PeakID (cmd=cIP1cIP2.mergepeaks.txt mm10 -m allmotifs.motif -mbed mergepeaks.motifs.bed)	Chr	Start	End	Strand	Peak Score	Focus Ratio/Region Size	Annotation	Detailed Annotation	Distance to TSS	Nearest PromoterID	Entrez ID	Nearest Unigene	Nearest Refseq	Nearest Ensembl	Gene Name	Gene Alias	Gene Description	Gene Type	CpG%	GC%
Merged-chr6-103649202-2	chr6	103649152	103649252	+	3315.299805	cIP1vsInput|cIP2vsInput	"intron (NM_007697, intron 4 of 26)"	SYNREP_MM|Satellite|Satellite	138326	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule with homology to L1CAM	protein-coding	0.02	0.346535
Merged-chr11-109011892-2	chr11	109011822	109011963	+	169.449997	cIP1vsInput|cIP2vsInput	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91543	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin2	protein-coding	0.092199	0.640845
Merged-chr7-73618566-2	chr7	73618513	73618619	+	167.449997	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-60171	NR_037569	69170	Mm.34955	NR_037569		1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	miscRNA	0.150943	0.757009
Merged-chr3-5860703-2	chr3	5860640	5860767	+	162.299988	cIP1vsInput|cIP2vsInput	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-284455	NM_001163305	19302	Mm.132336	NM_001163304	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding	0.133858	0.6875
Merged-chr11-121236749-2	chr11	121236697	121236801	+	156.950012	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026272)	promoter-TSS (NM_026272)	-487	NM_026272	67608	Mm.291832	NM_026272	ENSMUSG00000000056	Narf	4430402O11Rik	nuclear prelamin A recognition factor	protein-coding	0.115385	0.714286
Merged-chr16-57391619-2	chr16	57391561	57391678	+	156.700012	cIP1vsInput|cIP2vsInput	"intron (NM_001040397, intron 1 of 4)"	LSU-rRNA_Hsa|rRNA|rRNA	38342	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding	0.119658	0.70339
Merged-chr5-146261292-2	chr5	146261231	146261354	+	129.300003	cIP1vsInput|cIP2vsInput	"intron (NM_153599, intron 2 of 12)"	LSU-rRNA_Hsa|rRNA|rRNA	29617	NM_153599	264064	Mm.260576	NM_181570	ENSMUSG00000029635	Cdk8	-	cyclin-dependent kinase 8	protein-coding	0.130081	0.653226
Merged-chrM-16134-1	chrM	16084	16184	+	122.099998	cIP2vsInput	NA	Intergenic	NA	NA									0	0.415842
Merged-chr6-3201514-2	chr6	3201463	3201565	+	115.800003	cIP1vsInput|cIP2vsInput	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87005	NR_036696	667335	Mm.380219	NR_036696		Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo	0.107843	0.475728
Merged-chr4-150236932-2	chr4	150236878	150236986	+	109.199997	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001025388)	promoter-TSS (NM_001025388)	-265	NM_023119	13806	Mm.372389	NM_023119	ENSMUSG00000063524	Eno1	0610008I15|AL022784|Eno-1|MBP-1	"enolase 1, alpha non-neuron"	protein-coding	0.12963	0.770642
Merged-chr17-45736808-2	chr17	45736751	45736865	+	100.5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-2964	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding	0.114035	0.730435
Merged-chr8-46000075-2	chr8	46000023	46000128	+	99.600006	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001039562)	promoter-TSS (NM_001039562)	-225	NM_001039562	654824	Mm.334517	NM_001039562	ENSMUSG00000050914	Ankrd37	-	ankyrin repeat domain 37	protein-coding	0.066667	0.632075
Merged-chr16-11144097-2	chr16	11144047	11144147	+	93.199997	cIP1vsInput|cIP2vsInput	"intron (NR_027502, intron 19 of 22)"	LSU-rRNA_Hsa|rRNA|rRNA	-9565	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding	0.21	0.861386
Merged-chr4-33247673-2	chr4	33247622	33247725	+	85.600006	cIP1vsInput|cIP2vsInput	"intron (NM_001033225, intron 1 of 1)"	CpG	1114	NM_001033225	108767	Mm.27769	NM_001033225	ENSMUSG00000040128	Pnrc1	5730463C12Rik|B4-2|PRR2|Prol2	proline-rich nuclear receptor coactivator 1	protein-coding	0.116505	0.75
Merged-chr9-123461989-2	chr9	123461939	123462039	+	84.699997	cIP1vsInput|cIP2vsInput	"3' UTR (NM_153168, exon 21 of 21)"	"3' UTR (NM_153168, exon 21 of 21)"	-16712	NM_013860	29806	Mm.10987	NM_013860	ENSMUSG00000025239	Limd1	AW822033|D9Ertd192e	LIM domains containing 1	protein-coding	0.07	0.485149
Merged-chr13-97190586-1	chr13	97190536	97190636	+	74.5	cIP1vsInput	"intron (NM_010422, intron 3 of 13)"	LSU-rRNA_Hsa|rRNA|rRNA	7771	NM_010422	15212	Mm.27816	NM_010422	ENSMUSG00000021665	Hexb	-	hexosaminidase B	protein-coding	0.02	0.455446
Merged-chr2-5379329-2	chr2	5379279	5379379	+	62.400002	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_030601)	promoter-TSS (NR_030601)	-61	NR_030601	100124465		NR_030601		Mir466d	Mirn466d	microRNA 466d	miscRNA	0.08	0.564356
Merged-chr13-44869644-1	chr13	44869594	44869694	+	62.099998	cIP1vsInput	"intron (NM_001205043, intron 3 of 17)"	LSU-rRNA_Hsa|rRNA|rRNA	132452	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding	0.1	0.623762
Merged-chr2-71873279-2	chr2	71873227	71873332	+	59.100002	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172665)	promoter-TSS (NM_172665)	7	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	"pyruvate dehydrogenase kinase, isoenzyme 1"	protein-coding	0.133333	0.764151
Merged-chr6-49236512-2	chr6	49236462	49236562	+	58.099998	cIP1vsInput|cIP2vsInput	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-21558	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding	0.04	0.465347
Merged-chr19-41911772-2	chr19	41911721	41911824	+	55.349998	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_023418)	promoter-TSS (NM_023418)	-99	NM_023418	18648	Mm.391589	NM_023418	ENSMUSG00000011752	Pgam1	2310050F24Rik|Pgam-1	phosphoglycerate mutase 1	protein-coding	0.145631	0.673077
Merged-chr11-120950997-2	chr11	120950944	120951051	+	55	cIP1vsInput|cIP2vsInput	"intron (NM_001038654, intron 1 of 4)"	CpG	1930	NM_001038654	80879	Mm.28632	NM_001038653	ENSMUSG00000025161	Slc16a3	Mct3|Mct4	"solute carrier family 16 (monocarboxylic acid transporters), member 3"	protein-coding	0.102804	0.675926
Merged-chr17-36231559-2	chr17	36231507	36231611	+	54.75	cIP1vsInput|cIP2vsInput	Intergenic	CpG	26287	NM_026308	67676	Mm.27131	NM_026308		Rpp21	0610037N01Rik	ribonuclease P 21 subunit	protein-coding	0.105769	0.685714
Merged-chr12-54192127-2	chr12	54192068	54192187	+	53.299999	cIP1vsInput|cIP2vsInput	"intron (NM_028133, intron 1 of 4)"	"intron (NM_028133, intron 1 of 4)"	11747	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	EGL nine homolog 3 (C. elegans)	protein-coding	0.042017	0.65
Merged-chr4-119019601-2	chr4	119019550	119019653	+	51.599998	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	57634	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding	0.019417	0.634615
Merged-chr9-110281317-2	chr9	110281265	110281369	+	51.099998	cIP1vsInput|cIP2vsInput	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-23875	NM_001081381	72341	Mm.374250	NM_001081381	ENSMUSG00000054836	Elp6	2610001P13Rik|2610002I17Rik|AV159994|Tmem103	elongator acetyltransferase complex subunit 6	protein-coding	0.057692	0.561905
Merged-chr6-71633442-2	chr6	71633387	71633498	+	50.099998	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_173001)	promoter-TSS (NM_173001)	-537	NM_001038695	104263	Mm.260479	NM_001038695	ENSMUSG00000053470	Kdm3a	1700105C21Rik|C230043E16Rik|JHDM2a|Jmjd1|Jmjd1a|KDM2A|TGSA|Tsga|mKIAA0742	lysine (K)-specific demethylase 3A	protein-coding	0.081081	0.696429
Merged-chr17-36231300-1	chr17	36231250	36231350	+	49.299999	cIP2vsInput	Intergenic	CpG	26546	NM_026308	67676	Mm.27131	NM_026308		Rpp21	0610037N01Rik	ribonuclease P 21 subunit	protein-coding	0.1	0.70297
Merged-chr10-59323279-2	chr10	59323227	59323332	+	45.900002	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011030)	promoter-TSS (NM_011030)	-17	NM_011030	18451	Mm.2212	NM_011030	ENSMUSG00000019916	P4ha1	AL022634|P4ha	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha 1 polypeptide"	protein-coding	0.161905	0.792453
Merged-chr17-56036836-2	chr17	56036778	56036894	+	43.849998	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013664)	promoter-TSS (NM_013664)	-199	NM_001252471	20405	Mm.1773	NM_001252471	ENSMUSG00000003200	Sh3gl1	C77078|EEN|SH3P8|Sh3d2b	SH3-domain GRB2-like 1	protein-coding	0.051724	0.547009
Merged-chr6-125165747-2	chr6	125165694	125165801	+	42.450001	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008084)	promoter-TSS (NM_008084)	-164	NM_008084	14433	Mm.458416	NM_008084	ENSMUSG00000057666	Gapdh	Gapd	glyceraldehyde-3-phosphate dehydrogenase	protein-coding	0.056075	0.611111
Merged-chr9-44881450-2	chr9	44881385	44881515	+	41.049999	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081049)	promoter-TSS (NM_001081049)	-176	NM_001081049	214162	Mm.2389	NM_001081049	ENSMUSG00000002028	Mll1	6430520K01|ALL-1|All1|Cxxc7|HRX|HTRX1|KMT2A|Mll|mKIAA4050	myeloid/lymphoid or mixed-lineage leukemia 1	protein-coding	0.123077	0.755725
Merged-chr9-59657166-2	chr9	59657103	59657230	+	39.900002	cIP1vsInput|cIP2vsInput	"intron (NM_001253883, intron 1 of 10)"	CpG	798	NM_001253883	18746	Mm.488724	NM_001253883	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	"pyruvate kinase, muscle"	protein-coding	0.110236	0.679688
Merged-chr2-11503292-2	chr2	11503237	11503347	+	39.650002	cIP1vsInput|cIP2vsInput	"intron (NM_001177758, intron 1 of 14)"	CpG	-1202	NM_001177757	170768		NM_172976	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	"6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3"	protein-coding	0.109091	0.711712
Merged-chr3-95217941-2	chr3	95217891	95217992	+	38.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029885)	promoter-TSS (NM_029885)	1	NM_172512	213054	Mm.224820	NM_029885	ENSMUSG00000038766	Gabpb2	1810015F01Rik|5830427M07|9430006E19Rik|A430024B14Rik|AV050852|Gabpb2-1	"GA repeat binding protein, beta 2"	protein-coding	0.108911	0.578431
Merged-chr8-15519933-2	chr8	15519883	15519983	+	37.699997	cIP1vsInput|cIP2vsInput	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	462280	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding	0.08	0.50495
Merged-chr18-67774942-2	chr18	67774889	67774995	+	37.299999	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028112)	promoter-TSS (NM_028112)	66	NM_001039088	72124	Mm.307315	NM_001039088	ENSMUSG00000079614	Seh1l	2610007A16Rik|AW540070|SEC13L|SEH1A|SEH1B|Seh1	SEH1-like (S. cerevisiae	protein-coding	0.188679	0.850467
Merged-chr14-54996890-2	chr14	54996828	54996952	+	37.150002	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-2341	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	"myosin, heavy polypeptide 7, cardiac muscle, beta"	protein-coding	0.024194	0.56
Merged-chr7-138909626-2	chr7	138909572	138909680	+	35.949997	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009760)	promoter-TSS (NM_009760)	-120	NM_009760	12176	Mm.378890	NM_009760	ENSMUSG00000078566	Bnip3	Nip3	BCL2/adenovirus E1B interacting protein 3	protein-coding	0.12037	0.743119
Merged-chr16-36071677-2	chr16	36071621	36071733	+	33.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001159421)	promoter-TSS (NM_001159421)	17	NM_001159421	381045	Mm.310434	NM_001159421	ENSMUSG00000075229	Ccdc58	A930007B11Rik|AI413631	coiled-coil domain containing 58	protein-coding	0.142857	0.716814
Merged-chr15-36283287-2	chr15	36283233	36283341	+	32.450001	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013923)	promoter-TSS (NM_013923)	-140	NM_013923	30945	Mm.5181	NM_013923	ENSMUSG00000022280	Rnf19a	AA032313|Dorfin|Rnf19|UIP117|Ubce7ip2|XYbp	ring finger protein 19A	protein-coding	0.148148	0.733945
Merged-chr10-79704416-2	chr10	79704361	79704471	+	31.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009768)	promoter-TSS (NM_009768)	58	NM_009768	12215	Mm.726	NM_001077184	ENSMUSG00000023175	Bsg	AI115436|AI325119|CD147|EMMPRIN|HT-7	basigin	protein-coding	0.190909	0.783784
Merged-chr7-34234228-2	chr7	34234172	34234285	+	31.400002	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-3923	NM_008155	14751	Mm.589	XM_003689446		Gpi1	Amf|Gpi|Gpi-1|Gpi-1r|Gpi-1s|Gpi-1t|Gpi1-r|Gpi1-s|Gpi1-t|Gpi1s|MF|NK|NK/GPI|Org	glucose phosphate isomerase 1	protein-coding	0.106195	0.675439
Merged-chr12-86947186-2	chr12	86947134	86947239	+	31.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_173735)	promoter-TSS (NM_173735)	143	NR_033623	217732	Mm.22337	NM_173735	ENSMUSG00000034157	2310044G17Rik	AI842544|AI853744|Kiaa1737|mKIAA1737	RIKEN cDNA 2310044G17 gene	protein-coding	0.114286	0.641509
Merged-chr11-60537255-2	chr11	60537200	60537310	+	30.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172943)	promoter-TSS (NM_172943)	-428	NM_172943	268420	Mm.262056	NM_172943	ENSMUSG00000042650	Alkbh5	AW050020|AW215868|Abh5|E130207K11|Ofoxd	"alkB, alkylation repair homolog 5 (E. coli)"	protein-coding	0.163636	0.702703
Merged-chr5-114356770-2	chr5	114356712	114356828	+	30.6	cIP1vsInput|cIP2vsInput	"intron (NM_001164573, intron 21 of 30)"	"intron (NM_001164573, intron 21 of 30)"	23735	NM_026145	330171	Mm.490304	NM_001159941	ENSMUSG00000001098	Kctd10	AW536343|C87062|mBACURD3	potassium channel tetramerisation domain containing 10	protein-coding	0.017241	0.57265
Merged-chr7-46845779-2	chr7	46845723	46845835	+	29.599998	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010699)	promoter-TSS (NM_010699)	-25	NM_010699	16828	Mm.29324	NM_001136069	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding	0.125	0.734513
Merged-chr7-112298274-2	chr7	112298223	112298325	+	29.049999	cIP1vsInput|cIP2vsInput	"intron (NM_177282, intron 3 of 19)"	"intron (NM_177282, intron 3 of 19)"	-70034	NM_027587	100504195	Mm.291129	NM_027587	ENSMUSG00000030771	Micalcl	4921517J23Rik	MICAL C-terminal like	protein-coding	0.039216	0.563107
Merged-chr7-141221930-2	chr7	141221878	141221982	+	28.700001	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_029793)	promoter-TSS (NR_029793)	-437	NR_029793	387206		NR_029793	ENSMUSG00000065551	Mir210	Mirn210|mmu-mir-210	microRNA 210	miscRNA	0.115385	0.72381
Merged-chr4-34882956-2	chr4	34882905	34883008	+	28.549999	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013889)	promoter-TSS (NM_013889)	-8	NM_013889	30046	Mm.38193	NM_013889	ENSMUSG00000039967	Zfp292	5730450D02Rik|5830493J20Rik|9430062L07Rik|AI449016|Krox-10|Zfp-15|Zfp15|Zn-15|Zn-16|mKIAA0530	zinc finger protein 292	protein-coding	0.145631	0.663462
Merged-chr19-36736885-2	chr19	36736824	36736946	+	27.700001	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_016854)	promoter-TSS (NM_016854)	-281	NM_016854	53412	Mm.24724	NM_016854	ENSMUSG00000067279	Ppp1r3c	PTG|Ppp1r5	"protein phosphatase 1, regulatory (inhibitor) subunit 3C"	protein-coding	0.081967	0.691057
Merged-chr4-121215076-2	chr4	121215021	121215132	+	27.599998	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-26542	NM_001081013	109263	Mm.215745	NM_001081013	ENSMUSG00000049878	Rlf	9230110M18Rik|AI195322	rearranged L-myc fusion sequence	protein-coding	0.126126	0.758929
Merged-chr10-78009399-2	chr10	78009344	78009454	+	27.549999	cIP1vsInput|cIP2vsInput	"intron (NM_008826, intron 1 of 21)"	CpG	397	NM_008826	18641	Mm.269649	NM_008826	ENSMUSG00000020277	Pfkl	AA407869	"phosphofructokinase, liver, B-type"	protein-coding	0.1	0.738739
Merged-chrX-106186949-2	chrX	106186893	106187005	+	24.799999	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008828)	promoter-TSS (NM_008828)	-175	NM_008828	18655	Mm.336205	NM_008828	ENSMUSG00000062070	Pgk1	Pgk-1	phosphoglycerate kinase 1	protein-coding	0.080357	0.610619
Merged-chr9-59659924-2	chr9	59659871	59659978	+	23.799999	cIP1vsInput|cIP2vsInput	"intron (NM_001253883, intron 1 of 10)"	"intron (NM_001253883, intron 1 of 10)"	3556	NM_001253883	18746	Mm.488724	NM_001253883	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	"pyruvate kinase, muscle"	protein-coding	0.009346	0.574074
Merged-chr7-121034421-2	chr7	121034371	121034471	+	23.700001	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_021554)	promoter-TSS (NM_021554)	-24	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev	methyltransferase like 9	protein-coding	0.07	0.623762
Merged-chr6-124813632-2	chr6	124813581	124813683	+	22.9	cIP1vsInput|cIP2vsInput	"intron (NM_009415, intron 1 of 6)"	"intron (NM_009415, intron 1 of 6)"	664	NM_009415	21991	Mm.4222	NM_009415	ENSMUSG00000023456	Tpi1	AI255506|Tpi|Tpi-1	triosephosphate isomerase 1	protein-coding	0.098039	0.68932
Merged-chr17-74528368-2	chr17	74528312	74528424	+	21.599998	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007566)	promoter-TSS (NM_007566)	73	NM_007566	12211	Mm.447926	NM_007566	ENSMUSG00000024073	Birc6	A430032G04Rik|A430040A19Rik|AA501170|Bruce|D630005A10Rik|mKIAA1289	baculoviral IAP repeat-containing 6	protein-coding	0.098214	0.752212
Merged-chr4-120148853-2	chr4	120148798	120148909	+	20.799999	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-12571	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	VIC	endothelin 2	protein-coding	0.171171	0.732143
Merged-chr4-99929865-2	chr4	99929808	99929923	+	19.950001	cIP1vsInput|cIP2vsInput	"intron (NM_028132, intron 1 of 10)"	CpG	414	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding	0.156522	0.75
Merged-chr16-70314445-2	chr16	70314392	70314498	+	19.5	cIP1vsInput|cIP2vsInput	"intron (NM_028803, intron 1 of 15)"	CpG	496	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	"glucan (1,4-alpha-), branching enzyme 1"	protein-coding	0.103774	0.672897
Merged-chr8-124949301-2	chr8	124949248	124949354	+	19.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_053207)	promoter-TSS (NM_053207)	-47	NM_053207	112405	Mm.140619	NM_053207	ENSMUSG00000031987	Egln1	AI503754|C1orf12|HIF-PH2|HPH-2|Hif-p4h-2|ORF13|Phd2|SM-20	EGL nine homolog 1 (C. elegans)	protein-coding	0.207547	0.859813
Merged-chr9-92542104-2	chr9	92542053	92542156	+	19.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011961)	promoter-TSS (NM_011961)	-119	NM_011961	26432	Mm.79983	NM_001142916	ENSMUSG00000032374	Plod2	D530025C14Rik|LH2|Plod-2	"procollagen lysine, 2-oxoglutarate 5-dioxygenase 2"	protein-coding	0.097087	0.701923
Merged-chr17-26844616-1	chr17	26844566	26844666	+	18.799999	cIP1vsInput	Intergenic	CpG	-3051	NM_008700	18091	Mm.41974	NM_008700	ENSMUSG00000015579	Nkx2-5	Csx|Nkx-2.5|Nkx2.5|tinman	"NK2 transcription factor related, locus 5 (Drosophila)"	protein-coding	0.08	0.613861
Merged-chr13-43864709-2	chr13	43864656	43864763	+	18.700001	cIP1vsInput|cIP2vsInput	Intergenic	CpG	79602	NM_009856	12522	Mm.57175	NM_009856	ENSMUSG00000015396	Cd83	-	CD83 antigen	protein-coding	0.074766	0.703704
Merged-chr10-59951956-2	chr10	59951899	59952013	+	18.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029083)	promoter-TSS (NM_029083)	-186	NM_029083	74747	Mm.21697	NM_029083	ENSMUSG00000020108	Ddit4	5830413E08Rik|AA415483|REDD1|Rtp801|dig2	DNA-damage-inducible transcript 4	protein-coding	0.087719	0.704348
Merged-chr6-125166613-2	chr6	125166562	125166665	+	18.450001	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-1030	NM_008084	14433	Mm.458416	NM_008084	ENSMUSG00000057666	Gapdh	Gapd	glyceraldehyde-3-phosphate dehydrogenase	protein-coding	0.029126	0.644231
Merged-chr6-125165361-2	chr6	125165294	125165429	+	18.400002	cIP1vsInput|cIP2vsInput	"intron (NM_008084, intron 1 of 6)"	CpG-12474	222	NM_008084	14433	Mm.458416	NM_008084	ENSMUSG00000057666	Gapdh	Gapd	glyceraldehyde-3-phosphate dehydrogenase	protein-coding	0.066667	0.639706
Merged-chr17-34972474-1	chr17	34972424	34972524	+	18.299999	cIP1vsInput	promoter-TSS (NM_010479)	promoter-TSS (NM_010479)	-229	NM_013558	15482	Mm.14287	NM_013558	ENSMUSG00000007033	Hspa1l	Hsc70t|Msh5	heat shock protein 1-like	protein-coding	0.04	0.475248
Merged-chr1-193316243-2	chr1	193316190	193316296	+	18.25	cIP1vsInput|cIP2vsInput	"intron (NM_008484, intron 3 of 22)"	"intron (NM_008484, intron 3 of 22)"	14249	NM_008484	16780	Mm.435441	NM_008484	ENSMUSG00000026639	Lamb3	-	"laminin, beta 3"	protein-coding	0.018868	0.560748
Merged-chr13-55322047-2	chr13	55321988	55322106	+	17.950001	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009000)	promoter-TSS (NM_009000)	-8	NM_025596	66494	Mm.439805	NM_025596	ENSMUSG00000021486	Prelid1	2610524G07Rik|Preli	PRELI domain containing 1	protein-coding	0.118644	0.680672
Merged-chr13-35967892-2	chr13	35967842	35967942	+	17.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029628)	promoter-TSS (NM_029628)	-14	NM_029628	76487	Mm.44745	NM_029628	ENSMUSG00000050423	Ppp1r3g	1600032L17Rik	"protein phosphatase 1, regulatory (inhibitor) subunit 3G"	protein-coding	0.05	0.673267
Merged-chr3-86142666-2	chr3	86142609	86142723	+	17.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_016959)	promoter-TSS (NM_016959)	2	NM_016959	20091	Mm.399829	NM_016959	ENSMUSG00000028081	Rps3a1	Rps3a	ribosomal protein S3A1	protein-coding	0.149123	0.643478
Merged-chr11-69418912-2	chr11	69418862	69418963	+	17.849998	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-5237	NM_001017426	216850	Mm.472522	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding	0.049505	0.656863
Merged-chr14-62166803-2	chr14	62166749	62166857	+	17.700001	cIP1vsInput|cIP2vsInput	Intergenic	RMER17D2|LTR|ERVK	126176	NM_173419	239133	Mm.127330	NM_173419	ENSMUSG00000048281	Dleu7	BC038059	"deleted in lymphocytic leukemia, 7"	protein-coding	0.009259	0.513761
Merged-chr12-80146664-2	chr12	80146611	80146717	+	17.549999	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-13820	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	miscRNA	0.066038	0.570093
Merged-chr14-67008350-2	chr14	67008297	67008403	+	17.5	cIP1vsInput|cIP2vsInput	"intron (NM_009761, intron 1 of 5)"	CpG	527	NM_009761	12177	Mm.347081	NM_009761	ENSMUSG00000022051	Bnip3l	C86132|D14Ertd719e|Nip3L|Nix	BCL2/adenovirus E1B interacting protein 3-like	protein-coding	0.150943	0.785047
Merged-chr12-99563706-2	chr12	99563648	99563765	+	17.1	cIP1vsInput|cIP2vsInput	Intergenic	CpG	64268	NR_045288	73457	Mm.383439	NR_045288		1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	miscRNA	0.102564	0.762712
Merged-chr18-3004903-1	chr18	3004853	3004953	+	16.9	cIP2vsInput	Intergenic	B1_Mus1|SINE|Alu	118509	NM_001167539	100312476	Mm.480293	NM_001167539		Vmn1r238	-	"vomeronasal 1 receptor, 238"	protein-coding	0.01	0.425743
Merged-chr6-49319201-2	chr6	49319148	49319255	+	16.849998	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175098)	promoter-TSS (NM_175098)	-152	NM_175098	57895	Mm.32416	NM_175098	ENSMUSG00000050786	Ccdc126	6330407D12Rik|AA675040|AI465320|AL022711	coiled-coil domain containing 126	protein-coding	0.074766	0.638889
Merged-chr17-27204562-2	chr17	27204510	27204614	+	16.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_146075)	promoter-TSS (NM_146075)	-124	NM_146075	224640	Mm.29689	NM_146075	ENSMUSG00000044857	Lemd2	BC026588|Lem2|NET25	LEM domain containing 2	protein-coding	0.105769	0.647619
Merged-chr10-81266906-2	chr10	81266839	81266973	+	16.700001	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025317)	promoter-TSS (NM_025317)	20	NM_025317	66047	Mm.43397	NM_025317	ENSMUSG00000034932	Mrpl54	0610008M19Rik|D10Sut1e	mitochondrial ribosomal protein L54	protein-coding	0.11194	0.703704
Merged-chr4-119109107-2	chr4	119109049	119109165	+	16.700001	cIP1vsInput|cIP2vsInput	"intron (NM_011400, intron 1 of 9)"	CpG	362	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	"solute carrier family 2 (facilitated glucose transporter), member 1"	protein-coding	0.189655	0.820513
Merged-chr7-126799376-2	chr7	126799321	126799431	+	16.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007438)	promoter-TSS (NM_007438)	-122	NM_007438	11674	Mm.275831	NM_001177307	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	"aldolase A, fructose-bisphosphate"	protein-coding	0.063636	0.702703
Merged-chr11-72608504-2	chr11	72608452	72608556	+	16.450001	cIP1vsInput|cIP2vsInput	"intron (NM_025985, intron 1 of 5)"	"intron (NM_025985, intron 1 of 5)"	1243	NM_025985	67128	Mm.458052	NM_025985	ENSMUSG00000020794	Ube2g1	2700059C12Rik|AI256795|AU014992|AW552068|D130023C12Rik	ubiquitin-conjugating enzyme E2G 1	protein-coding	0.076923	0.67619
Merged-chr6-39256853-2	chr6	39256801	39256906	+	16.15	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-50080	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Jhdm1d	A630082K20Rik|BB041802|ENSMUSG00000073143|Kdm7a|mKIAA1718	jumonji C domain-containing histone demethylase 1 homolog D (S. cerevisiae)	protein-coding	0.152381	0.783019
Merged-chr14-45318649-2	chr14	45318597	45318701	+	16	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_015774)	promoter-TSS (NM_015774)	-77	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L	ERO1-like (S. cerevisiae)	protein-coding	0.182692	0.809524
Merged-chr1-75435940-2	chr1	75435883	75435997	+	15.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133708)	promoter-TSS (NM_133708)	-3	NM_133708	69080		NM_133708	ENSMUSG00000033021	Gmppa	1810012N01Rik	GDP-mannose pyrophosphorylase A	protein-coding	0.087719	0.582609
Merged-chr9-124256775-2	chr9	124256718	124256832	+	15.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	55919	NM_001243118	630836	Mm.458553	NM_001243117		2010315B03Rik	BC029716	RIKEN cDNA 2010315B03 gene	protein-coding	0	0.513043
Merged-chr3-21936082-2	chr3	21935999	21936165	+	15.65	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-140570	NM_030732	81004	Mm.446265	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding	0.03012	0.520958
Merged-chr19-26845517-2	chr19	26845458	26845577	+	15.400001	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-21610	NR_045306	70942	Mm.411548	NR_045306	ENSMUSG00000093772	4931403E22Rik	-	RIKEN cDNA 4931403E22 gene	miscRNA	0.02521	0.491667
Merged-chr3-103914280-2	chr3	103914227	103914333	+	15.25	cIP1vsInput|cIP2vsInput	"5' UTR (NM_172684, exon 1 of 7)"	"5' UTR (NM_172684, exon 1 of 7)"	160	NM_172684	229675	Mm.29366	NM_172684	ENSMUSG00000044098	Rsbn1	C230004D03Rik|E330004N01|Rosbin|Rsbn|Rsbp|mKIAA3002	"rosbin, round spermatid basic protein 1"	protein-coding	0.09434	0.719626
Merged-chr4-9669326-2	chr4	9669263	9669390	+	15.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_023066)	promoter-TSS (NM_023066)	-164	NM_001177849	65973	Mm.412008	NM_001177849	ENSMUSG00000028207	Asph	2310005F16Rik|3110001L23Rik|AI848629|AW261690|AW561901|BAH|C79816|cI-37	aspartate-beta-hydroxylase	protein-coding	0.070866	0.625
Merged-chr5-23433088-2	chr5	23433033	23433143	+	15.25	cIP1vsInput|cIP2vsInput	"non-coding (NR_040469, exon 1 of 1)"	"non-coding (NR_040469, exon 1 of 1)"	1265	NR_040469	269630	Mm.436103	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	miscRNA	0.090909	0.657658
Merged-chr7-45434566-2	chr7	45434513	45434619	+	15.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_030678)	promoter-TSS (NM_030678)	-102	NM_011304	20174	Mm.34410	NM_011304	ENSMUSG00000003868	Ruvbl2	mp47|p47	RuvB-like protein 2	protein-coding	0.037736	0.542056
Merged-chr15-66984999-2	chr15	66984940	66985058	+	15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-15358	NM_008681	17988	Mm.30837	NM_008681	ENSMUSG00000005125	Ndrg1	CAP43|CMT4D|DRG1|HMSNL|NMSL|Ndr1|Ndrl|PROXY1|RTP|TDD5	N-myc downstream regulated gene 1	protein-coding	0.042373	0.588235
Merged-chr12-32820220-2	chr12	32820164	32820276	+	14.900001	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_021524)	promoter-TSS (NM_021524)	-115	NM_021524	59027		NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding	0.107143	0.752212
Merged-chr3-51396773-2	chr3	51396717	51396829	+	14.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_028121)	promoter-TSS (NR_028121)	-226	NR_028121	67749	Mm.273339	NM_026358	ENSMUSG00000037161	Mgarp	4930583H14Rik|AI195347|CESP-1|HUMMR|Osap|Qsap	mitochondria localized glutamic acid rich protein	protein-coding	0.071429	0.566372
Merged-chr6-114920498-2	chr6	114920442	114920555	+	14.8	cIP1vsInput|cIP2vsInput	"intron (NM_177683, intron 1 of 4)"	"intron (NM_177683, intron 1 of 4)"	1254	NM_177683	232334	Mm.446323	NM_177683		Vgll4	BC048841|VGL-4	vestigial like 4 (Drosophila)	protein-coding	0.035398	0.570175
Merged-chr14-65332164-2	chr14	65332106	65332222	+	14.55	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-26512	NM_199029	380912	Mm.270087	NM_199029	ENSMUSG00000034522	Zfp395	BC053701|Gm910	zinc finger protein 395	protein-coding	0.137931	0.786325
Merged-chr3-133544397-2	chr3	133544346	133544448	+	14.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001040400)	promoter-TSS (NM_001040400)	-7	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding	0.166667	0.776699
Merged-chr16-32608907-2	chr16	32608850	32608964	+	14.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011638)	promoter-TSS (NM_011638)	11	NM_011638	22042	Mm.28683	NM_011638	ENSMUSG00000022797	Tfrc	2610028K12Rik|AI195355|AI426448|AU015758|CD71|E430033M20Rik|Mtvr-1|Mtvr1|TFR|TFR1|TR|Trfr|p90	transferrin receptor	protein-coding	0.078947	0.652174
Merged-chr10-75860262-2	chr10	75860199	75860326	+	14.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010798)	promoter-TSS (NM_010798)	-12	NM_010798	17319	Mm.2326	NM_010798	ENSMUSG00000033307	Mif	GIF|Glif	macrophage migration inhibitory factor	protein-coding	0.094488	0.664062
Merged-chr6-82774712-2	chr6	82774655	82774770	+	14.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013820)	promoter-TSS (NM_013820)	-258	NM_013820	15277	Mm.469167	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding	0.113043	0.706897
Merged-chr6-113076733-2	chr6	113076671	113076795	+	14.299999	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028385)	promoter-TSS (NM_028385)	511	NR_027010	14910	Mm.280950	NR_027008	ENSMUSG00000086429	Gt(ROSA)26Sor	AV258896|Gtrgeo26|Gtrosa26|R26|ROSA26	"gene trap ROSA 26, Philippe Soriano"	miscRNA	0.104839	0.752
Merged-chr1-73862889-2	chr1	73862827	73862951	+	14.200001	cIP1vsInput|cIP2vsInput	"non-coding (NR_045311, exon 2 of 9)"	"non-coding (NR_045311, exon 2 of 9)"	1577	NR_045311	109198	Mm.359721	NR_045311		6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	miscRNA	0.032258	0.6
Merged-chr9-69453534-2	chr9	69453478	69453591	+	14.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007585)	promoter-TSS (NM_007585)	-149	NM_007585	12306	Mm.238343	NM_007585	ENSMUSG00000032231	Anxa2	AW215814|Cal1h	annexin A2	protein-coding	0.035398	0.605263
Merged-chr13-80963021-2	chr13	80962965	80963078	+	14	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-1053	NR_015587	319983	Mm.343027	NR_015587	ENSMUSG00000097098	9330111N05Rik	-	RIKEN cDNA 9330111N05 gene	miscRNA	0.115044	0.719298
Merged-chr6-13677600-2	chr6	13677546	13677655	+	14	cIP1vsInput|cIP2vsInput	"intron (NM_175312, intron 1 of 4)"	CpG	366	NM_175312	101148	Mm.354863	NM_175312	ENSMUSG00000042742	B630005N14Rik	AI666701	RIKEN cDNA B630005N14 gene	protein-coding	0.110092	0.736364
Merged-chr10-31313691-2	chr10	31313632	31313751	+	13.950001	cIP1vsInput|cIP2vsInput	"intron (NM_027168, intron 1 of 5)"	CpG	286	NM_027168	69692	Mm.245537	NM_027168	ENSMUSG00000000295	Hddc2	2310057G13Rik	HD domain containing 2	protein-coding	0.067227	0.616667
Merged-chr18-68692131-2	chr18	68692081	68692182	+	13.9	cIP1vsInput|cIP2vsInput	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	259397	NR_038051	78931	Mm.160155	NR_038051		4930546C10Rik	-	RIKEN cDNA 4930546C10 gene	miscRNA	0.079208	0.539216
Merged-chr11-116842891-2	chr11	116842837	116842945	+	13.700001	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028865)	promoter-TSS (NM_028865)	558	NM_033398	107817	Mm.481684	NM_033398	ENSMUSG00000056962	Jmjd6	5730436I23Rik|D11Ertd195e|PSR|PtdSerR|Ptdsr|mKIAA0585	jumonji domain containing 6	protein-coding	0.111111	0.724771
Merged-chr4-119141312-2	chr4	119141250	119141375	+	13.700001	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	32544	NM_183140	195522	Mm.169620	NM_001145935	ENSMUSG00000045268	Zfp691	6430544H17Rik|Znf691	zinc finger protein 691	protein-coding	0.016	0.547619
Merged-chr11-94211288-2	chr11	94211229	94211348	+	13.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009427)	promoter-TSS (NM_009427)	-166	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding	0.109244	0.758333
Merged-chr13-59771518-2	chr13	59771465	59771572	+	13.599999	cIP1vsInput|cIP2vsInput	TTS (NM_153538)	TTS (NM_153538)	1552	NR_015349	13996	Mm.490435	NR_015349	ENSMUSG00000089875	Etohd2	AW491659	ethanol decreased 2	miscRNA	0.028037	0.611111
Merged-chr11-54100856-2	chr11	54100799	54100914	+	13.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001136076)	promoter-TSS (NM_001136076)	-68	NM_001136076	18452	Mm.3705	NM_001136076	ENSMUSG00000018906	P4ha2	AA407196|C76437|P4hl	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha II polypeptide"	protein-coding	0.130435	0.758621
Merged-chr10-127516831-2	chr10	127516781	127516881	+	13.450001	cIP1vsInput|cIP2vsInput	TTS (NM_028230)	TTS (NM_028230)	1892	NM_001098789	407790	Mm.336856	NM_001098789	ENSMUSG00000040280	Ndufa4l2	BC064011	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2"	protein-coding	0.08	0.653465
Merged-chr9-121857761-2	chr9	121857711	121857812	+	13.45	cIP1vsInput|cIP2vsInput	"5' UTR (NM_019814, exon 1 of 4)"	"5' UTR (NM_019814, exon 1 of 4)"	239	NM_019814	56295	Mm.347915	NM_019814	ENSMUSG00000038412	Higd1a	2210020B17Rik|7420700H20Rik|AI303276|AW049839|HIMP1|Hig1	"HIG1 domain family, member 1A"	protein-coding	0.148515	0.764706
Merged-chr2-91537730-2	chr2	91537666	91537795	+	13.3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-8592	NM_001165989	75786	Mm.168478	NM_001165989	ENSMUSG00000040549	Ckap5	3110043H24Rik|4930432B04Rik|D730027C18Rik|T25636|mKIAA0097	cytoskeleton associated protein 5	protein-coding	0.046512	0.623077
Merged-chr6-55203764-2	chr6	55203706	55203822	+	13.299999	cIP1vsInput|cIP2vsInput	"intron (NM_001142781, intron 1 of 17)"	"intron (NM_001142781, intron 1 of 17)"	381	NM_001142781	330323	Mm.268997	NM_001142781	ENSMUSG00000038022	Fam188b	C330043M08Rik|Gm1406	"family with sequence similarity 188, member B"	protein-coding	0.034483	0.615385
Merged-chr16-20498869-2	chr16	20498817	20498922	+	13.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172265)	promoter-TSS (NM_172265)	52	NM_172265	224045	Mm.233855	NM_172265	ENSMUSG00000003235	Eif2b5	C81315	"eukaryotic translation initiation factor 2B, subunit 5 epsilon"	protein-coding	0.07619	0.59434
Merged-chr7-121707509-2	chr7	121707443	121707576	+	13.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001033173)	promoter-TSS (NM_001033173)	-256	NM_001033173	76179	Mm.122538	NM_001033173	ENSMUSG00000063317	Usp31	6330567E21Rik|mKIAA1203	ubiquitin specific peptidase 31	protein-coding	0.067669	0.641791
Merged-chr5-136986983-2	chr5	136986933	136987034	+	13	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011962)	promoter-TSS (NM_011962)	-36	NM_011962	26433	Mm.251003	NM_011962	ENSMUSG00000004846	Plod3	AI414586|LH3	"procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3"	protein-coding	0.049505	0.509804
Merged-chr9-22002895-2	chr9	22002837	22002953	+	12.950001	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008925)	promoter-TSS (NM_008925)	-140	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H	protein kinase C substrate 80K-H	protein-coding	0.068966	0.555556
Merged-chr1-55027479-2	chr1	55027417	55027542	+	12.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_031179)	promoter-TSS (NM_031179)	-1	NM_031179	81898	Mm.279736	NM_031179	ENSMUSG00000025982	Sf3b1	155kDa|2810001M05Rik|AA409119|Prp10|SAP155|SF3b155|TA-8|Targ4	"splicing factor 3b, subunit 1"	protein-coding	0.112	0.65873
Merged-chr11-98931212-2	chr11	98931151	98931273	+	12.9	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-6484	NM_009024	19401	Mm.439744	NM_001176528	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	"retinoic acid receptor, alpha"	protein-coding	0.016393	0.593496
Merged-chr8-41239559-2	chr8	41239506	41239612	+	12.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_023662)	promoter-TSS (NM_023662)	-200	NM_023662	18536	Mm.117896	NM_023662	ENSMUSG00000031592	Pcm1	2600002H09Rik|9430077F19Rik|C030044G17Rik	pericentriolar material 1	protein-coding	0.075472	0.570093
Merged-chr2-172370923-2	chr2	172370865	172370982	+	12.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011497)	promoter-TSS (NM_011497)	-80	NM_024199	67337	Mm.26944	NM_024199		Cstf1	1700057K18Rik|AI788832	"cleavage stimulation factor, 3' pre-RNA, subunit 1"	protein-coding	0.111111	0.652542
Merged-chr12-73949908-2	chr12	73949846	73949971	+	12.75	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-14622	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	"small nuclear RNA activating complex, polypeptide 1"	protein-coding	0.12	0.753968
Merged-chr12-70227795-2	chr12	70227745	70227846	+	12.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133198)	promoter-TSS (NM_133198)	-46	NR_045174	414124	Mm.416164	NR_045174	ENSMUSG00000085298	F730035M05Rik	-	RIKEN cDNA F730035M05 gene	miscRNA	0.118812	0.72549
Merged-chr9-79617570-2	chr9	79617499	79617641	+	12.65	cIP1vsInput|cIP2vsInput	"intron (NM_007730, intron 53 of 65)"	"intron (NM_007730, intron 53 of 65)"	-98268	NR_045336	100038575	Mm.367838	NR_045336		Gm10635	ENSMUSG00000074174	predicted gene 10635	miscRNA	0.021127	0.524476
Merged-chr7-63939728-2	chr7	63939676	63939780	+	12.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_021366)	promoter-TSS (NM_021366)	-813	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding	0.048077	0.666667
Merged-chr12-51348120-2	chr12	51348066	51348175	+	12.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001167964)	promoter-TSS (NM_001167964)	-110	NM_001167964	217558	Mm.253264	NM_001015099	ENSMUSG00000035293	G2e3	6030408C04Rik|9030416F18|AW046379|D930034K21Rik|mKIAA1333	G2/M-phase specific E3 ubiquitin ligase	protein-coding	0.12844	0.718182
Merged-chr4-46389507-2	chr4	46389448	46389567	+	12.349999	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029086)	promoter-TSS (NM_029086)	-84	NM_029086	74753	Mm.45973	NM_029086	ENSMUSG00000028331	5830415F09Rik	AV014846|Nap1	RIKEN cDNA 5830415F09 gene	protein-coding	0.109244	0.666667
Merged-chr3-10140323-2	chr3	10140260	10140387	+	12.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	43562	NM_001030305	18857	Mm.371777	NM_001030305	ENSMUSG00000052468	Pmp2	P2	peripheral myelin protein 2	protein-coding	0.031496	0.46875
Merged-chr1-134556414-2	chr1	134556355	134556474	+	12.15	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-3764	NM_152895	75605	Mm.391994	NM_152895	ENSMUSG00000042207	Kdm5b	2010009J12Rik|2210016I17Rik|AW556288|D1Ertd202e|Jarid1b|PLU-1|PUT1|Plu1|RBBP2H1A|Rb-Bp2|mKIAA4034	lysine (K)-specific demethylase 5B	protein-coding	0.084034	0.75
Merged-chr1-118311308-2	chr1	118311241	118311375	+	12.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011650)	promoter-TSS (NM_011650)	-176	NM_011650	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding	0.134328	0.725926
Merged-chr12-54287086-2	chr12	54287030	54287143	+	12.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-83212	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	EGL nine homolog 3 (C. elegans)	protein-coding	0.035398	0.605263
Merged-chr10-59964683-2	chr10	59964629	59964738	+	12.05	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-12913	NM_029083	74747	Mm.21697	NM_029083	ENSMUSG00000020108	Ddit4	5830413E08Rik|AA415483|REDD1|Rtp801|dig2	DNA-damage-inducible transcript 4	protein-coding	0.055046	0.709091
Merged-chr19-36879295-2	chr19	36879242	36879349	+	11.950001	cIP1vsInput|cIP2vsInput	"exon (NM_001163635, exon 19 of 27)"	"exon (NM_001163635, exon 19 of 27)"	40304	NM_028263	72514	Mm.41674	NM_028263	ENSMUSG00000047632	Fgfbp3	2610306H15Rik|Fgf-bp3	fibroblast growth factor binding protein 3	protein-coding	0.028037	0.611111
Merged-chr8-75084049-2	chr8	75083985	75084114	+	11.950001	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-9569	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase (decycling) 1	protein-coding	0.077519	0.661538
Merged-chr2-120563853-2	chr2	120563795	120563912	+	11.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011743)	promoter-TSS (NM_011743)	-22	NM_011743	20402	Mm.195877	NM_011743	ENSMUSG00000027288	Zfp106	Cd-1|D2Dcr28|H3a|Sh3bp3|Znf106|sirm	zinc finger protein 106	protein-coding	0.128205	0.694915
Merged-chr5-33936298-2	chr5	33936243	33936353	+	11.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011914)	promoter-TSS (NM_011914)	-40	NM_011914	24116	Mm.332320	NM_011914		Nelfa	Whsc2|Whsc2h	"negative elongation factor complex member A, Whsc2"	protein-coding	0.163636	0.738739
Merged-chr7-105373720-2	chr7	105373658	105373782	+	11.799999	cIP1vsInput|cIP2vsInput	"3' UTR (NM_001242363, exon 13 of 13)"	"3' UTR (NM_001242363, exon 13 of 13)"	-1378	NM_001195727	100503879	Mm.380109	NM_001195727	ENSMUSG00000078611	Gm5901	EG545989	predicted gene 5901	protein-coding	0.008065	0.488
Merged-chrX-101222645-2	chrX	101222591	101222700	+	11.799999	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_018875)	promoter-TSS (NM_018875)	-82	NM_001110310	55988	Mm.206949	NM_001110310	ENSMUSG00000046032	Snx12	2610001F05Rik|AW045757|SDP8	sorting nexin 12	protein-coding	0.027523	0.545455
Merged-chr11-86757666-2	chr11	86757597	86757736	+	11.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001003908)	promoter-TSS (NM_001003908)	-174	NM_001003908	67300		NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	"clathrin, heavy polypeptide (Hc)"	protein-coding	0.107914	0.635714
Merged-chr9-114640321-2	chr9	114640269	114640373	+	11.700001	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_153585)	promoter-TSS (NM_153585)	-121	NM_153585	78893	Mm.486302	NM_153585	ENSMUSG00000056167	Cnot10	2600001P13Rik	"CCR4-NOT transcription complex, subunit 10"	protein-coding	0.019231	0.495238
Merged-chr10-17723124-2	chr10	17723071	17723178	+	11.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010828)	promoter-TSS (NM_010828)	-104	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	"Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2"	protein-coding	0.149533	0.703704
Merged-chr15-96286758-2	chr15	96286703	96286813	+	11.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175251)	promoter-TSS (NM_175251)	-764	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	"AT rich interactive domain 2 (ARID, RFX-like)"	protein-coding	0.1	0.630631
Merged-chr11-88047651-2	chr11	88047601	88047702	+	11.6	cIP1vsInput|cIP2vsInput	"5' UTR (NM_173374, exon 1 of 4)"	"5' UTR (NM_173374, exon 1 of 4)"	278	NM_173374	110809	Mm.478968	NM_001078167	ENSMUSG00000018379	Srsf1	1110054N12Rik|5730507C05Rik|6330415C05Rik|AI482334|AW491331|Asf|Sf2|Sfrs1	serine/arginine-rich splicing factor 1	protein-coding	0.09901	0.686275
Merged-chr16-4880400-2	chr16	4880337	4880464	+	11.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145359)	promoter-TSS (NM_145359)	-549	NM_145359	207740	Mm.268895	NM_145359		Ubald1	1500031H01Rik|BC013706|Fam100a	UBA-like domain containing 1	protein-coding	0.070866	0.578125
Merged-chr8-60993104-2	chr8	60993054	60993155	+	11.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175089)	promoter-TSS (NM_175089)	-116	NM_175089	18004	Mm.486881	NM_175089		Nek1	D8Ertd790e|kat	NIMA (never in mitosis gene a)-related expressed kinase 1	protein-coding	0.108911	0.735294
Merged-chr11-97315645-2	chr11	97315589	97315702	+	11.549999	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025927)	promoter-TSS (NM_025927)	-71	NM_025927	67036	Mm.5381	NM_025927	ENSMUSG00000018882	Mrpl45	2600005P05Rik|AU043542|R75241	mitochondrial ribosomal protein L45	protein-coding	0.123894	0.657895
Merged-chr3-53525873-2	chr3	53525817	53525930	+	11.5	cIP1vsInput|cIP2vsInput	"exon (NM_172862, exon 17 of 24)"	"exon (NM_172862, exon 17 of 24)"	37080	NM_153156	229277	Mm.222810	NM_153156		Stoml3	Epb7.2l|SLP3|sro	stomatin (Epb7.2)-like 3	protein-coding	0.088496	0.570175
Merged-chr15-81523342-2	chr15	81523287	81523397	+	11.45	cIP1vsInput|cIP2vsInput	Intergenic	CpG	57026	NM_019712	56438	Mm.29405	NM_019712	ENSMUSG00000022400	Rbx1	1500002P15Rik|AA517855|ROC1	ring-box 1	protein-coding	0.1	0.747748
Merged-chr3-96044867-1	chr3	96044817	96044917	+	11.4	cIP1vsInput	"intron (NM_013841, intron 7 of 14)"	"intron (NM_013841, intron 7 of 14)"	13588	NM_013841	22365	Mm.263185	NM_013841	ENSMUSG00000015747	Vps45	AI462172|AW554165|mVps45	vacuolar protein sorting 45 (yeast)	protein-coding	0	0.366337
Merged-chr17-32389487-2	chr17	32389429	32389545	+	11.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011717)	promoter-TSS (NM_011717)	-48	NR_033525	22404	Mm.274948	NM_011717	ENSMUSG00000024050	Wiz	-	widely-interspaced zinc finger motifs	protein-coding	0.094828	0.735043
Merged-chr19-3768546-1	chr19	3768496	3768596	+	11.2	cIP2vsInput	"intron (NM_001167886, intron 2 of 10)"	CpG-7172	1125	NM_001167884	225888	Mm.278578	NM_001167884	ENSMUSG00000045098	Suv420h1	AA117471|C630029K18Rik|KMT5B|Suv4-20h1	suppressor of variegation 4-20 homolog 1 (Drosophila)	protein-coding	0.06	0.435644
Merged-chr8-124633277-2	chr8	124633222	124633332	+	11.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	30092	NM_175149	69551	Mm.261920	NM_175149	ENSMUSG00000031983	2310022B05Rik	-	RIKEN cDNA 2310022B05 gene	protein-coding	0.054545	0.594595
Merged-chr15-68258591-2	chr15	68258533	68258650	+	11.1	cIP1vsInput|cIP2vsInput	"intron (NM_001145888, intron 1 of 15)"	CpG	265	NM_001145888	380993	Mm.309526	NM_001145888	ENSMUSG00000022335	Zfat	Gm922|Zfat1|Zfp406	zinc finger and AT hook domain containing	protein-coding	0.17094	0.813559
Merged-chr14-65358612-2	chr14	65358552	65358672	+	11.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_199029)	promoter-TSS (NM_199029)	-64	NM_199029	380912	Mm.270087	NM_199029	ENSMUSG00000034522	Zfp395	BC053701|Gm910	zinc finger protein 395	protein-coding	0.158333	0.801653
Merged-chr5-125465920-2	chr5	125465868	125465972	+	11.1	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-9953	NM_030210	78894	Mm.431573	NM_030210	ENSMUSG00000029482	Aacs	2210408B16Rik|SUR5	acetoacetyl-CoA synthetase	protein-coding	0.105769	0.67619
Merged-chr18-37883681-2	chr18	37883630	37883733	+	11.05	cIP1vsInput|cIP2vsInput	"intron (NM_007858, intron 16 of 26)"	"intron (NM_007858, intron 16 of 26)"	51730	NM_007858	13367	Mm.195916	NM_007858	ENSMUSG00000024456	Diap1	D18Wsu154e|Dia1|Diaph1|Drf1|mKIAA4062|p140mDia	diaphanous homolog 1 (Drosophila)	protein-coding	0.038835	0.480769
Merged-chr3-33800078-2	chr3	33800011	33800145	+	11.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027619)	promoter-TSS (NM_027619)	-117	NM_027619	67120	Mm.275710	NM_025978	ENSMUSG00000027677	Ttc14	2700016E08Rik|4930434D01Rik|4931403I22Rik|4933402I15Rik|AI662468|AU014779|AW561908|cI-44|mKIAA1980	tetratricopeptide repeat domain 14	protein-coding	0.104478	0.674074
Merged-chr5-129461690-2	chr5	129461635	129461746	+	11	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-39541	NM_172276	231769	Mm.288714	NM_001035259	ENSMUSG00000029439	Sfswap	1190005N23Rik|6330437E22Rik|AI197402|AW212079|SWAP|Sfrs8|Srsf8	"splicing factor, suppressor of white-apricot homolog (Drosophila)"	protein-coding	0.009009	0.348214
Merged-chr17-25579208-2	chr17	25579131	25579285	+	10.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029624)	promoter-TSS (NM_029624)	34	NR_045520	76483	Mm.12787	NM_029624	ENSMUSG00000002279	Lmf1	2400010G15Rik|AW822050|Tmem112|cld	lipase maturation factor 1	protein-coding	0.097403	0.651613
Merged-chr5-30869557-2	chr5	30869505	30869609	+	10.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_144525)	promoter-TSS (NM_144525)	-90	NM_144525	68796	Mm.205169	NM_144525		Tmem214	1110039B18Rik|4921530J21Rik|AI841294|AU018742|C76280	transmembrane protein 214	protein-coding	0.153846	0.752381
Merged-chr18-62548834-2	chr18	62548780	62548888	+	10.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_177829)	promoter-TSS (NM_177829)	-77	NM_177829	328971	Mm.312675	NM_177829	ENSMUSG00000044176	Spink10	A230091H23Rik	"serine peptidase inhibitor, Kazal type 10"	protein-coding	0.074074	0.614679
Merged-chr16-31740903-2	chr16	31740837	31740969	+	10.700001	cIP1vsInput|cIP2vsInput	"intron (NM_001252433, intron 4 of 24)"	RMER17D2|LTR|ERVK	-13447	NM_001252436	13383	Mm.382	NM_001252433	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	"discs, large homolog 1 (Drosophila)"	protein-coding	0.015152	0.518797
Merged-chr1-75192343-2	chr1	75192289	75192398	+	10.700001	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001003917)	promoter-TSS (NM_001003917)	183	NR_051999	52231	Mm.259326	NM_001267620	ENSMUSG00000026199	Ankzf1	1300008P06Rik|2810025E10Rik|D1Ertd161e	ankyrin repeat and zinc finger domain containing 1	protein-coding	0.036697	0.5
Merged-chr10-95324138-2	chr10	95324079	95324198	+	10.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009950)	promoter-TSS (NM_009950)	-41	NM_009950	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding	0.02521	0.466667
Merged-chr10-17722413-2	chr10	17722361	17722466	+	10.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010828)	promoter-TSS (NM_010828)	-815	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	"Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2"	protein-coding	0.07619	0.584906
Merged-chr4-44981433-2	chr4	44981382	44981485	+	10.549999	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_080289)	promoter-TSS (NM_080289)	22	NM_080289	76238	Mm.196574	NM_080289	ENSMUSG00000035637	Grhpr	1110059D05Rik|6430629L09Rik	glyoxylate reductase/hydroxypyruvate reductase	protein-coding	0.097087	0.625
Merged-chr19-29611162-2	chr19	29611107	29611217	+	10.450001	cIP1vsInput|cIP2vsInput	"3' UTR (NM_001081213, exon 15 of 15)"	"3' UTR (NM_001081213, exon 15 of 15)"	37258	NM_001081213	226090	Mm.267131	NM_001081213		Ermp1	D19Ertd410e|D19Wsu12e|Fxna|mKIAA1815	endoplasmic reticulum metallopeptidase 1	protein-coding	0.054545	0.468468
Merged-chr8-71668303-2	chr8	71668252	71668355	+	10.45	cIP1vsInput|cIP2vsInput	"intron (NM_001029873, intron 1 of 41)"	"intron (NM_001029873, intron 1 of 41)"	3454	NM_001029873	382018	Mm.334606	NM_001029873		Unc13a	2410078G03Rik|Munc13-1	unc-13 homolog A (C. elegans)	protein-coding	0.067961	0.625
Merged-chr19-3768716-1	chr19	3768666	3768766	+	10.4	cIP1vsInput	"intron (NM_001167886, intron 2 of 10)"	CpG-7172	1295	NM_001167884	225888	Mm.278578	NM_001167884	ENSMUSG00000045098	Suv420h1	AA117471|C630029K18Rik|KMT5B|Suv4-20h1	suppressor of variegation 4-20 homolog 1 (Drosophila)	protein-coding	0.17	0.792079
Merged-chr9-22071164-2	chr9	22071108	22071220	+	10.4	cIP1vsInput|cIP2vsInput	"exon (NM_177318, exon 1 of 9)"	"exon (NM_177318, exon 1 of 9)"	162	NR_040406	100503652	Mm.439941	NR_040406	ENSMUSG00000096981	Gm16845	-	"predicted gene, 16845"	miscRNA	0.151786	0.743363
Merged-chr16-31932922-2	chr16	31932865	31932980	+	10.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172822)	promoter-TSS (NM_172822)	-929	NM_172822	239827	Mm.440388	NM_172822	ENSMUSG00000045625	Pigz	F630022B06Rik	"phosphatidylinositol glycan anchor biosynthesis, class Z"	protein-coding	0.069565	0.637931
Merged-chr6-124769630-2	chr6	124769576	124769685	+	10.299999	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013509)	promoter-TSS (NM_013509)	-121	NM_013509	13807	Mm.3913	NM_013509	ENSMUSG00000004267	Eno2	AI837106|D6Ertd375e|Eno-2|NSE	"enolase 2, gamma neuronal"	protein-coding	0.100917	0.690909
Merged-chr1-128832752-2	chr1	128832690	128832815	+	10.299999	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-240453	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r	chemokine (C-X-C motif) receptor 4	protein-coding	0.032	0.52381
Merged-chr9-64738210-2	chr9	64738141	64738279	+	10.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_017382)	promoter-TSS (NM_017382)	-454	NM_017382	53869	Mm.1387	NM_017382	ENSMUSG00000004771	Rab11a	-	"RAB11a, member RAS oncogene family"	protein-coding	0	0.323741
Merged-chr11-116012332-2	chr11	116012271	116012394	+	10.25	cIP1vsInput|cIP2vsInput	"intron (NM_016905, intron 1 of 7)"	"intron (NM_016905, intron 1 of 7)"	387	NM_016905	14635	Mm.2820	NM_016905	ENSMUSG00000020766	Galk1	AA409894|GALK|Gk|Glk|Glk1	galactokinase 1	protein-coding	0.073171	0.66129
Merged-chr17-25274062-2	chr17	25273995	25274129	+	10.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_027452)	promoter-TSS (NR_027452)	-62	NR_027452	100272221	Mm.478766	NR_027452		Gm17801	-	"predicted gene, 17801"	miscRNA	0.097015	0.703704
Merged-chr9-90113916-2	chr9	90113845	90113988	+	10.200001	cIP1vsInput|cIP2vsInput	"intron (NM_001039147, intron 1 of 12)"	CpG	904	NM_001039147	21761		NM_001039147	ENSMUSG00000062270	Morf4l1	MORFRG15|MRG15|TEG-189|Tex189|mKIAA4002	mortality factor 4 like 1	protein-coding	0.104895	0.652778
Merged-chr3-116808246-2	chr3	116808179	116808313	+	10.200001	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081326)	promoter-TSS (NM_001081326)	-80	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	"amylo-1,6-glucosidase, 4-alpha-glucanotransferase"	protein-coding	0.11194	0.77037
Merged-chr4-70410570-2	chr4	70410519	70410621	+	10.200001	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145990)	promoter-TSS (NM_145990)	-203	NM_145990	214444	Mm.379344	NM_145990		Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding	0.04902	0.553398
Merged-chr5-34326979-2	chr5	34326926	34327033	+	10.15	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-9411	NM_011278	19822	Mm.21281	NM_011278	ENSMUSG00000029110	Rnf4	AU018689|Gtrgeo8	ring finger protein 4	protein-coding	0.084112	0.666667
Merged-chr5-125368734-2	chr5	125368662	125368807	+	10.1	cIP1vsInput|cIP2vsInput	Intergenic	(CA)n|Simple_repeat|Simple_repeat	21283	NM_019639	22190	Mm.419997	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding	0.013793	0.458904
Merged-chr3-153690215-2	chr3	153690162	153690269	+	10.05	cIP1vsInput|cIP2vsInput	"intron (NM_011372, intron 1 of 4)"	"intron (NM_011372, intron 1 of 4)"	34918	NM_011372	20447	Mm.440929	NM_011372		St6galnac3	Siat7c	"ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3"	protein-coding	0.018692	0.574074
Merged-chr11-102087628-2	chr11	102087567	102087690	+	10	cIP1vsInput|cIP2vsInput	"intron (NM_016695, intron 1 of 12)"	CpG	887	NM_016695	50997	Mm.36242	NM_016695	ENSMUSG00000017314	Mpp2	D11Bwg0652e|Dlg2|Dlgh2|Pals4	"membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)"	protein-coding	0.065041	0.653226
Merged-chr13-44730638-2	chr13	44730583	44730693	+	10	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001205044)	promoter-TSS (NM_001205044)	-136	NM_021878	16468	Mm.25059	NM_001205043	ENSMUSG00000038518	Jarid2	Jmj|jumonji	"jumonji, AT rich interactive domain 2"	protein-coding	0.109091	0.684685
Merged-chr17-45729628-2	chr17	45729578	45729679	+	9.950001	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	4216	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding	0.039604	0.617647
Merged-chr4-119073039-2	chr4	119072965	119073113	+	9.95	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-35706	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	"solute carrier family 2 (facilitated glucose transporter), member 1"	protein-coding	0.094595	0.724832
Merged-chr2-125673255-2	chr2	125673202	125673308	+	9.9	cIP1vsInput|cIP2vsInput	"exon (NM_025613, exon 1 of 1)"	"exon (NM_025613, exon 1 of 1)"	155	NM_025613	58521	Mm.490315	NM_025613	ENSMUSG00000091337	Eid1	2610002K20Rik|Cri1|EID-1|ORF12|PNAS-22|PTD014	EP300 interacting inhibitor of differentiation 1	protein-coding	0.113208	0.672897
Merged-chr16-16213196-2	chr16	16213139	16213254	+	9.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026163)	promoter-TSS (NM_026163)	-149	NM_026163	67451	Mm.2252	NM_026163	ENSMUSG00000041957	Pkp2	1200008D14Rik|1200012P04Rik|AA516617|Pkp2l	plakophilin 2	protein-coding	0.086957	0.689655
Merged-chr16-90405838-2	chr16	90405769	90405907	+	9.9	cIP1vsInput|cIP2vsInput	"intron (NM_015755, intron 1 of 10)"	"intron (NM_015755, intron 1 of 10)"	19441	NM_015755	26559	Mm.125874	NM_015755	ENSMUSG00000053414	Hunk	Bstk1|Mak-v	hormonally upregulated Neu-associated kinase	protein-coding	0.014493	0.618705
Merged-chr2-136892131-2	chr2	136892069	136892194	+	9.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028834)	promoter-TSS (NM_028834)	-132	NM_028834	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding	0.056	0.531746
Merged-chrX-126693323-2	chrX	126693268	126693379	+	9.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	140681	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding	0	0.258929
Merged-chr14-55722267-2	chr14	55722215	55722320	+	9.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019519)	promoter-TSS (NM_019519)	-91	NM_019519	56187	Mm.87216	NM_019519	ENSMUSG00000040472	Rabggta	gm	"Rab geranylgeranyl transferase, a subunit"	protein-coding	0.095238	0.716981
Merged-chr14-26535044-2	chr14	26534991	26535098	+	9.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-1304	NM_032008	83997	Mm.36769	NM_032008	ENSMUSG00000021870	Slmap	D330001L02Rik|Slap|mKIAA1601	sarcolemma associated protein	protein-coding	0.009346	0.490741
Merged-chr17-46031056-2	chr17	46030994	46031118	+	9.7	cIP1vsInput|cIP2vsInput	"intron (NM_001025250, intron 1 of 7)"	CpG	1321	NM_001025250	22339	Mm.282184	NM_001025250	ENSMUSG00000023951	Vegfa	Vegf|Vegf120|Vegf164|Vegf188|Vpf	vascular endothelial growth factor A	protein-coding	0.104839	0.736
Merged-chr11-33163415-2	chr11	33163356	33163475	+	9.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001252261)	promoter-TSS (NM_001252261)	-209	NM_008722	18148	Mm.485384	NM_001252260	ENSMUSG00000057113	Npm1	B23|NO38|Npm	nucleophosmin 1	protein-coding	0.084034	0.641667
Merged-chr12-108794225-2	chr12	108794167	108794284	+	9.55	cIP1vsInput|cIP2vsInput	"intron (NM_009537, intron 1 of 4)"	CpG-3499	914	NM_009537	22632	Mm.458511	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding	0.153846	0.762712
Merged-chr13-6647267-2	chr13	6647203	6647331	+	9.55	cIP1vsInput|cIP2vsInput	"intron (NM_019703, intron 1 of 21)"	"intron (NM_019703, intron 1 of 21)"	1457	NM_019703	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|PFK-C	"phosphofructokinase, platelet"	protein-coding	0.085938	0.682171
Merged-chr6-108660439-2	chr6	108660380	108660498	+	9.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011498)	promoter-TSS (NM_011498)	-190	NM_011498	20893	Mm.2436	NM_011498	ENSMUSG00000030103	Bhlhe40	Bhlhb2|C130042M06Rik|CR8|Clast5|Dec1|Sharp2|Stra13|Stra14	"basic helix-loop-helix family, member e40"	protein-coding	0.067797	0.655462
Merged-chr11-120573452-2	chr11	120573394	120573510	+	9.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011032)	promoter-TSS (NM_011032)	-516	NM_011032	18453	Mm.490258	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	"prolyl 4-hydroxylase, beta polypeptide"	protein-coding	0.094828	0.675214
Merged-chr8-57487979-2	chr8	57487925	57488033	+	9.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_021788)	promoter-TSS (NM_021788)	-119	NM_021788	60406	Mm.118	NM_021788	ENSMUSG00000031609	Sap30	30kDa	sin3 associated polypeptide	protein-coding	0.083333	0.53211
Merged-chr14-34503255-2	chr14	34503197	34503314	+	9.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009758)	promoter-TSS (NM_009758)	-709	NM_009758	12166	Mm.237825	NM_009758	ENSMUSG00000021796	Bmpr1a	1110037I22Rik|ALK3|AU045487|BMPR-IA|Bmpr	"bone morphogenetic protein receptor, type 1A"	protein-coding	0.119658	0.694915
Merged-chr7-19508734-2	chr7	19508674	19508795	+	9.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_177692)	promoter-TSS (NM_177692)	5	NM_025960	67091	Mm.442903	NM_025960	ENSMUSG00000002043	Trappc6a	1810073E21Rik|4930519D19Rik|AI480686|TRS33|mhyp	trafficking protein particle complex 6A	protein-coding	0.115702	0.655738
Merged-chr10-81627622-2	chr10	81627562	81627683	+	9.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027480)	promoter-TSS (NM_027480)	-14	NM_181586	50721	Mm.25643	NM_001163430	ENSMUSG00000034748	Sirt6	2810449N18Rik|AI043036|Sir2l6	"sirtuin 6 (silent mating type information regulation 2, homolog) 6 (S. cerevisiae)"	protein-coding	0.066116	0.565574
Merged-chr15-67039548-2	chr15	67039493	67039604	+	9.35	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-69907	NM_008681	17988	Mm.30837	NM_008681	ENSMUSG00000005125	Ndrg1	CAP43|CMT4D|DRG1|HMSNL|NMSL|Ndr1|Ndrl|PROXY1|RTP|TDD5	N-myc downstream regulated gene 1	protein-coding	0.018018	0.589286
Merged-chr17-12780309-2	chr17	12780249	12780370	+	9.35	cIP1vsInput|cIP2vsInput	"intron (NR_027784, intron 2 of 2)"	RMER20C_Mm|LTR|ERVK	-10603	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding	0.041322	0.598361
Merged-chr9-72662234-2	chr9	72662171	72662297	+	9.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010890)	promoter-TSS (NM_010890)	-113	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	"neural precursor cell expressed, developmentally down-regulated 4"	protein-coding	0.142857	0.826772
Merged-chr3-154597149-2	chr3	154597081	154597217	+	9.299999	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001168358)	promoter-TSS (NM_001168358)	-51	NM_172474	209584	Mm.347513	NM_001168358	ENSMUSG00000047583	Tyw3	5230400J09Rik	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	protein-coding	0.088235	0.627737
Merged-chr8-70873745-2	chr8	70873677	70873813	+	9.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026964)	promoter-TSS (NM_026964)	-255	NM_026964	234388	Mm.295791	NM_026964	ENSMUSG00000007721	Ccdc124	1810023B24Rik	coiled-coil domain containing 124	protein-coding	0.066176	0.576642
Merged-chr8-72517786-2	chr8	72517734	72517839	+	9.200001	cIP1vsInput|cIP2vsInput	"intron (NM_027485, intron 1 of 2)"	RMER17A2|LTR|ERVK	-25172	NM_177766	270066	Mm.291461	NM_177766		Slc35e1	6030458H05|AA408278	"solute carrier family 35, member E1"	protein-coding	0.028571	0.584906
Merged-chr2-77963168-1	chr2	77963118	77963218	+	9.2	cIP1vsInput	Intergenic	Intergenic	-16815	NM_030560	80744	Mm.288151	XM_003946079	ENSMUSG00000027014	Cwc22	AA684037|AI173004|AL022752|B230213M24|mKIAA1604	CWC22 spliceosome-associated protein homolog (S. cerevisiae)	protein-coding	0	0.376238
Merged-chr7-138907250-2	chr7	138907188	138907312	+	9.2	cIP1vsInput|cIP2vsInput	"intron (NM_009760, intron 1 of 5)"	"intron (NM_009760, intron 1 of 5)"	2256	NM_009760	12176	Mm.378890	NM_009760	ENSMUSG00000078566	Bnip3	Nip3	BCL2/adenovirus E1B interacting protein 3	protein-coding	0.016129	0.504
Merged-chr17-56626911-2	chr17	56626848	56626975	+	9.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028782)	promoter-TSS (NM_028782)	-8	NM_028782	74142	Mm.329136	NM_028782	ENSMUSG00000041168	Lonp1	1200017E13Rik|LON|Prss15	"lon peptidase 1, mitochondrial"	protein-coding	0.133858	0.664062
Merged-chr6-29272580-2	chr6	29272522	29272639	+	9.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001190461)	promoter-TSS (NM_001190461)	-46	NM_023516	69573	Mm.45161	NM_001190461	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding	0.128205	0.694915
Merged-chr9-21091764-2	chr9	21091702	21091827	+	9.15	cIP1vsInput|cIP2vsInput	"exon (NM_027911, exon 1 of 13)"	"exon (NM_027911, exon 1 of 13)"	224	NM_027911	71766	Mm.196137	NM_027911	ENSMUSG00000010205	Raver1	1300006N24Rik|AA050359|mKIAA1978	"ribonucleoprotein, PTB-binding 1"	protein-coding	0.12	0.68254
Merged-chr1-97977273-2	chr1	97977215	97977332	+	9.1	cIP1vsInput|cIP2vsInput	"intron (NM_013626, intron 1 of 25)"	"intron (NM_013626, intron 1 of 25)"	70520	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	miscRNA	0.051282	0.491525
Merged-chr6-82821917-2	chr6	82821856	82821978	+	9.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-47463	NM_013820	15277	Mm.469167	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding	0.016393	0.528455
Merged-chr5-134176792-2	chr5	134176723	134176862	+	9.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_033572)	promoter-TSS (NM_033572)	-25	NM_033572	94254	Mm.29508	NM_033572	ENSMUSG00000061979	Wbscr16	5730496C04Rik|AU019812	Williams-Beuren syndrome chromosome region 16 homolog (human)	protein-coding	0.064748	0.542857
Merged-chr17-26780966-2	chr17	26780913	26781019	+	9.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172149)	promoter-TSS (NM_172149)	-113	NM_172149	224630	Mm.21795	NM_172149	ENSMUSG00000024191	Bnip1	2010005M06Rik|5930429G21Rik|Sec20	BCL2/adenovirus E1B interacting protein 1	protein-coding	0.037736	0.495327
Merged-chrX-169982470-1	chrX	169982420	169982520	+	9	cIP1vsInput	"intron (NM_183151, intron 5 of 9)"	"intron (NM_183151, intron 5 of 9)"	-3553	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	miscRNA	0.02	0.39604
Merged-chr5-67306990-2	chr5	67306935	67307045	+	9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178651)	promoter-TSS (NM_178651)	33	NM_178651	109108	Mm.234455	NM_178651		Slc30a9	2310024J23Rik|AL024256|GAC63|HUEL	"solute carrier family 30 (zinc transporter), member 9"	protein-coding	0.163636	0.747748
Merged-chr15-41751472-2	chr15	41751415	41751529	+	9	cIP1vsInput|cIP2vsInput	"intron (NM_001130166, intron 3 of 16)"	"intron (NM_001130166, intron 3 of 16)"	-37562	NM_001130165	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding	0.017544	0.521739
Merged-chr5-93268506-2	chr5	93268437	93268575	+	8.950001	cIP1vsInput|cIP2vsInput	"intron (NM_007635, intron 1 of 7)"	CpG	933	NM_007635	12452	Mm.3527	NM_007635	ENSMUSG00000029385	Ccng2	-	cyclin G2	protein-coding	0.057971	0.654676
Merged-chr18-73815652-2	chr18	73815591	73815713	+	8.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145494)	promoter-TSS (NM_145494)	-260	NM_145494	107029	Mm.36817	NM_145494	ENSMUSG00000024556	Me2	AW120568|D030040L20Rik|NAD-ME	"malic enzyme 2, NAD(+)-dependent, mitochondrial"	protein-coding	0.106557	0.650407
Merged-chr10-79669402-2	chr10	79669345	79669459	+	8.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_148934)	promoter-TSS (NM_148934)	-8	NM_148934	110012	Mm.22623	NM_148934	ENSMUSG00000020308	Tpgs1	AV005629|Gm16517|Gtrgeo22|PGs1	tubulin polyglutamylase complex subunit 1	protein-coding	0.105263	0.634783
Merged-chr1-38471155-2	chr1	38471093	38471217	+	8.9	cIP1vsInput|cIP2vsInput	"intron (NM_010678, intron 5 of 22)"	(CA)n|Simple_repeat|Simple_repeat	193800	NM_010678	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	"AF4/FMR2 family, member 3"	protein-coding	0.024194	0.456
Merged-chr5-14954265-1	chr5	14954215	14954315	+	8.9	cIP1vsInput	"intron (NR_001584, intron 1 of 3)"	Lx|LINE|L1	8971	NR_001584	74062	Mm.394766	NR_001584		Speer8-ps1	4933405L09Rik|SPEER-8|Speer8-ps	"spermatogenesis associated glutamate (E)-rich protein 8, pseudogene 1"	pseudo	0	0.366337
Merged-chr17-56325576-2	chr17	56325512	56325641	+	8.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172132)	promoter-TSS (NM_172132)	-474	NM_172132	193796	Mm.45047	NM_172132	ENSMUSG00000024201	Kdm4b	4732474L06Rik|Jmjd2b|mKIAA0876	lysine (K)-specific demethylase 4B	protein-coding	0.054264	0.553846
Merged-chr4-14864167-2	chr4	14864103	14864232	+	8.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028264)	promoter-TSS (NM_028264)	-52	NM_028264	72519	Mm.279158	NM_028264	ENSMUSG00000028221	Tmem55a	2610319K07Rik|AI315591|AV001360	transmembrane protein 55A	protein-coding	0.062016	0.715385
Merged-chr6-112696702-2	chr6	112696644	112696760	+	8.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001167730)	promoter-TSS (NM_001167730)	-32	NM_001167730	58186	Mm.103812	NM_001167730	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 homolog (S. cerevisiae)	protein-coding	0.155172	0.623932
Merged-chr2-30967986-2	chr2	30967932	30968040	+	8.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_144884)	promoter-TSS (NM_144884)	-68	NM_144884	30931	Mm.154994	NM_144884	ENSMUSG00000026849	Tor1a	DQ2|Dyt1|torsinA	"torsin family 1, member A (torsin A)"	protein-coding	0.055556	0.59633
Merged-chr8-20424845-2	chr8	20424795	20424896	+	8.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_028428)	promoter-TSS (NR_028428)	-31	NR_028428	381598	Mm.483074	NM_001024708	ENSMUSG00000071793	2610005L07Rik	2810038F24Rik|6720476A01Rik	cadherin 11 pseudogene	pseudo	0.079208	0.666667
Merged-chr6-30047975-2	chr6	30047919	30048031	+	8.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001164230)	promoter-TSS (NM_001164230)	-13	NM_010938	18181	Mm.259258	NM_001164226	ENSMUSG00000058440	Nrf1	C87038|D6Ertd415e	nuclear respiratory factor 1	protein-coding	0.160714	0.787611
Merged-chr8-84712681-2	chr8	84712628	84712734	+	8.75	cIP1vsInput|cIP2vsInput	"intron (NM_010906, intron 8 of 8)"	"intron (NM_010906, intron 8 of 8)"	11224	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding	0.018868	0.588785
Merged-chr13-55714614-2	chr13	55714561	55714667	+	8.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175150)	promoter-TSS (NM_175150)	-36	NM_175150	69672	Mm.474297	NM_175150	ENSMUSG00000021497	Txndc15	2310047H23Rik|AI854086|C5orf14|UNQ335	thioredoxin domain containing 15	protein-coding	0.113208	0.700935
Merged-chr8-35376638-2	chr8	35376585	35376692	+	8.75	cIP1vsInput|cIP2vsInput	"intron (NM_177741, intron 1 of 1)"	CpG	897	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	"protein phosphatase 1, regulatory (inhibitor) subunit 3B"	protein-coding	0.056075	0.601852
Merged-chr2-154892936-2	chr2	154892884	154892989	+	8.700001	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026030)	promoter-TSS (NM_026030)	-30	NM_026030	67204	Mm.470088	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	"eukaryotic translation initiation factor 2, subunit 2 (beta)"	protein-coding	0.104762	0.59434
Merged-chr7-80134603-2	chr7	80134553	80134653	+	8.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	18412	NR_035491	100316758		NR_035491	ENSMUSG00000088619	Mir1965	mmu-mir-1965	microRNA 1965	miscRNA	0.03	0.60396
Merged-chr11-55113978-2	chr11	55113916	55114040	+	8.65	cIP1vsInput|cIP2vsInput	TTS (NM_010299)	TTS (NM_010299)	15993	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding	0.016129	0.552
Merged-chr7-41499538-2	chr7	41499477	41499600	+	8.65	cIP1vsInput|cIP2vsInput	"5' UTR (NM_001033530, exon 1 of 4)"	"5' UTR (NM_001033530, exon 1 of 4)"	352	NM_001033530	101835	Mm.370336	NM_001033530	ENSMUSG00000074166	AW146154	AI451288	expressed sequence AW146154	protein-coding	0.03252	0.508065
Merged-chr5-24445268-2	chr5	24445209	24445327	+	8.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_023229)	promoter-TSS (NM_023229)	-33	NM_023229	66587	Mm.28123	NM_023229	ENSMUSG00000028959	Fastk	0610011K02Rik|610011K02Rik	Fas-activated serine/threonine kinase	protein-coding	0.135593	0.764706
Merged-chr11-5902111-2	chr11	5902045	5902177	+	8.65	cIP1vsInput|cIP2vsInput	"exon (NM_010292, exon 9 of 10)"	"exon (NM_010292, exon 9 of 10)"	-3329	NM_022879	17898	Mm.46514	NM_022879	ENSMUSG00000020469	Myl7	MLC-2alpha|MLC2a|MYL2A|Mylc2a|RLC-A	"myosin, light polypeptide 7, regulatory"	protein-coding	0.106061	0.646617
Merged-chr4-116708536-2	chr4	116708483	116708589	+	8.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026714)	promoter-TSS (NM_026714)	-151	NM_025962	67096	Mm.252785	NM_025962	ENSMUSG00000028690	Mmachc	1810037K07Rik	"methylmalonic aciduria cblC type, with homocystinuria"	protein-coding	0.075472	0.53271
Merged-chr10-62340408-2	chr10	62340353	62340464	+	8.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_038038)	promoter-TSS (NR_038038)	13	NM_001146100	15275	Mm.196605	NM_001146100	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding	0.108108	0.678571
Merged-chr6-21949956-2	chr6	21949899	21950013	+	8.55	cIP1vsInput|cIP2vsInput	"intron (NM_023626, intron 1 of 11)"	CpG	341	NM_023626	71777	Mm.39999	NM_023626	ENSMUSG00000029670	Ing3	1300013A07Rik|P47ING3	"inhibitor of growth family, member 3"	protein-coding	0.149123	0.704348
Merged-chr4-154856344-2	chr4	154856276	154856413	+	8.5	cIP1vsInput|cIP2vsInput	"5' UTR (NM_172878, exon 1 of 7)"	"5' UTR (NM_172878, exon 1 of 7)"	144	NM_172878	242800	Mm.72944	NM_172878	ENSMUSG00000046637	Ttc34	4932418L02|B230396O12Rik	tetratricopeptide repeat domain 34	protein-coding	0.094891	0.688406
Merged-chr9-21225355-2	chr9	21225302	21225409	+	8.5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	13977	NM_016679	50868	Mm.248266	NM_001110305	ENSMUSG00000003308	Keap1	INRF2|mKIAA0132	kelch-like ECH-associated protein 1	protein-coding	0.046729	0.564815
Merged-chr9-49403893-2	chr9	49403837	49403949	+	8.5	cIP1vsInput|cIP2vsInput	"intron (NM_010077, intron 6 of 7)"	"intron (NM_010077, intron 6 of 7)"	23128	NM_172922	244859	Mm.119994	NM_172922	ENSMUSG00000032257	Ankk1	9930020N01Rik	ankyrin repeat and kinase domain containing 1	protein-coding	0.008929	0.424779
Merged-chrY-7030894-1	chrY	7030844	7030944	+	8.5	cIP1vsInput	Intergenic	Intergenic	136883	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.267327
Merged-chr3-152304605-2	chr3	152304530	152304680	+	8.5	cIP1vsInput|cIP2vsInput	"intron (NM_174868, intron 7 of 15)"	"intron (NM_174868, intron 7 of 15)"	35802	NM_001162375	215708	Mm.135018	NM_001162375	ENSMUSG00000054942	Fam73a	A930038D06|AI852168|C030011O14Rik	"family with sequence similarity 73, member A"	protein-coding	0.02	0.516556
Merged-chr7-19166225-2	chr7	19166157	19166294	+	8.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001080815)	promoter-TSS (NM_001080815)	-98	NM_001080815	381853	Mm.333633	NM_001080815	ENSMUSG00000030406	Gipr	GIP-R|Gm1081|Gm160	gastric inhibitory polypeptide receptor	protein-coding	0.036496	0.608696
Merged-chr9-115311001-2	chr9	115310942	115311061	+	8.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_024222)	promoter-TSS (NM_024222)	-580	NM_024222	68292	Mm.296158	NM_024222	ENSMUSG00000032437	Stt3b	1300006C19Rik|Simp	"STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"	protein-coding	0.07563	0.666667
Merged-chr11-44520492-2	chr11	44520427	44520558	+	8.4	cIP1vsInput|cIP2vsInput	"intron (NM_001166553, intron 1 of 5)"	"intron (NM_001166553, intron 1 of 5)"	1115	NM_001166553	74315	Mm.156771	NM_001166553	ENSMUSG00000019189	Rnf145	3732413I11Rik|TMRF1	ring finger protein 145	protein-coding	0.045802	0.560606
Merged-chr16-58670135-2	chr16	58670078	58670193	+	8.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007757)	promoter-TSS (NM_007757)	-73	NM_007757	12892	Mm.291519	NM_007757	ENSMUSG00000022742	Cpox	CPX|Cpo|HCP	coproporphyrinogen oxidase	protein-coding	0.052174	0.603448
Merged-chr4-153957020-2	chr4	153956963	153957077	+	8.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175287)	promoter-TSS (NM_175287)	-217	NM_175287	97159	Mm.7066	NM_001163019	ENSMUSG00000047613	A430005L14Rik	C79672	RIKEN cDNA A430005L14 gene	protein-coding	0.087719	0.686957
Merged-chrX-92796124-2	chrX	92796070	92796179	+	8.35	cIP1vsInput|cIP2vsInput	Intergenic	B1_Mm|SINE|Alu	-196552	NM_173783	215641	Mm.327999	NM_173783	ENSMUSG00000067649	Mageb18	B430216B18Rik	"melanoma antigen family B, 18"	protein-coding	0	0.5
Merged-chr11-79254785-2	chr11	79254722	79254849	+	8.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019653)	promoter-TSS (NM_019653)	-90	NM_019653	78889	Mm.474790	NM_001042565	ENSMUSG00000017677	Wsb1	1110056B13Rik|2700038M07Rik	WD repeat and SOCS box-containing 1	protein-coding	0.102362	0.632812
Merged-chr4-145446994-1	chr4	145446944	145447044	+	8.3	cIP1vsInput	Intergenic	Intergenic	-17216	NR_002888	545700	Mm.389595	NR_002888	ENSMUSG00000052912	Smarca5-ps	9230115A19Rik|OTTMUSG00000011029	"SWI/SNF related, matrix associated, actin depenent ragulator of chromatin, subfamily a, member 5, pseudogene"	pseudo	0	0.326733
Merged-chr15-9071383-2	chr15	9071322	9071445	+	8.3	cIP1vsInput|cIP2vsInput	"5' UTR (NM_001085410, exon 1 of 14)"	"5' UTR (NM_001085410, exon 1 of 14)"	123	NM_001040395	68646	Mm.468219	NM_001040395	ENSMUSG00000022253	Nadkd1	1110020G09Rik|4933430B08Rik	NAD kinase domain containing 1	protein-coding	0.138211	0.798387
Merged-chr8-60983481-2	chr8	60983420	60983542	+	8.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_173874)	promoter-TSS (NM_173874)	-170	NM_173874	12725	Mm.259751	NM_007711	ENSMUSG00000004319	Clcn3	Clc3	chloride channel 3	protein-coding	0.114754	0.699187
Merged-chr2-164785895-2	chr2	164785834	164785957	+	8.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133924)	promoter-TSS (NM_133924)	-126	NM_133924	101113	Mm.475604	NM_133924		Snx21	5730407K14Rik|AI481716	sorting nexin family member 21	protein-coding	0.138211	0.782258
Merged-chr9-53706134-2	chr9	53706081	53706187	+	8.299999	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175562)	promoter-TSS (NM_175562)	98	NM_175562	270160	Mm.290285	NM_175562	ENSMUSG00000055069	Rab39	C230094F14Rik|Rab39a	"RAB39, member RAS oncogene family"	protein-coding	0.084906	0.570093
Merged-chr13-52980628-2	chr13	52980565	52980692	+	8.25	cIP1vsInput|cIP2vsInput	"intron (NM_017373, intron 1 of 1)"	CpG	411	NM_017373	18030	Mm.136604	NM_017373	ENSMUSG00000056749	Nfil3	AV225605|E4BP4	"nuclear factor, interleukin 3, regulated"	protein-coding	0.086614	0.648438
Merged-chr8-19784734-2	chr8	19784639	19784829	+	8.25	cIP1vsInput|cIP2vsInput	"intron (NM_001270553, intron 6 of 9).2"	CpG	55158	NM_001039553	626415	Mm.425517	NM_001039553		4930467E23Rik	ENSMUSG00000074453|OTTMUSG00000018948|TSAP	RIKEN cDNA 4930467E23 gene	protein-coding	0.078947	0.643979
Merged-chr3-22076374-2	chr3	22076316	22076432	+	8.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_030732)	promoter-TSS (NM_030732)	-278	NM_030732	81004	Mm.446265	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding	0.034483	0.709402
Merged-chrX-93832194-2	chrX	93832134	93832255	+	8.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145630)	promoter-TSS (NM_145630)	-99	NM_145630	236900	Mm.12775	NM_145630	ENSMUSG00000035232	Pdk3	2610001M10Rik|AI035637	"pyruvate dehydrogenase kinase, isoenzyme 3"	protein-coding	0.165289	0.754098
Merged-chr18-75495125-2	chr18	75495052	75495198	+	8.15	cIP1vsInput|cIP2vsInput	"intron (NM_201354, intron 9 of 11)"	(TCCCC)n|Simple_repeat|Simple_repeat	-19520	NR_045879	100038353	Mm.440724	NR_045879	ENSMUSG00000097712	Gm10532	ENSMUSG00000073534	predicted gene 10532	miscRNA	0.054795	0.646259
Merged-chr9-119322915-2	chr9	119322850	119322980	+	8.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133985)	promoter-TSS (NM_133985)	-488	NM_133985	108737	Mm.293565	NM_133985	ENSMUSG00000036737	Oxsr1	2210022N24Rik|2810422B09Rik|AI462649|AW209236|Osr1|mKIAA1101	oxidative-stress responsive 1	protein-coding	0.130769	0.679389
Merged-chr4-105101584-2	chr4	105101522	105101646	+	8.15	cIP1vsInput|cIP2vsInput	"intron (NM_178143, intron 1 of 8)"	"intron (NM_178143, intron 1 of 8)"	8314	NM_178143	108079	Mm.48638	NM_178143	ENSMUSG00000028518	Prkaa2	2310008I11Rik|A830082D05|AMPKalpha2	"protein kinase, AMP-activated, alpha 2 catalytic subunit"	protein-coding	0.024194	0.376
Merged-chr11-31371405-2	chr11	31371333	31371478	+	8.1	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-1344	NM_011491	20856	Mm.32506	NM_011491		Stc2	AW125853|Stc2l|mustc2	stanniocalcin 2	protein-coding	0.082759	0.623288
Merged-chrY-7010901-1	chrY	7010851	7010951	+	8.1	cIP2vsInput	Intergenic	RLTR22_Mur|LTR|ERVK	156876	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.02	0.386139
Merged-chr6-38433645-2	chr6	38433587	38433704	+	8.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_177185)	promoter-TSS (NM_177185)	-280	NM_177185	320538	Mm.302831	NM_177185	ENSMUSG00000038538	Ubn2	2900060J04Rik|6030408G03Rik|BC060116|D130059P03Rik|mKIAA2030	ubinuclein 2	protein-coding	0.128205	0.70339
Merged-chr6-47651220-1	chr6	47651170	47651270	+	8	cIP1vsInput	Intergenic	CpG	3874	NR_002841	19799		NR_002841		Rn4.5s	-	4.5S RNA	rRNA	0.1	0.70297
Merged-chr1-51478336-2	chr1	51478277	51478396	+	8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028696)	promoter-TSS (NM_028696)	63	NM_028696	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a	nucleic acid binding protein 1	protein-coding	0.10084	0.658333
Merged-chr1-79776051-1	chr1	79776001	79776101	+	8	cIP2vsInput	promoter-TSS (NM_001081210)	promoter-TSS (NM_001081210)	33	NM_001081210	69163	Mm.238455	NM_001081210	ENSMUSG00000026248	Mrpl44	1810030E18Rik|5730593H20Rik|AI463302	mitochondrial ribosomal protein L44	protein-coding	0.08	0.643564
Merged-chr7-100706572-2	chr7	100706519	100706626	+	8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178764)	promoter-TSS (NM_178764)	-130	NM_178764	319604	Mm.260362	NM_178764	ENSMUSG00000029461	Fam168a	2610030B18Rik|B930006L02Rik|mKIAA0280	"family with sequence similarity 168, member A"	protein-coding	0.093458	0.685185
Merged-chr16-52074731-1	chr16	52074681	52074781	+	8	cIP2vsInput	"intron (NM_001033238, intron 3 of 17)"	(CACAT)n|Simple_repeat|Simple_repeat	43182	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding	0	0.326733
Merged-chr5-30701649-2	chr5	30701595	30701703	+	8	cIP1vsInput|cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	-10246	NM_023047	65254	Mm.27732	NM_023047	ENSMUSG00000029168	Dpysl5	CRAM|CRMP-5|Crmp5	dihydropyrimidinase-like 5	protein-coding	0.018519	0.568807
Merged-chr6-51470042-2	chr6	51469983	51470101	+	8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_182650)	promoter-TSS (NM_182650)	-148	NM_016806	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding	0.09322	0.588235
Merged-chr1-128416865-2	chr1	128416814	128416917	+	8	cIP1vsInput|cIP2vsInput	"intron (NM_177445, intron 1 of 15)"	CpG	551	NM_177445	226414	Mm.28693	NM_145507	ENSMUSG00000026356	Dars	5730439G15Rik	aspartyl-tRNA synthetase	protein-coding	0.097087	0.644231
Merged-chr7-24530566-2	chr7	24530512	24530621	+	7.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_153134)	promoter-TSS (NM_153134)	-82	NM_153134	210146	Mm.41108	NM_153134	ENSMUSG00000041037	Irgq	AF322649|FKSG27|Irgq1	"immunity-related GTPase family, Q"	protein-coding	0.082569	0.572727
Merged-chr16-64851660-2	chr16	64851610	64851710	+	7.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178647)	promoter-TSS (NM_178647)	-425	NM_178647	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding	0.16	0.772277
Merged-chr10-62865359-2	chr10	62865304	62865414	+	7.9	cIP1vsInput|cIP2vsInput	"intron (NM_001253857, intron 1 of 11)"	"intron (NM_001253857, intron 1 of 11)"	14655	NM_027384	52463	Mm.17774	NM_001253857	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding	0.009091	0.54955
Merged-chr11-105749444-2	chr11	105749369	105749520	+	7.9	cIP1vsInput|cIP2vsInput	"intron (NM_181071, intron 4 of 25)"	"intron (NM_181071, intron 4 of 25)"	159458	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	"tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2"	protein-coding	0	0.388158
Merged-chr11-98457568-2	chr11	98457511	98457625	+	7.9	cIP1vsInput|cIP2vsInput	Intergenic	CpG	10734	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding	0.061404	0.582609
Merged-chr3-135438680-1	chr3	135438630	135438730	+	7.9	cIP2vsInput	promoter-TSS (NR_030689)	promoter-TSS (NR_030689)	-15	NR_030689	319587	Mm.474537	NR_030689		4930539J05Rik	8030475D13Rik	RIKEN cDNA 4930539J05 gene	miscRNA	0.18	0.782178
Merged-chr14-64440607-2	chr14	64440553	64440662	+	7.9	cIP1vsInput|cIP2vsInput	"intron (NM_001253712, intron 1 of 5)"	CpG	419	NM_001253715	110265	Mm.26713	NM_001253712	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding	0.100917	0.709091
Merged-chr11-53098962-2	chr11	53098896	53099029	+	7.85	cIP1vsInput|cIP2vsInput	"intron (NM_177059, intron 6 of 15)"	"intron (NM_177059, intron 6 of 15)"	21094	NR_046047	790909	Mm.404626	NR_046047	ENSMUSG00000087668	Gm11186	OTTMUSG00000000039	predicted gene 11186	miscRNA	0.007519	0.470149
Merged-chr7-43579542-2	chr7	43579472	43579613	+	7.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172482)	promoter-TSS (NM_172482)	-44	NM_172482	210105	Mm.234422	NM_172482	ENSMUSG00000030469	Zfp719	8030458J18|9430094P17Rik|C630016O21Rik|mszf6	zinc finger protein 719	protein-coding	0.042553	0.528169
Merged-chr7-17060208-2	chr7	17060134	17060283	+	7.8	cIP1vsInput|cIP2vsInput	"intron (NM_001162950, intron 1 of 14)"	"intron (NM_001162950, intron 1 of 14)"	2219	NM_001162950	53417	Mm.135110	NM_001162950	ENSMUSG00000004328	Hif3a	Ipas|MOP7|NEPAS|bHLHe17	"hypoxia inducible factor 3, alpha subunit"	protein-coding	0.033557	0.66
Merged-chr10-38908415-2	chr10	38908350	38908480	+	7.8	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-57100	NM_010681	16775	Mm.258065	NM_010681	ENSMUSG00000019846	Lama4	-	"laminin, alpha 4"	protein-coding	0.007692	0.519084
Merged-chr15-98934110-2	chr15	98934057	98934163	+	7.8	cIP1vsInput|cIP2vsInput	"intron (NM_011654, intron 1 of 3)"	CpG	280	NM_011654	22143	Mm.405359	NM_011654	ENSMUSG00000023004	Tuba1b	Tuba2	"tubulin, alpha 1B"	protein-coding	0.066038	0.598131
Merged-chr19-44293837-2	chr19	44293785	44293890	+	7.8	cIP1vsInput|cIP2vsInput	"5' UTR (NM_009128, exon 1 of 6)"	"5' UTR (NM_009128, exon 1 of 6)"	161	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Scd-2|swty	stearoyl-Coenzyme A desaturase 2	protein-coding	0.038095	0.641509
Merged-chr9-22133206-1	chr9	22133156	22133256	+	7.8	cIP2vsInput	"intron (NM_001102405, intron 1 of 4)"	"intron (NM_001102405, intron 1 of 4)"	-1341	NM_001102404	11433	Mm.46354	NM_001102404	ENSMUSG00000001348	Acp5	TRACP|TRAP	"acid phosphatase 5, tartrate resistant"	protein-coding	0	0.475248
Merged-chr13-24566157-2	chr13	24566096	24566219	+	7.8	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	38610	NR_024599	76024	Mm.440710	NR_024599		Gm11346	5830431A10Rik|AI447617|Gm11347|OTTMUSG00000000601|OTTMUSG00000000602	X-linked lymphocyte-regulated 5 pseudogene	pseudo	0.00813	0.516129
Merged-chrY-90810792-1	chrY	90810742	90810842	+	7.8	cIP1vsInput	"intron (NM_133362, intron 2 of 2)"	"intron (NM_133362, intron 2 of 2)"	25350	NM_133362	170942	Mm.391385	XM_003946384	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding	0.01	0.336634
Merged-chr4-101420095-2	chr4	101420035	101420155	+	7.75	cIP1vsInput|cIP2vsInput	"intron (NM_001177605, intron 2 of 5)"	CpG	392	NM_009647	11639	Mm.42040	NM_001177602	ENSMUSG00000028527	Ak4	Ak-3|Ak-4|Ak3|Ak3l1|D4Ertd274e	adenylate kinase 4	protein-coding	0.191667	0.842975
Merged-chr8-105283241-2	chr8	105283183	105283300	+	7.75	cIP1vsInput|cIP2vsInput	"exon (NM_028888, exon 6 of 8)"	"exon (NM_028888, exon 6 of 8)"	6287	NM_001166394	74356	Mm.490326	NM_001166394	ENSMUSG00000014837	4931428F04Rik	AI426165|Kiaa0895l	RIKEN cDNA 4931428F04 gene	protein-coding	0.094017	0.635593
Merged-chr11-120949057-1	chr11	120949007	120949107	+	7.7	cIP2vsInput	promoter-TSS (NM_001038654)	promoter-TSS (NM_001038654)	-10	NM_001038653	80879	Mm.28632	NM_001038653	ENSMUSG00000025161	Slc16a3	Mct3|Mct4	"solute carrier family 16 (monocarboxylic acid transporters), member 3"	protein-coding	0.17	0.782178
Merged-chr6-86527172-1	chr6	86527122	86527222	+	7.7	cIP2vsInput	promoter-TSS (NR_037961)	promoter-TSS (NR_037961)	-158	NR_037960	72012	Mm.349174	NR_037960	ENSMUSG00000097048	1600020E01Rik	-	RIKEN cDNA 1600020E01 gene	miscRNA	0.1	0.663366
Merged-chr1-178318571-2	chr1	178318493	178318650	+	7.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025511)	promoter-TSS (NM_025511)	-582	NM_025511	66359	Mm.489720	NM_025511	ENSMUSG00000026500	Cox20	2310005N03Rik|Fam36a	COX20 Cox2 chaperone	protein-coding	0.11465	0.696203
Merged-chr19-44284142-2	chr19	44284091	44284194	+	7.7	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-9534	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Scd-2|swty	stearoyl-Coenzyme A desaturase 2	protein-coding	0.07767	0.644231
Merged-chr19-32757582-1	chr19	32757532	32757632	+	7.7	cIP2vsInput	promoter-TSS (NM_008960)	promoter-TSS (NM_008960)	5	NM_008960	19211	Mm.245395	NM_177096	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding	0.13	0.70297
Merged-chr5-30888820-2	chr5	30888769	30888871	+	7.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001048192)	promoter-TSS (NM_001048192)	-32	NM_174849	231093	Mm.440364	NM_001048190	ENSMUSG00000029165	Agbl5	4930455N08|9430057O19Rik|CCP5	ATP/GTP binding protein-like 5	protein-coding	0.107843	0.68932
Merged-chr8-36549340-2	chr8	36549276	36549404	+	7.7	cIP1vsInput|cIP2vsInput	Intergenic	CpG	60149	NM_176952	319582	Mm.180924	NM_176952	ENSMUSG00000039620	6430573F11Rik	Kiaa1456	RIKEN cDNA 6430573F11 gene	protein-coding	0.070312	0.682171
Merged-chr15-76576312-2	chr15	76576258	76576366	+	7.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172960)	promoter-TSS (NM_172960)	-47	NM_172960	268822	Mm.181624	NM_172960	ENSMUSG00000022550	Adck5	A230108P17	aarF domain containing kinase 5	protein-coding	0.083333	0.66055
Merged-chr10-81194533-2	chr10	81194477	81194590	+	7.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_015477)	promoter-TSS (NR_015477)	-158	NR_015477	69678	Mm.81562	NR_015477		2310050B05Rik	-	RIKEN cDNA 2310050B05 gene	miscRNA	0.088496	0.719298
Merged-chr3-89773365-2	chr3	89773309	89773421	+	7.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027315)	promoter-TSS (NM_027315)	-244	NM_027315	70093	Mm.41438	NM_027315	ENSMUSG00000042572	Ube2q1	1110002C01Rik|2310012M18Rik|AI854014|Gtap|NICE-5|PRO3094|Ube2q	ubiquitin-conjugating enzyme E2Q (putative) 1	protein-coding	0.116071	0.681416
Merged-chr8-84856937-2	chr8	84856877	84856997	+	7.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025648)	promoter-TSS (NM_025648)	-49	NM_025648	66590	Mm.292517	NM_025648	ENSMUSG00000003808	Farsa	0610012A19Rik|Farsla	"phenylalanyl-tRNA synthetase, alpha subunit"	protein-coding	0.091667	0.561983
Merged-chr8-109693350-2	chr8	109693297	109693403	+	7.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028018)	promoter-TSS (NM_028018)	-56	NM_028018	71955	Mm.290036	NM_028018	ENSMUSG00000031729	Ist1	2400003C14Rik|AW536298|mKIAA0174	increased sodium tolerance 1 homolog (yeast)	protein-coding	0.075472	0.654206
Merged-chr7-98656908-2	chr7	98656854	98656963	+	7.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172280)	promoter-TSS (NM_172280)	-339	NM_172280	233545	Mm.387819	NM_172280	ENSMUSG00000035401	2210018M11Rik	2310016L09Rik|AU019521|AU019557|Emsy	RIKEN cDNA 2210018M11 gene	protein-coding	0.100917	0.581818
Merged-chr2-173737550-2	chr2	173737496	173737605	+	7.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019806)	promoter-TSS (NM_019806)	-21	NM_019806	56491	Mm.260456	NM_019806	ENSMUSG00000054455	Vapb	AI225786|AI840687|AI848259|D2Abb2e|R75548|VAP33b|Vamp33b	"vesicle-associated membrane protein, associated protein B and C"	protein-coding	0.165138	0.709091
Merged-chr7-19361175-2	chr7	19361118	19361233	+	7.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001010836)	promoter-TSS (NM_001010836)	-41	NM_001010836	333654	Mm.333640	NM_001010836	ENSMUSG00000040734	Ppp1r13l	AV260376|IASPP|Nkip1|wa3	"protein phosphatase 1, regulatory (inhibitor) subunit 13 like"	protein-coding	0.06087	0.62069
Merged-chr5-23434365-1	chr5	23434315	23434415	+	7.6	cIP2vsInput	promoter-TSS (NM_026984)	promoter-TSS (NM_026984)	-12	NR_040469	269630	Mm.436103	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	miscRNA	0.13	0.782178
Merged-chr13-46728039-1	chr13	46727989	46728089	+	7.6	cIP2vsInput	promoter-TSS (NM_175749)	promoter-TSS (NM_175749)	-190	NM_175749	218210	Mm.445069	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding	0.12	0.673267
Merged-chr2-107227779-2	chr2	107227723	107227835	+	7.6	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-62810	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	"potassium voltage-gated channel, shaker-related subfamily, member 4"	protein-coding	0	0.40708
Merged-chr4-149426757-2	chr4	149426706	149426808	+	7.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_022022)	promoter-TSS (NM_022022)	-126	NM_022022	63958	Mm.415260	NM_022022	ENSMUSG00000028960	Ube4b	4930551I19Rik|4933406G05Rik|AU014668|D4Bwg0973e|UFD2|UFD2a|Ufd2p|mKIAA0684	"ubiquitination factor E4B, UFD2 homolog (S. cerevisiae)"	protein-coding	0.068627	0.718447
Merged-chr2-30441885-2	chr2	30441825	30441945	+	7.55	cIP1vsInput|cIP2vsInput	"intron (NM_138748, intron 8 of 9)"	"intron (NM_138748, intron 8 of 9)"	25835	NM_138748	110854	Mm.275393	NM_138748	ENSMUSG00000039515	Ppp2r4	2610042B21Rik|C77440|N28142|PR53	"protein phosphatase 2A, regulatory subunit B (PR 53)"	protein-coding	0.016667	0.578512
Merged-chr17-31746950-2	chr17	31746888	31747012	+	7.55	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	69005	NM_013501	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	AI323437|Acry-1|Crya-1|Crya1|DAcry-1|lop18	"crystallin, alpha A"	protein-coding	0.024194	0.624
Merged-chr10-42276797-2	chr10	42276744	42276850	+	7.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019740)	promoter-TSS (NM_019740)	-55	NM_019740	56484	Mm.466459	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding	0.103774	0.766355
Merged-chr5-93266987-2	chr5	93266925	93267049	+	7.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007635)	promoter-TSS (NM_007635)	-586	NM_007635	12452	Mm.3527	NM_007635	ENSMUSG00000029385	Ccng2	-	cyclin G2	protein-coding	0.064516	0.624
Merged-chr10-3973711-2	chr10	3973653	3973770	+	7.55	cIP1vsInput|cIP2vsInput	"intron (NM_001170786, intron 1 of 27)"	CpG	636	NM_172308	270685	Mm.184752	NM_001170785	ENSMUSG00000040675	Mthfd1l	2410004L15Rik|AI647056|Fthfsdc1	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	protein-coding	0.136752	0.737288
Merged-chr5-31811185-2	chr5	31811128	31811242	+	7.5	cIP1vsInput|cIP2vsInput	"intron (NM_181279, intron 6 of 13)"	"intron (NM_181279, intron 6 of 13)"	113135	NM_181282	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding	0.017544	0.504348
Merged-chr5-143527525-2	chr5	143527473	143527577	+	7.5	cIP1vsInput|cIP2vsInput	"intron (NM_009007, intron 1 of 5)"	CpG	468	NM_009007	19353	Mm.475073	NM_009007	ENSMUSG00000001847	Rac1	AL023026|D5Ertd559e	RAS-related C3 botulinum substrate 1	protein-coding	0.096154	0.628571
Merged-chr7-12010768-1	chr7	12010718	12010818	+	7.5	cIP1vsInput	Intergenic	Intergenic	-30531	NM_001166731	628946	Mm.484974	NM_001166731	ENSMUSG00000095864	Vmn1r77	Gm6935	vomeronasal 1 receptor 77	protein-coding	0.02	0.633663
Merged-chr4-141139904-2	chr4	141139851	141139958	+	7.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001025608)	promoter-TSS (NM_001025608)	-108	NR_102343	213491	Mm.332006	NM_174996	ENSMUSG00000040842	Szrd1	1110022I03|D4Ertd22e	SUZ RNA binding domain containing 1	protein-coding	0.046729	0.648148
Merged-chr18-35562084-2	chr18	35562012	35562157	+	7.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010771)	promoter-TSS (NM_010771)	-74	NM_010771	17184	Mm.215034	NM_010771	ENSMUSG00000037236	Matr3	1110061A14Rik|2810017I02Rik|AI841759|AW555618|D030046F20Rik|mKIAA0723	matrin 3	protein-coding	0.110345	0.705479
Merged-chr4-8647209-2	chr4	8647154	8647264	+	7.5	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-43197	NM_001277149	320790	Mm.138792	NM_001277149	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding	0.118182	0.720721
Merged-chr11-29373606-1	chr11	29373556	29373656	+	7.5	cIP2vsInput	promoter-TSS (NM_176841)	promoter-TSS (NM_176841)	-566	NM_176841	108686	Mm.441367	NM_176841	ENSMUSG00000032740	Ccdc88a	A430106J12Rik|AI848406|Ape|C130096N06Rik|C330012F17Rik|D130005J21Rik|Girdin|Giv|Grdn|Hkrp1	coiled coil domain containing 88A	protein-coding	0.15	0.782178
Merged-chr4-111414870-2	chr4	111414802	111414938	+	7.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026279)	promoter-TSS (NM_026279)	-136	NR_033793	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding	0.073529	0.532847
Merged-chr17-57105403-2	chr17	57105343	57105464	+	7.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009404)	promoter-TSS (NM_009404)	18	NM_009404	21950	Mm.41171	NM_009404	ENSMUSG00000035678	Tnfsf9	4-1BB-L|4-1BBL|AI848817|Cd137l|Ly63l	"tumor necrosis factor (ligand) superfamily, member 9"	protein-coding	0.066116	0.614754
Merged-chr14-54618091-2	chr14	54618035	54618148	+	7.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011186)	promoter-TSS (NM_011186)	-96	NM_011186	19173	Mm.8911	NM_011186	ENSMUSG00000022193	Psmb5	-	"proteasome (prosome, macropain) subunit, beta type 5"	protein-coding	0.079646	0.561404
Merged-chr19-46309266-1	chr19	46309216	46309316	+	7.4	cIP2vsInput	"exon (NM_001177369, exon 14 of 23)"	"exon (NM_001177369, exon 14 of 23)"	3336	NM_001177370	18034	Mm.102365	NM_001177369	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	"nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100"	protein-coding	0.12	0.653465
Merged-chr9-45984588-1	chr9	45984538	45984638	+	7.4	cIP2vsInput	"intron (NM_008775, intron 1 of 5)"	CpG	283	NM_008775	18475	Mm.200859	NM_008775	ENSMUSG00000003131	Pafah1b2	AI747451|AU021353|Pafahb|mus[b]	"platelet-activating factor acetylhydrolase, isoform 1b, subunit 2"	protein-coding	0.15	0.831683
Merged-chr16-30064279-2	chr16	30064229	30064330	+	7.4	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-1078	NM_008235	15205	Mm.390859	NM_008235	ENSMUSG00000022528	Hes1	Hry|bHLHb39	hairy and enhancer of split 1 (Drosophila)	protein-coding	0.128713	0.754902
Merged-chr8-126594671-2	chr8	126594621	126594722	+	7.4	cIP1vsInput|cIP2vsInput	Intergenic	CpG-14677	-1235	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding	0.089109	0.686275
Merged-chr6-108668560-2	chr6	108668509	108668612	+	7.4	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-7626	NR_040758	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	miscRNA	0.106796	0.605769
Merged-chr8-23388489-2	chr8	23388426	23388552	+	7.35	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-23013	NM_013834	20377	Mm.281691	NM_013834	ENSMUSG00000031548	Sfrp1	2210415K03Rik|AW011917|AW107218|AW742929|sFRP-1	secreted frizzled-related protein 1	protein-coding	0.007937	0.566929
Merged-chr1-64617835-2	chr1	64617778	64617892	+	7.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025964)	promoter-TSS (NM_025964)	-667	NM_025964	67099	Mm.46394	NM_025964	ENSMUSG00000025956	Mettl21a	2310038H17Rik|AI464204|Fam119a	methyltransferase like 21A	protein-coding	0.035088	0.608696
Merged-chr2-103797555-2	chr2	103797499	103797612	+	7.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001111292)	promoter-TSS (NM_001111292)	85	NM_001111291	53872	Mm.427589	NM_001111289	ENSMUSG00000027184	Caprin1	AL022980|Caprin-1|Gpiap|Gpiap1|Mmgpip137|P137|rng105	cell cycle associated protein 1	protein-coding	0.088496	0.692982
Merged-chr15-79347960-2	chr15	79347908	79348012	+	7.35	cIP1vsInput|cIP2vsInput	"intron (NM_010755, intron 1 of 2)"	CpG	282	NM_010755	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	"v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)"	protein-coding	0.125	0.714286
Merged-chr2-14140275-2	chr2	14140220	14140330	+	7.35	cIP1vsInput|cIP2vsInput	"intron (NM_011484, intron 12 of 13)"	RMER17B|LTR|ERVK	-34249	NM_001081310	625286	Mm.158781	NM_001081310	ENSMUSG00000061531	Tmem236	2010003H20Rik|Fam23a|Gm613	transmembrane protein 236	protein-coding	0.009091	0.576577
Merged-chr6-55016328-2	chr6	55016262	55016395	+	7.35	cIP1vsInput|cIP2vsInput	Intergenic	L1MB2|LINE|L1	-21673	NM_180678	353172	Mm.250004	NM_180678	ENSMUSG00000029777	Gars	Nmf249|Sgrp23	glycyl-tRNA synthetase	protein-coding	0.015038	0.447761
Merged-chr8-22859497-2	chr8	22859440	22859555	+	7.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081149)	promoter-TSS (NM_001081149)	-42	NM_001081149	244349	Mm.182776	NM_001081149	ENSMUSG00000031540	Kat6a	1500036M03|9930021N24Rik|MOZ|Myst3|Zfp220	K(lysine) acetyltransferase 6A	protein-coding	0.095652	0.741379
Merged-chr11-86285943-2	chr11	86285889	86285997	+	7.3	cIP1vsInput|cIP2vsInput	"intron (NM_001080931, intron 20 of 29)"	"intron (NM_001080931, intron 20 of 29)"	-28375	NM_027421	70422	Mm.440906	NM_027421	ENSMUSG00000018068	Ints2	2810417D08Rik|AA408260|AI987735|mKIAA1287	integrator complex subunit 2	protein-coding	0.037037	0.559633
Merged-chr7-128740563-2	chr7	128740509	128740618	+	7.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145955)	promoter-TSS (NM_145955)	-134	NM_145955	210711	Mm.490344	NM_145955	ENSMUSG00000048170	Mcmbp	1110007A13Rik|AU017382|BC025641|MCM-BP	MCM (minichromosome maintenance deficient) binding protein	protein-coding	0.110092	0.718182
Merged-chr10-38962174-2	chr10	38962120	38962229	+	7.3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-3341	NM_010681	16775	Mm.258065	NM_010681	ENSMUSG00000019846	Lama4	-	"laminin, alpha 4"	protein-coding	0.018349	0.572727
Merged-chr1-23188408-2	chr1	23188357	23188460	+	7.3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-83861	NR_029533	387225		NR_029533	ENSMUSG00000065405	Mir30a	Mirn30a|mmu-mir-30a	microRNA 30a	miscRNA	0.019417	0.461538
Merged-chr10-56777663-2	chr10	56777606	56777720	+	7.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	400363	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	"gap junction protein, alpha 1"	protein-coding	0.008772	0.4
Merged-chr7-110630420-2	chr7	110630363	110630477	+	7.25	cIP1vsInput|cIP2vsInput	TTS (NM_009627)	TTS (NM_009627)	2751	NM_009627	11535	Mm.1408	NM_009627	ENSMUSG00000030790	Adm	AM	adrenomedullin	protein-coding	0.04386	0.478261
Merged-chr7-30957640-2	chr7	30957576	30957704	+	7.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011680)	promoter-TSS (NM_011680)	-837	NM_011680	22282	Mm.466352	NM_011680		Usf2	Usf-2|bHLHb12	upstream transcription factor 2	protein-coding	0.132812	0.72093
Merged-chr9-15357898-2	chr9	15357845	15357952	+	7.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_176976)	promoter-TSS (NM_176976)	-110	NM_176976	319675	Mm.218317	NM_176976	ENSMUSG00000046111	5830418K08Rik	5832426L23Rik|Gm1131|Kiaa1731	RIKEN cDNA 5830418K08 gene	protein-coding	0.130841	0.694444
Merged-chr1-85280954-1	chr1	85280904	85281004	+	7.2	cIP1vsInput	Intergenic	Intergenic	-10388	NM_001037909	620078	Mm.461248	NM_001037909	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding	0	0.346535
Merged-chr11-116130625-2	chr11	116130572	116130679	+	7.2	cIP1vsInput|cIP2vsInput	"exon (NM_178802, exon 1 of 6)"	"exon (NM_178802, exon 1 of 6)"	503	NM_178802	338364	Mm.439976	NM_178802	ENSMUSG00000054517	Trim65	4732463G12Rik	tripartite motif-containing 65	protein-coding	0.149533	0.75
Merged-chr4-133369681-2	chr4	133369631	133369732	+	7.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_016981)	promoter-TSS (NM_016981)	-91	NM_016981	20544	Mm.4312	NM_016981	ENSMUSG00000028854	Slc9a1	AW554487|Apnh|Nhe1|swe	"solute carrier family 9 (sodium/hydrogen exchanger), member 1"	protein-coding	0.089109	0.647059
Merged-chr1-152738992-2	chr1	152738931	152739054	+	7.2	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-11559	NM_001081197	71281	Mm.158650	NM_001081197	ENSMUSG00000055547	Apobec4	4933431M11Rik	"apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)"	protein-coding	0.056911	0.604839
Merged-chr5-108065612-2	chr5	108065546	108065678	+	7.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013827)	promoter-TSS (NM_013827)	-62	NM_001253880	17765	Mm.257149	NM_001253877	ENSMUSG00000029267	Mtf2	9230112N11Rik|AA537621|C76717|M96|Pcl2	metal response element binding transcription factor 2	protein-coding	0.121212	0.661654
Merged-chr5-100322337-2	chr5	100322282	100322392	+	7.2	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	93897	NM_026969	69162	Mm.18634	NM_026969	ENSMUSG00000035325	Sec31a	1810024J13Rik|ABP125|ABP130|AU042160|HSPC275|Sec31l1	Sec31 homolog A (S. cerevisiae)	protein-coding	0.045455	0.54955
Merged-chr11-74925764-2	chr11	74925700	74925828	+	7.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001163311)	promoter-TSS (NM_001163311)	34	NM_013761	27364	Mm.412219	NM_001163311	ENSMUSG00000001323	Srr	Srs	serine racemase	protein-coding	0.09375	0.674419
Merged-chr4-151996437-2	chr4	151996363	151996511	+	7.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172705)	promoter-TSS (NM_172705)	-258	NM_172705	230936	Mm.25582	NM_172705	ENSMUSG00000047777	Phf13	BC029632|Phf5|SPOC1	PHD finger protein 13	protein-coding	0.101351	0.744966
Merged-chr16-4558716-2	chr16	4558645	4558788	+	7.15	cIP1vsInput|cIP2vsInput	"intron (NM_031182, intron 1 of 6)"	CpG	1004	NM_031182	83383	Mm.273210	NM_031182	ENSMUSG00000005718	Tfap4	AI642933|AP-4|D930048N17Rik|Tcfap4|bHLHc41	transcription factor AP4	protein-coding	0.097902	0.645833
Merged-chr18-76160997-2	chr18	76160934	76161061	+	7.15	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-62526	NR_045365	73009	Mm.443541	NR_045365		2900057B20Rik	-	RIKEN cDNA 2900057B20 gene	miscRNA	0.110236	0.679688
Merged-chr13-109776220-2	chr13	109776153	109776288	+	7.15	cIP1vsInput|cIP2vsInput	"intron (NM_011056, intron 7 of 16)"	"intron (NM_011056, intron 7 of 16)"	-127589	NR_035442	100316683		NR_035442		Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	miscRNA	0.051852	0.507353
Merged-chr7-44849962-2	chr7	44849899	44850026	+	7.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001253920)	promoter-TSS (NM_001253920)	-45	NM_001253920	67605	Mm.431538	NM_001253920	ENSMUSG00000011096	Akt1s1	1110012J22Rik|AI227026|Lobe|Lobel|PRAS40	AKT1 substrate 1 (proline-rich)	protein-coding	0.094488	0.65625
Merged-chr4-129926638-2	chr4	129926582	129926694	+	7.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	20412	NR_045190	319894	Mm.59196	NR_045190	ENSMUSG00000086369	E330017L17Rik	-	RIKEN cDNA E330017L17 gene	miscRNA	0.035714	0.566372
Merged-chr15-88819393-2	chr15	88819337	88819449	+	7.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029720)	promoter-TSS (NM_029720)	-75	NM_145477	223774	Mm.41512	NM_001142357	ENSMUSG00000035845	Alg12	ECM39	"asparagine-linked glycosylation 12 (alpha-1,6-mannosyltransferase)"	protein-coding	0.071429	0.663717
Merged-chr3-155093310-2	chr3	155093242	155093379	+	7.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029330)	promoter-TSS (NM_029330)	68	NM_029330	75540	Mm.35218	NM_029330	ENSMUSG00000053870	Fpgt	1700016E03Rik	fucose-1-phosphate guanylyltransferase	protein-coding	0.072993	0.615942
Merged-chr7-142533082-1	chr7	142533032	142533132	+	7.1	cIP2vsInput	promoter-TSS (NM_011288)	promoter-TSS (NM_011288)	-35	NM_011288	19935	Mm.12144	NM_011288	ENSMUSG00000037772	Mrpl23	L23mrp|Rpl23|Rpl23l	mitochondrial ribosomal protein L23	protein-coding	0.12	0.752475
Merged-chr4-145439836-1	chr4	145439786	145439886	+	7.1	cIP1vsInput	Intergenic	Intergenic	-24374	NR_002888	545700	Mm.389595	NR_002888	ENSMUSG00000052912	Smarca5-ps	9230115A19Rik|OTTMUSG00000011029	"SWI/SNF related, matrix associated, actin depenent ragulator of chromatin, subfamily a, member 5, pseudogene"	pseudo	0.01	0.376238
Merged-chr10-86705845-2	chr10	86705777	86705914	+	7.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011631)	promoter-TSS (NM_011631)	34	NM_001003939	103220	Mm.440762	NM_001003910	ENSMUSG00000044937	BC030307	AI449705|AU041509|Gnn	cDNA sequence BC030307	protein-coding	0.10219	0.550725
Merged-chr18-55134419-2	chr18	55134341	55134498	+	7.05	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-144239	NM_175751	269023	Mm.471753	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding	0.025478	0.436709
Merged-chr12-59131364-2	chr12	59131302	59131427	+	7.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001165253)	promoter-TSS (NM_001165253)	-89	NM_001165253	217615	Mm.438038	NM_001165253	ENSMUSG00000021000	Ctage5	D12Bwg0579e|Mea6|Mgea|Mgea6	"CTAGE family, member 5"	protein-coding	0.152	0.761905
Merged-chr13-36173240-2	chr13	36173186	36173294	+	7.05	cIP1vsInput|cIP2vsInput	"intron (NM_001039189, intron 1 of 5)"	RMER17D2|LTR|ERVK	55829	NM_001039189	69955	Mm.70690	NM_001039189	ENSMUSG00000021420	Fars2	2810431B21Rik|6720478K01Rik|Fars1	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding	0.009259	0.477064
Merged-chr14-105895105-2	chr14	105895052	105895158	+	7.05	cIP1vsInput|cIP2vsInput	"intron (NM_011897, intron 1 of 1)"	CpG	1714	NM_011897	24064	Mm.489870	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty homolog 2 (Drosophila)	protein-coding	0.075472	0.654206
Merged-chr12-54163009-2	chr12	54162927	54163092	+	7.05	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	40865	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	EGL nine homolog 3 (C. elegans)	protein-coding	0.048485	0.566265
Merged-chr5-149184608-2	chr5	149184545	149184672	+	7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001115153)	promoter-TSS (NM_001115153)	48	NM_001115149	231915	Mm.29402	NM_001013378	ENSMUSG00000041264	Uspl1	D030048C09|E430026A01Rik	ubiquitin specific peptidase like 1	protein-coding	0.070866	0.65625
Merged-chr1-171411020-2	chr1	171410957	171411084	+	7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009480)	promoter-TSS (NM_009480)	-661	NM_009480	22278	Mm.8	NM_009480	ENSMUSG00000026641	Usf1	bHLHb11	upstream transcription factor 1	protein-coding	0.023622	0.5
Merged-chr5-149052093-1	chr5	149052043	149052143	+	7	cIP2vsInput	"intron (NM_010439, intron 1 of 4)"	"intron (NM_010439, intron 1 of 4)"	944	NM_010439	15289	Mm.313345	NM_010439	ENSMUSG00000066551	Hmgb1	DEF|HMG-1|Hmg1|SBP-1|amphoterin|p30	high mobility group box 1	protein-coding	0.15	0.762376
Merged-chr16-58460137-2	chr16	58460085	58460189	+	7	cIP1vsInput|cIP2vsInput	"intron (NM_028523, intron 12 of 15)"	RMER17A2|LTR|ERVK	51602	NM_028523	73379	Mm.373589	NM_028523	ENSMUSG00000035107	Dcbld2	1700055P21Rik|AW146002|CLCP1|Esdn	"discoidin, CUB and LCCL domain containing 2"	protein-coding	0.019231	0.495238
Merged-chr1-137802331-2	chr1	137802277	137802386	+	7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-164124	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mmu-mir-213	microRNA 181a-1	miscRNA	0.018349	0.472727
Merged-chr7-142516428-2	chr7	142516376	142516481	+	7	cIP1vsInput|cIP2vsInput	TTS (NM_001163668)	TTS (NM_001163668)	-9657	NR_033261	677289	Mm.350054	NR_033261	ENSMUSG00000043795	Gm14492	ENSMUSG00000043795|OTTMUSG00000016823	predicted gene 14492	miscRNA	0.066667	0.650943
Merged-chr7-120865300-2	chr7	120865248	120865353	+	7	cIP1vsInput|cIP2vsInput	"intron (NM_001267710, intron 2 of 17)"	"intron (NM_001267710, intron 2 of 17)"	14111	NM_001267711	13631	Mm.470116	NM_001267710	ENSMUSG00000035064	Eef2k	C86191|eEF-2K	eukaryotic elongation factor-2 kinase	protein-coding	0.038095	0.528302
Merged-chr3-95882283-2	chr3	95882207	95882360	+	7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001033302)	promoter-TSS (NM_001033302)	-55	NM_001033302	229599	Mm.331218	NM_001033302	ENSMUSG00000038550	Gm129	-	predicted gene 129	protein-coding	0.065359	0.623377
Merged-chr5-125389862-1	chr5	125389812	125389912	+	7	cIP2vsInput	"intron (NM_019639, intron 1 of 1)"	CpG	155	NM_019639	22190	Mm.419997	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding	0.11	0.613861
Merged-chr4-154330211-2	chr4	154330158	154330264	+	6.95	cIP1vsInput|cIP2vsInput	"intron (NM_027504, intron 12 of 16)"	"intron (NM_027504, intron 12 of 16)"	-30316	NM_001112744	230972	Mm.38481	NM_001112744	ENSMUSG00000029032	Arhgef16	-	Rho guanine nucleotide exchange factor (GEF) 16	protein-coding	0.037736	0.579439
Merged-chr10-46786062-2	chr10	46786006	46786118	+	6.95	cIP1vsInput|cIP2vsInput	Intergenic	RLTR1F_Mm|LTR|ERVK	541313	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0.026786	0.424779
Merged-chr11-95310373-2	chr11	95310316	95310430	+	6.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001195004)	promoter-TSS (NM_001195004)	-127	NM_001195003	217127	Mm.472268	NM_001195003		Kat7	Hbo1|Hboa|Myst2	K(lysine) acetyltransferase 7	protein-coding	0.04386	0.504348
Merged-chr1-164586572-2	chr1	164586514	164586630	+	6.9	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-128217	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	"ATPase, Na+/K+ transporting, beta 1 polypeptide"	protein-coding	0.008621	0.478632
Merged-chr4-116075382-2	chr4	116075320	116075445	+	6.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025641)	promoter-TSS (NM_025641)	-83	NM_153521	230654	Mm.260786	NM_153521	ENSMUSG00000028703	Lrrc41	AA409966|AW555107|D630045E04Rik|D730026A16Rik|MUF1	leucine rich repeat containing 41	protein-coding	0.104	0.65873
Merged-chr10-128096805-1	chr10	128096755	128096855	+	6.9	cIP2vsInput	"intron (NM_054078, intron 2 of 29)"	CpG	4022	NM_054078	116848	Mm.252213	XM_003945867	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	"bromodomain adjacent to zinc finger domain, 2A"	protein-coding	0.13	0.762376
Merged-chr5-107900493-2	chr5	107900443	107900544	+	6.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_016980)	promoter-TSS (NM_016980)	-35	NM_016980	100503670	Mm.426204	NM_016980	ENSMUSG00000058558	Rpl5	U21RNA	ribosomal protein L5	protein-coding	0.069307	0.588235
Merged-chr4-145439950-1	chr4	145439900	145440000	+	6.9	cIP2vsInput	Intergenic	Intergenic	-24260	NR_002888	545700	Mm.389595	NR_002888	ENSMUSG00000052912	Smarca5-ps	9230115A19Rik|OTTMUSG00000011029	"SWI/SNF related, matrix associated, actin depenent ragulator of chromatin, subfamily a, member 5, pseudogene"	pseudo	0	0.346535
Merged-chr6-149141530-2	chr6	149141469	149141591	+	6.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001252096)	promoter-TSS (NM_001252096)	17	NM_177101	320204	Mm.274099	NM_001252094	ENSMUSG00000039958	Mettl20	4833442J19Rik|AI256744	methyltransferase like 20	protein-coding	0.122951	0.601626
Merged-chr8-70539543-2	chr8	70539489	70539597	+	6.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007924)	promoter-TSS (NM_007924)	-132	NM_007924	13716	Mm.271973	NM_007924	ENSMUSG00000070002	Ell	Ell1|Men	elongation factor RNA polymerase II	protein-coding	0.074074	0.651376
Merged-chr9-80607489-2	chr9	80607433	80607546	+	6.85	cIP1vsInput|cIP2vsInput	Intergenic	ID_B1|SINE|B4	-142051	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding	0	0.482456
Merged-chr16-70314010-2	chr16	70313922	70314098	+	6.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028803)	promoter-TSS (NM_028803)	61	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	"glucan (1,4-alpha-), branching enzyme 1"	protein-coding	0.107955	0.762712
Merged-chr9-63075468-2	chr9	63075404	63075532	+	6.85	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	71512	NM_172446	207667	Mm.447200	NM_001163755	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding	0.03125	0.565891
Merged-chr8-44938215-2	chr8	44938146	44938284	+	6.85	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-11993	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT tumor suppressor homolog 1 (Drosophila)	protein-coding	0.173913	0.805755
Merged-chr6-86472308-2	chr6	86472238	86472378	+	6.85	cIP1vsInput|cIP2vsInput	Intergenic	CpG	15919	NR_040293	381792	Mm.490854	NR_040292		2310040G24Rik	-	RIKEN cDNA 2310040G24 gene	miscRNA	0.15	0.70922
Merged-chr16-35022317-2	chr16	35022257	35022378	+	6.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_023587)	promoter-TSS (NM_023587)	-104	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Ptplb	6330408J20Rik|AI255777|AI481689|HACD2	"protein tyrosine phosphatase-like (proline instead of catalytic arginine), member b"	protein-coding	0.099174	0.663934
Merged-chr7-90130106-2	chr7	90130041	90130171	+	6.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001252523)	promoter-TSS (NM_001252523)	-126	NM_001252523	233489	Mm.394497	NM_001252520	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding	0.169231	0.801527
Merged-chr1-179668106-2	chr1	179668052	179668161	+	6.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178653)	promoter-TSS (NM_178653)	-125	NM_178653	109232	Mm.136458	NM_178653	ENSMUSG00000038936	Sccpdh	AW214504|C330023F11Rik	saccharopine dehydrogenase (putative)	protein-coding	0.155963	0.781818
Merged-chr6-29517316-2	chr6	29517253	29517379	+	6.8	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-9309	NM_012057	27056	Mm.6479	NM_001252382	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding	0.02381	0.543307
Merged-chr9-44320382-2	chr9	44320332	44320433	+	6.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027909)	promoter-TSS (NM_027909)	-100	NM_027909	71764	Mm.33869	NM_027909	ENSMUSG00000032120	C2cd2l	1300006O23Rik|Tmem24	C2 calcium-dependent domain containing 2-like	protein-coding	0.059406	0.617647
Merged-chr2-84465121-2	chr2	84465071	84465172	+	6.8	cIP1vsInput|cIP2vsInput	"intron (NM_011576, intron 2 of 8)"	"intron (NM_011576, intron 2 of 8)"	9053	NM_011576	21788	Mm.447013	NM_001177319	ENSMUSG00000027082	Tfpi	A630013F22Rik|AW552122|EPI|LACI	tissue factor pathway inhibitor	protein-coding	0.029703	0.529412
Merged-chr1-88277457-1	chr1	88277407	88277507	+	6.8	cIP2vsInput	promoter-TSS (NM_172505)	promoter-TSS (NM_172505)	100	NM_172505	212427	Mm.384762	NM_172505		A730008H23Rik	mFleg1	RIKEN cDNA A730008H23 gene	protein-coding	0.07	0.643564
Merged-chr7-110061668-1	chr7	110061618	110061718	+	6.8	cIP2vsInput	promoter-TSS (NM_009281)	promoter-TSS (NM_009281)	-34	NM_009281	20841	Mm.10815	NM_009281	ENSMUSG00000061079	Zfp143	AA959806|AU015869|D7Ertd805e|KRAB14|SBF|Staf|Zfp79|Zfp80-rs1|Znf143|pHZ-1	zinc finger protein 143	protein-coding	0.06	0.613861
Merged-chr6-134928531-1	chr6	134928481	134928581	+	6.8	cIP2vsInput	promoter-TSS (NR_037956)	promoter-TSS (NR_037956)	-561	NR_037956	381822	Mm.5935	NR_037955		1190002F15Rik	AI120476	RIKEN cDNA 1190002F15 gene	miscRNA	0.08	0.554455
Merged-chr18-65580768-1	chr18	65580718	65580818	+	6.8	cIP2vsInput	"intron (NM_207255, intron 1 of 5)"	CpG	538	NM_207255	328977	Mm.419081	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding	0.16	0.792079
Merged-chr9-124423905-1	chr9	124423855	124423955	+	6.8	cIP2vsInput	"non-coding (NR_027950, exon 2 of 2)"	"non-coding (NR_027950, exon 2 of 2)"	118	NR_015516	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	miscRNA	0.11	0.752475
Merged-chr7-122132969-1	chr7	122132919	122133019	+	6.8	cIP2vsInput	promoter-TSS (NM_001081238)	promoter-TSS (NM_001081238)	-23	NM_001081238	233826	Mm.38348	NM_001081238	ENSMUSG00000044702	Palb2	4732427B05|BC066140	partner and localizer of BRCA2	protein-coding	0.11	0.613861
Merged-chr11-103132899-1	chr11	103132849	103132949	+	6.8	cIP2vsInput	promoter-TSS (NM_027658)	promoter-TSS (NM_027658)	-440	NM_001130516	71059	Mm.273871	NM_001130515	ENSMUSG00000043372	Hexim2	4933402L21Rik	hexamethylene bis-acetamide inducible 2	protein-coding	0.15	0.722772
Merged-chr3-90293615-1	chr3	90293565	90293665	+	6.8	cIP2vsInput	Intergenic	C-rich|Low_complexity|Low_complexity	27081	NM_201407	229541	Mm.30571	NM_201407	ENSMUSG00000042404	Dennd4b	BC026996|mKIAA0476	DENN/MADD domain containing 4B	protein-coding	0.18	0.851485
Merged-chr10-40257690-2	chr10	40257628	40257752	+	6.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026113)	promoter-TSS (NM_026113)	-25	NM_026113	67371	Mm.64104	NM_026113	ENSMUSG00000019837	Gtf3c6	2410016F19Rik|AU019813	"general transcription factor IIIC, polypeptide 6, alpha"	protein-coding	0.112903	0.656
Merged-chr5-15638661-1	chr5	15638611	15638711	+	6.8	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	18398	NR_073011	381715		NR_073011	ENSMUSG00000069720	4930572O03Rik	-	spermatogenesis associated glutamate (E)-rich protein pseudogene	pseudo	0	0.267327
Merged-chr7-128461762-2	chr7	128461703	128461821	+	6.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009383)	promoter-TSS (NM_009383)	-249	NM_009383	21843	Mm.242072	NM_009383	ENSMUSG00000030846	Tial1	5330433G13Rik|AL033329|TIAR|mTIAR	Tia1 cytotoxic granule-associated RNA binding protein-like 1	protein-coding	0.118644	0.579832
Merged-chr8-79030550-2	chr8	79030500	79030600	+	6.8	cIP1vsInput|cIP2vsInput	"intron (NM_178267, intron 1 of 14)"	CpG	2113	NM_178267	622675	Mm.48724	NM_178267	ENSMUSG00000071064	Zfp827	2810449M09Rik|D630040G17Rik|Znf827	zinc finger protein 827	protein-coding	0.03	0.405941
Merged-chr11-11840971-2	chr11	11840918	11841024	+	6.8	cIP1vsInput|cIP2vsInput	"intron (NM_001190448, intron 7 of 14)"	"intron (NM_001190448, intron 7 of 14)"	-27152	NR_045178	73321	Mm.443306	NR_045178	ENSMUSG00000086391	1700042O10Rik	-	RIKEN cDNA 1700042O10 gene	miscRNA	0.009434	0.439252
Merged-chr18-69593302-2	chr18	69593251	69593354	+	6.75	cIP1vsInput|cIP2vsInput	"intron (NM_013685, intron 8 of 19)"	"intron (NM_013685, intron 8 of 19)"	247581	NM_001083967	21413	Mm.4269	NM_001083967	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding	0.116505	0.692308
Merged-chrX-126770755-2	chrX	126770704	126770806	+	6.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	63249	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding	0.019608	0.242718
Merged-chr4-62208504-2	chr4	62208448	62208561	+	6.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009554)	promoter-TSS (NM_009554)	42	NM_009554	22696	Mm.5011	NM_009554	ENSMUSG00000028389	Zfp37	AV042165|Tzn|Zfp-37	zinc finger protein 37	protein-coding	0.106195	0.701754
Merged-chr5-88929979-2	chr5	88929926	88930033	+	6.75	cIP1vsInput|cIP2vsInput	"intron (NM_001197147, intron 1 of 25)"	"intron (NM_001197147, intron 1 of 25)"	42719	NM_018760	54403	Mm.41044	NM_001136260	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	"solute carrier family 4 (anion exchanger), member 4"	protein-coding	0.028037	0.62963
Merged-chr1-171222462-2	chr1	171222411	171222513	+	6.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001037170)	promoter-TSS (NM_001037170)	52	NM_001037170	641376	Mm.288374	NM_001037170	ENSMUSG00000005674	Tomm40l	-	translocase of outer mitochondrial membrane 40 homolog-like (yeast)	protein-coding	0.029412	0.543689
Merged-chr19-53142278-2	chr19	53142214	53142342	+	6.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001164100)	promoter-TSS (NM_001164100)	-478	NM_001277100	27360	Mm.426080	NM_001164099	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding	0.078125	0.705426
Merged-chr11-119041137-2	chr11	119041084	119041191	+	6.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013926)	promoter-TSS (NM_013926)	-224	NM_013926	30951	Mm.99953	NM_013926		Cbx8	Pc3	chromobox 8	protein-coding	0.084112	0.685185
Merged-chr12-111038932-1	chr12	111038882	111038982	+	6.7	cIP2vsInput	promoter-TSS (NM_198023)	promoter-TSS (NM_198023)	-866	NM_198023	217864	Mm.23808	NM_198023	ENSMUSG00000037896	Rcor1	5730409O11|6720480E22Rik|AU042633|D12Wsu95e|mKIAA0071	REST corepressor 1	protein-coding	0.11	0.643564
Merged-chr2-128125848-2	chr2	128125772	128125924	+	6.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009754)	promoter-TSS (NM_009754)	-190	NM_207681	12125	Mm.453214	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod	BCL2-like 11 (apoptosis facilitator)	protein-coding	0.092105	0.732026
Merged-chr1-55087994-2	chr1	55087931	55088057	+	6.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008303)	promoter-TSS (NM_008303)	-62	NM_010477	15510	Mm.1777	NM_010477	ENSMUSG00000025980	Hspd1	60kDa|Hsp60	heat shock protein 1 (chaperonin)	protein-coding	0.119048	0.755906
Merged-chr7-127260931-2	chr7	127260880	127260983	+	6.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_023203)	promoter-TSS (NM_023203)	-264	NM_023203	66422	Mm.29898	NM_023203	ENSMUSG00000042462	Dctpp1	2410015N17Rik|AI854235|RS21-C6	dCTP pyrophosphatase 1	protein-coding	0.058252	0.519231
Merged-chr6-8730175-1	chr6	8730125	8730225	+	6.7	cIP1vsInput	"intron (NM_001252266, intron 5 of 11)"	B1_Mus1|SINE|Alu	28283	NM_001252266	15893	Mm.275683	NM_001252266	ENSMUSG00000062995	Ica1	69kDa|ICA69	islet cell autoantigen 1	protein-coding	0	0.534653
Merged-chr12-105685261-2	chr12	105685187	105685335	+	6.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178613)	promoter-TSS (NM_178613)	-20	NM_029654	76559	Mm.125279	NM_029654	ENSMUSG00000041341	Atg2b	2410024A21Rik|AI047755|AI503411|AW558123|C030004M05Rik|C630028L02Rik|mKIAA4067	autophagy related 2B	protein-coding	0.101351	0.604027
Merged-chr8-15011947-2	chr8	15011882	15012012	+	6.7	cIP1vsInput|cIP2vsInput	"intron (NM_029116, intron 1 of 1)"	CpG	922	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding	0.076923	0.618321
Merged-chr1-26687750-1	chr1	26687700	26687800	+	6.7	cIP2vsInput	promoter-TSS (NM_001033764)	promoter-TSS (NM_001033764)	-290	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding	0	0.346535
Merged-chr16-55822159-2	chr16	55822100	55822219	+	6.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001159394)	promoter-TSS (NM_001159394)	-21	NM_001159394	80859	Mm.247272	NM_001159394	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	"nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta"	protein-coding	0.12605	0.683333
Merged-chr2-153345869-2	chr2	153345808	153345931	+	6.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_040318)	promoter-TSS (NR_040318)	-59	NR_040318	72326	Mm.400102	NR_040318	ENSMUSG00000073236	2500004C02Rik	-	RIKEN cDNA 2500004C02 gene	miscRNA	0.089431	0.58871
Merged-chr18-32837199-2	chr18	32837137	32837262	+	6.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_045381)	promoter-TSS (NR_045381)	-26	NM_001110015	225348	Mm.38816	NM_001110015	ENSMUSG00000038299	Wdr36	5730444A13Rik|Ta-wdrp	WD repeat domain 36	protein-coding	0.064	0.563492
Merged-chr3-57847860-2	chr3	57847808	57847913	+	6.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019410)	promoter-TSS (NM_019410)	-103	NM_019410	18645	Mm.271744	NM_019410	ENSMUSG00000027805	Pfn2	Pfn	profilin 2	protein-coding	0.152381	0.792453
Merged-chr4-82513154-2	chr4	82513091	82513218	+	6.65	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-7846	NM_008687	18028	Mm.317947	NM_001113209	ENSMUSG00000008575	Nfib	6720429L07Rik|E030026I10Rik	nuclear factor I/B	protein-coding	0.141732	0.695312
Merged-chr2-165493381-2	chr2	165493315	165493448	+	6.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001007581)	promoter-TSS (NM_001007581)	-67	NM_001007581	381406	Mm.330785	NM_001007581	ENSMUSG00000039725	2810408M09Rik	-	RIKEN cDNA 2810408M09 gene	protein-coding	0.120301	0.634328
Merged-chr6-136468843-2	chr6	136468783	136468904	+	6.6	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-50008	NM_019426	54343	Mm.361788	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding	0.016529	0.614754
Merged-chr8-25101777-2	chr8	25101713	25101841	+	6.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_031257)	promoter-TSS (NM_031257)	34	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2"	protein-coding	0.070312	0.658915
Merged-chr11-60777331-2	chr11	60777258	60777405	+	6.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175491)	promoter-TSS (NM_175491)	34	NM_009410	21975	Mm.477819	NM_009410	ENSMUSG00000002814	Top3a	-	topoisomerase (DNA) III alpha	protein-coding	0.040816	0.527027
Merged-chr3-157534178-2	chr3	157534093	157534263	+	6.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_017381)	promoter-TSS (NM_017381)	-219	NM_017381	53861	Mm.259036	NM_017381	ENSMUSG00000028180	Zranb2	AI227013|Zfp265|Zis|Znf265	"zinc finger, RAN-binding domain containing 2"	protein-coding	0.105882	0.690058
Merged-chr11-116490612-1	chr11	116490562	116490662	+	6.6	cIP1vsInput	promoter-TSS (NM_026364)	promoter-TSS (NM_026364)	-266	NM_026364	67763	Mm.25125	NM_026364	ENSMUSG00000015869	Prpsap1	5730409F23Rik|PAP39	phosphoribosyl pyrophosphate synthetase-associated protein 1	protein-coding	0.06	0.514851
Merged-chr10-117014201-2	chr10	117014138	117014265	+	6.6	cIP1vsInput|cIP2vsInput	"intron (NM_001007583, intron 9 of 9)"	"intron (NM_001007583, intron 9 of 9)"	27887	NM_001007583	382427	Mm.339322	NM_001007583	ENSMUSG00000020169	Best3	Vmd2l3|mBest4	bestrophin 3	protein-coding	0.031496	0.507812
Merged-chr3-108210992-1	chr3	108210942	108211042	+	6.6	cIP2vsInput	promoter-TSS (NM_175183)	promoter-TSS (NM_175183)	-58	NM_175183	72522	Mm.187326	NM_175183	ENSMUSG00000048997	Atxn7l2	2610528J18Rik	ataxin 7-like 2	protein-coding	0.02	0.653465
Merged-chr4-133813434-1	chr4	133813384	133813484	+	6.6	cIP2vsInput	Intergenic	CpG	-59823	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding	0.13	0.782178
Merged-chr4-132422043-2	chr4	132421973	132422113	+	6.6	cIP1vsInput|cIP2vsInput	"intron (NM_001161797, intron 1 of 12)"	CpG	403	NM_001161797	100169	Mm.158361	NM_001161797	ENSMUSG00000066043	Phactr4	3110001B12Rik|AI527228|AW495572|C330013F19Rik|N28169|mKIAA4120	phosphatase and actin regulator 4	protein-coding	0.078571	0.673759
Merged-chrX-126777840-2	chrX	126777785	126777896	+	6.6	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	56164	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding	0.018018	0.446429
Merged-chr5-4326132-2	chr5	4326069	4326195	+	6.6	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	133765	NM_001042670	208595	Mm.129815	NM_001042670	ENSMUSG00000053178	Gm9897	ENSMUSG00000053178	predicted gene 9897	protein-coding	0.015873	0.448819
Merged-chr6-86526603-2	chr6	86526523	86526683	+	6.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_037961)	promoter-TSS (NR_037961)	-438	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1	poly(rC) binding protein 1	protein-coding	0.175	0.807453
Merged-chr11-87423069-1	chr11	87423019	87423119	+	6.6	cIP2vsInput	"intron (NM_031386, intron 1 of 30)"	"intron (NM_031386, intron 1 of 30)"	-4522	NM_001199293	83560	Mm.440758	NM_001199293	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding	0.05	0.415842
Merged-chr17-57032025-2	chr17	57031973	57032078	+	6.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010613)	promoter-TSS (NM_010613)	-518	NM_010613	16549	Mm.34296	NM_010613	ENSMUSG00000007670	Khsrp	6330409F21Rik|Fbp2|Fubp2|Ksrp	KH-type splicing regulatory protein	protein-coding	0.028571	0.481132
Merged-chr9-69290096-2	chr9	69290036	69290156	+	6.55	cIP1vsInput|cIP2vsInput	"intron (NM_013646, intron 2 of 10)"	CpG	-107902	NM_145618	93697	Mm.35911	NM_145618	ENSMUSG00000032235	Narg2	B230343B06Rik	NMDA receptor-regulated gene 2	protein-coding	0.116667	0.760331
Merged-chr13-58401593-2	chr13	58401541	58401646	+	6.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_031761)	promoter-TSS (NR_031761)	-655	NR_031761	74386	Mm.85289	NM_001168248	ENSMUSG00000035367	Rmi1	4932432N11Rik|C79893	"RMI1, RecQ mediated genome instability 1, homolog (S. cerevisiae)"	protein-coding	0.161905	0.735849
Merged-chr3-65829449-2	chr3	65829387	65829511	+	6.55	cIP1vsInput|cIP2vsInput	"intron (NM_001166659, intron 12 of 12)"	"intron (NM_001166659, intron 12 of 12)"	128776	NM_019937	56706	Mm.175612	NM_001025442	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding	0.032258	0.6
Merged-chr6-4733402-2	chr6	4733343	4733461	+	6.55	cIP1vsInput|cIP2vsInput	"intron (NM_001130188, intron 1 of 11)"	"intron (NM_001130188, intron 1 of 11)"	13802	NM_001130188	20392	Mm.8739	NM_001130188	ENSMUSG00000004631	Sgce	e-SG	"sarcoglycan, epsilon"	protein-coding	0.008475	0.478992
Merged-chr14-24487056-2	chr14	24486983	24487130	+	6.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081247)	promoter-TSS (NM_001081247)	-10	NM_001081247	218832	Mm.399136	NM_001081247	ENSMUSG00000025280	Polr3a	9330175N20Rik|BC053071|RPC1|RPC155	polymerase (RNA) III (DNA directed) polypeptide A	protein-coding	0.081633	0.614865
Merged-chr19-40894635-2	chr19	40894559	40894711	+	6.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028319)	promoter-TSS (NM_028319)	-70	NM_028319	72672	Mm.313523	NM_028319	ENSMUSG00000049164	Zfp518a	2810401C22Rik|6330417C12Rik|AI426493|Zfp518|Znf518|Znf518a|mKIAA0335	zinc finger protein 518A	protein-coding	0.138158	0.745098
Merged-chr3-97767900-2	chr3	97767841	97767959	+	6.5	cIP1vsInput|cIP2vsInput	"5' UTR (NM_178080, exon 1 of 17)"	"5' UTR (NM_178080, exon 1 of 17)"	114	NM_178080	83679	Mm.129840	NM_001039376	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding	0.09322	0.697479
Merged-chr16-16146782-2	chr16	16146720	16146844	+	6.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_146068)	promoter-TSS (NM_146068)	51	NM_146068	224008	Mm.244703	NM_146068	ENSMUSG00000041974	2310008H04Rik	Kiaa0146	RIKEN cDNA 2310008H04 gene	protein-coding	0.104839	0.68
Merged-chr11-103115627-1	chr11	103115577	103115677	+	6.5	cIP2vsInput	promoter-TSS (NM_138753)	promoter-TSS (NM_138753)	-698	NM_138753	192231		NM_138753	ENSMUSG00000048878	Hexim1	7330426E13Rik|CLP-1|Clp1|HIS1	hexamethylene bis-acetamide inducible 1	protein-coding	0.03	0.376238
Merged-chr6-13678249-2	chr6	13678184	13678314	+	6.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175312)	promoter-TSS (NM_175312)	-283	NM_175312	101148	Mm.354863	NM_175312	ENSMUSG00000042742	B630005N14Rik	AI666701	RIKEN cDNA B630005N14 gene	protein-coding	0.030769	0.564885
Merged-chr15-31224250-2	chr15	31224167	31224334	+	6.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_146057)	promoter-TSS (NM_146057)	-135	NM_146057	223453	Mm.222867	NM_146057	ENSMUSG00000039168	Dap	4921531N22Rik|AI789753|AU040360	death-associated protein	protein-coding	0.095808	0.660714
Merged-chr6-145865572-2	chr6	145865512	145865633	+	6.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_024469)	promoter-TSS (NM_024469)	-152	NM_024469	79362	Mm.396926	NM_001271768		Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	"basic helix-loop-helix family, member e41"	protein-coding	0.115702	0.762295
Merged-chr8-111732094-2	chr8	111732043	111732145	+	6.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001198839)	promoter-TSS (NM_001198839)	42	NM_001198839	12927	Mm.3758	NM_001198839	ENSMUSG00000031955	Bcar1	AI385681|Cas|Crkas	breast cancer anti-estrogen resistance 1	protein-coding	0.147059	0.747573
Merged-chr7-64287494-1	chr7	64287444	64287544	+	6.5	cIP2vsInput	promoter-TSS (NM_172742)	promoter-TSS (NM_172742)	-176	NM_172742	233315	Mm.214959	NM_172742	ENSMUSG00000030522	Mtmr10	BB128963|C79734	myotubularin related protein 10	protein-coding	0.12	0.683168
Merged-chrY-90732379-1	chrY	90732329	90732429	+	6.5	cIP1vsInput	Intergenic	Intergenic	-53063	NM_133362	170942	Mm.391385	XM_003946384	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding	0.03	0.435644
Merged-chr9-120492618-2	chr9	120492530	120492707	+	6.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026892)	promoter-TSS (NM_026892)	12	NM_026892	68969	Mm.28753	NM_026892	ENSMUSG00000006941	Eif1b	1500010M16Rik|3110001N14Rik|Gc20	eukaryotic translation initiation factor 1B	protein-coding	0.19209	0.792135
Merged-chr12-39195779-2	chr12	39195723	39195835	+	6.5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	412068	NM_001163154	14009	Mm.4866	NM_001163154	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant gene 1	protein-coding	0.017857	0.40708
Merged-chr5-137533290-2	chr5	137533193	137533388	+	6.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010312)	promoter-TSS (NM_010312)	-61	NM_010312	14693	Mm.30141	NM_010312	ENSMUSG00000029713	Gnb2	Gnb-2	"guanine nucleotide binding protein (G protein), beta 2"	protein-coding	0.117949	0.693878
Merged-chr8-36678009-2	chr8	36677947	36678071	+	6.45	cIP1vsInput|cIP2vsInput	"intron (NM_001194940, intron 5 of 17)"	"intron (NM_001194940, intron 5 of 17)"	55045	NM_001194941	50768	Mm.210875	NM_178735	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding	0.016129	0.56
Merged-chrX-103617087-2	chrX	103616994	103617180	+	6.45	cIP1vsInput|cIP2vsInput	"intron (NR_028381, intron 1 of 10)"	CpG	6667	NR_028381	78878	Mm.426420	NR_028380	ENSMUSG00000086370	Ftx	B230206F22Rik|BB219131|NCRNA00182|Thcytx	"Ftx transcript, Xist regulator (non-protein coding)"	miscRNA	0.069892	0.550802
Merged-chr11-96584686-2	chr11	96584636	96584737	+	6.45	cIP1vsInput|cIP2vsInput	"intron (NM_001033186, intron 4 of 12)"	"intron (NM_001033186, intron 4 of 12)"	120095	NM_001177898	78473	Mm.446811	NM_001033186		Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding	0	0.352941
Merged-chr6-88045353-2	chr6	88045269	88045437	+	6.45	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-31663	NM_009005	19349	Mm.486309	NM_009005		Rab7	Rab7a	"RAB7, member RAS oncogene family"	protein-coding	0.059524	0.615385
Merged-chr14-34502715-2	chr14	34502645	34502785	+	6.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009758)	promoter-TSS (NM_009758)	-169	NM_009758	12166	Mm.237825	NM_009758	ENSMUSG00000021796	Bmpr1a	1110037I22Rik|ALK3|AU045487|BMPR-IA|Bmpr	"bone morphogenetic protein receptor, type 1A"	protein-coding	0.157143	0.801418
Merged-chr7-30588785-2	chr7	30588722	30588848	+	6.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029274)	promoter-TSS (NM_029274)	-59	NM_029274	75410	Mm.168688	NM_029274	ENSMUSG00000006307	Wbp7	2610014H22Rik|Kmt2b|Mll2|mKIAA0304	WW domain binding protein 7	protein-coding	0.095238	0.779528
Merged-chr1-34439339-2	chr1	34439281	34439397	+	6.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178601)	promoter-TSS (NM_178601)	333	NM_027159	69668	Mm.379170	NM_027159	ENSMUSG00000042111	Ccdc115	2310061I09Rik|Ccp1	coiled-coil domain containing 115	protein-coding	0.068966	0.65812
Merged-chr8-33929920-2	chr8	33929868	33929972	+	6.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019733)	promoter-TSS (NM_019733)	-79	NM_001042675	19663	Mm.323997	NM_001042674	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|hermes	RNA binding protein gene with multiple splicing	protein-coding	0.096154	0.72381
Merged-chr14-57798117-2	chr14	57798044	57798191	+	6.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009119)	promoter-TSS (NM_009119)	-72	NM_009119	20220	Mm.344671	NM_009119	ENSMUSG00000021963	Sap18	C530046K05Rik|D11Ertd539e|EMegR4|Sinbp1	Sin3-associated polypeptide 18	protein-coding	0.115646	0.628378
Merged-chr19-53313097-2	chr19	53313036	53313159	+	6.4	cIP1vsInput|cIP2vsInput	"intron (NM_001008542, intron 1 of 5)"	CpG	2591	NM_001008542	17859	Mm.2154	NM_001008542	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	Max interacting protein 1	protein-coding	0.138211	0.782258
Merged-chr13-113618612-2	chr13	113618559	113618665	+	6.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_130796)	promoter-TSS (NM_130796)	-48	NM_130796	170625	Mm.33721	NM_130796	ENSMUSG00000042364	Snx18	Snag1	sorting nexin 18	protein-coding	0.150943	0.757009
Merged-chr7-16924158-2	chr7	16924095	16924222	+	6.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007590)	promoter-TSS (NM_007590)	-126	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding	0.149606	0.703125
Merged-chr12-102438114-2	chr12	102438059	102438170	+	6.4	cIP1vsInput|cIP2vsInput	"intron (NM_011175, intron 1 of 13)"	"intron (NM_011175, intron 1 of 13)"	1583	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding	0	0.5
Merged-chr6-136470984-2	chr6	136470922	136471047	+	6.4	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-47867	NM_019426	54343	Mm.361788	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding	0.096	0.730159
Merged-chr11-116490432-1	chr11	116490382	116490482	+	6.4	cIP2vsInput	promoter-TSS (NM_026364)	promoter-TSS (NM_026364)	-86	NM_026364	67763	Mm.25125	NM_026364	ENSMUSG00000015869	Prpsap1	5730409F23Rik|PAP39	phosphoribosyl pyrophosphate synthetase-associated protein 1	protein-coding	0.09	0.673267
Merged-chr1-125435806-2	chr1	125435726	125435886	+	6.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001205386)	promoter-TSS (NM_001205386)	-79	NM_001205386	74117	Mm.183102	NM_001205385	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding	0.09375	0.645963
Merged-chr11-116853680-1	chr11	116853630	116853730	+	6.4	cIP2vsInput	promoter-TSS (NM_178620)	promoter-TSS (NM_178620)	-335	NM_178620	69900	Mm.484423	NM_178620	ENSMUSG00000020818	Mfsd11	2600014M03Rik	major facilitator superfamily domain containing 11	protein-coding	0.12	0.70297
Merged-chr19-36409504-2	chr19	36409434	36409574	+	6.35	cIP1vsInput|cIP2vsInput	"intron (NM_029508, intron 1 of 8)"	"intron (NM_029508, intron 1 of 8)"	30437	NM_029508	76073	Mm.488093	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding	0.071429	0.652482
Merged-chr18-37841767-2	chr18	37841710	37841824	+	6.35	cIP1vsInput|cIP2vsInput	TTS (NM_033592)	TTS (NM_033592)	22221	NM_033583	93708	Mm.247203	NM_033583	ENSMUSG00000023036	Pcdhgc5	-	"protocadherin gamma subfamily C, 5"	protein-coding	0.04386	0.452174
Merged-chr10-70120051-2	chr10	70119997	70120105	+	6.35	cIP1vsInput|cIP2vsInput	"intron (NM_001111121, intron 1 of 8)"	"intron (NM_001111121, intron 1 of 8)"	22930	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding	0.027778	0.53211
Merged-chr5-150390577-2	chr5	150390507	150390648	+	6.35	cIP1vsInput|cIP2vsInput	"intron (NM_172887, intron 19 of 60)"	"intron (NM_172887, intron 19 of 60)"	111642	NR_024513	194292	Mm.300184	NR_024513		Gm5	Gm1812	predicted gene 5	miscRNA	0.021277	0.535211
Merged-chr6-128046963-2	chr6	128046911	128047015	+	6.3	cIP1vsInput|cIP2vsInput	"intron (NM_175414, intron 2 of 8)"	"intron (NM_175414, intron 2 of 8)"	96615	NM_175414	109246	Mm.21814	NM_175414	ENSMUSG00000030352	Tspan9	6720474K14Rik|9430079M16Rik|AU018597	tetraspanin 9	protein-coding	0.038462	0.590476
Merged-chr10-24869916-1	chr10	24869866	24869966	+	6.3	cIP2vsInput	promoter-TSS (NM_001166416)	promoter-TSS (NM_001166416)	-70	NM_001166416	70208	Mm.28020	NM_001166416	ENSMUSG00000019984	Med23	130kDa|3000002A17Rik|Crsp3|ESTM7|Sur2|X83317|mKIAA1216	mediator complex subunit 23	protein-coding	0.07	0.594059
Merged-chr3-52102126-1	chr3	52102076	52102176	+	6.3	cIP2vsInput	"intron (NM_001004176, intron 1 of 4)"	"intron (NM_001004176, intron 1 of 4)"	2880	NM_001004176	433586	Mm.481431	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding	0.08	0.772277
Merged-chr13-80883027-1	chr13	80882977	80883077	+	6.3	cIP2vsInput	promoter-TSS (NM_001042591)	promoter-TSS (NM_001042591)	-395	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0.09	0.712871
Merged-chr11-119602920-1	chr11	119602870	119602970	+	6.3	cIP2vsInput	promoter-TSS (NM_028898)	promoter-TSS (NM_028898)	-75	NM_028898	74370	Mm.209933	NM_028898	ENSMUSG00000025583	Rptor	4932417H02Rik|Rap|Raptor|mKIAA1303	"regulatory associated protein of MTOR, complex 1"	protein-coding	0.1	0.623762
Merged-chr15-102350825-2	chr15	102350762	102350888	+	6.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_153416)	promoter-TSS (NM_153416)	-66	NM_153416	223921	Mm.352946	NM_153416	ENSMUSG00000036678	Aaas	AAA|ADRACALA|D030041N15Rik|GL003	"achalasia, adrenocortical insufficiency, alacrimia"	protein-coding	0.142857	0.669291
Merged-chr13-63568017-1	chr13	63567967	63568067	+	6.3	cIP2vsInput	Intergenic	CpG	-2497	NM_008957	19206	Mm.488634	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes	patched homolog 1	protein-coding	0.13	0.70297
Merged-chr2-181929082-1	chr2	181929032	181929132	+	6.3	cIP1vsInput	Intergenic	(TTTC)n|Simple_repeat|Simple_repeat	-62144	NM_001205282	672125	Mm.489571	NM_001205282	ENSMUSG00000053277	Gm14496	OTTMUSG00000016837	predicted gene 14496	protein-coding	0	0.376238
Merged-chr5-142817703-1	chr5	142817653	142817753	+	6.3	cIP2vsInput	promoter-TSS (NM_001122730)	promoter-TSS (NM_001122730)	-316	NM_001122730	231861	Mm.480618	NM_001122730	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding	0.06	0.50495
Merged-chr3-53463677-1	chr3	53463627	53463727	+	6.3	cIP2vsInput	promoter-TSS (NM_173382)	promoter-TSS (NM_173382)	-140	NM_173382	212127	Mm.218697	NM_173382	ENSMUSG00000049504	Proser1	2810046L04Rik|9330161F11	proline and serine rich 1	protein-coding	0.08	0.673267
Merged-chrX-136273802-1	chrX	136273752	136273852	+	6.3	cIP1vsInput	Intergenic	Intergenic	3549	NM_001110234	12070	Mm.90787	NM_001110233	ENSMUSG00000046432	Ngfrap1	AL033356|Bex3|DXWsu67e|Gcap27|Nade	nerve growth factor receptor (TNFRSF16) associated protein 1	protein-coding	0	0.326733
Merged-chr18-74216170-2	chr18	74216119	74216222	+	6.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028868)	promoter-TSS (NM_028868)	-42	NM_028868	74322	Mm.17537	NM_028868	ENSMUSG00000024560	Cxxc1	2410002I16Rik|5830420C16Rik|AI426635|Cfp1|Cgbp|PHF18	CXXC finger 1 (PHD domain)	protein-coding	0.126214	0.653846
Merged-chr7-89941352-2	chr7	89941295	89941409	+	6.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026304)	promoter-TSS (NM_026304)	-167	NM_026304	67669	Mm.28679	NM_026304		l7Rn6	0610007P06Rik|1110002N09Rik|l(7)6Rn	"lethal, Chr 7, Rinchik 6"	protein-coding	0.035088	0.504348
Merged-chr2-30049182-2	chr2	30049130	30049234	+	6.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001008498)	promoter-TSS (NM_001008498)	-303	NM_001008498	71820	Mm.88053	NM_001008498	ENSMUSG00000039715	Wdr34	3200002I06Rik	WD repeat domain 34	protein-coding	0.096154	0.695238
Merged-chr16-50430376-2	chr16	50430309	50430443	+	6.3	cIP1vsInput|cIP2vsInput	"intron (NM_027444, intron 1 of 16)"	"intron (NM_027444, intron 1 of 16)"	2013	NM_027444	70508	Mm.28940	NM_027444	ENSMUSG00000022641	Bbx	5530401J07Rik|5730403O13Rik	bobby sox homolog (Drosophila)	protein-coding	0.059701	0.614815
Merged-chr8-125330803-2	chr8	125330753	125330854	+	6.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	161907	NM_001081337	244668	Mm.271668	NM_001081337	ENSMUSG00000001995	Sipa1l2	BC058408|mKIAA1389	signal-induced proliferation-associated 1 like 2	protein-coding	0	0.509804
Merged-chr5-149184313-2	chr5	149184260	149184366	+	6.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001115153)	promoter-TSS (NM_001115153)	-247	NM_001115153	231915	Mm.29402	NM_001013378	ENSMUSG00000041264	Uspl1	D030048C09|E430026A01Rik	ubiquitin specific peptidase like 1	protein-coding	0.103774	0.654206
Merged-chr10-54058170-2	chr10	54058112	54058228	+	6.25	cIP1vsInput|cIP2vsInput	"intron (NM_008548, intron 2 of 12)"	(TA)n|Simple_repeat|Simple_repeat	17626	NM_008548	17155	Mm.117294	NM_008548		Man1a	Man1a1|PCR1	"mannosidase 1, alpha"	protein-coding	0	0.213675
Merged-chr6-83156342-2	chr6	83156285	83156399	+	6.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027948)	promoter-TSS (NM_027948)	37	NM_023790	75659	Mm.130665	NM_023790		Wdr54	1700030E05Rik	WD repeat domain 54	protein-coding	0.096491	0.669565
Merged-chr7-25297639-2	chr7	25297582	25297696	+	6.2	cIP1vsInput|cIP2vsInput	"intron (NM_008776, intron 1 of 5)"	CpG-12842	316	NM_008776	18476	Mm.597	NM_008776	ENSMUSG00000005447	Pafah1b3	Pafahg|mus[g]	"platelet-activating factor acetylhydrolase, isoform 1b, subunit 3"	protein-coding	0.114035	0.652174
Merged-chr7-19308710-2	chr7	19308660	19308760	+	6.2	cIP1vsInput|cIP2vsInput	"intron (NM_008036, intron 1 of 3)"	CpG	1335	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding	0.15	0.732673
Merged-chrX-126077840-1	chrX	126077790	126077890	+	6.2	cIP1vsInput	Intergenic	Intergenic	756164	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding	0	0.29703
Merged-chr8-70302750-2	chr8	70302691	70302809	+	6.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_021538)	promoter-TSS (NM_021538)	-35	NM_021538	59042	Mm.28668	NM_021538		Cope	1110005D17Rik|Cope1	"coatomer protein complex, subunit epsilon"	protein-coding	0.059322	0.529412
Merged-chr8-33574284-2	chr8	33574232	33574336	+	6.2	cIP1vsInput|cIP2vsInput	"exon (NM_031374, exon 1 of 4)"	"exon (NM_031374, exon 1 of 4)"	3740	NM_031374	104271	Mm.488030	NM_031374	ENSMUSG00000009628	Tex15	2210014E14Rik|AL022622|AU022940	testis expressed gene 15	protein-coding	0	0.371429
Merged-chr18-84951535-1	chr18	84951485	84951585	+	6.2	cIP2vsInput	promoter-TSS (NM_025969)	promoter-TSS (NM_025969)	-11	NM_025969	67105	Mm.250617	NM_025969	ENSMUSG00000024645	Timm21	1700034H14Rik|2700002I20Rik	tranlocase of inner mitochondrial membrane 21	protein-coding	0.05	0.49505
Merged-chr6-86527321-1	chr6	86527271	86527371	+	6.2	cIP1vsInput	promoter-TSS (NR_037961)	promoter-TSS (NR_037961)	-9	NR_037960	72012	Mm.349174	NR_037960	ENSMUSG00000097048	1600020E01Rik	-	RIKEN cDNA 1600020E01 gene	miscRNA	0.09	0.653465
Merged-chr2-92185417-2	chr2	92185365	92185469	+	6.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001109691)	promoter-TSS (NM_001109691)	-66	NM_001109691	192285	Mm.330408	NM_001109690	ENSMUSG00000058318	Phf21a	80kDa|Bhc|Bhc80|D030065N23Rik|PFTF1	PHD finger protein 21A	protein-coding	0.115385	0.733333
Merged-chr6-24018522-2	chr6	24018454	24018590	+	6.2	cIP1vsInput|cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	-48462	NM_207022	387347	Mm.377909	NM_207022	ENSMUSG00000043865	Tas2r118	Gm465|T2R18|Tas2r16|Tas2r18|mGR18|mt2r40	"taste receptor, type 2, member 118"	protein-coding	0	0.481752
Merged-chr14-29978344-2	chr14	29978294	29978395	+	6.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027493)	promoter-TSS (NM_027493)	7	NM_027493	56249	Mm.215110	NM_027493	ENSMUSG00000015971	Actr8	5730542K05Rik|ARP8	ARP8 actin-related protein 8	protein-coding	0.089109	0.656863
Merged-chr2-180042476-2	chr2	180042414	180042538	+	6.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011969)	promoter-TSS (NM_011969)	-7	NM_178750	269397	Mm.63068	NM_178750	ENSMUSG00000039086	Ss18l1	A230053O16Rik|CREST	synovial sarcoma translocation gene on chromosome 18-like 1	protein-coding	0.137097	0.784
Merged-chr2-28641192-1	chr2	28641142	28641242	+	6.2	cIP2vsInput	promoter-TSS (NM_022887)	promoter-TSS (NM_022887)	-51	NM_022887	64930	Mm.224354	NM_022887	ENSMUSG00000026812	Tsc1	hamartin|mKIAA0243	tuberous sclerosis 1	protein-coding	0.09	0.613861
Merged-chr3-52105051-1	chr3	52105001	52105101	+	6.2	cIP2vsInput	promoter-TSS (NM_001004176)	promoter-TSS (NM_001004176)	-45	NM_001004176	433586	Mm.481431	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding	0.13	0.722772
Merged-chr7-142578248-2	chr7	142578168	142578329	+	6.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_001592)	promoter-TSS (NR_001592)	-102	NR_001592	14955	Mm.490776	NR_001592		H19	AI747191	H19 fetal liver mRNA	miscRNA	0.068323	0.635802
Merged-chr6-124712111-2	chr6	124712041	124712182	+	6.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013536)	promoter-TSS (NM_013536)	67	NM_013536	14791	Mm.6390	NM_013536	ENSMUSG00000004268	Emg1	C2f|Grcc2f	EMG1 nucleolar protein homolog (S. cerevisiae)	protein-coding	0.085106	0.549296
Merged-chr7-102441688-2	chr7	102441629	102441747	+	6.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009103)	promoter-TSS (NM_009103)	-7	NM_009103	20133	Mm.415177	NM_009103	ENSMUSG00000030978	Rrm1	RnrM1	ribonucleotide reductase M1	protein-coding	0.059322	0.596639
Merged-chr17-83123079-2	chr17	83123021	83123138	+	6.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-44854	NR_045094	100503434	Mm.187281	NR_045094		Gm19689	-	"predicted gene, 19689"	miscRNA	0.025641	0.59322
Merged-chr8-25720043-2	chr8	25719986	25720100	+	6.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028000)	promoter-TSS (NM_028000)	-5	NM_028000	71910	Mm.385055	NM_028000	ENSMUSG00000031570	Ppapdc1b	1810019D05Rik|2310022A04Rik|AW045471|Ppapdc1	phosphatidic acid phosphatase type 2 domain containing 1B	protein-coding	0.149123	0.730435
Merged-chr3-51701613-2	chr3	51701561	51701666	+	6.15	cIP1vsInput|cIP2vsInput	"intron (NM_001004176, intron 2 of 4)"	"intron (NM_001004176, intron 2 of 4)"	40420	NM_174995	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding	0.085714	0.688679
Merged-chrY-6825065-2	chrY	6824979	6825151	+	6.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	342712	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.416185
Merged-chr7-101905768-2	chr7	101905711	101905825	+	6.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025605)	promoter-TSS (NM_025605)	-69	NM_025605	66508	Mm.214841	NM_025605	ENSMUSG00000030842	Lamtor1	2400001E08Rik|Pdro|p18	"late endosomal/lysosomal adaptor, MAPK and MTOR activator 1"	protein-coding	0.087719	0.547826
Merged-chr12-80790468-2	chr12	80790415	80790521	+	6.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178682)	promoter-TSS (NM_178682)	-64	NM_178682	217684	Mm.341776	NM_001242419	ENSMUSG00000021133	4933426M11Rik	mKIAA0247	RIKEN cDNA 4933426M11 gene	protein-coding	0.150943	0.747664
Merged-chr17-4994294-2	chr17	4994233	4994356	+	6.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001085355)	promoter-TSS (NM_001085355)	-780	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding	0.154472	0.709677
Merged-chr7-110613844-2	chr7	110613777	110613911	+	6.15	cIP1vsInput|cIP2vsInput	"intron (NM_177324, intron 1 of 40)"	"intron (NM_177324, intron 1 of 40)"	1076	NM_177324	319934	Mm.102970	NM_178769	ENSMUSG00000038371	Sbf2	4833411B01Rik|AA414977|AI317167|B430219L04Rik|Mtmr13|mMTMH1	SET binding factor 2	protein-coding	0.037313	0.42963
Merged-chr19-44294845-2	chr19	44294776	44294914	+	6.15	cIP1vsInput|cIP2vsInput	"intron (NM_009128, intron 1 of 5)"	"intron (NM_009128, intron 1 of 5)"	1169	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Scd-2|swty	stearoyl-Coenzyme A desaturase 2	protein-coding	0.036232	0.553957
Merged-chr3-40847178-2	chr3	40847125	40847232	+	6.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028140)	promoter-TSS (NM_028140)	179	NR_038067	100039027	Mm.482948	NR_038067		Gm2011	-	predicted gene 2011	pseudo	0.056075	0.611111
Merged-chr13-51848800-1	chr13	51848750	51848850	+	6.1	cIP2vsInput	TTS (NM_011817)	TTS (NM_011817)	2125	NM_011817	23882	Mm.281298	NM_011817	ENSMUSG00000021453	Gadd45g	AI327420|C86281|CR6|DDIT2|OIG37	growth arrest and DNA-damage-inducible 45 gamma	protein-coding	0.04	0.643564
Merged-chr11-101658503-2	chr11	101658434	101658573	+	6.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-7038	NM_025404	80981	Mm.266840	NM_025404	ENSMUSG00000034936	Arl4d	1110036H21Rik|ARL6|AW456149|Arf4l|Arfl4|Arl5	ADP-ribosylation factor-like 4D	protein-coding	0.014388	0.342857
Merged-chr11-69368718-1	chr11	69368668	69368768	+	6.1	cIP2vsInput	"intron (NM_146019, intron 1 of 39)"	CpG	708	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding	0.16	0.841584
Merged-chr19-5845939-2	chr19	5845881	5845997	+	6.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_003513)	promoter-TSS (NR_003513)	-461	NR_003513	66961	Mm.472837	NR_003513		Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	miscRNA	0.112069	0.700855
Merged-chr11-52360802-1	chr11	52360752	52360852	+	6.1	cIP2vsInput	promoter-TSS (NM_011694)	promoter-TSS (NM_011694)	-313	NM_011694	22333	Mm.470023	NM_011694	ENSMUSG00000020402	Vdac1	AL033343|Vdac5	voltage-dependent anion channel 1	protein-coding	0.07	0.663366
Merged-chr10-53456540-2	chr10	53456485	53456596	+	6.1	cIP1vsInput|cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	62449	NR_037973	100502868	Mm.297722	NR_037973		Gm20597	B230314j19	"predicted gene, 20597"	miscRNA	0.027027	0.598214
Merged-chr4-59898910-2	chr4	59898853	59898967	+	6.1	cIP1vsInput|cIP2vsInput	"exon (NM_172468, exon 9 of 9)"	"exon (NM_172468, exon 9 of 9)"	16146	NM_021053	30936	Mm.284433	NM_021053		Slc46a2	5430429N04Rik|Ly110|TSO-1C12|Tscot	"solute carrier family 46, member 2"	protein-coding	0.026316	0.486957
Merged-chr11-62551676-1	chr11	62551626	62551726	+	6.1	cIP2vsInput	"intron (NR_002875, intron 1 of 2)"	CpG	172	NM_011664	22187	Mm.371592	NM_011664		Ubb	AL033289|Rps27a|Uba52|Ubb2|Ubc	ubiquitin B	protein-coding	0.08	0.623762
Merged-chr2-75659591-1	chr2	75659541	75659641	+	6.1	cIP2vsInput	"intron (NM_198090, intron 1 of 10)"	CpG	301	NR_033513	627828	Mm.459502	NR_033513	ENSMUSG00000092086	Gm6793	EG627828	heterogeneous nuclear ribonucleoprotein A3 pseudogene	pseudo	0.15	0.782178
Merged-chr17-29490449-2	chr17	29490398	29490501	+	6.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008842)	promoter-TSS (NM_008842)	-596	NM_008842	18712	Mm.485038	NM_008842		Pim1	Pim-1	proviral integration site 1	protein-coding	0.135922	0.701923
Merged-chr1-75597717-2	chr1	75597647	75597788	+	6.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	51451	NM_009208	20536	Mm.5053	NM_009208		Slc4a3	A930038D23Rik|Ae3	"solute carrier family 4 (anion exchanger), member 3"	protein-coding	0	0.288732
Merged-chr7-44849248-2	chr7	44849190	44849306	+	6.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001253920)	promoter-TSS (NM_001253920)	24	NM_026270	67605	Mm.431538	NM_001253920	ENSMUSG00000011096	Akt1s1	1110012J22Rik|AI227026|Lobe|Lobel|PRAS40	AKT1 substrate 1 (proline-rich)	protein-coding	0.051724	0.504274
Merged-chr11-88718993-2	chr11	88718931	88719056	+	6.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001201341)	promoter-TSS (NM_001201341)	350	NR_038058	193280	Mm.396842	NR_038058		C030037D09Rik	9330160M04	RIKEN cDNA C030037D09 gene	miscRNA	0.104	0.619048
Merged-chr11-118585050-2	chr11	118584988	118585113	+	6.05	cIP1vsInput|cIP2vsInput	"intron (NM_001024931, intron 4 of 14)"	"intron (NM_001024931, intron 4 of 14)"	108090	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding	0.072	0.611111
Merged-chr4-95288609-2	chr4	95288551	95288667	+	6.05	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-236387	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	Jun oncogene	protein-coding	0.008621	0.418803
Merged-chr10-82630138-2	chr10	82630067	82630209	+	6.05	cIP1vsInput|cIP2vsInput	"intron (NM_172552, intron 1 of 9)"	CpG	296	NR_037190	624784	Mm.284252	NR_037190	ENSMUSG00000085666	Gm9855	ENSMUSG00000051559	thymine DNA glycosylase pseudogene	pseudo	0.105634	0.727273
Merged-chr9-64253184-2	chr9	64253120	64253249	+	6.05	cIP1vsInput|cIP2vsInput	"intron (NM_008927, intron 1 of 10)"	CpG	421	NM_008927	26395	Mm.248907	NM_008927	ENSMUSG00000004936	Map2k1	MAPKK1|MEKK1|Mek1|Prkmk1	mitogen-activated protein kinase kinase 1	protein-coding	0.147287	0.753846
Merged-chr9-120933441-2	chr9	120933391	120933492	+	6.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001165902)	promoter-TSS (NM_001165902)	41	NM_007614	12387	Mm.291928	NM_001165902	ENSMUSG00000006932	Ctnnb1	Bfc|Catnb|Mesc	"catenin (cadherin associated protein), beta 1"	protein-coding	0.178218	0.686275
Merged-chr10-81378570-2	chr10	81378506	81378634	+	6.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019757)	promoter-TSS (NM_019757)	-200	NM_019757	56371	Mm.24202	NM_019757		Fzr1	AW108046|Cdh1|FZR|FZR2|Fyr|HCDH|HCDH1	fizzy/cell division cycle 20 related 1 (Drosophila)	protein-coding	0.085938	0.713178
Merged-chr17-84028750-2	chr17	84028681	84028820	+	6	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-49910	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	miscRNA	0.035971	0.642857
Merged-chr2-128968253-1	chr2	128968203	128968303	+	6	cIP2vsInput	"intron (NM_178404, intron 1 of 11)"	"intron (NM_178404, intron 1 of 11)"	851	NM_178404	78751	Mm.26377	NM_178404	ENSMUSG00000042851	Zc3h6	4631426G04Rik|4833425H18Rik|AU024389|AW060453|Zc3hdc6|mKIAA2035	zinc finger CCCH type containing 6	protein-coding	0.02	0.316832
Merged-chr4-135855723-2	chr4	135855646	135855800	+	6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010178)	promoter-TSS (NM_010178)	-369	NM_001080387	14105	Mm.472035	NM_001080387	ENSMUSG00000028676	Srsf10	FUSIP2|Fusip1|NSSR1|NSSR2|Nssr|SRrp40|Sfrs13a|Srsf13a|TASR|TASR1|TASR2	serine/arginine-rich splicing factor 10	protein-coding	0.058442	0.593548
Merged-chr9-24974378-1	chr9	24974328	24974428	+	6	cIP2vsInput	Intergenic	Intergenic	177403	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding	0.04	0.613861
Merged-chr9-82975464-1	chr9	82975414	82975514	+	6	cIP2vsInput	promoter-TSS (NM_001081216)	promoter-TSS (NM_001081216)	25	NM_001081216	83946	Mm.221688	NM_001081216	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding	0.12	0.712871
Merged-chr17-41548997-1	chr17	41548947	41549047	+	6	cIP2vsInput	Intergenic	Intergenic	614312	NM_008650	17850	Mm.259884	NM_008650	ENSMUSG00000023921	Mut	D230010K02Rik|Mcm	methylmalonyl-Coenzyme A mutase	protein-coding	0	0.386139
Merged-chr8-34154599-2	chr8	34154530	34154668	+	6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026432)	promoter-TSS (NM_026432)	36	NM_026432	67887	Mm.290353	NM_026432	ENSMUSG00000031532	Tmem66	1810045K07Rik|SARAF	transmembrane protein 66	protein-coding	0.115942	0.640288
Merged-chrY-90740532-2	chrY	90740476	90740589	+	6	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-44910	NM_133362	170942	Mm.391385	XM_003946384	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding	0.044248	0.517544
Merged-chr3-87885835-2	chr3	87885777	87885894	+	6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_033573)	promoter-TSS (NM_033573)	-273	NM_033573	94315	Mm.35089	NM_033573	ENSMUSG00000004895	Prcc	-	papillary renal cell carcinoma (translocation-associated)	protein-coding	0.042735	0.432203
Merged-chr12-3426582-2	chr12	3426529	3426636	+	6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001270988)	promoter-TSS (NM_001270988)	165	NR_030694	100043040	Mm.415417	NR_030694	ENSMUSG00000071456	1110002L01Rik	-	RIKEN cDNA 1110002L01 gene	miscRNA	0.065421	0.5
Merged-chr7-12978157-2	chr7	12978103	12978212	+	6	cIP1vsInput|cIP2vsInput	"5' UTR (NM_001168562, exon 1 of 5)"	"5' UTR (NM_001168562, exon 1 of 5)"	309	NM_001168561	269870	Mm.62083	NM_001168561		Zfp446	A630035I11Rik|A930031C22|AA120513|AV306632	zinc finger protein 446	protein-coding	0.091743	0.7
Merged-chrY-6793593-1	chrY	6793543	6793643	+	6	cIP2vsInput	Intergenic	Lx5b|LINE|L1	374184	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.326733
Merged-chr16-91534674-1	chr16	91534624	91534724	+	6	cIP2vsInput	Intergenic	Intergenic	-12420	NM_008338	15980	Mm.249364	NM_008338		Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding	0.07	0.683168
Merged-chr7-89980697-2	chr7	89980635	89980759	+	5.95	cIP1vsInput|cIP2vsInput	"5' UTR (NM_021876, exon 1 of 12)"	"5' UTR (NM_021876, exon 1 of 12)"	279	NM_021876	13626	Mm.380914	NM_021876	ENSMUSG00000030619	Eed	ENSMUSG00000039373|l(7)5Rn|l7Rn5|lusk	embryonic ectoderm development	protein-coding	0.169355	0.768
Merged-chr7-19228325-2	chr7	19228256	19228395	+	5.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_207525)	promoter-TSS (NM_207525)	-64	NM_207525	403187	Mm.239583	NM_207525		Opa3	D630048P19Rik|Gm1425|Gm472	optic atrophy 3	protein-coding	0.129496	0.685714
Merged-chr11-105505094-2	chr11	105505035	105505153	+	5.95	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-48359	NM_001039242	632687	Mm.121570	NM_001039242	ENSMUSG00000078627	10-Mar	4933417C16Rik|AV039223|OTTMUSG00000002847|Rnf190	membrane-associated ring finger (C3HC4) 10	protein-coding	0.008475	0.478992
Merged-chr10-63023896-2	chr10	63023840	63023953	+	5.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026085)	promoter-TSS (NM_026085)	-47	NM_001079824	432467	Mm.274784	NM_001079824	ENSMUSG00000020069	Hnrnph3	AA693301|AI666703|Hnrph3	heterogeneous nuclear ribonucleoprotein H3	protein-coding	0.097345	0.754386
Merged-chr8-126596470-2	chr8	126596391	126596550	+	5.95	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-3034	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding	0.018868	0.48125
Merged-chr5-32458941-2	chr5	32458887	32458996	+	5.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172707)	promoter-TSS (NM_172707)	-29	NM_172707	19046	Mm.456635	NM_172707		Ppp1cb	1200010B19	"protein phosphatase 1, catalytic subunit, beta isoform"	protein-coding	0.155963	0.763636
Merged-chr14-67009032-2	chr14	67008975	67009089	+	5.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009761)	promoter-TSS (NM_009761)	-155	NM_009761	12177	Mm.347081	NM_009761	ENSMUSG00000022051	Bnip3l	C86132|D14Ertd719e|Nip3L|Nix	BCL2/adenovirus E1B interacting protein 3-like	protein-coding	0.122807	0.669565
Merged-chr7-101837001-1	chr7	101836951	101837051	+	5.9	cIP2vsInput	"intron (NM_010567, intron 1 of 28)"	CpG-13418	823	NM_001122739	16332	Mm.476000	NM_001122739	ENSMUSG00000032737	Inppl1	51C|SHIP2	inositol polyphosphate phosphatase-like 1	protein-coding	0.06	0.653465
Merged-chr13-27343238-2	chr13	27343185	27343291	+	5.9	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-2451	NM_010088	13529	Mm.291450	NM_010088	ENSMUSG00000018259	Prl8a2	D/tPRP|DPRP|Dtprp|mdPRP	"prolactin family 8, subfamily a, member 2"	protein-coding	0	0.383178
Merged-chr3-121968797-2	chr3	121968747	121968848	+	5.9	cIP1vsInput|cIP2vsInput	"intron (NM_172525, intron 1 of 22)"	"intron (NM_172525, intron 1 of 22)"	15471	NM_172525	214137	Mm.229287	NM_172525	ENSMUSG00000039831	Arhgap29	6720461J18Rik|A830014I19|AU040217|B130017I01Rik|C76601|Parg1	Rho GTPase activating protein 29	protein-coding	0.039604	0.519608
Merged-chr3-8923600-1	chr3	8923550	8923650	+	5.9	cIP2vsInput	"exon (NM_025434, exon 1 of 3)"	"exon (NM_025434, exon 1 of 3)"	257	NM_025434	66230	Mm.38460	NM_025434	ENSMUSG00000040269	Mrps28	1500012D08Rik|AW061224	mitochondrial ribosomal protein S28	protein-coding	0.16	0.722772
Merged-chr5-92997969-2	chr5	92997906	92998032	+	5.9	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	47053	NM_175270	78088	Mm.245085	NM_175270	ENSMUSG00000045314	Sowahb	5730467H21Rik|Ankrd56	sosondowah ankyrin repeat domain family member B	protein-coding	0.015873	0.559055
Merged-chr6-36508048-2	chr6	36507990	36508106	+	5.9	cIP1vsInput|cIP2vsInput	"intron (NM_203491, intron 2 of 2)"	"intron (NM_203491, intron 2 of 2)"	86306	NR_030524	735279		NR_030524	ENSMUSG00000070075	Mir490	Mirn490|mmu-mir-490	microRNA 490	miscRNA	0.034483	0.487179
Merged-chr7-111157488-2	chr7	111157427	111157550	+	5.9	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-34813	NR_015573	75479	Mm.381620	NR_015573		1700012D14Rik	-	RIKEN cDNA 1700012D14 gene	miscRNA	0.03252	0.58871
Merged-chr4-34935817-1	chr4	34935767	34935867	+	5.9	cIP1vsInput	Intergenic	B2_Mm1a|SINE|B2	-24336	NR_040652	73696	Mm.296813	NR_040652	ENSMUSG00000085824	2410114N07Rik	-	RIKEN cDNA 2410114N07 gene	miscRNA	0	0.247525
Merged-chr2-39065544-2	chr2	39065477	39065612	+	5.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029793)	promoter-TSS (NM_029793)	-138	NM_029793	76899	Mm.131098	NM_029793	ENSMUSG00000026754	Golga1	0710001G09Rik|2210418B03Rik|AW107649|Golgi97|golgin-97	"golgi autoantigen, golgin subfamily a, 1"	protein-coding	0.177778	0.742647
Merged-chr2-25211487-1	chr2	25211437	25211537	+	5.9	cIP2vsInput	promoter-TSS (NM_021393)	promoter-TSS (NM_021393)	2	NM_021393	58202	Mm.116418	NM_021393	ENSMUSG00000013465	Nelfb	A730008L03Rik|AB041607|AI663983|Cobra1|Nelf-b	"negative elongation factor complex member B, Cobra1"	protein-coding	0.11	0.653465
Merged-chr1-86526328-1	chr1	86526278	86526378	+	5.9	cIP2vsInput	promoter-TSS (NM_008972)	promoter-TSS (NM_008972)	-408	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding	0.07	0.752475
Merged-chr2-117120713-1	chr2	117120663	117120763	+	5.9	cIP2vsInput	promoter-TSS (NM_001277256)	promoter-TSS (NM_001277256)	-358	NM_001277256	114715	Mm.397626	NM_001277256		Spred1	5730461F13Rik|AL024345|AW047647	"sprouty protein with EVH-1 domain 1, related sequence"	protein-coding	0.13	0.683168
Merged-chr18-16808708-1	chr18	16808658	16808758	+	5.9	cIP2vsInput	"5' UTR (NM_007664, exon 1 of 16)"	"5' UTR (NM_007664, exon 1 of 16)"	341	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-cadherin|Ncad	cadherin 2	protein-coding	0.13	0.70297
Merged-chr4-137048729-2	chr4	137048676	137048782	+	5.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_198248)	promoter-TSS (NM_198248)	-34	NM_198248	230848	Mm.31068	NM_198248	ENSMUSG00000060862	Zbtb40	BC059177|C230087D24|Gm571|mKIAA0478	zinc finger and BTB domain containing 40	protein-coding	0.04717	0.53271
Merged-chr11-69417611-2	chr11	69417544	69417678	+	5.9	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-3936	NM_001017426	216850	Mm.472522	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding	0.029851	0.592593
Merged-chr4-82506550-1	chr4	82506500	82506600	+	5.9	cIP2vsInput	Intergenic	CpG-9999	-1242	NM_008687	18028	Mm.317947	NM_001113209	ENSMUSG00000008575	Nfib	6720429L07Rik|E030026I10Rik	nuclear factor I/B	protein-coding	0.17	0.841584
Merged-chr1-155973165-1	chr1	155973115	155973215	+	5.9	cIP2vsInput	promoter-TSS (NM_001039184)	promoter-TSS (NM_001039184)	90	NM_001039184	74081	Mm.260247	NM_001039184	ENSMUSG00000033671	Cep350	4933409L06Rik|6430546F08Rik	centrosomal protein 350	protein-coding	0.12	0.732673
Merged-chr18-11133060-2	chr18	11132997	11133124	+	5.85	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	80550	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding	0	0.375
Merged-chr4-43058866-2	chr4	43058794	43058938	+	5.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_021468)	promoter-TSS (NM_021468)	-118	NM_001081413	22249	Mm.128892	NM_001081413	ENSMUSG00000028456	Unc13b	Munc13-1|Munc13-2|Unc13a|Unc13h1|Unc13h2	unc-13 homolog B (C. elegans)	protein-coding	0.076389	0.62069
Merged-chr7-111122464-2	chr7	111122398	111122531	+	5.85	cIP1vsInput|cIP2vsInput	"non-coding (NR_015573, exon 1 of 3)"	"non-coding (NR_015573, exon 1 of 3)"	211	NR_015573	75479	Mm.381620	NR_015573		1700012D14Rik	-	RIKEN cDNA 1700012D14 gene	miscRNA	0.097744	0.671642
Merged-chr8-95691173-2	chr8	95691105	95691241	+	5.8	cIP1vsInput|cIP2vsInput	Intergenic	L1MC4a|LINE|L1	-11864	NM_001195006	234593	Mm.29846	NM_001195006	ENSMUSG00000036564	Ndrg4	D8Bwg1337e|Ndr1-rs|Ndr4|R74996|SMAP-8	N-myc downstream regulated gene 4	protein-coding	0.007353	0.394161
Merged-chr3-90254151-2	chr3	90254100	90254203	+	5.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028881)	promoter-TSS (NM_028881)	-130	NM_028881	74343	Mm.35627	NM_028881	ENSMUSG00000027936	Crtc2	4632407F12Rik|Torc2|mTORC2	CREB regulated transcription coactivator 2	protein-coding	0.087379	0.692308
Merged-chr4-141546683-2	chr4	141546628	141546738	+	5.8	cIP1vsInput|cIP2vsInput	"non-coding (NR_030695, exon 1 of 1)"	"non-coding (NR_030695, exon 1 of 1)"	521	NR_030695	320456	Mm.32859	NM_177163		B330016D10Rik	-	RIKEN cDNA B330016D10 gene	miscRNA	0.172727	0.81982
Merged-chr3-108210187-2	chr3	108210125	108210250	+	5.8	cIP1vsInput|cIP2vsInput	"intron (NM_175183, intron 1 of 11)"	CpG	747	NM_175183	72522	Mm.187326	NM_175183	ENSMUSG00000048997	Atxn7l2	2610528J18Rik	ataxin 7-like 2	protein-coding	0.112	0.730159
Merged-chr15-81858354-2	chr15	81858296	81858412	+	5.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_020507)	promoter-TSS (NM_020507)	-28	NM_020507	57259	Mm.323595	NM_020507	ENSMUSG00000048546	Tob2	2900090N22Rik|4930545K18Rik|AV071822|mKIAA1663	"transducer of ERBB2, 2"	protein-coding	0.068966	0.649573
Merged-chr2-26572056-2	chr2	26571974	26572138	+	5.8	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-9000	NM_178444	353156	Mm.268933	NM_001164564	ENSMUSG00000026921	Egfl7	VE-statin|Zneu1	EGF-like domain 7	protein-coding	0.02439	0.618182
Merged-chr18-14103338-1	chr18	14103288	14103388	+	5.8	cIP1vsInput	Intergenic	B2_Mm1t|SINE|B2	-128968	NR_045373	74529	Mm.400519	NR_045373		8430422H06Rik	-	RIKEN cDNA 8430422H06 gene	miscRNA	0.05	0.554455
Merged-chrX-53057328-2	chrX	53057278	53057379	+	5.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_038185)	promoter-TSS (NR_038185)	-138	NR_038184	72575	Mm.59516	NR_038184		C430049B03Rik	2700063P19Rik|9430052C07Rik	RIKEN cDNA C430049B03 gene	miscRNA	0.089109	0.745098
Merged-chr8-34753392-2	chr8	34753326	34753459	+	5.8	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-54218	NM_176933	319520	Mm.392187	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding	0.015038	0.5
Merged-chr7-45466869-2	chr7	45466809	45466929	+	5.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007527)	promoter-TSS (NM_007527)	29	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding	0.125	0.68595
Merged-chr7-29983777-2	chr7	29983715	29983840	+	5.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001167873)	promoter-TSS (NM_001167873)	-178	NM_001167873	243905	Mm.322432	NM_001033355	ENSMUSG00000074221	Zfp568	C80731|Gm1691|chato	zinc finger protein 568	protein-coding	0.12	0.698413
Merged-chr9-65201665-1	chr9	65201615	65201715	+	5.8	cIP2vsInput	Intergenic	Intergenic	-13025	NM_177460	214424	Mm.31129	NM_177460	ENSMUSG00000032392	Parp16	ARTD15|BC055447|C79952|PARP-16	"poly (ADP-ribose) polymerase family, member 16"	protein-coding	0	0.287129
Merged-chr13-3893550-2	chr13	3893487	3893613	+	5.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001047159)	promoter-TSS (NM_001047159)	28	NM_001047159	56349	Mm.468637	NM_001047159	ENSMUSG00000021215	Net1	0610025H04Rik|9530071N24Rik|AI604373|AU015857|Net1a|mNET1	neuroepithelial cell transforming gene 1	protein-coding	0.095238	0.700787
Merged-chr17-35837097-1	chr17	35837047	35837147	+	5.8	cIP2vsInput	"intron (NM_011655, intron 1 of 3)"	CpG	1204	NM_011655	22154	Mm.472638	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	"tubulin, beta 5 class I"	protein-coding	0.08	0.683168
Merged-chrX-163958619-2	chrX	163958569	163958670	+	5.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009453)	promoter-TSS (NM_009453)	47	NM_009453	22184	Mm.426178	NM_009453	ENSMUSG00000031370	Zrsr2	35kDa|5031411E02Rik|A230052C13Rik|C77286|U2af1-rs2|URP	"zinc finger (CCCH type), RNA binding motif and serine/arginine rich 2"	protein-coding	0.089109	0.686275
Merged-chr11-54522510-1	chr11	54522460	54522560	+	5.8	cIP2vsInput	promoter-TSS (NM_175258)	promoter-TSS (NM_175258)	-335	NM_001252494	192786	Mm.254404	NM_001252494	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding	0.1	0.643564
Merged-chr5-136102319-1	chr5	136102269	136102369	+	5.8	cIP2vsInput	"exon (NM_133914, exon 13 of 21)"	"exon (NM_133914, exon 13 of 21)"	-14372	NM_011293	20022	Mm.4896	NM_011293	ENSMUSG00000039771	Polr2j	14.5kDa|Polr2i|Rpb11a|Rpo2-4	polymerase (RNA) II (DNA directed) polypeptide J	protein-coding	0.1	0.633663
Merged-chr11-87987683-1	chr11	87987633	87987733	+	5.8	cIP2vsInput	promoter-TSS (NM_026556)	promoter-TSS (NM_026556)	-150	NM_026556	68097	Mm.246436	NM_001168471	ENSMUSG00000020483	Dynll2	1700064A15Rik|6720463E02Rik|C87222|DLC8|DLC8b|Dlc2	dynein light chain LC8-type 2	protein-coding	0.05	0.663366
Merged-chr2-90745154-1	chr2	90745104	90745204	+	5.8	cIP2vsInput	promoter-TSS (NM_018828)	promoter-TSS (NM_018828)	-216	NM_018828	55935	Mm.489638	NM_018828	ENSMUSG00000008200	Fnbp4	FBP30|Fnbp30|mKIAA1014	formin binding protein 4	protein-coding	0	0.376238
Merged-chr19-6057948-2	chr19	6057882	6058015	+	5.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001160239)	promoter-TSS (NM_001160239)	-19	NM_001190436	14109	Mm.329631	NM_001160239	ENSMUSG00000038274	Fau	MNSFbeta	Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived)	protein-coding	0.135338	0.679104
Merged-chr8-86885396-2	chr8	86885339	86885454	+	5.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_030563)	promoter-TSS (NM_030563)	-138	NM_030563	80750	Mm.428374	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding	0.078261	0.594828
Merged-chr5-21701828-2	chr5	21701773	21701884	+	5.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178728)	promoter-TSS (NM_178728)	-483	NM_178728	242864	Mm.153292	NM_178728	ENSMUSG00000044968	Napepld	A530089G06|Mbldc1|NAPE-PLD	N-acyl phosphatidylethanolamine phospholipase D	protein-coding	0.063063	0.633929
Merged-chr5-24423761-1	chr5	24423711	24423811	+	5.8	cIP2vsInput	promoter-TSS (NM_007668)	promoter-TSS (NM_007668)	-231	NM_007668	12568	Mm.298798	NM_007668	ENSMUSG00000028969	Cdk5	AW048668|Crk6	cyclin-dependent kinase 5	protein-coding	0.1	0.613861
Merged-chr8-110919861-2	chr8	110919805	110919917	+	5.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009179)	promoter-TSS (NM_009179)	-4	NM_009179	20444	Mm.200388	NM_009179	ENSMUSG00000031749	St3gal2	AI429591|AW822065|ST3GalII|Siat5	"ST3 beta-galactoside alpha-2,3-sialyltransferase 2"	protein-coding	0.0625	0.734513
Merged-chr7-139364221-1	chr7	139364171	139364271	+	5.8	cIP2vsInput	Intergenic	Intergenic	-24888	NM_183144	212111	Mm.28308	NM_001127363	ENSMUSG00000025477	Inpp5a	-	inositol polyphosphate-5-phosphatase A	protein-coding	0.03	0.653465
Merged-chr7-127875761-1	chr7	127875711	127875811	+	5.8	cIP2vsInput	"intron (NM_146259, intron 1 of 2)"	CpG	1062	NM_146259	244219	Mm.425491	NM_146259	ENSMUSG00000049728	Zfp668	BC030314|E130018B19Rik|Znf668	zinc finger protein 668	protein-coding	0.12	0.722772
Merged-chr19-55743234-1	chr19	55743184	55743284	+	5.8	cIP2vsInput	"intron (NM_001142921, intron 3 of 11)"	CpG-7657	1424	NM_001142923	21416	Mm.139815	NM_001142918	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4|mTcf-4B|mTcf-4E	"transcription factor 7 like 2, T cell specific, HMG box"	protein-coding	0.11	0.821782
Merged-chr8-121170742-2	chr8	121170674	121170811	+	5.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	43057	NM_008024	14241	Mm.5111	NM_008024	ENSMUSG00000097084	Foxl1	FREAC7|Fkh6|fkh-6	forkhead box L1	protein-coding	0.029197	0.514493
Merged-chr8-109778521-2	chr8	109778465	109778578	+	5.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009677)	promoter-TSS (NM_009677)	-119	NM_009677	11765	Mm.37210	NM_009677		Ap1g1	AA409002|AU041323|AW551707|Adtg|D8Ertd374e	"adaptor protein complex AP-1, gamma 1 subunit"	protein-coding	0.061947	0.666667
Merged-chr14-120292796-2	chr14	120292731	120292862	+	5.75	cIP1vsInput|cIP2vsInput	"intron (NM_175341, intron 1 of 8)"	"intron (NM_175341, intron 1 of 8)"	17127	NM_175341	105559		NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding	0.022901	0.469697
Merged-chr2-164833420-2	chr2	164833365	164833475	+	5.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008906)	promoter-TSS (NM_008906)	176	NM_001082974	415115	Mm.474586	NM_001082974	ENSMUSG00000039873	Neurl2	Neur2|Ozz|Ozz-E3	neuralized-like 2 (Drosophila)	protein-coding	0.063636	0.693694
Merged-chr10-79766939-2	chr10	79766887	79766992	+	5.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_027505)	promoter-TSS (NR_027505)	13	NM_144528	70294	Mm.466670	NM_144528	ENSMUSG00000035890	Rnf126	2610010O19Rik	ring finger protein 126	protein-coding	0.2	0.783019
Merged-chr2-68436076-2	chr2	68436022	68436130	+	5.75	cIP1vsInput|cIP2vsInput	"intron (NM_016866, intron 1 of 17)"	"intron (NM_016866, intron 1 of 17)"	35905	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding	0.037037	0.605505
Merged-chr12-85452312-2	chr12	85452262	85452363	+	5.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-21589	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding	0.029703	0.568627
Merged-chr8-104609493-2	chr8	104609440	104609547	+	5.75	cIP1vsInput|cIP2vsInput	"intron (NM_001252628, intron 17 of 17)"	"intron (NM_001252628, intron 17 of 17)"	132	NR_029648	723945		NR_029648		Mir297-2	Mir297a-2|Mirn297-2	microRNA 297-2	miscRNA	0.046729	0.583333
Merged-chr12-80643930-2	chr12	80643857	80644003	+	5.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007951)	promoter-TSS (NM_007951)	-69	NM_007951	13877	Mm.378913	NM_007951		Erh	Mer|Prei1	enhancer of rudimentary homolog (Drosophila)	protein-coding	0.082192	0.530612
Merged-chr1-183794068-2	chr1	183793980	183794156	+	5.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	239930	NM_028516	73363	Mm.50115	NM_028516	ENSMUSG00000044854	1700056E22Rik	-	RIKEN cDNA 1700056E22 gene	protein-coding	0.028409	0.491525
Merged-chr7-100607675-2	chr7	100607614	100607737	+	5.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_024287)	promoter-TSS (NM_024287)	89	NM_001163663	19346	Mm.474075	NM_001163663	ENSMUSG00000030704	Rab6a	2610028L11Rik|AA419671|Rab6	"RAB6A, member RAS oncogene family"	protein-coding	0.146341	0.725806
Merged-chr16-26077421-2	chr16	26077350	26077492	+	5.7	cIP1vsInput|cIP2vsInput	"intron (NM_173379, intron 1 of 14)"	RMER17A2|LTR|ERVK	28363	NM_173379	210530		NM_173379		Leprel1	4832416N06|AW553532|Mlat4|P3H2	leprecan-like 1	protein-coding	0	0.51049
Merged-chr4-119294802-2	chr4	119294745	119294859	+	5.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011732)	promoter-TSS (NM_011732)	-289	NM_011732	22608	Mm.258204	NM_011732		Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding	0.131579	0.704348
Merged-chr10-36974189-1	chr10	36974139	36974239	+	5.7	cIP2vsInput	promoter-TSS (NM_008229)	promoter-TSS (NM_008229)	-355	NM_008229	15182	Mm.19806	NM_008229	ENSMUSG00000019777	Hdac2	D10Wsu179e|YAF1|Yy1bp|mRPD3	histone deacetylase 2	protein-coding	0.13	0.792079
Merged-chr18-9708692-2	chr18	9708629	9708755	+	5.7	cIP1vsInput|cIP2vsInput	"intron (NM_130449, intron 1 of 9)"	"intron (NM_130449, intron 1 of 9)"	1044	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding	0.039683	0.527559
Merged-chr4-119105938-2	chr4	119105886	119105991	+	5.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-2807	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	"solute carrier family 2 (facilitated glucose transporter), member 1"	protein-coding	0.104762	0.669811
Merged-chr15-101145663-2	chr15	101145606	101145721	+	5.7	cIP1vsInput|cIP2vsInput	TTS (NM_001277255)	TTS (NM_001277255)	17141	NM_001277257	11482	Mm.279542	NM_001277255	ENSMUSG00000000530	Acvrl1	AI115505|AI427544|Acvrlk1|Alk1	"activin A receptor, type II-like 1"	protein-coding	0.06087	0.663793
Merged-chr5-143180984-1	chr5	143180934	143181034	+	5.7	cIP2vsInput	promoter-TSS (NM_177880)	promoter-TSS (NM_177880)	-33	NM_177880	330228	Mm.255752	NM_177880	ENSMUSG00000029586	4933411G11Rik	-	RIKEN cDNA 4933411G11Rik gene	protein-coding	0.01	0.574257
Merged-chr11-105589622-1	chr11	105589572	105589672	+	5.7	cIP2vsInput	promoter-TSS (NM_181071)	promoter-TSS (NM_181071)	-364	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	"tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2"	protein-coding	0.14	0.80198
Merged-chr1-171247183-2	chr1	171247120	171247246	+	5.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_153064)	promoter-TSS (NM_153064)	-71	NM_153064	226646	Mm.21669	NM_153064	ENSMUSG00000013593	Ndufs2	AL033311	NADH dehydrogenase (ubiquinone) Fe-S protein 2	protein-coding	0.095238	0.629921
Merged-chr14-25606941-2	chr14	25606879	25607003	+	5.7	cIP1vsInput|cIP2vsInput	"intron (NM_183208, intron 6 of 23)"	CpG	20137	NR_033492	77592	Mm.444871	NM_175264		4931406H21Rik	-	RIKEN cDNA 4931406H21 gene	miscRNA	0.048387	0.632
Merged-chr7-5014863-2	chr7	5014795	5014931	+	5.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025324)	promoter-TSS (NM_025324)	-135	NM_001110329	23877	Mm.38911	NM_001110328	ENSMUSG00000061374	Fiz1	AI790204|mFLJ00416	Flt3 interacting zinc finger protein 1	protein-coding	0.066176	0.569343
Merged-chr9-107554678-2	chr9	107554613	107554744	+	5.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019713)	promoter-TSS (NM_019713)	95	NM_019713	56289	Mm.488708	NM_001243748	ENSMUSG00000010067	Rassf1	123F2|AA536941|AU044980|NORE2A|RDA32|REH3P21|Rassf1A|Rassf1B|Rassf1C	Ras association (RalGDS/AF-6) domain family member 1	protein-coding	0.145038	0.666667
Merged-chr9-60617184-2	chr9	60617130	60617238	+	5.65	cIP1vsInput|cIP2vsInput	"intron (NM_001146047, intron 10 of 16)"	"intron (NM_001146047, intron 10 of 16)"	70350	NM_001146047	102747	Mm.269413	NM_001146046	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding	0.055556	0.504587
Merged-chr1-171329252-2	chr1	171329177	171329327	+	5.65	cIP1vsInput|cIP2vsInput	"5' UTR (NM_011615, exon 1 of 5)"	"5' UTR (NM_011615, exon 1 of 5)"	107	NM_011615	21945	Mm.270139	NM_001128609	ENSMUSG00000013973	Dedd	CASP8IP1|DEFT|Dedpro1|FLDED1|KE05	death effector domain-containing	protein-coding	0.06	0.615894
Merged-chr12-108004167-2	chr12	108004109	108004225	+	5.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_021399)	promoter-TSS (NM_021399)	-753	NM_021399	58208	Mm.392694	NM_001079883	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding	0.051724	0.495726
Merged-chr2-127208250-2	chr2	127208169	127208332	+	5.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_198630)	promoter-TSS (NM_198630)	30	NM_198630	329509	Mm.120738	NM_198630	ENSMUSG00000044145	1810024B03Rik	-	RIKEN cDNA 1810024B03 gene	protein-coding	0.067485	0.54878
Merged-chr5-17897853-2	chr5	17897803	17897903	+	5.65	cIP1vsInput|cIP2vsInput	Intergenic	B1_Mus1|SINE|Alu	-8894	NM_001159558	12491	Mm.406799	NM_001159555	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding	0.01	0.445545
Merged-chr17-23829268-2	chr17	23829208	23829328	+	5.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026305)	promoter-TSS (NM_026305)	-159	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Tceb2	0610040H15Rik	"transcription elongation factor B (SIII), polypeptide 2"	protein-coding	0.083333	0.578512
Merged-chr1-38129709-2	chr1	38129644	38129774	+	5.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019570)	promoter-TSS (NM_019570)	-47	NM_019570	56210	Mm.389103	NM_019570	ENSMUSG00000026082	Rev1	1110027I23Rik|AU022044|Rev1l	REV1 homolog (S. cerevisiae)	protein-coding	0.184615	0.847328
Merged-chrX-126775879-2	chrX	126775828	126775931	+	5.6	cIP1vsInput|cIP2vsInput	Intergenic	AT_rich|Low_complexity|Low_complexity	58125	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding	0	0.221154
Merged-chr19-3248403-1	chr19	3248353	3248453	+	5.6	cIP1vsInput	Intergenic	Intergenic	34607	NM_009212	20589	Mm.3179	NM_009212		Ighmbp2	AEP|Catf1|RIPE3b1|Smbp-2|Smbp2|Smubp2|nmd|sma	immunoglobulin mu binding protein 2	protein-coding	0	0.306931
Merged-chr19-8774596-1	chr19	8774546	8774646	+	5.6	cIP2vsInput	promoter-TSS (NM_026325)	promoter-TSS (NM_026325)	111	NR_015538	100039957	Mm.220886	NR_015538		Gm2518	D630022E15Rik	interferon induced transmembrane protein 2 pseudogene	pseudo	0.14	0.742574
Merged-chr17-23802967-2	chr17	23802908	23803026	+	5.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175229)	promoter-TSS (NM_175229)	-220	NM_175229	75956	Mm.436876	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding	0.09322	0.647059
Merged-chr8-33732046-2	chr8	33731989	33732104	+	5.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026584)	promoter-TSS (NM_026584)	-21	NM_026584	68153	Mm.286104	NM_001167921	ENSMUSG00000031585	Gtf2e2	34kDa|AI462509|C330006J08Rik	"general transcription factor II E, polypeptide 2 (beta subunit)"	protein-coding	0.191304	0.801724
Merged-chr16-38550269-2	chr16	38550201	38550337	+	5.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172380)	promoter-TSS (NM_172380)	-85	NM_172380	224143	Mm.475345	NM_172380	ENSMUSG00000034064	Poglut1	9630046K23Rik|Ktelc1|Rumi	protein O-glucosyltransferase 1	protein-coding	0.088235	0.70073
Merged-chr5-15693631-2	chr5	15693579	15693683	+	5.6	cIP1vsInput|cIP2vsInput	"intron (NR_001585, intron 1 of 4)"	Lx|LINE|L1	12921	NR_001585	75858	Mm.359463	NR_001585	ENSMUSG00000089871	Speer7-ps1	4930568L21Rik|SPEER-7|Speer7-ps	"spermatogenesis associated glutamate (E)-rich protein 7, pseudogene 1"	pseudo	0	0.390476
Merged-chr11-49088488-2	chr11	49088419	49088558	+	5.6	cIP1vsInput|cIP2vsInput	"intron (NM_010999, intron 2 of 5)"	"intron (NM_010999, intron 2 of 5)"	1471	NM_008330	15953	Mm.24769	NM_001271676	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding	0.057554	0.671429
Merged-chr5-14964061-1	chr5	14964011	14964111	+	5.6	cIP1vsInput	"intron (NR_001584, intron 2 of 3)"	"intron (NR_001584, intron 2 of 3)"	18767	NR_001584	74062	Mm.394766	NR_001584		Speer8-ps1	4933405L09Rik|SPEER-8|Speer8-ps	"spermatogenesis associated glutamate (E)-rich protein 8, pseudogene 1"	pseudo	0.02	0.366337
Merged-chr8-40511733-2	chr8	40511674	40511792	+	5.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011135)	promoter-TSS (NM_011135)	21	NM_001271543	18983	Mm.272551	NM_001271542	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	"CCR4-NOT transcription complex, subunit 7"	protein-coding	0.169492	0.815126
Merged-chr4-133754381-1	chr4	133754331	133754431	+	5.6	cIP2vsInput	promoter-TSS (NM_001080819)	promoter-TSS (NM_001080819)	-770	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding	0.11	0.653465
Merged-chr7-51861666-2	chr7	51861611	51861722	+	5.6	cIP1vsInput|cIP2vsInput	"exon (NM_001115087, exon 1 of 1)"	"exon (NM_001115087, exon 1 of 1)"	601	NM_001115087	100040608	Mm.392015	NM_001115087	ENSMUSG00000092118	Fancf	A730016A17	"Fanconi anemia, complementation group F"	protein-coding	0.144144	0.723214
Merged-chr11-5099446-1	chr11	5099396	5099496	+	5.6	cIP2vsInput	promoter-TSS (NM_007968)	promoter-TSS (NM_007968)	8	NM_177370	279766	Mm.260866	NM_177370	ENSMUSG00000034175	Rhbdd3	5730411O18Rik|Ptag	rhomboid domain containing 3	protein-coding	0.11	0.683168
Merged-chr2-167632080-1	chr2	167632030	167632130	+	5.6	cIP2vsInput	promoter-TSS (NM_023230)	promoter-TSS (NM_023230)	-75	NM_023230	66589	Mm.360108	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding	0.13	0.712871
Merged-chr11-119306661-2	chr11	119306607	119306716	+	5.6	cIP1vsInput|cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	-6618	NM_138669	192170	Mm.490978	NM_138669	ENSMUSG00000025580	Eif4a3	2400003O03Rik|Ddx48|eIF4A-III|mKIAA0111	eukaryotic translation initiation factor 4A3	protein-coding	0.009174	0.554545
Merged-chr4-136310962-1	chr4	136310912	136311012	+	5.6	cIP2vsInput	promoter-TSS (NM_001277121)	promoter-TSS (NM_001277121)	20	NM_028871	74326	Mm.443495	NM_001277121	ENSMUSG00000066037	Hnrnpr	2610003J05Rik|2610528B01Rik|Hnrpr	heterogeneous nuclear ribonucleoprotein R	protein-coding	0.13	0.722772
Merged-chr1-168477152-2	chr1	168477092	168477213	+	5.6	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-44894	NM_008783	18514	Mm.440114	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|AI848790|AU015730|D230003C07Rik|Pbx-1|Pbx1a|Pbx1b	pre B cell leukemia homeobox 1	protein-coding	0.008264	0.491803
Merged-chr7-38107750-2	chr7	38107682	38107819	+	5.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007633)	promoter-TSS (NM_007633)	-260	NM_007633	12447	Mm.16110	NM_007633	ENSMUSG00000002068	Ccne1	AW538188|CycE1	cyclin E1	protein-coding	0.160584	0.789855
Merged-chr3-95357242-1	chr3	95357192	95357292	+	5.6	cIP2vsInput	promoter-TSS (NM_001163642)	promoter-TSS (NM_001163642)	-40	NM_001163642	84505	Mm.490259	NM_001163641	ENSMUSG00000015697	Setdb1	AU022152|ESET|KMT1E|mKIAA0067	"SET domain, bifurcated 1"	protein-coding	0.1	0.673267
Merged-chr17-47139928-2	chr17	47139875	47139982	+	5.6	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-1014	NM_001097623	224829	Mm.260989	NM_001097623	ENSMUSG00000064043	Trerf1	9430096I18Rik|AI429294|B830015H24|RAPA|Trep-132|Trep132	transcriptional regulating factor 1	protein-coding	0.130841	0.787037
Merged-chr8-57488654-2	chr8	57488603	57488705	+	5.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_021788)	promoter-TSS (NM_021788)	-794	NM_021788	60406	Mm.118	NM_021788	ENSMUSG00000031609	Sap30	30kDa	sin3 associated polypeptide	protein-coding	0.107843	0.669903
Merged-chr10-31609754-2	chr10	31609684	31609825	+	5.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001146349)	promoter-TSS (NM_001146349)	-29	NM_001146349	268291	Mm.295212	NM_001146349		Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding	0.078014	0.676056
Merged-chr11-3289727-2	chr11	3289662	3289792	+	5.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019574)	promoter-TSS (NM_019574)	596	NR_045109	56218	Mm.486715	NM_001253690	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding	0.1	0.687023
Merged-chr7-127745864-2	chr7	127745807	127745921	+	5.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172748)	promoter-TSS (NM_172748)	-911	NM_172748	233902	Mm.259353	NM_172748	ENSMUSG00000030811	Fbxl19	6030430O11|BC059812|Fbl19	F-box and leucine-rich repeat protein 19	protein-coding	0.061404	0.608696
Merged-chr3-134236370-2	chr3	134236315	134236426	+	5.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001004367)	promoter-TSS (NM_001004367)	-125	NM_001004367	319478	Mm.487501	NM_001004367	ENSMUSG00000044365	Cxxc4	9330210J02Rik|C030003J12Rik|Idax	CXXC finger 4	protein-coding	0.072072	0.678571
Merged-chr17-27056391-2	chr17	27056341	27056441	+	5.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_080553)	promoter-TSS (NM_080553)	-913	NM_080553	16440	Mm.458106	NM_080553	ENSMUSG00000042644	Itpr3	Ip3r3|Itpr-3	"inositol 1,4,5-triphosphate receptor 3"	protein-coding	0.04	0.633663
Merged-chr12-107011436-2	chr12	107011378	107011494	+	5.55	cIP1vsInput|cIP2vsInput	Intergenic	(TC)n|Simple_repeat|Simple_repeat	-295112	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	miscRNA	0.017241	0.470085
Merged-chr17-65614164-2	chr17	65614106	65614222	+	5.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013933)	promoter-TSS (NM_013933)	-609	NM_013933	30960	Mm.266767	NM_013933	ENSMUSG00000024091	Vapa	33kDa|VAP33	"vesicle-associated membrane protein, associated protein A"	protein-coding	0.068966	0.65812
Merged-chr5-25499766-2	chr5	25499699	25499833	+	5.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_030700)	promoter-TSS (NR_030700)	-31	NR_030700	320965	Mm.475726	NR_030700		4831440E17Rik	-	RIKEN cDNA 4831440E17 gene	miscRNA	0.119403	0.725926
Merged-chrY-87832768-2	chrY	87832718	87832819	+	5.55	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-2303249	NM_001160131	100040911	Mm.457993	NM_001160131	ENSMUSG00000095650	Gm20854	-	"predicted gene, 20854"	protein-coding	0	0.352941
Merged-chr5-15465129-1	chr5	15465079	15465179	+	5.5	cIP1vsInput	Intergenic	Intergenic	-153970	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0	0.425743
Merged-chr14-8098151-2	chr14	8098095	8098208	+	5.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145458)	promoter-TSS (NM_145458)	-62	NM_145458	218699	Mm.29515	NM_145458	ENSMUSG00000033885	Pxk	C230080L11Rik|D14Ertd813e|MONaKA	PX domain containing serine/threonine kinase	protein-coding	0.168142	0.754386
Merged-chr19-40873542-2	chr19	40873476	40873609	+	5.5	cIP1vsInput|cIP2vsInput	"intron (NR_045343, intron 1 of 4)"	CpG	5226	NR_045343	381223	Mm.136844	NR_045343		E030044B06Rik	E030007J07Rik|Gm1618	RIKEN cDNA E030044B06 gene	miscRNA	0.097744	0.656716
Merged-chr2-31670619-1	chr2	31670569	31670669	+	5.5	cIP2vsInput	promoter-TSS (NM_144886)	promoter-TSS (NM_144886)	-118	NM_144886	227715	Mm.150972	NM_144886	ENSMUSG00000039356	Exosc2	Rrp4	exosome component 2	protein-coding	0.01	0.455446
Merged-chr13-66431195-1	chr13	66431145	66431245	+	5.5	cIP1vsInput	"intron (NM_183119, intron 3 of 4)"	MMSAT4|Satellite|Satellite	9923	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding	0.01	0.425743
Merged-chr15-81585442-1	chr15	81585392	81585492	+	5.5	cIP2vsInput	promoter-TSS (NM_177821)	promoter-TSS (NM_177821)	-772	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding	0.05	0.683168
Merged-chr1-170623051-2	chr1	170622987	170623115	+	5.5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-21481	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding	0.015625	0.503876
Merged-chr18-6490417-1	chr18	6490367	6490467	+	5.5	cIP2vsInput	TTS (NR_035446)	TTS (NR_035446)	229	NR_035446	100316773		NR_035446		Mir1893	Mirn1893|mmu-mir-1893	microRNA 1893	miscRNA	0.14	0.732673
Merged-chr5-73975551-2	chr5	73975485	73975618	+	5.5	cIP1vsInput|cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	92860	NM_177561	69727	Mm.48795	NM_177561		Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding	0.007519	0.507463
Merged-chr16-44173212-2	chr16	44173161	44173264	+	5.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001029889)	promoter-TSS (NM_001029889)	-185	NM_001029889	207806	Mm.310566	NM_001029889	ENSMUSG00000068284	Gm608	5530400K22Rik|Gm1779|mKIAA2018	predicted gene 608	protein-coding	0.116505	0.798077
Merged-chr1-84839425-1	chr1	84839375	84839475	+	5.5	cIP2vsInput	promoter-TSS (NM_133975)	promoter-TSS (NM_133975)	-121	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding	0.12	0.762376
Merged-chr3-69044132-1	chr3	69044082	69044182	+	5.5	cIP2vsInput	"intron (NM_025863, intron 1 of 2)"	"intron (NM_025863, intron 1 of 2)"	610	NM_025863	66949		NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding	0.07	0.50495
Merged-chr15-38452888-2	chr15	38452832	38452945	+	5.5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	66378	NM_001102458	54375	Mm.250214	NM_001102458	ENSMUSG00000037458	Azin1	1700085L02Rik|AI414949|Oazi|Oazin	antizyme inhibitor 1	protein-coding	0.026549	0.640351
Merged-chr14-62760022-1	chr14	62759972	62760072	+	5.5	cIP2vsInput	promoter-TSS (NR_045503)	promoter-TSS (NR_045503)	-479	NR_045503	71000	Mm.399410	NR_045503	ENSMUSG00000097775	4931440J10Rik	-	RIKEN cDNA 4931440J10 gene	miscRNA	0.09	0.762376
Merged-chr4-88722564-1	chr4	88722514	88722614	+	5.5	cIP2vsInput	promoter-TSS (NM_172871)	promoter-TSS (NM_172871)	-56	NM_172871	242521	Mm.260601	NM_172871	ENSMUSG00000070923	Klhl9	8030469P05|C530050O22Rik|ENSMUSG00000070923|mKIAA1354	kelch-like 9	protein-coding	0.11	0.80198
Merged-chr19-8898063-2	chr19	8897992	8898135	+	5.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008060)	promoter-TSS (NM_008060)	-48	NM_008060	14376	Mm.3196	NM_008060	ENSMUSG00000071650	Ganab	AU042638|G2an|GluII|mKIAA0088	alpha glucosidase 2 alpha neutral subunit	protein-coding	0.097902	0.638889
Merged-chr2-25225075-1	chr2	25225025	25225125	+	5.5	cIP2vsInput	promoter-TSS (NM_146116)	promoter-TSS (NM_146116)	-373	NM_146116	227613	Mm.227260	NM_146116	ENSMUSG00000036752	Tubb4b	4930542G03Rik|Tubb2c|Tubb2c1	"tubulin, beta 4B class IVB"	protein-coding	0.07	0.643564
Merged-chr3-88950246-2	chr3	88950177	88950315	+	5.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_022994)	promoter-TSS (NM_022994)	36	NM_022994	65111	Mm.400397	NM_001164533	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3	death associated protein 3	protein-coding	0.123188	0.748201
Merged-chr1-172217336-2	chr1	172217281	172217392	+	5.45	cIP1vsInput|cIP2vsInput	"intron (NM_009813, intron 2 of 10)"	"intron (NM_009813, intron 2 of 10)"	2559	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding	0.036036	0.616071
Merged-chr10-82764129-2	chr10	82764070	82764189	+	5.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010914)	promoter-TSS (NM_010914)	12	NM_010914	18045	Mm.245998	NM_010914	ENSMUSG00000020248	Nfyb	AA985999|Cbf-A	nuclear transcription factor-Y beta	protein-coding	0.12605	0.741667
Merged-chr5-91598485-2	chr5	91598433	91598538	+	5.45	cIP1vsInput|cIP2vsInput	"intron (NM_145562, intron 2 of 3)"	"intron (NM_145562, intron 2 of 3)"	80785	NM_145562	231440	Mm.5002	NM_145562		Parm1	2210012L08Rik|9130213B05Rik|W91666	prostate androgen-regulated mucin-like protein 1	protein-coding	0.019048	0.490566
Merged-chr9-123021322-2	chr9	123021252	123021392	+	5.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001164823)	promoter-TSS (NM_001164823)	-4	NM_025339	66079	Mm.482265	NM_001164823	ENSMUSG00000066233	Tmem42	0610027O18Rik|4933429E06Rik|AV003444|D9Ertd662e	transmembrane protein 42	protein-coding	0.142857	0.765957
Merged-chr2-25168192-2	chr2	25168112	25168273	+	5.45	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-12566	NM_025980	67122	Mm.46539	NM_025980	ENSMUSG00000078202	Nrarp	2700054M22Rik	Notch-regulated ankyrin repeat protein	protein-coding	0.099379	0.759259
Merged-chr8-84198684-2	chr8	84198620	84198748	+	5.45	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-9834	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mmu-mir-23a	microRNA 23a	miscRNA	0.046875	0.666667
Merged-chr3-152340451-2	chr3	152340396	152340507	+	5.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001162375)	promoter-TSS (NM_001162375)	-44	NM_174868	215708	Mm.135018	NM_001162375	ENSMUSG00000054942	Fam73a	A930038D06|AI852168|C030011O14Rik	"family with sequence similarity 73, member A"	protein-coding	0.108108	0.660714
Merged-chr15-103215085-2	chr15	103215012	103215159	+	5.45	cIP1vsInput|cIP2vsInput	"5' UTR (NM_001110216, exon 2 of 6)"	"5' UTR (NM_001110216, exon 2 of 6)"	267	NM_007626	12419	Mm.262059	NM_001076789	ENSMUSG00000009575	Cbx5	2610029O15Rik|C75991|HP1|Hp1a|Hp1alpha	chromobox 5	protein-coding	0.013605	0.486486
Merged-chr2-71389084-2	chr2	71389028	71389140	+	5.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026115)	promoter-TSS (NM_026115)	-176	NM_026115	107435		NM_026115	ENSMUSG00000027018	Hat1	2410071B14Rik|AA536933|Hat-1|KAT1	histone aminotransferase 1	protein-coding	0.089286	0.699115
Merged-chr4-133814154-2	chr4	133814072	133814236	+	5.45	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-60543	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding	0.128049	0.769697
Merged-chr1-53485350-2	chr1	53485280	53485421	+	5.45	cIP1vsInput|cIP2vsInput	"intron (NM_001252070, intron 46 of 65)"	RMER17A2|LTR|ERVK	-132651	NM_133728	70396	Mm.285783	NM_133728	ENSMUSG00000026095	Asnsd1	2210409M21Rik	asparagine synthetase domain containing 1	protein-coding	0	0.471831
Merged-chr4-132270097-2	chr4	132270026	132270169	+	5.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_002865)	promoter-TSS (NR_002865)	89	NR_002865	353373	Mm.424675	NR_002865		Rnu11	MBII-407|Mirn801|mir-801|mmu-mir-801	U11 small nuclear RNA	snRNA	0.048951	0.416667
Merged-chr19-4510126-1	chr19	4510076	4510176	+	5.4	cIP2vsInput	promoter-TSS (NM_001162946)	promoter-TSS (NM_001162946)	-346	NM_001162946	18563	Mm.1845	NM_001162946	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding	0.07	0.544554
Merged-chr11-101425071-1	chr11	101425021	101425121	+	5.4	cIP2vsInput	promoter-TSS (NM_172566)	promoter-TSS (NM_172566)	-14	NM_172566	217201		NM_172566	ENSMUSG00000035007	Rundc1	AW125546|D930024B17	RUN domain containing 1	protein-coding	0.1	0.683168
Merged-chr14-65837308-2	chr14	65837243	65837373	+	5.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145944)	promoter-TSS (NM_145944)	6	NM_145944	67179	Mm.214576	NM_145944	ENSMUSG00000022035	Ccdc25	2610528H13Rik|NSrp70	coiled-coil domain containing 25	protein-coding	0.1	0.618321
Merged-chrX-103159728-2	chrX	103159664	103159793	+	5.4	cIP1vsInput|cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	26936	NM_008671	17954	Mm.388694	NM_008671	ENSMUSG00000082229	Nap1l2	Bpx	nucleosome assembly protein 1-like 2	protein-coding	0.007752	0.523077
Merged-chr13-91460806-1	chr13	91460756	91460856	+	5.4	cIP2vsInput	promoter-TSS (NM_024186)	promoter-TSS (NM_024186)	-291	NM_024272	66970	Mm.343095	NM_024186		Ssbp2	1500004K09Rik|2310079I02Rik|9330163K02Rik|A830008M03Rik|AU067692|AW558684|Hspc116|SSDP2	single-stranded DNA binding protein 2	protein-coding	0.1	0.653465
Merged-chr9-65885124-1	chr9	65885074	65885174	+	5.4	cIP2vsInput	promoter-TSS (NM_001170907)	promoter-TSS (NM_001170907)	49	NM_001170907	56404	Mm.208379	NM_001170907	ENSMUSG00000032386	Trip4	4930558E03Rik|ASC-1|Asc1|BB191711	thyroid hormone receptor interactor 4	protein-coding	0.13	0.673267
Merged-chr17-45573917-2	chr17	45573829	45574006	+	5.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008302)	promoter-TSS (NM_008302)	-656	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	"heat shock protein 90 alpha (cytosolic), class B member 1"	protein-coding	0.062147	0.679775
Merged-chr12-100199451-1	chr12	100199401	100199501	+	5.4	cIP2vsInput	promoter-TSS (NM_009790)	promoter-TSS (NM_009790)	-90	NM_009790	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding	0.17	0.762376
Merged-chr18-41951340-2	chr18	41951256	41951424	+	5.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029942)	promoter-TSS (NM_029942)	-146	NM_029942	77619	Mm.30649	NM_029942	ENSMUSG00000056671	Prelid2	1700003A01Rik|C330008K14Rik	PRELI domain containing 2	protein-coding	0.047619	0.544379
Merged-chr2-94010874-1	chr2	94010824	94010924	+	5.4	cIP2vsInput	promoter-TSS (NM_026944)	promoter-TSS (NM_026944)	-144	NM_026944	69113	Mm.272498	NM_026944	ENSMUSG00000040174	Alkbh3	1700108H04Rik|1810020C19Rik|Abh3|mABH3	"alkB, alkylation repair homolog 3 (E. coli)"	protein-coding	0.09	0.663366
Merged-chr7-126583587-1	chr7	126583537	126583637	+	5.4	cIP2vsInput	promoter-TSS (NM_009907)	promoter-TSS (NM_009907)	-351	NM_009907	12752	Mm.268930	NM_001146311	ENSMUSG00000030720	Cln3	AI323623	"ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)"	protein-coding	0.06	0.50495
Merged-chr9-77637586-2	chr9	77637525	77637647	+	5.4	cIP1vsInput|cIP2vsInput	"intron (NM_172925, intron 1 of 2)"	"intron (NM_172925, intron 1 of 2)"	854	NM_172925	244923	Mm.138238	NM_177238	ENSMUSG00000044938	Klhl31	9830147P19Rik|D930047P17Rik|Kbtbd1	kelch-like 31	protein-coding	0.02459	0.593496
Merged-chr6-50110076-2	chr6	50110002	50110151	+	5.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019939)	promoter-TSS (NM_019939)	-165	NM_019939	56524	Mm.463873	NM_001164734	ENSMUSG00000038388	Mpp6	P55t|Pals2	"membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)"	protein-coding	0.100671	0.733333
Merged-chr16-96145205-1	chr16	96145155	96145255	+	5.4	cIP2vsInput	promoter-TSS (NM_207301)	promoter-TSS (NM_207301)	-214	NM_207301	71446	Mm.255063	NM_207301	ENSMUSG00000023147	Wrb	5530402J05Rik|C030018G21Rik|Chd5	tryptophan rich basic protein	protein-coding	0.1	0.633663
Merged-chr8-111743909-1	chr8	111743859	111743959	+	5.4	cIP2vsInput	promoter-TSS (NM_009954)	promoter-TSS (NM_009954)	-60	NM_009954	12927	Mm.3758	NM_001198839	ENSMUSG00000031955	Bcar1	AI385681|Cas|Crkas	breast cancer anti-estrogen resistance 1	protein-coding	0.14	0.742574
Merged-chr2-152396537-1	chr2	152396487	152396587	+	5.4	cIP2vsInput	"3' UTR (NM_011438, exon 1 of 1)"	"3' UTR (NM_011438, exon 1 of 1)"	1509	NM_011438	20667	Mm.28424	NM_011438		Sox12	2010205A02Rik	SRY-box containing gene 12	protein-coding	0.03	0.653465
Merged-chrX-52961764-2	chrX	52961704	52961825	+	5.4	cIP1vsInput|cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	-26314	NM_013556	15452	Mm.299381	NM_013556	ENSMUSG00000025630	Hprt	C81579|HPGRT|Hprt1	hypoxanthine guanine phosphoribosyl transferase	protein-coding	0.008264	0.508197
Merged-chr9-96478631-1	chr9	96478581	96478681	+	5.4	cIP2vsInput	promoter-TSS (NM_011279)	promoter-TSS (NM_011279)	-36	NM_011279	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding	0.16	0.752475
Merged-chr12-81595040-1	chr12	81594990	81595090	+	5.4	cIP2vsInput	promoter-TSS (NM_027213)	promoter-TSS (NM_027213)	-82	NM_027213	69792	Mm.279993	NM_027213	ENSMUSG00000002679	Med6	1500012F11Rik|AU019660|AV213303	"mediator of RNA polymerase II transcription, subunit 6 homolog (yeast)"	protein-coding	0.16	0.663366
Merged-chr4-46390600-1	chr4	46390550	46390650	+	5.4	cIP1vsInput	Intergenic	Intergenic	-1177	NM_029086	74753	Mm.45973	NM_029086	ENSMUSG00000028331	5830415F09Rik	AV014846|Nap1	RIKEN cDNA 5830415F09 gene	protein-coding	0.04	0.49505
Merged-chr3-65871214-1	chr3	65871164	65871264	+	5.4	cIP2vsInput	Intergenic	Intergenic	87011	NM_019937	56706	Mm.175612	NM_001025442	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding	0.04	0.663366
Merged-chr3-32736990-1	chr3	32736940	32737040	+	5.4	cIP2vsInput	promoter-TSS (NM_025316)	promoter-TSS (NM_025316)	-73	NM_025316	66046	Mm.28058	NM_025316	ENSMUSG00000027673	Ndufb5	0610007D05Rik|AU015782|SGDH	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5"	protein-coding	0.08	0.663366
Merged-chr12-108792797-1	chr12	108792747	108792847	+	5.4	cIP2vsInput	promoter-TSS (NM_009537)	promoter-TSS (NM_009537)	-514	NM_009537	22632	Mm.458511	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding	0.12	0.80198
Merged-chr18-56678786-2	chr18	56678721	56678851	+	5.4	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-29027	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding	0.046154	0.564885
Merged-chr15-96460996-2	chr15	96460936	96461057	+	5.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028148)	promoter-TSS (NM_028148)	-153	NM_028148	72193	Mm.472183	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding	0.173554	0.811475
Merged-chr9-70657148-2	chr9	70657090	70657206	+	5.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172772)	promoter-TSS (NM_172772)	26	NM_172772	235461	Mm.170855	NM_172772	ENSMUSG00000042444	Fam63b	AI465301|B230380D07Rik|mKIAA1164	"family with sequence similarity 63, member B"	protein-coding	0.146552	0.74359
Merged-chr7-139234968-2	chr7	139234915	139235021	+	5.4	cIP1vsInput|cIP2vsInput	"intron (NM_027164, intron 8 of 10)"	"intron (NM_027164, intron 8 of 10)"	-13514	NM_001033206	101631	Mm.334300	NM_001033206	ENSMUSG00000060260	Pwwp2b	AI594893|D7Ertd517e|D930023J19Rik|Pwwp2	PWWP domain containing 2B	protein-coding	0.04717	0.560748
Merged-chr10-77606462-2	chr10	77606398	77606526	+	5.4	cIP1vsInput|cIP2vsInput	"intron (NM_019929, intron 1 of 3)"	CpG	228	NM_019929	20610	Mm.24433	NM_019929	ENSMUSG00000020265	Sumo3	2810014B19Rik|AA409334|AW121497|AW536077|D10Ertd345e|SMT3A|SUMO-3|Smt3B|Smt3h1	SMT3 suppressor of mif two 3 homolog 3 (yeast)	protein-coding	0.117188	0.79845
Merged-chr4-142015125-2	chr4	142015071	142015179	+	5.35	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-3474	NM_177868	329977	Mm.252019	NM_028429	ENSMUSG00000051435	Fhad1	2900090M10Rik|B230311F11	forkhead-associated (FHA) phosphopeptide binding domain 1	protein-coding	0.138889	0.733945
Merged-chr10-69213101-2	chr10	69213039	69213164	+	5.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001252637)	promoter-TSS (NM_001252637)	-93	NM_001252637	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding	0.112	0.730159
Merged-chr10-37078722-2	chr10	37078659	37078786	+	5.35	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	60204	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding	0.015748	0.5625
Merged-chr17-24469996-2	chr17	24469942	24470051	+	5.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025954)	promoter-TSS (NM_025954)	-477	NM_025954	67078	Mm.486259	NM_025954	ENSMUSG00000043445	Pgp	1700012G19Rik|AI481330	phosphoglycolate phosphatase	protein-coding	0.06422	0.581818
Merged-chr3-88685608-2	chr3	88685556	88685660	+	5.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028814)	promoter-TSS (NM_028814)	-186	NM_028814	74200	Mm.251800	NM_028814	ENSMUSG00000028060	2810403A07Rik	A430106P18Rik|AI256352|AI451678|Blom7|Kiaa0907	RIKEN cDNA 2810403A07 gene	protein-coding	0.038462	0.47619
Merged-chr16-22265418-2	chr16	22265355	22265481	+	5.35	cIP1vsInput|cIP2vsInput	"intron (NM_009186, intron 1 of 8)"	CpG	511	NM_009186	20462	Mm.442193	NM_009186		Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding	0.126984	0.692913
Merged-chr2-168207445-2	chr2	168207381	168207510	+	5.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009628)	promoter-TSS (NM_009628)	-383	NM_009628	11538	Mm.201322	NM_009628	ENSMUSG00000051149	Adnp	AA589558|mKIAA0784	activity-dependent neuroprotective protein	protein-coding	0.100775	0.7
Merged-chr12-98734684-2	chr12	98734624	98734745	+	5.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011877)	promoter-TSS (NM_011877)	-39	NM_011877	24000	Mm.483252	NM_001146199	ENSMUSG00000021009	Ptpn21	PTPD1|PTPRL10	"protein tyrosine phosphatase, non-receptor type 21"	protein-coding	0.115702	0.663934
Merged-chr11-83753675-2	chr11	83753618	83753733	+	5.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145432)	promoter-TSS (NM_145432)	38	NM_145432	217026	Mm.117874	NM_145432	ENSMUSG00000000976	Heatr6	2700008B19Rik|BB135312|BB249351	HEAT repeat containing 6	protein-coding	0.052174	0.577586
Merged-chr16-49855538-2	chr16	49855459	49855617	+	5.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010581)	promoter-TSS (NM_010581)	-116	NM_010581	16423	Mm.390865	NM_010581		Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	"CD47 antigen (Rh-related antigen, integrin-associated signal transducer)"	protein-coding	0.094937	0.72956
Merged-chr4-108459935-1	chr4	108459885	108459985	+	5.3	cIP2vsInput	"intron (NM_175472, intron 1 of 30)"	CpG	509	NM_175472	230594	Mm.446602	NM_175472	ENSMUSG00000034610	Zcchc11	6030404K05Rik|9230115F04Rik|PPAPD3|mKIAA0191	"zinc finger, CCHC domain containing 11"	protein-coding	0.06	0.732673
Merged-chr15-79546705-2	chr15	79546655	79546756	+	5.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_199079)	promoter-TSS (NM_199079)	36	NM_001040187	67040	Mm.298199	NM_001040187	ENSMUSG00000055065	Ddx17	2610007K22Rik|A430025E01Rik|AI047725|C80929|Gm926|p72	DEAD (Asp-Glu-Ala-Asp) box polypeptide 17	protein-coding	0.108911	0.637255
Merged-chr13-28957999-2	chr13	28957939	28958060	+	5.3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-4317	NM_009238	20677	Mm.455819	NM_009238		Sox4	AA682046|Sox-4	SRY-box containing gene 4	protein-coding	0.057851	0.647541
Merged-chr7-110319037-1	chr7	110318987	110319087	+	5.3	cIP2vsInput	"intron (NM_177324, intron 34 of 40)"	"intron (NM_177324, intron 34 of 40)"	97334	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding	0.02	0.564356
Merged-chr10-79854253-2	chr10	79854155	79854351	+	5.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008956)	promoter-TSS (NM_008956)	-352	NM_001077363	19205	Mm.265610	NM_001077363	ENSMUSG00000006498	Ptbp1	AA407203|AL033359|HNRPI|PTB-1|PTB2|PTB3|PTB4|Ptb|pPTB	polypyrimidine tract binding protein 1	protein-coding	0.061224	0.573604
Merged-chr7-46795939-1	chr7	46795889	46795989	+	5.3	cIP2vsInput	promoter-TSS (NM_008186)	promoter-TSS (NM_008186)	-58	NM_001005247	246694	Mm.379442	NM_178742	ENSMUSG00000014418	Hps5	AI646796|AL022647|C85120|haze|hz|maroon|mr|ru-2|ru2	Hermansky-Pudlak syndrome 5 homolog (human)	protein-coding	0.14	0.683168
Merged-chr4-121179859-1	chr4	121179809	121179909	+	5.3	cIP2vsInput	"intron (NM_001081013, intron 2 of 5)"	"intron (NM_001081013, intron 2 of 5)"	8675	NM_001081013	109263	Mm.215745	NM_001081013	ENSMUSG00000049878	Rlf	9230110M18Rik|AI195322	rearranged L-myc fusion sequence	protein-coding	0.01	0.405941
Merged-chr7-126503776-2	chr7	126503705	126503848	+	5.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_183020)	promoter-TSS (NM_183020)	-474	NM_183020	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding	0.104895	0.611111
Merged-chr1-86487532-1	chr1	86487482	86487582	+	5.3	cIP2vsInput	Intergenic	CpG	-39204	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding	0.14	0.663366
Merged-chr11-94328009-1	chr11	94327959	94328059	+	5.3	cIP2vsInput	promoter-TSS (NM_027799)	promoter-TSS (NM_027799)	8	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding	0.08	0.653465
Merged-chr3-89395024-1	chr3	89394974	89395074	+	5.3	cIP2vsInput	"intron (NR_040404, intron 1 of 1)"	"intron (NR_040404, intron 1 of 1)"	734	NR_040404	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	miscRNA	0.05	0.594059
Merged-chr6-117917239-1	chr6	117917189	117917289	+	5.3	cIP2vsInput	promoter-TSS (NM_001166427)	promoter-TSS (NM_001166427)	-55	NM_001166427	98758	Mm.476420	NM_001166427	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding	0.1	0.772277
Merged-chr6-83054597-2	chr6	83054536	83054658	+	5.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019752)	promoter-TSS (NM_019752)	-26	NM_019752	64704	Mm.21880	NM_019752	ENSMUSG00000068329	Htra2	AI481710|Omi|Prss25|mnd2	HtrA serine peptidase 2	protein-coding	0.090164	0.609756
Merged-chr7-28809131-1	chr7	28809081	28809181	+	5.3	cIP2vsInput	Intergenic	CpG	-1759	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding	0.12	0.732673
Merged-chr15-78913945-2	chr15	78913856	78914035	+	5.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_020271)	promoter-TSS (NM_020271)	26	NM_020271	57028	Mm.263169	NM_020271	ENSMUSG00000068221	Pdxp	1600027H05Rik|AB041662|PLPP	"pyridoxal (pyridoxine, vitamin B6) phosphatase"	protein-coding	0.145251	0.744444
Merged-chr5-142975028-2	chr5	142974960	142975096	+	5.3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	14673	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	"fascin homolog 1, actin bundling protein (Strongylocentrotus purpuratus)"	protein-coding	0.044118	0.613139
Merged-chr4-137489181-2	chr4	137489129	137489234	+	5.3	cIP1vsInput|cIP2vsInput	"intron (NM_008305, intron 1 of 96)"	"intron (NM_008305, intron 1 of 96)"	20378	NM_008305	15530	Mm.273662	NM_008305	ENSMUSG00000028763	Hspg2	AI852380|Pcn|Plc|per	perlecan (heparan sulfate proteoglycan 2)	protein-coding	0.028571	0.650943
Merged-chr2-25608512-1	chr2	25608462	25608562	+	5.3	cIP2vsInput	promoter-TSS (NM_001024616)	promoter-TSS (NM_001024616)	-66	NM_001024616	227624	Mm.443064	NM_001024616	ENSMUSG00000015087	Rabl6	B230208H17Rik|Rbel1|Rbel1a|Rbel1b|parf	"RAB, member of RAS oncogene family-like 6"	protein-coding	0.13	0.663366
Merged-chr4-130107303-1	chr4	130107253	130107353	+	5.3	cIP2vsInput	promoter-TSS (NM_026441)	promoter-TSS (NM_026441)	-253	NM_026441	67898	Mm.20818	NM_026441	ENSMUSG00000028779	Pef1	2600002E23Rik|Peflin	penta-EF hand domain containing 1	protein-coding	0.03	0.415842
Merged-chr4-106839836-1	chr4	106839786	106839886	+	5.3	cIP2vsInput	Intergenic	CpG	-40005	NM_025590	329910	Mm.222956	NM_025590	ENSMUSG00000034853	Acot11	1110020M10Rik|2010309H15Rik|AW060409|BFIT|BFIT1|Thea|Them1|mKIAA0707	acyl-CoA thioesterase 11	protein-coding	0.04	0.574257
Merged-chr15-103305482-1	chr15	103305432	103305532	+	5.3	cIP2vsInput	Intergenic	G-rich|Low_complexity|Low_complexity	4956	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding	0.16	0.782178
Merged-chr1-155973358-1	chr1	155973308	155973408	+	5.3	cIP1vsInput	promoter-TSS (NM_001039184)	promoter-TSS (NM_001039184)	-103	NM_001039184	74081	Mm.260247	NM_001039184	ENSMUSG00000033671	Cep350	4933409L06Rik|6430546F08Rik	centrosomal protein 350	protein-coding	0.1	0.653465
Merged-chr18-11967329-1	chr18	11967279	11967379	+	5.3	cIP1vsInput	Intergenic	Intergenic	-126891	NR_035447	100316686		NR_035447	ENSMUSG00000084565	Mir1901	Mirn1901|mmu-mir-1901	microRNA 1901	miscRNA	0.01	0.465347
Merged-chr1-172027264-1	chr1	172027214	172027314	+	5.3	cIP2vsInput	promoter-TSS (NM_033509)	promoter-TSS (NM_033509)	4	NM_033509	93840	Mm.392110	NM_033509	ENSMUSG00000026556	Vangl2	C530001F03Rik|Lp|Lpp1|Ltap|Vang1l2|loop-tail|ska17|ska<m17Jus>|stbm|strabismus	"vang-like 2 (van gogh, Drosophila)"	protein-coding	0.05	0.673267
Merged-chrY-90797938-2	chrY	90797880	90797996	+	5.3	cIP1vsInput|cIP2vsInput	"intron (NM_133362, intron 2 of 2)"	"intron (NM_133362, intron 2 of 2)"	12496	NM_133362	170942	Mm.391385	XM_003946384	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding	0.008621	0.282051
Merged-chr11-97187888-1	chr11	97187838	97187938	+	5.3	cIP2vsInput	promoter-TSS (NM_008379)	promoter-TSS (NM_008379)	4	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding	0.1	0.732673
Merged-chr11-77982322-1	chr11	77982272	77982372	+	5.3	cIP2vsInput	promoter-TSS (NM_174852)	promoter-TSS (NM_174852)	-494	NM_174852	268448	Mm.274329	NM_174852	ENSMUSG00000037791	Phf12	2410142K10Rik|F630045O13|PF1|mKIAA1523	PHD finger protein 12	protein-coding	0.03	0.524752
Merged-chr18-41950917-2	chr18	41950840	41950995	+	5.3	cIP1vsInput|cIP2vsInput	"intron (NM_029942, intron 1 of 6)"	CpG	277	NM_029942	77619	Mm.30649	NM_029942	ENSMUSG00000056671	Prelid2	1700003A01Rik|C330008K14Rik	PRELI domain containing 2	protein-coding	0.083871	0.679487
Merged-chr1-86525503-2	chr1	86525443	86525563	+	5.3	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-1233	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding	0.1	0.603306
Merged-chr11-24078075-2	chr11	24078010	24078141	+	5.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001242934)	promoter-TSS (NM_001242934)	19	NM_001159289	14025	Mm.53687	NM_001159289	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding	0.045802	0.537879
Merged-chr2-101886237-1	chr2	101886187	101886287	+	5.3	cIP2vsInput	promoter-TSS (NM_029635)	promoter-TSS (NM_029635)	-25	NM_029635	76501	Mm.330424	NM_029635	ENSMUSG00000027163	Commd9	1810029F08Rik|AA409293	COMM domain containing 9	protein-coding	0.07	0.60396
Merged-chr8-13104927-2	chr8	13104849	13105006	+	5.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_146207)	promoter-TSS (NM_146207)	416	NM_178708	234069	Mm.103427	NM_178708	ENSMUSG00000038542	Pcid2	A730042J05Rik	PCI domain containing 2	protein-coding	0.11465	0.683544
Merged-chr7-143438304-2	chr7	143438249	143438360	+	5.3	cIP1vsInput|cIP2vsInput	Intergenic	CpG	22746	NM_009876	12577	Mm.168789	NM_001161624	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding	0.108108	0.803571
Merged-chr9-56994903-1	chr9	56994853	56994953	+	5.3	cIP2vsInput	promoter-TSS (NM_019651)	promoter-TSS (NM_019651)	-65	NM_019651	56294	Mm.325643	NM_019651	ENSMUSG00000032290	Ptpn9	MEG2	"protein tyrosine phosphatase, non-receptor type 9"	protein-coding	0.12	0.762376
Merged-chr1-180813964-1	chr1	180813914	180814014	+	5.3	cIP2vsInput	promoter-TSS (NM_008210)	promoter-TSS (NM_008210)	-361	NM_008210	15078	Mm.442502	NM_008210	ENSMUSG00000060743	H3f3a	H3.3A	"H3 histone, family 3A"	protein-coding	0.16	0.851485
Merged-chr2-181930265-1	chr2	181930215	181930315	+	5.3	cIP2vsInput	Intergenic	RLTR33|LTR|ERVK	-60961	NM_001205282	672125	Mm.489571	NM_001205282	ENSMUSG00000053277	Gm14496	OTTMUSG00000016837	predicted gene 14496	protein-coding	0	0.425743
Merged-chr5-129007470-2	chr5	129007402	129007538	+	5.3	cIP1vsInput|cIP2vsInput	"intron (NM_007941, intron 1 of 10)"	"intron (NM_007941, intron 1 of 10)"	1094	NM_007941	13852	Mm.260716	NM_007941	ENSMUSG00000029428	Stx2	AW538950|Epim|G1-536-1|Syn-2|repro34	syntaxin 2	protein-coding	0	0.459854
Merged-chrY-7020095-2	chrY	7020028	7020162	+	5.3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	147682	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.007463	0.340741
Merged-chr1-178336486-1	chr1	178336436	178336536	+	5.3	cIP2vsInput	"intron (NM_016805, intron 1 of 13)"	CpG	1298	NM_016805	51810	Mm.482674	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding	0.12	0.762376
Merged-chr6-136804085-1	chr6	136804035	136804135	+	5.3	cIP2vsInput	"exon (NM_175652, exon 1 of 1)"	"exon (NM_175652, exon 1 of 1)"	346	NM_175652	320332	Mm.489077	NM_175652	ENSMUSG00000096010	Hist4h4	B130044J01Rik	"histone cluster 4, H4"	protein-coding	0.11	0.653465
Merged-chr7-80535185-2	chr7	80535102	80535268	+	5.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007550)	promoter-TSS (NM_007550)	-66	NM_001042527	12144	Mm.12932	NM_001042527	ENSMUSG00000030528	Blm	-	"Bloom syndrome, RecQ helicase-like"	protein-coding	0.078313	0.628743
Merged-chr15-98918174-2	chr15	98918123	98918226	+	5.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029098)	promoter-TSS (NM_029098)	-76	NM_029098	74775	Mm.385020	NM_029098	ENSMUSG00000022999	Lmbr1l	1110013E13Rik|AA415653|D15Ertd735e|Limr	limb region 1 like	protein-coding	0.097087	0.634615
Merged-chrX-101639976-1	chrX	101639926	101640026	+	5.3	cIP2vsInput	promoter-TSS (NM_139144)	promoter-TSS (NM_139144)	-88	NM_139144	108155	Mm.259191	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding	0.08	0.49505
Merged-chr18-68300237-2	chr18	68300179	68300295	+	5.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026440)	promoter-TSS (NM_026440)	96	NM_153794	108654	Mm.125857	NM_153794	ENSMUSG00000038121	Fam210a	4933403F05Rik|AA987140|AV134576|AW491926	"family with sequence similarity 210, member A"	protein-coding	0.12931	0.717949
Merged-chr18-5390426-2	chr18	5390365	5390488	+	5.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-55987	NM_178722	240186	Mm.118257	NM_178722	ENSMUSG00000050945	Zfp438	9430031G09|9430091M14Rik|B830013J05Rik	zinc finger protein 438	protein-coding	0.00813	0.435484
Merged-chr4-97887356-2	chr4	97887306	97887407	+	5.25	cIP1vsInput|cIP2vsInput	"intron (NM_001122953, intron 2 of 9)"	"intron (NM_001122953, intron 2 of 9)"	109730	NM_010905	18027	Mm.409646	NM_001122952	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|NF1-A|NF1A	nuclear factor I/A	protein-coding	0	0.401961
Merged-chr9-16115041-2	chr9	16114991	16115091	+	5.25	cIP1vsInput|cIP2vsInput	"intron (NM_001080814, intron 2 of 24)"	"intron (NM_001080814, intron 2 of 24)"	-240485	NM_145712	244701	Mm.222631	NM_145712	ENSMUSG00000050901	Mtnr1b	Mel-1B-R|Mel1b|Mt2	melatonin receptor 1B	protein-coding	0.03	0.49505
Merged-chr5-122158134-2	chr5	122158083	122158185	+	5.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013636)	promoter-TSS (NM_013636)	-145	NM_013636	19047	Mm.474554	NM_013636	ENSMUSG00000004455	Ppp1cc	PP-1G|PP1|dis2m1	"protein phosphatase 1, catalytic subunit, gamma isoform"	protein-coding	0.156863	0.757282
Merged-chr2-127008683-2	chr2	127008626	127008740	+	5.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175550)	promoter-TSS (NM_175550)	-28	NM_175550	108011	Mm.134045	NM_175550		Ap4e1	2310033A20Rik|9930028M04Rik|AV087807	"adaptor-related protein complex AP-4, epsilon 1"	protein-coding	0.114035	0.565217
Merged-chr3-103279681-2	chr3	103279626	103279737	+	5.25	cIP1vsInput|cIP2vsInput	"5' UTR (NM_001079830, exon 1 of 19)"	"5' UTR (NM_001079830, exon 1 of 19)"	388	NM_001079830	94093	Mm.195036	NM_001079830	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g|ectodermin|mKIAA1113	tripartite motif-containing 33	protein-coding	0.216216	0.8125
Merged-chr4-44168328-2	chr4	44168264	44168393	+	5.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175201)	promoter-TSS (NM_175201)	-45	NM_001038993	73469	Mm.262859	NM_001038993	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding	0.147287	0.776923
Merged-chr2-173020040-2	chr2	173019965	173020115	+	5.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-1862	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding	0.106667	0.741722
Merged-chr15-98872262-2	chr15	98872200	98872324	+	5.25	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-1057	NM_001033276	381022	Mm.264889	NM_001033388	ENSMUSG00000048154	Mll2	ALR|BC032281|BC058659|C430014K11Rik|KMT2B|KMT2D|Mll4	myeloid/lymphoid or mixed-lineage leukemia 2	protein-coding	0.08871	0.68
Merged-chr2-172440430-2	chr2	172440373	172440487	+	5.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025542)	promoter-TSS (NM_025542)	-148	NM_025542	66404	Mm.25157	NM_025542	ENSMUSG00000027502	Rtfdc1	1700067C04Rik|2410001C21Rik|5730427M17Rik|AA589417	replication termination factor 2 domain containing 1	protein-coding	0.078947	0.573913
Merged-chr4-97773267-2	chr4	97773204	97773331	+	5.25	cIP1vsInput|cIP2vsInput	"intron (NM_001122952, intron 1 of 10)"	"intron (NM_001122952, intron 1 of 10)"	-4359	NM_001122953	18027	Mm.409646	NM_001122952	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|NF1-A|NF1A	nuclear factor I/A	protein-coding	0.047244	0.5625
Merged-chr14-8666250-2	chr14	8666187	8666313	+	5.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028934)	promoter-TSS (NM_028934)	40	NM_028934	74430	Mm.271901	NM_028934	ENSMUSG00000021747	4930452B06Rik	4933406L09Rik|AI854000	RIKEN cDNA 4930452B06 gene	protein-coding	0.142857	0.732283
Merged-chr17-35000910-2	chr17	35000828	35000992	+	5.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011690)	promoter-TSS (NM_011690)	3	NM_011690	22321	Mm.28420	NM_011690	ENSMUSG00000007029	Vars	Bat6|D17H6S56E|G7a|Vars2	valyl-tRNA synthetase	protein-coding	0.134146	0.751515
Merged-chr9-62344643-2	chr9	62344589	62344698	+	5.2	cIP1vsInput|cIP2vsInput	"intron (NM_009672, intron 1 of 6)"	CpG	3300	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	"acidic (leucine-rich) nuclear phosphoprotein 32 family, member A"	protein-coding	0.100917	0.663636
Merged-chr9-62343698-1	chr9	62343648	62343748	+	5.2	cIP2vsInput	"intron (NM_009672, intron 1 of 6)"	CpG	2355	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	"acidic (leucine-rich) nuclear phosphoprotein 32 family, member A"	protein-coding	0.14	0.752475
Merged-chr11-94676864-2	chr11	94676805	94676924	+	5.2	cIP1vsInput|cIP2vsInput	"intron (NM_145828, intron 1 of 10)"	"intron (NM_145828, intron 1 of 10)"	629	NM_145828	217119	Mm.100638	NM_145828	ENSMUSG00000020868	Xylt2	E030002B02Rik|XT-II|XT2|xylT-II	xylosyltransferase II	protein-coding	0.042017	0.633333
Merged-chr1-163929746-1	chr1	163929696	163929796	+	5.2	cIP2vsInput	promoter-TSS (NM_028776)	promoter-TSS (NM_028776)	-318	NM_028776	240880	Mm.389213	NM_028776	ENSMUSG00000026584	Scyl3	1200016D23Rik|6030457O16|AW214499|Pace1	SCY1-like 3 (S. cerevisiae)	protein-coding	0.04	0.584158
Merged-chr7-19170448-1	chr7	19170398	19170498	+	5.2	cIP2vsInput	Intergenic	Intergenic	-4321	NM_001080815	381853	Mm.333633	NM_001080815	ENSMUSG00000030406	Gipr	GIP-R|Gm1081|Gm160	gastric inhibitory polypeptide receptor	protein-coding	0.02	0.544554
Merged-chr10-80264924-1	chr10	80264874	80264974	+	5.2	cIP2vsInput	promoter-TSS (NM_001122605)	promoter-TSS (NM_001122605)	-67	NM_001122604	70248	Mm.148693	NM_001122604	ENSMUSG00000069565	Dazap1	2410042M16Rik|mPrrp	DAZ associated protein 1	protein-coding	0.17	0.80198
Merged-chr18-82692483-1	chr18	82692433	82692533	+	5.2	cIP2vsInput	"intron (NM_177832, intron 1 of 29)"	GC_rich|Low_complexity|Low_complexity	251	NM_177832	329002		NM_177832	ENSMUSG00000041258	Zfp236	AI447957|Gm335	zinc finger protein 236	protein-coding	0.18	0.831683
Merged-chr7-28825255-2	chr7	28825189	28825322	+	5.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_016772)	promoter-TSS (NM_016772)	-83	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	"enoyl coenzyme A hydratase 1, peroxisomal"	protein-coding	0.082707	0.559701
Merged-chr19-4756509-1	chr19	4756459	4756559	+	5.2	cIP2vsInput	promoter-TSS (NM_025717)	promoter-TSS (NM_025717)	-16	NM_025717	66704	Mm.396734	NM_025717	ENSMUSG00000033760	Rbm4b	4921506I22Rik|AI504630|AI506404|Lark2	RNA binding motif protein 4B	protein-coding	0.14	0.762376
Merged-chr6-72538934-2	chr6	72538859	72539009	+	5.2	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-5457	NM_007599	12332	Mm.18626	NM_001042534	ENSMUSG00000056737	Capg	gCap39|mbh1	"capping protein (actin filament), gelsolin-like"	protein-coding	0.033333	0.543046
Merged-chr8-109565911-2	chr8	109565843	109565980	+	5.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175646)	promoter-TSS (NM_175646)	-75	NM_175646	234723	Mm.37667	NM_175646	ENSMUSG00000031723	Txnl4b	AI595343|D530025J19Rik|DLP|Dim2	thioredoxin-like 4B	protein-coding	0.094891	0.521739
Merged-chr8-39006331-2	chr8	39006270	39006392	+	5.2	cIP1vsInput|cIP2vsInput	"intron (NM_030254, intron 1 of 7)"	CpG	464	NM_030254	80286	Mm.272722	NM_030254		Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding	0.114754	0.747967
Merged-chr7-120842864-1	chr7	120842814	120842914	+	5.2	cIP2vsInput	promoter-TSS (NM_007908)	promoter-TSS (NM_007908)	33	NM_007908	13631	Mm.470116	NM_001267710	ENSMUSG00000035064	Eef2k	C86191|eEF-2K	eukaryotic elongation factor-2 kinase	protein-coding	0.08	0.752475
Merged-chr9-43106217-2	chr9	43106165	43106270	+	5.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027144)	promoter-TSS (NM_027144)	-499	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding	0.07619	0.622642
Merged-chr10-83543851-1	chr10	83543801	83543901	+	5.2	cIP2vsInput	promoter-TSS (NM_001033375)	promoter-TSS (NM_001033375)	-90	NM_001033375	319277	Mm.278577	NM_001033375	ENSMUSG00000034560	A230046K03Rik	AA589518|Kiaa1033|mKIAA1033	RIKEN cDNA A230046K03 gene	protein-coding	0.12	0.693069
Merged-chr4-88722220-2	chr4	88722156	88722285	+	5.2	cIP1vsInput|cIP2vsInput	"5' UTR (NM_172871, exon 1 of 1)"	"5' UTR (NM_172871, exon 1 of 1)"	288	NM_172871	242521	Mm.260601	NM_172871	ENSMUSG00000070923	Klhl9	8030469P05|C530050O22Rik|ENSMUSG00000070923|mKIAA1354	kelch-like 9	protein-coding	0.108527	0.692308
Merged-chr2-30807837-2	chr2	30807786	30807888	+	5.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_170592)	promoter-TSS (NM_170592)	-140	NM_170592	66617	Mm.33167	NM_170592	ENSMUSG00000026857	Ntmt1	2610205E22Rik|AL033331|AL033332|Mettl11a|NTM1A	N-terminal Xaa-Pro-Lys N-methyltransferase 1	protein-coding	0.058824	0.669903
Merged-chr13-21734994-2	chr13	21734935	21735053	+	5.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178210)	promoter-TSS (NM_178210)	-102	NM_178210	319159	Mm.486099	NM_178210		Hist1h4j	-	"histone cluster 1, H4j"	protein-coding	0.084746	0.596639
Merged-chr8-71908605-2	chr8	71908527	71908684	+	5.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001166645)	promoter-TSS (NM_001166645)	-1	NM_001166645	382019	Mm.251482	NM_001166645		Zfp882	ENSMUSG00000052439|Gm15468|OTTMUSG00000022410	zinc finger protein 882	protein-coding	0.050955	0.56962
Merged-chr9-25252598-1	chr9	25252548	25252648	+	5.2	cIP2vsInput	"5' UTR (NM_009859, exon 1 of 13)"	"5' UTR (NM_009859, exon 1 of 13)"	159	NM_001205367	235072	Mm.270259	NM_001205367	ENSMUSG00000001833	7-Sep	Cdc10|E430034N22	septin 7	protein-coding	0.16	0.732673
Merged-chr8-13869685-2	chr8	13869615	13869756	+	5.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_181854)	promoter-TSS (NM_181854)	44	NM_181854	101994	Mm.412576	NM_181854	ENSMUSG00000047710	Zfp828	AA675043|AI116001|Champ1|D8Ertd457e|D8Ertd569e|Znf828|mKIAA1802	zinc finger protein 828	protein-coding	0.120567	0.739437
Merged-chr3-108210491-1	chr3	108210441	108210541	+	5.2	cIP2vsInput	"5' UTR (NM_175183, exon 1 of 12)"	"5' UTR (NM_175183, exon 1 of 12)"	443	NM_175183	72522	Mm.187326	NM_175183	ENSMUSG00000048997	Atxn7l2	2610528J18Rik	ataxin 7-like 2	protein-coding	0.2	0.831683
Merged-chr9-75521971-1	chr9	75521921	75522021	+	5.2	cIP2vsInput	"intron (NM_016963, intron 3 of 9)"	B3|SINE|B2	37686	NM_016963	50875	Mm.38445	NM_016963	ENSMUSG00000058587	Tmod3	U-Tmod|UTMOD	tropomodulin 3	protein-coding	0.01	0.50495
Merged-chr11-75733373-1	chr11	75733323	75733423	+	5.2	cIP1vsInput	"intron (NM_009536, intron 1 of 5)"	CpG	486	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide"	protein-coding	0.09	0.742574
Merged-chr7-30563164-1	chr7	30563114	30563214	+	5.2	cIP2vsInput	promoter-TSS (NM_025498)	promoter-TSS (NM_025498)	20	NM_025498	66340	Mm.86557	NM_025498	ENSMUSG00000036835	Psenen	1700023M09Rik|Pen-2	presenilin enhancer 2 homolog (C. elegans)	protein-coding	0.06	0.544554
Merged-chr2-148681016-2	chr2	148680965	148681067	+	5.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028986)	promoter-TSS (NM_028986)	-104	NM_028986	74533	Mm.136913	NM_028986	ENSMUSG00000027439	Gzf1	8430437G08Rik|Zfp336|mGZF1	GDNF-inducible zinc finger protein 1	protein-coding	0.068627	0.572816
Merged-chr17-45748418-2	chr17	45748336	45748500	+	5.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-14574	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding	0.030488	0.654545
Merged-chr7-122969921-2	chr7	122969850	122969992	+	5.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175023)	promoter-TSS (NM_175023)	538	NR_045614	73951	Mm.389936	NR_045614		4930413G21Rik	-	RIKEN cDNA 4930413G21 gene	miscRNA	0.147887	0.748252
Merged-chr19-8837414-2	chr19	8837362	8837466	+	5.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001136064)	promoter-TSS (NM_001136064)	-53	NM_001136064	14705	Mm.345134	NM_001136064	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Bernardinelli-Seip congenital lipodystrophy 2 homolog (human)	protein-coding	0.086538	0.571429
Merged-chr13-49015614-2	chr13	49015553	49015676	+	5.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	47502	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A opposite strand	miscRNA	0.03252	0.516129
Merged-chr10-82701248-2	chr10	82701186	82701310	+	5.15	cIP1vsInput|cIP2vsInput	"intron (NM_001081218, intron 2 of 14)"	"intron (NM_001081218, intron 2 of 14)"	2241	NM_001081218	67933	Mm.458243	NM_001081218		Hcfc2	1700129L13Rik|AU019838	host cell factor C2	protein-coding	0	0.376
Merged-chr6-115676600-2	chr6	115676509	115676691	+	5.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029780)	promoter-TSS (NM_029780)	35	NM_029780	110157	Mm.184163	NM_029780	ENSMUSG00000000441	Raf1	6430402F14Rik|AA990557|BB129353|Craf1|D830050J10Rik|Raf-1|c-Raf|v-Raf	v-raf-leukemia viral oncogene 1	protein-coding	0.126374	0.688525
Merged-chr19-45783246-2	chr19	45783190	45783303	+	5.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_023799)	promoter-TSS (NM_023799)	45	NM_023799	76055	Mm.480399	NM_023799	ENSMUSG00000025220	Mgea5	2810009A20Rik|4833427O07Rik|5830447M11Rik|AA408215|Hy5|Ncoat|mKIAA0679	meningioma expressed antigen 5 (hyaluronidase)	protein-coding	0.115044	0.77193
Merged-chr7-45707769-2	chr7	45707695	45707844	+	5.15	cIP1vsInput|cIP2vsInput	"intron (NM_016974, intron 2 of 3)"	"intron (NM_016974, intron 2 of 3)"	2522	NM_016974	13170	Mm.378235	NM_016974	ENSMUSG00000059824	Dbp	-	D site albumin promoter binding protein	protein-coding	0.107383	0.686667
Merged-chr17-64559403-2	chr17	64559352	64559454	+	5.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-3813	NR_045899	100043582	Mm.11170	NR_045899	ENSMUSG00000073377	AU016765	-	expressed sequence AU016765	miscRNA	0.039216	0.533981
Merged-chr1-182908489-2	chr1	182908424	182908554	+	5.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-46299	NM_016928	53791	Mm.116894	NM_016928	ENSMUSG00000079164	Tlr5	-	toll-like receptor 5	protein-coding	0.038462	0.610687
Merged-chr5-15461283-2	chr5	15461221	15461345	+	5.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-157816	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0.008065	0.336
Merged-chr3-94837803-2	chr3	94837742	94837865	+	5.15	cIP1vsInput|cIP2vsInput	"intron (NM_001165948, intron 1 of 18)"	CpG	236	NM_172683	229584	Mm.274787	NM_001165948	ENSMUSG00000038902	Pogz	9530006B08Rik|AU015913|AU044539	pogo transposable element with ZNF domain	protein-coding	0.130081	0.66129
Merged-chr7-47008407-2	chr7	47008351	47008464	+	5.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175318)	promoter-TSS (NM_175318)	7	NM_175318	101685	Mm.155687	NM_175318	ENSMUSG00000049516	Spty2d1	5830435K17Rik|AI852426|P16H6	"SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)"	protein-coding	0.115044	0.570175
Merged-chr8-30629202-2	chr8	30629143	30629261	+	5.15	cIP1vsInput|cIP2vsInput	Intergenic	MIRb|SINE|MIR	60807	NR_045856	71314	Mm.158666	NR_045856	ENSMUSG00000097044	4933433F19Rik	-	RIKEN cDNA 4933433F19 gene	miscRNA	0.008475	0.445378
Merged-chr6-83456243-2	chr6	83456186	83456300	+	5.15	cIP1vsInput|cIP2vsInput	Intergenic	CpG	14488	NR_028382	320775	Mm.434334	NR_028382	ENSMUSG00000051844	B230319C09Rik	-	RIKEN cDNA B230319C09 gene	miscRNA	0.114035	0.791304
Merged-chr1-7746103-2	chr1	7746050	7746156	+	5.15	cIP1vsInput|cIP2vsInput	Intergenic	RLTR1A2_MM|LTR|ERV1	657183	NM_183028	319263		NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.028302	0.439252
Merged-chr7-142529434-1	chr7	142529384	142529484	+	5.1	cIP2vsInput	Intergenic	MER65D|LTR|ERV1	-3683	NM_011288	19935	Mm.12144	NM_011288	ENSMUSG00000037772	Mrpl23	L23mrp|Rpl23|Rpl23l	mitochondrial ribosomal protein L23	protein-coding	0.02	0.524752
Merged-chr11-9116341-1	chr11	9116291	9116391	+	5.1	cIP1vsInput	Intergenic	Intergenic	-1667	NM_001159401	22271	Mm.4610	NM_001159401	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding	0.05	0.554455
Merged-chr14-67716170-1	chr14	67716120	67716220	+	5.1	cIP2vsInput	promoter-TSS (NM_175384)	promoter-TSS (NM_175384)	72	NM_134073	105440	Mm.6720	NM_001111028	ENSMUSG00000034327	Kctd9	AA675328|AI854539	potassium channel tetramerisation domain containing 9	protein-coding	0.06	0.70297
Merged-chr7-64392243-1	chr7	64392193	64392293	+	5.1	cIP2vsInput	promoter-TSS (NM_028626)	promoter-TSS (NM_028626)	-7	NM_026483	67973	Mm.26973	NM_026483	ENSMUSG00000030521	Mphosph10	2810453H10Rik|5730405D16Rik|AI326008	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	protein-coding	0.1	0.623762
Merged-chr2-181520515-2	chr2	181520440	181520590	+	5.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_016775)	promoter-TSS (NM_016775)	30	NM_001271584	13002	Mm.391807	NM_001271584	ENSMUSG00000000826	Dnajc5	2610314I24Rik|AU018536|Csp	"DnaJ (Hsp40) homolog, subfamily C, member 5"	protein-coding	0.1	0.642384
Merged-chr4-155943783-2	chr4	155943722	155943844	+	5.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_021402)	promoter-TSS (NM_021402)	-48	NM_001039158	140499	Mm.371673	NM_001039157	ENSMUSG00000023286	Ube2j2	1200007B18Rik|2400008G19Rik|5730472G04Rik|AL022923|NCUBE-2|Ubc6|Ubc6p	ubiquitin-conjugating enzyme E2J 2	protein-coding	0.090164	0.682927
Merged-chr2-18028586-1	chr2	18028536	18028636	+	5.1	cIP2vsInput	"non-coding (NR_028378, exon 1 of 1)"	"non-coding (NR_028378, exon 1 of 1)"	1337	NR_028378	100034739	Mm.401643	NR_028378		Gm17762	-	"predicted gene, 17762"	miscRNA	0.05	0.673267
Merged-chr7-127026391-1	chr7	127026341	127026441	+	5.1	cIP1vsInput	promoter-TSS (NM_010772)	promoter-TSS (NM_010772)	88	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding	0.06	0.762376
Merged-chr2-80172094-2	chr2	80172040	80172148	+	5.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-42682	NM_001159582	18573	Mm.40678	NM_001009978	ENSMUSG00000059173	Pde1a	AI987702|AW125737	"phosphodiesterase 1A, calmodulin-dependent"	protein-coding	0	0.449541
Merged-chr5-151368895-1	chr5	151368845	151368945	+	5.1	cIP2vsInput	"intron (NR_045699, intron 1 of 3)"	CpG	220	NR_045699	625175	Mm.443286	NR_045699	ENSMUSG00000097321	1700028E10Rik	A630054D14|Gm6561	RIKEN cDNA 1700028E10 gene	miscRNA	0.11	0.683168
Merged-chr1-85273019-1	chr1	85272969	85273069	+	5.1	cIP1vsInput	Intergenic	Intergenic	-2453	NM_001037909	620078	Mm.461248	NM_001037909	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding	0.01	0.316832
Merged-chr4-41135519-1	chr4	41135469	41135569	+	5.1	cIP2vsInput	promoter-TSS (NM_026275)	promoter-TSS (NM_026275)	-502	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding	0.1	0.742574
Merged-chr12-52603818-1	chr12	52603768	52603868	+	5.1	cIP2vsInput	Intergenic	U6|snRNA|snRNA	-1496	NR_045910	73278	Mm.396209	NR_045910		1700031P21Rik	-	RIKEN cDNA 1700031P21 gene	miscRNA	0.08	0.514851
Merged-chr3-94837459-1	chr3	94837409	94837509	+	5.1	cIP2vsInput	promoter-TSS (NM_172683)	promoter-TSS (NM_172683)	-108	NM_001165948	229584	Mm.274787	NM_001165948	ENSMUSG00000038902	Pogz	9530006B08Rik|AU015913|AU044539	pogo transposable element with ZNF domain	protein-coding	0.09	0.732673
Merged-chr4-142166386-1	chr4	142166336	142166436	+	5.1	cIP2vsInput	"intron (NM_001109684, intron 1 of 6)"	"intron (NM_001109684, intron 1 of 6)"	43822	NM_144531	71529	Mm.255986	NM_001109684	ENSMUSG00000040606	Kazn	2310007B04Rik|9030409G11Rik|AI256607|AI666764|AW061099|Kaz|Kazrin	"kazrin, periplakin interacting protein"	protein-coding	0.03	0.693069
Merged-chr2-125859144-1	chr2	125859094	125859194	+	5.1	cIP2vsInput	promoter-TSS (NM_009939)	promoter-TSS (NM_009939)	-74	NM_175154	69976	Mm.20216	NM_175154	ENSMUSG00000027207	Galk2	2810017M24Rik|AI327030|Gk2	galactokinase 2	protein-coding	0.05	0.544554
Merged-chr17-80054515-2	chr17	80054455	80054575	+	5.1	cIP1vsInput|cIP2vsInput	"intron (NM_144802, intron 1 of 12)"	"intron (NM_144802, intron 1 of 12)"	7819	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082	heterogeneous nuclear ribonucleoprotein L-like	protein-coding	0.05	0.520661
Merged-chr15-38078308-1	chr15	38078258	38078358	+	5.1	cIP2vsInput	"intron (NM_001112721, intron 1 of 58)"	CpG	545	NM_001112721	70790	Mm.476840	NM_027553	ENSMUSG00000037487	Ubr5	4432411E13Rik|AW549941|C77315|D030042K14|Edd|Edd1|mKIAA0896	ubiquitin protein ligase E3 component n-recognin 5	protein-coding	0.07	0.762376
Merged-chr1-64122199-1	chr1	64122149	64122249	+	5.1	cIP2vsInput	promoter-TSS (NM_033563)	promoter-TSS (NM_033563)	-810	NM_033563	93691	Mm.458200	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding	0.04	0.594059
Merged-chr5-99978196-1	chr5	99978146	99978246	+	5.1	cIP2vsInput	"intron (NM_001077265, intron 1 of 8)"	CpG	742	NM_001077266	11991	Mm.150231	NM_001077265		Hnrnpd	Auf1|C230004L04|Hnrpd	heterogeneous nuclear ribonucleoprotein D	protein-coding	0.07	0.663366
Merged-chr7-16891164-2	chr7	16891110	16891219	+	5.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010320)	promoter-TSS (NM_010320)	-622	NM_010320	14709	Mm.103770	NM_010320	ENSMUSG00000063594	Gng8	G(y)8	"guanine nucleotide binding protein (G protein), gamma 8"	protein-coding	0.082569	0.709091
Merged-chr8-83997001-1	chr8	83996951	83997051	+	5.1	cIP2vsInput	promoter-TSS (NM_001081415)	promoter-TSS (NM_001081415)	-671	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding	0.13	0.851485
Merged-chr2-163535060-2	chr2	163535004	163535116	+	5.1	cIP1vsInput|cIP2vsInput	"intron (NR_027970, intron 1 of 3)"	"intron (NR_027970, intron 1 of 3)"	6661	NR_027970	68314	Mm.46190	NR_027970	ENSMUSG00000046840	0610008F07Rik	-	RIKEN cDNA 0610008F07 gene	miscRNA	0.053571	0.566372
Merged-chr8-111259186-2	chr8	111259126	111259247	+	5.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009149)	promoter-TSS (NM_009149)	16	NM_009149	20340	Mm.440619	NM_009149	ENSMUSG00000003316	Glg1	AI593353|AW537898|CFR|CFR-1|ESL-1|MG-160|MG160|Selel	golgi apparatus protein 1	protein-coding	0.157025	0.663934
Merged-chr5-86856735-2	chr5	86856681	86856789	+	5.1	cIP1vsInput|cIP2vsInput	Intergenic	RLTR1F_Mm|LTR|ERVK	50202	NM_153598	100727	Mm.281844	NM_153598	ENSMUSG00000029260	Ugt2b34	AI788959	"UDP glucuronosyltransferase 2 family, polypeptide B34"	protein-coding	0.027778	0.440367
Merged-chr1-178337983-1	chr1	178337933	178338033	+	5.1	cIP2vsInput	promoter-TSS (NM_016805)	promoter-TSS (NM_016805)	-199	NM_016805	51810	Mm.482674	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding	0.12	0.693069
Merged-chr16-15948343-2	chr16	15948289	15948398	+	5.1	cIP1vsInput|cIP2vsInput	"intron (NM_146068, intron 10 of 19)"	"intron (NM_146068, intron 10 of 19)"	61057	NM_007679	12609	Mm.347407	NM_007679		Cebpd	-	"CCAAT/enhancer binding protein (C/EBP), delta"	protein-coding	0.027523	0.5
Merged-chr15-102074100-1	chr15	102074050	102074150	+	5.1	cIP2vsInput	"intron (NM_145625, intron 1 of 14)"	CpG	327	NM_145625	75705	Mm.391795	NM_145625	ENSMUSG00000058655	Eif4b	2310046H11Rik|AL024095|C85189|Eif4a2	eukaryotic translation initiation factor 4B	protein-coding	0.07	0.693069
Merged-chr11-40694897-2	chr11	40694842	40694953	+	5.05	cIP1vsInput|cIP2vsInput	"5' UTR (NM_001199274, exon 1 of 7)"	"5' UTR (NM_001199274, exon 1 of 7)"	306	NM_001199274	108645	Mm.293771	NM_001199274	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	"methionine adenosyltransferase II, beta"	protein-coding	0.108108	0.633929
Merged-chr7-27481640-2	chr7	27481548	27481732	+	5.05	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-5313	NM_018820	55942	Mm.153684	NM_018820	ENSMUSG00000008384	Sertad1	1110032C13Rik|AV000455|AW456625|Sei-1|Sei1|TRIP-Br1	SERTA domain containing 1	protein-coding	0.059783	0.72973
Merged-chr1-46853565-2	chr1	46853508	46853623	+	5.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172653)	promoter-TSS (NM_172653)	-56	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0.130435	0.672414
Merged-chr6-87838721-2	chr6	87838671	87838772	+	5.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133934)	promoter-TSS (NM_133934)	38	NM_133934	57905	Mm.241546	NM_133934	ENSMUSG00000030056	Isy1	5830446M03Rik|AI181014|AU020769	ISY1 splicing factor homolog (S. cerevisiae)	protein-coding	0.09901	0.588235
Merged-chr14-52305210-2	chr14	52305159	52305261	+	5.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019721)	promoter-TSS (NM_019721)	-86	NM_019721	56335	Mm.271759	NM_019721	ENSMUSG00000022160	Mettl3	2310024F18Rik|M6A|Spo8	methyltransferase like 3	protein-coding	0.058824	0.504854
Merged-chr1-54439017-2	chr1	54438948	54439086	+	5.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001033194)	promoter-TSS (NM_001033194)	-46	NM_001033194	98488	Mm.25856	NM_001033194	ENSMUSG00000041303	Gtf3c3	AL022818|TF3C-gamma|TFIIIC102	"general transcription factor IIIC, polypeptide 3"	protein-coding	0.086957	0.690647
Merged-chr3-97158656-2	chr3	97158602	97158711	+	5.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019800)	promoter-TSS (NM_019800)	-121	NM_019800	66659	Mm.101368	NM_019800	ENSMUSG00000028093	Acp6	5730559A09Rik|ACPL1|AU022842|mPACPL1	"acid phosphatase 6, lysophosphatidic"	protein-coding	0.082569	0.681818
Merged-chrY-6799385-2	chrY	6799317	6799454	+	5.05	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	368392	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.282609
Merged-chr7-45526466-2	chr7	45526394	45526538	+	5.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008654)	promoter-TSS (NM_008654)	136	NM_148927	69217	Mm.274158	NM_148927	ENSMUSG00000040428	Plekha4	2410005C22Rik|C88169|Pepp1	"pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4"	protein-coding	0.0625	0.468966
Merged-chrY-6843319-2	chrY	6843265	6843374	+	5.05	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	324458	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.390909
Merged-chr2-118814127-2	chr2	118814072	118814182	+	5.05	cIP1vsInput|cIP2vsInput	"exon (NM_026412, exon 1 of 9)"	"exon (NM_026412, exon 1 of 9)"	124	NM_026412	51944	Mm.252695	NM_026412		Knstrn	1700025D04Rik|C15orf23|D2Ertd750e|SKAP|Traf4af1	kinetochore-localized astrin/SPAG5 binding	protein-coding	0.090909	0.648649
Merged-chr7-98361506-2	chr7	98361423	98361590	+	5.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001168539)	promoter-TSS (NM_001168539)	-178	NM_001168539	244152	Mm.25317	NM_001024619	ENSMUSG00000049580	Tsku	9530051K01Rik|E2ig4|Lrrc54|Tsk	tsukushi	protein-coding	0.05988	0.630952
Merged-chrY-6788519-2	chrY	6788442	6788596	+	5.05	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	379258	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.012987	0.212903
Merged-chr7-101933867-2	chr7	101933815	101933919	+	5.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001162973)	promoter-TSS (NM_001162973)	-10	NM_001162973	69358	Mm.214841	NM_001162973	ENSMUSG00000064307	Lrrc51	1700008D07Rik|Lrtomt	leucine rich repeat containing 51	protein-coding	0.086538	0.590476
Merged-chr16-56886088-2	chr16	56886038	56886139	+	5.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019631)	promoter-TSS (NM_019631)	75	NM_019631	56277	Mm.262328	NM_019631	ENSMUSG00000022754	Tmem45a	C630002M10Rik|M32486|p19.5	transmembrane protein 45a	protein-coding	0.029703	0.598039
Merged-chr8-118662402-2	chr8	118662346	118662459	+	5.05	cIP1vsInput|cIP2vsInput	"intron (NM_019707, intron 2 of 13)"	"intron (NM_019707, intron 2 of 13)"	378647	NM_019707	12554	Mm.334841	NM_019707		Cdh13	4932416G01Rik|Cdht|T-cadherin|Tcad	cadherin 13	protein-coding	0.00885	0.385965
Merged-chr11-60699687-2	chr11	60699631	60699743	+	5.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008502)	promoter-TSS (NM_008502)	-3	NM_001159405	16897	Mm.285453	NM_001159404	ENSMUSG00000020536	Llgl1	AI325176|Lgl1|Llglh|Mgl1	lethal giant larvae homolog 1 (Drosophila)	protein-coding	0.133929	0.787611
Merged-chr9-67047070-2	chr9	67047013	67047127	+	5.05	cIP1vsInput|cIP2vsInput	"intron (NM_001164249, intron 2 of 8)"	"intron (NM_001164249, intron 2 of 8)"	2143	NM_001164255	22003	Mm.121878	NM_001164248	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	"tropomyosin 1, alpha"	protein-coding	0.026316	0.617391
Merged-chr15-58135330-1	chr15	58135280	58135380	+	5	cIP2vsInput	promoter-TSS (NM_027435)	promoter-TSS (NM_027435)	-248	NM_027435	70472	Mm.221758	NM_153199	ENSMUSG00000022360	Atad2	2610509G12Rik	"ATPase family, AAA domain containing 2"	protein-coding	0.08	0.623762
Merged-chr6-17743540-1	chr6	17743490	17743590	+	5	cIP2vsInput	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-5676	NM_001083315	64213	Mm.12051	NM_001083315	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding	0.04	0.554455
Merged-chr11-93968375-1	chr11	93968325	93968425	+	5	cIP2vsInput	"5' UTR (NM_008704, exon 1 of 5)"	"5' UTR (NM_008704, exon 1 of 5)"	146	NM_008704	18102	Mm.439702	NM_008704		Nme1	AL024257|NDPK-A|NM23-M1|NM23A	NME/NM23 nucleoside diphosphate kinase 1	protein-coding	0.07	0.574257
Merged-chr3-51224591-2	chr3	51224514	51224669	+	5	cIP1vsInput|cIP2vsInput	"5' UTR (NM_009834, exon 1 of 3)"	"5' UTR (NM_009834, exon 1 of 3)"	144	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Ccrn4l	AU043840|Ccr4|nocturnin	CCR4 carbon catabolite repression 4-like (S. cerevisiae)	protein-coding	0.090323	0.666667
Merged-chr19-32181247-2	chr19	32181186	32181309	+	5	cIP1vsInput|cIP2vsInput	"intron (NM_001168525, intron 5 of 9)"	"intron (NM_001168525, intron 5 of 9)"	29766	NM_001168526	208449	Mm.329810	NM_001168525	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding	0.04065	0.483871
Merged-chr10-80398977-1	chr10	80398927	80399027	+	5	cIP1vsInput	"intron (NM_013595, intron 1 of 6)"	CpG	502	NM_013595	17192	Mm.7142	NM_013595	ENSMUSG00000035478	Mbd3	AI181826|AU019209	methyl-CpG binding domain protein 3	protein-coding	0.18	0.742574
Merged-chr2-28369892-2	chr2	28369810	28369975	+	5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-78049	NM_001005420	241289	Mm.330095	NM_001005420	ENSMUSG00000035829	Ppp1r26	Gm347|Kiaa0649|mKIAA0649	"protein phosphatase 1, regulatory subunit 26"	protein-coding	0.024242	0.566265
Merged-chr5-110135648-1	chr5	110135598	110135698	+	5	cIP2vsInput	promoter-TSS (NM_172717)	promoter-TSS (NM_172717)	-192	NM_172717	231600	Mm.30264	NM_172717	ENSMUSG00000014668	Chfr	5730484M20Rik|C230082M18|RNF116	checkpoint with forkhead and ring finger domains	protein-coding	0.03	0.534653
Merged-chrY-4155499-2	chrY	4155443	4155555	+	5	cIP1vsInput|cIP2vsInput	Intergenic	SYNREP_MM|Satellite|Satellite	383826	NM_001270516	100862398		NM_001270516		Gm21708	-	"predicted gene, 21708"	protein-coding	0	0.318584
Merged-chr2-154552748-2	chr2	154552696	154552801	+	5	cIP1vsInput|cIP2vsInput	"exon (NM_001171640, exon 1 of 1)"	"exon (NM_001171640, exon 1 of 1)"	972	NM_001171640	70362	Mm.479620	NM_001171640	ENSMUSG00000078129	Actl10	1700007I08Rik	actin-like 10	protein-coding	0.066667	0.632075
Merged-chr6-92214888-2	chr6	92214832	92214945	+	5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_030081)	promoter-TSS (NM_030081)	-77	NM_030081	78287	Mm.290734	NM_030081	ENSMUSG00000014550	Zfyve20	5330426D11Rik	"zinc finger, FYVE domain containing 20"	protein-coding	0.141593	0.692982
Merged-chr8-79030165-1	chr8	79030115	79030215	+	5	cIP2vsInput	"intron (NM_178267, intron 1 of 14)"	CpG	1728	NM_178267	622675	Mm.48724	NM_178267	ENSMUSG00000071064	Zfp827	2810449M09Rik|D630040G17Rik|Znf827	zinc finger protein 827	protein-coding	0.12	0.732673
Merged-chr19-5490841-1	chr19	5490791	5490891	+	5	cIP2vsInput	"intron (NM_007687, intron 1 of 3)"	CpG	386	NM_007687	12631	Mm.329655	NM_007687		Cfl1	AA959946|Cof	"cofilin 1, non-muscle"	protein-coding	0.1	0.762376
Merged-chr15-76724016-2	chr15	76723948	76724085	+	5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_176828)	promoter-TSS (NM_176828)	-171	NM_176828	223665	Mm.291713	NM_145472	ENSMUSG00000079002	C030006K11Rik	1110033I13Rik	RIKEN cDNA C030006K11 gene	protein-coding	0.058394	0.572464
Merged-chr8-36987296-2	chr8	36987237	36987355	+	5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-6279	NM_001039220	621080	Mm.373292	NM_001039220	ENSMUSG00000074384	AI429214	-	expressed sequence AI429214	protein-coding	0.016949	0.512605
Merged-chr8-111744024-1	chr8	111743974	111744074	+	5	cIP1vsInput	promoter-TSS (NM_009954)	promoter-TSS (NM_009954)	-175	NM_009954	12927	Mm.3758	NM_001198839	ENSMUSG00000031955	Bcar1	AI385681|Cas|Crkas	breast cancer anti-estrogen resistance 1	protein-coding	0.04	0.554455
Merged-chr11-88973897-1	chr11	88973847	88973947	+	5	cIP2vsInput	promoter-TSS (NM_016706)	promoter-TSS (NM_016706)	-38	NM_016706	12812	Mm.268004	NM_016706	ENSMUSG00000033983	Coil	C79982|Cln80|p80|p80-coilin	coilin	protein-coding	0.13	0.732673
Merged-chr3-90265815-2	chr3	90265761	90265870	+	5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_201407)	promoter-TSS (NM_201407)	-719	NM_201407	229541	Mm.30571	NM_201407	ENSMUSG00000042404	Dennd4b	BC026996|mKIAA0476	DENN/MADD domain containing 4B	protein-coding	0.119266	0.736364
Merged-chr10-68279769-2	chr10	68279703	68279835	+	5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-1043	NM_023598	71371		NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding	0.037879	0.511278
Merged-chr5-83355340-1	chr5	83355290	83355390	+	5	cIP2vsInput	promoter-TSS (NM_153801)	promoter-TSS (NM_153801)	-145	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	"trans-2,3-enoyl-CoA reductase-like"	protein-coding	0.01	0.376238
Merged-chr3-37640944-1	chr3	37640894	37640994	+	5	cIP2vsInput	"intron (NM_011896, intron 2 of 2)"	CpG-9115	994	NM_011896	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1	sprouty homolog 1 (Drosophila)	protein-coding	0.13	0.742574
Merged-chr3-58372734-1	chr3	58372684	58372784	+	5	cIP2vsInput	Intergenic	Intergenic	-42955	NM_001081229	72033	Mm.218409	NM_001081229	ENSMUSG00000027806	Tsc22d2	1810043J12Rik|5530402M19Rik	"TSC22 domain family, member 2"	protein-coding	0.02	0.445545
Merged-chr19-4397514-1	chr19	4397464	4397564	+	5	cIP2vsInput	promoter-TSS (NM_001001984)	promoter-TSS (NM_001001984)	-437	NM_001001984	225876	Mm.31941	NM_001001984	ENSMUSG00000054611	Kdm2a	100043628|5530401A10Rik|AA589516|AW536790|Cxxc8|Fbl11|Fbl7|Fbxl11|Gm4560|Jhdm1|Jhdm1a|lalina	lysine (K)-specific demethylase 2A	protein-coding	0.14	0.663366
Merged-chr13-48546159-1	chr13	48546109	48546209	+	5	cIP2vsInput	Intergenic	CpG	-7887	NR_029725	387244		NR_029725	ENSMUSG00000065421	Mirlet7a-1	Let-7a|Mirnlet7a|Mirnlet7a-1	microRNA let7a-1	miscRNA	0.12	0.841584
Merged-chr17-24745771-2	chr17	24745719	24745823	+	5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-7232	NM_001012402	328779	Mm.328848	NM_001012402	ENSMUSG00000039628	Hs3st6	-	heparan sulfate (glucosamine) 3-O-sulfotransferase 6	protein-coding	0.028846	0.504762
Merged-chr7-99183079-1	chr7	99183029	99183129	+	5	cIP2vsInput	promoter-TSS (NM_026384)	promoter-TSS (NM_026384)	-366	NM_026384	67800	Mm.180189	NM_026384	ENSMUSG00000030747	Dgat2	0610010B06Rik|ARAT|DGAT-2	diacylglycerol O-acyltransferase 2	protein-coding	0.06	0.633663
Merged-chr13-42657089-1	chr13	42657039	42657139	+	5	cIP2vsInput	Intergenic	Intergenic	-23534	NM_198419	218194	Mm.160124	NM_001005740	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding	0	0.425743
Merged-chr12-83922215-1	chr12	83922165	83922265	+	5	cIP2vsInput	promoter-TSS (NR_073564)	promoter-TSS (NR_073564)	-281	NR_073564	18222	Mm.447930	NM_001136075	ENSMUSG00000021224	Numb	Nb	numb gene homolog (Drosophila)	protein-coding	0.06	0.534653
Merged-chr11-98809707-2	chr11	98809621	98809794	+	5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_138660)	promoter-TSS (NM_138660)	-101	NM_138660	192160	Mm.40120	NM_138660	ENSMUSG00000078676	Casc3	Btz|Mln51	cancer susceptibility candidate 3	protein-coding	0.086705	0.655172
Merged-chr6-120666243-1	chr6	120666193	120666293	+	5	cIP2vsInput	promoter-TSS (NM_001128151)	promoter-TSS (NM_001128151)	-178	NM_001128151	330409	Mm.333357	NM_001128151	ENSMUSG00000071226	Cecr2	2610101O16Rik|2810409N01Rik|Gtl4|mKIAA1740	"cat eye syndrome chromosome region, candidate 2"	protein-coding	0.1	0.772277
Merged-chr8-125287879-1	chr8	125287829	125287929	+	5	cIP2vsInput	Intergenic	Intergenic	204831	NM_001081337	244668	Mm.271668	NM_001081337	ENSMUSG00000001995	Sipa1l2	BC058408|mKIAA1389	signal-induced proliferation-associated 1 like 2	protein-coding	0.02	0.49505
Merged-chr11-5098869-1	chr11	5098819	5098919	+	5	cIP2vsInput	promoter-TSS (NM_177370)	promoter-TSS (NM_177370)	208	NM_007968	14030	Mm.142822	NM_007968	ENSMUSG00000009079	Ewsr1	AU018891|Ews|Ewsh	Ewing sarcoma breakpoint region 1	protein-coding	0.11	0.722772
Merged-chr9-108347822-2	chr9	108347754	108347891	+	5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011678)	promoter-TSS (NM_011678)	-9	NM_011678	22258	Mm.3974	NM_011678	ENSMUSG00000032612	Usp4	F730026I20Rik|Unp|mKIAA4155	ubiquitin specific peptidase 4 (proto-oncogene)	protein-coding	0.175182	0.746377
Merged-chr2-29432862-2	chr2	29432806	29432918	+	5	cIP1vsInput|cIP2vsInput	"intron (NM_026896, intron 3 of 7)"	"intron (NM_026896, intron 3 of 7)"	86026	NM_026896	68975	Mm.330109	NM_026896	ENSMUSG00000026799	Med27	1500015J03Rik|2310042P07Rik|AA682045|Crsp8|D2Ertd434e	mediator complex subunit 27	protein-coding	0.017857	0.380531
Merged-chr2-32570808-2	chr2	32570746	32570870	+	5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010073)	promoter-TSS (NM_010073)	-50	NM_010073	13481	Mm.22001	NM_010073	ENSMUSG00000026810	Dpm2	AW557993|R75484	dolichol-phosphate (beta-D) mannosyltransferase 2	protein-coding	0.072581	0.56
Merged-chrX-152233121-1	chrX	152233071	152233171	+	5	cIP2vsInput	promoter-TSS (NM_013668)	promoter-TSS (NM_013668)	-109	NM_013668	20591	Mm.142655	NM_013668	ENSMUSG00000025332	Kdm5c	Jarid1c|Smcx|mKIAA0234	lysine (K)-specific demethylase 5C	protein-coding	0.03	0.386139
Merged-chr11-60220446-2	chr11	60220370	60220523	+	5	cIP1vsInput|cIP2vsInput	"intron (NM_011480, intron 1 of 18)"	CpG	158	NM_011480	20787	Mm.278701	NM_011480	ENSMUSG00000020538	Srebf1	ADD-1|ADD1|D630008H06|SREBP-1|SREBP-1a|SREBP-1c|SREBP1|SREBP1c|bHLHd1	sterol regulatory element binding transcription factor 1	protein-coding	0.130719	0.675325
Merged-chr7-25754764-2	chr7	25754711	25754818	+	5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178089)	promoter-TSS (NM_178089)	-44	NM_144922	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding	0.102804	0.675926
Merged-chr11-31370532-2	chr11	31370482	31370583	+	4.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011491)	promoter-TSS (NM_011491)	-471	NM_011491	20856	Mm.32506	NM_011491		Stc2	AW125853|Stc2l|mustc2	stanniocalcin 2	protein-coding	0.079208	0.529412
Merged-chr5-15037465-2	chr5	15037414	15037517	+	4.95	cIP1vsInput|cIP2vsInput	Intergenic	ORR1A1-int|LTR|ERVL-MaLR	-4458	NM_182957	66773	Mm.368256	NM_182957	ENSMUSG00000091897	Gm17019	-	predicted gene 17019	protein-coding	0.019417	0.413462
Merged-chr6-116635377-2	chr6	116635323	116635432	+	4.95	cIP1vsInput|cIP2vsInput	"3' UTR (NM_178045, exon 11 of 11)"	"3' UTR (NM_178045, exon 11 of 11)"	-6400	NM_026057	67255	Mm.18810	NM_026057	ENSMUSG00000059878	Zfp422	2900028O21Rik|AU041373|KOX15|Krox-25-2|Krox-26|Krox25|Krox26|Znf22	zinc finger protein 422	protein-coding	0.027523	0.518182
Merged-chr13-96435264-2	chr13	96435203	96435325	+	4.95	cIP1vsInput|cIP2vsInput	"intron (NM_001042714, intron 8 of 13)"	"intron (NM_001042714, intron 8 of 13)"	35896	NM_001042714	271144		NM_001042714	ENSMUSG00000047117	Ankdd1b	9330128J19Rik	ankyrin repeat and death domain containing 1B	protein-coding	0.008197	0.463415
Merged-chr8-3515324-2	chr8	3515274	3515375	+	4.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001122818)	promoter-TSS (NM_001122818)	-60	NM_001122818	50767	Mm.23085	NM_001122818	ENSMUSG00000004565	Pnpla6	AI661849|MSws|Nte	patatin-like phospholipase domain containing 6	protein-coding	0.079208	0.647059
Merged-chr10-19592028-2	chr10	19591974	19592083	+	4.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010511)	promoter-TSS (NM_010511)	70	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding	0.119266	0.727273
Merged-chr3-51484062-2	chr3	51484004	51484120	+	4.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_016858)	promoter-TSS (NM_016858)	96	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	"RAB33B, member of RAS oncogene family"	protein-coding	0.112069	0.683761
Merged-chr6-86585182-2	chr6	86585124	86585240	+	4.95	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-42992	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	"aspartic peptidase, retroviral-like 1"	protein-coding	0.034483	0.675214
Merged-chr9-49799030-2	chr9	49798956	49799104	+	4.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081445)	promoter-TSS (NM_001081445)	39	NM_001081445	17967	Mm.439182	NM_001081445		Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding	0.060811	0.624161
Merged-chr3-94932915-2	chr3	94932856	94932975	+	4.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009150)	promoter-TSS (NM_009150)	-168	NM_009150	20341	Mm.196558	NM_009150	ENSMUSG00000068874	Selenbp1	Lp56|Lpsb|SBP56	selenium binding protein 1	protein-coding	0.02521	0.475
Merged-chr11-85140231-2	chr11	85140168	85140294	+	4.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001029934)	promoter-TSS (NM_001029934)	-276	NM_001029934	237898	Mm.178524	NM_001029934	ENSMUSG00000000804	Usp32	2900074J03Rik|6430526O11Rik|AW045245	ubiquitin specific peptidase 32	protein-coding	0.111111	0.700787
Merged-chr14-101483511-2	chr14	101483458	101483564	+	4.95	cIP1vsInput|cIP2vsInput	"intron (NM_001081278, intron 8 of 18)"	"intron (NM_001081278, intron 8 of 18)"	125680	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	"TBC1 domain family, member 4"	protein-coding	0.009434	0.53271
Merged-chr7-28338871-2	chr7	28338820	28338922	+	4.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013676)	promoter-TSS (NM_013676)	-152	NM_013676	20924	Mm.285906	NM_013676	ENSMUSG00000003435	Supt5	AL033283|AL033321|AU019549|Spt5|Supt5h	suppressor of Ty 5	protein-coding	0.088235	0.592233
Merged-chr7-16948323-2	chr7	16948269	16948378	+	4.95	cIP1vsInput|cIP2vsInput	"3' UTR (NM_001099636, exon 1 of 1)"	"3' UTR (NM_001099636, exon 1 of 1)"	3641	NM_001099636	434128	Mm.483018	NM_001099636	ENSMUSG00000070802	Pnmal2	EG434128	PNMA-like 2	protein-coding	0.036697	0.590909
Merged-chr17-47688044-2	chr17	47687988	47688100	+	4.9	cIP1vsInput|cIP2vsInput	"non-coding (NR_045945, exon 1 of 3)"	"non-coding (NR_045945, exon 1 of 3)"	342	NM_025365	66119	Mm.89912	NM_001164729		Tomm6	1110002E23Rik|AI663970	translocase of outer mitochondrial membrane 6 homolog (yeast)	protein-coding	0.151786	0.654867
Merged-chr5-121545881-1	chr5	121545831	121545931	+	4.9	cIP2vsInput	promoter-TSS (NM_010765)	promoter-TSS (NM_010765)	11	NM_010765	17165	Mm.272206	NM_010765	ENSMUSG00000029454	Mapkapk5	MK5|PRAK	MAP kinase-activated protein kinase 5	protein-coding	0.17	0.772277
Merged-chr19-7267361-2	chr19	7267310	7267412	+	4.9	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-2403	NM_054048	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding	0.088235	0.757282
Merged-chr8-126971103-2	chr8	126971042	126971164	+	4.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172762)	promoter-TSS (NM_172762)	-24	NM_172762	52202	Mm.28199	NM_172762	ENSMUSG00000033931	Rbm34	4930547K05Rik|6330444B11|D8Ertd233e	RNA binding motif protein 34	protein-coding	0.081967	0.585366
Merged-chr11-79703672-1	chr11	79703622	79703722	+	4.9	cIP2vsInput	Intergenic	Intergenic	-8297	NR_029579	387188		NR_029579	ENSMUSG00000065395	Mir193	Mirn193|mmu-mir-193	microRNA 193	miscRNA	0.03	0.50495
Merged-chr9-88482734-1	chr9	88482684	88482784	+	4.9	cIP2vsInput	promoter-TSS (NM_019796)	promoter-TSS (NM_019796)	-337	NM_019796	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|pp68	"synaptotagmin binding, cytoplasmic RNA interacting protein"	protein-coding	0.12	0.70297
Merged-chr2-128967387-2	chr2	128967304	128967470	+	4.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178404)	promoter-TSS (NM_178404)	-15	NM_178404	78751	Mm.26377	NM_178404	ENSMUSG00000042851	Zc3h6	4631426G04Rik|4833425H18Rik|AU024389|AW060453|Zc3hdc6|mKIAA2035	zinc finger CCCH type containing 6	protein-coding	0.10241	0.652695
Merged-chr18-11353106-2	chr18	11353025	11353188	+	4.9	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-280170	NM_001252495	225182	Mm.154275	NM_175458	ENSMUSG00000041238	Rbbp8	9930104E21Rik|CtIP|RBBP-8|RIM|SAE2	retinoblastoma binding protein 8	protein-coding	0.04908	0.426829
Merged-chr11-78323091-2	chr11	78323024	78323158	+	4.9	cIP1vsInput|cIP2vsInput	TTS (NM_017407)	TTS (NM_017407)	-1107	NM_009657	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	"aldolase C, fructose-bisphosphate"	protein-coding	0.052239	0.614815
Merged-chr5-3596202-2	chr5	3596143	3596262	+	4.9	cIP1vsInput|cIP2vsInput	"exon (NM_172991, exon 1 of 5)"	"exon (NM_172991, exon 1 of 5)"	136	NM_027777	71382	Mm.379196	NM_027777	ENSMUSG00000005907	Pex1	5430414H02Rik|E330005K07Rik|ZWS1	peroxisomal biogenesis factor 1	protein-coding	0.092437	0.616667
Merged-chr5-14971265-1	chr5	14971215	14971315	+	4.9	cIP1vsInput	"intron (NR_001584, intron 2 of 3)"	"intron (NR_001584, intron 2 of 3)"	25971	NR_001584	74062	Mm.394766	NR_001584		Speer8-ps1	4933405L09Rik|SPEER-8|Speer8-ps	"spermatogenesis associated glutamate (E)-rich protein 8, pseudogene 1"	pseudo	0.03	0.425743
Merged-chr11-109611273-1	chr11	109611223	109611323	+	4.9	cIP2vsInput	"exon (NM_145940, exon 1 of 13)"	"exon (NM_145940, exon 1 of 13)"	116	NM_145940	52639	Mm.35817	NM_145940	ENSMUSG00000041895	Wipi1	4930533H01Rik|AW411817|D11Ertd498e	"WD repeat domain, phosphoinositide interacting 1"	protein-coding	0.1	0.663366
Merged-chrY-6810169-2	chrY	6810119	6810220	+	4.9	cIP1vsInput|cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	357608	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.343137
Merged-chr10-80264819-1	chr10	80264769	80264869	+	4.9	cIP1vsInput	promoter-TSS (NM_001122605)	promoter-TSS (NM_001122605)	-172	NM_001122604	70248	Mm.148693	NM_001122604	ENSMUSG00000069565	Dazap1	2410042M16Rik|mPrrp	DAZ associated protein 1	protein-coding	0.07	0.564356
Merged-chr5-21786722-1	chr5	21786672	21786772	+	4.9	cIP2vsInput	"exon (NM_011188, exon 2 of 13)"	"exon (NM_011188, exon 2 of 13)"	1439	NM_011188	19181	Mm.2462	NM_011188	ENSMUSG00000028932	Psmc2	-	"proteasome (prosome, macropain) 26S subunit, ATPase 2"	protein-coding	0.09	0.663366
Merged-chr1-162570529-1	chr1	162570479	162570579	+	4.9	cIP2vsInput	promoter-TSS (NM_016796)	promoter-TSS (NM_016796)	-299	NM_016796	53330	Mm.10699	NM_016796	ENSMUSG00000026696	Vamp4	D1Ertd147e	vesicle-associated membrane protein 4	protein-coding	0.12	0.693069
Merged-chr6-51163488-2	chr6	51163422	51163555	+	4.9	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	106422	NR_029719	387166		NR_029719	ENSMUSG00000065505	Mir148a	Mirn148|Mirn148a	microRNA 148a	miscRNA	0.022556	0.589552
Merged-chr18-60501543-1	chr18	60501493	60501593	+	4.9	cIP2vsInput	"5' UTR (NM_134133, exon 1 of 2)"	"5' UTR (NM_134133, exon 1 of 2)"	440	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding	0.14	0.732673
Merged-chr13-90828004-2	chr13	90827952	90828057	+	4.9	cIP1vsInput|cIP2vsInput	Intergenic	Plat_L3|LINE|CR1	77351	NM_001145879	435376	Mm.292579	NM_001145879	ENSMUSG00000078958	Atp6ap1l	EG435376	"ATPase, H+ transporting, lysosomal accessory protein 1-like"	protein-coding	0.028571	0.471698
Merged-chr7-82866191-1	chr7	82866141	82866241	+	4.9	cIP2vsInput	Intergenic	CpG	-1142	NM_175366	108797	Mm.306789	NM_175366	ENSMUSG00000057706	Mex3b	4931439A04Rik|M-04814|Rkhd3|mKIAA2009	mex3 homolog B (C. elegans)	protein-coding	0.11	0.742574
Merged-chr5-88764927-2	chr5	88764874	88764980	+	4.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007832)	promoter-TSS (NM_007832)	-86	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding	0.113208	0.747664
Merged-chr6-122308641-2	chr6	122308582	122308700	+	4.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010749)	promoter-TSS (NM_010749)	-369	NM_010749	17113	Mm.249225	NM_010749	ENSMUSG00000007458	M6pr	CD-MPR|Mpr46	"mannose-6-phosphate receptor, cation dependent"	protein-coding	0.042373	0.537815
Merged-chr4-149772589-2	chr4	149772525	149772654	+	4.9	cIP1vsInput|cIP2vsInput	"intron (NM_027460, intron 1 of 6)"	"intron (NM_027460, intron 1 of 6)"	1678	NM_027460	70556	Mm.41877	XM_003945705	ENSMUSG00000028982	Slc25a33	5730438N18Rik|Pnc1	"solute carrier family 25, member 33"	protein-coding	0.015504	0.515385
Merged-chr4-119539559-1	chr4	119539509	119539609	+	4.9	cIP2vsInput	promoter-TSS (NM_172699)	promoter-TSS (NM_172699)	-129	NM_172699	230700	Mm.259227	NM_172699	ENSMUSG00000032998	Foxj3	C330039G02Rik|Fhd6|mKIAA1041	forkhead box J3	protein-coding	0.15	0.752475
Merged-chr5-113771997-1	chr5	113771947	113772047	+	4.9	cIP2vsInput	promoter-TSS (NM_016926)	promoter-TSS (NM_016926)	-348	NM_016926	53890	Mm.29594	NM_016926	ENSMUSG00000018974	Sart3	AU045857|mKIAA0156	squamous cell carcinoma antigen recognized by T cells 3	protein-coding	0.09	0.584158
Merged-chr1-193317200-1	chr1	193317150	193317250	+	4.9	cIP2vsInput	"intron (NM_008484, intron 3 of 22)"	"intron (NM_008484, intron 3 of 22)"	15206	NM_008484	16780	Mm.435441	NM_008484	ENSMUSG00000026639	Lamb3	-	"laminin, beta 3"	protein-coding	0.02	0.633663
Merged-chr10-42502216-1	chr10	42502166	42502266	+	4.9	cIP2vsInput	"5' UTR (NM_017472, exon 1 of 4)"	"5' UTR (NM_017472, exon 1 of 4)"	162	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding	0.19	0.742574
Merged-chr11-72607864-1	chr11	72607814	72607914	+	4.9	cIP2vsInput	"intron (NM_025985, intron 1 of 5)"	CpG	603	NM_025985	67128	Mm.458052	NM_025985	ENSMUSG00000020794	Ube2g1	2700059C12Rik|AI256795|AU014992|AW552068|D130023C12Rik	ubiquitin-conjugating enzyme E2G 1	protein-coding	0.12	0.821782
Merged-chr11-80476625-2	chr11	80476575	80476676	+	4.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009871)	promoter-TSS (NM_009871)	-421	NM_009871	12569	Mm.474282	NM_009871	ENSMUSG00000048895	Cdk5r1	Cdk5r|D11Bwg0379e|p25|p35	"cyclin-dependent kinase 5, regulatory subunit 1 (p35)"	protein-coding	0.128713	0.794118
Merged-chr3-96597587-1	chr3	96597537	96597637	+	4.9	cIP2vsInput	"exon (NM_001024851, exon 2 of 2)"	"exon (NM_001024851, exon 2 of 2)"	951	NM_001024851	545554	Mm.267664	NM_001024851	ENSMUSG00000049097	Ankrd34a	AW060394|Ankrd34	ankyrin repeat domain 34A	protein-coding	0.07	0.633663
Merged-chr6-4004191-1	chr6	4004141	4004241	+	4.9	cIP2vsInput	"5' UTR (NM_025331, exon 1 of 2)"	"5' UTR (NM_025331, exon 1 of 2)"	204	NM_025331	66066	Mm.25547	NM_025331	ENSMUSG00000032766	Gng11	0610037B21Rik	"guanine nucleotide binding protein (G protein), gamma 11"	protein-coding	0.11	0.752475
Merged-chr17-87446900-1	chr17	87446850	87446950	+	4.9	cIP2vsInput	promoter-TSS (NM_007589)	promoter-TSS (NM_007589)	35	NM_007589	12314	Mm.329243	NM_007589	ENSMUSG00000036438	Calm2	1500001E21Rik|AL024017	calmodulin 2	protein-coding	0.06	0.613861
Merged-chr2-90904694-1	chr2	90904644	90904744	+	4.9	cIP2vsInput	promoter-TSS (NM_026688)	promoter-TSS (NM_026688)	27	NM_026688	68349	Mm.30113	NM_026688	ENSMUSG00000005510	Ndufs3	0610010M09Rik|CI-30kD	NADH dehydrogenase (ubiquinone) Fe-S protein 3	protein-coding	0.06	0.574257
Merged-chr17-79896102-1	chr17	79896052	79896152	+	4.9	cIP2vsInput	promoter-TSS (NM_019717)	promoter-TSS (NM_019717)	21	NM_178050	56298	Mm.175403	NM_019717	ENSMUSG00000059811	Atl2	2010110I21Rik|AA407293|AV334690|Aip-2|Arl6ip2	atlastin GTPase 2	protein-coding	0.14	0.722772
Merged-chr11-58330531-2	chr11	58330456	58330606	+	4.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_024480)	promoter-TSS (NM_024480)	-187	NM_001161338	79566	Mm.290534	NM_001161338	ENSMUSG00000013646	Sh3bp5l	2310074E09Rik|BC003251|mKIAA1720	SH3 binding domain protein 5 like	protein-coding	0.046667	0.496689
Merged-chr16-20141251-1	chr16	20141201	20141301	+	4.9	cIP2vsInput	"intron (NM_001033237, intron 1 of 29)"	CpG	188	NM_001145931	208146	Mm.390895	NM_001033237	ENSMUSG00000041215	Yeats2	BC042768|mKIAA1197	YEATS domain containing 2	protein-coding	0.13	0.752475
Merged-chr2-116065820-1	chr2	116065770	116065870	+	4.9	cIP2vsInput	promoter-TSS (NM_010825)	promoter-TSS (NM_010825)	-762	NM_010825	17536	Mm.247566	NM_001136072		Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding	0.12	0.732673
Merged-chr17-33929415-1	chr17	33929365	33929465	+	4.9	cIP2vsInput	promoter-TSS (NM_009059)	promoter-TSS (NM_009059)	-479	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding	0.18	0.732673
Merged-chr17-35549683-2	chr17	35549624	35549743	+	4.85	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-2445	NM_001008424	386463	Mm.426664	NM_001008424	ENSMUSG00000039518	Cdsn	AI747712	corneodesmosin	protein-coding	0.042017	0.65
Merged-chr11-31870637-2	chr11	31870568	31870707	+	4.85	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-1574	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	4930447D24Rik|AI851572|mKIAA1673	cytoplasmic polyadenylation element binding protein 4	protein-coding	0.079137	0.55
Merged-chr19-6909692-2	chr19	6909641	6909743	+	4.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_012021)	promoter-TSS (NM_012021)	-6	NM_001166370	67674	Mm.371597	NM_001166370	ENSMUSG00000038812	Trmt112	0610038D11Rik|Trm112p	tRNA methyltransferase 11-2	protein-coding	0.098039	0.728155
Merged-chr9-44397354-2	chr9	44397283	44397425	+	4.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008063)	promoter-TSS (NM_008063)	-822	NM_008063	14385	Mm.486672	NM_008063	ENSMUSG00000032114	Slc37a4	G6PT|G6pt1|GSD-1b|mG6PT	"solute carrier family 37 (glucose-6-phosphate transporter), member 4"	protein-coding	0.091549	0.692308
Merged-chr9-95857524-2	chr9	95857461	95857587	+	4.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019864)	promoter-TSS (NM_019864)	-7	NR_073361	73410	Mm.443314	NM_028533	ENSMUSG00000096655	1700065D16Rik	-	RIKEN cDNA 1700065D16 gene	protein-coding	0.071429	0.622047
Merged-chr10-36476229-2	chr10	36476173	36476286	+	4.85	cIP1vsInput|cIP2vsInput	Intergenic	B4A|SINE|B4	-30578	NM_001253355	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0	0.394737
Merged-chr7-28810836-2	chr7	28810780	28810892	+	4.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_177301)	promoter-TSS (NM_177301)	-54	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding	0.0625	0.663717
Merged-chr14-70153891-2	chr14	70153830	70153952	+	4.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_146055)	promoter-TSS (NM_146055)	-100	NM_146055	219158	Mm.218284	NM_146055	ENSMUSG00000033712	2610301G19Rik	mKIAA1967	RIKEN cDNA 2610301G19 gene	protein-coding	0.04918	0.520325
Merged-chr10-80249375-2	chr10	80249305	80249446	+	4.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029272)	promoter-TSS (NM_029272)	-77	NM_029272	75406	Mm.28712	NM_029272	ENSMUSG00000020153	Ndufs7	1010001M04Rik	NADH dehydrogenase (ubiquinone) Fe-S protein 7	protein-coding	0.099291	0.605634
Merged-chr18-3337519-2	chr18	3337432	3337607	+	4.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001110852)	promoter-TSS (NM_001110852)	70	NM_001110851	12916	Mm.5244	NM_001110850	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding	0.148571	0.732955
Merged-chr4-153975112-2	chr4	153975057	153975168	+	4.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007859)	promoter-TSS (NM_007859)	-31	NM_007859	13368	Mm.388918	NM_007859	ENSMUSG00000029027	Dffb	40kDa|5730477D02Rik|CAD|CPAN|DFF40|Didff	"DNA fragmentation factor, beta subunit"	protein-coding	0.108108	0.651786
Merged-chr8-20520529-2	chr8	20520477	20520581	+	4.85	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-94398	NM_001270553	100861668	Mm.445582	NM_001270553		Gm21119	-	"predicted gene, 21119"	protein-coding	0	0.285714
Merged-chr9-49976512-2	chr9	49976462	49976563	+	4.85	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-177443	NM_010875	17967	Mm.439182	NM_001081445		Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding	0.039604	0.480392
Merged-chr11-96065303-2	chr11	96065252	96065354	+	4.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172300)	promoter-TSS (NM_172300)	61	NM_172300	268470	Mm.38802	NM_172300	ENSMUSG00000014349	Ube2z	AW049199|C030047H17Rik|D11Moh35	ubiquitin-conjugating enzyme E2Z (putative)	protein-coding	0.127451	0.708738
Merged-chr2-132686850-2	chr2	132686787	132686913	+	4.85	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-3433	NM_028637	73747	Mm.284114	NM_028637	ENSMUSG00000044991	1110034G24Rik	-	RIKEN cDNA 1110034G24 gene	protein-coding	0.031746	0.503937
Merged-chr1-180850995-2	chr1	180850931	180851059	+	4.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145943)	promoter-TSS (NM_145943)	-156	NM_145943	208768	Mm.272625	NM_145943	ENSMUSG00000038806	Sde2	-	SDE2 telomere maintenance homolog (S. pombe)	protein-coding	0.109375	0.705426
Merged-chr8-109608527-2	chr8	109608438	109608616	+	4.85	cIP1vsInput|cIP2vsInput	"5' UTR (NM_020046, exon 1 of 9)"	"5' UTR (NM_020046, exon 1 of 9)"	146	NM_020046	56749	Mm.23894	NM_020046	ENSMUSG00000031730	Dhodh	2810417D19Rik|AI834883	dihydroorotate dehydrogenase	protein-coding	0.106742	0.648045
Merged-chr4-32373191-2	chr4	32373139	32373244	+	4.85	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-44244	NM_001109661	12014	Mm.431426	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology 2	protein-coding	0.047619	0.5
Merged-chr4-130307977-2	chr4	130307910	130308044	+	4.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010174)	promoter-TSS (NM_010174)	-801	NM_010174	14077	Mm.388886	NM_010174		Fabp3	Fabph-1|Fabph-4|Fabph1|Fabph4|H-FABP|Mdgi	"fatty acid binding protein 3, muscle and heart"	protein-coding	0.089552	0.666667
Merged-chr13-58128126-2	chr13	58128062	58128190	+	4.85	cIP1vsInput|cIP2vsInput	"exon (NM_029872, exon 1 of 1)"	"exon (NM_029872, exon 1 of 1)"	430	NM_029872	77134	Mm.490274	NM_029872	ENSMUSG00000007836	Hnrnpa0	1110055B05Rik|3010025E17Rik|Hnrpa0|hnRNP A0	heterogeneous nuclear ribonucleoprotein A0	protein-coding	0.164062	0.705426
Merged-chr2-13372434-1	chr2	13372384	13372484	+	4.8	cIP2vsInput	"intron (NM_001081084, intron 31 of 66)"	"intron (NM_001081084, intron 31 of 66)"	-101156	NM_009105	20163	Mm.905	NM_009105	ENSMUSG00000026727	Rsu1	RsuI|rsp-1	Ras suppressor protein 1	protein-coding	0.01	0.633663
Merged-chr1-180813671-1	chr1	180813621	180813721	+	4.8	cIP2vsInput	promoter-TSS (NM_008210)	promoter-TSS (NM_008210)	-68	NM_008210	15078	Mm.442502	NM_008210	ENSMUSG00000060743	H3f3a	H3.3A	"H3 histone, family 3A"	protein-coding	0.14	0.792079
Merged-chr7-12928141-1	chr7	12928091	12928191	+	4.8	cIP2vsInput	"exon (NM_029809, exon 2 of 2)"	"exon (NM_029809, exon 2 of 2)"	725	NM_029809	381845	Mm.439896	NM_029809	ENSMUSG00000033967	2310014L17Rik	AV237412|C77118	RIKEN cDNA 2310014L17 gene	protein-coding	0.09	0.594059
Merged-chr11-88718366-1	chr11	88718316	88718416	+	4.8	cIP2vsInput	promoter-TSS (NR_038058)	promoter-TSS (NR_038058)	-99	NM_001201341	76626	Mm.474737	NM_001201341	ENSMUSG00000069769	Msi2	1700105C15Rik|AI451722|AI563628|AW489193|Msi2h	musashi RNA-binding protein 2	protein-coding	0.06	0.752475
Merged-chr2-126933008-1	chr2	126932958	126933058	+	4.8	cIP2vsInput	"exon (NM_023220, exon 1 of 15)"	"exon (NM_023220, exon 1 of 15)"	227	NM_023220	66552	Mm.269928	NM_023220	ENSMUSG00000027366	Sppl2a	2010106G01Rik|C130089K23Rik	signal peptide peptidase like 2A	protein-coding	0.09	0.752475
Merged-chr4-147508490-1	chr4	147508440	147508540	+	4.8	cIP2vsInput	"intron (NM_001039209, intron 1 of 2)"	"intron (NM_001039209, intron 1 of 2)"	-44787	NM_001014397	433804	Mm.332047	XM_003946328	ENSMUSG00000065999	Gm13154	OTTMUSG00000010673	predicted gene 13154	protein-coding	0	0.346535
Merged-chr14-21500365-1	chr14	21500315	21500415	+	4.8	cIP2vsInput	"intron (NM_017479, intron 1 of 16)"	CpG	580	NM_017479	54169	Mm.248967	NM_001205241	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding	0.13	0.712871
Merged-chr13-111809757-2	chr13	111809681	111809834	+	4.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011945)	promoter-TSS (NM_011945)	-774	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding	0.039216	0.642857
Merged-chr7-118740657-2	chr7	118740604	118740710	+	4.8	cIP1vsInput|cIP2vsInput	"5' UTR (NM_027815, exon 1 of 31)"	"5' UTR (NM_027815, exon 1 of 31)"	386	NM_027815	71517	Mm.213298	NM_027815	ENSMUSG00000030982	9030624J02Rik	2610029J22Rik	RIKEN cDNA 9030624J02 gene	protein-coding	0.066038	0.616822
Merged-chr10-80398776-1	chr10	80398726	80398826	+	4.8	cIP2vsInput	"intron (NM_013595, intron 1 of 6)"	CpG	703	NM_013595	17192	Mm.7142	NM_013595	ENSMUSG00000035478	Mbd3	AI181826|AU019209	methyl-CpG binding domain protein 3	protein-coding	0.14	0.732673
Merged-chr13-21940412-1	chr13	21940362	21940462	+	4.8	cIP2vsInput	Intergenic	Intergenic	-4682	NM_183014	193452	Mm.187446	NM_183014	ENSMUSG00000006720	Zfp184	4930500C15Rik	zinc finger protein 184 (Kruppel-like)	protein-coding	0.01	0.465347
Merged-chr1-160213097-1	chr1	160213047	160213147	+	4.8	cIP2vsInput	promoter-TSS (NM_009786)	promoter-TSS (NM_009786)	-205	NM_009786	12301	Mm.10702	NM_009786	ENSMUSG00000014226	Cacybp	SIP	calcyclin binding protein	protein-coding	0.07	0.584158
Merged-chr4-141790813-1	chr4	141790763	141790863	+	4.8	cIP1vsInput	promoter-TSS (NM_172338)	promoter-TSS (NM_172338)	-169	NM_172338	214063	Mm.39102	NM_172338		Dnajc16	2900037O03Rik|4732437J24Rik|D030060M24|mKIAA0962	"DnaJ (Hsp40) homolog, subfamily C, member 16"	protein-coding	0.08	0.574257
Merged-chr3-103021003-1	chr3	103020953	103021053	+	4.8	cIP2vsInput	"intron (NM_144901, intron 1 of 19)"	CpG	457	NM_144901	229663	Mm.277713	NM_001161854	ENSMUSG00000068823	Csde1	AA960392|BC016898|D3Jfr1|mKIAA0885|unr	"cold shock domain containing E1, RNA binding"	protein-coding	0.09	0.663366
Merged-chr5-72905153-1	chr5	72905103	72905203	+	4.8	cIP2vsInput	Intergenic	Intergenic	-9164	NM_001113423	75991	Mm.121285	NM_001113423	ENSMUSG00000036087	Slain2	5033405K12Rik|8030444K12Rik|AI596370|mKIAA1458	"SLAIN motif family, member 2"	protein-coding	0.02	0.455446
Merged-chr12-51692272-1	chr12	51692222	51692322	+	4.8	cIP2vsInput	promoter-TSS (NM_001172098)	promoter-TSS (NM_001172098)	-358	NM_052973	94186	Mm.65979	NM_001172098	ENSMUSG00000020954	Strn3	Gs2na|SG2NA	"striatin, calmodulin binding protein 3"	protein-coding	0.07	0.623762
Merged-chr10-128059042-1	chr10	128058992	128059092	+	4.8	cIP2vsInput	promoter-TSS (NM_019766)	promoter-TSS (NM_019766)	60	NM_019766	56351	Mm.305816	NM_019766	ENSMUSG00000071072	Ptges3	5730442A20Rik|Ptges|Tebp|cPGES|p23|sid3177	prostaglandin E synthase 3 (cytosolic)	protein-coding	0.14	0.70297
Merged-chr2-131210360-2	chr2	131210304	131210416	+	4.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027129)	promoter-TSS (NM_027129)	-80	NM_027129	69596	Mm.2937	NM_027129	ENSMUSG00000068264	Ap5s1	0610038L13Rik|2310035K24Rik|AW060727	"adaptor-related protein 5 complex, sigma 1 subunit"	protein-coding	0.089286	0.654867
Merged-chr7-73524579-1	chr7	73524529	73524629	+	4.8	cIP2vsInput	"intron (NM_001081345, intron 2 of 38)"	"intron (NM_001081345, intron 2 of 38)"	17167	NM_001081345	244059	Mm.34955	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703	chromodomain helicase DNA binding protein 2	protein-coding	0.03	0.465347
Merged-chr17-80207400-1	chr17	80207350	80207450	+	4.8	cIP2vsInput	promoter-TSS (NR_036615)	promoter-TSS (NR_036615)	-95	NM_001195485	225027	Mm.292016	NM_001195485	ENSMUSG00000024097	Srsf7	35kDa|9430065L19Rik|9G8|NX-96|Sfrs7	serine/arginine-rich splicing factor 7	protein-coding	0.09	0.564356
Merged-chr3-153769433-1	chr3	153769383	153769483	+	4.8	cIP2vsInput	Intergenic	Intergenic	22654	NR_045801	70594	Mm.491050	NR_045801	ENSMUSG00000062046	5730460C07Rik	-	RIKEN cDNA 5730460C07 gene	miscRNA	0	0.386139
Merged-chr13-21750620-1	chr13	21750570	21750670	+	4.8	cIP2vsInput	promoter-TSS (NM_178211)	promoter-TSS (NM_178211)	-115	NM_178211	319160	Mm.255646	NM_178211	ENSMUSG00000064288	Hist1h4k	-	"histone cluster 1, H4k"	protein-coding	0.08	0.623762
Merged-chr1-52113954-1	chr1	52113904	52114004	+	4.8	cIP2vsInput	Intergenic	CpG	-5484	NM_009283	20846	Mm.487336	NM_001205313	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding	0.11	0.742574
Merged-chr16-4003862-1	chr16	4003812	4003912	+	4.8	cIP2vsInput	Intergenic	CpG	-2182	NM_177472	52864	Mm.29935	NM_177472	ENSMUSG00000039738	Slx4	AI256635|AI426760|Btbd12|D16Bwg1016e	SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)	protein-coding	0.11	0.613861
Merged-chr16-52031347-1	chr16	52031297	52031397	+	4.8	cIP2vsInput	promoter-TSS (NM_001033238)	promoter-TSS (NM_001033238)	-202	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding	0.03	0.49505
Merged-chr1-31793423-1	chr1	31793373	31793473	+	4.8	cIP1vsInput	Intergenic	Intergenic	-379383	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm1	"KH domain containing, RNA binding, signal transduction associated 2"	protein-coding	0	0.237624
Merged-chr16-32877792-1	chr16	32877742	32877842	+	4.8	cIP2vsInput	promoter-TSS (NM_001159349)	promoter-TSS (NM_001159349)	8	NM_001159349	69823	Mm.12831	NM_001159349	ENSMUSG00000022800	Fyttd1	2010005M05Rik|3830411L18Rik|3830421F13Rik|4933423A17Rik|AI098218|AW539567|C85190	forty-two-three domain containing 1	protein-coding	0.16	0.792079
Merged-chr2-174330726-1	chr2	174330676	174330776	+	4.8	cIP2vsInput	"intron (NM_001077510, intron 1 of 10)"	CpG-8943	637	NM_001077510	14683	Mm.125770	NM_001077507	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gsa|Nesp|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH	"GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus"	protein-coding	0.07	0.712871
Merged-chr7-144895957-2	chr7	144895907	144896008	+	4.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008003)	promoter-TSS (NM_008003)	-575	NM_008003	14170	Mm.3904	NM_008003	ENSMUSG00000031073	Fgf15	FGF19	fibroblast growth factor 15	protein-coding	0.069307	0.598039
Merged-chr11-57518415-2	chr11	57518347	57518483	+	4.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_180599)	promoter-TSS (NM_180599)	229	NM_001168667	67726	Mm.25632	NM_001168667	ENSMUSG00000020523	Fam114a2	1810073G14Rik|9030624B09Rik	"family with sequence similarity 114, member A2"	protein-coding	0.080882	0.671533
Merged-chr16-23107520-1	chr16	23107470	23107570	+	4.8	cIP2vsInput	promoter-TSS (NM_013506)	promoter-TSS (NM_013506)	41	NM_013506	13682	Mm.260084	NM_001123037	ENSMUSG00000022884	Eif4a2	4833432N07Rik|BM-010|Ddx2b|Eif4	eukaryotic translation initiation factor 4A2	protein-coding	0.15	0.663366
Merged-chr9-62344021-1	chr9	62343971	62344071	+	4.8	cIP2vsInput	"intron (NM_009672, intron 1 of 6)"	CpG	2678	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	"acidic (leucine-rich) nuclear phosphoprotein 32 family, member A"	protein-coding	0.15	0.762376
Merged-chr7-144170403-1	chr7	144170353	144170453	+	4.8	cIP2vsInput	"intron (NR_037302, intron 1 of 5)"	ID_B1|SINE|B4	-5117	NM_001113373	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding	0.02	0.514851
Merged-chr11-78550720-2	chr11	78550651	78550790	+	4.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133706)	promoter-TSS (NM_133706)	15	NM_133706	69071	Mm.29431	NM_133706	ENSMUSG00000037278	Tmem97	1810014L12Rik|AI115531|AL022956|D11Bhm182e	transmembrane protein 97	protein-coding	0.086331	0.628571
Merged-chr17-23803547-1	chr17	23803497	23803597	+	4.8	cIP2vsInput	"intron (NM_175229, intron 1 of 13)"	CpG	360	NM_175229	75956	Mm.436876	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding	0.14	0.762376
Merged-chr19-27217570-1	chr19	27217520	27217620	+	4.8	cIP2vsInput	"5' UTR (NM_001161420, exon 1 of 18)"	"5' UTR (NM_001161420, exon 1 of 18)"	550	NM_001161420	22359	Mm.4141	NM_001161420	ENSMUSG00000024924	Vldlr	AA408956|AI451093|AW047288	very low density lipoprotein receptor	protein-coding	0.12	0.663366
Merged-chr5-92137894-1	chr5	92137844	92137944	+	4.8	cIP1vsInput	promoter-TSS (NM_019490)	promoter-TSS (NM_019490)	-44	NM_019490	56041	Mm.15868	NM_019490	ENSMUSG00000029407	Uso1	115kDa|TAP|Vdp	USO1 vesicle docking factor	protein-coding	0.14	0.70297
Merged-chr5-15508651-1	chr5	15508601	15508701	+	4.8	cIP1vsInput	Intergenic	Intergenic	-110448	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0.02	0.415842
Merged-chr15-9222644-1	chr15	9222594	9222694	+	4.8	cIP1vsInput	Intergenic	RLTR45-int|LTR|ERVK	-57185	NM_207216	105887	Mm.482274	NM_207216	ENSMUSG00000072664	Ugt3a1	AI746432	"UDP glycosyltransferases 3 family, polypeptide A1"	protein-coding	0.02	0.277228
Merged-chr11-49203588-1	chr11	49203538	49203638	+	4.8	cIP2vsInput	promoter-TSS (NM_009562)	promoter-TSS (NM_009562)	88	NM_009562	22720	Mm.16650	NM_001024846	ENSMUSG00000046311	Zfp62	-	zinc finger protein 62	protein-coding	0.11	0.752475
Merged-chr9-120869563-2	chr9	120869505	120869621	+	4.8	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	45687	NR_040742	76402	Mm.436588	NR_040742		1700020M21Rik	-	RIKEN cDNA 1700020M21 gene	miscRNA	0.025862	0.521368
Merged-chr12-31654769-1	chr12	31654719	31654819	+	4.8	cIP2vsInput	promoter-TSS (NM_028002)	promoter-TSS (NM_028002)	57	NM_028002	71916	Mm.62979	NM_028002	ENSMUSG00000020648	Dus4l	2310069P03Rik|2700089B10Rik|AI482040|Pp35	dihydrouridine synthase 4-like (S. cerevisiae)	protein-coding	0.08	0.633663
Merged-chr4-150855456-1	chr4	150855406	150855506	+	4.8	cIP2vsInput	promoter-TSS (NR_040649)	promoter-TSS (NR_040649)	365	NM_133753	74155	Mm.318841	NM_133753	ENSMUSG00000028967	Errfi1	1300002F13Rik|AI788755|Mig-6|Mig6|RALT	ERBB receptor feedback inhibitor 1	protein-coding	0.15	0.762376
Merged-chr1-161034881-2	chr1	161034820	161034943	+	4.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_002840)	promoter-TSS (NR_002840)	-285	NR_002840	14455	Mm.486180	NR_002840	ENSMUSG00000053332	Gas5	Gas-5	growth arrest specific 5	miscRNA	0.073171	0.693548
Merged-chr17-12992688-2	chr17	12992638	12992738	+	4.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001113533)	promoter-TSS (NM_001113533)	-149	NM_175394	60532	Mm.275521	NM_001113532	ENSMUSG00000060475	Wtap	2810408K05Rik|9430038B09Rik	Wilms' tumour 1-associating protein	protein-coding	0.1	0.613861
Merged-chr8-19979985-1	chr8	19979935	19980035	+	4.8	cIP2vsInput	"intron (NM_001270553, intron 6 of 9).2"	CpG	250409	NM_001039553	626415	Mm.425517	NM_001039553		4930467E23Rik	ENSMUSG00000074453|OTTMUSG00000018948|TSAP	RIKEN cDNA 4930467E23 gene	protein-coding	0.08	0.693069
Merged-chr3-88410484-1	chr3	88410434	88410534	+	4.8	cIP2vsInput	promoter-TSS (NM_025928)	promoter-TSS (NM_025928)	-168	NM_025928	67037	Mm.36715	NM_025928	ENSMUSG00000028066	Pmf1	2600009M07Rik|AL033286|AW060657	polyamine-modulated factor 1	protein-coding	0.01	0.465347
Merged-chr10-13967020-1	chr10	13966970	13967070	+	4.8	cIP2vsInput	"intron (NM_010437, intron 1 of 8)"	CpG-904	641	NM_010437	15273	Mm.484135	NM_010437	ENSMUSG00000015501	Hivep2	MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding	0.12	0.752475
Merged-chr5-143235170-2	chr5	143235112	143235228	+	4.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_177681)	promoter-TSS (NM_177681)	-38	NM_177681	231866	Mm.55211	NM_177681	ENSMUSG00000029587	Zfp12	C530015C18|Krox-7|Zfp-12|Znf12	zinc finger protein 12	protein-coding	0.112069	0.666667
Merged-chr14-63606270-2	chr14	63606213	63606327	+	4.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_173393)	promoter-TSS (NM_173393)	-260	NM_173393	219149	Mm.450437	NM_173393	ENSMUSG00000035067	Xkr6	BC024502|Xrg6	X Kell blood group precursor related family member 6 homolog	protein-coding	0.070175	0.765217
Merged-chr15-76607528-1	chr15	76607478	76607578	+	4.8	cIP2vsInput	promoter-TSS (NM_053193)	promoter-TSS (NM_053193)	63	NM_053193	94230	Mm.45141	NM_053193	ENSMUSG00000034022	Cpsf1	-	cleavage and polyadenylation specific factor 1	protein-coding	0.17	0.762376
Merged-chr6-113624001-1	chr6	113623951	113624051	+	4.8	cIP2vsInput	promoter-TSS (NM_009507)	promoter-TSS (NM_009507)	-20	NM_009507	22346	Mm.29407	NM_009507	ENSMUSG00000033933	Vhl	Vhlh	von Hippel-Lindau tumor suppressor	protein-coding	0.13	0.762376
Merged-chr5-30887969-2	chr5	30887905	30888033	+	4.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_174849)	promoter-TSS (NM_174849)	-883	NM_174849	231093	Mm.440364	NM_001048190	ENSMUSG00000029165	Agbl5	4930455N08|9430057O19Rik|CCP5	ATP/GTP binding protein-like 5	protein-coding	0.070312	0.565891
Merged-chr9-45906356-1	chr9	45906306	45906406	+	4.8	cIP2vsInput	promoter-TSS (NM_008794)	promoter-TSS (NM_008794)	-213	NM_008794	18554	Mm.283283	NM_008794	ENSMUSG00000035382	Pcsk7	AA959856|PC7|SPC7	proprotein convertase subtilisin/kexin type 7	protein-coding	0.12	0.821782
Merged-chr6-117879550-1	chr6	117879500	117879600	+	4.8	cIP2vsInput	Intergenic	CpG	16473	NM_001001792	22685	Mm.249661	NM_001001792	ENSMUSG00000042097	Zfp239	Mok-2|Mok2|Znf239	zinc finger protein 239	protein-coding	0.15	0.722772
Merged-chr3-87114997-2	chr3	87114934	87115061	+	4.8	cIP1vsInput|cIP2vsInput	"intron (NM_001170985, intron 2 of 15)"	"intron (NM_001170985, intron 2 of 15)"	59750	NM_001170985	170643	Mm.89552	NM_001170985	ENSMUSG00000041734	Kirrel	6720469N11Rik|Kirrel1|Neph1	kin of IRRE like (Drosophila)	protein-coding	0.023622	0.601562
Merged-chr16-91647670-1	chr16	91647620	91647720	+	4.8	cIP2vsInput	promoter-TSS (NM_010256)	promoter-TSS (NM_010256)	-154	NM_019973	20658	Mm.328698	NM_019973	ENSMUSG00000022961	Son	2900011L12Rik|AA409051|AU067731|C81487|mKIAA1019|nrebp	Son DNA binding protein	protein-coding	0.13	0.653465
Merged-chr16-30185125-2	chr16	30185060	30185190	+	4.8	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	82407	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	"carboxypeptidase N, polypeptide 2"	protein-coding	0.046154	0.671756
Merged-chr6-8509811-1	chr6	8509761	8509861	+	4.8	cIP2vsInput	promoter-TSS (NR_040452)	promoter-TSS (NR_040452)	215	NM_133236	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding	0.18	0.811881
Merged-chr5-24383553-2	chr5	24383502	24383604	+	4.75	cIP1vsInput|cIP2vsInput	TTS (NM_001002897)	TTS (NM_001002897)	8590	NM_001002897	213948	Mm.332252	NM_001002897	ENSMUSG00000038295	Atg9b	Apg912|Apg9l2|Apgdc2|Gm574|Nos3as|eONE|sONE	autophagy related 9B	protein-coding	0.058824	0.601942
Merged-chr9-66713780-2	chr9	66713716	66713844	+	4.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178396)	promoter-TSS (NM_178396)	94	NM_178396	76459	Mm.277921	NM_178396	ENSMUSG00000032373	Car12	2310047E01Rik|AI314958|Ca12	carbonic anyhydrase 12	protein-coding	0.070312	0.635659
Merged-chr4-130663622-2	chr4	130663562	130663682	+	4.75	cIP1vsInput|cIP2vsInput	"intron (NM_001159604, intron 1 of 21)"	CpG	263	NM_001159603	80912	Mm.440206	NM_001159603	ENSMUSG00000028580	Pum1	AA517475|Pumm|mKIAA0099	pumilio 1 (Drosophila)	protein-coding	0.133333	0.702479
Merged-chr1-82724844-2	chr1	82724791	82724898	+	4.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029409)	promoter-TSS (NM_029409)	-74	NM_029409	75734	Mm.396863	NM_029409	ENSMUSG00000026150	Mff	5230400G24Rik|AI314724	mitochondrial fission factor	protein-coding	0.084112	0.555556
Merged-chr6-140623571-2	chr6	140623494	140623649	+	4.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009637)	promoter-TSS (NM_009637)	-118	NM_001005605	11569	Mm.479349	NM_001005605	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding	0.187097	0.814103
Merged-chr17-48042203-2	chr17	48042137	48042270	+	4.75	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-3910	NM_029689	76651	Mm.76918	NM_029689	ENSMUSG00000094928	1700122O11Rik	-	RIKEN cDNA 1700122O11 gene	protein-coding	0.075188	0.559701
Merged-chr10-111473165-2	chr10	111473090	111473241	+	4.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_015781)	promoter-TSS (NM_015781)	-27	NM_015781	53605	Mm.290407	NM_001146707	ENSMUSG00000058799	Nap1l1	AA407126|AI256722|D10Ertd68e|NAP-1	nucleosome assembly protein 1-like 1	protein-coding	0.10596	0.644737
Merged-chr4-134396105-2	chr4	134396030	134396180	+	4.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133880)	promoter-TSS (NM_133880)	-255	NM_133880	100163	Mm.22116	NM_133880	ENSMUSG00000037366	Pafah2	2310074E22Rik|AI507170	platelet-activating factor acetylhydrolase 2	protein-coding	0.08	0.589404
Merged-chr7-73558490-2	chr7	73558419	73558561	+	4.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_037569)	promoter-TSS (NR_037569)	-95	NR_037569	69170	Mm.34955	NR_037569		1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	miscRNA	0.091549	0.727273
Merged-chr19-3282994-2	chr19	3282943	3283046	+	4.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172252)	promoter-TSS (NM_172252)	16	NM_009212	20589	Mm.3179	NM_009212		Ighmbp2	AEP|Catf1|RIPE3b1|Smbp-2|Smbp2|Smubp2|nmd|sma	immunoglobulin mu binding protein 2	protein-coding	0.048544	0.567308
Merged-chr8-20145647-2	chr8	20145596	20145699	+	4.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	151785	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo	0.019417	0.432692
Merged-chr5-64092895-2	chr5	64092843	64092947	+	4.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025700)	promoter-TSS (NM_025700)	-55	NM_025700	66681	Mm.2325	NM_025700	ENSMUSG00000029171	Pgm1	3230402E02Rik|Pgm-1|Pgm2	phosphoglucomutase 1	protein-coding	0.076923	0.67619
Merged-chr9-21037745-2	chr9	21037679	21037812	+	4.75	cIP1vsInput|cIP2vsInput	"exon (NM_008319, exon 10 of 11)"	"exon (NM_008319, exon 10 of 11)"	-5417	NR_035438	100316681		NR_035438	ENSMUSG00000084663	Mir1900	Mirn1900|mmu-mir-1900	microRNA 1900	miscRNA	0.090226	0.671642
Merged-chr11-11948488-2	chr11	11948435	11948541	+	4.75	cIP1vsInput|cIP2vsInput	"intron (NM_001177629, intron 5 of 15)"	"intron (NM_001177629, intron 5 of 15)"	-50344	NM_001190448	13195	Mm.12906	NM_001190448	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding	0.037736	0.654206
Merged-chr2-151741352-2	chr2	151741292	151741412	+	4.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_212446)	promoter-TSS (NM_212446)	-59	NM_212446	228769	Mm.146984	NM_144889	ENSMUSG00000032869	Psmf1	AW048666|BC012260|PI31	"proteasome (prosome, macropain) inhibitor subunit 1"	protein-coding	0.091667	0.553719
Merged-chr19-11912418-2	chr19	11912367	11912469	+	4.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172635)	promoter-TSS (NM_172635)	19	NM_172635	225929	Mm.42711	NM_172635	ENSMUSG00000046139	Patl1	AV312086|D430024J04|Pat1b	protein associated with topoisomerase II homolog 1 (yeast)	protein-coding	0.196078	0.84466
Merged-chr5-14903561-2	chr5	14903503	14903620	+	4.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	11328	NM_198666	381714	Mm.368256	NM_198666	ENSMUSG00000033219	Gm9758	ENSMUSG00000033219	predicted gene 9758	protein-coding	0.025641	0.364407
Merged-chr7-73606983-2	chr7	73606903	73607063	+	4.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-48588	NR_037569	69170	Mm.34955	NR_037569		1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	miscRNA	0.1125	0.670807
Merged-chr8-3279634-2	chr8	3279581	3279687	+	4.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010568)	promoter-TSS (NM_010568)	-17	NM_010568	16337	Mm.268003	NM_010568		Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding	0.075472	0.691589
Merged-chr8-19910993-2	chr8	19910930	19911057	+	4.75	cIP1vsInput|cIP2vsInput	"intron (NM_001270553, intron 6 of 9).2"	L1Md_F3|LINE|L1	181417	NM_001039553	626415	Mm.425517	NM_001039553		4930467E23Rik	ENSMUSG00000074453|OTTMUSG00000018948|TSAP	RIKEN cDNA 4930467E23 gene	protein-coding	0.007874	0.34375
Merged-chr13-23446866-2	chr13	23446815	23446918	+	4.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-15849	NR_015492	320842	Mm.487476	NR_015492	ENSMUSG00000085024	C230035I16Rik	-	RIKEN cDNA C230035I16 gene	miscRNA	0.058252	0.5
Merged-chr2-33754068-2	chr2	33754008	33754128	+	4.75	cIP1vsInput|cIP2vsInput	"intron (NM_175184, intron 8 of 9)"	"intron (NM_175184, intron 8 of 9)"	-51748	NR_045729	320482	Mm.442057	NR_045729	ENSMUSG00000086484	Nron	A630071L07Rik|Gm24353	"non-protein coding RNA, repressor of NFAT"	miscRNA	0.033333	0.545455
Merged-chr18-80655758-2	chr18	80655708	80655808	+	4.75	cIP1vsInput|cIP2vsInput	"intron (NM_198429, intron 6 of 9)"	"intron (NM_198429, intron 6 of 9)"	52415	NM_001164111	18018	Mm.329560	NM_001164109	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	"nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1"	protein-coding	0.01	0.435644
Merged-chr5-65764042-1	chr5	65763992	65764092	+	4.7	cIP2vsInput	"intron (NM_001024917, intron 1 of 19)"	CpG	521	NM_001024917	333789	Mm.393231	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding	0.15	0.762376
Merged-chr9-25252177-1	chr9	25252127	25252227	+	4.7	cIP2vsInput	promoter-TSS (NM_009859)	promoter-TSS (NM_009859)	-262	NM_009859	235072	Mm.270259	NM_001205367	ENSMUSG00000001833	7-Sep	Cdc10|E430034N22	septin 7	protein-coding	0.12	0.70297
Merged-chr4-45342041-1	chr4	45341991	45342091	+	4.7	cIP2vsInput	promoter-TSS (NM_153167)	promoter-TSS (NM_153167)	-60	NM_153167	242418	Mm.317668	NM_153167	ENSMUSG00000035572	Dcaf10	AA959934|Wdr32	DDB1 and CUL4 associated factor 10	protein-coding	0.13	0.722772
Merged-chr14-47634620-2	chr14	47634560	47634681	+	4.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-29136	NM_008477	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding	0.041322	0.540984
Merged-chr9-119982055-2	chr9	119981999	119982111	+	4.7	cIP1vsInput|cIP2vsInput	"intron (NM_153287, intron 1 of 4)"	"intron (NM_153287, intron 1 of 4)"	2603	NM_153287	215418	Mm.125196	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding	0.017857	0.59292
Merged-chr1-45795332-2	chr1	45795234	45795430	+	4.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028599)	promoter-TSS (NM_028599)	-169	NM_028599	73674	Mm.270376	NM_028599	ENSMUSG00000025995	Wdr75	1300003A18Rik|2410118I19Rik|C77608	WD repeat domain 75	protein-coding	0.05102	0.51269
Merged-chr9-72133275-2	chr9	72133223	72133327	+	4.7	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-21456	NM_001253865	21406	Mm.480117	NM_001253862	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding	0.163462	0.771429
Merged-chr17-25434376-2	chr17	25434316	25434437	+	4.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001163691)	promoter-TSS (NM_001163691)	-593	NM_001163691	58226	Mm.268378	NM_001163691	ENSMUSG00000024112	Cacna1h	Cav3.2|MNCb-1209|alpha13.2	"calcium channel, voltage-dependent, T type, alpha 1H subunit"	protein-coding	0.115702	0.688525
Merged-chr12-52503940-1	chr12	52503890	52503990	+	4.7	cIP2vsInput	Intergenic	CpG	-12137	NM_009706	11855	Mm.474991	NM_009706	ENSMUSG00000035133	Arhgap5	p190-B|p190B	Rho GTPase activating protein 5	protein-coding	0.18	0.811881
Merged-chr3-101110686-2	chr3	101110631	101110742	+	4.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011197)	promoter-TSS (NM_011197)	-520	NM_011197	19221	Mm.24807	NM_011197	ENSMUSG00000027864	Ptgfrn	4833445A08Rik|AU042434|CD9P-1|FPRP|Trim45	prostaglandin F2 receptor negative regulator	protein-coding	0.063063	0.607143
Merged-chr14-65344078-1	chr14	65344028	65344128	+	4.7	cIP2vsInput	Intergenic	CpG	-14598	NM_199029	380912	Mm.270087	NM_199029	ENSMUSG00000034522	Zfp395	BC053701|Gm910	zinc finger protein 395	protein-coding	0.09	0.712871
Merged-chr9-119322579-1	chr9	119322529	119322629	+	4.7	cIP2vsInput	promoter-TSS (NM_133985)	promoter-TSS (NM_133985)	-152	NM_133985	108737	Mm.293565	NM_133985	ENSMUSG00000036737	Oxsr1	2210022N24Rik|2810422B09Rik|AI462649|AW209236|Osr1|mKIAA1101	oxidative-stress responsive 1	protein-coding	0.06	0.534653
Merged-chr8-20117094-1	chr8	20117044	20117144	+	4.7	cIP1vsInput	Intergenic	Lx5|LINE|L1	180338	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo	0	0.405941
Merged-chr13-38635163-1	chr13	38635113	38635213	+	4.7	cIP2vsInput	promoter-TSS (NM_139063)	promoter-TSS (NM_139063)	-54	NM_139063	17828	Mm.261554	NM_139063	ENSMUSG00000038982	Bloc1s5	1810074A19Rik|Muted|mu	"biogenesis of organelles complex-1, subunit 5, muted"	protein-coding	0.1	0.623762
Merged-chr14-55386920-1	chr14	55386870	55386970	+	4.7	cIP1vsInput	Intergenic	Intergenic	-91838	NM_001037938	28200	Mm.27427	NM_001037938	ENSMUSG00000022210	Dhrs4	AI043103|AI790593|CR|D14Ucla2|NDRD|PHCR|PSCD|RRD|mouNRDR	dehydrogenase/reductase (SDR family) member 4	protein-coding	0.01	0.485149
Merged-chr4-129742549-2	chr4	129742489	129742609	+	4.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011317)	promoter-TSS (NM_011317)	-246	NM_011317	20218	Mm.489797	NM_011317	ENSMUSG00000028790	Khdrbs1	Sam68|p62|p68	"KH domain containing, RNA binding, signal transduction associated 1"	protein-coding	0.133333	0.743802
Merged-chr17-4908385-2	chr17	4908307	4908464	+	4.7	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-86689	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding	0.146497	0.759494
Merged-chr10-42278197-1	chr10	42278147	42278247	+	4.7	cIP2vsInput	Intergenic	CpG-1005	-1455	NM_019740	56484	Mm.466459	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding	0.15	0.792079
Merged-chr10-79854469-1	chr10	79854419	79854519	+	4.7	cIP2vsInput	promoter-TSS (NM_008956)	promoter-TSS (NM_008956)	-136	NM_001077363	19205	Mm.265610	NM_001077363	ENSMUSG00000006498	Ptbp1	AA407203|AL033359|HNRPI|PTB-1|PTB2|PTB3|PTB4|Ptb|pPTB	polypyrimidine tract binding protein 1	protein-coding	0.09	0.613861
Merged-chrY-7036270-1	chrY	7036220	7036320	+	4.7	cIP1vsInput	Intergenic	Intergenic	131507	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.316832
Merged-chrY-6797547-1	chrY	6797497	6797597	+	4.7	cIP1vsInput	Intergenic	Lx5b|LINE|L1	370230	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.29703
Merged-chr7-44548872-1	chr7	44548822	44548922	+	4.7	cIP1vsInput	promoter-TSS (NM_011131)	promoter-TSS (NM_011131)	-57	NM_011131	18971	Mm.16549	NM_011131	ENSMUSG00000038644	Pold1	125kDa	"polymerase (DNA directed), delta 1, catalytic subunit"	protein-coding	0.1	0.70297
Merged-chr8-107588518-1	chr8	107588468	107588568	+	4.7	cIP2vsInput	promoter-TSS (NM_010817)	promoter-TSS (NM_010817)	-36	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	"proteasome (prosome, macropain) 26S subunit, non-ATPase, 7"	protein-coding	0.09	0.633663
Merged-chr8-107293417-2	chr8	107293362	107293473	+	4.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133957)	promoter-TSS (NM_133957)	-53	NM_018823	54446	Mm.390057	NM_018823	ENSMUSG00000003847	Nfat5	AI225870|B130038B15Rik|CAG-8|CAG80|NFATL1|OREBP|TonEBP|mKIAA0827|nfatz	nuclear factor of activated T cells 5	protein-coding	0.135135	0.785714
Merged-chr6-40325457-1	chr6	40325407	40325507	+	4.7	cIP2vsInput	promoter-TSS (NM_023538)	promoter-TSS (NM_023538)	-21	NM_023538	69923	Mm.32840	NM_023538	ENSMUSG00000029916	Agk	2610037M15Rik|6720408I04Rik|AI465370|Mulk	acylglycerol kinase	protein-coding	0.08	0.633663
Merged-chr10-62651454-1	chr10	62651404	62651504	+	4.7	cIP2vsInput	promoter-TSS (NM_053183)	promoter-TSS (NM_053183)	-256	NM_053183	94213	Mm.114116	NM_053183	ENSMUSG00000020076	Ddx50	4933429B04Rik|8430408E17Rik|GU2|RH-II	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	protein-coding	0.1	0.70297
Merged-chr11-94928858-2	chr11	94928791	94928926	+	4.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-7412	NM_007742	12842	Mm.458212	NM_007742		Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	"collagen, type I, alpha 1"	protein-coding	0.037037	0.669118
Merged-chr14-63247985-1	chr14	63247935	63248035	+	4.7	cIP2vsInput	Intergenic	Intergenic	-2725	NM_008092	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding	0.03	0.574257
Merged-chr7-67951876-1	chr7	67951826	67951926	+	4.7	cIP2vsInput	promoter-TSS (NM_010513)	promoter-TSS (NM_010513)	-381	NM_010513	16001	Mm.275742	NM_010513		Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding	0.19	0.792079
Merged-chr11-105508100-2	chr11	105508047	105508154	+	4.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-51365	NM_001039242	632687	Mm.121570	NM_001039242	ENSMUSG00000078627	10-Mar	4933417C16Rik|AV039223|OTTMUSG00000002847|Rnf190	membrane-associated ring finger (C3HC4) 10	protein-coding	0	0.472222
Merged-chr9-69129497-1	chr9	69129447	69129547	+	4.7	cIP2vsInput	"intron (NM_013646, intron 1 of 10)"	MTE2a|LTR|ERVL-MaLR	-268501	NM_145618	93697	Mm.35911	NM_145618	ENSMUSG00000032235	Narg2	B230343B06Rik	NMDA receptor-regulated gene 2	protein-coding	0.01	0.50495
Merged-chr5-129887564-2	chr5	129887488	129887640	+	4.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_024166)	promoter-TSS (NM_024166)	-94	NM_024166	14004	Mm.299062	NM_024166	ENSMUSG00000070493	Chchd2	AL033347|Etohi6	coiled-coil-helix-coiled-coil-helix domain containing 2	protein-coding	0.026316	0.503268
Merged-chr11-103360436-2	chr11	103360382	103360490	+	4.7	cIP1vsInput|cIP2vsInput	"exon (NM_183288, exon 3 of 3)"	"exon (NM_183288, exon 3 of 3)"	3256	NM_183288	544817	Mm.399816	NM_001205236	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Sh3d20	Rho GTPase activating protein 27	protein-coding	0.157407	0.779817
Merged-chr17-26508183-1	chr17	26508133	26508233	+	4.7	cIP2vsInput	"exon (NM_013642, exon 1 of 4)"	"exon (NM_013642, exon 1 of 4)"	289	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding	0.13	0.673267
Merged-chr17-27555446-2	chr17	27555366	27555526	+	4.7	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-1128	NM_001166536	15361	Mm.440289	NM_001025427	ENSMUSG00000046711	Hmga1	AL023995|Hmga1a|Hmga1b|Hmgi|Hmgiy|Hmgy	high mobility group AT-hook 1	protein-coding	0.11875	0.801242
Merged-chr7-45129036-2	chr7	45128983	45129090	+	4.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009438)	promoter-TSS (NM_009438)	-291	NM_009438	22121	Mm.180458	NM_009438	ENSMUSG00000074129	Rpl13a	1810026N22Rik|Tstap198-7|tum-antigen	ribosomal protein L13A	protein-coding	0.065421	0.583333
Merged-chr7-65393972-2	chr7	65393908	65394036	+	4.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-22728	NM_009386	21872	Mm.4342	NM_001163574	ENSMUSG00000030516	Tjp1	ZO1	tight junction protein 1	protein-coding	0.046875	0.503876
Merged-chr11-54882844-2	chr11	54882774	54882914	+	4.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	16406	NM_008248	15254	Mm.425	NM_008248	ENSMUSG00000020267	Hint1	AA673479|Hint|Ipk1|PKCI-1|PRKCNH1	histidine triad nucleotide binding protein 1	protein-coding	0.014286	0.574468
Merged-chr3-130818885-1	chr3	130818835	130818935	+	4.7	cIP2vsInput	Intergenic	Intergenic	-88556	NM_001199350	619547	Mm.391636	NM_001199350		Rpl34-ps1	EG619547|ENSMUSG00000068396|Gm10239	"ribosomal protein L34, pseudogene 1"	protein-coding	0.09	0.653465
Merged-chr5-73192106-2	chr5	73192033	73192179	+	4.7	cIP1vsInput|cIP2vsInput	"intron (NM_028194, intron 3 of 62)"	"intron (NM_028194, intron 3 of 62)"	64512	NM_028194	72313		NM_177136	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	furry homolog-like (Drosophila)	protein-coding	0.020548	0.442177
Merged-chr4-133756909-1	chr4	133756859	133756959	+	4.7	cIP2vsInput	Intergenic	CpG	-3298	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding	0.12	0.742574
Merged-chr14-20083051-1	chr14	20083001	20083101	+	4.7	cIP2vsInput	"exon (NM_026209, exon 1 of 2)"	"exon (NM_026209, exon 1 of 2)"	121	NM_026209	67509	Mm.292423	NM_026209	ENSMUSG00000045107	Saysd1	1810063B07Rik|4930488P03Rik	SAYSVFN motif domain containing 1	protein-coding	0.09	0.663366
Merged-chr5-129294688-2	chr5	129294630	129294746	+	4.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	197938	NM_001081342	243277	Mm.440501	NM_001081342	ENSMUSG00000044017	Gpr133	E230012M21Rik	G protein-coupled receptor 133	protein-coding	0	0.358974
Merged-chr19-57611026-1	chr19	57610976	57611076	+	4.7	cIP2vsInput	promoter-TSS (NM_181415)	promoter-TSS (NM_181415)	-8	NM_181415	226255	Mm.245340	NM_181415	ENSMUSG00000054843	Atrnl1	AI504415|AW555641|Alp|Atrnl|Atrnlp	attractin like 1	protein-coding	0.16	0.841584
Merged-chr1-178187379-2	chr1	178187310	178187449	+	4.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_024282)	promoter-TSS (NM_024282)	-38	NM_024282	78825	Mm.440132	NM_024282	ENSMUSG00000026502	Desi2	5830417C01Rik|DeSI-2|Fam152a|Pppde1	desumoylating isopeptidase 2	protein-coding	0.035971	0.514286
Merged-chr13-57983610-2	chr13	57983558	57983662	+	4.65	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	39590	NR_030544	100124491		NR_030544		Mir874	Mirn874|mmu-mir-874	microRNA 874	miscRNA	0.038462	0.552381
Merged-chr7-5015668-2	chr7	5015607	5015729	+	4.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001110329)	promoter-TSS (NM_001110329)	160	NM_025324	66056	Mm.19974	NM_025324	ENSMUSG00000051184	Zfp524	0610012F07Rik|2300009P13Rik|Znf524	zinc finger protein 524	protein-coding	0.163934	0.731707
Merged-chr3-103809507-2	chr3	103809423	103809592	+	4.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026193)	promoter-TSS (NM_026193)	-10	NM_001163552	67489	Mm.197568	NM_001163552	ENSMUSG00000032952	Ap4b1	1810038H16Rik|AV004952|Ap4b4	"adaptor-related protein complex AP-4, beta 1"	protein-coding	0.12426	0.752941
Merged-chr9-57765293-2	chr9	57765225	57765361	+	4.65	cIP1vsInput|cIP2vsInput	"exon (NM_007713, exon 1 of 13)"	"exon (NM_007713, exon 1 of 13)"	567	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding	0.088235	0.729927
Merged-chr7-100371885-2	chr7	100371833	100371937	+	4.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028292)	promoter-TSS (NM_028292)	11	NM_028292	72590	Mm.490280	NM_028292	ENSMUSG00000030718	Ppme1	1110069N17Rik|2700017M01Rik|PME-1|Pme1	protein phosphatase methylesterase 1	protein-coding	0.096154	0.609524
Merged-chr2-152414937-2	chr2	152414886	152414988	+	4.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_177656)	promoter-TSS (NM_177656)	107	NM_175126	67917	Mm.391810	NM_175126	ENSMUSG00000074682	Zcchc3	2810406K24Rik	"zinc finger, CCHC domain containing 3"	protein-coding	0.137255	0.679612
Merged-chr4-145195042-2	chr4	145194991	145195093	+	4.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001276465)	promoter-TSS (NM_001276465)	-37	NM_001276465	230895	Mm.476856	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13 D (yeast)	protein-coding	0.098039	0.650485
Merged-chr17-23673785-2	chr17	23673693	23673878	+	4.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001008425)	promoter-TSS (NM_001008425)	-15	NM_001008425	386612	Mm.328831	NM_001008425	ENSMUSG00000041319	Thoc6	F830014G06Rik|Wdr58	THO complex 6 homolog (Drosophila)	protein-coding	0.081081	0.580645
Merged-chr2-164912350-2	chr2	164912296	164912405	+	4.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_199027)	promoter-TSS (NM_199027)	-600	NM_199027	329559	Mm.330776	NM_199027	ENSMUSG00000039834	Zfp335	1810045J01Rik|NIF-1|Nif1|Znf335	zinc finger protein 335	protein-coding	0.06422	0.554545
Merged-chr2-152754514-2	chr2	152754462	152754567	+	4.65	cIP1vsInput|cIP2vsInput	"intron (NM_053091, intron 1 of 4)"	"intron (NM_053091, intron 1 of 4)"	341	NM_053091	84682	Mm.196668	NM_053091	ENSMUSG00000009876	Cox4i2	Cox4b|CoxIV-2	cytochrome c oxidase subunit IV isoform 2	protein-coding	0.066667	0.641509
Merged-chr2-174076247-2	chr2	174076185	174076309	+	4.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172675)	promoter-TSS (NM_172675)	-804	NM_172675	228960	Mm.277977	NM_001102423	ENSMUSG00000027522	Stx16	4930401D03|5430410K23Rik|6330500A18Rik|AI648908|AW553605|Syn16	syntaxin 16	protein-coding	0.080645	0.656
Merged-chr17-91092888-2	chr17	91092834	91092942	+	4.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_177284)	promoter-TSS (NM_177284)	-86	NM_020252	18189	Mm.312068	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0.074074	0.651376
Merged-chr5-15689850-2	chr5	15689800	15689900	+	4.65	cIP1vsInput|cIP2vsInput	"intron (NR_001585, intron 1 of 4)"	"intron (NR_001585, intron 1 of 4)"	9140	NR_001585	75858	Mm.359463	NR_001585	ENSMUSG00000089871	Speer7-ps1	4930568L21Rik|SPEER-7|Speer7-ps	"spermatogenesis associated glutamate (E)-rich protein 7, pseudogene 1"	pseudo	0	0.217822
Merged-chr14-55884751-2	chr14	55884661	55884842	+	4.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027143)	promoter-TSS (NM_027143)	-218	NM_027143	219094	Mm.37592	NM_027143	ENSMUSG00000047153	Khnyn	6330555F21|9130227C08Rik|AI605259|Kiaa0323|mKIAA0323	KH and NYN domain containing	protein-coding	0.033149	0.598901
Merged-chr10-80387794-2	chr10	80387738	80387851	+	4.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_198615)	promoter-TSS (NM_198615)	-143	NM_198615	237400	Mm.268389	NM_198615	ENSMUSG00000048696	Mex3d	BC059858|Rkhd1	mex3 homolog D (C. elegans)	protein-coding	0.123894	0.798246
Merged-chr9-48985056-2	chr9	48984991	48985122	+	4.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175482)	promoter-TSS (NM_175482)	-329	NM_175482	235323	Mm.21630	NM_175482	ENSMUSG00000032267	Usp28	9830148O20Rik|AU022237|mKIAA1515	ubiquitin specific peptidase 28	protein-coding	0.137405	0.727273
Merged-chr5-146221052-2	chr5	146220978	146221127	+	4.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001256085)	promoter-TSS (NM_001256085)	-81	NM_001256085	74132	Mm.26696	NM_001256085	ENSMUSG00000029634	Rnf6	1200013I08Rik|5730419H05Rik|AA537053	ring finger protein (C3H2C3 type) 6	protein-coding	0.053691	0.566667
Merged-chr9-106789226-2	chr9	106789173	106789280	+	4.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_030730)	promoter-TSS (NM_030730)	-13	NM_030730	81000	Mm.246689	NM_030730	ENSMUSG00000040661	Rad54l2	Arip4|D130058C05|G630026H09Rik|Srisnf2l	RAD54 like 2 (S. cerevisiae)	protein-coding	0.102804	0.703704
Merged-chr10-76684207-2	chr10	76684151	76684264	+	4.65	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	41837	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	"collagen, type VI, alpha 1"	protein-coding	0.053097	0.517544
Merged-chr13-115021525-1	chr13	115021475	115021575	+	4.6	cIP2vsInput	"intron (NM_001033228, intron 6 of 28)"	"intron (NM_001033228, intron 6 of 28)"	68633	NM_134058	105083	Mm.486295	NM_134058	ENSMUSG00000042275	Pelo	AA409897|AI852218	pelota homolog (Drosophila)	protein-coding	0.03	0.465347
Merged-chr19-6910035-2	chr19	6909966	6910104	+	4.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_012021)	promoter-TSS (NM_012021)	337	NM_026306	67674	Mm.371597	NM_001166370	ENSMUSG00000038812	Trmt112	0610038D11Rik|Trm112p	tRNA methyltransferase 11-2	protein-coding	0.086957	0.618705
Merged-chr4-156197788-1	chr4	156197738	156197838	+	4.6	cIP2vsInput	promoter-TSS (NM_021604)	promoter-TSS (NM_021604)	-300	NM_021604	11603	Mm.273098	NM_021604	ENSMUSG00000041936	Agrn	Agrin|nmf380	agrin	protein-coding	0.09	0.762376
Merged-chr7-111082746-1	chr7	111082696	111082796	+	4.6	cIP1vsInput	"intron (NM_001040131, intron 1 of 20)"	CpG	284	NM_001040131	13690	Mm.185453	NM_001040131	ENSMUSG00000005610	Eif4g2	AA589388|DAP-5|E130105L11Rik|Nat1|Natm1|p97	"eukaryotic translation initiation factor 4, gamma 2"	protein-coding	0.11	0.653465
Merged-chr5-93206727-1	chr5	93206677	93206777	+	4.6	cIP2vsInput	promoter-TSS (NM_017367)	promoter-TSS (NM_017367)	209	NM_029363	75610	Mm.175502	NM_029363	ENSMUSG00000029384	2010109A12Rik	-	RIKEN cDNA 2010109A12 gene	protein-coding	0.09	0.574257
Merged-chr4-41314888-1	chr4	41314838	41314938	+	4.6	cIP2vsInput	promoter-TSS (NM_026893)	promoter-TSS (NM_026893)	13	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding	0.11	0.70297
Merged-chr5-135186828-1	chr5	135186778	135186878	+	4.6	cIP2vsInput	promoter-TSS (NM_011714)	promoter-TSS (NM_011714)	-495	NM_011714	22385	Mm.40331	NM_011714	ENSMUSG00000002748	Baz1b	C87820|WSTF|Wbscr9	"bromodomain adjacent to zinc finger domain, 1B"	protein-coding	0.13	0.752475
Merged-chr2-30658472-1	chr2	30658422	30658522	+	4.6	cIP2vsInput	Intergenic	CpG	-62738	NR_037272	100526499		NR_037272	ENSMUSG00000093091	Mir3089	mmu-mir-3089	microRNA 3089	miscRNA	0.14	0.782178
Merged-chr8-22593888-2	chr8	22593836	22593940	+	4.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001198998)	promoter-TSS (NM_001198998)	-75	NM_011696	22335	Mm.227704	NM_001198998	ENSMUSG00000008892	Vdac3	-	voltage-dependent anion channel 3	protein-coding	0.163462	0.8
Merged-chr19-55743345-1	chr19	55743295	55743395	+	4.6	cIP1vsInput	"intron (NM_001142921, intron 3 of 11)"	"intron (NM_001142921, intron 3 of 11)"	1535	NM_001142923	21416	Mm.139815	NM_001142918	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4|mTcf-4B|mTcf-4E	"transcription factor 7 like 2, T cell specific, HMG box"	protein-coding	0.05	0.514851
Merged-chr9-56418703-2	chr9	56418619	56418788	+	4.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025812)	promoter-TSS (NM_025812)	-143	NM_025812	66867	Mm.150856	NM_025812	ENSMUSG00000032329	Hmg20a	1200004E06Rik|5730490E10Rik|Hmgxb1|Ibraf	high mobility group 20A	protein-coding	0.035503	0.394118
Merged-chr1-86442176-1	chr1	86442126	86442226	+	4.6	cIP2vsInput	Intergenic	CpG	15847	NM_027966	71863	Mm.179627	NM_027966	ENSMUSG00000036574	1700019O17Rik	-	RIKEN cDNA 1700019O17 gene	protein-coding	0.07	0.60396
Merged-chrY-6683691-1	chrY	6683641	6683741	+	4.6	cIP1vsInput	Intergenic	Intergenic	484086	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.336634
Merged-chr15-33083282-1	chr15	33083232	33083332	+	4.6	cIP2vsInput	"5' UTR (NM_176073, exon 1 of 8)"	"5' UTR (NM_176073, exon 1 of 8)"	153	NM_176073	54381	Mm.158251	NM_018755	ENSMUSG00000039007	Cpq	1190003P12Rik|2610034C17Rik|Hls2|Lal-1|Pgcp	carboxypeptidase Q	protein-coding	0.07	0.683168
Merged-chr11-86993978-2	chr11	86993919	86994037	+	4.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001005341)	promoter-TSS (NM_001005341)	-216	NM_001005341	77864	Mm.191894	NM_001005341	ENSMUSG00000018427	Ypel2	6430570G24|E130113K08Rik	yippee-like 2 (Drosophila)	protein-coding	0.076271	0.722689
Merged-chrY-6790615-1	chrY	6790565	6790665	+	4.6	cIP1vsInput	Intergenic	MT2A|LTR|ERVL	377162	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.376238
Merged-chr8-128685627-1	chr8	128685577	128685677	+	4.6	cIP2vsInput	promoter-TSS (NM_010578)	promoter-TSS (NM_010578)	-27	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding	0.1	0.673267
Merged-chr1-133661054-1	chr1	133661004	133661104	+	4.6	cIP2vsInput	promoter-TSS (NM_001166552)	promoter-TSS (NM_001166552)	-169	NM_001166552	667118	Mm.245357	NM_001166552		Zbed6	Gm8466|MGR	"zinc finger, BED domain containing 6"	protein-coding	0.08	0.742574
Merged-chr3-32736860-1	chr3	32736810	32736910	+	4.6	cIP1vsInput	promoter-TSS (NM_025316)	promoter-TSS (NM_025316)	-105	NM_029017	74600	Mm.288960	NM_029017		Mrpl47	4833424P18Rik|CGI-204|ENSMUSG00000051761|Gm9859|L47mt|MRP-L47|MTF/L47|NCM1	mitochondrial ribosomal protein L47	protein-coding	0.03	0.534653
Merged-chr4-141426073-1	chr4	141426023	141426123	+	4.6	cIP2vsInput	TTS (NM_013868)	TTS (NM_013868)	5294	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	"heat shock protein family, member 7 (cardiovascular)"	protein-coding	0.04	0.643564
Merged-chr7-25249662-1	chr7	25249612	25249712	+	4.6	cIP2vsInput	"intron (NM_010155, intron 1 of 3)"	CpG	1096	NM_010155	13875	Mm.8068	NM_010155	ENSMUSG00000040857	Erf	-	Ets2 repressor factor	protein-coding	0.1	0.752475
Merged-chr8-81015673-1	chr8	81015623	81015723	+	4.6	cIP2vsInput	promoter-TSS (NM_027554)	promoter-TSS (NM_027554)	-767	NM_027554	74841	Mm.246018	NM_027554	ENSMUSG00000038250	Usp38	4631402N15Rik|4833420O05Rik|AA536967|AU044701|AW544820|mKIAA1891	ubiquitin specific peptidase 38	protein-coding	0.03	0.356436
Merged-chr19-7268227-1	chr19	7268177	7268277	+	4.6	cIP2vsInput	Intergenic	Intergenic	-1537	NM_054048	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding	0.04	0.70297
Merged-chr3-95658902-1	chr3	95658852	95658952	+	4.6	cIP2vsInput	"exon (NM_008562, exon 1 of 3)"	"exon (NM_008562, exon 1 of 3)"	181	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding	0.16	0.722772
Merged-chr13-9276444-1	chr13	9276394	9276494	+	4.6	cIP2vsInput	promoter-TSS (NM_001081426)	promoter-TSS (NM_001081426)	-81	NM_001081426	208440	Mm.217326	NM_172459	ENSMUSG00000048264	Dip2c	2900024P20Rik|9630044M06|mKIAA0934	DIP2 disco-interacting protein 2 homolog C (Drosophila)	protein-coding	0.18	0.772277
Merged-chr1-4857717-1	chr1	4857667	4857767	+	4.6	cIP2vsInput	promoter-TSS (NM_001159751)	promoter-TSS (NM_001159751)	23	NM_011541	21399	Mm.207263	NM_001159750	ENSMUSG00000033813	Tcea1	S-II	transcription elongation factor A (SII) 1	protein-coding	0.11	0.613861
Merged-chr1-86587098-1	chr1	86587048	86587148	+	4.6	cIP2vsInput	promoter-TSS (NM_172974)	promoter-TSS (NM_172974)	-2	NM_172974	26895	Mm.12973	NM_172974	ENSMUSG00000026240	Cops7b	D1Wsu66e|E130114M23	"COP9 (constitutive photomorphogenic) homolog, subunit 7b (Arabidopsis thaliana)"	protein-coding	0.09	0.643564
Merged-chr13-59557393-2	chr13	59557307	59557479	+	4.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_023328)	promoter-TSS (NM_023328)	-74	NM_023328	67269	Mm.153008	NM_001048008	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|BB114605|CCP1|Nna1|mKIAA1035|nmf243|pcd	ATP/GTP binding protein 1	protein-coding	0.156977	0.797688
Merged-chr5-149831584-2	chr5	149831511	149831658	+	4.6	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-16163	NR_045758	70969	Mm.410799	NR_045758		4930500F04Rik	4931407C17Rik	RIKEN cDNA 4930500F04 gene	miscRNA	0.061224	0.52027
Merged-chr7-132852574-1	chr7	132852524	132852624	+	4.6	cIP2vsInput	promoter-TSS (NM_028095)	promoter-TSS (NM_028095)	73	NM_028095	72096	Mm.28631	NM_028095	ENSMUSG00000030960	Mettl10	2010208K18Rik	methyltransferase like 10	protein-coding	0.12	0.663366
Merged-chr8-125012979-2	chr8	125012920	125013038	+	4.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_016909)	promoter-TSS (NM_016909)	-18	NM_016909	53424	Mm.458292	NM_016909	ENSMUSG00000056820	Tsnax	R74833|Trax	translin-associated factor X	protein-coding	0.152542	0.781513
Merged-chr14-46822248-1	chr14	46822198	46822298	+	4.6	cIP2vsInput	promoter-TSS (NM_022023)	promoter-TSS (NM_022023)	-6	NM_022023	63985	Mm.87312	NM_022023	ENSMUSG00000062014	Gmfb	3110001H22Rik|3110001O16Rik|AI851627|C79176|D14Ertd630e	"glia maturation factor, beta"	protein-coding	0.14	0.712871
Merged-chr17-10474302-1	chr17	10474252	10474352	+	4.6	cIP2vsInput	TTS (NR_077238)	TTS (NR_077238)	18086	NR_077238	319750	Mm.383485	XR_105827	ENSMUSG00000089633	A230009B12Rik	-	RIKEN cDNA A230009B12 gene	miscRNA	0.02	0.524752
Merged-chr15-79547090-1	chr15	79547040	79547140	+	4.6	cIP2vsInput	promoter-TSS (NM_199079)	promoter-TSS (NM_199079)	-349	NM_199080	67040	Mm.298199	NM_001040187	ENSMUSG00000055065	Ddx17	2610007K22Rik|A430025E01Rik|AI047725|C80929|Gm926|p72	DEAD (Asp-Glu-Ala-Asp) box polypeptide 17	protein-coding	0.12	0.653465
Merged-chr2-181287768-2	chr2	181287716	181287821	+	4.6	cIP1vsInput|cIP2vsInput	"intron (NM_198169, intron 1 of 9)"	CpG	198	NM_198169	229004	Mm.220423	NM_198169	ENSMUSG00000038705	Gmeb2	AI839884	glucocorticoid modulatory element binding protein 2	protein-coding	0.161905	0.820755
Merged-chr5-15528461-1	chr5	15528411	15528511	+	4.6	cIP1vsInput	Intergenic	Intergenic	-90638	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0	0.455446
Merged-chr4-149166573-2	chr4	149166517	149166630	+	4.6	cIP1vsInput|cIP2vsInput	"intron (NM_001081274, intron 1 of 12)"	CpG	134	NM_001081274	110208	Mm.252080	NM_001081274	ENSMUSG00000028961	Pgd	0610042A05Rik|AU019875|C78335	phosphogluconate dehydrogenase	protein-coding	0.097345	0.675439
Merged-chr5-25529808-2	chr5	25529756	25529860	+	4.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_027388)	promoter-TSS (NR_027388)	-210	NR_027388	73571	Mm.105263	NR_027388		1700096K18Rik	-	RIKEN cDNA 1700096K18 gene	miscRNA	0.067308	0.685714
Merged-chr5-130364013-1	chr5	130363963	130364063	+	4.6	cIP2vsInput	Intergenic	Intergenic	-5445	NM_181045	140904	Mm.320206	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8	calneuron 1	protein-coding	0.02	0.465347
Merged-chr7-4866136-2	chr7	4866081	4866192	+	4.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026158)	promoter-TSS (NM_026158)	43	NM_026158	67441	Mm.41385	NM_026158	ENSMUSG00000052605	Isoc2b	0610042E07Rik|AI553388|Isoc2	isochorismatase domain containing 2b	protein-coding	0.063063	0.589286
Merged-chr10-95514847-2	chr10	95514792	95514903	+	4.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_080560)	promoter-TSS (NM_080560)	-315	NM_080560	93765	Mm.486592	NM_080560	ENSMUSG00000074781	Ube2n	1500026J17Rik|AL022654|BB101821|UBC13	ubiquitin-conjugating enzyme E2N	protein-coding	0.162162	0.732143
Merged-chr5-14989238-1	chr5	14989188	14989288	+	4.6	cIP2vsInput	Intergenic	Intergenic	43769	NM_182957	66773	Mm.368256	NM_182957	ENSMUSG00000091897	Gm17019	-	predicted gene 17019	protein-coding	0.01	0.356436
Merged-chr15-58888833-1	chr15	58888783	58888883	+	4.6	cIP2vsInput	promoter-TSS (NM_175226)	promoter-TSS (NM_175226)	-396	NM_175226	75841	Mm.460627	NM_175226	ENSMUSG00000037075	Rnf139	4930555P18Rik	ring finger protein 139	protein-coding	0.2	0.811881
Merged-chr9-64022964-1	chr9	64022914	64023014	+	4.6	cIP2vsInput	promoter-TSS (NM_008542)	promoter-TSS (NM_008542)	-905	NM_008542	17130	Mm.325757	NM_008542	ENSMUSG00000036867	Smad6	Madh6	SMAD family member 6	protein-coding	0.1	0.663366
Merged-chr6-108659729-2	chr6	108659642	108659816	+	4.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011498)	promoter-TSS (NM_011498)	-900	NM_011498	20893	Mm.2436	NM_011498	ENSMUSG00000030103	Bhlhe40	Bhlhb2|C130042M06Rik|CR8|Clast5|Dec1|Sharp2|Stra13|Stra14	"basic helix-loop-helix family, member e40"	protein-coding	0.114943	0.777143
Merged-chr15-61985001-1	chr15	61984951	61985051	+	4.6	cIP2vsInput	promoter-TSS (NM_001177352)	promoter-TSS (NM_001177352)	-340	NM_001177354	17869	Mm.2444	NM_001177352	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding	0.1	0.643564
Merged-chr10-4387229-2	chr10	4387166	4387292	+	4.6	cIP1vsInput|cIP2vsInput	"intron (NM_001033466, intron 1 of 2)"	CpG	879	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding	0.079365	0.732283
Merged-chr3-152265908-1	chr3	152265858	152265958	+	4.6	cIP2vsInput	"intron (NM_199465, intron 1 of 12)"	CpG	412	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding	0.08	0.722772
Merged-chr5-132543297-1	chr5	132543247	132543347	+	4.6	cIP2vsInput	promoter-TSS (NM_177047)	promoter-TSS (NM_177047)	-954	NM_177047	319974	Mm.488992	NM_177047		Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding	0.15	0.772277
Merged-chr8-115150601-2	chr8	115150549	115150653	+	4.6	cIP1vsInput|cIP2vsInput	"intron (NM_019573, intron 8 of 8)"	"intron (NM_019573, intron 8 of 8)"	556293	NM_001025577	17132	Mm.488377	NM_001025577		Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma (v-maf) AS42 oncogene homolog	protein-coding	0.038462	0.466667
Merged-chr15-80133046-1	chr15	80132996	80133096	+	4.6	cIP2vsInput	promoter-TSS (NM_025609)	promoter-TSS (NM_025609)	-108	NM_025609	66513	Mm.288245	NM_025609	ENSMUSG00000022414	Tab1	2310012M03Rik|Map3k7ip1	TGF-beta activated kinase 1/MAP3K7 binding protein 1	protein-coding	0.11	0.752475
Merged-chr7-82772711-1	chr7	82772661	82772761	+	4.6	cIP2vsInput	"intron (NM_001159672, intron 19 of 19)"	"intron (NM_001159672, intron 19 of 19)"	-17067	NR_046004	77800	Mm.447286	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	miscRNA	0.03	0.633663
Merged-chr9-65828165-1	chr9	65828115	65828215	+	4.6	cIP1vsInput	promoter-TSS (NM_172536)	promoter-TSS (NM_172536)	-601	NM_172536	214812	Mm.139231	NM_172536	ENSMUSG00000040524	Zfp609	9830165N24|BC016271|Znf609|mKIAA0295	zinc finger protein 609	protein-coding	0.03	0.465347
Merged-chr2-30237576-1	chr2	30237526	30237626	+	4.6	cIP2vsInput	promoter-TSS (NR_028299)	promoter-TSS (NR_028299)	55	NR_028299	67350	Mm.402683	NR_028299		1700084E18Rik	-	RIKEN cDNA 1700084E18 gene	miscRNA	0.07	0.594059
Merged-chr3-146521480-1	chr3	146521430	146521530	+	4.6	cIP1vsInput	promoter-TSS (NM_027371)	promoter-TSS (NM_027371)	-57	NM_027371	70285	Mm.28128	NM_027332	ENSMUSG00000028187	Rpf1	2210420E24Rik|2310066N05Rik|Bxdc5	ribosome production factor 1 homolog (S. cerevisiae)	protein-coding	0.06	0.50495
Merged-chr3-107631883-2	chr3	107631831	107631935	+	4.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_153563)	promoter-TSS (NM_153563)	-173	NM_153563	229707	Mm.278643	NM_153563	ENSMUSG00000014601	Strip1	6330569M22Rik|6530401O14Rik|Fam40a	striatin interacting protein 1	protein-coding	0.048077	0.514286
Merged-chr12-76370247-1	chr12	76370197	76370297	+	4.6	cIP2vsInput	promoter-TSS (NM_178744)	promoter-TSS (NM_178744)	-19	NM_178744	268564	Mm.470000	NM_178744		Zbtb1	9430077A12|AI256369|Bsg2|C430003J21Rik	zinc finger and BTB domain containing 1	protein-coding	0.06	0.683168
Merged-chr17-83706422-2	chr17	83706350	83706494	+	4.6	cIP1vsInput|cIP2vsInput	"intron (NM_001171052, intron 1 of 15)"	CpG	259	NM_001171052	116871	Mm.277668	NM_001171052	ENSMUSG00000055817	Mta3	1110002J22Rik|mKIAA1266	metastasis associated 3	protein-coding	0.104167	0.77931
Merged-chr4-134854102-2	chr4	134854041	134854163	+	4.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025382)	promoter-TSS (NM_025382)	-757	NM_025382	66146	Mm.99793	NM_025382	ENSMUSG00000028826	Tmem57	1110007C24Rik|9230118A01Rik|AI317300|AI606104|C61	transmembrane protein 57	protein-coding	0.131148	0.739837
Merged-chr8-68903130-1	chr8	68903080	68903180	+	4.6	cIP2vsInput	"intron (NM_008509, intron 9 of 9)"	"intron (NM_008509, intron 9 of 9)"	22575	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding	0.03	0.554455
Merged-chr7-110920512-2	chr7	110920458	110920567	+	4.55	cIP1vsInput|cIP2vsInput	"intron (NM_194464, intron 10 of 20)"	"intron (NM_194464, intron 10 of 20)"	15527	NR_045267	100504184	Mm.441327	NR_045267	ENSMUSG00000087160	Gm16336	OTTMUSG00000033852	predicted gene 16336	miscRNA	0.009174	0.481818
Merged-chr4-61855894-2	chr4	61855832	61855957	+	4.55	cIP1vsInput|cIP2vsInput	Intergenic	RLTR1F_Mm|LTR|ERVK	-20714	NM_008649	17844	Mm.445286	XM_003689354	ENSMUSG00000058523	Mup5	Mup18	major urinary protein 5	protein-coding	0.024	0.5
Merged-chr2-152411205-2	chr2	152411120	152411291	+	4.55	cIP1vsInput|cIP2vsInput	TTS (NM_175126)	TTS (NM_175126)	3839	NM_175126	67917	Mm.391810	NM_175126	ENSMUSG00000074682	Zcchc3	2810406K24Rik	"zinc finger, CCHC domain containing 3"	protein-coding	0.052632	0.645349
Merged-chr11-76201854-2	chr11	76201803	76201906	+	4.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027773)	promoter-TSS (NM_027773)	-202	NM_027773	116972	Mm.188413	NM_027773		Fam57a	2310047D13Rik|4932415L08Rik|5430402E13Rik|5430420K21Rik|Wdt3	"family with sequence similarity 57, member A"	protein-coding	0.087379	0.711538
Merged-chr2-69898497-2	chr2	69898434	69898561	+	4.55	cIP1vsInput|cIP2vsInput	"intron (NM_001081548, intron 1 of 38)"	"intron (NM_001081548, intron 1 of 38)"	1251	NM_001081548	68795	Mm.314576	NM_001081548	ENSMUSG00000044308	Ubr3	1110059H15Rik|4833421P10Rik|A130030D10Rik|AA409735|AA414972|AA422631|AI646861|AU016126|Zfp650|Znf650	ubiquitin protein ligase E3 component n-recognin 3	protein-coding	0.031496	0.5
Merged-chr5-115489658-2	chr5	115489558	115489758	+	4.55	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-5174	NM_133760	75387	Mm.332616	NM_001167691	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4 (silent mating type information regulation 2 homolog) 4 (S. cerevisiae)	protein-coding	0.015	0.328358
Merged-chr7-80246242-2	chr7	80246184	80246301	+	4.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_177765)	promoter-TSS (NM_177765)	-134	NM_177765	269954	Mm.276780	NM_177765	ENSMUSG00000045467	Ttll13	1700111A04Rik|4921538O11|BC024578	"tubulin tyrosine ligase-like family, member 13"	protein-coding	0.068376	0.542373
Merged-chr14-76963417-2	chr14	76963351	76963483	+	4.55	cIP1vsInput|cIP2vsInput	Intergenic	RMER17D2|LTR|ERVK	73200	NM_172488	210808	Mm.89278	NM_172488	ENSMUSG00000044350	Lacc1	9030625A04Rik	laccase (multicopper oxidoreductase) domain containing 1	protein-coding	0.007576	0.548872
Merged-chr8-3516915-2	chr8	3516863	3516967	+	4.55	cIP1vsInput|cIP2vsInput	"intron (NM_015801, intron 2 of 33)"	CpG	1531	NM_015801	50767	Mm.23085	NM_001122818	ENSMUSG00000004565	Pnpla6	AI661849|MSws|Nte	patatin-like phospholipase domain containing 6	protein-coding	0.048077	0.580952
Merged-chr18-31789130-2	chr18	31789079	31789181	+	4.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027002)	promoter-TSS (NM_027002)	-29	NM_027002	69241	Mm.279898	NM_027002	ENSMUSG00000024258	Polr2d	2310002G05Rik|2610028L19Rik|HSRBP4|RBP4	polymerase (RNA) II (DNA directed) polypeptide D	protein-coding	0.107843	0.660194
Merged-chr11-102156348-2	chr11	102156295	102156401	+	4.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029649)	promoter-TSS (NM_029649)	59	NM_029649	76547	Mm.46529	NM_029649	ENSMUSG00000020921	Tmem101	2610511E22Rik	transmembrane protein 101	protein-coding	0.075472	0.626168
Merged-chr1-131910166-2	chr1	131910114	131910219	+	4.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001145804)	promoter-TSS (NM_001145804)	-292	NM_175294	98415	Mm.246869	NM_001145804	ENSMUSG00000026434	Nucks1	2700010L10Rik|8430423A01Rik|AI647518|C78391|Nucks	nuclear casein kinase and cyclin-dependent kinase substrate 1	protein-coding	0	0.349057
Merged-chr3-6116138-2	chr3	6116087	6116190	+	4.55	cIP1vsInput|cIP2vsInput	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	504305	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding	0	0.509615
Merged-chr8-4239030-2	chr8	4238960	4239100	+	4.55	cIP1vsInput|cIP2vsInput	"exon (NM_001164172, exon 1 of 12)"	"exon (NM_001164172, exon 1 of 12)"	290	NM_001164172	26400	Mm.3906	NM_001042557	ENSMUSG00000002948	Map2k7	5930412N11Rik|JNKK 2|Jnkk2|MAPKK 7|MEK 7|Mapkk7|Mek7|Mkk7|Prkmk7|sek2	mitogen-activated protein kinase kinase 7	protein-coding	0.092857	0.730496
Merged-chr10-121626540-2	chr10	121626473	121626607	+	4.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081056)	promoter-TSS (NM_001081056)	-224	NM_001081056	73192	Mm.25042	NM_001081056	ENSMUSG00000034667	Xpot	1110004L07Rik|3110065H13Rik|AI452076|C79645|EXPORTIN-T	"exportin, tRNA (nuclear export receptor for tRNAs)"	protein-coding	0.104478	0.733333
Merged-chrX-139685006-2	chrX	139684954	139685059	+	4.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081499)	promoter-TSS (NM_001081499)	10	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	"TBC1 domain family, member 8B"	protein-coding	0.047619	0.603774
Merged-chr18-61634894-2	chr18	61634797	61634991	+	4.55	cIP1vsInput|cIP2vsInput	Intergenic	(GA)n|Simple_repeat|Simple_repeat	-4759	NR_045420	545261	Mm.426593	NR_045420		Gm20748	Bvht	"predicted gene, 20748"	miscRNA	0.020619	0.615385
Merged-chr19-61265583-2	chr19	61265521	61265645	+	4.55	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-37165	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	"colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)"	protein-coding	0	0.488
Merged-chr6-136828482-2	chr6	136828428	136828537	+	4.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178776)	promoter-TSS (NM_178776)	-266	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding	0.045872	0.472727
Merged-chr5-36661149-2	chr5	36661099	36661200	+	4.55	cIP1vsInput|cIP2vsInput	"intron (NM_001081232, intron 2 of 8)"	"intron (NM_001081232, intron 2 of 8)"	34820	NM_001081232	320661	Mm.486203	NM_001081232	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232|mKIAA0232	"DNA segment, Chr 5, ERATO Doi 579, expressed"	protein-coding	0	0.333333
Merged-chr17-55932095-2	chr17	55932033	55932158	+	4.5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	13164	NM_146249	240120	Mm.441018	NM_146249		Zfp119b	-	zinc finger protein 119b	protein-coding	0.032	0.650794
Merged-chr18-40219392-2	chr18	40219327	40219458	+	4.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_023311)	promoter-TSS (NM_023311)	7	NM_023311	67180	Mm.270382	NM_023311	ENSMUSG00000024487	Yipf5	2610311I19Rik|AA408236|Yip1a	"Yip1 domain family, member 5"	protein-coding	0.122137	0.719697
Merged-chr8-72135805-2	chr8	72135737	72135874	+	4.5	cIP1vsInput|cIP2vsInput	"intron (NM_001001491, intron 1 of 7)"	CpG	513	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik	tropomyosin 4	protein-coding	0.116788	0.688406
Merged-chr1-91250268-2	chr1	91250212	91250325	+	4.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026454)	promoter-TSS (NM_026454)	-51	NM_026454	67921	Mm.337238	NM_026454	ENSMUSG00000034343	Ube2f	2510010F15Rik|AI851109	ubiquitin-conjugating enzyme E2F (putative)	protein-coding	0.061947	0.517544
Merged-chr9-21592930-2	chr9	21592862	21592999	+	4.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001205158)	promoter-TSS (NM_001205158)	-99	NM_001205157	74766	Mm.475712	NM_001205157	ENSMUSG00000032182	Yipf2	1300010K09Rik	"Yip1 domain family, member 2"	protein-coding	0.072993	0.543478
Merged-chr1-21960592-2	chr1	21960528	21960657	+	4.5	cIP1vsInput|cIP2vsInput	"intron (NM_023872, intron 1 of 13)"	"intron (NM_023872, intron 1 of 13)"	1350	NM_001160139	226922	Mm.403737	NM_001160139	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	"potassium voltage-gated channel, subfamily Q, member 5"	protein-coding	0.046512	0.530769
Merged-chr2-19276462-1	chr2	19276412	19276512	+	4.5	cIP2vsInput	"intron (NM_001271565, intron 10 of 17)"	"intron (NM_001271565, intron 10 of 17)"	77344	NM_001081083	70882	Mm.276696	NM_001081083	ENSMUSG00000037683	Armc3	4921513G22Rik	armadillo repeat containing 3	protein-coding	0.05	0.594059
Merged-chr16-23500761-2	chr16	23500685	23500838	+	4.5	cIP1vsInput|cIP2vsInput	"intron (NM_008555, intron 2 of 15)"	"intron (NM_008555, intron 2 of 15)"	19829	NM_008555	17174	Mm.1213	NM_008555	ENSMUSG00000022887	Masp1	AW048060|CCPII|Crarf|Masp1/3	mannan-binding lectin serine peptidase 1	protein-coding	0.013072	0.467532
Merged-chr10-83360050-2	chr10	83359989	83360111	+	4.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026579)	promoter-TSS (NM_026579)	-171	NM_026579	28109	Mm.196210	NM_026579	ENSMUSG00000020255	D10Wsu102e	AI747614|C430041I18Rik	"DNA segment, Chr 10, Wayne State University 102, expressed"	protein-coding	0.090164	0.699187
Merged-chr14-51913092-2	chr14	51913040	51913145	+	4.5	cIP1vsInput|cIP2vsInput	"intron (NM_001145959, intron 1 of 14)"	CpG	396	NM_001145959	29811	Mm.26722	NM_001145959	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding	0.07619	0.59434
Merged-chr4-99194121-1	chr4	99194071	99194171	+	4.5	cIP2vsInput	promoter-TSS (NM_001145967)	promoter-TSS (NM_001145967)	-26	NM_001145967	242557	Mm.241663	NM_001145967	ENSMUSG00000028550	Atg4c	Apg4-C|Apg4c|Atg4cl|Autl1	"autophagy related 4C, cysteine peptidase"	protein-coding	0.16	0.752475
Merged-chr6-126961584-2	chr6	126961505	126961663	+	4.5	cIP1vsInput|cIP2vsInput	"intron (NM_138594, intron 9 of 13)"	"intron (NM_138594, intron 9 of 13)"	21618	NM_138594	28040	Mm.44228	NM_138594	ENSMUSG00000030347	D6Wsu163e	C12orf4	"DNA segment, Chr 6, Wayne State University 163, expressed"	protein-coding	0.012658	0.459119
Merged-chr5-135168428-2	chr5	135168354	135168502	+	4.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009745)	promoter-TSS (NM_009745)	56	NM_009745	12054	Mm.405834	NM_009745	ENSMUSG00000029681	Bcl7b	-	B cell CLL/lymphoma 7B	protein-coding	0.182432	0.785235
Merged-chr6-134567111-1	chr6	134567061	134567161	+	4.5	cIP2vsInput	promoter-TSS (NM_008514)	promoter-TSS (NM_008514)	-198	NM_008514	16974	Mm.321990	NM_008514	ENSMUSG00000030201	Lrp6	C030016K15Rik|Cd|Gw	low density lipoprotein receptor-related protein 6	protein-coding	0.18	0.792079
Merged-chr17-31520148-2	chr17	31520080	31520216	+	4.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001083891)	promoter-TSS (NM_001083891)	33	NM_001083891	78330	Mm.28349	NM_001083891	ENSMUSG00000024038	Ndufv3	1500032D16Rik	NADH dehydrogenase (ubiquinone) flavoprotein 3	protein-coding	0.095588	0.613139
Merged-chrY-6826990-2	chrY	6826936	6827044	+	4.5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	340787	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.009259	0.284404
Merged-chr5-15592364-1	chr5	15592314	15592414	+	4.5	cIP2vsInput	Intergenic	Intergenic	-26735	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0.01	0.336634
Merged-chr11-69097032-2	chr11	69096974	69097090	+	4.5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-1924	NM_011065	18626	Mm.7373	NM_001159367	ENSMUSG00000020893	Per1	Per|m-rigui|mPer1	period circadian clock 1	protein-coding	0.034483	0.555556
Merged-chr18-37877448-1	chr18	37877398	37877498	+	4.5	cIP1vsInput	"intron (NM_007858, intron 16 of 26)"	"intron (NM_007858, intron 16 of 26)"	57902	NM_033583	93708	Mm.247203	NM_033583	ENSMUSG00000023036	Pcdhgc5	-	"protocadherin gamma subfamily C, 5"	protein-coding	0.01	0.405941
Merged-chr12-76369646-2	chr12	76369583	76369710	+	4.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178744)	promoter-TSS (NM_178744)	-86	NM_028356	109929	Mm.41880	NM_001172104	ENSMUSG00000056459	Zbtb25	2810462M08Rik|2900064P18Rik|AI842128|Kup|Zfp-50|Zfp50	zinc finger and BTB domain containing 25	protein-coding	0.165354	0.789062
Merged-chr2-18049143-1	chr2	18049093	18049193	+	4.5	cIP2vsInput	promoter-TSS (NM_028317)	promoter-TSS (NM_028317)	-694	NM_028317	72668	Mm.482646	NM_028317	ENSMUSG00000054074	Skida1	2810030E01Rik|5730507N06Rik|BB088113	SKI/DACH domain containing 1	protein-coding	0.02	0.386139
Merged-chr2-6254966-2	chr2	6254896	6255036	+	4.5	cIP1vsInput|cIP2vsInput	"intron (NR_040333, intron 2 of 6)"	RMER17A2|LTR|ERVK	-41972	NM_024208	67856	Mm.38342	NM_024208	ENSMUSG00000039063	Echdc3	2310005D12Rik|AI662097	enoyl Coenzyme A hydratase domain containing 3	protein-coding	0.014286	0.531915
Merged-chr7-3629901-1	chr7	3629851	3629951	+	4.5	cIP2vsInput	promoter-TSS (NM_027328)	promoter-TSS (NM_027328)	-17	NM_023524	69714	Mm.358730	NM_023524	ENSMUSG00000006335	Tfpt	2400004F01Rik|AI450389|Amida|FB1	TCF3 (E2A) fusion partner	protein-coding	0.11	0.594059
Merged-chr9-90114840-1	chr9	90114790	90114890	+	4.5	cIP2vsInput	promoter-TSS (NM_024431)	promoter-TSS (NM_024431)	-20	NM_024431	21761		NM_001039147	ENSMUSG00000062270	Morf4l1	MORFRG15|MRG15|TEG-189|Tex189|mKIAA4002	mortality factor 4 like 1	protein-coding	0.07	0.70297
Merged-chr10-45469667-1	chr10	45469617	45469717	+	4.5	cIP2vsInput	"intron (NM_001031772, intron 1 of 4)"	"intron (NM_001031772, intron 1 of 4)"	534	NM_001031772	380669	Mm.440328	NM_001033152	ENSMUSG00000063804	Lin28b	2810403D23Rik|D030047M17Rik|Lin-28.2	lin-28 homolog B (C. elegans)	protein-coding	0.03	0.49505
Merged-chr2-18065217-1	chr2	18065167	18065267	+	4.5	cIP2vsInput	"intron (NR_045538, intron 2 of 22)"	CpG-7762	632	NM_001252561	17354	Mm.209175	NM_001252560	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10"	protein-coding	0.15	0.752475
Merged-chr19-6276766-1	chr19	6276716	6276816	+	4.5	cIP2vsInput	promoter-TSS (NM_010119)	promoter-TSS (NM_010119)	-130	NM_010119	13660	Mm.30169	NM_010119	ENSMUSG00000024772	Ehd1	AA409636|Past1|RME-1	EH-domain containing 1	protein-coding	0.16	0.712871
Merged-chr2-84742583-1	chr2	84742533	84742633	+	4.5	cIP2vsInput	Intergenic	Intergenic	-1405	NR_029544	387149		NR_029544	ENSMUSG00000065484	Mir130a	Mirn130|Mirn130a	microRNA 130a	miscRNA	0.01	0.613861
Merged-chr8-84687881-2	chr8	84687824	84687938	+	4.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025788)	promoter-TSS (NM_025788)	-19	NM_025788	66830	Mm.289698	NM_025788	ENSMUSG00000001910	Nacc1	2010001H03Rik|4930511N13Rik|Btbd14b|Nac1	"nucleus accumbens associated 1, BEN and BTB (POZ) domain containing"	protein-coding	0.122807	0.730435
Merged-chr5-134315048-1	chr5	134314998	134315098	+	4.5	cIP2vsInput	promoter-TSS (NM_001080747)	promoter-TSS (NM_001080747)	-302	NM_010365	14886	Mm.412191	NM_001080746	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding	0.06	0.712871
Merged-chr1-72243899-2	chr1	72243826	72243972	+	4.5	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-31592	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding	0.10274	0.612245
Merged-chr12-98259195-2	chr12	98259130	98259261	+	4.5	cIP1vsInput|cIP2vsInput	"exon (NM_008079, exon 1 of 17)"	"exon (NM_008079, exon 1 of 17)"	142	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding	0.129771	0.689394
Merged-chr9-106685949-2	chr9	106685894	106686004	+	4.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011573)	promoter-TSS (NM_011573)	-1	NM_001081654	21767	Mm.22266	NM_001081654	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding	0.136364	0.747748
Merged-chr4-31898896-1	chr4	31898846	31898946	+	4.5	cIP1vsInput	Intergenic	Intergenic	-65211	NM_009316	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.01	0.376238
Merged-chr4-57812993-2	chr4	57812938	57813049	+	4.5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-32255	NM_009649	11641	Mm.467752	NM_001035532	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding	0.018018	0.553571
Merged-chr10-85917107-1	chr10	85917057	85917157	+	4.5	cIP2vsInput	promoter-TSS (NM_181650)	promoter-TSS (NM_181650)	-162	NM_181650	72843	Mm.25307	NM_181650	ENSMUSG00000035529	Prdm4	1700031E19Rik|2810470D21Rik|AW552272|SC-1	PR domain containing 4	protein-coding	0.12	0.70297
Merged-chr8-83608260-1	chr8	83608210	83608310	+	4.5	cIP2vsInput	promoter-TSS (NM_018808)	promoter-TSS (NM_018808)	85	NM_018808	81489	Mm.282092	NM_018808	ENSMUSG00000005483	Dnajb1	0610007I11Rik|HSPF1|Hsp40	"DnaJ (Hsp40) homolog, subfamily B, member 1"	protein-coding	0.11	0.712871
Merged-chr19-46689933-2	chr19	46689839	46690027	+	4.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025563)	promoter-TSS (NM_025563)	27	NM_025563	66439	Mm.87163	NM_025563	ENSMUSG00000062376	2010012O05Rik	4930569L17Rik|AI413851|AI467257	RIKEN cDNA 2010012O05 gene	protein-coding	0.101064	0.608466
Merged-chr11-60454558-2	chr11	60454492	60454625	+	4.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_021354)	promoter-TSS (NM_021354)	-59	NM_021354	13495	Mm.41803	XM_003945908	ENSMUSG00000020537	Drg2	AI255295|AI461605	developmentally regulated GTP binding protein 2	protein-coding	0.075188	0.58209
Merged-chr5-15461771-1	chr5	15461721	15461821	+	4.5	cIP2vsInput	Intergenic	Intergenic	-157328	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0.02	0.386139
Merged-chr2-119662883-2	chr2	119662829	119662937	+	4.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027175)	promoter-TSS (NM_027175)	-85	NM_027175	69702	Mm.5390	NM_027175	ENSMUSG00000027305	Ndufaf1	2410001M24Rik|CGI-65|CIA30	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 1"	protein-coding	0.074074	0.504587
Merged-chr1-53313652-2	chr1	53313598	53313706	+	4.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028091)	promoter-TSS (NM_028091)	-11	NM_028091	72085	Mm.482256	NM_028091	ENSMUSG00000026096	Osgepl1	2610001M19Rik|AA416452	O-sialoglycoprotein endopeptidase-like 1	protein-coding	0.12037	0.678899
Merged-chr5-124425838-1	chr5	124425788	124425888	+	4.5	cIP2vsInput	promoter-TSS (NM_001081203)	promoter-TSS (NM_001081203)	76	NM_001081203	243272	Mm.439104	NM_001081203	ENSMUSG00000038095	Sbno1	9330180L10Rik|AI849128|AW557836|BC021875|Sbno|mSno1|sno	"sno, strawberry notch homolog 1 (Drosophila)"	protein-coding	0.08	0.673267
Merged-chr16-95990982-2	chr16	95990925	95991039	+	4.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019537)	promoter-TSS (NM_019537)	-79	NM_019537	56088	Mm.396248	NM_019537	ENSMUSG00000022913	Psmg1	AW552102|Dscr2	"proteasome (prosome, macropain) assembly chaperone 1"	protein-coding	0.131579	0.747826
Merged-chr3-16183174-1	chr3	16183124	16183224	+	4.5	cIP2vsInput	promoter-TSS (NM_001145919)	promoter-TSS (NM_001145919)	-9	NR_027375	229096	Mm.23834	NM_001145919	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding	0.11	0.693069
Merged-chrY-10011588-2	chrY	10011529	10011647	+	4.5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-1176419	NM_001017394	100039753	Mm.458473	NM_001017394	ENSMUSG00000096227	Gm20815	-	"predicted gene, 20815"	protein-coding	0	0.394958
Merged-chr1-167273596-2	chr1	167273527	167273666	+	4.5	cIP1vsInput|cIP2vsInput	"intron (NM_030724, intron 1 of 6)"	"intron (NM_030724, intron 1 of 6)"	11531	NM_030724	80914	Mm.440156	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding	0.05036	0.621429
Merged-chr7-81571798-2	chr7	81571741	81571856	+	4.5	cIP1vsInput|cIP2vsInput	"exon (NM_001004185, exon 1 of 10)"	"exon (NM_001004185, exon 1 of 10)"	506	NM_001004185	434204	Mm.181641	NM_001004185	ENSMUSG00000045795	Whamm	BB081391|Whdc1|mKIAA1971	"WAS protein homolog associated with actin, golgi membranes and microtubules"	protein-coding	0.121739	0.732759
Merged-chr5-100416438-1	chr5	100416388	100416488	+	4.5	cIP2vsInput	promoter-TSS (NM_026969)	promoter-TSS (NM_026969)	-204	NM_026969	69162	Mm.18634	NM_026969	ENSMUSG00000035325	Sec31a	1810024J13Rik|ABP125|ABP130|AU042160|HSPC275|Sec31l1	Sec31 homolog A (S. cerevisiae)	protein-coding	0.11	0.653465
Merged-chr5-65391499-1	chr5	65391449	65391549	+	4.5	cIP2vsInput	promoter-TSS (NM_011292)	promoter-TSS (NM_011292)	2	NM_024471	79464	Mm.195776	NM_024471		Lias	2900022L22Rik|4933425M12Rik|7a5ex|C77512|mLip1	lipoic acid synthetase	protein-coding	0.19	0.633663
Merged-chr4-149445455-2	chr4	149445386	149445525	+	4.5	cIP1vsInput|cIP2vsInput	Intergenic	CpG	9513	NM_022020	63954	Mm.46023	NM_022020	ENSMUSG00000028996	Rbp7	1110002J23Rik|CRBP-III	"retinol binding protein 7, cellular"	protein-coding	0.071942	0.642857
Merged-chr12-80062203-2	chr12	80062117	80062289	+	4.5	cIP1vsInput|cIP2vsInput	Intergenic	(CA)n|Simple_repeat|Simple_repeat	50810	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	"zinc finger protein 36, C3H type-like 1"	protein-coding	0.017442	0.514451
Merged-chr19-5024060-1	chr19	5024010	5024110	+	4.5	cIP2vsInput	promoter-TSS (NM_007854)	promoter-TSS (NM_007854)	54	NM_007854	13340	Mm.4930	NM_007854	ENSMUSG00000024891	Slc29a2	Der12|Ent2|Hnp36	"solute carrier family 29 (nucleoside transporters), member 2"	protein-coding	0.09	0.673267
Merged-chr19-53329344-1	chr19	53329294	53329394	+	4.5	cIP2vsInput	promoter-TSS (NM_010847)	promoter-TSS (NM_010847)	-69	NM_010847	17859	Mm.2154	NM_001008542	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	Max interacting protein 1	protein-coding	0.09	0.722772
Merged-chr19-10525766-1	chr19	10525716	10525816	+	4.5	cIP2vsInput	promoter-TSS (NM_025333)	promoter-TSS (NM_025333)	522	NM_172302	269061	Mm.490260	NM_001164272	ENSMUSG00000034820	Cpsf7	5730453I16Rik|AL022757|C330017N18Rik	cleavage and polyadenylation specific factor 7	protein-coding	0.14	0.80198
Merged-chr3-40894176-2	chr3	40894116	40894237	+	4.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026622)	promoter-TSS (NM_026622)	-101	NM_026622	269423	Mm.482948	NM_026622	ENSMUSG00000037818	3110057O12Rik	2310068E01Rik|4732404H23|AI645591	RIKEN cDNA 3110057O12 gene	protein-coding	0.066116	0.680328
Merged-chr18-45558542-2	chr18	45558472	45558612	+	4.45	cIP1vsInput|cIP2vsInput	Intergenic	L1MDb|LINE|L1	-1612	NM_080465	140492	Mm.458654	NM_080465		Kcnn2	KCa2.2|SK2|SKCA2|fri	"potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2"	protein-coding	0.107143	0.787234
Merged-chr14-24606920-2	chr14	24606870	24606971	+	4.45	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	116239	NM_011297	20088	Mm.16775	NM_011297	ENSMUSG00000025290	Rps24	-	ribosomal protein S24	protein-coding	0.029703	0.519608
Merged-chr17-12916446-2	chr17	12916352	12916540	+	4.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026310)	promoter-TSS (NM_026310)	-19	NM_013686	21454	Mm.229342	NM_013686	ENSMUSG00000068039	Tcp1	AI528772|CCT|Cct1|Ccta|TRic|Tcp-1|Tp63|c-cpn|p63	t-complex protein 1	protein-coding	0.117021	0.677249
Merged-chr3-108147966-2	chr3	108147910	108148023	+	4.45	cIP1vsInput|cIP2vsInput	TTS (NM_175470)	TTS (NM_175470)	-1852	NM_010306	14679	Mm.271703	NM_010306	ENSMUSG00000000001	Gnai3	AI158965|AW537698|Galphai3|Gnai-3	"guanine nucleotide binding protein (G protein), alpha inhibiting 3"	protein-coding	0	0.412281
Merged-chr9-65827814-2	chr9	65827727	65827902	+	4.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172536)	promoter-TSS (NM_172536)	-250	NM_172536	214812	Mm.139231	NM_172536	ENSMUSG00000040524	Zfp609	9830165N24|BC016271|Znf609|mKIAA0295	zinc finger protein 609	protein-coding	0.068571	0.579545
Merged-chr2-166996331-2	chr2	166996265	166996397	+	4.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001109906)	promoter-TSS (NM_001109906)	-53	NM_001109905	20853	Mm.73276	NM_001109905	ENSMUSG00000039536	Stau1	5830401L18Rik|AW549911|C85792|Stau	staufen (RNA binding protein) homolog 1 (Drosophila)	protein-coding	0.121212	0.774436
Merged-chr10-69533743-2	chr10	69533680	69533807	+	4.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_170689)	promoter-TSS (NM_170689)	35	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	"ankyrin 3, epithelial"	protein-coding	0.031496	0.546875
Merged-chr3-34020077-2	chr3	34019998	34020156	+	4.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001113189)	promoter-TSS (NM_001113189)	-2	NM_001113189	14359	Mm.259021	NM_001113188	ENSMUSG00000027680	Fxr1	1110050J02Rik|9530073J07Rik|AI851072|Fxr1h|Fxr1p	"fragile X mental retardation gene 1, autosomal homolog"	protein-coding	0.107595	0.691824
Merged-chr16-29579320-2	chr16	29579266	29579375	+	4.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133752)	promoter-TSS (NM_133752)	-14	NM_001199177	74143	Mm.274285	NM_001199177	ENSMUSG00000038084	Opa1	1200011N24Rik|AI225888|AI847218|lilr3|mKIAA0567	optic atrophy 1	protein-coding	0.100917	0.654545
Merged-chr5-111725026-2	chr5	111724975	111725077	+	4.45	cIP1vsInput|cIP2vsInput	Intergenic	(CACG)n|Simple_repeat|Simple_repeat	36702	NR_045832	269683	Mm.136946	NM_207252	ENSMUSG00000085271	E130006D01Rik	Gm16018|Gm681|OTTMUSG00000029083	RIKEN cDNA E130006D01 gene	miscRNA	0.068627	0.553398
Merged-chr3-146500178-2	chr3	146500109	146500248	+	4.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027617)	promoter-TSS (NM_027617)	342	NM_010318	14707	Mm.440505	NM_010318	ENSMUSG00000068523	Gng5	G(y)5	"guanine nucleotide binding protein (G protein), gamma 5"	protein-coding	0.129496	0.735714
Merged-chr4-147938911-2	chr4	147938857	147938965	+	4.45	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-1984	NM_029841	77034	Mm.470864	NM_029841	ENSMUSG00000044496	2510039O18Rik	Kiaa2013	RIKEN cDNA 2510039O18 gene	protein-coding	0.018519	0.486239
Merged-chr11-98682546-2	chr11	98682494	98682598	+	4.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009439)	promoter-TSS (NM_009439)	-8	NM_009439	22123	Mm.12194	NM_009439	ENSMUSG00000017221	Psmd3	AI255837|AntP91a|D11Bwg1349e|Psd3|Tstap91a	"proteasome (prosome, macropain) 26S subunit, non-ATPase, 3"	protein-coding	0.057692	0.6
Merged-chr2-60210050-2	chr2	60209993	60210107	+	4.45	cIP1vsInput|cIP2vsInput	"5' UTR (NM_020575, exon 1 of 10)"	"5' UTR (NM_020575, exon 1 of 10)"	114	NM_020575	57438	Mm.260635	NM_020575		7-Mar	Axo|Axot|Gtrgeo17	membrane-associated ring finger (C3HC4) 7	protein-coding	0.157895	0.73913
Merged-chr4-44072726-2	chr4	44072664	44072788	+	4.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001190414)	promoter-TSS (NM_001190414)	-53	NM_001190414	50798	Mm.256718	NM_001190414	ENSMUSG00000028479	Gne	2310066H07Rik|DMRV|GLCNE|IBM2|NM|Uae1	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	protein-coding	0.153226	0.736
Merged-chr6-37415325-2	chr6	37415266	37415385	+	4.45	cIP1vsInput|cIP2vsInput	"intron (NM_178661, intron 1 of 11)"	"intron (NM_178661, intron 1 of 11)"	26823	NM_178661	208647	Mm.482172	NM_178661		Creb3l2	BBF2H7|C530025K05Rik	cAMP responsive element binding protein 3-like 2	protein-coding	0.033613	0.533333
Merged-chr1-178646799-2	chr1	178646746	178646852	+	4.45	cIP1vsInput|cIP2vsInput	"intron (NM_001161665, intron 2 of 14)"	"intron (NM_001161665, intron 2 of 14)"	117674	NM_001161665	269152	Mm.138659	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding	0.018868	0.495327
Merged-chr3-97076634-2	chr3	97076568	97076700	+	4.45	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	44232	NM_008121	14613	Mm.281816	NM_001271628	ENSMUSG00000057123	Gja5	5730555N10Rik|Cnx40|Cx40|Gja-5	"gap junction protein, alpha 5"	protein-coding	0.030303	0.533835
Merged-chr11-100146147-2	chr11	100146093	100146201	+	4.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008471)	promoter-TSS (NM_008471)	-228	NM_008471	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding	0.018519	0.605505
Merged-chr2-28583038-2	chr2	28582971	28583106	+	4.45	cIP1vsInput|cIP2vsInput	"5' UTR (NM_148928, exon 1 of 12)"	"5' UTR (NM_148928, exon 1 of 12)"	241	NM_148928	70239	Mm.274120	NM_148928	ENSMUSG00000026816	Gtf3c5	2700084A09Rik|TFIIIC63|TFiiiC2-63	"general transcription factor IIIC, polypeptide 5"	protein-coding	0.081481	0.573529
Merged-chr19-44930991-2	chr19	44930940	44931042	+	4.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081225)	promoter-TSS (NM_001081225)	-128	NM_001081225	226151	Mm.212609	NM_001081225	ENSMUSG00000036097	Fam178a	3632432H19|6030443O07Rik|AU014917	"family with sequence similarity 178, member A"	protein-coding	0.107843	0.718447
Merged-chr7-65930698-2	chr7	65930641	65930755	+	4.45	cIP1vsInput|cIP2vsInput	"intron (NM_011048, intron 5 of 21)"	"intron (NM_011048, intron 5 of 21)"	68562	NM_011048	18553	Mm.294007	NM_011048	ENSMUSG00000030513	Pcsk6	C86343|Pace4|SPC4	proprotein convertase subtilisin/kexin type 6	protein-coding	0.035088	0.678261
Merged-chr14-79481093-2	chr14	79481036	79481151	+	4.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007920)	promoter-TSS (NM_007920)	-101	NM_007920	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding	0.156522	0.732759
Merged-chr13-51645027-2	chr13	51644971	51645083	+	4.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025415)	promoter-TSS (NM_025415)	-205	NM_025415	66197	Mm.222228	NM_025415	ENSMUSG00000062248	Cks2	1110038L14Rik|CKSHS2	CDC28 protein kinase regulatory subunit 2	protein-coding	0.098214	0.699115
Merged-chr9-105053209-2	chr9	105053145	105053274	+	4.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_053159)	promoter-TSS (NM_053159)	-59	NM_053159	94062	Mm.29746	NM_053159	ENSMUSG00000032563	Mrpl3	2010320L16Rik|5930422H18Rik|AA407889	mitochondrial ribosomal protein L3	protein-coding	0.046512	0.5
Merged-chr11-20632476-1	chr11	20632426	20632526	+	4.4	cIP2vsInput	"intron (NM_001038625, intron 1 of 1)"	CpG	499	NM_001038625	58172	Mm.339676	NM_001038625	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding	0.08	0.663366
Merged-chr10-80115792-2	chr10	80115728	80115856	+	4.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011492)	promoter-TSS (NM_011492)	-744	NM_011492	20869	Mm.44231	NM_011492		Stk11	AA408040|Lkb1|Par-4|R75140|mLKB1	serine/threonine kinase 11	protein-coding	0.171875	0.713178
Merged-chr15-102671949-2	chr15	102671890	102672009	+	4.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026468)	promoter-TSS (NM_026468)	-83	NR_030460	751542		NR_030460	ENSMUSG00000076009	Mir688	Mirn688|mmu-mir-688	microRNA 688	miscRNA	0.067227	0.658333
Merged-chr9-35421164-2	chr9	35421095	35421234	+	4.4	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-30912	NM_021339	57810	Mm.80509	NM_021339	ENSMUSG00000038119	Cdon	CDO|Cd0|Orcam	cell adhesion molecule-related/down-regulated by oncogenes	protein-coding	0.100719	0.707143
Merged-chr14-27429511-1	chr14	27429461	27429561	+	4.4	cIP1vsInput	"intron (NM_001114879, intron 1 of 23)"	CpG	664	NM_001114879	218850	Mm.247767	NM_028945	ENSMUSG00000040651	D14Abb1e	4732418E12|4933409E02Rik|Fam208a	"DNA segment, Chr 14, Abbott 1 expressed"	protein-coding	0.11	0.693069
Merged-chr4-147419665-1	chr4	147419615	147419715	+	4.4	cIP1vsInput	"intron (NM_001039209, intron 1 of 2)"	"intron (NM_001039209, intron 1 of 2)"	-133612	NM_001014397	433804	Mm.332047	XM_003946328	ENSMUSG00000065999	Gm13154	OTTMUSG00000010673	predicted gene 13154	protein-coding	0.01	0.376238
Merged-chr11-94989852-1	chr11	94989802	94989902	+	4.4	cIP2vsInput	Intergenic	Intergenic	-1360	NM_172261	217124		NM_172261	ENSMUSG00000038976	Ppp1r9b	SPL|Spn	"protein phosphatase 1, regulatory subunit 9B"	protein-coding	0.02	0.643564
Merged-chr5-145004658-2	chr5	145004597	145004720	+	4.4	cIP1vsInput|cIP2vsInput	"intron (NM_001013774, intron 6 of 12)"	"intron (NM_001013774, intron 6 of 12)"	4978	NM_001013774	381686	Mm.332837	NM_001013774	ENSMUSG00000038770	Kpna7	AW146299|Gm1055	karyopherin alpha 7 (importin alpha 8)	protein-coding	0.04878	0.612903
Merged-chr13-3611346-2	chr13	3611260	3611432	+	4.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_134063)	promoter-TSS (NM_134063)	-238	NM_134063	105203	Mm.221609	NM_134063		BC016423	AI645998|Fam208b|Pap20|mKIAA2006	cDNA sequence BC016423	protein-coding	0.046512	0.531792
Merged-chr3-87910636-1	chr3	87910586	87910686	+	4.4	cIP2vsInput	"intron (NM_008231, intron 1 of 5)"	"intron (NM_008231, intron 1 of 5)"	4315	NM_008231	15191	Mm.292208	NM_008231	ENSMUSG00000004897	Hdgf	AI118077|D3Ertd299e	hepatoma-derived growth factor	protein-coding	0.01	0.633663
Merged-chr17-29032869-1	chr17	29032819	29032919	+	4.4	cIP2vsInput	"intron (NM_013663, intron 1 of 5)"	CpG	209	NR_036613	20383	Mm.473125	NM_013663	ENSMUSG00000071172	Srsf3	AL024116|Sfrs3|X16	serine/arginine-rich splicing factor 3	protein-coding	0.09	0.653465
Merged-chrY-7035431-1	chrY	7035381	7035481	+	4.4	cIP1vsInput	Intergenic	Intergenic	132346	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.237624
Merged-chr19-8819436-1	chr19	8819386	8819486	+	4.4	cIP2vsInput	promoter-TSS (NM_027412)	promoter-TSS (NM_027412)	35	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding	0.08	0.554455
Merged-chr6-92943520-2	chr6	92943440	92943600	+	4.4	cIP1vsInput|cIP2vsInput	"intron (NR_015530, intron 1 of 2)"	CpG	2938	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	miscRNA	0.10625	0.726708
Merged-chr4-55349733-2	chr4	55349662	55349804	+	4.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009011)	promoter-TSS (NM_009011)	-309	NM_009011	19359	Mm.196846	NM_009011	ENSMUSG00000028426	Rad23b	0610007D13Rik|AV001138|HR23B|mHR23B|p58	RAD23b homolog (S. cerevisiae)	protein-coding	0.133803	0.713287
Merged-chr4-43969567-2	chr4	43969514	43969621	+	4.4	cIP1vsInput|cIP2vsInput	"intron (NM_027450, intron 3 of 4)"	"intron (NM_027450, intron 3 of 4)"	11865	NM_027450	384009	Mm.22213	NM_027450	ENSMUSG00000028480	Glipr2	5730414A08Rik|C77180|GAPR-1	GLI pathogenesis-related 2	protein-coding	0.009346	0.638889
Merged-chr10-127667703-1	chr10	127667653	127667753	+	4.4	cIP1vsInput	promoter-TSS (NM_008668)	promoter-TSS (NM_008668)	580	NR_045171	72243	Mm.482902	NR_045171	ENSMUSG00000040195	1700012D01Rik	-	RIKEN cDNA 1700012D01 gene	miscRNA	0.05	0.633663
Merged-chr11-116306797-2	chr11	116306723	116306872	+	4.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_016857)	promoter-TSS (NM_016857)	-59	NM_001162872	53413	Mm.22530	NM_001162872	ENSMUSG00000020792	Exoc7	Exo70|sec70	exocyst complex component 7	protein-coding	0.114094	0.7
Merged-chr1-20820243-2	chr1	20820189	20820297	+	4.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008563)	promoter-TSS (NM_008563)	-30	NM_008563	17215	Mm.4502	NM_008563	ENSMUSG00000041859	Mcm3	AL033361|C80350|Mcmd|P1|p1.m	minichromosome maintenance deficient 3 (S. cerevisiae)	protein-coding	0.111111	0.614679
Merged-chr1-176813410-1	chr1	176813360	176813460	+	4.4	cIP2vsInput	Intergenic	CpG	-1402	NM_029756	76816	Mm.171399	NM_029756	ENSMUSG00000026504	Sdccag8	2700048G21Rik|5730470G24Rik|Cccap	serologically defined colon cancer antigen 8	protein-coding	0.09	0.663366
Merged-chr2-115384874-1	chr2	115384824	115384924	+	4.4	cIP2vsInput	Intergenic	Intergenic	-40594	NR_040516	78193	Mm.189508	NR_040516	ENSMUSG00000087309	4930528P14Rik	-	RIKEN cDNA 4930528P14 gene	miscRNA	0.02	0.405941
Merged-chr15-102625616-2	chr15	102625544	102625688	+	4.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_146065)	promoter-TSS (NM_146065)	-195	NM_146065	223922	Mm.475149	NM_146065	ENSMUSG00000052414	Atf7	1110012F10Rik|9430065F09Rik|AI549878|C130020M04Rik	activating transcription factor 7	protein-coding	0.097222	0.648276
Merged-chr2-157204641-1	chr2	157204591	157204691	+	4.4	cIP2vsInput	promoter-TSS (NM_011249)	promoter-TSS (NM_011249)	-107	NM_001139516	19650	Mm.244671	NM_001139516	ENSMUSG00000027641	Rbl1	AW547426|PRB1|p107	retinoblastoma-like 1 (p107)	protein-coding	0.06	0.544554
Merged-chr8-121590394-2	chr8	121590340	121590449	+	4.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026160)	promoter-TSS (NM_026160)	-74	NM_026160	67443	Mm.28357	NM_026160		Map1lc3b	1010001C15Rik|Atg8|LC3b|Map1lc3	microtubule-associated protein 1 light chain 3 beta	protein-coding	0.174312	0.772727
Merged-chr6-135022313-2	chr6	135022254	135022372	+	4.4	cIP1vsInput|cIP2vsInput	"intron (NM_026360, intron 11 of 11)"	"intron (NM_026360, intron 11 of 11)"	10701	NM_026360	67755	Mm.166524	NM_026360	ENSMUSG00000030204	Ddx47	4930588A18Rik|C77285	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	protein-coding	0	0.361345
Merged-chr12-27343428-2	chr12	27343375	27343482	+	4.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009234)	promoter-TSS (NM_009234)	-710	NM_009234	20666	Mm.466344	NM_009234		Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY-box containing gene 11	protein-coding	0.074766	0.657407
Merged-chr14-60737228-1	chr14	60737178	60737278	+	4.4	cIP2vsInput	"intron (NM_001033272, intron 4 of 12)"	"intron (NM_001033272, intron 4 of 12)"	-30906	NM_183175	239126	Mm.319636	NM_183175	ENSMUSG00000071347	C1qtnf9	9130217G22Rik|CTRP9|Ciqtnf9	C1q and tumor necrosis factor related protein 9	protein-coding	0.03	0.60396
Merged-chr17-26202978-2	chr17	26202922	26203034	+	4.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081069)	promoter-TSS (NM_001081069)	16	NM_001081069	50782	Mm.109840	NM_001081069	ENSMUSG00000024186	Rgs11	C78048	regulator of G-protein signaling 11	protein-coding	0.107143	0.707965
Merged-chr5-92083551-1	chr5	92083501	92083601	+	4.4	cIP2vsInput	promoter-TSS (NM_001080797)	promoter-TSS (NM_001080797)	6	NM_001080794	23881	Mm.473827	NM_001080794	ENSMUSG00000029405	G3bp2	AA409541|E430034L04Rik|G3BP|mKIAA0660	GTPase activating protein (SH3 domain) binding protein 2	protein-coding	0.14	0.70297
Merged-chr13-45963629-2	chr13	45963565	45963693	+	4.4	cIP1vsInput|cIP2vsInput	"intron (NM_009124, intron 1 of 7)"	CpG	1362	NM_001199304	20238	Mm.487047	NM_001199304	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding	0.132812	0.790698
Merged-chr2-4559663-1	chr2	4559613	4559713	+	4.4	cIP2vsInput	promoter-TSS (NM_001177844)	promoter-TSS (NM_001177844)	-91	NM_001177844	209630	Mm.37932	NM_001177843	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding	0.06	0.584158
Merged-chr1-11117498-1	chr1	11117448	11117548	+	4.4	cIP2vsInput	"intron (NM_029525, intron 11 of 39)"	"intron (NM_029525, intron 11 of 39)"	124033	NM_029525	109294	Mm.123247	XM_003946036	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	"phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2"	protein-coding	0	0.326733
Merged-chr2-32362971-2	chr2	32362892	32363051	+	4.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028412)	promoter-TSS (NM_028412)	-39	NM_001252538	68379	Mm.170508	NM_001252534	ENSMUSG00000039205	Ciz1	0610038H21Rik|2900056O04Rik|LSFR1|ZNF356	CDKN1A interacting zinc finger protein 1	protein-coding	0.150943	0.74375
Merged-chr5-129725015-1	chr5	129724965	129725065	+	4.4	cIP2vsInput	promoter-TSS (NM_008095)	promoter-TSS (NM_008095)	-60	NM_008095	14467	Mm.12468	NM_008095	ENSMUSG00000029432	Gbas	AV006093|Nipsnap2	glioblastoma amplified sequence	protein-coding	0.09	0.782178
Merged-chr6-58596338-1	chr6	58596288	58596388	+	4.4	cIP1vsInput	promoter-TSS (NM_011920)	promoter-TSS (NM_011920)	-334	NM_011920	26357	Mm.333096	NM_011920	ENSMUSG00000029802	Abcg2	ABC15|ABCP|AI428558|BCRP|Bcrp1|MXR|MXR1	"ATP-binding cassette, sub-family G (WHITE), member 2"	protein-coding	0.04	0.475248
Merged-chr16-37540104-1	chr16	37540054	37540154	+	4.4	cIP2vsInput	promoter-TSS (NM_028812)	promoter-TSS (NM_028812)	210	NM_001042499	67657	Mm.28158	NM_026297	ENSMUSG00000022827	Rabl3	4930553C05Rik|AA958834	"RAB, member of RAS oncogene family-like 3"	protein-coding	0.05	0.534653
Merged-chr2-130284502-1	chr2	130284452	130284552	+	4.4	cIP2vsInput	promoter-TSS (NM_130884)	promoter-TSS (NM_130884)	-51	NM_130884	170718	Mm.29590	NM_130884	ENSMUSG00000027406	Idh3b	C78231	isocitrate dehydrogenase 3 (NAD+) beta	protein-coding	0.1	0.613861
Merged-chr17-78375011-1	chr17	78374961	78375061	+	4.4	cIP2vsInput	"3' UTR (NM_015800, exon 17 of 17)"	"3' UTR (NM_015800, exon 17 of 17)"	43092	NM_199448	225020	Mm.236835	NM_199448	ENSMUSG00000056121	Fez2	9030616F16|D17Ertd315e	fasciculation and elongation protein zeta 2 (zygin II)	protein-coding	0.04	0.564356
Merged-chr2-105726913-2	chr2	105726839	105726987	+	4.4	cIP1vsInput|cIP2vsInput	"intron (NM_023876, intron 9 of 9)"	"intron (NM_023876, intron 9 of 9)"	50784	NM_001244202	18508	Mm.487124	NM_001244198	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box gene 6	protein-coding	0.047297	0.590604
Merged-chr4-149485155-2	chr4	149485096	149485215	+	4.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133435)	promoter-TSS (NM_133435)	-13	NM_133435	66454	Mm.76062	NM_133435		Nmnat1	2610529L11Rik|5730441G13Rik|D4Cole1e|nmnat	nicotinamide nucleotide adenylyltransferase 1	protein-coding	0.067227	0.658333
Merged-chr16-45742900-1	chr16	45742850	45742950	+	4.4	cIP2vsInput	promoter-TSS (NM_172511)	promoter-TSS (NM_172511)	55	NM_001272070	213012	Mm.247453	NM_001272070		Abhd10	-	abhydrolase domain containing 10	protein-coding	0.12	0.752475
Merged-chr11-100939728-1	chr11	100939678	100939778	+	4.4	cIP2vsInput	promoter-TSS (NM_213660)	promoter-TSS (NM_213660)	-217	NM_011486	20848	Mm.249934	NM_011486	ENSMUSG00000004040	Stat3	1110034C02Rik|AW109958|Aprf	signal transducer and activator of transcription 3	protein-coding	0.06	0.60396
Merged-chr8-19728030-1	chr8	19727980	19728080	+	4.4	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-1546	NM_001270553	100861668	Mm.445582	NM_001270553		Gm21119	-	"predicted gene, 21119"	protein-coding	0.01	0.326733
Merged-chr6-13607912-1	chr6	13607862	13607962	+	4.4	cIP2vsInput	"5' UTR (NM_028990, exon 1 of 5)"	"5' UTR (NM_028990, exon 1 of 5)"	151	NM_028990	101118	Mm.254845	NM_028990	ENSMUSG00000029569	Tmem168	5730526F17Rik|8430437G11Rik|AI462344|AI504145	transmembrane protein 168	protein-coding	0.12	0.693069
Merged-chr3-79568004-1	chr3	79567954	79568054	+	4.4	cIP2vsInput	promoter-TSS (NM_001162999)	promoter-TSS (NM_001162999)	-325	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding	0.05	0.643564
Merged-chr11-102185152-1	chr11	102185102	102185202	+	4.4	cIP2vsInput	"exon (NM_172947, exon 1 of 5)"	"exon (NM_172947, exon 1 of 5)"	104	NM_172947	268490	Mm.259079	NM_172947		Lsm12	1110032E16Rik|1110059P07|2600001B17Rik	LSM12 homolog (S. cerevisiae)	protein-coding	0.1	0.683168
Merged-chr2-151494245-1	chr2	151494195	151494295	+	4.4	cIP2vsInput	promoter-TSS (NM_198326)	promoter-TSS (NM_198326)	-63	NM_198326	386649	Mm.419479	NM_198326	ENSMUSG00000027455	Nsfl1c	Munc-18c|Stxbp3a|p47	NSFL1 (p97) cofactor (p47)	protein-coding	0.13	0.693069
Merged-chr11-69672619-1	chr11	69672569	69672669	+	4.4	cIP2vsInput	promoter-TSS (NM_001159375)	promoter-TSS (NM_001159375)	-196	NM_001159375	13681	Mm.473799	NM_001159375	ENSMUSG00000059796	Eif4a1	BM-010|Ddx2a|Eif4	eukaryotic translation initiation factor 4A1	protein-coding	0.09	0.623762
Merged-chr2-26445240-1	chr2	26445190	26445290	+	4.4	cIP1vsInput	promoter-TSS (NM_153125)	promoter-TSS (NM_153125)	-24	NM_153125	227648	Mm.206371	NM_153125	ENSMUSG00000026924	Sec16a	AU024582|C230052J16Rik|RP23-306D20.10	SEC16 homolog A (S. cerevisiae)	protein-coding	0.11	0.653465
Merged-chr12-111039107-1	chr12	111039057	111039157	+	4.4	cIP1vsInput	promoter-TSS (NM_198023)	promoter-TSS (NM_198023)	-691	NM_198023	217864	Mm.23808	NM_198023	ENSMUSG00000037896	Rcor1	5730409O11|6720480E22Rik|AU042633|D12Wsu95e|mKIAA0071	REST corepressor 1	protein-coding	0.09	0.564356
Merged-chr18-34331065-2	chr18	34331011	34331119	+	4.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025527)	promoter-TSS (NM_025527)	-80	NM_025527	66384	Mm.29452	NM_025527	ENSMUSG00000014504	Srp19	2310020D23Rik	signal recognition particle 19	protein-coding	0.111111	0.633028
Merged-chr15-56014250-1	chr15	56014200	56014300	+	4.4	cIP2vsInput	Intergenic	Intergenic	-107301	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	"syntrophin, basic 1"	protein-coding	0.01	0.554455
Merged-chr11-97660503-1	chr11	97660453	97660553	+	4.4	cIP2vsInput	Intergenic	CpG	-2909	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6"	protein-coding	0.14	0.663366
Merged-chr6-136804724-1	chr6	136804674	136804774	+	4.4	cIP1vsInput	promoter-TSS (NM_175652)	promoter-TSS (NM_175652)	-293	NM_175652	320332	Mm.489077	NM_175652	ENSMUSG00000096010	Hist4h4	B130044J01Rik	"histone cluster 4, H4"	protein-coding	0.02	0.346535
Merged-chr6-71908777-2	chr6	71908683	71908871	+	4.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009088)	promoter-TSS (NM_009088)	-15	NM_027275	69956	Mm.30256	NM_027275	ENSMUSG00000063884	Ptcd3	2610034F17Rik|2810422B04Rik|AA589622|AU045708	pentatricopeptide repeat domain 3	protein-coding	0.111702	0.656085
Merged-chr16-13819216-1	chr16	13819166	13819266	+	4.4	cIP2vsInput	promoter-TSS (NM_010946)	promoter-TSS (NM_010946)	-61	NM_010946	18203	Mm.380410	NM_010946	ENSMUSG00000022681	Ntan1	-	N-terminal Asn amidase	protein-coding	0.13	0.70297
Merged-chr11-107189335-1	chr11	107189285	107189385	+	4.4	cIP2vsInput	promoter-TSS (NM_001161329)	promoter-TSS (NM_001161329)	46	NM_133702	68979	Mm.294617	NM_001161329	ENSMUSG00000018433	Nol11	1500002M01Rik|AU015220|AU019874	nucleolar protein 11	protein-coding	0.09	0.633663
Merged-chr19-10881954-1	chr19	10881904	10882004	+	4.4	cIP2vsInput	promoter-TSS (NM_134142)	promoter-TSS (NM_134142)	-211	NM_134142	68539	Mm.251890	NM_134142	ENSMUSG00000034659	Tmem109	1110006I15Rik|AA958958|C77652	transmembrane protein 109	protein-coding	0.07	0.564356
Merged-chr15-80255340-1	chr15	80255290	80255390	+	4.4	cIP2vsInput	"5' UTR (NM_009716, exon 1 of 3)"	"5' UTR (NM_009716, exon 1 of 3)"	156	NM_009716	11911	Mm.641	NM_009716	ENSMUSG00000042406	Atf4	Atf-4|C/ATF|CREB2|TAXREB67	activating transcription factor 4	protein-coding	0.07	0.613861
Merged-chr5-135489003-1	chr5	135488953	135489053	+	4.4	cIP2vsInput	"intron (NM_146001, intron 1 of 30)"	CpG	56119	NM_146001	215114	Mm.280805	NM_146001	ENSMUSG00000039959	Hip1	2610109B09Rik|A930014B11Rik|E130315I21Rik|mKIAA4113	huntingtin interacting protein 1	protein-coding	0.04	0.584158
Merged-chr2-18676868-2	chr2	18676809	18676927	+	4.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007552)	promoter-TSS (NM_007552)	-150	NM_007552	12151	Mm.289584	NM_007552	ENSMUSG00000026739	Bmi1	AW546694|Bmi-1|Pcgf4	Bmi1 polycomb ring finger oncogene	protein-coding	0.067797	0.680672
Merged-chr9-102406266-1	chr9	102406216	102406316	+	4.4	cIP2vsInput	Intergenic	Intergenic	-51573	NM_173447	270190	Mm.22897	NM_001168296	ENSMUSG00000032537	Ephb1	9330129L11|AW488255|C130099E04Rik|Cek6|ENSMUSG00000074119|Elk|Elkh|Hek6|Net	Eph receptor B1	protein-coding	0.03	0.564356
Merged-chr12-98746899-1	chr12	98746849	98746949	+	4.4	cIP2vsInput	promoter-TSS (NM_001160107)	promoter-TSS (NM_001160107)	-69	NM_001160107	75553	Mm.25549	NM_001008506	ENSMUSG00000021012	Zc3h14	1010001P15Rik|1700016A15Rik|2700069A02Rik|AU014748	zinc finger CCCH type containing 14	protein-coding	0.14	0.70297
Merged-chr5-122391807-1	chr5	122391757	122391857	+	4.4	cIP1vsInput	promoter-TSS (NM_019824)	promoter-TSS (NM_019824)	-121	NM_019824	56378	Mm.275942	NM_019824	ENSMUSG00000029465	Arpc3	1110006A04Rik|21kDa|AA408672|AI788639|p21-Ar|p21Arc	"actin related protein 2/3 complex, subunit 3"	protein-coding	0.11	0.60396
Merged-chr10-40258573-1	chr10	40258523	40258623	+	4.4	cIP2vsInput	promoter-TSS (NM_026113)	promoter-TSS (NM_026113)	-908	NM_026113	67371	Mm.64104	NM_026113	ENSMUSG00000019837	Gtf3c6	2410016F19Rik|AU019813	"general transcription factor IIIC, polypeptide 6, alpha"	protein-coding	0.04	0.524752
Merged-chr15-102510756-1	chr15	102510706	102510806	+	4.4	cIP2vsInput	"intron (NM_001163643, intron 1 of 15)"	CpG	6248	NM_001163643	26404	Mm.172897	NM_001163643	ENSMUSG00000023050	Map3k12	DLK|MUK|Zpk	mitogen-activated protein kinase kinase kinase 12	protein-coding	0.06	0.673267
Merged-chr5-32857982-1	chr5	32857932	32858032	+	4.4	cIP2vsInput	Intergenic	Intergenic	-3752	NM_194340	215476	Mm.248721	NM_194340	ENSMUSG00000054280	Prr14l	6030436E02Rik|C330019G07Rik|Prl14l	proline rich 14-like	protein-coding	0.03	0.435644
Merged-chr2-104467379-2	chr2	104467329	104467429	+	4.35	cIP1vsInput|cIP2vsInput	"intron (NM_001145824, intron 2 of 15)"	"intron (NM_001145824, intron 2 of 15)"	27110	NM_010434	15259	Mm.257925	NM_001145824	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY	homeodomain interacting protein kinase 3	protein-coding	0.01	0.465347
Merged-chr5-143528062-2	chr5	143528011	143528114	+	4.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009007)	promoter-TSS (NM_009007)	-69	NM_009007	19353	Mm.475073	NM_009007	ENSMUSG00000001847	Rac1	AL023026|D5Ertd559e	RAS-related C3 botulinum substrate 1	protein-coding	0.165049	0.836538
Merged-chr11-101442298-2	chr11	101442234	101442363	+	4.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011289)	promoter-TSS (NM_011289)	53	NM_011289	19942	Mm.439813	NM_011289	ENSMUSG00000063316	Rpl27	-	ribosomal protein L27	protein-coding	0.046512	0.584615
Merged-chr6-86684569-2	chr6	86684513	86684626	+	4.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025665)	promoter-TSS (NM_025665)	-78	NM_025665	66618	Mm.182650	NM_025665	ENSMUSG00000001158	Snrnp27	2610209M04Rik|AI449063|AU022368|Ry1	small nuclear ribonucleoprotein 27 (U4/U6.U5)	protein-coding	0.061947	0.570175
Merged-chr5-53590394-2	chr5	53590339	53590450	+	4.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001277116)	promoter-TSS (NM_001277116)	48	NM_001277116	19664	Mm.488709	NM_001080927	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding	0.099099	0.625
Merged-chr5-32854320-2	chr5	32854221	32854419	+	4.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_194340)	promoter-TSS (NM_194340)	-90	NM_194340	215476	Mm.248721	NM_194340	ENSMUSG00000054280	Prr14l	6030436E02Rik|C330019G07Rik|Prl14l	proline rich 14-like	protein-coding	0.106061	0.703518
Merged-chr17-28177390-2	chr17	28177323	28177457	+	4.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172617)	promoter-TSS (NM_172617)	-28	NM_172617	224656	Mm.267359	NM_172617	ENSMUSG00000024220	Zfp523	2810027J07|BC025615|Znf76	zinc finger protein 523	protein-coding	0.171642	0.777778
Merged-chr14-28507656-2	chr14	28507584	28507729	+	4.35	cIP1vsInput|cIP2vsInput	"intron (NM_009524, intron 1 of 4)"	"intron (NM_009524, intron 1 of 4)"	2183	NM_009524	22418	Mm.287544	NM_001256224	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-related MMTV integration site 5A	protein-coding	0.082759	0.636986
Merged-chr16-56717402-2	chr16	56717330	56717474	+	4.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019678)	promoter-TSS (NM_019678)	48	NM_019678	21787	Mm.489792	NM_001252443	ENSMUSG00000022757	Tfg	AI173908	Trk-fused gene	protein-coding	0.104167	0.668966
Merged-chr10-81496732-2	chr10	81496650	81496814	+	4.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_134009)	promoter-TSS (NM_134009)	-369	NM_134009	103425	Mm.302791	NM_134009	ENSMUSG00000020238	Ncln	3100002P13Rik|AW120537	nicalin homolog (zebrafish)	protein-coding	0.036585	0.424242
Merged-chr1-135799276-2	chr1	135799195	135799358	+	4.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_021467)	promoter-TSS (NM_021467)	-145	NM_021467	21952	Mm.44379	NM_001112702	ENSMUSG00000026418	Tnni1	2700018B22Rik|AI747285|ssTnI	"troponin I, skeletal, slow 1"	protein-coding	0.01227	0.597561
Merged-chr8-47990705-2	chr8	47990640	47990771	+	4.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133791)	promoter-TSS (NM_133791)	-154	NM_133791	52357	Mm.390033	NM_133791		Wwc2	5330431C14Rik|AU022508|C85457|D8Ertd594e	"WW, C2 and coiled-coil domain containing 2"	protein-coding	0.10687	0.757576
Merged-chr8-22521314-2	chr8	22521250	22521378	+	4.35	cIP1vsInput|cIP2vsInput	"intron (NM_011394, intron 1 of 10)"	"intron (NM_011394, intron 1 of 10)"	-44435	NM_001146117	102032	Mm.378231	NM_001012667	ENSMUSG00000031534	Smim19	AI316807|BG694986|EST-c39	small integral membrane protein 19	protein-coding	0	0.465116
Merged-chr10-105841424-2	chr10	105841371	105841477	+	4.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025602)	promoter-TSS (NM_025602)	-44	NM_207522	216292	Mm.250875	NM_207522	ENSMUSG00000036009	Mettl25	-	methyltransferase like 25	protein-coding	0.141509	0.672897
Merged-chr3-123115899-2	chr3	123115838	123115961	+	4.35	cIP1vsInput|cIP2vsInput	"intron (NM_080451, intron 3 of 4)"	"intron (NM_080451, intron 3 of 4)"	-80912	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding	0.00813	0.427419
Merged-chrX-52988528-2	chrX	52988457	52988600	+	4.35	cIP1vsInput|cIP2vsInput	"intron (NM_013556, intron 1 of 8)"	CpG	450	NM_013556	15452	Mm.299381	NM_013556	ENSMUSG00000025630	Hprt	C81579|HPGRT|Hprt1	hypoxanthine guanine phosphoribosyl transferase	protein-coding	0.097902	0.708333
Merged-chr2-32875813-2	chr2	32875748	32875878	+	4.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_146119)	promoter-TSS (NM_146119)	-321	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	"family with sequence similarity 129, member B"	protein-coding	0.046154	0.618321
Merged-chr10-11343390-2	chr10	11343321	11343459	+	4.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010146)	promoter-TSS (NM_010146)	-55	NM_010146	13853	Mm.89946	NM_010146		Epm2a	"TG-B|Tg(TcraK,TcrbK)TG-BFlv"	"epilepsy, progressive myoclonic epilepsy, type 2 gene alpha"	protein-coding	0.166667	0.776978
Merged-chr5-92675496-2	chr5	92675444	92675549	+	4.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_177230)	promoter-TSS (NM_177230)	-369	NM_177230	320696	Mm.209991	NM_177230	ENSMUSG00000050050	Ccdc158	4932413O14Rik	coiled-coil domain containing 158	protein-coding	0.07619	0.726415
Merged-chr11-72034906-2	chr11	72034850	72034962	+	4.35	cIP1vsInput|cIP2vsInput	"intron (NM_053245, intron 2 of 5)"	"intron (NM_053245, intron 2 of 5)"	2603	NM_053245	114230	Mm.95707	NM_053245		Aipl1	A930007I01Rik	aryl hydrocarbon receptor-interacting protein-like 1	protein-coding	0	0.39823
Merged-chr7-45460062-1	chr7	45460012	45460112	+	4.3	cIP2vsInput	promoter-TSS (NM_010240)	promoter-TSS (NM_010240)	-176	NM_010240	14325	Mm.486189	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light chain 1	protein-coding	0.08	0.673267
Merged-chr5-32725536-1	chr5	32725486	32725586	+	4.3	cIP1vsInput	Intergenic	RMER4A|LTR|ERVK	60090	NM_177298	320951	Mm.273765	NM_177298	ENSMUSG00000023452	Pisd	9030221M09Rik	phosphatidylserine decarboxylase	protein-coding	0	0.475248
Merged-chr2-164879474-1	chr2	164879424	164879524	+	4.3	cIP2vsInput	"5' UTR (NM_146129, exon 1 of 17)"	"5' UTR (NM_146129, exon 1 of 17)"	106	NM_146129	228866	Mm.241134	NM_146129		Pcif1	2310022K11Rik|C20orf67|F730014I05Rik	PDX1 C-terminal inhibiting factor 1	protein-coding	0.12	0.693069
Merged-chr2-15055206-1	chr2	15055156	15055256	+	4.3	cIP2vsInput	promoter-TSS (NM_001165941)	promoter-TSS (NM_001165941)	-156	NM_029466	75869	Mm.174068	NM_029466		Arl5b	4930587A11Rik|AW146430|Arl8	ADP-ribosylation factor-like 5B	protein-coding	0.16	0.732673
Merged-chr8-79294729-1	chr8	79294679	79294779	+	4.3	cIP2vsInput	promoter-TSS (NR_045822)	promoter-TSS (NR_045822)	227	NM_133823	109136	Mm.26510	NM_133823	ENSMUSG00000037022	Mmaa	2810018E08Rik|AI840684	methylmalonic aciduria (cobalamin deficiency) type A	protein-coding	0.05	0.60396
Merged-chr5-76588671-1	chr5	76588621	76588721	+	4.3	cIP2vsInput	Intergenic	CpG	-3043	NM_199032	381644	Mm.332452	NM_199032	ENSMUSG00000036403	Cep135	BC062951|Cep4|Gm1044	centrosomal protein 135	protein-coding	0.15	0.752475
Merged-chr2-25128367-1	chr2	25128317	25128417	+	4.3	cIP2vsInput	Intergenic	Intergenic	-33162	NM_172204	241275	Mm.218774	NM_001163626	ENSMUSG00000036805	Noxa1	NY-CO-31|SDCCAG31	NADPH oxidase activator 1	protein-coding	0.07	0.584158
Merged-chr10-59879839-1	chr10	59879789	59879889	+	4.3	cIP2vsInput	"intron (NM_019965, intron 1 of 8)"	CpG	248	NM_019965	56709	Mm.443586	NM_019965		Dnajb12	Dj10|mDj10	"DnaJ (Hsp40) homolog, subfamily B, member 12"	protein-coding	0.13	0.70297
Merged-chr11-87086815-2	chr11	87086757	87086874	+	4.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_024262)	promoter-TSS (NM_024262)	-38	NM_024262	74133	Mm.23257	NM_024262	ENSMUSG00000020495	Smg8	1200011M11Rik	"smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"	protein-coding	0.051282	0.584746
Merged-chr18-39491715-2	chr18	39491657	39491773	+	4.3	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-4470	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	"nuclear receptor subfamily 3, group C, member 1"	protein-coding	0.068966	0.555556
Merged-chr12-52799880-2	chr12	52799830	52799930	+	4.3	cIP1vsInput|cIP2vsInput	"intron (NM_198111, intron 2 of 13)"	"intron (NM_198111, intron 2 of 13)"	100497	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding	0.05	0.49505
Merged-chrX-126775076-1	chrX	126775026	126775126	+	4.3	cIP2vsInput	Intergenic	Intergenic	58928	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding	0.02	0.445545
Merged-chr13-46669397-1	chr13	46669347	46669447	+	4.3	cIP2vsInput	promoter-TSS (NM_001033192)	promoter-TSS (NM_001033192)	-125	NM_001033192	97863	Mm.275934	NM_001033192		C78339	-	expressed sequence C78339	protein-coding	0.09	0.673267
Merged-chr13-97071026-1	chr13	97070976	97071076	+	4.3	cIP2vsInput	promoter-TSS (NM_001100458)	promoter-TSS (NM_001100458)	-617	NM_001100458	320557	Mm.458280	NM_001100458	ENSMUSG00000041817	Fam169a	B230112C05Rik|SLAP75	"family with sequence similarity 169, member A"	protein-coding	0.06	0.594059
Merged-chr4-34123643-1	chr4	34123593	34123693	+	4.3	cIP2vsInput	Intergenic	Intergenic	-73576	NM_026293	67652	Mm.55848	NM_026293	ENSMUSG00000028264	Spaca1	1700124L11Rik|4930540L03Rik	sperm acrosome associated 1	protein-coding	0.02	0.425743
Merged-chr7-123500639-1	chr7	123500589	123500689	+	4.3	cIP2vsInput	promoter-TSS (NM_001081329)	promoter-TSS (NM_001081329)	-190	NM_001081329	210162	Mm.135397	NM_001081329	ENSMUSG00000030757	Zkscan2	9430065N20Rik|AW493225|Zfp694	zinc finger with KRAB and SCAN domains 2	protein-coding	0.16	0.742574
Merged-chr11-70646907-2	chr11	70646850	70646964	+	4.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027445)	promoter-TSS (NM_027445)	132	NM_024211	67863	Mm.296082	NM_024211	ENSMUSG00000014606	Slc25a11	2310022P18Rik|2oxoc	"solute carrier family 25 (mitochondrial carrier oxoglutarate carrier), member 11"	protein-coding	0.157895	0.73913
Merged-chr2-75658831-1	chr2	75658781	75658881	+	4.3	cIP2vsInput	promoter-TSS (NM_146130)	promoter-TSS (NM_146130)	-428	NM_146130	229279	Mm.379375	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding	0.05	0.485149
Merged-chr5-113993943-1	chr5	113993893	113993993	+	4.3	cIP2vsInput	promoter-TSS (NM_198109)	promoter-TSS (NM_198109)	-186	NM_198109	231637	Mm.389682	NM_198109	ENSMUSG00000042121	Ssh1	AW551225|Gm1394|Gm1395|SSH-1|mSSH-1L	slingshot homolog 1 (Drosophila)	protein-coding	0.17	0.821782
Merged-chr5-125475736-1	chr5	125475686	125475786	+	4.3	cIP2vsInput	promoter-TSS (NM_030210)	promoter-TSS (NM_030210)	-137	NM_030210	78894	Mm.431573	NM_030210	ENSMUSG00000029482	Aacs	2210408B16Rik|SUR5	acetoacetyl-CoA synthetase	protein-coding	0.11	0.633663
Merged-chr5-31048314-1	chr5	31048264	31048364	+	4.3	cIP2vsInput	promoter-TSS (NM_027855)	promoter-TSS (NM_027855)	-235	NM_177870	330064	Mm.205463	NM_001177621	ENSMUSG00000006641	Slc5a6	E430023I20	"solute carrier family 5 (sodium-dependent vitamin transporter), member 6"	protein-coding	0.1	0.742574
Merged-chr11-5788619-2	chr11	5788559	5788679	+	4.3	cIP1vsInput|cIP2vsInput	"exon (NM_001146308, exon 1 of 13)"	"exon (NM_001146308, exon 1 of 13)"	136	NM_013810	13169	Mm.256925	NM_001146308	ENSMUSG00000020476	Dbnl	Abp1|SH3P7|mAbp1	drebrin-like	protein-coding	0.125	0.702479
Merged-chr12-8632026-1	chr12	8631976	8632076	+	4.3	cIP2vsInput	Intergenic	Intergenic	-32960	NM_177802	328059	Mm.46326	NM_001038660	ENSMUSG00000020600	Slc7a15	2010001P20Rik|9030221C07Rik|Arpat	"solute carrier family 7 (cationic amino acid transporter, y+ system), member 15"	protein-coding	0.01	0.306931
Merged-chr13-93192641-1	chr13	93192591	93192691	+	4.3	cIP2vsInput	promoter-TSS (NM_133905)	promoter-TSS (NM_133905)	-358	NM_133905	100715	Mm.242865	NM_133905	ENSMUSG00000042167	Papd4	8030446C20Rik|AI649009|GLD-2|Gld2	PAP associated domain containing 4	protein-coding	0.06	0.613861
Merged-chr2-158028720-1	chr2	158028670	158028770	+	4.3	cIP2vsInput	promoter-TSS (NM_027434)	promoter-TSS (NM_027434)	-74	NM_027434	70470	Mm.290810	NM_027434		Rprd1b	2610304G08Rik|2810446G03Rik|Crept	regulation of nuclear pre-mRNA domain containing 1B	protein-coding	0.1	0.742574
Merged-chr13-14630228-1	chr13	14630178	14630278	+	4.3	cIP2vsInput	promoter-TSS (NM_134067)	promoter-TSS (NM_134067)	-17	NM_001104646	105351	Mm.41450	NM_001104646	ENSMUSG00000039182	AW209491	-	expressed sequence AW209491	protein-coding	0.09	0.673267
Merged-chr5-113908690-1	chr5	113908640	113908740	+	4.3	cIP2vsInput	promoter-TSS (NM_011779)	promoter-TSS (NM_011779)	16	NM_011779	23790	Mm.260158	NM_011779	ENSMUSG00000004530	Coro1c	AL022675|AW455561|AW548837	"coronin, actin binding protein 1C"	protein-coding	0.13	0.792079
Merged-chr12-100159639-1	chr12	100159589	100159689	+	4.3	cIP2vsInput	promoter-TSS (NM_183155)	promoter-TSS (NM_183155)	14	NM_183155	217827	Mm.224076	NM_183155	ENSMUSG00000021179	Nrde2	6720454P05Rik	"nrde-2 necessary for RNA interference, domain containing"	protein-coding	0.08	0.633663
Merged-chr4-46508264-2	chr4	46508213	46508315	+	4.3	cIP1vsInput|cIP2vsInput	"intron (NM_029077, intron 5 of 5)"	B3|SINE|B2	18935	NM_053179	94181	Mm.249349	NM_053179	ENSMUSG00000028334	Nans	4632418E04Rik|BB056474|Sas	N-acetylneuraminic acid synthase (sialic acid synthase)	protein-coding	0.04902	0.582524
Merged-chrY-6823309-2	chrY	6823239	6823380	+	4.3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	344468	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.014184	0.316901
Merged-chr4-97757495-1	chr4	97757445	97757545	+	4.3	cIP2vsInput	"intron (NM_001122952, intron 1 of 10)"	(CA)n|Simple_repeat|Simple_repeat	-20131	NM_001122953	18027	Mm.409646	NM_001122952	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|NF1-A|NF1A	nuclear factor I/A	protein-coding	0.04	0.534653
Merged-chr2-170221164-1	chr2	170221114	170221214	+	4.3	cIP1vsInput	Intergenic	Intergenic	-78489	NM_001159683	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding	0.06	0.554455
Merged-chr11-51763650-2	chr11	51763583	51763718	+	4.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025535)	promoter-TSS (NM_025535)	-13	NM_025535	66397	Mm.196592	NM_025535	ENSMUSG00000020386	Sar1b	2310075M17Rik|2900019I22Rik|CMRD|Sara1b|Sara2|Sarb	SAR1 gene homolog B (S. cerevisiae)	protein-coding	0.081481	0.705882
Merged-chr1-163281733-1	chr1	163281683	163281783	+	4.3	cIP2vsInput	"intron (NM_001025570, intron 1 of 2)"	"intron (NM_001025570, intron 1 of 2)"	31917	NM_011127	18933	Mm.288642	NM_001025570	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding	0	0.39604
Merged-chr10-128494169-1	chr10	128494119	128494219	+	4.3	cIP2vsInput	promoter-TSS (NM_010860)	promoter-TSS (NM_010860)	-344	NM_010860	17904	Mm.337074	NM_010860	ENSMUSG00000090841	Myl6	ESMLC|LC17|LC17-GI|LC17-NM|LC17A|LC17B|MLC-3|MLC1SM|MLC3SM|MLC3nm|Myln	"myosin, light polypeptide 6, alkali, smooth muscle and non-muscle"	protein-coding	0.04	0.465347
Merged-chr7-45343723-1	chr7	45343673	45343773	+	4.3	cIP2vsInput	"intron (NM_029741, intron 22 of 29)"	"intron (NM_029741, intron 22 of 29)"	8454	NM_010473	15464	Mm.39968	NM_010473	ENSMUSG00000038239	Hrc	-	histidine rich calcium binding protein	protein-coding	0.03	0.623762
Merged-chr7-27166717-1	chr7	27166667	27166767	+	4.3	cIP2vsInput	promoter-TSS (NM_053208)	promoter-TSS (NM_053208)	85	NM_053208	112406	Mm.29978	NM_053208	ENSMUSG00000058709	Egln2	0610011A13Rik|C85656|Hif-p4h-1|Ier4|Phd1|SM-20	EGL nine homolog 2 (C. elegans)	protein-coding	0.16	0.742574
Merged-chr5-129501163-1	chr5	129501113	129501213	+	4.3	cIP2vsInput	promoter-TSS (NM_172276)	promoter-TSS (NM_172276)	-68	NM_172276	231769	Mm.288714	NM_001035259	ENSMUSG00000029439	Sfswap	1190005N23Rik|6330437E22Rik|AI197402|AW212079|SWAP|Sfrs8|Srsf8	"splicing factor, suppressor of white-apricot homolog (Drosophila)"	protein-coding	0.07	0.475248
Merged-chr10-80755057-2	chr10	80754973	80755141	+	4.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_199322)	promoter-TSS (NM_199322)	-149	NM_199322	208266	Mm.393160	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"	protein-coding	0.190476	0.786982
Merged-chr3-65958267-1	chr3	65958217	65958317	+	4.3	cIP2vsInput	promoter-TSS (NM_019937)	promoter-TSS (NM_019937)	-42	NM_019937	56706	Mm.175612	NM_001025442	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding	0.16	0.762376
Merged-chr15-76973914-2	chr15	76973859	76973969	+	4.3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	25370	NM_054099	117171	Mm.480608	NM_054099		1110038F14Rik	-	RIKEN cDNA 1110038F14 gene	protein-coding	0.027273	0.567568
Merged-chrY-6802266-1	chrY	6802216	6802316	+	4.3	cIP2vsInput	Intergenic	L1Md_F3|LINE|L1	365511	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.405941
Merged-chr17-17625364-1	chr17	17625314	17625414	+	4.3	cIP2vsInput	promoter-TSS (NM_172827)	promoter-TSS (NM_172827)	-875	NM_172827	240028	Mm.393452	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding	0.09	0.613861
Merged-chr6-148944390-1	chr6	148944340	148944440	+	4.3	cIP1vsInput	"intron (NM_019643, intron 1 of 5)"	"intron (NM_019643, intron 1 of 5)"	2042	NM_019643	56306	Mm.18637	NM_019643	ENSMUSG00000039985	Fam60a	Ppcs1|Pptcs1|Tera	"family with sequence similarity 60, member A"	protein-coding	0.04	0.524752
Merged-chr3-94821428-1	chr3	94821378	94821478	+	4.3	cIP2vsInput	Intergenic	Intergenic	-16139	NM_001165948	229584	Mm.274787	NM_001165948	ENSMUSG00000038902	Pogz	9530006B08Rik|AU015913|AU044539	pogo transposable element with ZNF domain	protein-coding	0.11	0.732673
Merged-chr9-56950954-1	chr9	56950904	56951004	+	4.3	cIP2vsInput	promoter-TSS (NM_178374)	promoter-TSS (NM_178374)	30	NM_178374	66069	Mm.220984	NM_178374	ENSMUSG00000055334	Snupn	0610031A09Rik|Rnut1|Snupn1	snurportin 1	protein-coding	0.1	0.623762
Merged-chr7-30169765-1	chr7	30169715	30169815	+	4.3	cIP2vsInput	promoter-TSS (NM_011980)	promoter-TSS (NM_011980)	-38	NM_011980	26465	Mm.456449	XM_003946228	ENSMUSG00000037029	Zfp146	OZF|Znf146	zinc finger protein 146	protein-coding	0.05	0.584158
Merged-chr3-138442742-1	chr3	138442692	138442792	+	4.3	cIP1vsInput	promoter-TSS (NM_007410)	promoter-TSS (NM_007410)	-422	NM_007410	11532	Mm.3874	NM_007410	ENSMUSG00000028138	Adh5	Adh-5|Adh3|GSNOR	"alcohol dehydrogenase 5 (class III), chi polypeptide"	protein-coding	0.1	0.673267
Merged-chr8-46617403-1	chr8	46617353	46617453	+	4.3	cIP2vsInput	promoter-TSS (NM_009810)	promoter-TSS (NM_009810)	-46	NM_009810	12367	Mm.34405	NM_009810	ENSMUSG00000031628	Casp3	A830040C14Rik|AC-3|Apopain|CC3|CPP32|Caspase-3|Lice|Yama|mldy	caspase 3	protein-coding	0.06	0.673267
Merged-chr4-139642188-1	chr4	139642138	139642238	+	4.3	cIP2vsInput	"exon (NM_175438, exon 10 of 15)"	"exon (NM_175438, exon 10 of 15)"	-11350	NM_031873	83770	Mm.190612	NM_031873	ENSMUSG00000028738	Tas1r2	Gpr71|T1r2|TR2	"taste receptor, type 1, member 2"	protein-coding	0.14	0.673267
Merged-chr19-38224246-1	chr19	38224196	38224296	+	4.3	cIP2vsInput	promoter-TSS (NM_001081075)	promoter-TSS (NM_001081075)	-114	NM_001081075	70567	Mm.30607	NM_001081075	ENSMUSG00000054237	Fra10ac1	5730455O13Rik|AI448293	FRA10AC1 homolog (human)	protein-coding	0.08	0.623762
Merged-chr5-51899694-1	chr5	51899644	51899744	+	4.3	cIP2vsInput	Intergenic	Intergenic	290825	NM_001042620	13204	Mm.993	NM_001042620	ENSMUSG00000029169	Dhx15	DBP1|Ddx15|HRH2|mDEAH9	DEAH (Asp-Glu-Ala-His) box polypeptide 15	protein-coding	0.02	0.455446
Merged-chr19-8880937-2	chr19	8880875	8880999	+	4.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001160356)	promoter-TSS (NM_001160356)	-4	NM_001160356	107197		NM_001160356	ENSMUSG00000071654	AI462493	-	expressed sequence AI462493	protein-coding	0.064516	0.608
Merged-chr17-45574309-1	chr17	45574259	45574359	+	4.3	cIP2vsInput	Intergenic	Intergenic	-1048	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	"heat shock protein 90 alpha (cytosolic), class B member 1"	protein-coding	0.08	0.653465
Merged-chr6-124741082-1	chr6	124741032	124741132	+	4.3	cIP2vsInput	promoter-TSS (NM_013535)	promoter-TSS (NM_013535)	-3	NM_013535	14790	Mm.439877	NM_013535		Grcc10	2310033H05Rik|C10	"gene rich cluster, C10 gene"	protein-coding	0.08	0.643564
Merged-chr4-111415253-1	chr4	111415203	111415303	+	4.3	cIP2vsInput	"exon (NM_026279, exon 1 of 6)"	"exon (NM_026279, exon 1 of 6)"	247	NM_026279	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding	0.14	0.633663
Merged-chr10-37397491-1	chr10	37397441	37397541	+	4.3	cIP2vsInput	Intergenic	Intergenic	-258565	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding	0.02	0.584158
Merged-chr12-110696281-2	chr12	110696203	110696360	+	4.3	cIP1vsInput|cIP2vsInput	"5' UTR (NM_010480, exon 1 of 11)"	"5' UTR (NM_010480, exon 1 of 11)"	114	NM_010480	15519	Mm.486334	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	"heat shock protein 90, alpha (cytosolic), class A member 1"	protein-coding	0.11465	0.696203
Merged-chr11-74838275-1	chr11	74838225	74838325	+	4.3	cIP2vsInput	"intron (NM_010813, intron 4 of 5)"	CpG	7351	NM_010813	17428	Mm.3759	NM_010813	ENSMUSG00000000282	Mnt	Rox|bHLHd3	max binding protein	protein-coding	0.07	0.643564
Merged-chr2-49452042-1	chr2	49451992	49452092	+	4.3	cIP2vsInput	"intron (NM_172663, intron 1 of 13)"	CpG	556	NM_172663	227867	Mm.29167	NM_172663	ENSMUSG00000069495	Epc2	5830499L14|D2Ertd694e	enhancer of polycomb homolog 2 (Drosophila)	protein-coding	0.12	0.722772
Merged-chr18-80469780-1	chr18	80469730	80469830	+	4.3	cIP2vsInput	promoter-TSS (NM_026295)	promoter-TSS (NM_026295)	-113	NM_026295	67655	Mm.312893	NM_026295	ENSMUSG00000033323	Ctdp1	4930563P03Rik|AW553592	"CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1"	protein-coding	0.13	0.722772
Merged-chr5-149412087-1	chr5	149412037	149412137	+	4.3	cIP2vsInput	"exon (NM_027519, exon 1 of 5)"	"exon (NM_027519, exon 1 of 5)"	281	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding	0.08	0.693069
Merged-chr7-45124521-1	chr7	45124471	45124571	+	4.3	cIP2vsInput	promoter-TSS (NM_013725)	promoter-TSS (NM_013725)	-132	NM_013725	27207	Mm.389435	NM_013725	ENSMUSG00000003429	Rps11	-	ribosomal protein S11	protein-coding	0.08	0.584158
Merged-chr14-4807031-1	chr14	4806981	4807081	+	4.3	cIP2vsInput	Intergenic	Intergenic	-64125	NM_001242945	100041306	Mm.396155	NM_001242945	ENSMUSG00000094132	Gm3264	-	predicted gene 3264	protein-coding	0	0.346535
Merged-chr2-65995282-1	chr2	65995232	65995332	+	4.3	cIP2vsInput	"intron (NM_178634, intron 3 of 5)"	"intron (NM_178634, intron 3 of 5)"	129511	NM_015736	14425	Mm.439760	NM_015736	ENSMUSG00000026994	Galnt3	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3	protein-coding	0.03	0.49505
Merged-chr17-24073545-2	chr17	24073473	24073618	+	4.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027008)	promoter-TSS (NM_027008)	-60	NM_027008	69259	Mm.395963	NM_027008	ENSMUSG00000016946	Kctd5	2610030N08Rik|mKIAA0176	potassium channel tetramerisation domain containing 5	protein-coding	0.075862	0.59589
Merged-chr11-94990939-1	chr11	94990889	94990989	+	4.3	cIP2vsInput	promoter-TSS (NM_172261)	promoter-TSS (NM_172261)	-273	NM_172261	217124		NM_172261	ENSMUSG00000038976	Ppp1r9b	SPL|Spn	"protein phosphatase 1, regulatory subunit 9B"	protein-coding	0.1	0.70297
Merged-chr7-142330552-1	chr7	142330502	142330602	+	4.3	cIP1vsInput	"intron (NM_177265, intron 3 of 3)"	"intron (NM_177265, intron 3 of 3)"	27050	NM_015809	50775	Mm.389990	NM_015809	ENSMUSG00000045236	Krtap5-4	-	keratin associated protein 5-4	protein-coding	0	0.544554
Merged-chr15-76307366-1	chr15	76307316	76307416	+	4.3	cIP2vsInput	promoter-TSS (NM_153122)	promoter-TSS (NM_153122)	-121	NM_153122	75475	Mm.322738	NM_153122	ENSMUSG00000022562	Oplah	1700010G02Rik	5-oxoprolinase (ATP-hydrolysing)	protein-coding	0.05	0.60396
Merged-chr8-70797836-2	chr8	70797771	70797901	+	4.3	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-5403	NM_199308	546071	Mm.250731	NM_199308	ENSMUSG00000031833	Mast3	BC024265|mKIAA0561	microtubule associated serine/threonine kinase 3	protein-coding	0.069231	0.641221
Merged-chr9-24888557-1	chr9	24888507	24888607	+	4.3	cIP2vsInput	Intergenic	Intergenic	-114254	NM_001205085	57246	Mm.31452	NM_001205085	ENSMUSG00000031965	Tbx20	9430010M06Rik|AL022859|Tbx12	T-box 20	protein-coding	0.02	0.514851
Merged-chr12-8674582-1	chr12	8674532	8674632	+	4.3	cIP2vsInput	promoter-TSS (NM_030723)	promoter-TSS (NM_030723)	-99	NM_030723	80913	Mm.341243	NM_001160219	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2|mKIAA0235	pumilio 2 (Drosophila)	protein-coding	0.14	0.811881
Merged-chr8-33906016-1	chr8	33905966	33906066	+	4.3	cIP2vsInput	"intron (NM_001042674, intron 1 of 7)"	"intron (NM_001042674, intron 1 of 7)"	23825	NM_019733	19663	Mm.323997	NM_001042674	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|hermes	RNA binding protein gene with multiple splicing	protein-coding	0.01	0.445545
Merged-chr8-123102565-1	chr8	123102515	123102615	+	4.3	cIP2vsInput	promoter-TSS (NR_028128)	promoter-TSS (NR_028128)	215	NM_016738	270106	Mm.391834	NM_016738	ENSMUSG00000000740	Rpl13	A52|L13	ribosomal protein L13	protein-coding	0.1	0.762376
Merged-chr18-76930035-2	chr18	76929977	76930094	+	4.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025409)	promoter-TSS (NM_025409)	8	NM_025409	66191	Mm.28593	NM_025409	ENSMUSG00000090000	Ier3ip1	1110057H19Rik|AI644142|AL022842|AL022863|AV026606	immediate early response 3 interacting protein 1	protein-coding	0.153846	0.745763
Merged-chr15-84654442-1	chr15	84654392	84654492	+	4.3	cIP2vsInput	Intergenic	Intergenic	-26556	NM_146061	109270	Mm.291372	NM_146061	ENSMUSG00000036106	Prr5	AU043908|Arhgap8|C030017C09Rik|C78947|Protor-1|Protor1	proline rich 5 (renal)	protein-coding	0.04	0.663366
Merged-chr11-88969155-1	chr11	88969105	88969205	+	4.3	cIP1vsInput	Intergenic	RMER16-int|LTR|ERVK	-2238	NR_003564	217066	Mm.347543	NR_003564	ENSMUSG00000057534	Gm15698	OTTMUSG00000001305|OTTMUSG00000025408	"transcription elongation factor B (SIII), polypeptide 2 pseudogene"	pseudo	0	0.356436
Merged-chr17-25833298-2	chr17	25833203	25833393	+	4.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019719)	promoter-TSS (NM_019719)	63	NM_019719	56424	Mm.277599	NM_019719	ENSMUSG00000039615	Stub1	0610033N24Rik|2210017D18Rik|2310040B03Rik|AW046544|Chip	STIP1 homology and U-Box containing protein 1	protein-coding	0.084211	0.638743
Merged-chr4-15269561-1	chr4	15269511	15269611	+	4.3	cIP2vsInput	"intron (NM_181401, intron 1 of 2)"	"intron (NM_181401, intron 1 of 2)"	3741	NM_181401	100201	Mm.394111	NM_181401	ENSMUSG00000043252	Tmem64	9630015D15Rik|AI790744|AV300874	transmembrane protein 64	protein-coding	0.01	0.50495
Merged-chr1-166379006-1	chr1	166378956	166379056	+	4.3	cIP2vsInput	promoter-TSS (NM_030245)	promoter-TSS (NM_030245)	-161	NM_030245	27878	Mm.192094	NM_030245	ENSMUSG00000026563	Tada1	2900026B15Rik|D1Ertd251e|Staf42|Tada1l	transcriptional adaptor 1	protein-coding	0.15	0.782178
Merged-chr1-93478335-1	chr1	93478285	93478385	+	4.3	cIP1vsInput	promoter-TSS (NM_001159717)	promoter-TSS (NM_001159717)	473	NM_133808	110611	Mm.30012	NM_133808	ENSMUSG00000034088	Hdlbp	1110005P14Rik|AA960365|AI118566|D1Ertd101e	high density lipoprotein (HDL) binding protein	protein-coding	0.07	0.712871
Merged-chr9-104063345-1	chr9	104063295	104063395	+	4.3	cIP2vsInput	promoter-TSS (NM_175324)	promoter-TSS (NM_175324)	-224	NM_025692	66663	Mm.479441	NM_025692	ENSMUSG00000032557	Uba5	5730525G14Rik|AW240750|Ube1dc1	ubiquitin-like modifier activating enzyme 5	protein-coding	0.05	0.524752
Merged-chr13-17944427-1	chr13	17944377	17944477	+	4.3	cIP2vsInput	promoter-TSS (NM_019491)	promoter-TSS (NM_019491)	-210	NM_019491	56044	Mm.27348	NM_019491	ENSMUSG00000008859	Rala	3010001O15Rik|AW322615|Ral|Rasl1	v-ral simian leukemia viral oncogene homolog A (ras related)	protein-coding	0.12	0.712871
Merged-chr5-124425619-1	chr5	124425569	124425669	+	4.3	cIP1vsInput	"intron (NM_001081203, intron 1 of 31)"	CpG	295	NM_001081203	243272	Mm.439104	NM_001081203	ENSMUSG00000038095	Sbno1	9330180L10Rik|AI849128|AW557836|BC021875|Sbno|mSno1|sno	"sno, strawberry notch homolog 1 (Drosophila)"	protein-coding	0.16	0.811881
Merged-chr7-126566578-1	chr7	126566528	126566628	+	4.3	cIP2vsInput	promoter-TSS (NM_146200)	promoter-TSS (NM_146200)	-212	NM_146200	56347	Mm.22776	NM_146200	ENSMUSG00000030738	Eif3c	110kDa|3230401O13Rik|Eif3s8|NIPIL(A3)|NipilA3|Xs|Xsl	"eukaryotic translation initiation factor 3, subunit C"	protein-coding	0.04	0.49505
Merged-chr8-20324245-1	chr8	20324195	20324295	+	4.3	cIP2vsInput	Intergenic	L1_Mm|LINE|L1	-26813	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo	0	0.356436
Merged-chr3-145118771-2	chr3	145118673	145118870	+	4.3	cIP1vsInput|cIP2vsInput	"5' UTR (NM_001162538, exon 1 of 17)"	"5' UTR (NM_001162538, exon 1 of 17)"	171	NM_025714	52184	Mm.484158	NM_001162538	ENSMUSG00000028256	Odf2l	4733401D09Rik|9630045K08Rik|D3Ertd250e	outer dense fiber of sperm tails 2-like	protein-coding	0.091371	0.727273
Merged-chr10-37141017-1	chr10	37140967	37141067	+	4.3	cIP2vsInput	Intergenic	G-rich|Low_complexity|Low_complexity	-2091	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding	0.1	0.782178
Merged-chr3-90213778-1	chr3	90213728	90213828	+	4.3	cIP2vsInput	promoter-TSS (NR_033727)	promoter-TSS (NR_033727)	-130	NM_027015	57294	Mm.371611	NM_027015		Rps27	3200001M24Rik	ribosomal protein S27	protein-coding	0.1	0.564356
Merged-chr9-41935812-1	chr9	41935762	41935862	+	4.3	cIP2vsInput	Intergenic	Intergenic	188477	NM_011436	20660	Mm.121920	NM_011436		Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	"sortilin-related receptor, LDLR class A repeats-containing"	protein-coding	0.08	0.693069
Merged-chr3-152193853-1	chr3	152193803	152193903	+	4.3	cIP2vsInput	promoter-TSS (NM_025926)	promoter-TSS (NM_025926)	-10	NM_025926	67035	Mm.458538	NM_025926	ENSMUSG00000028035	Dnajb4	1700029A20Rik|2010306G19Rik|5730460G06Rik	"DnaJ (Hsp40) homolog, subfamily B, member 4"	protein-coding	0.08	0.554455
Merged-chr5-99978908-1	chr5	99978858	99978958	+	4.3	cIP2vsInput	promoter-TSS (NM_007516)	promoter-TSS (NM_007516)	30	NM_001077266	11991	Mm.150231	NM_001077265		Hnrnpd	Auf1|C230004L04|Hnrpd	heterogeneous nuclear ribonucleoprotein D	protein-coding	0.13	0.594059
Merged-chr18-47369023-1	chr18	47368973	47369073	+	4.3	cIP2vsInput	promoter-TSS (NM_018744)	promoter-TSS (NM_018744)	-155	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	9330158E07|A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	"sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A"	protein-coding	0.08	0.70297
Merged-chr14-69029731-1	chr14	69029681	69029781	+	4.3	cIP2vsInput	"intron (NM_009285, intron 1 of 3)"	"intron (NM_009285, intron 1 of 3)"	442	NM_009285	20855	Mm.20911	NM_009285	ENSMUSG00000014813	Stc1	Stc	stanniocalcin 1	protein-coding	0.03	0.455446
Merged-chr3-57574999-1	chr3	57574949	57575049	+	4.3	cIP2vsInput	"exon (NM_001168281, exon 2 of 7)"	"exon (NM_001168281, exon 2 of 7)"	877	NM_133784	97064	Mm.405029	NM_001168281	ENSMUSG00000027803	Wwtr1	2310058J06Rik|2610021I22Rik|C78399|Taz	WW domain containing transcription regulator 1	protein-coding	0.14	0.752475
Merged-chrX-107455343-1	chrX	107455293	107455393	+	4.3	cIP2vsInput	Intergenic	Intergenic	-51983	NM_008409	16431	Mm.193	NM_008409	ENSMUSG00000031239	Itm2a	AW108051|Bricd2a|E25|Itm2	integral membrane protein 2A	protein-coding	0	0.346535
Merged-chr11-89298423-1	chr11	89298373	89298473	+	4.3	cIP2vsInput	Intergenic	CpG	4136	NM_008711	18121	Mm.135266	NM_008711	ENSMUSG00000048616	Nog	-	noggin	protein-coding	0.12	0.70297
Merged-chr11-98202811-1	chr11	98202761	98202861	+	4.3	cIP2vsInput	promoter-TSS (NM_001109626)	promoter-TSS (NM_001109626)	-494	NM_001109628	69131	Mm.488484	NM_001109626	ENSMUSG00000003119	Cdk12	1810022J16Rik|AI646528|Crk7|Crkrs|D11Ertd752e|Pksc	cyclin-dependent kinase 12	protein-coding	0.06	0.574257
Merged-chr6-56797422-1	chr6	56797372	56797472	+	4.3	cIP2vsInput	"intron (NM_145958, intron 1 of 3)"	CpG	391	NM_145958	210973	Mm.57295	NM_145958	ENSMUSG00000059486	Kbtbd2	BC022962|Bklhd1|mKIAA1489	kelch repeat and BTB (POZ) domain containing 2	protein-coding	0.17	0.792079
Merged-chr7-126502255-1	chr7	126502205	126502305	+	4.3	cIP2vsInput	"intron (NM_183020, intron 1 of 22)"	CpG	1047	NM_183020	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding	0.06	0.633663
Merged-chr12-69582983-2	chr12	69582913	69583054	+	4.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001033236)	promoter-TSS (NM_001033236)	45	NM_001033236	207965	Mm.102487	NM_001033236	ENSMUSG00000049882	Mettl21d	Gm71|Mettl221d	methyltransferase like 21D	protein-coding	0.120567	0.732394
Merged-chr11-75630839-1	chr11	75630789	75630889	+	4.3	cIP2vsInput	promoter-TSS (NM_008916)	promoter-TSS (NM_008916)	-181	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding	0.1	0.70297
Merged-chr3-87987107-1	chr3	87987057	87987157	+	4.3	cIP2vsInput	TTS (NM_007529)	TTS (NM_007529)	13249	NM_007529	12032	Mm.4598	NM_001109758	ENSMUSG00000004892	Bcan	Cspg7	brevican	protein-coding	0.05	0.60396
Merged-chr2-167632246-1	chr2	167632196	167632296	+	4.3	cIP1vsInput	promoter-TSS (NM_023230)	promoter-TSS (NM_023230)	-241	NM_023230	66589	Mm.360108	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding	0.09	0.70297
Merged-chr1-186749369-1	chr1	186749319	186749419	+	4.3	cIP2vsInput	promoter-TSS (NM_026041)	promoter-TSS (NM_026041)	-11	NM_026041	67223	Mm.289841	NM_026041	ENSMUSG00000001305	Rrp15	2810430M08Rik|5430437H21Rik	ribosomal RNA processing 15 homolog (S. cerevisiae)	protein-coding	0.07	0.564356
Merged-chr3-142765145-1	chr3	142765095	142765195	+	4.3	cIP2vsInput	promoter-TSS (NM_145546)	promoter-TSS (NM_145546)	-102	NM_145546	229906	Mm.271756	NM_145546	ENSMUSG00000028271	Gtf2b	-	general transcription factor IIB	protein-coding	0.16	0.673267
Merged-chr13-77045598-1	chr13	77045548	77045648	+	4.3	cIP2vsInput	"intron (NM_134071, intron 20 of 20)"	"intron (NM_134071, intron 20 of 20)"	89870	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Ankrd32	2700017A04Rik|AW545819|Brctd1|Brctx|C730024G01Rik	ankyrin repeat domain 32	protein-coding	0	0.415842
Merged-chr3-95015244-1	chr3	95015194	95015294	+	4.3	cIP2vsInput	promoter-TSS (NM_030074)	promoter-TSS (NM_030074)	-6	NM_030074	78266	Mm.389478	NM_030074	ENSMUSG00000019338	Zfp687	4931408L03Rik|Znf687|mKIAA1441	zinc finger protein 687	protein-coding	0.07	0.762376
Merged-chr9-108137742-1	chr9	108137692	108137792	+	4.3	cIP2vsInput	"intron (NM_007567, intron 2 of 11)"	"intron (NM_007567, intron 2 of 11)"	-43262	NM_146226	235606	Mm.219639	NM_146226	ENSMUSG00000032590	Apeh	-	acylpeptide hydrolase	protein-coding	0.07	0.613861
Merged-chr17-20945429-1	chr17	20945379	20945479	+	4.3	cIP2vsInput	promoter-TSS (NM_016891)	promoter-TSS (NM_016891)	-25	NM_016891	51792	Mm.294138	NM_016891	ENSMUSG00000007564	Ppp2r1a	6330556D22Rik|PP2A|PR65	"protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform"	protein-coding	0.14	0.752475
Merged-chr6-30693657-1	chr6	30693607	30693707	+	4.3	cIP2vsInput	promoter-TSS (NM_031998)	promoter-TSS (NM_031998)	25	NM_031998	83922	Mm.65389	NM_031998	ENSMUSG00000029790	Tsga14	1700017E11Rik|2810431D15Rik|AI449046|AI503610	testis specific gene A14	protein-coding	0.07	0.633663
Merged-chr10-76468893-1	chr10	76468843	76468943	+	4.3	cIP2vsInput	promoter-TSS (NM_019434)	promoter-TSS (NM_019434)	-78	NM_019434	54387	Mm.30098	NM_019434	ENSMUSG00000001150	Mcm3ap	GANP|mKIAA0572	minichromosome maintenance deficient 3 (S. cerevisiae) associated protein	protein-coding	0.09	0.60396
Merged-chr1-137900362-1	chr1	137900312	137900412	+	4.3	cIP2vsInput	Intergenic	Intergenic	-66093	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mmu-mir-213	microRNA 181a-1	miscRNA	0.04	0.594059
Merged-chr16-8738941-1	chr16	8738891	8738991	+	4.3	cIP2vsInput	promoter-TSS (NM_001003918)	promoter-TSS (NM_001003918)	-599	NM_001003918	252870	Mm.295330	NM_001003918		Usp7	2210010O09Rik|AA409944|AA617399|AU019296|AW548146|C80752|Hausp	ubiquitin specific peptidase 7	protein-coding	0.15	0.70297
Merged-chr8-69903263-1	chr8	69903213	69903313	+	4.3	cIP2vsInput	promoter-TSS (NM_023312)	promoter-TSS (NM_023312)	-705	NM_023312	67184	Mm.21162	NM_023312	ENSMUSG00000036199	Ndufa13	2700054G14Rik|AU022060|CDA016|CGI-39|GRIM-19|Grim19	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13"	protein-coding	0.11	0.70297
Merged-chr14-45530396-1	chr14	45530346	45530446	+	4.3	cIP2vsInput	promoter-TSS (NM_146054)	promoter-TSS (NM_146054)	-331	NM_146054	218952	Mm.210018	NM_146054	ENSMUSG00000037712	Fermt2	AA960555|Kindlin-2|Mig2|Plekhc1	fermitin family homolog 2 (Drosophila)	protein-coding	0.12	0.742574
Merged-chr9-95511968-2	chr9	95511908	95512028	+	4.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001114977)	promoter-TSS (NM_001114977)	28	NM_026476	67958	Mm.392755	NM_001114977	ENSMUSG00000032407	U2surp	2610101N10Rik|AU023006|Sr140	U2 snRNP-associated SURP domain containing	protein-coding	0.166667	0.702479
Merged-chr1-82839409-1	chr1	82839359	82839459	+	4.3	cIP2vsInput	promoter-TSS (NM_010472)	promoter-TSS (NM_010472)	-74	NM_010472	15463	Mm.433409	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding	0.08	0.772277
Merged-chr11-60417103-2	chr11	60417053	60417154	+	4.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025757)	promoter-TSS (NM_025757)	-4	NM_145427	246782	Mm.475062	NM_145427	ENSMUSG00000042709	Atpaf2	ATP12|ATP12p	ATP synthase mitochondrial F1 complex assembly factor 2	protein-coding	0.138614	0.686275
Merged-chr10-81285926-2	chr10	81285857	81285996	+	4.25	cIP1vsInput|cIP2vsInput	"intron (NM_013769, intron 1 of 20)"	CpG	5341	NM_013769	27375	Mm.27984	NM_013769	ENSMUSG00000034917	Tjp3	ZO-3	tight junction protein 3	protein-coding	0.122302	0.678571
Merged-chr5-29195569-2	chr5	29195508	29195631	+	4.25	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-2437	NM_021470	56874	Mm.87352	NM_021470	ENSMUSG00000029130	Rnf32	1700009J01Rik|2700025B22Rik|4930542N22Rik|Lmbr2	ring finger protein 32	protein-coding	0.081301	0.58871
Merged-chr14-20765659-2	chr14	20765584	20765734	+	4.25	cIP1vsInput|cIP2vsInput	"intron (NM_001039139, intron 7 of 18)"	"intron (NM_001039139, intron 7 of 18)"	28429	NM_001039138	12325	Mm.235182	NM_001039138	ENSMUSG00000021820	Camk2g	5930429P18Rik|Camkg	calcium/calmodulin-dependent protein kinase II gamma	protein-coding	0.02	0.503311
Merged-chr19-44267368-2	chr19	44267308	44267428	+	4.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-26308	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Scd-2|swty	stearoyl-Coenzyme A desaturase 2	protein-coding	0.058333	0.636364
Merged-chr6-47778707-2	chr6	47778645	47778770	+	4.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	24945	NR_030485	735289		NR_030485		Mir704	Mirn704|mmu-mir-704	microRNA 704	miscRNA	0.008	0.396825
Merged-chr2-112265741-2	chr2	112265691	112265792	+	4.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133649)	promoter-TSS (NM_133649)	-573	NM_133649	107723	Mm.46449	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	"solute carrier family 12, member 6"	protein-coding	0.158416	0.843137
Merged-chr11-29526371-2	chr11	29526316	29526427	+	4.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133767)	promoter-TSS (NM_133767)	-86	NM_133767	76784	Mm.285429	NM_133767	ENSMUSG00000020459	Mtif2	2310038D14Rik|2410112O06Rik|IF-2mt	mitochondrial translational initiation factor 2	protein-coding	0.063063	0.633929
Merged-chr3-58692139-2	chr3	58692083	58692196	+	4.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_045167)	promoter-TSS (NR_045167)	249	NM_009174	20439	Mm.2847	NM_009174	ENSMUSG00000036432	Siah2	AA415433|Sinh2	seven in absentia 2	protein-coding	0.132743	0.72807
Merged-chr8-13159074-2	chr8	13158980	13159169	+	4.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010684)	promoter-TSS (NM_010684)	-61	NM_010684	16783	Mm.463967	NM_010684	ENSMUSG00000031447	Lamp1	AI196048|CD107a|Lamp-1	lysosomal-associated membrane protein 1	protein-coding	0.074074	0.621053
Merged-chr19-46045362-2	chr19	46045291	46045434	+	4.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001113408)	promoter-TSS (NM_001113408)	-151	NM_001113408	16825	Mm.327442	NM_001113408	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding	0.160839	0.715278
Merged-chr5-15606935-2	chr5	15606883	15606987	+	4.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-12164	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0.028846	0.47619
Merged-chr15-99972667-2	chr15	99972603	99972731	+	4.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001024526)	promoter-TSS (NM_001024526)	-113	NM_001024526	207214	Mm.490671	NM_001024526	ENSMUSG00000023025	Larp4	C530046N12|D330037H05Rik|DXErtd793|DXErtd793e	"La ribonucleoprotein domain family, member 4"	protein-coding	0.132812	0.666667
Merged-chr1-63176994-2	chr1	63176927	63177061	+	4.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001160040)	promoter-TSS (NM_001160040)	163	NM_018796	55949	Mm.2718	NM_018796	ENSMUSG00000025967	Eef1b2	2810017J07Rik|Eef1b	eukaryotic translation elongation factor 1 beta 2	protein-coding	0.059701	0.496296
Merged-chr13-32660116-2	chr13	32660065	32660167	+	4.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	121663	NM_001166030	238564	Mm.60041	NM_001166030	ENSMUSG00000044951	Mylk4	EG238564	"myosin light chain kinase family, member 4"	protein-coding	0	0.359223
Merged-chr19-4397205-1	chr19	4397155	4397255	+	4.2	cIP2vsInput	promoter-TSS (NM_001001984)	promoter-TSS (NM_001001984)	-128	NM_001001984	225876	Mm.31941	NM_001001984	ENSMUSG00000054611	Kdm2a	100043628|5530401A10Rik|AA589516|AW536790|Cxxc8|Fbl11|Fbl7|Fbxl11|Gm4560|Jhdm1|Jhdm1a|lalina	lysine (K)-specific demethylase 2A	protein-coding	0.11	0.70297
Merged-chr5-122821472-2	chr5	122821413	122821531	+	4.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_021505)	promoter-TSS (NM_021505)	-133	NM_001042491	59008	Mm.332667	NM_001042491	ENSMUSG00000029472	Anapc5	2510006G12Rik|AA408751|AA536819|AA986414|Anpc5	anaphase-promoting complex subunit 5	protein-coding	0.050847	0.521008
Merged-chr4-55350074-1	chr4	55350024	55350124	+	4.2	cIP2vsInput	promoter-TSS (NM_009011)	promoter-TSS (NM_009011)	32	NM_009011	19359	Mm.196846	NM_009011	ENSMUSG00000028426	Rad23b	0610007D13Rik|AV001138|HR23B|mHR23B|p58	RAD23b homolog (S. cerevisiae)	protein-coding	0.08	0.623762
Merged-chr4-82250479-2	chr4	82250428	82250531	+	4.2	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	185099	NR_040659	545641	Mm.216028	NR_040659	ENSMUSG00000085022	Gm5860	EG545641	predicted gene 5860	miscRNA	0.038835	0.538462
Merged-chr15-73336580-1	chr15	73336530	73336630	+	4.2	cIP2vsInput	"intron (NM_001130409, intron 4 of 29)"	"intron (NM_001130409, intron 4 of 29)"	86611	NM_007982	14083	Mm.254494	NM_001130409	ENSMUSG00000022607	Ptk2	FAK|FRNK|Fadk|mKIAA4203|p125FAK	PTK2 protein tyrosine kinase 2	protein-coding	0.01	0.405941
Merged-chr1-36939845-1	chr1	36939795	36939895	+	4.2	cIP2vsInput	promoter-TSS (NM_018872)	promoter-TSS (NM_018872)	-318	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding	0.1	0.732673
Merged-chr1-178369032-2	chr1	178368942	178369122	+	4.2	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-31248	NM_016805	51810	Mm.482674	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding	0.116667	0.718232
Merged-chr18-35771427-1	chr18	35771377	35771477	+	4.2	cIP2vsInput	promoter-TSS (NM_019912)	promoter-TSS (NM_019912)	-132	NM_019912	56550	Mm.180052	NM_019912	ENSMUSG00000091896	Ube2d2a	1500034D03Rik|Ubc2e|Ube2d2|ubc4	ubiquitin-conjugating enzyme E2D 2A	protein-coding	0.16	0.792079
Merged-chr2-30677180-2	chr2	30677106	30677255	+	4.2	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-44030	NR_037272	100526499		NR_037272	ENSMUSG00000093091	Mir3089	mmu-mir-3089	microRNA 3089	miscRNA	0.080537	0.633333
Merged-chr15-102203626-1	chr15	102203576	102203676	+	4.2	cIP2vsInput	Intergenic	CpG	-4641	NM_153194	68744	Mm.352945	NM_153194	ENSMUSG00000046897	Zfp740	1110034O07Rik|AW548228|Znf740	zinc finger protein 740	protein-coding	0.08	0.722772
Merged-chr8-83997379-1	chr8	83997329	83997429	+	4.2	cIP1vsInput	promoter-TSS (NM_001081415)	promoter-TSS (NM_001081415)	-293	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding	0.1	0.623762
Merged-chr11-72411111-2	chr11	72411057	72411166	+	4.2	cIP1vsInput|cIP2vsInput	"intron (NM_177776, intron 1 of 7)"	"intron (NM_177776, intron 1 of 7)"	602	NM_177776	276829	Mm.46732	NM_177776	ENSMUSG00000045667	Smtnl2	D130058I21Rik	smoothelin-like 2	protein-coding	0.06422	0.581818
Merged-chr1-92699095-1	chr1	92699045	92699145	+	4.2	cIP2vsInput	Intergenic	Intergenic	-50254	NM_153114	260301	Mm.219545	NM_153114	ENSMUSG00000044055	Otos	OTOSP	otospiralin	protein-coding	0.03	0.643564
Merged-chr10-95501951-1	chr10	95501901	95502001	+	4.2	cIP2vsInput	promoter-TSS (NM_026065)	promoter-TSS (NM_026065)	-24	NM_026065	67270	Mm.30008	NM_026065	ENSMUSG00000062981	Mrpl42	2700009F22Rik|2900055D03Rik|D10Ertd322e|HSPC204|L31mt|MRP-L31|PTD007|Rpml31	mitochondrial ribosomal protein L42	protein-coding	0.13	0.643564
Merged-chr15-81586360-1	chr15	81586310	81586410	+	4.2	cIP2vsInput	"5' UTR (NM_177821, exon 1 of 31)"	"5' UTR (NM_177821, exon 1 of 31)"	146	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding	0.08	0.613861
Merged-chr15-35371407-1	chr15	35371357	35371457	+	4.2	cIP2vsInput	promoter-TSS (NM_177151)	promoter-TSS (NM_177151)	-139	NM_177151	666173	Mm.309250	NM_177151	ENSMUSG00000037646	Vps13b	1810042B05Rik|2310042E16Rik|4732488H20|C330002D13Rik|C87206|Coh1|D230005K13|mKIAA0532|mKIAA5032	vacuolar protein sorting 13B (yeast)	protein-coding	0.09	0.663366
Merged-chr12-55443652-2	chr12	55443595	55443709	+	4.2	cIP1vsInput|cIP2vsInput	"intron (NR_035430, intron 1 of 3)"	"intron (NR_035430, intron 1 of 3)"	44827	NM_011968	26443	Mm.30210	NM_011968	ENSMUSG00000021024	Psma6	IOTA	"proteasome (prosome, macropain) subunit, alpha type 6"	protein-coding	0.017544	0.530435
Merged-chr11-115491728-2	chr11	115491678	115491779	+	4.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_015807)	promoter-TSS (NM_015807)	86	NM_015807	50773	Mm.390379	NM_015807	ENSMUSG00000020736	Nt5c	Dnt|Dnt1|Umph-2|Umph2	"5',3'-nucleotidase, cytosolic"	protein-coding	0.128713	0.666667
Merged-chr1-139422248-1	chr1	139422198	139422298	+	4.2	cIP2vsInput	promoter-TSS (NM_172643)	promoter-TSS (NM_172643)	-135	NM_172643	226470	Mm.119711	NM_172643	ENSMUSG00000033964	Zbtb41	8430415N23Rik|9430031N01|9830132G07Rik|AI316857	zinc finger and BTB domain containing 41 homolog	protein-coding	0.18	0.831683
Merged-chr1-178405633-1	chr1	178405583	178405683	+	4.2	cIP2vsInput	promoter-TSS (NM_026626)	promoter-TSS (NM_026626)	-248	NM_026626	68226	Mm.252132	NM_026626	ENSMUSG00000026495	Efcab2	1700073K01Rik|D830011E08Rik	EF-hand calcium binding domain 2	protein-coding	0.05	0.584158
Merged-chr3-144720170-1	chr3	144720120	144720220	+	4.2	cIP2vsInput	"5' UTR (NM_019464, exon 1 of 9)"	"5' UTR (NM_019464, exon 1 of 9)"	153	NM_019464	54673	Mm.474936	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding	0.17	0.811881
Merged-chr10-62792534-1	chr10	62792484	62792584	+	4.2	cIP2vsInput	promoter-TSS (NM_026201)	promoter-TSS (NM_026201)	-166	NM_026201	67500	Mm.196371	NM_026201	ENSMUSG00000020074	Ccar1	2610511G16Rik|9430036H15Rik|Carp1	cell division cycle and apoptosis regulator 1	protein-coding	0.08	0.60396
Merged-chr14-63271854-1	chr14	63271804	63271904	+	4.2	cIP2vsInput	Intergenic	Intergenic	-26594	NM_008092	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding	0.02	0.534653
Merged-chr5-15537565-1	chr5	15537515	15537615	+	4.2	cIP2vsInput	Intergenic	ETnERV3-int|LTR|ERVK	-81534	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0	0.326733
Merged-chr10-115384520-2	chr10	115384455	115384585	+	4.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025780)	promoter-TSS (NM_025780)	-85	NM_025780	66816	Mm.394447	NM_025780	ENSMUSG00000020137	Thap2	2900040O07Rik|9030625G08Rik|AI450385|AI649097	"THAP domain containing, apoptosis associated protein 2"	protein-coding	0.076923	0.664122
Merged-chr8-20389476-1	chr8	20389426	20389526	+	4.2	cIP2vsInput	"intron (NR_028428, intron 5 of 5)"	"intron (NR_028428, intron 5 of 5)"	-26274	NM_001177408	100040599	Mm.445582	NM_001177408	ENSMUSG00000074449	Gm15319	OTTMUSG00000020118	predicted gene 15319	protein-coding	0.02	0.455446
Merged-chr2-25255455-1	chr2	25255405	25255505	+	4.2	cIP2vsInput	promoter-TSS (NM_001252541)	promoter-TSS (NM_001252541)	16	NM_177344	227615	Mm.213925	NM_177344	ENSMUSG00000078201	Tmem203	C730025P13Rik|Hbebp1|RP23-132N23.14	transmembrane protein 203	protein-coding	0.09	0.653465
Merged-chr3-106721773-1	chr3	106721723	106721823	+	4.2	cIP2vsInput	promoter-TSS (NM_028081)	promoter-TSS (NM_028081)	91	NM_028081	321000	Mm.259638	NM_177309	ENSMUSG00000056260	Lrif1	2010012G17Rik|4933421E11Rik|AI450568|Rif1	ligand dependent nuclear receptor interacting factor 1	protein-coding	0.07	0.623762
Merged-chr9-72274916-1	chr9	72274866	72274966	+	4.2	cIP2vsInput	promoter-TSS (NM_146224)	promoter-TSS (NM_146224)	17	NM_146224	235469	Mm.242791	NM_146224	ENSMUSG00000038535	Zfp280d	A930005F02Rik|BC027163|Suhw4|ZNF634|Znf280d	zinc finger protein 280D	protein-coding	0.13	0.792079
Merged-chr11-95712888-1	chr11	95712838	95712938	+	4.2	cIP2vsInput	promoter-TSS (NR_045780)	promoter-TSS (NR_045780)	-134	NR_045780	432396	Mm.426849	NR_045780	ENSMUSG00000086191	1110035M17Rik	-	RIKEN cDNA 1110035M17 gene	miscRNA	0.15	0.811881
Merged-chr7-27474674-2	chr7	27474599	27474750	+	4.2	cIP1vsInput|cIP2vsInput	"intron (NM_133210, intron 1 of 1)"	"intron (NM_133210, intron 1 of 1)"	834	NM_133210	170742	Mm.200120	NM_133210	ENSMUSG00000055200	Sertad3	AW124805|D1Mgi51|Rbt1|Sei3	SERTA domain containing 3	protein-coding	0.07947	0.677632
Merged-chr4-95052780-1	chr4	95052730	95052830	+	4.2	cIP2vsInput	promoter-TSS (NM_010591)	promoter-TSS (NM_010591)	-558	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	Jun oncogene	protein-coding	0.08	0.623762
Merged-chr8-19908625-2	chr8	19908574	19908677	+	4.2	cIP1vsInput|cIP2vsInput	"intron (NM_001270553, intron 6 of 9).2"	Lx5|LINE|L1	179049	NM_001039553	626415	Mm.425517	NM_001039553		4930467E23Rik	ENSMUSG00000074453|OTTMUSG00000018948|TSAP	RIKEN cDNA 4930467E23 gene	protein-coding	0	0.375
Merged-chr7-126200569-2	chr7	126200494	126200644	+	4.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028816)	promoter-TSS (NM_028816)	-161	NM_028816	74204	Mm.235663	NM_028816	ENSMUSG00000000131	Xpo6	2610005L19Rik|AI854665|AL022631|C230091E20Rik|R75304|Ranbp20|mKIAA0370	exportin 6	protein-coding	0.08	0.649007
Merged-chr8-111643543-1	chr8	111643493	111643593	+	4.2	cIP2vsInput	promoter-TSS (NM_011742)	promoter-TSS (NM_011742)	100	NM_011742	22640	Mm.4184	NM_001037665	ENSMUSG00000055835	Zfp1	Fnp-1|Zfp-1|mkr-1	zinc finger protein 1	protein-coding	0.12	0.673267
Merged-chr6-43666151-2	chr6	43666101	43666201	+	4.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013861)	promoter-TSS (NM_013861)	24	NM_013861	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding	0.16	0.732673
Merged-chr1-85615712-1	chr1	85615662	85615762	+	4.2	cIP2vsInput	"intron (NM_001013817, intron 5 of 16)"	"intron (NM_001013817, intron 5 of 16)"	-11821	NM_175397	109032	Mm.461913	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding	0	0.29703
Merged-chr7-19359431-1	chr7	19359381	19359481	+	4.2	cIP2vsInput	promoter-TSS (NM_145822)	promoter-TSS (NM_145822)	52	NM_145822	70333	Mm.171370	NM_145822		Cd3eap	1190028F09|2610103M17Rik|ASE-1|Ase1|CAST|PAF49	"CD3E antigen, epsilon polypeptide associated protein"	protein-coding	0.07	0.70297
Merged-chr1-134955942-2	chr1	134955879	134956006	+	4.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081307)	promoter-TSS (NM_001081307)	-2	NM_001081307	329251	Mm.451578	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	"protein phosphatase 1, regulatory (inhibitor) subunit 12B"	protein-coding	0.094488	0.640625
Merged-chr7-105811059-2	chr7	105811008	105811110	+	4.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025301)	promoter-TSS (NM_025301)	28	NM_025301	27397	Mm.44225	NM_025301		Mrpl17	MRP-L26|Rpml26	mitochondrial ribosomal protein L17	protein-coding	0.117647	0.699029
Merged-chr17-45573333-1	chr17	45573283	45573383	+	4.2	cIP2vsInput	promoter-TSS (NM_008302)	promoter-TSS (NM_008302)	-72	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	"heat shock protein 90 alpha (cytosolic), class B member 1"	protein-coding	0.11	0.712871
Merged-chr16-50736548-1	chr16	50736498	50736598	+	4.2	cIP2vsInput	Intergenic	Intergenic	-3775	NR_028300	68190	Mm.482928	NR_028300		5330426P16Rik	-	RIKEN cDNA 5330426P16 gene	miscRNA	0	0.316832
Merged-chr7-68010411-2	chr7	68010361	68010461	+	4.2	cIP1vsInput|cIP2vsInput	"intron (NM_010513, intron 2 of 20)"	"intron (NM_010513, intron 2 of 20)"	58154	NM_010513	16001	Mm.275742	NM_010513		Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding	0.01	0.50495
Merged-chr17-47521948-1	chr17	47521898	47521998	+	4.2	cIP2vsInput	"intron (NM_001081635, intron 1 of 6)"	"intron (NM_001081635, intron 1 of 6)"	16897	NM_001081635	12445	Mm.27291	NM_001081635	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding	0.06	0.693069
Merged-chr9-44326804-1	chr9	44326754	44326854	+	4.2	cIP2vsInput	promoter-TSS (NM_007875)	promoter-TSS (NM_007875)	-41	NM_007875	13478	Mm.18353	NM_007875	ENSMUSG00000032123	Dpagt1	AU021132|Dpagt2|GPT|Gnpta	dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	protein-coding	0.06	0.524752
Merged-chr14-54426860-1	chr14	54426810	54426910	+	4.2	cIP2vsInput	promoter-TSS (NM_026851)	promoter-TSS (NM_026851)	-49	NM_026851	68836	Mm.248163	NM_026851	ENSMUSG00000010406	Mrpl52	1110047B07Rik	mitochondrial ribosomal protein L52	protein-coding	0.11	0.623762
Merged-chr11-119056534-1	chr11	119056484	119056584	+	4.2	cIP2vsInput	Intergenic	Intergenic	-15621	NM_013926	30951	Mm.99953	NM_013926		Cbx8	Pc3	chromobox 8	protein-coding	0.06	0.663366
Merged-chr19-53802109-1	chr19	53802059	53802159	+	4.2	cIP2vsInput	"intron (NM_001170847, intron 1 of 13)"	"intron (NM_001170847, intron 1 of 13)"	-90122	NM_011050	18569	Mm.1605	NM_001168491	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding	0.01	0.435644
Merged-chr4-32950944-1	chr4	32950894	32950994	+	4.2	cIP2vsInput	promoter-TSS (NM_001012451)	promoter-TSS (NM_001012451)	-118	NM_001012451	140577	Mm.214766	NM_001012450	ENSMUSG00000040183	Ankrd6	-	ankyrin repeat domain 6	protein-coding	0.12	0.732673
Merged-chr17-87107484-1	chr17	87107434	87107534	+	4.2	cIP2vsInput	promoter-TSS (NM_019654)	promoter-TSS (NM_019654)	-195	NM_019654	56468	Mm.126885	NM_019654	ENSMUSG00000037104	Socs5	1810018L08Rik|Cish5|mKIAA0671	suppressor of cytokine signaling 5	protein-coding	0.08	0.752475
Merged-chr16-92345475-1	chr16	92345425	92345525	+	4.2	cIP2vsInput	TTS (NM_008424)	TTS (NM_008424)	13993	NM_008424	16509	Mm.299425	NM_008424	ENSMUSG00000039639	Kcne1	Isk|MinK|nmf190	"potassium voltage-gated channel, Isk-related subfamily, member 1"	protein-coding	0.06	0.60396
Merged-chr7-105736540-1	chr7	105736490	105736590	+	4.2	cIP2vsInput	promoter-TSS (NM_010562)	promoter-TSS (NM_010562)	44	NM_025897	101867	Mm.231400	NM_025897		Rrp8	1500003O22Rik|2900001K19Rik|AW538116	"ribosomal RNA processing 8, methyltransferase, homolog (yeast)"	protein-coding	0.08	0.613861
Merged-chr4-136602831-1	chr4	136602781	136602881	+	4.2	cIP2vsInput	promoter-TSS (NM_133872)	promoter-TSS (NM_133872)	-108	NM_133872	99982	Mm.28540	NM_133872	ENSMUSG00000036940	Kdm1a	1810043O07Rik|AA408884|Aof2|D4Ertd478e|Kdm1|Lsd1|mKIAA0601	lysine (K)-specific demethylase 1A	protein-coding	0.12	0.683168
Merged-chr4-55532662-1	chr4	55532612	55532712	+	4.2	cIP2vsInput	promoter-TSS (NM_010637)	promoter-TSS (NM_010637)	-187	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding	0.13	0.722772
Merged-chr4-147508717-1	chr4	147508667	147508767	+	4.2	cIP1vsInput	"intron (NM_001039209, intron 1 of 2)"	"intron (NM_001039209, intron 1 of 2)"	-44560	NM_001014397	433804	Mm.332047	XM_003946328	ENSMUSG00000065999	Gm13154	OTTMUSG00000010673	predicted gene 13154	protein-coding	0	0.29703
Merged-chr3-81036983-1	chr3	81036933	81037033	+	4.2	cIP2vsInput	"5' UTR (NM_019971, exon 1 of 6)"	"5' UTR (NM_019971, exon 1 of 6)"	567	NM_019971	54635	Mm.331089	NM_019971	ENSMUSG00000028019	Pdgfc	1110064L01Rik|AI647969|PDGF-C	"platelet-derived growth factor, C polypeptide"	protein-coding	0.07	0.683168
Merged-chr14-69732581-2	chr14	69732512	69732651	+	4.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_134078)	promoter-TSS (NM_134078)	-11	NM_134078	105513	Mm.159637	NM_134078	ENSMUSG00000034190	Chmp7	4930596K11Rik|6330407G04Rik|AI450338|AW550775	charged multivesicular body protein 7	protein-coding	0.093525	0.65
Merged-chr16-42875076-2	chr16	42875026	42875127	+	4.2	cIP1vsInput|cIP2vsInput	"intron (NR_040522, intron 1 of 1)"	CpG	511	NR_040521	75722	Mm.243747	NR_040521	ENSMUSG00000075070	4932412D23Rik	ENSMUSG00000075070|Gm10809	RIKEN cDNA 4932412D23 gene	miscRNA	0.069307	0.696078
Merged-chr16-33184993-1	chr16	33184943	33185043	+	4.2	cIP2vsInput	promoter-TSS (NM_176840)	promoter-TSS (NM_176840)	-78	NM_176840	106326	Mm.486405	NM_176840	ENSMUSG00000022807	Osbpl11	9430097N02Rik|AI132306|AU019795|ORP-11	oxysterol binding protein-like 11	protein-coding	0.08	0.594059
Merged-chr3-107696601-2	chr3	107696542	107696661	+	4.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145542)	promoter-TSS (NM_145542)	-53	NM_145542	229709	Mm.220328	NM_145542	ENSMUSG00000027893	Ahcyl1	1110034F20Rik|AA409031|AA414901|Ahcy-rs3|DCAL|Irbit	S-adenosylhomocysteine hydrolase-like 1	protein-coding	0.092437	0.65
Merged-chr2-167063241-1	chr2	167063191	167063291	+	4.2	cIP2vsInput	promoter-TSS (NM_001033196)	promoter-TSS (NM_001033196)	-226	NM_001033196	98999	Mm.297074	NM_001033196	ENSMUSG00000039501	Znfx1	AI481105	"zinc finger, NFX1-type containing 1"	protein-coding	0.11	0.554455
Merged-chr13-13576529-2	chr13	13576471	13576588	+	4.2	cIP1vsInput|cIP2vsInput	Intergenic	L1MB3|LINE|L1	-13880	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding	0.017094	0.474576
Merged-chr4-131838423-1	chr4	131838373	131838473	+	4.2	cIP2vsInput	promoter-TSS (NM_011214)	promoter-TSS (NM_011214)	-145	NM_001083119	19273	Mm.4860	NM_001083119	ENSMUSG00000028909	Ptpru	Ftp-1|PCP-2|PTP|PTP-lambda|PTPlambda|Pcp2|Ptpf|Ptprl|R-PTP-U|R-PTP-psi|RPTPlambda	"protein tyrosine phosphatase, receptor type, U"	protein-coding	0.13	0.742574
Merged-chr11-51688949-1	chr11	51688899	51688999	+	4.2	cIP1vsInput	promoter-TSS (NM_025319)	promoter-TSS (NM_025319)	-315	NM_025319	66050	Mm.35693	NM_025319	ENSMUSG00000007777	0610009B22Rik	-	RIKEN cDNA 0610009B22 gene	protein-coding	0.07	0.613861
Merged-chr13-93499760-2	chr13	93499697	93499823	+	4.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_021310)	promoter-TSS (NM_021310)	48	NM_021310	57748	Mm.100273	NM_021310	ENSMUSG00000021690	Jmy	-	junction-mediating and regulatory protein	protein-coding	0.142857	0.661417
Merged-chr10-79908853-1	chr10	79908803	79908903	+	4.2	cIP2vsInput	promoter-TSS (NM_001163276)	promoter-TSS (NM_001163276)	85	NM_001163276	216154	Mm.260089	NM_001163276	ENSMUSG00000013833	Med16	95kDa|A630083L04|Thrap5|Trap95	mediator complex subunit 16	protein-coding	0.16	0.762376
Merged-chr19-46761821-1	chr19	46761771	46761871	+	4.2	cIP1vsInput	"exon (NM_001102471, exon 1 of 7)"	"exon (NM_001102471, exon 1 of 7)"	212	NM_033569	94219	Mm.306903	NM_001102471	ENSMUSG00000064105	Cnnm2	AU015877|AW048635|Acdp2|Clp2	cyclin M2	protein-coding	0.1	0.663366
Merged-chr2-25706662-2	chr2	25706587	25706738	+	4.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_023326)	promoter-TSS (NM_023326)	-217	NM_023326	107771	Mm.330057	NM_023326	ENSMUSG00000049086	Bmyc	2900002K07Rik|AW060705|Mycb	brain expressed myelocytomatosis oncogene	protein-coding	0.059603	0.532895
Merged-chr2-154613507-2	chr2	154613443	154613572	+	4.15	cIP1vsInput|cIP2vsInput	"intron (NM_199304, intron 1 of 14)"	CpG	139	NM_199304	228807	Mm.103555	NM_199304	ENSMUSG00000059842	Zfp341	Znf341	zinc finger protein 341	protein-coding	0.162791	0.861538
Merged-chr10-27916591-2	chr10	27916540	27916643	+	4.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-158229	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	"protein tyrosine phosphatase, receptor type, K"	protein-coding	0	0.365385
Merged-chr11-98754827-2	chr11	98754776	98754879	+	4.15	cIP1vsInput|cIP2vsInput	"intron (NM_178060, intron 2 of 8)"	"intron (NM_178060, intron 2 of 8)"	12954	NM_178060	21833	Mm.442648	NM_178060	ENSMUSG00000058756	Thra	6430529J03Rik|AW259572|Erba|Nr1a1|Rvr|T3R[a]|T3Ralpha|Thra1|Thra2	thyroid hormone receptor alpha	protein-coding	0.019417	0.625
Merged-chr4-108372366-2	chr4	108372305	108372428	+	4.15	cIP1vsInput|cIP2vsInput	"intron (NM_001099303, intron 2 of 2)"	"intron (NM_001099303, intron 2 of 2)"	11289	NM_001099303	545667	Mm.380025	NM_001099303	ENSMUSG00000059816	Fam159a	OTTMUSG00000008243	"family with sequence similarity 159, member A"	protein-coding	0.00813	0.483871
Merged-chr5-144014921-2	chr5	144014842	144015000	+	4.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_177682)	promoter-TSS (NM_177682)	-68	NM_177682	231874	Mm.320432	NM_177682	ENSMUSG00000029617	Ccz1	AU022870	CCZ1 vacuolar protein trafficking and biogenesis associated	protein-coding	0.075949	0.616352
Merged-chr1-72806279-2	chr1	72806215	72806343	+	4.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-18201	NM_008342	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding	0.015625	0.604651
Merged-chr2-27179315-2	chr2	27179238	27179392	+	4.15	cIP1vsInput|cIP2vsInput	"intron (NM_138942, intron 9 of 11)"	L1MB7|LINE|L1	13808	NM_138942	13166	Mm.167781	NM_138942	ENSMUSG00000000889	Dbh	-	dopamine beta hydroxylase	protein-coding	0.012987	0.516129
Merged-chr13-114018154-2	chr13	114018094	114018214	+	4.15	cIP1vsInput|cIP2vsInput	"intron (NM_172595, intron 4 of 4)"	"intron (NM_172595, intron 4 of 4)"	133438	NR_045836	319803	Mm.386896	NM_177004		A430090L17Rik	-	RIKEN cDNA A430090L17 gene	miscRNA	0.025	0.479339
Merged-chr11-23306481-2	chr11	23306389	23306574	+	4.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001190401)	promoter-TSS (NM_001190401)	-414	NM_001190401	17847	Mm.119155	NM_001190401	ENSMUSG00000056342	Usp34	A530081C03Rik|Murr2	ubiquitin specific peptidase 34	protein-coding	0.124324	0.747312
Merged-chr9-35176096-2	chr9	35176039	35176154	+	4.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027030)	promoter-TSS (NM_027030)	-109	NM_027030	69305	Mm.229110	NM_027030	ENSMUSG00000032040	Dcps	1700001E16Rik|AA408441	"decapping enzyme, scavenger"	protein-coding	0.069565	0.568966
Merged-chr9-118524444-2	chr9	118524386	118524503	+	4.15	cIP1vsInput|cIP2vsInput	"intron (NM_018748, intron 3 of 23)"	RMER17A2|LTR|ERVK	18126	NM_018748	54214	Mm.10409	NM_018748	ENSMUSG00000038708	Golga4	AI225887|AU019508|Olp-1	"golgi autoantigen, golgin subfamily a, 4"	protein-coding	0.008547	0.550847
Merged-chr4-120825739-2	chr4	120825686	120825793	+	4.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001277095)	promoter-TSS (NM_001277095)	2	NM_001277095	18046	Mm.477613	NM_001048168	ENSMUSG00000032897	Nfyc	-	nuclear transcription factor-Y gamma	protein-coding	0.121495	0.675926
Merged-chr9-86701558-2	chr9	86701496	86701621	+	4.15	cIP1vsInput|cIP2vsInput	TTS (NR_045835)	TTS (NR_045835)	-5644	NM_008615	17436	Mm.148155	NM_001198933	ENSMUSG00000032418	Me1	D9Ertd267e|Mdh-1|Mod-1|Mod1	"malic enzyme 1, NADP(+)-dependent, cytosolic"	protein-coding	0.016	0.460317
Merged-chr1-134093021-2	chr1	134092960	134093083	+	4.15	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-13866	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	"B cell translocation gene 2, anti-proliferative"	protein-coding	0.073171	0.733871
Merged-chr7-143465002-2	chr7	143464929	143465076	+	4.15	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-3952	NM_001161624	12577	Mm.168789	NM_001161624	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding	0.129252	0.763514
Merged-chr3-126746613-2	chr3	126746547	126746679	+	4.15	cIP1vsInput|cIP2vsInput	"intron (NM_001025438, intron 4 of 18)"	"intron (NM_001025438, intron 4 of 18)"	149640	NM_023813	108058	Mm.255822	NM_001025438	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|[d]-CaMKII|mKIAA4163	"calcium/calmodulin-dependent protein kinase II, delta"	protein-coding	0.022727	0.496241
Merged-chrY-6834957-2	chrY	6834895	6835019	+	4.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	332820	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.008065	0.312
Merged-chr2-156840961-2	chr2	156840906	156841016	+	4.15	cIP1vsInput|cIP2vsInput	"intron (NM_173396, intron 1 of 2)"	CpG	884	NM_173396	228839	Mm.488917	NM_173396	ENSMUSG00000062175	Tgif2	4921501K24|5730599O09Rik|C80753|C81206	TGFB-induced factor homeobox 2	protein-coding	0.127273	0.783784
Merged-chr11-59163375-2	chr11	59163307	59163444	+	4.15	cIP1vsInput|cIP2vsInput	"exon (NM_173785, exon 1 of 3)"	"exon (NM_173785, exon 1 of 3)"	370	NM_001270791	216792	Mm.487361	NM_183110	ENSMUSG00000049287	Iba57	4930543L23Rik|A230051G13Rik|C1orf69	"IBA57, iron-sulfur cluster assembly homolog (S. cerevisiae)"	protein-coding	0.10219	0.652174
Merged-chr5-21785270-2	chr5	21785213	21785328	+	4.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011188)	promoter-TSS (NM_011188)	-13	NM_011188	19181	Mm.2462	NM_011188	ENSMUSG00000028932	Psmc2	-	"proteasome (prosome, macropain) 26S subunit, ATPase 2"	protein-coding	0.121739	0.672414
Merged-chr2-14056213-2	chr2	14056163	14056264	+	4.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013935)	promoter-TSS (NM_013935)	-178	NM_013935	30963	Mm.241205	NM_001012396	ENSMUSG00000063275	Ptpla	HACD1	"protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"	protein-coding	0.089109	0.656863
Merged-chr12-78639649-2	chr12	78639598	78639701	+	4.15	cIP1vsInput|cIP2vsInput	"intron (NM_145965, intron 17 of 22)"	"intron (NM_145965, intron 17 of 22)"	-51886	NM_027597	70897	Mm.56514	NM_027597	ENSMUSG00000056987	Fam71d	4921509E07Rik|4930516C23Rik|GARI-L2	"family with sequence similarity 71, member D"	protein-coding	0.009709	0.461538
Merged-chr7-28350618-2	chr7	28350566	28350670	+	4.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013647)	promoter-TSS (NM_013647)	-71	NM_013647	20055	Mm.702	NM_013647	ENSMUSG00000037563	Rps16	AA420385|AI317031	ribosomal protein S16	protein-coding	0.105769	0.685714
Merged-chr14-21500034-2	chr14	21499978	21500091	+	4.15	cIP1vsInput|cIP2vsInput	"intron (NM_017479, intron 1 of 16)"	CpG	249	NM_017479	54169	Mm.248967	NM_001205241	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding	0.097345	0.701754
Merged-chr9-14042127-1	chr9	14042077	14042177	+	4.1	cIP2vsInput	Intergenic	Intergenic	214400	NM_176836	72826	Mm.246174	NM_176836	ENSMUSG00000037808	Fam76b	2810485I05Rik|C78303	"family with sequence similarity 76, member B"	protein-coding	0	0.386139
Merged-chr5-120613199-1	chr5	120613149	120613249	+	4.1	cIP2vsInput	promoter-TSS (NM_028041)	promoter-TSS (NM_028041)	69	NM_028041	71990	Mm.24495	NM_028041	ENSMUSG00000029599	Ddx54	2410015A15Rik|AI414901|DP97	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	protein-coding	0.12	0.693069
Merged-chr7-6797659-1	chr7	6797609	6797709	+	4.1	cIP2vsInput	"intron (NM_021323, intron 2 of 7)"	"intron (NM_021323, intron 2 of 7)"	-5928	NR_037213	100499513		NR_037213	ENSMUSG00000092815	Mir3099	mmu-mir-3099	microRNA 3099	miscRNA	0.01	0.613861
Merged-chr10-127063341-2	chr10	127063291	127063392	+	4.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009870)	promoter-TSS (NM_009870)	-262	NM_009870	12567	Mm.6839	NM_009870		Cdk4	Crk3	cyclin-dependent kinase 4	protein-coding	0.049505	0.637255
Merged-chr8-11009158-1	chr8	11009108	11009208	+	4.1	cIP2vsInput	promoter-TSS (NM_001081212)	promoter-TSS (NM_001081212)	-728	NM_001081212	384783	Mm.407207	NM_001081212	ENSMUSG00000038894	Irs2	Irs-2	insulin receptor substrate 2	protein-coding	0.11	0.752475
Merged-chr10-128176708-1	chr10	128176658	128176758	+	4.1	cIP2vsInput	promoter-TSS (NM_019711)	promoter-TSS (NM_019711)	-140	NM_019711	56516	Mm.42247	NM_001039080	ENSMUSG00000040043	Rbms2	2610315E04Rik|Scr3	"RNA binding motif, single stranded interacting protein 2"	protein-coding	0.02	0.455446
Merged-chr5-140704551-1	chr5	140704501	140704601	+	4.1	cIP2vsInput	promoter-TSS (NM_001276287)	promoter-TSS (NM_001276287)	-460	NM_181066	231841	Mm.271932	NM_001276287	ENSMUSG00000000148	Brat1	AA881470|Baat1	BRCA1-associated ATM activator 1	protein-coding	0.08	0.564356
Merged-chr10-11171789-1	chr10	11171739	11171839	+	4.1	cIP2vsInput	"intron (NM_001077707, intron 13 of 29)"	"intron (NM_001077707, intron 13 of 29)"	22359	NM_172937	268281	Mm.133101	NM_001077707	ENSMUSG00000090112	Shprh	2610103K11Rik|AA450458|AU024614|BC006883|D230017O13Rik|E130018M05	SNF2 histone linker PHD RING helicase	protein-coding	0	0.465347
Merged-chr4-97757671-1	chr4	97757621	97757721	+	4.1	cIP1vsInput	"intron (NM_001122952, intron 1 of 10)"	"intron (NM_001122952, intron 1 of 10)"	-19955	NM_001122953	18027	Mm.409646	NM_001122952	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|NF1-A|NF1A	nuclear factor I/A	protein-coding	0.09	0.663366
Merged-chr18-42511638-1	chr18	42511588	42511688	+	4.1	cIP2vsInput	"intron (NM_001039474, intron 1 of 21)"	CpG	151	NM_001039474	56070	Mm.270511	NM_001039474	ENSMUSG00000024498	Tcerg1	2410022J09Rik|2900090C16Rik|AI428505|CA150b|FBP23|FBP28|Taf2s|ca150|p144	transcription elongation regulator 1 (CA150)	protein-coding	0.1	0.673267
Merged-chr9-62828918-2	chr9	62828820	62829017	+	4.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-9869	NM_001033175	76524	Mm.283636	NM_001033175	ENSMUSG00000032245	Cln6	1810065L06Rik|AW743417|D9Bwg1455e|nclf	"ceroid-lipofuscinosis, neuronal 6"	protein-coding	0.076142	0.671717
Merged-chr10-58932653-1	chr10	58932603	58932703	+	4.1	cIP2vsInput	"intron (NM_172788, intron 1 of 9)"	"intron (NM_172788, intron 1 of 9)"	119294	NM_172788	237353	Mm.410104	NM_172788	ENSMUSG00000037990	Sh3rf3	4831416G18Rik|Igfbp5-ip|Sh3md4|Sh3rf31	SH3 domain containing ring finger 3	protein-coding	0.08	0.544554
Merged-chr12-54068028-2	chr12	54067971	54068086	+	4.1	cIP1vsInput|cIP2vsInput	"exon (NM_013780, exon 12 of 12)"	"exon (NM_013780, exon 12 of 12)"	135846	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	EGL nine homolog 3 (C. elegans)	protein-coding	0.130435	0.663793
Merged-chr9-72111841-1	chr9	72111791	72111891	+	4.1	cIP2vsInput	promoter-TSS (NM_001253865)	promoter-TSS (NM_001253865)	-22	NM_001253865	21406	Mm.480117	NM_001253862	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding	0.12	0.623762
Merged-chr2-26445910-1	chr2	26445860	26445960	+	4.1	cIP2vsInput	promoter-TSS (NM_153125)	promoter-TSS (NM_153125)	-694	NM_153125	227648	Mm.206371	NM_153125	ENSMUSG00000026924	Sec16a	AU024582|C230052J16Rik|RP23-306D20.10	SEC16 homolog A (S. cerevisiae)	protein-coding	0.11	0.673267
Merged-chr16-25058783-1	chr16	25058733	25058833	+	4.1	cIP2vsInput	promoter-TSS (NR_040374)	promoter-TSS (NR_040374)	-856	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	miscRNA	0.02	0.49505
Merged-chr3-131564825-2	chr3	131564761	131564890	+	4.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011863)	promoter-TSS (NM_011863)	57	NM_011863	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding	0.108527	0.761538
Merged-chr5-120503623-1	chr5	120503573	120503673	+	4.1	cIP2vsInput	promoter-TSS (NM_023625)	promoter-TSS (NM_023625)	0	NM_023625	71772	Mm.100065	NM_023625	ENSMUSG00000029598	Plbd2	1300012G16Rik|AU019810|P76	phospholipase B domain containing 2	protein-coding	0.12	0.772277
Merged-chr14-55004027-2	chr14	55003928	55004126	+	4.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-9478	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	"myosin, heavy polypeptide 7, cardiac muscle, beta"	protein-coding	0.005051	0.532663
Merged-chr11-20201061-1	chr11	20201011	20201111	+	4.1	cIP2vsInput	promoter-TSS (NM_008996)	promoter-TSS (NM_008996)	-541	NM_008996	19324	Mm.271944	NM_008996	ENSMUSG00000020149	Rab1	Gtbp|Rab-1|Rab1A|Ypt1|mKIAA3012	"RAB1, member RAS oncogene family"	protein-coding	0.08	0.663366
Merged-chr2-126707124-1	chr2	126707074	126707174	+	4.1	cIP2vsInput	promoter-TSS (NM_001252580)	promoter-TSS (NM_001252580)	-204	NM_001252580	84092	Mm.490069	NM_001252580	ENSMUSG00000027363	Usp8	AI574262|AW557536|Ubpy|mKIAA0055	ubiquitin specific peptidase 8	protein-coding	0.08	0.564356
Merged-chr8-22192778-1	chr8	22192728	22192828	+	4.1	cIP2vsInput	promoter-TSS (NM_027338)	promoter-TSS (NM_027338)	-82	NM_027338	70160	Mm.41453	NM_027338		Vps36	1700010A24Rik|2210415M20Rik|2810408E15Rik|Eap45	vacuolar protein sorting 36 (yeast)	protein-coding	0.13	0.792079
Merged-chr17-32166836-1	chr17	32166786	32166886	+	4.1	cIP2vsInput	promoter-TSS (NM_008716)	promoter-TSS (NM_008716)	16	NM_008716	18131	Mm.439741	NM_008716	ENSMUSG00000038146	Notch3	AW229011|N3|hpbk	notch 3	protein-coding	0.11	0.762376
Merged-chr6-113046185-1	chr6	113046135	113046235	+	4.1	cIP2vsInput	promoter-TSS (NM_008188)	promoter-TSS (NM_008188)	-142	NM_008188	14911	Mm.781	NM_008188	ENSMUSG00000030264	Thumpd3	AW556087|Gt(ROSA)26asSor|Gtrosa26as	THUMP domain containing 3	protein-coding	0.1	0.693069
Merged-chr10-93441615-1	chr10	93441565	93441665	+	4.1	cIP2vsInput	Intergenic	B4|SINE|B4	-11781	NM_008517	16993	Mm.271071	NM_008517	ENSMUSG00000015889	Lta4h	-	leukotriene A4 hydrolase	protein-coding	0.04	0.534653
Merged-chr6-146642695-1	chr6	146642645	146642745	+	4.1	cIP2vsInput	"intron (NM_025315, intron 1 of 3)"	CpG	116	NM_025315	108098	Mm.26212	NM_025315	ENSMUSG00000030291	Med21	0610007L03Rik|AI449604|D19234|D6Ertd782e|Srb7|Surb7	mediator complex subunit 21	protein-coding	0.08	0.653465
Merged-chr1-135729177-1	chr1	135729127	135729227	+	4.1	cIP2vsInput	promoter-TSS (NM_007791)	promoter-TSS (NM_007791)	-20	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding	0.1	0.643564
Merged-chrY-6802547-1	chrY	6802497	6802597	+	4.1	cIP2vsInput	Intergenic	L1Md_F3|LINE|L1	365230	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.366337
Merged-chr5-134184398-1	chr5	134184348	134184448	+	4.1	cIP2vsInput	"intron (NM_053266, intron 1 of 15)"	CpG	360	NM_053266	114674	Mm.218744	NM_053266	ENSMUSG00000015942	Gtf2ird2	1700012P16Rik	GTF2I repeat domain containing 2	protein-coding	0.13	0.712871
Merged-chr2-157279590-2	chr2	157279523	157279658	+	4.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001039557)	promoter-TSS (NM_001039557)	-41	NM_001039557	629499	Mm.384235	NM_001039557	ENSMUSG00000074627	Mroh8	4922505G16Rik	maestro heat-like repeat family member 8	protein-coding	0.111111	0.705882
Merged-chr8-124991702-2	chr8	124991638	124991767	+	4.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-21295	NM_016909	53424	Mm.458292	NM_016909	ENSMUSG00000056820	Tsnax	R74833|Trax	translin-associated factor X	protein-coding	0.023256	0.592308
Merged-chr8-107096485-1	chr8	107096435	107096535	+	4.1	cIP2vsInput	promoter-TSS (NM_001083118)	promoter-TSS (NM_001083118)	60	NM_001083118	21750	Mm.6402	NM_001083118	ENSMUSG00000031921	Terf2	TRF2	telomeric repeat binding factor 2	protein-coding	0.13	0.732673
Merged-chr17-29464183-1	chr17	29464133	29464233	+	4.1	cIP2vsInput	Intergenic	Intergenic	-26862	NM_008842	18712	Mm.485038	NM_008842		Pim1	Pim-1	proviral integration site 1	protein-coding	0.04	0.643564
Merged-chr3-89183119-2	chr3	89183058	89183181	+	4.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001014995)	promoter-TSS (NM_001014995)	-106	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	"family with sequence similarity 189, member B"	protein-coding	0.02439	0.629032
Merged-chr14-15439048-1	chr14	15438998	15439098	+	4.1	cIP2vsInput	promoter-TSS (NM_146052)	promoter-TSS (NM_146052)	-61	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding	0.05	0.60396
Merged-chr10-80742261-1	chr10	80742211	80742311	+	4.1	cIP2vsInput	promoter-TSS (NM_007460)	promoter-TSS (NM_007460)	-50	NM_007460	11776	Mm.209294	NM_007460	ENSMUSG00000020198	Ap3d1	AA407035|Ap3d|Bolvr|mBLVR1|mh|mocha	"adaptor-related protein complex 3, delta 1 subunit"	protein-coding	0.07	0.673267
Merged-chr3-96501646-1	chr3	96501596	96501696	+	4.1	cIP1vsInput	Intergenic	Intergenic	-23539	NM_027126	69585	Mm.171314	NM_027126	ENSMUSG00000038403	Hfe2	2310035L15Rik|5230400G09Rik|AI414844|AI789733|DL-M|HJV|Rgmc|hemojuvelin	hemochromatosis type 2 (juvenile) (human homolog)	protein-coding	0.05	0.326733
Merged-chr11-68638080-1	chr11	68638030	68638130	+	4.1	cIP2vsInput	Intergenic	Intergenic	51043	NM_177779	276920	Mm.123046	NM_177779	ENSMUSG00000045915	Ccdc42	A530001H01Rik	coiled-coil domain containing 42	protein-coding	0.01	0.50495
Merged-chr12-69987109-1	chr12	69987059	69987159	+	4.1	cIP2vsInput	promoter-TSS (NM_022028)	promoter-TSS (NM_022028)	-107	NM_022028	64010	Mm.390480	NM_022028	ENSMUSG00000021067	Sav1	1700040G09Rik|Salv|Sav|WW45|Wwp3|Wwp4	salvador homolog 1 (Drosophila)	protein-coding	0.17	0.762376
Merged-chr19-7418011-1	chr19	7417961	7418061	+	4.1	cIP2vsInput	"intron (NM_175381, intron 1 of 4)"	CpG	386	NM_175381	108899	Mm.386838	NM_175381	ENSMUSG00000053080	2700081O15Rik	AI255177|AI848741|AW742297	RIKEN cDNA 2700081O15 gene	protein-coding	0.12	0.792079
Merged-chr3-98013424-2	chr3	98013365	98013484	+	4.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010928)	promoter-TSS (NM_010928)	-114	NM_010928	18129	Mm.485843	NM_010928	ENSMUSG00000027878	Notch2	AI853703|N2	notch 2	protein-coding	0.142857	0.741667
Merged-chrX-169994108-1	chrX	169994058	169994158	+	4.1	cIP2vsInput	Intergenic	CpG	-15191	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	miscRNA	0.12	0.722772
Merged-chr19-47731410-1	chr19	47731360	47731460	+	4.1	cIP2vsInput	promoter-TSS (NM_026377)	promoter-TSS (NM_026377)	-346	NM_026377	67788	Mm.181610	NM_026377	ENSMUSG00000025066	Sfr1	6330577E15Rik|Meir5	SWI5 dependent recombination repair 1	protein-coding	0.08	0.70297
Merged-chr6-47595342-1	chr6	47595292	47595392	+	4.1	cIP2vsInput	promoter-TSS (NM_007971)	promoter-TSS (NM_007971)	-312	NM_001146689	14056	Mm.246688	NM_001146689	ENSMUSG00000029687	Ezh2	Enx-1|Enx1h|KMT6|mKIAA4065	enhancer of zeste homolog 2 (Drosophila)	protein-coding	0.1	0.752475
Merged-chr15-101977619-1	chr15	101977569	101977669	+	4.1	cIP2vsInput	Intergenic	Intergenic	-23332	NM_212487	332131	Mm.325105	NM_212487	ENSMUSG00000050463	Krt78	2310030B04Rik|Kb40	keratin 78	protein-coding	0.06	0.70297
Merged-chr16-44746182-1	chr16	44746132	44746232	+	4.1	cIP2vsInput	"exon (NM_025332, exon 1 of 6)"	"exon (NM_025332, exon 1 of 6)"	181	NM_001159329	66067	Mm.443456	NM_001159329		Gtpbp8	0610037H22Rik	GTP-binding protein 8 (putative)	protein-coding	0.08	0.623762
Merged-chr16-33056451-1	chr16	33056401	33056501	+	4.1	cIP2vsInput	promoter-TSS (NM_001130484)	promoter-TSS (NM_001130484)	-2	NM_001130485	57808	Mm.19355	NM_001130484	ENSMUSG00000060636	Rpl35a	2810431L15Rik|Rpl35	ribosomal protein L35A	protein-coding	0.13	0.712871
Merged-chr4-146050111-1	chr4	146050061	146050161	+	4.1	cIP1vsInput	Intergenic	Intergenic	-17413	NR_030771	627585	Mm.424988	NM_001039233	ENSMUSG00000082195	Gm13034	OTTMUSG00000010105	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 pseudogene"	pseudo	0	0.29703
Merged-chr12-21373600-1	chr12	21373550	21373650	+	4.1	cIP2vsInput	promoter-TSS (NR_102380)	promoter-TSS (NR_102380)	32	NR_102380	11491	Mm.27681	NM_001277266	ENSMUSG00000052593	Adam17	CD156b|Tace	a disintegrin and metallopeptidase domain 17	protein-coding	0.13	0.70297
Merged-chr4-120393004-2	chr4	120392934	120393075	+	4.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-12277	NM_013883	29871	Mm.427014	NM_001159630	ENSMUSG00000000085	Scmh1	AI315320|AI851618|Scml1|Scml3	sex comb on midleg homolog 1	protein-coding	0	0.415493
Merged-chr17-32036381-2	chr17	32036312	32036451	+	4.1	cIP1vsInput|cIP2vsInput	"5' UTR (NM_028244, exon 1 of 16)"	"5' UTR (NM_028244, exon 1 of 16)"	219	NM_028244	72462	Mm.102761	NM_001163734	ENSMUSG00000058392	Rrp1b	2600005C20Rik|D030064A17|Kiaa0179|mKIAA0179	ribosomal RNA processing 1 homolog B (S. cerevisiae)	protein-coding	0.194245	0.778571
Merged-chr4-46664818-2	chr4	46664753	46664883	+	4.1	cIP1vsInput|cIP2vsInput	"exon (NM_001081141, exon 19 of 19)"	"exon (NM_001081141, exon 19 of 19)"	-14619	NM_198664	381605	Mm.331595	NM_198664	ENSMUSG00000039813	Tbc1d2	A630005A06Rik|BC022630|Gm1037|PARIS-1|PARIS1	"TBC1 domain family, member 2"	protein-coding	0.069231	0.70229
Merged-chr17-70853546-1	chr17	70853496	70853596	+	4.1	cIP2vsInput	promoter-TSS (NM_001164074)	promoter-TSS (NM_001164074)	-14	NM_001164074	21815	Mm.101034	NM_001164074	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding	0.06	0.60396
Merged-chr4-151933695-1	chr4	151933645	151933745	+	4.1	cIP2vsInput	promoter-TSS (NM_172704)	promoter-TSS (NM_172704)	-25	NM_172704	230935	Mm.21353	NM_172704	ENSMUSG00000039768	Dnajc11	E030019A03Rik	"DnaJ (Hsp40) homolog, subfamily C, member 11"	protein-coding	0.15	0.732673
Merged-chr6-29735448-1	chr6	29735398	29735498	+	4.1	cIP2vsInput	promoter-TSS (NM_176996)	promoter-TSS (NM_176996)	-49	NM_176996	319757	Mm.29279	NM_176996	ENSMUSG00000001761	Smo	E130215L21Rik|Smoh|bnb|smoothened	smoothened homolog (Drosophila)	protein-coding	0.08	0.722772
Merged-chr6-42349948-1	chr6	42349898	42349998	+	4.1	cIP2vsInput	"5' UTR (NM_011777, exon 1 of 10)"	"5' UTR (NM_011777, exon 1 of 10)"	120	NM_011777	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding	0.08	0.732673
Merged-chr13-65631960-1	chr13	65631910	65632010	+	4.1	cIP2vsInput	Intergenic	Intergenic	353106	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding	0.01	0.316832
Merged-chr6-117574378-2	chr6	117574309	117574447	+	4.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	177391	NR_045731	72263	Mm.443289	NR_045731		1700030F04Rik	-	RIKEN cDNA 1700030F04 gene	miscRNA	0.021739	0.489209
Merged-chr7-127967614-1	chr7	127967564	127967664	+	4.1	cIP2vsInput	"intron (NM_139149, intron 1 of 14)"	CpG	135	NM_139149	233908	Mm.277680	NM_139149	ENSMUSG00000030795	Fus	D430004D17Rik|D930039C12Rik|Fus1|Tls	fused in sarcoma	protein-coding	0.12	0.673267
Merged-chr4-133910772-1	chr4	133910722	133910822	+	4.1	cIP2vsInput	Intergenic	CpG	-22973	NM_009097	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Rsk1|p90rsk|rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding	0.08	0.70297
Merged-chr9-63092171-1	chr9	63092121	63092221	+	4.1	cIP2vsInput	Intergenic	Intergenic	54809	NM_172446	207667	Mm.447200	NM_001163755	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding	0.04	0.594059
Merged-chr4-107253723-1	chr4	107253673	107253773	+	4.1	cIP2vsInput	promoter-TSS (NM_028394)	promoter-TSS (NM_028394)	-190	NM_029985	77809	Mm.29681	NM_029985	ENSMUSG00000028617	Lrrc42	A930011F22Rik|AA536996	leucine rich repeat containing 42	protein-coding	0.06	0.613861
Merged-chr10-31035024-2	chr10	31034946	31035102	+	4.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-192241	NM_013904	15214	Mm.103573	NM_013904	ENSMUSG00000019789	Hey2	CHF1|Herp1|Hrt2|bHLHb32|hesr2	hairy/enhancer-of-split related with YRPW motif 2	protein-coding	0.012821	0.535032
Merged-chr16-93770788-1	chr16	93770738	93770838	+	4.1	cIP2vsInput	"exon (NM_027293, exon 19 of 37)"	"exon (NM_027293, exon 19 of 37)"	58881	NM_027293	70028	Mm.23230	NM_026700	ENSMUSG00000022946	Dopey2	0610038M01Rik|2610510B01Rik|AI503246|C21orf5|mKIAA0933	dopey family member 2	protein-coding	0.02	0.643564
Merged-chr5-129670137-1	chr5	129670087	129670187	+	4.1	cIP2vsInput	promoter-TSS (NM_172462)	promoter-TSS (NM_172462)	-49	NM_172462	22648	Mm.135067	NM_172462	ENSMUSG00000051034	Zfp11	6720465D24|Krox-6|Zfp-11	zinc finger protein 11	protein-coding	0.12	0.673267
Merged-chr2-75703592-1	chr2	75703542	75703642	+	4.1	cIP2vsInput	"intron (NM_010902, intron 1 of 4)"	CpG	1049	NM_010902	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	AI194320|Nrf2	"nuclear factor, erythroid derived 2, like 2"	protein-coding	0.05	0.623762
Merged-chr1-153487480-1	chr1	153487430	153487530	+	4.1	cIP2vsInput	"intron (NM_007842, intron 1 of 27)"	CpG	180	NM_007842	13211	Mm.20000	NM_007842	ENSMUSG00000042699	Dhx9	AI326842|Ddx9|HEL-5|NDHII|RHA|mHEL-5	DEAH (Asp-Glu-Ala-His) box polypeptide 9	protein-coding	0.16	0.752475
Merged-chr1-65179259-1	chr1	65179209	65179309	+	4.1	cIP2vsInput	promoter-TSS (NM_010497)	promoter-TSS (NM_010497)	-117	NM_010497	15926	Mm.9925	NM_001111320	ENSMUSG00000025950	Idh1	AI314845|AI788952|E030024J03Rik|Id-1|Idh-1|Idpc	"isocitrate dehydrogenase 1 (NADP+), soluble"	protein-coding	0.07	0.60396
Merged-chr17-64473040-1	chr17	64472990	64473090	+	4.1	cIP2vsInput	Intergenic	Intergenic	82550	NR_045899	100043582	Mm.11170	NR_045899	ENSMUSG00000073377	AU016765	-	expressed sequence AU016765	miscRNA	0	0.39604
Merged-chr11-52744988-2	chr11	52744932	52745045	+	4.1	cIP1vsInput|cIP2vsInput	Intergenic	Tigger15a|DNA|TcMar-Tigger	-19718	NM_177059	320027	Mm.44518	NM_177059		Fstl4	B230374F23Rik|SPIG1|mKIAA1061	follistatin-like 4	protein-coding	0	0.429825
Merged-chr15-81745894-1	chr15	81745844	81745944	+	4.1	cIP2vsInput	"intron (NM_001081016, intron 1 of 22)"	CpG	1046	NM_001081016	20286	Mm.432075	NM_001081016	ENSMUSG00000022390	Zc3h7b	Gm627|Scrg3|Zc2h7b|mKIAA1031	zinc finger CCCH type containing 7B	protein-coding	0.14	0.762376
Merged-chr11-60634657-1	chr11	60634607	60634707	+	4.1	cIP1vsInput	Intergenic	MLTR31D_MM|LTR|ERVK	-65033	NM_001159405	16897	Mm.285453	NM_001159404	ENSMUSG00000020536	Llgl1	AI325176|Lgl1|Llglh|Mgl1	lethal giant larvae homolog 1 (Drosophila)	protein-coding	0	0.39604
Merged-chr1-133025223-1	chr1	133025173	133025273	+	4.1	cIP2vsInput	"intron (NM_008575, intron 1 of 11)"	CpG	125	NM_008575	17248	Mm.476028	NM_008575	ENSMUSG00000054387	Mdm4	4933417N07Rik|AA414968|AL023055|AU018793|AU021806|C85810|Mdmx	transformed mouse 3T3 cell double minute 4	protein-coding	0.09	0.70297
Merged-chr17-78916602-1	chr17	78916552	78916652	+	4.1	cIP2vsInput	"5' UTR (NM_001177403, exon 1 of 5)"	"5' UTR (NM_001177403, exon 1 of 5)"	103	NM_001177402	68554	Mm.391820	NM_001177402	ENSMUSG00000062691	1110001A16Rik	-	RIKEN cDNA 1110001A16 gene	protein-coding	0.1	0.663366
Merged-chr11-74724583-1	chr11	74724533	74724633	+	4.1	cIP2vsInput	promoter-TSS (NM_013625)	promoter-TSS (NM_013625)	-199	NM_013625	18472	Mm.397111	NM_013625	ENSMUSG00000020745	Pafah1b1	LIS-1|Lis1|MMS10-U|Mdsh|Ms10u|Pafaha	"platelet-activating factor acetylhydrolase, isoform 1b, subunit 1"	protein-coding	0.08	0.60396
Merged-chr14-54575797-2	chr14	54575715	54575879	+	4.1	cIP1vsInput|cIP2vsInput	"intron (NM_010590, intron 1 of 7)"	CpG	1864	NM_010590	16475	Mm.100253	NM_010590	ENSMUSG00000022178	Ajuba	Jub	ajuba LIM protein	protein-coding	0.140244	0.781818
Merged-chr1-150392760-1	chr1	150392710	150392810	+	4.1	cIP2vsInput	promoter-TSS (NM_133780)	promoter-TSS (NM_133780)	-78	NM_133780	108989	Mm.174256	NM_133780	ENSMUSG00000006005	Tpr	2610029M07Rik|C77892	translocated promoter region	protein-coding	0.07	0.584158
Merged-chr6-84105719-1	chr6	84105669	84105769	+	4.1	cIP2vsInput	"intron (NM_001077694, intron 22 of 54)"	CpG	86330	NM_021469	26903	Mm.220982	NM_001077694	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3|mFLJ00175	dysferlin	protein-coding	0.07	0.594059
Merged-chr4-149307956-1	chr4	149307906	149308006	+	4.1	cIP2vsInput	promoter-TSS (NM_008441)	promoter-TSS (NM_008441)	-258	NM_008441	16561	Mm.474289	NM_008441	ENSMUSG00000063077	Kif1b	A530096N05Rik|AI448212|AI506502|D4Mil1e|KIF1Bp130|KIF1Bp204|mKIAA0591	kinesin family member 1B	protein-coding	0.12	0.752475
Merged-chr9-121314188-1	chr9	121314138	121314238	+	4.1	cIP2vsInput	Intergenic	Intergenic	-37016	NM_177589	209012	Mm.371804	NM_177589	ENSMUSG00000040936	Ulk4	4932415A06Rik|A730098P15	unc-51-like kinase 4	protein-coding	0.03	0.60396
Merged-chr4-126753507-1	chr4	126753457	126753557	+	4.1	cIP2vsInput	promoter-TSS (NM_011986)	promoter-TSS (NM_011986)	-48	NM_001035525	100317	Mm.206206	NM_001035525	ENSMUSG00000028830	AU040320	A730047D20Rik|Kiaa0319l	expressed sequence AU040320	protein-coding	0.08	0.663366
Merged-chr1-59482076-1	chr1	59482026	59482126	+	4.1	cIP2vsInput	promoter-TSS (NM_008057)	promoter-TSS (NM_008057)	-71	NM_008057	14369	Mm.297906	NM_008057	ENSMUSG00000041075	Fzd7	Fz7	frizzled homolog 7 (Drosophila)	protein-coding	0.09	0.742574
Merged-chr14-30479590-1	chr14	30479540	30479640	+	4.1	cIP2vsInput	promoter-TSS (NM_133761)	promoter-TSS (NM_133761)	25	NM_133761	75901	Mm.28733	NM_133761	ENSMUSG00000021962	Dcp1a	1110066A22Rik|4930568L04Rik|AU019772|D14Ertd817e|Mitc1|SMIF	DCP1 decapping enzyme homolog A (S. cerevisiae)	protein-coding	0.04	0.594059
Merged-chr14-26638002-1	chr14	26637952	26638052	+	4.1	cIP2vsInput	promoter-TSS (NM_007479)	promoter-TSS (NM_007479)	-195	NM_007479	11843	Mm.297768	NM_007479	ENSMUSG00000021877	Arf4	AA407803	ADP-ribosylation factor 4	protein-coding	0.09	0.623762
Merged-chr11-61855127-1	chr11	61855077	61855177	+	4.1	cIP2vsInput	promoter-TSS (NM_013881)	promoter-TSS (NM_013881)	-35	NM_013881	29869	Mm.162025	NM_013881	ENSMUSG00000004798	Ulk2	A830085I22Rik|AU015340|Unc51.2|mKIAA0623	unc-51 like kinase 2	protein-coding	0.14	0.70297
Merged-chr6-51108500-1	chr6	51108450	51108550	+	4.1	cIP2vsInput	Intergenic	Intergenic	161410	NR_029719	387166		NR_029719	ENSMUSG00000065505	Mir148a	Mirn148|Mirn148a	microRNA 148a	miscRNA	0.03	0.633663
Merged-chr6-6371706-1	chr6	6371656	6371756	+	4.1	cIP2vsInput	Intergenic	MIR|SINE|MIR	-154533	NM_001177572	50799	Mm.24513	NM_001177572	ENSMUSG00000015112	Slc25a13	AI785475|Ctrn	"solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 13"	protein-coding	0.01	0.376238
Merged-chr12-4680095-1	chr12	4680045	4680145	+	4.1	cIP2vsInput	"intron (NM_011365, intron 28 of 38)"	"intron (NM_011365, intron 28 of 38)"	58288	NM_029107	74855	Mm.269534	NM_029107	ENSMUSG00000079177	Fam228a	4930417G10Rik	"family with sequence similarity 228, member A"	protein-coding	0.01	0.524752
Merged-chr6-122764811-1	chr6	122764761	122764861	+	4.1	cIP2vsInput	Intergenic	CpG	-22066	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	"solute carrier family 2 (facilitated glucose transporter), member 3"	protein-coding	0.13	0.752475
Merged-chr5-134099596-2	chr5	134099532	134099660	+	4.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_030719)	promoter-TSS (NM_030719)	-152	NM_030719	80909	Mm.426767	NM_030719		Gatsl2	7530428J21Rik|AW742413|Gats|Gatsl1	GATS protein-like 2	protein-coding	0.085938	0.658915
Merged-chr9-13296724-1	chr9	13296674	13296774	+	4.1	cIP2vsInput	Intergenic	Intergenic	49745	NM_025534	66396	Mm.290620	NM_025534		Ccdc82	2310043N13Rik	coiled-coil domain containing 82	protein-coding	0.02	0.663366
Merged-chr5-144966037-2	chr5	144965973	144966102	+	4.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029438)	promoter-TSS (NM_029438)	-207	NM_001038627	75788	Mm.27735	NM_001038627	ENSMUSG00000038780	Smurf1	4930431E10Rik|mKIAA1625	SMAD specific E3 ubiquitin protein ligase 1	protein-coding	0.077519	0.646154
Merged-chr10-86685484-2	chr10	86685414	86685555	+	4.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_015572)	promoter-TSS (NR_015572)	-43	NR_015572	66263	Mm.392261	NR_015572		1810014B01Rik	-	RIKEN cDNA 1810014B01 gene	pseudo	0.106383	0.612676
Merged-chr8-79562695-2	chr8	79562618	79562772	+	4.05	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-76981	NM_001256033	73945	Mm.34348	NM_001081164	ENSMUSG00000036990	Otud4	4930431L18Rik|AI449692|D8Ertd69e|mKIAA1046	OTU domain containing 4	protein-coding	0.006494	0.296774
Merged-chr15-76626100-2	chr15	76626043	76626157	+	4.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025842)	promoter-TSS (NM_025842)	-73	NM_025842	66914	Mm.30028	NM_025842	ENSMUSG00000062381	Vps28	1110014J03Rik|AI847241|D730005C08Rik	vacuolar protein sorting 28 (yeast)	protein-coding	0.078947	0.582609
Merged-chr17-47502322-2	chr17	47502252	47502392	+	4.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_022015)	promoter-TSS (NM_022015)	-35	NM_022015	63856	Mm.275901	NM_022015	ENSMUSG00000023980	Taf8	AW260255|Tbn	"TAF8 RNA polymerase II, TATA box binding protein (TBP)-associated factorq"	protein-coding	0.1	0.64539
Merged-chr5-74147773-2	chr5	74147722	74147824	+	4.05	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-47553	NM_026878	68939	Mm.293316	NM_026878	ENSMUSG00000049907	Rasl11b	1190017B18Rik	"RAS-like, family 11, member B"	protein-coding	0.039216	0.485437
Merged-chr8-24386426-2	chr8	24386370	24386482	+	4.05	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	52520	NM_026931	69068	Mm.25775	NM_026931	ENSMUSG00000056313	1810011O10Rik	1110065B09Rik|AW121743|AW321058	RIKEN cDNA 1810011O10 gene	protein-coding	0	0.353982
Merged-chr8-84761207-2	chr8	84761152	84761262	+	4.05	cIP1vsInput|cIP2vsInput	"intron (NM_010906, intron 2 of 8)"	"intron (NM_010906, intron 2 of 8)"	13162	NM_001081981	18032	Mm.9394	NM_001081981		Nfix	-	nuclear factor I/X	protein-coding	0	0.423423
Merged-chr2-35684178-2	chr2	35684110	35684246	+	4.05	cIP1vsInput|cIP2vsInput	"intron (NM_001114124, intron 3 of 15)"	"intron (NM_001114124, intron 3 of 15)"	-7816	NM_001001602	69601	Mm.29629	NM_001001602	ENSMUSG00000026883	Dab2ip	2310011D08Rik|AI480459|Aip1|mKIAA1743	disabled 2 interacting protein	protein-coding	0.014706	0.525547
Merged-chr16-8470844-2	chr16	8470793	8470896	+	4.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_146247)	promoter-TSS (NM_146247)	31	NM_146247	239706	Mm.214953	NM_146247		Mettl22	-	methyltransferase like 22	protein-coding	0.07767	0.682692
Merged-chr13-30974092-2	chr13	30974028	30974157	+	4.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025588)	promoter-TSS (NM_025588)	-45	NM_025588	66482	Mm.293510	NM_025588	ENSMUSG00000021357	Exoc2	2410030I24Rik|AI648199|Sec5|Sec5l1	exocyst complex component 2	protein-coding	0.139535	0.715385
Merged-chr16-84735273-2	chr16	84735220	84735326	+	4.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_017404)	promoter-TSS (NM_017404)	29	NM_017404	27393	Mm.103655	NM_017404	ENSMUSG00000022889	Mrpl39	C21orf8|MRP-L5|ORF22|Rpml5	mitochondrial ribosomal protein L39	protein-coding	0.122642	0.654206
Merged-chr6-148831634-2	chr6	148831557	148831712	+	4.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081113)	promoter-TSS (NM_001081113)	-167	NM_001081113	320727	Mm.468361	NM_001081113	ENSMUSG00000040029	Ipo8	6230418K12Rik|Abcc10|C130009K11Rik|MRP7|OM-1|Om1|Ranbp8	importin 8	protein-coding	0.058065	0.557692
Merged-chr11-102219040-2	chr11	102218973	102219108	+	4.05	cIP1vsInput|cIP2vsInput	"intron (NM_001077696, intron 2 of 26)"	"intron (NM_001077696, intron 2 of 26)"	11132	NM_001077696	15184	Mm.22665	NM_001077696	ENSMUSG00000008855	Hdac5	AI426555|Hdac4|mHDA1|mKIAA0600	histone deacetylase 5	protein-coding	0.044444	0.705882
Merged-chr17-74348792-2	chr17	74348724	74348860	+	4.05	cIP1vsInput|cIP2vsInput	"intron (NM_016962, intron 1 of 16)"	"intron (NM_016962, intron 1 of 16)"	9805	NM_016962	50850	Mm.19804	NM_001162870	ENSMUSG00000024068	Spast	Spg4|mKIAA1083	spastin	protein-coding	0	0.364964
Merged-chr4-40971181-2	chr4	40971123	40971240	+	4.05	cIP1vsInput|cIP2vsInput	"intron (NM_023739, intron 1 of 23)"	CpG	238	NM_023739	74164	Mm.439181	NM_023739	ENSMUSG00000028423	Nfx1	1300017N15Rik|3000003M19Rik|NFX.1|TEG-42|Tex42	"nuclear transcription factor, X-box binding 1"	protein-coding	0.111111	0.70339
Merged-chr11-50292578-2	chr11	50292499	50292658	+	4.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175334)	promoter-TSS (NM_175334)	-242	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding	0.062893	0.58125
Merged-chr3-95315182-2	chr3	95315120	95315244	+	4.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029789)	promoter-TSS (NM_029789)	-70	NM_029789	76893	Mm.181009	NM_029789	ENSMUSG00000015714	Cers2	0610013I17Rik|AI225939|Lass2|TRH3	ceramide synthase 2	protein-coding	0.112903	0.784
Merged-chr4-3835614-2	chr4	3835540	3835688	+	4.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026147)	promoter-TSS (NM_026147)	-14	NM_026147	67427	Mm.473992	NM_026147		Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding	0.135135	0.697987
Merged-chr7-29169627-2	chr7	29169574	29169680	+	4.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_182696)	promoter-TSS (NM_182696)	-583	NM_182694	243897	Mm.389886	NM_182696	ENSMUSG00000031493	Ggn	AI593290	gametogenetin	protein-coding	0.037736	0.672897
Merged-chr16-21423249-2	chr16	21423198	21423300	+	4.05	cIP1vsInput|cIP2vsInput	"intron (NM_001081366, intron 1 of 46)"	CpG	131	NM_001081366	209018	Mm.235683	NM_001081366	ENSMUSG00000033653	Vps8	AI315068|AU040738|mKIAA0804	vacuolar protein sorting 8 homolog (S. cerevisiae)	protein-coding	0.147059	0.747573
Merged-chr2-144270830-1	chr2	144270780	144270880	+	4	cIP2vsInput	promoter-TSS (NM_024225)	promoter-TSS (NM_024225)	72	NM_001199188	69178	Mm.273379	NM_001199188	ENSMUSG00000027423	Snx5	0910001N05Rik|1810032P22Rik|AU019504|D2Ertd52e	sorting nexin 5	protein-coding	0.15	0.663366
Merged-chr6-113696835-2	chr6	113696759	113696911	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001033463)	promoter-TSS (NM_001033463)	-664	NM_001033463	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding	0.072368	0.555556
Merged-chr11-49684744-1	chr11	49684694	49684794	+	4	cIP2vsInput	"intron (NM_212484, intron 6 of 11)"	(TG)n|Simple_repeat|Simple_repeat	21149	NM_170727	68662	Mm.22802	NM_054037	ENSMUSG00000064057	Scgb3a1	HIN-1|LuLeu2|Pnsp2|UGRP2|Utgrp2	"secretoglobin, family 3A, member 1"	protein-coding	0.08	0.49505
Merged-chr5-92310000-2	chr5	92309948	92310052	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172713)	promoter-TSS (NM_172713)	24	NM_172713	231452	Mm.86564	NM_172713	ENSMUSG00000029415	Sdad1	4931421J16|AA591032|AW538460	SDA1 domain containing 1	protein-coding	0.125	0.657143
Merged-chr14-20703052-2	chr14	20703002	20703103	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025366)	promoter-TSS (NM_025366)	25	NM_025366	66121	Mm.246996	NM_025366	ENSMUSG00000063787	Chchd1	1110001O19Rik|2400010G13Rik	coiled-coil-helix-coiled-coil-helix domain containing 1	protein-coding	0.138614	0.686275
Merged-chr8-105566807-2	chr8	105566753	105566861	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013477)	promoter-TSS (NM_013477)	-767	NM_013477	11972	Mm.17708	NM_013477	ENSMUSG00000013160	Atp6v0d1	AI267038|Ac39|Atp6d|P39|VATX|Vma6	"ATPase, H+ transporting, lysosomal V0 subunit D1"	protein-coding	0.083333	0.59633
Merged-chr17-31512299-1	chr17	31512249	31512349	+	4	cIP2vsInput	"exon (NM_021322, exon 1 of 11)"	"exon (NM_021322, exon 1 of 11)"	188	NM_021322	57773	Mm.143771	NM_021322	ENSMUSG00000024037	Wdr4	AI415180|AI448349|D530049K22Rik	WD repeat domain 4	protein-coding	0.18	0.732673
Merged-chr4-133967516-2	chr4	133967422	133967611	+	4	cIP1vsInput|cIP2vsInput	"intron (NM_016957, intron 1 of 5)"	CpG	475	NM_016957	15331	Mm.319660	NM_016957	ENSMUSG00000003038	Hmgn2	HMG-17|Hmg17	high mobility group nucleosomal binding domain 2	protein-coding	0.126984	0.742105
Merged-chr12-82169495-1	chr12	82169445	82169545	+	4	cIP2vsInput	promoter-TSS (NM_001167983)	promoter-TSS (NM_001167983)	-521	NM_001167983	217692	Mm.261333	NM_001167983	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding	0.13	0.683168
Merged-chr19-42518809-1	chr19	42518759	42518859	+	4	cIP2vsInput	promoter-TSS (NM_177464)	promoter-TSS (NM_177464)	4	NM_177464	52013	Mm.396211	NM_177464	ENSMUSG00000025184	R3hcc1l	1700036B12Rik|AI450607|C10orf28|D19Ertd386e|GIDRP86|Gidrp88	R3H domain and coiled-coil containing 1 like	protein-coding	0.14	0.742574
Merged-chr14-51884079-1	chr14	51884029	51884129	+	4	cIP2vsInput	promoter-TSS (NM_001029990)	promoter-TSS (NM_001029990)	-763	NM_001029990	52535	Mm.5750	NM_001029990	ENSMUSG00000004561	Mettl17	2310032K15Rik|D14Ertd209e|Mett11d1	methyltransferase like 17	protein-coding	0.02	0.386139
Merged-chr9-20385194-2	chr9	20385138	20385251	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001004190)	promoter-TSS (NM_001004190)	-36	NM_001004190	434377	Mm.379669	NM_001004190	ENSMUSG00000045519	Zfp560	2310030G09Rik|Znf560	zinc finger protein 560	protein-coding	0.097345	0.649123
Merged-chr6-32479268-1	chr6	32479218	32479318	+	4	cIP2vsInput	"intron (NM_175750, intron 3 of 31)"	"intron (NM_175750, intron 3 of 31)"	-31873	NR_040277	319849	Mm.440860	NR_040277	ENSMUSG00000086763	B230378P21Rik	-	RIKEN cDNA B230378P21 gene	miscRNA	0.02	0.633663
Merged-chr12-111537947-2	chr12	111537877	111538018	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_173363)	promoter-TSS (NM_173363)	-154	NM_178041	217869	Mm.470192	NM_173363	ENSMUSG00000021282	Eif5	2810011H21Rik|D12Ertd549e	eukaryotic translation initiation factor 5	protein-coding	0.092199	0.676056
Merged-chr7-113207792-1	chr7	113207742	113207842	+	4	cIP2vsInput	"intron (NM_007489, intron 1 of 19)"	CpG	327	NM_007489	11865	Mm.440371	NM_001243048	ENSMUSG00000055116	Arntl	Arnt3|BMAL1b|Bmal1|MOP3|bHLHe5|bmal1b'	aryl hydrocarbon receptor nuclear translocator-like	protein-coding	0.11	0.782178
Merged-chr11-52360912-1	chr11	52360862	52360962	+	4	cIP1vsInput	promoter-TSS (NM_011694)	promoter-TSS (NM_011694)	-203	NM_011694	22333	Mm.470023	NM_011694	ENSMUSG00000020402	Vdac1	AL033343|Vdac5	voltage-dependent anion channel 1	protein-coding	0.12	0.673267
Merged-chr4-155491324-2	chr4	155491261	155491388	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001160017)	promoter-TSS (NM_001160017)	-37	NM_008142	14688	Mm.2344	NM_001160016	ENSMUSG00000029064	Gnb1	AA409223|C77571|Gnb-1	"guanine nucleotide binding protein (G protein), beta 1"	protein-coding	0.173228	0.773438
Merged-chr13-100730685-1	chr13	100730635	100730735	+	4	cIP2vsInput	"intron (NM_009874, intron 1 of 11)"	"intron (NM_009874, intron 1 of 11)"	257	NM_009874	12572	Mm.259718	NM_009874	ENSMUSG00000069089	Cdk7	AI323415|AI528512|C230069N13|Cdkn7|Crk4	cyclin-dependent kinase 7	protein-coding	0.05	0.643564
Merged-chr5-137629105-1	chr5	137629055	137629155	+	4	cIP2vsInput	promoter-TSS (NM_146164)	promoter-TSS (NM_146164)	-18	NM_146164	231798	Mm.200763	NM_001168652	ENSMUSG00000093445	Lrch4	2810008P14Rik|2900069C24Rik|AI558103|LRN|LRRN4|SAP25|mFLJ00248	leucine-rich repeats and calponin homology (CH) domain containing 4	protein-coding	0.09	0.633663
Merged-chr16-96082689-2	chr16	96082591	96082787	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_176928)	promoter-TSS (NM_176928)	-261	NM_145125	93871	Mm.482469	NM_001103179	ENSMUSG00000022914	Brwd1	5330419I02Rik|D530019K20Rik|G1-403-16|Wdr9|repro5	bromodomain and WD repeat domain containing 1	protein-coding	0.142857	0.807107
Merged-chr1-191062942-2	chr1	191062873	191063011	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001163422)	promoter-TSS (NM_001163422)	-10	NM_026895	68972	Mm.237188	NM_001163421	ENSMUSG00000026632	Tatdn3	1500010M24Rik	TatD DNase domain containing 3	protein-coding	0.130435	0.690647
Merged-chr10-91171852-1	chr10	91171802	91171902	+	4	cIP2vsInput	promoter-TSS (NM_011605)	promoter-TSS (NM_011605)	-270	NM_001080130	21917	Mm.439157	NM_001080129	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding	0.09	0.653465
Merged-chr16-37994998-1	chr16	37994948	37995048	+	4	cIP1vsInput	"intron (NM_153394, intron 8 of 9)"	"intron (NM_153394, intron 8 of 9)"	-22325	NR_040565	75175	Mm.399335	NR_040565		4930542C21Rik	-	RIKEN cDNA 4930542C21 gene	miscRNA	0.05	0.564356
Merged-chr2-112454981-1	chr2	112454931	112455031	+	4	cIP2vsInput	promoter-TSS (NM_133749)	promoter-TSS (NM_133749)	-44	NM_133749	73024	Mm.489361	NM_133749		Emc7	2900064A13Rik|AI451465|ORF3|c11orf3	ER membrane protein complex subunit 7	protein-coding	0.13	0.70297
Merged-chr14-62837692-1	chr14	62837642	62837742	+	4	cIP2vsInput	promoter-TSS (NM_175546)	promoter-TSS (NM_175546)	2	NM_175546	268752	Mm.482243	NM_175546	ENSMUSG00000014547	Wdfy2	5830485M08|B130024L21Rik|ProF|ZFYVE22	WD repeat and FYVE domain containing 2	protein-coding	0.09	0.752475
Merged-chr1-136137746-2	chr1	136137672	136137821	+	4	cIP1vsInput|cIP2vsInput	"intron (NM_001039472, intron 1 of 34)"	(TG)n|Simple_repeat|Simple_repeat	6345	NM_001039472	16565	Mm.276135	NM_001039472	ENSMUSG00000041642	Kif21b	2610511N21Rik|mKIAA0449	kinesin family member 21B	protein-coding	0.020134	0.566667
Merged-chr18-6516288-1	chr18	6516238	6516338	+	4	cIP2vsInput	promoter-TSS (NM_007935)	promoter-TSS (NM_007935)	-180	NM_007935	13831	Mm.312133	NM_001276350	ENSMUSG00000024240	Epc1	2400007E14Rik|5730566F07Rik|A930032N02Rik	enhancer of polycomb homolog 1 (Drosophila)	protein-coding	0.07	0.633663
Merged-chr1-179546335-1	chr1	179546285	179546385	+	4	cIP2vsInput	promoter-TSS (NM_008249)	promoter-TSS (NM_008249)	-68	NM_008249	15278	Mm.293529	NM_008249	ENSMUSG00000026492	Tfb2m	Hkp1	"transcription factor B2, mitochondrial"	protein-coding	0.09	0.673267
Merged-chr2-91202884-2	chr2	91202817	91202952	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007387)	promoter-TSS (NM_007387)	-28	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	"acid phosphatase 2, lysosomal"	protein-coding	0.066667	0.595588
Merged-chr15-98568051-1	chr15	98568001	98568101	+	4	cIP2vsInput	promoter-TSS (NM_009833)	promoter-TSS (NM_009833)	-415	NM_009833	12455	Mm.86538	NM_009833	ENSMUSG00000011960	Ccnt1	2810478G24Rik|AI115585|CycT1	cyclin T1	protein-coding	0.08	0.554455
Merged-chr12-86983656-1	chr12	86983606	86983706	+	4	cIP2vsInput	"intron (NM_001080943, intron 1 of 1)"	"intron (NM_001080943, intron 1 of 1)"	5020	NM_001080943	238331	Mm.185890	NM_001080943	ENSMUSG00000048483	Zdhhc22	Gm262	"zinc finger, DHHC-type containing 22"	protein-coding	0.06	0.613861
Merged-chr6-83456564-1	chr6	83456514	83456614	+	4	cIP2vsInput	Intergenic	CpG	14809	NR_028382	320775	Mm.434334	NR_028382	ENSMUSG00000051844	B230319C09Rik	-	RIKEN cDNA B230319C09 gene	miscRNA	0.18	0.831683
Merged-chr12-108894283-2	chr12	108894226	108894341	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001164314)	promoter-TSS (NM_001164314)	11	NM_177602	212198	Mm.342082	NM_177602	ENSMUSG00000040877	Wdr25	B930090D16Rik	WD repeat domain 25	protein-coding	0.095652	0.646552
Merged-chr8-70700690-1	chr8	70700640	70700740	+	4	cIP2vsInput	TTS (NM_010592)	TTS (NM_010592)	2951	NM_010592	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	Jun proto-oncogene related gene d	protein-coding	0.02	0.732673
Merged-chr9-65032364-1	chr9	65032314	65032414	+	4	cIP2vsInput	promoter-TSS (NM_028906)	promoter-TSS (NM_028906)	-94	NM_028906	74388	Mm.391842	NM_028906	ENSMUSG00000032393	Dpp8	2310004I03Rik|4932434F09Rik|AI666706|DPP VIII	dipeptidylpeptidase 8	protein-coding	0.1	0.693069
Merged-chr17-85090331-2	chr17	85090264	85090398	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145984)	promoter-TSS (NM_145984)	-57	NM_001163624	213760	Mm.461481	NM_001163622	ENSMUSG00000024127	Prepl	2810457N15Rik|9530014L06Rik|D030028O16Rik|mKIAA0436	prolyl endopeptidase-like	protein-coding	0.052239	0.488889
Merged-chr3-86224127-2	chr3	86224053	86224202	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_030695)	promoter-TSS (NM_030695)	-563	NM_001077688	80877	Mm.439825	NM_001077687	ENSMUSG00000028080	Lrba	C80285|D3Ertd775e|Lab300|Lba	LPS-responsive beige-like anchor	protein-coding	0.174497	0.78
Merged-chr11-117654172-1	chr11	117654122	117654222	+	4	cIP2vsInput	promoter-TSS (NM_198022)	promoter-TSS (NM_198022)	-117	NM_198022	217351	Mm.473244	NM_198022	ENSMUSG00000025571	Tnrc6c	9930033H14Rik|mKIAA1582	trinucleotide repeat containing 6C	protein-coding	0.15	0.70297
Merged-chr9-40800720-1	chr9	40800670	40800770	+	4	cIP2vsInput	promoter-TSS (NM_031165)	promoter-TSS (NM_031165)	-553	NM_031165	15481	Mm.485345	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding	0.09	0.663366
Merged-chr18-33463512-1	chr18	33463462	33463562	+	4	cIP2vsInput	promoter-TSS (NR_045415)	promoter-TSS (NR_045415)	122	NM_001267717	27528	Mm.407415	NM_001109988	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding	0.02	0.653465
Merged-chr4-140624612-1	chr4	140624562	140624662	+	4	cIP2vsInput	"intron (NM_001112722, intron 1 of 27)"	(GA)n|Simple_repeat|Simple_repeat	24144	NM_001112723	72754	Mm.29329	NM_001112722	ENSMUSG00000040964	Arhgef10l	2810441C07Rik|mKIAA1626	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding	0.03	0.564356
Merged-chr19-8992932-1	chr19	8992882	8992982	+	4	cIP2vsInput	"intron (NM_001039959, intron 1 of 5)"	"intron (NM_001039959, intron 1 of 5)"	3648	NM_001039959	66395	Mm.392302	NM_175108	ENSMUSG00000069833	Ahnak	1110004P15Rik|2310047C17Rik|AA589382|AV091586|DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding	0.02	0.643564
Merged-chr7-127470937-1	chr7	127470887	127470987	+	4	cIP1vsInput	promoter-TSS (NM_145589)	promoter-TSS (NM_145589)	-677	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding	0.05	0.514851
Merged-chr1-188773103-1	chr1	188773053	188773153	+	4	cIP2vsInput	"intron (NM_021408, intron 46 of 70)"	"intron (NM_021408, intron 46 of 70)"	234737	NM_172650	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding	0.01	0.445545
Merged-chr4-132212372-2	chr4	132212312	132212432	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145393)	promoter-TSS (NM_145393)	-116	NM_145393	213541	Mm.23998	NM_145393	ENSMUSG00000040025	Ythdf2	9430020E02Rik|HGRG8|NY-REN-2	YTH domain family 2	protein-coding	0.091667	0.710744
Merged-chr4-134287249-2	chr4	134287182	134287317	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001163794)	promoter-TSS (NM_001163794)	4	NM_001163794	230809	Mm.22778	NM_001163794	ENSMUSG00000050890	Pdik1l	BC027088|stk35l2	PDLIM1 interacting kinase 1 like	protein-coding	0.140741	0.764706
Merged-chr9-116873348-1	chr9	116873298	116873398	+	4	cIP2vsInput	"intron (NM_001172126, intron 4 of 12)"	"intron (NM_001172126, intron 4 of 12)"	379135	NM_001172123	207181	Mm.326411	NM_001172121	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	"RNA binding motif, single stranded interacting protein"	protein-coding	0.05	0.524752
Merged-chr2-164911736-2	chr2	164911648	164911825	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_199027)	promoter-TSS (NM_199027)	14	NM_199027	329559	Mm.330776	NM_199027	ENSMUSG00000039834	Zfp335	1810045J01Rik|NIF-1|Nif1|Znf335	zinc finger protein 335	protein-coding	0.067797	0.606742
Merged-chr5-136198995-1	chr5	136198945	136199045	+	4	cIP2vsInput	promoter-TSS (NM_025774)	promoter-TSS (NM_025774)	-41	NM_025774	66801	Mm.425295	NM_025774		Prkrip1	8430424D23Rik|C114	Prkr interacting protein 1 (IL11 inducible)	protein-coding	0.12	0.663366
Merged-chr14-101883994-2	chr14	101883922	101884067	+	4	cIP1vsInput|cIP2vsInput	"intron (NM_201529, intron 7 of 30)"	"intron (NM_201529, intron 7 of 30)"	154066	NM_201529	380928		NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding	0.013793	0.479452
Merged-chr8-70527856-1	chr8	70527806	70527906	+	4	cIP2vsInput	promoter-TSS (NM_001199631)	promoter-TSS (NM_001199631)	10	NM_001199631	14232	Mm.482129	NM_001111066	ENSMUSG00000019428	Fkbp8	38kDa|FKBP-38|FKBP-8|Fkbp38	FK506 binding protein 8	protein-coding	0.12	0.782178
Merged-chr5-123749154-1	chr5	123749104	123749204	+	4	cIP2vsInput	promoter-TSS (NM_001042421)	promoter-TSS (NM_001042421)	260	NM_001005525	208606	Mm.276341	NM_001005523	ENSMUSG00000029422	Rsrc2	1500011J06Rik	arginine/serine-rich coiled-coil 2	protein-coding	0.09	0.683168
Merged-chr17-29717118-2	chr17	29717043	29717194	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026782)	promoter-TSS (NM_026782)	-101	NM_001163741	68597	Mm.390979	NM_001163741	ENSMUSG00000024018	Ccdc167	1110021J02Rik	coiled-coil domain containing 167	protein-coding	0.066225	0.585526
Merged-chr14-73524979-2	chr14	73524928	73525030	+	4	cIP1vsInput|cIP2vsInput	"intron (NM_172527, intron 3 of 4)"	CpG	14930	NM_026119	67381	Mm.282888	NM_026119	ENSMUSG00000022109	Med4	2410046H15Rik|DRIP36|HSPC126|TRAP36|Vdirp|Vdrip	"mediator of RNA polymerase II transcription, subunit 4 homolog (yeast)"	protein-coding	0.127451	0.631068
Merged-chr8-34995960-2	chr8	34995898	34996022	+	4	cIP1vsInput|cIP2vsInput	Intergenic	MER68|LTR|ERVL	-30270	NM_175091	21951	Mm.88364	NM_175091	ENSMUSG00000031529	Tnks	4930554K12Rik|AI662855|ARTD5|C86528|D130072O21Rik|TANK1|mTNKS1	"tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase"	protein-coding	0.032258	0.544
Merged-chr16-20610772-1	chr16	20610722	20610822	+	4	cIP2vsInput	promoter-TSS (NM_145939)	promoter-TSS (NM_145939)	-23	NM_145939	208624	Mm.24950	NM_145939	ENSMUSG00000033809	Alg3	D16Ertd36e	"asparagine-linked glycosylation 3 (alpha-1,3-mannosyltransferase)"	protein-coding	0.05	0.584158
Merged-chr3-157848724-1	chr3	157848674	157848774	+	4	cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	76339	NM_145953	107869	Mm.28301	NM_145953	ENSMUSG00000028179	Cth	0610010I13Rik|AI314617|BC019483|CSE|Cys3	cystathionase (cystathionine gamma-lyase)	protein-coding	0.01	0.445545
Merged-chr2-84799304-1	chr2	84799254	84799354	+	4	cIP2vsInput	"intron (NM_019949, intron 1 of 3)"	"intron (NM_019949, intron 1 of 3)"	476	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding	0.01	0.425743
Merged-chr15-83367451-2	chr15	83367380	83367523	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_027980)	promoter-TSS (NR_027980)	-154	NR_027980	69291	Mm.66794	NM_001033147		1700001L05Rik	-	RIKEN cDNA 1700001L05 gene	miscRNA	0.104895	0.708333
Merged-chr4-146050493-1	chr4	146050443	146050543	+	4	cIP1vsInput	Intergenic	Intergenic	-17031	NR_030771	627585	Mm.424988	NM_001039233	ENSMUSG00000082195	Gm13034	OTTMUSG00000010105	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 pseudogene"	pseudo	0	0.346535
Merged-chr8-11497459-1	chr8	11497409	11497509	+	4	cIP2vsInput	promoter-TSS (NM_001190357)	promoter-TSS (NM_001190357)	-47	NM_001190357	69225	Mm.64911	NM_001190357	ENSMUSG00000031505	Carkd	0710008K08Rik|2810407E01Rik	carbohydrate kinase domain containing	protein-coding	0.09	0.663366
Merged-chr4-32336855-1	chr4	32336805	32336905	+	4	cIP1vsInput	Intergenic	Intergenic	-80580	NM_001109661	12014	Mm.431426	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology 2	protein-coding	0.01	0.514851
Merged-chr18-77773955-1	chr18	77773905	77774005	+	4	cIP2vsInput	"5' UTR (NM_007505, exon 1 of 12)"	"5' UTR (NM_007505, exon 1 of 12)"	187	NM_007505	11946	Mm.276137	NM_007505	ENSMUSG00000025428	Atp5a1	AI035633|AL022851|AL023067|Atpm|D18Ertd206e|Mom2	"ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1"	protein-coding	0.08	0.623762
Merged-chr11-59163837-1	chr11	59163787	59163887	+	4	cIP1vsInput	promoter-TSS (NM_173785)	promoter-TSS (NM_173785)	-92	NM_173785	216792	Mm.487361	NM_183110	ENSMUSG00000049287	Iba57	4930543L23Rik|A230051G13Rik|C1orf69	"IBA57, iron-sulfur cluster assembly homolog (S. cerevisiae)"	protein-coding	0.04	0.594059
Merged-chr19-41503466-1	chr19	41503416	41503516	+	4	cIP1vsInput	Intergenic	Intergenic	-46173	NM_172154	212391	Mm.459119	NM_172154	ENSMUSG00000025019	Lcor	3110023F06Rik|A630025C20Rik|Mlr2|mKIAA1795	ligand dependent nuclear receptor corepressor	protein-coding	0	0.326733
Merged-chr6-51384175-2	chr6	51384125	51384226	+	4	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-48495	NM_010903	18025	Mm.42138	NM_010903	ENSMUSG00000029832	Nfe2l3	Nrf3	"nuclear factor, erythroid derived 2, like 3"	protein-coding	0.079208	0.519608
Merged-chr16-18248748-2	chr16	18248671	18248825	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011239)	promoter-TSS (NM_011239)	-54	NM_011239	19385	Mm.235287	NM_011239		Ranbp1	Htf9a	RAN binding protein 1	protein-coding	0.123377	0.664516
Merged-chr11-46202140-1	chr11	46202090	46202190	+	4	cIP2vsInput	"intron (NM_133769, intron 28 of 30)"	"intron (NM_133769, intron 28 of 30)"	-33417	NM_177075	320116	Mm.154358	NM_177075	ENSMUSG00000048721	Fndc9	C030019I05Rik	fibronectin type III domain containing 9	protein-coding	0.03	0.49505
Merged-chr12-12518994-2	chr12	12518928	12519060	+	4	cIP1vsInput|cIP2vsInput	Intergenic	L2a|LINE|L2	-126519	NR_045829	70858	Mm.410838	NR_045829		4921511I17Rik	-	RIKEN cDNA 4921511I17 gene	miscRNA	0.007576	0.390977
Merged-chr7-4915404-2	chr7	4915332	4915476	+	4	cIP1vsInput|cIP2vsInput	"5' UTR (NM_170759, exon 1 of 3)"	"5' UTR (NM_170759, exon 1 of 3)"	187	NM_170759	232816	Mm.27442	NM_170759	ENSMUSG00000074406	Zfp628	Zec|Znf628	zinc finger protein 628	protein-coding	0.104167	0.731034
Merged-chr9-44498877-1	chr9	44498827	44498927	+	4	cIP2vsInput	promoter-TSS (NM_030256)	promoter-TSS (NM_030256)	-259	NM_030256	80288	Mm.370270	NM_030256	ENSMUSG00000063382	Bcl9l	B9L|BC003321|BCL9-2|DLNB11	B cell CLL/lymphoma 9-like	protein-coding	0.04	0.643564
Merged-chr19-6084886-1	chr19	6084836	6084936	+	4	cIP2vsInput	promoter-TSS (NM_026410)	promoter-TSS (NM_026410)	5	NM_024231	81909	Mm.289471	NM_024231	ENSMUSG00000024792	Zfpl1	1500015B20Rik	zinc finger like protein 1	protein-coding	0.09	0.663366
Merged-chr2-114654858-2	chr2	114654797	114654920	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025675)	promoter-TSS (NM_025675)	70	NM_025675	66632	Mm.117809	NM_025675	ENSMUSG00000057147	Atpbd4	5730421E18Rik	ATP binding domain 4	protein-coding	0.105691	0.645161
Merged-chr3-132684084-2	chr3	132684012	132684156	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007926)	promoter-TSS (NM_007926)	-60	NM_001163455	271981	Mm.440106	NM_001163455	ENSMUSG00000028030	Tbck	1700120J03Rik|9430001M19|A630047E20Rik|C030007I09Rik|Tbckl	TBC1 domain containing kinase	protein-coding	0.083333	0.62069
Merged-chr2-80280607-1	chr2	80280557	80280657	+	4	cIP2vsInput	Intergenic	Intergenic	-11863	NM_177256	320769	Mm.60992	NR_033713	ENSMUSG00000050114	Prdx6b	1-cysPrx-P1|4930414C22Rik|Aop2-rs1|Prdx5-rs1|Prdx6-ps1|Prdx6-rs1|Prdx6-rs1-ps	peroxiredoxin 6B	protein-coding	0.02	0.366337
Merged-chr9-40414609-1	chr9	40414559	40414659	+	4	cIP2vsInput	"intron (NM_172768, intron 1 of 19)"	RLTR16C_MM|LTR|ERVK	41155	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding	0.06	0.663366
Merged-chr17-26252991-1	chr17	26252941	26253041	+	4	cIP2vsInput	promoter-TSS (NR_037906)	promoter-TSS (NR_037906)	81	NR_037905	66978	Mm.440216	NM_025881	ENSMUSG00000024188	Luc7l	1810045C04Rik|2410018D03Rik	Luc7 homolog (S. cerevisiae)-like	protein-coding	0.09	0.623762
Merged-chr9-114528152-2	chr9	114528096	114528209	+	4	cIP1vsInput|cIP2vsInput	"intron (NM_001042503, intron 1 of 3)"	"intron (NM_001042503, intron 1 of 3)"	-31608	NM_009916	12773	Mm.1337	NM_009916	ENSMUSG00000047898	Ccr4	C-C CKR-4|CHEMR1|Cmkbr4|LESTR|Sdf1r	chemokine (C-C motif) receptor 4	protein-coding	0.061947	0.640351
Merged-chr19-46338696-2	chr19	46338620	46338773	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_024192)	promoter-TSS (NM_024192)	-36	NM_024192	67116	Mm.218848	NM_001164290	ENSMUSG00000036748	Cuedc2	3010002G01Rik	CUE domain containing 2	protein-coding	0.052288	0.577922
Merged-chr2-26640285-1	chr2	26640235	26640335	+	4	cIP2vsInput	promoter-TSS (NR_028571)	promoter-TSS (NR_028571)	-41	NR_024068	72091	Mm.27103	NR_024068	ENSMUSG00000097052	Snhg7	2610002F03Rik|AI427062	small nucleolar RNA host gene (non-protein coding) 7	miscRNA	0.1	0.623762
Merged-chr16-32247109-1	chr16	32247059	32247159	+	4	cIP2vsInput	promoter-TSS (NM_001185162)	promoter-TSS (NM_001185162)	-84	NM_173439	268882	Mm.256137	NM_173439	ENSMUSG00000035764	Fbxo45	2610017J04Rik|AI463119|BC026799	F-box protein 45	protein-coding	0.16	0.782178
Merged-chr13-24831616-1	chr13	24831566	24831666	+	4	cIP2vsInput	promoter-TSS (NM_025790)	promoter-TSS (NM_025790)	-43	NM_019551	56196	Mm.427162	NM_019551	ENSMUSG00000035958	Tdp2	D13Ertd656e|Ttrap	tyrosyl-DNA phosphodiesterase 2	protein-coding	0.16	0.722772
Merged-chr6-122393788-2	chr6	122393735	122393842	+	4	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-53561	NM_001271579	13619	Mm.6822	NM_001042623	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding	0.037383	0.564815
Merged-chr5-122372439-2	chr5	122372382	122372496	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_024216)	promoter-TSS (NM_024216)	-69	NM_024216	68080		NM_024216	ENSMUSG00000029464	Gpn3	A930018B01Rik|Atpbd1c|D5Ertd708e	GPN-loop GTPase 3	protein-coding	0.105263	0.591304
Merged-chr11-84916430-2	chr11	84916365	84916495	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001005223)	promoter-TSS (NM_001005223)	-74	NM_001005223	448850	Mm.379733	NM_001005223	ENSMUSG00000020526	Znhit3	Myohd1|Trip3	"zinc finger, HIT type 3"	protein-coding	0.023077	0.458015
Merged-chr5-115327522-1	chr5	115327472	115327572	+	4	cIP2vsInput	"intron (NR_036616, intron 1 of 4)"	CpG	345	NR_036616	108014	Mm.287826	NM_025573	ENSMUSG00000029538	Srsf9	25kDa|2610029M16Rik|SRp30c|Sfrs9	serine/arginine-rich splicing factor 9	protein-coding	0.14	0.772277
Merged-chr17-74295500-1	chr17	74295450	74295550	+	4	cIP2vsInput	promoter-TSS (NM_133771)	promoter-TSS (NM_133771)	-637	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding	0.15	0.792079
Merged-chr2-69885666-1	chr2	69885616	69885716	+	4	cIP2vsInput	promoter-TSS (NM_029280)	promoter-TSS (NM_029280)	-62	NM_029280	75422	Mm.268657	NM_029280	ENSMUSG00000051730	Mettl5	2810410A08Rik	methyltransferase like 5	protein-coding	0.12	0.683168
Merged-chr4-41640275-1	chr4	41640225	41640325	+	4	cIP2vsInput	promoter-TSS (NM_027147)	promoter-TSS (NM_027147)	27	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding	0.14	0.752475
Merged-chr10-13553182-1	chr10	13553132	13553232	+	4	cIP2vsInput	promoter-TSS (NM_019961)	promoter-TSS (NM_019961)	-40	NM_001164195	56535	Mm.282711	NM_001164195	ENSMUSG00000019809	Pex3	1700014F15Rik|2810027F19Rik|2900010N04Rik	peroxisomal biogenesis factor 3	protein-coding	0.11	0.653465
Merged-chr3-38484915-2	chr3	38484815	38485015	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001167883)	promoter-TSS (NM_001167883)	-99	NM_001167883	99696	Mm.290937	NM_001033198	ENSMUSG00000044864	Ankrd50	AI662170|E430012K20Rik|mKIAA1223|mKIAA3019	ankyrin repeat domain 50	protein-coding	0.085	0.706468
Merged-chr7-45216625-1	chr7	45216575	45216675	+	4	cIP2vsInput	"intron (NM_011565, intron 1 of 11)"	"intron (NM_011565, intron 1 of 11)"	872	NM_011565	21677	Mm.3019	NM_011565	ENSMUSG00000030796	Tead2	ETF|Etdf|TEAD-2|TEF-4|TEF4	TEA domain family member 2	protein-coding	0.06	0.742574
Merged-chr11-87127196-1	chr11	87127146	87127246	+	4	cIP2vsInput	"5' UTR (NM_197987, exon 1 of 24)"	"5' UTR (NM_197987, exon 1 of 24)"	121	NM_197987	68729	Mm.17436	NM_197987	ENSMUSG00000018548	Trim37	1110032A10Rik|2810004E07Rik|AI848587|AU043018|MUL|TEF3|mKIAA0898	tripartite motif-containing 37	protein-coding	0.16	0.772277
Merged-chr2-162931349-2	chr2	162931298	162931401	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026499)	promoter-TSS (NM_026499)	-159	NM_026499	67996	Mm.24042	NM_026499	ENSMUSG00000016921	Srsf6	1210001E11Rik|AI314910|AW146126|Sfrs6	serine/arginine-rich splicing factor 6	protein-coding	0.097087	0.634615
Merged-chr3-97227207-1	chr3	97227157	97227257	+	4	cIP2vsInput	"intron (NM_029933, intron 1 of 9)"	GC_rich|Low_complexity|Low_complexity	157	NM_029933	77578	Mm.482931	NM_029933	ENSMUSG00000038256	Bcl9	2610202E01Rik|8030475K17Rik|A330041G23Rik|Gm130	B cell CLL/lymphoma 9	protein-coding	0.16	0.871287
Merged-chr9-108460499-2	chr9	108460421	108460578	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133744)	promoter-TSS (NM_133744)	-19	NM_133744	72454	Mm.46488	NM_133744	ENSMUSG00000049305	Ccdc71	2600016J21Rik	coiled-coil domain containing 71	protein-coding	0.076433	0.677215
Merged-chr19-6077278-2	chr19	6077220	6077337	+	4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081041)	promoter-TSS (NM_001081041)	-91	NM_001081041	68505	Mm.227361	NM_001081041	ENSMUSG00000024797	Vps51	1110014N23Rik|3110057M17Rik|AI837850|Ffr	vacuolar protein sorting 51 homolog (S. cerevisiae)	protein-coding	0.042735	0.525424
Merged-chr2-155473794-1	chr2	155473744	155473844	+	4	cIP2vsInput	Intergenic	Intergenic	-33011	NM_019825	56406	Mm.27592	NM_001242558	ENSMUSG00000038369	Ncoa6	AIB3|ASC-2|ASC2|NRC|Ncoa7|PRIP|RAP250|mKIAA0181	nuclear receptor coactivator 6	protein-coding	0.13	0.841584
Merged-chr8-89245278-1	chr8	89245228	89245328	+	4	cIP2vsInput	Intergenic	Intergenic	-201116	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding	0.05	0.50495
Merged-chr10-126978789-1	chr10	126978739	126978839	+	4	cIP2vsInput	promoter-TSS (NM_001113470)	promoter-TSS (NM_001113470)	72	NM_001113470	52468	Mm.29490	NM_001113470	ENSMUSG00000078429	Ctdsp2	AI586070|D10Ertd73e|OS-4|OS4|SCP2	"CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2"	protein-coding	0.14	0.772277
Merged-chr11-69671366-2	chr11	69671313	69671419	+	3.95	cIP1vsInput|cIP2vsInput	"intron (NM_144958, intron 1 of 10)"	CpG	1057	NM_144958	13681	Mm.473799	NM_001159375	ENSMUSG00000059796	Eif4a1	BM-010|Ddx2a|Eif4	eukaryotic translation initiation factor 4A1	protein-coding	0.113208	0.785047
Merged-chr11-21398733-2	chr11	21398677	21398789	+	3.95	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-27854	NM_139297	216558	Mm.28877	NM_139297	ENSMUSG00000001891	Ugp2	-	UDP-glucose pyrophosphorylase 2	protein-coding	0.035714	0.513274
Merged-chr7-127345627-2	chr7	127345570	127345684	+	3.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_146202)	promoter-TSS (NM_146202)	-313	NM_146202	233890	Mm.23031	NM_146202	ENSMUSG00000047371	Zfp768	BC026432|Znf768	zinc finger protein 768	protein-coding	0.096491	0.765217
Merged-chr5-137290966-2	chr5	137290906	137291026	+	3.95	cIP1vsInput|cIP2vsInput	"exon (NM_009599, exon 2 of 5)"	"exon (NM_009599, exon 2 of 5)"	2689	NM_009599	11423	Mm.489229	NM_009599	ENSMUSG00000023328	Ache	mE1a|mE1b|mE1c|mE1c-long|mE1d|mE1d'|mE1e	acetylcholinesterase	protein-coding	0.058333	0.578512
Merged-chr8-94838427-2	chr8	94838367	94838488	+	3.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_134141)	promoter-TSS (NM_134141)	10	NM_026452	67914	Mm.169234	NM_026452	ENSMUSG00000031782	Coq9	2310005O14Rik|C78387	coenzyme Q9 homolog (yeast)	protein-coding	0.123967	0.721311
Merged-chr18-37935582-2	chr18	37935530	37935634	+	3.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007858)	promoter-TSS (NM_007858)	-171	NM_007858	13367	Mm.195916	NM_007858	ENSMUSG00000024456	Diap1	D18Wsu154e|Dia1|Diaph1|Drf1|mKIAA4062|p140mDia	diaphanous homolog 1 (Drosophila)	protein-coding	0.096154	0.695238
Merged-chr6-88831651-2	chr6	88831593	88831709	+	3.95	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	10284	NM_030251	80283	Mm.166858	NM_030251	ENSMUSG00000030083	Abtb1	AI847549|BC003234|BPOZ|EF1ABP	ankyrin repeat and BTB (POZ) domain containing 1	protein-coding	0.034483	0.57265
Merged-chr5-135149413-2	chr5	135149356	135149471	+	3.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013763)	promoter-TSS (NM_013763)	-298	NM_013763	27368	Mm.441276	NM_013763		Tbl2	C76179|WS-bTRP	transducin (beta)-like 2	protein-coding	0.086957	0.715517
Merged-chr17-87974975-2	chr17	87974902	87975049	+	3.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010830)	promoter-TSS (NM_010830)	-75	NM_010830	17688	Mm.18210	NM_010830	ENSMUSG00000005370	Msh6	AU044881|AW550279|GTBP|Gtmbp	mutS homolog 6 (E. coli)	protein-coding	0.129252	0.763514
Merged-chr2-26933431-2	chr2	26933378	26933484	+	3.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_198628)	promoter-TSS (NM_198628)	80	NM_011512	20932	Mm.300594	NM_011512	ENSMUSG00000014867	Surf4	AL033340|AL033373|Surf-4	surfeit gene 4	protein-coding	0.132075	0.747664
Merged-chr11-97629856-2	chr11	97629803	97629909	+	3.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175332)	promoter-TSS (NM_175332)	-140	NM_175332	103551	Mm.24506	NM_175332	ENSMUSG00000043439	E130012A19Rik	AA409164|AI413509|AW539173|esPRC2p48	RIKEN cDNA E130012A19 gene	protein-coding	0.084906	0.691589
Merged-chr8-12463280-2	chr8	12463193	12463367	+	3.95	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	67761	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY-box containing gene 1	protein-coding	0.005747	0.422857
Merged-chr6-122761214-2	chr6	122761161	122761268	+	3.95	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-18469	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	"solute carrier family 2 (facilitated glucose transporter), member 3"	protein-coding	0.056075	0.574074
Merged-chrY-4154336-2	chrY	4154277	4154395	+	3.95	cIP1vsInput|cIP2vsInput	Intergenic	SYNREP_MM|Satellite|Satellite	382663	NM_001270516	100862398		NM_001270516		Gm21708	-	"predicted gene, 21708"	protein-coding	0.008475	0.260504
Merged-chr14-31251278-2	chr14	31251182	31251375	+	3.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027949)	promoter-TSS (NM_027949)	-60	NM_027949	71838	Mm.5348	NM_027949	ENSMUSG00000021902	Phf7	1700006H01Rik|1700010P14Rik|AI427892|AW555949	PHD finger protein 7	protein-coding	0.170984	0.716495
Merged-chr1-171294771-2	chr1	171294711	171294832	+	3.95	cIP1vsInput|cIP2vsInput	"5' UTR (NM_025388, exon 2 of 7)"	"5' UTR (NM_025388, exon 2 of 7)"	211	NM_025388	66155	Mm.2815	NM_025388	ENSMUSG00000062963	Ufc1	1110021H02Rik|AA062310|ESTM29	ubiquitin-fold modifier conjugating enzyme 1	protein-coding	0.082645	0.598361
Merged-chr11-88864583-2	chr11	88864524	88864643	+	3.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001042541)	promoter-TSS (NM_001042541)	3	NM_001042541	11640	Mm.2969	NM_001042541	ENSMUSG00000018428	Akap1	AKAP121|AKAP84|Akap|C76494|C81186|DAKAP1|S-AKAP84	A kinase (PRKA) anchor protein 1	protein-coding	0.151261	0.725
Merged-chr9-63109356-2	chr9	63109301	63109412	+	3.95	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	37624	NM_172446	207667	Mm.447200	NM_001163755	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding	0.036036	0.616071
Merged-chr8-104610407-2	chr8	104610346	104610468	+	3.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_029648)	promoter-TSS (NR_029648)	-782	NR_029648	723945		NR_029648		Mir297-2	Mir297a-2|Mirn297-2	microRNA 297-2	miscRNA	0.016393	0.577236
Merged-chr10-118799702-2	chr10	118799639	118799765	+	3.95	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	69201	NM_001014390	69181	Mm.458174	NM_001014390	ENSMUSG00000028630	Dyrk2	1810038L18Rik	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	protein-coding	0	0.283465
Merged-chr4-11322246-2	chr4	11322183	11322310	+	3.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081201)	promoter-TSS (NM_001081201)	-115	NM_001081201	381510	Mm.355656	NM_001081201		Dpy19l4	Gm1023|Narg3	dpy-19-like 4 (C. elegans)	protein-coding	0.110236	0.726562
Merged-chr15-85156574-2	chr15	85156509	85156640	+	3.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_040360)	promoter-TSS (NR_040360)	-442	NR_040360	100502602	Mm.390830	NR_040360		Gm19277	-	"predicted gene, 19277"	miscRNA	0.015267	0.492424
Merged-chr4-57670955-2	chr4	57670896	57671014	+	3.95	cIP1vsInput|cIP2vsInput	"intron (NM_172868, intron 3 of 5)"	"intron (NM_172868, intron 3 of 5)"	102707	NM_172868	242481	Mm.331630	NM_172868		Palm2	53-H12|B130066I24|R75368|pEN70	paralemmin 2	protein-coding	0.016949	0.462185
Merged-chr18-83011940-2	chr18	83011880	83012000	+	3.95	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-91380	NR_033307	75853	Mm.420737	NR_033307		4930592I03Rik	-	RIKEN cDNA 4930592I03 gene	miscRNA	0.05	0.528926
Merged-chr3-95434554-2	chr3	95434502	95434606	+	3.95	cIP1vsInput|cIP2vsInput	"exon (NM_009709, exon 1 of 21)"	"exon (NM_009709, exon 1 of 21)"	164	NM_001037737	11863	Mm.250265	NM_001037737	ENSMUSG00000015522	Arnt	D3Ertd557e|Drnt|ESTM42|Hif1b|W08714|bHLHe2|mKIAA4051	aryl hydrocarbon receptor nuclear translocator	protein-coding	0.076923	0.638095
Merged-chr11-116030494-2	chr11	116030432	116030556	+	3.95	cIP1vsInput|cIP2vsInput	"intron (NM_172569, intron 1 of 15)"	CpG	172	NM_172569	217331	Mm.297706	NM_172569	ENSMUSG00000020770	Unk	B230379M23Rik|Zc3h5|Zc3hdc5|mKIAA1753	unkempt homolog (Drosophila)	protein-coding	0.153226	0.736
Merged-chrX-151520523-2	chrX	151520466	151520580	+	3.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_177201)	promoter-TSS (NM_177201)	-149	NM_177201	320595	Mm.17156	NM_001113354	ENSMUSG00000041229	Phf8	9830141C09Rik|mKIAA1111	PHD finger protein 8	protein-coding	0.070175	0.6
Merged-chr12-13249229-1	chr12	13249179	13249279	+	3.9	cIP2vsInput	promoter-TSS (NM_134040)	promoter-TSS (NM_134040)	-55	NM_134040	104721	Mm.251255	NM_134040	ENSMUSG00000037149	Ddx1	AA409185|DBP-RB	DEAD (Asp-Glu-Ala-Asp) box polypeptide 1	protein-coding	0.15	0.653465
Merged-chrX-126773126-1	chrX	126773076	126773176	+	3.9	cIP1vsInput	Intergenic	Intergenic	60878	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding	0.01	0.257426
Merged-chr5-52783068-2	chr5	52783018	52783118	+	3.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_030185)	promoter-TSS (NM_030185)	1	NM_030185	78796	Mm.266886	NM_030185		Zcchc4	4930449I23Rik	"zinc finger, CCHC domain containing 4"	protein-coding	0.11	0.643564
Merged-chr13-46516447-1	chr13	46516397	46516497	+	3.9	cIP2vsInput	"intron (NM_026056, intron 1 of 12)"	B4A|SINE|B4	14544	NM_026056	67252	Mm.44529	NM_026056	ENSMUSG00000021373	Cap2	2810452G09Rik|AV045235	"CAP, adenylate cyclase-associated protein, 2 (yeast)"	protein-coding	0.02	0.554455
Merged-chr11-115604068-1	chr11	115604018	115604118	+	3.9	cIP2vsInput	promoter-TSS (NM_025305)	promoter-TSS (NM_025305)	-83	NM_025305	50529	Mm.193040	NM_025305		Mrps7	MRP-S7|Rpms7	mitchondrial ribosomal protein S7	protein-coding	0.07	0.584158
Merged-chr11-51689129-1	chr11	51689079	51689179	+	3.9	cIP2vsInput	promoter-TSS (NM_025319)	promoter-TSS (NM_025319)	-495	NM_025319	66050	Mm.35693	NM_025319	ENSMUSG00000007777	0610009B22Rik	-	RIKEN cDNA 0610009B22 gene	protein-coding	0.07	0.574257
Merged-chr5-135934304-1	chr5	135934254	135934354	+	3.9	cIP2vsInput	"intron (NM_018871, intron 1 of 1)"	CpG	337	NM_018871	22628	Mm.233813	NM_018871	ENSMUSG00000051391	Ywhag	14-3-3gamma|D7Bwg1348e	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide"	protein-coding	0.11	0.673267
Merged-chr10-80433942-1	chr10	80433892	80433992	+	3.9	cIP2vsInput	promoter-TSS (NM_001164150)	promoter-TSS (NM_001164150)	-289	NM_001164148	21423	Mm.3406	NM_001164147	ENSMUSG00000020167	Tcf3	A1|AA408400|ALF2|AW209082|E12|E12/E47|E2A|E47|ME2|Pan1|Pan2|Tcfe2a|VDIR|bHLHb21	transcription factor 3	protein-coding	0.09	0.524752
Merged-chr3-95110994-1	chr3	95110944	95111044	+	3.9	cIP2vsInput	promoter-TSS (NM_009336)	promoter-TSS (NM_009336)	-48	NM_009336	21427	Mm.133919	NM_009336	ENSMUSG00000008958	Vps72	Tcfl1|YL-1	vacuolar protein sorting 72 (yeast)	protein-coding	0.11	0.574257
Merged-chr2-32452195-1	chr2	32452145	32452245	+	3.9	cIP1vsInput	promoter-TSS (NM_146118)	promoter-TSS (NM_146118)	-725	NM_146118	227731	Mm.473265	NM_001164357	ENSMUSG00000026819	Slc25a25	1110030N17Rik|MCSC|mKIAA1896	"solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25"	protein-coding	0.09	0.673267
Merged-chr1-90754492-1	chr1	90754442	90754542	+	3.9	cIP2vsInput	Intergenic	Intergenic	89479	NM_001243009	12835	Mm.7562	NM_009935	ENSMUSG00000048126	Col6a3	AI507288|Col6a-3	"collagen, type VI, alpha 3"	protein-coding	0.04	0.60396
Merged-chr2-30472096-1	chr2	30472046	30472146	+	3.9	cIP2vsInput	TTS (NM_030244)	TTS (NM_030244)	2103	NM_030244	72500	Mm.295464	NM_030244	ENSMUSG00000089762	Ier5l	2610524G09Rik	immediate early response 5-like	protein-coding	0.07	0.762376
Merged-chr5-141241376-1	chr5	141241326	141241426	+	3.9	cIP2vsInput	promoter-TSS (NM_177879)	promoter-TSS (NM_177879)	-158	NM_177879	330222	Mm.406697	NM_177879	ENSMUSG00000039683	Sdk1	5330440E10|6720466O15Rik	sidekick homolog 1 (chicken)	protein-coding	0.15	0.722772
Merged-chr3-116562872-2	chr3	116562781	116562963	+	3.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175413)	promoter-TSS (NM_175413)	-101	NM_027321	109245	Mm.259648	NM_027321	ENSMUSG00000027961	Lrrc39	2010005E21Rik|9430028I06Rik	leucine rich repeat containing 39	protein-coding	0.021978	0.47541
Merged-chr3-8923840-1	chr3	8923790	8923890	+	3.9	cIP1vsInput	promoter-TSS (NM_025434)	promoter-TSS (NM_025434)	17	NM_025434	66230	Mm.38460	NM_025434	ENSMUSG00000040269	Mrps28	1500012D08Rik|AW061224	mitochondrial ribosomal protein S28	protein-coding	0.1	0.70297
Merged-chr3-87906094-2	chr3	87906031	87906158	+	3.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008231)	promoter-TSS (NM_008231)	-227	NM_008231	15191	Mm.292208	NM_008231	ENSMUSG00000004897	Hdgf	AI118077|D3Ertd299e	hepatoma-derived growth factor	protein-coding	0.047244	0.726562
Merged-chr9-20565844-2	chr9	20565782	20565906	+	3.9	cIP1vsInput|cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	-15484	NM_172919	244721	Mm.86627	NM_172919	ENSMUSG00000058192	Zfp846	2210010B09Rik|9130221F13|Znf846	zinc finger protein 846	protein-coding	0.016129	0.52
Merged-chr7-82721193-2	chr7	82721133	82721254	+	3.9	cIP1vsInput|cIP2vsInput	"intron (NM_001159672, intron 15 of 19)"	"intron (NM_001159672, intron 15 of 19)"	34451	NR_046004	77800	Mm.447286	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	miscRNA	0.024793	0.459016
Merged-chr17-69382846-1	chr17	69382796	69382896	+	3.9	cIP2vsInput	Intergenic	CpG	-1132	NM_009547	22666	Mm.29434	NM_009547	ENSMUSG00000049672	Zbtb14	ZF5|Zfp161	zinc finger and BTB domain containing 14	protein-coding	0.16	0.772277
Merged-chr3-32397141-1	chr3	32397091	32397191	+	3.9	cIP2vsInput	Intergenic	CpG	-31476	NM_009517	22401	Mm.35705	NM_009517	ENSMUSG00000027663	Zmat3	Wig1	zinc finger matrin type 3	protein-coding	0.04	0.49505
Merged-chr3-88121867-1	chr3	88121817	88121917	+	3.9	cIP1vsInput	TTS (NM_001033484)	TTS (NM_001033484)	-20528	NM_133665	17261	Mm.485397	NM_133665		Mef2d	C80750	myocyte enhancer factor 2D	protein-coding	0.04	0.49505
Merged-chr1-37890483-2	chr1	37890422	37890544	+	3.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026913)	promoter-TSS (NM_026913)	-70	NM_027098	107734	Mm.26614	NM_027098		Mrpl30	2310001L22Rik|MRP-L28|Rpml28	mitochondrial ribosomal protein L30	protein-coding	0.057377	0.512195
Merged-chr17-26716366-1	chr17	26716316	26716416	+	3.9	cIP2vsInput	"intron (NM_029870, intron 1 of 8)"	CpG	716	NM_029870	77128	Mm.275414	NM_029870	ENSMUSG00000048249	Crebrf	A930001N09Rik|LRF	CREB3 regulatory factor	protein-coding	0.07	0.722772
Merged-chr18-35118813-1	chr18	35118763	35118863	+	3.9	cIP2vsInput	promoter-TSS (NM_009818)	promoter-TSS (NM_009818)	-99	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	"catenin (cadherin associated protein), alpha 1"	protein-coding	0.18	0.841584
Merged-chr17-31565053-1	chr17	31565003	31565103	+	3.9	cIP2vsInput	"intron (NM_016670, intron 1 of 10)"	CpG	280	NM_016670	18771	Mm.259295	NM_016670	ENSMUSG00000006705	Pknox1	D17Wsu76e|PREP1	Pbx/knotted 1 homeobox	protein-coding	0.18	0.881188
Merged-chr5-15006495-1	chr5	15006445	15006545	+	3.9	cIP2vsInput	Intergenic	Intergenic	26512	NM_182957	66773	Mm.368256	NM_182957	ENSMUSG00000091897	Gm17019	-	predicted gene 17019	protein-coding	0	0.386139
Merged-chr19-7206114-1	chr19	7206064	7206164	+	3.9	cIP2vsInput	"intron (NM_134150, intron 1 of 6)"	CpG	170	NM_134150	107260	Mm.203921	NM_134150	ENSMUSG00000024767	Otub1	AI850305	"OTU domain, ubiquitin aldehyde binding 1"	protein-coding	0.11	0.742574
Merged-chr5-139460686-1	chr5	139460636	139460736	+	3.9	cIP2vsInput	promoter-TSS (NM_028469)	promoter-TSS (NM_028469)	-152	NM_028469	73212	Mm.84294	NM_028469	ENSMUSG00000053553	3110082I17Rik	AW411904	RIKEN cDNA 3110082I17 gene	protein-coding	0.07	0.633663
Merged-chr5-115158498-1	chr5	115158448	115158548	+	3.9	cIP2vsInput	promoter-TSS (NM_175403)	promoter-TSS (NM_175403)	-322	NM_175403	109154	Mm.153963	NM_175403	ENSMUSG00000048578	Mlec	2410014A08Rik|AI850530|ESTM19|X83352|mKIAA0152	malectin	protein-coding	0.09	0.663366
Merged-chr8-14279042-2	chr8	14278990	14279094	+	3.9	cIP1vsInput|cIP2vsInput	"intron (NM_001145965, intron 2 of 14)"	RMER17D2|LTR|ERVK	183167	NM_172910	244310	Mm.404697	NM_001145965	ENSMUSG00000047495	Dlgap2	6430596N04Rik|DAP2|Sapap2	"discs, large (Drosophila) homolog-associated protein 2"	protein-coding	0.009615	0.514286
Merged-chr11-5996183-2	chr11	5996126	5996240	+	3.9	cIP1vsInput|cIP2vsInput	"intron (NM_001174053, intron 5 of 19)"	"intron (NM_001174053, intron 5 of 19)"	40425	NM_019661	56418	Mm.294821	NM_019661	ENSMUSG00000002741	Ykt6	0610042I15Rik|1810013M05Rik|AW105923	YKT6 homolog (S. Cerevisiae)	protein-coding	0.026316	0.6
Merged-chr11-74649239-1	chr11	74649189	74649289	+	3.9	cIP2vsInput	promoter-TSS (NM_001081158)	promoter-TSS (NM_001081158)	-256	NM_001081158	74148	Mm.214574	NM_001081158	ENSMUSG00000020741	Cluh	1300001I01Rik|Kiaa0664|mKIAA0664	clustered mitochondria (cluA/CLU1) homolog	protein-coding	0.09	0.653465
Merged-chr1-74284995-1	chr1	74284945	74285045	+	3.9	cIP2vsInput	promoter-TSS (NM_001190444)	promoter-TSS (NM_001190444)	-39	NM_025580	56695	Mm.384726	NM_001039509	ENSMUSG00000026179	Pnkd	2210013N15Rik|2810403H05Rik|AI854243|Brp17|MNCb-5687|MR-1|Tahccp2	paroxysmal nonkinesiogenic dyskinesia	protein-coding	0.1	0.60396
Merged-chr12-85374809-2	chr12	85374755	85374863	+	3.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026775)	promoter-TSS (NM_026775)	-92	NM_026775	68581	Mm.472063	NM_026775	ENSMUSG00000021248	Tmed10	1110014C03Rik|Tmp21|p23|p24delta1	transmembrane emp24-like trafficking protein 10 (yeast)	protein-coding	0.027778	0.376147
Merged-chr10-53596749-1	chr10	53596699	53596799	+	3.9	cIP2vsInput	promoter-TSS (NM_025541)	promoter-TSS (NM_025541)	-212	NM_025541	66403	Mm.272989	NM_025541	ENSMUSG00000019857	Asf1a	2310079C17Rik|C79052	ASF1 anti-silencing function 1 homolog A (S. cerevisiae)	protein-coding	0.18	0.861386
Merged-chr4-81745078-1	chr4	81745028	81745128	+	3.9	cIP2vsInput	Intergenic	Intergenic	-258065	NR_030570	100124446		NR_030570		Mir466h	Mirn466h	microRNA 466h	miscRNA	0.03	0.455446
Merged-chr2-28468029-1	chr2	28467979	28468079	+	3.9	cIP2vsInput	promoter-TSS (NM_080452)	promoter-TSS (NM_080452)	-37	NM_080452	118451	Mm.294951	NM_001166031	ENSMUSG00000035772	Mrps2	1500019M10Rik	mitochondrial ribosomal protein S2	protein-coding	0.1	0.722772
Merged-chr12-68680714-2	chr12	68680649	68680780	+	3.9	cIP1vsInput|cIP2vsInput	Intergenic	MLTR11A|LTR|ERVK	478472	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding	0	0.431818
Merged-chr16-87454940-1	chr16	87454890	87454990	+	3.9	cIP2vsInput	promoter-TSS (NM_024258)	promoter-TSS (NM_024258)	-45	NM_024258	74112	Mm.152941	NM_024258	ENSMUSG00000025616	Usp16	1200004E02Rik|2810483I07Rik|6330514E22Rik|UBPM	ubiquitin specific peptidase 16	protein-coding	0.08	0.633663
Merged-chr13-99516619-1	chr13	99516569	99516669	+	3.9	cIP2vsInput	promoter-TSS (NM_008634)	promoter-TSS (NM_008634)	-17	NM_008634	17755	Mm.474896	NM_008634	ENSMUSG00000052727	Map1b	A230055D22|AI843217|LC1|MAP5|Mtap-5|Mtap1b|Mtap5	microtubule-associated protein 1B	protein-coding	0.13	0.772277
Merged-chr7-27490676-1	chr7	27490626	27490726	+	3.9	cIP2vsInput	TTS (NM_018820)	TTS (NM_018820)	3723	NM_018820	55942	Mm.153684	NM_018820	ENSMUSG00000008384	Sertad1	1110032C13Rik|AV000455|AW456625|Sei-1|Sei1|TRIP-Br1	SERTA domain containing 1	protein-coding	0.07	0.742574
Merged-chr4-61576337-1	chr4	61576287	61576387	+	3.9	cIP1vsInput	Intergenic	L1Md_F|LINE|L1	19488	NM_001134644	100048885	Mm.422695	NM_001134644		Gm2083	-	major urinary protein LOC100048885	protein-coding	0	0.336634
Merged-chr11-80378024-1	chr11	80377974	80378074	+	3.9	cIP2vsInput	promoter-TSS (NM_027472)	promoter-TSS (NM_027472)	-9	NM_027472	70591	Mm.86860	NM_027472	ENSMUSG00000057181	5730455P16Rik	-	RIKEN cDNA 5730455P16 gene	protein-coding	0.11	0.722772
Merged-chr7-27689612-1	chr7	27689562	27689662	+	3.9	cIP1vsInput	"intron (NM_001112731, intron 1 of 5)"	"intron (NM_001112731, intron 1 of 5)"	272	NM_001112731	112415	Mm.145362	NM_001112731	ENSMUSG00000057093	C030039L03Rik	-	RIKEN cDNA C030039L03 gene	protein-coding	0.03	0.465347
Merged-chr4-116221598-1	chr4	116221548	116221648	+	3.9	cIP2vsInput	promoter-TSS (NM_181585)	promoter-TSS (NM_181585)	-316	NM_181585	18710	Mm.253819	NM_181585	ENSMUSG00000028698	Pik3r3	AA414954|p55pik	"phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 3 (p55)"	protein-coding	0.04	0.643564
Merged-chr8-111033677-1	chr8	111033627	111033727	+	3.9	cIP2vsInput	promoter-TSS (NM_146217)	promoter-TSS (NM_146217)	-165	NM_146217	234734	Mm.24174	NM_146217	ENSMUSG00000031960	Aars	AI316495|C76919|sti	alanyl-tRNA synthetase	protein-coding	0.01	0.465347
Merged-chr18-58210690-1	chr18	58210640	58210740	+	3.9	cIP2vsInput	promoter-TSS (NM_010181)	promoter-TSS (NM_010181)	-764	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding	0.02	0.613861
Merged-chr17-28523134-1	chr17	28523084	28523184	+	3.9	cIP2vsInput	Intergenic	CpG	-7727	NM_026290	67645	Mm.46170	NM_026290	ENSMUSG00000024223	Armc12	4930511I11Rik|AV041658	armadillo repeat containing 12	protein-coding	0.11	0.693069
Merged-chr6-84883346-1	chr6	84883296	84883396	+	3.9	cIP2vsInput	"intron (NM_177077, intron 8 of 21)"	"intron (NM_177077, intron 8 of 21)"	186167	NM_177077	75914	Mm.159621	NM_177077	ENSMUSG00000033769	Exoc6b	4930569O18Rik|G430127E12Rik|Sec15b|Sec15l2|mKIAA0919	exocyst complex component 6B	protein-coding	0	0.445545
Merged-chr8-106011471-2	chr8	106011418	106011524	+	3.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028038)	promoter-TSS (NM_028038)	15	NM_028038	71986	Mm.307515	NM_028038	ENSMUSG00000045538	Ddx28	2410004K13Rik|AI449652|Mddx28	DEAD (Asp-Glu-Ala-Asp) box polypeptide 28	protein-coding	0.103774	0.607477
Merged-chr13-21440929-2	chr13	21440876	21440983	+	3.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001162919)	promoter-TSS (NM_001162919)	124	NM_001012311	319207	Mm.434384	NM_001012311	ENSMUSG00000055313	Pgbd1	4921509E05Rik	piggyBac transposable element derived 1	protein-coding	0.056075	0.527778
Merged-chr11-3964011-1	chr11	3963961	3964061	+	3.9	cIP1vsInput	promoter-TSS (NM_022889)	promoter-TSS (NM_022889)	36	NM_022889	64934	Mm.28659	NM_022889	ENSMUSG00000020430	Pes1	-	"pescadillo homolog 1, containing BRCT domain (zebrafish)"	protein-coding	0.03	0.574257
Merged-chr9-57910914-1	chr9	57910864	57910964	+	3.9	cIP2vsInput	promoter-TSS (NM_001122873)	promoter-TSS (NM_001122873)	-72	NM_027086	69459	Mm.41735	NM_001122873	ENSMUSG00000055720	Ubl7	2300004C15Rik	ubiquitin-like 7 (bone marrow stromal cell-derived)	protein-coding	0.05	0.574257
Merged-chr4-147095190-1	chr4	147095140	147095240	+	3.9	cIP1vsInput	Intergenic	L1VL4|LINE|L1	-26754	NR_045446	71270	Mm.460830	NR_045446	ENSMUSG00000093617	4933438K21Rik	-	RIKEN cDNA 4933438K21 gene	miscRNA	0	0.326733
Merged-chr4-129820684-1	chr4	129820634	129820734	+	3.9	cIP2vsInput	promoter-TSS (NM_001164745)	promoter-TSS (NM_001164745)	-24	NM_001164745	19244	Mm.193688	NM_001164745	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding	0.12	0.811881
Merged-chr18-6135950-1	chr18	6135900	6136000	+	3.9	cIP2vsInput	"5' UTR (NM_029277, exon 1 of 18)"	"5' UTR (NM_029277, exon 1 of 18)"	148	NM_029277	75415	Mm.239675	NM_001039692	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding	0.1	0.712871
Merged-chr6-38876364-1	chr6	38876314	38876414	+	3.9	cIP1vsInput	promoter-TSS (NM_010433)	promoter-TSS (NM_010433)	-174	NM_010433	15258	Mm.486937	NM_001136065	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding	0.18	0.80198
Merged-chr14-52244705-1	chr14	52244655	52244755	+	3.9	cIP2vsInput	Intergenic	Intergenic	-7133	NM_201637	67772	Mm.289934	NM_201637	ENSMUSG00000053754	Chd8	5830451P18Rik|AU015341|Duplin|HELSNF1|mKIAA1564	chromodomain helicase DNA binding protein 8	protein-coding	0.03	0.534653
Merged-chr15-82186502-1	chr15	82186452	82186552	+	3.9	cIP2vsInput	"intron (NM_033218, intron 11 of 18)"	"intron (NM_033218, intron 11 of 18)"	-11620	NR_029804	723897		NR_029804		Mir33	Mirn33|mmu-mir-33	microRNA 33	miscRNA	0.04	0.425743
Merged-chr17-29095372-2	chr17	29095280	29095464	+	3.9	cIP1vsInput|cIP2vsInput	"intron (NM_007669, intron 1 of 2)"	CpG	1600	NM_007669	12575	Mm.195663	NM_001111099	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding	0.103261	0.567568
Merged-chr11-75733238-1	chr11	75733188	75733288	+	3.9	cIP2vsInput	"intron (NM_009536, intron 1 of 5)"	CpG	351	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide"	protein-coding	0.1	0.742574
Merged-chr5-117120087-1	chr5	117120037	117120137	+	3.9	cIP2vsInput	promoter-TSS (NM_001199685)	promoter-TSS (NM_001199685)	-42	NM_001199685	330177	Mm.487518	NM_001081308	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding	0.1	0.673267
Merged-chr11-16508272-1	chr11	16508222	16508322	+	3.9	cIP1vsInput	"5' UTR (NM_011343, exon 1 of 4)"	"5' UTR (NM_011343, exon 1 of 4)"	212	NM_011343	20335	Mm.325350	NM_001109971	ENSMUSG00000078974	Sec61g	-	"SEC61, gamma subunit"	protein-coding	0.13	0.663366
Merged-chr6-29768303-1	chr6	29768253	29768353	+	3.9	cIP2vsInput	promoter-TSS (NM_001171000)	promoter-TSS (NM_001171000)	-140	NM_021414	74340	Mm.210899	NM_001171000	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding	0.09	0.623762
Merged-chr15-25941681-2	chr15	25941630	25941733	+	3.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001277317)	promoter-TSS (NM_001277317)	855	NM_025459	66270	Mm.25311	NM_001034851	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	"family with sequence similarity 134, member B"	protein-coding	0.067961	0.557692
Merged-chr9-75410083-1	chr9	75410033	75410133	+	3.9	cIP1vsInput	promoter-TSS (NM_015806)	promoter-TSS (NM_015806)	-69	NM_015806	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding	0.14	0.742574
Merged-chr5-29569158-1	chr5	29569108	29569208	+	3.9	cIP2vsInput	promoter-TSS (NM_133907)	promoter-TSS (NM_133907)	-84	NM_133907	100763	Mm.137746	NM_133907	ENSMUSG00000039000	Ube3c	AI853514|mKIAA0010	ubiquitin protein ligase E3C	protein-coding	0.18	0.762376
Merged-chr12-86884974-2	chr12	86884900	86885049	+	3.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145836)	promoter-TSS (NM_145836)	-160	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding	0.073826	0.673333
Merged-chr2-121956400-2	chr2	121956315	121956486	+	3.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008545)	promoter-TSS (NM_008545)	-53	NM_212450	329506	Mm.249405	NM_212450	ENSMUSG00000033411	Ctdspl2	D2Ertd485e	"CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2"	protein-coding	0.093567	0.697674
Merged-chr1-36558419-1	chr1	36558369	36558469	+	3.9	cIP2vsInput	promoter-TSS (NM_001126047)	promoter-TSS (NM_001126047)	-38	NM_001126047	20353	Mm.29558	NM_001126047	ENSMUSG00000026121	Sema4c	AI426163|Semacl1|Semaf|Semai|mKIAA1739	"sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C"	protein-coding	0.08	0.732673
Merged-chr18-40256877-2	chr18	40256819	40256936	+	3.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_045177)	promoter-TSS (NR_045177)	-85	NR_045177	73001	Mm.428647	NR_045177	ENSMUSG00000071860	2900055J20Rik	-	RIKEN cDNA 2900055J20 gene	miscRNA	0.102564	0.694915
Merged-chr10-62886306-1	chr10	62886256	62886356	+	3.9	cIP1vsInput	Intergenic	Intergenic	-6292	NM_001253857	52463	Mm.17774	NM_001253857	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding	0.09	0.643564
Merged-chr5-88554270-2	chr5	88554203	88554338	+	3.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_023054)	promoter-TSS (NM_023054)	-213	NM_023054	65961	Mm.490364	NM_023054	ENSMUSG00000070697	Utp3	2400011K09Rik|AW557551|C87704|Crl1|Crlz1|Sas10	"UTP3, small subunit (SSU) processome component, homolog (S. cerevisiae)"	protein-coding	0.096296	0.573529
Merged-chr1-36556590-1	chr1	36556540	36556640	+	3.9	cIP2vsInput	"intron (NM_001126047, intron 1 of 14)"	"intron (NM_001126047, intron 1 of 14)"	1791	NM_001126047	20353	Mm.29558	NM_001126047	ENSMUSG00000026121	Sema4c	AI426163|Semacl1|Semaf|Semai|mKIAA1739	"sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C"	protein-coding	0.06	0.673267
Merged-chr13-55600002-1	chr13	55599952	55600052	+	3.9	cIP2vsInput	promoter-TSS (NM_146045)	promoter-TSS (NM_146045)	-109	NM_146045	218271	Mm.139825	NM_146045		B4galt7	-	"xylosylprotein beta1,4-galactosyltransferase, polypeptide 7 (galactosyltransferase I)"	protein-coding	0.08	0.663366
Merged-chr18-61911765-1	chr18	61911715	61911815	+	3.9	cIP2vsInput	promoter-TSS (NM_001164491)	promoter-TSS (NM_001164491)	59	NM_198649	319713		NM_001164491	ENSMUSG00000032735	Ablim3	AW990719|D930036B08Rik	"actin binding LIM protein family, member 3"	protein-coding	0.08	0.663366
Merged-chr5-100798657-1	chr5	100798607	100798707	+	3.9	cIP2vsInput	promoter-TSS (NM_026826)	promoter-TSS (NM_026826)	-57	NM_001081107	191578	Mm.21469	NM_001081107	ENSMUSG00000035266	Helq	AU021725|D430018E21Rik|Hel308	"helicase, POLQ-like"	protein-coding	0.13	0.653465
Merged-chr11-86544857-1	chr11	86544807	86544907	+	3.9	cIP2vsInput	promoter-TSS (NM_001199045)	promoter-TSS (NM_001199045)	-50	NM_001114334	72508	Mm.479484	NM_001114334	ENSMUSG00000020516	Rps6kb1	2610318I15Rik|4732464A07Rik|70kDa|AA959758|AI256796|AI314060|S6K1|p70/85s6k|p70s6k	"ribosomal protein S6 kinase, polypeptide 1"	protein-coding	0.07	0.60396
Merged-chr3-104638744-1	chr3	104638694	104638794	+	3.9	cIP2vsInput	promoter-TSS (NM_009196)	promoter-TSS (NM_009196)	76	NM_009196	20501	Mm.9086	NM_009196	ENSMUSG00000032902	Slc16a1	AL022710|Mct1	"solute carrier family 16 (monocarboxylic acid transporters), member 1"	protein-coding	0.15	0.772277
Merged-chr5-74161731-1	chr5	74161681	74161781	+	3.9	cIP2vsInput	Intergenic	Intergenic	-33595	NM_026878	68939	Mm.293316	NM_026878	ENSMUSG00000049907	Rasl11b	1190017B18Rik	"RAS-like, family 11, member B"	protein-coding	0.02	0.643564
Merged-chr11-88968520-1	chr11	88968470	88968570	+	3.9	cIP1vsInput	Intergenic	RMER16B2|LTR|ERVK	-1603	NR_003564	217066	Mm.347543	NR_003564	ENSMUSG00000057534	Gm15698	OTTMUSG00000001305|OTTMUSG00000025408	"transcription elongation factor B (SIII), polypeptide 2 pseudogene"	pseudo	0.01	0.425743
Merged-chr2-157566791-1	chr2	157566741	157566841	+	3.9	cIP1vsInput	promoter-TSS (NM_016916)	promoter-TSS (NM_016916)	-430	NM_016916	53619	Mm.490288	NM_016916	ENSMUSG00000067787	Blcap	AI462828|Bc10	bladder cancer associated protein homolog (human)	protein-coding	0.02	0.544554
Merged-chr18-65207802-1	chr18	65207752	65207852	+	3.9	cIP2vsInput	"intron (NM_031881, intron 25 of 29)"	"intron (NM_031881, intron 25 of 29)"	-41059	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122a	Mirn122a|mmu-mir-122	microRNA 122a	miscRNA	0.03	0.49505
Merged-chr15-102203403-1	chr15	102203353	102203453	+	3.9	cIP1vsInput	Intergenic	Intergenic	-4864	NM_153194	68744	Mm.352945	NM_153194	ENSMUSG00000046897	Zfp740	1110034O07Rik|AW548228|Znf740	zinc finger protein 740	protein-coding	0.05	0.584158
Merged-chr1-121567967-2	chr1	121567868	121568067	+	3.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025860)	promoter-TSS (NM_025860)	13	NM_025860	66942	Mm.44219	NM_025860	ENSMUSG00000001674	Ddx18	2310005B10Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	protein-coding	0.095477	0.635
Merged-chr16-90934856-1	chr16	90934806	90934906	+	3.9	cIP2vsInput	promoter-TSS (NM_026502)	promoter-TSS (NM_026502)	-7	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding	0.12	0.623762
Merged-chr7-45092305-1	chr7	45092255	45092355	+	3.9	cIP2vsInput	promoter-TSS (NM_026555)	promoter-TSS (NM_026555)	-92	NM_026555	52377	Mm.29997	NM_026555	ENSMUSG00000019539	Rcn3	6030455P07Rik|D530026G20Rik|D7Ertd671e|RLP49	"reticulocalbin 3, EF-hand calcium binding domain"	protein-coding	0.06	0.574257
Merged-chr4-3875106-1	chr4	3875056	3875156	+	3.9	cIP2vsInput	Intergenic	CpG	-3001	NM_020021	17451	Mm.459300	NM_020021	ENSMUSG00000078365	Mos	c-mos	Moloney sarcoma oncogene	protein-coding	0.1	0.722772
Merged-chr9-116086868-1	chr9	116086818	116086918	+	3.9	cIP2vsInput	TTS (NM_029575)	TTS (NM_029575)	88495	NM_029575	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	"transforming growth factor, beta receptor II"	protein-coding	0	0.277228
Merged-chr19-5871378-1	chr19	5871328	5871428	+	3.9	cIP2vsInput	"intron (NM_026169, intron 3 of 10)"	"intron (NM_026169, intron 3 of 10)"	3830	NM_026169	67457	Mm.396413	NM_026169		Frmd8	1200004M23Rik|2310035N23Rik|4931429L16Rik|AU018809	FERM domain containing 8	protein-coding	0.01	0.60396
Merged-chr16-55973643-2	chr16	55973545	55973741	+	3.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_173026)	promoter-TSS (NM_173026)	-161	NM_173026	271377	Mm.282814	NM_173026	ENSMUSG00000022601	Zbtb11	9230110G02Rik|ZNF-U69274	zinc finger and BTB domain containing 11	protein-coding	0.071429	0.609137
Merged-chr4-150008415-2	chr4	150008362	150008468	+	3.85	cIP1vsInput|cIP2vsInput	"intron (NM_173371, intron 1 of 4)"	"intron (NM_173371, intron 1 of 4)"	608	NM_173371	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding	0.037736	0.53271
Merged-chr8-95833807-2	chr8	95833755	95833859	+	3.85	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	19684	NM_172758	234595	Mm.29267	NM_172758	ENSMUSG00000036534	Slc38a7	D430050E18	"solute carrier family 38, member 7"	protein-coding	0.038462	0.609524
Merged-chr1-85605540-2	chr1	85605486	85605594	+	3.85	cIP1vsInput|cIP2vsInput	"intron (NM_001013817, intron 1 of 16)"	"intron (NM_001013817, intron 1 of 16)"	-1649	NM_175397	109032	Mm.461913	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding	0.009259	0.394495
Merged-chr2-150749048-2	chr2	150748993	150749103	+	3.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172117)	promoter-TSS (NM_172117)	-33	NM_172117	12497	Mm.275524	NM_172117	ENSMUSG00000033068	Entpd6	2700026H11Rik|Cd39l2|NTPDase-6	ectonucleoside triphosphate diphosphohydrolase 6	protein-coding	0.118182	0.657658
Merged-chr11-115403704-2	chr11	115403635	115403773	+	3.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026729)	promoter-TSS (NM_026729)	-62	NM_026729	68572	Mm.271062	NM_026729	ENSMUSG00000018858	Ict1	1110001A02Rik|1110002E03Rik	immature colon carcinoma transcript 1	protein-coding	0.07971	0.661871
Merged-chr5-31526960-2	chr5	31526896	31527024	+	3.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009206)	promoter-TSS (NM_009206)	-35	NM_009206	20534	Mm.352407	NM_009206	ENSMUSG00000029141	Slc4a1ap	kanadaptin	"solute carrier family 4 (anion exchanger), member 1, adaptor protein"	protein-coding	0.046875	0.565891
Merged-chr7-131223275-2	chr7	131223199	131223351	+	3.85	cIP1vsInput|cIP2vsInput	"intron (NM_175166, intron 8 of 22)"	MTEb|LTR|ERVL-MaLR	48873	NM_175166	71395	Mm.118845	NM_175166	ENSMUSG00000006204	5430419D17Rik	-	RIKEN cDNA 5430419D17 gene	protein-coding	0	0.437908
Merged-chr5-65493049-2	chr5	65492977	65493121	+	3.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133697)	promoter-TSS (NM_133697)	-214	NM_133697	68552	Mm.393232	NM_133697		Smim14	1110003E01Rik|1700127H04Rik|5430439C17Rik|MAd4	small integral membrane protein 14	protein-coding	0.118056	0.731034
Merged-chr7-25267553-2	chr7	25267501	25267606	+	3.85	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-14626	NM_001110132	71722	Mm.28833	NM_001110131	ENSMUSG00000005442	Cic	1200010B10Rik|mKIAA0306	capicua homolog (Drosophila)	protein-coding	0.009524	0.537736
Merged-chr11-98149695-2	chr11	98149612	98149779	+	3.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028149)	promoter-TSS (NM_028149)	-79	NM_028149	72194	Mm.218350	NM_134030	ENSMUSG00000020883	Fbxl20	2610511F20Rik|4632423N09Rik|AI849362|AL117906|C86145|Fbl2|Scr|mKIAA4147	F-box and leucine-rich repeat protein 20	protein-coding	0.131737	0.779762
Merged-chr12-116485690-2	chr12	116485627	116485753	+	3.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011215)	promoter-TSS (NM_011215)	-30	NM_011215	19276	Mm.206054	NM_011215	ENSMUSG00000056553	Ptprn2	4930425H11Rik|IA2beta|PTP-NP|Phol|mKIAA0387|phogrin	"protein tyrosine phosphatase, receptor type, N polypeptide 2"	protein-coding	0.119048	0.755906
Merged-chr11-78032240-2	chr11	78032190	78032291	+	3.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_183286)	promoter-TSS (NM_183286)	-73	NM_183286	70451	Mm.390342	NM_183286	ENSMUSG00000020834	Dhrs13	2610209N15Rik	dehydrogenase/reductase (SDR family) member 13	protein-coding	0.118812	0.735294
Merged-chr6-48593860-2	chr6	48593795	48593926	+	3.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001079904)	promoter-TSS (NM_001079904)	-23	NM_001079903	58887	Mm.219183	NM_001079901	ENSMUSG00000052751	Repin1	AI425994|Ap4|E430037F08Rik|Zfp-464|Zfp464	replication initiator 1	protein-coding	0.099237	0.75
Merged-chr1-34678060-2	chr1	34677997	34678124	+	3.85	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-41850	NR_033627	241051	Mm.282827	NR_033627		AA619741	-	PHD finger protein 19 pseudogene	pseudo	0.094488	0.648438
Merged-chr15-62231125-2	chr15	62231067	62231184	+	3.85	cIP1vsInput|cIP2vsInput	"intron (NR_003368, intron 5 of 8)"	ID_B1|SINE|B4	-11674	NR_003523	67552	Mm.484027	NR_003523		H2afy3	4933432H23Rik	"H2A histone family, member Y3"	pseudo	0.017094	0.5
Merged-chr2-35504622-2	chr2	35504567	35504677	+	3.85	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-43197	NM_001145821	14594	Mm.281124	NM_001145821	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha3GalT	"glycoprotein galactosyltransferase alpha 1, 3"	protein-coding	0.027273	0.540541
Merged-chr16-30587874-2	chr16	30587822	30587926	+	3.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178069)	promoter-TSS (NM_178069)	-285	NM_178069	224092	Mm.567	NM_178069		Lsg1	5830465I20|AA409273|D16Bwg1547e	large subunit GTPase 1 homolog (S. cerevisiae)	protein-coding	0.067308	0.514286
Merged-chr12-84409032-2	chr12	84408977	84409087	+	3.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007647)	promoter-TSS (NM_007647)	-3	NM_001026214	12499	Mm.10211	NM_001026214	ENSMUSG00000021236	Entpd5	AI196558|AI987697|Cd39l4|ER-UDPase|NTPDase-5|NTPDase5|Pcph|mNTPase	ectonucleoside triphosphate diphosphohydrolase 5	protein-coding	0.218182	0.810811
Merged-chr7-127233197-2	chr7	127233144	127233250	+	3.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_030674)	promoter-TSS (NR_030674)	-67	NR_030674	100043580	Mm.482209	NR_030674		Gm4532	-	predicted gene 4532	miscRNA	0.150943	0.766355
Merged-chr17-33089476-2	chr17	33089414	33089538	+	3.85	cIP1vsInput|cIP2vsInput	"5' UTR (NM_001024950, exon 1 of 4)"	"5' UTR (NM_001024950, exon 1 of 4)"	109	NM_001024950	240068	Mm.121392	NM_001024950		Zfp563	D10628|D130054H01|NTfin7|Zfp413	zinc finger protein 563	protein-coding	0.040323	0.568
Merged-chr8-66486584-2	chr8	66486520	66486649	+	3.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025465)	promoter-TSS (NM_025465)	-77	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16 homolog (S. cerevisiae)	protein-coding	0.062016	0.569231
Merged-chr12-112743319-2	chr12	112743254	112743385	+	3.85	cIP1vsInput|cIP2vsInput	"intron (NM_001024602, intron 14 of 18)"	"intron (NM_001024602, intron 14 of 18)"	-17336	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	"phospholipase D family, member 4"	protein-coding	0.038168	0.606061
Merged-chr9-66593086-2	chr9	66593004	66593169	+	3.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_144937)	promoter-TSS (NM_144937)	-106	NM_144937	235441	Mm.38976	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding	0.109091	0.704819
Merged-chr10-91181844-1	chr10	91181794	91181894	+	3.8	cIP2vsInput	Intergenic	CpG	-10262	NM_001080130	21917	Mm.439157	NM_001080129	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding	0.12	0.643564
Merged-chr12-8921588-1	chr12	8921538	8921638	+	3.8	cIP2vsInput	"5' UTR (NM_008640, exon 1 of 7)"	"5' UTR (NM_008640, exon 1 of 7)"	281	NM_008640	17775	Mm.401534	NM_008640	ENSMUSG00000020585	Laptm4a	AA286466|LAPTM4|MTP|Mtrp|mKIAA0108	lysosomal-associated protein transmembrane 4A	protein-coding	0.06	0.643564
Merged-chr11-79993233-1	chr11	79993183	79993283	+	3.8	cIP2vsInput	"5' UTR (NM_199196, exon 1 of 16)"	"5' UTR (NM_199196, exon 1 of 16)"	127	NM_199196	52615	Mm.283410	NM_001163018	ENSMUSG00000017548	Suz12	2610028O16Rik|AI195385|AU016842|AW536442|D11Ertd530e|mKIAA0160	suppressor of zeste 12 homolog (Drosophila)	protein-coding	0.09	0.742574
Merged-chr14-19823951-2	chr14	19823896	19824007	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026528)	promoter-TSS (NM_026528)	-128	NM_026528	68045	Mm.21932	NM_026528	ENSMUSG00000021807	2700060E02Rik	-	RIKEN cDNA 2700060E02 gene	protein-coding	0.081081	0.535714
Merged-chr16-30510690-1	chr16	30510640	30510740	+	3.8	cIP2vsInput	"intron (NR_035427, intron 4 of 5)"	CpG	39888	NM_172614	224090	Mm.241459	NM_172614		Tmem44	1700007N03Rik|9330161C17Rik|B230220N21	transmembrane protein 44	protein-coding	0.06	0.633663
Merged-chr4-116220964-1	chr4	116220914	116221014	+	3.8	cIP2vsInput	promoter-TSS (NM_181585)	promoter-TSS (NM_181585)	-950	NM_181585	18710	Mm.253819	NM_181585	ENSMUSG00000028698	Pik3r3	AA414954|p55pik	"phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 3 (p55)"	protein-coding	0.12	0.732673
Merged-chr4-82447488-1	chr4	82447438	82447538	+	3.8	cIP2vsInput	"intron (NM_008687, intron 2 of 8)"	"intron (NM_008687, intron 2 of 8)"	57820	NM_001113210	18028	Mm.317947	NM_001113209	ENSMUSG00000008575	Nfib	6720429L07Rik|E030026I10Rik	nuclear factor I/B	protein-coding	0.02	0.485149
Merged-chrY-10324917-1	chrY	10324867	10324967	+	3.8	cIP2vsInput	Intergenic	T-rich|Low_complexity|Low_complexity	872931	NM_001199331	100040022	Mm.485767	NM_001199331	ENSMUSG00000095172	Gm20822	-	"predicted gene, 20822"	protein-coding	0	0.29703
Merged-chr6-143166931-1	chr6	143166881	143166981	+	3.8	cIP2vsInput	promoter-TSS (NM_029250)	promoter-TSS (NM_029250)	-299	NM_029250	75320	Mm.272548	NM_029250	ENSMUSG00000030275	Etnk1	1110061E11Rik|4930555L11Rik|AI195356|AI841245|C80956|D6Ertd3e|EKI1	ethanolamine kinase 1	protein-coding	0.11	0.673267
Merged-chr1-64616961-1	chr1	64616911	64617011	+	3.8	cIP1vsInput	"5' UTR (NM_025964, exon 1 of 3)"	"5' UTR (NM_025964, exon 1 of 3)"	207	NM_025964	67099	Mm.46394	NM_025964	ENSMUSG00000025956	Mettl21a	2310038H17Rik|AI464204|Fam119a	methyltransferase like 21A	protein-coding	0.09	0.673267
Merged-chr5-107055002-2	chr5	107054930	107055074	+	3.8	cIP1vsInput|cIP2vsInput	Intergenic	L2c|LINE|L2	90441	NM_001271566	12545	Mm.20842	NM_001271566	ENSMUSG00000029283	Cdc7	AI597260|Cdc7l1|muCdc7	cell division cycle 7 (S. cerevisiae)	protein-coding	0.006944	0.4
Merged-chr13-38204793-1	chr13	38204743	38204843	+	3.8	cIP2vsInput	promoter-TSS (NM_026382)	promoter-TSS (NM_026382)	-146	NM_026382	67797	Mm.250783	NM_026382	ENSMUSG00000021431	Snrnp48	1110050F08Rik|6530403A03Rik|C6orf151	small nuclear ribonucleoprotein 48 (U11/U12)	protein-coding	0.05	0.514851
Merged-chr8-25543461-1	chr8	25543411	25543511	+	3.8	cIP2vsInput	"intron (NM_001079909, intron 2 of 16)"	"intron (NM_001079909, intron 2 of 16)"	24689	NM_001079908	14182	Mm.265716	NM_001079908	ENSMUSG00000031565	Fgfr1	AW208770|Eask|FLG|Fgfr-1|Flt-2|Hspy	fibroblast growth factor receptor 1	protein-coding	0.05	0.673267
Merged-chr19-46619123-1	chr19	46619073	46619173	+	3.8	cIP1vsInput	"intron (NM_001177812, intron 2 of 4)"	"intron (NM_001177812, intron 2 of 4)"	-4278	NM_001177813	226178	Mm.329895	NM_001177812	ENSMUSG00000047731	Wbp1l	D19Wsu162e|Opal1	WW domain binding protein 1 like	protein-coding	0.08	0.584158
Merged-chr6-30463531-2	chr6	30463470	30463593	+	3.8	cIP1vsInput|cIP2vsInput	Intergenic	B1F|SINE|Alu	46175	NM_178625	72649	Mm.45418	NM_178625	ENSMUSG00000029782	Tmem209	2700094F01Rik|AI428435	transmembrane protein 209	protein-coding	0.01626	0.5
Merged-chr17-46752175-2	chr17	46752076	46752275	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028065)	promoter-TSS (NM_028065)	37	NM_028065	72029	Mm.240325	NM_028065	ENSMUSG00000023973	Cnpy3	1600025D17Rik|2410050O22Rik|AI413153|CAG4A|ERDA5|PRAT4A|Tnrc5	canopy 3 homolog (zebrafish)	protein-coding	0.125628	0.725
Merged-chr11-69766415-1	chr11	69766365	69766465	+	3.8	cIP2vsInput	"intron (NM_029348, intron 1 of 3)"	CpG	503	NM_029348	75580	Mm.426361	NM_029348	ENSMUSG00000018750	Zbtb4	2310026P19Rik|9230111I22Rik|RP23-422L16.16|mKIAA1538	zinc finger and BTB domain containing 4	protein-coding	0.03	0.683168
Merged-chr4-10874222-1	chr4	10874172	10874272	+	3.8	cIP2vsInput	promoter-TSS (NM_026005)	promoter-TSS (NM_026005)	-276	NM_026005	67157	Mm.440552	NM_026005	ENSMUSG00000059482	2610301B20Rik	AI428449	RIKEN cDNA 2610301B20 gene	protein-coding	0.04	0.534653
Merged-chr2-154372788-2	chr2	154372724	154372852	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025876)	promoter-TSS (NM_025876)	-69	NM_025876	66971	Mm.289427	NM_025876	ENSMUSG00000027487	Cdk5rap1	2310066P17Rik	CDK5 regulatory subunit associated protein 1	protein-coding	0.09375	0.612403
Merged-chr2-129471128-2	chr2	129471059	129471198	+	3.8	cIP1vsInput|cIP2vsInput	"intron (NM_177653, intron 3 of 6)"	"intron (NM_177653, intron 3 of 6)"	65474	NM_177653	228592	Mm.452175	NM_177653	ENSMUSG00000043727	F830045P16Rik	Sirpb3	RIKEN cDNA F830045P16 gene	protein-coding	0	0.435714
Merged-chr5-137307434-1	chr5	137307384	137307484	+	3.8	cIP2vsInput	"5' UTR (NM_001109909, exon 1 of 20)"	"5' UTR (NM_001109909, exon 1 of 20)"	240	NM_031405	83701	Mm.387734	NM_001109909	ENSMUSG00000037364	Srrt	2810019G02Rik|ASR2A|ASR2B|ASR2C|ASR2D|Ars2|Asr2	serrate RNA effector molecule homolog (Arabidopsis)	protein-coding	0.15	0.762376
Merged-chr1-128103949-1	chr1	128103899	128103999	+	3.8	cIP2vsInput	"intron (NM_181750, intron 1 of 26)"	CpG	643	NM_181750	226412	Mm.221041	NM_181750	ENSMUSG00000056211	R3hdm1	R3hdm	R3H domain containing 1	protein-coding	0.07	0.574257
Merged-chr11-105293194-1	chr11	105293144	105293244	+	3.8	cIP2vsInput	"intron (NM_008626, intron 1 of 29)"	"intron (NM_008626, intron 1 of 29)"	548	NM_008626	17534	Mm.235616	NM_008626	ENSMUSG00000020695	Mrc2	Endo180|mKIAA0709|uPARAP	"mannose receptor, C type 2"	protein-coding	0.06	0.742574
Merged-chr4-106678955-1	chr4	106678905	106679005	+	3.8	cIP2vsInput	promoter-TSS (NM_001172073)	promoter-TSS (NM_001172073)	-11	NM_028209	72354	Mm.25806	NM_001172073	ENSMUSG00000025413	Ttc4	2810002P21Rik|AF007005|L62	tetratricopeptide repeat domain 4	protein-coding	0.12	0.732673
Merged-chr4-43492946-1	chr4	43492896	43492996	+	3.8	cIP2vsInput	promoter-TSS (NM_001037913)	promoter-TSS (NM_001037913)	113	NR_001460	19782		NR_001460	ENSMUSG00000088088	Rmrp	1110032O22Rik|Rmrpr	RNA component of mitochondrial RNAase P	miscRNA	0.11	0.663366
Merged-chr12-4843440-2	chr12	4843387	4843494	+	3.8	cIP1vsInput|cIP2vsInput	"5' UTR (NM_173416, exon 1 of 2)"	"5' UTR (NM_173416, exon 1 of 2)"	137	NM_001170858	238037	Mm.146087	NM_001170858	ENSMUSG00000051721	BC068281	A430092C04	cDNA sequence BC068281	protein-coding	0.065421	0.574074
Merged-chr17-34894573-1	chr17	34894523	34894623	+	3.8	cIP2vsInput	promoter-TSS (NM_198886)	promoter-TSS (NM_198886)	14	NM_198886	193736	Mm.161119	NM_198886	ENSMUSG00000049823	Zbtb12	BC020447|Bat-9|Bat9|G10|NG35	zinc finger and BTB domain containing 12	protein-coding	0.11	0.722772
Merged-chr2-29619666-1	chr2	29619616	29619716	+	3.8	cIP2vsInput	promoter-TSS (NM_054050)	promoter-TSS (NM_054050)	-54	NM_054050	107746	Mm.298274	NM_001039086	ENSMUSG00000039844	Rapgef1	4932418O06Rik|C3G|Grf2	Rap guanine nucleotide exchange factor (GEF) 1	protein-coding	0.14	0.752475
Merged-chr7-28372676-1	chr7	28372626	28372726	+	3.8	cIP2vsInput	promoter-TSS (NM_138752)	promoter-TSS (NM_138752)	-14	NM_001083912	101497	Mm.235700	NM_001083912	ENSMUSG00000037552	Plekhg2	AI194308|Clg|Cslg	"pleckstrin homology domain containing, family G (with RhoGef domain) member 2"	protein-coding	0.09	0.683168
Merged-chr11-69332290-1	chr11	69332240	69332340	+	3.8	cIP2vsInput	"3' UTR (NM_010599, exon 14 of 14)"	"3' UTR (NM_010599, exon 14 of 14)"	6032	NM_010599	16499	Mm.232472	NM_010599	ENSMUSG00000018470	Kcnab3	C330022D06Rik|Kcnab4|mKv(beta)4	"potassium voltage-gated channel, shaker-related subfamily, beta member 3"	protein-coding	0.1	0.60396
Merged-chr11-101552961-1	chr11	101552911	101553011	+	3.8	cIP2vsInput	"intron (NM_008676, intron 1 of 23)"	"intron (NM_008676, intron 1 of 23)"	307	NM_001252223	17966	Mm.489817	NM_001252220	ENSMUSG00000017119	Nbr1	mKIAA0049	neighbor of Brca1 gene 1	protein-coding	0.05	0.60396
Merged-chr5-14997778-1	chr5	14997728	14997828	+	3.8	cIP1vsInput	Intergenic	Intergenic	35229	NM_182957	66773	Mm.368256	NM_182957	ENSMUSG00000091897	Gm17019	-	predicted gene 17019	protein-coding	0.01	0.425743
Merged-chr9-64045221-1	chr9	64045171	64045271	+	3.8	cIP2vsInput	Intergenic	Intergenic	-3756	NR_040726	73397	Mm.48745	NR_040726	ENSMUSG00000093616	1700055C04Rik	-	RIKEN cDNA 1700055C04 gene	miscRNA	0.02	0.60396
Merged-chr5-14952107-1	chr5	14952057	14952157	+	3.8	cIP2vsInput	"intron (NR_001584, intron 1 of 3)"	"intron (NR_001584, intron 1 of 3)"	6813	NR_001584	74062	Mm.394766	NR_001584		Speer8-ps1	4933405L09Rik|SPEER-8|Speer8-ps	"spermatogenesis associated glutamate (E)-rich protein 8, pseudogene 1"	pseudo	0.02	0.425743
Merged-chr15-68363343-2	chr15	68363275	68363411	+	3.8	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-22054	NR_029718	387228		NR_029718	ENSMUSG00000065437	Mir30d	Mirn30d|mmu-mir-30d	microRNA 30d	miscRNA	0.117647	0.715328
Merged-chr17-25015873-1	chr17	25015823	25015923	+	3.8	cIP2vsInput	promoter-TSS (NM_020608)	promoter-TSS (NM_020608)	-213	NM_134126	106633	Mm.32802	NM_134126	ENSMUSG00000024169	Ift140	AI661311|Tce5|Wdtc2|mKIAA0590	intraflagellar transport 140	protein-coding	0.11	0.643564
Merged-chr4-143413043-1	chr4	143412993	143413093	+	3.8	cIP2vsInput	"5' UTR (NM_172877, exon 1 of 5)"	"5' UTR (NM_172877, exon 1 of 5)"	617	NM_172877	242736	Mm.275953	NM_172877	ENSMUSG00000046862	Pramef8	4732496O08Rik|AU023234	PRAME family member 8	protein-coding	0.02	0.554455
Merged-chr2-13371951-1	chr2	13371901	13372001	+	3.8	cIP2vsInput	"intron (NM_001081084, intron 31 of 66)"	"intron (NM_001081084, intron 31 of 66)"	-100673	NM_009105	20163	Mm.905	NM_009105	ENSMUSG00000026727	Rsu1	RsuI|rsp-1	Ras suppressor protein 1	protein-coding	0.02	0.524752
Merged-chr2-32236628-2	chr2	32236574	32236683	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145145)	promoter-TSS (NM_145145)	-55	NM_145145	99011	Mm.31192	NM_145145	ENSMUSG00000039254	Pomt1	AI505244	protein-O-mannosyltransferase 1	protein-coding	0.137615	0.645455
Merged-chr17-34587570-1	chr17	34587520	34587620	+	3.8	cIP2vsInput	"exon (NM_010929, exon 30 of 30)"	"exon (NM_010929, exon 30 of 30)"	-2236	NM_134116	106512	Mm.26584	NM_134116	ENSMUSG00000034786	Gpsm3	AA960287|AGS4	"G-protein signalling modulator 3 (AGS3-like, C. elegans)"	protein-coding	0.16	0.772277
Merged-chr4-151517258-1	chr4	151517208	151517308	+	3.8	cIP2vsInput	"intron (NM_001081557, intron 4 of 23)"	"intron (NM_001081557, intron 4 of 23)"	344510	NM_001195565	100072	Mm.318846	NM_001166021	ENSMUSG00000014592	Camta1	1810059M14Rik|2310058O09Rik|AI316882|AW987475|mKIAA0833	calmodulin binding transcription activator 1	protein-coding	0.04	0.564356
Merged-chr2-18767119-1	chr2	18767069	18767169	+	3.8	cIP2vsInput	Intergenic	CpG	68097	NM_001001334	381350	Mm.330024	NM_001001334		BC061194	-	cDNA sequence BC061194	protein-coding	0.12	0.653465
Merged-chr17-22866968-1	chr17	22866918	22867018	+	3.8	cIP2vsInput	"intron (NM_001110254, intron 1 of 4)"	"intron (NM_001110254, intron 1 of 4)"	166	NM_177358	240041	Mm.328828	NM_001110254	ENSMUSG00000059142	Zfp945	A630033E08Rik|C730040L01Rik	zinc finger protein 945	protein-coding	0.04	0.663366
Merged-chr16-45913636-1	chr16	45913586	45913686	+	3.8	cIP2vsInput	Intergenic	Intergenic	-69258	NM_001252442	208177	Mm.211477	NM_001252442	ENSMUSG00000033149	Phldb2	AV253284|C820004H04Rik|LL5b|LL5beta	"pleckstrin homology-like domain, family B, member 2"	protein-coding	0	0.366337
Merged-chr5-139380647-1	chr5	139380597	139380697	+	3.8	cIP2vsInput	promoter-TSS (NM_030258)	promoter-TSS (NM_030258)	-20	NM_030258	80290	Mm.270003	NM_001038703	ENSMUSG00000044197	Gpr146	BC003323|PGR8	G protein-coupled receptor 146	protein-coding	0.13	0.772277
Merged-chr14-62837347-2	chr14	62837290	62837404	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175546)	promoter-TSS (NM_175546)	-343	NM_175546	268752	Mm.482243	NM_175546	ENSMUSG00000014547	Wdfy2	5830485M08|B130024L21Rik|ProF|ZFYVE22	WD repeat and FYVE domain containing 2	protein-coding	0.070175	0.547826
Merged-chr2-30783545-1	chr2	30783495	30783595	+	3.8	cIP2vsInput	Intergenic	MLT1J|LTR|ERVL-MaLR	18192	NM_198000	73598	Mm.34166	NM_198000	ENSMUSG00000044320	1700001O22Rik	1700113K14Rik|4930549G18Rik	RIKEN cDNA 1700001O22 gene	protein-coding	0.01	0.465347
Merged-chr14-74657404-1	chr14	74657354	74657454	+	3.8	cIP2vsInput	"intron (NM_172812, intron 2 of 2)"	"intron (NM_172812, intron 2 of 2)"	16564	NM_172812	15558	Mm.214351	NM_172812	ENSMUSG00000034997	Htr2a	E030013E04|Htr-2|Htr2	5-hydroxytryptamine (serotonin) receptor 2A	protein-coding	0.05	0.475248
Merged-chr2-14055382-1	chr2	14055332	14055432	+	3.8	cIP2vsInput	"intron (NM_001012396, intron 1 of 5)"	CpG	653	NM_001012396	30963	Mm.241205	NM_001012396	ENSMUSG00000063275	Ptpla	HACD1	"protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"	protein-coding	0.16	0.80198
Merged-chr2-39226308-1	chr2	39226258	39226358	+	3.8	cIP2vsInput	promoter-TSS (NM_024209)	promoter-TSS (NM_024209)	30	NM_024209	67857	Mm.392662	NM_024209		Ppp6c	2310003C10Rik	"protein phosphatase 6, catalytic subunit"	protein-coding	0.15	0.693069
Merged-chr2-125247184-1	chr2	125247134	125247234	+	3.8	cIP2vsInput	promoter-TSS (NM_001159646)	promoter-TSS (NM_001159646)	-64	NM_001159646	110074	Mm.471988	NM_001159646	ENSMUSG00000027203	Dut	5031412I06Rik|5133400F09Rik|D2Bwg0749e|Dutp|dUTPase	deoxyuridine triphosphatase	protein-coding	0.08	0.60396
Merged-chr7-45053395-1	chr7	45053345	45053445	+	3.8	cIP2vsInput	promoter-TSS (NM_175022)	promoter-TSS (NM_175022)	-514	NM_175022	233210	Mm.219137	NM_175022	ENSMUSG00000046574	Prr12	6720469B10|BC058674	proline rich 12	protein-coding	0.09	0.584158
Merged-chr6-124863765-1	chr6	124863715	124863815	+	3.8	cIP2vsInput	TTS (NM_013488)	TTS (NM_013488)	152	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding	0.07	0.772277
Merged-chr5-124579092-1	chr5	124579042	124579142	+	3.8	cIP2vsInput	promoter-TSS (NM_145371)	promoter-TSS (NM_145371)	-35	NM_145371	209354	Mm.28839	NM_145371	ENSMUSG00000029388	Eif2b1	26kDa|D5Ertd406e|EIF2B|EIF2BA	"eukaryotic translation initiation factor 2B, subunit 1 (alpha)"	protein-coding	0.18	0.693069
Merged-chr11-115564334-1	chr11	115564284	115564384	+	3.8	cIP2vsInput	promoter-TSS (NM_001002929)	promoter-TSS (NM_001002929)	-110	NM_001002929	445007	Mm.4379	NM_001002929	ENSMUSG00000020739	Nup85	Pcnt1|frount	nucleoporin 85	protein-coding	0.02	0.475248
Merged-chr6-87851063-1	chr6	87851013	87851113	+	3.8	cIP2vsInput	promoter-TSS (NM_001109745)	promoter-TSS (NM_001109745)	43	NM_001109746	12785	Mm.290251	NM_001109745	ENSMUSG00000030057	Cnbp	AA408710|Cnbp1|Znf9	cellular nucleic acid binding protein	protein-coding	0.1	0.683168
Merged-chr4-45084817-1	chr4	45084767	45084867	+	3.8	cIP2vsInput	promoter-TSS (NM_001024142)	promoter-TSS (NM_001024142)	-213	NM_001024142	269529	Mm.490989	NM_001024142	ENSMUSG00000048232	Fbxo10	FBX10|Gm634	F-box protein 10	protein-coding	0.03	0.60396
Merged-chr1-36557246-2	chr1	36557160	36557333	+	3.8	cIP1vsInput|cIP2vsInput	"intron (NM_001126047, intron 1 of 14)"	CpG	1135	NM_001126047	20353	Mm.29558	NM_001126047	ENSMUSG00000026121	Sema4c	AI426163|Semacl1|Semaf|Semai|mKIAA1739	"sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C"	protein-coding	0.075145	0.695402
Merged-chr2-30066232-1	chr2	30066182	30066282	+	3.8	cIP2vsInput	promoter-TSS (NM_001204875)	promoter-TSS (NM_001204875)	-242	NM_001204875	56086	Mm.335942	NM_001204875	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding	0.14	0.742574
Merged-chr11-111215045-1	chr11	111214995	111215095	+	3.8	cIP2vsInput	Intergenic	Intergenic	148881	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	"potassium inwardly-rectifying channel, subfamily J, member 2"	protein-coding	0.01	0.386139
Merged-chr14-20664640-1	chr14	20664590	20664690	+	3.8	cIP2vsInput	"intron (NM_175132, intron 3 of 3)"	"intron (NM_175132, intron 3 of 3)"	3666	NM_175132	68760	Mm.35789	NM_175132	ENSMUSG00000039376	Synpo2l	1110054M18Rik|Chap	synaptopodin 2-like	protein-coding	0.01	0.574257
Merged-chr18-35045786-1	chr18	35045736	35045836	+	3.8	cIP2vsInput	Intergenic	Intergenic	-73126	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	"catenin (cadherin associated protein), alpha 1"	protein-coding	0.01	0.574257
Merged-chrX-169973055-1	chrX	169973005	169973105	+	3.8	cIP1vsInput	"intron (NM_183151, intron 3 of 9)"	"intron (NM_183151, intron 3 of 9)"	5862	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	miscRNA	0.01	0.405941
Merged-chr8-95434825-1	chr8	95434775	95434875	+	3.8	cIP2vsInput	promoter-TSS (NM_008187)	promoter-TSS (NM_008187)	44	NM_008187	14894	Mm.2080	NM_008187	ENSMUSG00000031796	Gtl3	2600014O15Rik|AL024127|T10-2A2	gene trap locus 3	protein-coding	0.17	0.811881
Merged-chr8-105880840-1	chr8	105880790	105880890	+	3.8	cIP2vsInput	promoter-TSS (NM_181594)	promoter-TSS (NM_181594)	-111	NM_181594	234699	Mm.28979	NM_181594	ENSMUSG00000036270	Edc4	BC022641	enhancer of mRNA decapping 4	protein-coding	0.06	0.594059
Merged-chr11-119215513-1	chr11	119215463	119215563	+	3.8	cIP2vsInput	"intron (NM_172443, intron 1 of 11)"	"intron (NM_172443, intron 1 of 11)"	12986	NM_172443	207592	Mm.205263	NM_172443	ENSMUSG00000039976	Tbc1d16	B930087K01|BC026530|Tcd1d16	"TBC1 domain family, member 16"	protein-coding	0.04	0.554455
Merged-chr11-21371196-1	chr11	21371146	21371246	+	3.8	cIP2vsInput	promoter-TSS (NM_139297)	promoter-TSS (NM_139297)	-317	NM_139297	216558	Mm.28877	NM_139297	ENSMUSG00000001891	Ugp2	-	UDP-glucose pyrophosphorylase 2	protein-coding	0.06	0.712871
Merged-chr18-74778901-1	chr18	74778851	74778951	+	3.8	cIP1vsInput	promoter-TSS (NM_177470)	promoter-TSS (NM_177470)	-311	NM_177470	52538	Mm.245724	NM_177470	ENSMUSG00000036880	Acaa2	0610011L04Rik|AI255831|AI265397|D18Ertd240e	acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase)	protein-coding	0.05	0.653465
Merged-chr2-113849005-1	chr2	113848955	113849055	+	3.8	cIP2vsInput	promoter-TSS (NM_181416)	promoter-TSS (NM_181416)	-344	NM_181416	228482	Mm.45753	NM_181416	ENSMUSG00000041219	Arhgap11a	6530401L14Rik|mKIAA0013	Rho GTPase activating protein 11A	protein-coding	0.06	0.50495
Merged-chr14-54360796-1	chr14	54360746	54360846	+	3.8	cIP2vsInput	promoter-TSS (NM_026936)	promoter-TSS (NM_026936)	-45	NM_026936	69089	Mm.182340	NM_026936	ENSMUSG00000000959	Oxa1l	1810020M02Rik|AI894287	oxidase assembly 1-like	protein-coding	0.07	0.574257
Merged-chr15-89059684-2	chr15	89059620	89059748	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001002005)	promoter-TSS (NM_001002005)	-42	NM_001002005	406218	Mm.483059	NM_001002005	ENSMUSG00000058441	Panx2	-	pannexin 2	protein-coding	0.085938	0.534884
Merged-chr5-15020217-1	chr5	15020167	15020267	+	3.8	cIP1vsInput	Intergenic	Intergenic	12790	NM_182957	66773	Mm.368256	NM_182957	ENSMUSG00000091897	Gm17019	-	predicted gene 17019	protein-coding	0.02	0.386139
Merged-chr3-88336479-2	chr3	88336426	88336533	+	3.8	cIP1vsInput|cIP2vsInput	"exon (NM_178246, exon 1 of 22)"	"exon (NM_178246, exon 1 of 22)"	219	NM_178246	229512	Mm.439830	NM_173188	ENSMUSG00000001415	Smg5	BC024683|mKIAA1089	"Smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)"	protein-coding	0.065421	0.675926
Merged-chr6-3181511-1	chr6	3181461	3181561	+	3.8	cIP1vsInput	Intergenic	Intergenic	-107008	NR_036696	667335	Mm.380219	NR_036696		Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo	0.01	0.267327
Merged-chr5-48583697-2	chr5	48583628	48583767	+	3.8	cIP1vsInput|cIP2vsInput	"intron (NM_001199244, intron 1 of 7)"	"intron (NM_001199244, intron 1 of 7)"	15985	NM_001199245	80334	Mm.160172	NM_001199242	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding	0.007194	0.378571
Merged-chr9-66124813-1	chr9	66124763	66124863	+	3.8	cIP1vsInput	promoter-TSS (NM_019727)	promoter-TSS (NM_019727)	73	NM_019727	56440	Mm.271891	NM_019727	ENSMUSG00000032382	Snx1	-	sorting nexin 1	protein-coding	0.09	0.594059
Merged-chr3-30392402-1	chr3	30392352	30392452	+	3.8	cIP2vsInput	"intron (NM_021442, intron 1 of 2)"	"intron (NM_021442, intron 1 of 2)"	117085	NM_021442	14013	Mm.426829	NM_021442	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding	0.01	0.50495
Merged-chr6-86849413-1	chr6	86849363	86849463	+	3.8	cIP2vsInput	promoter-TSS (NM_177762)	promoter-TSS (NM_177762)	27	NR_028298	67170	Mm.392029	NR_028298		2610306M01Rik	-	RIKEN cDNA 2610306M01 gene	miscRNA	0.05	0.633663
Merged-chr17-17838238-1	chr17	17838188	17838288	+	3.8	cIP2vsInput	"exon (NM_001162909, exon 7 of 9)"	"exon (NM_001162909, exon 7 of 9)"	7263	NM_001162909	75202	Mm.227456	NM_001162909	ENSMUSG00000080316	Ncrna00085	4930546H06Rik|9530079D04Rik|B230206P06Rik	non-protein coding RNA 85	protein-coding	0.1	0.653465
Merged-chr7-13009723-1	chr7	13009673	13009773	+	3.8	cIP2vsInput	promoter-TSS (NM_001024699)	promoter-TSS (NM_001024699)	77	NM_001024699	232879	Mm.279272	NM_001024699	ENSMUSG00000049600	Zbtb45	BB161562|Gm157|Zfp499	zinc finger and BTB domain containing 45	protein-coding	0.09	0.70297
Merged-chr19-46962322-1	chr19	46962272	46962372	+	3.8	cIP2vsInput	promoter-TSS (NR_028353)	promoter-TSS (NR_028353)	29	NM_029810	76952	Mm.40965	NM_001164363	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	"5'-nucleotidase, cytosolic II"	protein-coding	0.19	0.831683
Merged-chr7-126487179-1	chr7	126487129	126487229	+	3.8	cIP2vsInput	promoter-TSS (NM_172745)	promoter-TSS (NM_172745)	-176	NM_172745	233870	Mm.197829	NM_001163713	ENSMUSG00000073838	Tufm	2300002G02Rik|C76308|C76389|EF-TuMT|EFTU	"Tu translation elongation factor, mitochondrial"	protein-coding	0.06	0.574257
Merged-chr2-84826911-1	chr2	84826861	84826961	+	3.8	cIP2vsInput	promoter-TSS (NM_013899)	promoter-TSS (NM_013899)	-110	NM_013899	30059	Mm.21826	NM_013899	ENSMUSG00000027076	Timm10	Tim13|Timm13a	translocase of inner mitochondrial membrane 10	protein-coding	0.04	0.514851
Merged-chr4-117682310-1	chr4	117682260	117682360	+	3.8	cIP2vsInput	promoter-TSS (NM_023178)	promoter-TSS (NM_023178)	-85	NM_023178	66233	Mm.29142	NM_023178	ENSMUSG00000009640	Dmap1	1500016M21Rik|DNMAP1|DNMTAP1|Dmtap1|mKIAA1425	DNA methyltransferase 1-associated protein 1	protein-coding	0.07	0.584158
Merged-chr17-80554096-2	chr17	80554040	80554153	+	3.8	cIP1vsInput|cIP2vsInput	"intron (NM_001033443, intron 3 of 9)"	(CGTG)n|Simple_repeat|Simple_repeat	9738	NM_001033443	381113	Mm.329216	NM_001033443	ENSMUSG00000033966	Cdkl4	AU067824|Gm942	cyclin-dependent kinase-like 4	protein-coding	0.070796	0.578947
Merged-chr7-6172458-1	chr7	6172408	6172508	+	3.8	cIP1vsInput	promoter-TSS (NM_028316)	promoter-TSS (NM_028316)	-55	NM_028316	72667	Mm.274089	NM_001146024		Zfp444	2810031J10Rik|6230401O10Rik|mFLJ00134	zinc finger protein 444	protein-coding	0.05	0.574257
Merged-chr8-69901593-1	chr8	69901543	69901643	+	3.8	cIP2vsInput	promoter-TSS (NM_032004)	promoter-TSS (NM_032004)	-622	NM_032004	83984	Mm.432504	NM_032004	ENSMUSG00000047654	Tssk6	Sstk	testis-specific serine kinase 6	protein-coding	0.1	0.683168
Merged-chr15-81730189-1	chr15	81730139	81730239	+	3.8	cIP2vsInput	promoter-TSS (NM_001146174)	promoter-TSS (NM_001146174)	-270	NM_001146174	19387	Mm.270975	NM_001146174	ENSMUSG00000022391	Rangap1	C79654|Fug1|mKIAA1835	RAN GTPase activating protein 1	protein-coding	0.08	0.544554
Merged-chr7-28277992-1	chr7	28277942	28278042	+	3.8	cIP2vsInput	"exon (NM_001177427, exon 1 of 1)"	"exon (NM_001177427, exon 1 of 1)"	286	NM_001177427	434156	Mm.118535	NM_001177427	ENSMUSG00000070705	Eid2b	3010005C08Rik	EP300 interacting inhibitor of differentiation 2B	protein-coding	0.12	0.70297
Merged-chr17-80290296-1	chr17	80290246	80290346	+	3.8	cIP2vsInput	promoter-TSS (NM_194269)	promoter-TSS (NM_194269)	84	NM_194269	378462	Mm.45208	NM_194269	ENSMUSG00000045257	Morn2	Mopt	MORN repeat containing 2	protein-coding	0.07	0.623762
Merged-chr13-91223687-1	chr13	91223637	91223737	+	3.8	cIP2vsInput	"intron (NM_025770, intron 1 of 7)"	"intron (NM_025770, intron 1 of 7)"	300	NM_025770	66795	Mm.235385	NM_025770	ENSMUSG00000021619	Atg10	5330424L23Rik|5430428K15Rik|AI852123|APG10|Agp10|Apg10l|Apg10p|Atg10l	autophagy related 10	protein-coding	0.02	0.534653
Merged-chr5-86804152-1	chr5	86804102	86804202	+	3.8	cIP1vsInput	promoter-TSS (NM_177680)	promoter-TSS (NM_177680)	-338	NM_177680	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding	0.13	0.712871
Merged-chr12-55492021-1	chr12	55491971	55492071	+	3.8	cIP2vsInput	TTS (NR_035430)	TTS (NR_035430)	626	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	"nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha"	protein-coding	0.19	0.861386
Merged-chr2-180171371-1	chr2	180171321	180171421	+	3.8	cIP2vsInput	promoter-TSS (NM_019822)	promoter-TSS (NM_019822)	-217	NM_019822	56436	Mm.379082	NM_019822	ENSMUSG00000039041	Adrm1	1110063P18Rik|2510006J17Rik|AA408205|ARM-1|AU043535|Arm1|Gp110|Rpn13	adhesion regulating molecule 1	protein-coding	0.13	0.782178
Merged-chr15-59030277-1	chr15	59030227	59030327	+	3.8	cIP1vsInput	"intron (NM_144800, intron 3 of 14)"	"intron (NM_144800, intron 3 of 14)"	51749	NM_001146180	211401	Mm.394414	NM_001146180	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	metastasis suppressor 1	protein-coding	0.02	0.564356
Merged-chr4-41569659-1	chr4	41569609	41569709	+	3.8	cIP2vsInput	promoter-TSS (NM_001159583)	promoter-TSS (NM_001159583)	-132	NM_027993	71901	Mm.39215	NM_001159583		Fam219a	2310028H24Rik	"family with sequence similarity 219, member A"	protein-coding	0.09	0.70297
Merged-chr14-73385339-1	chr14	73385289	73385389	+	3.8	cIP2vsInput	promoter-TSS (NM_008410)	promoter-TSS (NM_008410)	-68	NM_008410	16432	Mm.392973	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding	0.11	0.821782
Merged-chr13-92844721-1	chr13	92844671	92844771	+	3.8	cIP2vsInput	promoter-TSS (NM_001162945)	promoter-TSS (NM_001162945)	-66	NM_001162945	382793	Mm.296770	NM_001162945	ENSMUSG00000021704	Mtx3	4930470O13Rik|AA409304|AI853833|AU067765|EG624619|Gm1194|Gm6514	metaxin 3	protein-coding	0.06	0.633663
Merged-chr5-118155447-1	chr5	118155397	118155497	+	3.8	cIP2vsInput	promoter-TSS (NM_172721)	promoter-TSS (NM_172721)	11	NM_172721	231672	Mm.221769	NM_172721	ENSMUSG00000032867	Fbxw8	4930438M06Rik|FBW6|FBW8|FBXO29|Fbx29	F-box and WD-40 domain protein 8	protein-coding	0.11	0.683168
Merged-chrY-6728373-1	chrY	6728323	6728423	+	3.8	cIP2vsInput	Intergenic	Intergenic	439404	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.326733
Merged-chr13-100651286-2	chr13	100651205	100651367	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011233)	promoter-TSS (NM_011233)	-57	NM_027139	108143	Mm.301148	NM_001015889	ENSMUSG00000052293	Taf9	2310012M09Rik|2810046E22Rik|4921516M08Rik|AA673500|AU045423|Ak6|TAFII31|Taf2g	"TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor"	protein-coding	0.12963	0.723926
Merged-chr18-14657482-1	chr18	14657432	14657532	+	3.8	cIP1vsInput	"intron (NM_009280, intron 3 of 10)"	"intron (NM_009280, intron 3 of 10)"	25432	NM_001161369	268996	Mm.31761	NM_001161369	ENSMUSG00000037013	Ss18	D130059H17|Ssxt|Syt	"synovial sarcoma translocation, Chromosome 18"	protein-coding	0.01	0.534653
Merged-chr7-5080127-2	chr7	5080075	5080179	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001252454)	promoter-TSS (NM_001252454)	-108	NM_010147	13854	Mm.3091	NM_001252454	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding	0.125	0.647619
Merged-chr9-53667465-1	chr9	53667415	53667515	+	3.8	cIP2vsInput	promoter-TSS (NM_027807)	promoter-TSS (NM_027807)	42	NM_001161618	75717	Mm.218910	NM_001161618	ENSMUSG00000032030	Cul5	4921514I20Rik|8430423K24Rik|AI852817|C030032G03Rik|C330021I08Rik|VACM-1|VACM1	cullin 5	protein-coding	0.16	0.742574
Merged-chr11-120824853-1	chr11	120824803	120824903	+	3.8	cIP2vsInput	promoter-TSS (NM_007988)	promoter-TSS (NM_007988)	-306	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding	0.08	0.673267
Merged-chr6-97179175-1	chr6	97179125	97179225	+	3.8	cIP2vsInput	promoter-TSS (NM_001081111)	promoter-TSS (NM_001081111)	-51	NM_001081111	232286		NM_001081111		Tmf1	7030402D04Rik|Gm153|Tmf1`	TATA element modulatory factor 1	protein-coding	0.13	0.712871
Merged-chr13-98891077-1	chr13	98891027	98891127	+	3.8	cIP2vsInput	promoter-TSS (NM_001048267)	promoter-TSS (NM_001048267)	-35	NM_001048267	238799	Mm.173286	NM_001048267		Tnpo1	AU021749|D13Ertd688e|IPO2|Kpnb2|MIP|MIP1|TRN	transportin 1	protein-coding	0.06	0.623762
Merged-chr6-16958151-1	chr6	16958101	16958201	+	3.8	cIP1vsInput	Intergenic	Intergenic	-59710	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding	0.01	0.29703
Merged-chr15-99393074-1	chr15	99393024	99393124	+	3.8	cIP2vsInput	promoter-TSS (NM_001171035)	promoter-TSS (NM_001171035)	127	NM_001171034	110213	Mm.16769	NM_001171034	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding	0.07	0.584158
Merged-chr11-102316824-1	chr11	102316774	102316874	+	3.8	cIP2vsInput	"intron (NM_011551, intron 1 of 20)"	CpG	463	NM_001044383	21429	Mm.2845	NM_001044383	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF1	"upstream binding transcription factor, RNA polymerase I"	protein-coding	0.1	0.742574
Merged-chr4-98923064-1	chr4	98923014	98923114	+	3.8	cIP2vsInput	promoter-TSS (NM_146144)	promoter-TSS (NM_146144)	-746	NM_146144	230484	Mm.371692	NM_146144	ENSMUSG00000028560	Usp1	-	ubiquitin specific peptidase 1	protein-coding	0.1	0.623762
Merged-chr2-17462426-1	chr2	17462376	17462476	+	3.8	cIP2vsInput	"intron (NM_028757, intron 4 of 6)"	"intron (NM_028757, intron 4 of 6)"	268642	NM_028757	74103	Mm.440498	NM_028757		Nebl	1200007O21Rik|A630080F05Rik|BB140644|D830029A09Rik|Lnebl	nebulette	protein-coding	0.02	0.435644
Merged-chr3-138443017-1	chr3	138442967	138443067	+	3.8	cIP2vsInput	promoter-TSS (NM_007410)	promoter-TSS (NM_007410)	-147	NM_007410	11532	Mm.3874	NM_007410	ENSMUSG00000028138	Adh5	Adh-5|Adh3|GSNOR	"alcohol dehydrogenase 5 (class III), chi polypeptide"	protein-coding	0.13	0.742574
Merged-chr11-98740843-1	chr11	98740793	98740893	+	3.8	cIP2vsInput	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-1030	NM_178060	21833	Mm.442648	NM_178060	ENSMUSG00000058756	Thra	6430529J03Rik|AW259572|Erba|Nr1a1|Rvr|T3R[a]|T3Ralpha|Thra1|Thra2	thyroid hormone receptor alpha	protein-coding	0.03	0.514851
Merged-chr19-36834162-1	chr19	36834112	36834212	+	3.8	cIP2vsInput	promoter-TSS (NM_001163635)	promoter-TSS (NM_001163635)	-70	NM_001163635	74493	Mm.249310	NM_001163635	ENSMUSG00000024811	Tnks2	5430432P15Rik|AA517131|AI662480|ARTD6|TNKS-2|Tank2	"tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2"	protein-coding	0.1	0.70297
Merged-chr18-61786822-1	chr18	61786772	61786872	+	3.8	cIP2vsInput	promoter-TSS (NM_178928)	promoter-TSS (NM_178928)	-160	NM_178928	106877	Mm.26632	NM_178928	ENSMUSG00000033032	Afap1l1	AI173486	actin filament associated protein 1-like 1	protein-coding	0.08	0.70297
Merged-chrY-7035800-1	chrY	7035750	7035850	+	3.8	cIP2vsInput	Intergenic	L1MD|LINE|L1	131977	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.188119
Merged-chr3-147612013-1	chr3	147611963	147612063	+	3.8	cIP2vsInput	Intergenic	Intergenic	759646	NM_027594	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|Ttll7s	"tubulin tyrosine ligase-like family, member 7"	protein-coding	0.03	0.356436
Merged-chr4-150371817-2	chr4	150371722	150371912	+	3.8	cIP1vsInput|cIP2vsInput	"intron (NM_001085492, intron 1 of 22)"	CpG	89901	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding	0.078947	0.664921
Merged-chr10-40349104-1	chr10	40349054	40349154	+	3.8	cIP2vsInput	promoter-TSS (NM_001168304)	promoter-TSS (NM_001168304)	-204	NM_001168304	78334		NM_001168304	ENSMUSG00000038481	Cdk19	2700084L06Rik|AI845279|AW228747|CDK11|Cdc2l6|mKIAA1028	cyclin-dependent kinase 19	protein-coding	0.1	0.643564
Merged-chr3-114421751-1	chr3	114421701	114421801	+	3.8	cIP2vsInput	Intergenic	Intergenic	391211	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	"collagen, type XI, alpha 1"	protein-coding	0	0.336634
Merged-chr11-61175011-1	chr11	61174961	61175061	+	3.8	cIP2vsInput	promoter-TSS (NM_001004143)	promoter-TSS (NM_001004143)	48	NM_001004143	216825	Mm.30602	NM_001004143	ENSMUSG00000042506	Usp22	AI427806	ubiquitin specific peptidase 22	protein-coding	0.09	0.693069
Merged-chr7-113207093-2	chr7	113207021	113207165	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001243048)	promoter-TSS (NM_001243048)	-372	NM_001243048	11865	Mm.440371	NM_001243048	ENSMUSG00000055116	Arntl	Arnt3|BMAL1b|Bmal1|MOP3|bHLHe5|bmal1b'	aryl hydrocarbon receptor nuclear translocator-like	protein-coding	0.0625	0.634483
Merged-chr7-142330374-1	chr7	142330324	142330424	+	3.8	cIP2vsInput	"intron (NM_177265, intron 3 of 3)"	"intron (NM_177265, intron 3 of 3)"	26872	NM_015809	50775	Mm.389990	NM_015809	ENSMUSG00000045236	Krtap5-4	-	keratin associated protein 5-4	protein-coding	0.04	0.613861
Merged-chr2-30077617-2	chr2	30077544	30077691	+	3.8	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-1149	NM_153805	263803	Mm.233843	NM_153805	ENSMUSG00000026785	Pkn3	AW209115|BC034126	protein kinase N3	protein-coding	0.136054	0.736486
Merged-chr15-98993581-1	chr15	98993531	98993631	+	3.8	cIP2vsInput	Intergenic	RSINE1|SINE|B4	7616	NR_045991	75951	Mm.441657	NR_045991	ENSMUSG00000097587	4930578M01Rik	3010001K12Rik	RIKEN cDNA 4930578M01 gene	miscRNA	0.02	0.514851
Merged-chr7-51455254-1	chr7	51455204	51455304	+	3.8	cIP2vsInput	Intergenic	Intergenic	-55775	NR_073508	233246	Mm.411727	NM_001271879	ENSMUSG00000055489	Ano5	9330162L24|Gdd1|Tmem16e	anoctamin 5	protein-coding	0	0.346535
Merged-chrX-31230330-1	chrX	31230280	31230380	+	3.8	cIP1vsInput	Intergenic	L1_Mm|LINE|L1	-106039	NM_001243011	100042159	Mm.489579	NM_001243011	ENSMUSG00000095835	Gm3701	-	predicted gene 3701	protein-coding	0.01	0.346535
Merged-chr17-28328492-2	chr17	28328436	28328549	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011287)	promoter-TSS (NM_011287)	21	NM_011287	19896	Mm.467207	NM_011287	ENSMUSG00000037805	Rpl10a	CsA-19|Nedd6	ribosomal protein L10A	protein-coding	0.150442	0.719298
Merged-chr2-70661542-1	chr2	70661492	70661592	+	3.8	cIP2vsInput	promoter-TSS (NR_027343)	promoter-TSS (NR_027343)	33	NM_027352	70231	Mm.470827	NM_027352	ENSMUSG00000014959	Gorasp2	0610011A07Rik|2410043M02Rik|5730520M13Rik|9430094F20Rik|AW552058|GOLPH2|GRASP55|GRS2|p59	golgi reassembly stacking protein 2	protein-coding	0.16	0.792079
Merged-chr2-152669447-1	chr2	152669397	152669497	+	3.8	cIP2vsInput	promoter-TSS (NM_001159551)	promoter-TSS (NM_001159551)	-14	NM_010376	14950	Mm.277327	NM_001159551	ENSMUSG00000019188	H13	1200006O09Rik|4930443L17Rik|5031424B04Rik|AV020344|H-13|Hm13|PSL3|Spp	histocompatibility 13	protein-coding	0.14	0.643564
Merged-chr16-91406137-1	chr16	91406087	91406187	+	3.8	cIP2vsInput	promoter-TSS (NM_008349)	promoter-TSS (NM_008349)	-98	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	"interleukin 10 receptor, beta"	protein-coding	0.02	0.544554
Merged-chr5-41844428-1	chr5	41844378	41844478	+	3.8	cIP2vsInput	promoter-TSS (NM_001081422)	promoter-TSS (NM_001081422)	-113	NM_001081422	665775	Mm.158726	NM_001081422	ENSMUSG00000061755	Bod1l	A230054D04Rik|AI853319|FAM44A|mKIAA1327	biorientation of chromosomes in cell division 1-like	protein-coding	0.12	0.712871
Merged-chr13-23563282-1	chr13	23563232	23563332	+	3.8	cIP2vsInput	promoter-TSS (NM_178205)	promoter-TSS (NM_178205)	-917	NM_178205	319151	Mm.261658	NM_178205		Hist1h3e	H3-f|H3.1	"histone cluster 1, H3e"	protein-coding	0.02	0.405941
Merged-chr12-72761076-1	chr12	72761026	72761126	+	3.8	cIP2vsInput	promoter-TSS (NM_008910)	promoter-TSS (NM_008910)	-135	NM_008910	19042	Mm.261045	NM_008910	ENSMUSG00000021096	Ppm1a	2310003C21Rik|2900017D14Rik|AI427932|AU017636|MMPa-2|MPPa-1	"protein phosphatase 1A, magnesium dependent, alpha isoform"	protein-coding	0.11	0.752475
Merged-chr4-16660426-1	chr4	16660376	16660476	+	3.8	cIP1vsInput	Intergenic	Intergenic	496316	NR_045765	100415915	Mm.387180	NR_045765	ENSMUSG00000085112	A530072M11Rik	-	RIKEN cDNA gene A530072M11	miscRNA	0	0.326733
Merged-chr16-43889960-1	chr16	43889910	43890010	+	3.8	cIP2vsInput	promoter-TSS (NM_029128)	promoter-TSS (NM_029128)	58	NM_027801	212153	Mm.209835	NM_027801	ENSMUSG00000022701	2610015P09Rik	8430422M09Rik|AU040712	RIKEN cDNA 2610015P09 gene	protein-coding	0.06	0.60396
Merged-chr13-73298992-1	chr13	73298942	73299042	+	3.8	cIP2vsInput	Intergenic	Intergenic	29490	NR_033306	407785	Mm.29897	NM_010888	ENSMUSG00000021606	Ndufs6	BC059730|IP13	NADH dehydrogenase (ubiquinone) Fe-S protein 6	protein-coding	0.01	0.564356
Merged-chr10-24381012-1	chr10	24380962	24381062	+	3.8	cIP2vsInput	Intergenic	RLTR14|LTR|ERV1	157495	NM_021509	59012	Mm.285934	NM_021509	ENSMUSG00000020000	Moxd1	3230402N08Rik|MNCb-5203	"monooxygenase, DBH-like 1"	protein-coding	0.02	0.415842
Merged-chr12-71136996-1	chr12	71136946	71137046	+	3.8	cIP2vsInput	promoter-TSS (NM_013896)	promoter-TSS (NM_013896)	148	NM_001163378	76967	Mm.87290	NM_001163378	ENSMUSG00000034601	2700049A03Rik	Talpid3|mKIAA0586	RIKEN cDNA 2700049A03 gene	protein-coding	0.03	0.346535
Merged-chr2-91444778-1	chr2	91444728	91444828	+	3.8	cIP2vsInput	promoter-TSS (NM_175123)	promoter-TSS (NM_175123)	-136	NM_175123	228356	Mm.386861	NM_175123	ENSMUSG00000040591	1110051M20Rik	AI586322	RIKEN cDNA 1110051M20 gene	protein-coding	0.04	0.455446
Merged-chr16-64771040-2	chr16	64770982	64771099	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026273)	promoter-TSS (NM_026273)	-101	NM_026273	67609	Mm.212157	NM_026273		4930453N24Rik	AI649104	RIKEN cDNA 4930453N24 gene	protein-coding	0.051282	0.584746
Merged-chr18-16740932-1	chr18	16740882	16740982	+	3.8	cIP2vsInput	"intron (NM_007664, intron 2 of 15)"	"intron (NM_007664, intron 2 of 15)"	68117	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-cadherin|Ncad	cadherin 2	protein-coding	0.02	0.465347
Merged-chr13-103773996-2	chr13	103773936	103774057	+	3.8	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-9414	NM_172592	218543	Mm.458176	NM_172592	ENSMUSG00000032621	Srek1	8430401B01|AI450757|AI462342|SRrp508|SRrp86|Sfrs12|Srsf12	splicing regulatory glutamine/lysine-rich protein 1	protein-coding	0.066116	0.54918
Merged-chr10-77622324-1	chr10	77622274	77622374	+	3.8	cIP2vsInput	promoter-TSS (NM_019803)	promoter-TSS (NM_019803)	3	NM_019803	22213	Mm.458125	NM_019803	ENSMUSG00000009293	Ube2g2	1110003O05Rik|D10Xrf369|UBC7|Ubc7p	ubiquitin-conjugating enzyme E2G 2	protein-coding	0.18	0.762376
Merged-chr4-147497530-1	chr4	147497480	147497580	+	3.8	cIP1vsInput	"intron (NM_001039209, intron 1 of 2)"	"intron (NM_001039209, intron 1 of 2)"	-55747	NM_001014397	433804	Mm.332047	XM_003946328	ENSMUSG00000065999	Gm13154	OTTMUSG00000010673	predicted gene 13154	protein-coding	0.02	0.376238
Merged-chr16-17405916-1	chr16	17405866	17405966	+	3.8	cIP2vsInput	promoter-TSS (NM_023348)	promoter-TSS (NM_023348)	-84	NM_023348	67474	Mm.271992	NM_023348	ENSMUSG00000022765	Snap29	1300018G05Rik|AI891940|AU020222|BB131856|Gs32	synaptosomal-associated protein 29	protein-coding	0.07	0.752475
Merged-chr13-23544040-1	chr13	23543990	23544090	+	3.8	cIP2vsInput	promoter-TSS (NM_013548)	promoter-TSS (NM_013548)	-12	NM_013548	260423	Mm.474786	NM_013548	ENSMUSG00000059309	Hist1h3f	H3.2-221|Hist1	"histone cluster 1, H3f"	protein-coding	0.02	0.366337
Merged-chr10-80150785-1	chr10	80150735	80150835	+	3.8	cIP1vsInput	"intron (NM_021565, intron 2 of 8)"	CpG-1261	2495	NM_021565	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding	0.06	0.643564
Merged-chr3-97768327-1	chr3	97768277	97768377	+	3.8	cIP2vsInput	promoter-TSS (NM_178080)	promoter-TSS (NM_178080)	-313	NM_178080	83679	Mm.129840	NM_001039376	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding	0.06	0.633663
Merged-chr19-7494399-1	chr19	7494349	7494449	+	3.8	cIP2vsInput	promoter-TSS (NM_146091)	promoter-TSS (NM_146091)	-39	NM_146091	109168	Mm.264016	NM_001163505	ENSMUSG00000024759	Atl3	4633402C03Rik|5730596K20Rik|AI465397|AW228836	atlastin GTPase 3	protein-coding	0.19	0.742574
Merged-chr14-20294676-2	chr14	20294614	20294739	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026341)	promoter-TSS (NM_026341)	-14	NM_026341	67725	Mm.317636	NM_026341	ENSMUSG00000021809	Nudt13	4933433B15Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 13	protein-coding	0.032	0.460317
Merged-chr6-134659821-1	chr6	134659771	134659871	+	3.8	cIP2vsInput	"intron (NM_026371, intron 2 of 3)"	"intron (NM_026371, intron 2 of 3)"	18881	NM_026371	67774	Mm.41892	NM_001170479	ENSMUSG00000042992	Loh12cr1	5830457J20Rik|AW124643	"loss of heterozygosity, 12, chromosomal region 1 homolog (human)"	protein-coding	0	0.346535
Merged-chr10-42761580-1	chr10	42761530	42761630	+	3.8	cIP2vsInput	promoter-TSS (NM_153055)	promoter-TSS (NM_153055)	84	NM_153055	140740	Mm.214344	NM_153055	ENSMUSG00000019802	Sec63	5730478J10Rik|AI649014|AW319215	SEC63-like (S. cerevisiae)	protein-coding	0.18	0.792079
Merged-chr7-45522052-1	chr7	45522002	45522102	+	3.8	cIP1vsInput	TTS (NM_008654)	TTS (NM_008654)	4216	NM_008654	17872	Mm.4048	NM_008654	ENSMUSG00000040435	Ppp1r15a	9630030H21|Gadd34|Myd116	"protein phosphatase 1, regulatory (inhibitor) subunit 15A"	protein-coding	0.05	0.613861
Merged-chr1-184171085-1	chr1	184171035	184171135	+	3.8	cIP2vsInput	Intergenic	Intergenic	136624	NM_022019	63953	Mm.404024	NM_022019	ENSMUSG00000039384	Dusp10	2610306G15Rik|AI158871|MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0.01	0.613861
Merged-chr11-5522151-1	chr11	5522101	5522201	+	3.8	cIP2vsInput	"intron (NM_001271730, intron 2 of 5)"	"intron (NM_001271730, intron 2 of 5)"	1510	NM_001271730	22433	Mm.469937	NM_001271730	ENSMUSG00000020484	Xbp1	D11Ertd39e|TREB-5|TREB5|XBP-1	X-box binding protein 1	protein-coding	0.03	0.534653
Merged-chr6-147042787-1	chr6	147042737	147042837	+	3.8	cIP2vsInput	promoter-TSS (NM_145573)	promoter-TSS (NM_145573)	17	NM_145573	232536	Mm.46656	NM_145573	ENSMUSG00000040112	Mrps35	MDSO23|MRP-S28|MRPS28	mitochondrial ribosomal protein S35	protein-coding	0.13	0.742574
Merged-chr16-96127653-1	chr16	96127603	96127703	+	3.8	cIP2vsInput	promoter-TSS (NM_008251)	promoter-TSS (NM_008251)	72	NM_008251	15312	Mm.2756	NM_008251		Hmgn1	HMG-14|Hmg14	high mobility group nucleosomal binding domain 1	protein-coding	0.16	0.712871
Merged-chr8-85432803-1	chr8	85432753	85432853	+	3.8	cIP2vsInput	promoter-TSS (NM_025722)	promoter-TSS (NM_025722)	38	NR_033144	66714	Mm.272748	NM_025722	ENSMUSG00000036934	4921524J17Rik	-	RIKEN cDNA 4921524J17 gene	protein-coding	0.17	0.772277
Merged-chr13-3537866-1	chr13	3537816	3537916	+	3.8	cIP2vsInput	promoter-TSS (NM_008112)	promoter-TSS (NM_008112)	-209	NM_008112	14569	Mm.221609	NM_008112		Gdi2	GDI-B|GDIB|Gdi3	guanosine diphosphate (GDP) dissociation inhibitor 2	protein-coding	0.04	0.415842
Merged-chr13-96542676-1	chr13	96542626	96542726	+	3.8	cIP2vsInput	promoter-TSS (NM_012048)	promoter-TSS (NM_012048)	-59	NM_001164222	68018	Mm.24125	NM_001164222	ENSMUSG00000021669	Col4a3bp	2810404O15Rik|9230101K08Rik|AU016711|CERT|GPBP	"collagen, type IV, alpha 3 (Goodpasture antigen) binding protein"	protein-coding	0.1	0.772277
Merged-chr11-102296316-2	chr11	102296260	102296373	+	3.8	cIP1vsInput|cIP2vsInput	"intron (NM_001098837, intron 1 of 12)"	CpG	313	NM_001098836	217218	Mm.390381	NM_001098836	ENSMUSG00000059995	Atxn7l3	E030022H21Rik	ataxin 7-like 3	protein-coding	0.097345	0.815789
Merged-chr7-62420193-1	chr7	62420143	62420243	+	3.8	cIP2vsInput	promoter-TSS (NM_011746)	promoter-TSS (NM_011746)	-54	NM_011746	22652	Mm.146	NM_011746	ENSMUSG00000070527	Mkrn3	D7H15S9-1|Zfp127	"makorin, ring finger protein, 3"	protein-coding	0.05	0.514851
Merged-chr8-46551901-1	chr8	46551851	46551951	+	3.8	cIP2vsInput	promoter-TSS (NM_027973)	promoter-TSS (NM_027973)	-168	NM_027973	71876	Mm.217385	NM_027973	ENSMUSG00000031629	Mlf1ip	1700029A22Rik	myeloid leukemia factor 1 interacting protein	protein-coding	0.07	0.584158
Merged-chr1-172027370-1	chr1	172027320	172027420	+	3.8	cIP1vsInput	promoter-TSS (NM_033509)	promoter-TSS (NM_033509)	-102	NM_033509	93840	Mm.392110	NM_033509	ENSMUSG00000026556	Vangl2	C530001F03Rik|Lp|Lpp1|Ltap|Vang1l2|loop-tail|ska17|ska<m17Jus>|stbm|strabismus	"vang-like 2 (van gogh, Drosophila)"	protein-coding	0.08	0.762376
Merged-chr8-94179094-2	chr8	94179004	94179185	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013602)	promoter-TSS (NM_013602)	5	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding	0.093923	0.664835
Merged-chr1-180387576-1	chr1	180387526	180387626	+	3.8	cIP2vsInput	"intron (NM_001081175, intron 2 of 7)"	"intron (NM_001081175, intron 2 of 7)"	-57027	NR_003623	277333	Mm.490773	NR_003623		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0.06	0.643564
Merged-chr3-130060828-2	chr3	130060763	130060894	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_207209)	promoter-TSS (NM_207209)	79	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	"Sec24 related gene family, member B (S. cerevisiae)"	protein-coding	0.167939	0.810606
Merged-chr17-24479053-1	chr17	24479003	24479103	+	3.8	cIP2vsInput	promoter-TSS (NM_001252464)	promoter-TSS (NM_001252464)	25	NM_001252464	56716	Mm.289516	NM_001252463	ENSMUSG00000024142	Mlst8	0610033N12Rik|AA409454|AI505104|AI851821|Gbl	"MTOR associated protein, LST8 homolog (S. cerevisiae)"	protein-coding	0.1	0.613861
Merged-chr11-9011179-2	chr11	9011126	9011232	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008316)	promoter-TSS (NM_008316)	-42	NM_008316	15574	Mm.42201	NM_008316	ENSMUSG00000020413	Hus1	mHus1	Hus1 homolog (S. pombe)	protein-coding	0.113208	0.71028
Merged-chr17-47695075-1	chr17	47695025	47695125	+	3.8	cIP2vsInput	promoter-TSS (NM_144939)	promoter-TSS (NM_144939)	-132	NM_144939	107971	Mm.392206	NM_144939	ENSMUSG00000023266	Frs3	4930417B13Rik|AI449674|Frs2beta|Snt2	fibroblast growth factor receptor substrate 3	protein-coding	0.1	0.683168
Merged-chr19-53390498-1	chr19	53390448	53390548	+	3.8	cIP2vsInput	promoter-TSS (NM_172429)	promoter-TSS (NM_172429)	75	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding	0.15	0.70297
Merged-chr11-101171605-1	chr11	101171555	101171655	+	3.8	cIP2vsInput	promoter-TSS (NM_146030)	promoter-TSS (NM_146030)	-303	NM_146030	217198	Mm.273254	NM_146030	ENSMUSG00000035172	Plekhh3	BC020025	"pleckstrin homology domain containing, family H (with MyTH4 domain) member 3"	protein-coding	0.07	0.643564
Merged-chr14-50785520-1	chr14	50785470	50785570	+	3.8	cIP2vsInput	promoter-TSS (NM_177625)	promoter-TSS (NM_177625)	-2	NM_001080949	219022	Mm.276362	NM_001080949	ENSMUSG00000006288	Ttc5	5930437N14|AW743060	tetratricopeptide repeat domain 5	protein-coding	0.04	0.584158
Merged-chr2-164832884-1	chr2	164832834	164832934	+	3.8	cIP2vsInput	promoter-TSS (NM_008906)	promoter-TSS (NM_008906)	12	NM_001038492	19025	Mm.474586	NM_001038492	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding	0.08	0.60396
Merged-chr5-15054751-1	chr5	15054701	15054801	+	3.8	cIP1vsInput	Intergenic	T-rich|Low_complexity|Low_complexity	-21744	NM_182957	66773	Mm.368256	NM_182957	ENSMUSG00000091897	Gm17019	-	predicted gene 17019	protein-coding	0	0.306931
Merged-chrY-6392894-1	chrY	6392844	6392944	+	3.8	cIP1vsInput	Intergenic	MMERGLN-int|LTR|ERV1	774883	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.514851
Merged-chr7-45717953-1	chr7	45717903	45718003	+	3.8	cIP2vsInput	promoter-TSS (NM_203280)	promoter-TSS (NM_203280)	49	NM_203280	56632	Mm.24222	NM_001172561	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding	0.09	0.554455
Merged-chr2-60963234-1	chr2	60963184	60963284	+	3.8	cIP2vsInput	promoter-TSS (NM_020296)	promoter-TSS (NM_020296)	-30	NM_020296	56878	Mm.482338	NM_001141931	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	"RNA binding motif, single stranded interacting protein 1"	protein-coding	0.11	0.792079
Merged-chr6-142778472-1	chr6	142778422	142778522	+	3.8	cIP1vsInput	Intergenic	Intergenic	21786	NM_009908	12764	Mm.3820	NM_009908	ENSMUSG00000030282	Cmas	AW208911|CMPNeu5Ac|D6Bwg0250e	cytidine monophospho-N-acetylneuraminic acid synthetase	protein-coding	0	0.346535
Merged-chr3-97227569-1	chr3	97227519	97227619	+	3.8	cIP2vsInput	promoter-TSS (NM_029933)	promoter-TSS (NM_029933)	-205	NM_029933	77578	Mm.482931	NM_029933	ENSMUSG00000038256	Bcl9	2610202E01Rik|8030475K17Rik|A330041G23Rik|Gm130	B cell CLL/lymphoma 9	protein-coding	0.12	0.861386
Merged-chr10-69644079-2	chr10	69644020	69644138	+	3.8	cIP1vsInput|cIP2vsInput	"intron (NM_170730, intron 1 of 17)"	"intron (NM_170730, intron 1 of 17)"	110371	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	"ankyrin 3, epithelial"	protein-coding	0.016949	0.453782
Merged-chr11-104550310-1	chr11	104550260	104550360	+	3.8	cIP2vsInput	promoter-TSS (NM_010858)	promoter-TSS (NM_010858)	310	NM_145436	217232	Mm.89845	NM_145436	ENSMUSG00000020687	Cdc27	AI452358|APC3|BC023187	cell division cycle 27	protein-coding	0.1	0.70297
Merged-chr5-104022259-1	chr5	104022209	104022309	+	3.8	cIP2vsInput	promoter-TSS (NM_053262)	promoter-TSS (NM_053262)	-463	NM_053262	114664	Mm.46019	NM_053262	ENSMUSG00000029311	Hsd17b11	Dhrs8|Pan1b|SDR2|retSDR2	hydroxysteroid (17-beta) dehydrogenase 11	protein-coding	0.02	0.554455
Merged-chr18-12862016-1	chr18	12861966	12862066	+	3.8	cIP2vsInput	"intron (NM_001252489, intron 2 of 14)"	"intron (NM_001252489, intron 2 of 14)"	697	NM_001252493	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding	0.03	0.623762
Merged-chr12-69159760-1	chr12	69159710	69159810	+	3.8	cIP2vsInput	promoter-TSS (NM_009093)	promoter-TSS (NM_009093)	-574	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding	0.03	0.346535
Merged-chr5-114100302-1	chr5	114100252	114100352	+	3.8	cIP2vsInput	promoter-TSS (NM_001033202)	promoter-TSS (NM_001033202)	-31	NM_001033202	100756	Mm.240421	NM_001033202	ENSMUSG00000029592	Usp30	6330590F17Rik|AI851327|D5Ertd483e	ubiquitin specific peptidase 30	protein-coding	0.1	0.673267
Merged-chr5-18360518-2	chr5	18360465	18360571	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010305)	promoter-TSS (NM_010305)	-105	NM_010305	14677	Mm.254629	NM_010305	ENSMUSG00000057614	Gnai1	AU046200|Gialpha1|Gnai-1	"guanine nucleotide binding protein (G protein), alpha inhibiting 1"	protein-coding	0.226415	0.859813
Merged-chr10-76586351-1	chr10	76586301	76586401	+	3.8	cIP2vsInput	"intron (NM_080845, intron 10 of 13)"	"intron (NM_080845, intron 10 of 13)"	10703	NM_080845	14317	Mm.36278	NM_080845		Ftcd	-	formiminotransferase cyclodeaminase	protein-coding	0.01	0.544554
Merged-chr11-23255753-2	chr11	23255693	23255814	+	3.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_134014)	promoter-TSS (NM_134014)	-288	NM_001035226	103573	Mm.217547	NM_001035226	ENSMUSG00000020290	Xpo1	AA420417|Crm1|Exp1	"exportin 1, CRM1 homolog (yeast)"	protein-coding	0.066116	0.672131
Merged-chr18-19727755-1	chr18	19727705	19727805	+	3.8	cIP2vsInput	Intergenic	(CATTC)n|Simple_repeat|Simple_repeat	274342	NM_007882	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding	0	0.50495
Merged-chr13-54694013-1	chr13	54693963	54694063	+	3.8	cIP2vsInput	promoter-TSS (NR_027395)	promoter-TSS (NR_027395)	-53	NR_027396	105239	Mm.25366	NM_001146025	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding	0.13	0.732673
Merged-chr13-48968530-1	chr13	48968480	48968580	+	3.8	cIP2vsInput	promoter-TSS (NM_001033268)	promoter-TSS (NM_001033268)	418	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A opposite strand	miscRNA	0.13	0.772277
Merged-chr1-86487854-2	chr1	86487796	86487912	+	3.8	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-38882	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding	0.12069	0.632479
Merged-chr17-25792481-1	chr17	25792431	25792531	+	3.8	cIP2vsInput	promoter-TSS (NM_145410)	promoter-TSS (NM_145410)	-197	NM_145410	214917	Mm.26783	NM_145410	ENSMUSG00000057411	Fam173a	-	"family with sequence similarity 173, member A"	protein-coding	0.07	0.633663
Merged-chr4-21848006-1	chr4	21847956	21848056	+	3.8	cIP2vsInput	"non-coding (NR_028384, exon 1 of 1)"	"non-coding (NR_028384, exon 1 of 1)"	423	NM_025669	66625	Mm.100117	NM_025669	ENSMUSG00000028248	Sfrs18	5730406M06Rik|AA673174|Pnisr|Srsf18	serine/arginine-rich splicing factor 18	protein-coding	0.06	0.514851
Merged-chr8-119446623-1	chr8	119446573	119446673	+	3.8	cIP2vsInput	promoter-TSS (NM_054095)	promoter-TSS (NM_054095)	-96	NM_054095	117148	Mm.356184	NM_054095	ENSMUSG00000031837	Necab2	Efcbp2	N-terminal EF-hand calcium binding protein 2	protein-coding	0.08	0.673267
Merged-chr1-89580168-2	chr1	89580097	89580240	+	3.75	cIP1vsInput|cIP2vsInput	"intron (NM_001037136, intron 1 of 16)"	GC_rich|Low_complexity|Low_complexity	103724	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	miscRNA	0.181818	0.847222
Merged-chr13-91877550-2	chr13	91877499	91877602	+	3.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_198415)	promoter-TSS (NM_198415)	-665	NM_198415	76722	Mm.316438	NM_198415	ENSMUSG00000021622	Ckmt2	2300008A19Rik|ScCKmit	"creatine kinase, mitochondrial 2"	protein-coding	0.009709	0.509615
Merged-chr3-90446702-2	chr3	90446613	90446792	+	3.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-13066	NM_178876	229543	Mm.268564	NM_145540	ENSMUSG00000027933	Ints3	C77668	integrator complex subunit 3	protein-coding	0.027933	0.644444
Merged-chr2-156196702-2	chr2	156196651	156196753	+	3.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172674)	promoter-TSS (NM_172674)	55	NM_172674	228829	Mm.427078	NM_172674	ENSMUSG00000038116	Phf20	6820402O20Rik	PHD finger protein 20	protein-coding	0.127451	0.718447
Merged-chr14-77932385-2	chr14	77932322	77932448	+	3.75	cIP1vsInput|cIP2vsInput	"intron (NM_178825, intron 5 of 6)"	MIR|SINE|MIR	28146	NM_029495	108670	Mm.68134	NM_029495	ENSMUSG00000022014	Epsti1	2310046K10Rik|5033415K03Rik|BRESI1	epithelial stromal interaction 1 (breast)	protein-coding	0.02381	0.472441
Merged-chr4-98563723-2	chr4	98563663	98563783	+	3.75	cIP1vsInput|cIP2vsInput	"intron (NM_001005787, intron 1 of 15)"	"intron (NM_001005787, intron 1 of 15)"	17089	NM_001005787	12695	Mm.90218	NM_001005784	ENSMUSG00000061859	Inadl	Cipp|Patj	InaD-like (Drosophila)	protein-coding	0.016667	0.512397
Merged-chrY-90727405-2	chrY	90727352	90727458	+	3.75	cIP1vsInput|cIP2vsInput	Intergenic	L1MC|LINE|L1	-58037	NM_133362	170942	Mm.391385	XM_003946384	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding	0	0.158879
Merged-chr2-151702443-2	chr2	151702384	151702503	+	3.75	cIP1vsInput|cIP2vsInput	"5' UTR (NM_001160363, exon 1 of 2)"	"5' UTR (NM_001160363, exon 1 of 2)"	435	NM_001160363	108832	Mm.103494	NM_001160363	ENSMUSG00000044364	Tmem74b	5430405G05Rik	transmembrane protein 74b	protein-coding	0.159664	0.808333
Merged-chr16-42910224-2	chr16	42910164	42910284	+	3.75	cIP1vsInput|cIP2vsInput	"intron (NR_040402, intron 1 of 3)"	"intron (NR_040402, intron 1 of 3)"	1846	NR_040402	100503040	Mm.490721	NR_040402		Gm19522	-	"predicted gene, 19522"	miscRNA	0.008333	0.413223
Merged-chr15-99120439-2	chr15	99120367	99120511	+	3.75	cIP1vsInput|cIP2vsInput	Intergenic	RMER17D2|LTR|ERVK	-6406	NM_139140	72572	Mm.276650	NM_139140		Spats2	2700012F11Rik|59kDa|Scr59|p59	"spermatogenesis associated, serine-rich 2"	protein-coding	0.013889	0.565517
Merged-chr2-130424276-2	chr2	130424223	130424330	+	3.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178762)	promoter-TSS (NM_178762)	12	NM_178762	319513	Mm.482539	NM_001114541	ENSMUSG00000037773	Pced1a	A930025D01Rik|AI480484|Fam113a	PC-esterase domain containing 1A	protein-coding	0.130841	0.685185
Merged-chrY-6837664-2	chrY	6837613	6837715	+	3.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	330113	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.262136
Merged-chr5-115301150-2	chr5	115301100	115301200	+	3.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019682)	promoter-TSS (NM_019682)	-160	NM_019682	56455	Mm.256858	NM_019682	ENSMUSG00000009013	Dynll1	Dlc8|Dnclc1|Pin	dynein light chain LC8-type 1	protein-coding	0.14	0.732673
Merged-chr10-42478478-2	chr10	42478386	42478570	+	3.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145743)	promoter-TSS (NM_145743)	87	NM_145743	215951	Mm.89646	NM_145743	ENSMUSG00000038302	Lace1	CG8520	lactation elevated 1	protein-coding	0.065217	0.578378
Merged-chr7-29238435-2	chr7	29238381	29238490	+	3.75	cIP1vsInput|cIP2vsInput	"exon (NM_029887, exon 1 of 8)"	"exon (NM_029887, exon 1 of 8)"	112	NM_029887	77254	Mm.36699	NM_001110201	ENSMUSG00000030588	Yif1b	9430029K10Rik|Yip1b	Yip1 interacting factor homolog B (S. cerevisiae)	protein-coding	0.137615	0.709091
Merged-chr1-18961598-2	chr1	18961547	18961649	+	3.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-141424	NM_153154	226896	Mm.244858	NM_153154	ENSMUSG00000042596	Tfap2d	Tcfap2d	"transcription factor AP-2, delta"	protein-coding	0.029412	0.582524
Merged-chr8-4677668-2	chr8	4677589	4677747	+	3.75	cIP1vsInput|cIP2vsInput	Intergenic	CpG	64498	NM_145591	233987	Mm.102799	NM_145591		Zfp958	-	zinc finger protein 958	protein-coding	0.113924	0.691824
Merged-chr9-45055106-2	chr9	45055028	45055185	+	3.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_176993)	promoter-TSS (NM_176993)	-82	NM_176993	319742	Mm.49611	NM_001093749	ENSMUSG00000070305	Mpzl3	5430427F17Rik|A530065I17Rik|rc	myelin protein zero-like 3	protein-coding	0.057325	0.531646
Merged-chr7-44892563-2	chr7	44892496	44892631	+	3.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029365)	promoter-TSS (NM_029365)	-197	NM_029365	75613	Mm.157778	NM_029365	ENSMUSG00000002968	Med25	2610034E13Rik|2610529E18Rik|ESTM2|X83308	"mediator of RNA polymerase II transcription, subunit 25 homolog (yeast)"	protein-coding	0.051852	0.507353
Merged-chr4-134000920-2	chr4	134000844	134000996	+	3.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026144)	promoter-TSS (NM_026144)	-56	NM_026144	67422	Mm.100290	NM_026144	ENSMUSG00000012117	Dhdds	3222401G21Rik|CIT|DS|HDS|W91638	dehydrodolichyl diphosphate synthase	protein-coding	0.111842	0.660131
Merged-chr6-34852470-2	chr6	34852391	34852550	+	3.75	cIP1vsInput|cIP2vsInput	"intron (NM_178630, intron 18 of 18)"	"intron (NM_178630, intron 18 of 18)"	-10676	NM_197986	68487	Mm.332986	NM_197986	ENSMUSG00000057137	Tmem140	1110007F12Rik	transmembrane protein 140	protein-coding	0	0.3375
Merged-chr11-119079032-2	chr11	119078977	119079087	+	3.75	cIP1vsInput|cIP2vsInput	"3' UTR (NM_007625, exon 5 of 5)"	"3' UTR (NM_007625, exon 5 of 5)"	7205	NM_007625	12418	Mm.471550	NM_007625	ENSMUSG00000039989	Cbx4	MPc2|PC2	chromobox 4	protein-coding	0.054545	0.657658
Merged-chr5-110176830-2	chr5	110176776	110176885	+	3.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_040431)	promoter-TSS (NR_040431)	129	NM_008146	269682	Mm.393008	NM_008146	ENSMUSG00000029502	Golga3	5330413L04|5430416E01Rik|AI449376|AW490576|Mea-2|Mea2	"golgi autoantigen, golgin subfamily a, 3"	protein-coding	0.091743	0.663636
Merged-chr11-120932919-2	chr11	120932868	120932971	+	3.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027745)	promoter-TSS (NM_027745)	-47	NM_027745	71276	Mm.275751	NM_027745	ENSMUSG00000048445	Ccdc57	4933434G05Rik	coiled-coil domain containing 57	protein-coding	0.087379	0.615385
Merged-chr6-84583553-2	chr6	84583503	84583603	+	3.75	cIP1vsInput|cIP2vsInput	"intron (NM_001177713, intron 3 of 6)"	"intron (NM_001177713, intron 3 of 6)"	10257	NM_175475	232174	Mm.255246	NM_001177713	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	"cytochrome P450, family 26, subfamily b, polypeptide 1"	protein-coding	0.13	0.752475
Merged-chr3-88177771-2	chr3	88177715	88177827	+	3.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_045997)	promoter-TSS (NR_045997)	14	NR_045997	76642	Mm.424420	NR_045997	ENSMUSG00000096935	1700113A16Rik	2210408E11Rik|AA408983	RIKEN cDNA 1700113A16 gene	miscRNA	0.116071	0.690265
Merged-chr8-121829594-2	chr8	121829543	121829645	+	3.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145605)	promoter-TSS (NM_145605)	-25	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding	0.098039	0.631068
Merged-chr8-121585636-2	chr8	121585581	121585691	+	3.75	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-4832	NM_026160	67443	Mm.28357	NM_026160		Map1lc3b	1010001C15Rik|Atg8|LC3b|Map1lc3	microtubule-associated protein 1 light chain 3 beta	protein-coding	0.090909	0.666667
Merged-chr4-134612587-2	chr4	134612530	134612645	+	3.75	cIP1vsInput|cIP2vsInput	"intron (NM_207237, intron 2 of 11)"	L1M4|LINE|L1	-60421	NM_029100	74777	Mm.29773	NM_029100	ENSMUSG00000050989	Sepn1	1110019I12Rik|AI414492	"selenoprotein N, 1"	protein-coding	0.034783	0.5
Merged-chr17-66111626-2	chr17	66111559	66111693	+	3.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026833)	promoter-TSS (NM_026833)	-19	NM_001037757	68767	Mm.296545	NM_001037757	ENSMUSG00000024101	Wash	1110049F14Rik|ORF19|Wash1	WAS protein family homolog	protein-coding	0.097015	0.711111
Merged-chr18-37954998-2	chr18	37954947	37955049	+	3.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010411)	promoter-TSS (NM_010411)	-10	NM_010411	15183	Mm.20521	NM_010411	ENSMUSG00000024454	Hdac3	AW537363	histone deacetylase 3	protein-coding	0.127451	0.747573
Merged-chr13-100731021-2	chr13	100730967	100731075	+	3.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009874)	promoter-TSS (NM_009874)	-79	NM_009874	12572	Mm.259718	NM_009874	ENSMUSG00000069089	Cdk7	AI323415|AI528512|C230069N13|Cdkn7|Crk4	cyclin-dependent kinase 7	protein-coding	0.074074	0.66055
Merged-chr11-116274120-1	chr11	116274070	116274170	+	3.7	cIP2vsInput	promoter-TSS (NM_146032)	promoter-TSS (NM_146032)	97	NM_146032	217337	Mm.29655	NM_146032	ENSMUSG00000020780	Srp68	2610024I03Rik	signal recognition particle 68	protein-coding	0.08	0.633663
Merged-chr1-72255238-1	chr1	72255188	72255288	+	3.7	cIP2vsInput	Intergenic	Intergenic	29076	NM_023523	111175	Mm.281738	NM_023523	ENSMUSG00000026189	Pecr	2400003B18Rik|TERP	peroxisomal trans-2-enoyl-CoA reductase	protein-coding	0.01	0.445545
Merged-chr8-85071596-1	chr8	85071546	85071646	+	3.7	cIP2vsInput	promoter-TSS (NM_001039514)	promoter-TSS (NM_001039514)	-161	NM_001039514	330817	Mm.456030	NM_201408	ENSMUSG00000060038	Dhps	Dhs	deoxyhypusine synthase	protein-coding	0.01	0.485149
Merged-chr11-64073607-2	chr11	64073548	64073666	+	3.7	cIP1vsInput|cIP2vsInput	"exon (NM_178379, exon 2 of 7)"	"exon (NM_178379, exon 2 of 7)"	5865	NM_178379	70383	Mm.340211	NM_178379	ENSMUSG00000042148	Cox10	2410004F01Rik|AU042636	cytochrome c oxidase assembly protein 10	protein-coding	0.016949	0.487395
Merged-chr7-63897058-1	chr7	63897008	63897108	+	3.7	cIP2vsInput	"intron (NM_021366, intron 1 of 1)"	CpG	-19799	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding	0.05	0.574257
Merged-chr16-21846484-1	chr16	21846434	21846534	+	3.7	cIP2vsInput	Intergenic	Intergenic	-45485	NM_172821	71751	Mm.438136	NM_172821	ENSMUSG00000033618	Map3k13	C130026N12Rik|LZK	mitogen-activated protein kinase kinase kinase 13	protein-coding	0.03	0.475248
Merged-chr11-29515032-1	chr11	29514982	29515082	+	3.7	cIP2vsInput	promoter-TSS (NM_026465)	promoter-TSS (NM_026465)	1	NM_026465	67939	Mm.251087	NM_001163454	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding	0.07	0.663366
Merged-chr12-100187760-1	chr12	100187710	100187810	+	3.7	cIP2vsInput	promoter-TSS (NR_045282)	promoter-TSS (NR_045282)	-208	NR_045282	100038378	Mm.387075	NR_045282	ENSMUSG00000072884	Gm10433	ENSMUSG00000072884	predicted gene 10433	miscRNA	0.14	0.722772
Merged-chr13-25020452-1	chr13	25020402	25020502	+	3.7	cIP2vsInput	promoter-TSS (NM_001013389)	promoter-TSS (NM_001013389)	-73	NM_001013389	380836	Mm.387097	NM_001013389	ENSMUSG00000021339	Mrs2	Gm902|HPT|Mrs2l|RPT	MRS2 magnesium homeostasis factor homolog (S. cerevisiae)	protein-coding	0.07	0.564356
Merged-chrY-29619087-1	chrY	29619037	29619137	+	3.7	cIP1vsInput	Intergenic	Intergenic	-878642	NR_038299	100041346	Mm.490246	NR_038299		Gm20871	-	Sycp3 like Y-linked pseudogene	pseudo	0.02	0.425743
Merged-chr11-77078435-2	chr11	77078352	77078519	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_030756)	promoter-TSS (NR_030756)	2	NM_001012309	237859	Mm.156195	NM_001012309	ENSMUSG00000037958	Ccdc55	8030451K07|AI851076|AL022898|NSpr70|NSrp70|Nsrp1	coiled-coil domain containing 55	protein-coding	0.125749	0.636905
Merged-chr16-38562752-1	chr16	38562702	38562802	+	3.7	cIP2vsInput	promoter-TSS (NM_026407)	promoter-TSS (NM_026407)	-62	NM_026407	67846	Mm.489630	NM_001205286	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding	0.11	0.742574
Merged-chr11-3963740-1	chr11	3963690	3963790	+	3.7	cIP2vsInput	promoter-TSS (NM_022889)	promoter-TSS (NM_022889)	-235	NM_022889	64934	Mm.28659	NM_022889	ENSMUSG00000020430	Pes1	-	"pescadillo homolog 1, containing BRCT domain (zebrafish)"	protein-coding	0.03	0.475248
Merged-chr13-102599787-1	chr13	102599737	102599837	+	3.7	cIP2vsInput	Intergenic	Intergenic	-93771	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding	0	0.445545
Merged-chr19-6276630-1	chr19	6276580	6276680	+	3.7	cIP1vsInput	promoter-TSS (NM_010119)	promoter-TSS (NM_010119)	-266	NM_010119	13660	Mm.30169	NM_010119	ENSMUSG00000024772	Ehd1	AA409636|Past1|RME-1	EH-domain containing 1	protein-coding	0.09	0.613861
Merged-chr12-69893116-1	chr12	69893066	69893166	+	3.7	cIP2vsInput	promoter-TSS (NM_201519)	promoter-TSS (NM_201519)	11	NM_178628	73991	Mm.474462	NM_178628	ENSMUSG00000021066	Atl1	4930435M24Rik|Adfsp|Fsp1|Spg3|Spg3a	atlastin GTPase 1	protein-coding	0.16	0.772277
Merged-chr16-17201534-1	chr16	17201484	17201584	+	3.7	cIP2vsInput	promoter-TSS (NM_009456)	promoter-TSS (NM_009456)	-42	NM_009456	22195	Mm.3074	NM_009456	ENSMUSG00000038965	Ube2l3	C79827|UbcM4|Ubce7	ubiquitin-conjugating enzyme E2L 3	protein-coding	0.07	0.613861
Merged-chr18-11239836-1	chr18	11239786	11239886	+	3.7	cIP2vsInput	Intergenic	CpG	187326	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding	0.08	0.742574
Merged-chr4-155803531-2	chr4	155803479	155803583	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025570)	promoter-TSS (NM_025570)	-87	NM_025570	66448	Mm.23825	NM_025570	ENSMUSG00000029066	Mrpl20	2610008D01Rik|4930425I20Rik	mitochondrial ribosomal protein L20	protein-coding	0.086538	0.6
Merged-chr4-34687375-2	chr4	34687303	34687448	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011895)	promoter-TSS (NM_011895)	63	NM_011895	24060	Mm.281885	NM_011895	ENSMUSG00000028293	Slc35a1	AA408150|AI314851	"solute carrier family 35 (CMP-sialic acid transporter), member 1"	protein-coding	0.158621	0.719178
Merged-chr8-33978645-1	chr8	33978595	33978695	+	3.7	cIP2vsInput	Intergenic	Intergenic	-48804	NM_001042675	19663	Mm.323997	NM_001042674	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|hermes	RNA binding protein gene with multiple splicing	protein-coding	0.03	0.514851
Merged-chr7-122101569-1	chr7	122101519	122101619	+	3.7	cIP2vsInput	"intron (NM_028177, intron 1 of 4)"	"intron (NM_028177, intron 1 of 4)"	279	NM_028177	70316	Mm.347976	NM_028177		Ndufab1	2210401F17Rik|2310039H15Rik|2610003B19Rik|8kDa|9130423F15Rik|ACP|CI-SDAP|SDAP	"NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1"	protein-coding	0.05	0.683168
Merged-chr16-18187678-1	chr16	18187628	18187728	+	3.7	cIP2vsInput	Intergenic	Intergenic	25855	NR_027843	66779	Mm.387525	NR_015575		4933432I09Rik	-	RIKEN cDNA 4933432I09 gene	miscRNA	0	0.445545
Merged-chr6-57825073-1	chr6	57825023	57825123	+	3.7	cIP2vsInput	promoter-TSS (NM_146168)	promoter-TSS (NM_146168)	52	NM_146168	232023	Mm.24642	NM_146168	ENSMUSG00000037788	Vopp1	AW146242|Ecop	"vesicular, overexpressed in cancer, prosurvival protein 1"	protein-coding	0.14	0.732673
Merged-chr10-122544478-2	chr10	122544399	122544558	+	3.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	25413	NR_040616	319272	Mm.411763	NR_040616		A130077B15Rik	-	RIKEN cDNA A130077B15 gene	miscRNA	0.031447	0.44375
Merged-chr11-70540038-2	chr11	70539977	70540100	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008876)	promoter-TSS (NM_008876)	-126	NM_008876	18806	Mm.260177	NM_008876	ENSMUSG00000020828	Pld2	-	phospholipase D2	protein-coding	0.097561	0.669355
Merged-chr4-155601431-1	chr4	155601381	155601481	+	3.7	cIP2vsInput	promoter-TSS (NM_177186)	promoter-TSS (NM_177186)	15	NM_177186	320541	Mm.489769	NM_177186	ENSMUSG00000042202	Slc35e2	A530082C11Rik|AI957035	"solute carrier family 35, member E2"	protein-coding	0.09	0.594059
Merged-chr8-120488121-1	chr8	120488071	120488171	+	3.7	cIP2vsInput	promoter-TSS (NM_198671)	promoter-TSS (NM_198671)	-745	NM_198671	382034	Mm.334856	NM_001145896	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1	protein-coding	0.04	0.683168
Merged-chr11-103697842-1	chr11	103697792	103697892	+	3.7	cIP2vsInput	promoter-TSS (NM_019650)	promoter-TSS (NM_019650)	118	NR_102396	399609	Mm.462430	XR_106356		C130046K22Rik	-	RIKEN cDNA C130046K22 gene	miscRNA	0.12	0.673267
Merged-chr7-143154531-2	chr7	143154480	143154582	+	3.7	cIP1vsInput|cIP2vsInput	"intron (NM_008434, intron 2 of 15)"	"intron (NM_008434, intron 2 of 15)"	47277	NM_008434	16535	Mm.453037	NM_008434	ENSMUSG00000009545	Kcnq1	AW559127|KVLQT1|Kcna9	"potassium voltage-gated channel, subfamily Q, member 1"	protein-coding	0.068627	0.563107
Merged-chr9-122866034-1	chr9	122865984	122866084	+	3.7	cIP2vsInput	promoter-TSS (NM_173364)	promoter-TSS (NM_173364)	-28	NM_173364	235682	Mm.326477	NM_173364		Zfp445	AW610627|ZNF168|Znf445|mszf29|mszf50	zinc finger protein 445	protein-coding	0.06	0.594059
Merged-chr11-78189508-1	chr11	78189458	78189558	+	3.7	cIP2vsInput	"intron (NM_033475, intron 1 of 9)"	"intron (NM_033475, intron 1 of 9)"	760	NM_033475	19376	Mm.275864	NM_001159482	ENSMUSG00000002059	Rab34	AI326479|Narr|Rah|Rah1	"RAB34, member of RAS oncogene family"	protein-coding	0.04	0.663366
Merged-chr13-89730127-1	chr13	89730077	89730177	+	3.7	cIP2vsInput	"intron (NM_001134475, intron 2 of 12)"	"intron (NM_001134475, intron 2 of 12)"	12385	NM_001081249	13003	Mm.410783	NM_001081249	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding	0.01	0.386139
Merged-chrX-152232956-1	chrX	152232906	152233006	+	3.7	cIP1vsInput	promoter-TSS (NM_013668)	promoter-TSS (NM_013668)	-274	NM_013668	20591	Mm.142655	NM_013668	ENSMUSG00000025332	Kdm5c	Jarid1c|Smcx|mKIAA0234	lysine (K)-specific demethylase 5C	protein-coding	0.08	0.554455
Merged-chr15-58141214-2	chr15	58141164	58141265	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029734)	promoter-TSS (NM_029734)	-222	NM_029734	76773	Mm.26771	NM_029734	ENSMUSG00000022359	Wdyhv1	2410187C16Rik|AU014961|AW550036|Ntaq1	WDYHV motif containing 1	protein-coding	0.029703	0.598039
Merged-chr5-135078355-2	chr5	135078266	135078445	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001199677)	promoter-TSS (NM_001199677)	-89	NM_001199677	194309	Mm.44356	NM_001199677	ENSMUSG00000043614	Vps37d	Wbscr24	vacuolar protein sorting 37D (yeast)	protein-coding	0.122905	0.772222
Merged-chrY-6840707-1	chrY	6840657	6840757	+	3.7	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	327070	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.475248
Merged-chr1-136415497-1	chr1	136415447	136415547	+	3.7	cIP2vsInput	promoter-TSS (NR_024328)	promoter-TSS (NR_024328)	22	NR_024328	320054	Mm.208000	NR_024328	ENSMUSG00000097403	9230116N13Rik	-	RIKEN cDNA 9230116N13 gene	miscRNA	0.15	0.742574
Merged-chr17-6477376-1	chr17	6477326	6477426	+	3.7	cIP1vsInput	Intergenic	Intergenic	-26382	NR_033520	547127	Mm.381893	NR_033520		Tmem181b-ps	Tmem181b	"transmembrane protein 181B, pseudogene"	pseudo	0.03	0.465347
Merged-chr19-45006497-2	chr19	45006421	45006574	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_153796)	promoter-TSS (NM_153796)	-55	NM_053164	94067	Mm.44174	NM_053164	ENSMUSG00000025208	Mrpl43	4930442D21Rik|bMRP36a	mitochondrial ribosomal protein L43	protein-coding	0.117647	0.655844
Merged-chr3-90248145-1	chr3	90248095	90248195	+	3.7	cIP2vsInput	promoter-TSS (NM_013901)	promoter-TSS (NM_013901)	-47	NM_013901	30791	Mm.294709	NM_013901	ENSMUSG00000052310	Slc39a1	Zip1|Zirtl	"solute carrier family 39 (zinc transporter), member 1"	protein-coding	0.08	0.70297
Merged-chr11-69991057-2	chr11	69990997	69991118	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019749)	promoter-TSS (NM_019749)	-313	NM_019749	56486	Mm.272460	NM_019749	ENSMUSG00000018567	Gabarap	-	gamma-aminobutyric acid receptor associated protein	protein-coding	0.049587	0.5
Merged-chr5-15551488-1	chr5	15551438	15551538	+	3.7	cIP1vsInput	Intergenic	Intergenic	-67611	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0	0.346535
Merged-chr15-100228174-1	chr15	100228124	100228224	+	3.7	cIP2vsInput	"intron (NM_007497, intron 1 of 6)"	CpG	315	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding	0.2	0.881188
Merged-chr7-81762854-2	chr7	81762783	81762926	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025997)	promoter-TSS (NM_025997)	-99	NM_025997	67148	Mm.241472	NM_025997	ENSMUSG00000038646	Fam103a1	2410047I02Rik|2610204K14Rik|RAM	"family with sequence similarity 103, member A1"	protein-coding	0.090909	0.638889
Merged-chr2-135468097-1	chr2	135468047	135468147	+	3.7	cIP2vsInput	"intron (NM_019677, intron 32 of 32)"	"intron (NM_019677, intron 32 of 32)"	62267	NR_039540	100628568		NR_039540	ENSMUSG00000092830	Mir3963	mmu-mir-3963|mu-mir-3963	microRNA 3963	miscRNA	0.03	0.574257
Merged-chr8-45975320-2	chr8	45975259	45975381	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001033148)	promoter-TSS (NM_001033148)	-68	NM_001033148	69479	Mm.158282	NM_001033148	ENSMUSG00000071103	1700029J07Rik	-	RIKEN cDNA 1700029J07 gene	protein-coding	0.122951	0.585366
Merged-chr7-45715410-2	chr7	45715336	45715485	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_020011)	promoter-TSS (NM_020011)	-203	NM_020011	56632	Mm.24222	NM_001172561	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding	0.067114	0.566667
Merged-chr4-43442387-1	chr4	43442337	43442437	+	3.7	cIP2vsInput	"5' UTR (NM_011571, exon 1 of 10)"	"5' UTR (NM_011571, exon 1 of 10)"	110	NM_011571	21754	Mm.485441	NM_011571	ENSMUSG00000028458	Tesk1	AI326901	testis specific protein kinase 1	protein-coding	0.08	0.683168
Merged-chr4-136247934-2	chr4	136247880	136247988	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011542)	promoter-TSS (NM_011542)	-23	NM_011542	21401	Mm.112	NM_011542	ENSMUSG00000001604	Tcea3	S-II|SII-K1	"transcription elongation factor A (SII), 3"	protein-coding	0.092593	0.688073
Merged-chr19-42129257-1	chr19	42129207	42129307	+	3.7	cIP2vsInput	promoter-TSS (NM_027106)	promoter-TSS (NM_027106)	-264	NM_027106	69534	Mm.30060	NM_027106	ENSMUSG00000018821	Avpi1	2310008N12Rik|AA410041|VIT32|esu|mVIT32	arginine vasopressin-induced 1	protein-coding	0.09	0.722772
Merged-chr4-138217005-1	chr4	138216955	138217055	+	3.7	cIP2vsInput	promoter-TSS (NM_001122897)	promoter-TSS (NM_001122897)	-126	NM_001122897	15441	Mm.399941	NM_001122896	ENSMUSG00000028759	Hp1bp3	Hp1bp74	"heterochromatin protein 1, binding protein 3"	protein-coding	0.11	0.742574
Merged-chr9-108264123-1	chr9	108264073	108264173	+	3.7	cIP2vsInput	promoter-TSS (NM_001276481)	promoter-TSS (NM_001276481)	-165	NM_001276486	13138	Mm.7524	NM_001276481	ENSMUSG00000039952	Dag1	D9Wsu13e|DG|Dp427|Dp71	dystroglycan 1	protein-coding	0.05	0.594059
Merged-chr9-108517121-1	chr9	108517071	108517171	+	3.7	cIP2vsInput	promoter-TSS (NM_175143)	promoter-TSS (NM_175143)	34	NM_175143	69232	Mm.335449	NM_001114119	ENSMUSG00000006673	Qrich1	2610028H07Rik	glutamine-rich 1	protein-coding	0.08	0.623762
Merged-chr7-144941771-1	chr7	144941721	144941821	+	3.7	cIP1vsInput	Intergenic	CpG	-1846	NM_007631	12443	Mm.273049	NM_007631	ENSMUSG00000070348	Ccnd1	AI327039|CycD1|Cyl-1|PRAD1|bcl-1|cD1	cyclin D1	protein-coding	0.09	0.683168
Merged-chr5-90366651-1	chr5	90366601	90366701	+	3.7	cIP2vsInput	promoter-TSS (NR_045618)	promoter-TSS (NR_045618)	-346	NR_045618	791294	Mm.30508	NR_045618	ENSMUSG00000054945	Gm9958	ENSMUSG00000054945	predicted gene 9958	miscRNA	0.15	0.782178
Merged-chr9-59750834-1	chr9	59750784	59750884	+	3.7	cIP2vsInput	promoter-TSS (NM_027838)	promoter-TSS (NM_027838)	-185	NM_001172070	71599	Mm.279070	NM_001172068	ENSMUSG00000051705	Senp8	9130010J17Rik|AU020827|Den1|Nedp1|Prsc2	SUMO/sentrin specific peptidase 8	protein-coding	0.13	0.782178
Merged-chr9-64960872-2	chr9	64960789	64960956	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175153)	promoter-TSS (NM_175153)	40	NM_001077631	69882	Mm.272616	NM_001077631	ENSMUSG00000034263	Vwa9	2010321M09Rik	von Willebrand factor A domain containing 9	protein-coding	0.095808	0.64881
Merged-chr11-102189627-1	chr11	102189577	102189677	+	3.7	cIP2vsInput	promoter-TSS (NM_175935)	promoter-TSS (NM_175935)	-72	NM_175935	68401	Mm.22385	NM_175935	ENSMUSG00000034793	G6pc3	0710001K01Rik|AU019276|AU045429|AV128920|AW545836|UGRP	"glucose 6 phosphatase, catalytic, 3"	protein-coding	0.07	0.613861
Merged-chr7-81213198-1	chr7	81213148	81213248	+	3.7	cIP2vsInput	promoter-TSS (NM_008803)	promoter-TSS (NM_008803)	-606	NM_008803	18584	Mm.371577	NM_008803		Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding	0.13	0.752475
Merged-chr13-56703065-1	chr13	56703015	56703115	+	3.7	cIP2vsInput	promoter-TSS (NM_001164041)	promoter-TSS (NM_001164041)	13	NM_001164041	17129	Mm.272920	NM_001164041	ENSMUSG00000021540	Smad5	1110051M15Rik|AI451355|Dwf-C|Madh5|MusMLP	SMAD family member 5	protein-coding	0.19	0.752475
Merged-chr4-145533447-1	chr4	145533397	145533497	+	3.7	cIP2vsInput	Intergenic	Intergenic	69237	NR_002888	545700	Mm.389595	NR_002888	ENSMUSG00000052912	Smarca5-ps	9230115A19Rik|OTTMUSG00000011029	"SWI/SNF related, matrix associated, actin depenent ragulator of chromatin, subfamily a, member 5, pseudogene"	pseudo	0	0.326733
Merged-chr11-20333170-2	chr11	20333109	20333232	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_018861)	promoter-TSS (NM_018861)	-457	NM_018861	55963	Mm.6379	NM_018861	ENSMUSG00000020142	Slc1a4	ASCT-1|ASCT1|AW045657|SATT	"solute carrier family 1 (glutamate/neutral amino acid transporter), member 4"	protein-coding	0.02439	0.516129
Merged-chr1-167308748-1	chr1	167308698	167308798	+	3.7	cIP2vsInput	promoter-TSS (NM_001039483)	promoter-TSS (NM_001039483)	78	NM_001039483	68944	Mm.330045	NM_026881	ENSMUSG00000052428	Tmco1	1190006A08Rik|4930403O06Rik|AA109065|AU022572|ESTM39	transmembrane and coiled-coil domains 1	protein-coding	0.11	0.653465
Merged-chr11-97766737-1	chr11	97766687	97766787	+	3.7	cIP1vsInput	promoter-TSS (NM_026186)	promoter-TSS (NM_026186)	-124	NM_026186	67480	Mm.33206	NM_026186	ENSMUSG00000018541	Cwc25	1300013D05Rik|AA473636|Ccdc49|R75228	CWC25 spliceosome-associated protein homolog (S. cerevisiae)	protein-coding	0.03	0.554455
Merged-chr7-75430861-1	chr7	75430811	75430911	+	3.7	cIP1vsInput	Intergenic	Intergenic	-24673	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding	0.01	0.405941
Merged-chr7-127254428-1	chr7	127254378	127254478	+	3.7	cIP2vsInput	"exon (NM_177362, exon 3 of 3)"	"exon (NM_177362, exon 3 of 3)"	6239	NM_023203	66422	Mm.29898	NM_023203	ENSMUSG00000042462	Dctpp1	2410015N17Rik|AI854235|RS21-C6	dCTP pyrophosphatase 1	protein-coding	0.16	0.732673
Merged-chr14-31206644-1	chr14	31206594	31206694	+	3.7	cIP2vsInput	"exon (NM_022656, exon 1 of 21)"	"exon (NM_022656, exon 1 of 21)"	182	NM_022656	64652	Mm.298728	NM_022656	ENSMUSG00000021910	Nisch	1200007D05Rik|3202002H23Rik|AW494485|I-1	nischarin	protein-coding	0.15	0.752475
Merged-chr9-47529774-2	chr9	47529718	47529831	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_018770)	promoter-TSS (NM_018770)	-578	NM_207675	54725	Mm.234832	NM_001025600	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding	0.070796	0.587719
Merged-chr6-50566753-1	chr6	50566703	50566803	+	3.7	cIP2vsInput	promoter-TSS (NM_007808)	promoter-TSS (NM_007808)	110	NR_027892	73183	Mm.430720	NR_015581	ENSMUSG00000085776	5430402O13Rik	3110047M22Rik	RIKEN cDNA 5430402O13 gene	miscRNA	0.1	0.663366
Merged-chr2-91265283-1	chr2	91265233	91265333	+	3.7	cIP2vsInput	TTS (NM_030880)	TTS (NM_030880)	168	NM_023854	77038	Mm.386861	NM_001166024	ENSMUSG00000027255	Arfgap2	2310032E02Rik|Zfp289	ADP-ribosylation factor GTPase activating protein 2	protein-coding	0.13	0.70297
Merged-chr7-116423799-1	chr7	116423749	116423849	+	3.7	cIP1vsInput	"intron (NM_011083, intron 1 of 32)"	"intron (NM_011083, intron 1 of 32)"	19659	NM_011083	18704	Mm.3810	NM_011083	ENSMUSG00000030660	Pik3c2a	Cpk-m|PI3KC2	"phosphatidylinositol 3-kinase, C2 domain containing, alpha polypeptide"	protein-coding	0	0.326733
Merged-chr4-15957945-2	chr4	15957894	15957996	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013752)	promoter-TSS (NM_013752)	-22	NM_013752	27354	Mm.20866	NM_013752	ENSMUSG00000028224	Nbn	Nbs1	nibrin	protein-coding	0.137255	0.708738
Merged-chr15-85337429-1	chr15	85337379	85337479	+	3.7	cIP1vsInput	"intron (NM_016843, intron 1 of 11)"	"intron (NM_016843, intron 1 of 11)"	1048	NM_016843	54138	Mm.248906	NM_016843	ENSMUSG00000016541	Atxn10	AI325283|C77170|E46|Sca10|TEG-169|Tex169	ataxin 10	protein-coding	0.04	0.584158
Merged-chr5-14955352-1	chr5	14955302	14955402	+	3.7	cIP2vsInput	"intron (NR_001584, intron 1 of 3)"	Lx|LINE|L1	10058	NR_001584	74062	Mm.394766	NR_001584		Speer8-ps1	4933405L09Rik|SPEER-8|Speer8-ps	"spermatogenesis associated glutamate (E)-rich protein 8, pseudogene 1"	pseudo	0	0.277228
Merged-chr2-114201490-2	chr2	114201430	114201551	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175466)	promoter-TSS (NM_175466)	-58	NM_175466	228491	Mm.132523	NM_175466	ENSMUSG00000040321	Zfp770	6430601A21Rik|Znf770	zinc finger protein 770	protein-coding	0.07438	0.565574
Merged-chr6-115601797-2	chr6	115601736	115601859	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_023290)	promoter-TSS (NM_023290)	-141	NM_023290	67027	Mm.101316	NM_023290	ENSMUSG00000000439	Mkrn2	2610002L04Rik|C81377	"makorin, ring finger protein, 2"	protein-coding	0.065041	0.596774
Merged-chr11-103132771-1	chr11	103132721	103132821	+	3.7	cIP1vsInput	promoter-TSS (NM_027658)	promoter-TSS (NM_027658)	-568	NM_001130516	71059	Mm.273871	NM_001130515	ENSMUSG00000043372	Hexim2	4933402L21Rik	hexamethylene bis-acetamide inducible 2	protein-coding	0.12	0.772277
Merged-chr14-124308559-1	chr14	124308509	124308609	+	3.7	cIP2vsInput	"intron (NM_207667, intron 1 of 4)"	"intron (NM_207667, intron 1 of 4)"	-116013	NM_010201	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding	0	0.336634
Merged-chr18-75462710-1	chr18	75462660	75462760	+	3.7	cIP2vsInput	"intron (NM_201354, intron 10 of 11)"	"intron (NM_201354, intron 10 of 11)"	-51935	NR_045879	100038353	Mm.440724	NR_045879	ENSMUSG00000097712	Gm10532	ENSMUSG00000073534	predicted gene 10532	miscRNA	0	0.475248
Merged-chr9-37657399-1	chr9	37657349	37657449	+	3.7	cIP2vsInput	promoter-TSS (NM_025289)	promoter-TSS (NM_025289)	-87	NM_025289	21376	Mm.28689	NM_025289	ENSMUSG00000011114	Tbrg1	AA408552|AA409675|Niam|Tb-5|mFLJ00213	transforming growth factor beta regulated gene 1	protein-coding	0.04	0.564356
Merged-chr5-119670665-1	chr5	119670615	119670715	+	3.7	cIP2vsInput	promoter-TSS (NM_011535)	promoter-TSS (NM_011535)	-4	NM_011535	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding	0.07	0.683168
Merged-chr2-131160413-2	chr2	131160330	131160496	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026091)	promoter-TSS (NM_026091)	-393	NM_026091	67326	Mm.27711	NM_026091	ENSMUSG00000027327	1700037H04Rik	-	RIKEN cDNA 1700037H04 gene	protein-coding	0.054217	0.556886
Merged-chr11-69395972-1	chr11	69395922	69396022	+	3.7	cIP2vsInput	promoter-TSS (NM_001045525)	promoter-TSS (NM_001045525)	181	NM_030083	78304	Mm.45683	NM_030083		Lsmd1	1500034E06Rik	LSM domain containing 1	protein-coding	0.1	0.663366
Merged-chr2-59882310-1	chr2	59882260	59882360	+	3.7	cIP2vsInput	"intron (NM_028118, intron 1 of 10)"	CpG	296	NM_001159636	72137	Mm.488684	NM_001159636	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	"WD repeat, SAM and U-box domain containing 1"	protein-coding	0.1	0.732673
Merged-chr11-101064289-1	chr11	101064239	101064339	+	3.7	cIP2vsInput	TTS (NM_016920)	TTS (NM_016920)	-5805	NM_013792	27419	Mm.95452	NM_013792	ENSMUSG00000001751	Naglu	-	alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB)	protein-coding	0	0.49505
Merged-chr17-25115839-1	chr17	25115789	25115889	+	3.7	cIP2vsInput	promoter-TSS (NM_027880)	promoter-TSS (NM_027880)	66	NM_027880	71718	Mm.288702	NM_001163661	ENSMUSG00000024170	Telo2	1200003M09Rik|AI415602|Tel2|mKIAA0683	"TEL2, telomere maintenance 2, homolog (S. cerevisiae)"	protein-coding	0.08	0.564356
Merged-chr7-45589392-2	chr7	45589330	45589455	+	3.7	cIP1vsInput|cIP2vsInput	"3' UTR (NM_001243053, exon 12 of 12)"	"3' UTR (NM_001243053, exon 12 of 12)"	-14216	NR_038165	71661	Mm.439894	NR_038165	ENSMUSG00000085214	0610005C13Rik	AI182092	RIKEN cDNA 0610005C13 gene	miscRNA	0.048	0.579365
Merged-chr8-84639875-1	chr8	84639825	84639925	+	3.7	cIP1vsInput	"3' UTR (NM_001252061, exon 47 of 47)"	"3' UTR (NM_001252061, exon 47 of 47)"	22977	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding	0.08	0.544554
Merged-chr3-146521154-1	chr3	146521104	146521204	+	3.7	cIP2vsInput	"intron (NM_027332, intron 1 of 4)"	"intron (NM_027332, intron 1 of 4)"	269	NM_027332	70285	Mm.28128	NM_027332	ENSMUSG00000028187	Rpf1	2210420E24Rik|2310066N05Rik|Bxdc5	ribosome production factor 1 homolog (S. cerevisiae)	protein-coding	0.15	0.752475
Merged-chr5-15541894-1	chr5	15541844	15541944	+	3.7	cIP1vsInput	Intergenic	ETnERV3-int|LTR|ERVK	-77205	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0.01	0.336634
Merged-chr9-65196579-1	chr9	65196529	65196629	+	3.7	cIP2vsInput	Intergenic	U5|snRNA|snRNA	-18111	NM_177460	214424	Mm.31129	NM_177460	ENSMUSG00000032392	Parp16	ARTD15|BC055447|C79952|PARP-16	"poly (ADP-ribose) polymerase family, member 16"	protein-coding	0.01	0.386139
Merged-chr5-134456292-1	chr5	134456242	134456342	+	3.7	cIP2vsInput	promoter-TSS (NM_001081465)	promoter-TSS (NM_001081465)	-30	NM_001081465	57080	Mm.332735	NM_001081462	ENSMUSG00000023079	Gtf2ird1	1700012P16Rik|BEN|Cream1|ESTM9|GTF3|Gtf2il|MusTRD1|Tg(Alb1-Myc)166.8Sst|WBSCR11|X83320	general transcription factor II I repeat domain-containing 1	protein-coding	0.04	0.534653
Merged-chr5-146221484-1	chr5	146221434	146221534	+	3.7	cIP2vsInput	promoter-TSS (NM_001256085)	promoter-TSS (NM_001256085)	-27	NM_028774	74132	Mm.26696	NM_001256085	ENSMUSG00000029634	Rnf6	1200013I08Rik|5730419H05Rik|AA537053	ring finger protein (C3H2C3 type) 6	protein-coding	0.14	0.712871
Merged-chr6-145855872-2	chr6	145855806	145855938	+	3.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	9548	NM_001271768	79362	Mm.396926	NM_001271768		Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	"basic helix-loop-helix family, member e41"	protein-coding	0.098485	0.669173
Merged-chr4-102635380-2	chr4	102635323	102635437	+	3.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	45537	NM_001177981	18578	Mm.20181	NM_001177980	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	"phosphodiesterase 4B, cAMP specific"	protein-coding	0.035088	0.486957
Merged-chr8-25754506-1	chr8	25754456	25754556	+	3.7	cIP2vsInput	promoter-TSS (NM_028102)	promoter-TSS (NM_028102)	-226	NM_028102	72108	Mm.246875	NM_028102	ENSMUSG00000061313	Ddhd2	2010305K11Rik|SAMWD1|mKIAA0725	DDHD domain containing 2	protein-coding	0.15	0.782178
Merged-chr7-45154638-2	chr7	45154586	45154690	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145954)	promoter-TSS (NM_145954)	-100	NM_145954	69748	Mm.82139	NM_145954		Aldh16a1	2410004H02Rik|AI452234|mFLJ00209	"aldehyde dehydrogenase 16 family, member A1"	protein-coding	0.105769	0.6
Merged-chr10-93160644-1	chr10	93160594	93160694	+	3.7	cIP2vsInput	promoter-TSS (NM_146239)	promoter-TSS (NM_146239)	-232	NM_146239	237459		NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding	0.13	0.811881
Merged-chr12-99393137-2	chr12	99393053	99393222	+	3.7	cIP1vsInput|cIP2vsInput	"intron (NM_183186, intron 1 of 5)"	CpG	56937	NM_183186	71375	Mm.489662	NM_183186	ENSMUSG00000033713	Foxn3	5430426H20Rik|AA589593|AW556347|Ches1|Ches1l|HTLFL1	forkhead box N3	protein-coding	0.088757	0.688235
Merged-chr8-123949307-1	chr8	123949257	123949357	+	3.7	cIP2vsInput	promoter-TSS (NM_172288)	promoter-TSS (NM_172288)	-42	NM_172288	234865	Mm.267812	NM_172288	ENSMUSG00000039509	Nup133	mermaid	nucleoporin 133	protein-coding	0.11	0.653465
Merged-chr11-26387102-1	chr11	26387052	26387152	+	3.7	cIP2vsInput	promoter-TSS (NM_001277273)	promoter-TSS (NM_001277273)	18	NR_102382	67030	Mm.18875	NM_001277273		Fancl	2010322C19Rik|AW554273|B230118H11Rik|Phf9|Pog|gcd	"Fanconi anemia, complementation group L"	protein-coding	0.03	0.534653
Merged-chr9-53667594-1	chr9	53667544	53667644	+	3.7	cIP1vsInput	promoter-TSS (NM_027807)	promoter-TSS (NM_027807)	-87	NM_027807	75717	Mm.218910	NM_001161618	ENSMUSG00000032030	Cul5	4921514I20Rik|8430423K24Rik|AI852817|C030032G03Rik|C330021I08Rik|VACM-1|VACM1	cullin 5	protein-coding	0.13	0.722772
Merged-chr6-134830426-1	chr6	134830376	134830476	+	3.7	cIP2vsInput	"5' UTR (NM_177687, exon 1 of 5)"	"5' UTR (NM_177687, exon 1 of 5)"	227	NM_177687	232430	Mm.267010	NM_177687		Crebl2	AI046348|B230205M03	cAMP responsive element binding protein-like 2	protein-coding	0.09	0.712871
Merged-chr11-69088461-2	chr11	69088400	69088523	+	3.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009497)	promoter-TSS (NM_009497)	-67	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding	0.162602	0.782258
Merged-chr19-19737109-1	chr19	19737059	19737159	+	3.7	cIP2vsInput	Intergenic	Lx|LINE|L1	-625913	NM_001043354	225998		NM_001043354	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta	RAR-related orphan receptor beta	protein-coding	0.01	0.376238
Merged-chr19-10304950-1	chr19	10304900	10305000	+	3.7	cIP2vsInput	promoter-TSS (NM_198114)	promoter-TSS (NM_198114)	-73	NM_198114	269060	Mm.329718	NM_198114	ENSMUSG00000035735	Dagla	Nsddr	"diacylglycerol lipase, alpha"	protein-coding	0.16	0.742574
Merged-chr10-41303293-1	chr10	41303243	41303343	+	3.7	cIP2vsInput	promoter-TSS (NM_133999)	promoter-TSS (NM_133999)	-52	NM_133999	103199	Mm.277242	NM_133999	ENSMUSG00000038417	Fig4	A530089I17Rik|AI326867|Sac3	FIG4 homolog (S. cerevisiae)	protein-coding	0.06	0.663366
Merged-chr4-143212796-1	chr4	143212746	143212846	+	3.7	cIP2vsInput	promoter-TSS (NM_001256380)	promoter-TSS (NM_001256380)	-87	NM_001256380	110593	Mm.332020	NM_001081355	ENSMUSG00000057637	Prdm2	4833427P12Rik|E330024L24Rik|Gm1033|Gm19732|KMT8|Riz|Riz1|Znfpr1c1	"PR domain containing 2, with ZNF domain"	protein-coding	0.14	0.722772
Merged-chr8-70609645-1	chr8	70609595	70609695	+	3.7	cIP2vsInput	Intergenic	CpG	-1331	NM_133772	76900	Mm.6667	NM_133772	ENSMUSG00000070003	Ssbp4	1210002E11Rik|AW743380|Sspb4	single stranded DNA binding protein 4	protein-coding	0.08	0.752475
Merged-chr4-145000028-1	chr4	144999978	145000078	+	3.7	cIP2vsInput	"intron (NM_001276502, intron 66 of 68)"	"intron (NM_001276502, intron 66 of 68)"	106891	NM_011303	20148	Mm.14063	NM_001172424	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding	0.05	0.435644
Merged-chr15-101266607-2	chr15	101266552	101266663	+	3.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010444)	promoter-TSS (NM_010444)	-239	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	"nuclear receptor subfamily 4, group A, member 1"	protein-coding	0.117117	0.607143
Merged-chr9-80688671-2	chr9	80688605	80688737	+	3.65	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-223233	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding	0.015152	0.533835
Merged-chr7-19562281-2	chr7	19562221	19562342	+	3.65	cIP1vsInput|cIP2vsInput	"5' UTR (NM_199149, exon 1 of 13)"	"5' UTR (NM_199149, exon 1 of 13)"	117	NM_199149	232947	Mm.219662	NM_199149	ENSMUSG00000051403	Ppp1r37	Gm158|Lrrc68	"protein phosphatase 1, regulatory subunit 37"	protein-coding	0.099174	0.557377
Merged-chr5-28165551-2	chr5	28165476	28165627	+	3.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010134)	promoter-TSS (NM_010134)	-145	NM_010134	13799	Mm.4298	NM_010134		En2	BB131122|En-2	engrailed 2	protein-coding	0.112583	0.730263
Merged-chr3-31057182-2	chr3	31057100	31057265	+	3.65	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-37876	NM_011386	20482	Mm.15406	NM_001039090	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding	0.030303	0.554217
Merged-chrX-52651552-2	chrX	52651480	52651624	+	3.65	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-37578	NM_016697	14734	Mm.22515	NM_016697	ENSMUSG00000055653	Gpc3	OCI-5	glypican 3	protein-coding	0.020833	0.524138
Merged-chr1-36770999-2	chr1	36770928	36771070	+	3.65	cIP1vsInput|cIP2vsInput	"exon (NM_009539, exon 2 of 13)"	"exon (NM_009539, exon 2 of 13)"	9138	NM_009539	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	70kDa|AI327364|Srk|TZK|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding	0.133803	0.671329
Merged-chr11-20661839-2	chr11	20661779	20661899	+	3.65	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	29862	NM_001038625	58172	Mm.339676	NM_001038625	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding	0.008333	0.520661
Merged-chr4-152186146-2	chr4	152186086	152186207	+	3.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001146057)	promoter-TSS (NM_001146057)	12	NM_001146057	70025	Mm.296191	NM_001146057	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding	0.024793	0.57377
Merged-chr6-92869337-2	chr6	92869274	92869400	+	3.65	cIP1vsInput|cIP2vsInput	"intron (NM_175314, intron 12 of 29)"	"intron (NM_175314, intron 12 of 29)"	32104	NM_175314	101401	Mm.257557	NM_175314	ENSMUSG00000030022	Adamts9	1810011L16Rik|8430403M15Rik|AW743315|E030027K14Rik	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 9"	protein-coding	0.007937	0.448819
Merged-chr3-87512569-2	chr3	87512502	87512637	+	3.65	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-13009	NM_001083318	27049	Mm.219460	NM_001083318	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant gene 3	protein-coding	0.02963	0.566176
Merged-chr8-106683097-2	chr8	106683041	106683154	+	3.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_173037)	promoter-TSS (NM_173037)	29	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding	0.079646	0.640351
Merged-chr12-73964491-2	chr12	73964433	73964550	+	3.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178392)	promoter-TSS (NM_178392)	-39	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	"small nuclear RNA activating complex, polypeptide 1"	protein-coding	0.102564	0.661017
Merged-chr7-112242505-2	chr7	112242436	112242574	+	3.65	cIP1vsInput|cIP2vsInput	"intron (NM_177282, intron 2 of 19)"	"intron (NM_177282, intron 2 of 19)"	16669	NM_001193305	320878	Mm.488195	NM_001193305	ENSMUSG00000038244	Mical2	5330438E18Rik|9530064J02|MICAL-2|mKIAA0750	"microtubule associated monooxygenase, calponin and LIM domain containing 2"	protein-coding	0.007246	0.410072
Merged-chr15-58823584-2	chr15	58823532	58823637	+	3.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175212)	promoter-TSS (NM_175212)	-157	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding	0.12381	0.735849
Merged-chr19-6941614-2	chr19	6941560	6941668	+	3.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007522)	promoter-TSS (NM_007522)	-107	NM_001177362	107173	Mm.276555	NM_001177360	ENSMUSG00000024958	Gpr137	AI428855	G protein-coupled receptor 137	protein-coding	0.166667	0.715596
Merged-chr12-80168640-2	chr12	80168573	80168708	+	3.65	cIP1vsInput|cIP2vsInput	"intron (NM_134156, intron 20 of 20)"	"intron (NM_134156, intron 20 of 20)"	-35796	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	miscRNA	0.037037	0.323529
Merged-chr4-46507432-2	chr4	46507380	46507485	+	3.65	cIP1vsInput|cIP2vsInput	"intron (NM_029077, intron 5 of 5)"	CpG	18103	NM_053179	94181	Mm.249349	NM_053179	ENSMUSG00000028334	Nans	4632418E04Rik|BB056474|Sas	N-acetylneuraminic acid synthase (sialic acid synthase)	protein-coding	0.114286	0.726415
Merged-chr7-66109431-2	chr7	66109378	66109484	+	3.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081163)	promoter-TSS (NM_001081163)	-84	NM_001081163	269941	Mm.333916	NM_001081163	ENSMUSG00000032640	Chsy1	mKIAA0990	chondroitin sulfate synthase 1	protein-coding	0.150943	0.691589
Merged-chr14-75754664-2	chr14	75754590	75754738	+	3.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_177381)	promoter-TSS (NM_177381)	-171	NM_177381	338337	Mm.86507	NM_177381	ENSMUSG00000034893	Cog3	E430004N23	component of oligomeric golgi complex 3	protein-coding	0.047297	0.510067
Merged-chr6-71788507-2	chr6	71788455	71788560	+	3.65	cIP1vsInput|cIP2vsInput	"intron (NM_178608, intron 5 of 6)"	"intron (NM_178608, intron 5 of 6)"	35277	NM_025430	66223	Mm.28579	NM_025430	ENSMUSG00000052962	Mrpl35	1110066C01Rik	mitochondrial ribosomal protein L35	protein-coding	0.047619	0.632075
Merged-chr4-120613333-2	chr4	120613246	120613420	+	3.65	cIP1vsInput|cIP2vsInput	Intergenic	(CATATA)n|Simple_repeat|Simple_repeat	24588	NM_001101603	667063	Mm.90231	NM_001101603	ENSMUSG00000091297	Gm8439	EG667063|Gm1664	predicted gene 8439	protein-coding	0	0.32
Merged-chr9-71486000-2	chr9	71485910	71486090	+	3.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178602)	promoter-TSS (NM_178602)	-17	NM_178602	28015	Mm.21094	NM_001164793	ENSMUSG00000032199	Polr2m	AA407243|AA408799|AI303746|AW553238|D9Wsu138e|Grinl1a|mKIAA4185	polymerase (RNA) II (DNA directed) polypeptide M	protein-coding	0.088889	0.61326
Merged-chr15-76327341-2	chr15	76327245	76327438	+	3.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175399)	promoter-TSS (NM_175399)	-56	NM_175399	109075	Mm.322752	NM_175399	ENSMUSG00000034259	Exosc4	1110039I09Rik|1500001N04Rik|Rrp41	exosome component 4	protein-coding	0.082902	0.541237
Merged-chr8-4275937-2	chr8	4275867	4276008	+	3.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011592)	promoter-TSS (NM_011592)	-32	NM_011592	21856	Mm.195249	NM_011592	ENSMUSG00000002949	Timm44	0710005E20Rik|D8Ertd118e|Mimt44|Tim44	translocase of inner mitochondrial membrane 44	protein-coding	0.092199	0.661972
Merged-chr18-77565617-2	chr18	77565527	77565708	+	3.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001164504)	promoter-TSS (NM_001164504)	-481	NM_001164504	225743	Mm.23293	NM_001164504	ENSMUSG00000025427	Rnf165	2900024M11Rik|AI427432|G630064H08Rik|Gm96	ring finger protein 165	protein-coding	0.132597	0.703297
Merged-chr17-45686214-2	chr17	45686133	45686295	+	3.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026732)	promoter-TSS (NM_026732)	4	NM_198167	224807	Mm.157904	NM_198167	ENSMUSG00000036026	Tmem63b	BC026370	transmembrane protein 63b	protein-coding	0.104938	0.809816
Merged-chr12-40147578-1	chr12	40147528	40147628	+	3.6	cIP2vsInput	Intergenic	Intergenic	-13350	NM_001146196	20259	Mm.2416	NM_001146196	ENSMUSG00000002565	Scin	AW545522|adseverin	scinderin	protein-coding	0.01	0.366337
Merged-chr4-129513658-1	chr4	129513608	129513708	+	3.6	cIP2vsInput	promoter-TSS (NM_010807)	promoter-TSS (NM_010807)	77	NM_010807	17357	Mm.424974	NM_010807	ENSMUSG00000047945	Marcksl1	AL022768|AW215397|AW536807|D4Bc1|F52|MacMARCKS|Macs2|Macs3|Mlp|Mrp	MARCKS-like 1	protein-coding	0.15	0.772277
Merged-chr9-57836801-1	chr9	57836751	57836851	+	3.6	cIP2vsInput	Intergenic	CpG	-2567	NM_019689	56380	Mm.425588	NM_019689	ENSMUSG00000004661	Arid3b	Bdp|Dri2	AT rich interactive domain 3B (BRIGHT-like)	protein-coding	0.1	0.811881
Merged-chr2-65928751-1	chr2	65928701	65928801	+	3.6	cIP1vsInput	"intron (NM_178634, intron 2 of 5)"	"intron (NM_178634, intron 2 of 5)"	82984	NM_178634	77771	Mm.102025	NM_153409	ENSMUSG00000044647	Csrnp3	A330102K23Rik|CSRNP-3|Csnrp3|Mbu1|taip-2	cysteine-serine-rich nuclear protein 3	protein-coding	0.02	0.306931
Merged-chr3-105687539-2	chr3	105687477	105687602	+	3.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_017397)	promoter-TSS (NM_017397)	32	NM_017397	53975	Mm.272826	NM_017397	ENSMUSG00000027905	Ddx20	GEMIN3|dp103	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	protein-coding	0.056	0.531746
Merged-chr3-133310569-1	chr3	133310519	133310619	+	3.6	cIP2vsInput	"intron (NM_146141, intron 1 of 11)"	CpG	453	NM_146141	74776	Mm.210305	NM_146141	ENSMUSG00000028013	Ppa2	1110013G13Rik|Sid6306	pyrophosphatase (inorganic) 2	protein-coding	0.11	0.663366
Merged-chrY-6815984-1	chrY	6815934	6816034	+	3.6	cIP2vsInput	Intergenic	MLTR14|LTR|ERV1	351793	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.386139
Merged-chr13-41220383-1	chr13	41220333	41220433	+	3.6	cIP2vsInput	promoter-TSS (NM_019423)	promoter-TSS (NM_019423)	20	NM_019423	54326	Mm.2567	NM_019423	ENSMUSG00000021364	Elovl2	AI317360|Ssc2	"elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2"	protein-coding	0.17	0.772277
Merged-chr4-132843102-1	chr4	132843052	132843152	+	3.6	cIP2vsInput	promoter-TSS (NM_146154)	promoter-TSS (NM_146154)	67	NM_146154	100336	Mm.105230	NM_146154	ENSMUSG00000028882	Ppp1r8	6330548N22Rik|AU044684|NIPP1	"protein phosphatase 1, regulatory (inhibitor) subunit 8"	protein-coding	0.09	0.663366
Merged-chr10-108089344-1	chr10	108089294	108089394	+	3.6	cIP2vsInput	Intergenic	Intergenic	-73056	NM_027892	17931	Mm.489819	NM_027892	ENSMUSG00000019907	Ppp1r12a	1200015F06Rik|5730577I22Rik|AA792106|AV099298|D10Ertd625e|Mypt1	"protein phosphatase 1, regulatory (inhibitor) subunit 12A"	protein-coding	0.02	0.435644
Merged-chr7-81829147-1	chr7	81829097	81829197	+	3.6	cIP1vsInput	"exon (NM_146193, exon 1 of 8)"	"exon (NM_146193, exon 1 of 8)"	284	NM_146193	83962	Mm.439893	NM_146193	ENSMUSG00000025103	Btbd1	1190005H08Rik	BTB (POZ) domain containing 1	protein-coding	0.14	0.742574
Merged-chr13-66492927-1	chr13	66492877	66492977	+	3.6	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-51809	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding	0	0.316832
Merged-chr3-51652798-1	chr3	51652748	51652848	+	3.6	cIP2vsInput	Intergenic	Intergenic	-8395	NM_174995	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding	0.03	0.594059
Merged-chr5-108268793-1	chr5	108268743	108268843	+	3.6	cIP2vsInput	promoter-TSS (NM_026106)	promoter-TSS (NM_026106)	-104	NM_026106	13486	Mm.303534	NM_026106	ENSMUSG00000029265	Dr1	1700121L09Rik|Dr1l|NC2|NC2beta	down-regulator of transcription 1	protein-coding	0.15	0.811881
Merged-chr10-80826139-1	chr10	80826089	80826189	+	3.6	cIP1vsInput	promoter-TSS (NM_008753)	promoter-TSS (NM_008753)	-517	NM_008753	18245	Mm.398119	NM_008753	ENSMUSG00000035242	Oaz1	AZ-1|AZ1|Antizyme|ODC-Az|Oaz	ornithine decarboxylase antizyme 1	protein-coding	0.03	0.49505
Merged-chr2-173021880-1	chr2	173021830	173021930	+	3.6	cIP2vsInput	promoter-TSS (NM_019547)	promoter-TSS (NM_019547)	-22	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding	0.15	0.732673
Merged-chr2-180709995-1	chr2	180709945	180710045	+	3.6	cIP2vsInput	promoter-TSS (NM_177852)	promoter-TSS (NM_177852)	4	NM_177852	23856	Mm.490825	NM_011805	ENSMUSG00000038914	Dido1	6720461J16Rik|C530043I07|D130048F08Rik|DIO-1|Datf1|Dido2|Dido3|mKIAA0333	death inducer-obliterator 1	protein-coding	0.11	0.623762
Merged-chr1-121328025-2	chr1	121327956	121328095	+	3.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133748)	promoter-TSS (NM_133748)	-1	NM_133748	72999	Mm.27136	NM_001271531	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding	0.086331	0.65
Merged-chr13-73603926-2	chr13	73603864	73603988	+	3.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_146047)	promoter-TSS (NM_146047)	-76	NM_146047	218335	Mm.30099	NM_146047	ENSMUSG00000021610	Clptm1l	C130052I12Rik|Crr9	CLPTM1-like	protein-coding	0.145161	0.704
Merged-chr8-20287855-2	chr8	20287805	20287905	+	3.6	cIP1vsInput|cIP2vsInput	"intron (NR_030708, intron 1 of 4)"	B1_Mus1|SINE|Alu	9577	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo	0	0.435644
Merged-chr5-142367690-1	chr5	142367640	142367740	+	3.6	cIP2vsInput	Intergenic	CpG	-33807	NM_199068	17425	Mm.24214	NM_010812	ENSMUSG00000056493	Foxk1	A630048H08Rik|AI463295|ENSMUSG00000075577|Gm10868|Mnf	forkhead box K1	protein-coding	0.14	0.782178
Merged-chr11-50210274-2	chr11	50210209	50210339	+	3.6	cIP1vsInput|cIP2vsInput	"intron (NM_011018, intron 1 of 7)"	"intron (NM_011018, intron 1 of 7)"	516	NM_011018	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|p62	sequestosome 1	protein-coding	0.053846	0.656489
Merged-chr12-83489104-1	chr12	83489054	83489154	+	3.6	cIP1vsInput	Intergenic	Intergenic	-1368	NM_058212	70127	Mm.403230	NM_001267625	ENSMUSG00000021221	Dpf3	2810403B03Rik|6530402L11Rik|BAF45C|C78788|CERD4|cer-d4	"D4, zinc and double PHD fingers, family 3"	protein-coding	0.01	0.435644
Merged-chr1-85598095-1	chr1	85598045	85598145	+	3.6	cIP1vsInput	"intron (NM_175397, intron 2 of 12)"	"intron (NM_175397, intron 2 of 12)"	715	NM_030194	109032	Mm.461913	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding	0	0.415842
Merged-chr18-55252271-1	chr18	55252221	55252321	+	3.6	cIP1vsInput	Intergenic	Intergenic	-262091	NM_175751	269023	Mm.471753	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding	0.01	0.386139
Merged-chr17-3114887-1	chr17	3114837	3114937	+	3.6	cIP2vsInput	promoter-TSS (NM_134123)	promoter-TSS (NM_134123)	-85	NM_134123	106583	Mm.486401	NM_134123		Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding	0.16	0.772277
Merged-chr13-75943980-1	chr13	75943930	75944030	+	3.6	cIP2vsInput	promoter-TSS (NM_028493)	promoter-TSS (NM_028493)	-156	NM_028493	73296	Mm.276200	NM_028493	ENSMUSG00000021589	Rhobtb3	1700040C17Rik|2610033K01Rik|4930503C18Rik|AI317148|AW208826|mKIAA0878	Rho-related BTB domain containing 3	protein-coding	0.07	0.772277
Merged-chr4-44704498-2	chr4	44704442	44704555	+	3.6	cIP1vsInput|cIP2vsInput	"non-coding (NR_073462, exon 1 of 1)"	"non-coding (NR_073462, exon 1 of 1)"	1698	NR_073462	70602		XM_003945753		5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	miscRNA	0.132743	0.763158
Merged-chr14-62332172-1	chr14	62332122	62332222	+	3.6	cIP2vsInput	promoter-TSS (NM_026001)	promoter-TSS (NM_026001)	67	NM_026001	67153	Mm.26040	NM_026001	ENSMUSG00000021932	Rnaseh2b	1110019N06Rik|2610207P08Rik|Dleu8	"ribonuclease H2, subunit B"	protein-coding	0.11	0.70297
Merged-chr6-124828951-2	chr6	124828879	124829024	+	3.6	cIP1vsInput|cIP2vsInput	"intron (NM_013700, intron 1 of 19)"	"intron (NM_013700, intron 1 of 19)"	496	NM_013700	22225	Mm.3571	NM_013700	ENSMUSG00000038429	Usp5	AA407472|ISOT|ISOT-1|Ucht	ubiquitin specific peptidase 5 (isopeptidase T)	protein-coding	0.068966	0.554795
Merged-chr2-83644421-1	chr2	83644371	83644471	+	3.6	cIP2vsInput	promoter-TSS (NM_026934)	promoter-TSS (NM_026934)	-157	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding	0.15	0.742574
Merged-chr4-88094639-2	chr4	88094580	88094698	+	3.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081184)	promoter-TSS (NM_001081184)	9	NM_001081184	230393	Mm.287210	NM_001081184	ENSMUSG00000038368	Focad	Kiaa1797|mKIAA1797	focadhesin	protein-coding	0.084746	0.672269
Merged-chr15-81745103-1	chr15	81745053	81745153	+	3.6	cIP2vsInput	"5' UTR (NM_001081016, exon 1 of 23)"	"5' UTR (NM_001081016, exon 1 of 23)"	255	NM_001081016	20286	Mm.432075	NM_001081016	ENSMUSG00000022390	Zc3h7b	Gm627|Scrg3|Zc2h7b|mKIAA1031	zinc finger CCCH type containing 7B	protein-coding	0.09	0.712871
Merged-chr16-94526431-1	chr16	94526381	94526481	+	3.6	cIP1vsInput	"5' UTR (NM_007834, exon 1 of 8)"	"5' UTR (NM_007834, exon 1 of 8)"	198	NM_007834	13185	Mm.7472	NM_007834	ENSMUSG00000022898	Dscr3	AW538125|Dcra	Down syndrome critical region gene 3	protein-coding	0.1	0.673267
Merged-chr4-115828461-1	chr4	115828411	115828511	+	3.6	cIP2vsInput	"intron (NM_175308, intron 1 of 3)"	"intron (NM_175308, intron 1 of 3)"	369	NM_175308	100465	Mm.35571	NM_175308	ENSMUSG00000028709	Mob3c	AW822253|D130076I06Rik|Mobkl2c	MOB kinase activator 3C	protein-coding	0.04	0.633663
Merged-chr2-121449073-1	chr2	121449023	121449123	+	3.6	cIP2vsInput	promoter-TSS (NM_011354)	promoter-TSS (NM_011354)	-155	NM_011354	378702	Mm.262252	NM_011354	ENSMUSG00000074884	Serf2	C80083|Msmac1l|m4F5rel	small EDRK-rich factor 2	protein-coding	0.09	0.613861
Merged-chr8-94387344-1	chr8	94387294	94387394	+	3.6	cIP2vsInput	"intron (NM_022331, intron 1 of 7)"	"intron (NM_022331, intron 1 of 7)"	844	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	"homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1"	protein-coding	0.05	0.584158
Merged-chr10-110832516-1	chr10	110832466	110832566	+	3.6	cIP2vsInput	"intron (NR_045979, intron 2 of 2)"	"intron (NR_045979, intron 2 of 2)"	63991	NR_045979	75630	Mm.392786	NR_045979		1700020G17Rik	4930480D05Rik	RIKEN cDNA 1700020G17 gene	miscRNA	0.01	0.425743
Merged-chr5-15629455-1	chr5	15629405	15629505	+	3.6	cIP1vsInput	Intergenic	Intergenic	10356	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0.03	0.425743
Merged-chr9-21287979-1	chr9	21287929	21288029	+	3.6	cIP1vsInput	promoter-TSS (NM_145416)	promoter-TSS (NM_145416)	-10	NM_145416	215194	Mm.440165	NM_145416	ENSMUSG00000035047	Kri1	-	KRI1 homolog (S. cerevisiae)	protein-coding	0.13	0.732673
Merged-chr8-70282978-1	chr8	70282928	70283028	+	3.6	cIP2vsInput	promoter-TSS (NM_001146153)	promoter-TSS (NM_001146153)	-21	NM_011984	26558	Mm.440659	NM_001146153	ENSMUSG00000003573	Homer3	AW146114	homer homolog 3 (Drosophila)	protein-coding	0.11	0.80198
Merged-chr1-74588088-1	chr1	74588038	74588138	+	3.6	cIP2vsInput	promoter-TSS (NM_025784)	promoter-TSS (NM_025784)	-60	NM_029888	77264	Mm.207298	NM_029888	ENSMUSG00000026135	Zfp142	9330177B18Rik|BB154236|mKIAA0236	zinc finger protein 142	protein-coding	0.06	0.653465
Merged-chr14-76735251-1	chr14	76735201	76735301	+	3.6	cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	57683	NR_015485	73272	Mm.116804	NR_015485		1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	miscRNA	0.01	0.574257
Merged-chr8-44174962-1	chr8	44174912	44175012	+	3.6	cIP2vsInput	Intergenic	Intergenic	-475471	NM_001079931	384814	Mm.383288	NM_001079931		Gm5347	EG384814	predicted gene 5347	protein-coding	0	0.336634
Merged-chr1-93686548-1	chr1	93686498	93686598	+	3.6	cIP2vsInput	"exon (NM_016778, exon 2 of 5)"	"exon (NM_016778, exon 2 of 5)"	854	NM_016778	51800	Mm.3295	NM_016778	ENSMUSG00000026278	Bok	AI847676|AU021146|matador|mtd	BCL2-related ovarian killer protein	protein-coding	0.1	0.663366
Merged-chr4-141444757-1	chr4	141444707	141444807	+	3.6	cIP2vsInput	promoter-TSS (NM_009541)	promoter-TSS (NM_009541)	84	NM_009541	22642	Mm.389590	NM_009541		Zbtb17	AA589413|Lp-1|Miz1|Zfp100|mZ13	zinc finger and BTB domain containing 17	protein-coding	0.08	0.663366
Merged-chr6-145250286-1	chr6	145250236	145250336	+	3.6	cIP2vsInput	promoter-TSS (NM_021284)	promoter-TSS (NM_021284)	-55	NM_021284	16653	Mm.383182	NM_021284	ENSMUSG00000030265	Kras	AI929937|K-ras|Ki-ras|Kras-2|Kras2|p21B|ras	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	protein-coding	0.2	0.792079
Merged-chr9-104065635-1	chr9	104065585	104065685	+	3.6	cIP1vsInput	"intron (NM_175324, intron 1 of 19)"	L1M5|LINE|L1	1932	NM_175324	102632	Mm.41274	NM_175324	ENSMUSG00000090150	Acad11	5730439E10Rik|AI987948	"acyl-Coenzyme A dehydrogenase family, member 11"	protein-coding	0	0.316832
Merged-chr5-35921648-1	chr5	35921598	35921698	+	3.6	cIP2vsInput	"intron (NM_027373, intron 1 of 16)"	"intron (NM_027373, intron 1 of 16)"	28329	NM_027373	70292	Mm.125167	NM_027373	ENSMUSG00000029094	Afap1	2600003E23Rik|9630044L16Rik|AI848729|Afap|mKIAA3018	actin filament associated protein 1	protein-coding	0	0.524752
Merged-chr18-76944230-1	chr18	76944180	76944280	+	3.6	cIP2vsInput	promoter-TSS (NM_001039201)	promoter-TSS (NM_001039201)	115	NM_001039202	76987	Mm.236127	NM_001039201	ENSMUSG00000025421	Hdhd2	0610039H12Rik|3110052N05Rik	haloacid dehalogenase-like hydrolase domain containing 2	protein-coding	0.1	0.742574
Merged-chr2-50296703-1	chr2	50296653	50296753	+	3.6	cIP2vsInput	promoter-TSS (NR_040362)	promoter-TSS (NR_040362)	-26	NM_133839	109129	Mm.29214	NM_133839	ENSMUSG00000026766	Mmadhc	2010311D03Rik|AI314967	"methylmalonic aciduria (cobalamin deficiency) cblD type, with homocystinuria"	protein-coding	0.09	0.722772
Merged-chr10-82699066-1	chr10	82699016	82699116	+	3.6	cIP2vsInput	promoter-TSS (NM_001081218)	promoter-TSS (NM_001081218)	59	NM_001081218	67933	Mm.458243	NM_001081218		Hcfc2	1700129L13Rik|AU019838	host cell factor C2	protein-coding	0.16	0.811881
Merged-chr15-37135691-1	chr15	37135641	37135741	+	3.6	cIP2vsInput	Intergenic	CpG	-97345	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3	grainyhead-like 2 (Drosophila)	protein-coding	0.09	0.633663
Merged-chr3-80058900-1	chr3	80058850	80058950	+	3.6	cIP1vsInput	Intergenic	Intergenic	172970	NM_133187	68659	Mm.460017	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	"family with sequence similarity 198, member B"	protein-coding	0.01	0.376238
Merged-chr3-88043123-1	chr3	88043073	88043173	+	3.6	cIP2vsInput	promoter-TSS (NM_001110809)	promoter-TSS (NM_001110809)	15	NM_025663	66614	Mm.46029	NM_001110809	ENSMUSG00000028069	Gpatch4	2610029K21Rik|Gpatc4	G patch domain containing 4	protein-coding	0.04	0.544554
Merged-chr10-39518982-1	chr10	39518932	39519032	+	3.6	cIP2vsInput	"intron (NM_001122893, intron 5 of 13)"	"intron (NM_001122893, intron 5 of 13)"	-93952	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding	0	0.39604
Merged-chr6-88627442-2	chr6	88627377	88627507	+	3.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001142724)	promoter-TSS (NM_001142724)	3	NM_029013	74589	Mm.196226	NM_001142724	ENSMUSG00000033182	Kbtbd12	4833415F11Rik|4933428M03Rik|Klhdc6	kelch repeat and BTB (POZ) domain containing 12	protein-coding	0.092308	0.679389
Merged-chr2-75253806-1	chr2	75253756	75253856	+	3.6	cIP1vsInput	Intergenic	Intergenic	190373	NR_040635	77269	Mm.389278	NR_040635		9430019J16Rik	-	RIKEN cDNA 9430019J16 gene	miscRNA	0.01	0.366337
Merged-chr5-3343888-1	chr5	3343838	3343938	+	3.6	cIP2vsInput	promoter-TSS (NM_009873)	promoter-TSS (NM_009873)	-424	NM_009873	12571	Mm.399714	NM_009873		Cdk6	5830411I20|AI504062|Crk2	cyclin-dependent kinase 6	protein-coding	0.13	0.752475
Merged-chr13-17993378-1	chr13	17993328	17993428	+	3.6	cIP2vsInput	promoter-TSS (NM_025904)	promoter-TSS (NM_025904)	-27	NM_025904	67008	Mm.252918	NM_025904	ENSMUSG00000075054	Yae1d1	1600012F09Rik	Yae1 domain containing 1	protein-coding	0.13	0.722772
Merged-chr16-24393296-1	chr16	24393246	24393346	+	3.6	cIP2vsInput	promoter-TSS (NM_178665)	promoter-TSS (NM_178665)	-54	NM_178665	210126	Mm.450045	NM_001145952	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.12	0.772277
Merged-chr13-54621941-1	chr13	54621891	54621991	+	3.6	cIP2vsInput	"intron (NM_178397, intron 1 of 10)"	CpG	157	NM_178397	76577	Mm.194459	NM_178397	ENSMUSG00000025873	Faf2	2210404D11Rik|AI462440|Ubxd8|mKIAA0887	Fas associated factor family member 2	protein-coding	0.06	0.643564
Merged-chr11-113648375-1	chr11	113648325	113648425	+	3.6	cIP2vsInput	Intergenic	Intergenic	-1154	NM_013581	16834	Mm.261620	NM_013581		Cog1	6030445I15|Ldlb|mKIAA1381	component of oligomeric golgi complex 1	protein-coding	0.08	0.623762
Merged-chr15-78877409-2	chr15	78877342	78877476	+	3.6	cIP1vsInput|cIP2vsInput	"5' UTR (NM_145929, exon 1 of 17)"	"5' UTR (NM_145929, exon 1 of 17)"	219	NM_145929	106039	Mm.251331	NM_145929	ENSMUSG00000033128	Gga1	4930406E12Rik|AU016030|AW209092	"golgi associated, gamma adaptin ear containing, ARF binding protein 1"	protein-coding	0.164179	0.785185
Merged-chr1-52113826-1	chr1	52113776	52113876	+	3.6	cIP1vsInput	Intergenic	CpG	-5612	NM_009283	20846	Mm.487336	NM_001205313	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding	0.09	0.643564
Merged-chr18-7004854-1	chr18	7004804	7004904	+	3.6	cIP2vsInput	promoter-TSS (NM_177595)	promoter-TSS (NM_177595)	-75	NM_177595	210719	Mm.257186	NM_177595	ENSMUSG00000061013	Mkx	9430023B20Rik|Irxl1	mohawk homeobox	protein-coding	0.16	0.683168
Merged-chr18-67724451-1	chr18	67724401	67724501	+	3.6	cIP2vsInput	"exon (NM_001127177, exon 1 of 9)"	"exon (NM_001127177, exon 1 of 9)"	170	NM_001127177	19255	Mm.260433	NM_001127177	ENSMUSG00000024539	Ptpn2	AI325124|Ptpt|TC-PTP	"protein tyrosine phosphatase, non-receptor type 2"	protein-coding	0.11	0.643564
Merged-chr5-107437896-2	chr5	107437842	107437950	+	3.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001255991)	promoter-TSS (NM_001255991)	-101	NM_001255991	100503185	Mm.366650	NM_001255991	ENSMUSG00000070632	Btbd8	EG627196|Gm16115|OTTMUSG00000030610	BTB (POZ) domain containing 8	protein-coding	0.12037	0.678899
Merged-chr11-69863871-1	chr11	69863821	69863921	+	3.6	cIP1vsInput	Intergenic	RMER17D2|LTR|ERVK	-5141	NM_031880	83813	Mm.358793	NM_031880	ENSMUSG00000001583	Tnk1	Kos1|Tnk1a|Tnk1b	"tyrosine kinase, non-receptor, 1"	protein-coding	0.01	0.524752
Merged-chr8-27261122-2	chr8	27261071	27261174	+	3.6	cIP1vsInput|cIP2vsInput	"intron (NM_007918, intron 1 of 2)"	"intron (NM_007918, intron 1 of 2)"	795	NM_007918	13685	Mm.6700	NM_007918	ENSMUSG00000031490	Eif4ebp1	4e-bp1|AA959816|PHAS-I	eukaryotic translation initiation factor 4E binding protein 1	protein-coding	0.058252	0.644231
Merged-chr11-6476060-1	chr11	6476010	6476110	+	3.6	cIP2vsInput	promoter-TSS (NM_011221)	promoter-TSS (NM_011221)	16	NM_011221	19291	Mm.390332	NM_011221	ENSMUSG00000094483	Purb	2310015K15Rik|AA114818|Cager-2|D11Bwg0414e	purine rich element binding protein B	protein-coding	0.22	0.831683
Merged-chr1-170867831-1	chr1	170867781	170867881	+	3.6	cIP2vsInput	promoter-TSS (NM_001081304)	promoter-TSS (NM_001081304)	-60	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding	0.11	0.623762
Merged-chr6-124756808-1	chr6	124756758	124756858	+	3.6	cIP2vsInput	promoter-TSS (NM_007881)	promoter-TSS (NM_007881)	-321	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding	0.08	0.712871
Merged-chr10-54813855-1	chr10	54813805	54813905	+	3.6	cIP2vsInput	Intergenic	Intergenic	737933	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	"predicted gene, 16998"	miscRNA	0	0.376238
Merged-chr16-4594608-1	chr16	4594558	4594658	+	3.6	cIP2vsInput	promoter-TSS (NM_031184)	promoter-TSS (NM_031184)	-105	NM_031184	83396	Mm.134072	NM_031184	ENSMUSG00000014303	Glis2	Gli5|Klf16|Nkl	GLIS family zinc finger 2	protein-coding	0.1	0.732673
Merged-chr11-73138344-2	chr11	73138290	73138399	+	3.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010353)	promoter-TSS (NM_010353)	-50	NM_010353	14841	Mm.42045	NM_010353	ENSMUSG00000050107	Gsg2	Haspin	germ cell-specific gene 2	protein-coding	0.155963	0.781818
Merged-chr11-103102791-1	chr11	103102741	103102841	+	3.6	cIP2vsInput	"5' UTR (NM_025988, exon 2 of 10)"	"5' UTR (NM_025988, exon 2 of 10)"	1103	NM_025988	67131	Mm.390367	NM_001081495	ENSMUSG00000056938	Acbd4	2010009P05Rik|2010015A21Rik|AI849317	acyl-Coenzyme A binding domain containing 4	protein-coding	0.09	0.643564
Merged-chr4-43982553-2	chr4	43982501	43982606	+	3.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001002787)	promoter-TSS (NM_001002787)	-951	NM_001002787	442829	Mm.348215	NM_001002787	ENSMUSG00000070999	Ccin	4933417A14Rik	calicin	protein-coding	0.07619	0.641509
Merged-chr2-135658654-1	chr2	135658604	135658704	+	3.6	cIP2vsInput	Intergenic	Intergenic	-75434	NR_015544	320684	Mm.490820	NR_015544	ENSMUSG00000085631	9630028H03Rik	-	RIKEN cDNA 9630028H03 gene	miscRNA	0.09	0.70297
Merged-chr9-108339160-1	chr9	108339110	108339210	+	3.6	cIP2vsInput	promoter-TSS (NM_008160)	promoter-TSS (NM_008160)	80	NM_008160	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding	0.06	0.643564
Merged-chr13-43398338-1	chr13	43398288	43398388	+	3.6	cIP2vsInput	promoter-TSS (NM_023554)	promoter-TSS (NM_023554)	-38	NM_023554	70078	Mm.439927	NM_023554	ENSMUSG00000063200	Nol7	2210008F15Rik|5730556I21Rik|NOP27|RARG-1	nucleolar protein 7	protein-coding	0.15	0.712871
Merged-chr11-60104970-2	chr11	60104903	60105038	+	3.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009021)	promoter-TSS (NM_009021)	-43	NM_009021	19377	Mm.296366	NM_001037764	ENSMUSG00000062115	Rai1	Gt1	retinoic acid induced 1	protein-coding	0.148148	0.764706
Merged-chr15-11971999-1	chr15	11971949	11972049	+	3.6	cIP2vsInput	Intergenic	Intergenic	4937	NR_040447	73339	Mm.231975	NR_040447		1700047G03Rik	-	RIKEN cDNA 1700047G03 gene	miscRNA	0.02	0.534653
Merged-chr8-78508909-1	chr8	78508859	78508959	+	3.6	cIP2vsInput	promoter-TSS (NM_029736)	promoter-TSS (NM_029736)	19	NM_001252089	19656	Mm.24718	NM_001252089	ENSMUSG00000037070	Rbmxl1	Hnrpg|Rbmx|Rbmxrt	"RNA binding motif protein, X linked-like-1"	protein-coding	0.18	0.70297
Merged-chr3-27710731-1	chr3	27710681	27710781	+	3.6	cIP1vsInput	promoter-TSS (NM_173182)	promoter-TSS (NM_173182)	-292	NM_173182	72007	Mm.38832	NM_173182	ENSMUSG00000039286	Fndc3b	1600019O04Rik|AW550168|Fad104|mKIAA4164	fibronectin type III domain containing 3B	protein-coding	0.08	0.653465
Merged-chr3-80059065-1	chr3	80059015	80059115	+	3.6	cIP2vsInput	Intergenic	Intergenic	173135	NM_133187	68659	Mm.460017	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	"family with sequence similarity 198, member B"	protein-coding	0	0.29703
Merged-chr13-43479226-1	chr13	43479176	43479276	+	3.6	cIP2vsInput	"intron (NM_019930, intron 1 of 13)"	"intron (NM_019930, intron 1 of 13)"	1747	NM_019930	56705	Mm.148781	NM_019930	ENSMUSG00000038546	Ranbp9	IBAP-1|Ibap1|RanBPM	RAN binding protein 9	protein-coding	0.01	0.29703
Merged-chr19-43879770-2	chr19	43879707	43879834	+	3.6	cIP1vsInput|cIP2vsInput	"intron (NM_028029, intron 4 of 15)"	CpG	40967	NR_033472	100038628	Mm.212585	NR_033472	ENSMUSG00000074828	Gm10768	ENSMUSG00000074828	predicted gene 10768	miscRNA	0.070866	0.671875
Merged-chr2-122738571-1	chr2	122738521	122738621	+	3.6	cIP2vsInput	promoter-TSS (NM_019788)	promoter-TSS (NM_019788)	66	NM_019788	18457	Mm.268921	NM_019788	ENSMUSG00000005804	Bloc1s6	BLOC-1|Pldn|Stx13bp1|pa	"biogenesis of organelles complex-1, subunit 6, pallidin"	protein-coding	0.1	0.623762
Merged-chr8-26977223-1	chr8	26977173	26977273	+	3.6	cIP2vsInput	promoter-TSS (NM_001110508)	promoter-TSS (NM_001110508)	-113	NM_001101502	353310	Mm.212469	NM_001101502	ENSMUSG00000085795	Zfp703	1110032O19Rik|AI430822|AL022941|Csmn1|End2|Zeppo1|Znf703|Zpo1	zinc finger protein 703	protein-coding	0.22	0.841584
Merged-chr2-132815987-1	chr2	132815937	132816037	+	3.6	cIP2vsInput	promoter-TSS (NM_175113)	promoter-TSS (NM_175113)	67	NM_175113	66926	Mm.34199	NM_175113	ENSMUSG00000037376	Trmt6	3300001M20Rik|AU016412|AW492787|CGI-09|mKIAA1153	tRNA methyltransferase 6	protein-coding	0.09	0.653465
Merged-chr19-46623295-1	chr19	46623245	46623345	+	3.6	cIP2vsInput	promoter-TSS (NM_001177813)	promoter-TSS (NM_001177813)	-106	NM_001177813	226178	Mm.329895	NM_001177812	ENSMUSG00000047731	Wbp1l	D19Wsu162e|Opal1	WW domain binding protein 1 like	protein-coding	0.05	0.633663
Merged-chr1-61139394-2	chr1	61139341	61139447	+	3.6	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	161480	NM_017480	54167	Mm.42044	NM_017480	ENSMUSG00000026009	Icos	AILIM|CCLP|CRP-1|H4|Ly115	inducible T cell co-stimulator	protein-coding	0.018868	0.542056
Merged-chr6-121130210-1	chr6	121130160	121130260	+	3.6	cIP2vsInput	"intron (NM_001270475, intron 1 of 31)"	"intron (NM_001270475, intron 1 of 31)"	812	NM_001270475	194401	Mm.122399	NM_001270475	ENSMUSG00000003178	Mical3	C130040D16Rik|Mical-3|mKIAA1364	"microtubule associated monooxygenase, calponin and LIM domain containing 3"	protein-coding	0.07	0.673267
Merged-chr6-84856882-1	chr6	84856832	84856932	+	3.6	cIP1vsInput	"intron (NM_177077, intron 11 of 21)"	"intron (NM_177077, intron 11 of 21)"	212631	NM_177077	75914	Mm.159621	NM_177077	ENSMUSG00000033769	Exoc6b	4930569O18Rik|G430127E12Rik|Sec15b|Sec15l2|mKIAA0919	exocyst complex component 6B	protein-coding	0	0.29703
Merged-chr7-131371235-1	chr7	131371185	131371285	+	3.6	cIP2vsInput	promoter-TSS (NM_001039534)	promoter-TSS (NM_001039534)	89	NM_001039534	214580	Mm.272948	NM_177609	ENSMUSG00000063179	Pstk	5430423O14Rik|5730458D16Rik|Gm1099|R75284	phosphoseryl-tRNA kinase	protein-coding	0.12	0.673267
Merged-chr10-128626634-1	chr10	128626584	128626684	+	3.6	cIP2vsInput	promoter-TSS (NM_013765)	promoter-TSS (NM_013765)	-128	NM_013765	27370	Mm.261679	NM_013765	ENSMUSG00000025362	Rps26	-	ribosomal protein S26	protein-coding	0.01	0.356436
Merged-chr6-137704734-1	chr6	137704684	137704784	+	3.6	cIP1vsInput	Intergenic	Intergenic	-30348	NM_011499	20901	Mm.22584	NM_011499	ENSMUSG00000030224	Strap	AW557906|C78091|C79202|Unrip	serine/threonine kinase receptor associated protein	protein-coding	0.05	0.49505
Merged-chr4-152325682-1	chr4	152325632	152325732	+	3.6	cIP1vsInput	promoter-TSS (NM_001277114)	promoter-TSS (NM_001277114)	-44	NM_001277114	19934	Mm.307846	NM_001277113	ENSMUSG00000028936	Rpl22	2700038K18Rik	ribosomal protein L22	protein-coding	0.06	0.594059
Merged-chr19-24174056-1	chr19	24174006	24174106	+	3.6	cIP2vsInput	promoter-TSS (NM_001198985)	promoter-TSS (NM_001198985)	84	NM_001198985	21873	Mm.104744	NM_001198985	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding	0.13	0.712871
Merged-chr7-12897793-2	chr7	12897739	12897847	+	3.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001001447)	promoter-TSS (NM_001001447)	-22	NM_001001447	232878	Mm.40706	NM_001001447	ENSMUSG00000054715	Zscan22	AW227621|D530006B18Rik|Hkr2	zinc finger and SCAN domain containing 22	protein-coding	0.055556	0.587156
Merged-chr2-38926792-1	chr2	38926742	38926842	+	3.6	cIP2vsInput	promoter-TSS (NM_010264)	promoter-TSS (NM_010264)	-331	NM_010264	14536	Mm.439703	NM_001159548	ENSMUSG00000063972	Nr6a1	1700113M01Rik|Gcnf|NCNF|RTR	"nuclear receptor subfamily 6, group A, member 1"	protein-coding	0.04	0.643564
Merged-chr4-136135233-1	chr4	136135183	136135283	+	3.6	cIP2vsInput	Intergenic	CpG	-8589	NM_008321	15903	Mm.110	NM_008321		Id3	Hlh462|Idb3|bHLHb25	inhibitor of DNA binding 3	protein-coding	0.06	0.623762
Merged-chr2-93822620-2	chr2	93822546	93822694	+	3.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010163)	promoter-TSS (NM_010163)	-52	NM_010163	14043	Mm.4336	NM_010163	ENSMUSG00000027198	Ext2	AI893565	exostoses (multiple) 2	protein-coding	0.101351	0.657718
Merged-chr7-141328333-1	chr7	141328283	141328383	+	3.6	cIP2vsInput	promoter-TSS (NR_027769)	promoter-TSS (NR_027769)	203	NM_027797	71448	Mm.248960	NM_001141950	ENSMUSG00000025505	Tmem80	5530601I19Rik	transmembrane protein 80	protein-coding	0.05	0.554455
Merged-chr14-79587254-1	chr14	79587204	79587304	+	3.6	cIP2vsInput	promoter-TSS (NM_026474)	promoter-TSS (NM_026474)	-437	NM_026474	67955	Mm.18972	NM_026474	ENSMUSG00000022024	Sugt1	2410174K12Rik|SGT1	"SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)"	protein-coding	0.09	0.653465
Merged-chr1-110125877-1	chr1	110125827	110125927	+	3.6	cIP2vsInput	"intron (NM_172853, intron 11 of 11)"	Lx5b|LINE|L1	142140	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.326733
Merged-chr11-80081131-1	chr11	80081081	80081181	+	3.6	cIP2vsInput	promoter-TSS (NM_001277106)	promoter-TSS (NM_001277106)	-140	NM_018776	54394	Mm.272093	NM_001277106	ENSMUSG00000017561	Crlf3	BB164954|Creme9|Cytor4	cytokine receptor-like factor 3	protein-coding	0.06	0.613861
Merged-chr7-65371133-1	chr7	65371083	65371183	+	3.6	cIP2vsInput	"5' UTR (NM_001163574, exon 1 of 27)"	"5' UTR (NM_001163574, exon 1 of 27)"	111	NM_001163574	21872	Mm.4342	NM_001163574	ENSMUSG00000030516	Tjp1	ZO1	tight junction protein 1	protein-coding	0.13	0.722772
Merged-chr4-155993169-1	chr4	155993119	155993219	+	3.6	cIP2vsInput	promoter-TSS (NM_080445)	promoter-TSS (NM_080445)	255	NM_011341	20318	Mm.293517	NM_011341	ENSMUSG00000029076	Sdf4	Cab45	stromal cell derived factor 4	protein-coding	0.1	0.574257
Merged-chr2-119594645-1	chr2	119594595	119594695	+	3.6	cIP2vsInput	"intron (NR_015473, intron 1 of 2)"	CpG	349	NR_015473	66602	Mm.379181	NR_015473	ENSMUSG00000085438	1700020I14Rik	1190006L01Rik|4933437I03Rik|AI451541|AI585852|AW538376|AW558897	RIKEN cDNA 1700020I14 gene	miscRNA	0.09	0.623762
Merged-chr9-21265401-1	chr9	21265351	21265451	+	3.6	cIP2vsInput	"5' UTR (NM_153583, exon 1 of 10)"	"5' UTR (NM_153583, exon 1 of 10)"	102	NM_153583	235040	Mm.440165	NM_153583	ENSMUSG00000002820	Atg4d	9830134P12Rik|APG4-D|Apg4d|Atg4dl|Autl4	"autophagy related 4D, cysteine peptidase"	protein-coding	0.11	0.70297
Merged-chr1-190212492-1	chr1	190212442	190212542	+	3.6	cIP1vsInput	Intergenic	Lx8|LINE|L1	-41812	NM_008937	19130	Mm.392678	NM_008937		Prox1	A230003G05Rik	prospero-related homeobox 1	protein-coding	0.01	0.445545
Merged-chr2-126876400-1	chr2	126876350	126876450	+	3.6	cIP2vsInput	promoter-TSS (NM_021450)	promoter-TSS (NM_021450)	-139	NM_021450	58800	Mm.244705	NM_001164325	ENSMUSG00000027365	Trpm7	2310022G15Rik|4833414K03Rik|5033407O22Rik|CHAK|CHAK1|LTrpC-7|Ltpr7|Ltrpc7|TRPPLIK	"transient receptor potential cation channel, subfamily M, member 7"	protein-coding	0.06	0.564356
Merged-chr5-137786590-1	chr5	137786540	137786640	+	3.6	cIP2vsInput	"5' UTR (NM_144913, exon 1 of 4)"	"5' UTR (NM_144913, exon 1 of 4)"	111	NM_144913	231803	Mm.61193	NM_144913	ENSMUSG00000029726	Mepce	Bcdin3|D5Wsu46e	methylphosphate capping enzyme	protein-coding	0.05	0.584158
Merged-chr3-126780255-1	chr3	126780205	126780305	+	3.6	cIP2vsInput	"intron (NM_001025439, intron 6 of 19)"	"intron (NM_001025439, intron 6 of 19)"	163131	NM_001034168	109676	Mm.484610	NM_001034168	ENSMUSG00000032826	Ank2	AI835472|AW491075|Ank-2	"ankyrin 2, brain"	protein-coding	0	0.366337
Merged-chr9-119402114-1	chr9	119402064	119402164	+	3.6	cIP2vsInput	promoter-TSS (NM_007397)	promoter-TSS (NM_007397)	-387	NM_007397	11481	Mm.390239	NM_007397	ENSMUSG00000061393	Acvr2b	ActRIIB	activin receptor IIB	protein-coding	0.09	0.70297
Merged-chr11-107028380-1	chr11	107028330	107028430	+	3.6	cIP2vsInput	"5' UTR (NM_001163473, exon 2 of 3)"	"5' UTR (NM_001163473, exon 2 of 3)"	157	NM_001163473	69066	Mm.40679	NM_001163473		1810010H24Rik	OTTMUSG00000003581	RIKEN cDNA 1810010H24 gene	protein-coding	0.08	0.554455
Merged-chr17-5491498-1	chr17	5491448	5491548	+	3.6	cIP1vsInput	Intergenic	Intergenic	-1102	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	"zinc finger, DHHC domain containing 14"	protein-coding	0.05	0.544554
Merged-chr2-70661397-1	chr2	70661347	70661447	+	3.6	cIP1vsInput	promoter-TSS (NR_027343)	promoter-TSS (NR_027343)	-112	NR_027343	70231	Mm.470827	NM_027352	ENSMUSG00000014959	Gorasp2	0610011A07Rik|2410043M02Rik|5730520M13Rik|9430094F20Rik|AW552058|GOLPH2|GRASP55|GRS2|p59	golgi reassembly stacking protein 2	protein-coding	0.13	0.613861
Merged-chr4-152273982-1	chr4	152273932	152274032	+	3.6	cIP2vsInput	promoter-TSS (NM_178406)	promoter-TSS (NM_178406)	-380	NM_178406	100129	Mm.23235	NM_178406	ENSMUSG00000042804	Gpr153	1110065N12Rik|AI449320|PGR1	G protein-coupled receptor 153	protein-coding	0.1	0.742574
Merged-chr1-185394119-1	chr1	185394069	185394169	+	3.6	cIP2vsInput	"intron (NM_029735, intron 12 of 31)"	"intron (NM_029735, intron 12 of 31)"	31024	NM_029735	107508	Mm.490980	NM_029735	ENSMUSG00000026615	Eprs	2410081F06Rik|3010002K18Rik|C79379|Qprs	glutamyl-prolyl-tRNA synthetase	protein-coding	0	0.326733
Merged-chr17-80480526-1	chr17	80480476	80480576	+	3.6	cIP2vsInput	promoter-TSS (NM_009231)	promoter-TSS (NM_009231)	-73	NM_009231	20662	Mm.360004	NM_009231	ENSMUSG00000024241	Sos1	4430401P03Rik|9630010N06|AI449023	son of sevenless homolog 1 (Drosophila)	protein-coding	0.13	0.782178
Merged-chr5-114813778-1	chr5	114813728	114813828	+	3.6	cIP2vsInput	"intron (NR_027818, intron 1 of 1)"	CpG	198	NR_027818	66236	Mm.268546	NR_027817	ENSMUSG00000072694	1500011B03Rik	AI415201|AV141149|AW556386	RIKEN cDNA 1500011B03 gene	miscRNA	0.12	0.722772
Merged-chr10-75517922-2	chr10	75517835	75518010	+	3.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175133)	promoter-TSS (NM_175133)	-120	NM_026095	67332	Mm.392843	NM_026095	ENSMUSG00000020180	Snrpd3	1700043E15Rik|2310009E13Rik|AW046420|SMD3	small nuclear ribonucleoprotein D3	protein-coding	0.04	0.602273
Merged-chr14-20674077-1	chr14	20674027	20674127	+	3.6	cIP2vsInput	promoter-TSS (NM_172596)	promoter-TSS (NM_172596)	-244	NM_172596	218811	Mm.173119	NM_001168273	ENSMUSG00000039367	Sec24c	2610204K03Rik|mKIAA0079	"Sec24 related gene family, member C (S. cerevisiae)"	protein-coding	0.01	0.346535
Merged-chr3-144570260-1	chr3	144570210	144570310	+	3.6	cIP2vsInput	promoter-TSS (NM_053102)	promoter-TSS (NM_053102)	-44	NM_011828	23908	Mm.12863	NM_011828	ENSMUSG00000040151	Hs2st1	AW214369|Hs2st|mKIAA0448	heparan sulfate 2-O-sulfotransferase 1	protein-coding	0.11	0.762376
Merged-chr2-134786134-1	chr2	134786084	134786184	+	3.6	cIP2vsInput	promoter-TSS (NM_001145830)	promoter-TSS (NM_001145830)	-30	NM_019677	18795	Mm.330607	NM_001145830	ENSMUSG00000051177	Plcb1	3110043I21Rik|AI132408|Plcb|mKIAA0581	"phospholipase C, beta 1"	protein-coding	0.11	0.752475
Merged-chr2-80638727-2	chr2	80638659	80638795	+	3.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027091)	promoter-TSS (NM_027091)	-85	NM_027091	69482	Mm.29200	NM_001190179		Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding	0.036765	0.50365
Merged-chr1-37865131-2	chr1	37865074	37865189	+	3.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_207228)	promoter-TSS (NM_207228)	-52	NM_207228	211484	Mm.332756	NM_207228	ENSMUSG00000060771	Tsga10	4933432N21Rik|AI843383|Gm217|Mtsga10	testis specific 10	protein-coding	0.208696	0.741379
Merged-chr9-57130744-1	chr9	57130694	57130794	+	3.6	cIP2vsInput	promoter-TSS (NM_028636)	promoter-TSS (NM_028636)	-33	NM_028636	73744	Mm.474792	NM_028636	ENSMUSG00000032295	Man2c1	1110025H24Rik	"mannosidase, alpha, class 2C, member 1"	protein-coding	0.08	0.623762
Merged-chr8-60950979-1	chr8	60950929	60951029	+	3.6	cIP1vsInput	"intron (NM_007711, intron 1 of 11)"	"intron (NM_007711, intron 1 of 11)"	3820	NM_173876	12725	Mm.259751	NM_007711	ENSMUSG00000004319	Clcn3	Clc3	chloride channel 3	protein-coding	0	0.316832
Merged-chr15-81926536-1	chr15	81926486	81926586	+	3.6	cIP1vsInput	promoter-TSS (NM_030229)	promoter-TSS (NM_030229)	-323	NM_030229	78929	Mm.215115	NM_030229	ENSMUSG00000022476	Polr3h	5031409G22Rik|RPC8	polymerase (RNA) III (DNA directed) polypeptide H	protein-coding	0.03	0.445545
Merged-chr14-21988483-1	chr14	21988433	21988533	+	3.6	cIP1vsInput	"intron (NM_145459, intron 1 of 2)"	CpG-4314	1118	NM_145459	218820	Mm.292401	NM_145459	ENSMUSG00000039081	Zfp503	AI181838|B830002A16Rik|Nolz-1|Nolz1|Znf503	zinc finger protein 503	protein-coding	0.13	0.712871
Merged-chr2-32912628-1	chr2	32912578	32912678	+	3.6	cIP2vsInput	"intron (NM_146119, intron 5 of 13)"	"intron (NM_146119, intron 5 of 13)"	36494	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	"family with sequence similarity 129, member B"	protein-coding	0.05	0.524752
Merged-chr5-38039224-1	chr5	38039174	38039274	+	3.6	cIP2vsInput	promoter-TSS (NM_026959)	promoter-TSS (NM_026959)	-11	NM_026959	71116	Mm.18959	NM_026959	ENSMUSG00000029125	Stx18	1810035L21Rik|4933425D03Rik|AU041562	syntaxin 18	protein-coding	0.1	0.594059
Merged-chr18-80256140-1	chr18	80256090	80256190	+	3.6	cIP2vsInput	promoter-TSS (NM_001164422)	promoter-TSS (NM_001164422)	-86	NM_001164424	66943	Mm.29247	NM_001164420	ENSMUSG00000034006	Pqlc1	2310009N05Rik|4933425L21Rik|5730564E11Rik|C78974	PQ loop repeat containing 1	protein-coding	0.13	0.663366
Merged-chr3-65658914-1	chr3	65658864	65658964	+	3.6	cIP2vsInput	Intergenic	CpG	-7314	NM_001037923	624866	Mm.405524	NM_001166659	ENSMUSG00000074579	Lekr1	EG546798|EG624866|Gm6534	"leucine, glutamate and lysine rich 1"	protein-coding	0.1	0.752475
Merged-chr19-38819305-1	chr19	38819255	38819355	+	3.6	cIP2vsInput	promoter-TSS (NM_021315)	promoter-TSS (NM_021315)	-68	NM_021315	57753	Mm.86482	NM_021315	ENSMUSG00000024999	Noc3l	AF233884|Fad24	nucleolar complex associated 3 homolog (S. cerevisiae)	protein-coding	0.09	0.683168
Merged-chr13-21531145-1	chr13	21531095	21531195	+	3.6	cIP2vsInput	promoter-TSS (NM_001251834)	promoter-TSS (NM_001251834)	-31	NM_001251833	93681	Mm.489857	NM_001251833	ENSMUSG00000063894	Zkscan8	2510038J07Rik|D430019P06Rik|LD5-1|Zfp192	zinc finger with KRAB and SCAN domains 8	protein-coding	0.04	0.60396
Merged-chr18-33464040-1	chr18	33463990	33464090	+	3.6	cIP2vsInput	promoter-TSS (NR_045415)	promoter-TSS (NR_045415)	-11	NM_001109988	27528	Mm.407415	NM_001109988	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding	0.13	0.722772
Merged-chr18-55663932-1	chr18	55663882	55663982	+	3.6	cIP2vsInput	Intergenic	Intergenic	-673752	NM_175751	269023	Mm.471753	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding	0.02	0.50495
Merged-chr15-40656812-1	chr15	40656762	40656862	+	3.6	cIP1vsInput	"intron (NM_011766, intron 1 of 7)"	"intron (NM_011766, intron 1 of 7)"	1770	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	"zinc finger protein, multitype 2"	protein-coding	0	0.336634
Merged-chr12-21373732-1	chr12	21373682	21373782	+	3.6	cIP1vsInput	promoter-TSS (NR_102380)	promoter-TSS (NR_102380)	-100	NM_009615	11491	Mm.27681	NM_001277266	ENSMUSG00000052593	Adam17	CD156b|Tace	a disintegrin and metallopeptidase domain 17	protein-coding	0.1	0.722772
Merged-chr4-117190078-2	chr4	117190003	117190154	+	3.6	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-7454	NM_134471	73804	Mm.247651	NM_134471	ENSMUSG00000028678	Kif2c	4930402F02Rik|ESTM5|Knsl6|MCAK|X83316	kinesin family member 2C	protein-coding	0.006623	0.361842
Merged-chr9-106026285-2	chr9	106026233	106026337	+	3.6	cIP1vsInput|cIP2vsInput	"intron (NM_026763, intron 24 of 37)"	"intron (NM_026763, intron 24 of 37)"	-65642	NM_001167923	665033	Mm.39826	NM_001167923	ENSMUSG00000091345	Col6a5	Col29a1|EG665033|Gm7455	"collagen, type VI, alpha 5"	protein-coding	0	0.342857
Merged-chr19-45998557-2	chr19	45998493	45998622	+	3.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_198296)	promoter-TSS (NM_198296)	-69	NM_198296	71617	Mm.210949	NM_198296	ENSMUSG00000039901	9130011E15Rik	AI431055|AW050122	RIKEN cDNA 9130011E15 gene	protein-coding	0.108527	0.638462
Merged-chr4-136053057-1	chr4	136053007	136053107	+	3.6	cIP2vsInput	"intron (NM_025919, intron 1 of 5)"	CpG	314	NM_025919	67025	Mm.276856	NM_025919		Rpl11	2010203J19Rik	ribosomal protein L11	protein-coding	0.1	0.673267
Merged-chr17-5440280-2	chr17	5440228	5440333	+	3.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027457)	promoter-TSS (NM_027457)	-20	NM_027457	70544	Mm.46654	NM_027457	ENSMUSG00000004945	Tmem242	1110008A10Rik|2310046K16Rik|5730437N04Rik	transmembrane protein 242	protein-coding	0.047619	0.556604
Merged-chr5-72435342-2	chr5	72435277	72435407	+	3.55	cIP1vsInput|cIP2vsInput	"exon (NM_016869, exon 4 of 22)"	"exon (NM_016869, exon 4 of 22)"	68866	NM_016869	53419	Mm.332425	NM_001122756	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding	0.030769	0.48855
Merged-chr5-113133276-2	chr5	113133201	113133351	+	3.55	cIP1vsInput|cIP2vsInput	"intron (NM_172884, intron 1 of 7)"	"intron (NM_172884, intron 1 of 7)"	30037	NM_172884	243219	Mm.160131	NM_172884	ENSMUSG00000051339	2900026A02Rik	8430408O14Rik|A530094D01|AW539426|Gm449|Kiaa1671|mKIAA1671	RIKEN cDNA 2900026A02 gene	protein-coding	0.04	0.576159
Merged-chr15-89429999-2	chr15	89429942	89430057	+	3.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_004843)	promoter-TSS (NR_004843)	-72	NR_037153	12651	Mm.485045	NM_007692	ENSMUSG00000022617	Chkb	Chetk|Chkl|Ck|Ck/Ek|Ck/Ek-beta|Ckb|Ckekb|Ek	choline kinase beta	protein-coding	0.069565	0.568966
Merged-chr6-51858039-2	chr6	51857968	51858111	+	3.55	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	154510	NM_018773	54353	Mm.392558	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding	0.041958	0.555556
Merged-chr16-50542755-2	chr16	50542691	50542819	+	3.55	cIP1vsInput|cIP2vsInput	"intron (NR_040379, intron 4 of 5)"	"intron (NR_040379, intron 4 of 5)"	14253	NR_040379	619312	Mm.439483	NR_040379		G730013B05Rik	-	RIKEN cDNA G730013B05 gene	miscRNA	0.007812	0.496124
Merged-chr8-95539890-2	chr8	95539817	95539964	+	3.55	cIP1vsInput|cIP2vsInput	"intron (NM_172914, intron 3 of 8)"	MER44B|DNA|TcMar-Tigger	5790	NM_172914	244608	Mm.248902	NM_172914	ENSMUSG00000036598	Ccdc113	4933409I22|BC060957	coiled-coil domain containing 113	protein-coding	0.027211	0.412162
Merged-chr7-12478194-2	chr7	12478134	12478254	+	3.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026112)	promoter-TSS (NM_026112)	-111	NM_001039951	67370	Mm.98929	NM_001039951	ENSMUSG00000030386	Zfp606	2410022M24Rik|AW494727	zinc finger protein 606	protein-coding	0.05	0.53719
Merged-chr9-25481501-2	chr9	25481429	25481573	+	3.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026189)	promoter-TSS (NM_026189)	-96	NM_026189	67484	Mm.112977	NM_026189	ENSMUSG00000036611	Eepd1	2310005P05Rik|AI481005	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding	0.118056	0.765517
Merged-chr11-13032640-2	chr11	13032569	13032711	+	3.55	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-567680	NM_172496	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	4732460E13|C530045F18Rik|mKIAA0633	cordon-bleu	protein-coding	0.014085	0.405594
Merged-chr19-40589120-2	chr19	40589044	40589197	+	3.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019698)	promoter-TSS (NM_019698)	-657	NM_153554	56454	Mm.233117	NM_019698	ENSMUSG00000025007	Aldh18a1	2810433K04Rik|AI429789|Pycs	"aldehyde dehydrogenase 18 family, member A1"	protein-coding	0.013072	0.512987
Merged-chr9-98979909-2	chr9	98979828	98979990	+	3.55	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-6464	NM_001122851	23873	Mm.74605	NM_001122851	ENSMUSG00000032463	Faim	-	Fas apoptotic inhibitory molecule	protein-coding	0.055556	0.552147
Merged-chr17-35135175-2	chr17	35135080	35135271	+	3.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001252469)	promoter-TSS (NM_001252469)	-3	NM_001252468	224727	Mm.203962	NM_001252468	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding	0.141361	0.703125
Merged-chr9-108578841-2	chr9	108578783	108578900	+	3.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_031392)	promoter-TSS (NM_031392)	-171	NM_031392	83669	Mm.458081	NM_031392	ENSMUSG00000066357	Wdr6	mWDR6	WD repeat domain 6	protein-coding	0.051282	0.661017
Merged-chrX-169972632-2	chrX	169972582	169972682	+	3.55	cIP1vsInput|cIP2vsInput	"intron (NM_183151, intron 3 of 9)"	"intron (NM_183151, intron 3 of 9)"	6285	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	miscRNA	0	0.326733
Merged-chr14-63544026-2	chr14	63543957	63544095	+	3.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_177594)	promoter-TSS (NM_177594)	-73	NM_177594	210376	Mm.458343	NM_177594	ENSMUSG00000035078	Mtmr9	9430075G12Rik|AA516943|AF073881|LIP-STYX|MTMR8|mMTMH3	myotubularin related protein 9	protein-coding	0.057971	0.539568
Merged-chr2-144600002-2	chr2	144599915	144600090	+	3.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025314)	promoter-TSS (NM_025314)	49	NM_025314	66044	Mm.28109	NM_025314	ENSMUSG00000027430	Dtd1	0610006H08Rik|Hars2	D-tyrosyl-tRNA deacylase 1	protein-coding	0.108571	0.659091
Merged-chr8-83863087-2	chr8	83863013	83863161	+	3.55	cIP1vsInput|cIP2vsInput	Intergenic	MIRb|SINE|MIR	-37011	NM_181039	330814	Mm.260733	NM_181039	ENSMUSG00000013033	Lphn1	2900070I05Rik|AI182398|CLIBA|Lec2|mKIAA0821	latrophilin 1	protein-coding	0.02027	0.550336
Merged-chr18-8970661-2	chr18	8970588	8970734	+	3.55	cIP1vsInput|cIP2vsInput	Intergenic	L1MC5|LINE|L1	-242195	NM_008058	14370	Mm.184289	NM_008058	ENSMUSG00000036904	Fzd8	Fz8	frizzled homolog 8 (Drosophila)	protein-coding	0.013699	0.380952
Merged-chr4-129189828-2	chr4	129189776	129189881	+	3.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_134151)	promoter-TSS (NM_134151)	33	NM_134151	107271	Mm.410673	NM_134151	ENSMUSG00000028811	Yars	AL024047|AU018965	tyrosyl-tRNA synthetase	protein-coding	0.047619	0.556604
Merged-chr10-120876363-2	chr10	120876313	120876414	+	3.55	cIP1vsInput|cIP2vsInput	"intron (NM_177092, intron 1 of 6)"	MLT1I|LTR|ERVL-MaLR	18734	NR_038023	100504616	Mm.451174	NR_038023	ENSMUSG00000087480	Gm15910	OTTMUSG00000027725	predicted gene 15910	miscRNA	0.039604	0.568627
Merged-chr16-92466379-2	chr16	92466320	92466439	+	3.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081549)	promoter-TSS (NM_001081549)	-233	NM_001081549	54720	Mm.265744	NM_001081549	ENSMUSG00000022951	Rcan1	2410048A02Rik|AA408855|AI429645|AL024459|AV028423|Adapt78|CALP1L|CSP1|DSC1|Dscr1|MCIP1|RCN1	regulator of calcineurin 1	protein-coding	0.042017	0.55
Merged-chr11-59839432-2	chr11	59839370	59839494	+	3.55	cIP1vsInput|cIP2vsInput	"intron (NM_011991, intron 1 of 11)"	CpG	335	NM_011991	26572	Mm.40	NM_011991	ENSMUSG00000019373	Cops3	Csn3|Sgn3	"COP9 (constitutive photomorphogenic) homolog, subunit 3 (Arabidopsis thaliana)"	protein-coding	0.072581	0.728
Merged-chr4-48540034-2	chr4	48539975	48540093	+	3.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028137)	promoter-TSS (NM_028137)	-47	NM_001145924	66665	Mm.140749	NM_001145924	ENSMUSG00000039693	Msantd3	2410046L14Rik|2810429P03Rik|5730528L13Rik|Mysantd3	Myb/SANT-like DNA-binding domain containing 3	protein-coding	0.059322	0.621849
Merged-chr2-30416031-2	chr2	30415963	30416100	+	3.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007760)	promoter-TSS (NM_007760)	-19	NM_138748	110854	Mm.275393	NM_138748	ENSMUSG00000039515	Ppp2r4	2610042B21Rik|C77440|N28142|PR53	"protein phosphatase 2A, regulatory subunit B (PR 53)"	protein-coding	0.138686	0.717391
Merged-chr2-27540205-2	chr2	27540151	27540259	+	3.55	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	25058	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding	0.092593	0.587156
Merged-chr19-47067526-2	chr19	47067470	47067582	+	3.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_177342)	promoter-TSS (NM_177342)	-222	NM_177342	226182	Mm.301522	NM_177342	ENSMUSG00000025049	Taf5	6330528C20Rik|AV117817	"TAF5 RNA polymerase II, TATA box binding protein (TBP)-associated factor"	protein-coding	0.044643	0.362832
Merged-chr4-33154681-2	chr4	33154631	33154732	+	3.55	cIP1vsInput|cIP2vsInput	"intron (NM_008075, intron 5 of 9)"	(CATATA)n|Simple_repeat|Simple_repeat	22125	NM_008075	14408	Mm.14116	NM_008075	ENSMUSG00000028280	Gabrr1	GABA-C	"gamma-aminobutyric acid (GABA) C receptor, subunit rho 1"	protein-coding	0.009901	0.27451
Merged-chr12-4917319-2	chr12	4917253	4917386	+	3.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001099628)	promoter-TSS (NM_001099628)	-34	NM_001099628	320817	Mm.210966	NM_001099628		Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	"ATPase family, AAA domain containing 2B"	protein-coding	0.135338	0.738806
Merged-chr2-164867354-2	chr2	164867295	164867413	+	3.55	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-9646	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding	0.025424	0.546218
Merged-chr7-130669384-1	chr7	130669334	130669434	+	3.5	cIP2vsInput	"intron (NM_001004468, intron 4 of 21)"	"intron (NM_001004468, intron 4 of 21)"	-23172	NM_021314	57752	Mm.86322	NM_001004468	ENSMUSG00000030852	Tacc2	mKIAA4180	"transforming, acidic coiled-coil containing protein 2"	protein-coding	0.02	0.465347
Merged-chr3-95666281-1	chr3	95666231	95666331	+	3.5	cIP1vsInput	Intergenic	Intergenic	7560	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding	0.02	0.455446
Merged-chr10-94249555-1	chr10	94249505	94249605	+	3.5	cIP2vsInput	Intergenic	Intergenic	49148	NR_033209	215472	Mm.255656	NM_174999	ENSMUSG00000053420	Gm4792	E130012K09|EG215472	predicted gene 4792	miscRNA	0	0.386139
Merged-chr2-29787747-1	chr2	29787697	29787797	+	3.5	cIP2vsInput	promoter-TSS (NM_145520)	promoter-TSS (NM_145520)	-76	NM_145520	227682	Mm.245739	NM_145520		Trub2	G430055L02Rik	TruB pseudouridine (psi) synthase homolog 2 (E. coli)	protein-coding	0.04	0.50495
Merged-chr18-34759679-1	chr18	34759629	34759729	+	3.5	cIP2vsInput	"intron (NM_175104, intron 1 of 4)"	CpG	773	NM_175104	66306	Mm.29424	NM_175104	ENSMUSG00000034300	Fam53c	2810012G03Rik	"family with sequence similarity 53, member C"	protein-coding	0.12	0.762376
Merged-chr16-94209744-1	chr16	94209694	94209794	+	3.5	cIP1vsInput	"intron (NM_139145, intron 5 of 9)"	(TG)n|Simple_repeat|Simple_repeat	78112	NM_139145	110948	Mm.30921	NM_139145	ENSMUSG00000040820	Hlcs	410I21.SP6|D16Jhu34	holocarboxylase synthetase (biotin- [propriony-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)	protein-coding	0.02	0.544554
Merged-chr15-89075921-2	chr15	89075851	89075991	+	3.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_040417)	promoter-TSS (NR_040417)	-67	NR_040417	69120	Mm.276391	NR_040417	ENSMUSG00000087331	1810021B22Rik	-	RIKEN cDNA 1810021B22 gene	miscRNA	0.121429	0.765957
Merged-chr1-131053509-2	chr1	131053421	131053597	+	3.5	cIP1vsInput|cIP2vsInput	TTS (NM_008551)	TTS (NM_008551)	33664	NM_010548	16153	Mm.874	NM_010548	ENSMUSG00000016529	Il10	CSIF|Il-10	interleukin 10	protein-coding	0.028409	0.536723
Merged-chr6-91473647-1	chr6	91473597	91473697	+	3.5	cIP2vsInput	promoter-TSS (NM_028766)	promoter-TSS (NM_028766)	-104	NM_028766	74122	Mm.38801	NM_028766	ENSMUSG00000030095	Tmem43	1200015A22Rik|LUMA	transmembrane protein 43	protein-coding	0.08	0.50495
Merged-chr7-133124250-1	chr7	133124200	133124300	+	3.5	cIP2vsInput	promoter-TSS (NM_009980)	promoter-TSS (NM_009980)	-767	NM_009980	13017	Mm.389984	NM_001170744	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding	0.11	0.722772
Merged-chr3-65659023-1	chr3	65658973	65659073	+	3.5	cIP1vsInput	Intergenic	CpG	-7205	NM_001037923	624866	Mm.405524	NM_001166659	ENSMUSG00000074579	Lekr1	EG546798|EG624866|Gm6534	"leucine, glutamate and lysine rich 1"	protein-coding	0.11	0.633663
Merged-chr9-41951312-1	chr9	41951262	41951362	+	3.5	cIP2vsInput	Intergenic	Intergenic	172977	NM_011436	20660	Mm.121920	NM_011436		Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	"sortilin-related receptor, LDLR class A repeats-containing"	protein-coding	0.09	0.70297
Merged-chr5-135394626-1	chr5	135394576	135394676	+	3.5	cIP2vsInput	promoter-TSS (NM_148932)	promoter-TSS (NM_148932)	-80	NM_148932	107939	Mm.28399	NM_148932	ENSMUSG00000053293	Pom121	2610027A18Rik|C80273|mKIAA0618	nuclear pore membrane protein 121	protein-coding	0.15	0.643564
Merged-chrY-90724539-2	chrY	90724488	90724590	+	3.5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-60903	NM_133362	170942	Mm.391385	XM_003946384	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding	0.019608	0.300971
Merged-chr4-145539255-1	chr4	145539205	145539305	+	3.5	cIP2vsInput	Intergenic	RMER15|LTR|ERVL	75045	NR_002888	545700	Mm.389595	NR_002888	ENSMUSG00000052912	Smarca5-ps	9230115A19Rik|OTTMUSG00000011029	"SWI/SNF related, matrix associated, actin depenent ragulator of chromatin, subfamily a, member 5, pseudogene"	pseudo	0	0.336634
Merged-chr2-160367214-1	chr2	160367164	160367264	+	3.5	cIP2vsInput	promoter-TSS (NM_010658)	promoter-TSS (NM_010658)	-149	NM_010658	16658	Mm.330745	NM_010658	ENSMUSG00000074622	Mafb	Kreisler|Krml|Krml1|kr	"v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (avian)"	protein-coding	0.12	0.772277
Merged-chr7-39205151-1	chr7	39205101	39205201	+	3.5	cIP1vsInput	Intergenic	Intergenic	208009	NM_177890	330513	Mm.433234	NM_177890	ENSMUSG00000053742	Gm5114	4921507A12|EG330513	predicted gene 5114	protein-coding	0.01	0.534653
Merged-chr1-184033873-1	chr1	184033823	184033923	+	3.5	cIP2vsInput	promoter-TSS (NM_022019)	promoter-TSS (NM_022019)	125	NM_028516	73363	Mm.50115	NM_028516	ENSMUSG00000044854	1700056E22Rik	-	RIKEN cDNA 1700056E22 gene	protein-coding	0.13	0.782178
Merged-chr1-23922391-1	chr1	23922341	23922441	+	3.5	cIP2vsInput	promoter-TSS (NM_028534)	promoter-TSS (NM_028534)	-102	NM_028534	98366	Mm.329963	NM_028534	ENSMUSG00000026155	Smap1	1700056O10Rik|4921514B13Rik|4921525H11Rik|AI462175	stromal membrane-associated protein 1	protein-coding	0.19	0.821782
Merged-chr9-111118008-1	chr9	111117958	111118058	+	3.5	cIP2vsInput	promoter-TSS (NM_027742)	promoter-TSS (NM_027742)	-103	NM_027742	71268	Mm.302287	NM_001164838	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding	0.15	0.732673
Merged-chr11-106613081-1	chr11	106613031	106613131	+	3.5	cIP2vsInput	promoter-TSS (NM_198292)	promoter-TSS (NM_198292)	-151	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding	0.12	0.762376
Merged-chr3-88510304-1	chr3	88510254	88510354	+	3.5	cIP2vsInput	Intergenic	Intergenic	-6972	NM_001002011	16905	Mm.471227	NM_001002011	ENSMUSG00000028063	Lmna	Dhe	lamin A	protein-coding	0.05	0.584158
Merged-chr4-147094372-1	chr4	147094322	147094422	+	3.5	cIP1vsInput	Intergenic	L1VL4|LINE|L1	-25936	NR_045446	71270	Mm.460830	NR_045446	ENSMUSG00000093617	4933438K21Rik	-	RIKEN cDNA 4933438K21 gene	miscRNA	0.01	0.376238
Merged-chr1-185454578-1	chr1	185454528	185454628	+	3.5	cIP2vsInput	promoter-TSS (NM_001033286)	promoter-TSS (NM_001033286)	-270	NM_001033286	226781	Mm.227117	NM_001033286	ENSMUSG00000026614	Slc30a10	E130106K10Rik|Gm212	"solute carrier family 30, member 10"	protein-coding	0.04	0.574257
Merged-chr18-12236527-1	chr18	12236477	12236577	+	3.5	cIP2vsInput	promoter-TSS (NM_008720)	promoter-TSS (NM_008720)	-141	NM_008720	18145	Mm.3484	NM_008720	ENSMUSG00000024413	Npc1	A430089E03Rik|C85354|D18Ertd139e|D18Ertd723e|lcsd|nmf164|spm	Niemann Pick type C1	protein-coding	0.11	0.693069
Merged-chr3-63964694-2	chr3	63964628	63964761	+	3.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001272035)	promoter-TSS (NM_001272035)	39	NM_001272035	11416	Mm.135619	NM_001272035	ENSMUSG00000027822	Slc33a1	AI315656|AI788741|Acatn|D630022N01Rik	"solute carrier family 33 (acetyl-CoA transporter), member 1"	protein-coding	0.112782	0.589552
Merged-chr6-47877713-1	chr6	47877663	47877763	+	3.5	cIP2vsInput	"exon (NM_146175, exon 1 of 8)"	"exon (NM_146175, exon 1 of 8)"	158	NM_146175	101095	Mm.440186	NM_146175	ENSMUSG00000025821	Zfp282	AI449432|C81429|E430019K09Rik|HUB1	zinc finger protein 282	protein-coding	0.03	0.653465
Merged-chr2-91649978-1	chr2	91649928	91650028	+	3.5	cIP2vsInput	promoter-TSS (NM_001145902)	promoter-TSS (NM_001145902)	-140	NR_027372	228359	Mm.22413	NM_001145902	ENSMUSG00000027247	Arhgap1	B230365D05Rik|C76222|Cdc42GAP|RP23-12H6.2|p50rhoGAP	Rho GTPase activating protein 1	protein-coding	0.08	0.544554
Merged-chr14-83149083-1	chr14	83149033	83149133	+	3.5	cIP1vsInput	Intergenic	Intergenic	-1294480	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0	0.277228
Merged-chr6-120112469-1	chr6	120112419	120112519	+	3.5	cIP2vsInput	"intron (NM_016718, intron 1 of 3)"	G-rich|Low_complexity|Low_complexity	19089	NM_016718	29862	Mm.103668	NM_016718	ENSMUSG00000041377	Ninj2	-	ninjurin 2	protein-coding	0.08	0.742574
Merged-chr7-44554108-2	chr7	44554043	44554174	+	3.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009473)	promoter-TSS (NM_009473)	-185	NM_009473	22260	Mm.968	NM_009473	ENSMUSG00000060601	Nr1h2	AI194859|LXR|LXRB|LXRbeta|NER1|OR-1|RIP15|UR|Unr|Unr2	"nuclear receptor subfamily 1, group H, member 2"	protein-coding	0.038168	0.401515
Merged-chr8-84969559-1	chr8	84969509	84969609	+	3.5	cIP2vsInput	promoter-TSS (NM_011563)	promoter-TSS (NM_011563)	-89	NM_011563	21672	Mm.393373	NM_011563		Prdx2	AL022839|Band-8|NkefB|PRP|PrxII|TDX1|TPx|TPx-B|TR|TSA|Tdpx1|Torin	peroxiredoxin 2	protein-coding	0.1	0.70297
Merged-chr6-133105719-1	chr6	133105669	133105769	+	3.5	cIP2vsInput	"3' UTR (NM_001163445, exon 1 of 1)"	"3' UTR (NM_001163445, exon 1 of 1)"	480	NR_073368	381820	Mm.291762	NM_001163445	ENSMUSG00000072704	2700089E24Rik	AI662692	RIKEN cDNA 2700089E24 gene	protein-coding	0.09	0.623762
Merged-chr19-40588486-1	chr19	40588436	40588536	+	3.5	cIP1vsInput	promoter-TSS (NM_019698)	promoter-TSS (NM_019698)	-23	NM_153554	56454	Mm.233117	NM_019698	ENSMUSG00000025007	Aldh18a1	2810433K04Rik|AI429789|Pycs	"aldehyde dehydrogenase 18 family, member A1"	protein-coding	0.14	0.712871
Merged-chrY-6735446-1	chrY	6735396	6735496	+	3.5	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	432331	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.29703
Merged-chr5-15681747-1	chr5	15681697	15681797	+	3.5	cIP1vsInput	"intron (NR_001585, intron 1 of 4)"	"intron (NR_001585, intron 1 of 4)"	1037	NR_001585	75858	Mm.359463	NR_001585	ENSMUSG00000089871	Speer7-ps1	4930568L21Rik|SPEER-7|Speer7-ps	"spermatogenesis associated glutamate (E)-rich protein 7, pseudogene 1"	pseudo	0	0.366337
Merged-chr5-123311621-1	chr5	123311571	123311671	+	3.5	cIP2vsInput	Intergenic	L1MB7|LINE|L1	-32827	NM_029850	77045	Mm.151960	NM_029850	ENSMUSG00000029438	Bcl7a	4432415N06Rik|AI448316	B cell CLL/lymphoma 7A	protein-coding	0.03	0.405941
Merged-chr1-165237034-1	chr1	165236984	165237084	+	3.5	cIP2vsInput	promoter-TSS (NM_145513)	promoter-TSS (NM_145513)	-76	NM_145513	226591	Mm.21520	NM_145513		Tiprl	1810011K17Rik	"TIP41, TOR signalling pathway regulator-like (S. cerevisiae)"	protein-coding	0.09	0.633663
Merged-chr9-96119174-2	chr9	96119101	96119247	+	3.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_177352)	promoter-TSS (NM_177352)	-255	NM_177352	235533	Mm.213651	NM_177352		Gk5	AV095337|C330018K18Rik|G630067D24Rik	glycerol kinase 5 (putative)	protein-coding	0.082192	0.517007
Merged-chr18-45749368-1	chr18	45749318	45749418	+	3.5	cIP1vsInput	"intron (NR_040342, intron 3 of 3)"	L1MD2|LINE|L1	189214	NM_080465	140492	Mm.458654	NM_080465		Kcnn2	KCa2.2|SK2|SKCA2|fri	"potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2"	protein-coding	0.01	0.386139
Merged-chr10-128303071-1	chr10	128303021	128303121	+	3.5	cIP2vsInput	promoter-TSS (NM_001252326)	promoter-TSS (NM_001252326)	-264	NM_133992	103135	Mm.489673	NM_001252326	ENSMUSG00000005682	Pan2	1200014O24Rik|AI047843|AW742773|Usp52|mKIAA0710	PAN2 polyA specific ribonuclease subunit homolog (S. cerevisiae)	protein-coding	0.03	0.465347
Merged-chr7-143016223-2	chr7	143016150	143016297	+	3.5	cIP1vsInput|cIP2vsInput	"intron (NM_001128081, intron 5 of 6)"	"intron (NM_001128081, intron 5 of 6)"	10564	NM_001128081	27027	Mm.28172	NM_001128080	ENSMUSG00000000244	Tspan32	AW208513|Art-1|BB235973|D7Wsu37e|Phemx|Tssc6	tetraspanin 32	protein-coding	0	0.567568
Merged-chr2-76982011-1	chr2	76981961	76982061	+	3.5	cIP2vsInput	"intron (NM_028004, intron 1 of 191)"	"intron (NM_028004, intron 1 of 191)"	536	NM_028004	22138	Mm.473358	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding	0.02	0.425743
Merged-chr15-38078840-1	chr15	38078790	38078890	+	3.5	cIP2vsInput	promoter-TSS (NM_001081359)	promoter-TSS (NM_001081359)	13	NM_001112721	70790	Mm.476840	NM_027553	ENSMUSG00000037487	Ubr5	4432411E13Rik|AW549941|C77315|D030042K14|Edd|Edd1|mKIAA0896	ubiquitin protein ligase E3 component n-recognin 5	protein-coding	0.15	0.762376
Merged-chr7-118492023-1	chr7	118491973	118492073	+	3.5	cIP2vsInput	promoter-TSS (NM_001033380)	promoter-TSS (NM_001033380)	-48	NM_001033380	319622	Mm.323386	NM_001033380	ENSMUSG00000095115	Itpripl2	C130081G24|E030018N11Rik	"inositol 1,4,5-triphosphate receptor interacting protein-like 2"	protein-coding	0.1	0.752475
Merged-chr15-98108691-2	chr15	98108605	98108777	+	3.5	cIP1vsInput|cIP2vsInput	"intron (NM_001163487, intron 1 of 22)"	"intron (NM_001163487, intron 1 of 22)"	220	NM_001163487	18642	Mm.272582	NM_001163487	ENSMUSG00000033065	Pfkm	AI131669|PFK-A|PFK-M|Pfk-4|Pfk4|Pfka|Pfkx	"phosphofructokinase, muscle"	protein-coding	0.069767	0.65896
Merged-chr2-141279274-1	chr2	141279224	141279324	+	3.5	cIP2vsInput	"intron (NM_001013802, intron 5 of 18)"	"intron (NM_001013802, intron 5 of 18)"	-607798	NM_178382	71436	Mm.426781	NM_001172160	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0.02	0.50495
Merged-chr3-130730490-2	chr3	130730417	130730564	+	3.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001199350)	promoter-TSS (NM_001199350)	-161	NM_001199350	619547	Mm.391636	NM_001199350		Rpl34-ps1	EG619547|ENSMUSG00000068396|Gm10239	"ribosomal protein L34, pseudogene 1"	protein-coding	0.142857	0.641892
Merged-chr14-64949777-1	chr14	64949727	64949827	+	3.5	cIP2vsInput	promoter-TSS (NM_001253731)	promoter-TSS (NM_001253731)	70	NM_177338	219150	Mm.344074	NM_177338	ENSMUSG00000021972	Hmbox1	AI451877|AI604847|F830020C16Rik	homeobox containing 1	protein-coding	0.02	0.594059
Merged-chr16-86719604-1	chr16	86719554	86719654	+	3.5	cIP2vsInput	Intergenic	Intergenic	-634581	NM_001159331	67768	Mm.296532	NM_001159331	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding	0.01	0.475248
Merged-chr6-72512698-1	chr6	72512648	72512748	+	3.5	cIP2vsInput	Intergenic	Intergenic	-31693	NM_007599	12332	Mm.18626	NM_001042534	ENSMUSG00000056737	Capg	gCap39|mbh1	"capping protein (actin filament), gelsolin-like"	protein-coding	0.06	0.683168
Merged-chr17-12793014-1	chr17	12792964	12793064	+	3.5	cIP1vsInput	"intron (NR_027784, intron 2 of 2)"	"intron (NR_027784, intron 2 of 2)"	-23308	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding	0.02	0.475248
Merged-chr11-71004604-1	chr11	71004554	71004654	+	3.5	cIP2vsInput	promoter-TSS (NM_178367)	promoter-TSS (NM_178367)	-172	NM_178367	216877	Mm.35399	NM_178367	ENSMUSG00000040620	Dhx33	3110057P17Rik|9430096J02Rik|Ddx33	DEAH (Asp-Glu-Ala-His) box polypeptide 33	protein-coding	0.07	0.534653
Merged-chr1-171064612-2	chr1	171064560	171064664	+	3.5	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-5209	NM_010188	14131	Mm.22119	NM_010188	ENSMUSG00000059498	Fcgr3	CD16	"Fc receptor, IgG, low affinity III"	protein-coding	0.076923	0.638095
Merged-chr6-70844106-1	chr6	70844056	70844156	+	3.5	cIP2vsInput	promoter-TSS (NM_010121)	promoter-TSS (NM_010121)	-421	NM_010121	13666	Mm.247167	NM_010121	ENSMUSG00000031668	Eif2ak3	AI427929|Pek|Perk	eukaryotic translation initiation factor 2 alpha kinase 3	protein-coding	0.03	0.534653
Merged-chr10-34019801-1	chr10	34019751	34019851	+	3.5	cIP1vsInput	promoter-TSS (NM_025614)	promoter-TSS (NM_025614)	-185	NM_025614	66521	Mm.28528	NM_025614	ENSMUSG00000019782	Rwdd1	0710001K08Rik|2610002D06Rik|2700069A07Rik|IH1	RWD domain containing 1	protein-coding	0.09	0.633663
Merged-chr15-99126568-1	chr15	99126518	99126618	+	3.5	cIP2vsInput	promoter-TSS (NM_139140)	promoter-TSS (NM_139140)	-277	NM_139140	72572	Mm.276650	NM_139140		Spats2	2700012F11Rik|59kDa|Scr59|p59	"spermatogenesis associated, serine-rich 2"	protein-coding	0.21	0.782178
Merged-chr10-50592601-1	chr10	50592551	50592651	+	3.5	cIP2vsInput	promoter-TSS (NM_198007)	promoter-TSS (NM_198007)	-68	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.12	0.673267
Merged-chr2-94178920-1	chr2	94178870	94178970	+	3.5	cIP2vsInput	Intergenic	Intergenic	-21011	NM_019657	56348		NM_019657	ENSMUSG00000027195	Hsd17b12	2610510O05Rik|AI172963|KIK-I|Kik1	hydroxysteroid (17-beta) dehydrogenase 12	protein-coding	0.07	0.475248
Merged-chr14-67715500-2	chr14	67715405	67715595	+	3.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001111028)	promoter-TSS (NM_001111028)	110	NM_001110162	108912	Mm.33831	NM_001110162	ENSMUSG00000048922	Cdca2	2610311M19Rik|AI586158	cell division cycle associated 2	protein-coding	0.1	0.65445
Merged-chr9-21320783-1	chr9	21320733	21320833	+	3.5	cIP2vsInput	promoter-TSS (NM_001199186)	promoter-TSS (NM_001199186)	64	NM_001199186	68682	Mm.148425	NM_001199186	ENSMUSG00000057193	Slc44a2	1110028E10Rik|CTL2	"solute carrier family 44, member 2"	protein-coding	0.11	0.712871
Merged-chr4-3235457-1	chr4	3235407	3235507	+	3.5	cIP2vsInput	Intergenic	Lx|LINE|L1	-50152	NM_001167535	100312471	Mm.484976	NM_001167535	ENSMUSG00000095982	Vmn1r3	Gm11778|OTTMUSG00000004181	vomeronasal 1 receptor 3	protein-coding	0.01	0.346535
Merged-chr17-34592325-1	chr17	34592275	34592375	+	3.5	cIP2vsInput	promoter-TSS (NM_017463)	promoter-TSS (NM_017463)	-146	NM_017463	18515	Mm.390957	NM_017463	ENSMUSG00000034673	Pbx2	AU043397|G17	pre B cell leukemia homeobox 2	protein-coding	0.07	0.693069
Merged-chr10-78169769-2	chr10	78169713	78169826	+	3.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_138601)	promoter-TSS (NM_138601)	-1	NM_138601	28295	Mm.268691	NM_138601	ENSMUSG00000053329	D10Jhu81e	C21orf33|ES1	"DNA segment, Chr 10, Johns Hopkins University 81 expressed"	protein-coding	0.088496	0.666667
Merged-chr12-76837435-1	chr12	76837385	76837485	+	3.5	cIP1vsInput	promoter-TSS (NM_145927)	promoter-TSS (NM_145927)	-32	NM_145927	110606	Mm.151174	NM_145927	ENSMUSG00000033373	Fntb	2010013E13Rik|AA409500	"farnesyltransferase, CAAX box, beta"	protein-coding	0.09	0.485149
Merged-chr3-128049001-1	chr3	128048951	128049051	+	3.5	cIP2vsInput	Intergenic	Intergenic	132830	NR_040552	329753	Mm.119720	NR_040552		9830132P13Rik	9830132P13	RIKEN cDNA 9830132P13 gene	miscRNA	0.01	0.465347
Merged-chr9-44344192-2	chr9	44344130	44344255	+	3.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013551)	promoter-TSS (NM_013551)	36	NM_013551	15288	Mm.247676	NM_001110251	ENSMUSG00000032126	Hmbs	PBGD|T25658|Ups|Uros1	hydroxymethylbilane synthase	protein-coding	0.08	0.666667
Merged-chrX-169970927-1	chrX	169970877	169970977	+	3.5	cIP1vsInput	"intron (NM_183151, intron 3 of 9)"	"intron (NM_183151, intron 3 of 9)"	7990	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	miscRNA	0.03	0.267327
Merged-chr19-17837690-1	chr19	17837640	17837740	+	3.5	cIP2vsInput	promoter-TSS (NM_001163144)	promoter-TSS (NM_001163144)	-58	NM_001190483	18552	Mm.3401	NM_001163144	ENSMUSG00000024713	Pcsk5	PC5|PC5/6A|PC5A|PC6|SPC6|b2b585Clo	proprotein convertase subtilisin/kexin type 5	protein-coding	0.09	0.70297
Merged-chr8-122281326-1	chr8	122281276	122281376	+	3.5	cIP2vsInput	promoter-TSS (NM_009569)	promoter-TSS (NM_009569)	-815	NM_009569	22761	Mm.390068	NM_009569	ENSMUSG00000049577	Zfpm1	FOG|Fog1	"zinc finger protein, multitype 1"	protein-coding	0.06	0.712871
Merged-chr13-90012465-1	chr13	90012415	90012515	+	3.5	cIP2vsInput	"intron (NM_028012, intron 3 of 7)"	"intron (NM_028012, intron 3 of 7)"	77143	NM_028012	108138	Mm.37531	XM_003945936	ENSMUSG00000021615	Xrcc4	2310057B22Rik|AW413319|AW545101	X-ray repair complementing defective repair in Chinese hamster cells 4	protein-coding	0.03	0.455446
Merged-chr1-181204837-1	chr1	181204787	181204887	+	3.5	cIP1vsInput	"intron (NM_145514, intron 3 of 13)"	"intron (NM_145514, intron 3 of 13)"	7141	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding	0.01	0.326733
Merged-chr16-11909213-2	chr16	11909135	11909291	+	3.5	cIP1vsInput|cIP2vsInput	"intron (NR_033509, intron 2 of 2)"	CpG	210	NM_146067	223978	Mm.442728	NM_146067	ENSMUSG00000065979	Cpped1	C530044N13Rik	calcineurin-like phosphoesterase domain containing 1	protein-coding	0.076923	0.643312
Merged-chr11-23771071-1	chr11	23771021	23771121	+	3.5	cIP2vsInput	promoter-TSS (NM_009044)	promoter-TSS (NM_009044)	-101	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding	0.15	0.792079
Merged-chr12-46654001-1	chr12	46653951	46654051	+	3.5	cIP2vsInput	Intergenic	Lx6|LINE|L1	164774	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding	0.01	0.316832
Merged-chr11-83473304-1	chr11	83473254	83473354	+	3.5	cIP2vsInput	"intron (NM_027427, intron 1 of 15)"	CpG	196	NM_027427	70439	Mm.181050	NM_027427	ENSMUSG00000020680	Taf15	2610111C21Rik|68kDa|TAFII68|Taf2n	"TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor"	protein-coding	0.1	0.772277
Merged-chr18-34244277-1	chr18	34244227	34244327	+	3.5	cIP2vsInput	"intron (NM_007462, intron 1 of 15)"	LTR10_RN|LTR|ERVK	-22505	NR_040534	633395	Mm.414290	NR_040534	ENSMUSG00000073607	Gm10548	ENSMUSG00000073607	ribosomal protein L29 pseudogene	pseudo	0.03	0.514851
Merged-chr5-124862568-2	chr5	124862499	124862638	+	3.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	-137	NM_001081750	269704	Mm.138617	NM_001081750	ENSMUSG00000079215	Zfp664	AW060232|D930038J03Rik|ZFOC1|Znf664	zinc finger protein 664	protein-coding	0.107914	0.728571
Merged-chr4-155831517-1	chr4	155831467	155831567	+	3.5	cIP2vsInput	"5' UTR (NM_025338, exon 1 of 4)"	"5' UTR (NM_025338, exon 1 of 4)"	248	NM_025338	66077	Mm.28999	NM_025338	ENSMUSG00000065990	Aurkaip1	0610033H09Rik|Aip|Akip	aurora kinase A interacting protein 1	protein-coding	0.09	0.623762
Merged-chr2-7089045-1	chr2	7088995	7089095	+	3.5	cIP2vsInput	"intron (NM_001110232, intron 2 of 15)"	"intron (NM_001110232, intron 2 of 15)"	-7743	NM_001160292	14007	Mm.398543	NM_183219	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	"CUGBP, Elav-like family member 2"	protein-coding	0.02	0.435644
Merged-chr5-145191584-1	chr5	145191534	145191634	+	3.5	cIP2vsInput	promoter-TSS (NM_020582)	promoter-TSS (NM_020582)	8	NM_020582	57423	Mm.133551	NM_020582	ENSMUSG00000038690	Atp5j2	1110019H14Rik	"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F2"	protein-coding	0.07	0.643564
Merged-chr3-131976158-1	chr3	131976108	131976208	+	3.5	cIP1vsInput	Intergenic	Intergenic	-109134	NM_020265	56811	Mm.103593	NM_020265	ENSMUSG00000028031	Dkk2	-	dickkopf homolog 2 (Xenopus laevis)	protein-coding	0.02	0.485149
Merged-chr5-30587967-1	chr5	30587917	30588017	+	3.5	cIP2vsInput	promoter-TSS (NM_010608)	promoter-TSS (NM_010608)	-203	NM_010608	16527	Mm.439936	NM_010608	ENSMUSG00000049265	Kcnk3	TASK|cTBAK-1	"potassium channel, subfamily K, member 3"	protein-coding	0.07	0.732673
Merged-chr6-92862703-1	chr6	92862653	92862753	+	3.5	cIP1vsInput	"intron (NM_175314, intron 13 of 29)"	MER63D|DNA|hAT-Blackjack	38738	NM_175314	101401	Mm.257557	NM_175314	ENSMUSG00000030022	Adamts9	1810011L16Rik|8430403M15Rik|AW743315|E030027K14Rik	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 9"	protein-coding	0.02	0.455446
Merged-chr11-95824290-2	chr11	95824235	95824346	+	3.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_153104)	promoter-TSS (NM_153104)	-210	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	"phosphatase, orphan 1"	protein-coding	0.126126	0.741071
Merged-chr3-126596289-1	chr3	126596239	126596339	+	3.5	cIP2vsInput	promoter-TSS (NM_001025439)	promoter-TSS (NM_001025439)	-684	NM_001025438	108058	Mm.255822	NM_001025438	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|[d]-CaMKII|mKIAA4163	"calcium/calmodulin-dependent protein kinase II, delta"	protein-coding	0.07	0.643564
Merged-chr5-15538778-2	chr5	15538716	15538840	+	3.5	cIP1vsInput|cIP2vsInput	Intergenic	ETnERV3-int|LTR|ERVK	-80321	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0.008065	0.304
Merged-chr3-101507695-1	chr3	101507645	101507745	+	3.5	cIP2vsInput	Intergenic	Intergenic	97012	NM_144900	11928	Mm.280103	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	"ATPase, Na+/K+ transporting, alpha 1 polypeptide"	protein-coding	0.03	0.534653
Merged-chr2-69943636-1	chr2	69943586	69943686	+	3.5	cIP2vsInput	"intron (NM_001081548, intron 8 of 38)"	"intron (NM_001081548, intron 8 of 38)"	46390	NM_001081548	68795	Mm.314576	NM_001081548	ENSMUSG00000044308	Ubr3	1110059H15Rik|4833421P10Rik|A130030D10Rik|AA409735|AA414972|AA422631|AI646861|AU016126|Zfp650|Znf650	ubiquitin protein ligase E3 component n-recognin 3	protein-coding	0	0.366337
Merged-chr14-54653671-2	chr14	54653599	54653744	+	3.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001242606)	promoter-TSS (NM_001242606)	14	NM_001242605	56215	Mm.297078	NM_001085472	ENSMUSG00000022185	Acin1	2610036I19Rik|2610510L13Rik|Acinus|Acn|C79325|acinusL|acinusS|mKIAA0670	apoptotic chromatin condensation inducer 1	protein-coding	0.034483	0.60274
Merged-chr17-75552039-1	chr17	75551989	75552089	+	3.5	cIP2vsInput	promoter-TSS (NM_133747)	promoter-TSS (NM_133747)	-93	NM_133747	72722		NM_133747	ENSMUSG00000002017	Fam98a	2810405J04Rik|AL024114	"family with sequence similarity 98, member A"	protein-coding	0.05	0.633663
Merged-chr18-63692567-1	chr18	63692517	63692617	+	3.5	cIP2vsInput	promoter-TSS (NM_016792)	promoter-TSS (NM_016792)	-208	NM_016792	53382	Mm.19169	NM_016792	ENSMUSG00000024583	Txnl1	32kDa|TRP32|Txnl	thioredoxin-like 1	protein-coding	0.06	0.514851
Merged-chr4-40970877-1	chr4	40970827	40970927	+	3.5	cIP2vsInput	promoter-TSS (NM_023739)	promoter-TSS (NM_023739)	-66	NM_023739	74164	Mm.439181	NM_023739	ENSMUSG00000028423	Nfx1	1300017N15Rik|3000003M19Rik|NFX.1|TEG-42|Tex42	"nuclear transcription factor, X-box binding 1"	protein-coding	0.07	0.643564
Merged-chr2-30708053-1	chr2	30708003	30708103	+	3.5	cIP2vsInput	Intergenic	T-rich|Low_complexity|Low_complexity	-13157	NR_037272	100526499		NR_037272	ENSMUSG00000093091	Mir3089	mmu-mir-3089	microRNA 3089	miscRNA	0.08	0.534653
Merged-chr4-44801912-1	chr4	44801862	44801962	+	3.5	cIP2vsInput	"intron (NM_138590, intron 2 of 8)"	"intron (NM_138590, intron 2 of 8)"	45353	NM_138590	319885	Mm.486647	NM_177027	ENSMUSG00000035649	Zcchc7	4930572I07Rik|D4Wsu132e	"zinc finger, CCHC domain containing 7"	protein-coding	0	0.336634
Merged-chr17-32143405-2	chr17	32143346	32143465	+	3.5	cIP1vsInput|cIP2vsInput	"exon (NM_008716, exon 24 of 33)"	"exon (NM_008716, exon 24 of 33)"	23447	NM_008716	18131	Mm.439741	NM_008716	ENSMUSG00000038146	Notch3	AW229011|N3|hpbk	notch 3	protein-coding	0.05042	0.633333
Merged-chr12-119238532-1	chr12	119238482	119238582	+	3.5	cIP2vsInput	promoter-TSS (NM_177290)	promoter-TSS (NM_177290)	-256	NM_177290	320910	Mm.217000	NM_177290		Itgb8	4832412O06Rik	integrin beta 8	protein-coding	0.03	0.574257
Merged-chr3-109027802-1	chr3	109027752	109027852	+	3.5	cIP2vsInput	promoter-TSS (NM_001163567)	promoter-TSS (NM_001163567)	-195	NM_001163567	329739	Mm.69013	NM_001163567	ENSMUSG00000040339	Fam102b	1600010D10Rik|B430201A12Rik	"family with sequence similarity 102, member B"	protein-coding	0.1	0.633663
Merged-chr7-30095359-1	chr7	30095309	30095409	+	3.5	cIP2vsInput	"intron (NM_011981, intron 1 of 2)"	"intron (NM_011981, intron 1 of 2)"	283	NM_011981	26466	Mm.195092	NM_011981	ENSMUSG00000049421	Zfp260	AI480997|Ozrf1|PEX1|Zfp63|Znf260	zinc finger protein 260	protein-coding	0.05	0.623762
Merged-chr8-106935719-1	chr8	106935669	106935769	+	3.5	cIP2vsInput	promoter-TSS (NM_009229)	promoter-TSS (NM_009229)	-31	NM_009229	20650	Mm.30228	NM_009229	ENSMUSG00000041308	Sntb2	Snt2	"syntrophin, basic 2"	protein-coding	0.08	0.70297
Merged-chr16-87354307-1	chr16	87354257	87354357	+	3.5	cIP2vsInput	"exon (NM_001159331, exon 1 of 5)"	"exon (NM_001159331, exon 1 of 5)"	122	NM_026366	67768	Mm.296532	NM_001159331	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding	0.17	0.693069
Merged-chr5-142962056-1	chr5	142962006	142962106	+	3.5	cIP2vsInput	"intron (NM_007984, intron 1 of 4)"	CpG	1701	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	"fascin homolog 1, actin bundling protein (Strongylocentrotus purpuratus)"	protein-coding	0.09	0.762376
Merged-chr2-20869882-1	chr2	20869832	20869932	+	3.5	cIP2vsInput	"intron (NM_001128084, intron 10 of 24)"	"intron (NM_001128084, intron 10 of 24)"	97839	NM_001081364	71435	Mm.465492	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding	0.01	0.356436
Merged-chr16-60274188-1	chr16	60274138	60274238	+	3.5	cIP2vsInput	"intron (NM_007938, intron 3 of 17)"	Lx8|LINE|L1	331343	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0.02	0.435644
Merged-chr5-100429429-1	chr5	100429379	100429479	+	3.5	cIP2vsInput	"non-coding (NR_034038, exon 1 of 5)"	"non-coding (NR_034038, exon 1 of 5)"	106	NR_034038	100503199	Mm.392282	NR_034038	ENSMUSG00000097772	5430416N02Rik	100041797|Gm3514	RIKEN cDNA 5430416N02 gene	miscRNA	0.1	0.663366
Merged-chr7-129591846-1	chr7	129591796	129591896	+	3.5	cIP2vsInput	promoter-TSS (NM_172255)	promoter-TSS (NM_172255)	-17	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding	0.05	0.554455
Merged-chr5-150673646-1	chr5	150673596	150673696	+	3.5	cIP2vsInput	promoter-TSS (NM_175310)	promoter-TSS (NM_175310)	-181	NM_175310	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|mKIAA0979	"PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)"	protein-coding	0.19	0.811881
Merged-chr9-40800066-2	chr9	40799994	40800139	+	3.5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-1207	NM_031165	15481	Mm.485345	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding	0.068966	0.59589
Merged-chr11-87443614-1	chr11	87443564	87443664	+	3.5	cIP1vsInput	"intron (NM_031386, intron 2 of 30)"	"intron (NM_031386, intron 2 of 30)"	16023	NM_001199293	83560	Mm.440758	NM_001199293	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding	0	0.425743
Merged-chr6-83137741-2	chr6	83137675	83137807	+	3.5	cIP1vsInput|cIP2vsInput	"5' UTR (NM_133641, exon 1 of 12)"	"5' UTR (NM_133641, exon 1 of 12)"	657	NM_009106	20166	Mm.4139	NM_001136227	ENSMUSG00000034930	Rtkn	-	rhotekin	protein-coding	0.05303	0.669173
Merged-chr4-123282662-2	chr4	123282603	123282722	+	3.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_130881)	promoter-TSS (NM_130881)	-249	NM_130881	230721	Mm.277091	NM_130881	ENSMUSG00000011257	Pabpc4	-	"poly(A) binding protein, cytoplasmic 4"	protein-coding	0.084034	0.716667
Merged-chr3-89214427-1	chr3	89214377	89214477	+	3.5	cIP2vsInput	promoter-TSS (NM_013604)	promoter-TSS (NM_013604)	-92	NM_013604	17827	Mm.280943	NM_001161824	ENSMUSG00000064068	Mtx1	Gcap6|Mtx	metaxin 1	protein-coding	0.09	0.70297
Merged-chr6-130045213-1	chr6	130045163	130045263	+	3.5	cIP1vsInput	"intron (NM_053153, intron 6 of 6)"	"intron (NM_053153, intron 6 of 6)"	-18253	NM_053154	93971	Mm.14112	NM_053154		Klra19	Ly49s	"killer cell lectin-like receptor, subfamily A, member 19"	protein-coding	0	0.326733
Merged-chr13-100124844-1	chr13	100124794	100124894	+	3.5	cIP2vsInput	promoter-TSS (NM_011420)	promoter-TSS (NM_011420)	-11	NM_011420	20595	Mm.2025	NM_001252629	ENSMUSG00000021645	Smn1	AI849087|Gemin1|Smn	survival motor neuron 1	protein-coding	0.08	0.653465
Merged-chr1-36068291-1	chr1	36068241	36068341	+	3.5	cIP2vsInput	promoter-TSS (NM_015818)	promoter-TSS (NM_015818)	-109	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding	0.15	0.821782
Merged-chr13-12764969-1	chr13	12764919	12765019	+	3.5	cIP1vsInput	Intergenic	Intergenic	35089	NM_011954	26421	Mm.457984	NM_011954		Prl2c4	MRP-3|Mrpplf3|PLF-3|mrp/plf3	"prolactin family 2, subfamily c, member 4"	protein-coding	0	0.29703
Merged-chr8-59945940-1	chr8	59945890	59945990	+	3.5	cIP1vsInput	Intergenic	Intergenic	-560184	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|mKat-2	aminoadipate aminotransferase	protein-coding	0	0.326733
Merged-chr3-142285176-1	chr3	142285126	142285226	+	3.5	cIP2vsInput	"intron (NM_001190852, intron 7 of 15)"	"intron (NM_001190852, intron 7 of 15)"	106674	NM_022554	56376	Mm.117709	NM_001190852	ENSMUSG00000028273	Pdlim5	1110001A05Rik|AI987914|C87059|Enh|Enh1|Enh2|Enh3|LIM	PDZ and LIM domain 5	protein-coding	0	0.415842
Merged-chr3-127837677-1	chr3	127837627	127837727	+	3.5	cIP2vsInput	promoter-TSS (NM_145964)	promoter-TSS (NM_145964)	-185	NM_145964	211556	Mm.403486	NM_145964	ENSMUSG00000074238	Ap1ar	AA407621|C78909|Gadkin	adaptor-related protein complex 1 associated regulatory protein	protein-coding	0.06	0.584158
Merged-chr4-82440499-1	chr4	82440449	82440549	+	3.5	cIP1vsInput	"intron (NM_008687, intron 2 of 8)"	"intron (NM_008687, intron 2 of 8)"	64809	NM_001113210	18028	Mm.317947	NM_001113209	ENSMUSG00000008575	Nfib	6720429L07Rik|E030026I10Rik	nuclear factor I/B	protein-coding	0.02	0.306931
Merged-chr8-27023795-1	chr8	27023745	27023845	+	3.5	cIP2vsInput	promoter-TSS (NM_153592)	promoter-TSS (NM_153592)	-4	NM_153592	244373	Mm.277699	NM_153592	ENSMUSG00000031483	Erlin2	BC036333|C87251|Spfh2	ER lipid raft associated 2	protein-coding	0.09	0.475248
Merged-chr15-98993237-1	chr15	98993187	98993287	+	3.5	cIP1vsInput	Intergenic	CpG	7272	NR_045991	75951	Mm.441657	NR_045991	ENSMUSG00000097587	4930578M01Rik	3010001K12Rik	RIKEN cDNA 4930578M01 gene	miscRNA	0.14	0.732673
Merged-chr4-82622957-1	chr4	82622907	82623007	+	3.5	cIP2vsInput	Intergenic	Intergenic	-117649	NM_008687	18028	Mm.317947	NM_001113209	ENSMUSG00000008575	Nfib	6720429L07Rik|E030026I10Rik	nuclear factor I/B	protein-coding	0.01	0.39604
Merged-chr11-117654783-1	chr11	117654733	117654833	+	3.5	cIP1vsInput	"intron (NM_198022, intron 1 of 21)"	CpG	494	NM_198022	217351	Mm.473244	NM_198022	ENSMUSG00000025571	Tnrc6c	9930033H14Rik|mKIAA1582	trinucleotide repeat containing 6C	protein-coding	0.1	0.732673
Merged-chr1-59912702-2	chr1	59912650	59912755	+	3.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001037725)	promoter-TSS (NM_001037725)	-304	NM_001037725	72750	Mm.258250	NM_001037725	ENSMUSG00000041040	Fam117b	2810425F24Rik|6330416D14Rik|Als2cr13	"family with sequence similarity 117, member B"	protein-coding	0.152381	0.716981
Merged-chr3-142125735-1	chr3	142125685	142125785	+	3.5	cIP2vsInput	"intron (NM_001277216, intron 1 of 11)"	"intron (NM_001277216, intron 1 of 11)"	43493	NM_001277217	12167	Mm.39089	NM_001277216	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	"bone morphogenetic protein receptor, type 1B"	protein-coding	0.01	0.50495
Merged-chr9-85327536-1	chr9	85327486	85327586	+	3.5	cIP2vsInput	promoter-TSS (NM_001160379)	promoter-TSS (NM_001160379)	-386	NM_001160379	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	D930050G01Rik	"family with sequence similarity 46, member A"	protein-coding	0.07	0.534653
Merged-chr17-35046582-1	chr17	35046532	35046632	+	3.5	cIP2vsInput	promoter-TSS (NM_013600)	promoter-TSS (NM_013600)	24	NM_013600	17687	Mm.24192	NM_001146215	ENSMUSG00000007035	Msh5	G7|Mut5	mutS homolog 5 (E. coli)	protein-coding	0.1	0.673267
Merged-chr14-116925217-2	chr14	116925153	116925281	+	3.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011821)	promoter-TSS (NM_011821)	-98	NM_001079844	23888	Mm.440025	NM_001079844	ENSMUSG00000058571	Gpc6	6720429C22Rik|AI480529	glypican 6	protein-coding	0.046875	0.573643
Merged-chr4-34614882-2	chr4	34614828	34614937	+	3.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_181406)	promoter-TSS (NM_181406)	60	NM_001159563	50793	Mm.399624	NM_001159563		Orc3	Orc3l	"origin recognition complex, subunit 3"	protein-coding	0.119266	0.690909
Merged-chr2-152020441-1	chr2	152020391	152020491	+	3.5	cIP1vsInput	Intergenic	Intergenic	20575	NM_001164820	69698	Mm.258262	NM_001164819	ENSMUSG00000027463	Slc52a3	2310046K01Rik|RFT2	"solute carrier protein family 52, member 3"	protein-coding	0.03	0.584158
Merged-chr11-57951316-1	chr11	57951266	57951366	+	3.5	cIP2vsInput	Intergenic	Intergenic	-57748	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	"La ribonucleoprotein domain family, member 1"	protein-coding	0.02	0.386139
Merged-chr4-156031773-2	chr4	156031716	156031830	+	3.5	cIP1vsInput|cIP2vsInput	Intergenic	RLTR20B4_MM|LTR|ERVK	5431	NM_021985	21936	Mm.3180	NM_009400	ENSMUSG00000041954	Tnfrsf18	AITR|Gitr	"tumor necrosis factor receptor superfamily, member 18"	protein-coding	0.017544	0.547826
Merged-chr17-6828139-1	chr17	6828089	6828189	+	3.5	cIP2vsInput	Intergenic	CpG	-45359	NM_009510	22350	Mm.471952	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding	0.07	0.584158
Merged-chr8-123983033-1	chr8	123982983	123983083	+	3.5	cIP2vsInput	promoter-TSS (NM_019552)	promoter-TSS (NM_019552)	89	NM_019552	56199	Mm.274243	NM_019552	ENSMUSG00000031974	Abcb10	AU016331|Abc-me|Abcb12|C76534	"ATP-binding cassette, sub-family B (MDR/TAP), member 10"	protein-coding	0.13	0.732673
Merged-chr13-13358257-2	chr13	13358180	13358334	+	3.5	cIP1vsInput|cIP2vsInput	"3' UTR (NM_031999, exon 7 of 7)"	"3' UTR (NM_031999, exon 7 of 7)"	35367	NM_031999	83924	Mm.379269	NM_031999	ENSMUSG00000021306	Gpr137b	AI788917|AU016435|AW546472|C730041E01|C80550|C80741|D13Abb1e|Tm7sf1	G protein-coupled receptor 137B	protein-coding	0.038961	0.567742
Merged-chr8-121376308-1	chr8	121376258	121376358	+	3.5	cIP1vsInput	Intergenic	Intergenic	165646	NM_029597	76405	Mm.165697	NM_029597	ENSMUSG00000031809	1700018B08Rik	1700084O22Rik	RIKEN cDNA 1700018B08 gene	protein-coding	0.01	0.623762
Merged-chr18-80296121-2	chr18	80296063	80296180	+	3.45	cIP1vsInput|cIP2vsInput	"exon (NM_001190373, exon 4 of 4)"	"exon (NM_001190373, exon 4 of 4)"	39815	NM_001164423	66943	Mm.29247	NM_001164420	ENSMUSG00000034006	Pqlc1	2310009N05Rik|4933425L21Rik|5730564E11Rik|C78974	PQ loop repeat containing 1	protein-coding	0.162393	0.737288
Merged-chr4-134316479-2	chr4	134316412	134316547	+	3.45	cIP1vsInput|cIP2vsInput	"exon (NM_001039048, exon 2 of 9)"	"exon (NM_001039048, exon 2 of 9)"	1359	NM_001039048	433766	Mm.331961	NM_001039048	ENSMUSG00000028834	Trim63	MuRF1|RF1|Rnf28	tripartite motif-containing 63	protein-coding	0.059259	0.580882
Merged-chr2-152343953-2	chr2	152343894	152344013	+	3.45	cIP1vsInput|cIP2vsInput	"5' UTR (NM_175093, exon 1 of 4)"	"5' UTR (NM_175093, exon 1 of 4)"	107	NM_175093	228775	Mm.276018	NM_144554	ENSMUSG00000032715	Trib3	Ifld2|Nipk|SINK|SKIP3|TRB-3|Trb3	tribbles homolog 3 (Drosophila)	protein-coding	0.092437	0.666667
Merged-chr10-77259234-2	chr10	77259172	77259297	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_026944)	promoter-TSS (NR_026944)	-11	NR_026944	100169878	Mm.420901	NR_026944	ENSMUSG00000078444	Gm10941	ENSMUSG00000078444	predicted gene 10941	miscRNA	0.144	0.706349
Merged-chr9-46230126-2	chr9	46230066	46230187	+	3.45	cIP1vsInput|cIP2vsInput	"exon (NM_009692, exon 4 of 4)"	"exon (NM_009692, exon 4 of 4)"	1496	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2	apolipoprotein A-I	protein-coding	0.07438	0.622951
Merged-chr5-15539330-2	chr5	15539269	15539391	+	3.45	cIP1vsInput|cIP2vsInput	Intergenic	ETnERV3-int|LTR|ERVK	-79769	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0	0.382114
Merged-chr14-54254141-2	chr14	54254091	54254192	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001205181)	promoter-TSS (NM_001205181)	12	NM_001205181	105501	Mm.28771	NM_001205181	ENSMUSG00000040997	Abhd4	1110035H23Rik|AI429574|Abh4	abhydrolase domain containing 4	protein-coding	0.079208	0.578431
Merged-chr5-26904939-2	chr5	26904884	26904995	+	3.45	cIP1vsInput|cIP2vsInput	"5' UTR (NM_001198886, exon 1 of 26)"	"5' UTR (NM_001198886, exon 1 of 26)"	161	NM_001198886	13483	Mm.42078	NM_001136060	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding	0.081081	0.580357
Merged-chrY-6670828-2	chrY	6670776	6670880	+	3.45	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	496949	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.361905
Merged-chr9-89704992-2	chr9	89704926	89705059	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025360)	promoter-TSS (NM_025360)	51	NM_025360	66111	Mm.27606	NM_025360	ENSMUSG00000032353	Tmed3	1200002G13Rik|AW546672|P24b	transmembrane emp24 domain containing 3	protein-coding	0.097744	0.716418
Merged-chr1-133226945-2	chr1	133226889	133227002	+	3.45	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-19152	NM_001160268	240753	Mm.253559	NM_001160268	ENSMUSG00000041757	Plekha6	9530028L01Rik|AU042621|Pepp3	"pleckstrin homology domain containing, family A member 6"	protein-coding	0.017699	0.526316
Merged-chr10-111972641-2	chr10	111972549	111972734	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178610)	promoter-TSS (NM_178610)	-54	NM_178610	52705	Mm.34606	NM_178610	ENSMUSG00000063334	Krr1	2610511F02Rik|AI255219|AI428520|D10Ertd773e|Hrb2	"KRR1, small subunit (SSU) processome component, homolog (yeast)"	protein-coding	0.054054	0.526882
Merged-chr8-71592498-2	chr8	71592447	71592550	+	3.45	cIP1vsInput|cIP2vsInput	"exon (NM_025396, exon 1 of 5)"	"exon (NM_025396, exon 1 of 5)"	314	NM_025396	66171	Mm.402679	NM_025396	ENSMUSG00000031807	Pgls	1110030K05Rik|AI447866|Plgs	6-phosphogluconolactonase	protein-coding	0.184466	0.759615
Merged-chr13-13954569-2	chr13	13954511	13954627	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178640)	promoter-TSS (NM_178640)	-105	NM_178640	97884	Mm.21686	NM_178640	ENSMUSG00000039242	B3galnt2	A930105D20Rik|C80633|D230016N13Rik	"UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 2"	protein-coding	0.112069	0.717949
Merged-chr1-44102431-2	chr1	44102366	44102496	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029368)	promoter-TSS (NM_029368)	-43	NM_029368	75623	Mm.348017	NM_029368	ENSMUSG00000026049	Tex30	1700029F09Rik|3110030D08Rik	testis expressed 30	protein-coding	0.176923	0.748092
Merged-chr5-130171780-2	chr5	130171714	130171847	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001199059)	promoter-TSS (NM_001199059)	-39	NM_001199059	56715	Mm.288639	NM_019983	ENSMUSG00000025340	Rabgef1	Rab5ef|Rabex5|Rin2	RAB guanine nucleotide exchange factor (GEF) 1	protein-coding	0.157895	0.761194
Merged-chr9-42472275-2	chr9	42472218	42472333	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_173038)	promoter-TSS (NM_173038)	-49	NM_173038	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding	0.095652	0.646552
Merged-chr18-75697703-2	chr18	75697648	75697759	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_201354)	promoter-TSS (NM_201354)	-7	NM_201354	269037	Mm.36745	NM_201354	ENSMUSG00000052928	Ctif	Gm672	CBP80/20-dependent translation initiation factor	protein-coding	0.063063	0.598214
Merged-chr6-125081834-2	chr6	125081771	125081898	+	3.45	cIP1vsInput|cIP2vsInput	"exon (NM_001163269, exon 2 of 2)"	"exon (NM_001163269, exon 2 of 2)"	10557	NM_001163268	381810	Mm.333386	NM_001163268	ENSMUSG00000067714	Lpar5	GPR93|Gm1072|Gpr92|LPA5	lysophosphatidic acid receptor 5	protein-coding	0.102362	0.671875
Merged-chr12-103242779-2	chr12	103242728	103242831	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133364)	promoter-TSS (NM_133364)	-633	NM_133364	170952	Mm.217019	NM_178023	ENSMUSG00000041669	Prima1	B230212M13Rik|BB120497|PRiMA	proline rich membrane anchor 1	protein-coding	0.116505	0.586538
Merged-chr11-105363136-2	chr11	105363059	105363214	+	3.45	cIP1vsInput|cIP2vsInput	"intron (NM_172568, intron 11 of 11)"	CpG	70490	NM_008626	17534	Mm.235616	NM_008626	ENSMUSG00000020695	Mrc2	Endo180|mKIAA0709|uPARAP	"mannose receptor, C type 2"	protein-coding	0.083871	0.679487
Merged-chr4-45819306-2	chr4	45819256	45819356	+	3.45	cIP1vsInput|cIP2vsInput	"intron (NM_018741, intron 1 of 4)"	"intron (NM_018741, intron 1 of 4)"	7521	NM_018741	75426	Mm.3919	NM_018741	ENSMUSG00000035551	Igfbpl1	2810011G06Rik|2810453O06Rik|IGFBPL	insulin-like growth factor binding protein-like 1	protein-coding	0.01	0.613861
Merged-chr8-35411248-2	chr8	35411195	35411302	+	3.45	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	35507	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	"protein phosphatase 1, regulatory (inhibitor) subunit 3B"	protein-coding	0.028037	0.481481
Merged-chr11-47379133-2	chr11	47379050	47379217	+	3.45	cIP1vsInput|cIP2vsInput	"intron (NM_011891, intron 1 of 7)"	"intron (NM_011891, intron 1 of 7)"	169	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	"sarcoglycan, delta (dystrophin-associated glycoprotein)"	protein-coding	0.02994	0.553571
Merged-chr11-107132243-2	chr11	107132157	107132330	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_176850)	promoter-TSS (NM_176850)	-321	NM_176850	207165	Mm.343986	NM_176850	ENSMUSG00000040481	Bptf	9430093H17Rik|Falz	bromodomain PHD finger transcription factor	protein-coding	0.184971	0.827586
Merged-chr11-60046503-2	chr11	60046448	60046559	+	3.45	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-9664	NM_008819	18618	Mm.2731	NM_008819	ENSMUSG00000000301	Pemt	AI255394|Pempt|Pempt2	phosphatidylethanolamine N-methyltransferase	protein-coding	0.072072	0.651786
Merged-chr16-18812005-2	chr16	18811917	18812094	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011672)	promoter-TSS (NM_011672)	-33	NM_009862	12544	Mm.1248	NM_001161623	ENSMUSG00000000028	Cdc45	Cdc45l	cell division cycle 45	protein-coding	0.050847	0.404494
Merged-chr4-57143768-2	chr4	57143712	57143824	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019427)	promoter-TSS (NM_019427)	-612	NM_019427	54357	Mm.381403	NM_019427	ENSMUSG00000028434	Epb4.1l4b	6430543G08Rik|AA589614|AU021054|BB007528|D4Ertd346e|Ehm2|Epb41l4b|Lulu2	erythrocyte protein band 4.1-like 4b	protein-coding	0.098214	0.734513
Merged-chr9-123366940-2	chr9	123366879	123367001	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_153168)	promoter-TSS (NM_153168)	0	NM_153168	102436	Mm.276076	NM_153168	ENSMUSG00000035202	Lars2	AI035546|Kiaa0028|LEURS	"leucyl-tRNA synthetase, mitochondrial"	protein-coding	0.057377	0.585366
Merged-chr11-102027324-2	chr11	102027263	102027385	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007863)	promoter-TSS (NM_007863)	-369	NM_007863	13384	Mm.20449	NM_007863	ENSMUSG00000052373	Mpp3	6430514B01|Dlgh3	"membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)"	protein-coding	0.090164	0.650407
Merged-chr2-34826334-2	chr2	34826281	34826388	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001164770)	promoter-TSS (NM_001164770)	-99	NM_001164772	30050	Mm.4465	NM_001164768	ENSMUSG00000035949	Fbxw2	2700071L08Rik|FBW2|Fwd2|MD6	F-box and WD-40 domain protein 2	protein-coding	0.046729	0.555556
Merged-chr5-41768534-2	chr5	41768474	41768594	+	3.45	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-4314	NM_007524	12020	Mm.2530	NM_007524	ENSMUSG00000049691	Nkx3-2	Bapx1|NKX3.2|Nkx-3.2	NK3 homeobox 2	protein-coding	0.075	0.520661
Merged-chr4-12318155-2	chr4	12318059	12318251	+	3.45	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-146140	NM_026558	68099	Mm.25340	NM_026558	ENSMUSG00000028218	Fam92a	6720467C03Rik|Fam92a1	"family with sequence similarity 92, member A"	protein-coding	0	0.430052
Merged-chr1-181144309-2	chr1	181144224	181144394	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026171)	promoter-TSS (NM_026171)	-152	NM_026171	67459	Mm.263464	NM_026171	ENSMUSG00000026516	Nvl	1200009I24Rik	nuclear VCP-like	protein-coding	0.052941	0.567251
Merged-chr4-148444763-2	chr4	148444698	148444828	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027873)	promoter-TSS (NM_027873)	-12	NM_027873	71707	Mm.292503	NM_027873	ENSMUSG00000047719	Ubiad1	1200002M06Rik|AI426463|AW320947|Tere1	UbiA prenyltransferase domain containing 1	protein-coding	0.130769	0.748092
Merged-chr7-127512220-2	chr7	127512147	127512294	+	3.45	cIP1vsInput|cIP2vsInput	"non-coding (NR_024331, exon 1 of 1)"	"non-coding (NR_024331, exon 1 of 1)"	649	NR_024331	629159	Mm.256720	NR_024331		1700008J07Rik	AW048743	RIKEN cDNA 1700008J07 gene	miscRNA	0.068027	0.608108
Merged-chr1-74049678-2	chr1	74049624	74049732	+	3.45	cIP1vsInput|cIP2vsInput	"intron (NM_027884, intron 3 of 34)"	"intron (NM_027884, intron 3 of 34)"	74769	NM_027884	21961	Mm.309975	NM_177169	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding	0.037037	0.59633
Merged-chr19-8953839-2	chr19	8953762	8953916	+	3.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_197993)	promoter-TSS (NM_197993)	-11	NM_197993	70044	Mm.165979	NM_197993	ENSMUSG00000071645	Tut1	2700038E08Rik|PAPD2|Rbm21	"terminal uridylyl transferase 1, U6 snRNA-specific"	protein-coding	0.071429	0.496774
Merged-chr3-51559700-1	chr3	51559650	51559750	+	3.4	cIP2vsInput	promoter-TSS (NR_033624)	promoter-TSS (NR_033624)	-57	NR_033624	100039684	Mm.387178	NR_033624	ENSMUSG00000097885	5031434O11Rik	AI481280|Gm2370	RIKEN cDNA 5031434O11 gene	miscRNA	0.08	0.613861
Merged-chr5-139200405-1	chr5	139200355	139200455	+	3.4	cIP2vsInput	promoter-TSS (NM_024451)	promoter-TSS (NM_024451)	-232	NM_001256115	77053	Mm.210845	NM_001256115	ENSMUSG00000036817	Sun1	4632417G13Rik|5730434D03Rik|Unc84a|mKIAA0810	Sad1 and UNC84 domain containing 1	protein-coding	0.08	0.653465
Merged-chr2-26964429-2	chr2	26964377	26964481	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_207234)	promoter-TSS (NM_207234)	-43	NM_207234	227656	Mm.291874	NM_207234	ENSMUSG00000052406	Rexo4	Gm111|Xpmc2h	"REX4, RNA exonuclease 4 homolog (S. cerevisiae)"	protein-coding	0.076923	0.609524
Merged-chr7-127209038-1	chr7	127208988	127209088	+	3.4	cIP2vsInput	promoter-TSS (NM_144522)	promoter-TSS (NM_144522)	-570	NM_144522	68449	Mm.41420	NM_144522	ENSMUSG00000042492	Tbc1d10b	1110003P22Rik|C87963	"TBC1 domain family, member 10b"	protein-coding	0	0.465347
Merged-chr4-152325812-1	chr4	152325762	152325862	+	3.4	cIP2vsInput	promoter-TSS (NM_001277114)	promoter-TSS (NM_001277114)	86	NR_102291	19934	Mm.307846	NM_001277113	ENSMUSG00000028936	Rpl22	2700038K18Rik	ribosomal protein L22	protein-coding	0.09	0.653465
Merged-chr5-65335344-1	chr5	65335294	65335394	+	3.4	cIP2vsInput	"intron (NM_011258, intron 1 of 24)"	"intron (NM_011258, intron 1 of 24)"	295	NM_011258	19687	Mm.148877	NM_011258	ENSMUSG00000029191	Rfc1	140kDa|Alp145|RFC140|Recc1	replication factor C (activator 1) 1	protein-coding	0.04	0.613861
Merged-chr8-23257208-2	chr8	23257119	23257298	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_020585)	promoter-TSS (NM_020585)	-128	NM_001042484	57437	Mm.196269	NM_001042484	ENSMUSG00000015341	Golga7	AB041568|C130038N16Rik|GCP16|GOLGA3AP1|HSPC041|R75586	"golgi autoantigen, golgin subfamily a, 7"	protein-coding	0.111732	0.627778
Merged-chr3-145988446-1	chr3	145988396	145988496	+	3.4	cIP1vsInput	"exon (NM_001166064, exon 1 of 7)"	"exon (NM_001166064, exon 1 of 7)"	576	NM_001166064	214804	Mm.268854	NM_001166064	ENSMUSG00000036863	Syde2	C430017H16Rik	"synapse defective 1, Rho GTPase, homolog 2 (C. elegans)"	protein-coding	0.07	0.673267
Merged-chr10-81292838-2	chr10	81292786	81292891	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001146687)	promoter-TSS (NM_001146687)	-134	NM_008844	18717	Mm.29836	NM_001146687	ENSMUSG00000034902	Pip5k1c	AI115456|AI835305|Pip5kIgamma	"phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma"	protein-coding	0.104762	0.660377
Merged-chr9-65909920-1	chr9	65909870	65909970	+	3.4	cIP2vsInput	"intron (NM_173185, intron 1 of 13)"	"intron (NM_173185, intron 1 of 13)"	910	NM_173185	214897	Mm.325816	NM_173185	ENSMUSG00000032384	Csnk1g1	9130020E21Rik	"casein kinase 1, gamma 1"	protein-coding	0.02	0.376238
Merged-chr2-85037209-2	chr2	85037127	85037292	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_182990)	promoter-TSS (NM_182990)	89	NM_182990	20833	Mm.219793	NM_001136081	ENSMUSG00000027067	Ssrp1	C81323|Hmg1-rs1|Hmgi-rs3|Hmgox|T160	structure specific recognition protein 1	protein-coding	0.115152	0.704819
Merged-chr3-102204206-2	chr3	102204149	102204263	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001165951)	promoter-TSS (NM_001165951)	-243	NM_001165951	229658	Mm.118004	NM_001165951	ENSMUSG00000027860	Vangl1	Kitenin|Lpp2|Stb2|Stbm	"vang-like 1 (van gogh, Drosophila)"	protein-coding	0.087719	0.669565
Merged-chr16-56037878-1	chr16	56037828	56037928	+	3.4	cIP2vsInput	promoter-TSS (NM_029092)	promoter-TSS (NM_029092)	-104	NM_029092	52575	Mm.288742	NM_029092		Trmt10c	1300018J16Rik|D16Ertd454e|Rg9mtd1|Rnmtd1	tRNA methyltransferase 10C	protein-coding	0.09	0.663366
Merged-chr1-69139229-1	chr1	69139179	69139279	+	3.4	cIP2vsInput	Intergenic	Intergenic	-31170	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0.01	0.326733
Merged-chr5-148959327-2	chr5	148959271	148959383	+	3.4	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	9077	NR_040686	71473	Mm.90306	NR_040686	ENSMUSG00000079069	8430423G03Rik	-	RIKEN cDNA 8430423G03 gene	miscRNA	0.035714	0.59292
Merged-chr9-121710440-1	chr9	121710390	121710490	+	3.4	cIP2vsInput	promoter-TSS (NM_026794)	promoter-TSS (NM_026794)	51	NM_026794	26901	Mm.24848	NM_026794	ENSMUSG00000032526	Deb1	1110020I04Rik|AI463209|Ss18l2	differentially expressed in B16F10 1	protein-coding	0.07	0.544554
Merged-chr3-104818383-2	chr3	104818324	104818442	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008619)	promoter-TSS (NM_008619)	-78	NM_001163441	17454	Mm.1597	NM_001163440	ENSMUSG00000002227	Mov10	C77703|Mov-10	Moloney leukemia virus 10	protein-coding	0.050847	0.680672
Merged-chr10-80900925-1	chr10	80900875	80900975	+	3.4	cIP1vsInput	promoter-TSS (NM_013895)	promoter-TSS (NM_013895)	44	NM_013895	30055	Mm.142132	NM_013895	ENSMUSG00000020219	Timm13	D10Ertd378e|Tim9|Timm9	translocase of inner mitochondrial membrane 13	protein-coding	0.06	0.564356
Merged-chr4-132768186-1	chr4	132768136	132768236	+	3.4	cIP2vsInput	promoter-TSS (NM_011284)	promoter-TSS (NM_011284)	-174	NM_011284	19891	Mm.2870	NM_011284	ENSMUSG00000028884	Rpa2	AA409079|AI325195|AU020965|RPA34|Rf-A2	replication protein A2	protein-coding	0.04	0.49505
Merged-chr4-34778408-1	chr4	34778358	34778458	+	3.4	cIP2vsInput	promoter-TSS (NM_025471)	promoter-TSS (NM_025471)	-71	NM_025471	66291	Mm.28071	NM_025471	ENSMUSG00000028295	Smim8	1810030N24Rik|2810406B13Rik	small integral membrane protein 8	protein-coding	0.13	0.693069
Merged-chr16-57121642-1	chr16	57121592	57121692	+	3.4	cIP2vsInput	promoter-TSS (NM_138599)	promoter-TSS (NM_138599)	-72	NM_138599	28185	Mm.213292	NM_138599	ENSMUSG00000022752	Tomm70a	2610044B22Rik|D16Ium22|D16Ium22e|D16Wsu109e|Tom70|mKIAA0719	translocase of outer mitochondrial membrane 70 homolog A (yeast)	protein-coding	0.05	0.653465
Merged-chr10-21295951-1	chr10	21295901	21296001	+	3.4	cIP2vsInput	promoter-TSS (NM_001145209)	promoter-TSS (NM_001145209)	-28	NM_001042593	56422	Mm.25527	NM_001042593	ENSMUSG00000019977	Hbs1l	2810035F15Rik|AI326327|eRFS	Hbs1-like (S. cerevisiae)	protein-coding	0.17	0.732673
Merged-chr5-124327618-1	chr5	124327568	124327668	+	3.4	cIP2vsInput	promoter-TSS (NM_001134717)	promoter-TSS (NM_001134717)	-471	NM_028310	72650	Mm.121658	NM_001134717	ENSMUSG00000047635	2810006K23Rik	-	RIKEN cDNA 2810006K23 gene	protein-coding	0.1	0.653465
Merged-chr6-106800091-2	chr6	106800023	106800159	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_021449)	promoter-TSS (NM_021449)	-4	NM_175357	58799	Mm.290085	NM_021449		Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding	0.110294	0.715328
Merged-chr19-27218270-1	chr19	27218220	27218320	+	3.4	cIP2vsInput	"intron (NM_013703, intron 1 of 18)"	CpG	1250	NM_001161420	22359	Mm.4141	NM_001161420	ENSMUSG00000024924	Vldlr	AA408956|AI451093|AW047288	very low density lipoprotein receptor	protein-coding	0.12	0.732673
Merged-chrY-6674355-1	chrY	6674305	6674405	+	3.4	cIP1vsInput	Intergenic	Intergenic	493422	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.277228
Merged-chr5-133386202-2	chr5	133386146	133386258	+	3.4	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-713546	NM_030719	80909	Mm.426767	NM_030719		Gatsl2	7530428J21Rik|AW742413|Gats|Gatsl1	GATS protein-like 2	protein-coding	0.017857	0.460177
Merged-chr1-71652780-1	chr1	71652730	71652830	+	3.4	cIP1vsInput	promoter-TSS (NR_040308)	promoter-TSS (NR_040308)	454	NM_010233	14268	Mm.193099	NM_001276408	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding	0.1	0.613861
Merged-chr9-21546722-1	chr9	21546672	21546772	+	3.4	cIP2vsInput	promoter-TSS (NM_021531)	promoter-TSS (NM_021531)	-172	NM_021531	59035	Mm.178115	NM_021531	ENSMUSG00000032185	Carm1	Prmt4	coactivator-associated arginine methyltransferase 1	protein-coding	0.11	0.742574
Merged-chr3-152457759-2	chr3	152457700	152457818	+	3.4	cIP1vsInput|cIP2vsInput	"intron (NM_001080755, intron 12 of 13)"	"intron (NM_001080755, intron 12 of 13)"	61065	NM_198416	108946	Mm.379292	NM_001080755	ENSMUSG00000039068	Zzz3	3110065C23Rik|6430567E01Rik|AA408566|AI481057|AW556059|R75514	"zinc finger, ZZ domain containing 3"	protein-coding	0	0.453782
Merged-chr2-114046386-1	chr2	114046336	114046436	+	3.4	cIP2vsInput	TTS (NM_009608)	TTS (NM_009608)	6425	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	"actin, alpha, cardiac muscle 1"	protein-coding	0.01	0.435644
Merged-chr18-49755554-2	chr18	49755468	49755641	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001170960)	promoter-TSS (NM_001170960)	47	NM_026854	68857	Mm.96010	NM_001170960	ENSMUSG00000024505	Dtwd2	1190002H09Rik|8030470C17Rik|AI414673|BB115449	DTW domain containing 2	protein-coding	0.127168	0.735632
Merged-chrX-126771306-2	chrX	126771228	126771385	+	3.4	cIP1vsInput|cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	62698	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding	0.012739	0.348101
Merged-chr7-34168560-2	chr7	34168484	34168637	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_016682)	promoter-TSS (NM_016682)	-31	NM_016682	50995	Mm.27560	NM_016682	ENSMUSG00000052997	Uba2	AA986091|Arx|Sae2|UBA1|Ubl1a2|Uble1b	ubiquitin-like modifier activating enzyme 2	protein-coding	0.124183	0.733766
Merged-chr17-86963043-1	chr17	86962993	86963093	+	3.4	cIP2vsInput	promoter-TSS (NM_145491)	promoter-TSS (NM_145491)	-68	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	"ras homolog gene family, member Q"	protein-coding	0.07	0.712871
Merged-chr10-117013859-1	chr10	117013809	117013909	+	3.4	cIP2vsInput	"intron (NM_001007583, intron 9 of 9)"	"intron (NM_001007583, intron 9 of 9)"	27545	NM_001007583	382427	Mm.339322	NM_001007583	ENSMUSG00000020169	Best3	Vmd2l3|mBest4	bestrophin 3	protein-coding	0	0.356436
Merged-chrX-73966943-1	chrX	73966893	73966993	+	3.4	cIP2vsInput	promoter-TSS (NM_008224)	promoter-TSS (NM_008224)	-628	NM_008224	15161	Mm.439140	NM_008224	ENSMUSG00000031386	Hcfc1	AW060991|HCF|HCF1	host cell factor C1	protein-coding	0.06	0.534653
Merged-chr1-135800688-1	chr1	135800638	135800738	+	3.4	cIP2vsInput	"intron (NM_001112702, intron 2 of 8)"	"intron (NM_001112702, intron 2 of 8)"	1177	NM_001112702	21952	Mm.44379	NM_001112702	ENSMUSG00000026418	Tnni1	2700018B22Rik|AI747285|ssTnI	"troponin I, skeletal, slow 1"	protein-coding	0.01	0.623762
Merged-chr5-92435140-2	chr5	92435076	92435204	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_183392)	promoter-TSS (NM_183392)	59	NM_183392	269113	Mm.275289	NM_183392	ENSMUSG00000034826	Nup54	3110079L04Rik|54kDa	nucleoporin 54	protein-coding	0.117188	0.689922
Merged-chr11-121204719-2	chr11	121204665	121204773	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025402)	promoter-TSS (NM_025402)	-71	NM_025402	66179	Mm.390403	NM_025402	ENSMUSG00000025169	Ogfod3	1110031I02Rik	2-oxoglutarate and iron-dependent oxygenase domain containing 3	protein-coding	0.12963	0.733945
Merged-chr14-55095104-1	chr14	55095054	55095154	+	3.4	cIP2vsInput	"5' UTR (NM_153083, exon 1 of 2)"	"5' UTR (NM_153083, exon 1 of 2)"	320	NM_153083	105663	Mm.319204	NM_153083	ENSMUSG00000045691	Thtpa	AW122966	thiamine triphosphatase	protein-coding	0.06	0.623762
Merged-chr16-26105248-1	chr16	26105198	26105298	+	3.4	cIP2vsInput	"exon (NM_173379, exon 1 of 15)"	"exon (NM_173379, exon 1 of 15)"	536	NM_173379	210530		NM_173379		Leprel1	4832416N06|AW553532|Mlat4|P3H2	leprecan-like 1	protein-coding	0.1	0.623762
Merged-chr11-97975193-1	chr11	97975143	97975243	+	3.4	cIP2vsInput	"intron (NM_001163608, intron 2 of 13)"	RMER17A2|LTR|ERVK	11253	NM_028199	72324	Mm.482750	NM_001163608	ENSMUSG00000017417	Plxdc1	2410003I07Rik|AI848450|Tem7	plexin domain containing 1	protein-coding	0.01	0.564356
Merged-chr19-5273316-1	chr19	5273266	5273366	+	3.4	cIP2vsInput	promoter-TSS (NM_153129)	promoter-TSS (NM_153129)	-197	NM_153129	107975	Mm.234923	NM_153129	ENSMUSG00000024855	Pacs1	AI325977	phosphofurin acidic cluster sorting protein 1	protein-coding	0.14	0.772277
Merged-chr5-149636915-1	chr5	149636865	149636965	+	3.4	cIP2vsInput	promoter-TSS (NM_013559)	promoter-TSS (NM_013559)	-600	NM_013559	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I	heat shock 105kDa/110kDa protein 1	protein-coding	0.06	0.455446
Merged-chr1-161876816-1	chr1	161876766	161876866	+	3.4	cIP1vsInput	promoter-TSS (NM_172645)	promoter-TSS (NM_172645)	-155	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding	0.11	0.70297
Merged-chr11-95991371-1	chr11	95991321	95991421	+	3.4	cIP2vsInput	"intron (NM_009951, intron 2 of 14)"	CpG	14573	NM_009951	140486	Mm.294769	NM_009951	ENSMUSG00000013415	Igf2bp1	AL024068|AW549074|CRD-BP|Crdbp|D030026A21Rik|D11Moh40e|D11Moh45|IMP-1|Neilsen|Zbp1	insulin-like growth factor 2 mRNA binding protein 1	protein-coding	0.13	0.831683
Merged-chr6-113483894-1	chr6	113483844	113483944	+	3.4	cIP1vsInput	TTS (NM_178942)	TTS (NM_178942)	325	NM_133930	171508	Mm.41593	NM_133930	ENSMUSG00000030284	Creld1	AI843811	cysteine-rich with EGF-like domains 1	protein-coding	0.01	0.643564
Merged-chr12-24975071-1	chr12	24975021	24975121	+	3.4	cIP2vsInput	"intron (NM_001081378, intron 1 of 31)"	CpG	139	NM_001081378	77480	Mm.475357	NM_001081378	ENSMUSG00000036333	Kidins220	3110039L19Rik|AI194387|AI316525|C330002I19Rik|mKIAA1250	kinase D-interacting substrate 220	protein-coding	0.1	0.70297
Merged-chr8-81341725-1	chr8	81341675	81341775	+	3.4	cIP2vsInput	Intergenic	Intergenic	-326819	NM_027554	74841	Mm.246018	NM_027554	ENSMUSG00000038250	Usp38	4631402N15Rik|4833420O05Rik|AA536967|AU044701|AW544820|mKIAA1891	ubiquitin specific peptidase 38	protein-coding	0.05	0.60396
Merged-chr2-91963720-2	chr2	91963658	91963782	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_138306)	promoter-TSS (NM_138306)	-157	NM_138306	104418	Mm.314923	NM_001166597	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding	0.137097	0.784
Merged-chr19-27945900-1	chr19	27945850	27945950	+	3.4	cIP1vsInput	"intron (NM_001166414, intron 1 of 17)"	"intron (NM_001166414, intron 1 of 17)"	37048	NM_001166414	19726	Mm.313321	NM_001166414	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	"regulatory factor X, 3 (influences HLA class II expression)"	protein-coding	0	0.336634
Merged-chr2-5951440-1	chr2	5951390	5951490	+	3.4	cIP2vsInput	promoter-TSS (NM_001081132)	promoter-TSS (NM_001081132)	-29	NM_001081132	326622	Mm.31102	NM_001081132	ENSMUSG00000043241	Upf2	-	UPF2 regulator of nonsense transcripts homolog (yeast)	protein-coding	0.14	0.80198
Merged-chr1-180777819-1	chr1	180777769	180777869	+	3.4	cIP2vsInput	Intergenic	CpG	35784	NM_008210	15078	Mm.442502	NM_008210	ENSMUSG00000060743	H3f3a	H3.3A	"H3 histone, family 3A"	protein-coding	0.09	0.693069
Merged-chr17-80483060-1	chr17	80483010	80483110	+	3.4	cIP2vsInput	Intergenic	CpG	-2607	NM_009231	20662	Mm.360004	NM_009231	ENSMUSG00000024241	Sos1	4430401P03Rik|9630010N06|AI449023	son of sevenless homolog 1 (Drosophila)	protein-coding	0.1	0.673267
Merged-chr11-58938943-1	chr11	58938893	58938993	+	3.4	cIP2vsInput	promoter-TSS (NM_022423)	promoter-TSS (NM_022423)	-37	NM_022423	108660	Mm.249986	NM_022423		Rnf187	2410016F01Rik|AB030190|RACO-1	ring finger protein 187	protein-coding	0.14	0.742574
Merged-chr19-53038601-1	chr19	53038551	53038651	+	3.4	cIP2vsInput	promoter-TSS (NM_133216)	promoter-TSS (NM_133216)	53	NM_133216	170750	Mm.99776	NM_133216	ENSMUSG00000025027	Xpnpep1	D230045I08Rik|sAMP	"X-prolyl aminopeptidase (aminopeptidase P) 1, soluble"	protein-coding	0.09	0.732673
Merged-chr13-100492657-1	chr13	100492607	100492707	+	3.4	cIP2vsInput	promoter-TSS (NM_022011)	promoter-TSS (NM_022011)	-48	NM_022011	23894	Mm.272533	NM_022011	ENSMUSG00000021639	Gtf2h2	44kDa|BTF2 p44|BTF2-p44|Btf2p44|p44	"general transcription factor II H, polypeptide 2"	protein-coding	0.06	0.60396
Merged-chr5-15486558-1	chr5	15486508	15486608	+	3.4	cIP1vsInput	Intergenic	(TCTG)n|Simple_repeat|Simple_repeat	-132541	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0	0.455446
Merged-chr2-33216105-1	chr2	33216055	33216155	+	3.4	cIP2vsInput	"5' UTR (NM_011923, exon 1 of 5)"	"5' UTR (NM_011923, exon 1 of 5)"	144	NM_011923	26360	Mm.208919	NM_011923	ENSMUSG00000004105	Angptl2	AI593246|AW260363|Arp2	angiopoietin-like 2	protein-coding	0.03	0.60396
Merged-chr10-128626902-1	chr10	128626852	128626952	+	3.4	cIP2vsInput	promoter-TSS (NM_013765)	promoter-TSS (NM_013765)	-396	NM_013765	27370	Mm.261679	NM_013765	ENSMUSG00000025362	Rps26	-	ribosomal protein S26	protein-coding	0.06	0.50495
Merged-chr8-20297009-1	chr8	20296959	20297059	+	3.4	cIP2vsInput	"intron (NR_030708, intron 1 of 4)"	CpG	423	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo	0.09	0.693069
Merged-chr4-128925229-1	chr4	128925179	128925279	+	3.4	cIP2vsInput	Intergenic	Intergenic	37188	NM_172875	242669	Mm.215814	NM_172875	ENSMUSG00000028789	Adc	4933429I20Rik|AZIN2|Azi2|B930082O19|Odcp	arginine decarboxylase	protein-coding	0.04	0.594059
Merged-chr6-12814056-1	chr6	12814006	12814106	+	3.4	cIP1vsInput	Intergenic	RLTR1F_Mm|LTR|ERVK	-64803	NM_001164805	330267	Mm.400067	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	"thrombospondin, type I, domain containing 7A"	protein-coding	0.02	0.445545
Merged-chr6-17306236-1	chr6	17306186	17306286	+	3.4	cIP2vsInput	promoter-TSS (NM_007616)	promoter-TSS (NM_007616)	-99	NM_007616	12389	Mm.28278	NM_001243064	ENSMUSG00000007655	Cav1	Cav|Cav-1	"caveolin 1, caveolae protein"	protein-coding	0.06	0.663366
Merged-chr1-28067710-1	chr1	28067660	28067760	+	3.4	cIP2vsInput	Intergenic	Intergenic	712542	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0	0.247525
Merged-chr2-139258811-1	chr2	139258761	139258861	+	3.4	cIP1vsInput	Intergenic	Intergenic	-235109	NM_175467	228677	Mm.100450	NM_175467	ENSMUSG00000039092	Sptlc3	C130053K05Rik	"serine palmitoyltransferase, long chain base subunit 3"	protein-coding	0.03	0.336634
Merged-chr9-72628794-1	chr9	72628744	72628844	+	3.4	cIP2vsInput	Intergenic	Intergenic	-33553	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	"neural precursor cell expressed, developmentally down-regulated 4"	protein-coding	0.02	0.50495
Merged-chr12-80946092-1	chr12	80946042	80946142	+	3.4	cIP2vsInput	promoter-TSS (NR_045057)	promoter-TSS (NR_045057)	588	NM_009159	20384	Mm.43331	NM_001079694	ENSMUSG00000021134	Srsf5	Sfrs5	serine/arginine-rich splicing factor 5	protein-coding	0.14	0.722772
Merged-chr11-46069849-1	chr11	46069799	46069899	+	3.4	cIP2vsInput	"intron (NM_009616, intron 3 of 22)"	"intron (NM_009616, intron 3 of 22)"	13862	NM_009616	11492	Mm.89940	NM_009616	ENSMUSG00000011256	Adam19	AL024287|M[b]|Mltnb	a disintegrin and metallopeptidase domain 19 (meltrin beta)	protein-coding	0.04	0.643564
Merged-chr2-80054199-2	chr2	80054140	80054259	+	3.4	cIP1vsInput|cIP2vsInput	"intron (NM_016744, intron 1 of 14)"	"intron (NM_016744, intron 1 of 14)"	74772	NM_016744	18573	Mm.40678	NM_001009978	ENSMUSG00000059173	Pde1a	AI987702|AW125737	"phosphodiesterase 1A, calmodulin-dependent"	protein-coding	0	0.325
Merged-chr7-128238227-1	chr7	128238177	128238277	+	3.4	cIP2vsInput	promoter-TSS (NM_177001)	promoter-TSS (NM_177001)	-196	NM_177001	100043133	Mm.183647	NM_177001	ENSMUSG00000062944	9130023H24Rik	GLI4	RIKEN cDNA 9130023H24 gene	protein-coding	0.11	0.732673
Merged-chr9-124424424-1	chr9	124424374	124424474	+	3.4	cIP2vsInput	"non-coding (NR_027950, exon 2 of 2)"	"non-coding (NR_027950, exon 2 of 2)"	637	NR_015516	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	miscRNA	0.14	0.663366
Merged-chr13-55727332-1	chr13	55727282	55727382	+	3.4	cIP2vsInput	promoter-TSS (NM_028281)	promoter-TSS (NM_028281)	-36	NM_028281	72562	Mm.28145	NM_028281	ENSMUSG00000021496	Pcbd2	2700061N24Rik|Dcoh2|Dcohm	pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2	protein-coding	0.14	0.772277
Merged-chr18-80934061-1	chr18	80934011	80934111	+	3.4	cIP2vsInput	promoter-TSS (NM_001201569)	promoter-TSS (NM_001201569)	-3	NM_015805	50771	Mm.247138	NM_001201569	ENSMUSG00000024566	Atp9b	AA934181|Atpc2b|IIb|MMR	"ATPase, class II, type 9B"	protein-coding	0.14	0.712871
Merged-chr9-57521170-1	chr9	57521120	57521220	+	3.4	cIP2vsInput	promoter-TSS (NM_007747)	promoter-TSS (NM_007747)	-62	NM_007747	12858	Mm.273403	NM_007747	ENSMUSG00000000088	Cox5a	AA959768|CcOX	cytochrome c oxidase subunit Va	protein-coding	0.15	0.732673
Merged-chr18-30272485-1	chr18	30272435	30272535	+	3.4	cIP2vsInput	promoter-TSS (NM_181414)	promoter-TSS (NM_181414)	-411	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	"phosphoinositide-3-kinase, class 3"	protein-coding	0.01	0.316832
Merged-chr3-49841588-1	chr3	49841538	49841638	+	3.4	cIP2vsInput	Intergenic	Intergenic	-84272	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding	0	0.306931
Merged-chr4-137593862-1	chr4	137593812	137593912	+	3.4	cIP1vsInput	promoter-TSS (NM_130879)	promoter-TSS (NM_130879)	-327	NM_130879	170707	Mm.218478	NM_130879	ENSMUSG00000043411	Usp48	2810449C13Rik|AI115503|BC021769|D330022K21Rik|Usp31	ubiquitin specific peptidase 48	protein-coding	0.05	0.544554
Merged-chr12-17992705-2	chr12	17992650	17992761	+	3.4	cIP1vsInput|cIP2vsInput	Intergenic	CpG	301891	NM_016677	53602	Mm.489835	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding	0.09009	0.6875
Merged-chr16-90747347-2	chr16	90747283	90747412	+	3.4	cIP1vsInput|cIP2vsInput	"intron (NM_029844, intron 1 of 2)"	"intron (NM_029844, intron 1 of 2)"	9023	NM_029844	77037	Mm.22455	NM_029844	ENSMUSG00000039956	Mrap	1110025G12Rik|Falp|ORF61	melanocortin 2 receptor accessory protein	protein-coding	0.015504	0.523077
Merged-chr2-177531333-1	chr2	177531283	177531383	+	3.4	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	33107	NR_036450	433520	Mm.425117	NM_001024825		Gm14403	OTTMUSG00000016571	predicted gene 14403	miscRNA	0	0.376238
Merged-chr19-53365041-2	chr19	53364979	53365104	+	3.4	cIP1vsInput|cIP2vsInput	"intron (NM_001008542, intron 3 of 5)"	"intron (NM_001008542, intron 3 of 5)"	25532	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding	0.016	0.492063
Merged-chrX-103493472-1	chrX	103493422	103493522	+	3.4	cIP2vsInput	promoter-TSS (NR_015508)	promoter-TSS (NR_015508)	-104	NR_015508	70252	Mm.380486	NR_015508	ENSMUSG00000097571	Jpx	2010000I03Rik|2510040I06Rik|Enox	"Jpx transcript, Xist activator (non-protein coding)"	miscRNA	0.13	0.683168
Merged-chr2-130563671-2	chr2	130563591	130563752	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_040348)	promoter-TSS (NR_040348)	78	NR_040348	321014	Mm.442588	NR_040348	ENSMUSG00000060029	4930473A02Rik	-	RIKEN cDNA 4930473A02 gene	miscRNA	0.080745	0.691358
Merged-chr11-48823949-1	chr11	48823899	48823999	+	3.4	cIP2vsInput	Intergenic	Intergenic	-2189	NM_053166	94089	Mm.390335	NM_053166		Trim7	AI790312	tripartite motif-containing 7	protein-coding	0.03	0.465347
Merged-chr4-132608260-1	chr4	132608210	132608310	+	3.4	cIP2vsInput	Intergenic	ID_B1|SINE|B4	-30786	NM_210071	14050	Mm.227733	NM_211356	ENSMUSG00000028886	Eya3	AI844637	eyes absent 3 homolog (Drosophila)	protein-coding	0.02	0.534653
Merged-chr14-52020365-1	chr14	52020315	52020415	+	3.4	cIP2vsInput	promoter-TSS (NM_001253694)	promoter-TSS (NM_001253694)	368	NM_001253696	69890	Mm.475652	NM_001253694	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding	0.04	0.524752
Merged-chr6-39725345-1	chr6	39725295	39725395	+	3.4	cIP2vsInput	"5' UTR (NM_139294, exon 1 of 22)"	"5' UTR (NM_139294, exon 1 of 22)"	118	NM_139294	109880	Mm.489691	NM_139294	ENSMUSG00000002413	Braf	9930012E13Rik|AA120551|AA387315|AA473386|B-raf|Braf-2|Braf2|C230098H17|C87398|D6Ertd631e	Braf transforming gene	protein-coding	0.19	0.851485
Merged-chr13-81657852-1	chr13	81657802	81657902	+	3.4	cIP2vsInput	promoter-TSS (NM_030257)	promoter-TSS (NM_030257)	46	NM_030257	80289	Mm.439853	NM_030257	ENSMUSG00000035840	Lysmd3	1110030H10Rik|BC003322	"LysM, putative peptidoglycan-binding, domain containing 3"	protein-coding	0.14	0.70297
Merged-chr17-25941957-1	chr17	25941907	25942007	+	3.4	cIP2vsInput	promoter-TSS (NM_011822)	promoter-TSS (NM_011822)	5	NM_011822	14755	Mm.362054	NM_011822	ENSMUSG00000025728	Pigq	Gpi1|Gpi1h|Gpi1p|Gpih	"phosphatidylinositol glycan anchor biosynthesis, class Q"	protein-coding	0.15	0.732673
Merged-chrY-6700263-1	chrY	6700213	6700313	+	3.4	cIP1vsInput	Intergenic	MTD|LTR|ERVL-MaLR	467514	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.445545
Merged-chr5-54096196-2	chr5	54096127	54096266	+	3.4	cIP1vsInput|cIP2vsInput	"intron (NM_001081103, intron 3 of 11)"	"intron (NM_001081103, intron 3 of 11)"	97673	NM_001081103	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding	0.014388	0.457143
Merged-chr2-30133713-1	chr2	30133663	30133763	+	3.4	cIP2vsInput	promoter-TSS (NM_146252)	promoter-TSS (NM_146252)	-158	NM_146252	70296	Mm.490985	NM_146252	ENSMUSG00000039678	Tbc1d13	2600014A06Rik|BC025586	"TBC1 domain family, member 13"	protein-coding	0.13	0.683168
Merged-chr6-48444289-1	chr6	48444239	48444339	+	3.4	cIP2vsInput	"intron (NM_001085417, intron 1 of 4)"	"intron (NM_001085417, intron 1 of 4)"	801	NM_001085415	68910	Mm.2464	NM_001085415	ENSMUSG00000068551	Zfp467	1190001I08Rik|AB041616|AI426952|AV017623|EZI|Znf467	zinc finger protein 467	protein-coding	0.07	0.712871
Merged-chr15-100082249-2	chr15	100082181	100082317	+	3.4	cIP1vsInput|cIP2vsInput	"intron (NR_037311, intron 3 of 3)"	"intron (NR_037311, intron 3 of 3)"	43585	NM_001159361	239667	Mm.243658	NM_001159361	ENSMUSG00000023026	Dip2b	4932422C22|AI317237|AI854602|mKIAA1463	DIP2 disco-interacting protein 2 homolog B (Drosophila)	protein-coding	0.029412	0.554745
Merged-chr8-20324486-1	chr8	20324436	20324536	+	3.4	cIP1vsInput	Intergenic	L1_Mm|LINE|L1	-27054	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo	0	0.366337
Merged-chrX-13346933-1	chrX	13346883	13346983	+	3.4	cIP2vsInput	Intergenic	Intergenic	65911	NM_010028	13205	Mm.289662	NM_010028	ENSMUSG00000000787	Ddx3x	D1Pas1-rs2|Ddx3|Fin14	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked"	protein-coding	0.03	0.435644
Merged-chr1-163994819-1	chr1	163994769	163994869	+	3.4	cIP2vsInput	promoter-TSS (NM_201364)	promoter-TSS (NM_201364)	-38	NM_201364	381306	Mm.28152	NM_201364	ENSMUSG00000041406	BC055324	-	cDNA sequence BC055324	protein-coding	0.06	0.633663
Merged-chr10-96617024-1	chr10	96616974	96617074	+	3.4	cIP2vsInput	promoter-TSS (NM_007569)	promoter-TSS (NM_007569)	23	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	"B cell translocation gene 1, anti-proliferative"	protein-coding	0.1	0.643564
Merged-chr17-35700778-1	chr17	35700728	35700828	+	3.4	cIP2vsInput	promoter-TSS (NM_001198833)	promoter-TSS (NM_001198833)	-188	NM_001198833	12305	Mm.5021	NM_001198831	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	"discoidin domain receptor family, member 1"	protein-coding	0.07	0.70297
Merged-chr8-122775446-1	chr8	122775396	122775496	+	3.4	cIP2vsInput	promoter-TSS (NM_144932)	promoter-TSS (NM_144932)	-59	NM_144932	257633	Mm.334875	NM_144932	ENSMUSG00000015016	Acsf3	BB101783	acyl-CoA synthetase family member 3	protein-coding	0.11	0.544554
Merged-chr13-74208676-1	chr13	74208626	74208726	+	3.4	cIP1vsInput	promoter-TSS (NM_177333)	promoter-TSS (NM_177333)	24	NM_177333	211446		NM_177333	ENSMUSG00000034152	Exoc3	2810050O03Rik|E430013E20Rik|Sec6|Sec6l1	exocyst complex component 3	protein-coding	0.11	0.663366
Merged-chr5-29735862-2	chr5	29735781	29735943	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001127367)	promoter-TSS (NM_001127367)	-36	NM_001037941	23950	Mm.290110	NM_001037940	ENSMUSG00000029131	Dnajb6	Mrj|mDj4	"DnaJ (Hsp40) homolog, subfamily B, member 6"	protein-coding	0.111111	0.619632
Merged-chr9-72530428-1	chr9	72530378	72530478	+	3.4	cIP2vsInput	"intron (NR_045735, intron 1 of 2)"	"intron (NR_045735, intron 1 of 2)"	1430	NR_045735	75115	Mm.280755	NR_045735	ENSMUSG00000096986	4930509E16Rik	-	RIKEN cDNA 4930509E16 gene	miscRNA	0.07	0.564356
Merged-chr16-21794468-1	chr16	21794418	21794518	+	3.4	cIP2vsInput	"intron (NR_037957, intron 1 of 4)"	CpG	121	NR_037958	100043489	Mm.326535	NR_037957	ENSMUSG00000097290	1300002E11Rik	1500026P21Rik	RIKEN cDNA 1300002E11 gene	miscRNA	0.09	0.60396
Merged-chr8-123806148-1	chr8	123806098	123806198	+	3.4	cIP2vsInput	"exon (NM_009003, exon 1 of 8)"	"exon (NM_009003, exon 1 of 8)"	152	NM_009003	19341	Mm.9221	NM_009003	ENSMUSG00000019478	Rab4a	AI848268|Rab4	"RAB4A, member RAS oncogene family"	protein-coding	0.13	0.623762
Merged-chr18-80050550-1	chr18	80050500	80050600	+	3.4	cIP1vsInput	"intron (NM_053117, intron 1 of 2)"	"intron (NM_053117, intron 1 of 2)"	3655	NM_053117	93737	Mm.24678	NM_053117	ENSMUSG00000056214	Pard6g	2410049N21Rik|Par6a	par-6 partitioning defective 6 homolog gamma (C. elegans)	protein-coding	0	0.29703
Merged-chr19-11770298-2	chr19	11770230	11770367	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025606)	promoter-TSS (NM_025606)	-117	NM_025606	94063	Mm.203928	NM_025606	ENSMUSG00000024683	Mrpl16	2310039D06Rik	mitochondrial ribosomal protein L16	protein-coding	0.043796	0.550725
Merged-chr3-136725547-2	chr3	136725490	136725604	+	3.4	cIP1vsInput|cIP2vsInput	"intron (NM_008913, intron 1 of 13)"	"intron (NM_008913, intron 1 of 13)"	54777	NM_008913	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|AI841391|AW413465|CN|Caln|Calna|CnA	"protein phosphatase 3, catalytic subunit, alpha isoform"	protein-coding	0.008772	0.443478
Merged-chr16-90008691-1	chr16	90008641	90008741	+	3.4	cIP2vsInput	Intergenic	Tigger5|DNA|TcMar-Tigger	-33992	NM_001145886	21844	Mm.310902	NM_001145886	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding	0	0.49505
Merged-chr8-70865732-1	chr8	70865682	70865782	+	3.4	cIP2vsInput	Intergenic	CpG	7758	NM_026964	234388	Mm.295791	NM_026964	ENSMUSG00000007721	Ccdc124	1810023B24Rik	coiled-coil domain containing 124	protein-coding	0.11	0.712871
Merged-chr12-113000580-1	chr12	113000530	113000630	+	3.4	cIP2vsInput	promoter-TSS (NM_028193)	promoter-TSS (NM_028193)	41	NM_028193	72308	Mm.196721	NM_028193	ENSMUSG00000011158	Brf1	2510002F24Rik|GTF3B|TAF3C|TAFIII90|TFIIIB90|mTFIIIB90	"BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)"	protein-coding	0.16	0.693069
Merged-chr16-27389093-1	chr16	27389043	27389143	+	3.4	cIP1vsInput	"exon (NM_026202, exon 1 of 11)"	"exon (NM_026202, exon 1 of 11)"	116	NM_026202	67501	Mm.258985	NM_001025615	ENSMUSG00000038127	Ccdc50	2610529H08Rik|5730448P06Rik|AW048328|AW546090|C3orf6|D16Bwg1543e	coiled-coil domain containing 50	protein-coding	0.13	0.683168
Merged-chr6-83136945-1	chr6	83136895	83136995	+	3.4	cIP2vsInput	promoter-TSS (NM_133641)	promoter-TSS (NM_133641)	-139	NM_133641	20166	Mm.4139	NM_001136227	ENSMUSG00000034930	Rtkn	-	rhotekin	protein-coding	0.03	0.613861
Merged-chr5-67428093-1	chr5	67428043	67428143	+	3.4	cIP2vsInput	promoter-TSS (NM_001164806)	promoter-TSS (NM_001164806)	-294	NM_001164806	666938	Mm.101339	NM_001164806	ENSMUSG00000092060	Bend4	D330027G24Rik|EG666938	BEN domain containing 4	protein-coding	0.08	0.633663
Merged-chr3-108444768-1	chr3	108444718	108444818	+	3.4	cIP2vsInput	"intron (NM_011319, intron 1 of 11)"	CpG	491	NM_011319	20226	Mm.28688	NM_001204979	ENSMUSG00000068739	Sars	Sars1|Strs|serRS	seryl-aminoacyl-tRNA synthetase	protein-coding	0.08	0.633663
Merged-chr7-141172767-1	chr7	141172717	141172817	+	3.4	cIP2vsInput	promoter-TSS (NM_001172100)	promoter-TSS (NM_001172100)	84	NM_001172100	107702	Mm.279485	NM_001172100	ENSMUSG00000038650	Rnh1	AW546468|C80305|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding	0.08	0.574257
Merged-chr18-53744729-1	chr18	53744679	53744779	+	3.4	cIP2vsInput	promoter-TSS (NM_178686)	promoter-TSS (NM_178686)	-182	NM_178686	225523	Mm.193678	NM_178686	ENSMUSG00000048799	Cep120	A230075C01|AU016693|Ccdc100	centrosomal protein 120	protein-coding	0.09	0.673267
Merged-chr11-114830259-1	chr11	114830209	114830309	+	3.4	cIP2vsInput	Intergenic	Intergenic	-21273	NM_001110337	70355	Mm.242413	NM_001110337	ENSMUSG00000051043	Gprc5c	1110028I06Rik|3200002M13Rik|Raig3	"G protein-coupled receptor, family C, group 5, member C"	protein-coding	0.04	0.633663
Merged-chr8-20517941-2	chr8	20517847	20518035	+	3.4	cIP1vsInput|cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-93127	NR_028428	381598	Mm.483074	NM_001024708	ENSMUSG00000071793	2610005L07Rik	2810038F24Rik|6720476A01Rik	cadherin 11 pseudogene	pseudo	0.015957	0.428571
Merged-chr17-35879702-2	chr17	35879633	35879772	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026987)	promoter-TSS (NM_026987)	-76	NM_026987	69192	Mm.390986	NM_026987	ENSMUSG00000024422	Dhx16	2410006N22Rik|DBP2|Ddx16|mKIAA0577	DEAH (Asp-Glu-Ala-His) box polypeptide 16	protein-coding	0.093525	0.621429
Merged-chr4-123917311-1	chr4	123917261	123917361	+	3.4	cIP2vsInput	promoter-TSS (NM_017475)	promoter-TSS (NM_017475)	-122	NM_017475	54170	Mm.220922	NM_017475	ENSMUSG00000028646	Rragc	AU041672|Gtr2|RAGC|TIB929|YGR163W	Ras-related GTP binding C	protein-coding	0.06	0.613861
Merged-chr2-94157948-1	chr2	94157898	94157998	+	3.4	cIP2vsInput	promoter-TSS (NM_019657)	promoter-TSS (NM_019657)	-39	NM_019657	56348		NM_019657	ENSMUSG00000027195	Hsd17b12	2610510O05Rik|AI172963|KIK-I|Kik1	hydroxysteroid (17-beta) dehydrogenase 12	protein-coding	0.1	0.485149
Merged-chr3-107760347-1	chr3	107760297	107760397	+	3.4	cIP2vsInput	"5' UTR (NM_001113529, exon 1 of 9)"	"5' UTR (NM_001113529, exon 1 of 9)"	122	NM_001113530	12977	Mm.795	NM_001113529	ENSMUSG00000014599	Csf1	C87615|Csfm|MCSF|op	colony stimulating factor 1 (macrophage)	protein-coding	0.01	0.524752
Merged-chr8-74993630-1	chr8	74993580	74993680	+	3.4	cIP2vsInput	promoter-TSS (NM_178017)	promoter-TSS (NM_178017)	-73	NM_178017	70823	Mm.261739	NM_178017	ENSMUSG00000034518	Hmgxb4	4733401K04Rik|AI316803|E430025G12|Hmgb2l1	HMG box domain containing 4	protein-coding	0.14	0.663366
Merged-chr8-111717278-1	chr8	111717228	111717328	+	3.4	cIP2vsInput	"intron (NM_009954, intron 2 of 6)"	"intron (NM_009954, intron 2 of 6)"	14858	NM_001198839	12927	Mm.3758	NM_001198839	ENSMUSG00000031955	Bcar1	AI385681|Cas|Crkas	breast cancer anti-estrogen resistance 1	protein-coding	0.01	0.574257
Merged-chr15-59314851-1	chr15	59314801	59314901	+	3.4	cIP2vsInput	promoter-TSS (NM_009270)	promoter-TSS (NM_009270)	-241	NM_009270	20775	Mm.296169	NM_009270	ENSMUSG00000022351	Sqle	AI323792	squalene epoxidase	protein-coding	0.15	0.782178
Merged-chr8-111561814-2	chr8	111561742	111561886	+	3.4	cIP1vsInput|cIP2vsInput	"intron (NM_001168623, intron 1 of 4)"	"intron (NM_001168623, intron 1 of 4)"	23471	NM_001168623	170737	Mm.271578	NM_001168621	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding	0.006944	0.42069
Merged-chr5-142367475-1	chr5	142367425	142367525	+	3.4	cIP1vsInput	Intergenic	CpG	-34022	NM_199068	17425	Mm.24214	NM_010812	ENSMUSG00000056493	Foxk1	A630048H08Rik|AI463295|ENSMUSG00000075577|Gm10868|Mnf	forkhead box K1	protein-coding	0.13	0.643564
Merged-chr5-25530137-1	chr5	25530087	25530187	+	3.4	cIP1vsInput	"non-coding (NR_027388, exon 1 of 1)"	"non-coding (NR_027388, exon 1 of 1)"	119	NR_027388	73571	Mm.105263	NR_027388		1700096K18Rik	-	RIKEN cDNA 1700096K18 gene	miscRNA	0.1	0.663366
Merged-chr7-126776892-1	chr7	126776842	126776942	+	3.4	cIP2vsInput	promoter-TSS (NM_025347)	promoter-TSS (NM_025347)	-83	NM_026875	66090	Mm.27114	NM_025347	ENSMUSG00000042675	Ypel3	0610043B10Rik|1190001G19Rik|Suap	yippee-like 3 (Drosophila)	protein-coding	0.11	0.722772
Merged-chr4-117926800-2	chr4	117926745	117926856	+	3.4	cIP1vsInput|cIP2vsInput	"exon (NM_009711, exon 5 of 5)"	"exon (NM_009711, exon 5 of 5)"	2963	NM_009711	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding	0.117117	0.678571
Merged-chr19-4201725-1	chr19	4201675	4201775	+	3.4	cIP2vsInput	promoter-TSS (NM_011237)	promoter-TSS (NM_011237)	-122	NM_011237	19367	Mm.277629	NM_011237	ENSMUSG00000024824	Rad9a	Rad9	RAD9 homolog A	protein-coding	0.1	0.594059
Merged-chr8-84840598-1	chr8	84840548	84840648	+	3.4	cIP2vsInput	promoter-TSS (NM_009010)	promoter-TSS (NM_009010)	43	NM_009010	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23a homolog (S. cerevisiae)	protein-coding	0.12	0.693069
Merged-chr11-106272808-1	chr11	106272758	106272858	+	3.4	cIP2vsInput	"5' UTR (NM_001130187, exon 1 of 13)"	"5' UTR (NM_001130187, exon 1 of 13)"	164	NM_001130187	83796	Mm.21772	NM_001130187	ENSMUSG00000078619	Smarcd2	AW322457|Baf60b	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2"	protein-coding	0.11	0.574257
Merged-chr3-129532359-1	chr3	129532309	129532409	+	3.4	cIP2vsInput	promoter-TSS (NM_130450)	promoter-TSS (NM_130450)	-27	NM_130450	170439	Mm.314113	NM_130450	ENSMUSG00000041220	Elovl6	C77826|FAE|LCE	"ELOVL family member 6, elongation of long chain fatty acids (yeast)"	protein-coding	0.1	0.544554
Merged-chr11-62077053-1	chr11	62077003	62077103	+	3.4	cIP2vsInput	promoter-TSS (NM_001029936)	promoter-TSS (NM_001029936)	-44	NM_001029936	432572	Mm.459461	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb|mKIAA4061	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding	0.11	0.693069
Merged-chr18-44888985-1	chr18	44888935	44889035	+	3.4	cIP1vsInput	"3' UTR (NM_001163013, exon 30 of 30)"	"3' UTR (NM_001163013, exon 30 of 30)"	60320	NM_001163013	240255	Mm.244482	NM_001163013	ENSMUSG00000034653	Ythdc2	3010002F02Rik|BC037178	YTH domain containing 2	protein-coding	0	0.346535
Merged-chr4-123139937-2	chr4	123139853	123140021	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019489)	promoter-TSS (NM_019489)	4	NM_019489	56031	Mm.126873	NM_019489	ENSMUSG00000028651	Ppie	2010010D16Rik|Cyp33	peptidylprolyl isomerase E (cyclophilin E)	protein-coding	0.10119	0.680473
Merged-chr1-182683076-1	chr1	182683026	182683126	+	3.4	cIP2vsInput	Intergenic	MIRb|SINE|MIR	66104	NM_001033547	433386	Mm.338103	NM_001033547	ENSMUSG00000043429	4922505E12Rik	-	RIKEN cDNA 4922505E12 gene	protein-coding	0.03	0.633663
Merged-chr4-47438109-2	chr4	47438041	47438177	+	3.4	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	36258	NM_019998	56737	Mm.22218	NM_019998	ENSMUSG00000039740	Alg2	1110018A23Rik|1300013N08Rik|ALPG2|CDGIi|MNCb-5081	"asparagine-linked glycosylation 2 (alpha-1,3-mannosyltransferase)"	protein-coding	0.058824	0.605839
Merged-chr2-10048653-1	chr2	10048603	10048703	+	3.4	cIP2vsInput	promoter-TSS (NM_027748)	promoter-TSS (NM_027748)	-44	NM_027748	209361	Mm.401602	NM_027748	ENSMUSG00000025782	Taf3	140kDa|4933439M23Rik|AW539625|TAF140|TAFII-140|TAFII140|mTAFII140	"TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor"	protein-coding	0.12	0.712871
Merged-chr11-96789265-1	chr11	96789215	96789315	+	3.4	cIP2vsInput	"5' UTR (NM_007622, exon 1 of 6)"	"5' UTR (NM_007622, exon 1 of 6)"	129	NM_007622	12412	Mm.29055	NM_007622	ENSMUSG00000018666	Cbx1	Cbx|Cbx-rs2|E430007M08Rik|HP1B|Hp1beta|M31|MOD1	chromobox 1	protein-coding	0.17	0.712871
Merged-chr1-58711651-2	chr1	58711580	58711722	+	3.4	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-1635	NM_009805	12633	Mm.486313	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding	0.15493	0.713287
Merged-chr19-6128237-1	chr19	6128187	6128287	+	3.4	cIP2vsInput	promoter-TSS (NM_026912)	promoter-TSS (NM_026912)	-22	NM_026912	69024	Mm.329629	NM_026912	ENSMUSG00000024787	Snx15	1500032B08Rik|E130013C21Rik	sorting nexin 15	protein-coding	0.07	0.653465
Merged-chr8-95633406-1	chr8	95633356	95633456	+	3.4	cIP2vsInput	promoter-TSS (NM_030198)	promoter-TSS (NM_030198)	-153	NM_030198	78833	Mm.35546	NM_030198	ENSMUSG00000031669	Gins3	2700085M18Rik|AI616142	GINS complex subunit 3 (Psf3 homolog)	protein-coding	0.04	0.584158
Merged-chr9-64060241-1	chr9	64060191	64060291	+	3.4	cIP2vsInput	Intergenic	Intergenic	10412	NR_040713	68697	Mm.491042	NR_040713	ENSMUSG00000097036	1110036E04Rik	-	RIKEN cDNA 1110036E04 gene	miscRNA	0.03	0.524752
Merged-chr5-76974697-1	chr5	76974647	76974747	+	3.4	cIP2vsInput	promoter-TSS (NM_025691)	promoter-TSS (NM_025691)	-4	NM_025691	66661	Mm.461699	NM_025691	ENSMUSG00000036323	Srp72	5730576P14Rik|72kDa|AI132477|BC019196|C77589	signal recognition particle 72	protein-coding	0.06	0.712871
Merged-chr2-29965369-1	chr2	29965319	29965419	+	3.4	cIP2vsInput	promoter-TSS (NM_001177668)	promoter-TSS (NM_001177668)	-191	NM_001177668	20740	Mm.204969	NM_001076554	ENSMUSG00000057738	Sptan1	2610027H02Rik|Spna-2|Spna2	"spectrin alpha, non-erythrocytic 1"	protein-coding	0.11	0.742574
Merged-chr4-101356926-1	chr4	101356876	101356976	+	3.4	cIP2vsInput	promoter-TSS (NR_040708)	promoter-TSS (NR_040708)	-678	NR_040708	77866	Mm.137053	NR_040708	ENSMUSG00000086782	E130102H24Rik	-	RIKEN cDNA E130102H24 gene	miscRNA	0.12	0.712871
Merged-chr5-135934597-1	chr5	135934547	135934647	+	3.4	cIP2vsInput	promoter-TSS (NM_018871)	promoter-TSS (NM_018871)	44	NM_018871	22628	Mm.233813	NM_018871	ENSMUSG00000051391	Ywhag	14-3-3gamma|D7Bwg1348e	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide"	protein-coding	0.14	0.762376
Merged-chr12-55821055-1	chr12	55821005	55821105	+	3.4	cIP2vsInput	"5' UTR (NM_001112714, exon 1 of 41)"	"5' UTR (NM_001112714, exon 1 of 41)"	112	NM_019994	56784	Mm.292180	NM_001003719	ENSMUSG00000021027	Ralgapa1	2310003F20Rik|4930400K19Rik|AI563624|GRIPE|Garnl1|Tulip1|mKIAA0884	"Ral GTPase activating protein, alpha subunit 1"	protein-coding	0.11	0.722772
Merged-chr14-12284330-1	chr14	12284280	12284380	+	3.4	cIP2vsInput	"intron (NM_146051, intron 1 of 5)"	CpG	121	NM_178141	218734	Mm.44068	NM_146051	ENSMUSG00000033111	3830406C13Rik	3110059I09Rik|AV167947	RIKEN cDNA 3830406C13 gene	protein-coding	0.03	0.584158
Merged-chr9-107569353-1	chr9	107569303	107569403	+	3.4	cIP2vsInput	"intron (NM_010489, intron 1 of 3)"	CpG	190	NM_010489	15587	Mm.440982	NM_010489	ENSMUSG00000010047	Hyal2	AI256841|AU020858|AW555733	hyaluronoglucosaminidase 2	protein-coding	0.07	0.673267
Merged-chr5-14973694-1	chr5	14973644	14973744	+	3.4	cIP2vsInput	"intron (NR_001584, intron 2 of 3)"	"intron (NR_001584, intron 2 of 3)"	28400	NR_001584	74062	Mm.394766	NR_001584		Speer8-ps1	4933405L09Rik|SPEER-8|Speer8-ps	"spermatogenesis associated glutamate (E)-rich protein 8, pseudogene 1"	pseudo	0	0.405941
Merged-chr11-58846863-1	chr11	58846813	58846913	+	3.4	cIP2vsInput	Intergenic	L1MA7|LINE|L1	5747	NM_146537	258530	Mm.377556	NM_146537	ENSMUSG00000094805	Olfr311	MOR222-1	olfactory receptor 311	protein-coding	0	0.39604
Merged-chr4-3233380-1	chr4	3233330	3233430	+	3.4	cIP1vsInput	Intergenic	Lx|LINE|L1	-48075	NM_001167535	100312471	Mm.484976	NM_001167535	ENSMUSG00000095982	Vmn1r3	Gm11778|OTTMUSG00000004181	vomeronasal 1 receptor 3	protein-coding	0	0.366337
Merged-chr10-80053780-1	chr10	80053730	80053830	+	3.4	cIP2vsInput	promoter-TSS (NM_001037741)	promoter-TSS (NM_001037741)	-257	NM_001037741	625249	Mm.359573	NM_001037741	ENSMUSG00000075706	Gpx4	1700027O09Rik|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding	0.08	0.653465
Merged-chr1-125560481-1	chr1	125560431	125560531	+	3.4	cIP2vsInput	promoter-TSS (NM_028787)	promoter-TSS (NM_028787)	-535	NM_028787	74150	Mm.28654	NM_028787	ENSMUSG00000026342	Slc35f5	1300003P13Rik|AI646727	"solute carrier family 35, member F5"	protein-coding	0.13	0.663366
Merged-chr3-90490878-1	chr3	90490828	90490928	+	3.4	cIP2vsInput	"exon (NM_133854, exon 1 of 4)"	"exon (NM_133854, exon 1 of 4)"	135	NM_133854	20615	Mm.331182	NM_133854	ENSMUSG00000001018	Snapin	25kDa|AA407989|AV026596|Bloc1s7|Snap25bp|Snapap	SNAP-associated protein	protein-coding	0.11	0.712871
Merged-chr15-51865544-1	chr15	51865494	51865594	+	3.4	cIP2vsInput	promoter-TSS (NM_080635)	promoter-TSS (NM_080635)	-83	NM_080635	68135	Mm.289800	NM_080635	ENSMUSG00000022312	Eif3h	1110008A16Rik|40kD|9430017H16Rik|EIF3-P40|EIF3-gamma|Eif3s3	"eukaryotic translation initiation factor 3, subunit H"	protein-coding	0.09	0.693069
Merged-chr5-22550318-1	chr5	22550268	22550368	+	3.4	cIP2vsInput	promoter-TSS (NM_011959)	promoter-TSS (NM_011959)	13	NM_011959	26429	Mm.469664	NM_011959	ENSMUSG00000029012	Orc5	AL033327|MmORC5|Orc5l	"origin recognition complex, subunit 5"	protein-coding	0.08	0.643564
Merged-chr17-46084310-1	chr17	46084260	46084360	+	3.4	cIP2vsInput	Intergenic	Intergenic	-26694	NM_026768	68565	Mm.287443	NM_026768	ENSMUSG00000023967	Mrps18a	1110004O20Rik|C79712	mitochondrial ribosomal protein S18A	protein-coding	0.02	0.673267
Merged-chr4-114987298-1	chr4	114987248	114987348	+	3.4	cIP2vsInput	promoter-TSS (NM_025647)	promoter-TSS (NM_025647)	-70	NM_025647	66588	Mm.294159	NM_025647		Cmpk1	0610011D08Rik|Cmpk|UMP-CMPk	cytidine monophosphate (UMP-CMP) kinase 1	protein-coding	0.09	0.623762
Merged-chr9-56161015-1	chr9	56160965	56161065	+	3.4	cIP2vsInput	promoter-TSS (NM_019793)	promoter-TSS (NM_019793)	55	NM_019793	56434	Mm.393554	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding	0.12	0.752475
Merged-chr11-117115039-1	chr11	117114989	117115089	+	3.4	cIP2vsInput	promoter-TSS (NM_028777)	promoter-TSS (NM_028777)	-133	NR_029459	74136	Mm.272312	NM_001166506	ENSMUSG00000020823	Sec14l1	1200017E04Rik|2810012L19Rik|Naa-35	SEC14-like 1 (S. cerevisiae)	protein-coding	0.12	0.722772
Merged-chr2-25500829-1	chr2	25500779	25500879	+	3.4	cIP2vsInput	promoter-TSS (NM_027062)	promoter-TSS (NM_027062)	51	NM_013908	30839	Mm.29170	NM_013908	ENSMUSG00000015095	Fbxw5	AI159739|Fbw5	F-box and WD-40 domain protein 5	protein-coding	0.12	0.70297
Merged-chr10-33369762-1	chr10	33369712	33369812	+	3.4	cIP1vsInput	"intron (NM_029726, intron 21 of 37)"	"intron (NM_029726, intron 21 of 37)"	-113405	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	miscRNA	0.01	0.346535
Merged-chr11-70655067-1	chr11	70655017	70655117	+	3.4	cIP1vsInput	promoter-TSS (NM_011072)	promoter-TSS (NM_011072)	-417	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding	0.15	0.792079
Merged-chr10-75859594-1	chr10	75859544	75859644	+	3.4	cIP1vsInput	"intron (NM_010798, intron 2 of 2)"	"intron (NM_010798, intron 2 of 2)"	656	NM_010798	17319	Mm.2326	NM_010798	ENSMUSG00000033307	Mif	GIF|Glif	macrophage migration inhibitory factor	protein-coding	0.05	0.60396
Merged-chr4-31210666-1	chr4	31210616	31210716	+	3.4	cIP1vsInput	Intergenic	Intergenic	546070	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	miscRNA	0	0.326733
Merged-chr6-59208825-1	chr6	59208775	59208875	+	3.4	cIP2vsInput	promoter-TSS (NM_001081145)	promoter-TSS (NM_001081145)	-45	NM_001081145	68140	Mm.25843	NM_001081145	ENSMUSG00000049232	Tigd2	3632410O17Rik	tigger transposable element derived 2	protein-coding	0.14	0.772277
Merged-chr13-36735512-1	chr13	36735462	36735562	+	3.4	cIP1vsInput	Intergenic	Intergenic	-1035	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding	0.04	0.475248
Merged-chr8-9977735-1	chr8	9977685	9977785	+	3.4	cIP1vsInput	promoter-TSS (NM_001081119)	promoter-TSS (NM_001081119)	18	NM_026868	68904	Mm.395885	NM_001081119	ENSMUSG00000040396	Abhd13	1110065L07Rik|AI463703|AI788994	abhydrolase domain containing 13	protein-coding	0.08	0.643564
Merged-chr6-118419478-1	chr6	118419428	118419528	+	3.4	cIP2vsInput	promoter-TSS (NM_194339)	promoter-TSS (NM_194339)	-61	NM_194339	213895	Mm.25269	NM_194339	ENSMUSG00000030138	Bms1	AA408648|AU020092|AU043373|BB007109|BC030906|Bms1l|mKIAA0187	"BMS1 homolog, ribosome assembly protein (yeast)"	protein-coding	0.07	0.524752
Merged-chr8-84104557-1	chr8	84104507	84104607	+	3.4	cIP2vsInput	"intron (NM_172502, intron 1 of 12)"	C-rich|Low_complexity|Low_complexity	205	NM_172502	212123	Mm.260557	NM_172502	ENSMUSG00000037103	Dcaf15	6720484B16	DDB1 and CUL4 associated factor 15	protein-coding	0.15	0.831683
Merged-chr5-150522492-1	chr5	150522442	150522542	+	3.4	cIP2vsInput	promoter-TSS (NM_009765)	promoter-TSS (NM_009765)	-131	NM_009765	12190	Mm.236256	NM_001081001	ENSMUSG00000041147	Brca2	AI256696|AW045498|Fancd1|RAB163	breast cancer 2	protein-coding	0.05	0.564356
Merged-chr1-74387016-1	chr1	74386966	74387066	+	3.4	cIP2vsInput	TTS (NM_013612)	TTS (NM_013612)	-4593	NM_153088	227292	Mm.165042	NM_153088	ENSMUSG00000026176	Ctdsp1	GIP|NLIIF|Nif3|SCP1	"CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1"	protein-coding	0.02	0.584158
Merged-chr13-46430169-1	chr13	46430119	46430219	+	3.4	cIP2vsInput	"3' UTR (NM_001081425, exon 4 of 4)"	"3' UTR (NM_001081425, exon 4 of 4)"	11869	NM_001081425	666794	Mm.38269	NM_001081425	ENSMUSG00000038132	Rbm24	6330546B05Rik|AI606861	RNA binding motif protein 24	protein-coding	0.02	0.475248
Merged-chr2-145419262-1	chr2	145419212	145419312	+	3.4	cIP1vsInput	"intron (NM_053195, intron 2 of 16)"	"intron (NM_053195, intron 2 of 16)"	135720	NM_001037929	627302	Mm.445953	NM_001037929		Gm14092	OTTMUSG00000015643	predicted gene 14092	protein-coding	0.01	0.514851
Merged-chr5-29378460-1	chr5	29378410	29378510	+	3.4	cIP2vsInput	promoter-TSS (NM_020295)	promoter-TSS (NM_020295)	-70	NM_020295	56873	Mm.41572	NM_020295	ENSMUSG00000010721	Lmbr1	1110048D14Rik|AU017641	limb region 1	protein-coding	0.11	0.653465
Merged-chr3-65889062-1	chr3	65889012	65889112	+	3.4	cIP2vsInput	Intergenic	Intergenic	69163	NM_019937	56706	Mm.175612	NM_001025442	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding	0	0.554455
Merged-chr4-155600757-1	chr4	155600707	155600807	+	3.4	cIP2vsInput	promoter-TSS (NM_177186)	promoter-TSS (NM_177186)	-659	NM_177186	320541	Mm.489769	NM_177186	ENSMUSG00000042202	Slc35e2	A530082C11Rik|AI957035	"solute carrier family 35, member E2"	protein-coding	0	0.336634
Merged-chr1-5022908-1	chr1	5022858	5022958	+	3.4	cIP1vsInput	"intron (NM_001177795, intron 1 of 5)"	"intron (NM_001177795, intron 1 of 5)"	-3482	NM_021374	58175	Mm.103771	NM_001177795	ENSMUSG00000002459	Rgs20	2900073E09Rik|Rgsz1	regulator of G-protein signaling 20	protein-coding	0.08	0.712871
Merged-chr12-76962236-1	chr12	76962186	76962286	+	3.4	cIP2vsInput	promoter-TSS (NM_001146176)	promoter-TSS (NM_001146176)	12	NM_008558	17187	Mm.268548	NM_001146176	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding	0.12	0.673267
Merged-chr8-36528678-1	chr8	36528628	36528728	+	3.4	cIP2vsInput	Intergenic	Intergenic	39487	NM_176952	319582	Mm.180924	NM_176952	ENSMUSG00000039620	6430573F11Rik	Kiaa1456	RIKEN cDNA 6430573F11 gene	protein-coding	0	0.376238
Merged-chr10-81643609-1	chr10	81643559	81643659	+	3.4	cIP2vsInput	"exon (NM_027480, exon 17 of 20)"	"exon (NM_027480, exon 17 of 20)"	-5460	NM_001142963	100233208	Mm.327168	NM_001142963		Gm10778	ENSMUSG00000074860	predicted gene 10778	protein-coding	0.15	0.732673
Merged-chr10-80141393-1	chr10	80141343	80141443	+	3.4	cIP2vsInput	promoter-TSS (NM_025313)	promoter-TSS (NM_025313)	-922	NM_025313	66043	Mm.278560	NM_025313	ENSMUSG00000003072	Atp5d	0610008F14Rik|1500000I11Rik|AA960090|AI876556|AU020773|C85518	"ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit"	protein-coding	0.1	0.673267
Merged-chr16-56064513-2	chr16	56064459	56064568	+	3.4	cIP1vsInput|cIP2vsInput	Intergenic	(CACG)n|Simple_repeat|Simple_repeat	-10896	NM_025483	66315	Mm.255784	NM_001003971	ENSMUSG00000052917	Senp7	2410152H17Rik|2810413I22Rik|2900036C23Rik|6030449K19Rik|AI790676|mKIAA1707	SUMO1/sentrin specific peptidase 7	protein-coding	0.137615	0.563636
Merged-chrY-6840207-2	chrY	6840144	6840271	+	3.4	cIP1vsInput|cIP2vsInput	Intergenic	ID_B1|SINE|B4	327570	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.328125
Merged-chr6-13069906-1	chr6	13069856	13069956	+	3.4	cIP2vsInput	"5' UTR (NM_027992, exon 1 of 9)"	"5' UTR (NM_027992, exon 1 of 9)"	147	NM_027992	71900	Mm.27742	NM_027992	ENSMUSG00000029571	Tmem106b	2310036D22Rik|5830455K21Rik|6430519M21Rik|AI428776|AI661344	transmembrane protein 106B	protein-coding	0.16	0.772277
Merged-chr16-87263753-1	chr16	87263703	87263803	+	3.4	cIP2vsInput	Intergenic	Intergenic	-90432	NM_001159331	67768	Mm.296532	NM_001159331	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding	0.02	0.534653
Merged-chr2-174463979-1	chr2	174463929	174464029	+	3.4	cIP2vsInput	"exon (NM_025983, exon 1 of 3)"	"exon (NM_025983, exon 1 of 3)"	122	NM_025983	67126	Mm.20841	NM_025983	ENSMUSG00000016252	Atp5e	2410043G19Rik|ATPE|AV000645	"ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit"	protein-coding	0.11	0.693069
Merged-chr2-131352815-1	chr2	131352765	131352865	+	3.4	cIP2vsInput	promoter-TSS (NM_178607)	promoter-TSS (NM_178607)	77	NM_178607	51902	Mm.477523	NM_178607	ENSMUSG00000048911	Rnf24	2810473M14Rik|4930505A13Rik|AI317164|C86507|D2Ertd504e	ring finger protein 24	protein-coding	0.13	0.70297
Merged-chr18-44731080-1	chr18	44731030	44731130	+	3.4	cIP1vsInput	"intron (NM_001085373, intron 2 of 18)"	"intron (NM_001085373, intron 2 of 18)"	-68814	NM_001085374	328949	Mm.427116	NM_001033406	ENSMUSG00000071856	Mcc	D18Ertd451e|E330037C19	mutated in colorectal cancers	protein-coding	0.01	0.49505
Merged-chr15-35371260-1	chr15	35371210	35371310	+	3.4	cIP1vsInput	promoter-TSS (NM_177151)	promoter-TSS (NM_177151)	-286	NM_177151	666173	Mm.309250	NM_177151	ENSMUSG00000037646	Vps13b	1810042B05Rik|2310042E16Rik|4732488H20|C330002D13Rik|C87206|Coh1|D230005K13|mKIAA0532|mKIAA5032	vacuolar protein sorting 13B (yeast)	protein-coding	0.1	0.653465
Merged-chr4-133911033-1	chr4	133910983	133911083	+	3.4	cIP1vsInput	Intergenic	CpG	-23234	NM_009097	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Rsk1|p90rsk|rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding	0.1	0.693069
Merged-chr4-109280177-2	chr4	109280098	109280257	+	3.4	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007943)	promoter-TSS (NM_007943)	-98	NM_007943	13858	Mm.318250	NM_001159964	ENSMUSG00000028552	Eps15	2410112D09Rik	epidermal growth factor receptor pathway substrate 15	protein-coding	0.113208	0.725
Merged-chr9-31030471-1	chr9	31030421	31030521	+	3.4	cIP2vsInput	promoter-TSS (NM_001115130)	promoter-TSS (NM_001115130)	-173	NM_001115130	235132	Mm.393131	NM_177768	ENSMUSG00000047412	Zbtb44	6030404E16Rik|Btbd15|E230011F09	zinc finger and BTB domain containing 44	protein-coding	0.16	0.782178
Merged-chr5-44226742-1	chr5	44226692	44226792	+	3.4	cIP1vsInput	promoter-TSS (NM_173764)	promoter-TSS (NM_173764)	-136	NM_173764	231225	Mm.30688	NM_173764	ENSMUSG00000046985	Tapt1	4932414K18Rik	transmembrane anterior posterior transformation 1	protein-coding	0.21	0.851485
Merged-chr18-84950750-2	chr18	84950674	84950827	+	3.35	cIP1vsInput|cIP2vsInput	"intron (NM_025969, intron 1 of 5)"	"intron (NM_025969, intron 1 of 5)"	774	NM_025969	67105	Mm.250617	NM_025969	ENSMUSG00000024645	Timm21	1700034H14Rik|2700002I20Rik	tranlocase of inner mitochondrial membrane 21	protein-coding	0.039216	0.428571
Merged-chr6-91683951-2	chr6	91683880	91684022	+	3.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009320)	promoter-TSS (NM_009320)	-116	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	"solute carrier family 6 (neurotransmitter transporter, taurine), member 6"	protein-coding	0.169014	0.699301
Merged-chr4-84876580-2	chr4	84876518	84876643	+	3.35	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-7747	NM_175275	338349	Mm.440562	NM_175275	ENSMUSG00000038070	Cntln	AI448092|B430108F07Rik|D530005L17Rik	"centlein, centrosomal protein"	protein-coding	0.008	0.396825
Merged-chr6-48444688-2	chr6	48444631	48444745	+	3.35	cIP1vsInput|cIP2vsInput	"intron (NM_001085417, intron 1 of 4)"	"intron (NM_001085417, intron 1 of 4)"	402	NM_001085415	68910	Mm.2464	NM_001085415	ENSMUSG00000068551	Zfp467	1190001I08Rik|AB041616|AI426952|AV017623|EZI|Znf467	zinc finger protein 467	protein-coding	0.04386	0.669565
Merged-chr9-110333294-2	chr9	110333241	110333348	+	3.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001103162)	promoter-TSS (NM_001103162)	1	NM_001001144	235623	Mm.288741	NM_001001144	ENSMUSG00000032485	Scap	9530044G19|mKIAA0199	SREBF chaperone	protein-coding	0.11215	0.722222
Merged-chr16-34967656-2	chr16	34967593	34967719	+	3.35	cIP1vsInput|cIP2vsInput	"intron (NM_139300, intron 22 of 31)"	"intron (NM_139300, intron 22 of 31)"	-8662	NR_045723	278725	Mm.436927	NR_045722		E130310I04Rik	A930019C19Rik	RIKEN cDNA E130310I04 gene	miscRNA	0.015873	0.551181
Merged-chr7-15945938-2	chr7	15945859	15946017	+	3.35	cIP1vsInput|cIP2vsInput	"exon (NM_133831, exon 1 of 13)"	"exon (NM_133831, exon 1 of 13)"	170	NM_133831	68077	Mm.277634	NM_133831	ENSMUSG00000041560	Gltscr2	5330430H08Rik|9430097C02Rik|AU041936|AW536441|PICT-1|R74911	glioma tumor suppressor candidate region gene 2	protein-coding	0.101266	0.704403
Merged-chr14-118719944-2	chr14	118719889	118719999	+	3.35	cIP1vsInput|cIP2vsInput	Intergenic	ORSL-2b|DNA|hAT-Tip100	-13725	NM_001033336	239273	Mm.40537	NM_001033336	ENSMUSG00000032849	Abcc4	D630049P08Rik|MOATB|MRP4	"ATP-binding cassette, sub-family C (CFTR/MRP), member 4"	protein-coding	0.018182	0.468468
Merged-chr16-4642200-2	chr16	4642131	4642270	+	3.35	cIP1vsInput|cIP2vsInput	"intron (NM_139307, intron 1 of 1)"	"intron (NM_139307, intron 1 of 1)"	2255	NM_139307	246154	Mm.482140	NM_139307	ENSMUSG00000039646	Vasn	2610528G05Rik|Atia|Slitl2	vasorin	protein-coding	0.05036	0.557143
Merged-chr5-146379592-2	chr5	146379534	146379650	+	3.35	cIP1vsInput|cIP2vsInput	Intergenic	B1_Mus1|SINE|Alu	-5414	NM_145155	245880	Mm.472750	NM_145155		Wasf3	Scar3|Wave3	"WAS protein family, member 3"	protein-coding	0.017241	0.470085
Merged-chr11-50477117-2	chr11	50477059	50477175	+	3.35	cIP1vsInput|cIP2vsInput	Intergenic	L1ME4b|LINE|L1	-46006	NM_172557	216724	Mm.390400	NM_172557	ENSMUSG00000020375	Rufy1	3000002E04Rik|Rabip4|ZFYVE12	RUN and FYVE domain containing 1	protein-coding	0.008621	0.444444
Merged-chr5-15520621-2	chr5	15520570	15520673	+	3.35	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-98478	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0.019417	0.336538
Merged-chr14-64834901-2	chr14	64834838	64834964	+	3.35	cIP1vsInput|cIP2vsInput	"intron (NM_177338, intron 6 of 9)"	"intron (NM_177338, intron 6 of 9)"	114946	NM_177338	219150	Mm.344074	NM_177338	ENSMUSG00000021972	Hmbox1	AI451877|AI604847|F830020C16Rik	homeobox containing 1	protein-coding	0.031746	0.503937
Merged-chr2-30794701-2	chr2	30794610	30794793	+	3.35	cIP1vsInput|cIP2vsInput	TTS (NR_028486)	TTS (NR_028486)	7036	NM_198000	73598	Mm.34166	NM_198000	ENSMUSG00000044320	1700001O22Rik	1700113K14Rik|4930549G18Rik	RIKEN cDNA 1700001O22 gene	protein-coding	0.10929	0.657609
Merged-chr8-13757617-2	chr8	13757550	13757685	+	3.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027276)	promoter-TSS (NM_027276)	-73	NM_027276	69957	Mm.182412	NM_027276	ENSMUSG00000038416	Cdc16	2700071J12Rik|2810431D22Rik|APC6	CDC16 cell division cycle 16	protein-coding	0.088889	0.647059
Merged-chrX-126694579-2	chrX	126694526	126694632	+	3.35	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	139425	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding	0.009434	0.242991
Merged-chr15-78947743-2	chr15	78947684	78947802	+	3.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_138579)	promoter-TSS (NM_138579)	19	NM_001039155	110253	Mm.123714	NM_001024716	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding	0.09322	0.697479
Merged-chr11-102819243-2	chr11	102819178	102819309	+	3.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001159382)	promoter-TSS (NM_001159382)	-84	NM_001159382	14615	Mm.390369	NM_001159382	ENSMUSG00000034520	Gjc1	C130009G16Rik|Cnx45|Cx45|Gja-7|Gja7	"gap junction protein, gamma 1"	protein-coding	0.175573	0.840909
Merged-chr15-84829601-2	chr15	84829546	84829656	+	3.35	cIP1vsInput|cIP2vsInput	"intron (NM_001081166, intron 2 of 12)"	"intron (NM_001081166, intron 2 of 12)"	26528	NM_001081166	271305	Mm.101022	NM_001081166	ENSMUSG00000016624	Phf21b	A730032D07Rik	PHD finger protein 21B	protein-coding	0.063636	0.594595
Merged-chr15-88734321-2	chr15	88734235	88734408	+	3.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001033274)	promoter-TSS (NM_001033274)	-102	NM_001033274	223770	Mm.254438	NM_001033274	ENSMUSG00000022387	Brd1	1110059H06Rik|AI316859|mKIAA4191	bromodomain containing 1	protein-coding	0.150289	0.741379
Merged-chr10-108088340-2	chr10	108088273	108088407	+	3.35	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-74060	NM_027892	17931	Mm.489819	NM_027892	ENSMUSG00000019907	Ppp1r12a	1200015F06Rik|5730577I22Rik|AA792106|AV099298|D10Ertd625e|Mypt1	"protein phosphatase 1, regulatory (inhibitor) subunit 12A"	protein-coding	0.014925	0.422222
Merged-chr3-97658296-2	chr3	97658230	97658363	+	3.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_182997)	promoter-TSS (NM_182997)	84	NM_182997	108097	Mm.31175	NM_182997	ENSMUSG00000038205	Prkab2	5730553K21Rik|AW049591|BB124140	"protein kinase, AMP-activated, beta 2 non-catalytic subunit"	protein-coding	0.105263	0.58209
Merged-chr8-33653445-2	chr8	33653379	33653511	+	3.35	cIP1vsInput|cIP2vsInput	"5' UTR (NM_010344, exon 1 of 13)"	"5' UTR (NM_010344, exon 1 of 13)"	207	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding	0.106061	0.676692
Merged-chr14-71203663-2	chr14	71203598	71203728	+	3.35	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-47610	NR_046075	100043132	Mm.399336	NR_046075		Gm4251	-	predicted gene 4251	miscRNA	0.015385	0.473282
Merged-chr3-157947139-2	chr3	157947066	157947213	+	3.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001013806)	promoter-TSS (NM_001013806)	-327	NM_001013806	433667	Mm.265806	NM_001013806	ENSMUSG00000039988	Ankrd13c	AI505652|AU022220	ankyrin repeat domain 13c	protein-coding	0.081633	0.689189
Merged-chrX-51699163-2	chrX	51699099	51699227	+	3.35	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-17561	NM_001077202	50786	Mm.252561	NM_001077202	ENSMUSG00000062184	Hs6st2	6OST2	heparan sulfate 6-O-sulfotransferase 2	protein-coding	0.015625	0.48062
Merged-chr5-125566073-2	chr5	125566022	125566124	+	3.35	cIP1vsInput|cIP2vsInput	"intron (NM_001190352, intron 1 of 8)"	"intron (NM_001190352, intron 1 of 8)"	33655	NM_001190352	208151	Mm.40397	NM_001190352	ENSMUSG00000070498	Tmem132b	AK220418|mKIAA1786	transmembrane protein 132B	protein-coding	0.009804	0.475728
Merged-chr10-80509568-2	chr10	80509500	80509636	+	3.35	cIP1vsInput|cIP2vsInput	"intron (NM_139226, intron 1 of 1)"	B3A|SINE|B2	14662	NM_139226	246086	Mm.250572	NM_139226	ENSMUSG00000045518	Onecut3	OC-3|Oc3	"one cut domain, family member 3"	protein-coding	0.014706	0.49635
Merged-chr13-55622778-2	chr13	55622700	55622856	+	3.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007596)	promoter-TSS (NM_007596)	-227	NM_007596	12328	Mm.2313	NM_007596	ENSMUSG00000021501	Caml	AI385748|Camlg	calcium modulating ligand	protein-coding	0.038462	0.522293
Merged-chr17-87530683-2	chr17	87530601	87530765	+	3.35	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-83748	NM_007589	12314	Mm.329243	NM_007589	ENSMUSG00000036438	Calm2	1500001E21Rik|AL024017	calmodulin 2	protein-coding	0.073171	0.690909
Merged-chr4-75063618-1	chr4	75063568	75063668	+	3.3	cIP2vsInput	Intergenic	Intergenic	214668	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	3110001D03Rik	1700027K24Rik	RIKEN cDNA 3110001D03 gene	protein-coding	0	0.29703
Merged-chr4-147127505-1	chr4	147127455	147127555	+	3.3	cIP2vsInput	Intergenic	MLTR18A_MM|LTR|ERVK	-48361	NM_001039209	195531	Mm.489132	NM_001039209	ENSMUSG00000078496	Gm13152	OTTMUSG00000010671	predicted gene 13152	protein-coding	0.01	0.366337
Merged-chr9-108648772-1	chr9	108648722	108648822	+	3.3	cIP2vsInput	"intron (NM_011790, intron 1 of 15)"	CpG	608	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne homolog 2 (Drosophila)	protein-coding	0.16	0.722772
Merged-chr14-33290379-1	chr14	33290329	33290429	+	3.3	cIP2vsInput	"intron (NM_153800, intron 3 of 10)"	"intron (NM_153800, intron 3 of 10)"	73556	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding	0.02	0.425743
Merged-chr11-95859002-1	chr11	95858952	95859052	+	3.3	cIP1vsInput	"non-coding (NR_045187, exon 1 of 2)"	"non-coding (NR_045187, exon 1 of 2)"	185	NR_045187	73906	Mm.407342	NR_045187	ENSMUSG00000086015	4833417C18Rik	-	RIKEN cDNA 4833417C18 gene	miscRNA	0.09	0.554455
Merged-chr15-99333115-1	chr15	99333065	99333165	+	3.3	cIP2vsInput	"intron (NM_011711, intron 4 of 26)"	"intron (NM_011711, intron 4 of 26)"	37351	NM_011711	22379	Mm.29043	NM_011711	ENSMUSG00000023008	Fmnl3	2700073B04Rik|FBP11|Wbp3|mKIAA2014	formin-like 3	protein-coding	0.01	0.564356
Merged-chr15-80264359-1	chr15	80264309	80264409	+	3.3	cIP2vsInput	promoter-TSS (NM_175109)	promoter-TSS (NM_175109)	-53	NM_175109	66538	Mm.39485	NM_175109	ENSMUSG00000051518	Rps19bp1	2510038A11Rik|AI604923|S19BP	ribosomal protein S19 binding protein 1	protein-coding	0.08	0.623762
Merged-chr4-120705219-1	chr4	120705169	120705269	+	3.3	cIP2vsInput	"intron (NM_001081142, intron 9 of 13)"	"intron (NM_001081142, intron 9 of 13)"	38656	NM_019563	56222	Mm.272646	NM_019563	ENSMUSG00000070803	Cited4	MRG-2|Mrg2	"Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 4"	protein-coding	0.01	0.445545
Merged-chr11-97663138-1	chr11	97663088	97663188	+	3.3	cIP2vsInput	promoter-TSS (NM_139311)	promoter-TSS (NM_139311)	-274	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6"	protein-coding	0.2	0.881188
Merged-chr11-78261808-1	chr11	78261758	78261858	+	3.3	cIP2vsInput	promoter-TSS (NM_001002004)	promoter-TSS (NM_001002004)	54	NM_001002004	72503	Mm.237103	NM_001002004	ENSMUSG00000010277	2610507B11Rik	AU022687|D11Bhm178e|D11Bhm179e|E1|Kiaa0100|mKIAA0100	RIKEN cDNA 2610507B11 gene	protein-coding	0.15	0.782178
Merged-chr11-82871273-1	chr11	82871223	82871323	+	3.3	cIP2vsInput	promoter-TSS (NM_001164571)	promoter-TSS (NM_001164571)	-63	NM_001164571	67338	Mm.341608	NM_001007465	ENSMUSG00000020696	Rffl	1700051E09Rik|4930516L10Rik|BG080975|Carp2	ring finger and FYVE like domain containing protein	protein-coding	0.15	0.80198
Merged-chr1-12644812-1	chr1	12644762	12644862	+	3.3	cIP1vsInput	Intergenic	(GAATG)n|Simple_repeat|Simple_repeat	-22751	NR_045297	329096	Mm.417782	NR_045297	ENSMUSG00000097171	Gm17644	4932411L15	"predicted gene, 17644"	miscRNA	0	0.415842
Merged-chr16-20302416-1	chr16	20302366	20302466	+	3.3	cIP2vsInput	promoter-TSS (NM_001005767)	promoter-TSS (NM_001005767)	-54	NM_001005767	381038	Mm.371737	NM_001005767	ENSMUSG00000033918	Parl	D16Ertd607e|PRO2207|PSARL1|PSENIP2|Psarl	"presenilin associated, rhomboid-like"	protein-coding	0.07	0.524752
Merged-chr16-16302527-1	chr16	16302477	16302577	+	3.3	cIP2vsInput	promoter-TSS (NR_038046)	promoter-TSS (NR_038046)	-438	NM_198246	70120	Mm.37486	NM_198246	ENSMUSG00000022792	Yars2	2210023C10Rik|tyrRS	tyrosyl-tRNA synthetase 2 (mitochondrial)	protein-coding	0.05	0.594059
Merged-chr16-87246520-1	chr16	87246470	87246570	+	3.3	cIP2vsInput	Intergenic	Intergenic	-107665	NM_001159331	67768	Mm.296532	NM_001159331	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding	0.07	0.633663
Merged-chr5-69802314-1	chr5	69802264	69802364	+	3.3	cIP2vsInput	Intergenic	Intergenic	-210029	NM_001038015	67980	Mm.33830	NM_001038015	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding	0	0.39604
Merged-chr17-45506839-2	chr17	45506776	45506903	+	3.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_198608)	promoter-TSS (NM_198608)	-2	NM_198608	224805	Mm.329063	NM_198608	ENSMUSG00000023938	Aars2	Aarsl|AlaRS|Gm89	"alanyl-tRNA synthetase 2, mitochondrial (putative)"	protein-coding	0.110236	0.640625
Merged-chr18-82902277-1	chr18	82902227	82902327	+	3.3	cIP2vsInput	Intergenic	Intergenic	-8602	NM_183033	329003	Mm.326526	NM_001177464	ENSMUSG00000058881	Zfp516	C330029B10Rik|D230016L03|Zfp26l|Znf516|mKIAA0222	zinc finger protein 516	protein-coding	0.03	0.712871
Merged-chr4-155761180-1	chr4	155761130	155761230	+	3.3	cIP2vsInput	promoter-TSS (NM_179203)	promoter-TSS (NM_179203)	-12	NR_027971	70448	Mm.70636	NM_175157	ENSMUSG00000054514	2610204G22Rik	-	RIKEN cDNA 2610204G22 gene	miscRNA	0.1	0.60396
Merged-chr13-36019549-1	chr13	36019499	36019599	+	3.3	cIP1vsInput	"intron (NM_201358, intron 2 of 2)"	"intron (NM_201358, intron 2 of 2)"	51643	NM_029628	76487	Mm.44745	NM_029628	ENSMUSG00000050423	Ppp1r3g	1600032L17Rik	"protein phosphatase 1, regulatory (inhibitor) subunit 3G"	protein-coding	0	0.326733
Merged-chr11-74690035-1	chr11	74689985	74690085	+	3.3	cIP2vsInput	"intron (NR_037610, intron 4 of 10)"	"intron (NR_037610, intron 4 of 10)"	33823	NR_037610	18472	Mm.397111	NM_013625	ENSMUSG00000020745	Pafah1b1	LIS-1|Lis1|MMS10-U|Mdsh|Ms10u|Pafaha	"platelet-activating factor acetylhydrolase, isoform 1b, subunit 1"	protein-coding	0	0.336634
Merged-chr15-103182344-1	chr15	103182294	103182394	+	3.3	cIP2vsInput	Intergenic	CpG	-13467	NR_030558	100124494		NR_030558	ENSMUSG00000065509	Mir421	Mirn421|mmu-mir-421	microRNA 421	miscRNA	0.12	0.762376
Merged-chr18-56975391-1	chr18	56975341	56975441	+	3.3	cIP1vsInput	promoter-TSS (NM_029909)	promoter-TSS (NM_029909)	-12	NM_029909	77422	Mm.256874	NM_029909	ENSMUSG00000024592	C330018D20Rik	AU018666	RIKEN cDNA C330018D20 gene	protein-coding	0.17	0.80198
Merged-chr5-33658296-1	chr5	33658246	33658346	+	3.3	cIP1vsInput	promoter-TSS (NM_026698)	promoter-TSS (NM_026698)	149	NM_001040435	21335	Mm.379024	NM_011524	ENSMUSG00000037313	Tacc3	Aint|C86661|Eric1	"transforming, acidic coiled-coil containing protein 3"	protein-coding	0.06	0.544554
Merged-chr18-44612500-1	chr18	44612450	44612550	+	3.3	cIP2vsInput	"intron (NM_001085373, intron 3 of 18)"	"intron (NM_001085373, intron 3 of 18)"	-49165	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	miscRNA	0.01	0.445545
Merged-chr7-92874476-1	chr7	92874426	92874526	+	3.3	cIP2vsInput	promoter-TSS (NM_028243)	promoter-TSS (NM_028243)	-244	NM_001080995	74041	Mm.26468	NM_001080995	ENSMUSG00000030641	4632434I11Rik	noxin	RIKEN cDNA 4632434I11 gene	protein-coding	0.12	0.693069
Merged-chr11-23067857-1	chr11	23067807	23067907	+	3.3	cIP1vsInput	Intergenic	CpG	54470	NM_028672	73873	Mm.252406	NM_028672	ENSMUSG00000049811	Fam161a	4930430E16Rik	"family with sequence similarity 161, member A"	protein-coding	0.15	0.752475
Merged-chr12-76837553-1	chr12	76837503	76837603	+	3.3	cIP2vsInput	promoter-TSS (NM_145927)	promoter-TSS (NM_145927)	86	NM_145927	110606	Mm.151174	NM_145927	ENSMUSG00000033373	Fntb	2010013E13Rik|AA409500	"farnesyltransferase, CAAX box, beta"	protein-coding	0.05	0.514851
Merged-chr13-22049970-1	chr13	22049920	22050020	+	3.3	cIP2vsInput	Intergenic	Lx8|LINE|L1	6740	NM_178198	319183	Mm.371766	NM_178198	ENSMUSG00000069300	Hist1h2bj	-	"histone cluster 1, H2bj"	protein-coding	0.01	0.50495
Merged-chr5-137307787-1	chr5	137307737	137307837	+	3.3	cIP2vsInput	promoter-TSS (NM_001109909)	promoter-TSS (NM_001109909)	-113	NM_001109909	83701	Mm.387734	NM_001109909	ENSMUSG00000037364	Srrt	2810019G02Rik|ASR2A|ASR2B|ASR2C|ASR2D|Ars2|Asr2	serrate RNA effector molecule homolog (Arabidopsis)	protein-coding	0.05	0.564356
Merged-chrX-13071329-1	chrX	13071279	13071379	+	3.3	cIP2vsInput	promoter-TSS (NM_009481)	promoter-TSS (NM_009481)	-169	NM_009481	22284	Mm.242646	NM_009481	ENSMUSG00000031010	Usp9x	5730589N07Rik|AA407302|AA407699|AL022658|AL022749|Dffrx|FAF-X|Fafl	"ubiquitin specific peptidase 9, X chromosome"	protein-coding	0.04	0.653465
Merged-chr6-48554700-1	chr6	48554650	48554750	+	3.3	cIP2vsInput	promoter-TSS (NM_177736)	promoter-TSS (NM_177736)	-99	NM_001110160	243371	Mm.290764	NM_001110160	ENSMUSG00000073096	Lrrc61	BC027309	leucine rich repeat containing 61	protein-coding	0.07	0.623762
Merged-chr7-140137671-1	chr7	140137621	140137721	+	3.3	cIP2vsInput	"exon (NM_199301, exon 1 of 11)"	"exon (NM_199301, exon 1 of 11)"	107	NM_199301	212508	Mm.296088	NM_199301	ENSMUSG00000039018	Mtg1	Gm169|Gtpbp7	mitochondrial GTPase 1 homolog (S. cerevisiae)	protein-coding	0.11	0.693069
Merged-chr15-101177669-1	chr15	101177619	101177719	+	3.3	cIP2vsInput	"intron (NM_007395, intron 1 of 8)"	"intron (NM_007395, intron 1 of 8)"	3544	NM_007395	11479	Mm.308467	NM_007395		Acvr1b	6820432J04|ActR-IB|ActRIB|Acvrlk4|Alk4|SKR2	"activin A receptor, type 1B"	protein-coding	0.02	0.475248
Merged-chr19-30050291-1	chr19	30050241	30050341	+	3.3	cIP1vsInput	"intron (NM_144873, intron 2 of 15)"	"intron (NM_144873, intron 2 of 15)"	19778	NM_144873	109113	Mm.313364	NM_144873	ENSMUSG00000024817	Uhrf2	2310065A22Rik|AI426270|AW214556|D130071B19Rik|Nirf	"ubiquitin-like, containing PHD and RING finger domains 2"	protein-coding	0	0.316832
Merged-chr7-4137310-2	chr7	4137260	4137361	+	3.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_033548)	promoter-TSS (NR_033548)	254	NM_172736	232798	Mm.22831	NM_172736	ENSMUSG00000035545	Leng8	AW049671	leukocyte receptor cluster (LRC) member 8	protein-coding	0.148515	0.754902
Merged-chr11-3332343-1	chr11	3332293	3332393	+	3.3	cIP2vsInput	"intron (NM_178149, intron 3 of 5)"	CpG-1656	1612	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding	0.16	0.752475
Merged-chr17-33092405-1	chr17	33092355	33092455	+	3.3	cIP2vsInput	"intron (NM_001024950, intron 1 of 3)"	"intron (NM_001024950, intron 1 of 3)"	3038	NM_001024950	240068	Mm.121392	NM_001024950		Zfp563	D10628|D130054H01|NTfin7|Zfp413	zinc finger protein 563	protein-coding	0.03	0.554455
Merged-chr17-46772834-1	chr17	46772784	46772884	+	3.3	cIP2vsInput	"exon (NM_025966, exon 1 of 1)"	"exon (NM_025966, exon 1 of 1)"	199	NM_025966	67101	Mm.358702	NM_025966	ENSMUSG00000062619	2310039H08Rik	-	RIKEN cDNA 2310039H08 gene	protein-coding	0.09	0.673267
Merged-chr12-95294040-1	chr12	95293990	95294090	+	3.3	cIP2vsInput	Intergenic	MurERV4_19-int|LTR|ERVK	-398186	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0	0.336634
Merged-chr1-31793824-1	chr1	31793774	31793874	+	3.3	cIP1vsInput	Intergenic	Intergenic	-378982	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm1	"KH domain containing, RNA binding, signal transduction associated 2"	protein-coding	0	0.217822
Merged-chr8-21019597-2	chr8	21019522	21019672	+	3.3	cIP1vsInput|cIP2vsInput	Intergenic	Lx8b|LINE|L1	-5948	NM_183253	66298	Mm.482941	NM_183253	ENSMUSG00000074447	Defa21	2010016B13Rik|Defcr21	"defensin, alpha, 21"	protein-coding	0.006667	0.350993
Merged-chr16-94313087-1	chr16	94313037	94313137	+	3.3	cIP2vsInput	Intergenic	Intergenic	-15335	NM_133229	170765	Mm.42604	NM_133229	ENSMUSG00000022941	Ripply3	Dscr6	ripply3 homolog (zebrafish)	protein-coding	0.06	0.445545
Merged-chr6-124903791-1	chr6	124903741	124903841	+	3.3	cIP2vsInput	TTS (NM_008479)	TTS (NM_008479)	7914	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding	0.03	0.574257
Merged-chr10-59511747-2	chr10	59511679	59511816	+	3.3	cIP1vsInput|cIP2vsInput	"intron (NM_001033259, intron 1 of 7)"	"intron (NM_001033259, intron 1 of 7)"	-69968	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding	0.036496	0.456522
Merged-chr11-102624327-1	chr11	102624277	102624377	+	3.3	cIP2vsInput	promoter-TSS (NR_033474)	promoter-TSS (NR_033474)	89	NR_033474	77132	Mm.194729	NR_033474		2810433D01Rik	-	RIKEN cDNA 2810433D01 gene	miscRNA	0.02	0.613861
Merged-chr7-141476389-1	chr7	141476339	141476439	+	3.3	cIP2vsInput	promoter-TSS (NM_001252588)	promoter-TSS (NM_001252588)	9	NM_001252588	64540	Mm.489619	NM_001252588	ENSMUSG00000025511	Tspan4	AI325509|AI746565|D130042I01Rik|NAG-2|Tm4sf7|Tspan-4	tetraspanin 4	protein-coding	0.03	0.693069
Merged-chr2-35979905-1	chr2	35979855	35979955	+	3.3	cIP2vsInput	promoter-TSS (NM_029774)	promoter-TSS (NM_029774)	-281	NM_029774	74410	Mm.482520	NM_028921	ENSMUSG00000026885	Ttll11	4932702F08Rik|4933424A20Rik|AU043211|D2Ertd624e	"tubulin tyrosine ligase-like family, member 11"	protein-coding	0.04	0.594059
Merged-chr15-27782844-1	chr15	27782794	27782894	+	3.3	cIP2vsInput	"intron (NM_001081302, intron 34 of 56)"	"intron (NM_001081302, intron 34 of 56)"	-101302	NM_001242423	223433	Mm.266485	NM_001242423	ENSMUSG00000056069	Fam105a	9830126M18	"family with sequence similarity 105, member A"	protein-coding	0.02	0.544554
Merged-chr17-24849835-1	chr17	24849785	24849885	+	3.3	cIP2vsInput	promoter-TSS (NM_001159626)	promoter-TSS (NM_001159626)	467	NM_023480	68636	Mm.347964	NM_023480	ENSMUSG00000045316	Fahd1	1110025H10Rik|AV002085	fumarylacetoacetate hydrolase domain containing 1	protein-coding	0.06	0.633663
Merged-chr13-55571146-1	chr13	55571096	55571196	+	3.3	cIP2vsInput	promoter-TSS (NM_145382)	promoter-TSS (NM_145382)	-26	NM_145382	212483	Mm.35661	NM_145382	ENSMUSG00000021495	Fam193b	IRIZIO|Kiaa1931	"family with sequence similarity 193, member B"	protein-coding	0.13	0.752475
Merged-chr1-43974756-1	chr1	43974706	43974806	+	3.3	cIP2vsInput	"intron (NM_009418, intron 15 of 29)"	L2b|LINE|L2	40749	NM_009418	22019	Mm.401675	NM_009418	ENSMUSG00000041763	Tpp2	TPP-2|TppII	tripeptidyl peptidase II	protein-coding	0.01	0.316832
Merged-chr4-48043502-1	chr4	48043452	48043552	+	3.3	cIP2vsInput	Intergenic	Intergenic	-7746	NM_015743	18124	Mm.487935	NM_015743		Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	"nuclear receptor subfamily 4, group A, member 3"	protein-coding	0.11	0.663366
Merged-chr16-53054459-1	chr16	53054409	53054509	+	3.3	cIP2vsInput	Intergenic	Intergenic	-238715	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	miscRNA	0	0.29703
Merged-chr16-91044774-1	chr16	91044724	91044824	+	3.3	cIP2vsInput	promoter-TSS (NM_026110)	promoter-TSS (NM_026110)	-395	NM_026110	67367		NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding	0.04	0.633663
Merged-chr6-113307004-1	chr6	113306954	113307054	+	3.3	cIP2vsInput	promoter-TSS (NM_030178)	promoter-TSS (NM_030178)	-193	NM_030178	78783	Mm.474132	NM_030178	ENSMUSG00000001632	Brpf1	4833438B11Rik|4930540D11Rik|Brpf2	"bromodomain and PHD finger containing, 1"	protein-coding	0.07	0.554455
Merged-chr7-34133390-1	chr7	34133340	34133440	+	3.3	cIP2vsInput	promoter-TSS (NM_207212)	promoter-TSS (NM_207212)	-122	NM_207212	101543	Mm.422738	NM_207212	ENSMUSG00000036459	Wtip	-	WT1-interacting protein	protein-coding	0.09	0.712871
Merged-chr2-79454320-2	chr2	79454261	79454379	+	3.3	cIP1vsInput|cIP2vsInput	"exon (NM_010894, exon 2 of 2)"	"exon (NM_010894, exon 2 of 2)"	2316	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding	0.067797	0.655462
Merged-chr8-11274848-1	chr8	11274798	11274898	+	3.3	cIP2vsInput	"intron (NM_009931, intron 1 of 51)"	"intron (NM_009931, intron 1 of 51)"	37978	NM_009931	12826	Mm.738	NM_009931	ENSMUSG00000031502	Col4a1	Bru|Col4a-1|Del(8)44H|Raw|Svc	"collagen, type IV, alpha 1"	protein-coding	0.03	0.465347
Merged-chr19-36688380-1	chr19	36688330	36688430	+	3.3	cIP1vsInput	"intron (NR_033510, intron 1 of 4)"	"intron (NR_033510, intron 1 of 4)"	1099	NR_033510	668215	Mm.394223	NR_033510	ENSMUSG00000087579	1500017E21Rik	-	RIKEN cDNA 1500017E21 gene	miscRNA	0	0.544554
Merged-chr11-97988214-1	chr11	97988164	97988264	+	3.3	cIP1vsInput	Intergenic	Intergenic	-1768	NM_001163608	72324	Mm.482750	NM_001163608	ENSMUSG00000017417	Plxdc1	2410003I07Rik|AI848450|Tem7	plexin domain containing 1	protein-coding	0.04	0.465347
Merged-chr4-94603334-1	chr4	94603284	94603384	+	3.3	cIP2vsInput	promoter-TSS (NM_172695)	promoter-TSS (NM_172695)	-87	NM_172695	18786	Mm.490101	NM_172695		Plaa	2410007N06|AI536418|AU018445|AW208417|D4Ertd618e|PLA2P|PLAP|Ufd3	"phospholipase A2, activating protein"	protein-coding	0.1	0.643564
Merged-chr15-77306618-1	chr15	77306568	77306668	+	3.3	cIP2vsInput	"5' UTR (NM_175387, exon 1 of 13)"	"5' UTR (NM_175387, exon 1 of 13)"	435	NM_001110827	93686	Mm.202774	NM_001110827	ENSMUSG00000033565	Rbfox2	2810460A15Rik|AA407676|AI118529|Fbm2|Fxh|Hrnbp2|Rbm9	"RNA binding protein, fox-1 homolog (C. elegans) 2"	protein-coding	0.17	0.821782
Merged-chr11-51967626-1	chr11	51967576	51967676	+	3.3	cIP2vsInput	promoter-TSS (NM_029976)	promoter-TSS (NM_029976)	-5	NM_029976	52626	Mm.289456	NM_029976	ENSMUSG00000020392	Cdkn2aipnl	A430101B06Rik|AA409260|D11Ertd497e|MNCb-1520	CDKN2A interacting protein N-terminal like	protein-coding	0.15	0.732673
Merged-chr6-71707799-1	chr6	71707749	71707849	+	3.3	cIP2vsInput	"5' UTR (NM_178608, exon 1 of 7)"	"5' UTR (NM_178608, exon 1 of 7)"	118	NM_178608	52250	Mm.146332	NM_178608	ENSMUSG00000052852	Reep1	D6Ertd253e	receptor accessory protein 1	protein-coding	0.17	0.811881
Merged-chr6-61957816-1	chr6	61957766	61957866	+	3.3	cIP1vsInput	"intron (NM_001164316, intron 10 of 10)"	"intron (NM_001164316, intron 10 of 10)"	-777006	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	miscRNA	0	0.386139
Merged-chr7-130770602-1	chr7	130770552	130770652	+	3.3	cIP2vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	-3467	NM_001081038	330660	Mm.271550	NM_001081038	ENSMUSG00000040298	Btbd16	E330040A16Rik	BTB (POZ) domain containing 16	protein-coding	0.01	0.346535
Merged-chr14-121379304-1	chr14	121379254	121379354	+	3.3	cIP2vsInput	promoter-TSS (NM_145465)	promoter-TSS (NM_145465)	-74	NM_145465	223255	Mm.442081	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding	0.18	0.910891
Merged-chr15-6386605-1	chr15	6386555	6386655	+	3.3	cIP2vsInput	promoter-TSS (NM_001102400)	promoter-TSS (NM_001102400)	-143	NM_023118	13132	Mm.240830	NM_001008702	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	"disabled 2, mitogen-responsive phosphoprotein"	protein-coding	0.1	0.732673
Merged-chr18-18928245-1	chr18	18928195	18928295	+	3.3	cIP2vsInput	Intergenic	Lx2A1|LINE|L1	1073852	NM_007882	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding	0	0.336634
Merged-chr1-93445386-1	chr1	93445336	93445436	+	3.3	cIP2vsInput	"intron (NM_133808, intron 1 of 27)"	CpG	33422	NM_133808	110611	Mm.30012	NM_133808	ENSMUSG00000034088	Hdlbp	1110005P14Rik|AA960365|AI118566|D1Ertd101e	high density lipoprotein (HDL) binding protein	protein-coding	0.14	0.693069
Merged-chr4-126046963-2	chr4	126046884	126047042	+	3.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025544)	promoter-TSS (NM_025544)	35	NM_025544	66407	Mm.195628	NM_025544	ENSMUSG00000028861	Mrps15	1500003E24Rik|2410002B11Rik|Mprs15	mitochondrial ribosomal protein S15	protein-coding	0.101266	0.660377
Merged-chr18-49967420-1	chr18	49967370	49967470	+	3.3	cIP1vsInput	Intergenic	Intergenic	-12007	NM_001177760	106869	Mm.27740	NM_001177759	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2	"tumor necrosis factor, alpha-induced protein 8"	protein-coding	0.01	0.287129
Merged-chr3-94821552-1	chr3	94821502	94821602	+	3.3	cIP1vsInput	Intergenic	Intergenic	-16015	NM_001165948	229584	Mm.274787	NM_001165948	ENSMUSG00000038902	Pogz	9530006B08Rik|AU015913|AU044539	pogo transposable element with ZNF domain	protein-coding	0.03	0.574257
Merged-chr13-112927467-1	chr13	112927417	112927517	+	3.3	cIP1vsInput	promoter-TSS (NM_172594)	promoter-TSS (NM_172594)	-87	NM_028151	72198	Mm.291029	NM_028151	ENSMUSG00000016018	Skiv2l2	2610528A15Rik|mKIAA0052	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	protein-coding	0.08	0.60396
Merged-chr5-135689092-1	chr5	135689042	135689142	+	3.3	cIP2vsInput	promoter-TSS (NM_008898)	promoter-TSS (NM_008898)	-122	NM_008898	18984	Mm.3863	NM_008898	ENSMUSG00000005514	Por	4933424M13Rik|CPR|CYPOR	P450 (cytochrome) oxidoreductase	protein-coding	0.09	0.70297
Merged-chr1-92180824-2	chr1	92180754	92180895	+	3.3	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-32431	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|AI047285	histone deacetylase 4	protein-coding	0.078014	0.65493
Merged-chr7-138846320-1	chr7	138846270	138846370	+	3.3	cIP2vsInput	promoter-TSS (NM_026391)	promoter-TSS (NM_026391)	-53	NM_027115	69546	Mm.31598	NM_001045483	ENSMUSG00000041775	Mapk1ip1	2310009E07Rik|AU043776|MISS	mitogen-activated protein kinase 1 interacting protein 1	protein-coding	0.16	0.782178
Merged-chr13-66794524-1	chr13	66794474	66794574	+	3.3	cIP2vsInput	Intergenic	MurSatRep1|Unknown|Unknown	110826	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding	0.01	0.316832
Merged-chr12-105784617-1	chr12	105784567	105784667	+	3.3	cIP2vsInput	promoter-TSS (NM_011112)	promoter-TSS (NM_011112)	-85	NM_011112	18789	Mm.255877	NM_011112	ENSMUSG00000021111	Papola	Pap|PapIII|Plap	poly (A) polymerase alpha	protein-coding	0.14	0.762376
Merged-chr12-85339530-1	chr12	85339480	85339580	+	3.3	cIP2vsInput	promoter-TSS (NM_145138)	promoter-TSS (NM_145138)	-168	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding	0.08	0.584158
Merged-chr2-69808960-1	chr2	69808910	69809010	+	3.3	cIP1vsInput	Intergenic	RMER16-int|LTR|ERVK	-13410	NM_177784	277396	Mm.138073	NM_177784	ENSMUSG00000042155	Klhl23	C130068N17Rik	kelch-like 23	protein-coding	0	0.277228
Merged-chr17-27373585-1	chr17	27373535	27373635	+	3.3	cIP2vsInput	Intergenic	Intergenic	129719	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	"glutamate receptor, metabotropic 4"	protein-coding	0.04	0.50495
Merged-chr3-69316728-2	chr3	69316652	69316804	+	3.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178726)	promoter-TSS (NM_178726)	-190	NM_178726	242083	Mm.40577	NM_178726		Ppm1l	3222401G13|5930404J21Rik|AI481720|AW045850|PP2C|PP2Cepsilon|Pp2ce|Ppp2ce|mKIAA4175	protein phosphatase 1 (formerly 2C)-like	protein-coding	0.111842	0.732026
Merged-chr9-94379024-1	chr9	94378974	94379074	+	3.3	cIP2vsInput	Intergenic	Intergenic	159057	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49	RIKEN cDNA 1190002N15 gene	protein-coding	0.02	0.405941
Merged-chr5-77460029-1	chr5	77459979	77460079	+	3.3	cIP2vsInput	Intergenic	Intergenic	51719	NR_027806	231332	Mm.373616	NM_001010832		Pea15b	-	phosphoprotein enriched in astrocytes 15B	pseudo	0.04	0.60396
Merged-chr16-10665649-1	chr16	10665599	10665699	+	3.3	cIP1vsInput	"intron (NM_177562, intron 18 of 22)"	"intron (NM_177562, intron 18 of 22)"	119887	NM_001271603	12703	Mm.130	NM_001271603	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding	0.01	0.435644
Merged-chr7-143008251-1	chr7	143008201	143008301	+	3.3	cIP2vsInput	"intron (NM_001128081, intron 2 of 6)"	"intron (NM_001128081, intron 2 of 6)"	2592	NM_001128081	27027	Mm.28172	NM_001128080	ENSMUSG00000000244	Tspan32	AW208513|Art-1|BB235973|D7Wsu37e|Phemx|Tssc6	tetraspanin 32	protein-coding	0.04	0.584158
Merged-chr4-133088096-1	chr4	133088046	133088146	+	3.3	cIP1vsInput	Intergenic	Intergenic	-42537	NM_153423	242687	Mm.23566	NM_153423		Wasf2	AW742646|D4Ertd13e|WAVE2	"WAS protein family, member 2"	protein-coding	0.05	0.643564
Merged-chr14-31771239-1	chr14	31771189	31771289	+	3.3	cIP2vsInput	"intron (NM_001024604, intron 2 of 27)"	L1M2c|LINE|L1	59176	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding	0.01	0.306931
Merged-chr1-180726012-1	chr1	180725962	180726062	+	3.3	cIP2vsInput	promoter-TSS (NM_133225)	promoter-TSS (NM_133225)	-31	NM_133225	170760	Mm.472382	NM_133225	ENSMUSG00000026499	Acbd3	60kDa|8430407O11Rik|D1Ertd10e|GCP60|GOLPH1|Gocap1|Pap7	acyl-Coenzyme A binding domain containing 3	protein-coding	0.12	0.693069
Merged-chr7-112743922-1	chr7	112743872	112743972	+	3.3	cIP2vsInput	"intron (NM_001166584, intron 1 of 13)"	"intron (NM_001166584, intron 1 of 13)"	-15462	NM_001166585	21676	Mm.398985	NM_175559	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding	0.04	0.643564
Merged-chr4-124714771-1	chr4	124714721	124714821	+	3.3	cIP2vsInput	promoter-TSS (NM_029157)	promoter-TSS (NM_029157)	-90	NM_029157	75062	Mm.25779	NM_029157	ENSMUSG00000028902	Sf3a3	4930512K19Rik|60kDa	"splicing factor 3a, subunit 3"	protein-coding	0.09	0.594059
Merged-chr5-36696085-2	chr5	36696008	36696162	+	3.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081232)	promoter-TSS (NM_001081232)	-116	NM_001081232	320661	Mm.486203	NM_001081232	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232|mKIAA0232	"DNA segment, Chr 5, ERATO Doi 579, expressed"	protein-coding	0.11039	0.703226
Merged-chr12-54405207-1	chr12	54405157	54405257	+	3.3	cIP1vsInput	Intergenic	Intergenic	-13889	NR_033689	665239	Mm.26856	NR_033689		Gm7550	EG665239|Gm666	predicted gene 7550	miscRNA	0.02	0.594059
Merged-chr5-37198387-1	chr5	37198337	37198437	+	3.3	cIP2vsInput	Intergenic	Intergenic	-43671	NM_001136058	12933	Mm.290995	NM_001136058	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding	0.01	0.50495
Merged-chr7-73494254-1	chr7	73494204	73494304	+	3.3	cIP2vsInput	"intron (NM_001081345, intron 13 of 38)"	"intron (NM_001081345, intron 13 of 38)"	47492	NM_001081345	244059	Mm.34955	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703	chromodomain helicase DNA binding protein 2	protein-coding	0	0.376238
Merged-chr17-87613845-1	chr17	87613795	87613895	+	3.3	cIP2vsInput	Intergenic	Intergenic	-22134	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding	0.05	0.50495
Merged-chr18-51565020-1	chr18	51564970	51565070	+	3.3	cIP2vsInput	Intergenic	Intergenic	447122	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding	0.01	0.425743
Merged-chr11-52231870-1	chr11	52231820	52231920	+	3.3	cIP2vsInput	promoter-TSS (NM_011543)	promoter-TSS (NM_011543)	-125	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding	0.07	0.693069
Merged-chr11-69900807-1	chr11	69900757	69900857	+	3.3	cIP2vsInput	"5' UTR (NM_027419, exon 1 of 9)"	"5' UTR (NM_027419, exon 1 of 9)"	179	NM_027419	70419	Mm.272859	NM_027419	ENSMUSG00000018570	2810408A11Rik	1700019L01Rik|4930470J18Rik|RP23-172M21.16	RIKEN cDNA 2810408A11 gene	protein-coding	0.06	0.653465
Merged-chr11-117849041-1	chr11	117848991	117849091	+	3.3	cIP2vsInput	promoter-TSS (NM_009689)	promoter-TSS (NM_009689)	-196	NM_001012273	11799	Mm.8552	NM_001012273	ENSMUSG00000017716	Birc5	AAC-11|Api4|TIAP|survivin40	baculoviral IAP repeat-containing 5	protein-coding	0.06	0.653465
Merged-chr12-101913142-1	chr12	101913092	101913192	+	3.3	cIP2vsInput	promoter-TSS (NM_028446)	promoter-TSS (NM_028446)	29	NM_028446	109181	Mm.482284	NM_028446		Trip11	2610511G22Rik|3110031G15Rik|6030460N08Rik|AI450776|GMAP-210|TRIP230	thyroid hormone receptor interactor 11	protein-coding	0.1	0.643564
Merged-chr2-180034944-1	chr2	180034894	180034994	+	3.3	cIP2vsInput	"3' UTR (NM_177727, exon 9 of 9)"	"3' UTR (NM_177727, exon 9 of 9)"	7458	NM_011969	26444	Mm.21728	NM_011969	ENSMUSG00000027566	Psma7	C6-I	"proteasome (prosome, macropain) subunit, alpha type 7"	protein-coding	0.03	0.574257
Merged-chr11-94549034-1	chr11	94548984	94549084	+	3.3	cIP2vsInput	"exon (NM_001013381, exon 1 of 9)"	"exon (NM_001013381, exon 1 of 9)"	173	NM_001013381	237926	Mm.342275	NM_001013381	ENSMUSG00000039096	Rsad1	B430319G23|BC056485	radical S-adenosyl methionine domain containing 1	protein-coding	0.13	0.732673
Merged-chr13-53099836-1	chr13	53099786	53099886	+	3.3	cIP2vsInput	Intergenic	Intergenic	-118797	NM_017373	18030	Mm.136604	NM_017373	ENSMUSG00000056749	Nfil3	AV225605|E4BP4	"nuclear factor, interleukin 3, regulated"	protein-coding	0.03	0.574257
Merged-chr17-90446466-1	chr17	90446416	90446516	+	3.3	cIP1vsInput	"intron (NM_020252, intron 17 of 22)"	"intron (NM_020252, intron 17 of 22)"	-414703	NR_045463	78800	Mm.410772	NR_045463	ENSMUSG00000090160	4930480K15Rik	-	RIKEN cDNA 4930480K15 gene	miscRNA	0.02	0.356436
Merged-chr4-115785039-1	chr4	115784989	115785089	+	3.3	cIP2vsInput	"exon (NM_181040, exon 1 of 9)"	"exon (NM_181040, exon 1 of 9)"	225	NM_181040	230649	Mm.488437	NM_181040	ENSMUSG00000028710	Atpaf1	6330547J17Rik|AI593252|ATP11|ATP11p	ATP synthase mitochondrial F1 complex assembly factor 1	protein-coding	0.15	0.80198
Merged-chr8-20814247-1	chr8	20814197	20814297	+	3.3	cIP2vsInput	Intergenic	L1VL1|LINE|L1	-62252	NR_002880	654455	Mm.424927	NR_002880		Gm21944	Defb48-ps	defensin beta 48 pseudogene	pseudo	0	0.346535
Merged-chr11-102430258-1	chr11	102430208	102430308	+	3.3	cIP2vsInput	promoter-TSS (NM_008175)	promoter-TSS (NM_008175)	-64	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	epithelin	granulin	protein-coding	0.02	0.534653
Merged-chr8-112011600-1	chr8	112011550	112011650	+	3.3	cIP2vsInput	promoter-TSS (NM_053092)	promoter-TSS (NM_053092)	241	NM_020584	57321	Mm.213064	NM_020584	ENSMUSG00000033430	Terf2ip	Rap1	"telomeric repeat binding factor 2, interacting protein"	protein-coding	0.15	0.693069
Merged-chr8-122567991-2	chr8	122567918	122568065	+	3.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026014)	promoter-TSS (NM_026014)	-24	NM_026014	67177	Mm.21873	NM_026014	ENSMUSG00000006585	Cdt1	2610318F11Rik|AW545653|C76791|Ris2	chromatin licensing and DNA replication factor 1	protein-coding	0.115646	0.662162
Merged-chr2-125782843-1	chr2	125782793	125782893	+	3.3	cIP2vsInput	promoter-TSS (NM_177608)	promoter-TSS (NM_177608)	27	NM_177608	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding	0.12	0.712871
Merged-chr6-87888047-1	chr6	87887997	87888097	+	3.3	cIP2vsInput	promoter-TSS (NM_201244)	promoter-TSS (NM_201244)	75	NM_201244	54161	Mm.258785	NM_017477	ENSMUSG00000030058	Copg1	AU019265|BC056168|Copg|D6Ertd71e|D6Wsu16e	"coatomer protein complex, subunit gamma 1"	protein-coding	0.04	0.554455
Merged-chr1-84825235-2	chr1	84825164	84825306	+	3.3	cIP1vsInput|cIP2vsInput	"intron (NM_133975, intron 1 of 40)"	"intron (NM_133975, intron 1 of 40)"	14069	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding	0.014085	0.41958
Merged-chr3-101395469-2	chr3	101395396	101395543	+	3.3	cIP1vsInput|cIP2vsInput	"intron (NM_207205, intron 2 of 10)"	"intron (NM_207205, intron 2 of 10)"	18344	NM_207205	78908	Mm.489667	NM_207205	ENSMUSG00000042035	Igsf3	1700016K10Rik|2810035F16Rik|4833439O17Rik|mKIAA0466	"immunoglobulin superfamily, member 3"	protein-coding	0.013605	0.533784
Merged-chr3-34019701-1	chr3	34019651	34019751	+	3.3	cIP2vsInput	promoter-TSS (NM_001113189)	promoter-TSS (NM_001113189)	-378	NM_001113189	14359	Mm.259021	NM_001113188	ENSMUSG00000027680	Fxr1	1110050J02Rik|9530073J07Rik|AI851072|Fxr1h|Fxr1p	"fragile X mental retardation gene 1, autosomal homolog"	protein-coding	0.07	0.673267
Merged-chr11-22512713-1	chr11	22512663	22512763	+	3.3	cIP2vsInput	"intron (NM_153596, intron 1 of 3)"	CpG	430	NM_153596	103765	Mm.221274	NM_153596	ENSMUSG00000049904	Tmem17	AI503894|AW049890	transmembrane protein 17	protein-coding	0.11	0.732673
Merged-chr17-34850301-1	chr17	34850251	34850351	+	3.3	cIP2vsInput	promoter-TSS (NM_138580)	promoter-TSS (NM_138580)	-90	NM_138580	27632	Mm.279907	NM_001045863	ENSMUSG00000024369	Nelfe	D17H6S45|NELF-E|RD|Rdbp	"negative elongation factor complex member E, Rdbp"	protein-coding	0.13	0.742574
Merged-chr4-118179905-1	chr4	118179855	118179955	+	3.3	cIP2vsInput	"5' UTR (NM_001161823, exon 1 of 22)"	"5' UTR (NM_001161823, exon 1 of 22)"	138	NM_001161823	230674	Mm.234234	NM_001161823	ENSMUSG00000033326	Kdm4a	D4Ertd222e|JHDM3A|Jmjd2|Jmjd2a|mKIAA0677	lysine (K)-specific demethylase 4A	protein-coding	0.05	0.60396
Merged-chr10-81402058-1	chr10	81402008	81402108	+	3.3	cIP2vsInput	"intron (NM_026756, intron 8 of 8)"	"intron (NM_026756, intron 8 of 8)"	8994	NM_001099917	72273	Mm.253147	NM_001099917		2210404O07Rik	-	RIKEN cDNA 2210404O07 gene	protein-coding	0.04	0.653465
Merged-chr6-56715062-1	chr6	56715012	56715112	+	3.3	cIP2vsInput	"5' UTR (NM_030235, exon 1 of 16)"	"5' UTR (NM_030235, exon 1 of 16)"	157	NM_030235	78937	Mm.105343	NM_030235	ENSMUSG00000029787	Avl9	5830411G16Rik|D730049P16Rik|mKIAA0241	AVL9 homolog (S. cerevisiase)	protein-coding	0.16	0.752475
Merged-chr3-115978953-1	chr3	115978903	115979003	+	3.3	cIP2vsInput	"intron (NM_023214, intron 7 of 10)"	"intron (NM_023214, intron 7 of 10)"	28453	NM_023214	66500	Mm.34550	NM_023214	ENSMUSG00000054414	Slc30a7	1810059J10Rik|2610034N15Rik|4833428C12Rik|AI467242|ZnT-7|ZnT7|Zntl2	"solute carrier family 30 (zinc transporter), member 7"	protein-coding	0	0.306931
Merged-chr7-112852945-1	chr7	112852895	112852995	+	3.3	cIP2vsInput	"intron (NM_001166585, intron 3 of 10)"	"intron (NM_001166585, intron 3 of 10)"	93561	NM_001166585	21676	Mm.398985	NM_175559	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding	0	0.386139
Merged-chr5-149229091-1	chr5	149229041	149229141	+	3.3	cIP2vsInput	Intergenic	CpG	-35967	NM_009663	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding	0.14	0.673267
Merged-chr12-86801325-1	chr12	86801275	86801375	+	3.3	cIP2vsInput	Intergenic	Intergenic	66956	NM_001195767	627607	Mm.341880	NM_001195767	ENSMUSG00000059114	Gm6772	EG627607	predicted gene 6772	protein-coding	0.02	0.70297
Merged-chr2-144458957-1	chr2	144458907	144459007	+	3.3	cIP2vsInput	promoter-TSS (NR_033459)	promoter-TSS (NR_033459)	-323	NR_033459	668917	Mm.152805	NR_033459	ENSMUSG00000083674	Zfp133-ps	OTTMUSG00000003825|Zfp133	"zinc finger protein 133, pseudogene"	pseudo	0.02	0.524752
Merged-chr6-87424206-1	chr6	87424156	87424256	+	3.3	cIP2vsInput	Intergenic	Intergenic	-4796	NM_009756	12154	Mm.483321	NM_009756	ENSMUSG00000030046	Bmp10	-	bone morphogenetic protein 10	protein-coding	0.01	0.524752
Merged-chr9-57589650-1	chr9	57589600	57589700	+	3.3	cIP2vsInput	TTS (NM_022813)	TTS (NM_022813)	198	NM_027895	71742	Mm.155877	NM_027895	ENSMUSG00000032308	Ulk3	1200015E14Rik	unc-51-like kinase 3	protein-coding	0.09	0.663366
Merged-chr11-51916260-1	chr11	51916210	51916310	+	3.3	cIP2vsInput	Intergenic	Intergenic	-51371	NM_029976	52626	Mm.289456	NM_029976	ENSMUSG00000020392	Cdkn2aipnl	A430101B06Rik|AA409260|D11Ertd497e|MNCb-1520	CDKN2A interacting protein N-terminal like	protein-coding	0.01	0.623762
Merged-chr5-134456705-1	chr5	134456655	134456755	+	3.3	cIP2vsInput	promoter-TSS (NM_001081466)	promoter-TSS (NM_001081466)	11	NM_001081466	57080	Mm.332735	NM_001081462	ENSMUSG00000023079	Gtf2ird1	1700012P16Rik|BEN|Cream1|ESTM9|GTF3|Gtf2il|MusTRD1|Tg(Alb1-Myc)166.8Sst|WBSCR11|X83320	general transcription factor II I repeat domain-containing 1	protein-coding	0.2	0.891089
Merged-chr1-93668887-1	chr1	93668837	93668937	+	3.3	cIP2vsInput	Intergenic	Intergenic	-16807	NM_016778	51800	Mm.3295	NM_016778	ENSMUSG00000026278	Bok	AI847676|AU021146|matador|mtd	BCL2-related ovarian killer protein	protein-coding	0.05	0.623762
Merged-chr4-148804337-1	chr4	148804287	148804387	+	3.3	cIP2vsInput	promoter-TSS (NM_001159344)	promoter-TSS (NM_001159344)	-55	NM_027195	69743	Mm.233879	NM_001159344	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding	0.13	0.683168
Merged-chr6-147268631-1	chr6	147268581	147268681	+	3.3	cIP2vsInput	Intergenic	Intergenic	-4546	NM_008970	19227	Mm.28440	NM_008970	ENSMUSG00000048776	Pthlh	PTH-like|Pthrp	parathyroid hormone-like peptide	protein-coding	0.04	0.643564
Merged-chr1-186705337-1	chr1	186705287	186705387	+	3.3	cIP2vsInput	"5' UTR (NM_009367, exon 1 of 7)"	"5' UTR (NM_009367, exon 1 of 7)"	655	NM_009367	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	"transforming growth factor, beta 2"	protein-coding	0.17	0.722772
Merged-chrY-10017849-1	chrY	10017799	10017899	+	3.3	cIP2vsInput	Intergenic	Intergenic	1179999	NM_001199331	100040022	Mm.485767	NM_001199331	ENSMUSG00000095172	Gm20822	-	"predicted gene, 20822"	protein-coding	0.01	0.524752
Merged-chr15-58872429-1	chr15	58872379	58872479	+	3.3	cIP2vsInput	promoter-TSS (NM_026642)	promoter-TSS (NM_026642)	-220	NM_026642	68260	Mm.278805	NM_026642	ENSMUSG00000037085	Trmt12	4632406N01Rik|AI449275|Tyw2	tRNA methyltranferase 12	protein-coding	0.05	0.346535
Merged-chr12-85436246-1	chr12	85436196	85436296	+	3.3	cIP2vsInput	Intergenic	Intergenic	-37655	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding	0.03	0.554455
Merged-chr2-63200770-1	chr2	63200720	63200820	+	3.3	cIP1vsInput	Intergenic	Intergenic	-16483	NM_133207	170738	Mm.242532	NM_133207		Kcnh7	9330137I11Rik|Kv11.3|erg3	"potassium voltage-gated channel, subfamily H (eag-related), member 7"	protein-coding	0	0.287129
Merged-chr17-83527794-1	chr17	83527744	83527844	+	3.3	cIP2vsInput	Intergenic	RMER10A|LTR|ERVL	-13461	NM_001159529	20463	Mm.30072	NM_001159529	ENSMUSG00000024248	Cox7a2l	COX7AR|COX7RP|EB1|SIG-81|SIG81|Silg81	cytochrome c oxidase subunit VIIa polypeptide 2-like	protein-coding	0.02	0.574257
Merged-chr4-123606416-1	chr4	123606366	123606466	+	3.3	cIP2vsInput	"intron (NM_001199136, intron 1 of 97)"	"intron (NM_001199136, intron 1 of 97)"	77944	NM_001199136	11426	Mm.485351	NM_009600	ENSMUSG00000028649	Macf1	ABP620|Acf7|Aclp7|MACF|R74989|mKIAA0465	microtubule-actin crosslinking factor 1	protein-coding	0	0.376238
Merged-chr7-137437554-1	chr7	137437504	137437604	+	3.3	cIP2vsInput	promoter-TSS (NM_023140)	promoter-TSS (NM_023140)	-94	NM_023140	30926	Mm.267692	NM_023140	ENSMUSG00000031068	Glrx3	PICOT|Txnl2	glutaredoxin 3	protein-coding	0.09	0.693069
Merged-chr17-17374407-1	chr17	17374357	17374457	+	3.3	cIP2vsInput	promoter-TSS (NM_025934)	promoter-TSS (NM_025934)	75	NM_025934	67045	Mm.35117	NM_025934	ENSMUSG00000023846	Riok2	2010110K24Rik|2410085M17Rik	RIO kinase 2 (yeast)	protein-coding	0.02	0.306931
Merged-chr1-58423758-1	chr1	58423708	58423808	+	3.3	cIP2vsInput	"intron (NM_001042634, intron 1 of 12)"	CpG	330	NR_027853	12747	Mm.1761	NM_009905	ENSMUSG00000026034	Clk1	STY	CDC-like kinase 1	protein-coding	0.14	0.762376
Merged-chr11-87448935-2	chr11	87448869	87449002	+	3.3	cIP1vsInput|cIP2vsInput	"intron (NM_031386, intron 2 of 30)"	"intron (NM_031386, intron 2 of 30)"	21344	NM_001199293	83560	Mm.440758	NM_001199293	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding	0	0.268657
Merged-chr15-60824895-1	chr15	60824845	60824945	+	3.3	cIP2vsInput	"5' UTR (NM_001162926, exon 1 of 2)"	"5' UTR (NM_001162926, exon 1 of 2)"	185	NM_001162926	399603	Mm.230853	NM_207269	ENSMUSG00000072568	Fam84b	BF642811|D330050I23Rik	"family with sequence similarity 84, member B"	protein-coding	0.11	0.673267
Merged-chrX-164076560-1	chrX	164076510	164076610	+	3.3	cIP1vsInput	promoter-TSS (NM_009173)	promoter-TSS (NM_009173)	-511	NM_009173	20438	Mm.379013	NM_009173	ENSMUSG00000040749	Siah1b	AA960570|Sinh1b	seven in absentia 1B	protein-coding	0.07	0.574257
Merged-chr13-28418150-1	chr13	28418100	28418200	+	3.3	cIP2vsInput	Intergenic	Intergenic	275666	NM_023746	28078	Mm.155058	NM_023746	ENSMUSG00000017064	Prl5a1	1600013P04Rik|D13Wsu14e|PLP-L|Prlpl|RP23-231P12.2	"prolactin family 5, subfamily a, member 1"	protein-coding	0.02	0.574257
Merged-chr15-81802395-1	chr15	81802345	81802445	+	3.3	cIP2vsInput	promoter-TSS (NM_153484)	promoter-TSS (NM_153484)	-278	NM_153484	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding	0.02	0.673267
Merged-chr2-30124638-1	chr2	30124588	30124688	+	3.3	cIP2vsInput	promoter-TSS (NM_178694)	promoter-TSS (NM_178694)	-184	NM_178694	227693	Mm.44526	NM_178694	ENSMUSG00000039686	Zer1	C230075L19Rik|Zyg11bl	"zyg-11 related, cell cycle regulator"	protein-coding	0.08	0.653465
Merged-chr19-5424856-1	chr19	5424806	5424906	+	3.3	cIP2vsInput	promoter-TSS (NM_001256515)	promoter-TSS (NM_001256515)	60	NM_024176	66556	Mm.275446	NM_024176	ENSMUSG00000024914	Drap1	2310074H19Rik	Dr1 associated protein 1 (negative cofactor 2 alpha)	protein-coding	0.08	0.673267
Merged-chr1-91459268-1	chr1	91459218	91459318	+	3.3	cIP2vsInput	promoter-TSS (NM_011066)	promoter-TSS (NM_011066)	60	NM_011066	18627	Mm.482463	NM_011066	ENSMUSG00000055866	Per2	mKIAA0347|mPer2	period circadian clock 2	protein-coding	0.15	0.712871
Merged-chr14-74722882-1	chr14	74722832	74722932	+	3.3	cIP2vsInput	Intergenic	Intergenic	-9463	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|sid478	esterase D/formylglutathione hydrolase	protein-coding	0	0.346535
Merged-chr2-113980834-1	chr2	113980784	113980884	+	3.3	cIP2vsInput	Intergenic	Intergenic	-32731	NR_028423	320846	Mm.441458	NR_028423	ENSMUSG00000087694	A530058N18Rik	-	RIKEN cDNA A530058N18 gene	miscRNA	0.06	0.633663
Merged-chr16-11135286-1	chr16	11135236	11135336	+	3.3	cIP1vsInput	promoter-TSS (NM_029582)	promoter-TSS (NM_029582)	-754	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding	0	0.326733
Merged-chr1-76658301-1	chr1	76658251	76658351	+	3.3	cIP2vsInput	Intergenic	Intergenic	169168	NR_038013	620079	Mm.378379	NR_038012		Gm17751	-	"predicted gene, 17751"	miscRNA	0.01	0.445545
Merged-chr11-103017189-1	chr11	103017139	103017239	+	3.3	cIP2vsInput	promoter-TSS (NM_026551)	promoter-TSS (NM_026551)	-42	NM_026551	68087	Mm.277449	NM_026551	ENSMUSG00000020935	Dcakd	3010024O21Rik|6720485C15Rik|AI849483	dephospho-CoA kinase domain containing	protein-coding	0.14	0.772277
Merged-chr13-23368203-1	chr13	23368153	23368253	+	3.3	cIP1vsInput	"5' UTR (NM_172586, exon 2 of 4)"	"5' UTR (NM_172586, exon 2 of 4)"	999	NM_001111107	218100	Mm.286454	NM_001111107	ENSMUSG00000046351	Zfp322a	9630054P07Rik|Znf322|Znf322a	zinc finger protein 322A	protein-coding	0	0.376238
Merged-chr7-38271793-1	chr7	38271743	38271843	+	3.3	cIP2vsInput	promoter-TSS (NM_025390)	promoter-TSS (NM_025390)	-445	NM_025390	66161	Mm.22284	NM_025390	ENSMUSG00000030423	Pop4	1110023P21Rik|Rpp29	"processing of precursor 4, ribonuclease P/MRP family, (S. cerevisiae)"	protein-coding	0.02	0.336634
Merged-chr5-147658039-1	chr5	147657989	147658089	+	3.3	cIP2vsInput	"intron (NM_010228, intron 10 of 29)"	"intron (NM_010228, intron 10 of 29)"	67949	NM_010228	14254	Mm.389712	NM_010228	ENSMUSG00000029648	Flt1	AI323757|Flt-1|VEGFR-1|VEGFR1|sFlt1	FMS-like tyrosine kinase 1	protein-coding	0.04	0.594059
Merged-chr10-59132133-1	chr10	59132083	59132183	+	3.3	cIP2vsInput	"intron (NM_172788, intron 9 of 9)"	"intron (NM_172788, intron 9 of 9)"	89714	NM_001024911	103080	Mm.397041	NM_001024910	ENSMUSG00000019917	10-Sep	4921515A04Rik|9430099J10Rik|AA408298|AI874685	septin 10	protein-coding	0.03	0.514851
Merged-chr7-44974859-1	chr7	44974809	44974909	+	3.3	cIP2vsInput	promoter-TSS (NM_153679)	promoter-TSS (NM_153679)	-8	NM_001252470	78070	Mm.231465	NM_001252470	ENSMUSG00000007783	Cpt1c	6530437J22Rik|9630004I06Rik	carnitine palmitoyltransferase 1c	protein-coding	0.07	0.613861
Merged-chr1-134060931-1	chr1	134060881	134060981	+	3.3	cIP2vsInput	Intergenic	Intergenic	18224	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	"B cell translocation gene 2, anti-proliferative"	protein-coding	0.04	0.613861
Merged-chrX-168673531-1	chrX	168673481	168673581	+	3.3	cIP2vsInput	"intron (NM_010832, intron 1 of 11)"	CpG	371	NM_010832	17692	Mm.400572	NM_010832	ENSMUSG00000031358	Msl3	AU018931|Msl31|Msl3l1	male-specific lethal 3 homolog (Drosophila)	protein-coding	0.16	0.663366
Merged-chr11-120796454-2	chr11	120796400	120796508	+	3.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026824)	promoter-TSS (NM_026824)	-59	NM_026824	68730	Mm.180622	NM_026824	ENSMUSG00000025155	Dus1l	1110032N12Rik	dihydrouridine synthase 1-like (S. cerevisiae)	protein-coding	0.092593	0.605505
Merged-chr3-121344231-1	chr3	121344181	121344281	+	3.3	cIP1vsInput	"intron (NM_024178, intron 3 of 3)"	"intron (NM_024178, intron 3 of 3)"	52414	NM_024178	66789	Mm.269881	NM_024178	ENSMUSG00000039887	Alg14	5430428G01Rik|AI854024	asparagine-linked glycosylation 14	protein-coding	0.01	0.524752
Merged-chr18-73754488-1	chr18	73754438	73754538	+	3.3	cIP2vsInput	promoter-TSS (NM_053255)	promoter-TSS (NM_053255)	-9	NM_053255	114615	Mm.50642	NM_053255	ENSMUSG00000036941	Elac1	2610018O07Rik|8430417G19Rik	elaC homolog 1 (E. coli)	protein-coding	0.19	0.811881
Merged-chr3-88553306-1	chr3	88553256	88553356	+	3.3	cIP1vsInput	promoter-TSS (NM_031248)	promoter-TSS (NM_031248)	-379	NM_031248	83409	Mm.41680	NM_031248	ENSMUSG00000028062	Lamtor2	2010111E04Rik|AL022628|Mapbpip|P14|Rab25|Robld3	"late endosomal/lysosomal adaptor, MAPK and MTOR activator 2"	protein-coding	0.02	0.445545
Merged-chr4-132049206-1	chr4	132049156	132049256	+	3.3	cIP2vsInput	promoter-TSS (NM_001128606)	promoter-TSS (NM_001128606)	-128	NM_001128606	269587	Mm.30038	NM_001128606	ENSMUSG00000028906	Epb4.1	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb41|mKIAA4056	erythrocyte protein band 4.1	protein-coding	0.08	0.683168
Merged-chr13-113218439-1	chr13	113218389	113218489	+	3.3	cIP2vsInput	TTS (NM_023612)	TTS (NM_023612)	8780	NM_023612	71690	Mm.38929	NM_023612	ENSMUSG00000042379	Esm1	0610042H23Rik|AV004503|ESM-1	endothelial cell-specific molecule 1	protein-coding	0	0.277228
Merged-chr17-32364550-1	chr17	32364500	32364600	+	3.3	cIP2vsInput	"intron (NR_033525, intron 4 of 10)"	"intron (NR_033525, intron 4 of 10)"	-13973	NM_017476	54194	Mm.488380	NM_017476	ENSMUSG00000002625	Akap8l	HAP95|Nakap95	A kinase (PRKA) anchor protein 8-like	protein-coding	0.14	0.693069
Merged-chr4-53826052-1	chr4	53826002	53826102	+	3.3	cIP2vsInput	promoter-TSS (NM_028053)	promoter-TSS (NM_028053)	7	NM_028053	52076	Mm.27184	NM_028053	ENSMUSG00000028420	Tmem38b	1600017F22Rik|AA437809|AV051057|D4Ertd89e|TRIC-B|mg33b	transmembrane protein 38B	protein-coding	0.15	0.811881
Merged-chr2-152847866-2	chr2	152847811	152847922	+	3.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001141976)	promoter-TSS (NM_001141976)	-98	NM_001141975	72119	Mm.407737	NM_001141975	ENSMUSG00000027469	Tpx2	2610005B21Rik|DIL2|REPP86|p100	"TPX2, microtubule-associated protein homolog (Xenopus laevis)"	protein-coding	0.036036	0.517857
Merged-chr14-14012585-1	chr14	14012535	14012635	+	3.3	cIP2vsInput	promoter-TSS (NM_139227)	promoter-TSS (NM_139227)	94	NM_139227	246103	Mm.133625	NM_139227	ENSMUSG00000021738	Atxn7	A430107N12Rik|AI627028|Sca7|ataxin-7	ataxin 7	protein-coding	0.1	0.693069
Merged-chr1-161070777-1	chr1	161070727	161070827	+	3.3	cIP2vsInput	promoter-TSS (NM_172644)	promoter-TSS (NM_172644)	-115	NM_027429	70454	Mm.248212	NM_001159930	ENSMUSG00000026708	Cenpl	2610300B10Rik|AW121806|AW550697	centromere protein L	protein-coding	0.07	0.514851
Merged-chr5-97713818-1	chr5	97713768	97713868	+	3.3	cIP1vsInput	Intergenic	L1MDa|LINE|L1	-256810	NM_010294	14626	Mm.61206	NM_010294	ENSMUSG00000050553	Gk2	GKTA|Gk-rs2	glycerol kinase 2	protein-coding	0.01	0.336634
Merged-chrX-153497757-1	chrX	153497707	153497807	+	3.3	cIP2vsInput	promoter-TSS (NM_018798)	promoter-TSS (NM_018798)	-475	NM_018798	54609	Mm.430772	NM_018798	ENSMUSG00000050148	Ubqln2	Chap1|Dsk2|HRIHFB2157|Plic-2|Plic2	ubiquilin 2	protein-coding	0.05	0.514851
Merged-chr3-134190183-1	chr3	134190133	134190233	+	3.3	cIP2vsInput	Intergenic	Intergenic	-46312	NM_001004367	319478	Mm.487501	NM_001004367	ENSMUSG00000044365	Cxxc4	9330210J02Rik|C030003J12Rik|Idax	CXXC finger 4	protein-coding	0.05	0.524752
Merged-chr14-67072096-1	chr14	67072046	67072146	+	3.3	cIP2vsInput	"exon (NM_001205188, exon 1 of 10)"	"exon (NM_001205188, exon 1 of 10)"	375	NM_028032	71978	Mm.273997	NM_001205188	ENSMUSG00000022052	Ppp2r2a	2410004D02Rik|mKIAA1541	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform"	protein-coding	0.1	0.673267
Merged-chr8-71382128-1	chr8	71382078	71382178	+	3.3	cIP2vsInput	promoter-TSS (NM_010150)	promoter-TSS (NM_010150)	-176	NM_010150	13864	Mm.28989	NM_010150	ENSMUSG00000002393	Nr2f6	AV090102|COUP-TF3|EAR2|Erbal2	"nuclear receptor subfamily 2, group F, member 6"	protein-coding	0.14	0.792079
Merged-chr1-43098388-1	chr1	43098338	43098438	+	3.3	cIP2vsInput	promoter-TSS (NM_133818)	promoter-TSS (NM_133818)	234	NM_001013025	73122	Mm.246069	NM_001013025	ENSMUSG00000070939	Tgfbrap1	3110018K12Rik|AU024090|AU042859|AW742551|Trap1	"transforming growth factor, beta receptor associated protein 1"	protein-coding	0.02	0.445545
Merged-chr8-125054758-2	chr8	125054693	125054823	+	3.3	cIP1vsInput|cIP2vsInput	"intron (NM_174854, intron 1 of 12)"	CpG	563	NM_174854	244667	Mm.233504	NM_170596	ENSMUSG00000043051	Disc1	-	disrupted in schizophrenia 1	protein-coding	0.046154	0.580153
Merged-chr1-36369241-1	chr1	36369191	36369291	+	3.3	cIP2vsInput	promoter-TSS (NM_172652)	promoter-TSS (NM_172652)	-60	NM_172652	226976	Mm.24734	NM_172652	ENSMUSG00000010453	Kansl3	4632411B12Rik|4932435K23|AI431067|AI647574|C85723|Kiaa1310|mKIAA1310	KAT8 regulatory NSL complex subunit 3	protein-coding	0.16	0.722772
Merged-chr16-24902720-1	chr16	24902670	24902770	+	3.3	cIP2vsInput	"intron (NM_001145954, intron 5 of 7)"	"intron (NM_001145954, intron 5 of 7)"	-156919	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	miscRNA	0	0.366337
Merged-chr4-149099849-1	chr4	149099799	149099899	+	3.3	cIP2vsInput	promoter-TSS (NM_019781)	promoter-TSS (NM_019781)	-37	NM_019781	56273	Mm.184172	NM_019781	ENSMUSG00000028975	Pex14	Pex14p|R75137	peroxisomal biogenesis factor 14	protein-coding	0.07	0.574257
Merged-chr9-55209043-1	chr9	55208993	55209093	+	3.3	cIP2vsInput	"5' UTR (NM_028049, exon 1 of 7)"	"5' UTR (NM_028049, exon 1 of 7)"	108	NM_028049	71999	Mm.276429	NM_028049	ENSMUSG00000032309	Fbxo22	0610033L19Rik|1600016C16Rik	F-box protein 22	protein-coding	0.12	0.732673
Merged-chr2-118717034-1	chr2	118716984	118717084	+	3.3	cIP2vsInput	"exon (NM_177568, exon 16 of 32)"	"exon (NM_177568, exon 16 of 32)"	11404	NM_177568	18796	Mm.215156	NM_177568	ENSMUSG00000040061	Plcb2	AI550384|B230205M18Rik|B230399N12	"phospholipase C, beta 2"	protein-coding	0.03	0.50495
Merged-chr5-134639562-1	chr5	134639512	134639612	+	3.3	cIP2vsInput	promoter-TSS (NM_033561)	promoter-TSS (NM_033561)	-234	NM_033561	22384	Mm.27955	NM_033561	ENSMUSG00000040731	Eif4h	AU018978|D5Ertd355e|E430026L18Rik|Ef4h|Wbscr1|Wscr1|mKIAA0038	eukaryotic translation initiation factor 4H	protein-coding	0.1	0.70297
Merged-chr4-156235939-1	chr4	156235889	156235989	+	3.3	cIP2vsInput	promoter-TSS (NM_021303)	promoter-TSS (NM_021303)	-71	NM_021303	57741	Mm.486684	NM_021303	ENSMUSG00000095567	Noc2l	AA410003|AF155546|NIR	nucleolar complex associated 2 homolog (S. cerevisiae)	protein-coding	0.15	0.782178
Merged-chr9-83605770-1	chr9	83605720	83605820	+	3.3	cIP1vsInput	Intergenic	LTR41B|LTR|ERVL	57432	NM_172507	212531	Mm.100125	NM_172507	ENSMUSG00000032261	Sh3bgrl2	A930014C21Rik|AA408038|B930089I21	SH3 domain binding glutamic acid-rich protein like 2	protein-coding	0	0.316832
Merged-chr8-121653138-1	chr8	121653088	121653188	+	3.3	cIP2vsInput	Intergenic	CpG-14599	-1205	NM_080855	142682	Mm.475749	NM_080855	ENSMUSG00000061410	Zcchc14	AA792890|BDG29	"zinc finger, CCHC domain containing 14"	protein-coding	0.09	0.594059
Merged-chr6-39810965-2	chr6	39810906	39811024	+	3.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010270)	promoter-TSS (NM_010270)	-29	NM_001010930	14548	Mm.377071	NM_001010930	ENSMUSG00000029918	Mrps33	AI841153|CGI-139|Gdap3|MRP-S33|PTD003	mitochondrial ribosomal protein S33	protein-coding	0.067797	0.638655
Merged-chrY-6785475-1	chrY	6785425	6785525	+	3.3	cIP1vsInput	Intergenic	L1Md_F3|LINE|L1	382302	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.356436
Merged-chr10-13008239-1	chr10	13008189	13008289	+	3.3	cIP2vsInput	promoter-TSS (NM_175102)	promoter-TSS (NM_175102)	-211	NM_175102	66125	Mm.402225	NM_175102	ENSMUSG00000078348	Sf3b5	10kDa|1110005L13Rik|AU043053|Sf3b10	"splicing factor 3b, subunit 5"	protein-coding	0.02	0.425743
Merged-chr8-125617099-1	chr8	125617049	125617149	+	3.3	cIP1vsInput	TTS (NR_015535)	TTS (NR_015535)	32461	NR_015535	75930	Mm.234080	NR_015535		4930567H12Rik	4930579P07Rik	RIKEN cDNA 4930567H12 gene	miscRNA	0.01	0.643564
Merged-chr11-75190495-1	chr11	75190445	75190545	+	3.3	cIP2vsInput	promoter-TSS (NM_144491)	promoter-TSS (NM_144491)	-12	NM_144491	116905	Mm.41496	NM_144491	ENSMUSG00000078789	Dph1	2310011M22Rik|4930488F09Rik|AW551873|Dph2l1|Ovca1	DPH1 homolog (S. cerevisiae)	protein-coding	0.11	0.623762
Merged-chr4-98072001-1	chr4	98071951	98072051	+	3.3	cIP1vsInput	"intron (NM_001122953, intron 8 of 9)"	"intron (NM_001122953, intron 8 of 9)"	294375	NM_010905	18027	Mm.409646	NM_001122952	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|NF1-A|NF1A	nuclear factor I/A	protein-coding	0.01	0.386139
Merged-chr8-83652589-1	chr8	83652539	83652639	+	3.3	cIP2vsInput	promoter-TSS (NM_018771)	promoter-TSS (NM_018771)	-89	NM_018771	67903	Mm.20945	NM_018771	ENSMUSG00000019433	Gipc1	GIPC|Glut1CIP|Rgs19ip1|Semcap1|TIP-2|TaxIP2	"GIPC PDZ domain containing family, member 1"	protein-coding	0.14	0.712871
Merged-chr2-64462851-1	chr2	64462801	64462901	+	3.3	cIP2vsInput	Intergenic	Intergenic	-364813	NM_001267847	60344	Mm.483676	NM_001267846	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding	0.01	0.346535
Merged-chr13-12766342-1	chr13	12766292	12766392	+	3.3	cIP2vsInput	Intergenic	Intergenic	33716	NM_011954	26421	Mm.457984	NM_011954		Prl2c4	MRP-3|Mrpplf3|PLF-3|mrp/plf3	"prolactin family 2, subfamily c, member 4"	protein-coding	0	0.336634
Merged-chr7-127895502-1	chr7	127895452	127895552	+	3.3	cIP2vsInput	"exon (NM_178600, exon 1 of 3)"	"exon (NM_178600, exon 1 of 3)"	115	NM_178600	27973	Mm.29703	NM_178600	ENSMUSG00000096145	Vkorc1	D7Wsu86e	"vitamin K epoxide reductase complex, subunit 1"	protein-coding	0.15	0.663366
Merged-chr8-122551643-1	chr8	122551593	122551693	+	3.3	cIP2vsInput	promoter-TSS (NM_001037298)	promoter-TSS (NM_001037298)	-314	NM_001037298	234839		NM_001037298	ENSMUSG00000014444	Piezo1	9630020g22|Fam38a|mKIAA0233	piezo-type mechanosensitive ion channel component 1	protein-coding	0.06	0.584158
Merged-chr1-63730544-1	chr1	63730494	63730594	+	3.3	cIP2vsInput	promoter-TSS (NM_029696)	promoter-TSS (NM_029696)	-81	NM_172422	75619	Mm.30965	NM_172422		Fastkd2	2810421I24Rik	FAST kinase domains 2	protein-coding	0.05	0.445545
Merged-chr10-128566455-1	chr10	128566405	128566505	+	3.3	cIP2vsInput	promoter-TSS (NM_011119)	promoter-TSS (NM_011119)	-521	NM_011119	18813	Mm.4742	NM_011119	ENSMUSG00000025364	Pa2g4	38kDa|AA672939|Ebp1|Plfap	proliferation-associated 2G4	protein-coding	0.08	0.663366
Merged-chr16-52948076-1	chr16	52948026	52948126	+	3.3	cIP1vsInput	Intergenic	Intergenic	-132332	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	miscRNA	0.01	0.306931
Merged-chr2-48884972-1	chr2	48884922	48885022	+	3.3	cIP2vsInput	"intron (NM_007396, intron 4 of 10)"	"intron (NM_007396, intron 4 of 10)"	64295	NM_001177313	26428	Mm.314338	NM_001177313	ENSMUSG00000026761	Orc4	Orc4P|Orc4l|mMmORC4	"origin recognition complex, subunit 4"	protein-coding	0	0.366337
Merged-chr12-83950604-1	chr12	83950554	83950654	+	3.3	cIP2vsInput	promoter-TSS (NM_023633)	promoter-TSS (NM_023633)	-4	NM_023633	71952	Mm.251483	NM_023633	ENSMUSG00000046791	2410016O06Rik	MAPJD|NO66	RIKEN cDNA 2410016O06 gene	protein-coding	0.04	0.584158
Merged-chr1-133610048-1	chr1	133609998	133610098	+	3.3	cIP2vsInput	"intron (NM_009227, intron 1 of 4)"	CpG	232	NM_009227	20643	Mm.249110	NM_009227	ENSMUSG00000090553	Snrpe	AL022645|C76690|SME	small nuclear ribonucleoprotein E	protein-coding	0.14	0.772277
Merged-chr6-85451935-1	chr6	85451885	85451985	+	3.3	cIP2vsInput	promoter-TSS (NR_028081)	promoter-TSS (NR_028081)	35	NR_028081	73327	Mm.379221	NM_001163427	ENSMUSG00000030008	Pradc1	1700040I03Rik|Pap21	protease-associated domain containing 1	protein-coding	0.08	0.623762
Merged-chr4-156109887-1	chr4	156109837	156109937	+	3.3	cIP2vsInput	promoter-TSS (NM_177205)	promoter-TSS (NM_177205)	-111	NM_177205	230996	Mm.318925	NM_145557	ENSMUSG00000059939	9430015G10Rik	-	RIKEN cDNA 9430015G10 gene	protein-coding	0.09	0.623762
Merged-chr3-97610230-1	chr3	97610180	97610280	+	3.3	cIP2vsInput	promoter-TSS (NM_026539)	promoter-TSS (NM_026539)	-40	NM_026539	68058	Mm.41447	NM_026539	ENSMUSG00000028089	Chd1l	4432404A22Rik|Alc1|Snf2p	chromodomain helicase DNA binding protein 1-like	protein-coding	0.17	0.732673
Merged-chr3-40894494-1	chr3	40894444	40894544	+	3.3	cIP1vsInput	"intron (NM_026622, intron 1 of 12)"	CpG	217	NM_026622	269423	Mm.482948	NM_026622	ENSMUSG00000037818	3110057O12Rik	2310068E01Rik|4732404H23|AI645591	RIKEN cDNA 3110057O12 gene	protein-coding	0.07	0.633663
Merged-chr7-100121451-2	chr7	100121360	100121542	+	3.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133692)	promoter-TSS (NM_133692)	49	NM_133692	67967	Mm.37562	NM_133692	ENSMUSG00000030726	Pold3	2410142G14Rik|C85233|P66|P68	"polymerase (DNA-directed), delta 3, accessory subunit"	protein-coding	0.10989	0.63388
Merged-chr6-86438569-1	chr6	86438519	86438619	+	3.3	cIP2vsInput	promoter-TSS (NM_001243742)	promoter-TSS (NM_001243742)	-77	NM_001243742	232196		NR_027369	ENSMUSG00000046679	C87436	-	expressed sequence C87436	protein-coding	0.09	0.60396
Merged-chr4-116174893-1	chr4	116174843	116174943	+	3.3	cIP2vsInput	TTS (NM_001099295)	TTS (NM_001099295)	1521	NM_001099295	67323	Mm.45442	NM_001099295	ENSMUSG00000078593	1700042G07Rik	-	RIKEN cDNA 1700042G07 gene	protein-coding	0.01	0.633663
Merged-chr7-80947904-2	chr7	80947851	80947958	+	3.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019951)	promoter-TSS (NM_019951)	-354	NM_019951	56529	Mm.474025	NM_019951	ENSMUSG00000025724	Sec11a	1810012E07Rik|18kDa|Sec11l1|Sid2895p|Spc18|sid2895	SEC11 homolog A (S. cerevisiae)	protein-coding	0.074766	0.62963
Merged-chr2-15880456-1	chr2	15880406	15880506	+	3.3	cIP2vsInput	Intergenic	Intergenic	-475866	NM_026162	67448	Mm.394655	NM_026162		Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding	0	0.346535
Merged-chr2-61811655-1	chr2	61811605	61811705	+	3.3	cIP1vsInput	"exon (NM_009322, exon 6 of 6)"	"exon (NM_009322, exon 6 of 6)"	7202	NM_009322	21375	Mm.404741	NM_009322	ENSMUSG00000035033	Tbr1	-	T-box brain gene 1	protein-coding	0.14	0.683168
Merged-chr11-103029154-1	chr11	103029104	103029204	+	3.3	cIP2vsInput	"intron (NM_008707, intron 1 of 11)"	"intron (NM_008707, intron 1 of 11)"	592	NM_008707	18107	Mm.10265	NM_008707		Nmt1	AW536594	N-myristoyltransferase 1	protein-coding	0.02	0.346535
Merged-chr17-26663145-1	chr17	26663095	26663195	+	3.3	cIP2vsInput	Intergenic	Intergenic	-13251	NM_025272	11974	Mm.22602	NM_025272	ENSMUSG00000015575	Atp6v0e	Atp6k|Atp6v0e1|M9.2	"ATPase, H+ transporting, lysosomal V0 subunit E"	protein-coding	0.07	0.574257
Merged-chr4-134468298-1	chr4	134468248	134468348	+	3.3	cIP1vsInput	promoter-TSS (NM_019641)	promoter-TSS (NM_019641)	-22	NM_019641	16765	Mm.378957	NM_019641	ENSMUSG00000028832	Stmn1	19k|Lag|Lap18|Op18|P18|P19|Pig|Pp17|Pp18|Pp19|Pr22|Smn	stathmin 1	protein-coding	0.09	0.673267
Merged-chr7-24904330-1	chr7	24904280	24904380	+	3.3	cIP2vsInput	promoter-TSS (NM_001130152)	promoter-TSS (NM_001130152)	-16	NM_001130152	16801	Mm.3181	NM_001130150	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding	0.1	0.673267
Merged-chr13-94976438-1	chr13	94976388	94976488	+	3.3	cIP2vsInput	promoter-TSS (NM_172590)	promoter-TSS (NM_172590)	94	NM_172590	218460	Mm.33856	NM_172590	ENSMUSG00000042015	Wdr41	B830029I03Rik|MSTP048	WD repeat domain 41	protein-coding	0.12	0.722772
Merged-chr15-80219460-1	chr15	80219410	80219510	+	3.3	cIP2vsInput	Intergenic	Intergenic	-14620	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Smcr7l	A230016E22|AI452372	"Smith-Magenis syndrome chromosome region, candidate 7-like (human)"	protein-coding	0.04	0.574257
Merged-chr5-115436878-1	chr5	115436828	115436928	+	3.3	cIP2vsInput	"intron (NM_008629, intron 6 of 14)"	CpG	7193	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding	0.08	0.732673
Merged-chr3-136862652-1	chr3	136862602	136862702	+	3.3	cIP2vsInput	"intron (NM_008913, intron 2 of 13)"	"intron (NM_008913, intron 2 of 13)"	191882	NM_008913	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|AI841391|AW413465|CN|Caln|Calna|CnA	"protein phosphatase 3, catalytic subunit, alpha isoform"	protein-coding	0.01	0.435644
Merged-chr11-69340520-1	chr11	69340470	69340570	+	3.3	cIP1vsInput	promoter-TSS (NR_027827)	promoter-TSS (NR_027827)	-249	NR_027827	80515	Mm.5324	NM_020591	ENSMUSG00000043419	A030009H04Rik	2310043C11Rik|AA589459|AB041807|RNF21	RIKEN cDNA A030009H04 gene	miscRNA	0.06	0.594059
Merged-chrY-90829800-1	chrY	90829750	90829850	+	3.3	cIP1vsInput	Intergenic	Intergenic	44358	NM_133362	170942	Mm.391385	XM_003946384	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding	0.02	0.39604
Merged-chr12-79612887-1	chr12	79612837	79612937	+	3.3	cIP2vsInput	"intron (NM_009014, intron 7 of 10)"	"intron (NM_009014, intron 7 of 10)"	315536	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 homolog B	protein-coding	0.02	0.574257
Merged-chr10-79841318-1	chr10	79841268	79841368	+	3.3	cIP2vsInput	"intron (NR_038088, intron 3 of 4)"	"intron (NR_038088, intron 3 of 4)"	-13287	NM_001077363	19205	Mm.265610	NM_001077363	ENSMUSG00000006498	Ptbp1	AA407203|AL033359|HNRPI|PTB-1|PTB2|PTB3|PTB4|Ptb|pPTB	polypyrimidine tract binding protein 1	protein-coding	0.03	0.524752
Merged-chr13-98768485-1	chr13	98768435	98768535	+	3.3	cIP2vsInput	"intron (NM_172591, intron 8 of 25)"	"intron (NM_172591, intron 8 of 25)"	46964	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding	0.03	0.49505
Merged-chr16-3884572-1	chr16	3884522	3884622	+	3.3	cIP2vsInput	promoter-TSS (NM_029090)	promoter-TSS (NM_029090)	-47	NM_029090	74763	Mm.28403	NM_029090	ENSMUSG00000005982	Naa60	1200013P24Rik|AI315146|Nat15	"N(alpha)-acetyltransferase 60, NatF catalytic subunit"	protein-coding	0.08	0.693069
Merged-chr13-13860945-1	chr13	13860895	13860995	+	3.3	cIP1vsInput	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	76406	NM_010317	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	"guanine nucleotide binding protein (G protein), gamma 4"	protein-coding	0	0.544554
Merged-chr18-4921545-1	chr18	4921495	4921595	+	3.3	cIP2vsInput	Intergenic	Intergenic	109059	NR_045881	100038439	Mm.387569	NR_045881	ENSMUSG00000097043	Gm10556	ENSMUSG00000073646	predicted gene 10556	miscRNA	0.07	0.762376
Merged-chr7-139213321-2	chr7	139213266	139213377	+	3.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001162540)	promoter-TSS (NM_001162540)	-14	NM_001162540	57740	Mm.65336	NM_001162540	ENSMUSG00000015981	Stk32c	PKE|Pkek|YANK3	serine/threonine kinase 32C	protein-coding	0.099099	0.678571
Merged-chr8-20435853-1	chr8	20435803	20435903	+	3.3	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-11039	NR_028428	381598	Mm.483074	NM_001024708	ENSMUSG00000071793	2610005L07Rik	2810038F24Rik|6720476A01Rik	cadherin 11 pseudogene	pseudo	0	0.326733
Merged-chr16-86325537-1	chr16	86325487	86325587	+	3.3	cIP2vsInput	Intergenic	Intergenic	-424412	NM_011782	23794	Mm.437478	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|AI481094|ASMP-2	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"	protein-coding	0	0.316832
Merged-chr11-4594879-1	chr11	4594829	4594929	+	3.3	cIP1vsInput	promoter-TSS (NM_028860)	promoter-TSS (NM_028860)	-64	NM_028860	74302	Mm.425669	NM_028860	ENSMUSG00000034354	Mtmr3	1700092A20Rik|AI255150|AW557713|FYVE-DSP1|ZFYVE10|mKIAA0371	myotubularin related protein 3	protein-coding	0.15	0.792079
Merged-chr4-42949732-1	chr4	42949682	42949782	+	3.3	cIP2vsInput	Intergenic	CpG	-3362	NM_019874	56323	Mm.20437	NM_019874	ENSMUSG00000036052	Dnajb5	1110058L06Rik|AI462558|Hsc40|Hsp40-3	"DnaJ (Hsp40) homolog, subfamily B, member 5"	protein-coding	0.07	0.643564
Merged-chr11-53481321-1	chr11	53481271	53481371	+	3.3	cIP2vsInput	Intergenic	L2b|LINE|L2	-1126	NM_183173	237761	Mm.145208	NM_183173	ENSMUSG00000044352	Sowaha	A830006N08Rik|Ankrd43	sosondowah ankyrin repeat domain family member A	protein-coding	0.01	0.39604
Merged-chr14-61439934-1	chr14	61439884	61439984	+	3.3	cIP2vsInput	promoter-TSS (NM_008466)	promoter-TSS (NM_008466)	13	NM_008466	16648	Mm.25548	NM_008466	ENSMUSG00000021929	Kpna3	IPOA4	karyopherin (importin) alpha 3	protein-coding	0.17	0.811881
Merged-chr17-24669647-1	chr17	24669597	24669697	+	3.3	cIP2vsInput	promoter-TSS (NM_183149)	promoter-TSS (NM_183149)	-105	NM_183149	213753	Mm.219581	NM_183149	ENSMUSG00000041130	Zfp598	BC023040|Ntrap|Znf598	zinc finger protein 598	protein-coding	0.11	0.693069
Merged-chr6-24527591-1	chr6	24527541	24527641	+	3.3	cIP2vsInput	promoter-TSS (NM_080847)	promoter-TSS (NM_080847)	96	NM_026614	68202	Mm.275780	NM_026614		Ndufa5	2900002J19Rik	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5"	protein-coding	0.08	0.633663
Merged-chr9-120691643-1	chr9	120691593	120691693	+	3.3	cIP2vsInput	Intergenic	Intergenic	114312	NR_073359	76100	Mm.48212	XM_003945458		5830454E08Rik	-	RIKEN cDNA 5830454E08 gene	miscRNA	0.02	0.564356
Merged-chr19-24058307-1	chr19	24058257	24058357	+	3.3	cIP2vsInput	Intergenic	Intergenic	-27288	NM_001114174	381217	Mm.426078	NM_001114174	ENSMUSG00000071604	Fam189a2	AI414343|AI666772|Gm967	"family with sequence similarity 189, member A2"	protein-coding	0.04	0.514851
Merged-chr10-116950470-1	chr10	116950420	116950520	+	3.3	cIP2vsInput	promoter-TSS (NR_038026)	promoter-TSS (NR_038026)	-90	NM_001003950	216363	Mm.336394	NM_001003950	ENSMUSG00000064181	Rab3ip	B230311A06|Gtpat12|Rabin3	RAB3A interacting protein	protein-coding	0.15	0.831683
Merged-chr9-103202122-2	chr9	103202054	103202191	+	3.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009275)	promoter-TSS (NM_009275)	-57	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	"signal recognition particle receptor, B subunit"	protein-coding	0.065693	0.608696
Merged-chr8-95633203-1	chr8	95633153	95633253	+	3.3	cIP1vsInput	promoter-TSS (NM_030198)	promoter-TSS (NM_030198)	-356	NM_030198	78833	Mm.35546	NM_030198	ENSMUSG00000031669	Gins3	2700085M18Rik|AI616142	GINS complex subunit 3 (Psf3 homolog)	protein-coding	0.01	0.336634
Merged-chr7-127777010-1	chr7	127776960	127777060	+	3.3	cIP1vsInput	promoter-TSS (NM_178029)	promoter-TSS (NM_178029)	-379	NM_178029	233904	Mm.435494	NM_010940	ENSMUSG00000042308	Setd1a	BC010250|KMT2F|Nsccn1|mKIAA0339|mNSC1	SET domain containing 1A	protein-coding	0.13	0.673267
Merged-chr4-59438326-2	chr4	59438255	59438397	+	3.3	cIP1vsInput|cIP2vsInput	"5' UTR (NM_001163288, exon 1 of 17)"	"5' UTR (NM_001163288, exon 1 of 17)"	307	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding	0.112676	0.762238
Merged-chr9-65391216-1	chr9	65391166	65391266	+	3.3	cIP2vsInput	"exon (NM_028974, exon 1 of 1)"	"exon (NM_028974, exon 1 of 1)"	436	NM_028974	74492	Mm.159223	NM_028974	ENSMUSG00000054978	Kbtbd13	5430433E21Rik	kelch repeat and BTB (POZ) domain containing 13	protein-coding	0.14	0.732673
Merged-chr9-56041932-1	chr9	56041882	56041982	+	3.3	cIP2vsInput	promoter-TSS (NM_011992)	promoter-TSS (NM_011992)	87	NM_011992	26611	Mm.1782	NM_011992	ENSMUSG00000032320	Rcn2	AA408742|Tcbp49	reticulocalbin 2	protein-coding	0.08	0.732673
Merged-chr9-30704431-1	chr9	30704381	30704481	+	3.3	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	218021	NM_001024139	235130	Mm.65867	NM_001024139	ENSMUSG00000033453	Adamts15	-	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 15"	protein-coding	0	0.267327
Merged-chr5-129020473-2	chr5	129020408	129020538	+	3.3	cIP1vsInput|cIP2vsInput	"intron (NM_009391, intron 1 of 6)"	CpG	317	NM_009391	19384	Mm.386831	NM_009391	ENSMUSG00000029430	Ran	-	"RAN, member RAS oncogene family"	protein-coding	0.153846	0.740458
Merged-chr13-98004651-1	chr13	98004601	98004701	+	3.3	cIP2vsInput	"intron (NM_012026, intron 9 of 35)"	"intron (NM_012026, intron 9 of 35)"	201514	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding	0	0.326733
Merged-chr3-37639900-1	chr3	37639850	37639950	+	3.3	cIP2vsInput	promoter-TSS (NM_011896)	promoter-TSS (NM_011896)	-50	NM_011896	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1	sprouty homolog 1 (Drosophila)	protein-coding	0.15	0.70297
Merged-chr11-105181392-1	chr11	105181342	105181442	+	3.3	cIP1vsInput	promoter-TSS (NR_027956)	promoter-TSS (NR_027956)	41	NR_027956	73431	Mm.351426	NM_028539		1700052K11Rik	AI840954	RIKEN cDNA 1700052K11 gene	miscRNA	0.12	0.762376
Merged-chr4-156329970-1	chr4	156329920	156330020	+	3.3	cIP1vsInput	Intergenic	Intergenic	-1133	NR_028141	22314	Mm.458976	NR_028141	ENSMUSG00000057021	Vmn2r-ps159	V2r8|V2r9|Vmn2r-ps160	"vomeronasal 2, receptor, pseudogene 159"	pseudo	0	0.217822
Merged-chr5-119575360-1	chr5	119575310	119575410	+	3.3	cIP2vsInput	"non-coding (NR_045702, exon 2 of 5)"	"non-coding (NR_045702, exon 2 of 5)"	4998	NR_045702	100993	Mm.381453	NR_045702		AW549542	-	expressed sequence AW549542	miscRNA	0.05	0.594059
Merged-chr17-80728092-1	chr17	80728042	80728142	+	3.3	cIP2vsInput	promoter-TSS (NM_001081357)	promoter-TSS (NM_001081357)	1	NM_001081357	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding	0.15	0.792079
Merged-chr11-90391014-1	chr11	90390964	90391064	+	3.3	cIP2vsInput	promoter-TSS (NM_172563)	promoter-TSS (NM_172563)	-97	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding	0.11	0.722772
Merged-chr7-6410261-1	chr7	6410211	6410311	+	3.3	cIP2vsInput	Intergenic	Intergenic	-4914	NM_001134752	100042450	Mm.483282	NM_001134752		Gm16532	-	"predicted gene, 16532"	protein-coding	0.05	0.534653
Merged-chr1-85606269-1	chr1	85606219	85606319	+	3.3	cIP1vsInput	"intron (NM_001013817, intron 1 of 16)"	"intron (NM_001013817, intron 1 of 16)"	-2378	NM_175397	109032	Mm.461913	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding	0.02	0.376238
Merged-chr11-69795273-1	chr11	69795223	69795323	+	3.3	cIP2vsInput	"intron (NM_009601, intron 2 of 10)"	"intron (NM_009601, intron 2 of 10)"	664	NM_009601	11443	Mm.86425	NM_009601	ENSMUSG00000041189	Chrnb1	Achr-2|Acrb	"cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)"	protein-coding	0.03	0.465347
Merged-chr3-19311374-1	chr3	19311324	19311424	+	3.3	cIP2vsInput	promoter-TSS (NM_001122759)	promoter-TSS (NM_001122759)	-52	NM_001122759	18583	Mm.355614	NM_001122759		Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding	0.16	0.722772
Merged-chr4-28986545-1	chr4	28986495	28986595	+	3.3	cIP2vsInput	Intergenic	Intergenic	173400	NM_010141	13841	Mm.257266	NM_001122889	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding	0.01	0.336634
Merged-chr16-30009189-1	chr16	30009139	30009239	+	3.3	cIP2vsInput	"intron (NR_033631, intron 1 of 2)"	CpG	522	NR_033631	100043102	Mm.30797	NR_033631	ENSMUSG00000097184	4632428C04Rik	Gm4231	RIKEN cDNA 4632428C04 gene	miscRNA	0.12	0.762376
Merged-chr12-69242019-1	chr12	69241969	69242069	+	3.3	cIP2vsInput	"intron (NM_178253, intron 1 of 12)"	CpG	187	NM_178253	271005	Mm.180969	NM_178253		Klhdc1	-	kelch domain containing 1	protein-coding	0.1	0.722772
Merged-chr13-101978383-1	chr13	101978333	101978433	+	3.3	cIP1vsInput	Intergenic	Intergenic	-210166	NM_001077495	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	AA414921|C530050K14|PI3K|p50alpha|p55alpha|p85alpha	"phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)"	protein-coding	0	0.267327
Merged-chr9-61380833-1	chr9	61380783	61380883	+	3.3	cIP2vsInput	"intron (NM_001083927, intron 4 of 19)"	"intron (NM_001083927, intron 4 of 19)"	8467	NM_001083927	21887	Mm.469199	NM_001083927	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	"transducin-like enhancer of split 3, homolog of Drosophila E(spl)"	protein-coding	0.02	0.564356
Merged-chr3-15333988-1	chr3	15333938	15334038	+	3.3	cIP2vsInput	Intergenic	Intergenic	-1686	NM_001076679	751864	Mm.431296	NM_001076679	ENSMUSG00000078783	Gm9733	-	predicted gene 9733	protein-coding	0.01	0.356436
Merged-chr3-57736327-1	chr3	57736277	57736377	+	3.3	cIP2vsInput	"intron (NM_011883, intron 1 of 8)"	CpG	261	NM_001113413	24017	Mm.274360	NM_001113413	ENSMUSG00000036503	Rnf13	2010001H16Rik|Rzf	ring finger protein 13	protein-coding	0.08	0.683168
Merged-chr1-75546920-1	chr1	75546870	75546970	+	3.3	cIP2vsInput	"exon (NM_009208, exon 2 of 23)"	"exon (NM_009208, exon 2 of 23)"	654	NM_009208	20536	Mm.5053	NM_009208		Slc4a3	A930038D23Rik|Ae3	"solute carrier family 4 (anion exchanger), member 3"	protein-coding	0.06	0.742574
Merged-chr7-46100738-1	chr7	46100688	46100788	+	3.3	cIP2vsInput	promoter-TSS (NM_010602)	promoter-TSS (NM_010602)	26	NM_001204411	16514	Mm.428799	NM_001204411		Kcnj11	Kir6.2|mBIR	"potassium inwardly rectifying channel, subfamily J, member 11"	protein-coding	0.12	0.772277
Merged-chr3-9004617-1	chr3	9004567	9004667	+	3.3	cIP2vsInput	promoter-TSS (NM_009412)	promoter-TSS (NM_009412)	-102	NM_001025264	21985	Mm.371590	NM_001025261	ENSMUSG00000027506	Tpd52	AI043038|mD52	tumor protein D52	protein-coding	0.13	0.693069
Merged-chr2-127270740-1	chr2	127270690	127270790	+	3.3	cIP2vsInput	"exon (NM_139308, exon 1 of 8)"	"exon (NM_139308, exon 1 of 8)"	511	NM_139308	99138	Mm.41271	NM_139308	ENSMUSG00000027367	Stard7	AI852671|AL022671|AW544915	START domain containing 7	protein-coding	0.18	0.732673
Merged-chr9-72640180-2	chr9	72640106	72640255	+	3.3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-22167	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	"neural precursor cell expressed, developmentally down-regulated 4"	protein-coding	0.033557	0.553333
Merged-chr6-72217019-1	chr6	72216969	72217069	+	3.3	cIP2vsInput	"intron (NM_153778, intron 2 of 2)"	"intron (NM_153778, intron 2 of 2)"	18558	NM_153778	71093	Mm.87449	NM_153778	ENSMUSG00000037621	Atoh8	4933425C05Rik|Hath6|Math6|bHLHa21|okadin	atonal homolog 8 (Drosophila)	protein-coding	0.04	0.693069
Merged-chr16-14701598-1	chr16	14701548	14701648	+	3.3	cIP2vsInput	Intergenic	Intergenic	-4261	NM_011415	20583	Mm.4272	NM_011415	ENSMUSG00000022676	Snai2	Slug|Slugh|Snail2	snail homolog 2 (Drosophila)	protein-coding	0.02	0.415842
Merged-chr9-63124296-1	chr9	63124246	63124346	+	3.3	cIP2vsInput	Intergenic	Intergenic	22684	NM_172446	207667	Mm.447200	NM_001163755	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding	0.08	0.653465
Merged-chr11-86653375-1	chr11	86653325	86653425	+	3.3	cIP1vsInput	"intron (NM_029478, intron 5 of 11)"	"intron (NM_029478, intron 5 of 11)"	30447	NM_029478	75909	Mm.390398	NM_029478	ENSMUSG00000018171	Vmp1	3110098I04Rik|4930579A11Rik|AI787464|Tango5|Tmem49|ni-2	vacuole membrane protein 1	protein-coding	0.01	0.277228
Merged-chr14-63338699-1	chr14	63338649	63338749	+	3.3	cIP2vsInput	Intergenic	Intergenic	78488	NM_007549	12143	Mm.3962	NM_007549	ENSMUSG00000014453	Blk	-	B lymphoid kinase	protein-coding	0.04	0.613861
Merged-chr9-50006102-2	chr9	50006038	50006166	+	3.3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-207033	NM_010875	17967	Mm.439182	NM_001081445		Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding	0.015625	0.55814
Merged-chrY-6844821-2	chrY	6844766	6844876	+	3.3	cIP1vsInput|cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	322956	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.324324
Merged-chr7-127478225-1	chr7	127478175	127478275	+	3.3	cIP2vsInput	Intergenic	Intergenic	6611	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding	0.04	0.584158
Merged-chr12-112950813-1	chr12	112950763	112950863	+	3.3	cIP2vsInput	Intergenic	Intergenic	-8695	NM_025399	66174	Mm.7070	NM_025399	ENSMUSG00000002804	Nudt14	1110030M18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 14	protein-coding	0.04	0.524752
Merged-chr4-155150747-1	chr4	155150697	155150797	+	3.3	cIP2vsInput	Intergenic	CpG	64170	NM_001081100	76866	Mm.200590	NM_001081100	ENSMUSG00000029049	Morn1	2900057D20Rik|4930417P05Rik|AU042805	MORN repeat containing 1	protein-coding	0.16	0.80198
Merged-chr1-85606850-1	chr1	85606800	85606900	+	3.3	cIP1vsInput	"intron (NM_001013817, intron 1 of 16)"	B1_Mur1|SINE|Alu	-2959	NM_175397	109032	Mm.461913	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding	0.02	0.524752
Merged-chr1-132477085-1	chr1	132477035	132477135	+	3.3	cIP2vsInput	promoter-TSS (NM_172517)	promoter-TSS (NM_172517)	-282	NM_172517	213464	Mm.132868	NM_172517	ENSMUSG00000026439	Rbbp5	4933411J24Rik|C330016J05	retinoblastoma binding protein 5	protein-coding	0.08	0.574257
Merged-chr13-119488515-1	chr13	119488465	119488565	+	3.3	cIP2vsInput	promoter-TSS (NM_001177666)	promoter-TSS (NM_001177666)	-131	NR_027974	67304	Mm.474382	NM_026084	ENSMUSG00000074635	3110070M22Rik	-	RIKEN cDNA 3110070M22 gene	miscRNA	0.17	0.811881
Merged-chr1-38787583-1	chr1	38787533	38787633	+	3.3	cIP2vsInput	Intergenic	Intergenic	33632	NM_001029878	381338	Mm.487137	NM_001029878	ENSMUSG00000048814	Lonrf2	2900060P06Rik|AI851349	LON peptidase N-terminal domain and ring finger 2	protein-coding	0.02	0.49505
Merged-chr6-139848349-1	chr6	139848299	139848399	+	3.3	cIP2vsInput	"intron (NM_207683, intron 11 of 23)"	"intron (NM_207683, intron 11 of 23)"	6904	NM_011084	18705	Mm.391538	NM_207683	ENSMUSG00000030228	Pik3c2g	C80387|PI3K-C2-gamma	"phosphatidylinositol 3-kinase, C2 domain containing, gamma polypeptide"	protein-coding	0	0.336634
Merged-chr6-114875164-1	chr6	114875114	114875214	+	3.3	cIP2vsInput	"intron (NM_177683, intron 2 of 4)"	"intron (NM_177683, intron 2 of 4)"	46588	NM_177683	232334	Mm.446323	NM_177683		Vgll4	BC048841|VGL-4	vestigial like 4 (Drosophila)	protein-coding	0.08	0.70297
Merged-chr14-45920873-2	chr14	45920778	45920968	+	3.3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-163154	NR_002875	218963	Mm.282093	NR_002875		Gm1821	-	ubiquitin pseudogene	pseudo	0.015789	0.413613
Merged-chr11-32205624-2	chr11	32205562	32205687	+	3.3	cIP1vsInput|cIP2vsInput	"exon (NM_030093, exon 1 of 5)"	"exon (NM_030093, exon 1 of 5)"	209	NM_030093	78372	Mm.29952	NM_030093	ENSMUSG00000040767	Snrnp25	3300001G02Rik|AL033324|C16ORF33	small nuclear ribonucleoprotein 25 (U11/U12)	protein-coding	0.056	0.603175
Merged-chr16-17132969-1	chr16	17132919	17133019	+	3.3	cIP2vsInput	promoter-TSS (NM_022324)	promoter-TSS (NM_022324)	-586	NM_022324	64136	Mm.30222	NM_022324	ENSMUSG00000022769	Sdf2l1	-	stromal cell-derived factor 2-like 1	protein-coding	0.05	0.564356
Merged-chr9-18292214-1	chr9	18292164	18292264	+	3.3	cIP2vsInput	promoter-TSS (NM_025844)	promoter-TSS (NM_025844)	-53	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	"cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1"	protein-coding	0.09	0.643564
Merged-chr12-28048018-1	chr12	28047968	28048068	+	3.3	cIP2vsInput	Intergenic	Intergenic	500319	NM_001177964	68511	Mm.310284	NM_001177964		Dcdc2c	1110015M06Rik	doublecortin domain containing 2C	protein-coding	0	0.524752
Merged-chr11-115765468-1	chr11	115765418	115765518	+	3.3	cIP2vsInput	promoter-TSS (NM_028014)	promoter-TSS (NM_028014)	35	NM_028014	71947	Mm.23168	NM_028014	ENSMUSG00000020747	2310067B10Rik	Kiaa0195|mKIAA0195	RIKEN cDNA 2310067B10 gene	protein-coding	0.04	0.693069
Merged-chrX-103616391-1	chrX	103616341	103616441	+	3.3	cIP2vsInput	"intron (NR_028381, intron 1 of 10)"	"intron (NR_028381, intron 1 of 10)"	7363	NR_028381	78878	Mm.426420	NR_028380	ENSMUSG00000086370	Ftx	B230206F22Rik|BB219131|NCRNA00182|Thcytx	"Ftx transcript, Xist regulator (non-protein coding)"	miscRNA	0.09	0.514851
Merged-chr2-119787486-1	chr2	119787436	119787536	+	3.3	cIP2vsInput	promoter-TSS (NM_177294)	promoter-TSS (NM_177294)	51	NM_177294	68925	Mm.259223	NM_001163701	ENSMUSG00000034032	Rpap1	1190005L06Rik|A730023M06Rik|AU041788|AW107702|mKIAA1403	RNA polymerase II associated protein 1	protein-coding	0.08	0.623762
Merged-chr13-74463115-1	chr13	74463065	74463165	+	3.3	cIP1vsInput	Intergenic	Intergenic	30835	NM_146231	235956	Mm.296909	NM_146231		Zfp825	-	zinc finger protein 825	protein-coding	0.04	0.554455
Merged-chr5-76140578-2	chr5	76140494	76140662	+	3.3	cIP1vsInput|cIP2vsInput	"intron (NM_020611, intron 1 of 5)"	CpG	305	NM_020611	57357	Mm.289446	NM_020611	ENSMUSG00000029233	Srd5a3	1110025P14Rik|A430076C09|AV364670|AW987574|D730040M03Rik|H5ar|S5AR 3|Srd5a2l	steroid 5 alpha-reductase 3	protein-coding	0.113095	0.715976
Merged-chr7-6383432-1	chr7	6383382	6383482	+	3.3	cIP2vsInput	TTS (NM_177888)	TTS (NM_177888)	114	NM_175247	22690	Mm.127014	NM_175247	ENSMUSG00000062861	Zfp28	2810438M17Rik|Zfp-28|mkr-5	zinc finger protein 28	protein-coding	0.06	0.673267
Merged-chr8-70906328-2	chr8	70906253	70906404	+	3.3	cIP1vsInput|cIP2vsInput	"intron (NM_173013, intron 1 of 6)"	CpG	354	NM_173013	270058	Mm.248559	NM_173013	ENSMUSG00000019261	Map1s	6430517J16Rik|Bpy2ip1|Map8|Mtap1s|VCY2IP1	microtubule-associated protein 1S	protein-coding	0.099338	0.664474
Merged-chr14-113368521-1	chr14	113368471	113368571	+	3.3	cIP2vsInput	Intergenic	Intergenic	1347091	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0	0.366337
Merged-chr13-63642798-1	chr13	63642748	63642848	+	3.3	cIP2vsInput	Intergenic	Intergenic	-77278	NM_008957	19206	Mm.488634	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes	patched homolog 1	protein-coding	0	0.564356
Merged-chr7-109703771-1	chr7	109703721	109703821	+	3.3	cIP1vsInput	promoter-TSS (NM_020616)	promoter-TSS (NM_020616)	34	NM_020616	57373	Mm.334138	NM_020616	ENSMUSG00000031023	Akip1	BCA3|C11orf17|D7H11orf17|D930014E17Rik|ICRFP703B1614Q5.6|ORF27	A kinase (PRKA) interacting protein 1	protein-coding	0.1	0.693069
Merged-chr11-32642584-2	chr11	32642529	32642639	+	3.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001271349)	promoter-TSS (NM_001271349)	29	NM_001271347	103583	Mm.474118	NM_001271347	ENSMUSG00000020271	Fbxw11	2310065A07Rik|AA536858|BTRC2|BTRCP2|Fbxw1b|HOS	F-box and WD-40 domain protein 11	protein-coding	0.1	0.657658
Merged-chr5-15535143-1	chr5	15535093	15535193	+	3.3	cIP2vsInput	Intergenic	RMER6BA|LTR|ERVK	-83956	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0	0.237624
Merged-chr1-16656876-1	chr1	16656826	16656926	+	3.3	cIP1vsInput	promoter-TSS (NR_037998)	promoter-TSS (NR_037998)	-11	NM_026456	67923	Mm.289248	NM_026456	ENSMUSG00000079658	Tceb1	2610043E24Rik|2610301I15Rik|AA407206|AI987979|AW049146	"transcription elongation factor B (SIII), polypeptide 1"	protein-coding	0.08	0.722772
Merged-chr16-3337793-1	chr16	3337743	3337843	+	3.3	cIP2vsInput	Intergenic	RLTR21|LTR|ERVK	-254605	NM_146860	258859	Mm.377723	NM_146860		Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding	0	0.39604
Merged-chr4-42949999-1	chr4	42949949	42950049	+	3.3	cIP2vsInput	Intergenic	CpG	-3095	NM_019874	56323	Mm.20437	NM_019874	ENSMUSG00000036052	Dnajb5	1110058L06Rik|AI462558|Hsc40|Hsp40-3	"DnaJ (Hsp40) homolog, subfamily B, member 5"	protein-coding	0.12	0.762376
Merged-chr3-65929667-1	chr3	65929617	65929717	+	3.3	cIP2vsInput	Intergenic	Intergenic	28558	NM_019937	56706	Mm.175612	NM_001025442	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding	0.02	0.564356
Merged-chr15-57892765-1	chr15	57892715	57892815	+	3.3	cIP2vsInput	promoter-TSS (NM_024207)	promoter-TSS (NM_024207)	-347	NM_024207	67819	Mm.444431	NM_024207	ENSMUSG00000022365	Derl1	1110021N07Rik|AI195141|AW551338|Derlin-1	"Der1-like domain family, member 1"	protein-coding	0.01	0.39604
Merged-chr18-77714026-2	chr18	77713937	77714116	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_027978)	promoter-TSS (NR_027978)	-16	NM_178670	212163	Mm.158164	NM_178670	ENSMUSG00000047466	8030462N17Rik	Akd2	RIKEN cDNA 8030462N17 gene	protein-coding	0.150838	0.733333
Merged-chr4-63260740-2	chr4	63260667	63260814	+	3.25	cIP1vsInput|cIP2vsInput	"intron (NM_025685, intron 12 of 60)"	"intron (NM_025685, intron 12 of 60)"	3889	NR_030477	735262		NR_030477		Mir455	Mirn455|mmu-mir-455	microRNA 455	miscRNA	0.047619	0.635135
Merged-chr9-26999645-2	chr9	26999594	26999696	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025862)	promoter-TSS (NM_025862)	-32	NM_144543	77862	Mm.16925	NM_144543	ENSMUSG00000035443	Thyn1	D730042P09Rik|HSPC144|MDS012|MY105|Thy28	thymocyte nuclear protein 1	protein-coding	0.078431	0.582524
Merged-chr13-35027126-2	chr13	35027057	35027196	+	3.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-32982	NM_001110331	23986	Mm.28883	NM_001110332	ENSMUSG00000021417	Eci2	Acbd2|Drs1|Hca88|Peci	enoyl-Coenzyme A delta isomerase 2	protein-coding	0.021583	0.542857
Merged-chr8-94214458-2	chr8	94214402	94214515	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172410)	promoter-TSS (NM_172410)	-143	NM_172410	71805	Mm.458170	NM_172410	ENSMUSG00000032939	Nup93	2410008G02Rik	nucleoporin 93	protein-coding	0.097345	0.666667
Merged-chr18-46280852-2	chr18	46280767	46280937	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172627)	promoter-TSS (NM_172627)	-2	NM_172627	225467	Mm.393044	NM_172627	ENSMUSG00000024477	Pggt1b	2010207C17Rik|2610100E13|AI451237|AI551093|BGG1|GGT1	"protein geranylgeranyltransferase type I, beta subunit"	protein-coding	0.070588	0.637427
Merged-chrX-77510814-2	chrX	77510743	77510885	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_020601)	promoter-TSS (NM_020601)	-413	NM_020601	21372	Mm.258476	NM_020601		Tbl1x	5330429M20|Tbl1	transducin (beta)-like 1 X-linked	protein-coding	0.077465	0.755245
Merged-chr15-36728074-2	chr15	36728015	36728134	+	3.25	cIP1vsInput|cIP2vsInput	Intergenic	RMER17C-int|LTR|ERVK	62858	NM_001253807	22631	Mm.465895	NM_001253805	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide"	protein-coding	0.008403	0.475
Merged-chr6-145303830-2	chr6	145303770	145303890	+	3.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	53278	NR_045598	100039495	Mm.121014	NR_045598	ENSMUSG00000086013	Gm15706	OTTMUSG00000025463	predicted gene 15706	miscRNA	0.041667	0.471074
Merged-chr2-131096599-2	chr2	131096546	131096652	+	3.25	cIP1vsInput|cIP2vsInput	Intergenic	MIR|SINE|MIR	-9834	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	"sialic acid binding Ig-like lectin 1, sialoadhesin"	protein-coding	0.037736	0.53271
Merged-chr4-147969585-2	chr4	147969529	147969642	+	3.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-16204	NM_008726	18158	Mm.2740	NM_008726	ENSMUSG00000029019	Nppb	AA408272|BNP	natriuretic peptide type B	protein-coding	0.026549	0.596491
Merged-chr6-53337645-2	chr6	53337592	53337699	+	3.25	cIP1vsInput|cIP2vsInput	"intron (NR_015553, intron 1 of 4)"	"intron (NR_015553, intron 1 of 4)"	50350	NR_015553	320189		NR_015553		9430076C15Rik	-	RIKEN cDNA 9430076C15 gene	miscRNA	0.046729	0.537037
Merged-chr5-130222289-2	chr5	130222233	130222345	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027854)	promoter-TSS (NM_027854)	-46	NM_027854	71667	Mm.258508	NM_001081394	ENSMUSG00000053094	Tmem248	0610007L01Rik|A930023A16Rik|AW557951|G430067H08Rik	transmembrane protein 248	protein-coding	0.160714	0.716814
Merged-chr2-158128166-2	chr2	158128099	158128234	+	3.25	cIP1vsInput|cIP2vsInput	"intron (NM_009373, intron 8 of 12)"	"intron (NM_009373, intron 8 of 12)"	18226	NM_009373	21817	Mm.330731	NM_009373	ENSMUSG00000037820	Tgm2	G[a]h|TG2|TGase2|tTG|tTGas	"transglutaminase 2, C polypeptide"	protein-coding	0.007407	0.492647
Merged-chr5-123058219-2	chr5	123058154	123058284	+	3.25	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-11399	NM_029112	74890	Mm.141383	NM_029112	ENSMUSG00000029477	Morn3	4930438O03Rik	MORN repeat containing 3	protein-coding	0.084615	0.564885
Merged-chr9-8004641-2	chr9	8004574	8004708	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001171147)	promoter-TSS (NM_001171147)	-45	NM_009534	22601	Mm.486262	NM_001171147	ENSMUSG00000053110	Yap1	AI325207|Yap|Yap65|Yki|Yorkie	yes-associated protein 1	protein-coding	0.164179	0.733333
Merged-chr2-158702321-2	chr2	158702228	158702415	+	3.25	cIP1vsInput|cIP2vsInput	"intron (NM_001159662, intron 2 of 10)"	"intron (NM_001159662, intron 2 of 10)"	35186	NM_001159662	228852	Mm.150540	NM_001159662	ENSMUSG00000037754	Ppp1r16b	ANKRD4|C130078N17Rik|TIMAP|Wdt4	"protein phosphatase 1, regulatory (inhibitor) subunit 16B"	protein-coding	0.010695	0.361702
Merged-chr4-129696774-2	chr4	129696691	129696857	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_199305)	promoter-TSS (NM_199305)	64	NM_199305	230770	Mm.257157	NM_199305	ENSMUSG00000053730	Tmem39b	6330509E05Rik|BC037095	transmembrane protein 39b	protein-coding	0.114458	0.700599
Merged-chr12-102469179-2	chr12	102469105	102469254	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001199004)	promoter-TSS (NM_001199004)	45	NM_001199004	27277	Mm.273370	NM_001199004	ENSMUSG00000021192	Golga5	Ret-II	"golgi autoantigen, golgin subfamily a, 5"	protein-coding	0.127517	0.746667
Merged-chr2-156992169-2	chr2	156992119	156992220	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_180956)	promoter-TSS (NM_180956)	-58	NM_180956	29812	Mm.279256	NM_013865	ENSMUSG00000027634	Ndrg3	4833415O14Rik|AI747193|Ndr3	N-myc downstream regulated gene 3	protein-coding	0.059406	0.519608
Merged-chr15-101174028-2	chr15	101173956	101174100	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007395)	promoter-TSS (NM_007395)	-97	NM_007395	11479	Mm.308467	NM_007395		Acvr1b	6820432J04|ActR-IB|ActRIB|Acvrlk4|Alk4|SKR2	"activin A receptor, type 1B"	protein-coding	0.1875	0.855172
Merged-chr12-28636004-2	chr12	28635945	28636063	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011300)	promoter-TSS (NM_011300)	-51	NM_011300	20115	Mm.371579	NM_011300	ENSMUSG00000061477	Rps7	Rps7A|S7	ribosomal protein S7	protein-coding	0.059322	0.521008
Merged-chr2-155357539-2	chr2	155357483	155357596	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001004721)	promoter-TSS (NM_001004721)	-115	NM_001004721	228812	Mm.5434	NM_001004721	ENSMUSG00000038383	Pigu	5430426F17Rik|BC028278|Cdc91l1	"phosphatidylinositol glycan anchor biosynthesis, class U"	protein-coding	0.044248	0.517544
Merged-chr5-31202454-2	chr5	31202400	31202509	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001177901)	promoter-TSS (NM_001177901)	-151	NM_175311	101023	Mm.45033	NM_001177901	ENSMUSG00000043059	Zfp513	AW990386|D430028M17Rik|Znf513	zinc finger protein 513	protein-coding	0.055046	0.581818
Merged-chr2-38950386-2	chr2	38950316	38950456	+	3.25	cIP1vsInput|cIP2vsInput	"intron (NM_172854, intron 4 of 7)"	"intron (NM_172854, intron 4 of 7)"	18406	NM_172854	241327	Mm.103491	NM_172854		Olfml2a	4932431K08Rik|mFLJ00237	olfactomedin-like 2A	protein-coding	0.007143	0.595745
Merged-chr9-48836323-2	chr9	48836236	48836410	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001033324)	promoter-TSS (NM_001033324)	-378	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding	0.103448	0.765714
Merged-chr13-43365535-2	chr13	43365468	43365603	+	3.25	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-5181	NM_178848	68346	Mm.35325	NM_178848	ENSMUSG00000054021	Sirt5	0610012J09Rik|1500032M05Rik|AV001953	sirtuin 5 (silent mating type information regulation 2 homolog) 5 (S. cerevisiae)	protein-coding	0.074074	0.705882
Merged-chr5-115506632-2	chr5	115506575	115506689	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011223)	promoter-TSS (NM_011223)	-70	NM_011223	19303	Mm.18714	NM_011223	ENSMUSG00000029528	Pxn	AW108311|AW123232|Pax	paxillin	protein-coding	0.122807	0.782609
Merged-chr2-157367598-2	chr2	157367544	157367652	+	3.25	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026968)	promoter-TSS (NM_026968)	4	NM_026968	69161	Mm.228619	NM_026968	ENSMUSG00000063019	Manbal	1810024K12Rik|AI836500	"mannosidase, beta A, lysosomal-like"	protein-coding	0.111111	0.633028
Merged-chr14-55643437-1	chr14	55643387	55643487	+	3.2	cIP1vsInput	"5' UTR (NM_028780, exon 1 of 6)"	"5' UTR (NM_028780, exon 1 of 6)"	369	NM_028780	74140	Mm.132857	NM_028780	ENSMUSG00000002320	Tm9sf1	1200014D02Rik|AI893436|MP70	transmembrane 9 superfamily member 1	protein-coding	0.14	0.70297
Merged-chr10-80810358-1	chr10	80810308	80810408	+	3.2	cIP2vsInput	"exon (NM_028001, exon 5 of 7)"	"exon (NM_028001, exon 5 of 7)"	3140	NM_028001	71912	Mm.45137	NM_028001	ENSMUSG00000020216	Jsrp1	2300003C06Rik|2310032K21Rik|JP-45|JP45	junctional sarcoplasmic reticulum protein 1	protein-coding	0.08	0.653465
Merged-chr6-46068624-1	chr6	46068574	46068674	+	3.2	cIP1vsInput	"intron (NM_001004357, intron 8 of 23)"	"intron (NM_001004357, intron 8 of 23)"	1008563	NM_001004357	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0	0.336634
Merged-chr4-19709298-1	chr4	19709248	19709348	+	3.2	cIP1vsInput	promoter-TSS (NM_001276292)	promoter-TSS (NM_001276292)	-294	NR_074090	107568	Mm.78312	NM_001276292	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding	0.05	0.653465
Merged-chr4-51928867-1	chr4	51928817	51928917	+	3.2	cIP1vsInput	Intergenic	Intergenic	122243	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	miscRNA	0.02	0.336634
Merged-chr14-49061362-1	chr14	49061312	49061412	+	3.2	cIP1vsInput	"intron (NM_207214, intron 1 of 17)"	"intron (NM_207214, intron 1 of 17)"	-5133	NM_144535	74385	Mm.379235	NM_144535	ENSMUSG00000036291	Ap5m1	4932432K03Rik|Mu5|Mudeng	"adaptor-related protein complex 5, mu 1 subunit"	protein-coding	0	0.247525
Merged-chr6-124859908-1	chr6	124859858	124859958	+	3.2	cIP2vsInput	"intron (NM_013533, intron 3 of 4)"	"intron (NM_013533, intron 3 of 4)"	-2221	NM_013534	14789	Mm.35708	NM_013534	ENSMUSG00000023191	Leprel2	BC016431|Grcb|P3h3	leprecan-like 2	protein-coding	0.02	0.613861
Merged-chr15-98534114-1	chr15	98534064	98534164	+	3.2	cIP2vsInput	"5' UTR (NM_133714, exon 1 of 10)"	"5' UTR (NM_133714, exon 1 of 10)"	107	NM_133714	69612	Mm.296240	NM_133714	ENSMUSG00000022992	Kansl2	2310037I24Rik|B930009D17	KAT8 regulatory NSL complex subunit 2	protein-coding	0.08	0.643564
Merged-chr4-59233174-1	chr4	59233124	59233224	+	3.2	cIP2vsInput	Intergenic	Intergenic	43624	NM_011673	22234	Mm.198803	NM_011673	ENSMUSG00000028381	Ugcg	AU043821|C80537|Epcs21|GlcT-1|Ugcgl	UDP-glucose ceramide glucosyltransferase	protein-coding	0	0.29703
Merged-chr6-120406879-1	chr6	120406829	120406929	+	3.2	cIP1vsInput	"intron (NM_145997, intron 17 of 27)"	"intron (NM_145997, intron 17 of 27)"	-42510	NR_045558	67200	Mm.45767	NM_026028	ENSMUSG00000030177	Ccdc77	2400002C23Rik|2700091N06Rik|AV168274	coiled-coil domain containing 77	protein-coding	0	0.336634
Merged-chr13-51378368-1	chr13	51378318	51378418	+	3.2	cIP2vsInput	Intergenic	Intergenic	-30250	NM_010101	13610	Mm.136736	NM_010101	ENSMUSG00000067586	S1pr3	AI132464|Edg3|Lpb3|S1p3	sphingosine-1-phosphate receptor 3	protein-coding	0.01	0.584158
Merged-chr8-95080878-1	chr8	95080828	95080928	+	3.2	cIP2vsInput	promoter-TSS (NM_028805)	promoter-TSS (NM_028805)	-323	NM_028805	74187	Mm.28382	NM_028805	ENSMUSG00000031787	Katnb1	2410003J24Rik|KAT	katanin p80 (WD40-containing) subunit B 1	protein-coding	0.07	0.49505
Merged-chr3-40686961-1	chr3	40686911	40687011	+	3.2	cIP1vsInput	"intron (NM_175515, intron 7 of 14)"	"intron (NM_175515, intron 7 of 14)"	-21910	NM_178386	73333	Mm.78691	NM_178386		Slc25a31	1700034J06Rik|Ant4|Sfec	"solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 31"	protein-coding	0.04	0.445545
Merged-chr4-120674933-2	chr4	120674868	120674999	+	3.2	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	8370	NM_019563	56222	Mm.272646	NM_019563	ENSMUSG00000070803	Cited4	MRG-2|Mrg2	"Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 4"	protein-coding	0.030534	0.515152
Merged-chr4-47473972-2	chr4	47473915	47474030	+	3.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_024171)	promoter-TSS (NM_024171)	395	NM_019998	56737	Mm.22218	NM_019998	ENSMUSG00000039740	Alg2	1110018A23Rik|1300013N08Rik|ALPG2|CDGIi|MNCb-5081	"asparagine-linked glycosylation 2 (alpha-1,3-mannosyltransferase)"	protein-coding	0.095652	0.62069
Merged-chr18-35498579-1	chr18	35498529	35498629	+	3.2	cIP2vsInput	"intron (NM_030749, intron 1 of 9)"	"intron (NM_030749, intron 1 of 9)"	346	NM_030749	81500	Mm.291482	NM_030749	ENSMUSG00000024357	Sil1	1810057E01Rik|AI042831|wz	endoplasmic reticulum chaperone SIL1 homolog (S. cerevisiae)	protein-coding	0.04	0.643564
Merged-chr5-4104716-1	chr5	4104666	4104766	+	3.2	cIP2vsInput	promoter-TSS (NM_020010)	promoter-TSS (NM_020010)	-19	NM_020010	13121	Mm.140158	NM_020010	ENSMUSG00000001467	Cyp51	AI426508|CYPLI|Cyp51a1|Ldm|P450-14DM|P450LI	"cytochrome P450, family 51"	protein-coding	0.1	0.693069
Merged-chr3-118429526-1	chr3	118429476	118429576	+	3.2	cIP2vsInput	Intergenic	Intergenic	-4331	NR_029551	387155		NR_029551		Mir137	Mirn137|mmu-mir-137	microRNA 137	miscRNA	0	0.326733
Merged-chr9-92551812-1	chr9	92551762	92551862	+	3.2	cIP2vsInput	"intron (NM_001142916, intron 1 of 19)"	"intron (NM_001142916, intron 1 of 19)"	-8943	NR_029474	78575	Mm.407669	NR_029474		B430319G15Rik	D530025C14Rik	RIKEN cDNA B430319G15 gene	miscRNA	0.03	0.485149
Merged-chr3-64832166-1	chr3	64832116	64832216	+	3.2	cIP1vsInput	"intron (NR_003962, intron 1 of 8)"	"intron (NR_003962, intron 1 of 8)"	12577	NR_003962	319210	Mm.246646	NR_003962		Vmn2r-ps11	4930518C23Rik	"vomeronasal 2, receptor, pseudogene 11"	pseudo	0	0.316832
Merged-chr12-76895920-1	chr12	76895870	76895970	+	3.2	cIP1vsInput	"intron (NM_145927, intron 6 of 11)"	"intron (NM_145927, intron 6 of 11)"	58453	NM_145927	110606	Mm.151174	NM_145927	ENSMUSG00000033373	Fntb	2010013E13Rik|AA409500	"farnesyltransferase, CAAX box, beta"	protein-coding	0.01	0.544554
Merged-chr5-123907115-1	chr5	123907065	123907165	+	3.2	cIP2vsInput	promoter-TSS (NM_026603)	promoter-TSS (NM_026603)	-160	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding	0.1	0.712871
Merged-chr1-170764932-1	chr1	170764882	170764982	+	3.2	cIP2vsInput	"intron (NM_001081304, intron 14 of 15)"	"intron (NM_001081304, intron 14 of 15)"	102839	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding	0.01	0.316832
Merged-chr17-63863682-1	chr17	63863632	63863732	+	3.2	cIP2vsInput	Intergenic	CpG	-32336	NM_001037997	14158	Mm.23039	NM_001037997	ENSMUSG00000000127	Fert2	AV082135|C330004K01Rik|Fer|Fert	"fer (fms/fps related) protein kinase, testis specific 2"	protein-coding	0.13	0.653465
Merged-chr2-181680191-1	chr2	181680141	181680241	+	3.2	cIP2vsInput	promoter-TSS (NM_009326)	promoter-TSS (NM_009326)	-119	NM_009326	21400	Mm.24245	NM_009326	ENSMUSG00000059540	Tcea2	AI326274|S-II-T1|SII-T1|Tceat	"transcription elongation factor A (SII), 2"	protein-coding	0.12	0.683168
Merged-chr4-121098293-1	chr4	121098243	121098343	+	3.2	cIP1vsInput	promoter-TSS (NM_172700)	promoter-TSS (NM_172700)	-50	NM_172700	230709	Mm.34399	NM_172700	ENSMUSG00000043207	Zmpste24	A530043O15Rik|D030046F19|FACE1|Face-1|MADB|STE24|Ste24p	"zinc metallopeptidase, STE24"	protein-coding	0.06	0.574257
Merged-chrX-77433714-1	chrX	77433664	77433764	+	3.2	cIP2vsInput	"intron (NR_035475, intron 1 of 3)"	CpG	6500	NR_030558	100124494		NR_030558	ENSMUSG00000065509	Mir421	Mirn421|mmu-mir-421	microRNA 421	miscRNA	0.07	0.633663
Merged-chr19-4962375-2	chr19	4962315	4962436	+	3.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025553)	promoter-TSS (NM_025553)	69	NM_025553	66419	Mm.28494	NM_025553	ENSMUSG00000024902	Mrpl11	2410001P07Rik|L11mt	mitochondrial ribosomal protein L11	protein-coding	0.066116	0.54918
Merged-chr1-72237228-2	chr1	72237175	72237282	+	3.2	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-24921	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding	0.018692	0.324074
Merged-chr8-11785238-1	chr8	11785188	11785288	+	3.2	cIP1vsInput	"intron (NM_001113518, intron 3 of 20)"	"intron (NM_001113518, intron 3 of 20)"	26908	NM_001113518	54126	Mm.244068	NM_001113517	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding	0.03	0.663366
Merged-chr2-127722635-1	chr2	127722585	127722685	+	3.2	cIP2vsInput	"intron (NM_145532, intron 1 of 3)"	"intron (NM_145532, intron 1 of 3)"	7262	NM_145532	228576	Mm.133036	NM_145532	ENSMUSG00000027377	Mall	BC012256|BENE	"mal, T cell differentiation protein-like"	protein-coding	0.01	0.534653
Merged-chr5-15640023-1	chr5	15639973	15640073	+	3.2	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	17036	NR_073011	381715		NR_073011	ENSMUSG00000069720	4930572O03Rik	-	spermatogenesis associated glutamate (E)-rich protein pseudogene	pseudo	0.01	0.336634
Merged-chr7-101108144-1	chr7	101108094	101108194	+	3.2	cIP2vsInput	promoter-TSS (NM_001146010)	promoter-TSS (NM_001146010)	-631	NM_001146010	207278	Mm.263041	NM_001146010	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding	0.17	0.792079
Merged-chr19-4497741-1	chr19	4497691	4497791	+	3.2	cIP2vsInput	"intron (NM_027237, intron 1 of 1)"	"intron (NM_027237, intron 1 of 1)"	842	NM_027237	69861	Mm.282978	NM_027237	ENSMUSG00000042041	2010003K11Rik	-	RIKEN cDNA 2010003K11 gene	protein-coding	0.01	0.594059
Merged-chr17-47629644-1	chr17	47629594	47629694	+	3.2	cIP2vsInput	Intergenic	CpG	-1046	NM_198421	224836	Mm.59393	NM_198421		Usp49	C330046L10Rik|Gm545	ubiquitin specific peptidase 49	protein-coding	0.1	0.752475
Merged-chr15-66968882-1	chr15	66968832	66968932	+	3.2	cIP1vsInput	"intron (NM_008681, intron 1 of 15)"	CpG	759	NM_008681	17988	Mm.30837	NM_008681	ENSMUSG00000005125	Ndrg1	CAP43|CMT4D|DRG1|HMSNL|NMSL|Ndr1|Ndrl|PROXY1|RTP|TDD5	N-myc downstream regulated gene 1	protein-coding	0.12	0.70297
Merged-chr6-53573196-1	chr6	53573146	53573246	+	3.2	cIP2vsInput	promoter-TSS (NM_172728)	promoter-TSS (NM_172728)	-178	NM_172728	231991	Mm.321138	NM_172728	ENSMUSG00000053007	Creb5	Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding	0.02	0.534653
Merged-chr17-78200214-1	chr17	78200164	78200264	+	3.2	cIP2vsInput	promoter-TSS (NM_015800)	promoter-TSS (NM_015800)	-34	NM_015800	50766	Mm.311912	NM_015800	ENSMUSG00000024074	Crim1	AU015004	cysteine rich transmembrane BMP regulator 1 (chordin like)	protein-coding	0.11	0.732673
Merged-chr6-116338050-1	chr6	116338000	116338100	+	3.2	cIP2vsInput	promoter-TSS (NM_027920)	promoter-TSS (NM_027920)	-73	NM_027920	71779	Mm.27064	NM_027920	ENSMUSG00000025702	8-Mar	1300017E09Rik|Mir	membrane-associated ring finger (C3HC4) 8	protein-coding	0.14	0.742574
Merged-chr7-75455759-1	chr7	75455709	75455809	+	3.2	cIP2vsInput	"intron (NM_029332, intron 1 of 36)"	CpG	225	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding	0.11	0.712871
Merged-chr10-56229043-1	chr10	56228993	56229093	+	3.2	cIP2vsInput	promoter-TSS (NM_001033385)	promoter-TSS (NM_001033385)	-354	NM_001033385	544696	Mm.411188	NM_001033385	ENSMUSG00000038122	D630037F22Rik	Bromi	RIKEN cDNA D630037F22 gene	protein-coding	0.02	0.49505
Merged-chr11-120240441-1	chr11	120240391	120240491	+	3.2	cIP2vsInput	"intron (NM_198423, intron 2 of 27)"	"intron (NM_198423, intron 2 of 27)"	7494	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding	0.03	0.683168
Merged-chr8-84639318-1	chr8	84639268	84639368	+	3.2	cIP2vsInput	"exon (NM_001252061, exon 47 of 47)"	"exon (NM_001252061, exon 47 of 47)"	23534	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding	0.16	0.792079
Merged-chr2-156862879-1	chr2	156862829	156862929	+	3.2	cIP2vsInput	promoter-TSS (NR_015591)	promoter-TSS (NR_015591)	66	NR_015591	74487	Mm.490465	NR_015591	ENSMUSG00000085741	5430405H02Rik	2610307N17Rik	RIKEN cDNA 5430405H02 gene	miscRNA	0.11	0.663366
Merged-chr9-110305394-1	chr9	110305344	110305444	+	3.2	cIP2vsInput	"intron (NM_001081381, intron 1 of 6)"	CpG	202	NM_001081381	72341	Mm.374250	NM_001081381	ENSMUSG00000054836	Elp6	2610001P13Rik|2610002I17Rik|AV159994|Tmem103	elongator acetyltransferase complex subunit 6	protein-coding	0.12	0.663366
Merged-chr19-18670835-1	chr19	18670785	18670885	+	3.2	cIP2vsInput	promoter-TSS (NM_026120)	promoter-TSS (NM_026120)	55	NM_026120	67383	Mm.306602	XM_003946026	ENSMUSG00000024726	2410127L17Rik	-	RIKEN cDNA 2410127L17 gene	protein-coding	0.17	0.792079
Merged-chr19-44562765-1	chr19	44562715	44562815	+	3.2	cIP1vsInput	promoter-TSS (NM_176958)	promoter-TSS (NM_176958)	-89	NM_176958	319594	Mm.145278	NM_176958	ENSMUSG00000036450	Hif1an	2310046M24Rik|A830014H24Rik|FIH1	"hypoxia-inducible factor 1, alpha subunit inhibitor"	protein-coding	0.06	0.554455
Merged-chr17-42876541-1	chr17	42876491	42876591	+	3.2	cIP2vsInput	promoter-TSS (NM_009847)	promoter-TSS (NM_009847)	-117	NM_009847	12488	Mm.218637	NM_009847	ENSMUSG00000061665	Cd2ap	AL024079|C78928|METS-1|Mets1	CD2-associated protein	protein-coding	0.11	0.742574
Merged-chr15-72568748-2	chr15	72568695	72568801	+	3.2	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-22469	NM_001033876	223604	Mm.386856	NM_001033876	ENSMUSG00000036760	Kcnk9	Task3	"potassium channel, subfamily K, member 9"	protein-coding	0.056604	0.607477
Merged-chr6-72390216-1	chr6	72390166	72390266	+	3.2	cIP2vsInput	"intron (NM_016794, intron 1 of 2)"	"intron (NM_016794, intron 1 of 2)"	451	NM_016794	22320	Mm.1838	NM_016794	ENSMUSG00000050732	Vamp8	AU041171|Edb|endobrevin	vesicle-associated membrane protein 8	protein-coding	0.08	0.663366
Merged-chr19-34666455-1	chr19	34666405	34666505	+	3.2	cIP1vsInput	Intergenic	Intergenic	25566	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding	0	0.366337
Merged-chr17-25985754-1	chr17	25985704	25985804	+	3.2	cIP2vsInput	Intergenic	CpG	-20249	NM_015830	50817	Mm.486289	NM_015830	ENSMUSG00000037326	Solh	-	small optic lobes homolog (Drosophila)	protein-coding	0.15	0.752475
Merged-chr7-141447213-1	chr7	141447163	141447263	+	3.2	cIP2vsInput	promoter-TSS (NM_026020)	promoter-TSS (NM_026020)	-437	NM_026020	67186	Mm.380435	NM_026020	ENSMUSG00000025508	Rplp2	2700049I22Rik	"ribosomal protein, large P2"	protein-coding	0.02	0.554455
Merged-chr1-133363437-1	chr1	133363387	133363487	+	3.2	cIP2vsInput	promoter-TSS (NM_175443)	promoter-TSS (NM_175443)	-135	NM_175443	214253	Mm.52111	NM_175443	ENSMUSG00000070644	Etnk2	4933417N20Rik|AI197444|EKI 2|Eki2|Tuc1	ethanolamine kinase 2	protein-coding	0.05	0.683168
Merged-chr12-94756896-1	chr12	94756846	94756946	+	3.2	cIP2vsInput	Intergenic	LTR48B|LTR|ERV1	-935330	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0	0.346535
Merged-chr11-65788392-1	chr11	65788342	65788442	+	3.2	cIP2vsInput	promoter-TSS (NM_009157)	promoter-TSS (NM_009157)	-95	NM_009157	26398	Mm.412922	NM_009157	ENSMUSG00000033352	Map2k4	JNKK1|MEK4|MKK4|PRKMK4|Sek1|Serk1	mitogen-activated protein kinase kinase 4	protein-coding	0.09	0.712871
Merged-chr11-97150778-1	chr11	97150728	97150828	+	3.2	cIP1vsInput	Intergenic	CpG	-1066	NM_198100	73174	Mm.27882	NM_198100	ENSMUSG00000038517	Tbkbp1	3110043L15Rik|ProSAPiP2|SINTBAD	TBK1 binding protein 1	protein-coding	0.08	0.643564
Merged-chr15-77037731-1	chr15	77037681	77037781	+	3.2	cIP2vsInput	"intron (NM_013593, intron 1 of 3)"	"intron (NM_013593, intron 1 of 3)"	-7344	NM_001163621	71939	Mm.34173	NM_001163621	ENSMUSG00000033576	Apol6	2310076O14Rik	apolipoprotein L 6	protein-coding	0.02	0.60396
Merged-chr4-147410653-2	chr4	147410566	147410740	+	3.2	cIP1vsInput|cIP2vsInput	"intron (NM_001039209, intron 1 of 2)"	Lx2|LINE|L1	-142624	NM_001014397	433804	Mm.332047	XM_003946328	ENSMUSG00000065999	Gm13154	OTTMUSG00000010673	predicted gene 13154	protein-coding	0	0.342857
Merged-chr4-40757911-1	chr4	40757861	40757961	+	3.2	cIP2vsInput	promoter-TSS (NM_021535)	promoter-TSS (NM_021535)	-26	NM_021535	74255	Mm.289929	NM_021535		Smu1	2600001O03Rik|2610203K23Rik|AB044414|AI845086|AW556129|Bwd	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	protein-coding	0.13	0.712871
Merged-chr11-94989663-1	chr11	94989613	94989713	+	3.2	cIP1vsInput	Intergenic	Intergenic	-1549	NM_172261	217124		NM_172261	ENSMUSG00000038976	Ppp1r9b	SPL|Spn	"protein phosphatase 1, regulatory subunit 9B"	protein-coding	0.04	0.594059
Merged-chr5-111025817-1	chr5	111025767	111025867	+	3.2	cIP2vsInput	"intron (NM_001267622, intron 2 of 22)"	"intron (NM_001267622, intron 2 of 22)"	21673	NR_030482	735278		NR_030482		Mir701	Mirn701|mmu-mir-701	microRNA 701	miscRNA	0.07	0.554455
Merged-chr1-157382799-1	chr1	157382749	157382849	+	3.2	cIP1vsInput	"intron (NM_177644, intron 1 of 17)"	"intron (NM_177644, intron 1 of 17)"	-29553	NR_027984	69953	Mm.286863	NR_027984	ENSMUSG00000049881	2810025M15Rik	AI429618	RIKEN cDNA 2810025M15 gene	miscRNA	0.01	0.346535
Merged-chr5-124540621-1	chr5	124540571	124540671	+	3.2	cIP2vsInput	promoter-TSS (NM_019770)	promoter-TSS (NM_019770)	-170	NM_019770	56334	Mm.425279	NM_019770	ENSMUSG00000029390	Tmed2	1110032D12Rik|1810020N21Rik|Rnp24|Sid394|p24beta1	transmembrane emp24 domain trafficking protein 2	protein-coding	0.04	0.554455
Merged-chr10-89443838-2	chr10	89443749	89443927	+	3.2	cIP1vsInput|cIP2vsInput	"intron (NM_001033331, intron 1 of 10)"	"intron (NM_001033331, intron 1 of 10)"	129	NM_001079876	237436	Mm.11982	NM_001033331	ENSMUSG00000074802	Gas2l3	8430435B07Rik|Gm240	growth arrest-specific 2 like 3	protein-coding	0.05618	0.608939
Merged-chr12-113187776-1	chr12	113187726	113187826	+	3.2	cIP2vsInput	"intron (NM_153776, intron 1 of 1)"	CpG	1873	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding	0.09	0.70297
Merged-chr10-55874662-1	chr10	55874612	55874712	+	3.2	cIP2vsInput	Intergenic	Intergenic	-232255	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding	0	0.287129
Merged-chr13-53226591-1	chr13	53226541	53226641	+	3.2	cIP2vsInput	"intron (NM_013846, intron 1 of 8)"	"intron (NM_013846, intron 1 of 8)"	59518	NM_013846	26564	Mm.342774	NM_013846	ENSMUSG00000021464	Ror2	Ntrkr2|mRor2	receptor tyrosine kinase-like orphan receptor 2	protein-coding	0.01	0.405941
Merged-chr16-62786691-1	chr16	62786641	62786741	+	3.2	cIP2vsInput	promoter-TSS (NM_178925)	promoter-TSS (NM_178925)	25	NM_178925	106338	Mm.26321	NM_178925		Nsun3	6720484A09Rik|AU022521	NOL1/NOP2/Sun domain family member 3	protein-coding	0.13	0.70297
Merged-chr18-36454511-1	chr18	36454461	36454561	+	3.2	cIP2vsInput	promoter-TSS (NM_026027)	promoter-TSS (NM_026027)	-16	NM_026027	67199	Mm.30184	NM_026027	ENSMUSG00000024346	Pfdn1	2700086I23Rik|AA408327|AU044714	prefoldin 1	protein-coding	0.06	0.584158
Merged-chr3-9610096-1	chr3	9610046	9610146	+	3.2	cIP2vsInput	promoter-TSS (NM_133218)	promoter-TSS (NM_133218)	-11	NM_133218	170753	Mm.212908	NM_133218	ENSMUSG00000040209	Zfp704	C030026M03|C030034L19Rik|Gig1|Znf704	zinc finger protein 704	protein-coding	0.11	0.70297
Merged-chr2-155518221-1	chr2	155518171	155518271	+	3.2	cIP2vsInput	"exon (NM_019811, exon 1 of 18)"	"exon (NM_019811, exon 1 of 18)"	178	NM_019811	60525	Mm.255026	NM_019811	ENSMUSG00000027605	Acss2	1110017C11Rik|ACAS|Acas1|Acas2|AceCS1|Acs1	acyl-CoA synthetase short-chain family member 2	protein-coding	0.15	0.752475
Merged-chr3-67121860-1	chr3	67121810	67121910	+	3.2	cIP1vsInput	"intron (NM_025822, intron 4 of 9)"	L1_Mur3|LINE|L1	136188	NM_025822	66880	Mm.316418	NM_025822	ENSMUSG00000034544	Rsrc1	1200013F24Rik|SRrp53	arginine/serine-rich coiled-coil 1	protein-coding	0.01	0.29703
Merged-chr11-75051774-1	chr11	75051724	75051824	+	3.2	cIP2vsInput	"intron (NM_001002764, intron 12 of 18)"	"intron (NM_001002764, intron 12 of 18)"	14217	NR_030454	735274		NR_030454		Mir684-1	Mirn684-1	microRNA 684-1	miscRNA	0.01	0.633663
Merged-chr10-128409730-1	chr10	128409680	128409780	+	3.2	cIP2vsInput	promoter-TSS (NM_027257)	promoter-TSS (NM_027257)	66	NM_027257	69917	Mm.46614	NM_027257	ENSMUSG00000025374	Nabp2	2610036N15Rik|Obfc2b	nucleic acid binding protein 2	protein-coding	0.06	0.712871
Merged-chr9-87608196-1	chr9	87608146	87608246	+	3.2	cIP2vsInput	Intergenic	Intergenic	123064	NM_023814	76365	Mm.158789	NM_023814	ENSMUSG00000032419	Tbx18	2810012F10Rik|2810404D13Rik	T-box18	protein-coding	0	0.475248
Merged-chr18-24241709-1	chr18	24241659	24241759	+	3.2	cIP1vsInput	"intron (NM_001160404, intron 3 of 12)"	"intron (NM_001160404, intron 3 of 12)"	35715	NM_001160404	14423	Mm.30249	NM_001160404	ENSMUSG00000000420	Galnt1	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1	protein-coding	0	0.306931
Merged-chr1-131246692-1	chr1	131246642	131246742	+	3.2	cIP2vsInput	Intergenic	Intergenic	-1514	NM_018750	54354	Mm.248291	NM_018750	ENSMUSG00000026430	Rassf5	1300019G20Rik|AU042887|Maxp1|Nore1|Nore1A|Nore1B|Rapl	Ras association (RalGDS/AF-6) domain family member 5	protein-coding	0.01	0.554455
Merged-chr3-95025444-1	chr3	95025394	95025494	+	3.2	cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	-10206	NM_030074	78266	Mm.389478	NM_030074	ENSMUSG00000019338	Zfp687	4931408L03Rik|Znf687|mKIAA1441	zinc finger protein 687	protein-coding	0.01	0.49505
Merged-chr15-40811602-1	chr15	40811552	40811652	+	3.2	cIP1vsInput	"intron (NM_011766, intron 3 of 7)"	"intron (NM_011766, intron 3 of 7)"	156560	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	"zinc finger protein, multitype 2"	protein-coding	0	0.376238
Merged-chr11-73047772-1	chr11	73047722	73047822	+	3.2	cIP2vsInput	promoter-TSS (NM_025818)	promoter-TSS (NM_025818)	-95	NM_025818	66874	Mm.41903	NM_025818		1200014J11Rik	C130061O14Rik|C78393	RIKEN cDNA 1200014J11 gene	protein-coding	0.05	0.60396
Merged-chr14-120477770-1	chr14	120477720	120477820	+	3.2	cIP2vsInput	promoter-TSS (NM_029519)	promoter-TSS (NM_029519)	-691	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding	0.06	0.653465
Merged-chr15-99702094-1	chr15	99702044	99702144	+	3.2	cIP2vsInput	promoter-TSS (NM_031842)	promoter-TSS (NM_031842)	-193	NM_031842	83797	Mm.273756	NM_031842	ENSMUSG00000023018	Smarcd1	AA407987|Baf60a|D15Kz1	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1"	protein-coding	0.1	0.673267
Merged-chr7-16294499-1	chr7	16294449	16294549	+	3.2	cIP2vsInput	Intergenic	B3|SINE|B2	-7704	NM_001136471	243846	Mm.482401	NM_001136471	ENSMUSG00000041375	Ccdc9	2600011L02Rik	coiled-coil domain containing 9	protein-coding	0.01	0.415842
Merged-chr17-26916850-2	chr17	26916794	26916907	+	3.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_053173)	promoter-TSS (NM_053173)	-241	NM_053173	16580	Mm.258953	NM_016761	ENSMUSG00000024301	Kifc5b	Hset|KNSL2|Kifc5a	kinesin family member C5B	protein-coding	0.088496	0.666667
Merged-chr2-76115431-1	chr2	76115381	76115481	+	3.2	cIP2vsInput	"intron (NM_001081033, intron 9 of 19)"	"intron (NM_001081033, intron 9 of 19)"	-133464	NM_030188	78802	Mm.282339	NM_030188	ENSMUSG00000075271	Ttc30a1	4930506L13Rik	tetratricopeptide repeat domain 30A1	protein-coding	0.01	0.316832
Merged-chr5-34369887-1	chr5	34369837	34369937	+	3.2	cIP2vsInput	promoter-TSS (NM_001243123)	promoter-TSS (NM_001243123)	-46	NM_001243123	231128	Mm.286885	NM_001030306	ENSMUSG00000037210	Fam193a	-	"family with sequence similarity 193, member A"	protein-coding	0.13	0.80198
Merged-chr5-104046884-1	chr5	104046834	104046934	+	3.2	cIP2vsInput	promoter-TSS (NM_028794)	promoter-TSS (NM_028794)	-127	NM_028794	74167	Mm.241484	NM_028794	ENSMUSG00000029310	Nudt9	1190002C07Rik|AI462474	nudix (nucleoside diphosphate linked moiety X)-type motif 9	protein-coding	0.19	0.762376
Merged-chr19-38087307-1	chr19	38087257	38087357	+	3.2	cIP2vsInput	Intergenic	Intergenic	-9772	NM_181748	107221	Mm.35288	NM_181748	ENSMUSG00000054200	Ffar4	AI552415|GT01|Gpr120|Gpr129|KPG_013|O3far1|Pgr4	free fatty acid receptor 4	protein-coding	0.04	0.544554
Merged-chr11-100472703-1	chr11	100472653	100472753	+	3.2	cIP2vsInput	promoter-TSS (NM_172565)	promoter-TSS (NM_172565)	79	NM_172565	217194	Mm.183320	NM_172565	ENSMUSG00000048732	Klhl11	BC011167|RP23-392I3.12	kelch-like 11	protein-coding	0.12	0.70297
Merged-chr4-91564222-1	chr4	91564172	91564272	+	3.2	cIP2vsInput	Intergenic	Intergenic	-164238	NM_207685	15569	Mm.318042	NM_001177883	ENSMUSG00000008489	Elavl2	Hub|mel-N1	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)"	protein-coding	0	0.356436
Merged-chr3-58181975-1	chr3	58181925	58182025	+	3.2	cIP1vsInput	Intergenic	Intergenic	-18168	NR_040538	67850	Mm.416968	NR_040538		1700007F19Rik	-	RIKEN cDNA 1700007F19 gene	miscRNA	0.01	0.465347
Merged-chr8-67278435-1	chr8	67278385	67278485	+	3.2	cIP1vsInput	Intergenic	RMER17A2|LTR|ERVK	-212323	NM_008673	17960	Mm.14125	NM_008673	ENSMUSG00000025588	Nat1	Nat-1	N-acetyl transferase 1	protein-coding	0.02	0.524752
Merged-chr18-35829721-1	chr18	35829671	35829771	+	3.2	cIP2vsInput	promoter-TSS (NM_133687)	promoter-TSS (NM_133687)	-97	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding	0.1	0.742574
Merged-chr2-49047062-1	chr2	49047012	49047112	+	3.2	cIP1vsInput	"intron (NM_029924, intron 2 of 16)"	"intron (NM_029924, intron 2 of 16)"	97554	NM_029924	109241	Mm.440436	NM_029924		Mbd5	9430004D19Rik|AA536666|AI426407|C030040A15Rik|OTTMUSG00000012483	methyl-CpG binding domain protein 5	protein-coding	0	0.336634
Merged-chr8-69208523-1	chr8	69208473	69208573	+	3.2	cIP2vsInput	promoter-TSS (NM_001013379)	promoter-TSS (NM_001013379)	-523	NM_001013379	234358	Mm.334577	NM_001013379		Zfp930	-	zinc finger protein 930	protein-coding	0.01	0.405941
Merged-chr4-117019338-1	chr4	117019288	117019388	+	3.2	cIP2vsInput	promoter-TSS (NM_001111277)	promoter-TSS (NM_001111277)	-70	NM_001111277	108067	Mm.34612	NM_001111277	ENSMUSG00000028683	Eif2b3	1190002P15Rik	"eukaryotic translation initiation factor 2B, subunit 3"	protein-coding	0.11	0.60396
Merged-chr3-36065900-1	chr3	36065850	36065950	+	3.2	cIP2vsInput	promoter-TSS (NM_172678)	promoter-TSS (NM_172678)	-100	NM_172678	229211	Mm.260997	NM_172678		Acad9	2600017P15Rik|4732402K02|C630012L17Rik|NPD002	"acyl-Coenzyme A dehydrogenase family, member 9"	protein-coding	0.03	0.376238
Merged-chr10-80578009-1	chr10	80577959	80578059	+	3.2	cIP2vsInput	promoter-TSS (NM_078477)	promoter-TSS (NM_078477)	-713	NM_078477	118445	Mm.41513	NM_078477	ENSMUSG00000035397	Klf16	AI843742|BTEB4|DRRF	Kruppel-like factor 16	protein-coding	0.12	0.762376
Merged-chr2-154656842-2	chr2	154656754	154656931	+	3.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029362)	promoter-TSS (NM_029362)	-184	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding	0.050847	0.494382
Merged-chr10-86826105-1	chr10	86826055	86826155	+	3.2	cIP2vsInput	"intron (NM_175331, intron 12 of 13)"	"intron (NM_175331, intron 12 of 13)"	47100	NM_175331	103466	Mm.200446	NM_175331	ENSMUSG00000054027	Nt5dc3	AU040402|AW540062|C630002B14Rik|TU12B1-TY	5'-nucleotidase domain containing 3	protein-coding	0.02	0.643564
Merged-chr1-127038274-1	chr1	127038224	127038324	+	3.2	cIP2vsInput	Intergenic	Intergenic	-166712	NM_145128	107895	Mm.472488	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding	0	0.316832
Merged-chr15-75616605-1	chr15	75616555	75616655	+	3.2	cIP2vsInput	promoter-TSS (NM_011759)	promoter-TSS (NM_011759)	-80	NM_001044718	22701	Mm.87210	NM_001044718	ENSMUSG00000047003	Zfp41	CTfin92|Zfp-41	zinc finger protein 41	protein-coding	0.11	0.712871
Merged-chr10-17932717-1	chr10	17932667	17932767	+	3.2	cIP2vsInput	"intron (NM_001033432, intron 1 of 3)"	"intron (NM_001033432, intron 1 of 3)"	15350	NM_001033432	380629	Mm.473073	NM_001033432	ENSMUSG00000039879	Heca	Gm869|HDC|HDCL	headcase homolog (Drosophila)	protein-coding	0.01	0.306931
Merged-chr10-40737465-1	chr10	40737415	40737515	+	3.2	cIP2vsInput	"intron (NM_177793, intron 2 of 4)"	"intron (NM_177793, intron 2 of 4)"	54183	NM_177793	327747	Mm.80407	NM_177793	ENSMUSG00000045555	Mettl24	9030224M15Rik	methyltransferase like 24	protein-coding	0.03	0.475248
Merged-chr5-127617596-2	chr5	127617498	127617694	+	3.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133895)	promoter-TSS (NM_133895)	-204	NM_133895	100561	Mm.28506	NM_133895	ENSMUSG00000029416	Slc15a4	AA987064|AW742963|C130069N12Rik|PHT1|PTR4	"solute carrier family 15, member 4"	protein-coding	0.035714	0.563452
Merged-chr2-13544661-1	chr2	13544611	13544711	+	3.2	cIP2vsInput	promoter-TSS (NM_010067)	promoter-TSS (NM_010067)	3	NM_010067	13434	Mm.6979	NM_010067		Trdmt1	Dnmt2|Rnmt2	tRNA aspartic acid methyltransferase 1	protein-coding	0.1	0.633663
Merged-chr7-112317626-1	chr7	112317576	112317676	+	3.2	cIP2vsInput	"intron (NM_177282, intron 8 of 19)"	L4_B_Mam|LINE|RTE-X	-50682	NM_027587	100504195	Mm.291129	NM_027587	ENSMUSG00000030771	Micalcl	4921517J23Rik	MICAL C-terminal like	protein-coding	0.02	0.49505
Merged-chr18-7693258-1	chr18	7693208	7693308	+	3.2	cIP2vsInput	Intergenic	CpG	-66395	NM_001161620	75739	Mm.133293	NM_001081287	ENSMUSG00000057440	Mpp7	1110068J02Rik|2810038M04Rik|5430426E14Rik|AI415104|Gm955	"membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)"	protein-coding	0.15	0.722772
Merged-chr17-8283310-1	chr17	8283260	8283360	+	3.2	cIP2vsInput	promoter-TSS (NM_018819)	promoter-TSS (NM_018819)	-503	NM_018819	55951	Mm.288510	NM_018819	ENSMUSG00000023861	Mpc1	0610006G08Rik|3830411I18Rik|Brp44l	mitochondrial pyruvate carrier 1	protein-coding	0.04	0.613861
Merged-chr11-7125184-1	chr11	7125134	7125234	+	3.2	cIP2vsInput	"intron (NM_009622, intron 4 of 19)"	"intron (NM_009622, intron 4 of 19)"	61695	NM_009622	432530	Mm.259733	NM_009622	ENSMUSG00000020431	Adcy1	AC1|D11Bwg1392e|I-AC|brl|mKIAA4070	adenylate cyclase 1	protein-coding	0.03	0.514851
Merged-chr6-83860164-1	chr6	83860114	83860214	+	3.2	cIP2vsInput	Intergenic	Intergenic	-28423	NM_146169	232164	Mm.404420	NM_146169	ENSMUSG00000045896	Paip2b	-	poly(A) binding protein interacting protein 2B	protein-coding	0.02	0.465347
Merged-chr10-84383580-1	chr10	84383530	84383630	+	3.2	cIP1vsInput	"intron (NM_001004363, intron 4 of 6)"	"intron (NM_001004363, intron 4 of 6)"	56891	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	"NUAK family, SNF1-like kinase, 1"	protein-coding	0.03	0.544554
Merged-chr12-34447991-1	chr12	34447941	34448041	+	3.2	cIP2vsInput	"intron (NM_001271386, intron 4 of 27)"	"intron (NM_001271386, intron 4 of 27)"	80898	NM_024124	79221	Mm.483009	NM_001271386	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding	0.01	0.316832
Merged-chr15-5185716-1	chr15	5185666	5185766	+	3.2	cIP1vsInput	"5' UTR (NM_026213, exon 1 of 5)"	"5' UTR (NM_026213, exon 1 of 5)"	156	NM_026213	67515	Mm.438095	NM_026213	ENSMUSG00000022151	Ttc33	2410099M07Rik|2900001O04Rik|AI507072|AW538342|Osrf	tetratricopeptide repeat domain 33	protein-coding	0.05	0.524752
Merged-chrX-73054169-1	chrX	73054119	73054219	+	3.2	cIP2vsInput	Intergenic	Intergenic	-10618	NM_153169	245468	Mm.256249	NM_153169	ENSMUSG00000046287	Pnma3	-	paraneoplastic antigen MA3	protein-coding	0.01	0.594059
Merged-chr5-67260800-1	chr5	67260750	67260850	+	3.2	cIP2vsInput	"5' UTR (NM_028975, exon 1 of 8)"	"5' UTR (NM_028975, exon 1 of 8)"	148	NM_030108	67878	Mm.23217	NM_028975	ENSMUSG00000037720	Tmem33	1110006G02Rik|1600019D15Rik|2410089A21Rik|2700052H22Rik|5430406L04Rik|AA388285|AI314185|AI426615|db83	transmembrane protein 33	protein-coding	0.08	0.633663
Merged-chr5-143403836-2	chr5	143403784	143403889	+	3.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025841)	promoter-TSS (NM_025841)	16	NM_025841	66913	Mm.181880	NM_025841	ENSMUSG00000079111	Kdelr2	1110007A14Rik	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2	protein-coding	0.171429	0.764151
Merged-chr4-126321719-2	chr4	126321640	126321799	+	3.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133883)	promoter-TSS (NM_133883)	-16	NM_133883	100206	Mm.11285	NM_133883	ENSMUSG00000042558	Adprhl2	AI836109|Arh3	ADP-ribosylhydrolase like 2	protein-coding	0.113208	0.7
Merged-chr8-84067024-1	chr8	84066974	84067074	+	3.2	cIP2vsInput	"5' UTR (NM_009055, exon 1 of 21)"	"5' UTR (NM_009055, exon 1 of 21)"	188	NM_009055	19724	Mm.7892	NM_009055	ENSMUSG00000031706	Rfx1	AI047719|AI385641	"regulatory factor X, 1 (influences HLA class II expression)"	protein-coding	0.11	0.693069
Merged-chr13-111044448-1	chr13	111044398	111044498	+	3.2	cIP1vsInput	Intergenic	Intergenic	184983	NR_045908	73129	Mm.417826	NR_045908		3110015C05Rik	-	RIKEN cDNA 3110015C05 gene	miscRNA	0.03	0.534653
Merged-chr2-92007201-1	chr2	92007151	92007251	+	3.2	cIP2vsInput	"intron (NM_011957, intron 1 of 11)"	"intron (NM_011957, intron 1 of 11)"	16969	NM_011957	26427	Mm.10353	NM_011957	ENSMUSG00000027230	Creb3l1	Oasis	cAMP responsive element binding protein 3-like 1	protein-coding	0.05	0.633663
Merged-chr10-100299042-1	chr10	100298992	100299092	+	3.2	cIP1vsInput	Intergenic	RSINE1|SINE|B4	-36634	NM_001166636	100043247	Mm.478257	NM_001166636	ENSMUSG00000096640	Gm4312	-	predicted gene 4312	protein-coding	0	0.465347
Merged-chr2-155930035-1	chr2	155929985	155930085	+	3.2	cIP2vsInput	"exon (NM_018888, exon 1 of 10)"	"exon (NM_018888, exon 1 of 10)"	275	NM_018888	56046	Mm.158827	NM_018888	ENSMUSG00000005882	Uqcc	2310079L17Rik|2410003P15Rik|3110038N19Rik|Bfzb|Bfzp	"ubiquinol-cytochrome c reductase complex chaperone, CBP3 homolog (yeast)"	protein-coding	0.05	0.534653
Merged-chr11-83965000-1	chr11	83964950	83965050	+	3.2	cIP2vsInput	"intron (NM_194341, intron 1 of 19)"	"intron (NM_194341, intron 1 of 19)"	569	NM_194341	217030	Mm.441722	NM_001115009	ENSMUSG00000034940	Synrg	Ap1gbp1|SYNG	"synergin, gamma"	protein-coding	0	0.316832
Merged-chr6-86396747-1	chr6	86396697	86396797	+	3.2	cIP2vsInput	"intron (NM_025823, intron 1 of 5)"	"intron (NM_025823, intron 1 of 5)"	403	NM_025823	66881	Mm.30849	NM_025823	ENSMUSG00000029998	Pcyox1	1200015P13Rik|AI115532|AI448340|PCL1|Pcly	prenylcysteine oxidase 1	protein-coding	0.05	0.613861
Merged-chr4-86612262-1	chr4	86612212	86612312	+	3.2	cIP2vsInput	promoter-TSS (NM_173400)	promoter-TSS (NM_173400)	-240	NM_173400	230376	Mm.74730	NM_173400		Haus6	6230416J20Rik|9830144E06|D4Ertd27e|mKIAA1574	"HAUS augmin-like complex, subunit 6"	protein-coding	0.05	0.475248
Merged-chr14-52257987-1	chr14	52257937	52258037	+	3.2	cIP2vsInput	Intergenic	CpG	-20415	NM_201637	67772	Mm.289934	NM_201637	ENSMUSG00000053754	Chd8	5830451P18Rik|AU015341|Duplin|HELSNF1|mKIAA1564	chromodomain helicase DNA binding protein 8	protein-coding	0.09	0.732673
Merged-chr10-92181464-1	chr10	92181414	92181514	+	3.2	cIP2vsInput	"intron (NR_046027, intron 7 of 8)"	(ATATG)n|Simple_repeat|Simple_repeat	-16286	NR_028262	110333	Mm.429764	NR_028262	ENSMUSG00000097348	Rmst	AI853140|C230053E11Rik|D930049J19Rik|Dmt2|M2|Ncrms	rhabdomyosarcoma 2 associated transcript (non-coding RNA)	miscRNA	0	0.247525
Merged-chr16-94302942-1	chr16	94302892	94302992	+	3.2	cIP2vsInput	Intergenic	Intergenic	-15086	NM_139145	110948	Mm.30921	NM_139145	ENSMUSG00000040820	Hlcs	410I21.SP6|D16Jhu34	holocarboxylase synthetase (biotin- [propriony-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)	protein-coding	0.05	0.60396
Merged-chr11-30986541-1	chr11	30986491	30986591	+	3.2	cIP2vsInput	promoter-TSS (NM_026527)	promoter-TSS (NM_026527)	-176	NM_026527	68044	Mm.32656	NM_026527	ENSMUSG00000020309	Chac2	2510006C20Rik	"ChaC, cation transport regulator 2"	protein-coding	0.01	0.39604
Merged-chr12-54696938-1	chr12	54696888	54696988	+	3.2	cIP2vsInput	Intergenic	U1|snRNA|snRNA	-1073	NM_025456	66266	Mm.156440	NM_025456	ENSMUSG00000054302	Eapp	1810011O16Rik	E2F-associated phosphoprotein	protein-coding	0.05	0.445545
Merged-chr19-5425142-1	chr19	5425092	5425192	+	3.2	cIP2vsInput	promoter-TSS (NM_001256515)	promoter-TSS (NM_001256515)	-2	NM_001256515	107242	Mm.329658	NM_001256515	ENSMUSG00000047423	AI837181	Bles03|N28173	expressed sequence AI837181	protein-coding	0.1	0.643564
Merged-chr4-18864336-1	chr4	18864286	18864386	+	3.2	cIP2vsInput	Intergenic	MTEb|LTR|ERVL-MaLR	-416514	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding	0	0.376238
Merged-chr14-16364831-1	chr14	16364781	16364881	+	3.2	cIP2vsInput	promoter-TSS (NM_009409)	promoter-TSS (NM_009409)	-375	NM_009409	21974	Mm.130362	NM_009409	ENSMUSG00000017485	Top2b	D230016L12Rik|Top-2	topoisomerase (DNA) II beta	protein-coding	0.07	0.732673
Merged-chr10-67124358-1	chr10	67124308	67124408	+	3.2	cIP1vsInput	Intergenic	Intergenic	-2900	NM_207221	108829	Mm.23846	NM_001242396	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding	0.02	0.475248
Merged-chr12-111668623-1	chr12	111668573	111668673	+	3.2	cIP2vsInput	TTS (NM_021273)	TTS (NM_021273)	3715	NM_021273	12709	Mm.16831	NM_021273	ENSMUSG00000001270	Ckb	B-CK|Bck|Ck-3|Ck3|Ckbb	"creatine kinase, brain"	protein-coding	0.02	0.544554
Merged-chr5-58825714-1	chr5	58825664	58825764	+	3.2	cIP1vsInput	Intergenic	Intergenic	-372716	NR_046190	78163	Mm.243828	NR_046190		4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	miscRNA	0	0.326733
Merged-chr7-66956126-1	chr7	66956076	66956176	+	3.2	cIP2vsInput	"intron (NM_001033877, intron 7 of 22)"	"intron (NM_001033877, intron 7 of 22)"	116391	NM_001033877	233332	Mm.445763	NM_001033877	ENSMUSG00000058145	Adamts17	AU023434	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 17"	protein-coding	0.01	0.50495
Merged-chr2-114057590-1	chr2	114057540	114057640	+	3.2	cIP2vsInput	"intron (NR_028422, intron 2 of 2)"	"intron (NR_028422, intron 2 of 2)"	3194	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	miscRNA	0.01	0.623762
Merged-chr1-34843045-1	chr1	34842995	34843095	+	3.2	cIP2vsInput	promoter-TSS (NM_174997)	promoter-TSS (NM_174997)	5	NM_001160235	214469	Mm.120151	NM_001160235	ENSMUSG00000037503	Fam168b	mKIAA4042	"family with sequence similarity 168, member B"	protein-coding	0.2	0.80198
Merged-chr19-5609946-1	chr19	5609896	5609996	+	3.2	cIP2vsInput	promoter-TSS (NR_037603)	promoter-TSS (NR_037603)	148	NM_001199247	81601	Mm.228930	NM_001199247	ENSMUSG00000024926	Kat5	AI839539|CPLA2|Htatip|Htatip1|PLIP|Tip55|Tip60	K(lysine) acetyltransferase 5	protein-coding	0.08	0.742574
Merged-chr2-131423390-2	chr2	131423337	131423444	+	3.2	cIP1vsInput|cIP2vsInput	"intron (NR_037281, intron 1 of 2)"	"intron (NR_037281, intron 1 of 2)"	-68472	NM_001177834	228608	Mm.136586	NM_001177833	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding	0.009346	0.407407
Merged-chrX-85187054-1	chrX	85187004	85187104	+	3.2	cIP2vsInput	"intron (NM_007868, intron 76 of 78)"	"intron (NM_007868, intron 76 of 78)"	-62623	NM_028046	71996	Mm.20201	NM_028046	ENSMUSG00000035491	1600014K23Rik	AI324104	RIKEN cDNA 1600014K23 gene	protein-coding	0.01	0.336634
Merged-chr9-106203215-1	chr9	106203165	106203265	+	3.2	cIP2vsInput	"5' UTR (NM_011876, exon 1 of 9)"	"5' UTR (NM_011876, exon 1 of 9)"	107	NM_011876	23999	Mm.274346	NM_011876	ENSMUSG00000023277	Twf2	A6-related|AU014993|Ptk9l|Ptk9r	"twinfilin, actin-binding protein, homolog 2 (Drosophila)"	protein-coding	0.11	0.693069
Merged-chr1-8395119-1	chr1	8395069	8395169	+	3.2	cIP1vsInput	"intron (NM_027671, intron 20 of 20)"	L1_Mus2|LINE|L1	904611	NM_027671	71096	Mm.388998	NM_027671		Sntg1	4933426D16Rik|G1SYN|SYN4	"syntrophin, gamma 1"	protein-coding	0	0.336634
Merged-chr17-35821467-2	chr17	35821377	35821558	+	3.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133662)	promoter-TSS (NM_133662)	-246	NM_133662	15937	Mm.25613	NM_133662	ENSMUSG00000003541	Ier3	AI663993|IEX-1|cI-3|gly96	immediate early response 3	protein-coding	0.027624	0.527473
Merged-chr8-84655809-1	chr8	84655759	84655859	+	3.2	cIP2vsInput	Intergenic	Intergenic	7043	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding	0.02	0.613861
Merged-chr10-24479519-1	chr10	24479469	24479569	+	3.2	cIP2vsInput	Intergenic	Intergenic	-115923	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding	0.05	0.564356
Merged-chr11-106066047-2	chr11	106065995	106066099	+	3.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027346)	promoter-TSS (NM_027346)	-60	NM_027346	70207	Mm.343857	NM_027346	ENSMUSG00000001983	Taco1	2310066I18Rik|Ccdc44	translational activator of mitochondrially encoded cytochrome c oxidase I	protein-coding	0.096154	0.6
Merged-chr4-126968132-1	chr4	126968082	126968182	+	3.2	cIP2vsInput	promoter-TSS (NM_001114399)	promoter-TSS (NM_001114399)	-209	NM_001114399	67785	Mm.165401	NM_001114399	ENSMUSG00000042446	Zmym4	6330503C17Rik|AI480785|AW493829|CDIR|D630001M21|MYM|Zfp262|Znf262|mKIAA0425	"zinc finger, MYM-type 4"	protein-coding	0.04	0.564356
Merged-chr9-106170956-1	chr9	106170906	106171006	+	3.2	cIP2vsInput	promoter-TSS (NM_029896)	promoter-TSS (NM_029896)	27	NM_029896	77305	Mm.265125	NM_029896	ENSMUSG00000020257	Wdr82	9430077D24Rik|CDW5/WDR82	WD repeat domain containing 82	protein-coding	0.08	0.594059
Merged-chr1-128244368-1	chr1	128244318	128244418	+	3.2	cIP2vsInput	"5' UTR (NM_026390, exon 1 of 13)"	"5' UTR (NM_026390, exon 1 of 13)"	187	NM_026390	67812	Mm.293321	NM_026390	ENSMUSG00000026353	Ubxn4	1300013G12Rik|Ubxd2|mKIAA0242	UBX domain protein 4	protein-coding	0.1	0.722772
Merged-chr4-76018000-1	chr4	76017950	76018050	+	3.2	cIP1vsInput	"intron (NM_011211, intron 29 of 39)"	"intron (NM_011211, intron 29 of 39)"	-739714	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	3110001D03Rik	1700027K24Rik	RIKEN cDNA 3110001D03 gene	protein-coding	0	0.386139
Merged-chrX-134276897-1	chrX	134276847	134276947	+	3.2	cIP2vsInput	promoter-TSS (NM_172540)	promoter-TSS (NM_172540)	87	NM_172540	215201	Mm.289368	NM_001167994	ENSMUSG00000067369	Trmt2b	4732479N06Rik	TRM2 tRNA methyltransferase 2B	protein-coding	0.06	0.594059
Merged-chr11-120437775-2	chr11	120437698	120437852	+	3.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001195023)	promoter-TSS (NM_001195023)	-75	NM_199469	217365	Mm.309520	NM_001195023	ENSMUSG00000039703	Nploc4	AK129375|Npl4|mKIAA1499	nuclear protein localization 4 homolog (S. cerevisiae)	protein-coding	0.097403	0.716129
Merged-chr10-18055555-2	chr10	18055498	18055613	+	3.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009048)	promoter-TSS (NM_009048)	-385	NM_009048	19707	Mm.4479	NM_001111065	ENSMUSG00000019854	Reps1	BB161292	RalBP1 associated Eps domain containing protein	protein-coding	0.095652	0.689655
Merged-chr5-79409081-1	chr5	79409031	79409131	+	3.2	cIP1vsInput	"intron (NR_035474, intron 2 of 4)"	"intron (NR_035474, intron 2 of 4)"	106823	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0	0.316832
Merged-chr8-125343357-2	chr8	125343276	125343439	+	3.2	cIP1vsInput|cIP2vsInput	Intergenic	(TA)n|Simple_repeat|Simple_repeat	149353	NM_001081337	244668	Mm.271668	NM_001081337	ENSMUSG00000001995	Sipa1l2	BC058408|mKIAA1389	signal-induced proliferation-associated 1 like 2	protein-coding	0	0.195122
Merged-chr7-5038254-1	chr7	5038204	5038304	+	3.2	cIP2vsInput	"intron (NM_001039532, intron 1 of 1)"	"intron (NM_001039532, intron 1 of 1)"	192	NM_001039532	654801	Mm.333548	NM_001039532	ENSMUSG00000043290	Zfp784	C730049F21Rik|Znf784	zinc finger protein 784	protein-coding	0.06	0.633663
Merged-chr9-80165008-1	chr9	80164958	80165058	+	3.2	cIP2vsInput	promoter-TSS (NM_001039546)	promoter-TSS (NM_001039546)	-26	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding	0.09	0.732673
Merged-chr10-89522663-1	chr10	89522613	89522713	+	3.2	cIP2vsInput	"intron (NM_001163504, intron 1 of 9)"	"intron (NM_001163504, intron 1 of 9)"	10959	NM_001163504	20186	Mm.3095	NM_001163504	ENSMUSG00000047638	Nr1h4	AI957360|Fxr|HRR1|RIP14|Rxrip14	"nuclear receptor subfamily 1, group H, member 4"	protein-coding	0.03	0.445545
Merged-chr11-98150793-1	chr11	98150743	98150843	+	3.2	cIP1vsInput	Intergenic	Intergenic	-1177	NM_028149	72194	Mm.218350	NM_134030	ENSMUSG00000020883	Fbxl20	2610511F20Rik|4632423N09Rik|AI849362|AL117906|C86145|Fbl2|Scr|mKIAA4147	F-box and leucine-rich repeat protein 20	protein-coding	0.03	0.346535
Merged-chr17-33955856-1	chr17	33955806	33955906	+	3.2	cIP1vsInput	promoter-TSS (NM_011296)	promoter-TSS (NM_011296)	-26	NM_172620	224705	Mm.448614	XM_003689309	ENSMUSG00000024319	Vps52	ARE1|D130068D18|D430041K17Rik|Sacm2l	vacuolar protein sorting 52 (yeast)	protein-coding	0.11	0.564356
Merged-chr5-138280122-2	chr5	138280066	138280179	+	3.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_016964)	promoter-TSS (NM_016964)	-185	NM_172412	71951	Mm.77066	NM_172412	ENSMUSG00000029510	Gpc2	2410016G05Rik	glypican 2 (cerebroglycan)	protein-coding	0.079646	0.684211
Merged-chr4-52095841-1	chr4	52095791	52095891	+	3.2	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	-44731	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	miscRNA	0	0.425743
Merged-chr5-21737248-1	chr5	21737198	21737298	+	3.2	cIP2vsInput	promoter-TSS (NM_028431)	promoter-TSS (NM_028431)	88	NM_028431	73078	Mm.301655	NM_028431	ENSMUSG00000029017	Pmpcb	3110004O18Rik|MPP11|MPPB|MPPP52	peptidase (mitochondrial processing) beta	protein-coding	0.14	0.712871
Merged-chr16-27388945-1	chr16	27388895	27388995	+	3.2	cIP2vsInput	promoter-TSS (NM_026202)	promoter-TSS (NM_026202)	-32	NM_001025615	67501	Mm.258985	NM_001025615	ENSMUSG00000038127	Ccdc50	2610529H08Rik|5730448P06Rik|AW048328|AW546090|C3orf6|D16Bwg1543e	coiled-coil domain containing 50	protein-coding	0.12	0.752475
Merged-chrY-10378811-1	chrY	10378761	10378861	+	3.2	cIP1vsInput	Intergenic	IAPEy-int|LTR|ERVK	819037	NM_001199331	100040022	Mm.485767	NM_001199331	ENSMUSG00000095172	Gm20822	-	"predicted gene, 20822"	protein-coding	0	0.376238
Merged-chr2-16930142-1	chr2	16930092	16930192	+	3.2	cIP2vsInput	"intron (NR_040632, intron 2 of 3)"	"intron (NR_040632, intron 2 of 3)"	83584	NR_040632	75069	Mm.399263	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	miscRNA	0	0.425743
Merged-chr11-51756512-2	chr11	51756433	51756592	+	3.2	cIP1vsInput|cIP2vsInput	"5' UTR (NM_175255, exon 1 of 23)"	"5' UTR (NM_175255, exon 1 of 23)"	322	NM_175255	77371	Mm.33878	NM_175255	ENSMUSG00000036391	Sec24a	9430090N21Rik|AI504915	"Sec24 related gene family, member A (S. cerevisiae)"	protein-coding	0.100629	0.75625
Merged-chr10-121586932-1	chr10	121586882	121586982	+	3.2	cIP2vsInput	promoter-TSS (NM_019786)	promoter-TSS (NM_019786)	-138	NM_019786	56480	Mm.34580	NM_019786	ENSMUSG00000020115	Tbk1	1200008B05Rik|AI462036|AW048562	TANK-binding kinase 1	protein-coding	0.14	0.732673
Merged-chr13-37994125-1	chr13	37994075	37994175	+	3.2	cIP2vsInput	promoter-TSS (NM_025965)	promoter-TSS (NM_025965)	65	NM_025965	107513	Mm.490298	NM_025965	ENSMUSG00000021427	Ssr1	2510001K09Rik|6330400D04|AI159733|AI452176|SSR|TRAPA	"signal sequence receptor, alpha"	protein-coding	0.12	0.673267
Merged-chr12-34714722-2	chr12	34714658	34714786	+	3.2	cIP1vsInput|cIP2vsInput	"intron (NM_001271386, intron 3 of 27)"	"intron (NM_001271386, intron 3 of 27)"	-185833	NM_024124	79221	Mm.483009	NM_001271386	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding	0.023438	0.457364
Merged-chr19-8481957-1	chr19	8481907	8482007	+	3.2	cIP1vsInput	Intergenic	Intergenic	-76852	NM_177002	319800	Mm.426083	NM_177002	ENSMUSG00000052562	Slc22a30	AA986766|C730048C13Rik|UST1R	"solute carrier family 22, member 30"	protein-coding	0	0.376238
Merged-chr5-24352538-1	chr5	24352488	24352588	+	3.2	cIP2vsInput	promoter-TSS (NM_013569)	promoter-TSS (NM_013569)	-934	NM_013569	16511	Mm.6539	NM_013569	ENSMUSG00000038319	Kcnh2	AI326795|ERG1|LQT|Lqt2|M-erg|Merg1|merg1a|merg1b	"potassium voltage-gated channel, subfamily H (eag-related), member 2"	protein-coding	0.02	0.613861
Merged-chr7-96524744-2	chr7	96524680	96524809	+	3.2	cIP1vsInput|cIP2vsInput	"intron (NM_011858, intron 3 of 32)"	MIRb|SINE|MIR	-182780	NR_046043	670727	Mm.421352	NR_046043	ENSMUSG00000085751	Gm15412	OTTMUSG00000021245	predicted gene 15412	miscRNA	0.023256	0.484615
Merged-chr12-32615133-1	chr12	32615083	32615183	+	3.2	cIP1vsInput	Intergenic	MIRc|SINE|MIR	-205202	NM_021524	59027		NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding	0.01	0.336634
Merged-chr6-30617989-1	chr6	30617939	30618039	+	3.2	cIP2vsInput	"intron (NM_144537, intron 4 of 11)"	"intron (NM_144537, intron 4 of 11)"	6979	NM_144537	74649	Mm.159276	NM_144537	ENSMUSG00000029788	Cpa5	4930430M09Rik	carboxypeptidase A5	protein-coding	0.05	0.60396
Merged-chr7-127393516-1	chr7	127393466	127393566	+	3.2	cIP2vsInput	"5' UTR (NM_198011, exon 1 of 3)"	"5' UTR (NM_198011, exon 1 of 3)"	105	NM_198011	101604	Mm.334241	NM_198011		E430018J23Rik	AI480612	RIKEN cDNA E430018J23 gene	protein-coding	0.05	0.60396
Merged-chr1-33757755-1	chr1	33757705	33757805	+	3.2	cIP1vsInput	promoter-TSS (NM_145392)	promoter-TSS (NM_145392)	-5	NM_145392	213539	Mm.247037	NM_145392	ENSMUSG00000042215	Bag2	2610042A13Rik|BC016230	BCL2-associated athanogene 2	protein-coding	0.18	0.80198
Merged-chr1-173955254-1	chr1	173955204	173955304	+	3.2	cIP2vsInput	Intergenic	Intergenic	-12762	NM_001045481	15950	Mm.472787	NM_001045481	ENSMUSG00000039997	Ifi203	-	interferon activated gene 203	protein-coding	0	0.356436
Merged-chr10-45066816-1	chr10	45066766	45066866	+	3.2	cIP1vsInput	promoter-TSS (NM_011156)	promoter-TSS (NM_011156)	-398	NM_011156	19072	Mm.37294	NM_011156	ENSMUSG00000019849	Prep	AI047692|AI450383|D10Wsu136e|PEP|Pop	prolyl endopeptidase	protein-coding	0.03	0.524752
Merged-chr11-85800049-1	chr11	85799999	85800099	+	3.2	cIP2vsInput	"intron (NR_077059, intron 3 of 4)"	"intron (NR_077059, intron 3 of 4)"	-24369	NR_046194	78420	Mm.488197	NR_046194	ENSMUSG00000085514	9530048J24Rik	-	RIKEN cDNA 9530048J24 gene	miscRNA	0.09	0.673267
Merged-chr1-131097832-1	chr1	131097782	131097882	+	3.2	cIP2vsInput	promoter-TSS (NM_008551)	promoter-TSS (NM_008551)	-289	NM_008551	17164	Mm.490983	NM_008551	ENSMUSG00000016528	Mapkapk2	AA960234|MAPKAP-K2|MK-2|MK2|Rps6kc1	MAP kinase-activated protein kinase 2	protein-coding	0.13	0.70297
Merged-chr18-57354679-1	chr18	57354629	57354729	+	3.2	cIP1vsInput	promoter-TSS (NM_028447)	promoter-TSS (NM_028447)	-54	NM_028447	73137	Mm.29889	NM_028447	ENSMUSG00000024594	Prrc1	1190002C06Rik|2310058D16Rik|3110038B19Rik|9430085A19Rik	proline-rich coiled-coil 1	protein-coding	0.12	0.772277
Merged-chr17-72890381-1	chr17	72890331	72890431	+	3.2	cIP2vsInput	Intergenic	G-rich|Low_complexity|Low_complexity	-27924	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding	0.04	0.683168
Merged-chr3-97901155-1	chr3	97901105	97901205	+	3.2	cIP2vsInput	promoter-TSS (NM_011342)	promoter-TSS (NM_011342)	-72	NM_011342	20333	Mm.486379	NM_011342		Sec22b	4930564D15Rik|AA517334|AI480645|C81333|ERS-24|Sec22l1	SEC22 vesicle trafficking protein homolog B (S. cerevisiae)	protein-coding	0.06	0.554455
Merged-chr2-45672183-1	chr2	45672133	45672233	+	3.2	cIP1vsInput	Intergenic	Intergenic	-24422	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	miscRNA	0.01	0.346535
Merged-chr11-95666759-1	chr11	95666709	95666809	+	3.2	cIP2vsInput	promoter-TSS (NM_008831)	promoter-TSS (NM_008831)	-198	NM_008831	18673	Mm.263862	NM_008831	ENSMUSG00000038845	Phb	Bap32	prohibitin	protein-coding	0.05	0.49505
Merged-chr12-117200295-2	chr12	117200245	117200346	+	3.2	cIP1vsInput|cIP2vsInput	"intron (NM_011215, intron 14 of 22)"	"intron (NM_011215, intron 14 of 22)"	-49026	NR_033538	100038689	Mm.445351	NR_033538		Gm10421	ENSMUSG00000072792	predicted gene 10421	miscRNA	0.029703	0.529412
Merged-chr12-84417423-1	chr12	84417373	84417473	+	3.2	cIP2vsInput	"exon (NM_025525, exon 1 of 1)"	"exon (NM_025525, exon 1 of 1)"	223	NM_025525	66381	Mm.24846	NM_025525		Rnf113a2	2310020H19Rik|AI426758|Rnf113a	ring finger protein 113A2	protein-coding	0.1	0.643564
Merged-chr13-49505286-1	chr13	49505236	49505336	+	3.2	cIP2vsInput	"intron (NM_001012324, intron 1 of 9)"	"intron (NM_001012324, intron 1 of 9)"	476	NM_001012324	407800	Mm.386931	NM_001012324	ENSMUSG00000043631	Ecm2	9030618O22Rik|BC065151|tenonectin	"extracellular matrix protein 2, female organ and adipocyte specific"	protein-coding	0	0.306931
Merged-chr15-102377408-1	chr15	102377358	102377458	+	3.2	cIP2vsInput	Intergenic	Intergenic	-11137	NM_130458	170574	Mm.263284	NM_130458		Sp7	6430578P22Rik|C22|Osx	Sp7 transcription factor 7	protein-coding	0.01	0.653465
Merged-chr16-83758745-1	chr16	83758695	83758795	+	3.2	cIP2vsInput	Intergenic	MT2A|LTR|ERVL	-612398	NR_040567	75247	Mm.417813	NR_040567		4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	miscRNA	0	0.346535
Merged-chr5-31054958-1	chr5	31054908	31055008	+	3.2	cIP2vsInput	TTS (NM_027855)	TTS (NM_027855)	147	NM_023525	69719	Mm.305535	NM_023525	ENSMUSG00000013629	Cad	2410008J01Rik|AU018859|Cpad	"carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase"	protein-coding	0.11	0.732673
Merged-chr3-84040319-1	chr3	84040269	84040369	+	3.2	cIP2vsInput	promoter-TSS (NM_172681)	promoter-TSS (NM_172681)	-158	NM_172681	229473	Mm.28838	NM_172681	ENSMUSG00000033767	D930015E06Rik	Kiaa0922|mKIAA0922	RIKEN cDNA D930015E06 gene	protein-coding	0.16	0.693069
Merged-chr18-32068019-1	chr18	32067969	32068069	+	3.2	cIP1vsInput	"exon (NM_173441, exon 1 of 14)"	"exon (NM_173441, exon 1 of 14)"	285	NM_173441	73473	Mm.66853	NM_173441	ENSMUSG00000024384	Iws1	1700069O15Rik|3000008H23|AL117927|AW214353	IWS1 homolog (S. cerevisiae)	protein-coding	0.13	0.732673
Merged-chr7-45830661-1	chr7	45830611	45830711	+	3.2	cIP2vsInput	"exon (NM_153419, exon 1 of 7)"	"exon (NM_153419, exon 1 of 7)"	128	NM_153419	101612	Mm.274847	NM_153419	ENSMUSG00000053801	Grwd1	A301|AI504353|Grwd|Wdr28	glutamate-rich WD repeat containing 1	protein-coding	0.05	0.633663
Merged-chr8-72548299-1	chr8	72548249	72548349	+	3.2	cIP2vsInput	promoter-TSS (NM_027485)	promoter-TSS (NM_027485)	11	NM_027485	70625	Mm.440960	NM_027485	ENSMUSG00000045248	Med26	5730493L18Rik|AI414941|AW495270|Crsp7	mediator complex subunit 26	protein-coding	0.13	0.732673
Merged-chr3-8767080-1	chr3	8767030	8767130	+	3.2	cIP2vsInput	Intergenic	CpG	-100042	NM_010423	15213	Mm.29581	NM_010423	ENSMUSG00000040289	Hey1	AI316788|AI414254|CHF2|HRT1|Herp2|Hesr1|bHLHb31|hesr-1	hairy/enhancer-of-split related with YRPW motif 1	protein-coding	0.06	0.554455
Merged-chr8-106415483-1	chr8	106415433	106415533	+	3.2	cIP2vsInput	"5' UTR (NM_011764, exon 1 of 4)"	"5' UTR (NM_011764, exon 1 of 4)"	144	NM_011764	22751	Mm.295582	NM_011764	ENSMUSG00000031907	Zfp90	6430515L01Rik|KRAB17|NK10|Zfp64|Zfp83|mKIAA1954	zinc finger protein 90	protein-coding	0.11	0.683168
Merged-chrY-5051191-2	chrY	5051140	5051242	+	3.2	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	1279518	NM_001270516	100862398		NM_001270516		Gm21708	-	"predicted gene, 21708"	protein-coding	0.019608	0.320388
Merged-chr9-21616217-1	chr9	21616167	21616267	+	3.2	cIP2vsInput	promoter-TSS (NM_001174079)	promoter-TSS (NM_001174079)	48	NM_001174078	20586	Mm.286593	NM_001174078	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"	protein-coding	0.16	0.821782
Merged-chr1-157412626-1	chr1	157412576	157412676	+	3.2	cIP2vsInput	promoter-TSS (NM_177644)	promoter-TSS (NM_177644)	-31	NM_177644	226525	Mm.439484	NM_177644	ENSMUSG00000070565	Rasal2	6530401P13|A330066M24Rik	RAS protein activator like 2	protein-coding	0.11	0.653465
Merged-chr4-62470961-2	chr4	62470899	62471023	+	3.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_023597)	promoter-TSS (NM_023597)	-89	NM_023597	71354	Mm.155573	NM_023597	ENSMUSG00000028391	Wdr31	5430402I10Rik|spWD	WD repeat domain 31	protein-coding	0.120968	0.68
Merged-chr8-71526451-1	chr8	71526401	71526501	+	3.2	cIP2vsInput	Intergenic	Intergenic	10986	NM_198095	69550	Mm.260325	NM_198095	ENSMUSG00000046718	Bst2	2310015I10Rik|Bst-2|C87040|CD317|DAMP-1|GREG	bone marrow stromal cell antigen 2	protein-coding	0.02	0.49505
Merged-chr11-50431205-2	chr11	50431126	50431285	+	3.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172557)	promoter-TSS (NM_172557)	-94	NM_172557	216724	Mm.390400	NM_172557	ENSMUSG00000020375	Rufy1	3000002E04Rik|Rabip4|ZFYVE12	RUN and FYVE domain containing 1	protein-coding	0.062893	0.55625
Merged-chr3-138504095-1	chr3	138504045	138504145	+	3.2	cIP2vsInput	Intergenic	Intergenic	-14713	NM_175224	75624	Mm.26833	NM_175224	ENSMUSG00000005813	Metap1	1700029C17Rik|AW047992|mKIAA0094	methionyl aminopeptidase 1	protein-coding	0.01	0.465347
Merged-chr9-21368035-1	chr9	21367985	21368085	+	3.2	cIP2vsInput	promoter-TSS (NM_001277322)	promoter-TSS (NM_001277322)	164	NM_001042709	16201	Mm.440026	NM_001042707	ENSMUSG00000032178	Ilf3	MBII-26|MPHOSPH4|NF90|NFAR	interleukin enhancer binding factor 3	protein-coding	0.11	0.594059
Merged-chr17-70794297-1	chr17	70794247	70794347	+	3.2	cIP2vsInput	"intron (NM_027712, intron 8 of 9)"	"intron (NM_027712, intron 8 of 9)"	52480	NM_001164077	21815	Mm.101034	NM_001164074	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding	0.01	0.514851
Merged-chr5-45450549-1	chr5	45450499	45450599	+	3.2	cIP2vsInput	promoter-TSS (NM_024236)	promoter-TSS (NM_024236)	-320	NM_024236	110391	Mm.30204	NM_024236	ENSMUSG00000015806	Qdpr	2610008L04Rik|D5Ertd371e|Dhpr|PKU2	quinoid dihydropteridine reductase	protein-coding	0.07	0.673267
Merged-chr9-107612842-1	chr9	107612792	107612892	+	3.2	cIP2vsInput	Intergenic	CpG	-3601	NM_001042779	20347	Mm.4083	NM_001042779	ENSMUSG00000057969	Sema3b	AW208495|LUCA-1|SemA|Semaa|sema5|semaV	"sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B"	protein-coding	0.1	0.752475
Merged-chr5-96210106-1	chr5	96210056	96210156	+	3.2	cIP2vsInput	promoter-TSS (NM_053158)	promoter-TSS (NM_053158)	-9	NM_001039084	94061	Mm.295499	NM_001039084	ENSMUSG00000029486	Mrpl1	2410002L03Rik|5830418D04Rik|AI462572	mitochondrial ribosomal protein L1	protein-coding	0.08	0.564356
Merged-chr2-163364237-1	chr2	163364187	163364287	+	3.2	cIP2vsInput	"intron (NM_021566, intron 2 of 5)"	"intron (NM_021566, intron 2 of 5)"	33736	NM_021566	59091	Mm.34459	NM_197984	ENSMUSG00000017817	Jph2	1110002E14Rik|JP-2|Jp2	junctophilin 2	protein-coding	0.02	0.534653
Merged-chr1-131246487-1	chr1	131246437	131246537	+	3.2	cIP1vsInput	Intergenic	Intergenic	-1309	NM_018750	54354	Mm.248291	NM_018750	ENSMUSG00000026430	Rassf5	1300019G20Rik|AU042887|Maxp1|Nore1|Nore1A|Nore1B|Rapl	Ras association (RalGDS/AF-6) domain family member 5	protein-coding	0	0.415842
Merged-chr18-17371756-1	chr18	17371706	17371806	+	3.2	cIP1vsInput	Intergenic	Intergenic	-136274	NR_033607	664619	Mm.250005	NR_033607		4921533I20Rik	-	PRP18 pre-mRNA processing factor 18 homolog pseudogene	pseudo	0.01	0.316832
Merged-chr14-20794285-1	chr14	20794235	20794335	+	3.2	cIP2vsInput	promoter-TSS (NM_178597)	promoter-TSS (NM_178597)	-197	NM_178597	12325	Mm.235182	NM_001039138	ENSMUSG00000021820	Camk2g	5930429P18Rik|Camkg	calcium/calmodulin-dependent protein kinase II gamma	protein-coding	0.08	0.722772
Merged-chr5-135957893-1	chr5	135957843	135957943	+	3.2	cIP2vsInput	Intergenic	Intergenic	16583	NM_001160366	109267	Mm.332750	NM_001160366	ENSMUSG00000029699	Srcrb4d	C330016E03Rik|S4D-SRCRB|SRCRB-S4D	"scavenger receptor cysteine rich domain containing, group B (4 domains)"	protein-coding	0.06	0.574257
Merged-chr9-21238825-1	chr9	21238775	21238875	+	3.2	cIP2vsInput	"5' UTR (NM_016679, exon 1 of 5)"	"5' UTR (NM_016679, exon 1 of 5)"	507	NM_016679	50868	Mm.248266	NM_001110305	ENSMUSG00000003308	Keap1	INRF2|mKIAA0132	kelch-like ECH-associated protein 1	protein-coding	0.12	0.693069
Merged-chr1-55131140-2	chr1	55131047	55131233	+	3.2	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025283)	promoter-TSS (NM_025283)	-105	NM_025283	19070	Mm.291037	NM_025283	ENSMUSG00000025979	Mob4	2610109B12Rik|Mobkl3|Phocn|Prei3	"MOB family member 4, phocein"	protein-coding	0.134409	0.748663
Merged-chr11-76945635-1	chr11	76945585	76945685	+	3.2	cIP2vsInput	promoter-TSS (NM_178645)	promoter-TSS (NM_178645)	-21	NM_178645	104184	Mm.399785	NM_178645	ENSMUSG00000020840	Blmh	AI035728|Bh|Bmh	bleomycin hydrolase	protein-coding	0.11	0.772277
Merged-chr18-21002013-1	chr18	21001963	21002063	+	3.2	cIP2vsInput	"5' UTR (NM_019706, exon 2 of 7)"	"5' UTR (NM_019706, exon 2 of 7)"	672	NM_207623	56515	Mm.253542	NM_019706	ENSMUSG00000024317	Rnf138	2410015A17Rik|2810480D20Rik|STRIN|Trif|Trif-d	ring finger protein 138	protein-coding	0.11	0.742574
Merged-chr4-141147786-1	chr4	141147736	141147836	+	3.2	cIP2vsInput	promoter-TSS (NM_172518)	promoter-TSS (NM_172518)	-136	NM_172518	213499	Mm.28865	NM_172518	ENSMUSG00000028920	Fbxo42	6720460I06Rik|mKIAA1332	F-box protein 42	protein-coding	0.1	0.60396
Merged-chr1-164994520-1	chr1	164994470	164994570	+	3.2	cIP2vsInput	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-59010	NM_008510	16963	Mm.190	NM_008510	ENSMUSG00000026573	Xcl1	AI661682|ATAC|LTN|Lptn|SCM-1|SCM-1a|Scyc1	chemokine (C motif) ligand 1	protein-coding	0	0.50495
Merged-chr3-32529282-1	chr3	32529232	32529332	+	3.2	cIP2vsInput	promoter-TSS (NM_024200)	promoter-TSS (NM_024200)	-200	NM_024200	67414	Mm.290414	NM_024200	ENSMUSG00000027668	Mfn1	2310002F04Rik|6330416C07Rik|D3Ertd265e|HR2|mKIAA4032	mitofusin 1	protein-coding	0.01	0.455446
Merged-chr19-47919800-2	chr19	47919723	47919878	+	3.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001001738)	promoter-TSS (NM_001001738)	-501	NM_001001738	414801	Mm.29457	NM_001001738	ENSMUSG00000079254	Itprip	4833424O12Rik|DANGER|mKIAA1754	"inositol 1,4,5-triphosphate receptor interacting protein"	protein-coding	0.032258	0.461538
Merged-chr8-22398622-2	chr8	22398547	22398697	+	3.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_181325)	promoter-TSS (NM_181325)	-1	NM_181325	18408	Mm.200907	NM_181325	ENSMUSG00000031482	Slc25a15	D630044L02Rik|Ornt1	"solute carrier family 25 (mitochondrial carrier ornithine transporter), member 15"	protein-coding	0.073333	0.748344
Merged-chr9-23495387-2	chr9	23495306	23495469	+	3.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	272311	NM_028472	73230	Mm.335020	NM_028472	ENSMUSG00000031963	Bmper	3110056H04Rik|CV-2|Crim3|Cv2	BMP-binding endothelial regulator	protein-coding	0	0.341463
Merged-chr6-88446495-2	chr6	88446436	88446555	+	3.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_023060)	promoter-TSS (NM_023060)	44	NM_023060	65967	Mm.333237	NM_023060	ENSMUSG00000033216	Eefsec	Selb|sec	"eukaryotic elongation factor, selenocysteine-tRNA-specific"	protein-coding	0.12605	0.733333
Merged-chr2-30237273-2	chr2	30237183	30237363	+	3.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_177725)	promoter-TSS (NM_177725)	358	NR_028299	67350	Mm.402683	NR_028299		1700084E18Rik	-	RIKEN cDNA 1700084E18 gene	miscRNA	0.083333	0.524862
Merged-chr11-74811290-2	chr11	74811221	74811360	+	3.15	cIP1vsInput|cIP2vsInput	"intron (NM_026197, intron 8 of 9)"	RMER17D2|LTR|ERVK	-19634	NM_010813	17428	Mm.3759	NM_010813	ENSMUSG00000000282	Mnt	Rox|bHLHd3	max binding protein	protein-coding	0.007194	0.55
Merged-chr6-113740745-2	chr6	113740682	113740809	+	3.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_024206)	promoter-TSS (NM_024206)	-64	NM_024206	110379	Mm.29296	NM_024206	ENSMUSG00000030298	Sec13	1110003H02Rik|Sec13l1|Sec13r	SEC13 homolog (S. cerevisiae)	protein-coding	0.086614	0.640625
Merged-chr12-86726574-2	chr12	86726512	86726636	+	3.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_144524)	promoter-TSS (NM_144524)	-114	NM_144524	68737	Mm.63979	NM_144524	ENSMUSG00000021257	Angel1	1110030H02Rik|mKIAA0759	angel homolog 1 (Drosophila)	protein-coding	0.064516	0.632
Merged-chr15-76511902-2	chr15	76511850	76511954	+	3.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010046)	promoter-TSS (NM_010046)	-84	NM_010046	13350	Mm.22633	NM_010046	ENSMUSG00000022555	Dgat1	ARAT|C75990|D15Ertd23e|Dgat	diacylglycerol O-acyltransferase 1	protein-coding	0.134615	0.752381
Merged-chr7-44359995-2	chr7	44359938	44360052	+	3.15	cIP1vsInput|cIP2vsInput	TTS (NM_027049)	TTS (NM_027049)	15035	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding	0.070175	0.582609
Merged-chr4-127365316-2	chr4	127365261	127365371	+	3.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-7152	NM_010291	14622	Mm.26859	NM_010291	ENSMUSG00000042357	Gjb5	Cnx31.1|Cx31.1|Gjb-5	"gap junction protein, beta 5"	protein-coding	0.036364	0.513514
Merged-chr2-127792415-2	chr2	127792362	127792469	+	3.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_015476)	promoter-TSS (NR_015476)	73	NR_015476	67885	Mm.27359	NM_175125	ENSMUSG00000051319	1500011K16Rik	-	RIKEN cDNA 1500011K16 gene	miscRNA	0.084112	0.62963
Merged-chr13-38148584-2	chr13	38148511	38148657	+	3.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-2710	NM_023842	109620	Mm.355327	NM_023842	ENSMUSG00000054889	Dsp	2300002E22Rik|5730453H04Rik|AA407887|AA407888|AW109828|DP	desmoplakin	protein-coding	0.013699	0.503401
Merged-chr2-180385691-2	chr2	180385616	180385766	+	3.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_045331)	promoter-TSS (NR_045331)	87	NR_045331	622283	Mm.447602	NR_045331		Gm6307	EG622283	predicted gene 6307	miscRNA	0.046667	0.622517
Merged-chr1-169531503-2	chr1	169531414	169531592	+	3.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_023284)	promoter-TSS (NM_023284)	-39	NM_023284	66977	Mm.151315	NM_023284	ENSMUSG00000026683	Nuf2	2410003C07Rik|AU044112|C85691|Cdca1|NUF2R	"NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"	protein-coding	0.095506	0.597765
Merged-chr12-83424791-2	chr12	83424737	83424846	+	3.15	cIP1vsInput|cIP2vsInput	"intron (NM_001267625, intron 1 of 10)"	"intron (NM_001267625, intron 1 of 10)"	62945	NM_001267626	70127	Mm.403230	NM_001267625	ENSMUSG00000021221	Dpf3	2810403B03Rik|6530402L11Rik|BAF45C|C78788|CERD4|cer-d4	"D4, zinc and double PHD fingers, family 3"	protein-coding	0.018349	0.527273
Merged-chrY-9047421-2	chrY	9047370	9047472	+	3.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-212252	NM_001017394	100039753	Mm.458473	NM_001017394	ENSMUSG00000096227	Gm20815	-	"predicted gene, 20815"	protein-coding	0.019608	0.291262
Merged-chr14-78732823-2	chr14	78732769	78732877	+	3.15	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-7734	NM_001081336	380921	Mm.379505	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16	"diacylglycerol kinase, eta"	protein-coding	0.12037	0.761468
Merged-chrX-164419613-2	chrX	164419554	164419672	+	3.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011081)	promoter-TSS (NM_011081)	-174	NM_011081	18700	Mm.401070	NM_011081	ENSMUSG00000031381	Piga	AI194334|Pig-a	"phosphatidylinositol glycan anchor biosynthesis, class A"	protein-coding	0.084746	0.596639
Merged-chr5-15678587-2	chr5	15678535	15678640	+	3.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-2123	NR_001585	75858	Mm.359463	NR_001585	ENSMUSG00000089871	Speer7-ps1	4930568L21Rik|SPEER-7|Speer7-ps	"spermatogenesis associated glutamate (E)-rich protein 7, pseudogene 1"	pseudo	0	0.339623
Merged-chr2-91070330-2	chr2	91070268	91070393	+	3.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026721)	promoter-TSS (NM_026721)	-109	NM_026721	68427	Mm.192375	NM_026721	ENSMUSG00000002105	Slc39a13	1100001L14Rik|AA387663|ZIP13	"solute carrier family 39 (metal ion transporter), member 13"	protein-coding	0.144	0.761905
Merged-chrY-6681927-2	chrY	6681873	6681982	+	3.15	cIP1vsInput|cIP2vsInput	Intergenic	B1_Mur4|SINE|Alu	485850	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.4
Merged-chr16-12697143-2	chr16	12697080	12697206	+	3.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-114247	NR_040507	75493	Mm.396146	NR_040507		1700003L19Rik	-	RIKEN cDNA 1700003L19 gene	miscRNA	0.047619	0.496063
Merged-chr14-45388925-2	chr14	45388865	45388985	+	3.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019425)	promoter-TSS (NM_019425)	-129	NM_019425	54342	Mm.312945	NM_019425	ENSMUSG00000037722	Gnpnat1	AU017428|AU040593|EMeg32|Gpnat1|Gsnpat	glucosamine-phosphate N-acetyltransferase 1	protein-coding	0.133333	0.752066
Merged-chr13-65349664-2	chr13	65349610	65349719	+	3.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	70810	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding	0	0.372727
Merged-chr15-77928817-2	chr15	77928755	77928880	+	3.15	cIP1vsInput|cIP2vsInput	"intron (NM_019913, intron 1 of 3)"	"intron (NM_019913, intron 1 of 3)"	177	NM_019913	56551	Mm.462887	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding	0.056	0.706349
Merged-chr8-20410246-2	chr8	20410196	20410296	+	3.15	cIP1vsInput|cIP2vsInput	"intron (NR_028428, intron 2 of 5)"	(TTTG)n|Simple_repeat|Simple_repeat	14568	NR_028428	381598	Mm.483074	NM_001024708	ENSMUSG00000071793	2610005L07Rik	2810038F24Rik|6720476A01Rik	cadherin 11 pseudogene	pseudo	0.01	0.336634
Merged-chr19-56397415-2	chr19	56397337	56397493	+	3.15	cIP1vsInput|cIP2vsInput	"intron (NM_007611, intron 1 of 6)"	CpG	286	NM_007611	12369	Mm.35687	NM_007611	ENSMUSG00000025076	Casp7	AI314680|CMH-1|ICE-IAP3|Mch3|caspase-7|mCASP-7	caspase 7	protein-coding	0.102564	0.707006
Merged-chr9-21723432-2	chr9	21723359	21723506	+	3.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010700)	promoter-TSS (NM_010700)	-144	NM_001252658	16835	Mm.3213	NM_001252658	ENSMUSG00000032193	Ldlr	Hlb301	low density lipoprotein receptor	protein-coding	0.061224	0.581081
Merged-chr9-62828547-2	chr9	62828475	62828619	+	3.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-10240	NM_001033175	76524	Mm.283636	NM_001033175	ENSMUSG00000032245	Cln6	1810065L06Rik|AW743417|D9Bwg1455e|nclf	"ceroid-lipofuscinosis, neuronal 6"	protein-coding	0.034722	0.510345
Merged-chr14-54883348-2	chr14	54883288	54883408	+	3.15	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007537)	promoter-TSS (NM_007537)	-77	NM_007537	12050	Mm.397611	NM_007537	ENSMUSG00000089682	Bcl2l2	AW048834|Bcl-w|Gtrgal2|Gtrosa41|bclw|c98	BCL2-like 2	protein-coding	0.041667	0.702479
Merged-chr7-24507599-2	chr7	24507538	24507661	+	3.15	cIP1vsInput|cIP2vsInput	"intron (NM_146183, intron 1 of 2)"	CpG	512	NM_146183	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding	0.065041	0.709677
Merged-chr13-102334430-2	chr13	102334370	102334491	+	3.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-359128	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding	0.041322	0.590164
Merged-chr13-12293897-2	chr13	12293840	12293955	+	3.15	cIP1vsInput|cIP2vsInput	"intron (NM_033268, intron 9 of 20)"	"intron (NM_033268, intron 9 of 20)"	-35784	NM_001081128	238505	Mm.40335	NM_001081128	ENSMUSG00000021311	Mtr	AI894170|D830038K18Rik|MS	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding	0.026087	0.543103
Merged-chr11-89186920-2	chr11	89186869	89186971	+	3.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	113079	NM_001033266	217071	Mm.342127	NM_001033266	ENSMUSG00000072553	Gm525	RP23-176J13.10	predicted gene 525	protein-coding	0.039216	0.582524
Merged-chr16-64873597-1	chr16	64873547	64873647	+	3.1	cIP2vsInput	Intergenic	Intergenic	21512	NM_178647	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding	0.04	0.564356
Merged-chr19-20867455-2	chr19	20867387	20867523	+	3.1	cIP1vsInput|cIP2vsInput	"intron (NM_028953, intron 7 of 20)"	"intron (NM_028953, intron 7 of 20)"	86747	NM_028953	13409	Mm.219585	NM_028953	ENSMUSG00000024749	Tmc1	4933416G09Rik|Beethoven|Bth|CWEA1|dn	transmembrane channel-like gene family 1	protein-coding	0	0.343066
Merged-chr1-68962927-1	chr1	68962877	68962977	+	3.1	cIP2vsInput	"intron (NM_010154, intron 1 of 26)"	"intron (NM_010154, intron 1 of 26)"	145132	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0	0.19802
Merged-chr19-13140810-1	chr19	13140760	13140860	+	3.1	cIP1vsInput	Intergenic	RLTR45-int|LTR|ERVK	5847	NM_146689	258684	Mm.377638	NM_146689	ENSMUSG00000057503	Olfr1459	MOR202-17	olfactory receptor 1459	protein-coding	0	0.277228
Merged-chrX-94969380-1	chrX	94969330	94969430	+	3.1	cIP2vsInput	Intergenic	B1_Mus1|SINE|Alu	57302	NM_178753	270624	Mm.115205	NM_178753	ENSMUSG00000071722	Spin4	9630042H07Rik	"spindlin family, member 4"	protein-coding	0.01	0.514851
Merged-chr2-114123572-1	chr2	114123522	114123622	+	3.1	cIP2vsInput	"intron (NM_009702, intron 23 of 34)"	"intron (NM_009702, intron 23 of 34)"	51767	NM_009702	11834	Mm.2545	NM_009702	ENSMUSG00000040383	Aqr	AW495846|mKIAA0560	aquarius	protein-coding	0	0.514851
Merged-chr5-15539965-1	chr5	15539915	15540015	+	3.1	cIP1vsInput	Intergenic	ETnERV3-int|LTR|ERVK	-79134	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0.02	0.336634
Merged-chr2-172863247-2	chr2	172863188	172863307	+	3.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	77074	NM_007557	12162	Mm.392150	NM_007557		Bmp7	OP1	bone morphogenetic protein 7	protein-coding	0.05042	0.583333
Merged-chr13-97071629-1	chr13	97071579	97071679	+	3.1	cIP1vsInput	promoter-TSS (NM_001100458)	promoter-TSS (NM_001100458)	-14	NM_001100458	320557	Mm.458280	NM_001100458	ENSMUSG00000041817	Fam169a	B230112C05Rik|SLAP75	"family with sequence similarity 169, member A"	protein-coding	0.23	0.821782
Merged-chr4-97923933-1	chr4	97923883	97923983	+	3.1	cIP1vsInput	"intron (NM_001122953, intron 2 of 9)"	"intron (NM_001122953, intron 2 of 9)"	146307	NM_010905	18027	Mm.409646	NM_001122952	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|NF1-A|NF1A	nuclear factor I/A	protein-coding	0	0.455446
Merged-chr9-12391389-1	chr9	12391339	12391439	+	3.1	cIP2vsInput	Intergenic	Intergenic	714466	NR_040755	78219	Mm.414868	NR_040755		4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	miscRNA	0	0.346535
Merged-chr6-134897750-1	chr6	134897700	134897800	+	3.1	cIP2vsInput	promoter-TSS (NM_001167695)	promoter-TSS (NM_001167695)	75	NM_001167695	14760	Mm.4787	NM_001167693	ENSMUSG00000032641	Gpr19	-	G protein-coupled receptor 19	protein-coding	0.06	0.49505
Merged-chr17-92831975-1	chr17	92831925	92832025	+	3.1	cIP1vsInput	Intergenic	Intergenic	-367447	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0	0.326733
Merged-chrX-101332866-2	chrX	101332813	101332919	+	3.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	33687	NM_172932	245537	Mm.121508	NM_172932		Nlgn3	A230085M13Rik|HNL3|NL3	neuroligin 3	protein-coding	0.169811	0.766355
Merged-chr13-119462574-1	chr13	119462524	119462624	+	3.1	cIP2vsInput	promoter-TSS (NM_001113550)	promoter-TSS (NM_001113550)	-185	NM_001113550	67392	Mm.390641	NM_001113550	ENSMUSG00000062822	4833420G17Rik	2210017J06Rik|5730533D17Rik|AW107518|C85193	RIKEN cDNA 4833420G17 gene	protein-coding	0.03	0.376238
Merged-chr5-146833045-1	chr5	146832995	146833095	+	3.1	cIP2vsInput	"5' UTR (NM_019647, exon 1 of 6)"	"5' UTR (NM_019647, exon 1 of 6)"	155	NM_019647	19933	Mm.440507	NM_019647	ENSMUSG00000041453	Rpl21	8430440E03Rik|L21	ribosomal protein L21	protein-coding	0.12	0.653465
Merged-chr10-53398738-1	chr10	53398688	53398788	+	3.1	cIP2vsInput	Intergenic	Intergenic	-18887	NM_001204983	100038725	Mm.441403	NM_001204983	ENSMUSG00000038594	Cep85l	ENSMUSG00000038594|Gm9766	centrosomal protein 85-like	protein-coding	0.03	0.534653
Merged-chr5-69794811-1	chr5	69794761	69794861	+	3.1	cIP2vsInput	Intergenic	Intergenic	-202526	NM_001038015	67980	Mm.33830	NM_001038015	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding	0.01	0.485149
Merged-chr18-13804745-1	chr18	13804695	13804795	+	3.1	cIP2vsInput	"intron (NM_145492, intron 5 of 7)"	"intron (NM_145492, intron 5 of 7)"	167988	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding	0.01	0.524752
Merged-chr16-30599732-1	chr16	30599682	30599782	+	3.1	cIP2vsInput	promoter-TSS (NM_177632)	promoter-TSS (NM_177632)	9	NM_177632	224093	Mm.28244	NM_177632	ENSMUSG00000046546	Fam43a	Tuf1	"family with sequence similarity 43, member A"	protein-coding	0.13	0.623762
Merged-chr7-29954277-1	chr7	29954227	29954327	+	3.1	cIP2vsInput	Intergenic	Intergenic	-2384	NM_178384	72723	Mm.371648	NM_178384	ENSMUSG00000059975	Zfp74	2810054M15Rik|KRAB8|Zfp66|Znf569|mszf21|mszf77	zinc finger protein 74	protein-coding	0.02	0.514851
Merged-chr14-86808488-1	chr14	86808438	86808538	+	3.1	cIP2vsInput	"intron (NM_019670, intron 25 of 27)"	"intron (NM_019670, intron 25 of 27)"	332626	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diap3	4930417P13Rik|Dia2|Diaph3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous homolog 3 (Drosophila)	protein-coding	0	0.316832
Merged-chr2-152406358-1	chr2	152406308	152406408	+	3.1	cIP2vsInput	Intergenic	Intergenic	-8312	NM_011438	20667	Mm.28424	NM_011438		Sox12	2010205A02Rik	SRY-box containing gene 12	protein-coding	0.06	0.70297
Merged-chr3-107279011-1	chr3	107278961	107279061	+	3.1	cIP2vsInput	"exon (NM_026774, exon 1 of 4)"	"exon (NM_026774, exon 1 of 4)"	153	NM_026774	68576	Mm.290035	NM_026774	ENSMUSG00000087260	Lamtor5	1110003H18Rik|Hbxip|XIP	"late endosomal/lysosomal adaptor, MAPK and MTOR activator 5"	protein-coding	0.1	0.653465
Merged-chr11-49846584-1	chr11	49846534	49846634	+	3.1	cIP2vsInput	promoter-TSS (NM_016961)	promoter-TSS (NM_016961)	-167	NM_001163671	26420	Mm.68933	NM_001163671	ENSMUSG00000020366	Mapk9	AI851083|JNK2|Prkm9|p54aSAPK	mitogen-activated protein kinase 9	protein-coding	0.1	0.70297
Merged-chr5-23783693-1	chr5	23783643	23783743	+	3.1	cIP2vsInput	promoter-TSS (NM_178403)	promoter-TSS (NM_178403)	-32	NM_178403	78697	Mm.58660	NM_178403	ENSMUSG00000057541	Pus7	C330017I15Rik	pseudouridylate synthase 7 homolog (S. cerevisiae)	protein-coding	0.17	0.811881
Merged-chr12-31351659-1	chr12	31351609	31351709	+	3.1	cIP2vsInput	promoter-TSS (NM_007861)	promoter-TSS (NM_007861)	-222	NM_007861	13382	Mm.3131	NM_007861	ENSMUSG00000020664	Dld	AI315664|AI746344	dihydrolipoamide dehydrogenase	protein-coding	0	0.306931
Merged-chr5-30921389-1	chr5	30921339	30921439	+	3.1	cIP2vsInput	promoter-TSS (NM_008439)	promoter-TSS (NM_008439)	-506	NM_008439	16548	Mm.22451	NM_008439	ENSMUSG00000029162	Khk	-	ketohexokinase	protein-coding	0.06	0.643564
Merged-chr14-103070196-1	chr14	103070146	103070246	+	3.1	cIP2vsInput	promoter-TSS (NM_001033242)	promoter-TSS (NM_001033242)	-20	NM_001033242	211286	Mm.295289	NM_001033242	ENSMUSG00000022125	Cln5	A730075N08Rik	"ceroid-lipofuscinosis, neuronal 5"	protein-coding	0.14	0.742574
Merged-chr1-11329755-1	chr1	11329705	11329805	+	3.1	cIP1vsInput	Intergenic	Intergenic	65792	NM_001033636	109294	Mm.123247	XM_003946036	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	"phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2"	protein-coding	0.06	0.584158
Merged-chr9-107627029-1	chr9	107626979	107627079	+	3.1	cIP2vsInput	"intron (NM_008138, intron 1 of 8)"	"intron (NM_008138, intron 1 of 8)"	8313	NM_008138	14678	Mm.196464	NM_008138	ENSMUSG00000032562	Gnai2	C76432|Galphai2|Gia|Gnai-2	"guanine nucleotide binding protein (G protein), alpha inhibiting 2"	protein-coding	0.01	0.633663
Merged-chr9-65294200-1	chr9	65294150	65294250	+	3.1	cIP1vsInput	promoter-TSS (NM_011802)	promoter-TSS (NM_011802)	-95	NM_001044389	270166	Mm.30088	NM_001044389	ENSMUSG00000015357	Clpx	AU014732|E330029I21	caseinolytic peptidase X (E.coli)	protein-coding	0.13	0.673267
Merged-chr14-76811316-2	chr14	76811250	76811383	+	3.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	133748	NR_015485	73272	Mm.116804	NR_015485		1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	miscRNA	0.015038	0.5
Merged-chr5-59434171-1	chr5	59434121	59434221	+	3.1	cIP1vsInput	Intergenic	Intergenic	551831	NR_040683	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0	0.316832
Merged-chr15-31423241-2	chr15	31423177	31423306	+	3.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	30448	NM_145852	252967	Mm.436668	NM_145852	ENSMUSG00000022236	Ropn1l	ASP|AV047578|Akapasp	ropporin 1-like	protein-coding	0.007752	0.5
Merged-chr8-28486314-1	chr8	28486264	28486364	+	3.1	cIP1vsInput	Intergenic	Intergenic	-401461	NR_033590	666422	Mm.484413	NR_033590		Gm8096	EG666422	3-phosphoglycerate dehydrogenase pseudogene	pseudo	0	0.346535
Merged-chr11-78751603-1	chr11	78751553	78751653	+	3.1	cIP2vsInput	"exon (NM_197989, exon 1 of 1)"	"exon (NM_197989, exon 1 of 1)"	126	NM_197989	69109		NM_197989	ENSMUSG00000049489	Fam58b	1810009O10Rik|Fam58a	"family with sequence similarity 58, member B"	protein-coding	0.14	0.693069
Merged-chr8-70629918-1	chr8	70629868	70629968	+	3.1	cIP2vsInput	"exon (NM_011819, exon 2 of 2)"	"exon (NM_011819, exon 2 of 2)"	1717	NM_011819	23886	Mm.31325	NM_011819		Gdf15	MIC-1|NAG-1|SBF	growth differentiation factor 15	protein-coding	0.12	0.712871
Merged-chr16-4077900-1	chr16	4077850	4077950	+	3.1	cIP2vsInput	promoter-TSS (NM_026508)	promoter-TSS (NM_026508)	-90	NM_026508	68015	Mm.123366	NM_026508	ENSMUSG00000005981	Trap1	2410002K23Rik|HSP75	TNF receptor-associated protein 1	protein-coding	0.12	0.633663
Merged-chr2-91730093-2	chr2	91730021	91730165	+	3.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001080754)	promoter-TSS (NM_001080754)	-45	NM_172669	228361	Mm.436667	NM_001080754	ENSMUSG00000040506	Ambra1	2310079H06Rik|A130023A14|AA474864|AV021921|D030051N19Rik|mKIAA1736	autophagy/beclin 1 regulator 1	protein-coding	0.055556	0.510345
Merged-chr13-65112934-1	chr13	65112884	65112984	+	3.1	cIP2vsInput	promoter-TSS (NM_133680)	promoter-TSS (NM_133680)	48	NM_001083901	66631	Mm.239196	NM_001083901	ENSMUSG00000038212	Hiatl1	5730414C17Rik|AU045608|AW539692	hippocampus abundant transcript-like 1	protein-coding	0.1	0.683168
Merged-chr7-19094218-1	chr7	19094168	19094268	+	3.1	cIP2vsInput	promoter-TSS (NM_011383)	promoter-TSS (NM_011383)	-326	NM_011383	20475	Mm.3410	NM_011383	ENSMUSG00000040841	Six5	Dmahp|MDMAHP|TrexBF	sine oculis-related homeobox 5	protein-coding	0.12	0.712871
Merged-chr2-106974465-1	chr2	106974415	106974515	+	3.1	cIP2vsInput	promoter-TSS (NM_001025102)	promoter-TSS (NM_001025102)	-68	NM_001025102	212772	Mm.470117	NM_001025102	ENSMUSG00000027122	Arl14ep	2700007P21Rik|4930448O08Rik|ARF7EP	ADP-ribosylation factor-like 14 effector protein	protein-coding	0.05	0.673267
Merged-chrY-6735706-1	chrY	6735656	6735756	+	3.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	432071	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.356436
Merged-chr13-91068348-1	chr13	91068298	91068398	+	3.1	cIP2vsInput	"intron (NM_025770, intron 3 of 7)"	L1_Mus4|LINE|L1	145226	NM_024175	66475	Mm.306302	NM_024175		Rps23	2410044J15Rik	ribosomal protein S23	protein-coding	0	0.316832
Merged-chr11-102245373-1	chr11	102245323	102245423	+	3.1	cIP2vsInput	Intergenic	Intergenic	-3509	NM_153544	217216	Mm.247335	NM_153544	ENSMUSG00000034773	BC030867	-	cDNA sequence BC030867	protein-coding	0.09	0.60396
Merged-chr10-17291791-1	chr10	17291741	17291841	+	3.1	cIP1vsInput	Intergenic	Intergenic	-196009	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0.01	0.316832
Merged-chr3-89213907-1	chr3	89213857	89213957	+	3.1	cIP2vsInput	"exon (NM_013604, exon 1 of 8)"	"exon (NM_013604, exon 1 of 8)"	428	NM_001161824	17827	Mm.280943	NM_001161824	ENSMUSG00000064068	Mtx1	Gcap6|Mtx	metaxin 1	protein-coding	0.09	0.633663
Merged-chr15-55557392-1	chr15	55557342	55557442	+	3.1	cIP2vsInput	promoter-TSS (NM_026759)	promoter-TSS (NM_026759)	-16	NM_134092	105837	Mm.390829	NM_001168250	ENSMUSG00000022369	Mtbp	AI429604|MDM2BP	"Mdm2, transformed 3T3 cell double minute p53 binding protein"	protein-coding	0.12	0.673267
Merged-chr2-181319703-1	chr2	181319653	181319753	+	3.1	cIP2vsInput	promoter-TSS (NM_001166666)	promoter-TSS (NM_001166666)	-21	NM_001166665	269400	Mm.11333	NM_001001882	ENSMUSG00000038685	Rtel1	AI451565|AW540478|Rtel	regulator of telomere elongation helicase 1	protein-coding	0.1	0.60396
Merged-chr12-34146405-1	chr12	34146355	34146455	+	3.1	cIP2vsInput	"intron (NM_001271386, intron 24 of 27)"	"intron (NM_001271386, intron 24 of 27)"	188734	NM_011658	22160	Mm.3280	NM_011658	ENSMUSG00000035799	Twist1	AA960487|M-Twist|Pde|Ska10|Ska<m10Jus>|Twist|bHLHa38|pdt	twist basic helix-loop-helix transcription factor 1	protein-coding	0	0.356436
Merged-chr5-31526657-1	chr5	31526607	31526707	+	3.1	cIP2vsInput	promoter-TSS (NM_009206)	promoter-TSS (NM_009206)	105	NM_028150	72195	Mm.164187	NM_028150	ENSMUSG00000053134	Supt7l	2610524B01Rik|6030455L14Rik	suppressor of Ty 7-like	protein-coding	0.05	0.554455
Merged-chr14-46787811-1	chr14	46787761	46787861	+	3.1	cIP2vsInput	"intron (NM_009919, intron 1 of 4)"	"intron (NM_009919, intron 1 of 4)"	546	NM_009919	12793	Mm.3261	NM_009919	ENSMUSG00000015759	Cnih	0610007J15	cornichon homolog (Drosophila)	protein-coding	0.08	0.485149
Merged-chr18-54626425-1	chr18	54626375	54626475	+	3.1	cIP1vsInput	"intron (NR_045400, intron 1 of 2)"	MIR|SINE|MIR	14681	NR_045400	328957	Mm.402781	NR_045400		9330117O12Rik	9330117O12	RIKEN cDNA 9330117O12 gene	miscRNA	0	0.386139
Merged-chr8-106338258-1	chr8	106338208	106338308	+	3.1	cIP1vsInput	promoter-TSS (NM_021491)	promoter-TSS (NM_021491)	-270	NM_021491	58994	Mm.23298	NM_021491	ENSMUSG00000031906	Smpd3	4631433G07Rik|AI427456|AW537966|fro|nSMase2	"sphingomyelin phosphodiesterase 3, neutral"	protein-coding	0.02	0.633663
Merged-chr8-9423876-1	chr8	9423826	9423926	+	3.1	cIP2vsInput	"intron (NM_173446, intron 1 of 2)"	L1MA6|LINE|L1	279207	NR_073360	74688	Mm.159298	NR_073360		4930453L07Rik	-	RIKEN cDNA 4930453L07 gene	miscRNA	0.03	0.475248
Merged-chr11-83942214-1	chr11	83942164	83942264	+	3.1	cIP2vsInput	"exon (NM_030096, exon 1 of 15)"	"exon (NM_030096, exon 1 of 15)"	124	NM_030096	78394	Mm.280544	NM_030096	ENSMUSG00000020677	Ddx52	2700029C06Rik|ROK1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	protein-coding	0.1	0.574257
Merged-chr2-163419903-1	chr2	163419853	163419953	+	3.1	cIP2vsInput	promoter-TSS (NM_025699)	promoter-TSS (NM_025699)	-433	NM_025699	66680	Mm.390370	NM_025699	ENSMUSG00000035399	3230401D17Rik	AI256769|Perit1|RP23-297J14.5	RIKEN cDNA 3230401D17 gene	protein-coding	0.06	0.584158
Merged-chr3-106133092-1	chr3	106133042	106133142	+	3.1	cIP1vsInput	TTS (NM_023186)	TTS (NM_023186)	19710	NM_023186	81600	Mm.46418	NM_023186	ENSMUSG00000062778	Chia	2200003E03Rik|AMCase|YNL	"chitinase, acidic"	protein-coding	0	0.356436
Merged-chr17-48002116-1	chr17	48002066	48002166	+	3.1	cIP2vsInput	Intergenic	Intergenic	36177	NM_029689	76651	Mm.76918	NM_029689	ENSMUSG00000094928	1700122O11Rik	-	RIKEN cDNA 1700122O11 gene	protein-coding	0.02	0.554455
Merged-chr17-87044670-1	chr17	87044620	87044720	+	3.1	cIP2vsInput	Intergenic	Intergenic	19109	NM_019936	56724	Mm.109329	NM_019936	ENSMUSG00000024146	Cript	1200020A08Rik|AA589469	cysteine-rich PDZ-binding protein	protein-coding	0.04	0.49505
Merged-chr5-138187199-1	chr5	138187149	138187249	+	3.1	cIP2vsInput	promoter-TSS (NM_009315)	promoter-TSS (NM_009315)	-13	NM_009315	21343	Mm.248517	NM_009315	ENSMUSG00000036980	Taf6	80kDa|AW549759|TAF(II)80|TAFII70|Taf2e|p80	"TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor"	protein-coding	0.08	0.683168
Merged-chr12-54313776-2	chr12	54313717	54313835	+	3.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	77542	NR_033689	665239	Mm.26856	NR_033689		Gm7550	EG665239|Gm666	predicted gene 7550	miscRNA	0.025424	0.428571
Merged-chr6-83101431-1	chr6	83101381	83101481	+	3.1	cIP2vsInput	promoter-TSS (NM_001081266)	promoter-TSS (NM_001081266)	-85	NM_001081266	243510	Mm.436553	NM_001081266	ENSMUSG00000079511	Ccdc142	A230058J24Rik	coiled-coil domain containing 142	protein-coding	0.04	0.544554
Merged-chr4-139352352-1	chr4	139352302	139352402	+	3.1	cIP2vsInput	promoter-TSS (NM_146157)	promoter-TSS (NM_146157)	-54	NM_023536	69902	Mm.441201	NM_023536	ENSMUSG00000028741	Mrto4	2610012O22Rik|Mg684|Mrt4	"MRT4, mRNA turnover 4, homolog (S. cerevisiae)"	protein-coding	0.13	0.732673
Merged-chr4-107367928-1	chr4	107367878	107367978	+	3.1	cIP2vsInput	"5' UTR (NM_028355, exon 1 of 18)"	"5' UTR (NM_028355, exon 1 of 18)"	144	NM_028355	72787	Mm.28478	NM_028355		Tmem48	2810475A17Rik|AI450313|NDC1	transmembrane protein 48	protein-coding	0.05	0.623762
Merged-chr6-8472978-1	chr6	8472928	8473028	+	3.1	cIP2vsInput	Intergenic	L2c|LINE|L2	36183	NR_040452	320312	Mm.374890	NR_040452	ENSMUSG00000087305	A430035B10Rik	2810488G03Rik	RIKEN cDNA A430035B10 gene	miscRNA	0.02	0.485149
Merged-chr2-119288657-1	chr2	119288607	119288707	+	3.1	cIP2vsInput	promoter-TSS (NM_172269)	promoter-TSS (NM_172269)	-85	NM_172269	228545	Mm.294761	NM_172269	ENSMUSG00000034216	Vps18	9930024E13Rik	vacuolar protein sorting 18 (yeast)	protein-coding	0.08	0.683168
Merged-chr5-135806804-1	chr5	135806754	135806854	+	3.1	cIP2vsInput	Intergenic	Intergenic	-11302	NM_021403	58212	Mm.271230	NM_021403	ENSMUSG00000039860	Srrm3	2900083I11Rik|AB041661|SRm300-like|Srrm2l	serine/arginine repetitive matrix 3	protein-coding	0.06	0.643564
Merged-chr1-191802911-1	chr1	191802861	191802961	+	3.1	cIP1vsInput	Intergenic	Intergenic	-18562	NM_010892	18005	Mm.403999	NM_010892	ENSMUSG00000026622	Nek2	AA617254|C77054	NIMA (never in mitosis gene a)-related expressed kinase 2	protein-coding	0.03	0.49505
Merged-chr7-141693658-2	chr7	141693588	141693729	+	3.1	cIP1vsInput|cIP2vsInput	"exon (NM_023566, exon 6 of 46)"	"exon (NM_023566, exon 6 of 46)"	3318	NM_023566	17831	Mm.461296	XM_003688839		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding	0.113475	0.690141
Merged-chr5-61566238-1	chr5	61566188	61566288	+	3.1	cIP2vsInput	Intergenic	Intergenic	-242605	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding	0	0.326733
Merged-chr7-101158542-1	chr7	101158492	101158592	+	3.1	cIP2vsInput	"intron (NM_199012, intron 3 of 20)"	"intron (NM_199012, intron 3 of 20)"	49767	NM_199012	207278	Mm.263041	NM_001146010	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding	0	0.29703
Merged-chr3-89411851-1	chr3	89411801	89411901	+	3.1	cIP2vsInput	promoter-TSS (NM_177041)	promoter-TSS (NM_177041)	12	NM_177041	319945	Mm.258142	NM_177041	ENSMUSG00000042642	Flad1	A930017E24Rik|Pp591	"RFad1, flavin adenine dinucleotide synthetase, homolog (yeast)"	protein-coding	0.05	0.524752
Merged-chr13-99344740-1	chr13	99344690	99344790	+	3.1	cIP2vsInput	promoter-TSS (NM_026873)	promoter-TSS (NM_026873)	-46	NM_173757	218506	Mm.30208	NM_173757	ENSMUSG00000041632	Mrps27	2610028H14Rik	mitochondrial ribosomal protein S27	protein-coding	0.07	0.712871
Merged-chr4-134186967-1	chr4	134186917	134187017	+	3.1	cIP2vsInput	"5' UTR (NM_144527, exon 1 of 14)"	"5' UTR (NM_144527, exon 1 of 14)"	118	NM_144527	70012	Mm.26542	NM_144527	ENSMUSG00000037443	Cep85	2410030J07Rik|AI173272|AI173504|Ccdc21	centrosomal protein 85	protein-coding	0.1	0.653465
Merged-chr3-94442830-1	chr3	94442780	94442880	+	3.1	cIP1vsInput	promoter-TSS (NM_030116)	promoter-TSS (NM_030116)	-506	NM_030116	78523	Mm.218515	NM_030116	ENSMUSG00000028140	Mrpl9	8030480E20Rik|AA409733|C330013D18Rik|L9mt	mitochondrial ribosomal protein L9	protein-coding	0	0.326733
Merged-chr2-52306757-1	chr2	52306707	52306807	+	3.1	cIP1vsInput	"intron (NM_010889, intron 17 of 156)"	"intron (NM_010889, intron 17 of 156)"	15755	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	miscRNA	0	0.445545
Merged-chr6-86365707-1	chr6	86365657	86365757	+	3.1	cIP2vsInput	promoter-TSS (NM_025591)	promoter-TSS (NM_025591)	24	NM_025591	66488	Mm.422972	NM_025591	ENSMUSG00000057497	Fam136a	2010309E21Rik|AW124904|Hyccin	"family with sequence similarity 136, member A"	protein-coding	0.15	0.782178
Merged-chr1-74397557-1	chr1	74397507	74397607	+	3.1	cIP2vsInput	TTS (NM_153088)	TTS (NM_153088)	3247	NR_029743	387219		NR_029743		Mir26b	Mirn26b|mmu-mir-26b	microRNA 26b	miscRNA	0.05	0.683168
Merged-chr6-50358250-1	chr6	50358200	50358300	+	3.1	cIP2vsInput	"intron (NM_027881, intron 2 of 21)"	"intron (NM_027881, intron 2 of 21)"	24587	NM_027881	71720	Mm.44153	NM_001163645	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding	0.06	0.643564
Merged-chr16-86090103-1	chr16	86090053	86090153	+	3.1	cIP2vsInput	Intergenic	Intergenic	-188978	NM_011782	23794	Mm.437478	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|AI481094|ASMP-2	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"	protein-coding	0	0.316832
Merged-chr2-144280033-1	chr2	144279983	144280083	+	3.1	cIP2vsInput	"3' UTR (NM_028984, exon 5 of 5)"	"3' UTR (NM_028984, exon 5 of 5)"	8998	NM_028984	74528	Mm.386817	NM_028984	ENSMUSG00000027424	Mgme1	8430406I07Rik|AI426476	mitochondrial genome maintainance exonuclease 1	protein-coding	0.02	0.574257
Merged-chr4-125590727-2	chr4	125590669	125590785	+	3.1	cIP1vsInput|cIP2vsInput	"intron (NM_001081097, intron 1 of 15)"	"intron (NM_001081097, intron 1 of 15)"	99896	NM_001081097	14807	Mm.40896	NM_001081097	ENSMUSG00000001985	Grik3	9630027E11|GluK3|GluR7-3|Glur-7|Glur7	"glutamate receptor, ionotropic, kainate 3"	protein-coding	0.051724	0.615385
Merged-chr11-84819581-2	chr11	84819513	84819650	+	3.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145433)	promoter-TSS (NM_145433)	-66	NM_145433	217038	Mm.280825	NM_145433	ENSMUSG00000018405	Mrm1	A530065E19Rik|ENSMUSG00000054212	mitochondrial rRNA methyltransferase 1 homolog (S. cerevisiae)	protein-coding	0.072993	0.666667
Merged-chr18-60526192-1	chr18	60526142	60526242	+	3.1	cIP2vsInput	promoter-TSS (NM_026302)	promoter-TSS (NM_026302)	-29	NM_026302	67665	Mm.272801	NM_026302	ENSMUSG00000024603	Dctn4	1110001K06Rik|4930547K17Rik|C130039E17Rik|p62	dynactin 4	protein-coding	0.12	0.683168
Merged-chr10-70855136-1	chr10	70855086	70855186	+	3.1	cIP2vsInput	Intergenic	Intergenic	-199173	NR_045292	319646	Mm.483039	NR_045291	ENSMUSG00000037747	D630013N20Rik	-	RIKEN cDNA D630013N20 gene	miscRNA	0.01	0.366337
Merged-chr16-10785188-1	chr16	10785138	10785238	+	3.1	cIP2vsInput	"intron (NM_001271603, intron 1 of 1)"	CpG	348	NM_001271603	12703	Mm.130	NM_001271603	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding	0.12	0.762376
Merged-chr3-74317133-1	chr3	74317083	74317183	+	3.1	cIP2vsInput	Intergenic	Intergenic	-299856	NR_040450	100504692	Mm.394454	NR_040450		Gm20356	-	"predicted gene, 20356"	miscRNA	0.01	0.287129
Merged-chr8-34097601-1	chr8	34097551	34097651	+	3.1	cIP2vsInput	"intron (NM_011722, intron 2 of 6)"	"intron (NM_011722, intron 2 of 6)"	10910	NM_011722	22428	Mm.150373	NM_011722		Dctn6	AU044699|WS-3|p27	dynactin 6	protein-coding	0.05	0.514851
Merged-chr17-32166120-1	chr17	32166070	32166170	+	3.1	cIP1vsInput	"intron (NM_008716, intron 1 of 32)"	CpG	732	NM_008716	18131	Mm.439741	NM_008716	ENSMUSG00000038146	Notch3	AW229011|N3|hpbk	notch 3	protein-coding	0.11	0.712871
Merged-chr7-126695908-1	chr7	126695858	126695958	+	3.1	cIP2vsInput	promoter-TSS (NM_029420)	promoter-TSS (NM_029420)	-92	NM_175103	66162	Mm.358692	NM_175103		Bola2	1110025L05Rik|BolA-2	bolA-like 2 (E. coli)	protein-coding	0.06	0.643564
Merged-chr11-102393420-1	chr11	102393370	102393470	+	3.1	cIP2vsInput	promoter-TSS (NM_001252347)	promoter-TSS (NM_001252347)	17	NM_001252347	51799	Mm.2560	NM_001252347	ENSMUSG00000006575	Rundc3a	RPIP-8|Rap2ip|Rpip8	RUN domain containing 3A	protein-coding	0.1	0.742574
Merged-chr11-100414814-1	chr11	100414764	100414864	+	3.1	cIP1vsInput	promoter-TSS (NM_176830)	promoter-TSS (NM_176830)	5	NM_176830	66180	Mm.4940	NM_176830	ENSMUSG00000006931	Leprel4	1110036O03Rik|AI413214|Sc65	leprecan-like 4	protein-coding	0.08	0.643564
Merged-chr13-55536822-1	chr13	55536772	55536872	+	3.1	cIP1vsInput	promoter-TSS (NM_134059)	promoter-TSS (NM_134059)	-164	NM_134059	72935	Mm.205045	NM_134059	ENSMUSG00000021494	Ddx41	2900024F02Rik|AA958953|ABS|AI324246	DEAD (Asp-Glu-Ala-Asp) box polypeptide 41	protein-coding	0.08	0.554455
Merged-chr15-6206834-1	chr15	6206784	6206884	+	3.1	cIP2vsInput	Intergenic	Intergenic	-92955	NM_001008702	13132	Mm.240830	NM_001008702	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	"disabled 2, mitogen-responsive phosphoprotein"	protein-coding	0	0.336634
Merged-chr9-95709941-1	chr9	95709891	95709991	+	3.1	cIP1vsInput	"intron (NM_011643, intron 10 of 12)"	"intron (NM_011643, intron 10 of 12)"	40417	NM_011643	22063	Mm.149633	NM_011643	ENSMUSG00000032839	Trpc1	Mtrp1|Trp1|Trrp1	"transient receptor potential cation channel, subfamily C, member 1"	protein-coding	0	0.316832
Merged-chr6-99340816-1	chr6	99340766	99340866	+	3.1	cIP1vsInput	"intron (NM_053202, intron 1 of 18)"	"intron (NM_053202, intron 1 of 18)"	-74301	NM_001197321	108655	Mm.485266	NM_001197321	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding	0	0.326733
Merged-chr9-54734493-1	chr9	54734443	54734543	+	3.1	cIP2vsInput	promoter-TSS (NM_023191)	promoter-TSS (NM_023191)	1	NM_001025375	66317	Mm.28437	NM_001025375	ENSMUSG00000061559	Wdr61	2700038L12Rik|2810418I05Rik|REC14	WD repeat domain 61	protein-coding	0.08	0.633663
Merged-chr6-91515977-1	chr6	91515927	91516027	+	3.1	cIP2vsInput	promoter-TSS (NM_026309)	promoter-TSS (NM_026309)	-58	NM_026309	67678	Mm.410956	NM_026309	ENSMUSG00000034192	Lsm3	1010001J12Rik|2610005D18Rik|6030401D18Rik|SMX4|USS2	"LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)"	protein-coding	0.08	0.564356
Merged-chr5-24733297-1	chr5	24733247	24733347	+	3.1	cIP2vsInput	Intergenic	Intergenic	-2617	NM_001081441	269633	Mm.392539	NM_026621		Wdr86	2810046M22Rik|BC059069	WD repeat domain 86	protein-coding	0.03	0.544554
Merged-chr8-69774819-1	chr8	69774769	69774869	+	3.1	cIP2vsInput	promoter-TSS (NM_177899)	promoter-TSS (NM_177899)	92	NM_177899	330788	Mm.41364	NM_177899		Zfp866	9830167H18Rik|AI875089|C85843|D330038O06Rik	zinc finger protein 866	protein-coding	0.1	0.693069
Merged-chr1-171287918-2	chr1	171287865	171287972	+	3.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013919)	promoter-TSS (NM_013919)	43	NM_013919	30941	Mm.27510	NM_013919	ENSMUSG00000053483	Usp21	ESTM28|Usp16|Usp23|W53272	ubiquitin specific peptidase 21	protein-coding	0.093458	0.685185
Merged-chr7-99535124-1	chr7	99535074	99535174	+	3.1	cIP2vsInput	promoter-TSS (NM_178220)	promoter-TSS (NM_178220)	-362	NM_178220	109689	Mm.260193	NM_177231	ENSMUSG00000018909	Arrb1	1200006I17Rik|AW208571|G430100A01Rik	"arrestin, beta 1"	protein-coding	0.04	0.594059
Merged-chr14-25467709-1	chr14	25467659	25467759	+	3.1	cIP1vsInput	"intron (NM_183208, intron 1 of 23)"	"intron (NM_183208, intron 1 of 23)"	8524	NM_183208	328365	Mm.486339	NM_001033402	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	"zinc finger, MIZ-type containing 1"	protein-coding	0.01	0.435644
Merged-chr1-12416607-1	chr1	12416557	12416657	+	3.1	cIP2vsInput	Intergenic	Intergenic	-250956	NR_045297	329096	Mm.417782	NR_045297	ENSMUSG00000097171	Gm17644	4932411L15	"predicted gene, 17644"	miscRNA	0	0.405941
Merged-chr5-16997176-1	chr5	16997126	16997226	+	3.1	cIP1vsInput	Intergenic	ID_B1|SINE|B4	443626	NM_010427	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF/HGF	hepatocyte growth factor	protein-coding	0	0.376238
Merged-chr12-111908275-1	chr12	111908225	111908325	+	3.1	cIP2vsInput	promoter-TSS (NM_011625)	promoter-TSS (NM_011625)	-220	NM_011625	21981	Mm.313076	NM_011625	ENSMUSG00000021285	Ppp1r13b	AI449786|ASPP1|AW545810|Tp53bp2|Trp53bp2|p85	"protein phosphatase 1, regulatory (inhibitor) subunit 13B"	protein-coding	0.16	0.762376
Merged-chr1-10214604-1	chr1	10214554	10214654	+	3.1	cIP2vsInput	"intron (NM_001102430, intron 3 of 37)"	"intron (NM_001102430, intron 3 of 37)"	18066	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding	0	0.287129
Merged-chr10-67537677-1	chr10	67537627	67537727	+	3.1	cIP2vsInput	promoter-TSS (NM_010118)	promoter-TSS (NM_010118)	-192	NM_010118	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding	0.09	0.712871
Merged-chr14-32531081-2	chr14	32531023	32531140	+	3.1	cIP1vsInput|cIP2vsInput	"intron (NM_001081221, intron 5 of 20)"	"intron (NM_001081221, intron 5 of 20)"	17560	NM_001081221	319955	Mm.318310	NM_001081221	ENSMUSG00000054051	Ercc6	4732403I04|C130058G22Rik|CSB	"excision repair cross-complementing rodent repair deficiency, complementation group 6"	protein-coding	0.017094	0.483051
Merged-chr13-21090111-1	chr13	21090061	21090161	+	3.1	cIP2vsInput	Intergenic	Intergenic	-16812	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding	0	0.316832
Merged-chr5-15554569-1	chr5	15554519	15554619	+	3.1	cIP2vsInput	Intergenic	Intergenic	-64530	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0.01	0.386139
Merged-chr2-52571823-1	chr2	52571773	52571873	+	3.1	cIP1vsInput	"intron (NM_001037099, intron 2 of 13)"	"intron (NM_001037099, intron 2 of 13)"	-13256	NM_146123	12298	Mm.330223	NM_001037099	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lethargic|lh	"calcium channel, voltage-dependent, beta 4 subunit"	protein-coding	0.02	0.514851
Merged-chr16-14445315-2	chr16	14445261	14445370	+	3.1	cIP1vsInput|cIP2vsInput	"exon (NM_008576, exon 17 of 31)"	"exon (NM_008576, exon 17 of 31)"	83757	NM_008576	17250	Mm.196634	NM_008576	ENSMUSG00000023088	Abcc1	Abcc1a|Abcc1b|MRP|Mdrap|Mrp1	"ATP-binding cassette, sub-family C (CFTR/MRP), member 1"	protein-coding	0.027523	0.581818
Merged-chr9-6676435-1	chr9	6676385	6676485	+	3.1	cIP2vsInput	Intergenic	Intergenic	-409888	NM_027942	71829	Mm.141452	NM_027942	ENSMUSG00000047619	Ddi1	1700011N24Rik	"DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)"	protein-coding	0	0.326733
Merged-chr2-136678735-1	chr2	136678685	136678785	+	3.1	cIP2vsInput	Intergenic	CpG	-34715	NM_011428	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|SNAP-25|sp	synaptosomal-associated protein 25	protein-coding	0.1	0.762376
Merged-chr13-102905139-1	chr13	102905089	102905189	+	3.1	cIP1vsInput	"intron (NM_175171, intron 4 of 28)"	"intron (NM_175171, intron 4 of 28)"	211581	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding	0.01	0.306931
Merged-chr3-88913841-1	chr3	88913791	88913891	+	3.1	cIP2vsInput	"exon (NM_144898, exon 1 of 14)"	"exon (NM_144898, exon 1 of 14)"	109	NM_144898	229524	Mm.440405	NM_144898	ENSMUSG00000068922	Msto1	BC008103|mst	misato homolog 1 (Drosophila)	protein-coding	0.11	0.683168
Merged-chr3-37464327-1	chr3	37464277	37464377	+	3.1	cIP2vsInput	"intron (NM_001163511, intron 13 of 15)"	"intron (NM_001163511, intron 13 of 15)"	44047	NM_021343	57815	Mm.172679	NM_001163511	ENSMUSG00000027722	Spata5	2510048F20Rik|C78064|Spaf	spermatogenesis associated 5	protein-coding	0	0.29703
Merged-chr7-141902696-1	chr7	141902646	141902746	+	3.1	cIP2vsInput	promoter-TSS (NM_023764)	promoter-TSS (NM_023764)	-290	NM_023764	54473	Mm.103551	NM_023764	ENSMUSG00000025139	Tollip	4930403G24Rik|4931428G15Rik	toll interacting protein	protein-coding	0.06	0.574257
Merged-chr1-142009900-1	chr1	142009850	142009950	+	3.1	cIP2vsInput	Intergenic	Intergenic	-1353498	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0	0.29703
Merged-chr11-64079441-1	chr11	64079391	64079491	+	3.1	cIP2vsInput	promoter-TSS (NR_033780)	promoter-TSS (NR_033780)	31	NM_178379	70383	Mm.340211	NM_178379	ENSMUSG00000042148	Cox10	2410004F01Rik|AU042636	cytochrome c oxidase assembly protein 10	protein-coding	0.06	0.683168
Merged-chr5-118128372-1	chr5	118128322	118128422	+	3.1	cIP2vsInput	"intron (NM_172721, intron 3 of 10)"	"intron (NM_172721, intron 3 of 10)"	27086	NM_172721	231672	Mm.221769	NM_172721	ENSMUSG00000032867	Fbxw8	4930438M06Rik|FBW6|FBW8|FBXO29|Fbx29	F-box and WD-40 domain protein 8	protein-coding	0.01	0.49505
Merged-chr16-63796609-1	chr16	63796559	63796659	+	3.1	cIP1vsInput	"intron (NM_010140, intron 2 of 16)"	"intron (NM_010140, intron 2 of 16)"	67548	NM_010140	13837	Mm.1977	NM_010140		Epha3	AW492086|Cek4|ETK1|End3|Hek|Hek4|Mek4|Tyro4	Eph receptor A3	protein-coding	0	0.326733
Merged-chr7-127841526-1	chr7	127841476	127841576	+	3.1	cIP2vsInput	promoter-TSS (NM_009294)	promoter-TSS (NM_009294)	-282	NM_009294	20909	Mm.24867	NM_009294	ENSMUSG00000030805	Stx4a	Stx4|Syn-4|Syn4	syntaxin 4A (placental)	protein-coding	0.1	0.693069
Merged-chr1-53068238-1	chr1	53068188	53068288	+	3.1	cIP2vsInput	TTS (NM_010834)	TTS (NM_010834)	6575	NM_010834	17700	Mm.3514	NM_010834	ENSMUSG00000026100	Mstn	Cmpt|Gdf8	myostatin	protein-coding	0	0.336634
Merged-chr7-142061089-2	chr7	142061004	142061174	+	3.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028308)	promoter-TSS (NM_028308)	-55	NM_028308	101513	Mm.53259	NM_028308	ENSMUSG00000025147	Mob2	1110017M21Rik|2700078K21Rik|AI256456|Mmh	MOB kinase activator 2	protein-coding	0.147059	0.725146
Merged-chr2-123057925-1	chr2	123057875	123057975	+	3.1	cIP1vsInput	Intergenic	Lx8|LINE|L1	275926	NM_021507	59010	Mm.28986	NM_001162503	ENSMUSG00000005803	Sqrdl	0610039J17Rik|4930557M22Rik	sulfide quinone reductase-like (yeast)	protein-coding	0	0.287129
Merged-chrX-159942613-1	chrX	159942563	159942663	+	3.1	cIP2vsInput	"intron (NM_001135728, intron 7 of 12)"	"intron (NM_001135728, intron 7 of 12)"	-45820	NM_001163085	270672	Mm.386889	NM_001163085	ENSMUSG00000031303	Map3k15	BC031147|MEKK15	mitogen-activated protein kinase kinase kinase 15	protein-coding	0.02	0.534653
Merged-chr4-94752560-2	chr4	94752502	94752618	+	3.1	cIP1vsInput|cIP2vsInput	"intron (NM_013690, intron 1 of 22)"	"intron (NM_013690, intron 1 of 22)"	13260	NM_013690	21687	Mm.14313	NM_013690	ENSMUSG00000006386	Tek	AA517024|Cd202b|Hyk|Tie2|tie-2	endothelial-specific receptor tyrosine kinase	protein-coding	0.025862	0.589744
Merged-chr10-127195866-1	chr10	127195816	127195916	+	3.1	cIP2vsInput	promoter-TSS (NM_030714)	promoter-TSS (NM_030714)	-157	NM_030714	80904	Mm.271724	NM_030714	ENSMUSG00000040415	Dtx3	Deltex3|mg310	deltex 3 homolog (Drosophila)	protein-coding	0.04	0.633663
Merged-chr9-31972429-1	chr9	31972379	31972479	+	3.1	cIP2vsInput	Intergenic	Intergenic	-59144	NM_013800	12023	Mm.261044	NM_013800	ENSMUSG00000032033	Barx2	2310006E12Rik|Barx2b	BarH-like homeobox 2	protein-coding	0	0.613861
Merged-chr1-106796723-1	chr1	106796673	106796773	+	3.1	cIP2vsInput	promoter-TSS (NM_009190)	promoter-TSS (NM_009190)	2	NM_009190	20479	Mm.483448	NM_009190		Vps4b	8030489C12Rik|Skd1	vacuolar protein sorting 4b (yeast)	protein-coding	0.1	0.584158
Merged-chr16-22548509-1	chr16	22548459	22548559	+	3.1	cIP2vsInput	"intron (NM_138650, intron 20 of 24)"	"intron (NM_138650, intron 20 of 24)"	108722	NM_138650	110197	Mm.448158	NM_138650		Dgkg	2900055E17Rik|90kDa|AI854428|Dagk3|E430001K23Rik|mKIAA4131	"diacylglycerol kinase, gamma"	protein-coding	0.05	0.49505
Merged-chr3-17254426-1	chr3	17254376	17254476	+	3.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-535495	NR_033490	70441	Mm.458192	NR_033490		2610100L16Rik	100040120|Gm2612	RIKEN cDNA 2610100L16 gene	miscRNA	0	0.316832
Merged-chr18-75018781-1	chr18	75018731	75018831	+	3.1	cIP1vsInput	promoter-TSS (NM_027727)	promoter-TSS (NM_027727)	9	NM_027727	69190	Mm.173826	NM_027727	ENSMUSG00000035765	Dym	1810041M12Rik|4933427L07Rik|C030019K18Rik	dymeclin	protein-coding	0.13	0.693069
Merged-chr10-11343690-1	chr10	11343640	11343740	+	3.1	cIP1vsInput	"exon (NM_010146, exon 1 of 4)"	"exon (NM_010146, exon 1 of 4)"	245	NM_010146	13853	Mm.89946	NM_010146		Epm2a	"TG-B|Tg(TcraK,TcrbK)TG-BFlv"	"epilepsy, progressive myoclonic epilepsy, type 2 gene alpha"	protein-coding	0.13	0.722772
Merged-chr6-128066173-1	chr6	128066123	128066223	+	3.1	cIP1vsInput	"intron (NM_175414, intron 2 of 8)"	"intron (NM_175414, intron 2 of 8)"	77405	NM_175414	109246	Mm.21814	NM_175414	ENSMUSG00000030352	Tspan9	6720474K14Rik|9430079M16Rik|AU018597	tetraspanin 9	protein-coding	0.02	0.643564
Merged-chr9-59354101-1	chr9	59354051	59354151	+	3.1	cIP2vsInput	promoter-TSS (NM_175325)	promoter-TSS (NM_175325)	-593	NM_175325	102774	Mm.200714	NM_175325	ENSMUSG00000025235	Bbs4	AW537059|AW742241|D9Ertd464e	Bardet-Biedl syndrome 4 (human)	protein-coding	0	0.356436
Merged-chr11-83941366-1	chr11	83941316	83941416	+	3.1	cIP2vsInput	promoter-TSS (NM_030096)	promoter-TSS (NM_030096)	-724	NM_030096	78394	Mm.280544	NM_030096	ENSMUSG00000020677	Ddx52	2700029C06Rik|ROK1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	protein-coding	0.01	0.336634
Merged-chr3-89164747-2	chr3	89164679	89164815	+	3.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001163432)	promoter-TSS (NM_001163432)	-58	NM_007712	12748	Mm.288098	NM_001163432	ENSMUSG00000068917	Clk2	AU041688|Tu52	CDC-like kinase 2	protein-coding	0.102941	0.693431
Merged-chr6-58189287-1	chr6	58189237	58189337	+	3.1	cIP2vsInput	Intergenic	Intergenic	26730	NM_134436	171206	Mm.389781	NM_134436	ENSMUSG00000071428	Vmn1r27	V1rc33	vomeronasal 1 receptor 27	protein-coding	0	0.346535
Merged-chr3-54735105-1	chr3	54735055	54735155	+	3.1	cIP2vsInput	promoter-TSS (NM_025442)	promoter-TSS (NM_025442)	259	NM_027148	69639	Mm.29253	NM_001163570	ENSMUSG00000027752	Exosc8	2310032N20Rik|CIP3|mKIAA4013	exosome component 8	protein-coding	0.1	0.712871
Merged-chr11-102881057-1	chr11	102881007	102881107	+	3.1	cIP2vsInput	promoter-TSS (NM_011431)	promoter-TSS (NM_011431)	-82	NM_001109995	20624	Mm.873	NM_001109995	ENSMUSG00000020929	Eftud2	116kDa|Snrp116|U5-116kD	elongation factor Tu GTP binding domain containing 2	protein-coding	0.05	0.554455
Merged-chr11-88561415-1	chr11	88561365	88561465	+	3.1	cIP2vsInput	"intron (NM_054043, intron 6 of 13)"	"intron (NM_054043, intron 6 of 13)"	156814	NM_054043	76626	Mm.474737	NM_001201341	ENSMUSG00000069769	Msi2	1700105C15Rik|AI451722|AI563628|AW489193|Msi2h	musashi RNA-binding protein 2	protein-coding	0.02	0.524752
Merged-chr11-48871630-1	chr11	48871580	48871680	+	3.1	cIP2vsInput	promoter-TSS (NM_008326)	promoter-TSS (NM_008326)	-284	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding	0.03	0.564356
Merged-chr3-127369457-1	chr3	127369407	127369507	+	3.1	cIP1vsInput	Intergenic	Intergenic	-175771	NR_030403	723948		NR_030403	ENSMUSG00000076252	Mir302b	Mirn302b	microRNA 302b	miscRNA	0	0.277228
Merged-chr14-58300621-1	chr14	58300571	58300671	+	3.1	cIP2vsInput	Intergenic	Intergenic	227935	NM_013518	14180	Mm.8846	NM_013518		Fgf9	Eks	fibroblast growth factor 9	protein-coding	0.02	0.544554
Merged-chr1-36580606-1	chr1	36580556	36580656	+	3.1	cIP2vsInput	"intron (NM_027957, intron 2 of 5)"	"intron (NM_027957, intron 2 of 5)"	12726	NM_027957	381337	Mm.17413	NM_001126046	ENSMUSG00000046337	Fam178b	1700024G10Rik|Gm990	"family with sequence similarity 178, member B"	protein-coding	0.02	0.633663
Merged-chr6-84640939-1	chr6	84640889	84640989	+	3.1	cIP2vsInput	"intron (NM_177077, intron 20 of 21)"	"intron (NM_177077, intron 20 of 21)"	-47031	NM_001177713	232174	Mm.255246	NM_001177713	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	"cytochrome P450, family 26, subfamily b, polypeptide 1"	protein-coding	0.03	0.445545
Merged-chr6-115764604-1	chr6	115764554	115764654	+	3.1	cIP1vsInput	Intergenic	Intergenic	-2138	NM_001168257	94346	Mm.29739	NM_001168256	ENSMUSG00000059900	Tmem40	9030407H20Rik|AV091463|W64236	transmembrane protein 40	protein-coding	0.02	0.485149
Merged-chr15-100469049-1	chr15	100468999	100469099	+	3.1	cIP2vsInput	promoter-TSS (NM_134093)	promoter-TSS (NM_134093)	15	NM_134093	68614	Mm.275272	NM_134093	ENSMUSG00000037353	Letmd1	1110019O13Rik|AI593524|BB130465|BB235638|HCCR-2|HCCR1|MCC-32|Mccr	LETM1 domain containing 1	protein-coding	0.17	0.80198
Merged-chr16-4214046-1	chr16	4213996	4214096	+	3.1	cIP2vsInput	promoter-TSS (NM_001025432)	promoter-TSS (NM_001025432)	-642	NM_001025432	12914	Mm.392384	NM_001025432	ENSMUSG00000022521	Crebbp	AW558298|CBP|CBP/p300|KAT3A|p300/CBP	CREB binding protein	protein-coding	0.08	0.60396
Merged-chr17-36271566-1	chr17	36271516	36271616	+	3.1	cIP2vsInput	promoter-TSS (NM_178281)	promoter-TSS (NM_178281)	-133	NM_178281	79263	Mm.40624	NM_024468	ENSMUSG00000045409	Trim39	1100001D15Rik|E130103K13Rik|RBCC-B30.2|Rnf23|mKIAA4179|tfp	tripartite motif-containing 39	protein-coding	0.15	0.772277
Merged-chr2-163054594-1	chr2	163054544	163054644	+	3.1	cIP2vsInput	promoter-TSS (NM_008652)	promoter-TSS (NM_008652)	-41	NM_008652	17865	Mm.436712	NM_008652	ENSMUSG00000017861	Mybl2	B-Myb|Bmyb	myeloblastosis oncogene-like 2	protein-coding	0.14	0.693069
Merged-chr11-7055685-1	chr11	7055635	7055735	+	3.1	cIP2vsInput	Intergenic	Intergenic	-7804	NM_009622	432530	Mm.259733	NM_009622	ENSMUSG00000020431	Adcy1	AC1|D11Bwg1392e|I-AC|brl|mKIAA4070	adenylate cyclase 1	protein-coding	0.03	0.60396
Merged-chr7-100495973-1	chr7	100495923	100496023	+	3.1	cIP2vsInput	"intron (NM_011671, intron 2 of 7)"	"intron (NM_011671, intron 2 of 7)"	2628	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	"uncoupling protein 2 (mitochondrial, proton carrier)"	protein-coding	0.01	0.623762
Merged-chrX-108832800-2	chrX	108832715	108832886	+	3.1	cIP1vsInput|cIP2vsInput	"intron (NM_001081477, intron 4 of 40)"	"intron (NM_001081477, intron 4 of 40)"	1555	NM_001081477	382236	Mm.426127	NM_001081477		Brwd3	Brodl|D030064D06Rik|Gm596	bromodomain and WD repeat domain containing 3	protein-coding	0.02924	0.494186
Merged-chr15-83149746-1	chr15	83149696	83149796	+	3.1	cIP2vsInput	promoter-TSS (NM_178627)	promoter-TSS (NM_178627)	101	NR_004432	104307	Mm.471434	NR_004432	ENSMUSG00000065176	Rnu12	-	"RNA U12, small nuclear"	snRNA	0.07	0.554455
Merged-chr1-90650913-2	chr1	90650858	90650968	+	3.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	47488	NM_133805	108679	Mm.119177	NM_133805	ENSMUSG00000034432	Cops8	9430009J09Rik|AA408242|Csn8|Sgn8	"COP9 (constitutive photomorphogenic) homolog, subunit 8 (Arabidopsis thaliana)"	protein-coding	0.018182	0.54955
Merged-chr18-24121896-1	chr18	24121846	24121946	+	3.1	cIP2vsInput	promoter-TSS (NM_172625)	promoter-TSS (NM_172625)	-77	NM_172625	225280	Mm.258973	NM_172625	ENSMUSG00000047989	Ino80c	D030070L09Rik	INO80 complex subunit C	protein-coding	0.1	0.594059
Merged-chr13-34163246-2	chr13	34163166	34163327	+	3.1	cIP1vsInput|cIP2vsInput	"exon (NM_001110515, exon 1 of 2)"	"exon (NM_001110515, exon 1 of 2)"	269	NM_001110515	69666	Mm.24788	NM_001101430	ENSMUSG00000071451	Psmg4	2310047M15Rik	"proteasome (prosome, macropain) assembly chaperone 4"	protein-coding	0.080745	0.666667
Merged-chr3-88410300-1	chr3	88410250	88410350	+	3.1	cIP1vsInput	promoter-TSS (NM_025928)	promoter-TSS (NM_025928)	16	NM_025928	67037	Mm.36715	NM_025928	ENSMUSG00000028066	Pmf1	2600009M07Rik|AL033286|AW060657	polyamine-modulated factor 1	protein-coding	0.04	0.584158
Merged-chr2-104794721-1	chr2	104794671	104794771	+	3.1	cIP2vsInput	"intron (NM_001123327, intron 2 of 11)"	"intron (NM_001123327, intron 2 of 11)"	21975	NM_001123327	99003	Mm.274314	NM_001123327	ENSMUSG00000074994	Qser1	4732486I23Rik|AI502974	glutamine and serine rich 1	protein-coding	0	0.316832
Merged-chr9-85497942-1	chr9	85497892	85497992	+	3.1	cIP2vsInput	Intergenic	Intergenic	-170792	NM_001160379	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	D930050G01Rik	"family with sequence similarity 46, member A"	protein-coding	0	0.376238
Merged-chr16-58299656-1	chr16	58299606	58299706	+	3.1	cIP2vsInput	Intergenic	Intergenic	-108879	NM_028523	73379	Mm.373589	NM_028523	ENSMUSG00000035107	Dcbld2	1700055P21Rik|AW146002|CLCP1|Esdn	"discoidin, CUB and LCCL domain containing 2"	protein-coding	0.02	0.50495
Merged-chr18-46762106-1	chr18	46762056	46762156	+	3.1	cIP2vsInput	"intron (NM_009681, intron 3 of 5)"	"intron (NM_009681, intron 3 of 5)"	20189	NM_009681	11777	Mm.312536	NM_009681	ENSMUSG00000024480	Ap3s1	[s]3A	"adaptor-related protein complex 3, sigma 1 subunit"	protein-coding	0.01	0.346535
Merged-chr2-105399350-1	chr2	105399300	105399400	+	3.1	cIP2vsInput	promoter-TSS (NM_009037)	promoter-TSS (NM_009037)	-31	NM_009037	19672	Mm.4876	NM_009037	ENSMUSG00000005973	Rcn1	Rcn	reticulocalbin 1	protein-coding	0.14	0.821782
Merged-chr5-92375074-1	chr5	92375024	92375124	+	3.1	cIP2vsInput	"intron (NM_181728, intron 2 of 9)"	"intron (NM_181728, intron 2 of 9)"	-11778	NR_038116	56066	Mm.131723	NM_019494	ENSMUSG00000060183	Cxcl11	Cxc11|H174|I-tac|Ip9|Itac|Scyb11|Scyb9b|b-R1|betaR1	chemokine (C-X-C motif) ligand 11	protein-coding	0.03	0.445545
Merged-chr7-80861109-1	chr7	80861059	80861159	+	3.1	cIP2vsInput	promoter-TSS (NM_009553)	promoter-TSS (NM_009553)	-999	NM_009553	22691	Mm.358645	NM_009553	ENSMUSG00000038797	Zscan2	Zfp-29|Zfp29	zinc finger and SCAN domain containing 2	protein-coding	0.09	0.712871
Merged-chr8-109706012-1	chr8	109705962	109706062	+	3.1	cIP2vsInput	promoter-TSS (NM_029468)	promoter-TSS (NM_029468)	-76	NM_029468	75871	Mm.286964	NM_001167946	ENSMUSG00000031728	Zfp821	4930566A11Rik|Znf821	zinc finger protein 821	protein-coding	0.12	0.792079
Merged-chr12-31262146-1	chr12	31262096	31262196	+	3.1	cIP2vsInput	Intergenic	Intergenic	-3148	NM_008482	16777	Mm.172674	NM_008482	ENSMUSG00000002900	Lamb1	C77966|C80098|C81607|D130003D08Rik|Lamb-1|Lamb1-1	laminin B1	protein-coding	0.02	0.514851
Merged-chr1-72226522-1	chr1	72226472	72226572	+	3.1	cIP2vsInput	Intergenic	B1_Mus1|SINE|Alu	-14215	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding	0	0.39604
Merged-chr14-111676985-1	chr14	111676935	111677035	+	3.1	cIP2vsInput	"intron (NM_198865, intron 1 of 1)"	"intron (NM_198865, intron 1 of 1)"	1870	NM_198865	75409	Mm.417152	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	"SLIT and NTRK-like family, member 5"	protein-coding	0.04	0.594059
Merged-chr10-81606521-1	chr10	81606471	81606571	+	3.1	cIP1vsInput	"intron (NR_030677, intron 1 of 2)"	"intron (NR_030677, intron 1 of 2)"	213	NR_030677	268319	Mm.131825	NM_001033363	ENSMUSG00000074862	BC025920	-	zinc finger protein pseudogene	pseudo	0.04	0.524752
Merged-chr17-71032597-1	chr17	71032547	71032647	+	3.1	cIP2vsInput	"intron (NM_010867, intron 2 of 37)"	"intron (NM_010867, intron 2 of 37)"	13040	NM_001083934	17929	Mm.4103	NM_001083934	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding	0	0.366337
Merged-chr17-13552666-2	chr17	13552614	13552718	+	3.1	cIP1vsInput|cIP2vsInput	"intron (NR_045437, intron 1 of 3)"	(CTGTG)n|Simple_repeat|Simple_repeat	1428	NR_045436	72578	Mm.46549	NR_045436	ENSMUSG00000038347	2700054A10Rik	-	RIKEN cDNA 2700054A10 gene	miscRNA	0	0.571429
Merged-chrY-6787046-1	chrY	6786996	6787096	+	3.1	cIP1vsInput	Intergenic	L1Md_F|LINE|L1	380731	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.544554
Merged-chr11-55097973-1	chr11	55097923	55098023	+	3.1	cIP2vsInput	promoter-TSS (NM_010299)	promoter-TSS (NM_010299)	-12	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding	0.04	0.643564
Merged-chr12-38868599-1	chr12	38868549	38868649	+	3.1	cIP2vsInput	TTS (NM_007960)	TTS (NM_007960)	84888	NM_001163154	14009	Mm.4866	NM_001163154	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant gene 1	protein-coding	0	0.316832
Merged-chrY-6989045-1	chrY	6988995	6989095	+	3.1	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	178732	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.465347
Merged-chr10-37610391-1	chr10	37610341	37610441	+	3.1	cIP1vsInput	Intergenic	Intergenic	-471465	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding	0	0.29703
Merged-chr3-145683283-1	chr3	145683233	145683333	+	3.1	cIP1vsInput	Intergenic	Intergenic	-33298	NM_010516	16007	Mm.1231	NM_010516	ENSMUSG00000028195	Cyr61	AI325051|CCN1|Igfbp10	cysteine rich protein 61	protein-coding	0.01	0.346535
Merged-chr18-35752261-1	chr18	35752211	35752311	+	3.1	cIP1vsInput	Intergenic	Intergenic	-11707	NM_028261	72512	Mm.45995	NM_028261	ENSMUSG00000024349	Tmem173	2610307O08Rik|ERIS|MPYS|Mita|STING	transmembrane protein 173	protein-coding	0.07	0.594059
Merged-chr5-122602333-1	chr5	122602283	122602383	+	3.1	cIP1vsInput	"exon (NM_009879, exon 7 of 19)"	"exon (NM_009879, exon 7 of 19)"	12185	NM_009879	12589	Mm.10125	NM_009879	ENSMUSG00000029469	Ift81	AW060663|Cdv-1|Cdv-1r|Cdv1	intraflagellar transport 81	protein-coding	0.03	0.425743
Merged-chr6-3183983-1	chr6	3183933	3184033	+	3.1	cIP2vsInput	Intergenic	Intergenic	-104536	NR_036696	667335	Mm.380219	NR_036696		Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo	0.01	0.435644
Merged-chr17-35059496-1	chr17	35059446	35059546	+	3.1	cIP2vsInput	TTS (NM_033444)	TTS (NM_033444)	461	NM_016765	51793	Mm.1457	NM_001190449	ENSMUSG00000007039	Ddah2	1110003M04Rik|AU019324|AW413173|DDAH-2|DDAHII|Ddah|G6a|NG30	dimethylarginine dimethylaminohydrolase 2	protein-coding	0.08	0.623762
Merged-chr9-41736030-1	chr9	41735980	41736080	+	3.1	cIP2vsInput	Intergenic	Intergenic	154104	NR_029822	387236		NR_029822	ENSMUSG00000093354	Mir125b-1	Mirn125b|Mirn125b-1	microRNA 125b-1	miscRNA	0.03	0.633663
Merged-chr6-113638427-2	chr6	113638347	113638508	+	3.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001113553)	promoter-TSS (NM_001113553)	-40	NM_172161	108960	Mm.152142	NM_001113553	ENSMUSG00000060477	Irak2	6330415L08Rik|AI649099|IRAK-2	interleukin-1 receptor-associated kinase 2	protein-coding	0.099379	0.685185
Merged-chr2-52072848-1	chr2	52072798	52072898	+	3.1	cIP2vsInput	promoter-TSS (NM_175238)	promoter-TSS (NM_175238)	11	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	Rap1 interacting factor 1 homolog (yeast)	protein-coding	0.17	0.762376
Merged-chr2-57124359-1	chr2	57124309	57124409	+	3.1	cIP2vsInput	promoter-TSS (NM_001139509)	promoter-TSS (NM_001139509)	-356	NM_001139509	18227	Mm.3507	NM_001139509	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	"nuclear receptor subfamily 4, group A, member 2"	protein-coding	0.06	0.564356
Merged-chr7-127196007-2	chr7	127195934	127196081	+	3.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027353)	promoter-TSS (NM_027353)	-7	NM_027353	70233	Mm.28050	NM_027353	ENSMUSG00000042502	Cd2bp2	1500011B02Rik|2410024K20Rik|AW048183	CD2 antigen (cytoplasmic tail) binding protein 2	protein-coding	0.068027	0.547297
Merged-chr2-106522151-2	chr2	106522088	106522215	+	3.1	cIP1vsInput|cIP2vsInput	"intron (NR_040637, intron 1 of 2)"	RMER4A|LTR|ERVK	952	NR_040637	329483	Mm.246777	NR_040637	ENSMUSG00000087226	Gm14015	9330126M15|OTTMUSG00000015366	predicted gene 14015	miscRNA	0	0.382812
Merged-chr8-72421517-1	chr8	72421467	72421567	+	3.1	cIP1vsInput	promoter-TSS (NM_001122832)	promoter-TSS (NM_001122832)	-43	NM_007944	13859	Mm.288894	NM_001122832	ENSMUSG00000006276	Eps15l1	9830147J04Rik|AI593686|Eps15-rs|Eps15R	epidermal growth factor receptor pathway substrate 15-like 1	protein-coding	0.1	0.673267
Merged-chr17-15468419-1	chr17	15468369	15468469	+	3.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	29857	NM_011185	19170	Mm.32912	NM_011185	ENSMUSG00000014769	Psmb1	AA409053|C81484|Lmpc5	"proteasome (prosome, macropain) subunit, beta type 1"	protein-coding	0	0.316832
Merged-chr1-186835381-1	chr1	186835331	186835431	+	3.1	cIP2vsInput	Intergenic	Intergenic	-86023	NM_026041	67223	Mm.289841	NM_026041	ENSMUSG00000001305	Rrp15	2810430M08Rik|5430437H21Rik	ribosomal RNA processing 15 homolog (S. cerevisiae)	protein-coding	0	0.306931
Merged-chr1-191906759-1	chr1	191906709	191906809	+	3.1	cIP2vsInput	promoter-TSS (NM_009579)	promoter-TSS (NM_009579)	-22	NM_009579	22782	Mm.9024	NM_009579	ENSMUSG00000037434	Slc30a1	AI839647|C130040I11Rik|Znt1	"solute carrier family 30 (zinc transporter), member 1"	protein-coding	0.1	0.60396
Merged-chr10-98044735-1	chr10	98044685	98044785	+	3.1	cIP2vsInput	Intergenic	Intergenic	-77645	NR_033537	100038699	Mm.467933	NR_033537		Gm10754	ENSMUSG00000074776	predicted gene 10754	miscRNA	0	0.445545
Merged-chr4-117497034-2	chr4	117496968	117497101	+	3.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025739)	promoter-TSS (NM_025739)	-119	NM_025739	66743	Mm.470234	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding	0.06015	0.559701
Merged-chr9-58247236-1	chr9	58247186	58247286	+	3.1	cIP2vsInput	"exon (NM_178087, exon 2 of 9)"	"exon (NM_178087, exon 2 of 9)"	2550	NM_178087	18854	Mm.392123	NM_008884	ENSMUSG00000036986	Pml	1200009E24Rik|AI661194|Trim19	promyelocytic leukemia	protein-coding	0.09	0.643564
Merged-chr15-100599467-1	chr15	100599417	100599517	+	3.1	cIP2vsInput	Intergenic	CpG	-13102	NM_010127	19009	Mm.475483	NM_010127	ENSMUSG00000009739	Pou6f1	2310038G18Rik|Brn5.0|C79593|Emb|cns-1	"POU domain, class 6, transcription factor 1"	protein-coding	0.1	0.752475
Merged-chr6-58771462-1	chr6	58771412	58771512	+	3.1	cIP2vsInput	Intergenic	Intergenic	-62238	NM_028705	73998	Mm.191892	NM_028705	ENSMUSG00000029804	Herc3	5730409F18Rik|AI646603|mKIAA0032	hect domain and RLD 3	protein-coding	0	0.287129
Merged-chr16-52335601-1	chr16	52335551	52335651	+	3.1	cIP2vsInput	"intron (NM_009655, intron 1 of 15)"	"intron (NM_009655, intron 1 of 15)"	117396	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding	0	0.435644
Merged-chr14-120076217-1	chr14	120076167	120076267	+	3.1	cIP2vsInput	Intergenic	Intergenic	-33782	NM_001001490	239283	Mm.138520	NM_001001490	ENSMUSG00000044819	Oxgr1	Gm299|Gpr80|Gpr99|P2Y15	oxoglutarate (alpha-ketoglutarate) receptor 1	protein-coding	0.01	0.316832
Merged-chr5-110857260-1	chr5	110857210	110857310	+	3.1	cIP1vsInput	"intron (NM_016681, intron 6 of 14)"	"intron (NM_016681, intron 6 of 14)"	17243	NM_016681	50883	Mm.279308	NM_016681	ENSMUSG00000029521	Chek2	CHK2|Cds1|HUCDS1|Rad53	checkpoint kinase 2	protein-coding	0.02	0.425743
Merged-chr8-95488942-1	chr8	95488892	95488992	+	3.1	cIP2vsInput	promoter-TSS (NM_009974)	promoter-TSS (NM_009974)	-122	NM_009974	13000	Mm.440348	NM_009974	ENSMUSG00000046707	Csnk2a2	1110035J23Rik|C77789|CK2	"casein kinase 2, alpha prime polypeptide"	protein-coding	0.09	0.762376
Merged-chr5-114467532-1	chr5	114467482	114467582	+	3.1	cIP2vsInput	Intergenic	Intergenic	23226	NM_023556	17855	Mm.28088	NM_023556	ENSMUSG00000041939	Mvk	2310010A05Rik|AI256848|AI414037|MK	mevalonate kinase	protein-coding	0.03	0.752475
Merged-chr8-31919705-2	chr8	31919642	31919768	+	3.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-1502	NM_178591	211323	Mm.460675	NM_178591	ENSMUSG00000062991	Nrg1	6030402G23Rik|ARIA|D230005F13Rik|GGF|GGFII|HRG|HRGalpha|Hgl|NDF|SMDF	neuregulin 1	protein-coding	0.02381	0.448819
Merged-chr17-45584672-1	chr17	45584622	45584722	+	3.1	cIP2vsInput	TTS (NM_001199114)	TTS (NM_001199114)	7721	NM_022880	63959	Mm.486335	NM_001199113	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	"solute carrier family 29 (nucleoside transporters), member 1"	protein-coding	0	0.623762
Merged-chr19-5106748-1	chr19	5106698	5106798	+	3.1	cIP2vsInput	TTS (NM_008451)	TTS (NM_008451)	248	NM_029576	76308	Mm.182563	NM_029576	ENSMUSG00000024870	Rab1b	1110011F09Rik	"RAB1B, member RAS oncogene family"	protein-coding	0.06	0.722772
Merged-chr17-42883131-1	chr17	42883081	42883181	+	3.1	cIP2vsInput	Intergenic	Intergenic	-6707	NM_009847	12488	Mm.218637	NM_009847	ENSMUSG00000061665	Cd2ap	AL024079|C78928|METS-1|Mets1	CD2-associated protein	protein-coding	0	0.346535
Merged-chr17-63405382-1	chr17	63405332	63405432	+	3.1	cIP1vsInput	"intron (NM_015794, intron 4 of 8)"	"intron (NM_015794, intron 4 of 8)"	95198	NM_015794	50758	Mm.136366	NM_177143		Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding	0	0.336634
Merged-chr10-119615407-1	chr10	119615357	119615457	+	3.1	cIP1vsInput	"intron (NM_133442, intron 1 of 21)"	"intron (NM_133442, intron 1 of 21)"	146292	NR_045359	75321	Mm.402041	NR_045359	ENSMUSG00000084764	4930564G21Rik	-	RIKEN cDNA 4930564G21 gene	miscRNA	0	0.534653
Merged-chr1-31792183-2	chr1	31792112	31792255	+	3.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-380623	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm1	"KH domain containing, RNA binding, signal transduction associated 2"	protein-coding	0	0.270833
Merged-chr11-69662911-1	chr11	69662861	69662961	+	3.1	cIP2vsInput	promoter-TSS (NM_011900)	promoter-TSS (NM_011900)	-132	NR_035455	100316840		NR_035455	ENSMUSG00000088752	Mir1934	mmu-mir-1934	microRNA 1934	miscRNA	0.05	0.485149
Merged-chr5-142540298-2	chr5	142540204	142540392	+	3.1	cIP1vsInput|cIP2vsInput	"intron (NM_178702, intron 2 of 14)"	"intron (NM_178702, intron 2 of 14)"	-10222	NM_019943	56522	Mm.441372	NM_019943		Papolb	PAP|Paplob|Papola-ps|Papt|Plap-ps|Tpap	poly (A) polymerase beta (testis specific)	protein-coding	0.015957	0.492063
Merged-chr17-8283575-1	chr17	8283525	8283625	+	3.1	cIP2vsInput	promoter-TSS (NM_018819)	promoter-TSS (NM_018819)	-238	NM_018819	55951	Mm.288510	NM_018819	ENSMUSG00000023861	Mpc1	0610006G08Rik|3830411I18Rik|Brp44l	mitochondrial pyruvate carrier 1	protein-coding	0.07	0.732673
Merged-chr2-168154537-2	chr2	168154455	168154619	+	3.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_040327)	promoter-TSS (NR_040327)	-24	NR_040327	77017	Mm.407822	NR_040327	ENSMUSG00000087648	E130018N17Rik	-	RIKEN cDNA E130018N17 gene	miscRNA	0.018293	0.660606
Merged-chr13-64312626-1	chr13	64312576	64312676	+	3.1	cIP2vsInput	promoter-TSS (NM_025370)	promoter-TSS (NM_025370)	84	NM_025370	66129	Mm.227240	NM_025370	ENSMUSG00000021482	Aaed1	1110018J18Rik|AI849003	AhpC/TSA antioxidant enzyme domain containing 1	protein-coding	0.16	0.792079
Merged-chr5-136623283-1	chr5	136623233	136623333	+	3.1	cIP2vsInput	Intergenic	CpG	-55852	NM_009986	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	AA407197|CDP|Cutl1|Cux|Cux-1|Phox2|mKIAA4047	cut-like homeobox 1	protein-coding	0.13	0.663366
Merged-chr7-45395652-1	chr7	45395602	45395702	+	3.1	cIP2vsInput	promoter-TSS (NM_009224)	promoter-TSS (NM_009224)	-5	NM_009224	20637	Mm.216386	NM_009224	ENSMUSG00000063511	Snrnp70	2700022N21Rik|3200002N22Rik|70kDa|AI325098|R74807|Rnulp70|Snrp70|Srnp70|U1-70|U1-70K	small nuclear ribonucleoprotein 70 (U1)	protein-coding	0.13	0.693069
Merged-chr14-79488271-1	chr14	79488221	79488321	+	3.1	cIP1vsInput	"intron (NM_007920, intron 1 of 8)"	"intron (NM_007920, intron 1 of 8)"	-7003	NM_018765	22380	Mm.476813	NM_018765	ENSMUSG00000022023	Wbp4	AW545037|BB101031|FBP21	WW domain binding protein 4	protein-coding	0.01	0.29703
Merged-chr7-16993616-1	chr7	16993566	16993666	+	3.1	cIP2vsInput	promoter-TSS (NM_001101535)	promoter-TSS (NM_001101535)	-972	NM_001101535	434130	Mm.484826	NM_001101535		Ccdc8	ENSMUSG00000041117	coiled-coil domain containing 8	protein-coding	0.04	0.524752
Merged-chr4-116378566-1	chr4	116378516	116378616	+	3.1	cIP2vsInput	"intron (NM_001042743, intron 4 of 29)"	(TC)n|Simple_repeat|Simple_repeat	85617	NM_008641	17776	Mm.9287	NM_001042743	ENSMUSG00000003810	Mast2	MAST205|Mtssk|mKIAA0807	microtubule associated serine/threonine kinase 2	protein-coding	0	0.39604
Merged-chr4-153153136-2	chr4	153153083	153153190	+	3.1	cIP1vsInput|cIP2vsInput	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	329694	NM_001099299	230959	Mm.318874	NM_001099299	ENSMUSG00000039546	Ajap1	Gm573	adherens junction associated protein 1	protein-coding	0	0.5
Merged-chr9-86523464-1	chr9	86523414	86523514	+	3.1	cIP2vsInput	"intron (NM_177208, intron 23 of 38)"	L1ME1|LINE|L1	48378	NM_001163746	109785	Mm.390201	NM_001163746	ENSMUSG00000056131	Pgm3	2810473H05Rik|Agm1|BB187688|C77933|PAGM|Pgm-3	phosphoglucomutase 3	protein-coding	0	0.277228
Merged-chr10-78574052-1	chr10	78574002	78574102	+	3.1	cIP2vsInput	promoter-TSS (NM_173751)	promoter-TSS (NM_173751)	-448	NM_173751	216136	Mm.2644	NM_173751	ENSMUSG00000032763	Ilvbl	5830463I21|AI415009	ilvB (bacterial acetolactate synthase)-like	protein-coding	0	0.356436
Merged-chr9-22389258-1	chr9	22389208	22389308	+	3.1	cIP2vsInput	promoter-TSS (NM_028390)	promoter-TSS (NM_028390)	-52	NM_028390	68743	Mm.453238	NM_028390	ENSMUSG00000036777	Anln	1110037A17Rik|2900037I21Rik|C78101|Scraps	"anillin, actin binding protein"	protein-coding	0.12	0.752475
Merged-chr13-59625166-1	chr13	59625116	59625216	+	3.1	cIP2vsInput	"intron (NM_030153, intron 16 of 22)"	PB1|SINE|Alu	39833	NM_030153	78689	Mm.253902	NM_030153	ENSMUSG00000021555	Naa35	A330021G12Rik|A330027C19Rik|AI158944|C030004C14Rik|Mak10	"N(alpha)-acetyltransferase 35, NatC auxiliary subunit"	protein-coding	0.02	0.514851
Merged-chr5-77310224-1	chr5	77310174	77310274	+	3.1	cIP2vsInput	promoter-TSS (NM_019836)	promoter-TSS (NM_019836)	-138	NM_019836	56412	Mm.129136	NM_019836	ENSMUSG00000036285	Noa1	2610024G14Rik|AU022345|AtNOS1|mAtNOS1	nitric oxide associated 1	protein-coding	0.06	0.554455
Merged-chr19-46057123-1	chr19	46057073	46057173	+	3.1	cIP1vsInput	"intron (NM_001081214, intron 1 of 13)"	CpG	584	NM_001081214	226169	Mm.2415	NM_001081214	ENSMUSG00000055491	Pprc1	A930018M19|BC013720|PRC|mKIAA0595	"peroxisome proliferative activated receptor, gamma, coactivator-related 1"	protein-coding	0.11	0.732673
Merged-chr12-111713136-1	chr12	111713086	111713186	+	3.1	cIP2vsInput	promoter-TSS (NM_001163388)	promoter-TSS (NM_001163388)	120	NM_027404	70369	Mm.44239	NM_027404	ENSMUSG00000049792	Bag5	1600025G07Rik|4930405J06Rik	BCL2-associated athanogene 5	protein-coding	0.16	0.742574
Merged-chr10-81627244-1	chr10	81627194	81627294	+	3.1	cIP2vsInput	promoter-TSS (NM_001163430)	promoter-TSS (NM_001163430)	78	NM_001163430	50721	Mm.25643	NM_001163430	ENSMUSG00000034748	Sirt6	2810449N18Rik|AI043036|Sir2l6	"sirtuin 6 (silent mating type information regulation 2, homolog) 6 (S. cerevisiae)"	protein-coding	0.03	0.534653
Merged-chr14-52279173-1	chr14	52279123	52279223	+	3.1	cIP1vsInput	promoter-TSS (NM_023434)	promoter-TSS (NM_023434)	27	NM_023434	268741	Mm.246237	NM_023434	ENSMUSG00000016831	Tox4	5730589K01Rik|A630040M18|AA410149|LCP1	TOX high mobility group box family member 4	protein-coding	0.1	0.623762
Merged-chr18-35127521-1	chr18	35127471	35127571	+	3.1	cIP2vsInput	"intron (NM_009818, intron 1 of 17)"	"intron (NM_009818, intron 1 of 17)"	8609	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	"catenin (cadherin associated protein), alpha 1"	protein-coding	0.02	0.336634
Merged-chr16-44724066-1	chr16	44724016	44724116	+	3.1	cIP1vsInput	promoter-TSS (NM_145972)	promoter-TSS (NM_145972)	-235	NM_145972	212547	Mm.310573	NM_145972	ENSMUSG00000036208	BC027231	Nepro	cDNA sequence BC027231	protein-coding	0.05	0.39604
Merged-chr9-100452602-2	chr9	100452528	100452676	+	3.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	33871	NM_001033543	213208	Mm.242896	NM_001037246	ENSMUSG00000044244	Il20rb	AV228068|Fndc6|Gm186|Il20R2	interleukin 20 receptor beta	protein-coding	0.006757	0.483221
Merged-chr6-82652662-1	chr6	82652612	82652712	+	3.1	cIP2vsInput	"exon (NM_025882, exon 1 of 4)"	"exon (NM_025882, exon 1 of 4)"	203	NM_025882	66979	Mm.195753	NM_025882	ENSMUSG00000030042	Pole4	2400007P05Rik|5830430F06Rik	"polymerase (DNA-directed), epsilon 4 (p12 subunit)"	protein-coding	0.1	0.633663
Merged-chr15-33588488-1	chr15	33588438	33588538	+	3.1	cIP1vsInput	"intron (NM_018755, intron 8 of 8)"	L1_Mus3|LINE|L1	64948	NR_045070	75880	Mm.396109	NR_045070		4930592A05Rik	-	RIKEN cDNA 4930592A05 gene	miscRNA	0	0.287129
Merged-chr2-33641176-1	chr2	33641126	33641226	+	3.1	cIP2vsInput	promoter-TSS (NM_010725)	promoter-TSS (NM_010725)	-17	NR_046275	100504399	Mm.72070	NM_177842		C130021I20Rik	-	Riken cDNA C130021I20 gene	miscRNA	0.09	0.633663
Merged-chr3-21466053-1	chr3	21466003	21466103	+	3.1	cIP2vsInput	Intergenic	Intergenic	-610599	NM_030732	81004	Mm.446265	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding	0	0.326733
Merged-chr9-70448006-1	chr9	70447956	70448056	+	3.1	cIP2vsInput	"intron (NM_033604, intron 8 of 14)"	"intron (NM_033604, intron 8 of 14)"	-26452	NM_007630	12442	Mm.22592	NM_007630	ENSMUSG00000032218	Ccnb2	CycB2	cyclin B2	protein-coding	0.01	0.336634
Merged-chr3-96629999-1	chr3	96629949	96630049	+	3.1	cIP2vsInput	promoter-TSS (NM_001102407)	promoter-TSS (NM_001102407)	71	NM_001102407	60365	Mm.261972	NM_001102407	ENSMUSG00000038374	Rbm8a	2310057C03Rik|AA673428|Rbm8	RNA binding motif protein 8a	protein-coding	0.09	0.613861
Merged-chr5-121437019-1	chr5	121436969	121437069	+	3.1	cIP1vsInput	"intron (NM_172722, intron 20 of 23)"	(TTTG)n|Simple_repeat|Simple_repeat	15455	NM_026129	67397	Mm.154570	NM_026129		Erp29	1200015M03Rik|2810446M09Rik|AW209030|Erp28|Erp31|PDI-Db	endoplasmic reticulum protein 29	protein-coding	0	0.415842
Merged-chr13-69612003-2	chr13	69611950	69612056	+	3.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145354)	promoter-TSS (NM_145354)	-13	NM_145354	28114	Mm.260009	NM_145354	ENSMUSG00000021595	Nsun2	D13Wsu123e|Misu	NOL1/NOP2/Sun domain family member 2	protein-coding	0.066038	0.588785
Merged-chr18-14841721-1	chr18	14841671	14841771	+	3.1	cIP2vsInput	"intron (NM_001100449, intron 11 of 14)"	"intron (NM_001100449, intron 11 of 14)"	58476	NM_001100449	72504	Mm.312233	NM_001100449	ENSMUSG00000054321	Taf4b	105kDa|2610524B04Rik|4932409F03Rik|AW987595|TAFII105|Taf2c2	"TAF4B RNA polymerase II, TATA box binding protein (TBP)-associated factor"	protein-coding	0	0.316832
Merged-chr12-59220148-2	chr12	59220084	59220213	+	3.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001033156)	promoter-TSS (NM_001033156)	-665	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding	0.108527	0.6
Merged-chr1-171576376-1	chr1	171576326	171576426	+	3.1	cIP1vsInput	"intron (NM_018729, intron 3 of 8)"	"intron (NM_018729, intron 3 of 8)"	17183	NM_018729	18106	Mm.2299	NM_018729	ENSMUSG00000004709	Cd244	2B4|C9.1|F730046O15Rik|Ly90|NAIL|NKR2B4|Nmrk|SLAMF4	CD244 natural killer cell receptor 2B4	protein-coding	0.01	0.306931
Merged-chr7-67222740-1	chr7	67222690	67222790	+	3.1	cIP2vsInput	"5' UTR (NM_001191051, exon 1 of 3)"	"5' UTR (NM_001191051, exon 1 of 3)"	124	NM_001191051	75099	Mm.121691	NM_001191051	ENSMUSG00000043831	Lysmd4	4930506D23Rik	"LysM, putative peptidoglycan-binding, domain containing 4"	protein-coding	0.02	0.623762
Merged-chr2-84279315-1	chr2	84279265	84279365	+	3.1	cIP2vsInput	Intergenic	Intergenic	145951	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding	0.01	0.366337
Merged-chr10-71159920-1	chr10	71159870	71159970	+	3.1	cIP1vsInput	promoter-TSS (NM_031397)	promoter-TSS (NM_031397)	-286	NM_031397	83675	Mm.458090	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	bicaudal C homolog 1 (Drosophila)	protein-coding	0.16	0.782178
Merged-chr10-81426454-1	chr10	81426404	81426504	+	3.1	cIP2vsInput	"intron (NM_008688, intron 1 of 9)"	"intron (NM_008688, intron 1 of 9)"	719	NM_008688	18029	Mm.453078	NM_008688	ENSMUSG00000055053	Nfic	1110019L22Rik|1500041O16Rik|AA589446|AI746521|NF1-C	nuclear factor I/C	protein-coding	0.13	0.752475
Merged-chr15-13100595-1	chr15	13100545	13100645	+	3.1	cIP2vsInput	"intron (NM_007666, intron 1 of 11)"	"intron (NM_007666, intron 1 of 11)"	73044	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	K-cadherin|cad6|cadherin-6	cadherin 6	protein-coding	0.01	0.524752
Merged-chr11-76763464-2	chr11	76763394	76763535	+	3.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_016810)	promoter-TSS (NM_016810)	91	NM_016810	53334	Mm.20931	NM_016810	ENSMUSG00000010392	Gosr1	AI414660|AI426320|BB145494|GOS-28|GOSRI|GS28	golgi SNAP receptor complex member 1	protein-coding	0.021277	0.56338
Merged-chr2-26352106-1	chr2	26352056	26352156	+	3.1	cIP2vsInput	promoter-TSS (NM_001139503)	promoter-TSS (NM_001139503)	4	NM_026828	52838	Mm.31239	NM_001139503	ENSMUSG00000075467	Dnlz	1110034G11Rik|D2Bwg1335e	DNL-type zinc finger	protein-coding	0.1	0.653465
Merged-chr4-110422916-1	chr4	110422866	110422966	+	3.1	cIP2vsInput	"intron (NM_001048189, intron 1 of 12)"	"intron (NM_001048189, intron 1 of 12)"	25125	NM_030231	78933	Mm.435620	NM_001048189	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding	0	0.29703
Merged-chr19-4528787-1	chr19	4528737	4528837	+	3.1	cIP1vsInput	"intron (NM_001162946, intron 2 of 20)"	RMER17A2|LTR|ERVK	18315	NM_001162946	18563	Mm.1845	NM_001162946	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding	0.03	0.50495
Merged-chr16-13780824-1	chr16	13780774	13780874	+	3.1	cIP2vsInput	"exon (NM_001039521, exon 1 of 18)"	"exon (NM_001039521, exon 1 of 18)"	125	NM_001039521	106298	Mm.490362	NM_001039521	ENSMUSG00000022682	Rrn3	AL023001|E130302O19Rik|R75565|TIF-1A|Tif1a	RRN3 RNA polymerase I transcription factor homolog (yeast)	protein-coding	0.15	0.722772
Merged-chr16-56029853-1	chr16	56029803	56029903	+	3.1	cIP2vsInput	promoter-TSS (NM_001024622)	promoter-TSS (NM_001024622)	-136	NM_001024622	76302	Mm.310642	NM_001024622	ENSMUSG00000071533	Pcnp	1110018D06Rik|AI647035	PEST proteolytic signal containing nuclear protein	protein-coding	0.1	0.623762
Merged-chr11-50174821-1	chr11	50174771	50174871	+	3.1	cIP2vsInput	promoter-TSS (NM_026543)	promoter-TSS (NM_026543)	-30	NM_026543	68067	Mm.390357	NM_026543	ENSMUSG00000020381	3010026O09Rik	2900016G09Rik|AI851514|AW475975	RIKEN cDNA 3010026O09 gene	protein-coding	0.09	0.722772
Merged-chr15-84192300-1	chr15	84192250	84192350	+	3.1	cIP2vsInput	promoter-TSS (NM_178614)	promoter-TSS (NM_178614)	67	NM_178614	68653	Mm.290725	NM_178614	ENSMUSG00000022437	Samm50	1110030L07Rik	sorting and assembly machinery component 50 homolog (S. cerevisiae)	protein-coding	0.09	0.653465
Merged-chr1-133237117-1	chr1	133237067	133237167	+	3.1	cIP2vsInput	Intergenic	Intergenic	-8980	NM_001160268	240753	Mm.253559	NM_001160268	ENSMUSG00000041757	Plekha6	9530028L01Rik|AU042621|Pepp3	"pleckstrin homology domain containing, family A member 6"	protein-coding	0.02	0.544554
Merged-chr9-83833616-1	chr9	83833566	83833666	+	3.1	cIP1vsInput	Intergenic	Intergenic	-1073	NM_009445	22137	Mm.1904	NM_001110265	ENSMUSG00000038379	Ttk	AL022661|Esk1|Mps1|PYT|esk	Ttk protein kinase	protein-coding	0	0.316832
Merged-chr15-51865922-1	chr15	51865872	51865972	+	3.1	cIP1vsInput	promoter-TSS (NM_080635)	promoter-TSS (NM_080635)	-461	NM_080635	68135	Mm.289800	NM_080635	ENSMUSG00000022312	Eif3h	1110008A16Rik|40kD|9430017H16Rik|EIF3-P40|EIF3-gamma|Eif3s3	"eukaryotic translation initiation factor 3, subunit H"	protein-coding	0.02	0.376238
Merged-chr5-115662825-1	chr5	115662775	115662875	+	3.1	cIP1vsInput	"exon (NM_001080808, exon 6 of 9)"	"exon (NM_001080808, exon 6 of 9)"	30838	NM_198163	77407	Mm.27553	NM_198163		Rab35	9530019H02Rik|AU040256|H-ray|RAB1C|RAY	"RAB35, member RAS oncogene family"	protein-coding	0.08	0.613861
Merged-chr12-28675456-2	chr12	28675386	28675527	+	3.05	cIP1vsInput|cIP2vsInput	"intron (NM_134052, intron 1 of 3)"	CpG	249	NM_134052	104923	Mm.291504	NM_134052	ENSMUSG00000020629	Adi1	AL024210|Fe-ARD|MTCBP-1|Ni-ARD	acireductone dioxygenase 1	protein-coding	0.092199	0.683099
Merged-chr7-119720794-2	chr7	119720713	119720875	+	3.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145585)	promoter-TSS (NM_145585)	-29	NM_145585	233802	Mm.26392	NM_145585	ENSMUSG00000030942	Thumpd1	6330575P11Rik	THUMP domain containing 1	protein-coding	0.123457	0.668712
Merged-chr8-20503985-2	chr8	20503933	20504038	+	3.05	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-79171	NR_028428	381598	Mm.483074	NM_001024708	ENSMUSG00000071793	2610005L07Rik	2810038F24Rik|6720476A01Rik	cadherin 11 pseudogene	pseudo	0	0.339623
Merged-chr6-54327921-2	chr6	54327867	54327976	+	3.05	cIP1vsInput|cIP2vsInput	"intron (NM_030024, intron 1 of 1)"	CpG	909	NM_030024	78004	Mm.41984	NM_030024	ENSMUSG00000045725	Prr15	E130201N16Rik|G90	proline rich 15	protein-coding	0.119266	0.681818
Merged-chr2-91237151-2	chr2	91237099	91237203	+	3.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_015464)	promoter-TSS (NR_015464)	5	NR_015464	606735	Mm.443532	NR_015464	ENSMUSG00000097868	A330069E16Rik	-	RIKEN cDNA A330069E16 gene	miscRNA	0.067308	0.628571
Merged-chr6-70792141-2	chr6	70792047	70792235	+	3.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009075)	promoter-TSS (NM_009075)	34	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding	0.12766	0.783069
Merged-chr1-75400073-2	chr1	75399994	75400153	+	3.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001173477)	promoter-TSS (NM_001173477)	-12	NM_001173477	11790	Mm.275397	NM_001085370	ENSMUSG00000026207	Speg	AW125581|Apeg1|BPEG|D1Bwg1450e|SPEGalpha|SPEGbeta|mKIAA1297	SPEG complex locus	protein-coding	0.025157	0.70625
Merged-chr11-60699069-2	chr11	60699018	60699120	+	3.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008502)	promoter-TSS (NM_008502)	-621	NM_001159405	16897	Mm.285453	NM_001159404	ENSMUSG00000020536	Llgl1	AI325176|Lgl1|Llglh|Mgl1	lethal giant larvae homolog 1 (Drosophila)	protein-coding	0.039216	0.650485
Merged-chr17-42823050-2	chr17	42822991	42823109	+	3.05	cIP1vsInput|cIP2vsInput	"intron (NM_009847, intron 9 of 17)"	Lx8|LINE|L1	53374	NM_009847	12488	Mm.218637	NM_009847	ENSMUSG00000061665	Cd2ap	AL024079|C78928|METS-1|Mets1	CD2-associated protein	protein-coding	0.033898	0.529412
Merged-chr2-156547551-2	chr2	156547484	156547619	+	3.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001164818)	promoter-TSS (NM_001164818)	-25	NM_026661	68295	Mm.253648	NM_001164818	ENSMUSG00000027628	Aar2	0610011L14Rik	AAR2 splicing factor homolog (S. cerevisiae)	protein-coding	0.096296	0.595588
Merged-chr6-113494646-2	chr6	113494556	113494737	+	3.05	cIP1vsInput|cIP2vsInput	"exon (NM_172487, exon 4 of 4)"	"exon (NM_172487, exon 4 of 4)"	7172	NM_172487	210673	Mm.133060	NM_172487	ENSMUSG00000045009	Prrt3	6330505P20|B230206N24Rik	proline-rich transmembrane protein 3	protein-coding	0.149171	0.741758
Merged-chr16-55838959-2	chr16	55838892	55839027	+	3.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_030612)	promoter-TSS (NM_030612)	-318	NM_001159395	80859	Mm.247272	NM_001159394	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	"nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta"	protein-coding	0.074074	0.647059
Merged-chr5-41708183-2	chr5	41708113	41708253	+	3.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027295)	promoter-TSS (NM_027295)	-28	NM_027295	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	"RAB28, member RAS oncogene family"	protein-coding	0.064286	0.673759
Merged-chr4-149137630-2	chr4	149137559	149137701	+	3.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027263)	promoter-TSS (NM_027263)	-30	NM_027263	69928	Mm.260893	NM_027263	ENSMUSG00000073705	Apitd1	2610040C18Rik|2810407L01Rik|CENP-S	"apoptosis-inducing, TAF9-like domain 1"	protein-coding	0.133803	0.685315
Merged-chr8-40964614-2	chr8	40964542	40964687	+	3.05	cIP1vsInput|cIP2vsInput	"intron (NM_026840, intron 2 of 5)"	"intron (NM_026840, intron 2 of 5)"	38381	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding	0.02069	0.458904
Merged-chr4-141060279-2	chr4	141060228	141060330	+	3.05	cIP1vsInput|cIP2vsInput	"intron (NM_001145958, intron 1 of 35)"	CpG	266	NM_001145958	230872	Mm.80685	NM_001145958	ENSMUSG00000040860	Crocc	-	"ciliary rootlet coiled-coil, rootletin"	protein-coding	0.088235	0.776699
Merged-chr11-96849903-2	chr11	96849835	96849972	+	3.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019877)	promoter-TSS (NM_019877)	27	NM_019877	56358	Mm.22144	NM_019877	ENSMUSG00000018672	Copz2	1110012D12Rik|zeta2-COP	"coatomer protein complex, subunit zeta 2"	protein-coding	0.153285	0.826087
Merged-chr5-103911320-2	chr5	103911248	103911392	+	3.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178741)	promoter-TSS (NM_178741)	-91	NM_178741	246293	Mm.179871	NM_178741	ENSMUSG00000029312	Klhl8	2310001P09Rik|D5Ertd431e	kelch-like 8	protein-coding	0.097222	0.655172
Merged-chr6-6955860-2	chr6	6955806	6955914	+	3.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001077713)	promoter-TSS (NM_001077713)	-158	NM_001077713	71238	Mm.490412	NM_001077713		Acn9	0610005M07Rik|4933430A16Rik	ACN9 homolog (S. cerevisiae)	protein-coding	0.074074	0.522936
Merged-chr9-20581453-2	chr9	20581402	20581505	+	3.05	cIP1vsInput|cIP2vsInput	"5' UTR (NM_172919, exon 1 of 6)"	"5' UTR (NM_172919, exon 1 of 6)"	125	NM_172919	244721	Mm.86627	NM_172919	ENSMUSG00000058192	Zfp846	2210010B09Rik|9130221F13|Znf846	zinc finger protein 846	protein-coding	0.106796	0.701923
Merged-chr4-147499214-2	chr4	147499142	147499287	+	3.05	cIP1vsInput|cIP2vsInput	"intron (NM_001039209, intron 1 of 2)"	ORR1D2|LTR|ERVL-MaLR	-54063	NM_001014397	433804	Mm.332047	XM_003946328	ENSMUSG00000065999	Gm13154	OTTMUSG00000010673	predicted gene 13154	protein-coding	0	0.280822
Merged-chr10-120208728-2	chr10	120208672	120208785	+	3.05	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026617)	promoter-TSS (NM_026617)	-98	NM_026617	68212	Mm.157426	NM_026617	ENSMUSG00000020225	Tmbim4	0610007H07Rik|AU022431	transmembrane BAX inhibitor motif containing 4	protein-coding	0.079646	0.614035
Merged-chr3-97609397-1	chr3	97609347	97609447	+	3	cIP1vsInput	"intron (NM_026539, intron 1 of 22)"	"intron (NM_026539, intron 1 of 22)"	793	NM_026539	68058	Mm.41447	NM_026539	ENSMUSG00000028089	Chd1l	4432404A22Rik|Alc1|Snf2p	chromodomain helicase DNA binding protein 1-like	protein-coding	0.04	0.514851
Merged-chr9-86464668-1	chr9	86464618	86464718	+	3	cIP2vsInput	"intron (NM_027394, intron 1 of 9)"	CpG	248	NM_027394	70348	Mm.53469	NM_027394	ENSMUSG00000032415	Ube2cbp	2610018I03Rik|Ube3d	ubiquitin-conjugating enzyme E2C binding protein	protein-coding	0.19	0.80198
Merged-chr8-105289431-1	chr8	105289381	105289481	+	3	cIP2vsInput	promoter-TSS (NM_028888)	promoter-TSS (NM_028888)	97	NM_001166394	74356	Mm.490326	NM_001166394	ENSMUSG00000014837	4931428F04Rik	AI426165|Kiaa0895l	RIKEN cDNA 4931428F04 gene	protein-coding	0.12	0.693069
Merged-chr2-87273422-1	chr2	87273372	87273472	+	3	cIP1vsInput	Intergenic	L1_Mus4|LINE|L1	4576	NM_001011734	257875	Mm.424863	NM_001011734		Olfr1116-ps	MOR264-21P|Olfr1116	"olfactory receptor 1116, pseudogene"	protein-coding	0	0.326733
Merged-chr8-84831203-1	chr8	84831153	84831253	+	3	cIP1vsInput	"intron (NR_033145, intron 1 of 1)"	B3A|SINE|B2	1062	NR_033145	23863	Mm.304252	NM_201227	ENSMUSG00000053226	Dand5	Cerl-2|Cerr2|Dte|coco	"DAN domain family, member 5"	protein-coding	0	0.386139
Merged-chr8-84192666-1	chr8	84192616	84192716	+	3	cIP2vsInput	Intergenic	CpG	-13705	NR_029821	723819		NR_029821	ENSMUSG00000065483	Mir181c	Mirn181c	microRNA 181c	miscRNA	0.09	0.762376
Merged-chr4-119422782-1	chr4	119422732	119422832	+	3	cIP2vsInput	promoter-TSS (NM_026494)	promoter-TSS (NM_026494)	98	NM_001014900	332934	Mm.388911	NM_001014900	ENSMUSG00000070806	Zmynd12	AI414736	"zinc finger, MYND domain containing 12"	protein-coding	0.07	0.663366
Merged-chr11-21639866-1	chr11	21639816	21639916	+	3	cIP2vsInput	"intron (NM_145425, intron 1 of 17)"	"intron (NM_145425, intron 1 of 17)"	67585	NM_145425	216560	Mm.138090	NM_145425	ENSMUSG00000020319	Wdpcp	AV249152	WD repeat containing planar cell polarity effector	protein-coding	0	0.326733
Merged-chr18-42557799-1	chr18	42557749	42557849	+	3	cIP2vsInput	"intron (NM_001039474, intron 14 of 21)"	(TATATG)n|Simple_repeat|Simple_repeat	21853	NM_181543	240239	Mm.186779	NM_181543	ENSMUSG00000042816	Gpr151	C130082O03Rik|GalRL|PGR7|nGPCR-2037	G protein-coupled receptor 151	protein-coding	0	0.316832
Merged-chr3-140705222-1	chr3	140705172	140705272	+	3	cIP2vsInput	Intergenic	Intergenic	507133	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0.01	0.316832
Merged-chr17-35089232-1	chr17	35089182	35089282	+	3	cIP2vsInput	promoter-TSS (NM_178592)	promoter-TSS (NM_178592)	-59	NM_178592	193742	Mm.43745	NM_178592	ENSMUSG00000007036	Abhd16a	AI326074|Bat-5|Bat5|D17H6S82E|NG26	abhydrolase domain containing 16A	protein-coding	0.14	0.712871
Merged-chr8-7490186-1	chr8	7490136	7490236	+	3	cIP1vsInput	Intergenic	Intergenic	1170587	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding	0	0.39604
Merged-chr3-128935065-1	chr3	128935015	128935115	+	3	cIP1vsInput	Intergenic	Lx4A|LINE|L1	-264853	NM_011098	18741	Mm.246804	NM_001042502	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1a|Brx1b|Munc30|Otlx2|Pitx2a|Pitx2b|Pitx2c|Pitx2cbeta|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding	0	0.336634
Merged-chr8-18594918-1	chr8	18594868	18594968	+	3	cIP1vsInput	promoter-TSS (NM_173189)	promoter-TSS (NM_173189)	-255	NM_173189	244329	Mm.235296	NM_173189	ENSMUSG00000039842	Mcph1	5430437K10Rik|BRIT1|D030046N04Rik|MCT	"microcephaly, primary autosomal recessive 1"	protein-coding	0.03	0.445545
Merged-chr1-182585598-1	chr1	182585548	182585648	+	3	cIP1vsInput	"intron (NM_001145806, intron 2 of 9)"	"intron (NM_001145806, intron 2 of 9)"	20591	NM_130890	170725	Mm.189201	NM_001145806	ENSMUSG00000038599	Capn8	nCL-2|nCL-2'	calpain 8	protein-coding	0.03	0.524752
Merged-chr3-30074014-1	chr3	30073964	30074064	+	3	cIP2vsInput	Intergenic	Intergenic	-60810	NM_007963	14013	Mm.426829	NM_021442	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding	0.02	0.326733
Merged-chr6-72598656-1	chr6	72598606	72598706	+	3	cIP1vsInput	promoter-TSS (NM_026159)	promoter-TSS (NM_026159)	28	NM_026159	67442	Mm.305108	NM_026159	ENSMUSG00000056666	Retsat	0610039N19Rik|C80029|MMT-7|Ppsig	"retinol saturase (all trans retinol 13,14 reductase)"	protein-coding	0.04	0.60396
Merged-chr1-72969655-1	chr1	72969605	72969705	+	3	cIP2vsInput	Intergenic	Intergenic	46244	NM_009407	21958	Mm.425024	NM_009407	ENSMUSG00000026182	Tnp1	Stp-1|TP1|Tp-1	transition protein 1	protein-coding	0.01	0.564356
Merged-chr17-37029154-1	chr17	37029104	37029204	+	3	cIP1vsInput	Intergenic	Intergenic	-5756	NM_010814	17441	Mm.210857	NM_010814	ENSMUSG00000076439	Mog	B230317G11Rik	myelin oligodendrocyte glycoprotein	protein-coding	0.01	0.39604
Merged-chr8-3500359-1	chr8	3500309	3500409	+	3	cIP2vsInput	promoter-TSS (NM_053177)	promoter-TSS (NM_053177)	-160	NM_053177	94178	Mm.8356	NM_053177	ENSMUSG00000004567	Mcoln1	2210015I05Rik|TRPML1|mucolipidin	mucolipin 1	protein-coding	0.08	0.584158
Merged-chr14-29968125-1	chr14	29968075	29968175	+	3	cIP2vsInput	promoter-TSS (NM_019979)	promoter-TSS (NM_019979)	-255	NM_019979	80795	Mm.104491	NM_019979	ENSMUSG00000042682	Selk	1110001C03Rik|AA673253|HSPC030|Hsp30	selenoprotein K	protein-coding	0.07	0.594059
Merged-chr9-73560638-1	chr9	73560588	73560688	+	3	cIP2vsInput	"intron (NM_001081153, intron 21 of 30)"	"intron (NM_001081153, intron 21 of 30)"	372929	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|AU019458|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C (C. elegans)	protein-coding	0.01	0.316832
Merged-chr1-179446709-1	chr1	179446659	179446759	+	3	cIP2vsInput	"intron (NM_027188, intron 1 of 11)"	"intron (NM_027188, intron 1 of 11)"	71294	NM_027188	69726	Mm.222338	NM_027188		Smyd3	2410008A19Rik|Zmynd1	SET and MYND domain containing 3	protein-coding	0.04	0.574257
Merged-chr7-19573466-1	chr7	19573416	19573516	+	3	cIP2vsInput	promoter-TSS (NM_027189)	promoter-TSS (NM_027189)	-123	NM_027189	69731	Mm.24540	NM_027189	ENSMUSG00000044709	Gemin7	2400008I04Rik|AI120175|AI461688	gem (nuclear organelle) associated protein 7	protein-coding	0.07	0.673267
Merged-chr12-116262270-1	chr12	116262220	116262320	+	3	cIP2vsInput	"intron (NM_146039, intron 1 of 21)"	L1_Mur3|LINE|L1	755	NM_146039	217935	Mm.31382	NM_146039	ENSMUSG00000042050	Wdr60	D430033N04Rik	WD repeat domain 60	protein-coding	0.01	0.306931
Merged-chr7-79466401-1	chr7	79466351	79466451	+	3	cIP1vsInput	promoter-TSS (NM_017462)	promoter-TSS (NM_017462)	-128	NM_017462	18975	Mm.3616	NM_017462	ENSMUSG00000039176	Polg	AA409516|PolgA	"polymerase (DNA directed), gamma"	protein-coding	0.09	0.584158
Merged-chr19-55563575-2	chr19	55563484	55563667	+	3	cIP1vsInput|cIP2vsInput	"intron (NM_016862, intron 7 of 7)"	"intron (NM_016862, intron 7 of 7)"	138629	NR_045318	77594	Mm.329924	NR_045318	ENSMUSG00000097632	4930552P12Rik	-	RIKEN cDNA 4930552P12 gene	miscRNA	0.027322	0.527174
Merged-chr13-114337554-1	chr13	114337504	114337604	+	3	cIP1vsInput	"intron (NM_010887, intron 2 of 4)"	"intron (NM_010887, intron 2 of 4)"	50540	NM_010887	17993	Mm.253142	NM_010887	ENSMUSG00000021764	Ndufs4	6720411N02Rik|C1-18k	NADH dehydrogenase (ubiquinone) Fe-S protein 4	protein-coding	0.02	0.366337
Merged-chr2-177488850-1	chr2	177488800	177488900	+	3	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	-9376	NR_036450	433520	Mm.425117	NM_001024825		Gm14403	OTTMUSG00000016571	predicted gene 14403	miscRNA	0.01	0.386139
Merged-chr13-65631270-1	chr13	65631220	65631320	+	3	cIP2vsInput	Intergenic	Intergenic	352416	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding	0.01	0.415842
Merged-chr9-105630153-1	chr9	105630103	105630203	+	3	cIP1vsInput	Intergenic	Intergenic	-12842	NM_001081309	75669	Mm.274830	NM_001081309	ENSMUSG00000032571	Pik3r4	2210010O15Rik|C730038E05Rik|C85833|D9Ertd418e	"phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 4, p150"	protein-coding	0	0.336634
Merged-chr16-67373430-1	chr16	67373380	67373480	+	3	cIP1vsInput	"intron (NM_178721, intron 1 of 9)"	"intron (NM_178721, intron 1 of 9)"	247478	NM_001145977	239857	Mm.394300	NM_001145977	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0.02	0.29703
Merged-chr18-54424233-1	chr18	54424183	54424283	+	3	cIP2vsInput	"intron (NR_040338, intron 1 of 2)"	"intron (NR_040338, intron 1 of 2)"	1938	NR_040338	77433	Mm.159919	NR_040338		9430076G02Rik	-	RIKEN cDNA 9430076G02 gene	miscRNA	0	0.376238
Merged-chr14-30985001-1	chr14	30984951	30985051	+	3	cIP1vsInput	"intron (NM_011849, intron 14 of 14)"	L1MB7|LINE|L1	-16392	NM_001165930	76485	Mm.8766	NM_001165930	ENSMUSG00000021916	Glt8d1	2410004H05Rik|5430414N14Rik|AI450005	glycosyltransferase 8 domain containing 1	protein-coding	0	0.316832
Merged-chr2-158794730-1	chr2	158794680	158794780	+	3	cIP2vsInput	promoter-TSS (NM_145742)	promoter-TSS (NM_145742)	-90	NM_145742	71715	Mm.315652	NM_145742	ENSMUSG00000027655	Dhx35	1200009D07Rik|Ddx35	DEAH (Asp-Glu-Ala-His) box polypeptide 35	protein-coding	0.07	0.623762
Merged-chr12-85436469-1	chr12	85436419	85436519	+	3	cIP1vsInput	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-37432	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding	0	0.50495
Merged-chr9-44721465-1	chr9	44721415	44721515	+	3	cIP2vsInput	"intron (NM_153537, intron 4 of 21)"	G-rich|Low_complexity|Low_complexity	13733	NM_153537	102693	Mm.28639	NM_153537	ENSMUSG00000048537	Phldb1	AU041016|D330037A14Rik|Ll5a	"pleckstrin homology-like domain, family B, member 1"	protein-coding	0.05	0.70297
Merged-chr1-17097952-1	chr1	17097902	17098002	+	3	cIP1vsInput	promoter-TSS (NM_020604)	promoter-TSS (NM_020604)	-63	NM_020604	57339	Mm.143761	NM_020604	ENSMUSG00000042686	Jph1	ENSMUSG00000054314|JP-1|Jp1	junctophilin 1	protein-coding	0.15	0.861386
Merged-chr14-51089520-1	chr14	51089470	51089570	+	3	cIP2vsInput	Intergenic	tRNA-Tyr-TAC|tRNA|tRNA	-1557	NM_001161731	11727	Mm.202665	NM_001161731	ENSMUSG00000072115	Ang	AI385586|Ang1|Rnase5|Rnase5a	"angiogenin, ribonuclease, RNase A family, 5"	protein-coding	0.06	0.544554
Merged-chr1-91459730-1	chr1	91459680	91459780	+	3	cIP1vsInput	promoter-TSS (NM_011066)	promoter-TSS (NM_011066)	-402	NM_011066	18627	Mm.482463	NM_011066	ENSMUSG00000055866	Per2	mKIAA0347|mPer2	period circadian clock 2	protein-coding	0.08	0.584158
Merged-chr17-86997765-1	chr17	86997715	86997815	+	3	cIP1vsInput	"3' UTR (NM_145491, exon 5 of 5)"	"3' UTR (NM_145491, exon 5 of 5)"	27636	NM_008838	18701	Mm.219685	NM_008838	ENSMUSG00000024145	Pigf	-	"phosphatidylinositol glycan anchor biosynthesis, class F"	protein-coding	0	0.29703
Merged-chr8-49904061-1	chr8	49904011	49904111	+	3	cIP1vsInput	Intergenic	Intergenic	-464051	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.336634
Merged-chr10-19014815-1	chr10	19014765	19014865	+	3	cIP1vsInput	"intron (NM_009397, intron 1 of 8)"	"intron (NM_009397, intron 1 of 8)"	595	NM_009397	21929	Mm.116683	NM_001166402	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	"tumor necrosis factor, alpha-induced protein 3"	protein-coding	0.04	0.564356
Merged-chr18-27126219-1	chr18	27126169	27126269	+	3	cIP1vsInput	Intergenic	Intergenic	-1372236	NM_001174074	108013	Mm.266435	NM_001146292	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	"CUGBP, Elav-like family member 4"	protein-coding	0	0.316832
Merged-chr13-21362922-1	chr13	21362872	21362972	+	3	cIP2vsInput	"intron (NM_016684, intron 1 of 3)"	CpG	102	NM_016684	22758	Mm.399546	NM_016684		Zscan12	2510038J07Rik|FPM315|Zfp96|mKIAA0426	zinc finger and SCAN domain containing 12	protein-coding	0.06	0.663366
Merged-chr16-11134471-1	chr16	11134421	11134521	+	3	cIP2vsInput	promoter-TSS (NM_029582)	promoter-TSS (NM_029582)	61	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding	0.13	0.722772
Merged-chr6-72362340-2	chr6	72362284	72362397	+	3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025607)	promoter-TSS (NM_025607)	41	NM_025607	66510	Mm.170023	NM_025607	ENSMUSG00000055850	Rnf181	1700047F16Rik|2500002L14Rik|6230415N01Rik|C77350	ring finger protein 181	protein-coding	0.070796	0.578947
Merged-chr5-108669216-1	chr5	108669166	108669266	+	3	cIP2vsInput	"5' UTR (NM_008325, exon 1 of 14)"	"5' UTR (NM_008325, exon 1 of 14)"	110	NM_008325	15932	Mm.358608	NM_008325	ENSMUSG00000033540	Idua	6030426D08	"iduronidase, alpha-L-"	protein-coding	0.09	0.613861
Merged-chr18-65272227-1	chr18	65272177	65272277	+	3	cIP2vsInput	"intron (NM_001037294, intron 12 of 12)"	(GA)n|Simple_repeat|Simple_repeat	23366	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122a	Mirn122a|mmu-mir-122	microRNA 122a	miscRNA	0.02	0.564356
Merged-chr8-101114307-1	chr8	101114257	101114357	+	3	cIP1vsInput	Intergenic	Intergenic	1670804	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0	0.366337
Merged-chr7-112258684-1	chr7	112258634	112258734	+	3	cIP2vsInput	"intron (NM_177282, intron 2 of 19)"	"intron (NM_177282, intron 2 of 19)"	32848	NM_001193305	320878	Mm.488195	NM_001193305	ENSMUSG00000038244	Mical2	5330438E18Rik|9530064J02|MICAL-2|mKIAA0750	"microtubule associated monooxygenase, calponin and LIM domain containing 2"	protein-coding	0	0.50495
Merged-chr6-28423458-1	chr6	28423408	28423508	+	3	cIP2vsInput	promoter-TSS (NM_007480)	promoter-TSS (NM_007480)	-182	NM_007480	11844	Mm.389075	NM_007480	ENSMUSG00000020440	Arf5	-	ADP-ribosylation factor 5	protein-coding	0.05	0.673267
Merged-chr4-119320579-1	chr4	119320529	119320629	+	3	cIP2vsInput	promoter-TSS (NM_001110130)	promoter-TSS (NM_001110130)	-56	NM_001110130	66101	Mm.380651	NM_001110129	ENSMUSG00000060288	Ppih	1100001J08Rik|2010111B15Rik|4833408F11Rik|AI464484|CYP-20|CYPH|D4Wsu43e	peptidyl prolyl isomerase H	protein-coding	0.12	0.643564
Merged-chr18-50022969-1	chr18	50022919	50023019	+	3	cIP2vsInput	"intron (NM_001177759, intron 1 of 1)"	"intron (NM_001177759, intron 1 of 1)"	-30313	NM_134131	106869	Mm.27740	NM_001177759	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2	"tumor necrosis factor, alpha-induced protein 8"	protein-coding	0.03	0.445545
Merged-chr1-118459229-1	chr1	118459179	118459279	+	3	cIP2vsInput	promoter-TSS (NR_027901)	promoter-TSS (NR_027901)	36	NR_027901	68204	Mm.443536	NR_027901		2900060B14Rik	-	RIKEN cDNA 2900060B14 gene	miscRNA	0.06	0.544554
Merged-chr2-181581210-1	chr2	181581160	181581260	+	3	cIP1vsInput	TTS (NM_001164597)	TTS (NM_001164597)	763	NM_026765	68556	Mm.232400	NM_026765	ENSMUSG00000089917	Uckl1	1110007H10Rik|Urkl1	uridine-cytidine kinase 1-like 1	protein-coding	0.04	0.554455
Merged-chr9-20544801-1	chr9	20544751	20544851	+	3	cIP2vsInput	Intergenic	Intergenic	-23382	NM_001082485	77519	Mm.431849	NM_001082485	ENSMUSG00000060510	Zfp266	5330440G10Rik|5730601F06Rik|AW552317	zinc finger protein 266	protein-coding	0.04	0.534653
Merged-chr15-83345140-1	chr15	83345090	83345190	+	3	cIP1vsInput	"intron (NM_025445, intron 1 of 15)"	"intron (NM_025445, intron 1 of 15)"	5107	NM_025445	66251	Mm.258910	NM_025445	ENSMUSG00000054277	Arfgap3	0610009H19Rik|1810004P07Rik|1810035F16Rik|9130416J18Rik|Arfgap1	ADP-ribosylation factor GTPase activating protein 3	protein-coding	0.01	0.524752
Merged-chr1-138520752-1	chr1	138520702	138520802	+	3	cIP1vsInput	"intron (NM_021605, intron 5 of 9)"	"intron (NM_021605, intron 5 of 9)"	98944	NM_021605	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding	0	0.336634
Merged-chr16-45164990-1	chr16	45164940	45165040	+	3	cIP1vsInput	"intron (NM_026402, intron 2 of 11)"	"intron (NM_026402, intron 2 of 11)"	6161	NM_026402	67841	Mm.41775	NM_026402	ENSMUSG00000022663	Atg3	2610016C12Rik|APG3|Apg3l|Atg3l|PC3-96	autophagy related 3	protein-coding	0	0.316832
Merged-chr9-15279807-1	chr9	15279757	15279857	+	3	cIP2vsInput	promoter-TSS (NM_144933)	promoter-TSS (NM_144933)	60	NM_144933	234959	Mm.44151	NM_144933	ENSMUSG00000031935	Med17	77kDa|C330002H14Rik|Crsp6|Trap80	mediator complex subunit 17	protein-coding	0.13	0.683168
Merged-chr5-131640090-1	chr5	131640040	131640140	+	3	cIP1vsInput	"intron (NM_177047, intron 5 of 18)"	"intron (NM_177047, intron 5 of 18)"	-240179	NR_040704	75369	Mm.389696	NR_040704		4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	miscRNA	0	0.346535
Merged-chr15-86487198-1	chr15	86487148	86487248	+	3	cIP2vsInput	"intron (NM_145476, intron 12 of 12)"	"intron (NM_145476, intron 12 of 12)"	272739	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	"TBC1 domain family, member 22a"	protein-coding	0	0.39604
Merged-chr2-97434515-1	chr2	97434465	97434565	+	3	cIP1vsInput	Intergenic	Intergenic	-33159	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.306931
Merged-chr3-106076665-1	chr3	106076615	106076715	+	3	cIP1vsInput	Intergenic	Lx2B2|LINE|L1	-36717	NM_023186	81600	Mm.46418	NM_023186	ENSMUSG00000062778	Chia	2200003E03Rik|AMCase|YNL	"chitinase, acidic"	protein-coding	0	0.29703
Merged-chr19-43689258-1	chr19	43689208	43689308	+	3	cIP2vsInput	promoter-TSS (NM_053103)	promoter-TSS (NM_053103)	-431	NM_053103	93685	Mm.296789	NM_053103	ENSMUSG00000025192	Entpd7	1810012B13Rik|1810020C02Rik|2810003F23Rik|LALP1|Lysal2	ectonucleoside triphosphate diphosphohydrolase 7	protein-coding	0.03	0.455446
Merged-chr15-59374218-1	chr15	59374168	59374268	+	3	cIP2vsInput	promoter-TSS (NM_026746)	promoter-TSS (NM_026746)	20	NM_001164604	68501	Mm.27762	NM_001164604	ENSMUSG00000059586	Nsmce2	1110014D18Rik|AI661537	"non-SMC element 2 homolog (MMS21, S. cerevisiae)"	protein-coding	0.16	0.722772
Merged-chr1-49942730-1	chr1	49942680	49942780	+	3	cIP1vsInput	Intergenic	MTD|LTR|ERVL-MaLR	-984793	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.346535
Merged-chr2-115304312-1	chr2	115304262	115304362	+	3	cIP1vsInput	Intergenic	Lx5|LINE|L1	39968	NR_040516	78193	Mm.189508	NR_040516	ENSMUSG00000087309	4930528P14Rik	-	RIKEN cDNA 4930528P14 gene	miscRNA	0	0.306931
Merged-chr7-75782002-1	chr7	75781952	75782052	+	3	cIP2vsInput	Intergenic	CpG	-66336	NM_001122780	207952	Mm.206223	NM_001122780	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding	0.12	0.683168
Merged-chr19-53716825-1	chr19	53716775	53716875	+	3	cIP2vsInput	"intron (NM_001170847, intron 1 of 13)"	"intron (NM_001170847, intron 1 of 13)"	39519	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding	0.02	0.386139
Merged-chr14-55094673-1	chr14	55094623	55094723	+	3	cIP1vsInput	promoter-TSS (NM_153083)	promoter-TSS (NM_153083)	-111	NM_153083	105663	Mm.319204	NM_153083	ENSMUSG00000045691	Thtpa	AW122966	thiamine triphosphatase	protein-coding	0.04	0.50495
Merged-chr6-130828101-2	chr6	130828047	130828155	+	3	cIP1vsInput|cIP2vsInput	Intergenic	RMER13A2|LTR|ERVK	419261	NM_001170851	16633	Mm.4783	NM_001170851	ENSMUSG00000030187	Klra2	Klra30|Ly49b	"killer cell lectin-like receptor, subfamily A, member 2"	protein-coding	0	0.366972
Merged-chr13-12036864-1	chr13	12036814	12036914	+	3	cIP2vsInput	"intron (NM_023868, intron 1 of 104)"	MER67C|LTR|ERV1	70081	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	"ryanodine receptor 2, cardiac"	protein-coding	0	0.405941
Merged-chr18-24934932-1	chr18	24934882	24934982	+	3	cIP1vsInput	"intron (NM_175276, intron 5 of 26)"	"intron (NM_175276, intron 5 of 26)"	225487	NM_175276	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding	0	0.287129
Merged-chr7-84689505-2	chr7	84689446	84689565	+	3	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_038175)	promoter-TSS (NR_038175)	-135	NR_038175	72495	Mm.382914	NR_038175		2610206C17Rik	-	RIKEN cDNA 2610206C17 gene	miscRNA	0.067227	0.625
Merged-chr16-18289125-1	chr16	18289075	18289175	+	3	cIP2vsInput	promoter-TSS (NM_033324)	promoter-TSS (NM_033324)	43	NM_033324	94223	Mm.482156	NM_033324	ENSMUSG00000022718	Dgcr8	D16H22S1742E|D16H22S788E|D16Wis2|Gy1|N41|Vo59c07	DiGeorge syndrome critical region gene 8	protein-coding	0.17	0.811881
Merged-chr10-16548315-1	chr10	16548265	16548365	+	3	cIP2vsInput	Intergenic	L1MA9|LINE|L1	547467	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0	0.346535
Merged-chr13-79640069-1	chr13	79640019	79640119	+	3	cIP2vsInput	Intergenic	B3A|SINE|B2	-1243353	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0	0.366337
Merged-chr6-113624133-1	chr6	113624083	113624183	+	3	cIP1vsInput	"5' UTR (NM_009507, exon 1 of 3)"	"5' UTR (NM_009507, exon 1 of 3)"	112	NM_009507	22346	Mm.29407	NM_009507	ENSMUSG00000033933	Vhl	Vhlh	von Hippel-Lindau tumor suppressor	protein-coding	0.12	0.70297
Merged-chrX-13242908-1	chrX	13242858	13242958	+	3	cIP2vsInput	"intron (NR_045429, intron 1 of 2)"	"intron (NR_045429, intron 1 of 2)"	4825	NR_045429	72122	Mm.75434	NR_045429		2010308F09Rik	-	RIKEN cDNA 2010308F09 gene	miscRNA	0.01	0.643564
Merged-chr1-191556346-1	chr1	191556296	191556396	+	3	cIP1vsInput	"intron (NM_029766, intron 10 of 14)"	"intron (NM_029766, intron 10 of 14)"	19188	NM_029766	76843	Mm.189102	NM_029766	ENSMUSG00000037474	Dtl	2810047L02Rik|5730564G15Rik|Ramp	denticleless homolog (Drosophila)	protein-coding	0	0.386139
Merged-chr14-34290856-1	chr14	34290806	34290906	+	3	cIP1vsInput	"intron (NM_029389, intron 2 of 10)"	"intron (NM_029389, intron 2 of 10)"	19647	NM_029389	75698	Mm.45406	NM_029389	ENSMUSG00000041471	Fam35a	3110001K24Rik	"family with sequence similarity 35, member A"	protein-coding	0.01	0.316832
Merged-chr19-23632469-1	chr19	23632419	23632519	+	3	cIP2vsInput	"intron (NM_026188, intron 1 of 5)"	"intron (NM_026188, intron 1 of 5)"	20343	NM_026188	67483	Mm.443287	NM_026188	ENSMUSG00000033053	1700028P14Rik	AV209940	RIKEN cDNA 1700028P14 gene	protein-coding	0	0.316832
Merged-chr15-11745010-1	chr15	11744960	11745060	+	3	cIP2vsInput	Intergenic	Intergenic	160664	NM_008728	18162	Mm.25259	NM_001039181	ENSMUSG00000022206	Npr3	B430320C24Rik|C81222|NPR-C|lgj|stri	natriuretic peptide receptor 3	protein-coding	0.01	0.39604
Merged-chr18-75594117-2	chr18	75594033	75594201	+	3	cIP1vsInput|cIP2vsInput	"intron (NM_201354, intron 6 of 11)"	"intron (NM_201354, intron 6 of 11)"	79472	NR_045879	100038353	Mm.440724	NR_045879	ENSMUSG00000097712	Gm10532	ENSMUSG00000073534	predicted gene 10532	miscRNA	0.059524	0.662722
Merged-chr2-119873387-1	chr2	119873337	119873437	+	3	cIP1vsInput	Intergenic	CpG	-23841	NM_001164274	29808	Mm.437053	NM_001164274	ENSMUSG00000033943	Mga	AV312082|C130042M01Rik|C80739|D030062C11Rik|Mad5	MAX gene associated	protein-coding	0.12	0.643564
Merged-chr1-119504940-1	chr1	119504890	119504990	+	3	cIP2vsInput	promoter-TSS (NM_022327)	promoter-TSS (NM_022327)	-158	NM_022327	64143	Mm.27832	NM_022327	ENSMUSG00000004451	Ralb	5730472O18Rik	v-ral simian leukemia viral oncogene homolog B (ras related)	protein-coding	0.08	0.70297
Merged-chr8-23207215-1	chr8	23207165	23207265	+	3	cIP1vsInput	"intron (NM_018743, intron 1 of 12)"	"intron (NM_018743, intron 1 of 12)"	1238	NM_018743	102247	Mm.200898	NM_018743	ENSMUSG00000031545	Agpat6	AU041707|AW545732|GPAT4|Tsarg7	"1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta)"	protein-coding	0.01	0.336634
Merged-chr13-95765219-1	chr13	95765169	95765269	+	3	cIP2vsInput	"intron (NM_027711, intron 2 of 35)"	"intron (NM_027711, intron 2 of 35)"	68299	NM_010170	14064	Mm.440952	NM_010170	ENSMUSG00000021675	F2rl2	F730031A08|PAR3	coagulation factor II (thrombin) receptor-like 2	protein-coding	0.02	0.50495
Merged-chr6-108185606-2	chr6	108185553	108185659	+	3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145937)	promoter-TSS (NM_145937)	-23	NM_145937	58911	Mm.439876	NM_145937	ENSMUSG00000030101	Sumf1	AA543204|AI463102|AI851573|FGE	sulfatase modifying factor 1	protein-coding	0.028302	0.485981
Merged-chr14-21824086-1	chr14	21824036	21824136	+	3	cIP2vsInput	Intergenic	RMER20B|LTR|ERVK	-7475	NM_011695	22334	Mm.262327	NM_011695	ENSMUSG00000021771	Vdac2	Vdac6|mVDAC2|mVDAC6	voltage-dependent anion channel 2	protein-coding	0	0.49505
Merged-chr2-122348984-1	chr2	122348934	122349034	+	3	cIP2vsInput	TTS (NM_001013829)	TTS (NM_001013829)	19934	NM_001013829	435684	Mm.458215	NM_001013829	ENSMUSG00000033256	Shf	-	Src homology 2 domain containing F	protein-coding	0.13	0.831683
Merged-chr1-131867219-1	chr1	131867169	131867269	+	3	cIP1vsInput	promoter-TSS (NM_144875)	promoter-TSS (NM_144875)	-58	NM_144875	226422	Mm.34027	NM_144875	ENSMUSG00000026433	Rab7l1	-	"RAB7, member RAS oncogene family-like 1"	protein-coding	0.06	0.564356
Merged-chr2-155956369-1	chr2	155956319	155956419	+	3	cIP2vsInput	promoter-TSS (NM_001130000)	promoter-TSS (NM_001130000)	-189	NM_001129999	16328	Mm.288729	NM_001129999	ENSMUSG00000038241	Cep250	AW490617|B230210E21Rik|Cep2|Inmp	centrosomal protein 250	protein-coding	0.03	0.475248
Merged-chr4-132329500-1	chr4	132329450	132329550	+	3	cIP2vsInput	promoter-TSS (NM_027925)	promoter-TSS (NM_027925)	38	NM_027925	71787	Mm.239183	NM_027925	ENSMUSG00000028898	Trnau1ap	1110007F05Rik|AA387999|Secp43|Trspap1	tRNA selenocysteine 1 associated protein 1	protein-coding	0.11	0.722772
Merged-chr5-38260489-1	chr5	38260439	38260539	+	3	cIP2vsInput	"exon (NM_025480, exon 1 of 5)"	"exon (NM_025480, exon 1 of 5)"	114	NM_025480	66309	Mm.256185	NM_025480	ENSMUSG00000067365	Tmem128	2810021O14Rik	transmembrane protein 128	protein-coding	0.07	0.653465
Merged-chr12-81998583-1	chr12	81998533	81998633	+	3	cIP1vsInput	"3' UTR (NM_018814, exon 36 of 36)"	"3' UTR (NM_018814, exon 36 of 36)"	138553	NM_018814	54604	Mm.86584	NM_018814	ENSMUSG00000021140	Pcnx	2900024E21Rik|3526401J03Rik|AF096286|AI327143|AI413187|Pcnxl1	pecanex homolog (Drosophila)	protein-coding	0	0.326733
Merged-chr14-25842034-1	chr14	25841984	25842084	+	3	cIP2vsInput	promoter-TSS (NM_013469)	promoter-TSS (NM_013469)	-121	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding	0.06	0.584158
Merged-chr7-13799831-1	chr7	13799781	13799881	+	3	cIP1vsInput	"intron (NM_001111296, intron 5 of 5)"	"intron (NM_001111296, intron 5 of 5)"	37579	NM_001111296	20859	Mm.260026	NM_001111296	ENSMUSG00000078798	Sult2a1	ST2A1|Std|Sth1|mSTa1	"sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 1"	protein-coding	0	0.267327
Merged-chr2-34564736-1	chr2	34564686	34564786	+	3	cIP2vsInput	"intron (NM_177345, intron 7 of 10)"	L1M5|LINE|L1	132711	NM_177345	227743	Mm.270866	NM_177345	ENSMUSG00000038696	Mapkap1	AI591529|D230039K05Rik|Sin1	mitogen-activated protein kinase associated protein 1	protein-coding	0	0.376238
Merged-chr8-120736224-1	chr8	120736174	120736274	+	3	cIP1vsInput	promoter-TSS (NM_008320)	promoter-TSS (NM_008320)	-152	NM_008320	15900	Mm.334861	NM_008320	ENSMUSG00000041515	Irf8	AI893568|ICSBP|IRF-8|Icsbp1|Myls	interferon regulatory factor 8	protein-coding	0.08	0.594059
Merged-chr5-6859427-1	chr5	6859377	6859477	+	3	cIP1vsInput	"intron (NM_001163223, intron 2 of 3)"	HAL1|LINE|L1	-444737	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding	0	0.306931
Merged-chr11-111441423-1	chr11	111441373	111441473	+	3	cIP2vsInput	Intergenic	Intergenic	375259	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	"potassium inwardly-rectifying channel, subfamily J, member 2"	protein-coding	0	0.277228
Merged-chrY-6728684-1	chrY	6728634	6728734	+	3	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	439093	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.277228
Merged-chr7-67240755-1	chr7	67240705	67240805	+	3	cIP1vsInput	"intron (NM_001033713, intron 9 of 11)"	"intron (NM_001033713, intron 9 of 11)"	18139	NM_001191051	75099	Mm.121691	NM_001191051	ENSMUSG00000043831	Lysmd4	4930506D23Rik	"LysM, putative peptidoglycan-binding, domain containing 4"	protein-coding	0	0.287129
Merged-chr18-46982540-1	chr18	46982490	46982590	+	3	cIP1vsInput	"intron (NM_178377, intron 4 of 6)"	"intron (NM_178377, intron 4 of 6)"	23664	NM_178377	69456	Mm.210734	NM_178377	ENSMUSG00000042705	Commd10	2310003A05Rik|AU019438|DRWMS2	COMM domain containing 10	protein-coding	0	0.346535
Merged-chr9-67582023-1	chr9	67581973	67582073	+	3	cIP1vsInput	Intergenic	Intergenic	-22320	NM_001081242	70549	Mm.33645	NM_027458	ENSMUSG00000052698	Tln2	5730421P04Rik|AI507121|AI787438|AL118320|mKIAA0320	talin 2	protein-coding	0.01	0.435644
Merged-chr4-90374913-1	chr4	90374863	90374963	+	3	cIP2vsInput	Intergenic	Intergenic	-13599	NR_033610	619842	Mm.484218	NR_033610	ENSMUSG00000080756	Gm12633	OTTMUSG00000007790	zinc finger protein 352 pseudogene	pseudo	0	0.346535
Merged-chr2-163602215-1	chr2	163602165	163602265	+	3	cIP2vsInput	promoter-TSS (NM_181734)	promoter-TSS (NM_181734)	-99	NM_181734	76080	Mm.89828	NM_029512	ENSMUSG00000017679	Ttpal	3110080A02Rik|5830472M02Rik	tocopherol (alpha) transfer protein-like	protein-coding	0.03	0.594059
Merged-chr5-30775250-2	chr5	30775199	30775301	+	3	cIP1vsInput|cIP2vsInput	"intron (NM_023047, intron 2 of 12)"	"intron (NM_023047, intron 2 of 12)"	-39506	NM_133350	100732	Mm.471154	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3	"microtubule-associated protein, RP/EB family, member 3"	protein-coding	0.039216	0.553398
Merged-chr10-106685782-2	chr10	106685724	106685841	+	3	cIP1vsInput|cIP2vsInput	"intron (NM_177373, intron 3 of 31)"	"intron (NM_177373, intron 3 of 31)"	215472	NM_001205341	327814	Mm.391424	NM_001205341	ENSMUSG00000053825	Ppfia2	5330438O12|B230207K17Rik|E130120L08Rik|mKIAA4112	"protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2"	protein-coding	0.017094	0.389831
Merged-chr15-88861844-1	chr15	88861794	88861894	+	3	cIP1vsInput	promoter-TSS (NM_145478)	promoter-TSS (NM_145478)	-350	NM_145478	223775	Mm.474725	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding	0.1	0.633663
Merged-chr10-80053884-1	chr10	80053834	80053934	+	3	cIP1vsInput	promoter-TSS (NM_001037741)	promoter-TSS (NM_001037741)	-153	NM_001037741	625249	Mm.359573	NM_001037741	ENSMUSG00000075706	Gpx4	1700027O09Rik|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding	0.08	0.643564
Merged-chrY-88120062-1	chrY	88120012	88120112	+	3	cIP1vsInput	Intergenic	Intergenic	-2590543	NM_001160131	100040911	Mm.457993	NM_001160131	ENSMUSG00000095650	Gm20854	-	"predicted gene, 20854"	protein-coding	0	0.465347
Merged-chr14-77004430-1	chr14	77004380	77004480	+	3	cIP1vsInput	Intergenic	L2a|LINE|L2	32187	NM_172488	210808	Mm.89278	NM_172488	ENSMUSG00000044350	Lacc1	9030625A04Rik	laccase (multicopper oxidoreductase) domain containing 1	protein-coding	0.01	0.356436
Merged-chr9-115163589-1	chr9	115163539	115163639	+	3	cIP1vsInput	"intron (NM_148958, intron 2 of 9)"	"intron (NM_148958, intron 2 of 9)"	96310	NM_148958	74486	Mm.458474	NM_148958	ENSMUSG00000040875	Osbpl10	4933433D06Rik|C820004B04Rik|OPR-10	oxysterol binding protein-like 10	protein-coding	0.01	0.336634
Merged-chr17-50600268-1	chr17	50600218	50600318	+	3	cIP1vsInput	"intron (NM_013880, intron 1 of 5)"	RMER10A|LTR|ERVL	90721	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding	0.01	0.356436
Merged-chr10-39165825-1	chr10	39165775	39165875	+	3	cIP2vsInput	Intergenic	Intergenic	-2031	NM_001127376	327743	Mm.208111	NM_001127376	ENSMUSG00000062074	Wisp3	CCN6|ENSMUSG00000062074|Gm735|WISP-3	WNT1 inducible signaling pathway protein 3	protein-coding	0.01	0.514851
Merged-chrY-6672387-1	chrY	6672337	6672437	+	3	cIP1vsInput	Intergenic	Intergenic	495390	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.376238
Merged-chr9-123717420-1	chr9	123717370	123717470	+	3	cIP1vsInput	"intron (NM_033322, intron 1 of 9)"	CpG	137	NM_033322	93730	Mm.475504	NM_033322	ENSMUSG00000025245	Lztfl1	5530402H04Rik|6130400H19Rik|AI414725|AW048545	leucine zipper transcription factor-like 1	protein-coding	0.13	0.722772
Merged-chr15-8709853-1	chr15	8709803	8709903	+	3	cIP2vsInput	"intron (NM_148938, intron 1 of 9)"	"intron (NM_148938, intron 1 of 9)"	954	NM_148938	20512	Mm.204834	NM_148938	ENSMUSG00000005360	Slc1a3	AI504299|B430115D02Rik|Eaat1|GLAST|GLAST-1|GLU-T|GluT-1|Gmt1|MGluT1	"solute carrier family 1 (glial high affinity glutamate transporter), member 3"	protein-coding	0.06	0.594059
Merged-chr16-91931616-1	chr16	91931566	91931666	+	3	cIP2vsInput	promoter-TSS (NM_138597)	promoter-TSS (NM_138597)	14	NM_138597	28080	Mm.41	NM_138597	ENSMUSG00000022956	Atp5o	ATPO|D12Wsu28e|OSCP	"ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit"	protein-coding	0.13	0.60396
Merged-chr2-132781834-1	chr2	132781784	132781884	+	3	cIP2vsInput	"intron (NM_007694, intron 1 of 4)"	"intron (NM_007694, intron 1 of 4)"	556	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding	0.03	0.594059
Merged-chr10-32831528-1	chr10	32831478	32831578	+	3	cIP2vsInput	"intron (NM_001013411, intron 1 of 6)"	"intron (NM_001013411, intron 1 of 6)"	58387	NM_001013411	432450	Mm.49665	NM_001013411		Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding	0	0.346535
Merged-chr7-102250787-1	chr7	102250737	102250837	+	3	cIP2vsInput	promoter-TSS (NM_019566)	promoter-TSS (NM_019566)	-669	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	"ras homolog gene family, member G"	protein-coding	0.1	0.712871
Merged-chr11-101057158-1	chr11	101057108	101057208	+	3	cIP1vsInput	"intron (NM_001243050, intron 20 of 20)"	"intron (NM_001243050, intron 20 of 20)"	-12936	NM_013792	27419	Mm.95452	NM_013792	ENSMUSG00000001751	Naglu	-	alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB)	protein-coding	0.04	0.613861
Merged-chr6-71433790-1	chr6	71433740	71433840	+	3	cIP1vsInput	"intron (NM_024288, intron 1 of 8)"	"intron (NM_024288, intron 1 of 8)"	6847	NM_024288	68477	Mm.28474	NM_024288	ENSMUSG00000002222	Rmnd5a	1110007A06Rik|AJ237586|AW125795|Gid2|MTA.D02.090	required for meiotic nuclear division 5 homolog A (S. cerevisiae)	protein-coding	0	0.376238
Merged-chr3-134146820-1	chr3	134146770	134146870	+	3	cIP2vsInput	Intergenic	Intergenic	-89675	NM_001004367	319478	Mm.487501	NM_001004367	ENSMUSG00000044365	Cxxc4	9330210J02Rik|C030003J12Rik|Idax	CXXC finger 4	protein-coding	0.01	0.564356
Merged-chr11-102296971-1	chr11	102296921	102297021	+	3	cIP1vsInput	promoter-TSS (NM_001098836)	promoter-TSS (NM_001098836)	-342	NM_001098837	217218	Mm.390381	NM_001098836	ENSMUSG00000059995	Atxn7l3	E030022H21Rik	ataxin 7-like 3	protein-coding	0.14	0.693069
Merged-chr7-4740195-1	chr7	4740145	4740245	+	3	cIP2vsInput	promoter-TSS (NM_146177)	promoter-TSS (NM_146177)	68	NM_001115018	232811	Mm.247844	NM_001115018	ENSMUSG00000059851	Suv420h2	BC024816|KMT5C|Suv4-20h2	suppressor of variegation 4-20 homolog 2 (Drosophila)	protein-coding	0.11	0.712871
Merged-chr2-76172525-1	chr2	76172475	76172575	+	3	cIP1vsInput	"intron (NM_001081033, intron 5 of 19)"	"intron (NM_001081033, intron 5 of 19)"	166128	NM_001081033	241489	Mm.246613	NM_001081033		Pde11a	6330414F14Rik|A630086N24Rik|Gm350|PDE11A1	phosphodiesterase 11A	protein-coding	0.01	0.356436
Merged-chr1-183349879-1	chr1	183349829	183349929	+	3	cIP1vsInput	"intron (NM_177389, intron 6 of 26)"	"intron (NM_177389, intron 6 of 26)"	19686	NM_177389	338366	Mm.41152	NM_177389		Mia3	9130229H14Rik|A930039G15Rik|AU022327|B230399H06Rik|C80126|Gm1525|Tango	melanoma inhibitory activity 3	protein-coding	0.01	0.346535
Merged-chr5-146795154-1	chr5	146795104	146795204	+	3	cIP1vsInput	promoter-TSS (NM_011669)	promoter-TSS (NM_011669)	-198	NM_011669	22217	Mm.167971	NM_011669	ENSMUSG00000029640	Usp12	Ubh1	ubiquitin specific peptidase 12	protein-coding	0.11	0.673267
Merged-chr4-43010683-1	chr4	43010633	43010733	+	3	cIP2vsInput	promoter-TSS (NM_053081)	promoter-TSS (NM_053081)	-382	NM_053081	60534	Mm.23122	NM_001163233	ENSMUSG00000028453	Fancg	AU041407|Xrcc9	"Fanconi anemia, complementation group G"	protein-coding	0.02	0.50495
Merged-chr2-61967760-1	chr2	61967710	61967810	+	3	cIP1vsInput	Intergenic	Intergenic	-78755	NM_001242382	94229	Mm.314497	NM_001242378	ENSMUSG00000026904	Slc4a10	NCBE|mKIAA4136	"solute carrier family 4, sodium bicarbonate cotransporter-like, member 10"	protein-coding	0	0.366337
Merged-chr6-56831944-1	chr6	56831894	56831994	+	3	cIP2vsInput	promoter-TSS (NM_012056)	promoter-TSS (NM_012056)	-115	NM_012056	27055	Mm.487141	NM_012056	ENSMUSG00000029781	Fkbp9	1810014L23|AW549641|FKBP-63|FKBP-9|FKBP60|FKBP63|FKBP65RS	FK506 binding protein 9	protein-coding	0.07	0.623762
Merged-chr6-42754457-1	chr6	42754407	42754507	+	3	cIP1vsInput	Intergenic	L1ME1|LINE|L1	-7597	NM_146986	258988	Mm.377777	NM_146986	ENSMUSG00000095236	Olfr38	18A|MOR257-2	olfactory receptor 38	protein-coding	0.01	0.306931
Merged-chr9-3894420-1	chr9	3894370	3894470	+	3	cIP2vsInput	"intron (NM_001033322, intron 7 of 7)"	"intron (NM_001033322, intron 7 of 7)"	362071	NM_001033322	234889	Mm.91240	NM_001033322		Gucy1a2	6330407I18Rik|A230060L24Rik	"guanylate cyclase 1, soluble, alpha 2"	protein-coding	0	0.326733
Merged-chr5-142557539-1	chr5	142557489	142557589	+	3	cIP1vsInput	Intergenic	Intergenic	-6462	NM_178702	231858	Mm.33766	NM_178702	ENSMUSG00000029576	Radil	AI536456|D930005D10Rik	Ras association and DIL domains	protein-coding	0.11	0.653465
Merged-chr6-56809296-1	chr6	56809246	56809346	+	3	cIP2vsInput	Intergenic	Intergenic	-11483	NM_145958	210973	Mm.57295	NM_145958	ENSMUSG00000059486	Kbtbd2	BC022962|Bklhd1|mKIAA1489	kelch repeat and BTB (POZ) domain containing 2	protein-coding	0	0.306931
Merged-chr3-97240707-1	chr3	97240657	97240757	+	3	cIP1vsInput	Intergenic	Intergenic	-13343	NM_029933	77578	Mm.482931	NM_029933	ENSMUSG00000038256	Bcl9	2610202E01Rik|8030475K17Rik|A330041G23Rik|Gm130	B cell CLL/lymphoma 9	protein-coding	0.01	0.366337
Merged-chr5-15702946-2	chr5	15702859	15703034	+	3	cIP1vsInput|cIP2vsInput	"intron (NR_001585, intron 2 of 4)"	"intron (NR_001585, intron 2 of 4)"	22236	NR_001585	75858	Mm.359463	NR_001585	ENSMUSG00000089871	Speer7-ps1	4930568L21Rik|SPEER-7|Speer7-ps	"spermatogenesis associated glutamate (E)-rich protein 7, pseudogene 1"	pseudo	0.017143	0.340909
Merged-chr19-45451465-1	chr19	45451415	45451515	+	3	cIP1vsInput	"intron (NM_001037758, intron 2 of 14)"	"intron (NM_001037758, intron 2 of 14)"	87731	NM_001037758	12234	Mm.446448	NM_001037758	ENSMUSG00000025217	Btrc	Beta-Trcp1|FWD1|Fbw1a|HOS|Slimb|b-TrCP|beta-TrCP|mKIAA4123	beta-transducin repeat containing protein	protein-coding	0.01	0.316832
Merged-chr12-100110055-1	chr12	100110005	100110105	+	3	cIP2vsInput	Intergenic	CpG	-2276	NM_008947	19179	Mm.157105	NM_008947	ENSMUSG00000021178	Psmc1	AI325227|P26s4|S4	"protease (prosome, macropain) 26S subunit, ATPase 1"	protein-coding	0.06	0.49505
Merged-chr17-78724800-1	chr17	78724750	78724850	+	3	cIP2vsInput	"intron (NM_011500, intron 1 of 17)"	"intron (NM_011500, intron 1 of 17)"	11760	NM_011500	268980	Mm.486430	NM_011500		Strn	AU022939|D130055P19	"striatin, calmodulin binding protein"	protein-coding	0.02	0.554455
Merged-chr14-55560564-1	chr14	55560514	55560614	+	3	cIP1vsInput	promoter-TSS (NM_001199009)	promoter-TSS (NM_001199009)	-359	NM_001199009	28199	Mm.488383	NM_001199009	ENSMUSG00000022214	Dcaf11	0710008A13Rik|C76035|D14Ucla1|Dacf11|GLO14|Wdr23	DDB1 and CUL4 associated factor 11	protein-coding	0.14	0.683168
Merged-chr8-101123271-1	chr8	101123221	101123321	+	3	cIP1vsInput	Intergenic	Intergenic	1661840	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0	0.287129
Merged-chr4-12627345-1	chr4	12627295	12627395	+	3	cIP2vsInput	Intergenic	Intergenic	-279492	NM_173746	208820	Mm.12057	NM_001171801		Triqk	C130086A10|Gm11818|OTTMUSG00000004461	triple QxxK/R motif containing	protein-coding	0.01	0.386139
Merged-chr10-45394455-1	chr10	45394405	45394505	+	3	cIP2vsInput	"intron (NM_001031772, intron 4 of 4)"	Looper|DNA|PiggyBac	58693	NM_024285	23828	Mm.332793	NM_024285	ENSMUSG00000071317	Bves	Pop1|Popdc1|mBVES	blood vessel epicardial substance	protein-coding	0	0.326733
Merged-chr8-105693856-1	chr8	105693806	105693906	+	3	cIP2vsInput	"intron (NM_001033320, intron 8 of 16)"	CpG	2950	NM_001033320	234695	Mm.471640	NM_001033320	ENSMUSG00000050357	Rltpr	CG1399-PB|D130029J02Rik|Gm585	"RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing"	protein-coding	0.15	0.752475
Merged-chr3-103102946-1	chr3	103102896	103102996	+	3	cIP1vsInput	Intergenic	CpG	-24610	NM_177857	329727	Mm.293641	NM_177857	ENSMUSG00000007379	Dennd2c	A930010I20Rik	DENN/MADD domain containing 2C	protein-coding	0.13	0.70297
Merged-chr14-30437527-1	chr14	30437477	30437577	+	3	cIP1vsInput	"intron (NM_028981, intron 1 of 46)"	L1MDb|LINE|L1	-42038	NM_133761	75901	Mm.28733	NM_133761	ENSMUSG00000021962	Dcp1a	1110066A22Rik|4930568L04Rik|AU019772|D14Ertd817e|Mitc1|SMIF	DCP1 decapping enzyme homolog A (S. cerevisiae)	protein-coding	0.02	0.356436
Merged-chr11-6388975-1	chr11	6388925	6389025	+	3	cIP2vsInput	promoter-TSS (NM_028601)	promoter-TSS (NM_028601)	-389	NM_028601	52915	Mm.1144	NM_001005867	ENSMUSG00000041164	Zmiz2	2410117E06Rik|D11Bwg0280e|R74931|Zimp7	"zinc finger, MIZ-type containing 2"	protein-coding	0.06	0.623762
Merged-chr19-44135090-1	chr19	44135040	44135140	+	3	cIP1vsInput	"intron (NM_001081077, intron 1 of 13)"	"intron (NM_001081077, intron 1 of 13)"	786	NM_001081077	72502	Mm.276109	NM_001081077	ENSMUSG00000025200	Cwf19l1	2610528C06Rik|AI854304|AV336991	"CWF19-like 1, cell cycle control (S. pombe)"	protein-coding	0.01	0.316832
Merged-chr4-108328164-1	chr4	108328114	108328214	+	3	cIP1vsInput	promoter-TSS (NM_027250)	promoter-TSS (NM_027250)	12	NM_027250	69893	Mm.28354	NM_027250		Selrc1	2010305A19Rik|AI451324|D4Ertd796e	Sel1 repeat containing 1	protein-coding	0.06	0.613861
Merged-chr9-13241950-1	chr9	13241900	13242000	+	3	cIP1vsInput	TTS (NM_001033181)	TTS (NM_001033181)	3791	NM_001033181	77532	Mm.461740	NM_001033181	ENSMUSG00000079083	Jrkl	C030035D04Rik|HHMJG	jerky homolog-like (mouse)	protein-coding	0	0.316832
Merged-chr7-67797301-1	chr7	67797251	67797351	+	3	cIP2vsInput	"intron (NR_045954, intron 1 of 2)"	"intron (NR_045954, intron 1 of 2)"	6195	NR_045954	73904	Mm.70992	NR_045954	ENSMUSG00000097697	4833412C05Rik	-	RIKEN cDNA 4833412C05 gene	miscRNA	0.01	0.50495
Merged-chr14-89796129-1	chr14	89796079	89796179	+	3	cIP1vsInput	Intergenic	Intergenic	-100095	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0.01	0.336634
Merged-chr7-138919577-1	chr7	138919527	138919627	+	3	cIP2vsInput	Intergenic	Intergenic	-10071	NM_009760	12176	Mm.378890	NM_009760	ENSMUSG00000078566	Bnip3	Nip3	BCL2/adenovirus E1B interacting protein 3	protein-coding	0.05	0.514851
Merged-chr10-93648086-1	chr10	93648036	93648136	+	3	cIP1vsInput	"intron (NM_021320, intron 2 of 9)"	"intron (NM_021320, intron 2 of 9)"	7037	NM_021320	57764	Mm.483868	NM_021320		Ntn4	-	netrin 4	protein-coding	0	0.465347
Merged-chr1-139191507-1	chr1	139191457	139191557	+	3	cIP1vsInput	Intergenic	L1MA5A|LINE|L1	185569	NM_133239	170788	Mm.95700	NM_133239	ENSMUSG00000063681	Crb1	7530426H14Rik|A930008G09Rik	crumbs homolog 1 (Drosophila)	protein-coding	0	0.326733
Merged-chr8-84903185-1	chr8	84903135	84903235	+	3	cIP1vsInput	"exon (NM_010635, exon 2 of 3)"	"exon (NM_010635, exon 2 of 3)"	1257	NM_010635	16596	Mm.4847	NM_010635	ENSMUSG00000054191	Klf1	Eklf|Nan	Kruppel-like factor 1 (erythroid)	protein-coding	0.09	0.722772
Merged-chr13-37602522-1	chr13	37602472	37602572	+	3	cIP2vsInput	Intergenic	Intergenic	-223516	NM_026830	68750	Mm.132634	NM_001013392	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding	0.01	0.475248
Merged-chr17-73804778-2	chr17	73804716	73804841	+	3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_020578)	promoter-TSS (NM_020578)	-63	NM_020578	57440	Mm.18526	NM_020578	ENSMUSG00000024065	Ehd3	Ehd2	EH-domain containing 3	protein-coding	0.104	0.65873
Merged-chr1-75588178-1	chr1	75588128	75588228	+	3	cIP2vsInput	Intergenic	Intergenic	41912	NM_009208	20536	Mm.5053	NM_009208		Slc4a3	A930038D23Rik|Ae3	"solute carrier family 4 (anion exchanger), member 3"	protein-coding	0.02	0.465347
Merged-chr9-77840645-1	chr9	77840595	77840695	+	3	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-76720	NM_134255	68801	Mm.475262	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	"ELOVL family member 5, elongation of long chain fatty acids (yeast)"	protein-coding	0	0.356436
Merged-chrY-6685493-1	chrY	6685443	6685543	+	3	cIP2vsInput	Intergenic	Lx8|LINE|L1	482284	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.425743
Merged-chr15-96751504-1	chr15	96751454	96751554	+	3	cIP1vsInput	Intergenic	Intergenic	-51806	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	"solute carrier family 38, member 2"	protein-coding	0.02	0.49505
Merged-chr1-180568976-1	chr1	180568926	180569026	+	3	cIP2vsInput	promoter-TSS (NM_007415)	promoter-TSS (NM_007415)	1	NM_007415	11545	Mm.277779	NM_007415	ENSMUSG00000026496	Parp1	5830444G22Rik|AI893648|ARTD1|Adprp|Adprt1|C80510|PARP|PPOL|parp-1|sPARP-1	"poly (ADP-ribose) polymerase family, member 1"	protein-coding	0.14	0.683168
Merged-chr9-50686312-1	chr9	50686262	50686362	+	3	cIP1vsInput	"intron (NM_178118, intron 10 of 19)"	"intron (NM_178118, intron 10 of 19)"	-26532	NM_145614	235339	Mm.471144	NM_145614	ENSMUSG00000000168	Dlat	6332404G05Rik|DLTA|PDC-E2	dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex)	protein-coding	0.01	0.386139
Merged-chr2-131160978-1	chr2	131160928	131161028	+	3	cIP2vsInput	promoter-TSS (NM_026091)	promoter-TSS (NM_026091)	-958	NM_026091	67326	Mm.27711	NM_026091	ENSMUSG00000027327	1700037H04Rik	-	RIKEN cDNA 1700037H04 gene	protein-coding	0.04	0.475248
Merged-chr5-45857558-2	chr5	45857485	45857632	+	3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001163073)	promoter-TSS (NM_001163073)	-18	NM_001163073	209707	Mm.71498	NM_001163073	ENSMUSG00000015882	Lcorl	Mlr1	ligand dependent nuclear receptor corepressor-like	protein-coding	0.136054	0.695946
Merged-chr8-38869050-1	chr8	38869000	38869100	+	3	cIP2vsInput	Intergenic	Intergenic	-136817	NM_030254	80286	Mm.272722	NM_030254		Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding	0	0.316832
Merged-chr14-27956815-1	chr14	27956765	27956865	+	3	cIP1vsInput	"intron (NM_177814, intron 6 of 15)"	"intron (NM_177814, intron 6 of 15)"	334373	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding	0	0.415842
Merged-chr7-102440598-1	chr7	102440548	102440648	+	3	cIP1vsInput	Intergenic	Intergenic	-1097	NM_009103	20133	Mm.415177	NM_009103	ENSMUSG00000030978	Rrm1	RnrM1	ribonucleotide reductase M1	protein-coding	0.02	0.316832
Merged-chr13-104728340-1	chr13	104728290	104728390	+	3	cIP2vsInput	"intron (NM_026072, intron 10 of 13)"	"intron (NM_026072, intron 10 of 13)"	88613	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	protein-coding	0	0.336634
Merged-chr15-81190799-1	chr15	81190749	81190849	+	3	cIP2vsInput	promoter-TSS (NR_015603)	promoter-TSS (NR_015603)	-42	NM_001082536	223701	Mm.439814	NM_001082536	ENSMUSG00000042292	Mkl1	AI852829|AMKL|AW743281|AW821984|Bsac|Mal|Mrtf-A	MKL (megakaryoblastic leukemia)/myocardin-like 1	protein-coding	0.09	0.683168
Merged-chr14-28011467-1	chr14	28011417	28011517	+	3	cIP1vsInput	"intron (NM_177814, intron 7 of 15)"	"intron (NM_177814, intron 7 of 15)"	389025	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding	0	0.316832
Merged-chr18-57552537-1	chr18	57552487	57552587	+	3	cIP2vsInput	promoter-TSS (NR_027944)	promoter-TSS (NR_027944)	-140	NR_015494	75084	Mm.243841	NR_015494	ENSMUSG00000086607	4930511M06Rik	-	RIKEN cDNA 4930511M06 gene	miscRNA	0.02	0.405941
Merged-chr10-63339068-1	chr10	63339018	63339118	+	3	cIP2vsInput	promoter-TSS (NM_019812)	promoter-TSS (NM_019812)	-33	NM_001159589	93759	Mm.351459	NM_001159590	ENSMUSG00000020063	Sirt1	AA673258|SIR2L1|Sir2|Sir2a|Sir2alpha	"sirtuin 1 (silent mating type information regulation 2, homolog) 1 (S. cerevisiae)"	protein-coding	0.16	0.772277
Merged-chr2-177482662-1	chr2	177482612	177482712	+	3	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-15564	NR_036450	433520	Mm.425117	NM_001024825		Gm14403	OTTMUSG00000016571	predicted gene 14403	miscRNA	0.01	0.336634
Merged-chr5-139150121-1	chr5	139150071	139150171	+	3	cIP2vsInput	promoter-TSS (NM_001081265)	promoter-TSS (NM_001081265)	-102	NM_001081265	433956	Mm.5547	NM_001081265	ENSMUSG00000025857	Heatr2	BC053401|C76907	HEAT repeat containing 2	protein-coding	0.04	0.70297
Merged-chr7-3474998-1	chr7	3474948	3475048	+	3	cIP2vsInput	Intergenic	Intergenic	27554	NM_177363	245126	Mm.245747	NM_177363	ENSMUSG00000053338	Tarm1	9930022N03Rik|ENSMUSG00000053338|Gm9904|OLT-2	"T cell-interacting, activating receptor on myeloid cells 1"	protein-coding	0.02	0.633663
Merged-chr12-82430551-1	chr12	82430501	82430601	+	3	cIP1vsInput	"intron (NM_172579, intron 14 of 20)"	"intron (NM_172579, intron 14 of 20)"	119202	NM_172579	217692	Mm.261333	NM_001167983	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding	0.03	0.29703
Merged-chr1-41042167-2	chr1	41042084	41042250	+	3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	139085	NR_040475	74897	Mm.243822	NR_040475		4930448I06Rik	-	RIKEN cDNA 4930448I06 gene	miscRNA	0.036145	0.377246
Merged-chr13-52530781-1	chr13	52530731	52530831	+	3	cIP2vsInput	promoter-TSS (NM_001024474)	promoter-TSS (NM_001024474)	55	NM_001024474	68203	Mm.29362	NM_001024474	ENSMUSG00000047842	Diras2	2900052J15Rik|AI414999	"DIRAS family, GTP-binding RAS-like 2"	protein-coding	0.09	0.732673
Merged-chr5-114813628-1	chr5	114813578	114813678	+	3	cIP1vsInput	"intron (NR_027818, intron 1 of 1)"	RLTR10E|LTR|ERVK	348	NR_027818	66236	Mm.268546	NR_027817	ENSMUSG00000072694	1500011B03Rik	AI415201|AV141149|AW556386	RIKEN cDNA 1500011B03 gene	miscRNA	0.03	0.415842
Merged-chr10-50407703-1	chr10	50407653	50407753	+	3	cIP1vsInput	Intergenic	Intergenic	-184966	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.01	0.336634
Merged-chr5-122900328-1	chr5	122900278	122900378	+	3	cIP2vsInput	promoter-TSS (NM_013910)	promoter-TSS (NM_013910)	22	NM_013910	30841	Mm.86406	NM_001003953	ENSMUSG00000029475	Kdm2b	Cxxc2|E430001G17|Fbl10|Fbxl10|Jhdm1b|PCCX2|mKIAA3014	lysine (K)-specific demethylase 2B	protein-coding	0.2	0.861386
Merged-chr7-127842636-1	chr7	127842586	127842686	+	3	cIP2vsInput	"intron (NM_009294, intron 3 of 10)"	"intron (NM_009294, intron 3 of 10)"	828	NM_009294	20909	Mm.24867	NM_009294	ENSMUSG00000030805	Stx4a	Stx4|Syn-4|Syn4	syntaxin 4A (placental)	protein-coding	0.01	0.455446
Merged-chrY-6525354-1	chrY	6525304	6525404	+	3	cIP1vsInput	Intergenic	RLTR44-int|LTR|ERVK	642423	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.366337
Merged-chr7-105640693-1	chr7	105640643	105640743	+	3	cIP2vsInput	promoter-TSS (NM_029802)	promoter-TSS (NM_029802)	153	NM_019502	14356	Mm.220330	NM_019502		Timm10b	Fxc1|Tim10b|Tim9b	translocase of inner mitochondrial membrane 10B	protein-coding	0.07	0.60396
Merged-chr13-102319928-1	chr13	102319878	102319978	+	3	cIP2vsInput	Intergenic	Intergenic	-373630	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding	0.01	0.356436
Merged-chr1-119526288-1	chr1	119526238	119526338	+	3	cIP2vsInput	"5' UTR (NM_146103, exon 1 of 1)"	"5' UTR (NM_146103, exon 1 of 1)"	134	NM_146103	226351	Mm.439806	NM_146103		Tmem185b	2500001K11Rik	transmembrane protein 185B	protein-coding	0.12	0.663366
Merged-chr6-39592487-1	chr6	39592437	39592537	+	3	cIP2vsInput	promoter-TSS (NM_026612)	promoter-TSS (NM_026612)	-96	NM_026612	68198	Mm.29415	NM_026612	ENSMUSG00000002416	Ndufb2	1810011O01Rik|8kDa|AGGG|AI325567|CI-AGGG	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2"	protein-coding	0.05	0.584158
Merged-chr6-124415059-1	chr6	124415009	124415109	+	3	cIP2vsInput	promoter-TSS (NM_008995)	promoter-TSS (NM_008995)	8	NM_008995	19305	Mm.22418	NM_001277330	ENSMUSG00000005069	Pex5	AW212715|ESTM1|PTS1R|Pxr1|X83306	peroxisomal biogenesis factor 5	protein-coding	0.12	0.782178
Merged-chr14-112960491-1	chr14	112960441	112960541	+	3	cIP1vsInput	Intergenic	Intergenic	939061	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0	0.306931
Merged-chr10-82623343-1	chr10	82623293	82623393	+	3	cIP2vsInput	promoter-TSS (NM_001135569)	promoter-TSS (NM_001135569)	-115	NM_001135567	544717	Mm.334867	NM_001135567	ENSMUSG00000063320	1190007I07Rik	-	RIKEN cDNA 1190007I07 gene	protein-coding	0.02	0.534653
Merged-chr18-63508446-1	chr18	63508396	63508496	+	3	cIP1vsInput	Intergenic	Intergenic	-121263	NM_001039485	667742	Mm.158720	NM_172629	ENSMUSG00000041482	Piezo2	5930434P17|9030411M15Rik|9430028L06Rik|Fam38b|Fam38b2	piezo-type mechanosensitive ion channel component 2	protein-coding	0	0.326733
Merged-chr10-68136686-1	chr10	68136636	68136736	+	3	cIP2vsInput	"intron (NM_023598, intron 4 of 9)"	"intron (NM_023598, intron 4 of 9)"	142040	NM_023598	71371		NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding	0.02	0.574257
Merged-chr4-147810461-1	chr4	147810411	147810511	+	3	cIP1vsInput	promoter-TSS (NM_001127189)	promoter-TSS (NM_001127189)	-673	NM_001127189	100041677	Mm.327194	NM_001127189	ENSMUSG00000078495	Gm13157	OTTMUSG00000010679|Rp23-282c23.7	predicted gene 13157	protein-coding	0.01	0.336634
Merged-chr3-66304428-1	chr3	66304378	66304478	+	3	cIP1vsInput	Intergenic	L1M2|LINE|L1	-7591	NM_145820	72789	Mm.443526	NM_028357	ENSMUSG00000027831	Veph1	2810471M23Rik|Veph	ventricular zone expressed PH domain-containing 1	protein-coding	0	0.316832
Merged-chr4-25281788-1	chr4	25281738	25281838	+	3	cIP2vsInput	promoter-TSS (NM_026194)	promoter-TSS (NM_026194)	33	NM_026194	67490	Mm.226295	NM_026194	ENSMUSG00000040359	Ufl1	1810074P20Rik|AI429228|Kiaa0776|Maxer|Rcad|mKIAA0776	UFM1 specific ligase 1	protein-coding	0.12	0.712871
Merged-chr15-84714941-1	chr15	84714891	84714991	+	3	cIP2vsInput	"non-coding (NR_040347, exon 3 of 3)"	"non-coding (NR_040347, exon 3 of 3)"	-5111	NM_001164628	73167	Mm.128411	NM_001164627	ENSMUSG00000078954	Arhgap8	3110043J09Rik	Rho GTPase activating protein 8	protein-coding	0.06	0.643564
Merged-chr13-106036875-1	chr13	106036825	106036925	+	3	cIP1vsInput	Intergenic	L1VL4|LINE|L1	593182	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0	0.336634
Merged-chr18-80256271-1	chr18	80256221	80256321	+	3	cIP1vsInput	promoter-TSS (NM_001164422)	promoter-TSS (NM_001164422)	-35	NM_025861	66943	Mm.29247	NM_001164420	ENSMUSG00000034006	Pqlc1	2310009N05Rik|4933425L21Rik|5730564E11Rik|C78974	PQ loop repeat containing 1	protein-coding	0.08	0.673267
Merged-chr6-62531622-1	chr6	62531572	62531672	+	3	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	-725235	NM_008167	14804	Mm.447390	NM_008167		Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	"glutamate receptor, ionotropic, delta 2"	protein-coding	0	0.29703
Merged-chr4-41147699-1	chr4	41147649	41147749	+	3	cIP1vsInput	"intron (NM_026275, intron 1 of 4)"	"intron (NM_026275, intron 1 of 4)"	11678	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding	0	0.386139
Merged-chr7-70023492-1	chr7	70023442	70023542	+	3	cIP1vsInput	Intergenic	Intergenic	337101	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	"nuclear receptor subfamily 2, group F, member 2"	protein-coding	0	0.257426
Merged-chr10-35550356-1	chr10	35550306	35550406	+	3	cIP1vsInput	Intergenic	Intergenic	-956451	NM_001253355	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0.01	0.29703
Merged-chr2-34406550-1	chr2	34406500	34406600	+	3	cIP2vsInput	Intergenic	Lx8|LINE|L1	-25475	NM_177345	227743	Mm.270866	NM_177345	ENSMUSG00000038696	Mapkap1	AI591529|D230039K05Rik|Sin1	mitogen-activated protein kinase associated protein 1	protein-coding	0.01	0.346535
Merged-chr13-35309175-1	chr13	35309125	35309225	+	3	cIP1vsInput	Intergenic	L1MC|LINE|L1	127552	NR_045616	100503727	Mm.32214	NR_045616		1700011B04Rik	-	RIKEN cDNA 1700011B04 gene	miscRNA	0	0.287129
Merged-chr16-92552949-1	chr16	92552899	92552999	+	3	cIP2vsInput	Intergenic	Intergenic	54802	NM_172469	209195	Mm.44747	NM_172469	ENSMUSG00000022949	Clic6	5730466J16Rik|AL022908|AW045520|CLIC1L	chloride intracellular channel 6	protein-coding	0.01	0.514851
Merged-chr7-39199499-1	chr7	39199449	39199549	+	3	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	213661	NM_177890	330513	Mm.433234	NM_177890	ENSMUSG00000053742	Gm5114	4921507A12|EG330513	predicted gene 5114	protein-coding	0.01	0.277228
Merged-chr11-71004978-1	chr11	71004928	71005028	+	3	cIP1vsInput	promoter-TSS (NM_178367)	promoter-TSS (NM_178367)	-546	NM_178367	216877	Mm.35399	NM_178367	ENSMUSG00000040620	Dhx33	3110057P17Rik|9430096J02Rik|Ddx33	DEAH (Asp-Glu-Ala-His) box polypeptide 33	protein-coding	0	0.306931
Merged-chr9-7043672-1	chr9	7043622	7043722	+	3	cIP1vsInput	"intron (NM_029851, intron 64 of 88)"	RLTR25B|LTR|ERVK	133374	NM_029851	110350	Mm.237596	NM_029851	ENSMUSG00000047193	Dync2h1	4432416O06Rik|AI448217|D030010H02Rik|D330044F14Rik|DHC1b|DHC2|Dnchc2|b2b414Clo|mKIAA1997	dynein cytoplasmic 2 heavy chain 1	protein-coding	0	0.277228
Merged-chr19-6141331-1	chr19	6141281	6141381	+	3	cIP2vsInput	promoter-TSS (NM_019722)	promoter-TSS (NM_019722)	-194	NM_019722	56327	Mm.21071	NM_019722		Arl2	2610009M23Rik|AI115441|AW553335	ADP-ribosylation factor-like 2	protein-coding	0.05	0.594059
Merged-chr6-85254264-1	chr6	85254214	85254314	+	3	cIP2vsInput	"intron (NM_178639, intron 10 of 13)"	"intron (NM_178639, intron 10 of 13)"	66333	NM_010131	13796	Mm.391473	NM_010131		Emx1	-	empty spiracles homeobox 1	protein-coding	0.01	0.564356
Merged-chr7-3665434-1	chr7	3665384	3665484	+	3	cIP2vsInput	TTS (NM_181820)	TTS (NM_181820)	406	NM_027203	69757	Mm.389782	NM_027203	ENSMUSG00000078813	Leng1	1500001K17Rik	leukocyte receptor cluster (LRC) member 1	protein-coding	0.08	0.60396
Merged-chr7-84779701-2	chr7	84779624	84779779	+	3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-73870	NM_146415	258410	Mm.484702	NM_146415	ENSMUSG00000070460	Olfr291	MOR254-2	olfactory receptor 291	protein-coding	0.077419	0.557692
Merged-chr6-45189440-1	chr6	45189390	45189490	+	3	cIP1vsInput	"intron (NM_001004357, intron 1 of 23)"	"intron (NM_001004357, intron 1 of 23)"	129379	NM_001004357	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0.01	0.267327
Merged-chr6-58592182-1	chr6	58592132	58592232	+	3	cIP1vsInput	Intergenic	Intergenic	-4490	NM_011920	26357	Mm.333096	NM_011920	ENSMUSG00000029802	Abcg2	ABC15|ABCP|AI428558|BCRP|Bcrp1|MXR|MXR1	"ATP-binding cassette, sub-family G (WHITE), member 2"	protein-coding	0	0.257426
Merged-chr2-29538646-1	chr2	29538596	29538696	+	3	cIP1vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	-81074	NM_054050	107746	Mm.298274	NM_001039086	ENSMUSG00000039844	Rapgef1	4932418O06Rik|C3G|Grf2	Rap guanine nucleotide exchange factor (GEF) 1	protein-coding	0	0.316832
Merged-chr7-142284417-1	chr7	142284367	142284467	+	3	cIP1vsInput	Intergenic	ERVB4_1-I_MM-int|LTR|ERVK	-10054	NM_001199309	100043627	Mm.388589	NM_001199309	ENSMUSG00000056885	Gm4559	-	predicted gene 4559	protein-coding	0.09	0.623762
Merged-chr5-55428748-1	chr5	55428698	55428798	+	3	cIP2vsInput	Intergenic	Intergenic	1078756	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0.02	0.366337
Merged-chr7-127042510-2	chr7	127042440	127042580	+	3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145588)	promoter-TSS (NM_145588)	-90	NM_145588	110033	Mm.286488	NM_145588	ENSMUSG00000030677	Kif22	AU021460|C81217|Kid|Kif22a	kinesin family member 22	protein-coding	0.1	0.58156
Merged-chr8-25201849-1	chr8	25201799	25201899	+	3	cIP1vsInput	promoter-TSS (NM_177089)	promoter-TSS (NM_177089)	-400	NM_177089	320165	Mm.308452	NM_177089	ENSMUSG00000065954	Tacc1	4833447E04Rik|AA960202|B230378H13Rik	"transforming, acidic coiled-coil containing protein 1"	protein-coding	0.04	0.475248
Merged-chr3-104794643-1	chr3	104794593	104794693	+	3	cIP2vsInput	TTS (NM_001163440)	TTS (NM_001163440)	5609	NM_007484	11853	Mm.262	NM_007484	ENSMUSG00000002233	Rhoc	AI324259|Arh9|Arhc	"ras homolog gene family, member C"	protein-coding	0	0.554455
Merged-chr10-5294552-1	chr10	5294502	5294602	+	3	cIP2vsInput	Intergenic	Intergenic	-99845	NM_001079686	64009	Mm.331626	NM_001079686	ENSMUSG00000019769	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756	"spectrin repeat containing, nuclear envelope 1"	protein-coding	0.01	0.346535
Merged-chr3-99142029-1	chr3	99141979	99142079	+	3	cIP2vsInput	"intron (NM_027462, intron 1 of 5)"	"intron (NM_027462, intron 1 of 5)"	939	NM_027462	70560	Mm.316754	NM_027462	ENSMUSG00000004233	Wars2	5730427B17Rik|9430020O07Rik|AI413375|TrpRS	tryptophanyl tRNA synthetase 2 (mitochondrial)	protein-coding	0	0.386139
Merged-chr3-19263821-1	chr3	19263771	19263871	+	3	cIP1vsInput	"intron (NM_001122759, intron 1 of 12)"	MIR|SINE|MIR	1148	NM_008802	18583	Mm.355614	NM_001122759		Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding	0.01	0.306931
Merged-chr6-108736296-1	chr6	108736246	108736346	+	3	cIP1vsInput	Intergenic	Intergenic	-46763	NM_026011	67166	Mm.271178	NM_026011	ENSMUSG00000030105	Arl8b	2610313E07Rik|3100002J04Rik|Arl10c|gie1	ADP-ribosylation factor-like 8B	protein-coding	0.03	0.485149
Merged-chr5-149051850-1	chr5	149051800	149051900	+	3	cIP1vsInput	"intron (NM_010439, intron 1 of 4)"	"intron (NM_010439, intron 1 of 4)"	1187	NM_010439	15289	Mm.313345	NM_010439	ENSMUSG00000066551	Hmgb1	DEF|HMG-1|Hmg1|SBP-1|amphoterin|p30	high mobility group box 1	protein-coding	0.17	0.742574
Merged-chr9-100486113-1	chr9	100486063	100486163	+	3	cIP2vsInput	"intron (NM_001033543, intron 1 of 6)"	"intron (NM_001033543, intron 1 of 6)"	360	NM_001033543	213208	Mm.242896	NM_001037246	ENSMUSG00000044244	Il20rb	AV228068|Fndc6|Gm186|Il20R2	interleukin 20 receptor beta	protein-coding	0.01	0.316832
Merged-chr14-93126747-1	chr14	93126697	93126797	+	3	cIP1vsInput	"intron (NM_001081377, intron 3 of 3)"	"intron (NM_001081377, intron 3 of 3)"	762141	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.346535
Merged-chr12-44921369-1	chr12	44921319	44921419	+	3	cIP1vsInput	"intron (NM_144552, intron 2 of 5)"	"intron (NM_144552, intron 2 of 5)"	153114	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding	0	0.326733
Merged-chr14-20393574-1	chr14	20393524	20393624	+	3	cIP2vsInput	promoter-TSS (NM_025440)	promoter-TSS (NM_025440)	-19	NM_025440	66242	Mm.23747	NM_025440	ENSMUSG00000049960	Mrps16	1500011E11Rik|Mprs16	mitochondrial ribosomal protein S16	protein-coding	0.14	0.742574
Merged-chr13-52929633-1	chr13	52929583	52929683	+	3	cIP1vsInput	promoter-TSS (NM_016709)	promoter-TSS (NM_016709)	44	NM_016709	11992	Mm.252034	NM_016709	ENSMUSG00000021460	Auh	C77140|W91705	AU RNA binding protein/enoyl-coenzyme A hydratase	protein-coding	0.13	0.722772
Merged-chr8-62561114-1	chr8	62561064	62561164	+	3	cIP1vsInput	Intergenic	Intergenic	-390118	NM_001252620	72902	Mm.334552	NM_001252620	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3"	protein-coding	0.01	0.316832
Merged-chr7-100583142-1	chr7	100583092	100583192	+	3	cIP2vsInput	promoter-TSS (NM_198831)	promoter-TSS (NM_198831)	-12	NM_198831	52443	Mm.473730	XM_003946242		Mrpl48	1810030E20Rik|2610028L11Rik|CGI-118|D4Ertd786e	mitochondrial ribosomal protein L48	protein-coding	0.06	0.485149
Merged-chr14-61172886-1	chr14	61172836	61172936	+	3	cIP2vsInput	"intron (NM_172809, intron 2 of 9)"	CpG	34429	NM_172809	50720	Mm.446687	NM_172809	ENSMUSG00000048279	Sacs	A230052M14|DNAJC29|E130115J16Rik|mKIAA0730	sacsin	protein-coding	0.09	0.673267
Merged-chr10-63430243-1	chr10	63430193	63430293	+	3	cIP2vsInput	"intron (NM_177612, intron 1 of 17)"	"intron (NM_177612, intron 1 of 17)"	145	NM_177612	216033	Mm.444692	NM_001164376	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	"catenin (cadherin associated protein), alpha 3"	protein-coding	0.06	0.554455
Merged-chr5-36582247-1	chr5	36582197	36582297	+	3	cIP2vsInput	"intron (NM_001113362, intron 2 of 14)"	CpG	150	NM_133910	100855	Mm.486203	NM_001113362	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	"TBC1 domain family, member 14"	protein-coding	0.04	0.613861
Merged-chr2-32151061-1	chr2	32151011	32151111	+	3	cIP2vsInput	promoter-TSS (NM_172661)	promoter-TSS (NM_172661)	-87	NM_172661	227723	Mm.25504	NM_001159634	ENSMUSG00000039262	Prrc2b	5830434P21Rik|AI173903|Bat2l|Bat2l1|D430039P21|mKIAA0515	proline-rich coiled-coil 2B	protein-coding	0.23	0.920792
Merged-chr18-79379068-1	chr18	79379018	79379118	+	3	cIP2vsInput	Intergenic	L1MCa|LINE|L1	-269677	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding	0.01	0.29703
Merged-chr11-4096765-1	chr11	4096715	4096815	+	3	cIP2vsInput	TTS (NM_144520)	TTS (NM_144520)	-1334	NM_026443	67900	Mm.41719	NM_026443	ENSMUSG00000004748	Mtfp1	1700020C11Rik|2610507A21Rik|AV005788|Mtp18	mitochondrial fission process 1	protein-coding	0.1	0.633663
Merged-chr13-43171353-2	chr13	43171268	43171439	+	3	cIP1vsInput|cIP2vsInput	"5' UTR (NM_025935, exon 1 of 8)"	"5' UTR (NM_025935, exon 1 of 8)"	148	NM_001252639	67046	Mm.489645	NM_001252639	ENSMUSG00000021368	Tbc1d7	2610009C09Rik	"TBC1 domain family, member 7"	protein-coding	0.105263	0.674419
Merged-chr16-4542238-1	chr16	4542188	4542288	+	3	cIP1vsInput	Intergenic	L1MD3|LINE|L1	17482	NM_031182	83383	Mm.273210	NM_031182	ENSMUSG00000005718	Tfap4	AI642933|AP-4|D930048N17Rik|Tcfap4|bHLHc41	transcription factor AP4	protein-coding	0.01	0.356436
Merged-chr10-60958001-1	chr10	60957951	60958051	+	3	cIP1vsInput	Intergenic	Intergenic	-19869	NR_033616	73616	Mm.159038	NR_033616	ENSMUSG00000037247	Pldi	1700125F08Rik|Poldi	polymorphic derived intron containing	miscRNA	0.03	0.574257
Merged-chr15-45745730-1	chr15	45745680	45745780	+	3	cIP2vsInput	Intergenic	Intergenic	-578855	NR_045509	71120	Mm.158571	NR_045509		1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	miscRNA	0	0.405941
Merged-chrY-6080511-1	chrY	6080461	6080561	+	3	cIP1vsInput	Intergenic	MLT1A1|LTR|ERVL-MaLR	1087266	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.346535
Merged-chr12-79905911-1	chr12	79905861	79905961	+	3	cIP2vsInput	Intergenic	Intergenic	207102	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	"zinc finger protein 36, C3H type-like 1"	protein-coding	0.02	0.435644
Merged-chr12-99884621-1	chr12	99884571	99884671	+	3	cIP1vsInput	"intron (NM_028354, intron 1 of 15)"	CpG	106	NM_028354	104884	Mm.488658	NM_028354	ENSMUSG00000021177	Tdp1	2810481F14Rik|4921509N21Rik|AI838772|AW493413|E430034L06Rik|MLZ-501|SCAN1	tyrosyl-DNA phosphodiesterase 1	protein-coding	0.14	0.752475
Merged-chr4-117289480-1	chr4	117289430	117289530	+	3	cIP2vsInput	"intron (NM_025739, intron 5 of 14)"	"intron (NM_025739, intron 5 of 14)"	37491	NM_026837	68777	Mm.331805	NM_026837	ENSMUSG00000048772	Tmem53	1110038M16Rik|1500001P22Rik|1700012A05Rik	transmembrane protein 53	protein-coding	0.09	0.712871
Merged-chr8-68793800-2	chr8	68793728	68793872	+	3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027590)	promoter-TSS (NM_027590)	-154	NM_027590	70885	Mm.252421	NM_027590		Ints10	4921521J11Rik|AI462004	integrator complex subunit 10	protein-coding	0.104167	0.613793
Merged-chr15-3296015-1	chr15	3295965	3296065	+	3	cIP1vsInput	"intron (NM_001166063, intron 3 of 8)"	"intron (NM_001166063, intron 3 of 8)"	7511	NM_001166063	100039139	Mm.455610	NM_001166063	ENSMUSG00000091119	Ccdc152	ENSMUSG00000071814	coiled-coil domain containing 152	protein-coding	0.01	0.366337
Merged-chr17-71556941-1	chr17	71556891	71556991	+	3	cIP1vsInput	TTS (NR_027952)	TTS (NR_027952)	4880	NM_029254	70891	Mm.477599	NM_001142631	ENSMUSG00000052525	Spdya	4921517J08Rik|4930548B21Rik|GS4|MLZ-465|Spdy1	speedy homolog A (Xenopus laevis)	protein-coding	0.01	0.326733
Merged-chr19-32210929-1	chr19	32210879	32210979	+	3	cIP2vsInput	promoter-TSS (NM_001168526)	promoter-TSS (NM_001168526)	84	NM_001168526	208449	Mm.329810	NM_001168525	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding	0.06	0.683168
Merged-chr16-91073616-1	chr16	91073566	91073666	+	3	cIP1vsInput	Intergenic	Intergenic	-4471	NM_028905	74387	Mm.236220	NM_001163695	ENSMUSG00000039851	4932438H23Rik	4931406G06Rik|AI550392	RIKEN cDNA 4932438H23 gene	protein-coding	0.08	0.633663
Merged-chr8-83608727-1	chr8	83608677	83608777	+	3	cIP2vsInput	"intron (NM_018808, intron 1 of 2)"	CpG	552	NM_018808	81489	Mm.282092	NM_018808	ENSMUSG00000005483	Dnajb1	0610007I11Rik|HSPF1|Hsp40	"DnaJ (Hsp40) homolog, subfamily B, member 1"	protein-coding	0.1	0.70297
Merged-chr11-47461590-1	chr11	47461540	47461640	+	3	cIP2vsInput	Intergenic	L1MC5a|LINE|L1	-82288	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	"sarcoglycan, delta (dystrophin-associated glycoprotein)"	protein-coding	0	0.356436
Merged-chr13-16005508-1	chr13	16005458	16005558	+	3	cIP1vsInput	Intergenic	Intergenic	-8967	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding	0	0.326733
Merged-chr1-160832670-1	chr1	160832620	160832720	+	3	cIP1vsInput	Intergenic	Intergenic	-39732	NM_013862	29809	Mm.25833	NM_001038621	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding	0.01	0.356436
Merged-chr10-110812282-1	chr10	110812232	110812332	+	3	cIP2vsInput	"intron (NR_045979, intron 2 of 2)"	"intron (NR_045979, intron 2 of 2)"	66817	NM_178609	52679	Mm.11747	NM_178609	ENSMUSG00000020185	E2f7	A630014C11Rik|D10Ertd739e	E2F transcription factor 7	protein-coding	0	0.356436
Merged-chr1-72696403-1	chr1	72696353	72696453	+	3	cIP2vsInput	"intron (NM_176980, intron 2 of 23)"	SYNREP_MM|Satellite|Satellite	4161	NM_176980	319695	Mm.249056	NM_176980	ENSMUSG00000039342	Ankar	4932422E22Rik	ankyrin and armadillo repeat containing	protein-coding	0.01	0.316832
Merged-chr5-35895910-1	chr5	35895860	35895960	+	3	cIP1vsInput	"intron (NM_027373, intron 1 of 16)"	"intron (NM_027373, intron 1 of 16)"	2591	NM_027373	70292	Mm.125167	NM_027373	ENSMUSG00000029094	Afap1	2600003E23Rik|9630044L16Rik|AI848729|Afap|mKIAA3018	actin filament associated protein 1	protein-coding	0	0.415842
Merged-chr4-59711199-1	chr4	59711149	59711249	+	3	cIP2vsInput	"intron (NM_001015681, intron 2 of 3)"	"intron (NM_001015681, intron 2 of 3)"	72656	NM_001013577	66209	Mm.443220	NM_001013577	ENSMUSG00000038544	Inip	1110054O05Rik|2610312O17Rik|AA399876|Ssbip1	INTS3 and NABP interacting protein	protein-coding	0	0.405941
Merged-chr5-58512111-1	chr5	58512061	58512161	+	3	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-59113	NR_046190	78163	Mm.243828	NR_046190		4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	miscRNA	0	0.326733
Merged-chr15-51409444-1	chr15	51409394	51409494	+	3	cIP2vsInput	Intergenic	Intergenic	-13834	NR_045092	100502643	Mm.131987	NR_045092		Gm19303	-	"predicted gene, 19303"	miscRNA	0	0.306931
Merged-chr2-156344918-1	chr2	156344868	156344968	+	3	cIP2vsInput	"intron (NM_027585, intron 8 of 12)"	"intron (NM_027585, intron 8 of 12)"	-32214	NM_020255	19018	Mm.389346	NM_020255	ENSMUSG00000046229	Scand1	2310003H23Rik|Leap1|PGC-2|Ppargc2	SCAN domain-containing 1	protein-coding	0.01	0.514851
Merged-chr1-12397749-1	chr1	12397699	12397799	+	3	cIP1vsInput	Intergenic	Intergenic	-269814	NR_045297	329096	Mm.417782	NR_045297	ENSMUSG00000097171	Gm17644	4932411L15	"predicted gene, 17644"	miscRNA	0	0.316832
Merged-chr16-10545106-1	chr16	10545056	10545156	+	3	cIP1vsInput	promoter-TSS (NM_001204229)	promoter-TSS (NM_001204229)	-233	NM_177562	74374	Mm.159176	NM_001204229	ENSMUSG00000068663	Clec16a	4932416N17Rik|curt|mKIAA0350	"C-type lectin domain family 16, member A"	protein-coding	0.04	0.425743
Merged-chr19-25575419-1	chr19	25575369	25575469	+	3	cIP2vsInput	"intron (NM_015826, intron 4 of 4)"	"intron (NM_015826, intron 4 of 4)"	-35118	NM_177360	240590	Mm.62785	NM_177360	ENSMUSG00000042372	Dmrt3	-	doublesex and mab-3 related transcription factor 3	protein-coding	0	0.584158
Merged-chr14-113392657-1	chr14	113392607	113392707	+	3	cIP1vsInput	Intergenic	Intergenic	1371227	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0	0.346535
Merged-chr9-20898662-1	chr9	20898612	20898712	+	3	cIP1vsInput	promoter-TSS (NM_016876)	promoter-TSS (NM_016876)	-72	NM_016876	53356	Mm.427309	NM_016876	ENSMUSG00000070319	Eif3g	44kDa|D0Jmb4|Eif3s4|TU-189B2|eIF3-p44|p44	"eukaryotic translation initiation factor 3, subunit G"	protein-coding	0.12	0.712871
Merged-chr16-43192280-1	chr16	43192230	43192330	+	3	cIP1vsInput	Intergenic	Intergenic	-55004	NM_181058	56490	Mm.460947	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding	0	0.306931
Merged-chr3-150939889-1	chr3	150939839	150939939	+	3	cIP1vsInput	Intergenic	Lx|LINE|L1	-497993	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0	0.346535
Merged-chr1-24100371-1	chr1	24100321	24100421	+	3	cIP2vsInput	promoter-TSS (NM_026604)	promoter-TSS (NM_026604)	-30	NM_026604	68187	Mm.87130	NM_026604	ENSMUSG00000026153	Fam135a	4921533L14Rik|AI256732|AI835491	"family with sequence similarity 135, member A"	protein-coding	0.1	0.792079
Merged-chr11-85849407-1	chr11	85849357	85849457	+	3	cIP2vsInput	Intergenic	Intergenic	16792	NM_009324	21385	Mm.287052	NM_009324	ENSMUSG00000000093	Tbx2	-	T-box 2	protein-coding	0.03	0.613861
Merged-chr5-13629186-1	chr5	13629136	13629236	+	3	cIP2vsInput	Intergenic	Intergenic	-162433	NM_027650	71026	Mm.158536	NM_027650	ENSMUSG00000067855	Speer3	4933405P08Rik|SPEER-3	spermatogenesis associated glutamate (E)-rich protein 3	protein-coding	0.04	0.475248
Merged-chr1-143612109-1	chr1	143612059	143612159	+	3	cIP1vsInput	"intron (NM_145991, intron 15 of 16)"	"intron (NM_145991, intron 15 of 16)"	-28588	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0	0.326733
Merged-chr6-126939932-1	chr6	126939882	126939982	+	3	cIP2vsInput	promoter-TSS (NM_009013)	promoter-TSS (NM_009013)	-34	NM_138594	28040	Mm.44228	NM_138594	ENSMUSG00000030347	D6Wsu163e	C12orf4	"DNA segment, Chr 6, Wayne State University 163, expressed"	protein-coding	0.02	0.39604
Merged-chr15-38414926-1	chr15	38414876	38414976	+	3	cIP2vsInput	Intergenic	Intergenic	104340	NM_001102458	54375	Mm.250214	NM_001102458	ENSMUSG00000037458	Azin1	1700085L02Rik|AI414949|Oazi|Oazin	antizyme inhibitor 1	protein-coding	0	0.534653
Merged-chr14-45657276-1	chr14	45657226	45657326	+	3	cIP2vsInput	TTS (NR_039593)	TTS (NR_039593)	777	NR_039593	100628600		NR_039593		Mir5131	mmu-mir-5131|mu-mir-5131	microRNA 5131	miscRNA	0.09	0.643564
Merged-chr12-40257433-1	chr12	40257383	40257483	+	3	cIP1vsInput	Intergenic	Intergenic	34069	NR_045157	629820	Mm.435540	NR_045157	ENSMUSG00000035983	Gm7008	EG629820	predicted gene 7008	miscRNA	0.05	0.564356
Merged-chr5-150665503-1	chr5	150665453	150665553	+	3	cIP2vsInput	"5' UTR (NM_201369, exon 1 of 6)"	"5' UTR (NM_201369, exon 1 of 6)"	109	NM_201369	381695	Mm.246934	NM_201369	ENSMUSG00000029655	N4bp2l2	2700092H06Rik|zag1	NEDD4 binding protein 2-like 2	protein-coding	0.08	0.475248
Merged-chr1-165633359-1	chr1	165633309	165633409	+	3	cIP1vsInput	"intron (NM_001001880, intron 1 of 4)"	"intron (NM_001001880, intron 1 of 4)"	1182	NM_001001880	68481	Mm.46438	NM_001001880	ENSMUSG00000026566	Mpzl1	1110007A10Rik|PZR	myelin protein zero-like 1	protein-coding	0.02	0.336634
Merged-chr1-172206764-1	chr1	172206714	172206814	+	3	cIP2vsInput	promoter-TSS (NM_011063)	promoter-TSS (NM_011063)	17	NM_011063	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding	0.09	0.752475
Merged-chr8-64587021-1	chr8	64586971	64587071	+	3	cIP1vsInput	Intergenic	Intergenic	-72580	NR_030491	735270		NR_030491	ENSMUSG00000076042	Mir710	Mirn710|mmu-mir-710	microRNA 710	miscRNA	0	0.306931
Merged-chr11-58104116-1	chr11	58104066	58104166	+	3	cIP2vsInput	promoter-TSS (NM_026949)	promoter-TSS (NM_026949)	-37	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	"CCR4-NOT transcription complex, subunit 8"	protein-coding	0.09	0.693069
Merged-chr2-27210054-1	chr2	27210004	27210104	+	3	cIP2vsInput	"intron (NM_138665, intron 17 of 20)"	"intron (NM_138665, intron 17 of 20)"	37249	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding	0.05	0.60396
Merged-chr12-8618315-1	chr12	8618265	8618365	+	3	cIP1vsInput	Intergenic	Intergenic	-19249	NM_177802	328059	Mm.46326	NM_001038660	ENSMUSG00000020600	Slc7a15	2010001P20Rik|9030221C07Rik|Arpat	"solute carrier family 7 (cationic amino acid transporter, y+ system), member 15"	protein-coding	0	0.287129
Merged-chr5-30907758-1	chr5	30907708	30907808	+	3	cIP1vsInput	promoter-TSS (NM_024460)	promoter-TSS (NM_024460)	30	NM_024460	67695	Mm.21450	NM_001134692	ENSMUSG00000038803	Ost4	2310016E02Rik	oligosaccharyltransferase 4 homolog (S. cerevisiae)	protein-coding	0.13	0.663366
Merged-chr15-38927652-1	chr15	38927602	38927702	+	3	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-6257	NM_080640	118452	Mm.233837	NM_080640		Baalc	2810457D07Rik	"brain and acute leukemia, cytoplasmic"	protein-coding	0	0.455446
Merged-chr11-111766345-1	chr11	111766295	111766395	+	3	cIP1vsInput	Intergenic	Intergenic	700181	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	"potassium inwardly-rectifying channel, subfamily J, member 2"	protein-coding	0	0.326733
Merged-chr2-78526063-1	chr2	78526013	78526113	+	3	cIP1vsInput	Intergenic	Intergenic	288516	NM_177843	329436	Mm.235448	NM_177843		Gm14461	A830093M07|OTTMUSG00000016703	predicted gene 14461	protein-coding	0	0.29703
Merged-chr1-59481669-1	chr1	59481619	59481719	+	3	cIP1vsInput	promoter-TSS (NM_008057)	promoter-TSS (NM_008057)	-478	NM_008057	14369	Mm.297906	NM_008057	ENSMUSG00000041075	Fzd7	Fz7	frizzled homolog 7 (Drosophila)	protein-coding	0.07	0.544554
Merged-chr8-71881929-1	chr8	71881879	71881979	+	3	cIP2vsInput	promoter-TSS (NM_145624)	promoter-TSS (NM_145624)	-139	NM_145624	236193	Mm.290790	NM_145624		Zfp709	BC021921|GIOT-4|HIT-40	zinc finger protein 709	protein-coding	0.05	0.574257
Merged-chr16-25691477-1	chr16	25691427	25691527	+	3	cIP2vsInput	"intron (NM_001127259, intron 1 of 13)"	"intron (NM_001127259, intron 1 of 13)"	7712	NM_001127259	22061	Mm.20894	NM_001127259	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding	0.01	0.306931
Merged-chr4-133339315-1	chr4	133339265	133339365	+	3	cIP2vsInput	promoter-TSS (NM_199306)	promoter-TSS (NM_199306)	0	NM_199306	230796	Mm.226576	NM_199306	ENSMUSG00000037622	Wdtc1	Gm695|adipose|adp	WD and tetratricopeptide repeats 1	protein-coding	0.1	0.693069
Merged-chr5-57567543-1	chr5	57567493	57567593	+	3	cIP1vsInput	Intergenic	Intergenic	150376	NR_015588	319216	Mm.446765	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	miscRNA	0	0.257426
Merged-chr19-47295036-1	chr19	47294986	47295086	+	3	cIP1vsInput	"intron (NM_008018, intron 8 of 14)"	"intron (NM_008018, intron 8 of 14)"	66193	NM_001163480	18011	Mm.313651	NM_001163480	ENSMUSG00000006435	Neurl1a	2410129E16Rik|AI450910|AI481072|Neu1|Neur1|Neurl|Nlz|Rnf67	neuralized homolog 1A (Drosophila)	protein-coding	0.01	0.554455
Merged-chr7-120917675-1	chr7	120917625	120917725	+	3	cIP2vsInput	promoter-TSS (NM_025298)	promoter-TSS (NM_025298)	-69	NM_025298	26939	Mm.193632	NM_001164096	ENSMUSG00000030880	Polr3e	RPC5|Sin	polymerase (RNA) III (DNA directed) polypeptide E	protein-coding	0.13	0.683168
Merged-chr16-13780568-1	chr16	13780518	13780618	+	3	cIP1vsInput	promoter-TSS (NM_001039521)	promoter-TSS (NM_001039521)	-131	NM_001039521	106298	Mm.490362	NM_001039521	ENSMUSG00000022682	Rrn3	AL023001|E130302O19Rik|R75565|TIF-1A|Tif1a	RRN3 RNA polymerase I transcription factor homolog (yeast)	protein-coding	0.05	0.564356
Merged-chr2-71212062-1	chr2	71212012	71212112	+	3	cIP2vsInput	"5' UTR (NM_010064, exon 1 of 16)"	"5' UTR (NM_010064, exon 1 of 16)"	116	NM_010064	13427	Mm.249479	NM_001198872	ENSMUSG00000027012	Dync1i2	3110079H08Rik|AW554389|Dncic2	dynein cytoplasmic 1 intermediate chain 2	protein-coding	0.09	0.623762
Merged-chr7-15922304-1	chr7	15922254	15922354	+	3	cIP2vsInput	promoter-TSS (NM_009156)	promoter-TSS (NM_009156)	67	NM_009156	20364	Mm.42829	NM_009156	ENSMUSG00000041571	Sepw1	selW	"selenoprotein W, muscle 1"	protein-coding	0.11	0.613861
Merged-chr1-52119319-1	chr1	52119269	52119369	+	3	cIP2vsInput	promoter-TSS (NM_009283)	promoter-TSS (NM_009283)	-119	NM_009283	20846	Mm.487336	NM_001205313	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding	0.1	0.663366
Merged-chr2-152437722-1	chr2	152437672	152437772	+	3	cIP1vsInput	"intron (NM_177656, intron 6 of 11)"	"intron (NM_177656, intron 6 of 11)"	22135	NM_177656	228778	Mm.70959	NM_177656	ENSMUSG00000032680	6820408C15Rik	-	RIKEN cDNA 6820408C15 gene	protein-coding	0.06	0.60396
Merged-chr11-54192101-1	chr11	54192051	54192151	+	3	cIP1vsInput	"intron (NR_045506, intron 2 of 2)"	"intron (NR_045506, intron 2 of 2)"	21187	NR_045506	71056	Mm.56332	NR_045506	ENSMUSG00000086209	4933405E24Rik	-	RIKEN cDNA 4933405E24 gene	miscRNA	0	0.316832
Merged-chr2-111159053-1	chr2	111159003	111159103	+	3	cIP1vsInput	Intergenic	Intergenic	70547	NM_026248	67575	Mm.84331	NM_026248	ENSMUSG00000027157	4930430A15Rik	-	RIKEN cDNA 4930430A15 gene	protein-coding	0.01	0.336634
Merged-chr2-123984784-1	chr2	123984734	123984834	+	3	cIP1vsInput	Intergenic	Intergenic	145172	NR_040611	74702	Mm.410814	NR_040611	ENSMUSG00000085496	4930517E11Rik	-	RIKEN cDNA 4930517E11 gene	miscRNA	0	0.326733
Merged-chr13-34037874-1	chr13	34037824	34037924	+	3	cIP1vsInput	"intron (NM_026512, intron 1 of 6)"	CpG	233	NM_026512	68021	Mm.140243	NM_026512	ENSMUSG00000038286	Bphl	2010012D11Rik|5730533B08Rik|AI115341	"biphenyl hydrolase-like (serine hydrolase, breast epithelial mucin-associated antigen)"	protein-coding	0.06	0.594059
Merged-chr17-88529900-2	chr17	88529830	88529971	+	3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028658)	promoter-TSS (NM_028658)	-224	NM_028658	73825	Mm.271817	NM_028658	ENSMUSG00000034709	Ppp1r21	1110018J12Rik|AI426045|AW550781|Ccdc128|Klraq1	"protein phosphatase 1, regulatory subunit 21"	protein-coding	0.06383	0.584507
Merged-chr5-36530603-1	chr5	36530553	36530653	+	3	cIP2vsInput	promoter-TSS (NM_001113364)	promoter-TSS (NM_001113364)	20	NM_001113364	100855	Mm.486203	NM_001113362	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	"TBC1 domain family, member 14"	protein-coding	0.06	0.613861
Merged-chr11-109431812-1	chr11	109431762	109431862	+	3	cIP2vsInput	"intron (NM_001252193, intron 5 of 7)"	"intron (NM_001252193, intron 5 of 7)"	5592	NM_001252193	13929	Mm.211850	NM_001252193	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding	0.01	0.50495
Merged-chr9-55938011-1	chr9	55937961	55938061	+	3	cIP2vsInput	"intron (NM_001081341, intron 1 of 32)"	CpG	104	NM_001081341	244891	Mm.86588	NM_001081341	ENSMUSG00000034007	Scaper	C430017I08|D530014O03Rik|Zfp291	S phase cyclin A-associated protein in the ER	protein-coding	0.13	0.742574
Merged-chr6-6050281-1	chr6	6050231	6050331	+	3	cIP1vsInput	"intron (NM_015829, intron 15 of 17)"	Lx9|LINE|L1	-72888	NR_040255	72249	Mm.443268	NR_040255	ENSMUSG00000085416	1700019G24Rik	-	RIKEN cDNA 1700019G24 gene	miscRNA	0.01	0.376238
Merged-chr2-163472682-1	chr2	163472632	163472732	+	3	cIP2vsInput	promoter-TSS (NM_173397)	promoter-TSS (NM_173397)	-53	NM_173397	228859	Mm.242917	NM_173397		Fitm2	AI414861|D930001I22Rik|Fit2	fat storage-inducing transmembrane protein 2	protein-coding	0.07	0.673267
Merged-chr1-53144849-1	chr1	53144799	53144899	+	3	cIP1vsInput	Intergenic	Intergenic	42768	NM_027070	69397	Mm.307084	NM_027070	ENSMUSG00000060715	1700019A02Rik	-	RIKEN cDNA 1700019A02 gene	protein-coding	0	0.277228
Merged-chr14-92733469-1	chr14	92733419	92733519	+	3	cIP2vsInput	Intergenic	Intergenic	1155419	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.336634
Merged-chr16-3115160-1	chr16	3115110	3115210	+	3	cIP1vsInput	Intergenic	(CCTG)n|Simple_repeat|Simple_repeat	-477238	NM_146860	258859	Mm.377723	NM_146860		Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding	0	0.594059
Merged-chr11-116643555-1	chr11	116643505	116643605	+	3	cIP1vsInput	Intergenic	Intergenic	10758	NM_030206	114886	Mm.34598	NM_030206	ENSMUSG00000020810	Cygb	3110001K20Rik|HGb|Staap	cytoglobin	protein-coding	0.04	0.60396
Merged-chr5-139179077-1	chr5	139179027	139179127	+	3	cIP2vsInput	"intron (NM_001081265, intron 10 of 12)"	"intron (NM_001081265, intron 10 of 12)"	-21560	NM_001256115	77053	Mm.210845	NM_001256115	ENSMUSG00000036817	Sun1	4632417G13Rik|5730434D03Rik|Unc84a|mKIAA0810	Sad1 and UNC84 domain containing 1	protein-coding	0.06	0.633663
Merged-chr10-14705612-1	chr10	14705562	14705662	+	3	cIP2vsInput	promoter-TSS (NM_025418)	promoter-TSS (NM_025418)	3	NR_045824	69412		NR_045824		1700016L04Rik	-	RIKEN cDNA 1700016L04 gene	miscRNA	0.06	0.534653
Merged-chr5-25898629-1	chr5	25898579	25898679	+	3	cIP1vsInput	Intergenic	L1MEc|LINE|L1	138603	NM_001004365	242894	Mm.150319	NM_001004365	ENSMUSG00000056367	Actr3b	9630005C02|ARP11|AW047569|Arp3b|Arp3beta	ARP3 actin-related protein 3B	protein-coding	0	0.356436
Merged-chr7-127232925-1	chr7	127232875	127232975	+	3	cIP1vsInput	promoter-TSS (NM_146201)	promoter-TSS (NM_146201)	205	NR_030674	100043580	Mm.482209	NR_030674		Gm4532	-	predicted gene 4532	miscRNA	0.08	0.693069
Merged-chr13-76018561-1	chr13	76018511	76018611	+	3	cIP2vsInput	promoter-TSS (NM_178916)	promoter-TSS (NM_178916)	1	NM_178916	218341	Mm.266515	NM_001131068	ENSMUSG00000043190	Rfesd	AI256775|D030068K09	Rieske (Fe-S) domain containing	protein-coding	0.11	0.683168
Merged-chr16-3908711-1	chr16	3908661	3908761	+	3	cIP2vsInput	promoter-TSS (NM_028484)	promoter-TSS (NM_028484)	-22	NM_028484	73261	Mm.486226	NM_028484		1700037C18Rik	2810022L20Rik	RIKEN cDNA 1700037C18 gene	protein-coding	0.05	0.534653
Merged-chr5-138155455-1	chr5	138155405	138155505	+	3	cIP1vsInput	"intron (NM_019747, intron 1 of 4)"	CpG	289	NM_019747	56314	Mm.19274	NM_019747	ENSMUSG00000037007	Zfp113	4732456B05Rik|mKIAA4229	zinc finger protein 113	protein-coding	0.09	0.643564
Merged-chr3-158536378-1	chr3	158536328	158536428	+	3	cIP1vsInput	"intron (NM_001081358, intron 1 of 27)"	"intron (NM_001081358, intron 1 of 27)"	25843	NM_001081358	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding	0	0.316832
Merged-chr6-51592909-1	chr6	51592859	51592959	+	3	cIP2vsInput	Intergenic	CpG	48386	NM_001127348	71982		NM_001127348	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding	0.08	0.683168
Merged-chr10-47426782-1	chr10	47426732	47426832	+	3	cIP1vsInput	Intergenic	Lx|LINE|L1	1182033	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0.01	0.49505
Merged-chr11-30649264-1	chr11	30649214	30649314	+	3	cIP1vsInput	"intron (NM_029344, intron 1 of 3)"	CpG	132	NM_029344	75572	Mm.390319	NM_029344		Acyp2	2310004B09Rik	"acylphosphatase 2, muscle type"	protein-coding	0.05	0.574257
Merged-chr1-52874564-1	chr1	52874514	52874614	+	3	cIP1vsInput	"intron (NM_146108, intron 6 of 13)"	"intron (NM_146108, intron 6 of 13)"	29518	NM_146108	227095	Mm.222063	NM_146108	ENSMUSG00000041426	Hibch	2610509I15Rik|AI648812	3-hydroxyisobutyryl-Coenzyme A hydrolase	protein-coding	0	0.336634
Merged-chr1-177983135-1	chr1	177983085	177983185	+	3	cIP1vsInput	Intergenic	Intergenic	-8300	NM_001034899	545391	Mm.442974	NM_001034899	ENSMUSG00000091476	Gm16432	EG545391|EG666250	predicted gene 16432	protein-coding	0.02	0.554455
Merged-chr6-6299414-2	chr6	6299363	6299465	+	3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-82241	NM_001177572	50799	Mm.24513	NM_001177572	ENSMUSG00000015112	Slc25a13	AI785475|Ctrn	"solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 13"	protein-coding	0.039216	0.485437
Merged-chrX-151343834-1	chrX	151343784	151343884	+	3	cIP2vsInput	promoter-TSS (NM_198105)	promoter-TSS (NM_198105)	-389	NM_198105	207375	Mm.391339	NM_198105		Fam120c	D930001I21Rik|ORF34	"family with sequence similarity 120, member C"	protein-coding	0.04	0.584158
Merged-chr13-58040340-1	chr13	58040290	58040390	+	3	cIP2vsInput	"intron (NM_001195075, intron 8 of 16)"	PB1D7|SINE|Alu	-17140	NR_030544	100124491		NR_030544		Mir874	Mirn874|mmu-mir-874	microRNA 874	miscRNA	0.05	0.623762
Merged-chr10-72290987-1	chr10	72290937	72291037	+	3	cIP1vsInput	Intergenic	Intergenic	-310297	NR_003644	108950	Mm.212793	NR_003644	ENSMUSG00000043859	1700049L16Rik	-	hematological and neurological expressed 1-like pseudogene	pseudo	0	0.346535
Merged-chr8-69049731-2	chr8	69049675	69049788	+	3	cIP1vsInput|cIP2vsInput	"intron (NM_153054, intron 11 of 16)"	"intron (NM_153054, intron 11 of 16)"	-39005	NM_007509	11966	Mm.249096	NM_007509	ENSMUSG00000006273	Atp6v1b2	AI194269|AI790362|Atp6b2|HO57|R74844	"ATPase, H+ transporting, lysosomal V1 subunit B2"	protein-coding	0.017699	0.54386
Merged-chr12-73123559-1	chr12	73123509	73123609	+	3	cIP1vsInput	promoter-TSS (NM_008612)	promoter-TSS (NM_008612)	-158	NM_008612	17420	Mm.246750	NM_008612	ENSMUSG00000021103	Mnat1	E130115E11Rik|MAT1|P36	menage a trois 1	protein-coding	0.01	0.336634
Merged-chr2-17921405-1	chr2	17921355	17921455	+	3	cIP1vsInput	Intergenic	MYSERV16_I-int|LTR|ERVK	75541	NM_026627	68231	Mm.23887	NM_026627	ENSMUSG00000062651	H2afb1	1700113O17Rik|H2A.Bbd|H2al2|TSEG-1|Tseg1	"H2A histone family, member B1"	protein-coding	0	0.326733
Merged-chr3-106273266-1	chr3	106273216	106273316	+	3	cIP1vsInput	Intergenic	Intergenic	-53787	NM_145126	104183	Mm.425140	NM_145126	ENSMUSG00000063779	Chi3l4	Chil4|Ym2	"chitinase 3-like 4, Chil4"	protein-coding	0	0.336634
Merged-chr15-43282675-1	chr15	43282625	43282725	+	3	cIP2vsInput	promoter-TSS (NM_008388)	promoter-TSS (NM_008388)	61	NM_008388	16341	Mm.289992	NM_008388	ENSMUSG00000022336	Eif3e	48kDa|Eif3s6|Int6|eIF3-p46|eIF3-p48	"eukaryotic translation initiation factor 3, subunit E"	protein-coding	0.1	0.564356
Merged-chr10-58463152-1	chr10	58463102	58463202	+	3	cIP1vsInput	"intron (NM_011240, intron 9 of 28)"	"intron (NM_011240, intron 9 of 28)"	16300	NM_011240	19386	Mm.485644	NM_011240	ENSMUSG00000003226	Ranbp2	A430087B05Rik|AI256741|NUP358	RAN binding protein 2	protein-coding	0.01	0.306931
Merged-chr2-12507797-1	chr2	12507747	12507847	+	3	cIP1vsInput	Intergenic	Intergenic	-88337	NM_024185	66960	Mm.34059	NM_024185	ENSMUSG00000026767	Fam188a	1810041E18Rik|2310047O13Rik|5830410F13Rik|AI447827|AW111958	"family with sequence similarity 188, member A"	protein-coding	0	0.336634
Merged-chr4-105157393-1	chr4	105157343	105157443	+	3	cIP1vsInput	promoter-TSS (NM_080555)	promoter-TSS (NM_080555)	46	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Ppap2b	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b	phosphatidic acid phosphatase type 2B	protein-coding	0.06	0.643564
Merged-chr5-121185426-1	chr5	121185376	121185476	+	3	cIP1vsInput	"intron (NM_001109992, intron 1 of 15)"	"intron (NM_001109992, intron 1 of 15)"	5971	NM_001109992	19247	Mm.474046	NM_001109992	ENSMUSG00000043733	Ptpn11	2700084A17Rik|AW536184|PTP1D|PTP2C|SAP-2|SH-PTP2|SH-PTP3|SHP-2|Shp2|Syp	"protein tyrosine phosphatase, non-receptor type 11"	protein-coding	0.02	0.514851
Merged-chr17-24169556-1	chr17	24169506	24169606	+	3	cIP2vsInput	promoter-TSS (NM_009729)	promoter-TSS (NM_009729)	-127	NM_009729	11984	Mm.320896	NM_009729	ENSMUSG00000024121	Atp6v0c	Atp6c|Atp6c2|Atp6l|Atpl|Atpl-rs1|PL16|VATL|Vma3	"ATPase, H+ transporting, lysosomal V0 subunit C"	protein-coding	0.06	0.712871
Merged-chr18-44585058-1	chr18	44585008	44585108	+	3	cIP1vsInput	"intron (NM_001085373, intron 3 of 18)"	"intron (NM_001085373, intron 3 of 18)"	-76607	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	miscRNA	0.05	0.534653
Merged-chr12-36942395-1	chr12	36942345	36942445	+	3	cIP1vsInput	Intergenic	Lx6|LINE|L1	-166151	NM_008584	17286	Mm.341398	NM_008584		Meox2	AI528662|Gax|Mox-2|Mox2	mesenchyme homeobox 2	protein-coding	0	0.326733
Merged-chr8-19799341-1	chr8	19799291	19799391	+	3	cIP1vsInput	"intron (NM_001270553, intron 6 of 9).2"	"intron (NM_001270553, intron 6 of 9).2"	69765	NM_001039553	626415	Mm.425517	NM_001039553		4930467E23Rik	ENSMUSG00000074453|OTTMUSG00000018948|TSAP	RIKEN cDNA 4930467E23 gene	protein-coding	0.01	0.39604
Merged-chr4-17102690-1	chr4	17102640	17102740	+	3	cIP1vsInput	Intergenic	Lx10|LINE|L1	-750792	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0	0.356436
Merged-chr12-15605835-1	chr12	15605785	15605885	+	3	cIP1vsInput	Intergenic	Intergenic	210950	NM_144551	217410	Mm.266679	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles homolog 2 (Drosophila)	protein-coding	0	0.336634
Merged-chr17-46160415-1	chr17	46160365	46160465	+	3	cIP2vsInput	promoter-TSS (NM_001145979)	promoter-TSS (NM_001145979)	-617	NM_019581	56055	Mm.22147	NM_001145979	ENSMUSG00000023952	Gtpbp2	-	GTP binding protein 2	protein-coding	0.03	0.613861
Merged-chr11-106999649-1	chr11	106999599	106999699	+	3	cIP1vsInput	promoter-TSS (NM_010655)	promoter-TSS (NM_010655)	-124	NM_010655	16647	Mm.423000	NM_010655	ENSMUSG00000018362	Kpna2	2410044B12Rik|IPOA1|PTAC58|Rch1	karyopherin (importin) alpha 2	protein-coding	0.07	0.594059
Merged-chr8-56452896-1	chr8	56452846	56452946	+	3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	97670	NM_001009951	382010	Mm.425534	NM_001009951	ENSMUSG00000038215	Cep44	4933440G23Rik|mKIAA1712	centrosomal protein 44	protein-coding	0	0.346535
Merged-chr2-173000002-1	chr2	172999952	173000052	+	3	cIP2vsInput	promoter-TSS (NM_175112)	promoter-TSS (NM_175112)	-115	NM_175112	66679	Mm.4113	NM_175112	ENSMUSG00000027509	Rae1	3230401I12Rik|41|D2Ertd342e|MNRP|MNRP41	RAE1 RNA export 1 homolog (S. pombe)	protein-coding	0.06	0.554455
Merged-chr3-129831311-1	chr3	129831261	129831361	+	3	cIP2vsInput	promoter-TSS (NM_026578)	promoter-TSS (NM_026578)	85	NM_026578	68147	Mm.24873	NM_026578	ENSMUSG00000028010	Gar1	AA409823|AI326794|C430047J18Rik|Nola1	GAR1 ribonucleoprotein homolog (yeast)	protein-coding	0.09	0.643564
Merged-chr7-101664012-1	chr7	101663962	101664062	+	3	cIP2vsInput	"exon (NM_009191, exon 1 of 16)"	"exon (NM_009191, exon 1 of 16)"	244	NM_009191	20480	Mm.3990	NM_009191	ENSMUSG00000001829	Clpb	AL118244|Skd3	ClpB caseinolytic peptidase B	protein-coding	0.09	0.683168
Merged-chr10-41303577-1	chr10	41303527	41303627	+	3	cIP1vsInput	promoter-TSS (NM_133999)	promoter-TSS (NM_133999)	-336	NM_133999	103199	Mm.277242	NM_133999	ENSMUSG00000038417	Fig4	A530089I17Rik|AI326867|Sac3	FIG4 homolog (S. cerevisiae)	protein-coding	0.03	0.366337
Merged-chr16-62986084-1	chr16	62986034	62986134	+	3	cIP1vsInput	Intergenic	Intergenic	131750	NM_011173	19128	Mm.127156	NM_011173	ENSMUSG00000022912	Pros1	AW214361	protein S (alpha)	protein-coding	0	0.29703
Merged-chr2-175068101-1	chr2	175068051	175068151	+	3	cIP1vsInput	promoter-TSS (NM_001085546)	promoter-TSS (NM_001085546)	-338	NM_001085546	664987	Mm.452080	NM_001085546	ENSMUSG00000078905	Gm14393	OTTMUSG00000016546	predicted gene 14393	protein-coding	0	0.435644
Merged-chr5-34660280-1	chr5	34660230	34660330	+	3	cIP1vsInput	promoter-TSS (NM_019497)	promoter-TSS (NM_019497)	-99	NM_001080743	14772	Mm.117076	NM_001080743	ENSMUSG00000052783	Grk4	A830025H08Rik|GRK|Gprk2l|Gprk4	G protein-coupled receptor kinase 4	protein-coding	0.04	0.564356
Merged-chr3-90265094-2	chr3	90265035	90265153	+	3	cIP1vsInput|cIP2vsInput	TTS (NM_028881)	TTS (NM_028881)	-1440	NM_201407	229541	Mm.30571	NM_201407	ENSMUSG00000042404	Dennd4b	BC026996|mKIAA0476	DENN/MADD domain containing 4B	protein-coding	0.050847	0.680672
Merged-chr11-119034279-1	chr11	119034229	119034329	+	3	cIP2vsInput	Intergenic	Intergenic	6634	NM_013926	30951	Mm.99953	NM_013926		Cbx8	Pc3	chromobox 8	protein-coding	0.07	0.60396
Merged-chr12-76896031-1	chr12	76895981	76896081	+	3	cIP2vsInput	"intron (NM_145927, intron 6 of 11)"	"intron (NM_145927, intron 6 of 11)"	58564	NM_145927	110606	Mm.151174	NM_145927	ENSMUSG00000033373	Fntb	2010013E13Rik|AA409500	"farnesyltransferase, CAAX box, beta"	protein-coding	0.02	0.485149
Merged-chr1-167283788-1	chr1	167283738	167283838	+	3	cIP1vsInput	"intron (NM_030724, intron 1 of 6)"	CpG	1339	NM_030724	80914	Mm.440156	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding	0.08	0.653465
Merged-chr3-123184083-1	chr3	123184033	123184133	+	3	cIP2vsInput	"intron (NM_080451, intron 1 of 4)"	(TATAA)n|Simple_repeat|Simple_repeat	52066	NM_080451	118449	Mm.474733	NM_080451	ENSMUSG00000050315	Synpo2	1110069I04Rik|2310068J10Rik|9530006G20Rik|AI848603|Myo	synaptopodin 2	protein-coding	0	0.237624
Merged-chr1-25084437-1	chr1	25084387	25084487	+	3	cIP1vsInput	"intron (NM_175642, intron 28 of 30)"	"intron (NM_175642, intron 28 of 30)"	193517	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	"predicted gene, 20172"	protein-coding	0.01	0.316832
Merged-chr15-33831817-1	chr15	33831767	33831867	+	3	cIP1vsInput	Intergenic	RLTR45-int|LTR|ERVK	-143934	NM_001085421	239364	Mm.60794	NM_001085421	ENSMUSG00000038984	Tspyl5	6330530B20|E130308C19Rik	"testis-specific protein, Y-encoded-like 5"	protein-coding	0	0.29703
Merged-chr3-96172278-1	chr3	96172228	96172328	+	3	cIP2vsInput	promoter-TSS (NM_153053)	promoter-TSS (NM_153053)	-272	NM_153053	107701	Mm.219671	NM_153053	ENSMUSG00000068856	Sf3b4	49kDa|SF3b49|SF3b50|Sap49	"splicing factor 3b, subunit 4"	protein-coding	0.05	0.534653
Merged-chr17-81714568-1	chr17	81714518	81714618	+	3	cIP2vsInput	"intron (NM_011406, intron 1 of 10)"	"intron (NM_011406, intron 1 of 10)"	23809	NM_001112798	20541	Mm.489060	NM_001112798		Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	"solute carrier family 8 (sodium/calcium exchanger), member 1"	protein-coding	0	0.267327
Merged-chr1-165724776-1	chr1	165724726	165724826	+	3	cIP2vsInput	Intergenic	Intergenic	-16682	NM_001038846	226594	Mm.482459	NM_001038846	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872	RCSD domain containing 1	protein-coding	0.01	0.455446
Merged-chr3-130709632-1	chr3	130709582	130709682	+	3	cIP1vsInput	promoter-TSS (NM_025509)	promoter-TSS (NM_025509)	-188	NM_025509	66357	Mm.300697	NM_025509	ENSMUSG00000041084	Ostc	2310008M10Rik|5730557H03Rik	oligosaccharyltransferase complex subunit	protein-coding	0.02	0.455446
Merged-chr8-29397400-1	chr8	29397350	29397450	+	3	cIP1vsInput	Intergenic	(CATAT)n|Simple_repeat|Simple_repeat	-177764	NM_153135	210801	Mm.248433	NM_153135	ENSMUSG00000063626	Unc5d	D930029E11Rik|Unc5h4|mKIAA1777	unc-5 homolog D (C. elegans)	protein-coding	0	0.207921
Merged-chr12-64685642-1	chr12	64685592	64685692	+	3	cIP2vsInput	Intergenic	Intergenic	-210744	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.326733
Merged-chr3-89246602-1	chr3	89246552	89246652	+	3	cIP2vsInput	promoter-TSS (NM_183037)	promoter-TSS (NM_183037)	164	NM_025327	66059	Mm.177991	NM_025327	ENSMUSG00000042747	Krtcap2	0610010I12Rik|Kcp2	keratinocyte associated protein 2	protein-coding	0.06	0.594059
Merged-chr9-20976953-1	chr9	20976903	20977003	+	3	cIP2vsInput	promoter-TSS (NM_010333)	promoter-TSS (NM_010333)	-160	NM_010333	14739	Mm.46493	NM_010333	ENSMUSG00000043895	S1pr2	1100001A16Rik|Edg5|Gpcr13|H218|LPb2|S1P2	sphingosine-1-phosphate receptor 2	protein-coding	0.06	0.613861
Merged-chr2-144556109-1	chr2	144556059	144556159	+	3	cIP2vsInput	promoter-TSS (NM_001252544)	promoter-TSS (NM_001252544)	-120	NM_001252544	27054	Mm.487953	NM_001252543	ENSMUSG00000027429	Sec23b	-	SEC23B (S. cerevisiae)	protein-coding	0.01	0.415842
Merged-chr7-3644538-1	chr7	3644488	3644588	+	3	cIP1vsInput	promoter-TSS (NM_146176)	promoter-TSS (NM_146176)	-731	NM_146176	232791	Mm.358731	NM_146176	ENSMUSG00000035632	Cnot3	A930039N10Rik	"CCR4-NOT transcription complex, subunit 3"	protein-coding	0.03	0.425743
Merged-chr14-47568383-1	chr14	47568333	47568433	+	3	cIP2vsInput	promoter-TSS (NM_172599)	promoter-TSS (NM_172599)	51	NM_172599	100504663	Mm.470462	NM_172599	ENSMUSG00000037526	Atg14	4832427M01|Atg14L|D14Ertd114e|D14Ertd436e	autophagy related 14	protein-coding	0.08	0.653465
Merged-chr8-114018631-1	chr8	114018581	114018681	+	3	cIP2vsInput	Intergenic	Intergenic	-114948	NM_024446	67528	Mm.27889	NM_024437	ENSMUSG00000031767	Nudt7	1300007B24Rik|2210404C19Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 7	protein-coding	0	0.524752
Merged-chr3-96635491-1	chr3	96635441	96635541	+	3	cIP1vsInput	promoter-TSS (NR_027844)	promoter-TSS (NR_027844)	61	NM_001162387	18632	Mm.20901	NM_001162387	ENSMUSG00000028102	Pex11b	PEX11beta|Pex11pbeta	peroxisomal biogenesis factor 11 beta	protein-coding	0.07	0.564356
Merged-chr10-80141557-1	chr10	80141507	80141607	+	3	cIP1vsInput	promoter-TSS (NM_025313)	promoter-TSS (NM_025313)	-758	NM_025313	66043	Mm.278560	NM_025313	ENSMUSG00000003072	Atp5d	0610008F14Rik|1500000I11Rik|AA960090|AI876556|AU020773|C85518	"ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit"	protein-coding	0.09	0.643564
Merged-chr13-90161785-1	chr13	90161735	90161835	+	3	cIP1vsInput	Intergenic	Intergenic	72118	NM_025335	66074	Mm.241387	NM_025335		Tmem167	0610041E09Rik|5730424F14Rik|AU041184|AW537806|ENSMUSG00000060669|Gm10085|Tmem167a	transmembrane protein 167	protein-coding	0	0.366337
Merged-chr12-10128243-1	chr12	10128193	10128293	+	3	cIP2vsInput	Intergenic	Intergenic	-241728	NM_027588	70881	Mm.272843	NM_027588	ENSMUSG00000020622	Nt5c1b	4921514H13Rik|AIRP|CN-IB	"5'-nucleotidase, cytosolic IB"	protein-coding	0.01	0.435644
Merged-chr15-73186866-1	chr15	73186816	73186916	+	3	cIP2vsInput	Intergenic	Intergenic	-1919	NM_153178	239528	Mm.490340	NM_153178		Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding	0.04	0.564356
Merged-chr4-18221321-1	chr4	18221271	18221371	+	3	cIP1vsInput	Intergenic	Intergenic	367839	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0	0.306931
Merged-chr12-108334278-2	chr12	108334205	108334351	+	3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010010)	promoter-TSS (NM_010010)	-103	NM_010010	13116	Mm.41911	NM_010010	ENSMUSG00000021259	Cyp46a1	Cyp46	"cytochrome P450, family 46, subfamily a, polypeptide 1"	protein-coding	0.123288	0.789116
Merged-chr9-109097987-1	chr9	109097937	109098037	+	3	cIP2vsInput	"intron (NM_172775, intron 1 of 37)"	"intron (NM_172775, intron 1 of 37)"	2551	NM_172775	235611	Mm.53862	NM_172775	ENSMUSG00000053646	Plxnb1	2900002G15Rik|AU042020|mKIAA0407	plexin B1	protein-coding	0.02	0.653465
Merged-chr2-132856150-1	chr2	132856100	132856200	+	3	cIP2vsInput	"intron (NM_001024385, intron 3 of 6)"	L1M5|LINE|L1	8416	NM_025646	66586	Mm.357342	NM_001024384	ENSMUSG00000027357	Crls1	0610009I22Rik|4930557M15Rik|5730490M08Rik	cardiolipin synthase 1	protein-coding	0	0.316832
Merged-chr6-59657912-1	chr6	59657862	59657962	+	3	cIP1vsInput	Intergenic	Intergenic	-231622	NM_183183	243385	Mm.485751	NM_183183	ENSMUSG00000045441	Gprin3	C030038J10Rik|C730021L23	GPRIN family member 3	protein-coding	0	0.306931
Merged-chr16-42190269-1	chr16	42190219	42190319	+	3	cIP2vsInput	Intergenic	CpG	150382	NM_008083	14432	Mm.1222	NM_008083	ENSMUSG00000047261	Gap43	B-50|Basp2|GAP-43	growth associated protein 43	protein-coding	0.14	0.762376
Merged-chr2-32712407-1	chr2	32712357	32712457	+	3	cIP2vsInput	TTS (NR_039536)	TTS (NR_039536)	377	NM_130860	107951	Mm.27557	NM_130860		Cdk9	PITALRE	cyclin-dependent kinase 9 (CDC2-related kinase)	protein-coding	0.11	0.732673
Merged-chr2-6099214-1	chr2	6099164	6099264	+	3	cIP2vsInput	"3' UTR (NM_001159657, exon 4 of 4)"	"3' UTR (NM_001159657, exon 4 of 4)"	30971	NM_144883	227545	Mm.133542	NM_001159657		Proser2	5430407P10Rik|AU067770	proline and serine rich 2	protein-coding	0	0.455446
Merged-chr17-59358362-1	chr17	59358312	59358412	+	3	cIP1vsInput	Intergenic	Intergenic	-345040	NM_026497	67993	Mm.36507	NM_026497		Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0	0.336634
Merged-chr5-146272620-1	chr5	146272570	146272670	+	3	cIP1vsInput	"intron (NM_153599, intron 4 of 12)"	"intron (NM_153599, intron 4 of 12)"	40945	NM_153599	264064	Mm.260576	NM_181570	ENSMUSG00000029635	Cdk8	-	cyclin-dependent kinase 8	protein-coding	0.01	0.287129
Merged-chr16-13902951-1	chr16	13902901	13903001	+	3	cIP2vsInput	"5' UTR (NM_053181, exon 1 of 23)"	"5' UTR (NM_053181, exon 1 of 23)"	184	NM_001039533	94184	Mm.171484	NM_178853	ENSMUSG00000022680	Pdxdc1	2210010A19Rik|AA415817|Kiaa0251-hp	pyridoxal-dependent decarboxylase domain containing 1	protein-coding	0.13	0.732673
Merged-chr14-108392229-1	chr14	108392179	108392279	+	3	cIP2vsInput	Intergenic	Intergenic	522010	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	"SLIT and NTRK-like family, member 1"	protein-coding	0	0.336634
Merged-chr12-95213650-1	chr12	95213600	95213700	+	3	cIP1vsInput	Intergenic	Intergenic	-478576	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0	0.217822
Merged-chr7-41466151-1	chr7	41466101	41466201	+	3	cIP2vsInput	Intergenic	Intergenic	-17510	NM_177764	269902	Mm.483785	NM_177764	ENSMUSG00000066537	Vmn2r57	D430014M15|EG269902	"vomeronasal 2, receptor 57"	protein-coding	0	0.356436
Merged-chr6-23922429-1	chr6	23922379	23922479	+	3	cIP1vsInput	Intergenic	Intergenic	47631	NM_207022	387347	Mm.377909	NM_207022	ENSMUSG00000043865	Tas2r118	Gm465|T2R18|Tas2r16|Tas2r18|mGR18|mt2r40	"taste receptor, type 2, member 118"	protein-coding	0	0.267327
Merged-chr5-30960388-1	chr5	30960338	30960438	+	3	cIP2vsInput	promoter-TSS (NM_016703)	promoter-TSS (NM_016703)	-27	NM_016703	50907	Mm.272414	NM_016703	ENSMUSG00000045302	Preb	C85705	prolactin regulatory element binding	protein-coding	0.13	0.643564
Merged-chr4-155086469-2	chr4	155086405	155086534	+	2.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026395)	promoter-TSS (NM_026395)	-108	NM_001081100	76866	Mm.200590	NM_001081100	ENSMUSG00000029049	Morn1	2900057D20Rik|4930417P05Rik|AU042805	MORN repeat containing 1	protein-coding	0.124031	0.676923
Merged-chr2-180227823-2	chr2	180227764	180227882	+	2.95	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-1964	NM_001081171	16776	Mm.4339	NM_001081171	ENSMUSG00000015647	Lama5	AA408760|AA408762|AI853660|[a]5|laminin-511|mKIAA0533	"laminin, alpha 5"	protein-coding	0.025424	0.613445
Merged-chr16-95701879-2	chr16	95701807	95701951	+	2.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011809)	promoter-TSS (NM_011809)	-528	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	"E26 avian leukemia oncogene 2, 3' domain"	protein-coding	0.055556	0.558621
Merged-chr10-84622355-2	chr10	84622291	84622419	+	2.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027423)	promoter-TSS (NM_027423)	-82	NM_027423	70428	Mm.335007	NM_027423	ENSMUSG00000034453	Polr3b	2700078H01Rik|A330032P03Rik|C85372|RPC2	polymerase (RNA) III (DNA directed) polypeptide B	protein-coding	0.09375	0.635659
Merged-chr3-127258302-2	chr3	127258221	127258384	+	2.95	cIP1vsInput|cIP2vsInput	Intergenic	(GA)n|Simple_repeat|Simple_repeat	-259850	NM_178655	109676	Mm.484610	NM_001034168	ENSMUSG00000032826	Ank2	AI835472|AW491075|Ank-2	"ankyrin 2, brain"	protein-coding	0.067485	0.530488
Merged-chr4-99914072-2	chr4	99914019	99914126	+	2.95	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-15379	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding	0.009346	0.398148
Merged-chr6-54771419-2	chr6	54771355	54771483	+	2.95	cIP1vsInput|cIP2vsInput	Intergenic	MLT1F|LTR|ERVL-MaLR	-45497	NM_199143	387524	Mm.392146	NM_199143		Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding	0.023438	0.55814
Merged-chr1-131555398-2	chr1	131555327	131555469	+	2.95	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	27409	NM_175382	108900	Mm.31278	NM_175382	ENSMUSG00000055184	Fam72a	2700049P18Rik|P17	"family with sequence similarity 72, member A"	protein-coding	0.077465	0.524476
Merged-chr11-78163967-2	chr11	78163897	78164038	+	2.95	cIP1vsInput|cIP2vsInput	"intron (NM_009423, intron 1 of 6)"	G-rich|Low_complexity|Low_complexity	1583	NM_009423	22032	Mm.390418	NM_009423		Traf4	A530032M13Rik|CART1|msp2	TNF receptor associated factor 4	protein-coding	0.014184	0.647887
Merged-chr4-78283589-2	chr4	78283496	78283682	+	2.95	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-71694	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0	0.342246
Merged-chr19-56378670-2	chr19	56378604	56378736	+	2.95	cIP1vsInput|cIP2vsInput	"intron (NM_198059, intron 10 of 40)"	"intron (NM_198059, intron 10 of 40)"	11365	NM_198059	18175	Mm.386769	NM_008733	ENSMUSG00000049134	Nrap	-	nebulin-related anchoring protein	protein-coding	0.037879	0.43609
Merged-chr2-157102445-2	chr2	157102383	157102508	+	2.95	cIP1vsInput|cIP2vsInput	"intron (NM_001139520, intron 14 of 16)"	RMER17B|LTR|ERVK	15390	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding	0.016	0.515873
Merged-chr11-6626203-2	chr11	6626142	6626264	+	2.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_134011)	promoter-TSS (NM_134011)	-136	NM_134011	21379	Mm.247761	XM_003945887	ENSMUSG00000000384	Tbrg4	2310042P22Rik|AA120735|AA408001|AI527316|Cpr2|R74877|Tb-12|mKIAA0948	transforming growth factor beta regulated gene 4	protein-coding	0.07377	0.585366
Merged-chr2-92093750-2	chr2	92093697	92093804	+	2.95	cIP1vsInput|cIP2vsInput	Intergenic	(CCCTAA)n|Simple_repeat|Simple_repeat	-69580	NM_011957	26427	Mm.10353	NM_011957	ENSMUSG00000027230	Creb3l1	Oasis	cAMP responsive element binding protein 3-like 1	protein-coding	0.009346	0.5
Merged-chr5-19226777-2	chr5	19226721	19226834	+	2.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001170746)	promoter-TSS (NM_001170746)	-222	NR_102341	70832	Mm.398993	XR_106346	ENSMUSG00000097626	4921504A21Rik	-	RIKEN cDNA 4921504A21 gene	miscRNA	0.088496	0.640351
Merged-chrX-48454269-2	chrX	48454203	48454336	+	2.95	cIP1vsInput|cIP2vsInput	"intron (NM_019680, intron 1 of 8)"	CpG	8863	NM_019680	56501	Mm.36808	NM_019680	ENSMUSG00000031103	Elf4	AV314029|BC042423|ENSMUSG00000053512|Gm9907|Mef	E74-like factor 4 (ets domain transcription factor)	protein-coding	0.097744	0.686567
Merged-chr11-78080348-2	chr11	78080287	78080409	+	2.95	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_022313)	promoter-TSS (NM_022313)	35	NM_022313	57837	Mm.21096	NM_022313	ENSMUSG00000020832	Eral1	2610524P08Rik|9130407C09Rik|AU019798|Era|M-ERA|MERA-S|MERA-W	Era (G-protein)-like 1 (E. coli)	protein-coding	0.098361	0.650407
Merged-chr5-145204873-2	chr5	145204803	145204943	+	2.95	cIP1vsInput|cIP2vsInput	"5' UTR (NM_016683, exon 1 of 6)"	"5' UTR (NM_016683, exon 1 of 6)"	314	NM_001167944	22757	Mm.332842	NM_001167944	ENSMUSG00000055991	Zkscan5	AI132486|AI326970|Zfp95|hKraba1	zinc finger with KRAB and SCAN domains 5	protein-coding	0.028571	0.368794
Merged-chr2-4913693-2	chr2	4913625	4913762	+	2.95	cIP1vsInput|cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	-5303	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding	0.014599	0.557971
Merged-chr14-23682818-1	chr14	23682768	23682868	+	2.9	cIP2vsInput	"intron (NM_001253374, intron 1 of 28)"	"intron (NM_001253374, intron 1 of 28)"	321387	NM_001253375	16531	Mm.486347	NM_001253358	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	"potassium large conductance calcium-activated channel, subfamily M, alpha member 1"	protein-coding	0.03	0.554455
Merged-chr10-117905957-1	chr10	117905907	117906007	+	2.9	cIP1vsInput	Intergenic	Intergenic	-19502	NR_045342	71067	Mm.410793	NR_045342		4933411E08Rik	-	RIKEN cDNA 4933411E08 gene	miscRNA	0.07	0.623762
Merged-chr17-82413496-1	chr17	82413446	82413546	+	2.9	cIP2vsInput	Intergenic	Intergenic	664729	NR_045094	100503434	Mm.187281	NR_045094		Gm19689	-	"predicted gene, 19689"	miscRNA	0	0.346535
Merged-chr14-110727549-1	chr14	110727499	110727599	+	2.9	cIP1vsInput	Intergenic	Intergenic	27600	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	"SLIT and NTRK-like family, member 6"	protein-coding	0.01	0.346535
Merged-chr10-126778267-2	chr10	126778176	126778359	+	2.9	cIP1vsInput|cIP2vsInput	Intergenic	RLTR17B_Mm|LTR|ERVK	123104	NM_026858	68876	Mm.276769	NM_001159559	ENSMUSG00000025436	Xrcc6bp1	1110068E08Rik|2410012H02Rik	XRCC6 binding protein 1	protein-coding	0.005464	0.304348
Merged-chr8-5552207-1	chr8	5552157	5552257	+	2.9	cIP1vsInput	Intergenic	L2|LINE|L2	-446975	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.346535
Merged-chr18-58188818-1	chr18	58188768	58188868	+	2.9	cIP2vsInput	"intron (NM_010181, intron 5 of 64)"	"intron (NM_010181, intron 5 of 64)"	21108	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding	0	0.346535
Merged-chr6-91741332-1	chr6	91741282	91741382	+	2.9	cIP1vsInput	"intron (NM_009320, intron 9 of 14)"	"intron (NM_009320, intron 9 of 14)"	57265	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	"solute carrier family 6 (neurotransmitter transporter, taurine), member 6"	protein-coding	0.02	0.584158
Merged-chr6-60806002-1	chr6	60805952	60806052	+	2.9	cIP2vsInput	"intron (NM_001042451, intron 4 of 5)"	"intron (NM_001042451, intron 4 of 5)"	22994	NM_001042451	20617	Mm.17484	NM_001042451	ENSMUSG00000025889	Snca	NACP|alphaSYN	"synuclein, alpha"	protein-coding	0.01	0.316832
Merged-chr16-94080050-1	chr16	94080000	94080100	+	2.9	cIP1vsInput	Intergenic	Intergenic	-5210	NM_011377	20465	Mm.4775	NM_011377	ENSMUSG00000062713	Sim2	bHLHe15	single-minded homolog 2 (Drosophila)	protein-coding	0	0.405941
Merged-chr14-59076344-1	chr14	59076294	59076394	+	2.9	cIP2vsInput	Intergenic	(CACG)n|Simple_repeat|Simple_repeat	66549	NM_026461	67932	Mm.65550	NM_026461	ENSMUSG00000021977	1700129C05Rik	-	RIKEN cDNA 1700129C05 gene	protein-coding	0.13	0.623762
Merged-chr2-124206270-1	chr2	124206220	124206320	+	2.9	cIP1vsInput	Intergenic	Intergenic	16088	NR_040612	75946	Mm.415059	NR_040612	ENSMUSG00000086954	4930583P06Rik	-	RIKEN cDNA 4930583P06 gene	miscRNA	0	0.267327
Merged-chr4-52484551-1	chr4	52484501	52484601	+	2.9	cIP2vsInput	"intron (NM_008017, intron 24 of 24)"	"intron (NM_008017, intron 24 of 24)"	45302	NM_008017	14211	Mm.2999	NM_008017	ENSMUSG00000028312	Smc2	5730502P04Rik|AI255214|AW545314|CAP-E|CAPE|Fin16|SMC-2|Smc2l1	structural maintenance of chromosomes 2	protein-coding	0.01	0.316832
Merged-chr11-69913998-1	chr11	69913948	69914048	+	2.9	cIP2vsInput	promoter-TSS (NM_019726)	promoter-TSS (NM_019726)	-194	NM_019726	56310	Mm.477738	NM_019726	ENSMUSG00000023170	Gps2	AI505953	G protein pathway suppressor 2	protein-coding	0.11	0.613861
Merged-chr8-49392606-1	chr8	49392556	49392656	+	2.9	cIP1vsInput	Intergenic	Intergenic	-717916	NM_011857	23965	Mm.42191	NM_001145937	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding	0.01	0.316832
Merged-chr8-64688644-1	chr8	64688594	64688694	+	2.9	cIP1vsInput	"intron (NM_013494, intron 1 of 8)"	T-rich|Low_complexity|Low_complexity	4396	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|R74677|fat	carboxypeptidase E	protein-coding	0	0.267327
Merged-chr16-91688475-1	chr16	91688425	91688525	+	2.9	cIP2vsInput	promoter-TSS (NR_040389)	promoter-TSS (NR_040389)	253	NM_021720	60364		NM_021720	ENSMUSG00000022960	Donson	1110025J21Rik|AI845729|ORF60	downstream neighbor of SON	protein-coding	0.17	0.732673
Merged-chr9-102834830-1	chr9	102834780	102834880	+	2.9	cIP2vsInput	promoter-TSS (NM_013649)	promoter-TSS (NM_013649)	-90	NM_013649	20187	Mm.335391	NM_001042607	ENSMUSG00000032547	Ryk	AW536699|ERK-3|Vik	receptor-like tyrosine kinase	protein-coding	0.18	0.752475
Merged-chr2-81828078-1	chr2	81828028	81828128	+	2.9	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-225580	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0	0.287129
Merged-chr19-17715223-1	chr19	17715173	17715273	+	2.9	cIP1vsInput	"intron (NM_001190483, intron 3 of 37)"	"intron (NM_001190483, intron 3 of 37)"	122409	NM_001163144	18552	Mm.3401	NM_001163144	ENSMUSG00000024713	Pcsk5	PC5|PC5/6A|PC5A|PC6|SPC6|b2b585Clo	proprotein convertase subtilisin/kexin type 5	protein-coding	0.02	0.425743
Merged-chr2-7856640-1	chr2	7856590	7856690	+	2.9	cIP2vsInput	Intergenic	Intergenic	-460442	NM_001110231	14007	Mm.398543	NM_183219	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	"CUGBP, Elav-like family member 2"	protein-coding	0	0.356436
Merged-chr19-18412574-1	chr19	18412524	18412624	+	2.9	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	219239	NM_017375	20409	Mm.172222	NM_017375		Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding	0	0.316832
Merged-chr3-93768147-1	chr3	93768097	93768197	+	2.9	cIP1vsInput	Intergenic	RMER17C-int|LTR|ERVK	-28251	NM_207272	399675	Mm.377924	XM_003946379	ENSMUSG00000060256	Tdpoz4	-	TD and POZ domain containing 4	protein-coding	0	0.287129
Merged-chr13-67081468-1	chr13	67081418	67081518	+	2.9	cIP2vsInput	promoter-TSS (NM_001012448)	promoter-TSS (NM_001012448)	77	NM_001012448	432769	Mm.458849	NM_001012325	ENSMUSG00000058883	Zfp708	AU021768|BC038328|Rslcan11	zinc finger protein 708	protein-coding	0.06	0.594059
Merged-chr19-49517703-1	chr19	49517653	49517753	+	2.9	cIP2vsInput	Intergenic	Intergenic	1160943	NM_001252501	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0	0.326733
Merged-chr1-177797097-1	chr1	177797047	177797147	+	2.9	cIP2vsInput	promoter-TSS (NM_007422)	promoter-TSS (NM_007422)	-588	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	"adenylosuccinate synthetase, non muscle"	protein-coding	0	0.366337
Merged-chr1-130022303-1	chr1	130022253	130022353	+	2.9	cIP1vsInput	"intron (NM_172485, intron 15 of 27)"	Lx7|LINE|L1	400696	NM_007827	13137	Mm.436759	NM_007827	ENSMUSG00000026401	Daf2	AI323748|Cd55b|Daf|Daf-TM|TM-DAF	decay accelerating factor 2	protein-coding	0	0.29703
Merged-chr19-42779905-1	chr19	42779855	42779955	+	2.9	cIP1vsInput	promoter-TSS (NM_019424)	promoter-TSS (NM_019424)	71	NM_019424	192236	Mm.218381	NM_019424	ENSMUSG00000025188	Hps1	6030422N11Rik|BB405864|Hps|ep	Hermansky-Pudlak syndrome 1 homolog (human)	protein-coding	0.12	0.722772
Merged-chr11-88204192-1	chr11	88204142	88204242	+	2.9	cIP2vsInput	promoter-TSS (NM_024174)	promoter-TSS (NM_024174)	-226	NM_024174	64656	Mm.168680	NM_024174	ENSMUSG00000023723	Mrps23	2310047I09Rik|D11Bwg1153e|Rpms23	mitochondrial ribosomal protein S23	protein-coding	0.09	0.584158
Merged-chrX-123050049-1	chrX	123049999	123050099	+	2.9	cIP1vsInput	Intergenic	B1_Mus1|SINE|Alu	-53510	NM_028426	73061	Mm.292979	NM_028426		3110007F17Rik	-	RIKEN cDNA 3110007F17 gene	protein-coding	0	0.356436
Merged-chr15-22030121-1	chr15	22030071	22030171	+	2.9	cIP2vsInput	Intergenic	Intergenic	684863	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding	0	0.326733
Merged-chr8-26015713-1	chr8	26015663	26015763	+	2.9	cIP2vsInput	promoter-TSS (NM_008033)	promoter-TSS (NM_008033)	-112	NM_008033	14272	Mm.3496	NM_008033	ENSMUSG00000015994	Fnta	FTA	"farnesyltransferase, CAAX box, alpha"	protein-coding	0.05	0.663366
Merged-chr12-120028231-1	chr12	120028181	120028281	+	2.9	cIP2vsInput	Intergenic	Intergenic	82269	NM_001160385	217951	Mm.387395	NM_001160385	ENSMUSG00000048004	Tmem196	Gm528	transmembrane protein 196	protein-coding	0.01	0.356436
Merged-chr16-86215377-1	chr16	86215327	86215427	+	2.9	cIP2vsInput	Intergenic	Intergenic	-314252	NM_011782	23794	Mm.437478	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|AI481094|ASMP-2	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"	protein-coding	0	0.336634
Merged-chr13-67526435-1	chr13	67526385	67526485	+	2.9	cIP1vsInput	promoter-TSS (NM_133228)	promoter-TSS (NM_133228)	-204	NM_133228	170763	Mm.138283	NM_133228	ENSMUSG00000097333	Zfp87	2210039O17Rik|4631412O18Rik|KRAB4|Mzf22|Zfp72	zinc finger protein 87	protein-coding	0.01	0.287129
Merged-chr7-81900435-1	chr7	81900385	81900485	+	2.9	cIP1vsInput	"intron (NM_013886, intron 2 of 5)"	"intron (NM_013886, intron 2 of 5)"	34024	NM_013886	29877	Mm.392934	NM_013886	ENSMUSG00000025104	Hdgfrp3	2700022B06Rik|HRP-3	"hepatoma-derived growth factor, related protein 3"	protein-coding	0	0.356436
Merged-chr1-26533280-1	chr1	26533230	26533330	+	2.9	cIP1vsInput	Intergenic	Intergenic	154180	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding	0	0.316832
Merged-chr10-94198997-1	chr10	94198947	94199047	+	2.9	cIP2vsInput	promoter-TSS (NM_025551)	promoter-TSS (NM_025551)	-12	NM_025551	66414	Mm.461501	NM_025551	ENSMUSG00000020022	Ndufa12	2410011G03Rik|AW112974	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 12"	protein-coding	0.1	0.60396
Merged-chr19-47865527-1	chr19	47865477	47865577	+	2.9	cIP1vsInput	promoter-TSS (NM_030051)	promoter-TSS (NM_030051)	-18	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding	0.1	0.693069
Merged-chr4-51234432-1	chr4	51234382	51234482	+	2.9	cIP2vsInput	Intergenic	L1MC2|LINE|L1	17754	NM_001162865	74914	Mm.159368	NM_001162865	ENSMUSG00000039555	Cylc2	4930488P18Rik	"cylicin, basic protein of sperm head cytoskeleton 2"	protein-coding	0.01	0.316832
Merged-chr9-56427072-1	chr9	56427022	56427122	+	2.9	cIP2vsInput	"intron (NM_025812, intron 1 of 9)"	L1M2|LINE|L1	8226	NM_025812	66867	Mm.150856	NM_025812	ENSMUSG00000032329	Hmg20a	1200004E06Rik|5730490E10Rik|Hmgxb1|Ibraf	high mobility group 20A	protein-coding	0	0.326733
Merged-chr18-24872194-1	chr18	24872144	24872244	+	2.9	cIP2vsInput	"intron (NM_175276, intron 3 of 26)"	"intron (NM_175276, intron 3 of 26)"	162749	NM_175276	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding	0.04	0.623762
Merged-chr6-3498368-1	chr6	3498318	3498418	+	2.9	cIP2vsInput	promoter-TSS (NM_024260)	promoter-TSS (NM_024260)	-25	NM_001167751	73288	Mm.45539	NM_001167750	ENSMUSG00000001376	Ccdc132	1700034M03Rik|8430415E05Rik|BLM|C87205|mKIAA1861	coiled-coil domain containing 132	protein-coding	0.04	0.544554
Merged-chr10-13008098-1	chr10	13008048	13008148	+	2.9	cIP1vsInput	promoter-TSS (NM_175102)	promoter-TSS (NM_175102)	-352	NM_175102	66125	Mm.402225	NM_175102	ENSMUSG00000078348	Sf3b5	10kDa|1110005L13Rik|AU043053|Sf3b10	"splicing factor 3b, subunit 5"	protein-coding	0.03	0.485149
Merged-chr18-67279363-1	chr18	67279313	67279413	+	2.9	cIP2vsInput	Intergenic	Intergenic	-9860	NM_053261	114663	Mm.486871	NM_053261	ENSMUSG00000024525	Impa2	2210415D20Rik|AI326924|AW259601	inositol (myo)-1(or 4)-monophosphatase 2	protein-coding	0.02	0.544554
Merged-chr17-23586315-1	chr17	23586265	23586365	+	2.9	cIP1vsInput	"intron (NM_011747, intron 1 of 5)"	"intron (NM_011747, intron 1 of 5)"	13172	NM_011747	22654	Mm.40326	NM_011747	ENSMUSG00000062012	Zfp13	4933429B21|AI835008|Krox-8|Rhit|Zfp-13	zinc finger protein 13	protein-coding	0.01	0.554455
Merged-chr7-47001119-1	chr7	47001069	47001169	+	2.9	cIP2vsInput	"intron (NM_175318, intron 1 of 5)"	"intron (NM_175318, intron 1 of 5)"	7295	NM_175318	101685	Mm.155687	NM_175318	ENSMUSG00000049516	Spty2d1	5830435K17Rik|AI852426|P16H6	"SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)"	protein-coding	0	0.356436
Merged-chr18-82670122-1	chr18	82670072	82670172	+	2.9	cIP1vsInput	"intron (NM_177832, intron 5 of 29)"	ID_B1|SINE|B4	22612	NM_177832	329002		NM_177832	ENSMUSG00000041258	Zfp236	AI447957|Gm335	zinc finger protein 236	protein-coding	0.01	0.316832
Merged-chr5-142371989-1	chr5	142371939	142372039	+	2.9	cIP2vsInput	Intergenic	Intergenic	-29508	NM_199068	17425	Mm.24214	NM_010812	ENSMUSG00000056493	Foxk1	A630048H08Rik|AI463295|ENSMUSG00000075577|Gm10868|Mnf	forkhead box K1	protein-coding	0.04	0.613861
Merged-chr2-108574453-1	chr2	108574403	108574503	+	2.9	cIP2vsInput	Intergenic	L1MB1|LINE|L1	703837	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding	0	0.316832
Merged-chr6-126849166-1	chr6	126849116	126849216	+	2.9	cIP2vsInput	promoter-TSS (NM_025358)	promoter-TSS (NM_025358)	-22	NM_025358	66108	Mm.29939	NM_025358	ENSMUSG00000000399	Ndufa9	1010001N11Rik	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9"	protein-coding	0.08	0.594059
Merged-chr4-31505913-1	chr4	31505863	31505963	+	2.9	cIP2vsInput	Intergenic	Intergenic	-458194	NM_009316	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.01	0.386139
Merged-chr2-115096613-1	chr2	115096563	115096663	+	2.9	cIP2vsInput	Intergenic	Intergenic	247667	NR_040516	78193	Mm.189508	NR_040516	ENSMUSG00000087309	4930528P14Rik	-	RIKEN cDNA 4930528P14 gene	miscRNA	0.01	0.366337
Merged-chr12-78519262-1	chr12	78519212	78519312	+	2.9	cIP2vsInput	"intron (NM_145965, intron 9 of 22)"	"intron (NM_145965, intron 9 of 22)"	-172273	NM_027597	70897	Mm.56514	NM_027597	ENSMUSG00000056987	Fam71d	4921509E07Rik|4930516C23Rik|GARI-L2	"family with sequence similarity 71, member D"	protein-coding	0	0.316832
Merged-chr12-86008258-1	chr12	86008208	86008308	+	2.9	cIP2vsInput	"intron (NM_001081423, intron 30 of 33)"	"intron (NM_001081423, intron 30 of 33)"	70783	NM_009368	21809	Mm.3992	NM_009368	ENSMUSG00000021253	Tgfb3	Tgfb-3	"transforming growth factor, beta 3"	protein-coding	0.01	0.623762
Merged-chr1-63289519-1	chr1	63289469	63289569	+	2.9	cIP2vsInput	"intron (NM_028673, intron 4 of 6)"	L1M4|LINE|L1	16250	NM_001267872	73884	Mm.86986	NM_028673	ENSMUSG00000027520	Zdbf2	4930431J08Rik|9330107J05Rik	"zinc finger, DBF-type containing 2"	protein-coding	0	0.336634
Merged-chr12-63227474-1	chr12	63227424	63227524	+	2.9	cIP2vsInput	Intergenic	Intergenic	1247424	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.326733
Merged-chr11-53764042-2	chr11	53763967	53764118	+	2.9	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-5972	NM_001159393	16362	Mm.105218	NM_001159393	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding	0.086093	0.651316
Merged-chr6-16009321-1	chr6	16009271	16009371	+	2.9	cIP1vsInput	Intergenic	Intergenic	288660	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding	0	0.326733
Merged-chr14-46905234-1	chr14	46905184	46905284	+	2.9	cIP2vsInput	"intron (NM_001037221, intron 2 of 12)"	PB1D7|SINE|Alu	22269	NM_001037221	74480	Mm.214454	NM_001037221	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1	sterile alpha motif domain containing 4	protein-coding	0	0.366337
Merged-chr15-43459891-1	chr15	43459841	43459941	+	2.9	cIP2vsInput	"intron (NR_046064, intron 1 of 2)"	"intron (NR_046064, intron 1 of 2)"	17145	NR_046064	100038728	Mm.244168	NR_046064	ENSMUSG00000072592	Gm10373	ENSMUSG00000072592	predicted gene 10373	miscRNA	0	0.326733
Merged-chr18-67275829-1	chr18	67275779	67275879	+	2.9	cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	-13394	NM_053261	114663	Mm.486871	NM_053261	ENSMUSG00000024525	Impa2	2210415D20Rik|AI326924|AW259601	inositol (myo)-1(or 4)-monophosphatase 2	protein-coding	0.02	0.514851
Merged-chr18-10882962-1	chr18	10882912	10883012	+	2.9	cIP2vsInput	Intergenic	Intergenic	-97410	NR_029781	723959		NR_029781		Mir1a-2	Mir1-2|Mirn1-2|mmu-mir-1-2|mmu-mir-1a-2	microRNA 1a-2	miscRNA	0.02	0.524752
Merged-chr2-43588289-1	chr2	43588239	43588339	+	2.9	cIP1vsInput	"intron (NM_027552, intron 3 of 13)"	"intron (NM_027552, intron 3 of 13)"	32960	NM_027552	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding	0.01	0.356436
Merged-chr18-88001540-1	chr18	88001490	88001590	+	2.9	cIP2vsInput	Intergenic	Intergenic	892667	NM_018821	54607	Mm.476577	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding	0.02	0.376238
Merged-chr6-41516323-1	chr6	41516273	41516373	+	2.9	cIP1vsInput	Intergenic	Intergenic	-5453	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	"protease, serine, 2"	protein-coding	0	0.346535
Merged-chr18-31595735-1	chr18	31595685	31595785	+	2.9	cIP2vsInput	"intron (NM_026165, intron 6 of 7)"	"intron (NM_026165, intron 6 of 7)"	14167	NM_026165	67453	Mm.23896	NM_026165	ENSMUSG00000024259	Slc25a46	1200007B05Rik|AI325987	"solute carrier family 25, member 46"	protein-coding	0	0.346535
Merged-chr3-137172017-2	chr3	137171967	137172067	+	2.9	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-169061	NM_001163522	59308	Mm.27343	NM_001163522	ENSMUSG00000054690	Emcn	0610012K22Rik|AI315669|Muc14	endomucin	protein-coding	0	0.326733
Merged-chr11-97670022-2	chr11	97669966	97670078	+	2.9	cIP1vsInput|cIP2vsInput	"intron (NM_139311, intron 7 of 19)"	"intron (NM_139311, intron 7 of 19)"	6610	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6"	protein-coding	0.017857	0.539823
Merged-chr16-16493749-1	chr16	16493699	16493799	+	2.9	cIP1vsInput	"intron (NM_139232, intron 2 of 16)"	L1_Mur3|LINE|L1	10469	NM_139233	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	"FYVE, RhoGEF and PH domain containing 4"	protein-coding	0	0.336634
Merged-chr10-40247128-1	chr10	40247078	40247178	+	2.9	cIP1vsInput	promoter-TSS (NM_023323)	promoter-TSS (NM_023323)	-89	NM_023323	67239	Mm.11480	NM_001042556	ENSMUSG00000038510	Rpf2	2810470K21Rik|AU040229|AU043242|Bxdc1	ribosome production factor 2 homolog (S. cerevisiae)	protein-coding	0.09	0.564356
Merged-chr4-108058385-1	chr4	108058335	108058435	+	2.9	cIP2vsInput	"intron (NM_011327, intron 13 of 15)"	MTEb|LTR|ERVL-MaLR	-26295	NM_172874	242608	Mm.74710	NM_172874	ENSMUSG00000028600	Podn	9430070G18|Pcan|SLRR5A	podocan	protein-coding	0.04	0.455446
Merged-chr1-140331127-1	chr1	140331077	140331177	+	2.9	cIP2vsInput	"intron (NM_001081027, intron 1 of 27)"	"intron (NM_001081027, intron 1 of 27)"	84870	NM_001081027	240776	Mm.483845	NM_001081027	ENSMUSG00000052726	Kcnt2	E330038N15Rik|Slick	"potassium channel, subfamily T, member 2"	protein-coding	0	0.376238
Merged-chr17-27856520-1	chr17	27856470	27856570	+	2.9	cIP2vsInput	promoter-TSS (NM_001080769)	promoter-TSS (NM_001080769)	13	NM_001080769	224648	Mm.291291	NM_001080769	ENSMUSG00000039512	Uhrf1bp1	1110020K19Rik|AA408674|F830021D11Rik|mKIAA4127	UHRF1 (ICBP90) binding protein 1	protein-coding	0.17	0.792079
Merged-chr9-39494634-1	chr9	39494584	39494684	+	2.9	cIP2vsInput	promoter-TSS (NM_146830)	promoter-TSS (NM_146830)	-646	NM_146830	18343	Mm.246538	NM_146830	ENSMUSG00000062649	Olfr44	IB3|MOR171-5	olfactory receptor 44	protein-coding	0	0.29703
Merged-chr7-4690633-1	chr7	4690583	4690683	+	2.9	cIP2vsInput	promoter-TSS (NM_001168572)	promoter-TSS (NM_001168572)	-295	NM_001003920	381979	Mm.297064	NM_001003920	ENSMUSG00000035390	Brsk1	Gm1100|SAD-B|SADB	BR serine/threonine kinase 1	protein-coding	0.07	0.673267
Merged-chr6-72598454-1	chr6	72598404	72598504	+	2.9	cIP2vsInput	promoter-TSS (NM_026159)	promoter-TSS (NM_026159)	-41	NM_001253692	232089	Mm.489773	NM_001253692	ENSMUSG00000056698	Elmod3	AI844780|C330008I15Rik|RBM29|Rbed1	ELMO/CED-12 domain containing 3	protein-coding	0.02	0.435644
Merged-chr7-16119929-1	chr7	16119879	16119979	+	2.9	cIP2vsInput	promoter-TSS (NM_133727)	promoter-TSS (NM_133727)	53	NM_133727	70394	Mm.41101	NM_133727	ENSMUSG00000006021	Kptn	2310042D10Rik|2E4|C030013F01Rik	kaptin	protein-coding	0.06	0.643564
Merged-chrY-6711568-1	chrY	6711518	6711618	+	2.9	cIP1vsInput	Intergenic	MER2|DNA|TcMar-Tigger	456209	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.326733
Merged-chr16-35215555-1	chr16	35215505	35215605	+	2.9	cIP2vsInput	"intron (NM_001012765, intron 1 of 20)"	"intron (NM_001012765, intron 1 of 20)"	59919	NM_001012765	224129	Mm.41137	NM_001012765		Adcy5	AW121902|Ac5	adenylate cyclase 5	protein-coding	0	0.514851
Merged-chr7-38227989-1	chr7	38227939	38228039	+	2.9	cIP2vsInput	promoter-TSS (NM_024413)	promoter-TSS (NM_024413)	5	NM_024413	72287	Mm.333798	NM_024413	ENSMUSG00000074170	Plekhf1	1810013P09Rik|APPD|LAPF|PHAFIN1|ZFYVE15	"pleckstrin homology domain containing, family F (with FYVE domain) member 1"	protein-coding	0.12	0.693069
Merged-chr17-73142068-1	chr17	73142018	73142118	+	2.9	cIP2vsInput	"intron (NM_001081071, intron 1 of 5)"	"intron (NM_001081071, intron 1 of 5)"	34083	NM_001177967	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding	0	0.326733
Merged-chr2-6130101-1	chr2	6130051	6130151	+	2.9	cIP2vsInput	promoter-TSS (NM_001159657)	promoter-TSS (NM_001159657)	84	NM_144883	227545	Mm.133542	NM_001159657		Proser2	5430407P10Rik|AU067770	proline and serine rich 2	protein-coding	0.16	0.732673
Merged-chr3-87525444-1	chr3	87525394	87525494	+	2.9	cIP2vsInput	promoter-TSS (NM_012051)	promoter-TSS (NM_012051)	-134	NM_001083318	27049	Mm.219460	NM_001083318	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant gene 3	protein-coding	0.09	0.693069
Merged-chr3-128535550-1	chr3	128535500	128535600	+	2.9	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-303945	NR_045704	402774	Mm.209170	NR_045704		D030025E07Rik	-	RIKEN cDNA D030025E07 gene	miscRNA	0	0.346535
Merged-chr3-39513313-1	chr3	39513263	39513363	+	2.9	cIP1vsInput	Intergenic	Lx6|LINE|L1	626373	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT tumor suppressor homolog 4 (Drosophila)	protein-coding	0	0.356436
Merged-chr11-101733044-1	chr11	101732994	101733094	+	2.9	cIP1vsInput	promoter-TSS (NM_144831)	promoter-TSS (NM_144831)	88	NM_144831	217207	Mm.28186	NM_144831	ENSMUSG00000034931	Dhx8	Ddx8|mDEAH6|mKIAA4096	DEAH (Asp-Glu-Ala-His) box polypeptide 8	protein-coding	0.11	0.693069
Merged-chr2-138033490-1	chr2	138033440	138033540	+	2.9	cIP2vsInput	Intergenic	Intergenic	-223094	NM_001025431	228662	Mm.153405	NM_001025431	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding	0.01	0.346535
Merged-chr15-5116753-1	chr15	5116703	5116803	+	2.9	cIP1vsInput	"intron (NM_026069, intron 1 of 3)"	CpG	140	NM_026069	67281	Mm.10474	NM_026069	ENSMUSG00000041841	Rpl37	3110005M08Rik	ribosomal protein L37	protein-coding	0.07	0.613861
Merged-chr8-53639010-1	chr8	53638960	53639060	+	2.9	cIP2vsInput	promoter-TSS (NM_146208)	promoter-TSS (NM_146208)	55	NM_146208	234258	Mm.281749	NM_146208	ENSMUSG00000039396	Neil3	AI449477|BC034753|C85903	nei like 3 (E. coli)	protein-coding	0.06	0.633663
Merged-chr8-53812720-1	chr8	53812670	53812770	+	2.9	cIP1vsInput	Intergenic	Intergenic	-173655	NM_146208	234258	Mm.281749	NM_146208	ENSMUSG00000039396	Neil3	AI449477|BC034753|C85903	nei like 3 (E. coli)	protein-coding	0	0.376238
Merged-chr8-60632833-1	chr8	60632783	60632883	+	2.9	cIP2vsInput	promoter-TSS (NM_027756)	promoter-TSS (NM_027756)	-27	NM_027756	71306	Mm.23242	NM_001177881	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding	0.16	0.782178
Merged-chr8-36283634-1	chr8	36283584	36283684	+	2.9	cIP1vsInput	Intergenic	Intergenic	-34118	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding	0.03	0.485149
Merged-chr11-4953665-1	chr11	4953615	4953715	+	2.9	cIP2vsInput	"intron (NM_001243043, intron 1 of 22)"	"intron (NM_001243043, intron 1 of 22)"	-5601	NM_010904	380684	Mm.298283	NM_010904	ENSMUSG00000020396	Nefh	NF-H|NF200|Nfh|mKIAA0845	"neurofilament, heavy polypeptide"	protein-coding	0.03	0.70297
Merged-chr8-20592196-1	chr8	20592146	20592246	+	2.9	cIP1vsInput	Intergenic	Intergenic	-22731	NM_001270553	100861668	Mm.445582	NM_001270553		Gm21119	-	"predicted gene, 21119"	protein-coding	0.01	0.326733
Merged-chr4-29727077-1	chr4	29727027	29727127	+	2.9	cIP2vsInput	Intergenic	L1MC1|LINE|L1	913932	NM_010141	13841	Mm.257266	NM_001122889	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding	0	0.366337
Merged-chr7-125444733-1	chr7	125444683	125444783	+	2.9	cIP2vsInput	"5' UTR (NM_029842, exon 1 of 8)"	"5' UTR (NM_029842, exon 1 of 8)"	113	NM_029842	77035	Mm.307239	NM_029842	ENSMUSG00000030752	Kdm8	3110005O21Rik|Jmjd5	lysine (K)-specific demethylase 8	protein-coding	0.1	0.554455
Merged-chr5-98254269-1	chr5	98254219	98254319	+	2.9	cIP2vsInput	promoter-TSS (NM_001277268)	promoter-TSS (NM_001277268)	85	NM_010203	14176	Mm.5055	NM_001277268	ENSMUSG00000029337	Fgf5	Fgf-5|HBGF-5|angora|go	fibroblast growth factor 5	protein-coding	0.08	0.653465
Merged-chr12-96346139-1	chr12	96346089	96346189	+	2.9	cIP1vsInput	Intergenic	Intergenic	-298917	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0	0.366337
Merged-chr2-154390341-1	chr2	154390291	154390391	+	2.9	cIP2vsInput	"intron (NM_009228, intron 2 of 7)"	"intron (NM_009228, intron 2 of 7)"	-17622	NM_025876	66971	Mm.289427	NM_025876	ENSMUSG00000027487	Cdk5rap1	2310066P17Rik	CDK5 regulatory subunit associated protein 1	protein-coding	0.02	0.584158
Merged-chr12-110446956-1	chr12	110446906	110447006	+	2.9	cIP2vsInput	promoter-TSS (NM_001135001)	promoter-TSS (NM_001135001)	-223	NM_001135001	26931	Mm.490988	NM_001037934	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	"protein phosphatase 2, regulatory subunit B (B56), gamma isoform"	protein-coding	0.13	0.722772
Merged-chr12-102705319-1	chr12	102705269	102705369	+	2.9	cIP2vsInput	promoter-TSS (NM_172584)	promoter-TSS (NM_172584)	-450	NM_172584	217837	Mm.488700	NM_172584	ENSMUSG00000057963	Itpk1	BC031182	"inositol 1,3,4-triphosphate 5/6 kinase"	protein-coding	0.14	0.80198
Merged-chr11-120673048-1	chr11	120672998	120673098	+	2.9	cIP2vsInput	promoter-TSS (NM_026877)	promoter-TSS (NM_026877)	75	NM_026877	68938	Mm.294020	NM_001164224	ENSMUSG00000025142	Aspscr1	1190006K01Rik|ASPC|ASPCR1|ASPL|ASPS|RCC17|TUG	"alveolar soft part sarcoma chromosome region, candidate 1 (human)"	protein-coding	0.13	0.712871
Merged-chr1-91298501-1	chr1	91298451	91298551	+	2.9	cIP1vsInput	"intron (NM_016717, intron 1 of 11)"	CpG	163	NM_016717	50880	Mm.25724	NM_016717	ENSMUSG00000026307	Scly	9830169H08|A930015N15Rik|SCL|Scly1|Scly2	selenocysteine lyase	protein-coding	0.06	0.673267
Merged-chr19-60811579-1	chr19	60811529	60811629	+	2.9	cIP2vsInput	promoter-TSS (NM_001167829)	promoter-TSS (NM_001167829)	9	NM_001167829	67894		NM_001167829	ENSMUSG00000024993	Fam45a	1810055E12Rik	"family with sequence similarity 45, member A"	protein-coding	0.07	0.683168
Merged-chr6-97855122-1	chr6	97855072	97855172	+	2.9	cIP2vsInput	"intron (NM_001113198, intron 1 of 9)"	"intron (NM_001113198, intron 1 of 9)"	48064	NM_001113198	17342	Mm.454504	NM_001113198	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding	0.01	0.326733
Merged-chr10-28354964-1	chr10	28354914	28355014	+	2.9	cIP2vsInput	"intron (NM_008983, intron 6 of 31)"	"intron (NM_008983, intron 6 of 31)"	280144	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	"protein tyrosine phosphatase, receptor type, K"	protein-coding	0	0.29703
Merged-chr5-129715367-2	chr5	129715272	129715463	+	2.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025450)	promoter-TSS (NM_025450)	-161	NM_025450	66258	Mm.249809	NM_025450	ENSMUSG00000034211	Mrps17	1810006P02Rik|Mprs17	mitochondrial ribosomal protein S17	protein-coding	0.04712	0.494792
Merged-chr15-73826583-1	chr15	73826533	73826633	+	2.9	cIP1vsInput	"intron (NM_001033365, intron 1 of 10)"	Lx7|LINE|L1	13088	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding	0	0.336634
Merged-chr3-81225584-1	chr3	81225534	81225634	+	2.9	cIP2vsInput	Intergenic	Intergenic	189168	NM_019971	54635	Mm.331089	NM_019971	ENSMUSG00000028019	Pdgfc	1110064L01Rik|AI647969|PDGF-C	"platelet-derived growth factor, C polypeptide"	protein-coding	0	0.326733
Merged-chr8-33641935-1	chr8	33641885	33641985	+	2.9	cIP2vsInput	promoter-TSS (NM_178648)	promoter-TSS (NM_178648)	41	NM_178648	108159	Mm.29301	NM_178648	ENSMUSG00000052906	Ubxn8	D0H8S2298E|Rep-8|Rep8h|Ubxd6	UBX domain protein 8	protein-coding	0.1	0.693069
Merged-chr10-13869203-1	chr10	13869153	13869253	+	2.9	cIP2vsInput	promoter-TSS (NM_025446)	promoter-TSS (NM_025446)	-373	NM_025446	66253	Mm.45755	NM_025446		Aig1	1500031O19Rik|AV064870|AW413422|CGI-103	androgen-induced 1	protein-coding	0.02	0.574257
Merged-chr6-48010887-1	chr6	48010837	48010937	+	2.9	cIP2vsInput	Intergenic	Intergenic	37227	NM_001081382	72306	Mm.381553	NM_001081382	ENSMUSG00000071477	Zfp777	2500002G23Rik	zinc finger protein 777	protein-coding	0.01	0.534653
Merged-chr5-147430025-1	chr5	147429975	147430075	+	2.9	cIP1vsInput	promoter-TSS (NM_028291)	promoter-TSS (NM_028291)	-555	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 polyA specific ribonuclease subunit homolog (S. cerevisiae)	protein-coding	0.11	0.712871
Merged-chr8-56942705-1	chr8	56942655	56942755	+	2.9	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-378278	NM_010402	15111	Mm.430844	NM_010402	ENSMUSG00000038193	Hand2	AI225906|AI661148|Ehand2|Hed|Th2|Thing2|bHLHa26|dHAND	heart and neural crest derivatives expressed transcript 2	protein-coding	0.01	0.336634
Merged-chr10-70133976-1	chr10	70133926	70134026	+	2.9	cIP2vsInput	"intron (NM_001111121, intron 1 of 8)"	"intron (NM_001111121, intron 1 of 8)"	36855	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding	0.04	0.455446
Merged-chr10-45432389-1	chr10	45432339	45432439	+	2.9	cIP1vsInput	"intron (NM_001031772, intron 2 of 4)"	Lx|LINE|L1	37812	NM_001031772	380669	Mm.440328	NM_001033152	ENSMUSG00000063804	Lin28b	2810403D23Rik|D030047M17Rik|Lin-28.2	lin-28 homolog B (C. elegans)	protein-coding	0	0.376238
Merged-chr15-17019680-1	chr15	17019630	17019730	+	2.9	cIP1vsInput	Intergenic	Intergenic	241579	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0	0.306931
Merged-chr1-18616462-1	chr1	18616412	18616512	+	2.9	cIP2vsInput	Intergenic	Intergenic	-351324	NM_001040027	654464	Mm.99530	NM_001040027		Gm15386	BD-17|Defb17|OTTMUSG00000020946|OTTMUSG00000020948	predicted gene 15386	protein-coding	0	0.316832
Merged-chr8-123158392-1	chr8	123158342	123158442	+	2.9	cIP2vsInput	promoter-TSS (NM_020564)	promoter-TSS (NM_020564)	-112	NM_020564	57429	Mm.6562	NM_020564	ENSMUSG00000000739	Sult5a1	Sult-x1|Sultx1	"sulfotransferase family 5A, member 1"	protein-coding	0.03	0.514851
Merged-chr10-66920460-1	chr10	66920410	66920510	+	2.9	cIP2vsInput	Intergenic	Intergenic	176528	NM_001204915	28193	Mm.41272	NM_001204915	ENSMUSG00000019873	Reep3	D10Ucla1	receptor accessory protein 3	protein-coding	0.04	0.554455
Merged-chr11-20831107-1	chr11	20831057	20831157	+	2.9	cIP2vsInput	promoter-TSS (NM_173752)	promoter-TSS (NM_173752)	1	NM_173752	216551	Mm.76694	NM_173752	ENSMUSG00000042363	Lgalsl	1110067D22Rik|A530071M23|Grpa|Hspc159|Lgalsla	"lectin, galactoside binding-like"	protein-coding	0.2	0.851485
Merged-chr10-88826940-1	chr10	88826890	88826990	+	2.9	cIP2vsInput	promoter-TSS (NM_175158)	promoter-TSS (NM_175158)	-126	NM_175158	70683	Mm.29631	NM_175158	ENSMUSG00000004356	Utp20	3830408P06Rik|AA617408|Drim|mDRIM|mDRIN	"UTP20, small subunit (SSU) processome component, homolog (yeast)"	protein-coding	0.02	0.376238
Merged-chr8-33344879-1	chr8	33344829	33344929	+	2.9	cIP1vsInput	"intron (NM_001122822, intron 3 of 33)"	L1ME3Cz|LINE|L1	40648	NM_001122822	22427	Mm.228805	XM_003946269	ENSMUSG00000031583	Wrn	AI846146	Werner syndrome homolog (human)	protein-coding	0	0.267327
Merged-chr5-12871429-1	chr5	12871379	12871479	+	2.9	cIP2vsInput	Intergenic	Intergenic	488263	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	"sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D"	protein-coding	0.01	0.326733
Merged-chr2-52150092-1	chr2	52150042	52150142	+	2.9	cIP2vsInput	"intron (NM_010889, intron 151 of 156)"	"intron (NM_010889, intron 151 of 156)"	77255	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	Rap1 interacting factor 1 homolog (yeast)	protein-coding	0	0.316832
Merged-chr11-98400481-1	chr11	98400431	98400531	+	2.9	cIP1vsInput	promoter-TSS (NM_001033537)	promoter-TSS (NM_001033537)	9	NM_001033537	320655	Mm.86519	NM_001033537	ENSMUSG00000038208	Pgap3	CAB2|D430035D22Rik|Perld1	post-GPI attachment to proteins 3	protein-coding	0.08	0.524752
Merged-chrX-57053365-1	chrX	57053315	57053415	+	2.9	cIP2vsInput	promoter-TSS (NM_029371)	promoter-TSS (NM_029371)	-205	NM_028242	72459	Mm.2152	NM_028242	ENSMUSG00000067873	Htatsf1	1600023H17Rik|2600017A12Rik|2700077B20Rik|TAT-SF1	HIV TAT specific factor 1	protein-coding	0.09	0.613861
Merged-chr6-114968999-1	chr6	114968949	114969049	+	2.9	cIP2vsInput	Intergenic	CpG	-47247	NM_177683	232334	Mm.446323	NM_177683		Vgll4	BC048841|VGL-4	vestigial like 4 (Drosophila)	protein-coding	0.1	0.693069
Merged-chr18-5133097-1	chr18	5133047	5133147	+	2.9	cIP2vsInput	Intergenic	Intergenic	86508	NM_153153	225115	Mm.136791	NM_178046	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding	0.02	0.49505
Merged-chr9-57560687-1	chr9	57560637	57560737	+	2.9	cIP1vsInput	promoter-TSS (NM_022813)	promoter-TSS (NM_022813)	-257	NM_022813	24044	Mm.286069	NM_022813	ENSMUSG00000040188	Scamp2	AI875466|Sc2	secretory carrier membrane protein 2	protein-coding	0.01	0.425743
Merged-chr1-58253209-1	chr1	58253159	58253259	+	2.9	cIP1vsInput	"intron (NM_023631, intron 22 of 34)"	"intron (NM_023631, intron 22 of 34)"	-25117	NM_001008419	213043	Mm.414292	NM_001008419	ENSMUSG00000079554	Aox3l1	Aoh3	aldehyde oxidase 3-like 1	protein-coding	0	0.336634
Merged-chr11-121204281-1	chr11	121204231	121204331	+	2.9	cIP2vsInput	promoter-TSS (NM_001001333)	promoter-TSS (NM_001001333)	-152	NM_001001333	238023	Mm.275130	NM_001001333	ENSMUSG00000039307	Hexdc	BC069960	"hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing"	protein-coding	0.03	0.633663
Merged-chr18-32067858-1	chr18	32067808	32067908	+	2.9	cIP2vsInput	"5' UTR (NM_173441, exon 1 of 14)"	"5' UTR (NM_173441, exon 1 of 14)"	124	NM_173441	73473	Mm.66853	NM_173441	ENSMUSG00000024384	Iws1	1700069O15Rik|3000008H23|AL117927|AW214353	IWS1 homolog (S. cerevisiae)	protein-coding	0.14	0.70297
Merged-chr2-65378919-1	chr2	65378869	65378969	+	2.9	cIP2vsInput	Intergenic	Intergenic	-14893	NM_177074	320106	Mm.227703	NM_177074	ENSMUSG00000061171	Slc38a11	9330158F14Rik	"solute carrier family 38, member 11"	protein-coding	0.01	0.356436
Merged-chr14-85269057-1	chr14	85269007	85269107	+	2.9	cIP1vsInput	Intergenic	Intergenic	-792633	NR_015539	319903	Mm.440481	NR_015539		9630013A20Rik	-	RIKEN cDNA 9630013A20 gene	miscRNA	0	0.316832
Merged-chr11-120458155-1	chr11	120458105	120458205	+	2.9	cIP2vsInput	promoter-TSS (NM_025560)	promoter-TSS (NM_025560)	26	NM_152807	67291	Mm.103384	NM_152807	ENSMUSG00000049957	Ccdc137	3110023B02Rik|RP23-82I5.10	coiled-coil domain containing 137	protein-coding	0.1	0.643564
Merged-chr13-49341250-1	chr13	49341200	49341300	+	2.9	cIP2vsInput	promoter-TSS (NM_029791)	promoter-TSS (NM_029791)	-299	NM_001039179	76895	Mm.197387	NM_001039179	ENSMUSG00000037933	Bicd2	0610027D24Rik|1110005D12Rik|AA408834|mKIAA0699	bicaudal D homolog 2 (Drosophila)	protein-coding	0.05	0.653465
Merged-chr16-90629289-1	chr16	90629239	90629339	+	2.9	cIP2vsInput	Intergenic	Intergenic	98082	NM_025642	66578	Mm.180363	NM_025642	ENSMUSG00000022978	Mis18a	2610039C10Rik|2810018N07Rik	MIS18 kinetochore protein homolog A (S. pombe)	protein-coding	0	0.376238
Merged-chr1-173953813-1	chr1	173953763	173953863	+	2.9	cIP1vsInput	Intergenic	Intergenic	-11321	NM_001045481	15950	Mm.472787	NM_001045481	ENSMUSG00000039997	Ifi203	-	interferon activated gene 203	protein-coding	0.01	0.376238
Merged-chr18-48715412-1	chr18	48715362	48715462	+	2.9	cIP2vsInput	Intergenic	Intergenic	670077	NM_001025388	433182	Mm.372357	NM_001025388	ENSMUSG00000059040	Gm5506	EG433182|Eno1	predicted gene 5506	protein-coding	0	0.326733
Merged-chr17-84790883-2	chr17	84790825	84790941	+	2.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028233)	promoter-TSS (NM_028233)	-97	NM_028233	72416	Mm.217027	NM_028233	ENSMUSG00000024120	Lrpprc	3110001K13Rik|C76645|Gp130|Lrp130|Lsfc	leucine-rich PPR-motif containing	protein-coding	0.103448	0.692308
Merged-chr10-78019068-1	chr10	78019018	78019118	+	2.9	cIP2vsInput	Intergenic	CpG	-9272	NM_008826	18641	Mm.269649	NM_008826	ENSMUSG00000020277	Pfkl	AA407869	"phosphofructokinase, liver, B-type"	protein-coding	0.05	0.574257
Merged-chr13-100833327-1	chr13	100833277	100833377	+	2.9	cIP2vsInput	promoter-TSS (NM_022885)	promoter-TSS (NM_022885)	100	NM_022885	69048	Mm.402215	NM_022885	ENSMUSG00000021629	Slc30a5	1810010K08Rik|AF233321|ZNT5|ZTL1|ZnT-5|Zntl1	"solute carrier family 30 (zinc transporter), member 5"	protein-coding	0.15	0.752475
Merged-chr2-179976973-2	chr2	179976915	179977031	+	2.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081092)	promoter-TSS (NM_001081092)	120	NR_033782	66730	Mm.31773	NR_033782	ENSMUSG00000085704	4921531C22Rik	-	RIKEN cDNA 4921531C22 gene	miscRNA	0.112069	0.735043
Merged-chr7-80261081-1	chr7	80261031	80261131	+	2.9	cIP2vsInput	promoter-TSS (NM_031375)	promoter-TSS (NM_031375)	-134	NR_028053	83485	Mm.21175	NM_031375	ENSMUSG00000047084	Ngrn	AW552001	"neugrin, neurite outgrowth associated"	protein-coding	0	0.524752
Merged-chr12-64662978-1	chr12	64662928	64663028	+	2.9	cIP1vsInput	Intergenic	L1MA8|LINE|L1	-188080	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.326733
Merged-chr5-145167143-2	chr5	145167089	145167197	+	2.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_178576)	promoter-TSS (NM_178576)	-39	NM_133735	71799	Mm.474456	NM_133735	ENSMUSG00000029624	Ptcd1	1110069M14Rik	pentatricopeptide repeat domain 1	protein-coding	0.064815	0.559633
Merged-chr15-24974519-1	chr15	24974469	24974569	+	2.9	cIP1vsInput	Intergenic	Intergenic	439245	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	"brain abundant, membrane attached signal protein 1"	protein-coding	0	0.326733
Merged-chr12-111677840-1	chr12	111677790	111677890	+	2.9	cIP1vsInput	promoter-TSS (NM_001099792)	promoter-TSS (NM_001099792)	-265	NM_001099792	328162	Mm.425747	NM_001099792	ENSMUSG00000060950	Trmt61a	6720458F09Rik|AI606093|Gcd14|Trm61	tRNA methyltransferase 61A	protein-coding	0.04	0.544554
Merged-chr8-118850525-2	chr8	118850452	118850598	+	2.9	cIP1vsInput|cIP2vsInput	"intron (NM_019707, intron 4 of 13)"	"intron (NM_019707, intron 4 of 13)"	-494013	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding	0	0.510204
Merged-chr13-36789611-1	chr13	36789561	36789661	+	2.9	cIP2vsInput	Intergenic	Intergenic	-55134	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding	0	0.326733
Merged-chr5-81266506-1	chr5	81266456	81266556	+	2.9	cIP2vsInput	"intron (NM_198702, intron 3 of 27)"	"intron (NM_198702, intron 3 of 27)"	244913	NM_198702	319387	Mm.461016	NM_198702	ENSMUSG00000037605	Lphn3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|mKIAA0768	latrophilin 3	protein-coding	0	0.306931
Merged-chr6-3184474-1	chr6	3184424	3184524	+	2.9	cIP2vsInput	Intergenic	Intergenic	-104045	NR_036696	667335	Mm.380219	NR_036696		Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo	0	0.326733
Merged-chr3-42285199-1	chr3	42285149	42285249	+	2.9	cIP2vsInput	Intergenic	Intergenic	542581	NM_027271	73852	Mm.29006	NM_001099785	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	"DNA segment, Chr 3, ERATO Doi 751, expressed"	protein-coding	0.01	0.366337
Merged-chr18-54119227-1	chr18	54119177	54119277	+	2.9	cIP2vsInput	Intergenic	Intergenic	257114	NM_152809	70425	Mm.368668	NM_152809	ENSMUSG00000073563	Csnk1g3	3300002K07Rik|C330049O21Rik	"casein kinase 1, gamma 3"	protein-coding	0.02	0.455446
Merged-chr5-99729103-1	chr5	99729053	99729153	+	2.9	cIP2vsInput	promoter-TSS (NR_030692)	promoter-TSS (NR_030692)	-43	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	miscRNA	0.1	0.683168
Merged-chr1-72244783-1	chr1	72244733	72244833	+	2.9	cIP1vsInput	Intergenic	Intergenic	-32476	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding	0.01	0.366337
Merged-chr1-106371243-1	chr1	106371193	106371293	+	2.9	cIP1vsInput	"intron (NM_133821, intron 12 of 16)"	"intron (NM_133821, intron 12 of 16)"	199374	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0	0.366337
Merged-chr17-28313444-1	chr17	28313394	28313494	+	2.9	cIP2vsInput	promoter-TSS (NR_028297)	promoter-TSS (NR_028297)	-86	NR_028297	72775	Mm.201859	NM_001163819		Fance	2810451D06Rik|AI415634|AW209126	"Fanconi anemia, complementation group E"	protein-coding	0.07	0.633663
Merged-chr4-23528930-1	chr4	23528880	23528980	+	2.9	cIP1vsInput	Intergenic	L1MEg|LINE|L1	-967532	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	"MMS22-like, DNA repair protein"	protein-coding	0	0.326733
Merged-chr3-108562479-2	chr3	108562426	108562532	+	2.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026198)	promoter-TSS (NM_026198)	-13	NM_026198	67495	Mm.32615	NM_026198	ENSMUSG00000068732	Tmem167b	2010200O16Rik	transmembrane protein 167B	protein-coding	0.09434	0.570093
Merged-chr13-49173330-1	chr13	49173280	49173380	+	2.9	cIP2vsInput	Intergenic	Intergenic	-14217	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding	0.04	0.554455
Merged-chr15-19127893-1	chr15	19127843	19127943	+	2.9	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	307564	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0	0.316832
Merged-chr17-74338794-1	chr17	74338744	74338844	+	2.9	cIP1vsInput	promoter-TSS (NM_001162870)	promoter-TSS (NM_001162870)	-193	NM_001162870	50850	Mm.19804	NM_001162870	ENSMUSG00000024068	Spast	Spg4|mKIAA1083	spastin	protein-coding	0.07	0.722772
Merged-chr8-4285232-1	chr8	4285182	4285282	+	2.9	cIP2vsInput	"3' UTR (NM_010485, exon 6 of 6)"	"3' UTR (NM_010485, exon 6 of 6)"	-9327	NM_011592	21856	Mm.195249	NM_011592	ENSMUSG00000002949	Timm44	0710005E20Rik|D8Ertd118e|Mimt44|Tim44	translocase of inner mitochondrial membrane 44	protein-coding	0	0.326733
Merged-chr16-92400083-1	chr16	92400033	92400133	+	2.9	cIP1vsInput	promoter-TSS (NM_019466)	promoter-TSS (NM_019466)	-6	NM_019466	54720	Mm.265744	NM_001081549	ENSMUSG00000022951	Rcan1	2410048A02Rik|AA408855|AI429645|AL024459|AV028423|Adapt78|CALP1L|CSP1|DSC1|Dscr1|MCIP1|RCN1	regulator of calcineurin 1	protein-coding	0.06	0.613861
Merged-chr19-4510815-1	chr19	4510765	4510865	+	2.9	cIP2vsInput	"intron (NM_001162946, intron 1 of 20)"	CpG	343	NM_001162946	18563	Mm.1845	NM_001162946	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding	0.05	0.722772
Merged-chr16-66972823-1	chr16	66972773	66972873	+	2.9	cIP2vsInput	"intron (NM_178721, intron 1 of 9)"	"intron (NM_178721, intron 1 of 9)"	315705	NR_040512	75501	Mm.396161	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	miscRNA	0.01	0.336634
Merged-chr5-92698798-1	chr5	92698748	92698848	+	2.9	cIP1vsInput	"intron (NM_015756, intron 1 of 10)"	"intron (NM_015756, intron 1 of 10)"	15363	NM_015756	27428	Mm.46014	NM_001077595	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding	0.01	0.465347
Merged-chr9-122351853-1	chr9	122351803	122351903	+	2.9	cIP2vsInput	"intron (NM_026179, intron 1 of 6)"	CpG	237	NM_026179	67469	Mm.280254	NM_026179	ENSMUSG00000032540	Abhd5	1300003D03Rik|2010002J10Rik|CDS|CGI-58|IECN5|NCIE2	abhydrolase domain containing 5	protein-coding	0.12	0.742574
Merged-chr15-79659115-1	chr15	79659065	79659165	+	2.9	cIP1vsInput	promoter-TSS (NM_029407)	promoter-TSS (NM_029407)	-112	NM_028634	73739	Mm.294441	NM_028634	ENSMUSG00000022428	Cby1	1110014P06Rik|CBY|PGEA14|Pgea1|arb1	chibby homolog 1 (Drosophila)	protein-coding	0.07	0.584158
Merged-chr2-35588624-1	chr2	35588574	35588674	+	2.9	cIP2vsInput	"intron (NM_001114125, intron 1 of 16)"	"intron (NM_001114125, intron 1 of 16)"	-29922	NR_045894	100042194	Mm.330165	NR_045894		Gm13446	OTTMUSG00000012261	predicted gene 13446	miscRNA	0.02	0.623762
Merged-chr5-148995298-1	chr5	148995248	148995348	+	2.9	cIP2vsInput	promoter-TSS (NR_102383)	promoter-TSS (NR_102383)	-83	NR_102384	319982	Mm.33303	XR_104956		5930430L01Rik	-	RIKEN cDNA 5930430L01 gene	miscRNA	0.04	0.514851
Merged-chr19-35203053-1	chr19	35203003	35203103	+	2.9	cIP1vsInput	Intergenic	Intergenic	280695	NM_183046	240641	Mm.278471	NM_183046	ENSMUSG00000024795	Kif20b	B130024C23|C330014J10Rik|Mphosph1	kinesin family member 20B	protein-coding	0.01	0.326733
Merged-chr9-9881487-1	chr9	9881437	9881537	+	2.9	cIP1vsInput	"intron (NM_001033359, intron 9 of 20)"	L1_Mur3|LINE|L1	-642474	NM_027823	71544	Mm.334955	NM_027823	ENSMUSG00000050730	Arhgap42	9030420J04Rik|BE136619	Rho GTPase activating protein 42	protein-coding	0	0.306931
Merged-chr16-11322812-2	chr16	11322729	11322895	+	2.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028964)	promoter-TSS (NM_028964)	-92	NM_028964	74478	Mm.325831	NM_001163498	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding	0.090361	0.640719
Merged-chr9-100770839-1	chr9	100770789	100770889	+	2.9	cIP2vsInput	"intron (NM_009282, intron 5 of 33)"	"intron (NM_009282, intron 5 of 33)"	127216	NM_009282	20842	Mm.42135	NM_009282	ENSMUSG00000037286	Stag1	AU045003|SA-1|Scc3	stromal antigen 1	protein-coding	0	0.336634
Merged-chr15-25441371-1	chr15	25441321	25441421	+	2.9	cIP2vsInput	"intron (NR_027376, intron 1 of 1)"	"intron (NR_027376, intron 1 of 1)"	27179	NR_027376	432939	Mm.146555	NM_001013791		Gm5468	100040583|EG432939	predicted gene 5468	miscRNA	0.04	0.415842
Merged-chr15-85671199-1	chr15	85671149	85671249	+	2.9	cIP2vsInput	Intergenic	CpG	-35404	NR_029729	723966		NR_029729	ENSMUSG00000065608	Mirlet7c-2	Mirnlet7c-2	microRNA let7c-2	miscRNA	0.09	0.653465
Merged-chr12-76254819-1	chr12	76254769	76254869	+	2.9	cIP1vsInput	promoter-TSS (NM_138745)	promoter-TSS (NM_138745)	-413	NM_138745	108156	Mm.29584	NM_138745	ENSMUSG00000021048	Mthfd1	Dcs|E430024A07Rik|Mthfd	"methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthase"	protein-coding	0.03	0.49505
Merged-chr4-129276732-1	chr4	129276682	129276782	+	2.9	cIP1vsInput	Intergenic	Intergenic	-10889	NM_023485	68828	Mm.132243	NM_023485	ENSMUSG00000001333	Sync	1110057H03Rik|SNIP4	syncoilin	protein-coding	0.08	0.613861
Merged-chr2-115641364-1	chr2	115641314	115641414	+	2.9	cIP1vsInput	"intron (NM_001145898, intron 4 of 10)"	"intron (NM_001145898, intron 4 of 10)"	2639	NR_035476	100316703		NR_035476		Mir1951	mmu-mir-1951	microRNA 1951	miscRNA	0.01	0.356436
Merged-chr14-34867091-1	chr14	34867041	34867141	+	2.9	cIP1vsInput	"intron (NM_008166, intron 2 of 15)"	L1MA9|LINE|L1	-27518	NR_029774	723847		NR_029774		Mir346	Mirn346|mmu-mir-346	microRNA 346	miscRNA	0	0.346535
Merged-chr8-39269650-2	chr8	39269571	39269729	+	2.9	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-28330	NR_044988	621335	Mm.208080	NR_044988		Gm6213	EG621335	predicted gene 6213	miscRNA	0	0.352201
Merged-chr7-16412685-1	chr7	16412635	16412735	+	2.9	cIP2vsInput	"intron (NM_198631, intron 1 of 13)"	"intron (NM_198631, intron 1 of 13)"	11489	NM_198631	330474	Mm.490954	NM_198631	ENSMUSG00000059273	Zc3h4	Bwq1|Gm768|Kiaa1064-hp|mKIAA1064	zinc finger CCCH-type containing 4	protein-coding	0	0.465347
Merged-chr11-117940010-1	chr11	117939960	117940060	+	2.9	cIP2vsInput	Intergenic	Intergenic	29356	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding	0	0.524752
Merged-chr8-26556077-1	chr8	26556027	26556127	+	2.9	cIP2vsInput	Intergenic	Intergenic	268346	NR_045904	72316	Mm.490534	NR_045904		2310008N11Rik	-	RIKEN cDNA 2310008N11 gene	miscRNA	0.01	0.49505
Merged-chr6-88724575-1	chr6	88724525	88724625	+	2.9	cIP2vsInput	promoter-TSS (NM_001166251)	promoter-TSS (NM_001166251)	-129	NM_001166250	23945	Mm.272197	NM_001166249	ENSMUSG00000033174	Mgll	AA589436|Magl|Mgl	monoglyceride lipase	protein-coding	0.11	0.742574
Merged-chr5-140321616-1	chr5	140321566	140321666	+	2.9	cIP1vsInput	promoter-TSS (NM_010752)	promoter-TSS (NM_010752)	-64	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding	0.1	0.514851
Merged-chr15-35422759-1	chr15	35422709	35422809	+	2.9	cIP2vsInput	"intron (NM_177151, intron 5 of 61)"	"intron (NM_177151, intron 5 of 61)"	51213	NM_177151	666173	Mm.309250	NM_177151	ENSMUSG00000037646	Vps13b	1810042B05Rik|2310042E16Rik|4732488H20|C330002D13Rik|C87206|Coh1|D230005K13|mKIAA0532|mKIAA5032	vacuolar protein sorting 13B (yeast)	protein-coding	0	0.326733
Merged-chr2-170319292-2	chr2	170319230	170319354	+	2.9	cIP1vsInput|cIP2vsInput	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-37069	NR_040610	73303	Mm.443297	NR_040610	ENSMUSG00000086999	1700040N02Rik	-	RIKEN cDNA 1700040N02 gene	miscRNA	0.064516	0.568
Merged-chr11-53707342-1	chr11	53707292	53707392	+	2.9	cIP2vsInput	promoter-TSS (NM_009012)	promoter-TSS (NM_009012)	-23	NM_009012	19360	Mm.4888	NM_009012	ENSMUSG00000020380	Rad50	Mrell|Rad50l	RAD50 homolog (S. cerevisiae)	protein-coding	0.13	0.712871
Merged-chr16-64243763-1	chr16	64243713	64243813	+	2.9	cIP1vsInput	Intergenic	Intergenic	235371	NM_173861	224291	Mm.246580	NM_173861	ENSMUSG00000068167	Csnka2ip	Ckt2	"casein kinase 2, alpha prime interacting protein"	protein-coding	0.01	0.29703
Merged-chr1-171270237-1	chr1	171270187	171270287	+	2.9	cIP2vsInput	promoter-TSS (NM_020579)	promoter-TSS (NM_020579)	-91	NM_020579	57370	Mm.274011	NM_020579	ENSMUSG00000052423	B4galt3	9530061M23Rik|AA104562|AW125175|ESTM26|ESTM6|R74981	"UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 3"	protein-coding	0.04	0.643564
Merged-chr12-13322232-1	chr12	13322182	13322282	+	2.9	cIP1vsInput	"intron (NM_027706, intron 14 of 51)"	"intron (NM_027706, intron 14 of 51)"	53105	NM_027706	71169	Mm.177520	NM_027706	ENSMUSG00000020576	Nbas	4933425L03Rik|Nag	neuroblastoma amplified sequence	protein-coding	0.01	0.316832
Merged-chr2-152696952-1	chr2	152696902	152697002	+	2.9	cIP2vsInput	"intron (NM_010376, intron 10 of 11)"	"intron (NM_010376, intron 10 of 11)"	9804	NM_025543	66405	Mm.440291	NM_025543	ENSMUSG00000042814	Mcts2	2400002F11Rik|RP23-35I8.12	malignant T cell amplified sequence 2	protein-coding	0.04	0.613861
Merged-chr2-111104170-1	chr2	111104120	111104220	+	2.9	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	125430	NM_026248	67575	Mm.84331	NM_026248	ENSMUSG00000027157	4930430A15Rik	-	RIKEN cDNA 4930430A15 gene	protein-coding	0	0.336634
Merged-chr7-45062292-1	chr7	45062242	45062342	+	2.9	cIP2vsInput	promoter-TSS (NM_025533)	promoter-TSS (NM_025533)	-137	NM_001163684	66394	Mm.272139	NM_001163684	ENSMUSG00000003421	Nosip	2310061K06Rik|CGI-25	nitric oxide synthase interacting protein	protein-coding	0.05	0.544554
Merged-chr7-104778137-1	chr7	104778087	104778187	+	2.9	cIP1vsInput	promoter-TSS (NM_001256973)	promoter-TSS (NM_001256973)	-667	NM_001256973	625530	Mm.14130	NM_001256973		Usp17le	DUB-3|Dub3|Dub6|EG625530|Gm6596|USP17|Usp17l2	ubiquitin specific peptidase 17-like E	protein-coding	0	0.306931
Merged-chr16-21211051-1	chr16	21211001	21211101	+	2.9	cIP2vsInput	"intron (NM_010143, intron 1 of 15)"	"intron (NM_010143, intron 1 of 15)"	6256	NM_010143	13845	Mm.6972	NM_010143	ENSMUSG00000005958	Ephb3	AW456895|Cek10|Etk2|HEK2|MDK5|Sek4|Tyro6	Eph receptor B3	protein-coding	0.01	0.534653
Merged-chr10-103984216-1	chr10	103984166	103984266	+	2.9	cIP2vsInput	Intergenic	Intergenic	-158771	NM_001177535	100043292	Mm.339215	NM_001177535	ENSMUSG00000090854	Gm4340	-	predicted gene 4340	protein-coding	0.02	0.346535
Merged-chr9-25220046-1	chr9	25219996	25220096	+	2.9	cIP2vsInput	Intergenic	Intergenic	-32393	NM_009859	235072	Mm.270259	NM_001205367	ENSMUSG00000001833	7-Sep	Cdc10|E430034N22	septin 7	protein-coding	0.01	0.435644
Merged-chr13-16829945-1	chr13	16829895	16829995	+	2.9	cIP2vsInput	Intergenic	Intergenic	815470	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding	0.01	0.405941
Merged-chr7-66129838-1	chr7	66129788	66129888	+	2.9	cIP2vsInput	"intron (NM_001081163, intron 2 of 2)"	"intron (NM_001081163, intron 2 of 2)"	20323	NM_001081163	269941	Mm.333916	NM_001081163	ENSMUSG00000032640	Chsy1	mKIAA0990	chondroitin sulfate synthase 1	protein-coding	0	0.316832
Merged-chr3-52180977-1	chr3	52180927	52181027	+	2.9	cIP2vsInput	Intergenic	Intergenic	-75971	NM_001004176	433586	Mm.481431	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding	0.01	0.653465
Merged-chr16-72809187-1	chr16	72809137	72809237	+	2.9	cIP1vsInput	"intron (NM_019413, intron 2 of 28)"	"intron (NM_019413, intron 2 of 28)"	146038	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout homolog 1 (Drosophila)	protein-coding	0	0.336634
Merged-chr14-63860939-1	chr14	63860889	63860989	+	2.9	cIP2vsInput	"intron (NM_028228, intron 1 of 6)"	"intron (NM_028228, intron 1 of 6)"	627	NM_028228	72400	Mm.379214	NM_028228	ENSMUSG00000021958	Pinx1	2210403I16Rik|2610028A01Rik|67-11-3|AU024023|LPTS|LPTS1	"PIN2/TERF1 interacting, telomerase inhibitor 1"	protein-coding	0.02	0.475248
Merged-chr1-27916703-1	chr1	27916653	27916753	+	2.9	cIP1vsInput	Intergenic	Intergenic	863549	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0.01	0.346535
Merged-chr12-70235347-1	chr12	70235297	70235397	+	2.9	cIP2vsInput	Intergenic	Intergenic	7506	NR_045174	414124	Mm.416164	NR_045174	ENSMUSG00000085298	F730035M05Rik	-	RIKEN cDNA F730035M05 gene	miscRNA	0.06	0.554455
Merged-chr6-131293187-1	chr6	131293137	131293237	+	2.9	cIP2vsInput	promoter-TSS (NM_025564)	promoter-TSS (NM_025564)	57	NM_025564	66441	Mm.46623	NM_025564	ENSMUSG00000030188	Magohb	2010012C16Rik|Mago|Magoh|Magoh-rs1	mago-nashi homolog B (Drosophila)	protein-coding	0.12	0.594059
Merged-chr6-54826072-1	chr6	54826022	54826122	+	2.9	cIP2vsInput	"intron (NM_199143, intron 1 of 4)"	"intron (NM_199143, intron 1 of 4)"	9156	NM_199143	387524	Mm.392146	NM_199143		Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding	0.01	0.306931
Merged-chr10-76623497-2	chr10	76623438	76623557	+	2.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_146007)	promoter-TSS (NM_146007)	-93	NM_146007	12834	Mm.1949	NM_146007	ENSMUSG00000020241	Col6a2	Col6a-2	"collagen, type VI, alpha 2"	protein-coding	0.07563	0.716667
Merged-chr16-4586991-1	chr16	4586941	4587041	+	2.9	cIP2vsInput	Intergenic	CpG	-7722	NM_031184	83396	Mm.134072	NM_031184	ENSMUSG00000014303	Glis2	Gli5|Klf16|Nkl	GLIS family zinc finger 2	protein-coding	0.06	0.623762
Merged-chr12-75669395-1	chr12	75669345	75669445	+	2.9	cIP2vsInput	"intron (NM_028203, intron 1 of 1)"	CpG	142	NM_028203	72338	Mm.341719	NM_028203	ENSMUSG00000045690	Wdr89	2600001A11Rik	WD repeat domain 89	protein-coding	0.11	0.732673
Merged-chr11-101732826-1	chr11	101732776	101732876	+	2.9	cIP2vsInput	promoter-TSS (NM_144831)	promoter-TSS (NM_144831)	-130	NM_144831	217207	Mm.28186	NM_144831	ENSMUSG00000034931	Dhx8	Ddx8|mDEAH6|mKIAA4096	DEAH (Asp-Glu-Ala-His) box polypeptide 8	protein-coding	0.08	0.564356
Merged-chr13-110941640-1	chr13	110941590	110941690	+	2.9	cIP2vsInput	Intergenic	Intergenic	287791	NR_045908	73129	Mm.417826	NR_045908		3110015C05Rik	-	RIKEN cDNA 3110015C05 gene	miscRNA	0	0.29703
Merged-chr9-72170478-1	chr9	72170428	72170528	+	2.9	cIP2vsInput	Intergenic	(TGGGGG)n|Simple_repeat|Simple_repeat	-58659	NM_001253865	21406	Mm.480117	NM_001253862	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding	0.04	0.663366
Merged-chr16-77429177-1	chr16	77429127	77429227	+	2.9	cIP2vsInput	"intron (NR_015543, intron 2 of 4)"	"intron (NR_015543, intron 2 of 4)"	99849	NR_015543	77994	Mm.394688	NR_015543		2810055G20Rik	D730043B02Rik	RIKEN cDNA 2810055G20 gene	miscRNA	0	0.346535
Merged-chr2-167190280-1	chr2	167190230	167190330	+	2.9	cIP2vsInput	Intergenic	CpG	-1462	NM_008420	16500	Mm.490804	NM_008420		Kcnb1	Kcr1-1|Kv2.1|Shab	"potassium voltage gated channel, Shab-related subfamily, member 1"	protein-coding	0.09	0.722772
Merged-chr11-27329757-1	chr11	27329707	27329807	+	2.9	cIP1vsInput	Intergenic	Intergenic	544649	NR_002890	654472	Mm.347777	NR_002890	ENSMUSG00000069939	Gm12070	OTTMUSG00000005300	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0	0.29703
Merged-chr11-97400499-1	chr11	97400449	97400549	+	2.9	cIP2vsInput	Intergenic	Intergenic	37948	NM_138657	192157	Mm.34339	NM_138657	ENSMUSG00000038485	Socs7	2310063P06Rik|C85125|Nap4	suppressor of cytokine signaling 7	protein-coding	0.1	0.683168
Merged-chr15-85037065-1	chr15	85037015	85037115	+	2.9	cIP2vsInput	promoter-TSS (NM_177067)	promoter-TSS (NM_177067)	3	NM_133750	73225	Mm.247535	NM_133750	ENSMUSG00000022434	Fam118a	3110048E14Rik|C230014M12Rik	"family with sequence similarity 118, member A"	protein-coding	0.17	0.732673
Merged-chr2-164679285-2	chr2	164679225	164679345	+	2.9	cIP1vsInput|cIP2vsInput	Intergenic	B3|SINE|B2	-5198	NM_001161806	629761	Mm.389336	NM_001161806	ENSMUSG00000078940	Wfdc11	-	WAP four-disulfide core domain 11	protein-coding	0.033333	0.61157
Merged-chr9-48740353-1	chr9	48740303	48740403	+	2.9	cIP2vsInput	"intron (NM_001033324, intron 3 of 6)"	"intron (NM_001033324, intron 3 of 6)"	95592	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding	0.01	0.60396
Merged-chr14-74153385-1	chr14	74153335	74153435	+	2.9	cIP2vsInput	Intergenic	L1M2|LINE|L1	-202142	NR_046059	74425	Mm.399498	NR_046059		4933402J15Rik	-	RIKEN cDNA 4933402J15 gene	miscRNA	0	0.346535
Merged-chr13-49187420-1	chr13	49187370	49187470	+	2.9	cIP2vsInput	promoter-TSS (NM_013610)	promoter-TSS (NM_013610)	-127	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding	0.17	0.841584
Merged-chrY-6132689-1	chrY	6132639	6132739	+	2.9	cIP1vsInput	Intergenic	L1Md_T|LINE|L1	1035088	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.346535
Merged-chr4-48663389-1	chr4	48663339	48663439	+	2.9	cIP2vsInput	promoter-TSS (NM_026509)	promoter-TSS (NM_026509)	-125	NM_026509	68016	Mm.133444	NM_026509	ENSMUSG00000028348	Murc	2310039E09Rik	muscle-related coiled-coil protein	protein-coding	0.03	0.514851
Merged-chr6-21795448-1	chr6	21795398	21795498	+	2.9	cIP1vsInput	"intron (NM_173007, intron 8 of 8)"	"intron (NM_173007, intron 8 of 8)"	57067	NM_173007	269831	Mm.21950	NM_173007	ENSMUSG00000029669	Tspan12	9030619E17|AI426782|AI663988|AW111457|Tm4sf12	tetraspanin 12	protein-coding	0	0.257426
Merged-chr1-65699961-1	chr1	65699911	65700011	+	2.9	cIP1vsInput	Intergenic	Intergenic	-226561	NM_027010	12969	Mm.275362	NM_027010	ENSMUSG00000025945	Crygf	3110001K11Rik|Cryg-2|DGcry-2|Len-2	"crystallin, gamma F"	protein-coding	0	0.247525
Merged-chr11-77319961-1	chr11	77319911	77320011	+	2.9	cIP1vsInput	"intron (NM_177710, intron 1 of 14)"	"intron (NM_177710, intron 1 of 14)"	103536	NM_177710	237860	Mm.440381	NM_177710	ENSMUSG00000037926	Ssh2	BB104748|BC030940|SSH-2|mSSH-2L	slingshot homolog 2 (Drosophila)	protein-coding	0	0.376238
Merged-chr14-118089431-1	chr14	118089381	118089481	+	2.9	cIP2vsInput	Intergenic	Intergenic	-37185	NM_010024	13190	Mm.19987	NM_010024	ENSMUSG00000022129	Dct	DT|TRP-2|TRP2|Tyrp-2|Tyrp2|slaty|slt	dopachrome tautomerase	protein-coding	0.07	0.594059
Merged-chr8-56734669-1	chr8	56734619	56734719	+	2.9	cIP1vsInput	Intergenic	Intergenic	183535	NM_015791	50753	Mm.251174	NM_015791		Fbxo8	Fbx8	F-box protein 8	protein-coding	0.02	0.29703
Merged-chr13-21222565-1	chr13	21222515	21222615	+	2.9	cIP1vsInput	Intergenic	Intergenic	42634	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding	0.04	0.514851
Merged-chr5-73163534-1	chr5	73163484	73163584	+	2.9	cIP2vsInput	"intron (NM_028194, intron 3 of 62)"	"intron (NM_028194, intron 3 of 62)"	93084	NM_028194	72313		NM_177136	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	furry homolog-like (Drosophila)	protein-coding	0.01	0.336634
Merged-chr5-71245283-1	chr5	71245233	71245333	+	2.9	cIP2vsInput	Intergenic	Intergenic	-149434	NM_008066	14395	Mm.5304	NM_008066	ENSMUSG00000000560	Gabra2	C630048P16Rik|Gabra-2	"gamma-aminobutyric acid (GABA) A receptor, subunit alpha 2"	protein-coding	0.01	0.306931
Merged-chr10-80226247-1	chr10	80226197	80226297	+	2.9	cIP2vsInput	promoter-TSS (NM_023431)	promoter-TSS (NM_023431)	-351	NM_023431	68114	Mm.273418	NM_023431		Mum1	2610019J09|9430059D04Rik|UBE-1C2	melanoma associated antigen (mutated) 1	protein-coding	0.05	0.574257
Merged-chr11-89988986-1	chr11	89988936	89989036	+	2.9	cIP1vsInput	"intron (NM_008796, intron 2 of 5)"	"intron (NM_008796, intron 2 of 5)"	13908	NM_008796	18559	Mm.5062	NM_008796		Pctp	PC-TP|StarD2	phosphatidylcholine transfer protein	protein-coding	0.01	0.455446
Merged-chr10-101897238-1	chr10	101897188	101897288	+	2.9	cIP1vsInput	"intron (NM_001205098, intron 2 of 7)"	"intron (NM_001205098, intron 2 of 7)"	124546	NR_037211	100526516		NR_037211	ENSMUSG00000092952	Mir3059	mmu-mir-3059	microRNA 3059	miscRNA	0	0.346535
Merged-chr2-26409226-1	chr2	26409176	26409276	+	2.9	cIP2vsInput	promoter-TSS (NM_033134)	promoter-TSS (NM_033134)	-38	NM_033134	64436	Mm.330070	NM_033134	ENSMUSG00000026925	Inpp5e	1200002L24Rik|72kDa|mKIAA0123	inositol polyphosphate-5-phosphatase E	protein-coding	0.09	0.673267
Merged-chr4-114368058-1	chr4	114368008	114368108	+	2.9	cIP1vsInput	Intergenic	Intergenic	-38666	NM_001085549	666048	Mm.331779	NM_001085549	ENSMUSG00000070867	Trabd2b	Gm12824|OTTMUSG00000008561	TraB domain containing 2B	protein-coding	0.05	0.623762
Merged-chr13-88842506-1	chr13	88842456	88842556	+	2.9	cIP2vsInput	"intron (NM_001037987, intron 1 of 10)"	L1MA6|LINE|L1	21034	NM_001037987	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0	0.29703
Merged-chr6-66849033-1	chr6	66848983	66849083	+	2.9	cIP1vsInput	Intergenic	Intergenic	-43701	NM_001166720	546903	Mm.484975	NM_001166720		Vmn1r39	EG546903|Gm5993	vomeronasal 1 receptor 39	protein-coding	0.01	0.39604
Merged-chr6-147476355-1	chr6	147476305	147476405	+	2.9	cIP2vsInput	"intron (NM_025911, intron 1 of 12)"	CpG	484	NM_025911	67015	Mm.209774	NM_025911	ENSMUSG00000030301	Ccdc91	1700086G08Rik|1810060J02Rik|AU045683|AW555238|p56	coiled-coil domain containing 91	protein-coding	0.1	0.663366
Merged-chr10-37742099-1	chr10	37742049	37742149	+	2.9	cIP1vsInput	Intergenic	Intergenic	-603173	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding	0	0.306931
Merged-chr1-17588887-1	chr1	17588837	17588937	+	2.9	cIP1vsInput	Intergenic	Lx3A|LINE|L1	-13014	NM_053191	94227	Mm.442452	NM_053191	ENSMUSG00000067780	Pi15	P24TI|P25TI|PI-15|SugarCrisp	peptidase inhibitor 15	protein-coding	0	0.346535
Merged-chr1-52929479-1	chr1	52929429	52929529	+	2.9	cIP1vsInput	"intron (NM_144953, intron 1 of 1)"	L1_Rod|LINE|L1	23361	NM_144953	67080	Mm.236287	NM_144953		1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding	0	0.306931
Merged-chr18-29839516-1	chr18	29839466	29839566	+	2.9	cIP1vsInput	Intergenic	Intergenic	-343100	NR_045391	78058	Mm.416952	NR_045391		4930578E11Rik	-	RIKEN cDNA 4930578E11 gene	miscRNA	0.01	0.336634
Merged-chr11-88692335-2	chr11	88692253	88692417	+	2.9	cIP1vsInput|cIP2vsInput	"intron (NM_001201341, intron 5 of 7)"	"intron (NM_001201341, intron 5 of 7)"	25894	NM_054043	76626	Mm.474737	NM_001201341	ENSMUSG00000069769	Msi2	1700105C15Rik|AI451722|AI563628|AW489193|Msi2h	musashi RNA-binding protein 2	protein-coding	0.02439	0.430303
Merged-chr12-78206271-1	chr12	78206221	78206321	+	2.9	cIP1vsInput	Intergenic	Intergenic	-20384	NM_172952	268566	Mm.453131	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding	0	0.376238
Merged-chr5-150703189-1	chr5	150703139	150703239	+	2.9	cIP1vsInput	"intron (NM_175310, intron 1 of 34)"	"intron (NM_175310, intron 1 of 34)"	29362	NM_175310	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|mKIAA0979	"PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)"	protein-coding	0	0.306931
Merged-chr18-49721357-1	chr18	49721307	49721407	+	2.9	cIP2vsInput	"intron (NM_001170960, intron 2 of 3)"	L1M4c|LINE|L1	34244	NM_026854	68857	Mm.96010	NM_001170960	ENSMUSG00000024505	Dtwd2	1190002H09Rik|8030470C17Rik|AI414673|BB115449	DTW domain containing 2	protein-coding	0.01	0.346535
Merged-chr3-30122996-1	chr3	30122946	30123046	+	2.9	cIP1vsInput	Intergenic	Intergenic	-109792	NM_007963	14013	Mm.426829	NM_021442	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding	0	0.316832
Merged-chr12-90396714-1	chr12	90396664	90396764	+	2.9	cIP1vsInput	Intergenic	L1M4c|LINE|L1	341724	NM_010050	13371	Mm.408815	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	"deiodinase, iodothyronine, type II"	protein-coding	0	0.277228
Merged-chr8-124434686-1	chr8	124434636	124434736	+	2.9	cIP1vsInput	promoter-TSS (NM_171824)	promoter-TSS (NM_171824)	-750	NM_171824	209966	Mm.234233	NM_171824	ENSMUSG00000050751	Pgbd5	2900019M05Rik|AI854313	piggyBac transposable element derived 5	protein-coding	0.12	0.742574
Merged-chr10-77581847-1	chr10	77581797	77581897	+	2.9	cIP2vsInput	promoter-TSS (NM_145925)	promoter-TSS (NM_145925)	80	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding	0.1	0.673267
Merged-chr16-46010783-1	chr16	46010733	46010833	+	2.9	cIP2vsInput	promoter-TSS (NM_001134480)	promoter-TSS (NM_001134480)	-370	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	"phosphatidylinositol-specific phospholipase C, X domain containing 2"	protein-coding	0.03	0.425743
Merged-chr6-94018974-1	chr6	94018924	94019024	+	2.9	cIP1vsInput	"intron (NM_001029850, intron 1 of 23)"	"intron (NM_001029850, intron 1 of 23)"	-105284	NM_001083320	14924	Mm.217216	NM_001029850	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	"membrane associated guanylate kinase, WW and PDZ domain containing 1"	protein-coding	0	0.29703
Merged-chr3-87150804-1	chr3	87150754	87150854	+	2.9	cIP2vsInput	"intron (NM_001170985, intron 1 of 15)"	"intron (NM_001170985, intron 1 of 15)"	23943	NM_001170985	170643	Mm.89552	NM_001170985	ENSMUSG00000041734	Kirrel	6720469N11Rik|Kirrel1|Neph1	kin of IRRE like (Drosophila)	protein-coding	0.01	0.50495
Merged-chrX-13041764-2	chrX	13041700	13041829	+	2.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_038158)	promoter-TSS (NR_038158)	-251	NR_038158	70489	Mm.383563	NR_038158	ENSMUSG00000087424	5730405O15Rik	-	RIKEN cDNA 5730405O15 gene	miscRNA	0.116279	0.723077
Merged-chr14-93425387-1	chr14	93425337	93425437	+	2.9	cIP1vsInput	"intron (NM_001271798, intron 2 of 3)"	"intron (NM_001271798, intron 2 of 3)"	463501	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0.02	0.405941
Merged-chr6-78907539-1	chr6	78907489	78907589	+	2.9	cIP2vsInput	Intergenic	Intergenic	-124503	NR_040302	100504701	Mm.400420	NR_040301		Gm20362	-	"predicted gene, 20362"	miscRNA	0.01	0.366337
Merged-chr5-107688006-2	chr5	107687935	107688078	+	2.9	cIP1vsInput|cIP2vsInput	Intergenic	CpG	15474	NR_045871	654809	Mm.399159	NR_045871		4930428O21Rik	-	RIKEN cDNA 4930428O21 gene	miscRNA	0.111888	0.708333
Merged-chr10-33812050-1	chr10	33812000	33812100	+	2.9	cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	-29935	NM_001101452	215895	Mm.473684	NM_001101452	ENSMUSG00000090298	Gm4794	EG215895|Sult3a2	predicted gene 4794	protein-coding	0.01	0.50495
Merged-chr8-90302384-1	chr8	90302334	90302434	+	2.9	cIP2vsInput	"intron (NM_172913, intron 1 of 6)"	"intron (NM_172913, intron 1 of 6)"	45868	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding	0	0.366337
Merged-chr7-34702992-2	chr7	34702912	34703073	+	2.9	cIP1vsInput|cIP2vsInput	"intron (NM_175140, intron 2 of 3)"	"intron (NM_175140, intron 2 of 3)"	-50151	NM_146188	233107	Mm.486198	NM_146188	ENSMUSG00000030499	Kctd15	BC031749	potassium channel tetramerisation domain containing 15	protein-coding	0.043478	0.549383
Merged-chr12-50321994-1	chr12	50321944	50322044	+	2.9	cIP2vsInput	Intergenic	Intergenic	327229	NM_008858	18760	Mm.133719	NM_008858	ENSMUSG00000002688	Prkd1	PKD|PKD1|Pkcm|Prkcm	protein kinase D1	protein-coding	0.01	0.29703
Merged-chr18-82692254-1	chr18	82692204	82692304	+	2.9	cIP1vsInput	"intron (NM_177832, intron 1 of 29)"	CpG	480	NM_177832	329002		NM_177832	ENSMUSG00000041258	Zfp236	AI447957|Gm335	zinc finger protein 236	protein-coding	0.08	0.70297
Merged-chr10-108458338-1	chr10	108458288	108458388	+	2.9	cIP1vsInput	Intergenic	Lx8b|LINE|L1	126149	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	"PRKC, apoptosis, WT1, regulator"	protein-coding	0	0.405941
Merged-chr7-24507096-1	chr7	24507046	24507146	+	2.9	cIP2vsInput	promoter-TSS (NM_146183)	promoter-TSS (NM_146183)	9	NM_146183	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding	0.12	0.60396
Merged-chr4-151128756-2	chr4	151128680	151128832	+	2.9	cIP1vsInput|cIP2vsInput	"intron (NM_001081557, intron 11 of 23)"	CpG	-70803	NM_009498	22319	Mm.273930	NM_009498	ENSMUSG00000028955	Vamp3	D130027G05Rik|VAMP-3|ceb	vesicle-associated membrane protein 3	protein-coding	0.092105	0.627451
Merged-chr14-81355333-1	chr14	81355283	81355383	+	2.9	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	1355031	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0.01	0.346535
Merged-chr7-115233975-1	chr7	115233925	115234025	+	2.9	cIP2vsInput	Intergenic	Intergenic	282701	NR_040319	101786	Mm.395157	NR_040317		A730082K24Rik	AU044236	RIKEN cDNA A730082K24 gene	miscRNA	0.02	0.465347
Merged-chr11-55204298-2	chr11	55204230	55204367	+	2.9	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_153139)	promoter-TSS (NM_153139)	-42	NM_153139	215335	Mm.35732	NM_153139	ENSMUSG00000020261	Slc36a1	5830411H19Rik|AI839897|Pat1	"solute carrier family 36 (proton/amino acid symporter), member 1"	protein-coding	0.080292	0.673913
Merged-chr5-106709932-1	chr5	106709882	106709982	+	2.9	cIP2vsInput	Intergenic	RMER10B|LTR|ERVL	-13102	NM_026856	52397	Mm.440526	NM_026856	ENSMUSG00000049606	Zfp644	1110068L01Rik|AA408882|BM-005|D5Ertd689e|Zep-2	zinc finger protein 644	protein-coding	0.01	0.613861
Merged-chr13-99093524-1	chr13	99093474	99093574	+	2.9	cIP1vsInput	Intergenic	Intergenic	-5603	NR_045495	69603	Mm.390632	NR_045495		2310020H05Rik	-	RIKEN cDNA 2310020H05 gene	miscRNA	0.02	0.60396
Merged-chr6-41029381-1	chr6	41029331	41029431	+	2.9	cIP1vsInput	TTS (NM_023333)	TTS (NM_023333)	6128	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding	0	0.277228
Merged-chr19-4037770-1	chr19	4037720	4037820	+	2.9	cIP2vsInput	"intron (NM_013541, intron 1 of 6)"	"intron (NM_013541, intron 1 of 6)"	142	NM_013541	14870	Mm.299292	NM_013541	ENSMUSG00000060803	Gstp1	GstpiB	"glutathione S-transferase, pi 1"	protein-coding	0.07	0.683168
Merged-chr5-7111434-1	chr5	7111384	7111484	+	2.9	cIP2vsInput	"intron (NM_001163223, intron 1 of 3)"	"intron (NM_001163223, intron 1 of 3)"	-192730	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding	0	0.29703
Merged-chr5-15686221-1	chr5	15686171	15686271	+	2.9	cIP1vsInput	"intron (NR_001585, intron 1 of 4)"	MMERVK10C-int|LTR|ERVK	5511	NR_001585	75858	Mm.359463	NR_001585	ENSMUSG00000089871	Speer7-ps1	4930568L21Rik|SPEER-7|Speer7-ps	"spermatogenesis associated glutamate (E)-rich protein 7, pseudogene 1"	pseudo	0	0.336634
Merged-chr6-59154110-1	chr6	59154060	59154160	+	2.9	cIP2vsInput	Intergenic	Intergenic	-54760	NM_001081145	68140	Mm.25843	NM_001081145	ENSMUSG00000049232	Tigd2	3632410O17Rik	tigger transposable element derived 2	protein-coding	0.01	0.346535
Merged-chr7-145031107-1	chr7	145031057	145031157	+	2.9	cIP2vsInput	Intergenic	Intergenic	-91182	NM_007631	12443	Mm.273049	NM_007631	ENSMUSG00000070348	Ccnd1	AI327039|CycD1|Cyl-1|PRAD1|bcl-1|cD1	cyclin D1	protein-coding	0.05	0.663366
Merged-chr18-38250414-1	chr18	38250364	38250464	+	2.9	cIP2vsInput	promoter-TSS (NR_015475)	promoter-TSS (NR_015475)	151	NR_027904	73516	Mm.48776	NR_015475	ENSMUSG00000097080	1700086O06Rik	-	RIKEN cDNA 1700086O06 gene	miscRNA	0.1	0.663366
Merged-chr4-52438748-1	chr4	52438698	52438798	+	2.9	cIP1vsInput	promoter-TSS (NM_008017)	promoter-TSS (NM_008017)	216	NR_045175	72648	Mm.391869	NR_045175	ENSMUSG00000085763	2700081L22Rik	-	RIKEN cDNA 2700081L22 gene	miscRNA	0.01	0.425743
Merged-chr2-149878963-1	chr2	149878913	149879013	+	2.9	cIP2vsInput	"intron (NM_001085521, intron 1 of 3)"	"intron (NM_001085521, intron 1 of 3)"	48180	NM_001085521	433485	Mm.330649	NM_001085521	ENSMUSG00000074736	Syndig1	AW123113|DSPC2|Gm14134|H2C20orf39|OTTMUSG00000015750|Tmem90b	synapse differentiation inducing 1	protein-coding	0.01	0.316832
Merged-chr1-17065997-1	chr1	17065947	17066047	+	2.9	cIP1vsInput	"intron (NM_020604, intron 2 of 4)"	L1_Mus1|LINE|L1	31892	NM_020604	57339	Mm.143761	NM_020604	ENSMUSG00000042686	Jph1	ENSMUSG00000054314|JP-1|Jp1	junctophilin 1	protein-coding	0	0.306931
Merged-chr6-77913576-1	chr6	77913526	77913626	+	2.9	cIP1vsInput	"intron (NM_009819, intron 1 of 18)"	"intron (NM_009819, intron 1 of 18)"	66091	NM_145732	12386	Mm.34637	NM_001109764	ENSMUSG00000063063	Ctnna2	AI481747|Catna|Catna2|cdf|chp	"catenin (cadherin associated protein), alpha 2"	protein-coding	0	0.336634
Merged-chr2-117454868-1	chr2	117454818	117454918	+	2.9	cIP1vsInput	Intergenic	Intergenic	-111991	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding	0	0.336634
Merged-chr16-56277995-1	chr16	56277945	56278045	+	2.9	cIP2vsInput	Intergenic	Intergenic	73682	NM_174876	224224	Mm.151998	NM_174876	ENSMUSG00000035270	Impg2	IPM200|PG10.2|Rsbp|Spacrcan	interphotoreceptor matrix proteoglycan 2	protein-coding	0	0.306931
Merged-chr14-21686750-1	chr14	21686700	21686800	+	2.9	cIP2vsInput	"exon (NM_001013826, exon 3 of 4)"	"exon (NM_001013826, exon 3 of 4)"	27826	NM_001013826	435391	Mm.295860	NM_001013826	ENSMUSG00000063821	Dupd1	EG435391	dual specificity phosphatase and pro isomerase domain containing 1	protein-coding	0.15	0.663366
Merged-chr8-4238755-1	chr8	4238705	4238805	+	2.9	cIP1vsInput	promoter-TSS (NM_001164172)	promoter-TSS (NM_001164172)	15	NM_001164172	26400	Mm.3906	NM_001042557	ENSMUSG00000002948	Map2k7	5930412N11Rik|JNKK 2|Jnkk2|MAPKK 7|MEK 7|Mapkk7|Mek7|Mkk7|Prkmk7|sek2	mitogen-activated protein kinase kinase 7	protein-coding	0.1	0.683168
Merged-chr11-80142178-1	chr11	80142128	80142228	+	2.9	cIP2vsInput	promoter-TSS (NM_183275)	promoter-TSS (NM_183275)	-25	NM_183275	68550	Mm.18466	NM_183275	ENSMUSG00000046909	Tefm	1110002N22Rik	"transcription elongation factor, mitochondrial"	protein-coding	0.08	0.594059
Merged-chr7-97285806-1	chr7	97285756	97285856	+	2.9	cIP2vsInput	"intron (NM_001162477, intron 3 of 9)"	L1M2a|LINE|L1	40158	NM_001177412	244144	Mm.297541	NM_001177412	ENSMUSG00000035713	Usp35	Gm1088|Gm493	ubiquitin specific peptidase 35	protein-coding	0.01	0.326733
Merged-chr7-142611128-1	chr7	142611078	142611178	+	2.9	cIP2vsInput	Intergenic	Intergenic	-32982	NR_001592	14955	Mm.490776	NR_001592		H19	AI747191	H19 fetal liver mRNA	miscRNA	0	0.613861
Merged-chr9-122139570-1	chr9	122139520	122139620	+	2.9	cIP1vsInput	"intron (NM_133741, intron 3 of 6)"	"intron (NM_133741, intron 3 of 6)"	22304	NM_133741	20623	Mm.257989	XM_003946309	ENSMUSG00000038145	Snrk	2010012F07Rik|AI448042|AW547029|E030034B15|R74830|mKIAA0096	SNF related kinase	protein-coding	0	0.316832
Merged-chr9-100770574-1	chr9	100770524	100770624	+	2.9	cIP2vsInput	"intron (NM_009282, intron 5 of 33)"	"intron (NM_009282, intron 5 of 33)"	126951	NM_009282	20842	Mm.42135	NM_009282	ENSMUSG00000037286	Stag1	AU045003|SA-1|Scc3	stromal antigen 1	protein-coding	0.01	0.326733
Merged-chr5-47807098-1	chr5	47807048	47807148	+	2.9	cIP1vsInput	Intergenic	Intergenic	-176057	NM_178804	20563	Mm.289739	NM_178804		Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|mKIAA4141	slit homolog 2 (Drosophila)	protein-coding	0.01	0.346535
Merged-chr5-31571117-1	chr5	31571067	31571167	+	2.9	cIP2vsInput	"intron (NR_102275, intron 1 of 2)"	"intron (NR_102275, intron 1 of 2)"	280	NR_102275	100740	Mm.23370	XR_106452		AI839979	-	expressed sequence AI839979	miscRNA	0.06	0.732673
Merged-chr2-164443209-1	chr2	164443159	164443259	+	2.9	cIP2vsInput	promoter-TSS (NM_011521)	promoter-TSS (NM_011521)	-21	NM_011521	20971		NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding	0.1	0.722772
Merged-chr11-55428367-1	chr11	55428317	55428417	+	2.9	cIP2vsInput	Intergenic	Intergenic	-8287	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	AA517111|BM-40	secreted acidic cysteine rich glycoprotein	protein-coding	0.01	0.594059
Merged-chr13-29855696-1	chr13	29855646	29855746	+	2.9	cIP2vsInput	promoter-TSS (NM_144536)	promoter-TSS (NM_144536)	-108	NM_144536	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding	0.09	0.465347
Merged-chr19-24342769-1	chr19	24342719	24342819	+	2.9	cIP2vsInput	"intron (NM_008846, intron 13 of 14)"	"intron (NM_008846, intron 13 of 14)"	-62183	NM_008044	14297	Mm.7319	NM_008044	ENSMUSG00000059363	Fxn	FA|FARR|Frda|X25	frataxin	protein-coding	0	0.316832
Merged-chr2-33018207-1	chr2	33018157	33018257	+	2.9	cIP2vsInput	"intron (NM_178888, intron 15 of 28)"	"intron (NM_178888, intron 15 of 28)"	-36151	NM_019488	56017	Mm.305754	NM_019488	ENSMUSG00000026791	Slc2a8	D2Ertd44e|GLUT8|GlutX1	"solute carrier family 2, (facilitated glucose transporter), member 8"	protein-coding	0.02	0.554455
Merged-chr12-119325457-1	chr12	119325407	119325507	+	2.9	cIP1vsInput	Intergenic	Intergenic	-87181	NM_177290	320910	Mm.217000	NM_177290		Itgb8	4832412O06Rik	integrin beta 8	protein-coding	0	0.336634
Merged-chr4-132639013-1	chr4	132638963	132639063	+	2.9	cIP1vsInput	promoter-TSS (NM_010166)	promoter-TSS (NM_010166)	-33	NM_210071	14050	Mm.227733	NM_211356	ENSMUSG00000028886	Eya3	AI844637	eyes absent 3 homolog (Drosophila)	protein-coding	0.09	0.613861
Merged-chrY-6670415-1	chrY	6670365	6670465	+	2.9	cIP1vsInput	Intergenic	Lx3_Mus|LINE|L1	497362	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.356436
Merged-chr1-7398060-1	chr1	7398010	7398110	+	2.9	cIP2vsInput	Intergenic	CpG	309140	NM_183028	319263		NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.05	0.653465
Merged-chr3-37687290-1	chr3	37687240	37687340	+	2.9	cIP2vsInput	Intergenic	Intergenic	37070	NM_198657	381438	Mm.490549	NM_198657	ENSMUSG00000058174	Gm5148	EG381438	predicted gene 5148	protein-coding	0.03	0.60396
Merged-chr6-50276781-1	chr6	50276731	50276831	+	2.9	cIP2vsInput	Intergenic	Intergenic	-15012	NM_018769	54722	Mm.248361	NM_018769	ENSMUSG00000029821	Dfna5	2310037D07Rik|4932441K13Rik|Dfna5h|EG14210|Fin15	"deafness, autosomal dominant 5 (human)"	protein-coding	0.01	0.316832
Merged-chr18-37644438-1	chr18	37644388	37644488	+	2.9	cIP2vsInput	promoter-TSS (NM_175770)	promoter-TSS (NM_175770)	-234	NM_175770	24074	Mm.236009	NM_175770	ENSMUSG00000051316	Taf7	55kDa|AI607308|BB007175|TAFII55|Taf2f	"TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor"	protein-coding	0.06	0.475248
Merged-chr13-55471526-1	chr13	55471476	55471576	+	2.9	cIP2vsInput	"intron (NM_001030296, intron 1 of 2)"	CpG	7259	NM_001030296	432763	Mm.315457	NM_001030296	ENSMUSG00000034686	Prr7	XM_484263	proline rich 7 (synaptic)	protein-coding	0.11	0.693069
Merged-chr10-128704952-1	chr10	128704902	128705002	+	2.9	cIP2vsInput	promoter-TSS (NM_016756)	promoter-TSS (NM_016756)	99	NM_183417	12566	Mm.111326	NM_016756	ENSMUSG00000025358	Cdk2	A630093N05Rik	cyclin-dependent kinase 2	protein-coding	0.05	0.60396
Merged-chr19-61064289-1	chr19	61064239	61064339	+	2.9	cIP1vsInput	"intron (NM_018869, intron 4 of 15)"	"intron (NM_018869, intron 4 of 15)"	112020	NM_001177513	633057	Mm.426097	NM_001177513	ENSMUSG00000094649	Gm7102	EG633057	predicted gene 7102	protein-coding	0	0.445545
Merged-chr1-131827945-1	chr1	131827895	131827995	+	2.9	cIP2vsInput	promoter-TSS (NM_173865)	promoter-TSS (NM_173865)	-67	NM_173865	98396	Mm.389181	NM_173865	ENSMUSG00000013275	Slc41a1	AI573938|B230315F01Rik	"solute carrier family 41, member 1"	protein-coding	0.04	0.613861
Merged-chr11-12215777-1	chr11	12215727	12215827	+	2.9	cIP1vsInput	Intergenic	Intergenic	-178357	NM_010345	14783	Mm.273117	NM_001177629	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding	0	0.50495
Merged-chr1-119053724-1	chr1	119053674	119053774	+	2.9	cIP2vsInput	promoter-TSS (NM_001081125)	promoter-TSS (NM_001081125)	-105	NM_001081125	14633	Mm.273292	NM_001081125	ENSMUSG00000048402	Gli2	AW546128	GLI-Kruppel family member GLI2	protein-coding	0.12	0.673267
Merged-chr5-48372056-1	chr5	48372006	48372106	+	2.9	cIP2vsInput	promoter-TSS (NM_025755)	promoter-TSS (NM_025755)	-336	NM_025755	66768	Mm.29409	NM_025755	ENSMUSG00000029089	Pacrgl	4933428G09Rik	PARK2 co-regulated-like	protein-coding	0	0.445545
Merged-chr2-51429872-1	chr2	51429822	51429922	+	2.9	cIP2vsInput	Intergenic	Intergenic	188041	NR_040636	329404	Mm.417725	NR_040636	ENSMUSG00000086349	Gm13497	A730015I17|OTTMUSG00000012425	predicted gene 13497	miscRNA	0.01	0.475248
Merged-chr8-37187889-1	chr8	37187839	37187939	+	2.9	cIP2vsInput	Intergenic	Intergenic	194314	NM_001039220	621080	Mm.373292	NM_001039220	ENSMUSG00000074384	AI429214	-	expressed sequence AI429214	protein-coding	0.01	0.336634
Merged-chr16-58634263-1	chr16	58634213	58634313	+	2.9	cIP1vsInput	TTS (NM_175011)	TTS (NM_175011)	4140	NM_175011	224247	Mm.26145	NM_175011		E330017A01Rik	-	RIKEN cDNA E330017A01 gene	protein-coding	0.01	0.405941
Merged-chr18-14783008-1	chr18	14782958	14783058	+	2.9	cIP1vsInput	promoter-TSS (NM_001100449)	promoter-TSS (NM_001100449)	-237	NM_001100449	72504	Mm.312233	NM_001100449	ENSMUSG00000054321	Taf4b	105kDa|2610524B04Rik|4932409F03Rik|AW987595|TAFII105|Taf2c2	"TAF4B RNA polymerase II, TATA box binding protein (TBP)-associated factor"	protein-coding	0.11	0.653465
Merged-chr2-140935554-1	chr2	140935504	140935604	+	2.9	cIP2vsInput	"intron (NM_001013802, intron 4 of 18)"	"intron (NM_001013802, intron 4 of 18)"	-264078	NM_178382	71436	Mm.426781	NM_001172160	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0	0.326733
Merged-chr18-9463560-1	chr18	9463510	9463610	+	2.9	cIP1vsInput	Intergenic	Intergenic	-13410	NM_026484	67974	Mm.376607	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding	0.01	0.326733
Merged-chr14-89725811-1	chr14	89725761	89725861	+	2.9	cIP2vsInput	Intergenic	Intergenic	-170413	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0	0.336634
Merged-chr19-13980827-1	chr19	13980777	13980877	+	2.9	cIP1vsInput	Intergenic	Intergenic	61805	NM_001011850	258151	Mm.377361	NM_001011850	ENSMUSG00000062314	Olfr1505	MOR211-4P	olfactory receptor 1505	protein-coding	0.02	0.366337
Merged-chr1-172482068-1	chr1	172482018	172482118	+	2.9	cIP1vsInput	promoter-TSS (NM_033608)	promoter-TSS (NM_033608)	-145	NM_001145800	93842	Mm.214530	NM_001145800	ENSMUSG00000037995	Igsf9	644ETD8|Dasm1|Kiaa1355-hp|NRT1|Ncaml|mKIAA1355	"immunoglobulin superfamily, member 9"	protein-coding	0.12	0.693069
Merged-chr14-47334879-1	chr14	47334829	47334929	+	2.9	cIP1vsInput	Intergenic	Intergenic	36565	NM_178684	218975	Mm.405885	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding	0	0.366337
Merged-chr19-60924735-2	chr19	60924684	60924786	+	2.9	cIP1vsInput|cIP2vsInput	"intron (NM_018869, intron 1 of 15)"	IMPB_01|Satellite|Satellite	34986	NM_018869	14773	Mm.279400	NM_018869	ENSMUSG00000003228	Grk5	Gprk5	G protein-coupled receptor kinase 5	protein-coding	0	0.650485
Merged-chr5-48306738-1	chr5	48306688	48306788	+	2.9	cIP1vsInput	TTS (NM_178804)	TTS (NM_178804)	-65654	NM_025755	66768	Mm.29409	NM_025755	ENSMUSG00000029089	Pacrgl	4933428G09Rik	PARK2 co-regulated-like	protein-coding	0	0.316832
Merged-chr9-66946016-1	chr9	66945966	66946066	+	2.9	cIP2vsInput	promoter-TSS (NM_026467)	promoter-TSS (NM_026467)	-102	NM_026467	67941	Mm.30120	NM_026467	ENSMUSG00000036781	Rps27l	1810034D23Rik	ribosomal protein S27-like	protein-coding	0.08	0.643564
Merged-chr17-87044554-1	chr17	87044504	87044604	+	2.9	cIP1vsInput	Intergenic	Intergenic	18993	NM_019936	56724	Mm.109329	NM_019936	ENSMUSG00000024146	Cript	1200020A08Rik|AA589469	cysteine-rich PDZ-binding protein	protein-coding	0.08	0.544554
Merged-chr4-83524938-1	chr4	83524888	83524988	+	2.9	cIP2vsInput	promoter-TSS (NM_001081012)	promoter-TSS (NM_001081012)	-607	NM_001081012	320226	Mm.180032	NM_001081012	ENSMUSG00000052407	Ccdc171	4930418J05Rik|4930473A06Rik|A330015D16Rik	coiled-coil domain containing 171	protein-coding	0.02	0.49505
Merged-chr17-56935607-1	chr17	56935557	56935657	+	2.9	cIP2vsInput	promoter-TSS (NM_022328)	promoter-TSS (NM_022328)	-219	NM_022328	64144	Mm.148748	NM_022328	ENSMUSG00000024212	Mllt1	AA407901|BAM11|ENL|LTG19	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1"	protein-coding	0.13	0.732673
Merged-chr14-68845855-1	chr14	68845805	68845905	+	2.9	cIP2vsInput	Intergenic	Intergenic	-183434	NM_009285	20855	Mm.20911	NM_009285	ENSMUSG00000014813	Stc1	Stc	stanniocalcin 1	protein-coding	0	0.346535
Merged-chr5-107611825-1	chr5	107611775	107611875	+	2.9	cIP2vsInput	"intron (NM_001163461, intron 6 of 11)"	"intron (NM_001163461, intron 6 of 11)"	-13937	NM_001161738	170823	Mm.41417	NM_001161738	ENSMUSG00000029276	Glmn	9330160J16Rik|AW227515|Fap48|Fap68	"glomulin, FKBP associated protein"	protein-coding	0	0.336634
Merged-chr6-3934333-1	chr6	3934283	3934383	+	2.9	cIP2vsInput	Intergenic	Intergenic	34021	NM_009364	21789	Mm.25612	NM_009364	ENSMUSG00000029664	Tfpi2	AV000670|PP5/TFPI-2	tissue factor pathway inhibitor 2	protein-coding	0	0.306931
Merged-chr9-74436997-1	chr9	74436947	74437047	+	2.9	cIP2vsInput	Intergenic	Intergenic	326663	NM_001033500	546144	Mm.335289	NM_177908	ENSMUSG00000044976	Wdr72	AW558070|D230040E23	WD repeat domain 72	protein-coding	0.01	0.326733
Merged-chr15-38003252-1	chr15	38003202	38003302	+	2.9	cIP1vsInput	"intron (NM_001112721, intron 32 of 58)"	"intron (NM_001112721, intron 32 of 58)"	-42197	NM_199476	382985	Mm.24738	NM_199476	ENSMUSG00000022292	Rrm2b	p53R2	ribonucleotide reductase M2 B (TP53 inducible)	protein-coding	0	0.306931
Merged-chr2-26140367-1	chr2	26140317	26140417	+	2.9	cIP1vsInput	promoter-TSS (NM_001256522)	promoter-TSS (NM_001256522)	139	NM_001256521	109299	Mm.490529	NM_001256521		C330006A16Rik	AI551216	RIKEN cDNA C330006A16 gene	protein-coding	0.12	0.742574
Merged-chr12-52759696-1	chr12	52759646	52759746	+	2.9	cIP2vsInput	"intron (NM_198111, intron 1 of 13)"	L1MC|LINE|L1	60313	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding	0	0.346535
Merged-chr12-110591394-1	chr12	110591344	110591444	+	2.9	cIP2vsInput	promoter-TSS (NR_033340)	promoter-TSS (NR_033340)	20	NR_033340	319786	Mm.129691	NR_033340		B930059L03Rik	-	RIKEN cDNA B930059L03 gene	miscRNA	0.12	0.653465
Merged-chr10-50765104-1	chr10	50765054	50765154	+	2.9	cIP1vsInput	"intron (NM_198007, intron 34 of 41)"	"intron (NM_198007, intron 34 of 41)"	-130547	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding	0	0.316832
Merged-chr11-73177592-1	chr11	73177542	73177642	+	2.9	cIP2vsInput	promoter-TSS (NM_025318)	promoter-TSS (NM_025318)	509	NM_029564	76281	Mm.371656	NM_029564	ENSMUSG00000040158	Tax1bp3	1300011C24Rik|RP23-263M10.10|TIP-1	Tax1 (human T cell leukemia virus type I) binding protein 3	protein-coding	0.08	0.623762
Merged-chr1-92473817-1	chr1	92473767	92473867	+	2.9	cIP2vsInput	promoter-TSS (NM_024197)	promoter-TSS (NM_024197)	-59	NM_024197	67273	Mm.248778	NM_024197		Ndufa10	2900053E13Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 10	protein-coding	0.13	0.594059
Merged-chr4-134469033-1	chr4	134468983	134469083	+	2.9	cIP2vsInput	"intron (NM_019641, intron 1 of 4)"	CpG	713	NM_019641	16765	Mm.378957	NM_019641	ENSMUSG00000028832	Stmn1	19k|Lag|Lap18|Op18|P18|P19|Pig|Pp17|Pp18|Pp19|Pr22|Smn	stathmin 1	protein-coding	0.16	0.732673
Merged-chr16-77173429-2	chr16	77173372	77173487	+	2.9	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-155899	NR_015543	77994	Mm.394688	NR_015543		2810055G20Rik	D730043B02Rik	RIKEN cDNA 2810055G20 gene	miscRNA	0.008696	0.448276
Merged-chr6-122740139-1	chr6	122740089	122740189	+	2.9	cIP2vsInput	"intron (NM_011401, intron 2 of 9)"	"intron (NM_011401, intron 2 of 9)"	2606	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	"solute carrier family 2 (facilitated glucose transporter), member 3"	protein-coding	0.03	0.564356
Merged-chr2-106754466-1	chr2	106754416	106754516	+	2.9	cIP2vsInput	"intron (NM_001143683, intron 3 of 6)"	"intron (NM_001143683, intron 3 of 6)"	58865	NM_029837	77015	Mm.45628	NM_001143683	ENSMUSG00000016386	Mpped2	239Fb|2700082O15Rik|AV354767|AW060960	metallophosphoesterase domain containing 2	protein-coding	0.01	0.306931
Merged-chr2-25272492-1	chr2	25272442	25272542	+	2.9	cIP2vsInput	promoter-TSS (NM_023464)	promoter-TSS (NM_023464)	26	NM_175300	99152	Mm.291624	NM_175300	ENSMUSG00000026965	Anapc2	9230107K09Rik|AL024279|Apc2|Emi4|Imi4|mKIAA1406	anaphase promoting complex subunit 2	protein-coding	0.11	0.673267
Merged-chrX-74313012-1	chrX	74312962	74313062	+	2.9	cIP2vsInput	promoter-TSS (NM_138607)	promoter-TSS (NM_138607)	-21	NM_138607	108160	Mm.4370	NM_138607	ENSMUSG00000001962	Fam50a	D0HXS9928E|XAP-5	"family with sequence similarity 50, member A"	protein-coding	0.11	0.663366
Merged-chr17-80944709-1	chr17	80944659	80944759	+	2.9	cIP2vsInput	promoter-TSS (NM_026516)	promoter-TSS (NM_026516)	77	NM_026516	68027	Mm.357108	NM_026516	ENSMUSG00000024245	Tmem178	2810417M05Rik|Tmem178a	transmembrane protein 178	protein-coding	0.11	0.732673
Merged-chr12-40702369-2	chr12	40702281	40702458	+	2.9	cIP1vsInput|cIP2vsInput	"intron (NM_172803, intron 13 of 52)"	"intron (NM_172803, intron 13 of 52)"	256316	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding	0	0.421348
Merged-chr1-106759545-1	chr1	106759495	106759595	+	2.9	cIP2vsInput	"exon (NM_027534, exon 1 of 10)"	"exon (NM_027534, exon 1 of 10)"	197	NM_027534	70750	Mm.458911	NM_027534	ENSMUSG00000009905	Kdsr	6330410P18Rik|9430079B08Rik|Fvt1	3-ketodihydrosphingosine reductase	protein-coding	0.09	0.683168
Merged-chr2-83608095-1	chr2	83608045	83608145	+	2.9	cIP1vsInput	Intergenic	L1MD|LINE|L1	-36483	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding	0	0.306931
Merged-chr6-120175093-1	chr6	120175043	120175143	+	2.9	cIP1vsInput	"intron (NM_016718, intron 1 of 3)"	"intron (NM_016718, intron 1 of 3)"	81713	NM_016718	29862	Mm.103668	NM_016718	ENSMUSG00000041377	Ninj2	-	ninjurin 2	protein-coding	0	0.623762
Merged-chr17-91605178-1	chr17	91605128	91605228	+	2.9	cIP2vsInput	Intergenic	Intergenic	-512376	NM_020252	18189	Mm.312068	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0	0.29703
Merged-chr11-79423717-1	chr11	79423667	79423767	+	2.9	cIP1vsInput	"intron (NM_010897, intron 12 of 57)"	"intron (NM_010897, intron 12 of 57)"	60314	NR_045305	104522	Mm.436987	NR_045305	ENSMUSG00000091523	AU040972	AU040954	expressed sequence AU040972	miscRNA	0	0.376238
Merged-chr12-57594862-1	chr12	57594812	57594912	+	2.9	cIP1vsInput	"intron (NM_001037743, intron 2 of 4)"	"intron (NM_001037743, intron 2 of 4)"	30747	NM_001037743	70846	Mm.449996	NM_001037743	ENSMUSG00000046782	4921506M07Rik	-	RIKEN cDNA 4921506M07 gene	protein-coding	0.01	0.287129
Merged-chr19-6046351-1	chr19	6046301	6046401	+	2.9	cIP2vsInput	promoter-TSS (NM_028769)	promoter-TSS (NM_028769)	-225	NM_028769	74126	Mm.149870	NM_001164709	ENSMUSG00000024807	Syvn1	1200010C09Rik|AW211966|C85322|D530017H19Rik|Hrd1	"synovial apoptosis inhibitor 1, synoviolin"	protein-coding	0.07	0.643564
Merged-chr6-30390910-1	chr6	30390860	30390960	+	2.9	cIP2vsInput	promoter-TSS (NM_172735)	promoter-TSS (NM_172735)	100	NM_172735	232679	Mm.474686	NM_172735	ENSMUSG00000039130	Zc3hc1	1110054L24Rik|AU018540|AU019789|HSPC216|Nipa	"zinc finger, C3HC type 1"	protein-coding	0.04	0.534653
Merged-chr18-88398585-1	chr18	88398535	88398635	+	2.9	cIP2vsInput	Intergenic	Lx8b|LINE|L1	495622	NM_018821	54607	Mm.476577	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding	0	0.336634
Merged-chr9-46282986-1	chr9	46282936	46283036	+	2.9	cIP2vsInput	promoter-TSS (NM_146000)	promoter-TSS (NM_146000)	-26	NM_146000	215051	Mm.32648	NM_146000	ENSMUSG00000032077	Bud13	AV305342|D030060M11Rik	BUD13 homolog (yeast)	protein-coding	0.1	0.633663
Merged-chr8-83166745-1	chr8	83166695	83166795	+	2.9	cIP2vsInput	"intron (NM_027758, intron 1 of 17)"	"intron (NM_027758, intron 1 of 17)"	1393	NM_027758	71310	Mm.24031	NM_001111304	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	"TBC1 domain family, member 9"	protein-coding	0.01	0.306931
Merged-chr12-102039968-2	chr12	102039917	102040019	+	2.85	cIP1vsInput|cIP2vsInput	Intergenic	LTR72_RN|LTR|ERV1	63994	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding	0	0.427184
Merged-chr11-90418024-2	chr11	90417942	90418106	+	2.85	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-27107	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding	0.109756	0.715152
Merged-chr17-72997503-2	chr17	72997452	72997555	+	2.85	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	79198	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding	0.019417	0.576923
Merged-chrX-74393194-2	chrX	74393116	74393272	+	2.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001161424)	promoter-TSS (NM_001161424)	-55	NM_025473	66294	Mm.166485	NM_025473	ENSMUSG00000031399	Fam3a	1810037C20Rik|RP23-436K3.15	"family with sequence similarity 3, member A"	protein-coding	0.070513	0.630573
Merged-chr11-87462556-2	chr11	87462504	87462609	+	2.85	cIP1vsInput|cIP2vsInput	"intron (NM_031386, intron 2 of 30)"	"intron (NM_031386, intron 2 of 30)"	34965	NM_001199293	83560	Mm.440758	NM_001199293	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding	0.009524	0.349057
Merged-chr19-5366904-2	chr19	5366831	5366977	+	2.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011793)	promoter-TSS (NM_011793)	91	NM_027236	69860	Mm.299167	NM_027236	ENSMUSG00000024841	Eif1ad	2010003J03Rik|AI131644	eukaryotic translation initiation factor 1A domain containing	protein-coding	0.075342	0.605442
Merged-chr11-97309571-2	chr11	97309501	97309642	+	2.85	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-6145	NM_025927	67036	Mm.5381	NM_025927	ENSMUSG00000018882	Mrpl45	2600005P05Rik|AU043542|R75241	mitochondrial ribosomal protein L45	protein-coding	0.035461	0.619718
Merged-chr15-75929820-2	chr15	75929756	75929885	+	2.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_031201)	promoter-TSS (NM_031201)	-90	NM_031201	22122	Mm.22596	NM_031201	ENSMUSG00000022570	Tsta3	AI256181|FX|Tstap35b	tissue specific transplantation antigen P35B	protein-coding	0.054264	0.607692
Merged-chr16-18089145-2	chr16	18089080	18089210	+	2.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011172)	promoter-TSS (NM_011172)	45	NM_011172	19125	Mm.28456	NM_011172	ENSMUSG00000003526	Prodh	Pro-1|Pro1|Ym24d07	proline dehydrogenase	protein-coding	0.1	0.633588
Merged-chr8-20342363-2	chr8	20342313	20342413	+	2.85	cIP1vsInput|cIP2vsInput	"intron (NM_001177408, intron 7 of 9)"	"intron (NM_001177408, intron 7 of 9)"	20839	NM_001177408	100040599	Mm.445582	NM_001177408	ENSMUSG00000074449	Gm15319	OTTMUSG00000020118	predicted gene 15319	protein-coding	0.01	0.316832
Merged-chr7-28179449-2	chr7	28179384	28179515	+	2.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001271370)	promoter-TSS (NM_001271370)	-34	NM_001037957	13549	Mm.57249	NM_001037957	ENSMUSG00000002409	Dyrk1b	Mirk	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1b	protein-coding	0.091603	0.666667
Merged-chr13-49205701-2	chr13	49205615	49205787	+	2.85	cIP1vsInput|cIP2vsInput	"intron (NM_026738, intron 2 of 5)"	"intron (NM_026738, intron 2 of 5)"	10325	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	1110007C09Rik	AI851695|Bincard	RIKEN cDNA 1110007C09 gene	protein-coding	0.034884	0.462428
Merged-chr17-24163781-2	chr17	24163721	24163842	+	2.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172935)	promoter-TSS (NM_172935)	-48	NM_172935	245847	Mm.87319	NM_172935	ENSMUSG00000036820	Amdhd2	5730457F11Rik	amidohydrolase domain containing 2	protein-coding	0.090909	0.655738
Merged-chr11-101642092-2	chr11	101642039	101642146	+	2.85	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	14143	NM_025654	66599	Mm.41449	NM_025654	ENSMUSG00000010362	Rdm1	2410008M22Rik|AW212028|Rad52b	RAD52 motif 1	protein-coding	0.037383	0.444444
Merged-chr17-56831048-2	chr17	56830986	56831110	+	2.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009056)	promoter-TSS (NM_009056)	-40	NM_027787	19725	Mm.102	NM_009056	ENSMUSG00000024206	Rfx2	5430432H19Rik	"regulatory factor X, 2 (influences HLA class II expression)"	protein-coding	0.193548	0.88
Merged-chr11-72490090-2	chr11	72490018	72490163	+	2.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_153060)	promoter-TSS (NM_153060)	-170	NM_153060	216892	Mm.212812	NM_001276383	ENSMUSG00000040447	Spns2	-	spinster homolog 2	protein-coding	0.103448	0.760274
Merged-chr4-135963672-2	chr4	135963618	135963726	+	2.85	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-1493	NM_178389	74246	Mm.247946	NM_178389	ENSMUSG00000028671	Gale	2310002A12Rik|AI323962	"galactose-4-epimerase, UDP"	protein-coding	0.046296	0.642202
Merged-chrY-5844398-2	chrY	5844324	5844472	+	2.85	cIP1vsInput|cIP2vsInput	Intergenic	L1_Mm|LINE|L1	1323379	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.013514	0.362416
Merged-chr6-83109078-2	chr6	83109028	83109129	+	2.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026744)	promoter-TSS (NM_026744)	-30	NM_026744	68499	Mm.333183	NM_026744	ENSMUSG00000030037	Mrpl53	1110007K17Rik	mitochondrial ribosomal protein L53	protein-coding	0.118812	0.647059
Merged-chr5-120566751-2	chr5	120566679	120566823	+	2.85	cIP1vsInput|cIP2vsInput	"intron (NM_145853, intron 2 of 27)"	"intron (NM_145853, intron 2 of 27)"	21862	NM_145853	252972	Mm.114054	NM_145853	ENSMUSG00000032741	Tpcn1	5730403B01Rik|Tpc1|mKIAA1169	two pore channel 1	protein-coding	0.020833	0.524138
Merged-chr12-110979228-2	chr12	110979154	110979303	+	2.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175207)	promoter-TSS (NM_175207)	-207	NM_175207	74251	Mm.250989	NM_175207	ENSMUSG00000037904	Ankrd9	2500003O20Rik	ankyrin repeat domain 9	protein-coding	0.080537	0.7
Merged-chr18-36670289-2	chr18	36670220	36670359	+	2.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025291)	promoter-TSS (NM_025291)	22	NM_001164406	24068	Mm.29058	NM_001164406		Sra1	AA959952|Sra|Srap|Straa1|Strra1	steroid receptor RNA activator 1	protein-coding	0.100719	0.671429
Merged-chr8-115158765-2	chr8	115158706	115158825	+	2.85	cIP1vsInput|cIP2vsInput	"intron (NM_019573, intron 8 of 8)"	"intron (NM_019573, intron 8 of 8)"	548129	NM_001025577	17132	Mm.488377	NM_001025577		Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma (v-maf) AS42 oncogene homolog	protein-coding	0.008403	0.316667
Merged-chr2-143062996-2	chr2	143062935	143063058	+	2.85	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_021335)	promoter-TSS (NM_021335)	-73	NM_021335	20639	Mm.1323	NM_021335		Snrpb2	2810052G09Rik	U2 small nuclear ribonucleoprotein B	protein-coding	0.113821	0.629032
Merged-chr16-11203177-1	chr16	11203127	11203227	+	2.8	cIP2vsInput	promoter-TSS (NR_038156)	promoter-TSS (NR_038156)	115	NM_025546	66409	Mm.28291	NM_025546	ENSMUSG00000005846	Rsl1d1	2410005K20Rik|C76439|pBK1	ribosomal L1 domain containing 1	protein-coding	0.1	0.633663
Merged-chr15-102518505-1	chr15	102518455	102518555	+	2.8	cIP2vsInput	"5' UTR (NM_001253795, exon 1 of 7)"	"5' UTR (NM_001253795, exon 1 of 7)"	313	NM_009319	21357	Mm.291485	NM_001253795	ENSMUSG00000023051	Tarbp2	Prbp	TAR (HIV) RNA binding protein 2	protein-coding	0.1	0.712871
Merged-chr6-130876055-1	chr6	130876005	130876105	+	2.8	cIP2vsInput	Intergenic	L1VL1|LINE|L1	371307	NM_001170851	16633	Mm.4783	NM_001170851	ENSMUSG00000030187	Klra2	Klra30|Ly49b	"killer cell lectin-like receptor, subfamily A, member 2"	protein-coding	0	0.386139
Merged-chr14-25015928-1	chr14	25015878	25015978	+	2.8	cIP2vsInput	Intergenic	(GA)n|Simple_repeat|Simple_repeat	127313	NR_045718	75862	Mm.109191	NR_045718		4930572O13Rik	-	RIKEN cDNA 4930572O13 gene	miscRNA	0.01	0.514851
Merged-chr14-6972197-1	chr14	6972147	6972247	+	2.8	cIP1vsInput	Intergenic	Intergenic	55252	NM_001164727	100038847	Mm.483675	NM_001164727	ENSMUSG00000093985	Gm10406	ENSMUSG00000072735	predicted gene 10406	protein-coding	0	0.366337
Merged-chr17-39981710-1	chr17	39981660	39981760	+	2.8	cIP2vsInput	Intergenic	Intergenic	31190	NM_001256051	100126775	Mm.471585	NM_001256051		Gm21946	Esp38	"predicted gene, 21946"	protein-coding	0	0.376238
Merged-chr2-38513029-1	chr2	38512979	38513079	+	2.8	cIP2vsInput	"intron (NM_001159631, intron 1 of 9)"	"intron (NM_001159631, intron 1 of 9)"	1153	NM_001159631	59126	Mm.143818	NM_001159631	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding	0.02	0.653465
Merged-chr2-132283418-1	chr2	132283368	132283468	+	2.8	cIP2vsInput	"intron (NM_138651, intron 1 of 12)"	"intron (NM_138651, intron 1 of 12)"	20161	NM_138651	110911	Mm.284503	NM_138651	ENSMUSG00000058793	Cds2	5730450N06Rik|5730460C18Rik|AI854580|D2Wsu127e	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	protein-coding	0.04	0.49505
Merged-chr5-96374123-1	chr5	96374073	96374173	+	2.8	cIP2vsInput	"5' UTR (NM_175473, exon 1 of 74)"	"5' UTR (NM_175473, exon 1 of 74)"	168	NM_175473	231470	Mm.291120	NM_175473	ENSMUSG00000034687	Fras1	E130113P14Rik|bl|mKIAA1500	Fraser syndrome 1 homolog (human)	protein-coding	0.13	0.772277
Merged-chr6-16571638-1	chr6	16571588	16571688	+	2.8	cIP1vsInput	Intergenic	(TGAA)n|Simple_repeat|Simple_repeat	326803	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding	0	0.336634
Merged-chr7-100260855-1	chr7	100260805	100260905	+	2.8	cIP1vsInput	"intron (NM_027629, intron 6 of 13)"	L1MC5a|LINE|L1	-3689	NR_033563	14777	Mm.57225	NR_033563		Gpx2-ps1	AU041318	"glutathione peroxidase 2, pseudogene 1"	pseudo	0	0.346535
Merged-chr2-145832809-1	chr2	145832759	145832859	+	2.8	cIP2vsInput	"intron (NM_028724, intron 4 of 12)"	"intron (NM_028724, intron 4 of 12)"	46693	NM_028724	74030	Mm.433263	NM_028724	ENSMUSG00000001768	Rin2	2010003K16Rik|4632403N06Rik|AW821980|RASSF4	Ras and Rab interactor 2	protein-coding	0.01	0.554455
Merged-chr8-68520248-1	chr8	68520198	68520298	+	2.8	cIP1vsInput	"intron (NM_001252623, intron 4 of 10)"	L1M5|LINE|L1	151789	NR_038181	73609	Mm.443247	NR_038181	ENSMUSG00000085197	1700125H03Rik	4930510D22Rik	RIKEN cDNA 1700125H03 gene	miscRNA	0.01	0.287129
Merged-chr4-31476940-1	chr4	31476890	31476990	+	2.8	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-487167	NM_009316	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding	0	0.326733
Merged-chr15-82429908-1	chr15	82429858	82429958	+	2.8	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	-22469	NM_010006	13105	Mm.226708	NM_010006	ENSMUSG00000068086	Cyp2d9	Cyp2d|P450-2D	"cytochrome P450, family 2, subfamily d, polypeptide 9"	protein-coding	0	0.356436
Merged-chr5-136199602-1	chr5	136199552	136199652	+	2.8	cIP2vsInput	promoter-TSS (NM_025774)	promoter-TSS (NM_025774)	-648	NM_025774	66801	Mm.425295	NM_025774		Prkrip1	8430424D23Rik|C114	Prkr interacting protein 1 (IL11 inducible)	protein-coding	0.04	0.445545
Merged-chr9-113822247-1	chr9	113822197	113822297	+	2.8	cIP2vsInput	"intron (NM_001081960, intron 2 of 32)"	"intron (NM_001081960, intron 2 of 32)"	9661	NM_001081960	76499	Mm.222272	NM_001081960	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding	0	0.306931
Merged-chr16-21563513-1	chr16	21563463	21563563	+	2.8	cIP2vsInput	"intron (NM_001081366, intron 39 of 46)"	"intron (NM_001081366, intron 39 of 46)"	131152	NM_001001881	72190		NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding	0.04	0.594059
Merged-chr8-35469018-1	chr8	35468968	35469068	+	2.8	cIP2vsInput	"3' UTR (NM_026067, exon 7 of 7)"	"3' UTR (NM_026067, exon 7 of 7)"	26515	NM_026067	67276	Mm.207534	NM_026067	ENSMUSG00000031527	Eri1	3'hexo|3110010F15Rik|Thex1|eri-1	exoribonuclease 1	protein-coding	0	0.356436
Merged-chr19-32692148-1	chr19	32692098	32692198	+	2.8	cIP2vsInput	"intron (NM_026487, intron 6 of 9)"	"intron (NM_026487, intron 6 of 9)"	20150	NM_026487	67979	Mm.27123	NM_026487	ENSMUSG00000013662	Atad1	4921525H23Rik|AW107648|Thorase	"ATPase family, AAA domain containing 1"	protein-coding	0	0.346535
Merged-chr13-112801223-1	chr13	112801173	112801273	+	2.8	cIP2vsInput	"exon (NM_008903, exon 1 of 6)"	"exon (NM_008903, exon 1 of 6)"	300	NM_008903	19012	Mm.317186	NM_008247	ENSMUSG00000021759	Ppap2a	Hic53|Hpic53|LPP-1|LPP1|mPAP	phosphatidic acid phosphatase type 2A	protein-coding	0.1	0.60396
Merged-chr13-8855410-1	chr13	8855360	8855460	+	2.8	cIP2vsInput	"intron (NM_001039388, intron 3 of 13)"	"intron (NM_001039388, intron 3 of 13)"	15632	NM_001039389	207615	Mm.284654	NM_001039388	ENSMUSG00000021147	Wdr37	3110035P10Rik|4933417A01Rik|6430603N07|AI481191|mKIAA0982	WD repeat domain 37	protein-coding	0	0.316832
Merged-chr17-45848111-1	chr17	45848061	45848161	+	2.8	cIP1vsInput	Intergenic	Intergenic	-114267	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding	0.06	0.613861
Merged-chr17-24937002-1	chr17	24936952	24937052	+	2.8	cIP2vsInput	promoter-TSS (NM_001163451)	promoter-TSS (NM_001163451)	-25	NM_013931	30957	Mm.43081	NM_001163447	ENSMUSG00000024163	Mapk8ip3	BB120594|D17Wsu15e|JIP-3|JSAP1|JSAP1a|JSAP1b|JSAP1c|JSAP1d|Jip3|Syd2|mKIAA1066	mitogen-activated protein kinase 8 interacting protein 3	protein-coding	0.11	0.722772
Merged-chr7-12422804-1	chr7	12422754	12422854	+	2.8	cIP2vsInput	promoter-TSS (NM_001033820)	promoter-TSS (NM_001033820)	-313	NM_001033820	619331	Mm.361832	NM_001033820	ENSMUSG00000034071	Zfp551	9630004E07Rik|Znf551	zinc fingr protein 551	protein-coding	0.03	0.514851
Merged-chr11-59965026-1	chr11	59964976	59965076	+	2.8	cIP2vsInput	promoter-TSS (NM_009026)	promoter-TSS (NM_009026)	-84	NM_009026	19416	Mm.3903	NM_009026	ENSMUSG00000049892	Rasd1	Dexras1	"RAS, dexamethasone-induced 1"	protein-coding	0.11	0.712871
Merged-chr1-65223719-1	chr1	65223669	65223769	+	2.8	cIP2vsInput	"intron (NM_011086, intron 12 of 41)"	"intron (NM_011086, intron 12 of 41)"	37034	NM_011086	18711	Mm.38370	NM_011086		Pikfyve	5230400C17Rik|Pip5k|Pip5k3|Pipk5k3|p235	"phosphoinositide kinase, FYVE finger containing"	protein-coding	0.01	0.306931
Merged-chr4-26652391-1	chr4	26652341	26652441	+	2.8	cIP2vsInput	"intron (NR_040656, intron 2 of 2)"	Lx9|LINE|L1	53058	NR_040656	75360	Mm.67233	NR_040656	ENSMUSG00000086257	4930548K13Rik	-	RIKEN cDNA 4930548K13 gene	miscRNA	0	0.29703
Merged-chr10-60918177-1	chr10	60918127	60918227	+	2.8	cIP2vsInput	Intergenic	Intergenic	19955	NR_033616	73616	Mm.159038	NR_033616	ENSMUSG00000037247	Pldi	1700125F08Rik|Poldi	polymorphic derived intron containing	miscRNA	0	0.554455
Merged-chr4-62911967-1	chr4	62911917	62912017	+	2.8	cIP1vsInput	Intergenic	Intergenic	-53607	NM_028326	72701	Mm.482416	NM_028326	ENSMUSG00000028358	Zfp618	2810031P15Rik|2810040O04Rik|AI415580|AI505139|D430033D05Rik|Nedd10|Znf618|bM257P7.1	zinc finger protein 618	protein-coding	0.01	0.287129
Merged-chr1-151667755-1	chr1	151667705	151667805	+	2.8	cIP2vsInput	"intron (NM_022018, intron 5 of 13)"	"intron (NM_022018, intron 5 of 13)"	-87619	NM_001039644	66967	Mm.337691	NM_001039644	ENSMUSG00000043019	Edem3	2310050N11Rik	"ER degradation enhancer, mannosidase alpha-like 3"	protein-coding	0	0.346535
Merged-chr16-17619308-1	chr16	17619258	17619358	+	2.8	cIP2vsInput	promoter-TSS (NM_001164609)	promoter-TSS (NM_001164609)	-46	NM_001164610	77626	Mm.34659	NM_001164609	ENSMUSG00000005899	Smpd4	4122402O22Rik|mKIAA1418	sphingomyelin phosphodiesterase 4	protein-coding	0.07	0.524752
Merged-chr8-6072751-1	chr8	6072701	6072801	+	2.8	cIP2vsInput	Intergenic	Intergenic	-967519	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0.01	0.326733
Merged-chr4-24628076-1	chr4	24628026	24628126	+	2.8	cIP2vsInput	"intron (NM_001033531, intron 8 of 9)"	"intron (NM_001033531, intron 8 of 9)"	131614	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	"MMS22-like, DNA repair protein"	protein-coding	0	0.425743
Merged-chr5-14229256-1	chr5	14229206	14229306	+	2.8	cIP2vsInput	"intron (NM_011348, intron 9 of 16)"	"intron (NM_011348, intron 9 of 16)"	203980	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	"sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E"	protein-coding	0.01	0.316832
Merged-chr3-114131374-1	chr3	114131324	114131424	+	2.8	cIP1vsInput	"intron (NM_007729, intron 29 of 66)"	"intron (NM_007729, intron 29 of 66)"	100834	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	"collagen, type XI, alpha 1"	protein-coding	0	0.356436
Merged-chr16-86181218-1	chr16	86181168	86181268	+	2.8	cIP1vsInput	Intergenic	Intergenic	-280093	NM_011782	23794	Mm.437478	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|AI481094|ASMP-2	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"	protein-coding	0	0.306931
Merged-chr13-58035466-1	chr13	58035416	58035516	+	2.8	cIP2vsInput	"intron (NM_001195075, intron 8 of 16)"	"intron (NM_001195075, intron 8 of 16)"	-12266	NR_030544	100124491		NR_030544		Mir874	Mirn874|mmu-mir-874	microRNA 874	miscRNA	0.01	0.346535
Merged-chr8-99356357-1	chr8	99356307	99356407	+	2.8	cIP2vsInput	"intron (NM_001039154, intron 2 of 12)"	RMER5|LTR|ERV1	60100	NM_007667	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.366337
Merged-chr18-30272750-1	chr18	30272700	30272800	+	2.8	cIP1vsInput	promoter-TSS (NM_181414)	promoter-TSS (NM_181414)	-146	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	"phosphoinositide-3-kinase, class 3"	protein-coding	0.02	0.554455
Merged-chr10-25296929-1	chr10	25296879	25296979	+	2.8	cIP2vsInput	"intron (NM_018747, intron 1 of 7)"	CpG	2234	NM_018747	432442	Mm.487103	NM_018747		Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding	0.17	0.831683
Merged-chr18-40969041-1	chr18	40968991	40969091	+	2.8	cIP1vsInput	Intergenic	Intergenic	710680	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding	0	0.336634
Merged-chr1-78488872-1	chr1	78488822	78488922	+	2.8	cIP1vsInput	promoter-TSS (NM_011811)	promoter-TSS (NM_011811)	-26	NM_011811	23874	Mm.447792	NM_011811	ENSMUSG00000026245	Farsb	C76708|Farsa|Farsl|Farslb|Frsb	"phenylalanyl-tRNA synthetase, beta subunit"	protein-coding	0.11	0.653465
Merged-chr13-104948217-1	chr13	104948167	104948267	+	2.8	cIP2vsInput	"3' UTR (NM_029879, exon 6 of 6)"	"3' UTR (NM_029879, exon 6 of 6)"	-84324	NM_029984	77803	Mm.159995	NM_029984	ENSMUSG00000042655	Fam159b	A930021C24Rik	"family with sequence similarity 159, member B"	protein-coding	0.03	0.60396
Merged-chrX-65866499-1	chrX	65866449	65866549	+	2.8	cIP2vsInput	Intergenic	Intergenic	-782819	NM_001161431	245450	Mm.403134	NM_001161431	ENSMUSG00000036790	Slitrk2	A930040J07	"SLIT and NTRK-like family, member 2"	protein-coding	0	0.326733
Merged-chr6-99349076-1	chr6	99349026	99349126	+	2.8	cIP2vsInput	"intron (NM_053202, intron 1 of 18)"	"intron (NM_053202, intron 1 of 18)"	-82561	NM_001197321	108655	Mm.485266	NM_001197321	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding	0	0.277228
Merged-chr15-81836604-1	chr15	81836554	81836654	+	2.8	cIP1vsInput	Intergenic	Intergenic	21722	NM_020507	57259	Mm.323595	NM_020507	ENSMUSG00000048546	Tob2	2900090N22Rik|4930545K18Rik|AV071822|mKIAA1663	"transducer of ERBB2, 2"	protein-coding	0.11	0.683168
Merged-chr6-18086781-1	chr6	18086731	18086831	+	2.8	cIP2vsInput	"intron (NM_023729, intron 4 of 12)"	"intron (NM_023729, intron 4 of 12)"	22280	NM_023729	74068	Mm.73091	NM_023729	ENSMUSG00000010796	Asz1	4933400N19Rik|Gasz|ORF3	"ankyrin repeat, SAM and basic leucine zipper domain containing 1"	protein-coding	0	0.316832
Merged-chr1-54536244-1	chr1	54536194	54536294	+	2.8	cIP1vsInput	"intron (NM_001163314, intron 4 of 26)"	"intron (NM_001163314, intron 4 of 26)"	21440	NM_001163314	241062	Mm.103539	NM_175508	ENSMUSG00000073678	Pgap1	5033403E17Rik|9030223K07Rik|A530084K22|D230012E17Rik|oto	post-GPI attachment to proteins 1	protein-coding	0	0.326733
Merged-chr2-72169599-1	chr2	72169549	72169649	+	2.8	cIP2vsInput	"intron (NM_019688, intron 6 of 29)"	"intron (NM_019688, intron 6 of 29)"	114982	NM_001204166	56508	Mm.196153	NM_001204165	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding	0.04	0.534653
Merged-chr12-30584224-1	chr12	30584174	30584274	+	2.8	cIP2vsInput	promoter-TSS (NM_172049)	promoter-TSS (NM_172049)	-219	NM_172049	211986	Mm.34035	NM_172049	ENSMUSG00000043061	Tmem18	BC024093	transmembrane protein 18	protein-coding	0.06	0.653465
Merged-chr13-18933636-2	chr13	18933586	18933687	+	2.8	cIP1vsInput|cIP2vsInput	Intergenic	ETnERV3-int|LTR|ERVK	-14735	NM_175007	218038	Mm.101650	NM_175007	ENSMUSG00000021314	Amph	-	amphiphysin	protein-coding	0	0.245098
Merged-chr5-105415030-1	chr5	105414980	105415080	+	2.8	cIP1vsInput	promoter-TSS (NM_001033550)	promoter-TSS (NM_001033550)	-745	NM_001033550	433926	Mm.439828	NM_001033550	ENSMUSG00000070639	Lrrc8b	R75581|Ta-lrrp|mKIAA0231	"leucine rich repeat containing 8 family, member B"	protein-coding	0	0.405941
Merged-chr13-101323105-1	chr13	101323055	101323155	+	2.8	cIP2vsInput	Intergenic	Intergenic	68786	NR_045846	71174	Mm.399537	NR_045846		4933416M06Rik	-	RIKEN cDNA 4933416M06 gene	miscRNA	0	0.326733
Merged-chr3-8603084-1	chr3	8603034	8603134	+	2.8	cIP2vsInput	Intergenic	Intergenic	63954	NM_010423	15213	Mm.29581	NM_010423	ENSMUSG00000040289	Hey1	AI316788|AI414254|CHF2|HRT1|Herp2|Hesr1|bHLHb31|hesr-1	hairy/enhancer-of-split related with YRPW motif 1	protein-coding	0.01	0.455446
Merged-chr5-14692524-1	chr5	14692474	14692574	+	2.8	cIP2vsInput	"intron (NM_011995, intron 6 of 24)"	"intron (NM_011995, intron 6 of 24)"	177606	NM_001110796	26875	Mm.146275	NM_001110796	ENSMUSG00000061601	Pclo	Acz|Pico|mKIAA0559	piccolo (presynaptic cytomatrix protein)	protein-coding	0	0.316832
Merged-chr10-23081424-1	chr10	23081374	23081474	+	2.8	cIP2vsInput	Intergenic	Intergenic	-261296	NM_011545	21412	Mm.16497	NM_011545	ENSMUSG00000045680	Tcf21	Pod-1|Pod1|bHLHa23|capsulin|epc|epicardin	transcription factor 21	protein-coding	0.04	0.455446
Merged-chr13-111881651-1	chr13	111881601	111881701	+	2.8	cIP2vsInput	Intergenic	Lx8|LINE|L1	-72668	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding	0.02	0.336634
Merged-chr6-133713523-1	chr6	133713473	133713573	+	2.8	cIP2vsInput	Intergenic	Intergenic	53880	NM_001177652	545886	Mm.449716	NM_001177652		Gm5886	EG545886|smarp	predicted gene 5886	protein-coding	0	0.366337
Merged-chr8-19950021-1	chr8	19949971	19950071	+	2.8	cIP1vsInput	"intron (NM_001270553, intron 6 of 9).2"	RLTR28|LTR|ERVL	220445	NM_001039553	626415	Mm.425517	NM_001039553		4930467E23Rik	ENSMUSG00000074453|OTTMUSG00000018948|TSAP	RIKEN cDNA 4930467E23 gene	protein-coding	0	0.356436
Merged-chr12-114727734-1	chr12	114727684	114727784	+	2.8	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	1183826	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding	0	0.306931
Merged-chr7-113584256-1	chr7	113584206	113584306	+	2.8	cIP1vsInput	Intergenic	Lx5b|LINE|L1	70394	NM_027379	67420	Mm.477631	NM_026143	ENSMUSG00000030759	Far1	2600011M19Rik|2900034E22Rik|3732409C05Rik|AI850429|Mlstd2	fatty acyl CoA reductase 1	protein-coding	0	0.326733
Merged-chr7-83813843-1	chr7	83813793	83813893	+	2.8	cIP2vsInput	Intergenic	Intergenic	-19004	NM_029335	75556	Mm.17649	NM_029335	ENSMUSG00000011154	1700026D08Rik	AW047638|AW551802	RIKEN cDNA 1700026D08 gene	protein-coding	0	0.455446
Merged-chr16-21204782-1	chr16	21204732	21204832	+	2.8	cIP2vsInput	promoter-TSS (NM_010143)	promoter-TSS (NM_010143)	-13	NM_010143	13845	Mm.6972	NM_010143	ENSMUSG00000005958	Ephb3	AW456895|Cek10|Etk2|HEK2|MDK5|Sek4|Tyro6	Eph receptor B3	protein-coding	0.11	0.712871
Merged-chr19-31196678-1	chr19	31196628	31196728	+	2.8	cIP2vsInput	"intron (NM_001013833, intron 3 of 17)"	"intron (NM_001013833, intron 3 of 17)"	19718	NR_002849	78103	Mm.445198	NR_002849		8430431K14Rik	-	RIKEN cDNA 8430431K14 gene	miscRNA	0.01	0.326733
Merged-chr16-49873519-1	chr16	49873469	49873569	+	2.8	cIP2vsInput	"intron (NM_010581, intron 3 of 9)"	L1_Mur3|LINE|L1	17865	NM_010581	16423	Mm.390865	NM_010581		Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	"CD47 antigen (Rh-related antigen, integrin-associated signal transducer)"	protein-coding	0	0.336634
Merged-chr5-15677957-1	chr5	15677907	15678007	+	2.8	cIP2vsInput	Intergenic	MTD|LTR|ERVL-MaLR	-2753	NR_001585	75858	Mm.359463	NR_001585	ENSMUSG00000089871	Speer7-ps1	4930568L21Rik|SPEER-7|Speer7-ps	"spermatogenesis associated glutamate (E)-rich protein 7, pseudogene 1"	pseudo	0	0.445545
Merged-chr2-121448808-1	chr2	121448758	121448858	+	2.8	cIP1vsInput	promoter-TSS (NM_011354)	promoter-TSS (NM_011354)	-420	NM_011354	378702	Mm.262252	NM_011354	ENSMUSG00000074884	Serf2	C80083|Msmac1l|m4F5rel	small EDRK-rich factor 2	protein-coding	0.02	0.475248
Merged-chr12-85809991-1	chr12	85809941	85810041	+	2.8	cIP2vsInput	"intron (NM_145447, intron 9 of 9)"	"intron (NM_145447, intron 9 of 9)"	14554	NM_021446	58520	Mm.143795	NM_021446	ENSMUSG00000021252	0610007P14Rik	1190004E09Rik|AU019315|C77855|ORF11	RIKEN cDNA 0610007P14 gene	protein-coding	0.02	0.465347
Merged-chr9-113708087-1	chr9	113708037	113708137	+	2.8	cIP2vsInput	"exon (NM_001164677, exon 1 of 18)"	"exon (NM_001164677, exon 1 of 18)"	172	NM_001164678	18571	Mm.29816	NM_001164677	ENSMUSG00000032504	Pdcd6ip	AI480591|AW544830|Aip1|Alix|C76364|Eig2|mKIAA1375	programmed cell death 6 interacting protein	protein-coding	0.11	0.683168
Merged-chr15-27295960-1	chr15	27295910	27296010	+	2.8	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-170717	NM_020332	11732	Mm.265264	NM_020332	ENSMUSG00000022265	Ank	Ankh|D15Ertd221e|ank|mKIAA1581	progressive ankylosis	protein-coding	0	0.336634
Merged-chr5-63055341-1	chr5	63055291	63055391	+	2.8	cIP2vsInput	Intergenic	Intergenic	241518	NM_001170705	100322896	Mm.479821	NM_001170705	ENSMUSG00000090326	Gm17384	Dthd1	"predicted gene, 17384"	protein-coding	0	0.326733
Merged-chr5-70935965-1	chr5	70935915	70936015	+	2.8	cIP2vsInput	Intergenic	Intergenic	-93348	NM_010252	14405	Mm.255292	NM_010252	ENSMUSG00000001260	Gabrg1	GabaA|GabaA/BZ	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1"	protein-coding	0.01	0.346535
Merged-chr15-20195567-1	chr15	20195517	20195617	+	2.8	cIP1vsInput	Intergenic	RMER5|LTR|ERV1	471183	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding	0	0.356436
Merged-chr4-108847622-2	chr4	108847571	108847673	+	2.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_029571)	promoter-TSS (NM_029571)	-235	NM_029571	100087	Mm.440007	NM_029571	ENSMUSG00000073775	Kti12	1110001A12Rik|AI326810|AU014758	"KTI12 homolog, chromatin associated (S. cerevisiae)"	protein-coding	0.019608	0.368932
Merged-chr16-10358012-1	chr16	10357962	10358062	+	2.8	cIP2vsInput	Intergenic	Intergenic	37436	NM_001099275	70426	Mm.142181	NM_001099275	ENSMUSG00000039179	Tekt5	3300001K11Rik	tektin 5	protein-coding	0.05	0.49505
Merged-chr14-110995211-1	chr14	110995161	110995261	+	2.8	cIP2vsInput	Intergenic	Intergenic	-240062	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	"SLIT and NTRK-like family, member 6"	protein-coding	0	0.29703
Merged-chr14-69707422-1	chr14	69707372	69707472	+	2.8	cIP2vsInput	"intron (NM_001146012, intron 1 of 7)"	CpG	158	NM_001146012	71843	Mm.27738	NM_001146012	ENSMUSG00000034194	R3hcc1	1700020M16Rik|AA407796	R3H domain and coiled-coil containing 1	protein-coding	0.12	0.633663
Merged-chr16-38902374-1	chr16	38902324	38902424	+	2.8	cIP2vsInput	promoter-TSS (NM_170599)	promoter-TSS (NM_170599)	29	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	"immunoglobulin superfamily, member 11"	protein-coding	0.15	0.821782
Merged-chr7-119793944-1	chr7	119793894	119793994	+	2.8	cIP2vsInput	promoter-TSS (NM_028129)	promoter-TSS (NM_028129)	114	NM_027698	71151	Mm.274160	NM_027698		Eri2	4933424N09Rik|Exod1|mKIAA1504	exoribonuclease 2	protein-coding	0.1	0.653465
Merged-chr10-61622885-1	chr10	61622835	61622935	+	2.8	cIP1vsInput	"intron (NM_001177511, intron 2 of 3)"	L1MC4a|LINE|L1	-25736	NM_026438	67895	Mm.28897	NM_026438	ENSMUSG00000020089	Ppa1	2010317E03Rik|Pyp	pyrophosphatase (inorganic) 1	protein-coding	0	0.356436
Merged-chr10-37836826-1	chr10	37836776	37836876	+	2.8	cIP2vsInput	Intergenic	Intergenic	-697900	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding	0	0.316832
Merged-chr14-80666769-1	chr14	80666719	80666819	+	2.8	cIP1vsInput	Intergenic	Intergenic	666467	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.29703
Merged-chr5-65335747-1	chr5	65335697	65335797	+	2.8	cIP1vsInput	promoter-TSS (NM_011258)	promoter-TSS (NM_011258)	-108	NM_011258	19687	Mm.148877	NM_011258	ENSMUSG00000029191	Rfc1	140kDa|Alp145|RFC140|Recc1	replication factor C (activator 1) 1	protein-coding	0.11	0.683168
Merged-chr4-109816887-1	chr4	109816837	109816937	+	2.8	cIP2vsInput	"intron (NM_007983, intron 8 of 18)"	"intron (NM_007983, intron 8 of 18)"	140260	NM_007983	14084	Mm.318259	NM_007983	ENSMUSG00000010517	Faf1	AA408698|Dffrx|Fam	Fas-associated factor 1	protein-coding	0	0.326733
Merged-chr11-88187823-1	chr11	88187773	88187873	+	2.8	cIP2vsInput	"intron (NM_198013, intron 7 of 10)"	"intron (NM_198013, intron 7 of 10)"	-16595	NM_024174	64656	Mm.168680	NM_024174	ENSMUSG00000023723	Mrps23	2310047I09Rik|D11Bwg1153e|Rpms23	mitochondrial ribosomal protein S23	protein-coding	0.04	0.643564
Merged-chr18-9237294-1	chr18	9237244	9237344	+	2.8	cIP2vsInput	Intergenic	Intergenic	24438	NM_008058	14370	Mm.184289	NM_008058	ENSMUSG00000036904	Fzd8	Fz8	frizzled homolog 8 (Drosophila)	protein-coding	0.01	0.415842
Merged-chr15-73739999-1	chr15	73739949	73740049	+	2.8	cIP2vsInput	"intron (NM_001166388, intron 1 of 5)"	"intron (NM_001166388, intron 1 of 5)"	-8027	NM_008975	19245	Mm.390807	NM_001166388	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding	0.05	0.683168
Merged-chr1-183113196-1	chr1	183113146	183113246	+	2.8	cIP2vsInput	"intron (NM_026866, intron 4 of 9)"	"intron (NM_026866, intron 4 of 9)"	108333	NM_026866	68897	Mm.358721	NM_026866	ENSMUSG00000030768	Disp1	1190008H24Rik|DispA	dispatched homolog 1 (Drosophila)	protein-coding	0.01	0.544554
Merged-chr10-93959601-1	chr10	93959551	93959651	+	2.8	cIP2vsInput	Intergenic	Intergenic	4262	NR_029764	723908		NR_029764	ENSMUSG00000065607	Mir331	Mirn331|mmu-mir-331	microRNA 331	miscRNA	0.01	0.366337
Merged-chr6-17055691-1	chr6	17055641	17055741	+	2.8	cIP1vsInput	Intergenic	Intergenic	-9458	NM_207176	21753	Mm.436548	NM_011570	ENSMUSG00000029552	Tes	D6Ertd352e|TESS|Tes1|Tes2|testin2	testis derived transcript	protein-coding	0	0.366337
Merged-chr8-101080496-1	chr8	101080446	101080546	+	2.8	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-1664039	NM_001039154	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0.01	0.326733
Merged-chr3-50906066-1	chr3	50906016	50906116	+	2.8	cIP2vsInput	Intergenic	Intergenic	-318381	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Ccrn4l	AU043840|Ccr4|nocturnin	CCR4 carbon catabolite repression 4-like (S. cerevisiae)	protein-coding	0.02	0.445545
Merged-chr16-20673019-1	chr16	20672969	20673069	+	2.8	cIP2vsInput	"intron (NM_001005331, intron 1 of 31)"	CpG	270	NM_001005331	208643	Mm.260256	NM_001005331	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF4GI	"eukaryotic translation initiation factor 4, gamma 1"	protein-coding	0.12	0.831683
Merged-chr3-155210487-1	chr3	155210437	155210537	+	2.8	cIP2vsInput	Intergenic	Intergenic	117053	NM_028938	74435	Mm.195711	NM_028938	ENSMUSG00000028182	Lrriq3	4930438B07Rik|4930511J15Rik|4933403H06Rik|BB020367|Lrrc44	leucine-rich repeats and IQ motif containing 3	protein-coding	0	0.326733
Merged-chr4-6190942-1	chr4	6190892	6190992	+	2.8	cIP2vsInput	promoter-TSS (NM_026534)	promoter-TSS (NM_026534)	-163	NM_026534	68053	Mm.427021	NM_026534		Ubxn2b	3110003A22Rik|6430407D20Rik|AI451665|p37	UBX domain protein 2B	protein-coding	0.07	0.594059
Merged-chr8-54629327-1	chr8	54629277	54629377	+	2.8	cIP1vsInput	TTS (NM_028220)	TTS (NM_028220)	28546	NM_133711	69281	Mm.45833	NM_133711	ENSMUSG00000031518	Spata4	1700001N01Rik|Srg2|TSARG2	spermatogenesis associated 4	protein-coding	0.01	0.277228
Merged-chr18-43773134-1	chr18	43773084	43773184	+	2.8	cIP1vsInput	Intergenic	Intergenic	8807	NM_054038	117158	Mm.210437	NM_054038	ENSMUSG00000038791	Scgb3a2	LuLeu1|Pnsp1|UGRP1|Utgrp1	"secretoglobin, family 3A, member 2"	protein-coding	0	0.287129
Merged-chr6-124662640-1	chr6	124662590	124662690	+	2.8	cIP2vsInput	promoter-TSS (NM_145130)	promoter-TSS (NM_145130)	-464	NM_145130	14792	Mm.273915	NM_145130	ENSMUSG00000004270	Lpcat3	C3f|Grcc3f|Lpcat|Lpeat|Lplat5|Lpsat|Mboat5|Moact5|Oact5|PTG	lysophosphatidylcholine acyltransferase 3	protein-coding	0.09	0.70297
Merged-chr8-104534475-1	chr8	104534425	104534525	+	2.8	cIP2vsInput	"intron (NM_144931, intron 1 of 19)"	CpG	162	NM_144931	234664	Mm.237670	NM_144931	ENSMUSG00000031878	Nae1	59kDa|Appbp1	NEDD8 activating enzyme E1 subunit 1	protein-coding	0.08	0.70297
Merged-chr9-20544666-1	chr9	20544616	20544716	+	2.8	cIP1vsInput	Intergenic	Intergenic	-23247	NM_001082485	77519	Mm.431849	NM_001082485	ENSMUSG00000060510	Zfp266	5330440G10Rik|5730601F06Rik|AW552317	zinc finger protein 266	protein-coding	0.14	0.693069
Merged-chr9-114785387-1	chr9	114785337	114785437	+	2.8	cIP1vsInput	Intergenic	RLTR28B|LTR|ERVL	-3394	NM_001252479	102545	Mm.35600	NM_001252479	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding	0.02	0.455446
Merged-chr7-102222470-1	chr7	102222420	102222520	+	2.8	cIP2vsInput	promoter-TSS (NM_145583)	promoter-TSS (NM_145583)	-604	NM_145583	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding	0.04	0.544554
Merged-chr15-96339553-1	chr15	96339503	96339603	+	2.8	cIP2vsInput	"intron (NM_175251, intron 3 of 20)"	"intron (NM_175251, intron 3 of 20)"	52031	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	"AT rich interactive domain 2 (ARID, RFX-like)"	protein-coding	0.01	0.386139
Merged-chr11-31671894-1	chr11	31671844	31671944	+	2.8	cIP2vsInput	promoter-TSS (NM_001024919)	promoter-TSS (NM_001024919)	-32	NM_001024919	69556	Mm.34183	NM_001024919	ENSMUSG00000044502	Bod1	2310022M17Rik|BOD2.1|Fam44b	biorientation of chromosomes in cell division 1	protein-coding	0.11	0.613861
Merged-chr6-113326899-1	chr6	113326849	113326949	+	2.8	cIP2vsInput	promoter-TSS (NM_010957)	promoter-TSS (NM_010957)	-77	NM_010957	18294	Mm.43612	NM_010957	ENSMUSG00000030271	Ogg1	Mmh	8-oxoguanine DNA-glycosylase 1	protein-coding	0.1	0.663366
Merged-chrY-6581835-1	chrY	6581785	6581885	+	2.8	cIP2vsInput	Intergenic	B2_Mm2|SINE|B2	585942	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.306931
Merged-chr19-7217432-1	chr19	7217382	7217482	+	2.8	cIP2vsInput	"exon (NM_007750, exon 1 of 2)"	"exon (NM_007750, exon 1 of 2)"	184	NM_007750	12868	Mm.14022	NM_007750	ENSMUSG00000035885	Cox8a	COX8L	cytochrome c oxidase subunit VIIIa	protein-coding	0.14	0.762376
Merged-chr1-177074007-1	chr1	177073957	177074057	+	2.8	cIP2vsInput	"intron (NM_011785, intron 7 of 12)"	L1M2|LINE|L1	174760	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding	0.02	0.316832
Merged-chr17-56989965-1	chr17	56989915	56990015	+	2.8	cIP2vsInput	promoter-TSS (NM_017393)	promoter-TSS (NM_017393)	-299	NM_017393	53895	Mm.287892	NM_017393	ENSMUSG00000002660	Clpp	AU019820|D17Wsu160e	"ClpP caseinolytic peptidase, ATP-dependent, proteolytic subunit"	protein-coding	0.04	0.524752
Merged-chr5-13118145-1	chr5	13118095	13118195	+	2.8	cIP1vsInput	Intergenic	MTB_Mm|LTR|ERVL-MaLR	-278639	NM_001243072	20346	Mm.483774	NM_001243072	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	"sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A"	protein-coding	0	0.326733
Merged-chr1-155813040-1	chr1	155812990	155813090	+	2.8	cIP2vsInput	promoter-TSS (NM_023268)	promoter-TSS (NM_023268)	-141	NM_001024945	104009	Mm.27035	NM_001024945	ENSMUSG00000033684	Qsox1	1300003H02Rik|QSOX|Qscn6|SOx	quiescin Q6 sulfhydryl oxidase 1	protein-coding	0.13	0.732673
Merged-chr1-160646905-1	chr1	160646855	160646955	+	2.8	cIP1vsInput	"intron (NM_013862, intron 11 of 20)"	"intron (NM_013862, intron 11 of 20)"	-69152	NM_001146330	620246	Mm.478780	NM_001146330		Gpr52	EG620246	G protein-coupled receptor 52	protein-coding	0	0.306931
Merged-chr8-33312421-1	chr8	33312371	33312471	+	2.8	cIP2vsInput	"intron (NM_001122822, intron 15 of 33)"	L1VL2|LINE|L1	73106	NM_001122822	22427	Mm.228805	XM_003946269	ENSMUSG00000031583	Wrn	AI846146	Werner syndrome homolog (human)	protein-coding	0	0.326733
Merged-chr8-39755073-1	chr8	39755023	39755123	+	2.8	cIP2vsInput	"intron (NR_035426, intron 3 of 5)"	"intron (NR_035426, intron 3 of 5)"	-112395	NM_001113326	20288	Mm.239291	NM_001113326	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding	0.01	0.326733
Merged-chr15-38384485-1	chr15	38384435	38384535	+	2.8	cIP2vsInput	Intergenic	Intergenic	-83778	NM_013692	21847	Mm.4292	NM_013692	ENSMUSG00000037465	Klf10	AI115143|EGR[a]|Egral|Gdnfif|Tieg|Tieg1|mGIF	Kruppel-like factor 10	protein-coding	0.01	0.673267
Merged-chr1-51017684-1	chr1	51017634	51017734	+	2.8	cIP2vsInput	"intron (NM_019790, intron 4 of 9)"	"intron (NM_019790, intron 4 of 9)"	90161	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0.01	0.356436
Merged-chr16-94544853-1	chr16	94544803	94544903	+	2.8	cIP1vsInput	Intergenic	Intergenic	-18224	NM_007834	13185	Mm.7472	NM_007834	ENSMUSG00000022898	Dscr3	AW538125|Dcra	Down syndrome critical region gene 3	protein-coding	0.03	0.485149
Merged-chr1-50666710-1	chr1	50666660	50666760	+	2.8	cIP1vsInput	Intergenic	Lx8b|LINE|L1	-260813	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.287129
Merged-chr16-29873436-1	chr16	29873386	29873486	+	2.8	cIP1vsInput	Intergenic	L1ME2|LINE|L1	105688	NR_037689	328657	Mm.425982	NM_001033403		Gm1968	-	predicted gene 1968	miscRNA	0	0.29703
Merged-chr10-126919316-1	chr10	126919266	126919366	+	2.8	cIP1vsInput	Intergenic	Intergenic	-17945	NM_001159559	68876	Mm.276769	NM_001159559	ENSMUSG00000025436	Xrcc6bp1	1110068E08Rik|2410012H02Rik	XRCC6 binding protein 1	protein-coding	0.01	0.524752
Merged-chr1-29243667-1	chr1	29243617	29243717	+	2.8	cIP2vsInput	Intergenic	Lx|LINE|L1	-463415	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0	0.356436
Merged-chr7-16098450-1	chr7	16098400	16098500	+	2.8	cIP2vsInput	promoter-TSS (NM_025898)	promoter-TSS (NM_025898)	-193	NM_025898	108124	Mm.431371	NM_025898	ENSMUSG00000006024	Napa	1500039N14Rik|AW209189|RA81|SNAPA|SNARE|a-SNAP|hyh	N-ethylmaleimide sensitive fusion protein attachment protein alpha	protein-coding	0.07	0.70297
Merged-chr7-24399783-1	chr7	24399733	24399833	+	2.8	cIP2vsInput	"5' UTR (NM_028047, exon 1 of 14)"	"5' UTR (NM_028047, exon 1 of 14)"	155	NM_028047	71997	Mm.150977	NM_028047	ENSMUSG00000002210	Smg9	1500002O20Rik|AI429693|N28092	"smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)"	protein-coding	0.07	0.633663
Merged-chr2-31654476-1	chr2	31654426	31654526	+	2.8	cIP2vsInput	"exon (NM_001123362, exon 5 of 5)"	"exon (NM_001123362, exon 5 of 5)"	14439	NM_001123362	381359	Mm.379512	NM_001123362	ENSMUSG00000079466	Prdm12	Gm998	PR domain containing 12	protein-coding	0.19	0.821782
Merged-chr14-72887059-1	chr14	72887009	72887109	+	2.8	cIP2vsInput	Intergenic	L1MD3|LINE|L1	-138544	NR_027860	668489	Mm.491075	NR_027860		Gm9199	EG668489	glycine cleavage system protein H (aminomethyl carrier) pseudogene	pseudo	0.03	0.445545
Merged-chr13-63431479-1	chr13	63431429	63431529	+	2.8	cIP2vsInput	"5' UTR (NM_007985, exon 1 of 15)"	"5' UTR (NM_007985, exon 1 of 15)"	266	NM_007985	14088	Mm.126106	NM_001042673	ENSMUSG00000021461	Fancc	BB116513|Facc	"Fanconi anemia, complementation group C"	protein-coding	0.16	0.712871
Merged-chr10-37942389-1	chr10	37942339	37942439	+	2.8	cIP2vsInput	Intergenic	RMER6A|LTR|ERVK	-803463	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding	0	0.415842
Merged-chr11-87142186-1	chr11	87142136	87142236	+	2.8	cIP2vsInput	"intron (NM_197987, intron 4 of 23)"	"intron (NM_197987, intron 4 of 23)"	15111	NM_197987	68729	Mm.17436	NM_197987	ENSMUSG00000018548	Trim37	1110032A10Rik|2810004E07Rik|AI848587|AU043018|MUL|TEF3|mKIAA0898	tripartite motif-containing 37	protein-coding	0	0.277228
Merged-chr14-110724429-1	chr14	110724379	110724479	+	2.8	cIP2vsInput	Intergenic	Intergenic	30720	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	"SLIT and NTRK-like family, member 6"	protein-coding	0	0.346535
Merged-chr6-34072227-1	chr6	34072177	34072277	+	2.8	cIP2vsInput	"intron (NM_028886, intron 8 of 19)"	"intron (NM_028886, intron 8 of 19)"	42779	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding	0.01	0.514851
Merged-chr11-70764006-1	chr11	70763956	70764056	+	2.8	cIP2vsInput	promoter-TSS (NM_177565)	promoter-TSS (NM_177565)	-441	NM_177565	193043	Mm.40966	NM_177565	ENSMUSG00000043602	Zfp3	AI854635|B230309J24|Fnp-1|RP23-326P7.13|Zfp-3	zinc finger protein 3	protein-coding	0.03	0.574257
Merged-chr5-55371891-1	chr5	55371841	55371941	+	2.8	cIP2vsInput	Intergenic	Lx8b|LINE|L1	1021899	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0	0.316832
Merged-chr16-77105441-1	chr16	77105391	77105491	+	2.8	cIP2vsInput	"intron (NM_013918, intron 18 of 23)"	"intron (NM_013918, intron 18 of 23)"	91372	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding	0.01	0.29703
Merged-chr8-22209236-1	chr8	22209186	22209286	+	2.8	cIP2vsInput	"intron (NM_027338, intron 6 of 13)"	"intron (NM_027338, intron 6 of 13)"	16376	NM_027338	70160	Mm.41453	NM_027338		Vps36	1700010A24Rik|2210415M20Rik|2810408E15Rik|Eap45	vacuolar protein sorting 36 (yeast)	protein-coding	0.01	0.524752
Merged-chr13-30444627-1	chr13	30444577	30444677	+	2.8	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	100689	NM_025710	66694	Mm.181933	NM_025710	ENSMUSG00000038462	Uqcrfs1	4430402G14Rik|AI875505	"ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1"	protein-coding	0	0.386139
Merged-chr10-104489314-1	chr10	104489264	104489364	+	2.8	cIP2vsInput	Intergenic	Intergenic	295272	NM_001270900	667692		NM_001270900	ENSMUSG00000097878	Gm8764	EG667692	predicted gene 8764	protein-coding	0.01	0.336634
Merged-chr3-150395148-1	chr3	150395098	150395198	+	2.8	cIP2vsInput	Intergenic	Intergenic	-1042734	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0	0.29703
Merged-chr1-160287418-1	chr1	160287368	160287468	+	2.8	cIP2vsInput	"intron (NM_001038621, intron 2 of 8)"	"intron (NM_001038621, intron 2 of 8)"	64153	NM_001038621	29809	Mm.25833	NM_001038621	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding	0	0.376238
Merged-chr2-114336875-1	chr2	114336825	114336925	+	2.8	cIP2vsInput	Intergenic	Intergenic	-135443	NM_175466	228491	Mm.132523	NM_175466	ENSMUSG00000040321	Zfp770	6430601A21Rik|Znf770	zinc finger protein 770	protein-coding	0	0.306931
Merged-chr7-59259381-1	chr7	59259331	59259431	+	2.8	cIP2vsInput	"intron (NM_001033962, intron 2 of 10)"	L1M2|LINE|L1	29785	NR_033229	613263	Mm.404221	NR_033229		A230073K19Rik	-	RIKEN cDNA A230073K19 gene	miscRNA	0	0.237624
Merged-chr1-84992585-1	chr1	84992535	84992635	+	2.8	cIP1vsInput	Intergenic	Intergenic	-57502	NM_027921	71781	Mm.158754	NM_027921		Slc16a14	1110004H10Rik	"solute carrier family 16 (monocarboxylic acid transporters), member 14"	protein-coding	0.02	0.514851
Merged-chr4-102269825-1	chr4	102269775	102269875	+	2.8	cIP1vsInput	"intron (NM_019840, intron 1 of 14)"	"intron (NM_019840, intron 1 of 14)"	14886	NM_019840	18578	Mm.20181	NM_001177980	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	"phosphodiesterase 4B, cAMP specific"	protein-coding	0	0.346535
Merged-chr9-99568791-1	chr9	99568741	99568841	+	2.8	cIP1vsInput	"5' UTR (NM_028768, exon 1 of 22)"	"5' UTR (NM_028768, exon 1 of 22)"	108	NM_001166138	74125	Mm.234823	NM_001166138	ENSMUSG00000032468	Armc8	1200015K23Rik|Gid5|HSPC056	armadillo repeat containing 8	protein-coding	0.1	0.712871
Merged-chr10-42464296-1	chr10	42464246	42464346	+	2.8	cIP2vsInput	"intron (NM_145743, intron 1 of 12)"	"intron (NM_145743, intron 1 of 12)"	14269	NM_145743	215951	Mm.89646	NM_145743	ENSMUSG00000038302	Lace1	CG8520	lactation elevated 1	protein-coding	0.02	0.514851
Merged-chr2-159729480-1	chr2	159729430	159729530	+	2.8	cIP2vsInput	Intergenic	Intergenic	-217861	NR_040498	71081	Mm.383491	NR_040498	ENSMUSG00000085198	4933416E03Rik	-	RIKEN cDNA 4933416E03 gene	miscRNA	0.02	0.534653
Merged-chr2-167672243-1	chr2	167672193	167672293	+	2.8	cIP2vsInput	Intergenic	Intergenic	-10699	NM_145538	407243	Mm.4863	NM_145538		Tmem189	AI840826|Kua	transmembrane protein 189	protein-coding	0.01	0.544554
Merged-chr4-37742630-1	chr4	37742580	37742680	+	2.8	cIP2vsInput	Intergenic	Intergenic	-790886	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.01	0.287129
Merged-chr2-113153512-2	chr2	113153460	113153565	+	2.8	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-66675	NR_035479	100316776		NR_035479		Mir1954	mmu-mir-1954	microRNA 1954	miscRNA	0	0.471698
Merged-chr1-145343701-1	chr1	145343651	145343751	+	2.8	cIP1vsInput	Intergenic	Intergenic	-568280	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding	0	0.267327
Merged-chr9-50617215-1	chr9	50617165	50617265	+	2.8	cIP2vsInput	promoter-TSS (NM_028300)	promoter-TSS (NM_028300)	-106	NM_028300	72614	Mm.147232	NM_028300	ENSMUSG00000000167	Pih1d2	2700059L22Rik	PIH1 domain containing 2	protein-coding	0.11	0.663366
Merged-chr18-64516629-1	chr18	64516579	64516679	+	2.8	cIP1vsInput	promoter-TSS (NM_001142950)	promoter-TSS (NM_001142950)	-72	NM_001142950	70223	Mm.29192	NM_001142950	ENSMUSG00000024587	Nars	3010001M15Rik|AA960128|ASNRS|C78150	asparaginyl-tRNA synthetase	protein-coding	0.08	0.594059
Merged-chr2-81885347-1	chr2	81885297	81885397	+	2.8	cIP1vsInput	Intergenic	Intergenic	-168311	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0	0.336634
Merged-chr4-154011724-2	chr4	154011662	154011787	+	2.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_201226)	promoter-TSS (NM_201226)	-79	NM_201226	72946	Mm.260690	NM_201226	ENSMUSG00000029028	Lrrc47	2900010D03Rik|AA960559|mKIAA1185	leucine rich repeat containing 47	protein-coding	0.088	0.626984
Merged-chr15-36304922-1	chr15	36304872	36304972	+	2.8	cIP2vsInput	Intergenic	Intergenic	-21775	NM_013923	30945	Mm.5181	NM_013923	ENSMUSG00000022280	Rnf19a	AA032313|Dorfin|Rnf19|UIP117|Ubce7ip2|XYbp	ring finger protein 19A	protein-coding	0.01	0.336634
Merged-chr17-24141596-1	chr17	24141546	24141646	+	2.8	cIP2vsInput	promoter-TSS (NM_011062)	promoter-TSS (NM_011062)	-2	NM_011062	18607	Mm.10504	NM_001080773	ENSMUSG00000024122	Pdpk1	Pdk1	3-phosphoinositide dependent protein kinase 1	protein-coding	0.16	0.782178
Merged-chr9-21962560-1	chr9	21962510	21962610	+	2.8	cIP2vsInput	"intron (NM_010149, intron 1 of 7)"	CpG	1016	NM_010149	13857	Mm.2653	NM_010149	ENSMUSG00000006235	Epor	-	erythropoietin receptor	protein-coding	0.09	0.653465
Merged-chr5-137574767-1	chr5	137574717	137574817	+	2.8	cIP1vsInput	"intron (NM_015799, intron 7 of 19)"	CpG	4916	NM_015799	50765	Mm.21757	NM_015799	ENSMUSG00000029716	Tfr2	Trfr2	transferrin receptor 2	protein-coding	0.09	0.663366
Merged-chr6-117841429-1	chr6	117841379	117841479	+	2.8	cIP1vsInput	"intron (NM_177684, intron 1 of 2)"	CpG	187	NM_177684	232337	Mm.290847	NM_177684	ENSMUSG00000059689	Zfp637	AI646709|BC021601|Znf32	zinc finger protein 637	protein-coding	0.09	0.712871
Merged-chr18-37806324-1	chr18	37806274	37806374	+	2.8	cIP2vsInput	promoter-TSS (NM_033581)	promoter-TSS (NM_033581)	-86	NM_033581	93706	Mm.247203	NM_033581	ENSMUSG00000023036	Pcdhgc3	PC43|Pcdh2	"protocadherin gamma subfamily C, 3"	protein-coding	0.08	0.633663
Merged-chr12-71206476-1	chr12	71206426	71206526	+	2.8	cIP2vsInput	"intron (NM_029818, intron 27 of 27)"	"intron (NM_029818, intron 27 of 27)"	69628	NM_001163378	76967	Mm.87290	NM_001163378	ENSMUSG00000034601	2700049A03Rik	Talpid3|mKIAA0586	RIKEN cDNA 2700049A03 gene	protein-coding	0	0.336634
Merged-chr4-43381986-1	chr4	43381936	43382036	+	2.8	cIP2vsInput	promoter-TSS (NM_001037709)	promoter-TSS (NM_001037709)	4	NM_001037709	100213	Mm.235730	NM_001037709	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding	0.18	0.811881
Merged-chr13-117385036-1	chr13	117384986	117385086	+	2.8	cIP2vsInput	Intergenic	Intergenic	164463	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding	0	0.326733
Merged-chr11-115833360-1	chr11	115833310	115833410	+	2.8	cIP2vsInput	"intron (NM_145438, intron 1 of 25)"	"intron (NM_145438, intron 1 of 25)"	9302	NM_001252532	217325	Mm.290450	NM_001252532	ENSMUSG00000020782	Llgl2	9130006H11Rik|Llglh2	lethal giant larvae homolog 2 (Drosophila)	protein-coding	0.02	0.623762
Merged-chr1-60416607-1	chr1	60416557	60416657	+	2.8	cIP1vsInput	"intron (NM_198127, intron 1 of 8)"	L1ME1|LINE|L1	6988	NM_001198570	329165	Mm.465571	NM_001198570	ENSMUSG00000026782	Abi2	8430425M24Rik|AI839867|C130078H13	abl-interactor 2	protein-coding	0	0.336634
Merged-chr10-124382628-1	chr10	124382578	124382678	+	2.8	cIP1vsInput	Intergenic	Intergenic	-86446	NR_028310	75030	Mm.159403	NR_028310		4930503E24Rik	-	"eukaryotic translation initiation factor 3, subunit I pseudogene"	pseudo	0.01	0.425743
Merged-chr1-187215430-1	chr1	187215380	187215480	+	2.8	cIP2vsInput	promoter-TSS (NM_029067)	promoter-TSS (NM_029067)	16	NM_029067	74717	Mm.250430	NM_028848	ENSMUSG00000026611	Spata17	1700065F16Rik|4930504I07Rik|4930513F16Rik|MSRG-11	spermatogenesis associated 17	protein-coding	0.06	0.554455
Merged-chr15-18287521-1	chr15	18287471	18287571	+	2.8	cIP1vsInput	"intron (NR_045711, intron 6 of 11)"	"intron (NR_045711, intron 6 of 11)"	82106	NR_045711	70886	Mm.399021	NR_045711		4921515E04Rik	-	RIKEN cDNA 4921515E04 gene	miscRNA	0	0.306931
Merged-chr5-59427696-1	chr5	59427646	59427746	+	2.8	cIP2vsInput	Intergenic	Intergenic	558306	NR_040683	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0.01	0.29703
Merged-chr11-25320009-1	chr11	25319959	25320059	+	2.8	cIP1vsInput	Intergenic	Intergenic	-6098	NR_045853	71234	Mm.158627	NR_045853	ENSMUSG00000033015	4933427E13Rik	-	RIKEN cDNA 4933427E13 gene	miscRNA	0	0.326733
Merged-chr5-115631677-1	chr5	115631627	115631727	+	2.8	cIP2vsInput	promoter-TSS (NM_198163)	promoter-TSS (NM_198163)	139	NR_027810	66123	Mm.133063	NM_021417		1110006O24Rik	-	RIKEN cDNA 1110006O24 gene	miscRNA	0.09	0.663366
Merged-chr17-24455340-2	chr17	24455262	24455418	+	2.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007893)	promoter-TSS (NM_007893)	-29	NM_007893	13560	Mm.163132	NM_007893	ENSMUSG00000024137	E4f1	-	E4F transcription factor 1	protein-coding	0.115385	0.617834
Merged-chr8-93907989-1	chr8	93907939	93908039	+	2.8	cIP1vsInput	"intron (NM_010308, intron 3 of 8)"	"intron (NM_010308, intron 3 of 8)"	-94434	NR_026888	75809	Mm.443272	NR_026888		4930488L21Rik	4930452J22Rik	RIKEN cDNA 4930488L21 gene	miscRNA	0.02	0.584158
Merged-chr15-97831638-1	chr15	97831588	97831688	+	2.8	cIP2vsInput	"5' UTR (NM_001204276, exon 1 of 26)"	"5' UTR (NM_001204276, exon 1 of 26)"	129	NM_019572	56233	Mm.384027	NM_001204275	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding	0.09	0.752475
Merged-chr6-88106001-1	chr6	88105951	88106051	+	2.8	cIP2vsInput	TTS (NM_133933)	TTS (NM_133933)	21528	NM_133933	103963	Mm.188544	NM_133933	ENSMUSG00000030062	Rpn1	AU018702|D6Wsu137e|Rpn-1	ribophorin I	protein-coding	0.05	0.633663
Merged-chr1-160823487-1	chr1	160823437	160823537	+	2.8	cIP2vsInput	Intergenic	Intergenic	-30549	NM_013862	29809	Mm.25833	NM_001038621	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding	0	0.326733
Merged-chrY-6757840-1	chrY	6757790	6757890	+	2.8	cIP2vsInput	Intergenic	Intergenic	409937	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.39604
Merged-chr11-42887173-1	chr11	42887123	42887223	+	2.8	cIP2vsInput	Intergenic	Intergenic	-262704	NM_176999	319767	Mm.252339	NM_176999	ENSMUSG00000055415	Atp10b	5930426O13Rik|9030605H24Rik	"ATPase, class V, type 10B"	protein-coding	0	0.29703
Merged-chr10-125326027-1	chr10	125325977	125326077	+	2.8	cIP2vsInput	"intron (NM_011391, intron 1 of 6)"	"intron (NM_011391, intron 1 of 6)"	2508	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	"solute carrier family 16 (monocarboxylic acid transporters), member 7"	protein-coding	0	0.326733
Merged-chr1-75124815-1	chr1	75124765	75124865	+	2.8	cIP2vsInput	TTS (NM_194333)	TTS (NM_194333)	9075	NM_194333	22626	Mm.68157	NM_194333	ENSMUSG00000026205	Slc23a3	SVCT3|Yspl1	"solute carrier family 23 (nucleobase transporters), member 3"	protein-coding	0.08	0.623762
Merged-chr17-35134694-1	chr17	35134644	35134744	+	2.8	cIP1vsInput	promoter-TSS (NM_057171)	promoter-TSS (NM_057171)	-484	NM_001252468	224727	Mm.203962	NM_001252468	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding	0.02	0.346535
Merged-chr6-130881475-1	chr6	130881425	130881525	+	2.8	cIP2vsInput	Intergenic	L1VL1|LINE|L1	365887	NM_001170851	16633	Mm.4783	NM_001170851	ENSMUSG00000030187	Klra2	Klra30|Ly49b	"killer cell lectin-like receptor, subfamily A, member 2"	protein-coding	0	0.287129
Merged-chr7-92202027-1	chr7	92201977	92202077	+	2.8	cIP2vsInput	"intron (NM_011807, intron 13 of 22)"	"intron (NM_011807, intron 13 of 22)"	-32943	NM_001243047	23859	Mm.257035	NM_001243046		Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|PSD93	"discs, large homolog 2 (Drosophila)"	protein-coding	0	0.346535
Merged-chr3-67070656-1	chr3	67070606	67070706	+	2.8	cIP1vsInput	"intron (NM_025822, intron 3 of 9)"	"intron (NM_025822, intron 3 of 9)"	84984	NM_025822	66880	Mm.316418	NM_025822	ENSMUSG00000034544	Rsrc1	1200013F24Rik|SRrp53	arginine/serine-rich coiled-coil 1	protein-coding	0.02	0.336634
Merged-chr2-26459067-1	chr2	26459017	26459117	+	2.8	cIP2vsInput	"3' UTR (NM_008714, exon 34 of 34)"	"3' UTR (NM_008714, exon 34 of 34)"	-13851	NM_153125	227648	Mm.206371	NM_153125	ENSMUSG00000026924	Sec16a	AU024582|C230052J16Rik|RP23-306D20.10	SEC16 homolog A (S. cerevisiae)	protein-coding	0.02	0.594059
Merged-chr2-140143221-1	chr2	140143171	140143271	+	2.8	cIP2vsInput	"intron (NM_001081090, intron 9 of 13)"	"intron (NM_001081090, intron 9 of 13)"	27337	NM_001081090	66580	Mm.21228	NM_001081090	ENSMUSG00000045624	Esf1	2610101J03Rik|ABTAP|AW545818|C79684	"ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)"	protein-coding	0	0.316832
Merged-chr6-84965430-1	chr6	84965380	84965480	+	2.8	cIP1vsInput	"intron (NM_177077, intron 6 of 21)"	(TTTG)n|Simple_repeat|Simple_repeat	104083	NM_177077	75914	Mm.159621	NM_177077	ENSMUSG00000033769	Exoc6b	4930569O18Rik|G430127E12Rik|Sec15b|Sec15l2|mKIAA0919	exocyst complex component 6B	protein-coding	0	0.227723
Merged-chr18-46281350-1	chr18	46281300	46281400	+	2.8	cIP2vsInput	promoter-TSS (NM_172627)	promoter-TSS (NM_172627)	-500	NM_172627	225467	Mm.393044	NM_172627	ENSMUSG00000024477	Pggt1b	2010207C17Rik|2610100E13|AI451237|AI551093|BGG1|GGT1	"protein geranylgeranyltransferase type I, beta subunit"	protein-coding	0	0.326733
Merged-chr8-127193810-1	chr8	127193760	127193860	+	2.8	cIP1vsInput	"intron (NM_001122850, intron 2 of 15)"	(TATG)n|Simple_repeat|Simple_repeat	-105802	NM_001013581	93742	Mm.299254	NM_001013580	ENSMUSG00000025812	Pard3	AA960621|AI256638|ASIP|D8Ertd580e|PAR-3|Par3|Pard3a	par-3 (partitioning defective 3) homolog (C. elegans)	protein-coding	0	0.326733
Merged-chr3-76038410-1	chr3	76038360	76038460	+	2.8	cIP2vsInput	Intergenic	L1MB8|LINE|L1	-36151	NM_178673	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.316832
Merged-chr10-82985281-1	chr10	82985231	82985331	+	2.8	cIP2vsInput	promoter-TSS (NM_021439)	promoter-TSS (NM_021439)	-216	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding	0.12	0.722772
Merged-chr4-106359548-1	chr4	106359498	106359598	+	2.8	cIP2vsInput	"intron (NM_183225, intron 10 of 67)"	"intron (NM_183225, intron 10 of 67)"	43335	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding	0	0.356436
Merged-chr6-109994401-1	chr6	109994351	109994451	+	2.8	cIP1vsInput	Intergenic	ORR1F|LTR|ERVL-MaLR	-651197	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0.01	0.326733
Merged-chr4-138304770-1	chr4	138304720	138304820	+	2.8	cIP2vsInput	promoter-TSS (NM_007838)	promoter-TSS (NM_007838)	32	NM_007838	13200	Mm.7236	NM_007838	ENSMUSG00000028757	Ddost	-	dolichyl-di-phosphooligosaccharide-protein glycotransferase	protein-coding	0.14	0.742574
Merged-chr2-71845815-1	chr2	71845765	71845865	+	2.8	cIP1vsInput	"exon (NM_008397, exon 21 of 26)"	"exon (NM_008397, exon 21 of 26)"	-27457	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	"pyruvate dehydrogenase kinase, isoenzyme 1"	protein-coding	0.01	0.366337
Merged-chr18-82812595-1	chr18	82812545	82812645	+	2.8	cIP2vsInput	Intergenic	Intergenic	-53556	NR_045389	76961	Mm.396392	NR_045389		2210420H20Rik	-	RIKEN cDNA 2210420H20 gene	miscRNA	0.03	0.564356
Merged-chr8-91313312-1	chr8	91313262	91313362	+	2.8	cIP1vsInput	promoter-TSS (NM_011936)	promoter-TSS (NM_011936)	-90	NM_173431	244585	Mm.324592	NM_173431	ENSMUSG00000033282	Rpgrip1l	1700047E16Rik|4931437C01|Ftm|Nphp8	Rpgrip1-like	protein-coding	0.1	0.633663
Merged-chr15-89123152-1	chr15	89123102	89123202	+	2.8	cIP2vsInput	promoter-TSS (NM_001163319)	promoter-TSS (NM_001163319)	-2	NM_001163319	328580	Mm.380934	NM_001163319	ENSMUSG00000051786	Tubgcp6	AI843275|D430023H11|mKIAA1669	"tubulin, gamma complex associated protein 6"	protein-coding	0.12	0.663366
Merged-chr6-113690751-1	chr6	113690701	113690801	+	2.8	cIP2vsInput	"intron (NM_172161, intron 11 of 12)"	"intron (NM_172161, intron 11 of 12)"	-6748	NM_001033463	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding	0.05	0.574257
Merged-chr4-43031454-1	chr4	43031404	43031504	+	2.8	cIP2vsInput	promoter-TSS (NM_023231)	promoter-TSS (NM_023231)	-70	NM_023231	66592	Mm.331565	NM_023231	ENSMUSG00000028455	Stoml2	0610038F01Rik|MSLP2|SLP-2	stomatin (Epb7.2)-like 2	protein-coding	0.08	0.633663
Merged-chr11-8663863-1	chr11	8663813	8663913	+	2.8	cIP1vsInput	"intron (NM_001083587, intron 1 of 30)"	"intron (NM_001083587, intron 1 of 30)"	672	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding	0.04	0.653465
Merged-chr7-87250533-1	chr7	87250483	87250583	+	2.8	cIP2vsInput	"intron (NM_015760, intron 2 of 17)"	"intron (NM_015760, intron 2 of 17)"	3738	NM_015760	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding	0	0.356436
Merged-chr5-71322370-1	chr5	71322320	71322420	+	2.8	cIP2vsInput	Intergenic	Intergenic	225835	NM_030052	78174	Mm.60690	NM_030052	ENSMUSG00000049387	Cox7b2	4930503B16Rik	cytochrome c oxidase subunit VIIb2	protein-coding	0	0.326733
Merged-chr4-89749424-1	chr4	89749374	89749474	+	2.8	cIP2vsInput	Intergenic	Lx5|LINE|L1	61226	NM_175647	242523	Mm.130167	NM_175647	ENSMUSG00000043753	Dmrta1	Dmrt4	doublesex and mab-3 related transcription factor like family A1	protein-coding	0	0.336634
Merged-chr1-79574736-1	chr1	79574686	79574786	+	2.8	cIP2vsInput	Intergenic	L1MA9|LINE|L1	97236	NM_183027	252903	Mm.32409	NM_183027	ENSMUSG00000054702	Ap1s3	1190009B22|Jr2|[s]3A	"adaptor-related protein complex AP-1, sigma 3"	protein-coding	0	0.346535
Merged-chr9-22468238-1	chr9	22468188	22468288	+	2.8	cIP2vsInput	"5' UTR (NM_018739, exon 1 of 6)"	"5' UTR (NM_018739, exon 1 of 6)"	118	NM_018739	55934	Mm.38235	NM_018739	ENSMUSG00000032239	Rp9	PAP-1|Rp9h	retinitis pigmentosa 9 (human)	protein-coding	0.13	0.712871
Merged-chr18-13621073-1	chr18	13621023	13621123	+	2.8	cIP2vsInput	Intergenic	Intergenic	351660	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding	0.03	0.455446
Merged-chr12-75645981-1	chr12	75645931	75646031	+	2.8	cIP2vsInput	"intron (NM_028203, intron 1 of 1)"	B2_Mm2|SINE|B2	-14232	NR_038063	665931	Mm.341719	NR_038063		Rplp2-ps1	Gm7852	"ribosomal protein, large P2, pseudogene 1"	pseudo	0	0.524752
Merged-chr13-12300621-1	chr13	12300571	12300671	+	2.8	cIP2vsInput	"intron (NM_033268, intron 7 of 20)"	"intron (NM_033268, intron 7 of 20)"	40111	NM_033268	11472	Mm.37638	NM_033268	ENSMUSG00000052374	Actn2	1110008F24Rik	actinin alpha 2	protein-coding	0.01	0.39604
Merged-chr3-122048764-1	chr3	122048714	122048814	+	2.8	cIP2vsInput	"intron (NM_007378, intron 1 of 49)"	"intron (NM_007378, intron 1 of 49)"	4304	NM_007378	11304	Mm.3918	NM_007378	ENSMUSG00000028125	Abca4	AW050280|Abc10|Abcr|D430003I15Rik|RmP	"ATP-binding cassette, sub-family A (ABC1), member 4"	protein-coding	0.02	0.584158
Merged-chr17-83527327-1	chr17	83527277	83527377	+	2.8	cIP2vsInput	Intergenic	Intergenic	-12994	NM_001159529	20463	Mm.30072	NM_001159529	ENSMUSG00000024248	Cox7a2l	COX7AR|COX7RP|EB1|SIG-81|SIG81|Silg81	cytochrome c oxidase subunit VIIa polypeptide 2-like	protein-coding	0.02	0.574257
Merged-chr9-101211881-1	chr9	101211831	101211931	+	2.8	cIP2vsInput	"exon (NM_001161362, exon 2 of 14)"	"exon (NM_001161362, exon 2 of 14)"	-12808	NM_172144	235542	Mm.335386	NM_001161362	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	"protein phosphatase 2, regulatory subunit B'', alpha"	protein-coding	0.01	0.306931
Merged-chr12-36215606-1	chr12	36215556	36215656	+	2.8	cIP1vsInput	"intron (NM_001177877, intron 5 of 7)"	"intron (NM_001177877, intron 5 of 7)"	2596	NM_027699	71156	Mm.250837	NM_027699	ENSMUSG00000020545	Lrrc72	1700108M19Rik|4933421E18Rik	leucine rich repeat containing 72	protein-coding	0	0.405941
Merged-chr13-113794378-1	chr13	113794328	113794428	+	2.8	cIP2vsInput	promoter-TSS (NM_172595)	promoter-TSS (NM_172595)	-130	NM_172595	218639	Mm.79837	NM_172595	ENSMUSG00000042348	Arl15	A430036I03|Arfrp2|C230032K13Rik	ADP-ribosylation factor-like 15	protein-coding	0.11	0.752475
Merged-chr1-12832334-1	chr1	12832284	12832384	+	2.8	cIP2vsInput	"intron (NM_001198566, intron 11 of 20)"	"intron (NM_001198566, intron 11 of 20)"	113789	NM_172294	240725	Mm.45563	NM_001198565	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding	0	0.366337
Merged-chr2-50306408-1	chr2	50306358	50306458	+	2.8	cIP2vsInput	"intron (NR_040362, intron 1 of 2)"	"intron (NR_040362, intron 1 of 2)"	9598	NR_040362	100502624	Mm.412130	NR_040361	ENSMUSG00000085862	Gm13483	OTTMUSG00000012382	predicted gene 13483	miscRNA	0	0.386139
Merged-chr18-36783225-1	chr18	36783175	36783275	+	2.8	cIP2vsInput	promoter-TSS (NM_008214)	promoter-TSS (NM_008214)	-20	NM_008214	15115	Mm.10528	NM_008214	ENSMUSG00000001380	Hars	MMHRS	histidyl-tRNA synthetase	protein-coding	0.08	0.613861
Merged-chr7-41633836-1	chr7	41633786	41633886	+	2.8	cIP2vsInput	"intron (NM_023363, intron 1 of 5)"	"intron (NM_023363, intron 1 of 5)"	305	NM_023363	67607	Mm.384626	NM_023363	ENSMUSG00000074165	Zfp788	2810426N06Rik|AI256342|AI605193	zinc finger protein 788	protein-coding	0.04	0.663366
Merged-chr4-41755724-1	chr4	41755674	41755774	+	2.8	cIP2vsInput	"intron (NM_016658, intron 1 of 10)"	CpG	471	NM_016658	14430	Mm.439669	NM_016658		Galt	AW553376	galactose-1-phosphate uridyl transferase	protein-coding	0.09	0.653465
Merged-chr5-144356708-1	chr5	144356658	144356758	+	2.8	cIP2vsInput	"intron (NM_025833, intron 1 of 13)"	"intron (NM_025833, intron 1 of 13)"	-1215	NR_102374	100579137		NR_102372		Dmr	-	Dmrt1 related	miscRNA	0	0.326733
Merged-chr12-99257043-1	chr12	99256993	99257093	+	2.8	cIP1vsInput	"intron (NM_183186, intron 4 of 5)"	"intron (NM_183186, intron 4 of 5)"	-94235	NR_038130	67639	Mm.87374	NR_038130		4930474N09Rik	-	RIKEN cDNA 4930474N09 gene	miscRNA	0.02	0.49505
Merged-chr11-95384478-1	chr11	95384428	95384528	+	2.8	cIP2vsInput	promoter-TSS (NM_016752)	promoter-TSS (NM_016752)	-444	NM_016752	110172	Mm.4593	NM_016752		Slc35b1	Ugalt2	"solute carrier family 35, member B1"	protein-coding	0.07	0.554455
Merged-chr9-10142514-1	chr9	10142464	10142564	+	2.8	cIP2vsInput	"intron (NM_001170787, intron 6 of 24)"	"intron (NM_001170787, intron 6 of 24)"	762212	NM_001033359	244682	Mm.490683	NM_001033359	ENSMUSG00000039488	Cntn5	6720426O10Rik|A830025P08Rik|Gm507|NB-2	contactin 5	protein-coding	0	0.356436
Merged-chr5-86158278-1	chr5	86158228	86158328	+	2.8	cIP2vsInput	"intron (NM_172712, intron 6 of 32)"	"intron (NM_172712, intron 6 of 32)"	14465	NM_172712	231380	Mm.393083	NM_172712	ENSMUSG00000035898	Uba6	4930542H01|5730469D23Rik|AU021846|AW124799|E1-L2|Ube1l2	ubiquitin-like modifier activating enzyme 6	protein-coding	0.01	0.29703
Merged-chr16-73772812-1	chr16	73772762	73772862	+	2.8	cIP1vsInput	Intergenic	MER121|DNA|TcMar?	569255	NR_030464	751561		NR_030464		Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	miscRNA	0.01	0.29703
Merged-chr9-65094495-1	chr9	65094445	65094545	+	2.8	cIP2vsInput	Intergenic	Intergenic	-7000	NM_020043	56741	Mm.209041	NM_020043	ENSMUSG00000032816	Igdcc4	9330155G14Rik|DDM36|Nope|WI-16786|WI-18508|mKIAA1628	"immunoglobulin superfamily, DCC subclass, member 4"	protein-coding	0	0.554455
Merged-chr12-81071973-1	chr12	81071923	81072023	+	2.8	cIP2vsInput	"intron (NM_001146217, intron 1 of 12)"	"intron (NM_001146217, intron 1 of 12)"	45165	NM_022316	64075	Mm.273295	NM_001146217	ENSMUSG00000021136	Smoc1	2600002F22Rik|AI848508|SRG	SPARC related modular calcium binding 1	protein-coding	0	0.346535
Merged-chr17-66123678-1	chr17	66123628	66123728	+	2.8	cIP2vsInput	"5' UTR (NM_001003919, exon 1 of 27)"	"5' UTR (NM_001003919, exon 1 of 27)"	158	NM_001003919	320209	Mm.259605	NM_001003919	ENSMUSG00000035842	Ddx11	4732462I11Rik|CHL1|CHLR1|KRG2|essa15a	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	protein-coding	0.12	0.663366
Merged-chr5-73422101-1	chr5	73422051	73422151	+	2.8	cIP2vsInput	"intron (NM_181323, intron 8 of 15)"	"intron (NM_181323, intron 8 of 15)"	16023	NM_181323	231293	Mm.280211	NM_181323	ENSMUSG00000029154	Cwh43	C130090K23Rik|imds-60	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	protein-coding	0.01	0.346535
Merged-chr4-13605049-1	chr4	13604999	13605099	+	2.8	cIP2vsInput	Intergenic	Intergenic	-138253	NM_001111026	12395	Mm.470961	NM_001111026	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	"runt-related transcription factor 1; translocated to, 1 (cyclin D-related)"	protein-coding	0	0.326733
Merged-chr8-123373639-1	chr8	123373589	123373689	+	2.8	cIP2vsInput	promoter-TSS (NM_025804)	promoter-TSS (NM_025804)	-114	NM_025804	66855	Mm.178818	NM_001037877	ENSMUSG00000001472	Tcf25	1100001J13Rik|1810041K11Rik|D8Ertd325e|Nulp1|mKIAA1049	transcription factor 25 (basic helix-loop-helix)	protein-coding	0.12	0.693069
Merged-chr16-85024450-1	chr16	85024400	85024500	+	2.8	cIP2vsInput	"intron (NM_001198824, intron 10 of 16)"	"intron (NM_001198824, intron 10 of 16)"	52239	NR_045889	100038614	Mm.441351	NR_045889		Gm10791	ENSMUSG00000074933	predicted gene 10791	miscRNA	0	0.316832
Merged-chr1-75142940-1	chr1	75142890	75142990	+	2.8	cIP2vsInput	promoter-TSS (NM_026977)	promoter-TSS (NM_026977)	154	NM_170755	227298	Mm.392137	NM_170755	ENSMUSG00000049339	Fam134a	-	"family with sequence similarity 134, member A"	protein-coding	0.1	0.792079
Merged-chr16-20672803-1	chr16	20672753	20672853	+	2.8	cIP1vsInput	promoter-TSS (NM_145941)	promoter-TSS (NM_145941)	54	NM_001005331	208643	Mm.260256	NM_001005331	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF4GI	"eukaryotic translation initiation factor 4, gamma 1"	protein-coding	0.12	0.712871
Merged-chr1-188406997-1	chr1	188406947	188407047	+	2.8	cIP2vsInput	"intron (NM_021408, intron 12 of 70)"	"intron (NM_021408, intron 12 of 70)"	144159	NM_021408	22283	Mm.331238	NM_021408	ENSMUSG00000026609	Ush2a	A930011D15Rik|A930037M10Rik|Gm676|Gm983|Mush2a|Usherin	"Usher syndrome 2A (autosomal recessive, mild)"	protein-coding	0	0.326733
Merged-chr11-23403486-1	chr11	23403436	23403536	+	2.8	cIP2vsInput	"intron (NM_001190401, intron 30 of 79)"	"intron (NM_001190401, intron 30 of 79)"	94460	NM_172391	268390	Mm.13148	NM_172391	ENSMUSG00000020288	Ahsa2	1110064P04Rik|AI450991	"AHA1, activator of heat shock protein ATPase 2"	protein-coding	0.01	0.306931
Merged-chr17-23993662-1	chr17	23993612	23993712	+	2.8	cIP2vsInput	"3' UTR (NM_133731, exon 6 of 6)"	"3' UTR (NM_133731, exon 6 of 6)"	4438	NM_133731	70835	Mm.157351	NM_133731	ENSMUSG00000045027	Prss22	4733401N09Rik|BSSP-4|SP001LA	"protease, serine, 22"	protein-coding	0.1	0.60396
Merged-chrY-7009907-1	chrY	7009857	7009957	+	2.8	cIP2vsInput	Intergenic	GA-rich|Low_complexity|Low_complexity	157870	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.39604
Merged-chr15-79328506-1	chr15	79328456	79328556	+	2.8	cIP2vsInput	promoter-TSS (NM_016915)	promoter-TSS (NM_016915)	-135	NM_001199023	53357	Mm.155620	NM_001199023	ENSMUSG00000042632	Pla2g6	BB112799|PNPLA9|iPLA(2)beta|iPLA2|iPLA2beta	"phospholipase A2, group VI"	protein-coding	0.07	0.633663
Merged-chr1-23324436-1	chr1	23324386	23324486	+	2.8	cIP2vsInput	Intergenic	Intergenic	32735	NR_029717	723964		NR_029717	ENSMUSG00000065567	Mir30c-2	Mirn30c-2	microRNA 30c-2	miscRNA	0.02	0.316832
Merged-chr9-102864055-1	chr9	102864005	102864105	+	2.8	cIP1vsInput	"intron (NM_001042607, intron 2 of 14)"	"intron (NM_001042607, intron 2 of 14)"	29135	NM_001042607	20187	Mm.335391	NM_001042607	ENSMUSG00000032547	Ryk	AW536699|ERK-3|Vik	receptor-like tyrosine kinase	protein-coding	0.02	0.475248
Merged-chr12-93703957-1	chr12	93703907	93704007	+	2.8	cIP2vsInput	Intergenic	RMER6D|LTR|ERVK	-1854800	NM_011344	20338	Mm.250605	NM_001039089	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding	0	0.326733
Merged-chr4-35007081-1	chr4	35007031	35007131	+	2.8	cIP2vsInput	"intron (NM_178061, intron 2 of 3)"	"intron (NM_178061, intron 2 of 3)"	-95600	NR_040652	73696	Mm.296813	NR_040652	ENSMUSG00000085824	2410114N07Rik	-	RIKEN cDNA 2410114N07 gene	miscRNA	0.02	0.465347
Merged-chr6-52221711-1	chr6	52221661	52221761	+	2.8	cIP2vsInput	Intergenic	CpG	-3138	NM_010455	15404	Mm.294826	NM_010455		Hoxa7	AV118143|Hox-1.1	homeobox A7	protein-coding	0.03	0.49505
Merged-chr15-59404575-1	chr15	59404525	59404625	+	2.8	cIP1vsInput	"intron (NM_001164604, intron 2 of 4)"	"intron (NM_001164604, intron 2 of 4)"	30377	NM_001164604	68501	Mm.27762	NM_001164604	ENSMUSG00000059586	Nsmce2	1110014D18Rik|AI661537	"non-SMC element 2 homolog (MMS21, S. cerevisiae)"	protein-coding	0	0.336634
Merged-chr6-136672654-1	chr6	136672604	136672704	+	2.8	cIP2vsInput	Intergenic	Intergenic	-10761	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding	0.02	0.524752
Merged-chr9-30656162-1	chr9	30656112	30656212	+	2.8	cIP2vsInput	Intergenic	Intergenic	228833	NM_028874	102607	Mm.35084	NM_028874	ENSMUSG00000031993	Snx19	3526401K03Rik|AI195321|AI848208|mKIAA0254	sorting nexin 19	protein-coding	0	0.366337
Merged-chr18-44076812-1	chr18	44076762	44076862	+	2.8	cIP2vsInput	"intron (NM_001013797, intron 2 of 4)"	"intron (NM_001013797, intron 2 of 4)"	5419	NM_001013797	433180	Mm.57302	NM_001013797	ENSMUSG00000055095	Spink6	EG433180	"serine peptidase inhibitor, Kazal type 6"	protein-coding	0	0.316832
Merged-chr16-3128746-1	chr16	3128696	3128796	+	2.8	cIP2vsInput	Intergenic	RLTR21|LTR|ERVK	-463652	NM_146860	258859	Mm.377723	NM_146860		Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding	0	0.326733
Merged-chr14-115236327-1	chr14	115236277	115236377	+	2.8	cIP1vsInput	"intron (NM_175500, intron 2 of 7)"	"intron (NM_175500, intron 2 of 7)"	144112	NM_175500	103978	Mm.320791	NM_175500	ENSMUSG00000022112	Gpc5	A230034F01Rik	glypican 5	protein-coding	0	0.287129
Merged-chr9-106448561-1	chr9	106448511	106448611	+	2.8	cIP2vsInput	promoter-TSS (NM_145919)	promoter-TSS (NM_145919)	-79	NM_029631	76491	Mm.335427	NM_029631	ENSMUSG00000042073	Abhd14b	1810013B01Rik	abhydrolase domain containing 14b	protein-coding	0.04	0.544554
Merged-chr10-88622664-1	chr10	88622614	88622714	+	2.8	cIP2vsInput	Intergenic	Intergenic	-17512	NM_175418	109272	Mm.147208	NM_001252372	ENSMUSG00000020061	Mybpc1	8030451F13Rik	"myosin binding protein C, slow-type"	protein-coding	0.05	0.485149
Merged-chr9-41876851-1	chr9	41876801	41876901	+	2.8	cIP2vsInput	Intergenic	Intergenic	247438	NM_011436	20660	Mm.121920	NM_011436		Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	"sortilin-related receptor, LDLR class A repeats-containing"	protein-coding	0	0.445545
Merged-chr5-89882175-1	chr5	89882125	89882225	+	2.8	cIP2vsInput	"intron (NM_001081401, intron 1 of 21)"	"intron (NM_001081401, intron 1 of 21)"	1159	NM_177872	330119	Mm.133062	NM_001081401	ENSMUSG00000043635	Adamts3	1100001H14Rik|6330442E02Rik	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 3"	protein-coding	0.01	0.564356
Merged-chr2-120629183-1	chr2	120629133	120629233	+	2.8	cIP2vsInput	Intergenic	CpG	-19675	NM_001159609	66606	Mm.428639	NM_001159609	ENSMUSG00000027286	Lrrc57	2810002D13Rik|AA407405	leucine rich repeat containing 57	protein-coding	0.08	0.663366
Merged-chr5-58961585-1	chr5	58961535	58961635	+	2.8	cIP1vsInput	Intergenic	Intergenic	-508587	NR_046190	78163	Mm.243828	NR_046190		4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	miscRNA	0	0.326733
Merged-chr17-47151759-2	chr17	47151704	47151814	+	2.8	cIP1vsInput|cIP2vsInput	"intron (NM_001097623, intron 3 of 19)"	"intron (NM_001097623, intron 3 of 19)"	10817	NM_001097623	224829	Mm.260989	NM_001097623	ENSMUSG00000064043	Trerf1	9430096I18Rik|AI429294|B830015H24|RAPA|Trep-132|Trep132	transcriptional regulating factor 1	protein-coding	0.018182	0.468468
Merged-chr5-137072441-1	chr5	137072391	137072491	+	2.8	cIP2vsInput	promoter-TSS (NM_008871)	promoter-TSS (NM_008871)	-169	NM_008871	18787	Mm.250422	NM_008871	ENSMUSG00000037411	Serpine1	PAI-1|PAI1|Planh1	"serine (or cysteine) peptidase inhibitor, clade E, member 1"	protein-coding	0.02	0.584158
Merged-chr19-17567538-1	chr19	17567488	17567588	+	2.8	cIP1vsInput	"intron (NM_001190483, intron 17 of 37)"	"intron (NM_001190483, intron 17 of 37)"	173495	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding	0.01	0.415842
Merged-chr11-108173204-1	chr11	108173154	108173254	+	2.8	cIP1vsInput	"intron (NM_011101, intron 3 of 16)"	"intron (NM_011101, intron 3 of 16)"	170684	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	"protein kinase C, alpha"	protein-coding	0.01	0.366337
Merged-chrX-162749269-1	chrX	162749219	162749319	+	2.8	cIP2vsInput	"intron (NR_038088, intron 3 of 5)"	"intron (NR_038088, intron 3 of 5)"	-11103	NM_009031	245688	Mm.486181	NM_009031	ENSMUSG00000031353	Rbbp7	AA409861|AI173248|AU019541|BB114024|mRbAp46	retinoblastoma binding protein 7	protein-coding	0.03	0.50495
Merged-chr2-24367649-1	chr2	24367599	24367699	+	2.8	cIP2vsInput	Intergenic	CpG	-17748	NM_177611	215632	Mm.490434	NM_177611	ENSMUSG00000026979	Psd4	BC046518|EFA6B	pleckstrin and Sec7 domain containing 4	protein-coding	0.13	0.782178
Merged-chr6-84848403-1	chr6	84848353	84848453	+	2.8	cIP2vsInput	"intron (NM_177077, intron 16 of 21)"	"intron (NM_177077, intron 16 of 21)"	221110	NM_177077	75914	Mm.159621	NM_177077	ENSMUSG00000033769	Exoc6b	4930569O18Rik|G430127E12Rik|Sec15b|Sec15l2|mKIAA0919	exocyst complex component 6B	protein-coding	0	0.316832
Merged-chr13-116179688-1	chr13	116179638	116179738	+	2.8	cIP2vsInput	Intergenic	Intergenic	130000	NM_021459	16392	Mm.42242	NM_021459	ENSMUSG00000042258	Isl1	-	"ISL1 transcription factor, LIM/homeodomain"	protein-coding	0.01	0.405941
Merged-chr14-35831657-1	chr14	35831607	35831707	+	2.8	cIP2vsInput	Intergenic	L1M4c|LINE|L1	-19679	NM_001033766	239036	Mm.239970	NM_001033766	ENSMUSG00000041068	4930596D02Rik	-	RIKEN cDNA 4930596D02 gene	protein-coding	0	0.336634
Merged-chr3-118536210-1	chr3	118536160	118536260	+	2.8	cIP2vsInput	Intergenic	Intergenic	-25968	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding	0.01	0.346535
Merged-chr5-100819551-1	chr5	100819501	100819601	+	2.8	cIP2vsInput	"intron (NM_172405, intron 1 of 8)"	"intron (NM_172405, intron 1 of 8)"	1384	NM_172405	70681	Mm.486560	NM_172405	ENSMUSG00000035234	Fam175a	3830405G04Rik|5630400M01Rik|AI506069|AL024423|AV118690|Ccdc98	"family with sequence similarity 175, member A"	protein-coding	0	0.29703
Merged-chr4-55651462-1	chr4	55651412	55651512	+	2.8	cIP2vsInput	Intergenic	CpG	-118987	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding	0.14	0.851485
Merged-chr4-116940100-1	chr4	116940050	116940150	+	2.8	cIP2vsInput	"intron (NM_001029912, intron 1 of 13)"	"intron (NM_001029912, intron 1 of 13)"	54275	NM_009478	22275	Mm.46484	NM_009478	ENSMUSG00000028684	Urod	AI323803|Uro-d	uroporphyrinogen decarboxylase	protein-coding	0	0.336634
Merged-chr11-81595424-1	chr11	81595374	81595474	+	2.8	cIP2vsInput	"intron (NM_001034013, intron 1 of 9)"	"intron (NM_001034013, intron 1 of 9)"	-21885	NM_001033765	237880	Mm.435528	NM_001033765		1700071K01Rik	-	RIKEN cDNA 1700071K01 gene	protein-coding	0	0.485149
Merged-chr16-33684418-1	chr16	33684368	33684468	+	2.8	cIP2vsInput	promoter-TSS (NM_175256)	promoter-TSS (NM_175256)	-48	NM_175256	77446	Mm.245741	NM_172934		Heg1	4632417D23Rik|5530401I02Rik|9530025L16Rik|BC038614|Gm629|OTTMUSG00000027315	HEG homolog 1 (zebrafish)	protein-coding	0.14	0.811881
Merged-chr8-49553576-1	chr8	49553526	49553626	+	2.8	cIP1vsInput	Intergenic	L1MD|LINE|L1	-814536	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0.01	0.316832
Merged-chr7-67380563-1	chr7	67380513	67380613	+	2.8	cIP2vsInput	Intergenic	Intergenic	-7705	NM_001033713	17258	Mm.426509	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding	0.03	0.49505
Merged-chr9-108284628-1	chr9	108284578	108284678	+	2.8	cIP2vsInput	Intergenic	B3|SINE|B2	-5829	NM_025449	66257	Mm.10407	NM_025449	ENSMUSG00000032606	Nicn1	1500032A17Rik	nicolin 1	protein-coding	0.02	0.425743
Merged-chr15-43529273-1	chr15	43529223	43529323	+	2.8	cIP2vsInput	Intergenic	Intergenic	52044	NM_025736	66736	Mm.244512	NM_025736	ENSMUSG00000022337	Emc2	4921531G14Rik|AV060620|AW209495|Ttc35	ER membrane protein complex subunit 2	protein-coding	0	0.29703
Merged-chr14-89360070-1	chr14	89360020	89360120	+	2.8	cIP1vsInput	Intergenic	Lx9|LINE|L1	-536154	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0	0.326733
Merged-chr18-52529707-1	chr18	52529657	52529757	+	2.8	cIP2vsInput	promoter-TSS (NM_010728)	promoter-TSS (NM_010728)	1	NM_010728	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160	lysyl oxidase	protein-coding	0.07	0.623762
Merged-chr3-152458163-1	chr3	152458113	152458213	+	2.8	cIP2vsInput	"intron (NM_001080755, intron 13 of 13)"	"intron (NM_001080755, intron 13 of 13)"	61469	NM_198416	108946	Mm.379292	NM_001080755	ENSMUSG00000039068	Zzz3	3110065C23Rik|6430567E01Rik|AA408566|AI481057|AW556059|R75514	"zinc finger, ZZ domain containing 3"	protein-coding	0.01	0.336634
Merged-chr7-122832768-1	chr7	122832718	122832818	+	2.8	cIP2vsInput	Intergenic	RLTR14_RN|LTR|ERV1	137691	NR_045614	73951	Mm.389936	NR_045614		4930413G21Rik	-	RIKEN cDNA 4930413G21 gene	miscRNA	0	0.316832
Merged-chr4-28238745-1	chr4	28238695	28238795	+	2.8	cIP2vsInput	Intergenic	Intergenic	-574400	NM_001122889	13841	Mm.257266	NM_001122889	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding	0	0.316832
Merged-chr4-63558885-1	chr4	63558835	63558935	+	2.8	cIP2vsInput	Intergenic	CpG	-1475	NM_144905	230279	Mm.454458	NM_144905	ENSMUSG00000045917	6330416G13Rik	AW492431|bM230C2.2	RIKEN cDNA 6330416G13 gene	protein-coding	0.06	0.673267
Merged-chr1-51080392-1	chr1	51080342	51080442	+	2.8	cIP2vsInput	"intron (NM_019790, intron 5 of 9)"	"intron (NM_019790, intron 5 of 9)"	152869	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0.01	0.29703
Merged-chr13-107970527-1	chr13	107970477	107970577	+	2.8	cIP2vsInput	Intergenic	Intergenic	-73947	NM_001048250	75616	Mm.29464	NM_001048250		Smim15	2810008M24Rik	small integral membrane protein 15	protein-coding	0.02	0.544554
Merged-chr13-58996840-2	chr13	58996779	58996901	+	2.8	cIP1vsInput|cIP2vsInput	"intron (NM_001025074, intron 13 of 17)"	"intron (NM_001025074, intron 13 of 17)"	189007	NM_001025074	18212	Mm.130054	NM_001025074	ENSMUSG00000055254	Ntrk2	AI848316|C030027L06Rik|Tkrb|trkB	"neurotrophic tyrosine kinase, receptor, type 2"	protein-coding	0.008197	0.471545
Merged-chr8-8184811-1	chr8	8184761	8184861	+	2.8	cIP2vsInput	Intergenic	Intergenic	475962	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding	0	0.336634
Merged-chr13-12147075-1	chr13	12147025	12147125	+	2.8	cIP2vsInput	Intergenic	Intergenic	39413	NR_045170	328186	Mm.188154	NR_045170		Gm10336	B330003H21|ENSMUSG00000071543	predicted gene 10336	miscRNA	0	0.316832
Merged-chr7-55302865-1	chr7	55302815	55302915	+	2.8	cIP1vsInput	Intergenic	Intergenic	-465313	NM_178706	233274	Mm.44425	NM_178706	ENSMUSG00000051504	Siglech	6430529G09Rik|Siglec-H	sialic acid binding Ig-like lectin H	protein-coding	0	0.346535
Merged-chr2-99083199-1	chr2	99083149	99083249	+	2.8	cIP2vsInput	Intergenic	Intergenic	1615525	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.306931
Merged-chr2-123529090-1	chr2	123529040	123529140	+	2.8	cIP2vsInput	Intergenic	Intergenic	600866	NR_040611	74702	Mm.410814	NR_040611	ENSMUSG00000085496	4930517E11Rik	-	RIKEN cDNA 4930517E11 gene	miscRNA	0.01	0.425743
Merged-chr13-21453718-1	chr13	21453668	21453768	+	2.8	cIP2vsInput	promoter-TSS (NM_001013786)	promoter-TSS (NM_001013786)	9	NM_001013786	432731	Mm.441899	NM_001013786	ENSMUSG00000022228	Zscan26	BC068174|Zfp187|Znf187	zinc finger and SCAN domain containing 26	protein-coding	0.09	0.613861
Merged-chr8-95596808-1	chr8	95596758	95596858	+	2.8	cIP2vsInput	Intergenic	Intergenic	-21611	NM_027640	70993	Mm.486561	NM_027640	ENSMUSG00000048400	Prss54	4931432M23Rik|Klkbl4	"protease, serine, 54"	protein-coding	0.01	0.524752
Merged-chr10-69203903-1	chr10	69203853	69203953	+	2.8	cIP2vsInput	Intergenic	Intergenic	-4649	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding	0	0.455446
Merged-chr6-67046693-1	chr6	67046643	67046743	+	2.8	cIP2vsInput	"intron (NR_040278, intron 1 of 6)"	"intron (NR_040278, intron 1 of 6)"	-9286	NM_007836	13197	Mm.72235	NM_007836	ENSMUSG00000036390	Gadd45a	AA545191|Ddit1|GADD45	growth arrest and DNA-damage-inducible 45 alpha	protein-coding	0	0.336634
Merged-chr8-64850473-1	chr8	64850423	64850523	+	2.8	cIP2vsInput	Intergenic	Intergenic	-70608	NM_178633	77113	Mm.350347	NM_178633	ENSMUSG00000031605	Klhl2	6030411N21Rik|ABP-KELCH|AU020744|Mav|mKIAA4249	"kelch-like 2, Mayven"	protein-coding	0.04	0.50495
Merged-chr10-80342862-1	chr10	80342812	80342912	+	2.8	cIP2vsInput	"exon (NM_025629, exon 8 of 8)"	"exon (NM_025629, exon 8 of 8)"	5550	NM_025629	66548	Mm.268527	NM_001113548	ENSMUSG00000043822	Adamtsl5	2010109H09Rik|Thsd6	ADAMTS-like 5	protein-coding	0.02	0.564356
Merged-chr19-27364821-1	chr19	27364771	27364871	+	2.8	cIP2vsInput	Intergenic	Intergenic	42202	NM_183179	240595	Mm.269759	NM_183179	ENSMUSG00000047298	Kcnv2	KV11.1	"potassium channel, subfamily V, member 2"	protein-coding	0.01	0.514851
Merged-chr6-110918367-1	chr6	110918317	110918417	+	2.8	cIP1vsInput	"intron (NM_177328, intron 2 of 9)"	"intron (NM_177328, intron 2 of 9)"	272769	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0	0.306931
Merged-chr9-85106764-1	chr9	85106714	85106814	+	2.8	cIP2vsInput	Intergenic	Intergenic	220360	NM_001160378	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	D930050G01Rik	"family with sequence similarity 46, member A"	protein-coding	0	0.386139
Merged-chr1-75936651-1	chr1	75936601	75936701	+	2.8	cIP1vsInput	Intergenic	Intergenic	390385	NM_009208	20536	Mm.5053	NM_009208		Slc4a3	A930038D23Rik|Ae3	"solute carrier family 4 (anion exchanger), member 3"	protein-coding	0.03	0.554455
Merged-chr1-170006797-1	chr1	170006747	170006847	+	2.8	cIP2vsInput	"exon (NM_022563, exon 3 of 17)"	"exon (NM_022563, exon 3 of 17)"	37388	NR_040438	67303	Mm.396611	NR_040438	ENSMUSG00000097503	3110045C21Rik	AI838577	RIKEN cDNA 3110045C21 gene	miscRNA	0.01	0.524752
Merged-chr12-35992057-1	chr12	35992007	35992107	+	2.8	cIP2vsInput	promoter-TSS (NM_011783)	promoter-TSS (NM_011783)	-868	NM_011783	23795	Mm.7244	NM_011783	ENSMUSG00000020581	Agr2	Agr2h|Gob-4|HAG-2|XAG-2|mAG-2	anterior gradient 2 (Xenopus laevis)	protein-coding	0	0.415842
Merged-chr10-121038742-1	chr10	121038692	121038792	+	2.8	cIP1vsInput	"intron (NM_011915, intron 2 of 9)"	"intron (NM_011915, intron 2 of 9)"	4738	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding	0.01	0.366337
Merged-chr2-181365430-1	chr2	181365380	181365480	+	2.8	cIP2vsInput	promoter-TSS (NM_001165995)	promoter-TSS (NM_001165995)	7	NM_001048148	229007	Mm.272712	NM_001048148	ENSMUSG00000027582	Zgpat	1500006I01Rik|BC021513	"zinc finger, CCCH-type with G patch domain"	protein-coding	0.11	0.70297
Merged-chr14-95353234-1	chr14	95353184	95353284	+	2.8	cIP2vsInput	Intergenic	Intergenic	-528032	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.336634
Merged-chr4-80853884-1	chr4	80853834	80853934	+	2.8	cIP1vsInput	Intergenic	Intergenic	19654	NM_031202	22178	Mm.412291	NM_031202	ENSMUSG00000005994	Tyrp1	TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding	0	0.336634
Merged-chr5-29885015-1	chr5	29884965	29885065	+	2.8	cIP1vsInput	Intergenic	MER33|DNA|hAT-Charlie	-128146	NM_031168	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding	0.01	0.346535
Merged-chr4-29604042-1	chr4	29603992	29604092	+	2.8	cIP2vsInput	Intergenic	Intergenic	790897	NM_010141	13841	Mm.257266	NM_001122889	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding	0	0.316832
Merged-chr2-47296693-1	chr2	47296643	47296743	+	2.8	cIP2vsInput	Intergenic	Intergenic	-1517416	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding	0	0.29703
Merged-chr16-8471211-1	chr16	8471161	8471261	+	2.8	cIP2vsInput	"intron (NM_146247, intron 1 of 10)"	"intron (NM_146247, intron 1 of 10)"	398	NM_146247	239706	Mm.214953	NM_146247		Mettl22	-	methyltransferase like 22	protein-coding	0.02	0.613861
Merged-chr5-82390271-1	chr5	82390221	82390321	+	2.8	cIP2vsInput	Intergenic	Intergenic	408794	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mmu-mir-1187	microRNA 1187	miscRNA	0.02	0.336634
Merged-chr1-141131842-1	chr1	141131792	141131892	+	2.8	cIP1vsInput	Intergenic	Intergenic	-475440	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0.01	0.29703
Merged-chr8-65847244-1	chr8	65847194	65847294	+	2.8	cIP2vsInput	"intron (NM_175188, intron 1 of 7)"	Lx2B|LINE|L1	228719	NM_175188	72925	Mm.380457	NM_001166372	ENSMUSG00000036469	1-Mar	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding	0	0.346535
Merged-chr1-188154973-1	chr1	188154923	188155023	+	2.8	cIP2vsInput	"intron (NM_011935, intron 5 of 6)"	"intron (NM_011935, intron 5 of 6)"	-107865	NM_021408	22283	Mm.331238	NM_021408	ENSMUSG00000026609	Ush2a	A930011D15Rik|A930037M10Rik|Gm676|Gm983|Mush2a|Usherin	"Usher syndrome 2A (autosomal recessive, mild)"	protein-coding	0.03	0.564356
Merged-chr10-17112216-1	chr10	17112166	17112266	+	2.8	cIP2vsInput	Intergenic	Intergenic	-16434	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0	0.29703
Merged-chr8-91988137-1	chr8	91988087	91988187	+	2.8	cIP2vsInput	Intergenic	Intergenic	-186483	NM_008393	16373	Mm.238044	NM_001253822	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3 (Drosophila)	protein-coding	0.02	0.60396
Merged-chr5-129908685-1	chr5	129908635	129908735	+	2.8	cIP2vsInput	"exon (NM_026916, exon 1 of 3)"	"exon (NM_026916, exon 1 of 3)"	145	NM_026916	69034	Mm.211372	NM_026916		Nupr1l	1810010E01Rik|4930579G22Rik	nuclear protein transcriptional regulator 1 like	protein-coding	0.12	0.683168
Merged-chr17-60192951-1	chr17	60192901	60193001	+	2.8	cIP2vsInput	Intergenic	Intergenic	-1124801	NR_030569	100124495		NR_030569		Mir466g	Mirn466g	microRNA 466g	miscRNA	0	0.316832
Merged-chr2-111039626-1	chr2	111039576	111039676	+	2.8	cIP1vsInput	Intergenic	Intergenic	-89382	NM_001128103	228432	Mm.483325	NM_001128103	ENSMUSG00000074968	Ano3	AI838058|B230324K02Rik|Tmem16c	anoctamin 3	protein-coding	0	0.336634
Merged-chr16-34456644-1	chr16	34456594	34456694	+	2.8	cIP2vsInput	"intron (NM_001164268, intron 1 of 33)"	"intron (NM_001164268, intron 1 of 33)"	57383	NM_001164268	545156	Mm.353103	NM_001164268	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	"kalirin, RhoGEF kinase"	protein-coding	0.01	0.554455
Merged-chr14-104425510-1	chr14	104425460	104425560	+	2.8	cIP2vsInput	Intergenic	Intergenic	42489	NM_011143	18996	Mm.246550	NM_011143	ENSMUSG00000048349	Pou4f1	Brn-3|Brn-3.0|Brn3|Brn3.0|Brn3a|E130119J07Rik	"POU domain, class 4, transcription factor 1"	protein-coding	0	0.306931
Merged-chr8-70897158-1	chr8	70897108	70897208	+	2.8	cIP2vsInput	"intron (NM_029751, intron 1 of 4)"	CpG	285	NM_029751	76808	Mm.431334	NM_029751	ENSMUSG00000045128	Rpl18a	2510019J09Rik	ribosomal protein L18A	protein-coding	0.13	0.663366
Merged-chr11-104231292-1	chr11	104231242	104231342	+	2.8	cIP2vsInput	promoter-TSS (NM_010838)	promoter-TSS (NM_010838)	-144	NM_001038609	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding	0.17	0.80198
Merged-chr13-26208782-1	chr13	26208732	26208832	+	2.8	cIP2vsInput	Intergenic	Lx2B2|LINE|L1	103624	NR_045933	73576	Mm.45473	NR_045933		1700092E19Rik	-	RIKEN cDNA 1700092E19 gene	miscRNA	0	0.306931
Merged-chr10-52788670-1	chr10	52788620	52788720	+	2.8	cIP2vsInput	"intron (NM_178675, intron 1 of 7)"	"intron (NM_178675, intron 1 of 7)"	98169	NM_178675	215085	Mm.338690	NM_178675	ENSMUSG00000038602	Slc35f1	Duf6|E130016L02	"solute carrier family 35, member F1"	protein-coding	0	0.346535
Merged-chr1-9773004-1	chr1	9772954	9773054	+	2.8	cIP2vsInput	Intergenic	Intergenic	-24622	NM_173443	70675	Mm.440951	NM_173443		Vcpip1	4932442A08|5730421J18Rik|5730538E15Rik|VCIP135|mKIAA1850	valosin containing protein (p97)/p47 complex interacting protein 1	protein-coding	0.01	0.376238
Merged-chr6-68510983-1	chr6	68510933	68511033	+	2.8	cIP1vsInput	Intergenic	Intergenic	816191	NR_004434	19783		NR_004434		Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	miscRNA	0	0.346535
Merged-chr1-63632948-1	chr1	63632898	63632998	+	2.8	cIP2vsInput	"intron (NM_001081658, intron 14 of 14)"	"intron (NM_001081658, intron 14 of 14)"	53979	NM_001081658	241073	Mm.297680	NM_001081658	ENSMUSG00000069085	Dytn	Gm215	dystrotelin	protein-coding	0	0.39604
Merged-chr5-64382683-1	chr5	64382633	64382733	+	2.8	cIP2vsInput	Intergenic	Intergenic	85259	NR_040681	69999	Mm.261413	NR_040681		1700027F09Rik	-	RIKEN cDNA 1700027F09 gene	miscRNA	0.01	0.445545
Merged-chr15-79441299-1	chr15	79441249	79441349	+	2.8	cIP2vsInput	"intron (NM_013767, intron 1 of 10)"	"intron (NM_013767, intron 1 of 10)"	758	NM_013767	27373	Mm.30199	NM_013767	ENSMUSG00000022433	Csnk1e	AI426939|AI551861|AW457082|CK1epsilon|CKIe|KC1epsilon|tau	"casein kinase 1, epsilon"	protein-coding	0.02	0.445545
Merged-chr13-23193661-1	chr13	23193611	23193711	+	2.8	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	-9137	NM_134237	171271	Mm.377223	NM_134237	ENSMUSG00000096099	Vmn1r220	V1rh12	vomeronasal 1 receptor 220	protein-coding	0	0.346535
Merged-chr13-119689772-1	chr13	119689722	119689822	+	2.8	cIP2vsInput	promoter-TSS (NM_145942)	promoter-TSS (NM_145942)	-690	NM_145942	208715	Mm.61526	NM_145942	ENSMUSG00000093930	Hmgcs1	B130032C06Rik	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1	protein-coding	0.02	0.356436
Merged-chr9-44361798-1	chr9	44361748	44361848	+	2.8	cIP2vsInput	promoter-TSS (NM_027889)	promoter-TSS (NM_027889)	-128	NM_027889	71732	Mm.295013	NM_027889	ENSMUSG00000032127	Vps11	1200011A11Rik	vacuolar protein sorting 11 (yeast)	protein-coding	0.06	0.534653
Merged-chr1-85299394-1	chr1	85299344	85299444	+	2.8	cIP1vsInput	Intergenic	B2_Mm2|SINE|B2	-28828	NM_001037909	620078	Mm.461248	NM_001037909	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding	0.01	0.405941
Merged-chr17-6165084-1	chr17	6165034	6165134	+	2.8	cIP2vsInput	"intron (NM_054040, intron 1 of 13)"	"intron (NM_054040, intron 1 of 13)"	26936	NM_054040	68842	Mm.486644	NM_001033529	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding	0	0.366337
Merged-chrX-100948286-1	chrX	100948236	100948336	+	2.8	cIP2vsInput	"intron (NM_031384, intron 15 of 29)"	MTD|LTR|ERVL-MaLR	111353	NM_031384	83558	Mm.134024	NM_001167997	ENSMUSG00000009670	Tex11	4930565P14Rik|BB024231	testis expressed gene 11	protein-coding	0	0.336634
Merged-chr16-71529936-1	chr16	71529886	71529986	+	2.8	cIP2vsInput	Intergenic	Intergenic	280032	NR_040576	78221	Mm.399298	NR_040576		4930567J20Rik	-	RIKEN cDNA 4930567J20 gene	miscRNA	0	0.326733
Merged-chr17-26584968-1	chr17	26584918	26585018	+	2.8	cIP2vsInput	"intron (NM_026170, intron 1 of 9)"	"intron (NM_026170, intron 1 of 9)"	23456	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding	0.03	0.50495
Merged-chr5-83258436-1	chr5	83258386	83258486	+	2.8	cIP2vsInput	Intergenic	Lx7|LINE|L1	96759	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	"trans-2,3-enoyl-CoA reductase-like"	protein-coding	0.01	0.336634
Merged-chrX-136172465-1	chrX	136172415	136172515	+	2.8	cIP2vsInput	promoter-TSS (NM_001168578)	promoter-TSS (NM_001168578)	-214	NM_025703	66684	Mm.182094	NM_001168578	ENSMUSG00000051579	Tceal8	3930402F23Rik	transcription elongation factor A (SII)-like 8	protein-coding	0.02	0.50495
Merged-chr2-177228899-1	chr2	177228849	177228949	+	2.8	cIP1vsInput	Intergenic	MurSatRep1|Unknown|Unknown	-235843	NM_001177568	628308	Mm.460436	NM_001177568		Gm14420	OTTMUSG00000016588	predicted gene 14420	protein-coding	0	0.405941
Merged-chr2-7318836-1	chr2	7318786	7318886	+	2.8	cIP1vsInput	"intron (NM_001110232, intron 1 of 15)"	"intron (NM_001110232, intron 1 of 15)"	77164	NM_001110232	14007	Mm.398543	NM_183219	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	"CUGBP, Elav-like family member 2"	protein-coding	0	0.29703
Merged-chr2-136923037-1	chr2	136922987	136923087	+	2.8	cIP1vsInput	"intron (NM_001038641, intron 2 of 7)"	L1_Mus1|LINE|L1	23686	NM_001038641	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding	0.01	0.366337
Merged-chr7-95489890-1	chr7	95489840	95489940	+	2.8	cIP1vsInput	Intergenic	Intergenic	-720747	NM_011858	23966	Mm.391678	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding	0.03	0.49505
Merged-chrX-169312628-1	chrX	169312578	169312678	+	2.8	cIP2vsInput	"3' UTR (NM_008222, exon 7 of 7)"	"3' UTR (NM_008222, exon 7 of 7)"	7715	NM_008222	15159	Mm.284033	NM_008222	ENSMUSG00000031352	Hccs	-	holocytochrome c synthetase	protein-coding	0	0.326733
Merged-chr14-53684756-1	chr14	53684706	53684806	+	2.8	cIP1vsInput	Intergenic	Intergenic	18816	NM_001205242	100568452	Mm.486072	NM_001205242		A430107P09Rik	Va10	RIKEN cDNA A430107P09 gene	protein-coding	0	0.287129
Merged-chr1-164275135-1	chr1	164275085	164275185	+	2.8	cIP2vsInput	promoter-TSS (NM_029115)	promoter-TSS (NM_029115)	-463	NM_029115	74895	Mm.167258	NM_029115	ENSMUSG00000026578	Ccdc181	4930455F23Rik|AI427889	coiled-coil domain containing 181	protein-coding	0	0.39604
Merged-chr9-6724978-1	chr9	6724928	6725028	+	2.8	cIP1vsInput	Intergenic	MER63B|DNA|hAT-Blackjack	452068	NM_029851	110350	Mm.237596	NM_029851	ENSMUSG00000047193	Dync2h1	4432416O06Rik|AI448217|D030010H02Rik|D330044F14Rik|DHC1b|DHC2|Dnchc2|b2b414Clo|mKIAA1997	dynein cytoplasmic 2 heavy chain 1	protein-coding	0	0.287129
Merged-chr3-102491781-1	chr3	102491731	102491831	+	2.8	cIP1vsInput	"intron (NM_001112698, intron 1 of 2)"	"intron (NM_001112698, intron 1 of 2)"	21853	NM_013609	18049	Mm.1259	NM_001112698	ENSMUSG00000027859	Ngf	Ngfb	nerve growth factor	protein-coding	0.01	0.257426
Merged-chr17-37028687-1	chr17	37028637	37028737	+	2.8	cIP2vsInput	Intergenic	Intergenic	-5289	NM_010814	17441	Mm.210857	NM_010814	ENSMUSG00000076439	Mog	B230317G11Rik	myelin oligodendrocyte glycoprotein	protein-coding	0	0.554455
Merged-chr6-5951694-1	chr6	5951644	5951744	+	2.8	cIP1vsInput	"intron (NM_001191023, intron 9 of 15)"	"intron (NM_001191023, intron 9 of 15)"	25699	NR_040255	72249	Mm.443268	NR_040255	ENSMUSG00000085416	1700019G24Rik	-	RIKEN cDNA 1700019G24 gene	miscRNA	0	0.306931
Merged-chr8-91134433-1	chr8	91134383	91134483	+	2.8	cIP2vsInput	"5' UTR (NM_010241, exon 2 of 11)"	"5' UTR (NM_010241, exon 2 of 11)"	1063	NM_010241	14339	Mm.324588	NM_010241	ENSMUSG00000031667	Aktip	AL023020|Fif|Ft|Ft1|Fts	thymoma viral proto-oncogene 1 interacting protein	protein-coding	0.03	0.633663
Merged-chr6-129243551-1	chr6	129243501	129243601	+	2.8	cIP1vsInput	Intergenic	Intergenic	-5069	NR_040266	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	miscRNA	0	0.316832
Merged-chrX-101420373-1	chrX	101420323	101420423	+	2.8	cIP2vsInput	promoter-TSS (NM_001177988)	promoter-TSS (NM_001177988)	-151	NM_019831	56364	Mm.23458	NM_001177985	ENSMUSG00000031310	Zmym3	9030216B10Rik|AW122925|DXS6673E|DXS6673El|Zfp261	"zinc finger, MYM-type 3"	protein-coding	0.07	0.693069
Merged-chr1-66467865-2	chr1	66467806	66467924	+	2.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175510)	promoter-TSS (NM_175510)	-582	NM_175510	329178	Mm.44798	NM_175510	ENSMUSG00000055567	Unc80	C030018G13Rik|C230061B10Rik|UNC-80	unc-80 homolog (C. elegans)	protein-coding	0.025424	0.537815
Merged-chr12-38594286-1	chr12	38594236	38594336	+	2.8	cIP2vsInput	"intron (NR_045943, intron 1 of 8)"	"intron (NR_045943, intron 1 of 8)"	20235	NR_045943	73867	Mm.78933	NR_045943		4930428E07Rik	-	RIKEN cDNA 4930428E07 gene	miscRNA	0	0.386139
Merged-chr4-111687845-1	chr4	111687795	111687895	+	2.8	cIP1vsInput	Intergenic	Intergenic	-32165	NM_026470	67946	Mm.275526	NM_026470	ENSMUSG00000034401	Spata6	1700062C23Rik|AI790763|Hash|KRP|Mash	spermatogenesis associated 6	protein-coding	0.02	0.574257
Merged-chr8-53512088-1	chr8	53512038	53512138	+	2.8	cIP2vsInput	"intron (NM_001005847, intron 1 of 8)"	"intron (NM_001005847, intron 1 of 8)"	386	NM_001005847	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding	0	0.524752
Merged-chr10-75921303-1	chr10	75921253	75921353	+	2.8	cIP2vsInput	"exon (NM_011418, exon 1 of 9)"	"exon (NM_011418, exon 1 of 9)"	311	NM_011418	20587	Mm.405473	NM_001161853	ENSMUSG00000000902	Smarcb1	AU020204|Baf47|Ini1|SNF5/INI1|Snf5	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"	protein-coding	0.13	0.673267
Merged-chr1-33618923-1	chr1	33618873	33618973	+	2.8	cIP1vsInput	"intron (NM_008922, intron 7 of 13)"	"intron (NM_008922, intron 7 of 13)"	50835	NM_008922	19076	Mm.27705	NM_008922	ENSMUSG00000026134	Prim2	AI323589	"DNA primase, p58 subunit"	protein-coding	0	0.356436
Merged-chr10-58731807-1	chr10	58731757	58731857	+	2.8	cIP2vsInput	Intergenic	MER2|DNA|TcMar-Tigger	35062	NR_033565	103505	Mm.50261	NR_033565		BB019430	-	expressed sequence BB019430	miscRNA	0	0.326733
Merged-chr1-176023656-1	chr1	176023606	176023706	+	2.8	cIP2vsInput	"intron (NM_176916, intron 5 of 9)"	"intron (NM_176916, intron 5 of 9)"	142878	NM_012012	26909	Mm.283046	NM_012012	ENSMUSG00000039748	Exo1	5730442G03Rik|Msa	exonuclease 1	protein-coding	0	0.376238
Merged-chr10-85065375-1	chr10	85065325	85065425	+	2.8	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	37120	NM_010214	14202	Mm.46163	NM_010214	ENSMUSG00000050035	Fhl4	-	four and a half LIM domains 4	protein-coding	0.01	0.287129
Merged-chr2-140159455-1	chr2	140159405	140159505	+	2.8	cIP1vsInput	"intron (NM_001081090, intron 5 of 13)"	"intron (NM_001081090, intron 5 of 13)"	11103	NM_001081090	66580	Mm.21228	NM_001081090	ENSMUSG00000045624	Esf1	2610101J03Rik|ABTAP|AW545818|C79684	"ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)"	protein-coding	0	0.316832
Merged-chr5-110230976-1	chr5	110230926	110231026	+	2.8	cIP1vsInput	promoter-TSS (NM_001253814)	promoter-TSS (NM_001253814)	-28	NM_001253814	71782	Mm.288442	NM_001253814	ENSMUSG00000029501	Ankle2	1110001J12Rik|AI661024|D5Ertd585e	ankyrin repeat and LEM domain containing 2	protein-coding	0.12	0.732673
Merged-chr1-43119841-2	chr1	43119772	43119910	+	2.8	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	21131	NM_133818	98404	Mm.28817	NM_133818	ENSMUSG00000010290	AI597479	-	expressed sequence AI597479	protein-coding	0	0.410072
Merged-chr1-36203843-1	chr1	36203793	36203893	+	2.8	cIP2vsInput	"intron (NM_198899, intron 9 of 40)"	L1_Rod|LINE|L1	40459	NM_198899	320011	Mm.261022	NM_198899	ENSMUSG00000037470	Uggt1	0910001L17Rik|A930007H10Rik|AA589501|AI414429|AI448372|C820010P03Rik|GT|UGT1|Ugcgl1	UDP-glucose glycoprotein glucosyltransferase 1	protein-coding	0	0.356436
Merged-chr15-50092118-1	chr15	50092068	50092168	+	2.8	cIP1vsInput	Intergenic	Intergenic	796996	NR_035444	100316685		NR_035444	ENSMUSG00000084458	Mir1907	Mirn1907|mmu-mir-1907	microRNA 1907	miscRNA	0.01	0.326733
Merged-chr15-85879401-2	chr15	85879338	85879465	+	2.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028063)	promoter-TSS (NM_028063)	74	NM_028063	72026	Mm.158211	NM_028063	ENSMUSG00000022386	Trmu	1110005N20Rik|1600025P05Rik|AI314320|Trmt1	tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase	protein-coding	0.125984	0.695312
Merged-chr12-64067733-1	chr12	64067683	64067783	+	2.8	cIP2vsInput	Intergenic	Lx4B|LINE|L1	407165	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.336634
Merged-chr1-88008564-1	chr1	88008514	88008614	+	2.8	cIP2vsInput	promoter-TSS (NM_001198573)	promoter-TSS (NM_001198573)	-13	NM_001033291	227334	Mm.80484	NM_001033291	ENSMUSG00000005501	Usp40	B230215L03Rik|C730029K03	ubiquitin specific peptidase 40	protein-coding	0.07	0.60396
Merged-chr2-157367263-1	chr2	157367213	157367313	+	2.8	cIP1vsInput	promoter-TSS (NM_026968)	promoter-TSS (NM_026968)	-331	NM_026968	69161	Mm.228619	NM_026968	ENSMUSG00000063019	Manbal	1810024K12Rik|AI836500	"mannosidase, beta A, lysosomal-like"	protein-coding	0	0.326733
Merged-chr14-76011008-2	chr14	76010951	76011066	+	2.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026816)	promoter-TSS (NM_026816)	-143	NM_026816	68705	Mm.20415	NM_026816	ENSMUSG00000067995	Gtf2f2	1110031C13Rik|AI326315	"general transcription factor IIF, polypeptide 2"	protein-coding	0.069565	0.568966
Merged-chr10-17467714-1	chr10	17467664	17467764	+	2.8	cIP2vsInput	Intergenic	Intergenic	-255514	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	"Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2"	protein-coding	0	0.306931
Merged-chr8-72160819-1	chr8	72160769	72160869	+	2.8	cIP2vsInput	promoter-TSS (NM_023126)	promoter-TSS (NM_023126)	-381	NM_023126	17274	Mm.162811	NM_023126		Rab8a	AA409338|Mel	"RAB8A, member RAS oncogene family"	protein-coding	0.1	0.653465
Merged-chr6-98178894-1	chr6	98178844	98178944	+	2.8	cIP1vsInput	Intergenic	MLT1A-int|LTR|ERVL-MaLR	163860	NM_001128092	330390	Mm.484161	NM_001128092	ENSMUSG00000090667	Gm765	-	predicted gene 765	protein-coding	0	0.326733
Merged-chr2-60721330-1	chr2	60721280	60721380	+	2.8	cIP1vsInput	"intron (NM_001159564, intron 1 of 17)"	"intron (NM_001159564, intron 1 of 17)"	1273	NM_001159564	16420	Mm.98193	NM_001159564	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding	0	0.405941
Merged-chr10-128923343-1	chr10	128923293	128923393	+	2.8	cIP2vsInput	"intron (NM_015740, intron 1 of 3)"	CpG	181	NM_015740	14533	Mm.30118	NM_015740	ENSMUSG00000090247	Bloc1s1	AI839753|BLOS1|Gcn5l1	"biogenesis of lysosome-related organelles complex-1, subunit 1"	protein-coding	0.09	0.683168
Merged-chr2-122118185-1	chr2	122118135	122118235	+	2.8	cIP2vsInput	"exon (NM_145531, exon 1 of 40)"	"exon (NM_145531, exon 1 of 40)"	201	NM_145531	214585	Mm.222303	NM_172533	ENSMUSG00000033396	Spg11	6030465E24Rik|A330015I11|C530005A01Rik	spastic paraplegia 11	protein-coding	0.05	0.70297
Merged-chr6-64091651-1	chr6	64091601	64091701	+	2.8	cIP2vsInput	"intron (NM_008167, intron 7 of 15)"	"intron (NM_008167, intron 7 of 15)"	-637495	NM_007500	11921	Mm.57229	NM_007500	ENSMUSG00000073043	Atoh1	Hath1|MATH-1|Math1|bHLHa14	atonal homolog 1 (Drosophila)	protein-coding	0	0.376238
Merged-chr7-73482294-1	chr7	73482244	73482344	+	2.8	cIP1vsInput	"intron (NM_001081345, intron 17 of 38)"	"intron (NM_001081345, intron 17 of 38)"	59452	NM_001081345	244059	Mm.34955	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703	chromodomain helicase DNA binding protein 2	protein-coding	0	0.366337
Merged-chr19-4906688-1	chr19	4906638	4906738	+	2.8	cIP2vsInput	promoter-TSS (NM_001033128)	promoter-TSS (NM_001033128)	-61	NM_001033128	52028	Mm.23636	NM_001033128	ENSMUSG00000006464	Bbs1	AI451249|D19Ertd609e	Bardet-Biedl syndrome 1 (human)	protein-coding	0.06	0.524752
Merged-chr5-74556915-1	chr5	74556865	74556965	+	2.8	cIP1vsInput	"intron (NM_001159573, intron 8 of 17)"	"intron (NM_001159573, intron 8 of 17)"	21433	NM_001159574	66899	Mm.272468	NM_001159573		Fip1l1	1300019H17Rik|Rje	FIP1 like 1 (S. cerevisiae)	protein-coding	0.01	0.356436
Merged-chr4-7317937-1	chr4	7317887	7317987	+	2.8	cIP2vsInput	Intergenic	Lx9|LINE|L1	-242751	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	miscRNA	0.02	0.346535
Merged-chr10-101949151-1	chr10	101949101	101949201	+	2.8	cIP2vsInput	"intron (NM_001205098, intron 2 of 7)"	"intron (NM_001205098, intron 2 of 7)"	176459	NR_037211	100526516		NR_037211	ENSMUSG00000092952	Mir3059	mmu-mir-3059	microRNA 3059	miscRNA	0.01	0.336634
Merged-chr17-54653252-1	chr17	54653202	54653302	+	2.8	cIP1vsInput	Intergenic	RLTR21|LTR|ERVK	-283178	NR_045825	69418	Mm.391004	NR_045825		1700025K24Rik	-	RIKEN cDNA 1700025K24 gene	miscRNA	0	0.306931
Merged-chr6-128200526-1	chr6	128200476	128200576	+	2.8	cIP2vsInput	Intergenic	CpG	-16723	NR_077223	330427	Mm.426356	XR_105034		9330102E08Rik	-	RIKEN cDNA 9330102E08 gene	miscRNA	0.07	0.633663
Merged-chr4-147808945-1	chr4	147808895	147808995	+	2.8	cIP2vsInput	"intron (NM_001127189, intron 1 of 5)"	"intron (NM_001127189, intron 1 of 5)"	843	NM_001127189	100041677	Mm.327194	NM_001127189	ENSMUSG00000078495	Gm13157	OTTMUSG00000010679|Rp23-282c23.7	predicted gene 13157	protein-coding	0.02	0.415842
Merged-chr12-113156072-1	chr12	113156022	113156122	+	2.8	cIP2vsInput	promoter-TSS (NM_134041)	promoter-TSS (NM_134041)	-349	NM_134041	104732	Mm.87616	NM_134041	ENSMUSG00000037466	4930427A07Rik	AA536649|mFLJ00116	RIKEN cDNA 4930427A07 gene	protein-coding	0.09	0.693069
Merged-chr7-12921764-1	chr7	12921714	12921814	+	2.8	cIP2vsInput	promoter-TSS (NM_009095)	promoter-TSS (NM_009095)	-547	NM_009095	20103	Mm.5291	NM_009095	ENSMUSG00000012848	Rps5	AA617411	ribosomal protein S5	protein-coding	0.07	0.564356
Merged-chr17-84085928-1	chr17	84085878	84085978	+	2.8	cIP1vsInput	"non-coding (NR_045458, exon 4 of 6)"	"non-coding (NR_045458, exon 4 of 6)"	7268	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	miscRNA	0.02	0.554455
Merged-chr4-29397067-1	chr4	29397017	29397117	+	2.8	cIP2vsInput	Intergenic	MTE2a-int|LTR|ERVL-MaLR	583922	NM_010141	13841	Mm.257266	NM_001122889	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding	0	0.346535
Merged-chr1-12991486-2	chr1	12991386	12991586	+	2.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_172841)	promoter-TSS (NM_172841)	-351	NM_172841	240726	Mm.24481	NM_172841	ENSMUSG00000025938	Slco5a1	4732454B15|A630033C23Rik|AA407151	"solute carrier organic anion transporter family, member 5A1"	protein-coding	0.055	0.447761
Merged-chr1-93305929-1	chr1	93305879	93305979	+	2.8	cIP2vsInput	promoter-TSS (NM_178051)	promoter-TSS (NM_178051)	-59	NM_178051	69821	Mm.52809	NM_178051		Mterfd2	1810059A23Rik|4933412H03Rik|Mterf4	MTERF domain containing 2	protein-coding	0.1	0.643564
Merged-chr9-118952263-1	chr9	118952213	118952313	+	2.8	cIP1vsInput	"intron (NM_133710, intron 1 of 7)"	"intron (NM_133710, intron 1 of 7)"	25727	NM_133710	69274	Mm.439928	NM_133710	ENSMUSG00000047409	Ctdspl	2810418J22Rik|AI426263|HYA22|SCP3	"CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like"	protein-coding	0.05	0.524752
Merged-chr7-127912418-1	chr7	127912368	127912468	+	2.8	cIP2vsInput	promoter-TSS (NM_026370)	promoter-TSS (NM_026370)	-99	NM_026370	67773	Mm.425492	NM_026370	ENSMUSG00000030801	Kat8	2010203C02Rik|5830450F21Rik|D7Ertd629e|MOF|Myst1	K(lysine) acetyltransferase 8	protein-coding	0.04	0.50495
Merged-chr12-45380262-1	chr12	45380212	45380312	+	2.8	cIP1vsInput	Intergenic	RMER3D-int|LTR|ERVK	-305779	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding	0.01	0.356436
Merged-chr4-67923419-1	chr4	67923369	67923469	+	2.8	cIP2vsInput	Intergenic	RMER6C|LTR|ERVK	1030978	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Dbc1	BRINP|Brinp1|Dbccr1|Fam5a	deleted in bladder cancer 1 (human)	protein-coding	0	0.346535
Merged-chr8-109737730-1	chr8	109737680	109737780	+	2.8	cIP2vsInput	promoter-TSS (NM_001080930)	promoter-TSS (NM_001080930)	9	NM_001080930	52335	Mm.276770	NM_001080930	ENSMUSG00000069895	Atxn1l	AW558552|Boat|C330011L24Rik|D6Mgi37|D8Ertd587e|ENSMUSG00000069895	ataxin 1-like	protein-coding	0.14	0.821782
Merged-chr12-10089223-1	chr12	10089173	10089273	+	2.8	cIP2vsInput	Intergenic	Intergenic	-280748	NM_027588	70881	Mm.272843	NM_027588	ENSMUSG00000020622	Nt5c1b	4921514H13Rik|AIRP|CN-IB	"5'-nucleotidase, cytosolic IB"	protein-coding	0	0.287129
Merged-chr3-89998832-1	chr3	89998782	89998882	+	2.8	cIP2vsInput	promoter-TSS (NM_011826)	promoter-TSS (NM_011826)	72	NR_045749	100503469	Mm.440636	NR_045749		Gm19710	-	"predicted gene, 19710"	miscRNA	0.04	0.49505
Merged-chr7-127588464-1	chr7	127588414	127588514	+	2.8	cIP2vsInput	promoter-TSS (NM_172281)	promoter-TSS (NM_172281)	131	NM_001033040	233899	Mm.25220	NM_001033040	ENSMUSG00000057176	Gm166	-	predicted gene 166	protein-coding	0.07	0.574257
Merged-chr3-112778233-1	chr3	112778183	112778283	+	2.8	cIP1vsInput	Intergenic	L1MC|LINE|L1	378494	NM_001190404	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding	0.01	0.336634
Merged-chr1-155504585-1	chr1	155504535	155504635	+	2.8	cIP1vsInput	Intergenic	Intergenic	-53535	NM_001145781	72482	Mm.288249	NM_001145781	ENSMUSG00000033701	Acbd6	0610010G04Rik|2610100E10Rik	acyl-Coenzyme A binding domain containing 6	protein-coding	0	0.346535
Merged-chr6-66534065-1	chr6	66534015	66534115	+	2.8	cIP1vsInput	Intergenic	Intergenic	-1403	NM_019499	56150	Mm.489653	NM_019499	ENSMUSG00000029910	Mad2l1	AA673185|MAD2	MAD2 mitotic arrest deficient-like 1	protein-coding	0.01	0.316832
Merged-chrX-23220162-1	chrX	23220112	23220212	+	2.8	cIP2vsInput	"3' UTR (NM_026167, exon 9 of 9)"	"3' UTR (NM_026167, exon 9 of 9)"	144891	NM_026167	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik|mKIAA1309	kelch-like 13	protein-coding	0	0.306931
Merged-chr17-31766987-1	chr17	31766937	31767037	+	2.8	cIP2vsInput	Intergenic	Intergenic	88805	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding	0.08	0.653465
Merged-chr2-62103944-1	chr2	62103894	62103994	+	2.8	cIP2vsInput	"intron (NM_001242380, intron 1 of 26)"	Lx6|LINE|L1	57429	NM_033552	94229	Mm.314497	NM_001242378	ENSMUSG00000026904	Slc4a10	NCBE|mKIAA4136	"solute carrier family 4, sodium bicarbonate cotransporter-like, member 10"	protein-coding	0	0.336634
Merged-chr3-53350377-1	chr3	53350327	53350427	+	2.8	cIP2vsInput	Intergenic	Intergenic	112881	NM_172501	212114	Mm.85744	NM_172501		Nhlrc3	4833441N19|8030451K01Rik|mKIAA4083	NHL repeat containing 3	protein-coding	0.01	0.306931
Merged-chr2-46584008-1	chr2	46583958	46584058	+	2.8	cIP1vsInput	Intergenic	Intergenic	887403	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	miscRNA	0	0.277228
Merged-chr11-70983024-1	chr11	70982974	70983074	+	2.8	cIP2vsInput	promoter-TSS (NM_007573)	promoter-TSS (NM_007573)	2	NM_007573	12261	Mm.30049	NM_007573	ENSMUSG00000018446	C1qbp	AA407365|AA986492|D11Wsu182e|HABP1|P32|gC1qBP	"complement component 1, q subcomponent binding protein"	protein-coding	0.11	0.712871
Merged-chr8-38996221-1	chr8	38996171	38996271	+	2.8	cIP2vsInput	Intergenic	ORR1C2|LTR|ERVL-MaLR	-9646	NM_030254	80286	Mm.272722	NM_030254		Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding	0	0.386139
Merged-chr1-127921778-1	chr1	127921728	127921828	+	2.8	cIP2vsInput	"intron (NM_178690, intron 11 of 23)"	"intron (NM_178690, intron 11 of 23)"	53005	NM_178690	226407	Mm.489713	NM_178690	ENSMUSG00000036104	Rab3gap1	1700003B17Rik|4732493F09Rik|AL117896|Rab3gap|p130	RAB3 GTPase activating protein subunit 1	protein-coding	0.01	0.356436
Merged-chr18-18239083-1	chr18	18239033	18239133	+	2.8	cIP1vsInput	Intergenic	Intergenic	-658093	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	miscRNA	0	0.336634
Merged-chr12-12680869-1	chr12	12680819	12680919	+	2.8	cIP1vsInput	Intergenic	Intergenic	260967	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"	protein-coding	0.02	0.524752
Merged-chr4-106561365-1	chr4	106561315	106561415	+	2.8	cIP2vsInput	"exon (NM_053272, exon 1 of 9)"	"exon (NM_053272, exon 1 of 9)"	327	NM_053272	74754	Mm.133370	NM_053272	ENSMUSG00000034926	Dhcr24	2310076D10Rik|5830417J06Rik|mKIAA0018	24-dehydrocholesterol reductase	protein-coding	0.14	0.70297
Merged-chr5-45670122-1	chr5	45670072	45670172	+	2.8	cIP1vsInput	promoter-TSS (NR_073433)	promoter-TSS (NR_073433)	197	NM_019438	54392	Mm.32012	NM_019438	ENSMUSG00000015880	Ncapg	5730507H05Rik|Hcapg|MFT.M05.13	"non-SMC condensin I complex, subunit G"	protein-coding	0.13	0.70297
Merged-chr2-158113660-1	chr2	158113610	158113710	+	2.8	cIP2vsInput	Intergenic	Intergenic	-21863	NR_040609	72340	Mm.443395	NR_040609		2010009K17Rik	-	RIKEN cDNA 2010009K17 gene	miscRNA	0.01	0.465347
Merged-chr11-102230408-1	chr11	102230358	102230458	+	2.8	cIP2vsInput	promoter-TSS (NM_010412)	promoter-TSS (NM_010412)	-236	NM_010412	15184	Mm.22665	NM_001077696	ENSMUSG00000008855	Hdac5	AI426555|Hdac4|mHDA1|mKIAA0600	histone deacetylase 5	protein-coding	0.05	0.514851
Merged-chr17-55713516-1	chr17	55713466	55713566	+	2.8	cIP1vsInput	promoter-TSS (NM_028370)	promoter-TSS (NM_028370)	-888	NM_028370	72836	Mm.448349	NM_028370	ENSMUSG00000024174	Pot1b	2810458H16Rik	protection of telomeres 1B	protein-coding	0	0.326733
Merged-chr3-122668523-1	chr3	122668473	122668573	+	2.8	cIP2vsInput	Intergenic	L1MA4|LINE|L1	-48856	NM_153118	214459	Mm.470230	NM_001114665	ENSMUSG00000039735	Fnbp1l	2610318I01Rik|AW548221|TOCA1	formin binding protein 1-like	protein-coding	0	0.336634
Merged-chr14-93711436-1	chr14	93711386	93711486	+	2.8	cIP1vsInput	"intron (NM_001081377, intron 1 of 3)"	"intron (NM_001081377, intron 1 of 3)"	177452	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0.01	0.316832
Merged-chr11-103312228-2	chr11	103312172	103312285	+	2.8	cIP1vsInput|cIP2vsInput	Intergenic	CpG	32474	NM_133715	544817	Mm.399816	NM_001205236	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Sh3d20	Rho GTPase activating protein 27	protein-coding	0.106195	0.736842
Merged-chr8-84105238-1	chr8	84105188	84105288	+	2.8	cIP2vsInput	promoter-TSS (NM_172502)	promoter-TSS (NM_172502)	-476	NM_172502	212123	Mm.260557	NM_172502	ENSMUSG00000037103	Dcaf15	6720484B16	DDB1 and CUL4 associated factor 15	protein-coding	0.05	0.544554
Merged-chr11-120378669-1	chr11	120378619	120378719	+	2.8	cIP2vsInput	promoter-TSS (NM_027980)	promoter-TSS (NM_027980)	77	NM_027980	71885	Mm.274890	NM_027980	ENSMUSG00000025384	2310003H01Rik	Faap100	RIKEN cDNA 2310003H01 gene	protein-coding	0.15	0.732673
Merged-chr5-69857048-1	chr5	69856998	69857098	+	2.8	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-264763	NM_001038015	67980	Mm.33830	NM_001038015	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding	0	0.326733
Merged-chr18-45412447-1	chr18	45412397	45412497	+	2.8	cIP1vsInput	Intergenic	Intergenic	-147707	NM_080465	140492	Mm.458654	NM_080465		Kcnn2	KCa2.2|SK2|SKCA2|fri	"potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2"	protein-coding	0.01	0.277228
Merged-chr1-152670038-1	chr1	152669988	152670088	+	2.8	cIP2vsInput	Intergenic	Intergenic	-44927	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	"ral guanine nucleotide dissociation stimulator,-like 1"	protein-coding	0.02	0.524752
Merged-chr13-87584482-1	chr13	87584432	87584532	+	2.8	cIP2vsInput	Intergenic	Intergenic	-1236990	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0	0.336634
Merged-chr14-97362548-1	chr14	97362498	97362598	+	2.8	cIP1vsInput	Intergenic	Intergenic	806995	NM_001038610	13134	Mm.320593	NM_001038610	ENSMUSG00000055639	Dach1	AI182278|Dac|Dach|E130112M23Rik	dachshund 1 (Drosophila)	protein-coding	0	0.257426
Merged-chr2-32121837-1	chr2	32121787	32121887	+	2.8	cIP2vsInput	Intergenic	Intergenic	26186	NM_145521	227721	Mm.257236	NM_145521	ENSMUSG00000051373	Ppapdc3	D830019K17Rik|NET39	phosphatidic acid phosphatase type 2 domain containing 3	protein-coding	0	0.29703
Merged-chr14-18216590-1	chr14	18216540	18216640	+	2.8	cIP2vsInput	"intron (NM_011584, intron 4 of 7)"	"intron (NM_011584, intron 4 of 7)"	22516	NM_011584	353187	Mm.26587	NM_011584	ENSMUSG00000021775	Nr1d2	RVR|Rev-erb	"nuclear receptor subfamily 1, group D, member 2"	protein-coding	0.01	0.485149
Merged-chr15-85859532-1	chr15	85859482	85859582	+	2.8	cIP2vsInput	promoter-TSS (NM_001168672)	promoter-TSS (NM_001168672)	-175	NM_001168672	29870	Mm.20858	NM_001168672	ENSMUSG00000022385	Gtse1	B99|Gtse-1	G two S phase expressed protein 1	protein-coding	0.06	0.584158
Merged-chr16-96043813-1	chr16	96043763	96043863	+	2.8	cIP2vsInput	"intron (NM_145125, intron 19 of 41)"	"intron (NM_145125, intron 19 of 41)"	38615	NM_001103179	93871	Mm.482469	NM_001103179	ENSMUSG00000022914	Brwd1	5330419I02Rik|D530019K20Rik|G1-403-16|Wdr9|repro5	bromodomain and WD repeat domain containing 1	protein-coding	0	0.336634
Merged-chr4-134245480-1	chr4	134245430	134245530	+	2.8	cIP2vsInput	"non-coding (NR_040436, exon 5 of 5)"	"non-coding (NR_040436, exon 5 of 5)"	111	NM_024215	68040	Mm.426238	NM_024215	ENSMUSG00000028840	Zfp593	3110024A21Rik|AV062409|E130106C14Rik|ZNF593	zinc finger protein 593	protein-coding	0.1	0.633663
Merged-chr12-38750489-1	chr12	38750439	38750539	+	2.8	cIP2vsInput	Intergenic	Intergenic	-29769	NM_007960	14009	Mm.4866	NM_001163154	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant gene 1	protein-coding	0.01	0.346535
Merged-chr6-52750761-1	chr6	52750711	52750811	+	2.8	cIP2vsInput	"intron (NM_025816, intron 12 of 17)"	"intron (NM_025816, intron 12 of 17)"	37032	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding	0	0.316832
Merged-chr11-116581072-1	chr11	116581022	116581122	+	2.8	cIP2vsInput	"exon (NM_173755, exon 1 of 18)"	"exon (NM_173755, exon 1 of 18)"	375	NM_173755	217342	Mm.243950	NM_173755	ENSMUSG00000020802	Ube2o	9630022H21|B230113M03Rik|E2-230K|mKIAA1734	ubiquitin-conjugating enzyme E2O	protein-coding	0.13	0.752475
Merged-chr6-115764469-1	chr6	115764419	115764519	+	2.8	cIP2vsInput	Intergenic	Intergenic	-2003	NM_001168257	94346	Mm.29739	NM_001168256	ENSMUSG00000059900	Tmem40	9030407H20Rik|AV091463|W64236	transmembrane protein 40	protein-coding	0	0.544554
Merged-chr10-80928693-1	chr10	80928643	80928743	+	2.8	cIP2vsInput	Intergenic	CpG	-1398	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding	0.09	0.683168
Merged-chr12-119647596-1	chr12	119647546	119647646	+	2.8	cIP1vsInput	Intergenic	Intergenic	204186	NM_001163136	238455	Mm.31376	NM_001163136	ENSMUSG00000041886	Macc1	4732474O15Rik|Gm267	metastasis associated in colon cancer 1	protein-coding	0	0.346535
Merged-chr19-34334627-1	chr19	34334577	34334677	+	2.8	cIP2vsInput	Intergenic	Intergenic	43968	NM_001146708	14102	Mm.1626	NM_001146708	ENSMUSG00000024778	Fas	AI196731|APO1|APT1|CD95|TNFR6|Tnfrsf6|lpr	Fas (TNF receptor superfamily member 6)	protein-coding	0	0.356436
Merged-chr1-68632820-1	chr1	68632770	68632870	+	2.8	cIP2vsInput	"intron (NM_010154, intron 2 of 26)"	"intron (NM_010154, intron 2 of 26)"	475239	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0.01	0.287129
Merged-chr17-5249193-1	chr17	5249143	5249243	+	2.8	cIP1vsInput	"intron (NM_001085355, intron 5 of 19)"	"intron (NM_001085355, intron 5 of 19)"	169574	NM_175349	106557	Mm.432764	NM_175349		Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding	0.03	0.405941
Merged-chr16-74325115-1	chr16	74325065	74325165	+	2.8	cIP2vsInput	"intron (NM_175549, intron 2 of 27)"	"intron (NM_175549, intron 2 of 27)"	16952	NR_030464	751561		NR_030464		Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	miscRNA	0	0.306931
Merged-chr2-143062324-1	chr2	143062274	143062374	+	2.8	cIP2vsInput	promoter-TSS (NM_021335)	promoter-TSS (NM_021335)	-745	NM_021335	20639	Mm.1323	NM_021335		Snrpb2	2810052G09Rik	U2 small nuclear ribonucleoprotein B	protein-coding	0.02	0.316832
Merged-chr4-30444575-1	chr4	30444525	30444625	+	2.8	cIP2vsInput	Intergenic	Lx5|LINE|L1	-220021	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	miscRNA	0	0.336634
Merged-chr7-48800325-1	chr7	48800275	48800375	+	2.8	cIP2vsInput	"intron (NM_028031, intron 3 of 16)"	"intron (NM_028031, intron 3 of 16)"	11322	NM_028031	243983	Mm.279116	NM_028031	ENSMUSG00000030471	Zdhhc13	2410004E01Rik|C530010M18|HIP3RP|Hip14l|kojak|skc4	"zinc finger, DHHC domain containing 13"	protein-coding	0	0.277228
Merged-chr3-89035166-1	chr3	89035116	89035216	+	2.8	cIP1vsInput	"intron (NM_138679, intron 7 of 26)"	"intron (NM_138679, intron 7 of 26)"	54865	NM_001083808	72296	Mm.27687	NM_001083807	ENSMUSG00000041263	Rusc1	2210403N08Rik|AA408288|NESCA	RUN and SH3 domain containing 1	protein-coding	0	0.306931
Merged-chr12-44475444-1	chr12	44475394	44475494	+	2.8	cIP1vsInput	"intron (NM_176930, intron 3 of 30)"	"intron (NM_176930, intron 3 of 30)"	146559	NM_001146031	319504	Mm.208439	NM_001146031	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuron-glia-CAM-related cell adhesion molecule	protein-coding	0	0.306931
Merged-chr5-149246102-1	chr5	149246052	149246152	+	2.8	cIP2vsInput	Intergenic	Intergenic	-18956	NM_009663	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding	0.02	0.613861
Merged-chr3-45672362-1	chr3	45672312	45672412	+	2.8	cIP2vsInput	Intergenic	Intergenic	-233053	NR_040594	72274	Mm.396202	NR_040594		1700027H10Rik	-	RIKEN cDNA 1700027H10 gene	miscRNA	0	0.326733
Merged-chr8-33324349-1	chr8	33324299	33324399	+	2.8	cIP2vsInput	"exon (NM_011721, exon 9 of 34)"	"exon (NM_011721, exon 9 of 34)"	61178	NM_001122822	22427	Mm.228805	XM_003946269	ENSMUSG00000031583	Wrn	AI846146	Werner syndrome homolog (human)	protein-coding	0	0.366337
Merged-chr6-5382565-1	chr6	5382515	5382615	+	2.8	cIP2vsInput	promoter-TSS (NM_023048)	promoter-TSS (NM_023048)	-821	NM_023048	65255		NM_023048	ENSMUSG00000042607	Asb4	8430401O13Rik|AV117194|AW060255	ankyrin repeat and SOCS box-containing 4	protein-coding	0.02	0.29703
Merged-chr2-38258237-1	chr2	38258187	38258287	+	2.8	cIP2vsInput	"intron (NM_146122, intron 1 of 21)"	"intron (NM_146122, intron 1 of 21)"	29147	NM_146122	227801	Mm.461078	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding	0	0.346535
Merged-chr16-5204034-1	chr16	5203984	5204084	+	2.8	cIP2vsInput	promoter-TSS (NR_027804)	promoter-TSS (NR_027804)	-22	NR_027804	27426	Mm.215641	NM_013796	ENSMUSG00000023143	Nagpa	AI596180|UCE	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase	protein-coding	0.06	0.564356
Merged-chr3-54807736-1	chr3	54807686	54807786	+	2.8	cIP2vsInput	promoter-TSS (NM_133231)	promoter-TSS (NM_133231)	55	NM_133231	170767	Mm.185735	NM_133231	ENSMUSG00000036615	Rfxap	5730495K23Rik	regulatory factor X-associated protein	protein-coding	0.14	0.70297
Merged-chr4-85016343-1	chr4	85016293	85016393	+	2.8	cIP2vsInput	"intron (NM_175275, intron 12 of 25)"	L1_Mur2|LINE|L1	132016	NM_177385	338349	Mm.440562	NM_175275	ENSMUSG00000038070	Cntln	AI448092|B430108F07Rik|D530005L17Rik	"centlein, centrosomal protein"	protein-coding	0	0.366337
Merged-chr14-113484325-1	chr14	113484275	113484375	+	2.8	cIP2vsInput	Intergenic	Intergenic	-1347640	NR_045661	75822	Mm.410813	NR_045661		4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	miscRNA	0	0.326733
Merged-chr3-137444549-1	chr3	137444499	137444599	+	2.8	cIP2vsInput	Intergenic	L1MA6|LINE|L1	103471	NM_016885	59308	Mm.27343	NM_001163522	ENSMUSG00000054690	Emcn	0610012K22Rik|AI315669|Muc14	endomucin	protein-coding	0	0.356436
Merged-chr16-53689970-1	chr16	53689920	53690020	+	2.8	cIP2vsInput	Intergenic	Intergenic	-874226	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	miscRNA	0	0.336634
Merged-chr7-101663740-1	chr7	101663690	101663790	+	2.8	cIP2vsInput	promoter-TSS (NM_009191)	promoter-TSS (NM_009191)	-28	NM_009191	20480	Mm.3990	NM_009191	ENSMUSG00000001829	Clpb	AL118244|Skd3	ClpB caseinolytic peptidase B	protein-coding	0.11	0.653465
Merged-chr17-21733607-1	chr17	21733557	21733657	+	2.8	cIP2vsInput	promoter-TSS (NM_001164676)	promoter-TSS (NM_001164676)	-117	NM_001164676	381067	Mm.482723	NM_001164676	ENSMUSG00000061544	Zfp229	-	zinc finger protein 229	protein-coding	0.02	0.485149
Merged-chr2-152708022-1	chr2	152707972	152708072	+	2.8	cIP2vsInput	"3' UTR (NM_001159551, exon 13 of 13)"	"3' UTR (NM_001159551, exon 13 of 13)"	20874	NM_025543	66405	Mm.440291	NM_025543	ENSMUSG00000042814	Mcts2	2400002F11Rik|RP23-35I8.12	malignant T cell amplified sequence 2	protein-coding	0.05	0.49505
Merged-chr15-20690030-1	chr15	20689980	20690080	+	2.8	cIP2vsInput	Intergenic	Intergenic	-23280	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding	0	0.356436
Merged-chr7-116608635-1	chr7	116608585	116608685	+	2.8	cIP2vsInput	Intergenic	Intergenic	104266	NM_001130479	53322	Mm.9901	NM_016773	ENSMUSG00000030659	Nucb2	AI607786|Calnuc|Nefa|Nesfatin-1	nucleobindin 2	protein-coding	0.03	0.405941
Merged-chr16-22856315-1	chr16	22856265	22856365	+	2.8	cIP2vsInput	"intron (NM_001081368, intron 1 of 7)"	Lx8b|LINE|L1	1254	NM_001081368	70573	Mm.68291	NM_001081368	ENSMUSG00000004462	Tbccd1	5730478M09Rik|AU015083|BB165076	TBCC domain containing 1	protein-coding	0	0.336634
Merged-chr13-32994056-1	chr13	32994006	32994106	+	2.8	cIP1vsInput	Intergenic	RMER17D2|LTR|ERVK	-10485	NM_009256	20723	Mm.272569	NM_009256	ENSMUSG00000045827	Serpinb9	BB283241|CAP-3|CAP3|PI-9|PI9|Spi6|ovalbumin	"serine (or cysteine) peptidase inhibitor, clade B, member 9"	protein-coding	0	0.485149
Merged-chr6-37593054-1	chr6	37593004	37593104	+	2.8	cIP2vsInput	Intergenic	Intergenic	62881	NM_145364	208665	Mm.262635	NM_145364	ENSMUSG00000038641	Akr1d1	-	"aldo-keto reductase family 1, member D1"	protein-coding	0	0.39604
Merged-chr5-9759811-1	chr5	9759761	9759861	+	2.8	cIP2vsInput	Intergenic	Intergenic	-34459	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	"glutamate receptor, metabotropic 3"	protein-coding	0.01	0.356436
Merged-chr6-13620692-1	chr6	13620642	13620742	+	2.8	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-12629	NM_028990	101118	Mm.254845	NM_028990	ENSMUSG00000029569	Tmem168	5730526F17Rik|8430437G11Rik|AI462344|AI504145	transmembrane protein 168	protein-coding	0	0.326733
Merged-chr10-117224387-1	chr10	117224337	117224437	+	2.8	cIP2vsInput	"5' UTR (NM_026570, exon 1 of 7)"	"5' UTR (NM_026570, exon 1 of 7)"	120	NM_026570	64050	Mm.233529	NM_026570	ENSMUSG00000020171	Yeats4	4930573H17Rik|B230215M10Rik|GAS41|NuBI-1	YEATS domain containing 4	protein-coding	0.09	0.752475
Merged-chr8-26236467-1	chr8	26236417	26236517	+	2.8	cIP1vsInput	Intergenic	Intergenic	78298	NM_199042	73754	Mm.383241	NM_199042		Thap1	4833431A01Rik|AW490810	"THAP domain containing, apoptosis associated protein 1"	protein-coding	0	0.29703
Merged-chr6-93031014-1	chr6	93030964	93031064	+	2.8	cIP2vsInput	"intron (NR_015530, intron 1 of 2)"	L1MA8|LINE|L1	90432	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	miscRNA	0	0.306931
Merged-chr1-82882742-1	chr1	82882692	82882792	+	2.8	cIP2vsInput	"intron (NM_010472, intron 7 of 12)"	"intron (NM_010472, intron 7 of 12)"	43259	NM_010472	15463	Mm.433409	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding	0.01	0.336634
Merged-chr8-103333284-1	chr8	103333234	103333334	+	2.8	cIP1vsInput	Intergenic	Intergenic	-270515	NR_045730	71058	Mm.67707	NR_045730		4933400L20Rik	-	RIKEN cDNA 4933400L20 gene	miscRNA	0	0.326733
Merged-chr14-88933731-1	chr14	88933681	88933781	+	2.8	cIP1vsInput	Intergenic	Intergenic	-462335	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0	0.287129
Merged-chr5-43672421-1	chr5	43672371	43672471	+	2.8	cIP2vsInput	"intron (NM_172274, intron 4 of 39)"	"intron (NM_172274, intron 4 of 39)"	10042	NM_172274	231214	Mm.486802	NM_172274	ENSMUSG00000039765	Cc2d2a	5730509K17Rik	coiled-coil and C2 domain containing 2A	protein-coding	0.01	0.455446
Merged-chr14-25585915-1	chr14	25585865	25585965	+	2.8	cIP2vsInput	promoter-TSS (NR_033492)	promoter-TSS (NR_033492)	-889	NR_033492	77592	Mm.444871	NM_175264		4931406H21Rik	-	RIKEN cDNA 4931406H21 gene	miscRNA	0.04	0.653465
Merged-chr8-114439607-2	chr8	114439556	114439659	+	2.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019573)	promoter-TSS (NM_019573)	-45	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding	0.097087	0.634615
Merged-chr14-112923891-1	chr14	112923841	112923941	+	2.8	cIP1vsInput	Intergenic	LTR40b|LTR|ERVL	902461	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0	0.316832
Merged-chr6-75043209-1	chr6	75043159	75043259	+	2.8	cIP1vsInput	Intergenic	Intergenic	-1573542	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.336634
Merged-chr3-57651749-2	chr3	57651662	57651836	+	2.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_175095)	promoter-TSS (NM_175095)	-65	NM_175095	52245	Mm.21901	NM_175095		Commd2	1190017G07Rik|AI047739|D3Ertd176e|HSPC042	COMM domain containing 2	protein-coding	0.08046	0.617143
Merged-chr4-120630426-1	chr4	120630376	120630476	+	2.8	cIP2vsInput	Intergenic	L1MA6|LINE|L1	-36137	NM_019563	56222	Mm.272646	NM_019563	ENSMUSG00000070803	Cited4	MRG-2|Mrg2	"Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 4"	protein-coding	0.04	0.386139
Merged-chr8-20288981-1	chr8	20288931	20289031	+	2.8	cIP1vsInput	"intron (NR_030708, intron 1 of 4)"	"intron (NR_030708, intron 1 of 4)"	8451	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo	0	0.346535
Merged-chr5-110363224-1	chr5	110363174	110363274	+	2.8	cIP2vsInput	"exon (NM_028596, exon 12 of 12)"	"exon (NM_028596, exon 12 of 12)"	9128	NM_001033459	381667	Mm.332572	NM_001033459	ENSMUSG00000072754	Lrcol1	Clpsl3|Gm1679	leucine rich colipase-like 1	protein-coding	0.16	0.80198
Merged-chr2-166714081-1	chr2	166714031	166714131	+	2.8	cIP2vsInput	promoter-TSS (NM_177782)	promoter-TSS (NM_177782)	-249	NM_177782	277360	Mm.34420	NM_177782	ENSMUSG00000039621	Prex1	G630042G04|P-REX1|Setd6	"phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1"	protein-coding	0.11	0.712871
Merged-chr12-36215415-1	chr12	36215365	36215465	+	2.8	cIP2vsInput	"intron (NM_001177877, intron 5 of 7)"	"intron (NM_001177877, intron 5 of 7)"	2787	NM_027699	71156	Mm.250837	NM_027699	ENSMUSG00000020545	Lrrc72	1700108M19Rik|4933421E18Rik	leucine rich repeat containing 72	protein-coding	0	0.346535
Merged-chr12-76782667-1	chr12	76782617	76782717	+	2.8	cIP2vsInput	"intron (NM_206534, intron 3 of 3)"	"intron (NM_206534, intron 3 of 3)"	12887	NM_030677	14776	Mm.441856	NM_030677	ENSMUSG00000042808	Gpx2	GI-GPx|GPx-GI|GSHPx-2|GSHPx-GI	glutathione peroxidase 2	protein-coding	0	0.316832
Merged-chr19-3707554-1	chr19	3707504	3707604	+	2.8	cIP2vsInput	promoter-TSS (NM_028077)	promoter-TSS (NM_028077)	-779	NM_028077	72056	Mm.23780	NM_028077		1810055G02Rik	AI256204	RIKEN cDNA 1810055G02 gene	protein-coding	0.03	0.485149
Merged-chr6-89242564-1	chr6	89242514	89242614	+	2.8	cIP2vsInput	Intergenic	Intergenic	-26385	NR_033190	330379	Mm.297741	NM_201356		Gm839	-	predicted gene 839	miscRNA	0.02	0.653465
Merged-chr15-67302383-1	chr15	67302333	67302433	+	2.8	cIP1vsInput	"intron (NR_045140, intron 5 of 8)"	"intron (NR_045140, intron 5 of 8)"	75614	NR_045140	69334	Mm.63770	NR_045140		1700012I11Rik	-	RIKEN cDNA 1700012I11 gene	miscRNA	0.01	0.376238
Merged-chr8-27551735-1	chr8	27551685	27551785	+	2.8	cIP2vsInput	Intergenic	Intergenic	104065	NM_027618	70952	Mm.158160	NM_026256	ENSMUSG00000063932	Poteg	4921537P18Rik|4930456F22Rik|Gsarp1|Gsarp2	"POTE ankyrin domain family, member G"	protein-coding	0.01	0.356436
Merged-chr14-16575695-1	chr14	16575645	16575745	+	2.8	cIP2vsInput	promoter-TSS (NM_011243)	promoter-TSS (NM_011243)	-485	NM_011243	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2|RARbeta2	"retinoic acid receptor, beta"	protein-coding	0.13	0.70297
Merged-chr8-55832983-1	chr8	55832933	55833033	+	2.8	cIP2vsInput	Intergenic	Lx7|LINE|L1	73981	NM_175939	244486	Mm.67684	NM_175939	ENSMUSG00000046258	Adam29	-	a disintegrin and metallopeptidase domain 29	protein-coding	0.01	0.376238
Merged-chr9-13075574-1	chr9	13075524	13075624	+	2.8	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	30281	NR_040755	78219	Mm.414868	NR_040755		4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	miscRNA	0	0.336634
Merged-chr13-111868042-1	chr13	111867992	111868092	+	2.8	cIP2vsInput	Intergenic	Intergenic	-59059	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding	0.05	0.633663
Merged-chr13-105095119-1	chr13	105095069	105095169	+	2.8	cIP2vsInput	"intron (NM_025751, intron 1 of 7)"	"intron (NM_025751, intron 1 of 7)"	12997	NM_025751	66763	Mm.109093	NM_025751	ENSMUSG00000021718	4933425L06Rik	-	RIKEN cDNA 4933425L06 gene	protein-coding	0	0.316832
Merged-chr11-38564788-1	chr11	38564738	38564838	+	2.8	cIP1vsInput	Intergenic	L2a|LINE|L2	-44743	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0	0.316832
Merged-chr3-65586565-1	chr3	65586515	65586615	+	2.8	cIP1vsInput	Intergenic	Intergenic	-57151	NR_027955	71004	Mm.487418	NR_027955	ENSMUSG00000074580	4931440P22Rik	-	RIKEN cDNA 4931440P22 gene	miscRNA	0.05	0.60396
Merged-chr3-67582675-1	chr3	67582625	67582725	+	2.8	cIP2vsInput	promoter-TSS (NM_025813)	promoter-TSS (NM_025813)	-93	NM_025813	66868	Mm.271975	NM_025813	ENSMUSG00000027775	Mfsd1	1200003O06Rik	major facilitator superfamily domain containing 1	protein-coding	0.11	0.653465
Merged-chr6-53269025-1	chr6	53268975	53269075	+	2.8	cIP2vsInput	Intergenic	Intergenic	-18270	NR_015553	320189		NR_015553		9430076C15Rik	-	RIKEN cDNA 9430076C15 gene	miscRNA	0	0.346535
Merged-chr17-90212934-1	chr17	90212884	90212984	+	2.8	cIP1vsInput	"intron (NM_020252, intron 18 of 22)"	"intron (NM_020252, intron 18 of 22)"	-648235	NR_045463	78800	Mm.410772	NR_045463	ENSMUSG00000090160	4930480K15Rik	-	RIKEN cDNA 4930480K15 gene	miscRNA	0	0.267327
Merged-chr7-29767407-1	chr7	29767357	29767457	+	2.8	cIP1vsInput	Intergenic	Intergenic	-1145	NM_023750	74352	Mm.251083	NM_023750		Zfp84	2210410P13Rik|4633401C23Rik|AI415447|BB081605|C86188|KRAB18|Zfp69	zinc finger protein 84	protein-coding	0.03	0.49505
Merged-chr18-72195639-1	chr18	72195589	72195689	+	2.8	cIP1vsInput	"intron (NM_007831, intron 1 of 28)"	"intron (NM_007831, intron 1 of 28)"	155430	NM_007831	13176	Mm.167882	NM_007831		Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding	0.01	0.336634
Merged-chr3-118722077-1	chr3	118722027	118722127	+	2.8	cIP1vsInput	"intron (NM_170778, intron 3 of 22)"	"intron (NM_170778, intron 3 of 22)"	159899	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding	0	0.336634
Merged-chr1-185501434-1	chr1	185501384	185501484	+	2.8	cIP2vsInput	Intergenic	Intergenic	4128	NR_033600	114668	Mm.491071	NR_033600		5033404E19Rik	-	NSA2 ribosome biogenesis homolog pseudogene	pseudo	0	0.366337
Merged-chr14-121799591-1	chr14	121799541	121799641	+	2.8	cIP1vsInput	Intergenic	Intergenic	-1857	NM_134074	105445	Mm.441054	NM_001081039	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding	0.01	0.306931
Merged-chr8-84723091-1	chr8	84723041	84723141	+	2.8	cIP1vsInput	"intron (NM_010906, intron 6 of 8)"	"intron (NM_010906, intron 6 of 8)"	21634	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding	0.02	0.554455
Merged-chr2-114666211-1	chr2	114666161	114666261	+	2.8	cIP2vsInput	Intergenic	Intergenic	-11283	NM_025675	66632	Mm.117809	NM_025675	ENSMUSG00000057147	Atpbd4	5730421E18Rik	ATP binding domain 4	protein-coding	0	0.356436
Merged-chr13-107035764-1	chr13	107035714	107035814	+	2.8	cIP2vsInput	Intergenic	LTR16A|LTR|ERVL	13194	NR_015471	100040322	Mm.133867	NR_015471		3830408C21Rik	-	RIKEN cDNA 3830408C21 gene	miscRNA	0	0.405941
Merged-chr12-87472117-1	chr12	87472067	87472167	+	2.8	cIP2vsInput	"intron (NM_025507, intron 1 of 13)"	CpG	182	NM_025507	66354	Mm.271174	NM_025507	ENSMUSG00000021039	Snw1	2310008B08Rik|AW048543|NCoA-62|SKIP|Skiip	SNW domain containing 1	protein-coding	0.09	0.623762
Merged-chr10-95730108-1	chr10	95730058	95730158	+	2.8	cIP2vsInput	Intergenic	LTR72_RN|LTR|ERV1	-165941	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding	0.03	0.50495
Merged-chr15-80932594-1	chr15	80932544	80932644	+	2.8	cIP2vsInput	"3' UTR (NM_177124, exon 22 of 22)"	"3' UTR (NM_177124, exon 22 of 22)"	-7445	NR_039573	100628612		NR_039573	ENSMUSG00000092868	Mir5113	mmu-mir-5113|mu-mir-5113	microRNA 5113	miscRNA	0	0.316832
Merged-chr8-20282128-1	chr8	20282078	20282178	+	2.8	cIP1vsInput	"intron (NR_030708, intron 2 of 4)"	"intron (NR_030708, intron 2 of 4)"	15304	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo	0	0.316832
Merged-chr14-99932441-1	chr14	99932391	99932491	+	2.8	cIP2vsInput	"intron (NM_010636, intron 5 of 6)"	"intron (NM_010636, intron 5 of 6)"	217355	NM_010636	16597	Mm.458816	NM_010636		Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding	0	0.326733
Merged-chr11-75486491-1	chr11	75486441	75486541	+	2.8	cIP2vsInput	promoter-TSS (NM_138659)	promoter-TSS (NM_138659)	-286	NM_138659	192159	Mm.3757	NM_138659	ENSMUSG00000020850	Prpf8	AU019467|D11Bwg0410e|DBF3/PRP8|Prp8|Sfprp8l	pre-mRNA processing factor 8	protein-coding	0	0.336634
Merged-chr15-79229211-1	chr15	79229161	79229261	+	2.8	cIP1vsInput	promoter-TSS (NM_008837)	promoter-TSS (NM_008837)	37	NM_008837	18693	Mm.259464	NM_001045558	ENSMUSG00000068206	Pick1	Prkcabp	protein interacting with C kinase 1	protein-coding	0.08	0.594059
Merged-chr8-127948535-1	chr8	127948485	127948585	+	2.8	cIP1vsInput	Intergenic	Intergenic	-410538	NM_008737	18186	Mm.271745	NM_008737	ENSMUSG00000025810	Nrp1	C530029I03|NP-1|NPN-1|Npn1|Nrp	neuropilin 1	protein-coding	0	0.316832
Merged-chr8-74897225-1	chr8	74897175	74897275	+	2.8	cIP2vsInput	Intergenic	Intergenic	24051	NM_027837	71597	Mm.158735	NM_027837		Isx	9130012O13Rik|Pix-1	intestine specific homeobox	protein-coding	0	0.376238
Merged-chr18-38338325-1	chr18	38338275	38338375	+	2.8	cIP2vsInput	"intron (NM_011937, intron 1 of 6)"	"intron (NM_011937, intron 1 of 6)"	668	NM_011937	26384	Mm.22374	NM_011937	ENSMUSG00000052102	Gnpda1	GNPDA|Gnp1|Gnpi|oscillin	glucosamine-6-phosphate deaminase 1	protein-coding	0.05	0.623762
Merged-chr2-64715418-1	chr2	64715368	64715468	+	2.8	cIP1vsInput	Intergenic	Lx7|LINE|L1	307348	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding	0	0.29703
Merged-chr15-43283161-1	chr15	43283111	43283211	+	2.8	cIP2vsInput	promoter-TSS (NM_008388)	promoter-TSS (NM_008388)	-425	NM_008388	16341	Mm.289992	NM_008388	ENSMUSG00000022336	Eif3e	48kDa|Eif3s6|Int6|eIF3-p46|eIF3-p48	"eukaryotic translation initiation factor 3, subunit E"	protein-coding	0	0.39604
Merged-chr9-82991775-1	chr9	82991725	82991825	+	2.8	cIP1vsInput	Intergenic	Intergenic	-16286	NM_001081216	83946	Mm.221688	NM_001081216	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding	0	0.29703
Merged-chr10-38876220-1	chr10	38876170	38876270	+	2.8	cIP2vsInput	Intergenic	Intergenic	-54441	NM_001177783	215919	Mm.294313	NM_001177783	ENSMUSG00000094311	Rfpl4b	100040915|Gm3037|Gm62	ret finger protein-like 4B	protein-coding	0	0.306931
Merged-chr14-87511935-1	chr14	87511885	87511985	+	2.8	cIP2vsInput	"3' UTR (NM_001253755, exon 12 of 12)"	"3' UTR (NM_001253755, exon 12 of 12)"	95352	NM_001253755	219249	Mm.35168	NM_001253755	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding	0	0.306931
Merged-chr2-128180130-1	chr2	128180080	128180180	+	2.8	cIP2vsInput	Intergenic	Intergenic	54092	NM_009754	12125	Mm.453214	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod	BCL2-like 11 (apoptosis facilitator)	protein-coding	0.04	0.574257
Merged-chr4-18770601-2	chr4	18770551	18770652	+	2.8	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-510249	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding	0	0.264706
Merged-chr18-29833223-1	chr18	29833173	29833273	+	2.8	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-336807	NR_045391	78058	Mm.416952	NR_045391		4930578E11Rik	-	RIKEN cDNA 4930578E11 gene	miscRNA	0	0.336634
Merged-chr14-93859258-1	chr14	93859208	93859308	+	2.8	cIP2vsInput	"intron (NM_001081377, intron 1 of 3)"	"intron (NM_001081377, intron 1 of 3)"	29630	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.316832
Merged-chr9-77643243-1	chr9	77643193	77643293	+	2.8	cIP2vsInput	"intron (NM_172925, intron 1 of 2)"	Lx8|LINE|L1	6511	NM_172925	244923	Mm.138238	NM_177238	ENSMUSG00000044938	Klhl31	9830147P19Rik|D930047P17Rik|Kbtbd1	kelch-like 31	protein-coding	0.01	0.346535
Merged-chr11-85545363-1	chr11	85545313	85545413	+	2.8	cIP2vsInput	"intron (NM_138681, intron 18 of 25)"	"intron (NM_138681, intron 18 of 25)"	174381	NR_045875	71489	Mm.442482	NR_045875	ENSMUSG00000086199	8430403D17Rik	-	RIKEN cDNA 8430403D17 gene	miscRNA	0	0.336634
Merged-chr11-78042161-1	chr11	78042111	78042211	+	2.8	cIP2vsInput	"intron (NM_001040403, intron 1 of 10)"	Charlie4a|DNA|hAT-Charlie	4220	NM_008028	14252	Mm.130227	NM_001040403	ENSMUSG00000061981	Flot2	AI573412|Esa|reggie-2	flotillin 2	protein-coding	0.01	0.336634
Merged-chr3-70104239-1	chr3	70104189	70104289	+	2.8	cIP2vsInput	Intergenic	Intergenic	96626	NM_001018031	229389	Mm.331071	NM_001018031	ENSMUSG00000027788	Otol1	Gm414	otolin 1 homolog (zebrafish)	protein-coding	0.02	0.376238
Merged-chr10-24131549-1	chr10	24131499	24131599	+	2.8	cIP2vsInput	Intergenic	Intergenic	-17768	NM_016797	53331	Mm.248042	NM_016797	ENSMUSG00000019998	Stx7	AI315064|AI317144|AW107239|Syn7	syntaxin 7	protein-coding	0.01	0.326733
Merged-chr2-17218387-1	chr2	17218337	17218437	+	2.8	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-204661	NR_040632	75069	Mm.399263	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	miscRNA	0	0.386139
Merged-chr6-90868688-1	chr6	90868638	90868738	+	2.8	cIP2vsInput	Intergenic	RMER15|LTR|ERVL	-58565	NM_001134384	232227	Mm.473438	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43|mKIAA0763	IQ motif and Sec7 domain 1	protein-coding	0	0.346535
Merged-chr9-63195004-1	chr9	63194954	63195054	+	2.8	cIP2vsInput	"intron (NM_011840, intron 20 of 21)"	"intron (NM_011840, intron 20 of 21)"	-46043	NM_001163758	207667	Mm.447200	NM_001163755	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding	0.02	0.475248
Merged-chr9-44361951-1	chr9	44361901	44362001	+	2.8	cIP1vsInput	promoter-TSS (NM_027889)	promoter-TSS (NM_027889)	-281	NM_027889	71732	Mm.295013	NM_027889	ENSMUSG00000032127	Vps11	1200011A11Rik	vacuolar protein sorting 11 (yeast)	protein-coding	0.01	0.306931
Merged-chr8-15627173-1	chr8	15627123	15627223	+	2.8	cIP2vsInput	Intergenic	Intergenic	541665	NR_037214	100526464		NR_037214		Mir3106	mmu-mir-3106	microRNA 3106	miscRNA	0.01	0.326733
Merged-chr4-139599415-1	chr4	139599365	139599465	+	2.8	cIP2vsInput	"intron (NM_001205173, intron 1 of 8)"	"intron (NM_001205173, intron 1 of 8)"	-23479	NM_175438	212647	Mm.273571	NM_175438	ENSMUSG00000028737	Aldh4a1	A930035F14Rik|Ahd-1|Ahd1|Aldh4|Aldh5a1|E330022C09|P5cd|P5cdh|P5cdhl|P5cdhs|Ssdh1	"aldehyde dehydrogenase 4 family, member A1"	protein-coding	0.01	0.524752
Merged-chr2-105162931-1	chr2	105162881	105162981	+	2.8	cIP2vsInput	"intron (NM_144783, intron 5 of 9)"	"intron (NM_144783, intron 5 of 9)"	36402	NM_144783	22431	Mm.389339	NM_144783	ENSMUSG00000016458	Wt1	D630046I19Rik|Wt-1	Wilms tumor 1 homolog	protein-coding	0.03	0.475248
Merged-chr2-177332040-1	chr2	177331990	177332090	+	2.8	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	-132702	NM_001177568	628308	Mm.460436	NM_001177568		Gm14420	OTTMUSG00000016588	predicted gene 14420	protein-coding	0	0.306931
Merged-chr1-165663023-1	chr1	165662973	165663073	+	2.8	cIP2vsInput	"intron (NM_001038846, intron 2 of 5)"	"intron (NM_001038846, intron 2 of 5)"	-28482	NM_001083897	68481	Mm.46438	NM_001001880	ENSMUSG00000026566	Mpzl1	1110007A10Rik|PZR	myelin protein zero-like 1	protein-coding	0.01	0.445545
Merged-chr6-31011700-1	chr6	31011650	31011750	+	2.8	cIP2vsInput	Intergenic	(GA)n|Simple_repeat|Simple_repeat	51047	NR_029744	387222		NR_029744	ENSMUSG00000065610	Mir29a	Mirn29a|mmu-mir-29a	microRNA 29a	miscRNA	0.01	0.445545
Merged-chr11-116087587-1	chr11	116087537	116087637	+	2.8	cIP2vsInput	promoter-TSS (NM_016852)	promoter-TSS (NM_016852)	-623	NM_016852	22378	Mm.284792	NM_016852	ENSMUSG00000034341	Wbp2	-	WW domain binding protein 2	protein-coding	0.09	0.693069
Merged-chr16-20804932-1	chr16	20804882	20804982	+	2.8	cIP2vsInput	Intergenic	Intergenic	-70421	NM_009379	21832	Mm.3943	NM_001173505		Thpo	Mgdf|Ml|Mpllg|Tpo|Tpo1|Tpo2|Tpo3|Tpo4	thrombopoietin	protein-coding	0.03	0.60396
Merged-chr8-30655732-1	chr8	30655682	30655782	+	2.8	cIP2vsInput	Intergenic	Intergenic	87337	NR_045856	71314	Mm.158666	NR_045856	ENSMUSG00000097044	4933433F19Rik	-	RIKEN cDNA 4933433F19 gene	miscRNA	0.01	0.386139
Merged-chr17-50881744-1	chr17	50881694	50881794	+	2.8	cIP2vsInput	"intron (NM_028162, intron 13 of 21)"	L1_Mus3|LINE|L1	-266152	NR_035408	735256		NR_035408		Mir669a-1	Mir669a-1a|Mirn669a-1|Mirn669a-1a|mir-669a-1	microRNA 669a-1	miscRNA	0	0.316832
Merged-chr3-148030765-1	chr3	148030715	148030815	+	2.8	cIP1vsInput	Intergenic	Intergenic	923870	NM_001081298	99633	Mm.462301	NM_001081298	ENSMUSG00000028184	Lphn2	AI450192|Gm619|Lec1|Lphh1|mKIAA0786	latrophilin 2	protein-coding	0	0.306931
Merged-chr12-83632609-1	chr12	83632559	83632659	+	2.8	cIP2vsInput	"intron (NM_027349, intron 1 of 18)"	CpG	375	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding	0.08	0.732673
Merged-chr17-80148301-1	chr17	80148251	80148351	+	2.8	cIP1vsInput	"intron (NM_176963, intron 3 of 6)"	"intron (NM_176963, intron 3 of 6)"	20830	NM_176963	319625	Mm.29098	NM_176963	ENSMUSG00000035473	Galm	A530057M15Rik|AU015645|AU020959	galactose mutarotase	protein-coding	0.03	0.60396
Merged-chr10-99931255-1	chr10	99931205	99931305	+	2.8	cIP1vsInput	Intergenic	L1M3|LINE|L1	-84569	NM_013598	17311	Mm.45124	NM_013598	ENSMUSG00000019966	Kitl	Clo|Con|Gb|Kitlg|Mgf|SCF|SF|SLF|Sl|blz|contrasted	kit ligand	protein-coding	0.01	0.326733
Merged-chr11-106438364-1	chr11	106438314	106438414	+	2.8	cIP1vsInput	"intron (NM_023913, intron 2 of 21)"	"intron (NM_023913, intron 2 of 21)"	49432	NM_023913	78943	Mm.340943	NM_023913		Ern1	9030414B18Rik|AI225830|C85377|Ire1a|Ire1alpha|Ire1p	endoplasmic reticulum (ER) to nucleus signalling 1	protein-coding	0	0.346535
Merged-chr16-67122985-1	chr16	67122935	67123035	+	2.8	cIP2vsInput	"intron (NM_178721, intron 1 of 9)"	"intron (NM_178721, intron 1 of 9)"	465867	NR_040512	75501	Mm.396161	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	miscRNA	0.02	0.316832
Merged-chr17-45742408-1	chr17	45742358	45742458	+	2.8	cIP1vsInput	Intergenic	L1MB3|LINE|L1	-8564	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding	0	0.336634
Merged-chr11-88147503-1	chr11	88147453	88147553	+	2.8	cIP2vsInput	"intron (NM_198013, intron 1 of 10)"	L1MB4|LINE|L1	-22062	NM_001172099	103841	Mm.374846	NM_001172099	ENSMUSG00000018378	Cuedc1	AI841487|C330016O16Rik	CUE domain containing 1	protein-coding	0.02	0.514851
Merged-chr7-126475458-1	chr7	126475408	126475508	+	2.8	cIP2vsInput	promoter-TSS (NM_011363)	promoter-TSS (NM_011363)	-328	NM_011363	20399	Mm.8538	NM_001081459	ENSMUSG00000030733	Sh2b1	AI425885|C530001K22Rik|Irip|SH2-B|SH2-Bb|Sh2bpsm1|mKIAA1299	SH2B adaptor protein 1	protein-coding	0.05	0.594059
Merged-chr6-15038053-1	chr6	15038003	15038103	+	2.8	cIP2vsInput	"intron (NM_053242, intron 2 of 18)"	"intron (NM_053242, intron 2 of 18)"	136704	NM_053242	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding	0	0.366337
Merged-chr4-11156163-1	chr4	11156113	11156213	+	2.8	cIP2vsInput	promoter-TSS (NM_021897)	promoter-TSS (NM_021897)	-278	NM_021897	60599	Mm.393018	NM_021897	ENSMUSG00000028211	Trp53inp1	2700057G22Rik|SIP|SIP18|SIP27|Stinp|Teap	transformation related protein 53 inducible nuclear protein 1	protein-coding	0.1	0.742574
Merged-chr1-97688961-1	chr1	97688911	97689011	+	2.8	cIP1vsInput	Intergenic	Intergenic	-26943	NM_133825	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	"DNA segment, Chr 1, ERATO Doi 622, expressed"	protein-coding	0.01	0.475248
Merged-chr5-96072619-1	chr5	96072569	96072669	+	2.8	cIP2vsInput	Intergenic	Intergenic	89136	NM_178854	231464	Mm.384746	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	"CCR4-NOT transcription complex, subunit 6-like"	protein-coding	0	0.29703
Merged-chr2-19156661-1	chr2	19156611	19156711	+	2.8	cIP1vsInput	Intergenic	Intergenic	-42457	NM_001271563	70882	Mm.276696	NM_001081083	ENSMUSG00000037683	Armc3	4921513G22Rik	armadillo repeat containing 3	protein-coding	0	0.346535
Merged-chr2-146513033-1	chr2	146512983	146513083	+	2.8	cIP2vsInput	Intergenic	Intergenic	-1029	NM_001033348	241694	Mm.222310	NM_001033348	ENSMUSG00000037110	Ralgapa2	A230067G21Rik|AS250|BC053994|RGC2|pp250	"Ral GTPase activating protein, alpha subunit 2 (catalytic)"	protein-coding	0	0.376238
Merged-chr10-17155495-1	chr10	17155445	17155545	+	2.8	cIP1vsInput	Intergenic	Intergenic	-59713	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0	0.316832
Merged-chr6-47581957-1	chr6	47581907	47582007	+	2.8	cIP1vsInput	"intron (NM_001146689, intron 1 of 19)"	MMAR1|DNA|TcMar-Mariner	13073	NM_007971	14056	Mm.246688	NM_001146689	ENSMUSG00000029687	Ezh2	Enx-1|Enx1h|KMT6|mKIAA4065	enhancer of zeste homolog 2 (Drosophila)	protein-coding	0	0.316832
Merged-chr3-76302103-1	chr3	76302053	76302153	+	2.8	cIP1vsInput	"intron (NM_178673, intron 3 of 15)"	"intron (NM_178673, intron 3 of 15)"	226520	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.336634
Merged-chr5-140419285-1	chr5	140419235	140419335	+	2.8	cIP2vsInput	promoter-TSS (NM_133916)	promoter-TSS (NM_133916)	-20	NM_133916	27979	Mm.21671	NM_133916	ENSMUSG00000056076	Eif3b	AL033316|AL033334|AL033369|AW208965|D5Wsu45e|EIF3-ETA|EIF3-P110|EIF3-P116|Eif3s9|PRT1	"eukaryotic translation initiation factor 3, subunit B"	protein-coding	0.13	0.683168
Merged-chr3-9773720-1	chr3	9773670	9773770	+	2.8	cIP2vsInput	"intron (NM_053182, intron 1 of 7)"	"intron (NM_053182, intron 1 of 7)"	59959	NM_053182	94212	Mm.486503	NM_001195031	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding	0	0.326733
Merged-chr1-62123849-1	chr1	62123799	62123899	+	2.8	cIP2vsInput	"intron (NM_001081050, intron 4 of 22)"	"intron (NM_001081050, intron 4 of 22)"	485025	NM_001081050	72823	Mm.441881	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta|RP23-20G7.1	par-3 partitioning defective 3 homolog B (C. elegans)	protein-coding	0	0.356436
Merged-chr3-104442080-1	chr3	104442030	104442130	+	2.8	cIP1vsInput	Intergenic	Intergenic	69776	NM_001025067	269473	Mm.34855	NM_001025067	ENSMUSG00000032913	Lrig2	4632419I10Rik|BB096938	leucine-rich repeats and immunoglobulin-like domains 2	protein-coding	0.05	0.544554
Merged-chr2-140809796-1	chr2	140809746	140809846	+	2.8	cIP1vsInput	"intron (NM_001013802, intron 3 of 18)"	"intron (NM_001013802, intron 3 of 18)"	-138320	NM_178382	71436	Mm.426781	NM_001172160	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0	0.306931
Merged-chr18-23989593-1	chr18	23989543	23989643	+	2.8	cIP2vsInput	promoter-TSS (NM_011755)	promoter-TSS (NM_011755)	-41	NM_011755	22694	Mm.290596	NM_011755	ENSMUSG00000063281	Zfp35	Zfp-35|Znf271|mszf13|mszf20-1|mszf28|mszf68	zinc finger protein 35	protein-coding	0.06	0.554455
Merged-chr5-80518633-1	chr5	80518583	80518683	+	2.8	cIP1vsInput	Intergenic	Intergenic	-502960	NM_198702	319387	Mm.461016	NM_198702	ENSMUSG00000037605	Lphn3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|mKIAA0768	latrophilin 3	protein-coding	0.01	0.267327
Merged-chr8-33802593-1	chr8	33802543	33802643	+	2.8	cIP1vsInput	"intron (NM_001042674, intron 6 of 7)"	B4A|SINE|B4	-54823	NM_001206849	72632	Mm.443774	NM_001206849	ENSMUSG00000094500	Smim18	2700090O03Rik|AI835723	small integral membrane protein 18	protein-coding	0.03	0.544554
Merged-chr12-73895701-1	chr12	73895651	73895751	+	2.8	cIP1vsInput	Intergenic	Intergenic	-12166	NM_010431	15251	Mm.446610	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF1alpha|MOP1|bHLHe78	"hypoxia inducible factor 1, alpha subunit"	protein-coding	0.01	0.267327
Merged-chr12-15536184-1	chr12	15536134	15536234	+	2.8	cIP2vsInput	Intergenic	Intergenic	280601	NM_144551	217410	Mm.266679	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles homolog 2 (Drosophila)	protein-coding	0.01	0.336634
Merged-chr11-86570569-1	chr11	86570519	86570619	+	2.8	cIP2vsInput	Intergenic	Intergenic	13589	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21	Mirn21|mmu-mir-21	microRNA 21	miscRNA	0.02	0.465347
Merged-chr14-47534094-1	chr14	47534044	47534144	+	2.8	cIP1vsInput	Intergenic	Intergenic	34340	NM_172599	100504663	Mm.470462	NM_172599	ENSMUSG00000037526	Atg14	4832427M01|Atg14L|D14Ertd114e|D14Ertd436e	autophagy related 14	protein-coding	0	0.435644
Merged-chr6-87914212-1	chr6	87914162	87914262	+	2.8	cIP2vsInput	TTS (NM_017477)	TTS (NM_017477)	236	NM_173737	232210	Mm.246241	NM_173737	ENSMUSG00000030060	8430410A17Rik	C85376	RIKEN cDNA 8430410A17 gene	protein-coding	0.16	0.772277
Merged-chr9-37738527-1	chr9	37738477	37738577	+	2.8	cIP2vsInput	Intergenic	Intergenic	-7466	NM_207664	406176	Mm.356219	NM_207664		Olfr151	M71|MOR171-2	olfactory receptor 151	protein-coding	0.01	0.29703
Merged-chr5-143817447-1	chr5	143817397	143817497	+	2.8	cIP2vsInput	Intergenic	Intergenic	-54415	NM_013557	15467	Mm.431968	NM_013557		Eif2ak1	HCR|Hri	eukaryotic translation initiation factor 2 alpha kinase 1	protein-coding	0.05	0.485149
Merged-chr13-112927587-1	chr13	112927537	112927637	+	2.8	cIP2vsInput	promoter-TSS (NM_172594)	promoter-TSS (NM_172594)	-206	NM_172594	218629	Mm.35094	NM_172594	ENSMUSG00000042426	Dhx29	3732415M03|AU043276|Ddxx|E130202M19Rik	DEAH (Asp-Glu-Ala-His) box polypeptide 29	protein-coding	0.1	0.623762
Merged-chr14-101873051-1	chr14	101873001	101873101	+	2.8	cIP2vsInput	"intron (NM_201529, intron 4 of 30)"	"intron (NM_201529, intron 4 of 30)"	143123	NM_201529	380928		NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding	0.01	0.485149
Merged-chr11-98246086-1	chr11	98246036	98246136	+	2.8	cIP1vsInput	"3' UTR (NM_026952, exon 13 of 13)"	"3' UTR (NM_026952, exon 13 of 13)"	-16520	NR_039579	100628613		NR_039579	ENSMUSG00000093176	Mir5119	mmu-mir-5119|mu-mir-5119	microRNA 5119	miscRNA	0	0.366337
Merged-chr14-30549091-1	chr14	30549041	30549141	+	2.8	cIP2vsInput	promoter-TSS (NM_009388)	promoter-TSS (NM_009388)	-58	NM_009388	21881	Mm.290692	NM_009388	ENSMUSG00000021957	Tkt	p68	transketolase	protein-coding	0.11	0.752475
Merged-chr6-104896021-1	chr6	104895971	104896071	+	2.8	cIP2vsInput	Intergenic	L1M5|LINE|L1	402977	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding	0.01	0.29703
Merged-chr6-37144062-1	chr6	37144012	37144112	+	2.8	cIP2vsInput	"intron (NM_001081206, intron 2 of 33)"	"intron (NM_001081206, intron 2 of 33)"	155914	NM_001081206	320127	Mm.442505	NM_001081206	ENSMUSG00000038665	Dgki	C130010K08Rik	"diacylglycerol kinase, iota"	protein-coding	0.02	0.564356
Merged-chr6-20316236-1	chr6	20316186	20316286	+	2.8	cIP2vsInput	Intergenic	(TTTG)n|Simple_repeat|Simple_repeat	-899873	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	"potassium voltage-gated channel, Shal-related family, member 2"	protein-coding	0.01	0.29703
Merged-chr4-145680195-1	chr4	145680145	145680245	+	2.8	cIP2vsInput	"intron (NM_001103158, intron 2 of 4)"	"intron (NM_001103158, intron 2 of 4)"	9498	NM_001103158	100041379	Mm.276881	NM_001103158	ENSMUSG00000058186	Gm13242	OTTMUSG00000011070	predicted gene 13242	protein-coding	0.02	0.336634
Merged-chr11-41995841-1	chr11	41995791	41995891	+	2.8	cIP2vsInput	"intron (NM_177408, intron 1 of 8)"	"intron (NM_177408, intron 1 of 8)"	4873	NM_177408	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2"	protein-coding	0.01	0.346535
Merged-chr6-110046219-1	chr6	110046169	110046269	+	2.8	cIP2vsInput	Intergenic	Intergenic	-599379	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0.01	0.326733
Merged-chr5-74300267-1	chr5	74300217	74300317	+	2.8	cIP2vsInput	"intron (NM_001114660, intron 5 of 8)"	"intron (NM_001114660, intron 5 of 8)"	104941	NM_026878	68939	Mm.293316	NM_026878	ENSMUSG00000049907	Rasl11b	1190017B18Rik	"RAS-like, family 11, member B"	protein-coding	0.02	0.50495
Merged-chr11-96916696-2	chr11	96916621	96916772	+	2.8	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_030248)	promoter-TSS (NM_030248)	-215	NM_030248	80280	Mm.28297	NM_030248	ENSMUSG00000018669	Cdk5rap3	1810007E24Rik|BC002318|C53|C81486|HSF-27|IC53|MST016	CDK5 regulatory subunit associated protein 3	protein-coding	0.07947	0.618421
Merged-chr2-141571037-1	chr2	141570987	141571087	+	2.8	cIP1vsInput	"intron (NM_001013802, intron 6 of 18)"	"intron (NM_001013802, intron 6 of 18)"	-899561	NM_178382	71436	Mm.426781	NM_001172160	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0	0.376238
Merged-chr9-39689392-1	chr9	39689342	39689442	+	2.8	cIP2vsInput	Intergenic	Intergenic	13375	NM_207138	235256	Mm.478260	NM_207138	ENSMUSG00000062121	Olfr149	M31|MOR224-8	olfactory receptor 149	protein-coding	0.02	0.386139
Merged-chr12-52098582-1	chr12	52098532	52098632	+	2.8	cIP1vsInput	"intron (NM_029760, intron 2 of 10)"	"intron (NM_029760, intron 2 of 10)"	836	NM_029760	76826	Mm.244781	NM_029760		Nubpl	2410170E07Rik	nucleotide binding protein-like	protein-coding	0.01	0.405941
Merged-chr6-108632961-1	chr6	108632911	108633011	+	2.8	cIP1vsInput	"intron (NR_040758, intron 1 of 6)"	L1MC4|LINE|L1	-9794	NR_040757	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	miscRNA	0	0.336634
Merged-chr15-99724526-1	chr15	99724476	99724576	+	2.8	cIP2vsInput	"3' UTR (NM_010271, exon 8 of 8)"	"3' UTR (NM_010271, exon 8 of 8)"	-1092	NM_183256	66379	Mm.5265	NM_183256	ENSMUSG00000023020	Cox14	2310016M24Rik|AA959804	cytochrome c oxidase assembly protein 14	protein-coding	0.01	0.564356
Merged-chr17-51166443-1	chr17	51166393	51166493	+	2.8	cIP1vsInput	"intron (NR_035408, intron 2 of 6)"	L1M4|LINE|L1	12906	NM_028162	72238	Mm.120650	NM_028162	ENSMUSG00000023923	Tbc1d5	1600014N05Rik|mKIAA0210	"TBC1 domain family, member 5"	protein-coding	0	0.346535
Merged-chr9-75089349-1	chr9	75089299	75089399	+	2.8	cIP2vsInput	"intron (NM_010864, intron 1 of 40)"	"intron (NM_010864, intron 1 of 40)"	18143	NM_010864	17918	Mm.3645	NM_010864	ENSMUSG00000034593	Myo5a	9630007J19Rik|AI413174|AI661011|Dbv|MVa|Myo5|MyoVA|Sev-1|d|d-120J|flail|flr	myosin VA	protein-coding	0.01	0.326733
Merged-chr2-134060322-1	chr2	134060272	134060372	+	2.8	cIP2vsInput	Intergenic	Intergenic	494030	NM_010403	15112	Mm.26634	NM_010403	ENSMUSG00000027261	Hao1	GOX|Gox1|Hao-1	"hydroxyacid oxidase 1, liver"	protein-coding	0.01	0.376238
Merged-chr6-141541421-1	chr6	141541371	141541471	+	2.8	cIP2vsInput	"intron (NM_021471, intron 5 of 14)"	"intron (NM_021471, intron 5 of 14)"	17035	NM_021471	58807	Mm.284495	NM_001177772	ENSMUSG00000030235	Slco1c1	OATP-14|OATP-F|Oatp2|Oatpf|Slc21a14	"solute carrier organic anion transporter family, member 1c1"	protein-coding	0	0.425743
Merged-chr13-106203015-1	chr13	106202965	106203065	+	2.8	cIP2vsInput	Intergenic	Intergenic	733900	NM_029665	76582	Mm.482687	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding	0	0.356436
Merged-chr3-117439410-1	chr3	117439360	117439460	+	2.8	cIP2vsInput	Intergenic	Intergenic	-78534	NM_177664	229791	Mm.140138	NM_177664	ENSMUSG00000044667	D3Bwg0562e	A330086D10|Lppr4|PRG-1|mKIAA0455	"DNA segment, Chr 3, Brigham & Women's Genetics 0562 expressed"	protein-coding	0	0.316832
Merged-chr1-30166665-1	chr1	30166615	30166715	+	2.8	cIP1vsInput	Intergenic	Intergenic	696591	NM_001081080	213109	Mm.486727	NM_001081080	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding	0	0.356436
Merged-chr17-22889739-1	chr17	22889689	22889789	+	2.8	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-22605	NM_001110254	240041	Mm.328828	NM_001110254	ENSMUSG00000059142	Zfp945	A630033E08Rik|C730040L01Rik	zinc finger protein 945	protein-coding	0.01	0.306931
Merged-chr14-117055882-1	chr14	117055832	117055932	+	2.8	cIP1vsInput	"intron (NM_001079844, intron 1 of 9)"	"intron (NM_001079844, intron 1 of 9)"	130567	NM_011821	23888	Mm.440025	NM_001079844	ENSMUSG00000058571	Gpc6	6720429C22Rik|AI480529	glypican 6	protein-coding	0	0.316832
Merged-chr10-27622840-1	chr10	27622790	27622890	+	2.8	cIP2vsInput	Intergenic	Intergenic	-5898	NM_008481	16773	Mm.256087	NM_008481	ENSMUSG00000019899	Lama2	5830440B04|dy|mKIAA4087|mer|merosin	"laminin, alpha 2"	protein-coding	0	0.227723
Merged-chr3-51633805-1	chr3	51633755	51633855	+	2.8	cIP1vsInput	Intergenic	Intergenic	-27388	NM_174995	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding	0	0.39604
Merged-chr4-81860641-2	chr4	81860580	81860702	+	2.8	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-204739	NR_040659	545641	Mm.216028	NR_040659	ENSMUSG00000085022	Gm5860	EG545641	predicted gene 5860	miscRNA	0	0.357724
Merged-chr17-46283037-1	chr17	46282987	46283087	+	2.8	cIP2vsInput	promoter-TSS (NM_001252473)	promoter-TSS (NM_001252473)	-11	NM_028751	74094	Mm.490004	NM_001252473	ENSMUSG00000012296	Tjap1	0610041D19Rik|AI415281|AW121008|Pilt|Tjp4	tight junction associated protein 1	protein-coding	0.13	0.80198
Merged-chr18-73052422-1	chr18	73052372	73052472	+	2.8	cIP2vsInput	Intergenic	Intergenic	-520283	NM_001039214	240396	Mm.436942	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 homolog C (C. elegans)	protein-coding	0	0.326733
Merged-chr15-36635735-1	chr15	36635685	36635785	+	2.8	cIP2vsInput	Intergenic	Intergenic	-26762	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	"poly(A) binding protein, cytoplasmic 1"	protein-coding	0.04	0.534653
Merged-chr10-127311766-1	chr10	127311716	127311816	+	2.8	cIP2vsInput	promoter-TSS (NM_001171582)	promoter-TSS (NM_001171582)	20	NM_001003913	216443	Mm.28173	NM_001003913	ENSMUSG00000040354	Mars	Metrs|Mtrns	methionine-tRNA synthetase	protein-coding	0.1	0.574257
Merged-chr3-8916977-1	chr3	8916927	8917027	+	2.8	cIP1vsInput	"intron (NM_025434, intron 1 of 2)"	"intron (NM_025434, intron 1 of 2)"	6880	NM_025434	66230	Mm.38460	NM_025434	ENSMUSG00000040269	Mrps28	1500012D08Rik|AW061224	mitochondrial ribosomal protein S28	protein-coding	0	0.306931
Merged-chr4-116017701-1	chr4	116017651	116017751	+	2.8	cIP2vsInput	"5' UTR (NM_010173, exon 1 of 15)"	"5' UTR (NM_010173, exon 1 of 15)"	201	NM_010173	14073	Mm.256025	NM_010173	ENSMUSG00000034171	Faah	AW412498	fatty acid amide hydrolase	protein-coding	0.12	0.683168
Merged-chr2-67914562-1	chr2	67914512	67914612	+	2.8	cIP2vsInput	Intergenic	Intergenic	-190110	NM_020283	26877	Mm.490783	NM_020283	ENSMUSG00000034780	B3galt1	beta3Gal-T1	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1"	protein-coding	0.01	0.376238
Merged-chr4-32800270-1	chr4	32800220	32800320	+	2.8	cIP2vsInput	promoter-TSS (NM_175364)	promoter-TSS (NM_175364)	11	NM_175364	108755	Mm.1182	NM_175364		Lyrm2	2610208E05Rik	LYR motif containing 2	protein-coding	0.09	0.70297
Merged-chr17-74316578-1	chr17	74316528	74316628	+	2.8	cIP2vsInput	promoter-TSS (NM_001146224)	promoter-TSS (NM_001146224)	-145	NM_001146223	66310	Mm.28536	NM_001146222	ENSMUSG00000024067	Dpy30	2810410M20Rik|C87842	dpy-30 homolog (C. elegans)	protein-coding	0.06	0.613861
Merged-chr4-8584408-1	chr4	8584358	8584458	+	2.8	cIP2vsInput	"intron (NM_021518, intron 6 of 7)"	"intron (NM_021518, intron 6 of 7)"	48764	NM_021518	59021	Mm.467703	NM_021518	ENSMUSG00000047187	Rab2a	9330148M11Rik|C80220|Rab2	"RAB2A, member RAS oncogene family"	protein-coding	0	0.415842
Merged-chr11-77785607-2	chr11	77785551	77785663	+	2.8	cIP1vsInput|cIP2vsInput	"intron (NM_011586, intron 1 of 39)"	"intron (NM_011586, intron 1 of 39)"	8342	NM_011586	360013	Mm.476162	NM_011586	ENSMUSG00000000631	Myo18a	MyoPDZ|MysPDZ	myosin XVIIIA	protein-coding	0.026786	0.610619
Merged-chr1-91099150-1	chr1	91099100	91099200	+	2.8	cIP2vsInput	"intron (NM_008515, intron 10 of 22)"	"intron (NM_008515, intron 10 of 22)"	45706	NM_008515	16978	Mm.395990	NM_001111311	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding	0.02	0.564356
Merged-chr10-28267654-1	chr10	28267604	28267704	+	2.8	cIP2vsInput	"intron (NM_008983, intron 3 of 31)"	L1VL4|LINE|L1	192834	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	"protein tyrosine phosphatase, receptor type, K"	protein-coding	0	0.326733
Merged-chr8-99651218-1	chr8	99651168	99651268	+	2.8	cIP2vsInput	Intergenic	Intergenic	-234761	NM_001039154	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.376238
Merged-chr11-33369250-1	chr11	33369200	33369300	+	2.8	cIP2vsInput	"intron (NM_023146, intron 14 of 27)"	"intron (NM_023146, intron 14 of 27)"	144496	NM_023146	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	4932704E15Rik	RAN binding protein 17	protein-coding	0	0.316832
Merged-chr17-51689989-1	chr17	51689939	51690039	+	2.8	cIP1vsInput	Intergenic	(CAAA)n|Simple_repeat|Simple_repeat	122065	NM_001163630	20230	Mm.311655	NM_001163630	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding	0	0.346535
Merged-chr12-102387453-1	chr12	102387403	102387503	+	2.8	cIP1vsInput	"intron (NM_001161365, intron 8 of 9)"	"intron (NM_001161365, intron 8 of 9)"	52244	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding	0.03	0.60396
Merged-chr18-11648249-1	chr18	11648199	11648299	+	2.8	cIP1vsInput	"intron (NR_045527, intron 1 of 17)"	"intron (NR_045527, intron 1 of 17)"	-9100	NR_045526	225182	Mm.154275	NM_175458	ENSMUSG00000041238	Rbbp8	9930104E21Rik|CtIP|RBBP-8|RIM|SAE2	retinoblastoma binding protein 8	protein-coding	0	0.356436
Merged-chr10-17367229-1	chr10	17367179	17367279	+	2.8	cIP2vsInput	Intergenic	Intergenic	-271447	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0	0.39604
Merged-chr6-37017069-1	chr6	37017019	37017119	+	2.8	cIP1vsInput	"intron (NM_001081206, intron 17 of 33)"	"intron (NM_001081206, intron 17 of 33)"	-205708	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding	0	0.336634
Merged-chr13-111413456-1	chr13	111413406	111413506	+	2.8	cIP2vsInput	Intergenic	L3|LINE|CR1	76585	NM_028487	73274	Mm.441830	NM_001122963	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding	0.01	0.356436
Merged-chr14-34511600-1	chr14	34511550	34511650	+	2.8	cIP2vsInput	TTS (NM_030062)	TTS (NM_030062)	-9054	NM_009758	12166	Mm.237825	NM_009758	ENSMUSG00000021796	Bmpr1a	1110037I22Rik|ALK3|AU045487|BMPR-IA|Bmpr	"bone morphogenetic protein receptor, type 1A"	protein-coding	0.01	0.287129
Merged-chr10-47585755-1	chr10	47585705	47585805	+	2.8	cIP2vsInput	Intergenic	Intergenic	1341006	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0.01	0.326733
Merged-chr13-12803699-1	chr13	12803649	12803749	+	2.8	cIP2vsInput	Intergenic	Lx6|LINE|L1	-3620	NM_011118	18812	Mm.457984	NM_011118	ENSMUSG00000056457	Prl2c3	MRP-2|MRP-3|Mrpplf3|PLF-2|PLF-3|Plf2|Prl2c4|mrp/plf3	"prolactin family 2, subfamily c, member 3"	protein-coding	0	0.346535
Merged-chr6-3587391-1	chr6	3587341	3587441	+	2.8	cIP1vsInput	"intron (NM_001167750, intron 21 of 27)"	"intron (NM_001167750, intron 21 of 27)"	88998	NM_001167750	73288	Mm.45539	NM_001167750	ENSMUSG00000001376	Ccdc132	1700034M03Rik|8430415E05Rik|BLM|C87205|mKIAA1861	coiled-coil domain containing 132	protein-coding	0	0.306931
Merged-chr14-81751842-1	chr14	81751792	81751892	+	2.8	cIP1vsInput	Intergenic	Intergenic	1751540	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.306931
Merged-chr8-70897726-1	chr8	70897676	70897776	+	2.8	cIP2vsInput	promoter-TSS (NM_029751)	promoter-TSS (NM_029751)	-283	NM_029751	76808	Mm.431334	NM_029751	ENSMUSG00000045128	Rpl18a	2510019J09Rik	ribosomal protein L18A	protein-coding	0.01	0.366337
Merged-chr14-46674104-1	chr14	46674054	46674154	+	2.8	cIP1vsInput	Intergenic	Intergenic	-36681	NR_046460	74458	Mm.390708	NR_046460		4933425B07Rik	-	RIKEN cDNA 4933425B07 gene	miscRNA	0.01	0.346535
Merged-chr8-121393297-1	chr8	121393247	121393347	+	2.8	cIP2vsInput	Intergenic	Intergenic	148657	NM_029597	76405	Mm.165697	NM_029597	ENSMUSG00000031809	1700018B08Rik	1700084O22Rik	RIKEN cDNA 1700018B08 gene	protein-coding	0.01	0.594059
Merged-chr14-34653664-1	chr14	34653614	34653714	+	2.8	cIP2vsInput	promoter-TSS (NR_029647)	promoter-TSS (NR_029647)	-90	NR_029647	723831		NR_029647	ENSMUSG00000094316	Mir297-1	Mir297a-1|Mirn297-1	microRNA 297-1	miscRNA	0	0.267327
Merged-chr4-50976704-1	chr4	50976654	50976754	+	2.8	cIP2vsInput	Intergenic	L1MA7|LINE|L1	-239974	NM_001162865	74914	Mm.159368	NM_001162865	ENSMUSG00000039555	Cylc2	4930488P18Rik	"cylicin, basic protein of sperm head cytoskeleton 2"	protein-coding	0	0.346535
Merged-chr4-76087100-1	chr4	76087050	76087150	+	2.8	cIP2vsInput	"intron (NM_011211, intron 22 of 39)"	"intron (NM_011211, intron 22 of 39)"	-808814	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	3110001D03Rik	1700027K24Rik	RIKEN cDNA 3110001D03 gene	protein-coding	0	0.366337
Merged-chr2-181187883-1	chr2	181187833	181187933	+	2.8	cIP2vsInput	"exon (NM_025598, exon 3 of 5)"	"exon (NM_025598, exon 3 of 5)"	540	NM_025598	66496	Mm.213943	NM_025598	ENSMUSG00000016344	Ppdpf	0610012G23Rik|2610317A05Rik|2700038C09Rik|3110053G12Rik	pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish)RIKEN cDNA 2700038C09 gene	protein-coding	0.08	0.663366
Merged-chr2-79285924-1	chr2	79285874	79285974	+	2.8	cIP1vsInput	"intron (NM_010576, intron 10 of 27)"	"intron (NM_010576, intron 10 of 27)"	30498	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D	integrin alpha 4	protein-coding	0.01	0.326733
Merged-chr15-38198950-1	chr15	38198900	38199000	+	2.8	cIP2vsInput	Intergenic	Intergenic	-20253	NM_008757	18285	Mm.252830	NM_008757	ENSMUSG00000061923	Odf1	-	outer dense fiber of sperm tails 1	protein-coding	0.03	0.544554
Merged-chr18-5080919-1	chr18	5080869	5080969	+	2.8	cIP2vsInput	"intron (NM_153153, intron 14 of 34)"	"intron (NM_153153, intron 14 of 34)"	34330	NM_153153	225115	Mm.136791	NM_178046	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding	0	0.29703
Merged-chr15-45497842-1	chr15	45497792	45497892	+	2.8	cIP1vsInput	Intergenic	Lx3B|LINE|L1	-382908	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	"potassium channel, subfamily V, member 1"	protein-coding	0	0.346535
Merged-chr12-32185232-1	chr12	32185182	32185282	+	2.8	cIP1vsInput	"intron (NM_001146201, intron 10 of 10)"	"intron (NM_001146201, intron 10 of 10)"	23106	NM_001146201	30955	Mm.404021	NM_001146200	ENSMUSG00000020573	Pik3cg	5830428L06Rik|PI3Kgamma|p110gamma	"phosphoinositide-3-kinase, catalytic, gamma polypeptide"	protein-coding	0.02	0.326733
Merged-chr8-84811004-1	chr8	84810954	84811054	+	2.8	cIP2vsInput	Intergenic	Intergenic	-10664	NM_001081982	18032	Mm.9394	NM_001081981		Nfix	-	nuclear factor I/X	protein-coding	0.03	0.594059
Merged-chr5-115118992-1	chr5	115118942	115119042	+	2.8	cIP1vsInput	"intron (NM_007383, intron 1 of 9)"	"intron (NM_007383, intron 1 of 9)"	354	NM_007383	11409	Mm.18759	NM_007383	ENSMUSG00000029545	Acads	AI196007|Bcd-1|Bcd1|Hdlq8|SCAD	"acyl-Coenzyme A dehydrogenase, short chain"	protein-coding	0.05	0.60396
Merged-chr6-121272647-1	chr6	121272597	121272697	+	2.8	cIP2vsInput	Intergenic	ORR1D1|LTR|ERVL-MaLR	26741	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding	0.01	0.455446
Merged-chr13-74391125-1	chr13	74391075	74391175	+	2.8	cIP1vsInput	Intergenic	Intergenic	-14559	NM_001081680	238722	Mm.461254	NM_001081680	ENSMUSG00000069184	Zfp72	Zfp74	zinc finger protein 72	protein-coding	0	0.287129
Merged-chr14-36513465-1	chr14	36513415	36513515	+	2.8	cIP2vsInput	Intergenic	Lx6|LINE|L1	418500	NM_175008	218921	Mm.212464	NM_175008	ENSMUSG00000096405	4930474N05Rik	-	RIKEN cDNA 4930474N05 gene	protein-coding	0	0.306931
Merged-chr7-7171109-1	chr7	7171059	7171159	+	2.8	cIP2vsInput	promoter-TSS (NM_146179)	promoter-TSS (NM_146179)	-244	NM_146179	232854	Mm.184857	NM_146179	ENSMUSG00000034538	Zfp418	A230102I05Rik	zinc finger protein 418	protein-coding	0	0.376238
Merged-chr5-12527331-1	chr5	12527281	12527381	+	2.8	cIP2vsInput	"intron (NM_028882, intron 8 of 17)"	"intron (NM_028882, intron 8 of 17)"	144165	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	"sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D"	protein-coding	0	0.306931
Merged-chr18-17493585-1	chr18	17493535	17493635	+	2.8	cIP2vsInput	Intergenic	Intergenic	87405	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	miscRNA	0	0.287129
Merged-chr16-8513313-1	chr16	8513263	8513363	+	2.8	cIP2vsInput	promoter-TSS (NM_172961)	promoter-TSS (NM_172961)	-116	NM_001170978	268860	Mm.259315	NM_001170978	ENSMUSG00000057880	Abat	9630038C02Rik|AI255750|ENSMUSG00000051226|Gabaat|Gabat|Gm9851|I54|Laibat|X61497	4-aminobutyrate aminotransferase	protein-coding	0.12	0.792079
Merged-chr13-80242263-1	chr13	80242213	80242313	+	2.8	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-641159	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0	0.366337
Merged-chr5-45520231-1	chr5	45520181	45520281	+	2.8	cIP2vsInput	promoter-TSS (NM_025895)	promoter-TSS (NM_025895)	2	NM_025895	66999	Mm.283045	NM_025895	ENSMUSG00000015804	Med28	1500003D12Rik|AI451633|AU045690|Eg1|FKSG20|magicin	"mediator of RNA polymerase II transcription, subunit 28 homolog (yeast)"	protein-coding	0.08	0.594059
Merged-chr16-32360746-1	chr16	32360696	32360796	+	2.8	cIP2vsInput	"intron (NM_177633, intron 3 of 10)"	"intron (NM_177633, intron 3 of 10)"	28494	NM_177633	224111	Mm.31275	NM_177633	ENSMUSG00000053774	Ubxn7	A630090P18|AI196514|Ubxd7|mKIAA0794	UBX domain protein 7	protein-coding	0	0.326733
Merged-chr9-114583793-1	chr9	114583743	114583843	+	2.8	cIP2vsInput	Intergenic	Intergenic	-19424	NM_001042503	636931	Mm.17857	NM_001042503	ENSMUSG00000079259	Trim71	2610206G21Rik|AL022943|Gm1127|Lin41|Ripply2|lin-41|mLin41|mlin-41	tripartite motif-containing 71	protein-coding	0.01	0.287129
Merged-chr2-72242723-1	chr2	72242673	72242773	+	2.8	cIP2vsInput	"intron (NM_001204165, intron 28 of 30)"	"intron (NM_001204165, intron 28 of 30)"	-42914	NM_023057	65964	Mm.314618	NM_001164791	ENSMUSG00000004085	B230120H23Rik	AV006891|MLTK|MLTKalpha|MLTKbeta|Zak	RIKEN cDNA B230120H23 gene	protein-coding	0.01	0.346535
Merged-chr6-88841939-1	chr6	88841889	88841989	+	2.8	cIP2vsInput	promoter-TSS (NM_030251)	promoter-TSS (NM_030251)	-4	NM_030251	80283	Mm.166858	NM_030251	ENSMUSG00000030083	Abtb1	AI847549|BC003234|BPOZ|EF1ABP	ankyrin repeat and BTB (POZ) domain containing 1	protein-coding	0.16	0.792079
Merged-chr3-89963436-1	chr3	89963386	89963486	+	2.8	cIP2vsInput	promoter-TSS (NM_001081182)	promoter-TSS (NM_001081182)	-104	NM_001081182	54667	Mm.30455	NM_001081182	ENSMUSG00000060671	Atp8b2	Id	"ATPase, class I, type 8B, member 2"	protein-coding	0.1	0.70297
Merged-chr13-41579937-1	chr13	41579887	41579987	+	2.8	cIP2vsInput	Intergenic	MusHAL1|LINE|L1	-26279	NM_001163572	621976	Mm.408884	NM_001163572	ENSMUSG00000087370	Tmem170b	EG621976	transmembrane protein 170B	protein-coding	0.01	0.316832
Merged-chr2-43988442-1	chr2	43988392	43988492	+	2.8	cIP2vsInput	"intron (NM_153820, intron 6 of 13)"	"intron (NM_153820, intron 6 of 13)"	76882	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	A430092G05Rik	-	RIKEN cDNA A430092G05 gene	miscRNA	0	0.346535
Merged-chr19-44989331-1	chr19	44989281	44989381	+	2.8	cIP2vsInput	promoter-TSS (NM_011976)	promoter-TSS (NM_011976)	-13	NM_011976	26456	Mm.34404	NM_011976	ENSMUSG00000025207	Sema4g	AI507908|AW554132	"sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G"	protein-coding	0.09	0.70297
Merged-chr10-94091782-1	chr10	94091732	94091832	+	2.8	cIP1vsInput	"intron (NM_053072, intron 5 of 20)"	RLTR20B1|LTR|ERVK	55781	NM_053072	13998	Mm.269596	NM_053072	ENSMUSG00000020021	Fgd6	AA123052|Etohd4|ZFYVE24	"FYVE, RhoGEF and PH domain containing 6"	protein-coding	0	0.356436
Merged-chr10-96435204-1	chr10	96435154	96435254	+	2.8	cIP2vsInput	Intergenic	Intergenic	-181797	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	"B cell translocation gene 1, anti-proliferative"	protein-coding	0.01	0.306931
Merged-chr17-80223335-1	chr17	80223285	80223385	+	2.8	cIP2vsInput	Intergenic	Intergenic	-1154	NM_026053	67242	Mm.279985	NM_026053	ENSMUSG00000055760	Gemin6	2610019B15Rik|2810470M17Rik	gem (nuclear organelle) associated protein 6	protein-coding	0	0.306931
Merged-chr3-117547910-1	chr3	117547860	117547960	+	2.8	cIP2vsInput	Intergenic	Intergenic	-27551	NM_029425	75769	Mm.72187	NM_029425	ENSMUSG00000033342	4833424O15Rik	Lppr5|PRG-5|Pap2d	RIKEN cDNA 4833424O15 gene	protein-coding	0	0.306931
Merged-chr18-38296199-1	chr18	38296149	38296249	+	2.8	cIP1vsInput	promoter-TSS (NM_001164622)	promoter-TSS (NM_001164622)	-436	NM_020012	56736	Mm.228903	NM_001164621	ENSMUSG00000060450	Rnf14	2310075C09Rik|2610005D23Rik|AA986456|AU041447|D18Ertd188e|D7Bwg0165e|Triad2	ring finger protein 14	protein-coding	0.01	0.346535
Merged-chr1-189727442-1	chr1	189727392	189727492	+	2.8	cIP2vsInput	promoter-TSS (NM_008976)	promoter-TSS (NM_008976)	-826	NM_008976	19250	Mm.4498	NM_001033287	ENSMUSG00000026604	Ptpn14	C130080N23Rik|OTTMUSG00000022087|PTP36	"protein tyrosine phosphatase, non-receptor type 14"	protein-coding	0.05	0.643564
Merged-chr12-73684679-1	chr12	73684629	73684729	+	2.8	cIP2vsInput	"intron (NM_008856, intron 2 of 13)"	(TA)n|Simple_repeat|Simple_repeat	99638	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	"protein kinase C, eta"	protein-coding	0	0.217822
Merged-chrX-106027061-1	chrX	106027011	106027111	+	2.8	cIP2vsInput	promoter-TSS (NM_001109757)	promoter-TSS (NM_001109757)	-215	NM_001109757	11977	Mm.254297	NM_001109757		Atp7a	Blo|DXHXS1608e|I14|MNK|Mo|blotchy|br|brindled|mottled	"ATPase, Cu++ transporting, alpha polypeptide"	protein-coding	0.05	0.564356
Merged-chr7-24316973-1	chr7	24316923	24317023	+	2.8	cIP2vsInput	promoter-TSS (NM_001199321)	promoter-TSS (NM_001199321)	-307	NM_001199321	22756	Mm.487703	NM_001199321	ENSMUSG00000074282	Zfp94	-	zinc finger protein 94	protein-coding	0.04	0.455446
Merged-chr2-96201842-1	chr2	96201792	96201892	+	2.8	cIP2vsInput	Intergenic	Intergenic	-1265832	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0.01	0.316832
Merged-chr13-11969812-1	chr13	11969762	11969862	+	2.8	cIP2vsInput	"intron (NM_023868, intron 1 of 104)"	"intron (NM_023868, intron 1 of 104)"	137133	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	"ryanodine receptor 2, cardiac"	protein-coding	0	0.366337
Merged-chr13-49572511-1	chr13	49572461	49572561	+	2.8	cIP2vsInput	"intron (NM_025495, intron 5 of 7)"	"intron (NM_025495, intron 5 of 7)"	-10236	NM_012050	27047	Mm.390589	NM_012050	ENSMUSG00000048368	Omd	OSAD|SLRR2C	osteomodulin	protein-coding	0	0.336634
Merged-chr18-56029172-1	chr18	56029122	56029222	+	2.8	cIP2vsInput	Intergenic	Intergenic	-402960	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding	0.01	0.306931
Merged-chr3-47760937-1	chr3	47760887	47760987	+	2.8	cIP2vsInput	Intergenic	MLT1E2|LTR|ERVL-MaLR	265822	NR_040408	666202	Mm.465057	NR_040408		Gm7977	EG666202	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide pseudogene"	pseudo	0	0.326733
Merged-chr12-112976579-1	chr12	112976529	112976629	+	2.8	cIP2vsInput	promoter-TSS (NM_001145900)	promoter-TSS (NM_001145900)	16	NM_201646	399566	Mm.440140	NM_001145900	ENSMUSG00000002803	Btbd6	-	BTB (POZ) domain containing 6	protein-coding	0.11	0.80198
Merged-chr5-10122854-1	chr5	10122804	10122904	+	2.8	cIP2vsInput	Intergenic	Lx5|LINE|L1	-397502	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	"glutamate receptor, metabotropic 3"	protein-coding	0	0.326733
Merged-chr16-45922932-1	chr16	45922882	45922982	+	2.8	cIP1vsInput	Intergenic	Intergenic	-78554	NM_001252442	208177	Mm.211477	NM_001252442	ENSMUSG00000033149	Phldb2	AV253284|C820004H04Rik|LL5b|LL5beta	"pleckstrin homology-like domain, family B, member 2"	protein-coding	0.01	0.287129
Merged-chr12-33540919-1	chr12	33540869	33540969	+	2.8	cIP1vsInput	Intergenic	Intergenic	111295	NM_172253	28071	Mm.413045	NM_172253	ENSMUSG00000020561	Twistnb	2410173G11|2810024J17Rik|D16Wsu83e	TWIST neighbor	protein-coding	0	0.326733
Merged-chr4-11253968-1	chr4	11253918	11254018	+	2.8	cIP2vsInput	"intron (NM_001159595, intron 1 of 26)"	CpG	291	NM_178112	72656	Mm.246713	NM_001159595	ENSMUSG00000040738	Ints8	2810013E07Rik|AV063769|D130008D20Rik	integrator complex subunit 8	protein-coding	0.13	0.722772
Merged-chr4-91251879-1	chr4	91251829	91251929	+	2.8	cIP1vsInput	"3' UTR (NM_207686, exon 6 of 6)"	"3' UTR (NM_207686, exon 6 of 6)"	120176	NM_010486	15569	Mm.318042	NM_001177883	ENSMUSG00000008489	Elavl2	Hub|mel-N1	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)"	protein-coding	0	0.277228
Merged-chr10-89331176-1	chr10	89331126	89331226	+	2.8	cIP1vsInput	Intergenic	Intergenic	-73386	NM_178773	320091	Mm.417681	NM_178773	ENSMUSG00000035189	Ano4	A330096O15Rik|Gm65|Tmem16d	anoctamin 4	protein-coding	0	0.29703
Merged-chr4-74013653-1	chr4	74013603	74013703	+	2.8	cIP1vsInput	promoter-TSS (NM_001163732)	promoter-TSS (NM_001163732)	50	NM_001163732	242506	Mm.221597	NM_001163732	ENSMUSG00000049122	Frmd3	4.1O|9430066I12Rik|EPB41L4O|P410	FERM domain containing 3	protein-coding	0.12	0.693069
Merged-chr1-136769038-1	chr1	136768988	136769088	+	2.8	cIP2vsInput	Intergenic	Intergenic	72827	NR_037986	100503474	Mm.428276	NR_037986		Gm16880	-	"predicted gene, 16880"	miscRNA	0.03	0.663366
Merged-chr2-106356182-1	chr2	106356132	106356232	+	2.8	cIP2vsInput	Intergenic	Intergenic	166921	NR_040637	329483	Mm.246777	NR_040637	ENSMUSG00000087226	Gm14015	9330126M15|OTTMUSG00000015366	predicted gene 14015	miscRNA	0.01	0.524752
Merged-chr4-155308232-1	chr4	155308182	155308282	+	2.8	cIP2vsInput	"intron (NM_008860, intron 4 of 17)"	"intron (NM_008860, intron 4 of 17)"	37540	NM_001039079	18762	Mm.28561	NM_001039079	ENSMUSG00000029053	Prkcz	AI098070|C80388|Pkcz|R74924|aPKCzeta|zetaPKC	"protein kinase C, zeta"	protein-coding	0.04	0.574257
Merged-chr13-48947982-1	chr13	48947932	48948032	+	2.8	cIP2vsInput	"intron (NM_001033268, intron 2 of 17)"	"intron (NM_001033268, intron 2 of 17)"	19846	NM_001033268	218236	Mm.426571	NM_001033268	ENSMUSG00000038014	Fam120a	C9orf10|Ossa	"family with sequence similarity 120, member A"	protein-coding	0.01	0.356436
Merged-chr17-35235698-1	chr17	35235648	35235748	+	2.8	cIP2vsInput	promoter-TSS (NM_023179)	promoter-TSS (NM_023179)	117	NM_010909	18038	Mm.300795	NM_010909	ENSMUSG00000042419	Nfkbil1	Def-7|IKBL	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor like 1	protein-coding	0.04	0.653465
Merged-chrY-6910930-2	chrY	6910878	6910982	+	2.8	cIP1vsInput|cIP2vsInput	Intergenic	MER2|DNA|TcMar-Tigger	256847	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.352381
Merged-chr7-38019507-1	chr7	38019457	38019557	+	2.8	cIP2vsInput	promoter-TSS (NM_011274)	promoter-TSS (NM_011274)	45	NM_011274	19777	Mm.387220	NM_011274	ENSMUSG00000030421	Uri1	C80913|NNX3|Rmp	"URI1, prefoldin-like chaperone"	protein-coding	0.15	0.772277
Merged-chr11-77763248-1	chr11	77763198	77763298	+	2.8	cIP1vsInput	Intergenic	CpG	-14017	NM_011586	360013	Mm.476162	NM_011586	ENSMUSG00000000631	Myo18a	MyoPDZ|MysPDZ	myosin XVIIIA	protein-coding	0.19	0.811881
Merged-chr4-92592968-1	chr4	92592918	92593018	+	2.8	cIP2vsInput	Intergenic	Intergenic	-445747	NM_027034	69314	Mm.55891	NM_027034	ENSMUSG00000028533	Izumo3	1700011H22Rik	IZUMO family member 3	protein-coding	0	0.336634
Merged-chr2-45981832-1	chr2	45981782	45981882	+	2.8	cIP1vsInput	Intergenic	Intergenic	285227	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	miscRNA	0.01	0.287129
Merged-chr9-70109473-1	chr9	70109423	70109523	+	2.8	cIP2vsInput	"intron (NM_029784, intron 4 of 8)"	"intron (NM_029784, intron 4 of 8)"	32084	NM_029784	76886	Mm.44355	NM_029784	ENSMUSG00000032224	Fam81a	6430514L14Rik	"family with sequence similarity 81, member A"	protein-coding	0.02	0.465347
Merged-chr15-76069786-1	chr15	76069736	76069836	+	2.8	cIP2vsInput	promoter-TSS (NM_134089)	promoter-TSS (NM_134089)	-56	NM_134089	105782	Mm.25568	NM_134089	ENSMUSG00000022568	Scrib	AI118201|CRIB|Crc|SCRIB1|Scrb1|mKIAA0147|vartul	scribbled homolog (Drosophila)	protein-coding	0.13	0.722772
Merged-chr10-4432541-1	chr10	4432491	4432591	+	2.8	cIP2vsInput	promoter-TSS (NM_025343)	promoter-TSS (NM_025343)	-64	NM_024261	73419	Mm.346733	NM_024261	ENSMUSG00000061759	1700052N19Rik	AW320013|AW536799	RIKEN cDNA 1700052N19 gene	protein-coding	0.03	0.405941
Merged-chr11-70410081-1	chr11	70410031	70410131	+	2.8	cIP2vsInput	promoter-TSS (NM_029231)	promoter-TSS (NM_029231)	-50	NM_029231	75273	Mm.340601	NM_029231	ENSMUSG00000018921	Pelp1	4930563C04Rik|MNAR	"proline, glutamic acid and leucine rich protein 1"	protein-coding	0.09	0.663366
Merged-chr11-114040547-1	chr11	114040497	114040597	+	2.8	cIP2vsInput	"intron (NM_172800, intron 1 of 44)"	"intron (NM_172800, intron 1 of 44)"	25404	NM_172800	237979	Mm.401394	NM_172800		Sdk2	4632412F08Rik|5330435L01Rik|Sdk-2|mKIAA1514	sidekick homolog 2 (chicken)	protein-coding	0	0.653465
Merged-chr15-8312836-1	chr15	8312786	8312886	+	2.8	cIP1vsInput	"intron (NM_201232, intron 32 of 45)"	"intron (NM_201232, intron 32 of 45)"	131627	NM_027707	71175	Mm.440537	NM_027707	ENSMUSG00000022141	Nipbl	4921518A06Rik|4933421G18Rik|C79399|Idn3	Nipped-B homolog (Drosophila)	protein-coding	0	0.346535
Merged-chr14-61360502-1	chr14	61360452	61360552	+	2.8	cIP2vsInput	promoter-TSS (NM_026598)	promoter-TSS (NM_026598)	-57	NM_026598	68177	Mm.22758	NM_026598	ENSMUSG00000021928	Ebpl	5730442K12Rik|EBRP	emopamil binding protein-like	protein-coding	0.07	0.653465
Merged-chr6-108919841-1	chr6	108919791	108919891	+	2.8	cIP2vsInput	Intergenic	Intergenic	91200	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	"ER degradation enhancer, mannosidase alpha-like 1"	protein-coding	0	0.29703
Merged-chr4-49793586-1	chr4	49793536	49793636	+	2.8	cIP2vsInput	"intron (NM_001276355, intron 1 of 8)"	"intron (NM_001276355, intron 1 of 8)"	52183	NM_001033351	242443	Mm.440095	NM_001033351		Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	"glutamate receptor ionotropic, NMDA3A"	protein-coding	0	0.326733
Merged-chr3-103383362-1	chr3	103383312	103383412	+	2.8	cIP2vsInput	Intergenic	Intergenic	104069	NM_001079830	94093	Mm.195036	NM_001079830	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g|ectodermin|mKIAA1113	tripartite motif-containing 33	protein-coding	0.07	0.564356
Merged-chr6-67691695-1	chr6	67691645	67691745	+	2.8	cIP1vsInput	Intergenic	Intergenic	-125996	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo	0	0.217822
Merged-chr4-82393873-1	chr4	82393823	82393923	+	2.8	cIP2vsInput	"intron (NM_008687, intron 2 of 8)"	"intron (NM_008687, intron 2 of 8)"	111435	NM_001113210	18028	Mm.317947	NM_001113209	ENSMUSG00000008575	Nfib	6720429L07Rik|E030026I10Rik	nuclear factor I/B	protein-coding	0	0.316832
Merged-chr2-167661833-1	chr2	167661783	167661883	+	2.8	cIP2vsInput	promoter-TSS (NM_145538)	promoter-TSS (NM_145538)	-289	NM_145538	407243	Mm.4863	NM_145538		Tmem189	AI840826|Kua	transmembrane protein 189	protein-coding	0.12	0.633663
Merged-chr19-53723500-1	chr19	53723450	53723550	+	2.8	cIP2vsInput	"intron (NM_001170847, intron 1 of 13)"	MTEa|LTR|ERVL-MaLR	46194	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding	0.02	0.465347
Merged-chr9-108079288-1	chr9	108079238	108079338	+	2.8	cIP2vsInput	promoter-TSS (NM_032543)	promoter-TSS (NM_032543)	87	NM_032543	84585	Mm.379272	NM_032543	ENSMUSG00000041528	Rnf123	BC003945|Kpc1	ring finger protein 123	protein-coding	0.1	0.70297
Merged-chr2-39226844-1	chr2	39226794	39226894	+	2.8	cIP1vsInput	promoter-TSS (NM_024209)	promoter-TSS (NM_024209)	-506	NM_024209	67857	Mm.392662	NM_024209		Ppp6c	2310003C10Rik	"protein phosphatase 6, catalytic subunit"	protein-coding	0	0.346535
Merged-chr5-137502813-1	chr5	137502763	137502863	+	2.8	cIP2vsInput	promoter-TSS (NM_028753)	promoter-TSS (NM_028753)	-384	NM_028753	74097	Mm.290242	NM_028753	ENSMUSG00000029715	Pop7	0610037N12Rik|AI852017|Rpp20	"processing of precursor 7, ribonuclease P family, (S. cerevisiae)"	protein-coding	0.08	0.613861
Merged-chr2-92229521-1	chr2	92229471	92229571	+	2.8	cIP1vsInput	"intron (NM_001109691, intron 6 of 18)"	"intron (NM_001109691, intron 6 of 18)"	7959	NM_001109690	192285	Mm.330408	NM_001109690	ENSMUSG00000058318	Phf21a	80kDa|Bhc|Bhc80|D030065N23Rik|PFTF1	PHD finger protein 21A	protein-coding	0	0.336634
Merged-chr19-48599579-1	chr19	48599529	48599629	+	2.8	cIP2vsInput	"intron (NM_025696, intron 4 of 26)"	"intron (NM_025696, intron 4 of 26)"	393554	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding	0.01	0.346535
Merged-chr14-48664525-1	chr14	48664475	48664575	+	2.8	cIP2vsInput	Intergenic	Intergenic	-1653	NM_144841	18424	Mm.487292	NM_144841	ENSMUSG00000021848	Otx2	E130306E05Rik	orthodenticle homolog 2 (Drosophila)	protein-coding	0.01	0.376238
Merged-chr6-88075213-1	chr6	88075163	88075263	+	2.8	cIP2vsInput	Intergenic	Intergenic	-9260	NM_133933	103963	Mm.188544	NM_133933	ENSMUSG00000030062	Rpn1	AU018702|D6Wsu137e|Rpn-1	ribophorin I	protein-coding	0.09	0.613861
Merged-chr16-35939049-1	chr16	35938999	35939099	+	2.8	cIP2vsInput	promoter-TSS (NM_001013371)	promoter-TSS (NM_001013371)	-22	NM_001013371	209200	Mm.390852	NM_001013371	ENSMUSG00000049502	Dtx3l	AU042200|BC023741	deltex 3-like (Drosophila)	protein-coding	0.09	0.643564
Merged-chr2-26133133-2	chr2	26133034	26133232	+	2.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	6410	NM_001256522	109299	Mm.490529	NM_001256521		C330006A16Rik	AI551216	RIKEN cDNA C330006A16 gene	protein-coding	0.035354	0.613065
Merged-chr18-77767851-2	chr18	77767781	77767922	+	2.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_146089)	promoter-TSS (NM_146089)	-71	NM_146089	225745	Mm.39293	NM_146089	ENSMUSG00000041840	Haus1	BC024400|Ccdc5|HEI-C	"HAUS augmin-like complex, subunit 1"	protein-coding	0.06383	0.647887
Merged-chr10-80019005-2	chr10	80018905	80019105	+	2.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027521)	promoter-TSS (NM_027521)	-670	NM_027521	70719	Mm.243954	NM_001142701	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding	0.025	0.631841
Merged-chr5-100719826-2	chr5	100719751	100719901	+	2.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_152803)	promoter-TSS (NM_152803)	-143	NM_152803	15442	Mm.265786	NM_152803	ENSMUSG00000035273	Hpse	HSE1|Hpa|Hpr1	heparanase	protein-coding	0.066667	0.635762
Merged-chr15-96524300-2	chr15	96524249	96524351	+	2.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-63457	NM_028148	72193	Mm.472183	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding	0.039216	0.485437
Merged-chr12-32292435-2	chr12	32292366	32292505	+	2.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-83786	NM_001146200	30955	Mm.404021	NM_001146200	ENSMUSG00000020573	Pik3cg	5830428L06Rik|PI3Kgamma|p110gamma	"phosphoinositide-3-kinase, catalytic, gamma polypeptide"	protein-coding	0.021583	0.371429
Merged-chr17-45563852-2	chr17	45563788	45563916	+	2.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028662)	promoter-TSS (NM_028662)	-300	NM_028662	73836	Mm.289716	NM_028662	ENSMUSG00000037089	Slc35b2	1110003M08Rik|AA407792|AI842275|PAPST1|Slc35b1	"solute carrier family 35, member B2"	protein-coding	0.070312	0.697674
Merged-chr12-112693642-2	chr12	112693576	112693708	+	2.75	cIP1vsInput|cIP2vsInput	Intergenic	CpG	14802	NM_001100460	382639	Mm.11350	NM_001100460	ENSMUSG00000037638	Zbtb42	EG382639|Gm5188|simiRP58	zinc finger and BTB domain containing 42	protein-coding	0.151515	0.75188
Merged-chr8-20103509-2	chr8	20103454	20103565	+	2.75	cIP1vsInput|cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	193923	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo	0	0.348214
Merged-chr13-44293930-2	chr13	44293876	44293984	+	2.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-77443	NR_045088	100503592	Mm.488275	NR_045088		A330076C08Rik	-	RIKEN cDNA A330076C08 gene	miscRNA	0.055556	0.541284
Merged-chr15-74709330-2	chr15	74709249	74709411	+	2.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008415)	promoter-TSS (NM_008415)	-8	NM_008415	16469	Mm.87052	NM_008415	ENSMUSG00000046380	Jrk	-	jerky	protein-coding	0.111111	0.693252
Merged-chr3-96708561-2	chr3	96708506	96708616	+	2.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_030094)	promoter-TSS (NM_030094)	-1	NM_030094	78373	Mm.423186	NM_001162925	ENSMUSG00000028100	Nudt17	2410015C20Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 17	protein-coding	0.127273	0.765766
Merged-chr6-144222331-2	chr6	144222268	144222394	+	2.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-12763	NM_001243163	20678	Mm.1752	NM_001113559	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY-box containing gene 5	protein-coding	0.007937	0.322835
Merged-chr17-23599298-2	chr17	23599231	23599365	+	2.75	cIP1vsInput|cIP2vsInput	"5' UTR (NM_011747, exon 1 of 6)"	"5' UTR (NM_011747, exon 1 of 6)"	189	NM_011747	22654	Mm.40326	NM_011747	ENSMUSG00000062012	Zfp13	4933429B21|AI835008|Krox-8|Rhit|Zfp-13	zinc finger protein 13	protein-coding	0.037313	0.533333
Merged-chr2-69647311-2	chr2	69647254	69647369	+	2.75	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028284)	promoter-TSS (NM_028284)	56	NM_028284	72569	Mm.252136	NM_028284	ENSMUSG00000063145	Bbs5	1700049I01Rik|2700023J09Rik	Bardet-Biedl syndrome 5 (human)	protein-coding	0.104348	0.62931
Merged-chr7-83383380-2	chr7	83383325	83383435	+	2.75	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-201551	NM_177695	233424	Mm.486619	NM_177695		Tmc3	9030203A06	transmembrane channel-like gene family 3	protein-coding	0.018182	0.459459
Merged-chr1-86008405-1	chr1	86008355	86008455	+	2.7	cIP2vsInput	Intergenic	Intergenic	-13537	NM_001122732	70060	Mm.196313	NM_001122732	ENSMUSG00000026226	Spata3	1700011N12Rik|1700029H01Rik|4930424D10Rik|Mtsarg1|Tsarg1	spermatogenesis associated 3	protein-coding	0	0.366337
Merged-chr19-18149333-1	chr19	18149283	18149383	+	2.7	cIP2vsInput	Intergenic	Intergenic	-311701	NM_001190483	18552	Mm.3401	NM_001163144	ENSMUSG00000024713	Pcsk5	PC5|PC5/6A|PC5A|PC6|SPC6|b2b585Clo	proprotein convertase subtilisin/kexin type 5	protein-coding	0	0.346535
Merged-chr18-41985824-2	chr18	41985735	41985914	+	2.7	cIP1vsInput|cIP2vsInput	TTS (NM_001033426)	TTS (NM_001033426)	13225	NM_001033426	332309	Mm.240520	NM_001033426	ENSMUSG00000073574	Grxcr2	Gm851	"glutaredoxin, cysteine rich 2"	protein-coding	0.022346	0.477778
Merged-chr4-134579604-1	chr4	134579554	134579654	+	2.7	cIP2vsInput	"intron (NM_207237, intron 6 of 11)"	MIRb|SINE|MIR	-27438	NM_029100	74777	Mm.29773	NM_029100	ENSMUSG00000050989	Sepn1	1110019I12Rik|AI414492	"selenoprotein N, 1"	protein-coding	0.01	0.584158
Merged-chr14-10780807-1	chr14	10780757	10780857	+	2.7	cIP2vsInput	"intron (NM_010210, intron 2 of 8)"	MIRb|SINE|MIR	381225	NM_010210	14198	Mm.441926	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding	0.02	0.425743
Merged-chr5-5493787-1	chr5	5493737	5493837	+	2.7	cIP1vsInput	Intergenic	Intergenic	-14644	NM_001200025	381716	Mm.276086	NM_001200025	ENSMUSG00000079666	1700015F17Rik	Gm1686	RIKEN cDNA 1700015F17 gene	protein-coding	0.02	0.346535
Merged-chr9-52134221-1	chr9	52134171	52134271	+	2.7	cIP2vsInput	"intron (NM_001162921, intron 2 of 5)"	"intron (NM_001162921, intron 2 of 5)"	33890	NM_001162921	244871	Mm.390172	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding	0	0.346535
Merged-chr2-140679122-1	chr2	140679072	140679172	+	2.7	cIP2vsInput	"intron (NM_001013802, intron 3 of 18)"	"intron (NM_001013802, intron 3 of 18)"	-7646	NM_178382	71436	Mm.426781	NM_001172160	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0	0.306931
Merged-chr11-22925383-1	chr11	22925333	22925433	+	2.7	cIP1vsInput	"intron (NM_144514, intron 2 of 2)"	"intron (NM_144514, intron 2 of 2)"	-46622	NM_011663	22183	Mm.29542	NM_011663	ENSMUSG00000044068	Zrsr1	D11Ncvs75|Irlgs2|SP2|U2af1-rs1|U2afbp-rs	"zinc finger (CCCH type), RNA binding motif and serine/arginine rich 1"	protein-coding	0.01	0.39604
Merged-chrY-5693916-1	chrY	5693866	5693966	+	2.7	cIP1vsInput	Intergenic	Intergenic	1473861	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.306931
Merged-chr3-151300939-1	chr3	151300889	151300989	+	2.7	cIP1vsInput	Intergenic	Intergenic	-136943	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0	0.257426
Merged-chr10-128194677-1	chr10	128194627	128194727	+	2.7	cIP1vsInput	promoter-TSS (NM_001033264)	promoter-TSS (NM_001033264)	42	NM_001033264	216456	Mm.447148	NM_001033264	ENSMUSG00000044005	Gls2	A330074B06Rik|AI195532|GA|GLS|Lga	"glutaminase 2 (liver, mitochondrial)"	protein-coding	0.16	0.792079
Merged-chr14-104513832-1	chr14	104513782	104513882	+	2.7	cIP1vsInput	"intron (NM_026047, intron 1 of 5)"	L1MA4|LINE|L1	8834	NM_026047	72486	Mm.291811	NM_026047	ENSMUSG00000022120	Rnf219	2610206B13Rik|2810449K13Rik|AI451544	ring finger protein 219	protein-coding	0	0.316832
Merged-chr17-39601978-1	chr17	39601928	39602028	+	2.7	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-38979	NM_001244651	668200	Mm.464782	NM_001244651	ENSMUSG00000095104	Gm9041	EG668200|Esp16	predicted gene 9041	protein-coding	0	0.306931
Merged-chr1-168405826-1	chr1	168405776	168405876	+	2.7	cIP1vsInput	"intron (NM_183355, intron 2 of 8)"	"intron (NM_183355, intron 2 of 8)"	26432	NM_183355	18514	Mm.440114	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|AI848790|AU015730|D230003C07Rik|Pbx-1|Pbx1a|Pbx1b	pre B cell leukemia homeobox 1	protein-coding	0.01	0.425743
Merged-chr11-58008700-1	chr11	58008650	58008750	+	2.7	cIP1vsInput	promoter-TSS (NM_028451)	promoter-TSS (NM_028451)	-364	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	"La ribonucleoprotein domain family, member 1"	protein-coding	0.09	0.742574
Merged-chr7-34655143-2	chr7	34655062	34655224	+	2.7	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-2302	NM_146188	233107	Mm.486198	NM_146188	ENSMUSG00000030499	Kctd15	BC031749	potassium channel tetramerisation domain containing 15	protein-coding	0.074074	0.509202
Merged-chr6-30572904-1	chr6	30572854	30572954	+	2.7	cIP2vsInput	"intron (NM_027926, intron 1 of 10)"	"intron (NM_027926, intron 1 of 10)"	4528	NM_027926	71791	Mm.105759	NM_027926		Cpa4	1110019K20Rik|AV009555	carboxypeptidase A4	protein-coding	0.06	0.554455
Merged-chr19-30734507-1	chr19	30734457	30734557	+	2.7	cIP1vsInput	"intron (NM_001013833, intron 7 of 17)"	"intron (NM_001013833, intron 7 of 17)"	-185011	NM_010051	13380	Mm.214717	NM_010051	ENSMUSG00000024868	Dkk1	mdkk-1	dickkopf homolog 1 (Xenopus laevis)	protein-coding	0	0.257426
Merged-chr13-79270597-1	chr13	79270547	79270647	+	2.7	cIP1vsInput	Intergenic	Lx8b|LINE|L1	-1071615	NM_010151	13865	Mm.439653	NM_010151		Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR3|Erbal3|SVP44|Tcfcoup1	"nuclear receptor subfamily 2, group F, member 1"	protein-coding	0.01	0.366337
Merged-chr7-133698191-1	chr7	133698141	133698241	+	2.7	cIP2vsInput	"intron (NM_009479, intron 5 of 9)"	"intron (NM_009479, intron 5 of 9)"	11104	NM_009479	22276	Mm.3160	NM_009479	ENSMUSG00000030979	Uros	AI415298|Uros3	uroporphyrinogen III synthase	protein-coding	0.01	0.50495
Merged-chrY-6892971-1	chrY	6892921	6893021	+	2.7	cIP1vsInput	Intergenic	L1VL2|LINE|L1	274806	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.02	0.29703
Merged-chr12-4978868-1	chr12	4978818	4978918	+	2.7	cIP2vsInput	"intron (NM_001099628, intron 16 of 30)"	"intron (NM_001099628, intron 16 of 30)"	61515	NM_001099628	320817	Mm.210966	NM_001099628		Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	"ATPase family, AAA domain containing 2B"	protein-coding	0	0.316832
Merged-chr10-72986655-1	chr10	72986605	72986705	+	2.7	cIP1vsInput	"intron (NR_040646, intron 2 of 4)"	"intron (NR_040646, intron 2 of 4)"	100050	NR_040646	327768	Mm.417745	NR_040646		A330049N07Rik	-	RIKEN cDNA A330049N07 gene	miscRNA	0	0.346535
Merged-chr7-64049412-1	chr7	64049362	64049462	+	2.7	cIP1vsInput	Intergenic	Intergenic	-104423	NM_001039104	17364	Mm.38875	NM_001039104	ENSMUSG00000030523	Trpm1	4732499L03Rik|AI606771|Ltrpc1|Mlsn1|melastatin	"transient receptor potential cation channel, subfamily M, member 1"	protein-coding	0	0.534653
Merged-chr7-45570969-1	chr7	45570919	45571019	+	2.7	cIP1vsInput	promoter-TSS (NM_001243052)	promoter-TSS (NM_001243052)	-310	NM_001243052	12036	Mm.24210	NM_001243052	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	"branched chain aminotransferase 2, mitochondrial"	protein-coding	0.02	0.435644
Merged-chr9-75888730-1	chr9	75888680	75888780	+	2.7	cIP2vsInput	"intron (NM_007555, intron 5 of 6)"	Lx8b|LINE|L1	113365	NM_007555	12160	Mm.428950	NM_007555		Bmp5	AU023399|se	bone morphogenetic protein 5	protein-coding	0	0.356436
Merged-chr13-79544394-1	chr13	79544344	79544444	+	2.7	cIP1vsInput	Intergenic	Intergenic	-1339028	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0	0.267327
Merged-chr2-115536927-1	chr2	115536877	115536977	+	2.7	cIP1vsInput	Intergenic	Intergenic	-24726	NR_030712	100043232	Mm.240112	NR_030712	ENSMUSG00000085582	3110099E03Rik	-	RIKEN cDNA 3110099E03 gene	miscRNA	0	0.336634
Merged-chr8-20264265-1	chr8	20264215	20264315	+	2.7	cIP2vsInput	Intergenic	L1MB7|LINE|L1	33167	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo	0	0.445545
Merged-chr8-43068323-1	chr8	43068273	43068373	+	2.7	cIP2vsInput	Intergenic	Intergenic	73163	NM_177742	244448	Mm.64542	NM_177742	ENSMUSG00000031651	Triml1	4933403D14|BC050188	tripartite motif family-like 1	protein-coding	0	0.376238
Merged-chr1-37783451-2	chr1	37783396	37783506	+	2.7	cIP1vsInput|cIP2vsInput	"intron (NM_207228, intron 16 of 19)"	"intron (NM_207228, intron 16 of 19)"	-63640	NM_028096	72097	Mm.142607	NM_028096	ENSMUSG00000026090	2010300C02Rik	-	RIKEN cDNA 2010300C02 gene	protein-coding	0	0.396396
Merged-chr7-87411999-1	chr7	87411949	87412049	+	2.7	cIP2vsInput	Intergenic	Intergenic	81412	NM_011661	22173	Mm.238127	NM_011661	ENSMUSG00000004651	Tyr	albino|c|skc35	tyrosinase	protein-coding	0	0.346535
Merged-chrX-74305214-1	chrX	74305164	74305264	+	2.7	cIP2vsInput	TTS (NM_018794)	TTS (NM_018794)	202	NM_010273	14567	Mm.205830	NM_010273	ENSMUSG00000015291	Gdi1	GDIA|GDIalpha	guanosine diphosphate (GDP) dissociation inhibitor 1	protein-coding	0.09	0.633663
Merged-chr2-79859401-1	chr2	79859351	79859451	+	2.7	cIP2vsInput	"intron (NM_001009979, intron 12 of 13)"	"intron (NM_001009979, intron 12 of 13)"	48998	NM_001009979	18573	Mm.40678	NM_001009978	ENSMUSG00000059173	Pde1a	AI987702|AW125737	"phosphodiesterase 1A, calmodulin-dependent"	protein-coding	0.01	0.316832
Merged-chr2-14099786-1	chr2	14099736	14099836	+	2.7	cIP2vsInput	"intron (NM_011484, intron 1 of 13)"	MTD|LTR|ERVL-MaLR	25674	NM_011484	20844	Mm.273174	NM_011484	ENSMUSG00000026718	Stam	STAM1	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	protein-coding	0	0.356436
Merged-chr14-120137844-1	chr14	120137794	120137894	+	2.7	cIP1vsInput	Intergenic	Intergenic	-95409	NM_001001490	239283	Mm.138520	NM_001001490	ENSMUSG00000044819	Oxgr1	Gm299|Gpr80|Gpr99|P2Y15	oxoglutarate (alpha-ketoglutarate) receptor 1	protein-coding	0.04	0.514851
Merged-chr8-111652691-1	chr8	111652641	111652741	+	2.7	cIP2vsInput	"intron (NM_001037665, intron 1 of 3)"	L1_Mur2|LINE|L1	9248	NM_011742	22640	Mm.4184	NM_001037665	ENSMUSG00000055835	Zfp1	Fnp-1|Zfp-1|mkr-1	zinc finger protein 1	protein-coding	0	0.346535
Merged-chr4-80938402-1	chr4	80938352	80938452	+	2.7	cIP2vsInput	"intron (NM_026821, intron 1 of 1)"	"intron (NM_026821, intron 1 of 1)"	27716	NM_026821	52829	Mm.273986	NM_026821		Lurap1l	1110029A09Rik|AV077978|AV175137|D4Bwg0951e|WI-13707|bM350F23.1	leucine rich adaptor protein 1-like	protein-coding	0.01	0.316832
Merged-chr17-34604276-1	chr17	34604226	34604326	+	2.7	cIP2vsInput	promoter-TSS (NM_019403)	promoter-TSS (NM_019403)	-715	NM_019403	54197	Mm.274542	NM_019403	ENSMUSG00000015478	Rnf5	2410131O05Rik|AA407576|NG2	ring finger protein 5	protein-coding	0.05	0.613861
Merged-chr16-81334006-1	chr16	81333956	81334056	+	2.7	cIP2vsInput	"intron (NM_001113208, intron 1 of 17)"	"intron (NM_001113208, intron 1 of 17)"	133309	NM_010954	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.306931
Merged-chr16-82614802-1	chr16	82614752	82614852	+	2.7	cIP1vsInput	Intergenic	Intergenic	1414105	NM_010954	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.316832
Merged-chr14-79300828-1	chr14	79300778	79300878	+	2.7	cIP2vsInput	"exon (NM_025427, exon 2 of 5)"	"exon (NM_025427, exon 2 of 5)"	807	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding	0.13	0.653465
Merged-chr15-42301696-1	chr15	42301646	42301746	+	2.7	cIP1vsInput	Intergenic	Intergenic	375099	NM_009640	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding	0.01	0.277228
Merged-chr7-78596067-1	chr7	78596017	78596117	+	2.7	cIP1vsInput	"intron (NR_015542, intron 8 of 10)"	"intron (NR_015542, intron 8 of 10)"	-18229	NM_182809	18213	Mm.421361	NM_008746		Ntrk3	AW125844|Ntrk3_tv3|TrkC	"neurotrophic tyrosine kinase, receptor, type 3"	protein-coding	0.01	0.574257
Merged-chr14-89509751-1	chr14	89509701	89509801	+	2.7	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-386473	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0	0.29703
Merged-chr10-120554372-1	chr10	120554322	120554422	+	2.7	cIP2vsInput	Intergenic	Intergenic	-77437	NM_010441	15364	Mm.157190	NM_010441	ENSMUSG00000056758	Hmga2	9430083A20Rik|HMGI-C|Hmgic|pg|pygmy	high mobility group AT-hook 2	protein-coding	0.01	0.356436
Merged-chr4-24496167-1	chr4	24496117	24496217	+	2.7	cIP2vsInput	promoter-TSS (NM_199467)	promoter-TSS (NM_199467)	-295	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	"MMS22-like, DNA repair protein"	protein-coding	0.03	0.673267
Merged-chr6-113377537-1	chr6	113377487	113377587	+	2.7	cIP2vsInput	promoter-TSS (NM_133932)	promoter-TSS (NM_133932)	-17	NM_133932	101206	Mm.266811	NM_133932	ENSMUSG00000048930	Tada3	1110004B19Rik|ADA3|AI987856|Tada3l	transcriptional adaptor 3	protein-coding	0.07	0.70297
Merged-chr15-55306493-1	chr15	55306443	55306543	+	2.7	cIP2vsInput	Intergenic	Intergenic	-1257	NM_181277	12818	Mm.297859	NM_181277	ENSMUSG00000022371	Col14a1	5730412L22Rik|AW108078	"collagen, type XIV, alpha 1"	protein-coding	0.13	0.663366
Merged-chr8-90013977-1	chr8	90013927	90014027	+	2.7	cIP2vsInput	Intergenic	Intergenic	334275	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding	0.01	0.445545
Merged-chr19-10949233-1	chr19	10949183	10949283	+	2.7	cIP2vsInput	promoter-TSS (NM_023731)	promoter-TSS (NM_023731)	33	NM_023731	108673	Mm.294908	NM_023731	ENSMUSG00000024732	Ccdc86	4933411H20Rik|6720480F16Rik|D19Ertd678e	coiled-coil domain containing 86	protein-coding	0.09	0.613861
Merged-chr10-98292201-1	chr10	98292151	98292251	+	2.7	cIP1vsInput	Intergenic	Intergenic	59666	NR_045179	667438	Mm.414522	NR_045179		Gm8633	EG667438	predicted gene 8633	miscRNA	0.02	0.465347
Merged-chr13-75374236-1	chr13	75374186	75374286	+	2.7	cIP2vsInput	Intergenic	Charlie1a|DNA|hAT-Charlie	-270810	NR_030451	751556		NR_030451	ENSMUSG00000076236	Mir682	Mirn682|mir-682|mmu-mir-682	microRNA 682	miscRNA	0	0.316832
Merged-chr12-94501941-1	chr12	94501891	94501991	+	2.7	cIP1vsInput	Intergenic	Intergenic	-1190285	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0.01	0.346535
Merged-chr4-78228061-1	chr4	78228011	78228111	+	2.7	cIP1vsInput	Intergenic	Intergenic	-16166	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0.01	0.336634
Merged-chr6-24573881-1	chr6	24573831	24573931	+	2.7	cIP1vsInput	TTS (NM_080847)	TTS (NM_080847)	-23890	NM_053098	93677	Mm.332941	NM_053098	ENSMUSG00000029683	Lmod2	C-Lmod	leiomodin 2 (cardiac)	protein-coding	0	0.326733
Merged-chr10-114704327-1	chr10	114704277	114704377	+	2.7	cIP2vsInput	"intron (NM_146241, intron 2 of 18)"	"intron (NM_146241, intron 2 of 18)"	97043	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding	0.01	0.306931
Merged-chr7-142968276-2	chr7	142968200	142968352	+	2.7	cIP1vsInput|cIP2vsInput	"exon (NM_008554, exon 2 of 3)"	"exon (NM_008554, exon 2 of 3)"	988	NM_008554	17173	Mm.196417	NM_008554	ENSMUSG00000009248	Ascl2	2410083I15Rik|Mash2|bHLHa45	achaete-scute complex homolog 2 (Drosophila)	protein-coding	0.131579	0.647059
Merged-chr12-17544893-1	chr12	17544843	17544943	+	2.7	cIP2vsInput	promoter-TSS (NM_013614)	promoter-TSS (NM_013614)	20	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	"ornithine decarboxylase, structural 1"	protein-coding	0.15	0.712871
Merged-chr4-15833217-1	chr4	15833167	15833267	+	2.7	cIP2vsInput	Intergenic	Intergenic	-48047	NM_009788	12307	Mm.277665	NM_009788		Calb1	Brain-2|CB|Calb|Calb-1	calbindin 1	protein-coding	0	0.316832
Merged-chr10-127030928-1	chr10	127030878	127030978	+	2.7	cIP2vsInput	promoter-TSS (NM_025537)	promoter-TSS (NM_025537)	-114	NM_025537	66399	Mm.29900	NM_025537	ENSMUSG00000040521	Tsfm	2310050B20Rik|9430024O13Rik|EF-TS|EF-Tsmt	"Ts translation elongation factor, mitochondrial"	protein-coding	0.06	0.485149
Merged-chr1-99550419-1	chr1	99550369	99550469	+	2.7	cIP1vsInput	Intergenic	MTD|LTR|ERVL-MaLR	-222346	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding	0	0.376238
Merged-chrX-13461710-1	chrX	13461660	13461760	+	2.7	cIP2vsInput	Intergenic	CpG	-5962	NM_173415	236690	Mm.90233	NM_173415		Nyx	CLNP|CSNB1|CSNB4|nob	nyctalopin	protein-coding	0.07	0.673267
Merged-chr5-14973934-1	chr5	14973884	14973984	+	2.7	cIP1vsInput	"intron (NR_001584, intron 2 of 3)"	"intron (NR_001584, intron 2 of 3)"	28640	NR_001584	74062	Mm.394766	NR_001584		Speer8-ps1	4933405L09Rik|SPEER-8|Speer8-ps	"spermatogenesis associated glutamate (E)-rich protein 8, pseudogene 1"	pseudo	0	0.336634
Merged-chr2-66762735-1	chr2	66762685	66762785	+	2.7	cIP1vsInput	"intron (NM_009135, intron 1 of 24)"	"intron (NM_009135, intron 1 of 24)"	22175	NM_009135	20272	Mm.38127	NM_009135	ENSMUSG00000034810	Scn7a	1110034K09Rik|AI642000|NaG|Nav2|Nav2.3|Nax|Scn6a	"sodium channel, voltage-gated, type VII, alpha"	protein-coding	0.01	0.405941
Merged-chr14-100242011-1	chr14	100241961	100242061	+	2.7	cIP1vsInput	Intergenic	Intergenic	-92215	NM_010636	16597	Mm.458816	NM_010636		Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding	0.01	0.554455
Merged-chr16-89789979-1	chr16	89789929	89790029	+	2.7	cIP1vsInput	"intron (NM_001145887, intron 12 of 12)"	"intron (NM_001145887, intron 12 of 12)"	28373	NM_001145887	21844	Mm.310902	NM_001145886	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding	0.03	0.564356
Merged-chr10-112736473-1	chr10	112736423	112736523	+	2.7	cIP2vsInput	"intron (NR_040579, intron 2 of 6)"	"intron (NR_040579, intron 2 of 6)"	9547	NR_040579	69355	Mm.84337	NR_040579		1700010J16Rik	-	RIKEN cDNA 1700010J16 gene	miscRNA	0	0.29703
Merged-chr18-63306490-1	chr18	63306440	63306540	+	2.7	cIP2vsInput	"intron (NM_001039485, intron 2 of 53)"	L1_Mur3|LINE|L1	80693	NM_001039485	667742	Mm.158720	NM_172629	ENSMUSG00000041482	Piezo2	5930434P17|9030411M15Rik|9430028L06Rik|Fam38b|Fam38b2	piezo-type mechanosensitive ion channel component 2	protein-coding	0	0.366337
Merged-chr19-10688852-1	chr19	10688802	10688902	+	2.7	cIP2vsInput	promoter-TSS (NM_181403)	promoter-TSS (NM_181403)	37	NM_181403	107305	Mm.19091	NM_181403	ENSMUSG00000048832	Vps37c	5730409F24Rik|AU042646	vacuolar protein sorting 37C (yeast)	protein-coding	0.09	0.673267
Merged-chr1-73604514-1	chr1	73604464	73604564	+	2.7	cIP2vsInput	Intergenic	Intergenic	-196945	NR_003202	723792	Mm.486048	NR_003202		Pinc	-	pregnancy induced noncoding RNA	miscRNA	0	0.346535
Merged-chr19-51559367-1	chr19	51559317	51559417	+	2.7	cIP1vsInput	Intergenic	Intergenic	-704956	NM_008386	16333	Mm.46269	NM_008386	ENSMUSG00000035804	Ins1	Ins-1|Ins2-rs1	insulin I	protein-coding	0	0.326733
Merged-chr5-144100376-1	chr5	144100326	144100426	+	2.7	cIP2vsInput	promoter-TSS (NM_001081109)	promoter-TSS (NM_001081109)	-60	NM_001081109	231876	Mm.288726	NM_001081109	ENSMUSG00000038970	Lmtk2	2900041G10Rik|A330101P12Rik|BREK|KPI-2|KPI2|aatyk2|cprk	lemur tyrosine kinase 2	protein-coding	0.12	0.732673
Merged-chr3-56221602-1	chr3	56221552	56221652	+	2.7	cIP2vsInput	Intergenic	L1MA6|LINE|L1	-37901	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding	0	0.356436
Merged-chr13-110952815-1	chr13	110952765	110952865	+	2.7	cIP2vsInput	Intergenic	Lx7|LINE|L1	276616	NR_045908	73129	Mm.417826	NR_045908		3110015C05Rik	-	RIKEN cDNA 3110015C05 gene	miscRNA	0	0.306931
Merged-chr4-98383327-1	chr4	98383277	98383377	+	2.7	cIP1vsInput	promoter-TSS (NM_053157)	promoter-TSS (NM_053157)	-62	NM_053157	94043	Mm.331719	NM_053157	ENSMUSG00000028563	Tm2d1	2310026L18Rik|AA990549|Bbp	TM2 domain containing 1	protein-coding	0.03	0.554455
Merged-chr4-43499599-1	chr4	43499549	43499649	+	2.7	cIP2vsInput	promoter-TSS (NM_001013377)	promoter-TSS (NM_001013377)	61	NM_001013377	230098	Mm.331567	NM_001013377	ENSMUSG00000051517	Arhgef39	E130306D19Rik	Rho guanine nucleotide exchange factor (GEF) 39	protein-coding	0.12	0.643564
Merged-chr15-13181058-1	chr15	13181008	13181108	+	2.7	cIP1vsInput	Intergenic	Intergenic	-7419	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	K-cadherin|cad6|cadherin-6	cadherin 6	protein-coding	0	0.356436
Merged-chr3-96238280-1	chr3	96238230	96238330	+	2.7	cIP2vsInput	"3' UTR (NM_054045, exon 1 of 1)"	"3' UTR (NM_054045, exon 1 of 1)"	847	NM_054045	97114	Mm.358797	NM_054045	ENSMUSG00000081058	Hist2h3c2	H3-614|H3.2-614|Hist2h3c2-ps|Hist2h3ca1|M32461	"histone cluster 2, H3c2"	protein-coding	0.04	0.465347
Merged-chr15-3301306-1	chr15	3301256	3301356	+	2.7	cIP2vsInput	"intron (NM_001166063, intron 1 of 8)"	"intron (NM_001166063, intron 1 of 8)"	2220	NM_001166063	100039139	Mm.455610	NM_001166063	ENSMUSG00000091119	Ccdc152	ENSMUSG00000071814	coiled-coil domain containing 152	protein-coding	0.02	0.326733
Merged-chr9-3878591-1	chr9	3878541	3878641	+	2.7	cIP1vsInput	"intron (NM_001033322, intron 7 of 7)"	"intron (NM_001033322, intron 7 of 7)"	346242	NM_001033322	234889	Mm.91240	NM_001033322		Gucy1a2	6330407I18Rik|A230060L24Rik	"guanylate cyclase 1, soluble, alpha 2"	protein-coding	0	0.316832
Merged-chr3-36032219-1	chr3	36032169	36032269	+	2.7	cIP2vsInput	"intron (NM_178418, intron 5 of 11)"	"intron (NM_178418, intron 5 of 11)"	21328	NM_178418	241943	Mm.269018	NM_178418	ENSMUSG00000047696	Ccdc144b	-	coiled-coil domain containing 144B	protein-coding	0.03	0.425743
Merged-chr9-101397823-1	chr9	101397773	101397873	+	2.7	cIP1vsInput	Intergenic	L1M2|LINE|L1	-145991	NM_001161362	235542	Mm.335386	NM_001161362	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	"protein phosphatase 2, regulatory subunit B'', alpha"	protein-coding	0.01	0.336634
Merged-chr3-123283313-1	chr3	123283263	123283363	+	2.7	cIP2vsInput	"intron (NM_027135, intron 3 of 22)"	"intron (NM_027135, intron 3 of 22)"	15817	NM_027135	69608	Mm.29293	NM_027135	ENSMUSG00000039234	Sec24d	2310020L09Rik|Gm1349	"Sec24 related gene family, member D (S. cerevisiae)"	protein-coding	0.03	0.475248
Merged-chrX-107457714-1	chrX	107457664	107457764	+	2.7	cIP1vsInput	Intergenic	Lx9|LINE|L1	-54354	NM_008409	16431	Mm.193	NM_008409	ENSMUSG00000031239	Itm2a	AW108051|Bricd2a|E25|Itm2	integral membrane protein 2A	protein-coding	0	0.435644
Merged-chr4-31525556-1	chr4	31525506	31525606	+	2.7	cIP1vsInput	Intergenic	Intergenic	-438551	NM_009316	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding	0	0.346535
Merged-chr6-15082076-1	chr6	15082026	15082126	+	2.7	cIP2vsInput	"intron (NM_053242, intron 2 of 18)"	L2a|LINE|L2	-103430	NM_212435	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding	0.01	0.39604
Merged-chr18-23943300-1	chr18	23943250	23943350	+	2.7	cIP2vsInput	Intergenic	Intergenic	-11388	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding	0	0.336634
Merged-chr7-13055015-1	chr7	13054965	13055065	+	2.7	cIP1vsInput	promoter-TSS (NM_145819)	promoter-TSS (NM_145819)	-251	NM_145819	109889	Mm.10103	NM_145819	ENSMUSG00000030380	Mzf1	Mzf-2|Mzf2|Zfp121|Zfp98|Znf42	myeloid zinc finger 1	protein-coding	0.03	0.514851
Merged-chr11-35799053-1	chr11	35799003	35799103	+	2.7	cIP2vsInput	promoter-TSS (NM_001004147)	promoter-TSS (NM_001004147)	-169	NM_001004147	237730	Mm.189222	NM_001004147	ENSMUSG00000051062	Fbll1	AI595406	fibrillarin-like 1	protein-coding	0.05	0.554455
Merged-chr2-4918926-1	chr2	4918876	4918976	+	2.7	cIP2vsInput	promoter-TSS (NM_010726)	promoter-TSS (NM_010726)	-70	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding	0.04	0.70297
Merged-chr2-124938493-2	chr2	124938437	124938550	+	2.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-129634	NM_175034	317750	Mm.330538	NM_175034	ENSMUSG00000035183	Slc24a5	F630045L20Rik|JSX|NCKX5|NCX5	"solute carrier family 24, member 5"	protein-coding	0.00885	0.412281
Merged-chr1-108913343-1	chr1	108913293	108913393	+	2.7	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	996084	NR_102307	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0.01	0.326733
Merged-chr7-86799425-1	chr7	86799375	86799475	+	2.7	cIP1vsInput	"intron (NM_001105188, intron 1 of 5)"	"intron (NM_001105188, intron 1 of 5)"	4284	NM_001105188	546983	Mm.469904	NM_001105188	ENSMUSG00000090949	Vmn2r77	EG546983	"vomeronasal 2, receptor 77"	protein-coding	0	0.257426
Merged-chr10-28809014-1	chr10	28808964	28809064	+	2.7	cIP2vsInput	"intron (NM_178666, intron 4 of 5)"	L1M4|LINE|L1	114493	NR_033601	114676	Mm.484516	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo	0.02	0.346535
Merged-chr10-62740785-1	chr10	62740735	62740835	+	2.7	cIP2vsInput	Intergenic	Intergenic	-14686	NM_001033260	216021	Mm.39821	NM_001033260	ENSMUSG00000036923	Stox1	4732470K04Rik|Gm63	storkhead box 1	protein-coding	0	0.287129
Merged-chr3-60239380-1	chr3	60239330	60239430	+	2.7	cIP1vsInput	Intergenic	Lx7|LINE|L1	157511	NM_032400	84112	Mm.125110	NM_032400	ENSMUSG00000027762	Sucnr1	Gpr91	succinate receptor 1	protein-coding	0	0.336634
Merged-chr3-47322690-1	chr3	47322640	47322740	+	2.7	cIP2vsInput	Intergenic	Lx6|LINE|L1	704069	NR_040408	666202	Mm.465057	NR_040408		Gm7977	EG666202	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide pseudogene"	pseudo	0.01	0.346535
Merged-chr4-21727653-1	chr4	21727603	21727703	+	2.7	cIP2vsInput	promoter-TSS (NM_001122982)	promoter-TSS (NM_001122982)	-50	NM_001122982	51813	Mm.278584	NM_001122982	ENSMUSG00000028252	Ccnc	AI451004|AU020987|CG1C	cyclin C	protein-coding	0.11	0.653465
Merged-chrX-36817183-1	chrX	36817133	36817233	+	2.7	cIP2vsInput	Intergenic	Intergenic	21531	NM_007451	11740	Mm.371544	NM_007451	ENSMUSG00000016319	Slc25a5	Ant2	"solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 5"	protein-coding	0.01	0.623762
Merged-chr12-62693717-1	chr12	62693667	62693767	+	2.7	cIP1vsInput	Intergenic	Intergenic	1169085	NM_178714	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0	0.336634
Merged-chr10-57106795-1	chr10	57106745	57106845	+	2.7	cIP2vsInput	Intergenic	L1MA5|LINE|L1	379558	NR_045353	74928	Mm.416643	NR_045353	ENSMUSG00000097370	4930467K11Rik	-	RIKEN cDNA 4930467K11 gene	miscRNA	0.01	0.326733
Merged-chr10-62980167-1	chr10	62980117	62980217	+	2.7	cIP2vsInput	promoter-TSS (NM_027425)	promoter-TSS (NM_027425)	-56	NM_027425	70432	Mm.274784	NM_027425		Rufy2	2610111M19Rik|AI844453|Denn|LZ-FYVE|ZFYVE13	RUN and FYVE domain-containing 2	protein-coding	0.08	0.683168
Merged-chr7-25268542-1	chr7	25268492	25268592	+	2.7	cIP2vsInput	Intergenic	CpG	-13637	NM_001110132	71722	Mm.28833	NM_001110131	ENSMUSG00000005442	Cic	1200010B10Rik|mKIAA0306	capicua homolog (Drosophila)	protein-coding	0.1	0.772277
Merged-chr19-55643619-1	chr19	55643569	55643669	+	2.7	cIP2vsInput	"intron (NR_045318, intron 2 of 3)"	MIR3|SINE|MIR	58585	NR_045318	77594	Mm.329924	NR_045318	ENSMUSG00000097632	4930552P12Rik	-	RIKEN cDNA 4930552P12 gene	miscRNA	0.02	0.485149
Merged-chr15-102525155-1	chr15	102525105	102525205	+	2.7	cIP1vsInput	promoter-TSS (NR_033409)	promoter-TSS (NR_033409)	-213	NR_033409	54615	Mm.445915	NM_018787	ENSMUSG00000023052	Npff	-	neuropeptide FF-amide peptide precursor	protein-coding	0	0.415842
Merged-chr6-136249184-1	chr6	136249134	136249234	+	2.7	cIP2vsInput	Intergenic	Intergenic	-75673	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	"glutamate receptor, ionotropic, NMDA2B (epsilon 2)"	protein-coding	0	0.386139
Merged-chr1-149035574-1	chr1	149035524	149035624	+	2.7	cIP2vsInput	Intergenic	Intergenic	925710	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0	0.326733
Merged-chr4-70942890-1	chr4	70942840	70942940	+	2.7	cIP2vsInput	Intergenic	MLT2C1|LTR|ERVL	-407962	NM_172694	230316	Mm.251188	NM_172694		Megf9	4933405H16Rik|9630025C07|Egfl5|mKIAA0818	multiple EGF-like-domains 9	protein-coding	0	0.316832
Merged-chr8-98391681-1	chr8	98391631	98391731	+	2.7	cIP1vsInput	Intergenic	Intergenic	1024776	NM_007667	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.326733
Merged-chr5-90931482-1	chr5	90931432	90931532	+	2.7	cIP2vsInput	"intron (NM_026788, intron 1 of 7)"	GC_rich|Low_complexity|Low_complexity	286	NM_026788	665563	Mm.153030	NM_026788	ENSMUSG00000029376	Mthfd2l	1110019K23Rik|C630010D07Rik	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like	protein-coding	0.15	0.821782
Merged-chr1-188058969-1	chr1	188058919	188059019	+	2.7	cIP2vsInput	"intron (NM_011935, intron 2 of 6)"	"intron (NM_011935, intron 2 of 6)"	-49979	NR_038007	320272	Mm.446274	NR_038007		9330162B11Rik	-	RIKEN cDNA 9330162B11 gene	miscRNA	0	0.366337
Merged-chr7-97171045-1	chr7	97170995	97171095	+	2.7	cIP1vsInput	"intron (NM_001162477, intron 1 of 9)"	"intron (NM_001162477, intron 1 of 9)"	89294	NM_010248	14389	Mm.42033	NM_001162477	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding	0	0.405941
Merged-chr14-22895114-1	chr14	22895064	22895164	+	2.7	cIP2vsInput	"intron (NM_028275, intron 6 of 6)"	"intron (NM_028275, intron 6 of 6)"	199457	NR_033550	791307	Mm.364384	NR_033550	ENSMUSG00000068680	Gm10248	ENSMUSG00000068680	predicted gene 10248	miscRNA	0	0.316832
Merged-chr16-22428875-1	chr16	22428825	22428925	+	2.7	cIP2vsInput	"intron (NM_023794, intron 5 of 12)"	"intron (NM_023794, intron 5 of 12)"	10695	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant gene 5	protein-coding	0.01	0.465347
Merged-chr3-84692828-1	chr3	84692778	84692878	+	2.7	cIP1vsInput	"intron (NM_177260, intron 6 of 6)"	"intron (NM_177260, intron 6 of 6)"	26636	NM_177260	320782	Mm.107370	NM_177260	ENSMUSG00000056498	Tmem154	9930117H01Rik	transmembrane protein 154	protein-coding	0.01	0.405941
Merged-chr13-87535437-1	chr13	87535387	87535487	+	2.7	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-1286035	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0	0.346535
Merged-chr5-100878954-1	chr5	100878904	100879004	+	2.7	cIP1vsInput	"intron (NM_172715, intron 3 of 12)"	"intron (NM_172715, intron 3 of 12)"	32725	NM_172715	231510		NM_172715	ENSMUSG00000029314	Agpat9	1-AGPAT|1-AGPAT 9|4933407I02Rik|4933408F15|9|A230097K15Rik|GPAT-3|mGPAT3	1-acylglycerol-3-phosphate O-acyltransferase 9	protein-coding	0	0.287129
Merged-chr5-99479604-1	chr5	99479554	99479654	+	2.7	cIP2vsInput	"intron (NR_030692, intron 2 of 3)"	"intron (NR_030692, intron 2 of 3)"	-226677	NM_145839	320292	Mm.259074	NM_145839	ENSMUSG00000029333	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	"RasGEF domain family, member 1B"	protein-coding	0.04	0.574257
Merged-chr6-24955250-1	chr6	24955200	24955300	+	2.7	cIP2vsInput	"exon (NM_177013, exon 1 of 1)"	"exon (NM_177013, exon 1 of 1)"	875	NM_177013	319832	Mm.127446	NM_177013	ENSMUSG00000048022	Tmem229a	6332401O19Rik	transmembrane protein 229A	protein-coding	0.12	0.673267
Merged-chr15-5994444-1	chr15	5994394	5994494	+	2.7	cIP1vsInput	Intergenic	MLTR18_MM|LTR|ERVK	-305345	NM_001008702	13132	Mm.240830	NM_001008702	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	"disabled 2, mitogen-responsive phosphoprotein"	protein-coding	0.01	0.455446
Merged-chr4-31999055-1	chr4	31999005	31999105	+	2.7	cIP2vsInput	"intron (NM_009316, intron 12 of 16)"	"intron (NM_009316, intron 12 of 16)"	34948	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding	0	0.326733
Merged-chr7-27178722-1	chr7	27178672	27178772	+	2.7	cIP2vsInput	"intron (NM_029391, intron 1 of 7)"	CpG	161	NM_029391	19342	Mm.482114	NM_029391	ENSMUSG00000053291	Rab4b	1500031G17Rik	"RAB4B, member RAS oncogene family"	protein-coding	0.07	0.673267
Merged-chr9-26072840-1	chr9	26072790	26072890	+	2.7	cIP1vsInput	Intergenic	Intergenic	591243	NM_026189	67484	Mm.112977	NM_026189	ENSMUSG00000036611	Eepd1	2310005P05Rik|AI481005	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding	0	0.277228
Merged-chr6-4782829-1	chr6	4782779	4782879	+	2.7	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	35523	NM_130877	170676	Mm.320575	NM_001040611	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding	0.01	0.366337
Merged-chr2-118883497-1	chr2	118883447	118883547	+	2.7	cIP1vsInput	Intergenic	CpG	-18118	NM_001045523	228536	Mm.330487	NM_001045523	ENSMUSG00000040007	Bahd1	AL022997|AW541238|Gm117|mKIAA0945	bromo adjacent homology domain containing 1	protein-coding	0.07	0.574257
Merged-chr16-9632775-1	chr16	9632725	9632825	+	2.7	cIP1vsInput	"intron (NM_008170, intron 9 of 11)"	L1VL4|LINE|L1	359758	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	"glutamate receptor, ionotropic, NMDA2A (epsilon 1)"	protein-coding	0.01	0.336634
Merged-chr4-137495239-1	chr4	137495189	137495289	+	2.7	cIP2vsInput	"intron (NM_008305, intron 1 of 96)"	"intron (NM_008305, intron 1 of 96)"	26436	NM_008305	15530	Mm.273662	NM_008305	ENSMUSG00000028763	Hspg2	AI852380|Pcn|Plc|per	perlecan (heparan sulfate proteoglycan 2)	protein-coding	0.01	0.60396
Merged-chr13-102444855-1	chr13	102444805	102444905	+	2.7	cIP1vsInput	Intergenic	(ATATG)n|Simple_repeat|Simple_repeat	-248703	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding	0	0.277228
Merged-chr17-10864943-1	chr17	10864893	10864993	+	2.7	cIP2vsInput	"intron (NM_016694, intron 1 of 11)"	"intron (NM_016694, intron 1 of 11)"	24559	NM_016694	50873	Mm.311110	NM_016694		Park2	PRKN	"Parkinson disease (autosomal recessive, juvenile) 2, parkin"	protein-coding	0	0.29703
Merged-chr12-83632052-2	chr12	83631965	83632139	+	2.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_027349)	promoter-TSS (NM_027349)	-182	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding	0.045977	0.514286
Merged-chr16-68064186-1	chr16	68064136	68064236	+	2.7	cIP2vsInput	Intergenic	Intergenic	-443278	NM_178721	239857	Mm.394300	NM_001145977	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0.01	0.29703
Merged-chr3-89430387-1	chr3	89430337	89430437	+	2.7	cIP2vsInput	promoter-TSS (NM_026869)	promoter-TSS (NM_026869)	-450	NM_026869	68911	Mm.22521	NM_026869	ENSMUSG00000047824	Pygo2	1190004M21Rik|mpygo2	pygopus 2	protein-coding	0.07	0.673267
Merged-chrY-6988928-1	chrY	6988878	6988978	+	2.7	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	178849	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.326733
Merged-chr18-25263737-1	chr18	25263687	25263787	+	2.7	cIP1vsInput	"intron (NM_001033532, intron 5 of 10)"	"intron (NM_001033532, intron 5 of 10)"	94717	NM_001033532	225289	Mm.391081	NM_001033532	ENSMUSG00000033632	AW554918	4921538P22|AI461742|Kiaa1328|mKIAA1328	expressed sequence AW554918	protein-coding	0	0.346535
Merged-chr10-5287860-1	chr10	5287810	5287910	+	2.7	cIP1vsInput	Intergenic	Intergenic	-93153	NM_001079686	64009	Mm.331626	NM_001079686	ENSMUSG00000019769	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756	"spectrin repeat containing, nuclear envelope 1"	protein-coding	0	0.306931
Merged-chr9-58679746-1	chr9	58679696	58679796	+	2.7	cIP1vsInput	"intron (NM_028598, intron 2 of 5)"	L1_Mur3|LINE|L1	61813	NM_028598	73673	Mm.205196	NM_028598	ENSMUSG00000074269	2410076I21Rik	4930527A11Rik	RIKEN cDNA 2410076I21 gene	protein-coding	0.01	0.306931
Merged-chr7-105769878-1	chr7	105769828	105769928	+	2.7	cIP2vsInput	"intron (NM_001162943, intron 2 of 20)"	L2a|LINE|L2	-17671	NM_009906	12751	Mm.20837	NM_009906	ENSMUSG00000030894	Tpp1	Cln2|TPP-I	tripeptidyl peptidase I	protein-coding	0.01	0.346535
Merged-chr4-7595075-1	chr4	7595025	7595125	+	2.7	cIP1vsInput	Intergenic	Arthur1|DNA|hAT-Tip100	34387	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	miscRNA	0	0.326733
Merged-chr2-34031689-1	chr2	34031639	34031739	+	2.7	cIP2vsInput	Intergenic	Intergenic	-143743	NM_175184	72543	Mm.254914	NM_175184	ENSMUSG00000038740	Mvb12b	2610200O14Rik|2610528K11Rik|AI414895|Fam125b	multivesicular body subunit 12B	protein-coding	0.02	0.673267
Merged-chr19-41071831-1	chr19	41071781	41071881	+	2.7	cIP2vsInput	"intron (NM_153520, intron 2 of 5)"	"intron (NM_153520, intron 2 of 5)"	5282	NM_153520	226115	Mm.54119	NM_153520		Opalin	Tmem10|Tmp10	oligodendrocytic myelin paranodal and inner loop protein	protein-coding	0.01	0.346535
Merged-chr1-35885965-1	chr1	35885915	35886015	+	2.7	cIP1vsInput	Intergenic	Intergenic	-182435	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding	0.05	0.574257
Merged-chr8-63198491-1	chr8	63198441	63198541	+	2.7	cIP2vsInput	"intron (NM_001252620, intron 5 of 11)"	L1MC|LINE|L1	247146	NM_023689	72902	Mm.334552	NM_001252620	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3"	protein-coding	0	0.356436
Merged-chr19-50014050-1	chr19	50014000	50014100	+	2.7	cIP1vsInput	Intergenic	Intergenic	664596	NM_001252501	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0	0.316832
Merged-chr13-12770422-1	chr13	12770372	12770472	+	2.7	cIP1vsInput	Intergenic	L1VL1|LINE|L1	29636	NM_011954	26421	Mm.457984	NM_011954		Prl2c4	MRP-3|Mrpplf3|PLF-3|mrp/plf3	"prolactin family 2, subfamily c, member 4"	protein-coding	0	0.287129
Merged-chr16-4541672-1	chr16	4541622	4541722	+	2.7	cIP1vsInput	Intergenic	Intergenic	18048	NM_031182	83383	Mm.273210	NM_031182	ENSMUSG00000005718	Tfap4	AI642933|AP-4|D930048N17Rik|Tcfap4|bHLHc41	transcription factor AP4	protein-coding	0.03	0.405941
Merged-chr17-62534906-1	chr17	62534856	62534956	+	2.7	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	346411	NM_207654	13640	Mm.401670	NM_010109		Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding	0	0.316832
Merged-chrY-6516661-2	chrY	6516610	6516713	+	2.7	cIP1vsInput|cIP2vsInput	Intergenic	Lx5b|LINE|L1	651116	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.326923
Merged-chr2-135243581-1	chr2	135243531	135243631	+	2.7	cIP2vsInput	"intron (NM_019677, intron 4 of 32)"	"intron (NM_019677, intron 4 of 32)"	-27965	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	miscRNA	0	0.306931
Merged-chr5-103377912-1	chr5	103377862	103377962	+	2.7	cIP2vsInput	Intergenic	Intergenic	-47280	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|Ptpri|RIP	"protein tyrosine phosphatase, non-receptor type 13"	protein-coding	0.02	0.415842
Merged-chr1-86814894-1	chr1	86814844	86814944	+	2.7	cIP2vsInput	"intron (NM_001172157, intron 6 of 21)"	"intron (NM_001172157, intron 6 of 21)"	111090	NM_001172157	208718	Mm.389152	NM_001172157	ENSMUSG00000053333	Dis3l2	4930429A22Rik|8030493P09Rik	DIS3 mitotic control homolog (S. cerevisiae)-like 2	protein-coding	0	0.336634
Merged-chr10-21702656-1	chr10	21702606	21702706	+	2.7	cIP2vsInput	Intergenic	Intergenic	11811	NR_045843	432436	Mm.244553	NM_001004162	ENSMUSG00000056716	Gm5420	EG432436	predicted gene 5420	miscRNA	0.01	0.346535
Merged-chr6-13349798-1	chr6	13349748	13349848	+	2.7	cIP2vsInput	Intergenic	L1MA7|LINE|L1	-63539	NR_038149	69413	Mm.177847	NR_038149		1700016P04Rik	-	RIKEN cDNA 1700016P04 gene	miscRNA	0.01	0.346535
Merged-chr15-102065861-1	chr15	102065811	102065911	+	2.7	cIP2vsInput	Intergenic	Intergenic	-7912	NM_145625	75705	Mm.391795	NM_145625	ENSMUSG00000058655	Eif4b	2310046H11Rik|AL024095|C85189|Eif4a2	eukaryotic translation initiation factor 4B	protein-coding	0.07	0.623762
Merged-chr7-128611361-1	chr7	128611311	128611411	+	2.7	cIP2vsInput	promoter-TSS (NM_178641)	promoter-TSS (NM_178641)	-4	NM_178641	101490	Mm.490344	NM_178641	ENSMUSG00000042105	Inpp5f	5830435P03Rik|AI115354|AW561896|SAC2|cI-27|mKIAA0966	inositol polyphosphate-5-phosphatase F	protein-coding	0.05	0.663366
Merged-chr3-112031052-1	chr3	112031002	112031102	+	2.7	cIP1vsInput	"intron (NR_045362, intron 2 of 3)"	Lx3C|LINE|L1	149149	NR_045362	625585	Mm.389497	NR_045362		Gm6602	-	predicted gene 6602	miscRNA	0	0.306931
Merged-chr15-90329830-1	chr15	90329780	90329880	+	2.7	cIP1vsInput	Intergenic	L1ME3A|LINE|L1	105519	NM_001033441	380959	Mm.17853	NM_001033441	ENSMUSG00000075470	Alg10b	AA469671|AU045404|AW123895|C85569|Gm917	"asparagine-linked glycosylation 10B (alpha-1,2-glucosyltransferase)"	protein-coding	0	0.316832
Merged-chr8-49960929-1	chr8	49960879	49960979	+	2.7	cIP1vsInput	Intergenic	Intergenic	-407183	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.356436
Merged-chr2-78048475-1	chr2	78048425	78048525	+	2.7	cIP2vsInput	Intergenic	Intergenic	-102122	NM_030560	80744	Mm.288151	XM_003946079	ENSMUSG00000027014	Cwc22	AA684037|AI173004|AL022752|B230213M24|mKIAA1604	CWC22 spliceosome-associated protein homolog (S. cerevisiae)	protein-coding	0.01	0.386139
Merged-chr7-128474078-1	chr7	128474028	128474128	+	2.7	cIP1vsInput	Intergenic	Intergenic	-12565	NM_009383	21843	Mm.242072	NM_009383	ENSMUSG00000030846	Tial1	5330433G13Rik|AL033329|TIAR|mTIAR	Tia1 cytotoxic granule-associated RNA binding protein-like 1	protein-coding	0	0.405941
Merged-chr18-65076133-1	chr18	65076083	65076183	+	2.7	cIP2vsInput	"intron (NM_031881, intron 2 of 29)"	"intron (NM_031881, intron 2 of 29)"	52606	NM_031881	83814	Mm.98668	NM_001114386	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	"neural precursor cell expressed, developmentally down-regulated gene 4-like"	protein-coding	0.01	0.574257
Merged-chr1-173831521-1	chr1	173831471	173831571	+	2.7	cIP1vsInput	Intergenic	Intergenic	48666	NM_001170853	100040462	Mm.463437	NM_001170853	ENSMUSG00000090272	Mndal	Gm2785	myeloid nuclear differentiation antigen like	protein-coding	0	0.316832
Merged-chr14-54265242-1	chr14	54265192	54265292	+	2.7	cIP2vsInput	"intron (NM_134076, intron 4 of 6)"	PB1D11|SINE|Alu	6010	NM_134076	105501	Mm.28771	NM_001205181	ENSMUSG00000040997	Abhd4	1110035H23Rik|AI429574|Abh4	abhydrolase domain containing 4	protein-coding	0.03	0.613861
Merged-chr5-76118512-1	chr5	76118462	76118562	+	2.7	cIP2vsInput	Intergenic	Intergenic	-21761	NM_020611	57357	Mm.289446	NM_020611	ENSMUSG00000029233	Srd5a3	1110025P14Rik|A430076C09|AV364670|AW987574|D730040M03Rik|H5ar|S5AR 3|Srd5a2l	steroid 5 alpha-reductase 3	protein-coding	0.01	0.336634
Merged-chr16-55934153-1	chr16	55934103	55934203	+	2.7	cIP1vsInput	"intron (NM_001159366, intron 1 of 4)"	CpG	695	NM_001159365	74201	Mm.178427	NM_001159364	ENSMUSG00000022604	Cep97	2810403B08Rik|4932439K18Rik|AA437768|E130116N02Rik|Lrriq2	centrosomal protein 97	protein-coding	0.04	0.594059
Merged-chr1-148331120-1	chr1	148331070	148331170	+	2.7	cIP2vsInput	Intergenic	Intergenic	1630164	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0	0.326733
Merged-chr8-107425189-1	chr8	107425139	107425239	+	2.7	cIP2vsInput	promoter-TSS (NM_026277)	promoter-TSS (NM_026277)	-151	NM_026277	67619	Mm.334793	NM_026277	ENSMUSG00000003848	Nob1	1700021I09Rik|ART-4|Nob1p|Psmd8bp1	NIN1/RPN12 binding protein 1 homolog (S. cerevisiae)	protein-coding	0.07	0.653465
Merged-chr2-88752336-1	chr2	88752286	88752386	+	2.7	cIP1vsInput	Intergenic	Lx9|LINE|L1	4337	NM_146458	258450	Mm.271378	NM_146458	ENSMUSG00000089892	Olfr1199	MOR230-8	olfactory receptor 1199	protein-coding	0	0.267327
Merged-chr10-33039735-1	chr10	33039685	33039785	+	2.7	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	-43748	NM_029726	76757	Mm.338508	NM_029726	ENSMUSG00000019787	Trdn	2310045H21Rik|EG432451|TDN	triadin	protein-coding	0	0.29703
Merged-chr7-91225834-1	chr7	91225784	91225884	+	2.7	cIP2vsInput	"intron (NM_011807, intron 1 of 22)"	"intron (NM_011807, intron 1 of 22)"	135048	NM_011807	23859	Mm.257035	NM_001243046		Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|PSD93	"discs, large homolog 2 (Drosophila)"	protein-coding	0	0.366337
Merged-chr5-57308463-1	chr5	57308413	57308513	+	2.7	cIP2vsInput	Intergenic	Intergenic	409456	NR_015588	319216	Mm.446765	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	miscRNA	0	0.316832
Merged-chr12-3469960-1	chr12	3469910	3470010	+	2.7	cIP2vsInput	"intron (NM_172421, intron 5 of 10)"	"intron (NM_172421, intron 5 of 10)"	43103	NM_172421	75302	Mm.120475	NM_001270988	ENSMUSG00000037486	Asxl2	4930556B16Rik|mKIAA1685	additional sex combs like 2 (Drosophila)	protein-coding	0.01	0.316832
Merged-chr14-104033818-1	chr14	104033768	104033868	+	2.7	cIP1vsInput	Intergenic	Intergenic	-6676	NR_045953	73877	Mm.399172	NR_045953		4930432J09Rik	-	RIKEN cDNA 4930432J09 gene	miscRNA	0	0.346535
Merged-chr14-122676610-1	chr14	122676560	122676660	+	2.7	cIP1vsInput	"intron (NM_144844, intron 12 of 23)"	"intron (NM_144844, intron 12 of 23)"	142282	NM_144844	110821	Mm.23876	NM_144844	ENSMUSG00000041650	Pcca	C79630	"propionyl-Coenzyme A carboxylase, alpha polypeptide"	protein-coding	0	0.29703
Merged-chr10-128909857-1	chr10	128909807	128909907	+	2.7	cIP2vsInput	promoter-TSS (NM_007653)	promoter-TSS (NM_007653)	-9	NM_007653	12512	Mm.371552	NM_001042580	ENSMUSG00000025351	Cd63	C75951|ME491|Tspan30	CD63 antigen	protein-coding	0.11	0.831683
Merged-chr16-27517264-1	chr16	27517214	27517314	+	2.7	cIP1vsInput	Intergenic	Intergenic	128287	NM_026202	67501	Mm.258985	NM_001025615	ENSMUSG00000038127	Ccdc50	2610529H08Rik|5730448P06Rik|AW048328|AW546090|C3orf6|D16Bwg1543e	coiled-coil domain containing 50	protein-coding	0	0.346535
Merged-chr2-174453871-1	chr2	174453821	174453921	+	2.7	cIP2vsInput	"intron (NM_001080971, intron 1 of 3)"	"intron (NM_001080971, intron 1 of 3)"	3276	NM_001080971	545486	Mm.45285	NM_001080971	ENSMUSG00000016255	Tubb1	2810484G07Rik|M(beta)1	"tubulin, beta 1 class VI"	protein-coding	0.01	0.564356
Merged-chr18-8039294-1	chr18	8039244	8039344	+	2.7	cIP1vsInput	Intergenic	Intergenic	170097	NM_153085	225131	Mm.204524	NM_001146298	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding	0	0.326733
Merged-chr16-70090666-1	chr16	70090616	70090716	+	2.7	cIP2vsInput	Intergenic	Intergenic	-223283	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	"glucan (1,4-alpha-), branching enzyme 1"	protein-coding	0	0.346535
Merged-chr6-124857073-1	chr6	124857023	124857123	+	2.7	cIP2vsInput	"intron (NM_013534, intron 1 of 14)"	CpG	614	NM_013534	14789	Mm.35708	NM_013534	ENSMUSG00000023191	Leprel2	BC016431|Grcb|P3h3	leprecan-like 2	protein-coding	0.08	0.613861
Merged-chr18-79240015-1	chr18	79239965	79240065	+	2.7	cIP2vsInput	Intergenic	(CATAT)n|Simple_repeat|Simple_repeat	-130624	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding	0	0.405941
Merged-chr10-103529893-1	chr10	103529843	103529943	+	2.7	cIP2vsInput	Intergenic	Lx9|LINE|L1	162085	NM_175328	103098	Mm.458408	NM_001252330	ENSMUSG00000019894	Slc6a15	AA536730|AI326450|AI326451|v7-3	"solute carrier family 6 (neurotransmitter transporter), member 15"	protein-coding	0	0.326733
Merged-chr13-12798157-1	chr13	12798107	12798207	+	2.7	cIP2vsInput	"intron (NM_011118, intron 1 of 4)"	"intron (NM_011118, intron 1 of 4)"	1901	NM_011954	26421	Mm.457984	NM_011954		Prl2c4	MRP-3|Mrpplf3|PLF-3|mrp/plf3	"prolactin family 2, subfamily c, member 4"	protein-coding	0	0.287129
Merged-chr10-18318671-1	chr10	18318621	18318721	+	2.7	cIP2vsInput	Intergenic	CpG	-83690	NM_144820	215814	Mm.296565	NM_144820	ENSMUSG00000059554	Ccdc28a	1700009P13Rik|AI480677	coiled-coil domain containing 28A	protein-coding	0.08	0.673267
Merged-chr8-53606416-1	chr8	53606366	53606466	+	2.7	cIP2vsInput	"intron (NM_146208, intron 5 of 9)"	"intron (NM_146208, intron 5 of 9)"	32649	NM_146208	234258	Mm.281749	NM_146208	ENSMUSG00000039396	Neil3	AI449477|BC034753|C85903	nei like 3 (E. coli)	protein-coding	0.01	0.316832
Merged-chr19-37100856-1	chr19	37100806	37100906	+	2.7	cIP2vsInput	"intron (NM_198300, intron 5 of 10)"	"intron (NM_198300, intron 5 of 10)"	-72987	NR_045329	319931	Mm.446730	NR_045329	ENSMUSG00000097591	A330032B11Rik	-	RIKEN cDNA A330032B11 gene	miscRNA	0	0.574257
Merged-chr9-4295325-1	chr9	4295275	4295375	+	2.7	cIP1vsInput	"3' UTR (NM_026276, exon 6 of 6)"	"3' UTR (NM_026276, exon 6 of 6)"	14169	NM_026276	67618	Mm.33970	NM_026276	ENSMUSG00000025894	Aasdhppt	2010309J24Rik|2810407B07Rik|AASD-PPT|CGI-80|LYS2|LYS5	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	protein-coding	0	0.326733
Merged-chr3-150101180-1	chr3	150101130	150101230	+	2.7	cIP2vsInput	Intergenic	Intergenic	826443	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	miscRNA	0.01	0.326733
Merged-chr1-52652073-1	chr1	52652023	52652123	+	2.7	cIP2vsInput	TTS (NR_024590)	TTS (NR_024590)	21368	NM_001142647	227094	Mm.83541	NM_172654	ENSMUSG00000043015	Tmem194b	5330401P04Rik|9830163O08	transmembrane protein 194B	protein-coding	0.02	0.514851
Merged-chr1-25228794-1	chr1	25228744	25228844	+	2.7	cIP2vsInput	"intron (NM_175642, intron 16 of 30)"	"intron (NM_175642, intron 16 of 30)"	49160	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	"predicted gene, 20172"	protein-coding	0.1	0.683168
Merged-chr10-99106924-1	chr10	99106874	99106974	+	2.7	cIP1vsInput	promoter-TSS (NM_027740)	promoter-TSS (NM_027740)	-247	NM_027740	382406	Mm.440656	NM_027740	ENSMUSG00000019952	Poc1b	4933430F16Rik|Wdr51b	POC1 centriolar protein homolog B (Chlamydomonas)	protein-coding	0.12	0.653465
Merged-chr3-145576185-1	chr3	145576135	145576235	+	2.7	cIP1vsInput	promoter-TSS (NM_001081094)	promoter-TSS (NM_001081094)	-23	NM_001081094	229937	Mm.24586	NM_001081094	ENSMUSG00000074182	Znhit6	2410019A14Rik	"zinc finger, HIT type 6"	protein-coding	0.12	0.643564
Merged-chr3-112087606-1	chr3	112087556	112087656	+	2.7	cIP2vsInput	Intergenic	B1F|SINE|Alu	205703	NR_045362	625585	Mm.389497	NR_045362		Gm6602	-	predicted gene 6602	miscRNA	0.01	0.336634
Merged-chr11-109425753-1	chr11	109425703	109425803	+	2.7	cIP1vsInput	promoter-TSS (NM_025275)	promoter-TSS (NM_025275)	-193	NM_025275	13929	Mm.211850	NM_001252193	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding	0.06	0.544554
Merged-chr5-40222224-1	chr5	40222174	40222274	+	2.7	cIP1vsInput	Intergenic	Intergenic	-577593	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding	0.01	0.316832
Merged-chr2-142472009-1	chr2	142471959	142472059	+	2.7	cIP2vsInput	Intergenic	Intergenic	429455	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0	0.356436
Merged-chrX-31171351-1	chrX	31171301	31171401	+	2.7	cIP1vsInput	Intergenic	ETnERV3-int|LTR|ERVK	-165018	NM_001243011	100042159	Mm.489579	NM_001243011	ENSMUSG00000095835	Gm3701	-	predicted gene 3701	protein-coding	0	0.415842
Merged-chr2-156440163-1	chr2	156440113	156440213	+	2.7	cIP2vsInput	"intron (NM_001003815, intron 2 of 21)"	"intron (NM_001003815, intron 2 of 21)"	19111	NM_013510	13821	Mm.20852	NM_001003815	ENSMUSG00000027624	Epb4.1l1	4.1N|Epb41l1|NBL1|mKIAA0338	erythrocyte protein band 4.1-like 1	protein-coding	0.03	0.623762
Merged-chr1-80858280-1	chr1	80858230	80858330	+	2.7	cIP2vsInput	Intergenic	Intergenic	-99727	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding	0.02	0.376238
Merged-chr2-161271022-1	chr2	161270972	161271072	+	2.7	cIP2vsInput	Intergenic	A-rich|Low_complexity|Low_complexity	-161966	NM_173368	71389	Mm.122738	NM_173368	ENSMUSG00000057133	Chd6	5430439G14Rik|6330406J24Rik	chromodomain helicase DNA binding protein 6	protein-coding	0	0.257426
Merged-chr8-118120793-1	chr8	118120743	118120843	+	2.7	cIP1vsInput	Intergenic	L1MDa|LINE|L1	-162962	NM_019707	12554	Mm.334841	NM_019707		Cdh13	4932416G01Rik|Cdht|T-cadherin|Tcad	cadherin 13	protein-coding	0.01	0.326733
Merged-chr5-15021049-1	chr5	15020999	15021099	+	2.7	cIP2vsInput	Intergenic	Intergenic	11958	NM_182957	66773	Mm.368256	NM_182957	ENSMUSG00000091897	Gm17019	-	predicted gene 17019	protein-coding	0	0.39604
Merged-chr7-135736257-1	chr7	135736207	135736307	+	2.7	cIP1vsInput	Intergenic	Intergenic	-19878	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding	0.02	0.39604
Merged-chr3-128372706-1	chr3	128372656	128372756	+	2.7	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-141101	NR_045704	402774	Mm.209170	NR_045704		D030025E07Rik	-	RIKEN cDNA D030025E07 gene	miscRNA	0	0.356436
Merged-chr16-49693111-1	chr16	49693061	49693161	+	2.7	cIP1vsInput	Intergenic	MER34A|LTR|ERV1	-6183	NM_028680	73916	Mm.404371	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding	0.01	0.29703
Merged-chr8-56294731-1	chr8	56294681	56294781	+	2.7	cIP2vsInput	"intron (NM_008278, intron 1 of 6)"	CpG	179	NM_008278	15446	Mm.18832	NM_008278	ENSMUSG00000031613	Hpgd	15-PGDH|AV026552	hydroxyprostaglandin dehydrogenase 15 (NAD)	protein-coding	0.08	0.693069
Merged-chr8-63136377-1	chr8	63136327	63136427	+	2.7	cIP1vsInput	"intron (NM_001252620, intron 4 of 11)"	"intron (NM_001252620, intron 4 of 11)"	185032	NM_023689	72902	Mm.334552	NM_001252620	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3"	protein-coding	0.01	0.356436
Merged-chr4-75064143-1	chr4	75064093	75064193	+	2.7	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	214143	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	3110001D03Rik	1700027K24Rik	RIKEN cDNA 3110001D03 gene	protein-coding	0	0.356436
Merged-chr13-55330125-1	chr13	55330075	55330175	+	2.7	cIP2vsInput	promoter-TSS (NM_016662)	promoter-TSS (NM_016662)	-395	NM_016662	17121	Mm.20350	NM_016662	ENSMUSG00000021485	Mxd3	4631412E13Rik|Mad3|bHLHc13	Max dimerization protein 3	protein-coding	0.14	0.712871
Merged-chr1-61969441-1	chr1	61969391	61969491	+	2.7	cIP1vsInput	"intron (NM_001081050, intron 2 of 22)"	"intron (NM_001081050, intron 2 of 22)"	330617	NM_001081050	72823	Mm.441881	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta|RP23-20G7.1	par-3 partitioning defective 3 homolog B (C. elegans)	protein-coding	0	0.336634
Merged-chr12-77135420-1	chr12	77135370	77135470	+	2.7	cIP1vsInput	Intergenic	Intergenic	-102684	NM_001252614	53618	Mm.489686	NM_001252614	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding	0	0.316832
Merged-chr13-23307762-1	chr13	23307712	23307812	+	2.7	cIP1vsInput	Intergenic	Intergenic	29412	NR_046038	74061	Mm.399501	NR_046038	ENSMUSG00000085122	4933404K08Rik	-	RIKEN cDNA 4933404K08 gene	miscRNA	0	0.425743
Merged-chr1-161149988-1	chr1	161149938	161150038	+	2.7	cIP2vsInput	"intron (NM_028664, intron 1 of 6)"	RMER12|LTR|ERVK	7276	NM_028664	73844	Mm.38830	NM_028664		Ankrd45	4933409K03Rik	ankyrin repeat domain 45	protein-coding	0	0.336634
Merged-chr17-35059158-1	chr17	35059108	35059208	+	2.7	cIP1vsInput	TTS (NM_033444)	TTS (NM_033444)	123	NM_016765	51793	Mm.1457	NM_001190449	ENSMUSG00000007039	Ddah2	1110003M04Rik|AU019324|AW413173|DDAH-2|DDAHII|Ddah|G6a|NG30	dimethylarginine dimethylaminohydrolase 2	protein-coding	0.06	0.574257
Merged-chr14-35422485-1	chr14	35422435	35422535	+	2.7	cIP2vsInput	"intron (NM_008166, intron 8 of 15)"	MLT1H1-int|LTR|ERVL-MaLR	389493	NM_001033766	239036	Mm.239970	NM_001033766	ENSMUSG00000041068	4930596D02Rik	-	RIKEN cDNA 4930596D02 gene	protein-coding	0	0.326733
Merged-chr13-39166646-1	chr13	39166596	39166696	+	2.7	cIP1vsInput	Intergenic	Intergenic	-205771	NM_001170431	108652	Mm.255506	NM_001170430	ENSMUSG00000021432	Slc35b3	4921526O06Rik|AI428480|CGI-19|PABST2|PAPST2	"solute carrier family 35, member B3"	protein-coding	0	0.356436
Merged-chr12-69743867-1	chr12	69743817	69743917	+	2.7	cIP1vsInput	"3' UTR (NM_026536, exon 5 of 5)"	"3' UTR (NM_026536, exon 5 of 5)"	18905	NM_026536	68055	Mm.27844	NM_026536	ENSMUSG00000054894	Atp5s	1110015E18Rik|ATPW	"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit s"	protein-coding	0	0.306931
Merged-chr2-54768132-1	chr2	54768082	54768182	+	2.7	cIP2vsInput	"intron (NM_173030, intron 4 of 12)"	L1_Mur3|LINE|L1	331745	NM_173030	271786	Mm.330227	NM_173030	ENSMUSG00000060988	Galnt13	A230002A12|A230020F20|BB182356	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13	protein-coding	0	0.306931
Merged-chr3-22036505-1	chr3	22036455	22036555	+	2.7	cIP2vsInput	Intergenic	Intergenic	-40147	NM_030732	81004	Mm.446265	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding	0	0.326733
Merged-chr15-23618430-1	chr15	23618380	23618480	+	2.7	cIP2vsInput	Intergenic	Intergenic	581967	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l	cadherin 18	protein-coding	0	0.415842
Merged-chr11-111814062-1	chr11	111814012	111814112	+	2.7	cIP1vsInput	Intergenic	MER58B|DNA|hAT-Charlie	747898	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	"potassium inwardly-rectifying channel, subfamily J, member 2"	protein-coding	0.02	0.316832
Merged-chr3-53863903-1	chr3	53863853	53863953	+	2.7	cIP2vsInput	promoter-TSS (NM_026435)	promoter-TSS (NM_026435)	-96	NM_026435	67890	Mm.23067	NM_026435		Ufm1	1810045K17Rik|AI132708|AI463323|ENSMUSG00000074598|Gm10726	ubiquitin-fold modifier 1	protein-coding	0.03	0.475248
Merged-chr1-172206565-1	chr1	172206515	172206615	+	2.7	cIP1vsInput	"intron (NM_011063, intron 1 of 3)"	"intron (NM_011063, intron 1 of 3)"	216	NM_011063	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding	0.06	0.633663
Merged-chr3-89281391-1	chr3	89281341	89281441	+	2.7	cIP1vsInput	promoter-TSS (NM_001162425)	promoter-TSS (NM_001162425)	-440	NM_001162425	13636	Mm.15675	NM_001162425	ENSMUSG00000027954	Efna1	AI325262|B61|Efl1|Epl1|Eplg1|Lerk1	ephrin A1	protein-coding	0.1	0.653465
Merged-chr15-18993687-1	chr15	18993637	18993737	+	2.7	cIP2vsInput	"intron (NM_009865, intron 8 of 11)"	"intron (NM_009865, intron 8 of 11)"	173358	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0	0.386139
Merged-chr12-42820862-1	chr12	42820812	42820912	+	2.7	cIP1vsInput	Intergenic	RLTR14-int|LTR|ERV1	1192098	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding	0	0.346535
Merged-chr11-84234749-1	chr11	84234699	84234799	+	2.7	cIP1vsInput	"intron (NM_133360, intron 8 of 53)"	L1MEg|LINE|L1	39311	NM_133360	107476	Mm.31374	NM_133360	ENSMUSG00000020532	Acaca	A530025K05Rik|Acac|Acc1|Gm738	acetyl-Coenzyme A carboxylase alpha	protein-coding	0	0.306931
Merged-chr13-53033344-1	chr13	53033294	53033394	+	2.7	cIP1vsInput	Intergenic	Intergenic	-52305	NM_017373	18030	Mm.136604	NM_017373	ENSMUSG00000056749	Nfil3	AV225605|E4BP4	"nuclear factor, interleukin 3, regulated"	protein-coding	0.03	0.445545
Merged-chr12-107979977-1	chr12	107979927	107980027	+	2.7	cIP1vsInput	"intron (NM_001079883, intron 2 of 3)"	"intron (NM_001079883, intron 2 of 3)"	23437	NM_001079883	58208	Mm.392694	NM_001079883	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding	0.07	0.712871
Merged-chrX-101429413-1	chrX	101429363	101429463	+	2.7	cIP2vsInput	promoter-TSS (NM_001252518)	promoter-TSS (NM_001252518)	-238	NM_023144	53610	Mm.280069	NM_001252518	ENSMUSG00000031311	Nono	AA407051|AV149256|NRB54|P54NRB|nonA	"non-POU-domain-containing, octamer binding protein"	protein-coding	0.06	0.653465
Merged-chr3-93754738-1	chr3	93754688	93754788	+	2.7	cIP2vsInput	Intergenic	Lx4A|LINE|L1	-41660	NM_207272	399675	Mm.377924	XM_003946379	ENSMUSG00000060256	Tdpoz4	-	TD and POZ domain containing 4	protein-coding	0	0.29703
Merged-chr9-30480714-1	chr9	30480664	30480764	+	2.7	cIP1vsInput	Intergenic	Intergenic	53385	NM_028874	102607	Mm.35084	NM_028874	ENSMUSG00000031993	Snx19	3526401K03Rik|AI195321|AI848208|mKIAA0254	sorting nexin 19	protein-coding	0.02	0.524752
Merged-chr4-143412526-1	chr4	143412476	143412576	+	2.7	cIP2vsInput	promoter-TSS (NM_172877)	promoter-TSS (NM_172877)	100	NM_172877	242736	Mm.275953	NM_172877	ENSMUSG00000046862	Pramef8	4732496O08Rik|AU023234	PRAME family member 8	protein-coding	0.07	0.524752
Merged-chr8-35593765-1	chr8	35593715	35593815	+	2.7	cIP2vsInput	"intron (NM_001081279, intron 1 of 2)"	"intron (NM_001081279, intron 1 of 2)"	-4745	NR_040376	100504714	Mm.381744	NR_040376	ENSMUSG00000097357	Gm16793	-	"predicted gene, 16793"	miscRNA	0	0.326733
Merged-chr16-92451917-1	chr16	92451867	92451967	+	2.7	cIP2vsInput	"intron (NM_001081549, intron 1 of 3)"	"intron (NM_001081549, intron 1 of 3)"	14229	NM_001081549	54720	Mm.265744	NM_001081549	ENSMUSG00000022951	Rcan1	2410048A02Rik|AA408855|AI429645|AL024459|AV028423|Adapt78|CALP1L|CSP1|DSC1|Dscr1|MCIP1|RCN1	regulator of calcineurin 1	protein-coding	0.08	0.633663
Merged-chr4-89312978-1	chr4	89312928	89313028	+	2.7	cIP1vsInput	Intergenic	Intergenic	-1946	NM_007670	12579	Mm.423094	NM_007670	ENSMUSG00000073802	Cdkn2b	AV083695|INK4b|MTS2|p15|p15(INK4b)|p15INK4b	"cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)"	protein-coding	0.01	0.39604
Merged-chr5-15054153-1	chr5	15054103	15054203	+	2.7	cIP1vsInput	Intergenic	Intergenic	-21146	NM_182957	66773	Mm.368256	NM_182957	ENSMUSG00000091897	Gm17019	-	predicted gene 17019	protein-coding	0.01	0.287129
Merged-chr17-94040860-1	chr17	94040810	94040910	+	2.7	cIP2vsInput	Intergenic	L1MC3|LINE|L1	709032	NM_176917	76781	Mm.486648	NM_176917	ENSMUSG00000055660	Mettl4	2410198H06Rik|A730091E08Rik|AV296509|HsT661	methyltransferase like 4	protein-coding	0	0.326733
Merged-chr9-67106155-1	chr9	67106105	67106205	+	2.7	cIP1vsInput	Intergenic	Intergenic	-27406	NR_045748	100502636	Mm.412607	NR_045748		Gm19299	-	"predicted gene, 19299"	miscRNA	0.04	0.554455
Merged-chr11-87461830-1	chr11	87461780	87461880	+	2.7	cIP2vsInput	"intron (NM_031386, intron 2 of 30)"	"intron (NM_031386, intron 2 of 30)"	34239	NM_001199293	83560	Mm.440758	NM_001199293	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding	0.02	0.425743
Merged-chr11-79973358-1	chr11	79973308	79973408	+	2.7	cIP2vsInput	Intergenic	Intergenic	-10971	NM_144826	216987	Mm.274961	NM_144826	ENSMUSG00000035575	Utp6	4732497O03Rik|HCA66	"UTP6, small subunit (SSU) processome component, homolog (yeast)"	protein-coding	0.03	0.316832
Merged-chr1-155537414-1	chr1	155537364	155537464	+	2.7	cIP2vsInput	Intergenic	Intergenic	-20706	NM_001145781	72482	Mm.288249	NM_001145781	ENSMUSG00000033701	Acbd6	0610010G04Rik|2610100E10Rik	acyl-Coenzyme A binding domain containing 6	protein-coding	0.02	0.465347
Merged-chr7-123068639-1	chr7	123068589	123068689	+	2.7	cIP2vsInput	Intergenic	L1M6|LINE|L1	-55246	NM_144925	233833	Mm.102305	NM_144925	ENSMUSG00000052707	Tnrc6a	2010321I05Rik|3110054G10Rik|AW557223|CAGH26|D130023A07Rik|GW182|Tnrc6	trinucleotide repeat containing 6a	protein-coding	0	0.336634
Merged-chr7-51875473-1	chr7	51875423	51875523	+	2.7	cIP1vsInput	Intergenic	Lx7|LINE|L1	-3672	NM_008087	14453	Mm.471773	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding	0	0.336634
Merged-chr10-91072378-1	chr10	91072328	91072428	+	2.7	cIP1vsInput	"intron (NM_001042558, intron 4 of 26)"	"intron (NM_001042558, intron 4 of 26)"	10365	NM_001042558	11783	Mm.220289	NM_001042558	ENSMUSG00000019979	Apaf1	6230400I06Rik|Apaf-1|Apaf1l|fog|mKIAA0413	apoptotic peptidase activating factor 1	protein-coding	0	0.287129
Merged-chr3-150964295-1	chr3	150964245	150964345	+	2.7	cIP2vsInput	Intergenic	Intergenic	-473587	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0.01	0.336634
Merged-chr12-98230851-1	chr12	98230801	98230901	+	2.7	cIP2vsInput	"intron (NM_008079, intron 9 of 16)"	L1_Mus3|LINE|L1	28486	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding	0	0.346535
Merged-chr2-132283305-1	chr2	132283255	132283355	+	2.7	cIP1vsInput	"intron (NM_138651, intron 1 of 12)"	"intron (NM_138651, intron 1 of 12)"	20048	NM_138651	110911	Mm.284503	NM_138651	ENSMUSG00000058793	Cds2	5730450N06Rik|5730460C18Rik|AI854580|D2Wsu127e	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	protein-coding	0	0.336634
Merged-chr3-121171761-1	chr3	121171711	121171811	+	2.7	cIP2vsInput	promoter-TSS (NM_028456)	promoter-TSS (NM_028456)	-66	NM_025637	66568	Mm.263163	NM_025637	ENSMUSG00000028133	Rwdd3	2510027J23Rik|3110037C01Rik|AI035684|AI662458|X2CR1	RWD domain containing 3	protein-coding	0.11	0.782178
Merged-chr7-45923374-1	chr7	45923324	45923424	+	2.7	cIP2vsInput	Intergenic	Intergenic	-1948	NM_010129	13732	Mm.20829	NM_001146346	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding	0.03	0.524752
Merged-chr19-14487036-1	chr19	14486986	14487086	+	2.7	cIP2vsInput	"intron (NM_011600, intron 8 of 19)"	"intron (NM_011600, intron 8 of 19)"	-48530	NR_003027	19862		NR_003027	ENSMUSG00000095132	Rnu6	-	U6 small nuclear RNA	snRNA	0	0.326733
Merged-chr3-119249099-1	chr3	119249049	119249149	+	2.7	cIP1vsInput	"intron (NM_170778, intron 18 of 22)"	L1ME1|LINE|L1	534289	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0	0.326733
Merged-chr5-122621700-1	chr5	122621650	122621750	+	2.7	cIP2vsInput	Intergenic	Intergenic	-7182	NM_009879	12589	Mm.10125	NM_009879	ENSMUSG00000029469	Ift81	AW060663|Cdv-1|Cdv-1r|Cdv1	intraflagellar transport 81	protein-coding	0	0.514851
Merged-chr8-49187691-1	chr8	49187641	49187741	+	2.7	cIP1vsInput	Intergenic	Intergenic	-513001	NM_011857	23965	Mm.42191	NM_001145937	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding	0.01	0.29703
Merged-chr18-18286363-1	chr18	18286313	18286413	+	2.7	cIP2vsInput	Intergenic	Intergenic	-705373	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	miscRNA	0	0.326733
Merged-chr15-11914123-2	chr15	11914066	11914181	+	2.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-8449	NM_001039181	18162	Mm.25259	NM_001039181	ENSMUSG00000022206	Npr3	B430320C24Rik|C81222|NPR-C|lgj|stri	natriuretic peptide receptor 3	protein-coding	0.017391	0.344828
Merged-chr3-23883016-1	chr3	23882966	23883066	+	2.7	cIP1vsInput	Intergenic	Intergenic	1631646	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	miscRNA	0.01	0.336634
Merged-chr7-57434438-1	chr7	57434388	57434488	+	2.7	cIP1vsInput	"intron (NM_176942, intron 6 of 9)"	Lx7|LINE|L1	47166	NR_033504	791383	Mm.403104	NR_033504		Gm9962	ENSMUSG00000055048	predicted gene 9962	miscRNA	0.01	0.267327
Merged-chr2-70864526-1	chr2	70864476	70864576	+	2.7	cIP2vsInput	Intergenic	Intergenic	-39046	NM_172664	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding	0	0.306931
Merged-chr2-134259985-1	chr2	134259935	134260035	+	2.7	cIP2vsInput	Intergenic	Intergenic	294367	NM_010403	15112	Mm.26634	NM_010403	ENSMUSG00000027261	Hao1	GOX|Gox1|Hao-1	"hydroxyacid oxidase 1, liver"	protein-coding	0	0.306931
Merged-chr8-32126610-1	chr8	32126560	32126660	+	2.7	cIP1vsInput	Intergenic	Intergenic	-25285	NR_046039	666589	Mm.367675	NR_046039		Gm8179	EG666589	predicted gene 8179	miscRNA	0	0.336634
Merged-chr6-107313027-1	chr6	107312977	107313077	+	2.7	cIP1vsInput	Intergenic	Intergenic	-216699	NM_008516	16979	Mm.488119	NM_008516	ENSMUSG00000034648	Lrrn1	2810047E21Rik|NLRR-1	"leucine rich repeat protein 1, neuronal"	protein-coding	0	0.306931
Merged-chr8-6747290-1	chr8	6747240	6747340	+	2.7	cIP2vsInput	Intergenic	Intergenic	-1642058	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.306931
Merged-chr10-32069719-1	chr10	32069669	32069769	+	2.7	cIP2vsInput	"intron (NM_001013411, intron 3 of 6)"	"intron (NM_001013411, intron 3 of 6)"	-459994	NM_001146349	268291	Mm.295212	NM_001146349		Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding	0	0.257426
Merged-chr6-130789671-1	chr6	130789621	130789721	+	2.7	cIP1vsInput	Intergenic	Lx4A|LINE|L1	-402797	NM_016659	16627	Mm.333431	NM_016659	ENSMUSG00000079853	Klra1	A1|Klra22|Ly49a|Ly49o<129>|Ly49v	"killer cell lectin-like receptor, subfamily A, member 1"	protein-coding	0.01	0.336634
Merged-chr2-98518791-1	chr2	98518741	98518841	+	2.7	cIP2vsInput	Intergenic	L1MC1|LINE|L1	1051117	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.346535
Merged-chr17-15285548-1	chr17	15285498	15285598	+	2.7	cIP2vsInput	Intergenic	Intergenic	-44765	NR_046164	328747	Mm.256835	NR_046164	ENSMUSG00000097624	Gm5091	C330048F19	predicted gene 5091	miscRNA	0.01	0.594059
Merged-chr10-89478610-1	chr10	89478560	89478660	+	2.7	cIP1vsInput	"intron (NM_001163700, intron 5 of 8)"	"intron (NM_001163700, intron 5 of 8)"	28048	NM_001163700	20186	Mm.3095	NM_001163504	ENSMUSG00000047638	Nr1h4	AI957360|Fxr|HRR1|RIP14|Rxrip14	"nuclear receptor subfamily 1, group H, member 4"	protein-coding	0	0.326733
Merged-chr2-129606342-1	chr2	129606292	129606392	+	2.7	cIP1vsInput	"intron (NM_001177646, intron 2 of 8)"	"intron (NM_001177646, intron 2 of 8)"	13147	NM_001177647	19261	Mm.1682	NM_001177646	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding	0	0.514851
Merged-chr13-104717619-1	chr13	104717569	104717669	+	2.7	cIP1vsInput	"intron (NM_026072, intron 11 of 13)"	L1_Mus2|LINE|L1	99334	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	protein-coding	0	0.316832
Merged-chr5-52476439-1	chr5	52476389	52476489	+	2.7	cIP1vsInput	Intergenic	CpG	-4896	NM_001256059	100503884	Mm.483034	NM_001256059	ENSMUSG00000045790	Ccdc149	Gm447	coiled-coil domain containing 149	protein-coding	0.06	0.633663
Merged-chr7-71674778-1	chr7	71674728	71674828	+	2.7	cIP2vsInput	Intergenic	Intergenic	631817	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	"multiple C2 domains, transmembrane 2"	protein-coding	0	0.29703
Merged-chr12-97113927-1	chr12	97113877	97113977	+	2.7	cIP1vsInput	Intergenic	Lx7|LINE|L1	-1066705	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0	0.356436
Merged-chr18-33935902-1	chr18	33935852	33935952	+	2.7	cIP2vsInput	"intron (NM_013512, intron 2 of 23)"	"intron (NM_013512, intron 2 of 23)"	71304	NM_013512	13824	Mm.3465	NM_013512	ENSMUSG00000024376	Epb4.1l4a	Epb4.1l4|Epb41l4a|NBL4	erythrocyte protein band 4.1-like 4a	protein-coding	0.01	0.29703
Merged-chr1-36017433-1	chr1	36017383	36017483	+	2.7	cIP2vsInput	Intergenic	Intergenic	-50967	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding	0.02	0.49505
Merged-chr8-69716600-2	chr8	69716527	69716673	+	2.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_181274)	promoter-TSS (NM_181274)	-114	NM_181274	66869	Mm.334581	NM_001039965		Zfp869	1200003I07Rik	zinc finger protein 869	protein-coding	0.09589	0.666667
Merged-chr7-57493014-1	chr7	57492964	57493064	+	2.7	cIP1vsInput	"intron (NM_176942, intron 2 of 9)"	"intron (NM_176942, intron 2 of 9)"	16995	NM_176942	110886	Mm.273114	NM_176942	ENSMUSG00000055078	Gabra5	A230018I05Rik	"gamma-aminobutyric acid (GABA) A receptor, subunit alpha 5"	protein-coding	0.01	0.346535
Merged-chr13-96735508-1	chr13	96735458	96735558	+	2.7	cIP1vsInput	Intergenic	Intergenic	-64572	NM_008255	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding	0.01	0.366337
Merged-chr6-8574762-1	chr6	8574712	8574812	+	2.7	cIP1vsInput	"intron (NM_133236, intron 4 of 7)"	"intron (NM_133236, intron 4 of 7)"	65166	NM_133236	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding	0.01	0.39604
Merged-chr17-32027745-1	chr17	32027695	32027795	+	2.7	cIP1vsInput	"intron (NM_028902, intron 2 of 7)"	"intron (NM_028902, intron 2 of 7)"	6763	NM_028902	74377	Mm.75856	NM_028902	ENSMUSG00000002076	Hsf2bp	4932437G14Rik	heat shock transcription factor 2 binding protein	protein-coding	0	0.386139
Merged-chr3-131246464-1	chr3	131246414	131246514	+	2.7	cIP2vsInput	"intron (NM_008212, intron 3 of 7)"	"intron (NM_008212, intron 3 of 7)"	25573	NM_008212	15107	Mm.260164	NM_008212	ENSMUSG00000027984	Hadh	AA409008|AU019341|AW742602|Hadhsc|Schad	hydroxyacyl-Coenzyme A dehydrogenase	protein-coding	0.03	0.623762
Merged-chr11-53795870-2	chr11	53795776	53795964	+	2.7	cIP1vsInput|cIP2vsInput	"intron (NR_033332, intron 3 of 3)"	"intron (NR_033332, intron 3 of 3)"	25397	NM_001159396	16362	Mm.105218	NM_001159393	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding	0.026596	0.439153
Merged-chr6-48048555-1	chr6	48048505	48048605	+	2.7	cIP2vsInput	promoter-TSS (NM_001081382)	promoter-TSS (NM_001081382)	-441	NM_001081382	72306	Mm.381553	NM_001081382	ENSMUSG00000071477	Zfp777	2500002G23Rik	zinc finger protein 777	protein-coding	0.07	0.613861
Merged-chr7-25619147-1	chr7	25619097	25619197	+	2.7	cIP2vsInput	promoter-TSS (NM_025504)	promoter-TSS (NM_025504)	-346	NM_025504	66349	Mm.159956	NM_025504	ENSMUSG00000057229	Atp5sl	2310004L02Rik|C030044E10Rik	ATP5S-like	protein-coding	0.08	0.455446
Merged-chr12-70148353-1	chr12	70148303	70148403	+	2.7	cIP2vsInput	Intergenic	Intergenic	-5818	NM_001195033	100504285	Mm.291105	NM_001195033	ENSMUSG00000090121	Abhd12b	Gm804	abhydrolase domain containing 12B	protein-coding	0.02	0.544554
Merged-chr5-86045673-1	chr5	86045623	86045723	+	2.7	cIP2vsInput	"intron (NM_007683, intron 6 of 18)"	"intron (NM_007683, intron 6 of 18)"	19910	NM_007683	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	Cenpc	centromere protein C1	protein-coding	0.01	0.326733
Merged-chr9-87253991-1	chr9	87253941	87254041	+	2.7	cIP2vsInput	"5' UTR (NM_199316, exon 2 of 27)"	"5' UTR (NM_199316, exon 2 of 27)"	1541	NM_199316	382090	Mm.335338	NM_199316		4922501C03Rik	Kiaa1009|mKIAA1009	RIKEN cDNA 4922501C03 gene	protein-coding	0.02	0.326733
Merged-chr15-9497258-1	chr15	9497208	9497308	+	2.7	cIP1vsInput	Intergenic	L1_Mus4|LINE|L1	32618	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding	0	0.386139
Merged-chr1-84554049-1	chr1	84553999	84554099	+	2.7	cIP2vsInput	"intron (NM_152915, intron 4 of 12)"	"intron (NM_152915, intron 4 of 12)"	-141790	NR_039588	100628595		NR_039588	ENSMUSG00000093254	Mir5126	mmu-mir-5126|mu-mir-5126	microRNA 5126	miscRNA	0	0.316832
Merged-chr18-10321870-1	chr18	10321820	10321920	+	2.7	cIP1vsInput	Intergenic	L1MB8|LINE|L1	-3309	NM_001083628	381157	Mm.261535	NM_001083628	ENSMUSG00000042942	Greb1l	mKIAA4095	growth regulation by estrogen in breast cancer-like	protein-coding	0	0.356436
Merged-chr10-101835035-1	chr10	101834985	101835085	+	2.7	cIP2vsInput	"intron (NM_001205098, intron 1 of 7)"	"intron (NM_001205098, intron 1 of 7)"	62343	NR_037211	100526516		NR_037211	ENSMUSG00000092952	Mir3059	mmu-mir-3059	microRNA 3059	miscRNA	0	0.306931
Merged-chr2-65240444-1	chr2	65240394	65240494	+	2.7	cIP1vsInput	Intergenic	Intergenic	-1818	NM_027225	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding	0.01	0.336634
Merged-chr5-138397864-1	chr5	138397814	138397914	+	2.7	cIP2vsInput	Intergenic	RMER17D2|LTR|ERVK	-43612	NM_028130	72154	Mm.20263	NM_028130	ENSMUSG00000036898	Zfp157	2610020C11Rik|A630094N24Rik|AI327407|mszf12|mszf23-1	zinc finger protein 157	protein-coding	0	0.524752
Merged-chr1-19765967-1	chr1	19765917	19766017	+	2.7	cIP1vsInput	Intergenic	A-rich|Low_complexity|Low_complexity	553913	NM_001025305	21419	Mm.137021	NM_001025305	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding	0	0.326733
Merged-chr14-50870282-1	chr14	50870232	50870332	+	2.7	cIP1vsInput	"intron (NM_009351, intron 1 of 54)"	"intron (NM_009351, intron 1 of 54)"	272	NM_009351	21745	Mm.318736	NM_009351	ENSMUSG00000006281	Tep1	Tp1	telomerase associated protein 1	protein-coding	0.03	0.594059
Merged-chr3-29908420-1	chr3	29908370	29908470	+	2.7	cIP1vsInput	Intergenic	Intergenic	104784	NM_007963	14013	Mm.426829	NM_021442	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding	0	0.346535
Merged-chr1-141916894-1	chr1	141916844	141916944	+	2.7	cIP2vsInput	Intergenic	MTEa|LTR|ERVL-MaLR	-1260492	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0.01	0.316832
Merged-chr14-102935751-1	chr14	102935701	102935801	+	2.7	cIP2vsInput	Intergenic	Intergenic	46881	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mmu-mir-5130|mu-mir-5130	microRNA 5130	miscRNA	0	0.386139
Merged-chr13-49421065-1	chr13	49421015	49421115	+	2.7	cIP1vsInput	promoter-TSS (NM_001276399)	promoter-TSS (NM_001276399)	-158	NR_075085	75678	Mm.390586	NM_001276399	ENSMUSG00000021385	Ippk	1810043M15Rik|InsP6	"inositol 1,3,4,5,6-pentakisphosphate 2-kinase"	protein-coding	0.11	0.673267
Merged-chr13-31927485-1	chr13	31927435	31927535	+	2.7	cIP2vsInput	"intron (NM_146041, intron 8 of 10)"	"intron (NM_146041, intron 8 of 10)"	120839	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding	0.01	0.435644
Merged-chr7-73399843-1	chr7	73399793	73399893	+	2.7	cIP1vsInput	"intron (NM_177740, intron 2 of 3)"	"intron (NM_177740, intron 2 of 3)"	-24069	NR_040324	319783	Mm.349813	NR_040324	ENSMUSG00000097756	A730056A06Rik	C76391	RIKEN cDNA A730056A06 gene	miscRNA	0.06	0.60396
Merged-chr1-92934173-1	chr1	92934123	92934223	+	2.7	cIP2vsInput	promoter-TSS (NM_011796)	promoter-TSS (NM_011796)	-235	NM_011796	23830	Mm.294315	NM_011796	ENSMUSG00000026270	Capn10	AW049679|Capn8|mKIAA1845	calpain 10	protein-coding	0.06	0.544554
Merged-chr3-23931696-1	chr3	23931646	23931746	+	2.7	cIP2vsInput	Intergenic	Intergenic	1680326	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	miscRNA	0	0.336634
Merged-chr6-110990875-1	chr6	110990825	110990925	+	2.7	cIP1vsInput	"intron (NM_177328, intron 2 of 9)"	"intron (NM_177328, intron 2 of 9)"	345277	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0.01	0.267327
Merged-chr19-25963438-1	chr19	25963388	25963488	+	2.7	cIP2vsInput	Intergenic	Intergenic	291027	NM_145831	226049	Mm.275572	NM_145831	ENSMUSG00000048138	Dmrt2	Terra	doublesex and mab-3 related transcription factor 2	protein-coding	0	0.277228
Merged-chr14-52279298-1	chr14	52279248	52279348	+	2.7	cIP2vsInput	promoter-TSS (NM_172601)	promoter-TSS (NM_172601)	97	NM_172601	76338	Mm.32870	NM_172601	ENSMUSG00000022159	Rab2b	1500012D09Rik|4930528G15Rik|A230002G14|D530043M21Rik	"RAB2B, member RAS oncogene family"	protein-coding	0.06	0.574257
Merged-chr2-8431582-1	chr2	8431532	8431632	+	2.7	cIP2vsInput	Intergenic	Intergenic	-757933	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	miscRNA	0	0.29703
Merged-chr13-21066575-1	chr13	21066525	21066625	+	2.7	cIP1vsInput	Intergenic	RLTR21|LTR|ERVK	6724	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding	0	0.29703
Merged-chr8-51485411-1	chr8	51485361	51485461	+	2.7	cIP2vsInput	Intergenic	Intergenic	1117299	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0.01	0.277228
Merged-chr8-102917855-1	chr8	102917805	102917905	+	2.7	cIP1vsInput	Intergenic	Intergenic	-132744	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0	0.336634
Merged-chr18-50711648-1	chr18	50711598	50711698	+	2.7	cIP1vsInput	Intergenic	Intergenic	-142949	NM_026108	67365	Mm.158150	NM_026108	ENSMUSG00000048875	Hdhd1a	1700121L12Rik|GS1|Hdhd1	haloacid dehalogenase-like hydrolase domain containing 1A	protein-coding	0.01	0.445545
Merged-chr14-93547178-1	chr14	93547128	93547228	+	2.7	cIP1vsInput	"intron (NM_001271798, intron 2 of 3)"	"intron (NM_001271798, intron 2 of 3)"	341710	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.316832
Merged-chr2-14674120-1	chr2	14674070	14674170	+	2.7	cIP1vsInput	"intron (NM_023116, intron 2 of 13)"	Lx7|LINE|L1	-46522	NR_028497	625342	Mm.484784	NR_028497		Gm13315	OTTMUSG00000011384	lactate dehydrogenase A pseudogene	pseudo	0	0.306931
Merged-chr1-100879832-1	chr1	100879782	100879882	+	2.7	cIP1vsInput	Intergenic	Intergenic	-275936	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.306931
Merged-chr1-68361748-1	chr1	68361698	68361798	+	2.7	cIP1vsInput	"intron (NM_010154, intron 5 of 26)"	"intron (NM_010154, intron 5 of 26)"	746311	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0	0.257426
Merged-chr7-94798157-1	chr7	94798107	94798207	+	2.7	cIP2vsInput	Intergenic	Intergenic	-1412480	NM_011858	23966	Mm.391678	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding	0.04	0.465347
Merged-chr14-55918806-1	chr14	55918756	55918856	+	2.7	cIP2vsInput	Intergenic	Intergenic	-18574	NM_001082975	654795	Mm.486218	NM_001082975	ENSMUSG00000022223	Sdr39u1	2310014G06Rik	"short chain dehydrogenase/reductase family 39U, member 1"	protein-coding	0.01	0.386139
Merged-chr16-93711687-1	chr16	93711637	93711737	+	2.7	cIP2vsInput	promoter-TSS (NM_026700)	promoter-TSS (NM_026700)	-220	NM_026700	70028	Mm.23230	NM_026700	ENSMUSG00000022946	Dopey2	0610038M01Rik|2610510B01Rik|AI503246|C21orf5|mKIAA0933	dopey family member 2	protein-coding	0.08	0.683168
Merged-chr9-117447092-1	chr9	117447042	117447142	+	2.7	cIP1vsInput	"intron (NM_001172121, intron 1 of 14)"	"intron (NM_001172121, intron 1 of 14)"	182821	NM_001172121	207181	Mm.326411	NM_001172121	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	"RNA binding motif, single stranded interacting protein"	protein-coding	0.01	0.366337
Merged-chr9-114752952-1	chr9	114752902	114753002	+	2.7	cIP2vsInput	Intergenic	CpG	21749	NM_026036	67213	Mm.28858	NM_026036	ENSMUSG00000032434	Cmtm6	2810051A14Rik|AA536733|Cklfsf6	CKLF-like MARVEL transmembrane domain containing 6	protein-coding	0.09	0.70297
Merged-chr13-111868172-1	chr13	111868122	111868222	+	2.7	cIP1vsInput	Intergenic	Intergenic	-59189	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding	0.03	0.584158
Merged-chr17-36257868-1	chr17	36257818	36257918	+	2.7	cIP2vsInput	promoter-TSS (NM_026308)	promoter-TSS (NM_026308)	-22	NM_026308	67676	Mm.27131	NM_026308		Rpp21	0610037N01Rik	ribonuclease P 21 subunit	protein-coding	0.08	0.663366
Merged-chr10-98012468-1	chr10	98012418	98012518	+	2.7	cIP2vsInput	Intergenic	Intergenic	-45378	NR_033537	100038699	Mm.467933	NR_033537		Gm10754	ENSMUSG00000074776	predicted gene 10754	miscRNA	0	0.336634
Merged-chr11-22129522-1	chr11	22129472	22129572	+	2.7	cIP1vsInput	"intron (NM_001252515, intron 11 of 24)"	"intron (NM_001252515, intron 11 of 24)"	-127871	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homolog 1 (Drosophila)	protein-coding	0	0.356436
Merged-chr2-124320208-1	chr2	124320158	124320258	+	2.7	cIP2vsInput	Intergenic	Intergenic	-97850	NR_040612	75946	Mm.415059	NR_040612	ENSMUSG00000086954	4930583P06Rik	-	RIKEN cDNA 4930583P06 gene	miscRNA	0	0.366337
Merged-chr4-147804346-1	chr4	147804296	147804396	+	2.7	cIP1vsInput	"intron (NM_001127189, intron 2 of 5)"	"intron (NM_001127189, intron 2 of 5)"	5442	NM_001127189	100041677	Mm.327194	NM_001127189	ENSMUSG00000078495	Gm13157	OTTMUSG00000010679|Rp23-282c23.7	predicted gene 13157	protein-coding	0.01	0.455446
Merged-chr6-38835357-1	chr6	38835307	38835407	+	2.7	cIP1vsInput	"intron (NM_010433, intron 1 of 14)"	"intron (NM_010433, intron 1 of 14)"	1867	NM_001136065	15258	Mm.486937	NM_001136065	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding	0	0.465347
Merged-chr17-43372361-1	chr17	43372311	43372411	+	2.7	cIP1vsInput	Intergenic	Intergenic	-17105	NM_001081178	224792	Mm.23478	NM_001081178	ENSMUSG00000056492	Gpr116	8430401C09Rik|9330185D23|AI528491|mKIAA0758	G protein-coupled receptor 116	protein-coding	0	0.346535
Merged-chr1-64587823-1	chr1	64587773	64587873	+	2.7	cIP1vsInput	"intron (NM_001037726, intron 6 of 6)"	L1MB2|LINE|L1	29345	NM_025964	67099	Mm.46394	NM_025964	ENSMUSG00000025956	Mettl21a	2310038H17Rik|AI464204|Fam119a	methyltransferase like 21A	protein-coding	0.01	0.29703
Merged-chr2-32847419-1	chr2	32847369	32847469	+	2.7	cIP2vsInput	promoter-TSS (NM_009295)	promoter-TSS (NM_009295)	-182	NM_001113569	20910	Mm.278865	NM_001113569	ENSMUSG00000026797	Stxbp1	AI317162|AI326233|MMS10-G|Ms10g|Munc-18a|Munc18-1|N-sec1|Rb-sec1|Sxtbp1|Unc18-1|Unc18h|nsec1	syntaxin binding protein 1	protein-coding	0.09	0.742574
Merged-chr16-87764015-1	chr16	87763965	87764065	+	2.7	cIP1vsInput	Intergenic	L1MC5a|LINE|L1	65061	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1	protein-coding	0	0.386139
Merged-chr19-57925797-1	chr19	57925747	57925847	+	2.7	cIP2vsInput	"intron (NM_181415, intron 26 of 28)"	"intron (NM_181415, intron 26 of 28)"	314763	NM_181415	226255	Mm.245340	NM_181415	ENSMUSG00000054843	Atrnl1	AI504415|AW555641|Alp|Atrnl|Atrnlp	attractin like 1	protein-coding	0	0.425743
Merged-chr2-122630799-1	chr2	122630749	122630849	+	2.7	cIP2vsInput	"exon (NM_001033256, exon 1 of 2)"	"exon (NM_001033256, exon 1 of 2)"	174	NM_001033256	214616	Mm.271306	NM_001033256		Spata5l1	AV141009|C130039A10Rik	spermatogenesis associated 5-like 1	protein-coding	0.15	0.792079
Merged-chr6-44320783-1	chr6	44320733	44320833	+	2.7	cIP2vsInput	Intergenic	Intergenic	-654608	NM_013861	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding	0.01	0.326733
Merged-chr1-137307715-1	chr1	137307665	137307765	+	2.7	cIP2vsInput	Intergenic	Lx|LINE|L1	-347267	NM_030676	26424	Mm.16794	NM_001159769	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	"nuclear receptor subfamily 5, group A, member 2"	protein-coding	0.01	0.326733
Merged-chr11-17771967-1	chr11	17771917	17772017	+	2.7	cIP2vsInput	Intergenic	MER5A|DNA|hAT-Charlie	181908	NM_026576	68145	Mm.178684	NM_026576	ENSMUSG00000016984	Etaa1	5730466H23Rik|AA672646	Ewing's tumor-associated antigen 1	protein-coding	0	0.316832
Merged-chr15-8034488-1	chr15	8034438	8034538	+	2.7	cIP2vsInput	"intron (NM_001081402, intron 8 of 17)"	"intron (NM_001081402, intron 8 of 17)"	64721	NM_001081402	545085	Mm.321312	NM_001081402	ENSMUSG00000039828	Wdr70	4833422F06Rik	WD repeat domain 70	protein-coding	0.01	0.366337
Merged-chr3-101026902-1	chr3	101026852	101026952	+	2.7	cIP2vsInput	"intron (NM_001167906, intron 1 of 8)"	"intron (NM_001167906, intron 1 of 8)"	2593	NM_001167906	630146	Mm.190915	NM_001099332	ENSMUSG00000086564	Cd101	Gm1016|Gm734|Igsf2	CD101 antigen	protein-coding	0	0.544554
Merged-chr18-89725139-1	chr18	89725089	89725189	+	2.7	cIP1vsInput	"intron (NM_001039173, intron 1 of 7)"	"intron (NM_001039173, intron 1 of 7)"	43997	NM_001039173	623279	Mm.447164	NM_001039173		Dok6	Dok-6	docking protein 6	protein-coding	0	0.376238
Merged-chr5-80239595-1	chr5	80239545	80239645	+	2.7	cIP2vsInput	Intergenic	Intergenic	-723691	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0	0.306931
Merged-chr14-107453006-1	chr14	107452956	107453056	+	2.7	cIP1vsInput	Intergenic	RMER17A2|LTR|ERVK	-966486	NR_045938	73631	Mm.48862	NR_045938		1700128A07Rik	-	RIKEN cDNA 1700128A07 gene	miscRNA	0.01	0.554455
Merged-chr17-82191334-1	chr17	82191284	82191384	+	2.7	cIP1vsInput	Intergenic	Intergenic	-452957	NM_011406	20541	Mm.489060	NM_001112798		Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	"solute carrier family 8 (sodium/calcium exchanger), member 1"	protein-coding	0	0.29703
Merged-chr15-78935244-1	chr15	78935194	78935294	+	2.7	cIP2vsInput	"intron (NM_133800, intron 1 of 5)"	CpG	311	NM_133800	97961	Mm.157216	NM_133800		Nol12	C78541|Nop25	nucleolar protein 12	protein-coding	0.11	0.693069
Merged-chr17-34982151-1	chr17	34982101	34982201	+	2.7	cIP1vsInput	promoter-TSS (NM_001204273)	promoter-TSS (NM_001204273)	21	NM_030597	27756	Mm.165735	NM_001110101	ENSMUSG00000007050	Lsm2	D17H6S56E-2|D17H6S56E2|Dmapl|Dmpkap|G7b|Sm-X5|SmX5|snRNP	"LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae)"	protein-coding	0.16	0.762376
Merged-chr10-87644374-1	chr10	87644324	87644424	+	2.7	cIP2vsInput	Intergenic	Intergenic	122579	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding	0	0.316832
Merged-chr5-61152658-1	chr5	61152608	61152708	+	2.7	cIP1vsInput	Intergenic	Intergenic	-656185	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding	0	0.287129
Merged-chr13-88595385-1	chr13	88595335	88595435	+	2.7	cIP2vsInput	Intergenic	Lx9|LINE|L1	-226087	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0	0.376238
Merged-chr2-130906452-1	chr2	130906402	130906502	+	2.7	cIP2vsInput	promoter-TSS (NM_009730)	promoter-TSS (NM_009730)	-44	NM_009730	11990	Mm.119936	NM_009730	ENSMUSG00000027312	Atrn	AW558010|Mgca|mKIAA0548|mahogany|mg	attractin	protein-coding	0.13	0.782178
Merged-chr12-66014713-1	chr12	66014663	66014763	+	2.7	cIP1vsInput	Intergenic	Lx3_Mus|LINE|L1	269688	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding	0	0.346535
Merged-chr14-16546190-1	chr14	16546140	16546240	+	2.7	cIP2vsInput	"intron (NM_011243, intron 2 of 7)"	"intron (NM_011243, intron 2 of 7)"	29020	NM_011243	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2|RARbeta2	"retinoic acid receptor, beta"	protein-coding	0	0.267327
Merged-chr17-47887617-1	chr17	47887567	47887667	+	2.7	cIP2vsInput	"intron (NM_028767, intron 3 of 16)"	"intron (NM_028767, intron 3 of 16)"	37015	NM_028767	74123	Mm.240062	NM_001110824	ENSMUSG00000023991	Foxp4	1200010K03Rik|2310007G05Rik|mFKHLA	forkhead box P4	protein-coding	0.03	0.673267
Merged-chr18-3758096-1	chr18	3758046	3758146	+	2.7	cIP2vsInput	Intergenic	Lx5b|LINE|L1	250139	NM_026505	68010	Mm.284863	NM_026505	ENSMUSG00000024232	Bambi	2610003H06Rik	BMP and activin membrane-bound inhibitor	protein-coding	0	0.346535
Merged-chr18-5162642-1	chr18	5162592	5162692	+	2.7	cIP2vsInput	Intergenic	Intergenic	116053	NM_153153	225115	Mm.136791	NM_178046	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding	0.06	0.653465
Merged-chr8-12756902-1	chr8	12756852	12756952	+	2.7	cIP2vsInput	promoter-TSS (NM_015804)	promoter-TSS (NM_015804)	-114	NM_015804	50770	Mm.257837	NM_015804	ENSMUSG00000031441	Atp11a	4930558F19Rik|AU040868|Atpc1h|Ih	"ATPase, class VI, type 11A"	protein-coding	0.11	0.772277
Merged-chr1-152038061-1	chr1	152038011	152038111	+	2.7	cIP1vsInput	"intron (NM_197990, intron 1 of 5)"	"intron (NM_197990, intron 1 of 5)"	52259	NM_197990	69399	Mm.278031	NM_197990	ENSMUSG00000032666	1700025G04Rik	2610510E02Rik|2900042O04Rik|ENSMUSG00000073540	RIKEN cDNA 1700025G04 gene	protein-coding	0	0.336634
Merged-chr9-21963638-1	chr9	21963588	21963688	+	2.7	cIP2vsInput	promoter-TSS (NM_010149)	promoter-TSS (NM_010149)	-62	NM_010149	13857	Mm.2653	NM_010149	ENSMUSG00000006235	Epor	-	erythropoietin receptor	protein-coding	0.01	0.633663
Merged-chr5-40279518-1	chr5	40279468	40279568	+	2.7	cIP1vsInput	Intergenic	Intergenic	-634887	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding	0	0.287129
Merged-chr4-147499893-1	chr4	147499843	147499943	+	2.7	cIP2vsInput	"intron (NM_001039209, intron 1 of 2)"	"intron (NM_001039209, intron 1 of 2)"	-53384	NM_001014397	433804	Mm.332047	XM_003946328	ENSMUSG00000065999	Gm13154	OTTMUSG00000010673	predicted gene 13154	protein-coding	0	0.356436
Merged-chr15-30075959-1	chr15	30075909	30076009	+	2.7	cIP1vsInput	Intergenic	(CAAAAA)n|Simple_repeat|Simple_repeat	-96634	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	"catenin (cadherin associated protein), delta 2"	protein-coding	0.02	0.277228
Merged-chr10-41690396-1	chr10	41690346	41690446	+	2.7	cIP2vsInput	Intergenic	Intergenic	-102643	NM_001177571	75973	Mm.228517	NM_029493	ENSMUSG00000075225	Ccdc162	5033413D22Rik|Ccdc162p|Gm61	coiled-coil domain containing 162	protein-coding	0.07	0.564356
Merged-chr11-105777850-1	chr11	105777800	105777900	+	2.7	cIP1vsInput	"intron (NM_181071, intron 5 of 25)"	"intron (NM_181071, intron 5 of 25)"	166297	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding	0	0.306931
Merged-chr9-93559864-1	chr9	93559814	93559914	+	2.7	cIP2vsInput	Intergenic	Intergenic	-554131	NR_040756	78349	Mm.52612	NR_040756		1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	miscRNA	0	0.346535
Merged-chr3-76264266-1	chr3	76264216	76264316	+	2.7	cIP1vsInput	"intron (NM_178673, intron 3 of 15)"	"intron (NM_178673, intron 3 of 15)"	188683	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.326733
Merged-chr14-11067050-1	chr14	11067000	11067100	+	2.7	cIP1vsInput	"intron (NM_010210, intron 2 of 8)"	"intron (NM_010210, intron 2 of 8)"	94982	NM_010210	14198	Mm.441926	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding	0	0.267327
Merged-chr4-59034783-2	chr4	59034726	59034840	+	2.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025277)	promoter-TSS (NM_025277)	-373	NM_025277	14700	Mm.41780	NM_025277	ENSMUSG00000038607	Gng10	AV006524	"guanine nucleotide binding protein (G protein), gamma 10"	protein-coding	0.017544	0.382609
Merged-chr4-10874081-1	chr4	10874031	10874131	+	2.7	cIP1vsInput	promoter-TSS (NM_026005)	promoter-TSS (NM_026005)	-417	NM_026005	67157	Mm.440552	NM_026005	ENSMUSG00000059482	2610301B20Rik	AI428449	RIKEN cDNA 2610301B20 gene	protein-coding	0.06	0.514851
Merged-chr12-58414234-1	chr12	58414184	58414284	+	2.7	cIP1vsInput	Intergenic	Intergenic	-144976	NM_025809	66864	Mm.280563	NM_025809	ENSMUSG00000045930	Clec14a	1200003C23Rik|AI642649	"C-type lectin domain family 14, member a"	protein-coding	0.01	0.267327
Merged-chr2-152636880-1	chr2	152636830	152636930	+	2.7	cIP2vsInput	Intergenic	Intergenic	9872	NM_009047	19700	Mm.8752	NM_009047	ENSMUSG00000000359	Rem1	E030011C07Rik|Rem	rad and gem related GTP binding protein 1	protein-coding	0.07	0.60396
Merged-chr2-65095756-1	chr2	65095706	65095806	+	2.7	cIP2vsInput	"exon (NM_027225, exon 12 of 13)"	"exon (NM_027225, exon 12 of 13)"	-72990	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding	0.04	0.524752
Merged-chr1-151177735-1	chr1	151177685	151177785	+	2.7	cIP2vsInput	Intergenic	L2|LINE|L2	39701	NR_038011	402734	Mm.337666	NR_038011		C730036E19Rik	-	RIKEN cDNA C730036E19 gene	miscRNA	0	0.465347
Merged-chr1-71458332-1	chr1	71458282	71458382	+	2.7	cIP2vsInput	Intergenic	Intergenic	-43422	NM_175210	74591	Mm.159251	NM_175210	ENSMUSG00000050296	Abca12	4832428G11Rik|4833417A11Rik	"ATP-binding cassette, sub-family A (ABC1), member 12"	protein-coding	0.01	0.306931
Merged-chr9-81225171-2	chr9	81225118	81225225	+	2.7	cIP1vsInput|cIP2vsInput	Intergenic	B1_Mus1|SINE|Alu	-406759	NR_040394	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	miscRNA	0	0.527778
Merged-chr19-5176904-1	chr19	5176854	5176954	+	2.7	cIP2vsInput	"intron (NM_153129, intron 1 of 23)"	"intron (NM_153129, intron 1 of 23)"	-58496	NM_008451	16594	Mm.271648	NM_008451	ENSMUSG00000024862	Klc2	8030455F02Rik|AW212649|KLC 2|KLC-2	kinesin light chain 2	protein-coding	0.01	0.306931
Merged-chr2-114342902-1	chr2	114342852	114342952	+	2.7	cIP2vsInput	Intergenic	Intergenic	-141470	NM_175466	228491	Mm.132523	NM_175466	ENSMUSG00000040321	Zfp770	6430601A21Rik|Znf770	zinc finger protein 770	protein-coding	0	0.316832
Merged-chr4-129082860-1	chr4	129082810	129082910	+	2.7	cIP1vsInput	"exon (NM_029219, exon 8 of 9)"	"exon (NM_029219, exon 8 of 9)"	-22670	NM_133881	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding	0.05	0.544554
Merged-chr6-74829739-1	chr6	74829689	74829789	+	2.7	cIP1vsInput	Intergenic	Intergenic	-1360072	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.316832
Merged-chr3-36496980-1	chr3	36496930	36497030	+	2.7	cIP2vsInput	Intergenic	Intergenic	9829	NR_040590	329623	Mm.490730	NR_040590	ENSMUSG00000085320	Gm11548	E330009D11|OTTMUSG00000002110	predicted gene 11548	miscRNA	0.05	0.544554
Merged-chr3-12194894-1	chr3	12194844	12194944	+	2.7	cIP2vsInput	Intergenic	Intergenic	-350535	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.376238
Merged-chr5-147860447-1	chr5	147860397	147860497	+	2.7	cIP2vsInput	promoter-TSS (NM_025624)	promoter-TSS (NM_025624)	-181	NM_025624	66537	Mm.332855	NM_025624	ENSMUSG00000029649	Pomp	2510048O06Rik	proteasome maturation protein	protein-coding	0.09	0.683168
Merged-chr3-90830746-1	chr3	90830696	90830796	+	2.7	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	103840	NM_207263	384997	Mm.316644	NM_001165968	ENSMUSG00000042250	Pglyrp4	Gm1478|Gm413	peptidoglycan recognition protein 4	protein-coding	0	0.316832
Merged-chr15-13096355-1	chr15	13096305	13096405	+	2.7	cIP1vsInput	"intron (NM_007666, intron 1 of 11)"	MamRep434|DNA|TcMar-Tigger	77284	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	K-cadherin|cad6|cadherin-6	cadherin 6	protein-coding	0	0.366337
Merged-chr4-79901745-1	chr4	79901695	79901795	+	2.7	cIP2vsInput	Intergenic	Intergenic	-932485	NM_031202	22178	Mm.412291	NM_031202	ENSMUSG00000005994	Tyrp1	TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding	0	0.29703
Merged-chr18-87236264-1	chr18	87236214	87236314	+	2.7	cIP1vsInput	Intergenic	ORR1B2-int|LTR|ERVL-MaLR	523216	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding	0	0.376238
Merged-chr4-30321842-1	chr4	30321792	30321892	+	2.7	cIP2vsInput	Intergenic	Intergenic	-342754	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	miscRNA	0.01	0.326733
Merged-chr5-114175605-1	chr5	114175555	114175655	+	2.7	cIP1vsInput	"intron (NM_133904, intron 1 of 51)"	"intron (NM_133904, intron 1 of 51)"	10087	NM_133904	100705	Mm.81793	NM_133904	ENSMUSG00000042010	Acacb	AI597064|AW743042|Acc2|Accb	acetyl-Coenzyme A carboxylase beta	protein-coding	0.05	0.613861
Merged-chr13-4173650-1	chr13	4173600	4173700	+	2.7	cIP1vsInput	Intergenic	Intergenic	-17537	NM_013778	27384	Mm.27447	NM_013778	ENSMUSG00000021213	Akr1c13	mKIAA4014	"aldo-keto reductase family 1, member C13"	protein-coding	0.01	0.29703
Merged-chr17-75005967-2	chr17	75005885	75006049	+	2.7	cIP1vsInput|cIP2vsInput	"exon (NM_019919, exon 1 of 34)"	"exon (NM_019919, exon 1 of 34)"	438	NM_019919	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Tgfb	latent transforming growth factor beta binding protein 1	protein-coding	0.103659	0.739394
Merged-chr11-115841988-1	chr11	115841938	115842038	+	2.7	cIP1vsInput	"intron (NM_145438, intron 2 of 25)"	"intron (NM_145438, intron 2 of 25)"	17930	NM_001252532	217325	Mm.290450	NM_001252532	ENSMUSG00000020782	Llgl2	9130006H11Rik|Llglh2	lethal giant larvae homolog 2 (Drosophila)	protein-coding	0.01	0.534653
Merged-chr14-69029370-1	chr14	69029320	69029420	+	2.7	cIP2vsInput	promoter-TSS (NM_009285)	promoter-TSS (NM_009285)	81	NM_009285	20855	Mm.20911	NM_009285	ENSMUSG00000014813	Stc1	Stc	stanniocalcin 1	protein-coding	0.03	0.49505
Merged-chr15-76925605-1	chr15	76925555	76925655	+	2.7	cIP2vsInput	promoter-TSS (NM_172817)	promoter-TSS (NM_172817)	-157	NM_001168276	239546	Mm.183650	NM_001168276		Zfp647	6030449J21|Es492|Znf250	zinc finger protein 647	protein-coding	0.1	0.70297
Merged-chr18-8788909-1	chr18	8788859	8788959	+	2.7	cIP1vsInput	Intergenic	L2|LINE|L2	-423947	NM_008058	14370	Mm.184289	NM_008058	ENSMUSG00000036904	Fzd8	Fz8	frizzled homolog 8 (Drosophila)	protein-coding	0.01	0.366337
Merged-chr11-65869555-1	chr11	65869505	65869605	+	2.7	cIP1vsInput	"intron (NM_001099633, intron 61 of 68)"	L1M4|LINE|L1	62311	NM_026107	52712	Mm.340052	NM_026107	ENSMUSG00000018347	Zkscan6	1700128E15Rik|D11Ertd714e|KOX11|Zfp535|Znf18	zinc finger with KRAB and SCAN domains 6	protein-coding	0	0.326733
Merged-chr11-108449826-1	chr11	108449776	108449876	+	2.7	cIP1vsInput	"intron (NM_029606, intron 5 of 27)"	"intron (NM_029606, intron 5 of 27)"	24560	NM_029606	76380	Mm.344071	NM_029586	ENSMUSG00000020728	Cep112	1700001M19Rik|1700029K01Rik|8430407H02Rik|AV043680|AV207351|Ccdc46|Macoco	centrosomal protein 112	protein-coding	0	0.316832
Merged-chr12-77285210-1	chr12	77285160	77285260	+	2.7	cIP1vsInput	"intron (NM_001252614, intron 3 of 12)"	"intron (NM_001252614, intron 3 of 12)"	46471	NR_045554	53618	Mm.489686	NM_001252614	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding	0	0.277228
Merged-chr15-73137178-1	chr15	73137128	73137228	+	2.7	cIP1vsInput	"intron (NM_153178, intron 3 of 18)"	"intron (NM_153178, intron 3 of 18)"	46766	NM_053068	93696	Mm.23095	NM_053068	ENSMUSG00000068391	Chrac1	2410152E03Rik|2810406L04Rik|YCL1	chromatin accessibility complex 1	protein-coding	0.03	0.584158
Merged-chr7-25681269-1	chr7	25681219	25681319	+	2.7	cIP2vsInput	"5' UTR (NM_172148, exon 1 of 3)"	"5' UTR (NM_172148, exon 1 of 3)"	111	NM_172148	232987	Mm.22849	NM_172148	ENSMUSG00000063439	B9d2	stumpy	B9 protein domain 2	protein-coding	0.01	0.455446
Merged-chr18-19839818-1	chr18	19839768	19839868	+	2.7	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	162279	NM_007882	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding	0.01	0.326733
Merged-chr14-54518119-1	chr14	54518069	54518169	+	2.7	cIP1vsInput	promoter-TSS (NM_013768)	promoter-TSS (NM_013768)	-649	NM_013768	27374	Mm.196585	NM_013768	ENSMUSG00000023110	Prmt5	Jbp1|Skb1	protein arginine N-methyltransferase 5	protein-coding	0.02	0.425743
Merged-chr1-184645450-1	chr1	184645400	184645500	+	2.7	cIP1vsInput	Intergenic	Intergenic	-67047	NR_040627	74971	Mm.410816	NR_040627	ENSMUSG00000092578	4930488B22Rik	-	RIKEN cDNA 4930488B22 gene	miscRNA	0.03	0.584158
Merged-chr3-120639307-1	chr3	120639257	120639357	+	2.7	cIP1vsInput	Intergenic	L1MC|LINE|L1	532388	NM_028456	66568	Mm.263163	NM_025637	ENSMUSG00000028133	Rwdd3	2510027J23Rik|3110037C01Rik|AI035684|AI662458|X2CR1	RWD domain containing 3	protein-coding	0.01	0.336634
Merged-chr12-80260690-1	chr12	80260640	80260740	+	2.7	cIP2vsInput	promoter-TSS (NM_134156)	promoter-TSS (NM_134156)	-319	NM_134156	109711	Mm.403477	NM_134156	ENSMUSG00000015143	Actn1	3110023F10Rik|Actn1a	"actinin, alpha 1"	protein-coding	0.08	0.693069
Merged-chr5-83229826-1	chr5	83229776	83229876	+	2.7	cIP2vsInput	Intergenic	Intergenic	125369	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	"trans-2,3-enoyl-CoA reductase-like"	protein-coding	0	0.346535
Merged-chr12-50297337-1	chr12	50297287	50297387	+	2.7	cIP1vsInput	Intergenic	Intergenic	351886	NM_008858	18760	Mm.133719	NM_008858	ENSMUSG00000002688	Prkd1	PKD|PKD1|Pkcm|Prkcm	protein kinase D1	protein-coding	0	0.306931
Merged-chr5-14489862-1	chr5	14489812	14489912	+	2.7	cIP1vsInput	Intergenic	Intergenic	-25056	NM_011995	26875	Mm.146275	NM_001110796	ENSMUSG00000061601	Pclo	Acz|Pico|mKIAA0559	piccolo (presynaptic cytomatrix protein)	protein-coding	0	0.326733
Merged-chr5-10182363-1	chr5	10182313	10182413	+	2.7	cIP2vsInput	Intergenic	Intergenic	-457011	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	"glutamate receptor, metabotropic 3"	protein-coding	0	0.306931
Merged-chr4-15304630-1	chr4	15304580	15304680	+	2.7	cIP2vsInput	Intergenic	Intergenic	38810	NM_181401	100201	Mm.394111	NM_181401	ENSMUSG00000043252	Tmem64	9630015D15Rik|AI790744|AV300874	transmembrane protein 64	protein-coding	0.01	0.306931
Merged-chr2-81612176-1	chr2	81612126	81612226	+	2.7	cIP2vsInput	Intergenic	Intergenic	-441482	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0	0.257426
Merged-chr5-25261899-1	chr5	25261849	25261949	+	2.7	cIP1vsInput	"intron (NM_144908, intron 8 of 11)"	"intron (NM_144908, intron 8 of 11)"	39006	NM_144908	231050	Mm.246718	NM_144908	ENSMUSG00000038072	Galnt11	A430075I06Rik|AI648252|E430002F06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11	protein-coding	0	0.316832
Merged-chr11-47789704-1	chr11	47789654	47789754	+	2.7	cIP2vsInput	Intergenic	Intergenic	-410402	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	"sarcoglycan, delta (dystrophin-associated glycoprotein)"	protein-coding	0	0.356436
Merged-chr16-60631330-1	chr16	60631280	60631380	+	2.7	cIP1vsInput	Intergenic	L1MA9|LINE|L1	-25799	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0	0.326733
Merged-chr6-98371035-1	chr6	98370985	98371085	+	2.7	cIP1vsInput	Intergenic	Intergenic	-28281	NM_001128092	330390	Mm.484161	NM_001128092	ENSMUSG00000090667	Gm765	-	predicted gene 765	protein-coding	0	0.356436
Merged-chr6-8333868-1	chr6	8333818	8333918	+	2.7	cIP2vsInput	"intron (NR_033518, intron 2 of 3)"	"intron (NR_033518, intron 2 of 3)"	74580	NR_033518	100036521	Mm.458518	NR_033518	ENSMUSG00000089862	Gm16039	OTTMUSG00000029336	predicted gene 16039	miscRNA	0	0.267327
Merged-chr16-15071005-1	chr16	15070955	15071055	+	2.7	cIP2vsInput	Intergenic	Intergenic	164359	NM_025769	66793	Mm.100270	NM_025769		Efcab1	4930449A16Rik|5430404L10Rik	EF hand calcium binding domain 1	protein-coding	0.01	0.267327
Merged-chr5-80771732-1	chr5	80771682	80771782	+	2.7	cIP1vsInput	Intergenic	Intergenic	-249861	NM_198702	319387	Mm.461016	NM_198702	ENSMUSG00000037605	Lphn3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|mKIAA0768	latrophilin 3	protein-coding	0	0.306931
Merged-chr17-31892945-1	chr17	31892895	31892995	+	2.7	cIP2vsInput	Intergenic	Intergenic	-37153	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding	0.01	0.683168
Merged-chr3-126369530-1	chr3	126369480	126369580	+	2.7	cIP1vsInput	"intron (NM_173451, intron 1 of 1)"	L2|LINE|L2	5678	NM_173451	271970	Mm.317021	NM_173451	ENSMUSG00000046561	Arsj	9330196J05Rik|D830047F08	arylsulfatase J	protein-coding	0	0.356436
Merged-chr18-33176484-1	chr18	33176434	33176534	+	2.7	cIP2vsInput	"intron (NM_009793, intron 8 of 10)"	"intron (NM_009793, intron 8 of 10)"	37332	NM_133774	170459	Mm.393277	NM_133774		Stard4	4632419C16Rik|9030213J02Rik|AA517649|AW324468	StAR-related lipid transfer (START) domain containing 4	protein-coding	0.01	0.346535
Merged-chr10-50449299-1	chr10	50449249	50449349	+	2.7	cIP1vsInput	Intergenic	Lx4A|LINE|L1	-143370	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0	0.306931
Merged-chr1-16508035-1	chr1	16507985	16508085	+	2.7	cIP1vsInput	"intron (NM_025303, intron 2 of 13)"	MER2|DNA|TcMar-Tigger	11267	NM_025303	29819	Mm.216257	NM_001111272	ENSMUSG00000025920	Stau2	-	staufen (RNA binding protein) homolog 2 (Drosophila)	protein-coding	0	0.336634
Merged-chr7-84329675-1	chr7	84329625	84329725	+	2.7	cIP2vsInput	"intron (NM_007488, intron 5 of 18)"	"intron (NM_007488, intron 5 of 18)"	80363	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding	0	0.346535
Merged-chr12-30894215-1	chr12	30894165	30894265	+	2.7	cIP2vsInput	TTS (NM_001159743)	TTS (NM_001159743)	9891	NM_001159743	100294583	Mm.399726	NM_001159743	ENSMUSG00000054204	Fam150b	6230419C23Rik	"family with sequence similarity 150, member B"	protein-coding	0.02	0.435644
Merged-chr3-55845358-1	chr3	55845308	55845408	+	2.7	cIP2vsInput	"intron (NM_030595, intron 38 of 57)"	L1_Mur2|LINE|L1	-1747	NR_033592	71182	Mm.195603	NR_033592		4933417G07Rik	-	SEC13 homolog pseudogene	pseudo	0	0.29703
Merged-chr10-100488627-1	chr10	100488577	100488677	+	2.7	cIP2vsInput	"exon (NM_146009, exon 2 of 53)"	"exon (NM_146009, exon 2 of 53)"	338	NM_146009	216274	Mm.229114	NM_146009	ENSMUSG00000019971	Cep290	BC004690|Nphp6|b2b1454Clo	centrosomal protein 290	protein-coding	0	0.306931
Merged-chr2-42713290-1	chr2	42713240	42713340	+	2.7	cIP1vsInput	Intergenic	Intergenic	-59692	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0	0.257426
Merged-chr1-68463476-1	chr1	68463426	68463526	+	2.7	cIP1vsInput	"intron (NM_010154, intron 3 of 26)"	"intron (NM_010154, intron 3 of 26)"	644583	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0	0.316832
Merged-chr3-97819259-1	chr3	97819209	97819309	+	2.7	cIP2vsInput	"intron (NM_001039376, intron 4 of 46)"	RMER17D2|LTR|ERVK	5362	NM_001110163	83679	Mm.129840	NM_001039376	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding	0.01	0.50495
Merged-chr2-79868900-1	chr2	79868850	79868950	+	2.7	cIP2vsInput	"intron (NM_001009979, intron 9 of 13)"	"intron (NM_001009979, intron 9 of 13)"	39499	NM_001009979	18573	Mm.40678	NM_001009978	ENSMUSG00000059173	Pde1a	AI987702|AW125737	"phosphodiesterase 1A, calmodulin-dependent"	protein-coding	0	0.267327
Merged-chr1-12896856-1	chr1	12896806	12896906	+	2.7	cIP2vsInput	"intron (NM_172841, intron 4 of 8)"	L1_Mus1|LINE|L1	94279	NM_172841	240726	Mm.24481	NM_172841	ENSMUSG00000025938	Slco5a1	4732454B15|A630033C23Rik|AA407151	"solute carrier organic anion transporter family, member 5A1"	protein-coding	0	0.366337
Merged-chr5-72803268-1	chr5	72803218	72803318	+	2.7	cIP2vsInput	"intron (NM_001113464, intron 2 of 17)"	"intron (NM_001113464, intron 2 of 17)"	-50495	NM_001122754	22165	Mm.3264	NM_001122754	ENSMUSG00000054892	Txk	A130089B16Rik|Btkl|PTK4|Rlk	TXK tyrosine kinase	protein-coding	0.02	0.534653
Merged-chr2-29100350-1	chr2	29100300	29100400	+	2.7	cIP1vsInput	Intergenic	Intergenic	-24642	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding	0	0.356436
Merged-chr16-83697639-1	chr16	83697589	83697689	+	2.7	cIP1vsInput	Intergenic	Intergenic	-673504	NR_040567	75247	Mm.417813	NR_040567		4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	miscRNA	0	0.217822
Merged-chr8-7521498-1	chr8	7521448	7521548	+	2.7	cIP2vsInput	Intergenic	Intergenic	1139275	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding	0	0.29703
Merged-chr3-110233785-1	chr3	110233735	110233835	+	2.7	cIP2vsInput	Intergenic	Intergenic	17213	NM_178891	99890	Mm.393526	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding	0	0.356436
Merged-chr19-25635810-1	chr19	25635760	25635860	+	2.7	cIP2vsInput	Intergenic	Intergenic	25273	NM_177360	240590	Mm.62785	NM_177360	ENSMUSG00000042372	Dmrt3	-	doublesex and mab-3 related transcription factor 3	protein-coding	0.04	0.544554
Merged-chr1-67116107-1	chr1	67116057	67116157	+	2.7	cIP2vsInput	Intergenic	Intergenic	-6959	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding	0.01	0.386139
Merged-chr3-144905101-1	chr3	144905051	144905151	+	2.7	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	-9090	NM_001039222	622139	Mm.447150	NM_001039222	ENSMUSG00000074196	Gm6289	EG622139	predicted gene 6289	protein-coding	0	0.326733
Merged-chr8-58445090-1	chr8	58445040	58445140	+	2.7	cIP1vsInput	"intron (NM_175032, intron 3 of 11)"	"intron (NM_175032, intron 3 of 11)"	255706	NM_001177534	100271928	Mm.484123	NM_001177534		Gm15881	OTTMUSG00000027193	predicted gene 15881	protein-coding	0.01	0.356436
Merged-chr11-30849963-1	chr11	30849913	30850013	+	2.7	cIP2vsInput	"intron (NM_134013, intron 36 of 46)"	"intron (NM_134013, intron 36 of 46)"	-35395	NM_175490	237716	Mm.338361	NM_175490	ENSMUSG00000043999	Gpr75	-	G protein-coupled receptor 75	protein-coding	0.02	0.306931
Merged-chr7-67759897-1	chr7	67759847	67759947	+	2.7	cIP2vsInput	promoter-TSS (NM_201639)	promoter-TSS (NM_201639)	-155	NM_207663	233335	Mm.60526	NM_183312	ENSMUSG00000030554	Synm	4930412K21Rik|AI852401|Dmn|E130104F11|Syn|Synemin	"synemin, intermediate filament protein"	protein-coding	0.07	0.712871
Merged-chr1-135766202-1	chr1	135766152	135766252	+	2.7	cIP2vsInput	"5' UTR (NM_013750, exon 1 of 2)"	"5' UTR (NM_013750, exon 1 of 2)"	117	NM_013750	27280	Mm.34346	NM_013750	ENSMUSG00000041801	Phlda3	Tih1	"pleckstrin homology-like domain, family A, member 3"	protein-coding	0.16	0.792079
Merged-chr12-47469545-2	chr12	47469464	47469627	+	2.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-650770	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding	0.01227	0.323171
Merged-chr2-132043538-1	chr2	132043488	132043588	+	2.7	cIP1vsInput	Intergenic	Intergenic	-13550	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding	0.02	0.475248
Merged-chr3-144381000-1	chr3	144380950	144381050	+	2.7	cIP2vsInput	Intergenic	Intergenic	-175745	NM_010723	16911	Mm.29187	NM_001161769	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding	0.03	0.50495
Merged-chr1-191224497-1	chr1	191224447	191224547	+	2.7	cIP2vsInput	Intergenic	CpG	-41164	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding	0.14	0.683168
Merged-chr2-87858021-1	chr2	87857971	87858071	+	2.7	cIP1vsInput	TTS (NM_146638)	TTS (NM_146638)	844	NM_146638	258631	Mm.377602	NM_146638	ENSMUSG00000047039	Olfr1151	MOR177-9	olfactory receptor 1151	protein-coding	0	0.346535
Merged-chr4-150288212-1	chr4	150288162	150288262	+	2.7	cIP2vsInput	"intron (NM_001085492, intron 1 of 22)"	"intron (NM_001085492, intron 1 of 22)"	6296	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding	0	0.326733
Merged-chr13-44206215-1	chr13	44206165	44206265	+	2.7	cIP2vsInput	"intron (NR_045088, intron 2 of 3)"	MIR|SINE|MIR	10272	NR_045088	100503592	Mm.488275	NR_045088		A330076C08Rik	-	RIKEN cDNA A330076C08 gene	miscRNA	0.01	0.425743
Merged-chr17-29796147-1	chr17	29796097	29796197	+	2.7	cIP2vsInput	Intergenic	L2a|LINE|L2	-79130	NM_001163741	68597	Mm.390979	NM_001163741	ENSMUSG00000024018	Ccdc167	1110021J02Rik	coiled-coil domain containing 167	protein-coding	0.02	0.346535
Merged-chr3-55374394-1	chr3	55374344	55374444	+	2.7	cIP1vsInput	"intron (NM_001195538, intron 3 of 16)"	"intron (NM_001195538, intron 3 of 16)"	-87364	NM_001195539	13175	Mm.472264	NM_001111051	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding	0.01	0.415842
Merged-chr17-88531120-1	chr17	88531070	88531170	+	2.7	cIP2vsInput	"intron (NM_028658, intron 1 of 21)"	"intron (NM_028658, intron 1 of 21)"	996	NM_028658	73825	Mm.271817	NM_028658	ENSMUSG00000034709	Ppp1r21	1110018J12Rik|AI426045|AW550781|Ccdc128|Klraq1	"protein phosphatase 1, regulatory subunit 21"	protein-coding	0.03	0.326733
Merged-chr2-21958076-1	chr2	21958026	21958126	+	2.7	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-269427	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding	0.01	0.346535
Merged-chr5-36830659-1	chr5	36830609	36830709	+	2.7	cIP2vsInput	promoter-TSS (NM_008550)	promoter-TSS (NM_008550)	-10	NM_008550	17160	Mm.761	NM_008550	ENSMUSG00000029119	Man2b2	mKIAA0935	"mannosidase 2, alpha B2"	protein-coding	0.13	0.722772
Merged-chr8-107150489-1	chr8	107150439	107150539	+	2.7	cIP2vsInput	promoter-TSS (NM_025558)	promoter-TSS (NM_025558)	-172	NM_025558	66427	Mm.20242	NM_025558	ENSMUSG00000031924	Cyb5b	1810044O22Rik|AU015618|Cyb5m	cytochrome b5 type B	protein-coding	0.05	0.594059
Merged-chr17-83197496-1	chr17	83197446	83197546	+	2.7	cIP2vsInput	Intergenic	Intergenic	-17787	NM_134117	106522	Mm.311974	NM_134117	ENSMUSG00000024247	Pkdcc	AI115348|AW548124|Adtk1|ESTM17|MAd1|Sgk493|Vlk|X83346	"protein kinase domain containing, cytoplasmic"	protein-coding	0.01	0.584158
Merged-chr11-103568008-1	chr11	103567958	103568058	+	2.7	cIP2vsInput	"intron (NM_001033434, intron 7 of 13)"	MYSERV6-int|LTR|ERVK	46731	NM_001033434	380730	Mm.380214	NM_001033434	ENSMUSG00000034239	Gm884	-	predicted gene 884	protein-coding	0	0.29703
Merged-chr12-29291213-1	chr12	29291163	29291263	+	2.7	cIP2vsInput	Intergenic	Intergenic	-237171	NM_001093775	17933	Mm.418721	NM_001093775	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding	0.05	0.584158
Merged-chr5-95880578-1	chr5	95880528	95880628	+	2.7	cIP1vsInput	Intergenic	ID2|SINE|ID	-76361	NM_018866	55985	Mm.10116	NM_018866	ENSMUSG00000023078	Cxcl13	4631412M08Rik|ANGIE2|Angie|BCA-1|BLC|BLR1L|Scyb13	chemokine (C-X-C motif) ligand 13	protein-coding	0.01	0.326733
Merged-chr1-45510847-1	chr1	45510797	45510897	+	2.7	cIP1vsInput	Intergenic	MIR|SINE|MIR	-7565	NM_007737	12832	Mm.10299	NM_007737	ENSMUSG00000026042	Col5a2	1110014L14Rik|D230017N05	"collagen, type V, alpha 2"	protein-coding	0	0.29703
Merged-chr1-37430112-1	chr1	37430062	37430162	+	2.7	cIP2vsInput	promoter-TSS (NM_026123)	promoter-TSS (NM_026123)	-9	NM_198006	76178	Mm.28085	NM_198006	ENSMUSG00000026112	Coa5	1700001A24Rik|6330578E17Rik|Pet191	cytochrome C oxidase assembly factor 5	protein-coding	0.11	0.584158
Merged-chr7-35334445-1	chr7	35334395	35334495	+	2.7	cIP2vsInput	"intron (NM_027897, intron 1 of 14)"	CpG	208	NM_027897	52428	Mm.286600	NM_027897	ENSMUSG00000030494	Rhpn2	1300002E07Rik|AA536890|C85860|D7Ertd784e	"rhophilin, Rho GTPase binding protein 2"	protein-coding	0.07	0.594059
Merged-chr5-120116642-1	chr5	120116592	120116692	+	2.7	cIP2vsInput	"exon (NM_028762, exon 1 of 24)"	"exon (NM_028762, exon 1 of 24)"	129	NM_028762	74111	Mm.41022	NM_028762		Rbm19	1200009A02Rik|AV302714|NPO	RNA binding motif protein 19	protein-coding	0.08	0.633663
Merged-chr6-56705011-1	chr6	56704961	56705061	+	2.7	cIP2vsInput	promoter-TSS (NM_025520)	promoter-TSS (NM_025520)	-312	NM_025520	66373	Mm.25642	NM_025520	ENSMUSG00000091625	Lsm5	2010208O10Rik|2310034K10Rik	"LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae)"	protein-coding	0.01	0.29703
Merged-chr10-81384567-1	chr10	81384517	81384617	+	2.7	cIP2vsInput	"5' UTR (NM_133964, exon 1 of 5)"	"5' UTR (NM_133964, exon 1 of 5)"	139	NM_133964	102115	Mm.294975	NM_133964	ENSMUSG00000078440	Dohh	1110033C18Rik|AI585913|AL022869|Hlrc1	deoxyhypusine hydroxylase/monooxygenase	protein-coding	0.06	0.564356
Merged-chr10-123623135-1	chr10	123623085	123623185	+	2.7	cIP2vsInput	"intron (NM_001252387, intron 2 of 4)"	"intron (NM_001252387, intron 2 of 4)"	359059	NM_001252387	268354	Mm.51939	NM_001252387	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	"family with sequence similarity 19, member A2"	protein-coding	0.01	0.386139
Merged-chr18-33342883-1	chr18	33342833	33342933	+	2.7	cIP1vsInput	Intergenic	Intergenic	120751	NM_001267717	27528	Mm.407415	NM_001109988	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding	0.02	0.326733
Merged-chr2-128339622-1	chr2	128339572	128339672	+	2.7	cIP1vsInput	"intron (NR_028589, intron 1 of 2)"	"intron (NR_028589, intron 1 of 2)"	89729	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	miscRNA	0.02	0.435644
Merged-chr3-47907394-1	chr3	47907344	47907444	+	2.7	cIP1vsInput	Intergenic	Intergenic	119365	NR_040408	666202	Mm.465057	NR_040408		Gm7977	EG666202	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide pseudogene"	pseudo	0	0.316832
Merged-chr2-36151587-1	chr2	36151537	36151637	+	2.7	cIP1vsInput	"intron (NM_026422, intron 3 of 6)"	"intron (NM_026422, intron 3 of 6)"	-14883	NR_027515	67889	Mm.205937	NM_001159635	ENSMUSG00000026889	Rbm18	2010004P11Rik|AU015530	RNA binding motif protein 18	protein-coding	0.01	0.435644
Merged-chr11-59191901-1	chr11	59191851	59191951	+	2.7	cIP2vsInput	promoter-TSS (NM_008193)	promoter-TSS (NM_008193)	51	NM_008193	14923	Mm.3624	NM_001159410	ENSMUSG00000020444	Guk1	AA409738|AL033299|AL033300|AV026611|Gmk|Guk-1	guanylate kinase 1	protein-coding	0.11	0.663366
Merged-chr10-75304576-1	chr10	75304526	75304626	+	2.7	cIP2vsInput	"intron (NM_001145826, intron 16 of 18)"	"intron (NM_001145826, intron 16 of 18)"	-12367	NM_009630	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding	0.02	0.633663
Merged-chr1-146049617-1	chr1	146049567	146049667	+	2.7	cIP2vsInput	Intergenic	Intergenic	-446049	NM_153539	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.336634
Merged-chr4-155223211-2	chr4	155223151	155223271	+	2.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_011385)	promoter-TSS (NM_011385)	-676	NM_011385	20481	Mm.28520	NM_011385	ENSMUSG00000029050	Ski	2310012I02Rik|2610001A11Rik|AA062172|AA589460|BC004088	ski sarcoma viral oncogene homolog (avian)	protein-coding	0.116667	0.719008
Merged-chr10-56757619-1	chr10	56757569	56757669	+	2.7	cIP1vsInput	Intergenic	Intergenic	380319	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	"gap junction protein, alpha 1"	protein-coding	0	0.306931
Merged-chr11-69546938-1	chr11	69546888	69546988	+	2.7	cIP2vsInput	"intron (NM_001081330, intron 1 of 85)"	"intron (NM_001081330, intron 1 of 85)"	2170	NM_001081330	327954	Mm.247478	NM_001081330	ENSMUSG00000005237	Dnahc2	2900022L05Rik|4930564A01|D130094J20|D330014H01Rik|Dnah2|Dnhd3	"dynein, axonemal, heavy chain 2"	protein-coding	0.05	0.60396
Merged-chr7-127691775-1	chr7	127691725	127691825	+	2.7	cIP2vsInput	Intergenic	Intergenic	-16712	NR_030428	791073		NR_030428	ENSMUSG00000076454	Mir762	Mirn762|mir-762|mmu-mir-762	microRNA 762	miscRNA	0.05	0.712871
Merged-chr11-97575866-1	chr11	97575816	97575916	+	2.7	cIP2vsInput	promoter-TSS (NM_018873)	promoter-TSS (NM_018873)	-740	NM_018873	56013	Mm.342665	NM_018873	ENSMUSG00000038453	Srcin1	P140|SNIP|mKIAA1684|p140Cap	SRC kinase signaling inhibitor 1	protein-coding	0.05	0.693069
Merged-chr5-21433261-1	chr5	21433211	21433311	+	2.7	cIP1vsInput	"intron (NM_177869, intron 2 of 7)"	"intron (NM_177869, intron 2 of 7)"	8358	NM_177869	330050	Mm.40655	NM_177869	ENSMUSG00000047221	Fam185a	4631428I10|AI847670	"family with sequence similarity 185, member A"	protein-coding	0.01	0.306931
Merged-chr12-72772854-1	chr12	72772804	72772904	+	2.7	cIP2vsInput	"intron (NM_008910, intron 1 of 5)"	"intron (NM_008910, intron 1 of 5)"	11643	NM_008910	19042	Mm.261045	NM_008910	ENSMUSG00000021096	Ppm1a	2310003C21Rik|2900017D14Rik|AI427932|AU017636|MMPa-2|MPPa-1	"protein phosphatase 1A, magnesium dependent, alpha isoform"	protein-coding	0	0.287129
Merged-chr13-74009435-1	chr13	74009385	74009485	+	2.7	cIP2vsInput	promoter-TSS (NM_182839)	promoter-TSS (NM_182839)	16	NM_182839	72948	Mm.39752	NM_182839	ENSMUSG00000021573	Tppp	2900041A09Rik|AI849835	tubulin polymerization promoting protein	protein-coding	0.12	0.772277
Merged-chr5-74960163-1	chr5	74960113	74960213	+	2.7	cIP1vsInput	"intron (NR_045866, intron 2 of 4)"	B3A|SINE|B2	10969	NR_045866	619945	Mm.359372	NM_001037908	ENSMUSG00000072874	Gm6116	EG619945	predicted gene 6116	miscRNA	0	0.485149
Merged-chr1-110446273-1	chr1	110446223	110446323	+	2.7	cIP1vsInput	Intergenic	Intergenic	462536	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.336634
Merged-chr10-28620681-1	chr10	28620631	28620731	+	2.7	cIP2vsInput	Intergenic	Lx7|LINE|L1	-47714	NM_178666	210757	Mm.123021	NM_178666		Themis	A430108D01|BB160712|E430004N04Rik|Gasp|Tsepa|thylex	thymocyte selection associated	protein-coding	0	0.356436
Merged-chr18-31001609-1	chr18	31001559	31001659	+	2.7	cIP1vsInput	"intron (NM_009065, intron 4 of 4)"	"intron (NM_009065, intron 4 of 4)"	315519	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding	0	0.366337
Merged-chr4-19840029-1	chr4	19839979	19840079	+	2.7	cIP2vsInput	"intron (NM_028746, intron 3 of 3)"	"intron (NM_028746, intron 3 of 3)"	21302	NM_028746	74087	Mm.173833	NM_028746	ENSMUSG00000041052	Slc7a13	0610009O04Rik|AGT-1|AGT1|XAT2	"solute carrier family 7, (cationic amino acid transporter, y+ system) member 13"	protein-coding	0.01	0.326733
Merged-chr3-60803651-1	chr3	60803601	60803701	+	2.7	cIP1vsInput	Intergenic	Intergenic	-199144	NM_008772	18441	Mm.281452	NM_008772	ENSMUSG00000027765	P2ry1	P2Y1	"purinergic receptor P2Y, G-protein coupled 1"	protein-coding	0	0.356436
Merged-chr12-30806185-1	chr12	30806135	30806235	+	2.7	cIP2vsInput	Intergenic	Lx6|LINE|L1	-78139	NM_001159743	100294583	Mm.399726	NM_001159743	ENSMUSG00000054204	Fam150b	6230419C23Rik	"family with sequence similarity 150, member B"	protein-coding	0	0.29703
Merged-chr2-59249576-1	chr2	59249526	59249626	+	2.7	cIP2vsInput	"intron (NM_175464, intron 2 of 20)"	"intron (NM_175464, intron 2 of 20)"	88726	NM_175464	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding	0.01	0.346535
Merged-chr16-81466848-1	chr16	81466798	81466898	+	2.7	cIP1vsInput	"intron (NM_001113208, intron 8 of 17)"	"intron (NM_001113208, intron 8 of 17)"	266151	NM_010954	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.306931
Merged-chr5-15518896-1	chr5	15518846	15518946	+	2.7	cIP1vsInput	Intergenic	Intergenic	-100203	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0.02	0.316832
Merged-chr12-33147700-2	chr12	33147646	33147755	+	2.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028139)	promoter-TSS (NM_028139)	14	NM_028139	380753	Mm.41540	NM_001033436	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding	0.137615	0.7
Merged-chr7-30626116-1	chr7	30626066	30626166	+	2.7	cIP2vsInput	promoter-TSS (NM_025628)	promoter-TSS (NM_025628)	35	NM_025628	110323	Mm.400	XM_003946224	ENSMUSG00000036751	Cox6b1	2010000G05Rik|Cox6b	"cytochrome c oxidase, subunit VIb polypeptide 1"	protein-coding	0.08	0.564356
Merged-chr9-59539614-1	chr9	59539564	59539664	+	2.7	cIP2vsInput	promoter-TSS (NM_010421)	promoter-TSS (NM_010421)	-53	NM_010421	15211	Mm.2284	NM_010421	ENSMUSG00000025232	Hexa	Hex-1	hexosaminidase A	protein-coding	0.11	0.633663
Merged-chr9-57505853-1	chr9	57505803	57505903	+	2.7	cIP2vsInput	TTS (NM_133982)	TTS (NM_133982)	1751	NM_133982	102614	Mm.274421	NM_133982	ENSMUSG00000062309	Rpp25	AI851155	ribonuclease P/MRP 25 subunit	protein-coding	0	0.574257
Merged-chr4-150311635-1	chr4	150311585	150311685	+	2.7	cIP1vsInput	"intron (NM_001085492, intron 1 of 22)"	MLT1C|LTR|ERVL-MaLR	29719	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding	0	0.346535
Merged-chr1-85345080-1	chr1	85345030	85345130	+	2.7	cIP1vsInput	Intergenic	Intergenic	-74514	NM_001037909	620078	Mm.461248	NM_001037909	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding	0	0.524752
Merged-chr3-132708594-1	chr3	132708544	132708644	+	2.7	cIP1vsInput	"intron (NM_173032, intron 5 of 23)"	"intron (NM_173032, intron 5 of 23)"	24450	NM_173032	271981	Mm.440106	NM_001163455	ENSMUSG00000028030	Tbck	1700120J03Rik|9430001M19|A630047E20Rik|C030007I09Rik|Tbckl	TBC1 domain containing kinase	protein-coding	0	0.306931
Merged-chr10-108866893-1	chr10	108866843	108866943	+	2.7	cIP2vsInput	"intron (NM_001252342, intron 2 of 10)"	"intron (NM_001252342, intron 2 of 10)"	144082	NM_009306	20979	Mm.489829	NM_001252341	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding	0.01	0.356436
Merged-chr3-81687365-1	chr3	81687315	81687415	+	2.7	cIP1vsInput	Intergenic	Intergenic	-245251	NM_177662	229445	Mm.254642	NM_177662	ENSMUSG00000028015	Ctso	A330105D01Rik|A430056C07|AI118514	cathepsin O	protein-coding	0	0.267327
Merged-chr1-189727993-1	chr1	189727943	189728043	+	2.7	cIP1vsInput	promoter-TSS (NM_008976)	promoter-TSS (NM_008976)	-275	NM_008976	19250	Mm.4498	NM_001033287	ENSMUSG00000026604	Ptpn14	C130080N23Rik|OTTMUSG00000022087|PTP36	"protein tyrosine phosphatase, non-receptor type 14"	protein-coding	0.1	0.663366
Merged-chr16-13160446-1	chr16	13160396	13160496	+	2.7	cIP1vsInput	Intergenic	Intergenic	50710	NM_015769	50505	Mm.287837	NM_015769		Ercc4	AI606920|Xpf	"excision repair cross-complementing rodent repair deficiency, complementation group 4"	protein-coding	0.01	0.554455
Merged-chr10-16194589-1	chr10	16194539	16194639	+	2.7	cIP2vsInput	Intergenic	Intergenic	901193	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0	0.356436
Merged-chr11-78571956-1	chr11	78571906	78572006	+	2.7	cIP2vsInput	"intron (NM_008702, intron 9 of 10)"	"intron (NM_008702, intron 9 of 10)"	-21221	NM_133706	69071	Mm.29431	NM_133706	ENSMUSG00000037278	Tmem97	1810014L12Rik|AI115531|AL022956|D11Bhm182e	transmembrane protein 97	protein-coding	0.01	0.316832
Merged-chr2-69913717-1	chr2	69913667	69913767	+	2.7	cIP1vsInput	"intron (NM_001081548, intron 1 of 38)"	"intron (NM_001081548, intron 1 of 38)"	16471	NM_001081548	68795	Mm.314576	NM_001081548	ENSMUSG00000044308	Ubr3	1110059H15Rik|4833421P10Rik|A130030D10Rik|AA409735|AA414972|AA422631|AI646861|AU016126|Zfp650|Znf650	ubiquitin protein ligase E3 component n-recognin 3	protein-coding	0	0.227723
Merged-chr3-112630243-1	chr3	112630193	112630293	+	2.7	cIP1vsInput	Intergenic	Intergenic	526484	NM_001190404	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding	0	0.356436
Merged-chr17-5397600-1	chr17	5397550	5397650	+	2.7	cIP2vsInput	Intergenic	Intergenic	21167	NM_175349	106557	Mm.432764	NM_175349		Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding	0.07	0.643564
Merged-chr2-128943655-1	chr2	128943605	128943705	+	2.7	cIP2vsInput	"intron (NM_020594, intron 1 of 8)"	CpG	365	NM_020594	57432	Mm.11675	NM_020594	ENSMUSG00000027387	Zc3h8	AU020882|E130108N08Rik|Fliz1|Zc3hdc8	zinc finger CCCH type containing 8	protein-coding	0.09	0.742574
Merged-chr7-30445485-1	chr7	30445435	30445535	+	2.7	cIP2vsInput	promoter-TSS (NM_007467)	promoter-TSS (NM_007467)	97	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding	0.12	0.80198
Merged-chr1-3563700-1	chr1	3563650	3563750	+	2.7	cIP2vsInput	"intron (NM_001011874, intron 1 of 2)"	L1_Mur3|LINE|L1	107798	NM_001011874	497097	Mm.489375	NM_001011874		Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X Kell blood group precursor related family member 4	protein-coding	0.02	0.356436
Merged-chr7-19381903-1	chr7	19381853	19381953	+	2.7	cIP1vsInput	promoter-TSS (NM_007949)	promoter-TSS (NM_007949)	-136	NM_007949	13871	Mm.36524	NM_007949	ENSMUSG00000030400	Ercc2	AA407812|AU020867|AW240756|CXPD|Ercc-2|XPD	"excision repair cross-complementing rodent repair deficiency, complementation group 2"	protein-coding	0.12	0.633663
Merged-chr13-88016740-1	chr13	88016690	88016790	+	2.7	cIP1vsInput	Intergenic	Intergenic	-804732	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0	0.247525
Merged-chr17-33909355-1	chr17	33909305	33909405	+	2.7	cIP1vsInput	promoter-TSS (NM_007829)	promoter-TSS (NM_007829)	-90	NM_007829	13163	Mm.271809	NM_001199733	ENSMUSG00000002307	Daxx	-	Fas death domain-associated protein	protein-coding	0.16	0.772277
Merged-chr15-97964041-1	chr15	97963991	97964091	+	2.7	cIP1vsInput	promoter-TSS (NM_201359)	promoter-TSS (NM_201359)	-188	NM_201359	380967	Mm.489364	NM_001252153	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding	0.06	0.584158
Merged-chr12-48931620-1	chr12	48931570	48931670	+	2.7	cIP1vsInput	Intergenic	L1M2|LINE|L1	-451263	NM_001160112	15228	Mm.4704	NM_001160112	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding	0	0.227723
Merged-chr16-25931812-1	chr16	25931762	25931862	+	2.7	cIP1vsInput	Intergenic	Intergenic	129896	NM_001127264	22061	Mm.20894	NM_001127259	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding	0	0.336634
Merged-chr5-100158430-1	chr5	100158380	100158480	+	2.7	cIP1vsInput	"intron (NM_182841, intron 1 of 7)"	"intron (NM_182841, intron 1 of 7)"	1378	NM_182841	231503	Mm.99790	NM_182841	ENSMUSG00000050640	Tmem150c	-	transmembrane protein 150C	protein-coding	0.04	0.485149
Merged-chr6-113237677-1	chr6	113237627	113237727	+	2.7	cIP2vsInput	promoter-TSS (NM_026849)	promoter-TSS (NM_026849)	-166	NM_026849	97287	Mm.197816	NM_026849	ENSMUSG00000030269	Mtmr14	1110061O04Rik|AW553738|C76151	myotubularin related protein 14	protein-coding	0.09	0.70297
Merged-chr3-70539291-1	chr3	70539241	70539341	+	2.7	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	268000	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	miscRNA	0	0.306931
Merged-chr6-60423876-1	chr6	60423826	60423926	+	2.7	cIP2vsInput	Intergenic	L1VL1|LINE|L1	-20169	NR_015565	208079	Mm.490691	NR_015565		A530053G22Rik	-	RIKEN cDNA A530053G22 gene	miscRNA	0	0.366337
Merged-chr15-41831043-1	chr15	41830993	41831093	+	2.7	cIP1vsInput	promoter-TSS (NM_001130164)	promoter-TSS (NM_001130164)	85	NM_001130164	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding	0.02	0.445545
Merged-chr7-13805416-1	chr7	13805366	13805466	+	2.7	cIP1vsInput	"intron (NM_001111296, intron 3 of 5)"	Lx8|LINE|L1	31994	NM_001111296	20859	Mm.260026	NM_001111296	ENSMUSG00000078798	Sult2a1	ST2A1|Std|Sth1|mSTa1	"sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 1"	protein-coding	0	0.356436
Merged-chr6-134526552-1	chr6	134526502	134526602	+	2.7	cIP1vsInput	"intron (NM_008514, intron 2 of 22)"	"intron (NM_008514, intron 2 of 22)"	40361	NM_008514	16974	Mm.321990	NM_008514	ENSMUSG00000030201	Lrp6	C030016K15Rik|Cd|Gw	low density lipoprotein receptor-related protein 6	protein-coding	0	0.39604
Merged-chr11-5803807-1	chr11	5803757	5803857	+	2.7	cIP2vsInput	promoter-TSS (NM_018870)	promoter-TSS (NM_018870)	-11	NM_018870	56012	Mm.219627	NM_018870	ENSMUSG00000020475	Pgam2	-	phosphoglycerate mutase 2	protein-coding	0	0.60396
Merged-chr17-16151065-1	chr17	16151015	16151115	+	2.7	cIP1vsInput	Intergenic	Intergenic	-324479	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	"RGM domain family, member B"	protein-coding	0	0.316832
Merged-chr6-10114690-1	chr6	10114640	10114740	+	2.7	cIP2vsInput	Intergenic	MYSERV6-int|LTR|ERVK	859688	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	miscRNA	0	0.326733
Merged-chr10-21017315-1	chr10	21017265	21017365	+	2.7	cIP2vsInput	"intron (NM_026203, intron 17 of 23)"	"intron (NM_026203, intron 17 of 23)"	-23505	NM_001177776	52906	Mm.486431	NM_001177776	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding	0.03	0.316832
Merged-chr2-133187549-1	chr2	133187499	133187599	+	2.7	cIP1vsInput	Intergenic	Intergenic	-241513	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family homolog 1 (Drosophila)	protein-coding	0	0.29703
Merged-chr7-97286306-1	chr7	97286256	97286356	+	2.7	cIP1vsInput	"intron (NM_001162477, intron 3 of 9)"	Tigger5|DNA|TcMar-Tigger	39658	NM_001177412	244144	Mm.297541	NM_001177412	ENSMUSG00000035713	Usp35	Gm1088|Gm493	ubiquitin specific peptidase 35	protein-coding	0	0.316832
Merged-chr13-106862350-1	chr13	106862300	106862400	+	2.7	cIP2vsInput	"intron (NM_029665, intron 21 of 29)"	"intron (NM_029665, intron 21 of 29)"	74565	NM_029665	76582	Mm.482687	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding	0	0.306931
Merged-chr1-155733358-1	chr1	155733308	155733408	+	2.7	cIP1vsInput	"intron (NM_010712, intron 1 of 5)"	"intron (NM_010712, intron 1 of 5)"	8669	NM_010712	16872	Mm.351266	NM_010712		Lhx4	A330062J17Rik|Gsh-4|Gsh4	LIM homeobox protein 4	protein-coding	0	0.356436
Merged-chr7-125444552-1	chr7	125444502	125444602	+	2.7	cIP1vsInput	promoter-TSS (NM_029842)	promoter-TSS (NM_029842)	-68	NM_029842	77035	Mm.307239	NM_029842	ENSMUSG00000030752	Kdm8	3110005O21Rik|Jmjd5	lysine (K)-specific demethylase 8	protein-coding	0.02	0.465347
Merged-chr2-140436124-1	chr2	140436074	140436174	+	2.7	cIP2vsInput	"intron (NM_001013802, intron 2 of 18)"	"intron (NM_001013802, intron 2 of 18)"	40689	NM_028387	72899	Mm.229466	NM_001013802	ENSMUSG00000068205	Macrod2	1110033L15Rik|2610107G07Rik|2900006F19Rik	MACRO domain containing 2	protein-coding	0.01	0.366337
Merged-chr10-113160392-1	chr10	113160342	113160442	+	2.7	cIP1vsInput	Intergenic	Intergenic	-231366	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132|ENSMUSG00000074747	ataxin 7-like 3B	protein-coding	0	0.366337
Merged-chr11-41912965-1	chr11	41912915	41913015	+	2.7	cIP1vsInput	"intron (NM_177408, intron 8 of 8)"	"intron (NM_177408, intron 8 of 8)"	87749	NM_177408	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2"	protein-coding	0	0.306931
Merged-chr13-83162249-1	chr13	83162199	83162299	+	2.7	cIP1vsInput	Intergenic	L1MB7|LINE|L1	-341785	NM_001170537	17260	Mm.487610	NM_001170537	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding	0	0.366337
Merged-chr10-77581451-1	chr10	77581401	77581501	+	2.7	cIP1vsInput	promoter-TSS (NM_145925)	promoter-TSS (NM_145925)	-316	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding	0.03	0.554455
Merged-chr4-129811045-1	chr4	129810995	129811095	+	2.7	cIP2vsInput	Intergenic	CpG	-9434	NM_008974	19244	Mm.193688	NM_001164745	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding	0.06	0.683168
Merged-chr4-133575101-1	chr4	133575051	133575151	+	2.7	cIP2vsInput	"exon (NM_172876, exon 1 of 7)"	"exon (NM_172876, exon 1 of 7)"	356	NM_172876	242691	Mm.40110	NM_172876	ENSMUSG00000028850	Gpatch3	D930035B09Rik|Gpatc3	G patch domain containing 3	protein-coding	0.11	0.70297
Merged-chr12-31968225-1	chr12	31968175	31968275	+	2.7	cIP2vsInput	"intron (NM_011158, intron 6 of 10)"	"intron (NM_011158, intron 6 of 10)"	-17690	NM_153198	73389	Mm.458534	NM_153198	ENSMUSG00000002996	Hbp1	1700058O05Rik|BE629963|C330012F01Rik|C86454	high mobility group box transcription factor 1	protein-coding	0	0.277228
Merged-chr8-96584043-1	chr8	96583993	96584093	+	2.7	cIP2vsInput	Intergenic	Intergenic	-38070	NR_039538	100628567		NR_039538		Mir28c	mmu-mir-28c	microRNA 28c	miscRNA	0	0.316832
Merged-chr11-102267787-1	chr11	102267737	102267837	+	2.7	cIP2vsInput	Intergenic	Intergenic	-1036	NM_148953	217217	Mm.216432	NM_148953		Asb16	-	ankyrin repeat and SOCS box-containing 16	protein-coding	0.02	0.49505
Merged-chr1-145421054-1	chr1	145421004	145421104	+	2.7	cIP2vsInput	Intergenic	Intergenic	-645633	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding	0.01	0.306931
Merged-chr5-56759423-1	chr5	56759373	56759473	+	2.7	cIP2vsInput	Intergenic	Intergenic	958496	NR_015588	319216	Mm.446765	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	miscRNA	0	0.336634
Merged-chr17-46680871-1	chr17	46680821	46680921	+	2.7	cIP2vsInput	promoter-TSS (NM_001163729)	promoter-TSS (NM_001163729)	59	NM_001163729	71765	Mm.254784	NM_001163729	ENSMUSG00000063576	Klhdc3	1300011D16Rik|Peas	kelch domain containing 3	protein-coding	0.1	0.653465
Merged-chr16-80492139-1	chr16	80492089	80492189	+	2.7	cIP2vsInput	Intergenic	Intergenic	-708558	NM_001113208	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.267327
Merged-chr14-100271540-1	chr14	100271490	100271590	+	2.7	cIP1vsInput	Intergenic	L1M5|LINE|L1	-121744	NM_010636	16597	Mm.458816	NM_010636		Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding	0	0.346535
Merged-chr3-86642253-1	chr3	86642203	86642303	+	2.7	cIP2vsInput	"intron (NM_001077687, intron 45 of 50)"	"intron (NM_001077687, intron 45 of 50)"	-93970	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding	0	0.366337
Merged-chr3-88221014-2	chr3	88220963	88221065	+	2.7	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	5416	NR_029817	387133		NR_029817		Mir9-1	Mirn9|Mirn9-1|mmu-mir-9-1	microRNA 9-1	miscRNA	0.039216	0.660194
Merged-chr13-105236425-1	chr13	105236375	105236475	+	2.7	cIP2vsInput	"intron (NM_027934, intron 5 of 7)"	L1M2|LINE|L1	56589	NM_027934	71816	Mm.317015	NM_027934		Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding	0	0.336634
Merged-chr13-118029724-1	chr13	118029674	118029774	+	2.7	cIP1vsInput	Intergenic	Intergenic	-309713	NR_045508	71100	Mm.416966	NR_045508	ENSMUSG00000079048	4933413L06Rik	-	RIKEN cDNA 4933413L06 gene	miscRNA	0	0.306931
Merged-chr5-24685919-1	chr5	24685869	24685969	+	2.7	cIP1vsInput	"5' UTR (NM_016736, exon 1 of 15)"	"5' UTR (NM_016736, exon 1 of 15)"	104	NM_016736	53312	Mm.5856	NM_016736	ENSMUSG00000028954	Nub1	4931404D21Rik|6330412F12Rik|BS4|NY-REN-18	negative regulator of ubiquitin-like proteins 1	protein-coding	0.13	0.732673
Merged-chr5-18087867-1	chr5	18087817	18087917	+	2.7	cIP1vsInput	Intergenic	Intergenic	125297	NM_001081143	242851	Mm.332230	NM_001081143	ENSMUSG00000028777	Gnat3	Ggust|Gtn	"guanine nucleotide binding protein, alpha transducing 3"	protein-coding	0	0.306931
Merged-chr14-115798279-1	chr14	115798229	115798329	+	2.7	cIP2vsInput	"intron (NM_175500, intron 7 of 7)"	"intron (NM_175500, intron 7 of 7)"	-388727	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	miscRNA	0	0.376238
Merged-chr11-98413028-1	chr11	98412978	98413078	+	2.7	cIP2vsInput	"intron (NM_001003817, intron 1 of 26)"	CpG	544	NM_001003817	13866	Mm.290822	NM_001003817	ENSMUSG00000062312	Erbb2	Erbb-2|HER-2|HER2|Neu|c-erbB2|c-neu|mKIAA3023	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"	protein-coding	0.08	0.584158
Merged-chr8-39697568-1	chr8	39697518	39697618	+	2.7	cIP1vsInput	"intron (NR_035426, intron 3 of 5)"	Lx8|LINE|L1	-54890	NM_001113326	20288	Mm.239291	NM_001113326	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding	0	0.346535
Merged-chr3-57448759-1	chr3	57448709	57448809	+	2.7	cIP1vsInput	Intergenic	Intergenic	23349	NM_145539	229302	Mm.26618	NM_145539	ENSMUSG00000027801	Tm4sf4	Iltmp	transmembrane 4 superfamily member 4	protein-coding	0.02	0.405941
Merged-chr9-44773153-1	chr9	44773103	44773203	+	2.7	cIP1vsInput	"5' UTR (NM_023831, exon 1 of 12)"	"5' UTR (NM_023831, exon 1 of 12)"	144	NM_023831	76568	Mm.278597	NM_023831	ENSMUSG00000002031	Ift46	1500035H01Rik|AA408110|AI663846|R75047|c11orf2	intraflagellar transport 46	protein-coding	0.04	0.554455
Merged-chr12-48073566-1	chr12	48073516	48073616	+	2.7	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	227896	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0	0.336634
Merged-chr16-56175342-1	chr16	56175292	56175392	+	2.7	cIP1vsInput	"intron (NM_001003971, intron 15 of 22)"	"intron (NM_001003971, intron 15 of 22)"	-28971	NM_174876	224224	Mm.151998	NM_174876	ENSMUSG00000035270	Impg2	IPM200|PG10.2|Rsbp|Spacrcan	interphotoreceptor matrix proteoglycan 2	protein-coding	0	0.316832
Merged-chr1-97654502-1	chr1	97654452	97654552	+	2.7	cIP2vsInput	"intron (NM_133825, intron 2 of 2)"	"intron (NM_133825, intron 2 of 2)"	7516	NM_133825	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	"DNA segment, Chr 1, ERATO Doi 622, expressed"	protein-coding	0.02	0.346535
Merged-chr16-81200606-1	chr16	81200556	81200656	+	2.7	cIP2vsInput	promoter-TSS (NM_010954)	promoter-TSS (NM_010954)	-91	NM_001113208	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0.17	0.821782
Merged-chr13-110062773-1	chr13	110062723	110062823	+	2.7	cIP2vsInput	"intron (NM_023852, intron 4 of 4)"	"intron (NM_023852, intron 4 of 4)"	158964	NR_035442	100316683		NR_035442		Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	miscRNA	0.01	0.316832
Merged-chr15-58595005-1	chr15	58594955	58595055	+	2.7	cIP2vsInput	Intergenic	(CTG)n|Simple_repeat|Simple_repeat	179537	NM_145959	210998	Mm.3224	NM_145959	ENSMUSG00000037119	D15Ertd621e	AV220772|BC033609|Fam91a1|SKIN|mKIAA0493	"DNA segment, Chr 15, ERATO Doi 621, expressed"	protein-coding	0.01	0.584158
Merged-chr3-76067954-1	chr3	76067904	76068004	+	2.7	cIP1vsInput	Intergenic	Lx7|LINE|L1	-6607	NM_178673	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0.01	0.326733
Merged-chr1-156869204-1	chr1	156869154	156869254	+	2.7	cIP1vsInput	"intron (NM_001159968, intron 7 of 18)"	"intron (NM_001159968, intron 7 of 18)"	30181	NM_028333	72713	Mm.389206	NM_028333	ENSMUSG00000033544	Angptl1	2810039D03Rik|ANG3|ANGPT3|ANGY|ARP1	angiopoietin-like 1	protein-coding	0.01	0.316832
Merged-chr13-109343760-1	chr13	109343710	109343810	+	2.7	cIP2vsInput	"intron (NM_011056, intron 3 of 16)"	"intron (NM_011056, intron 3 of 16)"	19016	NR_030644	100124489		NR_030644		Mir582	Mirn582|mmu-mir-582	microRNA 582	miscRNA	0.01	0.554455
Merged-chr13-32493333-1	chr13	32493283	32493383	+	2.7	cIP1vsInput	Intergenic	Intergenic	-154789	NM_146041	218138	Mm.247143	NM_146041	ENSMUSG00000038372	Gmds	BC031788|C87208	"GDP-mannose 4, 6-dehydratase"	protein-coding	0.01	0.356436
Merged-chr2-152081949-1	chr2	152081899	152081999	+	2.7	cIP2vsInput	"5' UTR (NM_001160410, exon 1 of 2)"	"5' UTR (NM_001160410, exon 1 of 2)"	420	NM_001160410	545474	Mm.214317	NM_001160410	ENSMUSG00000060257	Scrt2	AW060659	"scratch homolog 2, zinc finger protein (Drosophila)"	protein-coding	0.19	0.811881
Merged-chr15-80404747-1	chr15	80404697	80404797	+	2.7	cIP1vsInput	Intergenic	ORR1A3|LTR|ERVL-MaLR	117509	NM_001044308	239556	Mm.291058	NM_001044308	ENSMUSG00000022416	Cacna1i	Ca(V)3.3	"calcium channel, voltage-dependent, alpha 1I subunit"	protein-coding	0	0.356436
Merged-chr2-112239712-1	chr2	112239662	112239762	+	2.7	cIP2vsInput	promoter-TSS (NM_207206)	promoter-TSS (NM_207206)	-129	NM_207206	99010	Mm.33438	NM_207206	ENSMUSG00000027134	Lpcat4	AI505034|Agpat7|Aytl3|LPEAT2	lysophosphatidylcholine acyltransferase 4	protein-coding	0.19	0.80198
Merged-chr10-89408613-1	chr10	89408563	89408663	+	2.7	cIP1vsInput	TTS (NM_001079876)	TTS (NM_001079876)	35354	NM_001079876	237436	Mm.11982	NM_001033331	ENSMUSG00000074802	Gas2l3	8430435B07Rik|Gm240	growth arrest-specific 2 like 3	protein-coding	0	0.386139
Merged-chr15-62378883-1	chr15	62378833	62378933	+	2.7	cIP2vsInput	Intergenic	Intergenic	-159432	NR_003523	67552	Mm.484027	NR_003523		H2afy3	4933432H23Rik	"H2A histone family, member Y3"	pseudo	0	0.366337
Merged-chr8-35557075-1	chr8	35557025	35557125	+	2.7	cIP2vsInput	Intergenic	Intergenic	-30723	NM_001081279	52065	Mm.103246	NM_001081279	ENSMUSG00000070056	Mfhas1	2310066G09Rik|D8Ertd91e	malignant fibrous histiocytoma amplified sequence 1	protein-coding	0	0.326733
Merged-chr5-150746730-1	chr5	150746680	150746780	+	2.7	cIP2vsInput	"exon (NM_175310, exon 11 of 35)"	"exon (NM_175310, exon 11 of 35)"	72903	NM_175310	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|mKIAA0979	"PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)"	protein-coding	0.02	0.39604
Merged-chr12-55695741-1	chr12	55695691	55695791	+	2.7	cIP1vsInput	"intron (NM_001003719, intron 27 of 39)"	L1_Mur1|LINE|L1	96824	NM_020287	56856	Mm.114886	NM_020287	ENSMUSG00000045440	Insm2	Mlt1	insulinoma-associated 2	protein-coding	0.01	0.306931
Merged-chr19-3907207-1	chr19	3907157	3907257	+	2.7	cIP2vsInput	promoter-TSS (NM_001167784)	promoter-TSS (NM_001167784)	-74	NM_001136091	27060	Mm.271689	NM_001136091	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	"T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3"	protein-coding	0.1	0.623762
Merged-chr4-110720012-1	chr4	110719962	110720062	+	2.7	cIP2vsInput	"intron (NM_001048189, intron 3 of 12)"	"intron (NM_001048189, intron 3 of 12)"	322221	NM_030231	78933	Mm.435620	NM_001048189	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding	0.01	0.306931
Merged-chr12-77483706-1	chr12	77483656	77483756	+	2.7	cIP2vsInput	Intergenic	Intergenic	73565	NM_001252616	53618	Mm.489686	NM_001252614	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding	0.03	0.554455
Merged-chr1-67038514-1	chr1	67038464	67038564	+	2.7	cIP2vsInput	"exon (NM_001190985, exon 1 of 9)"	"exon (NM_001190985, exon 1 of 9)"	320	NM_001190984	14768	Mm.20522	NM_001190984	ENSMUSG00000026000	Lancl1	AW124738|Gpr69|Gpr69a|p40	LanC (bacterial lantibiotic synthetase component C)-like 1	protein-coding	0.04	0.49505
Merged-chr10-80039962-1	chr10	80039912	80040012	+	2.7	cIP2vsInput	promoter-TSS (NM_025554)	promoter-TSS (NM_025554)	-303	NM_025554	66420	Mm.18579	NM_025554	ENSMUSG00000004667	Polr2e	2410021N14Rik|25kDa|AW208866|RPB5|XAP4	polymerase (RNA) II (DNA directed) polypeptide E	protein-coding	0.06	0.60396
Merged-chr3-39815157-1	chr3	39815107	39815207	+	2.7	cIP2vsInput	Intergenic	Intergenic	707755	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	miscRNA	0.01	0.356436
Merged-chr2-45715909-1	chr2	45715859	45715959	+	2.7	cIP2vsInput	Intergenic	Intergenic	19304	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	miscRNA	0	0.277228
Merged-chr14-68413466-1	chr14	68413416	68413516	+	2.7	cIP2vsInput	Intergenic	Intergenic	120223	NM_007402	11500	Mm.261495	NM_007402	ENSMUSG00000022056	Adam7	9230104J12Rik|EAP1|EAPI	a disintegrin and metallopeptidase domain 7	protein-coding	0	0.316832
Merged-chr7-136609444-1	chr7	136609394	136609494	+	2.7	cIP1vsInput	Intergenic	Intergenic	101160	NR_046021	621677	Mm.207290	NR_046021		Gm6249	EG621677	predicted gene 6249	miscRNA	0.02	0.336634
Merged-chr3-109491424-1	chr3	109491374	109491474	+	2.7	cIP1vsInput	"intron (NM_020505, intron 2 of 26)"	"intron (NM_020505, intron 2 of 26)"	-82583	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding	0.01	0.366337
Merged-chr4-12352387-1	chr4	12352337	12352437	+	2.7	cIP1vsInput	Intergenic	Intergenic	-180372	NM_026558	68099	Mm.25340	NM_026558	ENSMUSG00000028218	Fam92a	6720467C03Rik|Fam92a1	"family with sequence similarity 92, member A"	protein-coding	0	0.207921
Merged-chr13-25640249-1	chr13	25640199	25640299	+	2.7	cIP2vsInput	Intergenic	MTD|LTR|ERVL-MaLR	326067	NR_045062	100503530	Mm.86763	NR_045062	ENSMUSG00000086531	Gm11351	OTTMUSG00000000620	predicted gene 11351	miscRNA	0.01	0.386139
Merged-chr15-53752394-1	chr15	53752344	53752444	+	2.7	cIP2vsInput	"intron (NM_177225, intron 2 of 4)"	"intron (NM_177225, intron 2 of 4)"	150042	NM_177225	320679	Mm.442455	NM_177225	ENSMUSG00000058656	Samd12	A830094I09Rik	sterile alpha motif domain containing 12	protein-coding	0.01	0.316832
Merged-chr16-37225977-1	chr16	37225927	37226027	+	2.7	cIP1vsInput	"intron (NM_001114613, intron 12 of 26)"	L1MA8|LINE|L1	158981	NM_001114613	207227	Mm.403226	NM_001114611		Stxbp5l	9430094L02|A830015P08Rik|LLGL4|T2dm1|t2md1|tomosyn-2	syntaxin binding protein 5-like	protein-coding	0.01	0.326733
Merged-chr7-89919911-1	chr7	89919861	89919961	+	2.7	cIP2vsInput	"intron (NM_026304, intron 4 of 4)"	"intron (NM_026304, intron 4 of 4)"	-16282	NM_001162979	70884	Mm.252823	NM_001162979	ENSMUSG00000039391	Ccdc81	4921513D09Rik	coiled-coil domain containing 81	protein-coding	0.01	0.346535
Merged-chr3-33854074-1	chr3	33854024	33854124	+	2.7	cIP1vsInput	Intergenic	Intergenic	-9764	NM_026222	51938	Mm.474546	NM_026222	ENSMUSG00000027676	Ccdc39	4921507O14Rik|AI447426|AI844750|D3Ertd789e	coiled-coil domain containing 39	protein-coding	0.01	0.346535
Merged-chr11-3894739-1	chr11	3894689	3894789	+	2.7	cIP1vsInput	promoter-TSS (NM_173745)	promoter-TSS (NM_173745)	387	NM_026150	67430	Mm.347950	NM_026150	ENSMUSG00000020434	4921536K21Rik	AV043724	RIKEN cDNA 4921536K21 gene	protein-coding	0.06	0.544554
Merged-chr3-48664824-1	chr3	48664774	48664874	+	2.7	cIP2vsInput	Intergenic	Intergenic	-55724	NR_003617	66332	Mm.46124	NR_003617		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo	0	0.346535
Merged-chr9-84938336-1	chr9	84938286	84938386	+	2.7	cIP2vsInput	Intergenic	Intergenic	163938	NR_040739	75253	Mm.401984	NR_040739		4930554C24Rik	-	RIKEN cDNA 4930554C24 gene	miscRNA	0.02	0.346535
Merged-chr10-35003802-1	chr10	35003752	35003852	+	2.7	cIP1vsInput	Intergenic	Lx|LINE|L1	520402	NM_010237	14302	Mm.332432	NM_001159544	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding	0	0.336634
Merged-chr17-93967963-1	chr17	93967913	93968013	+	2.7	cIP2vsInput	Intergenic	Intergenic	768541	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0.01	0.326733
Merged-chr7-50581915-1	chr7	50581865	50581965	+	2.7	cIP2vsInput	"intron (NM_001037906, intron 14 of 19)"	"intron (NM_001037906, intron 14 of 19)"	-6031	NR_045928	73515	Mm.437440	NR_045928	ENSMUSG00000085265	1700081H22Rik	-	RIKEN cDNA 1700081H22 gene	miscRNA	0	0.356436
Merged-chr8-119671116-1	chr8	119671066	119671166	+	2.7	cIP2vsInput	"intron (NM_023395, intron 1 of 6)"	"intron (NM_023395, intron 1 of 6)"	4751	NM_023395	67866	Mm.87599	NM_023395		Wfdc1	2310058A03Rik|ps20	WAP four-disulfide core domain 1	protein-coding	0.01	0.465347
Merged-chr11-95605977-1	chr11	95605927	95606027	+	2.7	cIP1vsInput	Intergenic	RMER16-int|LTR|ERVK	-18279	NM_033217	18053	Mm.283893	NM_033217	ENSMUSG00000000120	Ngfr	LNGFR|Tnfrsf16|p75|p75NGFR|p75NTR	"nerve growth factor receptor (TNFR superfamily, member 16)"	protein-coding	0.01	0.306931
Merged-chr13-90299534-1	chr13	90299484	90299584	+	2.7	cIP2vsInput	Intergenic	L1M2|LINE|L1	209867	NM_025335	66074	Mm.241387	NM_025335		Tmem167	0610041E09Rik|5730424F14Rik|AU041184|AW537806|ENSMUSG00000060669|Gm10085|Tmem167a	transmembrane protein 167	protein-coding	0.01	0.29703
Merged-chr12-35296836-1	chr12	35296786	35296886	+	2.7	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	238153	NM_013464	11622	Mm.341377	NM_013464	ENSMUSG00000019256	Ahr	Ah|Ahh|Ahre|In|bHLHe76	aryl-hydrocarbon receptor	protein-coding	0	0.376238
Merged-chr19-31972185-1	chr19	31972135	31972235	+	2.7	cIP2vsInput	Intergenic	Intergenic	103424	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf	APOBEC1 complementation factor	protein-coding	0.03	0.514851
Merged-chr5-50157877-1	chr5	50157827	50157927	+	2.7	cIP1vsInput	Intergenic	L1MA4A|LINE|L1	6544	NR_040696	73965	Mm.243823	NR_040696		4930448I18Rik	-	RIKEN cDNA 4930448I18 gene	miscRNA	0	0.346535
Merged-chr13-101399279-1	chr13	101399229	101399329	+	2.7	cIP1vsInput	Intergenic	Intergenic	-1699	NR_046187	78136	Mm.399065	NR_046187		4922502H24Rik	-	RIKEN cDNA 4922502H24 gene	miscRNA	0.01	0.346535
Merged-chr16-71567274-1	chr16	71567224	71567324	+	2.7	cIP2vsInput	Intergenic	Intergenic	317370	NR_040576	78221	Mm.399298	NR_040576		4930567J20Rik	-	RIKEN cDNA 4930567J20 gene	miscRNA	0	0.287129
Merged-chr9-3851428-1	chr9	3851378	3851478	+	2.7	cIP2vsInput	"intron (NM_001033322, intron 6 of 7)"	"intron (NM_001033322, intron 6 of 7)"	319079	NM_001033322	234889	Mm.91240	NM_001033322		Gucy1a2	6330407I18Rik|A230060L24Rik	"guanylate cyclase 1, soluble, alpha 2"	protein-coding	0	0.326733
Merged-chr2-150786537-1	chr2	150786487	150786587	+	2.7	cIP1vsInput	promoter-TSS (NM_153781)	promoter-TSS (NM_153781)	-259	NM_153781	110078	Mm.222584	NM_153781	ENSMUSG00000033059	Pygb	-	brain glycogen phosphorylase	protein-coding	0.03	0.50495
Merged-chr19-30381148-1	chr19	30381098	30381198	+	2.7	cIP1vsInput	Intergenic	UCON12A|Unknown|Unknown	148191	NM_010776	17195	Mm.30045	NM_010776	ENSMUSG00000024863	Mbl2	L-MBP|MBL|MBL-C|MBP-C	mannose-binding lectin (protein C) 2	protein-coding	0	0.356436
Merged-chr14-76444916-1	chr14	76444866	76444966	+	2.7	cIP2vsInput	"intron (NM_207652, intron 1 of 2)"	"intron (NM_207652, intron 1 of 2)"	29095	NM_207652	21807	Mm.153272	NM_001177751	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	"TSC22 domain family, member 1"	protein-coding	0	0.346535
Merged-chr7-28742165-1	chr7	28742115	28742215	+	2.7	cIP1vsInput	promoter-TSS (NM_011885)	promoter-TSS (NM_011885)	197	NM_023637	71984	Mm.333725	NM_023637	ENSMUSG00000070699	Sars2	2410015F05Rik|D7Ertd353e|SerRS|SerRSmt	seryl-aminoacyl-tRNA synthetase 2	protein-coding	0.1	0.594059
Merged-chr2-97916116-1	chr2	97916066	97916166	+	2.7	cIP2vsInput	Intergenic	Intergenic	448442	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.346535
Merged-chr11-115506762-1	chr11	115506712	115506812	+	2.7	cIP2vsInput	"intron (NM_008258, intron 1 of 4)"	"intron (NM_008258, intron 1 of 4)"	7608	NM_008258	15374	Mm.1775	NM_008258	ENSMUSG00000020737	Hn1	-	hematological and neurological expressed sequence 1	protein-coding	0.01	0.564356
Merged-chr11-37601347-1	chr11	37601297	37601397	+	2.7	cIP1vsInput	Intergenic	Intergenic	-657104	NM_011856	23964	Mm.445432	NM_011856	ENSMUSG00000049336	Tenm2	2610040L17Rik|9330187F13Rik|D3Bwg1534e|Odz2|Odz3|Ten-m2|mKIAA1127	teneurin transmembrane protein 2	protein-coding	0	0.336634
Merged-chr18-19379291-1	chr18	19379241	19379341	+	2.7	cIP2vsInput	Intergenic	Intergenic	622806	NM_007882	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding	0.01	0.326733
Merged-chr18-24121772-1	chr18	24121722	24121822	+	2.7	cIP1vsInput	promoter-TSS (NM_172625)	promoter-TSS (NM_172625)	47	NM_172625	225280	Mm.258973	NM_172625	ENSMUSG00000047989	Ino80c	D030070L09Rik	INO80 complex subunit C	protein-coding	0.05	0.613861
Merged-chr1-28964152-1	chr1	28964102	28964202	+	2.7	cIP2vsInput	Intergenic	Intergenic	-183900	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0.01	0.326733
Merged-chr8-110998155-2	chr8	110998082	110998228	+	2.7	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007916)	promoter-TSS (NM_007916)	-332	NM_007916	13680	Mm.287901	NM_007916	ENSMUSG00000015023	Ddx19a	DBP5|Ddx19|Eif4a-rs1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19a	protein-coding	0.027397	0.387755
Merged-chr6-17891740-1	chr6	17891690	17891790	+	2.7	cIP1vsInput	"intron (NM_001083315, intron 9 of 14)"	"intron (NM_001083315, intron 9 of 14)"	138705	NM_023653	22413	Mm.33653	NM_023653	ENSMUSG00000010797	Wnt2	2610510E18Rik|Int1l1|Irp|Mirp|Wnt-2|Wnt2a	wingless-related MMTV integration site 2	protein-coding	0	0.29703
Merged-chr17-86753419-1	chr17	86753369	86753469	+	2.7	cIP2vsInput	promoter-TSS (NM_010137)	promoter-TSS (NM_010137)	-445	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding	0.08	0.60396
Merged-chr3-22359010-1	chr3	22358960	22359060	+	2.7	cIP2vsInput	Intergenic	Intergenic	107640	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	miscRNA	0	0.326733
Merged-chr15-99075163-1	chr15	99075113	99075213	+	2.7	cIP2vsInput	"intron (NM_030159, intron 1 of 13)"	"intron (NM_030159, intron 1 of 13)"	190	NM_030159	78733	Mm.124905	NM_001162506	ENSMUSG00000032783	Troap	AW476063|E130301L11Rik|tastin	trophinin associated protein	protein-coding	0.04	0.60396
Merged-chr9-83354304-1	chr9	83354254	83354354	+	2.7	cIP1vsInput	Intergenic	Intergenic	86795	NM_027448	75782	Mm.199698	NM_027448	ENSMUSG00000032258	Lca5	4930431B11Rik|5730406O13Rik|AV274874|ORF64	Leber congenital amaurosis 5 (human)	protein-coding	0	0.306931
Merged-chr3-125383899-1	chr3	125383849	125383949	+	2.7	cIP1vsInput	Intergenic	Intergenic	-20192	NM_022565	64580	Mm.444289	NM_022565	ENSMUSG00000027971	Ndst4	4930439H17Rik	N-deacetylase/N-sulfotransferase (heparin glucosaminyl) 4	protein-coding	0.01	0.316832
Merged-chr3-4999843-1	chr3	4999793	4999893	+	2.7	cIP1vsInput	Intergenic	Intergenic	201135	NR_045272	100503859	Mm.75172	NR_045272		1110015O18Rik	-	RIKEN cDNA 1110015O18 gene	miscRNA	0	0.336634
Merged-chr5-122588356-1	chr5	122588306	122588406	+	2.7	cIP1vsInput	"intron (NM_009879, intron 11 of 18)"	"intron (NM_009879, intron 11 of 18)"	26162	NM_009879	12589	Mm.10125	NM_009879	ENSMUSG00000029469	Ift81	AW060663|Cdv-1|Cdv-1r|Cdv1	intraflagellar transport 81	protein-coding	0	0.346535
Merged-chr1-108589714-1	chr1	108589664	108589764	+	2.7	cIP1vsInput	Intergenic	Intergenic	672455	NR_102307	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0	0.306931
Merged-chr12-84362005-1	chr12	84361955	84362055	+	2.7	cIP2vsInput	promoter-TSS (NM_172581)	promoter-TSS (NM_172581)	37	NM_172582	217707	Mm.280062	NM_172582	ENSMUSG00000021235	Coq6	5930427M12Rik|AW742344	coenzyme Q6 homolog (yeast)	protein-coding	0.06	0.60396
Merged-chr6-148927397-1	chr6	148927347	148927447	+	2.7	cIP1vsInput	"intron (NM_019643, intron 4 of 5)"	"intron (NM_019643, intron 4 of 5)"	19035	NM_019643	56306	Mm.18637	NM_019643	ENSMUSG00000039985	Fam60a	Ppcs1|Pptcs1|Tera	"family with sequence similarity 60, member A"	protein-coding	0	0.326733
Merged-chr17-57250782-1	chr17	57250732	57250832	+	2.7	cIP1vsInput	"exon (NM_001242390, exon 2 of 15)"	"exon (NM_001242390, exon 2 of 15)"	1331	NM_001242389	106628	Mm.37368	NM_001242389	ENSMUSG00000019487	Trip10	AI646975|Cip4	thyroid hormone receptor interactor 10	protein-coding	0.07	0.544554
Merged-chr2-105089875-1	chr2	105089825	105089925	+	2.7	cIP2vsInput	"intron (NR_015462, intron 3 of 6)"	"intron (NR_015462, intron 3 of 6)"	36635	NR_015462	329480	Mm.246679	NR_015462	ENSMUSG00000074987	AI314831	6030498F17	expressed sequence AI314831	miscRNA	0.01	0.326733
Merged-chr2-143862993-1	chr2	143862943	143863043	+	2.7	cIP2vsInput	"5' UTR (NM_009751, exon 1 of 8)"	"5' UTR (NM_009751, exon 1 of 8)"	180	NM_009751	12075	Mm.275937	NM_009751	ENSMUSG00000027420	Bfsp1	-	"beaded filament structural protein 1, in lens-CP94"	protein-coding	0.11	0.712871
Merged-chr10-81106073-1	chr10	81106023	81106123	+	2.7	cIP2vsInput	"5' UTR (NM_023138, exon 1 of 11)"	"5' UTR (NM_023138, exon 1 of 11)"	126	NM_023138	26396	Mm.275436	NM_023138	ENSMUSG00000035027	Map2k2	AA589381|MEK2|MK2|Prkmk2	mitogen-activated protein kinase kinase 2	protein-coding	0.15	0.821782
Merged-chr1-17812388-1	chr1	17812338	17812438	+	2.7	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	84971	NM_031402	83691	Mm.289625	NM_031402	ENSMUSG00000025776	Crispld1	Cocoacrisp|Lcrisp1	cysteine-rich secretory protein LCCL domain containing 1	protein-coding	0	0.336634
Merged-chr3-23733938-1	chr3	23733888	23733988	+	2.7	cIP1vsInput	Intergenic	Intergenic	1482568	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	miscRNA	0	0.316832
Merged-chr7-19024278-1	chr7	19024228	19024328	+	2.7	cIP1vsInput	promoter-TSS (NM_026605)	promoter-TSS (NM_026605)	-99	NM_026605	68188	Mm.130902	NM_026605	ENSMUSG00000023118	Sympk	1500016F02Rik|4632415H16Rik|AA125406|AI449890|SPK|SYM	symplekin	protein-coding	0.14	0.742574
Merged-chr6-133287795-2	chr6	133287735	133287856	+	2.65	cIP1vsInput|cIP2vsInput	Intergenic	RMER12B|LTR|ERVK	-4421	NM_027784	232426	Mm.158689	NM_027784	ENSMUSG00000055594	5530400C23Rik	GRP	RIKEN cDNA 5530400C23 gene	protein-coding	0	0.303279
Merged-chr13-67683739-2	chr13	67683640	67683839	+	2.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001001187)	promoter-TSS (NM_001001187)	-227	NM_001001187	408068	Mm.435551	NM_175676	ENSMUSG00000048280	Zfp738	3830402I07Rik|6720487G11Rik	zinc finger protein 738	protein-coding	0.020101	0.41
Merged-chrX-106171580-2	chrX	106171520	106171640	+	2.65	cIP1vsInput|cIP2vsInput	Intergenic	B4A|SINE|B4	-15544	NM_008828	18655	Mm.336205	NM_008828	ENSMUSG00000062070	Pgk1	Pgk-1	phosphoglycerate kinase 1	protein-coding	0.033333	0.578512
Merged-chr11-114198596-2	chr11	114198537	114198655	+	2.65	cIP1vsInput|cIP2vsInput	"intron (NR_045930, intron 1 of 2)"	"intron (NR_045930, intron 1 of 2)"	338	NR_045930	73536	Mm.54275	NR_045930	ENSMUSG00000078600	1700092K14Rik	-	RIKEN cDNA 1700092K14 gene	miscRNA	0.008475	0.630252
Merged-chr11-121283152-2	chr11	121283097	121283208	+	2.65	cIP1vsInput|cIP2vsInput	"intron (NM_001080932, intron 1 of 8)"	ID4_|SINE|ID	23165	NM_001080932	68837	Mm.209750	NM_001080932	ENSMUSG00000039275	Foxk2	1110054H05Rik|5730434B08Rik|6230415M23Rik|ILF|Ilf1	forkhead box K2	protein-coding	0.027027	0.517857
Merged-chr17-24696150-2	chr17	24696095	24696206	+	2.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_023040)	promoter-TSS (NM_023040)	6	NM_023040	11692	Mm.28124	NM_212443	ENSMUSG00000040888	Gfer	Alr|ERV1	"growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration)"	protein-coding	0.153153	0.803571
Merged-chrY-7001502-2	chrY	7001451	7001553	+	2.65	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	166275	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.009804	0.300971
Merged-chr8-85312255-2	chr8	85312183	85312328	+	2.65	cIP1vsInput|cIP2vsInput	Intergenic	Lx7|LINE|L1	12623	NR_028268	56452	Mm.29709	NM_001163791	ENSMUSG00000031697	Orc6	6720420I10Rik|Orc6l	"origin recognition complex, subunit 6"	protein-coding	0	0.315068
Merged-chr5-119713065-2	chr5	119712980	119713151	+	2.65	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-21847	NR_040416	433944	Mm.491053	NR_040416	ENSMUSG00000086847	Gm16065	OTTMUSG00000029666	predicted gene 16065	miscRNA	0.064327	0.593023
Merged-chr7-140036521-2	chr7	140036466	140036577	+	2.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133755)	promoter-TSS (NM_133755)	130	NM_027201	69752	Mm.200818	NM_027201	ENSMUSG00000025470	Zfp511	2410004P19Rik|C86579|Znf511	zinc finger protein 511	protein-coding	0.117117	0.732143
Merged-chr6-133712046-2	chr6	133711965	133712127	+	2.65	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	55357	NM_001177652	545886	Mm.449716	NM_001177652		Gm5886	EG545886|smarp	predicted gene 5886	protein-coding	0.006173	0.368098
Merged-chr10-85871686-2	chr10	85871608	85871765	+	2.65	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133993)	promoter-TSS (NM_133993)	-145	NM_133993	103136	Mm.18834	NM_133993	ENSMUSG00000001785	Pwp1	2310058A11Rik|2610205J09Rik|AI098170|AL022879|AV083409|AW550690	PWP1 homolog (S. cerevisiae)	protein-coding	0	0.474684
Merged-chr13-74208809-1	chr13	74208759	74208859	+	2.6	cIP2vsInput	promoter-TSS (NM_177333)	promoter-TSS (NM_177333)	-109	NM_177333	211446		NM_177333	ENSMUSG00000034152	Exoc3	2810050O03Rik|E430013E20Rik|Sec6|Sec6l1	exocyst complex component 3	protein-coding	0.03	0.50495
Merged-chr15-58292910-1	chr15	58292860	58292960	+	2.6	cIP2vsInput	Intergenic	Intergenic	31259	NM_177755	268807	Mm.124498	NM_177755	ENSMUSG00000022357	Klhl38	8230402K04Rik	kelch-like 38	protein-coding	0.03	0.594059
Merged-chr8-102261033-1	chr8	102260983	102261083	+	2.6	cIP1vsInput	Intergenic	Intergenic	524078	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0	0.29703
Merged-chr7-19920614-1	chr7	19920564	19920664	+	2.6	cIP2vsInput	"intron (NM_027514, intron 1 of 7)"	"intron (NM_027514, intron 1 of 7)"	529	NM_027514	52118	Mm.227506	NM_027514	ENSMUSG00000040511	Pvr	3830421F03Rik|CD155|D7Ertd458e|HVED|PVS|Taa1|Tage4|mE4|necl-5	poliovirus receptor	protein-coding	0.13	0.49505
Merged-chr16-23100158-1	chr16	23100108	23100208	+	2.6	cIP2vsInput	Intergenic	Intergenic	-7321	NM_001123038	13682	Mm.260084	NM_001123037	ENSMUSG00000022884	Eif4a2	4833432N07Rik|BM-010|Ddx2b|Eif4	eukaryotic translation initiation factor 4A2	protein-coding	0.02	0.683168
Merged-chrX-139610213-1	chrX	139610163	139610263	+	2.6	cIP2vsInput	promoter-TSS (NM_023270)	promoter-TSS (NM_023270)	-407	NM_023270	66889	Mm.27764	NM_001254761	ENSMUSG00000031438	Rnf128	1300002C13Rik|AI987883|GRAIL|Greul1	ring finger protein 128	protein-coding	0.01	0.574257
Merged-chr17-59847930-1	chr17	59847880	59847980	+	2.6	cIP1vsInput	Intergenic	Intergenic	-834608	NM_026497	67993	Mm.36507	NM_026497		Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0.01	0.287129
Merged-chr15-96797735-1	chr15	96797685	96797785	+	2.6	cIP2vsInput	Intergenic	Intergenic	-98037	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	"solute carrier family 38, member 2"	protein-coding	0.01	0.465347
Merged-chr10-48364004-1	chr10	48363954	48364054	+	2.6	cIP2vsInput	Intergenic	Lx3B|LINE|L1	731839	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	"proteasome (prosome, macropain) subunit, alpha type 6 pseudogene"	pseudo	0.01	0.326733
Merged-chr2-114379009-1	chr2	114378959	114379059	+	2.6	cIP1vsInput	Intergenic	UCON31|Unknown|Unknown	-177577	NM_175466	228491	Mm.132523	NM_175466	ENSMUSG00000040321	Zfp770	6430601A21Rik|Znf770	zinc finger protein 770	protein-coding	0	0.465347
Merged-chr8-101820475-1	chr8	101820425	101820525	+	2.6	cIP1vsInput	Intergenic	Intergenic	964636	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0	0.277228
Merged-chr15-84853971-1	chr15	84853921	84854021	+	2.6	cIP2vsInput	"intron (NM_001081166, intron 2 of 12)"	CpG	2158	NM_001081166	271305	Mm.101022	NM_001081166	ENSMUSG00000016624	Phf21b	A730032D07Rik	PHD finger protein 21B	protein-coding	0.15	0.782178
Merged-chr15-12433560-1	chr15	12433510	12433610	+	2.6	cIP1vsInput	"intron (NM_001081064, intron 5 of 23)"	"intron (NM_001081064, intron 5 of 23)"	112064	NM_025673	66629	Mm.250936	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding	0	0.316832
Merged-chr4-68778202-1	chr4	68778152	68778252	+	2.6	cIP1vsInput	"intron (NM_019967, intron 7 of 7)"	"intron (NM_019967, intron 7 of 7)"	176195	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Dbc1	BRINP|Brinp1|Dbccr1|Fam5a	deleted in bladder cancer 1 (human)	protein-coding	0	0.316832
Merged-chr4-58863801-1	chr4	58863751	58863851	+	2.6	cIP2vsInput	"intron (NM_172381, intron 8 of 48)"	"intron (NM_172381, intron 8 of 48)"	48924	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding	0	0.386139
Merged-chr13-77302893-1	chr13	77302843	77302943	+	2.6	cIP1vsInput	"intron (NM_001145676, intron 13 of 19)"	"intron (NM_001145676, intron 13 of 19)"	167357	NM_001145676	72371	Mm.371098	NM_028215	ENSMUSG00000071252	2210408I21Rik	-	RIKEN cDNA 2210408I21 gene	protein-coding	0	0.287129
Merged-chr15-32270960-1	chr15	32270910	32271010	+	2.6	cIP1vsInput	"intron (NM_009154, intron 1 of 22)"	"intron (NM_009154, intron 1 of 22)"	26147	NM_009154	20356	Mm.260374	NM_009154	ENSMUSG00000022231	Sema5a	5930434A13|9130201M22Rik|AI464145|Semaf|semF	"sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A"	protein-coding	0	0.316832
Merged-chr4-125085005-1	chr4	125084955	125085055	+	2.6	cIP2vsInput	promoter-TSS (NM_027310)	promoter-TSS (NM_027310)	-142	NM_027310	70088	Mm.291214	NM_027310	ENSMUSG00000028863	Meaf6	2310005N01Rik|2810036M01Rik	MYST/Esa1-associated factor 6	protein-coding	0.09	0.653465
Merged-chr3-101462298-1	chr3	101462248	101462348	+	2.6	cIP2vsInput	"3' UTR (NM_207205, exon 11 of 11)"	"3' UTR (NM_207205, exon 11 of 11)"	85173	NM_207205	78908	Mm.489667	NM_207205	ENSMUSG00000042035	Igsf3	1700016K10Rik|2810035F16Rik|4833439O17Rik|mKIAA0466	"immunoglobulin superfamily, member 3"	protein-coding	0.02	0.336634
Merged-chr1-177319570-1	chr1	177319520	177319620	+	2.6	cIP1vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	-70803	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding	0	0.326733
Merged-chr1-70738226-1	chr1	70738176	70738276	+	2.6	cIP2vsInput	"intron (NM_177164, intron 2 of 3)"	"intron (NM_177164, intron 2 of 3)"	12511	NM_177164	320460	Mm.360649	NM_177164	ENSMUSG00000045648	Vwc2l	A830006F12Rik|Brl	von Willebrand factor C domain-containing protein 2-like	protein-coding	0	0.326733
Merged-chr2-97423581-1	chr2	97423531	97423631	+	2.6	cIP2vsInput	Intergenic	Intergenic	-44093	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.376238
Merged-chr18-41457824-1	chr18	41457774	41457874	+	2.6	cIP1vsInput	Intergenic	Intergenic	493370	NM_029942	77619	Mm.30649	NM_029942	ENSMUSG00000056671	Prelid2	1700003A01Rik|C330008K14Rik	PRELI domain containing 2	protein-coding	0	0.316832
Merged-chr4-5896011-1	chr4	5895961	5896061	+	2.6	cIP2vsInput	Intergenic	Lx2|LINE|L1	251832	NM_173426	242297	Mm.458843	NM_173426		Fam110b	1700012H17Rik|5031405P22|AW049855	"family with sequence similarity 110, member B"	protein-coding	0	0.326733
Merged-chr1-117382486-1	chr1	117382436	117382536	+	2.6	cIP1vsInput	Intergenic	L1MD|LINE|L1	928646	NM_011650	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding	0	0.336634
Merged-chr9-57158322-2	chr9	57158247	57158397	+	2.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025417)	promoter-TSS (NM_025417)	-23	NM_025417	66199	Mm.41687	NM_025417	ENSMUSG00000032299	Commd4	1110039H05Rik	COMM domain containing 4	protein-coding	0.02	0.496689
Merged-chr16-86949204-1	chr16	86949154	86949254	+	2.6	cIP2vsInput	Intergenic	Intergenic	-404981	NM_001159331	67768	Mm.296532	NM_001159331	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding	0	0.316832
Merged-chr6-141778828-1	chr6	141778778	141778878	+	2.6	cIP2vsInput	Intergenic	Intergenic	77343	NM_030687	28250	Mm.255586	NM_030687	ENSMUSG00000030237	Slco1a4	AI785519|Oatp1a4|Oatp2|Slc21a5	"solute carrier organic anion transporter family, member 1a4"	protein-coding	0	0.287129
Merged-chr11-48420985-1	chr11	48420935	48421035	+	2.6	cIP1vsInput	Intergenic	Intergenic	-379375	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Gnb2l1	AL033335|GB-like|Gnb2-rs1|Rack1|p205	"guanine nucleotide binding protein (G protein), beta polypeptide 2 like 1"	protein-coding	0	0.415842
Merged-chr13-59491177-1	chr13	59491127	59491227	+	2.6	cIP1vsInput	"intron (NM_023328, intron 17 of 25)"	"intron (NM_023328, intron 17 of 25)"	66142	NM_001048008	67269	Mm.153008	NM_001048008	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|BB114605|CCP1|Nna1|mKIAA1035|nmf243|pcd	ATP/GTP binding protein 1	protein-coding	0	0.277228
Merged-chr6-62940449-1	chr6	62940399	62940499	+	2.6	cIP1vsInput	Intergenic	Intergenic	-316408	NM_008167	14804	Mm.447390	NM_008167		Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	"glutamate receptor, ionotropic, delta 2"	protein-coding	0	0.29703
Merged-chr9-101303107-1	chr9	101303057	101303157	+	2.6	cIP2vsInput	Intergenic	L1MEd|LINE|L1	-51275	NM_001161362	235542	Mm.335386	NM_001161362	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	"protein phosphatase 2, regulatory subunit B'', alpha"	protein-coding	0	0.29703
Merged-chr10-23473400-1	chr10	23473350	23473450	+	2.6	cIP2vsInput	Intergenic	L1Md_T|LINE|L1	-123497	NM_010167	14051	Mm.446298	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	eyes absent 4 homolog (Drosophila)	protein-coding	0.01	0.356436
Merged-chr13-56806960-1	chr13	56806910	56807010	+	2.6	cIP2vsInput	"intron (NM_012035, intron 6 of 11)"	"intron (NM_012035, intron 6 of 11)"	88628	NM_012035	26946	Mm.62409	NM_012035	ENSMUSG00000021541	Trpc7	TRP-7|TRP7|Trrp8	"transient receptor potential cation channel, subfamily C, member 7"	protein-coding	0.1	0.673267
Merged-chr5-60019806-1	chr5	60019756	60019856	+	2.6	cIP2vsInput	Intergenic	Intergenic	-33804	NR_040682	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0	0.287129
Merged-chr19-14644250-1	chr19	14644200	14644300	+	2.6	cIP1vsInput	Intergenic	Intergenic	-46267	NM_011600	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333	"transducin-like enhancer of split 4, homolog of Drosophila E(spl)"	protein-coding	0.01	0.316832
Merged-chr6-8251102-1	chr6	8251052	8251152	+	2.6	cIP2vsInput	Intergenic	MYSERV-int|LTR|ERVK	8039	NM_026632	68240	Mm.29073	NM_026632	ENSMUSG00000012483	Rpa3	14kDa|C330026P08Rik	replication protein A3	protein-coding	0.01	0.326733
Merged-chr5-36797703-1	chr5	36797653	36797753	+	2.6	cIP1vsInput	promoter-TSS (NM_026242)	promoter-TSS (NM_026242)	-949	NM_026242	67568	Mm.490257	NM_026242	ENSMUSG00000055302	Mrfap1	9130413I22Rik|AL022827|Pam14	Morf4 family associated protein 1	protein-coding	0.01	0.376238
Merged-chr6-29467678-1	chr6	29467628	29467728	+	2.6	cIP1vsInput	promoter-TSS (NM_025381)	promoter-TSS (NM_025381)	-105	NM_025381	66144	Mm.371614	NM_025381	ENSMUSG00000004285	Atp6v1f	1110004G16Rik	"ATPase, H+ transporting, lysosomal V1 subunit F"	protein-coding	0.06	0.544554
Merged-chr12-93571311-1	chr12	93571261	93571361	+	2.6	cIP2vsInput	Intergenic	Intergenic	-1722154	NM_011344	20338	Mm.250605	NM_001039089	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding	0.01	0.287129
Merged-chr14-79301566-1	chr14	79301516	79301616	+	2.6	cIP2vsInput	promoter-TSS (NM_025427)	promoter-TSS (NM_025427)	69	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding	0.07	0.673267
Merged-chr19-9609303-1	chr19	9609253	9609353	+	2.6	cIP2vsInput	Intergenic	RMER15|LTR|ERVL	-50055	NR_073559	619371	Mm.391205	NM_001030317		Stxbp3b	Munc18c(L)|Stxbp3-1	syntaxin-binding protein 3B	pseudo	0.01	0.316832
Merged-chrX-73008261-2	chrX	73008202	73008320	+	2.6	cIP1vsInput|cIP2vsInput	"intron (NM_001109043, intron 12 of 18)"	"intron (NM_001109043, intron 12 of 18)"	16182	NR_035517	100316779		NR_035517	ENSMUSG00000089357	Mir2137	mmu-mir-2137	microRNA 2137	miscRNA	0.042373	0.596639
Merged-chr15-41456317-1	chr15	41456267	41456367	+	2.6	cIP2vsInput	"intron (NM_001130166, intron 1 of 16)"	"intron (NM_001130166, intron 1 of 16)"	8835	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding	0.01	0.346535
Merged-chr3-38034616-1	chr3	38034566	38034666	+	2.6	cIP1vsInput	Intergenic	Intergenic	135803	NR_040559	626410	Mm.389417	NR_040559		Gm20755	-	"predicted gene, 20755"	miscRNA	0	0.346535
Merged-chr1-53166532-1	chr1	53166482	53166582	+	2.6	cIP1vsInput	"intron (NM_027070, intron 7 of 8)"	L1_Rod|LINE|L1	21085	NM_027070	69397	Mm.307084	NM_027070	ENSMUSG00000060715	1700019A02Rik	-	RIKEN cDNA 1700019A02 gene	protein-coding	0	0.346535
Merged-chr3-69702050-1	chr3	69702000	69702100	+	2.6	cIP2vsInput	Intergenic	Intergenic	-20005	NM_133787	97112	Mm.439485	NM_133787	ENSMUSG00000027787	Nmd3	C87860	NMD3 homolog (S. cerevisiae)	protein-coding	0	0.356436
Merged-chr16-8207285-1	chr16	8207235	8207335	+	2.6	cIP1vsInput	Intergenic	Intergenic	217851	NM_029070	74720	Mm.159318	NM_029070	ENSMUSG00000022715	Cldn26	4930511J11Rik|Tmem114	claudin 26	protein-coding	0	0.475248
Merged-chr9-101689903-1	chr9	101689853	101689953	+	2.6	cIP1vsInput	Intergenic	Intergenic	-438071	NM_001161362	235542	Mm.335386	NM_001161362	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	"protein phosphatase 2, regulatory subunit B'', alpha"	protein-coding	0	0.485149
Merged-chr17-16305073-1	chr17	16305023	16305123	+	2.6	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-478487	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	"RGM domain family, member B"	protein-coding	0	0.336634
Merged-chr19-10240819-1	chr19	10240769	10240869	+	2.6	cIP2vsInput	promoter-TSS (NM_001033481)	promoter-TSS (NM_001033481)	-71	NM_001033481	225908	Mm.329716	NM_001033481	ENSMUSG00000036098	Myrf	6030439E18|Gm1804|Gm98|Mrf	myelin regulatory factor	protein-coding	0.14	0.792079
Merged-chr1-173982160-1	chr1	173982110	173982210	+	2.6	cIP2vsInput	"intron (NM_008327, intron 1 of 6)"	"intron (NM_008327, intron 1 of 6)"	684	NM_008327	26388	Mm.218770	XM_003689227	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding	0.03	0.386139
Merged-chr18-30705811-1	chr18	30705761	30705861	+	2.6	cIP2vsInput	Intergenic	Intergenic	432915	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	"phosphoinositide-3-kinase, class 3"	protein-coding	0	0.29703
Merged-chr3-45857525-1	chr3	45857475	45857575	+	2.6	cIP1vsInput	Intergenic	Intergenic	-418216	NR_040594	72274	Mm.396202	NR_040594		1700027H10Rik	-	RIKEN cDNA 1700027H10 gene	miscRNA	0	0.356436
Merged-chr19-4625564-1	chr19	4625514	4625614	+	2.6	cIP2vsInput	promoter-TSS (NM_023131)	promoter-TSS (NM_023131)	53	NM_023131	19671	Mm.391143	NM_023131	ENSMUSG00000024889	Rce1	D19Ertd283e|D19Ertd98e	"RCE1 homolog, prenyl protein peptidase (S. cerevisiae)"	protein-coding	0.15	0.762376
Merged-chr11-4218036-1	chr11	4217986	4218086	+	2.6	cIP1vsInput	promoter-TSS (NM_028022)	promoter-TSS (NM_028022)	-215	NM_028022	71962	Mm.7852	NM_028022	ENSMUSG00000020424	Gatsl3	2410008K03Rik	GATS protein-like 3	protein-coding	0.06	0.633663
Merged-chr8-54153374-1	chr8	54153324	54153424	+	2.6	cIP1vsInput	"intron (NM_009506, intron 1 of 6)"	"intron (NM_009506, intron 1 of 6)"	75842	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding	0.01	0.376238
Merged-chr9-122027759-1	chr9	122027709	122027809	+	2.6	cIP1vsInput	Intergenic	Intergenic	-31733	NM_153540	215494	Mm.402151	NM_153540	ENSMUSG00000066235	Gtdc2	Ago61|C85492	glycosyltransferase-like domain containing 2	protein-coding	0.01	0.544554
Merged-chr11-68938799-1	chr11	68938749	68938849	+	2.6	cIP1vsInput	Intergenic	Intergenic	-11718	NM_145746	252868	Mm.76826	NM_145746	ENSMUSG00000032921	Odf4	Oppo1	outer dense fiber of sperm tails 4	protein-coding	0.02	0.445545
Merged-chr10-50335876-1	chr10	50335826	50335926	+	2.6	cIP2vsInput	Intergenic	Intergenic	-256793	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0	0.346535
Merged-chr11-33360823-1	chr11	33360773	33360873	+	2.6	cIP1vsInput	"intron (NM_023146, intron 14 of 27)"	"intron (NM_023146, intron 14 of 27)"	152923	NM_023146	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	4932704E15Rik	RAN binding protein 17	protein-coding	0	0.326733
Merged-chr6-100563428-1	chr6	100563378	100563478	+	2.6	cIP2vsInput	Intergenic	CpG	36028	NR_040525	73395	Mm.69413	NR_040525		1700049E22Rik	-	RIKEN cDNA 1700049E22 gene	miscRNA	0.07	0.663366
Merged-chr6-64657139-1	chr6	64657089	64657189	+	2.6	cIP1vsInput	"intron (NM_008167, intron 14 of 15)"	ETnERV3-int|LTR|ERVK	-72007	NM_007500	11921	Mm.57229	NM_007500	ENSMUSG00000073043	Atoh1	Hath1|MATH-1|Math1|bHLHa14	atonal homolog 1 (Drosophila)	protein-coding	0.01	0.405941
Merged-chr6-122703364-2	chr6	122703308	122703420	+	2.6	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-4204	NM_028016	71950	Mm.6047	NM_028016		Nanog	2410002E02Rik|ENK|ecat4	Nanog homeobox	protein-coding	0.008929	0.39823
Merged-chr3-10230199-1	chr3	10230149	10230249	+	2.6	cIP2vsInput	Intergenic	Intergenic	-21623	NM_024406	11770	Mm.582	NM_024406	ENSMUSG00000062515	Fabp4	422/aP2|ALBP/Ap2|Ap2|Lbpl	"fatty acid binding protein 4, adipocyte"	protein-coding	0	0.29703
Merged-chr16-80191319-1	chr16	80191269	80191369	+	2.6	cIP1vsInput	Intergenic	Intergenic	-1009378	NM_001113208	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.326733
Merged-chr13-54565516-1	chr13	54565466	54565566	+	2.6	cIP2vsInput	promoter-TSS (NM_133797)	promoter-TSS (NM_133797)	-134	NM_133797	97820	Mm.489745	NM_001252645	ENSMUSG00000025871	4833439L19Rik	4930558H15Rik|C81457|Kiaa1191|P33monox	RIKEN cDNA 4833439L19 gene	protein-coding	0.02	0.465347
Merged-chr8-98404600-1	chr8	98404550	98404650	+	2.6	cIP1vsInput	Intergenic	Intergenic	1011857	NM_007667	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.405941
Merged-chr5-81375493-1	chr5	81375443	81375543	+	2.6	cIP2vsInput	"intron (NM_198702, intron 5 of 27)"	"intron (NM_198702, intron 5 of 27)"	353900	NM_198702	319387	Mm.461016	NM_198702	ENSMUSG00000037605	Lphn3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|mKIAA0768	latrophilin 3	protein-coding	0.02	0.386139
Merged-chr9-65060143-1	chr9	65060093	65060193	+	2.6	cIP2vsInput	"intron (NM_028906, intron 12 of 20)"	"intron (NM_028906, intron 12 of 20)"	27685	NM_028906	74388	Mm.391842	NM_028906	ENSMUSG00000032393	Dpp8	2310004I03Rik|4932434F09Rik|AI666706|DPP VIII	dipeptidylpeptidase 8	protein-coding	0	0.267327
Merged-chr3-106266119-1	chr3	106266069	106266169	+	2.6	cIP1vsInput	Intergenic	Intergenic	-46640	NM_145126	104183	Mm.425140	NM_145126	ENSMUSG00000063779	Chi3l4	Chil4|Ym2	"chitinase 3-like 4, Chil4"	protein-coding	0	0.257426
Merged-chr18-61707592-1	chr18	61707542	61707642	+	2.6	cIP1vsInput	promoter-TSS (NM_172832)	promoter-TSS (NM_172832)	43	NM_172832	240334	Mm.234457	NM_172832	ENSMUSG00000024579	Pcyox1l	BC060677|C630049M13	prenylcysteine oxidase 1 like	protein-coding	0.13	0.742574
Merged-chr12-83631754-1	chr12	83631704	83631804	+	2.6	cIP2vsInput	promoter-TSS (NM_027349)	promoter-TSS (NM_027349)	-480	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding	0.03	0.415842
Merged-chr3-132759713-1	chr3	132759663	132759763	+	2.6	cIP1vsInput	"intron (NM_173032, intron 22 of 23)"	"intron (NM_173032, intron 22 of 23)"	75569	NM_173032	271981	Mm.440106	NM_001163455	ENSMUSG00000028030	Tbck	1700120J03Rik|9430001M19|A630047E20Rik|C030007I09Rik|Tbckl	TBC1 domain containing kinase	protein-coding	0	0.316832
Merged-chr17-80470001-1	chr17	80469951	80470051	+	2.6	cIP2vsInput	"intron (NM_009231, intron 1 of 21)"	"intron (NM_009231, intron 1 of 21)"	10452	NM_009231	20662	Mm.360004	NM_009231	ENSMUSG00000024241	Sos1	4430401P03Rik|9630010N06|AI449023	son of sevenless homolog 1 (Drosophila)	protein-coding	0	0.326733
Merged-chr12-52577095-1	chr12	52577045	52577145	+	2.6	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	25227	NR_045910	73278	Mm.396209	NR_045910		1700031P21Rik	-	RIKEN cDNA 1700031P21 gene	miscRNA	0	0.316832
Merged-chr4-75023334-1	chr4	75023284	75023384	+	2.6	cIP2vsInput	Intergenic	Intergenic	254952	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	3110001D03Rik	1700027K24Rik	RIKEN cDNA 3110001D03 gene	protein-coding	0.01	0.316832
Merged-chr1-157371667-1	chr1	157371617	157371717	+	2.6	cIP1vsInput	"intron (NM_177644, intron 1 of 17)"	"intron (NM_177644, intron 1 of 17)"	-40685	NR_027984	69953	Mm.286863	NR_027984	ENSMUSG00000049881	2810025M15Rik	AI429618	RIKEN cDNA 2810025M15 gene	miscRNA	0	0.386139
Merged-chr5-133287283-1	chr5	133287233	133287333	+	2.6	cIP2vsInput	Intergenic	Intergenic	-744940	NM_177047	319974	Mm.488992	NM_177047		Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding	0	0.336634
Merged-chr14-78482627-1	chr14	78482577	78482677	+	2.6	cIP2vsInput	Intergenic	Intergenic	54233	NM_001164503	219181	Mm.89413	NM_001164503	ENSMUSG00000022016	Akap11	6330501D17Rik|AKAP220|Gm80|PRKA11|mKIAA0629	A kinase (PRKA) anchor protein 11	protein-coding	0.01	0.594059
Merged-chr3-102898320-1	chr3	102898270	102898370	+	2.6	cIP2vsInput	"intron (NM_011516, intron 18 of 32)"	MER2|DNA|TcMar-Tigger	37780	NM_011516	20957	Mm.243849	NM_011516	ENSMUSG00000027855	Sycp1	SCP1	synaptonemal complex protein 1	protein-coding	0	0.356436
Merged-chr12-116047929-1	chr12	116047879	116047979	+	2.6	cIP2vsInput	"intron (NM_001004066, intron 1 of 2)"	CpG	205	NM_019565	56220	Mm.254997	NM_001004066	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding	0.14	0.772277
Merged-chr1-15792101-1	chr1	15792051	15792151	+	2.6	cIP2vsInput	Intergenic	Intergenic	-13557	NM_009352	21749	Mm.4306	NM_009352	ENSMUSG00000025925	Terf1	Pin2|Trbf1|Trf1	telomeric repeat binding factor 1	protein-coding	0.03	0.376238
Merged-chr1-4162773-1	chr1	4162723	4162823	+	2.6	cIP2vsInput	Intergenic	Intergenic	197541	NM_011283	19888	Mm.294263	NM_001195662	ENSMUSG00000025900	Rp1	Dcdc3|Orp1|Rp1h|mG145	retinitis pigmentosa 1 (human)	protein-coding	0	0.326733
Merged-chr18-79864529-1	chr18	79864479	79864579	+	2.6	cIP1vsInput	Intergenic	Intergenic	-182366	NM_053117	93737	Mm.24678	NM_053117	ENSMUSG00000056214	Pard6g	2410049N21Rik|Par6a	par-6 partitioning defective 6 homolog gamma (C. elegans)	protein-coding	0	0.267327
Merged-chr16-36817836-1	chr16	36817786	36817886	+	2.6	cIP1vsInput	"intron (NM_134111, intron 2 of 5)"	"intron (NM_134111, intron 2 of 5)"	-9131	NM_001113405	106389	Mm.432078	NM_001113401	ENSMUSG00000022838	Eaf2	AW048865|FESTA-L|FESTA-S|Festa|Traits|U19	ELL associated factor 2	protein-coding	0.01	0.425743
Merged-chr10-127938012-1	chr10	127937962	127938062	+	2.6	cIP2vsInput	Intergenic	Intergenic	39477	NM_027301	70061	Mm.158320	NM_027301	ENSMUSG00000040127	Sdr9c7	1810054F20Rik|Rdh20|Rdhs|SDR-O|Sdro	"4short chain dehydrogenase/reductase family 9C, member 7"	protein-coding	0	0.356436
Merged-chr15-7243412-1	chr15	7243362	7243462	+	2.6	cIP1vsInput	"intron (NM_178748, intron 13 of 21)"	"intron (NM_178748, intron 13 of 21)"	102870	NM_013584	16880	Mm.149720	NM_001113386	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	leukemia inhibitory factor receptor	protein-coding	0	0.316832
Merged-chr13-118698805-1	chr13	118698755	118698855	+	2.6	cIP2vsInput	Intergenic	Intergenic	-15894	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding	0.01	0.29703
Merged-chr11-109197797-1	chr11	109197747	109197847	+	2.6	cIP1vsInput	Intergenic	Intergenic	-53428	NR_037978	268498	Mm.227970	NM_001085512	ENSMUSG00000078605	E030025P04Rik	Gm664	RIKEN cDNA E030025P04 gene	miscRNA	0	0.366337
Merged-chr5-59886110-1	chr5	59886060	59886160	+	2.6	cIP2vsInput	Intergenic	Lx8b|LINE|L1	99892	NR_040683	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0.01	0.336634
Merged-chr10-23543184-1	chr10	23543134	23543234	+	2.6	cIP2vsInput	Intergenic	Intergenic	-193281	NM_010167	14051	Mm.446298	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	eyes absent 4 homolog (Drosophila)	protein-coding	0.02	0.306931
Merged-chr2-34406889-1	chr2	34406839	34406939	+	2.6	cIP2vsInput	Intergenic	CpG	-25136	NM_177345	227743	Mm.270866	NM_177345	ENSMUSG00000038696	Mapkap1	AI591529|D230039K05Rik|Sin1	mitogen-activated protein kinase associated protein 1	protein-coding	0.14	0.742574
Merged-chr13-95398627-1	chr13	95398577	95398677	+	2.6	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	-23293	NM_025630	66549	Mm.36785	NM_025630	ENSMUSG00000021681	Aggf1	2010009L17Rik|2310029P06Rik|AW112072|Peg3|VG5Q	angiogenic factor with G patch and FHA domains 1	protein-coding	0	0.306931
Merged-chr18-38904504-1	chr18	38904454	38904554	+	2.6	cIP2vsInput	"intron (NM_001033789, intron 3 of 4)"	"intron (NM_001033789, intron 3 of 4)"	12048	NM_001033789	545253	Mm.244585	NM_001033789		Gm5820	EG545253	predicted gene 5820	protein-coding	0	0.346535
Merged-chr1-33081433-1	chr1	33081383	33081483	+	2.6	cIP1vsInput	Intergenic	MTE2b|LTR|ERVL-MaLR	-534140	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding	0	0.326733
Merged-chr6-91129920-1	chr6	91129870	91129970	+	2.6	cIP2vsInput	Intergenic	Intergenic	-13094	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding	0.01	0.356436
Merged-chr18-58602940-1	chr18	58602890	58602990	+	2.6	cIP2vsInput	"intron (NM_001081072, intron 5 of 9)"	"intron (NM_001081072, intron 5 of 9)"	46700	NM_001081072	225579	Mm.258517	NM_001081072	ENSMUSG00000024600	Slc27a6	4732438L20Rik|FACVL2|FATP6|VLCS-H1	"solute carrier family 27 (fatty acid transporter), member 6"	protein-coding	0.01	0.316832
Merged-chr2-27009964-1	chr2	27009914	27010014	+	2.6	cIP2vsInput	promoter-TSS (NM_001243240)	promoter-TSS (NM_001243240)	38	NM_001243239	381356	Mm.150270	NM_001243239	ENSMUSG00000015488	Cacfd1	5930434B04Rik|mFwe	calcium channel flower domain containing 1	protein-coding	0.16	0.732673
Merged-chr18-30304765-1	chr18	30304715	30304815	+	2.6	cIP1vsInput	"intron (NM_181414, intron 12 of 24)"	"intron (NM_181414, intron 12 of 24)"	31869	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	"phosphoinositide-3-kinase, class 3"	protein-coding	0.01	0.415842
Merged-chr15-50002867-1	chr15	50002817	50002917	+	2.6	cIP2vsInput	Intergenic	Intergenic	886247	NR_035444	100316685		NR_035444	ENSMUSG00000084458	Mir1907	Mirn1907|mmu-mir-1907	microRNA 1907	miscRNA	0.01	0.306931
Merged-chr3-141485742-1	chr3	141485692	141485792	+	2.6	cIP1vsInput	"intron (NM_009472, intron 1 of 15)"	"intron (NM_009472, intron 1 of 15)"	20178	NM_009472	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	6030473H24|AI047720|B130051O18Rik|Unc5h3|rcm	unc-5 homolog C (C. elegans)	protein-coding	0.01	0.336634
Merged-chr9-42486383-1	chr9	42486333	42486433	+	2.6	cIP1vsInput	Intergenic	L1MB4|LINE|L1	-14157	NM_173038	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding	0.02	0.326733
Merged-chr2-45759116-1	chr2	45759066	45759166	+	2.6	cIP2vsInput	Intergenic	Intergenic	62511	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	miscRNA	0.01	0.306931
Merged-chr12-8640858-1	chr12	8640808	8640908	+	2.6	cIP2vsInput	Intergenic	Intergenic	-33276	NM_001160221	80913	Mm.341243	NM_001160219	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2|mKIAA0235	pumilio 2 (Drosophila)	protein-coding	0.04	0.643564
Merged-chr7-116237866-1	chr7	116237816	116237916	+	2.6	cIP2vsInput	Intergenic	CpG	-48025	NM_172743	233765	Mm.3741	NM_172743	ENSMUSG00000045659	Plekha7	A430081P20Rik|AI414265	"pleckstrin homology domain containing, family A member 7"	protein-coding	0.07	0.712871
Merged-chr1-140474372-1	chr1	140474322	140474422	+	2.6	cIP2vsInput	"intron (NM_001081027, intron 13 of 27)"	Lx9|LINE|L1	182030	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0	0.326733
Merged-chr10-105657017-1	chr10	105656967	105657067	+	2.6	cIP1vsInput	Intergenic	Intergenic	82466	NR_038032	327812	Mm.191660	NR_038032	ENSMUSG00000085282	Gm15663	9330159K06|OTTMUSG00000025047	predicted gene 15663	miscRNA	0	0.465347
Merged-chr16-84089592-1	chr16	84089542	84089642	+	2.6	cIP2vsInput	Intergenic	Intergenic	-281551	NR_040567	75247	Mm.417813	NR_040567		4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	miscRNA	0	0.316832
Merged-chr10-101826792-1	chr10	101826742	101826842	+	2.6	cIP1vsInput	"intron (NM_001205098, intron 1 of 7)"	"intron (NM_001205098, intron 1 of 7)"	54100	NR_037211	100526516		NR_037211	ENSMUSG00000092952	Mir3059	mmu-mir-3059	microRNA 3059	miscRNA	0.01	0.316832
Merged-chr2-42877888-1	chr2	42877838	42877938	+	2.6	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	-224290	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0.02	0.326733
Merged-chr8-72443655-1	chr8	72443605	72443705	+	2.6	cIP1vsInput	promoter-TSS (NM_028170)	promoter-TSS (NM_028170)	123	NM_028500	73316	Mm.196315	NM_029782	ENSMUSG00000019732	Calr3	1700031L01Rik|6330586I20Rik|Crt2|cspn	calreticulin 3	protein-coding	0.06	0.584158
Merged-chr6-15967119-1	chr6	15967069	15967169	+	2.6	cIP2vsInput	Intergenic	Intergenic	246458	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding	0	0.316832
Merged-chr13-11954202-1	chr13	11954152	11954252	+	2.6	cIP2vsInput	"intron (NM_023868, intron 1 of 104)"	"intron (NM_023868, intron 1 of 104)"	152743	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	"ryanodine receptor 2, cardiac"	protein-coding	0.01	0.386139
Merged-chr5-123609252-1	chr5	123609202	123609302	+	2.6	cIP1vsInput	"exon (NM_019765, exon 17 of 24)"	"exon (NM_019765, exon 17 of 24)"	-36237	NM_029929	77573	Mm.41372	NM_029929	ENSMUSG00000029434	Vps33a	3830421M04Rik|AI503300|AW048546|AW554476|bf	vacuolar protein sorting 33A (yeast)	protein-coding	0	0.346535
Merged-chr4-77185204-1	chr4	77185154	77185254	+	2.6	cIP2vsInput	"intron (NM_011211, intron 7 of 39)"	"intron (NM_011211, intron 7 of 39)"	1026691	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0	0.277228
Merged-chr18-68757553-1	chr18	68757503	68757603	+	2.6	cIP1vsInput	Intergenic	Intergenic	193975	NR_038051	78931	Mm.160155	NR_038051		4930546C10Rik	-	RIKEN cDNA 4930546C10 gene	miscRNA	0	0.346535
Merged-chr2-58373065-1	chr2	58373015	58373115	+	2.6	cIP1vsInput	Intergenic	Intergenic	-15307	NM_001111030	269275	Mm.77751	NM_001033369	ENSMUSG00000026834	Acvr1c	ACVRLK7|ALK7|Alk-7|C230097P10	"activin A receptor, type IC"	protein-coding	0	0.336634
Merged-chr4-117770793-1	chr4	117770743	117770843	+	2.6	cIP1vsInput	Intergenic	Lx7|LINE|L1	-5127	NM_029416	75753	Mm.3848	XM_003946144		Klf17	7420700M05Rik|AA420409|AU043468|C85123|D4Ertd561e|Gzf|Zfp393	Kruppel-like factor 17	protein-coding	0	0.346535
Merged-chr9-110790698-1	chr9	110790648	110790748	+	2.6	cIP2vsInput	Intergenic	L1MB8|LINE|L1	-7487	NM_153099	235628	Mm.292285	NM_153099	ENSMUSG00000044664	Prss42	Tessp2	"protease, serine, 42"	protein-coding	0	0.346535
Merged-chr11-22366173-1	chr11	22366123	22366223	+	2.6	cIP1vsInput	Intergenic	Lx8|LINE|L1	-79378	NM_001252515	216565	Mm.281732	NM_001252515	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding	0	0.326733
Merged-chr15-73739893-1	chr15	73739843	73739943	+	2.6	cIP1vsInput	"intron (NM_001166388, intron 1 of 5)"	"intron (NM_001166388, intron 1 of 5)"	-8133	NM_008975	19245	Mm.390807	NM_001166388	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding	0.03	0.574257
Merged-chr17-41318385-1	chr17	41318335	41318435	+	2.6	cIP2vsInput	Intergenic	Intergenic	383700	NM_008650	17850	Mm.259884	NM_008650	ENSMUSG00000023921	Mut	D230010K02Rik|Mcm	methylmalonyl-Coenzyme A mutase	protein-coding	0	0.336634
Merged-chr10-14452244-1	chr10	14452194	14452294	+	2.6	cIP2vsInput	"intron (NM_001002268, intron 5 of 24)"	"intron (NM_001002268, intron 5 of 24)"	92792	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Gpr126	1190004A11Rik|AI449247|AW045736|DREG|Gm222	G protein-coupled receptor 126	protein-coding	0.01	0.336634
Merged-chr2-14088673-1	chr2	14088623	14088723	+	2.6	cIP1vsInput	"intron (NM_011484, intron 1 of 13)"	"intron (NM_011484, intron 1 of 13)"	14561	NM_011484	20844	Mm.273174	NM_011484	ENSMUSG00000026718	Stam	STAM1	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	protein-coding	0	0.386139
Merged-chr13-76982887-1	chr13	76982837	76982937	+	2.6	cIP1vsInput	"intron (NM_030174, intron 17 of 20)"	L1_Mus3|LINE|L1	152581	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Ankrd32	2700017A04Rik|AW545819|Brctd1|Brctx|C730024G01Rik	ankyrin repeat domain 32	protein-coding	0	0.287129
Merged-chr7-48749164-1	chr7	48749114	48749214	+	2.6	cIP2vsInput	Intergenic	L1MA6|LINE|L1	-39839	NM_028031	243983	Mm.279116	NM_028031	ENSMUSG00000030471	Zdhhc13	2410004E01Rik|C530010M18|HIP3RP|Hip14l|kojak|skc4	"zinc finger, DHHC domain containing 13"	protein-coding	0	0.306931
Merged-chr15-75909226-1	chr15	75909176	75909276	+	2.6	cIP2vsInput	promoter-TSS (NM_178646)	promoter-TSS (NM_178646)	114	NM_023240	66656	Mm.258927	NM_023240	ENSMUSG00000055762	Eef1d	1700026P12Rik|5730529A16Rik|AL023999	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	protein-coding	0.11	0.732673
Merged-chr12-112492128-1	chr12	112492078	112492178	+	2.6	cIP2vsInput	"intron (NM_177039, intron 1 of 4)"	"intron (NM_177039, intron 1 of 4)"	2680	NM_177039	319942	Mm.185209	NM_177039	ENSMUSG00000043122	A530016L24Rik	Nrac	RIKEN cDNA A530016L24 gene	protein-coding	0.03	0.554455
Merged-chr12-28286266-1	chr12	28286216	28286316	+	2.6	cIP1vsInput	Intergenic	Intergenic	262071	NM_001177964	68511	Mm.310284	NM_001177964		Dcdc2c	1110015M06Rik	doublecortin domain containing 2C	protein-coding	0	0.287129
Merged-chr4-71153356-1	chr4	71153306	71153406	+	2.6	cIP2vsInput	Intergenic	MurERV4-int|LTR|ERVK	-618428	NM_172694	230316	Mm.251188	NM_172694		Megf9	4933405H16Rik|9630025C07|Egfl5|mKIAA0818	multiple EGF-like-domains 9	protein-coding	0	0.366337
Merged-chr8-51301887-1	chr8	51301837	51301937	+	2.6	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	933775	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0.01	0.29703
Merged-chr2-57767997-1	chr2	57767947	57768047	+	2.6	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-230158	NM_172855	241391	Mm.484118	NM_172855	ENSMUSG00000026828	Galnt5	4832424J23	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5	protein-coding	0.01	0.366337
Merged-chr6-27037462-1	chr6	27037412	27037512	+	2.6	cIP1vsInput	Intergenic	Intergenic	899288	NR_030420	735266		NR_030420		Mir592	Mirn592|mir-592|mmu-mir-592	microRNA 592	miscRNA	0	0.356436
Merged-chr1-174669121-1	chr1	174669071	174669171	+	2.6	cIP2vsInput	"intron (NM_019445, intron 8 of 17)"	"intron (NM_019445, intron 8 of 17)"	167296	NM_019445	54418	Mm.330620	NM_019445	ENSMUSG00000028354	Fmn2	AU024104	formin 2	protein-coding	0	0.316832
Merged-chr10-51253108-1	chr10	51253058	51253158	+	2.6	cIP2vsInput	Intergenic	Intergenic	-227571	NM_008147	14727	Mm.439661	NM_008147	ENSMUSG00000089672	Gp49a	gp49	glycoprotein 49 A	protein-coding	0	0.316832
Merged-chr6-5669098-1	chr6	5669048	5669148	+	2.6	cIP2vsInput	Intergenic	Intergenic	-56541	NM_001191023	13426	Mm.20893	NM_001191023	ENSMUSG00000029757	Dync1i1	DH IC-1|DHIC-1|DIC|Dncic1|IC74	dynein cytoplasmic 1 intermediate chain 1	protein-coding	0	0.287129
Merged-chr3-27681207-1	chr3	27681157	27681257	+	2.6	cIP2vsInput	"intron (NM_173182, intron 1 of 25)"	"intron (NM_173182, intron 1 of 25)"	29232	NM_173182	72007	Mm.38832	NM_173182	ENSMUSG00000039286	Fndc3b	1600019O04Rik|AW550168|Fad104|mKIAA4164	fibronectin type III domain containing 3B	protein-coding	0.01	0.336634
Merged-chr12-112490639-1	chr12	112490589	112490689	+	2.6	cIP2vsInput	"intron (NM_177039, intron 1 of 4)"	"intron (NM_177039, intron 1 of 4)"	1191	NM_177039	319942	Mm.185209	NM_177039	ENSMUSG00000043122	A530016L24Rik	Nrac	RIKEN cDNA A530016L24 gene	protein-coding	0	0.574257
Merged-chr13-119342407-1	chr13	119342357	119342457	+	2.6	cIP2vsInput	"intron (NR_003544, intron 14 of 16)"	"intron (NR_003544, intron 14 of 16)"	66604	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding	0	0.326733
Merged-chr2-40969087-1	chr2	40969037	40969137	+	2.6	cIP1vsInput	"intron (NM_053011, intron 43 of 90)"	RLTR25A|LTR|ERVK	1684511	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0	0.316832
Merged-chr5-143548473-1	chr5	143548423	143548523	+	2.6	cIP1vsInput	promoter-TSS (NM_133703)	promoter-TSS (NM_133703)	-233	NM_133703	67238	Mm.383219	NM_026050	ENSMUSG00000048910	Fam220a	1500026F15Rik|2810453I06Rik|AW047776|Acpin1|Sipar	"family with sequence similarity 220, member A"	protein-coding	0.02	0.514851
Merged-chr8-35483094-1	chr8	35483044	35483144	+	2.6	cIP1vsInput	"intron (NM_026067, intron 2 of 6)"	"intron (NM_026067, intron 2 of 6)"	12439	NM_026067	67276	Mm.207534	NM_026067	ENSMUSG00000031527	Eri1	3'hexo|3110010F15Rik|Thex1|eri-1	exoribonuclease 1	protein-coding	0	0.356436
Merged-chr18-40943581-1	chr18	40943531	40943631	+	2.6	cIP2vsInput	Intergenic	Intergenic	685220	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding	0	0.287129
Merged-chr4-150415793-1	chr4	150415743	150415843	+	2.6	cIP1vsInput	"intron (NM_001085492, intron 2 of 22)"	"intron (NM_001085492, intron 2 of 22)"	133877	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding	0.02	0.39604
Merged-chr17-29348193-1	chr17	29348143	29348243	+	2.6	cIP1vsInput	promoter-TSS (NM_019880)	promoter-TSS (NM_019880)	-289	NM_019880	56462	Mm.486273	NM_019880	ENSMUSG00000024012	Mtch1	2310034O17Rik|AI255158|AU018396|C77849|PSAP	mitochondrial carrier homolog 1 (C. elegans)	protein-coding	0.03	0.524752
Merged-chr9-45412045-1	chr9	45411995	45412095	+	2.6	cIP1vsInput	Intergenic	Intergenic	5968	NM_007503	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding	0.04	0.475248
Merged-chr18-78660151-1	chr18	78660101	78660201	+	2.6	cIP1vsInput	Intergenic	Intergenic	-63201	NM_030683	27411	Mm.44158	NM_001110273	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	"solute carrier family 14 (urea transporter), member 2"	protein-coding	0.02	0.356436
Merged-chr16-26437695-1	chr16	26437645	26437745	+	2.6	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-25440	NM_053241	114141	Mm.275205	NM_053241	ENSMUSG00000038148	Cldn16	PCLN1|claudin-16	claudin 16	protein-coding	0	0.336634
Merged-chr4-52528000-1	chr4	52527950	52528050	+	2.6	cIP1vsInput	Intergenic	MLT2C1|LTR|ERVL	-68274	NM_026652	68274	Mm.475827	NM_026652	ENSMUSG00000028314	4930547C10Rik	-	RIKEN cDNA 4930547C10 gene	protein-coding	0.01	0.306931
Merged-chr9-79190891-1	chr9	79190841	79190941	+	2.6	cIP2vsInput	Intergenic	L1VL2|LINE|L1	328411	NR_045336	100038575	Mm.367838	NR_045336		Gm10635	ENSMUSG00000074174	predicted gene 10635	miscRNA	0.01	0.356436
Merged-chr8-42120498-1	chr8	42120448	42120548	+	2.6	cIP1vsInput	Intergenic	Intergenic	293231	NR_045497	69966	Mm.416903	NR_045497		2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	miscRNA	0.01	0.306931
Merged-chr5-32863666-1	chr5	32863616	32863716	+	2.6	cIP2vsInput	promoter-TSS (NM_001170567)	promoter-TSS (NM_001170567)	-55	NM_177786	277854	Mm.101524	NM_001025426	ENSMUSG00000037426	Depdc5	AV016528	DEP domain containing 5	protein-coding	0.11	0.762376
Merged-chr9-21073213-1	chr9	21073163	21073263	+	2.6	cIP2vsInput	TTS (NM_027911)	TTS (NM_027911)	301	NM_001039824	68165	Mm.490294	NM_001039824	ENSMUSG00000079677	Fdx1l	B230118G17Rik	ferredoxin 1-like	protein-coding	0.05	0.683168
Merged-chr2-89096540-1	chr2	89096490	89096590	+	2.6	cIP1vsInput	TTS (NM_146900)	TTS (NM_146900)	1423	NM_146900	258902	Mm.223312	NM_146900	ENSMUSG00000075103	Olfr1220	MOR2335	olfactory receptor 1220	protein-coding	0.01	0.346535
Merged-chr15-76504943-1	chr15	76504893	76504993	+	2.6	cIP1vsInput	"intron (NM_010046, intron 2 of 16)"	"intron (NM_010046, intron 2 of 16)"	6875	NM_010046	13350	Mm.22633	NM_010046	ENSMUSG00000022555	Dgat1	ARAT|C75990|D15Ertd23e|Dgat	diacylglycerol O-acyltransferase 1	protein-coding	0	0.465347
Merged-chr4-102935420-1	chr4	102935370	102935470	+	2.6	cIP2vsInput	"intron (NM_144906, intron 17 of 23)"	"intron (NM_144906, intron 17 of 23)"	-50959	NM_026100	67344	Mm.111346	NM_001163767	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding	0	0.316832
Merged-chr11-102040568-1	chr11	102040518	102040618	+	2.6	cIP2vsInput	promoter-TSS (NM_001160712)	promoter-TSS (NM_001160712)	-943	NM_001160711	52685	Mm.266885	NM_001160711	ENSMUSG00000017309	Cd300lg	2310016B05Rik|Clm9|D11Ertd736e	CD300 antigen like family member G	protein-coding	0.02	0.405941
Merged-chr10-97878185-1	chr10	97878135	97878235	+	2.6	cIP1vsInput	"intron (NR_033537, intron 2 of 4)"	"intron (NR_033537, intron 2 of 4)"	88905	NR_033537	100038699	Mm.467933	NR_033537		Gm10754	ENSMUSG00000074776	predicted gene 10754	miscRNA	0.02	0.386139
Merged-chr7-80232835-1	chr7	80232785	80232885	+	2.6	cIP1vsInput	promoter-TSS (NM_178752)	promoter-TSS (NM_178752)	-58	NM_178752	269952	Mm.187733	NM_178752	ENSMUSG00000050973	Gdpgp1	D330012F22Rik	GDP-D-glucose phosphorylase 1	protein-coding	0.13	0.742574
Merged-chr4-77781379-1	chr4	77781329	77781429	+	2.6	cIP2vsInput	"intron (NM_011211, intron 2 of 39)"	"intron (NM_011211, intron 2 of 39)"	430516	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0.01	0.316832
Merged-chr19-60974875-1	chr19	60974825	60974925	+	2.6	cIP2vsInput	"intron (NM_018869, intron 1 of 15)"	RMER17C-int|LTR|ERVK	85126	NM_018869	14773	Mm.279400	NM_018869	ENSMUSG00000003228	Grk5	Gprk5	G protein-coupled receptor kinase 5	protein-coding	0	0.435644
Merged-chr16-70567720-1	chr16	70567670	70567770	+	2.6	cIP1vsInput	"intron (NM_028803, intron 15 of 15)"	"intron (NM_028803, intron 15 of 15)"	-48705	NR_040474	52645	Mm.188475	NR_040474		D16Ertd519e	-	"DNA segment, Chr 16, ERATO Doi 519, expressed"	miscRNA	0.01	0.267327
Merged-chr4-49251777-1	chr4	49251727	49251827	+	2.6	cIP1vsInput	"intron (NM_178756, intron 2 of 7)"	"intron (NM_178756, intron 2 of 7)"	156374	NM_145368	209186	Mm.35071	NM_145368	ENSMUSG00000060317	Acnat2	C730036D15Rik	acyl-coenzyme A amino acid N-acyltransferase 2	protein-coding	0	0.386139
Merged-chr15-64808300-1	chr15	64808250	64808350	+	2.6	cIP2vsInput	"intron (NM_009623, intron 4 of 17)"	"intron (NM_009623, intron 4 of 17)"	113996	NM_009623	11514	Mm.1425	NM_009623	ENSMUSG00000022376	Adcy8	AC8|AW060868	adenylate cyclase 8	protein-coding	0	0.287129
Merged-chr8-68256863-1	chr8	68256813	68256913	+	2.6	cIP2vsInput	Intergenic	Intergenic	-19665	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding	0.01	0.376238
Merged-chr7-101822194-1	chr7	101822144	101822244	+	2.6	cIP1vsInput	TTS (NM_010567)	TTS (NM_010567)	3881	NM_008887	11859	Mm.5028	NM_008887		Phox2a	Arix|Phox2|Pmx2|Pmx2a	paired-like homeobox 2a	protein-coding	0.05	0.653465
Merged-chr4-22473019-1	chr4	22472969	22473069	+	2.6	cIP1vsInput	Intergenic	L1MA9|LINE|L1	15347	NM_008899	18992	Mm.487875	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	"POU domain, class 3, transcription factor 2"	protein-coding	0	0.306931
Merged-chr13-87540420-1	chr13	87540370	87540470	+	2.6	cIP1vsInput	Intergenic	ORR1B2-int|LTR|ERVL-MaLR	-1281052	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0.01	0.336634
Merged-chr7-18873642-1	chr7	18873592	18873692	+	2.6	cIP2vsInput	Intergenic	Intergenic	-11048	NM_009402	21946	Mm.21855	NM_009402	ENSMUSG00000030413	Pglyrp1	PGRP|PGRP-S|Pglyrp|Tag7|Tasg7|Tnfsf3l	peptidoglycan recognition protein 1	protein-coding	0.01	0.475248
Merged-chr14-123820784-1	chr14	123820734	123820834	+	2.6	cIP2vsInput	"intron (NM_145467, intron 2 of 10)"	"intron (NM_145467, intron 2 of 10)"	160644	NM_145467	223272	Mm.383176	NM_145467		Itgbl1	B930011D01Rik	"integrin, beta-like 1"	protein-coding	0	0.29703
Merged-chr6-87187120-1	chr6	87187070	87187170	+	2.6	cIP2vsInput	"intron (NM_054041, intron 16 of 17)"	"intron (NM_054041, intron 16 of 17)"	82374	NM_001167937	52372	Mm.282851	NM_001167937		D6Ertd527e	AU043841	"DNA segment, Chr 6, ERATO Doi 527, expressed"	protein-coding	0.05	0.554455
Merged-chr6-17047624-1	chr6	17047574	17047674	+	2.6	cIP2vsInput	Intergenic	URR1A|DNA|hAT-Charlie	-17525	NM_207176	21753	Mm.436548	NM_011570	ENSMUSG00000029552	Tes	D6Ertd352e|TESS|Tes1|Tes2|testin2	testis derived transcript	protein-coding	0	0.356436
Merged-chr2-65008946-1	chr2	65008896	65008996	+	2.6	cIP2vsInput	"intron (NM_016719, intron 2 of 13)"	"intron (NM_016719, intron 2 of 13)"	13820	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding	0	0.326733
Merged-chr17-60334815-1	chr17	60334765	60334865	+	2.6	cIP1vsInput	Intergenic	Intergenic	-982937	NR_030569	100124495		NR_030569		Mir466g	Mirn466g	microRNA 466g	miscRNA	0.01	0.346535
Merged-chr9-87599512-1	chr9	87599462	87599562	+	2.6	cIP1vsInput	Intergenic	Intergenic	131748	NM_023814	76365	Mm.158789	NM_023814	ENSMUSG00000032419	Tbx18	2810012F10Rik|2810404D13Rik	T-box18	protein-coding	0	0.287129
Merged-chr15-18235375-1	chr15	18235325	18235425	+	2.6	cIP2vsInput	"intron (NR_045711, intron 7 of 11)"	"intron (NR_045711, intron 7 of 11)"	134252	NR_045711	70886	Mm.399021	NR_045711		4921515E04Rik	-	RIKEN cDNA 4921515E04 gene	miscRNA	0	0.316832
Merged-chr2-174964929-1	chr2	174964879	174964979	+	2.6	cIP1vsInput	Intergenic	Intergenic	102834	NM_001085546	664987	Mm.452080	NM_001085546	ENSMUSG00000078905	Gm14393	OTTMUSG00000016546	predicted gene 14393	protein-coding	0	0.336634
Merged-chr8-4670842-1	chr8	4670792	4670892	+	2.6	cIP2vsInput	Intergenic	MurSatRep1|Unknown|Unknown	57672	NM_145591	233987	Mm.102799	NM_145591		Zfp958	-	zinc finger protein 958	protein-coding	0	0.346535
Merged-chr6-105350260-1	chr6	105350210	105350310	+	2.6	cIP1vsInput	Intergenic	Intergenic	142408	NR_040297	100503536	Mm.366960	NR_040297		Gm19757	-	"predicted gene, 19757"	miscRNA	0	0.287129
Merged-chr6-18819685-1	chr6	18819635	18819735	+	2.6	cIP2vsInput	Intergenic	Intergenic	-28950	NM_133939	76522	Mm.275158	NM_133939	ENSMUSG00000044155	Naa38	2010003I05Rik|AW214405|Lsm8	"N(alpha)-acetyltransferase 38, NatC auxiliary subunit"	protein-coding	0	0.287129
Merged-chr4-95703515-1	chr4	95703465	95703565	+	2.6	cIP2vsInput	"intron (NM_029347, intron 6 of 10)"	"intron (NM_029347, intron 6 of 10)"	124094	NM_029347	75578	Mm.276098	NM_001113412	ENSMUSG00000028573	Fggy	2310009E04Rik	FGGY carbohydrate kinase domain containing	protein-coding	0	0.346535
Merged-chr9-93092876-1	chr9	93092826	93092926	+	2.6	cIP2vsInput	Intergenic	L1MA4|LINE|L1	-87143	NR_040756	78349	Mm.52612	NR_040756		1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	miscRNA	0.01	0.346535
Merged-chr13-27181456-1	chr13	27181406	27181506	+	2.6	cIP1vsInput	Intergenic	Lx3A|LINE|L1	-15204	NM_013766	27372	Mm.291456	NM_013766	ENSMUSG00000017922	Prl3c1	PLP-J|Prlpi|Prlpj|decidualin	"prolactin family 3, subfamily c, member 1"	protein-coding	0	0.376238
Merged-chr11-13039574-1	chr11	13039524	13039624	+	2.6	cIP1vsInput	Intergenic	Intergenic	-574614	NM_172496	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	4732460E13|C530045F18Rik|mKIAA0633	cordon-bleu	protein-coding	0	0.306931
Merged-chr12-71157178-1	chr12	71157128	71157228	+	2.6	cIP1vsInput	"intron (NM_001163378, intron 9 of 29)"	"intron (NM_001163378, intron 9 of 29)"	20330	NM_001163378	76967	Mm.87290	NM_001163378	ENSMUSG00000034601	2700049A03Rik	Talpid3|mKIAA0586	RIKEN cDNA 2700049A03 gene	protein-coding	0	0.346535
Merged-chr16-69527326-1	chr16	69527276	69527376	+	2.6	cIP2vsInput	Intergenic	Intergenic	336418	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding	0	0.287129
Merged-chr6-113038320-1	chr6	113038270	113038370	+	2.6	cIP1vsInput	Intergenic	Intergenic	-8007	NM_008188	14911	Mm.781	NM_008188	ENSMUSG00000030264	Thumpd3	AW556087|Gt(ROSA)26asSor|Gtrosa26as	THUMP domain containing 3	protein-coding	0.02	0.336634
Merged-chr16-70760798-1	chr16	70760748	70760848	+	2.6	cIP1vsInput	Intergenic	Intergenic	144373	NR_040474	52645	Mm.188475	NR_040474		D16Ertd519e	-	"DNA segment, Chr 16, ERATO Doi 519, expressed"	miscRNA	0	0.316832
Merged-chr4-54567314-1	chr4	54567264	54567364	+	2.6	cIP1vsInput	Intergenic	Intergenic	-380631	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding	0	0.356436
Merged-chr3-83994377-1	chr3	83994327	83994427	+	2.6	cIP2vsInput	"intron (NM_172681, intron 3 of 34)"	"intron (NM_172681, intron 3 of 34)"	45784	NM_172681	229473	Mm.28838	NM_172681	ENSMUSG00000033767	D930015E06Rik	Kiaa0922|mKIAA0922	RIKEN cDNA D930015E06 gene	protein-coding	0.04	0.613861
Merged-chr9-52761535-1	chr9	52761485	52761585	+	2.6	cIP2vsInput	"intron (NR_045333, intron 2 of 4)"	"intron (NR_045333, intron 2 of 4)"	81672	NR_045333	382139	Mm.335162	NR_045333		Gm1715	-	predicted gene 1715	miscRNA	0.01	0.326733
Merged-chr5-116453613-1	chr5	116453563	116453663	+	2.6	cIP1vsInput	"exon (NM_026886, exon 9 of 13)"	"exon (NM_026886, exon 9 of 13)"	14891	NR_015595	76798	Mm.444322	NR_015595	ENSMUSG00000086219	2410137F16Rik	-	RIKEN cDNA 2410137F16 gene	miscRNA	0.13	0.712871
Merged-chr12-86957057-1	chr12	86957007	86957107	+	2.6	cIP1vsInput	"intron (NM_173735, intron 2 of 3)"	"intron (NM_173735, intron 2 of 3)"	9714	NM_173735	217732	Mm.22337	NM_173735	ENSMUSG00000034157	2310044G17Rik	AI842544|AI853744|Kiaa1737|mKIAA1737	RIKEN cDNA 2310044G17 gene	protein-coding	0	0.39604
Merged-chr14-102209291-1	chr14	102209241	102209341	+	2.6	cIP2vsInput	Intergenic	Intergenic	479363	NM_201529	380928		NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding	0	0.366337
Merged-chr5-98648783-1	chr5	98648733	98648833	+	2.6	cIP2vsInput	"intron (NM_001024614, intron 3 of 5)"	"intron (NM_001024614, intron 3 of 5)"	-173119	NR_030484	735265		NR_030484		Mir703	Mirn703|mmu-mir-703	microRNA 703	miscRNA	0	0.29703
Merged-chr1-68355110-1	chr1	68355060	68355160	+	2.6	cIP2vsInput	"intron (NM_010154, intron 5 of 26)"	"intron (NM_010154, intron 5 of 26)"	752949	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0.01	0.405941
Merged-chr14-31963677-1	chr14	31963627	31963727	+	2.6	cIP2vsInput	Intergenic	Intergenic	-65426	NM_030166	78754	Mm.40681	NM_030166		Galnt15	4631401E18Rik|Galntl2|mpp-GalNAc-T15	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15	protein-coding	0.01	0.524752
Merged-chr9-3343917-1	chr9	3343867	3343967	+	2.6	cIP1vsInput	"intron (NM_026303, intron 3 of 11)"	L1_Mur3|LINE|L1	8686	NM_026303	67667	Mm.440994	NM_026303		Alkbh8	4930562C03Rik|8030431D03Rik|9430088N01Rik|Abh8	"alkB, alkylation repair homolog 8 (E. coli)"	protein-coding	0	0.306931
Merged-chr13-93051956-1	chr13	93051906	93052006	+	2.6	cIP2vsInput	"intron (NM_023821, intron 9 of 12)"	"intron (NM_023821, intron 9 of 12)"	-21348	NR_036451	100502942	Mm.441946	NM_177623		Gm4814	C920025J10|EG218444	predicted gene 4814	miscRNA	0.02	0.39604
Merged-chr6-115808913-1	chr6	115808863	115808963	+	2.6	cIP1vsInput	promoter-TSS (NM_172086)	promoter-TSS (NM_172086)	-170	NM_172086	19951	Mm.104368	NM_172086	ENSMUSG00000057841	Rpl32	AU020185|rpL32-3A	ribosomal protein L32	protein-coding	0	0.306931
Merged-chr5-147697915-1	chr5	147697865	147697965	+	2.6	cIP1vsInput	"intron (NM_010228, intron 3 of 29)"	"intron (NM_010228, intron 3 of 29)"	28073	NM_010228	14254	Mm.389712	NM_010228	ENSMUSG00000029648	Flt1	AI323757|Flt-1|VEGFR-1|VEGFR1|sFlt1	FMS-like tyrosine kinase 1	protein-coding	0.02	0.425743
Merged-chr1-161195995-1	chr1	161195945	161196045	+	2.6	cIP2vsInput	Intergenic	Intergenic	-36681	NM_001195189	100502590	Mm.449990	NM_001195189		4930469G21Rik	-	RIKEN cDNA 4930469G21 gene	protein-coding	0.03	0.39604
Merged-chr10-16723712-1	chr10	16723662	16723762	+	2.6	cIP1vsInput	Intergenic	Intergenic	372070	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0	0.287129
Merged-chr11-64718856-1	chr11	64718806	64718906	+	2.6	cIP2vsInput	Intergenic	Intergenic	-260179	NM_023479	68626	Mm.157711	NM_023479	ENSMUSG00000020549	Elac2	1110017O07Rik|D11Wsu80e|Hpc2	elaC homolog 2 (E. coli)	protein-coding	0.01	0.50495
Merged-chr15-4148589-1	chr15	4148539	4148639	+	2.6	cIP2vsInput	"intron (NM_024188, intron 16 of 16)"	"intron (NM_024188, intron 16 of 16)"	-121183	NR_028266	414066	Mm.394461	NR_028266		BC037032	-	cDNA Sequence BC037032	miscRNA	0.02	0.346535
Merged-chr8-65497638-1	chr8	65497588	65497688	+	2.6	cIP2vsInput	Intergenic	Intergenic	-120402	NM_001166372	72925	Mm.380457	NM_001166372	ENSMUSG00000036469	1-Mar	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding	0	0.316832
Merged-chr12-116235266-1	chr12	116235216	116235316	+	2.6	cIP1vsInput	"intron (NM_146039, intron 8 of 21)"	"intron (NM_146039, intron 8 of 21)"	27759	NM_146039	217935	Mm.31382	NM_146039	ENSMUSG00000042050	Wdr60	D430033N04Rik	WD repeat domain 60	protein-coding	0	0.376238
Merged-chr8-66220297-1	chr8	66220247	66220347	+	2.6	cIP2vsInput	"intron (NM_001166372, intron 3 of 7)"	"intron (NM_001166372, intron 3 of 7)"	-166004	NM_001166375	72925	Mm.380457	NM_001166372	ENSMUSG00000036469	1-Mar	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding	0	0.316832
Merged-chr10-114325699-1	chr10	114325649	114325749	+	2.6	cIP1vsInput	Intergenic	L2|LINE|L2	475671	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding	0	0.346535
Merged-chr10-50106949-1	chr10	50106899	50106999	+	2.6	cIP1vsInput	Intergenic	Intergenic	-318195	NM_001111268	14806	Mm.332838	NM_001111268	ENSMUSG00000056073	Grik2	AW124492|GluK2|Glur-6|Glur6|Glurbeta2	"glutamate receptor, ionotropic, kainate 2 (beta 2)"	protein-coding	0	0.267327
Merged-chr18-38934930-1	chr18	38934880	38934980	+	2.6	cIP1vsInput	"intron (NM_001033789, intron 4 of 4)"	L1MEg|LINE|L1	-16231	NM_010197	14164	Mm.241282	NM_010197	ENSMUSG00000036585	Fgf1	Dffrx|Fam|Fgf-1|Fgfa	fibroblast growth factor 1	protein-coding	0	0.366337
Merged-chr6-51026870-1	chr6	51026820	51026920	+	2.6	cIP2vsInput	Intergenic	Intergenic	243040	NR_029719	387166		NR_029719	ENSMUSG00000065505	Mir148a	Mirn148|Mirn148a	microRNA 148a	miscRNA	0	0.306931
Merged-chr14-7766089-1	chr14	7766039	7766139	+	2.6	cIP1vsInput	Intergenic	Intergenic	-51868	NM_134080	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016	"filamin, beta"	protein-coding	0.04	0.683168
Merged-chr7-57434007-1	chr7	57433957	57434057	+	2.6	cIP2vsInput	"intron (NM_176942, intron 6 of 9)"	Lx7|LINE|L1	46735	NR_033504	791383	Mm.403104	NR_033504		Gm9962	ENSMUSG00000055048	predicted gene 9962	miscRNA	0	0.346535
Merged-chr16-78999570-1	chr16	78999520	78999620	+	2.6	cIP1vsInput	"intron (NM_178855, intron 18 of 26)"	"intron (NM_178855, intron 18 of 26)"	68622	NM_139134	246048	Mm.77895	NM_139134	ENSMUSG00000022860	Chodl	3110074E07Rik|MT75|PRED12	chondrolectin	protein-coding	0.01	0.277228
Merged-chr15-22412949-1	chr15	22412899	22412999	+	2.6	cIP2vsInput	Intergenic	Intergenic	302035	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding	0	0.316832
Merged-chr7-130547390-1	chr7	130547340	130547440	+	2.6	cIP2vsInput	promoter-TSS (NM_001162855)	promoter-TSS (NM_001162855)	-9	NM_001162855	67872	Mm.411879	NM_001162855	ENSMUSG00000040331	Nsmce4a	2410003A14Rik	non-SMC element 4 homolog A (S. cerevisiae)	protein-coding	0.13	0.742574
Merged-chr4-68368928-1	chr4	68368878	68368978	+	2.6	cIP1vsInput	Intergenic	Lx6|LINE|L1	585469	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Dbc1	BRINP|Brinp1|Dbccr1|Fam5a	deleted in bladder cancer 1 (human)	protein-coding	0.02	0.277228
Merged-chr2-87175933-1	chr2	87175883	87175983	+	2.6	cIP2vsInput	Intergenic	Lx5|LINE|L1	-15756	NM_146661	258655	Mm.377618	NM_146661	ENSMUSG00000044487	Olfr1112	MOR264-6	olfactory receptor 1112	protein-coding	0	0.346535
Merged-chr11-45955576-1	chr11	45955526	45955626	+	2.6	cIP1vsInput	promoter-TSS (NM_001080969)	promoter-TSS (NM_001080969)	-82	NM_001080969	66628	Mm.269083	NM_001080969		Thg1l	1700121M19Rik|5730409G07Rik|AA387658	tRNA-histidine guanylyltransferase 1-like (S. cerevisiae)	protein-coding	0.03	0.564356
Merged-chr14-89821054-1	chr14	89821004	89821104	+	2.6	cIP2vsInput	Intergenic	RMER4A|LTR|ERVK	-75170	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0.02	0.306931
Merged-chr17-46202878-1	chr17	46202828	46202928	+	2.6	cIP1vsInput	promoter-TSS (NM_030715)	promoter-TSS (NM_030715)	23	NM_028198	72322	Mm.275039	NM_028198	ENSMUSG00000067150	Xpo5	2410004H11Rik|2700038C24Rik|AI648907|AW549301|Exp5|RanBp21|mKIAA1291	exportin 5	protein-coding	0.12	0.693069
Merged-chr5-96652435-1	chr5	96652385	96652485	+	2.6	cIP1vsInput	"intron (NM_175473, intron 27 of 73)"	"intron (NM_175473, intron 27 of 73)"	-140950	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding	0.01	0.336634
Merged-chr14-101458649-1	chr14	101458599	101458699	+	2.6	cIP1vsInput	"intron (NM_001081278, intron 13 of 18)"	"intron (NM_001081278, intron 13 of 18)"	150542	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	"TBC1 domain family, member 4"	protein-coding	0	0.356436
Merged-chr1-9023222-1	chr1	9023172	9023272	+	2.6	cIP2vsInput	"intron (NM_027671, intron 2 of 20)"	"intron (NM_027671, intron 2 of 20)"	276508	NM_027671	71096	Mm.388998	NM_027671		Sntg1	4933426D16Rik|G1SYN|SYN4	"syntrophin, gamma 1"	protein-coding	0	0.356436
Merged-chr5-54992012-1	chr5	54991962	54992062	+	2.6	cIP1vsInput	Intergenic	Lx4A|LINE|L1	642020	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0	0.29703
Merged-chr10-58549098-1	chr10	58549048	58549148	+	2.6	cIP1vsInput	"intron (NM_001162956, intron 13 of 15)"	URR1A|DNA|hAT-Charlie	51161	NM_001162956	76138	Mm.211744	NM_001162956	ENSMUSG00000038010	Ccdc138	6230424H07Rik|BC042726	coiled-coil domain containing 138	protein-coding	0.01	0.366337
Merged-chr12-83633442-1	chr12	83633392	83633492	+	2.6	cIP1vsInput	"intron (NM_027349, intron 1 of 18)"	"intron (NM_027349, intron 1 of 18)"	1208	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding	0.01	0.376238
Merged-chr7-105581256-1	chr7	105581206	105581306	+	2.6	cIP2vsInput	"5' UTR (NM_001253885, exon 1 of 14)"	"5' UTR (NM_001253885, exon 1 of 14)"	235	NM_001253885	11785	Mm.490092	NM_001253885	ENSMUSG00000037032	Apbb1	Fe65|Rir	"amyloid beta (A4) precursor protein-binding, family B, member 1"	protein-coding	0.15	0.782178
Merged-chr1-68581200-1	chr1	68581150	68581250	+	2.6	cIP2vsInput	"intron (NM_010154, intron 2 of 26)"	"intron (NM_010154, intron 2 of 26)"	526859	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0	0.287129
Merged-chr13-77084247-1	chr13	77084197	77084297	+	2.6	cIP1vsInput	"intron (NM_134071, intron 13 of 20)"	"intron (NM_134071, intron 13 of 20)"	51221	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Ankrd32	2700017A04Rik|AW545819|Brctd1|Brctx|C730024G01Rik	ankyrin repeat domain 32	protein-coding	0	0.306931
Merged-chr11-44507657-1	chr11	44507607	44507707	+	2.6	cIP2vsInput	Intergenic	Intergenic	-11307	NM_028862	74315	Mm.156771	NM_001166553	ENSMUSG00000019189	Rnf145	3732413I11Rik|TMRF1	ring finger protein 145	protein-coding	0.01	0.386139
Merged-chr14-90634461-1	chr14	90634411	90634511	+	2.6	cIP1vsInput	Intergenic	MIR3|SINE|MIR	507570	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0	0.316832
Merged-chr8-33533270-1	chr8	33533220	33533320	+	2.6	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-37274	NM_031374	104271	Mm.488030	NM_031374	ENSMUSG00000009628	Tex15	2210014E14Rik|AL022622|AU022940	testis expressed gene 15	protein-coding	0	0.277228
Merged-chr1-112261046-1	chr1	112260996	112261096	+	2.6	cIP2vsInput	Intergenic	MT2B1|LTR|ERVL	-396128	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik	dermatan sulfate epimerase-like	protein-coding	0	0.326733
Merged-chr14-91728646-1	chr14	91728596	91728696	+	2.6	cIP1vsInput	Intergenic	Lx7|LINE|L1	1601755	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0	0.306931
Merged-chr6-108292058-1	chr6	108292008	108292108	+	2.6	cIP2vsInput	"intron (NM_010585, intron 4 of 61)"	"intron (NM_010585, intron 4 of 61)"	78962	NM_010585	16438	Mm.227912	NM_010585	ENSMUSG00000030102	Itpr1	D6Pas2|ENSMUSG00000072853|Gm10429|IP3R1|InsP3R|Ip3r|Itpr-1|P400|Pcp-1|Pcp1|opt	"inositol 1,4,5-trisphosphate receptor 1"	protein-coding	0.01	0.306931
Merged-chr15-22777383-1	chr15	22777333	22777433	+	2.6	cIP2vsInput	Intergenic	Intergenic	-62399	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding	0.01	0.336634
Merged-chr8-99868612-1	chr8	99868562	99868662	+	2.6	cIP2vsInput	Intergenic	Intergenic	-452155	NM_001039154	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0.01	0.267327
Merged-chr14-124411324-1	chr14	124411274	124411374	+	2.6	cIP1vsInput	"intron (NM_207667, intron 1 of 4)"	"intron (NM_207667, intron 1 of 4)"	-218778	NM_010201	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding	0.01	0.326733
Merged-chr16-52790971-1	chr16	52790921	52791021	+	2.6	cIP2vsInput	Intergenic	L1M4|LINE|L1	24773	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	miscRNA	0.01	0.326733
Merged-chr7-126428795-1	chr7	126428745	126428845	+	2.6	cIP2vsInput	promoter-TSS (NM_030566)	promoter-TSS (NM_030566)	28	NM_030566	70314	Mm.35467	NM_030566	ENSMUSG00000030727	Rabep2	2610011A08Rik|AI462746|Fra	"rabaptin, RAB GTPase binding effector protein 2"	protein-coding	0.1	0.70297
Merged-chr12-82487420-1	chr12	82487370	82487470	+	2.6	cIP2vsInput	Intergenic	B4|SINE|B4	-129618	NM_015812	50779	Mm.153013	NM_015812		Rgs6	-	regulator of G-protein signaling 6	protein-coding	0	0.584158
Merged-chr9-66295078-1	chr9	66295028	66295128	+	2.6	cIP2vsInput	Intergenic	Intergenic	-55372	NM_145617	235439	Mm.244179	NM_145617	ENSMUSG00000038664	Herc1	2810449H11Rik|B230218H07|D130015N03Rik|tbl	hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1	protein-coding	0.01	0.524752
Merged-chr5-63066361-1	chr5	63066311	63066411	+	2.6	cIP1vsInput	Intergenic	Lx9|LINE|L1	252538	NM_001170705	100322896	Mm.479821	NM_001170705	ENSMUSG00000090326	Gm17384	Dthd1	"predicted gene, 17384"	protein-coding	0	0.326733
Merged-chr16-68356315-1	chr16	68356265	68356365	+	2.6	cIP1vsInput	Intergenic	Intergenic	-735407	NM_178721	239857	Mm.394300	NM_001145977	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0	0.346535
Merged-chr4-94148361-1	chr4	94148311	94148411	+	2.6	cIP2vsInput	Intergenic	Intergenic	408435	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0	0.306931
Merged-chr1-90603397-1	chr1	90603347	90603447	+	2.6	cIP2vsInput	promoter-TSS (NM_133805)	promoter-TSS (NM_133805)	-28	NM_133805	108679	Mm.119177	NM_133805	ENSMUSG00000034432	Cops8	9430009J09Rik|AA408242|Csn8|Sgn8	"COP9 (constitutive photomorphogenic) homolog, subunit 8 (Arabidopsis thaliana)"	protein-coding	0.15	0.693069
Merged-chr19-26921458-1	chr19	26921408	26921508	+	2.6	cIP1vsInput	Intergenic	MYSERV-int|LTR|ERVK	35533	NM_001033407	329047	Mm.293289	NM_001033407	ENSMUSG00000074913	Gm815	-	predicted gene 815	protein-coding	0	0.356436
Merged-chr2-7056515-1	chr2	7056465	7056565	+	2.6	cIP1vsInput	"intron (NM_001110232, intron 2 of 15)"	"intron (NM_001110232, intron 2 of 15)"	24787	NM_001110230	14007	Mm.398543	NM_183219	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	"CUGBP, Elav-like family member 2"	protein-coding	0	0.356436
Merged-chr13-52079483-1	chr13	52079433	52079533	+	2.6	cIP1vsInput	Intergenic	Intergenic	-17258	NR_045061	74050	Mm.84860	NR_045061		4921525O09Rik	-	RIKEN cDNA 4921525O09 gene	miscRNA	0.02	0.445545
Merged-chr13-8516894-1	chr13	8516844	8516944	+	2.6	cIP2vsInput	"intron (NM_052977, intron 1 of 9)"	L1MD1|LINE|L1	313985	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	"adenosine deaminase, RNA-specific, B2"	protein-coding	0	0.366337
Merged-chr8-71831240-1	chr8	71831190	71831290	+	2.6	cIP1vsInput	Intergenic	Intergenic	-50828	NM_145624	236193	Mm.290790	NM_145624		Zfp709	BC021921|GIOT-4|HIT-40	zinc finger protein 709	protein-coding	0	0.237624
Merged-chr14-77054005-1	chr14	77053955	77054055	+	2.6	cIP2vsInput	"intron (NM_175369, intron 1 of 5)"	"intron (NM_175369, intron 1 of 5)"	17233	NM_175369	108811	Mm.102168	NM_175369	ENSMUSG00000034795	Ccdc122	4933415L06Rik	coiled-coil domain containing 122	protein-coding	0	0.376238
Merged-chr12-89868312-1	chr12	89868262	89868362	+	2.6	cIP2vsInput	"intron (NM_001252074, intron 1 of 6)"	MLT1B|LTR|ERVL-MaLR	55829	NM_001252074	18191	Mm.487864	NM_001198587	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding	0	0.287129
Merged-chr7-79721868-1	chr7	79721818	79721918	+	2.6	cIP2vsInput	"intron (NM_001113471, intron 8 of 8)"	"intron (NM_001113471, intron 8 of 8)"	-7682	NM_010626	16576	Mm.101633	NM_010626	ENSMUSG00000050382	Kif7	-	kinesin family member 7	protein-coding	0.04	0.623762
Merged-chr11-35283306-1	chr11	35283256	35283356	+	2.6	cIP2vsInput	"intron (NM_011412, intron 4 of 35)"	"intron (NM_011412, intron 4 of 35)"	161850	NM_011412	20564	Mm.478604	NM_011412	ENSMUSG00000056427	Slit3	Slil2|Slit1	slit homolog 3 (Drosophila)	protein-coding	0.02	0.564356
Merged-chr3-21241809-1	chr3	21241759	21241859	+	2.6	cIP1vsInput	Intergenic	Intergenic	-834843	NM_030732	81004	Mm.446265	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding	0	0.415842
Merged-chr14-69805466-1	chr14	69805416	69805516	+	2.6	cIP2vsInput	promoter-TSS (NM_153514)	promoter-TSS (NM_153514)	79	NM_153514	246710	Mm.102367	NM_153514	ENSMUSG00000022075	Rhobtb2	Dbc2|E130206H14Rik|mKIAA0717	Rho-related BTB domain containing 2	protein-coding	0.19	0.762376
Merged-chr12-85280639-1	chr12	85280589	85280689	+	2.6	cIP2vsInput	promoter-TSS (NM_025421)	promoter-TSS (NM_025421)	-204	NM_025421	66204	Mm.311985	NM_025421	ENSMUSG00000008822	Acyp1	1110039O14Rik|AI325944	"acylphosphatase 1, erythrocyte (common) type"	protein-coding	0.02	0.455446
Merged-chr9-21901594-1	chr9	21901544	21901644	+	2.6	cIP2vsInput	Intergenic	Intergenic	16527	NM_031874	19340	Mm.260157	NM_031874	ENSMUSG00000019066	Rab3d	C130057E11Rik	"RAB3D, member RAS oncogene family"	protein-coding	0.03	0.435644
Merged-chr14-110487097-1	chr14	110487047	110487147	+	2.6	cIP1vsInput	Intergenic	Intergenic	268052	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	"SLIT and NTRK-like family, member 6"	protein-coding	0	0.346535
Merged-chr5-114707745-1	chr5	114707695	114707795	+	2.6	cIP2vsInput	promoter-TSS (NM_029992)	promoter-TSS (NM_029992)	-34	NM_029992	77832	Mm.239698	NM_029992	ENSMUSG00000002486	Tchp	A930031F18Rik|AV279199	"trichoplein, keratin filament binding"	protein-coding	0.08	0.594059
Merged-chr5-65020626-1	chr5	65020576	65020676	+	2.6	cIP2vsInput	"intron (NM_026667, intron 7 of 13)"	URR1A|DNA|hAT-Charlie	50308	NR_030577	100124451		NR_030577	ENSMUSG00000077042	Mir574	Mirn574|mmu-mir-574	microRNA 574	miscRNA	0	0.356436
Merged-chr1-55346382-1	chr1	55346332	55346432	+	2.6	cIP2vsInput	"exon (NM_029267, exon 5 of 10)"	"exon (NM_029267, exon 5 of 10)"	16325	NM_001113367	75388	Mm.483408	NM_001113367	ENSMUSG00000025977	Boll	4930554P13Rik|4930597B14Rik	"bol, boule-like (Drosophila)"	protein-coding	0.01	0.346535
Merged-chr2-134383440-1	chr2	134383390	134383490	+	2.6	cIP2vsInput	Intergenic	Intergenic	170912	NM_010403	15112	Mm.26634	NM_010403	ENSMUSG00000027261	Hao1	GOX|Gox1|Hao-1	"hydroxyacid oxidase 1, liver"	protein-coding	0	0.326733
Merged-chr11-61366603-1	chr11	61366553	61366653	+	2.6	cIP2vsInput	"intron (NM_026183, intron 6 of 16)"	"intron (NM_026183, intron 6 of 16)"	11472	NM_026183	67473	Mm.100741	NM_026183	ENSMUSG00000010122	Slc47a1	1300013J15Rik|AI036982|MATE1|mMATE1	"solute carrier family 47, member 1"	protein-coding	0.02	0.60396
Merged-chr4-148558615-1	chr4	148558565	148558665	+	2.6	cIP2vsInput	TTS (NM_020009)	TTS (NM_020009)	188	NM_016699	50912	Mm.266635	NM_016699	ENSMUSG00000017264	Exosc10	PM-Scl|PM/Scl-100|Pmscl2|RRP6|p2|p3|p4	exosome component 10	protein-coding	0.09	0.683168
Merged-chr10-81105804-1	chr10	81105754	81105854	+	2.6	cIP2vsInput	promoter-TSS (NM_023138)	promoter-TSS (NM_023138)	-143	NM_023138	26396	Mm.275436	NM_023138	ENSMUSG00000035027	Map2k2	AA589381|MEK2|MK2|Prkmk2	mitogen-activated protein kinase kinase 2	protein-coding	0.11	0.60396
Merged-chr4-33396820-1	chr4	33396770	33396870	+	2.6	cIP1vsInput	"intron (NM_011884, intron 12 of 15)"	"intron (NM_011884, intron 12 of 15)"	86509	NM_011884	24018	Mm.464346	NM_011884	ENSMUSG00000028274	Rngtt	AU020997	RNA guanylyltransferase and 5'-phosphatase	protein-coding	0	0.316832
Merged-chr17-87398457-1	chr17	87398407	87398507	+	2.6	cIP1vsInput	"intron (NM_029298, intron 5 of 6)"	MTC-int|LTR|ERVL-MaLR	29284	NM_029298	75467	Mm.50108	NM_029298	ENSMUSG00000036557	1700011E24Rik	-	RIKEN cDNA 1700011E24 gene	protein-coding	0	0.257426
Merged-chr4-96283378-1	chr4	96283328	96283428	+	2.6	cIP2vsInput	Intergenic	ETnERV2-int|LTR|ERVK	65302	NM_001004141	100066	Mm.26915	NM_001004141	ENSMUSG00000066097	Cyp2j11	AI314783|Cyp2j11-ps	"cytochrome P450, family 2, subfamily j, polypeptide 11"	protein-coding	0.02	0.326733
Merged-chr19-55305297-1	chr19	55305247	55305347	+	2.6	cIP1vsInput	"intron (NM_001033573, intron 6 of 10)"	"intron (NM_001033573, intron 6 of 10)"	10735	NM_025883	66980	Mm.386789	NM_001033573	ENSMUSG00000024982	Zdhhc6	2400007G07Rik|5930409M18Rik|AI462345|C77369	"zinc finger, DHHC domain containing 6"	protein-coding	0	0.267327
Merged-chr4-94683111-1	chr4	94683061	94683161	+	2.6	cIP2vsInput	"intron (NM_026319, intron 16 of 19)"	"intron (NM_026319, intron 16 of 19)"	17954	NR_030604	100124456		NR_030604		Mir872	Mirn872|mmu-mir-872	microRNA 872	miscRNA	0.02	0.405941
Merged-chr15-50581381-1	chr15	50581331	50581431	+	2.6	cIP2vsInput	Intergenic	Intergenic	307733	NR_035444	100316685		NR_035444	ENSMUSG00000084458	Mir1907	Mirn1907|mmu-mir-1907	microRNA 1907	miscRNA	0.01	0.326733
Merged-chr3-81560494-1	chr3	81560444	81560544	+	2.6	cIP1vsInput	Intergenic	BLACKJACK|DNA|hAT-Blackjack	-372122	NM_177662	229445	Mm.254642	NM_177662	ENSMUSG00000028015	Ctso	A330105D01Rik|A430056C07|AI118514	cathepsin O	protein-coding	0	0.277228
Merged-chr10-80039684-1	chr10	80039634	80039734	+	2.6	cIP2vsInput	promoter-TSS (NM_025554)	promoter-TSS (NM_025554)	-25	NM_025554	66420	Mm.18579	NM_025554	ENSMUSG00000004667	Polr2e	2410021N14Rik|25kDa|AW208866|RPB5|XAP4	polymerase (RNA) II (DNA directed) polypeptide E	protein-coding	0.12	0.70297
Merged-chr7-12477746-1	chr7	12477696	12477796	+	2.6	cIP1vsInput	promoter-TSS (NM_026112)	promoter-TSS (NM_026112)	-559	NM_001039951	67370	Mm.98929	NM_001039951	ENSMUSG00000030386	Zfp606	2410022M24Rik|AW494727	zinc finger protein 606	protein-coding	0.01	0.306931
Merged-chr6-106778878-1	chr6	106778828	106778928	+	2.6	cIP2vsInput	"exon (NM_027296, exon 7 of 9)"	"exon (NM_027296, exon 7 of 9)"	9740	NM_001242358	70047	Mm.196332	NM_001242358	ENSMUSG00000013736	Trnt1	2410043H24Rik|2610044E04Rik|9830143O18Rik|AA408384|C76540|CGI-47|mt-Trat	"tRNA nucleotidyl transferase, CCA-adding, 1"	protein-coding	0	0.326733
Merged-chr2-83812594-1	chr2	83812544	83812644	+	2.6	cIP2vsInput	promoter-TSS (NM_175514)	promoter-TSS (NM_175514)	-134	NM_175514	241520	Mm.436122	NM_175514		Fam171b	D430039N05Rik	"family with sequence similarity 171, member B"	protein-coding	0.13	0.732673
Merged-chr8-77630334-1	chr8	77630284	77630384	+	2.6	cIP2vsInput	Intergenic	Intergenic	6162	NR_045467	67357	Mm.71129	NR_045467	ENSMUSG00000086781	1700092C02Rik	-	RIKEN cDNA 1700092C02 gene	miscRNA	0.08	0.60396
Merged-chr1-192834969-1	chr1	192834919	192835019	+	2.6	cIP2vsInput	Intergenic	CpG	-6736	NR_040468	73455	Mm.414869	NR_040468		1700065J18Rik	-	RIKEN cDNA 1700065J18 gene	miscRNA	0.1	0.693069
Merged-chr1-145421896-1	chr1	145421846	145421946	+	2.6	cIP1vsInput	Intergenic	Intergenic	-646475	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding	0	0.346535
Merged-chr2-127801322-1	chr2	127801272	127801372	+	2.6	cIP2vsInput	"exon (NM_001113179, exon 25 of 25)"	"exon (NM_001113179, exon 25 of 25)"	-8834	NR_015476	67885	Mm.27359	NM_175125	ENSMUSG00000051319	1500011K16Rik	-	RIKEN cDNA 1500011K16 gene	miscRNA	0.01	0.346535
Merged-chr17-24736370-1	chr17	24736320	24736420	+	2.6	cIP2vsInput	promoter-TSS (NM_013759)	promoter-TSS (NM_013759)	-272	NM_013759	27361	Mm.28212	NM_013759	ENSMUSG00000075705	Msrb1	D17Wsu82e|SELX|SelR|Sepr|Sepx1	methionine sulfoxide reductase B1	protein-coding	0.01	0.445545
Merged-chr4-125814512-1	chr4	125814462	125814562	+	2.6	cIP2vsInput	Intergenic	Intergenic	107798	NR_015560	72395	Mm.112888	NR_015560	ENSMUSG00000085562	2610028E06Rik	BB043107	RIKEN cDNA 2610028E06 gene	miscRNA	0.09	0.653465
Merged-chr17-80767029-1	chr17	80766979	80767079	+	2.6	cIP2vsInput	Intergenic	Intergenic	-38936	NM_001081357	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding	0.01	0.366337
Merged-chr10-55729204-1	chr10	55729154	55729254	+	2.6	cIP1vsInput	Intergenic	Intergenic	-377713	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding	0	0.287129
Merged-chr11-106246298-1	chr11	106246248	106246348	+	2.6	cIP2vsInput	"intron (NM_028074, intron 16 of 17)"	"intron (NM_028074, intron 16 of 17)"	9504	NM_025310	56095	Mm.29795	NM_025310	ENSMUSG00000020706	Ftsj3	AA537063|AU045295|C79843|D11Ertd400e|Epcs3	FtsJ homolog 3 (E. coli)	protein-coding	0.01	0.336634
Merged-chr15-56252099-1	chr15	56252049	56252149	+	2.6	cIP1vsInput	Intergenic	Intergenic	-345150	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	"syntrophin, basic 1"	protein-coding	0	0.247525
Merged-chr18-51373122-1	chr18	51373072	51373172	+	2.6	cIP1vsInput	Intergenic	L1M8|LINE|L1	255224	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding	0	0.346535
Merged-chr6-143313852-1	chr6	143313802	143313902	+	2.6	cIP2vsInput	Intergenic	Intergenic	67964	NR_027803	52285	Mm.354898	NM_001033129		D6Ertd474e	1700001I24Rik|AU023129	"DNA segment, Chr 6, ERATO Doi 474, expressed"	miscRNA	0	0.376238
Merged-chr11-44723184-1	chr11	44723134	44723234	+	2.6	cIP2vsInput	"intron (NM_007897, intron 6 of 15)"	"intron (NM_007897, intron 6 of 15)"	105050	NM_007897	13591	Mm.440346	NM_007897		Ebf1	9830166E18Rik|AW990631|Ebf|O/E-1|Olf-1|Olf1	early B cell factor 1	protein-coding	0	0.346535
Merged-chr4-30899571-1	chr4	30899521	30899621	+	2.6	cIP1vsInput	Intergenic	Intergenic	234975	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	miscRNA	0.01	0.336634
Merged-chr19-43832606-1	chr19	43832556	43832656	+	2.6	cIP1vsInput	"intron (NM_013806, intron 29 of 31)"	"intron (NM_013806, intron 29 of 31)"	-6197	NR_033472	100038628	Mm.212585	NR_033472	ENSMUSG00000074828	Gm10768	ENSMUSG00000074828	predicted gene 10768	miscRNA	0.05	0.554455
Merged-chr6-105192721-1	chr6	105192671	105192771	+	2.6	cIP1vsInput	Intergenic	Intergenic	299947	NR_040297	100503536	Mm.366960	NR_040297		Gm19757	-	"predicted gene, 19757"	miscRNA	0	0.316832
Merged-chr5-131250904-1	chr5	131250854	131250954	+	2.6	cIP2vsInput	"intron (NM_145218, intron 1 of 10)"	MER58B|DNA|hAT-Charlie	56618	NM_145218	212996	Mm.299204	NM_145218		Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding	0.01	0.455446
Merged-chr4-147674535-1	chr4	147674485	147674585	+	2.6	cIP1vsInput	"exon (NM_001127188, exon 4 of 4)"	"exon (NM_001127188, exon 4 of 4)"	28018	NM_001127188	100503584	Mm.327194	XM_003945679	ENSMUSG00000062518	Zfp534	Gm13159|OTTMUSG00000010681|Rp23-282c23.3	zinc finger protein 534	protein-coding	0	0.336634
Merged-chr4-147804852-1	chr4	147804802	147804902	+	2.6	cIP1vsInput	"intron (NM_001127189, intron 2 of 5)"	"intron (NM_001127189, intron 2 of 5)"	4936	NM_001127189	100041677	Mm.327194	NM_001127189	ENSMUSG00000078495	Gm13157	OTTMUSG00000010679|Rp23-282c23.7	predicted gene 13157	protein-coding	0.01	0.326733
Merged-chr1-85704327-1	chr1	85704277	85704377	+	2.6	cIP2vsInput	"intron (NM_013673, intron 17 of 19)"	"intron (NM_013673, intron 17 of 19)"	32279	NM_177055	319997	Mm.116691	NM_177055		A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding	0	0.326733
Merged-chr16-67681485-1	chr16	67681435	67681535	+	2.6	cIP2vsInput	Intergenic	Intergenic	-60577	NM_178721	239857	Mm.394300	NM_001145977	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0.02	0.346535
Merged-chr18-67391498-1	chr18	67391448	67391548	+	2.6	cIP2vsInput	"intron (NM_026473, intron 2 of 3)"	CpG-7052	767	NM_026473	67951	Mm.181860	NM_026473	ENSMUSG00000001473	Tubb6	2310057H16Rik|BB220206	"tubulin, beta 6 class V"	protein-coding	0.09	0.722772
Merged-chr12-97450158-1	chr12	97450108	97450208	+	2.6	cIP1vsInput	Intergenic	RLTR19-int|LTR|ERVK	809179	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding	0	0.376238
Merged-chr16-82323604-1	chr16	82323554	82323654	+	2.6	cIP2vsInput	Intergenic	Intergenic	1122907	NM_010954	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.326733
Merged-chr7-27804186-1	chr7	27804136	27804236	+	2.6	cIP2vsInput	Intergenic	Intergenic	-34398	NM_011762	22717	Mm.379046	NM_011762		Zfp59	Mfg-2|Mfg2	zinc finger protein 59	protein-coding	0	0.306931
Merged-chr17-22845088-1	chr17	22845038	22845138	+	2.6	cIP1vsInput	Intergenic	Intergenic	22046	NM_177358	240041	Mm.328828	NM_001110254	ENSMUSG00000059142	Zfp945	A630033E08Rik|C730040L01Rik	zinc finger protein 945	protein-coding	0	0.405941
Merged-chr4-38545040-1	chr4	38544990	38545090	+	2.6	cIP2vsInput	Intergenic	Intergenic	-905253	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding	0	0.306931
Merged-chr1-177400137-1	chr1	177400087	177400187	+	2.6	cIP1vsInput	Intergenic	Intergenic	-44524	NM_001012330	30928	Mm.330700	NM_001012330	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding	0	0.356436
Merged-chr3-43756913-1	chr3	43756863	43756963	+	2.6	cIP1vsInput	Intergenic	Intergenic	1621347	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	miscRNA	0	0.277228
Merged-chr2-52083290-1	chr2	52083240	52083340	+	2.6	cIP1vsInput	"intron (NM_175238, intron 9 of 35)"	"intron (NM_175238, intron 9 of 35)"	10453	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	Rap1 interacting factor 1 homolog (yeast)	protein-coding	0	0.316832
Merged-chr2-77342395-1	chr2	77342345	77342445	+	2.6	cIP2vsInput	Intergenic	Intergenic	-61803	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding	0.01	0.326733
Merged-chr9-12774995-1	chr9	12774945	12775045	+	2.6	cIP2vsInput	Intergenic	Intergenic	330860	NR_040755	78219	Mm.414868	NR_040755		4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	miscRNA	0	0.336634
Merged-chr1-69255484-1	chr1	69255434	69255534	+	2.6	cIP1vsInput	Intergenic	Intergenic	-147425	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0.01	0.316832
Merged-chr15-19877634-1	chr15	19877584	19877684	+	2.6	cIP2vsInput	Intergenic	Intergenic	789116	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding	0	0.326733
Merged-chr15-101327451-1	chr15	101327401	101327501	+	2.6	cIP2vsInput	Intergenic	Intergenic	34239	NR_033803	77717	Mm.391998	NR_033803		6030408B16Rik	AI225877	RIKEN cDNA 6030408B16 gene	miscRNA	0.04	0.60396
Merged-chr8-73048797-1	chr8	73048747	73048847	+	2.6	cIP1vsInput	"intron (NM_010687, intron 5 of 14)"	"intron (NM_010687, intron 5 of 14)"	32285	NR_039551	100628574		NR_039551	ENSMUSG00000093140	Mir28b	mmu-mir-28b	microRNA 28b	miscRNA	0	0.336634
Merged-chr15-96489505-1	chr15	96489455	96489555	+	2.6	cIP2vsInput	Intergenic	Intergenic	-28662	NM_028148	72193	Mm.472183	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding	0.02	0.435644
Merged-chr10-30825158-1	chr10	30825108	30825208	+	2.6	cIP2vsInput	Intergenic	Intergenic	17625	NM_013904	15214	Mm.103573	NM_013904	ENSMUSG00000019789	Hey2	CHF1|Herp1|Hrt2|bHLHb32|hesr2	hairy/enhancer-of-split related with YRPW motif 2	protein-coding	0	0.346535
Merged-chr1-153402040-1	chr1	153401990	153402090	+	2.6	cIP2vsInput	Intergenic	Intergenic	12193	NR_033736	626058	Mm.31556	NM_001177359		E330020D12Rik	EG626058|F430003O07Rik|Gm6648	Riken cDNA E330020D12 gene	miscRNA	0.03	0.514851
Merged-chr1-135524054-1	chr1	135524004	135524104	+	2.6	cIP2vsInput	"intron (NM_173437, intron 3 of 28)"	"intron (NM_173437, intron 3 of 28)"	61301	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding	0.03	0.594059
Merged-chr11-6447999-1	chr11	6447949	6448049	+	2.6	cIP1vsInput	Intergenic	L1M4|LINE|L1	-3556	NM_029938	77605	Mm.27624	NM_029938	ENSMUSG00000041126	H2afv	C530002L11Rik|H2av	"H2A histone family, member V"	protein-coding	0	0.326733
Merged-chr10-61626327-1	chr10	61626277	61626377	+	2.6	cIP1vsInput	TTS (NM_001177511)	TTS (NM_001177511)	-22294	NM_026438	67895	Mm.28897	NM_026438	ENSMUSG00000020089	Ppa1	2010317E03Rik|Pyp	pyrophosphatase (inorganic) 1	protein-coding	0.04	0.663366
Merged-chr11-102547136-1	chr11	102547086	102547186	+	2.6	cIP2vsInput	"intron (NM_001159492, intron 1 of 7)"	"intron (NM_001159492, intron 1 of 7)"	9022	NM_001159492	237943	Mm.260282	NM_001159492	ENSMUSG00000034621	Gpatch8	5430405G24Rik|AU018890|ENSMUSG00000075516|Fbm1|Gpatc8|mKIAA0553	G patch domain containing 8	protein-coding	0	0.346535
Merged-chr9-91451050-1	chr9	91451000	91451100	+	2.6	cIP1vsInput	Intergenic	Intergenic	82078	NM_009576	22774	Mm.434835	NM_009576		Zic4	-	zinc finger protein of the cerebellum 4	protein-coding	0	0.356436
Merged-chr12-40837550-1	chr12	40837500	40837600	+	2.6	cIP1vsInput	"intron (NM_172803, intron 50 of 52)"	"intron (NM_172803, intron 50 of 52)"	391497	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding	0	0.356436
Merged-chr9-91083082-1	chr9	91083032	91083132	+	2.6	cIP2vsInput	Intergenic	Intergenic	282717	NM_009573	22771	Mm.477226	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding	0.01	0.336634
Merged-chr9-62174989-1	chr9	62174939	62175039	+	2.6	cIP1vsInput	Intergenic	Intergenic	-52395	NR_039595	100628602		NR_039595	ENSMUSG00000092696	Mir5133	mmu-mir-5133|mu-mir-5133	microRNA 5133	miscRNA	0.01	0.376238
Merged-chr18-79015150-1	chr18	79015100	79015200	+	2.6	cIP2vsInput	"intron (NM_053099, intron 2 of 5)"	"intron (NM_053099, intron 2 of 5)"	94241	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding	0	0.415842
Merged-chr11-107012980-1	chr11	107012930	107013030	+	2.6	cIP2vsInput	Intergenic	Intergenic	-13455	NM_010655	16647	Mm.423000	NM_010655	ENSMUSG00000018362	Kpna2	2410044B12Rik|IPOA1|PTAC58|Rch1	karyopherin (importin) alpha 2	protein-coding	0.04	0.356436
Merged-chr5-71796258-1	chr5	71796208	71796308	+	2.6	cIP2vsInput	"intron (NM_008069, intron 3 of 8)"	"intron (NM_008069, intron 3 of 8)"	96242	NM_008069	14400	Mm.38567	NM_008069		Gabrb1	AW061132|B230208N19Rik|Gabrb-1	"gamma-aminobutyric acid (GABA) A receptor, subunit beta 1"	protein-coding	0	0.29703
Merged-chr2-98893277-1	chr2	98893227	98893327	+	2.6	cIP1vsInput	Intergenic	Intergenic	1425603	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0.02	0.306931
Merged-chr13-90198873-1	chr13	90198823	90198923	+	2.6	cIP1vsInput	Intergenic	ETnERV2-int|LTR|ERVK	109206	NM_025335	66074	Mm.241387	NM_025335		Tmem167	0610041E09Rik|5730424F14Rik|AU041184|AW537806|ENSMUSG00000060669|Gm10085|Tmem167a	transmembrane protein 167	protein-coding	0	0.336634
Merged-chr3-136642387-1	chr3	136642337	136642437	+	2.6	cIP1vsInput	Intergenic	Intergenic	-28383	NM_008913	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|AI841391|AW413465|CN|Caln|Calna|CnA	"protein phosphatase 3, catalytic subunit, alpha isoform"	protein-coding	0.01	0.326733
Merged-chr6-137317827-1	chr6	137317777	137317877	+	2.6	cIP2vsInput	"intron (NM_001164401, intron 1 of 25)"	"intron (NM_001164401, intron 1 of 25)"	65528	NM_011216	19277	Mm.186361	NM_001164401	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	"protein tyrosine phosphatase, receptor type, O"	protein-coding	0.02	0.386139
Merged-chr8-68556117-1	chr8	68556067	68556167	+	2.6	cIP2vsInput	"intron (NM_001252623, intron 4 of 10)"	"intron (NM_001252623, intron 4 of 10)"	179029	NM_001252623	234356	Mm.489712	NM_001252623	ENSMUSG00000036356	Csgalnact1	4732435N03Rik|CSGalNAcT-1	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.01	0.346535
Merged-chr15-27189539-1	chr15	27189489	27189589	+	2.6	cIP1vsInput	Intergenic	Intergenic	-277138	NM_020332	11732	Mm.265264	NM_020332	ENSMUSG00000022265	Ank	Ankh|D15Ertd221e|ank|mKIAA1581	progressive ankylosis	protein-coding	0.01	0.316832
Merged-chr2-32694284-1	chr2	32694234	32694334	+	2.6	cIP1vsInput	promoter-TSS (NM_010236)	promoter-TSS (NM_010236)	-109	NM_010236	14287	Mm.3830	NM_010236	ENSMUSG00000009566	Fpgs	AA408187	folylpolyglutamyl synthetase	protein-coding	0.08	0.633663
Merged-chr4-72699142-1	chr4	72699092	72699192	+	2.6	cIP2vsInput	Intergenic	MTC|LTR|ERVL-MaLR	153492	NM_001199270	353204	Mm.317892	NM_001199270	ENSMUSG00000059343	Aldoart1	4921524E03Rik|Aldo1-ps|Aldo1-ps2|Aldoa-ps2	aldolase 1 A retrogene 1	protein-coding	0	0.356436
Merged-chr2-65183022-1	chr2	65182972	65183072	+	2.6	cIP2vsInput	"intron (NM_177025, intron 1 of 13)"	"intron (NM_177025, intron 1 of 13)"	55604	NM_177025	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding	0	0.366337
Merged-chr7-117857467-2	chr7	117857406	117857529	+	2.6	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	258680	NM_170669	267019	Mm.288212	NM_170669	ENSMUSG00000008683	Rps15a	A630031B11Rik	ribosomal protein S15A	protein-coding	0.02439	0.5
Merged-chr11-67025110-1	chr11	67025060	67025160	+	2.6	cIP2vsInput	promoter-TSS (NM_177392)	promoter-TSS (NM_177392)	-44	NM_177392	338369	Mm.128138	NM_177392	ENSMUSG00000050270	Tmem220	A730055C05Rik	transmembrane protein 220	protein-coding	0.06	0.752475
Merged-chr9-14809409-1	chr9	14809359	14809459	+	2.6	cIP2vsInput	"intron (NM_018736, intron 9 of 19)"	"intron (NM_018736, intron 9 of 19)"	24702	NM_018736	17535	Mm.149071	NM_018736	ENSMUSG00000031928	Mre11a	Mre11|Mre11b	meiotic recombination 11 homolog A (S. cerevisiae)	protein-coding	0	0.366337
Merged-chr5-149030911-1	chr5	149030861	149030961	+	2.6	cIP1vsInput	Intergenic	MER2|DNA|TcMar-Tigger	22126	NM_010439	15289	Mm.313345	NM_010439	ENSMUSG00000066551	Hmgb1	DEF|HMG-1|Hmg1|SBP-1|amphoterin|p30	high mobility group box 1	protein-coding	0.01	0.386139
Merged-chr16-9504880-1	chr16	9504830	9504930	+	2.6	cIP2vsInput	Intergenic	Intergenic	487653	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	"glutamate receptor, ionotropic, NMDA2A (epsilon 1)"	protein-coding	0	0.346535
Merged-chr9-79362715-1	chr9	79362665	79362765	+	2.6	cIP1vsInput	Intergenic	Intergenic	156587	NR_045336	100038575	Mm.367838	NR_045336		Gm10635	ENSMUSG00000074174	predicted gene 10635	miscRNA	0	0.326733
Merged-chr19-28453756-1	chr19	28453706	28453806	+	2.6	cIP2vsInput	"intron (NM_175459, intron 4 of 10)"	"intron (NM_175459, intron 4 of 10)"	-224468	NR_045330	320176	Mm.406716	NR_045330	ENSMUSG00000097735	D930032P07Rik	-	RIKEN cDNA D930032P07 gene	miscRNA	0	0.39604
Merged-chr2-124470163-1	chr2	124470113	124470213	+	2.6	cIP1vsInput	Intergenic	Intergenic	-140133	NM_199240	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|Sema6D-1|Sema6D-2|Sema6D-4|Sema6D-5|Sema6D-6|mKIAA1479	"sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D"	protein-coding	0	0.376238
Merged-chr1-29157504-1	chr1	29157454	29157554	+	2.6	cIP1vsInput	Intergenic	Intergenic	-377252	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0.01	0.366337
Merged-chr7-99556062-1	chr7	99556012	99556112	+	2.6	cIP2vsInput	"intron (NM_177231, intron 1 of 15)"	"intron (NM_177231, intron 1 of 15)"	3793	NR_029760	723840		NR_029760		Mir326	Mirn326|mmu-mir-326	microRNA 326	miscRNA	0.01	0.584158
Merged-chr8-42209278-1	chr8	42209228	42209328	+	2.6	cIP2vsInput	Intergenic	Intergenic	382011	NR_045497	69966	Mm.416903	NR_045497		2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	miscRNA	0	0.376238
Merged-chr14-6156621-1	chr14	6156571	6156671	+	2.6	cIP2vsInput	Intergenic	Intergenic	130629	NM_001270812	100861615	Mm.399319	NM_001270812	ENSMUSG00000079396	LOC100861615	-	alpha takusan-like	protein-coding	0	0.386139
Merged-chr4-61614362-1	chr4	61614312	61614412	+	2.6	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	-18530	NM_001200006	100039206	Mm.475721	NM_001200006	ENSMUSG00000096688	Mup17	Gm12557|MUP 17|OTTMUSG00000007480	major urinary protein 17	protein-coding	0	0.316832
Merged-chr14-46489875-1	chr14	46489825	46489925	+	2.6	cIP1vsInput	Intergenic	Intergenic	85976	NR_046459	100873094	Mm.318596	NR_046459		Rubie	-	RNA upstream of Bmp4 expressed in inner ear	miscRNA	0.01	0.356436
Merged-chr5-40388000-1	chr5	40387950	40388050	+	2.6	cIP1vsInput	Intergenic	Intergenic	-743369	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding	0	0.326733
Merged-chr15-91674790-1	chr15	91674740	91674840	+	2.6	cIP1vsInput	"intron (NM_025730, intron 2 of 50)"	"intron (NM_025730, intron 2 of 50)"	1566	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding	0	0.346535
Merged-chr3-112934967-1	chr3	112934917	112935017	+	2.6	cIP1vsInput	Intergenic	Intergenic	221760	NM_001190404	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding	0	0.376238
Merged-chr12-117483319-1	chr12	117483269	117483369	+	2.6	cIP2vsInput	Intergenic	Intergenic	-33160	NM_175930	217944	Mm.227642	NM_175930	ENSMUSG00000041992	Rapgef5	4932413M22|C86120|D030051B22Rik|GFR|Mrgef|mKIAA0277|mmr-gef	Rap guanine nucleotide exchange factor (GEF) 5	protein-coding	0	0.39604
Merged-chr13-15009286-1	chr13	15009236	15009336	+	2.6	cIP2vsInput	Intergenic	Intergenic	379028	NM_134067	105351	Mm.41450	NM_001104646	ENSMUSG00000039182	AW209491	-	expressed sequence AW209491	protein-coding	0	0.267327
Merged-chr8-50008017-1	chr8	50007967	50008067	+	2.6	cIP2vsInput	Intergenic	Intergenic	-360095	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.287129
Merged-chr7-143069555-1	chr7	143069505	143069605	+	2.6	cIP1vsInput	"intron (NM_001115085, intron 1 of 2)"	CpG	187	NM_001115085	56844	Mm.139675	NM_001115085	ENSMUSG00000045752	Tssc4	AA241958|ESTM671070	tumor-suppressing subchromosomal transferable fragment 4	protein-coding	0.08	0.673267
Merged-chr5-7017028-1	chr5	7016978	7017078	+	2.6	cIP2vsInput	"intron (NM_001163223, intron 1 of 3)"	Tigger1|DNA|TcMar-Tigger	-287136	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding	0	0.346535
Merged-chr4-114405844-1	chr4	114405794	114405894	+	2.6	cIP2vsInput	promoter-TSS (NM_001085549)	promoter-TSS (NM_001085549)	-880	NM_001085549	666048	Mm.331779	NM_001085549	ENSMUSG00000070867	Trabd2b	Gm12824|OTTMUSG00000008561	TraB domain containing 2B	protein-coding	0.05	0.643564
Merged-chr5-87570657-1	chr5	87570607	87570707	+	2.6	cIP2vsInput	Intergenic	Intergenic	-1651	NM_016771	53315	Mm.6824	NM_016771	ENSMUSG00000029273	Sult1d1	5033411P13Rik|AI987815|ST1d1|SULT-N|Sultn	"sulfotransferase family 1D, member 1"	protein-coding	0.01	0.386139
Merged-chr6-125426515-1	chr6	125426465	125426565	+	2.6	cIP2vsInput	Intergenic	Intergenic	-46011	NM_198604	213522	Mm.333396	NM_198604	ENSMUSG00000038167	Plekhg6	BC026778|Gm155	"pleckstrin homology domain containing, family G (with RhoGef domain) member 6"	protein-coding	0.06	0.663366
Merged-chr7-110109455-1	chr7	110109405	110109505	+	2.6	cIP1vsInput	Intergenic	Intergenic	-12604	NM_009516	22390	Mm.287173	NM_009516		Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding	0.05	0.564356
Merged-chr12-85763427-1	chr12	85763377	85763477	+	2.6	cIP1vsInput	"intron (NM_145447, intron 1 of 9)"	"intron (NM_145447, intron 1 of 9)"	16888	NM_145447	217721	Mm.301076	NM_145447	ENSMUSG00000034258	Mfsd7c	CCT|Flvcr2	major facilitator superfamily domain containing 7C	protein-coding	0	0.415842
Merged-chr5-84009910-1	chr5	84009860	84009960	+	2.6	cIP1vsInput	Intergenic	Intergenic	407472	NM_007937	13839	Mm.438006	NM_007937		Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding	0.01	0.306931
Merged-chr17-49735531-1	chr17	49735481	49735581	+	2.6	cIP2vsInput	"intron (NM_177052, intron 10 of 22)"	"intron (NM_177052, intron 10 of 22)"	120359	NM_177052	319991	Mm.441340	NM_177052	ENSMUSG00000023999	Kif6	D130004B10Rik|D130084M03Rik	kinesin family member 6	protein-coding	0	0.326733
Merged-chr11-45992631-1	chr11	45992581	45992681	+	2.6	cIP2vsInput	"intron (NM_173384, intron 4 of 4)"	"intron (NM_173384, intron 4 of 4)"	12321	NM_173384	214105	Mm.66708	NM_173384	ENSMUSG00000040489	Sox30	-	SRY-box containing gene 30	protein-coding	0.02	0.366337
Merged-chr5-56036625-1	chr5	56036575	56036675	+	2.6	cIP1vsInput	Intergenic	Intergenic	1681294	NR_015588	319216	Mm.446765	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	miscRNA	0.01	0.287129
Merged-chr3-137275985-1	chr3	137275935	137276035	+	2.6	cIP1vsInput	Intergenic	Intergenic	-65093	NM_001163522	59308	Mm.27343	NM_001163522	ENSMUSG00000054690	Emcn	0610012K22Rik|AI315669|Muc14	endomucin	protein-coding	0.01	0.415842
Merged-chr14-17803082-1	chr14	17803032	17803132	+	2.6	cIP2vsInput	"intron (NM_001113417, intron 1 of 9)"	"intron (NM_001113417, intron 1 of 9)"	142122	NM_001113417	21834	Mm.32563	NM_001113417	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding	0	0.306931
Merged-chr11-108657829-1	chr11	108657779	108657879	+	2.6	cIP2vsInput	"intron (NM_029606, intron 21 of 27)"	"intron (NM_029606, intron 21 of 27)"	-24780	NM_145688	76380	Mm.344071	NM_029586	ENSMUSG00000020728	Cep112	1700001M19Rik|1700029K01Rik|8430407H02Rik|AV043680|AV207351|Ccdc46|Macoco	centrosomal protein 112	protein-coding	0	0.366337
Merged-chr8-32318376-1	chr8	32318326	32318426	+	2.6	cIP1vsInput	Intergenic	Intergenic	166481	NR_046039	666589	Mm.367675	NR_046039		Gm8179	EG666589	predicted gene 8179	miscRNA	0	0.316832
Merged-chr6-61978652-1	chr6	61978602	61978702	+	2.6	cIP2vsInput	"intron (NM_001164316, intron 10 of 10)"	"intron (NM_001164316, intron 10 of 10)"	-797842	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	miscRNA	0	0.415842
Merged-chr9-64759299-1	chr9	64759249	64759349	+	2.6	cIP1vsInput	Intergenic	Intergenic	-21543	NM_017382	53869	Mm.1387	NM_017382	ENSMUSG00000004771	Rab11a	-	"RAB11a, member RAS oncogene family"	protein-coding	0	0.356436
Merged-chr2-177483158-1	chr2	177483108	177483208	+	2.6	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-15068	NR_036450	433520	Mm.425117	NM_001024825		Gm14403	OTTMUSG00000016571	predicted gene 14403	miscRNA	0	0.316832
Merged-chr7-28766725-1	chr7	28766675	28766775	+	2.6	cIP1vsInput	promoter-TSS (NM_010908)	promoter-TSS (NM_010908)	-27	NM_022432	64383	Mm.272443	NM_001122765	ENSMUSG00000015149	Sirt2	5730427M03Rik|SIR2L2|Sir2l	"sirtuin 2 (silent mating type information regulation 2, homolog) 2 (S. cerevisiae)"	protein-coding	0.04	0.445545
Merged-chr1-31896416-1	chr1	31896366	31896466	+	2.6	cIP2vsInput	Intergenic	MLT2C1|LTR|ERVL	-276390	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm1	"KH domain containing, RNA binding, signal transduction associated 2"	protein-coding	0.01	0.29703
Merged-chr5-60274331-1	chr5	60274281	60274381	+	2.6	cIP2vsInput	Intergenic	Lx3_Mus|LINE|L1	-288329	NR_040682	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0.01	0.306931
Merged-chr9-119937459-1	chr9	119937409	119937509	+	2.6	cIP2vsInput	promoter-TSS (NM_028735)	promoter-TSS (NM_028735)	99	NM_028976	74498	Mm.473239	NM_028976	ENSMUSG00000032513	Gorasp1	5430411C10Rik|GOLPH5|GRASP65|P65	golgi reassembly stacking protein 1	protein-coding	0.08	0.712871
Merged-chr1-183388770-1	chr1	183388720	183388820	+	2.6	cIP2vsInput	promoter-TSS (NM_021466)	promoter-TSS (NM_021466)	-115	NM_021466	21339	Mm.383556	NM_021466		Taf1a	mTAFI48	"TATA box binding protein (Tbp)-associated factor, RNA polymerase I, A"	protein-coding	0.04	0.475248
Merged-chr10-105378660-1	chr10	105378610	105378710	+	2.6	cIP1vsInput	"intron (NM_177368, intron 2 of 11)"	"intron (NM_177368, intron 2 of 11)"	195819	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding	0.01	0.336634
Merged-chr11-88099270-1	chr11	88099220	88099320	+	2.6	cIP2vsInput	"non-coding (NR_045499, exon 4 of 4)"	"non-coding (NR_045499, exon 4 of 4)"	124	NM_198013	103841	Mm.374846	NM_001172099	ENSMUSG00000018378	Cuedc1	AI841487|C330016O16Rik	CUE domain containing 1	protein-coding	0.2	0.891089
Merged-chr12-89895540-1	chr12	89895490	89895590	+	2.6	cIP2vsInput	"intron (NM_001252074, intron 1 of 6)"	"intron (NM_001252074, intron 1 of 6)"	83057	NM_001252074	18191	Mm.487864	NM_001198587	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding	0	0.316832
Merged-chr3-94443232-1	chr3	94443182	94443282	+	2.6	cIP1vsInput	promoter-TSS (NM_030116)	promoter-TSS (NM_030116)	-104	NM_030116	78523	Mm.218515	NM_030116	ENSMUSG00000028140	Mrpl9	8030480E20Rik|AA409733|C330013D18Rik|L9mt	mitochondrial ribosomal protein L9	protein-coding	0.09	0.633663
Merged-chr5-143818978-1	chr5	143818928	143819028	+	2.6	cIP1vsInput	Intergenic	Intergenic	-52884	NM_013557	15467	Mm.431968	NM_013557		Eif2ak1	HCR|Hri	eukaryotic translation initiation factor 2 alpha kinase 1	protein-coding	0.01	0.356436
Merged-chr7-97986330-1	chr7	97986280	97986380	+	2.6	cIP2vsInput	"intron (NM_177696, intron 11 of 17)"	"intron (NM_177696, intron 11 of 17)"	66372	NM_177696	233537	Mm.375772	NM_177696	ENSMUSG00000035582	Gdpd4	4921513O04	glycerophosphodiester phosphodiesterase domain containing 4	protein-coding	0	0.376238
Merged-chr11-60728492-1	chr11	60728442	60728542	+	2.6	cIP2vsInput	promoter-TSS (NR_039559)	promoter-TSS (NR_039559)	94	NM_001009927	237781	Mm.339760	NM_001009927	ENSMUSG00000018599	Smcr7	AI482195|Gm11	"Smith-Magenis syndrome chromosome region, candidate 7 homolog (human)"	protein-coding	0.09	0.663366
Merged-chr8-5635786-1	chr8	5635736	5635836	+	2.6	cIP1vsInput	Intergenic	Lx2B|LINE|L1	-530554	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.356436
Merged-chr8-104655360-1	chr8	104655310	104655410	+	2.6	cIP2vsInput	Intergenic	Intergenic	-13632	NM_026753	68523	Mm.279	NM_026753	ENSMUSG00000031879	Fam96b	1110019N10Rik	"family with sequence similarity 96, member B"	protein-coding	0	0.306931
Merged-chr4-54389286-1	chr4	54389236	54389336	+	2.6	cIP2vsInput	Intergenic	Intergenic	-558659	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding	0.01	0.386139
Merged-chr16-81706567-1	chr16	81706517	81706617	+	2.6	cIP1vsInput	Intergenic	Intergenic	505870	NM_010954	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.316832
Merged-chr14-98434136-1	chr14	98434086	98434186	+	2.6	cIP1vsInput	Intergenic	Intergenic	-264593	NM_007826	13134	Mm.320593	NM_001038610	ENSMUSG00000055639	Dach1	AI182278|Dac|Dach|E130112M23Rik	dachshund 1 (Drosophila)	protein-coding	0	0.29703
Merged-chr14-17584840-1	chr14	17584790	17584890	+	2.6	cIP2vsInput	Intergenic	L1M4|LINE|L1	-76120	NM_001113417	21834	Mm.32563	NM_001113417	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding	0	0.356436
Merged-chr1-162445538-1	chr1	162445488	162445588	+	2.6	cIP1vsInput	"intron (NM_001038619, intron 1 of 20)"	"intron (NM_001038619, intron 1 of 20)"	32492	NM_001038619	103967	Mm.441620	NM_172646	ENSMUSG00000040265	Dnm3	9630020E24Rik|AW061159|B230343F03Rik|C530045C17|mKIAA0820	dynamin 3	protein-coding	0	0.346535
Merged-chr13-78475494-1	chr13	78475444	78475544	+	2.6	cIP2vsInput	Intergenic	Tigger6b|DNA|TcMar-Tigger	-276512	NM_010151	13865	Mm.439653	NM_010151		Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR3|Erbal3|SVP44|Tcfcoup1	"nuclear receptor subfamily 2, group F, member 1"	protein-coding	0	0.287129
Merged-chr2-90594839-1	chr2	90594789	90594889	+	2.6	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-14192	NM_008982	19271	Mm.330393	NM_001135657	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	"protein tyrosine phosphatase, receptor type, J"	protein-coding	0	0.366337
Merged-chr3-116976489-1	chr3	116976439	116976539	+	2.6	cIP1vsInput	"intron (NR_040596, intron 2 of 2)"	L1_Mur3|LINE|L1	-7537	NM_023245	114301	Mm.253736	NM_023245	ENSMUSG00000033377	Palmd	4631423C22Rik|PALML	palmdelphin	protein-coding	0	0.316832
Merged-chr2-126117918-1	chr2	126117868	126117968	+	2.6	cIP1vsInput	"intron (NM_029455, intron 9 of 16)"	"intron (NM_029455, intron 9 of 16)"	34086	NM_029455	75823	Mm.444732	NM_029455	ENSMUSG00000027209	Fam227b	4930525F21Rik	"family with sequence similarity 227, member B"	protein-coding	0	0.277228
Merged-chr16-44063444-1	chr16	44063394	44063494	+	2.6	cIP2vsInput	Intergenic	CpG	-35499	NM_001172107	207798	Mm.19316	NM_001172107	ENSMUSG00000036292	Gramd1c	4921521N14Rik	GRAM domain containing 1C	protein-coding	0.07	0.564356
Merged-chr8-78821609-1	chr8	78821559	78821659	+	2.6	cIP1vsInput	promoter-TSS (NM_001191004)	promoter-TSS (NM_001191004)	-457	NM_030145	78651	Mm.28694	NM_001191004	ENSMUSG00000031683	Lsm6	1500031N17Rik|2410088K19Rik|AI747288	"LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae)"	protein-coding	0.02	0.306931
Merged-chr10-16906635-1	chr10	16906585	16906685	+	2.6	cIP2vsInput	Intergenic	Intergenic	189147	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0	0.306931
Merged-chr7-127244329-1	chr7	127244279	127244379	+	2.6	cIP2vsInput	promoter-TSS (NM_177362)	promoter-TSS (NM_177362)	-197	NM_177362	244216	Mm.41038	NM_177362	ENSMUSG00000054716	Zfp771	G630024C07Rik|Znf771	zinc finger protein 771	protein-coding	0.06	0.663366
Merged-chr19-43370720-1	chr19	43370670	43370770	+	2.6	cIP2vsInput	"intron (NM_001081257, intron 2 of 11)"	L1MB7|LINE|L1	17635	NM_001081257	545291	Mm.442200	NM_001081257	ENSMUSG00000074852	Hpse2	Gm968|Hpa2	heparanase 2	protein-coding	0	0.326733
Merged-chr10-78244791-1	chr10	78244741	78244841	+	2.6	cIP2vsInput	promoter-TSS (NM_001081055)	promoter-TSS (NM_001081055)	-149	NM_001081055	216131	Mm.27539	NM_001081055	ENSMUSG00000000374	Trappc10	B230307C21Rik|Gm870|Tmem1	trafficking protein particle complex 10	protein-coding	0.1	0.732673
Merged-chr4-14756322-1	chr4	14756272	14756372	+	2.6	cIP1vsInput	"intron (NM_028499, intron 5 of 7)"	"intron (NM_028499, intron 5 of 7)"	39730	NM_028499	73314	Mm.52613	NM_028499	ENSMUSG00000023151	Lrrc69	1700034K16Rik	leucine rich repeat containing 69	protein-coding	0	0.326733
Merged-chr1-127055183-1	chr1	127055133	127055233	+	2.6	cIP1vsInput	Intergenic	Lx5c|LINE|L1	-149803	NM_145128	107895	Mm.472488	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding	0.01	0.386139
Merged-chr16-52041688-1	chr16	52041638	52041738	+	2.6	cIP2vsInput	"intron (NM_001033238, intron 2 of 17)"	"intron (NM_001033238, intron 2 of 17)"	10139	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding	0.01	0.316832
Merged-chr9-49987308-1	chr9	49987258	49987358	+	2.6	cIP2vsInput	Intergenic	Intergenic	-188239	NM_010875	17967	Mm.439182	NM_001081445		Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding	0	0.326733
Merged-chr7-138828108-1	chr7	138828058	138828158	+	2.6	cIP2vsInput	Intergenic	Intergenic	18159	NM_001045483	69546	Mm.31598	NM_001045483	ENSMUSG00000041775	Mapk1ip1	2310009E07Rik|AU043776|MISS	mitogen-activated protein kinase 1 interacting protein 1	protein-coding	0.04	0.386139
Merged-chr6-72380406-1	chr6	72380356	72380456	+	2.6	cIP2vsInput	promoter-TSS (NM_016872)	promoter-TSS (NM_016872)	62	NM_016872	53620	Mm.440321	NM_001080742	ENSMUSG00000073002	Vamp5	AF119384|Camp	vesicle-associated membrane protein 5	protein-coding	0.13	0.762376
Merged-chr5-150229580-1	chr5	150229530	150229630	+	2.6	cIP1vsInput	Intergenic	L1MEd|LINE|L1	-30350	NM_172887	320365	Mm.454348	NM_178781	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	furry homolog (Drosophila)	protein-coding	0	0.247525
Merged-chr8-20834923-1	chr8	20834873	20834973	+	2.6	cIP1vsInput	Intergenic	Intergenic	-41576	NR_002880	654455	Mm.424927	NR_002880		Gm21944	Defb48-ps	defensin beta 48 pseudogene	pseudo	0	0.267327
Merged-chr9-94277043-1	chr9	94276993	94277093	+	2.6	cIP2vsInput	Intergenic	Intergenic	261038	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49	RIKEN cDNA 1190002N15 gene	protein-coding	0.01	0.336634
Merged-chr7-30184229-1	chr7	30184179	30184279	+	2.6	cIP1vsInput	promoter-TSS (NM_009944)	promoter-TSS (NM_009944)	58	NM_009944	12865	Mm.423030	NM_009944	ENSMUSG00000074218	Cox7a1	COX7A|COX7AH|COX7AM	cytochrome c oxidase subunit VIIa 1	protein-coding	0.07	0.673267
Merged-chr13-32696904-1	chr13	32696854	32696954	+	2.6	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	84875	NM_001166030	238564	Mm.60041	NM_001166030	ENSMUSG00000044951	Mylk4	EG238564	"myosin light chain kinase family, member 4"	protein-coding	0	0.316832
Merged-chr3-25920695-1	chr3	25920645	25920745	+	2.6	cIP1vsInput	"intron (NM_138666, intron 3 of 7)"	"intron (NM_138666, intron 3 of 7)"	232612	NM_001163387	192167	Mm.316080	NM_001163387	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|mKIAA1070	neuroligin 1	protein-coding	0	0.267327
Merged-chr2-91777187-1	chr2	91777137	91777237	+	2.6	cIP2vsInput	"intron (NM_172669, intron 7 of 17)"	"intron (NM_172669, intron 7 of 17)"	47049	NM_001080754	228361	Mm.436667	NM_001080754	ENSMUSG00000040506	Ambra1	2310079H06Rik|A130023A14|AA474864|AV021921|D030051N19Rik|mKIAA1736	autophagy/beclin 1 regulator 1	protein-coding	0	0.336634
Merged-chr16-53749764-1	chr16	53749714	53749814	+	2.6	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-934020	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	miscRNA	0	0.29703
Merged-chr15-4090729-1	chr15	4090679	4090779	+	2.6	cIP1vsInput	"intron (NM_024188, intron 7 of 16)"	"intron (NM_024188, intron 7 of 16)"	-63323	NR_028266	414066	Mm.394461	NR_028266		BC037032	-	cDNA Sequence BC037032	miscRNA	0.01	0.336634
Merged-chr14-81309416-1	chr14	81309366	81309466	+	2.6	cIP2vsInput	Intergenic	Intergenic	1309114	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.29703
Merged-chr3-117536568-1	chr3	117536518	117536618	+	2.6	cIP1vsInput	Intergenic	Intergenic	-38893	NM_029425	75769	Mm.72187	NM_029425	ENSMUSG00000033342	4833424O15Rik	Lppr5|PRG-5|Pap2d	RIKEN cDNA 4833424O15 gene	protein-coding	0	0.346535
Merged-chr4-76408418-1	chr4	76408368	76408468	+	2.6	cIP2vsInput	"intron (NM_011211, intron 10 of 39)"	"intron (NM_011211, intron 10 of 39)"	-1130132	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	3110001D03Rik	1700027K24Rik	RIKEN cDNA 3110001D03 gene	protein-coding	0	0.306931
Merged-chr3-6219917-1	chr3	6219867	6219967	+	2.6	cIP1vsInput	Intergenic	Intergenic	400526	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding	0	0.316832
Merged-chr3-110485063-1	chr3	110485013	110485113	+	2.6	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-234065	NR_024139	99890	Mm.393526	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding	0	0.316832
Merged-chr14-87905596-1	chr14	87905546	87905646	+	2.6	cIP1vsInput	Intergenic	Intergenic	489013	NM_001253755	219249	Mm.35168	NM_001253755	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding	0	0.217822
Merged-chr1-193915508-1	chr1	193915458	193915558	+	2.6	cIP2vsInput	Intergenic	Intergenic	307251	NR_040477	74942	Mm.60689	NR_040477		4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	miscRNA	0	0.316832
Merged-chr3-35826346-1	chr3	35826296	35826396	+	2.6	cIP1vsInput	"intron (NM_029570, intron 19 of 29)"	"intron (NM_029570, intron 19 of 29)"	72208	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	"ATPase, class VI, type 11B"	protein-coding	0	0.316832
Merged-chr9-121329298-1	chr9	121329248	121329348	+	2.6	cIP1vsInput	Intergenic	Intergenic	-37660	NM_175114	67095	Mm.305318	NM_175114	ENSMUSG00000032536	Trak1	2310001H13Rik|AI413908|AI467545|hyrt|mKIAA1042	"trafficking protein, kinesin binding 1"	protein-coding	0.02	0.544554
Merged-chr17-59405180-1	chr17	59405130	59405230	+	2.6	cIP1vsInput	Intergenic	Intergenic	-391858	NM_026497	67993	Mm.36507	NM_026497		Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0	0.356436
Merged-chr4-141310479-1	chr4	141310429	141310529	+	2.6	cIP2vsInput	"intron (NM_010139, intron 3 of 16)"	"intron (NM_010139, intron 3 of 16)"	9258	NM_010139	13836	Mm.2581	NM_010139	ENSMUSG00000006445	Epha2	AW545284|Eck|Myk2|Sek-2|Sek2	Eph receptor A2	protein-coding	0.02	0.584158
Merged-chr6-22032318-1	chr6	22032268	22032368	+	2.6	cIP2vsInput	"intron (NM_001081351, intron 2 of 21)"	"intron (NM_001081351, intron 2 of 21)"	46408	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding	0.01	0.316832
Merged-chr4-5695234-1	chr4	5695184	5695284	+	2.6	cIP1vsInput	"intron (NM_173426, intron 1 of 2)"	"intron (NM_173426, intron 1 of 2)"	51055	NM_173426	242297	Mm.458843	NM_173426		Fam110b	1700012H17Rik|5031405P22|AW049855	"family with sequence similarity 110, member B"	protein-coding	0.01	0.336634
Merged-chr14-6965379-1	chr14	6965329	6965429	+	2.6	cIP1vsInput	Intergenic	Intergenic	62070	NM_001164727	100038847	Mm.483675	NM_001164727	ENSMUSG00000093985	Gm10406	ENSMUSG00000072735	predicted gene 10406	protein-coding	0	0.326733
Merged-chr9-67446924-1	chr9	67446874	67446974	+	2.6	cIP1vsInput	"intron (NM_001081242, intron 2 of 57)"	"intron (NM_001081242, intron 2 of 57)"	112779	NM_001081242	70549	Mm.33645	NM_027458	ENSMUSG00000052698	Tln2	5730421P04Rik|AI507121|AI787438|AL118320|mKIAA0320	talin 2	protein-coding	0.01	0.336634
Merged-chr1-99660626-1	chr1	99660576	99660676	+	2.6	cIP1vsInput	Intergenic	RMER16-int|LTR|ERVK	-112139	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding	0	0.316832
Merged-chr5-59661495-1	chr5	59661445	59661545	+	2.6	cIP1vsInput	Intergenic	Lx9|LINE|L1	324507	NR_040683	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0.01	0.326733
Merged-chr1-70046647-1	chr1	70046597	70046697	+	2.6	cIP1vsInput	"intron (NM_025728, intron 2 of 7)"	"intron (NM_025728, intron 2 of 7)"	95032	NM_025728	66722	Mm.440554	NM_001271533	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding	0	0.287129
Merged-chr19-38829125-1	chr19	38829075	38829175	+	2.6	cIP1vsInput	Intergenic	Intergenic	-7454	NM_145952	209478	Mm.391153	NM_145952	ENSMUSG00000048720	Tbc1d12	BC033574	"TBC1D12: TBC1 domain family, member 12"	protein-coding	0.01	0.356436
Merged-chr8-90828793-1	chr8	90828743	90828843	+	2.6	cIP2vsInput	promoter-TSS (NM_177224)	promoter-TSS (NM_177224)	-42	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding	0.08	0.683168
Merged-chr3-148236321-1	chr3	148236271	148236371	+	2.6	cIP1vsInput	Intergenic	Intergenic	718314	NM_001081298	99633	Mm.462301	NM_001081298	ENSMUSG00000028184	Lphn2	AI450192|Gm619|Lec1|Lphh1|mKIAA0786	latrophilin 2	protein-coding	0	0.425743
Merged-chr16-42791016-1	chr16	42790966	42791066	+	2.6	cIP2vsInput	"intron (NR_040521, intron 1 of 3)"	"intron (NR_040521, intron 1 of 3)"	84571	NR_040521	75722	Mm.243747	NR_040521	ENSMUSG00000075070	4932412D23Rik	ENSMUSG00000075070|Gm10809	RIKEN cDNA 4932412D23 gene	miscRNA	0	0.386139
Merged-chr6-33833450-1	chr6	33833400	33833500	+	2.6	cIP2vsInput	"intron (NM_009148, intron 12 of 17)"	"intron (NM_009148, intron 12 of 17)"	-195998	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding	0	0.29703
Merged-chr9-90478175-1	chr9	90478125	90478225	+	2.6	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-207406	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	"TBC1 domain family, member 2B"	protein-coding	0	0.366337
Merged-chr14-46678676-1	chr14	46678626	46678726	+	2.6	cIP2vsInput	Intergenic	B3A|SINE|B2	-41253	NR_046460	74458	Mm.390708	NR_046460		4933425B07Rik	-	RIKEN cDNA 4933425B07 gene	miscRNA	0	0.49505
Merged-chr12-73750821-1	chr12	73750771	73750871	+	2.6	cIP1vsInput	"intron (NM_008856, intron 10 of 13)"	"intron (NM_008856, intron 10 of 13)"	-157046	NM_010431	15251	Mm.446610	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF1alpha|MOP1|bHLHe78	"hypoxia inducible factor 1, alpha subunit"	protein-coding	0	0.405941
Merged-chr5-123079118-1	chr5	123079068	123079168	+	2.6	cIP1vsInput	"intron (NM_001039723, intron 1 of 11)"	"intron (NM_001039723, intron 1 of 11)"	2843	NM_001039723	330189	Mm.391872	NM_001039723	ENSMUSG00000054434	Tmem120b	-	transmembrane protein 120B	protein-coding	0	0.405941
Merged-chr3-158748203-1	chr3	158748153	158748253	+	2.6	cIP1vsInput	Intergenic	Intergenic	-185982	NM_001081358	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding	0.01	0.386139
Merged-chr16-16324906-1	chr16	16324856	16324956	+	2.6	cIP2vsInput	"intron (NM_001025947, intron 9 of 17)"	L1M2|LINE|L1	21941	NR_038046	70120	Mm.37486	NM_198246	ENSMUSG00000022792	Yars2	2210023C10Rik|tyrRS	tyrosyl-tRNA synthetase 2 (mitochondrial)	protein-coding	0	0.356436
Merged-chr7-66661815-1	chr7	66661765	66661865	+	2.6	cIP2vsInput	"intron (NM_080443, intron 4 of 5)"	B3A|SINE|B2	27746	NM_080443	117589	Mm.34785	NM_178236	ENSMUSG00000030509	Asb7	AI449039|Asb-7|D030055C23Rik	ankyrin repeat and SOCS box-containing 7	protein-coding	0.01	0.50495
Merged-chr19-36569881-1	chr19	36569831	36569931	+	2.6	cIP1vsInput	"intron (NM_001163471, intron 2 of 20)"	"intron (NM_001163471, intron 2 of 20)"	15242	NM_001163471	226098	Mm.61107	NM_001163471	ENSMUSG00000041180	Hectd2	4921524L07|A630025O09Rik|AW212605	HECT domain containing 2	protein-coding	0.01	0.316832
Merged-chr2-146855786-1	chr2	146855736	146855836	+	2.6	cIP2vsInput	promoter-TSS (NM_001033298)	promoter-TSS (NM_001033298)	-103	NM_001033298	228730	Mm.292352	NM_001033298	ENSMUSG00000074749	Plk1s1	Gm114|Ncrna00153	polo-like kinase 1 substrate 1	protein-coding	0.1	0.732673
Merged-chr12-35831442-1	chr12	35831392	35831492	+	2.6	cIP1vsInput	Intergenic	Intergenic	-94179	NM_207531	403205	Mm.190508	NM_207531	ENSMUSG00000036231	Agr3	BCMP11|E030025L21Rik|Gm888	anterior gradient 3	protein-coding	0.01	0.39604
Merged-chr9-21798055-1	chr9	21798005	21798105	+	2.6	cIP2vsInput	"intron (NM_145611, intron 1 of 11)"	"intron (NM_145611, intron 1 of 11)"	491	NM_145611	235041	Mm.257371	NM_145611	ENSMUSG00000032194	Kank2	AI504612|Ankrd25|BC010245	KN motif and ankyrin repeat domains 2	protein-coding	0.08	0.752475
Merged-chr15-27647952-1	chr15	27647902	27648002	+	2.6	cIP2vsInput	Intergenic	(TTTTTG)n|Simple_repeat|Simple_repeat	-17259	NM_001013792	432940	Mm.309164	NM_001013792	ENSMUSG00000046034	Fam105b	C79097	"family with sequence similarity 105, member B"	protein-coding	0.01	0.29703
Merged-chr14-10562198-1	chr14	10562148	10562248	+	2.6	cIP1vsInput	"intron (NM_010210, intron 3 of 8)"	L1M5|LINE|L1	599834	NM_010210	14198	Mm.441926	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding	0.01	0.356436
Merged-chr1-143559289-1	chr1	143559239	143559339	+	2.6	cIP2vsInput	Intergenic	Intergenic	-81408	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0	0.316832
Merged-chr2-79140826-1	chr2	79140776	79140876	+	2.6	cIP2vsInput	Intergenic	MIR|SINE|MIR	-114600	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D	integrin alpha 4	protein-coding	0	0.356436
Merged-chr17-92342294-1	chr17	92342244	92342344	+	2.6	cIP2vsInput	Intergenic	L1MA4A|LINE|L1	-857128	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0	0.316832
Merged-chr7-10214816-1	chr7	10214766	10214866	+	2.6	cIP1vsInput	Intergenic	MYSERV16_I-int|LTR|ERVK	-38530	NM_001105191	384534	Mm.389802	NM_001105191	ENSMUSG00000091930	Vmn2r52	EG384534	"vomeronasal 2, receptor 52"	protein-coding	0	0.316832
Merged-chr5-66894739-1	chr5	66894689	66894789	+	2.6	cIP1vsInput	"intron (NM_001001980, intron 3 of 25)"	"intron (NM_001001980, intron 3 of 25)"	-73677	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding	0	0.435644
Merged-chr6-5229138-1	chr6	5229088	5229188	+	2.6	cIP2vsInput	"intron (NM_173006, intron 8 of 8)"	"intron (NM_173006, intron 8 of 8)"	27095	NM_173006	269823	Mm.9122	NM_173006	ENSMUSG00000029759	Pon3	2810004E20|AI786302	paraoxonase 3	protein-coding	0	0.306931
Merged-chr19-19784503-1	chr19	19784453	19784553	+	2.6	cIP2vsInput	Intergenic	Intergenic	606168	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding	0.01	0.356436
Merged-chr10-51427889-1	chr10	51427839	51427939	+	2.6	cIP2vsInput	Intergenic	L1VL2|LINE|L1	-52790	NM_008147	14727	Mm.439661	NM_008147	ENSMUSG00000089672	Gp49a	gp49	glycoprotein 49 A	protein-coding	0	0.287129
Merged-chr10-103470867-1	chr10	103470817	103470917	+	2.6	cIP2vsInput	Intergenic	Intergenic	103059	NM_175328	103098	Mm.458408	NM_001252330	ENSMUSG00000019894	Slc6a15	AA536730|AI326450|AI326451|v7-3	"solute carrier family 6 (neurotransmitter transporter), member 15"	protein-coding	0	0.287129
Merged-chr5-150489211-1	chr5	150489161	150489261	+	2.6	cIP2vsInput	"intron (NM_172887, intron 58 of 60)"	"intron (NM_172887, intron 58 of 60)"	13008	NR_024513	194292	Mm.300184	NR_024513		Gm5	Gm1812	predicted gene 5	miscRNA	0.01	0.356436
Merged-chr9-45518130-1	chr9	45518080	45518180	+	2.6	cIP2vsInput	"intron (NM_001081270, intron 3 of 32)"	"intron (NM_001081270, intron 3 of 32)"	-86898	NR_040732	74602	Mm.394117	NR_040732	ENSMUSG00000097074	4833428L15Rik	-	RIKEN cDNA 4833428L15 gene	miscRNA	0.01	0.534653
Merged-chr8-119605270-1	chr8	119605220	119605320	+	2.6	cIP2vsInput	promoter-TSS (NM_021441)	promoter-TSS (NM_021441)	-30	NM_021441	21341	Mm.475128	NM_021441	ENSMUSG00000031832	Taf1c	Tafi95|mTAFI95	"TATA box binding protein (Tbp)-associated factor, RNA polymerase I, C"	protein-coding	0.06	0.60396
Merged-chr1-41287252-1	chr1	41287202	41287302	+	2.6	cIP2vsInput	Intergenic	Intergenic	-106000	NR_040475	74897	Mm.243822	NR_040475		4930448I06Rik	-	RIKEN cDNA 4930448I06 gene	miscRNA	0	0.336634
Merged-chr15-5995295-1	chr15	5995245	5995345	+	2.6	cIP2vsInput	Intergenic	Intergenic	-304494	NM_001008702	13132	Mm.240830	NM_001008702	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	"disabled 2, mitogen-responsive phosphoprotein"	protein-coding	0	0.277228
Merged-chr14-61610587-1	chr14	61610537	61610637	+	2.6	cIP1vsInput	"intron (NM_206974, intron 1 of 1)"	"intron (NM_206974, intron 1 of 1)"	3130	NM_001039105	328424	Mm.224464	NM_001039105	ENSMUSG00000046168	Kcnrg	Clld4|E030012H22Rik|Gm745	potassium channel regulator	protein-coding	0	0.356436
Merged-chr6-60000619-1	chr6	60000569	60000669	+	2.6	cIP1vsInput	Intergenic	Intergenic	403088	NR_015565	208079	Mm.490691	NR_015565		A530053G22Rik	-	RIKEN cDNA A530053G22 gene	miscRNA	0.01	0.336634
Merged-chr10-113532538-1	chr10	113532488	113532588	+	2.6	cIP1vsInput	Intergenic	Intergenic	-54040	NR_035418	100316831		NR_035418		Mir669h	Mirn669h|mmu-mir-669h	microRNA 669h	miscRNA	0	0.39604
Merged-chr18-52836527-1	chr18	52836477	52836577	+	2.6	cIP2vsInput	"intron (NR_035420, intron 1 of 2)"	"intron (NR_035420, intron 1 of 2)"	66120	NR_035420	100316749		NR_035420	ENSMUSG00000080573	Mir467f	Mirn467f|mmu-mir-467f	microRNA 467f	miscRNA	0	0.366337
Merged-chr2-69462319-1	chr2	69462269	69462369	+	2.6	cIP2vsInput	"intron (NM_001081088, intron 53 of 78)"	MYSERV16_I-int|LTR|ERVK	81857	NM_175512	241452	Mm.211655	NM_175512		Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding	0	0.366337
Merged-chr8-100175108-1	chr8	100175058	100175158	+	2.6	cIP1vsInput	Intergenic	Intergenic	-758651	NM_001039154	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.29703
Merged-chrX-94177469-1	chrX	94177419	94177519	+	2.6	cIP2vsInput	Intergenic	Intergenic	35182	NM_012010	26905	Mm.218851	NM_012010	ENSMUSG00000035150	Eif2s3x	AA409828|AA547477|AI314668|Eif-2gx	"eukaryotic translation initiation factor 2, subunit 3, structural gene X-linked"	protein-coding	0.03	0.366337
Merged-chr3-93521032-1	chr3	93520982	93521082	+	2.6	cIP1vsInput	"intron (NM_016740, intron 1 of 2)"	"intron (NM_016740, intron 1 of 2)"	536	NM_016740	20195	Mm.280038	NM_016740	ENSMUSG00000027907	S100a11	EMAPI|Emap1|S100a14|S100c|cal	S100 calcium binding protein A11 (calgizzarin)	protein-coding	0.03	0.554455
Merged-chr2-90593990-1	chr2	90593940	90594040	+	2.6	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-13343	NM_008982	19271	Mm.330393	NM_001135657	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	"protein tyrosine phosphatase, receptor type, J"	protein-coding	0	0.326733
Merged-chr9-110101036-1	chr9	110100986	110101086	+	2.6	cIP2vsInput	promoter-TSS (NM_001252683)	promoter-TSS (NM_001252683)	51	NM_001252683	72831	Mm.276305	NM_001252682	ENSMUSG00000032480	Dhx30	2810477H02Rik|C130058C04Rik|Ddx30|HELG|Ret-CoR	DEAH (Asp-Glu-Ala-His) box polypeptide 30	protein-coding	0.11	0.712871
Merged-chr1-62795726-1	chr1	62795676	62795776	+	2.6	cIP2vsInput	promoter-TSS (NR_040601)	promoter-TSS (NR_040601)	-994	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	miscRNA	0.04	0.683168
Merged-chr11-36744052-1	chr11	36744002	36744102	+	2.6	cIP2vsInput	"intron (NM_011856, intron 2 of 28)"	"intron (NM_011856, intron 2 of 28)"	200191	NM_011856	23964	Mm.445432	NM_011856	ENSMUSG00000049336	Tenm2	2610040L17Rik|9330187F13Rik|D3Bwg1534e|Odz2|Odz3|Ten-m2|mKIAA1127	teneurin transmembrane protein 2	protein-coding	0	0.346535
Merged-chr2-129129635-1	chr2	129129585	129129685	+	2.6	cIP1vsInput	promoter-TSS (NM_025395)	promoter-TSS (NM_025395)	-65	NM_025395	66170	Mm.40621	NM_025395	ENSMUSG00000037938	Chchd5	1110027L01Rik|AW045710	coiled-coil-helix-coiled-coil-helix domain containing 5	protein-coding	0.07	0.534653
Merged-chr15-24987513-1	chr15	24987463	24987563	+	2.6	cIP2vsInput	Intergenic	Lx5|LINE|L1	426251	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	"brain abundant, membrane attached signal protein 1"	protein-coding	0	0.326733
Merged-chrY-5219047-2	chrY	5218997	5219098	+	2.6	cIP1vsInput|cIP2vsInput	Intergenic	Lx5b|LINE|L1	1447374	NM_001270516	100862398		NM_001270516		Gm21708	-	"predicted gene, 21708"	protein-coding	0.009901	0.303922
Merged-chr5-110269952-1	chr5	110269902	110270002	+	2.6	cIP2vsInput	promoter-TSS (NM_001163538)	promoter-TSS (NM_001163538)	-53	NM_028273	72542	Mm.61682	NM_001163538	ENSMUSG00000029500	Pgam5	2610528A17Rik	phosphoglycerate mutase family member 5	protein-coding	0.09	0.70297
Merged-chr5-13660617-1	chr5	13660567	13660667	+	2.6	cIP1vsInput	Intergenic	Intergenic	-131002	NM_027650	71026	Mm.158536	NM_027650	ENSMUSG00000067855	Speer3	4933405P08Rik|SPEER-3	spermatogenesis associated glutamate (E)-rich protein 3	protein-coding	0	0.316832
Merged-chr19-23730879-1	chr19	23730829	23730929	+	2.6	cIP2vsInput	Intergenic	Intergenic	-27997	NM_177034	319924	Mm.22879	NM_177034	ENSMUSG00000024897	Apba1	6430513E09Rik|Lin-10|Mint|Mint1|Urop11|X11|X11alpha	"amyloid beta (A4) precursor protein binding, family A, member 1"	protein-coding	0.01	0.386139
Merged-chr8-73402996-1	chr8	73402946	73403046	+	2.6	cIP1vsInput	Intergenic	RMER16-int|LTR|ERVK	-50440	NM_010687	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large	BPFD#36|Gyltl1a|Mbp-1|Mbp1|enr|fg|froggy|mKIAA0609|myd	like-glycosyltransferase	protein-coding	0	0.29703
Merged-chr8-87473101-2	chr8	87473049	87473154	+	2.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	289	NR_033430	100040294	Mm.213632	NR_033430	ENSMUSG00000097248	Gm2694	-	predicted gene 2694	miscRNA	0.171429	0.773585
Merged-chr4-40630252-1	chr4	40630202	40630302	+	2.6	cIP2vsInput	Intergenic	Lx5|LINE|L1	72664	NM_025545	66408	Mm.430710	NM_001025445	ENSMUSG00000028411	Aptx	2410016G21Rik|AA388047	aprataxin	protein-coding	0	0.336634
Merged-chr11-88955475-1	chr11	88955425	88955525	+	2.6	cIP1vsInput	promoter-TSS (NM_029023)	promoter-TSS (NM_029023)	-33	NM_029023	74617	Mm.34126	NM_029023	ENSMUSG00000000278	Scpep1	2410018F01Rik|4833411K15Rik|AI957256|Risc	serine carboxypeptidase 1	protein-coding	0.09	0.70297
Merged-chr19-15985058-1	chr19	15985008	15985108	+	2.6	cIP2vsInput	promoter-TSS (NR_045355)	promoter-TSS (NR_045355)	-17	NR_045355	100502653	Mm.149980	NR_045355	ENSMUSG00000097557	C130060C02Rik	-	RIKEN cDNA C130060C02 gene	miscRNA	0.16	0.712871
Merged-chr11-31843948-1	chr11	31843898	31843998	+	2.6	cIP2vsInput	Intergenic	Intergenic	-19401	NR_102312	414116	Mm.150222	NR_102310		D630024D03Rik	-	RIKEN cDNA D630024D03 gene	miscRNA	0.01	0.534653
Merged-chr2-128339502-1	chr2	128339452	128339552	+	2.6	cIP2vsInput	"intron (NR_028589, intron 1 of 2)"	"intron (NR_028589, intron 1 of 2)"	89849	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	miscRNA	0	0.435644
Merged-chr17-50795337-1	chr17	50795287	50795387	+	2.6	cIP2vsInput	"intron (NM_028162, intron 17 of 21)"	"intron (NM_028162, intron 17 of 21)"	285790	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding	0.01	0.277228
Merged-chr7-136924793-1	chr7	136924743	136924843	+	2.6	cIP2vsInput	"intron (NM_008598, intron 1 of 4)"	"intron (NM_008598, intron 1 of 4)"	30182	NM_008598	17314	Mm.440219	NM_008598	ENSMUSG00000054612	Mgmt	AGT|AI267024|Agat	O-6-methylguanine-DNA methyltransferase	protein-coding	0.04	0.524752
Merged-chr10-43353633-1	chr10	43353583	43353683	+	2.6	cIP1vsInput	"intron (NM_001168289, intron 3 of 7)"	"intron (NM_001168289, intron 3 of 7)"	-125507	NM_199028	331623	Mm.490388	NM_199028	ENSMUSG00000038214	Bend3	mKIAA1553	BEN domain containing 3	protein-coding	0.01	0.29703
Merged-chr11-120087094-1	chr11	120087044	120087144	+	2.6	cIP2vsInput	promoter-TSS (NM_009734)	promoter-TSS (NM_009734)	-267	NM_009734	12009	Mm.2556	NM_009734	ENSMUSG00000039781	Azi1	AZ1|Azi	5-azacytidine induced gene 1	protein-coding	0.06	0.60396
Merged-chr5-92809073-1	chr5	92809023	92809123	+	2.6	cIP2vsInput	promoter-TSS (NM_001077595)	promoter-TSS (NM_001077595)	-315	NM_001077595	27428	Mm.46014	NM_001077595	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding	0.04	0.613861
Merged-chr17-78417859-1	chr17	78417809	78417909	+	2.6	cIP1vsInput	"exon (NM_199448, exon 1 of 8)"	"exon (NM_199448, exon 1 of 8)"	244	NM_199448	225020	Mm.236835	NM_199448	ENSMUSG00000056121	Fez2	9030616F16|D17Ertd315e	fasciculation and elongation protein zeta 2 (zygin II)	protein-coding	0.13	0.782178
Merged-chr3-122312455-1	chr3	122312405	122312505	+	2.6	cIP1vsInput	Intergenic	L1MC4|LINE|L1	-18752	NR_030439	791077		NR_030439	ENSMUSG00000076456	Mir760	Mirn760|mir-760|mmu-mir-760	microRNA 760	miscRNA	0	0.346535
Merged-chr5-107088320-1	chr5	107088270	107088370	+	2.6	cIP2vsInput	Intergenic	Intergenic	123759	NM_001271566	12545	Mm.20842	NM_001271566	ENSMUSG00000029283	Cdc7	AI597260|Cdc7l1|muCdc7	cell division cycle 7 (S. cerevisiae)	protein-coding	0.05	0.70297
Merged-chr1-110414407-1	chr1	110414357	110414457	+	2.6	cIP2vsInput	Intergenic	Intergenic	430670	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.346535
Merged-chr14-81159324-1	chr14	81159274	81159374	+	2.6	cIP2vsInput	Intergenic	Intergenic	1159022	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0.01	0.346535
Merged-chr2-78544850-1	chr2	78544800	78544900	+	2.6	cIP1vsInput	Intergenic	Intergenic	307303	NM_177843	329436	Mm.235448	NM_177843		Gm14461	A830093M07|OTTMUSG00000016703	predicted gene 14461	protein-coding	0	0.326733
Merged-chr2-12520651-1	chr2	12520601	12520701	+	2.6	cIP2vsInput	Intergenic	Intergenic	-101191	NM_024185	66960	Mm.34059	NM_024185	ENSMUSG00000026767	Fam188a	1810041E18Rik|2310047O13Rik|5830410F13Rik|AI447827|AW111958	"family with sequence similarity 188, member A"	protein-coding	0	0.306931
Merged-chr6-85587611-2	chr6	85587559	85587664	+	2.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_145223)	promoter-TSS (NM_145223)	80	NM_145223	236266	Mm.246967	NM_145223	ENSMUSG00000063810	Alms1	bbb	Alstrom syndrome 1	protein-coding	0.057143	0.669811
Merged-chr4-86899335-1	chr4	86899285	86899385	+	2.6	cIP1vsInput	"intron (NM_139306, intron 3 of 5)"	MIR3|SINE|MIR	24921	NM_139306	230379	Mm.458684	NM_139306	ENSMUSG00000038007	Acer2	2410116I05Rik|Asah3l|CRG-L1|maCER2	alkaline ceramidase 2	protein-coding	0.05	0.574257
Merged-chr9-84442310-1	chr9	84442260	84442360	+	2.6	cIP1vsInput	Intergenic	MERVL_2A-int|LTR|ERVL	-332088	NR_040739	75253	Mm.401984	NR_040739		4930554C24Rik	-	RIKEN cDNA 4930554C24 gene	miscRNA	0	0.326733
Merged-chr11-37913786-1	chr11	37913736	37913836	+	2.6	cIP1vsInput	Intergenic	Intergenic	606259	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0	0.376238
Merged-chr9-79662288-1	chr9	79662238	79662338	+	2.6	cIP1vsInput	"intron (NM_007730, intron 26 of 65)"	"intron (NM_007730, intron 26 of 65)"	56390	NM_007730	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	AW743884	"collagen, type XII, alpha 1"	protein-coding	0	0.287129
Merged-chr9-40469392-1	chr9	40469342	40469442	+	2.6	cIP2vsInput	Intergenic	Intergenic	-13628	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding	0.02	0.39604
Merged-chr9-65102382-1	chr9	65102332	65102432	+	2.6	cIP2vsInput	"intron (NM_020043, intron 1 of 19)"	"intron (NM_020043, intron 1 of 19)"	887	NM_020043	56741	Mm.209041	NM_020043	ENSMUSG00000032816	Igdcc4	9330155G14Rik|DDM36|Nope|WI-16786|WI-18508|mKIAA1628	"immunoglobulin superfamily, DCC subclass, member 4"	protein-coding	0.03	0.564356
Merged-chr14-35646716-1	chr14	35646666	35646766	+	2.6	cIP1vsInput	Intergenic	L1ME1|LINE|L1	165262	NM_001033766	239036	Mm.239970	NM_001033766	ENSMUSG00000041068	4930596D02Rik	-	RIKEN cDNA 4930596D02 gene	protein-coding	0	0.366337
Merged-chr9-20460072-1	chr9	20460022	20460122	+	2.6	cIP2vsInput	promoter-TSS (NM_011753)	promoter-TSS (NM_011753)	88	NM_011753	22688	Mm.107441	NM_011753		Zfp26	5033428C05Rik|KRAB15|Zfp-26|Zfp70|Zfp81-rs1|mKIAA4196|mkr-3|mszf14|mszf52	zinc finger protein 26	protein-coding	0.06	0.455446
Merged-chr16-53252749-1	chr16	53252699	53252799	+	2.6	cIP2vsInput	Intergenic	L1MC1|LINE|L1	-437005	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	miscRNA	0	0.316832
Merged-chr11-109331624-1	chr11	109331574	109331674	+	2.6	cIP1vsInput	Intergenic	Intergenic	-15243	NR_027883	67927	Mm.394490	NR_027883		1700096J18Rik	-	RIKEN cDNA 1700096J18 gene	miscRNA	0.01	0.50495
Merged-chr8-41639728-1	chr8	41639678	41639778	+	2.6	cIP1vsInput	Intergenic	Intergenic	-187539	NR_045497	69966	Mm.416903	NR_045497		2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	miscRNA	0	0.366337
Merged-chr5-87860270-1	chr5	87860220	87860320	+	2.6	cIP1vsInput	Intergenic	Intergenic	9911	NR_003652	654494	Mm.475331	NM_001039193	ENSMUSG00000067156	Gm7337	EG654494	DAZ interacting protein 1 pseudogene	pseudo	0.01	0.316832
Merged-chr11-82971141-1	chr11	82971091	82971191	+	2.6	cIP2vsInput	Intergenic	Intergenic	-10460	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	1700003F17Rik	-	RIKEN cDNA 1700003F17 gene	miscRNA	0.15	0.732673
Merged-chr3-158289090-1	chr3	158289040	158289140	+	2.6	cIP1vsInput	"intron (NM_001081358, intron 7 of 27)"	"intron (NM_001081358, intron 7 of 27)"	252387	NM_024194	67144	Mm.358704	NM_024194	ENSMUSG00000063052	Lrrc40	2610040E16Rik|AI837674	leucine rich repeat containing 40	protein-coding	0.01	0.29703
Merged-chr15-12679880-1	chr15	12679830	12679930	+	2.6	cIP2vsInput	Intergenic	Intergenic	-87324	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding	0.01	0.306931
Merged-chr11-56096102-1	chr11	56096052	56096152	+	2.6	cIP1vsInput	Intergenic	Intergenic	-55115	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding	0.03	0.346535
Merged-chr15-46376414-1	chr15	46376364	46376464	+	2.6	cIP2vsInput	Intergenic	Intergenic	51829	NR_045509	71120	Mm.158571	NR_045509		1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	miscRNA	0	0.326733
Merged-chr5-14680637-1	chr5	14680587	14680687	+	2.6	cIP2vsInput	"exon (NM_001110796, exon 6 of 20)"	"exon (NM_001110796, exon 6 of 20)"	165719	NM_001110796	26875	Mm.146275	NM_001110796	ENSMUSG00000061601	Pclo	Acz|Pico|mKIAA0559	piccolo (presynaptic cytomatrix protein)	protein-coding	0.01	0.455446
Merged-chr13-42619118-1	chr13	42619068	42619168	+	2.6	cIP2vsInput	Intergenic	Intergenic	-61505	NM_198419	218194	Mm.160124	NM_001005740	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding	0.01	0.306931
Merged-chr9-80505502-1	chr9	80505452	80505552	+	2.6	cIP1vsInput	Intergenic	Intergenic	-40064	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding	0	0.356436
Merged-chr3-36964296-1	chr3	36964246	36964346	+	2.6	cIP1vsInput	"intron (NM_172679, intron 37 of 85)"	PB1|SINE|Alu	-99360	NM_009350	21744	Mm.8122	NM_009350	ENSMUSG00000027719	Adad1	Tenr	adenosine deaminase domain containing 1 (testis specific)	protein-coding	0	0.366337
Merged-chr12-3235716-1	chr12	3235666	3235766	+	2.6	cIP1vsInput	promoter-TSS (NR_015551)	promoter-TSS (NR_015551)	-75	NR_015551	74173	Mm.309774	NR_015551	ENSMUSG00000079179	1700012B15Rik	1810036A22Rik	RIKEN cDNA 1700012B15 gene	miscRNA	0.12	0.643564
Merged-chr5-5944887-2	chr5	5944814	5944961	+	2.6	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-195570	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding	0.013605	0.297297
Merged-chr15-94313111-1	chr15	94313061	94313161	+	2.6	cIP1vsInput	"intron (NM_177431, intron 28 of 38)"	"intron (NM_177431, intron 28 of 38)"	65909	NR_045629	328594	Mm.135523	NR_045629		D630010B17Rik	Gm811	RIKEN cDNA D630010B17 gene	miscRNA	0	0.316832
Merged-chr12-67922607-1	chr12	67922557	67922657	+	2.6	cIP2vsInput	Intergenic	Intergenic	-253336	NR_033146	100316870	Mm.379794	NR_033146		Gm17821	-	DDB1 and CUL4 associated factor 5 pseudogene	pseudo	0	0.287129
Merged-chr12-37685995-1	chr12	37685945	37686045	+	2.6	cIP2vsInput	Intergenic	Intergenic	-194710	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	"diacylglycerol kinase, beta"	protein-coding	0	0.29703
Merged-chr14-54449165-1	chr14	54449115	54449215	+	2.6	cIP2vsInput	Intergenic	Intergenic	-14982	NM_022993	65107	Mm.472719	NM_022993		Lrp10	Lrp9	low-density lipoprotein receptor-related protein 10	protein-coding	0.05	0.613861
Merged-chr17-14913849-1	chr17	14913799	14913899	+	2.6	cIP1vsInput	"exon (NM_175173, exon 15 of 25)"	"exon (NM_175173, exon 15 of 25)"	29275	NM_175173	71682		NM_175173	ENSMUSG00000046991	Wdr27	0610012K18Rik	WD repeat domain 27	protein-coding	0	0.316832
Merged-chr9-85374489-1	chr9	85374439	85374539	+	2.6	cIP1vsInput	Intergenic	Intergenic	-47339	NM_001160379	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	D930050G01Rik	"family with sequence similarity 46, member A"	protein-coding	0.01	0.356436
Merged-chr5-28180195-1	chr5	28180145	28180245	+	2.6	cIP1vsInput	Intergenic	Intergenic	14499	NM_010134	13799	Mm.4298	NM_010134		En2	BB131122|En-2	engrailed 2	protein-coding	0.04	0.50495
Merged-chrY-8837491-1	chrY	8837441	8837541	+	2.6	cIP1vsInput	Intergenic	Intergenic	-2322	NM_001017394	100039753	Mm.458473	NM_001017394	ENSMUSG00000096227	Gm20815	-	"predicted gene, 20815"	protein-coding	0	0.386139
Merged-chr12-28649610-1	chr12	28649560	28649660	+	2.6	cIP2vsInput	promoter-TSS (NM_011275)	promoter-TSS (NM_011275)	8	NM_011275	19819	Mm.10152	NM_011275	ENSMUSG00000020630	Rnaseh1	-	ribonuclease H1	protein-coding	0.16	0.752475
Merged-chr3-120301436-1	chr3	120301386	120301486	+	2.6	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	-518048	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.01	0.306931
Merged-chr9-101035155-1	chr9	101035105	101035205	+	2.6	cIP1vsInput	promoter-TSS (NM_025835)	promoter-TSS (NM_025835)	-280	NM_025835	66904	Mm.335385	NM_025835	ENSMUSG00000032527	Pccb	1300012P06Rik|AI314687|R74805	"propionyl Coenzyme A carboxylase, beta polypeptide"	protein-coding	0.02	0.445545
Merged-chr16-74226974-1	chr16	74226924	74227024	+	2.6	cIP2vsInput	"intron (NM_175549, intron 2 of 27)"	"intron (NM_175549, intron 2 of 27)"	115093	NR_030464	751561		NR_030464		Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	miscRNA	0	0.326733
Merged-chr10-85957682-1	chr10	85957632	85957732	+	2.6	cIP1vsInput	"exon (NM_145422, exon 1 of 12)"	"exon (NM_145422, exon 1 of 12)"	111	NM_145422	28088	Mm.9257	NM_145422	ENSMUSG00000001783	D10Wsu52e	AI255213|AI463255|FAAP|HSPC117	"DNA segment, Chr 10, Wayne State University 52, expressed"	protein-coding	0.05	0.49505
Merged-chr17-51257647-1	chr17	51257597	51257697	+	2.6	cIP1vsInput	"intron (NR_035408, intron 2 of 6)"	"intron (NR_035408, intron 2 of 6)"	-20341	NR_037260	100526491		NR_037260		Mir669a-9	mmu-mir-669a-9	microRNA 4669a-9	miscRNA	0.01	0.366337
Merged-chr4-13300478-1	chr4	13300428	13300528	+	2.6	cIP2vsInput	Intergenic	Intergenic	393641	NM_001171801	208820	Mm.12057	NM_001171801		Triqk	C130086A10|Gm11818|OTTMUSG00000004461	triple QxxK/R motif containing	protein-coding	0.01	0.485149
Merged-chr10-29641754-1	chr10	29641704	29641804	+	2.6	cIP1vsInput	Intergenic	Intergenic	-105887	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3 homolog (Xenopus laevis)	protein-coding	0.01	0.39604
Merged-chr16-66135352-1	chr16	66135302	66135402	+	2.6	cIP2vsInput	Intergenic	Intergenic	319719	NM_028572	73569	Mm.482366	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like 3 (Drosophila)	protein-coding	0	0.346535
Merged-chr7-5051689-1	chr7	5051639	5051739	+	2.6	cIP2vsInput	"5' UTR (NM_026900, exon 1 of 2)"	"5' UTR (NM_026900, exon 1 of 2)"	157	NM_026900	68992	Mm.41484	NM_026900	ENSMUSG00000055633	Zfp580	1500015O20Rik|AI838225|Znf580	zinc finger protein 580	protein-coding	0.11	0.762376
Merged-chr1-168784176-1	chr1	168784126	168784226	+	2.6	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-351918	NM_008783	18514	Mm.440114	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|AI848790|AU015730|D230003C07Rik|Pbx-1|Pbx1a|Pbx1b	pre B cell leukemia homeobox 1	protein-coding	0	0.267327
Merged-chr15-103147079-1	chr15	103147029	103147129	+	2.6	cIP1vsInput	promoter-TSS (NR_045743)	promoter-TSS (NR_045743)	-251	NR_045743	432989	Mm.383979	NR_045743	ENSMUSG00000097003	D930007P13Rik	-	Riken cDNA D930007P13 gene	miscRNA	0.09	0.683168
Merged-chr11-25501796-1	chr11	25501746	25501846	+	2.6	cIP1vsInput	Intergenic	Lx3A|LINE|L1	175689	NR_045853	71234	Mm.158627	NR_045853	ENSMUSG00000033015	4933427E13Rik	-	RIKEN cDNA 4933427E13 gene	miscRNA	0	0.316832
Merged-chr6-120916753-1	chr6	120916703	120916803	+	2.6	cIP2vsInput	promoter-TSS (NM_007544)	promoter-TSS (NM_007544)	67	NM_007544	12122	Mm.235081	NM_007544	ENSMUSG00000004446	Bid	2700049M22Rik|AI875481|AU022477	BH3 interacting domain death agonist	protein-coding	0.12	0.693069
Merged-chr4-39298239-1	chr4	39298189	39298289	+	2.6	cIP1vsInput	Intergenic	ORR1D2|LTR|ERVL-MaLR	-152054	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding	0	0.376238
Merged-chr1-15250030-1	chr1	15249980	15250080	+	2.6	cIP2vsInput	Intergenic	Intergenic	-62422	NM_001098528	98741	Mm.156081	NM_001033195		Kcnb2	9630047L19Rik|BB130875|Kv2.2	"potassium voltage gated channel, Shab-related subfamily, member 2"	protein-coding	0	0.336634
Merged-chr8-24117443-1	chr8	24117393	24117493	+	2.6	cIP1vsInput	Intergenic	Lx7|LINE|L1	321503	NM_026931	69068	Mm.25775	NM_026931	ENSMUSG00000056313	1810011O10Rik	1110065B09Rik|AW121743|AW321058	RIKEN cDNA 1810011O10 gene	protein-coding	0.01	0.336634
Merged-chr7-35754532-1	chr7	35754482	35754582	+	2.6	cIP2vsInput	promoter-TSS (NM_178704)	promoter-TSS (NM_178704)	-78	NM_178704	233115	Mm.257808	NM_178704	ENSMUSG00000043671	Dpy19l3	6030410G08|9330164H19Rik	dpy-19-like 3 (C. elegans)	protein-coding	0.14	0.732673
Merged-chr5-68469225-1	chr5	68469175	68469275	+	2.6	cIP2vsInput	Intergenic	Intergenic	437390	NM_001018019	433899	Mm.332422	NM_001018019	ENSMUSG00000068082	Grxcr1	Tg(Eno2-Gabrb3)0370Brll|pi|tde	"glutaredoxin, cysteine rich 1"	protein-coding	0	0.356436
Merged-chr1-46040689-1	chr1	46040639	46040739	+	2.6	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-10252	NR_037691	212225	Mm.78540	NM_172504	ENSMUSG00000044457	Gm4776	4930509O22|EG212225	sperm motility kinase W	pseudo	0.01	0.326733
Merged-chr18-60848382-1	chr18	60848332	60848432	+	2.6	cIP2vsInput	"intron (NM_011552, intron 1 of 24)"	"intron (NM_011552, intron 1 of 24)"	582	NM_011552	21453	Mm.486251	NM_001198984	ENSMUSG00000024613	Tcof1	AA408847|AW209012|treacle	"Treacher Collins Franceschetti syndrome 1, homolog"	protein-coding	0.04	0.554455
Merged-chr4-22529960-1	chr4	22529910	22530010	+	2.6	cIP2vsInput	Intergenic	MTD-int|LTR|ERVL-MaLR	-41594	NM_008899	18992	Mm.487875	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	"POU domain, class 3, transcription factor 2"	protein-coding	0	0.29703
Merged-chr19-57329154-1	chr19	57329104	57329204	+	2.6	cIP2vsInput	"intron (NR_040316, intron 1 of 2)"	"intron (NR_040316, intron 1 of 2)"	31745	NR_040316	320879	Mm.375089	NR_040316	ENSMUSG00000097785	B230217O12Rik	-	RIKEN cDNA B230217O12 gene	miscRNA	0	0.316832
Merged-chr1-28137579-1	chr1	28137529	28137629	+	2.6	cIP2vsInput	Intergenic	Lx3A|LINE|L1	642673	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0.01	0.326733
Merged-chr6-60377570-1	chr6	60377520	60377620	+	2.6	cIP2vsInput	"intron (NR_015565, intron 1 of 1)"	"intron (NR_015565, intron 1 of 1)"	26137	NR_015565	208079	Mm.490691	NR_015565		A530053G22Rik	-	RIKEN cDNA A530053G22 gene	miscRNA	0	0.386139
Merged-chr12-87861411-1	chr12	87861361	87861461	+	2.6	cIP1vsInput	promoter-TSS (NR_033562)	promoter-TSS (NR_033562)	61	NR_033562	100038982	Mm.16926	NR_033562		Gm1995	-	"REX1, RNA exonuclease 1 homolog pseudogene"	pseudo	0.01	0.49505
Merged-chr1-70501157-1	chr1	70501107	70501207	+	2.6	cIP2vsInput	"intron (NM_025728, intron 7 of 7)"	"intron (NM_025728, intron 7 of 7)"	-224558	NM_177164	320460	Mm.360649	NM_177164	ENSMUSG00000045648	Vwc2l	A830006F12Rik|Brl	von Willebrand factor C domain-containing protein 2-like	protein-coding	0	0.366337
Merged-chr8-71131385-1	chr8	71131335	71131435	+	2.6	cIP1vsInput	Intergenic	Intergenic	-104630	NR_045487	69419	Mm.188688	NR_045487		1700026F02Rik	-	RIKEN cDNA 1700026F02 gene	miscRNA	0	0.267327
Merged-chr2-106084937-1	chr2	106084887	106084987	+	2.6	cIP2vsInput	Intergenic	Intergenic	-81388	NR_033993	99349	Mm.25661	NM_026992	ENSMUSG00000027166	Dnajc24	1700030A21Rik|2610027M02Rik|AV066965|AW240712|Dph4|MmDjC7|Zcsl3	"DnaJ (Hsp40) homolog, subfamily C, member 24"	protein-coding	0	0.326733
Merged-chr10-116772154-1	chr10	116772104	116772204	+	2.6	cIP1vsInput	Intergenic	Intergenic	-42977	NR_045345	72286	Mm.396207	NR_045345		1700030O20Rik	-	RIKEN cDNA 1700030O20 gene	miscRNA	0.02	0.415842
Merged-chr16-75109280-1	chr16	75109230	75109330	+	2.6	cIP1vsInput	Intergenic	Intergenic	458402	NM_177142	320355	Mm.99517	NM_001252513		Lipi	D930038D03Rik|lpd1	"lipase, member I"	protein-coding	0	0.346535
Merged-chr18-54745367-1	chr18	54745317	54745417	+	2.6	cIP1vsInput	Intergenic	Intergenic	133623	NR_045400	328957	Mm.402781	NR_045400		9330117O12Rik	9330117O12	RIKEN cDNA 9330117O12 gene	miscRNA	0	0.287129
Merged-chr18-16470533-1	chr18	16470483	16470583	+	2.6	cIP2vsInput	Intergenic	Intergenic	338516	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-cadherin|Ncad	cadherin 2	protein-coding	0	0.356436
Merged-chr3-56413647-1	chr3	56413597	56413697	+	2.6	cIP2vsInput	Intergenic	Intergenic	-229946	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding	0.01	0.415842
Merged-chrY-6668650-1	chrY	6668600	6668700	+	2.6	cIP1vsInput	Intergenic	Intergenic	499127	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.39604
Merged-chr15-7659634-1	chr15	7659584	7659684	+	2.6	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-151377	NM_010275	14573	Mm.4679	NM_010275	ENSMUSG00000022144	Gdnf	AI385739	glial cell line derived neurotrophic factor	protein-coding	0	0.326733
Merged-chr1-101225631-1	chr1	101225581	101225681	+	2.6	cIP2vsInput	Intergenic	Intergenic	69863	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0.01	0.376238
Merged-chr13-63902129-1	chr13	63902079	63902179	+	2.6	cIP2vsInput	Intergenic	Intergenic	86795	NM_023507	76251	Mm.186610	NM_001013608	ENSMUSG00000021470	Ercc6l2	0610007P08Rik|1700019D06Rik|9330134C04Rik|Rad26l|Sr278	"excision repair cross-complementing rodent repair deficiency, complementation group 6 like 2"	protein-coding	0.05	0.663366
Merged-chr13-87804459-1	chr13	87804409	87804509	+	2.6	cIP2vsInput	Intergenic	Intergenic	-1017013	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0	0.356436
Merged-chr6-109739221-1	chr6	109739171	109739271	+	2.6	cIP2vsInput	Intergenic	Intergenic	-906377	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0.01	0.346535
Merged-chr18-43322341-1	chr18	43322291	43322391	+	2.6	cIP1vsInput	Intergenic	Intergenic	50931	NM_001136086	22240	Mm.428551	NM_001136086	ENSMUSG00000024501	Dpysl3	CRMP-4|TUC4|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding	0	0.346535
Merged-chr17-14173706-1	chr17	14173656	14173756	+	2.6	cIP2vsInput	Intergenic	Intergenic	30125	NM_172826	240025	Mm.79993	NM_172826	ENSMUSG00000048826	Dact2	2900084M21Rik|A630024E20|Dpr2|Frd2|dapper2	"dapper homolog 2, antagonist of beta-catenin (xenopus)"	protein-coding	0	0.49505
Merged-chr8-70042721-1	chr8	70042671	70042771	+	2.6	cIP1vsInput	promoter-TSS (NM_027481)	promoter-TSS (NM_027481)	13	NM_001167939	74549	Mm.269061	NM_001167939	ENSMUSG00000031858	Mau2	9130404D08Rik|A930019L04Rik|C77863|C79014|Mau-2|mKIAA0892	MAU2 chromatid cohesion factor homolog (C. elegans)	protein-coding	0.1	0.683168
Merged-chr1-188443994-1	chr1	188443944	188444044	+	2.6	cIP1vsInput	"intron (NM_021408, intron 16 of 70)"	"intron (NM_021408, intron 16 of 70)"	181156	NM_021408	22283	Mm.331238	NM_021408	ENSMUSG00000026609	Ush2a	A930011D15Rik|A930037M10Rik|Gm676|Gm983|Mush2a|Usherin	"Usher syndrome 2A (autosomal recessive, mild)"	protein-coding	0	0.316832
Merged-chr17-92735659-1	chr17	92735609	92735709	+	2.6	cIP2vsInput	Intergenic	Intergenic	-463763	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0	0.29703
Merged-chr1-11443284-1	chr1	11443234	11443334	+	2.6	cIP2vsInput	"intron (NM_001160371, intron 1 of 7)"	"intron (NM_001160371, intron 1 of 7)"	29179	NM_001160371	320492	Mm.52021	NM_001160369	ENSMUSG00000057715	A830018L16Rik	-	RIKEN cDNA A830018L16 gene	protein-coding	0.01	0.346535
Merged-chr14-79451448-1	chr14	79451398	79451498	+	2.6	cIP2vsInput	promoter-TSS (NM_001034882)	promoter-TSS (NM_001034882)	-387	NM_001034882	432879	Mm.308666	NM_001034882	ENSMUSG00000075502	Zbtbd6	EG432879|Gm5465	kelch repeat and BTB (POZ) domain containing 6	protein-coding	0.01	0.267327
Merged-chr6-135246700-1	chr6	135246650	135246750	+	2.6	cIP1vsInput	"intron (NM_001080553, intron 1 of 5)"	Lx8b|LINE|L1	1184	NM_001080552	14840	Mm.272306	NM_001080552	ENSMUSG00000030206	Gsg1	-	germ cell-specific gene 1	protein-coding	0	0.376238
Merged-chr4-28341042-1	chr4	28340992	28341092	+	2.6	cIP2vsInput	Intergenic	Intergenic	-472103	NM_001122889	13841	Mm.257266	NM_001122889	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding	0	0.287129
Merged-chr10-129116802-1	chr10	129116752	129116852	+	2.6	cIP1vsInput	Intergenic	Intergenic	-4379	NM_146267	257667	Mm.377271	NM_146267	ENSMUSG00000042801	Olfr769	MOR114-14	olfactory receptor 769	protein-coding	0	0.277228
Merged-chr10-121022351-1	chr10	121022301	121022401	+	2.6	cIP2vsInput	Intergenic	Intergenic	-11653	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding	0	0.465347
Merged-chr3-11012609-1	chr3	11012559	11012659	+	2.6	cIP2vsInput	Intergenic	L1MA4|LINE|L1	-572485	NM_001127191	74718	Mm.440548	NM_001127191	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding	0	0.346535
Merged-chr12-101410854-1	chr12	101410804	101410904	+	2.6	cIP2vsInput	"intron (NM_173023, intron 2 of 26)"	MER34A|LTR|ERV1	6181	NM_173023	271036	Mm.84218	NM_173023	ENSMUSG00000047014	Catsperb	4931410B03|4932415G16Rik	catsper channel auxiliary subunit beta	protein-coding	0	0.366337
Merged-chr14-68524001-1	chr14	68523951	68524051	+	2.6	cIP2vsInput	"intron (NM_007402, intron 7 of 22)"	"intron (NM_007402, intron 7 of 22)"	9688	NM_007402	11500	Mm.261495	NM_007402	ENSMUSG00000022056	Adam7	9230104J12Rik|EAP1|EAPI	a disintegrin and metallopeptidase domain 7	protein-coding	0	0.306931
Merged-chr10-94198861-1	chr10	94198811	94198911	+	2.6	cIP1vsInput	promoter-TSS (NM_025551)	promoter-TSS (NM_025551)	-148	NM_025551	66414	Mm.461501	NM_025551	ENSMUSG00000020022	Ndufa12	2410011G03Rik|AW112974	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 12"	protein-coding	0.04	0.49505
Merged-chr10-53579827-1	chr10	53579777	53579877	+	2.6	cIP1vsInput	"intron (NM_027830, intron 8 of 13)"	L1MC2|LINE|L1	-17134	NM_025541	66403	Mm.272989	NM_025541	ENSMUSG00000019857	Asf1a	2310079C17Rik|C79052	ASF1 anti-silencing function 1 homolog A (S. cerevisiae)	protein-coding	0	0.316832
Merged-chr1-75479365-1	chr1	75479315	75479415	+	2.6	cIP2vsInput	promoter-TSS (NM_177056)	promoter-TSS (NM_177056)	106	NM_001001565	74241	Mm.260577	NM_001001565	ENSMUSG00000032997	Chpf	1700028N03Rik|AI414328|D1Bwg1363e	chondroitin polymerizing factor	protein-coding	0.09	0.683168
Merged-chr11-99385873-1	chr11	99385823	99385923	+	2.6	cIP2vsInput	"intron (NM_010660, intron 7 of 7)"	"intron (NM_010660, intron 7 of 7)"	3491	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding	0.01	0.336634
Merged-chr2-63812241-1	chr2	63812191	63812291	+	2.6	cIP2vsInput	Intergenic	Intergenic	285797	NM_001267846	60344	Mm.483676	NM_001267846	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding	0	0.277228
Merged-chr9-124066609-1	chr9	124066559	124066659	+	2.6	cIP1vsInput	Intergenic	L1MC|LINE|L1	-35574	NM_009915	12772	Mm.6272	NM_009915	ENSMUSG00000049103	Ccr2	Cc-ckr-2|Ccr2a|Ccr2b|Ckr2|Ckr2a|Ckr2b|Cmkbr2|mJe-r	chemokine (C-C motif) receptor 2	protein-coding	0	0.29703
Merged-chr17-93102460-1	chr17	93102410	93102510	+	2.6	cIP1vsInput	Intergenic	Intergenic	-96962	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0	0.376238
Merged-chr13-51418560-1	chr13	51418510	51418610	+	2.6	cIP1vsInput	"intron (NM_010101, intron 1 of 1)"	"intron (NM_010101, intron 1 of 1)"	9942	NM_010101	13610	Mm.136736	NM_010101	ENSMUSG00000067586	S1pr3	AI132464|Edg3|Lpb3|S1p3	sphingosine-1-phosphate receptor 3	protein-coding	0.03	0.524752
Merged-chr2-129638364-1	chr2	129638314	129638414	+	2.6	cIP1vsInput	Intergenic	Lx9|LINE|L1	45169	NM_001177647	19261	Mm.1682	NM_001177646	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding	0.01	0.306931
Merged-chr6-81965988-1	chr6	81965938	81966038	+	2.6	cIP2vsInput	promoter-TSS (NM_026490)	promoter-TSS (NM_026490)	-39	NM_026490	56284	Mm.276293	NM_026490	ENSMUSG00000030045	Mrpl19	9030416F12Rik|9130412E02Rik|D6Ertd157e|MRP-L15|RLX1|Rpml15	mitochondrial ribosomal protein L19	protein-coding	0.06	0.564356
Merged-chr7-45154272-1	chr7	45154222	45154322	+	2.6	cIP2vsInput	promoter-TSS (NM_029406)	promoter-TSS (NM_029406)	-126	NM_029406	68845	Mm.181689	NM_029406	ENSMUSG00000003423	Pih1d1	1110061L23Rik|4933413A04Rik|Nop17	PIH1 domain containing 1	protein-coding	0.1	0.70297
Merged-chr5-115844928-1	chr5	115844878	115844978	+	2.6	cIP2vsInput	promoter-TSS (NM_007708)	promoter-TSS (NM_007708)	-728	NM_007708	12704	Mm.426282	NM_007708	ENSMUSG00000029516	Cit	C030025P15Rik|CRIK|CRIK-SK|Cit-k	citron	protein-coding	0.03	0.564356
Merged-chr10-104435450-1	chr10	104435400	104435500	+	2.6	cIP2vsInput	Intergenic	Intergenic	241408	NM_001270900	667692		NM_001270900	ENSMUSG00000097878	Gm8764	EG667692	predicted gene 8764	protein-coding	0	0.346535
Merged-chr1-42243598-1	chr1	42243548	42243648	+	2.6	cIP2vsInput	Intergenic	Intergenic	451227	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	2610017I09Rik	-	RIKEN cDNA 2610017I09 gene	miscRNA	0.02	0.534653
Merged-chr17-56924138-1	chr17	56924088	56924188	+	2.6	cIP2vsInput	"intron (NM_022328, intron 2 of 11)"	L1_Mur2|LINE|L1	11250	NM_022328	64144	Mm.148748	NM_022328	ENSMUSG00000024212	Mllt1	AA407901|BAM11|ENL|LTG19	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1"	protein-coding	0	0.287129
Merged-chr17-42653788-1	chr17	42653738	42653838	+	2.6	cIP2vsInput	Intergenic	Intergenic	38496	NM_030067	78249	Mm.66217	NM_030067	ENSMUSG00000023918	Gpr115	4632435A09Rik|AV239010	G protein-coupled receptor 115	protein-coding	0	0.326733
Merged-chr14-81551438-1	chr14	81551388	81551488	+	2.6	cIP1vsInput	Intergenic	Intergenic	1551136	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.39604
Merged-chr5-79377309-1	chr5	79377259	79377359	+	2.6	cIP2vsInput	"intron (NR_035474, intron 2 of 4)"	"intron (NR_035474, intron 2 of 4)"	138595	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0.01	0.277228
Merged-chr2-24949607-2	chr2	24949544	24949671	+	2.6	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026021)	promoter-TSS (NM_026021)	-195	NM_026021	67187	Mm.296106	NM_026021		Zmynd19	2700064H14Rik|AA536891|AU014915|mizip	"zinc finger, MYND domain containing 19"	protein-coding	0.133858	0.679688
Merged-chr12-89201576-1	chr12	89201526	89201626	+	2.6	cIP1vsInput	"intron (NM_001198587, intron 5 of 19)"	"intron (NM_001198587, intron 5 of 19)"	248186	NM_172544	18191	Mm.487864	NM_001198587	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding	0	0.366337
Merged-chr14-107841643-1	chr14	107841593	107841693	+	2.6	cIP1vsInput	Intergenic	Intergenic	1072596	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	"SLIT and NTRK-like family, member 1"	protein-coding	0.01	0.356436
Merged-chr1-156752169-1	chr1	156752119	156752219	+	2.6	cIP2vsInput	Intergenic	Intergenic	-33259	NM_145413	215015	Mm.229107	NM_145413	ENSMUSG00000033557	Fam20b	C530043G21Rik|mKIAA0475	"family with sequence similarity 20, member B"	protein-coding	0.02	0.455446
Merged-chr9-7230861-1	chr9	7230811	7230911	+	2.6	cIP2vsInput	Intergenic	Lx|LINE|L1	-41653	NM_008607	17386	Mm.5022	NM_008607	ENSMUSG00000050578	Mmp13	Clg|MMP-13|Mmp1	matrix metallopeptidase 13	protein-coding	0	0.316832
Merged-chr18-15725689-1	chr18	15725639	15725739	+	2.6	cIP1vsInput	Intergenic	Intergenic	-7643	NM_199055	71367	Mm.329304	NM_199055	ENSMUSG00000047161	Chst9	5430438D01Rik	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	protein-coding	0.01	0.336634
Merged-chr9-62550799-1	chr9	62550749	62550849	+	2.6	cIP2vsInput	Intergenic	Intergenic	-13755	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	"coronin, actin binding protein, 2B"	protein-coding	0.03	0.613861
Merged-chr5-31116567-1	chr5	31116517	31116617	+	2.6	cIP2vsInput	promoter-TSS (NM_021447)	promoter-TSS (NM_021447)	-45	NM_021447	58522	Mm.402047	NM_021447	ENSMUSG00000062077	Trim54	4930486E09Rik|4930566I02Rik|MURF|MURF-3|MuRF3|Rnf30	tripartite motif-containing 54	protein-coding	0.01	0.50495
Merged-chr3-98374815-1	chr3	98374765	98374865	+	2.6	cIP1vsInput	Intergenic	Intergenic	-7666	NM_172863	242109	Mm.490503	NM_172863	ENSMUSG00000050064	Zfp697	9430053K19|AI467503|Znf697	zinc finger protein 697	protein-coding	0.01	0.336634
Merged-chr4-138326335-1	chr4	138326285	138326385	+	2.6	cIP2vsInput	promoter-TSS (NM_026880)	promoter-TSS (NM_026880)	-39	NM_026880	68943	Mm.18539	NM_026880	ENSMUSG00000028756	Pink1	1190006F07Rik|AU042772|AW557854|BRPK|mFLJ00387	PTEN induced putative kinase 1	protein-coding	0.12	0.752475
Merged-chr1-39879142-1	chr1	39879092	39879192	+	2.6	cIP1vsInput	Intergenic	Intergenic	-21771	NM_001252202	26921	Mm.19073	NM_001252200	ENSMUSG00000026074	Map4k4	9430080K19Rik|AU043147|AU045934|AW046177|HGK|Nik	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding	0	0.29703
Merged-chr17-79873951-1	chr17	79873901	79874001	+	2.6	cIP2vsInput	"intron (NM_178050, intron 1 of 11)"	"intron (NM_178050, intron 1 of 11)"	22077	NM_019717	56298	Mm.175403	NM_019717	ENSMUSG00000059811	Atl2	2010110I21Rik|AA407293|AV334690|Aip-2|Arl6ip2	atlastin GTPase 2	protein-coding	0.01	0.346535
Merged-chr13-62964695-1	chr13	62964645	62964745	+	2.6	cIP2vsInput	Intergenic	B1_Mus2|SINE|Alu	-50239	NM_028079	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|Aopep	RIKEN cDNA 2010111I01 gene	protein-coding	0.03	0.455446
Merged-chr2-163266793-1	chr2	163266743	163266843	+	2.6	cIP2vsInput	"intron (NM_001098799, intron 2 of 8)"	L1MD|LINE|L1	41339	NM_001098799	269389	Mm.207709	NM_001098799	ENSMUSG00000074607	Tox2	AI851523|AV026525|BI987407|Gcx1|RxHMG1	TOX high mobility group box family member 2	protein-coding	0	0.366337
Merged-chr5-143315399-1	chr5	143315349	143315449	+	2.6	cIP1vsInput	promoter-TSS (NM_172726)	promoter-TSS (NM_172726)	-39	NM_172726	231868	Mm.440105	NM_172726	ENSMUSG00000039244	E130309D02Rik	A630028N22	RIKEN cDNA E130309D02 gene	protein-coding	0.16	0.821782
Merged-chr6-95587841-1	chr6	95587791	95587891	+	2.6	cIP2vsInput	"intron (NM_011507, intron 5 of 10)"	"intron (NM_011507, intron 5 of 10)"	130996	NM_011507	20917	Mm.371585	NM_011507	ENSMUSG00000061838	Suclg2	AF171077|AW556404|D6Wsu120e	"succinate-Coenzyme A ligase, GDP-forming, beta subunit"	protein-coding	0	0.306931
Merged-chr1-110916412-1	chr1	110916362	110916462	+	2.6	cIP2vsInput	"intron (NM_001081386, intron 8 of 11)"	"intron (NM_001081386, intron 8 of 11)"	60960	NM_001081386	227485	Mm.322070	NM_001081386	ENSMUSG00000047216	Cdh19	-	"cadherin 19, type 2"	protein-coding	0	0.287129
Merged-chr1-59119712-1	chr1	59119662	59119762	+	2.6	cIP2vsInput	promoter-TSS (NM_001037812)	promoter-TSS (NM_001037812)	94	NM_001037812	381259	Mm.261275	NM_001037812	ENSMUSG00000038079	Tmem237	AI853305|Als2cr4|Gm972	transmembrane protein 237	protein-coding	0.04	0.554455
Merged-chr16-70074770-1	chr16	70074720	70074820	+	2.6	cIP1vsInput	Intergenic	Intergenic	-211026	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding	0	0.346535
Merged-chrX-11664826-1	chrX	11664776	11664876	+	2.6	cIP2vsInput	Intergenic	CpG	337004	NM_001114529	236663	Mm.473680	NM_001114529	ENSMUSG00000069038	Gm4906	EG236663	predicted gene 4906	protein-coding	0.12	0.742574
Merged-chr5-108410294-1	chr5	108410244	108410344	+	2.6	cIP1vsInput	"intron (NM_008806, intron 3 of 21)"	L1MC3|LINE|L1	21921	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	"phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide"	protein-coding	0	0.366337
Merged-chr4-20525954-1	chr4	20525904	20526004	+	2.6	cIP2vsInput	"intron (NM_172987, intron 1 of 4)"	"intron (NM_172987, intron 1 of 4)"	252714	NM_172987	269513		NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding	0	0.306931
Merged-chr15-6315091-1	chr15	6315041	6315141	+	2.6	cIP1vsInput	"intron (NM_001008702, intron 1 of 13)"	"intron (NM_001008702, intron 1 of 13)"	15302	NM_001008702	13132	Mm.240830	NM_001008702	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	"disabled 2, mitogen-responsive phosphoprotein"	protein-coding	0	0.326733
Merged-chr13-63941426-1	chr13	63941376	63941476	+	2.6	cIP2vsInput	Intergenic	ORR1D1|LTR|ERVL-MaLR	126092	NM_023507	76251	Mm.186610	NM_001013608	ENSMUSG00000021470	Ercc6l2	0610007P08Rik|1700019D06Rik|9330134C04Rik|Rad26l|Sr278	"excision repair cross-complementing rodent repair deficiency, complementation group 6 like 2"	protein-coding	0.01	0.445545
Merged-chr1-135313984-1	chr1	135313934	135314034	+	2.6	cIP2vsInput	promoter-TSS (NM_011590)	promoter-TSS (NM_011590)	-247	NM_011590	21854	Mm.2368	NM_011590	ENSMUSG00000062580	Timm17a	17kDa|mTim17a	translocase of inner mitochondrial membrane 17a	protein-coding	0.03	0.50495
Merged-chr7-63492092-1	chr7	63492042	63492142	+	2.6	cIP1vsInput	"intron (NM_130880, intron 1 of 13)"	Lx7|LINE|L1	47320	NM_130880	170711	Mm.156872	NM_130880	ENSMUSG00000033510	Otud7a	AJ430384|Otud7	OTU domain containing 7A	protein-coding	0	0.316832
Merged-chr13-3518586-1	chr13	3518536	3518636	+	2.6	cIP1vsInput	Intergenic	L1MA7|LINE|L1	-19489	NM_008112	14569	Mm.221609	NM_008112		Gdi2	GDI-B|GDIB|Gdi3	guanosine diphosphate (GDP) dissociation inhibitor 2	protein-coding	0	0.346535
Merged-chr18-31475714-1	chr18	31475664	31475764	+	2.6	cIP1vsInput	Intergenic	Intergenic	-28299	NM_009308	20983		NM_009308	ENSMUSG00000024261	Syt4	SytIV	synaptotagmin IV	protein-coding	0	0.257426
Merged-chr5-138161095-1	chr5	138161045	138161145	+	2.6	cIP2vsInput	promoter-TSS (NM_012002)	promoter-TSS (NM_012002)	-7	NM_012002	26893	Mm.3981	NM_012002	ENSMUSG00000019494	Cops6	Sgn3|VIP/MOV34	"COP9 (constitutive photomorphogenic) homolog, subunit 6 (Arabidopsis thaliana)"	protein-coding	0.14	0.752475
Merged-chr8-50661859-1	chr8	50661809	50661909	+	2.6	cIP2vsInput	Intergenic	Intergenic	293747	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0.01	0.356436
Merged-chr10-20170631-1	chr10	20170581	20170681	+	2.6	cIP2vsInput	"intron (NM_008635, intron 1 of 17)"	"intron (NM_008635, intron 1 of 17)"	21711	NM_001198635	17761	Mm.20928	NM_001198636	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding	0.02	0.643564
Merged-chr12-98856599-1	chr12	98856549	98856649	+	2.6	cIP2vsInput	"intron (NM_001081191, intron 14 of 43)"	"intron (NM_001081191, intron 14 of 43)"	44885	NM_001081191	319670	Mm.463212	NM_001081191	ENSMUSG00000051166	Eml5	BC027154|C130068M19Rik	echinoderm microtubule associated protein like 5	protein-coding	0	0.336634
Merged-chr6-107417950-1	chr6	107417900	107418000	+	2.6	cIP1vsInput	Intergenic	Intergenic	-111776	NM_008516	16979	Mm.488119	NM_008516	ENSMUSG00000034648	Lrrn1	2810047E21Rik|NLRR-1	"leucine rich repeat protein 1, neuronal"	protein-coding	0	0.316832
Merged-chr2-12349296-1	chr2	12349246	12349346	+	2.6	cIP2vsInput	"intron (NM_024185, intron 14 of 14)"	"intron (NM_024185, intron 14 of 14)"	-47376	NM_001001309	241226	Mm.329997	NM_001001309	ENSMUSG00000026768	Itga8	AI447669	integrin alpha 8	protein-coding	0	0.356436
Merged-chr1-98031632-1	chr1	98031582	98031682	+	2.6	cIP1vsInput	"non-coding (NR_037993, exon 3 of 3)"	"non-coding (NR_037993, exon 3 of 3)"	16161	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	miscRNA	0.01	0.485149
Merged-chr1-184675725-1	chr1	184675675	184675775	+	2.6	cIP2vsInput	Intergenic	Intergenic	-36772	NR_040627	74971	Mm.410816	NR_040627	ENSMUSG00000092578	4930488B22Rik	-	RIKEN cDNA 4930488B22 gene	miscRNA	0.05	0.613861
Merged-chr3-37906744-1	chr3	37906694	37906794	+	2.6	cIP1vsInput	"intron (NR_040559, intron 1 of 3)"	"intron (NR_040559, intron 1 of 3)"	7931	NR_040559	626410	Mm.389417	NR_040559		Gm20755	-	"predicted gene, 20755"	miscRNA	0.03	0.277228
Merged-chr16-92565556-1	chr16	92565506	92565606	+	2.6	cIP2vsInput	Intergenic	Intergenic	67409	NM_172469	209195	Mm.44747	NM_172469	ENSMUSG00000022949	Clic6	5730466J16Rik|AL022908|AW045520|CLIC1L	chloride intracellular channel 6	protein-coding	0.02	0.376238
Merged-chr2-104685480-1	chr2	104685430	104685530	+	2.6	cIP1vsInput	"exon (NM_177190, exon 8 of 10)"	"exon (NM_177190, exon 8 of 10)"	26682	NM_177190	320554	Mm.249065	NM_177190	ENSMUSG00000027175	Tcp11l1	C130096D04Rik	t-complex 11 like 1	protein-coding	0.06	0.623762
Merged-chr15-98181098-1	chr15	98181048	98181148	+	2.6	cIP2vsInput	Intergenic	Intergenic	13292	NM_177716	239650	Mm.54140	NM_177716	ENSMUSG00000029875	AI836003	5630400A08	expressed sequence AI836003	protein-coding	0.06	0.564356
Merged-chr13-90302618-1	chr13	90302568	90302668	+	2.6	cIP1vsInput	Intergenic	Intergenic	212951	NM_025335	66074	Mm.241387	NM_025335		Tmem167	0610041E09Rik|5730424F14Rik|AU041184|AW537806|ENSMUSG00000060669|Gm10085|Tmem167a	transmembrane protein 167	protein-coding	0	0.336634
Merged-chr3-21614148-1	chr3	21614098	21614198	+	2.6	cIP2vsInput	Intergenic	L1Md_T|LINE|L1	-462504	NM_030732	81004	Mm.446265	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding	0.01	0.564356
Merged-chr4-116994594-1	chr4	116994544	116994644	+	2.6	cIP1vsInput	promoter-TSS (NM_009478)	promoter-TSS (NM_009478)	-219	NM_009478	22275	Mm.46484	NM_009478	ENSMUSG00000028684	Urod	AI323803|Uro-d	uroporphyrinogen decarboxylase	protein-coding	0.03	0.425743
Merged-chr9-76677594-1	chr9	76677544	76677644	+	2.6	cIP2vsInput	Intergenic	Intergenic	-131790	NM_001045518	208994	Mm.256929	NM_001045518	ENSMUSG00000032358	Fam83b	C530008M07Rik|Gm516	"family with sequence similarity 83, member B"	protein-coding	0.01	0.356436
Merged-chr2-149807380-1	chr2	149807330	149807430	+	2.6	cIP1vsInput	Intergenic	Intergenic	-23403	NM_001085521	433485	Mm.330649	NM_001085521	ENSMUSG00000074736	Syndig1	AW123113|DSPC2|Gm14134|H2C20orf39|OTTMUSG00000015750|Tmem90b	synapse differentiation inducing 1	protein-coding	0.01	0.366337
Merged-chr12-46991444-1	chr12	46991394	46991494	+	2.6	cIP2vsInput	Intergenic	Lx9|LINE|L1	-172669	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding	0	0.306931
Merged-chr3-146133999-1	chr3	146133949	146134049	+	2.6	cIP2vsInput	"intron (NM_134160, intron 8 of 11)"	"intron (NM_134160, intron 8 of 11)"	12208	NM_134160	171166	Mm.114683	NM_134160		Mcoln3	6720490O21Rik|TRPML3|Va	mucolipin 3	protein-coding	0.01	0.386139
Merged-chr14-55148750-1	chr14	55148700	55148800	+	2.6	cIP1vsInput	Intergenic	Intergenic	-31815	NM_177049	319984	Mm.486015	NM_001003829	ENSMUSG00000022208	Jph4	9330157P13Rik|JP-4|JPHL1	junctophilin 4	protein-coding	0	0.445545
Merged-chr7-98951259-1	chr7	98951209	98951309	+	2.6	cIP1vsInput	"intron (NM_178635, intron 12 of 14)"	L1MC5|LINE|L1	112414	NM_009519	22411	Mm.22182	NM_009519		Wnt11	-	wingless-related MMTV integration site 11	protein-coding	0	0.336634
Merged-chr8-56485898-1	chr8	56485848	56485948	+	2.6	cIP1vsInput	Intergenic	Intergenic	64668	NM_001009951	382010	Mm.425534	NM_001009951	ENSMUSG00000038215	Cep44	4933440G23Rik|mKIAA1712	centrosomal protein 44	protein-coding	0	0.346535
Merged-chr16-37239949-1	chr16	37239899	37239999	+	2.6	cIP2vsInput	"intron (NM_001114613, intron 11 of 26)"	"intron (NM_001114613, intron 11 of 26)"	145009	NM_001114613	207227	Mm.403226	NM_001114611		Stxbp5l	9430094L02|A830015P08Rik|LLGL4|T2dm1|t2md1|tomosyn-2	syntaxin binding protein 5-like	protein-coding	0	0.336634
Merged-chr1-14777738-1	chr1	14777688	14777788	+	2.6	cIP2vsInput	Intergenic	Intergenic	-21772	NM_010827	17681	Mm.5820	NM_010827	ENSMUSG00000025930	Msc	MyoR|bHLHa22	musculin	protein-coding	0	0.326733
Merged-chr13-25863952-1	chr13	25863902	25864002	+	2.6	cIP2vsInput	Intergenic	Intergenic	102364	NR_045062	100503530	Mm.86763	NR_045062	ENSMUSG00000086531	Gm11351	OTTMUSG00000000620	predicted gene 11351	miscRNA	0	0.356436
Merged-chr19-56513708-1	chr19	56513658	56513758	+	2.6	cIP2vsInput	Intergenic	Intergenic	34514	NM_018831	55947	Mm.2805	NM_018831	ENSMUSG00000025077	Dclre1a	2810043H12Rik|AU022226|Pso2|Smn1a|Snm1|mKIAA0086	"DNA cross-link repair 1A, PSO2 homolog (S. cerevisiae)"	protein-coding	0.01	0.554455
Merged-chr15-95697708-1	chr15	95697658	95697758	+	2.6	cIP1vsInput	Intergenic	Intergenic	-42937	NM_207533	223843	Mm.152937	NM_207533		Dbx2	9430056A22Rik|9630005K15|AI846217|Gm1229	developing brain homeobox 2	protein-coding	0.01	0.346535
Merged-chr9-18318546-1	chr9	18318496	18318596	+	2.6	cIP2vsInput	Intergenic	Intergenic	26279	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	"cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1"	protein-coding	0.01	0.306931
Merged-chr3-150436782-1	chr3	150436732	150436832	+	2.6	cIP2vsInput	Intergenic	Intergenic	-1001100	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0.01	0.326733
Merged-chr2-51501956-1	chr2	51501906	51502006	+	2.6	cIP2vsInput	Intergenic	MER34A1|LTR|ERV1	-125555	NM_199158	387511	Mm.377918	NM_199158	ENSMUSG00000056115	Tas2r134	T2R134|Tas2r34	"taste receptor, type 2, member 134"	protein-coding	0	0.366337
Merged-chr7-35073194-1	chr7	35073144	35073244	+	2.6	cIP1vsInput	Intergenic	Intergenic	-16628	NM_009884	12611	Mm.273090	NM_009884	ENSMUSG00000056216	Cebpg	C/EBP[g]|C/EBPgamma|GPE1-BP|Gpe1bp|Ig/EBP	"CCAAT/enhancer binding protein (C/EBP), gamma"	protein-coding	0	0.287129
Merged-chr11-54413398-1	chr11	54413348	54413448	+	2.6	cIP2vsInput	"intron (NM_029105, intron 12 of 13)"	L1M6|LINE|L1	-24781	NM_173753	216742	Mm.34087	NM_173753	ENSMUSG00000035992	Fnip1	A730024A03Rik|AI838773|AW557298	folliculin interacting protein 1	protein-coding	0.01	0.386139
Merged-chr12-67994695-1	chr12	67994645	67994745	+	2.6	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-325424	NR_033146	100316870	Mm.379794	NR_033146		Gm17821	-	DDB1 and CUL4 associated factor 5 pseudogene	pseudo	0	0.336634
Merged-chr8-6333340-1	chr8	6333290	6333390	+	2.6	cIP1vsInput	Intergenic	Intergenic	-1228108	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0.02	0.405941
Merged-chr14-68937313-1	chr14	68937263	68937363	+	2.6	cIP1vsInput	Intergenic	Intergenic	-91976	NM_009285	20855	Mm.20911	NM_009285	ENSMUSG00000014813	Stc1	Stc	stanniocalcin 1	protein-coding	0	0.287129
Merged-chr2-57133085-1	chr2	57133035	57133135	+	2.6	cIP1vsInput	"intron (NR_040356, intron 1 of 2)"	"intron (NR_040356, intron 1 of 2)"	-9082	NM_001139509	18227	Mm.3507	NM_001139509	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	"nuclear receptor subfamily 4, group A, member 2"	protein-coding	0.02	0.306931
Merged-chr8-59354945-1	chr8	59354895	59354995	+	2.6	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	443190	NM_173411	234290	Mm.39244	NM_173411	ENSMUSG00000049946	BC030500	-	cDNA sequence BC030500	protein-coding	0	0.316832
Merged-chr14-73525260-1	chr14	73525210	73525310	+	2.6	cIP1vsInput	"5' UTR (NM_172527, exon 3 of 5)"	"5' UTR (NM_172527, exon 3 of 5)"	15211	NM_026119	67381	Mm.282888	NM_026119	ENSMUSG00000022109	Med4	2410046H15Rik|DRIP36|HSPC126|TRAP36|Vdirp|Vdrip	"mediator of RNA polymerase II transcription, subunit 4 homolog (yeast)"	protein-coding	0.07	0.574257
Merged-chrY-7043783-1	chrY	7043733	7043833	+	2.6	cIP2vsInput	Intergenic	Intergenic	123994	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.306931
Merged-chr7-87868636-1	chr7	87868586	87868686	+	2.6	cIP1vsInput	"intron (NM_001081414, intron 4 of 9)"	"intron (NM_001081414, intron 4 of 9)"	284468	NM_001143834	108071	Mm.235018	NM_001033224	ENSMUSG00000049583	Grm5	6430542K11Rik|AI850523|Gprc1e|mGluR5|mGluR5b	"glutamate receptor, metabotropic 5"	protein-coding	0	0.306931
Merged-chr5-43402414-1	chr5	43402364	43402464	+	2.6	cIP2vsInput	Intergenic	Intergenic	-113155	NM_001135172	109323	Mm.275553	NM_001135172	ENSMUSG00000061535	C1qtnf7	5530401N20Rik|8430425G24Rik|Ctrp7	C1q and tumor necrosis factor related protein 7	protein-coding	0	0.306931
Merged-chr19-20833737-1	chr19	20833687	20833787	+	2.6	cIP2vsInput	"intron (NM_028953, intron 9 of 20)"	"intron (NM_028953, intron 9 of 20)"	-106181	NM_011921	26358	Mm.14609	NM_011921	ENSMUSG00000024747	Aldh1a7	AI987940|Ahd2-like|Aldh-pb|Aldh1a4|Aldhpb	"aldehyde dehydrogenase family 1, subfamily A7"	protein-coding	0	0.386139
Merged-chr9-66294925-1	chr9	66294875	66294975	+	2.6	cIP1vsInput	Intergenic	Intergenic	-55525	NM_145617	235439	Mm.244179	NM_145617	ENSMUSG00000038664	Herc1	2810449H11Rik|B230218H07|D130015N03Rik|tbl	hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1	protein-coding	0.02	0.524752
Merged-chr3-82199044-1	chr3	82198994	82199094	+	2.6	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-53167	NM_021896	60596	Mm.143831	NM_021896	ENSMUSG00000033910	Gucy1a3	1200016O07Rik	"guanylate cyclase 1, soluble, alpha 3"	protein-coding	0	0.316832
Merged-chr11-55461438-1	chr11	55461388	55461488	+	2.6	cIP1vsInput	promoter-TSS (NM_009720)	promoter-TSS (NM_009720)	-300	NM_009720	11927	Mm.217759	NM_009720	ENSMUSG00000018585	Atox1	AI256639|Atx1	ATX1 (antioxidant protein 1) homolog 1 (yeast)	protein-coding	0.06	0.514851
Merged-chr11-24368447-1	chr11	24368397	24368497	+	2.6	cIP1vsInput	Intergenic	Intergenic	-113462	NR_045857	71316	Mm.79162	NR_045857	ENSMUSG00000086892	4933430M04Rik	-	RIKEN cDNA 4933430M04 gene	miscRNA	0	0.326733
Merged-chr2-60615506-1	chr2	60615456	60615556	+	2.6	cIP1vsInput	"intron (NM_021359, intron 12 of 14)"	"intron (NM_021359, intron 12 of 14)"	58187	NM_021359	16420	Mm.98193	NM_001159564	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding	0	0.306931
Merged-chr15-93422585-1	chr15	93422535	93422635	+	2.6	cIP2vsInput	"intron (NM_146062, intron 3 of 9)"	B1_Mur2|SINE|Alu	24235	NM_175363	223828	Mm.74208	NM_001083114	ENSMUSG00000036167	Pphln1	1110063K05Rik|1600022A19Rik|CR|HSPC206|HSPC232	periphilin 1	protein-coding	0	0.485149
Merged-chr17-92885436-1	chr17	92885386	92885486	+	2.6	cIP2vsInput	Intergenic	Intergenic	-313986	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0	0.29703
Merged-chr2-125839230-1	chr2	125839180	125839280	+	2.6	cIP2vsInput	"intron (NM_009939, intron 8 of 12)"	"intron (NM_009939, intron 8 of 12)"	19788	NM_009939	12848	Mm.3596	NM_009939	ENSMUSG00000027206	Cops2	AI315723|C85265|Csn2|Sgn2|Trip15|alien-like	"COP9 (constitutive photomorphogenic) homolog, subunit 2 (Arabidopsis thaliana)"	protein-coding	0.01	0.316832
Merged-chr4-83516569-1	chr4	83516519	83516619	+	2.6	cIP1vsInput	Intergenic	Intergenic	-8976	NM_001081012	320226	Mm.180032	NM_001081012	ENSMUSG00000052407	Ccdc171	4930418J05Rik|4930473A06Rik|A330015D16Rik	coiled-coil domain containing 171	protein-coding	0.01	0.376238
Merged-chr4-109908362-1	chr4	109908312	109908412	+	2.6	cIP2vsInput	"intron (NM_007983, intron 15 of 18)"	"intron (NM_007983, intron 15 of 18)"	-69663	NM_172296	242620	Mm.32825	NM_172296	ENSMUSG00000047143	Dmrta2	Dmrt5	doublesex and mab-3 related transcription factor like family A2	protein-coding	0	0.287129
Merged-chr3-114170228-1	chr3	114170178	114170278	+	2.6	cIP1vsInput	"intron (NM_007729, intron 46 of 66)"	"intron (NM_007729, intron 46 of 66)"	139688	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	"collagen, type XI, alpha 1"	protein-coding	0	0.287129
Merged-chr7-19291503-1	chr7	19291453	19291553	+	2.6	cIP1vsInput	"intron (NM_001025364, intron 1 of 6)"	"intron (NM_001025364, intron 1 of 6)"	434	NM_001025364	20167	Mm.24142	NM_001025364	ENSMUSG00000030401	Rtn2	MMS10-P|Ms10p|NSPLI|Nspl1	reticulon 2 (Z-band associated protein)	protein-coding	0.07	0.712871
Merged-chr7-49245530-1	chr7	49245480	49245580	+	2.6	cIP2vsInput	promoter-TSS (NM_175272)	promoter-TSS (NM_175272)	-659	NM_175272	78286	Mm.471488	NM_001111016	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding	0.03	0.594059
Merged-chr3-56000442-1	chr3	56000392	56000492	+	2.6	cIP2vsInput	"intron (NM_030595, intron 24 of 57)"	"intron (NM_030595, intron 24 of 57)"	153337	NR_033592	71182	Mm.195603	NR_033592		4933417G07Rik	-	SEC13 homolog pseudogene	pseudo	0	0.405941
Merged-chr3-155805016-1	chr3	155804966	155805066	+	2.6	cIP1vsInput	Intergenic	Intergenic	-171338	NR_040553	329780	Mm.119000	NR_040553		9330178D15Rik	9330178D15	RIKEN cDNA 9330178D15 gene	miscRNA	0	0.326733
Merged-chr13-88038481-1	chr13	88038431	88038531	+	2.6	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-782991	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0	0.316832
Merged-chr9-73576075-1	chr9	73576025	73576125	+	2.6	cIP1vsInput	"intron (NM_001081153, intron 18 of 30)"	"intron (NM_001081153, intron 18 of 30)"	357492	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|AU019458|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C (C. elegans)	protein-coding	0.01	0.267327
Merged-chr17-28232587-1	chr17	28232537	28232637	+	2.6	cIP1vsInput	promoter-TSS (NM_011145)	promoter-TSS (NM_011145)	-167	NM_011145	19015	Mm.328914	NM_011145	ENSMUSG00000002250	Ppard	NUC-1|NUC1|Nr1c2|PPAR-beta|PPAR-delta|PPAR[b]|PPARdelta|Pparb|Pparb/d	peroxisome proliferator activator receptor delta	protein-coding	0.1	0.70297
Merged-chr9-106789541-1	chr9	106789491	106789591	+	2.6	cIP2vsInput	promoter-TSS (NM_030730)	promoter-TSS (NM_030730)	-328	NM_030730	81000	Mm.246689	NM_030730	ENSMUSG00000040661	Rad54l2	Arip4|D130058C05|G630026H09Rik|Srisnf2l	RAD54 like 2 (S. cerevisiae)	protein-coding	0.05	0.405941
Merged-chr14-55745628-1	chr14	55745578	55745678	+	2.6	cIP2vsInput	promoter-TSS (NM_026819)	promoter-TSS (NM_026819)	56	NM_026819	52585	Mm.21623	NM_026819	ENSMUSG00000002332	Dhrs1	1110029G07Rik|AW112170|D14Ertd484e	dehydrogenase/reductase (SDR family) member 1	protein-coding	0.05	0.663366
Merged-chr10-109748938-1	chr10	109748888	109748988	+	2.6	cIP2vsInput	"intron (NM_001081035, intron 20 of 38)"	"intron (NM_001081035, intron 20 of 38)"	251281	NM_001081035	260315	Mm.461280	NM_001081035	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding	0	0.306931
Merged-chr18-15015127-1	chr18	15015077	15015177	+	2.6	cIP2vsInput	"intron (NM_134112, intron 1 of 4)"	"intron (NM_134112, intron 1 of 4)"	26132	NR_045372	74456	Mm.391075	NR_045372		4933424G05Rik	-	RIKEN cDNA 4933424G05 gene	miscRNA	0.03	0.544554
Merged-chr16-84842017-1	chr16	84841967	84842067	+	2.6	cIP1vsInput	"intron (NM_008065, intron 3 of 9)"	"intron (NM_008065, intron 3 of 9)"	-6443	NM_016755	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	-	"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F"	protein-coding	0.01	0.227723
Merged-chr12-33623681-1	chr12	33623631	33623731	+	2.6	cIP2vsInput	Intergenic	Intergenic	194057	NM_172253	28071	Mm.413045	NM_172253	ENSMUSG00000020561	Twistnb	2410173G11|2810024J17Rik|D16Wsu83e	TWIST neighbor	protein-coding	0	0.287129
Merged-chr12-96749451-1	chr12	96749401	96749501	+	2.6	cIP1vsInput	Intergenic	Intergenic	-702229	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0.02	0.455446
Merged-chr1-134221791-1	chr1	134221741	134221841	+	2.6	cIP1vsInput	"intron (NM_001008533, intron 1 of 1)"	L1MA4|LINE|L1	13636	NM_001008533	11539	Mm.298908	NM_009629	ENSMUSG00000042429	Adora1	A1-AR|A1AR|A1R|AA1R|AI848715|BB176431|Ri	adenosine A1 receptor	protein-coding	0	0.346535
Merged-chr1-145314113-1	chr1	145314063	145314163	+	2.6	cIP2vsInput	Intergenic	Intergenic	-538692	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding	0	0.356436
Merged-chr11-104934003-1	chr11	104933953	104934053	+	2.6	cIP1vsInput	Intergenic	Intergenic	-158216	NM_001081046	70894	Mm.87320	NM_001081046	ENSMUSG00000020690	Efcab3	4921510J17Rik	EF-hand calcium binding domain 3	protein-coding	0	0.316832
Merged-chr7-36708059-1	chr7	36708009	36708109	+	2.6	cIP2vsInput	"intron (NM_172298, intron 1 of 1)"	"intron (NM_172298, intron 1 of 1)"	9941	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding	0.03	0.50495
Merged-chr17-37708287-1	chr17	37708237	37708337	+	2.6	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	11602	NM_001011830	258095	Mm.329042	NM_001011830	ENSMUSG00000059964	Olfr119	MOR263-7	olfactory receptor 119	protein-coding	0	0.336634
Merged-chr9-116198995-1	chr9	116198945	116199045	+	2.6	cIP1vsInput	Intergenic	Intergenic	-23632	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	"transforming growth factor, beta receptor II"	protein-coding	0	0.257426
Merged-chr11-61476390-1	chr11	61476340	61476440	+	2.6	cIP1vsInput	Intergenic	RLTR42-int|LTR|ERVK	-9054	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding	0.01	0.39604
Merged-chr12-43292283-1	chr12	43292233	43292333	+	2.6	cIP1vsInput	Intergenic	ID_B1|SINE|B4	917785	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	"DnaJ (Hsp40) homolog, subfamily B, member 9"	protein-coding	0	0.386139
Merged-chr9-83019219-1	chr9	83019169	83019269	+	2.6	cIP1vsInput	Intergenic	Intergenic	-43730	NM_001081216	83946	Mm.221688	NM_001081216	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding	0.01	0.257426
Merged-chr3-136918858-1	chr3	136918808	136918908	+	2.6	cIP2vsInput	"intron (NM_008913, intron 10 of 13)"	"intron (NM_008913, intron 10 of 13)"	248088	NM_008913	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|AI841391|AW413465|CN|Caln|Calna|CnA	"protein phosphatase 3, catalytic subunit, alpha isoform"	protein-coding	0.01	0.366337
Merged-chr14-8172920-1	chr14	8172870	8172970	+	2.6	cIP2vsInput	promoter-TSS (NM_024221)	promoter-TSS (NM_024221)	72	NM_024221	68263	Mm.301527	NM_024221	ENSMUSG00000021748	Pdhb	2610103L06Rik|AL024199|C81408	pyruvate dehydrogenase (lipoamide) beta	protein-coding	0.07	0.653465
Merged-chr1-17616572-1	chr1	17616522	17616622	+	2.6	cIP2vsInput	"intron (NM_053191, intron 2 of 5)"	"intron (NM_053191, intron 2 of 5)"	14671	NM_053191	94227	Mm.442452	NM_053191	ENSMUSG00000067780	Pi15	P24TI|P25TI|PI-15|SugarCrisp	peptidase inhibitor 15	protein-coding	0	0.356436
Merged-chr2-108533010-1	chr2	108532960	108533060	+	2.6	cIP1vsInput	Intergenic	Intergenic	745280	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding	0	0.366337
Merged-chr6-52838901-1	chr6	52838851	52838951	+	2.6	cIP2vsInput	"intron (NM_001168277, intron 2 of 4)"	"intron (NM_001168277, intron 2 of 4)"	70719	NM_001168277	231986	Mm.386865	NM_001168277		Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding	0.02	0.485149
Merged-chr10-8078023-1	chr10	8077973	8078073	+	2.6	cIP2vsInput	Intergenic	Intergenic	-121900	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding	0	0.326733
Merged-chr3-146328132-1	chr3	146328082	146328182	+	2.6	cIP1vsInput	Intergenic	Intergenic	50812	NR_033542	100038607	Mm.365888	NR_033542		Gm10636	ENSMUSG00000074175	predicted gene 10636	miscRNA	0.02	0.475248
Merged-chr14-57065412-1	chr14	57065362	57065462	+	2.6	cIP2vsInput	Intergenic	RLTR17D_Mm|LTR|ERVK	-7382	NM_016975	14611	Mm.57207	NM_001271623	ENSMUSG00000048582	Gja3	Cnx46|Cx43|Cx46|Gja-3	"gap junction protein, alpha 3"	protein-coding	0.01	0.326733
Merged-chr2-41722175-1	chr2	41722125	41722225	+	2.6	cIP2vsInput	"intron (NM_053011, intron 6 of 90)"	L1_Mur2|LINE|L1	931423	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0	0.326733
Merged-chr6-8845712-1	chr6	8845662	8845762	+	2.6	cIP2vsInput	Intergenic	Intergenic	-67228	NM_010492	15893	Mm.275683	NM_001252266	ENSMUSG00000062995	Ica1	69kDa|ICA69	islet cell autoantigen 1	protein-coding	0.01	0.366337
Merged-chr13-6633692-1	chr13	6633642	6633742	+	2.6	cIP2vsInput	"intron (NM_019703, intron 2 of 21)"	"intron (NM_019703, intron 2 of 21)"	15032	NM_019703	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|PFK-C	"phosphofructokinase, platelet"	protein-coding	0.03	0.564356
Merged-chr10-76694953-2	chr10	76694899	76695008	+	2.6	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	31091	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	"collagen, type VI, alpha 1"	protein-coding	0.027523	0.563636
Merged-chr19-24777079-1	chr19	24777029	24777129	+	2.6	cIP1vsInput	"intron (NM_175013, intron 6 of 10)"	"intron (NM_175013, intron 6 of 10)"	84763	NM_175013	226041	Mm.391170	NM_175013		Pgm5	4833423B07|9530034F03Rik|D830025G17|aciculin	phosphoglucomutase 5	protein-coding	0	0.415842
Merged-chr7-99441919-1	chr7	99441869	99441969	+	2.6	cIP1vsInput	"exon (NM_201352, exon 7 of 18)"	"exon (NM_201352, exon 7 of 18)"	-24085	NM_028145	72184	Mm.153585	NM_028145	ENSMUSG00000035298	Klhl35	2810406K13Rik	kelch-like 35	protein-coding	0.01	0.564356
Merged-chr18-87991946-1	chr18	87991896	87991996	+	2.6	cIP1vsInput	Intergenic	MYSERV-int|LTR|ERVK	902261	NM_018821	54607	Mm.476577	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding	0	0.336634
Merged-chr15-64216839-1	chr15	64216789	64216889	+	2.6	cIP1vsInput	"intron (NM_001276462, intron 1 of 27)"	"intron (NM_001276462, intron 1 of 27)"	95834	NM_001276462	13196	Mm.277236	NM_001276461	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	"ArfGAP with SH3 domain, ankyrin repeat and PH domain1"	protein-coding	0.01	0.366337
Merged-chr9-12645944-1	chr9	12645894	12645994	+	2.6	cIP2vsInput	Intergenic	Intergenic	459911	NR_040755	78219	Mm.414868	NR_040755		4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	miscRNA	0	0.287129
Merged-chr5-135489375-1	chr5	135489325	135489425	+	2.6	cIP1vsInput	"intron (NM_146001, intron 1 of 30)"	CpG	55747	NM_146001	215114	Mm.280805	NM_146001	ENSMUSG00000039959	Hip1	2610109B09Rik|A930014B11Rik|E130315I21Rik|mKIAA4113	huntingtin interacting protein 1	protein-coding	0.09	0.693069
Merged-chr18-90458922-1	chr18	90458872	90458972	+	2.6	cIP1vsInput	Intergenic	Intergenic	-51232	NM_198295	67988	Mm.268041	NM_198295	ENSMUSG00000024614	Tmx3	6430411B10Rik|A730024F05Rik|AV259382|Txndc10|mKIAA1830	thioredoxin-related transmembrane protein 3	protein-coding	0	0.277228
Merged-chr17-74835296-1	chr17	74835246	74835346	+	2.6	cIP1vsInput	"intron (NM_152817, intron 14 of 19)"	"intron (NM_152817, intron 14 of 19)"	117546	NM_152817	74196	Mm.209503	NM_152817	ENSMUSG00000024078	Ttc27	2610511O17Rik	tetratricopeptide repeat domain 27	protein-coding	0	0.346535
Merged-chr5-10556590-1	chr5	10556540	10556640	+	2.6	cIP1vsInput	Intergenic	Intergenic	-308439	NR_003596	623849	Mm.335888	NR_003596	ENSMUSG00000091422	Gm6455	EG623849	predicted gene 6455	pseudo	0	0.306931
Merged-chr12-108407094-1	chr12	108407044	108407144	+	2.6	cIP1vsInput	Intergenic	L1MB7|LINE|L1	-3561	NM_001043336	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL	echinoderm microtubule associated protein like 1	protein-coding	0	0.277228
Merged-chr10-81496390-1	chr10	81496340	81496440	+	2.6	cIP2vsInput	promoter-TSS (NM_134009)	promoter-TSS (NM_134009)	-27	NM_134009	103425	Mm.302791	NM_134009	ENSMUSG00000020238	Ncln	3100002P13Rik|AW120537	nicalin homolog (zebrafish)	protein-coding	0.11	0.732673
Merged-chr4-8666703-1	chr4	8666653	8666753	+	2.6	cIP1vsInput	Intergenic	Intergenic	-23703	NM_001277149	320790	Mm.138792	NM_001277149	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding	0.02	0.445545
Merged-chr9-4601856-1	chr9	4601806	4601906	+	2.6	cIP1vsInput	"intron (NM_019691, intron 4 of 16)"	"intron (NM_019691, intron 4 of 16)"	194378	NM_001113180	14802	Mm.209263	NM_001113180	ENSMUSG00000025892	Gria4	GluA4|GluR-D|Glur-4|Glur4|Gluralpha4|spkw1	"glutamate receptor, ionotropic, AMPA4 (alpha 4)"	protein-coding	0.02	0.366337
Merged-chr17-43699528-1	chr17	43699478	43699578	+	2.6	cIP1vsInput	"intron (NM_018887, intron 6 of 11)"	"intron (NM_018887, intron 6 of 11)"	32103	NM_018887	56050	Mm.376968	NM_018887	ENSMUSG00000023963	Cyp39a1	-	"cytochrome P450, family 39, subfamily a, polypeptide 1"	protein-coding	0.01	0.405941
Merged-chr16-41089985-1	chr16	41089935	41090035	+	2.6	cIP1vsInput	Intergenic	Intergenic	-443357	NM_175548	268890	Mm.473653	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding	0	0.29703
Merged-chr7-142284700-1	chr7	142284650	142284750	+	2.6	cIP2vsInput	Intergenic	ERVB4_1-I_MM-int|LTR|ERVK	-10337	NM_001199309	100043627	Mm.388589	NM_001199309	ENSMUSG00000056885	Gm4559	-	predicted gene 4559	protein-coding	0.05	0.524752
Merged-chr8-49488835-1	chr8	49488785	49488885	+	2.6	cIP1vsInput	Intergenic	Intergenic	-814145	NM_011857	23965	Mm.42191	NM_001145937	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding	0.01	0.386139
Merged-chr5-97802349-1	chr5	97802299	97802399	+	2.6	cIP2vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	228613	NM_133738	71914	Mm.24842	NM_133738		Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding	0.01	0.326733
Merged-chr2-17742053-1	chr2	17742003	17742103	+	2.6	cIP2vsInput	Intergenic	Intergenic	-10985	NM_028757	74103	Mm.440498	NM_028757		Nebl	1200007O21Rik|A630080F05Rik|BB140644|D830029A09Rik|Lnebl	nebulette	protein-coding	0.02	0.346535
Merged-chr4-111328055-1	chr4	111328005	111328105	+	2.6	cIP2vsInput	"intron (NM_001048189, intron 5 of 12)"	"intron (NM_001048189, intron 5 of 12)"	-86951	NR_033793	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding	0	0.306931
Merged-chr17-62403677-1	chr17	62403627	62403727	+	2.6	cIP2vsInput	Intergenic	MTD|LTR|ERVL-MaLR	477640	NM_207654	13640	Mm.401670	NM_010109		Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding	0	0.346535
Merged-chr3-96094320-2	chr3	96094237	96094403	+	2.55	cIP1vsInput|cIP2vsInput	"intron (NR_035496, intron 1 of 1)"	"intron (NR_035496, intron 1 of 1)"	-10207	NM_001025613	229603	Mm.487453	NM_001025613	ENSMUSG00000038495	Otud7b	2900060B22Rik|4930463P07Rik|AI462125|CEZANNE|Trabid2|Za20d1	OTU domain containing 7B	protein-coding	0.042169	0.556886
Merged-chr8-84872144-2	chr8	84872061	84872228	+	2.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NR_031759)	promoter-TSS (NR_031759)	33	NM_001168246	71846	Mm.229128	NM_001168244	ENSMUSG00000003824	Syce2	1700013H19Rik|AA407907|Cesc1	synaptonemal complex central element protein 2	protein-coding	0.107784	0.744048
Merged-chr3-78167339-2	chr3	78167250	78167428	+	2.55	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	978536	NM_001099624	76089	Mm.462396	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding	0	0.318436
Merged-chr2-30171575-2	chr2	30171505	30171645	+	2.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_007931)	promoter-TSS (NM_007931)	51	NM_007931	13804	Mm.474473	NM_007931	ENSMUSG00000015337	Endog	-	endonuclease G	protein-coding	0.114286	0.716312
Merged-chr7-145206213-2	chr7	145206161	145206265	+	2.55	cIP1vsInput|cIP2vsInput	"non-coding (NR_033626, exon 3 of 3)"	"non-coding (NR_033626, exon 3 of 3)"	1906	NR_033626	100040049	Mm.102235	NR_033626		1810010D01Rik	Gm2572	RIKEN cDNA 1810010D01 gene	miscRNA	0.048077	0.609524
Merged-chr11-102138599-2	chr11	102138544	102138655	+	2.55	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-6914	NM_145829	217214	Mm.31686	NM_178053		Nags	1700120E20Rik|argA	N-acetylglutamate synthase	protein-coding	0.081081	0.553571
Merged-chr14-14120989-2	chr14	14120912	14121066	+	2.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025550)	promoter-TSS (NM_025550)	-85	NM_025550	66413	Mm.27591	NM_025550	ENSMUSG00000021737	Psmd6	2400006A19Rik	"proteasome (prosome, macropain) 26S subunit, non-ATPase, 6"	protein-coding	0.084416	0.683871
Merged-chrX-169320525-2	chrX	169320463	169320587	+	2.55	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008222)	promoter-TSS (NM_008222)	-182	NM_008222	15159	Mm.284033	NM_008222	ENSMUSG00000031352	Hccs	-	holocytochrome c synthetase	protein-coding	0.137097	0.712
Merged-chr2-84549789-2	chr2	84549734	84549845	+	2.55	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-42916	NR_046046	672763	Mm.491046	NR_046046	ENSMUSG00000087362	Gm13710	OTTMUSG00000013441	predicted gene 13710	miscRNA	0.009009	0.517857
Merged-chr3-38612613-2	chr3	38612563	38612663	+	2.55	cIP1vsInput|cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	-127797	NM_001167883	99696	Mm.290937	NM_001033198	ENSMUSG00000044864	Ankrd50	AI662170|E430012K20Rik|mKIAA1223|mKIAA3019	ankyrin repeat domain 50	protein-coding	0.01	0.50495
Merged-chr12-93711309-2	chr12	93711238	93711381	+	2.55	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-1862152	NM_011344	20338	Mm.250605	NM_001039089	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding	0.006993	0.326389
Merged-chr6-34028675-1	chr6	34028625	34028725	+	2.5	cIP1vsInput	promoter-TSS (NM_028886)	promoter-TSS (NM_028886)	-773	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding	0	0.356436
Merged-chr14-60140356-1	chr14	60140306	60140406	+	2.5	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-53522	NM_015803	50769	Mm.319599	NM_015803	ENSMUSG00000021983	Atp8a2	AI415030|Atpc1b|Ib	"ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"	protein-coding	0.01	0.326733
Merged-chr17-61542578-1	chr17	61542528	61542628	+	2.5	cIP1vsInput	Intergenic	Intergenic	224826	NR_030569	100124495		NR_030569		Mir466g	Mirn466g	microRNA 466g	miscRNA	0	0.336634
Merged-chr3-136548234-2	chr3	136548180	136548289	+	2.5	cIP1vsInput|cIP2vsInput	Intergenic	L1MCa|LINE|L1	-98885	NR_040592	70055	Mm.261063	NR_040592		1700030L20Rik	-	RIKEN cDNA 1700030L20 gene	miscRNA	0.009174	0.336364
Merged-chr5-115230734-1	chr5	115230684	115230784	+	2.5	cIP1vsInput	Intergenic	PB1D10|SINE|Alu	-5117	NM_026398	117109	Mm.24636	NM_026398	ENSMUSG00000060152	Pop5	1500019J17Rik|2700077E03Rik|AW049989|Rnasep3	"processing of precursor 5, ribonuclease P/MRP family (S. cerevisiae)"	protein-coding	0	0.39604
Merged-chr7-24175016-1	chr7	24174966	24175066	+	2.5	cIP1vsInput	promoter-TSS (NM_001029933)	promoter-TSS (NM_001029933)	-29	NM_001029933	232966	Mm.435485	NM_001029933		Zfp114	Gm1957|Zfp110	zinc finger protein 114	protein-coding	0.02	0.49505
Merged-chr1-137550275-1	chr1	137550225	137550325	+	2.5	cIP2vsInput	Intergenic	L1M2|LINE|L1	-416180	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mmu-mir-213	microRNA 181a-1	miscRNA	0.01	0.336634
Merged-chr3-29072525-1	chr3	29072475	29072575	+	2.5	cIP1vsInput	Intergenic	Lx9|LINE|L1	-10052	NM_001167748	75740	Mm.330948	NM_001167748	ENSMUSG00000063600	Egfem1	6130401L20Rik|Efcab11	EGF-like and EMI domain containing 1	protein-coding	0.01	0.405941
Merged-chr1-48767034-1	chr1	48766984	48767084	+	2.5	cIP2vsInput	Intergenic	Intergenic	-1913525	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.336634
Merged-chr1-99308728-1	chr1	99308678	99308778	+	2.5	cIP2vsInput	Intergenic	MTE2a|LTR|ERVL-MaLR	-464037	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding	0.01	0.356436
Merged-chr1-73641149-1	chr1	73641099	73641199	+	2.5	cIP1vsInput	"intron (NR_045311, intron 7 of 8)"	"intron (NR_045311, intron 7 of 8)"	223317	NR_045311	109198	Mm.359721	NR_045311		6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	miscRNA	0.01	0.49505
Merged-chr12-76409819-1	chr12	76409769	76409869	+	2.5	cIP2vsInput	Intergenic	Intergenic	5449	NM_008301	15512	Mm.296181	NM_001002012	ENSMUSG00000059970	Hspa2	70kDa|HSP70.2|HSP70A2|Hsp70-2	heat shock protein 2	protein-coding	0.01	0.356436
Merged-chr10-12987201-1	chr10	12987151	12987251	+	2.5	cIP2vsInput	Intergenic	Intergenic	-21249	NM_175102	66125	Mm.402225	NM_175102	ENSMUSG00000078348	Sf3b5	10kDa|1110005L13Rik|AU043053|Sf3b10	"splicing factor 3b, subunit 5"	protein-coding	0.02	0.50495
Merged-chr16-89367346-1	chr16	89367296	89367396	+	2.5	cIP1vsInput	Intergenic	Intergenic	36428	NM_028621	170656	Mm.46109	NM_028621	ENSMUSG00000058368	Krtap21-1	1110017B05Rik|AI506979|KAP21.1|Krtap16-7	keratin associated protein 21-1	protein-coding	0	0.346535
Merged-chr11-41371870-1	chr11	41371820	41371920	+	2.5	cIP1vsInput	Intergenic	Intergenic	-616584	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding	0	0.306931
Merged-chr15-55090430-1	chr15	55090380	55090480	+	2.5	cIP1vsInput	promoter-TSS (NM_183089)	promoter-TSS (NM_183089)	48	NM_183089	72107	Mm.486550	NM_183089	ENSMUSG00000022422	Dscc1	2010006I05Rik|2600005O03Rik|Dcc1	defective in sister chromatid cohesion 1 homolog (S. cerevisiae)	protein-coding	0.11	0.653465
Merged-chr17-41237184-1	chr17	41237134	41237234	+	2.5	cIP2vsInput	Intergenic	L1M3c|LINE|L1	302499	NM_008650	17850	Mm.259884	NM_008650	ENSMUSG00000023921	Mut	D230010K02Rik|Mcm	methylmalonyl-Coenzyme A mutase	protein-coding	0.01	0.277228
Merged-chr2-58595628-1	chr2	58595578	58595678	+	2.5	cIP2vsInput	Intergenic	Intergenic	-28800	NM_001110204	11477	Mm.689	NM_001110204	ENSMUSG00000026836	Acvr1	ALK2|ActR-I|ActRIA|Acvr|Acvrlk2|Alk-2|Alk8|D330013D15Rik|SKR1|Tsk7L	"activin A receptor, type 1"	protein-coding	0.01	0.405941
Merged-chr1-182752635-1	chr1	182752585	182752685	+	2.5	cIP1vsInput	Intergenic	L1MA6|LINE|L1	-3455	NM_001033547	433386	Mm.338103	NM_001033547	ENSMUSG00000043429	4922505E12Rik	-	RIKEN cDNA 4922505E12 gene	protein-coding	0	0.257426
Merged-chr4-115878556-1	chr4	115878506	115878606	+	2.5	cIP2vsInput	"3' UTR (NM_021461, exon 13 of 13)"	"3' UTR (NM_021461, exon 13 of 13)"	-5844	NM_001039124	654462	Mm.388913	NM_001039124	ENSMUSG00000073774	Kncn	Kino|L5	kinocilin	protein-coding	0.03	0.60396
Merged-chr12-70680418-1	chr12	70680368	70680468	+	2.5	cIP2vsInput	Intergenic	Intergenic	-145096	NM_028127	319710	Mm.2962	NM_028127	ENSMUSG00000048285	Frmd6	2610019M19Rik|4930488L10Rik|AW212977	FERM domain containing 6	protein-coding	0.04	0.534653
Merged-chr8-57775239-1	chr8	57775189	57775289	+	2.5	cIP2vsInput	"3' UTR (NM_175032, exon 12 of 12)"	"3' UTR (NM_175032, exon 12 of 12)"	-122184	NM_144731	108150	Mm.62886	NM_001167981	ENSMUSG00000031608	Galnt7	AI225872	UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.01	0.326733
Merged-chrX-7422734-1	chrX	7422684	7422784	+	2.5	cIP2vsInput	"intron (NR_027924, intron 1 of 1)"	"intron (NR_027924, intron 1 of 1)"	254	NR_027924	68355	Mm.45111	NR_027924		2010204K13Rik	0610010M13Rik|Cip7	RIKEN cDNA 2010204K13 gene	miscRNA	0.09	0.623762
Merged-chr11-103141112-1	chr11	103141062	103141162	+	2.5	cIP2vsInput	Intergenic	MIRc|SINE|MIR	7753	NM_027658	71059	Mm.273871	NM_001130515	ENSMUSG00000043372	Hexim2	4933402L21Rik	hexamethylene bis-acetamide inducible 2	protein-coding	0.02	0.524752
Merged-chr14-69767623-1	chr14	69767573	69767673	+	2.5	cIP1vsInput	"5' UTR (NM_020275, exon 1 of 8)"	"5' UTR (NM_020275, exon 1 of 8)"	151	NM_020275	21933	Mm.193430	NM_020275	ENSMUSG00000022074	Tnfrsf10b	DR5|KILLER|Ly98|MK|TRAILR2|TRICK2A|TRICK2B|TRICKB	"tumor necrosis factor receptor superfamily, member 10b"	protein-coding	0.03	0.564356
Merged-chr2-148732867-1	chr2	148732817	148732917	+	2.5	cIP2vsInput	promoter-TSS (NM_019632)	promoter-TSS (NM_019632)	-447	NM_019632	17957	Mm.391579	NM_019632	ENSMUSG00000027438	Napb	Brp14|E161|I47|SNARE|b-SNAP	N-ethylmaleimide sensitive fusion protein attachment protein beta	protein-coding	0	0.336634
Merged-chr3-132883814-1	chr3	132883764	132883864	+	2.5	cIP1vsInput	"3' UTR (NM_033525, exon 13 of 13)"	"3' UTR (NM_033525, exon 13 of 13)"	-5218	NR_102298	101243624	Mm.306256	NR_102297		LOC101243624	-	uncharacterized LOC101243624	miscRNA	0.01	0.366337
Merged-chr9-96616699-1	chr9	96616649	96616749	+	2.5	cIP1vsInput	"intron (NM_053268, intron 1 of 23)"	"intron (NM_053268, intron 1 of 23)"	14804	NM_053268	114713	Mm.124502	NM_053268	ENSMUSG00000032413	Rasa2	5430433H21Rik|AA517451|AU023900|GAP1m	RAS p21 protein activator 2	protein-coding	0	0.336634
Merged-chr5-9108289-1	chr5	9108239	9108339	+	2.5	cIP2vsInput	"intron (NM_001081029, intron 2 of 4)"	"intron (NM_001081029, intron 2 of 4)"	7552	NM_001081029	652925	Mm.439954	NM_001081029	ENSMUSG00000079659	Tmem243	4930420K17Rik|E030031F02Rik	"transmembrane protein 243, mitochondrial"	protein-coding	0	0.306931
Merged-chr11-30986389-1	chr11	30986339	30986439	+	2.5	cIP1vsInput	promoter-TSS (NM_026527)	promoter-TSS (NM_026527)	-24	NM_026527	68044	Mm.32656	NM_026527	ENSMUSG00000020309	Chac2	2510006C20Rik	"ChaC, cation transport regulator 2"	protein-coding	0.04	0.594059
Merged-chr16-83469366-1	chr16	83469316	83469416	+	2.5	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-901777	NR_040567	75247	Mm.417813	NR_040567		4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	miscRNA	0	0.366337
Merged-chr15-53775109-1	chr15	53775059	53775159	+	2.5	cIP1vsInput	"intron (NM_177225, intron 2 of 4)"	ORR1D2|LTR|ERVL-MaLR	127327	NM_177225	320679	Mm.442455	NM_177225	ENSMUSG00000058656	Samd12	A830094I09Rik	sterile alpha motif domain containing 12	protein-coding	0	0.366337
Merged-chr5-19587656-1	chr5	19587606	19587706	+	2.5	cIP2vsInput	"intron (NM_001170746, intron 1 of 22)"	Tigger6a|DNA|TcMar-Tigger	-319862	NM_001170745	50791	Mm.441283	NM_001170745	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	"membrane associated guanylate kinase, WW and PDZ domain containing 2"	protein-coding	0	0.326733
Merged-chr6-45333500-1	chr6	45333450	45333550	+	2.5	cIP1vsInput	"intron (NM_001004357, intron 1 of 23)"	"intron (NM_001004357, intron 1 of 23)"	273439	NM_001004357	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0	0.366337
Merged-chr14-97280333-1	chr14	97280283	97280383	+	2.5	cIP1vsInput	Intergenic	Intergenic	-761299	NM_053105	93688	Mm.308735	NM_053105	ENSMUSG00000022076	Klhl1	mKIAA1490	kelch-like 1	protein-coding	0	0.277228
Merged-chr4-67148303-1	chr4	67148253	67148353	+	2.5	cIP1vsInput	Intergenic	Intergenic	320492	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding	0	0.287129
Merged-chrX-103289193-1	chrX	103289143	103289243	+	2.5	cIP2vsInput	Intergenic	Intergenic	-32205	NM_007674	12592	Mm.4353	NM_007674	ENSMUSG00000031326	Cdx4	Cdx-3|Cdx-4|Cdx3	caudal type homeobox 4	protein-coding	0.06	0.683168
Merged-chr16-70436615-1	chr16	70436565	70436665	+	2.5	cIP2vsInput	"intron (NM_028803, intron 5 of 15)"	"intron (NM_028803, intron 5 of 15)"	122666	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	"glucan (1,4-alpha-), branching enzyme 1"	protein-coding	0	0.306931
Merged-chr2-124588828-1	chr2	124588778	124588878	+	2.5	cIP2vsInput	Intergenic	Intergenic	-21468	NM_199240	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|Sema6D-1|Sema6D-2|Sema6D-4|Sema6D-5|Sema6D-6|mKIAA1479	"sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D"	protein-coding	0	0.356436
Merged-chr5-64265032-1	chr5	64264982	64265082	+	2.5	cIP1vsInput	"intron (NM_019636, intron 6 of 19)"	"intron (NM_019636, intron 6 of 19)"	104821	NM_019636	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Tbc1|mKIAA1108	"TBC1 domain family, member 1"	protein-coding	0	0.326733
Merged-chr8-11706018-1	chr8	11705968	11706068	+	2.5	cIP2vsInput	Intergenic	Intergenic	-11504	NR_028307	624710	Mm.482623	NR_028307		Gm6524	EG624710	katanin p60 (ATPase-containing) subunit A1 pseudogene	pseudo	0.04	0.544554
Merged-chr15-53744581-1	chr15	53744531	53744631	+	2.5	cIP2vsInput	"intron (NM_177225, intron 2 of 4)"	L1MA4A|LINE|L1	157855	NM_177225	320679	Mm.442455	NM_177225	ENSMUSG00000058656	Samd12	A830094I09Rik	sterile alpha motif domain containing 12	protein-coding	0	0.346535
Merged-chr9-15639775-1	chr9	15639725	15639825	+	2.5	cIP2vsInput	"intron (NR_040746, intron 4 of 4)"	Lx5c|LINE|L1	-11842	NM_181816	234964	Mm.32237	NM_181816	ENSMUSG00000039977	Ccdc67	4933401K09Rik	coiled-coil domain containing 67	protein-coding	0	0.346535
Merged-chr2-42322326-1	chr2	42322276	42322376	+	2.5	cIP1vsInput	"intron (NM_053011, intron 2 of 90)"	L1MB8|LINE|L1	331272	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0	0.326733
Merged-chr9-108578523-1	chr9	108578473	108578573	+	2.5	cIP2vsInput	TTS (NM_028944)	TTS (NM_028944)	147	NM_031392	83669	Mm.458081	NM_031392	ENSMUSG00000066357	Wdr6	mWDR6	WD repeat domain 6	protein-coding	0.08	0.653465
Merged-chr14-103389474-1	chr14	103389424	103389524	+	2.5	cIP1vsInput	Intergenic	Intergenic	-42674	NM_207215	105689	Mm.6478	NM_207215	ENSMUSG00000033004	Mycbp2	AU023734|AW107953|AW546647|C130061D10Rik|Pam|Phr1|R75243	MYC binding protein 2	protein-coding	0	0.326733
Merged-chr5-16833994-1	chr5	16833944	16834044	+	2.5	cIP2vsInput	Intergenic	Intergenic	280444	NM_010427	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF/HGF	hepatocyte growth factor	protein-coding	0	0.277228
Merged-chr9-11142530-1	chr9	11142480	11142580	+	2.5	cIP1vsInput	Intergenic	MYSERV-int|LTR|ERVK	-237755	NM_001170787	244682	Mm.490683	NM_001033359	ENSMUSG00000039488	Cntn5	6720426O10Rik|A830025P08Rik|Gm507|NB-2	contactin 5	protein-coding	0	0.267327
Merged-chr2-42890171-1	chr2	42890121	42890221	+	2.5	cIP1vsInput	Intergenic	Intergenic	-236573	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0.01	0.277228
Merged-chr9-40397481-1	chr9	40397431	40397531	+	2.5	cIP2vsInput	"intron (NM_172768, intron 2 of 19)"	"intron (NM_172768, intron 2 of 19)"	58283	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding	0	0.415842
Merged-chr15-63391511-1	chr15	63391461	63391561	+	2.5	cIP1vsInput	Intergenic	Intergenic	88097	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	"predicted gene, 20740"	miscRNA	0	0.316832
Merged-chr6-63675602-1	chr6	63675552	63675652	+	2.5	cIP2vsInput	"intron (NM_008167, intron 2 of 15)"	MLT1B|LTR|ERVL-MaLR	418745	NM_008167	14804	Mm.447390	NM_008167		Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	"glutamate receptor, ionotropic, delta 2"	protein-coding	0	0.306931
Merged-chr2-129514895-1	chr2	129514845	129514945	+	2.5	cIP1vsInput	"intron (NM_177653, intron 1 of 6)"	"intron (NM_177653, intron 1 of 6)"	21707	NM_177653	228592	Mm.452175	NM_177653	ENSMUSG00000043727	F830045P16Rik	Sirpb3	RIKEN cDNA F830045P16 gene	protein-coding	0	0.425743
Merged-chr4-68174033-1	chr4	68173983	68174083	+	2.5	cIP1vsInput	Intergenic	Intergenic	780364	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Dbc1	BRINP|Brinp1|Dbccr1|Fam5a	deleted in bladder cancer 1 (human)	protein-coding	0	0.29703
Merged-chr3-149746328-1	chr3	149746278	149746378	+	2.5	cIP2vsInput	Intergenic	Intergenic	471591	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	miscRNA	0	0.356436
Merged-chr18-32129291-1	chr18	32129241	32129341	+	2.5	cIP1vsInput	"intron (NR_045173, intron 6 of 8)"	Lx7|LINE|L1	8914	NR_045173	19123	Mm.489734	NM_001042767	ENSMUSG00000024386	Proc	PC	protein C	protein-coding	0	0.405941
Merged-chr1-53412012-1	chr1	53411962	53412062	+	2.5	cIP2vsInput	"intron (NM_001252070, intron 63 of 65)"	"intron (NM_001252070, intron 63 of 65)"	-59313	NM_133728	70396	Mm.285783	NM_133728	ENSMUSG00000026095	Asnsd1	2210409M21Rik	asparagine synthetase domain containing 1	protein-coding	0	0.326733
Merged-chr2-39611946-1	chr2	39611896	39611996	+	2.5	cIP1vsInput	Intergenic	MYSERV-int|LTR|ERVK	-385608	NM_024209	67857	Mm.392662	NM_024209		Ppp6c	2310003C10Rik	"protein phosphatase 6, catalytic subunit"	protein-coding	0	0.29703
Merged-chr13-36724632-1	chr13	36724582	36724682	+	2.5	cIP2vsInput	TTS (NM_153529)	TTS (NM_153529)	9845	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding	0.07	0.60396
Merged-chr1-39192844-1	chr1	39192794	39192894	+	2.5	cIP1vsInput	Intergenic	Intergenic	-1428	NM_008719	18143	Mm.2380	NM_008719	ENSMUSG00000026077	Npas2	MOP4|bHLHe9	neuronal PAS domain protein 2	protein-coding	0.02	0.465347
Merged-chr8-36836665-1	chr8	36836615	36836715	+	2.5	cIP1vsInput	"intron (NM_001194940, intron 4 of 17)"	RCHARR1|DNA|hAT-Charlie	-103611	NM_001194941	50768	Mm.210875	NM_178735	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding	0.01	0.306931
Merged-chr8-100428035-1	chr8	100427985	100428085	+	2.5	cIP1vsInput	Intergenic	MTE2a-int|LTR|ERVL-MaLR	-1011578	NM_001039154	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0.01	0.306931
Merged-chr1-51565872-1	chr1	51565822	51565922	+	2.5	cIP1vsInput	Intergenic	Intergenic	-87473	NM_028696	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a	nucleic acid binding protein 1	protein-coding	0	0.306931
Merged-chr2-43641521-1	chr2	43641471	43641571	+	2.5	cIP2vsInput	"intron (NM_027552, intron 10 of 13)"	L1_Mur3|LINE|L1	86192	NM_027552	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding	0	0.326733
Merged-chr5-139345180-1	chr5	139345130	139345230	+	2.5	cIP1vsInput	promoter-TSS (NM_197980)	promoter-TSS (NM_197980)	-14	NM_197980	68033	Mm.261064	NM_197980		Cox19	1810074D02Rik|2810437L13Rik	cytochrome c oxidase assembly protein 19	protein-coding	0.14	0.643564
Merged-chr18-17712662-1	chr18	17712612	17712712	+	2.5	cIP1vsInput	Intergenic	Intergenic	-131672	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	miscRNA	0	0.267327
Merged-chr18-38164927-1	chr18	38164877	38164977	+	2.5	cIP2vsInput	Intergenic	L1ME3G|LINE|L1	44835	NM_029357	75599	Mm.458851	NM_029357	ENSMUSG00000051375	Pcdh1	2010005A06Rik|AI585920	protocadherin 1	protein-coding	0	0.445545
Merged-chr3-26631978-1	chr3	26631928	26632028	+	2.5	cIP2vsInput	Intergenic	Intergenic	-5653	NM_029150	70862	Mm.330943	NM_027583	ENSMUSG00000039335	Spata16	4921511F01Rik|4930503K02Rik|Nyd-sp12	spermatogenesis associated 16	protein-coding	0	0.316832
Merged-chr18-21962273-1	chr18	21962223	21962323	+	2.5	cIP2vsInput	"intron (NM_027616, intron 20 of 22)"	"intron (NM_027616, intron 20 of 22)"	209123	NM_027616	70950	Mm.235716	NM_027616	ENSMUSG00000024306	Ccdc178	4921528I01Rik	coiled coil domain containing 178	protein-coding	0.01	0.306931
Merged-chr6-26456781-1	chr6	26456731	26456831	+	2.5	cIP2vsInput	Intergenic	Intergenic	525355	NR_040771	626904	Mm.126787	NR_040771		Gm20756	-	"predicted gene, 20756"	miscRNA	0.02	0.376238
Merged-chr5-42982696-1	chr5	42982646	42982746	+	2.5	cIP1vsInput	Intergenic	L1ME4b|LINE|L1	-250767	NM_175937	231207	Mm.7233	NM_001177379	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding	0	0.257426
Merged-chr5-77646390-1	chr5	77646340	77646440	+	2.5	cIP2vsInput	Intergenic	Tigger13a|DNA|TcMar-Tigger	-134642	NR_027806	231332	Mm.373616	NM_001010832		Pea15b	-	phosphoprotein enriched in astrocytes 15B	pseudo	0.01	0.366337
Merged-chr4-83709465-1	chr4	83709415	83709515	+	2.5	cIP1vsInput	"intron (NM_001081012, intron 21 of 25)"	"intron (NM_001081012, intron 21 of 25)"	183920	NM_001081012	320226	Mm.180032	NM_001081012	ENSMUSG00000052407	Ccdc171	4930418J05Rik|4930473A06Rik|A330015D16Rik	coiled-coil domain containing 171	protein-coding	0.01	0.237624
Merged-chr4-70482285-1	chr4	70482235	70482335	+	2.5	cIP2vsInput	"intron (NM_172694, intron 2 of 5)"	"intron (NM_172694, intron 2 of 5)"	52643	NM_172694	230316	Mm.251188	NM_172694		Megf9	4933405H16Rik|9630025C07|Egfl5|mKIAA0818	multiple EGF-like-domains 9	protein-coding	0.01	0.356436
Merged-chr5-17091993-1	chr5	17091943	17092043	+	2.5	cIP2vsInput	Intergenic	Intergenic	-384129	NM_027609	70935	Mm.332225	NM_027609	ENSMUSG00000058643	Speer4f	4922502J04Rik|SPEER-4F	spermatogenesis associated glutamate (E)-rich protein 4f	protein-coding	0.01	0.39604
Merged-chr9-89594687-1	chr9	89594637	89594737	+	2.5	cIP1vsInput	"intron (NM_153509, intron 3 of 3)"	IMPB_01|Satellite|Satellite	28299	NM_153509	209743	Mm.458520	NM_153509	ENSMUSG00000039313	AF529169	DD1|Kiaa1024	cDNA sequence AF529169	protein-coding	0	0.405941
Merged-chr2-107462011-1	chr2	107461961	107462061	+	2.5	cIP1vsInput	Intergenic	Intergenic	171422	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	"potassium voltage-gated channel, shaker-related subfamily, member 4"	protein-coding	0	0.227723
Merged-chr3-17496762-1	chr3	17496712	17496812	+	2.5	cIP2vsInput	Intergenic	MLT2D|LTR|ERVL	-293159	NR_033490	70441	Mm.458192	NR_033490		2610100L16Rik	100040120|Gm2612	RIKEN cDNA 2610100L16 gene	miscRNA	0	0.336634
Merged-chr2-159386725-1	chr2	159386675	159386775	+	2.5	cIP1vsInput	Intergenic	Intergenic	-560616	NR_040498	71081	Mm.383491	NR_040498	ENSMUSG00000085198	4933416E03Rik	-	RIKEN cDNA 4933416E03 gene	miscRNA	0.01	0.316832
Merged-chr13-12262777-1	chr13	12262727	12262827	+	2.5	cIP1vsInput	Intergenic	Intergenic	-4664	NM_001081128	238505	Mm.40335	NM_001081128	ENSMUSG00000021311	Mtr	AI894170|D830038K18Rik|MS	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding	0	0.39604
Merged-chr4-134510876-2	chr4	134510826	134510926	+	2.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_001081099)	promoter-TSS (NM_001081099)	-123	NM_001081099	69885	Mm.141592	NM_001081099	ENSMUSG00000078521	Clhc1	2610002D18Rik|Aunip	clathrin heavy chain linker domain containing 1	protein-coding	0	0.445545
Merged-chr1-5389117-1	chr1	5389067	5389167	+	2.5	cIP1vsInput	Intergenic	Lx4A|LINE|L1	-199376	NM_011011	18387	Mm.7977	NM_001204371	ENSMUSG00000025905	Oprk1	K-OR-1|KOR|KOR-1|MSL-1|Oprk2|R21	"opioid receptor, kappa 1"	protein-coding	0.02	0.336634
Merged-chr12-82122938-1	chr12	82122888	82122988	+	2.5	cIP2vsInput	Intergenic	Intergenic	-47078	NM_001167983	217692	Mm.261333	NM_001167983	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding	0.01	0.336634
Merged-chr12-95970862-1	chr12	95970812	95970912	+	2.5	cIP2vsInput	Intergenic	Intergenic	76360	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0.01	0.326733
Merged-chr17-43327070-1	chr17	43327020	43327120	+	2.5	cIP2vsInput	Intergenic	Intergenic	56723	NM_133776	77596	Mm.159950	NM_133776	ENSMUSG00000041293	Gpr110	5031409J19Rik|KPG_009	G protein-coupled receptor 110	protein-coding	0.02	0.514851
Merged-chr13-119632346-1	chr13	119632296	119632396	+	2.5	cIP2vsInput	"intron (NM_020279, intron 1 of 2)"	ID4_|SINE|ID	8527	NM_020279	56838	Mm.143745	NM_020279	ENSMUSG00000074715	Ccl28	CCK1|MEC|Scya28	chemokine (C-C motif) ligand 28	protein-coding	0.02	0.386139
Merged-chr6-110145171-1	chr6	110145121	110145221	+	2.5	cIP1vsInput	Intergenic	Intergenic	-500427	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0.01	0.316832
Merged-chr11-51916818-1	chr11	51916768	51916868	+	2.5	cIP2vsInput	Intergenic	Intergenic	-50813	NM_029976	52626	Mm.289456	NM_029976	ENSMUSG00000020392	Cdkn2aipnl	A430101B06Rik|AA409260|D11Ertd497e|MNCb-1520	CDKN2A interacting protein N-terminal like	protein-coding	0.06	0.712871
Merged-chr12-97033974-1	chr12	97033924	97034024	+	2.5	cIP1vsInput	Intergenic	Intergenic	-986752	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0	0.306931
Merged-chr2-8543427-1	chr2	8543377	8543477	+	2.5	cIP1vsInput	Intergenic	L1M4|LINE|L1	-646088	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	miscRNA	0	0.237624
Merged-chr11-28942975-1	chr11	28942925	28943025	+	2.5	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	89770	NM_146015	216616	Mm.44176	NM_146015	ENSMUSG00000020467	Efemp1	-	epidermal growth factor-containing fibulin-like extracellular matrix protein 1	protein-coding	0	0.386139
Merged-chr5-48325148-1	chr5	48325098	48325198	+	2.5	cIP2vsInput	Intergenic	Intergenic	-47244	NM_025755	66768	Mm.29409	NM_025755	ENSMUSG00000029089	Pacrgl	4933428G09Rik	PARK2 co-regulated-like	protein-coding	0	0.346535
Merged-chr16-53876181-1	chr16	53876131	53876231	+	2.5	cIP1vsInput	Intergenic	Intergenic	-1060437	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	miscRNA	0	0.257426
Merged-chr17-60683046-1	chr17	60682996	60683096	+	2.5	cIP1vsInput	Intergenic	L1MD1|LINE|L1	-634706	NR_030569	100124495		NR_030569		Mir466g	Mirn466g	microRNA 466g	miscRNA	0	0.336634
Merged-chr17-91408853-1	chr17	91408803	91408903	+	2.5	cIP2vsInput	Intergenic	Intergenic	-316051	NM_020252	18189	Mm.312068	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0	0.376238
Merged-chr11-106648513-1	chr11	106648463	106648563	+	2.5	cIP2vsInput	Intergenic	Intergenic	-35583	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding	0.06	0.554455
Merged-chr1-110467684-1	chr1	110467634	110467734	+	2.5	cIP2vsInput	Intergenic	Intergenic	483947	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.316832
Merged-chr4-91425778-1	chr4	91425728	91425828	+	2.5	cIP1vsInput	Intergenic	Intergenic	-25794	NM_207685	15569	Mm.318042	NM_001177883	ENSMUSG00000008489	Elavl2	Hub|mel-N1	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)"	protein-coding	0.01	0.326733
Merged-chr8-73965238-1	chr8	73965188	73965288	+	2.5	cIP2vsInput	Intergenic	L1M2|LINE|L1	-612682	NM_010687	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large	BPFD#36|Gyltl1a|Mbp-1|Mbp1|enr|fg|froggy|mKIAA0609|myd	like-glycosyltransferase	protein-coding	0	0.316832
Merged-chr17-40546150-1	chr17	40546100	40546200	+	2.5	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-15357	NM_001177529	433107	Mm.353122	NM_001177529	ENSMUSG00000092043	Gm5494	EG433107|Esp5|Esp6	predicted gene 5494	protein-coding	0	0.346535
Merged-chr1-68454034-1	chr1	68453984	68454084	+	2.5	cIP1vsInput	"intron (NM_010154, intron 3 of 26)"	"intron (NM_010154, intron 3 of 26)"	654025	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0.01	0.306931
Merged-chr2-104712314-1	chr2	104712264	104712364	+	2.5	cIP2vsInput	promoter-TSS (NM_177190)	promoter-TSS (NM_177190)	-152	NM_177190	320554	Mm.249065	NM_177190	ENSMUSG00000027175	Tcp11l1	C130096D04Rik	t-complex 11 like 1	protein-coding	0.09	0.683168
Merged-chr5-79575111-1	chr5	79575061	79575161	+	2.5	cIP2vsInput	Intergenic	Intergenic	-59207	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0	0.356436
Merged-chr17-88474927-1	chr17	88474877	88474977	+	2.5	cIP1vsInput	"intron (NM_180974, intron 2 of 5)"	"intron (NM_180974, intron 2 of 5)"	34215	NM_180974	14236	Mm.393597	NM_180974	ENSMUSG00000034998	Foxn2	3230402J05Rik|6030465J18Rik|Fkh19|Foxn1|HTLF	forkhead box N2	protein-coding	0	0.306931
Merged-chr6-45571061-1	chr6	45571011	45571111	+	2.5	cIP2vsInput	"intron (NM_001004357, intron 1 of 23)"	"intron (NM_001004357, intron 1 of 23)"	511000	NM_001004357	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0	0.326733
Merged-chr8-111094565-1	chr8	111094515	111094615	+	2.5	cIP2vsInput	promoter-TSS (NM_198308)	promoter-TSS (NM_198308)	-180	NM_198308	319518	Mm.370024	NM_198308		Pdpr	4930402E16Rik|AU018056|mKIAA1990	pyruvate dehydrogenase phosphatase regulatory subunit	protein-coding	0.18	0.792079
Merged-chr9-18230364-1	chr9	18230314	18230414	+	2.5	cIP2vsInput	Intergenic	Intergenic	-61903	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	"cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1"	protein-coding	0.01	0.376238
Merged-chrX-48285267-1	chrX	48285217	48285317	+	2.5	cIP2vsInput	"intron (NR_045916, intron 1 of 3)"	"intron (NR_045916, intron 1 of 3)"	159	NR_045916	100500713	Mm.396609	NR_045916	ENSMUSG00000097197	9530027J09Rik	-	RIKEN cDNA 9530027J09 gene	miscRNA	0.06	0.693069
Merged-chr16-81934651-1	chr16	81934601	81934701	+	2.5	cIP2vsInput	Intergenic	Intergenic	733954	NM_010954	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.326733
Merged-chr6-65698398-1	chr6	65698348	65698448	+	2.5	cIP1vsInput	"intron (NM_172399, intron 2 of 3)"	"intron (NM_172399, intron 2 of 3)"	26787	NM_172399	68169	Mm.52392	NM_172399	ENSMUSG00000049001	Ndnf	A930038C07Rik|epidermacan	neuron-derived neurotrophic factor	protein-coding	0	0.356436
Merged-chr10-49322887-1	chr10	49322837	49322937	+	2.5	cIP2vsInput	"intron (NM_010349, intron 11 of 17)"	"intron (NM_010349, intron 11 of 17)"	-227044	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	"proteasome (prosome, macropain) subunit, alpha type 6 pseudogene"	pseudo	0	0.306931
Merged-chr10-51908778-1	chr10	51908728	51908828	+	2.5	cIP2vsInput	Intergenic	Intergenic	-113908	NM_153786	215031	Mm.87237	NM_153786	ENSMUSG00000049641	Vgll2	C130057C21Rik|VITO-1|Vito1	vestigial like 2 homolog (Drosophila)	protein-coding	0	0.29703
Merged-chr13-18907292-1	chr13	18907242	18907342	+	2.5	cIP1vsInput	Intergenic	L1M2|LINE|L1	-41079	NM_175007	218038	Mm.101650	NM_175007	ENSMUSG00000021314	Amph	-	amphiphysin	protein-coding	0	0.29703
Merged-chr2-133327201-1	chr2	133327151	133327251	+	2.5	cIP1vsInput	Intergenic	Intergenic	-224958	NM_007553	12156	Mm.103205	NM_007553		Bmp2	AI467020|Bmp2a	bone morphogenetic protein 2	protein-coding	0.01	0.306931
Merged-chr15-103777127-1	chr15	103777077	103777177	+	2.5	cIP2vsInput	"intron (NM_009268, intron 2 of 4)"	"intron (NM_009268, intron 2 of 4)"	122173	NM_009268	20771	Mm.30276	XM_003945554		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding	0	0.39604
Merged-chr11-50931982-1	chr11	50931932	50932032	+	2.5	cIP2vsInput	promoter-TSS (NM_013744)	promoter-TSS (NM_013744)	-347	NM_013744	27274	Mm.74670	NM_013744	ENSMUSG00000020335	Zfp354b	Kid2|Tcf17l1|Znf354b	zinc finger protein 354B	protein-coding	0	0.356436
Merged-chr18-29777715-1	chr18	29777665	29777765	+	2.5	cIP1vsInput	Intergenic	MARNA|DNA|TcMar-Mariner	-281299	NR_045391	78058	Mm.416952	NR_045391		4930578E11Rik	-	RIKEN cDNA 4930578E11 gene	miscRNA	0	0.306931
Merged-chr14-83614735-1	chr14	83614685	83614785	+	2.5	cIP2vsInput	Intergenic	Intergenic	-828828	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0	0.326733
Merged-chr6-125215575-1	chr6	125215525	125215625	+	2.5	cIP2vsInput	promoter-TSS (NM_009496)	promoter-TSS (NM_009496)	-6	NM_009496	22317	Mm.32321	NM_001080557	ENSMUSG00000030337	Vamp1	Syb-1|Syb1|VAMP-1|lew	vesicle-associated membrane protein 1	protein-coding	0.07	0.564356
Merged-chr7-52644679-1	chr7	52644629	52644729	+	2.5	cIP1vsInput	Intergenic	RLTR15|LTR|ERVK	-628963	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding	0	0.356436
Merged-chr2-168584977-1	chr2	168584927	168585027	+	2.5	cIP2vsInput	"intron (NM_001037177, intron 1 of 6)"	"intron (NM_001037177, intron 1 of 6)"	5214	NM_001136073	18019	Mm.116802	NM_001136073	ENSMUSG00000027544	Nfatc2	AI607462|NF-ATc2|NFAT1|NFAT1-D|Nfatp	"nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2"	protein-coding	0.01	0.445545
Merged-chr6-7377587-1	chr6	7377537	7377637	+	2.5	cIP2vsInput	Intergenic	Intergenic	-177484	NM_009311	21333	Mm.410823	NM_009311	ENSMUSG00000061762	Tac1	4930528L02Rik|NK-1|NK1|Nkna|PPT-A|PPTA|SP	tachykinin 1	protein-coding	0	0.366337
Merged-chr8-91206106-1	chr8	91206056	91206156	+	2.5	cIP1vsInput	Intergenic	Intergenic	-70610	NM_010241	14339	Mm.324588	NM_010241	ENSMUSG00000031667	Aktip	AL023020|Fif|Ft|Ft1|Fts	thymoma viral proto-oncogene 1 interacting protein	protein-coding	0.01	0.534653
Merged-chr15-25642455-1	chr15	25642405	25642505	+	2.5	cIP2vsInput	"intron (NM_019472, intron 1 of 40)"	"intron (NM_019472, intron 1 of 40)"	19905	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799	myosin X	protein-coding	0.02	0.544554
Merged-chr10-27940155-1	chr10	27940105	27940205	+	2.5	cIP2vsInput	Intergenic	Intergenic	-134665	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	"protein tyrosine phosphatase, receptor type, K"	protein-coding	0.01	0.306931
Merged-chr9-121760347-1	chr9	121760297	121760397	+	2.5	cIP2vsInput	promoter-TSS (NR_033503)	promoter-TSS (NR_033503)	314	NM_001166644	270210	Mm.473702	NM_001166644	ENSMUSG00000013419	Zfp651	4732420M22Rik|BC030045|R74626	zinc finger protein 651	protein-coding	0.09	0.742574
Merged-chr3-124472195-1	chr3	124472145	124472245	+	2.5	cIP2vsInput	Intergenic	Intergenic	-46167	NM_027939	71824	Mm.331353	NM_027939	ENSMUSG00000027973	1700006A11Rik	-	RIKEN cDNA 1700006A11 gene	protein-coding	0	0.306931
Merged-chr8-62427169-1	chr8	62427119	62427219	+	2.5	cIP1vsInput	Intergenic	Intergenic	-304051	NM_011922	26359	Mm.42179	NM_001136089	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding	0.01	0.326733
Merged-chr2-157066567-1	chr2	157066517	157066617	+	2.5	cIP2vsInput	"intron (NM_001164663, intron 1 of 14)"	Charlie4a|DNA|hAT-Charlie	12698	NM_001164663	320706	Mm.79466	NM_001164663		Soga1	9830001H06Rik|AI426038|D430036N24Rik|Soga	"suppressor of glucose, autophagy associated 1"	protein-coding	0	0.326733
Merged-chr8-40991164-1	chr8	40991114	40991214	+	2.5	cIP1vsInput	TTS (NM_026840)	TTS (NM_026840)	-26304	NR_015457	78849	Mm.440930	NR_015457	ENSMUSG00000084960	B430010I23Rik	-	RIKEN cDNA B430010I23 gene	miscRNA	0.03	0.405941
Merged-chr11-89914892-1	chr11	89914842	89914942	+	2.5	cIP1vsInput	Intergenic	L1MD|LINE|L1	88002	NM_008796	18559	Mm.5062	NM_008796		Pctp	PC-TP|StarD2	phosphatidylcholine transfer protein	protein-coding	0.01	0.386139
Merged-chr1-52748547-1	chr1	52748497	52748597	+	2.5	cIP1vsInput	Intergenic	Intergenic	-21229	NM_133829	98682	Mm.269793	NM_133829	ENSMUSG00000041439	Mfsd6	2210010L05Rik|9630025I22Rik|AI836200|AW212394|MMR2	major facilitator superfamily domain containing 6	protein-coding	0.01	0.415842
Merged-chr6-93075588-1	chr6	93075538	93075638	+	2.5	cIP2vsInput	"intron (NR_015530, intron 1 of 2)"	"intron (NR_015530, intron 1 of 2)"	135006	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	miscRNA	0.02	0.316832
Merged-chr11-39439353-1	chr11	39439303	39439403	+	2.5	cIP1vsInput	Intergenic	Intergenic	-919308	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0.01	0.336634
Merged-chr17-71562137-1	chr17	71562087	71562187	+	2.5	cIP1vsInput	"intron (NR_015549, intron 5 of 6)"	"intron (NR_015549, intron 5 of 6)"	10076	NM_029254	70891	Mm.477599	NM_001142631	ENSMUSG00000052525	Spdya	4921517J08Rik|4930548B21Rik|GS4|MLZ-465|Spdy1	speedy homolog A (Xenopus laevis)	protein-coding	0	0.277228
Merged-chr8-5764914-1	chr8	5764864	5764964	+	2.5	cIP2vsInput	Intergenic	Intergenic	-659682	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.356436
Merged-chr1-23900260-1	chr1	23900210	23900310	+	2.5	cIP1vsInput	"intron (NM_028534, intron 1 of 9)"	"intron (NM_028534, intron 1 of 9)"	22029	NM_028534	98366	Mm.329963	NM_028534	ENSMUSG00000026155	Smap1	1700056O10Rik|4921514B13Rik|4921525H11Rik|AI462175	stromal membrane-associated protein 1	protein-coding	0	0.257426
Merged-chr8-83595004-1	chr8	83594954	83595054	+	2.5	cIP1vsInput	promoter-TSS (NM_134118)	promoter-TSS (NM_134118)	-513	NM_134118	106529	Mm.352239	NM_027179	ENSMUSG00000031708	Tecr	2410016D23Rik|A230102P12Rik|AI173355|D17Ertd178e|Gpsn2|SC2	"trans-2,3-enoyl-CoA reductase"	protein-coding	0.02	0.445545
Merged-chr8-13338310-1	chr8	13338260	13338360	+	2.5	cIP1vsInput	Intergenic	Intergenic	-1364	NM_009361	21781	Mm.925	NM_009361	ENSMUSG00000038482	Tfdp1	Dp1|Drtf1	transcription factor Dp 1	protein-coding	0.05	0.534653
Merged-chr2-30667660-1	chr2	30667610	30667710	+	2.5	cIP2vsInput	Intergenic	Intergenic	-53550	NR_037272	100526499		NR_037272	ENSMUSG00000093091	Mir3089	mmu-mir-3089	microRNA 3089	miscRNA	0.03	0.574257
Merged-chr6-21169779-1	chr6	21169729	21169829	+	2.5	cIP1vsInput	Intergenic	Intergenic	-46330	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	"potassium voltage-gated channel, Shal-related family, member 2"	protein-coding	0	0.326733
Merged-chr17-89423029-1	chr17	89422979	89423079	+	2.5	cIP2vsInput	Intergenic	Intergenic	43788	NR_045952	100043904	Mm.396198	NR_045952		Gm4719	-	predicted gene 4719	miscRNA	0.01	0.336634
Merged-chr7-69364415-1	chr7	69364365	69364465	+	2.5	cIP2vsInput	Intergenic	L1MC3|LINE|L1	-131679	NR_045940	73796	Mm.410832	NR_045940		4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	miscRNA	0	0.316832
Merged-chr2-47781539-1	chr2	47781489	47781589	+	2.5	cIP2vsInput	Intergenic	Lx3A|LINE|L1	-1032570	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding	0	0.316832
Merged-chr16-69676326-1	chr16	69676276	69676376	+	2.5	cIP2vsInput	Intergenic	Intergenic	187418	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding	0.01	0.326733
Merged-chr8-20906078-1	chr8	20906028	20906128	+	2.5	cIP1vsInput	Intergenic	Intergenic	-4105	NM_001177471	100504014	Mm.490239	NM_001177471	ENSMUSG00000082976	Gm15056	Defb52|OTTMUSG00000018888	predicted gene 15056	protein-coding	0.04	0.445545
Merged-chr6-47843202-1	chr6	47843152	47843252	+	2.5	cIP1vsInput	"intron (NM_027477, intron 2 of 5)"	"intron (NM_027477, intron 2 of 5)"	7541	NM_027477	272347	Mm.395440	NM_027477	ENSMUSG00000062519	Zfp398	5730513I23Rik|6430539K21	zinc finger protein 398	protein-coding	0	0.346535
Merged-chr13-11998118-1	chr13	11998068	11998168	+	2.5	cIP2vsInput	"intron (NM_023868, intron 1 of 104)"	"intron (NM_023868, intron 1 of 104)"	108827	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	"ryanodine receptor 2, cardiac"	protein-coding	0	0.336634
Merged-chr15-57946006-1	chr15	57945956	57946056	+	2.5	cIP1vsInput	"intron (NM_001167679, intron 10 of 17)"	L1MC5a|LINE|L1	33807	NM_001167679	210544	Mm.390835	NM_199300	ENSMUSG00000022364	Wdr67	4B3|D330013L20Rik|Gm85	WD repeat domain 67	protein-coding	0.01	0.485149
Merged-chr9-39205246-1	chr9	39205196	39205296	+	2.5	cIP1vsInput	Intergenic	Intergenic	-12113	NM_146507	258500	Mm.271417	NM_146507	ENSMUSG00000096555	Olfr944	MOR171-19	olfactory receptor 944	protein-coding	0	0.316832
Merged-chr5-115135027-1	chr5	115134977	115135077	+	2.5	cIP2vsInput	promoter-TSS (NM_175352)	promoter-TSS (NM_175352)	-52	NM_175352	106840	Mm.29241	NM_175352	ENSMUSG00000046562	Unc119b	AA407659|AI414892	unc-119 homolog B (C. elegans)	protein-coding	0.07	0.782178
Merged-chr1-23062211-1	chr1	23062161	23062261	+	2.5	cIP2vsInput	Intergenic	Intergenic	40042	NM_025746	66755	Mm.431297	NM_025746	ENSMUSG00000073730	4933415F23Rik	-	RIKEN cDNA 4933415F23 gene	protein-coding	0.05	0.534653
Merged-chr13-82654704-1	chr13	82654654	82654754	+	2.5	cIP2vsInput	Intergenic	L1M2|LINE|L1	-849330	NM_001170537	17260	Mm.487610	NM_001170537	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding	0.01	0.326733
Merged-chr4-23800238-1	chr4	23800188	23800288	+	2.5	cIP1vsInput	Intergenic	Intergenic	-696224	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	"MMS22-like, DNA repair protein"	protein-coding	0	0.326733
Merged-chr12-57068567-1	chr12	57068517	57068617	+	2.5	cIP2vsInput	"intron (NM_172577, intron 1 of 9)"	"intron (NM_172577, intron 1 of 9)"	92076	NM_001167976	217593	Mm.32835	NM_001167976	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	"solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21"	protein-coding	0	0.346535
Merged-chr6-13003689-1	chr6	13003639	13003739	+	2.5	cIP2vsInput	Intergenic	Lx7|LINE|L1	-66070	NM_027992	71900	Mm.27742	NM_027992	ENSMUSG00000029571	Tmem106b	2310036D22Rik|5830455K21Rik|6430519M21Rik|AI428776|AI661344	transmembrane protein 106B	protein-coding	0	0.376238
Merged-chr13-110388448-1	chr13	110388398	110388498	+	2.5	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-6596	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding	0	0.316832
Merged-chr18-72047472-1	chr18	72047422	72047522	+	2.5	cIP1vsInput	"intron (NM_007831, intron 1 of 28)"	"intron (NM_007831, intron 1 of 28)"	303597	NM_007831	13176	Mm.167882	NM_007831		Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding	0	0.376238
Merged-chr17-13847493-1	chr17	13847443	13847543	+	2.5	cIP1vsInput	"intron (NM_010806, intron 15 of 32)"	"intron (NM_010806, intron 15 of 32)"	-86099	NM_022311	21646	Mm.486358	NM_022311		Tcte2	AI429268|Tcte-2	t-complex-associated testis expressed 2	protein-coding	0	0.316832
Merged-chr13-72181150-1	chr13	72181100	72181200	+	2.5	cIP2vsInput	Intergenic	Intergenic	-217427	NM_010573	16371	Mm.316056	NM_010573	ENSMUSG00000060969	Irx1	-	Iroquois related homeobox 1 (Drosophila)	protein-coding	0	0.326733
Merged-chr16-32487372-1	chr16	32487322	32487422	+	2.5	cIP2vsInput	"intron (NM_145932, intron 1 of 8)"	"intron (NM_145932, intron 1 of 8)"	507	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	"solute carrier family 51, alpha subunit"	protein-coding	0.03	0.574257
Merged-chr12-60805151-1	chr12	60805101	60805201	+	2.5	cIP1vsInput	Intergenic	Intergenic	716669	NR_045049	100504101	Mm.235026	NR_045049		Gm20063	-	"predicted gene, 20063"	miscRNA	0.01	0.336634
Merged-chr1-16916450-1	chr1	16916400	16916500	+	2.5	cIP1vsInput	Intergenic	Intergenic	181439	NM_020604	57339	Mm.143761	NM_020604	ENSMUSG00000042686	Jph1	ENSMUSG00000054314|JP-1|Jp1	junctophilin 1	protein-coding	0	0.346535
Merged-chr18-39651812-1	chr18	39651762	39651862	+	2.5	cIP2vsInput	Intergenic	Intergenic	-121685	NM_011033	18459	Mm.9493	NM_011033	ENSMUSG00000051732	Pabpc2	Pabp|Pabp+|Pabp2	"poly(A) binding protein, cytoplasmic 2"	protein-coding	0	0.277228
Merged-chr4-33310297-1	chr4	33310247	33310347	+	2.5	cIP2vsInput	promoter-TSS (NM_011884)	promoter-TSS (NM_011884)	-14	NM_011884	24018	Mm.464346	NM_011884	ENSMUSG00000028274	Rngtt	AU020997	RNA guanylyltransferase and 5'-phosphatase	protein-coding	0.08	0.663366
Merged-chr18-89381399-1	chr18	89381349	89381449	+	2.5	cIP1vsInput	"intron (NM_001039173, intron 7 of 7)"	"intron (NM_001039173, intron 7 of 7)"	183972	NM_001039149	225825	Mm.139293	NM_001039148	ENSMUSG00000034028	Cd226	BC051526|DNAM-1|DNAM1|Pta1|TLiSA1	CD226 antigen	protein-coding	0	0.326733
Merged-chr19-33176394-1	chr19	33176344	33176444	+	2.5	cIP1vsInput	"intron (NM_001146342, intron 3 of 4)"	"intron (NM_001146342, intron 3 of 4)"	215901	NM_001167818	67795	Mm.204591	NM_001146342	ENSMUSG00000071573	Rnls	6530404N21Rik|AI452315|AW060440|C10orf59	"renalase, FAD-dependent amine oxidase"	protein-coding	0	0.376238
Merged-chr12-48460795-1	chr12	48460745	48460845	+	2.5	cIP1vsInput	Intergenic	Intergenic	-159333	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0	0.306931
Merged-chr14-77134486-1	chr14	77134436	77134536	+	2.5	cIP2vsInput	Intergenic	Intergenic	-22277	NM_001253759	239188	Mm.490096	NM_001253759	ENSMUSG00000022012	Enox1	B230207J08|D230005D02Rik	ecto-NOX disulfide-thiol exchanger 1	protein-coding	0.02	0.356436
Merged-chr2-88641930-1	chr2	88641880	88641980	+	2.5	cIP1vsInput	Intergenic	Intergenic	-35927	NM_001011517	329460	Mm.377885	NM_001011517	ENSMUSG00000060827	Olfr1193	MOR226-1|MOR230-9|Olfr1193-ps1|Olfr1194-ps1	olfactory receptor 1193	protein-coding	0	0.326733
Merged-chr15-47986515-1	chr15	47986465	47986565	+	2.5	cIP1vsInput	"intron (NM_001081391, intron 16 of 70)"	ID_B1|SINE|B4	805474	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0	0.346535
Merged-chr10-111908493-1	chr10	111908443	111908543	+	2.5	cIP1vsInput	Intergenic	Intergenic	-34117	NR_046029	629206	Mm.391444	NR_046029		Gm20758	-	"predicted gene, 20758"	miscRNA	0	0.366337
Merged-chr6-53657118-1	chr6	53657068	53657168	+	2.5	cIP2vsInput	"intron (NM_172728, intron 3 of 6)"	"intron (NM_172728, intron 3 of 6)"	83744	NM_172728	231991	Mm.321138	NM_172728	ENSMUSG00000053007	Creb5	Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding	0	0.316832
Merged-chr11-99938131-1	chr11	99938081	99938181	+	2.5	cIP1vsInput	TTS (NM_001025244)	TTS (NM_001025244)	1840	NM_001025244	432602	Mm.246878	NM_001025244	ENSMUSG00000051481	Krtap31-2	OTTMUSG00000002177	keratin associated protein 31-2	protein-coding	0.01	0.376238
Merged-chr11-65893279-1	chr11	65893229	65893329	+	2.5	cIP2vsInput	"intron (NM_001099633, intron 56 of 68)"	L1MA6|LINE|L1	86035	NM_026107	52712	Mm.340052	NM_026107	ENSMUSG00000018347	Zkscan6	1700128E15Rik|D11Ertd714e|KOX11|Zfp535|Znf18	zinc finger with KRAB and SCAN domains 6	protein-coding	0	0.336634
Merged-chr17-71981041-1	chr17	71980991	71981091	+	2.5	cIP2vsInput	"intron (NM_007439, intron 8 of 28)"	"intron (NM_007439, intron 8 of 28)"	199094	NM_030179	78785	Mm.196382	NM_001271483	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	"CAP-GLY domain containing linker protein family, member 4"	protein-coding	0.01	0.574257
Merged-chr3-6033399-1	chr3	6033349	6033449	+	2.5	cIP1vsInput	Intergenic	Intergenic	-457151	NM_001163305	19302	Mm.132336	NM_001163304	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding	0	0.306931
Merged-chr18-17161197-1	chr18	17161147	17161247	+	2.5	cIP2vsInput	Intergenic	L1M4|LINE|L1	74285	NR_033607	664619	Mm.250005	NR_033607		4921533I20Rik	-	PRP18 pre-mRNA processing factor 18 homolog pseudogene	pseudo	0	0.326733
Merged-chr4-26211665-1	chr4	26211615	26211715	+	2.5	cIP1vsInput	Intergenic	Intergenic	134987	NM_172865	242362	Mm.245602	NM_172865	ENSMUSG00000040520	Manea	4932703L02Rik	"mannosidase, endo-alpha"	protein-coding	0	0.346535
Merged-chr16-85292574-1	chr16	85292524	85292624	+	2.5	cIP2vsInput	Intergenic	PB1D10|SINE|Alu	-118867	NM_001198823	11820	Mm.490986	NM_001198823	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding	0.01	0.405941
Merged-chr3-155737087-1	chr3	155737037	155737137	+	2.5	cIP2vsInput	Intergenic	Intergenic	-239267	NR_040553	329780	Mm.119000	NR_040553		9330178D15Rik	9330178D15	RIKEN cDNA 9330178D15 gene	miscRNA	0.01	0.326733
Merged-chr11-98374569-1	chr11	98374519	98374619	+	2.5	cIP1vsInput	"intron (NM_021547, intron 2 of 14)"	"intron (NM_021547, intron 2 of 14)"	-9242	NM_011540	21393	Mm.10762	NM_011540	ENSMUSG00000007877	Tcap	AI503981|AJ223855	titin-cap	protein-coding	0.05	0.584158
Merged-chr13-56088134-1	chr13	56088084	56088184	+	2.5	cIP2vsInput	"intron (NM_001159513, intron 6 of 8)"	"intron (NM_001159513, intron 6 of 8)"	47416	NM_012015	26914	Mm.478369	NM_001159513	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	"H2A histone family, member Y"	protein-coding	0.03	0.584158
Merged-chr16-86687894-1	chr16	86687844	86687944	+	2.5	cIP2vsInput	Intergenic	L4_C_Mam|LINE|RTE-X	-666291	NM_001159331	67768	Mm.296532	NM_001159331	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding	0	0.29703
Merged-chr12-15019481-1	chr12	15019431	15019531	+	2.5	cIP1vsInput	"intron (NR_045960, intron 3 of 7)"	"intron (NR_045960, intron 3 of 7)"	30908	NR_045960	73972	Mm.107680	NR_045960		4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	miscRNA	0.01	0.346535
Merged-chr1-94695270-1	chr1	94695220	94695320	+	2.5	cIP1vsInput	Intergenic	Intergenic	-102172	NR_040473	74689	Mm.399187	NR_040473		4930440C22Rik	-	RIKEN cDNA 4930440C22 gene	miscRNA	0.01	0.316832
Merged-chr4-72561870-1	chr4	72561820	72561920	+	2.5	cIP2vsInput	Intergenic	Intergenic	290764	NM_001199270	353204	Mm.317892	NM_001199270	ENSMUSG00000059343	Aldoart1	4921524E03Rik|Aldo1-ps|Aldo1-ps2|Aldoa-ps2	aldolase 1 A retrogene 1	protein-coding	0	0.306931
Merged-chr9-46129157-1	chr9	46129107	46129207	+	2.5	cIP1vsInput	"intron (NM_027498, intron 3 of 24)"	"intron (NM_027498, intron 3 of 24)"	-99473	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2	apolipoprotein A-I	protein-coding	0	0.346535
Merged-chr5-137510195-1	chr5	137510145	137510245	+	2.5	cIP2vsInput	Intergenic	Intergenic	-7766	NM_028753	74097	Mm.290242	NM_028753	ENSMUSG00000029715	Pop7	0610037N12Rik|AI852017|Rpp20	"processing of precursor 7, ribonuclease P family, (S. cerevisiae)"	protein-coding	0.07	0.712871
Merged-chr16-7140245-1	chr16	7140195	7140295	+	2.5	cIP1vsInput	"intron (NM_183188, intron 1 of 12)"	"intron (NM_183188, intron 1 of 12)"	70410	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	"RNA binding protein, fox-1 homolog (C. elegans) 1"	protein-coding	0	0.336634
Merged-chr6-79073521-1	chr6	79073471	79073571	+	2.5	cIP2vsInput	Intergenic	Intergenic	41479	NR_040301	100504701	Mm.400420	NR_040301		Gm20362	-	"predicted gene, 20362"	miscRNA	0	0.336634
Merged-chr10-17281448-1	chr10	17281398	17281498	+	2.5	cIP2vsInput	Intergenic	Intergenic	-185666	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0.01	0.346535
Merged-chr14-85289981-1	chr14	85289931	85290031	+	2.5	cIP2vsInput	Intergenic	Intergenic	-813557	NR_015539	319903	Mm.440481	NR_015539		9630013A20Rik	-	RIKEN cDNA 9630013A20 gene	miscRNA	0	0.326733
Merged-chr3-52844123-1	chr3	52844073	52844173	+	2.5	cIP1vsInput	Intergenic	Intergenic	83543	NR_040555	622124	Mm.389434	NR_040555		Gm20750	-	"predicted gene, 20750"	miscRNA	0.01	0.475248
Merged-chr6-80610597-1	chr6	80610547	80610647	+	2.5	cIP1vsInput	Intergenic	Intergenic	590954	NM_178731	243499	Mm.483425	NM_001134743	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding	0	0.326733
Merged-chr7-94122673-1	chr7	94122623	94122723	+	2.5	cIP2vsInput	Intergenic	Intergenic	1042794	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0	0.277228
Merged-chr12-89961582-1	chr12	89961532	89961632	+	2.5	cIP2vsInput	"intron (NM_001252074, intron 1 of 6)"	"intron (NM_001252074, intron 1 of 6)"	149099	NM_001252074	18191	Mm.487864	NM_001198587	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding	0	0.356436
Merged-chr7-28014826-1	chr7	28014776	28014876	+	2.5	cIP1vsInput	promoter-TSS (NM_001254951)	promoter-TSS (NM_001254951)	-711	NM_001254951	100043772	Mm.129275	NM_001100456		Gm4636	C130069I09Rik|Zfp850	predicted gene 4636	protein-coding	0.01	0.29703
Merged-chr1-79352809-1	chr1	79352759	79352859	+	2.5	cIP1vsInput	Intergenic	Intergenic	87281	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding	0	0.316832
Merged-chr16-60516005-1	chr16	60515955	60516055	+	2.5	cIP2vsInput	"intron (NM_007938, intron 2 of 17)"	"intron (NM_007938, intron 2 of 17)"	89526	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0.02	0.356436
Merged-chr4-50334265-1	chr4	50334215	50334315	+	2.5	cIP2vsInput	Intergenic	MLTR73|LTR|ERV1	-488496	NM_001276355	242443	Mm.440095	NM_001033351		Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	"glutamate receptor ionotropic, NMDA3A"	protein-coding	0	0.326733
Merged-chr15-6625569-1	chr15	6625519	6625619	+	2.5	cIP2vsInput	"intron (NM_011815, intron 2 of 17)"	L2|LINE|L2	45698	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik	FYN binding protein	protein-coding	0	0.386139
Merged-chr16-50935194-1	chr16	50935144	50935244	+	2.5	cIP2vsInput	Intergenic	Intergenic	-202421	NR_028300	68190	Mm.482928	NR_028300		5330426P16Rik	-	RIKEN cDNA 5330426P16 gene	miscRNA	0.01	0.316832
Merged-chr1-108216475-1	chr1	108216425	108216525	+	2.5	cIP1vsInput	Intergenic	L2a|LINE|L2	299216	NR_102307	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0	0.287129
Merged-chr4-98653270-1	chr4	98653220	98653320	+	2.5	cIP1vsInput	"intron (NM_001005787, intron 8 of 15)"	"intron (NM_001005787, intron 8 of 15)"	-73484	NM_001081202	381591	Mm.34340	NM_001081202	ENSMUSG00000087166	L1td1	AA546746|AB211064|D76865|ECAT11	LINE-1 type transposase domain containing 1	protein-coding	0	0.39604
Merged-chrX-116581479-1	chrX	116581429	116581529	+	2.5	cIP1vsInput	Intergenic	Intergenic	132535	NM_001033471	382239	Mm.336224	NM_001033471	ENSMUSG00000072995	Cpxcr1	Gm1143	"CPX chromosome region, candidate 1"	protein-coding	0	0.346535
Merged-chr17-69811166-1	chr17	69811116	69811216	+	2.5	cIP1vsInput	Intergenic	Lx5|LINE|L1	371840	NM_001145192	320722	Mm.400254	NM_001145192	ENSMUSG00000091636	A330050F15Rik	-	RIKEN cDNA A330050F15 gene	protein-coding	0	0.326733
Merged-chr1-85823899-1	chr1	85823849	85823949	+	2.5	cIP1vsInput	"intron (NM_133781, intron 2 of 8)"	"intron (NM_133781, intron 2 of 8)"	30452	NM_133781	12283	Mm.26135	NM_133781	ENSMUSG00000036707	Cab39	AA408805|AA960512|C78372|MO25|MO25alpha	calcium binding protein 39	protein-coding	0	0.316832
Merged-chr4-82684902-1	chr4	82684852	82684952	+	2.5	cIP2vsInput	Intergenic	Intergenic	174759	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	"zinc finger, DHHC domain containing 21"	protein-coding	0.02	0.455446
Merged-chr10-89192206-1	chr10	89192156	89192256	+	2.5	cIP1vsInput	"intron (NR_102339, intron 1 of 26)"	"intron (NR_102339, intron 1 of 26)"	65584	NM_001277188	320091	Mm.417681	NM_178773	ENSMUSG00000035189	Ano4	A330096O15Rik|Gm65|Tmem16d	anoctamin 4	protein-coding	0	0.247525
Merged-chr1-94712729-1	chr1	94712679	94712779	+	2.5	cIP2vsInput	Intergenic	Intergenic	-84713	NR_040473	74689	Mm.399187	NR_040473		4930440C22Rik	-	RIKEN cDNA 4930440C22 gene	miscRNA	0	0.39604
Merged-chr17-90349050-1	chr17	90349000	90349100	+	2.5	cIP1vsInput	"intron (NM_020252, intron 18 of 22)"	"intron (NM_020252, intron 18 of 22)"	-512119	NR_045463	78800	Mm.410772	NR_045463	ENSMUSG00000090160	4930480K15Rik	-	RIKEN cDNA 4930480K15 gene	miscRNA	0	0.326733
Merged-chr3-25314656-1	chr3	25314606	25314706	+	2.5	cIP1vsInput	Intergenic	Lx5|LINE|L1	838651	NM_001163387	192167	Mm.316080	NM_001163387	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|mKIAA1070	neuroligin 1	protein-coding	0	0.316832
Merged-chr12-48703426-1	chr12	48703376	48703476	+	2.5	cIP1vsInput	Intergenic	L1MB1|LINE|L1	-401964	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0	0.326733
Merged-chrX-31185303-1	chrX	31185253	31185353	+	2.5	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	-151066	NM_001243011	100042159	Mm.489579	NM_001243011	ENSMUSG00000095835	Gm3701	-	predicted gene 3701	protein-coding	0	0.287129
Merged-chr9-80235805-1	chr9	80235755	80235855	+	2.5	cIP2vsInput	"intron (NM_001039546, intron 5 of 32)"	L1MA5A|LINE|L1	70771	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding	0	0.336634
Merged-chr10-94877673-1	chr10	94877623	94877723	+	2.5	cIP1vsInput	"intron (NM_018797, intron 5 of 30)"	"intron (NM_018797, intron 5 of 30)"	66905	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding	0	0.237624
Merged-chr16-26216776-2	chr16	26216693	26216859	+	2.5	cIP1vsInput|cIP2vsInput	Intergenic	L1M2|LINE|L1	-110992	NM_173379	210530		NM_173379		Leprel1	4832416N06|AW553532|Mlat4|P3H2	leprecan-like 1	protein-coding	0	0.299401
Merged-chr15-52599587-1	chr15	52599537	52599637	+	2.5	cIP1vsInput	Intergenic	Intergenic	-112858	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding	0	0.386139
Merged-chr9-95703358-1	chr9	95703308	95703408	+	2.5	cIP1vsInput	Intergenic	Intergenic	47000	NM_011643	22063	Mm.149633	NM_011643	ENSMUSG00000032839	Trpc1	Mtrp1|Trp1|Trrp1	"transient receptor potential cation channel, subfamily C, member 1"	protein-coding	0.01	0.306931
Merged-chr18-20591501-1	chr18	20591451	20591551	+	2.5	cIP1vsInput	"intron (NM_007883, intron 9 of 14)"	"intron (NM_007883, intron 9 of 14)"	33385	NM_007883	13511	Mm.345891	NM_007883	ENSMUSG00000044393	Dsg2	AA408168|D18Ertd293e	desmoglein 2	protein-coding	0.01	0.346535
Merged-chr14-81884777-1	chr14	81884727	81884827	+	2.5	cIP1vsInput	Intergenic	Intergenic	1884475	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.316832
Merged-chr7-72965980-1	chr7	72965930	72966030	+	2.5	cIP1vsInput	Intergenic	Intergenic	136088	NR_046024	625243	Mm.261798	NR_046024		Gm6567	-	predicted gene 6567	miscRNA	0	0.346535
Merged-chr16-61749051-1	chr16	61749001	61749101	+	2.5	cIP1vsInput	Intergenic	Intergenic	1037665	NM_178925	106338	Mm.26321	NM_178925		Nsun3	6720484A09Rik|AU022521	NOL1/NOP2/Sun domain family member 3	protein-coding	0	0.29703
Merged-chr2-19371621-1	chr2	19371571	19371671	+	2.5	cIP2vsInput	promoter-TSS (NM_029619)	promoter-TSS (NM_029619)	-15	NM_029619	76467	Mm.27166	NM_029619	ENSMUSG00000023094	Msrb2	2310050L06Rik|Mrsb|Msrb|Pilb	methionine sulfoxide reductase B2	protein-coding	0.03	0.643564
Merged-chr14-98971974-1	chr14	98971924	98972024	+	2.5	cIP2vsInput	Intergenic	Intergenic	74162	NM_175245	76789	Mm.38912	NM_175245	ENSMUSG00000033186	Mzt1	2410129H14Rik|AI120158|Mozart1	mitotic spindle organizing protein 1	protein-coding	0	0.267327
Merged-chr14-78915719-1	chr14	78915669	78915769	+	2.5	cIP2vsInput	"intron (NM_173758, intron 4 of 25)"	B3A|SINE|B2	66541	NM_173758	219189	Mm.159651	NM_027906	ENSMUSG00000058997	Vwa8	1300010F03Rik|4932416F07Rik|AI957255|Kiaa0564|mKIAA0564	von Willebrand factor A domain containing 8	protein-coding	0.01	0.435644
Merged-chr11-66645566-1	chr11	66645516	66645616	+	2.5	cIP2vsInput	Intergenic	Lx5b|LINE|L1	-119440	NM_001034874	380702	Mm.351764	NM_001034874	ENSMUSG00000053930	Shisa6	Gm879	shisa homolog 6 (Xenopus laevis)	protein-coding	0	0.306931
Merged-chr7-41599110-1	chr7	41599060	41599160	+	2.5	cIP2vsInput	Intergenic	Intergenic	-34421	NM_023363	67607	Mm.384626	NM_023363	ENSMUSG00000074165	Zfp788	2810426N06Rik|AI256342|AI605193	zinc finger protein 788	protein-coding	0.02	0.475248
Merged-chr14-6494265-1	chr14	6494215	6494315	+	2.5	cIP2vsInput	Intergenic	Intergenic	-207015	NM_001270812	100861615	Mm.399319	NM_001270812	ENSMUSG00000079396	LOC100861615	-	alpha takusan-like	protein-coding	0.01	0.50495
Merged-chr6-94347812-1	chr6	94347762	94347862	+	2.5	cIP1vsInput	Intergenic	ORR1C2|LTR|ERVL-MaLR	-63908	NM_001029850	14924	Mm.217216	NM_001029850	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	"membrane associated guanylate kinase, WW and PDZ domain containing 1"	protein-coding	0	0.386139
Merged-chr17-84975059-1	chr17	84975009	84975109	+	2.5	cIP2vsInput	"intron (NM_001159498, intron 1 of 6)"	RMER16-int|LTR|ERVK	1007	NM_001159498	19043	Mm.249695	NM_001159496	ENSMUSG00000061130	Ppm1b	PP2CB	"protein phosphatase 1B, magnesium dependent, beta isoform"	protein-coding	0.01	0.336634
Merged-chr13-88912578-1	chr13	88912528	88912628	+	2.5	cIP2vsInput	"intron (NM_001037987, intron 1 of 10)"	"intron (NM_001037987, intron 1 of 10)"	91106	NM_001037987	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0.01	0.366337
Merged-chr15-103651522-1	chr15	103651472	103651572	+	2.5	cIP2vsInput	Intergenic	Intergenic	-86444	NM_008134	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	Sgp50	glycosylation dependent cell adhesion molecule 1	protein-coding	0	0.336634
Merged-chr10-82354351-1	chr10	82354301	82354401	+	2.5	cIP2vsInput	Intergenic	Intergenic	-113076	NM_001105557	237411		NM_172789	ENSMUSG00000062931	Zfp938	B230315N10Rik	zinc finger protein 938	protein-coding	0.05	0.623762
Merged-chr12-111946834-1	chr12	111946784	111946884	+	2.5	cIP2vsInput	Intergenic	Intergenic	-2352	NR_029464	77675	Mm.98331	NR_029464		5033406O09Rik	9130204G15Rik	RIKEN cDNA 5033406O09 gene	miscRNA	0	0.594059
Merged-chr15-52368134-1	chr15	52368084	52368184	+	2.5	cIP2vsInput	Intergenic	Intergenic	72581	NM_172816	239436	Mm.208831	NM_172816	ENSMUSG00000022315	Slc30a8	C820002P14Rik|ZnT-8|ZnT8	"solute carrier family 30 (zinc transporter), member 8"	protein-coding	0.01	0.415842
Merged-chr14-38443333-1	chr14	38443283	38443383	+	2.5	cIP1vsInput	"intron (NM_001190187, intron 4 of 9)"	"intron (NM_001190187, intron 4 of 9)"	-454969	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	4930529F24Rik	-	RIKEN cDNA 4930529F24 gene	miscRNA	0.02	0.405941
Merged-chr5-77407790-1	chr5	77407740	77407840	+	2.5	cIP2vsInput	"exon (NM_008048, exon 1 of 5)"	"exon (NM_008048, exon 1 of 5)"	255	NM_001159518	29817	Mm.233470	NM_001159518	ENSMUSG00000036256	Igfbp7	AGM|Fstl2|Mac25	insulin-like growth factor binding protein 7	protein-coding	0.15	0.772277
Merged-chr7-86693936-1	chr7	86693886	86693986	+	2.5	cIP1vsInput	"intron (NM_146620, intron 1 of 1)"	"intron (NM_146620, intron 1 of 1)"	5595	NM_146620	258613	Mm.271466	NM_146620	ENSMUSG00000060688	Olfr292	MOR220-2	olfactory receptor 292	protein-coding	0	0.287129
Merged-chr5-39273679-1	chr5	39273629	39273729	+	2.5	cIP1vsInput	Intergenic	Intergenic	329895	NR_045416	75095	Mm.332354	NR_045416		4930513D17Rik	-	RIKEN cDNA 4930513D17 gene	miscRNA	0.01	0.356436
Merged-chr15-47034555-1	chr15	47034505	47034605	+	2.5	cIP1vsInput	Intergenic	Lx8b|LINE|L1	411250	NR_045811	75281	Mm.159487	NR_045811		4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	miscRNA	0	0.306931
Merged-chr7-77122174-1	chr7	77122124	77122224	+	2.5	cIP1vsInput	"intron (NM_001199224, intron 22 of 22)"	"intron (NM_001199224, intron 22 of 22)"	892287	NM_001199224	244071	Mm.322829	NM_001199224		Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding	0.01	0.346535
Merged-chr3-73938517-1	chr3	73938467	73938567	+	2.5	cIP1vsInput	Intergenic	Intergenic	78760	NR_040450	100504692	Mm.394454	NR_040450		Gm20356	-	"predicted gene, 20356"	miscRNA	0	0.336634
Merged-chr1-179340185-1	chr1	179340135	179340235	+	2.5	cIP2vsInput	"intron (NM_027188, intron 5 of 11)"	"intron (NM_027188, intron 5 of 11)"	177818	NM_027188	69726	Mm.222338	NM_027188		Smyd3	2410008A19Rik|Zmynd1	SET and MYND domain containing 3	protein-coding	0	0.356436
Merged-chr3-92201770-1	chr3	92201720	92201820	+	2.5	cIP1vsInput	Intergenic	Intergenic	-14065	NM_001164787	100303744	Mm.429851	NM_001164787	ENSMUSG00000068893	Sprr2a2	-	small proline-rich protein 2A2	protein-coding	0	0.306931
Merged-chr4-94859348-1	chr4	94859298	94859398	+	2.5	cIP1vsInput	"intron (NM_013690, intron 17 of 22)"	"intron (NM_013690, intron 17 of 22)"	69462	NM_027089	67753	Mm.25097	NM_027089	ENSMUSG00000028575	Eqtn	1700028B15Rik|4930579C15Rik|Afaf|C81058|Eqtl|Eqts|equatorin	"equatorin, sperm acrosome associated"	protein-coding	0.02	0.39604
Merged-chr8-57831061-1	chr8	57831011	57831111	+	2.5	cIP1vsInput	"intron (NM_175032, intron 9 of 11)"	"intron (NM_175032, intron 9 of 11)"	-178006	NM_144731	108150	Mm.62886	NM_001167981	ENSMUSG00000031608	Galnt7	AI225872	UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.02	0.425743
Merged-chr9-91346955-1	chr9	91346905	91347005	+	2.5	cIP1vsInput	Intergenic	Intergenic	18844	NM_009573	22771	Mm.477226	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding	0	0.217822
Merged-chr18-33783553-1	chr18	33783503	33783603	+	2.5	cIP1vsInput	Intergenic	Intergenic	-11339	NR_038152	69749	Mm.248787	NR_038151	ENSMUSG00000087590	2410004N09Rik	-	RIKEN cDNA 2410004N09 gene	miscRNA	0	0.237624
Merged-chr4-63985050-1	chr4	63985000	63985100	+	2.5	cIP2vsInput	"intron (NM_011607, intron 14 of 25)"	"intron (NM_011607, intron 14 of 25)"	61965	NM_011607	21923	Mm.454219	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding	0	0.356436
Merged-chr2-52821307-1	chr2	52821257	52821357	+	2.5	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-36561	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding	0	0.326733
Merged-chr13-21134611-1	chr13	21134561	21134661	+	2.5	cIP1vsInput	TTS (NM_010984)	TTS (NM_010984)	1834	NM_010984	18341	Mm.246536	NM_010984	ENSMUSG00000071522	Olfr263	GA_x5J8B7TTCWC-858-415|IA3|MOR256-31|MOR256-37P|MOR256-61|Olfr263-ps1|Olfr42	olfactory receptor 263	protein-coding	0.01	0.39604
Merged-chr1-169969539-1	chr1	169969489	169969589	+	2.5	cIP2vsInput	promoter-TSS (NM_010476)	promoter-TSS (NM_010476)	130	NR_040438	67303	Mm.396611	NR_040438	ENSMUSG00000097503	3110045C21Rik	AI838577	RIKEN cDNA 3110045C21 gene	miscRNA	0.02	0.346535
Merged-chr2-30795038-1	chr2	30794988	30795088	+	2.5	cIP1vsInput	TTS (NR_028486)	TTS (NR_028486)	6699	NM_198000	73598	Mm.34166	NM_198000	ENSMUSG00000044320	1700001O22Rik	1700113K14Rik|4930549G18Rik	RIKEN cDNA 1700001O22 gene	protein-coding	0.03	0.574257
Merged-chr11-63748762-1	chr11	63748712	63748812	+	2.5	cIP1vsInput	Intergenic	Intergenic	173522	NM_018805	54710	Mm.274426	NM_018805	ENSMUSG00000070407	Hs3st3b1	3-OST-3B|3OST3B1|3Ost3b|AU041882|AW536289|Hs3st3b|m3-OST-3B	heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1	protein-coding	0	0.306931
Merged-chr2-44530425-1	chr2	44530375	44530475	+	2.5	cIP1vsInput	Intergenic	Intergenic	331197	NM_172662	227835	Mm.488285	NM_172662	ENSMUSG00000036890	Gtdc1	E330008O22Rik	glycosyltransferase-like domain containing 1	protein-coding	0	0.356436
Merged-chr7-12401826-1	chr7	12401776	12401876	+	2.5	cIP2vsInput	Intergenic	L1M4|LINE|L1	20665	NM_001033820	619331	Mm.361832	NM_001033820	ENSMUSG00000034071	Zfp551	9630004E07Rik|Znf551	zinc fingr protein 551	protein-coding	0	0.366337
Merged-chr3-71173195-1	chr3	71173145	71173245	+	2.5	cIP1vsInput	Intergenic	Lx8|LINE|L1	-365904	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	miscRNA	0.03	0.346535
Merged-chr15-48916437-1	chr15	48916387	48916487	+	2.5	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-124448	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0	0.306931
Merged-chr17-65539723-1	chr17	65539673	65539773	+	2.5	cIP1vsInput	"intron (NM_001008973, intron 1 of 14)"	"intron (NM_001008973, intron 1 of 14)"	1059	NM_001008973	381107	Mm.141275	NM_001008973	ENSMUSG00000045036	Tmem232	E130009J12Rik|Gm940|Tes13-L|Tes13-S	transmembrane protein 232	protein-coding	0	0.287129
Merged-chr6-50788534-1	chr6	50788484	50788584	+	2.5	cIP1vsInput	"intron (NR_045984, intron 2 of 4)"	L1M5|LINE|L1	12419	NR_045984	319981	Mm.131454	NR_045984		C530044C16Rik	-	RIKEN cDNA C530044C16 gene	miscRNA	0	0.336634
Merged-chr6-56083704-1	chr6	56083654	56083754	+	2.5	cIP1vsInput	"intron (NM_011054, intron 18 of 18)"	"intron (NM_011054, intron 18 of 18)"	66189	NM_011153	19051	Mm.42096	NM_011153	ENSMUSG00000002930	Ppp1r17	Gsbs|Ppp1r2	"protein phosphatase 1, regulatory subunit 17"	protein-coding	0	0.366337
Merged-chr5-47547643-1	chr5	47547593	47547693	+	2.5	cIP2vsInput	Intergenic	Intergenic	-435512	NM_178804	20563	Mm.289739	NM_178804		Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|mKIAA4141	slit homolog 2 (Drosophila)	protein-coding	0.01	0.346535
Merged-chr12-60330361-1	chr12	60330311	60330411	+	2.5	cIP1vsInput	Intergenic	Intergenic	-1110878	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding	0	0.287129
Merged-chr9-71189050-1	chr9	71189000	71189100	+	2.5	cIP1vsInput	Intergenic	MLT1D|LTR|ERVL-MaLR	-25761	NM_022026	64008	Mm.485117	NM_001271843	ENSMUSG00000032204	Aqp9	1700020I22Rik|AI266899|AQP-9	aquaporin 9	protein-coding	0.01	0.445545
Merged-chr6-73987615-1	chr6	73987565	73987665	+	2.5	cIP2vsInput	Intergenic	Intergenic	-517948	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.376238
Merged-chr10-57537941-1	chr10	57537891	57537991	+	2.5	cIP2vsInput	Intergenic	Intergenic	-5412	NM_019760	56442	Mm.29344	NM_019760	ENSMUSG00000019877	Serinc1	1500011D18Rik|AI315070|AIGP-2|TMS-2|Tde1l|Tde2|Tms2|mKIAA1253	serine incorporator 1	protein-coding	0	0.326733
Merged-chr17-86022346-1	chr17	86022296	86022396	+	2.5	cIP2vsInput	"intron (NM_030133, intron 16 of 20)"	MLT1F1|LTR|ERVL-MaLR	122829	NM_030133	78586	Mm.146236	NM_030133	ENSMUSG00000024135	Srbd1	AI461933|C85414|D530025C17Rik	S1 RNA binding domain 1	protein-coding	0.01	0.524752
Merged-chr6-36114601-1	chr6	36114551	36114651	+	2.5	cIP2vsInput	Intergenic	L1M4a2|LINE|L1	-273483	NM_203491	243764	Mm.448632	NM_203491		Chrm2	AChR-M2|Chrm-2|M2	"cholinergic receptor, muscarinic 2, cardiac"	protein-coding	0	0.376238
Merged-chr18-37644321-1	chr18	37644271	37644371	+	2.5	cIP1vsInput	promoter-TSS (NM_175770)	promoter-TSS (NM_175770)	-117	NM_175770	24074	Mm.236009	NM_175770	ENSMUSG00000051316	Taf7	55kDa|AI607308|BB007175|TAFII55|Taf2f	"TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor"	protein-coding	0.06	0.455446
Merged-chr2-158361575-1	chr2	158361525	158361625	+	2.5	cIP2vsInput	promoter-TSS (NR_015463)	promoter-TSS (NR_015463)	-53	NR_027887	68108	Mm.119198	NR_015463		9430008C03Rik	-	RIKEN cDNA 9430008C03 gene	miscRNA	0.08	0.643564
Merged-chr15-44385467-1	chr15	44385417	44385517	+	2.5	cIP2vsInput	"intron (NM_026149, intron 8 of 9)"	"intron (NM_026149, intron 8 of 9)"	-42644	NM_175009	223527	Mm.490404	NM_175009	ENSMUSG00000022338	Eny2	1810057B09Rik|6720481I12|DC6|Ey2	enhancer of yellow 2 homolog (Drosophila)	protein-coding	0	0.386139
Merged-chr4-123990796-2	chr4	123990730	123990863	+	2.5	cIP1vsInput|cIP2vsInput	Intergenic	CpG	73363	NM_017475	54170	Mm.220922	NM_017475	ENSMUSG00000028646	Rragc	AU041672|Gtr2|RAGC|TIB929|YGR163W	Ras-related GTP binding C	protein-coding	0.082707	0.738806
Merged-chr18-52075391-1	chr18	52075341	52075441	+	2.5	cIP2vsInput	Intergenic	Intergenic	48155	NR_029788	723830		NR_029788		Mir28	Mirn28|mmu-mir-28	microRNA 28	miscRNA	0	0.316832
Merged-chr10-48791147-1	chr10	48791097	48791197	+	2.5	cIP2vsInput	Intergenic	Intergenic	304696	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	"proteasome (prosome, macropain) subunit, alpha type 6 pseudogene"	pseudo	0.01	0.336634
Merged-chr15-42726266-1	chr15	42726216	42726316	+	2.5	cIP1vsInput	Intergenic	Lx|LINE|L1	-49471	NM_009640	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding	0	0.326733
Merged-chr1-49956846-1	chr1	49956796	49956896	+	2.5	cIP1vsInput	Intergenic	Intergenic	-970677	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0.01	0.29703
Merged-chr17-4175419-1	chr17	4175369	4175469	+	2.5	cIP1vsInput	Intergenic	Intergenic	-53317	NR_045462	78043	Mm.460785	NR_045462		4930548J01Rik	1700113K09Rik	RIKEN cDNA 4930548J01 gene	miscRNA	0.01	0.405941
Merged-chr13-85748769-1	chr13	85748719	85748819	+	2.5	cIP2vsInput	Intergenic	Intergenic	298026	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0.01	0.316832
Merged-chr3-48833073-1	chr3	48833023	48833123	+	2.5	cIP2vsInput	Intergenic	Intergenic	-223973	NR_003617	66332	Mm.46124	NR_003617		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo	0	0.356436
Merged-chr7-97332503-1	chr7	97332453	97332553	+	2.5	cIP2vsInput	"intron (NM_001039039, intron 1 of 1)"	CpG	180	NM_001039039	622320	Mm.334029	NM_001039039	ENSMUSG00000044952	Kctd21	EG622320	potassium channel tetramerisation domain containing 21	protein-coding	0.09	0.663366
Merged-chr1-47331626-1	chr1	47331576	47331676	+	2.5	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-478117	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.277228
Merged-chr2-97191384-1	chr2	97191334	97191434	+	2.5	cIP2vsInput	Intergenic	Intergenic	-276290	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.415842
Merged-chr2-22384902-1	chr2	22384852	22384952	+	2.5	cIP1vsInput	"intron (NM_148413, intron 16 of 19)"	"intron (NM_148413, intron 16 of 19)"	157399	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding	0	0.336634
Merged-chr15-71050138-1	chr15	71050088	71050188	+	2.5	cIP2vsInput	Intergenic	Intergenic	677700	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	"family with sequence similarity 135, member B"	protein-coding	0	0.287129
Merged-chr7-104771996-1	chr7	104771946	104772046	+	2.5	cIP1vsInput	"intron (NM_001256973, intron 1 of 2)"	"intron (NM_001256973, intron 1 of 2)"	5474	NM_001256973	625530	Mm.14130	NM_001256973		Usp17le	DUB-3|Dub3|Dub6|EG625530|Gm6596|USP17|Usp17l2	ubiquitin specific peptidase 17-like E	protein-coding	0	0.366337
Merged-chr3-84155741-1	chr3	84155691	84155791	+	2.5	cIP2vsInput	promoter-TSS (NM_029797)	promoter-TSS (NM_029797)	45	NM_029797	76915	Mm.274829	NM_029797	ENSMUSG00000033752	Mnd1	2610034E18Rik|AI591601|Gaj	meiotic nuclear divisions 1 homolog (S. cerevisiae)	protein-coding	0.08	0.693069
Merged-chr10-101360108-1	chr10	101360058	101360158	+	2.5	cIP2vsInput	Intergenic	Intergenic	-321379	NM_001205098	67569	Mm.403713	NM_001162368	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"	protein-coding	0.01	0.326733
Merged-chr7-41656798-1	chr7	41656748	41656848	+	2.5	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	-11216	NR_004441	75835	Mm.429459	NR_004441	ENSMUSG00000074164	Vmn2r-ps54	1700108E19Rik|4930562N12Rik|Casr-rs5|ENSMUSG00000078527|Gm10948|Gprc2a-rs5	"vomeronasal 2, receptor, pseudogene 54"	pseudo	0	0.346535
Merged-chr5-91595080-1	chr5	91595030	91595130	+	2.5	cIP1vsInput	"intron (NM_145562, intron 2 of 3)"	"intron (NM_145562, intron 2 of 3)"	77380	NM_145562	231440	Mm.5002	NM_145562		Parm1	2210012L08Rik|9130213B05Rik|W91666	prostate androgen-regulated mucin-like protein 1	protein-coding	0.03	0.386139
Merged-chr11-97071326-1	chr11	97071276	97071376	+	2.5	cIP2vsInput	Intergenic	Intergenic	20506	NM_001081434	71240	Mm.190450	NM_001081434	ENSMUSG00000038534	Osbpl7	4933437E18Rik	oxysterol binding protein-like 7	protein-coding	0	0.485149
Merged-chr7-124157643-1	chr7	124157593	124157693	+	2.5	cIP1vsInput	"intron (NM_001252072, intron 1 of 1)"	"intron (NM_001252072, intron 1 of 1)"	174462	NM_001252072	628779	Mm.40210	NM_001252072	ENSMUSG00000078591	Hs3st4	EG628779|Gm6915	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	protein-coding	0	0.326733
Merged-chr17-86606305-1	chr17	86606255	86606355	+	2.5	cIP2vsInput	"intron (NM_011104, intron 11 of 14)"	B3|SINE|B2	-147559	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding	0	0.386139
Merged-chr16-29759635-1	chr16	29759585	29759685	+	2.5	cIP2vsInput	Intergenic	Intergenic	180301	NM_133752	74143	Mm.274285	NM_001199177	ENSMUSG00000038084	Opa1	1200011N24Rik|AI225888|AI847218|lilr3|mKIAA0567	optic atrophy 1	protein-coding	0.02	0.465347
Merged-chr5-88459019-1	chr5	88458969	88459069	+	2.5	cIP1vsInput	"intron (NM_009664, intron 2 of 10)"	"intron (NM_009664, intron 2 of 10)"	3008	NM_009664	11698	Mm.8437	NM_009664	ENSMUSG00000029288	Ambn	-	ameloblastin	protein-coding	0.01	0.316832
Merged-chr10-98095912-1	chr10	98095862	98095962	+	2.5	cIP1vsInput	Intergenic	Intergenic	-128822	NR_033537	100038699	Mm.467933	NR_033537		Gm10754	ENSMUSG00000074776	predicted gene 10754	miscRNA	0	0.326733
Merged-chr9-107024407-1	chr9	107024357	107024457	+	2.5	cIP1vsInput	"intron (NM_153413, intron 11 of 52)"	"intron (NM_153413, intron 11 of 52)"	-132469	NM_029103	74840	Mm.29778	NM_029103	ENSMUSG00000032575	Manf	3230402M22Rik|AA407711|AA408789|AA673178|Armet|D17914|D18Mgi17	mesencephalic astrocyte-derived neurotrophic factor	protein-coding	0	0.346535
Merged-chr3-67222934-1	chr3	67222884	67222984	+	2.5	cIP2vsInput	"intron (NM_025822, intron 6 of 9)"	"intron (NM_025822, intron 6 of 9)"	-151163	NM_010801	17349	Mm.10414	NM_001039543	ENSMUSG00000048416	Mlf1	HLS7	myeloid leukemia factor 1	protein-coding	0	0.326733
Merged-chr13-70637919-1	chr13	70637869	70637969	+	2.5	cIP1vsInput	promoter-TSS (NM_144837)	promoter-TSS (NM_144837)	-285	NM_144837	218333	Mm.139738	NM_144837	ENSMUSG00000034525	BC018507	C77245|mKIAA0947	cDNA sequence BC018507	protein-coding	0.04	0.49505
Merged-chr15-70598420-1	chr15	70598370	70598470	+	2.5	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	674187	NR_045071	100503580	Mm.404646	NR_045071		Gm19782	-	"predicted gene, 19782"	miscRNA	0	0.29703
Merged-chr7-125393764-1	chr7	125393714	125393814	+	2.5	cIP2vsInput	Intergenic	CpG	24903	NM_001145759	75861	Mm.349600	NM_001145759	ENSMUSG00000090457	4930571K23Rik	AI428146	RIKEN cDNA 4930571K23 gene	protein-coding	0.12	0.663366
Merged-chr5-6576929-1	chr5	6576879	6576979	+	2.5	cIP2vsInput	Intergenic	Intergenic	-727235	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding	0	0.336634
Merged-chr14-27368150-1	chr14	27368100	27368200	+	2.5	cIP1vsInput	"intron (NM_027871, intron 3 of 10)"	ID_B1|SINE|B4	-60697	NM_028945	218850	Mm.247767	NM_028945	ENSMUSG00000040651	D14Abb1e	4732418E12|4933409E02Rik|Fam208a	"DNA segment, Chr 14, Abbott 1 expressed"	protein-coding	0.01	0.435644
Merged-chr1-27826966-1	chr1	27826916	27827016	+	2.5	cIP1vsInput	Intergenic	Intergenic	953286	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0	0.257426
Merged-chr19-48034252-1	chr19	48034202	48034302	+	2.5	cIP1vsInput	"intron (NM_001163267, intron 17 of 17)"	"intron (NM_001163267, intron 17 of 17)"	96540	NM_001163267	381229	Mm.300553	NM_001163267	ENSMUSG00000046585	Ccdc147	Gm969	coiled-coil domain containing 147	protein-coding	0	0.316832
Merged-chr7-93815108-1	chr7	93815058	93815158	+	2.5	cIP1vsInput	Intergenic	Intergenic	735229	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0.01	0.316832
Merged-chr15-53181438-1	chr15	53181388	53181488	+	2.5	cIP2vsInput	"intron (NM_010162, intron 1 of 10)"	"intron (NM_010162, intron 1 of 10)"	164745	NM_010162	14042	Mm.309395	NM_010162		Ext1	AA409028	exostoses (multiple) 1	protein-coding	0.01	0.346535
Merged-chr14-78724819-1	chr14	78724769	78724869	+	2.5	cIP2vsInput	"intron (NM_001081336, intron 1 of 28)"	CpG	270	NM_001081336	380921	Mm.379505	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16	"diacylglycerol kinase, eta"	protein-coding	0.1	0.722772
Merged-chr14-120867331-1	chr14	120867281	120867381	+	2.5	cIP1vsInput	Intergenic	Intergenic	-43863	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding	0	0.425743
Merged-chr10-81502942-1	chr10	81502892	81502992	+	2.5	cIP1vsInput	"exon (NM_010304, exon 7 of 7)"	"exon (NM_010304, exon 7 of 7)"	-2805	NM_010102	13611	Mm.33065	NM_010102	ENSMUSG00000044199	S1pr4	Edg6|Lpc1|S1p4	sphingosine-1-phosphate receptor 4	protein-coding	0.12	0.633663
Merged-chr5-91827633-1	chr5	91827583	91827683	+	2.5	cIP1vsInput	Intergenic	L1MEc|LINE|L1	-60333	NR_045383	73452	Mm.396233	NR_045383		1700063O14Rik	-	RIKEN cDNA 1700063O14 gene	miscRNA	0.01	0.316832
Merged-chr6-140234636-1	chr6	140234586	140234686	+	2.5	cIP1vsInput	Intergenic	Intergenic	-189463	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	"pleckstrin homology domain containing, family A member 5"	protein-coding	0	0.376238
Merged-chr5-60927698-1	chr5	60927648	60927748	+	2.5	cIP2vsInput	Intergenic	Intergenic	-881145	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding	0	0.306931
Merged-chr8-49405617-1	chr8	49405567	49405667	+	2.5	cIP2vsInput	Intergenic	Intergenic	-730927	NM_011857	23965	Mm.42191	NM_001145937	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding	0.01	0.316832
Merged-chr4-143238812-1	chr4	143238762	143238862	+	2.5	cIP2vsInput	Intergenic	Intergenic	-26103	NM_001256380	110593	Mm.332020	NM_001081355	ENSMUSG00000057637	Prdm2	4833427P12Rik|E330024L24Rik|Gm1033|Gm19732|KMT8|Riz|Riz1|Znfpr1c1	"PR domain containing 2, with ZNF domain"	protein-coding	0.03	0.405941
Merged-chr1-26809290-1	chr1	26809240	26809340	+	2.5	cIP2vsInput	Intergenic	Intergenic	-121830	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding	0	0.316832
Merged-chr1-88424509-1	chr1	88424459	88424559	+	2.5	cIP1vsInput	"intron (NM_029269, intron 7 of 7)"	(CATAT)n|Simple_repeat|Simple_repeat	17490	NM_029269	75396	Mm.173058	NM_029269	ENSMUSG00000026295	Spp2	0610038O04Rik|pp-24|spp24	secreted phosphoprotein 2	protein-coding	0.01	0.306931
Merged-chr5-80541164-1	chr5	80541114	80541214	+	2.5	cIP2vsInput	Intergenic	Intergenic	-480429	NM_198702	319387	Mm.461016	NM_198702	ENSMUSG00000037605	Lphn3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|mKIAA0768	latrophilin 3	protein-coding	0	0.287129
Merged-chr1-94932542-1	chr1	94932492	94932592	+	2.5	cIP2vsInput	Intergenic	Intergenic	135100	NR_040473	74689	Mm.399187	NR_040473		4930440C22Rik	-	RIKEN cDNA 4930440C22 gene	miscRNA	0.02	0.326733
Merged-chr8-41026186-1	chr8	41026136	41026236	+	2.5	cIP2vsInput	"intron (NM_001005863, intron 5 of 13)"	PB1|SINE|Alu	8718	NR_015457	78849	Mm.440930	NR_015457	ENSMUSG00000084960	B430010I23Rik	-	RIKEN cDNA B430010I23 gene	miscRNA	0.01	0.554455
Merged-chr18-16887806-1	chr18	16887756	16887856	+	2.5	cIP1vsInput	Intergenic	Intergenic	71399	NR_045399	328906	Mm.136064	NR_045399	ENSMUSG00000086095	Gm15328	D830029L11|OTTMUSG00000020196	predicted gene 15328	miscRNA	0.02	0.336634
Merged-chr14-109984849-1	chr14	109984799	109984899	+	2.5	cIP1vsInput	Intergenic	Intergenic	524619	NR_039542	100628607		NR_039542	ENSMUSG00000092639	Mir3964	mmu-mir-3964|mu-mir-3964	microRNA 3964	miscRNA	0.01	0.267327
Merged-chr10-125742820-1	chr10	125742770	125742870	+	2.5	cIP1vsInput	Intergenic	Intergenic	-223399	NM_177152	320398	Mm.275586	NM_177152	ENSMUSG00000020105	Lrig3	9030421L11Rik|9130004I02Rik|9430095K15Rik|mKIAA3016	leucine-rich repeats and immunoglobulin-like domains 3	protein-coding	0.01	0.277228
Merged-chr1-142438204-1	chr1	142438154	142438254	+	2.5	cIP1vsInput	Intergenic	Lx9|LINE|L1	-1202493	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0	0.326733
Merged-chr5-42716494-1	chr5	42716444	42716544	+	2.5	cIP2vsInput	Intergenic	Intergenic	-516969	NM_175937	231207	Mm.7233	NM_001177379	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding	0	0.366337
Merged-chr3-49636300-1	chr3	49636250	49636350	+	2.5	cIP1vsInput	Intergenic	Intergenic	121016	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding	0	0.346535
Merged-chr8-73829604-1	chr8	73829554	73829654	+	2.5	cIP2vsInput	Intergenic	Intergenic	-477048	NM_010687	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large	BPFD#36|Gyltl1a|Mbp-1|Mbp1|enr|fg|froggy|mKIAA0609|myd	like-glycosyltransferase	protein-coding	0	0.346535
Merged-chr5-130163966-1	chr5	130163916	130164016	+	2.5	cIP2vsInput	Intergenic	LTR41|LTR|ERVL	-7853	NM_001199059	56715	Mm.288639	NM_019983	ENSMUSG00000025340	Rabgef1	Rab5ef|Rabex5|Rin2	RAB guanine nucleotide exchange factor (GEF) 1	protein-coding	0.03	0.386139
Merged-chr14-122721316-1	chr14	122721266	122721366	+	2.5	cIP1vsInput	"intron (NM_144844, intron 18 of 23)"	"intron (NM_144844, intron 18 of 23)"	186988	NM_144844	110821	Mm.23876	NM_144844	ENSMUSG00000041650	Pcca	C79630	"propionyl-Coenzyme A carboxylase, alpha polypeptide"	protein-coding	0.01	0.356436
Merged-chr5-71164256-1	chr5	71164206	71164306	+	2.5	cIP1vsInput	Intergenic	Intergenic	-68407	NM_008066	14395	Mm.5304	NM_008066	ENSMUSG00000000560	Gabra2	C630048P16Rik|Gabra-2	"gamma-aminobutyric acid (GABA) A receptor, subunit alpha 2"	protein-coding	0	0.326733
Merged-chr8-70898165-1	chr8	70898115	70898215	+	2.5	cIP1vsInput	promoter-TSS (NM_029751)	promoter-TSS (NM_029751)	-722	NM_029751	76808	Mm.431334	NM_029751	ENSMUSG00000045128	Rpl18a	2510019J09Rik	ribosomal protein L18A	protein-coding	0.04	0.475248
Merged-chr1-11124561-1	chr1	11124511	11124611	+	2.5	cIP2vsInput	"intron (NM_029525, intron 13 of 39)"	(TAGA)n|Simple_repeat|Simple_repeat	131096	NM_029525	109294	Mm.123247	XM_003946036	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	"phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2"	protein-coding	0	0.336634
Merged-chr2-157502729-1	chr2	157502679	157502779	+	2.5	cIP2vsInput	Intergenic	Intergenic	-57381	NM_010923	18111	Mm.486979	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding	0.01	0.544554
Merged-chr4-51710026-1	chr4	51709976	51710076	+	2.5	cIP1vsInput	Intergenic	Intergenic	341084	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	miscRNA	0.01	0.306931
Merged-chr1-102772822-1	chr1	102772772	102772872	+	2.5	cIP2vsInput	Intergenic	Intergenic	1617054	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0.02	0.267327
Merged-chr5-70791678-1	chr5	70791628	70791728	+	2.5	cIP1vsInput	"intron (NM_010252, intron 3 of 8)"	"intron (NM_010252, intron 3 of 8)"	50939	NM_010252	14405	Mm.255292	NM_010252	ENSMUSG00000001260	Gabrg1	GabaA|GabaA/BZ	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1"	protein-coding	0.01	0.267327
Merged-chr4-66052691-1	chr4	66052641	66052741	+	2.5	cIP1vsInput	"intron (NM_019514, intron 4 of 21)"	"intron (NM_019514, intron 4 of 21)"	351792	NM_019514	56079	Mm.445312	NM_019514	ENSMUSG00000028373	Astn2	1d8|Astnl|bM452J22.1	astrotactin 2	protein-coding	0.01	0.306931
Merged-chr3-122122188-1	chr3	122122138	122122238	+	2.5	cIP2vsInput	"intron (NM_007378, intron 19 of 49)"	"intron (NM_007378, intron 19 of 49)"	77728	NM_007378	11304	Mm.3918	NM_007378	ENSMUSG00000028125	Abca4	AW050280|Abc10|Abcr|D430003I15Rik|RmP	"ATP-binding cassette, sub-family A (ABC1), member 4"	protein-coding	0.04	0.623762
Merged-chr10-126531738-1	chr10	126531688	126531788	+	2.5	cIP2vsInput	Intergenic	Intergenic	369633	NM_026858	68876	Mm.276769	NM_001159559	ENSMUSG00000025436	Xrcc6bp1	1110068E08Rik|2410012H02Rik	XRCC6 binding protein 1	protein-coding	0	0.346535
Merged-chr17-44913087-1	chr17	44913037	44913137	+	2.5	cIP2vsInput	"intron (NM_178652, intron 2 of 11)"	"intron (NM_178652, intron 2 of 11)"	-32202	NM_029257	75341	Mm.386821	XM_001003502		4930564C03Rik	-	RIKEN cDNA 4930564C03 gene	protein-coding	0	0.29703
Merged-chr16-21667160-1	chr16	21667110	21667210	+	2.5	cIP1vsInput	"intron (NM_001001881, intron 1 of 1)"	L1M2|LINE|L1	27505	NM_001001881	72190		NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding	0.01	0.316832
Merged-chr4-29062862-1	chr4	29062812	29062912	+	2.5	cIP2vsInput	Intergenic	Intergenic	249717	NM_010141	13841	Mm.257266	NM_001122889	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding	0	0.306931
Merged-chr17-84790479-1	chr17	84790429	84790529	+	2.5	cIP2vsInput	"exon (NM_028233, exon 1 of 38)"	"exon (NM_028233, exon 1 of 38)"	307	NM_028233	72416	Mm.217027	NM_028233	ENSMUSG00000024120	Lrpprc	3110001K13Rik|C76645|Gp130|Lrp130|Lsfc	leucine-rich PPR-motif containing	protein-coding	0.13	0.772277
Merged-chr7-39204092-1	chr7	39204042	39204142	+	2.5	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	209068	NM_177890	330513	Mm.433234	NM_177890	ENSMUSG00000053742	Gm5114	4921507A12|EG330513	predicted gene 5114	protein-coding	0	0.326733
Merged-chrX-169283512-1	chrX	169283462	169283562	+	2.5	cIP1vsInput	"intron (NM_009707, intron 10 of 12)"	"intron (NM_009707, intron 10 of 12)"	36831	NM_008222	15159	Mm.284033	NM_008222	ENSMUSG00000031352	Hccs	-	holocytochrome c synthetase	protein-coding	0.01	0.306931
Merged-chr4-37120480-1	chr4	37120430	37120530	+	2.5	cIP2vsInput	Intergenic	Intergenic	-168736	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.01	0.316832
Merged-chr1-50525825-1	chr1	50525775	50525875	+	2.5	cIP2vsInput	Intergenic	Intergenic	-401698	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.346535
Merged-chr8-95556682-1	chr8	95556632	95556732	+	2.5	cIP1vsInput	"intron (NM_172914, intron 7 of 8)"	L1M4b|LINE|L1	18515	NM_027640	70993	Mm.486561	NM_027640	ENSMUSG00000048400	Prss54	4931432M23Rik|Klkbl4	"protease, serine, 54"	protein-coding	0.02	0.435644
Merged-chr15-44759073-1	chr15	44759023	44759123	+	2.5	cIP1vsInput	"intron (NM_176998, intron 1 of 7)"	"intron (NM_176998, intron 1 of 7)"	-6615	NM_178765	319613	Mm.207715	NM_001032727	ENSMUSG00000022340	Sybu	5730410E15Rik|A830027B17Rik|Golsyn|mKIAA1472	syntabulin (syntaxin-interacting)	protein-coding	0	0.346535
Merged-chr17-62147158-1	chr17	62147108	62147208	+	2.5	cIP1vsInput	Intergenic	Intergenic	734159	NM_207654	13640	Mm.401670	NM_010109		Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding	0	0.326733
Merged-chr11-111757959-1	chr11	111757909	111758009	+	2.5	cIP1vsInput	Intergenic	Intergenic	691795	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	"potassium inwardly-rectifying channel, subfamily J, member 2"	protein-coding	0	0.29703
Merged-chr7-91996753-1	chr7	91996703	91996803	+	2.5	cIP2vsInput	"intron (NM_011807, intron 9 of 22)"	MLT1J|LTR|ERVL-MaLR	-65641	NM_001243046	23859	Mm.257035	NM_001243046		Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|PSD93	"discs, large homolog 2 (Drosophila)"	protein-coding	0.01	0.386139
Merged-chr15-18812930-1	chr15	18812880	18812980	+	2.5	cIP2vsInput	Intergenic	L1MA7|LINE|L1	-7399	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0	0.29703
Merged-chr1-153814226-1	chr1	153814176	153814276	+	2.5	cIP1vsInput	"intron (NM_001243223, intron 9 of 20)"	"intron (NM_001243223, intron 9 of 20)"	29915	NM_001243223	240816	Mm.329340	NM_001243223	ENSMUSG00000042641	Rgsl1	4930415K13Rik|Gm202|Rgsl2	regulator of G-protein signaling like 1	protein-coding	0	0.316832
Merged-chr15-91754625-1	chr15	91754575	91754675	+	2.5	cIP2vsInput	"intron (NM_025730, intron 31 of 50)"	"intron (NM_025730, intron 31 of 50)"	81401	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding	0.01	0.356436
Merged-chr1-75546260-1	chr1	75546210	75546310	+	2.5	cIP2vsInput	promoter-TSS (NM_009208)	promoter-TSS (NM_009208)	-6	NM_009208	20536	Mm.5053	NM_009208		Slc4a3	A930038D23Rik|Ae3	"solute carrier family 4 (anion exchanger), member 3"	protein-coding	0.05	0.653465
Merged-chr5-60451439-1	chr5	60451389	60451489	+	2.5	cIP2vsInput	Intergenic	RLTR40|LTR|ERVK	-465437	NR_040682	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0	0.316832
Merged-chr3-69686740-1	chr3	69686690	69686790	+	2.5	cIP1vsInput	Intergenic	Intergenic	-35315	NM_133787	97112	Mm.439485	NM_133787	ENSMUSG00000027787	Nmd3	C87860	NMD3 homolog (S. cerevisiae)	protein-coding	0	0.356436
Merged-chr10-42265255-1	chr10	42265205	42265305	+	2.5	cIP1vsInput	"intron (NM_019740, intron 2 of 3)"	"intron (NM_019740, intron 2 of 3)"	11487	NM_019740	56484	Mm.466459	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding	0.03	0.475248
Merged-chr8-80136480-1	chr8	80136430	80136530	+	2.5	cIP1vsInput	Intergenic	Intergenic	-78472	NM_020259	15245	Mm.254493	NM_020259		Hhip	Hhip1	Hedgehog-interacting protein	protein-coding	0	0.29703
Merged-chr4-53006149-1	chr4	53006099	53006199	+	2.5	cIP2vsInput	Intergenic	Intergenic	-5775	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding	0	0.316832
Merged-chr4-71397793-1	chr4	71397743	71397843	+	2.5	cIP2vsInput	Intergenic	MT2B1|LTR|ERVL	803126	NM_011599	21885	Mm.399716	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg1|Tle4l	"transducin-like enhancer of split 1, homolog of Drosophila E(spl)"	protein-coding	0	0.326733
Merged-chr9-84997741-1	chr9	84997691	84997791	+	2.5	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	223343	NR_040739	75253	Mm.401984	NR_040739		4930554C24Rik	-	RIKEN cDNA 4930554C24 gene	miscRNA	0	0.326733
Merged-chr2-22019222-1	chr2	22019172	22019272	+	2.5	cIP2vsInput	Intergenic	Intergenic	-208281	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding	0	0.29703
Merged-chr9-18522686-1	chr9	18522636	18522736	+	2.5	cIP1vsInput	Intergenic	Intergenic	44291	NM_028557	73503	Mm.160088	NM_028557	ENSMUSG00000038691	Mbd3l1	1700070G05Rik|1700095H13Rik|Mbd3l	methyl-CpG binding domain protein 3-like 1	protein-coding	0	0.346535
Merged-chr10-18022909-1	chr10	18022859	18022959	+	2.5	cIP2vsInput	"intron (NM_028440, intron 1 of 2)"	CpG	343	NM_028440	73112	Mm.276041	NM_028440	ENSMUSG00000078453	Abracl	1700028I04Rik|3110003A17Rik	ABRA C-terminal like	protein-coding	0.1	0.693069
Merged-chr11-81534739-1	chr11	81534689	81534789	+	2.5	cIP1vsInput	"intron (NM_001034013, intron 1 of 9)"	MIRb|SINE|MIR	38800	NM_001033765	237880	Mm.435528	NM_001033765		1700071K01Rik	-	RIKEN cDNA 1700071K01 gene	protein-coding	0.01	0.29703
Merged-chr6-46095131-1	chr6	46095081	46095181	+	2.5	cIP2vsInput	"intron (NM_001004357, intron 8 of 23)"	L1M3|LINE|L1	1035070	NM_001004357	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0	0.336634
Merged-chr18-50394729-1	chr18	50394679	50394779	+	2.5	cIP1vsInput	Intergenic	Intergenic	116360	NM_001004061	225497	Mm.329435	NM_001004061	ENSMUSG00000035420	Fam170a	Gm93|Znfd	"family with sequence similarity 170, member A"	protein-coding	0	0.346535
Merged-chr9-105448652-1	chr9	105448602	105448702	+	2.5	cIP2vsInput	"intron (NM_001253831, intron 11 of 26)"	"intron (NM_001253831, intron 11 of 26)"	46481	NM_175025	235574	Mm.489853	NM_001253831	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	"ATPase, Ca++-sequestering"	protein-coding	0.02	0.326733
Merged-chr6-143229685-1	chr6	143229635	143229735	+	2.5	cIP1vsInput	Intergenic	Intergenic	-16203	NR_027803	52285	Mm.354898	NM_001033129		D6Ertd474e	1700001I24Rik|AU023129	"DNA segment, Chr 6, ERATO Doi 474, expressed"	miscRNA	0	0.346535
Merged-chr1-185903955-1	chr1	185903905	185904005	+	2.5	cIP2vsInput	"intron (NR_030555, intron 5 of 6)"	"intron (NR_030555, intron 5 of 6)"	213355	NM_146106	226791	Mm.257116	NM_146106	ENSMUSG00000039246	Lyplal1	BC027340|Q96AVO	lysophospholipase-like 1	protein-coding	0	0.316832
Merged-chr4-77544654-1	chr4	77544604	77544704	+	2.5	cIP2vsInput	"intron (NM_011211, intron 4 of 39)"	Lx8b|LINE|L1	667241	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0	0.356436
Merged-chr1-134120202-1	chr1	134120152	134120252	+	2.5	cIP2vsInput	"intron (NM_027979, intron 1 of 11)"	"intron (NM_027979, intron 1 of 11)"	8960	NM_027979	71884	Mm.328268	NM_027979	ENSMUSG00000026450	Chit1	2300002L19Rik	chitinase 1 (chitotriosidase)	protein-coding	0	0.425743
Merged-chr14-63171769-1	chr14	63171719	63171819	+	2.5	cIP2vsInput	"intron (NM_010191, intron 1 of 7)"	"intron (NM_010191, intron 1 of 7)"	6024	NM_010191	14137	Mm.474432	NM_010191	ENSMUSG00000021273	Fdft1	SQS|SS	farnesyl diphosphate farnesyl transferase 1	protein-coding	0.01	0.49505
Merged-chrY-6685299-1	chrY	6685249	6685349	+	2.5	cIP1vsInput	Intergenic	MER2|DNA|TcMar-Tigger	482478	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.306931
Merged-chr13-10446914-1	chr13	10446864	10446964	+	2.5	cIP1vsInput	Intergenic	Intergenic	-86111	NM_033269	12671	Mm.342315	NM_033269		Chrm3	Chrm-3|M3|M3R	"cholinergic receptor, muscarinic 3, cardiac"	protein-coding	0.01	0.39604
Merged-chr4-85668897-1	chr4	85668847	85668947	+	2.5	cIP1vsInput	Intergenic	Intergenic	-385018	NM_029967	77739	Mm.331690	NM_029967	ENSMUSG00000066113	Adamtsl1	5930437A14Rik|6720426B09Rik|ADAMTSL-1	ADAMTS-like 1	protein-coding	0	0.306931
Merged-chr19-45545183-1	chr19	45545133	45545233	+	2.5	cIP2vsInput	Intergenic	CpG	15360	NM_020032	56626	Mm.46509	NM_020032	ENSMUSG00000025218	Poll	1110003P06Rik|AV007317	"polymerase (DNA directed), lambda"	protein-coding	0.13	0.70297
Merged-chrX-52819484-1	chrX	52819434	52819534	+	2.5	cIP2vsInput	Intergenic	Tigger5|DNA|TcMar-Tigger	28284	NM_001034059	434778	Mm.23411	NM_001034059	ENSMUSG00000073207	Ccdc160	6330534C20Rik	coiled-coil domain containing 160	protein-coding	0.01	0.455446
Merged-chr18-64144150-1	chr18	64144100	64144200	+	2.5	cIP2vsInput	Intergenic	Intergenic	-110209	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	"ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3"	protein-coding	0	0.316832
Merged-chr5-14844153-1	chr5	14844103	14844203	+	2.5	cIP2vsInput	"intron (NM_011995, intron 22 of 24)"	"intron (NM_011995, intron 22 of 24)"	70736	NM_198666	381714	Mm.368256	NM_198666	ENSMUSG00000033219	Gm9758	ENSMUSG00000033219	predicted gene 9758	protein-coding	0	0.326733
Merged-chr13-7280441-1	chr13	7280391	7280491	+	2.5	cIP1vsInput	Intergenic	Intergenic	-631717	NM_019703	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|PFK-C	"phosphofructokinase, platelet"	protein-coding	0	0.425743
Merged-chr10-18283980-1	chr10	18283930	18284030	+	2.5	cIP1vsInput	Intergenic	Intergenic	-48999	NM_144820	215814	Mm.296565	NM_144820	ENSMUSG00000059554	Ccdc28a	1700009P13Rik|AI480677	coiled-coil domain containing 28A	protein-coding	0.01	0.306931
Merged-chr2-152405913-1	chr2	152405863	152405963	+	2.5	cIP1vsInput	Intergenic	PB1D7|SINE|Alu	-7867	NM_011438	20667	Mm.28424	NM_011438		Sox12	2010205A02Rik	SRY-box containing gene 12	protein-coding	0.06	0.49505
Merged-chr8-46697358-1	chr8	46697308	46697408	+	2.5	cIP1vsInput	Intergenic	Intergenic	42157	NR_045750	100503498	Mm.187358	NR_045750	ENSMUSG00000097534	Gm16675	-	"predicted gene, 16675"	miscRNA	0	0.306931
Merged-chr6-71860672-1	chr6	71860622	71860722	+	2.5	cIP1vsInput	"intron (NM_001253681, intron 7 of 14)"	"intron (NM_001253681, intron 7 of 14)"	29352	NM_001253688	76614	Mm.490578	NM_001253681	ENSMUSG00000052337	Immt	1700082C19Rik|D830041H16Rik|HMP|P87|P87/89|P89	"inner membrane protein, mitochondrial"	protein-coding	0	0.326733
Merged-chr1-194151516-1	chr1	194151466	194151566	+	2.5	cIP1vsInput	Intergenic	L1MA8|LINE|L1	71243	NR_040477	74942	Mm.60689	NR_040477		4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	miscRNA	0	0.29703
Merged-chr5-80099292-1	chr5	80099242	80099342	+	2.5	cIP1vsInput	Intergenic	Intergenic	-583388	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0	0.277228
Merged-chr11-63072993-1	chr11	63072943	63073043	+	2.5	cIP1vsInput	"intron (NM_027660, intron 2 of 7)"	"intron (NM_027660, intron 2 of 7)"	11334	NM_027660	71062	Mm.23534	NM_027660	ENSMUSG00000042189	Tekt3	4933407G07Rik	tektin 3	protein-coding	0	0.227723
Merged-chr13-87264568-1	chr13	87264518	87264618	+	2.5	cIP2vsInput	Intergenic	MT2B1|LTR|ERVL	-1217773	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0	0.346535
Merged-chr8-112098421-1	chr8	112098371	112098471	+	2.5	cIP2vsInput	Intergenic	Intergenic	87062	NM_020584	57321	Mm.213064	NM_020584	ENSMUSG00000033430	Terf2ip	Rap1	"telomeric repeat binding factor 2, interacting protein"	protein-coding	0.02	0.485149
Merged-chr13-99267844-1	chr13	99267794	99267894	+	2.5	cIP2vsInput	Intergenic	Lx5|LINE|L1	76834	NM_026873	68927	Mm.276502	NM_026873	ENSMUSG00000021650	Ptcd2	1190005P08Rik	pentatricopeptide repeat domain 2	protein-coding	0	0.336634
Merged-chr5-34860258-1	chr5	34860208	34860308	+	2.5	cIP1vsInput	"intron (NM_010414, intron 37 of 66)"	L1_Mus1|LINE|L1	-55657	NM_207277	403174	Mm.291225	NM_207277	ENSMUSG00000051246	Msantd1	A930005I04Rik|Gm144	Myb/SANT-like DNA-binding domain containing 1	protein-coding	0	0.326733
Merged-chr9-108049228-1	chr9	108049178	108049278	+	2.5	cIP2vsInput	promoter-TSS (NM_177910)	promoter-TSS (NM_177910)	-62	NM_177910	331026	Mm.379272	NM_177910		Gmppb	AI317178|E430010H19	GDP-mannose pyrophosphorylase B	protein-coding	0.11	0.623762
Merged-chr15-77367290-1	chr15	77367240	77367340	+	2.5	cIP2vsInput	Intergenic	Intergenic	31820	NM_029419	75761	Mm.232636	NM_001164640	ENSMUSG00000010601	Apol7a	9130022K13Rik|Apol3	apolipoprotein L 7a	protein-coding	0.04	0.544554
Merged-chr5-89836142-1	chr5	89836092	89836192	+	2.5	cIP1vsInput	"intron (NM_001081401, intron 3 of 21)"	"intron (NM_001081401, intron 3 of 21)"	47192	NM_177872	330119	Mm.133062	NM_001081401	ENSMUSG00000043635	Adamts3	1100001H14Rik|6330442E02Rik	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 3"	protein-coding	0	0.306931
Merged-chr10-108602702-1	chr10	108602652	108602752	+	2.5	cIP1vsInput	"intron (NM_001252342, intron 8 of 10)"	"intron (NM_001252342, intron 8 of 10)"	97458	NM_203660	368203	Mm.452758	NM_203660		Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding	0.02	0.39604
Merged-chr4-106195254-1	chr4	106195204	106195304	+	2.5	cIP1vsInput	Intergenic	Intergenic	-120959	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding	0.01	0.514851
Merged-chr10-128015051-1	chr10	128015001	128015101	+	2.5	cIP2vsInput	promoter-TSS (NM_008921)	promoter-TSS (NM_008921)	-164	NM_008921	19075	Mm.2903	NM_008921	ENSMUSG00000025395	Prim1	AI324982	"DNA primase, p49 subunit"	protein-coding	0.02	0.445545
Merged-chr2-19528817-1	chr2	19528767	19528867	+	2.5	cIP1vsInput	"intron (NM_027600, intron 4 of 16)"	"intron (NM_027600, intron 4 of 16)"	25093	NM_027600	70909	Mm.158488	NM_027600	ENSMUSG00000026734	4921504E06Rik	4921522E24Rik	RIKEN cDNA 4921504E06 gene	protein-coding	0	0.267327
Merged-chr16-85906344-1	chr16	85906294	85906394	+	2.5	cIP2vsInput	Intergenic	Intergenic	-5219	NM_011782	23794	Mm.437478	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|AI481094|ASMP-2	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"	protein-coding	0	0.336634
Merged-chrY-7044065-1	chrY	7044015	7044115	+	2.5	cIP1vsInput	Intergenic	YREP_Mm|Unknown|Unknown	123712	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.257426
Merged-chr2-24060205-1	chr2	24060155	24060255	+	2.5	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	-10826	NM_080462	140483	Mm.33120	NM_080462	ENSMUSG00000026986	Hnmt	1500031F01Rik|AI788969	histamine N-methyltransferase	protein-coding	0	0.346535
Merged-chr3-135485651-1	chr3	135485601	135485701	+	2.5	cIP2vsInput	promoter-TSS (NM_027288)	promoter-TSS (NM_027288)	40	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	"mannosidase, beta A, lysosomal"	protein-coding	0.07	0.653465
Merged-chr15-45486944-1	chr15	45486894	45486994	+	2.5	cIP1vsInput	Intergenic	Tigger6a|DNA|TcMar-Tigger	-372010	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	"potassium channel, subfamily V, member 1"	protein-coding	0	0.277228
Merged-chr11-108759327-1	chr11	108759277	108759377	+	2.5	cIP1vsInput	"intron (NM_145688, intron 3 of 6)"	"intron (NM_145688, intron 3 of 6)"	76709	NM_029586	76380	Mm.344071	NM_029586	ENSMUSG00000020728	Cep112	1700001M19Rik|1700029K01Rik|8430407H02Rik|AV043680|AV207351|Ccdc46|Macoco	centrosomal protein 112	protein-coding	0	0.336634
Merged-chr13-25055420-1	chr13	25055370	25055470	+	2.5	cIP1vsInput	promoter-TSS (NM_177577)	promoter-TSS (NM_177577)	-584	NM_001195617	195208	Mm.284719	NM_001195617	ENSMUSG00000035910	Dcdc2a	AW492955|Dcdc2|RU2	doublecortin domain containing 2a	protein-coding	0.08	0.732673
Merged-chr5-139364506-1	chr5	139364456	139364556	+	2.5	cIP1vsInput	"intron (NM_028469, intron 2 of 4)"	"intron (NM_028469, intron 2 of 4)"	5239	NR_029768	723898		NR_029768		Mir339	Mirn339|mmu-mir-339	microRNA 339	miscRNA	0.01	0.584158
Merged-chr7-74641904-1	chr7	74641854	74641954	+	2.5	cIP2vsInput	Intergenic	Intergenic	-87124	NM_001038643	108116	Mm.425467	NM_001038643	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	"solute carrier organic anion transporter family, member 3a1"	protein-coding	0	0.326733
Merged-chr6-113531588-1	chr6	113531538	113531638	+	2.5	cIP2vsInput	promoter-TSS (NM_175101)	promoter-TSS (NM_175101)	50	NM_175101	66087	Mm.275989	NM_175101	ENSMUSG00000030286	Emc3	0610039A15Rik|AI225901|AW260416|Pob|Tmem111	ER membrane protein complex subunit 3	protein-coding	0.07	0.673267
Merged-chr16-69405330-1	chr16	69405280	69405380	+	2.5	cIP2vsInput	Intergenic	Intergenic	458414	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding	0	0.29703
Merged-chr6-9912000-1	chr6	9911950	9912050	+	2.5	cIP1vsInput	Intergenic	L1VL4|LINE|L1	961981	NM_008751	18231	Mm.46954	NM_008751		Nxph1	C130005L03Rik	neurexophilin 1	protein-coding	0	0.376238
Merged-chr13-51202862-1	chr13	51202812	51202912	+	2.5	cIP2vsInput	Intergenic	CpG	31837	NM_029173	75124	Mm.179243	NM_029173	ENSMUSG00000021396	Nxnl2	4930519N16Rik|Rdcvf2	nucleoredoxin-like 2	protein-coding	0.11	0.653465
Merged-chr9-32264151-1	chr9	32264101	32264201	+	2.5	cIP1vsInput	"3' UTR (NM_177379, exon 13 of 13)"	"3' UTR (NM_177379, exon 13 of 13)"	39902	NM_177379	330914	Mm.46683	NM_001195632	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding	0	0.39604
Merged-chr2-145555655-1	chr2	145555605	145555705	+	2.5	cIP2vsInput	promoter-TSS (NM_001037929)	promoter-TSS (NM_001037929)	-673	NM_001037929	627302	Mm.445953	NM_001037929		Gm14092	OTTMUSG00000015643	predicted gene 14092	protein-coding	0	0.316832
Merged-chr10-55723559-1	chr10	55723509	55723609	+	2.5	cIP2vsInput	Intergenic	Lx8|LINE|L1	-383358	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding	0	0.356436
Merged-chr10-46166148-1	chr10	46166098	46166198	+	2.5	cIP2vsInput	Intergenic	Intergenic	-78600	NR_028274	100302593		NR_028274		Snord14d	Gm23710	"small nucleolar RNA, C/D box 14D"	snoRNA	0	0.316832
Merged-chr14-13456352-1	chr14	13456302	13456402	+	2.5	cIP1vsInput	"intron (NM_001163032, intron 1 of 4)"	"intron (NM_001163032, intron 1 of 4)"	2394	NM_001163032	72003	Mm.317515	NM_001163032	ENSMUSG00000056296	Synpr	1500003F20Rik|SPO	synaptoporin	protein-coding	0	0.356436
Merged-chr1-95762103-1	chr1	95762053	95762153	+	2.5	cIP1vsInput	Intergenic	Intergenic	-45585	NR_040479	75381	Mm.417807	NR_040479		4930598F16Rik	-	RIKEN cDNA 4930598F16 gene	miscRNA	0	0.19802
Merged-chr5-9169714-1	chr5	9169664	9169764	+	2.5	cIP1vsInput	Intergenic	Intergenic	-7938	NM_011806	23857	Mm.22480	NM_001110327	ENSMUSG00000042508	Dmtf1	Dimp|Dmp1	cyclin D binding myb-like transcription factor 1	protein-coding	0	0.306931
Merged-chr12-96765035-1	chr12	96764985	96765085	+	2.5	cIP1vsInput	Intergenic	Intergenic	-717813	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0	0.316832
Merged-chr4-97273540-1	chr4	97273490	97273590	+	2.5	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	-308403	NM_001122952	18027	Mm.409646	NM_001122952	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|NF1-A|NF1A	nuclear factor I/A	protein-coding	0	0.346535
Merged-chr1-129250218-1	chr1	129250168	129250268	+	2.5	cIP1vsInput	Intergenic	Intergenic	-23086	NM_172485	210417	Mm.380518	NM_172485	ENSMUSG00000042581	Thsd7b	1700074E13Rik|B930082A18|D130067I03Rik	"thrombospondin, type I, domain containing 7B"	protein-coding	0	0.336634
Merged-chr8-32475502-1	chr8	32475452	32475552	+	2.5	cIP2vsInput	Intergenic	Intergenic	323607	NR_046039	666589	Mm.367675	NR_046039		Gm8179	EG666589	predicted gene 8179	miscRNA	0	0.376238
Merged-chr6-5974821-1	chr6	5974771	5974871	+	2.5	cIP1vsInput	"intron (NM_001191023, intron 13 of 15)"	L1MC5|LINE|L1	2572	NR_040255	72249	Mm.443268	NR_040255	ENSMUSG00000085416	1700019G24Rik	-	RIKEN cDNA 1700019G24 gene	miscRNA	0.02	0.346535
Merged-chr8-104471828-1	chr8	104471778	104471878	+	2.5	cIP2vsInput	"intron (NM_180958, intron 14 of 19)"	ID_B1|SINE|B4	-28781	NM_001013380	234663	Mm.289583	NM_001013380	ENSMUSG00000035770	Dync1li2	AA409702|C920003I06|Dncli2|Dnclic2|LIC2	"dynein, cytoplasmic 1 light intermediate chain 2"	protein-coding	0	0.435644
Merged-chr10-26633771-1	chr10	26633721	26633821	+	2.5	cIP1vsInput	Intergenic	ETnERV2-int|LTR|ERVK	40880	NR_033633	667572	Mm.482728	NR_033633		Gm8709	EG667572	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0	0.336634
Merged-chr5-87696532-1	chr5	87696482	87696582	+	2.5	cIP2vsInput	"intron (NM_009972, intron 4 of 8)"	"intron (NM_009972, intron 4 of 8)"	2889	NM_009972	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding	0	0.346535
Merged-chr2-135142912-1	chr2	135142862	135142962	+	2.5	cIP1vsInput	"intron (NM_019677, intron 3 of 32)"	"intron (NM_019677, intron 3 of 32)"	72704	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	miscRNA	0	0.386139
Merged-chr8-3469431-1	chr8	3469381	3469481	+	2.5	cIP2vsInput	Intergenic	RMER15|LTR|ERVL	-1431	NM_029598	76406	Mm.74996	NM_029598	ENSMUSG00000040340	1700019B03Rik	-	RIKEN cDNA 1700019B03 gene	protein-coding	0.01	0.425743
Merged-chr18-29643010-1	chr18	29642960	29643060	+	2.5	cIP1vsInput	Intergenic	Intergenic	-146594	NR_045391	78058	Mm.416952	NR_045391		4930578E11Rik	-	RIKEN cDNA 4930578E11 gene	miscRNA	0	0.39604
Merged-chr1-48305161-1	chr1	48305111	48305211	+	2.5	cIP1vsInput	Intergenic	Intergenic	-1451652	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.306931
Merged-chr8-104799785-1	chr8	104799735	104799835	+	2.5	cIP1vsInput	TTS (NM_001002775)	TTS (NM_001002775)	4548	NM_001002775	442809	Mm.444779	NM_001002775		4932416K20Rik	-	RIKEN cDNA 4932416K20 gene	protein-coding	0	0.455446
Merged-chr7-122670997-1	chr7	122670947	122671047	+	2.5	cIP2vsInput	promoter-TSS (NM_019430)	promoter-TSS (NM_019430)	-747	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	"calcium channel, voltage-dependent, gamma subunit 3"	protein-coding	0.07	0.653465
Merged-chr1-33814540-1	chr1	33814490	33814590	+	2.5	cIP2vsInput	promoter-TSS (NM_133817)	promoter-TSS (NM_133817)	-113	NM_133817	98403	Mm.440137	NM_133817	ENSMUSG00000042197	Zfp451	4930515K21Rik|4933435G09Rik|AI596398|COASTER|Kiaa0576-hp|Znf451|mKIAA1702	zinc finger protein 451	protein-coding	0.14	0.752475
Merged-chr10-101280847-1	chr10	101280797	101280897	+	2.5	cIP1vsInput	Intergenic	Lx5c|LINE|L1	-400640	NM_001205098	67569	Mm.403713	NM_001162368	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"	protein-coding	0	0.346535
Merged-chr9-60969804-1	chr9	60969754	60969854	+	2.5	cIP1vsInput	Intergenic	L1MD|LINE|L1	-47265	NR_040767	330956	Mm.207985	NR_040767		Gm5122	A430102L10	predicted gene 5122	miscRNA	0	0.346535
Merged-chr1-146676422-1	chr1	146676372	146676472	+	2.5	cIP2vsInput	"intron (NM_153539, intron 2 of 7)"	RMER16B3|LTR|ERVK	178735	NM_001145807	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.306931
Merged-chr4-146190325-1	chr4	146190275	146190375	+	2.5	cIP1vsInput	"intron (NM_001177545, intron 3 of 4)"	"intron (NM_001177545, intron 3 of 4)"	32635	NM_001177545	667666	Mm.459230	NM_001177545	ENSMUSG00000066007	Zfp600	Gm13164|OTTMUSG00000010694	zinc finger protein 600	protein-coding	0	0.306931
Merged-chr10-109174137-1	chr10	109174087	109174187	+	2.5	cIP2vsInput	Intergenic	L1MC|LINE|L1	-163162	NM_001252341	20979	Mm.489829	NM_001252341	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding	0	0.326733
Merged-chr8-64362603-1	chr8	64362553	64362653	+	2.5	cIP2vsInput	Intergenic	Intergenic	151838	NR_030491	735270		NR_030491	ENSMUSG00000076042	Mir710	Mirn710|mmu-mir-710	microRNA 710	miscRNA	0.03	0.376238
Merged-chr7-76718823-1	chr7	76718773	76718873	+	2.5	cIP1vsInput	"intron (NM_001199224, intron 19 of 22)"	MLT1I|LTR|ERVL-MaLR	488936	NM_001199224	244071	Mm.322829	NM_001199224		Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding	0	0.326733
Merged-chr14-73782206-1	chr14	73782156	73782256	+	2.5	cIP1vsInput	Intergenic	L1MA5|LINE|L1	229420	NM_011506	20916	Mm.38951	NM_011506	ENSMUSG00000022110	Sucla2	4930547K18Rik	"succinate-Coenzyme A ligase, ADP-forming, beta subunit"	protein-coding	0.02	0.356436
Merged-chr8-47787585-1	chr8	47787535	47787635	+	2.5	cIP1vsInput	Intergenic	Intergenic	-34558	NM_001111318	100039801	Mm.471595	NM_001111318	ENSMUSG00000061974	Cldn24	ENSMUSG00000061974|Gm10107	claudin 24	protein-coding	0.03	0.574257
Merged-chr3-151449354-1	chr3	151449304	151449404	+	2.5	cIP2vsInput	"intron (NM_133222, intron 2 of 15)"	"intron (NM_133222, intron 2 of 15)"	11472	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0	0.287129
Merged-chr6-103859713-1	chr6	103859663	103859763	+	2.5	cIP1vsInput	Intergenic	Intergenic	348837	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule with homology to L1CAM	protein-coding	0.01	0.336634
Merged-chr3-62658791-1	chr3	62658741	62658841	+	2.5	cIP1vsInput	Intergenic	Intergenic	-53651	NM_177346	229357	Mm.95181	NM_177346		Gpr149	9630018L10Rik|PGR10	G protein-coupled receptor 149	protein-coding	0.01	0.306931
Merged-chr10-44177854-1	chr10	44177804	44177904	+	2.5	cIP1vsInput	"intron (NR_001582, intron 2 of 6)"	L1_Mus3|LINE|L1	7407	NR_001582	70365	Mm.87073	NR_001582		Speer5-ps1	1700007C10Rik|SPEER-5|Speer5-ps	"spermatogenesis associated glutamate (E)-rich protein 5, pseudogene 1"	pseudo	0.01	0.386139
Merged-chr10-35507309-1	chr10	35507259	35507359	+	2.5	cIP2vsInput	Intergenic	Intergenic	-999498	NM_001253355	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0	0.316832
Merged-chr2-96720002-1	chr2	96719952	96720052	+	2.5	cIP1vsInput	Intergenic	(CAAAAA)n|Simple_repeat|Simple_repeat	-747672	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.316832
Merged-chr12-101386178-1	chr12	101386128	101386228	+	2.5	cIP1vsInput	Intergenic	Lx3_Mus|LINE|L1	-18495	NM_173023	271036	Mm.84218	NM_173023	ENSMUSG00000047014	Catsperb	4931410B03|4932415G16Rik	catsper channel auxiliary subunit beta	protein-coding	0.02	0.336634
Merged-chr6-29559347-1	chr6	29559297	29559397	+	2.5	cIP2vsInput	"intron (NM_177296, intron 16 of 22)"	"intron (NM_177296, intron 16 of 22)"	30065	NM_001252382	27056	Mm.6479	NM_001252382	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding	0	0.326733
Merged-chr3-25716141-1	chr3	25716091	25716191	+	2.5	cIP2vsInput	"intron (NM_001163387, intron 3 of 5)"	"intron (NM_001163387, intron 3 of 5)"	437166	NM_001163387	192167	Mm.316080	NM_001163387	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|mKIAA1070	neuroligin 1	protein-coding	0	0.306931
Merged-chr1-107023822-1	chr1	107023772	107023872	+	2.5	cIP1vsInput	Intergenic	Intergenic	28481	NM_009126	20248	Mm.482944	NM_009126	ENSMUSG00000044594	Serpinb3a	1110001H02Rik|1110013A16Rik|Scca2|Serpinb4|Sqn5	"serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 3A"	protein-coding	0	0.29703
Merged-chr6-57430544-1	chr6	57430494	57430594	+	2.5	cIP2vsInput	Intergenic	Intergenic	-1147	NM_001101533	434017	Mm.473685	NM_001101533	ENSMUSG00000093679	Vmn1r20	EG434017|Gm5569	vomeronasal 1 receptor 20	protein-coding	0	0.306931
Merged-chr15-6024704-1	chr15	6024654	6024754	+	2.5	cIP1vsInput	Intergenic	MIR|SINE|MIR	-275085	NM_001008702	13132	Mm.240830	NM_001008702	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	"disabled 2, mitogen-responsive phosphoprotein"	protein-coding	0	0.346535
Merged-chr4-69444113-1	chr4	69444063	69444163	+	2.5	cIP2vsInput	Intergenic	Intergenic	-489716	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Dbc1	BRINP|Brinp1|Dbccr1|Fam5a	deleted in bladder cancer 1 (human)	protein-coding	0	0.39604
Merged-chr2-83331017-1	chr2	83330967	83331067	+	2.5	cIP1vsInput	Intergenic	Intergenic	-313561	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding	0.01	0.386139
Merged-chr5-60307511-1	chr5	60307461	60307561	+	2.5	cIP2vsInput	Intergenic	Intergenic	-321509	NR_040682	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0	0.306931
Merged-chr13-85906195-1	chr13	85906145	85906245	+	2.5	cIP1vsInput	Intergenic	L1MA4|LINE|L1	140600	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0	0.277228
Merged-chr18-43803807-1	chr18	43803757	43803857	+	2.5	cIP1vsInput	Intergenic	Intergenic	-10929	NM_001033280	225443	Mm.100304	NM_001033280	ENSMUSG00000071858	Gm94	-	predicted gene 94	protein-coding	0.01	0.326733
Merged-chr3-14051821-1	chr3	14051771	14051871	+	2.5	cIP2vsInput	"intron (NM_178631, intron 4 of 9)"	MER67C|LTR|ERV1	105449	NM_001163330	76897	Mm.422625	NM_001163328	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0	0.356436
Merged-chr13-7428862-1	chr13	7428812	7428912	+	2.5	cIP1vsInput	Intergenic	Intergenic	-774047	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	"adenosine deaminase, RNA-specific, B2"	protein-coding	0	0.415842
Merged-chr15-46070074-1	chr15	46070024	46070124	+	2.5	cIP1vsInput	Intergenic	Lx8|LINE|L1	-254511	NR_045509	71120	Mm.158571	NR_045509		1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	miscRNA	0	0.405941
Merged-chr12-49876945-1	chr12	49876895	49876995	+	2.5	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-396083	NR_045472	69054	Mm.417838	NR_045472		1810007C17Rik	-	RIKEN cDNA 1810007C17 gene	miscRNA	0	0.306931
Merged-chr1-22679240-1	chr1	22679190	22679290	+	2.5	cIP2vsInput	"intron (NM_001012623, intron 2 of 14).2"	"intron (NM_001012623, intron 2 of 14).2"	126484	NM_001012625	116837	Mm.461684	NM_001012623		Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding	0	0.405941
Merged-chr19-29234625-1	chr19	29234575	29234675	+	2.5	cIP2vsInput	Intergenic	L1M5|LINE|L1	-17203	NM_001048177	16452	Mm.275839	NM_001048177	ENSMUSG00000024789	Jak2	AI504024|C81284|Fd17	Janus kinase 2	protein-coding	0.01	0.316832
Merged-chr1-83449723-1	chr1	83449673	83449773	+	2.5	cIP1vsInput	Intergenic	Zaphod3|DNA|hAT-Tip100	-41523	NM_172430	77629	Mm.154303	NM_172430		Sphkap	4930544G21Rik|A930009L15Rik|AI852220|SKIP|mKIAA1678	"SPHK1 interactor, AKAP domain containing"	protein-coding	0	0.366337
Merged-chr8-30173663-1	chr8	30173613	30173713	+	2.5	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-394732	NR_045856	71314	Mm.158666	NR_045856	ENSMUSG00000097044	4933433F19Rik	-	RIKEN cDNA 4933433F19 gene	miscRNA	0	0.326733
Merged-chr8-38190404-1	chr8	38190354	38190454	+	2.5	cIP1vsInput	"intron (NM_145841, intron 1 of 7)"	"intron (NM_145841, intron 1 of 7)"	61798	NR_029884	723860		NR_029884		Mir383	Mirn383|mmu-mir-383	microRNA 383	miscRNA	0	0.326733
Merged-chr15-48003761-1	chr15	48003711	48003811	+	2.5	cIP1vsInput	"intron (NM_001081391, intron 15 of 70)"	"intron (NM_001081391, intron 15 of 70)"	788228	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0.01	0.316832
Merged-chr10-127342142-1	chr10	127342092	127342192	+	2.5	cIP2vsInput	promoter-TSS (NM_010296)	promoter-TSS (NM_010296)	-563	NM_010296	14632	Mm.391450	NM_010296	ENSMUSG00000025407	Gli1	AV235269|Zfp-5|Zfp5	GLI-Kruppel family member GLI1	protein-coding	0.06	0.554455
Merged-chr5-75632507-1	chr5	75632457	75632557	+	2.5	cIP2vsInput	"intron (NM_021099, intron 7 of 20)"	"intron (NM_021099, intron 7 of 20)"	57516	NM_021099	16590	Mm.247073	NM_001122733	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	kit oncogene	protein-coding	0.01	0.415842
Merged-chr2-56924298-1	chr2	56924248	56924348	+	2.5	cIP2vsInput	Intergenic	Intergenic	190740	NM_013613	18227	Mm.3507	NM_001139509	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	"nuclear receptor subfamily 4, group A, member 2"	protein-coding	0	0.346535
Merged-chr7-49778295-1	chr7	49778245	49778345	+	2.5	cIP2vsInput	promoter-TSS (NM_133740)	promoter-TSS (NM_133740)	-63	NM_133740	71974	Mm.349442	NM_133740	ENSMUSG00000030505	Prmt3	2010005E20Rik|2410018A17Rik|AL033309|Hrmt1l3	protein arginine N-methyltransferase 3	protein-coding	0.13	0.70297
Merged-chr6-36642222-1	chr6	36642172	36642272	+	2.5	cIP1vsInput	Intergenic	Intergenic	169139	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding	0	0.326733
Merged-chr5-10082691-1	chr5	10082641	10082741	+	2.5	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-357339	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	"glutamate receptor, metabotropic 3"	protein-coding	0	0.346535
Merged-chr5-20022350-1	chr5	20022300	20022400	+	2.5	cIP2vsInput	"intron (NM_015823, intron 1 of 21)"	"intron (NM_015823, intron 1 of 21)"	114832	NM_015823	50791	Mm.441283	NM_001170745	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	"membrane associated guanylate kinase, WW and PDZ domain containing 2"	protein-coding	0	0.336634
Merged-chr12-10328820-1	chr12	10328770	10328870	+	2.5	cIP1vsInput	Intergenic	Intergenic	-41151	NM_027588	70881	Mm.272843	NM_027588	ENSMUSG00000020622	Nt5c1b	4921514H13Rik|AIRP|CN-IB	"5'-nucleotidase, cytosolic IB"	protein-coding	0	0.306931
Merged-chr7-51819624-1	chr7	51819574	51819674	+	2.5	cIP2vsInput	Intergenic	Intergenic	42643	NM_001115087	100040608	Mm.392015	NM_001115087	ENSMUSG00000092118	Fancf	A730016A17	"Fanconi anemia, complementation group F"	protein-coding	0	0.326733
Merged-chr8-42644396-1	chr8	42644346	42644446	+	2.5	cIP2vsInput	Intergenic	Intergenic	497090	NM_177742	244448	Mm.64542	NM_177742	ENSMUSG00000031651	Triml1	4933403D14|BC050188	tripartite motif family-like 1	protein-coding	0	0.376238
Merged-chr14-7203384-1	chr14	7203334	7203434	+	2.5	cIP1vsInput	Intergenic	Intergenic	-97927	NM_001024712	100042149	Mm.483675	NM_001024712	ENSMUSG00000092167	Gm3696	544988|ENSMUSG00000056940|Gm10014	predicted gene 3696	protein-coding	0.02	0.346535
Merged-chr6-148390629-1	chr6	148390579	148390679	+	2.5	cIP1vsInput	"intron (NM_198967, intron 5 of 19)"	"intron (NM_198967, intron 5 of 19)"	35973	NR_003634	66184	Mm.391542	NR_003634	ENSMUSG00000063171	Rps4y2	1110033J19Rik|AA407494	"ribosomal protein S4, Y-linked 2"	pseudo	0	0.316832
Merged-chr6-61515097-1	chr6	61515047	61515147	+	2.5	cIP2vsInput	"intron (NM_001164316, intron 5 of 10)"	"intron (NM_001164316, intron 5 of 10)"	-334287	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	miscRNA	0	0.306931
Merged-chr14-124409210-1	chr14	124409160	124409260	+	2.5	cIP2vsInput	"intron (NM_207667, intron 1 of 4)"	"intron (NM_207667, intron 1 of 4)"	-216664	NM_010201	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding	0	0.316832
Merged-chr2-87820499-1	chr2	87820449	87820549	+	2.5	cIP1vsInput	Intergenic	Intergenic	10677	NM_146320	258317	Mm.377433	NM_146320	ENSMUSG00000068814	Olfr1145	MOR264-19	olfactory receptor 1145	protein-coding	0.01	0.287129
Merged-chr8-8820754-1	chr8	8820704	8820804	+	2.5	cIP2vsInput	Intergenic	Intergenic	-130217	NM_176849	234023	Mm.251655	NM_176849	ENSMUSG00000040459	Arglu1	9430010O03Rik|C130008N12	arginine and glutamate rich 1	protein-coding	0.01	0.386139
Merged-chr15-102279499-1	chr15	102279449	102279549	+	2.5	cIP2vsInput	promoter-TSS (NM_134100)	promoter-TSS (NM_134100)	43	NM_134100	106073	Mm.287740	NM_134100	ENSMUSG00000045665	Mfsd5	AA409375|AW556797|D15Mgi27	major facilitator superfamily domain containing 5	protein-coding	0.13	0.752475
Merged-chr10-30188960-1	chr10	30188910	30189010	+	2.5	cIP1vsInput	Intergenic	Intergenic	11580	NM_001109747	66311	Mm.251779	NM_001109747	ENSMUSG00000075266	Cenpw	2610036L11Rik|Cug2	centromere protein W	protein-coding	0	0.336634
Merged-chr14-67621087-1	chr14	67621037	67621137	+	2.5	cIP1vsInput	Intergenic	Intergenic	94523	NM_001110162	108912	Mm.33831	NM_001110162	ENSMUSG00000048922	Cdca2	2610311M19Rik|AI586158	cell division cycle associated 2	protein-coding	0	0.465347
Merged-chr6-52687524-1	chr6	52687474	52687574	+	2.5	cIP1vsInput	Intergenic	Intergenic	-26205	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding	0	0.247525
Merged-chr2-96422242-1	chr2	96422192	96422292	+	2.5	cIP1vsInput	Intergenic	Intergenic	-1045432	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.306931
Merged-chr2-181694100-1	chr2	181694050	181694150	+	2.5	cIP2vsInput	promoter-TSS (NM_026446)	promoter-TSS (NM_026446)	-176	NM_026446	56470	Mm.274366	NM_026446	ENSMUSG00000002458	Rgs19	2610042F04Rik|AI324841|AW547781|GAIP	regulator of G-protein signaling 19	protein-coding	0.1	0.663366
Merged-chr12-85683718-1	chr12	85683668	85683768	+	2.5	cIP2vsInput	Intergenic	Intergenic	-3002	NM_016767	53314	Mm.6672	NM_016767	ENSMUSG00000034266	Batf	B-ATF|SFA-2	"basic leucine zipper transcription factor, ATF-like"	protein-coding	0	0.326733
Merged-chr13-109130381-1	chr13	109130331	109130431	+	2.5	cIP2vsInput	"intron (NM_011056, intron 3 of 16)"	L1MA7|LINE|L1	-194363	NR_030644	100124489		NR_030644		Mir582	Mirn582|mmu-mir-582	microRNA 582	miscRNA	0	0.336634
Merged-chr6-53509214-1	chr6	53509164	53509264	+	2.5	cIP2vsInput	Intergenic	Intergenic	-64160	NM_172728	231991	Mm.321138	NM_172728	ENSMUSG00000053007	Creb5	Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding	0	0.39604
Merged-chr4-23068151-1	chr4	23068101	23068201	+	2.5	cIP1vsInput	Intergenic	Lx9|LINE|L1	-579785	NM_008899	18992	Mm.487875	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	"POU domain, class 3, transcription factor 2"	protein-coding	0	0.29703
Merged-chr15-3953075-1	chr15	3953025	3953125	+	2.5	cIP1vsInput	Intergenic	Intergenic	26498	NM_134099	106052	Mm.234191	NM_134099		Fbxo4	1700096C12Rik|AI851261|AW494535|Fbx4	F-box protein 4	protein-coding	0	0.366337
Merged-chr3-5472418-1	chr3	5472368	5472468	+	2.5	cIP2vsInput	Intergenic	Lx6|LINE|L1	103830	NM_001163301	19302	Mm.132336	NM_001163304	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding	0	0.316832
Merged-chr14-10328722-1	chr14	10328672	10328772	+	2.5	cIP2vsInput	"intron (NM_010210, intron 4 of 8)"	Lx|LINE|L1	444627	NR_030680	100042415	Mm.235938	NR_030680		Gm3833	-	meiotic nuclear divisions 1 homolog pseudogene	pseudo	0	0.376238
Merged-chr1-16353199-1	chr1	16353149	16353249	+	2.5	cIP2vsInput	"intron (NM_001111272, intron 10 of 12)"	Lx5|LINE|L1	166103	NM_025303	29819	Mm.216257	NM_001111272	ENSMUSG00000025920	Stau2	-	staufen (RNA binding protein) homolog 2 (Drosophila)	protein-coding	0	0.306931
Merged-chr12-43619406-1	chr12	43619356	43619456	+	2.5	cIP2vsInput	Intergenic	Intergenic	590662	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	"DnaJ (Hsp40) homolog, subfamily B, member 9"	protein-coding	0	0.306931
Merged-chr12-4818196-1	chr12	4818146	4818246	+	2.5	cIP1vsInput	"intron (NM_025323, intron 1 of 3)"	"intron (NM_025323, intron 1 of 3)"	588	NM_025323	66055	Mm.102627	NM_025323	ENSMUSG00000037361	0610009D07Rik	6030419K15Rik|AV001342|Sf3b14	RIKEN cDNA 0610009D07 gene	protein-coding	0.01	0.366337
Merged-chr3-110979348-1	chr3	110979298	110979398	+	2.5	cIP2vsInput	Intergenic	Intergenic	-728350	NR_024139	99890	Mm.393526	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding	0	0.29703
Merged-chr2-157310767-1	chr2	157310717	157310817	+	2.5	cIP1vsInput	"intron (NM_019642, intron 10 of 16)"	URR1B|DNA|hAT-Charlie	-31218	NM_001039557	629499	Mm.384235	NM_001039557	ENSMUSG00000074627	Mroh8	4922505G16Rik	maestro heat-like repeat family member 8	protein-coding	0	0.386139
Merged-chr17-84541519-1	chr17	84541469	84541569	+	2.5	cIP2vsInput	"intron (NM_177606, intron 2 of 29)"	"intron (NM_177606, intron 2 of 29)"	29624	NM_177606	213556	Mm.215159	NM_177606	ENSMUSG00000040852	Plekhh2	AI256725|E030001K05|mKIAA2028	"pleckstrin homology domain containing, family H (with MyTH4 domain) member 2"	protein-coding	0	0.277228
Merged-chr11-100460515-1	chr11	100460465	100460565	+	2.5	cIP2vsInput	Intergenic	Intergenic	12267	NM_172565	217194	Mm.183320	NM_172565	ENSMUSG00000048732	Klhl11	BC011167|RP23-392I3.12	kelch-like 11	protein-coding	0.01	0.356436
Merged-chr1-68267406-1	chr1	68267356	68267456	+	2.5	cIP2vsInput	"intron (NM_010154, intron 16 of 26)"	"intron (NM_010154, intron 16 of 26)"	840653	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0	0.29703
Merged-chr6-100644059-1	chr6	100644009	100644109	+	2.5	cIP1vsInput	"intron (NM_181590, intron 6 of 10)"	"intron (NM_181590, intron 6 of 10)"	27098	NM_181590	72171	Mm.256022	NM_181590	ENSMUSG00000035378	Shq1	2810403P18Rik|Grim-1	SHQ1 homolog (S. cerevisiae)	protein-coding	0	0.316832
Merged-chr1-101484680-1	chr1	101484630	101484730	+	2.5	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	328912	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.356436
Merged-chr1-155603836-1	chr1	155603786	155603886	+	2.5	cIP1vsInput	"intron (NM_028250, intron 4 of 7)"	"intron (NM_028250, intron 4 of 7)"	45716	NM_026683	72482	Mm.288249	NM_001145781	ENSMUSG00000033701	Acbd6	0610010G04Rik|2610100E10Rik	acyl-Coenzyme A binding domain containing 6	protein-coding	0.01	0.316832
Merged-chr1-117212258-1	chr1	117212208	117212308	+	2.5	cIP1vsInput	Intergenic	Intergenic	1098874	NM_011650	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding	0.01	0.29703
Merged-chr6-124723031-1	chr6	124722981	124723081	+	2.5	cIP2vsInput	"intron (NM_001077705, intron 11 of 15)"	B4A|SINE|B4	-4641	NR_029792	723944		NR_029792	ENSMUSG00000065462	Mir200c	Mirn200c	microRNA 200c	miscRNA	0.02	0.50495
Merged-chr15-47668568-1	chr15	47668518	47668618	+	2.5	cIP1vsInput	"intron (NM_001081391, intron 49 of 70)"	"intron (NM_001081391, intron 49 of 70)"	1045263	NR_045811	75281	Mm.159487	NR_045811		4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	miscRNA	0	0.267327
Merged-chr14-34008948-1	chr14	34008898	34008998	+	2.5	cIP2vsInput	Intergenic	Lx5b|LINE|L1	-30184	NM_001013777	382867	Mm.343728	NM_001013777	ENSMUSG00000044519	Zfp488	Gm1206|Znf488	zinc finger protein 488	protein-coding	0.01	0.366337
Merged-chr4-96069153-1	chr4	96069103	96069203	+	2.5	cIP1vsInput	"intron (NM_145548, intron 2 of 8)"	"intron (NM_145548, intron 2 of 8)"	8387	NM_145548	230459	Mm.268175	NM_145548	ENSMUSG00000028571	Cyp2j13	-	"cytochrome P450, family 2, subfamily j, polypeptide 13"	protein-coding	0	0.336634
Merged-chr14-84152502-1	chr14	84152452	84152552	+	2.5	cIP2vsInput	Intergenic	Intergenic	-291061	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0.01	0.366337
Merged-chr3-78713927-1	chr3	78713877	78713977	+	2.5	cIP2vsInput	Intergenic	Lx|LINE|L1	431948	NM_001099624	76089	Mm.462396	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding	0	0.306931
Merged-chr4-43431889-1	chr4	43431839	43431939	+	2.5	cIP2vsInput	Intergenic	Intergenic	-2755	NM_177377	329831	Mm.454466	NM_001162381	ENSMUSG00000042788	Fam166b	4833436C18Rik	"family with sequence similarity 166, member B"	protein-coding	0.02	0.49505
Merged-chr12-41891620-1	chr12	41891570	41891670	+	2.5	cIP2vsInput	"intron (NM_053122, intron 2 of 2)"	"intron (NM_053122, intron 2 of 2)"	262856	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding	0.01	0.287129
Merged-chr7-16974333-1	chr7	16974283	16974383	+	2.5	cIP2vsInput	Intergenic	Intergenic	14538	NM_001007569	71691	Mm.275673	NM_001007569	ENSMUSG00000041141	Pnmal1	0710005I19Rik	PNMA-like 1	protein-coding	0.01	0.524752
Merged-chr19-30509376-1	chr19	30509326	30509426	+	2.5	cIP1vsInput	Intergenic	L1ME3F|LINE|L1	30303	NR_003650	546723	Mm.301509	NR_003650		Ppp1r2-ps3	EG546723|Gm5972	"protein phosphatase 1, regulatory (inhibitor) subunit 2, pseudogene 3"	pseudo	0.02	0.29703
Merged-chr1-147052450-1	chr1	147052400	147052500	+	2.5	cIP2vsInput	Intergenic	Intergenic	554763	NM_001145807	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0.01	0.366337
Merged-chr15-83595036-1	chr15	83594986	83595086	+	2.5	cIP2vsInput	"exon (NM_183017, exon 1 of 14)"	"exon (NM_183017, exon 1 of 14)"	121	NM_183017	223723	Mm.46778	NM_183017	ENSMUSG00000016757	Ttll12	BC055368|D430005B17	"tubulin tyrosine ligase-like family, member 12"	protein-coding	0.16	0.742574
Merged-chr8-60328216-1	chr8	60328166	60328266	+	2.5	cIP1vsInput	Intergenic	A-rich|Low_complexity|Low_complexity	-177908	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|mKat-2	aminoadipate aminotransferase	protein-coding	0	0.267327
Merged-chr3-104541806-1	chr3	104541756	104541856	+	2.5	cIP2vsInput	Intergenic	Intergenic	-29950	NM_001025067	269473	Mm.34855	NM_001025067	ENSMUSG00000032913	Lrig2	4632419I10Rik|BB096938	leucine-rich repeats and immunoglobulin-like domains 2	protein-coding	0.02	0.514851
Merged-chr10-55328075-1	chr10	55328025	55328125	+	2.5	cIP2vsInput	Intergenic	Intergenic	-778842	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding	0	0.316832
Merged-chr6-26007546-1	chr6	26007496	26007596	+	2.5	cIP1vsInput	Intergenic	Intergenic	76120	NR_040771	626904	Mm.126787	NR_040771		Gm20756	-	"predicted gene, 20756"	miscRNA	0	0.356436
Merged-chr10-65109052-1	chr10	65109002	65109102	+	2.5	cIP1vsInput	Intergenic	Intergenic	1015012	NR_038039	69433	Mm.23366	NR_038039		1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	miscRNA	0	0.366337
Merged-chr10-99655326-1	chr10	99655276	99655376	+	2.5	cIP2vsInput	"intron (NR_038019, intron 2 of 2)"	"intron (NR_038019, intron 2 of 2)"	-13406	NR_038018	100417125	Mm.391428	NR_038018		Gm18409	-	mediator of cell motility 1 pseudogene	pseudo	0	0.346535
Merged-chr6-92787759-1	chr6	92787709	92787809	+	2.5	cIP1vsInput	"intron (NM_175314, intron 27 of 29)"	"intron (NM_175314, intron 27 of 29)"	-81575	NM_001081146	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle homolog 2 (Drosophila)	protein-coding	0.03	0.485149
Merged-chr16-48351908-1	chr16	48351858	48351958	+	2.5	cIP2vsInput	Intergenic	Intergenic	41634	NM_028615	73703	Mm.27857	NM_028615	ENSMUSG00000072419	Dppa2	2410088E07Rik|C80932|D19Mgi18|ECAT15-2	developmental pluripotency associated 2	protein-coding	0	0.326733
Merged-chr2-14013551-1	chr2	14013501	14013601	+	2.5	cIP1vsInput	Intergenic	Intergenic	42484	NM_001012396	30963	Mm.241205	NM_001012396	ENSMUSG00000063275	Ptpla	HACD1	"protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"	protein-coding	0	0.326733
Merged-chr19-49738424-1	chr19	49738374	49738474	+	2.5	cIP1vsInput	Intergenic	Intergenic	940222	NM_001252501	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0	0.316832
Merged-chr11-43634310-1	chr11	43634260	43634360	+	2.5	cIP2vsInput	Intergenic	Intergenic	-32748	NM_008375	16204	Mm.142716	NM_008375	ENSMUSG00000020405	Fabp6	GT|I-15P|I-BABP|ILBP|ILBP3|Illbp	"fatty acid binding protein 6, ileal (gastrotropin)"	protein-coding	0.05	0.613861
Merged-chr5-73383452-1	chr5	73383402	73383502	+	2.5	cIP1vsInput	Intergenic	Arthur1|DNA|hAT-Tip100	-22626	NM_181323	231293	Mm.280211	NM_181323	ENSMUSG00000029154	Cwh43	C130090K23Rik|imds-60	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	protein-coding	0	0.425743
Merged-chr2-179698401-1	chr2	179698351	179698451	+	2.5	cIP1vsInput	"intron (NM_009867, intron 2 of 15)"	"intron (NM_009867, intron 2 of 15)"	255923	NM_009867	12561	Mm.184711	NM_009867	ENSMUSG00000000305	Cdh4	AW120700|R-Cadh|R-cadherin|Rcad	cadherin 4	protein-coding	0.02	0.653465
Merged-chr7-56751419-1	chr7	56751369	56751469	+	2.5	cIP1vsInput	"intron (NM_008074, intron 6 of 9)"	L1MD2|LINE|L1	511648	NM_021879	18431	Mm.137052	NM_021879	ENSMUSG00000030450	Oca2	D7H15S12|D7Icr28RN|D7Nic1|p	oculocutaneous albinism II	protein-coding	0.01	0.376238
Merged-chr3-135024433-1	chr3	135024383	135024483	+	2.5	cIP2vsInput	Intergenic	RLTR17D_Mm|LTR|ERVK	-188130	NM_173762	229841	Mm.161470	NM_173762	ENSMUSG00000045328	Cenpe	312kDa|AU019344|BC049989|C530022J18|CENP-E|Kif10	centromere protein E	protein-coding	0.02	0.376238
Merged-chr8-116347152-1	chr8	116347102	116347202	+	2.5	cIP2vsInput	Intergenic	MTE2b|LTR|ERVL-MaLR	-157863	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding	0.02	0.475248
Merged-chr7-94622425-1	chr7	94622375	94622475	+	2.5	cIP1vsInput	Intergenic	Intergenic	1542546	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0	0.336634
Merged-chr16-71875095-1	chr16	71875045	71875145	+	2.5	cIP1vsInput	Intergenic	Intergenic	625191	NR_040576	78221	Mm.399298	NR_040576		4930567J20Rik	-	RIKEN cDNA 4930567J20 gene	miscRNA	0	0.287129
Merged-chr3-49285522-1	chr3	49285472	49285572	+	2.5	cIP1vsInput	Intergenic	Tigger1|DNA|TcMar-Tigger	471794	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding	0.01	0.356436
Merged-chr8-84147858-1	chr8	84147808	84147908	+	2.5	cIP2vsInput	promoter-TSS (NM_145970)	promoter-TSS (NM_145970)	-105	NM_145970	212139	Mm.41424	NM_145970	ENSMUSG00000036686	Cc2d1a	BC016188|Freud-1|Tape	coiled-coil and C2 domain containing 1A	protein-coding	0.11	0.712871
Merged-chr2-14354756-1	chr2	14354706	14354806	+	2.5	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-33642	NM_001012305	277468	Mm.44662	NM_001012305	ENSMUSG00000036949	Slc39a12	AW046938|Gm731	"solute carrier family 39 (zinc transporter), member 12"	protein-coding	0	0.336634
Merged-chr1-160061239-1	chr1	160061189	160061289	+	2.5	cIP1vsInput	"intron (NM_001162896, intron 1 of 2)"	"intron (NM_001162896, intron 1 of 2)"	16679	NR_038030	75255	Mm.414845	NR_038030	ENSMUSG00000026729	4930562F07Rik	-	RIKEN cDNA 4930562F07 gene	miscRNA	0.01	0.485149
Merged-chr5-135369804-1	chr5	135369754	135369854	+	2.5	cIP1vsInput	promoter-TSS (NM_145414)	promoter-TSS (NM_145414)	-149	NM_145414	100609	Mm.281189	NM_145414	ENSMUSG00000000916	Nsun5	9830109N13Rik|AI326939|Nol1r|Wbscr20|Wbscr20a	"NOL1/NOP2/Sun domain family, member 5"	protein-coding	0.07	0.50495
Merged-chr16-42781234-1	chr16	42781184	42781284	+	2.5	cIP1vsInput	"intron (NR_040521, intron 1 of 3)"	"intron (NR_040521, intron 1 of 3)"	94353	NR_040521	75722	Mm.243747	NR_040521	ENSMUSG00000075070	4932412D23Rik	ENSMUSG00000075070|Gm10809	RIKEN cDNA 4932412D23 gene	miscRNA	0.04	0.376238
Merged-chr2-15346161-1	chr2	15346111	15346211	+	2.5	cIP2vsInput	Intergenic	Intergenic	290799	NM_029466	75869	Mm.174068	NM_029466		Arl5b	4930587A11Rik|AW146430|Arl8	ADP-ribosylation factor-like 5B	protein-coding	0	0.336634
Merged-chr2-79818066-1	chr2	79818016	79818116	+	2.5	cIP1vsInput	Intergenic	Intergenic	90333	NM_001009979	18573	Mm.40678	NM_001009978	ENSMUSG00000059173	Pde1a	AI987702|AW125737	"phosphodiesterase 1A, calmodulin-dependent"	protein-coding	0	0.326733
Merged-chr12-41084416-1	chr12	41084366	41084466	+	2.5	cIP2vsInput	Intergenic	Intergenic	401641	NM_001271708	16981	Mm.39913	NM_001271708	ENSMUSG00000036295	Lrrn3	NLRR-3	"leucine rich repeat protein 3, neuronal"	protein-coding	0	0.386139
Merged-chr10-13016939-1	chr10	13016889	13016989	+	2.5	cIP2vsInput	Intergenic	B1_Mur3|SINE|Alu	8489	NM_175102	66125	Mm.402225	NM_175102	ENSMUSG00000078348	Sf3b5	10kDa|1110005L13Rik|AU043053|Sf3b10	"splicing factor 3b, subunit 5"	protein-coding	0.01	0.435644
Merged-chr5-5229231-1	chr5	5229181	5229281	+	2.5	cIP1vsInput	"intron (NM_011074, intron 3 of 14)"	"intron (NM_011074, intron 3 of 14)"	151020	NM_011074	18647	Mm.404502	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding	0.01	0.287129
Merged-chr8-61206690-1	chr8	61206640	61206740	+	2.5	cIP2vsInput	Intergenic	Intergenic	-17481	NM_021506	59009	Mm.27949	NM_198678	ENSMUSG00000031642	Sh3rf1	2200003J05Rik|Posh|R75531|Sh3md2	SH3 domain containing ring finger 1	protein-coding	0	0.267327
Merged-chr16-78348344-1	chr16	78348294	78348394	+	2.5	cIP1vsInput	"intron (NM_009988, intron 7 of 7)"	"intron (NM_009988, intron 7 of 7)"	28413	NR_002700	654432	Mm.458574	NR_002700	ENSMUSG00000044645	Gm7334	EG654432	B-cell translocation gene 3 pseudogene	pseudo	0	0.277228
Merged-chr10-53088139-1	chr10	53088089	53088189	+	2.5	cIP1vsInput	"intron (NM_178675, intron 6 of 7)"	"intron (NM_178675, intron 6 of 7)"	-192131	NR_038015	100502820	Mm.55827	NR_038015		Gm19395	-	"predicted gene, 19395"	miscRNA	0	0.386139
Merged-chr10-42401013-1	chr10	42400963	42401063	+	2.5	cIP2vsInput	"intron (NM_145743, intron 6 of 12)"	"intron (NM_145743, intron 6 of 12)"	77552	NM_145743	215951	Mm.89646	NM_145743	ENSMUSG00000038302	Lace1	CG8520	lactation elevated 1	protein-coding	0	0.306931
Merged-chr6-19497252-1	chr6	19497202	19497302	+	2.5	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	630934	NM_001167757	75196	Mm.67665	NM_001167757	ENSMUSG00000029517	Ankrd7	4930532L20Rik|AV278427	ankyrin repeat domain 7	protein-coding	0	0.326733
Merged-chr1-57511916-1	chr1	57511866	57511966	+	2.5	cIP2vsInput	Intergenic	Intergenic	-105242	NM_001037742	68736	Mm.288490	NM_001037742	ENSMUSG00000048495	Tyw5	1110034B05Rik	tRNA-yW synthesizing protein 5	protein-coding	0	0.316832
Merged-chr17-92682618-1	chr17	92682568	92682668	+	2.5	cIP1vsInput	Intergenic	Intergenic	-516804	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0	0.366337
Merged-chr4-66865777-1	chr4	66865727	66865827	+	2.5	cIP2vsInput	Intergenic	Lx7|LINE|L1	37966	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding	0.01	0.39604
Merged-chr10-29559065-1	chr10	29559015	29559115	+	2.5	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-23198	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3 homolog (Xenopus laevis)	protein-coding	0	0.316832
Merged-chr10-91811985-1	chr10	91811935	91812035	+	2.5	cIP1vsInput	Intergenic	Intergenic	260200	NR_029812	723955		NR_029812	ENSMUSG00000065524	Mir135a-2	Mirn135a-2	microRNA 135a-2	miscRNA	0	0.336634
Merged-chr11-39494151-1	chr11	39494101	39494201	+	2.5	cIP1vsInput	Intergenic	Intergenic	-974106	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0.01	0.326733
Merged-chr2-78160642-1	chr2	78160592	78160692	+	2.5	cIP2vsInput	Intergenic	Intergenic	-76905	NM_177843	329436	Mm.235448	NM_177843		Gm14461	A830093M07|OTTMUSG00000016703	predicted gene 14461	protein-coding	0.01	0.316832
Merged-chr11-41988325-1	chr11	41988275	41988375	+	2.5	cIP2vsInput	"intron (NM_177408, intron 1 of 8)"	"intron (NM_177408, intron 1 of 8)"	12389	NM_177408	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2"	protein-coding	0.02	0.356436
Merged-chr9-21950492-1	chr9	21950442	21950542	+	2.5	cIP1vsInput	Intergenic	Intergenic	-5261	NM_025870	66962	Mm.46647	NM_025870	ENSMUSG00000051238	Swsap1	2310047B19Rik	SWIM type zinc finger 7 associated protein 1	protein-coding	0.04	0.574257
Merged-chr15-15545176-1	chr15	15545126	15545226	+	2.5	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-1232925	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0	0.326733
Merged-chr1-9829401-1	chr1	9829351	9829451	+	2.5	cIP2vsInput	"intron (NM_133220, intron 2 of 17)"	"intron (NM_133220, intron 2 of 17)"	-18880	NM_001037759	170755	Mm.336410	NM_001037759	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding	0	0.306931
Merged-chr15-59425776-1	chr15	59425726	59425826	+	2.5	cIP2vsInput	"intron (NM_001164604, intron 3 of 4)"	"intron (NM_001164604, intron 3 of 4)"	51578	NM_001164604	68501	Mm.27762	NM_001164604	ENSMUSG00000059586	Nsmce2	1110014D18Rik|AI661537	"non-SMC element 2 homolog (MMS21, S. cerevisiae)"	protein-coding	0.01	0.326733
Merged-chr5-146844988-1	chr5	146844938	146845038	+	2.5	cIP2vsInput	promoter-TSS (NM_026864)	promoter-TSS (NM_026864)	-83	NM_026864	68895	Mm.266978	NM_026864	ENSMUSG00000029641	Rasl11a	1110065D03Rik|AI852031	"RAS-like, family 11, member A"	protein-coding	0.12	0.752475
Merged-chr6-64359683-1	chr6	64359633	64359733	+	2.5	cIP2vsInput	"intron (NM_008167, intron 11 of 15)"	"intron (NM_008167, intron 11 of 15)"	-369463	NM_007500	11921	Mm.57229	NM_007500	ENSMUSG00000073043	Atoh1	Hath1|MATH-1|Math1|bHLHa14	atonal homolog 1 (Drosophila)	protein-coding	0	0.306931
Merged-chr7-115453482-1	chr7	115453432	115453532	+	2.5	cIP2vsInput	Intergenic	Intergenic	348127	NM_001277328	20679	Mm.487065	NM_001025559	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY-box containing gene 6	protein-coding	0.03	0.643564
Merged-chr10-46925962-1	chr10	46925912	46926012	+	2.5	cIP2vsInput	Intergenic	RLTR12B|LTR|ERVK	681213	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0	0.366337
Merged-chr2-54943660-1	chr2	54943610	54943710	+	2.5	cIP2vsInput	"intron (NM_173030, intron 9 of 12)"	"intron (NM_173030, intron 9 of 12)"	-493496	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK1|Kcnf3|Kir3.1	"potassium inwardly-rectifying channel, subfamily J, member 3"	protein-coding	0.01	0.326733
Merged-chr13-82819380-1	chr13	82819330	82819430	+	2.5	cIP2vsInput	Intergenic	L1MA4A|LINE|L1	-684654	NM_001170537	17260	Mm.487610	NM_001170537	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding	0	0.326733
Merged-chr3-76461797-1	chr3	76461747	76461847	+	2.5	cIP1vsInput	"intron (NM_178673, intron 6 of 15)"	"intron (NM_178673, intron 6 of 15)"	386214	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.316832
Merged-chr15-4764940-1	chr15	4764890	4764990	+	2.5	cIP1vsInput	"intron (NM_016704, intron 8 of 15)"	"intron (NM_016704, intron 8 of 15)"	37730	NM_016704	12274	Mm.20247	NM_016704	ENSMUSG00000022181	C6	AW111623	complement component 6	protein-coding	0.01	0.277228
Merged-chr4-144971090-1	chr4	144971040	144971140	+	2.5	cIP1vsInput	Intergenic	Intergenic	77953	NM_011303	20148	Mm.14063	NM_001172424	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding	0	0.306931
Merged-chr16-89104897-1	chr16	89104847	89104947	+	2.5	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-40895	NM_001276278	68637	Mm.384089	XM_003945561		1110025L11Rik	-	RIKEN cDNA 1110025L11 gene	protein-coding	0	0.336634
Merged-chr2-118598177-2	chr2	118598102	118598252	+	2.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_009773)	promoter-TSS (NM_009773)	-34	NM_009773	12236	Mm.29133	NM_009773	ENSMUSG00000040084	Bub1b	AU045529|BUBR1	"budding uninhibited by benzimidazoles 1 homolog, beta (S. cerevisiae)"	protein-coding	0.073333	0.549669
Merged-chr1-55930971-1	chr1	55930921	55931021	+	2.5	cIP1vsInput	promoter-TSS (NR_045837)	promoter-TSS (NR_045837)	-270	NR_045837	329159	Mm.98697	NR_045837		9130227L01Rik	-	RIKEN cDNA 9130227L01 gene	miscRNA	0	0.376238
Merged-chr9-28831080-1	chr9	28831030	28831130	+	2.5	cIP2vsInput	"intron (NM_177906, intron 4 of 7)"	L1MD|LINE|L1	1039811	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding	0	0.346535
Merged-chr4-137450691-1	chr4	137450641	137450741	+	2.5	cIP1vsInput	Intergenic	Intergenic	-2605	NM_027063	69380	Mm.272519	NM_027063	ENSMUSG00000041399	1700013G24Rik	AI507018	RIKEN cDNA 1700013G24 gene	protein-coding	0	0.415842
Merged-chr7-92690203-1	chr7	92690153	92690253	+	2.5	cIP1vsInput	Intergenic	Intergenic	-20291	NM_029078	74737	Mm.288645	NM_029078	ENSMUSG00000041328	Pcf11	2500001H09Rik|5730417B17Rik|C77803	cleavage and polyadenylation factor subunit homolog (S. cerevisiae)	protein-coding	0.01	0.405941
Merged-chr1-191855641-1	chr1	191855591	191855691	+	2.5	cIP2vsInput	Intergenic	Intergenic	34168	NM_010892	18005	Mm.403999	NM_010892	ENSMUSG00000026622	Nek2	AA617254|C77054	NIMA (never in mitosis gene a)-related expressed kinase 2	protein-coding	0.02	0.574257
Merged-chr7-52700596-1	chr7	52700546	52700646	+	2.5	cIP2vsInput	Intergenic	Intergenic	-684880	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding	0.01	0.346535
Merged-chr17-81722963-1	chr17	81722913	81723013	+	2.5	cIP2vsInput	"intron (NM_011406, intron 1 of 10)"	"intron (NM_011406, intron 1 of 10)"	15414	NM_001112798	20541	Mm.489060	NM_001112798		Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	"solute carrier family 8 (sodium/calcium exchanger), member 1"	protein-coding	0	0.386139
Merged-chr3-150931856-1	chr3	150931806	150931906	+	2.5	cIP2vsInput	Intergenic	(CATAT)n|Simple_repeat|Simple_repeat	-506026	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0	0.19802
Merged-chr5-41515913-1	chr5	41515863	41515963	+	2.5	cIP2vsInput	Intergenic	L1M4|LINE|L1	192242	NM_027295	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	"RAB28, member RAS oncogene family"	protein-coding	0	0.326733
Merged-chr2-55705568-1	chr2	55705518	55705618	+	2.5	cIP2vsInput	Intergenic	Lx9|LINE|L1	268412	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK1|Kcnf3|Kir3.1	"potassium inwardly-rectifying channel, subfamily J, member 3"	protein-coding	0	0.336634
Merged-chr10-88260786-1	chr10	88260736	88260836	+	2.5	cIP1vsInput	Intergenic	Intergenic	59689	NM_027487	67282	Mm.208465	NM_001122960	ENSMUSG00000020056	Ccdc53	2900091E11Rik|5730495F03Rik	coiled-coil domain containing 53	protein-coding	0	0.267327
Merged-chr17-31964699-1	chr17	31964649	31964749	+	2.5	cIP1vsInput	"intron (NM_028902, intron 7 of 7)"	L1_Mur2|LINE|L1	69809	NM_028902	74377	Mm.75856	NM_028902	ENSMUSG00000002076	Hsf2bp	4932437G14Rik	heat shock transcription factor 2 binding protein	protein-coding	0	0.366337
Merged-chr1-46985575-1	chr1	46985525	46985625	+	2.5	cIP1vsInput	Intergenic	Intergenic	-132066	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.386139
Merged-chr14-83904659-1	chr14	83904609	83904709	+	2.5	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-538904	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0	0.39604
Merged-chr9-86948869-1	chr9	86948819	86948919	+	2.5	cIP1vsInput	Intergenic	RLTR17D_Mm|LTR|ERVK	-66668	NM_001037907	382089	Mm.92244	NM_001037907	ENSMUSG00000047897	Ripply2	C030002E08Rik|Gm1122	ripply2 homolog (zebrafish)	protein-coding	0	0.316832
Merged-chr10-53110275-1	chr10	53110225	53110325	+	2.5	cIP2vsInput	"3' UTR (NM_178675, exon 8 of 8)"	"3' UTR (NM_178675, exon 8 of 8)"	-169995	NR_038015	100502820	Mm.55827	NR_038015		Gm19395	-	"predicted gene, 19395"	miscRNA	0	0.356436
Merged-chr9-123644798-1	chr9	123644748	123644848	+	2.5	cIP2vsInput	"intron (NM_139142, intron 7 of 10)"	ORR1D1-int|LTR|ERVL-MaLR	-12233	NM_011731	22599	Mm.41963	NM_011731	ENSMUSG00000025243	Slc6a20b	AA986306|Sit1|Slc6a20|XT3|Xtrp3	"solute carrier family 6 (neurotransmitter transporter), member 20B"	protein-coding	0.01	0.326733
Merged-chr8-28849212-1	chr8	28849162	28849262	+	2.5	cIP2vsInput	"intron (NM_153135, intron 3 of 17)"	"intron (NM_153135, intron 3 of 17)"	370424	NM_153135	210801	Mm.248433	NM_153135	ENSMUSG00000063626	Unc5d	D930029E11Rik|Unc5h4|mKIAA1777	unc-5 homolog D (C. elegans)	protein-coding	0.01	0.366337
Merged-chr7-96411941-1	chr7	96411891	96411991	+	2.5	cIP1vsInput	"intron (NM_011858, intron 2 of 32)"	"intron (NM_011858, intron 2 of 32)"	-69977	NR_046043	670727	Mm.421352	NR_046043	ENSMUSG00000085751	Gm15412	OTTMUSG00000021245	predicted gene 15412	miscRNA	0	0.346535
Merged-chr9-17417886-1	chr9	17417836	17417936	+	2.5	cIP1vsInput	Intergenic	Intergenic	-874381	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	"cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1"	protein-coding	0	0.29703
Merged-chr11-38597871-1	chr11	38597821	38597921	+	2.5	cIP1vsInput	Intergenic	MusHAL1|LINE|L1	-77826	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0.01	0.39604
Merged-chr4-51819751-1	chr4	51819701	51819801	+	2.5	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	231359	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	miscRNA	0	0.326733
Merged-chr1-48617195-1	chr1	48617145	48617245	+	2.5	cIP1vsInput	Intergenic	Intergenic	-1763686	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.277228
Merged-chr11-86105999-1	chr11	86105949	86106049	+	2.5	cIP2vsInput	"intron (NM_178309, intron 16 of 19)"	"intron (NM_178309, intron 16 of 19)"	-81649	NR_046030	629393	Mm.372867	NR_046030		Gm20759	-	"predicted gene, 20759"	miscRNA	0.01	0.336634
Merged-chr11-43137144-1	chr11	43137094	43137194	+	2.5	cIP1vsInput	Intergenic	Tigger20a|DNA|TcMar-Tigger	-12733	NM_176999	319767	Mm.252339	NM_176999	ENSMUSG00000055415	Atp10b	5930426O13Rik|9030605H24Rik	"ATPase, class V, type 10B"	protein-coding	0	0.326733
Merged-chr4-28355819-1	chr4	28355769	28355869	+	2.5	cIP1vsInput	Intergenic	Intergenic	-457326	NM_001122889	13841	Mm.257266	NM_001122889	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding	0	0.306931
Merged-chr4-126375032-1	chr4	126374982	126375082	+	2.5	cIP1vsInput	"intron (NM_153402, intron 6 of 18)"	"intron (NM_153402, intron 6 of 18)"	-49833	NM_011902	24084	Mm.23895	NM_011902	ENSMUSG00000028845	Tekt2	AU014974|tektin-t	tektin 2	protein-coding	0	0.306931
Merged-chr1-73742428-1	chr1	73742378	73742478	+	2.5	cIP1vsInput	"intron (NR_045311, intron 6 of 8)"	"intron (NR_045311, intron 6 of 8)"	122038	NR_045311	109198	Mm.359721	NR_045311		6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	miscRNA	0	0.356436
Merged-chr14-53574896-1	chr14	53574846	53574946	+	2.5	cIP2vsInput	Intergenic	ETnERV2-int|LTR|ERVK	-91044	NM_001205242	100568452	Mm.486072	NM_001205242		A430107P09Rik	Va10	RIKEN cDNA A430107P09 gene	protein-coding	0	0.257426
Merged-chr12-91783639-1	chr12	91783589	91783689	+	2.5	cIP2vsInput	"intron (NM_175367, intron 1 of 6)"	"intron (NM_175367, intron 1 of 6)"	2797	NM_175367	108800	Mm.23125	NM_175367		Ston2	4933401N24Rik|AI425999|AW544599	stonin 2	protein-coding	0.01	0.306931
Merged-chr8-53258473-1	chr8	53258423	53258523	+	2.5	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-253229	NM_001205054	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding	0	0.306931
Merged-chr5-51320771-1	chr5	51320721	51320821	+	2.5	cIP1vsInput	Intergenic	Intergenic	233150	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PGC-1v|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	"peroxisome proliferative activated receptor, gamma, coactivator 1 alpha"	protein-coding	0	0.326733
Merged-chr19-24596490-1	chr19	24596440	24596540	+	2.5	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-40663	NM_008846	18719	Mm.217214	NM_008846	ENSMUSG00000024867	Pip5k1b	AI844522|Pip5k1a|Pipk5a|Pipk5b|STM7	"phosphatidylinositol-4-phosphate 5-kinase, type 1 beta"	protein-coding	0.01	0.326733
Merged-chr16-75064900-1	chr16	75064850	75064950	+	2.5	cIP1vsInput	Intergenic	Intergenic	502782	NM_177142	320355	Mm.99517	NM_001252513		Lipi	D930038D03Rik|lpd1	"lipase, member I"	protein-coding	0	0.346535
Merged-chr3-144058396-1	chr3	144058346	144058446	+	2.5	cIP1vsInput	Intergenic	Intergenic	143936	NM_001161770	16911	Mm.29187	NM_001161769	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding	0	0.336634
Merged-chr18-66254848-1	chr18	66254798	66254898	+	2.5	cIP2vsInput	"intron (NM_178793, intron 2 of 10)"	"intron (NM_178793, intron 2 of 10)"	-35515	NR_030467	751558		NR_030467		Mir694	Mirn694|mmu-mir-694	microRNA 694	miscRNA	0	0.29703
Merged-chr11-102097177-1	chr11	102097127	102097227	+	2.5	cIP1vsInput	Intergenic	Intergenic	4123	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding	0.07	0.712871
Merged-chr3-86941781-1	chr3	86941731	86941831	+	2.5	cIP1vsInput	Intergenic	Lx7|LINE|L1	-20897	NM_001195500	70762	Mm.44490	NM_001195496	ENSMUSG00000028078	Dclk2	6330415M09Rik|AU044875|CL2|CLICK2|Click-II|Dcamkl2	doublecortin-like kinase 2	protein-coding	0.01	0.326733
Merged-chr6-22905420-1	chr6	22905370	22905470	+	2.5	cIP1vsInput	"intron (NM_001081306, intron 1 of 29)"	"intron (NM_001081306, intron 1 of 29)"	29918	NM_001081306	19283	Mm.41639	NM_001081306	ENSMUSG00000068748	Ptprz1	AI850339|DSD-1-PG|PTPbeta|PTPzeta|Ptprz|Ptpz|RPTPz|Rptpbeta	"protein tyrosine phosphatase, receptor type Z, polypeptide 1"	protein-coding	0	0.287129
Merged-chr19-17583384-1	chr19	17583334	17583434	+	2.5	cIP1vsInput	"intron (NM_001190483, intron 13 of 37)"	MER2|DNA|TcMar-Tigger	189341	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding	0.01	0.336634
Merged-chr17-35126458-1	chr17	35126408	35126508	+	2.5	cIP2vsInput	promoter-TSS (NM_033477)	promoter-TSS (NM_033477)	56	NM_033477	114585	Mm.42070	NM_033477	ENSMUSG00000043311	D17H6S53E	G4|NG34	"DNA segment, Chr 17, human D6S53E"	protein-coding	0.06	0.594059
Merged-chr16-9636534-1	chr16	9636484	9636584	+	2.5	cIP2vsInput	"intron (NM_008170, intron 9 of 11)"	L1MC4a|LINE|L1	355999	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	"glutamate receptor, ionotropic, NMDA2A (epsilon 1)"	protein-coding	0	0.326733
Merged-chr6-66026093-1	chr6	66026043	66026143	+	2.5	cIP2vsInput	Intergenic	Lx9|LINE|L1	73522	NM_001161773	67653	Mm.389756	NR_003637	ENSMUSG00000036463	4930544G11Rik	-	RIKEN cDNA 4930544G11 gene	protein-coding	0	0.277228
Merged-chr5-69001552-1	chr5	69001502	69001602	+	2.5	cIP1vsInput	Intergenic	Kanga1d|DNA|TcMar-Tc2	340157	NM_175519	243043	Mm.234821	NM_175519	ENSMUSG00000037653	Kctd8	A730087N02Rik	potassium channel tetramerisation domain containing 8	protein-coding	0.01	0.405941
Merged-chr16-17508859-1	chr16	17508809	17508909	+	2.5	cIP2vsInput	promoter-TSS (NM_025808)	promoter-TSS (NM_025808)	-112	NM_025808	66863	Mm.161726	NM_025808	ENSMUSG00000022761	Lztr1	1200003E21Rik|AI591627|AW550890	"leucine-zipper-like transcriptional regulator, 1"	protein-coding	0.14	0.623762
Merged-chr16-80327322-1	chr16	80327272	80327372	+	2.5	cIP1vsInput	Intergenic	Intergenic	-873375	NM_001113208	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.29703
Merged-chr9-74051588-1	chr9	74051538	74051638	+	2.5	cIP1vsInput	Intergenic	L1MEc|LINE|L1	-58746	NM_001033500	546144	Mm.335289	NM_177908	ENSMUSG00000044976	Wdr72	AW558070|D230040E23	WD repeat domain 72	protein-coding	0	0.306931
Merged-chr17-60058359-1	chr17	60058309	60058409	+	2.5	cIP2vsInput	Intergenic	Intergenic	-1045037	NM_026497	67993	Mm.36507	NM_026497		Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0	0.29703
Merged-chr3-20339905-1	chr3	20339855	20339955	+	2.5	cIP2vsInput	"intron (NM_175086, intron 1 of 1)"	"intron (NM_175086, intron 1 of 1)"	27272	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	"angiotensin II receptor, type 1b"	protein-coding	0	0.405941
Merged-chr13-90877033-1	chr13	90876983	90877083	+	2.5	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	28322	NM_001145879	435376	Mm.292579	NM_001145879	ENSMUSG00000078958	Atp6ap1l	EG435376	"ATPase, H+ transporting, lysosomal accessory protein 1-like"	protein-coding	0	0.326733
Merged-chr5-83859800-1	chr5	83859750	83859850	+	2.5	cIP1vsInput	Intergenic	Intergenic	-504605	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	"trans-2,3-enoyl-CoA reductase-like"	protein-coding	0	0.29703
Merged-chr8-6485014-1	chr8	6484964	6485064	+	2.5	cIP1vsInput	Intergenic	Intergenic	-1379782	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.326733
Merged-chrX-11807623-1	chrX	11807573	11807673	+	2.5	cIP2vsInput	Intergenic	CpG	272930	NM_175045	71458	Mm.196328	NM_001168321	ENSMUSG00000040363	Bcor	5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding	0.11	0.742574
Merged-chr19-43479100-2	chr19	43479029	43479171	+	2.5	cIP1vsInput|cIP2vsInput	"intron (NM_031396, intron 6 of 10)"	"intron (NM_031396, intron 6 of 10)"	38664	NM_031396	83674	Mm.329864	NM_031396	ENSMUSG00000025189	Cnnm1	AI846314|Acdp1|CLP-1	cyclin M1	protein-coding	0.021127	0.447552
Merged-chr1-142443763-1	chr1	142443713	142443813	+	2.5	cIP1vsInput	Intergenic	RMER6A|LTR|ERVK	-1196934	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0.01	0.415842
Merged-chr15-10185062-1	chr15	10185012	10185112	+	2.5	cIP1vsInput	"intron (NM_011169, intron 1 of 9)"	L1_Rod|LINE|L1	7824	NM_011169	19116	Mm.442446	NR_045590	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding	0.01	0.306931
Merged-chr9-107201282-1	chr9	107201232	107201332	+	2.5	cIP2vsInput	"intron (NM_153413, intron 1 of 52)"	L1M2|LINE|L1	8475	NR_102273	100417434		NR_102273		AA543401	Mycs-like	"myc-like oncogene, s-myc protein pseudogene"	pseudo	0.01	0.356436
Merged-chr4-97266621-1	chr4	97266571	97266671	+	2.5	cIP1vsInput	Intergenic	MIR|SINE|MIR	-315322	NM_001122952	18027	Mm.409646	NM_001122952	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|NF1-A|NF1A	nuclear factor I/A	protein-coding	0	0.29703
Merged-chr2-55506518-1	chr2	55506468	55506568	+	2.5	cIP1vsInput	"intron (NM_008426, intron 2 of 2)"	"intron (NM_008426, intron 2 of 2)"	69362	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK1|Kcnf3|Kir3.1	"potassium inwardly-rectifying channel, subfamily J, member 3"	protein-coding	0.01	0.267327
Merged-chr3-64272100-1	chr3	64272050	64272150	+	2.5	cIP2vsInput	"intron (NM_001104614, intron 3 of 5)"	"intron (NM_001104614, intron 3 of 5)"	15317	NM_001104614	637004	Mm.469887	NM_001104614	ENSMUSG00000091572	Vmn2r3	EG637004	"vomeronasal 2, receptor 3"	protein-coding	0	0.346535
Merged-chr18-86722617-1	chr18	86722567	86722667	+	2.5	cIP2vsInput	Intergenic	Intergenic	9569	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding	0	0.316832
Merged-chr10-126950709-1	chr10	126950659	126950759	+	2.5	cIP1vsInput	Intergenic	Intergenic	-28008	NM_001113470	52468	Mm.29490	NM_001113470	ENSMUSG00000078429	Ctdsp2	AI586070|D10Ertd73e|OS-4|OS4|SCP2	"CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2"	protein-coding	0.03	0.49505
Merged-chr4-109883087-1	chr4	109883037	109883137	+	2.5	cIP2vsInput	"intron (NM_007983, intron 13 of 18)"	"intron (NM_007983, intron 13 of 18)"	-94938	NM_172296	242620	Mm.32825	NM_172296	ENSMUSG00000047143	Dmrta2	Dmrt5	doublesex and mab-3 related transcription factor like family A2	protein-coding	0.01	0.29703
Merged-chr15-57049290-1	chr15	57049240	57049340	+	2.5	cIP2vsInput	Intergenic	Intergenic	-354744	NM_008216	15117	Mm.5148	NM_008216	ENSMUSG00000022367	Has2	-	hyaluronan synthase 2	protein-coding	0.01	0.336634
Merged-chr9-119244521-1	chr9	119244471	119244571	+	2.5	cIP1vsInput	"intron (NR_045693, intron 16 of 18)"	"intron (NR_045693, intron 16 of 18)"	-12829	NR_033303	109280	Mm.261557	NM_175420	ENSMUSG00000092212	Slc22a13b-ps	9330176C04Rik|Slc22a13b	"solute carrier family 22 (organic cation transporter), member 13b, pseudogene"	pseudo	0.02	0.346535
Merged-chr14-14482236-1	chr14	14482186	14482286	+	2.5	cIP2vsInput	Intergenic	Lx8b|LINE|L1	135741	NM_008369	16188	Mm.425857	NM_008369	ENSMUSG00000068758	Il3ra	CD123|CDw123|SUT-1	"interleukin 3 receptor, alpha chain"	protein-coding	0.01	0.366337
Merged-chr7-61608187-1	chr7	61608137	61608237	+	2.5	cIP2vsInput	"intron (NR_045727, intron 1 of 4)"	Lx2|LINE|L1	7140	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	miscRNA	0	0.386139
Merged-chr9-27897046-1	chr9	27896996	27897096	+	2.5	cIP2vsInput	"intron (NM_177906, intron 1 of 7)"	(TATATG)n|Simple_repeat|Simple_repeat	105777	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding	0	0.346535
Merged-chr4-134036208-1	chr4	134036158	134036258	+	2.5	cIP2vsInput	Intergenic	L2a|LINE|L2	-17392	NM_145833	83557	Mm.302567	NM_145833	ENSMUSG00000050966	Lin28a	AL024421|ENSMUSG00000070700|Gm10299|Lin-28|Lin28|Tex17|lin-28A	lin-28 homolog A (C. elegans)	protein-coding	0.02	0.514851
Merged-chr17-26813501-2	chr17	26813422	26813581	+	2.5	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	28064	NM_008700	18091	Mm.41974	NM_008700	ENSMUSG00000015579	Nkx2-5	Csx|Nkx-2.5|Nkx2.5|tinman	"NK2 transcription factor related, locus 5 (Drosophila)"	protein-coding	0.018868	0.51875
Merged-chr3-95348327-1	chr3	95348277	95348377	+	2.5	cIP2vsInput	"intron (NM_018877, intron 4 of 21)"	"intron (NM_018877, intron 4 of 21)"	8875	NM_001163641	84505	Mm.490259	NM_001163641	ENSMUSG00000015697	Setdb1	AU022152|ESET|KMT1E|mKIAA0067	"SET domain, bifurcated 1"	protein-coding	0	0.336634
Merged-chr14-78330941-1	chr14	78330891	78330991	+	2.5	cIP1vsInput	Intergenic	Intergenic	-22898	NM_011613	21943	Mm.249221	NM_011613	ENSMUSG00000022015	Tnfsf11	Ly109l|ODF|OPG|OPGL|RANKL|Trance	"tumor necrosis factor (ligand) superfamily, member 11"	protein-coding	0.01	0.39604
Merged-chr3-96798960-1	chr3	96798910	96799010	+	2.5	cIP2vsInput	"3' UTR (NM_001163496, exon 5 of 5)"	"3' UTR (NM_001163496, exon 5 of 5)"	15561	NM_018767	54215	Mm.34693	NM_001163496	ENSMUSG00000038304	Cd160	AU045688|By55	CD160 antigen	protein-coding	0	0.316832
Merged-chr6-147302608-1	chr6	147302558	147302658	+	2.5	cIP2vsInput	Intergenic	Intergenic	-38523	NM_008970	19227	Mm.28440	NM_008970	ENSMUSG00000048776	Pthlh	PTH-like|Pthrp	parathyroid hormone-like peptide	protein-coding	0	0.326733
Merged-chr2-24664885-1	chr2	24664835	24664935	+	2.5	cIP2vsInput	"intron (NM_001042528, intron 20 of 46)"	"intron (NM_001042528, intron 20 of 46)"	98162	NM_001042528	12287	Mm.4424	NM_001042528	ENSMUSG00000004113	Cacna1b	AW050276|AW060892|AW822256|Cav2.2|Cchn1a|alpha(1B)	"calcium channel, voltage-dependent, N type, alpha 1B subunit"	protein-coding	0.03	0.683168
Merged-chr2-3489885-1	chr2	3489835	3489935	+	2.5	cIP2vsInput	"intron (NM_015765, intron 12 of 13)"	"intron (NM_015765, intron 12 of 13)"	-14899	NR_027509	64707	Mm.128273	NM_022724	ENSMUSG00000026646	Suv39h2	4930507K23Rik|AA536750|D030054H19Rik|D2Ertd544e|KMT1B	suppressor of variegation 3-9 homolog 2 (Drosophila)	protein-coding	0	0.366337
Merged-chr1-79896310-1	chr1	79896260	79896360	+	2.5	cIP1vsInput	Intergenic	Intergenic	-37645	NM_009255	20720	Mm.3093	NM_009255	ENSMUSG00000026249	Serpine2	B230326M24Rik|PAI-1|PI-7|PI7|PN-1|Spi4	"serine (or cysteine) peptidase inhibitor, clade E, member 2"	protein-coding	0	0.346535
Merged-chr10-25849845-1	chr10	25849795	25849895	+	2.5	cIP1vsInput	Intergenic	Intergenic	-12408	NR_045349	73803	Mm.258921	NR_045349		4930401C15Rik	-	RIKEN cDNA 4930401C15 gene	miscRNA	0.02	0.435644
Merged-chr12-96786065-1	chr12	96786015	96786115	+	2.5	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-738843	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0	0.336634
Merged-chr3-116064976-1	chr3	116064926	116065026	+	2.5	cIP2vsInput	Intergenic	Intergenic	56679	NM_001163514	58193	Mm.41739	NM_001163514	ENSMUSG00000027963	Extl2	3000001D04Rik|AW146439	exostoses (multiple)-like 2	protein-coding	0	0.326733
Merged-chr2-145645820-1	chr2	145645770	145645870	+	2.5	cIP2vsInput	Intergenic	Intergenic	-55375	NR_033220	408057	Mm.486711	NR_033220	ENSMUSG00000087594	BC039771	-	cDNA sequence BC039771	miscRNA	0	0.306931
Merged-chr16-59011979-1	chr16	59011929	59012029	+	2.5	cIP2vsInput	Intergenic	Intergenic	15926	NM_146321	258318	Mm.377434	NM_146321	ENSMUSG00000047960	Olfr186	MOR183-9	olfactory receptor 186	protein-coding	0.01	0.356436
Merged-chr4-81184344-1	chr4	81184294	81184394	+	2.5	cIP1vsInput	Intergenic	Intergenic	258461	NM_010820	17475	Mm.153039	NM_010820	ENSMUSG00000028402	Mpdz	AI225843|B930003D11Rik|MUPP1	multiple PDZ domain protein	protein-coding	0.01	0.277228
Merged-chr8-34623375-1	chr8	34623325	34623425	+	2.5	cIP2vsInput	"intron (NR_040706, intron 1 of 4)"	"intron (NR_040706, intron 1 of 4)"	16941	NR_040706	330734	Mm.149998	NR_040706		B930018H19Rik	B930018H19	RIKEN cDNA B930018H19 gene	miscRNA	0.01	0.306931
Merged-chr13-8263268-1	chr13	8263218	8263318	+	2.5	cIP2vsInput	"intron (NM_052977, intron 1 of 9)"	"intron (NM_052977, intron 1 of 9)"	60359	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	"adenosine deaminase, RNA-specific, B2"	protein-coding	0	0.346535
Merged-chr13-26906234-1	chr13	26906184	26906284	+	2.5	cIP2vsInput	Intergenic	Lx7|LINE|L1	104111	NR_039552	100628575		NR_039552		Mir3970	mmu-mir-3970|mu-mir-3970	microRNA 3970	miscRNA	0	0.366337
Merged-chr17-13729672-1	chr17	13729622	13729722	+	2.5	cIP2vsInput	"intron (NM_022311, intron 1 of 2)"	"intron (NM_022311, intron 1 of 2)"	-30869	NM_010806	17356	Mm.59167	NM_010806	ENSMUSG00000068036	Mllt4	5033403D15Rik|AF6|Af-6|Afadin|Gm314|I-afadin|S-afadin	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4"	protein-coding	0	0.356436
Merged-chr10-80103192-1	chr10	80103142	80103242	+	2.5	cIP1vsInput	promoter-TSS (NM_183426)	promoter-TSS (NM_183426)	-490	NM_183426	216161	Mm.262102	NM_183426	ENSMUSG00000035673	Sbno2	BC019206|F730040C21|Sno|Stno	strawberry notch homolog 2 (Drosophila)	protein-coding	0	0.564356
Merged-chr8-105254250-2	chr8	105254170	105254331	+	2.5	cIP1vsInput|cIP2vsInput	"exon (NM_178879, exon 2 of 2)"	"exon (NM_178879, exon 2 of 2)"	903	NM_001271915	97440	Mm.489600	NM_001271915	ENSMUSG00000069920	B3gnt9	3-Gn-T9|B3gnt9-ps|BGnT-9|C76565|C76566|beta-1|beta3Gn-T9	"UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9"	protein-coding	0.093168	0.685185
Merged-chr2-119787602-1	chr2	119787552	119787652	+	2.5	cIP1vsInput	promoter-TSS (NM_177294)	promoter-TSS (NM_177294)	-65	NM_001163701	68925	Mm.259223	NM_001163701	ENSMUSG00000034032	Rpap1	1190005L06Rik|A730023M06Rik|AU041788|AW107702|mKIAA1403	RNA polymerase II associated protein 1	protein-coding	0.12	0.722772
Merged-chr8-127843778-1	chr8	127843728	127843828	+	2.5	cIP1vsInput	Intergenic	Intergenic	-515295	NM_008737	18186	Mm.271745	NM_008737	ENSMUSG00000025810	Nrp1	C530029I03|NP-1|NPN-1|Npn1|Nrp	neuropilin 1	protein-coding	0.02	0.386139
Merged-chr10-54852391-1	chr10	54852341	54852441	+	2.5	cIP1vsInput	Intergenic	Intergenic	776469	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	"predicted gene, 16998"	miscRNA	0	0.267327
Merged-chr2-15977302-1	chr2	15977252	15977352	+	2.5	cIP2vsInput	Intergenic	Intergenic	-379020	NM_026162	67448	Mm.394655	NM_026162		Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding	0.01	0.287129
Merged-chr3-136455387-1	chr3	136455337	136455437	+	2.5	cIP1vsInput	Intergenic	Intergenic	-6038	NR_040592	70055	Mm.261063	NR_040592		1700030L20Rik	-	RIKEN cDNA 1700030L20 gene	miscRNA	0	0.306931
Merged-chr3-93762658-1	chr3	93762608	93762708	+	2.5	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-33740	NM_207272	399675	Mm.377924	XM_003946379	ENSMUSG00000060256	Tdpoz4	-	TD and POZ domain containing 4	protein-coding	0.01	0.415842
Merged-chr6-14103285-1	chr6	14103235	14103335	+	2.5	cIP1vsInput	Intergenic	Intergenic	231716	NR_045995	76311	Mm.367129	NR_045995	ENSMUSG00000097616	1110019D14Rik	-	RIKEN cDNA 1110019D14 gene	miscRNA	0	0.287129
Merged-chr3-4411956-1	chr3	4411906	4412006	+	2.5	cIP2vsInput	Intergenic	Intergenic	-386752	NR_045272	100503859	Mm.75172	NR_045272		1110015O18Rik	-	RIKEN cDNA 1110015O18 gene	miscRNA	0.01	0.356436
Merged-chr7-74820021-1	chr7	74819971	74820071	+	2.5	cIP2vsInput	Intergenic	MER44A|DNA|TcMar-Tigger	-265241	NM_001038643	108116	Mm.425467	NM_001038643	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	"solute carrier organic anion transporter family, member 3a1"	protein-coding	0	0.316832
Merged-chr7-46192506-1	chr7	46192456	46192556	+	2.5	cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	-12473	NM_011510	20927	Mm.259076	NM_011510	ENSMUSG00000040136	Abcc8	D930031B21Rik|SUR1|Sur	"ATP-binding cassette, sub-family C (CFTR/MRP), member 8"	protein-coding	0	0.455446
Merged-chr19-33391832-1	chr19	33391782	33391882	+	2.5	cIP1vsInput	"intron (NM_001167818, intron 1 of 6)"	CpG	463	NM_001167818	67795	Mm.204591	NM_001146342	ENSMUSG00000071573	Rnls	6530404N21Rik|AI452315|AW060440|C10orf59	"renalase, FAD-dependent amine oxidase"	protein-coding	0.09	0.653465
Merged-chr12-101610433-1	chr12	101610383	101610483	+	2.5	cIP1vsInput	"intron (NM_173023, intron 23 of 26)"	Lx2|LINE|L1	101140	NM_028924	74413	Mm.390521	NM_001082976	ENSMUSG00000021187	Tc2n	4933406D09Rik|Mtac2d1|Tac2-N	"tandem C2 domains, nuclear"	protein-coding	0	0.326733
Merged-chr8-6869144-1	chr8	6869094	6869194	+	2.5	cIP2vsInput	Intergenic	Intergenic	-1763912	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.277228
Merged-chr8-42788358-1	chr8	42788308	42788408	+	2.5	cIP1vsInput	Intergenic	L1M3|LINE|L1	353128	NM_177742	244448	Mm.64542	NM_177742	ENSMUSG00000031651	Triml1	4933403D14|BC050188	tripartite motif family-like 1	protein-coding	0.01	0.346535
Merged-chr13-65247575-1	chr13	65247525	65247625	+	2.5	cIP2vsInput	Intergenic	MurSatRep1|Unknown|Unknown	-31279	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding	0	0.356436
Merged-chr11-29161882-1	chr11	29161832	29161932	+	2.5	cIP2vsInput	TTS (NM_027869)	TTS (NM_027869)	-11025	NM_134034	104570	Mm.276386	NM_134034	ENSMUSG00000020463	Smek2	AW011752|AW557776|mKIAA1387	"SMEK homolog 2, suppressor of mek1 (Dictyostelium)"	protein-coding	0	0.366337
Merged-chr11-47685744-1	chr11	47685694	47685794	+	2.5	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-306442	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	"sarcoglycan, delta (dystrophin-associated glycoprotein)"	protein-coding	0	0.346535
Merged-chr9-62456250-1	chr9	62456200	62456300	+	2.5	cIP1vsInput	"intron (NM_175484, intron 2 of 11)"	"intron (NM_175484, intron 2 of 11)"	80794	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	"coronin, actin binding protein, 2B"	protein-coding	0.01	0.564356
Merged-chr16-9156497-1	chr16	9156447	9156547	+	2.5	cIP1vsInput	Intergenic	Intergenic	326397	NM_001081400	69053	Mm.426413	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding	0	0.386139
Merged-chr1-119561680-1	chr1	119561630	119561730	+	2.5	cIP2vsInput	"intron (NM_145506, intron 20 of 24)"	L1_Mur3|LINE|L1	35526	NM_146103	226351	Mm.439806	NM_146103		Tmem185b	2500001K11Rik	transmembrane protein 185B	protein-coding	0	0.336634
Merged-chr4-147618559-1	chr4	147618509	147618609	+	2.5	cIP1vsInput	"intron (NM_145078, intron 2 of 4)"	"intron (NM_145078, intron 2 of 4)"	23949	NM_145078	112422	Mm.440486	XM_003945706	ENSMUSG00000066000	2610305D13Rik	-	RIKEN cDNA 2610305D13 gene	protein-coding	0	0.326733
Merged-chr5-27769736-1	chr5	27769686	27769786	+	2.5	cIP1vsInput	"intron (NM_018878, intron 6 of 20)"	"intron (NM_018878, intron 6 of 20)"	21814	NM_018878	55982	Mm.444095	NM_018878	ENSMUSG00000002221	Paxip1	D5Ertd149e|PTIP	PAX interacting (with transcription-activation domain) protein 1	protein-coding	0.01	0.514851
Merged-chr9-83548309-1	chr9	83548259	83548359	+	2.5	cIP2vsInput	promoter-TSS (NM_172507)	promoter-TSS (NM_172507)	-29	NM_172507	212531	Mm.100125	NM_172507	ENSMUSG00000032261	Sh3bgrl2	A930014C21Rik|AA408038|B930089I21	SH3 domain binding glutamic acid-rich protein like 2	protein-coding	0.17	0.80198
Merged-chr10-61648606-1	chr10	61648556	61648656	+	2.5	cIP1vsInput	promoter-TSS (NM_026438)	promoter-TSS (NM_026438)	-15	NM_026438	67895	Mm.28897	NM_026438	ENSMUSG00000020089	Ppa1	2010317E03Rik|Pyp	pyrophosphatase (inorganic) 1	protein-coding	0.14	0.732673
Merged-chr4-90451169-1	chr4	90451119	90451219	+	2.5	cIP2vsInput	Intergenic	Intergenic	-89855	NR_033610	619842	Mm.484218	NR_033610	ENSMUSG00000080756	Gm12633	OTTMUSG00000007790	zinc finger protein 352 pseudogene	pseudo	0	0.376238
Merged-chr2-70010349-1	chr2	70010299	70010399	+	2.5	cIP2vsInput	"intron (NM_001081548, intron 32 of 38)"	"intron (NM_001081548, intron 32 of 38)"	-28777	NM_177376	329421	Mm.99648	NM_001042509	ENSMUSG00000042064	Myo3b	A430065P19Rik	myosin IIIB	protein-coding	0	0.257426
Merged-chr18-11758160-1	chr18	11758110	11758210	+	2.5	cIP1vsInput	Intergenic	Intergenic	-81114	NM_022021	63955	Mm.40717	NM_001146287	ENSMUSG00000040957	Cables1	Cables|ik3-1	CDK5 and Abl enzyme substrate 1	protein-coding	0	0.39604
Merged-chr17-82046908-1	chr17	82046858	82046958	+	2.5	cIP1vsInput	Intergenic	Intergenic	-308531	NM_011406	20541	Mm.489060	NM_001112798		Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	"solute carrier family 8 (sodium/calcium exchanger), member 1"	protein-coding	0	0.316832
Merged-chr4-20009305-1	chr4	20009255	20009355	+	2.5	cIP2vsInput	"intron (NM_015767, intron 1 of 4)"	"intron (NM_015767, intron 1 of 4)"	877	NM_015767	50500	Mm.24375	NM_015767	ENSMUSG00000073988	Ttpa	alpha-TTP	tocopherol (alpha) transfer protein	protein-coding	0	0.29703
Merged-chr9-107231989-1	chr9	107231939	107232039	+	2.5	cIP2vsInput	promoter-TSS (NM_153413)	promoter-TSS (NM_153413)	-80	NM_153413	208869	Mm.150259	NM_153413	ENSMUSG00000039716	Dock3	MOCA|PBP|mKIAA0299	dedicator of cyto-kinesis 3	protein-coding	0.13	0.712871
Merged-chr10-26575430-1	chr10	26575380	26575480	+	2.5	cIP2vsInput	Intergenic	Intergenic	99221	NR_033633	667572	Mm.482728	NR_033633		Gm8709	EG667572	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0.02	0.306931
Merged-chr18-81916656-1	chr18	81916606	81916706	+	2.5	cIP2vsInput	Intergenic	Intergenic	75424	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	miscRNA	0.06	0.534653
Merged-chr3-89858038-1	chr3	89857988	89858088	+	2.5	cIP2vsInput	"3' UTR (NM_172530, exon 6 of 6)"	"3' UTR (NM_172530, exon 6 of 6)"	26668	NM_172530	214547	Mm.225	NM_172530	ENSMUSG00000046280	She	9430022A14	src homology 2 domain-containing transforming protein E	protein-coding	0.01	0.415842
Merged-chr3-65441225-1	chr3	65441175	65441275	+	2.5	cIP2vsInput	Intergenic	Intergenic	-48672	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	"signal sequence receptor, gamma"	protein-coding	0.01	0.29703
Merged-chr16-37404605-1	chr16	37404555	37404655	+	2.5	cIP2vsInput	Intergenic	MLT1N2|LTR|ERVL-MaLR	-19647	NM_001114612	207227	Mm.403226	NM_001114611		Stxbp5l	9430094L02|A830015P08Rik|LLGL4|T2dm1|t2md1|tomosyn-2	syntaxin binding protein 5-like	protein-coding	0.01	0.29703
Merged-chr1-149901830-1	chr1	149901780	149901880	+	2.5	cIP1vsInput	"intron (NM_008869, intron 4 of 17)"	"intron (NM_008869, intron 4 of 17)"	59454	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0.01	0.267327
Merged-chr8-69716338-1	chr8	69716288	69716388	+	2.5	cIP1vsInput	"5' UTR (NM_181274, exon 1 of 5)"	"5' UTR (NM_181274, exon 1 of 5)"	148	NM_181274	66869	Mm.334581	NM_001039965		Zfp869	1200003I07Rik	zinc finger protein 869	protein-coding	0.02	0.366337
Merged-chr3-151093529-1	chr3	151093479	151093579	+	2.5	cIP1vsInput	Intergenic	Intergenic	-344353	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0	0.356436
Merged-chr12-37447658-1	chr12	37447608	37447708	+	2.5	cIP1vsInput	"intron (NM_178767, intron 12 of 12)"	"intron (NM_178767, intron 12 of 12)"	206019	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding	0	0.277228
Merged-chr10-103992073-1	chr10	103992023	103992123	+	2.5	cIP2vsInput	Intergenic	Intergenic	-150914	NM_001177535	100043292	Mm.339215	NM_001177535	ENSMUSG00000090854	Gm4340	-	predicted gene 4340	protein-coding	0	0.267327
Merged-chr15-42249424-1	chr15	42249374	42249474	+	2.5	cIP1vsInput	Intergenic	Intergenic	-379704	NM_175456	223513	Mm.148913	NM_175456	ENSMUSG00000042895	Abra	C130068O12Rik|STARS	actin-binding Rho activating protein	protein-coding	0	0.247525
Merged-chr4-111735816-1	chr4	111735766	111735866	+	2.5	cIP1vsInput	"intron (NM_026470, intron 1 of 12)"	"intron (NM_026470, intron 1 of 12)"	15806	NM_026470	67946	Mm.275526	NM_026470	ENSMUSG00000034401	Spata6	1700062C23Rik|AI790763|Hash|KRP|Mash	spermatogenesis associated 6	protein-coding	0	0.386139
Merged-chr19-9117545-1	chr19	9117495	9117595	+	2.5	cIP2vsInput	"intron (NM_025610, intron 4 of 6)"	ID4_|SINE|ID	18021	NM_025610	66514	Mm.272847	NM_025610		Asrgl1	2410004D18Rik|ALP|ALP1|AU040643|AW060375	asparaginase like 1	protein-coding	0.03	0.524752
Merged-chr7-67428828-1	chr7	67428778	67428878	+	2.5	cIP1vsInput	Intergenic	Intergenic	-55970	NM_001033713	17258	Mm.426509	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding	0	0.227723
Merged-chr9-44239758-1	chr9	44239708	44239808	+	2.5	cIP2vsInput	promoter-TSS (NM_001081369)	promoter-TSS (NM_001081369)	-919	NM_001081369	270150	Mm.347681	NM_001081369	ENSMUSG00000070306	Ccdc153	-	coiled-coil domain containing 153	protein-coding	0	0.475248
Merged-chr16-61675321-1	chr16	61675271	61675371	+	2.5	cIP1vsInput	Intergenic	Lx2|LINE|L1	-1069790	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0	0.326733
Merged-chr11-43433874-1	chr11	43433824	43433924	+	2.5	cIP2vsInput	"intron (NM_198936, intron 1 of 15)"	CpG	143	NM_198936	193116	Mm.28200	NM_148673	ENSMUSG00000020409	Slu7	AU018913|D11Ertd730e|D3Bwg0878e	SLU7 splicing factor homolog (S. cerevisiae)	protein-coding	0.09	0.643564
Merged-chr11-29946171-1	chr11	29946121	29946221	+	2.5	cIP1vsInput	"intron (NM_146016, intron 2 of 41)"	RLTR17D_Mm|LTR|ERVK	79862	NM_146016	237711	Mm.445271	NM_146016	ENSMUSG00000044072	Eml6	2900083P10Rik|C230094A16Rik|EMAP-6	echinoderm microtubule associated protein like 6	protein-coding	0.01	0.29703
Merged-chr11-14336327-1	chr11	14336277	14336377	+	2.5	cIP1vsInput	Intergenic	MTD|LTR|ERVL-MaLR	262898	NR_045918	73307	Mm.399291	NR_045918	ENSMUSG00000085561	1700046C09Rik	-	RIKEN cDNA 1700046C09 gene	miscRNA	0.01	0.336634
Merged-chr12-118199606-1	chr12	118199556	118199656	+	2.5	cIP1vsInput	promoter-TSS (NM_010060)	promoter-TSS (NM_010060)	-563	NM_010060	13411	Mm.390540	NM_010060	ENSMUSG00000018581	Dnahc11	b2b1203Clo|b2b1279Clo|b2b1289Clo|b2b1727Clo|b2b598Clo|iv|lrd	"dynein, axonemal, heavy chain 11"	protein-coding	0.01	0.336634
Merged-chrY-7004080-1	chrY	7004030	7004130	+	2.5	cIP1vsInput	Intergenic	Intergenic	163697	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.277228
Merged-chr6-42641320-1	chr6	42641270	42641370	+	2.5	cIP2vsInput	"intron (NM_146174, intron 2 of 7)"	"intron (NM_146174, intron 2 of 7)"	3721	NM_146174	232748	Mm.279659	NM_146174	ENSMUSG00000029851	Fam115c	-	"family with sequence similarity 115, member C"	protein-coding	0	0.346535
Merged-chr13-84439259-1	chr13	84439209	84439309	+	2.5	cIP2vsInput	Intergenic	Intergenic	216963	NM_175187	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding	0.01	0.336634
Merged-chr4-107950281-1	chr4	107950231	107950331	+	2.5	cIP1vsInput	Intergenic	Intergenic	-18053	NM_146255	242607	Mm.192040	NM_146255	ENSMUSG00000008932	Slc1a7	A930031E15Rik|Eaat5	"solute carrier family 1 (glutamate transporter), member 7"	protein-coding	0	0.356436
Merged-chr10-27412254-1	chr10	27412204	27412304	+	2.5	cIP2vsInput	"intron (NM_008481, intron 4 of 63)"	"intron (NM_008481, intron 4 of 63)"	204688	NM_008481	16773	Mm.256087	NM_008481	ENSMUSG00000019899	Lama2	5830440B04|dy|mKIAA4087|mer|merosin	"laminin, alpha 2"	protein-coding	0.01	0.306931
Merged-chr4-128669821-1	chr4	128669771	128669871	+	2.5	cIP2vsInput	"intron (NM_001195130, intron 1 of 14)"	L1MEf|LINE|L1	15119	NM_001195130	54383	Mm.490300	NM_001195083	ENSMUSG00000028796	Phc2	A3galt2|AA415044|D130050K19Rik|D4Ertd810e|Edr2|Mph2|p36	polyhomeotic-like 2 (Drosophila)	protein-coding	0	0.287129
Merged-chr7-71960885-1	chr7	71960835	71960935	+	2.5	cIP2vsInput	Intergenic	Intergenic	345710	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	"multiple C2 domains, transmembrane 2"	protein-coding	0.01	0.524752
Merged-chr3-143717756-1	chr3	143717706	143717806	+	2.5	cIP1vsInput	Intergenic	Intergenic	-5613	NR_040405	621809	Mm.360134	NR_040405		Gm6260	EG621809	predicted gene 6260	miscRNA	0	0.346535
Merged-chr6-138001730-1	chr6	138001680	138001780	+	2.5	cIP2vsInput	"intron (NM_177787, intron 7 of 8)"	"intron (NM_177787, intron 7 of 8)"	78186	NM_177787	277898	Mm.269823	NM_177787	ENSMUSG00000044378	Slc15a5	9830102E05Rik	"solute carrier family 15, member 5"	protein-coding	0.01	0.356436
Merged-chr12-39809238-1	chr12	39809188	39809288	+	2.5	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	228138	NM_007487	11861	Mm.12723	NM_001039515	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding	0	0.29703
Merged-chr7-116431751-1	chr7	116431701	116431801	+	2.5	cIP1vsInput	"intron (NM_011083, intron 1 of 32)"	"intron (NM_011083, intron 1 of 32)"	11707	NM_011083	18704	Mm.3810	NM_011083	ENSMUSG00000030660	Pik3c2a	Cpk-m|PI3KC2	"phosphatidylinositol 3-kinase, C2 domain containing, alpha polypeptide"	protein-coding	0.01	0.386139
Merged-chr1-41304768-1	chr1	41304718	41304818	+	2.5	cIP1vsInput	Intergenic	Intergenic	-123516	NR_040475	74897	Mm.243822	NR_040475		4930448I06Rik	-	RIKEN cDNA 4930448I06 gene	miscRNA	0	0.316832
Merged-chr10-72579012-1	chr10	72578962	72579062	+	2.5	cIP2vsInput	Intergenic	Intergenic	-75883	NM_025635	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding	0	0.39604
Merged-chr7-34912424-2	chr7	34912355	34912494	+	2.5	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008820)	promoter-TSS (NM_008820)	17	NM_008820	18624	Mm.69751	NM_008820	ENSMUSG00000063931	Pepd	Pep-4|Pep4	peptidase D	protein-coding	0.079137	0.671429
Merged-chr2-80732114-1	chr2	80732064	80732164	+	2.5	cIP2vsInput	Intergenic	Intergenic	92850	NM_001190179	69482	Mm.29200	NM_001190179		Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding	0	0.316832
Merged-chr15-8689187-1	chr15	8689137	8689237	+	2.5	cIP2vsInput	"intron (NM_148938, intron 2 of 9)"	"intron (NM_148938, intron 2 of 9)"	21620	NM_148938	20512	Mm.204834	NM_148938	ENSMUSG00000005360	Slc1a3	AI504299|B430115D02Rik|Eaat1|GLAST|GLAST-1|GLU-T|GluT-1|Gmt1|MGluT1	"solute carrier family 1 (glial high affinity glutamate transporter), member 3"	protein-coding	0	0.316832
Merged-chr4-36845730-1	chr4	36845680	36845780	+	2.5	cIP2vsInput	"intron (NM_001165999, intron 1 of 7)"	"intron (NM_001165999, intron 1 of 7)"	106014	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0	0.316832
Merged-chr1-81901914-1	chr1	81901864	81901964	+	2.5	cIP2vsInput	Intergenic	Intergenic	389525	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding	0	0.306931
Merged-chr2-154534900-1	chr2	154534850	154534950	+	2.5	cIP2vsInput	"exon (NM_009823, exon 11 of 11)"	"exon (NM_009823, exon 11 of 11)"	-14004	NM_029305	75480	Mm.440434	NM_029305	ENSMUSG00000038523	1700003F12Rik	-	RIKEN cDNA 1700003F12 gene	protein-coding	0.05	0.564356
Merged-chr3-39150527-1	chr3	39150477	39150577	+	2.5	cIP2vsInput	Intergenic	L1MA5|LINE|L1	263587	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT tumor suppressor homolog 4 (Drosophila)	protein-coding	0	0.326733
Merged-chr2-173198045-1	chr2	173197995	173198095	+	2.5	cIP2vsInput	Intergenic	Lx6|LINE|L1	20877	NM_021394	58203	Mm.116687	NM_001139519	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding	0	0.366337
Merged-chr10-75108062-1	chr10	75108012	75108112	+	2.5	cIP2vsInput	"intron (NM_001081412, intron 1 of 22)"	L1MEf|LINE|L1	47166	NM_001081412	110279		NM_001081412	ENSMUSG00000009681	Bcr	5133400C09Rik|AI561783|AI853148|mKIAA3017	breakpoint cluster region	protein-coding	0	0.306931
Merged-chr5-15902086-1	chr5	15902036	15902136	+	2.5	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-18320	NR_045974	75058	Mm.183467	NR_045974		4930519H02Rik	-	RIKEN cDNA 4930519H02 gene	miscRNA	0	0.287129
Merged-chr2-166564019-1	chr2	166563969	166564069	+	2.5	cIP2vsInput	Intergenic	Intergenic	116568	NR_015558	319684	Mm.399746	NR_015558		5031425F14Rik	-	RIKEN cDNA 5031425F14 gene	miscRNA	0	0.584158
Merged-chr2-67138188-1	chr2	67138138	67138238	+	2.5	cIP1vsInput	Intergenic	Intergenic	-35646	NM_001033477	383709	Mm.244520	NM_001033477		Gm1322	-	predicted gene 1322	protein-coding	0	0.29703
Merged-chr8-83189432-1	chr8	83189382	83189482	+	2.5	cIP1vsInput	"intron (NM_027758, intron 1 of 17)"	"intron (NM_027758, intron 1 of 17)"	24080	NM_027758	71310	Mm.24031	NM_001111304	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	"TBC1 domain family, member 9"	protein-coding	0	0.316832
Merged-chr3-158948493-1	chr3	158948443	158948543	+	2.5	cIP2vsInput	Intergenic	Intergenic	-127871	NR_040750	624759	Mm.491054	NR_040750		Gm20752	-	"predicted gene, 20752"	miscRNA	0	0.356436
Merged-chr13-84320396-1	chr13	84320346	84320446	+	2.5	cIP1vsInput	Intergenic	Intergenic	98100	NM_175187	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding	0	0.356436
Merged-chr9-54482769-1	chr9	54482719	54482819	+	2.5	cIP1vsInput	"intron (NM_172771, intron 1 of 43)"	B4|SINE|B4	18857	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding	0	0.39604
Merged-chr9-99080375-1	chr9	99080325	99080425	+	2.5	cIP1vsInput	"intron (NM_029094, intron 8 of 23)"	B3|SINE|B2	-44685	NM_001080776	382097	Mm.293727	NM_001080776	ENSMUSG00000044860	Gm1123	AV052824|CLSP	predicted gene 1123	protein-coding	0	0.465347
Merged-chr7-60166251-1	chr7	60166201	60166301	+	2.5	cIP1vsInput	Intergenic	Intergenic	-26032	NM_001082962	20646	Mm.274995	NM_001082961	ENSMUSG00000000948	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding	0	0.29703
Merged-chr5-88966397-1	chr5	88966347	88966447	+	2.5	cIP1vsInput	"intron (NM_001197147, intron 3 of 25)"	"intron (NM_001197147, intron 3 of 25)"	79137	NM_018760	54403	Mm.41044	NM_001136260	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	"solute carrier family 4 (anion exchanger), member 4"	protein-coding	0	0.346535
Merged-chr8-37709198-1	chr8	37709148	37709248	+	2.5	cIP1vsInput	"intron (NM_145841, intron 3 of 7)"	"intron (NM_145841, intron 3 of 7)"	543004	NR_029884	723860		NR_029884		Mir383	Mirn383|mmu-mir-383	microRNA 383	miscRNA	0.01	0.336634
Merged-chr10-106879017-1	chr10	106878967	106879067	+	2.5	cIP2vsInput	"intron (NM_177373, intron 21 of 31)"	"intron (NM_177373, intron 21 of 31)"	244647	NM_001142804	380660	Mm.336072	NM_001142804	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding	0	0.326733
Merged-chr13-55495350-1	chr13	55495300	55495400	+	2.5	cIP2vsInput	Intergenic	Intergenic	-7274	NM_001177372	56320	Mm.19016	NM_001177371	ENSMUSG00000034675	Dbn1	-	drebrin 1	protein-coding	0.03	0.633663
Merged-chr11-68566587-1	chr11	68566537	68566637	+	2.5	cIP2vsInput	Intergenic	Intergenic	10401	NM_146004	215723	Mm.131205	NM_146004	ENSMUSG00000048329	Mfsd6l	-	major facilitator superfamily domain containing 6-like	protein-coding	0	0.534653
Merged-chr3-57862494-1	chr3	57862444	57862544	+	2.5	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-14737	NM_019410	18645	Mm.271744	NM_019410	ENSMUSG00000027805	Pfn2	Pfn	profilin 2	protein-coding	0	0.336634
Merged-chr8-126421690-1	chr8	126421640	126421740	+	2.5	cIP2vsInput	promoter-TSS (NM_174987)	promoter-TSS (NM_174987)	-811	NM_174987	67892	Mm.31946	NM_174987	ENSMUSG00000051671	Coa6	1810063B05Rik|AI447995	cytochrome c oxidase assembly factor 6	protein-coding	0.01	0.376238
Merged-chr5-84881519-1	chr5	84881469	84881569	+	2.5	cIP2vsInput	Intergenic	MIRb|SINE|MIR	-464137	NM_007937	13839	Mm.438006	NM_007937		Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding	0	0.306931
Merged-chr15-66142057-1	chr15	66142007	66142107	+	2.5	cIP1vsInput	"intron (NM_152923, intron 1 of 14)"	RMER5|LTR|ERV1	144167	NM_152923	110862	Mm.255585	NM_152923	ENSMUSG00000056258	Kcnq3	-	"potassium voltage-gated channel, subfamily Q, member 3"	protein-coding	0.01	0.336634
Merged-chrX-140504075-1	chrX	140504025	140504125	+	2.5	cIP2vsInput	Intergenic	Intergenic	39110	NM_010286	14605	Mm.22216	NM_001077364	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	"TSC22 domain family, member 3"	protein-coding	0.06	0.594059
Merged-chr6-19565713-1	chr6	19565663	19565763	+	2.5	cIP1vsInput	Intergenic	Intergenic	699395	NM_001167757	75196	Mm.67665	NM_001167757	ENSMUSG00000029517	Ankrd7	4930532L20Rik|AV278427	ankyrin repeat domain 7	protein-coding	0	0.316832
Merged-chr14-75787071-1	chr14	75787021	75787121	+	2.5	cIP1vsInput	promoter-TSS (NM_026232)	promoter-TSS (NM_026232)	-34	NM_026232	67554	Mm.46067	NM_026232	ENSMUSG00000022003	Slc25a30	4933433D23Rik|AV025504|AV221431|AW319655|KMCP1	"solute carrier family 25, member 30"	protein-coding	0.13	0.70297
Merged-chr3-119261846-1	chr3	119261796	119261896	+	2.5	cIP1vsInput	"intron (NM_170778, intron 18 of 22)"	MIR|SINE|MIR	521542	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0	0.316832
Merged-chr1-27223011-1	chr1	27222961	27223061	+	2.5	cIP2vsInput	Intergenic	Lx8|LINE|L1	-535551	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding	0	0.376238
Merged-chr9-115813024-1	chr9	115812974	115813074	+	2.5	cIP2vsInput	Intergenic	MYSERV6-int|LTR|ERVK	-96431	NM_028638	73748	Mm.485018	NM_028638	ENSMUSG00000056880	Gadl1	1110027M19Rik	glutamate decarboxylase-like 1	protein-coding	0	0.336634
Merged-chrX-45302387-1	chrX	45302337	45302437	+	2.5	cIP2vsInput	Intergenic	Intergenic	211483	NM_026841	68800	Mm.336041	NM_026841	ENSMUSG00000037086	1110059M19Rik	-	RIKEN cDNA 1110059M19 gene	protein-coding	0	0.346535
Merged-chr15-42809222-1	chr15	42809172	42809272	+	2.5	cIP1vsInput	Intergenic	Intergenic	-132427	NM_009640	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding	0.01	0.326733
Merged-chr4-92039753-1	chr4	92039703	92039803	+	2.5	cIP1vsInput	Intergenic	Intergenic	107468	NM_027034	69314	Mm.55891	NM_027034	ENSMUSG00000028533	Izumo3	1700011H22Rik	IZUMO family member 3	protein-coding	0	0.346535
Merged-chr16-81819538-1	chr16	81819488	81819588	+	2.5	cIP1vsInput	Intergenic	RLTR22_Mur|LTR|ERVK	618841	NM_010954	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.277228
Merged-chr6-84673878-1	chr6	84673828	84673928	+	2.5	cIP2vsInput	"intron (NM_177077, intron 20 of 21)"	"intron (NM_177077, intron 20 of 21)"	-79970	NM_001177713	232174	Mm.255246	NM_001177713	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	"cytochrome P450, family 26, subfamily b, polypeptide 1"	protein-coding	0	0.306931
Merged-chr14-100024352-1	chr14	100024302	100024402	+	2.5	cIP1vsInput	"intron (NM_010636, intron 2 of 6)"	"intron (NM_010636, intron 2 of 6)"	125444	NM_010636	16597	Mm.458816	NM_010636		Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding	0	0.326733
Merged-chr5-60422425-1	chr5	60422375	60422475	+	2.5	cIP1vsInput	Intergenic	Intergenic	-436423	NR_040682	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0	0.316832
Merged-chr9-75107218-1	chr9	75107168	75107268	+	2.5	cIP2vsInput	"intron (NM_010864, intron 1 of 40)"	"intron (NM_010864, intron 1 of 40)"	36012	NM_010864	17918	Mm.3645	NM_010864	ENSMUSG00000034593	Myo5a	9630007J19Rik|AI413174|AI661011|Dbv|MVa|Myo5|MyoVA|Sev-1|d|d-120J|flail|flr	myosin VA	protein-coding	0	0.277228
Merged-chr5-149015508-1	chr5	149015458	149015558	+	2.5	cIP2vsInput	Intergenic	CpG	8546	NR_040429	100503307	Mm.188008	NR_040429	ENSMUSG00000086610	Gm15408	OTTMUSG00000021225	predicted gene 15408	miscRNA	0.04	0.663366
Merged-chr8-39458668-1	chr8	39458618	39458718	+	2.5	cIP1vsInput	Intergenic	Intergenic	160688	NR_044988	621335	Mm.208080	NR_044988		Gm6213	EG621335	predicted gene 6213	miscRNA	0	0.247525
Merged-chr2-174602432-1	chr2	174602382	174602482	+	2.5	cIP2vsInput	Intergenic	Intergenic	-41102	NM_001099328	100043757	Mm.48711	NM_001099328	ENSMUSG00000050600	Zfp831	ENSMUSG00000050600|OTTMUSG00000017459|Rp23-45p4.1	zinc finger protein 831	protein-coding	0.02	0.554455
Merged-chr5-135632646-1	chr5	135632596	135632696	+	2.5	cIP2vsInput	promoter-TSS (NM_146002)	promoter-TSS (NM_146002)	-8	NM_146002	215160	Mm.295438	NM_146002	ENSMUSG00000039917	Rhbdd2	0610011L13Rik|AI480532|Rhbdl7|Usmg1	rhomboid domain containing 2	protein-coding	0.05	0.683168
Merged-chr8-76316887-1	chr8	76316837	76316937	+	2.5	cIP1vsInput	Intergenic	Intergenic	583286	NR_028579	100039211	Mm.367571	NR_028579	ENSMUSG00000074235	Gm10649	ENSMUSG00000074235	predicted gene 10649	miscRNA	0	0.316832
Merged-chr2-77112344-1	chr2	77112294	77112394	+	2.5	cIP1vsInput	"intron (NM_001025576, intron 5 of 23)"	"intron (NM_001025576, intron 5 of 23)"	58291	NM_001025576	545428	Mm.26579	NM_001025576	ENSMUSG00000044033	Ccdc141	2610301F02Rik|CAMDI|ENSMUSG00000075261	coiled-coil domain containing 141	protein-coding	0	0.29703
Merged-chr17-87613195-1	chr17	87613145	87613245	+	2.5	cIP2vsInput	Intergenic	Intergenic	-22784	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding	0.04	0.485149
Merged-chr18-43945619-1	chr18	43945569	43945669	+	2.5	cIP2vsInput	Intergenic	L1Md_A|LINE|L1	-17622	NM_001081180	72432	Mm.35369	NM_001081180	ENSMUSG00000055561	Spink5	2310065D10Rik|AV238912|LEKT1|LETK1|VAKT1	"serine peptidase inhibitor, Kazal type 5"	protein-coding	0	0.336634
Merged-chr6-129366881-1	chr6	129366831	129366931	+	2.5	cIP2vsInput	Intergenic	Intergenic	16637	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	"C-type lectin domain family 12, member a"	protein-coding	0.01	0.306931
Merged-chr13-82354348-1	chr13	82354298	82354398	+	2.5	cIP2vsInput	Intergenic	Intergenic	571056	NM_007684	12626	Mm.12481	NM_007684	ENSMUSG00000021537	Cetn3	MmCEN3	centrin 3	protein-coding	0	0.356436
Merged-chr16-75851812-1	chr16	75851762	75851862	+	2.5	cIP2vsInput	Intergenic	Intergenic	57454	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	"SAM domain, SH3 domain and nuclear localization signals, 1"	protein-coding	0	0.316832
Merged-chr1-115149700-1	chr1	115149650	115149750	+	2.5	cIP1vsInput	Intergenic	MurERV4_19-int|LTR|ERVK	-535437	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0	0.306931
Merged-chrX-159988663-1	chrX	159988613	159988713	+	2.5	cIP2vsInput	"exon (NM_001163085, exon 1 of 29)"	"exon (NM_001163085, exon 1 of 29)"	230	NM_001163085	270672	Mm.386889	NM_001163085	ENSMUSG00000031303	Map3k15	BC031147|MEKK15	mitogen-activated protein kinase kinase kinase 15	protein-coding	0.15	0.772277
Merged-chr7-79715834-1	chr7	79715784	79715884	+	2.5	cIP2vsInput	Intergenic	CpG	-1648	NM_010626	16576	Mm.101633	NM_010626	ENSMUSG00000050382	Kif7	-	kinesin family member 7	protein-coding	0.12	0.821782
Merged-chr8-59498053-1	chr8	59498003	59498103	+	2.5	cIP2vsInput	Intergenic	L1VL4|LINE|L1	586298	NM_173411	234290	Mm.39244	NM_173411	ENSMUSG00000049946	BC030500	-	cDNA sequence BC030500	protein-coding	0	0.316832
Merged-chr16-17987021-1	chr16	17986971	17987071	+	2.5	cIP2vsInput	Intergenic	Intergenic	6456	NM_016983	22363	Mm.377118	NM_016983	ENSMUSG00000059280	Vpreb2	CD179b|VpreB1|Vpreb-2	pre-B lymphocyte gene 2	protein-coding	0.01	0.425743
Merged-chr10-82991843-1	chr10	82991793	82991893	+	2.5	cIP2vsInput	"intron (NM_021439, intron 1 of 2)"	"intron (NM_021439, intron 1 of 2)"	6346	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding	0.02	0.514851
Merged-chr1-137978109-1	chr1	137978059	137978159	+	2.5	cIP2vsInput	Intergenic	Intergenic	11470	NR_029820	723890		NR_029820	ENSMUSG00000065458	Mir181b-1	Mirn181b-1	microRNA 181b-1	miscRNA	0	0.346535
Merged-chr1-79339561-1	chr1	79339511	79339611	+	2.5	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	100529	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding	0	0.316832
Merged-chr13-118386729-1	chr13	118386679	118386779	+	2.5	cIP2vsInput	"exon (NM_021556, exon 1 of 5)"	"exon (NM_021556, exon 1 of 5)"	523	NM_021556	59054	Mm.143810	NM_021556	ENSMUSG00000021731	Mrps30	2610020A16Rik|AA968347|PAP|Pdcd9	mitochondrial ribosomal protein S30	protein-coding	0.11	0.693069
Merged-chr18-18663145-1	chr18	18663095	18663195	+	2.5	cIP2vsInput	Intergenic	Intergenic	-1082155	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	miscRNA	0	0.346535
Merged-chr10-31152936-1	chr10	31152886	31152986	+	2.5	cIP1vsInput	Intergenic	Intergenic	-160469	NM_027168	69692	Mm.245537	NM_027168	ENSMUSG00000000295	Hddc2	2310057G13Rik	HD domain containing 2	protein-coding	0	0.277228
Merged-chr13-80476316-1	chr13	80476266	80476366	+	2.5	cIP1vsInput	Intergenic	Intergenic	-407106	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0.02	0.257426
Merged-chr6-16348188-1	chr6	16348138	16348238	+	2.5	cIP1vsInput	Intergenic	Intergenic	550253	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding	0	0.346535
Merged-chr19-26037580-1	chr19	26037530	26037630	+	2.5	cIP1vsInput	Intergenic	Intergenic	365169	NM_145831	226049	Mm.275572	NM_145831	ENSMUSG00000048138	Dmrt2	Terra	doublesex and mab-3 related transcription factor 2	protein-coding	0	0.49505
Merged-chr5-54541519-1	chr5	54541469	54541569	+	2.5	cIP2vsInput	Intergenic	Intergenic	191527	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0	0.356436
Merged-chr6-117536477-1	chr6	117536427	117536527	+	2.5	cIP1vsInput	Intergenic	L1MA4|LINE|L1	215292	NR_045731	72263	Mm.443289	NR_045731		1700030F04Rik	-	RIKEN cDNA 1700030F04 gene	miscRNA	0.01	0.336634
Merged-chr7-98489937-1	chr7	98489887	98489987	+	2.5	cIP2vsInput	Intergenic	CpG	-4285	NM_001113379	434215	Mm.323057	XM_003689425	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding	0.12	0.742574
Merged-chr6-56753514-1	chr6	56753464	56753564	+	2.5	cIP1vsInput	"intron (NM_030235, intron 14 of 15)"	"intron (NM_030235, intron 14 of 15)"	38609	NM_030235	78937	Mm.105343	NM_030235	ENSMUSG00000029787	Avl9	5830411G16Rik|D730049P16Rik|mKIAA0241	AVL9 homolog (S. cerevisiase)	protein-coding	0	0.326733
Merged-chr2-180589500-1	chr2	180589450	180589550	+	2.5	cIP2vsInput	promoter-TSS (NM_031373)	promoter-TSS (NM_031373)	93	NM_031373	72075	Mm.250418	NM_031373	ENSMUSG00000049401	Ogfr	2010013E17Rik	opioid growth factor receptor	protein-coding	0.12	0.663366
Merged-chr19-10422427-1	chr19	10422377	10422477	+	2.5	cIP1vsInput	"intron (NM_173067, intron 4 of 9)"	"intron (NM_173067, intron 4 of 9)"	33337	NM_173068	54525	Mm.182654	NM_018801	ENSMUSG00000024743	Syt7	AI851541|B230112P13Rik	synaptotagmin VII	protein-coding	0.05	0.653465
Merged-chr15-9383611-1	chr15	9383561	9383661	+	2.5	cIP2vsInput	Intergenic	Intergenic	48013	NM_144845	223337	Mm.422853	NM_144845	ENSMUSG00000049152	Ugt3a2	AI313915	"UDP glycosyltransferases 3 family, polypeptide A2"	protein-coding	0	0.336634
Merged-chr10-51288900-1	chr10	51288850	51288950	+	2.5	cIP1vsInput	Intergenic	Intergenic	-191779	NM_008147	14727	Mm.439661	NM_008147	ENSMUSG00000089672	Gp49a	gp49	glycoprotein 49 A	protein-coding	0.01	0.386139
Merged-chr8-62227539-1	chr8	62227489	62227589	+	2.5	cIP2vsInput	Intergenic	Lx4A|LINE|L1	-104421	NM_011922	26359	Mm.42179	NM_001136089	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding	0	0.326733
Merged-chr10-103297578-1	chr10	103297528	103297628	+	2.5	cIP2vsInput	Intergenic	Intergenic	-61256	NM_029134	74978	Mm.483817	NM_001163559	ENSMUSG00000019892	Lrriq1	4930503E15Rik|Gm1557	leucine-rich repeats and IQ motif containing 1	protein-coding	0.02	0.386139
Merged-chr4-7321131-1	chr4	7321081	7321181	+	2.5	cIP2vsInput	Intergenic	Lx9|LINE|L1	-239557	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	miscRNA	0	0.316832
Merged-chr14-89348283-1	chr14	89348233	89348333	+	2.5	cIP2vsInput	Intergenic	Intergenic	-547941	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0	0.277228
Merged-chr2-155412504-1	chr2	155412454	155412554	+	2.5	cIP2vsInput	"intron (NM_001242558, intron 8 of 12)"	"intron (NM_001242558, intron 8 of 12)"	28279	NM_001242558	56406	Mm.27592	NM_001242558	ENSMUSG00000038369	Ncoa6	AIB3|ASC-2|ASC2|NRC|Ncoa7|PRIP|RAP250|mKIAA0181	nuclear receptor coactivator 6	protein-coding	0	0.316832
Merged-chr8-30173187-1	chr8	30173137	30173237	+	2.5	cIP2vsInput	Intergenic	L1M4|LINE|L1	-395208	NR_045856	71314	Mm.158666	NR_045856	ENSMUSG00000097044	4933433F19Rik	-	RIKEN cDNA 4933433F19 gene	miscRNA	0	0.326733
Merged-chr4-95129797-1	chr4	95129747	95129847	+	2.5	cIP2vsInput	Intergenic	Intergenic	-77575	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	Jun oncogene	protein-coding	0	0.346535
Merged-chr15-20838388-1	chr15	20838338	20838438	+	2.5	cIP1vsInput	Intergenic	Intergenic	-171638	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding	0	0.346535
Merged-chr8-75500606-1	chr8	75500556	75500656	+	2.5	cIP2vsInput	"intron (NM_001164235, intron 2 of 13)"	L1_Mur3|LINE|L1	51912	NM_001164235	71831	Mm.443238	NM_001164235	ENSMUSG00000031620	1700007B14Rik	-	RIKEN cDNA 1700007B14 gene	protein-coding	0	0.306931
Merged-chr6-133287478-2	chr6	133287384	133287573	+	2.45	cIP1vsInput|cIP2vsInput	Intergenic	MYSERV16_I-int|LTR|ERVK	-4738	NM_027784	232426	Mm.158689	NM_027784	ENSMUSG00000055594	5530400C23Rik	GRP	RIKEN cDNA 5530400C23 gene	protein-coding	0.005291	0.315789
Merged-chr17-31448691-2	chr17	31448638	31448744	+	2.45	cIP1vsInput|cIP2vsInput	"intron (NM_001163748, intron 7 of 18)"	B2_Mm2|SINE|B2	62457	NM_001163748	18585	Mm.10812	NM_001163748	ENSMUSG00000041119	Pde9a	PDE9A1	phosphodiesterase 9A	protein-coding	0	0.373832
Merged-chrY-6115422-2	chrY	6115372	6115473	+	2.45	cIP1vsInput|cIP2vsInput	Intergenic	MURVY-LTR|LTR|ERV1	1052355	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.009901	0.421569
Merged-chr9-62436084-2	chr9	62436024	62436144	+	2.45	cIP1vsInput|cIP2vsInput	"intron (NM_175484, intron 3 of 11)"	"intron (NM_175484, intron 3 of 11)"	94741	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	"acidic (leucine-rich) nuclear phosphoprotein 32 family, member A"	protein-coding	0.025	0.578512
Merged-chr9-41207879-2	chr9	41207793	41207965	+	2.45	cIP1vsInput|cIP2vsInput	"intron (NR_040392, intron 1 of 4)"	"intron (NR_040392, intron 1 of 4)"	1724	NR_040392	78500	Mm.275715	NR_040392		1700063D05Rik	-	RIKEN cDNA 1700063D05 gene	miscRNA	0.011628	0.323699
Merged-chr17-46782632-2	chr17	46782544	46782720	+	2.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_025433)	promoter-TSS (NM_025433)	24	NM_025433	66229	Mm.218533	NM_025433	ENSMUSG00000063888	Rpl7l1	1500016H10Rik	ribosomal protein L7-like 1	protein-coding	0.068182	0.564972
Merged-chr6-58560151-2	chr6	58560096	58560206	+	2.45	cIP1vsInput|cIP2vsInput	Intergenic	Lx6|LINE|L1	-36521	NM_011920	26357	Mm.333096	NM_011920	ENSMUSG00000029802	Abcg2	ABC15|ABCP|AI428558|BCRP|Bcrp1|MXR|MXR1	"ATP-binding cassette, sub-family G (WHITE), member 2"	protein-coding	0	0.297297
Merged-chr5-36661535-2	chr5	36661480	36661590	+	2.45	cIP1vsInput|cIP2vsInput	"intron (NM_001081232, intron 2 of 8)"	"intron (NM_001081232, intron 2 of 8)"	34434	NM_001081232	320661	Mm.486203	NM_001081232	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232|mKIAA0232	"DNA segment, Chr 5, ERATO Doi 579, expressed"	protein-coding	0	0.342342
Merged-chr11-7178939-2	chr11	7178880	7178999	+	2.45	cIP1vsInput|cIP2vsInput	TTS (NM_009622)	TTS (NM_009622)	9630	NR_045101	100041347	Mm.300962	NR_045101		Gm11985	OTTMUSG00000005133	predicted gene 11985	miscRNA	0.008403	0.483333
Merged-chrY-6699448-2	chrY	6699397	6699499	+	2.45	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	468329	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.009804	0.339806
Merged-chr4-139469236-2	chr4	139469160	139469313	+	2.45	cIP1vsInput|cIP2vsInput	"intron (NM_001160319, intron 90 of 105)"	"intron (NM_001160319, intron 90 of 105)"	-61312	NM_183148	212632	Mm.30464	NM_001205173	ENSMUSG00000041025	Iffo2	C79267	intermediate filament family orphan 2	protein-coding	0.013072	0.467532
Merged-chr7-46710641-2	chr7	46710585	46710697	+	2.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_030233)	promoter-TSS (NM_030233)	10	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding	0.125	0.663717
Merged-chr15-74487708-2	chr15	74487630	74487786	+	2.45	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-28488	NM_174991	107831	Mm.43133	NM_174991	ENSMUSG00000034730	Bai1	B830018M07Rik|R75078|mKIAA4089	brain-specific angiogenesis inhibitor 1	protein-coding	0.096154	0.675159
Merged-chr4-129542930-2	chr4	129542852	129543009	+	2.45	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008228)	promoter-TSS (NM_008228)	-284	NM_008228	433759	Mm.391033	NM_008228	ENSMUSG00000028800	Hdac1	HD1|Hdac1-ps|MommeD5|RPD3	histone deacetylase 1	protein-coding	0.082803	0.626582
Merged-chr12-33593652-1	chr12	33593602	33593702	+	2.4	cIP1vsInput	Intergenic	Intergenic	164028	NM_172253	28071	Mm.413045	NM_172253	ENSMUSG00000020561	Twistnb	2410173G11|2810024J17Rik|D16Wsu83e	TWIST neighbor	protein-coding	0.02	0.366337
Merged-chr14-16473988-1	chr14	16473938	16474038	+	2.4	cIP2vsInput	"intron (NM_011243, intron 3 of 7)"	Lx|LINE|L1	101222	NM_011243	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2|RARbeta2	"retinoic acid receptor, beta"	protein-coding	0	0.316832
Merged-chr3-39629322-1	chr3	39629272	39629372	+	2.4	cIP2vsInput	Intergenic	Intergenic	742382	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT tumor suppressor homolog 4 (Drosophila)	protein-coding	0.01	0.386139
Merged-chr10-24424507-1	chr10	24424457	24424557	+	2.4	cIP2vsInput	Intergenic	MIR|SINE|MIR	-170935	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding	0.01	0.376238
Merged-chr5-91739141-1	chr5	91739091	91739191	+	2.4	cIP2vsInput	Intergenic	RLTR18B|LTR|ERVK	28159	NR_045383	73452	Mm.396233	NR_045383		1700063O14Rik	-	RIKEN cDNA 1700063O14 gene	miscRNA	0	0.356436
Merged-chr19-27042696-1	chr19	27042646	27042746	+	2.4	cIP1vsInput	Intergenic	L1M4b|LINE|L1	156771	NM_001033407	329047	Mm.293289	NM_001033407	ENSMUSG00000074913	Gm815	-	predicted gene 815	protein-coding	0	0.326733
Merged-chr15-19870912-1	chr15	19870862	19870962	+	2.4	cIP2vsInput	Intergenic	Intergenic	795838	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding	0	0.29703
Merged-chr6-118585142-1	chr6	118585092	118585192	+	2.4	cIP2vsInput	Intergenic	L1MB3|LINE|L1	-22886	NM_001081112	232339	Mm.276116	NM_001081112	ENSMUSG00000007827	Ankrd26	5730521P14Rik|BC008111|mKIAA1074	ankyrin repeat domain 26	protein-coding	0.01	0.306931
Merged-chr4-37767191-1	chr4	37767141	37767241	+	2.4	cIP2vsInput	Intergenic	Intergenic	-815447	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0	0.316832
Merged-chr3-70669779-1	chr3	70669729	70669829	+	2.4	cIP2vsInput	Intergenic	Lx5|LINE|L1	137512	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	miscRNA	0	0.316832
Merged-chr4-78574066-1	chr4	78574016	78574116	+	2.4	cIP2vsInput	Intergenic	MERVL_2A-int|LTR|ERVL	-362171	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0.01	0.326733
Merged-chr2-64485056-1	chr2	64485006	64485106	+	2.4	cIP2vsInput	Intergenic	Intergenic	-387018	NM_001267847	60344	Mm.483676	NM_001267846	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding	0	0.336634
Merged-chr4-63496094-1	chr4	63496044	63496144	+	2.4	cIP2vsInput	promoter-TSS (NM_001008791)	promoter-TSS (NM_001008791)	-103	NM_001276371	73750	Mm.300397	NM_001008791	ENSMUSG00000039137	Whrn	1110035G07Rik|AW122018|AW742671|C430046P22Rik|Dfnb31|wi	whirlin	protein-coding	0.11	0.772277
Merged-chrX-101532736-1	chrX	101532686	101532786	+	2.4	cIP2vsInput	promoter-TSS (NM_001081008)	promoter-TSS (NM_001081008)	1	NM_001081008	270627	Mm.261750	NM_001081008	ENSMUSG00000031314	Taf1	250kDa|AU015687|B430306D02Rik|Ccg-1|Ccg1|KAT4|N-TAF1|TAFII250|Taf2a	"TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor"	protein-coding	0.05	0.574257
Merged-chr3-148153382-1	chr3	148153332	148153432	+	2.4	cIP1vsInput	Intergenic	Intergenic	801253	NM_001081298	99633	Mm.462301	NM_001081298	ENSMUSG00000028184	Lphn2	AI450192|Gm619|Lec1|Lphh1|mKIAA0786	latrophilin 2	protein-coding	0.01	0.346535
Merged-chr12-40593752-1	chr12	40593702	40593802	+	2.4	cIP2vsInput	"intron (NM_172803, intron 1 of 52)"	"intron (NM_172803, intron 1 of 52)"	147699	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding	0.01	0.356436
Merged-chr7-99865549-1	chr7	99865499	99865599	+	2.4	cIP2vsInput	"intron (NM_001164258, intron 2 of 18)"	"intron (NM_001164258, intron 2 of 18)"	6331	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding	0.01	0.405941
Merged-chr6-58505246-1	chr6	58505196	58505296	+	2.4	cIP1vsInput	Intergenic	RLTR22_Mur|LTR|ERVK	-32368	NM_001166729	626828	Mm.480268	NM_001166729	ENSMUSG00000093379	Vmn1r31	EG626828|Gm6709	vomeronasal 1 receptor 31	protein-coding	0	0.29703
Merged-chr12-45740091-1	chr12	45740041	45740141	+	2.4	cIP2vsInput	Intergenic	Intergenic	-665608	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding	0	0.326733
Merged-chr9-3380751-1	chr9	3380701	3380801	+	2.4	cIP1vsInput	"intron (NM_026303, intron 10 of 11)"	"intron (NM_026303, intron 10 of 11)"	-23334	NM_027545	244672	Mm.245482	NM_027545		Cwf19l2	3230401L03Rik|9030209E10	"CWF19-like 2, cell cycle control (S. pombe)"	protein-coding	0	0.316832
Merged-chr5-3081133-1	chr5	3081083	3081183	+	2.4	cIP2vsInput	Intergenic	Lx2A1|LINE|L1	-263179	NM_009873	12571	Mm.399714	NM_009873		Cdk6	5830411I20|AI504062|Crk2	cyclin-dependent kinase 6	protein-coding	0	0.316832
Merged-chr10-83060250-1	chr10	83060200	83060300	+	2.4	cIP2vsInput	"intron (NM_021439, intron 1 of 2)"	"intron (NM_021439, intron 1 of 2)"	74753	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding	0.02	0.564356
Merged-chr6-101554769-1	chr6	101554719	101554819	+	2.4	cIP2vsInput	Intergenic	Intergenic	-176872	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding	0.01	0.356436
Merged-chr17-20596251-1	chr17	20596201	20596301	+	2.4	cIP1vsInput	promoter-TSS (NM_001104572)	promoter-TSS (NM_001104572)	8	NM_001104572	224582	Mm.469851	NM_001104572	ENSMUSG00000091259	Vmn2r110	EG224582	"vomeronasal 2, receptor 110"	protein-coding	0	0.336634
Merged-chr7-61295284-1	chr7	61295234	61295334	+	2.4	cIP1vsInput	Intergenic	Intergenic	320043	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	miscRNA	0	0.267327
Merged-chrY-10319405-1	chrY	10319355	10319455	+	2.4	cIP2vsInput	Intergenic	MTD|LTR|ERVL-MaLR	878443	NM_001199331	100040022	Mm.485767	NM_001199331	ENSMUSG00000095172	Gm20822	-	"predicted gene, 20822"	protein-coding	0	0.415842
Merged-chr2-170757559-1	chr2	170757509	170757609	+	2.4	cIP1vsInput	"intron (NM_029761, intron 1 of 7)"	"intron (NM_029761, intron 1 of 7)"	25752	NM_001163686	76829	Mm.41633	NM_001163686	ENSMUSG00000027560	Dok5	2700055C10Rik	docking protein 5	protein-coding	0.04	0.49505
Merged-chr1-28166937-1	chr1	28166887	28166987	+	2.4	cIP2vsInput	Intergenic	Intergenic	613315	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0	0.356436
Merged-chr10-8813453-1	chr10	8813403	8813503	+	2.4	cIP2vsInput	"intron (NM_175155, intron 4 of 19)"	(CA)n|Simple_repeat|Simple_repeat	72617	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding	0.08	0.554455
Merged-chr12-86855887-2	chr12	86855831	86855943	+	2.4	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	28927	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding	0.017857	0.628319
Merged-chr10-115700681-1	chr10	115700631	115700731	+	2.4	cIP1vsInput	Intergenic	Intergenic	-112901	NM_010195	14160	Mm.42103	NM_010195	ENSMUSG00000020140	Lgr5	FEX|Gpr49	leucine rich repeat containing G protein coupled receptor 5	protein-coding	0	0.356436
Merged-chr3-105156923-1	chr3	105156873	105156973	+	2.4	cIP1vsInput	Intergenic	Intergenic	90079	NM_029228	75269	Mm.307994	NM_029228	ENSMUSG00000051788	4930564D02Rik	-	RIKEN cDNA 4930564D02 gene	protein-coding	0	0.326733
Merged-chr17-91968498-1	chr17	91968448	91968548	+	2.4	cIP2vsInput	Intergenic	ORR1C1|LTR|ERVL-MaLR	-875696	NM_020252	18189	Mm.312068	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0	0.326733
Merged-chr3-44240770-1	chr3	44240720	44240820	+	2.4	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	1137490	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	miscRNA	0	0.346535
Merged-chr3-66332208-1	chr3	66332158	66332258	+	2.4	cIP2vsInput	Intergenic	Intergenic	-35371	NM_145820	72789	Mm.443526	NM_028357	ENSMUSG00000027831	Veph1	2810471M23Rik|Veph	ventricular zone expressed PH domain-containing 1	protein-coding	0.02	0.316832
Merged-chr13-74993902-1	chr13	74993852	74993952	+	2.4	cIP2vsInput	Intergenic	Intergenic	-96085	NM_013628	18548	Mm.1333	NM_013628	ENSMUSG00000021587	Pcsk1	Nec-1|Nec1|PC1|PC3|Phpp-1|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0.01	0.306931
Merged-chr3-143921684-1	chr3	143921634	143921734	+	2.4	cIP2vsInput	Intergenic	L1MEd|LINE|L1	-209541	NR_040405	621809	Mm.360134	NR_040405		Gm6260	EG621809	predicted gene 6260	miscRNA	0	0.326733
Merged-chr4-35847378-1	chr4	35847328	35847428	+	2.4	cIP1vsInput	"intron (NM_001166000, intron 8 of 8)"	"intron (NM_001166000, intron 8 of 8)"	-2174	NM_001166001	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0	0.336634
Merged-chr2-122919193-1	chr2	122919143	122919243	+	2.4	cIP1vsInput	Intergenic	Intergenic	137194	NM_021507	59010	Mm.28986	NM_001162503	ENSMUSG00000005803	Sqrdl	0610039J17Rik|4930557M22Rik	sulfide quinone reductase-like (yeast)	protein-coding	0	0.346535
Merged-chr7-54158627-1	chr7	54158577	54158677	+	2.4	cIP1vsInput	Intergenic	Intergenic	-676618	NM_178705	233271	Mm.474990	NM_178705		Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding	0	0.306931
Merged-chrX-7638643-1	chrX	7638593	7638693	+	2.4	cIP2vsInput	promoter-TSS (NM_009305)	promoter-TSS (NM_009305)	63	NM_009305	20977	Mm.223674	NM_009305	ENSMUSG00000031144	Syp	A230093K24Rik|AI848995|Syn|p38	synaptophysin	protein-coding	0.14	0.752475
Merged-chr15-41907174-1	chr15	41907124	41907224	+	2.4	cIP2vsInput	Intergenic	Intergenic	-37454	NM_175456	223513	Mm.148913	NM_175456	ENSMUSG00000042895	Abra	C130068O12Rik|STARS	actin-binding Rho activating protein	protein-coding	0	0.356436
Merged-chr12-8617188-1	chr12	8617138	8617238	+	2.4	cIP1vsInput	Intergenic	Intergenic	-18122	NM_177802	328059	Mm.46326	NM_001038660	ENSMUSG00000020600	Slc7a15	2010001P20Rik|9030221C07Rik|Arpat	"solute carrier family 7 (cationic amino acid transporter, y+ system), member 15"	protein-coding	0	0.267327
Merged-chr16-55863340-1	chr16	55863290	55863390	+	2.4	cIP1vsInput	"intron (NM_001134457, intron 3 of 5)"	"intron (NM_001134457, intron 3 of 5)"	-24699	NM_001159395	80859	Mm.247272	NM_001159394	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	"nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta"	protein-coding	0	0.455446
Merged-chr6-73223398-1	chr6	73223348	73223448	+	2.4	cIP2vsInput	Intergenic	Intergenic	-1767	NM_001164669	330355	Mm.333166	NM_001164669	ENSMUSG00000052861	Dnahc6	9830168K20|A730004I20Rik|mKIAA1697|mdhc6	"dynein, axonemal, heavy chain 6"	protein-coding	0	0.485149
Merged-chr5-85687897-1	chr5	85687847	85687947	+	2.4	cIP1vsInput	Intergenic	Intergenic	377686	NM_007683	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	Cenpc	centromere protein C1	protein-coding	0	0.366337
Merged-chr10-56572975-1	chr10	56572925	56573025	+	2.4	cIP2vsInput	Intergenic	Intergenic	195675	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	"gap junction protein, alpha 1"	protein-coding	0.01	0.316832
Merged-chr18-18784361-1	chr18	18784311	18784411	+	2.4	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-1203371	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	miscRNA	0	0.346535
Merged-chr14-8944950-1	chr14	8944900	8945000	+	2.4	cIP2vsInput	Intergenic	L1ME3|LINE|L1	278560	NR_045968	74859	Mm.84041	NR_045968	ENSMUSG00000097898	4930455B14Rik	1700027C12Rik	RIKEN cDNA 4930455B14 gene	miscRNA	0	0.29703
Merged-chr19-27410176-1	chr19	27410126	27410226	+	2.4	cIP1vsInput	"intron (NM_177474, intron 13 of 17)"	"intron (NM_177474, intron 13 of 17)"	19644	NM_177474	52874	Mm.261027	NM_177474	ENSMUSG00000041360	D19Bwg1357e	1110069H02Rik|AA675048|Kiaa0020	"DNA segment, Chr 19, Brigham & Women's Genetics 1357 expressed"	protein-coding	0	0.346535
Merged-chr11-28490617-1	chr11	28490567	28490667	+	2.4	cIP1vsInput	"intron (NM_181577, intron 2 of 4)"	MER103C|DNA|hAT-Charlie	93679	NM_001166661	216613	Mm.93759	NM_001166661	ENSMUSG00000032878	Ccdc85a	E030025D05Rik	coiled-coil domain containing 85A	protein-coding	0.01	0.326733
Merged-chr7-73275739-1	chr7	73275689	73275789	+	2.4	cIP1vsInput	Intergenic	Intergenic	-99781	NM_177740	244058	Mm.333943	NM_177740	ENSMUSG00000070509	Rgma	BC059072|C230063O06	"RGM domain family, member A"	protein-coding	0.03	0.465347
Merged-chr1-41718810-1	chr1	41718760	41718860	+	2.4	cIP1vsInput	Intergenic	Intergenic	-537558	NR_040475	74897	Mm.243822	NR_040475		4930448I06Rik	-	RIKEN cDNA 4930448I06 gene	miscRNA	0	0.435644
Merged-chr12-59762902-1	chr12	59762852	59762952	+	2.4	cIP1vsInput	Intergenic	Intergenic	-543419	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding	0	0.316832
Merged-chr1-99949201-1	chr1	99949151	99949251	+	2.4	cIP2vsInput	"intron (NM_172851, intron 2 of 23)"	L1VL2|LINE|L1	176436	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding	0	0.326733
Merged-chr11-36526565-1	chr11	36526515	36526615	+	2.4	cIP2vsInput	"intron (NM_011856, intron 2 of 28)"	"intron (NM_011856, intron 2 of 28)"	417678	NM_011856	23964	Mm.445432	NM_011856	ENSMUSG00000049336	Tenm2	2610040L17Rik|9330187F13Rik|D3Bwg1534e|Odz2|Odz3|Ten-m2|mKIAA1127	teneurin transmembrane protein 2	protein-coding	0.04	0.594059
Merged-chr16-96157952-1	chr16	96157902	96158002	+	2.4	cIP2vsInput	TTS (NM_207301)	TTS (NM_207301)	12533	NM_207301	71446	Mm.255063	NM_207301	ENSMUSG00000023147	Wrb	5530402J05Rik|C030018G21Rik|Chd5	tryptophan rich basic protein	protein-coding	0	0.445545
Merged-chr12-44339490-1	chr12	44339440	44339540	+	2.4	cIP1vsInput	"intron (NM_176930, intron 1 of 30)"	"intron (NM_176930, intron 1 of 30)"	10605	NM_001146031	319504	Mm.208439	NM_001146031	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuron-glia-CAM-related cell adhesion molecule	protein-coding	0	0.346535
Merged-chr5-34547502-1	chr5	34547452	34547552	+	2.4	cIP2vsInput	"intron (NM_001145858, intron 1 of 12)"	L1M4|LINE|L1	-2074	NM_001145859	24055	Mm.5012	NM_001136088	ENSMUSG00000054520	Sh3bp2	3BP2	SH3-domain binding protein 2	protein-coding	0	0.306931
Merged-chr12-4946114-1	chr12	4946064	4946164	+	2.4	cIP2vsInput	"intron (NM_001099628, intron 7 of 30)"	"intron (NM_001099628, intron 7 of 30)"	28761	NM_001099628	320817	Mm.210966	NM_001099628		Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	"ATPase family, AAA domain containing 2B"	protein-coding	0.01	0.386139
Merged-chr5-8509534-1	chr5	8509484	8509584	+	2.4	cIP2vsInput	"intron (NM_198620, intron 8 of 9)"	"intron (NM_198620, intron 8 of 9)"	86684	NM_178766	319653	Mm.146262	NM_178766	ENSMUSG00000054099	Slc25a40	B230315F11Rik	"solute carrier family 25, member 40"	protein-coding	0.01	0.356436
Merged-chr5-41029269-1	chr5	41029219	41029319	+	2.4	cIP1vsInput	Intergenic	Intergenic	678886	NM_027295	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	"RAB28, member RAS oncogene family"	protein-coding	0	0.356436
Merged-chr17-79448845-1	chr17	79448795	79448895	+	2.4	cIP1vsInput	Intergenic	Intergenic	29040	NR_033463	74622	Mm.311921	NR_033463		4930429F11Rik	-	RIKEN cDNA 4930429F11 gene	miscRNA	0.01	0.366337
Merged-chr1-46260053-1	chr1	46260003	46260103	+	2.4	cIP1vsInput	"intron (NM_001160386, intron 48 of 65)"	MMERVK9C_I-int|LTR|ERVK	193315	NM_001160386	227058	Mm.296880	NM_001160386	ENSMUSG00000041144	Dnahc7b	Gm107	"dynein, axonemal, heavy chain 7B"	protein-coding	0.01	0.316832
Merged-chr16-75460119-1	chr16	75460069	75460169	+	2.4	cIP1vsInput	Intergenic	Intergenic	107563	NM_177142	320355	Mm.99517	NM_001252513		Lipi	D930038D03Rik|lpd1	"lipase, member I"	protein-coding	0	0.227723
Merged-chr19-7246887-1	chr19	7246837	7246937	+	2.4	cIP2vsInput	Intergenic	Intergenic	-5665	NM_027643	70999	Mm.474361	NM_027643	ENSMUSG00000024764	Naa40	4931433E08Rik|AU023197|Nat11	"N(alpha)-acetyltransferase 40, NatD catalytic subunit, homolog (S. cerevisiae)"	protein-coding	0	0.376238
Merged-chrX-110474908-1	chrX	110474858	110474958	+	2.4	cIP1vsInput	Intergenic	L1MA9|LINE|L1	102155	NR_033597	634340	Mm.66709	NR_033597	ENSMUSG00000082853	Gm7134	EG634340	kinesin family member 18B pseudogene	pseudo	0	0.356436
Merged-chr10-94408943-1	chr10	94408893	94408993	+	2.4	cIP2vsInput	Intergenic	Intergenic	-105914	NM_172051	319880	Mm.23047	NM_001168684	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding	0.01	0.435644
Merged-chr19-24046726-1	chr19	24046676	24046776	+	2.4	cIP1vsInput	Intergenic	Intergenic	-15707	NM_001114174	381217	Mm.426078	NM_001114174	ENSMUSG00000071604	Fam189a2	AI414343|AI666772|Gm967	"family with sequence similarity 189, member A2"	protein-coding	0.03	0.455446
Merged-chr6-50365227-1	chr6	50365177	50365277	+	2.4	cIP2vsInput	"intron (NM_027881, intron 2 of 21)"	RMER17D|LTR|ERVK	17610	NM_027881	71720	Mm.44153	NM_001163645	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding	0.02	0.544554
Merged-chr11-47633046-1	chr11	47632996	47633096	+	2.4	cIP1vsInput	Intergenic	Intergenic	-253744	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	"sarcoglycan, delta (dystrophin-associated glycoprotein)"	protein-coding	0	0.405941
Merged-chr2-41144175-1	chr2	41144125	41144225	+	2.4	cIP2vsInput	"intron (NM_053011, intron 35 of 90)"	L1_Mur2|LINE|L1	1509423	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0	0.346535
Merged-chr6-42887435-1	chr6	42887385	42887485	+	2.4	cIP1vsInput	Intergenic	L1VL4|LINE|L1	-9018	NM_146273	258270	Mm.377404	NM_146273	ENSMUSG00000043119	Olfr448	MOR261-13	olfactory receptor 448	protein-coding	0	0.346535
Merged-chr1-181089718-1	chr1	181089668	181089768	+	2.4	cIP2vsInput	Intergenic	Intergenic	38481	NM_001033819	619326	Mm.355174	NM_001033819	ENSMUSG00000038768	9130409I23Rik	-	RIKEN cDNA 9130409I23 gene	protein-coding	0.01	0.366337
Merged-chr8-43087808-1	chr8	43087758	43087858	+	2.4	cIP1vsInput	Intergenic	Intergenic	53678	NM_177742	244448	Mm.64542	NM_177742	ENSMUSG00000031651	Triml1	4933403D14|BC050188	tripartite motif family-like 1	protein-coding	0	0.326733
Merged-chr1-48373116-1	chr1	48373066	48373166	+	2.4	cIP2vsInput	Intergenic	L1MC4|LINE|L1	-1519607	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.326733
Merged-chr13-102009907-1	chr13	102009857	102009957	+	2.4	cIP1vsInput	Intergenic	Intergenic	-241690	NM_001077495	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	AA414921|C530050K14|PI3K|p50alpha|p55alpha|p85alpha	"phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)"	protein-coding	0	0.336634
Merged-chr2-127241468-1	chr2	127241418	127241518	+	2.4	cIP1vsInput	"3' UTR (NM_025296, exon 7 of 7)"	"3' UTR (NM_025296, exon 7 of 7)"	6348	NM_025296	26371	Mm.45179	NM_025296	ENSMUSG00000003662	Ciao1	AW210570|Wdr39	cytosolic iron-sulfur protein assembly 1	protein-coding	0	0.29703
Merged-chr6-16459944-1	chr6	16459894	16459994	+	2.4	cIP1vsInput	Intergenic	LTR78B|LTR|ERV1	438497	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding	0	0.316832
Merged-chr12-95588597-1	chr12	95588547	95588647	+	2.4	cIP1vsInput	Intergenic	Intergenic	-103629	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0	0.336634
Merged-chr4-17787336-1	chr4	17787286	17787386	+	2.4	cIP2vsInput	Intergenic	Intergenic	-66146	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0	0.306931
Merged-chr3-81578065-1	chr3	81578015	81578115	+	2.4	cIP2vsInput	Intergenic	Lx10|LINE|L1	-354551	NM_177662	229445	Mm.254642	NM_177662	ENSMUSG00000028015	Ctso	A330105D01Rik|A430056C07|AI118514	cathepsin O	protein-coding	0	0.336634
Merged-chr1-8300175-1	chr1	8300125	8300225	+	2.4	cIP2vsInput	Intergenic	L1M2|LINE|L1	999555	NM_027671	71096	Mm.388998	NM_027671		Sntg1	4933426D16Rik|G1SYN|SYN4	"syntrophin, gamma 1"	protein-coding	0	0.336634
Merged-chr5-135256736-1	chr5	135256686	135256786	+	2.4	cIP1vsInput	Intergenic	RSINE1|SINE|B4	-5689	NM_010246	14371	Mm.6256	NM_010246	ENSMUSG00000049551	Fzd9	mfz9	frizzled homolog 9 (Drosophila)	protein-coding	0.03	0.49505
Merged-chr1-173819159-2	chr1	173819109	173819209	+	2.4	cIP1vsInput|cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-52240	NM_008329	15951	Mm.261270	NM_008329	ENSMUSG00000073489	Ifi204	Ifi16|p204	interferon activated gene 204	protein-coding	0	0.326733
Merged-chr9-94333968-1	chr9	94333918	94334018	+	2.4	cIP1vsInput	Intergenic	Intergenic	204113	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49	RIKEN cDNA 1190002N15 gene	protein-coding	0	0.306931
Merged-chr8-58228198-1	chr8	58228148	58228248	+	2.4	cIP1vsInput	"intron (NM_175032, intron 4 of 11)"	"intron (NM_175032, intron 4 of 11)"	472598	NM_001177534	100271928	Mm.484123	NM_001177534		Gm15881	OTTMUSG00000027193	predicted gene 15881	protein-coding	0.01	0.29703
Merged-chr1-106438660-1	chr1	106438610	106438710	+	2.4	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	266791	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.01	0.326733
Merged-chr15-22865611-1	chr15	22865561	22865661	+	2.4	cIP1vsInput	Intergenic	Intergenic	-150627	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding	0.01	0.29703
Merged-chr6-26244230-1	chr6	26244180	26244280	+	2.4	cIP1vsInput	Intergenic	L1MA6|LINE|L1	312804	NR_040771	626904	Mm.126787	NR_040771		Gm20756	-	"predicted gene, 20756"	miscRNA	0	0.326733
Merged-chr11-44647012-1	chr11	44646962	44647062	+	2.4	cIP1vsInput	"intron (NM_007897, intron 6 of 15)"	"intron (NM_007897, intron 6 of 15)"	28878	NM_007897	13591	Mm.440346	NM_007897		Ebf1	9830166E18Rik|AW990631|Ebf|O/E-1|Olf-1|Olf1	early B cell factor 1	protein-coding	0.01	0.346535
Merged-chr1-142491023-1	chr1	142490973	142491073	+	2.4	cIP1vsInput	Intergenic	L1M3|LINE|L1	-1149674	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0	0.287129
Merged-chr17-77782242-1	chr17	77782192	77782292	+	2.4	cIP2vsInput	Intergenic	Intergenic	-418006	NM_015800	50766	Mm.311912	NM_015800	ENSMUSG00000024074	Crim1	AU015004	cysteine rich transmembrane BMP regulator 1 (chordin like)	protein-coding	0.01	0.336634
Merged-chr14-39981199-1	chr14	39981149	39981249	+	2.4	cIP1vsInput	Intergenic	Intergenic	325536	NR_045936	73591	Mm.65499	NR_045936		1700109I08Rik	-	RIKEN cDNA 1700109I08 gene	miscRNA	0	0.326733
Merged-chr6-110717591-1	chr6	110717541	110717641	+	2.4	cIP2vsInput	"intron (NM_177328, intron 1 of 9)"	"intron (NM_177328, intron 1 of 9)"	71993	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0	0.316832
Merged-chr6-54391753-1	chr6	54391703	54391803	+	2.4	cIP2vsInput	"intron (NR_033635, intron 3 of 13)"	"intron (NR_033635, intron 3 of 13)"	38468	NR_033635	100042056	Mm.448157	NM_198118	ENSMUSG00000073067	9130019P16Rik	6430501H15Rik|OTTMUSG00000023151	RIKEN cDNA 9130019P16 gene	miscRNA	0.01	0.425743
Merged-chr11-25804912-1	chr11	25804862	25804962	+	2.4	cIP1vsInput	"intron (NR_027973, intron 2 of 5)"	"intron (NR_027973, intron 2 of 5)"	405664	NR_027973	70626	Mm.379180	NR_027973		5730522E02Rik	-	RIKEN cDNA 5730522E02 gene	miscRNA	0	0.366337
Merged-chr12-72038529-1	chr12	72038479	72038579	+	2.4	cIP1vsInput	Intergenic	Lx6|LINE|L1	32462	NM_181752	238252	Mm.390508	NM_181752	ENSMUSG00000043398	Gpr135	PAFR	G protein-coupled receptor 135	protein-coding	0.02	0.326733
Merged-chr19-15575360-1	chr19	15575310	15575410	+	2.4	cIP1vsInput	Intergenic	Intergenic	349262	NM_001205339	107272	Mm.470456	NM_001205339	ENSMUSG00000024640	Psat1	D8Ertd814e|EPIP|PSA|Psat	phosphoserine aminotransferase 1	protein-coding	0.01	0.346535
Merged-chr6-146535692-1	chr6	146535642	146535742	+	2.4	cIP1vsInput	Intergenic	Intergenic	-33469	NM_019923	16439	Mm.7800	NM_010586		Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	"inositol 1,4,5-triphosphate receptor 2"	protein-coding	0.01	0.405941
Merged-chr2-14192648-1	chr2	14192598	14192698	+	2.4	cIP1vsInput	"intron (NM_001081310, intron 2 of 3)"	"intron (NM_001081310, intron 2 of 3)"	18124	NM_001081310	625286	Mm.158781	NM_001081310	ENSMUSG00000061531	Tmem236	2010003H20Rik|Fam23a|Gm613	transmembrane protein 236	protein-coding	0	0.326733
Merged-chr1-9489269-1	chr1	9489219	9489319	+	2.4	cIP1vsInput	Intergenic	Lx3B|LINE|L1	-56139	NM_021511	59014	Mm.29061	NM_021511	ENSMUSG00000061024	Rrs1	5730466A07Rik|AA415037|D1Ertd701e|Rrr	RRS1 ribosome biogenesis regulator homolog (S. cerevisiae)	protein-coding	0	0.326733
Merged-chr2-105155301-1	chr2	105155251	105155351	+	2.4	cIP1vsInput	"intron (NM_144783, intron 5 of 9)"	"intron (NM_144783, intron 5 of 9)"	28772	NM_144783	22431	Mm.389339	NM_144783	ENSMUSG00000016458	Wt1	D630046I19Rik|Wt-1	Wilms tumor 1 homolog	protein-coding	0	0.376238
Merged-chr6-104052486-1	chr6	104052436	104052536	+	2.4	cIP2vsInput	Intergenic	Intergenic	-440558	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding	0	0.306931
Merged-chr15-51466559-1	chr15	51466509	51466609	+	2.4	cIP2vsInput	Intergenic	Intergenic	-70949	NR_045092	100502643	Mm.131987	NR_045092		Gm19303	-	"predicted gene, 19303"	miscRNA	0.01	0.336634
Merged-chr3-62637067-1	chr3	62637017	62637117	+	2.4	cIP1vsInput	Intergenic	L1VL2|LINE|L1	-31927	NM_177346	229357	Mm.95181	NM_177346		Gpr149	9630018L10Rik|PGR10	G protein-coupled receptor 149	protein-coding	0	0.287129
Merged-chr15-83350317-1	chr15	83350267	83350367	+	2.4	cIP1vsInput	promoter-TSS (NM_025445)	promoter-TSS (NM_025445)	-70	NM_025445	66251	Mm.258910	NM_025445	ENSMUSG00000054277	Arfgap3	0610009H19Rik|1810004P07Rik|1810035F16Rik|9130416J18Rik|Arfgap1	ADP-ribosylation factor GTPase activating protein 3	protein-coding	0.13	0.683168
Merged-chr1-65664059-1	chr1	65664009	65664109	+	2.4	cIP1vsInput	Intergenic	MLTR14|LTR|ERV1	-262463	NM_027010	12969	Mm.275362	NM_027010	ENSMUSG00000025945	Crygf	3110001K11Rik|Cryg-2|DGcry-2|Len-2	"crystallin, gamma F"	protein-coding	0.01	0.267327
Merged-chr12-67230334-1	chr12	67230284	67230384	+	2.4	cIP1vsInput	Intergenic	Intergenic	-7785	NM_207010	320772	Mm.227680	NM_001193266		Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding	0.01	0.336634
Merged-chr15-29266888-1	chr15	29266838	29266938	+	2.4	cIP2vsInput	Intergenic	L1MA5A|LINE|L1	-905705	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	"catenin (cadherin associated protein), delta 2"	protein-coding	0	0.366337
Merged-chr16-84315840-1	chr16	84315790	84315890	+	2.4	cIP1vsInput	Intergenic	Intergenic	-55303	NR_040567	75247	Mm.417813	NR_040567		4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	miscRNA	0.01	0.346535
Merged-chr17-72657420-1	chr17	72657370	72657470	+	2.4	cIP2vsInput	Intergenic	Intergenic	-53113	NM_007439	11682	Mm.311854	NM_007439	ENSMUSG00000055471	Alk	CD246|Tcrz	anaplastic lymphoma kinase	protein-coding	0.01	0.316832
Merged-chr13-17369758-1	chr13	17369708	17369808	+	2.4	cIP2vsInput	"intron (NM_138654, intron 9 of 13)"	"intron (NM_138654, intron 9 of 13)"	325007	NM_138654	192136	Mm.364180	NM_138654		5033411D12Rik	D17907	RIKEN cDNA 5033411D12 gene	protein-coding	0	0.356436
Merged-chr1-186489262-1	chr1	186489212	186489312	+	2.4	cIP2vsInput	Intergenic	Intergenic	216730	NM_009367	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	"transforming growth factor, beta 2"	protein-coding	0.02	0.326733
Merged-chr3-140820918-1	chr3	140820868	140820968	+	2.4	cIP1vsInput	Intergenic	L2a|LINE|L2	391437	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0	0.267327
Merged-chr3-62868494-1	chr3	62868444	62868544	+	2.4	cIP1vsInput	Intergenic	Intergenic	-263354	NM_177346	229357	Mm.95181	NM_177346		Gpr149	9630018L10Rik|PGR10	G protein-coupled receptor 149	protein-coding	0	0.346535
Merged-chr7-45682918-1	chr7	45682868	45682968	+	2.4	cIP2vsInput	"intron (NM_001271578, intron 3 of 3)"	"intron (NM_001271578, intron 3 of 3)"	-1496	NM_001033356	243967	Mm.291240	NM_001033356	ENSMUSG00000070564	Ntn5	Gm484	netrin 5	protein-coding	0.04	0.60396
Merged-chr10-127121186-1	chr10	127121136	127121236	+	2.4	cIP2vsInput	promoter-TSS (NM_001171026)	promoter-TSS (NM_001171026)	-26	NM_001171026	216440	Mm.295246	NM_001171026	ENSMUSG00000040462	Os9	4632413K17Rik|AU022351	amplified in osteosarcoma	protein-coding	0.07	0.613861
Merged-chr3-62641623-1	chr3	62641573	62641673	+	2.4	cIP1vsInput	Intergenic	Intergenic	-36483	NM_177346	229357	Mm.95181	NM_177346		Gpr149	9630018L10Rik|PGR10	G protein-coupled receptor 149	protein-coding	0	0.346535
Merged-chr1-72537160-1	chr1	72537110	72537210	+	2.4	cIP2vsInput	promoter-TSS (NM_001045533)	promoter-TSS (NM_001045533)	-596	NM_001045533	381270	Mm.337023	NM_001045533	ENSMUSG00000039372	4-Mar	BC056494|mKIAA1399	membrane-associated ring finger (C3HC4) 4	protein-coding	0.09	0.712871
Merged-chr5-57184389-1	chr5	57184339	57184439	+	2.4	cIP2vsInput	Intergenic	Intergenic	533530	NR_015588	319216	Mm.446765	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	miscRNA	0	0.356436
Merged-chr2-99655164-1	chr2	99655114	99655214	+	2.4	cIP2vsInput	Intergenic	B3|SINE|B2	-1969584	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding	0	0.425743
Merged-chr4-98261882-1	chr4	98261832	98261932	+	2.4	cIP2vsInput	Intergenic	Intergenic	121383	NM_053157	94043	Mm.331719	NM_053157	ENSMUSG00000028563	Tm2d1	2310026L18Rik|AA990549|Bbp	TM2 domain containing 1	protein-coding	0.01	0.356436
Merged-chr13-53377397-1	chr13	53377347	53377447	+	2.4	cIP2vsInput	promoter-TSS (NM_009269)	promoter-TSS (NM_009269)	-36	NM_009269	268656	Mm.240336	NM_009269	ENSMUSG00000021468	Sptlc1	AW552086|C77762|E030036H05|Lcb1	"serine palmitoyltransferase, long chain base subunit 1"	protein-coding	0.12	0.693069
Merged-chr17-34850188-1	chr17	34850138	34850238	+	2.4	cIP1vsInput	promoter-TSS (NM_138580)	promoter-TSS (NM_138580)	16	NM_021337	108077	Mm.18845	NM_178062	ENSMUSG00000040356	Skiv2l	4930534J06Rik|AW214248|Ddx13|SKI|Ski2w	superkiller viralicidic activity 2-like (S. cerevisiae)	protein-coding	0.11	0.683168
Merged-chr2-97590917-1	chr2	97590867	97590967	+	2.4	cIP2vsInput	"intron (NM_178725, intron 1 of 2)"	"intron (NM_178725, intron 1 of 2)"	123243	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.326733
Merged-chr3-147473151-1	chr3	147473101	147473201	+	2.4	cIP2vsInput	Intergenic	L1MC1|LINE|L1	620784	NM_027594	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|Ttll7s	"tubulin tyrosine ligase-like family, member 7"	protein-coding	0	0.346535
Merged-chr16-54641848-1	chr16	54641798	54641898	+	2.4	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	641389	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding	0	0.306931
Merged-chr2-43444669-1	chr2	43444619	43444719	+	2.4	cIP1vsInput	Intergenic	Intergenic	-110660	NM_027552	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding	0	0.326733
Merged-chr3-133721162-1	chr3	133721112	133721212	+	2.4	cIP2vsInput	Intergenic	ID_B1|SINE|B4	-176772	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding	0	0.415842
Merged-chr9-39161131-1	chr9	39161081	39161181	+	2.4	cIP1vsInput	Intergenic	Intergenic	-5179	NM_146326	258323	Mm.223019	NM_146326	ENSMUSG00000094970	Olfr943	MOR171-44	olfactory receptor 943	protein-coding	0	0.336634
Merged-chr1-105158656-1	chr1	105158606	105158706	+	2.4	cIP2vsInput	Intergenic	Intergenic	198054	NM_178779	320311	Mm.389162	NM_001160368	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding	0	0.386139
Merged-chr1-102857919-1	chr1	102857869	102857969	+	2.4	cIP1vsInput	Intergenic	Intergenic	1702151	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.39604
Merged-chr5-40403298-1	chr5	40403248	40403348	+	2.4	cIP1vsInput	Intergenic	Intergenic	-758667	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding	0	0.326733
Merged-chr11-120784148-1	chr11	120784098	120784198	+	2.4	cIP1vsInput	promoter-TSS (NM_145370)	promoter-TSS (NM_145370)	56	NM_009053	19719	Mm.871	NM_009053	ENSMUSG00000025158	Rfng	-	RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding	0.16	0.792079
Merged-chr16-94101471-1	chr16	94101421	94101521	+	2.4	cIP2vsInput	"intron (NM_011377, intron 3 of 10)"	"intron (NM_011377, intron 3 of 10)"	16211	NM_011377	20465	Mm.4775	NM_011377	ENSMUSG00000062713	Sim2	bHLHe15	single-minded homolog 2 (Drosophila)	protein-coding	0	0.316832
Merged-chr14-6156996-1	chr14	6156946	6157046	+	2.4	cIP1vsInput	Intergenic	Intergenic	130254	NM_001270812	100861615	Mm.399319	NM_001270812	ENSMUSG00000079396	LOC100861615	-	alpha takusan-like	protein-coding	0	0.217822
Merged-chr3-74566769-1	chr3	74566719	74566819	+	2.4	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-549492	NR_040450	100504692	Mm.394454	NR_040450		Gm20356	-	"predicted gene, 20356"	miscRNA	0	0.316832
Merged-chr2-57628634-1	chr2	57628584	57628684	+	2.4	cIP1vsInput	Intergenic	Intergenic	-369521	NM_172855	241391	Mm.484118	NM_172855	ENSMUSG00000026828	Galnt5	4832424J23	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5	protein-coding	0	0.366337
Merged-chr5-14000153-1	chr5	14000103	14000203	+	2.4	cIP1vsInput	Intergenic	L2|LINE|L2	-25123	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	"sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E"	protein-coding	0	0.386139
Merged-chr11-51805698-1	chr11	51805648	51805748	+	2.4	cIP2vsInput	Intergenic	Intergenic	42035	NM_025535	66397	Mm.196592	NM_025535	ENSMUSG00000020386	Sar1b	2310075M17Rik|2900019I22Rik|CMRD|Sara1b|Sara2|Sarb	SAR1 gene homolog B (S. cerevisiae)	protein-coding	0.02	0.574257
Merged-chr12-4464749-1	chr12	4464699	4464799	+	2.4	cIP1vsInput	"intron (NM_010881, intron 1 of 22)"	Charlie7|DNA|hAT-Charlie	12433	NM_010881	17977	Mm.301039	NM_010881	ENSMUSG00000020647	Ncoa1	KAT13A|SRC-1|SRC1|bHLHe74	nuclear receptor coactivator 1	protein-coding	0	0.316832
Merged-chr18-62586891-1	chr18	62586841	62586941	+	2.4	cIP1vsInput	"intron (NM_177829, intron 1 of 8)"	"intron (NM_177829, intron 1 of 8)"	9373	NM_001001803	408198	Mm.478742	NM_001001803	ENSMUSG00000060201	Spink7	EG408198|Ecg2	"serine peptidase inhibitor, Kazal type 7 (putative)"	protein-coding	0	0.207921
Merged-chr2-99598590-1	chr2	99598540	99598640	+	2.4	cIP2vsInput	Intergenic	Intergenic	-2026158	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding	0	0.366337
Merged-chr7-68961072-1	chr7	68961022	68961122	+	2.4	cIP2vsInput	Intergenic	L1ME1|LINE|L1	-211834	NM_025549	66412	Mm.251199	NM_001042592	ENSMUSG00000042659	Arrdc4	2410003C09Rik|AV216361	arrestin domain containing 4	protein-coding	0	0.346535
Merged-chr1-149278716-1	chr1	149278666	149278766	+	2.4	cIP1vsInput	Intergenic	Intergenic	682568	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0.01	0.287129
Merged-chr14-30746330-1	chr14	30746280	30746380	+	2.4	cIP1vsInput	"intron (NM_001166531, intron 2 of 21)"	"intron (NM_001166531, intron 2 of 21)"	30715	NM_001166532	54650	Mm.294662	NM_175254	ENSMUSG00000006527	Sfmbt1	4930442N21Rik|9330180L21Rik|AA536974|Sfmbt|Smr	Scm-like with four mbt domains 1	protein-coding	0	0.415842
Merged-chr6-58943429-1	chr6	58943379	58943479	+	2.4	cIP2vsInput	"intron (NM_153574, intron 15 of 17)"	"intron (NM_153574, intron 15 of 17)"	-36303	NM_021432	58243	Mm.389747	NM_021432	ENSMUSG00000055430	Nap1l5	1110020M21Rik	nucleosome assembly protein 1-like 5	protein-coding	0	0.306931
Merged-chr10-92669148-1	chr10	92669098	92669198	+	2.4	cIP1vsInput	Intergenic	Intergenic	53270	NM_008682	17997	Mm.2998	NM_008682	ENSMUSG00000019988	Nedd1	-	"neural precursor cell expressed, developmentally down-regulated gene 1"	protein-coding	0	0.326733
Merged-chr2-95716982-1	chr2	95716932	95717032	+	2.4	cIP2vsInput	Intergenic	Intergenic	-1278835	NM_007466	11800	Mm.486651	NM_007466	ENSMUSG00000027193	Api5	AAC-11|AI196452	apoptosis inhibitor 5	protein-coding	0	0.277228
Merged-chr7-75848421-1	chr7	75848371	75848471	+	2.4	cIP2vsInput	promoter-TSS (NM_029652)	promoter-TSS (NM_029652)	83	NM_029652	207952	Mm.206223	NM_001122780	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding	0.15	0.792079
Merged-chr13-29678588-1	chr13	29678538	29678638	+	2.4	cIP2vsInput	"intron (NM_144536, intron 8 of 15)"	B3|SINE|B2	177000	NM_144536	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding	0.01	0.346535
Merged-chr12-56330171-1	chr12	56330121	56330221	+	2.4	cIP2vsInput	"intron (NM_145442, intron 8 of 8)"	"intron (NM_145442, intron 8 of 8)"	15723	NM_145442	217588	Mm.25656	NM_145442	ENSMUSG00000021028	Mbip	4933408E06Rik	MAP3K12 binding inhibitory protein 1	protein-coding	0	0.326733
Merged-chr6-26932179-1	chr6	26932129	26932229	+	2.4	cIP1vsInput	Intergenic	Intergenic	1000753	NR_040771	626904	Mm.126787	NR_040771		Gm20756	-	"predicted gene, 20756"	miscRNA	0	0.306931
Merged-chr15-79455762-1	chr15	79455712	79455812	+	2.4	cIP2vsInput	Intergenic	Intergenic	-13705	NM_013767	27373	Mm.30199	NM_013767	ENSMUSG00000022433	Csnk1e	AI426939|AI551861|AW457082|CK1epsilon|CKIe|KC1epsilon|tau	"casein kinase 1, epsilon"	protein-coding	0.02	0.623762
Merged-chr3-116327426-1	chr3	116327376	116327476	+	2.4	cIP2vsInput	"intron (NM_001173553, intron 7 of 13)"	"intron (NM_001173553, intron 7 of 13)"	-73942	NM_022427	64378	Mm.40025	NM_022427	ENSMUSG00000068696	Gpr88	AW061286|Strg	G-protein coupled receptor 88	protein-coding	0.05	0.49505
Merged-chr3-20530184-1	chr3	20530134	20530234	+	2.4	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-163007	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	"angiotensin II receptor, type 1b"	protein-coding	0.02	0.366337
Merged-chr8-102849284-1	chr8	102849234	102849334	+	2.4	cIP1vsInput	Intergenic	Intergenic	-64173	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0	0.316832
Merged-chr10-107669342-1	chr10	107669292	107669392	+	2.4	cIP1vsInput	"intron (NM_001081432, intron 14 of 44)"	L2|LINE|L2	50685	NM_001081432	237523	Mm.391418	NM_001081432	ENSMUSG00000035916	Ptprq	-	"protein tyrosine phosphatase, receptor type, Q"	protein-coding	0.01	0.455446
Merged-chr18-85326457-1	chr18	85326407	85326507	+	2.4	cIP1vsInput	Intergenic	Intergenic	-374933	NM_025969	67105	Mm.250617	NM_025969	ENSMUSG00000024645	Timm21	1700034H14Rik|2700002I20Rik	tranlocase of inner mitochondrial membrane 21	protein-coding	0	0.326733
Merged-chr9-53984046-1	chr9	53983996	53984096	+	2.4	cIP1vsInput	Intergenic	(CATATA)n|Simple_repeat|Simple_repeat	-8745	NM_177769	270162	Mm.259791	NM_177769	ENSMUSG00000041986	Elmod1	4831417L10|AI428506|AI834991	ELMO/CED-12 domain containing 1	protein-coding	0	0.316832
Merged-chr2-88238551-1	chr2	88238501	88238601	+	2.4	cIP1vsInput	Intergenic	Intergenic	-13521	NM_146532	258525	Mm.377552	NM_146532	ENSMUSG00000075133	Olfr1170	MOR174-12	olfactory receptor 1170	protein-coding	0	0.277228
Merged-chr16-62721258-1	chr16	62721208	62721308	+	2.4	cIP1vsInput	Intergenic	Intergenic	65458	NM_178925	106338	Mm.26321	NM_178925		Nsun3	6720484A09Rik|AU022521	NOL1/NOP2/Sun domain family member 3	protein-coding	0.02	0.257426
Merged-chr1-9024069-1	chr1	9024019	9024119	+	2.4	cIP2vsInput	"intron (NM_027671, intron 2 of 20)"	"intron (NM_027671, intron 2 of 20)"	275661	NM_027671	71096	Mm.388998	NM_027671		Sntg1	4933426D16Rik|G1SYN|SYN4	"syntrophin, gamma 1"	protein-coding	0	0.346535
Merged-chr4-98018752-1	chr4	98018702	98018802	+	2.4	cIP2vsInput	"intron (NM_001122953, intron 5 of 9)"	"intron (NM_001122953, intron 5 of 9)"	241126	NM_010905	18027	Mm.409646	NM_001122952	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|NF1-A|NF1A	nuclear factor I/A	protein-coding	0	0.29703
Merged-chr1-7567352-1	chr1	7567302	7567402	+	2.4	cIP1vsInput	Intergenic	Intergenic	478432	NM_183028	319263		NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0	0.366337
Merged-chr9-41744065-1	chr9	41744015	41744115	+	2.4	cIP2vsInput	Intergenic	ID_B1|SINE|B4	162139	NR_029822	387236		NR_029822	ENSMUSG00000093354	Mir125b-1	Mirn125b|Mirn125b-1	microRNA 125b-1	miscRNA	0	0.306931
Merged-chrX-138980517-1	chrX	138980467	138980567	+	2.4	cIP2vsInput	"intron (NM_013724, intron 14 of 27)"	"intron (NM_013724, intron 14 of 27)"	66087	NM_013724	27206	Mm.482319	NM_013724	ENSMUSG00000052854	Nrk	AA407323|AA409510|AI225895|AV168563|AW538185|Nesk	Nik related kinase	protein-coding	0	0.455446
Merged-chr9-22150669-1	chr9	22150619	22150719	+	2.4	cIP1vsInput	"intron (NR_030448, intron 3 of 4)"	RLTR13D3|LTR|ERVK	-6177	NM_001082532	66268	Mm.28924	NM_001082532	ENSMUSG00000010607	Pigyl	1810008A14Rik|PIG-Y|Pigy	"phosphatidylinositol glycan anchor biosynthesis, class Y-like"	protein-coding	0	0.326733
Merged-chr11-65795890-1	chr11	65795840	65795940	+	2.4	cIP2vsInput	Intergenic	Intergenic	-7593	NM_009157	26398	Mm.412922	NM_009157	ENSMUSG00000033352	Map2k4	JNKK1|MEK4|MKK4|PRKMK4|Sek1|Serk1	mitogen-activated protein kinase kinase 4	protein-coding	0	0.247525
Merged-chr4-152283394-2	chr4	152283342	152283447	+	2.4	cIP1vsInput|cIP2vsInput	"exon (NM_178406, exon 6 of 6)"	"exon (NM_178406, exon 6 of 6)"	8268	NM_008237	15207	Mm.3516	NM_008237	ENSMUSG00000028946	Hes3	Hes-3|bHLHb43	hairy and enhancer of split 3 (Drosophila)	protein-coding	0.133333	0.773585
Merged-chr4-21062769-1	chr4	21062719	21062819	+	2.4	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-284101	NM_172987	269513		NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding	0	0.316832
Merged-chr9-3586051-1	chr9	3586001	3586101	+	2.4	cIP1vsInput	"intron (NM_001033322, intron 3 of 7)"	Lx2A1|LINE|L1	53702	NM_001033322	234889	Mm.91240	NM_001033322		Gucy1a2	6330407I18Rik|A230060L24Rik	"guanylate cyclase 1, soluble, alpha 2"	protein-coding	0	0.366337
Merged-chr2-41941946-1	chr2	41941896	41941996	+	2.4	cIP1vsInput	"intron (NM_053011, intron 3 of 90)"	"intron (NM_053011, intron 3 of 90)"	711652	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0	0.316832
Merged-chr13-54072345-1	chr13	54072295	54072395	+	2.4	cIP1vsInput	"intron (NM_027324, intron 1 of 10)"	"intron (NM_027324, intron 1 of 10)"	500	NM_027324	14057	Mm.134191	NM_027324	ENSMUSG00000021474	Sfxn1	2810002O05Rik|A930015P12Rik|f	sideroflexin 1	protein-coding	0.06	0.613861
Merged-chr10-59036234-1	chr10	59036184	59036284	+	2.4	cIP1vsInput	"intron (NM_172788, intron 3 of 9)"	Lx2B|LINE|L1	185613	NM_001024911	103080	Mm.397041	NM_001024910	ENSMUSG00000019917	10-Sep	4921515A04Rik|9430099J10Rik|AA408298|AI874685	septin 10	protein-coding	0	0.356436
Merged-chr11-15918315-1	chr11	15918265	15918365	+	2.4	cIP1vsInput	Intergenic	Intergenic	-339409	NM_145967	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	9330184N17Rik|BC027127|Vstm2	V-set and transmembrane domain containing 2A	protein-coding	0	0.306931
Merged-chr18-27502003-1	chr18	27501953	27502053	+	2.4	cIP1vsInput	Intergenic	Intergenic	-1058161	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	miscRNA	0.02	0.346535
Merged-chr13-105378425-1	chr13	105378375	105378475	+	2.4	cIP1vsInput	Intergenic	L1M3|LINE|L1	-65268	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0	0.306931
Merged-chr14-124046755-1	chr14	124046705	124046805	+	2.4	cIP2vsInput	"intron (NM_207667, intron 3 of 4)"	"intron (NM_207667, intron 3 of 4)"	59120	NR_045479	69393	Mm.206362	NR_045479		1700024B18Rik	-	RIKEN cDNA 1700024B18 gene	miscRNA	0	0.326733
Merged-chr2-153248634-1	chr2	153248584	153248684	+	2.4	cIP1vsInput	"intron (NM_080463, intron 3 of 6)"	"intron (NM_080463, intron 3 of 6)"	7102	NM_080463	140484	Mm.293761	NM_001039055	ENSMUSG00000046020	Pofut1	O-FucT-1|mKIAA0180	protein O-fucosyltransferase 1	protein-coding	0.01	0.50495
Merged-chr10-57237579-1	chr10	57237529	57237629	+	2.4	cIP2vsInput	Intergenic	Intergenic	248774	NR_045353	74928	Mm.416643	NR_045353	ENSMUSG00000097370	4930467K11Rik	-	RIKEN cDNA 4930467K11 gene	miscRNA	0	0.356436
Merged-chr15-93933190-1	chr15	93933140	93933240	+	2.4	cIP2vsInput	Intergenic	Intergenic	-6079	NR_045737	77248	Mm.410768	NR_045737		9430014N10Rik	-	RIKEN cDNA 9430014N10 gene	miscRNA	0	0.475248
Merged-chr9-86787465-1	chr9	86787415	86787515	+	2.4	cIP1vsInput	"intron (NM_013669, intron 22 of 29)"	"intron (NM_013669, intron 22 of 29)"	43832	NM_178738	244954	Mm.257629	NM_178738	ENSMUSG00000033491	Prss35	6030424L22Rik|P3D9	"protease, serine, 35"	protein-coding	0.01	0.386139
Merged-chr16-66063448-1	chr16	66063398	66063498	+	2.4	cIP1vsInput	Intergenic	Intergenic	247815	NM_028572	73569	Mm.482366	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like 3 (Drosophila)	protein-coding	0.02	0.326733
Merged-chr18-29533427-1	chr18	29533377	29533477	+	2.4	cIP1vsInput	Intergenic	Lx5c|LINE|L1	-37011	NR_045391	78058	Mm.416952	NR_045391		4930578E11Rik	-	RIKEN cDNA 4930578E11 gene	miscRNA	0.04	0.366337
Merged-chr16-11534193-1	chr16	11534143	11534243	+	2.4	cIP1vsInput	"intron (NM_028964, intron 14 of 20)"	"intron (NM_028964, intron 14 of 20)"	211289	NM_028964	74478	Mm.325831	NM_001163498	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding	0	0.386139
Merged-chr14-107801253-1	chr14	107801203	107801303	+	2.4	cIP1vsInput	Intergenic	RMER6C|LTR|ERVK	1112986	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	"SLIT and NTRK-like family, member 1"	protein-coding	0	0.336634
Merged-chr5-64219988-1	chr5	64219938	64220038	+	2.4	cIP2vsInput	"intron (NM_019636, intron 2 of 19)"	"intron (NM_019636, intron 2 of 19)"	59777	NM_019636	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Tbc1|mKIAA1108	"TBC1 domain family, member 1"	protein-coding	0.01	0.316832
Merged-chr10-35804593-1	chr10	35804543	35804643	+	2.4	cIP2vsInput	Intergenic	Intergenic	-702214	NM_001253355	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0	0.326733
Merged-chr5-45975047-1	chr5	45974997	45975097	+	2.4	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-117507	NM_001163073	209707	Mm.71498	NM_001163073	ENSMUSG00000015882	Lcorl	Mlr1	ligand dependent nuclear receptor corepressor-like	protein-coding	0	0.356436
Merged-chr5-120438269-1	chr5	120438219	120438319	+	2.4	cIP2vsInput	"intron (NM_008499, intron 4 of 4)"	CpG	6383	NM_008499	16873	Mm.5151	NM_008499	ENSMUSG00000029595	Lhx5	Lim2	LIM homeobox protein 5	protein-coding	0.12	0.663366
Merged-chr13-55444287-1	chr13	55444237	55444337	+	2.4	cIP1vsInput	Intergenic	L2a|LINE|L2	-1047	NM_011938	26385	Mm.10193	NM_001038018	ENSMUSG00000074886	Grk6	Gprk6	G protein-coupled receptor kinase 6	protein-coding	0.03	0.514851
Merged-chr3-49308277-1	chr3	49308227	49308327	+	2.4	cIP1vsInput	Intergenic	Intergenic	449039	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding	0	0.366337
Merged-chr2-181998382-1	chr2	181998332	181998432	+	2.4	cIP1vsInput	"intron (NM_001205282, intron 4 of 5)"	"intron (NM_001205282, intron 4 of 5)"	7156	NM_001205282	672125	Mm.489571	NM_001205282	ENSMUSG00000053277	Gm14496	OTTMUSG00000016837	predicted gene 14496	protein-coding	0	0.287129
Merged-chr10-107950497-1	chr10	107950447	107950547	+	2.4	cIP2vsInput	Intergenic	L1MC|LINE|L1	-38363	NM_001177567	628870	Mm.336090	NM_001177567	ENSMUSG00000091455	Otogl	EG628870|Gm6924	otogelin-like	protein-coding	0	0.316832
Merged-chr11-31623874-1	chr11	31623824	31623924	+	2.4	cIP1vsInput	Intergenic	Intergenic	47988	NM_001024919	69556	Mm.34183	NM_001024919	ENSMUSG00000044502	Bod1	2310022M17Rik|BOD2.1|Fam44b	biorientation of chromosomes in cell division 1	protein-coding	0	0.316832
Merged-chr9-83350795-1	chr9	83350745	83350845	+	2.4	cIP2vsInput	Intergenic	Intergenic	90304	NM_027448	75782	Mm.199698	NM_027448	ENSMUSG00000032258	Lca5	4930431B11Rik|5730406O13Rik|AV274874|ORF64	Leber congenital amaurosis 5 (human)	protein-coding	0	0.534653
Merged-chr5-62866599-1	chr5	62866549	62866649	+	2.4	cIP2vsInput	"intron (NM_001170705, intron 7 of 8)"	"intron (NM_001170705, intron 7 of 8)"	52776	NM_001170705	100322896	Mm.479821	NM_001170705	ENSMUSG00000090326	Gm17384	Dthd1	"predicted gene, 17384"	protein-coding	0	0.376238
Merged-chr8-78602472-1	chr8	78602422	78602522	+	2.4	cIP2vsInput	"intron (NM_029736, intron 5 of 11)"	"intron (NM_029736, intron 5 of 11)"	93137	NM_029736	76775	Mm.334631	NM_001009980	ENSMUSG00000031684	Slc10a7	2410193C02Rik|P7	"solute carrier family 10 (sodium/bile acid cotransporter family), member 7"	protein-coding	0	0.366337
Merged-chr3-76811663-1	chr3	76811613	76811713	+	2.4	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	736080	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.336634
Merged-chr11-58867105-1	chr11	58867055	58867155	+	2.4	cIP2vsInput	promoter-TSS (NM_172403)	promoter-TSS (NM_172403)	-135	NM_172403	69944	Mm.32118	NM_172403		2810021J22Rik	AI449137	RIKEN cDNA 2810021J22 gene	protein-coding	0.05	0.485149
Merged-chr14-52316215-1	chr14	52316165	52316265	+	2.4	cIP2vsInput	"5' UTR (NM_001244916, exon 1 of 2)"	"5' UTR (NM_001244916, exon 1 of 2)"	108	NM_001244916	50524	Mm.489795	NM_001244916	ENSMUSG00000049532	Sall2	AI225809|AW559097|Msal-2|Sal-2|mKIAA0360|p150(Sal2)	sal-like 2 (Drosophila)	protein-coding	0.1	0.762376
Merged-chr1-29447304-1	chr1	29447254	29447354	+	2.4	cIP1vsInput	Intergenic	Intergenic	-667052	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0.01	0.356436
Merged-chr1-25069813-1	chr1	25069763	25069863	+	2.4	cIP1vsInput	"intron (NM_175642, intron 30 of 30)"	"intron (NM_175642, intron 30 of 30)"	208141	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	"predicted gene, 20172"	protein-coding	0	0.326733
Merged-chr19-13224633-1	chr19	13224583	13224683	+	2.4	cIP1vsInput	Intergenic	Lx4A|LINE|L1	-9619	NM_001011840	258120	Mm.329753	NM_001011840	ENSMUSG00000096365	Olfr1463	MOR202-29P	olfactory receptor 1463	protein-coding	0	0.366337
Merged-chr1-68403608-1	chr1	68403558	68403658	+	2.4	cIP1vsInput	"intron (NM_010154, intron 3 of 26)"	"intron (NM_010154, intron 3 of 26)"	704451	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0	0.257426
Merged-chrX-93260992-1	chrX	93260942	93261042	+	2.4	cIP1vsInput	Intergenic	Intergenic	-25654	NM_007492	11878	Mm.275547	NM_007492	ENSMUSG00000035277	Arx	-	aristaless related homeobox	protein-coding	0	0.326733
Merged-chr6-104180219-1	chr6	104180169	104180269	+	2.4	cIP2vsInput	Intergenic	Intergenic	-312825	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding	0	0.29703
Merged-chr5-90805045-1	chr5	90804995	90805095	+	2.4	cIP1vsInput	Intergenic	Intergenic	10511	NM_011339	20309	Mm.64326	NM_011339	ENSMUSG00000029375	Il8	Cxcl15|Scyb15|lungkine|weche	interleukin 8	protein-coding	0.01	0.316832
Merged-chr12-43365759-1	chr12	43365709	43365809	+	2.4	cIP2vsInput	Intergenic	Lx9|LINE|L1	844309	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	"DnaJ (Hsp40) homolog, subfamily B, member 9"	protein-coding	0	0.366337
Merged-chr12-109535375-1	chr12	109535325	109535425	+	2.4	cIP1vsInput	Intergenic	Intergenic	-5621	NR_046475	17263	Mm.442513	NR_003633	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	miscRNA	0.01	0.514851
Merged-chr3-52540638-1	chr3	52540588	52540688	+	2.4	cIP2vsInput	Intergenic	Intergenic	-199086	NR_038079	329639	Mm.131245	NR_038079		Gm2447	100039832|A530017F20	predicted gene 2447	miscRNA	0	0.306931
Merged-chr12-36209757-1	chr12	36209707	36209807	+	2.4	cIP1vsInput	"intron (NM_027699, intron 3 of 4)"	"intron (NM_027699, intron 3 of 4)"	8445	NM_027699	71156	Mm.250837	NM_027699	ENSMUSG00000020545	Lrrc72	1700108M19Rik|4933421E18Rik	leucine rich repeat containing 72	protein-coding	0	0.277228
Merged-chr10-68303578-1	chr10	68303528	68303628	+	2.4	cIP1vsInput	Intergenic	Intergenic	17564	NR_045357	75148	Mm.23505	NR_045357		4930545H06Rik	-	RIKEN cDNA 4930545H06 gene	miscRNA	0	0.386139
Merged-chr6-49227901-1	chr6	49227851	49227951	+	2.4	cIP1vsInput	Intergenic	Intergenic	-12947	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding	0	0.29703
Merged-chr4-102873298-1	chr4	102873248	102873348	+	2.4	cIP1vsInput	"intron (NM_144906, intron 7 of 23)"	"intron (NM_144906, intron 7 of 23)"	112935	NM_144906	73094	Mm.238094	NM_144906	ENSMUSG00000028524	Sgip1	3110007P09Rik|SGIP1alpha|gag	SH3-domain GRB2-like (endophilin) interacting protein 1	protein-coding	0.01	0.336634
Merged-chr19-32210624-1	chr19	32210574	32210674	+	2.4	cIP1vsInput	"intron (NM_001168525, intron 5 of 9)"	"intron (NM_001168525, intron 5 of 9)"	389	NM_001168526	208449	Mm.329810	NM_001168525	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding	0.03	0.524752
Merged-chr1-107902172-1	chr1	107902122	107902222	+	2.4	cIP1vsInput	Intergenic	Intergenic	-15087	NR_102306	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0	0.326733
Merged-chr12-41014543-1	chr12	41014493	41014593	+	2.4	cIP1vsInput	Intergenic	Intergenic	471514	NM_001271708	16981	Mm.39913	NM_001271708	ENSMUSG00000036295	Lrrn3	NLRR-3	"leucine rich repeat protein 3, neuronal"	protein-coding	0	0.306931
Merged-chr3-110504722-1	chr3	110504672	110504772	+	2.4	cIP1vsInput	Intergenic	MER5B|DNA|hAT-Charlie	-253724	NR_024139	99890	Mm.393526	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding	0	0.346535
Merged-chr5-15587568-1	chr5	15587518	15587618	+	2.4	cIP1vsInput	Intergenic	Intergenic	-31531	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0.04	0.425743
Merged-chr14-114567975-1	chr14	114567925	114568025	+	2.4	cIP1vsInput	Intergenic	Intergenic	-263990	NR_045661	75822	Mm.410813	NR_045661		4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	miscRNA	0	0.366337
Merged-chr17-75591916-1	chr17	75591866	75591966	+	2.4	cIP1vsInput	Intergenic	Intergenic	-39970	NM_133747	72722		NM_133747	ENSMUSG00000002017	Fam98a	2810405J04Rik|AL024114	"family with sequence similarity 98, member A"	protein-coding	0	0.306931
Merged-chr6-104414875-1	chr6	104414825	104414925	+	2.4	cIP2vsInput	Intergenic	Intergenic	-78169	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding	0.01	0.405941
Merged-chr5-51307620-1	chr5	51307570	51307670	+	2.4	cIP1vsInput	Intergenic	HAL1b|LINE|L1	246301	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PGC-1v|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	"peroxisome proliferative activated receptor, gamma, coactivator 1 alpha"	protein-coding	0.01	0.257426
Merged-chr10-15037506-1	chr10	15037456	15037556	+	2.4	cIP2vsInput	Intergenic	Intergenic	277217	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding	0	0.366337
Merged-chr2-109794568-1	chr2	109794518	109794618	+	2.4	cIP2vsInput	Intergenic	Intergenic	-96310	NM_011699	22343	Mm.478053	NM_011699	ENSMUSG00000027162	Lin7c	9130007B12Rik|AI303698|AU019331|AW125731|D2Ertd520e|LIN-7-C|LIN-7C|MALS-3|Veli3	lin-7 homolog C (C. elegans)	protein-coding	0	0.336634
Merged-chr13-26957097-1	chr13	26957047	26957147	+	2.4	cIP1vsInput	Intergenic	Intergenic	53248	NR_039552	100628575		NR_039552		Mir3970	mmu-mir-3970|mu-mir-3970	microRNA 3970	miscRNA	0	0.326733
Merged-chr15-16125204-1	chr15	16125154	16125254	+	2.4	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-652897	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0	0.326733
Merged-chr11-12685211-1	chr11	12685161	12685261	+	2.4	cIP2vsInput	Intergenic	Intergenic	-220251	NM_172496	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	4732460E13|C530045F18Rik|mKIAA0633	cordon-bleu	protein-coding	0.01	0.316832
Merged-chr4-123687036-1	chr4	123686986	123687086	+	2.4	cIP2vsInput	Intergenic	CpG	-2676	NM_001199137	11426	Mm.485351	NM_009600	ENSMUSG00000028649	Macf1	ABP620|Acf7|Aclp7|MACF|R74989|mKIAA0465	microtubule-actin crosslinking factor 1	protein-coding	0.15	0.792079
Merged-chr12-61736568-1	chr12	61736518	61736618	+	2.4	cIP2vsInput	"intron (NM_178714, intron 2 of 3)"	"intron (NM_178714, intron 2 of 3)"	211936	NM_178714	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.01	0.316832
Merged-chr1-181706125-1	chr1	181706075	181706175	+	2.4	cIP1vsInput	Intergenic	L1M2|LINE|L1	136276	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding	0	0.29703
Merged-chr9-35247059-1	chr9	35247009	35247109	+	2.4	cIP1vsInput	"intron (NM_194257, intron 1 of 7)"	"intron (NM_194257, intron 1 of 7)"	20708	NM_194257	109229	Mm.24197	NM_175411	ENSMUSG00000050471	Fam118b	2310022O21Rik|2700018L24Rik|C030004A17Rik|Ppp4r1l	"family with sequence similarity 118, member B"	protein-coding	0	0.29703
Merged-chr1-105599895-1	chr1	105599845	105599945	+	2.4	cIP1vsInput	"intron (NM_013784, intron 14 of 30)"	"intron (NM_013784, intron 14 of 30)"	63781	NM_013784	27392	Mm.268911	NM_013784	ENSMUSG00000056536	Pign	Gm20308|PIG-N	"phosphatidylinositol glycan anchor biosynthesis, class N"	protein-coding	0	0.306931
Merged-chr1-58156627-1	chr1	58156577	58156677	+	2.4	cIP1vsInput	"intron (NM_023617, intron 16 of 34)"	"intron (NM_023617, intron 16 of 34)"	43491	NM_023617	71724	Mm.20108	NM_023617	ENSMUSG00000064294	Aox3	1200011D03Rik|AI326299|Aoh1|Aoh2	aldehyde oxidase 3	protein-coding	0.02	0.405941
Merged-chr6-58707684-1	chr6	58707634	58707734	+	2.4	cIP1vsInput	Intergenic	Lx9|LINE|L1	111012	NM_011920	26357	Mm.333096	NM_011920	ENSMUSG00000029802	Abcg2	ABC15|ABCP|AI428558|BCRP|Bcrp1|MXR|MXR1	"ATP-binding cassette, sub-family G (WHITE), member 2"	protein-coding	0	0.277228
Merged-chr16-76246790-1	chr16	76246740	76246840	+	2.4	cIP2vsInput	Intergenic	Intergenic	124177	NR_040575	78215	Mm.243885	NR_040575		4930578N18Rik	-	RIKEN cDNA 4930578N18 gene	miscRNA	0.01	0.287129
Merged-chr8-20630963-1	chr8	20630913	20631013	+	2.4	cIP2vsInput	"intron (NM_001270553, intron 6 of 9)"	L1_Mus4|LINE|L1	16036	NM_001270553	100861668	Mm.445582	NM_001270553		Gm21119	-	"predicted gene, 21119"	protein-coding	0	0.425743
Merged-chr15-54515636-1	chr15	54515586	54515686	+	2.4	cIP1vsInput	Intergenic	Intergenic	-55730	NM_178920	105853	Mm.410994	NM_178920	ENSMUSG00000024479	Mal2	AI461653	"mal, T cell differentiation protein 2"	protein-coding	0	0.306931
Merged-chr6-112729079-1	chr6	112729029	112729129	+	2.4	cIP1vsInput	"intron (NM_080448, intron 20 of 21)"	"intron (NM_080448, intron 20 of 21)"	-32409	NM_001167730	58186	Mm.103812	NM_001167730	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 homolog (S. cerevisiae)	protein-coding	0.02	0.455446
Merged-chr16-59070672-1	chr16	59070622	59070722	+	2.4	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	4406	NM_146397	258392	Mm.377476	NM_146397	ENSMUSG00000064006	Olfr190	MOR183-4	olfactory receptor 190	protein-coding	0	0.306931
Merged-chr7-124583233-1	chr7	124583183	124583283	+	2.4	cIP2vsInput	Intergenic	Intergenic	125702	NR_045907	73076	Mm.417827	NR_045907	ENSMUSG00000086254	3100003L05Rik	-	RIKEN cDNA 3100003L05 gene	miscRNA	0	0.356436
Merged-chr10-47064348-1	chr10	47064298	47064398	+	2.4	cIP2vsInput	Intergenic	Lx5|LINE|L1	819599	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0	0.356436
Merged-chr4-10353301-1	chr4	10353251	10353351	+	2.4	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-435904	NR_004448	74662	Mm.483401	NR_004448		4930448K20Rik	1700009K09Rik	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0.01	0.346535
Merged-chr4-30211660-1	chr4	30211610	30211710	+	2.4	cIP1vsInput	Intergenic	Intergenic	-452936	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	miscRNA	0	0.425743
Merged-chr3-85052257-1	chr3	85052207	85052307	+	2.4	cIP1vsInput	Intergenic	Intergenic	-86677	NM_001040461	654362	Mm.466598	NM_001040461		Dear1	Dear|Despr	dual endothelin 1/angiotensin II receptor 1	protein-coding	0	0.386139
Merged-chrX-151017633-1	chrX	151017583	151017683	+	2.4	cIP2vsInput	promoter-TSS (NM_198110)	promoter-TSS (NM_198110)	-311	NM_198110	237107	Mm.45987	NM_001168600	ENSMUSG00000025266	Gnl3l	BC020354	guanine nucleotide binding protein-like 3 (nucleolar)-like	protein-coding	0.01	0.465347
Merged-chr4-24019734-1	chr4	24019684	24019784	+	2.4	cIP1vsInput	Intergenic	Intergenic	-476728	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	"MMS22-like, DNA repair protein"	protein-coding	0	0.465347
Merged-chr7-99316336-1	chr7	99316286	99316386	+	2.4	cIP1vsInput	"intron (NM_001043355, intron 2 of 2)"	"intron (NM_001043355, intron 2 of 2)"	36903	NM_009825	12406	Mm.444951	NM_001111043	ENSMUSG00000070436	Serpinh1	BERF-1|Cbp1|Cbp2|Hsp47|J6|Serpinh2|colligin|gp46	"serine (or cysteine) peptidase inhibitor, clade H, member 1"	protein-coding	0.01	0.564356
Merged-chr9-78724581-1	chr9	78724531	78724631	+	2.4	cIP2vsInput	Intergenic	Intergenic	109035	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding	0	0.326733
Merged-chr6-69805385-1	chr6	69805335	69805435	+	2.4	cIP2vsInput	Intergenic	Lx7|LINE|L1	-478211	NR_004434	19783		NR_004434		Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	miscRNA	0	0.326733
Merged-chr1-54016345-1	chr1	54016295	54016395	+	2.4	cIP1vsInput	"intron (NM_001001883, intron 2 of 28)"	"intron (NM_001001883, intron 2 of 28)"	178689	NM_001001883	329152	Mm.447527	NM_001001883	ENSMUSG00000042807	Hecw2	A730039N16Rik|D030049F17Rik|Gm971|Nedl2|mKIAA1301	"HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2"	protein-coding	0	0.336634
Merged-chr18-78741547-1	chr18	78741497	78741597	+	2.4	cIP2vsInput	Intergenic	Intergenic	-144597	NM_030683	27411	Mm.44158	NM_001110273	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	"solute carrier family 14 (urea transporter), member 2"	protein-coding	0	0.376238
Merged-chr4-146427177-1	chr4	146427127	146427227	+	2.4	cIP1vsInput	"intron (NM_001083918, intron 3 of 6)"	L1_Mus3|LINE|L1	-21853	NM_001085522	433791	Mm.441417	NM_001085522	ENSMUSG00000070605	Gm13251	OTTMUSG00000011097	predicted gene 13251	protein-coding	0	0.356436
Merged-chr7-66711167-1	chr7	66711117	66711217	+	2.4	cIP1vsInput	"intron (NM_152815, intron 6 of 7)"	"intron (NM_152815, intron 6 of 7)"	21278	NR_034030	72635	Mm.289796	NM_001191001		Lins	2700083B01Rik|AW547219|Lins2|Wins2	lines homolog (Drosophila)	protein-coding	0.01	0.425743
Merged-chr16-61750302-1	chr16	61750252	61750352	+	2.4	cIP1vsInput	Intergenic	Intergenic	1036414	NM_178925	106338	Mm.26321	NM_178925		Nsun3	6720484A09Rik|AU022521	NOL1/NOP2/Sun domain family member 3	protein-coding	0	0.326733
Merged-chr9-116727850-1	chr9	116727800	116727900	+	2.4	cIP2vsInput	"intron (NM_001172126, intron 6 of 12)"	"intron (NM_001172126, intron 6 of 12)"	524633	NM_001172123	207181	Mm.326411	NM_001172121	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	"RNA binding motif, single stranded interacting protein"	protein-coding	0	0.376238
Merged-chr10-103470297-1	chr10	103470247	103470347	+	2.4	cIP1vsInput	Intergenic	(TTTTG)n|Simple_repeat|Simple_repeat	102489	NM_175328	103098	Mm.458408	NM_001252330	ENSMUSG00000019894	Slc6a15	AA536730|AI326450|AI326451|v7-3	"solute carrier family 6 (neurotransmitter transporter), member 15"	protein-coding	0.03	0.326733
Merged-chr15-71122250-1	chr15	71122200	71122300	+	2.4	cIP1vsInput	Intergenic	Intergenic	605588	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	"family with sequence similarity 135, member B"	protein-coding	0	0.29703
Merged-chr2-92306927-1	chr2	92306877	92306977	+	2.4	cIP1vsInput	"intron (NM_001109691, intron 7 of 18)"	"intron (NM_001109691, intron 7 of 18)"	64109	NM_172670	228366	Mm.31158	NM_001166633	ENSMUSG00000040434	Gyltl1b	5730485C17Rik|AI891893|Large2|Largel|mKIAA4105	glycosyltransferase-like 1B	protein-coding	0.01	0.29703
Merged-chr4-95989383-1	chr4	95989333	95989433	+	2.4	cIP2vsInput	"intron (NM_030014, intron 2 of 21)"	"intron (NM_030014, intron 2 of 21)"	-21728	NR_045776	319247	Mm.473527	NM_175680	ENSMUSG00000044125	9530080O11Rik	-	RIKEN cDNA 9530080O11 gene	miscRNA	0	0.326733
Merged-chr4-88219253-1	chr4	88219203	88219303	+	2.4	cIP1vsInput	"intron (NM_001081184, intron 11 of 43)"	"intron (NM_001081184, intron 11 of 43)"	97213	NR_030478	735282		NR_030478		Mir491	Mirn491|mmu-mir-491	microRNA 491	miscRNA	0	0.326733
Merged-chr16-21710520-1	chr16	21710470	21710570	+	2.4	cIP2vsInput	Intergenic	Intergenic	-15855	NM_001001881	72190		NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding	0.01	0.584158
Merged-chr8-101138963-1	chr8	101138913	101139013	+	2.4	cIP1vsInput	Intergenic	Intergenic	1646148	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0	0.346535
Merged-chr9-118147342-1	chr9	118147292	118147392	+	2.4	cIP1vsInput	"intron (NM_026442, intron 1 of 3)"	"intron (NM_026442, intron 1 of 3)"	2854	NM_026442	67899	Mm.9953	NM_026442	ENSMUSG00000039163	Cmc1	2010110K16Rik|2010312P05Rik|AI596001	COX assembly mitochondrial protein 1	protein-coding	0	0.415842
Merged-chr2-43240468-1	chr2	43240418	43240518	+	2.4	cIP1vsInput	Intergenic	Intergenic	-314861	NM_027552	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding	0	0.316832
Merged-chr1-173943493-2	chr1	173943425	173943561	+	2.4	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-1001	NM_001045481	15950	Mm.472787	NM_001045481	ENSMUSG00000039997	Ifi203	-	interferon activated gene 203	protein-coding	0	0.379562
Merged-chr12-81342054-1	chr12	81342004	81342104	+	2.4	cIP1vsInput	Intergenic	MusHAL1|LINE|L1	-8874	NM_080440	110893	Mm.443748	NM_001167920	ENSMUSG00000079055	Slc8a3	AW742262|Ncx3	"solute carrier family 8 (sodium/calcium exchanger), member 3"	protein-coding	0	0.366337
Merged-chr17-89655136-1	chr17	89655086	89655186	+	2.4	cIP1vsInput	Intergenic	Intergenic	275895	NR_045952	100043904	Mm.396198	NR_045952		Gm4719	-	predicted gene 4719	miscRNA	0	0.425743
Merged-chr18-90340241-1	chr18	90340191	90340291	+	2.4	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-169913	NM_198295	67988	Mm.268041	NM_198295	ENSMUSG00000024614	Tmx3	6430411B10Rik|A730024F05Rik|AV259382|Txndc10|mKIAA1830	thioredoxin-related transmembrane protein 3	protein-coding	0.01	0.376238
Merged-chr18-87945717-1	chr18	87945667	87945767	+	2.4	cIP1vsInput	Intergenic	Intergenic	948490	NM_018821	54607	Mm.476577	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding	0	0.29703
Merged-chr2-132016290-1	chr2	132016240	132016340	+	2.4	cIP2vsInput	"intron (NM_175445, intron 1 of 10)"	L1M5|LINE|L1	13698	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding	0	0.326733
Merged-chr12-96276966-1	chr12	96276916	96277016	+	2.4	cIP1vsInput	Intergenic	Intergenic	-229744	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0	0.306931
Merged-chr10-19285939-1	chr10	19285889	19285989	+	2.4	cIP2vsInput	Intergenic	L1MA5|LINE|L1	-70600	NM_053008	94222	Mm.156946	NM_053008	ENSMUSG00000045591	Olig3	Bhlhb7|bHLHe20	oligodendrocyte transcription factor 3	protein-coding	0	0.326733
Merged-chr11-41286774-1	chr11	41286724	41286824	+	2.4	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-531488	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding	0	0.306931
Merged-chr1-185309140-1	chr1	185309090	185309190	+	2.4	cIP2vsInput	"intron (NM_198653, intron 12 of 22)"	"intron (NM_198653, intron 12 of 22)"	-4179	NR_029580	387189		NR_029580	ENSMUSG00000065581	Mir194-1	Mirn194|Mirn194-1|miR-194	microRNA 194-1	miscRNA	0.02	0.584158
Merged-chr9-14850267-1	chr9	14850217	14850317	+	2.4	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-9987	NM_010287	14608	Mm.4672	NM_010287		Gpr83	AW045253|Gir|Gpr72|RP105|RP39|RP82	G protein-coupled receptor 83	protein-coding	0	0.445545
Merged-chr13-19851442-1	chr13	19851392	19851492	+	2.4	cIP2vsInput	Intergenic	Lx2A|LINE|L1	-27185	NM_181754	353346	Mm.239268	NM_181754	ENSMUSG00000053101	Gpr141	PGR13	G protein-coupled receptor 141	protein-coding	0	0.316832
Merged-chr2-47005324-1	chr2	47005274	47005374	+	2.4	cIP1vsInput	Intergenic	Lx8b|LINE|L1	1308719	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	miscRNA	0	0.405941
Merged-chr1-47019911-1	chr1	47019861	47019961	+	2.4	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-166402	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0.01	0.376238
Merged-chr1-79143312-1	chr1	79143262	79143362	+	2.4	cIP2vsInput	Intergenic	Intergenic	296778	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding	0	0.336634
Merged-chr4-37542743-1	chr4	37542693	37542793	+	2.4	cIP2vsInput	Intergenic	Intergenic	-590999	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0	0.326733
Merged-chr1-193984913-1	chr1	193984863	193984963	+	2.4	cIP2vsInput	Intergenic	MER2|DNA|TcMar-Tigger	237846	NR_040477	74942	Mm.60689	NR_040477		4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	miscRNA	0	0.386139
Merged-chr11-105126267-1	chr11	105126217	105126317	+	2.4	cIP2vsInput	promoter-TSS (NM_172567)	promoter-TSS (NM_172567)	-158	NM_172567	52686	Mm.270091	NM_172567		Mettl2	2810438F06Rik|AW493404|C130031G21Rik|D11Ertd768e|METL|PSENIP1	methyltransferase like 2	protein-coding	0.05	0.564356
Merged-chr3-35669836-1	chr3	35669786	35669886	+	2.4	cIP2vsInput	Intergenic	L1VL2|LINE|L1	-3673	NR_040748	625963	Mm.251506	NR_040748		Gm6639	-	predicted gene 6639	miscRNA	0	0.336634
Merged-chr17-22896095-1	chr17	22896045	22896145	+	2.4	cIP2vsInput	Intergenic	Intergenic	-28961	NM_001110254	240041	Mm.328828	NM_001110254	ENSMUSG00000059142	Zfp945	A630033E08Rik|C730040L01Rik	zinc finger protein 945	protein-coding	0	0.346535
Merged-chr10-112262030-1	chr10	112261980	112262080	+	2.4	cIP1vsInput	Intergenic	MLT1F-int|LTR|ERVL-MaLR	-9093	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	"potassium voltage gated channel, Shaw-related subfamily, member 2"	protein-coding	0.01	0.415842
Merged-chr15-39195101-1	chr15	39195051	39195151	+	2.4	cIP1vsInput	Intergenic	Intergenic	-3185	NM_001256382	116838	Mm.309296	NM_001256382		Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding	0.02	0.336634
Merged-chr3-12451996-1	chr3	12451946	12452046	+	2.4	cIP1vsInput	Intergenic	Intergenic	-607637	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0.01	0.267327
Merged-chr7-124142322-1	chr7	124142272	124142372	+	2.4	cIP1vsInput	"intron (NM_001252072, intron 1 of 1)"	"intron (NM_001252072, intron 1 of 1)"	159141	NM_001252072	628779	Mm.40210	NM_001252072	ENSMUSG00000078591	Hs3st4	EG628779|Gm6915	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	protein-coding	0.01	0.415842
Merged-chr19-53528832-1	chr19	53528782	53528882	+	2.4	cIP2vsInput	promoter-TSS (NM_001085390)	promoter-TSS (NM_001085390)	-486	NM_001085390	240672	Mm.482424	NM_001085390		Dusp5	Gm337	dual specificity phosphatase 5	protein-coding	0.11	0.732673
Merged-chr14-55122347-1	chr14	55122297	55122397	+	2.4	cIP2vsInput	Intergenic	Intergenic	-5412	NM_177049	319984	Mm.486015	NM_001003829	ENSMUSG00000022208	Jph4	9330157P13Rik|JP-4|JPHL1	junctophilin 4	protein-coding	0.01	0.524752
Merged-chr6-16538437-1	chr6	16538387	16538487	+	2.4	cIP2vsInput	Intergenic	Intergenic	360004	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding	0	0.29703
Merged-chr2-168115099-1	chr2	168115049	168115149	+	2.4	cIP1vsInput	Intergenic	Intergenic	34095	NM_021409	58220	Mm.292834	NM_021409	ENSMUSG00000044641	Pard6b	AV025615|Par6b	par-6 (partitioning defective 6) homolog beta (C. elegans)	protein-coding	0.03	0.584158
Merged-chr1-6958673-1	chr1	6958623	6958723	+	2.4	cIP2vsInput	Intergenic	Lx7|LINE|L1	-130247	NM_183028	319263		NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0	0.306931
Merged-chr7-142059428-1	chr7	142059378	142059478	+	2.4	cIP2vsInput	"intron (NM_028308, intron 1 of 4)"	"intron (NM_028308, intron 1 of 4)"	1606	NM_028308	101513	Mm.53259	NM_028308	ENSMUSG00000025147	Mob2	1110017M21Rik|2700078K21Rik|AI256456|Mmh	MOB kinase activator 2	protein-coding	0	0.366337
Merged-chr11-100574929-1	chr11	100574879	100574979	+	2.4	cIP2vsInput	promoter-TSS (NM_009923)	promoter-TSS (NM_009923)	-10	NM_009923	12799	Mm.453219	NM_001146318	ENSMUSG00000006782	Cnp	CNPase|Cnp-1|Cnp1	"2',3'-cyclic nucleotide 3' phosphodiesterase"	protein-coding	0.12	0.80198
Merged-chr8-31121240-1	chr8	31121190	31121290	+	2.4	cIP1vsInput	"intron (NM_175136, intron 2 of 5)"	"intron (NM_175136, intron 2 of 5)"	9394	NM_175136	68867	Mm.400167	NM_175136	ENSMUSG00000039328	Rnf122	1110063C11Rik	ring finger protein 122	protein-coding	0.03	0.613861
Merged-chr10-126928788-1	chr10	126928738	126928838	+	2.4	cIP2vsInput	Intergenic	Intergenic	-27417	NM_001159559	68876	Mm.276769	NM_001159559	ENSMUSG00000025436	Xrcc6bp1	1110068E08Rik|2410012H02Rik	XRCC6 binding protein 1	protein-coding	0.01	0.534653
Merged-chrY-41754067-1	chrY	41754017	41754117	+	2.4	cIP2vsInput	Intergenic	Intergenic	-1176256	NR_038299	100041346	Mm.490246	NR_038299		Gm20871	-	Sycp3 like Y-linked pseudogene	pseudo	0.01	0.386139
Merged-chr14-60458490-1	chr14	60458440	60458540	+	2.4	cIP2vsInput	Intergenic	Intergenic	80204	NM_001164705	72125	Mm.275499	NM_001164705	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding	0.01	0.316832
Merged-chr2-46282492-1	chr2	46282442	46282542	+	2.4	cIP2vsInput	Intergenic	Intergenic	585887	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	miscRNA	0	0.306931
Merged-chr12-116405551-1	chr12	116405501	116405601	+	2.4	cIP1vsInput	promoter-TSS (NR_028421)	promoter-TSS (NR_028421)	149	NM_133762	76044	Mm.21516	NM_133762	ENSMUSG00000042029	Ncapg2	5830426I05Rik|Luzp5|Mtb|mCAP-G2	"non-SMC condensin II complex, subunit G2"	protein-coding	0.19	0.762376
Merged-chr2-56391878-1	chr2	56391828	56391928	+	2.4	cIP1vsInput	Intergenic	Intergenic	723160	NM_013613	18227	Mm.3507	NM_001139509	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	"nuclear receptor subfamily 4, group A, member 2"	protein-coding	0	0.287129
Merged-chr6-63712505-1	chr6	63712455	63712555	+	2.4	cIP2vsInput	"intron (NM_008167, intron 2 of 15)"	Lx7|LINE|L1	455648	NM_008167	14804	Mm.447390	NM_008167		Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	"glutamate receptor, ionotropic, delta 2"	protein-coding	0	0.405941
Merged-chr5-68636373-1	chr5	68636323	68636423	+	2.4	cIP2vsInput	Intergenic	Intergenic	604538	NM_001018019	433899	Mm.332422	NM_001018019	ENSMUSG00000068082	Grxcr1	Tg(Eno2-Gabrb3)0370Brll|pi|tde	"glutaredoxin, cysteine rich 1"	protein-coding	0.02	0.336634
Merged-chr1-180863683-1	chr1	180863633	180863733	+	2.4	cIP1vsInput	"intron (NM_145943, intron 6 of 6)"	"intron (NM_145943, intron 6 of 6)"	12532	NM_145943	208768	Mm.272625	NM_145943	ENSMUSG00000038806	Sde2	-	SDE2 telomere maintenance homolog (S. pombe)	protein-coding	0	0.435644
Merged-chr10-77383349-1	chr10	77383299	77383399	+	2.4	cIP2vsInput	"intron (NM_001024837, intron 1 of 10)"	"intron (NM_001024837, intron 1 of 10)"	34924	NM_130895	110532	Mm.276815	NM_001024837	ENSMUSG00000020262	Adarb1	1700057H01Rik|AW124433|AW558573|Adar2|BB220382|D10Bwg0447e|Red1	"adenosine deaminase, RNA-specific, B1"	protein-coding	0.02	0.39604
Merged-chr10-53577801-1	chr10	53577751	53577851	+	2.4	cIP2vsInput	"intron (NM_027830, intron 8 of 13)"	L1MC2|LINE|L1	-19160	NM_025541	66403	Mm.272989	NM_025541	ENSMUSG00000019857	Asf1a	2310079C17Rik|C79052	ASF1 anti-silencing function 1 homolog A (S. cerevisiae)	protein-coding	0	0.39604
Merged-chr5-22488575-1	chr5	22488525	22488625	+	2.4	cIP1vsInput	"intron (NM_011959, intron 13 of 13)"	"intron (NM_011959, intron 13 of 13)"	40455	NR_004442	100042049	Mm.21724	NR_004442		Gm15421	OTTMUSG00000021442	ribosomal protein L22 like 1 pseudogene	pseudo	0	0.237624
Merged-chr13-88511898-1	chr13	88511848	88511948	+	2.4	cIP1vsInput	Intergenic	Intergenic	-309574	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0.01	0.316832
Merged-chr12-7773007-1	chr12	7772957	7773057	+	2.4	cIP2vsInput	Intergenic	Intergenic	-204670	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding	0	0.326733
Merged-chr16-74228406-1	chr16	74228356	74228456	+	2.4	cIP2vsInput	"intron (NM_175549, intron 2 of 27)"	"intron (NM_175549, intron 2 of 27)"	113661	NR_030464	751561		NR_030464		Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	miscRNA	0.02	0.39604
Merged-chr4-77632770-1	chr4	77632720	77632820	+	2.4	cIP1vsInput	"intron (NM_011211, intron 2 of 39)"	"intron (NM_011211, intron 2 of 39)"	579125	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0	0.29703
Merged-chr1-35096257-1	chr1	35096207	35096307	+	2.4	cIP1vsInput	Intergenic	A-rich|Low_complexity|Low_complexity	246298	NM_145516	226971	Mm.292751	NM_145516	ENSMUSG00000026123	Plekhb2	2310009M15Rik|AU018239|Evt2|Phdc|evt-2	"pleckstrin homology domain containing, family B (evectins) member 2"	protein-coding	0.01	0.326733
Merged-chr1-134885806-1	chr1	134885756	134885856	+	2.4	cIP2vsInput	"intron (NM_001081307, intron 8 of 23)"	MER2|DNA|TcMar-Tigger	70134	NM_001081307	329251	Mm.451578	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	"protein phosphatase 1, regulatory (inhibitor) subunit 12B"	protein-coding	0	0.316832
Merged-chr1-105586121-1	chr1	105586071	105586171	+	2.4	cIP2vsInput	"intron (NM_013784, intron 20 of 30)"	"intron (NM_013784, intron 20 of 30)"	77555	NM_013784	27392	Mm.268911	NM_013784	ENSMUSG00000056536	Pign	Gm20308|PIG-N	"phosphatidylinositol glycan anchor biosynthesis, class N"	protein-coding	0	0.336634
Merged-chr5-133456454-2	chr5	133456367	133456541	+	2.4	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-643294	NM_030719	80909	Mm.426767	NM_030719		Gatsl2	7530428J21Rik|AW742413|Gats|Gatsl1	GATS protein-like 2	protein-coding	0.005747	0.308571
Merged-chr17-94084071-1	chr17	94084021	94084121	+	2.4	cIP1vsInput	Intergenic	Intergenic	665821	NM_176917	76781	Mm.486648	NM_176917	ENSMUSG00000055660	Mettl4	2410198H06Rik|A730091E08Rik|AV296509|HsT661	methyltransferase like 4	protein-coding	0	0.237624
Merged-chr8-45467433-1	chr8	45467383	45467483	+	2.4	cIP1vsInput	Intergenic	Intergenic	-40355	NM_172752	234214	Mm.447653	NM_001205219	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777	sorbin and SH3 domain containing 2	protein-coding	0.02	0.376238
Merged-chr6-72408058-1	chr6	72408008	72408108	+	2.4	cIP1vsInput	Intergenic	Intergenic	-6250	NM_019802	56316	Mm.19937	NM_019802	ENSMUSG00000053460	Ggcx	-	gamma-glutamyl carboxylase	protein-coding	0	0.356436
Merged-chr3-158693415-1	chr3	158693365	158693465	+	2.4	cIP2vsInput	Intergenic	Intergenic	-131194	NM_001081358	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding	0	0.326733
Merged-chr5-118315875-1	chr5	118315825	118315925	+	2.4	cIP2vsInput	Intergenic	Intergenic	70648	NM_001081236	76792	Mm.103428	NM_001081236		2410131K14Rik	-	RIKEN cDNA 2410131K14 gene	protein-coding	0.01	0.445545
Merged-chr14-87500207-1	chr14	87500157	87500257	+	2.4	cIP2vsInput	"intron (NM_172605, intron 10 of 13)"	L1_Mur3|LINE|L1	83624	NM_001253755	219249	Mm.35168	NM_001253755	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding	0	0.346535
Merged-chr1-152120345-1	chr1	152120295	152120395	+	2.4	cIP1vsInput	Intergenic	Intergenic	-30025	NM_197990	69399	Mm.278031	NM_197990	ENSMUSG00000032666	1700025G04Rik	2610510E02Rik|2900042O04Rik|ENSMUSG00000073540	RIKEN cDNA 1700025G04 gene	protein-coding	0.01	0.366337
Merged-chr12-62890620-1	chr12	62890570	62890670	+	2.4	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	1365988	NM_178714	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0	0.306931
Merged-chr4-21903581-1	chr4	21903531	21903631	+	2.4	cIP2vsInput	"intron (NM_172687, intron 5 of 6)"	Lx6|LINE|L1	23906	NM_172687	230027	Mm.5662	NM_172687	ENSMUSG00000028247	Coq3	4732433J24|C77934	"coenzyme Q3 homolog, methyltransferase (yeast)"	protein-coding	0	0.376238
Merged-chr19-18482367-1	chr19	18482317	18482417	+	2.4	cIP1vsInput	Intergenic	Lx7|LINE|L1	149446	NM_017375	20409	Mm.172222	NM_017375		Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding	0	0.336634
Merged-chr1-105630763-1	chr1	105630713	105630813	+	2.4	cIP2vsInput	"intron (NM_013784, intron 14 of 30)"	"intron (NM_013784, intron 14 of 30)"	32913	NM_013784	27392	Mm.268911	NM_013784	ENSMUSG00000056536	Pign	Gm20308|PIG-N	"phosphatidylinositol glycan anchor biosynthesis, class N"	protein-coding	0	0.356436
Merged-chr14-57753632-1	chr14	57753582	57753682	+	2.4	cIP2vsInput	Intergenic	Intergenic	-7509	NM_015771	50523	Mm.347899	NM_015771	ENSMUSG00000021959	Lats2	4932411G09Rik|AV277261|AW228608	large tumor suppressor 2	protein-coding	0.01	0.465347
Merged-chr4-41286719-1	chr4	41286669	41286769	+	2.4	cIP2vsInput	Intergenic	Intergenic	-11584	NM_026872	68926	Mm.41864	NM_026872	ENSMUSG00000028433	Ubap2	1190005K07Rik|AA408600|AU045235|UBAP-2|mKIAA1491	ubiquitin-associated protein 2	protein-coding	0	0.405941
Merged-chr19-36057387-1	chr19	36057337	36057437	+	2.4	cIP2vsInput	promoter-TSS (NM_008315)	promoter-TSS (NM_008315)	-27	NM_008315	15566	Mm.254266	NM_008315	ENSMUSG00000024798	Htr7	5-HT7	5-hydroxytryptamine (serotonin) receptor 7	protein-coding	0.14	0.811881
Merged-chr4-75870618-1	chr4	75870568	75870668	+	2.4	cIP2vsInput	Intergenic	Intergenic	-592332	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	3110001D03Rik	1700027K24Rik	RIKEN cDNA 3110001D03 gene	protein-coding	0	0.287129
Merged-chr5-86337329-1	chr5	86337279	86337379	+	2.4	cIP1vsInput	"intron (NM_145561, intron 3 of 9)"	"intron (NM_145561, intron 3 of 9)"	36058	NM_145561	231382	Mm.240139	NM_145561		Tmprss11d	AST|AsP|BC020151	"transmembrane protease, serine 11d"	protein-coding	0.02	0.366337
Merged-chr8-7364000-1	chr8	7363950	7364050	+	2.4	cIP2vsInput	Intergenic	Intergenic	1296773	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding	0.01	0.346535
Merged-chr14-115315439-1	chr14	115315389	115315489	+	2.4	cIP2vsInput	"intron (NM_175500, intron 2 of 7)"	RLTR12A|LTR|ERVK	94113	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	miscRNA	0	0.336634
Merged-chr11-64785240-1	chr11	64785190	64785290	+	2.4	cIP2vsInput	Intergenic	Intergenic	-193795	NM_023479	68626	Mm.157711	NM_023479	ENSMUSG00000020549	Elac2	1110017O07Rik|D11Wsu80e|Hpc2	elaC homolog 2 (E. coli)	protein-coding	0	0.405941
Merged-chr3-45358761-1	chr3	45358711	45358811	+	2.4	cIP1vsInput	"intron (NR_045172, intron 4 of 8)"	"intron (NR_045172, intron 4 of 8)"	19499	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	miscRNA	0.01	0.336634
Merged-chr1-106249487-1	chr1	106249437	106249537	+	2.4	cIP2vsInput	"intron (NM_133821, intron 1 of 16)"	L1_Mus1|LINE|L1	77618	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0	0.346535
Merged-chr18-19985162-1	chr18	19985112	19985212	+	2.4	cIP1vsInput	"intron (NM_007882, intron 6 of 15)"	"intron (NM_007882, intron 6 of 15)"	16935	NM_007882	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding	0.01	0.376238
Merged-chr9-50299661-1	chr9	50299611	50299711	+	2.4	cIP1vsInput	Intergenic	Intergenic	-194864	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	1600029D21Rik	0610037B23Rik|AA407923|AU043048|PLET1	RIKEN cDNA 1600029D21 gene	protein-coding	0.01	0.306931
Merged-chr6-80244530-1	chr6	80244480	80244580	+	2.4	cIP1vsInput	Intergenic	Intergenic	224887	NM_178731	243499	Mm.483425	NM_001134743	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding	0	0.346535
Merged-chr2-134629470-1	chr2	134629420	134629520	+	2.4	cIP2vsInput	"intron (NM_029148, intron 2 of 7)"	MYSERV6-int|LTR|ERVK	14651	NM_029148	52837	Mm.264096	NM_029148	ENSMUSG00000034723	Tmx4	2810417D04Rik|4930500L08Rik|AI843224|AW046784|D2Bwg1356e|Txndc13|mKIAA1162	thioredoxin-related transmembrane protein 4	protein-coding	0	0.257426
Merged-chr6-118538130-1	chr6	118538080	118538180	+	2.4	cIP2vsInput	"intron (NM_001081112, intron 15 of 33)"	"intron (NM_001081112, intron 15 of 33)"	24126	NM_001081112	232339	Mm.276116	NM_001081112	ENSMUSG00000007827	Ankrd26	5730521P14Rik|BC008111|mKIAA1074	ankyrin repeat domain 26	protein-coding	0	0.336634
Merged-chr17-12147917-1	chr17	12147867	12147967	+	2.4	cIP2vsInput	"intron (NM_026644, intron 1 of 8)"	"intron (NM_026644, intron 1 of 8)"	28633	NM_026644	68262	Mm.258300	NM_026644	ENSMUSG00000023827	Agpat4	1500003P24Rik	"1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)"	protein-coding	0	0.366337
Merged-chr7-90681098-1	chr7	90681048	90681148	+	2.4	cIP1vsInput	Intergenic	Intergenic	-205103	NM_026734	68472	Mm.289791	NM_026734		Tmem126b	1110001A23Rik	transmembrane protein 126B	protein-coding	0.01	0.346535
Merged-chr3-45036590-1	chr3	45036540	45036640	+	2.4	cIP2vsInput	Intergenic	Intergenic	341670	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	miscRNA	0	0.336634
Merged-chr7-42505745-1	chr7	42505695	42505795	+	2.4	cIP1vsInput	Intergenic	CpG	-57665	NM_027702	71162	Mm.158598	NM_027702	ENSMUSG00000030463	4933421I07Rik	-	RIKEN cDNA 4933421I07 gene	protein-coding	0.05	0.50495
Merged-chr2-80714071-1	chr2	80714021	80714121	+	2.4	cIP2vsInput	Intergenic	L1M2|LINE|L1	74807	NM_001190179	69482	Mm.29200	NM_001190179		Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding	0	0.326733
Merged-chr5-96441970-1	chr5	96441920	96442020	+	2.4	cIP1vsInput	"intron (NM_175473, intron 2 of 73)"	MIRc|SINE|MIR	68015	NM_175473	231470	Mm.291120	NM_175473	ENSMUSG00000034687	Fras1	E130113P14Rik|bl|mKIAA1500	Fraser syndrome 1 homolog (human)	protein-coding	0.01	0.425743
Merged-chr15-20692392-1	chr15	20692342	20692442	+	2.4	cIP2vsInput	Intergenic	Intergenic	-25642	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding	0	0.316832
Merged-chr6-86497574-1	chr6	86497524	86497624	+	2.4	cIP2vsInput	Intergenic	MLT1O|LTR|ERVL-MaLR	-9347	NR_040292	381792	Mm.490854	NR_040292		2310040G24Rik	-	RIKEN cDNA 2310040G24 gene	miscRNA	0.03	0.544554
Merged-chr1-121905001-1	chr1	121904951	121905051	+	2.4	cIP2vsInput	Intergenic	Intergenic	-337021	NM_025860	66942	Mm.44219	NM_025860	ENSMUSG00000001674	Ddx18	2310005B10Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	protein-coding	0	0.316832
Merged-chr9-12320465-1	chr9	12320415	12320515	+	2.4	cIP1vsInput	Intergenic	Lx2B|LINE|L1	785390	NR_040755	78219	Mm.414868	NR_040755		4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	miscRNA	0.02	0.346535
Merged-chr8-26878265-1	chr8	26878215	26878315	+	2.4	cIP2vsInput	Intergenic	Intergenic	-53842	NR_045904	72316	Mm.490534	NR_045904		2310008N11Rik	-	RIKEN cDNA 2310008N11 gene	miscRNA	0.01	0.39604
Merged-chr15-18793777-1	chr15	18793727	18793827	+	2.4	cIP2vsInput	Intergenic	MTE-int|LTR|ERVL-MaLR	-26552	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0	0.29703
Merged-chr1-100995281-1	chr1	100995231	100995331	+	2.4	cIP1vsInput	Intergenic	Lx|LINE|L1	-160487	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.326733
Merged-chr5-114594969-1	chr5	114594919	114595019	+	2.4	cIP2vsInput	"intron (NM_001004180, intron 2 of 2)"	"intron (NM_001004180, intron 2 of 2)"	26718	NM_001004180	433940	Mm.194212	NM_001004180	ENSMUSG00000041930	Fam222a	-	"family with sequence similarity 222, member A"	protein-coding	0.07	0.574257
Merged-chr19-51761063-1	chr19	51761013	51761113	+	2.4	cIP1vsInput	Intergenic	Intergenic	-503260	NM_008386	16333	Mm.46269	NM_008386	ENSMUSG00000035804	Ins1	Ins-1|Ins2-rs1	insulin I	protein-coding	0	0.376238
Merged-chr16-20702849-1	chr16	20702799	20702899	+	2.4	cIP2vsInput	TTS (NM_009900)	TTS (NM_009900)	7792	NM_133778	78408	Mm.196512	NM_133778	ENSMUSG00000050821	Fam131a	2900046G09Rik	"family with sequence similarity 131, member A"	protein-coding	0.03	0.623762
Merged-chr5-42872837-1	chr5	42872787	42872887	+	2.4	cIP2vsInput	Intergenic	Intergenic	-360626	NM_175937	231207	Mm.7233	NM_001177379	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding	0.01	0.346535
Merged-chr4-110893970-1	chr4	110893920	110894020	+	2.4	cIP1vsInput	"intron (NM_001048189, intron 3 of 12)"	L1_Mur3|LINE|L1	496179	NM_030231	78933	Mm.435620	NM_001048189	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding	0	0.356436
Merged-chr1-127660570-1	chr1	127660520	127660620	+	2.4	cIP2vsInput	"intron (NM_028135, intron 2 of 7)"	"intron (NM_028135, intron 2 of 7)"	17451	NM_028135	72160	Mm.281287	NM_028135	ENSMUSG00000026347	Tmem163	2610024A01Rik|SV31	transmembrane protein 163	protein-coding	0.03	0.445545
Merged-chrX-107182752-1	chrX	107182702	107182802	+	2.4	cIP2vsInput	Intergenic	Lx8b|LINE|L1	33137	NM_175442	213438	Mm.265244	NM_001122595	ENSMUSG00000054293	A630033H20Rik	AI662791|P2ry10	RIKEN cDNA A630033H20 gene	protein-coding	0.01	0.39604
Merged-chr9-93880717-1	chr9	93880667	93880767	+	2.4	cIP2vsInput	Intergenic	Intergenic	657364	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49	RIKEN cDNA 1190002N15 gene	protein-coding	0.01	0.356436
Merged-chr9-3459249-1	chr9	3459199	3459299	+	2.4	cIP1vsInput	"intron (NM_027545, intron 15 of 17)"	"intron (NM_027545, intron 15 of 17)"	55164	NM_027545	244672	Mm.245482	NM_027545		Cwf19l2	3230401L03Rik|9030209E10	"CWF19-like 2, cell cycle control (S. pombe)"	protein-coding	0	0.267327
Merged-chr4-74861107-1	chr4	74861057	74861157	+	2.4	cIP1vsInput	Intergenic	Intergenic	417179	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	3110001D03Rik	1700027K24Rik	RIKEN cDNA 3110001D03 gene	protein-coding	0.01	0.227723
Merged-chr12-29291459-1	chr12	29291409	29291509	+	2.4	cIP1vsInput	Intergenic	Intergenic	-236925	NM_001093775	17933	Mm.418721	NM_001093775	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding	0.02	0.435644
Merged-chr17-48336824-1	chr17	48336774	48336874	+	2.4	cIP2vsInput	Intergenic	Intergenic	-9577	NM_031254	83433	Mm.261623	NM_001272078	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding	0	0.267327
Merged-chr6-132509233-1	chr6	132509183	132509283	+	2.4	cIP2vsInput	Intergenic	Intergenic	-60609	NM_011174	19131	Mm.484054	NM_011174	ENSMUSG00000059934	Prh1	MP2|Prp	proline rich protein HaeIII subfamily 1	protein-coding	0	0.316832
Merged-chr13-112823886-1	chr13	112823836	112823936	+	2.4	cIP1vsInput	"intron (NM_008903, intron 1 of 5)"	"intron (NM_008903, intron 1 of 5)"	22963	NM_008903	19012	Mm.317186	NM_008247	ENSMUSG00000021759	Ppap2a	Hic53|Hpic53|LPP-1|LPP1|mPAP	phosphatidic acid phosphatase type 2A	protein-coding	0	0.366337
Merged-chr14-113777975-1	chr14	113777925	113778025	+	2.4	cIP2vsInput	Intergenic	L4_C_Mam|LINE|RTE-X	-1053990	NR_045661	75822	Mm.410813	NR_045661		4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	miscRNA	0	0.356436
Merged-chr1-148661093-1	chr1	148661043	148661143	+	2.4	cIP2vsInput	Intergenic	Intergenic	1300191	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0	0.287129
Merged-chr1-94523231-1	chr1	94523181	94523281	+	2.4	cIP2vsInput	Intergenic	Intergenic	-274211	NR_040473	74689	Mm.399187	NR_040473		4930440C22Rik	-	RIKEN cDNA 4930440C22 gene	miscRNA	0	0.336634
Merged-chr4-61821324-1	chr4	61821274	61821374	+	2.4	cIP1vsInput	Intergenic	L1Md_T|LINE|L1	13856	NM_008649	17844	Mm.445286	XM_003689354	ENSMUSG00000058523	Mup5	Mup18	major urinary protein 5	protein-coding	0	0.336634
Merged-chr2-73976224-1	chr2	73976174	73976274	+	2.4	cIP2vsInput	Intergenic	Intergenic	-64930	NM_175015	228033	Mm.2966	NM_175015	ENSMUSG00000018770	Atp5g3	6030447M23	"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9)"	protein-coding	0	0.326733
Merged-chr14-120680615-1	chr14	120680565	120680665	+	2.4	cIP1vsInput	Intergenic	L1MEc|LINE|L1	202154	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding	0	0.29703
Merged-chr16-73022040-1	chr16	73021990	73022090	+	2.4	cIP1vsInput	"intron (NM_019413, intron 24 of 28)"	"intron (NM_019413, intron 24 of 28)"	358891	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout homolog 1 (Drosophila)	protein-coding	0	0.306931
Merged-chr8-26708421-1	chr8	26708371	26708471	+	2.4	cIP2vsInput	Intergenic	(TA)n|Simple_repeat|Simple_repeat	116002	NR_045904	72316	Mm.490534	NR_045904		2310008N11Rik	-	RIKEN cDNA 2310008N11 gene	miscRNA	0	0.277228
Merged-chr15-42136023-1	chr15	42135973	42136073	+	2.4	cIP1vsInput	Intergenic	Intergenic	-266303	NM_175456	223513	Mm.148913	NM_175456	ENSMUSG00000042895	Abra	C130068O12Rik|STARS	actin-binding Rho activating protein	protein-coding	0	0.346535
Merged-chr8-43705764-1	chr8	43705714	43705814	+	2.4	cIP2vsInput	Intergenic	Lx7|LINE|L1	-6273	NM_001079931	384814	Mm.383288	NM_001079931		Gm5347	EG384814	predicted gene 5347	protein-coding	0	0.306931
Merged-chr8-43930252-1	chr8	43930202	43930302	+	2.4	cIP1vsInput	Intergenic	Intergenic	-230761	NM_001079931	384814	Mm.383288	NM_001079931		Gm5347	EG384814	predicted gene 5347	protein-coding	0	0.336634
Merged-chr15-47557291-1	chr15	47557241	47557341	+	2.4	cIP1vsInput	Intergenic	L1_Mur1|LINE|L1	933986	NR_045811	75281	Mm.159487	NR_045811		4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	miscRNA	0	0.316832
Merged-chr11-93641168-1	chr11	93641118	93641218	+	2.4	cIP2vsInput	Intergenic	Intergenic	244598	NM_001013375	217109	Mm.379350	NM_001013375	ENSMUSG00000054079	Utp18	6230425C22Rik|6430513M13|Wdr50	"UTP18, small subunit (SSU) processome component, homolog (yeast)"	protein-coding	0.01	0.485149
Merged-chr6-10326836-1	chr6	10326786	10326886	+	2.4	cIP2vsInput	Intergenic	Intergenic	647542	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	miscRNA	0	0.366337
Merged-chr15-29786982-1	chr15	29786932	29787032	+	2.4	cIP2vsInput	Intergenic	Intergenic	-385611	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	"catenin (cadherin associated protein), delta 2"	protein-coding	0	0.29703
Merged-chr12-18319154-1	chr12	18319104	18319204	+	2.4	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-195356	NM_001033157	236366	Mm.352227	NM_001033157		5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding	0.01	0.435644
Merged-chr1-35836112-1	chr1	35836062	35836162	+	2.4	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	-232288	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding	0	0.39604
Merged-chr14-36765055-1	chr14	36765005	36765105	+	2.4	cIP2vsInput	Intergenic	Charlie7|DNA|hAT-Charlie	170513	NM_028407	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding	0	0.287129
Merged-chr2-86857408-1	chr2	86857358	86857458	+	2.4	cIP2vsInput	Intergenic	Intergenic	-5712	NM_146730	258725	Mm.377658	NM_146730	ENSMUSG00000075171	Olfr1095	MOR179-1	olfactory receptor 1095	protein-coding	0	0.306931
Merged-chr11-35766769-1	chr11	35766719	35766819	+	2.4	cIP2vsInput	Intergenic	Intergenic	-2726	NM_145962	211347	Mm.255044	NM_145962	ENSMUSG00000018846	Pank3	-	pantothenate kinase 3	protein-coding	0.01	0.336634
Merged-chr4-118904579-1	chr4	118904529	118904629	+	2.4	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	11494	NM_146334	258331	Mm.223025	NM_146334	ENSMUSG00000073768	Olfr1330	MOR259-8	olfactory receptor 1330	protein-coding	0.01	0.306931
Merged-chr15-83086132-1	chr15	83086082	83086182	+	2.4	cIP2vsInput	Intergenic	Intergenic	-14073	NM_023475	68607	Mm.30056	NM_023475	ENSMUSG00000058586	Serhl	0610008B10Rik|1110019M09Rik|AU019786	serine hydrolase-like	protein-coding	0.02	0.70297
Merged-chr5-78394333-1	chr5	78394283	78394383	+	2.4	cIP1vsInput	Intergenic	Intergenic	-882585	NR_027806	231332	Mm.373616	NM_001010832		Pea15b	-	phosphoprotein enriched in astrocytes 15B	pseudo	0.01	0.336634
Merged-chr8-45421472-1	chr8	45421422	45421522	+	2.4	cIP2vsInput	Intergenic	Intergenic	-10933	NM_126166	142980	Mm.33874	NM_126166	ENSMUSG00000031639	Tlr3	AI957183	toll-like receptor 3	protein-coding	0	0.39604
Merged-chr12-7304340-1	chr12	7304290	7304390	+	2.4	cIP2vsInput	Intergenic	Intergenic	75990	NR_045045	73575	Mm.179463	NR_045045		1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	miscRNA	0	0.29703
Merged-chr18-12925328-1	chr18	12925278	12925378	+	2.4	cIP2vsInput	"intron (NM_207530, intron 4 of 27)"	"intron (NM_207530, intron 4 of 27)"	16513	NM_207530	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding	0.01	0.277228
Merged-chr17-38739127-1	chr17	38739077	38739177	+	2.4	cIP2vsInput	Intergenic	Intergenic	99680	NM_001177586	100126768	Mm.471528	NM_001177586	ENSMUSG00000092342	Gm20516	Esp31	predicted gene 20516	protein-coding	0.01	0.306931
Merged-chr6-89644136-1	chr6	89644086	89644186	+	2.4	cIP2vsInput	"exon (NM_001178059, exon 1 of 14)"	"exon (NM_001178059, exon 1 of 14)"	148	NM_001178058	232223	Mm.229332	NM_001178058	ENSMUSG00000000811	Txnrd3	AI196535|TR2|Tgr	thioredoxin reductase 3	protein-coding	0.13	0.762376
Merged-chr17-39809286-1	chr17	39809236	39809336	+	2.4	cIP1vsInput	Intergenic	MTC-int|LTR|ERVL-MaLR	-33711	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA	0	0.39604
Merged-chr4-62008848-1	chr4	62008798	62008898	+	2.4	cIP1vsInput	Intergenic	L1VL4|LINE|L1	45269	NM_001012323	381530	Mm.460005	NM_001012323	ENSMUSG00000078672	Mup20	Gm12560|Mup24|OTTMUSG00000007485|darcin	major urinary protein 20	protein-coding	0	0.306931
Merged-chr5-79763135-1	chr5	79763085	79763185	+	2.4	cIP2vsInput	Intergenic	Intergenic	-247231	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0	0.326733
Merged-chr14-12074982-1	chr14	12074932	12075032	+	2.4	cIP1vsInput	"intron (NM_008981, intron 5 of 29)"	"intron (NM_008981, intron 5 of 29)"	-209227	NM_146051	218734	Mm.44068	NM_146051	ENSMUSG00000033111	3830406C13Rik	3110059I09Rik|AV167947	RIKEN cDNA 3830406C13 gene	protein-coding	0	0.39604
Merged-chr15-47247179-1	chr15	47247129	47247229	+	2.4	cIP1vsInput	Intergenic	Intergenic	623874	NR_045811	75281	Mm.159487	NR_045811		4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	miscRNA	0	0.346535
Merged-chr2-140885356-1	chr2	140885306	140885406	+	2.4	cIP2vsInput	"intron (NM_001013802, intron 4 of 18)"	LTR16C|LTR|ERVL	-213880	NM_178382	71436	Mm.426781	NM_001172160	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0	0.49505
Merged-chr7-91304434-1	chr7	91304384	91304484	+	2.4	cIP2vsInput	"intron (NM_011807, intron 1 of 22)"	L1_Mm|LINE|L1	213648	NM_011807	23859	Mm.257035	NM_001243046		Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|PSD93	"discs, large homolog 2 (Drosophila)"	protein-coding	0	0.346535
Merged-chr10-32003614-1	chr10	32003564	32003664	+	2.4	cIP1vsInput	"intron (NM_001013411, intron 3 of 6)"	"intron (NM_001013411, intron 3 of 6)"	-393889	NM_001146349	268291	Mm.295212	NM_001146349		Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding	0	0.306931
Merged-chr16-83414089-1	chr16	83414039	83414139	+	2.4	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-957054	NR_040567	75247	Mm.417813	NR_040567		4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	miscRNA	0	0.247525
Merged-chr1-94674599-1	chr1	94674549	94674649	+	2.4	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	-122843	NR_040473	74689	Mm.399187	NR_040473		4930440C22Rik	-	RIKEN cDNA 4930440C22 gene	miscRNA	0	0.336634
Merged-chr9-76702890-1	chr9	76702840	76702940	+	2.4	cIP2vsInput	Intergenic	RMER6-int|LTR|ERVK	-157086	NM_001045518	208994	Mm.256929	NM_001045518	ENSMUSG00000032358	Fam83b	C530008M07Rik|Gm516	"family with sequence similarity 83, member B"	protein-coding	0	0.366337
Merged-chr15-28332371-1	chr15	28332321	28332421	+	2.4	cIP2vsInput	"intron (NM_133365, intron 39 of 78)"	"intron (NM_133365, intron 39 of 78)"	128605	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnahc5	AU022615|Dnah5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	"dynein, axonemal, heavy chain 5"	protein-coding	0	0.326733
Merged-chr3-59069945-1	chr3	59069895	59069995	+	2.4	cIP1vsInput	"intron (NM_177855, intron 5 of 43)"	RSINE1|SINE|B4	31876	NM_173398	229323	Mm.123648	NM_173398	ENSMUSG00000050075	Gpr171	A630006E05|F730001G15Rik|H963	G protein-coupled receptor 171	protein-coding	0.01	0.376238
Merged-chr16-62369729-1	chr16	62369679	62369779	+	2.4	cIP2vsInput	Intergenic	Intergenic	416987	NM_178925	106338	Mm.26321	NM_178925		Nsun3	6720484A09Rik|AU022521	NOL1/NOP2/Sun domain family member 3	protein-coding	0.01	0.346535
Merged-chr14-114004595-1	chr14	114004545	114004645	+	2.4	cIP1vsInput	Intergenic	Intergenic	-827370	NR_045661	75822	Mm.410813	NR_045661		4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	miscRNA	0	0.346535
Merged-chr6-66370538-1	chr6	66370488	66370588	+	2.4	cIP1vsInput	Intergenic	MER119|DNA|hAT-Charlie	-164930	NM_019499	56150	Mm.489653	NM_019499	ENSMUSG00000029910	Mad2l1	AA673185|MAD2	MAD2 mitotic arrest deficient-like 1	protein-coding	0.01	0.386139
Merged-chr15-31730291-2	chr15	31730235	31730347	+	2.4	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	128175	NM_026546	68073	Mm.119185	NM_026546	ENSMUSG00000039065	Fam173b	A930016P21Rik|AA987072	"family with sequence similarity 173, member B"	protein-coding	0.008929	0.469027
Merged-chr13-7232571-1	chr13	7232521	7232621	+	2.4	cIP2vsInput	Intergenic	Intergenic	-583847	NM_019703	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|PFK-C	"phosphofructokinase, platelet"	protein-coding	0	0.29703
Merged-chr14-35791102-1	chr14	35791052	35791152	+	2.4	cIP2vsInput	Intergenic	Intergenic	20876	NM_001033766	239036	Mm.239970	NM_001033766	ENSMUSG00000041068	4930596D02Rik	-	RIKEN cDNA 4930596D02 gene	protein-coding	0	0.39604
Merged-chr6-89362688-1	chr6	89362638	89362738	+	2.4	cIP2vsInput	promoter-TSS (NM_008881)	promoter-TSS (NM_008881)	-75	NM_008881	18844	Mm.3789	NM_008881	ENSMUSG00000030084	Plxna1	2600013D04Rik|NOV|PlexA1|Plxn1|mKIAA4053	plexin A1	protein-coding	0.19	0.90099
Merged-chr15-28592328-1	chr15	28592278	28592378	+	2.4	cIP2vsInput	Intergenic	Intergenic	388562	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnahc5	AU022615|Dnah5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	"dynein, axonemal, heavy chain 5"	protein-coding	0	0.326733
Merged-chr11-30000590-1	chr11	30000540	30000640	+	2.4	cIP2vsInput	"intron (NM_146016, intron 2 of 41)"	L1_Mur1|LINE|L1	25443	NM_146016	237711	Mm.445271	NM_146016	ENSMUSG00000044072	Eml6	2900083P10Rik|C230094A16Rik|EMAP-6	echinoderm microtubule associated protein like 6	protein-coding	0.01	0.346535
Merged-chr13-40438669-1	chr13	40438619	40438719	+	2.4	cIP1vsInput	Intergenic	Intergenic	-150658	NM_172143	218165	Mm.364096	NM_172143	ENSMUSG00000047094	Ofcc1	opo	orofacial cleft 1 candidate 1	protein-coding	0	0.346535
Merged-chr14-66069382-1	chr14	66069332	66069432	+	2.4	cIP1vsInput	"intron (NM_009618, intron 4 of 20)"	"intron (NM_009618, intron 4 of 20)"	8351	NM_009618	11495	Mm.422850	NM_009618	ENSMUSG00000022039	Adam2	AI323749|Ftnb|Ph30-beta	a disintegrin and metallopeptidase domain 2	protein-coding	0.01	0.326733
Merged-chr8-49464698-1	chr8	49464648	49464748	+	2.4	cIP1vsInput	Intergenic	Intergenic	-790008	NM_011857	23965	Mm.42191	NM_001145937	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding	0	0.257426
Merged-chr2-78080085-1	chr2	78080035	78080135	+	2.4	cIP2vsInput	Intergenic	Intergenic	-133732	NM_030560	80744	Mm.288151	XM_003946079	ENSMUSG00000027014	Cwc22	AA684037|AI173004|AL022752|B230213M24|mKIAA1604	CWC22 spliceosome-associated protein homolog (S. cerevisiae)	protein-coding	0	0.316832
Merged-chr16-20213785-1	chr16	20213735	20213835	+	2.4	cIP1vsInput	"intron (NM_001033237, intron 21 of 29)"	"intron (NM_001033237, intron 21 of 29)"	27573	NM_198599	208158	Mm.326383	NM_198599	ENSMUSG00000041205	Map6d1	A330066I15Rik	MAP6 domain containing 1	protein-coding	0	0.455446
Merged-chr13-6166699-1	chr13	6166649	6166749	+	2.4	cIP2vsInput	Intergenic	Intergenic	305210	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding	0	0.326733
Merged-chr9-65364098-1	chr9	65364048	65364148	+	2.4	cIP2vsInput	"intron (NM_001111145, intron 1 of 6)"	"intron (NM_001111145, intron 1 of 6)"	3038	NM_001111145	208080	Mm.291862	NM_001111145	ENSMUSG00000086228	Gm514	-	predicted gene 514	protein-coding	0.01	0.326733
Merged-chr7-94143287-1	chr7	94143237	94143337	+	2.4	cIP1vsInput	Intergenic	Intergenic	1063408	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0	0.287129
Merged-chr16-94358566-1	chr16	94358516	94358616	+	2.4	cIP2vsInput	TTS (NM_001159620)	TTS (NM_001159620)	11764	NM_001159619	56176	Mm.474449	NM_001159616	ENSMUSG00000022940	Pigp	Dcrc|Dscr5	"phosphatidylinositol glycan anchor biosynthesis, class P"	protein-coding	0.01	0.465347
Merged-chr2-7332595-1	chr2	7332545	7332645	+	2.4	cIP2vsInput	"intron (NM_001110232, intron 1 of 15)"	"intron (NM_001110232, intron 1 of 15)"	63405	NM_001110232	14007	Mm.398543	NM_183219	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	"CUGBP, Elav-like family member 2"	protein-coding	0	0.336634
Merged-chr12-47348910-1	chr12	47348860	47348960	+	2.4	cIP1vsInput	Intergenic	Intergenic	-530135	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding	0.02	0.386139
Merged-chr16-57980744-1	chr16	57980694	57980794	+	2.4	cIP2vsInput	Intergenic	MIR|SINE|MIR	-226007	NM_007739	12837	Mm.130388	NM_007739	ENSMUSG00000068196	Col8a1	Col8a-1	"collagen, type VIII, alpha 1"	protein-coding	0.01	0.356436
Merged-chr4-67704084-1	chr4	67704034	67704134	+	2.4	cIP1vsInput	Intergenic	Intergenic	876273	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding	0	0.306931
Merged-chr2-66410635-1	chr2	66410585	66410685	+	2.4	cIP2vsInput	"intron (NM_018733, intron 1 of 26)"	"intron (NM_018733, intron 1 of 26)"	30202	NM_018733	20265	Mm.439704	NM_018733	ENSMUSG00000064329	Scn1a	B230332M13|Nav1.1	"sodium channel, voltage-gated, type I, alpha"	protein-coding	0.04	0.415842
Merged-chr13-78725575-1	chr13	78725525	78725625	+	2.4	cIP1vsInput	Intergenic	L1_Mur1|LINE|L1	-526593	NM_010151	13865	Mm.439653	NM_010151		Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR3|Erbal3|SVP44|Tcfcoup1	"nuclear receptor subfamily 2, group F, member 1"	protein-coding	0	0.306931
Merged-chr8-41285034-1	chr8	41284984	41285084	+	2.4	cIP2vsInput	"intron (NM_023662, intron 16 of 37)"	"intron (NM_023662, intron 16 of 37)"	45275	NM_023662	18536	Mm.117896	NM_023662	ENSMUSG00000031592	Pcm1	2600002H09Rik|9430077F19Rik|C030044G17Rik	pericentriolar material 1	protein-coding	0	0.29703
Merged-chr19-59764823-1	chr19	59764773	59764873	+	2.4	cIP1vsInput	Intergenic	RMER3D-int|LTR|ERVK	178541	NM_001033172	74998	Mm.24167	NM_001033172	ENSMUSG00000040022	Rab11fip2	4930470G04Rik|A830046J09Rik|AW558126|Nrip11	RAB11 family interacting protein 2 (class I)	protein-coding	0	0.346535
Merged-chr6-105182504-1	chr6	105182454	105182554	+	2.4	cIP2vsInput	Intergenic	L1ME2|LINE|L1	310164	NR_040297	100503536	Mm.366960	NR_040297		Gm19757	-	"predicted gene, 19757"	miscRNA	0	0.336634
Merged-chr17-33629174-1	chr17	33629124	33629224	+	2.4	cIP2vsInput	promoter-TSS (NM_026712)	promoter-TSS (NM_026712)	82	NM_026712	328801	Mm.181488	NM_026712	ENSMUSG00000073423	Zfp414	0610030H11Rik|Znf414	zinc finger protein 414	protein-coding	0.08	0.633663
Merged-chr6-44575085-1	chr6	44575035	44575135	+	2.4	cIP1vsInput	Intergenic	Intergenic	-484976	NM_001004357	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0.01	0.316832
Merged-chr5-78579162-1	chr5	78579112	78579212	+	2.4	cIP2vsInput	Intergenic	Intergenic	936742	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0	0.29703
Merged-chr1-33078672-1	chr1	33078622	33078722	+	2.4	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	-531379	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding	0	0.267327
Merged-chr7-109740739-1	chr7	109740689	109740789	+	2.4	cIP2vsInput	"intron (NM_020050, intron 4 of 4)"	"intron (NM_020050, intron 4 of 4)"	-9007	NM_020051	56787	Mm.29275	NM_020051	ENSMUSG00000035951	Ascl3	Sgn1|bHLHa42	achaete-scute complex homolog 3 (Drosophila)	protein-coding	0	0.425743
Merged-chr15-33531622-1	chr15	33531572	33531672	+	2.4	cIP1vsInput	"intron (NM_018755, intron 8 of 8)"	MER117|DNA|hAT-Charlie	121814	NR_045070	75880	Mm.396109	NR_045070		4930592A05Rik	-	RIKEN cDNA 4930592A05 gene	miscRNA	0.01	0.356436
Merged-chr4-16454560-1	chr4	16454510	16454610	+	2.4	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	290450	NR_045765	100415915	Mm.387180	NR_045765	ENSMUSG00000085112	A530072M11Rik	-	RIKEN cDNA gene A530072M11	miscRNA	0	0.316832
Merged-chr11-46165445-1	chr11	46165395	46165495	+	2.4	cIP2vsInput	"intron (NM_172524, intron 1 of 5)"	RSINE1|SINE|B4	914	NM_172524	214112	Mm.225253	NM_172524	ENSMUSG00000020411	Nipal4	9530066K23Rik	NIPA-like domain containing 4	protein-coding	0	0.415842
Merged-chr14-78333138-1	chr14	78333088	78333188	+	2.4	cIP2vsInput	Intergenic	Intergenic	-25095	NM_011613	21943	Mm.249221	NM_011613	ENSMUSG00000022015	Tnfsf11	Ly109l|ODF|OPG|OPGL|RANKL|Trance	"tumor necrosis factor (ligand) superfamily, member 11"	protein-coding	0	0.415842
Merged-chr11-37292735-1	chr11	37292685	37292785	+	2.4	cIP1vsInput	Intergenic	Intergenic	-348492	NM_011856	23964	Mm.445432	NM_011856	ENSMUSG00000049336	Tenm2	2610040L17Rik|9330187F13Rik|D3Bwg1534e|Odz2|Odz3|Ten-m2|mKIAA1127	teneurin transmembrane protein 2	protein-coding	0.01	0.326733
Merged-chr15-56284203-1	chr15	56284153	56284253	+	2.4	cIP2vsInput	Intergenic	RMER15|LTR|ERVL	-377254	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	"syntrophin, basic 1"	protein-coding	0	0.346535
Merged-chr8-66784747-1	chr8	66784697	66784797	+	2.4	cIP2vsInput	Intergenic	MT2A|LTR|ERVL	-75470	NM_001163564	234344	Mm.334561	NM_001163564	ENSMUSG00000014907	Naf1	Gm174	nuclear assembly factor 1 homolog (S. cerevisiae)	protein-coding	0.01	0.405941
Merged-chr7-88107052-1	chr7	88107002	88107102	+	2.4	cIP1vsInput	"intron (NM_001081414, intron 9 of 9)"	"intron (NM_001081414, intron 9 of 9)"	-171041	NM_009982	13032	Mm.322945	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|DPP1|DPPI	cathepsin C	protein-coding	0.01	0.346535
Merged-chr3-135959912-1	chr3	135959862	135959962	+	2.4	cIP1vsInput	Intergenic	Intergenic	-119643	NR_040540	71038	Mm.410798	NR_040540		4933401H06Rik	-	RIKEN cDNA 4933401H06 gene	miscRNA	0	0.39604
Merged-chr3-54720230-1	chr3	54720180	54720280	+	2.4	cIP2vsInput	Intergenic	Intergenic	15134	NM_027148	69639	Mm.29253	NM_001163570	ENSMUSG00000027752	Exosc8	2310032N20Rik|CIP3|mKIAA4013	exosome component 8	protein-coding	0	0.336634
Merged-chr14-109682593-1	chr14	109682543	109682643	+	2.4	cIP2vsInput	Intergenic	Intergenic	222363	NR_039542	100628607		NR_039542	ENSMUSG00000092639	Mir3964	mmu-mir-3964|mu-mir-3964	microRNA 3964	miscRNA	0	0.29703
Merged-chr8-18291946-1	chr8	18291896	18291996	+	2.4	cIP1vsInput	Intergenic	Intergenic	-303227	NM_173189	244329	Mm.235296	NM_173189	ENSMUSG00000039842	Mcph1	5430437K10Rik|BRIT1|D030046N04Rik|MCT	"microcephaly, primary autosomal recessive 1"	protein-coding	0	0.405941
Merged-chr2-98602388-1	chr2	98602338	98602438	+	2.4	cIP1vsInput	Intergenic	Intergenic	1134714	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0.01	0.356436
Merged-chr16-94758257-1	chr16	94758207	94758307	+	2.4	cIP1vsInput	"intron (NM_001025584, intron 4 of 4)"	"intron (NM_001025584, intron 4 of 4)"	98433	NM_001025590	16522	Mm.328720	NM_001025584	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	"potassium inwardly-rectifying channel, subfamily J, member 6"	protein-coding	0.02	0.435644
Merged-chr16-47110008-1	chr16	47109958	47110058	+	2.4	cIP1vsInput	Intergenic	Intergenic	-613041	NM_021497	58998	Mm.328072	NM_021495	ENSMUSG00000022656	Pvrl3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113	poliovirus receptor-related 3	protein-coding	0	0.29703
Merged-chr17-46546363-1	chr17	46546313	46546413	+	2.4	cIP2vsInput	promoter-TSS (NM_001081335)	promoter-TSS (NM_001081335)	25	NM_001081335	78309	Mm.329076	NM_001081335	ENSMUSG00000040327	Cul9	1810035I07Rik|Cul-9|Parc|mKIAA0708	cullin 9	protein-coding	0.15	0.712871
Merged-chr12-57645802-1	chr12	57645752	57645852	+	2.4	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	81687	NM_001037743	70846	Mm.449996	NM_001037743	ENSMUSG00000046782	4921506M07Rik	-	RIKEN cDNA 4921506M07 gene	protein-coding	0.02	0.336634
Merged-chr17-81867762-1	chr17	81867712	81867812	+	2.4	cIP1vsInput	Intergenic	Intergenic	-129385	NM_011406	20541	Mm.489060	NM_001112798		Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	"solute carrier family 8 (sodium/calcium exchanger), member 1"	protein-coding	0	0.277228
Merged-chr17-84455504-1	chr17	84455454	84455554	+	2.4	cIP1vsInput	"intron (NM_183021, intron 4 of 37)"	"intron (NM_183021, intron 4 of 37)"	10704	NM_183021	240174	Mm.246767	NM_177826	ENSMUSG00000024251	Thada	6530405K19|A930021O22|AU019899|BC052885|GITA	thyroid adenoma associated	protein-coding	0	0.326733
Merged-chr8-50758498-1	chr8	50758448	50758548	+	2.4	cIP1vsInput	Intergenic	Intergenic	390386	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.366337
Merged-chr9-31442881-1	chr9	31442831	31442931	+	2.4	cIP1vsInput	"intron (NM_144936, intron 1 of 5)"	"intron (NM_144936, intron 1 of 5)"	21357	NM_144936	235135	Mm.390134	NM_144936	ENSMUSG00000041737	Tmem45b	BC018222	transmembrane protein 45b	protein-coding	0	0.356436
Merged-chr1-21162148-1	chr1	21162098	21162198	+	2.4	cIP1vsInput	Intergenic	Intergenic	-56483	NM_029398	75712	Mm.441478	NM_029398	ENSMUSG00000025933	Tmem14a	5730496E24Rik|C85783|PTD011	transmembrane protein 14A	protein-coding	0	0.267327
Merged-chr5-40275810-1	chr5	40275760	40275860	+	2.4	cIP2vsInput	Intergenic	Intergenic	-631179	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding	0	0.336634
Merged-chr1-77124674-1	chr1	77124624	77124724	+	2.4	cIP2vsInput	Intergenic	Intergenic	390414	NM_007936	13838	Mm.400747	NM_007936	ENSMUSG00000026235	Epha4	2900005C20Rik|AI385584|Cek8|Hek8|Sek|Sek1|Tyro1|rb	Eph receptor A4	protein-coding	0	0.316832
Merged-chr11-35407519-1	chr11	35407469	35407569	+	2.4	cIP1vsInput	"intron (NM_011412, intron 4 of 35)"	"intron (NM_011412, intron 4 of 35)"	-209297	NR_029799	723924		NR_029799		Mir218-2	Mirn218-2|mir-218-2	microRNA 218-2	miscRNA	0.01	0.435644
Merged-chr13-110350534-1	chr13	110350484	110350584	+	2.4	cIP1vsInput	Intergenic	MLT1A|LTR|ERVL-MaLR	6638	NM_177713	238875	Mm.30533	NM_177713	ENSMUSG00000046006	Gapt	9830130M13Rik	"Grb2-binding adaptor, transmembrane"	protein-coding	0	0.376238
Merged-chr12-33471465-1	chr12	33471415	33471515	+	2.4	cIP1vsInput	Intergenic	Lx5c|LINE|L1	41841	NM_172253	28071	Mm.413045	NM_172253	ENSMUSG00000020561	Twistnb	2410173G11|2810024J17Rik|D16Wsu83e	TWIST neighbor	protein-coding	0	0.336634
Merged-chr9-19249482-1	chr9	19249432	19249532	+	2.4	cIP2vsInput	promoter-TSS (NM_146567)	promoter-TSS (NM_146567)	-19	NM_146567	258560	Mm.377569	NM_146567	ENSMUSG00000048391	Olfr843	MOR155-2	olfactory receptor 843	protein-coding	0.01	0.306931
Merged-chr14-109120142-1	chr14	109120092	109120192	+	2.4	cIP2vsInput	Intergenic	Intergenic	-205903	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	"SLIT and NTRK-like family, member 1"	protein-coding	0	0.29703
Merged-chr8-90656184-1	chr8	90656134	90656234	+	2.4	cIP1vsInput	Intergenic	Lx8|LINE|L1	-172651	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding	0.01	0.366337
Merged-chr1-23153637-1	chr1	23153587	23153687	+	2.4	cIP2vsInput	Intergenic	Intergenic	-51384	NM_025746	66755	Mm.431297	NM_025746	ENSMUSG00000073730	4933415F23Rik	-	RIKEN cDNA 4933415F23 gene	protein-coding	0	0.326733
Merged-chr4-50846269-1	chr4	50846219	50846319	+	2.4	cIP2vsInput	Intergenic	RLTR17D_Mm|LTR|ERVK	-370409	NM_001162865	74914	Mm.159368	NM_001162865	ENSMUSG00000039555	Cylc2	4930488P18Rik	"cylicin, basic protein of sperm head cytoskeleton 2"	protein-coding	0	0.306931
Merged-chr8-72296055-1	chr8	72296005	72296105	+	2.4	cIP1vsInput	Intergenic	Intergenic	-23007	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding	0	0.475248
Merged-chr2-149586155-1	chr2	149586105	149586205	+	2.4	cIP2vsInput	Intergenic	Intergenic	180906	NM_021405	58214	Mm.117117	NM_021405	ENSMUSG00000033156	Cst10	DD72	cystatin 10 (chondrocytes)	protein-coding	0	0.316832
Merged-chr5-15588409-1	chr5	15588359	15588459	+	2.4	cIP1vsInput	Intergenic	Intergenic	-30690	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0	0.277228
Merged-chr4-51671778-1	chr4	51671728	51671828	+	2.4	cIP1vsInput	Intergenic	Intergenic	379332	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	miscRNA	0	0.386139
Merged-chr11-15258463-1	chr11	15258413	15258513	+	2.4	cIP1vsInput	Intergenic	Intergenic	659223	NM_001164166	432536	Mm.33646	NR_002893		Pom121l12	1700054H16Rik	POM121 membrane glycoprotein-like 12	protein-coding	0	0.306931
Merged-chr14-83156769-1	chr14	83156719	83156819	+	2.4	cIP1vsInput	Intergenic	Intergenic	-1286794	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0	0.346535
Merged-chr17-76831893-1	chr17	76831843	76831943	+	2.4	cIP2vsInput	Intergenic	Intergenic	970870	NR_033456	100043885	Mm.127562	NR_033456		Gm4710	-	predicted gene 4710	miscRNA	0.01	0.356436
Merged-chr9-19748355-1	chr9	19748305	19748405	+	2.4	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-31928	NM_011001	18358	Mm.248950	NM_011001	ENSMUSG00000058659	Olfr58	IG6|MOR146-3|MOR146-7P	olfactory receptor 58	protein-coding	0.01	0.346535
Merged-chr13-38658679-1	chr13	38658629	38658729	+	2.4	cIP2vsInput	"intron (NM_025380, intron 1 of 3)"	CpG	349	NM_025380	66143	Mm.490319	NM_025380	ENSMUSG00000001707	Eef1e1	1110003A02Rik	eukaryotic translation elongation factor 1 epsilon 1	protein-coding	0.09	0.673267
Merged-chr7-94787308-1	chr7	94787258	94787358	+	2.4	cIP1vsInput	Intergenic	Intergenic	-1423329	NM_011858	23966	Mm.391678	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding	0	0.267327
Merged-chr12-43427054-1	chr12	43427004	43427104	+	2.4	cIP2vsInput	Intergenic	Intergenic	783014	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	"DnaJ (Hsp40) homolog, subfamily B, member 9"	protein-coding	0.01	0.356436
Merged-chr15-46371264-1	chr15	46371214	46371314	+	2.4	cIP1vsInput	"intron (NR_045509, intron 3 of 3)"	Lx|LINE|L1	46679	NR_045509	71120	Mm.158571	NR_045509		1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	miscRNA	0.01	0.366337
Merged-chr2-137037479-1	chr2	137037429	137037529	+	2.4	cIP2vsInput	"intron (NM_001038641, intron 4 of 7)"	"intron (NM_001038641, intron 4 of 7)"	79041	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding	0.01	0.346535
Merged-chr4-121141167-1	chr4	121141117	121141217	+	2.4	cIP2vsInput	Intergenic	MYSERV6-int|LTR|ERVK	-31941	NM_001081312	69469	Mm.481120	NM_001081312	ENSMUSG00000078577	Tmco2	1700028F16Rik	transmembrane and coiled-coil domains 2	protein-coding	0	0.326733
Merged-chr6-121896439-1	chr6	121896389	121896489	+	2.4	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	57898	NM_008645	17836	Mm.1311	NM_008645	ENSMUSG00000059908	Mug1	-	murinoglobulin 1	protein-coding	0	0.287129
Merged-chr3-73434765-1	chr3	73434715	73434815	+	2.4	cIP1vsInput	"intron (NR_040547, intron 2 of 7)"	MLT1B|LTR|ERVL-MaLR	46886	NR_040547	74693	Mm.292227	NR_040547		4930509J09Rik	-	RIKEN cDNA 4930509J09 gene	miscRNA	0	0.326733
Merged-chr2-108203808-1	chr2	108203758	108203858	+	2.4	cIP2vsInput	Intergenic	Intergenic	913219	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	"potassium voltage-gated channel, shaker-related subfamily, member 4"	protein-coding	0	0.316832
Merged-chr10-109479125-1	chr10	109479075	109479175	+	2.4	cIP2vsInput	Intergenic	Intergenic	-468150	NM_001252341	20979	Mm.489829	NM_001252341	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding	0	0.386139
Merged-chr15-54306993-1	chr15	54306943	54307043	+	2.4	cIP2vsInput	Intergenic	Intergenic	-28509	NM_008764	18383	Mm.15383	NM_008764	ENSMUSG00000063727	Tnfrsf11b	OCIF|Opg|TR1	"tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)"	protein-coding	0	0.346535
Merged-chr12-9230190-1	chr12	9230140	9230240	+	2.4	cIP1vsInput	Intergenic	Intergenic	200193	NM_029321	75516	Mm.37581	NM_029321	ENSMUSG00000066637	Ttc32	1700013G20Rik	tetratricopeptide repeat domain 32	protein-coding	0.01	0.455446
Merged-chr4-48290758-1	chr4	48290708	48290808	+	2.4	cIP2vsInput	"intron (NM_010569, intron 2 of 16)"	"intron (NM_010569, intron 2 of 16)"	10956	NM_010569	16348	Mm.317706	NM_010569	ENSMUSG00000028344	Invs	AI428552|AW455512|Nphp2|inv	inversin	protein-coding	0	0.326733
Merged-chr10-80348519-1	chr10	80348469	80348569	+	2.4	cIP2vsInput	promoter-TSS (NM_001113548)	promoter-TSS (NM_001113548)	-73	NM_001113548	66548	Mm.268527	NM_001113548	ENSMUSG00000043822	Adamtsl5	2010109H09Rik|Thsd6	ADAMTS-like 5	protein-coding	0.12	0.792079
Merged-chr2-29060091-1	chr2	29060041	29060141	+	2.4	cIP2vsInput	promoter-TSS (NM_009442)	promoter-TSS (NM_009442)	-172	NM_009442	22130	Mm.252195	NM_009442	ENSMUSG00000026803	Ttf1	AV245725|TTF-1|TTF-I	"transcription termination factor, RNA polymerase I"	protein-coding	0	0.475248
Merged-chr14-111259399-1	chr14	111259349	111259449	+	2.4	cIP2vsInput	Intergenic	Intergenic	-415716	NM_198865	75409	Mm.417152	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	"SLIT and NTRK-like family, member 5"	protein-coding	0	0.277228
Merged-chr6-88465193-1	chr6	88465143	88465243	+	2.4	cIP2vsInput	promoter-TSS (NM_019685)	promoter-TSS (NM_019685)	-230	NM_019685	56505	Mm.42195	NM_019685	ENSMUSG00000030079	Ruvbl1	2510009G06Rik|Pontin52|Tip49a	RuvB-like protein 1	protein-coding	0	0.277228
Merged-chr1-113889218-1	chr1	113889168	113889268	+	2.4	cIP2vsInput	Intergenic	RMER15|LTR|ERVL	-1795919	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0.01	0.405941
Merged-chr9-83762143-1	chr9	83762093	83762193	+	2.4	cIP2vsInput	Intergenic	Intergenic	44162	NM_148941	83603	Mm.83949	NM_148941	ENSMUSG00000032262	Elovl4	-	"elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 4"	protein-coding	0	0.316832
Merged-chr6-25766829-1	chr6	25766779	25766879	+	2.4	cIP2vsInput	"intron (NM_133931, intron 8 of 17)"	"intron (NM_133931, intron 8 of 17)"	42397	NM_133931	101185	Mm.397208	NM_133931	ENSMUSG00000029676	Pot1a	1500031H18Rik|AI851169|Pot1	protection of telomeres 1A	protein-coding	0	0.29703
Merged-chr2-51284077-1	chr2	51284027	51284127	+	2.4	cIP1vsInput	"intron (NR_040636, intron 1 of 2)"	"intron (NR_040636, intron 1 of 2)"	42246	NR_040636	329404	Mm.417725	NR_040636	ENSMUSG00000086349	Gm13497	A730015I17|OTTMUSG00000012425	predicted gene 13497	miscRNA	0	0.277228
Merged-chr9-28350830-1	chr9	28350780	28350880	+	2.4	cIP1vsInput	"intron (NM_177906, intron 1 of 7)"	"intron (NM_177906, intron 1 of 7)"	559561	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding	0	0.306931
Merged-chr15-35169820-1	chr15	35169770	35169870	+	2.4	cIP2vsInput	Intergenic	MYSERV6-int|LTR|ERVK	-14014	NM_019635	56274	Mm.262330	NM_019635	ENSMUSG00000022329	Stk3	0610042I06Rik|MST|Mst2|Mst3|Ste20|mess1	serine/threonine kinase 3	protein-coding	0	0.316832
Merged-chr15-23407565-1	chr15	23407515	23407615	+	2.4	cIP1vsInput	"intron (NM_001081299, intron 7 of 11)"	"intron (NM_001081299, intron 7 of 11)"	371102	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l	cadherin 18	protein-coding	0	0.336634
Merged-chr6-94501026-1	chr6	94500976	94501076	+	2.4	cIP2vsInput	"intron (NM_026255, intron 1 of 9)"	"intron (NM_026255, intron 1 of 9)"	712	NM_026255	67582	Mm.280725	NM_026255	ENSMUSG00000045100	Slc25a26	4930433D19Rik|4933433F13Rik|AW557176|D6Bwg0781e|Slc25a6	"solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 26"	protein-coding	0	0.366337
Merged-chr4-117133962-1	chr4	117133912	117134012	+	2.4	cIP2vsInput	promoter-TSS (NM_013807)	promoter-TSS (NM_013807)	-10	NM_013807	12795	Mm.259022	NM_013807	ENSMUSG00000028680	Plk3	Cnk|Fnk|PRK	polo-like kinase 3	protein-coding	0.12	0.683168
Merged-chr18-58314791-1	chr18	58314741	58314841	+	2.4	cIP2vsInput	Intergenic	Intergenic	-104865	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding	0	0.356436
Merged-chr13-26231638-1	chr13	26231588	26231688	+	2.4	cIP2vsInput	Intergenic	MLT1H-int|LTR|ERVL-MaLR	80768	NR_045933	73576	Mm.45473	NR_045933		1700092E19Rik	-	RIKEN cDNA 1700092E19 gene	miscRNA	0	0.336634
Merged-chr3-151868577-1	chr3	151868527	151868627	+	2.4	cIP1vsInput	Intergenic	L2|LINE|L2	-31049	NM_008966	19220	Mm.460678	NM_008966	ENSMUSG00000028036	Ptgfr	AI957154|PGF|fp	prostaglandin F receptor	protein-coding	0	0.425743
Merged-chr17-65146090-1	chr17	65146040	65146140	+	2.4	cIP1vsInput	Intergenic	Intergenic	394692	NM_001008973	381107	Mm.141275	NM_001008973	ENSMUSG00000045036	Tmem232	E130009J12Rik|Gm940|Tes13-L|Tes13-S	transmembrane protein 232	protein-coding	0.02	0.346535
Merged-chr5-84290273-1	chr5	84290223	84290323	+	2.4	cIP1vsInput	"intron (NM_007937, intron 3 of 15)"	"intron (NM_007937, intron 3 of 15)"	127109	NM_007937	13839	Mm.438006	NM_007937		Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding	0.01	0.29703
Merged-chr1-147831109-1	chr1	147831059	147831159	+	2.4	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	1333422	NM_001145807	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.336634
Merged-chr6-80952905-1	chr6	80952855	80952955	+	2.4	cIP1vsInput	Intergenic	Intergenic	933262	NM_178731	243499	Mm.483425	NM_001134743	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding	0.01	0.366337
Merged-chr2-111778880-1	chr2	111778830	111778930	+	2.4	cIP1vsInput	Intergenic	Intergenic	-1433	NM_146889	258891	Mm.223301	NM_146889	ENSMUSG00000044560	Olfr1302	MOR248-3	olfactory receptor 1302	protein-coding	0	0.356436
Merged-chr8-67772376-1	chr8	67772326	67772426	+	2.4	cIP1vsInput	"intron (NM_027626, intron 2 of 7)"	L1MCa|LINE|L1	45919	NM_027626	234353	Mm.32525	NM_177698	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding	0	0.386139
Merged-chr12-5717887-1	chr12	5717837	5717937	+	2.4	cIP2vsInput	Intergenic	Intergenic	341385	NR_015579	72669	Mm.10434	NR_015579		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	miscRNA	0	0.29703
Merged-chr6-33654890-1	chr6	33654840	33654940	+	2.4	cIP1vsInput	"intron (NM_009148, intron 10 of 17)"	"intron (NM_009148, intron 10 of 17)"	-374558	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding	0	0.346535
Merged-chr15-8473932-1	chr15	8473882	8473982	+	2.4	cIP1vsInput	Intergenic	Intergenic	-29469	NM_201232	71175	Mm.440537	NM_027707	ENSMUSG00000022141	Nipbl	4921518A06Rik|4933421G18Rik|C79399|Idn3	Nipped-B homolog (Drosophila)	protein-coding	0	0.405941
Merged-chr4-85592375-1	chr4	85592325	85592425	+	2.4	cIP2vsInput	Intergenic	Intergenic	386919	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding	0	0.287129
Merged-chr11-27831909-1	chr11	27831859	27831959	+	2.4	cIP2vsInput	Intergenic	Lx|LINE|L1	752387	NM_001166661	216613	Mm.93759	NM_001166661	ENSMUSG00000032878	Ccdc85a	E030025D05Rik	coiled-coil domain containing 85A	protein-coding	0	0.356436
Merged-chr1-110108029-1	chr1	110107979	110108079	+	2.4	cIP1vsInput	"intron (NM_172853, intron 10 of 11)"	"intron (NM_172853, intron 10 of 11)"	124292	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.326733
Merged-chr10-65194225-1	chr10	65194175	65194275	+	2.4	cIP1vsInput	Intergenic	Intergenic	929839	NR_038039	69433	Mm.23366	NR_038039		1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	miscRNA	0	0.336634
Merged-chr11-16341907-1	chr11	16341857	16341957	+	2.4	cIP1vsInput	Intergenic	MTD|LTR|ERVL-MaLR	84183	NM_145967	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	9330184N17Rik|BC027127|Vstm2	V-set and transmembrane domain containing 2A	protein-coding	0	0.405941
Merged-chr3-19679876-1	chr3	19679826	19679926	+	2.4	cIP2vsInput	"intron (NM_001081281, intron 9 of 9)"	L1MC|LINE|L1	15520	NM_205769	12918	Mm.290689	NM_205769	ENSMUSG00000049796	Crh	CRF|Gm1347	corticotropin releasing hormone	protein-coding	0	0.346535
Merged-chr15-20894245-1	chr15	20894195	20894295	+	2.4	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-217207	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding	0.01	0.356436
Merged-chr10-113447799-1	chr10	113447749	113447849	+	2.4	cIP1vsInput	Intergenic	Intergenic	-138779	NR_035418	100316831		NR_035418		Mir669h	Mirn669h|mmu-mir-669h	microRNA 669h	miscRNA	0	0.29703
Merged-chr14-81986166-1	chr14	81986116	81986216	+	2.4	cIP1vsInput	Intergenic	Intergenic	1985864	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.237624
Merged-chr12-94819091-1	chr12	94819041	94819141	+	2.4	cIP1vsInput	Intergenic	Intergenic	-873135	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0	0.336634
Merged-chr5-8432773-1	chr5	8432723	8432823	+	2.4	cIP1vsInput	"intron (NM_178766, intron 5 of 11)"	Lx2|LINE|L1	9923	NM_178766	319653	Mm.146262	NM_178766	ENSMUSG00000054099	Slc25a40	B230315F11Rik	"solute carrier family 25, member 40"	protein-coding	0	0.356436
Merged-chr15-53056685-1	chr15	53056635	53056735	+	2.4	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	289498	NM_010162	14042	Mm.309395	NM_010162		Ext1	AA409028	exostoses (multiple) 1	protein-coding	0	0.277228
Merged-chr15-47390162-1	chr15	47390112	47390212	+	2.4	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	766857	NR_045811	75281	Mm.159487	NR_045811		4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	miscRNA	0.01	0.356436
Merged-chr3-144744643-1	chr3	144744593	144744693	+	2.4	cIP1vsInput	"intron (NM_009899, intron 11 of 13)"	"intron (NM_009899, intron 11 of 13)"	16096	NM_009899	12722	Mm.454553	NM_009899	ENSMUSG00000056025	Clca1	Cacc	chloride channel calcium activated 1	protein-coding	0	0.316832
Merged-chr1-150260422-1	chr1	150260372	150260472	+	2.4	cIP2vsInput	Intergenic	Intergenic	-58995	NM_024458	20028	Mm.440883	NM_001159730	ENSMUSG00000006007	Pdc	Rpr-1|Rpr1	phosducin	protein-coding	0	0.366337
Merged-chr14-109508834-1	chr14	109508784	109508884	+	2.4	cIP1vsInput	Intergenic	Intergenic	48604	NR_039542	100628607		NR_039542	ENSMUSG00000092639	Mir3964	mmu-mir-3964|mu-mir-3964	microRNA 3964	miscRNA	0	0.316832
Merged-chr16-79168333-1	chr16	79168283	79168383	+	2.4	cIP1vsInput	Intergenic	Intergenic	-77236	NM_008941	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	"transmembrane protease, serine 15"	protein-coding	0.02	0.356436
Merged-chr5-129583940-1	chr5	129583890	129583990	+	2.4	cIP1vsInput	promoter-TSS (NM_011846)	promoter-TSS (NM_011846)	-274	NM_011846	23948	Mm.42047	NM_011846	ENSMUSG00000029436	Mmp17	MT4-MMP|MT4MMP|MTMMP4	matrix metallopeptidase 17	protein-coding	0.08	0.613861
Merged-chrX-166510317-1	chrX	166510267	166510367	+	2.4	cIP2vsInput	"5' UTR (NM_001007577, exon 1 of 5)"	"5' UTR (NM_001007577, exon 1 of 5)"	161	NM_001007577	245695	Mm.336318	NM_001007577	ENSMUSG00000051224	Tceanc	A630018P17Rik|Gm390	transcription elongation factor A (SII) N-terminal and central domain containing	protein-coding	0.06	0.653465
Merged-chr1-142340942-1	chr1	142340892	142340992	+	2.4	cIP1vsInput	Intergenic	Intergenic	-1299755	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0	0.316832
Merged-chr5-50214356-1	chr5	50214306	50214406	+	2.4	cIP1vsInput	Intergenic	Lx8b|LINE|L1	63023	NR_040696	73965	Mm.243823	NR_040696		4930448I18Rik	-	RIKEN cDNA 4930448I18 gene	miscRNA	0	0.267327
Merged-chr1-101574332-1	chr1	101574282	101574382	+	2.4	cIP2vsInput	Intergenic	Intergenic	418564	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.306931
Merged-chr7-44496515-1	chr7	44496465	44496565	+	2.4	cIP2vsInput	promoter-TSS (NM_028169)	promoter-TSS (NM_028169)	-2	NM_197991	69683	Mm.294759	NM_197991	ENSMUSG00000008140	Emc10	2310044H10Rik|5430410O10Rik|Inm02	ER membrane protein complex subunit 10	protein-coding	0.09	0.663366
Merged-chr1-32239569-1	chr1	32239519	32239619	+	2.4	cIP2vsInput	"intron (NM_133235, intron 1 of 8)"	"intron (NM_133235, intron 1 of 8)"	66763	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm1	"KH domain containing, RNA binding, signal transduction associated 2"	protein-coding	0.01	0.316832
Merged-chr13-17261502-1	chr13	17261452	17261552	+	2.4	cIP1vsInput	"intron (NM_138654, intron 11 of 13)"	Lx9|LINE|L1	433263	NM_138654	192136	Mm.364180	NM_138654		5033411D12Rik	D17907	RIKEN cDNA 5033411D12 gene	protein-coding	0	0.326733
Merged-chr10-124134222-1	chr10	124134172	124134272	+	2.4	cIP2vsInput	Intergenic	Lx7|LINE|L1	-334852	NR_028310	75030	Mm.159403	NR_028310		4930503E24Rik	-	"eukaryotic translation initiation factor 3, subunit I pseudogene"	pseudo	0	0.376238
Merged-chr14-81564695-1	chr14	81564645	81564745	+	2.4	cIP2vsInput	Intergenic	Intergenic	1564393	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.326733
Merged-chr3-72919766-1	chr3	72919716	72919816	+	2.4	cIP1vsInput	"intron (NM_001081137, intron 30 of 46)"	"intron (NM_001081137, intron 30 of 46)"	47100	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding	0	0.257426
Merged-chrX-48343681-1	chrX	48343631	48343731	+	2.4	cIP2vsInput	"intron (NM_178782, intron 2 of 14)"	CpG	2323	NM_178782	320376	Mm.210146	NM_178782	ENSMUSG00000036959	Bcorl1	6720425J07Rik|B930011H20Rik	BCL6 co-repressor-like 1	protein-coding	0.11	0.683168
Merged-chr9-44096969-1	chr9	44096919	44097019	+	2.4	cIP2vsInput	Intergenic	Intergenic	-4801	NM_001190314	259172	Mm.227110	NM_001190314	ENSMUSG00000034739	Mfrp	rd6	membrane-type frizzled-related protein	protein-coding	0.02	0.50495
Merged-chr16-55577784-1	chr16	55577734	55577834	+	2.4	cIP2vsInput	Intergenic	Intergenic	244354	NM_001159394	80859	Mm.247272	NM_001159394	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	"nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta"	protein-coding	0	0.346535
Merged-chr16-86505225-1	chr16	86505175	86505275	+	2.4	cIP1vsInput	Intergenic	MIRb|SINE|MIR	-604100	NM_011782	23794	Mm.437478	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|AI481094|ASMP-2	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"	protein-coding	0	0.326733
Merged-chr10-107184150-1	chr10	107184100	107184200	+	2.4	cIP2vsInput	Intergenic	Intergenic	-60486	NM_198636	380660	Mm.336072	NM_001142804	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding	0	0.316832
Merged-chr1-7177418-1	chr1	7177368	7177468	+	2.4	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	88498	NM_183028	319263		NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0	0.356436
Merged-chr15-96205234-1	chr15	96205184	96205284	+	2.4	cIP1vsInput	Intergenic	L1M2|LINE|L1	-7260	NR_040423	70040	Mm.490780	NR_040423	ENSMUSG00000097536	2610037D02Rik	AU024679	RIKEN cDNA 2610037D02 gene	miscRNA	0.02	0.405941
Merged-chr15-99596204-1	chr15	99596154	99596254	+	2.4	cIP2vsInput	Intergenic	Intergenic	5176	NM_009701	11830	Mm.45580	NM_009701	ENSMUSG00000044217	Aqp5	-	aquaporin 5	protein-coding	0.01	0.544554
Merged-chr3-124809878-1	chr3	124809828	124809928	+	2.4	cIP1vsInput	Intergenic	Intergenic	-228787	NR_015460	384775	Mm.489851	NR_015460	ENSMUSG00000039174	1700003H04Rik	4930538K10Rik|4933400D22Rik	RIKEN cDNA 1700003H04 gene	miscRNA	0	0.346535
Merged-chr3-125468762-1	chr3	125468712	125468812	+	2.4	cIP2vsInput	"intron (NM_022565, intron 2 of 13)"	"intron (NM_022565, intron 2 of 13)"	64671	NM_022565	64580	Mm.444289	NM_022565	ENSMUSG00000027971	Ndst4	4930439H17Rik	N-deacetylase/N-sulfotransferase (heparin glucosaminyl) 4	protein-coding	0.01	0.405941
Merged-chr5-137924415-1	chr5	137924365	137924465	+	2.4	cIP1vsInput	Intergenic	L1M2|LINE|L1	-2796	NM_007819	13113	Mm.289886	NM_007819	ENSMUSG00000029727	Cyp3a13	IIIAm2	"cytochrome P450, family 3, subfamily a, polypeptide 13"	protein-coding	0	0.316832
Merged-chr6-67781596-1	chr6	67781546	67781646	+	2.4	cIP1vsInput	Intergenic	L1_Mur1|LINE|L1	-215897	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo	0	0.376238
Merged-chr8-57066301-1	chr8	57066251	57066351	+	2.4	cIP1vsInput	Intergenic	Intergenic	-254682	NM_010402	15111	Mm.430844	NM_010402	ENSMUSG00000038193	Hand2	AI225906|AI661148|Ehand2|Hed|Th2|Thing2|bHLHa26|dHAND	heart and neural crest derivatives expressed transcript 2	protein-coding	0.01	0.386139
Merged-chr2-90728847-1	chr2	90728797	90728897	+	2.4	cIP1vsInput	"intron (NM_021512, intron 33 of 36)"	"intron (NM_021512, intron 33 of 36)"	-16523	NM_018828	55935	Mm.489638	NM_018828	ENSMUSG00000008200	Fnbp4	FBP30|Fnbp30|mKIAA1014	formin binding protein 4	protein-coding	0.01	0.346535
Merged-chr6-18172293-1	chr6	18172243	18172343	+	2.4	cIP2vsInput	"intron (NM_021050, intron 1 of 26)"	"intron (NM_021050, intron 1 of 26)"	1606	NM_021050	12638	Mm.15621	NM_021050	ENSMUSG00000041301	Cftr	AW495489|Abcc7	cystic fibrosis transmembrane conductance regulator	protein-coding	0	0.316832
Merged-chr14-103334497-1	chr14	103334447	103334547	+	2.4	cIP1vsInput	"intron (NM_207215, intron 1 of 84)"	L1MC1|LINE|L1	12303	NM_207215	105689	Mm.6478	NM_207215	ENSMUSG00000033004	Mycbp2	AU023734|AW107953|AW546647|C130061D10Rik|Pam|Phr1|R75243	MYC binding protein 2	protein-coding	0.01	0.336634
Merged-chr6-59701467-1	chr6	59701417	59701517	+	2.4	cIP1vsInput	Intergenic	Intergenic	-275177	NM_183183	243385	Mm.485751	NM_183183	ENSMUSG00000045441	Gprin3	C030038J10Rik|C730021L23	GPRIN family member 3	protein-coding	0	0.316832
Merged-chr12-42570497-1	chr12	42570447	42570547	+	2.4	cIP2vsInput	Intergenic	Intergenic	941733	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding	0.01	0.29703
Merged-chr10-34902726-1	chr10	34902676	34902776	+	2.4	cIP1vsInput	Intergenic	Intergenic	419326	NM_010237	14302	Mm.332432	NM_001159544	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding	0	0.39604
Merged-chr15-44004949-1	chr15	44004899	44004999	+	2.4	cIP1vsInput	Intergenic	Intergenic	-134920	NM_175502	239408	Mm.461451	NM_175502	ENSMUSG00000054409	Tmem74	AA549547|B230382K22Rik	transmembrane protein 74	protein-coding	0	0.306931
Merged-chr7-78371270-1	chr7	78371220	78371320	+	2.4	cIP1vsInput	"intron (NM_182809, intron 11 of 13)"	"intron (NM_182809, intron 11 of 13)"	206568	NM_008746	18213	Mm.421361	NM_008746		Ntrk3	AW125844|Ntrk3_tv3|TrkC	"neurotrophic tyrosine kinase, receptor, type 3"	protein-coding	0	0.326733
Merged-chr6-43435568-1	chr6	43435518	43435618	+	2.4	cIP2vsInput	"intron (NM_013861, intron 7 of 8)"	"intron (NM_013861, intron 7 of 8)"	-6861	NR_045988	319812	Mm.446393	NR_045988		9430018G01Rik	-	RIKEN cDNA 9430018G01 gene	miscRNA	0	0.29703
Merged-chr10-123646589-1	chr10	123646539	123646639	+	2.4	cIP2vsInput	"intron (NM_001252387, intron 2 of 4)"	"intron (NM_001252387, intron 2 of 4)"	382513	NM_001252387	268354	Mm.51939	NM_001252387	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	"family with sequence similarity 19, member A2"	protein-coding	0	0.376238
Merged-chr14-91387736-1	chr14	91387686	91387786	+	2.4	cIP1vsInput	Intergenic	Intergenic	1260845	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0	0.287129
Merged-chr5-24751072-1	chr5	24751022	24751122	+	2.4	cIP1vsInput	TTS (NM_153076)	TTS (NM_153076)	6771	NM_153076	214301	Mm.63484	NM_153076		Crygn	-	"crystallin, gamma N"	protein-coding	0.11	0.663366
Merged-chr11-13360151-1	chr11	13360101	13360201	+	2.4	cIP1vsInput	Intergenic	Intergenic	-895191	NM_172496	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	4732460E13|C530045F18Rik|mKIAA0633	cordon-bleu	protein-coding	0	0.326733
Merged-chr2-49181902-1	chr2	49181852	49181952	+	2.4	cIP2vsInput	"intron (NM_029924, intron 6 of 16)"	L1_Mur2|LINE|L1	232394	NM_029924	109241	Mm.440436	NM_029924		Mbd5	9430004D19Rik|AA536666|AI426407|C030040A15Rik|OTTMUSG00000012483	methyl-CpG binding domain protein 5	protein-coding	0	0.306931
Merged-chr13-117497268-1	chr13	117497218	117497318	+	2.4	cIP1vsInput	Intergenic	Intergenic	-105052	NM_010408	15165	Mm.343429	NM_010408		Hcn1	Bcng1|C630013B14Rik|HAC2	"hyperpolarization-activated, cyclic nucleotide-gated K+ 1"	protein-coding	0	0.287129
Merged-chr2-103364152-1	chr2	103364102	103364202	+	2.4	cIP1vsInput	"intron (NR_040332, intron 1 of 2)"	"intron (NR_040332, intron 1 of 2)"	8612	NR_040332	319854	Mm.403818	NR_040332	ENSMUSG00000087278	A930006I01Rik	-	RIKEN cDNA A930006I01 gene	miscRNA	0.01	0.356436
Merged-chr2-12035903-1	chr2	12035853	12035953	+	2.4	cIP2vsInput	Intergenic	L1MB7|LINE|L1	258150	NM_177268	320816	Mm.260201	NM_177268		Ankrd16	2810455F06Rik|AI646698|D430029B21Rik	ankyrin repeat domain 16	protein-coding	0.01	0.356436
Merged-chr3-12207308-1	chr3	12207258	12207358	+	2.4	cIP1vsInput	Intergenic	Intergenic	-362949	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.247525
Merged-chr1-68681615-1	chr1	68681565	68681665	+	2.4	cIP1vsInput	"intron (NM_010154, intron 2 of 26)"	"intron (NM_010154, intron 2 of 26)"	426444	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0	0.316832
Merged-chr15-33634733-1	chr15	33634683	33634783	+	2.4	cIP1vsInput	"intron (NR_045070, intron 3 of 5)"	"intron (NR_045070, intron 3 of 5)"	18703	NR_045070	75880	Mm.396109	NR_045070		4930592A05Rik	-	RIKEN cDNA 4930592A05 gene	miscRNA	0	0.316832
Merged-chr14-56582638-1	chr14	56582588	56582688	+	2.4	cIP2vsInput	"intron (NM_001145978, intron 1 of 34)"	"intron (NM_001145978, intron 1 of 34)"	7019	NM_001145978	328417	Mm.379357	NM_001145978	ENSMUSG00000054509	Parp4	Adprtl1|C030027K23Rik|E230037B21Rik|Gm743|PARPL|PH5P|VAULT3|VPARP|p193	"poly (ADP-ribose) polymerase family, member 4"	protein-coding	0.01	0.445545
Merged-chr8-50293680-1	chr8	50293630	50293730	+	2.4	cIP2vsInput	Intergenic	Intergenic	-74432	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0.02	0.366337
Merged-chr4-10500131-1	chr4	10500081	10500181	+	2.4	cIP1vsInput	Intergenic	MusHAL1|LINE|L1	297671	NR_045185	73624	Mm.67392	NR_045185	ENSMUSG00000086080	1700123O12Rik	-	RIKEN cDNA 1700123O12 gene	miscRNA	0	0.415842
Merged-chr4-8138897-1	chr4	8138847	8138947	+	2.4	cIP1vsInput	Intergenic	L1M4b|LINE|L1	100144	NM_007592	12319	Mm.119320	NM_007592		Car8	AW546993|Ca8|Cals|Cals1|Carp|wdl	carbonic anhydrase 8	protein-coding	0	0.316832
Merged-chr9-69507905-1	chr9	69507855	69507955	+	2.4	cIP1vsInput	Intergenic	Intergenic	50961	NR_037296	100526560		NR_037296	ENSMUSG00000093042	Mir3109	mmu-mir-3109	microRNA 3109	miscRNA	0.02	0.415842
Merged-chr7-28796909-1	chr7	28796859	28796959	+	2.4	cIP2vsInput	"exon (NM_177158, exon 9 of 12)"	"exon (NM_177158, exon 9 of 12)"	7940	NM_177158	320435	Mm.74632	NM_177158	ENSMUSG00000051735	Rinl	5830482F20Rik|9930116N10Rik	Ras and Rab interactor-like	protein-coding	0.14	0.673267
Merged-chr12-34681783-1	chr12	34681733	34681833	+	2.4	cIP1vsInput	"intron (NM_001271386, intron 3 of 27)"	"intron (NM_001271386, intron 3 of 27)"	-152894	NM_024124	79221	Mm.483009	NM_001271386	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding	0	0.306931
Merged-chr1-104648241-1	chr1	104648191	104648291	+	2.4	cIP2vsInput	Intergenic	Intergenic	-120578	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0.01	0.336634
Merged-chr7-113380644-1	chr7	113380594	113380694	+	2.4	cIP1vsInput	Intergenic	L1MA4A|LINE|L1	7929	NM_020623	19226	Mm.284168	NM_020623	ENSMUSG00000059077	Pth	Pthp	parathyroid hormone	protein-coding	0.01	0.346535
Merged-chr9-116726853-1	chr9	116726803	116726903	+	2.4	cIP2vsInput	"intron (NM_001172126, intron 6 of 12)"	"intron (NM_001172126, intron 6 of 12)"	525630	NM_001172123	207181	Mm.326411	NM_001172121	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	"RNA binding motif, single stranded interacting protein"	protein-coding	0	0.326733
Merged-chr6-137723968-1	chr6	137723918	137724018	+	2.4	cIP1vsInput	Intergenic	Intergenic	-11114	NM_011499	20901	Mm.22584	NM_011499	ENSMUSG00000030224	Strap	AW557906|C78091|C79202|Unrip	serine/threonine kinase receptor associated protein	protein-coding	0.01	0.287129
Merged-chr7-55992544-1	chr7	55992494	55992594	+	2.4	cIP1vsInput	"intron (NM_153578, intron 3 of 4)"	L1M4|LINE|L1	27029	NM_153578	233280	Mm.443911	NM_153578		Nipa1	1110027G09Rik|A830014A18Rik|FSP3|Spg6	non imprinted in Prader-Willi/Angelman syndrome 1 homolog (human)	protein-coding	0	0.306931
Merged-chr5-49155828-1	chr5	49155778	49155878	+	2.4	cIP1vsInput	"intron (NM_001199244, intron 1 of 7)"	"intron (NM_001199244, intron 1 of 7)"	129831	NM_001199244	80334	Mm.160172	NM_001199242	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding	0.01	0.306931
Merged-chr3-50391490-1	chr3	50391440	50391540	+	2.4	cIP1vsInput	"intron (NM_011990, intron 6 of 11)"	"intron (NM_011990, intron 6 of 11)"	52123	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	"solute carrier family 7 (cationic amino acid transporter, y+ system), member 11"	protein-coding	0	0.306931
Merged-chr12-44197041-1	chr12	44196991	44197091	+	2.4	cIP2vsInput	Intergenic	RMER12|LTR|ERVK	13027	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	"DnaJ (Hsp40) homolog, subfamily B, member 9"	protein-coding	0	0.336634
Merged-chr8-49801319-1	chr8	49801269	49801369	+	2.4	cIP1vsInput	Intergenic	Intergenic	-566793	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.306931
Merged-chr17-54014786-1	chr17	54014736	54014836	+	2.4	cIP2vsInput	Intergenic	MurERV4-int|LTR|ERVK	-24155	NM_018751	20888	Mm.10108	NM_018751	ENSMUSG00000023943	Sult1c1	(PST)G|P-SULT|ST1C1|Stp2|Sult1a2|mOLFST	"sulfotransferase family, cytosolic, 1C, member 1"	protein-coding	0	0.366337
Merged-chr12-93954420-1	chr12	93954370	93954470	+	2.4	cIP1vsInput	Intergenic	Intergenic	-1737806	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0	0.356436
Merged-chr4-58578627-1	chr4	58578577	58578677	+	2.4	cIP2vsInput	Intergenic	Intergenic	-25136	NM_010336	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	5031439C20|AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding	0.01	0.465347
Merged-chr2-110101481-1	chr2	110101431	110101531	+	2.4	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-51002	NR_040508	75517	Mm.363927	NR_040508	ENSMUSG00000086186	1700024P03Rik	-	RIKEN cDNA 1700024P03 gene	miscRNA	0	0.366337
Merged-chr13-24170099-1	chr13	24170049	24170149	+	2.4	cIP1vsInput	"intron (NM_026825, intron 4 of 37)"	"intron (NM_026825, intron 4 of 37)"	110691	NM_026825	68732	Mm.211047	NM_177807	ENSMUSG00000021338	Lrrc16a	1110037D04Rik|AI425970|CARMIL|D130057M20|Lrrc16	leucine rich repeat containing 16A	protein-coding	0	0.326733
Merged-chr10-45931120-1	chr10	45931070	45931170	+	2.4	cIP1vsInput	Intergenic	Intergenic	123416	NR_040624	320363	Mm.123343	NR_040624		D030045P18Rik	-	RIKEN cDNA D030045P18 gene	miscRNA	0	0.346535
Merged-chr6-111341448-1	chr6	111341398	111341498	+	2.4	cIP1vsInput	"intron (NM_177328, intron 7 of 9)"	B4A|SINE|B4	695850	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0.01	0.376238
Merged-chr3-32746379-1	chr3	32746329	32746429	+	2.4	cIP2vsInput	"intron (NM_025316, intron 2 of 5)"	"intron (NM_025316, intron 2 of 5)"	9316	NM_025316	66046	Mm.28058	NM_025316	ENSMUSG00000027673	Ndufb5	0610007D05Rik|AU015782|SGDH	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5"	protein-coding	0	0.306931
Merged-chr3-150524468-1	chr3	150524418	150524518	+	2.4	cIP2vsInput	Intergenic	Intergenic	-913414	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0	0.435644
Merged-chr9-73857840-1	chr9	73857790	73857890	+	2.4	cIP1vsInput	"intron (NM_001081153, intron 1 of 30)"	"intron (NM_001081153, intron 1 of 30)"	75727	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|AU019458|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C (C. elegans)	protein-coding	0	0.326733
Merged-chr6-12980497-1	chr6	12980447	12980547	+	2.4	cIP2vsInput	Intergenic	Intergenic	-89262	NM_027992	71900	Mm.27742	NM_027992	ENSMUSG00000029571	Tmem106b	2310036D22Rik|5830455K21Rik|6430519M21Rik|AI428776|AI661344	transmembrane protein 106B	protein-coding	0	0.346535
Merged-chr4-17111944-1	chr4	17111894	17111994	+	2.4	cIP1vsInput	Intergenic	Intergenic	-741538	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0.01	0.306931
Merged-chr1-18143321-1	chr1	18143271	18143371	+	2.4	cIP2vsInput	Intergenic	Intergenic	-6270	NM_030033	78081	Mm.319913	NM_030033	ENSMUSG00000025774	Crisp4	9230112K08Rik	cysteine-rich secretory protein 4	protein-coding	0.01	0.306931
Merged-chr2-81632840-1	chr2	81632790	81632890	+	2.4	cIP1vsInput	Intergenic	Intergenic	-420818	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0	0.316832
Merged-chr1-41134110-2	chr1	41134043	41134177	+	2.4	cIP1vsInput|cIP2vsInput	Intergenic	MER89|LTR|ERV1	47142	NR_040475	74897	Mm.243822	NR_040475		4930448I06Rik	-	RIKEN cDNA 4930448I06 gene	miscRNA	0.022388	0.451852
Merged-chr1-40330803-1	chr1	40330753	40330853	+	2.4	cIP1vsInput	"intron (NM_133193, intron 4 of 10)"	L1MEg|LINE|L1	6176	NM_133193	107527	Mm.155583	NM_133193	ENSMUSG00000070942	Il1rl2	AI481289|AW551444|IL-1Rrp2	interleukin 1 receptor-like 2	protein-coding	0.03	0.356436
Merged-chr16-66677721-1	chr16	66677671	66677771	+	2.4	cIP2vsInput	"intron (NM_001145977, intron 7 of 8)"	"intron (NM_001145977, intron 7 of 8)"	20603	NR_040512	75501	Mm.396161	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	miscRNA	0	0.346535
Merged-chr7-30373648-1	chr7	30373598	30373698	+	2.4	cIP2vsInput	Intergenic	Intergenic	-10876	NM_175478	233067	Mm.23157	NM_175478	ENSMUSG00000036957	Lrfn3	A530045B06Rik|SALM4	leucine rich repeat and fibronectin type III domain containing 3	protein-coding	0.07	0.574257
Merged-chr14-81799576-1	chr14	81799526	81799626	+	2.4	cIP1vsInput	Intergenic	L1MD2|LINE|L1	1799274	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0.01	0.336634
Merged-chr13-90535121-1	chr13	90535071	90535171	+	2.4	cIP2vsInput	Intergenic	Intergenic	370234	NM_001145879	435376	Mm.292579	NM_001145879	ENSMUSG00000078958	Atp6ap1l	EG435376	"ATPase, H+ transporting, lysosomal accessory protein 1-like"	protein-coding	0	0.306931
Merged-chr11-117263029-1	chr11	117262979	117263079	+	2.4	cIP2vsInput	"intron (NM_001113486, intron 2 of 11)"	(TATG)n|Simple_repeat|Simple_repeat	-3217	NM_001113487	53860	Mm.38450	NM_001113486	ENSMUSG00000059248	9-Sep	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding	0	0.287129
Merged-chr5-39905401-1	chr5	39905351	39905451	+	2.4	cIP1vsInput	Intergenic	Intergenic	-260770	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding	0	0.386139
Merged-chr1-43855659-1	chr1	43855609	43855709	+	2.4	cIP2vsInput	Intergenic	Intergenic	-27951	NM_026430	67883	Mm.387202	NM_026430		Uxs1	1600025I13Rik|AI451869|AI649125|AW550562	UDP-glucuronate decarboxylase 1	protein-coding	0	0.306931
Merged-chr18-35661997-1	chr18	35661947	35662047	+	2.4	cIP2vsInput	"intron (NM_027733, intron 1 of 3)"	"intron (NM_027733, intron 1 of 3)"	189	NM_029485	71242	Mm.443473	NM_027733	ENSMUSG00000024352	Spata24	2700012K08Rik|4930583E11Rik|5133400G04Rik|AU016220|TIPT|TIPT2	spermatogenesis associated 24	protein-coding	0.05	0.663366
Merged-chr6-62690512-1	chr6	62690462	62690562	+	2.4	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-566345	NM_008167	14804	Mm.447390	NM_008167		Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	"glutamate receptor, ionotropic, delta 2"	protein-coding	0.01	0.356436
Merged-chr3-10832102-1	chr3	10832052	10832152	+	2.4	cIP1vsInput	Intergenic	Intergenic	-391978	NM_001127191	74718	Mm.440548	NM_001127191	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding	0.01	0.336634
Merged-chr10-21773240-1	chr10	21773190	21773290	+	2.4	cIP2vsInput	Intergenic	Intergenic	82395	NR_045843	432436	Mm.244553	NM_001004162	ENSMUSG00000056716	Gm5420	EG432436	predicted gene 5420	miscRNA	0	0.306931
Merged-chr15-19586746-1	chr15	19586696	19586796	+	2.4	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	766417	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0	0.326733
Merged-chr2-117541896-1	chr2	117541846	117541946	+	2.4	cIP2vsInput	Intergenic	Intergenic	-199019	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding	0	0.386139
Merged-chr7-87781850-1	chr7	87781800	87781900	+	2.4	cIP1vsInput	"intron (NM_001081414, intron 3 of 9)"	L1_Mur1|LINE|L1	197682	NM_001143834	108071	Mm.235018	NM_001033224	ENSMUSG00000049583	Grm5	6430542K11Rik|AI850523|Gprc1e|mGluR5|mGluR5b	"glutamate receptor, metabotropic 5"	protein-coding	0	0.356436
Merged-chr3-12758817-1	chr3	12758767	12758867	+	2.4	cIP2vsInput	Intergenic	Intergenic	-712838	NM_178631	76897	Mm.422625	NM_001163328	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0	0.366337
Merged-chr11-38962883-1	chr11	38962833	38962933	+	2.4	cIP1vsInput	Intergenic	Intergenic	-442838	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0	0.306931
Merged-chr10-115323645-1	chr10	115323595	115323695	+	2.4	cIP1vsInput	Intergenic	Intergenic	-8054	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	"RAB21, member RAS oncogene family"	protein-coding	0.02	0.39604
Merged-chr11-64391346-1	chr11	64391296	64391396	+	2.4	cIP1vsInput	Intergenic	Intergenic	-43986	NM_178870	15478	Mm.340214	NM_178870	ENSMUSG00000047759	Hs3st3a1	3Ost3a|Hs3st3a	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	protein-coding	0	0.386139
Merged-chr9-3653073-1	chr9	3653023	3653123	+	2.4	cIP1vsInput	"intron (NM_001033322, intron 4 of 7)"	L1_Mus1|LINE|L1	120724	NM_001033322	234889	Mm.91240	NM_001033322		Gucy1a2	6330407I18Rik|A230060L24Rik	"guanylate cyclase 1, soluble, alpha 2"	protein-coding	0	0.346535
Merged-chr16-38562586-1	chr16	38562536	38562636	+	2.4	cIP1vsInput	promoter-TSS (NM_026407)	promoter-TSS (NM_026407)	-228	NM_026407	67846	Mm.489630	NM_001205286	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding	0.03	0.475248
Merged-chr14-102721366-1	chr14	102721316	102721416	+	2.4	cIP1vsInput	Intergenic	Intergenic	261266	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mmu-mir-5130|mu-mir-5130	microRNA 5130	miscRNA	0	0.306931
Merged-chr11-3409276-1	chr11	3409226	3409326	+	2.4	cIP2vsInput	promoter-TSS (NM_010718)	promoter-TSS (NM_010718)	-41	NM_010718	16886	Mm.442189	NM_001034030		Limk2	9430059K01|A930024P04Rik|C85310|Limk2a|Limk2b	LIM motif-containing protein kinase 2	protein-coding	0.12	0.722772
Merged-chr1-49213523-1	chr1	49213473	49213573	+	2.4	cIP1vsInput	Intergenic	Lx5|LINE|L1	-1714000	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.306931
Merged-chr12-96113005-1	chr12	96112955	96113055	+	2.4	cIP1vsInput	Intergenic	Intergenic	-65783	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0	0.316832
Merged-chr13-106108839-1	chr13	106108789	106108889	+	2.4	cIP1vsInput	Intergenic	Intergenic	665146	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0	0.237624
Merged-chr15-14361515-1	chr15	14361465	14361565	+	2.4	cIP1vsInput	Intergenic	Intergenic	-1187876	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	K-cadherin|cad6|cadherin-6	cadherin 6	protein-coding	0	0.237624
Merged-chr10-89602485-1	chr10	89602435	89602535	+	2.4	cIP1vsInput	"intron (NM_182959, intron 2 of 11)"	L1MB1|LINE|L1	18764	NM_182959	216227	Mm.233921	NM_182959	ENSMUSG00000019935	Slc17a8	BC042593|Vglut3	"solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8"	protein-coding	0.01	0.376238
Merged-chr17-29532482-1	chr17	29532432	29532532	+	2.4	cIP1vsInput	"intron (NM_001162902, intron 1 of 1)"	MLT1J|LTR|ERVL-MaLR	17111	NM_001162901	71138	Mm.158581	NM_001162901	ENSMUSG00000079580	Tmem217	4933413N12Rik|EG622644	transmembrane protein 217	protein-coding	0.02	0.524752
Merged-chr3-82408995-1	chr3	82408945	82409045	+	2.4	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	50923	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding	0	0.257426
Merged-chr6-132986396-1	chr6	132986346	132986446	+	2.4	cIP2vsInput	Intergenic	Intergenic	-5431	NM_207017	387343	Mm.377905	NM_207017	ENSMUSG00000062528	Tas2r109	T2R09|Tas2r9|mGR09|mt2r62	"taste receptor, type 2, member 109"	protein-coding	0.01	0.227723
Merged-chr16-70797304-1	chr16	70797254	70797354	+	2.4	cIP1vsInput	Intergenic	Intergenic	180879	NR_040474	52645	Mm.188475	NR_040474		D16Ertd519e	-	"DNA segment, Chr 16, ERATO Doi 519, expressed"	miscRNA	0	0.287129
Merged-chr3-12743122-1	chr3	12743072	12743172	+	2.4	cIP1vsInput	Intergenic	Intergenic	-728533	NM_178631	76897	Mm.422625	NM_001163328	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0	0.376238
Merged-chr3-131063280-1	chr3	131063230	131063330	+	2.4	cIP1vsInput	Intergenic	Intergenic	-47017	NM_010703	16842	Mm.255219	NM_001276402		Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding	0	0.366337
Merged-chr4-30477526-1	chr4	30477476	30477576	+	2.4	cIP2vsInput	Intergenic	Intergenic	-187070	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	miscRNA	0	0.336634
Merged-chr4-58221606-1	chr4	58221556	58221656	+	2.4	cIP1vsInput	Intergenic	Intergenic	-15010	NM_022814	64817	Mm.261024	NM_022814	ENSMUSG00000028369	Svep1	1110021D17Rik|4833413O10Rik|AA387071|D430029O09Rik|Polydom	"sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1"	protein-coding	0	0.207921
Merged-chr3-20313622-1	chr3	20313572	20313672	+	2.4	cIP2vsInput	TTS (NM_175086)	TTS (NM_175086)	-37893	NM_029706	76703	Mm.34692	NM_029706		Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding	0	0.306931
Merged-chr1-49836146-1	chr1	49836096	49836196	+	2.4	cIP1vsInput	Intergenic	RLTR17|LTR|ERVK	-1091377	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.257426
Merged-chr10-33073559-1	chr10	33073509	33073609	+	2.4	cIP2vsInput	Intergenic	Intergenic	-9924	NM_029726	76757	Mm.338508	NM_029726	ENSMUSG00000019787	Trdn	2310045H21Rik|EG432451|TDN	triadin	protein-coding	0	0.336634
Merged-chr1-148871378-1	chr1	148871328	148871428	+	2.4	cIP2vsInput	Intergenic	Intergenic	1089906	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0.01	0.336634
Merged-chr15-24596163-1	chr15	24596113	24596213	+	2.4	cIP2vsInput	Intergenic	MLT1B|LTR|ERVL-MaLR	817601	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	"brain abundant, membrane attached signal protein 1"	protein-coding	0	0.366337
Merged-chrY-5983484-1	chrY	5983434	5983534	+	2.4	cIP2vsInput	Intergenic	Intergenic	1184293	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.326733
Merged-chr9-39336519-1	chr9	39336469	39336569	+	2.4	cIP1vsInput	Intergenic	Intergenic	-16907	NM_001011756	257912	Mm.377297	NM_001011756	ENSMUSG00000057349	Olfr948	MOR171-45|MOR171-51	olfactory receptor 948	protein-coding	0	0.336634
Merged-chr6-75830896-1	chr6	75830846	75830946	+	2.4	cIP1vsInput	Intergenic	Intergenic	-1411821	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0	0.306931
Merged-chr1-157533558-1	chr1	157533508	157533608	+	2.4	cIP1vsInput	"intron (NM_033354, intron 7 of 27)"	"intron (NM_033354, intron 7 of 27)"	7388	NM_001159986	89867	Mm.87114	NM_001159986	ENSMUSG00000026589	Sec16b	Lztr2|Rgpr|Rgpr-p117	SEC16 homolog B (S. cerevisiae)	protein-coding	0	0.306931
Merged-chr13-83687585-1	chr13	83687535	83687635	+	2.4	cIP1vsInput	Intergenic	Intergenic	-40521	NR_015561	320203	Mm.245636	NR_015561		C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	miscRNA	0.02	0.336634
Merged-chr6-110307306-1	chr6	110307256	110307356	+	2.4	cIP1vsInput	Intergenic	Intergenic	-338292	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0.01	0.415842
Merged-chr4-78004759-1	chr4	78004709	78004809	+	2.4	cIP1vsInput	"intron (NM_011211, intron 1 of 39)"	"intron (NM_011211, intron 1 of 39)"	207136	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0	0.326733
Merged-chr17-6513704-1	chr17	6513654	6513754	+	2.4	cIP1vsInput	Intergenic	HAL1|LINE|L1	-62710	NR_033520	547127	Mm.381893	NR_033520		Tmem181b-ps	Tmem181b	"transmembrane protein 181B, pseudogene"	pseudo	0.01	0.336634
Merged-chr1-182215893-1	chr1	182215843	182215943	+	2.4	cIP2vsInput	Intergenic	MurERV4-int|LTR|ERVK	-57795	NM_001166728	625823	Mm.479992	NM_001166728		Vmn1r1	EG625823|Gm6628	vomeronasal 1 receptor 1	protein-coding	0	0.29703
Merged-chr18-71764714-1	chr18	71764664	71764764	+	2.4	cIP2vsInput	"intron (NM_007831, intron 5 of 28)"	"intron (NM_007831, intron 5 of 28)"	586355	NM_007831	13176	Mm.167882	NM_007831		Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding	0.01	0.316832
Merged-chr8-18595231-1	chr8	18595181	18595281	+	2.4	cIP2vsInput	promoter-TSS (NM_173189)	promoter-TSS (NM_173189)	58	NM_173189	244329	Mm.235296	NM_173189	ENSMUSG00000039842	Mcph1	5430437K10Rik|BRIT1|D030046N04Rik|MCT	"microcephaly, primary autosomal recessive 1"	protein-coding	0.11	0.772277
Merged-chr5-12550972-1	chr5	12550922	12551022	+	2.4	cIP2vsInput	"intron (NM_028882, intron 10 of 17)"	"intron (NM_028882, intron 10 of 17)"	167806	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	"sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D"	protein-coding	0	0.336634
Merged-chr1-29085481-1	chr1	29085431	29085531	+	2.4	cIP1vsInput	Intergenic	MTC|LTR|ERVL-MaLR	-305229	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0	0.326733
Merged-chr5-124232665-1	chr5	124232615	124232715	+	2.4	cIP2vsInput	"intron (NR_045369, intron 2 of 5)"	"intron (NR_045369, intron 2 of 5)"	2940	NR_045369	75927	Mm.410803	NR_045369	ENSMUSG00000090220	4930568K20Rik	-	RIKEN cDNA 4930568K20 gene	miscRNA	0.02	0.574257
Merged-chr13-105464013-1	chr13	105463963	105464063	+	2.4	cIP2vsInput	Intergenic	Intergenic	20320	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0.01	0.366337
Merged-chr1-48154472-1	chr1	48154422	48154522	+	2.4	cIP2vsInput	Intergenic	Intergenic	-1300963	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.29703
Merged-chr15-49861771-1	chr15	49861721	49861821	+	2.4	cIP2vsInput	Intergenic	Intergenic	1027343	NR_035444	100316685		NR_035444	ENSMUSG00000084458	Mir1907	Mirn1907|mmu-mir-1907	microRNA 1907	miscRNA	0	0.356436
Merged-chr13-58547887-1	chr13	58547837	58547937	+	2.4	cIP1vsInput	Intergenic	Intergenic	62990	NM_022317	114304	Mm.18188	NM_022317	ENSMUSG00000021553	Slc28a3	Cnt3	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 3"	protein-coding	0.02	0.455446
Merged-chr6-12701269-1	chr6	12701219	12701319	+	2.4	cIP1vsInput	"intron (NM_001164805, intron 1 of 26)"	MLT1F|LTR|ERVL-MaLR	47984	NM_001164805	330267	Mm.400067	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	"thrombospondin, type I, domain containing 7A"	protein-coding	0	0.29703
Merged-chr16-60012491-1	chr16	60012441	60012541	+	2.4	cIP1vsInput	"intron (NM_007938, intron 6 of 17)"	"intron (NM_007938, intron 6 of 17)"	-373152	NM_019665	56297	Mm.392505	NM_019665	ENSMUSG00000022722	Arl6	1110018H24Rik|2210411E14Rik|BBS3	ADP-ribosylation factor-like 6	protein-coding	0.02	0.336634
Merged-chr7-104633785-1	chr7	104633735	104633835	+	2.4	cIP1vsInput	Intergenic	Intergenic	-1891	NM_146312	258309	Mm.377429	NM_146312	ENSMUSG00000073923	Olfr657	MOR40-13	olfactory receptor 657	protein-coding	0	0.316832
Merged-chr17-27133869-1	chr17	27133819	27133919	+	2.4	cIP2vsInput	promoter-TSS (NM_026063)	promoter-TSS (NM_026063)	22	NM_026063	67267	Mm.272389	NM_026063	ENSMUSG00000024208	Mnf1	2900010M23Rik|M19	mitochondrial nucleoid factor 1	protein-coding	0.07	0.653465
Merged-chr13-21132549-1	chr13	21132499	21132599	+	2.4	cIP1vsInput	promoter-TSS (NM_010984)	promoter-TSS (NM_010984)	-228	NM_010984	18341	Mm.246536	NM_010984	ENSMUSG00000071522	Olfr263	GA_x5J8B7TTCWC-858-415|IA3|MOR256-31|MOR256-37P|MOR256-61|Olfr263-ps1|Olfr42	olfactory receptor 263	protein-coding	0	0.306931
Merged-chr2-5206175-1	chr2	5206125	5206225	+	2.4	cIP1vsInput	"intron (NM_028804, intron 2 of 2)"	L1MA8|LINE|L1	68399	NM_028804	74186	Mm.274715	NM_028804	ENSMUSG00000026676	Ccdc3	2310045O21Rik	coiled-coil domain containing 3	protein-coding	0	0.326733
Merged-chr3-124623264-1	chr3	124623214	124623314	+	2.4	cIP2vsInput	Intergenic	Intergenic	-42173	NR_015460	384775	Mm.489851	NR_015460	ENSMUSG00000039174	1700003H04Rik	4930538K10Rik|4933400D22Rik	RIKEN cDNA 1700003H04 gene	miscRNA	0	0.336634
Merged-chr1-105405694-1	chr1	105405644	105405744	+	2.4	cIP2vsInput	Intergenic	Intergenic	-48984	NM_001160368	320311	Mm.389162	NM_001160368	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding	0	0.306931
Merged-chr6-112245623-1	chr6	112245573	112245673	+	2.4	cIP2vsInput	Intergenic	Intergenic	-28135	NM_144799	30937	Mm.234441	NM_144799	ENSMUSG00000057604	Lmcd1	AW455500|AW553074|dyxin	LIM and cysteine-rich domains 1	protein-coding	0	0.544554
Merged-chr1-188893274-1	chr1	188893224	188893324	+	2.4	cIP2vsInput	"intron (NM_021408, intron 60 of 70)"	"intron (NM_021408, intron 60 of 70)"	114566	NM_172650	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding	0.01	0.346535
Merged-chr6-26430121-1	chr6	26430071	26430171	+	2.4	cIP1vsInput	Intergenic	Intergenic	498695	NR_040771	626904	Mm.126787	NR_040771		Gm20756	-	"predicted gene, 20756"	miscRNA	0.01	0.247525
Merged-chr12-46999379-1	chr12	46999329	46999429	+	2.4	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-180604	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding	0	0.287129
Merged-chr3-76372770-1	chr3	76372720	76372820	+	2.4	cIP2vsInput	"intron (NM_178673, intron 4 of 15)"	Lx7|LINE|L1	297187	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.306931
Merged-chr17-76591155-1	chr17	76591105	76591205	+	2.4	cIP1vsInput	Intergenic	Intergenic	730132	NR_033456	100043885	Mm.127562	NR_033456		Gm4710	-	predicted gene 4710	miscRNA	0	0.336634
Merged-chr7-144914866-1	chr7	144914816	144914916	+	2.4	cIP2vsInput	promoter-TSS (NM_028184)	promoter-TSS (NM_028184)	-328	NM_028184	72284	Mm.389995	NM_028184	ENSMUSG00000031072	Oraov1	2210010N10Rik|TAOS1	oral cancer overexpressed 1	protein-coding	0.03	0.50495
Merged-chr14-15893710-1	chr14	15893660	15893760	+	2.4	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-355604	NM_021504	59007	Mm.258381	NM_021504	ENSMUSG00000021785	Ngly1	1110002C09Rik|PNGase|Png1	N-glycanase 1	protein-coding	0	0.346535
Merged-chr1-93176590-1	chr1	93176540	93176640	+	2.4	cIP2vsInput	Intergenic	Intergenic	-15642	NM_172411	71874	Mm.158766	NM_001159940	ENSMUSG00000034159	2310007B03Rik	-	RIKEN cDNA 2310007B03 gene	protein-coding	0.09	0.70297
Merged-chr10-37311233-1	chr10	37311183	37311283	+	2.4	cIP1vsInput	Intergenic	L1VL2|LINE|L1	-172307	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding	0	0.346535
Merged-chr18-78429475-1	chr18	78429425	78429525	+	2.4	cIP1vsInput	"intron (NM_207651, intron 2 of 21)"	L1MA4|LINE|L1	167475	NM_207651	27411	Mm.44158	NM_001110273	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	"solute carrier family 14 (urea transporter), member 2"	protein-coding	0	0.287129
Merged-chr4-79949151-1	chr4	79949101	79949201	+	2.4	cIP1vsInput	Intergenic	Intergenic	-885079	NM_031202	22178	Mm.412291	NM_031202	ENSMUSG00000005994	Tyrp1	TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding	0.01	0.316832
Merged-chr1-142452715-1	chr1	142452665	142452765	+	2.4	cIP1vsInput	Intergenic	Intergenic	-1187982	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0	0.386139
Merged-chr12-41264116-1	chr12	41264066	41264166	+	2.4	cIP2vsInput	Intergenic	Intergenic	221941	NM_001271708	16981	Mm.39913	NM_001271708	ENSMUSG00000036295	Lrrn3	NLRR-3	"leucine rich repeat protein 3, neuronal"	protein-coding	0	0.316832
Merged-chr11-30336083-1	chr11	30336033	30336133	+	2.4	cIP2vsInput	Intergenic	Lx7|LINE|L1	-116311	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	"spectrin beta, non-erythrocytic 1"	protein-coding	0	0.287129
Merged-chr6-72291106-1	chr6	72291056	72291156	+	2.4	cIP2vsInput	Intergenic	Lx3_Mus|LINE|L1	-12142	NM_147779	20388	Mm.46033	NM_147779		Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding	0	0.336634
Merged-chr5-82082542-1	chr5	82082492	82082592	+	2.4	cIP2vsInput	Intergenic	Intergenic	716523	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mmu-mir-1187	microRNA 1187	miscRNA	0	0.287129
Merged-chr15-48491376-1	chr15	48491326	48491426	+	2.4	cIP1vsInput	"intron (NM_001081391, intron 4 of 70)"	RMER5|LTR|ERV1	300613	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0	0.366337
Merged-chr14-88462957-1	chr14	88462907	88463007	+	2.4	cIP2vsInput	Intergenic	Intergenic	8439	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0	0.356436
Merged-chr11-99395598-1	chr11	99395548	99395648	+	2.4	cIP1vsInput	Intergenic	Intergenic	-6234	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding	0.01	0.386139
Merged-chr17-24895072-1	chr17	24895022	24895122	+	2.4	cIP2vsInput	promoter-TSS (NM_001163102)	promoter-TSS (NM_001163102)	15	NM_001163102	193838	Mm.440199	NM_001163102	ENSMUSG00000073436	Eme2	2810013J18Rik	essential meiotic endonuclease 1 homolog 2 (S. pombe)	protein-coding	0.1	0.60396
Merged-chr11-56603074-1	chr11	56603024	56603124	+	2.4	cIP2vsInput	Intergenic	(TATAA)n|Simple_repeat|Simple_repeat	-408544	NM_001113325	14799	Mm.4920	NM_001113325	ENSMUSG00000020524	Gria1	2900051M01Rik|Glr-1|Glr1|GluA1|GluR-A|GluRA|Glur-1|Glur1|HIPA1|gluR-K1	"glutamate receptor, ionotropic, AMPA1 (alpha 1)"	protein-coding	0	0.237624
Merged-chr15-5915733-1	chr15	5915683	5915783	+	2.4	cIP2vsInput	Intergenic	Intergenic	-384056	NM_001008702	13132	Mm.240830	NM_001008702	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	"disabled 2, mitogen-responsive phosphoprotein"	protein-coding	0	0.306931
Merged-chrX-22210230-1	chrX	22210180	22210280	+	2.4	cIP2vsInput	Intergenic	Intergenic	-251366	NR_033731	76705	Mm.399727	NM_029707		Ppp1r2-ps7	1700023I07Rik	"protein phosphatase 1, regulatory (inhibitor) subunit 2, pseudogene 7"	pseudo	0	0.356436
Merged-chr8-54095987-1	chr8	54095937	54096037	+	2.4	cIP1vsInput	"intron (NM_009506, intron 1 of 6)"	"intron (NM_009506, intron 1 of 6)"	18455	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding	0.01	0.316832
Merged-chr19-42255988-1	chr19	42255938	42256038	+	2.4	cIP1vsInput	"5' UTR (NM_001141983, exon 3 of 7)"	"5' UTR (NM_001141983, exon 3 of 7)"	249	NM_027694	71146	Mm.329851	NM_001141983	ENSMUSG00000042532	Golga7b	4933417O08Rik|AI839934	"golgi autoantigen, golgin subfamily a, 7B"	protein-coding	0.13	0.70297
Merged-chr17-10834795-1	chr17	10834745	10834845	+	2.4	cIP1vsInput	"intron (NM_027032, intron 1 of 4)"	"intron (NM_027032, intron 1 of 4)"	5396	NM_027032	69310	Mm.18889	NM_027032	ENSMUSG00000037196	Pacrg	1700008H23Rik	PARK2 co-regulated	protein-coding	0	0.376238
Merged-chr8-111717133-1	chr8	111717083	111717183	+	2.4	cIP1vsInput	"intron (NM_009954, intron 2 of 6)"	"intron (NM_009954, intron 2 of 6)"	15003	NM_001198839	12927	Mm.3758	NM_001198839	ENSMUSG00000031955	Bcar1	AI385681|Cas|Crkas	breast cancer anti-estrogen resistance 1	protein-coding	0.01	0.623762
Merged-chr9-81690337-1	chr9	81690287	81690387	+	2.4	cIP2vsInput	Intergenic	Intergenic	-57785	NM_010482	15551	Mm.445308	NM_010482	ENSMUSG00000049511	Htr1b	-	5-hydroxytryptamine (serotonin) receptor 1B	protein-coding	0	0.366337
Merged-chr14-63860257-1	chr14	63860207	63860307	+	2.4	cIP1vsInput	promoter-TSS (NM_028228)	promoter-TSS (NM_028228)	-55	NM_028228	72400	Mm.379214	NM_028228	ENSMUSG00000021958	Pinx1	2210403I16Rik|2610028A01Rik|67-11-3|AU024023|LPTS|LPTS1	"PIN2/TERF1 interacting, telomerase inhibitor 1"	protein-coding	0.09	0.623762
Merged-chr2-129189848-1	chr2	129189798	129189898	+	2.4	cIP1vsInput	Intergenic	RLTR17C_Mm|LTR|ERVK	-8925	NM_015747	20515	Mm.272675	NM_001159593	ENSMUSG00000027397	Slc20a1	AI607883|Glvr-1|Glvr1	"solute carrier family 20, member 1"	protein-coding	0	0.306931
Merged-chr1-108238728-1	chr1	108238678	108238778	+	2.4	cIP2vsInput	Intergenic	MurERV4_19-int|LTR|ERVK	321469	NR_102307	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0	0.316832
Merged-chr17-40824300-1	chr17	40824250	40824350	+	2.4	cIP1vsInput	"intron (NM_011269, intron 1 of 9)"	"intron (NM_011269, intron 1 of 9)"	13151	NM_011269	19743	Mm.12961	NM_011269	ENSMUSG00000023926	Rhag	CD241|Rh50|Rh50A	Rhesus blood group-associated A glycoprotein	protein-coding	0.01	0.316832
Merged-chr4-98845624-1	chr4	98845574	98845674	+	2.4	cIP1vsInput	Intergenic	Intergenic	-28087	NM_172872	242553	Mm.440211	NM_172872	ENSMUSG00000035407	Kank4	AU021071|Ankrd38|BC060737|C130031J23	KN motif and ankyrin repeat domains 4	protein-coding	0	0.455446
Merged-chr18-46847837-1	chr18	46847787	46847887	+	2.4	cIP2vsInput	Intergenic	L1MB4|LINE|L1	-2202	NM_029008	74574	Mm.26379	NM_029008	ENSMUSG00000024481	4833403I15Rik	Aqpep|Lvrn	RIKEN cDNA 4833403I15 gene	protein-coding	0	0.336634
Merged-chr9-32272988-1	chr9	32272938	32273038	+	2.4	cIP2vsInput	Intergenic	Intergenic	48739	NM_177379	330914	Mm.46683	NM_001195632	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding	0	0.39604
Merged-chr1-104921786-1	chr1	104921736	104921836	+	2.4	cIP2vsInput	"intron (NM_011800, intron 1 of 11)"	"intron (NM_011800, intron 1 of 11)"	152967	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0.01	0.29703
Merged-chr15-42733599-1	chr15	42733549	42733649	+	2.4	cIP1vsInput	Intergenic	Intergenic	-56804	NM_009640	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding	0	0.29703
Merged-chr14-46031212-1	chr14	46031162	46031262	+	2.4	cIP2vsInput	Intergenic	L1MA9|LINE|L1	-52815	NR_002875	218963	Mm.282093	NR_002875		Gm1821	-	ubiquitin pseudogene	pseudo	0	0.287129
Merged-chr6-4920518-1	chr6	4920468	4920568	+	2.4	cIP1vsInput	"intron (NM_181595, intron 2 of 15)"	"intron (NM_181595, intron 2 of 15)"	17198	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	"protein phosphatase 1, regulatory (inhibitor) subunit 9A"	protein-coding	0.01	0.356436
Merged-chr11-52911156-1	chr11	52911106	52911206	+	2.4	cIP1vsInput	"intron (NM_177059, intron 3 of 15)"	"intron (NM_177059, intron 3 of 15)"	146450	NM_177059	320027	Mm.44518	NM_177059		Fstl4	B230374F23Rik|SPIG1|mKIAA1061	follistatin-like 4	protein-coding	0.02	0.50495
Merged-chr12-7652708-1	chr12	7652658	7652758	+	2.4	cIP2vsInput	Intergenic	MER94|DNA|hAT-Blackjack	-272378	NR_045045	73575	Mm.179463	NR_045045		1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	miscRNA	0	0.356436
Merged-chr2-65429964-1	chr2	65429914	65430014	+	2.4	cIP1vsInput	Intergenic	Intergenic	-65938	NM_177074	320106	Mm.227703	NM_177074	ENSMUSG00000061171	Slc38a11	9330158F14Rik	"solute carrier family 38, member 11"	protein-coding	0	0.217822
Merged-chrX-110670516-1	chrX	110670466	110670566	+	2.4	cIP2vsInput	Intergenic	L1M4|LINE|L1	-143949	NM_008901	18994	Mm.405149	NM_008901	ENSMUSG00000056854	Pou3f4	Brn-4|Brn4|OTF-9|Otf9|Slf|oct-9	"POU domain, class 3, transcription factor 4"	protein-coding	0	0.287129
Merged-chr10-24424058-1	chr10	24424008	24424108	+	2.4	cIP1vsInput	Intergenic	MTC|LTR|ERVL-MaLR	-171384	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding	0	0.366337
Merged-chr14-121203817-1	chr14	121203767	121203867	+	2.4	cIP2vsInput	"intron (NM_134082, intron 2 of 26)"	"intron (NM_134082, intron 2 of 26)"	168243	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	"FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)"	protein-coding	0.02	0.346535
Merged-chr18-21525307-1	chr18	21525257	21525357	+	2.4	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-126258	NM_001271580	74644	Mm.329311	XR_168573		4930426D05Rik	-	RIKEN cDNA 4930426D05 gene	protein-coding	0	0.336634
Merged-chr4-31152882-1	chr4	31152832	31152932	+	2.4	cIP2vsInput	Intergenic	Intergenic	488286	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	miscRNA	0.01	0.326733
Merged-chr3-99018550-1	chr3	99018500	99018600	+	2.4	cIP1vsInput	Intergenic	Intergenic	-122540	NM_027462	70560	Mm.316754	NM_027462	ENSMUSG00000004233	Wars2	5730427B17Rik|9430020O07Rik|AI413375|TrpRS	tryptophanyl tRNA synthetase 2 (mitochondrial)	protein-coding	0	0.376238
Merged-chr18-18321688-1	chr18	18321638	18321738	+	2.4	cIP2vsInput	Intergenic	Intergenic	-740698	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	miscRNA	0	0.376238
Merged-chr1-4279103-1	chr1	4279053	4279153	+	2.4	cIP1vsInput	Intergenic	L1M3|LINE|L1	81211	NM_011283	19888	Mm.294263	NM_001195662	ENSMUSG00000025900	Rp1	Dcdc3|Orp1|Rp1h|mG145	retinitis pigmentosa 1 (human)	protein-coding	0	0.257426
Merged-chr5-85027573-1	chr5	85027523	85027623	+	2.4	cIP2vsInput	Intergenic	Intergenic	-610191	NM_007937	13839	Mm.438006	NM_007937		Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding	0	0.366337
Merged-chr4-28519967-1	chr4	28519917	28520017	+	2.4	cIP1vsInput	Intergenic	Intergenic	-293178	NM_001122889	13841	Mm.257266	NM_001122889	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding	0	0.336634
Merged-chr15-9862249-1	chr15	9862199	9862299	+	2.4	cIP2vsInput	Intergenic	Intergenic	-113443	NM_177123	320277	Mm.127822	NM_177123		Spef2	C230086A09Rik	sperm flagellar 2	protein-coding	0	0.336634
Merged-chr8-19771199-1	chr8	19771149	19771249	+	2.4	cIP2vsInput	"intron (NM_001270553, intron 6 of 9).2"	L1_Mus4|LINE|L1	41623	NM_001039553	626415	Mm.425517	NM_001039553		4930467E23Rik	ENSMUSG00000074453|OTTMUSG00000018948|TSAP	RIKEN cDNA 4930467E23 gene	protein-coding	0	0.306931
Merged-chr10-3461101-1	chr10	3461051	3461151	+	2.4	cIP1vsInput	"intron (NM_133485, intron 3 of 3)"	"intron (NM_133485, intron 3 of 3)"	-79178	NM_027391	70337	Mm.24153	NM_027391		Iyd	0610009A07Rik|AI265638|Dehal1	iodotyrosine deiodinase	protein-coding	0	0.445545
Merged-chr10-26793676-1	chr10	26793626	26793726	+	2.4	cIP2vsInput	"intron (NM_176837, intron 1 of 14)"	"intron (NM_176837, intron 1 of 14)"	21164	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding	0	0.336634
Merged-chr5-9610507-1	chr5	9610457	9610557	+	2.4	cIP1vsInput	"intron (NM_181850, intron 1 of 5)"	"intron (NM_181850, intron 1 of 5)"	114845	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	"glutamate receptor, metabotropic 3"	protein-coding	0	0.336634
Merged-chr18-81288197-1	chr18	81288147	81288247	+	2.4	cIP2vsInput	Intergenic	Lx5b|LINE|L1	-301619	NM_178280	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	sal-like 3 (Drosophila)	protein-coding	0	0.366337
Merged-chr15-57320502-1	chr15	57320452	57320552	+	2.4	cIP2vsInput	"intron (NM_172378, intron 2 of 11)"	"intron (NM_172378, intron 2 of 11)"	157123	NM_172378	210463	Mm.26555	NM_172378	ENSMUSG00000022366	Slc22a22	oat-pg	"solute carrier family 22 (organic cation transporter), member 22"	protein-coding	0	0.346535
Merged-chr4-92938608-1	chr4	92938558	92938658	+	2.4	cIP2vsInput	Intergenic	Intergenic	396903	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding	0	0.336634
Merged-chr8-78923675-1	chr8	78923625	78923725	+	2.4	cIP1vsInput	Intergenic	Lx5|LINE|L1	-102523	NM_030145	78651	Mm.28694	NM_001191004	ENSMUSG00000031683	Lsm6	1500031N17Rik|2410088K19Rik|AI747288	"LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae)"	protein-coding	0	0.287129
Merged-chr5-15053256-1	chr5	15053206	15053306	+	2.4	cIP1vsInput	Intergenic	Intergenic	-20249	NM_182957	66773	Mm.368256	NM_182957	ENSMUSG00000091897	Gm17019	-	predicted gene 17019	protein-coding	0.01	0.257426
Merged-chr9-38266286-1	chr9	38266236	38266336	+	2.4	cIP1vsInput	Intergenic	Intergenic	-2229	NM_146875	258875	Mm.223290	NM_146875	ENSMUSG00000096427	Olfr895	MOR170-1	olfactory receptor 895	protein-coding	0	0.346535
Merged-chr9-106281113-1	chr9	106281063	106281163	+	2.4	cIP1vsInput	promoter-TSS (NM_027354)	promoter-TSS (NM_027354)	52	NM_027354	70235	Mm.23054	NM_027354	ENSMUSG00000023345	Poc1a	2510040D07Rik|Wdr51a	POC1 centriolar protein homolog A (Chlamydomonas)	protein-coding	0.05	0.455446
Merged-chr4-81399375-1	chr4	81399325	81399425	+	2.4	cIP1vsInput	"intron (NM_010820, intron 3 of 46)"	"intron (NM_010820, intron 3 of 46)"	43430	NM_010820	17475	Mm.153039	NM_010820	ENSMUSG00000028402	Mpdz	AI225843|B930003D11Rik|MUPP1	multiple PDZ domain protein	protein-coding	0	0.346535
Merged-chr8-120736062-1	chr8	120736012	120736112	+	2.4	cIP2vsInput	promoter-TSS (NM_008320)	promoter-TSS (NM_008320)	-314	NM_008320	15900	Mm.334861	NM_008320	ENSMUSG00000041515	Irf8	AI893568|ICSBP|IRF-8|Icsbp1|Myls	interferon regulatory factor 8	protein-coding	0.05	0.623762
Merged-chr6-144222763-1	chr6	144222713	144222813	+	2.4	cIP1vsInput	Intergenic	Intergenic	-13195	NM_001243163	20678	Mm.1752	NM_001113559	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY-box containing gene 5	protein-coding	0.01	0.336634
Merged-chr14-61790669-1	chr14	61790619	61790719	+	2.4	cIP1vsInput	Intergenic	Intergenic	-108296	NR_028264	668253	Mm.483605	NR_028264		Dleu2	1810047A16Rik|4932411A06Rik|7730401J12Rik|AI197277|AI788824|Alt1|Gm9069|Leu2	"deleted in lymphocytic leukemia, 2"	miscRNA	0	0.346535
Merged-chr15-96783329-1	chr15	96783279	96783379	+	2.4	cIP1vsInput	Intergenic	Intergenic	-83631	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	"solute carrier family 38, member 2"	protein-coding	0.01	0.356436
Merged-chr11-90547357-1	chr11	90547307	90547407	+	2.4	cIP2vsInput	"intron (NM_011505, intron 13 of 17)"	"intron (NM_011505, intron 13 of 17)"	90751	NM_011505	20913	Mm.207203	NM_011505	ENSMUSG00000020546	Stxbp4	6030470M02Rik|Synip	syntaxin binding protein 4	protein-coding	0.04	0.554455
Merged-chr2-19037625-1	chr2	19037575	19037675	+	2.4	cIP1vsInput	Intergenic	Intergenic	39306	NR_024323	74629	Mm.117687	NR_024323	ENSMUSG00000026736	4930426L09Rik	-	RIKEN cDNA 4930426L09 gene	miscRNA	0.01	0.366337
Merged-chr16-90799979-1	chr16	90799929	90800029	+	2.4	cIP1vsInput	"intron (NM_029497, intron 5 of 38)"	"intron (NM_029497, intron 5 of 38)"	10434	NM_029497	207932	Mm.473093	NM_029497	ENSMUSG00000039929	Urb1	4921511H13Rik|5730405K23Rik|AA670781|AI645590|mKIAA0539	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	protein-coding	0.02	0.564356
Merged-chr4-34454236-1	chr4	34454186	34454286	+	2.4	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-96379	NM_001007589	433693	Mm.399624	NM_026019	ENSMUSG00000028291	Akirin2	2700059D21Rik|AA114675|AA522011|AU019887|Akirin-2	akirin 2	protein-coding	0	0.346535
Merged-chr2-64310681-1	chr2	64310631	64310731	+	2.4	cIP2vsInput	Intergenic	Intergenic	-212643	NM_001267847	60344	Mm.483676	NM_001267846	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding	0	0.326733
Merged-chr19-38581382-1	chr19	38581332	38581432	+	2.4	cIP2vsInput	"intron (NM_019588, intron 1 of 31)"	"intron (NM_019588, intron 1 of 31)"	57185	NM_019588	74055	Mm.34031	NM_019588	ENSMUSG00000024998	Plce1	4933403A21Rik|PLCepsilon|Plce|mKIAA1516	"phospholipase C, epsilon 1"	protein-coding	0.01	0.366337
Merged-chr10-81233330-1	chr10	81233280	81233380	+	2.4	cIP2vsInput	"intron (NM_001034895, intron 1 of 17)"	(CGGGG)n|Simple_repeat|Simple_repeat	167	NM_001034895	103406	Mm.416021	NM_001034895	ENSMUSG00000034949	Zfr2	2010013I23Rik|9130206N08Rik|AW045600|mKIAA1086	zinc finger RNA binding protein 2	protein-coding	0.15	0.821782
Merged-chr14-113935655-1	chr14	113935605	113935705	+	2.4	cIP1vsInput	Intergenic	Intergenic	-896310	NR_045661	75822	Mm.410813	NR_045661		4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	miscRNA	0.01	0.336634
Merged-chr6-10981997-1	chr6	10981947	10982047	+	2.4	cIP1vsInput	Intergenic	Intergenic	-7619	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	miscRNA	0	0.257426
Merged-chr18-9498350-1	chr18	9498300	9498400	+	2.4	cIP1vsInput	Intergenic	Intergenic	-48200	NM_026484	67974	Mm.376607	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding	0	0.277228
Merged-chr12-93845547-1	chr12	93845497	93845597	+	2.4	cIP1vsInput	Intergenic	Intergenic	-1846679	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0	0.247525
Merged-chr18-31099156-1	chr18	31099106	31099206	+	2.4	cIP2vsInput	"intron (NM_009065, intron 4 of 4)"	Lx2|LINE|L1	217972	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding	0	0.346535
Merged-chr5-146927595-1	chr5	146927545	146927645	+	2.4	cIP2vsInput	Intergenic	Intergenic	-21062	NM_025652	66596	Mm.196528	NM_025652	ENSMUSG00000016503	Gtf3a	2010015D03Rik|2610111I01Rik|5330403M05Rik	general transcription factor III A	protein-coding	0	0.326733
Merged-chr5-21474069-1	chr5	21474019	21474119	+	2.4	cIP2vsInput	"intron (NM_177869, intron 7 of 7)"	Lx6|LINE|L1	49166	NM_177869	330050	Mm.40655	NM_177869	ENSMUSG00000047221	Fam185a	4631428I10|AI847670	"family with sequence similarity 185, member A"	protein-coding	0	0.316832
Merged-chr11-15420026-1	chr11	15419976	15420076	+	2.4	cIP2vsInput	Intergenic	Intergenic	820786	NM_001164166	432536	Mm.33646	NR_002893		Pom121l12	1700054H16Rik	POM121 membrane glycoprotein-like 12	protein-coding	0.01	0.356436
Merged-chr15-15401154-1	chr15	15401104	15401204	+	2.4	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-1376947	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0	0.336634
Merged-chr4-10731249-1	chr4	10731199	10731299	+	2.4	cIP2vsInput	"intron (NR_045185, intron 4 of 4)"	"intron (NR_045185, intron 4 of 4)"	66553	NR_045185	73624	Mm.67392	NR_045185	ENSMUSG00000086080	1700123O12Rik	-	RIKEN cDNA 1700123O12 gene	miscRNA	0	0.346535
Merged-chr5-57611245-1	chr5	57611195	57611295	+	2.4	cIP1vsInput	"intron (NR_015588, intron 3 of 4)"	"intron (NR_015588, intron 3 of 4)"	106674	NR_015588	319216	Mm.446765	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	miscRNA	0.01	0.336634
Merged-chr12-73254047-1	chr12	73253997	73254097	+	2.4	cIP2vsInput	"intron (NM_008612, intron 7 of 7)"	L1_Rod|LINE|L1	32664	NM_029580	76357	Mm.311344	NM_029580	ENSMUSG00000034442	Trmt5	2610027O18Rik|mKIAA1393	TRM5 tRNA methyltransferase 5	protein-coding	0.01	0.267327
Merged-chr7-93455038-1	chr7	93454988	93455088	+	2.4	cIP2vsInput	Intergenic	Intergenic	375159	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0	0.346535
Merged-chr18-23579715-1	chr18	23579665	23579765	+	2.4	cIP2vsInput	"intron (NM_010087, intron 5 of 11)"	Lx7|LINE|L1	164300	NM_207650	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|A0|Dtn|a-DB-1|adbn	dystrobrevin alpha	protein-coding	0	0.39604
Merged-chr12-64657664-1	chr12	64657614	64657714	+	2.4	cIP2vsInput	Intergenic	Intergenic	-182766	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.346535
Merged-chr2-124042040-1	chr2	124041990	124042090	+	2.4	cIP1vsInput	Intergenic	ORR1E-int|LTR|ERVL-MaLR	87916	NR_040611	74702	Mm.410814	NR_040611	ENSMUSG00000085496	4930517E11Rik	-	RIKEN cDNA 4930517E11 gene	miscRNA	0	0.306931
Merged-chr6-5218776-1	chr6	5218726	5218826	+	2.4	cIP1vsInput	Intergenic	L1MA6|LINE|L1	-24830	NM_011134	18979	Mm.237657	NM_011134	ENSMUSG00000002588	Pon1	Pon	paraoxonase 1	protein-coding	0	0.316832
Merged-chr13-109102869-1	chr13	109102819	109102919	+	2.4	cIP1vsInput	"intron (NM_011056, intron 3 of 16)"	"intron (NM_011056, intron 3 of 16)"	-221875	NR_030644	100124489		NR_030644		Mir582	Mirn582|mmu-mir-582	microRNA 582	miscRNA	0	0.306931
Merged-chr14-95814281-1	chr14	95814231	95814331	+	2.4	cIP1vsInput	Intergenic	Intergenic	-66985	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0.01	0.29703
Merged-chr5-99174576-1	chr5	99174526	99174626	+	2.4	cIP2vsInput	Intergenic	A-rich|Low_complexity|Low_complexity	78351	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000029333	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	"RasGEF domain family, member 1B"	protein-coding	0	0.326733
Merged-chr6-132977655-1	chr6	132977605	132977705	+	2.4	cIP1vsInput	Intergenic	Intergenic	3310	NM_207017	387343	Mm.377905	NM_207017	ENSMUSG00000062528	Tas2r109	T2R09|Tas2r9|mGR09|mt2r62	"taste receptor, type 2, member 109"	protein-coding	0	0.326733
Merged-chr14-95791626-1	chr14	95791576	95791676	+	2.4	cIP1vsInput	Intergenic	Intergenic	-89640	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.356436
Merged-chr3-70260330-1	chr3	70260280	70260380	+	2.4	cIP1vsInput	Intergenic	Intergenic	252717	NM_001018031	229389	Mm.331071	NM_001018031	ENSMUSG00000027788	Otol1	Gm414	otolin 1 homolog (zebrafish)	protein-coding	0.01	0.306931
Merged-chr9-38614975-1	chr9	38614925	38615025	+	2.4	cIP1vsInput	Intergenic	Lx3_Mus|LINE|L1	8508	NM_146786	258782	Mm.390144	NM_146786	ENSMUSG00000047050	Olfr914	MOR165-7	olfactory receptor 914	protein-coding	0	0.326733
Merged-chr8-123332847-1	chr8	123332797	123332897	+	2.4	cIP2vsInput	"exon (NM_172287, exon 1 of 15)"	"exon (NM_172287, exon 1 of 15)"	134	NM_172287	234857	Mm.150200	NM_172287	ENSMUSG00000010154	Spire2	BC026502|Spir-2|Spir2	spire homolog 2 (Drosophila)	protein-coding	0.12	0.712871
Merged-chr17-76492533-1	chr17	76492483	76492583	+	2.4	cIP1vsInput	Intergenic	Intergenic	631510	NR_033456	100043885	Mm.127562	NR_033456		Gm4710	-	predicted gene 4710	miscRNA	0	0.336634
Merged-chr17-42408417-1	chr17	42408367	42408467	+	2.4	cIP2vsInput	"intron (NM_028474, intron 3 of 3)"	"intron (NM_028474, intron 3 of 3)"	92470	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding	0	0.336634
Merged-chr18-76890861-1	chr18	76890811	76890911	+	2.4	cIP1vsInput	"intron (NM_001109743, intron 7 of 8)"	"intron (NM_001109743, intron 7 of 8)"	34456	NM_001109743	664805	Mm.329543	NM_001109743	ENSMUSG00000091519	Skor2	Corl2|EG664805|Fussel18|Gm7348	SKI family transcriptional corepressor 2	protein-coding	0.01	0.405941
Merged-chr7-104218601-1	chr7	104218551	104218651	+	2.4	cIP2vsInput	promoter-TSS (NM_001013616)	promoter-TSS (NM_001013616)	-194	NM_001013616	94088	Mm.274843	NM_001013616	ENSMUSG00000072244	Trim6	C430046K18Rik|D7Ertd684e	tripartite motif-containing 6	protein-coding	0	0.316832
Merged-chr3-60720852-1	chr3	60720802	60720902	+	2.4	cIP2vsInput	Intergenic	Intergenic	219600	NM_001253708	56758	Mm.255723	NM_001253708	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding	0	0.306931
Merged-chr6-57005418-1	chr6	57005368	57005468	+	2.4	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	3063	NM_134175	171193	Mm.377173	NM_134175	ENSMUSG00000058923	Vmn1r6	V1rc20	vomeronasal 1 receptor 6	protein-coding	0	0.356436
Merged-chrX-147522789-1	chrX	147522739	147522839	+	2.4	cIP2vsInput	"intron (NM_001081173, intron 2 of 20)"	MIRb|SINE|MIR	31292	NM_001081173	210297	Mm.30506	NM_001081173		Lrch2	AI316885|mKIAA1495	leucine-rich repeats and calponin homology (CH) domain containing 2	protein-coding	0	0.326733
Merged-chr2-69312617-1	chr2	69312567	69312667	+	2.4	cIP1vsInput	"intron (NM_021022, intron 5 of 27)"	L1MB7|LINE|L1	29999	NM_021022	27413	Mm.439855	NM_021022	ENSMUSG00000027048	Abcb11	ABC16|Bsep|Lith1|PFIC2|PGY4|SPGP	"ATP-binding cassette, sub-family B (MDR/TAP), member 11"	protein-coding	0.01	0.316832
Merged-chr19-22750845-1	chr19	22750795	22750895	+	2.4	cIP2vsInput	TTS (NR_029591)	TTS (NR_029591)	240	NR_029591	387200		NR_029591		Mir204	Mirn204|mmu-mir-204	microRNA 204	miscRNA	0	0.386139
Merged-chr6-5228391-1	chr6	5228341	5228441	+	2.4	cIP2vsInput	"intron (NM_173006, intron 8 of 8)"	"intron (NM_173006, intron 8 of 8)"	27842	NM_173006	269823	Mm.9122	NM_173006	ENSMUSG00000029759	Pon3	2810004E20|AI786302	paraoxonase 3	protein-coding	0	0.316832
Merged-chr17-9388299-1	chr17	9388249	9388349	+	2.4	cIP1vsInput	Intergenic	Intergenic	-220277	NR_027881	67791	Mm.158175	NR_027881	ENSMUSG00000097049	6530411M01Rik	-	RIKEN cDNA 6530411M01 gene	miscRNA	0	0.287129
Merged-chr3-130715334-1	chr3	130715284	130715384	+	2.4	cIP2vsInput	Intergenic	Intergenic	-5890	NM_025509	66357	Mm.300697	NM_025509	ENSMUSG00000041084	Ostc	2310008M10Rik|5730557H03Rik	oligosaccharyltransferase complex subunit	protein-coding	0.03	0.29703
Merged-chr7-6763181-1	chr7	6763131	6763231	+	2.4	cIP2vsInput	"intron (NM_021323, intron 2 of 7)"	(TAGA)n|Simple_repeat|Simple_repeat	32440	NM_021323	57775	Mm.394138	NM_021323		Usp29	Ocat	ubiquitin specific peptidase 29	protein-coding	0.01	0.336634
Merged-chr2-98221968-1	chr2	98221918	98222018	+	2.4	cIP2vsInput	Intergenic	Intergenic	754294	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.336634
Merged-chr1-48931864-1	chr1	48931814	48931914	+	2.4	cIP2vsInput	Intergenic	Lx9|LINE|L1	-1995659	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.366337
Merged-chr18-40916944-1	chr18	40916894	40916994	+	2.4	cIP2vsInput	Intergenic	Intergenic	658583	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding	0	0.287129
Merged-chr10-104493102-1	chr10	104493052	104493152	+	2.4	cIP2vsInput	Intergenic	Intergenic	299060	NM_001270900	667692		NM_001270900	ENSMUSG00000097878	Gm8764	EG667692	predicted gene 8764	protein-coding	0	0.356436
Merged-chr17-93762375-1	chr17	93762325	93762425	+	2.4	cIP2vsInput	Intergenic	Intergenic	562953	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0	0.326733
Merged-chr9-94266666-1	chr9	94266616	94266716	+	2.4	cIP1vsInput	Intergenic	Intergenic	271415	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49	RIKEN cDNA 1190002N15 gene	protein-coding	0	0.29703
Merged-chr7-53967804-1	chr7	53967754	53967854	+	2.4	cIP1vsInput	Intergenic	Intergenic	-867441	NM_178705	233271	Mm.474990	NM_178705		Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding	0	0.336634
Merged-chr6-24405907-1	chr6	24405857	24405957	+	2.4	cIP2vsInput	Intergenic	Intergenic	109160	NM_172535	214704	Mm.61131	NM_172535	ENSMUSG00000046192	Iqub	4932408B21Rik|Trs4	IQ motif and ubiquitin domain containing	protein-coding	0	0.366337
Merged-chr6-94466731-1	chr6	94466681	94466781	+	2.4	cIP2vsInput	Intergenic	B3|SINE|B2	-33583	NM_026255	67582	Mm.280725	NM_026255	ENSMUSG00000045100	Slc25a26	4930433D19Rik|4933433F13Rik|AW557176|D6Bwg0781e|Slc25a6	"solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 26"	protein-coding	0.02	0.534653
Merged-chr4-30878156-1	chr4	30878106	30878206	+	2.4	cIP1vsInput	Intergenic	Intergenic	213560	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	miscRNA	0	0.267327
Merged-chr18-18563256-1	chr18	18563206	18563306	+	2.4	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-982266	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	miscRNA	0	0.356436
Merged-chr17-20997232-1	chr17	20997182	20997282	+	2.4	cIP2vsInput	Intergenic	Lx9|LINE|L1	-2546	NM_134202	171236	Mm.377192	NM_134202	ENSMUSG00000045575	Vmn1r233	V1rf5	vomeronasal 1 receptor 233	protein-coding	0	0.29703
Merged-chr5-104819194-1	chr5	104819144	104819244	+	2.4	cIP1vsInput	"intron (NM_001039231, intron 1 of 4)"	L1_Mur2|LINE|L1	40874	NM_001039231	626391	Mm.484585	NM_001039231		Zfp951	C230055K05Rik	zinc finger protein 951	protein-coding	0.01	0.326733
Merged-chr11-43865917-1	chr11	43865867	43865967	+	2.4	cIP2vsInput	Intergenic	Intergenic	-29585	NM_007416	11548	Mm.39086	NM_007416	ENSMUSG00000050541	Adra1b	[a]1b	"adrenergic receptor, alpha 1b"	protein-coding	0	0.485149
Merged-chr16-80862086-1	chr16	80862036	80862136	+	2.4	cIP1vsInput	Intergenic	Intergenic	-338611	NM_001113208	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0.02	0.386139
Merged-chrX-130162725-1	chrX	130162675	130162775	+	2.4	cIP2vsInput	"intron (NM_172493, intron 22 of 26)"	"intron (NM_172493, intron 22 of 26)"	412983	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diap2	Dia3|Diaph2|Drf2|E430022I22Rik	diaphanous homolog 2 (Drosophila)	protein-coding	0	0.29703
Merged-chr1-159105557-1	chr1	159105507	159105607	+	2.4	cIP1vsInput	Intergenic	L1MEc|LINE|L1	-126769	NM_011931	26374	Mm.328135	NM_011931	ENSMUSG00000040782	Rfwd2	AI316802|C80879|Cop1	ring finger and WD repeat domain 2	protein-coding	0	0.247525
Merged-chr1-31939705-1	chr1	31939655	31939755	+	2.4	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	-233101	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm1	"KH domain containing, RNA binding, signal transduction associated 2"	protein-coding	0	0.316832
Merged-chr6-81797468-1	chr6	81797418	81797518	+	2.4	cIP1vsInput	Intergenic	Intergenic	99208	NR_030151	723871		NR_030151		Mir468	Mirn468|mmu-mir-468	microRNA 468	miscRNA	0	0.316832
Merged-chr3-11760217-1	chr3	11760167	11760267	+	2.4	cIP1vsInput	Intergenic	Intergenic	84142	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.306931
Merged-chr7-123046958-1	chr7	123046908	123047008	+	2.4	cIP2vsInput	Intergenic	Charlie25|DNA|hAT-Charlie	76394	NM_175023	19647	Mm.4480	NM_011247	ENSMUSG00000030779	Rbbp6	4933422O15Rik|AI316869|BB233631|C030034J04Rik|C77662|P2P-R|PACT	retinoblastoma binding protein 6	protein-coding	0	0.405941
Merged-chr6-79881184-1	chr6	79881134	79881234	+	2.4	cIP1vsInput	Intergenic	Intergenic	63153	NM_001190732	100463512	Mm.461086	NM_001190732	ENSMUSG00000096887	Gm20594	Mtrnr2l	"predicted gene, 20594"	protein-coding	0	0.257426
Merged-chr14-84151680-1	chr14	84151630	84151730	+	2.4	cIP1vsInput	Intergenic	MIR|SINE|MIR	-291883	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0	0.316832
Merged-chr11-99385464-1	chr11	99385414	99385514	+	2.4	cIP2vsInput	"3' UTR (NM_010660, exon 8 of 8)"	"3' UTR (NM_010660, exon 8 of 8)"	3900	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding	0.02	0.405941
Merged-chr13-19724762-1	chr13	19724712	19724812	+	2.4	cIP2vsInput	Intergenic	Intergenic	8189	NM_175688	319293	Mm.246657	NM_175688	ENSMUSG00000047462	A530099J19Rik	-	RIKEN cDNA A530099J19 gene	protein-coding	0	0.326733
Merged-chr2-41993980-1	chr2	41993930	41994030	+	2.4	cIP1vsInput	"intron (NM_053011, intron 2 of 90)"	"intron (NM_053011, intron 2 of 90)"	659618	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0	0.326733
Merged-chr11-74017166-1	chr11	74017116	74017216	+	2.4	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	28106	NM_147003	259005	Mm.377784	NM_147003	ENSMUSG00000047444	Olfr139	M5|MOR255-2	olfactory receptor 139	protein-coding	0	0.316832
Merged-chr14-68398776-1	chr14	68398726	68398826	+	2.4	cIP2vsInput	Intergenic	Intergenic	134913	NM_007402	11500	Mm.261495	NM_007402	ENSMUSG00000022056	Adam7	9230104J12Rik|EAP1|EAPI	a disintegrin and metallopeptidase domain 7	protein-coding	0	0.356436
Merged-chr4-56871000-1	chr4	56870950	56871050	+	2.4	cIP1vsInput	Intergenic	Intergenic	-5789	NM_018761	54366	Mm.218891	NM_018761	ENSMUSG00000038816	Ctnnal1	ACRP|AI616177|AW545119|C86009|Catnal1	"catenin (cadherin associated protein), alpha-like 1"	protein-coding	0	0.356436
Merged-chr12-66268238-1	chr12	66268188	66268288	+	2.4	cIP1vsInput	Intergenic	Intergenic	16163	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding	0.01	0.247525
Merged-chr2-44498278-1	chr2	44498228	44498328	+	2.4	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	363344	NM_172662	227835	Mm.488285	NM_172662	ENSMUSG00000036890	Gtdc1	E330008O22Rik	glycosyltransferase-like domain containing 1	protein-coding	0	0.306931
Merged-chr4-38339690-1	chr4	38339640	38339740	+	2.4	cIP2vsInput	Intergenic	Lx2|LINE|L1	-1110603	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding	0	0.346535
Merged-chr6-72407283-1	chr6	72407233	72407333	+	2.4	cIP2vsInput	Intergenic	B3|SINE|B2	-7025	NM_019802	56316	Mm.19937	NM_019802	ENSMUSG00000053460	Ggcx	-	gamma-glutamyl carboxylase	protein-coding	0.02	0.544554
Merged-chr6-79000409-1	chr6	79000359	79000459	+	2.4	cIP1vsInput	Intergenic	L1M3|LINE|L1	-31633	NR_040302	100504701	Mm.400420	NR_040301		Gm20362	-	"predicted gene, 20362"	miscRNA	0	0.29703
Merged-chr2-28420128-1	chr2	28420078	28420178	+	2.4	cIP2vsInput	Intergenic	Intergenic	-27813	NM_001005420	241289	Mm.330095	NM_001005420	ENSMUSG00000035829	Ppp1r26	Gm347|Kiaa0649|mKIAA0649	"protein phosphatase 1, regulatory subunit 26"	protein-coding	0.01	0.613861
Merged-chr6-130696760-1	chr6	130696710	130696810	+	2.4	cIP2vsInput	Intergenic	Intergenic	-309886	NM_016659	16627	Mm.333431	NM_016659	ENSMUSG00000079853	Klra1	A1|Klra22|Ly49a|Ly49o<129>|Ly49v	"killer cell lectin-like receptor, subfamily A, member 1"	protein-coding	0	0.346535
Merged-chr5-82916844-1	chr5	82916794	82916894	+	2.4	cIP1vsInput	Intergenic	Intergenic	-117779	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mmu-mir-1187	microRNA 1187	miscRNA	0	0.356436
Merged-chr1-74520092-1	chr1	74520042	74520142	+	2.4	cIP2vsInput	"intron (NM_021383, intron 3 of 7)"	"intron (NM_021383, intron 3 of 7)"	14032	NM_021383	58184	Mm.291708	NM_021383	ENSMUSG00000026174	Rqcd1	2610007F23Rik|AI593551|Fl10	rcd1 (required for cell differentiation) homolog 1 (S. pombe)	protein-coding	0	0.39604
Merged-chr10-79430035-1	chr10	79429985	79430085	+	2.4	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-38923	NM_001104537	625029	Mm.469865	NM_001104537	ENSMUSG00000091381	Vmn2r83	EG625029	"vomeronasal 2, receptor 83"	protein-coding	0	0.326733
Merged-chr18-50763666-1	chr18	50763616	50763716	+	2.4	cIP1vsInput	Intergenic	Intergenic	-194967	NM_026108	67365	Mm.158150	NM_026108	ENSMUSG00000048875	Hdhd1a	1700121L12Rik|GS1|Hdhd1	haloacid dehalogenase-like hydrolase domain containing 1A	protein-coding	0	0.405941
Merged-chr18-29465667-1	chr18	29465617	29465717	+	2.4	cIP2vsInput	"intron (NR_045395, intron 3 of 3)"	"intron (NR_045395, intron 3 of 3)"	23467	NR_045395	78199	Mm.243850	NR_045395		4930527G23Rik	-	RIKEN cDNA 4930527G23 gene	miscRNA	0	0.287129
Merged-chr3-48266724-1	chr3	48266674	48266774	+	2.4	cIP1vsInput	Intergenic	L1VL2|LINE|L1	-239965	NR_040408	666202	Mm.465057	NR_040408		Gm7977	EG666202	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide pseudogene"	pseudo	0	0.306931
Merged-chr5-55904161-1	chr5	55904111	55904211	+	2.4	cIP1vsInput	Intergenic	Intergenic	1554169	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0.01	0.267327
Merged-chr5-132975043-1	chr5	132974993	132975093	+	2.4	cIP2vsInput	Intergenic	Intergenic	-432700	NM_177047	319974	Mm.488992	NM_177047		Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding	0	0.475248
Merged-chr10-21050261-1	chr10	21050211	21050311	+	2.4	cIP2vsInput	"intron (NM_026203, intron 19 of 23)"	"intron (NM_026203, intron 19 of 23)"	9441	NM_001177776	52906	Mm.486431	NM_001177776	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding	0.01	0.356436
Merged-chr3-143161310-1	chr3	143161260	143161360	+	2.4	cIP2vsInput	Intergenic	Intergenic	-81745	NR_040551	320072	Mm.136397	NR_040551		A830019L24Rik	-	RIKEN cDNA A830019L24 gene	miscRNA	0.03	0.326733
Merged-chr1-104287021-1	chr1	104286971	104287071	+	2.4	cIP1vsInput	Intergenic	Intergenic	-481798	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0	0.267327
Merged-chr4-93034808-1	chr4	93034758	93034858	+	2.4	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	300703	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding	0	0.316832
Merged-chr18-67364550-1	chr18	67364500	67364600	+	2.4	cIP2vsInput	"intron (NM_007702, intron 3 of 4)"	"intron (NM_007702, intron 3 of 4)"	-20447	NR_033214	338360	Mm.486871	NR_033214	ENSMUSG00000046415	B430212C06Rik	-	RIKEN cDNA B430212C06 gene	miscRNA	0.02	0.554455
Merged-chr11-111214728-1	chr11	111214678	111214778	+	2.4	cIP1vsInput	Intergenic	Intergenic	148564	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	"potassium inwardly-rectifying channel, subfamily J, member 2"	protein-coding	0	0.326733
Merged-chr4-81708375-1	chr4	81708325	81708425	+	2.4	cIP1vsInput	Intergenic	Lx7|LINE|L1	-221362	NR_030570	100124446		NR_030570		Mir466h	Mirn466h	microRNA 466h	miscRNA	0	0.336634
Merged-chr11-44568594-1	chr11	44568544	44568644	+	2.4	cIP2vsInput	Intergenic	MYSERV-int|LTR|ERVK	49217	NM_001166553	74315	Mm.156771	NM_001166553	ENSMUSG00000019189	Rnf145	3732413I11Rik|TMRF1	ring finger protein 145	protein-coding	0.02	0.405941
Merged-chr5-83478489-1	chr5	83478439	83478539	+	2.4	cIP1vsInput	Intergenic	Intergenic	-123294	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	"trans-2,3-enoyl-CoA reductase-like"	protein-coding	0	0.306931
Merged-chr14-121746883-1	chr14	121746833	121746933	+	2.4	cIP2vsInput	"intron (NM_134074, intron 1 of 52)"	"intron (NM_134074, intron 1 of 52)"	-7954	NM_001128307	105445	Mm.441054	NM_001081039	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding	0	0.386139
Merged-chr18-71266542-1	chr18	71266492	71266592	+	2.4	cIP1vsInput	"intron (NM_007831, intron 27 of 28)"	"intron (NM_007831, intron 27 of 28)"	698250	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding	0	0.336634
Merged-chr12-112146306-1	chr12	112146256	112146356	+	2.4	cIP2vsInput	promoter-TSS (NM_001097621)	promoter-TSS (NM_001097621)	98	NM_001097621	668303	Mm.313104	NM_001097621	ENSMUSG00000021294	Kif26a	mKIAA1236	kinesin family member 26A	protein-coding	0.05	0.653465
Merged-chr4-106109556-1	chr4	106109506	106109606	+	2.4	cIP2vsInput	Intergenic	L1M5|LINE|L1	-206657	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding	0	0.336634
Merged-chr1-112434761-1	chr1	112434711	112434811	+	2.4	cIP1vsInput	Intergenic	Lx7|LINE|L1	-569843	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik	dermatan sulfate epimerase-like	protein-coding	0	0.376238
Merged-chr6-20590174-1	chr6	20590124	20590224	+	2.4	cIP1vsInput	Intergenic	Intergenic	-625935	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	"potassium voltage-gated channel, Shal-related family, member 2"	protein-coding	0.01	0.376238
Merged-chr15-33820913-1	chr15	33820863	33820963	+	2.4	cIP2vsInput	Intergenic	Intergenic	-133030	NM_001085421	239364	Mm.60794	NM_001085421	ENSMUSG00000038984	Tspyl5	6330530B20|E130308C19Rik	"testis-specific protein, Y-encoded-like 5"	protein-coding	0.01	0.287129
Merged-chr2-139109666-1	chr2	139109616	139109716	+	2.4	cIP2vsInput	Intergenic	Intergenic	289737	NR_035477	100316816		NR_035477	ENSMUSG00000088983	Mir1952	mmu-mir-1952	microRNA 1952	miscRNA	0	0.29703
Merged-chr12-96637627-1	chr12	96637577	96637677	+	2.4	cIP2vsInput	Intergenic	Intergenic	-590405	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0	0.336634
Merged-chr7-56588804-1	chr7	56588754	56588854	+	2.4	cIP1vsInput	Intergenic	(CAAAA)n|Simple_repeat|Simple_repeat	349033	NM_021879	18431	Mm.137052	NM_021879	ENSMUSG00000030450	Oca2	D7H15S12|D7Icr28RN|D7Nic1|p	oculocutaneous albinism II	protein-coding	0	0.306931
Merged-chr11-28148603-1	chr11	28148553	28148653	+	2.4	cIP1vsInput	Intergenic	Intergenic	435693	NM_001166661	216613	Mm.93759	NM_001166661	ENSMUSG00000032878	Ccdc85a	E030025D05Rik	coiled-coil domain containing 85A	protein-coding	0.01	0.306931
Merged-chr13-102635769-1	chr13	102635719	102635819	+	2.4	cIP1vsInput	Intergenic	Intergenic	-57789	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding	0	0.445545
Merged-chr13-39094269-1	chr13	39094219	39094319	+	2.4	cIP2vsInput	Intergenic	Intergenic	-133394	NM_001170431	108652	Mm.255506	NM_001170430	ENSMUSG00000021432	Slc35b3	4921526O06Rik|AI428480|CGI-19|PABST2|PAPST2	"solute carrier family 35, member B3"	protein-coding	0	0.346535
Merged-chr3-48206092-1	chr3	48206042	48206142	+	2.4	cIP2vsInput	Intergenic	Intergenic	-179333	NR_040408	666202	Mm.465057	NR_040408		Gm7977	EG666202	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide pseudogene"	pseudo	0	0.316832
Merged-chr1-163063951-1	chr1	163063901	163064001	+	2.4	cIP1vsInput	"intron (NM_030071, intron 8 of 21)"	L1MEc|LINE|L1	21719	NM_030071	78258	Mm.78368	NM_030071	ENSMUSG00000071890	Mroh9	4921528O07Rik|Armc11	maestro heat-like repeat family member 9	protein-coding	0	0.227723
Merged-chr1-141296639-1	chr1	141296589	141296689	+	2.4	cIP1vsInput	Intergenic	Intergenic	-640237	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0	0.346535
Merged-chr6-93074234-1	chr6	93074184	93074284	+	2.4	cIP2vsInput	"intron (NR_015530, intron 1 of 2)"	"intron (NR_015530, intron 1 of 2)"	133652	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	miscRNA	0	0.366337
Merged-chr18-4486378-1	chr18	4486328	4486428	+	2.4	cIP1vsInput	Intergenic	Intergenic	110786	NM_026157	67440	Mm.49826	NM_026157	ENSMUSG00000024234	Mtpap	0610027A18Rik|AW551379|Papd1	mitochondrial poly(A) polymerase	protein-coding	0	0.326733
Merged-chr3-140285554-1	chr3	140285504	140285604	+	2.4	cIP2vsInput	Intergenic	Intergenic	926801	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0.02	0.356436
Merged-chr11-14410386-1	chr11	14410336	14410436	+	2.4	cIP1vsInput	Intergenic	Intergenic	188839	NR_045918	73307	Mm.399291	NR_045918	ENSMUSG00000085561	1700046C09Rik	-	RIKEN cDNA 1700046C09 gene	miscRNA	0.01	0.227723
Merged-chr4-36263198-1	chr4	36263148	36263248	+	2.4	cIP2vsInput	"intron (NM_001165999, intron 3 of 7)"	"intron (NM_001165999, intron 3 of 7)"	382255	NR_030545	100124458		NR_030545	ENSMUSG00000077851	Mir876	Mirn876|mmu-mir-876	microRNA 876	miscRNA	0	0.306931
Merged-chr12-63624913-1	chr12	63624863	63624963	+	2.4	cIP2vsInput	Intergenic	Intergenic	849985	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.336634
Merged-chr4-49090267-1	chr4	49090217	49090317	+	2.4	cIP1vsInput	"intron (NM_178756, intron 1 of 7)"	MARNA|DNA|TcMar-Mariner	30805	NM_178756	272031	Mm.299460	NM_178756	ENSMUSG00000063446	E130309F12Rik	Lppr1|PRG-3|mKIAA4247	RIKEN cDNA E130309F12 gene	protein-coding	0	0.346535
Merged-chr4-53359886-1	chr4	53359836	53359936	+	2.4	cIP1vsInput	Intergenic	Intergenic	-80527	NM_001159633	100434	Mm.482207	NM_001159633	ENSMUSG00000028412	Slc44a1	2210409B22Rik|4833416H08Rik|AW547365|CHTL1|CTL1|Cdw92	"solute carrier family 44, member 1"	protein-coding	0	0.306931
Merged-chr16-60682622-1	chr16	60682572	60682672	+	2.4	cIP2vsInput	Intergenic	Intergenic	-77091	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0	0.346535
Merged-chr4-55991051-1	chr4	55991001	55991101	+	2.4	cIP1vsInput	Intergenic	Intergenic	-458576	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding	0	0.366337
Merged-chr2-133576473-1	chr2	133576423	133576523	+	2.4	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	24314	NM_007553	12156	Mm.103205	NM_007553		Bmp2	AI467020|Bmp2a	bone morphogenetic protein 2	protein-coding	0	0.415842
Merged-chr12-96580399-1	chr12	96580349	96580449	+	2.4	cIP1vsInput	Intergenic	Intergenic	-533177	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0	0.356436
Merged-chr2-128396055-1	chr2	128396005	128396105	+	2.4	cIP2vsInput	"intron (NR_028591, intron 1 of 1)"	"intron (NR_028591, intron 1 of 1)"	33296	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	miscRNA	0.04	0.653465
Merged-chr14-24399135-1	chr14	24399085	24399185	+	2.4	cIP1vsInput	Intergenic	L1_Mur1|LINE|L1	87911	NM_001081247	218832	Mm.399136	NM_001081247	ENSMUSG00000025280	Polr3a	9330175N20Rik|BC053071|RPC1|RPC155	polymerase (RNA) III (DNA directed) polypeptide A	protein-coding	0	0.336634
Merged-chr8-95586628-1	chr8	95586578	95586678	+	2.4	cIP1vsInput	Intergenic	L1MA9|LINE|L1	-11431	NM_027640	70993	Mm.486561	NM_027640	ENSMUSG00000048400	Prss54	4931432M23Rik|Klkbl4	"protease, serine, 54"	protein-coding	0	0.326733
Merged-chr19-15890272-1	chr19	15890222	15890322	+	2.4	cIP2vsInput	Intergenic	Lx5c|LINE|L1	34350	NM_001205339	107272	Mm.470456	NM_001205339	ENSMUSG00000024640	Psat1	D8Ertd814e|EPIP|PSA|Psat	phosphoserine aminotransferase 1	protein-coding	0	0.316832
Merged-chr5-36936683-1	chr5	36936633	36936733	+	2.4	cIP2vsInput	"intron (NM_172994, intron 5 of 8)"	"intron (NM_172994, intron 5 of 8)"	52299	NM_011716	22393	Mm.20916	NM_011716	ENSMUSG00000039474	Wfs1	AI481085|wolframin	Wolfram syndrome 1 homolog (human)	protein-coding	0.04	0.534653
Merged-chr9-50463102-1	chr9	50463052	50463152	+	2.4	cIP2vsInput	Intergenic	Intergenic	-31423	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	1600029D21Rik	0610037B23Rik|AA407923|AU043048|PLET1	RIKEN cDNA 1600029D21 gene	protein-coding	0.01	0.524752
Merged-chrX-47985358-2	chrX	47985302	47985414	+	2.4	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	49494	NM_013912	30878	Mm.29262	NM_013912	ENSMUSG00000037010	Apln	6030430G11Rik|Apel	apelin	protein-coding	0.151786	0.628319
Merged-chr1-97088186-1	chr1	97088136	97088236	+	2.4	cIP1vsInput	"intron (NM_028942, intron 6 of 13)"	"intron (NM_028942, intron 6 of 13)"	40117	NM_028942	74441	Mm.60362	NM_028942	ENSMUSG00000026331	Slco6c1	4933404A18Rik|C79179	"solute carrier organic anion transporter family, member 6c1"	protein-coding	0	0.306931
Merged-chr7-15851166-1	chr7	15851116	15851216	+	2.4	cIP1vsInput	Intergenic	RLTR45-int|LTR|ERVK	-11487	NM_145710	252830	Mm.25863	NM_145710	ENSMUSG00000041583	Obox6	D17Ertd599e	oocyte specific homeobox 6	protein-coding	0	0.29703
Merged-chr18-32485093-1	chr18	32485043	32485143	+	2.4	cIP2vsInput	Intergenic	Intergenic	74941	NM_001048207	71683	Mm.292145	NM_027863	ENSMUSG00000090523	Gypc	0610037F22Rik|Cd236r	glycophorin C	protein-coding	0.04	0.524752
Merged-chr15-96411975-1	chr15	96411925	96412025	+	2.4	cIP2vsInput	"3' UTR (NM_028148, exon 15 of 15)"	"3' UTR (NM_028148, exon 15 of 15)"	48868	NM_028148	72193	Mm.472183	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding	0	0.267327
Merged-chr5-47710068-1	chr5	47710018	47710118	+	2.4	cIP2vsInput	Intergenic	L1MDa|LINE|L1	-273087	NM_178804	20563	Mm.289739	NM_178804		Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|mKIAA4141	slit homolog 2 (Drosophila)	protein-coding	0.01	0.316832
Merged-chr8-71676817-1	chr8	71676767	71676867	+	2.4	cIP2vsInput	"intron (NM_001190830, intron 1 of 23)"	B1F1|SINE|Alu	434	NM_010589	16453	Mm.249645	NM_001190830	ENSMUSG00000031805	Jak3	fae|wil	Janus kinase 3	protein-coding	0.04	0.415842
Merged-chr7-67537970-1	chr7	67537920	67538020	+	2.4	cIP1vsInput	"intron (NR_028144, intron 6 of 8)"	"intron (NR_028144, intron 6 of 8)"	107266	NM_175124	67867	Mm.31247	NM_027413	ENSMUSG00000030556	Lrrc28	1300004K21Rik|2210012C09Rik|2310058O11Rik	leucine rich repeat containing 28	protein-coding	0.01	0.306931
Merged-chr11-111417222-1	chr11	111417172	111417272	+	2.4	cIP1vsInput	Intergenic	Intergenic	351058	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	"potassium inwardly-rectifying channel, subfamily J, member 2"	protein-coding	0.01	0.326733
Merged-chr8-89853790-1	chr8	89853740	89853840	+	2.4	cIP2vsInput	Intergenic	Intergenic	494462	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding	0	0.29703
Merged-chr4-79711695-1	chr4	79711645	79711745	+	2.4	cIP1vsInput	Intergenic	Intergenic	-1122535	NM_031202	22178	Mm.412291	NM_031202	ENSMUSG00000005994	Tyrp1	TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding	0	0.316832
Merged-chr1-127055645-1	chr1	127055595	127055695	+	2.4	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-149341	NM_145128	107895	Mm.472488	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding	0.01	0.316832
Merged-chr2-51716912-1	chr2	51716862	51716962	+	2.4	cIP1vsInput	"intron (NR_040639, intron 1 of 6)"	"intron (NR_040639, intron 1 of 6)"	15097	NR_040639	433426	Mm.244381	NR_040639	ENSMUSG00000085014	Gm13490	OTTMUSG00000012405	predicted gene 13490	miscRNA	0	0.326733
Merged-chr4-21712404-1	chr4	21712354	21712454	+	2.4	cIP1vsInput	Intergenic	RMER21A|LTR|ERV1	-15299	NM_001122982	51813	Mm.278584	NM_001122982	ENSMUSG00000028252	Ccnc	AI451004|AU020987|CG1C	cyclin C	protein-coding	0.06	0.623762
Merged-chr16-27730881-1	chr16	27730831	27730931	+	2.4	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-119049	NR_033475	100038623	Mm.387135	NR_033475		Gm10823	ENSMUSG00000075290	predicted gene 10823	miscRNA	0	0.346535
Merged-chr12-96656022-1	chr12	96655972	96656072	+	2.4	cIP2vsInput	Intergenic	Intergenic	-608800	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0.01	0.336634
Merged-chr4-58579555-1	chr4	58579505	58579605	+	2.4	cIP2vsInput	Intergenic	Intergenic	-26064	NM_010336	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	5031439C20|AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding	0.01	0.306931
Merged-chr12-114499513-1	chr12	114499463	114499563	+	2.4	cIP1vsInput	Intergenic	Intergenic	955605	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding	0	0.376238
Merged-chr9-84086953-1	chr9	84086903	84087003	+	2.4	cIP1vsInput	"intron (NM_199195, intron 9 of 10)"	"intron (NM_199195, intron 9 of 10)"	138172	NM_199195	12040	Mm.12819	NM_199195		Bckdhb	-	"branched chain ketoacid dehydrogenase E1, beta polypeptide"	protein-coding	0.01	0.346535
Merged-chr15-5490265-2	chr15	5490213	5490317	+	2.4	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-6053	NR_045274	71432	Mm.291087	NR_045274		5430437J10Rik	-	RIKEN cDNA 5430437J10 gene	miscRNA	0	0.361905
Merged-chr11-31861408-1	chr11	31861358	31861458	+	2.4	cIP2vsInput	Intergenic	Intergenic	-10803	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	4930447D24Rik|AI851572|mKIAA1673	cytoplasmic polyadenylation element binding protein 4	protein-coding	0.02	0.435644
Merged-chr19-30829959-1	chr19	30829909	30830009	+	2.4	cIP1vsInput	"intron (NM_001013833, intron 5 of 17)"	"intron (NM_001013833, intron 5 of 17)"	101003	NR_033643	625995	Mm.490410	NR_033643		Gm6642	EG625995	ubiquitin-like 5 pseudogene	pseudo	0.02	0.267327
Merged-chr19-46707608-1	chr19	46707558	46707658	+	2.4	cIP2vsInput	"intron (NM_020577, intron 1 of 10)"	"intron (NM_020577, intron 1 of 10)"	165	NM_020577	57344	Mm.28566	NM_020577	ENSMUSG00000003559	As3mt	2310045H08Rik|Cyt19	arsenic (+3 oxidation state) methyltransferase	protein-coding	0.03	0.693069
Merged-chr1-11967809-1	chr1	11967759	11967859	+	2.4	cIP1vsInput	"intron (NM_177173, intron 12 of 13)"	L1MEg|LINE|L1	553704	NM_001160371	320492	Mm.52021	NM_001160369	ENSMUSG00000057715	A830018L16Rik	-	RIKEN cDNA A830018L16 gene	protein-coding	0	0.316832
Merged-chr12-119045664-1	chr12	119045614	119045714	+	2.4	cIP2vsInput	Intergenic	Intergenic	-79243	NM_029961	77706	Mm.261496	NM_029961	ENSMUSG00000072791	Abcb5	9230106F14Rik	"ATP-binding cassette, sub-family B (MDR/TAP), member 5"	protein-coding	0	0.29703
Merged-chr18-87376703-1	chr18	87376653	87376753	+	2.4	cIP1vsInput	Intergenic	Intergenic	663655	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding	0	0.376238
Merged-chr1-195100121-1	chr1	195100071	195100171	+	2.4	cIP1vsInput	Intergenic	Intergenic	-7873	NM_010778	17221	Mm.12884	NM_010778	ENSMUSG00000016493	Cd46	Mcp	"CD46 antigen, complement regulatory protein"	protein-coding	0	0.346535
Merged-chr3-39513590-1	chr3	39513540	39513640	+	2.4	cIP1vsInput	Intergenic	Lx6|LINE|L1	626650	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT tumor suppressor homolog 4 (Drosophila)	protein-coding	0.01	0.356436
Merged-chr6-5589777-1	chr6	5589727	5589827	+	2.4	cIP2vsInput	Intergenic	Intergenic	-93499	NM_013743	27273	Mm.235547	NM_013743	ENSMUSG00000019577	Pdk4	AV005916	"pyruvate dehydrogenase kinase, isoenzyme 4"	protein-coding	0.03	0.445545
Merged-chr3-96198067-1	chr3	96198017	96198117	+	2.4	cIP1vsInput	promoter-TSS (NM_026975)	promoter-TSS (NM_026975)	-481	NM_026975	69168	Mm.104531	NM_026975	ENSMUSG00000015943	Bola1	1810037G04Rik	bolA-like 1 (E. coli)	protein-coding	0.01	0.475248
Merged-chr13-28483010-1	chr13	28482960	28483060	+	2.4	cIP2vsInput	"intron (NR_045054, intron 7 of 7)"	"intron (NR_045054, intron 7 of 7)"	340526	NM_023746	28078	Mm.155058	NM_023746	ENSMUSG00000017064	Prl5a1	1600013P04Rik|D13Wsu14e|PLP-L|Prlpl|RP23-231P12.2	"prolactin family 5, subfamily a, member 1"	protein-coding	0	0.366337
Merged-chr16-58225049-1	chr16	58224999	58225099	+	2.4	cIP1vsInput	Intergenic	Intergenic	-183486	NM_028523	73379	Mm.373589	NM_028523	ENSMUSG00000035107	Dcbld2	1700055P21Rik|AW146002|CLCP1|Esdn	"discoidin, CUB and LCCL domain containing 2"	protein-coding	0.01	0.356436
Merged-chr4-128609701-1	chr4	128609651	128609751	+	2.4	cIP2vsInput	"intron (NM_177758, intron 1 of 7)"	"intron (NM_177758, intron 1 of 7)"	397	NM_177758	269585	Mm.153291	NM_177758	ENSMUSG00000061894	Zscan20	C130001F22|Zfp31|Zkscan20	zinc finger and SCAN domains 20	protein-coding	0.04	0.554455
Merged-chr2-91078876-1	chr2	91078826	91078926	+	2.4	cIP2vsInput	Intergenic	Intergenic	-8655	NM_026721	68427	Mm.192375	NM_026721	ENSMUSG00000002105	Slc39a13	1100001L14Rik|AA387663|ZIP13	"solute carrier family 39 (metal ion transporter), member 13"	protein-coding	0.11	0.752475
Merged-chr9-73113276-1	chr9	73113226	73113326	+	2.4	cIP2vsInput	promoter-TSS (NM_198609)	promoter-TSS (NM_198609)	-193	NM_198609	225215	Mm.379366	NM_198609	ENSMUSG00000032215	Rsl24d1	2410159K22Rik	ribosomal L24 domain containing 1	protein-coding	0.04	0.574257
Merged-chr10-16197917-1	chr10	16197867	16197967	+	2.4	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	897865	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0	0.346535
Merged-chr17-39170130-1	chr17	39170080	39170180	+	2.4	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-93093	NM_001177582	100126779	Mm.471589	NM_001177582	ENSMUSG00000096697	Gm20581	Esp23	"predicted gene, 20581"	protein-coding	0	0.346535
Merged-chr2-173836844-1	chr2	173836794	173836894	+	2.4	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	99273	NM_019806	56491	Mm.260456	NM_019806	ENSMUSG00000054455	Vapb	AI225786|AI840687|AI848259|D2Abb2e|R75548|VAP33b|Vamp33b	"vesicle-associated membrane protein, associated protein B and C"	protein-coding	0	0.316832
Merged-chr2-12523848-1	chr2	12523798	12523898	+	2.4	cIP1vsInput	Intergenic	Intergenic	-104388	NM_024185	66960	Mm.34059	NM_024185	ENSMUSG00000026767	Fam188a	1810041E18Rik|2310047O13Rik|5830410F13Rik|AI447827|AW111958	"family with sequence similarity 188, member A"	protein-coding	0.01	0.287129
Merged-chr7-136821562-1	chr7	136821512	136821612	+	2.4	cIP2vsInput	Intergenic	Intergenic	-73049	NM_008598	17314	Mm.440219	NM_008598	ENSMUSG00000054612	Mgmt	AGT|AI267024|Agat	O-6-methylguanine-DNA methyltransferase	protein-coding	0.01	0.356436
Merged-chr5-87140811-1	chr5	87140761	87140861	+	2.4	cIP2vsInput	promoter-TSS (NM_009467)	promoter-TSS (NM_009467)	-471	NM_009467	22238	Mm.291575	NM_009467	ENSMUSG00000054630	Ugt2b5	AI118071|M-1|Udpgt-3|Udpgt2b5|Ugt2b17	"UDP glucuronosyltransferase 2 family, polypeptide B5"	protein-coding	0	0.29703
Merged-chr16-53252912-1	chr16	53252862	53252962	+	2.4	cIP1vsInput	Intergenic	Intergenic	-437168	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	miscRNA	0	0.247525
Merged-chr11-72466985-1	chr11	72466935	72467035	+	2.4	cIP2vsInput	"intron (NM_153060, intron 2 of 12)"	MER63B|DNA|hAT-Blackjack	8042	NM_001276383	216892	Mm.212812	NM_001276383	ENSMUSG00000040447	Spns2	-	spinster homolog 2	protein-coding	0.01	0.356436
Merged-chr5-56186137-1	chr5	56186087	56186187	+	2.4	cIP1vsInput	Intergenic	Intergenic	1531782	NR_015588	319216	Mm.446765	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	miscRNA	0	0.39604
Merged-chr13-19593780-1	chr13	19593730	19593830	+	2.4	cIP2vsInput	"intron (NM_134065, intron 2 of 2)"	L1MB3|LINE|L1	26050	NM_134065	105298	Mm.275054	NM_134065	ENSMUSG00000002808	Epdr1	AU040950|AV006210|Epdm2|Epdr2|MERP-1|MERP-2|MERP2|Ucc1	ependymin related protein 1 (zebrafish)	protein-coding	0	0.366337
Merged-chr13-38580907-1	chr13	38580857	38580957	+	2.4	cIP2vsInput	Intergenic	Intergenic	-52447	NM_145367	105245	Mm.28622	NM_145367	ENSMUSG00000038991	Txndc5	AL022641|ERp46|PC-TRP	thioredoxin domain containing 5	protein-coding	0.04	0.514851
Merged-chr15-45659317-1	chr15	45659267	45659367	+	2.4	cIP1vsInput	Intergenic	Intergenic	-544383	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	"potassium channel, subfamily V, member 1"	protein-coding	0	0.346535
Merged-chr5-110653318-1	chr5	110653268	110653368	+	2.4	cIP2vsInput	promoter-TSS (NM_027156)	promoter-TSS (NM_027156)	64	NM_153570	100608	Mm.29960	NM_153570	ENSMUSG00000033294	Noc4l	AI326906	nucleolar complex associated 4 homolog (S. cerevisiae)	protein-coding	0.11	0.712871
Merged-chr3-36710258-1	chr3	36710208	36710308	+	2.4	cIP2vsInput	Intergenic	Intergenic	-20091	NM_019510	22065	Mm.74363	NM_019510	ENSMUSG00000027716	Trpc3	Mwk|Trcp3|Trp3|Trrp3	"transient receptor potential cation channel, subfamily C, member 3"	protein-coding	0.01	0.366337
Merged-chr4-100036606-1	chr4	100036556	100036656	+	2.4	cIP1vsInput	Intergenic	Intergenic	-59185	NM_013845	26563	Mm.485829	NM_013845		Ror1	2810404D04Rik|Ntrkr1|mRor1	receptor tyrosine kinase-like orphan receptor 1	protein-coding	0	0.336634
Merged-chr5-102149399-1	chr5	102149349	102149449	+	2.4	cIP1vsInput	Intergenic	Intergenic	-79478	NM_172882	72145	Mm.447999	NM_172882	ENSMUSG00000043940	Wdfy3	2610509D04Rik|ALFY|AW319683|B930017C24|BWF1|Bchs|D5Ertd66e|Ggtb3|ZFYVE25|mKIAA0993	WD repeat and FYVE domain containing 3	protein-coding	0.02	0.366337
Merged-chr6-6849557-1	chr6	6849507	6849607	+	2.4	cIP2vsInput	"intron (NR_015388, intron 1 of 1)"	"intron (NR_015388, intron 1 of 1)"	-13777	NM_010057	13396	Mm.439763	NM_010057	ENSMUSG00000029754	Dlx6	-	distal-less homeobox 6	protein-coding	0	0.356436
Merged-chr2-51935388-1	chr2	51935338	51935438	+	2.4	cIP1vsInput	promoter-TSS (NM_001141982)	promoter-TSS (NM_001141982)	-379	NM_001141981	71684	Mm.28309	NM_001141981	ENSMUSG00000036249	Rbm43	0610033I05Rik	RNA binding motif protein 43	protein-coding	0.02	0.405941
Merged-chr1-181612188-1	chr1	181612138	181612238	+	2.4	cIP2vsInput	Intergenic	Lx9|LINE|L1	-100737	NM_207280	403180	Mm.220754	NM_207280	ENSMUSG00000050625	Ccdc121	6530421E24Rik|Gm755	coiled-coil domain containing 121	protein-coding	0	0.326733
Merged-chr15-52096833-1	chr15	52096783	52096883	+	2.4	cIP2vsInput	Intergenic	RMER17A2|LTR|ERVK	56726	NM_175503	239435	Mm.24204	NM_175503	ENSMUSG00000068522	Aard	A5D3|AV328152	alanine and arginine rich domain containing protein	protein-coding	0.02	0.534653
Merged-chr2-107537460-1	chr2	107537410	107537510	+	2.4	cIP2vsInput	Intergenic	Intergenic	246871	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	"potassium voltage-gated channel, shaker-related subfamily, member 4"	protein-coding	0.01	0.346535
Merged-chr15-28078372-1	chr15	28078322	28078422	+	2.4	cIP2vsInput	Intergenic	L1MB8|LINE|L1	-52524	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding	0	0.376238
Merged-chr17-81987645-1	chr17	81987595	81987695	+	2.4	cIP2vsInput	Intergenic	Intergenic	-249268	NM_011406	20541	Mm.489060	NM_001112798		Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	"solute carrier family 8 (sodium/calcium exchanger), member 1"	protein-coding	0	0.316832
Merged-chr5-150376997-1	chr5	150376947	150377047	+	2.4	cIP1vsInput	"intron (NM_172887, intron 14 of 60)"	L1MC|LINE|L1	117067	NM_172887	320365	Mm.454348	NM_178781	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	furry homolog (Drosophila)	protein-coding	0.01	0.435644
Merged-chr16-58960538-1	chr16	58960488	58960588	+	2.4	cIP1vsInput	Intergenic	Intergenic	-31894	NM_146999	259001	Mm.223388	NM_146999	ENSMUSG00000090951	Olfr181	MOR184-4	olfactory receptor 181	protein-coding	0	0.346535
Merged-chr4-17665720-1	chr4	17665670	17665770	+	2.4	cIP2vsInput	Intergenic	Intergenic	-187762	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0	0.257426
Merged-chr12-64297792-1	chr12	64297742	64297842	+	2.4	cIP1vsInput	Intergenic	L1MDb|LINE|L1	177106	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.316832
Merged-chr8-82616657-1	chr8	82616607	82616707	+	2.4	cIP1vsInput	Intergenic	Intergenic	157469	NM_145600	30932	Mm.269248	NM_145600	ENSMUSG00000031711	Zfp330	BC008086|Noa36|Znf330	zinc finger protein 330	protein-coding	0	0.346535
Merged-chr5-15632470-2	chr5	15632420	15632520	+	2.4	cIP1vsInput|cIP2vsInput	Intergenic	RMER6D|LTR|ERVK	13371	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0.01	0.366337
Merged-chr14-80593918-1	chr14	80593868	80593968	+	2.4	cIP1vsInput	Intergenic	Intergenic	593616	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0.01	0.306931
Merged-chr1-158418189-1	chr1	158418139	158418239	+	2.4	cIP1vsInput	"intron (NM_001205204, intron 1 of 22)"	"intron (NM_001205204, intron 1 of 22)"	55885	NM_001205204	11899	Mm.329586	NM_001205204	ENSMUSG00000026587	Astn1	Astn|GC14|mKIAA0289	astrotactin 1	protein-coding	0	0.316832
Merged-chr16-79779285-1	chr16	79779235	79779335	+	2.4	cIP1vsInput	Intergenic	Intergenic	-688188	NM_008941	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	"transmembrane protease, serine 15"	protein-coding	0	0.336634
Merged-chr3-63113764-1	chr3	63113714	63113814	+	2.4	cIP1vsInput	Intergenic	Intergenic	-182108	NM_008604	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding	0.01	0.326733
Merged-chr5-82696407-1	chr5	82696357	82696457	+	2.4	cIP1vsInput	Intergenic	Intergenic	102658	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mmu-mir-1187	microRNA 1187	miscRNA	0	0.29703
Merged-chr14-47597992-1	chr14	47597942	47598042	+	2.4	cIP1vsInput	Intergenic	Intergenic	-29558	NM_172599	100504663	Mm.470462	NM_172599	ENSMUSG00000037526	Atg14	4832427M01|Atg14L|D14Ertd114e|D14Ertd436e	autophagy related 14	protein-coding	0.03	0.475248
Merged-chr5-17328574-1	chr5	17328524	17328624	+	2.4	cIP1vsInput	Intergenic	Intergenic	-147548	NM_027609	70935	Mm.332225	NM_027609	ENSMUSG00000058643	Speer4f	4922502J04Rik|SPEER-4F	spermatogenesis associated glutamate (E)-rich protein 4f	protein-coding	0	0.237624
Merged-chr1-3341447-1	chr1	3341397	3341497	+	2.4	cIP1vsInput	"intron (NM_001011874, intron 2 of 2)"	MMERVK9C_I-int|LTR|ERVK	330051	NM_001011874	497097	Mm.489375	NM_001011874		Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X Kell blood group precursor related family member 4	protein-coding	0	0.237624
Merged-chr4-95205477-1	chr4	95205427	95205527	+	2.4	cIP1vsInput	Intergenic	MTC|LTR|ERVL-MaLR	-153255	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	Jun oncogene	protein-coding	0	0.465347
Merged-chr3-147369381-1	chr3	147369331	147369431	+	2.4	cIP1vsInput	Intergenic	Intergenic	517014	NM_027594	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|Ttll7s	"tubulin tyrosine ligase-like family, member 7"	protein-coding	0	0.336634
Merged-chr16-16997178-1	chr16	16997128	16997228	+	2.4	cIP1vsInput	"intron (NM_001038663, intron 1 of 7)"	"intron (NM_001038663, intron 1 of 7)"	13796	NM_001038663	26413	Mm.196581	NM_001038663	ENSMUSG00000063358	Mapk1	9030612K14Rik|AA407128|AU018647|C78273|ERK|Erk2|MAPK2|PRKM2|Prkm1|p41mapk|p42mapk	mitogen-activated protein kinase 1	protein-coding	0	0.336634
Merged-chr8-68322219-1	chr8	68322169	68322269	+	2.4	cIP2vsInput	"intron (NM_028182, intron 4 of 8)"	"intron (NM_028182, intron 4 of 8)"	45691	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding	0	0.39604
Merged-chr7-13436190-1	chr7	13436140	13436240	+	2.4	cIP1vsInput	Intergenic	Intergenic	-14651	NM_001033418	330470	Mm.291102	NM_001033418	ENSMUSG00000074378	Bsph1	Gm767	binder of sperm protein homolog 1	protein-coding	0	0.376238
Merged-chr16-93876030-1	chr16	93875980	93876080	+	2.4	cIP1vsInput	TTS (NM_001045529)	TTS (NM_001045529)	-7871	NM_028083	110749	Mm.274222	NM_028083	ENSMUSG00000022945	Chaf1b	2600017H24Rik|C76145|CAF-I p60|CAF-Ip60|CAF1|CAF1A|CAF1P60|MPHOSPH7	"chromatin assembly factor 1, subunit B (p60)"	protein-coding	0.02	0.29703
Merged-chr1-40971650-1	chr1	40971600	40971700	+	2.4	cIP2vsInput	Intergenic	Intergenic	166049	NM_001081198	381339	Mm.395273	NM_001081198		Tmem182	2310079P10Rik|AI414494	transmembrane protein 182	protein-coding	0	0.336634
Merged-chr15-57243927-1	chr15	57243877	57243977	+	2.4	cIP1vsInput	"3' UTR (NM_172378, exon 12 of 12)"	"3' UTR (NM_172378, exon 12 of 12)"	233698	NM_172378	210463	Mm.26555	NM_172378	ENSMUSG00000022366	Slc22a22	oat-pg	"solute carrier family 22 (organic cation transporter), member 22"	protein-coding	0.02	0.356436
Merged-chr1-96507160-1	chr1	96507110	96507210	+	2.4	cIP2vsInput	Intergenic	Lx8b|LINE|L1	155413	NR_040478	75159	Mm.243854	NR_040478		4930533P14Rik	-	RIKEN cDNA 4930533P14 gene	miscRNA	0	0.366337
Merged-chr15-73764338-1	chr15	73764288	73764388	+	2.4	cIP1vsInput	Intergenic	Intergenic	16312	NM_008975	19245	Mm.390807	NM_001166388	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding	0.01	0.514851
Merged-chr1-87041296-1	chr1	87041246	87041346	+	2.4	cIP2vsInput	"intron (NM_001172157, intron 15 of 21)"	"intron (NM_001172157, intron 15 of 21)"	48632	NM_007433	11650	Mm.195224	NM_007433	ENSMUSG00000026246	Alppl2	Akp5|C77216|D1Ertd816e|EAP	"alkaline phosphatase, placental-like 2"	protein-coding	0.01	0.584158
Merged-chr5-27737367-2	chr5	27737312	27737423	+	2.35	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	54183	NM_018878	55982	Mm.444095	NM_018878	ENSMUSG00000002221	Paxip1	D5Ertd149e|PTIP	PAX interacting (with transcription-activation domain) protein 1	protein-coding	0.009009	0.553571
Merged-chr10-81037477-2	chr10	81037426	81037528	+	2.35	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-3565	NM_134135	106947	Mm.5353	NM_134135	ENSMUSG00000046822	Slc39a3	AI845814|Zip3	"solute carrier family 39 (zinc transporter), member 3"	protein-coding	0.029412	0.456311
Merged-chr2-12630339-2	chr2	12630278	12630401	+	2.35	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-210879	NM_024185	66960	Mm.34059	NM_024185	ENSMUSG00000026767	Fam188a	1810041E18Rik|2310047O13Rik|5830410F13Rik|AI447827|AW111958	"family with sequence similarity 188, member A"	protein-coding	0	0.330645
Merged-chr2-72279375-2	chr2	72279307	72279443	+	2.35	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-6262	NM_023057	65964	Mm.314618	NM_001164791	ENSMUSG00000004085	B230120H23Rik	AV006891|MLTK|MLTKalpha|MLTKbeta|Zak	RIKEN cDNA B230120H23 gene	protein-coding	0.022059	0.306569
Merged-chr18-90602053-2	chr18	90601999	90602107	+	2.35	cIP1vsInput|cIP2vsInput	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	91899	NM_198295	67988	Mm.268041	NM_198295	ENSMUSG00000024614	Tmx3	6430411B10Rik|A730024F05Rik|AV259382|Txndc10|mKIAA1830	thioredoxin-related transmembrane protein 3	protein-coding	0	0.605505
Merged-chr4-141010576-2	chr4	141010487	141010665	+	2.35	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_008546)	promoter-TSS (NM_008546)	-61	NM_008546	17150	Mm.7386	NM_001161799	ENSMUSG00000060572	Mfap2	AI893631|Magp|Magp1	microfibrillar-associated protein 2	protein-coding	0.08427	0.709497
Merged-chrY-10423991-2	chrY	10423932	10424050	+	2.35	cIP1vsInput|cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	773857	NM_001199331	100040022	Mm.485767	NM_001199331	ENSMUSG00000095172	Gm20822	-	"predicted gene, 20822"	protein-coding	0	0.277311
Merged-chr2-177278862-1	chr2	177278812	177278912	+	2.3	cIP1vsInput	Intergenic	MMERVK9E_I-int|LTR|ERVK	-185880	NM_001177568	628308	Mm.460436	NM_001177568		Gm14420	OTTMUSG00000016588	predicted gene 14420	protein-coding	0	0.376238
Merged-chr6-44826657-1	chr6	44826607	44826707	+	2.3	cIP1vsInput	Intergenic	Lx6|LINE|L1	-233404	NM_001004357	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0	0.415842
Merged-chr3-133190971-1	chr3	133190921	133191021	+	2.3	cIP2vsInput	"intron (NM_029953, intron 2 of 3)"	"intron (NM_029953, intron 2 of 3)"	43918	NM_029953	77669	Mm.98630	NM_029953	ENSMUSG00000040969	Arhgef38	9130221D24Rik	Rho guanine nucleotide exchange factor (GEF) 38	protein-coding	0.01	0.326733
Merged-chr10-89898841-1	chr10	89898791	89898891	+	2.3	cIP1vsInput	"intron (NM_001128086, intron 1 of 24)"	"intron (NM_001128086, intron 1 of 24)"	25332	NM_001128086	77531	Mm.440605	NM_001128086		Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding	0.01	0.326733
Merged-chr15-60952610-1	chr15	60952560	60952660	+	2.3	cIP1vsInput	Intergenic	MTC|LTR|ERVL-MaLR	-31340	NM_001081067	117586	Mm.291499	NM_001081067	ENSMUSG00000022347	A1bg	C44	alpha-1-B glycoprotein	protein-coding	0.01	0.425743
Merged-chr5-49027011-1	chr5	49026961	49027061	+	2.3	cIP2vsInput	"intron (NM_001199244, intron 1 of 7)"	"intron (NM_001199244, intron 1 of 7)"	-137454	NM_030265	80334	Mm.160172	NM_001199242	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding	0.01	0.405941
Merged-chr13-118983656-1	chr13	118983606	118983706	+	2.3	cIP2vsInput	Intergenic	Intergenic	268957	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding	0	0.336634
Merged-chr8-24554622-1	chr8	24554572	24554672	+	2.3	cIP2vsInput	"intron (NM_145949, intron 2 of 9)"	"intron (NM_145949, intron 2 of 9)"	21711	NM_145949	209176	Mm.219580	NM_145949	ENSMUSG00000031549	Ido2	AI265623|C230043N17Rik|Ido-2|Indol1	"indoleamine 2,3-dioxygenase 2"	protein-coding	0.05	0.623762
Merged-chr15-100600178-1	chr15	100600128	100600228	+	2.3	cIP1vsInput	Intergenic	Intergenic	-13813	NM_010127	19009	Mm.475483	NM_010127	ENSMUSG00000009739	Pou6f1	2310038G18Rik|Brn5.0|C79593|Emb|cns-1	"POU domain, class 6, transcription factor 1"	protein-coding	0.1	0.732673
Merged-chr14-75066787-1	chr14	75066737	75066837	+	2.3	cIP2vsInput	"intron (NR_030568, intron 2 of 3)"	"intron (NR_030568, intron 2 of 3)"	50760	NM_198642	271221	Mm.320280	NM_198642	ENSMUSG00000034959	5031414D18Rik	Gm744|Gm911|Kiaa0226l	RIKEN cDNA 5031414D18 gene	protein-coding	0	0.326733
Merged-chr1-111319734-1	chr1	111319684	111319784	+	2.3	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-342362	NM_001081386	227485	Mm.322070	NM_001081386	ENSMUSG00000047216	Cdh19	-	"cadherin 19, type 2"	protein-coding	0	0.386139
Merged-chr9-112326217-1	chr9	112326167	112326267	+	2.3	cIP2vsInput	"intron (NR_033433, intron 2 of 3)"	"intron (NR_033433, intron 2 of 3)"	69643	NR_033433	620760	Mm.259863	NR_015468	ENSMUSG00000087038	2900079G21Rik	C130083B14|Gm6179	RIKEN cDNA 2900079G21 gene	miscRNA	0	0.356436
Merged-chr6-27095600-1	chr6	27095550	27095650	+	2.3	cIP2vsInput	Intergenic	Lx4A|LINE|L1	841150	NR_030420	735266		NR_030420		Mir592	Mirn592|mir-592|mmu-mir-592	microRNA 592	miscRNA	0.01	0.336634
Merged-chr13-76184123-1	chr13	76184073	76184173	+	2.3	cIP1vsInput	"intron (NM_001081352, intron 42 of 43)"	"intron (NM_001081352, intron 42 of 43)"	85389	NM_001081352	218343	Mm.277964	NM_001081352	ENSMUSG00000033991	Ttc37	mKIAA0372	tetratricopeptide repeat domain 37	protein-coding	0	0.217822
Merged-chr14-89219947-1	chr14	89219897	89219997	+	2.3	cIP2vsInput	Intergenic	Intergenic	-676277	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0.01	0.356436
Merged-chr1-124535588-1	chr1	124535538	124535638	+	2.3	cIP2vsInput	Intergenic	B1F|SINE|Alu	-490029	NM_199021	269109	Mm.483255	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding	0.01	0.326733
Merged-chr3-157779141-1	chr3	157779091	157779191	+	2.3	cIP2vsInput	Intergenic	Intergenic	145922	NM_145953	107869	Mm.28301	NM_145953	ENSMUSG00000028179	Cth	0610010I13Rik|AI314617|BC019483|CSE|Cys3	cystathionase (cystathionine gamma-lyase)	protein-coding	0	0.326733
Merged-chr5-42475371-1	chr5	42475321	42475421	+	2.3	cIP2vsInput	Intergenic	Intergenic	-631056	NM_001081422	665775	Mm.158726	NM_001081422	ENSMUSG00000061755	Bod1l	A230054D04Rik|AI853319|FAM44A|mKIAA1327	biorientation of chromosomes in cell division 1-like	protein-coding	0	0.336634
Merged-chr16-75602273-1	chr16	75602223	75602323	+	2.3	cIP2vsInput	"3' UTR (NM_198302, exon 5 of 5)"	"3' UTR (NM_198302, exon 5 of 5)"	9382	NM_198302	224344	Mm.273214	NM_198302	ENSMUSG00000032940	Rbm11	A330018F01	RNA binding motif protein 11	protein-coding	0.01	0.267327
Merged-chr6-66443463-1	chr6	66443413	66443513	+	2.3	cIP1vsInput	Intergenic	RMER6A|LTR|ERVK	-92005	NM_019499	56150	Mm.489653	NM_019499	ENSMUSG00000029910	Mad2l1	AA673185|MAD2	MAD2 mitotic arrest deficient-like 1	protein-coding	0	0.425743
Merged-chr7-71705302-1	chr7	71705252	71705352	+	2.3	cIP2vsInput	Intergenic	Intergenic	601293	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	"multiple C2 domains, transmembrane 2"	protein-coding	0	0.346535
Merged-chr1-78174550-1	chr1	78174500	78174600	+	2.3	cIP2vsInput	"intron (NM_008781, intron 4 of 7)"	"intron (NM_008781, intron 4 of 7)"	22586	NM_008781	18505	Mm.1371	NM_001159520	ENSMUSG00000004872	Pax3	Pax-3|Sp|splotch	paired box gene 3	protein-coding	0.02	0.277228
Merged-chr2-51451829-1	chr2	51451779	51451879	+	2.3	cIP2vsInput	Intergenic	Intergenic	-175682	NM_199158	387511	Mm.377918	NM_199158	ENSMUSG00000056115	Tas2r134	T2R134|Tas2r34	"taste receptor, type 2, member 134"	protein-coding	0.01	0.366337
Merged-chr8-120589485-1	chr8	120589435	120589535	+	2.3	cIP2vsInput	promoter-TSS (NM_178856)	promoter-TSS (NM_178856)	-410	NM_178856	272551	Mm.275910	NM_178856		Gins2	2210013I18Rik|4833427B12Rik|AI323585|Pfs2	GINS complex subunit 2 (Psf2 homolog)	protein-coding	0.1	0.70297
Merged-chr15-80479283-1	chr15	80479233	80479333	+	2.3	cIP2vsInput	"intron (NM_001163189, intron 4 of 5)"	"intron (NM_001163189, intron 4 of 5)"	81187	NM_001163189	383075	Mm.297626	NM_001163189	ENSMUSG00000050439	Enthd1	Gm1242|Gm86	ENTH domain containing 1	protein-coding	0	0.306931
Merged-chr6-101450707-1	chr6	101450657	101450757	+	2.3	cIP1vsInput	Intergenic	MIRb|SINE|MIR	-72810	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding	0	0.336634
Merged-chr17-61296977-1	chr17	61296927	61297027	+	2.3	cIP1vsInput	Intergenic	Intergenic	-20775	NR_030569	100124495		NR_030569		Mir466g	Mirn466g	microRNA 466g	miscRNA	0	0.277228
Merged-chr5-56818281-1	chr5	56818231	56818331	+	2.3	cIP2vsInput	Intergenic	Intergenic	899638	NR_015588	319216	Mm.446765	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	miscRNA	0	0.277228
Merged-chr13-85008560-1	chr13	85008510	85008610	+	2.3	cIP2vsInput	Intergenic	Lx|LINE|L1	-180917	NM_023243	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding	0	0.326733
Merged-chr6-96736768-1	chr6	96736718	96736818	+	2.3	cIP2vsInput	Intergenic	Intergenic	323643	NM_177233	320701	Mm.131700	NM_177233	ENSMUSG00000046500	Fam19a4	C130034I18Rik|Fam19a4 Tafa-4|Tafa-4	"family with sequence similarity 19, member A4"	protein-coding	0	0.306931
Merged-chr4-61973892-1	chr4	61973842	61973942	+	2.3	cIP2vsInput	Intergenic	B3|SINE|B2	80225	NM_001012323	381530	Mm.460005	NM_001012323	ENSMUSG00000078672	Mup20	Gm12560|Mup24|OTTMUSG00000007485|darcin	major urinary protein 20	protein-coding	0	0.356436
Merged-chr3-89430148-2	chr3	89430073	89430224	+	2.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_026869)	promoter-TSS (NM_026869)	-689	NM_026869	68911	Mm.22521	NM_026869	ENSMUSG00000047824	Pygo2	1190004M21Rik|mpygo2	pygopus 2	protein-coding	0.07947	0.677632
Merged-chr7-89289239-1	chr7	89289189	89289289	+	2.3	cIP2vsInput	"intron (NM_028343, intron 3 of 14)"	"intron (NM_028343, intron 3 of 14)"	49548	NM_028343	72759	Mm.208477	NM_028343	ENSMUSG00000039428	Tmem135	2810439K08Rik|AW319712|PMP52	transmembrane protein 135	protein-coding	0.01	0.306931
Merged-chr2-111609892-1	chr2	111609842	111609942	+	2.3	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	12180	NM_146888	258890	Mm.472596	NM_146888	ENSMUSG00000094858	Olfr1297	MOR248-4	olfactory receptor 1297	protein-coding	0	0.336634
Merged-chrY-10072994-1	chrY	10072944	10073044	+	2.3	cIP2vsInput	Intergenic	Intergenic	1124854	NM_001199331	100040022	Mm.485767	NM_001199331	ENSMUSG00000095172	Gm20822	-	"predicted gene, 20822"	protein-coding	0	0.287129
Merged-chr19-56316108-1	chr19	56316058	56316158	+	2.3	cIP2vsInput	"intron (NM_146101, intron 9 of 11)"	"intron (NM_146101, intron 9 of 11)"	28170	NM_146101	226243	Mm.25791	NM_146101	ENSMUSG00000025075	Habp2	AI035669|FSAP|HABP|HGFAL|PHBP	hyaluronic acid binding protein 2	protein-coding	0.01	0.29703
Merged-chr1-152461941-1	chr1	152461891	152461991	+	2.3	cIP2vsInput	"intron (NM_177756, intron 1 of 11)"	"intron (NM_177756, intron 1 of 11)"	62074	NM_177756	269132	Mm.23782	NM_177756	ENSMUSG00000032649	Colgalt2	AI427652|D730024P12|Glt25d2	collagen beta(1-O)galactosyltransferase 2	protein-coding	0.02	0.594059
Merged-chr9-97854267-1	chr9	97854217	97854317	+	2.3	cIP2vsInput	"intron (NM_022319, intron 1 of 17)"	"intron (NM_022319, intron 1 of 17)"	178900	NM_022319	64085	Mm.440903	NM_022319	ENSMUSG00000032452	Clstn2	2900042C18Rik|AI448973|CSTN2|Cs2|Cst-2|mKIAA4134	calsyntenin 2	protein-coding	0	0.326733
Merged-chr6-149075531-1	chr6	149075481	149075581	+	2.3	cIP1vsInput	"intron (NM_177192, intron 2 of 20)"	"intron (NM_177192, intron 2 of 20)"	26149	NM_177192	320560	Mm.426874	NM_177192	ENSMUSG00000030313	Dennd5b	9330160C06Rik|AI852444|D030011O10Rik|ENSMUSG00000072657|Gm17524	DENN/MADD domain containing 5B	protein-coding	0	0.346535
Merged-chr15-48673536-1	chr15	48673486	48673586	+	2.3	cIP1vsInput	"exon (NM_001081391, exon 2 of 71)"	"exon (NM_001081391, exon 2 of 71)"	118453	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0.02	0.376238
Merged-chr6-12418826-1	chr6	12418776	12418876	+	2.3	cIP2vsInput	"intron (NM_001164805, intron 6 of 26)"	"intron (NM_001164805, intron 6 of 26)"	-309246	NR_003631	625347	Mm.389084	NR_003631	ENSMUSG00000057223	Gm6578	EG625347	mitochondrial ribosomal protein L32 pseudogene	pseudo	0	0.306931
Merged-chr9-43000113-1	chr9	43000063	43000163	+	2.3	cIP2vsInput	"intron (NM_027144, intron 19 of 40)"	"intron (NM_027144, intron 19 of 40)"	-55742	NM_175481	110637	Mm.370291	NM_175481	ENSMUSG00000032017	Grik4	6330551K01Rik|GluK4|GluRgamma1|KA-1|KA1	"glutamate receptor, ionotropic, kainate 4"	protein-coding	0.01	0.376238
Merged-chr19-52546481-1	chr19	52546431	52546531	+	2.3	cIP2vsInput	Intergenic	B1_Mur2|SINE|Alu	282158	NM_008386	16333	Mm.46269	NM_008386	ENSMUSG00000035804	Ins1	Ins-1|Ins2-rs1	insulin I	protein-coding	0	0.455446
Merged-chr9-7811281-1	chr9	7811231	7811331	+	2.3	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	23974	NM_007465	11797	Mm.335659	NM_007465	ENSMUSG00000057367	Birc2	AW146227|Api1|Api2|Birc3|HIAP1|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF48|cIAP1|cIAP2|mcIAP1	baculoviral IAP repeat-containing 2	protein-coding	0	0.336634
Merged-chr14-48303081-1	chr14	48303031	48303131	+	2.3	cIP2vsInput	Intergenic	Intergenic	104365	NR_003630	624367	Mm.445185	NR_003630		Gm6498	EG624367	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0	0.564356
Merged-chr8-29843228-1	chr8	29843178	29843278	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-623592	NM_153135	210801	Mm.248433	NM_153135	ENSMUSG00000063626	Unc5d	D930029E11Rik|Unc5h4|mKIAA1777	unc-5 homolog D (C. elegans)	protein-coding	0	0.316832
Merged-chr5-10134660-1	chr5	10134610	10134710	+	2.3	cIP2vsInput	Intergenic	Lx2|LINE|L1	-409308	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	"glutamate receptor, metabotropic 3"	protein-coding	0	0.366337
Merged-chr7-71636965-1	chr7	71636915	71637015	+	2.3	cIP2vsInput	Intergenic	Intergenic	669630	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	"multiple C2 domains, transmembrane 2"	protein-coding	0	0.277228
Merged-chr15-80173444-1	chr15	80173394	80173494	+	2.3	cIP2vsInput	promoter-TSS (NM_010795)	promoter-TSS (NM_010795)	-277	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding	0.13	0.752475
Merged-chr12-96683847-1	chr12	96683797	96683897	+	2.3	cIP2vsInput	Intergenic	Intergenic	-636625	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0	0.316832
Merged-chr5-13747535-1	chr5	13747485	13747585	+	2.3	cIP1vsInput	Intergenic	Intergenic	-44084	NM_027650	71026	Mm.158536	NM_027650	ENSMUSG00000067855	Speer3	4933405P08Rik|SPEER-3	spermatogenesis associated glutamate (E)-rich protein 3	protein-coding	0	0.29703
Merged-chr1-108564633-1	chr1	108564583	108564683	+	2.3	cIP1vsInput	Intergenic	Intergenic	647374	NR_102307	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0	0.316832
Merged-chr2-108349835-1	chr2	108349785	108349885	+	2.3	cIP1vsInput	Intergenic	L1MA5|LINE|L1	928455	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding	0.01	0.336634
Merged-chr11-9865322-1	chr11	9865272	9865372	+	2.3	cIP2vsInput	Intergenic	Intergenic	673380	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	"ATP-binding cassette, sub-family A (ABC1), member 13"	protein-coding	0	0.346535
Merged-chr5-80654282-1	chr5	80654232	80654332	+	2.3	cIP2vsInput	Intergenic	Intergenic	-367311	NM_198702	319387	Mm.461016	NM_198702	ENSMUSG00000037605	Lphn3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|mKIAA0768	latrophilin 3	protein-coding	0	0.29703
Merged-chr1-108459309-1	chr1	108459259	108459359	+	2.3	cIP2vsInput	Intergenic	Intergenic	542050	NR_102307	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0	0.336634
Merged-chr19-51187496-1	chr19	51187446	51187546	+	2.3	cIP2vsInput	Intergenic	Intergenic	-508850	NM_021377	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0	0.326733
Merged-chr8-37913564-1	chr8	37913514	37913614	+	2.3	cIP2vsInput	"intron (NM_145841, intron 2 of 7)"	"intron (NM_145841, intron 2 of 7)"	338638	NR_029884	723860		NR_029884		Mir383	Mirn383|mmu-mir-383	microRNA 383	miscRNA	0	0.316832
Merged-chr4-140495596-1	chr4	140495546	140495646	+	2.3	cIP1vsInput	Intergenic	(TGAA)n|Simple_repeat|Simple_repeat	153160	NM_001112723	72754	Mm.29329	NM_001112722	ENSMUSG00000040964	Arhgef10l	2810441C07Rik|mKIAA1626	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding	0	0.306931
Merged-chr15-96477240-1	chr15	96477190	96477290	+	2.3	cIP2vsInput	Intergenic	Intergenic	-16397	NM_028148	72193	Mm.472183	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding	0.02	0.39604
Merged-chr3-62138308-1	chr3	62138258	62138358	+	2.3	cIP2vsInput	Intergenic	Intergenic	-200469	NM_001081295	622434		NM_001081295	ENSMUSG00000036885	Arhgef26	4631416L12Rik|8430436L14Rik|AI303572|AW491953|SGEF	Rho guanine nucleotide exchange factor (GEF) 26	protein-coding	0	0.316832
Merged-chr8-100530370-1	chr8	100530320	100530420	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1113913	NM_001039154	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.336634
Merged-chr8-91040680-1	chr8	91040630	91040730	+	2.3	cIP1vsInput	"intron (NM_177224, intron 35 of 39)"	"intron (NM_177224, intron 35 of 39)"	-29414	NM_011250	19651	Mm.235580	NM_011250	ENSMUSG00000031666	Rbl2	Rb2|p130	retinoblastoma-like 2	protein-coding	0	0.445545
Merged-chr3-30164650-1	chr3	30164600	30164700	+	2.3	cIP2vsInput	Intergenic	Intergenic	-151446	NM_007963	14013	Mm.426829	NM_021442	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding	0.01	0.326733
Merged-chr16-69317537-1	chr16	69317487	69317587	+	2.3	cIP2vsInput	Intergenic	Intergenic	546207	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding	0	0.356436
Merged-chr13-94958708-1	chr13	94958658	94958758	+	2.3	cIP2vsInput	Intergenic	(TATAG)n|Simple_repeat|Simple_repeat	-17636	NM_172590	218460	Mm.33856	NM_172590	ENSMUSG00000042015	Wdr41	B830029I03Rik|MSTP048	WD repeat domain 41	protein-coding	0	0.356436
Merged-chr16-73677539-1	chr16	73677489	73677589	+	2.3	cIP1vsInput	Intergenic	L3|LINE|CR1	664528	NR_030464	751561		NR_030464		Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	miscRNA	0	0.316832
Merged-chr14-36631201-1	chr14	36631151	36631251	+	2.3	cIP2vsInput	Intergenic	L1M4|LINE|L1	304367	NM_028407	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding	0	0.306931
Merged-chr1-100872462-1	chr1	100872412	100872512	+	2.3	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-283306	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.326733
Merged-chr9-21852498-1	chr9	21852448	21852548	+	2.3	cIP1vsInput	"intron (NM_177030, intron 1 of 49)"	CpG	137	NM_177030	319899	Mm.128153	NM_177030	ENSMUSG00000032198	Dock6	2410095B20Rik|4931431C02Rik|C330023D02Rik|mKIAA1395	dedicator of cytokinesis 6	protein-coding	0.12	0.742574
Merged-chr9-76727665-1	chr9	76727615	76727715	+	2.3	cIP1vsInput	Intergenic	Intergenic	-181861	NM_001045518	208994	Mm.256929	NM_001045518	ENSMUSG00000032358	Fam83b	C530008M07Rik|Gm516	"family with sequence similarity 83, member B"	protein-coding	0.01	0.386139
Merged-chr15-20609762-1	chr15	20609712	20609812	+	2.3	cIP2vsInput	Intergenic	Intergenic	56988	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding	0	0.306931
Merged-chr16-93875453-1	chr16	93875403	93875503	+	2.3	cIP2vsInput	"3' UTR (NM_001045529, exon 17 of 17)"	"3' UTR (NM_001045529, exon 17 of 17)"	-8448	NM_028083	110749	Mm.274222	NM_028083	ENSMUSG00000022945	Chaf1b	2600017H24Rik|C76145|CAF-I p60|CAF-Ip60|CAF1|CAF1A|CAF1P60|MPHOSPH7	"chromatin assembly factor 1, subunit B (p60)"	protein-coding	0	0.386139
Merged-chr18-20505586-1	chr18	20505536	20505636	+	2.3	cIP2vsInput	Intergenic	MusHAL1|LINE|L1	-4718	NM_030596	13512	Mm.106811	NM_030596	ENSMUSG00000056632	Dsg3	bal|balding	desmoglein 3	protein-coding	0	0.346535
Merged-chr6-59244212-1	chr6	59244162	59244262	+	2.3	cIP1vsInput	Intergenic	Lx9|LINE|L1	35342	NM_001081145	68140	Mm.25843	NM_001081145	ENSMUSG00000049232	Tigd2	3632410O17Rik	tigger transposable element derived 2	protein-coding	0	0.336634
Merged-chr7-96710810-1	chr7	96710760	96710860	+	2.3	cIP1vsInput	"intron (NM_011858, intron 8 of 32)"	"intron (NM_011858, intron 8 of 32)"	90739	NR_045874	791381	Mm.402112	NR_045874	ENSMUSG00000053049	Gm15413	ENSMUSG00000053049|OTTMUSG00000021246	predicted gene 15413	miscRNA	0.01	0.415842
Merged-chr7-77718889-1	chr7	77718839	77718939	+	2.3	cIP2vsInput	Intergenic	Intergenic	858949	NM_008746	18213	Mm.421361	NM_008746		Ntrk3	AW125844|Ntrk3_tv3|TrkC	"neurotrophic tyrosine kinase, receptor, type 3"	protein-coding	0.02	0.336634
Merged-chr2-58310287-1	chr2	58310237	58310337	+	2.3	cIP2vsInput	"intron (NM_001111030, intron 2 of 8)"	"intron (NM_001111030, intron 2 of 8)"	14520	NM_001033369	269275	Mm.77751	NM_001033369	ENSMUSG00000026834	Acvr1c	ACVRLK7|ALK7|Alk-7|C230097P10	"activin A receptor, type IC"	protein-coding	0	0.227723
Merged-chr10-28847582-1	chr10	28847532	28847632	+	2.3	cIP1vsInput	"intron (NM_178666, intron 4 of 5)"	"intron (NM_178666, intron 4 of 5)"	75925	NR_033601	114676	Mm.484516	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo	0	0.356436
Merged-chr11-10412512-1	chr11	10412462	10412562	+	2.3	cIP2vsInput	Intergenic	Lx5|LINE|L1	-701504	NM_177033	319922	Mm.487612	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding	0	0.376238
Merged-chr16-25240228-1	chr16	25240178	25240278	+	2.3	cIP1vsInput	Intergenic	Intergenic	-46589	NM_175165	71338	Mm.126851	NM_175165	ENSMUSG00000048399	Tprg	5430420C16Rik|Tprg1	transformation related protein 63 regulated	protein-coding	0.01	0.376238
Merged-chr19-20177530-1	chr19	20177480	20177580	+	2.3	cIP2vsInput	Intergenic	Intergenic	213141	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding	0.01	0.316832
Merged-chr14-75632970-1	chr14	75632920	75633020	+	2.3	cIP1vsInput	Intergenic	Kanga1d|DNA|TcMar-Tc2	-9289	NM_029230	75272	Mm.159483	NM_029230	ENSMUSG00000022002	4930564B18Rik	-	RIKEN cDNA 4930564B18 gene	protein-coding	0.01	0.306931
Merged-chr13-105891016-1	chr13	105890966	105891066	+	2.3	cIP1vsInput	Intergenic	Intergenic	447323	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0	0.257426
Merged-chr6-122475190-1	chr6	122475140	122475240	+	2.3	cIP2vsInput	"intron (NM_027664, intron 1 of 5)"	PB1D9|SINE|Alu	11115	NM_027664	108653	Mm.277939	NM_027664	ENSMUSG00000040649	Rimklb	4931417E21Rik|4933426K21Rik|AA097693|AI325948|AU015629|Naags	ribosomal modification protein rimK-like family member B	protein-coding	0.02	0.544554
Merged-chr17-65220411-1	chr17	65220361	65220461	+	2.3	cIP2vsInput	Intergenic	Intergenic	320371	NM_001008973	381107	Mm.141275	NM_001008973	ENSMUSG00000045036	Tmem232	E130009J12Rik|Gm940|Tes13-L|Tes13-S	transmembrane protein 232	protein-coding	0	0.386139
Merged-chr8-83715576-1	chr8	83715526	83715626	+	2.3	cIP2vsInput	"intron (NM_197982, intron 1 of 10)"	CpG	399	NM_197982	68278	Mm.28222	NM_197982	ENSMUSG00000005481	Ddx39	2610307C23Rik|BAT1|DDXL|Ddx39a|URH49	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39	protein-coding	0.11	0.663366
Merged-chr8-39185093-1	chr8	39185043	39185143	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-112887	NR_044988	621335	Mm.208080	NR_044988		Gm6213	EG621335	predicted gene 6213	miscRNA	0.01	0.287129
Merged-chr8-56344885-1	chr8	56344835	56344935	+	2.3	cIP2vsInput	Intergenic	Intergenic	50333	NM_008278	15446	Mm.18832	NM_008278	ENSMUSG00000031613	Hpgd	15-PGDH|AV026552	hydroxyprostaglandin dehydrogenase 15 (NAD)	protein-coding	0.02	0.356436
Merged-chr4-37233581-1	chr4	37233531	37233631	+	2.3	cIP2vsInput	Intergenic	Intergenic	-281837	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.02	0.366337
Merged-chr7-10170010-1	chr7	10169960	10170060	+	2.3	cIP1vsInput	"intron (NM_001105191, intron 3 of 5)"	(CA)n|Simple_repeat|Simple_repeat	6276	NM_001105191	384534	Mm.389802	NM_001105191	ENSMUSG00000091930	Vmn2r52	EG384534	"vomeronasal 2, receptor 52"	protein-coding	0	0.29703
Merged-chr18-33834360-1	chr18	33834310	33834410	+	2.3	cIP2vsInput	"intron (NM_013512, intron 13 of 23)"	"intron (NM_013512, intron 13 of 23)"	39468	NR_038151	69749	Mm.248787	NR_038151	ENSMUSG00000087590	2410004N09Rik	-	RIKEN cDNA 2410004N09 gene	miscRNA	0.01	0.425743
Merged-chr10-116666303-1	chr10	116666253	116666353	+	2.3	cIP1vsInput	Intergenic	Intergenic	62874	NR_045345	72286	Mm.396207	NR_045345		1700030O20Rik	-	RIKEN cDNA 1700030O20 gene	miscRNA	0	0.316832
Merged-chr7-142851663-1	chr7	142851613	142851713	+	2.3	cIP2vsInput	Intergenic	Intergenic	48303	NM_009377	21823	Mm.1292	NM_009377	ENSMUSG00000000214	Th	-	tyrosine hydroxylase	protein-coding	0.01	0.326733
Merged-chr4-87684709-1	chr4	87684659	87684759	+	2.3	cIP2vsInput	Intergenic	MusHAL1|LINE|L1	121605	NM_029931	70122	Mm.472285	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3"	protein-coding	0	0.386139
Merged-chr17-76062419-1	chr17	76062369	76062469	+	2.3	cIP2vsInput	Intergenic	Intergenic	201396	NR_033456	100043885	Mm.127562	NR_033456		Gm4710	-	predicted gene 4710	miscRNA	0	0.336634
Merged-chr1-65787792-1	chr1	65787742	65787842	+	2.3	cIP1vsInput	Intergenic	Intergenic	-138730	NM_027010	12969	Mm.275362	NM_027010	ENSMUSG00000025945	Crygf	3110001K11Rik|Cryg-2|DGcry-2|Len-2	"crystallin, gamma F"	protein-coding	0.01	0.336634
Merged-chr6-19134780-1	chr6	19134730	19134830	+	2.3	cIP2vsInput	Intergenic	Intergenic	268462	NM_001167757	75196	Mm.67665	NM_001167757	ENSMUSG00000029517	Ankrd7	4930532L20Rik|AV278427	ankyrin repeat domain 7	protein-coding	0	0.346535
Merged-chr3-12630407-1	chr3	12630357	12630457	+	2.3	cIP2vsInput	Intergenic	Intergenic	-786048	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.247525
Merged-chr2-148807912-1	chr2	148807862	148807962	+	2.3	cIP1vsInput	Intergenic	Intergenic	9073	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding	0	0.39604
Merged-chr18-72226552-1	chr18	72226502	72226602	+	2.3	cIP1vsInput	"intron (NM_007831, intron 1 of 28)"	"intron (NM_007831, intron 1 of 28)"	124517	NM_007831	13176	Mm.167882	NM_007831		Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding	0	0.287129
Merged-chr14-31630604-1	chr14	31630554	31630654	+	2.3	cIP1vsInput	"intron (NM_019975, intron 6 of 16)"	"intron (NM_019975, intron 6 of 16)"	10361	NM_019975	56794	Mm.38887	NM_019975	ENSMUSG00000021884	Hacl1	1600020H07Rik|Hpcl|Phyh2	2-hydroxyacyl-CoA lyase 1	protein-coding	0	0.316832
Merged-chr6-50858214-1	chr6	50858164	50858264	+	2.3	cIP2vsInput	Intergenic	L1MCa|LINE|L1	82099	NR_045984	319981	Mm.131454	NR_045984		C530044C16Rik	-	RIKEN cDNA C530044C16 gene	miscRNA	0	0.376238
Merged-chr12-96214010-1	chr12	96213960	96214060	+	2.3	cIP2vsInput	Intergenic	Intergenic	-166788	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0	0.326733
Merged-chr16-24561346-1	chr16	24561296	24561396	+	2.3	cIP2vsInput	"intron (NM_001145952, intron 3 of 11)"	"intron (NM_001145952, intron 3 of 11)"	32032	NR_038091	624582	Mm.439775	NR_038091		A730098P11Rik	-	mortality factor 4 like 1 pseudogene	pseudo	0	0.376238
Merged-chr13-88544951-1	chr13	88544901	88545001	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-276521	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0	0.336634
Merged-chr17-8508490-1	chr17	8508440	8508540	+	2.3	cIP2vsInput	Intergenic	Intergenic	74067	NM_009309	20997	Mm.913	NM_009309	ENSMUSG00000062327	T	Bra|D17Mit170|Low|Lr|T1|Tl2|Tl3|cou|me75	brachyury	protein-coding	0.09	0.712871
Merged-chr10-79554847-1	chr10	79554797	79554897	+	2.3	cIP2vsInput	"intron (NM_027422, intron 1 of 13)"	CpG	244	NM_027422	70427	Mm.334193	NM_027422	ENSMUSG00000042570	Mier2	2700087H15Rik|mKIAA1193	"mesoderm induction early response 1, family member 2"	protein-coding	0.2	0.90099
Merged-chr14-93707002-1	chr14	93706952	93707052	+	2.3	cIP2vsInput	"intron (NM_001081377, intron 1 of 3)"	"intron (NM_001081377, intron 1 of 3)"	181886	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0.01	0.366337
Merged-chr6-44648825-1	chr6	44648775	44648875	+	2.3	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	-411236	NM_001004357	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0	0.346535
Merged-chr15-36238483-1	chr15	36238433	36238533	+	2.3	cIP2vsInput	Intergenic	Intergenic	44664	NM_013923	30945	Mm.5181	NM_013923	ENSMUSG00000022280	Rnf19a	AA032313|Dorfin|Rnf19|UIP117|Ubce7ip2|XYbp	ring finger protein 19A	protein-coding	0	0.336634
Merged-chr2-139966355-1	chr2	139966305	139966405	+	2.3	cIP1vsInput	"intron (NM_001159640, intron 8 of 13)"	"intron (NM_001159640, intron 8 of 13)"	100405	NM_175225	75812	Mm.293449	NM_001159640	ENSMUSG00000039033	Tasp1	4930485D02Rik|AW986064	"taspase, threonine aspartase 1"	protein-coding	0.01	0.346535
Merged-chr9-63323093-1	chr9	63323043	63323143	+	2.3	cIP2vsInput	"intron (NM_011840, intron 7 of 21)"	"intron (NM_011840, intron 7 of 21)"	54759	NM_011840	23938	Mm.325746	NM_011840	ENSMUSG00000058444	Map2k5	AI324775|AI428457|MEK5|Mapkk5|Prkmk5	mitogen-activated protein kinase kinase 5	protein-coding	0	0.326733
Merged-chrY-6837285-1	chrY	6837235	6837335	+	2.3	cIP2vsInput	Intergenic	RLTR24B_MM|LTR|ERV1	330492	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.346535
Merged-chr9-61920778-1	chr9	61920728	61920828	+	2.3	cIP1vsInput	"intron (NM_024245, intron 19 of 22)"	B3|SINE|B2	-6268	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	"ribosomal protein, large, P1"	protein-coding	0	0.376238
Merged-chr12-63669859-1	chr12	63669809	63669909	+	2.3	cIP2vsInput	Intergenic	Intergenic	805039	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.316832
Merged-chr16-69284265-1	chr16	69284215	69284315	+	2.3	cIP2vsInput	Intergenic	Intergenic	579479	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding	0	0.366337
Merged-chr16-91512638-1	chr16	91512588	91512688	+	2.3	cIP1vsInput	Intergenic	Intergenic	27423	NM_010508	15975	Mm.502	NM_010508		Ifnar1	CD118|Ifar|Ifnar|Ifrc|Infar	interferon (alpha and beta) receptor 1	protein-coding	0	0.39604
Merged-chr3-51349065-1	chr3	51349015	51349115	+	2.3	cIP2vsInput	Intergenic	Intergenic	-23078	NM_023502	69257	Mm.131038	NM_023502	ENSMUSG00000037174	Elf2	2610036A20Rik|A230104O07Rik|AW111824|BB183398|EU32|NERF|NERF-1A|NERF-1B|NERF-2	E74-like factor 2	protein-coding	0	0.49505
Merged-chr15-17901314-1	chr15	17901264	17901364	+	2.3	cIP2vsInput	Intergenic	Intergenic	468313	NR_045711	70886	Mm.399021	NR_045711		4921515E04Rik	-	RIKEN cDNA 4921515E04 gene	miscRNA	0	0.356436
Merged-chr15-103939062-1	chr15	103939012	103939112	+	2.3	cIP1vsInput	Intergenic	RLTR40|LTR|ERVK	-39750	NM_009267	20770	Mm.1280	NM_009267	ENSMUSG00000036925	Spt1	Spt-1	salivary protein 1	protein-coding	0.02	0.39604
Merged-chr16-52490271-1	chr16	52490221	52490321	+	2.3	cIP2vsInput	Intergenic	Intergenic	-37274	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding	0	0.326733
Merged-chr3-59343551-1	chr3	59343501	59343601	+	2.3	cIP2vsInput	"intron (NM_001162884, intron 1 of 6)"	"intron (NM_001162884, intron 1 of 6)"	705	NM_001162884	242050	Mm.444186	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	"immunoglobulin superfamily, member 10"	protein-coding	0	0.356436
Merged-chr11-109312327-1	chr11	109312277	109312377	+	2.3	cIP2vsInput	Intergenic	Intergenic	-14146	NM_011268	19739	Mm.38548	NM_001165934	ENSMUSG00000020599	Rgs9	RGS9-1|Rgs9-2	regulator of G-protein signaling 9	protein-coding	0.06	0.623762
Merged-chr8-90854839-1	chr8	90854789	90854889	+	2.3	cIP2vsInput	"intron (NM_177224, intron 2 of 39)"	"intron (NM_177224, intron 2 of 39)"	26004	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding	0.03	0.653465
Merged-chr3-103178801-1	chr3	103178751	103178851	+	2.3	cIP1vsInput	"3' UTR (NM_026602, exon 7 of 7)"	"3' UTR (NM_026602, exon 7 of 7)"	7090	NM_026602	68183	Mm.104919	NM_026602	ENSMUSG00000005687	Bcas2	6430539P16Rik|AI132645|C76366|C80030	breast carcinoma amplified sequence 2	protein-coding	0	0.336634
Merged-chr9-5972990-1	chr9	5972940	5973040	+	2.3	cIP1vsInput	Intergenic	Intergenic	-195622	NM_027924	71785	Mm.390122	NM_027924	ENSMUSG00000032006	Pdgfd	1110003I09Rik	"platelet-derived growth factor, D polypeptide"	protein-coding	0	0.29703
Merged-chr6-63554651-1	chr6	63554601	63554701	+	2.3	cIP2vsInput	"intron (NM_008167, intron 2 of 15)"	"intron (NM_008167, intron 2 of 15)"	297794	NM_008167	14804	Mm.447390	NM_008167		Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	"glutamate receptor, ionotropic, delta 2"	protein-coding	0	0.29703
Merged-chr9-57645687-1	chr9	57645637	57645737	+	2.3	cIP2vsInput	promoter-TSS (NM_007783)	promoter-TSS (NM_007783)	-507	NM_007783	12988	Mm.21974	NM_007783	ENSMUSG00000032312	Csk	AW212630	c-src tyrosine kinase	protein-coding	0.13	0.782178
Merged-chr11-26038258-1	chr11	26038208	26038308	+	2.3	cIP2vsInput	"intron (NR_027973, intron 1 of 5)"	UCON18|Unknown|Unknown	172318	NR_027973	70626	Mm.379180	NR_027973		5730522E02Rik	-	RIKEN cDNA 5730522E02 gene	miscRNA	0	0.336634
Merged-chr15-22519715-1	chr15	22519665	22519765	+	2.3	cIP1vsInput	Intergenic	Intergenic	195269	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding	0	0.29703
Merged-chr2-86528493-1	chr2	86528443	86528543	+	2.3	cIP2vsInput	promoter-TSS (NR_033507)	promoter-TSS (NR_033507)	-66	NR_033507	625853	Mm.365699	NR_033507		Olfr1077-ps1	MOR189-4P|OTTMUSG00000013632	"olfactory receptor 1077, pseudogene 1"	pseudo	0	0.326733
Merged-chr14-94835825-1	chr14	94835775	94835875	+	2.3	cIP1vsInput	Intergenic	Intergenic	-945156	NM_001271798	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0.01	0.376238
Merged-chr9-94130377-1	chr9	94130327	94130427	+	2.3	cIP2vsInput	Intergenic	Intergenic	407704	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49	RIKEN cDNA 1190002N15 gene	protein-coding	0.01	0.356436
Merged-chr10-126051106-1	chr10	126051056	126051156	+	2.3	cIP2vsInput	Intergenic	Intergenic	84887	NM_177152	320398	Mm.275586	NM_177152	ENSMUSG00000020105	Lrig3	9030421L11Rik|9130004I02Rik|9430095K15Rik|mKIAA3016	leucine-rich repeats and immunoglobulin-like domains 3	protein-coding	0.01	0.326733
Merged-chr4-134300386-1	chr4	134300336	134300436	+	2.3	cIP2vsInput	Intergenic	Intergenic	-12540	NM_146156	230809	Mm.22778	NM_001163794	ENSMUSG00000050890	Pdik1l	BC027088|stk35l2	PDLIM1 interacting kinase 1 like	protein-coding	0.02	0.524752
Merged-chr4-68218929-1	chr4	68218879	68218979	+	2.3	cIP2vsInput	Intergenic	Lx7|LINE|L1	735468	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Dbc1	BRINP|Brinp1|Dbccr1|Fam5a	deleted in bladder cancer 1 (human)	protein-coding	0	0.326733
Merged-chr3-72579316-1	chr3	72579266	72579366	+	2.3	cIP2vsInput	Intergenic	MER34|LTR|ERV1	387550	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding	0	0.326733
Merged-chr1-140068534-1	chr1	140068484	140068584	+	2.3	cIP1vsInput	Intergenic	RMER16-int|LTR|ERVK	114877	NM_009888	12628	Mm.8655	NM_009888	ENSMUSG00000026365	Cfh	Mud-1|NOM|Sas-1|Sas1	complement component factor h	protein-coding	0	0.326733
Merged-chr1-91351409-1	chr1	91351359	91351459	+	2.3	cIP1vsInput	"intron (NM_027551, intron 1 of 7)"	"intron (NM_027551, intron 1 of 7)"	336	NM_027551	70788	Mm.68617	NM_027551	ENSMUSG00000026308	Klhl30	4631423F02Rik	kelch-like 30	protein-coding	0.01	0.554455
Merged-chr8-25835204-1	chr8	25835154	25835254	+	2.3	cIP1vsInput	"intron (NM_001080793, intron 4 of 15)"	MTE2a|LTR|ERVL-MaLR	5575	NM_011791	23808	Mm.27706	NM_001080793	ENSMUSG00000031575	Ash2l	-	"ash2 (absent, small, or homeotic)-like (Drosophila)"	protein-coding	0	0.366337
Merged-chr1-101465892-1	chr1	101465842	101465942	+	2.3	cIP2vsInput	Intergenic	Intergenic	310124	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.336634
Merged-chr17-35293985-1	chr17	35293935	35294035	+	2.3	cIP2vsInput	Intergenic	MYSERV6-int|LTR|ERVK	-26573	NM_010390	15006	Mm.466882	NM_010390	ENSMUSG00000079507	H2-Q1	H-2Q1|Q1|Q1b|Q1d|Q1k|Qa-1|Qa1|Qed-1	"histocompatibility 2, Q region locus 1"	protein-coding	0	0.346535
Merged-chr16-58762901-1	chr16	58762851	58762951	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1661	NM_147001	259003	Mm.390862	NM_147001	ENSMUSG00000071510	Olfr172	MOR184-2	olfactory receptor 172	protein-coding	0	0.306931
Merged-chr5-65064486-1	chr5	65064436	65064536	+	2.3	cIP1vsInput	Intergenic	Intergenic	-66745	NM_175174	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding	0.01	0.445545
Merged-chr12-71042086-1	chr12	71042036	71042136	+	2.3	cIP1vsInput	"intron (NM_001081195, intron 8 of 23)"	B1_Mus2|SINE|Alu	26119	NM_001081195	238247	Mm.241601	NM_001081195	ENSMUSG00000048118	Arid4a	A630009N03|A630067N03Rik|MmRBBP1|Rbbp1	AT rich interactive domain 4A (RBP1-like)	protein-coding	0	0.445545
Merged-chr5-13693070-1	chr5	13693020	13693120	+	2.3	cIP2vsInput	Intergenic	Intergenic	-98549	NM_027650	71026	Mm.158536	NM_027650	ENSMUSG00000067855	Speer3	4933405P08Rik|SPEER-3	spermatogenesis associated glutamate (E)-rich protein 3	protein-coding	0	0.326733
Merged-chr2-131222238-1	chr2	131222188	131222288	+	2.3	cIP1vsInput	"intron (NR_037281, intron 2 of 2)"	LTR67B|LTR|ERVL	11798	NM_027129	69596	Mm.2937	NM_027129	ENSMUSG00000068264	Ap5s1	0610038L13Rik|2310035K24Rik|AW060727	"adaptor-related protein 5 complex, sigma 1 subunit"	protein-coding	0.01	0.39604
Merged-chr12-63130311-1	chr12	63130261	63130361	+	2.3	cIP1vsInput	Intergenic	Intergenic	1344587	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.29703
Merged-chr17-26645228-1	chr17	26645178	26645278	+	2.3	cIP2vsInput	"intron (NM_026170, intron 9 of 9)"	"intron (NM_026170, intron 9 of 9)"	-31168	NM_025272	11974	Mm.22602	NM_025272	ENSMUSG00000015575	Atp6v0e	Atp6k|Atp6v0e1|M9.2	"ATPase, H+ transporting, lysosomal V0 subunit E"	protein-coding	0.01	0.613861
Merged-chr13-25179194-1	chr13	25179144	25179244	+	2.3	cIP2vsInput	"intron (NM_177577, intron 7 of 9)"	"intron (NM_177577, intron 7 of 9)"	90802	NM_009513	22360	Mm.4766	NM_009513	ENSMUSG00000048978	Nrsn1	Neurensin-1|Neuro-p24|Vmp	neurensin 1	protein-coding	0	0.465347
Merged-chr13-118332221-1	chr13	118332171	118332271	+	2.3	cIP1vsInput	Intergenic	Intergenic	55031	NM_021556	59054	Mm.143810	NM_021556	ENSMUSG00000021731	Mrps30	2610020A16Rik|AA968347|PAP|Pdcd9	mitochondrial ribosomal protein S30	protein-coding	0	0.336634
Merged-chr12-57113814-1	chr12	57113764	57113864	+	2.3	cIP2vsInput	"intron (NM_172577, intron 1 of 9)"	L1MC4|LINE|L1	46829	NM_001167976	217593	Mm.32835	NM_001167976	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	"solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21"	protein-coding	0.01	0.29703
Merged-chr6-117864466-1	chr6	117864416	117864516	+	2.3	cIP1vsInput	"intron (NM_008616, intron 1 of 2)"	"intron (NM_008616, intron 1 of 2)"	1389	NM_001001792	22685	Mm.249661	NM_001001792	ENSMUSG00000042097	Zfp239	Mok-2|Mok2|Znf239	zinc finger protein 239	protein-coding	0	0.306931
Merged-chr8-100131446-1	chr8	100131396	100131496	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-714989	NM_001039154	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.39604
Merged-chr4-8252531-1	chr4	8252481	8252581	+	2.3	cIP2vsInput	Intergenic	Intergenic	-13490	NM_007592	12319	Mm.119320	NM_007592		Car8	AW546993|Ca8|Cals|Cals1|Carp|wdl	carbonic anhydrase 8	protein-coding	0.01	0.336634
Merged-chr9-65076307-1	chr9	65076257	65076357	+	2.3	cIP2vsInput	"intron (NM_028906, intron 18 of 20)"	"intron (NM_028906, intron 18 of 20)"	-25188	NM_020043	56741	Mm.209041	NM_020043	ENSMUSG00000032816	Igdcc4	9330155G14Rik|DDM36|Nope|WI-16786|WI-18508|mKIAA1628	"immunoglobulin superfamily, DCC subclass, member 4"	protein-coding	0	0.29703
Merged-chr15-6594217-1	chr15	6594167	6594267	+	2.3	cIP2vsInput	"intron (NM_011815, intron 1 of 17)"	"intron (NM_011815, intron 1 of 17)"	14346	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik	FYN binding protein	protein-coding	0	0.306931
Merged-chr5-24795956-1	chr5	24795906	24796006	+	2.3	cIP2vsInput	Intergenic	MYSERV-int|LTR|ERVK	-38113	NM_153076	214301	Mm.63484	NM_153076		Crygn	-	"crystallin, gamma N"	protein-coding	0.01	0.287129
Merged-chr5-62712934-1	chr5	62712884	62712984	+	2.3	cIP1vsInput	"intron (NM_178407, intron 7 of 32)"	"intron (NM_178407, intron 7 of 32)"	53243	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	"ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2"	protein-coding	0	0.346535
Merged-chr1-145926725-1	chr1	145926675	145926775	+	2.3	cIP1vsInput	Intergenic	Intergenic	-568941	NM_153539	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.326733
Merged-chr16-26763307-1	chr16	26763257	26763357	+	2.3	cIP2vsInput	Intergenic	Intergenic	181602	NM_008364	16180	Mm.253424	NM_001159317	ENSMUSG00000022514	Il1rap	6430709H04Rik|AI255955|AV239853|IL-1RAcP	interleukin 1 receptor accessory protein	protein-coding	0	0.316832
Merged-chr11-16560186-1	chr11	16560136	16560236	+	2.3	cIP2vsInput	Intergenic	Intergenic	-51702	NM_001109971	20335	Mm.325350	NM_001109971	ENSMUSG00000078974	Sec61g	-	"SEC61, gamma subunit"	protein-coding	0.02	0.405941
Merged-chr5-79223747-1	chr5	79223697	79223797	+	2.3	cIP1vsInput	"intron (NR_035474, intron 3 of 4)"	"intron (NR_035474, intron 3 of 4)"	292157	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0.01	0.326733
Merged-chr13-110356354-1	chr13	110356304	110356404	+	2.3	cIP1vsInput	"intron (NM_177713, intron 1 of 2)"	"intron (NM_177713, intron 1 of 2)"	818	NM_177713	238875	Mm.30533	NM_177713	ENSMUSG00000046006	Gapt	9830130M13Rik	"Grb2-binding adaptor, transmembrane"	protein-coding	0.01	0.336634
Merged-chr9-45212089-1	chr9	45212039	45212139	+	2.3	cIP1vsInput	"intron (NM_001198971, intron 1 of 4)"	ORR1F|LTR|ERVL-MaLR	-8014	NM_145403	214523	Mm.436756	NM_145403	ENSMUSG00000032091	Tmprss4	mCAP2	"transmembrane protease, serine 4"	protein-coding	0.02	0.445545
Merged-chr1-47575290-1	chr1	47575240	47575340	+	2.3	cIP2vsInput	Intergenic	Intergenic	-721781	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.306931
Merged-chr1-13953252-1	chr1	13953202	13953302	+	2.3	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	-166323	NR_004447	433273	Mm.363045	NR_004447	ENSMUSG00000097711	Gm5523	EG433273	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0.01	0.346535
Merged-chr6-45875144-1	chr6	45875094	45875194	+	2.3	cIP2vsInput	"intron (NM_001004357, intron 3 of 23)"	"intron (NM_001004357, intron 3 of 23)"	815083	NM_001004357	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0	0.336634
Merged-chr7-52981560-1	chr7	52981510	52981610	+	2.3	cIP1vsInput	Intergenic	AT_rich|Low_complexity|Low_complexity	-965844	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding	0.01	0.267327
Merged-chr2-42235152-1	chr2	42235102	42235202	+	2.3	cIP1vsInput	"intron (NM_053011, intron 2 of 90)"	"intron (NM_053011, intron 2 of 90)"	418446	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0.01	0.326733
Merged-chr6-21073661-1	chr6	21073611	21073711	+	2.3	cIP2vsInput	Intergenic	Intergenic	-142448	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	"potassium voltage-gated channel, Shal-related family, member 2"	protein-coding	0.01	0.237624
Merged-chr1-37290214-1	chr1	37290164	37290264	+	2.3	cIP1vsInput	Intergenic	L1M4|LINE|L1	-9679	NM_030266	269180	Mm.5294	NM_030266	ENSMUSG00000026113	Inpp4a	107kDa|9630012D15|D130048C09Rik|R74740	"inositol polyphosphate-4-phosphatase, type I"	protein-coding	0.01	0.415842
Merged-chr7-65223197-1	chr7	65223147	65223247	+	2.3	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-66669	NM_183087	70638	Mm.441986	NM_183087	ENSMUSG00000030518	Fam189a1	5730507A09Rik|AW047451	"family with sequence similarity 189, member A1"	protein-coding	0	0.356436
Merged-chr1-137810970-1	chr1	137810920	137811020	+	2.3	cIP2vsInput	Intergenic	Intergenic	-155485	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mmu-mir-213	microRNA 181a-1	miscRNA	0.01	0.306931
Merged-chr16-88478449-1	chr16	88478399	88478499	+	2.3	cIP2vsInput	Intergenic	Intergenic	28529	NM_181490	239931	Mm.126860	NM_181490	ENSMUSG00000055811	Cldn17	-	claudin 17	protein-coding	0	0.306931
Merged-chr2-56755640-1	chr2	56755590	56755690	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	359398	NM_013613	18227	Mm.3507	NM_001139509	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	"nuclear receptor subfamily 4, group A, member 2"	protein-coding	0.01	0.326733
Merged-chr14-116997022-1	chr14	116996972	116997072	+	2.3	cIP1vsInput	"intron (NM_001079844, intron 1 of 9)"	"intron (NM_001079844, intron 1 of 9)"	71707	NM_011821	23888	Mm.440025	NM_001079844	ENSMUSG00000058571	Gpc6	6720429C22Rik|AI480529	glypican 6	protein-coding	0	0.316832
Merged-chr7-86753019-1	chr7	86752969	86753069	+	2.3	cIP2vsInput	"intron (NM_016770, intron 7 of 18)"	L1MEc|LINE|L1	22845	NM_016770	53320	Mm.269137	NM_001159706	ENSMUSG00000001773	Folh1	GCP2|mopsm	folate hydrolase 1	protein-coding	0	0.336634
Merged-chr12-63219819-1	chr12	63219769	63219869	+	2.3	cIP2vsInput	Intergenic	Intergenic	1255079	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.306931
Merged-chr17-46783575-1	chr17	46783525	46783625	+	2.3	cIP2vsInput	promoter-TSS (NM_025433)	promoter-TSS (NM_025433)	-919	NM_025433	66229	Mm.218533	NM_025433	ENSMUSG00000063888	Rpl7l1	1500016H10Rik	ribosomal protein L7-like 1	protein-coding	0.01	0.39604
Merged-chr17-57096957-1	chr17	57096907	57097007	+	2.3	cIP1vsInput	"intron (NR_033508, intron 3 of 3)"	B3|SINE|B2	-8428	NM_009404	21950	Mm.41171	NM_009404	ENSMUSG00000035678	Tnfsf9	4-1BB-L|4-1BBL|AI848817|Cd137l|Ly63l	"tumor necrosis factor (ligand) superfamily, member 9"	protein-coding	0.01	0.475248
Merged-chr10-104652050-1	chr10	104652000	104652100	+	2.3	cIP2vsInput	Intergenic	Intergenic	458008	NM_001270900	667692		NM_001270900	ENSMUSG00000097878	Gm8764	EG667692	predicted gene 8764	protein-coding	0	0.326733
Merged-chr12-38585222-1	chr12	38585172	38585272	+	2.3	cIP2vsInput	"intron (NR_045943, intron 4 of 8)"	"intron (NR_045943, intron 4 of 8)"	29299	NR_045943	73867	Mm.78933	NR_045943		4930428E07Rik	-	RIKEN cDNA 4930428E07 gene	miscRNA	0	0.39604
Merged-chr2-8957413-1	chr2	8957363	8957463	+	2.3	cIP2vsInput	Intergenic	Intergenic	-232102	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	miscRNA	0	0.287129
Merged-chr4-30258540-1	chr4	30258490	30258590	+	2.3	cIP1vsInput	Intergenic	Intergenic	-406056	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	miscRNA	0	0.247525
Merged-chr1-95921798-1	chr1	95921748	95921848	+	2.3	cIP2vsInput	Intergenic	Intergenic	99960	NR_040467	73454	Mm.396229	NR_040467		1700063A18Rik	-	RIKEN cDNA 1700063A18 gene	miscRNA	0	0.326733
Merged-chr17-75135624-1	chr17	75135574	75135674	+	2.3	cIP1vsInput	"intron (NM_019919, intron 3 of 33)"	"intron (NM_019919, intron 3 of 33)"	-43186	NM_206958	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Tgfb	latent transforming growth factor beta binding protein 1	protein-coding	0	0.287129
Merged-chr12-93405681-1	chr12	93405631	93405731	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1556524	NM_011344	20338	Mm.250605	NM_001039089	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding	0.01	0.29703
Merged-chr1-180901505-1	chr1	180901455	180901555	+	2.3	cIP2vsInput	Intergenic	Intergenic	-2769	NM_133705	69051	Mm.274180	NM_133705	ENSMUSG00000026520	Pycr2	1810018M05Rik|P5cr2	"pyrroline-5-carboxylate reductase family, member 2"	protein-coding	0.01	0.356436
Merged-chr16-48570687-1	chr16	48570637	48570737	+	2.3	cIP2vsInput	"intron (NM_010816, intron 17 of 26)"	"intron (NM_010816, intron 17 of 26)"	139450	NM_010816	17450	Mm.250060	NM_010816	ENSMUSG00000022652	Morc1	Morc	microrchidia 1	protein-coding	0	0.287129
Merged-chr10-12964582-1	chr10	12964532	12964632	+	2.3	cIP2vsInput	promoter-TSS (NM_001163591)	promoter-TSS (NM_001163591)	-323	NM_001163591	74732	Mm.248648	NM_001163590	ENSMUSG00000039232	Stx11	5830405C08Rik	syntaxin 11	protein-coding	0.08	0.584158
Merged-chr15-34504649-1	chr15	34504599	34504699	+	2.3	cIP2vsInput	"intron (NM_026340, intron 3 of 15)"	"intron (NM_026340, intron 3 of 15)"	9338	NM_152894	67724	Mm.248779	NM_026340	ENSMUSG00000022325	Pop1	4932434G09Rik	"processing of precursor 1, ribonuclease P/MRP family, (S. cerevisiae)"	protein-coding	0	0.316832
Merged-chr6-43518966-1	chr6	43518916	43519016	+	2.3	cIP1vsInput	"intron (NM_013861, intron 5 of 8)"	"intron (NM_013861, intron 5 of 8)"	76537	NR_045988	319812	Mm.446393	NR_045988		9430018G01Rik	-	RIKEN cDNA 9430018G01 gene	miscRNA	0	0.316832
Merged-chr8-43033758-1	chr8	43033708	43033808	+	2.3	cIP2vsInput	Intergenic	RLTR11A|LTR|ERVK	107728	NM_177742	244448	Mm.64542	NM_177742	ENSMUSG00000031651	Triml1	4933403D14|BC050188	tripartite motif family-like 1	protein-coding	0	0.39604
Merged-chr6-48177894-1	chr6	48177844	48177944	+	2.3	cIP2vsInput	Intergenic	Intergenic	-91301	NM_001163475	69228	Mm.207555	NM_001163475	ENSMUSG00000057691	Zfp746	2810407L07Rik|AI317225|Znf746	zinc finger protein 746	protein-coding	0	0.415842
Merged-chrX-127009087-1	chrX	127009037	127009137	+	2.3	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-30885	NM_001033241	211208	Mm.300684	NM_001033241	ENSMUSG00000062791	Gm382	-	predicted gene 382	protein-coding	0	0.306931
Merged-chr17-92752993-1	chr17	92752943	92753043	+	2.3	cIP2vsInput	Intergenic	Intergenic	-446429	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0.01	0.306931
Merged-chr15-52514263-1	chr15	52514213	52514313	+	2.3	cIP2vsInput	Intergenic	Intergenic	-198182	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding	0	0.326733
Merged-chr19-19138659-1	chr19	19138609	19138709	+	2.3	cIP1vsInput	Intergenic	Intergenic	-27463	NM_001043354	225998		NM_001043354	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta	RAR-related orphan receptor beta	protein-coding	0	0.366337
Merged-chr19-6399640-1	chr19	6399590	6399690	+	2.3	cIP2vsInput	promoter-TSS (NM_011242)	promoter-TSS (NM_011242)	-943	NM_011242	19395	Mm.77017	NM_011242	ENSMUSG00000032946	Rasgrp2	CDC25L|Caldaggef1	"RAS, guanyl releasing protein 2"	protein-coding	0.1	0.752475
Merged-chr15-80694698-1	chr15	80694648	80694748	+	2.3	cIP2vsInput	"non-coding (NR_045310, exon 3 of 3)"	"non-coding (NR_045310, exon 3 of 3)"	2912	NR_045309	106059	Mm.442457	NR_045309		A430088P11Rik	-	RIKEN cDNA A430088P11 gene	miscRNA	0.02	0.60396
Merged-chr8-42325690-1	chr8	42325640	42325740	+	2.3	cIP2vsInput	Intergenic	Intergenic	498423	NR_045497	69966	Mm.416903	NR_045497		2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	miscRNA	0	0.287129
Merged-chr15-62412280-1	chr15	62412230	62412330	+	2.3	cIP2vsInput	Intergenic	Intergenic	-192829	NR_003523	67552	Mm.484027	NR_003523		H2afy3	4933432H23Rik	"H2A histone family, member Y3"	pseudo	0	0.316832
Merged-chr1-141070094-1	chr1	141070044	141070144	+	2.3	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-413692	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0	0.346535
Merged-chr3-115900920-1	chr3	115900870	115900970	+	2.3	cIP2vsInput	"intron (NM_027193, intron 4 of 7)"	"intron (NM_027193, intron 4 of 7)"	12737	NM_027193	69740	Mm.5915	NM_027193	ENSMUSG00000033554	Dph5	2410012M04Rik|AU045680|C80186	DPH5 homolog (S. cerevisiae)	protein-coding	0.02	0.316832
Merged-chr3-140529725-1	chr3	140529675	140529775	+	2.3	cIP2vsInput	Intergenic	Intergenic	682630	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0	0.336634
Merged-chr1-151395634-1	chr1	151395584	151395684	+	2.3	cIP1vsInput	"intron (NM_025819, intron 12 of 19)"	"intron (NM_025819, intron 12 of 19)"	32801	NM_025819	66875	Mm.290905	NM_025819	ENSMUSG00000052748	Swt1	1200016B10Rik|C1orf26	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	protein-coding	0	0.267327
Merged-chr18-46198923-1	chr18	46198873	46198973	+	2.3	cIP2vsInput	promoter-TSS (NM_001170855)	promoter-TSS (NM_001170855)	-105	NM_001170855	28105	Mm.277382	NM_001170855	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding	0.1	0.742574
Merged-chr12-27856617-1	chr12	27856567	27856667	+	2.3	cIP1vsInput	Intergenic	Lx2B|LINE|L1	-513899	NM_009234	20666	Mm.466344	NM_009234		Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY-box containing gene 11	protein-coding	0	0.326733
Merged-chr1-85480954-1	chr1	85480904	85481004	+	2.3	cIP1vsInput	Intergenic	RLTR31B2|LTR|ERVK	117856	NM_030194	109032	Mm.461913	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding	0	0.405941
Merged-chr16-9193797-2	chr16	9193704	9193891	+	2.3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	363697	NM_001081400	69053	Mm.426413	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding	0.026738	0.484043
Merged-chr15-31895465-1	chr15	31895415	31895515	+	2.3	cIP2vsInput	Intergenic	Intergenic	-281824	NM_020503	57254	Mm.377133	NM_020503	ENSMUSG00000045267	Tas2r119	T2r19|Tas2r19|mGR19|mt2r19	"taste receptor, type 2, member 119"	protein-coding	0	0.465347
Merged-chr5-96560051-1	chr5	96560001	96560101	+	2.3	cIP1vsInput	"intron (NM_175473, intron 10 of 73)"	"intron (NM_175473, intron 10 of 73)"	186096	NM_175473	231470	Mm.291120	NM_175473	ENSMUSG00000034687	Fras1	E130113P14Rik|bl|mKIAA1500	Fraser syndrome 1 homolog (human)	protein-coding	0	0.287129
Merged-chr3-127780432-1	chr3	127780382	127780482	+	2.3	cIP1vsInput	promoter-TSS (NM_027808)	promoter-TSS (NM_027808)	95	NM_027808	71481	Mm.158704	NM_027808	ENSMUSG00000028028	Alpk1	8430410J10Rik|LAK	alpha-kinase 1	protein-coding	0.06	0.554455
Merged-chr3-133023658-1	chr3	133023608	133023708	+	2.3	cIP2vsInput	"intron (NM_026231, intron 5 of 11)"	"intron (NM_026231, intron 5 of 11)"	68082	NM_026231	67553	Mm.304899	NM_026231	ENSMUSG00000028018	Gstcd	4933434L15Rik	"glutathione S-transferase, C-terminal domain containing"	protein-coding	0.02	0.336634
Merged-chr17-42198724-1	chr17	42198674	42198774	+	2.3	cIP2vsInput	Intergenic	L1MA6|LINE|L1	-117223	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding	0	0.346535
Merged-chr16-78237738-1	chr16	78237688	78237788	+	2.3	cIP2vsInput	Intergenic	Intergenic	17716	NR_045698	100503619	Mm.387531	NR_045698		E330011O21Rik	-	RIKEN cDNA E330011O21 gene	miscRNA	0	0.425743
Merged-chr13-79632915-1	chr13	79632865	79632965	+	2.3	cIP2vsInput	Intergenic	RLTR18B|LTR|ERVK	-1250507	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0	0.29703
Merged-chr11-10829630-1	chr11	10829580	10829680	+	2.3	cIP2vsInput	Intergenic	Intergenic	-284386	NM_177033	319922	Mm.487612	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding	0.01	0.386139
Merged-chr3-6813001-1	chr3	6812951	6813051	+	2.3	cIP2vsInput	Intergenic	Intergenic	-192558	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding	0	0.346535
Merged-chr19-42779771-1	chr19	42779721	42779821	+	2.3	cIP2vsInput	"intron (NM_019424, intron 1 of 19)"	CpG	205	NM_019424	192236	Mm.218381	NM_019424	ENSMUSG00000025188	Hps1	6030422N11Rik|BB405864|Hps|ep	Hermansky-Pudlak syndrome 1 homolog (human)	protein-coding	0.07	0.623762
Merged-chr17-44996675-1	chr17	44996625	44996725	+	2.3	cIP2vsInput	"intron (NM_178652, intron 5 of 11)"	L1M4b|LINE|L1	-115790	NM_029257	75341	Mm.386821	XM_001003502		4930564C03Rik	-	RIKEN cDNA 4930564C03 gene	protein-coding	0	0.356436
Merged-chr15-89373851-1	chr15	89373801	89373901	+	2.3	cIP2vsInput	promoter-TSS (NM_001111288)	promoter-TSS (NM_001111288)	-33	NM_001111288	100126824	Mm.287977	NM_001111288	ENSMUSG00000091780	Sco2	-	SCO cytochrome oxidase deficient homolog 2 (yeast)	protein-coding	0.05	0.594059
Merged-chr18-24714646-1	chr18	24714596	24714696	+	2.3	cIP1vsInput	"intron (NM_175276, intron 1 of 26)"	"intron (NM_175276, intron 1 of 26)"	5201	NM_175276	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding	0.03	0.49505
Merged-chr8-106647675-1	chr8	106647625	106647725	+	2.3	cIP2vsInput	"intron (NM_009864, intron 2 of 15)"	"intron (NM_009864, intron 2 of 15)"	-35393	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding	0.01	0.485149
Merged-chr1-99338401-1	chr1	99338351	99338451	+	2.3	cIP1vsInput	Intergenic	Intergenic	-434364	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding	0	0.356436
Merged-chr15-22641827-1	chr15	22641777	22641877	+	2.3	cIP1vsInput	Intergenic	Intergenic	73157	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding	0	0.366337
Merged-chr13-39562958-1	chr13	39562908	39563008	+	2.3	cIP2vsInput	Intergenic	Intergenic	-602083	NM_001170431	108652	Mm.255506	NM_001170430	ENSMUSG00000021432	Slc35b3	4921526O06Rik|AI428480|CGI-19|PABST2|PAPST2	"solute carrier family 35, member B3"	protein-coding	0	0.287129
Merged-chr19-56997469-1	chr19	56997419	56997519	+	2.3	cIP2vsInput	"intron (NM_146102, intron 1 of 20)"	"intron (NM_146102, intron 1 of 20)"	11106	NM_146102	226250	Mm.226284	NM_001177796	ENSMUSG00000025083	Afap1l2	AU041783|C86904|mKIAA1914	actin filament associated protein 1-like 2	protein-coding	0.04	0.653465
Merged-chr9-55224304-1	chr9	55224254	55224354	+	2.3	cIP2vsInput	"3' UTR (NM_028049, exon 7 of 7)"	"3' UTR (NM_028049, exon 7 of 7)"	15369	NM_028049	71999	Mm.276429	NM_028049	ENSMUSG00000032309	Fbxo22	0610033L19Rik|1600016C16Rik	F-box protein 22	protein-coding	0.01	0.336634
Merged-chr5-3854468-1	chr5	3854418	3854518	+	2.3	cIP2vsInput	"intron (NM_172879, intron 2 of 5)"	ID4|SINE|ID	9295	NM_172879	242838	Mm.482273	NM_172879	ENSMUSG00000040367	Lrrd1	4932412H11Rik	leucine rich repeats and death domain containing 1	protein-coding	0	0.386139
Merged-chr12-78780605-1	chr12	78780555	78780655	+	2.3	cIP2vsInput	"intron (NM_019579, intron 1 of 14)"	"intron (NM_019579, intron 1 of 14)"	31658	NM_019579	56217	Mm.425777	NM_019579	ENSMUSG00000021112	Mpp5	3830420B02Rik|AI255216|AI644496|Pals1	"membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5)"	protein-coding	0.01	0.29703
Merged-chr4-88262312-1	chr4	88262262	88262362	+	2.3	cIP2vsInput	"intron (NM_001081184, intron 15 of 43)"	"intron (NM_001081184, intron 15 of 43)"	140272	NR_030478	735282		NR_030478		Mir491	Mirn491|mmu-mir-491	microRNA 491	miscRNA	0	0.336634
Merged-chr4-77148880-1	chr4	77148830	77148930	+	2.3	cIP2vsInput	"intron (NM_011211, intron 7 of 39)"	"intron (NM_011211, intron 7 of 39)"	1063015	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0	0.405941
Merged-chr7-26437677-1	chr7	26437627	26437727	+	2.3	cIP2vsInput	"intron (NM_172896, intron 2 of 10)"	"intron (NM_172896, intron 2 of 10)"	2564	NM_172896	243880	Mm.322356	NM_172896	ENSMUSG00000040601	Nlrp4a	E330021B02|E330028A19Rik|NALP4|Nalp-eta|Nalp-ita|Nalp4a	"NLR family, pyrin domain containing 4A"	protein-coding	0	0.366337
Merged-chr1-48895253-1	chr1	48895203	48895303	+	2.3	cIP2vsInput	Intergenic	Lx9|LINE|L1	-2032270	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.366337
Merged-chr10-56890992-1	chr10	56890942	56891042	+	2.3	cIP2vsInput	Intergenic	L1VL4|LINE|L1	513692	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	"gap junction protein, alpha 1"	protein-coding	0	0.277228
Merged-chr14-88033260-1	chr14	88033210	88033310	+	2.3	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	438136	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0	0.326733
Merged-chr2-54859105-1	chr2	54859055	54859155	+	2.3	cIP2vsInput	"intron (NM_173030, intron 7 of 12)"	"intron (NM_173030, intron 7 of 12)"	422718	NM_173030	271786	Mm.330227	NM_173030	ENSMUSG00000060988	Galnt13	A230002A12|A230020F20|BB182356	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13	protein-coding	0	0.326733
Merged-chr1-142752594-1	chr1	142752544	142752644	+	2.3	cIP1vsInput	Intergenic	L1VL4|LINE|L1	-888103	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0	0.346535
Merged-chr10-106990441-1	chr10	106990391	106990491	+	2.3	cIP1vsInput	"intron (NM_001142804, intron 8 of 15)"	"intron (NM_001142804, intron 8 of 15)"	133223	NM_001142804	380660	Mm.336072	NM_001142804	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding	0.01	0.386139
Merged-chr1-151586061-1	chr1	151586011	151586111	+	2.3	cIP2vsInput	"intron (NM_022018, intron 1 of 13)"	"intron (NM_022018, intron 1 of 13)"	14688	NM_022018	63913	Mm.482559	NM_022018		Fam129a	AI256368|AU019833|Niban	"family with sequence similarity 129, member A"	protein-coding	0	0.326733
Merged-chr3-24707958-1	chr3	24707908	24708008	+	2.3	cIP2vsInput	Intergenic	Intergenic	1445349	NM_001163387	192167	Mm.316080	NM_001163387	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|mKIAA1070	neuroligin 1	protein-coding	0	0.366337
Merged-chr10-127256223-1	chr10	127256173	127256273	+	2.3	cIP2vsInput	"intron (NM_001039000, intron 1 of 28)"	"intron (NM_001039000, intron 1 of 28)"	7140	NM_008447	16572	Mm.30355	NM_001039000	ENSMUSG00000074657	Kif5a	D10Bwg0738e|Khc|Kif5|Kns|mKIAA4086	kinesin family member 5A	protein-coding	0.04	0.514851
Merged-chr10-100259833-1	chr10	100259783	100259883	+	2.3	cIP2vsInput	Intergenic	Intergenic	-75843	NM_001166636	100043247	Mm.478257	NM_001166636	ENSMUSG00000096640	Gm4312	-	predicted gene 4312	protein-coding	0	0.366337
Merged-chr19-12157997-1	chr19	12157947	12158047	+	2.3	cIP1vsInput	"intron (NR_030566, intron 2 of 3)"	L1M3|LINE|L1	-37323	NM_146682	258677	Mm.261576	NM_146682	ENSMUSG00000067522	Olfr76	MOR215-3|V5	olfactory receptor 76	protein-coding	0	0.316832
Merged-chr6-103717734-1	chr6	103717684	103717784	+	2.3	cIP1vsInput	"intron (NM_007697, intron 26 of 26)"	L1_Mus3|LINE|L1	206858	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule with homology to L1CAM	protein-coding	0	0.386139
Merged-chr15-48876647-1	chr15	48876597	48876697	+	2.3	cIP2vsInput	Intergenic	Lx2|LINE|L1	-84658	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0	0.356436
Merged-chr2-69096827-1	chr2	69096777	69096877	+	2.3	cIP1vsInput	"intron (NM_172856, intron 8 of 9)"	"intron (NM_172856, intron 8 of 9)"	-38973	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding	0	0.425743
Merged-chr3-20798748-1	chr3	20798698	20798798	+	2.3	cIP2vsInput	Intergenic	L1MEb|LINE|L1	-431571	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	"angiotensin II receptor, type 1b"	protein-coding	0	0.336634
Merged-chr6-109941740-1	chr6	109941690	109941790	+	2.3	cIP2vsInput	Intergenic	L1MDa|LINE|L1	-703858	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0	0.316832
Merged-chr8-5204874-1	chr8	5204824	5204924	+	2.3	cIP2vsInput	Intergenic	MTD|LTR|ERVL-MaLR	-99642	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.356436
Merged-chr1-16530510-1	chr1	16530460	16530560	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-11208	NM_001111272	29819	Mm.216257	NM_001111272	ENSMUSG00000025920	Stau2	-	staufen (RNA binding protein) homolog 2 (Drosophila)	protein-coding	0	0.326733
Merged-chr7-69278385-1	chr7	69278335	69278435	+	2.3	cIP2vsInput	Intergenic	Intergenic	-217709	NR_045940	73796	Mm.410832	NR_045940		4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	miscRNA	0	0.336634
Merged-chr16-66199576-1	chr16	66199526	66199626	+	2.3	cIP2vsInput	Intergenic	Intergenic	383943	NM_028572	73569	Mm.482366	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like 3 (Drosophila)	protein-coding	0.01	0.316832
Merged-chr13-113234441-1	chr13	113234391	113234491	+	2.3	cIP1vsInput	Intergenic	Intergenic	24782	NM_023612	71690	Mm.38929	NM_023612	ENSMUSG00000042379	Esm1	0610042H23Rik|AV004503|ESM-1	endothelial cell-specific molecule 1	protein-coding	0	0.237624
Merged-chr15-78892553-1	chr15	78892503	78892603	+	2.3	cIP2vsInput	"exon (NM_145929, exon 14 of 17)"	"exon (NM_145929, exon 14 of 17)"	-7233	NM_009164	20401	Mm.4462	NM_009164	ENSMUSG00000022436	Sh3bp1	3BP-1	SH3-domain binding protein 1	protein-coding	0.03	0.693069
Merged-chr2-102798960-1	chr2	102798910	102799010	+	2.3	cIP1vsInput	Intergenic	Intergenic	92522	NM_001077515	20511	Mm.371582	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	"solute carrier family 1 (glial high affinity glutamate transporter), member 2"	protein-coding	0	0.306931
Merged-chr12-64493036-1	chr12	64492986	64493086	+	2.3	cIP2vsInput	Intergenic	Intergenic	-18138	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.316832
Merged-chr13-106481261-1	chr13	106481211	106481311	+	2.3	cIP1vsInput	Intergenic	Intergenic	455654	NM_029665	76582	Mm.482687	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding	0	0.415842
Merged-chr13-91653357-1	chr13	91653307	91653407	+	2.3	cIP2vsInput	"intron (NM_024272, intron 5 of 16)"	Lx3C|LINE|L1	-88164	NM_028790	74156	Mm.275963	NM_028790	ENSMUSG00000021620	Acot12	1300004O04Rik|4930449F15Rik|AV027244|Cach|mCACH-1	acyl-CoA thioesterase 12	protein-coding	0.01	0.346535
Merged-chr15-48491547-1	chr15	48491497	48491597	+	2.3	cIP2vsInput	"intron (NM_001081391, intron 4 of 70)"	RMER5|LTR|ERV1	300442	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0.01	0.326733
Merged-chr1-92091358-1	chr1	92091308	92091408	+	2.3	cIP1vsInput	"intron (NM_207225, intron 1 of 25)"	"intron (NM_207225, intron 1 of 25)"	57035	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|AI047285	histone deacetylase 4	protein-coding	0	0.29703
Merged-chr6-59753582-1	chr6	59753532	59753632	+	2.3	cIP1vsInput	Intergenic	Intergenic	-327292	NM_183183	243385	Mm.485751	NM_183183	ENSMUSG00000045441	Gprin3	C030038J10Rik|C730021L23	GPRIN family member 3	protein-coding	0	0.346535
Merged-chr18-49265300-1	chr18	49265250	49265350	+	2.3	cIP2vsInput	Intergenic	Intergenic	-257989	NR_033785	67321	Mm.245802	NR_033785		1700044K03Rik	-	RIKEN cDNA 1700044K03 gene	miscRNA	0.01	0.326733
Merged-chr11-88173303-1	chr11	88173253	88173353	+	2.3	cIP1vsInput	"intron (NM_198013, intron 2 of 10)"	"intron (NM_198013, intron 2 of 10)"	3738	NM_001172099	103841	Mm.374846	NM_001172099	ENSMUSG00000018378	Cuedc1	AI841487|C330016O16Rik	CUE domain containing 1	protein-coding	0.01	0.534653
Merged-chr3-58839166-1	chr3	58839116	58839216	+	2.3	cIP2vsInput	Intergenic	ORR1B2-int|LTR|ERVL-MaLR	46046	NM_153386	229320	Mm.131502	NM_153384	ENSMUSG00000043850	Clrn1	A130002D11Rik|USH3|Ush3a	clarin 1	protein-coding	0	0.346535
Merged-chr10-130185156-1	chr10	130185106	130185206	+	2.3	cIP1vsInput	Intergenic	Intergenic	-4278	NM_146676	258671	Mm.271513	NM_146676	ENSMUSG00000059862	Olfr826	MOR210-2	olfactory receptor 826	protein-coding	0	0.336634
Merged-chr14-86040588-1	chr14	86040538	86040638	+	2.3	cIP2vsInput	Intergenic	Intergenic	-205382	NR_040457	75155	Mm.399239	NR_040457		4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	miscRNA	0	0.306931
Merged-chr1-44529651-1	chr1	44529601	44529701	+	2.3	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	-22020	NM_028450	70676	Mm.133132	NM_027506	ENSMUSG00000056870	Gulp1	3110030A04Rik|5730529O06Rik|CED-6|Ced6|GULP|Gulp-2	"GULP, engulfment adaptor PTB domain containing 1"	protein-coding	0	0.316832
Merged-chr11-61644201-1	chr11	61644151	61644251	+	2.3	cIP1vsInput	Intergenic	Tigger5b|DNA|TcMar-Tigger	-9120	NM_027817	71520	Mm.202760	NM_027817	ENSMUSG00000004837	Grap	8430435N19Rik|BB233594	GRB2-related adaptor protein	protein-coding	0	0.287129
Merged-chr10-38231879-1	chr10	38231829	38231929	+	2.3	cIP1vsInput	Intergenic	Intergenic	589900	NM_001177783	215919	Mm.294313	NM_001177783	ENSMUSG00000094311	Rfpl4b	100040915|Gm3037|Gm62	ret finger protein-like 4B	protein-coding	0.03	0.267327
Merged-chr5-87786940-1	chr5	87786890	87786990	+	2.3	cIP1vsInput	"intron (NM_007785, intron 12 of 13)"	"intron (NM_007785, intron 12 of 13)"	12373	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csn1s2b|Csng	casein alpha s2-like A	protein-coding	0	0.267327
Merged-chr15-49564837-1	chr15	49564787	49564887	+	2.3	cIP2vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	-772848	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0.01	0.306931
Merged-chr9-106844146-1	chr9	106844096	106844196	+	2.3	cIP2vsInput	"exon (NM_001015507, exon 9 of 23)"	"exon (NM_001015507, exon 9 of 23)"	22170	NM_001015507	321006	Mm.440089	NM_001015507	ENSMUSG00000040325	Vprbp	AI447437|B930007L02Rik|mKIAA0800	Vpr (HIV-1) binding protein	protein-coding	0	0.376238
Merged-chr14-92189649-1	chr14	92189599	92189699	+	2.3	cIP1vsInput	Intergenic	Intergenic	1699239	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.356436
Merged-chr4-29610270-1	chr4	29610220	29610320	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	797125	NM_010141	13841	Mm.257266	NM_001122889	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding	0.01	0.356436
Merged-chr16-73988766-1	chr16	73988716	73988816	+	2.3	cIP1vsInput	"intron (NM_175549, intron 6 of 27)"	"intron (NM_175549, intron 6 of 27)"	353301	NR_030464	751561		NR_030464		Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	miscRNA	0	0.287129
Merged-chr13-88053572-1	chr13	88053522	88053622	+	2.3	cIP1vsInput	Intergenic	Intergenic	-767900	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0.01	0.316832
Merged-chr17-8755688-1	chr17	8755638	8755738	+	2.3	cIP2vsInput	Intergenic	Intergenic	-46057	NM_011866	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding	0	0.326733
Merged-chr5-83518746-1	chr5	83518696	83518796	+	2.3	cIP2vsInput	Intergenic	Intergenic	-163551	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	"trans-2,3-enoyl-CoA reductase-like"	protein-coding	0.01	0.306931
Merged-chr1-17162668-1	chr1	17162618	17162718	+	2.3	cIP2vsInput	"3' UTR (NM_010267, exon 6 of 6)"	"3' UTR (NM_010267, exon 6 of 6)"	17295	NM_010267	14545	Mm.18218	NM_010267	ENSMUSG00000025777	Gdap1	-	ganglioside-induced differentiation-associated-protein 1	protein-coding	0	0.316832
Merged-chr12-57211271-1	chr12	57211221	57211321	+	2.3	cIP2vsInput	Intergenic	Intergenic	-13799	NM_172577	217593	Mm.32835	NM_001167976	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	"solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21"	protein-coding	0.01	0.316832
Merged-chr18-17687238-1	chr18	17687188	17687288	+	2.3	cIP2vsInput	Intergenic	Intergenic	-106248	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	miscRNA	0	0.445545
Merged-chr2-23385299-1	chr2	23385249	23385349	+	2.3	cIP2vsInput	"intron (NM_008752, intron 1 of 1)"	L1_Mus3|LINE|L1	64053	NM_008752	18232	Mm.131616	NM_008752	ENSMUSG00000069132	Nxph2	-	neurexophilin 2	protein-coding	0	0.29703
Merged-chr4-38010223-1	chr4	38010173	38010273	+	2.3	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-1058479	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0	0.336634
Merged-chr17-60841217-2	chr17	60841135	60841299	+	2.3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-476535	NR_030569	100124495		NR_030569		Mir466g	Mirn466g	microRNA 466g	miscRNA	0.006098	0.333333
Merged-chr15-30802779-1	chr15	30802729	30802829	+	2.3	cIP2vsInput	"intron (NM_008729, intron 10 of 22)"	L1MC1|LINE|L1	-236347	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	miscRNA	0	0.29703
Merged-chr18-21043893-1	chr18	21043843	21043943	+	2.3	cIP2vsInput	Intergenic	A-rich|Low_complexity|Low_complexity	-28451	NM_008586	17288	Mm.2682	NM_008586	ENSMUSG00000024313	Mep1b	Mep-1b	meprin 1 beta	protein-coding	0	0.346535
Merged-chr14-93591943-1	chr14	93591893	93591993	+	2.3	cIP1vsInput	"intron (NM_001081377, intron 1 of 3)"	"intron (NM_001081377, intron 1 of 3)"	296945	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0.01	0.277228
Merged-chr3-38718834-1	chr3	38718784	38718884	+	2.3	cIP1vsInput	Intergenic	Intergenic	-168106	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT tumor suppressor homolog 4 (Drosophila)	protein-coding	0	0.306931
Merged-chr17-20067734-1	chr17	20067684	20067784	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-19529	NM_001104566	22313	Mm.379039	NM_001104566	ENSMUSG00000090315	Vmn2r104	V2r7	"vomeronasal 2, receptor 104"	protein-coding	0.01	0.29703
Merged-chr16-67234179-1	chr16	67234129	67234229	+	2.3	cIP2vsInput	"intron (NM_178721, intron 1 of 9)"	"intron (NM_178721, intron 1 of 9)"	386729	NM_001145977	239857	Mm.394300	NM_001145977	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0	0.326733
Merged-chr7-36112602-1	chr7	36112552	36112652	+	2.3	cIP1vsInput	Intergenic	ORR1E|LTR|ERVL-MaLR	-309613	NM_177739	668501	Mm.286296	NM_177739	ENSMUSG00000044452	Zfp507	1810022O10Rik|A230056M16Rik|AL024009|AU021817|BB105092|Gm480|Znf507|mKIAA1084	zinc finger protein 507	protein-coding	0	0.287129
Merged-chr5-88631240-1	chr5	88631190	88631290	+	2.3	cIP1vsInput	"intron (NM_027530, intron 8 of 12)"	"intron (NM_027530, intron 8 of 12)"	44340	NM_001098476	231413	Mm.332474	NM_001098476	ENSMUSG00000044221	Grsf1	B130010H02|BB232551|C80280|D5Wsu31e	G-rich RNA sequence binding factor 1	protein-coding	0.01	0.376238
Merged-chr17-10804486-1	chr17	10804436	10804536	+	2.3	cIP2vsInput	"intron (NM_027032, intron 1 of 4)"	L1MEc|LINE|L1	35705	NM_027032	69310	Mm.18889	NM_027032	ENSMUSG00000037196	Pacrg	1700008H23Rik	PARK2 co-regulated	protein-coding	0	0.316832
Merged-chr6-61620803-1	chr6	61620753	61620853	+	2.3	cIP2vsInput	"intron (NM_001164316, intron 6 of 10)"	"intron (NM_001164316, intron 6 of 10)"	-439993	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	miscRNA	0.01	0.29703
Merged-chr1-148683296-1	chr1	148683246	148683346	+	2.3	cIP1vsInput	Intergenic	L1MB5|LINE|L1	1277988	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0	0.287129
Merged-chr4-94787069-1	chr4	94787019	94787119	+	2.3	cIP2vsInput	"intron (NM_013690, intron 2 of 22)"	"intron (NM_013690, intron 2 of 22)"	47769	NM_013690	21687	Mm.14313	NM_013690	ENSMUSG00000006386	Tek	AA517024|Cd202b|Hyk|Tie2|tie-2	endothelial-specific receptor tyrosine kinase	protein-coding	0	0.316832
Merged-chr2-144172747-1	chr2	144172697	144172797	+	2.3	cIP2vsInput	TTS (NM_001033778)	TTS (NM_001033778)	16543	NM_001033778	433481	Mm.330630	NM_001033778		Gm5535	EG433481	predicted gene 5535	protein-coding	0.01	0.435644
Merged-chr12-47909439-1	chr12	47909389	47909489	+	2.3	cIP2vsInput	Intergenic	L1M2|LINE|L1	392023	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0	0.316832
Merged-chr15-18019489-1	chr15	18019439	18019539	+	2.3	cIP1vsInput	Intergenic	Intergenic	350138	NR_045711	70886	Mm.399021	NR_045711		4921515E04Rik	-	RIKEN cDNA 4921515E04 gene	miscRNA	0	0.316832
Merged-chr9-14246585-1	chr9	14246535	14246635	+	2.3	cIP2vsInput	Intergenic	Intergenic	-29716	NM_030261	75747	Mm.439776	NM_030261	ENSMUSG00000032009	Sesn3	5630400E15Rik|BC003348|SEST3	sestrin 3	protein-coding	0.02	0.50495
Merged-chr11-59264862-1	chr11	59264812	59264912	+	2.3	cIP1vsInput	"intron (NM_009522, intron 2 of 3)"	"intron (NM_009522, intron 2 of 3)"	25889	NM_009522	22416	Mm.1367	NM_009522	ENSMUSG00000009900	Wnt3a	Wnt-3a|vt	wingless-related MMTV integration site 3A	protein-coding	0.01	0.613861
Merged-chr5-5482474-1	chr5	5482424	5482524	+	2.3	cIP1vsInput	Intergenic	Intergenic	-3331	NM_001200025	381716	Mm.276086	NM_001200025	ENSMUSG00000079666	1700015F17Rik	Gm1686	RIKEN cDNA 1700015F17 gene	protein-coding	0.01	0.336634
Merged-chr2-101926813-1	chr2	101926763	101926863	+	2.3	cIP2vsInput	Intergenic	Intergenic	40551	NM_029635	76501	Mm.330424	NM_029635	ENSMUSG00000027163	Commd9	1810029F08Rik|AA409293	COMM domain containing 9	protein-coding	0	0.386139
Merged-chr1-154378932-1	chr1	154378882	154378982	+	2.3	cIP2vsInput	Intergenic	B4A|SINE|B4	-122026	NR_040629	78112	Mm.401935	NR_040629		4930452N14Rik	-	RIKEN cDNA 4930452N14 gene	miscRNA	0	0.425743
Merged-chr1-174795001-1	chr1	174794951	174795051	+	2.3	cIP1vsInput	"intron (NM_019445, intron 16 of 17)"	"intron (NM_019445, intron 16 of 17)"	126818	NM_011825	23893	Mm.25760	NM_011825	ENSMUSG00000050069	Grem2	Gremlin2|Prdc	"gremlin 2 homolog, cysteine knot superfamily (Xenopus laevis)"	protein-coding	0	0.346535
Merged-chr15-45950498-1	chr15	45950448	45950548	+	2.3	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-374087	NR_045509	71120	Mm.158571	NR_045509		1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	miscRNA	0	0.336634
Merged-chr6-25345065-1	chr6	25345015	25345115	+	2.3	cIP2vsInput	Intergenic	Intergenic	344915	NM_010338	14763	Mm.409670	NM_010338		Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding	0	0.306931
Merged-chr19-50879166-1	chr19	50879116	50879216	+	2.3	cIP2vsInput	Intergenic	Intergenic	-200520	NM_021377	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0.01	0.356436
Merged-chr5-89889859-1	chr5	89889809	89889909	+	2.3	cIP1vsInput	Intergenic	Intergenic	-6525	NM_001081401	330119	Mm.133062	NM_001081401	ENSMUSG00000043635	Adamts3	1100001H14Rik|6330442E02Rik	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 3"	protein-coding	0.01	0.346535
Merged-chr14-88475999-1	chr14	88475949	88476049	+	2.3	cIP2vsInput	Intergenic	Intergenic	-4603	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0.01	0.336634
Merged-chr10-113698394-1	chr10	113698344	113698444	+	2.3	cIP2vsInput	Intergenic	Intergenic	111816	NR_035418	100316831		NR_035418		Mir669h	Mirn669h|mmu-mir-669h	microRNA 669h	miscRNA	0	0.287129
Merged-chr14-100803655-1	chr14	100803605	100803705	+	2.3	cIP2vsInput	Intergenic	Intergenic	396414	NM_029680	76627	Mm.31415	NM_029680	ENSMUSG00000042888	1700110M21Rik	-	RIKEN cDNA 1700110M21 gene	protein-coding	0	0.415842
Merged-chr2-131456008-1	chr2	131455958	131456058	+	2.3	cIP2vsInput	"intron (NR_037281, intron 1 of 2)"	Lx7|LINE|L1	-35854	NM_001177834	228608	Mm.136586	NM_001177833	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding	0.01	0.346535
Merged-chr2-48670744-1	chr2	48670694	48670794	+	2.3	cIP1vsInput	Intergenic	Intergenic	-143365	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding	0.01	0.336634
Merged-chr13-102660769-1	chr13	102660719	102660819	+	2.3	cIP2vsInput	Intergenic	L1M5|LINE|L1	-32789	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding	0	0.306931
Merged-chr17-78809185-1	chr17	78809135	78809235	+	2.3	cIP2vsInput	"intron (NM_001081179, intron 17 of 35)"	"intron (NM_001081179, intron 17 of 35)"	26196	NM_001081179	320473	Mm.210489	NM_001081179	ENSMUSG00000039414	Heatr5b	2010013B10Rik|A230048G03Rik|AV071430|D330050P16Rik|mKIAA1414	HEAT repeat containing 5B	protein-coding	0	0.435644
Merged-chr5-13975421-1	chr5	13975371	13975471	+	2.3	cIP2vsInput	Intergenic	Intergenic	-49855	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	"sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E"	protein-coding	0.01	0.29703
Merged-chr1-121747522-1	chr1	121747472	121747572	+	2.3	cIP1vsInput	Intergenic	Lx|LINE|L1	-179542	NM_025860	66942	Mm.44219	NM_025860	ENSMUSG00000001674	Ddx18	2310005B10Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	protein-coding	0	0.346535
Merged-chr15-19798350-1	chr15	19798300	19798400	+	2.3	cIP2vsInput	Intergenic	Intergenic	868400	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding	0	0.326733
Merged-chr8-24107418-1	chr8	24107368	24107468	+	2.3	cIP1vsInput	Intergenic	Lx2B2|LINE|L1	331528	NM_026931	69068	Mm.25775	NM_026931	ENSMUSG00000056313	1810011O10Rik	1110065B09Rik|AW121743|AW321058	RIKEN cDNA 1810011O10 gene	protein-coding	0	0.29703
Merged-chr10-116330471-1	chr10	116330421	116330521	+	2.3	cIP2vsInput	"intron (NM_029928, intron 8 of 31)"	"intron (NM_029928, intron 8 of 31)"	29097	NM_029928	19263	Mm.489025	NM_029928	ENSMUSG00000020154	Ptprb	3230402H02Rik|C130094E24|Ptpz|Rptpb|VE-PTP|Veptp	"protein tyrosine phosphatase, receptor type, B"	protein-coding	0	0.326733
Merged-chrX-131737926-1	chrX	131737876	131737976	+	2.3	cIP2vsInput	Intergenic	Intergenic	1951067	NM_001105245	279653	Mm.39738	NM_001105245	ENSMUSG00000051323	Pcdh19	B530002L05Rik|Gm717|mKIAA1313	protocadherin 19	protein-coding	0.01	0.306931
Merged-chr7-58032646-1	chr7	58032596	58032696	+	2.3	cIP2vsInput	Intergenic	Intergenic	441473	NM_008071	14402	Mm.8004	NM_001038701	ENSMUSG00000033676	Gabrb3	A230092K12Rik|AW049585|Cp1|Gabrb-3|beta3	"gamma-aminobutyric acid (GABA) A receptor, subunit beta 3"	protein-coding	0	0.326733
Merged-chr17-76627971-1	chr17	76627921	76628021	+	2.3	cIP1vsInput	Intergenic	L1ME3A|LINE|L1	766948	NR_033456	100043885	Mm.127562	NR_033456		Gm4710	-	predicted gene 4710	miscRNA	0	0.277228
Merged-chr16-23627721-1	chr16	23627671	23627771	+	2.3	cIP2vsInput	Intergenic	Intergenic	17802	NM_023386	67775	Mm.475107	NM_023386	ENSMUSG00000033355	Rtp4	5830458K16Rik|Ifrg28	receptor transporter protein 4	protein-coding	0	0.336634
Merged-chr11-15235562-1	chr11	15235512	15235612	+	2.3	cIP2vsInput	Intergenic	Lx2|LINE|L1	636322	NM_001164166	432536	Mm.33646	NR_002893		Pom121l12	1700054H16Rik	POM121 membrane glycoprotein-like 12	protein-coding	0	0.287129
Merged-chr3-158176437-1	chr3	158176387	158176487	+	2.3	cIP2vsInput	"intron (NM_001081358, intron 17 of 27)"	"intron (NM_001081358, intron 17 of 27)"	139734	NM_024194	67144	Mm.358704	NM_024194	ENSMUSG00000063052	Lrrc40	2610040E16Rik|AI837674	leucine rich repeat containing 40	protein-coding	0.01	0.366337
Merged-chrX-7948256-2	chrX	7948192	7948320	+	2.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_010413)	promoter-TSS (NM_010413)	-367	NM_010413	15185	Mm.29854	NM_001130416	ENSMUSG00000031161	Hdac6	Hd6|Hdac5|Sfc6|mHDA2	histone deacetylase 6	protein-coding	0.070312	0.643411
Merged-chr17-65916295-1	chr17	65916245	65916345	+	2.3	cIP2vsInput	Intergenic	Intergenic	-30540	NM_009067	19765	Mm.486223	NM_001198949	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding	0.02	0.564356
Merged-chr6-97058389-1	chr6	97058339	97058439	+	2.3	cIP2vsInput	"intron (NM_177233, intron 1 of 5)"	"intron (NM_177233, intron 1 of 5)"	2022	NM_177233	320701	Mm.131700	NM_177233	ENSMUSG00000046500	Fam19a4	C130034I18Rik|Fam19a4 Tafa-4|Tafa-4	"family with sequence similarity 19, member A4"	protein-coding	0	0.386139
Merged-chr9-38215184-1	chr9	38215134	38215234	+	2.3	cIP2vsInput	Intergenic	Intergenic	-3634	NM_146868	258868	Mm.377728	NM_146868	ENSMUSG00000070311	Olfr894	MOR170-5	olfactory receptor 894	protein-coding	0.01	0.306931
Merged-chr7-43151230-1	chr7	43151180	43151280	+	2.3	cIP1vsInput	Intergenic	MurSatRep1|Unknown|Unknown	-26358	NM_001034893	668620		NM_001034893		Zfp936	EG435970|EG668620|Gm9272|I1C0022H11Rik	zinc finger protein 936	protein-coding	0	0.405941
Merged-chr18-6040913-1	chr18	6040863	6040963	+	2.3	cIP2vsInput	"intron (NM_001039692, intron 10 of 18)"	"intron (NM_001039692, intron 10 of 18)"	95185	NM_029277	75415	Mm.239675	NM_001039692	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding	0	0.306931
Merged-chr11-20004985-1	chr11	20004935	20005035	+	2.3	cIP2vsInput	"intron (NM_033523, intron 2 of 5)"	"intron (NM_033523, intron 2 of 5)"	80543	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	"sprouty-related, EVH1 domain containing 2"	protein-coding	0	0.29703
Merged-chr11-56321419-1	chr11	56321369	56321469	+	2.3	cIP2vsInput	Intergenic	Intergenic	-280432	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding	0	0.356436
Merged-chr9-62838850-1	chr9	62838800	62838900	+	2.3	cIP2vsInput	promoter-TSS (NM_001033175)	promoter-TSS (NM_001033175)	63	NM_001033175	76524	Mm.283636	NM_001033175	ENSMUSG00000032245	Cln6	1810065L06Rik|AW743417|D9Bwg1455e|nclf	"ceroid-lipofuscinosis, neuronal 6"	protein-coding	0.19	0.792079
Merged-chr10-51405514-1	chr10	51405464	51405564	+	2.3	cIP2vsInput	Intergenic	Intergenic	-75165	NM_008147	14727	Mm.439661	NM_008147	ENSMUSG00000089672	Gp49a	gp49	glycoprotein 49 A	protein-coding	0	0.316832
Merged-chr11-113565800-1	chr11	113565750	113565850	+	2.3	cIP2vsInput	promoter-TSS (NM_027216)	promoter-TSS (NM_027216)	15	NM_001166503	69806	Mm.341021	NM_001166503	ENSMUSG00000041654	Slc39a11	1810074D23Rik	"solute carrier family 39 (metal ion transporter), member 11"	protein-coding	0.08	0.643564
Merged-chr1-41483789-1	chr1	41483739	41483839	+	2.3	cIP2vsInput	Intergenic	Lx7|LINE|L1	-302537	NR_040475	74897	Mm.243822	NR_040475		4930448I06Rik	-	RIKEN cDNA 4930448I06 gene	miscRNA	0	0.405941
Merged-chr2-50541092-1	chr2	50541042	50541142	+	2.3	cIP1vsInput	Intergenic	Intergenic	244282	NR_040362	100502624	Mm.412130	NR_040361	ENSMUSG00000085862	Gm13483	OTTMUSG00000012382	predicted gene 13483	miscRNA	0	0.277228
Merged-chr9-113895179-1	chr9	113895129	113895229	+	2.3	cIP1vsInput	"intron (NM_001081960, intron 23 of 32)"	"intron (NM_001081960, intron 23 of 32)"	-35755	NM_001083319	22221	Mm.386808	NM_001083319	ENSMUSG00000009741	Ubp1	Cp2b|LBP-1a|LBP-1b|NF2d9	upstream binding protein 1	protein-coding	0	0.306931
Merged-chr6-55721226-1	chr6	55721176	55721276	+	2.3	cIP1vsInput	Intergenic	Intergenic	36655	NR_046071	100041339	Mm.403680	NR_046071		Gm3279	-	predicted gene 3279	miscRNA	0	0.346535
Merged-chr3-11283918-1	chr3	11283868	11283968	+	2.3	cIP2vsInput	Intergenic	Intergenic	560441	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.376238
Merged-chr6-27206189-1	chr6	27206139	27206239	+	2.3	cIP2vsInput	Intergenic	Intergenic	730561	NR_030420	735266		NR_030420		Mir592	Mirn592|mir-592|mmu-mir-592	microRNA 592	miscRNA	0	0.306931
Merged-chr16-65890383-1	chr16	65890333	65890433	+	2.3	cIP2vsInput	Intergenic	Intergenic	74750	NM_028572	73569	Mm.482366	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like 3 (Drosophila)	protein-coding	0.01	0.326733
Merged-chr1-103556304-1	chr1	103556254	103556354	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1212515	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0.02	0.306931
Merged-chr14-37165297-1	chr14	37165247	37165347	+	2.3	cIP2vsInput	Intergenic	Intergenic	-29975	NM_078478	66092	Mm.486242	NM_001199122	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010	growth hormone inducible transmembrane protein	protein-coding	0	0.346535
Merged-chr12-81500256-1	chr12	81500206	81500306	+	2.3	cIP2vsInput	"3' UTR (NM_025292, exon 4 of 4)"	"3' UTR (NM_025292, exon 4 of 4)"	-15146	NM_025461	66272	Mm.439970	NM_025461	ENSMUSG00000091803	Cox16	1810020G14Rik|1810055I05Rik|BB388670	cytochrome c oxidase assembly protein 16	protein-coding	0	0.366337
Merged-chr1-156118105-1	chr1	156118055	156118155	+	2.3	cIP2vsInput	"intron (NM_177838, intron 1 of 4)"	"intron (NM_177838, intron 1 of 4)"	77244	NM_022329	240832	Mm.253335	NM_001160180	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding	0	0.316832
Merged-chr15-70571472-1	chr15	70571422	70571522	+	2.3	cIP1vsInput	Intergenic	Intergenic	647239	NR_045071	100503580	Mm.404646	NR_045071		Gm19782	-	"predicted gene, 19782"	miscRNA	0	0.277228
Merged-chr3-137166301-1	chr3	137166251	137166351	+	2.3	cIP2vsInput	Intergenic	Intergenic	-174777	NM_001163522	59308	Mm.27343	NM_001163522	ENSMUSG00000054690	Emcn	0610012K22Rik|AI315669|Muc14	endomucin	protein-coding	0	0.346535
Merged-chr1-84201637-1	chr1	84201587	84201687	+	2.3	cIP1vsInput	"intron (NM_001003948, intron 1 of 2)"	"intron (NM_001003948, intron 1 of 2)"	83008	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding	0	0.356436
Merged-chr3-12566029-1	chr3	12565979	12566079	+	2.3	cIP1vsInput	Intergenic	L1MA8|LINE|L1	-721670	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.316832
Merged-chr8-98153337-1	chr8	98153287	98153387	+	2.3	cIP2vsInput	Intergenic	L1MC|LINE|L1	1263120	NM_007667	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.316832
Merged-chr18-23666977-1	chr18	23666927	23667027	+	2.3	cIP2vsInput	Intergenic	Intergenic	-85356	NM_001162942	212307	Mm.132237	NM_001162941	ENSMUSG00000024277	Mapre2	AI314113|C820009F03Rik|D18Abb1e|EB1|EB2|RP1	"microtubule-associated protein, RP/EB family, member 2"	protein-coding	0	0.356436
Merged-chr1-42764020-1	chr1	42763970	42764070	+	2.3	cIP1vsInput	Intergenic	Intergenic	63684	NR_027891	73100	Mm.480115	NR_027891		2900092D14Rik	-	RIKEN cDNA 2900092D14 gene	miscRNA	0.01	0.366337
Merged-chr14-49686877-1	chr14	49686827	49686927	+	2.3	cIP2vsInput	"intron (NM_026142, intron 6 of 7)"	"intron (NM_026142, intron 6 of 7)"	96490	NM_026142	67419	Mm.318710	NM_026142	ENSMUSG00000036242	3632451O06Rik	AU067705	RIKEN cDNA 3632451O06 gene	protein-coding	0	0.425743
Merged-chr5-30193130-1	chr5	30193080	30193180	+	2.3	cIP2vsInput	TTS (NM_001014394)	TTS (NM_001014394)	12592	NM_001014394	381628	Mm.291148	NM_001014394	ENSMUSG00000067642	Gpr113	Gm1041|Pgr23	G protein-coupled receptor 113	protein-coding	0	0.336634
Merged-chr3-65806624-1	chr3	65806574	65806674	+	2.3	cIP2vsInput	"intron (NM_001166659, intron 10 of 12)"	L1MEc|LINE|L1	140396	NM_001166659	624866	Mm.405524	NM_001166659	ENSMUSG00000074579	Lekr1	EG546798|EG624866|Gm6534	"leucine, glutamate and lysine rich 1"	protein-coding	0	0.386139
Merged-chr13-72175313-1	chr13	72175263	72175363	+	2.3	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-211590	NM_010573	16371	Mm.316056	NM_010573	ENSMUSG00000060969	Irx1	-	Iroquois related homeobox 1 (Drosophila)	protein-coding	0	0.316832
Merged-chr1-63824299-1	chr1	63824249	63824349	+	2.3	cIP2vsInput	Intergenic	Intergenic	-55032	NM_001256158	74426	Mm.159197	NM_001256158	ENSMUSG00000025961	4933402D24Rik	-	RIKEN cDNA 4933402D24 gene	protein-coding	0	0.336634
Merged-chr6-22956387-1	chr6	22956337	22956437	+	2.3	cIP2vsInput	"intron (NM_001081306, intron 2 of 29)"	"intron (NM_001081306, intron 2 of 29)"	80885	NM_001081306	19283	Mm.41639	NM_001081306	ENSMUSG00000068748	Ptprz1	AI850339|DSD-1-PG|PTPbeta|PTPzeta|Ptprz|Ptpz|RPTPz|Rptpbeta	"protein tyrosine phosphatase, receptor type Z, polypeptide 1"	protein-coding	0.01	0.267327
Merged-chr1-12650648-1	chr1	12650598	12650698	+	2.3	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-16915	NR_045297	329096	Mm.417782	NR_045297	ENSMUSG00000097171	Gm17644	4932411L15	"predicted gene, 17644"	miscRNA	0.01	0.376238
Merged-chr17-23924305-1	chr17	23924255	23924355	+	2.3	cIP2vsInput	Intergenic	Intergenic	6847	NM_001077633	620253	Mm.390964	XM_003945992	ENSMUSG00000057417	Dcpp3	Dcpp-3|EG620253|SPT-3	demilune cell and parotid protein 3	protein-coding	0.01	0.306931
Merged-chr8-24061304-1	chr8	24061254	24061354	+	2.3	cIP2vsInput	"3' UTR (NM_001277239, exon 8 of 8)"	"3' UTR (NM_001277239, exon 8 of 8)"	377642	NM_026931	69068	Mm.25775	NM_026931	ENSMUSG00000056313	1810011O10Rik	1110065B09Rik|AW121743|AW321058	RIKEN cDNA 1810011O10 gene	protein-coding	0	0.326733
Merged-chr14-123408365-1	chr14	123408315	123408415	+	2.3	cIP2vsInput	"intron (NM_177393, intron 14 of 43)"	"intron (NM_177393, intron 14 of 43)"	218779	NM_177393	338370	Mm.255348	NM_177754	ENSMUSG00000000197	Nalcn	A530023G15Rik|AI849508|Vgcnl1	"sodium leak channel, non-selective"	protein-coding	0	0.336634
Merged-chr4-73428040-1	chr4	73427990	73428090	+	2.3	cIP2vsInput	Intergenic	Lx9|LINE|L1	-22968	NM_001013393	433719	Mm.348294	NM_001013393	ENSMUSG00000066137	Gm11487	OTTMUSG00000001246	predicted gene 11487	protein-coding	0	0.316832
Merged-chr18-33589193-1	chr18	33589143	33589243	+	2.3	cIP2vsInput	Intergenic	Intergenic	125030	NR_045415	433171	Mm.353332	NR_045415		Gm10549	ENSMUSG00000073610	predicted gene 10549	miscRNA	0	0.316832
Merged-chr3-3786289-1	chr3	3786239	3786339	+	2.3	cIP1vsInput	Intergenic	Intergenic	278259	NM_013920	30942	Mm.330897	NM_013920		Hnf4g	NR2A2	"hepatocyte nuclear factor 4, gamma"	protein-coding	0.01	0.306931
Merged-chr11-66773683-1	chr11	66773633	66773733	+	2.3	cIP2vsInput	Intergenic	Charlie25|DNA|hAT-Charlie	-138308	NM_178656	193003	Mm.440256	NM_178656		Pirt	A530088H08Rik	phosphoinositide-interacting regulator of transient receptor potential channels	protein-coding	0	0.316832
Merged-chr1-149046232-1	chr1	149046182	149046282	+	2.3	cIP2vsInput	Intergenic	Intergenic	915052	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0	0.237624
Merged-chr6-35979610-1	chr6	35979560	35979660	+	2.3	cIP2vsInput	Intergenic	Intergenic	-408474	NM_203491	243764	Mm.448632	NM_203491		Chrm2	AChR-M2|Chrm-2|M2	"cholinergic receptor, muscarinic 2, cardiac"	protein-coding	0	0.306931
Merged-chr19-38788494-1	chr19	38788444	38788544	+	2.3	cIP2vsInput	"3' UTR (NM_021315, exon 21 of 21)"	"3' UTR (NM_021315, exon 21 of 21)"	30743	NM_021315	57753	Mm.86482	NM_021315	ENSMUSG00000024999	Noc3l	AF233884|Fad24	nucleolar complex associated 3 homolog (S. cerevisiae)	protein-coding	0.01	0.425743
Merged-chr3-42879853-1	chr3	42879803	42879903	+	2.3	cIP1vsInput	Intergenic	RMER6D|LTR|ERVK	1137235	NM_027271	73852	Mm.29006	NM_001099785	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	"DNA segment, Chr 3, ERATO Doi 751, expressed"	protein-coding	0	0.346535
Merged-chr1-74660770-1	chr1	74660720	74660820	+	2.3	cIP1vsInput	promoter-TSS (NM_001014974)	promoter-TSS (NM_001014974)	-984	NM_001014974	67534	Mm.260714	NM_001014974	ENSMUSG00000033257	Ttll4	4632407P03Rik|AI451681|mKIAA0173	"tubulin tyrosine ligase-like family, member 4"	protein-coding	0	0.247525
Merged-chr6-7299521-1	chr6	7299471	7299571	+	2.3	cIP2vsInput	Intergenic	Intergenic	-255550	NM_009311	21333	Mm.410823	NM_009311	ENSMUSG00000061762	Tac1	4930528L02Rik|NK-1|NK1|Nkna|PPT-A|PPTA|SP	tachykinin 1	protein-coding	0	0.326733
Merged-chr16-17276259-1	chr16	17276209	17276309	+	2.3	cIP2vsInput	promoter-TSS (NM_177473)	promoter-TSS (NM_177473)	-41	NM_177473	224019	Mm.246388	NM_177473	ENSMUSG00000055692	Tmem191c	4933405M22Rik|D16Bwg1494e	transmembrane protein 191C	protein-coding	0.11	0.693069
Merged-chr17-38594810-1	chr17	38594760	38594860	+	2.3	cIP2vsInput	Intergenic	Intergenic	40618	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Gm20410	Esp34	predicted gene 20410	protein-coding	0	0.326733
Merged-chr8-100101794-1	chr8	100101744	100101844	+	2.3	cIP2vsInput	Intergenic	Intergenic	-685337	NM_001039154	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.287129
Merged-chr3-25162486-1	chr3	25162436	25162536	+	2.3	cIP2vsInput	Intergenic	L1M4|LINE|L1	990821	NM_001163387	192167	Mm.316080	NM_001163387	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|mKIAA1070	neuroligin 1	protein-coding	0	0.306931
Merged-chr1-82072244-1	chr1	82072194	82072294	+	2.3	cIP1vsInput	Intergenic	Intergenic	219195	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding	0.01	0.366337
Merged-chr14-40687275-1	chr14	40687225	40687325	+	2.3	cIP2vsInput	Intergenic	Intergenic	205690	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding	0	0.376238
Merged-chr12-53904513-1	chr12	53904463	53904563	+	2.3	cIP1vsInput	"intron (NM_013780, intron 5 of 11)"	"intron (NM_013780, intron 5 of 11)"	299361	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	EGL nine homolog 3 (C. elegans)	protein-coding	0.01	0.29703
Merged-chr17-21605897-1	chr17	21605847	21605947	+	2.3	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	38851	NM_001002008	381066	Mm.441097	NM_001002008	ENSMUSG00000067931	Zfp948	-	zinc finger protein 948	protein-coding	0	0.366337
Merged-chr12-93650568-1	chr12	93650518	93650618	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1801411	NM_011344	20338	Mm.250605	NM_001039089	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding	0	0.405941
Merged-chr2-113223228-1	chr2	113223178	113223278	+	2.3	cIP2vsInput	"intron (NR_035479, intron 2 of 3)"	"intron (NR_035479, intron 2 of 3)"	3041	NR_035479	100316776		NR_035479		Mir1954	mmu-mir-1954	microRNA 1954	miscRNA	0	0.316832
Merged-chr17-52576942-1	chr17	52576892	52576992	+	2.3	cIP2vsInput	Intergenic	RLTR25B|LTR|ERVK	-25767	NM_001031811	211468	Mm.490760	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	"potassium voltage-gated channel, subfamily H (eag-related), member 8"	protein-coding	0	0.336634
Merged-chr5-7523703-1	chr5	7523653	7523753	+	2.3	cIP2vsInput	Intergenic	Intergenic	-179325	NM_001163223	207618	Mm.478808	NM_001163223	ENSMUSG00000092094	Zfp804b	Gm441	zinc finger protein 804B	protein-coding	0.01	0.336634
Merged-chr5-6405162-1	chr5	6405112	6405212	+	2.3	cIP1vsInput	Intergenic	Lx5b|LINE|L1	-655845	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding	0	0.366337
Merged-chr8-59067574-1	chr8	59067524	59067624	+	2.3	cIP1vsInput	Intergenic	Intergenic	155819	NM_173411	234290	Mm.39244	NM_173411	ENSMUSG00000049946	BC030500	-	cDNA sequence BC030500	protein-coding	0	0.277228
Merged-chr8-65325075-1	chr8	65325025	65325125	+	2.3	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-195538	NR_033217	407795	Mm.387876	NR_033217		BC030870	-	cDNA sequence BC030870	miscRNA	0	0.336634
Merged-chr1-29450617-1	chr1	29450567	29450667	+	2.3	cIP2vsInput	Intergenic	Intergenic	-670365	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0	0.376238
Merged-chr8-24736685-1	chr8	24736635	24736735	+	2.3	cIP1vsInput	"intron (NM_001272057, intron 18 of 18)"	L1_Mur2|LINE|L1	-10860	NM_009619	11497	Mm.5168	NM_009619	ENSMUSG00000031553	Adam3	Cyrn1|Taz83|tMDC	a disintegrin and metallopeptidase domain 3 (cyritestin)	protein-coding	0.01	0.386139
Merged-chr11-92136292-1	chr11	92136242	92136342	+	2.3	cIP2vsInput	Intergenic	Intergenic	-558737	NM_028547	73470	Mm.67677	NM_028547	ENSMUSG00000046755	Kif2b	1700063D03Rik	kinesin family member 2B	protein-coding	0	0.306931
Merged-chr5-79149730-1	chr5	79149680	79149780	+	2.3	cIP2vsInput	"intron (NR_035474, intron 3 of 4)"	MusHAL1|LINE|L1	366174	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0	0.326733
Merged-chr15-33426126-1	chr15	33426076	33426176	+	2.3	cIP2vsInput	"intron (NM_018755, intron 6 of 8)"	MLTR25A|LTR|ERVK	-20187	NR_033608	73486	Mm.483393	NR_033608		1700084J12Rik	-	ribosomal protein L7-like 1 pseudogene	pseudo	0	0.316832
Merged-chr3-7044439-1	chr3	7044389	7044489	+	2.3	cIP2vsInput	Intergenic	Intergenic	-322165	NM_008862	18767	Mm.3193	NM_008862	ENSMUSG00000027499	Pkia	AI415001|PKIalpha	"protein kinase inhibitor, alpha"	protein-coding	0.01	0.326733
Merged-chr2-85123701-1	chr2	85123651	85123751	+	2.3	cIP1vsInput	Intergenic	Intergenic	-12659	NM_011784	23796	Mm.29368	NM_011784	ENSMUSG00000044338	Aplnr	APJ|Agtrl1|msr/apj	apelin receptor	protein-coding	0.01	0.386139
Merged-chr3-64569201-1	chr3	64569151	64569251	+	2.3	cIP2vsInput	Intergenic	Intergenic	-9383	NM_001104619	667069	Mm.484956	NM_001104619	ENSMUSG00000090581	Vmn2r6	EG620718|EG667069	"vomeronasal 2, receptor 6"	protein-coding	0	0.39604
Merged-chr17-38096524-1	chr17	38096474	38096574	+	2.3	cIP2vsInput	Intergenic	Intergenic	-13548	NM_146867	258867	Mm.377727	NM_146867	ENSMUSG00000043312	Olfr131	MOR256-4	olfactory receptor 131	protein-coding	0	0.306931
Merged-chr9-37054288-1	chr9	37054238	37054338	+	2.3	cIP2vsInput	"intron (NM_001029838, intron 2 of 12)"	"intron (NM_001029838, intron 2 of 12)"	92978	NM_001029838	208076	Mm.260335	NM_001029838	ENSMUSG00000035934	Pknox2	D230005H23Rik|Prep2	Pbx/knotted 1 homeobox 2	protein-coding	0.04	0.584158
Merged-chr13-86646533-1	chr13	86646483	86646583	+	2.3	cIP2vsInput	Intergenic	Intergenic	-599738	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0.01	0.29703
Merged-chr19-9890049-1	chr19	9889999	9890099	+	2.3	cIP2vsInput	"intron (NM_016692, intron 4 of 17)"	Lx9|LINE|L1	9484	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding	0	0.356436
Merged-chr2-173870283-1	chr2	173870233	173870333	+	2.3	cIP1vsInput	Intergenic	Lx2|LINE|L1	132712	NM_019806	56491	Mm.260456	NM_019806	ENSMUSG00000054455	Vapb	AI225786|AI840687|AI848259|D2Abb2e|R75548|VAP33b|Vamp33b	"vesicle-associated membrane protein, associated protein B and C"	protein-coding	0.02	0.306931
Merged-chr2-131127367-2	chr2	131127313	131127422	+	2.3	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_028306)	promoter-TSS (NM_028306)	-45	NM_028306	72630	Mm.277465	NM_028306	ENSMUSG00000074793	Hspa12b	2700081N06Rik	heat shock protein 12B	protein-coding	0.110092	0.8
Merged-chr12-74765342-1	chr12	74765292	74765392	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	411990	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	"potassium voltage-gated channel, subfamily H (eag-related), member 5"	protein-coding	0	0.386139
Merged-chr18-32716020-1	chr18	32715970	32716070	+	2.3	cIP2vsInput	"intron (NR_045381, intron 4 of 4)"	"intron (NR_045381, intron 4 of 4)"	-99363	NM_021367	53603	Mm.143716	NM_021367	ENSMUSG00000024379	Tslp	-	thymic stromal lymphopoietin	protein-coding	0	0.336634
Merged-chr6-76103233-1	chr6	76103183	76103283	+	2.3	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-1139484	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0.03	0.267327
Merged-chr13-85000788-1	chr13	85000738	85000838	+	2.3	cIP1vsInput	Intergenic	ORR1B1-int|LTR|ERVL-MaLR	-188689	NM_023243	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding	0	0.306931
Merged-chr10-12142078-1	chr10	12142028	12142128	+	2.3	cIP1vsInput	Intergenic	Intergenic	719657	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding	0	0.277228
Merged-chr5-51217985-1	chr5	51217935	51218035	+	2.3	cIP2vsInput	Intergenic	Intergenic	335936	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PGC-1v|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	"peroxisome proliferative activated receptor, gamma, coactivator 1 alpha"	protein-coding	0	0.306931
Merged-chr10-15790197-1	chr10	15790147	15790247	+	2.3	cIP1vsInput	Intergenic	Intergenic	1029908	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding	0	0.29703
Merged-chr1-90896885-2	chr1	90896793	90896978	+	2.3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-18215	NM_053015	171531	Mm.105208	NM_053015	ENSMUSG00000026303	Mlph	2210418F23Rik|5031433I09Rik|AW228792|D1Wsu84e|Slac-2a|l(1)-3Rk|l1Rk3|ln	melanophilin	protein-coding	0.027027	0.623656
Merged-chr4-92307014-1	chr4	92306964	92307064	+	2.3	cIP2vsInput	Intergenic	Intergenic	-159793	NM_027034	69314	Mm.55891	NM_027034	ENSMUSG00000028533	Izumo3	1700011H22Rik	IZUMO family member 3	protein-coding	0	0.306931
Merged-chr18-39371793-1	chr18	39371743	39371843	+	2.3	cIP2vsInput	"3' UTR (NM_175164, exon 23 of 23)"	"3' UTR (NM_175164, exon 23 of 23)"	115452	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	"nuclear receptor subfamily 3, group C, member 1"	protein-coding	0.03	0.514851
Merged-chr3-12944110-1	chr3	12944060	12944160	+	2.3	cIP2vsInput	Intergenic	Intergenic	-527545	NM_178631	76897	Mm.422625	NM_001163328	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0	0.306931
Merged-chr3-63880840-1	chr3	63880790	63880890	+	2.3	cIP2vsInput	Intergenic	L1M5|LINE|L1	-29849	NM_001177732	269437	Mm.316391	NM_001177732	ENSMUSG00000036834	Plch1	BC042549|PLCeta1|Plcl3	"phospholipase C, eta 1"	protein-coding	0	0.356436
Merged-chr14-10764094-1	chr14	10764044	10764144	+	2.3	cIP1vsInput	"intron (NM_010210, intron 2 of 8)"	L1MA4|LINE|L1	397938	NM_010210	14198	Mm.441926	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding	0	0.336634
Merged-chr3-126451853-1	chr3	126451803	126451903	+	2.3	cIP2vsInput	Intergenic	Intergenic	88001	NM_173451	271970	Mm.317021	NM_173451	ENSMUSG00000046561	Arsj	9330196J05Rik|D830047F08	arylsulfatase J	protein-coding	0	0.376238
Merged-chr14-95293534-1	chr14	95293484	95293584	+	2.3	cIP2vsInput	Intergenic	Lx8|LINE|L1	-587732	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.376238
Merged-chr2-153632844-1	chr2	153632794	153632894	+	2.3	cIP2vsInput	promoter-TSS (NM_001195390)	promoter-TSS (NM_001195390)	-63	NM_133850	99311	Mm.294478	NM_001195390	ENSMUSG00000056941	Commd7	2310010I22Rik|AW060956|mU3	COMM domain containing 7	protein-coding	0.05	0.574257
Merged-chr8-19170481-1	chr8	19170431	19170531	+	2.3	cIP2vsInput	Intergenic	Lx10|LINE|L1	12594	NM_153115	78128	Mm.229357	NM_153115	ENSMUSG00000079842	Spag11a	9230111C08Rik|Bin1b|EP2Q|EP2e|Spag11	sperm associated antigen 11A	protein-coding	0	0.336634
Merged-chr12-20248176-1	chr12	20248126	20248226	+	2.3	cIP2vsInput	Intergenic	Intergenic	567603	NR_015521	69513	Mm.273972	NR_015521		1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	miscRNA	0	0.356436
Merged-chr2-73050535-1	chr2	73050485	73050585	+	2.3	cIP1vsInput	Intergenic	Intergenic	-70089	NM_001018042	20687	Mm.465887	NM_001018042	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding	0.02	0.50495
Merged-chr14-87555328-1	chr14	87555278	87555378	+	2.3	cIP2vsInput	Intergenic	L1ME2z|LINE|L1	138745	NM_001253755	219249	Mm.35168	NM_001253755	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding	0.01	0.356436
Merged-chr2-40226274-1	chr2	40226224	40226324	+	2.3	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-999936	NM_024209	67857	Mm.392662	NM_024209		Ppp6c	2310003C10Rik	"protein phosphatase 6, catalytic subunit"	protein-coding	0	0.267327
Merged-chr1-104122387-1	chr1	104122337	104122437	+	2.3	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-646432	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0	0.277228
Merged-chr3-71931959-1	chr3	71931909	71932009	+	2.3	cIP2vsInput	Intergenic	ORR1D1-int|LTR|ERVL-MaLR	1034907	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding	0	0.306931
Merged-chr6-56490112-1	chr6	56490062	56490162	+	2.3	cIP1vsInput	Intergenic	Intergenic	-120478	NM_001159955	18575	Mm.5145	NM_001025568	ENSMUSG00000004347	Pde1c	-	phosphodiesterase 1C	protein-coding	0.01	0.336634
Merged-chr16-66542878-1	chr16	66542828	66542928	+	2.3	cIP2vsInput	Intergenic	Intergenic	-114240	NR_040512	75501	Mm.396161	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	miscRNA	0	0.346535
Merged-chr15-69812195-1	chr15	69812145	69812245	+	2.3	cIP1vsInput	Intergenic	Lx7|LINE|L1	-112038	NR_045071	100503580	Mm.404646	NR_045071		Gm19782	-	"predicted gene, 19782"	miscRNA	0	0.336634
Merged-chr12-75020341-1	chr12	75020291	75020391	+	2.3	cIP1vsInput	"intron (NM_172805, intron 7 of 10)"	"intron (NM_172805, intron 7 of 10)"	156991	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	"potassium voltage-gated channel, subfamily H (eag-related), member 5"	protein-coding	0	0.287129
Merged-chr3-47472248-1	chr3	47472198	47472298	+	2.3	cIP2vsInput	Intergenic	Intergenic	554511	NR_040408	666202	Mm.465057	NR_040408		Gm7977	EG666202	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide pseudogene"	pseudo	0	0.287129
Merged-chrX-134686443-1	chrX	134686393	134686493	+	2.3	cIP2vsInput	promoter-TSS (NM_001202500)	promoter-TSS (NM_001202500)	19	NR_045454	77983	Mm.153204	NR_045454	ENSMUSG00000087024	B230119M05Rik	-	RIKEN cDNA B230119M05 gene	miscRNA	0.05	0.643564
Merged-chr14-86862553-1	chr14	86862503	86862603	+	2.3	cIP2vsInput	"intron (NM_019670, intron 21 of 27)"	"intron (NM_019670, intron 21 of 27)"	278561	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diap3	4930417P13Rik|Dia2|Diaph3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous homolog 3 (Drosophila)	protein-coding	0.02	0.405941
Merged-chr2-51915211-1	chr2	51915161	51915261	+	2.3	cIP2vsInput	Intergenic	Intergenic	19433	NM_001141982	71684	Mm.28309	NM_001141981	ENSMUSG00000036249	Rbm43	0610033I05Rik	RNA binding motif protein 43	protein-coding	0.01	0.435644
Merged-chr2-45716177-1	chr2	45716127	45716227	+	2.3	cIP1vsInput	Intergenic	Intergenic	19572	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	miscRNA	0	0.336634
Merged-chr8-18883631-1	chr8	18883581	18883681	+	2.3	cIP1vsInput	"3' UTR (NM_026792, exon 8 of 8)"	"3' UTR (NM_026792, exon 8 of 8)"	37352	NM_026792	52123	Mm.24117	NM_026792		Agpat5	1110013A05Rik|D8Ertd319e	"1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)"	protein-coding	0.01	0.316832
Merged-chr5-83607369-1	chr5	83607319	83607419	+	2.3	cIP1vsInput	Intergenic	Intergenic	-252174	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	"trans-2,3-enoyl-CoA reductase-like"	protein-coding	0.01	0.316832
Merged-chr14-112261955-1	chr14	112261905	112262005	+	2.3	cIP2vsInput	Intergenic	Intergenic	240525	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0	0.316832
Merged-chr15-17403005-1	chr15	17402955	17403055	+	2.3	cIP2vsInput	Intergenic	Intergenic	624904	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0	0.366337
Merged-chr1-168170884-1	chr1	168170834	168170934	+	2.3	cIP2vsInput	"intron (NM_183355, intron 8 of 8)"	L1ME4a|LINE|L1	261374	NM_183355	18514	Mm.440114	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|AI848790|AU015730|D230003C07Rik|Pbx-1|Pbx1a|Pbx1b	pre B cell leukemia homeobox 1	protein-coding	0	0.306931
Merged-chr14-112456406-1	chr14	112456356	112456456	+	2.3	cIP2vsInput	Intergenic	Intergenic	434976	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0.01	0.356436
Merged-chr12-62699087-1	chr12	62699037	62699137	+	2.3	cIP2vsInput	Intergenic	Intergenic	1174455	NM_178714	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0	0.346535
Merged-chr5-121618217-1	chr5	121618167	121618267	+	2.3	cIP2vsInput	"intron (NM_178799, intron 1 of 10)"	B1_Mur4|SINE|Alu	721	NM_178799	338350	Mm.482918	NM_178799	ENSMUSG00000042647	Acad12	9330129D05Rik	"acyl-Coenzyme A dehydrogenase family, member 12"	protein-coding	0.03	0.524752
Merged-chr3-66679914-1	chr3	66679864	66679964	+	2.3	cIP2vsInput	Intergenic	L1ME3G|LINE|L1	301857	NM_013665	20429	Mm.39093	NM_013665		Shox2	6330543G17Rik|OG12|Og12x|Prx3|SHOT	short stature homeobox 2	protein-coding	0.01	0.356436
Merged-chr9-72402473-1	chr9	72402423	72402523	+	2.3	cIP2vsInput	Intergenic	Intergenic	-36056	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding	0	0.336634
Merged-chr2-12714696-1	chr2	12714646	12714746	+	2.3	cIP2vsInput	Intergenic	Intergenic	-209345	NM_008961	19212	Mm.229322	NM_008961	ENSMUSG00000026730	Pter	AI790318|Mpr56-1	phosphotriesterase related	protein-coding	0.02	0.29703
Merged-chr6-142585190-1	chr6	142585140	142585240	+	2.3	cIP1vsInput	Intergenic	Intergenic	-13834	NM_008428	16523	Mm.1482	NM_008428	ENSMUSG00000030247	Kcnj8	AI448900|Kir6.1|gnite|slmbr|sltr	"potassium inwardly-rectifying channel, subfamily J, member 8"	protein-coding	0.01	0.306931
Merged-chr13-25360628-1	chr13	25360578	25360678	+	2.3	cIP1vsInput	Intergenic	Intergenic	-90632	NM_009513	22360	Mm.4766	NM_009513	ENSMUSG00000048978	Nrsn1	Neurensin-1|Neuro-p24|Vmp	neurensin 1	protein-coding	0	0.326733
Merged-chr18-72994534-1	chr18	72994484	72994584	+	2.3	cIP2vsInput	Intergenic	Intergenic	-578171	NM_001039214	240396	Mm.436942	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 homolog C (C. elegans)	protein-coding	0	0.366337
Merged-chr17-70738404-1	chr17	70738354	70738454	+	2.3	cIP2vsInput	"intron (NM_001128181, intron 5 of 9)"	"intron (NM_001128181, intron 5 of 9)"	108373	NM_001164077	21815	Mm.101034	NM_001164074	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding	0.04	0.544554
Merged-chr5-119332834-1	chr5	119332784	119332884	+	2.3	cIP2vsInput	Intergenic	Intergenic	-132816	NR_046033	665194	Mm.491047	NR_046033		Gm7538	EG665194	predicted gene 7538	miscRNA	0.05	0.544554
Merged-chr1-14445676-1	chr1	14445626	14445726	+	2.3	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	-135477	NM_010164	14048	Mm.250185	NM_001252192	ENSMUSG00000025932	Eya1	bor	eyes absent 1 homolog (Drosophila)	protein-coding	0	0.346535
Merged-chr7-85744262-1	chr7	85744212	85744312	+	2.3	cIP2vsInput	"intron (NM_001105185, intron 5 of 5)"	Lx6|LINE|L1	10719	NM_001105185	244114	Mm.469907	NM_001105185	ENSMUSG00000051877	Vmn2r72	EG244114|Vmn2r72-ps	"vomeronasal 2, receptor 72"	protein-coding	0	0.316832
Merged-chr3-125565480-1	chr3	125565430	125565530	+	2.3	cIP2vsInput	"intron (NM_022565, intron 3 of 13)"	"intron (NM_022565, intron 3 of 13)"	161389	NM_022565	64580	Mm.444289	NM_022565	ENSMUSG00000027971	Ndst4	4930439H17Rik	N-deacetylase/N-sulfotransferase (heparin glucosaminyl) 4	protein-coding	0.01	0.366337
Merged-chr10-34123713-1	chr10	34123663	34123763	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	4259	NM_175449	215900	Mm.34479	NM_175449	ENSMUSG00000046031	Fam26f	A630077B13Rik	"family with sequence similarity 26, member F"	protein-coding	0	0.346535
Merged-chr13-115633637-1	chr13	115633587	115633687	+	2.3	cIP2vsInput	Intergenic	Intergenic	-531673	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding	0	0.366337
Merged-chr2-68658969-1	chr2	68658919	68659019	+	2.3	cIP2vsInput	"intron (NM_183113, intron 1 of 28)"	"intron (NM_183113, intron 1 of 28)"	1085	NM_183113	75721	Mm.65456	NM_183113	ENSMUSG00000079324	4932414N04Rik	-	RIKEN cDNA 4932414N04 gene	protein-coding	0	0.287129
Merged-chr15-68999324-1	chr15	68999274	68999374	+	2.3	cIP2vsInput	"intron (NM_010158, intron 2 of 8)"	L1_Mur2|LINE|L1	70904	NM_010158	13992	Mm.17964	NM_010158	ENSMUSG00000022332	Khdrbs3	Etle|SLM-2|Slm2|T-STAR	"KH domain containing, RNA binding, signal transduction associated 3"	protein-coding	0	0.277228
Merged-chr12-66286372-1	chr12	66286322	66286422	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1971	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding	0	0.386139
Merged-chr18-16172852-1	chr18	16172802	16172902	+	2.3	cIP2vsInput	Intergenic	MusHAL1|LINE|L1	-454806	NM_199055	71367	Mm.329304	NM_199055	ENSMUSG00000047161	Chst9	5430438D01Rik	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	protein-coding	0	0.326733
Merged-chr5-41768020-1	chr5	41767970	41768070	+	2.3	cIP2vsInput	Intergenic	Intergenic	-3800	NM_007524	12020	Mm.2530	NM_007524	ENSMUSG00000049691	Nkx3-2	Bapx1|NKX3.2|Nkx-3.2	NK3 homeobox 2	protein-coding	0	0.435644
Merged-chr8-82400711-1	chr8	82400661	82400761	+	2.3	cIP2vsInput	"intron (NM_001254747, intron 1 of 7)"	"intron (NM_001254747, intron 1 of 7)"	1875	NM_001254747	16168	Mm.490053	NM_001254747		Il15	AI503618|IL-15	interleukin 15	protein-coding	0.01	0.316832
Merged-chr9-37329991-1	chr9	37329941	37330041	+	2.3	cIP2vsInput	"intron (NM_001081429, intron 4 of 15)"	"intron (NM_001081429, intron 4 of 15)"	18401	NM_001081429	245902	Mm.390150	NM_001081429	ENSMUSG00000034303	Ccdc15	A630039F14Rik|D030074L19	coiled-coil domain containing 15	protein-coding	0.01	0.29703
Merged-chr15-4433598-1	chr15	4433548	4433648	+	2.3	cIP2vsInput	"intron (NM_177355, intron 1 of 2)"	"intron (NM_177355, intron 1 of 2)"	58107	NM_177355	239318	Mm.308996	NM_177355	ENSMUSG00000049148	Plcxd3	B130016O10Rik	"phosphatidylinositol-specific phospholipase C, X domain containing 3"	protein-coding	0.01	0.336634
Merged-chr1-119570095-1	chr1	119570045	119570145	+	2.3	cIP2vsInput	"exon (NM_145506, exon 19 of 25)"	"exon (NM_145506, exon 19 of 25)"	43941	NM_146103	226351	Mm.439806	NM_146103		Tmem185b	2500001K11Rik	transmembrane protein 185B	protein-coding	0	0.386139
Merged-chr7-98431131-1	chr7	98431081	98431181	+	2.3	cIP2vsInput	Intergenic	(TCCA)n|Simple_repeat|Simple_repeat	-12291	NM_001130693	14918	Mm.389928	NM_001034890	ENSMUSG00000074003	Gucy2d	-	guanylate cyclase 2d	protein-coding	0	0.386139
Merged-chr3-124806125-1	chr3	124806075	124806175	+	2.3	cIP1vsInput	Intergenic	Intergenic	-225034	NR_015460	384775	Mm.489851	NR_015460	ENSMUSG00000039174	1700003H04Rik	4930538K10Rik|4933400D22Rik	RIKEN cDNA 1700003H04 gene	miscRNA	0.01	0.356436
Merged-chr13-113510308-1	chr13	113510258	113510358	+	2.3	cIP1vsInput	Intergenic	L1MC3|LINE|L1	-7464	NR_045501	70917	Mm.491036	NR_045501		4921509O07Rik	-	RIKEN cDNA 4921509O07 gene	miscRNA	0.02	0.386139
Merged-chr5-145737277-1	chr5	145737227	145737327	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-17141	NM_017396	53973	Mm.379071	XM_003946424	ENSMUSG00000075551	Cyp3a41a	Cyp3a41	"cytochrome P450, family 3, subfamily a, polypeptide 41A"	protein-coding	0	0.316832
Merged-chr6-35892584-1	chr6	35892534	35892634	+	2.3	cIP2vsInput	Intergenic	Intergenic	-352696	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding	0.01	0.356436
Merged-chr10-64530316-1	chr10	64530266	64530366	+	2.3	cIP2vsInput	"intron (NM_001164519, intron 6 of 12)"	"intron (NM_001164519, intron 6 of 12)"	-440061	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding	0.01	0.306931
Merged-chr10-75984433-1	chr10	75984383	75984483	+	2.3	cIP2vsInput	"intron (NM_198635, intron 6 of 13)"	RMER12B|LTR|ERVK	29919	NM_198635	333669	Mm.31077	NM_198635	ENSMUSG00000033255	Gm5134	EG333669	predicted gene 5134	protein-coding	0	0.336634
Merged-chr14-123543114-1	chr14	123543064	123543164	+	2.3	cIP2vsInput	"intron (NM_177393, intron 7 of 43)"	"intron (NM_177393, intron 7 of 43)"	84030	NM_177393	338370	Mm.255348	NM_177754	ENSMUSG00000000197	Nalcn	A530023G15Rik|AI849508|Vgcnl1	"sodium leak channel, non-selective"	protein-coding	0.02	0.277228
Merged-chr17-94624356-1	chr17	94624306	94624406	+	2.3	cIP2vsInput	Intergenic	Intergenic	125536	NM_176917	76781	Mm.486648	NM_176917	ENSMUSG00000055660	Mettl4	2410198H06Rik|A730091E08Rik|AV296509|HsT661	methyltransferase like 4	protein-coding	0	0.346535
Merged-chr14-87870456-1	chr14	87870406	87870506	+	2.3	cIP1vsInput	Intergenic	Intergenic	453873	NM_001253755	219249	Mm.35168	NM_001253755	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding	0	0.336634
Merged-chr15-17997179-1	chr15	17997129	17997229	+	2.3	cIP2vsInput	Intergenic	Lx8|LINE|L1	372448	NR_045711	70886	Mm.399021	NR_045711		4921515E04Rik	-	RIKEN cDNA 4921515E04 gene	miscRNA	0	0.326733
Merged-chr13-67538624-1	chr13	67538574	67538674	+	2.3	cIP2vsInput	TTS (NM_001035231)	TTS (NM_001035231)	-12393	NM_133228	170763	Mm.138283	NM_133228	ENSMUSG00000097333	Zfp87	2210039O17Rik|4631412O18Rik|KRAB4|Mzf22|Zfp72	zinc finger protein 87	protein-coding	0	0.346535
Merged-chr4-90109811-1	chr4	90109761	90109861	+	2.3	cIP2vsInput	Intergenic	Intergenic	-109009	NM_153102	236537	Mm.214642	NM_153102	ENSMUSG00000070902	Zfp352	2czf48	zinc finger protein 352	protein-coding	0	0.306931
Merged-chr7-127406306-1	chr7	127406256	127406356	+	2.3	cIP2vsInput	"intron (NM_001167832, intron 1 of 2)"	"intron (NM_001167832, intron 1 of 2)"	516	NM_146203	233893	Mm.297097	NM_001167832	ENSMUSG00000045757	Zfp764	8030466O12Rik	zinc finger protein 764	protein-coding	0.04	0.564356
Merged-chr1-38305157-1	chr1	38305107	38305207	+	2.3	cIP2vsInput	"intron (NM_010678, intron 9 of 22)"	"intron (NM_010678, intron 9 of 22)"	-175495	NM_019570	56210	Mm.389103	NM_019570	ENSMUSG00000026082	Rev1	1110027I23Rik|AU022044|Rev1l	REV1 homolog (S. cerevisiae)	protein-coding	0.01	0.435644
Merged-chr1-142210194-1	chr1	142210144	142210244	+	2.3	cIP1vsInput	Intergenic	Intergenic	-1430503	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0.03	0.405941
Merged-chr2-114514886-1	chr2	114514836	114514936	+	2.3	cIP1vsInput	Intergenic	Intergenic	140042	NM_025675	66632	Mm.117809	NM_025675	ENSMUSG00000057147	Atpbd4	5730421E18Rik	ATP binding domain 4	protein-coding	0	0.336634
Merged-chr14-26686863-1	chr14	26686813	26686913	+	2.3	cIP2vsInput	Intergenic	Lx7|LINE|L1	-17017	NM_178668	211948	Mm.297768	NM_178668		Pde12	2'-PDE|E430028B21Rik	phosphodiesterase 12	protein-coding	0	0.316832
Merged-chr8-6563416-1	chr8	6563366	6563466	+	2.3	cIP1vsInput	Intergenic	Intergenic	-1458184	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.29703
Merged-chr7-77590310-1	chr7	77590260	77590360	+	2.3	cIP2vsInput	Intergenic	L1MCb|LINE|L1	987528	NM_008746	18213	Mm.421361	NM_008746		Ntrk3	AW125844|Ntrk3_tv3|TrkC	"neurotrophic tyrosine kinase, receptor, type 3"	protein-coding	0	0.306931
Merged-chr9-8650152-1	chr9	8650102	8650202	+	2.3	cIP1vsInput	"intron (NM_013838, intron 6 of 12)"	"intron (NM_013838, intron 6 of 12)"	106010	NM_013838	22068	Mm.325086	NM_013838	ENSMUSG00000031997	Trpc6	AV025995|LLHWJM002|LLHWJM003|LLHWJM004|TRP-6|Trrp6|mtrp6	"transient receptor potential cation channel, subfamily C, member 6"	protein-coding	0	0.326733
Merged-chr17-68156291-1	chr17	68156241	68156341	+	2.3	cIP2vsInput	Intergenic	Intergenic	-117506	NM_177278	320858	Mm.137356	NM_177278		L3mbtl4	A730037L19Rik|D930040M24Rik	l(3)mbt-like 4 (Drosophila)	protein-coding	0.01	0.326733
Merged-chr14-10475331-1	chr14	10475281	10475381	+	2.3	cIP2vsInput	"intron (NM_010210, intron 3 of 8)"	"intron (NM_010210, intron 3 of 8)"	591236	NR_030680	100042415	Mm.235938	NR_030680		Gm3833	-	meiotic nuclear divisions 1 homolog pseudogene	pseudo	0.02	0.346535
Merged-chr15-31249683-1	chr15	31249633	31249733	+	2.3	cIP2vsInput	"intron (NM_146057, intron 2 of 3)"	"intron (NM_146057, intron 2 of 3)"	25298	NM_146057	223453	Mm.222867	NM_146057	ENSMUSG00000039168	Dap	4921531N22Rik|AI789753|AU040360	death-associated protein	protein-coding	0	0.386139
Merged-chr4-9415507-1	chr4	9415457	9415557	+	2.3	cIP2vsInput	"intron (NM_028940, intron 3 of 5)"	L1_Rod|LINE|L1	146190	NM_028940	74438	Mm.473368	NM_028940	ENSMUSG00000041216	Clvs1	4933402J24Rik|Clvl1|Rlbp1l1	clavesin 1	protein-coding	0.01	0.366337
Merged-chr14-85287784-1	chr14	85287734	85287834	+	2.3	cIP1vsInput	Intergenic	Intergenic	-811360	NR_015539	319903	Mm.440481	NR_015539		9630013A20Rik	-	RIKEN cDNA 9630013A20 gene	miscRNA	0	0.287129
Merged-chr13-118075045-1	chr13	118074995	118075095	+	2.3	cIP2vsInput	Intergenic	Intergenic	312207	NM_021556	59054	Mm.143810	NM_021556	ENSMUSG00000021731	Mrps30	2610020A16Rik|AA968347|PAP|Pdcd9	mitochondrial ribosomal protein S30	protein-coding	0	0.346535
Merged-chr12-103367972-1	chr12	103367922	103368022	+	2.3	cIP1vsInput	Intergenic	Intergenic	-8922	NR_033587	68149	Mm.127378	NM_001177841	ENSMUSG00000021203	Otub2	2010015L18Rik|4930586I02Rik|AI413508|AW557219|OTB2|OTU2	"OTU domain, ubiquitin aldehyde binding 2"	protein-coding	0.01	0.554455
Merged-chr5-35525555-1	chr5	35525505	35525605	+	2.3	cIP2vsInput	promoter-TSS (NM_153107)	promoter-TSS (NM_153107)	71	NM_153107	242939	Mm.108557	NM_153107	ENSMUSG00000036596	Cpz	AV136066	carboxypeptidase Z	protein-coding	0.12	0.712871
Merged-chr15-79774295-1	chr15	79774245	79774345	+	2.3	cIP2vsInput	"intron (NM_017470, intron 1 of 3)"	CpG	172	NM_017470	54152	Mm.288159	NM_017470	ENSMUSG00000022420	Dnalc4	D15Ertd424e|Dnal4	"dynein, axonemal, light chain 4"	protein-coding	0.09	0.772277
Merged-chr3-43778092-1	chr3	43778042	43778142	+	2.3	cIP1vsInput	Intergenic	Lx3C|LINE|L1	1600168	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	miscRNA	0	0.376238
Merged-chr10-48346227-1	chr10	48346177	48346277	+	2.3	cIP1vsInput	Intergenic	MurERV4_19-int|LTR|ERVK	749616	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	"proteasome (prosome, macropain) subunit, alpha type 6 pseudogene"	pseudo	0	0.326733
Merged-chr3-134690906-1	chr3	134690856	134690956	+	2.3	cIP2vsInput	Intergenic	Lx3C|LINE|L1	-138101	NM_021382	21338	Mm.103810	NM_021382	ENSMUSG00000028172	Tacr3	Nk3r|Nkr|Tac3r	tachykinin receptor 3	protein-coding	0	0.346535
Merged-chr9-79007261-1	chr9	79007211	79007311	+	2.3	cIP2vsInput	Intergenic	Intergenic	391715	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding	0.01	0.257426
Merged-chr3-88775097-1	chr3	88775047	88775147	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1960	NR_028359	100302730	Mm.482358	NR_028359		5830417I10Rik	3632445O20Rik|AA387005	gon-4-like pseudogene	pseudo	0.02	0.485149
Merged-chr10-64109501-1	chr10	64109451	64109551	+	2.3	cIP2vsInput	"intron (NM_001164519, intron 2 of 12)"	"intron (NM_001164519, intron 2 of 12)"	-19246	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding	0	0.336634
Merged-chr6-53893852-1	chr6	53893802	53893902	+	2.3	cIP2vsInput	"intron (NM_027749, intron 12 of 12)"	L1MEg|LINE|L1	-73027	NM_025817	66873	Mm.480530	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding	0.01	0.346535
Merged-chr5-67099436-1	chr5	67099386	67099486	+	2.3	cIP1vsInput	promoter-TSS (NM_008888)	promoter-TSS (NM_008888)	-310	NM_008888	18935	Mm.62505	NM_008888	ENSMUSG00000012520	Phox2b	Dilp1|NBPhox|Pmx2b	paired-like homeobox 2b	protein-coding	0.01	0.366337
Merged-chr8-127132203-1	chr8	127132153	127132253	+	2.3	cIP2vsInput	"intron (NM_001122850, intron 1 of 15)"	L1MD|LINE|L1	68147	NM_001122850	93742	Mm.299254	NM_001013580	ENSMUSG00000025812	Pard3	AA960621|AI256638|ASIP|D8Ertd580e|PAR-3|Par3|Pard3a	par-3 (partitioning defective 3) homolog (C. elegans)	protein-coding	0	0.386139
Merged-chr8-105708229-1	chr8	105708179	105708279	+	2.3	cIP2vsInput	promoter-TSS (NM_027655)	promoter-TSS (NM_027655)	-61	NM_198299	102124	Mm.276087	NM_198299	ENSMUSG00000013155	Enkd1	AI606951|E130303B06Rik	enkurin domain containing 1	protein-coding	0.02	0.524752
Merged-chr5-60013856-1	chr5	60013806	60013906	+	2.3	cIP2vsInput	Intergenic	Intergenic	-27854	NR_040682	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0	0.326733
Merged-chr7-56981405-1	chr7	56981355	56981455	+	2.3	cIP2vsInput	"intron (NM_008074, intron 5 of 9)"	"intron (NM_008074, intron 5 of 9)"	405466	NM_008074	14407	Mm.434343	NM_008074		Gabrg3	B230362M20Rik|Gabrg-3	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 3"	protein-coding	0	0.287129
Merged-chr2-159578797-1	chr2	159578747	159578847	+	2.3	cIP2vsInput	Intergenic	Intergenic	-368544	NR_040498	71081	Mm.383491	NR_040498	ENSMUSG00000085198	4933416E03Rik	-	RIKEN cDNA 4933416E03 gene	miscRNA	0	0.326733
Merged-chr10-69964989-1	chr10	69964939	69965039	+	2.3	cIP2vsInput	"intron (NM_170729, intron 27 of 40)"	"intron (NM_170729, intron 27 of 40)"	39457	NM_009670	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	"ankyrin 3, epithelial"	protein-coding	0.02	0.346535
Merged-chr7-131545277-1	chr7	131545227	131545327	+	2.3	cIP2vsInput	TTS (NM_008257)	TTS (NM_008257)	2314	NM_008257	15373	Mm.323562	NM_008257	ENSMUSG00000040148	Hmx3	Nkx-5.1|Nkx5-1|Nkx5.1	H6 homeobox 3	protein-coding	0.01	0.386139
Merged-chr12-60589766-1	chr12	60589716	60589816	+	2.3	cIP1vsInput	Intergenic	Intergenic	932054	NR_045049	100504101	Mm.235026	NR_045049		Gm20063	-	"predicted gene, 20063"	miscRNA	0	0.366337
Merged-chr13-118925076-1	chr13	118925026	118925126	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	210377	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding	0.01	0.356436
Merged-chr3-23600728-1	chr3	23600678	23600778	+	2.3	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	1349358	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	miscRNA	0	0.326733
Merged-chr12-64489059-1	chr12	64489009	64489109	+	2.3	cIP2vsInput	Intergenic	Intergenic	-14161	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.346535
Merged-chrX-133746400-1	chrX	133746350	133746450	+	2.3	cIP1vsInput	Intergenic	Lx8|LINE|L1	-57407	NM_001105246	279653	Mm.39738	NM_001105245	ENSMUSG00000051323	Pcdh19	B530002L05Rik|Gm717|mKIAA1313	protocadherin 19	protein-coding	0	0.336634
Merged-chr2-110230212-1	chr2	110230162	110230262	+	2.3	cIP2vsInput	Intergenic	Intergenic	75513	NM_130452	170442	Mm.27335	NM_130452		Bbox1	AI874739	"butyrobetaine (gamma), 2-oxoglutarate dioxygenase 1 (gamma-butyrobetaine hydroxylase)"	protein-coding	0	0.277228
Merged-chr2-148408096-1	chr2	148408046	148408146	+	2.3	cIP2vsInput	promoter-TSS (NM_009378)	promoter-TSS (NM_009378)	92	NM_009378	21824	Mm.24096	NM_009378	ENSMUSG00000074743	Thbd	AI385582|CD141|TM	thrombomodulin	protein-coding	0.03	0.544554
Merged-chr5-143818764-1	chr5	143818714	143818814	+	2.3	cIP2vsInput	Intergenic	ID4_|SINE|ID	-53098	NM_013557	15467	Mm.431968	NM_013557		Eif2ak1	HCR|Hri	eukaryotic translation initiation factor 2 alpha kinase 1	protein-coding	0.01	0.455446
Merged-chr6-35853027-1	chr6	35852977	35853077	+	2.3	cIP2vsInput	Intergenic	Intergenic	-313139	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding	0.01	0.386139
Merged-chr8-39719722-1	chr8	39719672	39719772	+	2.3	cIP2vsInput	"intron (NR_035426, intron 3 of 5)"	"intron (NR_035426, intron 3 of 5)"	-77044	NM_001113326	20288	Mm.239291	NM_001113326	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding	0	0.316832
Merged-chr13-103559395-1	chr13	103559345	103559445	+	2.3	cIP2vsInput	Intergenic	Intergenic	205187	NM_172592	218543	Mm.458176	NM_172592	ENSMUSG00000032621	Srek1	8430401B01|AI450757|AI462342|SRrp508|SRrp86|Sfrs12|Srsf12	splicing regulatory glutamine/lysine-rich protein 1	protein-coding	0.01	0.356436
Merged-chr9-42048871-1	chr9	42048821	42048921	+	2.3	cIP2vsInput	"intron (NM_011436, intron 12 of 47)"	"intron (NM_011436, intron 12 of 47)"	75418	NM_011436	20660	Mm.121920	NM_011436		Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	"sortilin-related receptor, LDLR class A repeats-containing"	protein-coding	0	0.29703
Merged-chr16-56109564-1	chr16	56109514	56109614	+	2.3	cIP2vsInput	"intron (NM_001003971, intron 3 of 22)"	L1M2|LINE|L1	34155	NM_001003973	66315	Mm.255784	NM_001003971	ENSMUSG00000052917	Senp7	2410152H17Rik|2810413I22Rik|2900036C23Rik|6030449K19Rik|AI790676|mKIAA1707	SUMO1/sentrin specific peptidase 7	protein-coding	0.01	0.336634
Merged-chr11-55607914-1	chr11	55607864	55607964	+	2.3	cIP2vsInput	promoter-TSS (NM_020492)	promoter-TSS (NM_020492)	-124	NM_020492	14654	Mm.89320	NM_020492		Glra1	B230397M16Rik|nmf11|oscillator|ot|spasmodic|spd	"glycine receptor, alpha 1 subunit"	protein-coding	0.09	0.663366
Merged-chr8-6778515-1	chr8	6778465	6778565	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1673283	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.277228
Merged-chr1-109419313-1	chr1	109419263	109419363	+	2.3	cIP2vsInput	Intergenic	Intergenic	-564424	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.306931
Merged-chr10-92839598-1	chr10	92839548	92839648	+	2.3	cIP1vsInput	Intergenic	Intergenic	-3252	NR_040653	380653	Mm.391437	NR_040653	ENSMUSG00000020014	Gm872	-	predicted gene 872	miscRNA	0	0.326733
Merged-chr11-66788330-1	chr11	66788280	66788380	+	2.3	cIP1vsInput	Intergenic	L1M4|LINE|L1	-123661	NM_178656	193003	Mm.440256	NM_178656		Pirt	A530088H08Rik	phosphoinositide-interacting regulator of transient receptor potential channels	protein-coding	0	0.366337
Merged-chr7-100521032-1	chr7	100520982	100521082	+	2.3	cIP2vsInput	Intergenic	B3A|SINE|B2	-6217	NM_153527	69387	Mm.278554	NM_153527	ENSMUSG00000030708	Dnajb13	1700014P03Rik|Tsarg	"DnaJ (Hsp40) related, subfamily B, member 13"	protein-coding	0.01	0.514851
Merged-chr11-119524637-1	chr11	119524587	119524687	+	2.3	cIP1vsInput	Intergenic	CpG	23183	NM_008730	18164	Mm.5142	NM_008730	ENSMUSG00000025582	Nptx1	D11Bwg1004e|Np1	neuronal pentraxin 1	protein-coding	0.08	0.673267
Merged-chr17-25868385-1	chr17	25868335	25868435	+	2.3	cIP2vsInput	"intron (NM_026633, intron 2 of 4)"	CpG	353	NM_026633	68241	Mm.328870	NM_026633	ENSMUSG00000025732	Fam195a	9530058B02Rik	"family with sequence similarity 195, member A"	protein-coding	0.06	0.712871
Merged-chr12-71424163-1	chr12	71424113	71424213	+	2.3	cIP2vsInput	Intergenic	Intergenic	114279	NM_001190466	59036	Mm.46662	NM_001190466	ENSMUSG00000044548	Dact1	4921528D17Rik|AI115603|DAPPER|DAPPER1|FRODO|Frd1|Frodo1|MDpr1|MTNG3|THYEX3	"dapper homolog 1, antagonist of beta-catenin (xenopus)"	protein-coding	0.01	0.366337
Merged-chr3-139845561-1	chr3	139845511	139845611	+	2.3	cIP1vsInput	Intergenic	Intergenic	639668	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding	0	0.257426
Merged-chr4-86930931-1	chr4	86930881	86930981	+	2.3	cIP1vsInput	Intergenic	L1Md_F|LINE|L1	56517	NM_139306	230379	Mm.458684	NM_139306	ENSMUSG00000038007	Acer2	2410116I05Rik|Asah3l|CRG-L1|maCER2	alkaline ceramidase 2	protein-coding	0.09	0.643564
Merged-chr13-66773814-1	chr13	66773764	66773864	+	2.3	cIP2vsInput	Intergenic	Intergenic	131536	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding	0.01	0.287129
Merged-chr12-54308358-1	chr12	54308308	54308408	+	2.3	cIP1vsInput	Intergenic	Intergenic	82960	NR_033689	665239	Mm.26856	NR_033689		Gm7550	EG665239|Gm666	predicted gene 7550	miscRNA	0	0.267327
Merged-chr4-68336294-1	chr4	68336244	68336344	+	2.3	cIP2vsInput	Intergenic	B4|SINE|B4	618103	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Dbc1	BRINP|Brinp1|Dbccr1|Fam5a	deleted in bladder cancer 1 (human)	protein-coding	0	0.425743
Merged-chr7-130756298-1	chr7	130756248	130756348	+	2.3	cIP2vsInput	"intron (NM_001004468, intron 18 of 21)"	"intron (NM_001004468, intron 18 of 21)"	-17771	NM_001081038	330660	Mm.271550	NM_001081038	ENSMUSG00000040298	Btbd16	E330040A16Rik	BTB (POZ) domain containing 16	protein-coding	0.02	0.435644
Merged-chrY-6054474-1	chrY	6054424	6054524	+	2.3	cIP2vsInput	Intergenic	MT2A|LTR|ERVL	1113303	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.386139
Merged-chr19-26639185-1	chr19	26639135	26639235	+	2.3	cIP2vsInput	"intron (NM_011416, intron 4 of 32)"	"intron (NM_011416, intron 4 of 32)"	34025	NM_011416	67155	Mm.313303	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2"	protein-coding	0	0.346535
Merged-chr13-79854640-1	chr13	79854590	79854690	+	2.3	cIP2vsInput	Intergenic	Lx3B|LINE|L1	-1028782	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0	0.346535
Merged-chr8-62456835-1	chr8	62456785	62456885	+	2.3	cIP2vsInput	Intergenic	Intergenic	-333717	NM_011922	26359	Mm.42179	NM_001136089	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding	0	0.336634
Merged-chr18-63131506-1	chr18	63131456	63131556	+	2.3	cIP2vsInput	"intron (NM_001039485, intron 7 of 53)"	"intron (NM_001039485, intron 7 of 53)"	153590	NM_028017	108123	Mm.292687	NM_028017	ENSMUSG00000024581	Napg	2400003O04Rik|SNARE	N-ethylmaleimide sensitive fusion protein attachment protein gamma	protein-coding	0.01	0.306931
Merged-chr5-58479048-1	chr5	58478998	58479098	+	2.3	cIP2vsInput	Intergenic	L1M2|LINE|L1	-26050	NR_046190	78163	Mm.243828	NR_046190		4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	miscRNA	0	0.316832
Merged-chr13-86077514-1	chr13	86077464	86077564	+	2.3	cIP2vsInput	Intergenic	Intergenic	-30719	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0	0.336634
Merged-chr17-53505400-1	chr17	53505350	53505450	+	2.3	cIP2vsInput	"intron (NM_025887, intron 5 of 5)"	"intron (NM_025887, intron 5 of 5)"	26166	NM_025887	271457	Mm.329123	NM_025887	ENSMUSG00000017831	Rab5a	2410015H04Rik|AI663973|AU021172|nnyRab5a	"RAB5A, member RAS oncogene family"	protein-coding	0	0.356436
Merged-chr16-39269290-1	chr16	39269240	39269340	+	2.3	cIP2vsInput	Intergenic	Intergenic	366945	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	"immunoglobulin superfamily, member 11"	protein-coding	0	0.346535
Merged-chr2-110980567-1	chr2	110980517	110980617	+	2.3	cIP2vsInput	Intergenic	Intergenic	-30323	NM_001128103	228432	Mm.483325	NM_001128103	ENSMUSG00000074968	Ano3	AI838058|B230324K02Rik|Tmem16c	anoctamin 3	protein-coding	0.01	0.316832
Merged-chr1-101066863-1	chr1	101066813	101066913	+	2.3	cIP1vsInput	Intergenic	Intergenic	-88905	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.346535
Merged-chr4-24253927-1	chr4	24253877	24253977	+	2.3	cIP2vsInput	Intergenic	Intergenic	-242535	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	"MMS22-like, DNA repair protein"	protein-coding	0	0.29703
Merged-chr4-117219000-1	chr4	117218950	117219050	+	2.3	cIP2vsInput	"intron (NM_001033774, intron 7 of 7)"	"intron (NM_001033774, intron 7 of 7)"	32917	NM_001145637	381544	Mm.23504	NM_001033774	ENSMUSG00000060268	Gm1661	Gm1662|Ncrna00082	predicted gene 1661	protein-coding	0.03	0.544554
Merged-chr3-102854158-1	chr3	102854108	102854208	+	2.3	cIP2vsInput	"exon (NM_011516, exon 25 of 33)"	"exon (NM_011516, exon 25 of 33)"	-71444	NM_001165940	22094	Mm.110730	NM_001165939	ENSMUSG00000027857	Tshb	-	"thyroid stimulating hormone, beta subunit"	protein-coding	0	0.326733
Merged-chr9-4607132-1	chr9	4607082	4607182	+	2.3	cIP1vsInput	"intron (NM_019691, intron 4 of 16)"	"intron (NM_019691, intron 4 of 16)"	189102	NM_001113180	14802	Mm.209263	NM_001113180	ENSMUSG00000025892	Gria4	GluA4|GluR-D|Glur-4|Glur4|Gluralpha4|spkw1	"glutamate receptor, ionotropic, AMPA4 (alpha 4)"	protein-coding	0	0.336634
Merged-chr1-110419082-1	chr1	110419032	110419132	+	2.3	cIP2vsInput	Intergenic	L1VL4|LINE|L1	435345	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.386139
Merged-chr14-38816177-1	chr14	38816127	38816227	+	2.3	cIP2vsInput	"intron (NM_001190187, intron 2 of 9)"	"intron (NM_001190187, intron 2 of 9)"	-82125	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	4930529F24Rik	-	RIKEN cDNA 4930529F24 gene	miscRNA	0	0.316832
Merged-chr16-36779970-1	chr16	36779920	36780020	+	2.3	cIP2vsInput	"intron (NM_021301, intron 3 of 21)"	"intron (NM_021301, intron 3 of 21)"	4992	NM_001145899	57738	Mm.281804	NM_001145899	ENSMUSG00000022899	Slc15a2	8430408C16Rik|C78862|Pept2	"solute carrier family 15 (H+/peptide transporter), member 2"	protein-coding	0.01	0.376238
Merged-chr14-15814688-1	chr14	15814638	15814738	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-375701	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding	0	0.29703
Merged-chr14-79660844-1	chr14	79660794	79660894	+	2.3	cIP2vsInput	"intron (NM_010701, intron 2 of 6)"	"intron (NM_010701, intron 2 of 6)"	1326	NM_010701	16840	Mm.46561	NM_010701	ENSMUSG00000022025	Lect1	Bricd3|ChM-I	leukocyte cell derived chemotaxin 1	protein-coding	0	0.316832
Merged-chr1-96785219-1	chr1	96785169	96785269	+	2.3	cIP1vsInput	Intergenic	Intergenic	86952	NM_172658	227394	Mm.11662	NM_172658	ENSMUSG00000040693	Slco4c1	9530051F04|C330017E21Rik|OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20|oatp-R	"solute carrier organic anion transporter family, member 4C1"	protein-coding	0.02	0.39604
Merged-chr3-72599737-1	chr3	72599687	72599787	+	2.3	cIP2vsInput	Intergenic	Intergenic	367129	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding	0	0.306931
Merged-chr1-31683692-1	chr1	31683642	31683742	+	2.3	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	418845	NR_015347	226957	Mm.25966	NR_015347		Gm4850	EG226957	THO complex 4 pseudogene	pseudo	0.01	0.277228
Merged-chr10-103898547-1	chr10	103898497	103898597	+	2.3	cIP1vsInput	Intergenic	Intergenic	-244440	NM_001177535	100043292	Mm.339215	NM_001177535	ENSMUSG00000090854	Gm4340	-	predicted gene 4340	protein-coding	0	0.29703
Merged-chr3-115017780-1	chr3	115017730	115017830	+	2.3	cIP1vsInput	"intron (NM_153458, intron 1 of 5)"	"intron (NM_153458, intron 1 of 5)"	-63185	NM_153157	229759	Mm.54183	NM_153157	ENSMUSG00000027965	Olfm3	B230206G02Rik	olfactomedin 3	protein-coding	0	0.386139
Merged-chr13-71011082-1	chr13	71011032	71011132	+	2.3	cIP2vsInput	Intergenic	Lx5|LINE|L1	128134	NM_029873	77166	Mm.159859	NM_029873	ENSMUSG00000021600	8030423J24Rik	-	RIKEN cDNA 8030423J24 gene	protein-coding	0	0.316832
Merged-chr5-39346445-1	chr5	39346395	39346495	+	2.3	cIP2vsInput	Intergenic	Intergenic	257129	NR_045416	75095	Mm.332354	NR_045416		4930513D17Rik	-	RIKEN cDNA 4930513D17 gene	miscRNA	0	0.346535
Merged-chr5-50826210-1	chr5	50826160	50826260	+	2.3	cIP2vsInput	Intergenic	Lx7|LINE|L1	674877	NR_040696	73965	Mm.243823	NR_040696		4930448I18Rik	-	RIKEN cDNA 4930448I18 gene	miscRNA	0	0.316832
Merged-chr4-146486746-1	chr4	146486696	146486796	+	2.3	cIP1vsInput	Intergenic	Intergenic	-15254	NM_001243138	100041433	Mm.441741	NM_001243138	ENSMUSG00000056300	Gm13247	OTTMUSG00000011075	predicted gene 13247	protein-coding	0	0.306931
Merged-chr11-67317302-1	chr11	67317252	67317352	+	2.3	cIP2vsInput	Intergenic	Intergenic	-9801	NM_001081250	544791	Mm.461064	NM_001081250	ENSMUSG00000060180	Myh13	MyHC-eo	"myosin, heavy polypeptide 13, skeletal muscle"	protein-coding	0	0.366337
Merged-chr13-57332054-1	chr13	57332004	57332104	+	2.3	cIP2vsInput	Intergenic	Intergenic	-436466	NM_012035	26946	Mm.62409	NM_012035	ENSMUSG00000021541	Trpc7	TRP-7|TRP7|Trrp8	"transient receptor potential cation channel, subfamily C, member 7"	protein-coding	0.02	0.524752
Merged-chr3-134057443-1	chr3	134057393	134057493	+	2.3	cIP1vsInput	Intergenic	Lx7|LINE|L1	-179052	NM_001004367	319478	Mm.487501	NM_001004367	ENSMUSG00000044365	Cxxc4	9330210J02Rik|C030003J12Rik|Idax	CXXC finger 4	protein-coding	0	0.287129
Merged-chr4-79234560-1	chr4	79234510	79234610	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1022665	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0	0.316832
Merged-chr17-82347509-1	chr17	82347459	82347559	+	2.3	cIP2vsInput	Intergenic	Intergenic	-609132	NM_011406	20541	Mm.489060	NM_001112798		Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	"solute carrier family 8 (sodium/calcium exchanger), member 1"	protein-coding	0.01	0.346535
Merged-chr7-85876077-1	chr7	85876027	85876127	+	2.3	cIP2vsInput	promoter-TSS (NM_001105186)	promoter-TSS (NM_001105186)	-139	NM_001105186	620928	Mm.469906	NM_001105186	ENSMUSG00000070458	Vmn2r73	EG620928	"vomeronasal 2, receptor 73"	protein-coding	0	0.376238
Merged-chr13-32350320-1	chr13	32350270	32350370	+	2.3	cIP2vsInput	Intergenic	Intergenic	-11776	NM_146041	218138	Mm.247143	NM_146041	ENSMUSG00000038372	Gmds	BC031788|C87208	"GDP-mannose 4, 6-dehydratase"	protein-coding	0	0.336634
Merged-chr6-148527657-1	chr6	148527607	148527707	+	2.3	cIP2vsInput	Intergenic	B1F1|SINE|Alu	-83305	NM_198967	387314	Mm.137858	NM_198967	ENSMUSG00000030306	Tmtc1	Arg99|BC023818	transmembrane and tetratricopeptide repeat containing 1	protein-coding	0	0.376238
Merged-chr7-13352453-1	chr7	13352403	13352503	+	2.3	cIP1vsInput	"intron (NM_001004762, intron 13 of 15)"	Lx3B|LINE|L1	23131	NM_001004762	232889	Mm.223639	NM_001004762	ENSMUSG00000033847	Pla2g4c	D7Ertd445e	"phospholipase A2, group IVC (cytosolic, calcium-independent)"	protein-coding	0.02	0.376238
Merged-chr14-99815036-1	chr14	99814986	99815086	+	2.3	cIP2vsInput	Intergenic	Intergenic	334760	NM_010636	16597	Mm.458816	NM_010636		Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding	0.01	0.336634
Merged-chr12-42282347-1	chr12	42282297	42282397	+	2.3	cIP1vsInput	Intergenic	Intergenic	653583	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding	0.01	0.356436
Merged-chr9-81169379-1	chr9	81169329	81169429	+	2.3	cIP1vsInput	Intergenic	Intergenic	-462551	NR_040394	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	miscRNA	0.01	0.316832
Merged-chr4-145687909-1	chr4	145687859	145687959	+	2.3	cIP1vsInput	"intron (NM_001103158, intron 2 of 4)"	"intron (NM_001103158, intron 2 of 4)"	17212	NM_001103158	100041379	Mm.276881	NM_001103158	ENSMUSG00000058186	Gm13242	OTTMUSG00000011070	predicted gene 13242	protein-coding	0.01	0.346535
Merged-chr11-95298517-1	chr11	95298467	95298567	+	2.3	cIP2vsInput	"intron (NM_177619, intron 3 of 12)"	"intron (NM_177619, intron 3 of 12)"	11729	NM_001195004	217127	Mm.472268	NM_001195003		Kat7	Hbo1|Hboa|Myst2	K(lysine) acetyltransferase 7	protein-coding	0	0.366337
Merged-chr19-20589665-1	chr19	20589615	20589715	+	2.3	cIP2vsInput	Intergenic	Intergenic	-12317	NM_013467	11668	Mm.250866	NM_013467	ENSMUSG00000053279	Aldh1a1	Ahd-2|Ahd2|Aldh1|Aldh1a2|E1|Raldh1	"aldehyde dehydrogenase family 1, subfamily A1"	protein-coding	0	0.316832
Merged-chr13-99748823-1	chr13	99748773	99748873	+	2.3	cIP2vsInput	Intergenic	Intergenic	151860	NM_013732	27220	Mm.75498	NM_001081493	ENSMUSG00000021647	Cartpt	Cart	CART prepropeptide	protein-coding	0	0.336634
Merged-chr10-4990970-1	chr10	4990920	4991020	+	2.3	cIP2vsInput	"intron (NM_007956, intron 7 of 8)"	"intron (NM_007956, intron 7 of 8)"	78093	NM_022027	64009	Mm.331626	NM_001079686	ENSMUSG00000019769	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756	"spectrin repeat containing, nuclear envelope 1"	protein-coding	0.02	0.356436
Merged-chr16-38476631-1	chr16	38476581	38476681	+	2.3	cIP2vsInput	"intron (NM_009855, intron 2 of 4)"	"intron (NM_009855, intron 2 of 4)"	17698	NM_009855	12519	Mm.89474	NM_009855	ENSMUSG00000075122	Cd80	B71|Cd28l|Ly-53|Ly53|MIC17|TSA1	CD80 antigen	protein-coding	0.05	0.584158
Merged-chr13-11778049-1	chr13	11777999	11778099	+	2.3	cIP1vsInput	"intron (NM_023868, intron 25 of 104)"	"intron (NM_023868, intron 25 of 104)"	255997	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	"zona pellucida glycoprotein 4, pseudogene"	pseudo	0	0.237624
Merged-chr8-98037111-1	chr8	98037061	98037161	+	2.3	cIP1vsInput	Intergenic	Intergenic	1379346	NM_007667	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.336634
Merged-chr12-38450766-1	chr12	38450716	38450816	+	2.3	cIP2vsInput	"intron (NM_178681, intron 22 of 24)"	"intron (NM_178681, intron 22 of 24)"	163755	NR_045943	73867	Mm.78933	NR_045943		4930428E07Rik	-	RIKEN cDNA 4930428E07 gene	miscRNA	0.01	0.306931
Merged-chr7-105105153-1	chr7	105105103	105105203	+	2.3	cIP1vsInput	Intergenic	RLTR17D_Mm|LTR|ERVK	-16306	NM_207557	404318	Mm.377938	NM_207557	ENSMUSG00000095248	Olfr681	MOR4014	olfactory receptor 681	protein-coding	0	0.306931
Merged-chr15-28904684-1	chr15	28904634	28904734	+	2.3	cIP2vsInput	Intergenic	L1M2|LINE|L1	700918	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnahc5	AU022615|Dnah5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	"dynein, axonemal, heavy chain 5"	protein-coding	0	0.316832
Merged-chr1-83378195-1	chr1	83378145	83378245	+	2.3	cIP2vsInput	"intron (NM_172430, intron 1 of 10)"	ORR1D1|LTR|ERVL-MaLR	30005	NM_172430	77629	Mm.154303	NM_172430		Sphkap	4930544G21Rik|A930009L15Rik|AI852220|SKIP|mKIAA1678	"SPHK1 interactor, AKAP domain containing"	protein-coding	0	0.386139
Merged-chr2-103002491-1	chr2	103002441	103002541	+	2.3	cIP1vsInput	Intergenic	Intergenic	71022	NM_175094	27402	Mm.315011	NM_175094	ENSMUSG00000010914	Pdhx	AI481367|E3bp|Pdx1	"pyruvate dehydrogenase complex, component X"	protein-coding	0.02	0.465347
Merged-chrX-78368816-1	chrX	78368766	78368866	+	2.3	cIP2vsInput	promoter-TSS (NM_001177966)	promoter-TSS (NM_001177966)	-827	NM_001177966	74910	Mm.159364	NM_001177966	ENSMUSG00000035651	4930480E11Rik	-	RIKEN cDNA 4930480E11 gene	protein-coding	0	0.306931
Merged-chr15-73553672-1	chr15	73553622	73553722	+	2.3	cIP2vsInput	"intron (NM_001081066, intron 13 of 22)"	"intron (NM_001081066, intron 13 of 22)"	41112	NM_001081066	105841	Mm.322557	NM_001081066	ENSMUSG00000036661	Dennd3	AI447457|E030003N15Rik	DENN/MADD domain containing 3	protein-coding	0.01	0.326733
Merged-chr10-129889640-1	chr10	129889590	129889690	+	2.3	cIP2vsInput	Intergenic	L1VL4|LINE|L1	13086	NM_146670	258665	Mm.377627	NM_146670	ENSMUSG00000061961	Olfr815	MOR113-3	olfactory receptor 815	protein-coding	0.01	0.326733
Merged-chr15-35379543-1	chr15	35379493	35379593	+	2.3	cIP2vsInput	"intron (NM_177151, intron 3 of 61)"	"intron (NM_177151, intron 3 of 61)"	7997	NM_177151	666173	Mm.309250	NM_177151	ENSMUSG00000037646	Vps13b	1810042B05Rik|2310042E16Rik|4732488H20|C330002D13Rik|C87206|Coh1|D230005K13|mKIAA0532|mKIAA5032	vacuolar protein sorting 13B (yeast)	protein-coding	0	0.29703
Merged-chr15-45535093-1	chr15	45535043	45535143	+	2.3	cIP1vsInput	Intergenic	Lx3A|LINE|L1	-420159	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	"potassium channel, subfamily V, member 1"	protein-coding	0	0.376238
Merged-chr9-82026260-1	chr9	82026210	82026310	+	2.3	cIP2vsInput	"3' UTR (NM_175213, exon 5 of 5)"	"3' UTR (NM_175213, exon 5 of 5)"	162516	NM_175213	75033	Mm.457083	NM_175213	ENSMUSG00000043289	Mei4	4930486G11Rik	"meiosis-specific, MEI4 homolog (S. cerevisiae)"	protein-coding	0	0.267327
Merged-chr14-34363242-1	chr14	34363192	34363292	+	2.3	cIP2vsInput	Intergenic	Intergenic	-7849	NM_183278	69134	Mm.27156	NM_183278	ENSMUSG00000043681	Fam25c	2200001I15Rik|Fam25	"family with sequence similarity 25, member C"	protein-coding	0.01	0.564356
Merged-chr4-78745726-1	chr4	78745676	78745776	+	2.3	cIP1vsInput	Intergenic	Intergenic	-533831	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0	0.277228
Merged-chr1-86842704-1	chr1	86842654	86842754	+	2.3	cIP2vsInput	"intron (NM_001172157, intron 7 of 21)"	ORR1D2-int|LTR|ERVL-MaLR	138900	NM_001172157	208718	Mm.389152	NM_001172157	ENSMUSG00000053333	Dis3l2	4930429A22Rik|8030493P09Rik	DIS3 mitotic control homolog (S. cerevisiae)-like 2	protein-coding	0	0.425743
Merged-chr8-49457038-1	chr8	49456988	49457088	+	2.3	cIP1vsInput	Intergenic	Intergenic	-782348	NM_011857	23965	Mm.42191	NM_001145937	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding	0.02	0.326733
Merged-chr1-28112383-1	chr1	28112333	28112433	+	2.3	cIP1vsInput	Intergenic	Intergenic	667869	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0	0.356436
Merged-chr9-18036101-1	chr9	18036051	18036151	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-256166	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	"cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1"	protein-coding	0	0.326733
Merged-chr13-88553585-1	chr13	88553535	88553635	+	2.3	cIP1vsInput	Intergenic	Intergenic	-267887	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0	0.316832
Merged-chr3-49346503-1	chr3	49346453	49346553	+	2.3	cIP2vsInput	Intergenic	Intergenic	410813	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding	0	0.326733
Merged-chr8-56530374-1	chr8	56530324	56530424	+	2.3	cIP1vsInput	Intergenic	Intergenic	20192	NM_001009951	382010	Mm.425534	NM_001009951	ENSMUSG00000038215	Cep44	4933440G23Rik|mKIAA1712	centrosomal protein 44	protein-coding	0	0.306931
Merged-chr14-27708805-1	chr14	27708755	27708855	+	2.3	cIP1vsInput	"intron (NM_177814, intron 2 of 15)"	"intron (NM_177814, intron 2 of 15)"	86363	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding	0	0.386139
Merged-chr1-136685289-1	chr1	136685239	136685339	+	2.3	cIP1vsInput	"intron (NR_045325, intron 1 of 2)"	"intron (NR_045325, intron 1 of 2)"	1660	NR_045325	100503460	Mm.30630	NR_045324	ENSMUSG00000097113	Gm19705	-	"predicted gene, 19705"	miscRNA	0	0.415842
Merged-chr18-52440286-1	chr18	52440236	52440336	+	2.3	cIP2vsInput	Intergenic	Intergenic	-25407	NM_026040	67222	Mm.100617	XM_003946020	ENSMUSG00000024528	Srfbp1	2810036K01Rik|p49/STRAP	serum response factor binding protein 1	protein-coding	0	0.346535
Merged-chr17-91712061-1	chr17	91712011	91712111	+	2.3	cIP1vsInput	Intergenic	Intergenic	-619259	NM_020252	18189	Mm.312068	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0	0.306931
Merged-chr2-136203203-1	chr2	136203153	136203253	+	2.3	cIP1vsInput	"intron (NM_172858, intron 2 of 9)"	Lx8b|LINE|L1	145276	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	"lysosomal-associated membrane protein family, member 5"	protein-coding	0	0.39604
Merged-chr16-59421219-1	chr16	59421169	59421269	+	2.3	cIP1vsInput	"intron (NM_001081190, intron 2 of 8)"	L1_Mur3|LINE|L1	13837	NM_001081190	328699	Mm.451970	NM_001081190	ENSMUSG00000074991	Gabrr3	-	"gamma-aminobutyric acid (GABA) receptor, rho 3"	protein-coding	0.01	0.356436
Merged-chr3-17154106-1	chr3	17154056	17154156	+	2.3	cIP2vsInput	Intergenic	Intergenic	-635815	NR_033490	70441	Mm.458192	NR_033490		2610100L16Rik	100040120|Gm2612	RIKEN cDNA 2610100L16 gene	miscRNA	0.01	0.336634
Merged-chr16-71197162-1	chr16	71197112	71197212	+	2.3	cIP2vsInput	Intergenic	Intergenic	-52742	NR_040576	78221	Mm.399298	NR_040576		4930567J20Rik	-	RIKEN cDNA 4930567J20 gene	miscRNA	0.01	0.386139
Merged-chr8-115528682-1	chr8	115528632	115528732	+	2.3	cIP2vsInput	Intergenic	Intergenic	178212	NM_001025577	17132	Mm.488377	NM_001025577		Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma (v-maf) AS42 oncogene homolog	protein-coding	0	0.376238
Merged-chr3-112800697-1	chr3	112800647	112800747	+	2.3	cIP2vsInput	Intergenic	Intergenic	356030	NM_001190404	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding	0.01	0.386139
Merged-chr10-124954596-1	chr10	124954546	124954646	+	2.3	cIP1vsInput	Intergenic	Intergenic	373939	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	"solute carrier family 16 (monocarboxylic acid transporters), member 7"	protein-coding	0.01	0.29703
Merged-chr3-159373279-1	chr3	159373229	159373329	+	2.3	cIP2vsInput	Intergenic	Intergenic	-122154	NM_001172092	76131	Mm.371655	NM_001172092	ENSMUSG00000028175	Depdc1a	5830484J08Rik|Depdc1	DEP domain containing 1a	protein-coding	0	0.336634
Merged-chr1-11391800-1	chr1	11391750	11391850	+	2.3	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-22305	NM_001160369	320492	Mm.52021	NM_001160369	ENSMUSG00000057715	A830018L16Rik	-	RIKEN cDNA A830018L16 gene	protein-coding	0	0.366337
Merged-chr1-68458733-1	chr1	68458683	68458783	+	2.3	cIP2vsInput	"intron (NM_010154, intron 3 of 26)"	"intron (NM_010154, intron 3 of 26)"	649326	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0	0.346535
Merged-chr13-119632097-1	chr13	119632047	119632147	+	2.3	cIP1vsInput	"intron (NM_020279, intron 1 of 2)"	"intron (NM_020279, intron 1 of 2)"	8278	NM_020279	56838	Mm.143745	NM_020279	ENSMUSG00000074715	Ccl28	CCK1|MEC|Scya28	chemokine (C-C motif) ligand 28	protein-coding	0	0.346535
Merged-chr18-89641841-1	chr18	89641791	89641891	+	2.3	cIP2vsInput	"intron (NM_001039173, intron 1 of 7)"	"intron (NM_001039173, intron 1 of 7)"	127295	NM_001039173	623279	Mm.447164	NM_001039173		Dok6	Dok-6	docking protein 6	protein-coding	0	0.257426
Merged-chr16-66014130-1	chr16	66014080	66014180	+	2.3	cIP2vsInput	Intergenic	Intergenic	198497	NM_028572	73569	Mm.482366	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like 3 (Drosophila)	protein-coding	0	0.356436
Merged-chr11-101130473-1	chr11	101130423	101130523	+	2.3	cIP2vsInput	Intergenic	Intergenic	10342	NM_134024	103733	Mm.479145	NM_134024	ENSMUSG00000035198	Tubg1	1500010O08Rik|AI451582|AI503389|Tubg	"tubulin, gamma 1"	protein-coding	0.04	0.435644
Merged-chr3-110944455-1	chr3	110944405	110944505	+	2.3	cIP2vsInput	Intergenic	Intergenic	-693457	NR_024139	99890	Mm.393526	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding	0.02	0.366337
Merged-chr3-77332140-1	chr3	77332090	77332190	+	2.3	cIP1vsInput	Intergenic	Intergenic	1256557	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.257426
Merged-chr12-64161915-1	chr12	64161865	64161965	+	2.3	cIP2vsInput	Intergenic	Intergenic	312983	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.366337
Merged-chr10-66206185-1	chr10	66206135	66206235	+	2.3	cIP2vsInput	Intergenic	Intergenic	-82121	NR_038039	69433	Mm.23366	NR_038039		1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	miscRNA	0	0.247525
Merged-chr4-147498133-1	chr4	147498083	147498183	+	2.3	cIP2vsInput	"intron (NM_001039209, intron 1 of 2)"	"intron (NM_001039209, intron 1 of 2)"	-55144	NM_001014397	433804	Mm.332047	XM_003946328	ENSMUSG00000065999	Gm13154	OTTMUSG00000010673	predicted gene 13154	protein-coding	0	0.257426
Merged-chr6-18756596-1	chr6	18756546	18756646	+	2.3	cIP2vsInput	Intergenic	Intergenic	-92039	NM_133939	76522	Mm.275158	NM_133939	ENSMUSG00000044155	Naa38	2010003I05Rik|AW214405|Lsm8	"N(alpha)-acetyltransferase 38, NatC auxiliary subunit"	protein-coding	0.01	0.336634
Merged-chr16-70471593-1	chr16	70471543	70471643	+	2.3	cIP2vsInput	"intron (NM_028803, intron 7 of 15)"	"intron (NM_028803, intron 7 of 15)"	-144832	NR_040474	52645	Mm.188475	NR_040474		D16Ertd519e	-	"DNA segment, Chr 16, ERATO Doi 519, expressed"	miscRNA	0	0.207921
Merged-chr15-19374204-1	chr15	19374154	19374254	+	2.3	cIP1vsInput	Intergenic	Intergenic	553875	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0	0.29703
Merged-chr9-79289767-1	chr9	79289717	79289817	+	2.3	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	229535	NR_045336	100038575	Mm.367838	NR_045336		Gm10635	ENSMUSG00000074174	predicted gene 10635	miscRNA	0	0.326733
Merged-chr1-145099688-1	chr1	145099638	145099738	+	2.3	cIP2vsInput	Intergenic	Tigger1|DNA|TcMar-Tigger	-324267	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding	0	0.29703
Merged-chr2-5041216-1	chr2	5041166	5041266	+	2.3	cIP2vsInput	"intron (NM_181848, intron 5 of 14)"	"intron (NM_181848, intron 5 of 14)"	22722	NM_181848	71648	Mm.116942	NM_181848	ENSMUSG00000026672	Optn	4930441O07Rik|FIP2|HYPL|NRP	optineurin	protein-coding	0	0.277228
Merged-chr3-44307286-1	chr3	44307236	44307336	+	2.3	cIP1vsInput	Intergenic	Intergenic	1070974	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	miscRNA	0	0.306931
Merged-chrX-87619939-1	chrX	87619889	87619989	+	2.3	cIP1vsInput	"intron (NM_001160403, intron 2 of 10)"	"intron (NM_001160403, intron 2 of 10)"	495684	NM_001160403	331461	Mm.426143	NM_001160403		Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding	0	0.316832
Merged-chr7-29626936-1	chr7	29626886	29626986	+	2.3	cIP2vsInput	Intergenic	MYSERV16_I-int|LTR|ERVK	100079	NM_029714	76718	Mm.69030	NM_029714	ENSMUSG00000049123	Catsperg2	1700067C01Rik|CATSPERG	catsper channel auxiliary subunit gamma 2	protein-coding	0	0.346535
Merged-chr11-57352370-1	chr11	57352320	57352420	+	2.3	cIP2vsInput	Intergenic	Lx7|LINE|L1	166274	NM_001168667	67726	Mm.25632	NM_001168667	ENSMUSG00000020523	Fam114a2	1810073G14Rik|9030624B09Rik	"family with sequence similarity 114, member A2"	protein-coding	0	0.39604
Merged-chr2-109358645-1	chr2	109358595	109358695	+	2.3	cIP2vsInput	Intergenic	Intergenic	77907	NM_139303	228421	Mm.274086	NM_139303	ENSMUSG00000027115	Kif18a	AU024633|B130001M12Rik	kinesin family member 18A	protein-coding	0	0.326733
Merged-chr14-109612567-1	chr14	109612517	109612617	+	2.3	cIP2vsInput	Intergenic	Intergenic	152337	NR_039542	100628607		NR_039542	ENSMUSG00000092639	Mir3964	mmu-mir-3964|mu-mir-3964	microRNA 3964	miscRNA	0	0.326733
Merged-chr9-49684331-1	chr9	49684281	49684381	+	2.3	cIP1vsInput	"intron (NM_001113204, intron 1 of 18)"	"intron (NM_001113204, intron 1 of 18)"	114738	NM_001081445	17967	Mm.439182	NM_001081445		Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding	0.02	0.306931
Merged-chr13-87133758-1	chr13	87133708	87133808	+	2.3	cIP2vsInput	Intergenic	MYSERV-int|LTR|ERVK	-1086963	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0	0.316832
Merged-chr5-83382342-1	chr5	83382292	83382392	+	2.3	cIP2vsInput	Intergenic	Intergenic	-27147	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	"trans-2,3-enoyl-CoA reductase-like"	protein-coding	0.01	0.346535
Merged-chr17-67741418-1	chr17	67741368	67741468	+	2.3	cIP1vsInput	"intron (NM_008480, intron 5 of 62)"	(CCCTAA)n|Simple_repeat|Simple_repeat	44153	NM_008480	16772	Mm.303386	NM_008480	ENSMUSG00000032796	Lama1	AA408497|Lama	"laminin, alpha 1"	protein-coding	0	0.50495
Merged-chr6-44797744-1	chr6	44797694	44797794	+	2.3	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-262317	NM_001004357	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0	0.306931
Merged-chr3-67327274-1	chr3	67327224	67327324	+	2.3	cIP1vsInput	"intron (NM_025822, intron 7 of 9)"	L1_Mus3|LINE|L1	-46823	NM_010801	17349	Mm.10414	NM_001039543	ENSMUSG00000048416	Mlf1	HLS7	myeloid leukemia factor 1	protein-coding	0.01	0.435644
Merged-chr5-66936958-1	chr5	66936908	66937008	+	2.3	cIP2vsInput	"intron (NM_001001980, intron 3 of 25)"	"intron (NM_001001980, intron 3 of 25)"	-31458	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding	0.04	0.415842
Merged-chr5-5054674-1	chr5	5054624	5054724	+	2.3	cIP2vsInput	"intron (NM_011074, intron 8 of 14)"	LTR104_Mam|LTR|Gypsy	-296458	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled homolog 1 (Drosophila)	protein-coding	0	0.346535
Merged-chr11-117479272-1	chr11	117479222	117479322	+	2.3	cIP2vsInput	Intergenic	Intergenic	-131975	NR_015489	78403	Mm.212543	NR_015489		2900041M22Rik	-	RIKEN cDNA 2900041M22 gene	miscRNA	0.03	0.643564
Merged-chr16-71492071-1	chr16	71492021	71492121	+	2.3	cIP1vsInput	Intergenic	Intergenic	242167	NR_040576	78221	Mm.399298	NR_040576		4930567J20Rik	-	RIKEN cDNA 4930567J20 gene	miscRNA	0	0.257426
Merged-chr15-85036721-1	chr15	85036671	85036771	+	2.3	cIP2vsInput	promoter-TSS (NM_177067)	promoter-TSS (NM_177067)	-341	NM_177067	73225	Mm.247535	NM_133750	ENSMUSG00000022434	Fam118a	3110048E14Rik|C230014M12Rik	"family with sequence similarity 118, member A"	protein-coding	0.04	0.623762
Merged-chr14-113163401-1	chr14	113163351	113163451	+	2.3	cIP1vsInput	Intergenic	Intergenic	1141971	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0.02	0.356436
Merged-chr13-20747116-1	chr13	20747066	20747166	+	2.3	cIP1vsInput	Intergenic	Intergenic	-47003	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding	0	0.287129
Merged-chr14-71143845-1	chr14	71143795	71143895	+	2.3	cIP2vsInput	Intergenic	L1MD1|LINE|L1	-107428	NR_046075	100043132	Mm.399336	NR_046075		Gm4251	-	predicted gene 4251	miscRNA	0.01	0.29703
Merged-chr9-53595097-1	chr9	53595047	53595147	+	2.3	cIP1vsInput	"intron (NM_144784, intron 3 of 11)"	"intron (NM_144784, intron 3 of 11)"	15253	NM_144784	110446	Mm.293233	NM_144784	ENSMUSG00000032047	Acat1	6330585C21Rik|Acat	acetyl-Coenzyme A acetyltransferase 1	protein-coding	0	0.376238
Merged-chr6-148301705-1	chr6	148301655	148301755	+	2.3	cIP2vsInput	"intron (NM_198967, intron 9 of 19)"	"intron (NM_198967, intron 9 of 19)"	-52951	NR_003634	66184	Mm.391542	NR_003634	ENSMUSG00000063171	Rps4y2	1110033J19Rik|AA407494	"ribosomal protein S4, Y-linked 2"	pseudo	0	0.306931
Merged-chr5-7262461-1	chr5	7262411	7262511	+	2.3	cIP1vsInput	"intron (NM_001163223, intron 1 of 3)"	Lx7|LINE|L1	-41703	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding	0.01	0.366337
Merged-chr10-22019524-1	chr10	22019474	22019574	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	24858	NM_011361	20393	Mm.28405	NM_001161845	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding	0.01	0.346535
Merged-chr6-105654882-1	chr6	105654832	105654932	+	2.3	cIP2vsInput	Intergenic	Intergenic	-22863	NM_001109749	269784	Mm.321683	NM_001109749	ENSMUSG00000064293	Cntn4	9630050B05|Axcam|BIG-2	contactin 4	protein-coding	0	0.39604
Merged-chr8-119779491-1	chr8	119779441	119779541	+	2.3	cIP1vsInput	Intergenic	Intergenic	-1075	NM_028883	74347	Mm.358759	NM_028883	ENSMUSG00000034105	Tldc1	4632415K11Rik|Kiaa1609	TBC/LysM associated domain containing 1	protein-coding	0.02	0.475248
Merged-chr12-12959037-1	chr12	12958987	12959087	+	2.3	cIP1vsInput	Intergenic	Intergenic	-17201	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"	protein-coding	0	0.316832
Merged-chr7-6560509-1	chr7	6560459	6560559	+	2.3	cIP2vsInput	Intergenic	Lx3C|LINE|L1	-9484	NM_146389	258384	Mm.271316	NM_146389	ENSMUSG00000056696	Olfr1350	MOR222-3	olfactory receptor 1350	protein-coding	0.01	0.346535
Merged-chrX-83188088-1	chrX	83188038	83188138	+	2.3	cIP2vsInput	"intron (NM_007868, intron 2 of 78)"	"intron (NM_007868, intron 2 of 78)"	239218	NM_007868	13405	Mm.416750	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|mdx|pke	"dystrophin, muscular dystrophy"	protein-coding	0	0.29703
Merged-chr3-39283816-1	chr3	39283766	39283866	+	2.3	cIP1vsInput	Intergenic	Lx9|LINE|L1	396876	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT tumor suppressor homolog 4 (Drosophila)	protein-coding	0	0.435644
Merged-chr5-67663225-1	chr5	67663175	67663275	+	2.3	cIP2vsInput	"intron (NM_001038999, intron 27 of 36)"	"intron (NM_001038999, intron 27 of 36)"	55342	NM_001033415	330096	Mm.442747	NM_001033415	ENSMUSG00000050010	Shisa3	D830007B15Rik	shisa homolog 3 (Xenopus laevis)	protein-coding	0	0.287129
Merged-chr15-40461047-1	chr15	40460997	40461097	+	2.3	cIP2vsInput	Intergenic	Intergenic	66230	NR_046185	432945	Mm.321981	NR_046185	ENSMUSG00000056332	Gm16294	EG432945|OTTMUSG00000033304	predicted gene 16294	miscRNA	0	0.287129
Merged-chr15-16450773-1	chr15	16450723	16450823	+	2.3	cIP1vsInput	Intergenic	Intergenic	-327328	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0.01	0.376238
Merged-chr5-51185674-1	chr5	51185624	51185724	+	2.3	cIP2vsInput	Intergenic	Intergenic	368247	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PGC-1v|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	"peroxisome proliferative activated receptor, gamma, coactivator 1 alpha"	protein-coding	0.01	0.356436
Merged-chr14-116151147-1	chr14	116151097	116151197	+	2.3	cIP2vsInput	"intron (NM_175500, intron 7 of 7)"	"intron (NM_175500, intron 7 of 7)"	-741595	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	miscRNA	0	0.316832
Merged-chr8-121786737-1	chr8	121786687	121786787	+	2.3	cIP2vsInput	"intron (NM_020605, intron 4 of 4)"	"intron (NM_020605, intron 4 of 4)"	42832	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding	0.01	0.524752
Merged-chr4-77424017-1	chr4	77423967	77424067	+	2.3	cIP2vsInput	"intron (NM_011211, intron 4 of 39)"	"intron (NM_011211, intron 4 of 39)"	787878	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0.01	0.366337
Merged-chr5-112584201-1	chr5	112584151	112584251	+	2.3	cIP1vsInput	"non-coding (NR_045396, exon 4 of 5)"	"non-coding (NR_045396, exon 4 of 5)"	5795	NR_045397	67325	Mm.490791	NR_045396		1700034G24Rik	-	RIKEN cDNA 1700034G24 gene	miscRNA	0	0.366337
Merged-chr6-19206396-1	chr6	19206346	19206446	+	2.3	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	340078	NM_001167757	75196	Mm.67665	NM_001167757	ENSMUSG00000029517	Ankrd7	4930532L20Rik|AV278427	ankyrin repeat domain 7	protein-coding	0	0.366337
Merged-chr12-119645647-1	chr12	119645597	119645697	+	2.3	cIP2vsInput	Intergenic	Intergenic	202237	NM_001163136	238455	Mm.31376	NM_001163136	ENSMUSG00000041886	Macc1	4732474O15Rik|Gm267	metastasis associated in colon cancer 1	protein-coding	0.01	0.336634
Merged-chr1-55196255-1	chr1	55196205	55196305	+	2.3	cIP1vsInput	"intron (NM_028713, intron 5 of 8)"	"intron (NM_028713, intron 5 of 8)"	30527	NM_028713	74013	Mm.292050	NM_028713	ENSMUSG00000025978	Rftn2	2700010E02Rik|3222401M22Rik	raftlin family member 2	protein-coding	0	0.316832
Merged-chr10-102274948-1	chr10	102274898	102274998	+	2.3	cIP2vsInput	"intron (NM_001162369, intron 1 of 5)"	"intron (NM_001162369, intron 1 of 5)"	-99489	NM_026243	67569	Mm.403713	NM_001162368	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"	protein-coding	0.01	0.376238
Merged-chr2-123618737-1	chr2	123618687	123618787	+	2.3	cIP2vsInput	Intergenic	Intergenic	511219	NR_040611	74702	Mm.410814	NR_040611	ENSMUSG00000085496	4930517E11Rik	-	RIKEN cDNA 4930517E11 gene	miscRNA	0.01	0.326733
Merged-chr5-80991573-1	chr5	80991523	80991623	+	2.3	cIP1vsInput	Intergenic	L1MA5|LINE|L1	-30020	NM_198702	319387	Mm.461016	NM_198702	ENSMUSG00000037605	Lphn3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|mKIAA0768	latrophilin 3	protein-coding	0	0.356436
Merged-chr14-107804157-1	chr14	107804107	107804207	+	2.3	cIP2vsInput	Intergenic	L1VL4|LINE|L1	1110082	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	"SLIT and NTRK-like family, member 1"	protein-coding	0	0.376238
Merged-chr17-16571862-1	chr17	16571812	16571912	+	2.3	cIP1vsInput	Intergenic	Intergenic	-492241	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding	0	0.306931
Merged-chr3-51516057-1	chr3	51516007	51516107	+	2.3	cIP2vsInput	"3' UTR (NM_080793, exon 8 of 8)"	"3' UTR (NM_080793, exon 8 of 8)"	32091	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	"RAB33B, member of RAS oncogene family"	protein-coding	0	0.287129
Merged-chr9-42264552-1	chr9	42264502	42264602	+	2.3	cIP1vsInput	promoter-TSS (NM_172769)	promoter-TSS (NM_172769)	-252	NM_172769	235293	Mm.470142	NM_172769	ENSMUSG00000032018	Sc5d	A830037K02|A830073K23Rik|Sc5dl	"sterol-C5-desaturase (fungal ERG3, delta-5-desaturase) homolog (S. cerevisae)"	protein-coding	0.05	0.50495
Merged-chr13-10644992-1	chr13	10644942	10645042	+	2.3	cIP2vsInput	Intergenic	L1M5|LINE|L1	-284189	NM_033269	12671	Mm.342315	NM_033269		Chrm3	Chrm-3|M3|M3R	"cholinergic receptor, muscarinic 3, cardiac"	protein-coding	0.01	0.336634
Merged-chr6-53749217-1	chr6	53749167	53749267	+	2.3	cIP2vsInput	Intergenic	L1MEc|LINE|L1	71608	NM_025817	66873	Mm.480530	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding	0	0.346535
Merged-chr6-21200407-1	chr6	21200357	21200457	+	2.3	cIP2vsInput	Intergenic	RLTR44-int|LTR|ERVK	-15702	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	"potassium voltage-gated channel, Shal-related family, member 2"	protein-coding	0	0.356436
Merged-chr15-80948539-1	chr15	80948489	80948589	+	2.3	cIP2vsInput	promoter-TSS (NM_009634)	promoter-TSS (NM_009634)	49	NM_009634	11564	Mm.38151	NM_009634		Adsl	Adl|Asl	adenylosuccinate lyase	protein-coding	0.09	0.623762
Merged-chr14-119113475-1	chr14	119113425	119113525	+	2.3	cIP2vsInput	Intergenic	Intergenic	-14041	NM_001081252	66435	Mm.490593	NM_025561	ENSMUSG00000042104	Uggt2	1810064L21Rik|3110001A05Rik|3110027P15Rik|A230065J02Rik|AW047562|Ugcgl2	UDP-glucose glycoprotein glucosyltransferase 2	protein-coding	0	0.277228
Merged-chr11-10803826-1	chr11	10803776	10803876	+	2.3	cIP1vsInput	Intergenic	Intergenic	-310190	NM_177033	319922	Mm.487612	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding	0.02	0.316832
Merged-chr2-20005655-1	chr2	20005605	20005705	+	2.3	cIP2vsInput	Intergenic	Lx3_Mus|LINE|L1	-284258	NM_001081006	208618	Mm.237935	NM_001081006	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding	0.01	0.316832
Merged-chr18-14368057-1	chr18	14368007	14368107	+	2.3	cIP2vsInput	Intergenic	Intergenic	135751	NR_045373	74529	Mm.400519	NR_045373		8430422H06Rik	-	RIKEN cDNA 8430422H06 gene	miscRNA	0	0.336634
Merged-chr11-24168119-1	chr11	24168069	24168169	+	2.3	cIP2vsInput	"3' UTR (NM_001242934, exon 4 of 4)"	"3' UTR (NM_001242934, exon 4 of 4)"	87424	NM_001159290	14025	Mm.53687	NM_001159289	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding	0.01	0.306931
Merged-chr16-61219610-1	chr16	61219560	61219660	+	2.3	cIP1vsInput	Intergenic	Intergenic	-614079	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0	0.346535
Merged-chr8-85796649-1	chr8	85796599	85796699	+	2.3	cIP2vsInput	"intron (NM_028007, intron 6 of 17)"	RLTR22_Mur|LTR|ERVK	44300	NM_028007	71927	Mm.61018	NM_028007	ENSMUSG00000031703	Itfg1	2310047C21Rik|AI314457|Cda08|D8Wsu49e	integrin alpha FG-GAP repeat containing 1	protein-coding	0	0.336634
Merged-chr5-103083397-1	chr5	103083347	103083447	+	2.3	cIP2vsInput	"intron (NM_001081567, intron 2 of 13)"	L1_Mur2|LINE|L1	127937	NM_001081567	26414	Mm.472459	NM_001081567	ENSMUSG00000046709	Mapk10	C230008H04Rik|JNK3|JNK3B1|JNK3B2|SAPK(beta)|Serk2|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding	0	0.336634
Merged-chr16-73623869-1	chr16	73623819	73623919	+	2.3	cIP2vsInput	Intergenic	Intergenic	718198	NR_030464	751561		NR_030464		Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	miscRNA	0	0.356436
Merged-chr14-116740931-1	chr14	116740881	116740981	+	2.3	cIP2vsInput	Intergenic	L1MC1|LINE|L1	-184384	NM_001079844	23888	Mm.440025	NM_001079844	ENSMUSG00000058571	Gpc6	6720429C22Rik|AI480529	glypican 6	protein-coding	0	0.306931
Merged-chr15-53735641-1	chr15	53735591	53735691	+	2.3	cIP2vsInput	"intron (NM_177225, intron 2 of 4)"	"intron (NM_177225, intron 2 of 4)"	166795	NM_177225	320679	Mm.442455	NM_177225	ENSMUSG00000058656	Samd12	A830094I09Rik	sterile alpha motif domain containing 12	protein-coding	0	0.326733
Merged-chr4-124448323-1	chr4	124448273	124448373	+	2.3	cIP2vsInput	Intergenic	L1ME1|LINE|L1	37636	NR_040774	78460	Mm.452060	NR_040774		1700057H15Rik	-	RIKEN cDNA 1700057H15 gene	miscRNA	0	0.316832
Merged-chr18-17356397-1	chr18	17356347	17356447	+	2.3	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-120915	NR_033607	664619	Mm.250005	NR_033607		4921533I20Rik	-	PRP18 pre-mRNA processing factor 18 homolog pseudogene	pseudo	0	0.336634
Merged-chr12-41182357-1	chr12	41182307	41182407	+	2.3	cIP2vsInput	Intergenic	Intergenic	303700	NM_001271708	16981	Mm.39913	NM_001271708	ENSMUSG00000036295	Lrrn3	NLRR-3	"leucine rich repeat protein 3, neuronal"	protein-coding	0	0.336634
Merged-chr3-5796199-1	chr3	5796149	5796249	+	2.3	cIP1vsInput	Intergenic	Intergenic	-219951	NM_001163305	19302	Mm.132336	NM_001163304	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding	0	0.415842
Merged-chr3-151709854-1	chr3	151709804	151709904	+	2.3	cIP1vsInput	Intergenic	L1M5|LINE|L1	40105	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding	0.01	0.346535
Merged-chr8-38905951-1	chr8	38905901	38906001	+	2.3	cIP2vsInput	Intergenic	Intergenic	-99916	NM_030254	80286	Mm.272722	NM_030254		Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding	0.02	0.39604
Merged-chr3-74882214-1	chr3	74882164	74882264	+	2.3	cIP2vsInput	Intergenic	L1ME1|LINE|L1	261509	NM_172515	213234	Mm.80075	NM_172515	ENSMUSG00000034151	Zbbx	4931432L23	"zinc finger, B-box domain containing"	protein-coding	0.02	0.316832
Merged-chr12-28266033-1	chr12	28265983	28266083	+	2.3	cIP2vsInput	Intergenic	MusHAL1|LINE|L1	282304	NM_001177964	68511	Mm.310284	NM_001177964		Dcdc2c	1110015M06Rik	doublecortin domain containing 2C	protein-coding	0	0.316832
Merged-chr9-85778007-1	chr9	85777957	85778057	+	2.3	cIP1vsInput	Intergenic	Intergenic	-28673	NM_001081282	108837	Mm.487092	NM_175371	ENSMUSG00000035941	Ibtk	5430411K16Rik|AA409502|BTKI|mKIAA1417	inhibitor of Bruton agammaglobulinemia tyrosine kinase	protein-coding	0.01	0.376238
Merged-chr2-72065968-1	chr2	72065918	72066018	+	2.3	cIP2vsInput	"intron (NM_001204166, intron 1 of 27)"	MER45B|DNA|hAT-Tip100	11351	NM_001204166	56508	Mm.196153	NM_001204165	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding	0	0.316832
Merged-chr9-37788085-1	chr9	37788035	37788135	+	2.3	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	15448	NM_146749	258744	Mm.347661	NM_146749	ENSMUSG00000058628	Olfr875	MOR161-4	olfactory receptor 875	protein-coding	0.01	0.425743
Merged-chr3-120722209-1	chr3	120722159	120722259	+	2.3	cIP1vsInput	Intergenic	L1VL4|LINE|L1	449486	NM_028456	66568	Mm.263163	NM_025637	ENSMUSG00000028133	Rwdd3	2510027J23Rik|3110037C01Rik|AI035684|AI662458|X2CR1	RWD domain containing 3	protein-coding	0	0.346535
Merged-chr1-91313450-1	chr1	91313400	91313500	+	2.3	cIP2vsInput	"intron (NM_016717, intron 7 of 11)"	"intron (NM_016717, intron 7 of 11)"	-8625	NM_001033292	227357	Mm.318167	NM_001033292	ENSMUSG00000049515	Espnl	Gm556	espin-like	protein-coding	0.01	0.524752
Merged-chr13-87061191-1	chr13	87061141	87061241	+	2.3	cIP1vsInput	Intergenic	Intergenic	-1014396	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0	0.247525
Merged-chr2-68170537-1	chr2	68170487	68170587	+	2.3	cIP2vsInput	Intergenic	Intergenic	65865	NM_020283	26877	Mm.490783	NM_020283	ENSMUSG00000034780	B3galt1	beta3Gal-T1	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1"	protein-coding	0	0.415842
Merged-chrX-18235981-1	chrX	18235931	18236031	+	2.3	cIP2vsInput	"intron (NM_009483, intron 7 of 28)"	"intron (NM_009483, intron 7 of 28)"	73314	NM_009483	22289	Mm.417709	NM_009483	ENSMUSG00000037369	Kdm6a	Utx	lysine (K)-specific demethylase 6A	protein-coding	0.02	0.316832
Merged-chr4-21177175-1	chr4	21177125	21177225	+	2.3	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-398507	NM_172987	269513		NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding	0	0.306931
Merged-chr13-116278991-1	chr13	116278941	116279041	+	2.3	cIP2vsInput	Intergenic	Intergenic	30697	NM_021459	16392	Mm.42242	NM_021459	ENSMUSG00000042258	Isl1	-	"ISL1 transcription factor, LIM/homeodomain"	protein-coding	0	0.356436
Merged-chr16-28840052-1	chr16	28840002	28840102	+	2.3	cIP2vsInput	"intron (NM_177718, intron 1 of 1)"	"intron (NM_177718, intron 1 of 1)"	-86809	NM_010199	14167	Mm.7996	NM_001276419	ENSMUSG00000022523	Fgf12	AV114868|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding	0	0.445545
Merged-chr1-78629721-1	chr1	78629671	78629771	+	2.3	cIP1vsInput	Intergenic	Intergenic	-28104	NM_001033606	74205	Mm.276016	NM_001033606	ENSMUSG00000032883	Acsl3	2610510B12Rik|Acs3|C85929|Facl3|Pro2194	acyl-CoA synthetase long-chain family member 3	protein-coding	0	0.336634
Merged-chr13-74655785-1	chr13	74655735	74655835	+	2.3	cIP2vsInput	"intron (NM_030711, intron 2 of 18)"	L1_Mur2|LINE|L1	15913	NM_030711	80898	Mm.83526	NM_030711	ENSMUSG00000021583	Erap1	Arts1|ERAAP|PILSA|PILSAP	endoplasmic reticulum aminopeptidase 1	protein-coding	0	0.366337
Merged-chr15-49227403-1	chr15	49227353	49227453	+	2.3	cIP2vsInput	Intergenic	MTD|LTR|ERVL-MaLR	-435414	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0	0.326733
Merged-chr9-44570074-1	chr9	44570024	44570124	+	2.3	cIP2vsInput	Intergenic	L1ME4c|LINE|L1	-34818	NM_001110826	13209	Mm.267061	NM_001110826	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding	0.02	0.29703
Merged-chr16-57945950-1	chr16	57945900	57946000	+	2.3	cIP2vsInput	Intergenic	Intergenic	-191213	NM_007739	12837	Mm.130388	NM_007739	ENSMUSG00000068196	Col8a1	Col8a-1	"collagen, type VIII, alpha 1"	protein-coding	0.01	0.306931
Merged-chr3-110997610-1	chr3	110997560	110997660	+	2.3	cIP2vsInput	Intergenic	Lx|LINE|L1	-746612	NR_024139	99890	Mm.393526	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding	0.01	0.326733
Merged-chr15-102722165-1	chr15	102722115	102722215	+	2.3	cIP2vsInput	promoter-TSS (NM_026192)	promoter-TSS (NM_026192)	13	NM_026192	67488	Mm.71682	NM_026192	ENSMUSG00000023055	Calcoco1	1810009B06Rik|Cocoa|Gcap11|mKIAA1536	calcium binding and coiled coil domain 1	protein-coding	0.03	0.534653
Merged-chr19-5309147-1	chr19	5309097	5309197	+	2.3	cIP2vsInput	TTS (NM_001024717)	TTS (NM_001024717)	10816	NM_001024717	545276	Mm.447174	NM_001024717	ENSMUSG00000047658	Gal3st3	-	galactose-3-O-sulfotransferase 3	protein-coding	0.01	0.594059
Merged-chr2-89601575-1	chr2	89601525	89601625	+	2.3	cIP2vsInput	Intergenic	L1M3|LINE|L1	8578	NM_146966	258968	Mm.489196	NM_146966	ENSMUSG00000075081	Olfr1247	MOR231-6	olfactory receptor 1247	protein-coding	0.02	0.366337
Merged-chr14-111879884-1	chr14	111879834	111879934	+	2.3	cIP2vsInput	Intergenic	Intergenic	-141546	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0	0.346535
Merged-chr4-89755265-1	chr4	89755215	89755315	+	2.3	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	67067	NM_175647	242523	Mm.130167	NM_175647	ENSMUSG00000043753	Dmrta1	Dmrt4	doublesex and mab-3 related transcription factor like family A1	protein-coding	0	0.39604
Merged-chr5-45481700-1	chr5	45481650	45481750	+	2.3	cIP2vsInput	Intergenic	Intergenic	-11674	NM_024434	66988	Mm.286830	NM_024434	ENSMUSG00000039682	Lap3	2410015L10Rik|AA410100|LAP-3|Lap|Lapep|Pep-7|Pep-S|Pep7|Peps	leucine aminopeptidase 3	protein-coding	0	0.386139
Merged-chr14-67329143-1	chr14	67329093	67329193	+	2.3	cIP2vsInput	"intron (NM_001276387, intron 7 of 16)"	"intron (NM_001276387, intron 7 of 16)"	-14432	NM_001037931	628416	Mm.390723	NM_001037931	ENSMUSG00000075549	Gm6878	EG628416	predicted gene 6878	protein-coding	0	0.277228
Merged-chr5-86575338-1	chr5	86575288	86575388	+	2.3	cIP1vsInput	"intron (NM_178730, intron 2 of 10)"	L1M2|LINE|L1	-56738	NM_177162	320454	Mm.184522	NM_177162	ENSMUSG00000079451	Tmprss11g	9930032O22Rik|Desc4	"transmembrane protease, serine 11g"	protein-coding	0	0.326733
Merged-chr12-45275495-1	chr12	45275445	45275545	+	2.3	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-201012	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding	0.01	0.346535
Merged-chr14-35546420-1	chr14	35546370	35546470	+	2.3	cIP2vsInput	"intron (NM_008166, intron 13 of 15)"	L1_Rod|LINE|L1	265558	NM_001033766	239036	Mm.239970	NM_001033766	ENSMUSG00000041068	4930596D02Rik	-	RIKEN cDNA 4930596D02 gene	protein-coding	0	0.386139
Merged-chr15-63076136-1	chr15	63076086	63076186	+	2.3	cIP1vsInput	Intergenic	L1Md_A|LINE|L1	403472	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	"predicted gene, 20740"	miscRNA	0	0.346535
Merged-chr10-109391339-1	chr10	109391289	109391389	+	2.3	cIP1vsInput	Intergenic	Lx6|LINE|L1	-380364	NM_001252341	20979	Mm.489829	NM_001252341	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding	0.01	0.306931
Merged-chr7-86136200-1	chr7	86136150	86136250	+	2.3	cIP2vsInput	Intergenic	MurERV4_19-int|LTR|ERVK	35524	NM_001102578	546981	Mm.469835	NM_001102578	ENSMUSG00000090436	Vmn2r75	EG546981	"vomeronasal 2, receptor 75"	protein-coding	0.01	0.287129
Merged-chr4-4707353-1	chr4	4707303	4707403	+	2.3	cIP2vsInput	Intergenic	Intergenic	85953	NM_177730	242291	Mm.369779	NM_177730		Impad1	1110001C20Rik|AA408880|AI451589|AL022796|B230207P20|Jaws|gPAPP	inositol monophosphatase domain containing 1	protein-coding	0.01	0.336634
Merged-chr5-78392315-1	chr5	78392265	78392365	+	2.3	cIP1vsInput	Intergenic	Intergenic	-880567	NR_027806	231332	Mm.373616	NM_001010832		Pea15b	-	phosphoprotein enriched in astrocytes 15B	pseudo	0	0.39604
Merged-chr18-52137148-1	chr18	52137098	52137198	+	2.3	cIP2vsInput	Intergenic	Intergenic	-13602	NR_029788	723830		NR_029788		Mir28	Mirn28|mmu-mir-28	microRNA 28	miscRNA	0	0.306931
Merged-chr1-100114222-1	chr1	100114172	100114272	+	2.3	cIP2vsInput	"intron (NM_172851, intron 7 of 23)"	"intron (NM_172851, intron 7 of 23)"	341457	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding	0	0.356436
Merged-chr17-64509348-1	chr17	64509298	64509398	+	2.3	cIP2vsInput	Intergenic	Intergenic	46242	NR_045899	100043582	Mm.11170	NR_045899	ENSMUSG00000073377	AU016765	-	expressed sequence AU016765	miscRNA	0.01	0.366337
Merged-chrX-83131442-1	chrX	83131392	83131492	+	2.3	cIP2vsInput	"intron (NM_007868, intron 1 of 78)"	"intron (NM_007868, intron 1 of 78)"	182572	NM_007868	13405	Mm.416750	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|mdx|pke	"dystrophin, muscular dystrophy"	protein-coding	0	0.346535
Merged-chr10-104723744-1	chr10	104723694	104723794	+	2.3	cIP1vsInput	Intergenic	Intergenic	529702	NM_001270900	667692		NM_001270900	ENSMUSG00000097878	Gm8764	EG667692	predicted gene 8764	protein-coding	0	0.277228
Merged-chr8-119862378-1	chr8	119862328	119862428	+	2.3	cIP2vsInput	promoter-TSS (NM_146219)	promoter-TSS (NM_146219)	73	NM_146219	234796	Mm.86446	NM_146219	ENSMUSG00000031828	Klhl36	-	kelch-like 36	protein-coding	0.14	0.742574
Merged-chr7-53128221-1	chr7	53128171	53128271	+	2.3	cIP1vsInput	Intergenic	Intergenic	-1112505	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding	0	0.287129
Merged-chr14-114692354-1	chr14	114692304	114692404	+	2.3	cIP2vsInput	Intergenic	Intergenic	-139611	NR_045661	75822	Mm.410813	NR_045661		4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	miscRNA	0.01	0.306931
Merged-chr14-76940971-1	chr14	76940921	76941021	+	2.3	cIP1vsInput	Intergenic	Intergenic	95646	NM_172488	210808	Mm.89278	NM_172488	ENSMUSG00000044350	Lacc1	9030625A04Rik	laccase (multicopper oxidoreductase) domain containing 1	protein-coding	0	0.386139
Merged-chr13-85421121-1	chr13	85421071	85421171	+	2.3	cIP1vsInput	Intergenic	RMER20B|LTR|ERVK	-131635	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding	0.01	0.336634
Merged-chr4-147789052-1	chr4	147789002	147789102	+	2.3	cIP1vsInput	"intron (NM_001127189, intron 3 of 5)"	MYSERV16_I-int|LTR|ERVK	20736	NM_001127189	100041677	Mm.327194	NM_001127189	ENSMUSG00000078495	Gm13157	OTTMUSG00000010679|Rp23-282c23.7	predicted gene 13157	protein-coding	0.01	0.376238
Merged-chr4-4277660-1	chr4	4277610	4277710	+	2.3	cIP1vsInput	Intergenic	L1MA4A|LINE|L1	-139215	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding	0.01	0.326733
Merged-chr17-90525774-1	chr17	90525724	90525824	+	2.3	cIP2vsInput	"intron (NM_020252, intron 17 of 22)"	"intron (NM_020252, intron 17 of 22)"	-335395	NR_045463	78800	Mm.410772	NR_045463	ENSMUSG00000090160	4930480K15Rik	-	RIKEN cDNA 4930480K15 gene	miscRNA	0.01	0.376238
Merged-chr10-109539481-1	chr10	109539431	109539531	+	2.3	cIP2vsInput	Intergenic	Intergenic	460738	NM_001081035	260315	Mm.461280	NM_001081035	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding	0.01	0.346535
Merged-chr7-18892390-1	chr7	18892340	18892440	+	2.3	cIP2vsInput	"intron (NM_001033314, intron 10 of 13)"	CpG	7700	NM_009402	21946	Mm.21855	NM_009402	ENSMUSG00000030413	Pglyrp1	PGRP|PGRP-S|Pglyrp|Tag7|Tasg7|Tnfsf3l	peptidoglycan recognition protein 1	protein-coding	0.06	0.673267
Merged-chr3-58218880-1	chr3	58218830	58218930	+	2.3	cIP2vsInput	Intergenic	L1VL2|LINE|L1	-55073	NR_040538	67850	Mm.416968	NR_040538		1700007F19Rik	-	RIKEN cDNA 1700007F19 gene	miscRNA	0	0.326733
Merged-chr3-24299672-1	chr3	24299622	24299722	+	2.3	cIP2vsInput	Intergenic	Intergenic	1853635	NM_001163387	192167	Mm.316080	NM_001163387	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|mKIAA1070	neuroligin 1	protein-coding	0	0.346535
Merged-chr10-125245744-1	chr10	125245694	125245794	+	2.3	cIP2vsInput	"intron (NM_011391, intron 4 of 6)"	Lx5|LINE|L1	82791	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	"solute carrier family 16 (monocarboxylic acid transporters), member 7"	protein-coding	0.01	0.306931
Merged-chr19-10635244-1	chr19	10635194	10635294	+	2.3	cIP2vsInput	"intron (NM_027913, intron 1 of 19)"	"intron (NM_027913, intron 1 of 19)"	1011	NM_027913	71768	Mm.169261	NM_027913	ENSMUSG00000043789	Vwce	1300015B04Rik	von Willebrand factor C and EGF domains	protein-coding	0.05	0.663366
Merged-chr9-124295064-1	chr9	124295014	124295114	+	2.3	cIP1vsInput	"intron (NM_001243119, intron 3 of 3)"	MurSatRep1|Unknown|Unknown	17630	NM_001243118	630836	Mm.458553	NM_001243117		2010315B03Rik	BC029716	RIKEN cDNA 2010315B03 gene	protein-coding	0	0.346535
Merged-chr3-118836754-1	chr3	118836704	118836804	+	2.3	cIP2vsInput	"intron (NM_170778, intron 8 of 22)"	"intron (NM_170778, intron 8 of 22)"	274576	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding	0	0.287129
Merged-chr3-144948253-1	chr3	144948203	144948303	+	2.3	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	-15724	NM_001033199	99709	Mm.440040	NM_001033199	ENSMUSG00000074195	AI747448	Clca7	expressed sequence AI747448	protein-coding	0	0.277228
Merged-chr18-11034901-1	chr18	11034851	11034951	+	2.3	cIP1vsInput	Intergenic	ID_B1|SINE|B4	-17609	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding	0	0.356436
Merged-chr14-115744221-1	chr14	115744171	115744271	+	2.3	cIP1vsInput	"intron (NM_175500, intron 6 of 7)"	"intron (NM_175500, intron 6 of 7)"	-334669	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	miscRNA	0.01	0.257426
Merged-chr3-3485222-1	chr3	3485172	3485272	+	2.3	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	-22808	NM_013920	30942	Mm.330897	NM_013920		Hnf4g	NR2A2	"hepatocyte nuclear factor 4, gamma"	protein-coding	0	0.405941
Merged-chr18-66269112-1	chr18	66269062	66269162	+	2.3	cIP2vsInput	"intron (NM_178793, intron 2 of 10)"	"intron (NM_178793, intron 2 of 10)"	22726	NM_178793	320924	Mm.442049	NM_178793	ENSMUSG00000046318	Ccbe1	4933426F18Rik|9430093N24Rik|mKIAA1983	collagen and calcium binding EGF domains 1	protein-coding	0.01	0.326733
Merged-chr3-47057900-1	chr3	47057850	47057950	+	2.3	cIP1vsInput	Intergenic	Intergenic	-609959	NM_001101479	241989	Mm.475785	NM_001101479	ENSMUSG00000090919	Pabpc4l	C330050A14Rik|EG241989	"poly(A) binding protein, cytoplasmic 4-like"	protein-coding	0.01	0.336634
Merged-chr8-43981502-1	chr8	43981452	43981552	+	2.3	cIP2vsInput	Intergenic	Intergenic	-282011	NM_001079931	384814	Mm.383288	NM_001079931		Gm5347	EG384814	predicted gene 5347	protein-coding	0	0.336634
Merged-chr13-35554673-1	chr13	35554623	35554723	+	2.3	cIP2vsInput	Intergenic	Lx8|LINE|L1	-105189	NM_009881	12593	Mm.29002	NM_001123386	ENSMUSG00000059288	Cdyl	AI325931	"chromodomain protein, Y chromosome-like"	protein-coding	0.01	0.326733
Merged-chr2-78115664-1	chr2	78115614	78115714	+	2.3	cIP2vsInput	Intergenic	Intergenic	-121883	NM_177843	329436	Mm.235448	NM_177843		Gm14461	A830093M07|OTTMUSG00000016703	predicted gene 14461	protein-coding	0	0.287129
Merged-chr15-13985823-1	chr15	13985773	13985873	+	2.3	cIP2vsInput	Intergenic	(CAAAAA)n|Simple_repeat|Simple_repeat	-812184	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	K-cadherin|cad6|cadherin-6	cadherin 6	protein-coding	0	0.287129
Merged-chr13-71332386-1	chr13	71332336	71332436	+	2.3	cIP1vsInput	Intergenic	Intergenic	449438	NM_029873	77166	Mm.159859	NM_029873	ENSMUSG00000021600	8030423J24Rik	-	RIKEN cDNA 8030423J24 gene	protein-coding	0.01	0.445545
Merged-chr3-3215697-1	chr3	3215647	3215747	+	2.3	cIP2vsInput	Intergenic	Lx2B|LINE|L1	-292333	NM_013920	30942	Mm.330897	NM_013920		Hnf4g	NR2A2	"hepatocyte nuclear factor 4, gamma"	protein-coding	0	0.316832
Merged-chr4-120951817-1	chr4	120951767	120951867	+	2.3	cIP1vsInput	promoter-TSS (NM_001005788)	promoter-TSS (NM_001005788)	-116	NM_001005788	381549	Mm.331840	NM_001005788	ENSMUSG00000064141	Zfp69	Gm1029|Krab2|Zfp63	zinc finger protein 69	protein-coding	0.12	0.772277
Merged-chr11-29897043-1	chr11	29896993	29897093	+	2.3	cIP1vsInput	"intron (NM_146016, intron 4 of 41)"	"intron (NM_146016, intron 4 of 41)"	-71375	NM_176829	216622	Mm.443260	NM_176829	ENSMUSG00000078157	4931440F15Rik	Fem1ab	RIKEN cDNA 4931440F15 gene	protein-coding	0.02	0.29703
Merged-chr1-128906683-1	chr1	128906633	128906733	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-314384	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r	chemokine (C-X-C motif) receptor 4	protein-coding	0	0.376238
Merged-chr4-93135676-1	chr4	93135626	93135726	+	2.3	cIP2vsInput	Intergenic	Intergenic	199835	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding	0.01	0.376238
Merged-chr12-35831784-1	chr12	35831734	35831834	+	2.3	cIP2vsInput	Intergenic	Intergenic	-93837	NM_207531	403205	Mm.190508	NM_207531	ENSMUSG00000036231	Agr3	BCMP11|E030025L21Rik|Gm888	anterior gradient 3	protein-coding	0.02	0.316832
Merged-chr17-74489268-1	chr17	74489218	74489318	+	2.3	cIP1vsInput	promoter-TSS (NM_026417)	promoter-TSS (NM_026417)	-225	NM_026417	67864	Mm.41891	NM_026417	ENSMUSG00000024072	Yipf4	2310034L04Rik	"Yip1 domain family, member 4"	protein-coding	0.04	0.376238
Merged-chr1-30614136-1	chr1	30614086	30614186	+	2.3	cIP2vsInput	Intergenic	L1VL4|LINE|L1	249120	NM_001081080	213109	Mm.486727	NM_001081080	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding	0.01	0.326733
Merged-chr9-47193149-1	chr9	47193099	47193199	+	2.3	cIP2vsInput	Intergenic	L1MD2|LINE|L1	194408	NM_001243258	215467	Mm.246572	NM_001243258		Gm4791	D930036J05	predicted gene 4791	protein-coding	0	0.336634
Merged-chr18-57414312-1	chr18	57414262	57414362	+	2.3	cIP2vsInput	Intergenic	Intergenic	-54174	NM_001134697	629147	Mm.57415	NM_001134697	ENSMUSG00000069372	Ctxn3	ENSMUSG00000069372	cortexin 3	protein-coding	0.02	0.356436
Merged-chr9-23549145-1	chr9	23549095	23549195	+	2.3	cIP1vsInput	Intergenic	Intergenic	326069	NM_028472	73230	Mm.335020	NM_028472	ENSMUSG00000031963	Bmper	3110056H04Rik|CV-2|Crim3|Cv2	BMP-binding endothelial regulator	protein-coding	0	0.316832
Merged-chr15-3756960-1	chr15	3756910	3757010	+	2.3	cIP2vsInput	Intergenic	RMER4B|LTR|ERVK	-173730	NM_010284	14600	Mm.3986	NM_001048147	ENSMUSG00000055737	Ghr	AA986417|GHBP|GHR/BP	growth hormone receptor	protein-coding	0	0.386139
Merged-chr3-113649177-1	chr3	113649127	113649227	+	2.3	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-19028	NM_001038696	67225	Mm.316928	NM_001038696	ENSMUSG00000027981	Rnpc3	2810441O16Rik|AI447568|C030014B17Rik	"RNA-binding region (RNP1, RRM) containing 3"	protein-coding	0	0.326733
Merged-chr15-78584870-1	chr15	78584820	78584920	+	2.3	cIP1vsInput	Intergenic	L1MA9|LINE|L1	-12087	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding	0.01	0.475248
Merged-chr3-141322584-1	chr3	141322534	141322634	+	2.3	cIP2vsInput	Intergenic	Intergenic	-110229	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0.01	0.316832
Merged-chr15-60057642-1	chr15	60057592	60057692	+	2.3	cIP2vsInput	Intergenic	Intergenic	-41024	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding	0.01	0.346535
Merged-chr15-78448169-1	chr15	78448119	78448219	+	2.3	cIP1vsInput	"intron (NM_027902, intron 10 of 17)"	"intron (NM_027902, intron 10 of 17)"	19541	NM_001081367	72844	Mm.390816	NM_001081367		Kctd17	2900008M13Rik|AA414907|AW742389|N28155	potassium channel tetramerisation domain containing 17	protein-coding	0.02	0.415842
Merged-chr3-114563733-1	chr3	114563683	114563783	+	2.3	cIP1vsInput	Intergenic	Intergenic	-299520	NR_030469	735255		NR_030469		Mir669b	Mirn669b	microRNA 669b	miscRNA	0.01	0.336634
Merged-chr9-77019667-1	chr9	77019617	77019717	+	2.3	cIP2vsInput	"intron (NM_012033, intron 4 of 10)"	"intron (NM_012033, intron 4 of 10)"	26114	NM_012033	26944	Mm.23199	NM_012033	ENSMUSG00000032357	Tinag	AI452335|TIN-ag	tubulointerstitial nephritis antigen	protein-coding	0	0.346535
Merged-chr1-37224371-1	chr1	37224321	37224421	+	2.3	cIP1vsInput	"intron (NM_009918, intron 1 of 5)"	L1MB7|LINE|L1	5110	NM_009918	12790	Mm.214224	NM_009918	ENSMUSG00000026114	Cnga3	CNG3	cyclic nucleotide gated channel alpha 3	protein-coding	0.01	0.346535
Merged-chr15-56406864-1	chr15	56406814	56406914	+	2.3	cIP2vsInput	Intergenic	Intergenic	-283080	NR_002874	594843	Mm.484850	NR_002874	ENSMUSG00000086541	Has2as	EG594843|Hasnt	HAS2 antisense RNA (non-protein coding)	miscRNA	0	0.316832
Merged-chr9-45886825-1	chr9	45886775	45886875	+	2.3	cIP2vsInput	"intron (NM_178709, intron 6 of 13)"	"intron (NM_178709, intron 6 of 13)"	-19744	NM_008794	18554	Mm.283283	NM_008794	ENSMUSG00000035382	Pcsk7	AA959856|PC7|SPC7	proprotein convertase subtilisin/kexin type 7	protein-coding	0	0.356436
Merged-chr3-110206248-1	chr3	110206198	110206298	+	2.3	cIP2vsInput	Intergenic	Intergenic	44750	NM_178891	99890	Mm.393526	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding	0	0.376238
Merged-chr7-108321137-1	chr7	108321087	108321187	+	2.3	cIP2vsInput	Intergenic	Intergenic	2537	NM_146497	258490	Mm.377532	NM_146497		Olfr492	MOR204-18	olfactory receptor 492	protein-coding	0	0.29703
Merged-chr6-11235867-1	chr6	11235817	11235917	+	2.3	cIP2vsInput	Intergenic	L1M2|LINE|L1	-261489	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	miscRNA	0	0.326733
Merged-chr16-55720203-1	chr16	55720153	55720253	+	2.3	cIP1vsInput	Intergenic	Intergenic	101935	NM_001159394	80859	Mm.247272	NM_001159394	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	"nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta"	protein-coding	0	0.455446
Merged-chr17-25727938-1	chr17	25727888	25727988	+	2.3	cIP1vsInput	promoter-TSS (NM_145409)	promoter-TSS (NM_145409)	187	NM_028009	106707	Mm.24603	NM_028009	ENSMUSG00000041199	Rpusd1	2310051D06Rik|AU019540|Rlucl	RNA pseudouridylate synthase domain containing 1	protein-coding	0.03	0.544554
Merged-chr8-52047282-1	chr8	52047232	52047332	+	2.3	cIP1vsInput	Intergenic	Intergenic	-1464420	NM_001205054	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding	0	0.316832
Merged-chr7-14554369-1	chr7	14554319	14554419	+	2.3	cIP1vsInput	"intron (NR_045120, intron 12 of 12)"	Lx|LINE|L1	7802	NM_001244031	627280	Mm.372763	NM_001039146	ENSMUSG00000097425	Vmn1r90	B430211C08Rik	vomeronasal 1 receptor 90	protein-coding	0	0.376238
Merged-chr8-63223034-1	chr8	63222984	63223084	+	2.3	cIP1vsInput	"intron (NM_001252620, intron 6 of 11)"	"intron (NM_001252620, intron 6 of 11)"	271689	NM_023689	72902	Mm.334552	NM_001252620	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3"	protein-coding	0	0.29703
Merged-chrX-71524282-1	chrX	71524232	71524332	+	2.3	cIP1vsInput	Intergenic	Intergenic	-31433	NM_001199349	171486	Mm.283879	NM_001199349	ENSMUSG00000035776	Cd99l2	AW548191|Mic2l1|Xap89	CD99 antigen-like 2	protein-coding	0.01	0.336634
Merged-chr18-84809934-1	chr18	84809884	84809984	+	2.3	cIP2vsInput	Intergenic	Intergenic	-41480	NM_025797	109672	Mm.31018	NM_025797		Cyb5	0610009N12Rik|Cyb5a	cytochrome b-5	protein-coding	0.01	0.316832
Merged-chr15-22168539-1	chr15	22168489	22168589	+	2.3	cIP2vsInput	Intergenic	Intergenic	546445	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding	0	0.356436
Merged-chr3-93804486-1	chr3	93804436	93804536	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	8088	NM_207272	399675	Mm.377924	XM_003946379	ENSMUSG00000060256	Tdpoz4	-	TD and POZ domain containing 4	protein-coding	0	0.277228
Merged-chr15-62204472-1	chr15	62204422	62204522	+	2.3	cIP2vsInput	"intron (NR_003368, intron 5 of 8)"	"intron (NR_003368, intron 5 of 8)"	14979	NR_003523	67552	Mm.484027	NR_003523		H2afy3	4933432H23Rik	"H2A histone family, member Y3"	pseudo	0.01	0.524752
Merged-chr6-19105233-1	chr6	19105183	19105283	+	2.3	cIP2vsInput	Intergenic	Intergenic	238915	NM_001167757	75196	Mm.67665	NM_001167757	ENSMUSG00000029517	Ankrd7	4930532L20Rik|AV278427	ankyrin repeat domain 7	protein-coding	0.01	0.29703
Merged-chr17-73213805-1	chr17	73213755	73213855	+	2.3	cIP2vsInput	"intron (NM_001081071, intron 5 of 5)"	"intron (NM_001081071, intron 5 of 5)"	105820	NM_001177967	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding	0	0.475248
Merged-chr3-121279492-1	chr3	121279442	121279542	+	2.3	cIP2vsInput	Intergenic	Intergenic	-12325	NM_024178	66789	Mm.269881	NM_024178	ENSMUSG00000039887	Alg14	5430428G01Rik|AI854024	asparagine-linked glycosylation 14	protein-coding	0.02	0.415842
Merged-chr4-147476108-1	chr4	147476058	147476158	+	2.3	cIP2vsInput	"intron (NM_001039209, intron 1 of 2)"	"intron (NM_001039209, intron 1 of 2)"	-77169	NM_001014397	433804	Mm.332047	XM_003946328	ENSMUSG00000065999	Gm13154	OTTMUSG00000010673	predicted gene 13154	protein-coding	0	0.267327
Merged-chr13-57976053-1	chr13	57976003	57976103	+	2.3	cIP2vsInput	Intergenic	Intergenic	47147	NR_030544	100124491		NR_030544		Mir874	Mirn874|mmu-mir-874	microRNA 874	miscRNA	0.01	0.356436
Merged-chr16-22089818-1	chr16	22089768	22089868	+	2.3	cIP1vsInput	"intron (NM_183029, intron 2 of 15)"	"intron (NM_183029, intron 2 of 15)"	73481	NM_183029	319765	Mm.489442	NM_183029	ENSMUSG00000033581	Igf2bp2	C330012H03Rik|IMP-2|Imp2|Neilsen	insulin-like growth factor 2 mRNA binding protein 2	protein-coding	0	0.306931
Merged-chr15-10677695-1	chr15	10677645	10677745	+	2.3	cIP1vsInput	"intron (NM_030690, intron 2 of 17)"	"intron (NM_030690, intron 2 of 17)"	35845	NM_030690	75646	Mm.212395	NM_001166408	ENSMUSG00000022246	Rai14	1700008J19Rik|1700020L11Rik|Ankycorbin|Norpeg|mKIAA1334	retinoic acid induced 14	protein-coding	0	0.316832
Merged-chr2-111681723-1	chr2	111681673	111681773	+	2.3	cIP2vsInput	"intron (NR_033534, intron 1 of 3)"	"intron (NR_033534, intron 1 of 3)"	14286	NR_033534	258199	Mm.437874	NR_033534		Olfr1300-ps1	MOR248-12	"olfactory receptor 1300, pseudogene 1"	pseudo	0	0.316832
Merged-chr1-187090081-1	chr1	187090031	187090131	+	2.3	cIP1vsInput	"intron (NM_028848, intron 9 of 9)"	L1MC4|LINE|L1	-35057	NR_040554	69308	Mm.490882	NR_040554		1700007P06Rik	-	RIKEN cDNA 1700007P06 gene	miscRNA	0	0.306931
Merged-chr2-128734298-1	chr2	128734248	128734348	+	2.3	cIP1vsInput	"intron (NM_008587, intron 2 of 18)"	"intron (NM_008587, intron 2 of 18)"	35301	NM_008587	17289	Mm.239655	XM_003689343	ENSMUSG00000014361	Mertk	Eyk|Mer|Nyk|nmf12	c-mer proto-oncogene tyrosine kinase	protein-coding	0	0.386139
Merged-chr6-78290819-1	chr6	78290769	78290869	+	2.3	cIP1vsInput	Intergenic	Lx2B|LINE|L1	-80066	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding	0	0.356436
Merged-chr14-103957357-1	chr14	103957307	103957407	+	2.3	cIP2vsInput	Intergenic	Intergenic	69785	NR_045953	73877	Mm.399172	NR_045953		4930432J09Rik	-	RIKEN cDNA 4930432J09 gene	miscRNA	0	0.287129
Merged-chr15-91164261-1	chr15	91164211	91164311	+	2.3	cIP2vsInput	"intron (NM_011994, intron 6 of 9)"	RMER12C|LTR|ERVK	27546	NM_011994	26874	Mm.295456	NM_011994	ENSMUSG00000055782	Abcd2	ABC39|ALDL1|ALDR|ALDRP	"ATP-binding cassette, sub-family D (ALD), member 2"	protein-coding	0	0.29703
Merged-chr1-27957558-1	chr1	27957508	27957608	+	2.3	cIP1vsInput	Intergenic	L1_Mur1|LINE|L1	822694	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0	0.326733
Merged-chr8-62784940-1	chr8	62784890	62784990	+	2.3	cIP1vsInput	Intergenic	Intergenic	-166292	NM_001252620	72902	Mm.334552	NM_001252620	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3"	protein-coding	0	0.287129
Merged-chr10-48883377-1	chr10	48883327	48883427	+	2.3	cIP2vsInput	Intergenic	Intergenic	212466	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	"proteasome (prosome, macropain) subunit, alpha type 6 pseudogene"	pseudo	0	0.29703
Merged-chr15-28739414-1	chr15	28739364	28739464	+	2.3	cIP2vsInput	Intergenic	L1MC1|LINE|L1	535648	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnahc5	AU022615|Dnah5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	"dynein, axonemal, heavy chain 5"	protein-coding	0	0.346535
Merged-chr17-82308923-1	chr17	82308873	82308973	+	2.3	cIP2vsInput	Intergenic	Intergenic	-570546	NM_011406	20541	Mm.489060	NM_001112798		Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	"solute carrier family 8 (sodium/calcium exchanger), member 1"	protein-coding	0	0.346535
Merged-chr11-47271486-1	chr11	47271436	47271536	+	2.3	cIP2vsInput	"intron (NM_011891, intron 2 of 7)"	"intron (NM_011891, intron 2 of 7)"	107816	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	"sarcoglycan, delta (dystrophin-associated glycoprotein)"	protein-coding	0	0.306931
Merged-chr16-25277776-1	chr16	25277726	25277826	+	2.3	cIP2vsInput	Intergenic	L1MA4|LINE|L1	-9041	NM_175165	71338	Mm.126851	NM_175165	ENSMUSG00000048399	Tprg	5430420C16Rik|Tprg1	transformation related protein 63 regulated	protein-coding	0	0.287129
Merged-chr8-15405436-1	chr8	15405386	15405486	+	2.3	cIP2vsInput	Intergenic	Intergenic	347783	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding	0	0.386139
Merged-chr4-118134675-1	chr4	118134625	118134725	+	2.3	cIP2vsInput	"5' UTR (NM_009176, exon 1 of 12)"	"5' UTR (NM_009176, exon 1 of 12)"	215	NM_009176	20441	Mm.251002	NM_001161774	ENSMUSG00000028538	St3gal3	ST3N|Siat3|Siat6	"ST3 beta-galactoside alpha-2,3-sialyltransferase 3"	protein-coding	0.13	0.821782
Merged-chr16-79735913-1	chr16	79735863	79735963	+	2.3	cIP2vsInput	Intergenic	Intergenic	-644816	NM_008941	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	"transmembrane protease, serine 15"	protein-coding	0.01	0.376238
Merged-chr3-51085635-1	chr3	51085585	51085685	+	2.3	cIP1vsInput	Intergenic	Intergenic	-138812	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Ccrn4l	AU043840|Ccr4|nocturnin	CCR4 carbon catabolite repression 4-like (S. cerevisiae)	protein-coding	0	0.39604
Merged-chr11-32147588-1	chr11	32147538	32147638	+	2.3	cIP1vsInput	Intergenic	L1M4|LINE|L1	52691	NM_001134458	16199	Mm.384	NM_001134458		Il9r	-	interleukin 9 receptor	protein-coding	0	0.336634
Merged-chr17-35309430-1	chr17	35309380	35309480	+	2.3	cIP1vsInput	Intergenic	Intergenic	-11128	NM_010390	15006	Mm.466882	NM_010390	ENSMUSG00000079507	H2-Q1	H-2Q1|Q1|Q1b|Q1d|Q1k|Qa-1|Qa1|Qed-1	"histocompatibility 2, Q region locus 1"	protein-coding	0	0.425743
Merged-chr5-48753465-1	chr5	48753415	48753515	+	2.3	cIP2vsInput	"intron (NM_001199244, intron 1 of 7)"	LTR106_Mam|LTR|LTR	136092	NM_030265	80334	Mm.160172	NM_001199242	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding	0	0.356436
Merged-chr2-4461720-1	chr2	4461670	4461770	+	2.3	cIP2vsInput	"intron (NM_172475, intron 2 of 22)"	(CCCCCT)n|Simple_repeat|Simple_repeat	60744	NM_001177843	209630	Mm.37932	NM_001177843	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding	0	0.554455
Merged-chr2-168478679-1	chr2	168478629	168478729	+	2.3	cIP2vsInput	"3' UTR (NM_001136073, exon 11 of 11)"	"3' UTR (NM_001136073, exon 11 of 11)"	111512	NM_001136073	18019	Mm.116802	NM_001136073	ENSMUSG00000027544	Nfatc2	AI607462|NF-ATc2|NFAT1|NFAT1-D|Nfatp	"nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2"	protein-coding	0.03	0.564356
Merged-chr8-113428757-1	chr8	113428707	113428807	+	2.3	cIP2vsInput	Intergenic	Intergenic	-206829	NM_001048143	270096	Mm.74689	NM_001048143	ENSMUSG00000078908	Mon1b	5031407H10|5033413H12Rik	MON1 homolog b (yeast)	protein-coding	0.01	0.287129
Merged-chr7-51593517-1	chr7	51593467	51593567	+	2.3	cIP1vsInput	"intron (NM_001271879, intron 20 of 20)"	"intron (NM_001271879, intron 20 of 20)"	-28313	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	"solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6"	protein-coding	0	0.336634
Merged-chr6-74838693-1	chr6	74838643	74838743	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1369026	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.29703
Merged-chr1-110085557-1	chr1	110085507	110085607	+	2.3	cIP2vsInput	"intron (NM_172853, intron 7 of 11)"	"intron (NM_172853, intron 7 of 11)"	101820	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.277228
Merged-chr7-77564544-1	chr7	77564494	77564594	+	2.3	cIP2vsInput	Intergenic	Intergenic	1013294	NM_008746	18213	Mm.421361	NM_008746		Ntrk3	AW125844|Ntrk3_tv3|TrkC	"neurotrophic tyrosine kinase, receptor, type 3"	protein-coding	0	0.326733
Merged-chr3-70325548-1	chr3	70325498	70325598	+	2.3	cIP2vsInput	Intergenic	Intergenic	317935	NM_001018031	229389	Mm.331071	NM_001018031	ENSMUSG00000027788	Otol1	Gm414	otolin 1 homolog (zebrafish)	protein-coding	0	0.306931
Merged-chr1-25370526-1	chr1	25370476	25370576	+	2.3	cIP1vsInput	"intron (NM_175642, intron 16 of 30)"	"intron (NM_175642, intron 16 of 30)"	-92572	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	"predicted gene, 20172"	protein-coding	0.01	0.336634
Merged-chr8-43806966-1	chr8	43806916	43807016	+	2.3	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-107475	NM_001079931	384814	Mm.383288	NM_001079931		Gm5347	EG384814	predicted gene 5347	protein-coding	0	0.316832
Merged-chr13-25326370-1	chr13	25326320	25326420	+	2.3	cIP2vsInput	Intergenic	Intergenic	-56374	NM_009513	22360	Mm.4766	NM_009513	ENSMUSG00000048978	Nrsn1	Neurensin-1|Neuro-p24|Vmp	neurensin 1	protein-coding	0.01	0.326733
Merged-chr3-5155797-1	chr3	5155747	5155847	+	2.3	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-62757	NM_030708	80892	Mm.41522	NM_030708	ENSMUSG00000025255	Zfhx4	A930021B15|C130041O22Rik|Zfh-4|Zfh4	zinc finger homeodomain 4	protein-coding	0	0.326733
Merged-chr3-25262556-1	chr3	25262506	25262606	+	2.3	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	890751	NM_001163387	192167	Mm.316080	NM_001163387	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|mKIAA1070	neuroligin 1	protein-coding	0	0.306931
Merged-chr9-84171066-1	chr9	84171016	84171116	+	2.3	cIP1vsInput	Intergenic	Lx10|LINE|L1	222285	NM_199195	12040	Mm.12819	NM_199195		Bckdhb	-	"branched chain ketoacid dehydrogenase E1, beta polypeptide"	protein-coding	0	0.326733
Merged-chr12-31513684-1	chr12	31513634	31513734	+	2.3	cIP2vsInput	Intergenic	Intergenic	-14068	NM_001253848	104836	Mm.273270	NM_001253847	ENSMUSG00000020659	Cbll1	AI467391|Hakai|c-Cbl-like	Casitas B-lineage lymphoma-like 1	protein-coding	0	0.306931
Merged-chr7-104963104-1	chr7	104963054	104963154	+	2.3	cIP2vsInput	Intergenic	Intergenic	-2374	NM_207146	384703	Mm.377901	NM_207146	ENSMUSG00000044705	Olfr670	GA_x5J8B7W6B6J-141796-141659|MOR32-8	olfactory receptor 670	protein-coding	0	0.336634
Merged-chr2-122846924-1	chr2	122846874	122846974	+	2.3	cIP2vsInput	Intergenic	MTD|LTR|ERVL-MaLR	64925	NM_021507	59010	Mm.28986	NM_001162503	ENSMUSG00000005803	Sqrdl	0610039J17Rik|4930557M22Rik	sulfide quinone reductase-like (yeast)	protein-coding	0	0.316832
Merged-chr4-62591525-1	chr4	62591475	62591575	+	2.3	cIP2vsInput	"intron (NM_019492, intron 3 of 19)"	MLT1F1|LTR|ERVL-MaLR	-28147	NM_001081650	50780	Mm.286753	NM_001081650	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding	0.03	0.554455
Merged-chr18-72844416-1	chr18	72844366	72844466	+	2.3	cIP1vsInput	Intergenic	Intergenic	-493347	NM_007831	13176	Mm.167882	NM_007831		Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding	0	0.356436
Merged-chr1-162149498-1	chr1	162149448	162149548	+	2.3	cIP2vsInput	"intron (NM_001038619, intron 14 of 20)"	ORR1E|LTR|ERVL-MaLR	-68125	NR_002870	474332	Mm.485366	NR_002870	ENSMUSG00000078190	Dnm3os	6030416H16Rik|Hag2|Npn1|P/L01	"dynamin 3, opposite strand"	miscRNA	0.01	0.376238
Merged-chr9-27125403-1	chr9	27125353	27125453	+	2.3	cIP2vsInput	"intron (NM_023277, intron 1 of 8)"	L1_Rod|LINE|L1	30018	NM_023277	83964	Mm.28770	NM_023277	ENSMUSG00000031990	Jam3	1110002N23Rik|JAM-3|JAM-C|Jcam3	junction adhesion molecule 3	protein-coding	0	0.326733
Merged-chr4-132732688-1	chr4	132732638	132732738	+	2.3	cIP2vsInput	promoter-TSS (NM_201368)	promoter-TSS (NM_201368)	-142	NM_201368	381560	Mm.44558	NM_201368	ENSMUSG00000037752	Xkr8	4931440N07Rik|AI597014|Gm1031|XRG8	X Kell blood group precursor related family member 8 homolog	protein-coding	0.01	0.455446
Merged-chr3-17763702-1	chr3	17763652	17763752	+	2.3	cIP2vsInput	Intergenic	Intergenic	-26219	NR_033490	70441	Mm.458192	NR_033490		2610100L16Rik	100040120|Gm2612	RIKEN cDNA 2610100L16 gene	miscRNA	0.01	0.366337
Merged-chr19-16971516-1	chr19	16971466	16971566	+	2.3	cIP2vsInput	"intron (NM_181348, intron 1 of 19)"	"intron (NM_181348, intron 1 of 19)"	15398	NM_181348	353211	Mm.489758	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2 (Drosophila)	protein-coding	0.03	0.455446
Merged-chr2-38658401-1	chr2	38658351	38658451	+	2.3	cIP2vsInput	Intergenic	Intergenic	-14495	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	"proteasome (prosome, macropain) subunit, beta type 7"	protein-coding	0.05	0.653465
Merged-chr17-51055235-1	chr17	51055185	51055285	+	2.3	cIP2vsInput	"intron (NM_028162, intron 2 of 21)"	"intron (NM_028162, intron 2 of 21)"	-92661	NR_035408	735256		NR_035408		Mir669a-1	Mir669a-1a|Mirn669a-1|Mirn669a-1a|mir-669a-1	microRNA 669a-1	miscRNA	0	0.326733
Merged-chr1-67654057-1	chr1	67654007	67654107	+	2.3	cIP2vsInput	Intergenic	Intergenic	530991	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding	0	0.336634
Merged-chr12-44298097-1	chr12	44298047	44298147	+	2.3	cIP2vsInput	"intron (NM_026164, intron 6 of 9)"	"intron (NM_026164, intron 6 of 9)"	28943	NM_026164	67452	Mm.54126	NM_026164		Pnpla8	1200006O19Rik|AI467579|Ipla2(gamma)	patatin-like phospholipase domain containing 8	protein-coding	0	0.326733
Merged-chr12-63234655-1	chr12	63234605	63234705	+	2.3	cIP2vsInput	Intergenic	MT2A|LTR|ERVL	1240243	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.356436
Merged-chr5-123655135-1	chr5	123655085	123655185	+	2.3	cIP2vsInput	"intron (NM_019765, intron 2 of 23)"	"intron (NM_019765, intron 2 of 23)"	29156	NM_019765	56430	Mm.441802	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding	0.02	0.465347
Merged-chr3-124050138-1	chr3	124050088	124050188	+	2.3	cIP2vsInput	Intergenic	Intergenic	-270899	NM_146140	229801	Mm.165810	NM_146140	ENSMUSG00000044528	Tram1l1	A830091N21Rik	translocation associated membrane protein 1-like 1	protein-coding	0	0.336634
Merged-chr18-49559588-1	chr18	49559538	49559638	+	2.3	cIP2vsInput	Intergenic	Intergenic	36299	NR_033785	67321	Mm.245802	NR_033785		1700044K03Rik	-	RIKEN cDNA 1700044K03 gene	miscRNA	0.01	0.574257
Merged-chr1-149277943-1	chr1	149277893	149277993	+	2.3	cIP1vsInput	Intergenic	Intergenic	683341	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0.01	0.326733
Merged-chr14-47255825-1	chr14	47255775	47255875	+	2.3	cIP2vsInput	"intron (NM_172598, intron 15 of 24)"	L1MB8|LINE|L1	21032	NM_172598	218973	Mm.265615	NM_172598	ENSMUSG00000037572	Wdhd1	A630092E18|AND-1|D630024B06Rik	WD repeat and HMG-box DNA binding protein 1	protein-coding	0.01	0.356436
Merged-chr11-28762724-1	chr11	28762674	28762774	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1004	NR_029828	387213		NR_029828	ENSMUSG00000065415	Mir217	Mirn217|mmu-mir-217	microRNA 217	miscRNA	0.01	0.405941
Merged-chr10-34216865-1	chr10	34216815	34216915	+	2.3	cIP2vsInput	Intergenic	Intergenic	-9314	NM_172508	212898	Mm.34557	NM_172508	ENSMUSG00000039497	Dse	6030499O08|AI480506|B130024B19Rik|Sart2	dermatan sulfate epimerase	protein-coding	0	0.376238
Merged-chr15-43991327-1	chr15	43991277	43991377	+	2.3	cIP2vsInput	Intergenic	Intergenic	-121298	NM_175502	239408	Mm.461451	NM_175502	ENSMUSG00000054409	Tmem74	AA549547|B230382K22Rik	transmembrane protein 74	protein-coding	0.01	0.336634
Merged-chr5-16715655-1	chr5	16715605	16715705	+	2.3	cIP2vsInput	Intergenic	Intergenic	162105	NM_010427	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF/HGF	hepatocyte growth factor	protein-coding	0.01	0.306931
Merged-chr6-67376475-1	chr6	67376425	67376525	+	2.3	cIP1vsInput	promoter-TSS (NM_008354)	promoter-TSS (NM_008354)	-338	NM_008354	16162	Mm.188337	NM_008354	ENSMUSG00000018341	Il12rb2	A930027I18Rik|IL-12RB2|Ifnm	"interleukin 12 receptor, beta 2"	protein-coding	0.01	0.336634
Merged-chr15-4477273-1	chr15	4477223	4477323	+	2.3	cIP2vsInput	"intron (NM_177355, intron 1 of 2)"	"intron (NM_177355, intron 1 of 2)"	101782	NM_177355	239318	Mm.308996	NM_177355	ENSMUSG00000049148	Plcxd3	B130016O10Rik	"phosphatidylinositol-specific phospholipase C, X domain containing 3"	protein-coding	0	0.346535
Merged-chr12-35457920-1	chr12	35457870	35457970	+	2.3	cIP2vsInput	Intergenic	Intergenic	77069	NM_013464	11622	Mm.341377	NM_013464	ENSMUSG00000019256	Ahr	Ah|Ahh|Ahre|In|bHLHe76	aryl-hydrocarbon receptor	protein-coding	0	0.316832
Merged-chr11-28643555-1	chr11	28643505	28643605	+	2.3	cIP2vsInput	Intergenic	Intergenic	-38009	NR_045906	72818	Mm.410846	NR_045906	ENSMUSG00000084966	2810471M01Rik	-	RIKEN cDNA 2810471M01 gene	miscRNA	0	0.356436
Merged-chrX-66459461-1	chrX	66459411	66459511	+	2.3	cIP1vsInput	Intergenic	L1M2|LINE|L1	-189857	NM_001161431	245450	Mm.403134	NM_001161431	ENSMUSG00000036790	Slitrk2	A930040J07	"SLIT and NTRK-like family, member 2"	protein-coding	0	0.29703
Merged-chr14-102903035-1	chr14	102902985	102903085	+	2.3	cIP2vsInput	Intergenic	Intergenic	79597	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mmu-mir-5130|mu-mir-5130	microRNA 5130	miscRNA	0.01	0.485149
Merged-chr19-16895445-1	chr19	16895395	16895495	+	2.3	cIP2vsInput	Intergenic	L1M2|LINE|L1	-21615	NM_008023	14240	Mm.7971	NM_008023	ENSMUSG00000056829	Foxb2	Fkh4	forkhead box B2	protein-coding	0	0.346535
Merged-chr18-28737943-1	chr18	28737893	28737993	+	2.3	cIP2vsInput	"intron (NR_045398, intron 2 of 4)"	"intron (NR_045398, intron 2 of 4)"	177779	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	miscRNA	0.01	0.326733
Merged-chr1-92928142-1	chr1	92928092	92928192	+	2.3	cIP1vsInput	Intergenic	MTD-int|LTR|ERVL-MaLR	-6266	NM_011796	23830	Mm.294315	NM_011796	ENSMUSG00000026270	Capn10	AW049679|Capn8|mKIAA1845	calpain 10	protein-coding	0	0.356436
Merged-chr9-9196052-1	chr9	9196002	9196102	+	2.3	cIP2vsInput	"intron (NM_027823, intron 1 of 22)"	"intron (NM_027823, intron 1 of 22)"	-40236	NR_045754	100579151	Mm.412450	NR_045754		Gm16833	-	"predicted gene, 16833"	miscRNA	0	0.346535
Merged-chr13-7466927-1	chr13	7466877	7466977	+	2.3	cIP1vsInput	Intergenic	Intergenic	-735982	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	"adenosine deaminase, RNA-specific, B2"	protein-coding	0.02	0.386139
Merged-chr18-11425358-1	chr18	11425308	11425408	+	2.3	cIP2vsInput	Intergenic	Intergenic	-207918	NM_001252495	225182	Mm.154275	NM_175458	ENSMUSG00000041238	Rbbp8	9930104E21Rik|CtIP|RBBP-8|RIM|SAE2	retinoblastoma binding protein 8	protein-coding	0	0.336634
Merged-chr14-95974795-1	chr14	95974745	95974845	+	2.3	cIP1vsInput	Intergenic	L1VL4|LINE|L1	93529	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.386139
Merged-chr13-81278230-1	chr13	81278180	81278280	+	2.3	cIP2vsInput	"intron (NM_054053, intron 84 of 89)"	"intron (NM_054053, intron 84 of 89)"	314156	NR_015587	319983	Mm.343027	NR_015587	ENSMUSG00000097098	9330111N05Rik	-	RIKEN cDNA 9330111N05 gene	miscRNA	0.01	0.287129
Merged-chr1-133520840-1	chr1	133520790	133520890	+	2.3	cIP2vsInput	Intergenic	Intergenic	89440	NM_009227	20643	Mm.249110	NM_009227	ENSMUSG00000090553	Snrpe	AL022645|C76690|SME	small nuclear ribonucleoprotein E	protein-coding	0.01	0.594059
Merged-chr17-64100222-1	chr17	64100172	64100272	+	2.3	cIP2vsInput	"intron (NM_001037997, intron 15 of 17)"	"intron (NM_001037997, intron 15 of 17)"	162250	NM_008000	14158	Mm.23039	NM_001037997	ENSMUSG00000000127	Fert2	AV082135|C330004K01Rik|Fer|Fert	"fer (fms/fps related) protein kinase, testis specific 2"	protein-coding	0	0.445545
Merged-chr7-46888611-1	chr7	46888561	46888661	+	2.3	cIP1vsInput	TTS (NM_021884)	TTS (NM_021884)	27348	NM_013580	16833	Mm.16563	NM_013580	ENSMUSG00000030851	Ldhc	LDH-C4|Ldh-3|Ldh-x|Ldh3|Ldhc4	lactate dehydrogenase C	protein-coding	0.02	0.326733
Merged-chr18-24941826-1	chr18	24941776	24941876	+	2.3	cIP1vsInput	"intron (NM_175276, intron 5 of 26)"	"intron (NM_175276, intron 5 of 26)"	224139	NM_001142697	66648	Mm.441171	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding	0.03	0.376238
Merged-chr16-85587606-1	chr16	85587556	85587656	+	2.3	cIP2vsInput	Intergenic	Intergenic	-37233	NM_144853	224405		NM_144853		Cyyr1	-	cysteine and tyrosine-rich protein 1	protein-coding	0.02	0.356436
Merged-chr4-89989866-1	chr4	89989816	89989916	+	2.3	cIP2vsInput	Intergenic	Intergenic	-228954	NM_153102	236537	Mm.214642	NM_153102	ENSMUSG00000070902	Zfp352	2czf48	zinc finger protein 352	protein-coding	0	0.376238
Merged-chr16-11233586-1	chr16	11233536	11233636	+	2.3	cIP2vsInput	"intron (NM_001130008, intron 6 of 14)"	"intron (NM_001130008, intron 6 of 14)"	20739	NM_001130008	14852	Mm.325827	NM_001130008		Gspt1	AI314175|AI326449|AV307676|C79774|G1st|Gst-1	G1 to S phase transition 1	protein-coding	0.01	0.267327
Merged-chr16-72025610-1	chr16	72025560	72025660	+	2.3	cIP1vsInput	Intergenic	Intergenic	-637539	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout homolog 1 (Drosophila)	protein-coding	0	0.346535
Merged-chr7-95385516-1	chr7	95385466	95385566	+	2.3	cIP2vsInput	Intergenic	L1M3|LINE|L1	-825121	NM_011858	23966	Mm.391678	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding	0	0.326733
Merged-chr9-92855090-1	chr9	92855040	92855140	+	2.3	cIP1vsInput	Intergenic	Intergenic	136374	NR_040770	331003	Mm.50805	NR_040770		4933400C23Rik	4933400C23	RIKEN cDNA 4933400C23 gene	miscRNA	0	0.306931
Merged-chr3-19151613-1	chr3	19151563	19151663	+	2.3	cIP2vsInput	"intron (NM_028840, intron 2 of 6)"	"intron (NM_028840, intron 2 of 6)"	11452	NM_028840	74252	Mm.316007	XM_003689346	ENSMUSG00000027599	Armc1	2310016N05Rik|2900046P06Rik|3110009G21Rik|AA409258|AW048872|Arcp|C330014L16Rik	armadillo repeat containing 1	protein-coding	0.02	0.277228
Merged-chr1-28640514-1	chr1	28640464	28640564	+	2.3	cIP2vsInput	Intergenic	Intergenic	139738	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0.01	0.356436
Merged-chr3-143275786-1	chr3	143275736	143275836	+	2.3	cIP2vsInput	Intergenic	Intergenic	32731	NR_040551	320072	Mm.136397	NR_040551		A830019L24Rik	-	RIKEN cDNA A830019L24 gene	miscRNA	0	0.326733
Merged-chr11-36289353-1	chr11	36289303	36289403	+	2.3	cIP1vsInput	"intron (NM_011856, intron 4 of 28)"	"intron (NM_011856, intron 4 of 28)"	-309264	NM_170779	211652	Mm.31267	NM_170779		Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	"WW, C2 and coiled-coil domain containing 1"	protein-coding	0	0.336634
Merged-chr10-39766029-1	chr10	39765979	39766079	+	2.3	cIP2vsInput	"intron (NM_011264, intron 1 of 31)"	"intron (NM_011264, intron 1 of 31)"	33869	NM_011264	19714	Mm.439723	NM_011264	ENSMUSG00000019841	Rev3l	Rev|Rev3|Sez4	"REV3-like, catalytic subunit of DNA polymerase zeta RAD54 like (S. cerevisiae)"	protein-coding	0	0.316832
Merged-chr14-80199774-1	chr14	80199724	80199824	+	2.3	cIP2vsInput	Intergenic	L1ME2|LINE|L1	199472	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.287129
Merged-chr3-60810625-1	chr3	60810575	60810675	+	2.3	cIP1vsInput	Intergenic	Intergenic	-192170	NM_008772	18441	Mm.281452	NM_008772	ENSMUSG00000027765	P2ry1	P2Y1	"purinergic receptor P2Y, G-protein coupled 1"	protein-coding	0	0.366337
Merged-chr5-13723300-1	chr5	13723250	13723350	+	2.3	cIP2vsInput	Intergenic	Intergenic	-68319	NM_027650	71026	Mm.158536	NM_027650	ENSMUSG00000067855	Speer3	4933405P08Rik|SPEER-3	spermatogenesis associated glutamate (E)-rich protein 3	protein-coding	0	0.336634
Merged-chr3-4633794-1	chr3	4633744	4633844	+	2.3	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-164914	NR_045272	100503859	Mm.75172	NR_045272		1110015O18Rik	-	RIKEN cDNA 1110015O18 gene	miscRNA	0	0.29703
Merged-chr8-115431328-1	chr8	115431278	115431378	+	2.3	cIP2vsInput	Intergenic	Intergenic	275566	NM_001025577	17132	Mm.488377	NM_001025577		Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma (v-maf) AS42 oncogene homolog	protein-coding	0	0.366337
Merged-chr4-93843246-1	chr4	93843196	93843296	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-507735	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding	0	0.336634
Merged-chr8-65970198-1	chr8	65970148	65970248	+	2.3	cIP1vsInput	"intron (NM_175188, intron 3 of 7)"	"intron (NM_175188, intron 3 of 7)"	351673	NM_175188	72925	Mm.380457	NM_001166372	ENSMUSG00000036469	1-Mar	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding	0	0.326733
Merged-chr13-118326040-1	chr13	118325990	118326090	+	2.3	cIP2vsInput	Intergenic	Lx7|LINE|L1	61212	NM_021556	59054	Mm.143810	NM_021556	ENSMUSG00000021731	Mrps30	2610020A16Rik|AA968347|PAP|Pdcd9	mitochondrial ribosomal protein S30	protein-coding	0.01	0.376238
Merged-chr18-66817761-1	chr18	66817711	66817811	+	2.3	cIP1vsInput	Intergenic	Intergenic	42726	NM_016977	17202	Mm.229447	NM_016977	ENSMUSG00000047259	Mc4r	Mc4-r	melanocortin 4 receptor	protein-coding	0	0.376238
Merged-chr8-66917112-1	chr8	66917062	66917162	+	2.3	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	56895	NM_001163564	234344	Mm.334561	NM_001163564	ENSMUSG00000014907	Naf1	Gm174	nuclear assembly factor 1 homolog (S. cerevisiae)	protein-coding	0	0.306931
Merged-chr7-61843280-1	chr7	61843230	61843330	+	2.3	cIP2vsInput	"intron (NR_015533, intron 6 of 8)"	"intron (NR_015533, intron 6 of 8)"	-5878	NR_037286	100526506		NR_037286	ENSMUSG00000077107	Mir344c	mmu-mir-344c	microRNA 344c	miscRNA	0	0.366337
Merged-chr8-56345576-1	chr8	56345526	56345626	+	2.3	cIP2vsInput	Intergenic	Intergenic	51024	NM_008278	15446	Mm.18832	NM_008278	ENSMUSG00000031613	Hpgd	15-PGDH|AV026552	hydroxyprostaglandin dehydrogenase 15 (NAD)	protein-coding	0.01	0.257426
Merged-chr11-13217691-1	chr11	13217641	13217741	+	2.3	cIP1vsInput	Intergenic	Intergenic	-752731	NM_172496	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	4732460E13|C530045F18Rik|mKIAA0633	cordon-bleu	protein-coding	0.01	0.306931
Merged-chr14-89181450-1	chr14	89181400	89181500	+	2.3	cIP2vsInput	Intergenic	Intergenic	-710054	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0	0.336634
Merged-chr10-47457248-1	chr10	47457198	47457298	+	2.3	cIP2vsInput	Intergenic	MLT1H-int|LTR|ERVL-MaLR	1212499	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0.01	0.356436
Merged-chr9-92821458-1	chr9	92821408	92821508	+	2.3	cIP2vsInput	Intergenic	Intergenic	102742	NR_040770	331003	Mm.50805	NR_040770		4933400C23Rik	4933400C23	RIKEN cDNA 4933400C23 gene	miscRNA	0	0.316832
Merged-chr15-97718369-1	chr15	97718319	97718419	+	2.3	cIP2vsInput	"intron (NM_001168693, intron 6 of 9)"	"intron (NM_001168693, intron 6 of 9)"	2781	NM_008902	19011	Mm.1001	NM_001168693	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	"endonuclease, polyU-specific"	protein-coding	0.02	0.574257
Merged-chr6-41125156-1	chr6	41125106	41125206	+	2.3	cIP1vsInput	Intergenic	Intergenic	-89647	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding	0.01	0.306931
Merged-chr14-92320653-1	chr14	92320603	92320703	+	2.3	cIP2vsInput	Intergenic	Intergenic	1568235	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.366337
Merged-chr1-47420506-1	chr1	47420456	47420556	+	2.3	cIP1vsInput	Intergenic	L1M2|LINE|L1	-566997	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.316832
Merged-chr6-6499187-1	chr6	6499137	6499237	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	79471	NM_009169	20422	Mm.2469	NM_009169		Shfm1	DSS1|Shfdg1|Shfg	split hand/foot malformation (ectrodactyly) type 1	protein-coding	0	0.326733
Merged-chr17-33940378-1	chr17	33940328	33940428	+	2.3	cIP2vsInput	promoter-TSS (NM_001185182)	promoter-TSS (NM_001185182)	-35	NM_010385	14976	Mm.2948	NM_001185182	ENSMUSG00000024309	H2-Ke2	H-2Ke2|Ke-2|Pfdn6	H2-K region expressed gene 2	protein-coding	0.07	0.50495
Merged-chr10-124424951-1	chr10	124424901	124425001	+	2.3	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-44123	NR_028310	75030	Mm.159403	NR_028310		4930503E24Rik	-	"eukaryotic translation initiation factor 3, subunit I pseudogene"	pseudo	0	0.366337
Merged-chr10-52963573-1	chr10	52963523	52963623	+	2.3	cIP2vsInput	"intron (NM_178675, intron 2 of 7)"	"intron (NM_178675, intron 2 of 7)"	273072	NM_178675	215085	Mm.338690	NM_178675	ENSMUSG00000038602	Slc35f1	Duf6|E130016L02	"solute carrier family 35, member F1"	protein-coding	0	0.336634
Merged-chr16-56283785-1	chr16	56283735	56283835	+	2.3	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	79472	NM_174876	224224	Mm.151998	NM_174876	ENSMUSG00000035270	Impg2	IPM200|PG10.2|Rsbp|Spacrcan	interphotoreceptor matrix proteoglycan 2	protein-coding	0.01	0.306931
Merged-chr5-139518865-1	chr5	139518815	139518915	+	2.3	cIP2vsInput	Intergenic	B4A|SINE|B4	-4886	NR_040701	74973	Mm.141282	NR_040701		4930500L23Rik	-	RIKEN cDNA 4930500L23 gene	miscRNA	0.01	0.534653
Merged-chr9-5087392-1	chr9	5087342	5087442	+	2.3	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-211125	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding	0	0.287129
Merged-chr1-31316119-1	chr1	31316069	31316169	+	2.3	cIP2vsInput	Intergenic	Intergenic	51272	NR_015347	226957	Mm.25966	NR_015347		Gm4850	EG226957	THO complex 4 pseudogene	pseudo	0.01	0.386139
Merged-chr14-96528821-1	chr14	96528771	96528871	+	2.3	cIP1vsInput	Intergenic	Intergenic	-9787	NM_053105	93688	Mm.308735	NM_053105	ENSMUSG00000022076	Klhl1	mKIAA1490	kelch-like 1	protein-coding	0	0.306931
Merged-chr11-121092395-1	chr11	121092345	121092445	+	2.3	cIP2vsInput	Intergenic	Intergenic	-11256	NM_145373	209588	Mm.69553	NM_145373	ENSMUSG00000025165	Sectm1a	BC010462	secreted and transmembrane 1A	protein-coding	0	0.366337
Merged-chr13-39043475-1	chr13	39043425	39043525	+	2.3	cIP1vsInput	Intergenic	ORR1C2-int|LTR|ERVL-MaLR	-82600	NM_001170431	108652	Mm.255506	NM_001170430	ENSMUSG00000021432	Slc35b3	4921526O06Rik|AI428480|CGI-19|PABST2|PAPST2	"solute carrier family 35, member B3"	protein-coding	0	0.346535
Merged-chr7-95427289-1	chr7	95427239	95427339	+	2.3	cIP2vsInput	Intergenic	Lx9|LINE|L1	-783348	NM_011858	23966	Mm.391678	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding	0.01	0.356436
Merged-chr7-51922939-1	chr7	51922889	51922989	+	2.3	cIP2vsInput	"intron (NM_008087, intron 3 of 7)"	"intron (NM_008087, intron 3 of 7)"	43794	NM_008087	14453	Mm.471773	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding	0.01	0.306931
Merged-chr5-105035238-1	chr5	105035188	105035288	+	2.3	cIP1vsInput	"intron (NM_029509, intron 3 of 9)"	L1_Mur2|LINE|L1	18323	NM_029509	76074	Mm.458519	NM_029509	ENSMUSG00000034438	Gbp8	5830443L24Rik|mGBP8	guanylate-binding protein 8	protein-coding	0	0.346535
Merged-chr3-77207333-1	chr3	77207283	77207383	+	2.3	cIP2vsInput	Intergenic	ERVB4_1B-I_MM-int|LTR|ERVK	1131750	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0.01	0.39604
Merged-chr1-31621311-1	chr1	31621261	31621361	+	2.3	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	356464	NR_015347	226957	Mm.25966	NR_015347		Gm4850	EG226957	THO complex 4 pseudogene	pseudo	0.01	0.326733
Merged-chr3-145542378-1	chr3	145542328	145542428	+	2.3	cIP1vsInput	"intron (NM_027770, intron 58 of 59)"	"intron (NM_027770, intron 58 of 59)"	-33830	NM_001081094	229937	Mm.24586	NM_001081094	ENSMUSG00000074182	Znhit6	2410019A14Rik	"zinc finger, HIT type 6"	protein-coding	0.01	0.326733
Merged-chr11-43783861-1	chr11	43783811	43783911	+	2.3	cIP2vsInput	"intron (NM_007416, intron 1 of 1)"	"intron (NM_007416, intron 1 of 1)"	-35888	NM_133795	66827	Mm.271974	NM_133795	ENSMUSG00000041278	Ttc1	4833412C19Rik|C79328|TPR1	tetratricopeptide repeat domain 1	protein-coding	0.01	0.475248
Merged-chr12-60478933-1	chr12	60478883	60478983	+	2.3	cIP2vsInput	Intergenic	Intergenic	1042887	NR_045049	100504101	Mm.235026	NR_045049		Gm20063	-	"predicted gene, 20063"	miscRNA	0.01	0.277228
Merged-chr2-101905511-1	chr2	101905461	101905561	+	2.3	cIP2vsInput	Intergenic	Intergenic	19249	NM_029635	76501	Mm.330424	NM_029635	ENSMUSG00000027163	Commd9	1810029F08Rik|AA409293	COMM domain containing 9	protein-coding	0.01	0.346535
Merged-chr15-32506628-1	chr15	32506578	32506678	+	2.3	cIP2vsInput	"intron (NM_009154, intron 5 of 22)"	"intron (NM_009154, intron 5 of 22)"	261815	NM_009154	20356	Mm.260374	NM_009154	ENSMUSG00000022231	Sema5a	5930434A13|9130201M22Rik|AI464145|Semaf|semF	"sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A"	protein-coding	0	0.326733
Merged-chr10-89055015-1	chr10	89054965	89055065	+	2.3	cIP2vsInput	"intron (NR_102339, intron 7 of 26)"	"intron (NR_102339, intron 7 of 26)"	169023	NM_145423	216225	Mm.77381	NM_145423	ENSMUSG00000020062	Slc5a8	Ait|SMCT	"solute carrier family 5 (iodide transporter), member 8"	protein-coding	0	0.386139
Merged-chr5-104265157-1	chr5	104265107	104265207	+	2.3	cIP2vsInput	Intergenic	Intergenic	-34130	NM_008318	15891	Mm.4987	XM_003689386	ENSMUSG00000029306	Ibsp	BSP|BSP II|BSPII|Bsp2	integrin binding sialoprotein	protein-coding	0	0.29703
Merged-chr15-56457960-1	chr15	56457910	56458010	+	2.3	cIP2vsInput	Intergenic	Intergenic	-231984	NR_002874	594843	Mm.484850	NR_002874	ENSMUSG00000086541	Has2as	EG594843|Hasnt	HAS2 antisense RNA (non-protein coding)	miscRNA	0	0.306931
Merged-chr11-77173720-1	chr11	77173670	77173770	+	2.3	cIP1vsInput	"intron (NM_176965, intron 1 of 17)"	"intron (NM_176965, intron 1 of 17)"	15248	NM_176965	319634	Mm.108786	NM_176965	ENSMUSG00000050944	Efcab5	4930563A03Rik	EF-hand calcium binding domain 5	protein-coding	0.01	0.465347
Merged-chr10-13453799-1	chr10	13453749	13453849	+	2.3	cIP2vsInput	"intron (NM_001195065, intron 1 of 12)"	"intron (NM_001195065, intron 1 of 12)"	20597	NM_001195065	215789	Mm.487722	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding	0.01	0.425743
Merged-chr2-40899353-1	chr2	40899303	40899403	+	2.3	cIP2vsInput	"intron (NM_053011, intron 49 of 90)"	Lx9|LINE|L1	-1673015	NM_024209	67857	Mm.392662	NM_024209		Ppp6c	2310003C10Rik	"protein phosphatase 6, catalytic subunit"	protein-coding	0	0.445545
Merged-chr2-89689784-1	chr2	89689734	89689834	+	2.3	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-21900	NM_001011529	259145	Mm.376637	NM_001011529	ENSMUSG00000075077	Olfr1251	GA_x5J8B7TT7VM-20-924|MOR231-15P	olfactory receptor 1251	protein-coding	0.01	0.346535
Merged-chr5-87880364-1	chr5	87880314	87880414	+	2.3	cIP2vsInput	Intergenic	Intergenic	-5331	NM_027128	69592	Mm.389652	NM_027128	ENSMUSG00000009580	Odam	2310011G06Rik|APIN	"odontogenic, ameloblast asssociated"	protein-coding	0	0.316832
Merged-chr14-65791742-1	chr14	65791692	65791792	+	2.3	cIP1vsInput	Intergenic	Intergenic	-14169	NM_023209	52033	Mm.24337	NM_023209	ENSMUSG00000022033	Pbk	2810434B10Rik|AW538537|D14Ertd732e|TOPK	PDZ binding kinase	protein-coding	0.01	0.316832
Merged-chr6-141708092-1	chr6	141708042	141708142	+	2.3	cIP2vsInput	Intergenic	Intergenic	78574	NM_020495	28253	Mm.272223	NM_020495	ENSMUSG00000030236	Slco1b2	7330442B20Rik|OATP-C|OATP2|Oatp1b2|Oatp4|Slc21a10|Slc21a6|lst-1|mlst-1	"solute carrier organic anion transporter family, member 1b2"	protein-coding	0	0.326733
Merged-chr8-116733650-1	chr8	116733600	116733700	+	2.3	cIP2vsInput	promoter-TSS (NM_029441)	promoter-TSS (NM_029441)	-659	NM_029441	75796	Mm.159575	NM_029441	ENSMUSG00000031758	Cdyl2	1700029M19Rik|4930453I21Rik|Gm20194	"chromodomain protein, Y chromosome-like 2"	protein-coding	0.03	0.60396
Merged-chr3-47047686-1	chr3	47047636	47047736	+	2.3	cIP2vsInput	Intergenic	Lx6|LINE|L1	-599745	NM_001101479	241989	Mm.475785	NM_001101479	ENSMUSG00000090919	Pabpc4l	C330050A14Rik|EG241989	"poly(A) binding protein, cytoplasmic 4-like"	protein-coding	0	0.336634
Merged-chr12-67304945-1	chr12	67304895	67304995	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-82396	NM_207010	320772	Mm.227680	NM_001193266		Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding	0	0.346535
Merged-chr5-80997364-1	chr5	80997314	80997414	+	2.3	cIP2vsInput	Intergenic	Intergenic	-24229	NM_198702	319387	Mm.461016	NM_198702	ENSMUSG00000037605	Lphn3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|mKIAA0768	latrophilin 3	protein-coding	0	0.29703
Merged-chr15-22802238-1	chr15	22802188	22802288	+	2.3	cIP2vsInput	Intergenic	Lx9|LINE|L1	-87254	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding	0.01	0.405941
Merged-chr8-124644100-1	chr8	124644050	124644150	+	2.3	cIP2vsInput	"intron (NM_175149, intron 2 of 3)"	"intron (NM_175149, intron 2 of 3)"	19269	NM_175149	69551	Mm.261920	NM_175149	ENSMUSG00000031983	2310022B05Rik	-	RIKEN cDNA 2310022B05 gene	protein-coding	0.02	0.524752
Merged-chr13-79648296-1	chr13	79648246	79648346	+	2.3	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-1235126	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0	0.326733
Merged-chr12-28012862-1	chr12	28012812	28012912	+	2.3	cIP1vsInput	Intergenic	ORR1C1|LTR|ERVL-MaLR	535475	NM_001177964	68511	Mm.310284	NM_001177964		Dcdc2c	1110015M06Rik	doublecortin domain containing 2C	protein-coding	0	0.405941
Merged-chr17-76209200-1	chr17	76209150	76209250	+	2.3	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	348177	NR_033456	100043885	Mm.127562	NR_033456		Gm4710	-	predicted gene 4710	miscRNA	0.01	0.376238
Merged-chr5-90930860-1	chr5	90930810	90930910	+	2.3	cIP2vsInput	promoter-TSS (NM_026788)	promoter-TSS (NM_026788)	-336	NM_026788	665563	Mm.153030	NM_026788	ENSMUSG00000029376	Mthfd2l	1110019K23Rik|C630010D07Rik	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like	protein-coding	0	0.39604
Merged-chr12-62679373-1	chr12	62679323	62679423	+	2.3	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	1154741	NM_178714	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.01	0.29703
Merged-chr1-115925971-1	chr1	115925921	115926021	+	2.3	cIP2vsInput	"intron (NM_001077425, intron 3 of 23)"	"intron (NM_001077425, intron 3 of 23)"	240834	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0.01	0.316832
Merged-chr14-38893302-1	chr14	38893252	38893352	+	2.3	cIP1vsInput	"intron (NM_001190187, intron 2 of 9)"	L1ME4c|LINE|L1	-5000	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	4930529F24Rik	-	RIKEN cDNA 4930529F24 gene	miscRNA	0	0.336634
Merged-chr1-131736717-1	chr1	131736667	131736767	+	2.3	cIP2vsInput	Intergenic	Intergenic	-7305	NM_177243	320718	Mm.482704	NM_177243		Slc26a9	E030002L01Rik	"solute carrier family 26, member 9"	protein-coding	0.03	0.514851
Merged-chr5-144290134-1	chr5	144290084	144290184	+	2.3	cIP2vsInput	"intron (NM_025833, intron 3 of 13)"	"intron (NM_025833, intron 3 of 13)"	13073	NR_040432	100504231	Mm.453004	NR_040432	ENSMUSG00000086894	Gm15708	OTTMUSG00000025583	predicted gene 15708	miscRNA	0	0.386139
Merged-chr2-168072866-1	chr2	168072816	168072916	+	2.3	cIP2vsInput	Intergenic	Intergenic	-8138	NM_021409	58220	Mm.292834	NM_021409	ENSMUSG00000044641	Pard6b	AV025615|Par6b	par-6 (partitioning defective 6) homolog beta (C. elegans)	protein-coding	0.01	0.663366
Merged-chr18-52044004-1	chr18	52043954	52044054	+	2.3	cIP2vsInput	Intergenic	Intergenic	79542	NR_029788	723830		NR_029788		Mir28	Mirn28|mmu-mir-28	microRNA 28	miscRNA	0.01	0.316832
Merged-chr12-44046297-1	chr12	44046247	44046347	+	2.3	cIP2vsInput	Intergenic	Intergenic	163771	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	"DnaJ (Hsp40) homolog, subfamily B, member 9"	protein-coding	0	0.306931
Merged-chr14-110635852-1	chr14	110635802	110635902	+	2.3	cIP2vsInput	Intergenic	MLT2B3|LTR|ERVL	119297	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	"SLIT and NTRK-like family, member 6"	protein-coding	0	0.356436
Merged-chr13-7750491-1	chr13	7750441	7750541	+	2.3	cIP2vsInput	Intergenic	Intergenic	-452418	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	"adenosine deaminase, RNA-specific, B2"	protein-coding	0	0.29703
Merged-chr18-8324393-1	chr18	8324343	8324443	+	2.3	cIP2vsInput	Intergenic	Intergenic	455196	NM_153085	225131	Mm.204524	NM_001146298	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding	0	0.336634
Merged-chr12-48765030-1	chr12	48764980	48765080	+	2.3	cIP2vsInput	Intergenic	Lx9|LINE|L1	-463568	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0	0.326733
Merged-chr16-39810067-1	chr16	39810017	39810117	+	2.3	cIP2vsInput	Intergenic	MIR|SINE|MIR	907722	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	"immunoglobulin superfamily, member 11"	protein-coding	0	0.287129
Merged-chr5-14417821-1	chr5	14417771	14417871	+	2.3	cIP1vsInput	Intergenic	Intergenic	-97097	NM_011995	26875	Mm.146275	NM_001110796	ENSMUSG00000061601	Pclo	Acz|Pico|mKIAA0559	piccolo (presynaptic cytomatrix protein)	protein-coding	0	0.376238
Merged-chr5-43218346-1	chr5	43218296	43218396	+	2.3	cIP2vsInput	"intron (NR_028417, intron 1 of 7)"	"intron (NR_028417, intron 1 of 7)"	-15117	NM_175937	231207	Mm.7233	NM_001177379	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding	0	0.346535
Merged-chr14-16484409-1	chr14	16484359	16484459	+	2.3	cIP2vsInput	"intron (NM_011243, intron 3 of 7)"	"intron (NM_011243, intron 3 of 7)"	90801	NM_011243	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2|RARbeta2	"retinoic acid receptor, beta"	protein-coding	0.01	0.475248
Merged-chr4-134511773-1	chr4	134511723	134511823	+	2.3	cIP2vsInput	"intron (NM_001081099, intron 1 of 2)"	"intron (NM_001081099, intron 1 of 2)"	774	NM_001081099	69885	Mm.141592	NM_001081099	ENSMUSG00000078521	Clhc1	2610002D18Rik|Aunip	clathrin heavy chain linker domain containing 1	protein-coding	0	0.366337
Merged-chr1-148666225-1	chr1	148666175	148666275	+	2.3	cIP2vsInput	Intergenic	Intergenic	1295059	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0	0.287129
Merged-chr10-64820211-1	chr10	64820161	64820261	+	2.3	cIP2vsInput	"intron (NM_001164519, intron 8 of 12)"	"intron (NM_001164519, intron 8 of 12)"	-729956	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding	0	0.306931
Merged-chr12-61198637-1	chr12	61198587	61198687	+	2.3	cIP2vsInput	Intergenic	Intergenic	323183	NR_045049	100504101	Mm.235026	NR_045049		Gm20063	-	"predicted gene, 20063"	miscRNA	0	0.306931
Merged-chr5-51089991-1	chr5	51089941	51090041	+	2.3	cIP2vsInput	Intergenic	Lx8b|LINE|L1	463930	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PGC-1v|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	"peroxisome proliferative activated receptor, gamma, coactivator 1 alpha"	protein-coding	0	0.336634
Merged-chr14-97680516-1	chr14	97680466	97680566	+	2.3	cIP2vsInput	Intergenic	RMER15|LTR|ERVL	489027	NM_001038610	13134	Mm.320593	NM_001038610	ENSMUSG00000055639	Dach1	AI182278|Dac|Dach|E130112M23Rik	dachshund 1 (Drosophila)	protein-coding	0	0.336634
Merged-chr5-62793102-1	chr5	62793052	62793152	+	2.3	cIP2vsInput	Intergenic	Intergenic	-20721	NM_001170705	100322896	Mm.479821	NM_001170705	ENSMUSG00000090326	Gm17384	Dthd1	"predicted gene, 17384"	protein-coding	0	0.346535
Merged-chr16-58919174-1	chr16	58919124	58919224	+	2.3	cIP1vsInput	promoter-TSS (NM_001011662)	promoter-TSS (NM_001011662)	-688	NM_001011662	258178	Mm.489195	NM_001011662	ENSMUSG00000090629	Olfr180	MOR184-11P|MOR184-9|Olfr1563-ps1	olfactory receptor 180	protein-coding	0.01	0.386139
Merged-chr15-71018021-1	chr15	71017971	71018071	+	2.3	cIP2vsInput	Intergenic	MLT2B3|LTR|ERVL	709817	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	"family with sequence similarity 135, member B"	protein-coding	0	0.336634
Merged-chr3-148042232-1	chr3	148042182	148042282	+	2.3	cIP1vsInput	Intergenic	Intergenic	912403	NM_001081298	99633	Mm.462301	NM_001081298	ENSMUSG00000028184	Lphn2	AI450192|Gm619|Lec1|Lphh1|mKIAA0786	latrophilin 2	protein-coding	0.01	0.405941
Merged-chr6-129884770-1	chr6	129884720	129884820	+	2.3	cIP1vsInput	Intergenic	L1VL2|LINE|L1	-8098	NM_133203	170733	Mm.155514	NM_133203	ENSMUSG00000014543	Klra17	Ly49q|Ly49q1	"killer cell lectin-like receptor, subfamily A, member 17"	protein-coding	0	0.316832
Merged-chr15-31645546-1	chr15	31645496	31645596	+	2.3	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	43430	NM_026546	68073	Mm.119185	NM_026546	ENSMUSG00000039065	Fam173b	A930016P21Rik|AA987072	"family with sequence similarity 173, member B"	protein-coding	0.01	0.435644
Merged-chr16-80499217-1	chr16	80499167	80499267	+	2.3	cIP1vsInput	Intergenic	Intergenic	-701480	NM_001113208	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.306931
Merged-chr1-167449587-1	chr1	167449537	167449637	+	2.3	cIP2vsInput	"intron (NM_001013382, intron 1 of 1)"	L1M5|LINE|L1	17193	NM_001013382	240899	Mm.159799	NM_001013382	ENSMUSG00000040485	Lrrc52	4930413P14Rik	leucine rich repeat containing 52	protein-coding	0.01	0.316832
Merged-chr18-33579452-1	chr18	33579402	33579502	+	2.3	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	115289	NR_045415	433171	Mm.353332	NR_045415		Gm10549	ENSMUSG00000073610	predicted gene 10549	miscRNA	0.01	0.366337
Merged-chr4-146481689-1	chr4	146481639	146481739	+	2.3	cIP1vsInput	Intergenic	Intergenic	-20311	NM_001243138	100041433	Mm.441741	NM_001243138	ENSMUSG00000056300	Gm13247	OTTMUSG00000011075	predicted gene 13247	protein-coding	0	0.306931
Merged-chr18-43555649-1	chr18	43555599	43555699	+	2.3	cIP1vsInput	"intron (NM_001163637, intron 16 of 21)"	"intron (NM_001163637, intron 16 of 21)"	132124	NM_001163637	76217	Mm.134602	NM_001163637	ENSMUSG00000024502	Jakmip2	6430702L21Rik|AI850334|D930046L20Rik	janus kinase and microtubule interacting protein 2	protein-coding	0	0.316832
Merged-chr2-98947330-1	chr2	98947280	98947380	+	2.3	cIP2vsInput	Intergenic	Intergenic	1479656	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.356436
Merged-chr4-17242093-1	chr4	17242043	17242143	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-611389	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0	0.356436
Merged-chr16-74989758-1	chr16	74989708	74989808	+	2.3	cIP1vsInput	Intergenic	Intergenic	577924	NM_177142	320355	Mm.99517	NM_001252513		Lipi	D930038D03Rik|lpd1	"lipase, member I"	protein-coding	0	0.29703
Merged-chr8-3295015-1	chr8	3294965	3295065	+	2.3	cIP2vsInput	Intergenic	Lx4B|LINE|L1	-15398	NM_010568	16337	Mm.268003	NM_010568		Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding	0	0.356436
Merged-chr2-116245748-1	chr2	116245698	116245798	+	2.3	cIP2vsInput	Intergenic	L1ME2|LINE|L1	-169652	NR_033447	69974	Mm.440293	NR_033447		2810405F15Rik	-	RIKEN cDNA 2810405F15 gene	miscRNA	0	0.316832
Merged-chr15-19267764-1	chr15	19267714	19267814	+	2.3	cIP2vsInput	Intergenic	Intergenic	447435	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0	0.316832
Merged-chr3-75720690-1	chr3	75720640	75720740	+	2.3	cIP2vsInput	Intergenic	Intergenic	-64959	NR_040539	69193	Mm.374088	NR_040539		2410007B07Rik	-	RIKEN cDNA 2410007B07 gene	miscRNA	0	0.336634
Merged-chr4-65564085-1	chr4	65564035	65564135	+	2.3	cIP1vsInput	"intron (NM_019514, intron 16 of 21)"	"intron (NM_019514, intron 16 of 21)"	-40901	NM_053084	69807	Mm.22786	NM_001161782	ENSMUSG00000051675	Trim32	1810045E12Rik|3f3|BBS11|Zfp117	tripartite motif-containing 32	protein-coding	0	0.326733
Merged-chr17-94367783-1	chr17	94367733	94367833	+	2.3	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	382109	NM_176917	76781	Mm.486648	NM_176917	ENSMUSG00000055660	Mettl4	2410198H06Rik|A730091E08Rik|AV296509|HsT661	methyltransferase like 4	protein-coding	0	0.306931
Merged-chr4-22732715-1	chr4	22732665	22732765	+	2.3	cIP2vsInput	Intergenic	Lx2B2|LINE|L1	-244349	NM_008899	18992	Mm.487875	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	"POU domain, class 3, transcription factor 2"	protein-coding	0	0.356436
Merged-chr3-82422299-1	chr3	82422249	82422349	+	2.3	cIP2vsInput	Intergenic	Intergenic	64227	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding	0.01	0.336634
Merged-chr3-61511086-1	chr3	61511036	61511136	+	2.3	cIP2vsInput	Intergenic	Lx5c|LINE|L1	146579	NM_028712	74012	Mm.477648	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	"RAP2B, member of RAS oncogene family"	protein-coding	0	0.29703
Merged-chr18-82717512-1	chr18	82717462	82717562	+	2.3	cIP2vsInput	Intergenic	Intergenic	-2769	NR_039572	100628586		NR_039572	ENSMUSG00000092638	Mir5112	mmu-mir-5112|mu-mir-5112	microRNA 5112	miscRNA	0	0.564356
Merged-chr6-20249514-1	chr6	20249464	20249564	+	2.3	cIP1vsInput	Intergenic	Intergenic	-966595	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	"potassium voltage-gated channel, Shal-related family, member 2"	protein-coding	0	0.29703
Merged-chr11-47803464-1	chr11	47803414	47803514	+	2.3	cIP1vsInput	Intergenic	L3|LINE|CR1	-424162	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	"sarcoglycan, delta (dystrophin-associated glycoprotein)"	protein-coding	0	0.415842
Merged-chr1-169123997-1	chr1	169123947	169124047	+	2.3	cIP2vsInput	Intergenic	Intergenic	407467	NM_023284	66977	Mm.151315	NM_023284	ENSMUSG00000026683	Nuf2	2410003C07Rik|AU044112|C85691|Cdca1|NUF2R	"NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"	protein-coding	0	0.356436
Merged-chr2-110396567-1	chr2	110396517	110396617	+	2.3	cIP2vsInput	Intergenic	Intergenic	-33574	NM_026271	67606	Mm.291809	NM_026271	ENSMUSG00000074971	Fibin	1110018M03Rik	fin bud initiation factor homolog (zebrafish)	protein-coding	0	0.326733
Merged-chr8-68012937-1	chr8	68012887	68012987	+	2.3	cIP2vsInput	Intergenic	Intergenic	-101991	NM_030263	234353	Mm.32525	NM_177698	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding	0.01	0.316832
Merged-chr12-119248991-1	chr12	119248941	119249041	+	2.3	cIP1vsInput	Intergenic	Intergenic	-10715	NM_177290	320910	Mm.217000	NM_177290		Itgb8	4832412O06Rik	integrin beta 8	protein-coding	0	0.207921
Merged-chr3-22812278-1	chr3	22812228	22812328	+	2.3	cIP1vsInput	Intergenic	Intergenic	560908	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	miscRNA	0	0.326733
Merged-chr4-149737921-1	chr4	149737871	149737971	+	2.3	cIP2vsInput	"exon (NM_177672, exon 1 of 6)"	"exon (NM_177672, exon 1 of 6)"	113	NM_001025106	230917	Mm.266704	XM_003945703	ENSMUSG00000044700	Tmem201	9430091K04|AV028368|D4Ertd429e|Net5|Samp1	transmembrane protein 201	protein-coding	0.13	0.782178
Merged-chr19-19200111-1	chr19	19200061	19200161	+	2.3	cIP1vsInput	Intergenic	L1M4|LINE|L1	-88915	NM_001043354	225998		NM_001043354	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta	RAR-related orphan receptor beta	protein-coding	0	0.346535
Merged-chr2-139772660-1	chr2	139772610	139772710	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	94482	NM_001276489	319909	Mm.41113	NM_001126490	ENSMUSG00000074766	Ism1	5430433G21Rik|Ism	isthmin 1 homolog (zebrafish)	protein-coding	0	0.356436
Merged-chr7-101374440-1	chr7	101374390	101374490	+	2.3	cIP2vsInput	"intron (NM_001040111, intron 3 of 33)"	"intron (NM_001040111, intron 3 of 33)"	-3682	NM_001040112	69710	Mm.277687	NM_001040111	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	"ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1"	protein-coding	0	0.485149
Merged-chr4-102772838-1	chr4	102772788	102772888	+	2.3	cIP2vsInput	"intron (NM_144906, intron 1 of 23)"	"intron (NM_144906, intron 1 of 23)"	12475	NM_144906	73094	Mm.238094	NM_144906	ENSMUSG00000028524	Sgip1	3110007P09Rik|SGIP1alpha|gag	SH3-domain GRB2-like (endophilin) interacting protein 1	protein-coding	0.01	0.306931
Merged-chr12-8120637-1	chr12	8120587	8120687	+	2.3	cIP2vsInput	Intergenic	Intergenic	-87470	NM_172401	68832	Mm.25608	NM_001167767	ENSMUSG00000037669	1110057K04Rik	-	RIKEN cDNA 1110057K04 gene	protein-coding	0.01	0.50495
Merged-chr4-92550435-1	chr4	92550385	92550485	+	2.3	cIP2vsInput	Intergenic	Intergenic	-403214	NM_027034	69314	Mm.55891	NM_027034	ENSMUSG00000028533	Izumo3	1700011H22Rik	IZUMO family member 3	protein-coding	0	0.316832
Merged-chr14-82036234-1	chr14	82036184	82036284	+	2.3	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	2035932	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.326733
Merged-chr1-34392764-1	chr1	34392714	34392814	+	2.3	cIP2vsInput	Intergenic	Intergenic	40435	NR_039562	100628580		NR_039562	ENSMUSG00000092852	Mir5103	mmu-mir-5103|mu-mir-5103	microRNA 5103	miscRNA	0.02	0.336634
Merged-chr8-97326884-1	chr8	97326834	97326934	+	2.3	cIP2vsInput	Intergenic	Intergenic	-780911	NR_039538	100628567		NR_039538		Mir28c	mmu-mir-28c	microRNA 28c	miscRNA	0.01	0.316832
Merged-chr12-14418176-1	chr12	14418126	14418226	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	156642	NR_045003	791361	Mm.217963	NR_045003		Gm16497	ENSMUSG00000066623	predicted gene 16497	miscRNA	0.02	0.326733
Merged-chr7-25396403-1	chr7	25396353	25396453	+	2.3	cIP2vsInput	promoter-TSS (NM_010719)	promoter-TSS (NM_010719)	-416	NM_010719	16890	Mm.333679	NM_001039507	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	"lipase, hormone sensitive"	protein-coding	0.09	0.633663
Merged-chr5-40289003-1	chr5	40288953	40289053	+	2.3	cIP1vsInput	Intergenic	Lx8b|LINE|L1	-644372	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding	0	0.336634
Merged-chr5-114443990-1	chr5	114443940	114444040	+	2.3	cIP2vsInput	promoter-TSS (NM_023556)	promoter-TSS (NM_023556)	37	NM_029956	77697	Mm.105182	NM_029956	ENSMUSG00000029575	Mmab	9130222L19Rik|ATR	methylmalonic aciduria (cobalamin deficiency) type B homolog (human)	protein-coding	0.11	0.693069
Merged-chr4-85162951-1	chr4	85162901	85163001	+	2.3	cIP1vsInput	Intergenic	Intergenic	-42505	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding	0.06	0.514851
Merged-chr4-80053977-1	chr4	80053927	80054027	+	2.3	cIP2vsInput	Intergenic	Intergenic	-780253	NM_031202	22178	Mm.412291	NM_031202	ENSMUSG00000005994	Tyrp1	TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding	0	0.267327
Merged-chr8-50128466-1	chr8	50128416	50128516	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-239646	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.277228
Merged-chr6-57181428-1	chr6	57181378	57181478	+	2.3	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	22508	NM_001101579	626397	Mm.475092	NM_001101579	ENSMUSG00000057981	Vmn1r12	EG626397|Gm6674	vomeronasal 1 receptor 12	protein-coding	0	0.316832
Merged-chr8-100594519-1	chr8	100594469	100594569	+	2.3	cIP1vsInput	Intergenic	Intergenic	-1178062	NM_001039154	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.326733
Merged-chr1-147886012-1	chr1	147885962	147886062	+	2.3	cIP2vsInput	Intergenic	Intergenic	1388325	NM_001145807	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.336634
Merged-chr1-107663440-1	chr1	107663390	107663490	+	2.3	cIP2vsInput	Intergenic	Intergenic	73434	NM_001159748	20725	Mm.83909	NM_001159748	ENSMUSG00000026315	Serpinb8	CAP-2|CAP2|NK10|Spi8|ovalbumin	"serine (or cysteine) peptidase inhibitor, clade B, member 8"	protein-coding	0	0.336634
Merged-chr18-77083467-1	chr18	77083417	77083517	+	2.3	cIP2vsInput	"intron (NM_001164170, intron 1 of 12)"	"intron (NM_001164170, intron 1 of 12)"	17787	NM_001164168	17344	Mm.6370	NM_001164167	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding	0	0.316832
Merged-chr12-15315093-1	chr12	15315043	15315143	+	2.3	cIP2vsInput	Intergenic	Intergenic	-264704	NR_045960	73972	Mm.107680	NR_045960		4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	miscRNA	0	0.306931
Merged-chr4-27287661-1	chr4	27287611	27287711	+	2.3	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-582212	NR_040656	75360	Mm.67233	NR_040656	ENSMUSG00000086257	4930548K13Rik	-	RIKEN cDNA 4930548K13 gene	miscRNA	0	0.336634
Merged-chr3-47739493-1	chr3	47739443	47739543	+	2.3	cIP2vsInput	Intergenic	Intergenic	287266	NR_040408	666202	Mm.465057	NR_040408		Gm7977	EG666202	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide pseudogene"	pseudo	0	0.287129
Merged-chr14-83934609-1	chr14	83934559	83934659	+	2.3	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	-508954	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0	0.316832
Merged-chr17-61778739-1	chr17	61778689	61778789	+	2.3	cIP1vsInput	Intergenic	MTD-int|LTR|ERVL-MaLR	460987	NR_030569	100124495		NR_030569		Mir466g	Mirn466g	microRNA 466g	miscRNA	0	0.336634
Merged-chr16-38080847-1	chr16	38080797	38080897	+	2.3	cIP2vsInput	Intergenic	ORR1A4|LTR|ERVL-MaLR	-8154	NM_019827	56637	Mm.394930	NM_019827	ENSMUSG00000022812	Gsk3b	7330414F15Rik|8430431H08Rik|C86142|GSK-3|GSK-3beta|GSK3	glycogen synthase kinase 3 beta	protein-coding	0	0.425743
Merged-chr6-143254545-1	chr6	143254495	143254595	+	2.3	cIP2vsInput	"intron (NR_027803, intron 3 of 3)"	"intron (NR_027803, intron 3 of 3)"	8657	NR_027803	52285	Mm.354898	NM_001033129		D6Ertd474e	1700001I24Rik|AU023129	"DNA segment, Chr 6, ERATO Doi 474, expressed"	miscRNA	0.01	0.306931
Merged-chr8-57271038-1	chr8	57270988	57271088	+	2.3	cIP2vsInput	Intergenic	Intergenic	-49945	NM_010402	15111	Mm.430844	NM_010402	ENSMUSG00000038193	Hand2	AI225906|AI661148|Ehand2|Hed|Th2|Thing2|bHLHa26|dHAND	heart and neural crest derivatives expressed transcript 2	protein-coding	0.01	0.316832
Merged-chr12-26349496-1	chr12	26349446	26349546	+	2.3	cIP1vsInput	"intron (NM_080563, intron 2 of 8)"	Lx9|LINE|L1	65760	NM_001081977	108089	Mm.214932	NM_001081977	ENSMUSG00000020642	Rnf144a	AI316797|Rnf144|UIP4|Ubce7ip4	ring finger protein 144A	protein-coding	0	0.336634
Merged-chr6-19067297-1	chr6	19067247	19067347	+	2.3	cIP1vsInput	Intergenic	Intergenic	200979	NM_001167757	75196	Mm.67665	NM_001167757	ENSMUSG00000029517	Ankrd7	4930532L20Rik|AV278427	ankyrin repeat domain 7	protein-coding	0	0.306931
Merged-chrX-23689364-1	chrX	23689314	23689414	+	2.3	cIP2vsInput	Intergenic	Intergenic	-3753	NM_175180	72404	Mm.423	NM_175180	ENSMUSG00000036769	Wdr44	2610034K17Rik|9130203L06|RAB11BP|RPH11	WD repeat domain 44	protein-coding	0	0.277228
Merged-chr4-49345244-1	chr4	49345194	49345294	+	2.3	cIP1vsInput	Intergenic	Intergenic	62907	NM_145368	209186	Mm.35071	NM_145368	ENSMUSG00000060317	Acnat2	C730036D15Rik	acyl-coenzyme A amino acid N-acyltransferase 2	protein-coding	0	0.306931
Merged-chr19-49370740-1	chr19	49370690	49370790	+	2.3	cIP2vsInput	Intergenic	Intergenic	1164715	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding	0	0.376238
Merged-chr13-88997576-1	chr13	88997526	88997626	+	2.3	cIP2vsInput	"intron (NM_001037987, intron 3 of 10)"	L1_Mur3|LINE|L1	176104	NM_001037987	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0	0.346535
Merged-chr1-20585361-1	chr1	20585311	20585411	+	2.3	cIP1vsInput	"intron (NM_153179, intron 9 of 66)"	"intron (NM_153179, intron 9 of 66)"	32696	NM_153179	241035	Mm.249253	NM_153179	ENSMUSG00000043760	Pkhd1	AI118496|AI182499|FPC|Tigm1	polycystic kidney and hepatic disease 1	protein-coding	0	0.326733
Merged-chr13-37403681-1	chr13	37403631	37403731	+	2.3	cIP2vsInput	"intron (NM_010745, intron 3 of 4)"	L1MA7|LINE|L1	58336	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1	lymphocyte antigen 86	protein-coding	0	0.386139
Merged-chr17-17927228-1	chr17	17927178	17927278	+	2.3	cIP2vsInput	Intergenic	RMER12|LTR|ERVK	39404	NM_008039	14289		NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding	0.01	0.267327
Merged-chr11-37336923-1	chr11	37336873	37336973	+	2.3	cIP2vsInput	Intergenic	Intergenic	-392680	NM_011856	23964	Mm.445432	NM_011856	ENSMUSG00000049336	Tenm2	2610040L17Rik|9330187F13Rik|D3Bwg1534e|Odz2|Odz3|Ten-m2|mKIAA1127	teneurin transmembrane protein 2	protein-coding	0.01	0.356436
Merged-chr1-128446723-1	chr1	128446673	128446773	+	2.3	cIP1vsInput	Intergenic	Intergenic	-29307	NM_145507	226414	Mm.28693	NM_145507	ENSMUSG00000026356	Dars	5730439G15Rik	aspartyl-tRNA synthetase	protein-coding	0	0.405941
Merged-chr18-52521030-1	chr18	52520980	52521080	+	2.3	cIP2vsInput	"intron (NM_010728, intron 5 of 6)"	"intron (NM_010728, intron 5 of 6)"	8678	NM_010728	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160	lysyl oxidase	protein-coding	0	0.336634
Merged-chr12-78206149-1	chr12	78206099	78206199	+	2.3	cIP2vsInput	Intergenic	Intergenic	-20506	NM_172952	268566	Mm.453131	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding	0	0.326733
Merged-chr8-20870920-1	chr8	20870870	20870970	+	2.3	cIP1vsInput	Intergenic	L1_Mus4|LINE|L1	-5579	NR_002880	654455	Mm.424927	NR_002880		Gm21944	Defb48-ps	defensin beta 48 pseudogene	pseudo	0	0.287129
Merged-chr7-69599776-1	chr7	69599726	69599826	+	2.3	cIP1vsInput	Intergenic	Intergenic	103682	NR_045940	73796	Mm.410832	NR_045940		4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	miscRNA	0	0.316832
Merged-chr10-35685956-1	chr10	35685906	35686006	+	2.3	cIP1vsInput	Intergenic	RMER3D-int|LTR|ERVK	-820851	NM_001253355	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0.01	0.366337
Merged-chr11-62781506-1	chr11	62781456	62781556	+	2.3	cIP2vsInput	"intron (NM_138949, intron 5 of 5)"	"intron (NM_138949, intron 5 of 5)"	7911	NM_138949	192651	Mm.168530	NM_138949	ENSMUSG00000047342	Zfp286	BC027023	zinc finger protein 286	protein-coding	0.01	0.346535
Merged-chr11-97874286-1	chr11	97874236	97874336	+	2.3	cIP2vsInput	"intron (NM_001081435, intron 3 of 10)"	"intron (NM_001081435, intron 3 of 10)"	9868	NM_001081435	72973	Mm.245939	NM_001081435		Fbxo47	2900052P03Rik|Gm1562	F-box protein 47	protein-coding	0	0.336634
Merged-chr7-68960733-1	chr7	68960683	68960783	+	2.3	cIP1vsInput	Intergenic	Intergenic	-211495	NM_025549	66412	Mm.251199	NM_001042592	ENSMUSG00000042659	Arrdc4	2410003C09Rik|AV216361	arrestin domain containing 4	protein-coding	0	0.247525
Merged-chr10-34827514-1	chr10	34827464	34827564	+	2.3	cIP2vsInput	Intergenic	Charlie10|DNA|hAT-Charlie	344114	NM_010237	14302	Mm.332432	NM_001159544	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding	0	0.346535
Merged-chr3-109147048-1	chr3	109146998	109147098	+	2.3	cIP1vsInput	"intron (NM_172685, intron 2 of 9)"	L1VL2|LINE|L1	23899	NM_172685	229731	Mm.33574	NM_172685	ENSMUSG00000040322	Slc25a24	2610016M12Rik	"solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 24"	protein-coding	0	0.346535
Merged-chr4-143904075-1	chr4	143904025	143904125	+	2.3	cIP2vsInput	Intergenic	Intergenic	-3695	NM_001085414	195555	Mm.389601	NM_001085414	ENSMUSG00000078512	Pramef6	Gm13099|OTTMUSG00000010429	PRAME family member 6	protein-coding	0.01	0.356436
Merged-chr7-83794255-1	chr7	83794205	83794305	+	2.3	cIP2vsInput	"intron (NM_029335, intron 1 of 6)"	"intron (NM_029335, intron 1 of 6)"	584	NM_029335	75556	Mm.17649	NM_029335	ENSMUSG00000011154	1700026D08Rik	AW047638|AW551802	RIKEN cDNA 1700026D08 gene	protein-coding	0.04	0.544554
Merged-chr3-47122024-1	chr3	47121974	47122074	+	2.3	cIP1vsInput	Intergenic	Intergenic	-674083	NM_001101479	241989	Mm.475785	NM_001101479	ENSMUSG00000090919	Pabpc4l	C330050A14Rik|EG241989	"poly(A) binding protein, cytoplasmic 4-like"	protein-coding	0	0.316832
Merged-chr13-37526223-1	chr13	37526173	37526273	+	2.3	cIP1vsInput	Intergenic	Intergenic	180878	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1	lymphocyte antigen 86	protein-coding	0.03	0.49505
Merged-chr9-81127341-1	chr9	81127291	81127391	+	2.3	cIP2vsInput	Intergenic	Intergenic	-504589	NR_040394	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	miscRNA	0.01	0.29703
Merged-chr17-94175052-1	chr17	94175002	94175102	+	2.3	cIP2vsInput	Intergenic	Intergenic	574840	NM_176917	76781	Mm.486648	NM_176917	ENSMUSG00000055660	Mettl4	2410198H06Rik|A730091E08Rik|AV296509|HsT661	methyltransferase like 4	protein-coding	0	0.346535
Merged-chr19-57767288-1	chr19	57767238	57767338	+	2.3	cIP2vsInput	"intron (NM_181415, intron 24 of 28)"	"intron (NM_181415, intron 24 of 28)"	156254	NM_181415	226255	Mm.245340	NM_181415	ENSMUSG00000054843	Atrnl1	AI504415|AW555641|Alp|Atrnl|Atrnlp	attractin like 1	protein-coding	0.01	0.346535
Merged-chr8-40537376-1	chr8	40537326	40537426	+	2.3	cIP2vsInput	"intron (NM_033560, intron 5 of 11)"	"intron (NM_033560, intron 5 of 11)"	-21529	NM_001271542	18983	Mm.272551	NM_001271542	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	"CCR4-NOT transcription complex, subunit 7"	protein-coding	0	0.356436
Merged-chr17-28232711-1	chr17	28232661	28232761	+	2.3	cIP2vsInput	promoter-TSS (NM_011145)	promoter-TSS (NM_011145)	-43	NM_011145	19015	Mm.328914	NM_011145	ENSMUSG00000002250	Ppard	NUC-1|NUC1|Nr1c2|PPAR-beta|PPAR-delta|PPAR[b]|PPARdelta|Pparb|Pparb/d	peroxisome proliferator activator receptor delta	protein-coding	0.12	0.772277
Merged-chr12-15239874-1	chr12	15239824	15239924	+	2.3	cIP2vsInput	Intergenic	Intergenic	-189485	NR_045960	73972	Mm.107680	NR_045960		4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	miscRNA	0	0.326733
Merged-chr12-94856024-1	chr12	94855974	94856074	+	2.3	cIP2vsInput	Intergenic	Intergenic	-836202	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0	0.257426
Merged-chr9-5831151-1	chr9	5831101	5831201	+	2.3	cIP2vsInput	Intergenic	Intergenic	-337461	NM_027924	71785	Mm.390122	NM_027924	ENSMUSG00000032006	Pdgfd	1110003I09Rik	"platelet-derived growth factor, D polypeptide"	protein-coding	0	0.287129
Merged-chr1-70186876-1	chr1	70186826	70186926	+	2.3	cIP2vsInput	"intron (NM_025728, intron 2 of 7)"	L1M4c|LINE|L1	235261	NM_025728	66722	Mm.440554	NM_001271533	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding	0	0.356436
Merged-chr11-94265397-1	chr11	94265347	94265447	+	2.3	cIP2vsInput	Intergenic	Intergenic	-22818	NM_181819	278507	Mm.342216	NM_181819	ENSMUSG00000044177	Wfikkn2	2610304F08Rik|AY100450|Gasp1|WFIKKNRP	"WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2"	protein-coding	0.03	0.534653
Merged-chr12-32624432-1	chr12	32624382	32624482	+	2.3	cIP1vsInput	Intergenic	Intergenic	-195903	NM_021524	59027		NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding	0	0.29703
Merged-chr16-64690275-1	chr16	64690225	64690325	+	2.3	cIP2vsInput	Intergenic	Intergenic	80664	NM_026273	67609	Mm.212157	NM_026273		4930453N24Rik	AI649104	RIKEN cDNA 4930453N24 gene	protein-coding	0	0.346535
Merged-chr8-104565111-1	chr8	104565061	104565161	+	2.3	cIP2vsInput	"intron (NR_029648, intron 1 of 2)"	"intron (NR_029648, intron 1 of 2)"	24304	NM_053070	12354	Mm.129265	NM_053070	ENSMUSG00000031883	Car7	AV343731|Ca7	carbonic anhydrase 7	protein-coding	0.04	0.594059
Merged-chr17-3603346-1	chr17	3603296	3603396	+	2.3	cIP2vsInput	Intergenic	Intergenic	45522	NR_045302	68230	Mm.431352	NR_045302		1700102H20Rik	-	RIKEN cDNA 1700102H20 gene	miscRNA	0.01	0.405941
Merged-chr16-72767298-1	chr16	72767248	72767348	+	2.3	cIP2vsInput	"intron (NM_019413, intron 2 of 28)"	"intron (NM_019413, intron 2 of 28)"	104149	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout homolog 1 (Drosophila)	protein-coding	0	0.386139
Merged-chr16-65371399-1	chr16	65371349	65371449	+	2.3	cIP2vsInput	Intergenic	Intergenic	-149230	NM_008849	18736	Mm.355440	NM_008849		Pou1f1	GHF-1|Hmp1|Pit-1|Pit1|Pit1-rs1|dw|dwarf	"POU domain, class 1, transcription factor 1"	protein-coding	0.01	0.326733
Merged-chr3-120202583-1	chr3	120202533	120202633	+	2.3	cIP2vsInput	Intergenic	MamRep1151|LTR?|LTR?	-419195	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.01	0.326733
Merged-chr16-16184590-1	chr16	16184540	16184640	+	2.3	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-28755	NM_026163	67451	Mm.2252	NM_026163	ENSMUSG00000041957	Pkp2	1200008D14Rik|1200012P04Rik|AA516617|Pkp2l	plakophilin 2	protein-coding	0.01	0.336634
Merged-chr7-24438267-1	chr7	24438217	24438317	+	2.3	cIP2vsInput	"intron (NM_199013, intron 1 of 2)"	"intron (NM_199013, intron 1 of 2)"	7415	NM_199013	210145	Mm.33811	NM_199013		Irgc1	F630044M05Rik|Gm1102|Gm474|Ifgge|Iigp5|Irgc	"immunity-related GTPase family, cinema 1"	protein-coding	0.05	0.60396
Merged-chr15-22496055-1	chr15	22496005	22496105	+	2.3	cIP1vsInput	Intergenic	Intergenic	218929	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding	0	0.346535
Merged-chr12-62046504-1	chr12	62046454	62046554	+	2.3	cIP1vsInput	Intergenic	Intergenic	521872	NM_178714	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0	0.336634
Merged-chr10-3297511-1	chr10	3297461	3297561	+	2.3	cIP2vsInput	Intergenic	Lx|LINE|L1	-29740	NM_001204916	670558	Mm.398582	NM_001204916		H60c	4632413I24Rik|Gm9491	histocompatibility 60c	protein-coding	0	0.405941
Merged-chr7-81186073-1	chr7	81186023	81186123	+	2.3	cIP1vsInput	Intergenic	RLTR13D3A1|LTR|ERVK	-27731	NM_008803	18584	Mm.371577	NM_008803		Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding	0	0.326733
Merged-chr19-9864856-1	chr19	9864806	9864906	+	2.3	cIP1vsInput	Intergenic	RMER6A|LTR|ERVK	34677	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding	0	0.376238
Merged-chr3-124454419-1	chr3	124454369	124454469	+	2.3	cIP1vsInput	Intergenic	Intergenic	-28391	NM_027939	71824	Mm.331353	NM_027939	ENSMUSG00000027973	1700006A11Rik	-	RIKEN cDNA 1700006A11 gene	protein-coding	0	0.346535
Merged-chr10-27429189-1	chr10	27429139	27429239	+	2.3	cIP2vsInput	"intron (NM_008481, intron 3 of 63)"	"intron (NM_008481, intron 3 of 63)"	187753	NM_008481	16773	Mm.256087	NM_008481	ENSMUSG00000019899	Lama2	5830440B04|dy|mKIAA4087|mer|merosin	"laminin, alpha 2"	protein-coding	0	0.326733
Merged-chr7-48734607-1	chr7	48734557	48734657	+	2.3	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-54396	NM_028031	243983	Mm.279116	NM_028031	ENSMUSG00000030471	Zdhhc13	2410004E01Rik|C530010M18|HIP3RP|Hip14l|kojak|skc4	"zinc finger, DHHC domain containing 13"	protein-coding	0.01	0.29703
Merged-chr1-104379811-1	chr1	104379761	104379861	+	2.3	cIP1vsInput	Intergenic	Intergenic	-389008	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0.02	0.326733
Merged-chr17-35737948-1	chr17	35737898	35737998	+	2.3	cIP1vsInput	Intergenic	Intergenic	-33809	NM_172962	12305	Mm.5021	NM_001198831	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	"discoidin domain receptor family, member 1"	protein-coding	0.06	0.514851
Merged-chr2-110555139-1	chr2	110555089	110555189	+	2.3	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-42160	NM_001003915	241612	Mm.277148	NM_001003915		Slc5a12	AI315119|D630015G19|SMCT2	"solute carrier family 5 (sodium/glucose cotransporter), member 12"	protein-coding	0	0.346535
Merged-chr9-44750338-1	chr9	44750288	44750388	+	2.3	cIP2vsInput	"exon (NM_145985, exon 8 of 10)"	"exon (NM_145985, exon 8 of 10)"	-15140	NM_153537	102693	Mm.28639	NM_153537	ENSMUSG00000048537	Phldb1	AU041016|D330037A14Rik|Ll5a	"pleckstrin homology-like domain, family B, member 1"	protein-coding	0.02	0.386139
Merged-chr7-128485405-1	chr7	128485355	128485455	+	2.3	cIP1vsInput	Intergenic	ORR1C2-int|LTR|ERVL-MaLR	-23892	NM_009383	21843	Mm.242072	NM_009383	ENSMUSG00000030846	Tial1	5330433G13Rik|AL033329|TIAR|mTIAR	Tia1 cytotoxic granule-associated RNA binding protein-like 1	protein-coding	0	0.425743
Merged-chr10-6505267-1	chr10	6505217	6505317	+	2.3	cIP2vsInput	Intergenic	Intergenic	-283334	NM_001039652	18390	Mm.439715	NM_011013	ENSMUSG00000000766	Oprm1	M-OR-1|MOP-R|MOR-1|MOR-1O|Oprm|mor|muOR	"opioid receptor, mu 1"	protein-coding	0.01	0.356436
Merged-chr2-63633457-1	chr2	63633407	63633507	+	2.3	cIP1vsInput	Intergenic	Intergenic	-449170	NM_133207	170738	Mm.242532	NM_133207		Kcnh7	9330137I11Rik|Kv11.3|erg3	"potassium voltage-gated channel, subfamily H (eag-related), member 7"	protein-coding	0	0.326733
Merged-chr12-12318695-1	chr12	12318645	12318745	+	2.3	cIP2vsInput	"intron (NM_001146119, intron 2 of 11)"	Lx4A|LINE|L1	56556	NM_001146119	76820	Mm.440802	NM_001146119	ENSMUSG00000020589	Fam49a	2410157M17Rik|9630047E15|D12Ertd553e	"family with sequence similarity 49, member A"	protein-coding	0.01	0.445545
Merged-chr9-81205799-1	chr9	81205749	81205849	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-426131	NR_040394	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	miscRNA	0	0.306931
Merged-chr4-154611470-2	chr4	154611409	154611532	+	2.3	cIP1vsInput|cIP2vsInput	"intron (NM_027504, intron 1 of 16)"	"intron (NM_027504, intron 1 of 16)"	24897	NR_045643	320939	Mm.436738	NR_045643		5930403L14Rik	-	RIKEN cDNA 5930403L14 gene	miscRNA	0.02439	0.5
Merged-chr3-70563363-1	chr3	70563313	70563413	+	2.3	cIP2vsInput	Intergenic	Intergenic	243928	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	miscRNA	0.01	0.346535
Merged-chr18-9461578-1	chr18	9461528	9461628	+	2.3	cIP2vsInput	Intergenic	Intergenic	-11428	NM_026484	67974	Mm.376607	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding	0	0.326733
Merged-chr6-81214834-1	chr6	81214784	81214884	+	2.3	cIP2vsInput	Intergenic	Intergenic	681842	NR_030151	723871		NR_030151		Mir468	Mirn468|mmu-mir-468	microRNA 468	miscRNA	0	0.356436
Merged-chr13-60675510-1	chr13	60675460	60675560	+	2.3	cIP2vsInput	"intron (NM_134062, intron 2 of 26)"	"intron (NM_134062, intron 2 of 26)"	73299	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	2310039H24Rik|2810425C21Rik|AI642003|D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding	0	0.514851
Merged-chr11-12239849-1	chr11	12239799	12239899	+	2.3	cIP2vsInput	"intron (NM_172496, intron 14 of 14)"	"intron (NM_172496, intron 14 of 14)"	-202429	NM_010345	14783	Mm.273117	NM_001177629	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding	0	0.425743
Merged-chr15-10527453-1	chr15	10527403	10527503	+	2.3	cIP2vsInput	"intron (NM_029430, intron 7 of 10)"	"intron (NM_029430, intron 7 of 10)"	31215	NM_029430	75777	Mm.48812	NM_029430	ENSMUSG00000022249	Ttc23l	4930401A09Rik	tetratricopeptide repeat domain 23-like	protein-coding	0	0.287129
Merged-chr8-79759151-1	chr8	79759101	79759201	+	2.3	cIP2vsInput	"intron (NM_026904, intron 4 of 4)"	L1_Mus4|LINE|L1	47331	NM_026904	68999	Mm.257445	NM_026904	ENSMUSG00000036977	Anapc10	1500026N15Rik|A830003M23Rik|APC10	anaphase promoting complex subunit 10	protein-coding	0	0.316832
Merged-chr2-180257373-1	chr2	180257323	180257423	+	2.3	cIP1vsInput	promoter-TSS (NR_037274)	promoter-TSS (NR_037274)	-6	NM_025587	66481	Mm.289669	NM_025587	ENSMUSG00000039001	Rps21	1810049N11Rik|2410030A14Rik	ribosomal protein S21	protein-coding	0.07	0.60396
Merged-chr12-82869152-1	chr12	82869102	82869202	+	2.3	cIP1vsInput	"intron (NM_015812, intron 2 of 16)"	"intron (NM_015812, intron 2 of 16)"	70003	NR_046045	74283	Mm.398247	NR_046045		1700085C21Rik	-	RIKEN cDNA 1700085C21 gene	miscRNA	0	0.386139
Merged-chr10-107676779-1	chr10	107676729	107676829	+	2.3	cIP2vsInput	"intron (NM_001081432, intron 14 of 44)"	L1_Mur3|LINE|L1	43248	NM_001081432	237523	Mm.391418	NM_001081432	ENSMUSG00000035916	Ptprq	-	"protein tyrosine phosphatase, receptor type, Q"	protein-coding	0	0.306931
Merged-chr13-47675852-1	chr13	47675802	47675902	+	2.3	cIP2vsInput	Intergenic	Intergenic	-234583	NR_045156	619327	Mm.412752	NR_045156		G630093K05Rik	-	RIKEN cDNA G630093K05 gene	miscRNA	0.02	0.386139
Merged-chr17-38302589-1	chr17	38302539	38302639	+	2.3	cIP2vsInput	Intergenic	RMER5|LTR|ERV1	2870	NM_146488	258481	Mm.377526	NM_146488	ENSMUSG00000054940	Olfr137	MOR256-18	olfactory receptor 137	protein-coding	0.01	0.356436
Merged-chr9-85517818-1	chr9	85517768	85517868	+	2.3	cIP1vsInput	Intergenic	Intergenic	-190668	NM_001160379	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	D930050G01Rik	"family with sequence similarity 46, member A"	protein-coding	0	0.346535
Merged-chr13-87238476-1	chr13	87238426	87238526	+	2.3	cIP1vsInput	Intergenic	Intergenic	-1191681	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0.01	0.287129
Merged-chr13-64431459-1	chr13	64431409	64431509	+	2.3	cIP2vsInput	Intergenic	L1M2|LINE|L1	-1094	NM_053180	105278	Mm.74982	NM_053180	ENSMUSG00000021483	Cdk20	4932702G04Rik|AU019450|AW558027|CDCH|Ccrk|PNQLARE|p42	cyclin-dependent kinase 20	protein-coding	0.01	0.336634
Merged-chr12-26473970-1	chr12	26473920	26474020	+	2.3	cIP1vsInput	"intron (NM_020557, intron 2 of 4)"	"intron (NM_020557, intron 2 of 4)"	4755	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	"cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial"	protein-coding	0.02	0.415842
Merged-chr11-68901925-1	chr11	68901875	68901975	+	2.3	cIP2vsInput	"intron (NM_009080, intron 1 of 3)"	"intron (NM_009080, intron 1 of 3)"	336	NR_003373	100034726	Mm.3229	NR_003373		Gm15772	ENSMUSG00000062353|OTTMUSG00000026108	ribosomal protein L26 pseudogene	pseudo	0.05	0.623762
Merged-chr17-58905678-1	chr17	58905628	58905728	+	2.3	cIP2vsInput	"intron (NM_027001, intron 8 of 12)"	"intron (NM_027001, intron 8 of 12)"	85697	NM_027001	69239	Mm.246732	NM_027001	ENSMUSG00000024227	2610034M16Rik	AV114557	RIKEN cDNA 2610034M16 gene	protein-coding	0	0.336634
Merged-chr16-25456598-1	chr16	25456548	25456648	+	2.3	cIP2vsInput	Intergenic	Lx7|LINE|L1	169781	NM_175165	71338	Mm.126851	NM_175165	ENSMUSG00000048399	Tprg	5430420C16Rik|Tprg1	transformation related protein 63 regulated	protein-coding	0	0.366337
Merged-chr15-46163724-1	chr15	46163674	46163774	+	2.3	cIP1vsInput	Intergenic	Intergenic	-160861	NR_045509	71120	Mm.158571	NR_045509		1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	miscRNA	0	0.277228
Merged-chr1-42681857-1	chr1	42681807	42681907	+	2.3	cIP1vsInput	"intron (NR_027826, intron 1 of 3)"	"intron (NR_027826, intron 1 of 3)"	12968	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	2610017I09Rik	-	RIKEN cDNA 2610017I09 gene	miscRNA	0.02	0.306931
Merged-chr4-140658377-1	chr4	140658327	140658427	+	2.3	cIP2vsInput	"intron (NM_001112722, intron 1 of 27)"	"intron (NM_001112722, intron 1 of 27)"	7528	NM_001112722	72754	Mm.29329	NM_001112722	ENSMUSG00000040964	Arhgef10l	2810441C07Rik|mKIAA1626	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding	0.01	0.60396
Merged-chr1-142765985-1	chr1	142765935	142766035	+	2.3	cIP2vsInput	Intergenic	Intergenic	-874712	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0	0.326733
Merged-chr19-52576113-1	chr19	52576063	52576163	+	2.3	cIP1vsInput	Intergenic	Intergenic	311790	NM_008386	16333	Mm.46269	NM_008386	ENSMUSG00000035804	Ins1	Ins-1|Ins2-rs1	insulin I	protein-coding	0	0.386139
Merged-chr17-14790326-1	chr17	14790276	14790376	+	2.3	cIP2vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	-96064	NM_011581	21826	Mm.26688	NM_011581	ENSMUSG00000023885	Thbs2	TSP2|Thbs-2	thrombospondin 2	protein-coding	0.01	0.306931
Merged-chr7-94515078-1	chr7	94515028	94515128	+	2.3	cIP2vsInput	Intergenic	Intergenic	1435199	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0	0.356436
Merged-chr14-30470451-1	chr14	30470401	30470501	+	2.3	cIP1vsInput	"intron (NM_028981, intron 1 of 46)"	"intron (NM_028981, intron 1 of 46)"	-9114	NM_133761	75901	Mm.28733	NM_133761	ENSMUSG00000021962	Dcp1a	1110066A22Rik|4930568L04Rik|AU019772|D14Ertd817e|Mitc1|SMIF	DCP1 decapping enzyme homolog A (S. cerevisiae)	protein-coding	0.01	0.306931
Merged-chr12-25161537-1	chr12	25161487	25161587	+	2.3	cIP2vsInput	Intergenic	Intergenic	32363	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	"predicted gene, 17746"	miscRNA	0.06	0.514851
Merged-chr9-79375106-1	chr9	79375056	79375156	+	2.3	cIP2vsInput	Intergenic	Intergenic	144196	NR_045336	100038575	Mm.367838	NR_045336		Gm10635	ENSMUSG00000074174	predicted gene 10635	miscRNA	0	0.336634
Merged-chr10-50134210-1	chr10	50134160	50134260	+	2.3	cIP2vsInput	Intergenic	Intergenic	-345456	NM_001111268	14806	Mm.332838	NM_001111268	ENSMUSG00000056073	Grik2	AW124492|GluK2|Glur-6|Glur6|Glurbeta2	"glutamate receptor, ionotropic, kainate 2 (beta 2)"	protein-coding	0	0.306931
Merged-chr14-115266465-1	chr14	115266415	115266515	+	2.3	cIP2vsInput	"intron (NM_175500, intron 2 of 7)"	"intron (NM_175500, intron 2 of 7)"	143087	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	miscRNA	0	0.306931
Merged-chr1-89621740-1	chr1	89621690	89621790	+	2.3	cIP2vsInput	"intron (NM_001037136, intron 3 of 16)"	"intron (NM_001037136, intron 3 of 16)"	62152	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	miscRNA	0.02	0.336634
Merged-chr16-79468360-1	chr16	79468310	79468410	+	2.3	cIP1vsInput	Intergenic	Intergenic	-377263	NM_008941	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	"transmembrane protease, serine 15"	protein-coding	0	0.326733
Merged-chr3-75022668-1	chr3	75022618	75022718	+	2.3	cIP1vsInput	Intergenic	Intergenic	121055	NM_172515	213234	Mm.80075	NM_172515	ENSMUSG00000034151	Zbbx	4931432L23	"zinc finger, B-box domain containing"	protein-coding	0	0.346535
Merged-chr2-58383151-1	chr2	58383101	58383201	+	2.3	cIP2vsInput	Intergenic	Lx8|LINE|L1	-25393	NM_001111030	269275	Mm.77751	NM_001033369	ENSMUSG00000026834	Acvr1c	ACVRLK7|ALK7|Alk-7|C230097P10	"activin A receptor, type IC"	protein-coding	0	0.336634
Merged-chr3-71436267-1	chr3	71436217	71436317	+	2.3	cIP2vsInput	Intergenic	Intergenic	-628976	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	miscRNA	0	0.326733
Merged-chr8-6901937-1	chr8	6901887	6901987	+	2.3	cIP2vsInput	Intergenic	Intergenic	1758836	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding	0.01	0.455446
Merged-chr4-129959670-1	chr4	129959620	129959720	+	2.3	cIP2vsInput	promoter-TSS (NR_040647)	promoter-TSS (NR_040647)	-704	NR_040647	72225	Mm.102193	NR_040647		1700003M07Rik	-	RIKEN cDNA 1700003M07 gene	miscRNA	0.04	0.673267
Merged-chr8-123254069-1	chr8	123254019	123254119	+	2.3	cIP1vsInput	promoter-TSS (NM_020497)	promoter-TSS (NM_020497)	106	NM_028200	72325	Mm.276193	NM_028200	ENSMUSG00000001062	Vps9d1	1300018I17Rik|2410004N05Rik|5DOS1|Vsp9d1	VPS9 domain containing 1	protein-coding	0.12	0.772277
Merged-chr6-42727897-1	chr6	42727847	42727947	+	2.3	cIP1vsInput	Intergenic	Intergenic	-16142	NM_001011799	258016	Mm.377328	NM_001011799	ENSMUSG00000095831	Olfr453	MOR257-8P	olfactory receptor 453	protein-coding	0.01	0.336634
Merged-chr10-21235836-1	chr10	21235786	21235886	+	2.3	cIP1vsInput	Intergenic	L1MA4|LINE|L1	-60143	NM_001042593	56422	Mm.25527	NM_001042593	ENSMUSG00000019977	Hbs1l	2810035F15Rik|AI326327|eRFS	Hbs1-like (S. cerevisiae)	protein-coding	0	0.366337
Merged-chr2-150645246-1	chr2	150645196	150645296	+	2.3	cIP2vsInput	"intron (NM_080575, intron 2 of 13)"	"intron (NM_080575, intron 2 of 13)"	-22248	NR_040331	109344	Mm.440012	NR_040331	ENSMUSG00000087406	E130215H24Rik	-	RIKEN cDNA E130215H24 gene	miscRNA	0	0.50495
Merged-chr16-42406894-1	chr16	42406844	42406944	+	2.3	cIP2vsInput	Intergenic	MT2A|LTR|ERVL	-66243	NM_008083	14432	Mm.1222	NM_008083	ENSMUSG00000047261	Gap43	B-50|Basp2|GAP-43	growth associated protein 43	protein-coding	0	0.316832
Merged-chr14-85999212-1	chr14	85999162	85999262	+	2.3	cIP1vsInput	Intergenic	Intergenic	-246758	NR_040457	75155	Mm.399239	NR_040457		4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	miscRNA	0	0.326733
Merged-chr2-10288927-1	chr2	10288877	10288977	+	2.3	cIP2vsInput	Intergenic	L1M2|LINE|L1	-81524	NM_001198808	353282	Mm.329991	NM_001198808	ENSMUSG00000061186	Sfmbt2	D2Wsu23e|D330030P06Rik	Scm-like with four mbt domains 2	protein-coding	0	0.29703
Merged-chr5-150180640-1	chr5	150180590	150180690	+	2.3	cIP1vsInput	Intergenic	Intergenic	-79290	NM_172887	320365	Mm.454348	NM_178781	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	furry homolog (Drosophila)	protein-coding	0	0.277228
Merged-chr3-18249160-1	chr3	18249110	18249210	+	2.3	cIP2vsInput	Intergenic	Intergenic	-5822	NM_007825	13123	Mm.316000	NM_007825	ENSMUSG00000039519	Cyp7b1	AW261589|D3Ertd552e|hct-1	"cytochrome P450, family 7, subfamily b, polypeptide 1"	protein-coding	0	0.415842
Merged-chr14-95965851-1	chr14	95965801	95965901	+	2.3	cIP2vsInput	Intergenic	ERVL-B4-int|LTR|ERVL	84585	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.366337
Merged-chr12-48097860-1	chr12	48097810	48097910	+	2.3	cIP2vsInput	Intergenic	Intergenic	203602	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0.01	0.316832
Merged-chr7-105170655-1	chr7	105170605	105170705	+	2.3	cIP1vsInput	Intergenic	Intergenic	10656	NM_001011857	258160	Mm.377366	NM_001011857	ENSMUSG00000047794	Olfr685	MOR37-1	olfactory receptor 685	protein-coding	0	0.336634
Merged-chr13-86958796-1	chr13	86958746	86958846	+	2.3	cIP2vsInput	Intergenic	Intergenic	-912001	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0	0.376238
Merged-chr7-92784956-1	chr7	92784906	92785006	+	2.3	cIP2vsInput	"intron (NM_029494, intron 1 of 4)"	PB1D7|SINE|Alu	43242	NM_029494	75985	Mm.389966	NM_029494	ENSMUSG00000030643	Rab30	5033421K01Rik|AI323892|Rsb30	"RAB30, member RAS oncogene family"	protein-coding	0	0.425743
Merged-chr13-84050522-1	chr13	84050472	84050572	+	2.3	cIP2vsInput	Intergenic	Intergenic	159314	NR_036594	72677	Mm.245636	NR_036594		2810049E08Rik	-	RIKEN cDNA 2810049E08 gene	miscRNA	0	0.366337
Merged-chr5-104072419-1	chr5	104072369	104072469	+	2.3	cIP2vsInput	"intron (NM_001163772, intron 6 of 9)"	"intron (NM_001163772, intron 6 of 9)"	5189	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	"predicted gene, 17660"	protein-coding	0.01	0.465347
Merged-chr9-4277201-1	chr9	4277151	4277251	+	2.3	cIP2vsInput	Intergenic	L1VL1|LINE|L1	32293	NM_026276	67618	Mm.33970	NM_026276	ENSMUSG00000025894	Aasdhppt	2010309J24Rik|2810407B07Rik|AASD-PPT|CGI-80|LYS2|LYS5	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	protein-coding	0	0.326733
Merged-chr1-40126876-1	chr1	40126826	40126926	+	2.3	cIP2vsInput	Intergenic	Lx8|LINE|L1	-41025	NR_037980	100047133	Mm.447052	NR_037980	ENSMUSG00000097899	Gm16894	-	"predicted gene, 16894"	miscRNA	0	0.39604
Merged-chr15-95163985-1	chr15	95163935	95164035	+	2.3	cIP1vsInput	Intergenic	Lx7|LINE|L1	-14667	NR_015482	100043315	Mm.159041	NR_015482		LOC100043315	-	uncharacterized LOC100043315	miscRNA	0	0.316832
Merged-chr7-94358680-1	chr7	94358630	94358730	+	2.3	cIP2vsInput	Intergenic	Intergenic	1278801	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0	0.316832
Merged-chr2-106533670-1	chr2	106533620	106533720	+	2.3	cIP2vsInput	Intergenic	Intergenic	-10567	NR_040637	329483	Mm.246777	NR_040637	ENSMUSG00000087226	Gm14015	9330126M15|OTTMUSG00000015366	predicted gene 14015	miscRNA	0.01	0.336634
Merged-chr11-108954635-1	chr11	108954585	108954685	+	2.3	cIP2vsInput	Intergenic	Lx9|LINE|L1	34286	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin2	protein-coding	0	0.346535
Merged-chr3-42331455-1	chr3	42331405	42331505	+	2.3	cIP1vsInput	Intergenic	ORR1F|LTR|ERVL-MaLR	588837	NM_027271	73852	Mm.29006	NM_001099785	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	"DNA segment, Chr 3, ERATO Doi 751, expressed"	protein-coding	0	0.336634
Merged-chr4-117211041-1	chr4	117210991	117211091	+	2.3	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	-28417	NM_134471	73804	Mm.247651	NM_134471	ENSMUSG00000028678	Kif2c	4930402F02Rik|ESTM5|Knsl6|MCAK|X83316	kinesin family member 2C	protein-coding	0.01	0.376238
Merged-chr1-94296258-1	chr1	94296208	94296308	+	2.3	cIP1vsInput	Intergenic	Intergenic	-243705	NM_008798	18566	Mm.5024	NM_008798	ENSMUSG00000026285	Pdcd1	Ly101|PD-1|Pdc1	programmed cell death 1	protein-coding	0.01	0.346535
Merged-chr13-15838966-1	chr13	15838916	15839016	+	2.3	cIP2vsInput	Intergenic	Intergenic	31723	NR_046131	328190	Mm.446957	NR_046131		A530046M15Rik	A530046M15	RIKEN cDNA A530046M15 gene	miscRNA	0	0.267327
Merged-chr13-91044616-1	chr13	91044566	91044666	+	2.3	cIP2vsInput	"intron (NM_025770, intron 3 of 7)"	L1M5|LINE|L1	121494	NM_024175	66475	Mm.306302	NM_024175		Rps23	2410044J15Rik	ribosomal protein S23	protein-coding	0	0.316832
Merged-chr12-97662937-1	chr12	97662887	97662987	+	2.3	cIP2vsInput	Intergenic	Intergenic	596400	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding	0.01	0.29703
Merged-chr18-24735633-1	chr18	24735583	24735683	+	2.3	cIP1vsInput	"intron (NM_175276, intron 1 of 26)"	"intron (NM_175276, intron 1 of 26)"	26188	NM_175276	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding	0.01	0.356436
Merged-chr7-26102063-1	chr7	26102013	26102113	+	2.3	cIP2vsInput	Intergenic	Lx4B|LINE|L1	40568	NM_007813	13089	Mm.482696	NM_007813	ENSMUSG00000040583	Cyp2b13	-	"cytochrome P450, family 2, subfamily b, polypeptide 13"	protein-coding	0	0.376238
Merged-chr16-39878614-1	chr16	39878564	39878664	+	2.3	cIP1vsInput	Intergenic	Intergenic	976269	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	"immunoglobulin superfamily, member 11"	protein-coding	0	0.336634
Merged-chr1-142393865-1	chr1	142393815	142393915	+	2.3	cIP1vsInput	Intergenic	Intergenic	-1246832	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0	0.306931
Merged-chr8-112865529-1	chr8	112865479	112865579	+	2.3	cIP1vsInput	"intron (NM_130457, intron 21 of 23)"	"intron (NM_130457, intron 21 of 23)"	-201733	NR_033584	791378	Mm.350576	NR_033584		Gm10280	ENSMUSG00000069883	predicted gene 10280	miscRNA	0.01	0.346535
Merged-chr2-26707227-1	chr2	26707177	26707277	+	2.3	cIP1vsInput	Intergenic	MurERV4_19-int|LTR|ERVK	-35945	NM_010695	16821	Mm.123925	NM_010695	ENSMUSG00000026919	Lcn4	A630045M08Rik|Vnsp2	lipocalin 4	protein-coding	0	0.336634
Merged-chr4-9702850-1	chr4	9702800	9702900	+	2.3	cIP1vsInput	Intergenic	L1M2|LINE|L1	-33688	NM_001177849	65973	Mm.412008	NM_001177849	ENSMUSG00000028207	Asph	2310005F16Rik|3110001L23Rik|AI848629|AW261690|AW561901|BAH|C79816|cI-37	aspartate-beta-hydroxylase	protein-coding	0	0.316832
Merged-chr12-17881892-1	chr12	17881842	17881942	+	2.3	cIP2vsInput	Intergenic	CpG	191078	NM_016677	53602	Mm.489835	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding	0.12	0.70297
Merged-chr18-30360128-1	chr18	30360078	30360178	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	87232	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	"phosphoinositide-3-kinase, class 3"	protein-coding	0	0.316832
Merged-chr3-71028645-1	chr3	71028595	71028695	+	2.3	cIP2vsInput	Intergenic	Intergenic	-221354	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	miscRNA	0	0.306931
Merged-chr7-23926724-1	chr7	23926674	23926774	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1662	NM_207545	404286	Mm.377930	NM_207545	ENSMUSG00000046924	Vmn1r179	V1rd17	vomeronasal 1 receptor 179	protein-coding	0.01	0.346535
Merged-chr1-58603125-1	chr1	58603075	58603175	+	2.3	cIP2vsInput	Intergenic	Intergenic	16526	NM_025597	66495	Mm.2033	NM_025597		Ndufb3	2700033I16Rik|AI415450	NADH dehydrogenase (ubiquinone) 1 beta subcomplex 3	protein-coding	0.01	0.336634
Merged-chr3-137424823-1	chr3	137424773	137424873	+	2.3	cIP2vsInput	"intron (NM_001163522, intron 10 of 11)"	"intron (NM_001163522, intron 10 of 11)"	83745	NM_016885	59308	Mm.27343	NM_001163522	ENSMUSG00000054690	Emcn	0610012K22Rik|AI315669|Muc14	endomucin	protein-coding	0.01	0.376238
Merged-chr10-82070533-1	chr10	82070483	82070583	+	2.3	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	22406	NM_001024626	408062	Mm.479503	NM_001024626		Zfp873	-	zinc finger protein 873	protein-coding	0	0.336634
Merged-chr12-100289883-1	chr12	100289833	100289933	+	2.3	cIP2vsInput	"intron (NR_045741, intron 1 of 3)"	"intron (NR_045741, intron 1 of 3)"	13274	NR_045741	100038713	Mm.470751	NR_045741		Gm10432	ENSMUSG00000072882	predicted gene 10432	miscRNA	0.02	0.623762
Merged-chr14-8618035-1	chr14	8617985	8618085	+	2.3	cIP2vsInput	"intron (NM_028934, intron 4 of 15)"	"intron (NM_028934, intron 4 of 15)"	48255	NM_028934	74430	Mm.271901	NM_028934	ENSMUSG00000021747	4930452B06Rik	4933406L09Rik|AI854000	RIKEN cDNA 4930452B06 gene	protein-coding	0.01	0.346535
Merged-chr4-69166731-1	chr4	69166681	69166781	+	2.3	cIP2vsInput	Intergenic	Intergenic	-212334	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Dbc1	BRINP|Brinp1|Dbccr1|Fam5a	deleted in bladder cancer 1 (human)	protein-coding	0	0.326733
Merged-chr4-89023883-1	chr4	89023833	89023933	+	2.3	cIP1vsInput	Intergenic	Intergenic	-26424	NR_033533	100040617	Mm.171720	NR_033533	ENSMUSG00000085183	Gm12603	OTTMUSG00000007693	predicted gene 12603	miscRNA	0	0.316832
Merged-chr13-87486674-1	chr13	87486624	87486724	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1334798	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0.02	0.346535
Merged-chrX-38182042-1	chrX	38181992	38182092	+	2.3	cIP2vsInput	Intergenic	(TGGGGG)n|Simple_repeat|Simple_repeat	-7751	NM_020256	56805	Mm.391248	NM_001079513	ENSMUSG00000048047	Zbtb33	AW260253|E130014G12Rik|Kaiso|Znf-kaiso	zinc finger and BTB domain containing 33	protein-coding	0.04	0.732673
Merged-chr1-105946873-1	chr1	105946823	105946923	+	2.3	cIP1vsInput	Intergenic	Intergenic	-43533	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	"zinc finger, CCHC domain containing 2"	protein-coding	0.02	0.405941
Merged-chr3-85734997-1	chr3	85734947	85735047	+	2.3	cIP2vsInput	"intron (NM_172682, intron 2 of 11)"	"intron (NM_172682, intron 2 of 11)"	11212	NM_172682	229488	Mm.119926	NM_172682	ENSMUSG00000051000	Fam160a1	9930021J17Rik	"family with sequence similarity 160, member A1"	protein-coding	0	0.316832
Merged-chr4-129455550-1	chr4	129455500	129455600	+	2.3	cIP1vsInput	Intergenic	Intergenic	-6129	NM_133889	100383	Mm.17918	NM_133889	ENSMUSG00000040859	Bsdc1	1110063F24Rik|AW011758	BSD domain containing 1	protein-coding	0.03	0.475248
Merged-chr16-59934008-1	chr16	59933958	59934058	+	2.3	cIP2vsInput	"intron (NM_007938, intron 10 of 17)"	"intron (NM_007938, intron 10 of 17)"	-294669	NM_019665	56297	Mm.392505	NM_019665	ENSMUSG00000022722	Arl6	1110018H24Rik|2210411E14Rik|BBS3	ADP-ribosylation factor-like 6	protein-coding	0	0.316832
Merged-chr15-94520982-1	chr15	94520932	94521032	+	2.3	cIP2vsInput	Intergenic	Intergenic	22525	NM_172437	78895	Mm.34344	NM_172437	ENSMUSG00000033356	Pus7l	3000003F02Rik	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	protein-coding	0.02	0.356436
Merged-chr15-37379358-1	chr15	37379308	37379408	+	2.3	cIP2vsInput	"intron (NM_001170868, intron 2 of 3)"	"intron (NM_001170868, intron 2 of 3)"	-46196	NM_029113	74892	Mm.107630	NM_029113	ENSMUSG00000022288	4930447A16Rik	-	RIKEN cDNA 4930447A16 gene	protein-coding	0.01	0.39604
Merged-chr1-68136026-1	chr1	68135976	68136076	+	2.3	cIP2vsInput	"intron (NM_010154, intron 20 of 26)"	"intron (NM_010154, intron 20 of 26)"	972033	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0	0.29703
Merged-chr4-50618243-1	chr4	50618193	50618293	+	2.3	cIP2vsInput	Intergenic	Intergenic	-598435	NM_001162865	74914	Mm.159368	NM_001162865	ENSMUSG00000039555	Cylc2	4930488P18Rik	"cylicin, basic protein of sperm head cytoskeleton 2"	protein-coding	0.01	0.29703
Merged-chr1-164720600-1	chr1	164720550	164720650	+	2.3	cIP1vsInput	Intergenic	Intergenic	-76132	NM_019759	56429	Mm.28935	NM_019759	ENSMUSG00000026574	Dpt	1810032B19Rik|5033416F05Rik|EQ-1|Eq1	dermatopontin	protein-coding	0	0.346535
Merged-chr19-6577335-1	chr19	6577285	6577385	+	2.3	cIP2vsInput	Intergenic	Intergenic	-34265	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	"solute carrier family 22 (organic anion/cation transporter), member 12"	protein-coding	0.05	0.673267
Merged-chr1-182125515-1	chr1	182125465	182125565	+	2.3	cIP2vsInput	"intron (NM_012058, intron 1 of 2)"	"intron (NM_012058, intron 1 of 2)"	778	NM_012058	27058	Mm.303071	NM_012058	ENSMUSG00000026511	Srp9	9kDa	signal recognition particle 9	protein-coding	0.02	0.485149
Merged-chr8-83179647-1	chr8	83179597	83179697	+	2.3	cIP2vsInput	"intron (NM_027758, intron 1 of 17)"	"intron (NM_027758, intron 1 of 17)"	14295	NM_027758	71310	Mm.24031	NM_001111304	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	"TBC1 domain family, member 9"	protein-coding	0.01	0.306931
Merged-chr14-123466116-1	chr14	123466066	123466166	+	2.3	cIP2vsInput	"intron (NM_177393, intron 11 of 43)"	"intron (NM_177393, intron 11 of 43)"	161028	NM_177393	338370	Mm.255348	NM_177754	ENSMUSG00000000197	Nalcn	A530023G15Rik|AI849508|Vgcnl1	"sodium leak channel, non-selective"	protein-coding	0	0.366337
Merged-chr2-21842472-1	chr2	21842422	21842522	+	2.3	cIP2vsInput	Intergenic	Intergenic	-385031	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding	0.01	0.356436
Merged-chr12-65688019-1	chr12	65687969	65688069	+	2.3	cIP2vsInput	Intergenic	L1M3b|LINE|L1	462502	NM_027614	70948	Mm.219475	NM_027614	ENSMUSG00000035560	Wdr20b	4921538B03Rik|4930427E19Rik|Wdr20	WD repeat domain 20b	protein-coding	0.01	0.287129
Merged-chr14-39954338-1	chr14	39954288	39954388	+	2.3	cIP2vsInput	Intergenic	MIR|SINE|MIR	298675	NR_045936	73591	Mm.65499	NR_045936		1700109I08Rik	-	RIKEN cDNA 1700109I08 gene	miscRNA	0	0.39604
Merged-chr4-73360433-1	chr4	73360383	73360483	+	2.3	cIP2vsInput	Intergenic	Intergenic	44639	NM_001013393	433719	Mm.348294	NM_001013393	ENSMUSG00000066137	Gm11487	OTTMUSG00000001246	predicted gene 11487	protein-coding	0	0.316832
Merged-chr12-72377180-1	chr12	72377130	72377230	+	2.3	cIP2vsInput	"intron (NM_153457, intron 1 of 8)"	"intron (NM_153457, intron 1 of 8)"	31759	NM_153457	104001	Mm.221275	NM_001007596	ENSMUSG00000021087	Rtn1	0710005K15Rik|4930441F12Rik|Nsp|R75279|Rtn1-a|Rtn1-b|Rtn1-c	reticulon 1	protein-coding	0.01	0.366337
Merged-chr14-109314634-1	chr14	109314584	109314684	+	2.3	cIP2vsInput	Intergenic	Intergenic	-145596	NR_039542	100628607		NR_039542	ENSMUSG00000092639	Mir3964	mmu-mir-3964|mu-mir-3964	microRNA 3964	miscRNA	0	0.306931
Merged-chr6-138366138-1	chr6	138366088	138366188	+	2.3	cIP2vsInput	"intron (NM_207222, intron 4 of 4)"	"intron (NM_207222, intron 4 of 4)"	215830	NM_207222	109593	Mm.490545	NM_207222		Lmo3	AI854781|BB106490|Rbtn-3|Rbtn3	LIM domain only 3	protein-coding	0.02	0.336634
Merged-chr12-55857369-1	chr12	55857319	55857419	+	2.3	cIP2vsInput	"intron (NM_001037756, intron 4 of 9)"	RLTR13D3|LTR|ERVK	21003	NM_001037756	52592	Mm.24761	NM_001037756	ENSMUSG00000012076	Brms1l	0710008O11Rik|AI159718|BRMS1|D12Ertd407e	breast cancer metastasis-suppressor 1-like	protein-coding	0.03	0.405941
Merged-chr3-79841311-1	chr3	79841261	79841361	+	2.3	cIP1vsInput	"intron (NM_027495, intron 1 of 11)"	"intron (NM_027495, intron 1 of 11)"	1351	NM_027495	70652		NM_027495	ENSMUSG00000027956	Tmem144	1110057I03Rik|5730537D05Rik	transmembrane protein 144	protein-coding	0.01	0.39604
Merged-chr11-44453563-2	chr11	44453499	44453627	+	2.3	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	16985	NM_024475	79560	Mm.338784	XM_003945884	ENSMUSG00000041231	Ublcp1	4930527B16Rik|8430435I17Rik|BC002236	ubiquitin-like domain containing CTD phosphatase 1	protein-coding	0	0.434109
Merged-chr9-29374234-1	chr9	29374184	29374284	+	2.3	cIP2vsInput	"intron (NM_172290, intron 2 of 7)"	"intron (NM_172290, intron 2 of 7)"	588895	NM_172290	235106	Mm.283138	NM_172290		Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding	0	0.336634
Merged-chr12-91412743-1	chr12	91412693	91412793	+	2.3	cIP1vsInput	"intron (NM_001113404, intron 1 of 8)"	"intron (NM_001113404, intron 1 of 8)"	11750	NM_011648	22095	Mm.173847	NM_001113404	ENSMUSG00000020963	Tshr	AI481368|hypothroid|hyt|pet	thyroid stimulating hormone receptor	protein-coding	0.01	0.415842
Merged-chr1-49871203-1	chr1	49871153	49871253	+	2.3	cIP2vsInput	Intergenic	L1MB7|LINE|L1	-1056320	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0.02	0.356436
Merged-chr6-29507656-1	chr6	29507606	29507706	+	2.3	cIP2vsInput	"intron (NM_001029985, intron 1 of 37)"	"intron (NM_001029985, intron 1 of 37)"	296	NM_001029985	333088	Mm.332961	NM_001029985	ENSMUSG00000059022	Kcp	AW060220|CRIM-2|Crim2|Gm793|KCP-1	kielin/chordin-like protein	protein-coding	0.03	0.643564
Merged-chr1-80640866-1	chr1	80640816	80640916	+	2.3	cIP1vsInput	"intron (NM_175291, intron 2 of 55)"	"intron (NM_175291, intron 2 of 55)"	117687	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding	0	0.29703
Merged-chr7-16479484-1	chr7	16479434	16479534	+	2.3	cIP1vsInput	Intergenic	RSINE1|SINE|B4	-2704	NM_008718	18142	Mm.145821	NM_008718	ENSMUSG00000001988	Npas1	MOP5|bHLHe11	neuronal PAS domain protein 1	protein-coding	0	0.584158
Merged-chrY-5251732-1	chrY	5251682	5251782	+	2.3	cIP1vsInput	Intergenic	RLTR22_Mus|LTR|ERVK	1480059	NM_001270516	100862398		NM_001270516		Gm21708	-	"predicted gene, 21708"	protein-coding	0	0.336634
Merged-chr3-146700056-1	chr3	146700006	146700106	+	2.3	cIP1vsInput	Intergenic	Lx7|LINE|L1	-48739	NM_029144	75015	Mm.475299	NM_029144		4930503B20Rik	1700013A07Rik|1700095G21Rik|4930483N21Rik	RIKEN cDNA 4930503B20 gene	protein-coding	0.02	0.534653
Merged-chr15-26930906-1	chr15	26930856	26930956	+	2.3	cIP2vsInput	Intergenic	Intergenic	-35342	NM_176959	448987	Mm.253378	NM_176959		Fbxl7	AL023057|D230018M15Rik|FBL7|Fbl6	F-box and leucine-rich repeat protein 7	protein-coding	0.01	0.366337
Merged-chr8-55875735-1	chr8	55875685	55875785	+	2.3	cIP2vsInput	"intron (NM_175939, intron 1 of 1)"	L1_Mus2|LINE|L1	31229	NM_175939	244486	Mm.67684	NM_175939	ENSMUSG00000046258	Adam29	-	a disintegrin and metallopeptidase domain 29	protein-coding	0	0.336634
Merged-chr1-145989624-1	chr1	145989574	145989674	+	2.3	cIP1vsInput	Intergenic	Intergenic	-506042	NM_153539	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0.01	0.326733
Merged-chr8-72880653-1	chr8	72880603	72880703	+	2.3	cIP2vsInput	"intron (NM_010687, intron 9 of 14)"	L1M5|LINE|L1	118773	NM_007975	14065	Mm.12948	NM_007975	ENSMUSG00000050147	F2rl3	PAR4	coagulation factor II (thrombin) receptor-like 3	protein-coding	0.02	0.326733
Merged-chr9-5483337-1	chr9	5483287	5483387	+	2.3	cIP1vsInput	Intergenic	Intergenic	137861	NM_009808	12364	Mm.42163	NM_009808	ENSMUSG00000025887	Casp12	-	caspase 12	protein-coding	0	0.316832
Merged-chr13-86897654-1	chr13	86897604	86897704	+	2.3	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-850859	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0	0.316832
Merged-chr7-113124237-1	chr7	113124187	113124287	+	2.3	cIP2vsInput	"intron (NR_045978, intron 2 of 5)"	L1MDa|LINE|L1	17778	NR_045978	75239	Mm.381688	NR_045978		4930543E12Rik	4930545H14Rik	RIKEN cDNA 4930543E12 gene	miscRNA	0	0.277228
Merged-chr3-11602651-1	chr3	11602601	11602701	+	2.3	cIP2vsInput	Intergenic	Intergenic	241708	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.29703
Merged-chr10-57052309-1	chr10	57052259	57052359	+	2.3	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	434044	NR_045353	74928	Mm.416643	NR_045353	ENSMUSG00000097370	4930467K11Rik	-	RIKEN cDNA 4930467K11 gene	miscRNA	0	0.316832
Merged-chr6-59208289-1	chr6	59208239	59208339	+	2.3	cIP1vsInput	promoter-TSS (NM_001081145)	promoter-TSS (NM_001081145)	-581	NM_001081145	68140	Mm.25843	NM_001081145	ENSMUSG00000049232	Tigd2	3632410O17Rik	tigger transposable element derived 2	protein-coding	0	0.237624
Merged-chr6-13520566-1	chr6	13520516	13520616	+	2.3	cIP2vsInput	Intergenic	L1MC|LINE|L1	87497	NM_028990	101118	Mm.254845	NM_028990	ENSMUSG00000029569	Tmem168	5730526F17Rik|8430437G11Rik|AI462344|AI504145	transmembrane protein 168	protein-coding	0	0.306931
Merged-chr17-3596581-1	chr17	3596531	3596631	+	2.3	cIP2vsInput	Intergenic	Intergenic	38757	NR_045302	68230	Mm.431352	NR_045302		1700102H20Rik	-	RIKEN cDNA 1700102H20 gene	miscRNA	0	0.267327
Merged-chr6-102713208-1	chr6	102713158	102713258	+	2.3	cIP2vsInput	Intergenic	L1M4|LINE|L1	-248541	NM_008779	18488	Mm.435479	NM_008779	ENSMUSG00000030075	Cntn3	Pang	contactin 3	protein-coding	0	0.346535
Merged-chr17-29975916-1	chr17	29975866	29975966	+	2.3	cIP2vsInput	Intergenic	Intergenic	-29171	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	"zinc finger, AN1-type domain 3"	protein-coding	0.03	0.643564
Merged-chr4-78652984-1	chr4	78652934	78653034	+	2.3	cIP2vsInput	Intergenic	L1M5|LINE|L1	-441089	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0	0.287129
Merged-chr10-46651683-1	chr10	46651633	46651733	+	2.3	cIP2vsInput	Intergenic	Intergenic	406934	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0.01	0.306931
Merged-chr11-99547829-1	chr11	99547779	99547879	+	2.3	cIP1vsInput	Intergenic	Intergenic	3034	NM_025524	66380	Mm.30539	NM_025524	ENSMUSG00000069722	Krtap3-3	2310020D06Rik|KAP3.3|KRTAP3.3	keratin associated protein 3-3	protein-coding	0.01	0.326733
Merged-chr4-27063436-1	chr4	27063386	27063486	+	2.3	cIP2vsInput	Intergenic	Intergenic	-357987	NR_040656	75360	Mm.67233	NR_040656	ENSMUSG00000086257	4930548K13Rik	-	RIKEN cDNA 4930548K13 gene	miscRNA	0.01	0.247525
Merged-chr13-90331588-1	chr13	90331538	90331638	+	2.3	cIP1vsInput	Intergenic	RLTR12B|LTR|ERVK	241921	NM_025335	66074	Mm.241387	NM_025335		Tmem167	0610041E09Rik|5730424F14Rik|AU041184|AW537806|ENSMUSG00000060669|Gm10085|Tmem167a	transmembrane protein 167	protein-coding	0	0.316832
Merged-chr4-26525105-1	chr4	26525055	26525155	+	2.3	cIP1vsInput	Intergenic	B4|SINE|B4	-178453	NM_172865	242362	Mm.245602	NM_172865	ENSMUSG00000040520	Manea	4932703L02Rik	"mannosidase, endo-alpha"	protein-coding	0.01	0.415842
Merged-chr18-26398249-1	chr18	26398199	26398299	+	2.3	cIP2vsInput	Intergenic	Lx4A|LINE|L1	-644266	NM_001174074	108013	Mm.266435	NM_001146292	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	"CUGBP, Elav-like family member 4"	protein-coding	0	0.336634
Merged-chr11-72440957-1	chr11	72440907	72441007	+	2.3	cIP2vsInput	promoter-TSS (NM_016776)	promoter-TSS (NM_016776)	-421	NM_016776	18432	Mm.147946	NM_016776	ENSMUSG00000040463	Mybbp1a	AL024407|AU019902|P160|p160MBP|p67MBP	MYB binding protein (P160) 1a	protein-coding	0.01	0.366337
Merged-chr2-55182546-1	chr2	55182496	55182596	+	2.3	cIP2vsInput	Intergenic	Intergenic	-254610	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK1|Kcnf3|Kir3.1	"potassium inwardly-rectifying channel, subfamily J, member 3"	protein-coding	0	0.39604
Merged-chr17-90021610-1	chr17	90021560	90021660	+	2.3	cIP2vsInput	Intergenic	MusHAL1|LINE|L1	642369	NR_045952	100043904	Mm.396198	NR_045952		Gm4719	-	predicted gene 4719	miscRNA	0.01	0.346535
Merged-chr8-102678931-1	chr8	102678881	102678981	+	2.3	cIP2vsInput	"intron (NM_009866, intron 3 of 12)"	"intron (NM_009866, intron 3 of 12)"	106180	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0	0.29703
Merged-chr15-91665802-1	chr15	91665752	91665852	+	2.3	cIP1vsInput	Intergenic	Intergenic	-7422	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding	0	0.366337
Merged-chr7-114561976-1	chr7	114561926	114562026	+	2.3	cIP2vsInput	"intron (NM_177382, intron 1 of 4)"	"intron (NM_177382, intron 1 of 4)"	996	NM_177382	244209	Mm.108037	NM_177382	ENSMUSG00000030670	Cyp2r1	-	"cytochrome P450, family 2, subfamily r, polypeptide 1"	protein-coding	0.02	0.287129
Merged-chr7-41381606-1	chr7	41381556	41381656	+	2.3	cIP2vsInput	"intron (NM_183167, intron 1 of 3)"	L1_Mur2|LINE|L1	11654	NM_183167	233168	Mm.379390	NM_001199330		AI987944	-	expressed sequence AI987944	protein-coding	0	0.306931
Merged-chr5-71624334-1	chr5	71624284	71624384	+	2.3	cIP2vsInput	"intron (NM_010251, intron 7 of 8)"	"intron (NM_010251, intron 7 of 8)"	33974	NM_010251	14397	Mm.248731	NM_010251	ENSMUSG00000029211	Gabra4	Gabra-4	"gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4"	protein-coding	0	0.306931
Merged-chr8-68309070-1	chr8	68309020	68309120	+	2.3	cIP2vsInput	"intron (NM_028182, intron 4 of 8)"	RCHARR1|DNA|hAT-Charlie	32542	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding	0	0.287129
Merged-chr12-8947878-1	chr12	8947828	8947928	+	2.3	cIP2vsInput	promoter-TSS (NM_010770)	promoter-TSS (NM_010770)	-51	NM_010770	17182	Mm.42226	NM_010770	ENSMUSG00000020583	Matn3	AV009181	matrilin 3	protein-coding	0.06	0.663366
Merged-chr19-46086471-1	chr19	46086421	46086521	+	2.3	cIP2vsInput	TTS (NM_053086)	TTS (NM_053086)	10608	NM_001039351	70769	Mm.486316	NM_001039351	ENSMUSG00000015176	Nolc1	3230402K17Rik|AA408077|AA536818|AU046071|NOPP130|NOPP140|P130|mKIAA0035	nucleolar and coiled-body phosphoprotein 1	protein-coding	0	0.326733
Merged-chr3-75384856-1	chr3	75384806	75384906	+	2.3	cIP2vsInput	Intergenic	Intergenic	-114778	NM_026460	67931	Mm.259446	NM_026460	ENSMUSG00000034139	Serpini2	Spi14	"serine (or cysteine) peptidase inhibitor, clade I, member 2"	protein-coding	0	0.376238
Merged-chr5-72068538-1	chr5	72068488	72068588	+	2.3	cIP2vsInput	"intron (NM_008069, intron 5 of 8)"	"intron (NM_008069, intron 5 of 8)"	99645	NM_178599	27784	Mm.44223	NM_178599	ENSMUSG00000029213	Commd8	C77770|D5Buc26e	COMM domain containing 8	protein-coding	0.01	0.316832
Merged-chr1-26245438-1	chr1	26245388	26245488	+	2.3	cIP2vsInput	Intergenic	Intergenic	-415731	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Bai3	A830096D10Rik	brain-specific angiogenesis inhibitor 3	protein-coding	0	0.346535
Merged-chr7-117775291-1	chr7	117775241	117775341	+	2.3	cIP2vsInput	Intergenic	Intergenic	340856	NM_170669	267019	Mm.288212	NM_170669	ENSMUSG00000008683	Rps15a	A630031B11Rik	ribosomal protein S15A	protein-coding	0	0.386139
Merged-chr1-28253809-1	chr1	28253759	28253859	+	2.3	cIP2vsInput	Intergenic	Intergenic	526443	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0	0.336634
Merged-chr3-135149927-1	chr3	135149877	135149977	+	2.3	cIP1vsInput	Intergenic	Intergenic	-62636	NM_173762	229841	Mm.161470	NM_173762	ENSMUSG00000045328	Cenpe	312kDa|AU019344|BC049989|C530022J18|CENP-E|Kif10	centromere protein E	protein-coding	0	0.326733
Merged-chr13-27963395-1	chr13	27963345	27963445	+	2.3	cIP2vsInput	Intergenic	ETnERV2-int|LTR|ERVK	-52828	NM_011165	19110	Mm.18607	NM_011165	ENSMUSG00000005891	Prl4a1	AA409771|PLP-A|Prlpa	"prolactin family 4, subfamily a, member 1"	protein-coding	0	0.277228
Merged-chr1-49582537-1	chr1	49582487	49582587	+	2.3	cIP1vsInput	Intergenic	Intergenic	-1344986	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.29703
Merged-chr1-147475881-1	chr1	147475831	147475931	+	2.3	cIP2vsInput	Intergenic	Intergenic	978194	NM_001145807	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.326733
Merged-chr1-102833973-1	chr1	102833923	102834023	+	2.3	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	1678205	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.316832
Merged-chr3-83841523-1	chr3	83841473	83841573	+	2.3	cIP2vsInput	promoter-TSS (NM_011905)	promoter-TSS (NM_011905)	85	NM_011905	24088	Mm.87596	NM_011905	ENSMUSG00000027995	Tlr2	Ly105	toll-like receptor 2	protein-coding	0.06	0.70297
Merged-chr14-40373615-1	chr14	40373565	40373665	+	2.3	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	519350	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding	0	0.39604
Merged-chr12-50657561-1	chr12	50657511	50657611	+	2.3	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	-8338	NM_008858	18760	Mm.133719	NM_008858	ENSMUSG00000002688	Prkd1	PKD|PKD1|Pkcm|Prkcm	protein kinase D1	protein-coding	0	0.316832
Merged-chr5-19185620-1	chr5	19185570	19185670	+	2.3	cIP1vsInput	Intergenic	Intergenic	40935	NR_102342	70832	Mm.398993	XR_106346	ENSMUSG00000097626	4921504A21Rik	-	RIKEN cDNA 4921504A21 gene	miscRNA	0.01	0.346535
Merged-chr10-121089941-1	chr10	121089891	121089991	+	2.3	cIP2vsInput	"intron (NM_011915, intron 6 of 9)"	"intron (NM_011915, intron 6 of 9)"	55937	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding	0.04	0.346535
Merged-chr8-75818842-1	chr8	75818792	75818892	+	2.3	cIP2vsInput	"intron (NM_001164235, intron 12 of 13)"	Tigger7|DNA|TcMar-Tigger	370148	NM_001164235	71831	Mm.443238	NM_001164235	ENSMUSG00000031620	1700007B14Rik	-	RIKEN cDNA 1700007B14 gene	protein-coding	0	0.346535
Merged-chr1-26119577-1	chr1	26119527	26119627	+	2.3	cIP1vsInput	Intergenic	Intergenic	-289870	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Bai3	A830096D10Rik	brain-specific angiogenesis inhibitor 3	protein-coding	0	0.326733
Merged-chr4-104422372-1	chr4	104422322	104422422	+	2.3	cIP1vsInput	"intron (NM_177259, intron 1 of 14)"	"intron (NM_177259, intron 1 of 14)"	54801	NM_177259	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding	0	0.376238
Merged-chr8-66441294-1	chr8	66441244	66441344	+	2.3	cIP2vsInput	"intron (NM_001166372, intron 6 of 7)"	"intron (NM_001166372, intron 6 of 7)"	45213	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16 homolog (S. cerevisiae)	protein-coding	0	0.356436
Merged-chr10-119169465-1	chr10	119169415	119169515	+	2.3	cIP1vsInput	Intergenic	Intergenic	70590	NM_027994	71902	Mm.203965	NM_027994	ENSMUSG00000020114	Cand1	2310038O07Rik|6330512O03Rik|AI195005|AI846556|D10Ertd516e|Tp120a|mKIAA0829	cullin associated and neddylation disassociated 1	protein-coding	0.03	0.39604
Merged-chr9-7536754-1	chr9	7536704	7536804	+	2.3	cIP1vsInput	Intergenic	Lx3B|LINE|L1	-21675	NM_008611	17394	Mm.16415	NM_008611	ENSMUSG00000005800	Mmp8	BB138268	matrix metallopeptidase 8	protein-coding	0	0.316832
Merged-chr10-46050989-1	chr10	46050939	46051039	+	2.3	cIP2vsInput	Intergenic	Intergenic	-193759	NR_028274	100302593		NR_028274		Snord14d	Gm23710	"small nucleolar RNA, C/D box 14D"	snoRNA	0	0.386139
Merged-chr15-37536838-1	chr15	37536788	37536888	+	2.3	cIP2vsInput	"intron (NM_134094, intron 4 of 6)"	"intron (NM_134094, intron 4 of 6)"	-77456	NM_001170868	52589	Mm.472945	NM_001170866	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding	0	0.366337
Merged-chr6-30205774-1	chr6	30205724	30205824	+	2.3	cIP2vsInput	Intergenic	CpG	29151	NR_038124	100463519	Mm.361139	NR_038124		BB283400	BF465573	expressed sequence BB283400	miscRNA	0.12	0.752475
Merged-chr17-82782805-1	chr17	82782755	82782855	+	2.3	cIP2vsInput	Intergenic	Intergenic	295420	NR_045094	100503434	Mm.187281	NR_045094		Gm19689	-	"predicted gene, 19689"	miscRNA	0	0.376238
Merged-chr3-93505388-1	chr3	93505338	93505438	+	2.3	cIP2vsInput	Intergenic	Looper|DNA|PiggyBac	-15108	NM_016740	20195	Mm.280038	NM_016740	ENSMUSG00000027907	S100a11	EMAPI|Emap1|S100a14|S100c|cal	S100 calcium binding protein A11 (calgizzarin)	protein-coding	0	0.376238
Merged-chr3-64182936-1	chr3	64182886	64182986	+	2.3	cIP2vsInput	Intergenic	ETnERV2-int|LTR|ERVK	-45456	NM_001104592	100125586	Mm.469888	NM_001104592	ENSMUSG00000043897	Vmn2r2	ENSMUSG00000043897	"vomeronasal 2, receptor 2"	protein-coding	0.01	0.29703
Merged-chr10-63526279-1	chr10	63526229	63526329	+	2.3	cIP2vsInput	"intron (NM_001164376, intron 2 of 17)"	"intron (NM_001164376, intron 2 of 17)"	68768	NM_001164376	216033	Mm.444692	NM_001164376	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	"catenin (cadherin associated protein), alpha 3"	protein-coding	0.04	0.514851
Merged-chr13-56522520-1	chr13	56522470	56522570	+	2.3	cIP2vsInput	promoter-TSS (NM_178674)	promoter-TSS (NM_178674)	12	NM_178674	213311	Mm.233904	NM_178674	ENSMUSG00000035509	Fbxl21	D630045D17Rik|FBL3B|FBXL3B	F-box and leucine-rich repeat protein 21	protein-coding	0.09	0.613861
Merged-chr9-19876875-1	chr9	19876825	19876925	+	2.3	cIP2vsInput	Intergenic	Intergenic	7428	NM_146562	258555	Mm.434360	NM_146562	ENSMUSG00000063842	Olfr862	MOR146-1	olfactory receptor 862	protein-coding	0	0.217822
Merged-chr4-75625143-1	chr4	75625093	75625193	+	2.3	cIP2vsInput	Intergenic	Intergenic	-346857	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	3110001D03Rik	1700027K24Rik	RIKEN cDNA 3110001D03 gene	protein-coding	0	0.287129
Merged-chr5-46758212-1	chr5	46758162	46758262	+	2.3	cIP2vsInput	Intergenic	Intergenic	-900672	NM_001163073	209707	Mm.71498	NM_001163073	ENSMUSG00000015882	Lcorl	Mlr1	ligand dependent nuclear receptor corepressor-like	protein-coding	0.01	0.485149
Merged-chr16-54508750-1	chr16	54508700	54508800	+	2.3	cIP2vsInput	Intergenic	Intergenic	774487	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding	0	0.287129
Merged-chr9-28956865-1	chr9	28956815	28956915	+	2.3	cIP1vsInput	Intergenic	Intergenic	1006264	NM_172290	235106	Mm.283138	NM_172290		Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding	0	0.346535
Merged-chr6-5841914-1	chr6	5841864	5841964	+	2.3	cIP2vsInput	"intron (NM_001191023, intron 5 of 15)"	"intron (NM_001191023, intron 5 of 15)"	116275	NM_001191026	13426	Mm.20893	NM_001191023	ENSMUSG00000029757	Dync1i1	DH IC-1|DHIC-1|DIC|Dncic1|IC74	dynein cytoplasmic 1 intermediate chain 1	protein-coding	0	0.336634
Merged-chr8-96748541-1	chr8	96748491	96748591	+	2.3	cIP2vsInput	Intergenic	Intergenic	-202568	NR_039538	100628567		NR_039538		Mir28c	mmu-mir-28c	microRNA 28c	miscRNA	0	0.376238
Merged-chr9-22919267-1	chr9	22919217	22919317	+	2.3	cIP2vsInput	Intergenic	Intergenic	-303809	NM_028472	73230	Mm.335020	NM_028472	ENSMUSG00000031963	Bmper	3110056H04Rik|CV-2|Crim3|Cv2	BMP-binding endothelial regulator	protein-coding	0	0.326733
Merged-chr14-34775321-1	chr14	34775271	34775371	+	2.3	cIP1vsInput	Intergenic	RLTR40|LTR|ERVK	-44815	NM_008166	14803	Mm.413604	NM_008166		Grid1	GluD1|GluRdelta1	"glutamate receptor, ionotropic, delta 1"	protein-coding	0	0.287129
Merged-chr4-34000554-1	chr4	34000504	34000604	+	2.3	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	49513	NM_026293	67652	Mm.55848	NM_026293	ENSMUSG00000028264	Spaca1	1700124L11Rik|4930540L03Rik	sperm acrosome associated 1	protein-coding	0.01	0.376238
Merged-chr8-21093484-1	chr8	21093434	21093534	+	2.3	cIP2vsInput	Intergenic	Intergenic	2566	NM_001177482	634825	Mm.429748	NM_001177482		Gm14851	CRS1C-2|OTTMUSG00000018260	predicted gene 14851	protein-coding	0	0.316832
Merged-chr12-94414316-1	chr12	94414266	94414366	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1277910	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0	0.366337
Merged-chr17-47180417-1	chr17	47180367	47180467	+	2.3	cIP1vsInput	"intron (NM_001097623, intron 3 of 19)"	"intron (NM_001097623, intron 3 of 19)"	39475	NM_001097623	224829	Mm.260989	NM_001097623	ENSMUSG00000064043	Trerf1	9430096I18Rik|AI429294|B830015H24|RAPA|Trep-132|Trep132	transcriptional regulating factor 1	protein-coding	0.01	0.277228
Merged-chr8-37758264-1	chr8	37758214	37758314	+	2.3	cIP1vsInput	"intron (NM_145841, intron 2 of 7)"	"intron (NM_145841, intron 2 of 7)"	493938	NR_029884	723860		NR_029884		Mir383	Mirn383|mmu-mir-383	microRNA 383	miscRNA	0	0.287129
Merged-chrX-71364787-1	chrX	71364737	71364837	+	2.3	cIP2vsInput	promoter-TSS (NM_016985)	promoter-TSS (NM_016985)	27	NM_016985	53332	Mm.219672	NM_016985	ENSMUSG00000015214	Mtmr1	AW049210	myotubularin related protein 1	protein-coding	0.16	0.742574
Merged-chr14-102527595-1	chr14	102527545	102527645	+	2.3	cIP2vsInput	Intergenic	Intergenic	455037	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mmu-mir-5130|mu-mir-5130	microRNA 5130	miscRNA	0.01	0.316832
Merged-chr6-115193316-1	chr6	115193266	115193366	+	2.3	cIP2vsInput	"intron (NM_001111015, intron 1 of 12)"	L1M3|LINE|L1	58414	NM_001111015	20965	Mm.466323	NM_001111015	ENSMUSG00000009394	Syn2	2900074L19Rik|AI836018|AI841723	synapsin II	protein-coding	0	0.356436
Merged-chrX-52934367-1	chrX	52934317	52934417	+	2.3	cIP2vsInput	"intron (NM_027642, intron 5 of 10)"	ID4|SINE|ID	22101	NM_027642	70998	Mm.26870	NM_027642	ENSMUSG00000025626	Phf6	2700007B13Rik|4931428F02Rik|mKIAA1823	PHD finger protein 6	protein-coding	0	0.435644
Merged-chr2-162658568-1	chr2	162658518	162658618	+	2.3	cIP2vsInput	"intron (NM_021464, intron 1 of 29)"	"intron (NM_021464, intron 1 of 29)"	2579	NM_021464	19281	Mm.381206	NM_021464	ENSMUSG00000053141	Ptprt	RPTP-rfo|RPTPrho|mKIAA0283	"protein tyrosine phosphatase, receptor type, T"	protein-coding	0	0.267327
Merged-chr15-21671693-1	chr15	21671643	21671743	+	2.3	cIP1vsInput	Intergenic	Intergenic	560241	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding	0	0.316832
Merged-chr1-142221401-1	chr1	142221351	142221451	+	2.3	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-1419296	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0	0.29703
Merged-chr6-141641460-1	chr6	141641410	141641510	+	2.3	cIP2vsInput	"intron (NM_020495, intron 3 of 15)"	"intron (NM_020495, intron 3 of 15)"	11942	NM_020495	28253	Mm.272223	NM_020495	ENSMUSG00000030236	Slco1b2	7330442B20Rik|OATP-C|OATP2|Oatp1b2|Oatp4|Slc21a10|Slc21a6|lst-1|mlst-1	"solute carrier organic anion transporter family, member 1b2"	protein-coding	0	0.326733
Merged-chr12-60986101-1	chr12	60986051	60986151	+	2.3	cIP2vsInput	Intergenic	Intergenic	535719	NR_045049	100504101	Mm.235026	NR_045049		Gm20063	-	"predicted gene, 20063"	miscRNA	0	0.356436
Merged-chr1-173379947-1	chr1	173379897	173379997	+	2.3	cIP2vsInput	Intergenic	L1ME4b|LINE|L1	-12252	NM_053199	94332	Mm.330524	NM_053199	ENSMUSG00000005338	Cadm3	BIgR|Igsf4b|Necl-1|Necl1|SynCAM3|Tsll1	cell adhesion molecule 3	protein-coding	0	0.316832
Merged-chr1-10504980-1	chr1	10504930	10505030	+	2.3	cIP1vsInput	"intron (NM_177834, intron 2 of 10)"	L1M5|LINE|L1	214963	NM_177834	329093	Mm.336423	NM_177834	ENSMUSG00000042501	Cpa6	9030616D13Rik	carboxypeptidase A6	protein-coding	0.01	0.346535
Merged-chr8-79926331-1	chr8	79926281	79926381	+	2.3	cIP1vsInput	Intergenic	Lx8b|LINE|L1	131677	NM_020259	15245	Mm.254493	NM_020259		Hhip	Hhip1	Hedgehog-interacting protein	protein-coding	0	0.316832
Merged-chr9-122366817-1	chr9	122366767	122366867	+	2.3	cIP2vsInput	"intron (NM_026179, intron 2 of 6)"	"intron (NM_026179, intron 2 of 6)"	15201	NM_026179	67469	Mm.280254	NM_026179	ENSMUSG00000032540	Abhd5	1300003D03Rik|2010002J10Rik|CDS|CGI-58|IECN5|NCIE2	abhydrolase domain containing 5	protein-coding	0	0.336634
Merged-chr19-31116456-1	chr19	31116406	31116506	+	2.3	cIP2vsInput	"intron (NM_001013833, intron 3 of 17)"	"intron (NM_001013833, intron 3 of 17)"	33615	NM_031249	83410		NM_031249	ENSMUSG00000053536	Cstf2t	64kDa|C77975|tCstF-64|tauCstF-64	"cleavage stimulation factor, 3' pre-RNA subunit 2, tau"	protein-coding	0	0.356436
Merged-chr8-96859236-1	chr8	96859186	96859286	+	2.3	cIP2vsInput	Intergenic	Intergenic	-313263	NR_039538	100628567		NR_039538		Mir28c	mmu-mir-28c	microRNA 28c	miscRNA	0	0.336634
Merged-chr8-33059191-1	chr8	33059141	33059241	+	2.3	cIP1vsInput	Intergenic	Intergenic	-109165	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding	0.01	0.336634
Merged-chr5-72350349-1	chr5	72350299	72350399	+	2.3	cIP2vsInput	"intron (NM_001122756, intron 10 of 21)"	"intron (NM_001122756, intron 10 of 21)"	147006	NM_153389	231287	Mm.441066	NM_153389	ENSMUSG00000046808	Atp10d	9830145H18Rik|ATPVD|D5Buc24e	"ATPase, class V, type 10D"	protein-coding	0	0.326733
Merged-chr1-103454394-1	chr1	103454344	103454444	+	2.3	cIP1vsInput	Intergenic	Lx4A|LINE|L1	-1314425	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0	0.336634
Merged-chr8-28035663-1	chr8	28035613	28035713	+	2.3	cIP2vsInput	Intergenic	Intergenic	49190	NR_033590	666422	Mm.484413	NR_033590		Gm8096	EG666422	3-phosphoglycerate dehydrogenase pseudogene	pseudo	0.01	0.326733
Merged-chr18-37178354-1	chr18	37178304	37178404	+	2.3	cIP2vsInput	"intron (NM_001003671, intron 3 of 3)"	"intron (NM_001003671, intron 3 of 3)"	34385	NM_001003672	353237	Mm.308500	NM_001003672	ENSMUSG00000007440	Pcdhac2	CNRc2	"protocadherin alpha subfamily C, 2"	protein-coding	0.03	0.574257
Merged-chrX-88832126-1	chrX	88832076	88832176	+	2.3	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-72573	NR_037313	100499530		NR_037313	ENSMUSG00000084559	Mir1906-2	mmu-mir-1906-2	microRNA 1906-2	miscRNA	0	0.29703
Merged-chr18-88939153-1	chr18	88939103	88939203	+	2.3	cIP2vsInput	Intergenic	Intergenic	-32637	NM_175542	246102	Mm.772	NM_175542	ENSMUSG00000023066	Rttn	4921538A15Rik|AI666264|C530033I08Rik|D230040K24	rotatin	protein-coding	0	0.336634
Merged-chr14-81565311-1	chr14	81565261	81565361	+	2.3	cIP2vsInput	Intergenic	Intergenic	1565009	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.415842
Merged-chr12-21185543-1	chr12	21185493	21185593	+	2.3	cIP2vsInput	"intron (NM_001004364, intron 3 of 26)"	"intron (NM_001004364, intron 3 of 26)"	73787	NM_001135192	211914	Mm.358946	NM_001004364	ENSMUSG00000052632	Asap2	6530401G17Rik|Ddef2|Gm1523|Gm592|PAG3|PAP	"ArfGAP with SH3 domain, ankyrin repeat and PH domain 2"	protein-coding	0	0.39604
Merged-chr5-55560239-1	chr5	55560189	55560289	+	2.3	cIP1vsInput	Intergenic	Intergenic	1210247	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0	0.366337
Merged-chr4-15945461-1	chr4	15945411	15945511	+	2.3	cIP2vsInput	promoter-TSS (NM_026172)	promoter-TSS (NM_026172)	46	NM_026172	67460	Mm.393293	NM_026172	ENSMUSG00000028223	Decr1	1200012F07Rik|Decr|Nadph	"2,4-dienoyl CoA reductase 1, mitochondrial"	protein-coding	0.08	0.742574
Merged-chr18-18115061-1	chr18	18115011	18115111	+	2.3	cIP1vsInput	Intergenic	Intergenic	-534071	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	miscRNA	0	0.366337
Merged-chr19-8251841-1	chr19	8251791	8251891	+	2.3	cIP2vsInput	Intergenic	MMERVK10C-int|LTR|ERVK	-33002	NM_172776	236293	Mm.440581	NM_172776	ENSMUSG00000075044	Slc22a29	D630002G06Rik	solute carrier family 22. member 29	protein-coding	0.01	0.346535
Merged-chr7-30394722-1	chr7	30394672	30394772	+	2.3	cIP2vsInput	Intergenic	Intergenic	-19066	NM_011662	22177	Mm.46301	NM_011662	ENSMUSG00000030579	Tyrobp	DAP12|KARAP|Ly83	TYRO protein tyrosine kinase binding protein	protein-coding	0.02	0.60396
Merged-chr7-112428248-1	chr7	112428198	112428298	+	2.3	cIP2vsInput	"intron (NM_020606, intron 1 of 12)"	CpG	542	NM_020606	57342	Mm.143763	NM_020606	ENSMUSG00000030770	Parva	2010012A22Rik|5430400F08Rik|AI225929|AU042898|Actp|CH-ILKBP|Parvin	"parvin, alpha"	protein-coding	0.05	0.673267
Merged-chr18-46686248-1	chr18	46686198	46686298	+	2.3	cIP1vsInput	Intergenic	Intergenic	42094	NM_033037	12583	Mm.241056	NM_033037	ENSMUSG00000033022	Cdo1	1300002L19Rik|Cdo|D18Ucla3	"cysteine dioxygenase 1, cytosolic"	protein-coding	0.01	0.326733
Merged-chrX-159371997-1	chrX	159371947	159372047	+	2.3	cIP2vsInput	promoter-TSS (NM_025437)	promoter-TSS (NM_025437)	-198	NM_025437	66235	Mm.294623	NM_025437		Eif1ax	1500010B24Rik|AI426898|Eif1ay	"eukaryotic translation initiation factor 1A, X-linked"	protein-coding	0.07	0.732673
Merged-chr1-79531817-1	chr1	79531767	79531867	+	2.3	cIP1vsInput	Intergenic	Charlie1b|DNA|hAT-Charlie	-91727	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding	0	0.29703
Merged-chr6-27260343-1	chr6	27260293	27260393	+	2.3	cIP1vsInput	Intergenic	Lx8|LINE|L1	676407	NR_030420	735266		NR_030420		Mir592	Mirn592|mir-592|mmu-mir-592	microRNA 592	miscRNA	0	0.346535
Merged-chr4-21759625-1	chr4	21759575	21759675	+	2.3	cIP2vsInput	"exon (NM_029840, exon 2 of 4)"	"exon (NM_029840, exon 2 of 4)"	7586	NM_029840	77032	Mm.87238	NM_029840	ENSMUSG00000028251	Tstd3	2610029I01Rik	thiosulfate sulfurtransferase (rhodanese)-like domain containing 3	protein-coding	0	0.316832
Merged-chr6-135168334-1	chr6	135168284	135168384	+	2.3	cIP1vsInput	promoter-TSS (NM_013546)	promoter-TSS (NM_013546)	-119	NM_013546	15199	Mm.378937	NM_013546	ENSMUSG00000042770	Hebp1	Hebp	heme binding protein 1	protein-coding	0.01	0.485149
Merged-chr9-103936078-1	chr9	103936028	103936128	+	2.3	cIP1vsInput	Intergenic	Intergenic	-66466	NM_172460	74025	Mm.479273	NM_028721	ENSMUSG00000032558	Nphp3	3632410F03Rik|AI550417|C230078J01|D330020E01Rik|pcy	nephronophthisis 3 (adolescent)	protein-coding	0	0.336634
Merged-chr3-154346113-1	chr3	154346063	154346163	+	2.3	cIP2vsInput	Intergenic	Intergenic	15292	NR_040387	99686	Mm.38082	NR_040387	ENSMUSG00000093738	AI606473	-	expressed sequence AI606473	miscRNA	0.01	0.326733
Merged-chr1-147293213-1	chr1	147293163	147293263	+	2.3	cIP2vsInput	Intergenic	Intergenic	795526	NM_001145807	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0.01	0.366337
Merged-chr16-71271801-1	chr16	71271751	71271851	+	2.3	cIP2vsInput	Intergenic	Intergenic	21897	NR_040576	78221	Mm.399298	NR_040576		4930567J20Rik	-	RIKEN cDNA 4930567J20 gene	miscRNA	0	0.306931
Merged-chr5-13786756-1	chr5	13786706	13786806	+	2.3	cIP1vsInput	Intergenic	Lx2A1|LINE|L1	-4863	NM_027650	71026	Mm.158536	NM_027650	ENSMUSG00000067855	Speer3	4933405P08Rik|SPEER-3	spermatogenesis associated glutamate (E)-rich protein 3	protein-coding	0.01	0.277228
Merged-chr6-43615438-1	chr6	43615388	43615488	+	2.3	cIP2vsInput	"intron (NM_013861, intron 2 of 8)"	"intron (NM_013861, intron 2 of 8)"	50737	NM_013861	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding	0.01	0.346535
Merged-chr6-113419586-1	chr6	113419536	113419636	+	2.3	cIP1vsInput	promoter-TSS (NM_001033204)	promoter-TSS (NM_001033204)	-246	NM_001033204	101122	Mm.31204	NM_001033204	ENSMUSG00000051169	Rpusd3	AI527266	RNA pseudouridylate synthase domain containing 3	protein-coding	0.04	0.435644
Merged-chr17-3704470-1	chr17	3704420	3704520	+	2.3	cIP2vsInput	Intergenic	Intergenic	-8209	NM_198958	224480	Mm.328756	NM_198958	ENSMUSG00000023802	Nox3	GP91-3|het|nmf250	NADPH oxidase 3	protein-coding	0.01	0.376238
Merged-chr11-99066190-1	chr11	99066140	99066240	+	2.3	cIP2vsInput	"3' UTR (NM_172564, exon 13 of 13)"	"3' UTR (NM_172564, exon 13 of 13)"	23116	NM_172564	217169	Mm.262067	NM_172564	ENSMUSG00000017607	Tns4	9930017A07Rik|AA589547|AU016405|Cten	tensin 4	protein-coding	0	0.50495
Merged-chr1-190751786-1	chr1	190751736	190751836	+	2.3	cIP1vsInput	Intergenic	Intergenic	159984	NM_178775	320119	Mm.220912	NM_178775	ENSMUSG00000089872	Rps6kc1	AA682037|B130003F20Rik|C80612|Rpk118	ribosomal protein S6 kinase polypeptide 1	protein-coding	0	0.257426
Merged-chr12-97058385-1	chr12	97058335	97058435	+	2.3	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-1011163	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0	0.326733
Merged-chr1-165252214-1	chr1	165252164	165252264	+	2.3	cIP1vsInput	Intergenic	Intergenic	-15256	NM_145513	226591	Mm.21520	NM_145513		Tiprl	1810011K17Rik	"TIP41, TOR signalling pathway regulator-like (S. cerevisiae)"	protein-coding	0.01	0.534653
Merged-chr4-8226204-1	chr4	8226154	8226254	+	2.3	cIP2vsInput	"intron (NM_007592, intron 2 of 8)"	Lx9|LINE|L1	12837	NM_007592	12319	Mm.119320	NM_007592		Car8	AW546993|Ca8|Cals|Cals1|Carp|wdl	carbonic anhydrase 8	protein-coding	0	0.326733
Merged-chr3-28160062-1	chr3	28160012	28160112	+	2.3	cIP1vsInput	Intergenic	Intergenic	-103152	NM_001163007	665113	Mm.483052	NM_001163007	ENSMUSG00000027692	Tnik	1500031A17Rik|4831440I19Rik|AI451411|C530008O15Rik|C630040K21Rik	TRAF2 and NCK interacting kinase	protein-coding	0.01	0.356436
Merged-chr1-175880707-1	chr1	175880657	175880757	+	2.3	cIP2vsInput	promoter-TSS (NM_012012)	promoter-TSS (NM_012012)	-71	NM_012012	26909	Mm.283046	NM_012012	ENSMUSG00000039748	Exo1	5730442G03Rik|Msa	exonuclease 1	protein-coding	0.07	0.623762
Merged-chr4-137809070-1	chr4	137809020	137809120	+	2.3	cIP1vsInput	Intergenic	(ATATG)n|Simple_repeat|Simple_repeat	-12693	NM_007431	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	APTNAP|Akp-2|Akp2|TNAP|TNSALP	"alkaline phosphatase, liver/bone/kidney"	protein-coding	0.01	0.207921
Merged-chr12-71814156-1	chr12	71814106	71814206	+	2.3	cIP2vsInput	Intergenic	Intergenic	-16922	NM_026102	208846	Mm.474935	NM_026102	ENSMUSG00000034574	Daam1	1700066F09Rik|2310028E21Rik|AI503486|E130308H01|mKIAA0666	dishevelled associated activator of morphogenesis 1	protein-coding	0	0.39604
Merged-chr3-87971060-1	chr3	87971010	87971110	+	2.3	cIP1vsInput	promoter-TSS (NM_016701)	promoter-TSS (NM_016701)	-33	NM_016701	18008	Mm.331129	NM_016701	ENSMUSG00000004891	Nes	AA166324|C78523|ESTM46	nestin	protein-coding	0.1	0.673267
Merged-chr4-89654433-1	chr4	89654383	89654483	+	2.3	cIP2vsInput	Intergenic	Intergenic	-33765	NM_175647	242523	Mm.130167	NM_175647	ENSMUSG00000043753	Dmrta1	Dmrt4	doublesex and mab-3 related transcription factor like family A1	protein-coding	0.01	0.356436
Merged-chr5-8381829-1	chr5	8381779	8381879	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-13748	NM_001098225	11496	Mm.275895	NM_001007220	ENSMUSG00000040537	Adam22	2900022I03Rik|AI854032|MDC2	a disintegrin and metallopeptidase domain 22	protein-coding	0	0.29703
Merged-chr10-52035750-1	chr10	52035700	52035800	+	2.3	cIP2vsInput	Intergenic	Intergenic	13064	NM_153786	215031	Mm.87237	NM_153786	ENSMUSG00000049641	Vgll2	C130057C21Rik|VITO-1|Vito1	vestigial like 2 homolog (Drosophila)	protein-coding	0	0.376238
Merged-chrX-134601575-1	chrX	134601525	134601625	+	2.3	cIP2vsInput	promoter-TSS (NM_013463)	promoter-TSS (NM_013463)	289	NM_019868	56258	Mm.315909	NM_019868	ENSMUSG00000045427	Hnrnph2	DXHXS1271E|Ftp-3|Ftp3|H'|HNRNP|Hnrph2	heterogeneous nuclear ribonucleoprotein H2	protein-coding	0.06	0.514851
Merged-chr16-68471729-1	chr16	68471679	68471779	+	2.3	cIP1vsInput	Intergenic	Intergenic	-850821	NM_178721	239857	Mm.394300	NM_001145977	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0	0.336634
Merged-chr15-67606448-1	chr15	67606398	67606498	+	2.3	cIP2vsInput	Intergenic	Lx10|LINE|L1	379679	NR_045140	69334	Mm.63770	NR_045140		1700012I11Rik	-	RIKEN cDNA 1700012I11 gene	miscRNA	0	0.366337
Merged-chr1-137545625-1	chr1	137545575	137545675	+	2.3	cIP2vsInput	Intergenic	Intergenic	-420830	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mmu-mir-213	microRNA 181a-1	miscRNA	0.01	0.336634
Merged-chr1-13565353-1	chr1	13565303	13565403	+	2.3	cIP2vsInput	"3' UTR (NM_028173, exon 11 of 11)"	"3' UTR (NM_028173, exon 11 of 11)"	24511	NM_028173	72265	Mm.28765	NM_028173	ENSMUSG00000025935	Tram1	1810049E02Rik|TRAMP	translocating chain-associating membrane protein 1	protein-coding	0.01	0.326733
Merged-chr12-91877942-1	chr12	91877892	91877992	+	2.3	cIP2vsInput	Intergenic	Intergenic	-28785	NM_011344	20338	Mm.250605	NM_001039089	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding	0.01	0.376238
Merged-chr3-43233381-1	chr3	43233331	43233431	+	2.3	cIP2vsInput	Intergenic	Intergenic	1490763	NM_027271	73852	Mm.29006	NM_001099785	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	"DNA segment, Chr 3, ERATO Doi 751, expressed"	protein-coding	0	0.306931
Merged-chr5-129379811-1	chr5	129379761	129379861	+	2.3	cIP1vsInput	Intergenic	L1MA5|LINE|L1	-121420	NM_172276	231769	Mm.288714	NM_001035259	ENSMUSG00000029439	Sfswap	1190005N23Rik|6330437E22Rik|AI197402|AW212079|SWAP|Sfrs8|Srsf8	"splicing factor, suppressor of white-apricot homolog (Drosophila)"	protein-coding	0.01	0.326733
Merged-chr1-129775708-1	chr1	129775658	129775758	+	2.3	cIP1vsInput	"intron (NM_172485, intron 9 of 27)"	"intron (NM_172485, intron 9 of 27)"	502404	NM_172485	210417	Mm.380518	NM_172485	ENSMUSG00000042581	Thsd7b	1700074E13Rik|B930082A18|D130067I03Rik	"thrombospondin, type I, domain containing 7B"	protein-coding	0	0.336634
Merged-chr14-89612341-1	chr14	89612291	89612391	+	2.3	cIP2vsInput	Intergenic	Intergenic	-283883	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0.01	0.326733
Merged-chr8-7660899-1	chr8	7660849	7660949	+	2.3	cIP1vsInput	Intergenic	Lx7|LINE|L1	999874	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding	0	0.346535
Merged-chr15-17939392-1	chr15	17939342	17939442	+	2.3	cIP2vsInput	Intergenic	RMER6C|LTR|ERVK	430235	NR_045711	70886	Mm.399021	NR_045711		4921515E04Rik	-	RIKEN cDNA 4921515E04 gene	miscRNA	0.02	0.405941
Merged-chr10-112444557-1	chr10	112444507	112444607	+	2.3	cIP2vsInput	"intron (NM_001025581, intron 2 of 4)"	"intron (NM_001025581, intron 2 of 4)"	173434	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	"potassium voltage gated channel, Shaw-related subfamily, member 2"	protein-coding	0	0.306931
Merged-chr19-60485715-1	chr19	60485665	60485765	+	2.3	cIP2vsInput	Intergenic	Intergenic	-17411	NM_201615	226278	Mm.377241	NM_201615	ENSMUSG00000045052	Prlhr	Gm339|Gpr10|Gr3|Prrpr	prolactin releasing hormone receptor	protein-coding	0	0.356436
Merged-chr18-37142913-1	chr18	37142863	37142963	+	2.3	cIP1vsInput	"intron (NM_001003671, intron 1 of 3)"	"intron (NM_001003671, intron 1 of 3)"	-1056	NM_001003672	353237	Mm.308500	NM_001003672	ENSMUSG00000007440	Pcdhac2	CNRc2	"protocadherin alpha subfamily C, 2"	protein-coding	0.01	0.326733
Merged-chr9-9208407-1	chr9	9208357	9208457	+	2.3	cIP2vsInput	"intron (NM_027823, intron 1 of 22)"	"intron (NM_027823, intron 1 of 22)"	-27881	NR_045754	100579151	Mm.412450	NR_045754		Gm16833	-	"predicted gene, 16833"	miscRNA	0	0.336634
Merged-chr3-11910102-1	chr3	11910052	11910152	+	2.3	cIP1vsInput	Intergenic	Intergenic	-65743	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0.01	0.326733
Merged-chr7-94469309-1	chr7	94469259	94469359	+	2.3	cIP2vsInput	Intergenic	Intergenic	1389430	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0	0.346535
Merged-chr3-116333205-1	chr3	116333155	116333255	+	2.3	cIP2vsInput	"intron (NM_001173553, intron 5 of 13)"	"intron (NM_001173553, intron 5 of 13)"	-79721	NM_022427	64378	Mm.40025	NM_022427	ENSMUSG00000068696	Gpr88	AW061286|Strg	G-protein coupled receptor 88	protein-coding	0.01	0.306931
Merged-chr3-75804709-1	chr3	75804659	75804759	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-148978	NR_040539	69193	Mm.374088	NR_040539		2410007B07Rik	-	RIKEN cDNA 2410007B07 gene	miscRNA	0	0.356436
Merged-chr17-38817800-1	chr17	38817750	38817850	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	178353	NM_001177586	100126768	Mm.471528	NM_001177586	ENSMUSG00000092342	Gm20516	Esp31	predicted gene 20516	protein-coding	0	0.336634
Merged-chr10-14481450-1	chr10	14481400	14481500	+	2.3	cIP2vsInput	"intron (NM_001002268, intron 2 of 24)"	"intron (NM_001002268, intron 2 of 24)"	63586	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Gpr126	1190004A11Rik|AI449247|AW045736|DREG|Gm222	G protein-coupled receptor 126	protein-coding	0.01	0.29703
Merged-chr6-58233354-1	chr6	58233304	58233404	+	2.3	cIP2vsInput	Intergenic	Lx4B|LINE|L1	-17337	NM_134436	171206	Mm.389781	NM_134436	ENSMUSG00000071428	Vmn1r27	V1rc33	vomeronasal 1 receptor 27	protein-coding	0.01	0.336634
Merged-chr2-46957776-1	chr2	46957726	46957826	+	2.3	cIP2vsInput	Intergenic	Intergenic	1261171	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	miscRNA	0	0.306931
Merged-chr9-80476830-1	chr9	80476780	80476880	+	2.3	cIP1vsInput	Intergenic	L1M5|LINE|L1	-11392	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding	0	0.29703
Merged-chr5-49199081-1	chr5	49199031	49199131	+	2.3	cIP2vsInput	"intron (NM_001199244, intron 1 of 7)"	"intron (NM_001199244, intron 1 of 7)"	86578	NM_001199244	80334	Mm.160172	NM_001199242	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding	0	0.316832
Merged-chr10-49906739-1	chr10	49906689	49906789	+	2.3	cIP2vsInput	Intergenic	MMERVK9C_I-int|LTR|ERVK	-117985	NM_001111268	14806	Mm.332838	NM_001111268	ENSMUSG00000056073	Grik2	AW124492|GluK2|Glur-6|Glur6|Glurbeta2	"glutamate receptor, ionotropic, kainate 2 (beta 2)"	protein-coding	0.01	0.366337
Merged-chr19-4993124-1	chr19	4993074	4993174	+	2.3	cIP2vsInput	Intergenic	Intergenic	-3153	NM_153553	225872	Mm.287867	NM_153553	ENSMUSG00000045903	Npas4	LE-PAS|Nxf	neuronal PAS domain protein 4	protein-coding	0.03	0.613861
Merged-chr3-143233826-1	chr3	143233776	143233876	+	2.3	cIP1vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	-9229	NR_040551	320072	Mm.136397	NR_040551		A830019L24Rik	-	RIKEN cDNA A830019L24 gene	miscRNA	0	0.306931
Merged-chr15-61236657-1	chr15	61236607	61236707	+	2.3	cIP1vsInput	Intergenic	MLT2B2|LTR|ERVL	-315387	NM_001081067	117586	Mm.291499	NM_001081067	ENSMUSG00000022347	A1bg	C44	alpha-1-B glycoprotein	protein-coding	0	0.247525
Merged-chr12-67470615-1	chr12	67470565	67470665	+	2.3	cIP2vsInput	Intergenic	RMER12B|LTR|ERVK	198656	NR_033146	100316870	Mm.379794	NR_033146		Gm17821	-	DDB1 and CUL4 associated factor 5 pseudogene	pseudo	0	0.376238
Merged-chr1-55520282-1	chr1	55520232	55520332	+	2.3	cIP2vsInput	"intron (NM_001114663, intron 1 of 5)"	"intron (NM_001114663, intron 1 of 5)"	114336	NM_001114663	227120	Mm.194183	NM_001114663		Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding	0	0.346535
Merged-chr2-32857813-1	chr2	32857763	32857863	+	2.3	cIP2vsInput	Intergenic	Intergenic	-10576	NM_001113569	20910	Mm.278865	NM_001113569	ENSMUSG00000026797	Stxbp1	AI317162|AI326233|MMS10-G|Ms10g|Munc-18a|Munc18-1|N-sec1|Rb-sec1|Sxtbp1|Unc18-1|Unc18h|nsec1	syntaxin binding protein 1	protein-coding	0.02	0.60396
Merged-chr6-26623070-1	chr6	26623020	26623120	+	2.3	cIP2vsInput	Intergenic	Lx9|LINE|L1	691644	NR_040771	626904	Mm.126787	NR_040771		Gm20756	-	"predicted gene, 20756"	miscRNA	0	0.326733
Merged-chr2-67949261-1	chr2	67949211	67949311	+	2.3	cIP1vsInput	Intergenic	Intergenic	-155411	NM_020283	26877	Mm.490783	NM_020283	ENSMUSG00000034780	B3galt1	beta3Gal-T1	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1"	protein-coding	0	0.316832
Merged-chr19-21504180-1	chr19	21504130	21504230	+	2.3	cIP1vsInput	Intergenic	Lx7|LINE|L1	-31519	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581	guanine deaminase	protein-coding	0.01	0.287129
Merged-chr2-141112482-1	chr2	141112432	141112532	+	2.3	cIP2vsInput	"intron (NM_001013802, intron 5 of 18)"	"intron (NM_001013802, intron 5 of 18)"	-441006	NM_178382	71436	Mm.426781	NM_001172160	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0	0.346535
Merged-chr6-42044575-1	chr6	42044525	42044625	+	2.3	cIP2vsInput	Intergenic	Intergenic	6181	NM_009299	20939	Mm.4119	NM_009299	ENSMUSG00000023289	Sva	-	seminal vesicle antigen	protein-coding	0	0.287129
Merged-chr13-109229601-1	chr13	109229551	109229651	+	2.3	cIP1vsInput	"intron (NM_011056, intron 3 of 16)"	"intron (NM_011056, intron 3 of 16)"	-95143	NR_030644	100124489		NR_030644		Mir582	Mirn582|mmu-mir-582	microRNA 582	miscRNA	0	0.336634
Merged-chr17-17982053-1	chr17	17982003	17982103	+	2.3	cIP2vsInput	Intergenic	Intergenic	11595	NM_008042	14294	Mm.378918	NM_008042	ENSMUSG00000079700	Fpr3	ALX|Fpr-rs1|Fpr-s1|Fprl1|LXA4-R|Lxa4r	formyl peptide receptor 3	protein-coding	0	0.29703
Merged-chr1-108706810-1	chr1	108706760	108706860	+	2.3	cIP1vsInput	Intergenic	Intergenic	789551	NR_102307	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0.01	0.217822
Merged-chr7-76665182-1	chr7	76665132	76665232	+	2.3	cIP1vsInput	"intron (NM_001199224, intron 18 of 22)"	"intron (NM_001199224, intron 18 of 22)"	435295	NM_001199224	244071	Mm.322829	NM_001199224		Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding	0	0.316832
Merged-chr3-145976818-1	chr3	145976768	145976868	+	2.3	cIP2vsInput	Intergenic	B3|SINE|B2	-11052	NM_001166064	214804	Mm.268854	NM_001166064	ENSMUSG00000036863	Syde2	C430017H16Rik	"synapse defective 1, Rho GTPase, homolog 2 (C. elegans)"	protein-coding	0	0.485149
Merged-chr11-11764672-1	chr11	11764622	11764722	+	2.3	cIP2vsInput	"intron (NM_001025597, intron 7 of 7)"	"intron (NM_001025597, intron 7 of 7)"	44290	NM_021891	60530	Mm.236114	NM_001163359	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding	0	0.39604
Merged-chr3-112272430-1	chr3	112272380	112272480	+	2.3	cIP1vsInput	Intergenic	Intergenic	390527	NR_045362	625585	Mm.389497	NR_045362		Gm6602	-	predicted gene 6602	miscRNA	0	0.267327
Merged-chr18-54299531-1	chr18	54299481	54299581	+	2.3	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-122764	NR_040338	77433	Mm.159919	NR_040338		9430076G02Rik	-	RIKEN cDNA 9430076G02 gene	miscRNA	0	0.326733
Merged-chr5-58493368-1	chr5	58493318	58493418	+	2.3	cIP2vsInput	Intergenic	Intergenic	-40370	NR_046190	78163	Mm.243828	NR_046190		4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	miscRNA	0	0.277228
Merged-chr3-11540773-1	chr3	11540723	11540823	+	2.3	cIP2vsInput	Intergenic	Intergenic	303586	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0.01	0.386139
Merged-chr6-117041855-1	chr6	117041805	117041905	+	2.3	cIP1vsInput	Intergenic	L1MEc|LINE|L1	-126680	NM_001012477	20315	Mm.303231	NM_001012477	ENSMUSG00000061353	Cxcl12	AI174028|Pbsf|Scyb12|Sdf1|Sdf1a|Sdf1b|Tlsf|Tlsfa|Tlsfb|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding	0.01	0.316832
Merged-chr1-20160320-1	chr1	20160270	20160370	+	2.3	cIP2vsInput	"intron (NM_153179, intron 60 of 66)"	"intron (NM_153179, intron 60 of 66)"	-196134	NR_045734	75028	Mm.417820	NR_045734		4930486I03Rik	-	RIKEN cDNA 4930486I03 gene	miscRNA	0	0.356436
Merged-chr15-19373531-1	chr15	19373481	19373581	+	2.3	cIP1vsInput	Intergenic	Intergenic	553202	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0	0.277228
Merged-chr1-47214610-1	chr1	47214560	47214660	+	2.3	cIP2vsInput	Intergenic	Intergenic	-361101	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.366337
Merged-chr3-14105644-1	chr3	14105594	14105694	+	2.3	cIP1vsInput	"intron (NM_178631, intron 5 of 9)"	L1_Mur2|LINE|L1	159272	NM_001163330	76897	Mm.422625	NM_001163328	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0	0.346535
Merged-chr3-156460104-1	chr3	156460054	156460154	+	2.3	cIP2vsInput	Intergenic	Intergenic	101583	NR_040398	329782	Mm.183459	NR_040398	ENSMUSG00000085084	4930570G19Rik	C630015G22	RIKEN cDNA 4930570G19 gene	miscRNA	0	0.475248
Merged-chr13-111718097-1	chr13	111718047	111718147	+	2.3	cIP2vsInput	"3' UTR (NM_172593, exon 13 of 13)"	"3' UTR (NM_172593, exon 13 of 13)"	31919	NM_172593	218613	Mm.31012	NM_172593	ENSMUSG00000032727	Mier3	5730509D14|AU015422|D130064H19Rik	"mesoderm induction early response 1, family member 3"	protein-coding	0.03	0.29703
Merged-chr19-42742026-1	chr19	42741976	42742076	+	2.3	cIP2vsInput	"intron (NM_029011, intron 5 of 15)"	"intron (NM_029011, intron 5 of 15)"	10749	NM_029011	74580	Mm.329858	NM_029011	ENSMUSG00000060224	Pyroxd2	3830409H07Rik|4833409A17Rik	pyridine nucleotide-disulphide oxidoreductase domain 2	protein-coding	0.02	0.544554
Merged-chr8-62804755-1	chr8	62804705	62804805	+	2.3	cIP2vsInput	Intergenic	Intergenic	-146477	NM_001252620	72902	Mm.334552	NM_001252620	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3"	protein-coding	0	0.316832
Merged-chr18-70219263-1	chr18	70219213	70219313	+	2.3	cIP2vsInput	Intergenic	Intergenic	25321	NM_029346	75577	Mm.58214	NM_029346	ENSMUSG00000024512	Dynap	2310002L13Rik	dynactin associated protein	protein-coding	0	0.306931
Merged-chr7-55376945-1	chr7	55376895	55376995	+	2.3	cIP2vsInput	Intergenic	Intergenic	-391233	NM_178706	233274	Mm.44425	NM_178706	ENSMUSG00000051504	Siglech	6430529G09Rik|Siglec-H	sialic acid binding Ig-like lectin H	protein-coding	0	0.306931
Merged-chr10-10407145-1	chr10	10407095	10407195	+	2.3	cIP2vsInput	"exon (NM_001127353, exon 15 of 37)"	"exon (NM_001127353, exon 15 of 37)"	65169	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding	0.01	0.346535
Merged-chr3-111182151-1	chr3	111182101	111182201	+	2.3	cIP1vsInput	Intergenic	Intergenic	-699752	NR_045362	625585	Mm.389497	NR_045362		Gm6602	-	predicted gene 6602	miscRNA	0.01	0.336634
Merged-chr13-62445844-1	chr13	62445794	62445894	+	2.3	cIP1vsInput	Intergenic	ERVB4_1-I_MM-int|LTR|ERVK	20968	NM_178875	71508	Mm.442497	NM_001136496		Zfp935	8430426H19Rik|Es113	zinc finger protein 935	protein-coding	0	0.435644
Merged-chr8-37708885-1	chr8	37708835	37708935	+	2.3	cIP2vsInput	"intron (NM_145841, intron 3 of 7)"	Lx7|LINE|L1	543317	NR_029884	723860		NR_029884		Mir383	Mirn383|mmu-mir-383	microRNA 383	miscRNA	0.01	0.346535
Merged-chr18-27744484-1	chr18	27744434	27744534	+	2.3	cIP2vsInput	Intergenic	Intergenic	-815680	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	miscRNA	0	0.356436
Merged-chr11-91785948-1	chr11	91785898	91785998	+	2.3	cIP2vsInput	Intergenic	L1MB8|LINE|L1	-208393	NM_028547	73470	Mm.67677	NM_028547	ENSMUSG00000046755	Kif2b	1700063D03Rik	kinesin family member 2B	protein-coding	0.01	0.366337
Merged-chr12-61212607-1	chr12	61212557	61212657	+	2.3	cIP2vsInput	Intergenic	Lx6|LINE|L1	309213	NR_045049	100504101	Mm.235026	NR_045049		Gm20063	-	"predicted gene, 20063"	miscRNA	0	0.316832
Merged-chr13-67500796-1	chr13	67500746	67500846	+	2.3	cIP2vsInput	promoter-TSS (NM_001007575)	promoter-TSS (NM_001007575)	-274	NM_001007575	238693	Mm.478914	NM_001007575	ENSMUSG00000071291	Zfp58	A530094I17Rik|Mfg-1|Mfg1|Rslcan5|Zfp817	zinc finger protein 58	protein-coding	0.02	0.386139
Merged-chr15-56462948-1	chr15	56462898	56462998	+	2.3	cIP2vsInput	Intergenic	Intergenic	-226996	NR_002874	594843	Mm.484850	NR_002874	ENSMUSG00000086541	Has2as	EG594843|Hasnt	HAS2 antisense RNA (non-protein coding)	miscRNA	0	0.316832
Merged-chr14-110351231-1	chr14	110351181	110351281	+	2.3	cIP1vsInput	Intergenic	Intergenic	403918	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	"SLIT and NTRK-like family, member 6"	protein-coding	0.01	0.326733
Merged-chr14-78138931-1	chr14	78138881	78138981	+	2.3	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	-49924	NM_177629	219170	Mm.320428	NM_177629	ENSMUSG00000045655	Fam216b	9330158N17|AU021034	"family with sequence similarity 216, member B"	protein-coding	0.01	0.326733
Merged-chr3-5678943-1	chr3	5678893	5678993	+	2.3	cIP1vsInput	Intergenic	L1VL1|LINE|L1	-102695	NM_001163305	19302	Mm.132336	NM_001163304	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding	0	0.326733
Merged-chr11-116615832-1	chr11	116615782	116615882	+	2.3	cIP2vsInput	"intron (NM_172572, intron 1 of 18)"	"intron (NM_172572, intron 1 of 18)"	8420	NM_001167680	217344	Mm.89695	NM_001167680	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6	rhomboid 5 homolog 2 (Drosophila)	protein-coding	0.05	0.594059
Merged-chr14-80509069-1	chr14	80509019	80509119	+	2.3	cIP2vsInput	Intergenic	Lx6|LINE|L1	508767	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.366337
Merged-chr7-77060286-1	chr7	77060236	77060336	+	2.3	cIP1vsInput	"intron (NM_001199224, intron 22 of 22)"	L1M4a2|LINE|L1	830399	NM_001199224	244071	Mm.322829	NM_001199224		Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding	0	0.376238
Merged-chr14-48367340-1	chr14	48367290	48367390	+	2.3	cIP1vsInput	Intergenic	Intergenic	-79012	NM_172600	218989	Mm.85211	NM_172600	ENSMUSG00000036339	Tmem260	5930435P15|6720456H20Rik	transmembrane protein 260	protein-coding	0.01	0.366337
Merged-chr2-17330932-1	chr2	17330882	17330982	+	2.3	cIP2vsInput	Intergenic	Lx|LINE|L1	-317206	NR_040632	75069	Mm.399263	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	miscRNA	0	0.316832
Merged-chr16-93543911-1	chr16	93543861	93543961	+	2.3	cIP1vsInput	Intergenic	Intergenic	59904	NM_145482	224440	Mm.10628	NM_145482	ENSMUSG00000022948	Setd4	AY037804|C21orf18|ORF21	SET domain containing 4	protein-coding	0.02	0.455446
Merged-chr1-40423949-1	chr1	40423899	40423999	+	2.3	cIP2vsInput	Intergenic	Intergenic	-15700	NM_010743	17082	Mm.289824	NM_001025602	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding	0	0.366337
Merged-chr6-52174748-1	chr6	52174698	52174798	+	2.3	cIP2vsInput	"intron (NM_010452, intron 3 of 4)"	"intron (NM_010452, intron 3 of 4)"	-9917	NM_010451	15399	Mm.131	NM_010451		Hoxa2	AI324701|HOX1.11|Hox-1.11	homeobox A2	protein-coding	0.02	0.326733
Merged-chr16-53634640-1	chr16	53634590	53634690	+	2.3	cIP2vsInput	Intergenic	RLTR40|LTR|ERVK	-818896	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	miscRNA	0	0.366337
Merged-chr6-4338910-1	chr6	4338860	4338960	+	2.3	cIP2vsInput	Intergenic	L1MA9|LINE|L1	-166787	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	"collagen, type I, alpha 2"	protein-coding	0	0.326733
Merged-chr15-20138775-1	chr15	20138725	20138825	+	2.3	cIP2vsInput	Intergenic	Intergenic	527975	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding	0.01	0.316832
Merged-chr2-149198979-1	chr2	149198929	149199029	+	2.3	cIP2vsInput	Intergenic	MTE-int|LTR|ERVL-MaLR	-206270	NM_021405	58214	Mm.117117	NM_021405	ENSMUSG00000033156	Cst10	DD72	cystatin 10 (chondrocytes)	protein-coding	0	0.316832
Merged-chr3-23497537-1	chr3	23497487	23497587	+	2.3	cIP1vsInput	Intergenic	Lx5|LINE|L1	1246167	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	miscRNA	0	0.346535
Merged-chr6-83215356-1	chr6	83215306	83215406	+	2.3	cIP1vsInput	Intergenic	Intergenic	-22019	NM_001166067	232156	Mm.333189	NM_001166067	ENSMUSG00000068323	Slc4a5	C330006M16|C330016K18Rik	"solute carrier family 4, sodium bicarbonate cotransporter, member 5"	protein-coding	0.01	0.465347
Merged-chr17-52291267-1	chr17	52291217	52291317	+	2.3	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-311442	NM_001031811	211468	Mm.490760	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	"potassium voltage-gated channel, subfamily H (eag-related), member 8"	protein-coding	0	0.326733
Merged-chr15-23775456-1	chr15	23775406	23775506	+	2.3	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	738993	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l	cadherin 18	protein-coding	0	0.306931
Merged-chr8-56253410-1	chr8	56253360	56253460	+	2.3	cIP2vsInput	Intergenic	Intergenic	-41142	NM_008278	15446	Mm.18832	NM_008278	ENSMUSG00000031613	Hpgd	15-PGDH|AV026552	hydroxyprostaglandin dehydrogenase 15 (NAD)	protein-coding	0.01	0.356436
Merged-chr4-106059660-1	chr4	106059610	106059710	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-256553	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding	0	0.366337
Merged-chr11-98674625-1	chr11	98674575	98674675	+	2.3	cIP1vsInput	"intron (NM_021347, intron 10 of 11)"	"intron (NM_021347, intron 10 of 11)"	-7929	NM_009439	22123	Mm.12194	NM_009439	ENSMUSG00000017221	Psmd3	AI255837|AntP91a|D11Bwg1349e|Psd3|Tstap91a	"proteasome (prosome, macropain) 26S subunit, non-ATPase, 3"	protein-coding	0.01	0.435644
Merged-chr16-63836261-1	chr16	63836211	63836311	+	2.3	cIP1vsInput	"intron (NM_010140, intron 2 of 16)"	"intron (NM_010140, intron 2 of 16)"	27896	NM_010140	13837	Mm.1977	NM_010140		Epha3	AW492086|Cek4|ETK1|End3|Hek|Hek4|Mek4|Tyro4	Eph receptor A3	protein-coding	0	0.366337
Merged-chr10-111710966-1	chr10	111710916	111711016	+	2.3	cIP2vsInput	Intergenic	Intergenic	-116693	NR_045344	71321	Mm.410785	NR_045344	ENSMUSG00000097082	4933440J02Rik	-	RIKEN cDNA 4933440J02 gene	miscRNA	0.01	0.326733
Merged-chr6-20802760-1	chr6	20802710	20802810	+	2.3	cIP2vsInput	Intergenic	Intergenic	-413349	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	"potassium voltage-gated channel, Shal-related family, member 2"	protein-coding	0.01	0.316832
Merged-chr6-9245064-1	chr6	9245014	9245114	+	2.3	cIP1vsInput	"intron (NM_008751, intron 1 of 1)"	"intron (NM_008751, intron 1 of 1)"	295045	NM_008751	18231	Mm.46954	NM_008751		Nxph1	C130005L03Rik	neurexophilin 1	protein-coding	0	0.366337
Merged-chr4-97328620-1	chr4	97328570	97328670	+	2.3	cIP2vsInput	Intergenic	Intergenic	-253323	NM_001122952	18027	Mm.409646	NM_001122952	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|NF1-A|NF1A	nuclear factor I/A	protein-coding	0	0.336634
Merged-chr16-94694704-1	chr16	94694654	94694754	+	2.3	cIP1vsInput	"3' UTR (NM_001113389, exon 12 of 12)"	"3' UTR (NM_001113389, exon 12 of 12)"	123797	NM_001113389	13548	Mm.310973	NM_001113389	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding	0	0.376238
Merged-chr16-74157620-1	chr16	74157570	74157670	+	2.3	cIP1vsInput	"intron (NM_175549, intron 2 of 27)"	"intron (NM_175549, intron 2 of 27)"	184447	NR_030464	751561		NR_030464		Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	miscRNA	0	0.306931
Merged-chr10-25644441-1	chr10	25644391	25644491	+	2.3	cIP1vsInput	Intergenic	Intergenic	-108169	NM_001195596	100504474	Mm.46323	NM_001195596	ENSMUSG00000096546	Smlr1	2010003K15Rik	small leucine-rich protein 1	protein-coding	0	0.39604
Merged-chr5-102366951-1	chr5	102366901	102367001	+	2.3	cIP1vsInput	Intergenic	Intergenic	-114440	NM_146161	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding	0.02	0.465347
Merged-chr8-56101507-1	chr8	56101457	56101557	+	2.3	cIP2vsInput	"intron (NM_080438, intron 7 of 9)"	"intron (NM_080438, intron 7 of 9)"	160682	NM_080438	110304	Mm.307061	NM_080438		Glra3	-	"glycine receptor, alpha 3 subunit"	protein-coding	0	0.316832
Merged-chr13-100928521-1	chr13	100928471	100928571	+	2.3	cIP2vsInput	Intergenic	Intergenic	-95094	NM_022885	69048	Mm.402215	NM_022885	ENSMUSG00000021629	Slc30a5	1810010K08Rik|AF233321|ZNT5|ZTL1|ZnT-5|Zntl1	"solute carrier family 30 (zinc transporter), member 5"	protein-coding	0.01	0.346535
Merged-chr3-73797377-1	chr3	73797327	73797427	+	2.3	cIP1vsInput	Intergenic	MLT1D|LTR|ERVL-MaLR	-88962	NM_009738	12038	Mm.250719	NM_009738	ENSMUSG00000027792	Bche	C730038G20Rik	butyrylcholinesterase	protein-coding	0	0.356436
Merged-chr11-11913368-1	chr11	11913318	11913418	+	2.3	cIP1vsInput	Intergenic	Lx8|LINE|L1	-15224	NM_001190448	13195	Mm.12906	NM_001190448	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding	0	0.326733
Merged-chr3-79215360-1	chr3	79215310	79215410	+	2.3	cIP2vsInput	"intron (NR_045502, intron 1 of 2)"	"intron (NR_045502, intron 1 of 2)"	2441	NR_045502	70924	Mm.444622	NR_045502		4921511C10Rik	-	RIKEN cDNA 4921511C10 gene	miscRNA	0	0.316832
Merged-chr13-87097426-1	chr13	87097376	87097476	+	2.3	cIP2vsInput	Intergenic	Lx3A|LINE|L1	-1050631	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0	0.336634
Merged-chr1-170038949-1	chr1	170038899	170038999	+	2.3	cIP2vsInput	"intron (NM_022563, intron 1 of 16)"	"intron (NM_022563, intron 1 of 16)"	49995	NM_022563	18214	Mm.229249	NM_022563	ENSMUSG00000026674	Ddr2	AW495251|Ntrkr3|tyro10	"discoidin domain receptor family, member 2"	protein-coding	0	0.287129
Merged-chr12-89955284-1	chr12	89955234	89955334	+	2.3	cIP2vsInput	"intron (NM_001252074, intron 1 of 6)"	ID_B1|SINE|B4	142801	NM_001252074	18191	Mm.487864	NM_001198587	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding	0	0.346535
Merged-chr7-94079649-1	chr7	94079599	94079699	+	2.3	cIP2vsInput	Intergenic	Intergenic	999770	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0	0.306931
Merged-chr16-88371821-1	chr16	88371771	88371871	+	2.3	cIP1vsInput	Intergenic	Arthur1|DNA|hAT-Tip100	-81563	NM_010348	14805	Mm.5134	NM_010348		Grik1	A830007B11Rik|D16Ium24|D16Ium24e|GluK1|GluK5|Glur-5|Glur5|Glurbeta1	"glutamate receptor, ionotropic, kainate 1"	protein-coding	0.02	0.316832
Merged-chr13-82520945-1	chr13	82520895	82520995	+	2.3	cIP1vsInput	Intergenic	Lx|LINE|L1	737653	NM_007684	12626	Mm.12481	NM_007684	ENSMUSG00000021537	Cetn3	MmCEN3	centrin 3	protein-coding	0	0.29703
Merged-chr4-119592993-1	chr4	119592943	119593043	+	2.3	cIP2vsInput	"intron (NM_172699, intron 4 of 12)"	"intron (NM_172699, intron 4 of 12)"	-44739	NM_008190	14915	Mm.2614	NM_008190	ENSMUSG00000023247	Guca2a	Guca2	guanylate cyclase activator 2a (guanylin)	protein-coding	0	0.336634
Merged-chr16-84887299-1	chr16	84887249	84887349	+	2.3	cIP1vsInput	Intergenic	Intergenic	-51725	NM_016755	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	-	"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F"	protein-coding	0	0.356436
Merged-chr1-91436510-1	chr1	91436460	91436560	+	2.3	cIP1vsInput	"intron (NM_011066, intron 9 of 22)"	"intron (NM_011066, intron 9 of 22)"	22818	NM_011066	18627	Mm.482463	NM_011066	ENSMUSG00000055866	Per2	mKIAA0347|mPer2	period circadian clock 2	protein-coding	0	0.524752
Merged-chr11-45866870-1	chr11	45866820	45866920	+	2.3	cIP2vsInput	"intron (NM_001045520, intron 1 of 11)"	"intron (NM_001045520, intron 1 of 11)"	14906	NM_001045520	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding	0	0.346535
Merged-chr2-83183299-1	chr2	83183249	83183349	+	2.3	cIP2vsInput	Intergenic	L1MB1|LINE|L1	-461279	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding	0	0.336634
Merged-chr13-114739455-1	chr13	114739405	114739505	+	2.3	cIP1vsInput	Intergenic	Intergenic	-78782	NM_013826	17434	Mm.19027	NM_001113374		Mocs2	AI415403	molybdenum cofactor synthesis 2	protein-coding	0	0.287129
Merged-chr11-49074631-1	chr11	49074581	49074681	+	2.3	cIP2vsInput	"intron (NM_010999, intron 1 of 5)"	L1_Mur3|LINE|L1	-1956	NM_001271677	15953	Mm.24769	NM_001271676	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding	0.02	0.366337
Merged-chr6-75390943-1	chr6	75390893	75390993	+	2.3	cIP1vsInput	Intergenic	Intergenic	-1851774	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0	0.336634
Merged-chr2-25428520-1	chr2	25428470	25428570	+	2.3	cIP2vsInput	promoter-TSS (NM_007379)	promoter-TSS (NM_007379)	-154	NM_007379	11305	Mm.2210	NM_007379	ENSMUSG00000026944	Abca2	AI413825|Abc2|D2H0S1474E|mKIAA1062	"ATP-binding cassette, sub-family A (ABC1), member 2"	protein-coding	0.1	0.70297
Merged-chr4-79498274-1	chr4	79498224	79498324	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1286379	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0.01	0.376238
Merged-chr1-173361908-1	chr1	173361858	173361958	+	2.3	cIP2vsInput	"intron (NM_053199, intron 1 of 8)"	"intron (NM_053199, intron 1 of 8)"	5787	NM_053199	94332	Mm.330524	NM_053199	ENSMUSG00000005338	Cadm3	BIgR|Igsf4b|Necl-1|Necl1|SynCAM3|Tsll1	cell adhesion molecule 3	protein-coding	0	0.485149
Merged-chr17-26794755-1	chr17	26794705	26794805	+	2.3	cIP2vsInput	Intergenic	Intergenic	13676	NM_172149	224630	Mm.21795	NM_172149	ENSMUSG00000024191	Bnip1	2010005M06Rik|5930429G21Rik|Sec20	BCL2/adenovirus E1B interacting protein 1	protein-coding	0.02	0.485149
Merged-chr14-111588978-1	chr14	111588928	111589028	+	2.3	cIP1vsInput	Intergenic	Intergenic	-86137	NM_198865	75409	Mm.417152	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	"SLIT and NTRK-like family, member 5"	protein-coding	0.01	0.29703
Merged-chr5-100704958-1	chr5	100704908	100705008	+	2.3	cIP1vsInput	"intron (NM_152803, intron 3 of 11)"	Tigger1|DNA|TcMar-Tigger	14725	NM_152803	15442	Mm.265786	NM_152803	ENSMUSG00000035273	Hpse	HSE1|Hpa|Hpr1	heparanase	protein-coding	0	0.326733
Merged-chr6-82996896-1	chr6	82996846	82996946	+	2.3	cIP2vsInput	"intron (NM_033079, intron 4 of 9)"	"intron (NM_033079, intron 4 of 9)"	36575	NM_010070	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding	0.04	0.524752
Merged-chr13-27467240-1	chr13	27467190	27467290	+	2.3	cIP2vsInput	Intergenic	Intergenic	-28552	NM_001271378	19112	Mm.142728	NM_001271378	ENSMUSG00000021345	Prl8a6	PLP-C1|PLP-Ca|PLP-calpha|Prlpc|Prlpc1	"prolactin family 8, subfamily a, member 6"	protein-coding	0	0.405941
Merged-chr1-192565061-1	chr1	192565011	192565111	+	2.3	cIP2vsInput	"intron (NM_144881, intron 10 of 11)"	MTC-int|LTR|ERVL-MaLR	206158	NM_144881	226861	Mm.145857	NM_144881	ENSMUSG00000037375	Hhat	2810432O22Rik|AI462858|AP-2CRE|Skn|Tg(TFAP2A-cre)1Will	hedgehog acyltransferase	protein-coding	0	0.366337
Merged-chr6-11043256-1	chr6	11043206	11043306	+	2.3	cIP1vsInput	Intergenic	Intergenic	-68878	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	miscRNA	0	0.29703
Merged-chr18-36265842-1	chr18	36265792	36265892	+	2.3	cIP2vsInput	Intergenic	Intergenic	-15320	NM_008989	19290	Mm.482241	NM_008989		Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding	0.02	0.346535
Merged-chrX-59576514-1	chrX	59576464	59576564	+	2.3	cIP1vsInput	Intergenic	RMER5|LTR|ERV1	-422950	NM_007979	14071	Mm.391283	NM_007979	ENSMUSG00000031138	F9	AW111646|Cf-9|Cf9	coagulation factor IX	protein-coding	0.01	0.29703
Merged-chr3-159164951-1	chr3	159164901	159165001	+	2.3	cIP2vsInput	"intron (NR_040750, intron 2 of 4)"	Lx7|LINE|L1	88587	NR_040750	624759	Mm.491054	NR_040750		Gm20752	-	"predicted gene, 20752"	miscRNA	0	0.336634
Merged-chr14-62572680-1	chr14	62572630	62572730	+	2.3	cIP2vsInput	"intron (NM_001243857, intron 2 of 3)"	RLTR19-int|LTR|ERVK	16943	NM_001243857	629059	Mm.291864	NM_001243857	ENSMUSG00000035184	Fam124a	EG629059	"family with sequence similarity 124, member A"	protein-coding	0.01	0.376238
Merged-chr18-8998678-1	chr18	8998628	8998728	+	2.3	cIP2vsInput	Intergenic	Lx|LINE|L1	-214178	NM_008058	14370	Mm.184289	NM_008058	ENSMUSG00000036904	Fzd8	Fz8	frizzled homolog 8 (Drosophila)	protein-coding	0	0.405941
Merged-chr15-47776131-1	chr15	47776081	47776181	+	2.3	cIP2vsInput	"intron (NM_001081391, intron 32 of 70)"	"intron (NM_001081391, intron 32 of 70)"	1015858	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0	0.356436
Merged-chr13-55041447-1	chr13	55041397	55041497	+	2.3	cIP2vsInput	"intron (NM_011307, intron 10 of 14)"	"intron (NM_011307, intron 10 of 14)"	-20062	NM_001033245	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding	0	0.346535
Merged-chr3-3483527-1	chr3	3483477	3483577	+	2.3	cIP2vsInput	Intergenic	Lx3_Mus|LINE|L1	-24503	NM_013920	30942	Mm.330897	NM_013920		Hnf4g	NR2A2	"hepatocyte nuclear factor 4, gamma"	protein-coding	0	0.316832
Merged-chr1-21770584-1	chr1	21770534	21770634	+	2.3	cIP1vsInput	"intron (NM_023872, intron 1 of 13)"	"intron (NM_023872, intron 1 of 13)"	191358	NM_001160139	226922	Mm.403737	NM_001160139	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	"potassium voltage-gated channel, subfamily Q, member 5"	protein-coding	0	0.346535
Merged-chrX-166509991-1	chrX	166509941	166510041	+	2.3	cIP2vsInput	"intron (NM_001007577, intron 1 of 4)"	"intron (NM_001007577, intron 1 of 4)"	487	NM_001007577	245695	Mm.336318	NM_001007577	ENSMUSG00000051224	Tceanc	A630018P17Rik|Gm390	transcription elongation factor A (SII) N-terminal and central domain containing	protein-coding	0.02	0.485149
Merged-chr1-144197694-1	chr1	144197644	144197744	+	2.3	cIP1vsInput	Intergenic	Intergenic	-20322	NM_153171	246709	Mm.38271	NM_153171	ENSMUSG00000051079	Rgs13	-	regulator of G-protein signaling 13	protein-coding	0.01	0.306931
Merged-chr7-62238480-1	chr7	62238430	62238530	+	2.3	cIP1vsInput	Intergenic	Intergenic	-109797	NM_010882	17984	Mm.400253	NM_010882	ENSMUSG00000033585	Ndn	AI528698|Peg6	necdin	protein-coding	0.01	0.356436
Merged-chr8-15153273-1	chr8	15153223	15153323	+	2.3	cIP2vsInput	Intergenic	Intergenic	95620	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding	0	0.316832
Merged-chr5-106281003-1	chr5	106280953	106281053	+	2.3	cIP2vsInput	Intergenic	Intergenic	177163	NM_001005477	104382	Mm.271593	NM_001005477	ENSMUSG00000034384	Barhl2	E130309B19Rik|MBH1	BarH-like 2 (Drosophila)	protein-coding	0	0.356436
Merged-chr13-62952231-1	chr13	62952181	62952281	+	2.3	cIP1vsInput	Intergenic	RMER21B|LTR|ERV1	-62703	NM_028079	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|Aopep	RIKEN cDNA 2010111I01 gene	protein-coding	0.01	0.584158
Merged-chr2-127037785-1	chr2	127037735	127037835	+	2.3	cIP2vsInput	"intron (NM_175550, intron 7 of 20)"	"intron (NM_175550, intron 7 of 20)"	29074	NM_175550	108011	Mm.134045	NM_175550		Ap4e1	2310033A20Rik|9930028M04Rik|AV087807	"adaptor-related protein complex AP-4, epsilon 1"	protein-coding	0.03	0.356436
Merged-chr6-26536782-1	chr6	26536732	26536832	+	2.3	cIP2vsInput	Intergenic	Intergenic	605356	NR_040771	626904	Mm.126787	NR_040771		Gm20756	-	"predicted gene, 20756"	miscRNA	0.01	0.356436
Merged-chr5-61562426-1	chr5	61562376	61562476	+	2.3	cIP1vsInput	Intergenic	Intergenic	-246417	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding	0	0.336634
Merged-chr2-141638428-1	chr2	141638378	141638478	+	2.3	cIP2vsInput	"intron (NM_001013802, intron 6 of 18)"	"intron (NM_001013802, intron 6 of 18)"	-966952	NM_178382	71436	Mm.426781	NM_001172160	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0	0.356436
Merged-chr18-17702129-1	chr18	17702079	17702179	+	2.3	cIP2vsInput	Intergenic	Intergenic	-121139	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	miscRNA	0	0.336634
Merged-chr6-79857172-1	chr6	79857122	79857222	+	2.3	cIP2vsInput	Intergenic	Intergenic	39141	NM_001190732	100463512	Mm.461086	NM_001190732	ENSMUSG00000096887	Gm20594	Mtrnr2l	"predicted gene, 20594"	protein-coding	0	0.277228
Merged-chr16-79464925-1	chr16	79464875	79464975	+	2.3	cIP2vsInput	Intergenic	Intergenic	-373828	NM_008941	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	"transmembrane protease, serine 15"	protein-coding	0	0.336634
Merged-chr12-112749343-1	chr12	112749293	112749393	+	2.3	cIP2vsInput	Intergenic	Intergenic	-11312	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	"phospholipase D family, member 4"	protein-coding	0	0.336634
Merged-chr18-20344073-1	chr18	20344023	20344123	+	2.3	cIP2vsInput	TTS (NM_010079)	TTS (NM_010079)	-32762	NM_181682	225256	Mm.355485	NM_181682	ENSMUSG00000061928	Dsg1b	Dsg5	desmoglein 1 beta	protein-coding	0	0.316832
Merged-chr1-17439252-1	chr1	17439202	17439302	+	2.3	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-162649	NM_053191	94227	Mm.442452	NM_053191	ENSMUSG00000067780	Pi15	P24TI|P25TI|PI-15|SugarCrisp	peptidase inhibitor 15	protein-coding	0	0.356436
Merged-chr13-75227814-1	chr13	75227764	75227864	+	2.3	cIP2vsInput	Intergenic	Intergenic	137827	NM_013628	18548	Mm.1333	NM_013628	ENSMUSG00000021587	Pcsk1	Nec-1|Nec1|PC1|PC3|Phpp-1|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0.02	0.524752
Merged-chr4-20574159-1	chr4	20574109	20574209	+	2.3	cIP1vsInput	"intron (NM_172987, intron 1 of 4)"	"intron (NM_172987, intron 1 of 4)"	204509	NM_172987	269513		NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding	0	0.316832
Merged-chr2-147885073-1	chr2	147885023	147885123	+	2.3	cIP1vsInput	Intergenic	Intergenic	161896	NM_010446	15376	Mm.938	NM_010446	ENSMUSG00000037025	Foxa2	HNF3-beta|HNF3beta|Hnf-3b|Hnf3b|Tcf-3b|Tcf3b	forkhead box A2	protein-coding	0	0.356436
Merged-chr6-102958139-1	chr6	102958089	102958189	+	2.3	cIP2vsInput	Intergenic	Intergenic	-493472	NM_008779	18488	Mm.435479	NM_008779	ENSMUSG00000030075	Cntn3	Pang	contactin 3	protein-coding	0	0.346535
Merged-chr15-89591839-1	chr15	89591789	89591889	+	2.3	cIP1vsInput	promoter-TSS (NM_026817)	promoter-TSS (NM_026817)	84	NM_026817	68708	Mm.23258	NM_026817	ENSMUSG00000022621	Rabl2	1110031N17Rik|AW549303|Rabl2a	"RAB, member of RAS oncogene family-like 2"	protein-coding	0.11	0.693069
Merged-chr5-150476674-1	chr5	150476624	150476724	+	2.3	cIP2vsInput	"intron (NM_172887, intron 55 of 60)"	L1_Rod|LINE|L1	25545	NR_024513	194292	Mm.300184	NR_024513		Gm5	Gm1812	predicted gene 5	miscRNA	0.03	0.376238
Merged-chr2-89682518-1	chr2	89682468	89682568	+	2.3	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-14634	NM_001011529	259145	Mm.376637	NM_001011529	ENSMUSG00000075077	Olfr1251	GA_x5J8B7TT7VM-20-924|MOR231-15P	olfactory receptor 1251	protein-coding	0.01	0.376238
Merged-chr4-80781379-1	chr4	80781329	80781429	+	2.3	cIP2vsInput	Intergenic	Lx7|LINE|L1	-52851	NM_031202	22178	Mm.412291	NM_031202	ENSMUSG00000005994	Tyrp1	TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding	0	0.326733
Merged-chr8-128578791-1	chr8	128578741	128578841	+	2.3	cIP2vsInput	Intergenic	Intergenic	-106863	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding	0.02	0.356436
Merged-chr13-65309646-1	chr13	65309596	65309696	+	2.3	cIP2vsInput	Intergenic	Intergenic	30792	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding	0	0.386139
Merged-chr6-132925610-1	chr6	132925560	132925660	+	2.3	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	15959	NM_207027	387352	Mm.377913	NM_207027	ENSMUSG00000059410	Tas2r125	T2R26|Tas2r25|mGR25|mt2r59	"taste receptor, type 2, member 125"	protein-coding	0	0.376238
Merged-chr10-110193675-1	chr10	110193625	110193725	+	2.3	cIP2vsInput	Intergenic	Intergenic	-193456	NM_001081035	260315	Mm.461280	NM_001081035	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding	0	0.356436
Merged-chr19-33675808-1	chr19	33675758	33675858	+	2.3	cIP1vsInput	Intergenic	Intergenic	-85497	NM_001013770	381236	Mm.329814	NM_001013770	ENSMUSG00000024766	Lipo1	AI747699	"lipase, member O1"	protein-coding	0	0.29703
Merged-chr9-51571419-1	chr9	51571369	51571469	+	2.3	cIP2vsInput	Intergenic	Intergenic	-193933	NM_175535	244867	Mm.443529	NM_175535	ENSMUSG00000053199	Arhgap20	6530403F17Rik|A530023E23Rik|mKIAA1391	Rho GTPase activating protein 20	protein-coding	0	0.306931
Merged-chr9-64805384-1	chr9	64805334	64805434	+	2.3	cIP1vsInput	Intergenic	B3|SINE|B2	-5627	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding	0	0.415842
Merged-chr16-76884458-1	chr16	76884408	76884508	+	2.3	cIP2vsInput	Intergenic	Intergenic	126423	NR_040573	76601	Mm.396217	NR_040573		1700041M19Rik	-	RIKEN cDNA 1700041M19 gene	miscRNA	0.02	0.326733
Merged-chr4-73199393-1	chr4	73199343	73199443	+	2.3	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	205679	NM_001013393	433719	Mm.348294	NM_001013393	ENSMUSG00000066137	Gm11487	OTTMUSG00000001246	predicted gene 11487	protein-coding	0	0.316832
Merged-chr19-50840966-1	chr19	50840916	50841016	+	2.3	cIP2vsInput	Intergenic	Intergenic	-162320	NM_021377	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0.01	0.346535
Merged-chr11-16478828-1	chr11	16478778	16478878	+	2.3	cIP2vsInput	Intergenic	LTR87|LTR|ERVL?	29656	NM_011343	20335	Mm.325350	NM_001109971	ENSMUSG00000078974	Sec61g	-	"SEC61, gamma subunit"	protein-coding	0	0.346535
Merged-chr1-40120938-1	chr1	40120888	40120988	+	2.3	cIP1vsInput	"exon (NM_010555, exon 7 of 9)"	"exon (NM_010555, exon 7 of 9)"	-35087	NR_037980	100047133	Mm.447052	NR_037980	ENSMUSG00000097899	Gm16894	-	"predicted gene, 16894"	miscRNA	0.01	0.49505
Merged-chr10-87834394-1	chr10	87834344	87834444	+	2.3	cIP1vsInput	Intergenic	LTR16E1|LTR|ERVL	-24662	NM_001111275	16000	Mm.268521	NM_001111274	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding	0	0.336634
Merged-chr16-4814322-1	chr16	4814272	4814372	+	2.3	cIP2vsInput	Intergenic	MurERV4_19-int|LTR|ERVK	-21094	NM_030192	78809	Mm.325551	NM_030192	ENSMUSG00000022518	4930562C15Rik	-	RIKEN cDNA 4930562C15 gene	protein-coding	0	0.306931
Merged-chr3-87610564-1	chr3	87610514	87610614	+	2.3	cIP2vsInput	Intergenic	MERVL_2A-int|LTR|ERVL	-8187	NM_001003912	213498	Mm.287267	NM_001003912	ENSMUSG00000041977	Arhgef11	B930073M02|E130307F09|RhoGEF|mKIAA0380	Rho guanine nucleotide exchange factor (GEF) 11	protein-coding	0	0.366337
Merged-chr13-20823399-1	chr13	20823349	20823449	+	2.3	cIP1vsInput	"intron (NM_012054, intron 2 of 20)"	"intron (NM_012054, intron 2 of 20)"	29280	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding	0.01	0.386139
Merged-chr13-76780346-1	chr13	76780296	76780396	+	2.3	cIP1vsInput	"intron (NM_030174, intron 8 of 20)"	L1_Mus2|LINE|L1	355122	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Ankrd32	2700017A04Rik|AW545819|Brctd1|Brctx|C730024G01Rik	ankyrin repeat domain 32	protein-coding	0	0.336634
Merged-chr9-12191156-1	chr9	12191106	12191206	+	2.3	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	914699	NR_040755	78219	Mm.414868	NR_040755		4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	miscRNA	0	0.316832
Merged-chr14-57720305-1	chr14	57720255	57720355	+	2.3	cIP2vsInput	"intron (NM_015771, intron 2 of 7)"	L1_Mur3|LINE|L1	14113	NM_153382	50523	Mm.347899	NM_015771	ENSMUSG00000021959	Lats2	4932411G09Rik|AV277261|AW228608	large tumor suppressor 2	protein-coding	0.01	0.366337
Merged-chr3-101225573-1	chr3	101225523	101225623	+	2.3	cIP2vsInput	Intergenic	ID4_|SINE|ID	62366	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding	0	0.405941
Merged-chr3-127038260-1	chr3	127038210	127038310	+	2.3	cIP1vsInput	Intergenic	Intergenic	-39808	NM_178655	109676	Mm.484610	NM_001034168	ENSMUSG00000032826	Ank2	AI835472|AW491075|Ank-2	"ankyrin 2, brain"	protein-coding	0	0.29703
Merged-chr4-129415400-1	chr4	129415350	129415450	+	2.3	cIP2vsInput	Intergenic	Intergenic	25418	NM_153541	215627	Mm.458339	NM_153541	ENSMUSG00000048485	Zbtb8b	AV220464|BC023839|BOZF1|Zbtb8	zinc finger and BTB domain containing 8b	protein-coding	0.01	0.29703
Merged-chr13-81583492-1	chr13	81583442	81583542	+	2.3	cIP2vsInput	"intron (NM_054053, intron 5 of 89)"	"intron (NM_054053, intron 5 of 89)"	49652	NM_054053	110789	Mm.288694	NM_054053	ENSMUSG00000069170	Gpr98	Frings|Mass1|Mgr1|VLGR1	G protein-coupled receptor 98	protein-coding	0	0.316832
Merged-chr3-63489934-1	chr3	63489884	63489984	+	2.3	cIP2vsInput	Intergenic	Intergenic	194062	NM_008604	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding	0.01	0.316832
Merged-chr2-54650327-1	chr2	54650277	54650377	+	2.3	cIP1vsInput	"intron (NM_173030, intron 3 of 12)"	"intron (NM_173030, intron 3 of 12)"	213940	NM_173030	271786	Mm.330227	NM_173030	ENSMUSG00000060988	Galnt13	A230002A12|A230020F20|BB182356	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13	protein-coding	0.01	0.306931
Merged-chr16-72731544-1	chr16	72731494	72731594	+	2.3	cIP2vsInput	"intron (NM_019413, intron 1 of 28)"	"intron (NM_019413, intron 1 of 28)"	68395	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout homolog 1 (Drosophila)	protein-coding	0	0.356436
Merged-chr3-151781703-1	chr3	151781653	151781753	+	2.3	cIP2vsInput	Intergenic	Intergenic	-18812	NM_031367	15061	Mm.219544	NM_031367		Ifi44l	H-28|H28|H28-1|NS1178	interferon-induced protein 44 like	protein-coding	0	0.326733
Merged-chr15-41576280-1	chr15	41576230	41576330	+	2.3	cIP2vsInput	"intron (NM_001130166, intron 2 of 16)"	"intron (NM_001130166, intron 2 of 16)"	128798	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding	0	0.316832
Merged-chr1-102593339-1	chr1	102593289	102593389	+	2.3	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	1437571	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.326733
Merged-chr17-20465629-1	chr17	20465579	20465679	+	2.3	cIP1vsInput	"intron (NM_001104570, intron 5 of 5)"	"intron (NM_001104570, intron 5 of 5)"	15607	NM_001104570	627805	Mm.469853	NM_001104570	ENSMUSG00000091805	Vmn2r108	EG627805	"vomeronasal 2, receptor 108"	protein-coding	0	0.336634
Merged-chr17-51474007-1	chr17	51473957	51474057	+	2.3	cIP2vsInput	"intron (NR_037260, intron 3 of 4)"	"intron (NR_037260, intron 3 of 4)"	-25738	NR_046166	328837	Mm.236143	NR_046166		C330011F03Rik	C330011F03	RIKEN cDNA C330011F03 gene	miscRNA	0	0.366337
Merged-chr16-67970427-1	chr16	67970377	67970477	+	2.3	cIP2vsInput	Intergenic	Lx9|LINE|L1	-349519	NM_178721	239857	Mm.394300	NM_001145977	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0	0.39604
Merged-chr6-103953137-1	chr6	103953087	103953187	+	2.3	cIP2vsInput	Intergenic	Intergenic	442261	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule with homology to L1CAM	protein-coding	0	0.346535
Merged-chr15-10584207-1	chr15	10584157	10584257	+	2.3	cIP1vsInput	"intron (NM_030690, intron 12 of 17)"	AT_rich|Low_complexity|Low_complexity	-16086	NR_033541	100038608	Mm.450744	NR_033541		Gm10389	ENSMUSG00000072658	predicted gene 10389	miscRNA	0	0.267327
Merged-chr13-31792817-1	chr13	31792767	31792867	+	2.3	cIP2vsInput	Intergenic	Intergenic	-13829	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding	0.01	0.445545
Merged-chr14-94424027-1	chr14	94423977	94424077	+	2.3	cIP2vsInput	Intergenic	Intergenic	-533358	NM_001271798	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.356436
Merged-chr3-4872399-1	chr3	4872349	4872449	+	2.3	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	73691	NR_045272	100503859	Mm.75172	NR_045272		1110015O18Rik	-	RIKEN cDNA 1110015O18 gene	miscRNA	0.01	0.346535
Merged-chr3-136313098-1	chr3	136313048	136313148	+	2.3	cIP2vsInput	"intron (NM_001033350, intron 1 of 16)"	"intron (NM_001033350, intron 1 of 16)"	12948	NM_001033350	242248	Mm.30832	NM_001033350	ENSMUSG00000037922	Bank1	A530094C12Rik|AI451642|AVIEF|BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.01	0.267327
Merged-chr19-46740752-1	chr19	46740702	46740802	+	2.3	cIP2vsInput	"3' UTR (NM_020577, exon 11 of 11)"	"3' UTR (NM_020577, exon 11 of 11)"	-20857	NM_001102471	94219	Mm.306903	NM_001102471	ENSMUSG00000064105	Cnnm2	AU015877|AW048635|Acdp2|Clp2	cyclin M2	protein-coding	0.01	0.39604
Merged-chr14-94700459-1	chr14	94700409	94700509	+	2.3	cIP2vsInput	Intergenic	B4A|SINE|B4	-809790	NM_001271798	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.287129
Merged-chr3-140500451-1	chr3	140500401	140500501	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	711904	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0	0.346535
Merged-chr19-50171942-1	chr19	50171892	50171992	+	2.3	cIP1vsInput	"intron (NM_001252501, intron 23 of 25)"	"intron (NM_001252501, intron 23 of 25)"	506704	NM_001252501	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0	0.445545
Merged-chr11-5563411-1	chr11	5563361	5563461	+	2.3	cIP1vsInput	Intergenic	Intergenic	-6273	NM_023816	76389	Mm.67300	NM_023816	ENSMUSG00000020481	Ankrd36	1700008J08Rik|1700012M14Rik|Ankrd48	ankyrin repeat domain 36	protein-coding	0	0.29703
Merged-chr3-115445928-1	chr3	115445878	115445978	+	2.3	cIP2vsInput	Intergenic	Lx6|LINE|L1	269127	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding	0	0.287129
Merged-chr12-12866502-1	chr12	12866452	12866552	+	2.3	cIP1vsInput	Intergenic	Intergenic	75334	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"	protein-coding	0.01	0.39604
Merged-chr13-80656069-1	chr13	80656019	80656119	+	2.3	cIP1vsInput	Intergenic	Intergenic	-227353	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0	0.316832
Merged-chr7-103228706-1	chr7	103228656	103228756	+	2.3	cIP2vsInput	Intergenic	Lx6|LINE|L1	8986	NM_207143	258246	Mm.377390	NM_207143	ENSMUSG00000073954	Olfr594	MOR32-10	olfactory receptor 594	protein-coding	0	0.39604
Merged-chr2-41082180-1	chr2	41082130	41082230	+	2.3	cIP2vsInput	"intron (NM_053011, intron 41 of 90)"	L1_Mur2|LINE|L1	1571418	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0	0.376238
Merged-chr8-72336524-1	chr8	72336474	72336574	+	2.3	cIP1vsInput	Intergenic	Intergenic	17462	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding	0.01	0.336634
Merged-chr12-78687548-1	chr12	78687498	78687598	+	2.3	cIP2vsInput	Intergenic	Intergenic	-3987	NM_027597	70897	Mm.56514	NM_027597	ENSMUSG00000056987	Fam71d	4921509E07Rik|4930516C23Rik|GARI-L2	"family with sequence similarity 71, member D"	protein-coding	0.02	0.435644
Merged-chr16-70903918-1	chr16	70903868	70903968	+	2.3	cIP2vsInput	Intergenic	Intergenic	-227158	NR_040561	70972	Mm.399391	NR_040561		4931420L22Rik	-	RIKEN cDNA 4931420L22 gene	miscRNA	0	0.346535
Merged-chr5-122071086-1	chr5	122071036	122071136	+	2.3	cIP2vsInput	Intergenic	Intergenic	-23261	NM_007804	13048	Mm.332661	NM_007804	ENSMUSG00000042589	Cux2	1700051K22Rik|Cutl2|Cux-2|ENSMUSG00000072641	cut-like homeobox 2	protein-coding	0.02	0.584158
Merged-chr4-54895128-1	chr4	54895078	54895178	+	2.3	cIP1vsInput	Intergenic	Intergenic	-52817	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding	0	0.346535
Merged-chr9-39167180-1	chr9	39167130	39167230	+	2.3	cIP2vsInput	"intron (NM_146326, intron 1 of 2)"	"intron (NM_146326, intron 1 of 2)"	870	NM_146326	258323	Mm.223019	NM_146326	ENSMUSG00000094970	Olfr943	MOR171-44	olfactory receptor 943	protein-coding	0	0.287129
Merged-chr7-39456000-1	chr7	39455950	39456050	+	2.3	cIP2vsInput	"intron (NM_001243021, intron 1 of 5)"	RMER21A|LTR|ERV1	6482	NM_001243021	233147	Mm.148946	NM_001243021	ENSMUSG00000030424	Zfp939	9430025M13Rik	zinc finger protein 939	protein-coding	0	0.574257
Merged-chr16-70828802-1	chr16	70828752	70828852	+	2.3	cIP1vsInput	Intergenic	Intergenic	212377	NR_040474	52645	Mm.188475	NR_040474		D16Ertd519e	-	"DNA segment, Chr 16, ERATO Doi 519, expressed"	miscRNA	0	0.346535
Merged-chr11-50841868-1	chr11	50841818	50841918	+	2.3	cIP1vsInput	promoter-TSS (NM_173387)	promoter-TSS (NM_173387)	-316	NM_173387	214779	Mm.191846	NM_173387	ENSMUSG00000044296	Zfp879	9630041N07Rik|Znf879	zinc finger protein 879	protein-coding	0.01	0.316832
Merged-chr8-60617079-1	chr8	60617029	60617129	+	2.3	cIP2vsInput	Intergenic	Intergenic	-15781	NM_027756	71306	Mm.23242	NM_001177881	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding	0	0.39604
Merged-chr14-90803147-1	chr14	90803097	90803197	+	2.3	cIP2vsInput	Intergenic	MERVL_2A-int|LTR|ERVL	676256	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0	0.346535
Merged-chr1-163020341-1	chr1	163020291	163020391	+	2.3	cIP2vsInput	Intergenic	Lx5b|LINE|L1	-35850	NM_008030	14262	Mm.2900	NM_008030	ENSMUSG00000026691	Fmo3	AW111792	flavin containing monooxygenase 3	protein-coding	0	0.326733
Merged-chr19-59239693-1	chr19	59239643	59239743	+	2.3	cIP2vsInput	Intergenic	Intergenic	20045	NM_207261	332396	Mm.329947	NM_207261	ENSMUSG00000040901	Kcnk18	Gm781|Tresk|Tresk-2|Trik	"potassium channel, subfamily K, member 18"	protein-coding	0.07	0.623762
Merged-chr16-93832064-1	chr16	93832014	93832114	+	2.3	cIP1vsInput	promoter-TSS (NM_001045529)	promoter-TSS (NM_001045529)	-57	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding	0.15	0.693069
Merged-chr13-5078050-1	chr13	5078000	5078100	+	2.3	cIP2vsInput	Intergenic	Lx6|LINE|L1	-468886	NM_018859	56043	Mm.251908	NM_018859	ENSMUSG00000045410	Akr1e1	1810061I10Rik|Akr1e2	"aldo-keto reductase family 1, member E1"	protein-coding	0	0.336634
Merged-chr13-63434121-1	chr13	63434071	63434171	+	2.3	cIP2vsInput	Intergenic	Intergenic	-2376	NM_001042673	14088	Mm.126106	NM_001042673	ENSMUSG00000021461	Fancc	BB116513|Facc	"Fanconi anemia, complementation group C"	protein-coding	0.02	0.39604
Merged-chr9-37932666-1	chr9	37932616	37932716	+	2.3	cIP2vsInput	Intergenic	Intergenic	14118	NM_146798	258794	Mm.377695	NM_146798	ENSMUSG00000066747	Olfr878	MOR163-1	olfactory receptor 878	protein-coding	0.04	0.455446
Merged-chr1-52279411-1	chr1	52279361	52279461	+	2.3	cIP2vsInput	Intergenic	Intergenic	-46179	NM_001113383	14660	Mm.398608	NM_001081081	ENSMUSG00000026103	Gls	6330442B14|AI314027|B230365M23Rik	glutaminase	protein-coding	0.01	0.475248
Merged-chr7-53264781-1	chr7	53264731	53264831	+	2.3	cIP1vsInput	Intergenic	Intergenic	-1249065	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding	0	0.306931
Merged-chr11-64710795-1	chr11	64710745	64710845	+	2.3	cIP1vsInput	Intergenic	Intergenic	-268240	NM_023479	68626	Mm.157711	NM_023479	ENSMUSG00000020549	Elac2	1110017O07Rik|D11Wsu80e|Hpc2	elaC homolog 2 (E. coli)	protein-coding	0	0.346535
Merged-chrX-47892051-1	chrX	47892001	47892101	+	2.3	cIP2vsInput	"intron (NM_053123, intron 1 of 23)"	"intron (NM_053123, intron 1 of 23)"	501	NM_053123	93761	Mm.229151	NM_053123	ENSMUSG00000031099	Smarca1	5730494M04Rik|Snf2l	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1"	protein-coding	0.09	0.782178
Merged-chr8-105949602-1	chr8	105949552	105949652	+	2.3	cIP1vsInput	"intron (NM_009195, intron 12 of 23)"	"intron (NM_009195, intron 12 of 23)"	-6200	NM_008490	16816	Mm.1593	NM_008490	ENSMUSG00000035237	Lcat	AI046659|D8Wsu61e	lecithin cholesterol acyltransferase	protein-coding	0.05	0.613861
Merged-chr8-75431075-1	chr8	75431025	75431125	+	2.3	cIP2vsInput	Intergenic	RMER19C|LTR|ERVK	-17619	NM_027944	71831	Mm.443238	NM_001164235	ENSMUSG00000031620	1700007B14Rik	-	RIKEN cDNA 1700007B14 gene	protein-coding	0	0.415842
Merged-chr12-62801485-1	chr12	62801435	62801535	+	2.3	cIP2vsInput	Intergenic	Intergenic	1276853	NM_178714	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0	0.366337
Merged-chr18-57085682-1	chr18	57085632	57085732	+	2.3	cIP2vsInput	Intergenic	Intergenic	-47408	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding	0.02	0.445545
Merged-chr5-103627979-1	chr5	103627929	103628029	+	2.3	cIP2vsInput	"intron (NM_029415, intron 1 of 5)"	"intron (NM_029415, intron 1 of 5)"	1424	NM_029415	75750	Mm.7446	NM_029415	ENSMUSG00000029321	Slc10a6	8430417G17Rik|C78479|Soat	"solute carrier family 10 (sodium/bile acid cotransporter family), member 6"	protein-coding	0	0.356436
Merged-chr2-43633641-1	chr2	43633591	43633691	+	2.3	cIP1vsInput	"intron (NM_027552, intron 10 of 13)"	"intron (NM_027552, intron 10 of 13)"	78312	NM_027552	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding	0	0.326733
Merged-chr7-126272049-1	chr7	126271999	126272099	+	2.3	cIP2vsInput	promoter-TSS (NM_145587)	promoter-TSS (NM_145587)	-570	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding	0.02	0.524752
Merged-chr1-68210608-1	chr1	68210558	68210658	+	2.3	cIP1vsInput	"intron (NM_010154, intron 19 of 26)"	"intron (NM_010154, intron 19 of 26)"	897451	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0	0.316832
Merged-chr14-119210429-1	chr14	119210379	119210479	+	2.3	cIP1vsInput	"intron (NM_015820, intron 1 of 1)"	"intron (NM_015820, intron 1 of 1)"	72164	NM_015820	50787	Mm.445777	NM_015820		Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding	0.01	0.336634
Merged-chr11-104740057-1	chr11	104740007	104740107	+	2.3	cIP2vsInput	Intergenic	Intergenic	132057	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding	0	0.455446
Merged-chr7-80623780-1	chr7	80623730	80623830	+	2.3	cIP2vsInput	"intron (NM_173863, intron 3 of 14)"	"intron (NM_173863, intron 3 of 14)"	-12237	NR_040343	100504375	Mm.322881	NR_040343	ENSMUSG00000084821	Gm15880	OTTMUSG00000027171	predicted gene 15880	miscRNA	0	0.366337
Merged-chr5-15026363-1	chr5	15026313	15026413	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	6644	NM_182957	66773	Mm.368256	NM_182957	ENSMUSG00000091897	Gm17019	-	predicted gene 17019	protein-coding	0	0.29703
Merged-chr11-119586103-1	chr11	119586053	119586153	+	2.3	cIP2vsInput	Intergenic	Intergenic	-16892	NM_028898	74370	Mm.209933	NM_028898	ENSMUSG00000025583	Rptor	4932417H02Rik|Rap|Raptor|mKIAA1303	"regulatory associated protein of MTOR, complex 1"	protein-coding	0.02	0.594059
Merged-chr4-99750849-1	chr4	99750799	99750899	+	2.3	cIP1vsInput	"intron (NM_001081264, intron 12 of 14)"	"intron (NM_001081264, intron 12 of 14)"	35219	NM_001081264	320438	Mm.32408	NM_001081264	ENSMUSG00000073792	Alg6	E230028F23Rik	"asparagine-linked glycosylation 6 (alpha-1,3,-glucosyltransferase)"	protein-coding	0	0.207921
Merged-chr13-27179875-1	chr13	27179825	27179925	+	2.3	cIP1vsInput	Intergenic	Lx3A|LINE|L1	-16785	NM_013766	27372	Mm.291456	NM_013766	ENSMUSG00000017922	Prl3c1	PLP-J|Prlpi|Prlpj|decidualin	"prolactin family 3, subfamily c, member 1"	protein-coding	0.01	0.316832
Merged-chr12-90811350-1	chr12	90811300	90811400	+	2.3	cIP2vsInput	Intergenic	L1MB7|LINE|L1	-72912	NM_010050	13371	Mm.408815	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	"deiodinase, iodothyronine, type II"	protein-coding	0.02	0.336634
Merged-chr19-44094318-1	chr19	44094268	44094368	+	2.3	cIP2vsInput	"intron (NM_001162410, intron 9 of 20)"	"intron (NM_001162410, intron 9 of 20)"	13159	NM_007700	12675	Mm.3996	NM_001162410	ENSMUSG00000025199	Chuk	AI256658|Chuk1|Fbx24|Fbxo24|IKBKA|IKK1|Ikka|NFKBIKA	conserved helix-loop-helix ubiquitous kinase	protein-coding	0	0.326733
Merged-chr3-47709082-1	chr3	47709032	47709132	+	2.3	cIP1vsInput	Intergenic	Intergenic	317677	NR_040408	666202	Mm.465057	NR_040408		Gm7977	EG666202	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide pseudogene"	pseudo	0.01	0.326733
Merged-chr2-111227765-1	chr2	111227715	111227815	+	2.3	cIP2vsInput	"intron (NM_026248, intron 3 of 15)"	"intron (NM_026248, intron 3 of 15)"	1835	NM_026248	67575	Mm.84331	NM_026248	ENSMUSG00000027157	4930430A15Rik	-	RIKEN cDNA 4930430A15 gene	protein-coding	0	0.316832
Merged-chr9-15591212-1	chr9	15591162	15591262	+	2.3	cIP2vsInput	"intron (NM_181816, intron 8 of 11)"	"intron (NM_181816, intron 8 of 11)"	-28645	NR_040746	78025	Mm.55983	NR_040746		4930540M03Rik	-	RIKEN cDNA 4930540M03 gene	miscRNA	0	0.346535
Merged-chr15-36820327-1	chr15	36820277	36820377	+	2.3	cIP2vsInput	Intergenic	Intergenic	-23398	NM_001253806	22631	Mm.465895	NM_001253805	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide"	protein-coding	0.03	0.50495
Merged-chr17-29222086-1	chr17	29222036	29222136	+	2.3	cIP1vsInput	"intron (NM_153166, intron 3 of 20)"	"intron (NM_153166, intron 3 of 20)"	15704	NM_153166	240058	Mm.39905	NM_153166	ENSMUSG00000024008	Cpne5	A830083G22Rik	copine V	protein-coding	0	0.386139
Merged-chrX-31166456-1	chrX	31166406	31166506	+	2.3	cIP2vsInput	Intergenic	L1Md_F|LINE|L1	-169913	NM_001243011	100042159	Mm.489579	NM_001243011	ENSMUSG00000095835	Gm3701	-	predicted gene 3701	protein-coding	0	0.326733
Merged-chr3-95389418-1	chr3	95389368	95389468	+	2.3	cIP2vsInput	"intron (NR_015490, intron 1 of 1)"	L1MB8|LINE|L1	13423	NR_015490	67654	Mm.75066	NR_015490		4930558C23Rik	-	RIKEN cDNA 4930558C23 gene	miscRNA	0	0.287129
Merged-chr3-149715286-1	chr3	149715236	149715336	+	2.3	cIP2vsInput	Intergenic	Intergenic	440549	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	miscRNA	0	0.316832
Merged-chr5-123067602-1	chr5	123067552	123067652	+	2.3	cIP2vsInput	Intergenic	Intergenic	-8673	NM_001039723	330189	Mm.391872	NM_001039723	ENSMUSG00000054434	Tmem120b	-	transmembrane protein 120B	protein-coding	0.01	0.415842
Merged-chr4-76203861-1	chr4	76203811	76203911	+	2.3	cIP1vsInput	"intron (NM_011211, intron 13 of 39)"	"intron (NM_011211, intron 13 of 39)"	-925575	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	3110001D03Rik	1700027K24Rik	RIKEN cDNA 3110001D03 gene	protein-coding	0.01	0.336634
Merged-chr17-14408607-1	chr17	14408557	14408657	+	2.3	cIP1vsInput	Intergenic	Intergenic	-9665	NR_027986	74917	Mm.32228	NM_183107		4930474M22Rik	-	RIKEN cDNA 4930474M22 gene	miscRNA	0	0.316832
Merged-chr2-90404465-2	chr2	90404404	90404527	+	2.3	cIP1vsInput|cIP2vsInput	Intergenic	L1_Rod|LINE|L1	3825	NM_146263	258330	Mm.330392	NM_146263		Olfr1274-ps	GA_x5J8B7W2BV0-3116-4045|MOR228-4|MOR228-5|Olfr1274	"olfactory receptor 1274, pseudogene"	protein-coding	0.00813	0.330645
Merged-chr13-62467854-1	chr13	62467804	62467904	+	2.3	cIP2vsInput	Intergenic	MT2B1|LTR|ERVL	-1042	NM_001136496	71508	Mm.442497	NM_001136496		Zfp935	8430426H19Rik|Es113	zinc finger protein 935	protein-coding	0	0.306931
Merged-chr6-106762928-1	chr6	106762878	106762978	+	2.3	cIP2vsInput	Intergenic	Intergenic	-6210	NM_027296	70047	Mm.196332	NM_001242358	ENSMUSG00000013736	Trnt1	2410043H24Rik|2610044E04Rik|9830143O18Rik|AA408384|C76540|CGI-47|mt-Trat	"tRNA nucleotidyl transferase, CCA-adding, 1"	protein-coding	0	0.356436
Merged-chr11-41404952-1	chr11	41404902	41405002	+	2.3	cIP2vsInput	Intergenic	Intergenic	595762	NM_177408	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2"	protein-coding	0	0.316832
Merged-chr7-112488082-1	chr7	112488032	112488132	+	2.3	cIP1vsInput	"intron (NM_020606, intron 1 of 12)"	L1M2|LINE|L1	60376	NM_020606	57342	Mm.143763	NM_020606	ENSMUSG00000030770	Parva	2010012A22Rik|5430400F08Rik|AI225929|AU042898|Actp|CH-ILKBP|Parvin	"parvin, alpha"	protein-coding	0	0.29703
Merged-chr17-32891331-1	chr17	32891281	32891381	+	2.3	cIP2vsInput	"intron (NM_207245, intron 1 of 3)"	"intron (NM_207245, intron 1 of 3)"	272	NM_207245	240066	Mm.26636	NM_207245	ENSMUSG00000095325	Zfp870	AI173952	zinc finger protein 870	protein-coding	0.05	0.613861
Merged-chr11-38082105-1	chr11	38082055	38082155	+	2.3	cIP1vsInput	Intergenic	Intergenic	437940	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0	0.287129
Merged-chr6-60397655-1	chr6	60397605	60397705	+	2.3	cIP2vsInput	"intron (NR_015565, intron 1 of 1)"	"intron (NR_015565, intron 1 of 1)"	6052	NR_015565	208079	Mm.490691	NR_015565		A530053G22Rik	-	RIKEN cDNA A530053G22 gene	miscRNA	0	0.366337
Merged-chr7-93778238-1	chr7	93778188	93778288	+	2.3	cIP2vsInput	Intergenic	Intergenic	698359	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0.01	0.386139
Merged-chr8-68941781-1	chr8	68941731	68941831	+	2.3	cIP2vsInput	Intergenic	Intergenic	61226	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding	0	0.366337
Merged-chr13-64306322-1	chr13	64306272	64306372	+	2.3	cIP2vsInput	"intron (NM_025370, intron 4 of 5)"	"intron (NM_025370, intron 4 of 5)"	6388	NM_025370	66129	Mm.227240	NM_025370	ENSMUSG00000021482	Aaed1	1110018J18Rik|AI849003	AhpC/TSA antioxidant enzyme domain containing 1	protein-coding	0	0.49505
Merged-chr5-106895564-1	chr5	106895514	106895614	+	2.3	cIP2vsInput	"intron (NM_177873, intron 16 of 39)"	"intron (NM_177873, intron 16 of 39)"	30326	NM_177873	330149	Mm.121664	NM_001252516	ENSMUSG00000043410	Hfm1	A330009G12Rik|Gm1046|Sec63d1	"HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)"	protein-coding	0	0.257426
Merged-chr15-69230913-1	chr15	69230863	69230963	+	2.3	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	302493	NM_010158	13992	Mm.17964	NM_010158	ENSMUSG00000022332	Khdrbs3	Etle|SLM-2|Slm2|T-STAR	"KH domain containing, RNA binding, signal transduction associated 3"	protein-coding	0.02	0.316832
Merged-chr5-109758604-1	chr5	109758554	109758654	+	2.3	cIP2vsInput	Intergenic	RLTR22_Mus|LTR|ERVK	75538	NR_027964	667213	Mm.454429	NR_027964		Gm10416	EG667213|ENSMUSG00000072761	zinc finger protein pseudogene	pseudo	0	0.316832
Merged-chr7-102311550-1	chr7	102311500	102311600	+	2.3	cIP1vsInput	"intron (NM_009287, intron 1 of 11)"	"intron (NM_009287, intron 1 of 11)"	43726	NM_009287	20866	Mm.645	NM_009287	ENSMUSG00000030987	Stim1	SIM	stromal interaction molecule 1	protein-coding	0	0.326733
Merged-chr3-118095349-1	chr3	118095299	118095399	+	2.3	cIP2vsInput	Intergenic	Intergenic	-226413	NM_029655	76561	Mm.33824	NM_001190156	ENSMUSG00000028007	Snx7	2510028H01Rik	sorting nexin 7	protein-coding	0	0.366337
Merged-chr14-122173521-1	chr14	122173471	122173571	+	2.3	cIP1vsInput	Intergenic	Intergenic	-8173	NM_029556	69634	Mm.34608	NM_029556	ENSMUSG00000025545	Clybl	0610033J05Rik|2310014M14Rik|AI256068|Clb	citrate lyase beta like	protein-coding	0	0.29703
Merged-chr3-70232143-1	chr3	70232093	70232193	+	2.3	cIP1vsInput	Intergenic	Intergenic	224530	NM_001018031	229389	Mm.331071	NM_001018031	ENSMUSG00000027788	Otol1	Gm414	otolin 1 homolog (zebrafish)	protein-coding	0	0.29703
Merged-chr1-37359924-1	chr1	37359874	37359974	+	2.3	cIP1vsInput	"intron (NM_030266, intron 4 of 25)"	L1ME3A|LINE|L1	-9297	NM_172971	269180	Mm.5294	NM_030266	ENSMUSG00000026113	Inpp4a	107kDa|9630012D15|D130048C09Rik|R74740	"inositol polyphosphate-4-phosphatase, type I"	protein-coding	0	0.306931
Merged-chr9-40807257-1	chr9	40807207	40807307	+	2.3	cIP1vsInput	Intergenic	Intergenic	5984	NM_031165	15481	Mm.485345	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding	0.02	0.366337
Merged-chr11-19322600-1	chr11	19322550	19322650	+	2.3	cIP2vsInput	Intergenic	Lx2|LINE|L1	257325	NR_046037	74059	Mm.292321	NR_046037	ENSMUSG00000086025	4933406G16Rik	-	RIKEN cDNA 4933406G16 gene	miscRNA	0.01	0.356436
Merged-chr9-85992303-1	chr9	85992253	85992353	+	2.3	cIP1vsInput	Intergenic	MLT1B|LTR|ERVL-MaLR	149451	NM_001164792	21983	Mm.484180	NM_001164792	ENSMUSG00000035274	Tpbg	5T4|AW495680	trophoblast glycoprotein	protein-coding	0	0.376238
Merged-chr9-62588930-1	chr9	62588880	62588980	+	2.3	cIP2vsInput	Intergenic	(TGAA)n|Simple_repeat|Simple_repeat	-51886	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	"coronin, actin binding protein, 2B"	protein-coding	0	0.306931
Merged-chr15-18965572-1	chr15	18965522	18965622	+	2.3	cIP1vsInput	"intron (NM_009865, intron 3 of 11)"	"intron (NM_009865, intron 3 of 11)"	145243	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0.01	0.306931
Merged-chr5-70815780-1	chr5	70815730	70815830	+	2.3	cIP2vsInput	"intron (NM_010252, intron 2 of 8)"	"intron (NM_010252, intron 2 of 8)"	26837	NM_010252	14405	Mm.255292	NM_010252	ENSMUSG00000001260	Gabrg1	GabaA|GabaA/BZ	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1"	protein-coding	0	0.356436
Merged-chr9-39257072-1	chr9	39257022	39257122	+	2.3	cIP2vsInput	TTS (NM_146506)	TTS (NM_146506)	1607	NM_146506	258499	Mm.377538	NM_146506	ENSMUSG00000063380	Olfr945	MOR171-20	olfactory receptor 945	protein-coding	0	0.29703
Merged-chr3-123407100-1	chr3	123407050	123407150	+	2.3	cIP2vsInput	Intergenic	Intergenic	-21110	NM_201638	210529	Mm.260039	NM_201638	ENSMUSG00000028114	Mettl14	G430022H21Rik|mKIAA1627	methyltransferase like 14	protein-coding	0	0.277228
Merged-chr1-192190679-1	chr1	192190629	192190729	+	2.3	cIP2vsInput	promoter-TSS (NM_010600)	promoter-TSS (NM_010600)	-193	NM_001038607	16510	Mm.4489	NM_001038607	ENSMUSG00000058248	Kcnh1	Kv10.1|M-eag	"potassium voltage-gated channel, subfamily H (eag-related), member 1"	protein-coding	0.08	0.653465
Merged-chr11-29130852-1	chr11	29130802	29130902	+	2.3	cIP2vsInput	"exon (NM_027869, exon 1 of 28)"	"exon (NM_027869, exon 1 of 28)"	101	NM_027869	71701	Mm.211131	XM_003689261	ENSMUSG00000020464	Pnpt1	1200003F12Rik|Old35|PNPase|Pnptl1	polyribonucleotide nucleotidyltransferase 1	protein-coding	0.1	0.693069
Merged-chr16-82503821-1	chr16	82503771	82503871	+	2.3	cIP2vsInput	Intergenic	Intergenic	1303124	NM_010954	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.336634
Merged-chr17-40946442-1	chr17	40946392	40946492	+	2.3	cIP1vsInput	"intron (NM_008650, intron 5 of 12)"	"intron (NM_008650, intron 5 of 12)"	11757	NM_008650	17850	Mm.259884	NM_008650	ENSMUSG00000023921	Mut	D230010K02Rik|Mcm	methylmalonyl-Coenzyme A mutase	protein-coding	0	0.287129
Merged-chr4-152520040-1	chr4	152519990	152520090	+	2.3	cIP1vsInput	"intron (NM_153424, intron 10 of 29)"	"intron (NM_153424, intron 10 of 29)"	41898	NM_153424	260305	Mm.302496	NM_153424	ENSMUSG00000039577	Nphp4	4930564O18Rik|nmf192	nephronophthisis 4 (juvenile) homolog (human)	protein-coding	0	0.435644
Merged-chr16-23135710-1	chr16	23135660	23135760	+	2.3	cIP2vsInput	Intergenic	Intergenic	-7980	NM_145480	106344	Mm.386835	NM_145480	ENSMUSG00000022881	Rfc4	A1|AI894123|AU040575|RFC37	replication factor C (activator 1) 4	protein-coding	0	0.356436
Merged-chr18-38778286-1	chr18	38778236	38778336	+	2.3	cIP2vsInput	Intergenic	Intergenic	-114170	NM_001033789	545253	Mm.244585	NM_001033789		Gm5820	EG545253	predicted gene 5820	protein-coding	0.01	0.514851
Merged-chr5-100489346-1	chr5	100489296	100489396	+	2.3	cIP2vsInput	"intron (NM_172714, intron 1 of 12)"	L1M5|LINE|L1	9227	NM_001115010	231506	Mm.212568	NM_001115010	ENSMUSG00000035310	Lin54	4832414L08|AI461788|mKIAA2037	lin-54 homolog (C. elegans)	protein-coding	0	0.29703
Merged-chr8-62179588-1	chr8	62179538	62179638	+	2.3	cIP2vsInput	Intergenic	Intergenic	-56470	NM_011922	26359	Mm.42179	NM_001136089	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding	0.01	0.336634
Merged-chr19-19148306-1	chr19	19148256	19148356	+	2.3	cIP1vsInput	Intergenic	Intergenic	-37110	NM_001043354	225998		NM_001043354	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta	RAR-related orphan receptor beta	protein-coding	0	0.326733
Merged-chr14-91723637-1	chr14	91723587	91723687	+	2.3	cIP2vsInput	Intergenic	RMER6-int|LTR|ERVK	1596746	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0	0.356436
Merged-chr17-79423204-1	chr17	79423154	79423254	+	2.3	cIP2vsInput	Intergenic	Intergenic	54681	NR_033463	74622	Mm.311921	NR_033463		4930429F11Rik	-	RIKEN cDNA 4930429F11 gene	miscRNA	0	0.356436
Merged-chr5-116271769-1	chr5	116271719	116271819	+	2.3	cIP2vsInput	"intron (NM_177759, intron 1 of 13)"	"intron (NM_177759, intron 1 of 13)"	17216	NM_177759	269693	Mm.10946	NM_177759		Ccdc60	AU018954|C130098D09	coiled-coil domain containing 60	protein-coding	0.02	0.574257
Merged-chr9-25089253-1	chr9	25089203	25089303	+	2.3	cIP2vsInput	Intergenic	(TTTG)n|Simple_repeat|Simple_repeat	62528	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding	0.02	0.316832
Merged-chr12-61746142-1	chr12	61746092	61746192	+	2.3	cIP2vsInput	"intron (NM_178714, intron 2 of 3)"	L1_Mus3|LINE|L1	221510	NM_178714	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.01	0.346535
Merged-chr15-35655248-1	chr15	35655198	35655298	+	2.3	cIP1vsInput	"intron (NM_177151, intron 30 of 61)"	L1MB7|LINE|L1	5670	NR_035527	100316736		NR_035527	ENSMUSG00000076333	Mir599	mmu-mir-599	microRNA 599	miscRNA	0	0.247525
Merged-chr2-87898172-1	chr2	87898122	87898222	+	2.3	cIP2vsInput	Intergenic	Intergenic	1995	NM_146640	258633	Mm.377603	NM_146640	ENSMUSG00000048197	Olfr1153	MOR177-7	olfactory receptor 1153	protein-coding	0	0.366337
Merged-chr16-60234429-1	chr16	60234379	60234479	+	2.3	cIP1vsInput	"intron (NM_007938, intron 3 of 17)"	L1MA4|LINE|L1	371102	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0	0.346535
Merged-chr2-113327690-1	chr2	113327640	113327740	+	2.3	cIP2vsInput	promoter-TSS (NM_010230)	promoter-TSS (NM_010230)	-46	NM_001043322	14260	Mm.4938	NM_001043322	ENSMUSG00000044042	Fmn1	BB164513|Fmn|formin-1|ld	formin 1	protein-coding	0.06	0.653465
Merged-chr18-60180852-1	chr18	60180802	60180902	+	2.3	cIP2vsInput	Intergenic	Intergenic	-31225	NM_001033767	240327	Mm.475204	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding	0	0.346535
Merged-chr13-21117903-1	chr13	21117853	21117953	+	2.3	cIP2vsInput	Intergenic	Intergenic	-14874	NM_010984	18341	Mm.246536	NM_010984	ENSMUSG00000071522	Olfr263	GA_x5J8B7TTCWC-858-415|IA3|MOR256-31|MOR256-37P|MOR256-61|Olfr263-ps1|Olfr42	olfactory receptor 263	protein-coding	0	0.287129
Merged-chr3-34692912-1	chr3	34692862	34692962	+	2.3	cIP1vsInput	Intergenic	Intergenic	23750	NR_038347	100041108	Mm.484676	NR_038347		Gm3143	-	predicted gene 3143	miscRNA	0.02	0.336634
Merged-chr13-13687422-1	chr13	13687372	13687472	+	2.3	cIP2vsInput	"intron (NM_010748, intron 28 of 52)"	"intron (NM_010748, intron 28 of 52)"	97013	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding	0	0.356436
Merged-chr4-104246951-1	chr4	104246901	104247001	+	2.3	cIP2vsInput	Intergenic	Intergenic	-120609	NM_010014	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding	0	0.425743
Merged-chr5-151479201-1	chr5	151479151	151479251	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	107723	NM_001102582	632671	Mm.469837	NM_001102582	ENSMUSG00000091794	Vmn2r18	EG632671|Vn2r18	"vomeronasal 2, receptor 18"	protein-coding	0	0.29703
Merged-chr6-111365316-1	chr6	111365266	111365366	+	2.3	cIP2vsInput	"intron (NM_177328, intron 8 of 9)"	"intron (NM_177328, intron 8 of 9)"	719718	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0	0.326733
Merged-chrX-115223444-1	chrX	115223394	115223494	+	2.3	cIP1vsInput	Intergenic	ERVL-int|LTR|ERVL	315862	NM_001081661	75097	Mm.50414	NM_001081661	ENSMUSG00000047079	Ube2dnl2	4930524E20Rik	ubiquitin-conjugating enzyme E2D N-terminal like 2	protein-coding	0	0.356436
Merged-chr1-22713469-1	chr1	22713419	22713519	+	2.3	cIP2vsInput	"intron (NM_001012623, intron 2 of 14).2"	"intron (NM_001012623, intron 2 of 14).2"	92255	NM_001012625	116837	Mm.461684	NM_001012623		Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding	0.01	0.376238
Merged-chr2-79461268-1	chr2	79461218	79461318	+	2.3	cIP1vsInput	Intergenic	Intergenic	-4632	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding	0	0.326733
Merged-chr14-95454277-1	chr14	95454227	95454327	+	2.3	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-426989	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.316832
Merged-chr19-42256095-1	chr19	42256045	42256145	+	2.3	cIP2vsInput	"5' UTR (NM_001141983, exon 3 of 7)"	"5' UTR (NM_001141983, exon 3 of 7)"	356	NM_027694	71146	Mm.329851	NM_001141983	ENSMUSG00000042532	Golga7b	4933417O08Rik|AI839934	"golgi autoantigen, golgin subfamily a, 7B"	protein-coding	0.09	0.722772
Merged-chr3-43661665-1	chr3	43661615	43661715	+	2.3	cIP2vsInput	Intergenic	Intergenic	1716595	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	miscRNA	0	0.316832
Merged-chr6-80681539-1	chr6	80681489	80681589	+	2.3	cIP2vsInput	Intergenic	Intergenic	661896	NM_178731	243499	Mm.483425	NM_001134743	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding	0	0.326733
Merged-chr16-73638674-1	chr16	73638624	73638724	+	2.3	cIP2vsInput	Intergenic	L1MA9|LINE|L1	703393	NR_030464	751561		NR_030464		Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	miscRNA	0	0.336634
Merged-chr10-68722423-1	chr10	68722373	68722473	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1323	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding	0	0.405941
Merged-chr11-38564647-1	chr11	38564597	38564697	+	2.3	cIP2vsInput	Intergenic	Intergenic	-44602	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0	0.336634
Merged-chr18-44250088-1	chr18	44250038	44250138	+	2.3	cIP2vsInput	Intergenic	Intergenic	-20039	NM_010935	18169	Mm.57234	NM_010935	ENSMUSG00000038071	Npy6r	-	neuropeptide Y receptor Y6	protein-coding	0	0.336634
Merged-chr15-12739716-1	chr15	12739666	12739766	+	2.3	cIP2vsInput	Intergenic	CpG	84941	NM_029998	77877	Mm.207311	NM_001166360	ENSMUSG00000022195	6030458C11Rik	-	RIKEN cDNA 6030458C11 gene	protein-coding	0.15	0.80198
Merged-chr4-64548652-1	chr4	64548602	64548702	+	2.3	cIP2vsInput	Intergenic	Intergenic	-501637	NM_011607	21923	Mm.454219	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding	0	0.376238
Merged-chr9-47026032-1	chr9	47025982	47026082	+	2.3	cIP2vsInput	Intergenic	L1M3a|LINE|L1	27291	NM_001243258	215467	Mm.246572	NM_001243258		Gm4791	D930036J05	predicted gene 4791	protein-coding	0	0.29703
Merged-chr11-4135113-1	chr11	4135063	4135163	+	2.3	cIP2vsInput	promoter-TSS (NM_027859)	promoter-TSS (NM_027859)	-47	NM_027859	71673	Mm.240586	NM_027859	ENSMUSG00000003581	Rnf215	0610009J22Rik|AW557025|C77903	ring finger protein 215	protein-coding	0.06	0.693069
Merged-chr6-77964266-1	chr6	77964216	77964316	+	2.3	cIP2vsInput	"intron (NM_145732, intron 1 of 18)"	L1MB7|LINE|L1	15401	NM_145732	12386	Mm.34637	NM_001109764	ENSMUSG00000063063	Ctnna2	AI481747|Catna|Catna2|cdf|chp	"catenin (cadherin associated protein), alpha 2"	protein-coding	0.01	0.376238
Merged-chr10-45547092-1	chr10	45547042	45547142	+	2.3	cIP1vsInput	Intergenic	Intergenic	-30737	NM_172473	209462	Mm.458633	NM_172473	ENSMUSG00000038822	Hace1	1700042J16Rik|A730034A22Rik|BC025474	"HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1"	protein-coding	0.01	0.455446
Merged-chr13-5642109-1	chr13	5642059	5642159	+	2.3	cIP1vsInput	Intergenic	Intergenic	215983	NR_045891	71867	Mm.179181	NR_045891		1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	miscRNA	0.01	0.336634
Merged-chr1-155919847-1	chr1	155919797	155919897	+	2.3	cIP2vsInput	"intron (NM_001039184, intron 15 of 37)"	L1_Mur1|LINE|L1	53408	NM_001039184	74081	Mm.260247	NM_001039184	ENSMUSG00000033671	Cep350	4933409L06Rik|6430546F08Rik	centrosomal protein 350	protein-coding	0	0.336634
Merged-chr9-19032816-1	chr9	19032766	19032866	+	2.3	cIP2vsInput	Intergenic	Intergenic	-2309	NM_001012266	257872	Mm.377280	NM_001012266	ENSMUSG00000045204	Olfr835	MOR150-3	olfactory receptor 835	protein-coding	0	0.336634
Merged-chr7-142387737-1	chr7	142387687	142387787	+	2.3	cIP2vsInput	"exon (NM_009983, exon 1 of 9)"	"exon (NM_009983, exon 1 of 9)"	133	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding	0.08	0.633663
Merged-chr15-16822916-1	chr15	16822866	16822966	+	2.3	cIP2vsInput	"intron (NM_009869, intron 1 of 10)"	"intron (NM_009869, intron 1 of 10)"	44815	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0.01	0.29703
Merged-chr8-116980179-1	chr8	116980129	116980229	+	2.3	cIP2vsInput	Intergenic	PB1D9|SINE|Alu	-1236	NM_027103	69528	Mm.272846	NM_027103	ENSMUSG00000031847	1700030J22Rik	-	RIKEN cDNA 1700030J22 gene	protein-coding	0.01	0.50495
Merged-chr7-87120773-1	chr7	87120723	87120823	+	2.3	cIP2vsInput	Intergenic	Intergenic	124308	NM_001105190	621430	Mm.469903	NM_001105190	ENSMUSG00000090362	Vmn2r79	EG621430	"vomeronasal 2, receptor 79"	protein-coding	0	0.326733
Merged-chr16-27830510-1	chr16	27830460	27830560	+	2.3	cIP2vsInput	Intergenic	Intergenic	-19420	NR_033475	100038623	Mm.387135	NR_033475		Gm10823	ENSMUSG00000075290	predicted gene 10823	miscRNA	0	0.39604
Merged-chr16-82315542-1	chr16	82315492	82315592	+	2.3	cIP1vsInput	Intergenic	Intergenic	1114845	NM_010954	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.277228
Merged-chr3-94811639-1	chr3	94811589	94811689	+	2.3	cIP2vsInput	Intergenic	B1_Mus2|SINE|Alu	-25124	NM_001037711	70737	Mm.87634	NM_001037711	ENSMUSG00000068876	Cgn	6330408J11Rik|AI647528|AI987749	cingulin	protein-coding	0	0.386139
Merged-chr7-86980727-1	chr7	86980677	86980777	+	2.3	cIP1vsInput	Intergenic	Intergenic	-15738	NM_001105190	621430	Mm.469903	NM_001105190	ENSMUSG00000090362	Vmn2r79	EG621430	"vomeronasal 2, receptor 79"	protein-coding	0.01	0.306931
Merged-chr8-86692892-1	chr8	86692842	86692942	+	2.3	cIP1vsInput	"intron (NM_025827, intron 11 of 14)"	"intron (NM_025827, intron 11 of 14)"	41323	NM_001168591	66887	Mm.324550	NM_001168591	ENSMUSG00000047866	Lonp2	1300002A08Rik|AU015403|Lonp	"lon peptidase 2, peroxisomal"	protein-coding	0	0.326733
Merged-chr1-139901842-1	chr1	139901792	139901892	+	2.3	cIP2vsInput	Intergenic	Lx3_Mus|LINE|L1	-43143	NM_001025575	545366	Mm.439660	NM_001025575	ENSMUSG00000033898	Cfhr2	Cfhrb_4/2	complement factor H-related 2	protein-coding	0	0.356436
Merged-chr4-94787456-1	chr4	94787406	94787506	+	2.3	cIP2vsInput	"intron (NM_013690, intron 2 of 22)"	"intron (NM_013690, intron 2 of 22)"	48156	NM_013690	21687	Mm.14313	NM_013690	ENSMUSG00000006386	Tek	AA517024|Cd202b|Hyk|Tie2|tie-2	endothelial-specific receptor tyrosine kinase	protein-coding	0	0.287129
Merged-chr4-35665666-1	chr4	35665616	35665716	+	2.3	cIP2vsInput	Intergenic	Intergenic	179538	NM_175516	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0	0.346535
Merged-chr1-109657854-1	chr1	109657804	109657904	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-325883	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.326733
Merged-chr2-161116030-1	chr2	161115980	161116080	+	2.3	cIP2vsInput	Intergenic	MTE2a|LTR|ERVL-MaLR	-6974	NM_173368	71389	Mm.122738	NM_173368	ENSMUSG00000057133	Chd6	5430439G14Rik|6330406J24Rik	chromodomain helicase DNA binding protein 6	protein-coding	0	0.346535
Merged-chr9-34538027-1	chr9	34537977	34538077	+	2.3	cIP1vsInput	"intron (NM_001190912, intron 1 of 15)"	"intron (NM_001190912, intron 1 of 15)"	49296	NM_001190911	67703	Mm.220710	NM_001190911		Kirrel3	1500010O20Rik|2900036G11Rik|NEPH2|SST4|mKIAA1867	kin of IRRE like 3 (Drosophila)	protein-coding	0	0.287129
Merged-chr1-131153110-1	chr1	131153060	131153160	+	2.3	cIP2vsInput	promoter-TSS (NM_010709)	promoter-TSS (NM_010709)	-97	NM_001136070	16865	Mm.276294	NM_001136070	ENSMUSG00000026427	Eif2d	D1Ertd5e|Lgtn	eukaryotic translation initiation factor 2D	protein-coding	0.07	0.574257
Merged-chr4-155654667-1	chr4	155654617	155654717	+	2.3	cIP2vsInput	"3' UTR (NM_001256108, exon 20 of 20)"	"3' UTR (NM_001256108, exon 20 of 20)"	-1283	NM_011985	26561	Mm.29373	NM_011985	ENSMUSG00000029061	Mmp23	CA-MMP	matrix metallopeptidase 23	protein-coding	0.02	0.50495
Merged-chr10-93919555-1	chr10	93919505	93919605	+	2.3	cIP1vsInput	Intergenic	Intergenic	-28353	NM_019648	56307	Mm.289329	NM_019648	ENSMUSG00000036112	Metap2	4930584B20Rik|A930035J23Rik|AI047573|AL024412|AU014659|Amp2|Mnpep|p67|p67eIF2	methionine aminopeptidase 2	protein-coding	0.03	0.524752
Merged-chr6-145662862-1	chr6	145662812	145662912	+	2.3	cIP2vsInput	Intergenic	Intergenic	46899	NM_009449	22147	Mm.270295	NM_009449	ENSMUSG00000067338	Tuba3b	M[a]7|Tuba7	"tubulin, alpha 3B"	protein-coding	0	0.376238
Merged-chr5-111581958-1	chr5	111581908	111582008	+	2.3	cIP2vsInput	"intron (NR_015546, intron 1 of 3)"	"intron (NR_015546, intron 1 of 3)"	397	NR_015546	330164	Mm.193276	NR_015546		C130026L21Rik	-	RIKEN cDNA C130026L21 gene	miscRNA	0.01	0.514851
Merged-chr7-88092061-1	chr7	88092011	88092111	+	2.3	cIP2vsInput	"intron (NM_001081414, intron 9 of 9)"	"intron (NM_001081414, intron 9 of 9)"	-186032	NM_009982	13032	Mm.322945	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|DPP1|DPPI	cathepsin C	protein-coding	0.01	0.306931
Merged-chr11-87372532-1	chr11	87372482	87372582	+	2.3	cIP2vsInput	Intergenic	Intergenic	-13538	NM_177167	320472	Mm.341988	NM_177167	ENSMUSG00000046442	Ppm1e	AW049266|B930008A12Rik|POPX1|PP2CH|mKIAA1072	protein phosphatase 1E (PP2C domain containing)	protein-coding	0	0.336634
Merged-chr3-61268955-1	chr3	61268905	61269005	+	2.3	cIP1vsInput	Intergenic	Intergenic	-95552	NM_028712	74012	Mm.477648	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	"RAP2B, member of RAS oncogene family"	protein-coding	0	0.287129
Merged-chr4-30526868-1	chr4	30526818	30526918	+	2.3	cIP1vsInput	Intergenic	Intergenic	-137728	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	miscRNA	0	0.316832
Merged-chr9-8591441-1	chr9	8591391	8591491	+	2.3	cIP1vsInput	"intron (NM_013838, intron 1 of 12)"	"intron (NM_013838, intron 1 of 12)"	47299	NM_013838	22068	Mm.325086	NM_013838	ENSMUSG00000031997	Trpc6	AV025995|LLHWJM002|LLHWJM003|LLHWJM004|TRP-6|Trrp6|mtrp6	"transient receptor potential cation channel, subfamily C, member 6"	protein-coding	0	0.326733
Merged-chr14-95433694-1	chr14	95433644	95433744	+	2.3	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-447572	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0.01	0.386139
Merged-chr6-141602974-1	chr6	141602924	141603024	+	2.3	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-26544	NM_020495	28253	Mm.272223	NM_020495	ENSMUSG00000030236	Slco1b2	7330442B20Rik|OATP-C|OATP2|Oatp1b2|Oatp4|Slc21a10|Slc21a6|lst-1|mlst-1	"solute carrier organic anion transporter family, member 1b2"	protein-coding	0	0.287129
Merged-chr14-92029368-1	chr14	92029318	92029418	+	2.3	cIP2vsInput	Intergenic	Intergenic	1859520	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.316832
Merged-chr15-81153740-1	chr15	81153690	81153790	+	2.3	cIP1vsInput	"intron (NM_001082536, intron 1 of 13)"	RMER12|LTR|ERVK	37017	NM_001082536	223701	Mm.439814	NM_001082536	ENSMUSG00000042292	Mkl1	AI852829|AMKL|AW743281|AW821984|Bsac|Mal|Mrtf-A	MKL (megakaryoblastic leukemia)/myocardin-like 1	protein-coding	0	0.386139
Merged-chr5-44237085-1	chr5	44237035	44237135	+	2.3	cIP2vsInput	Intergenic	Intergenic	-10479	NM_173764	231225	Mm.30688	NM_173764	ENSMUSG00000046985	Tapt1	4932414K18Rik	transmembrane anterior posterior transformation 1	protein-coding	0.01	0.415842
Merged-chr4-80209009-1	chr4	80208959	80209059	+	2.3	cIP1vsInput	Intergenic	Intergenic	-625221	NM_031202	22178	Mm.412291	NM_031202	ENSMUSG00000005994	Tyrp1	TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding	0.01	0.366337
Merged-chr16-48853967-1	chr16	48853917	48854017	+	2.3	cIP2vsInput	Intergenic	Intergenic	11415	NM_020509	57262	Mm.441868	NM_020509	ENSMUSG00000061100	Retnla	1810019L16Rik|Fizz-1|Fizz1|HIMF|RELM-alpha|RELMa|RELMalpha|Xcp2	resistin like alpha	protein-coding	0.01	0.336634
Merged-chr11-27931812-1	chr11	27931762	27931862	+	2.3	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	652484	NM_001166661	216613	Mm.93759	NM_001166661	ENSMUSG00000032878	Ccdc85a	E030025D05Rik	coiled-coil domain containing 85A	protein-coding	0	0.29703
Merged-chr2-111036108-1	chr2	111036058	111036158	+	2.3	cIP2vsInput	Intergenic	Intergenic	-85864	NM_001128103	228432	Mm.483325	NM_001128103	ENSMUSG00000074968	Ano3	AI838058|B230324K02Rik|Tmem16c	anoctamin 3	protein-coding	0	0.306931
Merged-chr16-85201285-1	chr16	85201235	85201335	+	2.3	cIP2vsInput	Intergenic	Intergenic	-27578	NM_001198823	11820	Mm.490986	NM_001198823	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding	0	0.336634
Merged-chr7-61923306-1	chr7	61923256	61923356	+	2.3	cIP2vsInput	"intron (NR_015533, intron 2 of 8)"	"intron (NR_015533, intron 2 of 8)"	4268	NR_015533	319893	Mm.490684	NR_015533		A230057D06Rik	-	RIKEN cDNA A230057D06 gene	miscRNA	0.01	0.356436
Merged-chr13-67638554-1	chr13	67638504	67638604	+	2.3	cIP2vsInput	promoter-TSS (NM_183146)	promoter-TSS (NM_183146)	-801	NM_183146	212281	Mm.342918	NM_183146	ENSMUSG00000021510	A530054K11Rik	Rslcan3	RIKEN cDNA A530054K11 gene	protein-coding	0.02	0.356436
Merged-chr6-74812462-1	chr6	74812412	74812512	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1342795	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.316832
Merged-chrX-98938056-1	chrX	98938006	98938106	+	2.3	cIP2vsInput	"5' UTR (NM_207633, exon 1 of 7)"	"5' UTR (NM_207633, exon 1 of 7)"	275	NM_207633	77929	Mm.212290	NM_207633	ENSMUSG00000047694	Yipf6	A430107J06Rik	"Yip1 domain family, member 6"	protein-coding	0.12	0.683168
Merged-chr6-82964068-1	chr6	82964018	82964118	+	2.3	cIP2vsInput	"intron (NM_033079, intron 2 of 9)"	"intron (NM_033079, intron 2 of 9)"	17146	NM_033079	110958	Mm.100652	NM_033079	ENSMUSG00000030041	M1ap	D6Mm5e	meiosis 1 associated protein	protein-coding	0	0.316832
Merged-chr2-88834509-1	chr2	88834459	88834559	+	2.3	cIP2vsInput	Intergenic	Intergenic	3390	NM_146896	258898	Mm.223308	NM_146896	ENSMUSG00000057447	Olfr1205	MOR230-1|MOR230-3|Olfr1203|Olfr1205-ps1	olfactory receptor 1205	protein-coding	0.02	0.326733
Merged-chr17-88956711-1	chr17	88956661	88956761	+	2.3	cIP1vsInput	Intergenic	Intergenic	-164735	NM_013582	16867	Mm.1644	NM_013582	ENSMUSG00000024107	Lhcgr	Gpcr19-rs1|LH-R|Lhr	luteinizing hormone/choriogonadotropin receptor	protein-coding	0.03	0.366337
Merged-chr15-46608881-1	chr15	46608831	46608931	+	2.3	cIP2vsInput	Intergenic	Lx3C|LINE|L1	-14424	NR_045811	75281	Mm.159487	NR_045811		4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	miscRNA	0	0.366337
Merged-chr17-30306650-1	chr17	30306600	30306700	+	2.3	cIP1vsInput	"intron (NM_027060, intron 7 of 10)"	"intron (NM_027060, intron 7 of 10)"	89530	NR_030688	623169	Mm.440508	NR_030688		Gm6402	EG623169	ribosomal protein S17 pseudogene	pseudo	0.01	0.316832
Merged-chr15-31568821-1	chr15	31568771	31568871	+	2.3	cIP2vsInput	promoter-TSS (NM_181588)	promoter-TSS (NM_181588)	-91	NM_181588	69574	Mm.28108	NM_181588	ENSMUSG00000022235	Cmbl	2310016A09Rik	carboxymethylenebutenolidase-like (Pseudomonas)	protein-coding	0.04	0.613861
Merged-chr3-79683746-2	chr3	79683674	79683818	+	2.3	cIP1vsInput|cIP2vsInput	"intron (NM_212452, intron 3 of 17)"	"intron (NM_212452, intron 3 of 17)"	54048	NM_212452	381489	Mm.331086	NM_212452	ENSMUSG00000034009	Rxfp1	Gm1018|Lgr7	relaxin/insulin-like family peptide receptor 1	protein-coding	0.027778	0.503448
Merged-chr2-82329512-1	chr2	82329462	82329562	+	2.3	cIP1vsInput	Intergenic	Intergenic	275854	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0	0.346535
Merged-chr14-109321355-1	chr14	109321305	109321405	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-138875	NR_039542	100628607		NR_039542	ENSMUSG00000092639	Mir3964	mmu-mir-3964|mu-mir-3964	microRNA 3964	miscRNA	0	0.287129
Merged-chr6-33073308-1	chr6	33073258	33073358	+	2.3	cIP1vsInput	Intergenic	RLTR25B|LTR|ERVK	-13156	NM_025336	66075	Mm.21501	NM_025336	ENSMUSG00000053768	Chchd3	0610041L09Rik|1700039J09Rik|AW558177	coiled-coil-helix-coiled-coil-helix domain containing 3	protein-coding	0	0.336634
Merged-chr3-21521734-1	chr3	21521684	21521784	+	2.3	cIP1vsInput	Intergenic	Intergenic	-554918	NM_030732	81004	Mm.446265	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding	0.02	0.366337
Merged-chr5-45124365-1	chr5	45124315	45124415	+	2.3	cIP2vsInput	Intergenic	Intergenic	158164	NR_073013	75783	Mm.218472	NR_073013		4930431F12Rik	-	RIKEN cDNA 4930431F12 gene	miscRNA	0	0.346535
Merged-chr5-21868201-1	chr5	21868151	21868251	+	2.3	cIP1vsInput	Intergenic	MusHAL1|LINE|L1	-2597	NM_030727	80979	Mm.160370	NM_030727	ENSMUSG00000029015	Slc26a5	Pres|prestin	"solute carrier family 26, member 5"	protein-coding	0	0.316832
Merged-chr17-17253016-1	chr17	17252966	17253066	+	2.3	cIP2vsInput	Intergenic	Intergenic	-121316	NM_025934	67045	Mm.35117	NM_025934	ENSMUSG00000023846	Riok2	2010110K24Rik|2410085M17Rik	RIO kinase 2 (yeast)	protein-coding	0.01	0.326733
Merged-chr2-74281199-1	chr2	74281149	74281249	+	2.3	cIP1vsInput	Intergenic	Intergenic	26518	NR_040501	73962	Mm.50289	NR_040501	ENSMUSG00000085405	4930441J16Rik	-	RIKEN cDNA 4930441J16 gene	miscRNA	0.02	0.356436
Merged-chr2-20128958-1	chr2	20128908	20129008	+	2.3	cIP2vsInput	Intergenic	L1MC1|LINE|L1	-160955	NM_001081006	208618	Mm.237935	NM_001081006	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding	0.01	0.336634
Merged-chr13-80011975-1	chr13	80011925	80012025	+	2.3	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-871447	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0	0.336634
Merged-chr13-80464706-1	chr13	80464656	80464756	+	2.3	cIP2vsInput	Intergenic	Intergenic	-418716	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0.01	0.29703
Merged-chr4-85368965-1	chr4	85368915	85369015	+	2.3	cIP2vsInput	"intron (NM_019535, intron 3 of 8)"	Lx7|LINE|L1	163509	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding	0	0.306931
Merged-chr7-52579483-1	chr7	52579433	52579533	+	2.3	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-563767	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding	0	0.306931
Merged-chr2-94598060-1	chr2	94598010	94598110	+	2.3	cIP2vsInput	Intergenic	Lx3A|LINE|L1	-159913	NM_007466	11800	Mm.486651	NM_007466	ENSMUSG00000027193	Api5	AAC-11|AI196452	apoptosis inhibitor 5	protein-coding	0	0.39604
Merged-chr6-139477448-1	chr6	139477398	139477498	+	2.3	cIP2vsInput	Intergenic	Intergenic	24461	NM_001128090	632971	Mm.475610	NM_001128090	ENSMUSG00000092164	Rergl	EG632971	RERG/RAS-like	protein-coding	0.01	0.287129
Merged-chr2-26351949-1	chr2	26351899	26351999	+	2.3	cIP1vsInput	TTS (NM_001037747)	TTS (NM_001037747)	161	NM_026828	52838	Mm.31239	NM_001139503	ENSMUSG00000075467	Dnlz	1110034G11Rik|D2Bwg1335e	DNL-type zinc finger	protein-coding	0.13	0.653465
Merged-chr8-96147200-1	chr8	96147150	96147250	+	2.3	cIP1vsInput	Intergenic	L1_Mus4|LINE|L1	183656	NR_037310	100499527		NR_037310	ENSMUSG00000093084	Mir1186b	mmu-mir-1186b	microRNA 1186b	miscRNA	0	0.346535
Merged-chr15-52976964-1	chr15	52976914	52977014	+	2.3	cIP1vsInput	Intergenic	ORR1D2|LTR|ERVL-MaLR	264519	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding	0.01	0.514851
Merged-chr2-51414904-1	chr2	51414854	51414954	+	2.3	cIP2vsInput	Intergenic	Lx7|LINE|L1	173073	NR_040636	329404	Mm.417725	NR_040636	ENSMUSG00000086349	Gm13497	A730015I17|OTTMUSG00000012425	predicted gene 13497	miscRNA	0	0.29703
Merged-chr17-22286507-1	chr17	22286457	22286557	+	2.3	cIP2vsInput	Intergenic	Intergenic	-60893	NM_001205095	240038	Mm.227945	NM_001205095	ENSMUSG00000096433	Gm4944	EG240038	predicted gene 4944	protein-coding	0	0.316832
Merged-chr12-60900911-1	chr12	60900861	60900961	+	2.3	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	620909	NR_045049	100504101	Mm.235026	NR_045049		Gm20063	-	"predicted gene, 20063"	miscRNA	0	0.336634
Merged-chr6-74318608-1	chr6	74318558	74318658	+	2.3	cIP2vsInput	Intergenic	Intergenic	-848941	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.346535
Merged-chr7-52424748-1	chr7	52424698	52424798	+	2.3	cIP2vsInput	Intergenic	Intergenic	-409032	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding	0.01	0.29703
Merged-chr2-22775927-1	chr2	22775877	22775977	+	2.3	cIP2vsInput	"intron (NM_019456, intron 1 of 13)"	"intron (NM_019456, intron 1 of 13)"	1600	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	"amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein"	protein-coding	0.01	0.336634
Merged-chr10-3854309-1	chr10	3854259	3854359	+	2.3	cIP2vsInput	"intron (NM_001159942, intron 2 of 16)"	RLTR31_Mur|LTR|ERVK	-18358	NM_001033253	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	"pleckstrin homology domain containing, family G (with RhoGef domain) member 1"	protein-coding	0.01	0.346535
Merged-chr7-94247726-1	chr7	94247676	94247776	+	2.3	cIP2vsInput	Intergenic	Intergenic	1167847	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0.01	0.29703
Merged-chr4-109572669-1	chr4	109572619	109572719	+	2.3	cIP2vsInput	Intergenic	Intergenic	-41372	NM_026291	67646	Mm.45820	NM_001199090	ENSMUSG00000060491	4930522H14Rik	1700007J23Rik	RIKEN cDNA 4930522H14 gene	protein-coding	0	0.316832
Merged-chrY-6705172-1	chrY	6705122	6705222	+	2.3	cIP1vsInput	Intergenic	Intergenic	462605	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.287129
Merged-chr14-112944201-1	chr14	112944151	112944251	+	2.3	cIP1vsInput	Intergenic	Intergenic	922771	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0	0.316832
Merged-chr15-47032129-1	chr15	47032079	47032179	+	2.3	cIP1vsInput	Intergenic	L1VL4|LINE|L1	408824	NR_045811	75281	Mm.159487	NR_045811		4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	miscRNA	0	0.277228
Merged-chr6-46885699-1	chr6	46885649	46885749	+	2.3	cIP2vsInput	"intron (NM_001004357, intron 15 of 23)"	"intron (NM_001004357, intron 15 of 23)"	-358697	NM_025771	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0	0.336634
Merged-chr6-102806207-1	chr6	102806157	102806257	+	2.3	cIP2vsInput	Intergenic	Intergenic	-341540	NM_008779	18488	Mm.435479	NM_008779	ENSMUSG00000030075	Cntn3	Pang	contactin 3	protein-coding	0	0.316832
Merged-chr3-99262629-1	chr3	99262579	99262679	+	2.3	cIP2vsInput	"intron (NM_009323, intron 1 of 7)"	"intron (NM_009323, intron 1 of 7)"	8869	NM_009323	21384	Mm.88761	NM_009323	ENSMUSG00000027868	Tbx15	Tbx14|Tbx8|de	T-box 15	protein-coding	0.01	0.336634
Merged-chr3-52909580-1	chr3	52909530	52909630	+	2.3	cIP1vsInput	"non-coding (NR_040555, exon 5 of 5)"	"non-coding (NR_040555, exon 5 of 5)"	18086	NR_040555	622124	Mm.389434	NR_040555		Gm20750	-	"predicted gene, 20750"	miscRNA	0.01	0.366337
Merged-chr5-71008344-1	chr5	71008294	71008394	+	2.3	cIP2vsInput	"intron (NM_008066, intron 6 of 9)"	"intron (NM_008066, intron 6 of 9)"	87505	NM_008066	14395	Mm.5304	NM_008066	ENSMUSG00000000560	Gabra2	C630048P16Rik|Gabra-2	"gamma-aminobutyric acid (GABA) A receptor, subunit alpha 2"	protein-coding	0	0.356436
Merged-chr11-107325929-1	chr11	107325879	107325979	+	2.3	cIP2vsInput	"intron (NM_145823, intron 2 of 9)"	"intron (NM_145823, intron 2 of 9)"	-136548	NM_001161329	68979	Mm.294617	NM_001161329	ENSMUSG00000018433	Nol11	1500002M01Rik|AU015220|AU019874	nucleolar protein 11	protein-coding	0.04	0.574257
Merged-chr6-12510006-1	chr6	12509956	12510056	+	2.3	cIP2vsInput	"intron (NM_001164805, intron 2 of 26)"	Lx8|LINE|L1	239247	NM_001164805	330267	Mm.400067	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	"thrombospondin, type I, domain containing 7A"	protein-coding	0	0.356436
Merged-chr3-15562488-1	chr3	15562438	15562538	+	2.3	cIP2vsInput	"intron (NM_001173460, intron 1 of 5)"	"intron (NM_001173460, intron 1 of 5)"	12577	NM_001173460	668101	Mm.423523	NM_001173460	ENSMUSG00000095028	Sirpb1b	-	signal-regulatory protein beta 1B	protein-coding	0	0.346535
Merged-chr17-56997100-1	chr17	56997050	56997150	+	2.3	cIP2vsInput	promoter-TSS (NM_025538)	promoter-TSS (NM_025538)	-239	NM_025538	66400	Mm.196150	NM_025538	ENSMUSG00000002661	Alkbh7	2310045B01Rik|2510008E23Rik|Abh7|Spata11	"alkB, alkylation repair homolog 7 (E. coli)"	protein-coding	0.02	0.485149
Merged-chr10-25979112-1	chr10	25979062	25979162	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-84607	NR_030449	751520		NR_030449	ENSMUSG00000076253	Mir680-3	Mirn680-3	microRNA 680-3	miscRNA	0	0.29703
Merged-chr13-31083128-1	chr13	31083078	31083178	+	2.3	cIP2vsInput	Intergenic	Intergenic	-109081	NM_025588	66482	Mm.293510	NM_025588	ENSMUSG00000021357	Exoc2	2410030I24Rik|AI648199|Sec5|Sec5l1	exocyst complex component 2	protein-coding	0	0.316832
Merged-chr10-73780091-1	chr10	73780041	73780141	+	2.3	cIP2vsInput	Intergenic	Lx9|LINE|L1	-41776	NM_001142760	11994	Mm.338933	NM_001142735	ENSMUSG00000052613	Pcdh15	BB078305|ENSMUSG00000046980|Gm9815|Ush1f|av|nmf19	protocadherin 15	protein-coding	0	0.29703
Merged-chr5-32435684-1	chr5	32435634	32435734	+	2.3	cIP1vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	-23286	NM_172707	19046	Mm.456635	NM_172707		Ppp1cb	1200010B19	"protein phosphatase 1, catalytic subunit, beta isoform"	protein-coding	0	0.277228
Merged-chr17-81281798-1	chr17	81281748	81281848	+	2.3	cIP2vsInput	Intergenic	Intergenic	-216713	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding	0.01	0.316832
Merged-chr12-57387023-1	chr12	57386973	57387073	+	2.3	cIP2vsInput	"intron (NM_001164370, intron 8 of 9)"	L1M5|LINE|L1	156598	NM_001164370	73490	Mm.268180	NM_001164370	ENSMUSG00000047022	Mipol1	1700081O04Rik|6030439O22Rik|AU021838|AW536152|D12Ertd19e	mirror-image polydactyly gene 1 homolog (human)	protein-coding	0	0.326733
Merged-chr10-36949587-1	chr10	36949537	36949637	+	2.3	cIP1vsInput	Intergenic	Lx4A|LINE|L1	-24957	NM_008229	15182	Mm.19806	NM_008229	ENSMUSG00000019777	Hdac2	D10Wsu179e|YAF1|Yy1bp|mRPD3	histone deacetylase 2	protein-coding	0.01	0.306931
Merged-chr4-66368738-1	chr4	66368688	66368788	+	2.3	cIP1vsInput	"intron (NM_019514, intron 1 of 21)"	L1MB8|LINE|L1	35745	NM_019514	56079	Mm.445312	NM_019514	ENSMUSG00000028373	Astn2	1d8|Astnl|bM452J22.1	astrotactin 2	protein-coding	0.02	0.326733
Merged-chr18-37969816-1	chr18	37969766	37969866	+	2.3	cIP2vsInput	promoter-TSS (NM_175684)	promoter-TSS (NM_175684)	-85	NM_175684	319262	Mm.285060	NM_175684	ENSMUSG00000038524	Fchsd1	A030002D08Rik	FCH and double SH3 domains 1	protein-coding	0.12	0.742574
Merged-chr4-50110691-1	chr4	50110641	50110741	+	2.3	cIP1vsInput	Intergenic	Intergenic	-264922	NM_001276355	242443	Mm.440095	NM_001033351		Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	"glutamate receptor ionotropic, NMDA3A"	protein-coding	0	0.376238
Merged-chr17-4185880-1	chr17	4185830	4185930	+	2.3	cIP1vsInput	Intergenic	Intergenic	-63778	NR_045462	78043	Mm.460785	NR_045462		4930548J01Rik	1700113K09Rik	RIKEN cDNA 4930548J01 gene	miscRNA	0	0.217822
Merged-chr14-92757601-1	chr14	92757551	92757651	+	2.3	cIP1vsInput	Intergenic	Intergenic	1131287	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0.01	0.316832
Merged-chr8-31291803-1	chr8	31291753	31291853	+	2.3	cIP2vsInput	Intergenic	L1MDa|LINE|L1	-75946	NR_046272	74517	Mm.390001	NR_046272		7420700N18Rik	-	RIKEN cDNA 7420700N18 gene	miscRNA	0	0.316832
Merged-chr13-88409437-1	chr13	88409387	88409487	+	2.3	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	-412035	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0	0.287129
Merged-chr10-28882462-1	chr10	28882412	28882512	+	2.3	cIP2vsInput	"3' UTR (NM_178666, exon 6 of 6)"	"3' UTR (NM_178666, exon 6 of 6)"	41045	NR_033601	114676	Mm.484516	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo	0	0.376238
Merged-chr4-61560609-1	chr4	61560559	61560659	+	2.3	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	35216	NM_001134644	100048885	Mm.422695	NM_001134644		Gm2083	-	major urinary protein LOC100048885	protein-coding	0	0.356436
Merged-chr3-16931169-1	chr3	16931119	16931219	+	2.3	cIP1vsInput	Intergenic	L1MB8|LINE|L1	747986	NM_001145919	229096	Mm.23834	NM_001145919	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding	0.02	0.287129
Merged-chr1-147300813-1	chr1	147300763	147300863	+	2.3	cIP1vsInput	Intergenic	Intergenic	803126	NM_001145807	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.336634
Merged-chr6-98914035-1	chr6	98913985	98914085	+	2.3	cIP2vsInput	Intergenic	Intergenic	114263	NM_001197322	108655	Mm.485266	NM_001197321	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding	0.01	0.29703
Merged-chr5-44881277-1	chr5	44881227	44881327	+	2.3	cIP2vsInput	Intergenic	Intergenic	-81570	NM_001077398	16826	Mm.25785	NM_001077398	ENSMUSG00000039706	Ldb2	AI035351|AW146358|CLIM1|CLP-36|Ldb3	LIM domain binding 2	protein-coding	0	0.356436
Merged-chr4-54128896-1	chr4	54128846	54128946	+	2.3	cIP1vsInput	Intergenic	Intergenic	302851	NM_028053	52076	Mm.27184	NM_028053	ENSMUSG00000028420	Tmem38b	1600017F22Rik|AA437809|AV051057|D4Ertd89e|TRIC-B|mg33b	transmembrane protein 38B	protein-coding	0.01	0.326733
Merged-chr5-59673517-1	chr5	59673467	59673567	+	2.3	cIP2vsInput	Intergenic	Intergenic	312485	NR_040683	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0.01	0.316832
Merged-chr8-54275629-1	chr8	54275579	54275679	+	2.3	cIP1vsInput	Intergenic	Intergenic	198097	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding	0	0.415842
Merged-chr1-55499411-1	chr1	55499361	55499461	+	2.3	cIP1vsInput	"intron (NM_001114663, intron 1 of 5)"	"intron (NM_001114663, intron 1 of 5)"	93465	NM_001114663	227120	Mm.194183	NM_001114663		Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding	0	0.29703
Merged-chr6-78408649-1	chr6	78408599	78408699	+	2.3	cIP2vsInput	TTS (NM_009043)	TTS (NM_009043)	3494	NM_009043	19693	Mm.46360	NM_009043	ENSMUSG00000023140	Reg2	RegII	regenerating islet-derived 2	protein-coding	0	0.336634
Merged-chr3-94235663-1	chr3	94235613	94235713	+	2.3	cIP2vsInput	Intergenic	URR1A|DNA|hAT-Charlie	-57470	NM_001146107	100043188	Mm.304029	NM_001146107	ENSMUSG00000074424	Gm10696	ENSMUSG00000074424	predicted gene 10696	protein-coding	0	0.336634
Merged-chr6-135087896-1	chr6	135087846	135087946	+	2.3	cIP2vsInput	Intergenic	Intergenic	22234	NM_181444	232431	Mm.477015	NM_181444	ENSMUSG00000046733	Gprc5a	Rai3|Raig1	"G protein-coupled receptor, family C, group 5, member A"	protein-coding	0.04	0.485149
Merged-chr8-109254737-1	chr8	109254687	109254787	+	2.3	cIP2vsInput	Intergenic	Intergenic	86171	NR_002928	384864	Mm.390083	NR_002928		Gm1943	-	WD repeat domain 70 pseudogene	pseudo	0	0.346535
Merged-chr1-4904724-1	chr1	4904674	4904774	+	2.3	cIP1vsInput	Intergenic	RMER12C|LTR|ERVK	46396	NM_001159751	21399	Mm.207263	NM_001159750	ENSMUSG00000033813	Tcea1	S-II	transcription elongation factor A (SII) 1	protein-coding	0	0.316832
Merged-chr1-94766077-1	chr1	94766027	94766127	+	2.3	cIP2vsInput	Intergenic	Intergenic	-31365	NR_040473	74689	Mm.399187	NR_040473		4930440C22Rik	-	RIKEN cDNA 4930440C22 gene	miscRNA	0.01	0.336634
Merged-chr16-56406473-1	chr16	56406423	56406523	+	2.3	cIP2vsInput	Intergenic	Intergenic	-71373	NM_001014422	320712	Mm.209236	NM_001014399	ENSMUSG00000035258	Abi3bp	5033411B22Rik|AI506287|BG172926|D930038M13Rik|TARSH|eratin	"ABI gene family, member 3 (NESH) binding protein"	protein-coding	0	0.346535
Merged-chr5-147854093-1	chr5	147854043	147854143	+	2.3	cIP2vsInput	Intergenic	Lx8|LINE|L1	-6535	NM_025624	66537	Mm.332855	NM_025624	ENSMUSG00000029649	Pomp	2510048O06Rik	proteasome maturation protein	protein-coding	0	0.346535
Merged-chr1-85909826-1	chr1	85909776	85909876	+	2.3	cIP2vsInput	Intergenic	Intergenic	15316	NM_022417	64294	Mm.29870	NM_022417	ENSMUSG00000026223	Itm2c	3110038L02Rik|BRI3|Bricd2c|E25|E25C|ITM3	integral membrane protein 2C	protein-coding	0.01	0.356436
Merged-chr9-98974150-1	chr9	98974100	98974200	+	2.3	cIP2vsInput	Intergenic	Intergenic	-12223	NM_001122851	23873	Mm.74605	NM_001122851	ENSMUSG00000032463	Faim	-	Fas apoptotic inhibitory molecule	protein-coding	0.01	0.376238
Merged-chr17-24457061-1	chr17	24457011	24457111	+	2.3	cIP2vsInput	Intergenic	L1M4|LINE|L1	-1750	NM_007893	13560	Mm.163132	NM_007893	ENSMUSG00000024137	E4f1	-	E4F transcription factor 1	protein-coding	0.01	0.277228
Merged-chr5-43404126-1	chr5	43404076	43404176	+	2.3	cIP2vsInput	Intergenic	Intergenic	-111443	NM_001135172	109323	Mm.275553	NM_001135172	ENSMUSG00000061535	C1qtnf7	5530401N20Rik|8430425G24Rik|Ctrp7	C1q and tumor necrosis factor related protein 7	protein-coding	0	0.356436
Merged-chr18-63648200-1	chr18	63648150	63648250	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	44159	NM_016792	53382	Mm.19169	NM_016792	ENSMUSG00000024583	Txnl1	32kDa|TRP32|Txnl	thioredoxin-like 1	protein-coding	0	0.316832
Merged-chr16-80602925-1	chr16	80602875	80602975	+	2.3	cIP2vsInput	Intergenic	Intergenic	-597772	NM_001113208	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.29703
Merged-chr7-108200023-1	chr7	108199973	108200073	+	2.3	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	12504	NM_001011811	258042	Mm.377337	NM_001011811	ENSMUSG00000095929	Olfr487	MOR204-29P|MOR204-31P|Olfr1538-ps1	olfactory receptor 487	protein-coding	0	0.346535
Merged-chr2-13053180-1	chr2	13053130	13053230	+	2.3	cIP2vsInput	Intergenic	Intergenic	-42316	NM_153155	227580	Mm.477072	NM_153155		C1ql3	1110065A22Rik|AI661623|C1ql|C1qtnf13|K100	C1q-like 3	protein-coding	0.02	0.366337
Merged-chr16-58033185-1	chr16	58033135	58033235	+	2.3	cIP2vsInput	Intergenic	Intergenic	-278448	NM_007739	12837	Mm.130388	NM_007739	ENSMUSG00000068196	Col8a1	Col8a-1	"collagen, type VIII, alpha 1"	protein-coding	0	0.336634
Merged-chr8-66637419-1	chr8	66637369	66637469	+	2.3	cIP2vsInput	Intergenic	Intergenic	50675	NM_016708	18168	Mm.10685	NM_016708	ENSMUSG00000044014	Npy5r	NPY5-R|NPYY5-R|Y5R	neuropeptide Y receptor Y5	protein-coding	0	0.29703
Merged-chr2-132032784-1	chr2	132032734	132032834	+	2.3	cIP1vsInput	Intergenic	Lx9|LINE|L1	-2796	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding	0	0.287129
Merged-chr2-96894256-1	chr2	96894206	96894306	+	2.3	cIP2vsInput	Intergenic	Intergenic	-573418	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0.01	0.336634
Merged-chr10-48156258-1	chr10	48156208	48156308	+	2.3	cIP2vsInput	Intergenic	Lx2|LINE|L1	939585	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	"proteasome (prosome, macropain) subunit, alpha type 6 pseudogene"	pseudo	0	0.336634
Merged-chr7-129586728-1	chr7	129586678	129586778	+	2.3	cIP1vsInput	Intergenic	Intergenic	-5135	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding	0.01	0.287129
Merged-chr12-93079553-1	chr12	93079503	93079603	+	2.3	cIP2vsInput	Intergenic	Intergenic	-1230396	NM_011344	20338	Mm.250605	NM_001039089	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding	0	0.277228
Merged-chr2-6078273-1	chr2	6078223	6078323	+	2.3	cIP2vsInput	Intergenic	Intergenic	51912	NM_144883	227545	Mm.133542	NM_001159657		Proser2	5430407P10Rik|AU067770	proline and serine rich 2	protein-coding	0	0.257426
Merged-chr18-47626292-1	chr18	47626242	47626342	+	2.3	cIP2vsInput	"intron (NR_033454, intron 1 of 5)"	"intron (NR_033454, intron 1 of 5)"	88557	NR_033454	328953	Mm.246768	NR_033454		Gm5095	A730092B10	predicted gene 5095	miscRNA	0	0.316832
Merged-chr17-57897514-1	chr17	57897464	57897564	+	2.3	cIP2vsInput	"intron (NM_001081653, intron 3 of 23)"	Lx|LINE|L1	127944	NM_001081653	620292	Mm.391030	NM_001081653	ENSMUSG00000038048	Cntnap5c	Caspr5-3|EG620292|Gm325	contactin associated protein-like 5C	protein-coding	0.02	0.29703
Merged-chr3-134427762-1	chr3	134427712	134427812	+	2.3	cIP2vsInput	Intergenic	Intergenic	-4127	NR_040600	75208	Mm.84580	NR_040600		4930539C22Rik	-	RIKEN cDNA 4930539C22 gene	miscRNA	0.02	0.366337
Merged-chr1-170857217-1	chr1	170857167	170857267	+	2.3	cIP2vsInput	"intron (NM_001081304, intron 1 of 15)"	L2|LINE|L2	10554	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding	0	0.366337
Merged-chr17-20665246-1	chr17	20665196	20665296	+	2.3	cIP2vsInput	Intergenic	Intergenic	-22262	NM_134191	171225	Mm.377184	NM_134191	ENSMUSG00000042848	Vmn1r226	V1re2	vomeronasal 1 receptor 226	protein-coding	0	0.316832
Merged-chr7-86436884-1	chr7	86436834	86436934	+	2.3	cIP2vsInput	Intergenic	B3|SINE|B2	-28529	NM_001011767	257929	Mm.377305	NM_001011767	ENSMUSG00000020168	Olfr299	MOR221-2	olfactory receptor 299	protein-coding	0	0.376238
Merged-chr1-156304431-1	chr1	156304381	156304481	+	2.3	cIP1vsInput	Intergenic	Intergenic	-1083	NM_001134741	214575	Mm.252800	NM_001134741	ENSMUSG00000060985	Tdrd5	Gm103	tudor domain containing 5	protein-coding	0.01	0.346535
Merged-chr8-6289544-1	chr8	6289494	6289594	+	2.3	cIP1vsInput	Intergenic	Intergenic	-1184312	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.29703
Merged-chr3-64345943-1	chr3	64345893	64345993	+	2.3	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-58526	NM_001104614	637004	Mm.469887	NM_001104614	ENSMUSG00000091572	Vmn2r3	EG637004	"vomeronasal 2, receptor 3"	protein-coding	0	0.336634
Merged-chr3-12874137-1	chr3	12874087	12874187	+	2.3	cIP2vsInput	Intergenic	L1MA5|LINE|L1	-597518	NM_178631	76897	Mm.422625	NM_001163328	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0	0.366337
Merged-chr10-5033539-1	chr10	5033489	5033589	+	2.3	cIP1vsInput	"intron (NM_001079686, intron 51 of 54)"	"intron (NM_001079686, intron 51 of 54)"	35524	NM_022027	64009	Mm.331626	NM_001079686	ENSMUSG00000019769	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756	"spectrin repeat containing, nuclear envelope 1"	protein-coding	0.01	0.336634
Merged-chr15-48811845-1	chr15	48811795	48811895	+	2.3	cIP2vsInput	Intergenic	Intergenic	-19856	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0	0.316832
Merged-chr7-18117742-1	chr7	18117692	18117792	+	2.3	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	51813	NM_001162523	67315	Mm.46089	NM_001162523	ENSMUSG00000030366	Ceacam12	1600031J20Rik|Ceacam12-C1|Ceacam12-C3|Ceacam12C1|Ceacam12C3	carcinoembryonic antigen-related cell adhesion molecule 12	protein-coding	0.01	0.415842
Merged-chrY-5084762-1	chrY	5084712	5084812	+	2.3	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	1313089	NM_001270516	100862398		NM_001270516		Gm21708	-	"predicted gene, 21708"	protein-coding	0.01	0.346535
Merged-chr2-81236181-1	chr2	81236131	81236231	+	2.3	cIP2vsInput	Intergenic	Intergenic	596917	NM_001190179	69482	Mm.29200	NM_001190179		Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding	0	0.306931
Merged-chr11-48478866-1	chr11	48478816	48478916	+	2.3	cIP2vsInput	Intergenic	ORR1D1|LTR|ERVL-MaLR	-321494	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Gnb2l1	AL033335|GB-like|Gnb2-rs1|Rack1|p205	"guanine nucleotide binding protein (G protein), beta polypeptide 2 like 1"	protein-coding	0.01	0.49505
Merged-chr5-17020976-1	chr5	17020926	17021026	+	2.3	cIP2vsInput	Intergenic	Intergenic	-455146	NM_027609	70935	Mm.332225	NM_027609	ENSMUSG00000058643	Speer4f	4922502J04Rik|SPEER-4F	spermatogenesis associated glutamate (E)-rich protein 4f	protein-coding	0.01	0.306931
Merged-chr12-90002813-1	chr12	90002763	90002863	+	2.3	cIP2vsInput	"intron (NM_001252074, intron 2 of 6)"	"intron (NM_001252074, intron 2 of 6)"	190330	NM_001252074	18191	Mm.487864	NM_001198587	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding	0	0.336634
Merged-chr14-57907786-1	chr14	57907736	57907836	+	2.3	cIP2vsInput	Intergenic	RMER17D2|LTR|ERVK	-17524	NM_029492	75965	Mm.29044	NM_029492	ENSMUSG00000021969	Zdhhc20	5033406L14Rik|AI448102|B230110O18Rik|HK11	"zinc finger, DHHC domain containing 20"	protein-coding	0	0.485149
Merged-chr11-12915298-1	chr11	12915248	12915348	+	2.3	cIP2vsInput	Intergenic	Intergenic	-450338	NM_172496	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	4732460E13|C530045F18Rik|mKIAA0633	cordon-bleu	protein-coding	0	0.346535
Merged-chrX-23132026-1	chrX	23131976	23132076	+	2.3	cIP1vsInput	Intergenic	Intergenic	233027	NM_026167	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik|mKIAA1309	kelch-like 13	protein-coding	0	0.326733
Merged-chr7-96506782-1	chr7	96506732	96506832	+	2.3	cIP1vsInput	"intron (NM_011858, intron 3 of 32)"	L1MB1|LINE|L1	-164818	NR_046043	670727	Mm.421352	NR_046043	ENSMUSG00000085751	Gm15412	OTTMUSG00000021245	predicted gene 15412	miscRNA	0.01	0.39604
Merged-chr4-105914885-1	chr4	105914835	105914935	+	2.3	cIP2vsInput	Intergenic	LTR16A|LTR|ERVL	-401328	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding	0	0.465347
Merged-chr14-69228123-1	chr14	69228073	69228173	+	2.3	cIP1vsInput	Intergenic	L1MA4A|LINE|L1	37431	NM_010921	18095	Mm.3520	NM_010921	ENSMUSG00000022061	Nkx3-1	Bax|NKX3.1|NKX3A|Nkx-3.1|bagpipe	"NK-3 transcription factor, locus 1 (Drosophila)"	protein-coding	0.01	0.356436
Merged-chr18-23047085-1	chr18	23047035	23047135	+	2.3	cIP2vsInput	Intergenic	Intergenic	-5432	NM_199024	319211	Mm.209896	NM_001161483	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding	0	0.356436
Merged-chr10-34766168-1	chr10	34766118	34766218	+	2.3	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	282768	NM_010237	14302	Mm.332432	NM_001159544	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding	0	0.366337
Merged-chr14-80413852-1	chr14	80413802	80413902	+	2.3	cIP2vsInput	Intergenic	Intergenic	413550	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.376238
Merged-chr6-42908447-1	chr6	42908397	42908497	+	2.3	cIP1vsInput	Intergenic	Intergenic	-3078	NM_146988	258990	Mm.377779	NM_146988	ENSMUSG00000045708	Olfr447	MOR261-1	olfactory receptor 447	protein-coding	0	0.277228
Merged-chr15-103823969-1	chr15	103823919	103824019	+	2.3	cIP1vsInput	"intron (NM_009268, intron 2 of 4)"	"intron (NM_009268, intron 2 of 4)"	75331	NM_009268	20771	Mm.30276	XM_003945554		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding	0.02	0.366337
Merged-chr4-69725465-1	chr4	69725415	69725515	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	684902	NM_145990	214444	Mm.379344	NM_145990		Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding	0	0.316832
Merged-chr4-105462876-1	chr4	105462826	105462926	+	2.3	cIP1vsInput	Intergenic	Intergenic	305529	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Ppap2b	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b	phosphatidic acid phosphatase type 2B	protein-coding	0	0.346535
Merged-chr4-147096900-1	chr4	147096850	147096950	+	2.3	cIP1vsInput	Intergenic	ORR1C1|LTR|ERVL-MaLR	-28464	NR_045446	71270	Mm.460830	NR_045446	ENSMUSG00000093617	4933438K21Rik	-	RIKEN cDNA 4933438K21 gene	miscRNA	0	0.415842
Merged-chr10-48434580-1	chr10	48434530	48434630	+	2.3	cIP2vsInput	Intergenic	Intergenic	661263	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	"proteasome (prosome, macropain) subunit, alpha type 6 pseudogene"	pseudo	0.01	0.336634
Merged-chr10-40869967-1	chr10	40869917	40870017	+	2.3	cIP1vsInput	"intron (NM_027879, intron 1 of 14)"	Lx7|LINE|L1	13176	NM_027879	71713	Mm.46063	NM_027879	ENSMUSG00000038446	Cdc40	1200003H23Rik|EHB3|PRP17	cell division cycle 40	protein-coding	0	0.336634
Merged-chr3-49605874-1	chr3	49605824	49605924	+	2.3	cIP2vsInput	Intergenic	ERVB4_1B-I_MM-int|LTR|ERVK	151442	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding	0	0.287129
Merged-chr2-129955649-1	chr2	129955599	129955699	+	2.3	cIP1vsInput	Intergenic	Intergenic	-56725	NM_009374	21818	Mm.2961	NM_009374	ENSMUSG00000027401	Tgm3	AI893889	"transglutaminase 3, E polypeptide"	protein-coding	0.01	0.524752
Merged-chr18-84146510-1	chr18	84146460	84146560	+	2.3	cIP2vsInput	Intergenic	Intergenic	58352	NM_146090	225791	Mm.440718	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik	"zinc binding alcohol dehydrogenase, domain containing 2"	protein-coding	0	0.326733
Merged-chr18-52872798-1	chr18	52872748	52872848	+	2.3	cIP2vsInput	"intron (NM_001199151, intron 5 of 11)"	L2c|LINE|L2	29849	NR_035420	100316749		NR_035420	ENSMUSG00000080573	Mir467f	Mirn467f|mmu-mir-467f	microRNA 467f	miscRNA	0	0.39604
Merged-chr7-61450375-1	chr7	61450325	61450425	+	2.3	cIP2vsInput	Intergenic	Intergenic	164952	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	miscRNA	0.01	0.346535
Merged-chr3-42962262-1	chr3	42962212	42962312	+	2.3	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	1219644	NM_027271	73852	Mm.29006	NM_001099785	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	"DNA segment, Chr 3, ERATO Doi 751, expressed"	protein-coding	0	0.356436
Merged-chr3-152089087-1	chr3	152089037	152089137	+	2.3	cIP1vsInput	Intergenic	Intergenic	76813	NM_016867	54120	Mm.97	NM_016867		Gipc2	2200002N01Rik|AU021850|Semcap2	"GIPC PDZ domain containing family, member 2"	protein-coding	0.03	0.326733
Merged-chr7-61034176-1	chr7	61034126	61034226	+	2.3	cIP2vsInput	Intergenic	Intergenic	581151	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	miscRNA	0	0.346535
Merged-chr4-74151348-1	chr4	74151298	74151398	+	2.3	cIP2vsInput	"intron (NM_172869, intron 7 of 13)"	Lx9|LINE|L1	-91149	NM_001172095	76804	Mm.209059	NM_001172095	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding	0	0.29703
Merged-chr1-166639353-1	chr1	166639303	166639403	+	2.3	cIP1vsInput	"intron (NM_001164312, intron 5 of 8)"	"intron (NM_001164312, intron 5 of 8)"	8340	NM_001164312	226604	Mm.330032	NM_001164312	ENSMUSG00000051081	Gm4847	EG226604|Fmo12	predicted gene 4847	protein-coding	0	0.316832
Merged-chr14-36389368-1	chr14	36389318	36389418	+	2.3	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	294403	NM_175008	218921	Mm.212464	NM_175008	ENSMUSG00000096405	4930474N05Rik	-	RIKEN cDNA 4930474N05 gene	protein-coding	0	0.445545
Merged-chr5-97947838-1	chr5	97947788	97947888	+	2.3	cIP1vsInput	"intron (NM_133738, intron 14 of 16)"	"intron (NM_133738, intron 14 of 16)"	83124	NM_133738	71914	Mm.24842	NM_133738		Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding	0	0.306931
Merged-chrX-74249993-1	chrX	74249943	74250043	+	2.3	cIP2vsInput	Intergenic	Intergenic	-3459	NM_010227	192176	Mm.295533	NM_010227	ENSMUSG00000031328	Flna	ABP-280|Dilp2|F730004A14Rik|Fln1|filamin-1	"filamin, alpha"	protein-coding	0.1	0.712871
Merged-chr12-32442971-1	chr12	32442921	32443021	+	2.3	cIP2vsInput	Intergenic	Intergenic	64182	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding	0	0.336634
Merged-chr8-34262480-1	chr8	34262430	34262530	+	2.3	cIP2vsInput	Intergenic	(CTATG)n|Simple_repeat|Simple_repeat	107917	NM_026432	67887	Mm.290353	NM_026432	ENSMUSG00000031532	Tmem66	1810045K07Rik|SARAF	transmembrane protein 66	protein-coding	0	0.306931
Merged-chr12-43416686-2	chr12	43416619	43416753	+	2.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	793382	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	"DnaJ (Hsp40) homolog, subfamily B, member 9"	protein-coding	0	0.303704
Merged-chr2-10143022-2	chr2	10142957	10143088	+	2.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-10521	NM_172471	209378	Mm.313876	NM_172471	ENSMUSG00000025780	Itih5	4631408O11Rik|5430408M01Rik|E130106B02	inter-alpha (globulin) inhibitor H5	protein-coding	0	0.477273
Merged-chrX-66554812-2	chrX	66554752	66554873	+	2.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-94506	NM_001161431	245450	Mm.403134	NM_001161431	ENSMUSG00000036790	Slitrk2	A930040J07	"SLIT and NTRK-like family, member 2"	protein-coding	0	0.401639
Merged-chr8-63221417-2	chr8	63221338	63221496	+	2.25	cIP1vsInput|cIP2vsInput	"intron (NM_001252620, intron 6 of 11)"	"intron (NM_001252620, intron 6 of 11)"	270072	NM_023689	72902	Mm.334552	NM_001252620	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3"	protein-coding	0	0.339623
Merged-chr2-89564327-2	chr2	89564277	89564378	+	2.25	cIP1vsInput|cIP2vsInput	Intergenic	MYSERV6-int|LTR|ERVK	11446	NM_146788	258784	Mm.377688	NM_146788	ENSMUSG00000075083	Olfr1245	MOR23112	olfactory receptor 1245	protein-coding	0	0.303922
Merged-chr12-18266015-2	chr12	18265919	18266111	+	2.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-248495	NM_001033157	236366	Mm.352227	NM_001033157		5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding	0.005208	0.42487
Merged-chr7-45481607-2	chr7	45481552	45481663	+	2.25	cIP1vsInput|cIP2vsInput	"intron (NM_027903, intron 4 of 6)"	"intron (NM_027903, intron 4 of 6)"	7189	NM_027903	71755	Mm.34208	NM_027903	ENSMUSG00000011382	Dhdh	1300018L09Rik|AA591799|Xld-1|Xld1	dihydrodiol dehydrogenase (dimeric)	protein-coding	0.018018	0.464286
Merged-chr10-104197045-2	chr10	104196987	104197104	+	2.25	cIP1vsInput|cIP2vsInput	TTS (NM_001270644)	TTS (NM_001270644)	3003	NM_001270900	667692		NM_001270900	ENSMUSG00000097878	Gm8764	EG667692	predicted gene 8764	protein-coding	0	0.381356
Merged-chr2-69635182-2	chr2	69635104	69635261	+	2.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-12073	NM_028284	72569	Mm.252136	NM_028284	ENSMUSG00000063145	Bbs5	1700049I01Rik|2700023J09Rik	Bardet-Biedl syndrome 5 (human)	protein-coding	0.038217	0.436709
Merged-chr15-31578443-2	chr15	31578356	31578531	+	2.25	cIP1vsInput|cIP2vsInput	"intron (NM_181588, intron 1 of 5)"	"intron (NM_181588, intron 1 of 5)"	9531	NM_181588	69574	Mm.28108	NM_181588	ENSMUSG00000022235	Cmbl	2310016A09Rik	carboxymethylenebutenolidase-like (Pseudomonas)	protein-coding	0	0.357955
Merged-chr12-4705830-2	chr12	4705754	4705906	+	2.25	cIP1vsInput|cIP2vsInput	"intron (NM_011365, intron 31 of 38)"	"intron (NM_011365, intron 31 of 38)"	32553	NM_029107	74855	Mm.269534	NM_029107	ENSMUSG00000079177	Fam228a	4930417G10Rik	"family with sequence similarity 228, member A"	protein-coding	0.013158	0.581699
Merged-chr7-61327195-2	chr7	61327121	61327270	+	2.25	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	288132	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	miscRNA	0.006711	0.346667
Merged-chr18-15539391-1	chr18	15539341	15539441	+	2.2	cIP1vsInput	"intron (NM_199055, intron 2 of 3)"	"intron (NM_199055, intron 2 of 3)"	-135707	NM_009700	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding	0	0.366337
Merged-chr11-6366148-1	chr11	6366098	6366198	+	2.2	cIP1vsInput	Intergenic	Intergenic	-23216	NM_028601	52915	Mm.1144	NM_001005867	ENSMUSG00000041164	Zmiz2	2410117E06Rik|D11Bwg0280e|R74931|Zimp7	"zinc finger, MIZ-type containing 2"	protein-coding	0.06	0.564356
Merged-chr2-116163411-1	chr2	116163361	116163461	+	2.2	cIP2vsInput	Intergenic	Intergenic	-87315	NR_033447	69974	Mm.440293	NR_033447		2810405F15Rik	-	RIKEN cDNA 2810405F15 gene	miscRNA	0	0.336634
Merged-chr9-19493914-1	chr9	19493864	19493964	+	2.2	cIP2vsInput	Intergenic	Intergenic	-2836	NM_146905	258907	Mm.377744	NM_146905	ENSMUSG00000052625	Olfr851	MOR155-1	olfactory receptor 851	protein-coding	0	0.287129
Merged-chr5-22092509-1	chr5	22092459	22092559	+	2.2	cIP2vsInput	"intron (NM_011261, intron 10 of 63)"	"intron (NM_011261, intron 10 of 63)"	-226905	NM_030727	80979	Mm.160370	NM_030727	ENSMUSG00000029015	Slc26a5	Pres|prestin	"solute carrier family 26, member 5"	protein-coding	0	0.326733
Merged-chr1-78159365-1	chr1	78159315	78159415	+	2.2	cIP2vsInput	"intron (NM_008781, intron 4 of 7)"	"intron (NM_008781, intron 4 of 7)"	37771	NM_008781	18505	Mm.1371	NM_001159520	ENSMUSG00000004872	Pax3	Pax-3|Sp|splotch	paired box gene 3	protein-coding	0.02	0.346535
Merged-chr3-75105946-1	chr3	75105896	75105996	+	2.2	cIP2vsInput	"intron (NM_172515, intron 5 of 16)"	"intron (NM_172515, intron 5 of 16)"	37777	NM_172515	213234	Mm.80075	NM_172515	ENSMUSG00000034151	Zbbx	4931432L23	"zinc finger, B-box domain containing"	protein-coding	0	0.316832
Merged-chr3-5784299-1	chr3	5784249	5784349	+	2.2	cIP2vsInput	Intergenic	Intergenic	-208051	NM_001163305	19302	Mm.132336	NM_001163304	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding	0.01	0.326733
Merged-chr15-60372716-1	chr15	60372666	60372766	+	2.2	cIP2vsInput	Intergenic	Intergenic	-356098	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding	0	0.336634
Merged-chr15-69763159-1	chr15	69763109	69763209	+	2.2	cIP1vsInput	Intergenic	MusHAL1|LINE|L1	-161074	NR_045071	100503580	Mm.404646	NR_045071		Gm19782	-	"predicted gene, 19782"	miscRNA	0.01	0.316832
Merged-chr7-85413798-1	chr7	85413748	85413848	+	2.2	cIP1vsInput	"intron (NM_001105182, intron 1 of 5)"	"intron (NM_001105182, intron 1 of 5)"	1878	NM_001105182	330581	Mm.469909	NM_001105182	ENSMUSG00000091006	Vmn2r69	-	"vomeronasal 2, receptor 69"	protein-coding	0	0.29703
Merged-chr3-69984093-1	chr3	69984043	69984143	+	2.2	cIP1vsInput	Intergenic	L1M2|LINE|L1	-23520	NM_001018031	229389	Mm.331071	NM_001018031	ENSMUSG00000027788	Otol1	Gm414	otolin 1 homolog (zebrafish)	protein-coding	0.01	0.316832
Merged-chr4-18340346-1	chr4	18340296	18340396	+	2.2	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	486864	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0.01	0.376238
Merged-chr1-52984137-1	chr1	52984087	52984187	+	2.2	cIP1vsInput	Intergenic	Lx|LINE|L1	-31297	NM_144953	67080	Mm.236287	NM_144953		1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding	0	0.326733
Merged-chr3-113798263-1	chr3	113798213	113798313	+	2.2	cIP2vsInput	Intergenic	B1_Mur1|SINE|Alu	-168114	NM_001038696	67225	Mm.316928	NM_001038696	ENSMUSG00000027981	Rnpc3	2810441O16Rik|AI447568|C030014B17Rik	"RNA-binding region (RNP1, RRM) containing 3"	protein-coding	0	0.405941
Merged-chr3-83263279-1	chr3	83263229	83263329	+	2.2	cIP2vsInput	Intergenic	Intergenic	207741	NM_016784	53317	Mm.286349	NM_016784	ENSMUSG00000027998	Plrg1	AA958940|C80566|Tango4	"pleiotropic regulator 1, PRL1 homolog (Arabidopsis)"	protein-coding	0	0.39604
Merged-chr1-148048074-1	chr1	148048024	148048124	+	2.2	cIP1vsInput	Intergenic	Intergenic	1550387	NM_001145807	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.346535
Merged-chr11-16103666-1	chr11	16103616	16103716	+	2.2	cIP2vsInput	Intergenic	Intergenic	-154058	NM_145967	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	9330184N17Rik|BC027127|Vstm2	V-set and transmembrane domain containing 2A	protein-coding	0.01	0.287129
Merged-chr17-83000855-1	chr17	83000805	83000905	+	2.2	cIP1vsInput	Intergenic	Intergenic	77370	NR_045094	100503434	Mm.187281	NR_045094		Gm19689	-	"predicted gene, 19689"	miscRNA	0	0.415842
Merged-chr15-22331695-1	chr15	22331645	22331745	+	2.2	cIP1vsInput	Intergenic	Intergenic	383289	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding	0.02	0.415842
Merged-chr15-54834994-1	chr15	54834944	54835044	+	2.2	cIP2vsInput	Intergenic	L1ME1|LINE|L1	84967	NM_001136077	18606	Mm.250256	NM_001136077	ENSMUSG00000022425	Enpp2	ATX|Npps2|PD-Ialpha|Pdnp2	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding	0.01	0.326733
Merged-chr13-101566488-1	chr13	101566438	101566538	+	2.2	cIP2vsInput	Intergenic	MER45R|DNA|hAT-Tip100	126159	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	AA414921|C530050K14|PI3K|p50alpha|p55alpha|p85alpha	"phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)"	protein-coding	0	0.267327
Merged-chr13-115253917-1	chr13	115253867	115253967	+	2.2	cIP2vsInput	Intergenic	Intergenic	-151953	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding	0.01	0.336634
Merged-chr6-10710510-1	chr6	10710460	10710560	+	2.2	cIP2vsInput	Intergenic	Lx3_Mus|LINE|L1	263868	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	miscRNA	0	0.306931
Merged-chr18-34663368-1	chr18	34663318	34663418	+	2.2	cIP1vsInput	Intergenic	Intergenic	-11632	NM_178347	52563	Mm.196638	NM_178347	ENSMUSG00000024370	Cdc23	6030435O18|D18Ertd243e	CDC23 cell division cycle 23	protein-coding	0.04	0.554455
Merged-chr2-85241363-1	chr2	85241313	85241413	+	2.2	cIP1vsInput	Intergenic	Intergenic	-44664	NM_001033346	241528	Mm.476412	NM_001033346	ENSMUSG00000075224	Lrrc55	A330097E02Rik|Gm351	leucine rich repeat containing 55	protein-coding	0.01	0.405941
Merged-chr3-88193356-1	chr3	88193306	88193406	+	2.2	cIP1vsInput	Intergenic	ORR1C2|LTR|ERVL-MaLR	-15571	NR_045997	76642	Mm.424420	NR_045997	ENSMUSG00000096935	1700113A16Rik	2210408E11Rik|AA408983	RIKEN cDNA 1700113A16 gene	miscRNA	0	0.445545
Merged-chr3-44503169-1	chr3	44503119	44503219	+	2.2	cIP1vsInput	Intergenic	Intergenic	875091	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	miscRNA	0	0.326733
Merged-chr16-88777331-1	chr16	88777281	88777381	+	2.2	cIP1vsInput	Intergenic	Intergenic	-3125	NM_027170	69696	Mm.358728	NM_027170	ENSMUSG00000048830	2310057N15Rik	Krtap13-1	RIKEN cDNA 2310057N15 gene	protein-coding	0	0.356436
Merged-chr11-91949530-1	chr11	91949480	91949580	+	2.2	cIP2vsInput	Intergenic	Intergenic	-371975	NM_028547	73470	Mm.67677	NM_028547	ENSMUSG00000046755	Kif2b	1700063D03Rik	kinesin family member 2B	protein-coding	0	0.306931
Merged-chr11-116319031-1	chr11	116318981	116319081	+	2.2	cIP2vsInput	Intergenic	Intergenic	-12293	NM_001162872	53413	Mm.22530	NM_001162872	ENSMUSG00000020792	Exoc7	Exo70|sec70	exocyst complex component 7	protein-coding	0.03	0.415842
Merged-chr12-33511366-1	chr12	33511316	33511416	+	2.2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	81742	NM_172253	28071	Mm.413045	NM_172253	ENSMUSG00000020561	Twistnb	2410173G11|2810024J17Rik|D16Wsu83e	TWIST neighbor	protein-coding	0	0.326733
Merged-chr12-86625656-1	chr12	86625606	86625706	+	2.2	cIP1vsInput	Intergenic	Intergenic	-53044	NM_177354	238328	Mm.216101	NM_177354		Vash1	AI834978|D930046M13Rik|G630009D10Rik	vasohibin 1	protein-coding	0	0.336634
Merged-chr11-61825936-1	chr11	61825886	61825986	+	2.2	cIP2vsInput	"intron (NM_013881, intron 10 of 26)"	"intron (NM_013881, intron 10 of 26)"	29156	NM_013881	29869	Mm.162025	NM_013881	ENSMUSG00000004798	Ulk2	A830085I22Rik|AU015340|Unc51.2|mKIAA0623	unc-51 like kinase 2	protein-coding	0	0.326733
Merged-chr10-50066167-1	chr10	50066117	50066217	+	2.2	cIP2vsInput	Intergenic	Intergenic	-277413	NM_001111268	14806	Mm.332838	NM_001111268	ENSMUSG00000056073	Grik2	AW124492|GluK2|Glur-6|Glur6|Glurbeta2	"glutamate receptor, ionotropic, kainate 2 (beta 2)"	protein-coding	0.01	0.326733
Merged-chrX-153918654-1	chrX	153918604	153918704	+	2.2	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	86361	NM_001005370	278240	Mm.293363	NM_001005370	ENSMUSG00000046550	Spin2	BC068162	"spindlin family, member 2"	protein-coding	0.01	0.306931
Merged-chr6-5840472-1	chr6	5840422	5840522	+	2.2	cIP2vsInput	"intron (NM_001191023, intron 5 of 15)"	"intron (NM_001191023, intron 5 of 15)"	114833	NM_001191026	13426	Mm.20893	NM_001191023	ENSMUSG00000029757	Dync1i1	DH IC-1|DHIC-1|DIC|Dncic1|IC74	dynein cytoplasmic 1 intermediate chain 1	protein-coding	0	0.346535
Merged-chr3-150268720-1	chr3	150268670	150268770	+	2.2	cIP2vsInput	Intergenic	L1VL4|LINE|L1	993983	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	miscRNA	0	0.366337
Merged-chrX-131919737-1	chrX	131919687	131919787	+	2.2	cIP1vsInput	Intergenic	Intergenic	1769256	NM_001105245	279653	Mm.39738	NM_001105245	ENSMUSG00000051323	Pcdh19	B530002L05Rik|Gm717|mKIAA1313	protocadherin 19	protein-coding	0	0.277228
Merged-chr5-78032490-1	chr5	78032440	78032540	+	2.2	cIP1vsInput	Intergenic	Intergenic	-520742	NR_027806	231332	Mm.373616	NM_001010832		Pea15b	-	phosphoprotein enriched in astrocytes 15B	pseudo	0	0.336634
Merged-chr5-10167037-1	chr5	10166987	10167087	+	2.2	cIP2vsInput	Intergenic	Intergenic	-441685	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	"glutamate receptor, metabotropic 3"	protein-coding	0.01	0.277228
Merged-chr10-49895389-1	chr10	49895339	49895439	+	2.2	cIP1vsInput	Intergenic	Intergenic	-106635	NM_001111268	14806	Mm.332838	NM_001111268	ENSMUSG00000056073	Grik2	AW124492|GluK2|Glur-6|Glur6|Glurbeta2	"glutamate receptor, ionotropic, kainate 2 (beta 2)"	protein-coding	0	0.237624
Merged-chr7-93709739-1	chr7	93709689	93709789	+	2.2	cIP2vsInput	Intergenic	L1M5|LINE|L1	629860	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0	0.277228
Merged-chr11-47613343-1	chr11	47613293	47613393	+	2.2	cIP2vsInput	Intergenic	L1MD|LINE|L1	-234041	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	"sarcoglycan, delta (dystrophin-associated glycoprotein)"	protein-coding	0	0.336634
Merged-chr9-115829680-1	chr9	115829630	115829730	+	2.2	cIP2vsInput	Intergenic	MYSERV6-int|LTR|ERVK	-79775	NM_028638	73748	Mm.485018	NM_028638	ENSMUSG00000056880	Gadl1	1110027M19Rik	glutamate decarboxylase-like 1	protein-coding	0	0.336634
Merged-chr12-92985075-1	chr12	92985025	92985125	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1135918	NM_011344	20338	Mm.250605	NM_001039089	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding	0.01	0.306931
Merged-chr5-57274627-1	chr5	57274577	57274677	+	2.2	cIP2vsInput	Intergenic	Intergenic	443292	NR_015588	319216	Mm.446765	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	miscRNA	0.02	0.316832
Merged-chr19-37937247-1	chr19	37937197	37937297	+	2.2	cIP2vsInput	"intron (NM_001099634, intron 31 of 52)"	"intron (NM_001099634, intron 31 of 52)"	106330	NM_001099634	226101	Mm.34674	NM_001099634	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding	0	0.346535
Merged-chr3-5747497-1	chr3	5747447	5747547	+	2.2	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	-171249	NM_001163305	19302	Mm.132336	NM_001163304	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding	0	0.346535
Merged-chr12-47623748-1	chr12	47623698	47623798	+	2.2	cIP1vsInput	Intergenic	Intergenic	677714	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0.01	0.326733
Merged-chr15-55106521-1	chr15	55106471	55106571	+	2.2	cIP2vsInput	"intron (NR_045093, intron 4 of 4)"	"intron (NR_045093, intron 4 of 4)"	-5962	NM_145470	97998	Mm.393497	NM_001037937	ENSMUSG00000022419	Deptor	4731402B04Rik|9130412E02Rik|D15Ertd336e|D15Ertd597e|Depdc6|Depdc6-001|Depdc6-002|R75183|mKIAA4200	DEP domain containing MTOR-interacting protein	protein-coding	0	0.316832
Merged-chr18-26396262-1	chr18	26396212	26396312	+	2.2	cIP1vsInput	Intergenic	Intergenic	-642279	NM_001174074	108013	Mm.266435	NM_001146292	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	"CUGBP, Elav-like family member 4"	protein-coding	0	0.415842
Merged-chr15-14783143-1	chr15	14783093	14783193	+	2.2	cIP2vsInput	Intergenic	Intergenic	-1609504	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	K-cadherin|cad6|cadherin-6	cadherin 6	protein-coding	0	0.346535
Merged-chr4-38657838-1	chr4	38657788	38657888	+	2.2	cIP1vsInput	Intergenic	L1MEc|LINE|L1	-792455	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding	0	0.39604
Merged-chr8-71835162-1	chr8	71835112	71835212	+	2.2	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-46906	NM_145624	236193	Mm.290790	NM_145624		Zfp709	BC021921|GIOT-4|HIT-40	zinc finger protein 709	protein-coding	0.01	0.336634
Merged-chr1-66034475-1	chr1	66034425	66034525	+	2.2	cIP2vsInput	Intergenic	L1M5|LINE|L1	107953	NM_027010	12969	Mm.275362	NM_027010	ENSMUSG00000025945	Crygf	3110001K11Rik|Cryg-2|DGcry-2|Len-2	"crystallin, gamma F"	protein-coding	0	0.346535
Merged-chr2-116382802-1	chr2	116382752	116382852	+	2.2	cIP2vsInput	Intergenic	Intergenic	-306706	NR_033447	69974	Mm.440293	NR_033447		2810405F15Rik	-	RIKEN cDNA 2810405F15 gene	miscRNA	0	0.326733
Merged-chr1-49868706-1	chr1	49868656	49868756	+	2.2	cIP1vsInput	Intergenic	Lx9|LINE|L1	-1058817	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.326733
Merged-chr3-7256605-1	chr3	7256555	7256655	+	2.2	cIP2vsInput	Intergenic	Intergenic	-109999	NM_008862	18767	Mm.3193	NM_008862	ENSMUSG00000027499	Pkia	AI415001|PKIalpha	"protein kinase inhibitor, alpha"	protein-coding	0.01	0.287129
Merged-chr1-159062011-1	chr1	159061961	159062061	+	2.2	cIP2vsInput	Intergenic	L1MA7|LINE|L1	-104573	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding	0	0.237624
Merged-chr19-17612338-1	chr19	17612288	17612388	+	2.2	cIP1vsInput	"intron (NM_001190483, intron 10 of 37)"	MTB_Mm|LTR|ERVL-MaLR	218295	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding	0	0.346535
Merged-chr6-108504130-1	chr6	108504080	108504180	+	2.2	cIP2vsInput	"intron (NM_010585, intron 53 of 61)"	"intron (NM_010585, intron 53 of 61)"	119037	NR_040757	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	miscRNA	0.02	0.405941
Merged-chr1-151677774-1	chr1	151677724	151677824	+	2.2	cIP1vsInput	"intron (NM_022018, intron 5 of 13)"	"intron (NM_022018, intron 5 of 13)"	-77600	NM_001039644	66967	Mm.337691	NM_001039644	ENSMUSG00000043019	Edem3	2310050N11Rik	"ER degradation enhancer, mannosidase alpha-like 3"	protein-coding	0	0.346535
Merged-chr9-108729741-1	chr9	108729691	108729791	+	2.2	cIP1vsInput	"intron (NM_008924, intron 5 of 10)"	"intron (NM_008924, intron 5 of 10)"	37598	NM_008924	19087	Mm.486392	NM_008924	ENSMUSG00000032601	Prkar2a	1110061A24Rik|AI317181|AI836829|RII(alpha)	"protein kinase, cAMP dependent regulatory, type II alpha"	protein-coding	0	0.386139
Merged-chr17-91231928-1	chr17	91231878	91231978	+	2.2	cIP1vsInput	Intergenic	Lx|LINE|L1	-139126	NM_020252	18189	Mm.312068	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0	0.356436
Merged-chr17-64375590-1	chr17	64375540	64375640	+	2.2	cIP2vsInput	Intergenic	Intergenic	-43707	NM_001025309	224938	Mm.489681	NM_001025309	ENSMUSG00000024083	Pja2	AI447901|AL022700|Neurodap1|mKIAA0438	"praja 2, RING-H2 motif containing"	protein-coding	0	0.514851
Merged-chr16-66584607-1	chr16	66584557	66584657	+	2.2	cIP2vsInput	Intergenic	Intergenic	-72511	NR_040512	75501	Mm.396161	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	miscRNA	0.01	0.346535
Merged-chr1-147339763-2	chr1	147339702	147339825	+	2.2	cIP1vsInput|cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	842076	NM_001145807	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0.01626	0.33871
Merged-chr2-45422556-1	chr2	45422506	45422606	+	2.2	cIP1vsInput	Intergenic	Intergenic	-274049	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	miscRNA	0	0.247525
Merged-chr2-86228069-1	chr2	86228019	86228119	+	2.2	cIP2vsInput	TTS (NM_147012)	TTS (NM_147012)	900	NM_147012	259014	Mm.377789	NM_147012	ENSMUSG00000075196	Olfr1047	MOR188-3	olfactory receptor 1047	protein-coding	0	0.277228
Merged-chr10-102282096-1	chr10	102282046	102282146	+	2.2	cIP2vsInput	"intron (NM_001162369, intron 1 of 5)"	Lx6|LINE|L1	-92341	NM_026243	67569	Mm.403713	NM_001162368	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"	protein-coding	0	0.376238
Merged-chr2-134320339-1	chr2	134320289	134320389	+	2.2	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	234013	NM_010403	15112	Mm.26634	NM_010403	ENSMUSG00000027261	Hao1	GOX|Gox1|Hao-1	"hydroxyacid oxidase 1, liver"	protein-coding	0	0.287129
Merged-chr10-129509950-1	chr10	129509900	129510000	+	2.2	cIP1vsInput	Intergenic	ID_B1|SINE|B4	9064	NM_146933	258935	Mm.377756	NM_146933	ENSMUSG00000044025	Olfr790	MOR112-1	olfactory receptor 790	protein-coding	0	0.386139
Merged-chr4-73182327-1	chr4	73182277	73182377	+	2.2	cIP1vsInput	Intergenic	Intergenic	222745	NM_001013393	433719	Mm.348294	NM_001013393	ENSMUSG00000066137	Gm11487	OTTMUSG00000001246	predicted gene 11487	protein-coding	0	0.326733
Merged-chr5-85780806-1	chr5	85780756	85780856	+	2.2	cIP1vsInput	Intergenic	Intergenic	284777	NM_007683	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	Cenpc	centromere protein C1	protein-coding	0.01	0.376238
Merged-chr14-43279154-1	chr14	43279104	43279204	+	2.2	cIP1vsInput	Intergenic	Intergenic	68657	NM_027940	71826	Mm.335855	XM_003945954	ENSMUSG00000095384	1700001F09Rik	Gm10377	RIKEN cDNA 1700001F09 gene	protein-coding	0	0.376238
Merged-chr5-80005089-1	chr5	80005039	80005139	+	2.2	cIP2vsInput	Intergenic	Intergenic	-489185	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0	0.326733
Merged-chr5-90203143-1	chr5	90203093	90203193	+	2.2	cIP2vsInput	Intergenic	Intergenic	20853	NR_028088	231430	Mm.319697	NM_001033310	ENSMUSG00000035505	Cox18	BC038311	cytochrome c oxidase assembly protein 18	protein-coding	0.01	0.257426
Merged-chr5-132453078-1	chr5	132453028	132453128	+	2.2	cIP2vsInput	"intron (NM_177047, intron 1 of 18)"	"intron (NM_177047, intron 1 of 18)"	89265	NM_177047	319974	Mm.488992	NM_177047		Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding	0	0.346535
Merged-chr8-76882500-1	chr8	76882450	76882550	+	2.2	cIP2vsInput	"intron (NR_028579, intron 1 of 1)"	Lx5|LINE|L1	17673	NR_028579	100039211	Mm.367571	NR_028579	ENSMUSG00000074235	Gm10649	ENSMUSG00000074235	predicted gene 10649	miscRNA	0	0.386139
Merged-chr3-119437783-1	chr3	119437733	119437833	+	2.2	cIP2vsInput	Intergenic	Intergenic	345605	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0	0.316832
Merged-chr13-76519527-1	chr13	76519477	76519577	+	2.2	cIP1vsInput	"intron (NM_030174, intron 1 of 20)"	L1VL4|LINE|L1	134566	NM_030174	78771	Mm.316249	NM_030174		Mctp1	2810465F10Rik	"multiple C2 domains, transmembrane 1"	protein-coding	0	0.366337
Merged-chr8-127656177-1	chr8	127656127	127656227	+	2.2	cIP1vsInput	Intergenic	Intergenic	356525	NM_001013580	93742	Mm.299254	NM_001013580	ENSMUSG00000025812	Pard3	AA960621|AI256638|ASIP|D8Ertd580e|PAR-3|Par3|Pard3a	par-3 (partitioning defective 3) homolog (C. elegans)	protein-coding	0	0.366337
Merged-chr19-12696408-1	chr19	12696358	12696458	+	2.2	cIP1vsInput	"intron (NM_029550, intron 1 of 5)"	"intron (NM_029550, intron 1 of 5)"	618	NM_029550	64697	Mm.218561	NM_029550	ENSMUSG00000024694	Keg1	0610008P16Rik|AI316519|GS4059	kidney expressed gene 1	protein-coding	0	0.376238
Merged-chr13-26173426-1	chr13	26173376	26173476	+	2.2	cIP1vsInput	Intergenic	Intergenic	138980	NR_045933	73576	Mm.45473	NR_045933		1700092E19Rik	-	RIKEN cDNA 1700092E19 gene	miscRNA	0	0.306931
Merged-chr8-13613654-1	chr8	13613604	13613704	+	2.2	cIP2vsInput	"intron (NM_009025, intron 3 of 23)"	"intron (NM_009025, intron 3 of 23)"	-51206	NM_001080781	66501	Mm.46136	NM_001080781	ENSMUSG00000031452	1700029H14Rik	-	RIKEN cDNA 1700029H14 gene	protein-coding	0	0.50495
Merged-chrX-75603682-1	chrX	75603632	75603732	+	2.2	cIP1vsInput	Intergenic	Intergenic	-25478	NM_175122	67790	Mm.45148	NM_175122	ENSMUSG00000031202	Rab39b	6330580M05Rik	"RAB39B, member RAS oncogene family"	protein-coding	0	0.306931
Merged-chr1-94117812-1	chr1	94117762	94117862	+	2.2	cIP2vsInput	Intergenic	Intergenic	-65259	NM_008798	18566	Mm.5024	NM_008798	ENSMUSG00000026285	Pdcd1	Ly101|PD-1|Pdc1	programmed cell death 1	protein-coding	0	0.326733
Merged-chr14-115625076-1	chr14	115625026	115625126	+	2.2	cIP1vsInput	"intron (NM_175500, intron 6 of 7)"	"intron (NM_175500, intron 6 of 7)"	-215524	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	miscRNA	0	0.316832
Merged-chr12-117990269-1	chr12	117990219	117990319	+	2.2	cIP2vsInput	"intron (NM_010060, intron 55 of 81)"	"intron (NM_010060, intron 55 of 81)"	146408	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding	0	0.356436
Merged-chr2-136455838-1	chr2	136455788	136455888	+	2.2	cIP1vsInput	Intergenic	MLT1B|LTR|ERVL-MaLR	-67871	NM_172858	241656	Mm.131572	NM_172858	ENSMUSG00000039913	Pak7	2900083L08Rik|6430627N20|Pak5	p21 protein (Cdc42/Rac)-activated kinase 7	protein-coding	0	0.39604
Merged-chr19-30249293-1	chr19	30249243	30249343	+	2.2	cIP2vsInput	Intergenic	Intergenic	16336	NM_010776	17195	Mm.30045	NM_010776	ENSMUSG00000024863	Mbl2	L-MBP|MBL|MBL-C|MBP-C	mannose-binding lectin (protein C) 2	protein-coding	0	0.306931
Merged-chr4-100454618-1	chr4	100454568	100454668	+	2.2	cIP1vsInput	Intergenic	Lx7|LINE|L1	-24249	NM_001033773	381534	Mm.318133	NM_001033773	ENSMUSG00000069733	Ube2u	-	ubiquitin-conjugating enzyme E2U (putative)	protein-coding	0	0.336634
Merged-chr17-54981050-1	chr17	54981000	54981100	+	2.2	cIP1vsInput	Intergenic	Lx|LINE|L1	-464667	NM_172829	240119	Mm.311687	NM_172829	ENSMUSG00000024172	St6gal2	C230064G14Rik|St6galII|mKIAA1877	"beta galactoside alpha 2,6 sialyltransferase 2"	protein-coding	0	0.386139
Merged-chr2-22370403-1	chr2	22370353	22370453	+	2.2	cIP1vsInput	"intron (NM_148413, intron 16 of 19)"	L1M2|LINE|L1	142900	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding	0	0.326733
Merged-chr17-71332954-1	chr17	71332904	71333004	+	2.2	cIP1vsInput	TTS (NR_028023)	TTS (NR_028023)	8850	NR_028023	100043644	Mm.362377	NR_028023		Gm4566	-	ubiquitin specific peptidase 16 pseudogene	pseudo	0.01	0.346535
Merged-chr8-84800316-1	chr8	84800266	84800366	+	2.2	cIP2vsInput	promoter-TSS (NM_001081982)	promoter-TSS (NM_001081982)	24	NM_010906	18032	Mm.9394	NM_001081981		Nfix	-	nuclear factor I/X	protein-coding	0.21	0.772277
Merged-chr6-69975228-1	chr6	69975178	69975278	+	2.2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-648054	NR_004434	19783		NR_004434		Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	miscRNA	0	0.346535
Merged-chr13-112541045-1	chr13	112540995	112541095	+	2.2	cIP2vsInput	"intron (NM_139299, intron 10 of 16)"	"intron (NM_139299, intron 10 of 16)"	39617	NM_139299	218624	Mm.380801	NM_139299	ENSMUSG00000050377	Il31ra	CRL3|GLM-R|GPL|Glmr|NR10	interleukin 31 receptor A	protein-coding	0.02	0.524752
Merged-chr14-93948340-1	chr14	93948290	93948390	+	2.2	cIP1vsInput	Intergenic	Intergenic	-57671	NM_001271798	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.29703
Merged-chr3-24684837-1	chr3	24684787	24684887	+	2.2	cIP1vsInput	Intergenic	Intergenic	1468470	NM_001163387	192167	Mm.316080	NM_001163387	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|mKIAA1070	neuroligin 1	protein-coding	0	0.326733
Merged-chr18-40986284-1	chr18	40986234	40986334	+	2.2	cIP2vsInput	Intergenic	Intergenic	727923	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding	0.01	0.29703
Merged-chr5-96533662-1	chr5	96533612	96533712	+	2.2	cIP1vsInput	"intron (NM_175473, intron 3 of 73)"	"intron (NM_175473, intron 3 of 73)"	159707	NM_175473	231470	Mm.291120	NM_175473	ENSMUSG00000034687	Fras1	E130113P14Rik|bl|mKIAA1500	Fraser syndrome 1 homolog (human)	protein-coding	0	0.267327
Merged-chr2-154276837-1	chr2	154276787	154276887	+	2.2	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	18958	NM_175167	71425	Mm.389341	NM_175167	ENSMUSG00000067998	Bpifb9a	4833413D08Rik|AI413838	"BPI fold containing family B, member 9A"	protein-coding	0.01	0.376238
Merged-chr18-77190373-1	chr18	77190323	77190423	+	2.2	cIP1vsInput	"intron (NM_153124, intron 1 of 6)"	"intron (NM_153124, intron 1 of 6)"	4526	NM_013666	225742	Mm.365178	NM_013666	ENSMUSG00000025425	St8sia5	ST8SiaV|Siat8e	"ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5"	protein-coding	0	0.326733
Merged-chr9-80599025-1	chr9	80598975	80599075	+	2.2	cIP1vsInput	Intergenic	Intergenic	-133587	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding	0	0.257426
Merged-chr15-72753077-1	chr15	72753027	72753127	+	2.2	cIP2vsInput	"intron (NM_029640, intron 17 of 21)"	L1MC|LINE|L1	57247	NR_002864	353342	Mm.440245	NR_002864		Peg13	-	paternally expressed 13	miscRNA	0	0.356436
Merged-chr1-175242948-1	chr1	175242898	175242998	+	2.2	cIP1vsInput	"intron (NM_001199003, intron 3 of 17)"	"intron (NM_001199003, intron 3 of 17)"	249597	NM_011880	24012	Mm.7956	NM_001199003		Rgs7	-	regulator of G protein signaling 7	protein-coding	0.01	0.366337
Merged-chr15-19255972-1	chr15	19255922	19256022	+	2.2	cIP2vsInput	Intergenic	Intergenic	435643	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0	0.366337
Merged-chrX-44624928-1	chrX	44624878	44624978	+	2.2	cIP2vsInput	Intergenic	Intergenic	165233	NM_001190718	245404	Mm.55685	NM_001190718	ENSMUSG00000045284	Dcaf12l1	9330180J20|A230038L21Rik|Decaf12l1|Wdr40b	DDB1 and CUL4 associated factor 12-like 1	protein-coding	0.01	0.336634
Merged-chr12-55080208-1	chr12	55080158	55080258	+	2.2	cIP2vsInput	promoter-TSS (NM_011899)	promoter-TSS (NM_011899)	-98	NM_028314	72658	Mm.434380	NM_028314	ENSMUSG00000062198	2700097O09Rik	AW552125	RIKEN cDNA 2700097O09 gene	protein-coding	0.13	0.70297
Merged-chr8-85577508-1	chr8	85577458	85577558	+	2.2	cIP2vsInput	Intergenic	Intergenic	-22237	NM_019794	56445	Mm.475573	NM_019794	ENSMUSG00000031701	Dnaja2	1500017M13Rik|2010206B19Rik|DNAJ|DNJ3|Dnaj3|HIRIP4|PRO3015|mDj3	"DnaJ (Hsp40) homolog, subfamily A, member 2"	protein-coding	0	0.346535
Merged-chr1-142860444-1	chr1	142860394	142860494	+	2.2	cIP2vsInput	Intergenic	Intergenic	-780253	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0	0.376238
Merged-chr2-65792743-1	chr2	65792693	65792793	+	2.2	cIP2vsInput	Intergenic	RLTR20A3_MM|LTR|ERVK	-53024	NM_153409	77771	Mm.102025	NM_153409	ENSMUSG00000044647	Csrnp3	A330102K23Rik|CSRNP-3|Csnrp3|Mbu1|taip-2	cysteine-serine-rich nuclear protein 3	protein-coding	0.01	0.366337
Merged-chr3-143931026-1	chr3	143930976	143931076	+	2.2	cIP2vsInput	Intergenic	Intergenic	-218883	NR_040405	621809	Mm.360134	NR_040405		Gm6260	EG621809	predicted gene 6260	miscRNA	0.01	0.346535
Merged-chr18-47735784-1	chr18	47735734	47735834	+	2.2	cIP1vsInput	Intergenic	Intergenic	-187057	NR_045404	414127	Mm.450768	NR_045404		G630055G22Rik	-	RIKEN cDNA G630055G22 gene	miscRNA	0.01	0.49505
Merged-chr7-82434204-1	chr7	82434154	82434254	+	2.2	cIP2vsInput	"intron (NM_001190374, intron 4 of 29)"	"intron (NM_001190374, intron 4 of 29)"	98510	NM_001190374	269959	Mm.65306	NM_001190374	ENSMUSG00000070469	Adamtsl3	9230119C12Rik|C130057K09|mKIAA1233	ADAMTS-like 3	protein-coding	0	0.356436
Merged-chr10-13452863-1	chr10	13452813	13452913	+	2.2	cIP1vsInput	"intron (NM_001195065, intron 1 of 12)"	"intron (NM_001195065, intron 1 of 12)"	21533	NM_001195065	215789	Mm.487722	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding	0.01	0.346535
Merged-chr3-98579081-1	chr3	98579031	98579131	+	2.2	cIP1vsInput	Intergenic	Intergenic	-15043	NM_008294	15495	Mm.475664	NM_001111336	ENSMUSG00000095143	Hsd3b4	-	"hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4"	protein-coding	0	0.425743
Merged-chr12-49836720-1	chr12	49836670	49836770	+	2.2	cIP2vsInput	Intergenic	Intergenic	-355858	NR_045472	69054	Mm.417838	NR_045472		1810007C17Rik	-	RIKEN cDNA 1810007C17 gene	miscRNA	0	0.306931
Merged-chrX-94996878-1	chrX	94996828	94996928	+	2.2	cIP1vsInput	Intergenic	Intergenic	29804	NM_178753	270624	Mm.115205	NM_178753	ENSMUSG00000071722	Spin4	9630042H07Rik	"spindlin family, member 4"	protein-coding	0.01	0.306931
Merged-chr1-103514950-1	chr1	103514900	103515000	+	2.2	cIP2vsInput	Intergenic	Intergenic	-1253869	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0	0.336634
Merged-chr1-9731470-1	chr1	9731420	9731520	+	2.2	cIP2vsInput	"intron (NM_173443, intron 2 of 2)"	"intron (NM_173443, intron 2 of 2)"	-16178	NR_040462	73331	Mm.460470	NR_040462		1700034P13Rik	-	RIKEN cDNA 1700034P13 gene	miscRNA	0	0.326733
Merged-chr4-17247112-1	chr4	17247062	17247162	+	2.2	cIP1vsInput	Intergenic	RMER6D|LTR|ERVK	-606370	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0	0.326733
Merged-chr6-43119118-1	chr6	43119068	43119168	+	2.2	cIP2vsInput	Intergenic	L1VL2|LINE|L1	3374	NM_146655	258649	Mm.271494	NM_146655	ENSMUSG00000094669	Olfr441	MOR261-3	olfactory receptor 441	protein-coding	0	0.356436
Merged-chr11-60199714-1	chr11	60199664	60199764	+	2.2	cIP2vsInput	TTS (NM_009021)	TTS (NM_009021)	20890	NM_011480	20787	Mm.278701	NM_011480	ENSMUSG00000020538	Srebf1	ADD-1|ADD1|D630008H06|SREBP-1|SREBP-1a|SREBP-1c|SREBP1|SREBP1c|bHLHd1	sterol regulatory element binding transcription factor 1	protein-coding	0.01	0.564356
Merged-chr14-33459895-1	chr14	33459845	33459945	+	2.2	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-12737	NM_016700	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding	0	0.346535
Merged-chr7-87984542-1	chr7	87984492	87984592	+	2.2	cIP1vsInput	"intron (NM_001081414, intron 5 of 9)"	"intron (NM_001081414, intron 5 of 9)"	-293551	NM_009982	13032	Mm.322945	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|DPP1|DPPI	cathepsin C	protein-coding	0	0.316832
Merged-chr8-32399759-1	chr8	32399709	32399809	+	2.2	cIP2vsInput	Intergenic	Intergenic	247864	NR_046039	666589	Mm.367675	NR_046039		Gm8179	EG666589	predicted gene 8179	miscRNA	0	0.287129
Merged-chr5-50942917-1	chr5	50942867	50942967	+	2.2	cIP2vsInput	Intergenic	Intergenic	611004	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PGC-1v|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	"peroxisome proliferative activated receptor, gamma, coactivator 1 alpha"	protein-coding	0	0.326733
Merged-chr6-26691436-1	chr6	26691386	26691486	+	2.2	cIP2vsInput	Intergenic	Intergenic	760010	NR_040771	626904	Mm.126787	NR_040771		Gm20756	-	"predicted gene, 20756"	miscRNA	0.01	0.336634
Merged-chr5-43633477-1	chr5	43633427	43633527	+	2.2	cIP1vsInput	Intergenic	Lx3C|LINE|L1	-28902	NM_172274	231214	Mm.486802	NM_172274	ENSMUSG00000039765	Cc2d2a	5730509K17Rik	coiled-coil and C2 domain containing 2A	protein-coding	0.02	0.346535
Merged-chr3-35374459-1	chr3	35374409	35374509	+	2.2	cIP2vsInput	Intergenic	Lx|LINE|L1	291704	NR_040748	625963	Mm.251506	NR_040748		Gm6639	-	predicted gene 6639	miscRNA	0	0.39604
Merged-chr1-22913965-1	chr1	22913915	22914015	+	2.2	cIP1vsInput	Intergenic	Intergenic	-108241	NM_001012624	116837	Mm.461684	NM_001012623		Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding	0	0.346535
Merged-chr10-63971065-1	chr10	63971015	63971115	+	2.2	cIP1vsInput	"intron (NM_178678, intron 2 of 2)"	"intron (NM_178678, intron 2 of 2)"	119190	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding	0	0.336634
Merged-chr5-70644321-1	chr5	70644271	70644371	+	2.2	cIP1vsInput	Intergenic	LTR69|LTR|ERVL	198296	NM_010252	14405	Mm.255292	NM_010252	ENSMUSG00000001260	Gabrg1	GabaA|GabaA/BZ	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1"	protein-coding	0	0.29703
Merged-chr12-72893002-1	chr12	72892952	72893052	+	2.2	cIP2vsInput	"intron (NM_029444, intron 14 of 17)"	"intron (NM_029444, intron 14 of 17)"	24763	NM_029444	75801	Mm.242892	NM_029444	ENSMUSG00000021098	4930447C04Rik	4921504I02Rik|A930035O15Rik|Six6OS|Six6as|Six6os1	RIKEN cDNA 4930447C04 gene	protein-coding	0	0.346535
Merged-chr5-6845141-1	chr5	6845091	6845191	+	2.2	cIP2vsInput	"intron (NM_001163223, intron 2 of 3)"	"intron (NM_001163223, intron 2 of 3)"	-459023	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding	0	0.316832
Merged-chr1-102486933-1	chr1	102486883	102486983	+	2.2	cIP1vsInput	Intergenic	Lx3A|LINE|L1	1331165	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.39604
Merged-chr5-63063219-1	chr5	63063169	63063269	+	2.2	cIP2vsInput	Intergenic	Intergenic	249396	NM_001170705	100322896	Mm.479821	NM_001170705	ENSMUSG00000090326	Gm17384	Dthd1	"predicted gene, 17384"	protein-coding	0	0.336634
Merged-chr18-22961478-1	chr18	22961428	22961528	+	2.2	cIP1vsInput	"intron (NM_199024, intron 1 of 9)"	"intron (NM_199024, intron 1 of 9)"	77185	NM_001161483	319211	Mm.209896	NM_001161483	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding	0	0.287129
Merged-chr1-26708722-1	chr1	26708672	26708772	+	2.2	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-21262	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding	0.01	0.336634
Merged-chr13-19972381-1	chr13	19972331	19972431	+	2.2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-118126	NM_080288	140580	Mm.342392	NR_038122		Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding	0.01	0.316832
Merged-chr1-98879381-1	chr1	98879331	98879431	+	2.2	cIP1vsInput	Intergenic	MTD|LTR|ERVL-MaLR	458257	NM_027584	70866	Mm.389164	NM_001164233	ENSMUSG00000026336	Slco6d1	4921511I05Rik	"solute carrier organic anion transporter family, member 6d1"	protein-coding	0	0.316832
Merged-chr18-83555859-1	chr18	83555809	83555909	+	2.2	cIP2vsInput	Intergenic	Intergenic	-229975	NR_045361	70960	Mm.410834	NR_045361		4921531P14Rik	1700108N05Rik	RIKEN cDNA 4921531P14 gene	miscRNA	0	0.29703
Merged-chr11-45290548-1	chr11	45290498	45290598	+	2.2	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-173620	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	OTTMUSG00000005475	predicted gene 12159	miscRNA	0.01	0.326733
Merged-chr3-11849310-1	chr3	11849260	11849360	+	2.2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-4951	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.336634
Merged-chr17-15787753-1	chr17	15787703	15787803	+	2.2	cIP1vsInput	Intergenic	Intergenic	38833	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	"RGM domain family, member B"	protein-coding	0.01	0.277228
Merged-chr9-95373681-1	chr9	95373631	95373731	+	2.2	cIP1vsInput	Intergenic	RMER6C|LTR|ERVK	33589	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding	0.01	0.415842
Merged-chr1-99593912-1	chr1	99593862	99593962	+	2.2	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	-178853	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding	0	0.277228
Merged-chr11-39042271-1	chr11	39042221	39042321	+	2.2	cIP2vsInput	Intergenic	Intergenic	-522226	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0.02	0.316832
Merged-chr6-11040101-1	chr6	11040051	11040151	+	2.2	cIP2vsInput	Intergenic	Intergenic	-65723	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	miscRNA	0	0.306931
Merged-chr12-43024281-1	chr12	43024231	43024331	+	2.2	cIP2vsInput	Intergenic	Intergenic	1185787	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	"DnaJ (Hsp40) homolog, subfamily B, member 9"	protein-coding	0.02	0.366337
Merged-chr7-98295748-1	chr7	98295698	98295798	+	2.2	cIP2vsInput	"intron (NM_025408, intron 1 of 10)"	"intron (NM_025408, intron 1 of 10)"	13779	NM_025408	66190	Mm.334041	NM_025408	ENSMUSG00000030760	Acer3	1110057L18Rik|5430429L08Rik|AV015045|Phca	alkaline ceramidase 3	protein-coding	0	0.346535
Merged-chr14-120698483-1	chr14	120698433	120698533	+	2.2	cIP2vsInput	Intergenic	Intergenic	-212711	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding	0	0.336634
Merged-chr7-44594020-1	chr7	44593970	44594070	+	2.2	cIP2vsInput	"intron (NM_008422, intron 1 of 3)"	"intron (NM_008422, intron 1 of 3)"	3134	NM_008422	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	"potassium voltage gated channel, Shaw-related subfamily, member 3"	protein-coding	0.09	0.732673
Merged-chr15-33573896-1	chr15	33573846	33573946	+	2.2	cIP2vsInput	"intron (NM_018755, intron 8 of 8)"	Lx3_Mus|LINE|L1	79540	NR_045070	75880	Mm.396109	NR_045070		4930592A05Rik	-	RIKEN cDNA 4930592A05 gene	miscRNA	0	0.326733
Merged-chr6-118431940-1	chr6	118431890	118431990	+	2.2	cIP2vsInput	"intron (NM_028335, intron 5 of 5)"	"intron (NM_028335, intron 5 of 5)"	-12523	NM_194339	213895	Mm.25269	NM_194339	ENSMUSG00000030138	Bms1	AA408648|AU020092|AU043373|BB007109|BC030906|Bms1l|mKIAA0187	"BMS1 homolog, ribosome assembly protein (yeast)"	protein-coding	0	0.356436
Merged-chr8-75109331-1	chr8	75109281	75109381	+	2.2	cIP2vsInput	promoter-TSS (NM_008566)	promoter-TSS (NM_008566)	-197	NM_008566	17218	Mm.5048	NM_008566	ENSMUSG00000005410	Mcm5	AA617332|AI324988|AL033333|Cdc46|Mcmd5|P1-CDC46|mCD46|mCDC46	"minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)"	protein-coding	0.08	0.554455
Merged-chr4-56341157-1	chr4	56341107	56341207	+	2.2	cIP2vsInput	Intergenic	Intergenic	400268	NM_025271	11471	Mm.251434	NM_025271	ENSMUSG00000070980	Actl7b	Tact1	actin-like 7b	protein-coding	0.01	0.316832
Merged-chr5-100506677-1	chr5	100506627	100506727	+	2.2	cIP2vsInput	Intergenic	Intergenic	-6038	NM_172714	231506	Mm.212568	NM_001115010	ENSMUSG00000035310	Lin54	4832414L08|AI461788|mKIAA2037	lin-54 homolog (C. elegans)	protein-coding	0	0.366337
Merged-chr19-43015194-1	chr19	43015144	43015244	+	2.2	cIP2vsInput	"intron (NM_001081257, intron 3 of 11)"	"intron (NM_001081257, intron 3 of 11)"	-235218	NM_019424	192236	Mm.218381	NM_019424	ENSMUSG00000025188	Hps1	6030422N11Rik|BB405864|Hps|ep	Hermansky-Pudlak syndrome 1 homolog (human)	protein-coding	0	0.336634
Merged-chr2-155275416-1	chr2	155275366	155275466	+	2.2	cIP1vsInput	promoter-TSS (NM_025735)	promoter-TSS (NM_025735)	-948	NM_025735	66734	Mm.196239	NM_025735	ENSMUSG00000027602	Map1lc3a	1010001H21Rik|4922501H04Rik|LC3|LC3a	microtubule-associated protein 1 light chain 3 alpha	protein-coding	0.01	0.356436
Merged-chr8-101510809-1	chr8	101510759	101510859	+	2.2	cIP2vsInput	Intergenic	Intergenic	1274302	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0	0.366337
Merged-chr15-103916976-1	chr15	103916926	103917026	+	2.2	cIP2vsInput	Intergenic	Lx8|LINE|L1	-17664	NM_009267	20770	Mm.1280	NM_009267	ENSMUSG00000036925	Spt1	Spt-1	salivary protein 1	protein-coding	0	0.455446
Merged-chr8-77133303-1	chr8	77133253	77133353	+	2.2	cIP1vsInput	"intron (NM_001083906, intron 3 of 8)"	"intron (NM_001083906, intron 3 of 8)"	230795	NM_001083906	110784	Mm.324393	NM_001083906	ENSMUSG00000031618	Nr3c2	MR|Mlr	"nuclear receptor subfamily 3, group C, member 2"	protein-coding	0	0.29703
Merged-chr13-118442478-1	chr13	118442428	118442528	+	2.2	cIP2vsInput	Intergenic	L3|LINE|CR1	-55226	NM_021556	59054	Mm.143810	NM_021556	ENSMUSG00000021731	Mrps30	2610020A16Rik|AA968347|PAP|Pdcd9	mitochondrial ribosomal protein S30	protein-coding	0	0.346535
Merged-chr3-86883002-1	chr3	86882952	86883052	+	2.2	cIP1vsInput	"intron (NM_001195497, intron 2 of 15)"	"intron (NM_001195497, intron 2 of 15)"	37882	NM_001195496	70762	Mm.44490	NM_001195496	ENSMUSG00000028078	Dclk2	6330415M09Rik|AU044875|CL2|CLICK2|Click-II|Dcamkl2	doublecortin-like kinase 2	protein-coding	0.01	0.336634
Merged-chr1-83471872-1	chr1	83471822	83471922	+	2.2	cIP1vsInput	Intergenic	Intergenic	-63672	NM_172430	77629	Mm.154303	NM_172430		Sphkap	4930544G21Rik|A930009L15Rik|AI852220|SKIP|mKIAA1678	"SPHK1 interactor, AKAP domain containing"	protein-coding	0.01	0.316832
Merged-chr14-20234275-1	chr14	20234225	20234325	+	2.2	cIP1vsInput	Intergenic	Intergenic	34887	NM_029006	74571	Mm.105571	NM_029006	ENSMUSG00000023387	Kcnk16	4731413G05Rik|TALK-1|TALK1	"potassium channel, subfamily K, member 16"	protein-coding	0	0.366337
Merged-chr3-52234349-1	chr3	52234299	52234399	+	2.2	cIP1vsInput	Intergenic	Intergenic	-33988	NM_019739	56458	Mm.29891	NM_019739	ENSMUSG00000044167	Foxo1	AI876417|Afxh|FKHR|Fkhr1|Foxo1a	forkhead box O1	protein-coding	0	0.277228
Merged-chr8-38069156-1	chr8	38069106	38069206	+	2.2	cIP1vsInput	"intron (NM_145841, intron 1 of 7)"	"intron (NM_145841, intron 1 of 7)"	183046	NR_029884	723860		NR_029884		Mir383	Mirn383|mmu-mir-383	microRNA 383	miscRNA	0	0.336634
Merged-chr16-69708180-1	chr16	69708130	69708230	+	2.2	cIP1vsInput	Intergenic	L1_Mus4|LINE|L1	155564	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding	0.01	0.316832
Merged-chr5-70437537-1	chr5	70437487	70437587	+	2.2	cIP1vsInput	Intergenic	RLTR11A2|LTR|ERVK	405080	NM_010252	14405	Mm.255292	NM_010252	ENSMUSG00000001260	Gabrg1	GabaA|GabaA/BZ	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1"	protein-coding	0	0.316832
Merged-chr5-144663573-1	chr5	144663523	144663623	+	2.2	cIP1vsInput	Intergenic	(TA)n|Simple_repeat|Simple_repeat	98005	NM_177735	243339	Mm.126793	NM_177735	ENSMUSG00000043388	Tmem130	BC067004|C130036G08	transmembrane protein 130	protein-coding	0.01	0.19802
Merged-chr13-10231440-1	chr13	10231390	10231490	+	2.2	cIP1vsInput	"intron (NM_033269, intron 1 of 4)"	"intron (NM_033269, intron 1 of 4)"	129363	NM_033269	12671	Mm.342315	NM_033269		Chrm3	Chrm-3|M3|M3R	"cholinergic receptor, muscarinic 3, cardiac"	protein-coding	0.01	0.386139
Merged-chr2-146354755-1	chr2	146354705	146354805	+	2.2	cIP1vsInput	"intron (NM_001033348, intron 27 of 40)"	"intron (NM_001033348, intron 27 of 40)"	95469	NR_040619	77806	Mm.392819	NR_040619	ENSMUSG00000085958	A930019D19Rik	-	RIKEN cDNA A930019D19 gene	miscRNA	0	0.306931
Merged-chr1-117108484-1	chr1	117108434	117108534	+	2.2	cIP1vsInput	Intergenic	Intergenic	1202648	NM_011650	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding	0	0.366337
Merged-chr14-111148448-1	chr14	111148398	111148498	+	2.2	cIP2vsInput	Intergenic	Intergenic	-393299	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	"SLIT and NTRK-like family, member 6"	protein-coding	0	0.326733
Merged-chr17-17041419-1	chr17	17041369	17041469	+	2.2	cIP2vsInput	Intergenic	Intergenic	-22684	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding	0.01	0.405941
Merged-chr1-113792508-1	chr1	113792458	113792558	+	2.2	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-1892629	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0	0.336634
Merged-chr4-91680003-1	chr4	91679953	91680053	+	2.2	cIP2vsInput	Intergenic	Intergenic	-280019	NM_207685	15569	Mm.318042	NM_001177883	ENSMUSG00000008489	Elavl2	Hub|mel-N1	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)"	protein-coding	0.01	0.356436
Merged-chr6-128212656-1	chr6	128212606	128212706	+	2.2	cIP1vsInput	Intergenic	L1MC4|LINE|L1	-28853	NR_077223	330427	Mm.426356	XR_105034		9330102E08Rik	-	RIKEN cDNA 9330102E08 gene	miscRNA	0	0.247525
Merged-chr14-86233291-1	chr14	86233241	86233341	+	2.2	cIP1vsInput	Intergenic	Intergenic	-12679	NR_040457	75155	Mm.399239	NR_040457		4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	miscRNA	0	0.356436
Merged-chr12-55505953-1	chr12	55505903	55506003	+	2.2	cIP1vsInput	Intergenic	Intergenic	-13306	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	"nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha"	protein-coding	0	0.336634
Merged-chr3-12103309-1	chr3	12103259	12103359	+	2.2	cIP1vsInput	Intergenic	Intergenic	-258950	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.277228
Merged-chr10-106336451-1	chr10	106336401	106336501	+	2.2	cIP1vsInput	Intergenic	Intergenic	-133859	NM_177373	327814	Mm.391424	NM_001205341	ENSMUSG00000053825	Ppfia2	5330438O12|B230207K17Rik|E130120L08Rik|mKIAA4112	"protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2"	protein-coding	0	0.455446
Merged-chr1-32340477-1	chr1	32340427	32340527	+	2.2	cIP1vsInput	"intron (NM_133235, intron 3 of 8)"	"intron (NM_133235, intron 3 of 8)"	167671	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm1	"KH domain containing, RNA binding, signal transduction associated 2"	protein-coding	0	0.257426
Merged-chr8-3621305-1	chr8	3621255	3621355	+	2.2	cIP1vsInput	promoter-TSS (NM_026156)	promoter-TSS (NM_026156)	-9	NM_026156	67439	Mm.23739	NM_026156	ENSMUSG00000019470	Xab2	0610041O14Rik|AV025587	XPA binding protein 2	protein-coding	0.1	0.623762
Merged-chr7-126701356-1	chr7	126701306	126701406	+	2.2	cIP1vsInput	"exon (NM_009898, exon 6 of 11)"	"exon (NM_009898, exon 6 of 11)"	3398	NM_009898	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	"coronin, actin binding protein 1A"	protein-coding	0.06	0.574257
Merged-chr17-56507998-1	chr17	56507948	56508048	+	2.2	cIP1vsInput	Intergenic	PB1D10|SINE|Alu	4485	NM_011483	20834	Mm.76862	NM_011483	ENSMUSG00000044526	Znrf4	1700094M01Rik|Ssrzf1|spzn	zinc and ring finger 4	protein-coding	0.05	0.584158
Merged-chr2-129341500-1	chr2	129341450	129341550	+	2.2	cIP2vsInput	Intergenic	Intergenic	-28402	NR_015474	329514	Mm.207315	NR_015474	ENSMUSG00000074805	Gm14047	9430083I22|OTTMUSG00000015529	predicted gene 14047	miscRNA	0	0.247525
Merged-chr19-24884226-1	chr19	24884176	24884276	+	2.2	cIP1vsInput	Intergenic	Intergenic	17083	NM_008022	14237	Mm.377080	NM_008022	ENSMUSG00000051490	Foxd4	FREAC5|Fkh2	forkhead box D4	protein-coding	0	0.326733
Merged-chr7-102791753-1	chr7	102791703	102791803	+	2.2	cIP1vsInput	Intergenic	Lx8|LINE|L1	-11727	NM_146359	258356	Mm.457775	NM_146359	ENSMUSG00000048469	Olfr564	MOR14-10	olfactory receptor 564	protein-coding	0	0.39604
Merged-chr4-78883624-1	chr4	78883574	78883674	+	2.2	cIP1vsInput	Intergenic	Intergenic	-671729	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0.01	0.306931
Merged-chr6-123816618-1	chr6	123816568	123816668	+	2.2	cIP2vsInput	TTS (NM_001104639)	TTS (NM_001104639)	36572	NM_001104641	545874	Mm.484595	NM_001104641	ENSMUSG00000094672	Vmn2r25	EG545874	"vomeronasal 2, receptor 25"	protein-coding	0	0.316832
Merged-chr16-6824703-1	chr16	6824653	6824753	+	2.2	cIP2vsInput	"intron (NM_021477, intron 5 of 16)"	"intron (NM_021477, intron 5 of 16)"	-245132	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	"RNA binding protein, fox-1 homolog (C. elegans) 1"	protein-coding	0	0.277228
Merged-chr10-113238130-1	chr10	113238080	113238180	+	2.2	cIP1vsInput	Intergenic	Intergenic	-309104	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132|ENSMUSG00000074747	ataxin 7-like 3B	protein-coding	0	0.326733
Merged-chr8-129219984-1	chr8	129219934	129220034	+	2.2	cIP2vsInput	"intron (NM_153780, intron 4 of 4)"	MurSatRep1|Unknown|Unknown	14019	NM_153780	72139	Mm.456686	NM_153780		2610044O15Rik8	2610044O15Rik	RIKEN cDNA 2610044O15 gene	protein-coding	0	0.326733
Merged-chr8-9274652-1	chr8	9274602	9274702	+	2.2	cIP1vsInput	"intron (NM_173446, intron 1 of 2)"	"intron (NM_173446, intron 1 of 2)"	129983	NR_073360	74688	Mm.159298	NR_073360		4930453L07Rik	-	RIKEN cDNA 4930453L07 gene	miscRNA	0	0.306931
Merged-chr13-86794857-1	chr13	86794807	86794907	+	2.2	cIP2vsInput	Intergenic	Intergenic	-748062	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0.01	0.247525
Merged-chr13-15292694-1	chr13	15292644	15292744	+	2.2	cIP2vsInput	Intergenic	Lx|LINE|L1	-171029	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding	0.01	0.445545
Merged-chr2-54648102-1	chr2	54648052	54648152	+	2.2	cIP1vsInput	"intron (NM_173030, intron 3 of 12)"	"intron (NM_173030, intron 3 of 12)"	211715	NM_173030	271786	Mm.330227	NM_173030	ENSMUSG00000060988	Galnt13	A230002A12|A230020F20|BB182356	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13	protein-coding	0	0.326733
Merged-chr19-26441019-1	chr19	26440969	26441069	+	2.2	cIP2vsInput	Intergenic	Intergenic	-164141	NM_011416	67155	Mm.313303	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2"	protein-coding	0.02	0.376238
Merged-chr1-78871693-1	chr1	78871643	78871743	+	2.2	cIP1vsInput	Intergenic	L1VL4|LINE|L1	54744	NM_021342	57814	Mm.24386	NM_021342	ENSMUSG00000047330	Kcne4	AW487937|MiRP3	"potassium voltage-gated channel, Isk-related subfamily, gene 4"	protein-coding	0	0.29703
Merged-chr1-162125133-1	chr1	162125083	162125183	+	2.2	cIP2vsInput	"intron (NM_001038619, intron 15 of 20)"	"intron (NM_001038619, intron 15 of 20)"	-92490	NR_002870	474332	Mm.485366	NR_002870	ENSMUSG00000078190	Dnm3os	6030416H16Rik|Hag2|Npn1|P/L01	"dynamin 3, opposite strand"	miscRNA	0	0.366337
Merged-chr16-16413325-1	chr16	16413275	16413375	+	2.2	cIP1vsInput	Intergenic	Lx|LINE|L1	-54294	NM_001025947	74006	Mm.218820	NM_001025947	ENSMUSG00000022789	Dnm1l	6330417M19Rik|AI450666|Dlp1|Dnmlp1|Drp1|python	dynamin 1-like	protein-coding	0	0.356436
Merged-chr17-91540026-1	chr17	91539976	91540076	+	2.2	cIP2vsInput	Intergenic	Intergenic	-447224	NM_020252	18189	Mm.312068	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0	0.326733
Merged-chr11-12116170-1	chr11	12116120	12116220	+	2.2	cIP2vsInput	Intergenic	Intergenic	-78750	NM_010345	14783	Mm.273117	NM_001177629	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding	0.01	0.356436
Merged-chr4-113903011-1	chr4	113902961	113903061	+	2.2	cIP1vsInput	"intron (NM_001167876, intron 8 of 58)"	MurERV4-int|LTR|ERVK	96492	NM_001167876	242627	Mm.484115	NM_001167876	ENSMUSG00000078598	Skint5	OTTMUSG00000008560|Skint-5	selection and upkeep of intraepithelial T cells 5	protein-coding	0	0.267327
Merged-chr13-53109456-1	chr13	53109406	53109506	+	2.2	cIP2vsInput	"3' UTR (NM_013846, exon 9 of 9)"	"3' UTR (NM_013846, exon 9 of 9)"	-128417	NM_017373	18030	Mm.136604	NM_017373	ENSMUSG00000056749	Nfil3	AV225605|E4BP4	"nuclear factor, interleukin 3, regulated"	protein-coding	0.01	0.306931
Merged-chr14-17798635-1	chr14	17798585	17798685	+	2.2	cIP1vsInput	"intron (NM_001113417, intron 1 of 9)"	L1_Mus3|LINE|L1	137675	NM_001113417	21834	Mm.32563	NM_001113417	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding	0	0.316832
Merged-chr12-60606361-1	chr12	60606311	60606411	+	2.2	cIP1vsInput	Intergenic	Intergenic	915459	NR_045049	100504101	Mm.235026	NR_045049		Gm20063	-	"predicted gene, 20063"	miscRNA	0.01	0.29703
Merged-chr9-29723254-1	chr9	29723204	29723304	+	2.2	cIP1vsInput	"intron (NM_172290, intron 1 of 7)"	ORR1E|LTR|ERVL-MaLR	239875	NM_172290	235106	Mm.283138	NM_172290		Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding	0	0.455446
Merged-chr13-37482885-1	chr13	37482835	37482935	+	2.2	cIP2vsInput	Intergenic	Intergenic	137540	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1	lymphocyte antigen 86	protein-coding	0.01	0.564356
Merged-chr6-76008184-1	chr6	76008134	76008234	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1234533	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0.01	0.326733
Merged-chr1-74713114-1	chr1	74713064	74713164	+	2.2	cIP2vsInput	promoter-TSS (NM_024264)	promoter-TSS (NM_024264)	-460	NM_024264	104086	Mm.85083	NM_024264	ENSMUSG00000026170	Cyp27a1	1300013A03Rik|Cyp27	"cytochrome P450, family 27, subfamily a, polypeptide 1"	protein-coding	0.02	0.415842
Merged-chr16-71341542-1	chr16	71341492	71341592	+	2.2	cIP1vsInput	Intergenic	Intergenic	91638	NR_040576	78221	Mm.399298	NR_040576		4930567J20Rik	-	RIKEN cDNA 4930567J20 gene	miscRNA	0	0.267327
Merged-chr3-140468904-1	chr3	140468854	140468954	+	2.2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	743451	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0.02	0.405941
Merged-chr6-131281594-1	chr6	131281544	131281644	+	2.2	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	11650	NM_025564	66441	Mm.46623	NM_025564	ENSMUSG00000030188	Magohb	2010012C16Rik|Mago|Magoh|Magoh-rs1	mago-nashi homolog B (Drosophila)	protein-coding	0.01	0.356436
Merged-chr18-49429482-1	chr18	49429432	49429532	+	2.2	cIP1vsInput	Intergenic	MLT1A1-int|LTR|ERVL-MaLR	-93807	NR_033785	67321	Mm.245802	NR_033785		1700044K03Rik	-	RIKEN cDNA 1700044K03 gene	miscRNA	0.02	0.29703
Merged-chr3-107605666-1	chr3	107605616	107605716	+	2.2	cIP2vsInput	"3' UTR (NM_007441, exon 4 of 4)"	"3' UTR (NM_007441, exon 4 of 4)"	10635	NM_007441	11694	Mm.10112	NM_007441	ENSMUSG00000014603	Alx3	-	aristaless-like homeobox 3	protein-coding	0	0.346535
Merged-chrY-10001116-1	chrY	10001066	10001166	+	2.2	cIP2vsInput	Intergenic	MTE2a-int|LTR|ERVL-MaLR	-1165947	NM_001017394	100039753	Mm.458473	NM_001017394	ENSMUSG00000096227	Gm20815	-	"predicted gene, 20815"	protein-coding	0	0.267327
Merged-chr11-15892566-1	chr11	15892516	15892616	+	2.2	cIP2vsInput	Intergenic	Intergenic	-365158	NM_145967	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	9330184N17Rik|BC027127|Vstm2	V-set and transmembrane domain containing 2A	protein-coding	0	0.346535
Merged-chr14-90791550-1	chr14	90791500	90791600	+	2.2	cIP1vsInput	Intergenic	UCON29|DNA|PiggyBac?	664659	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0.01	0.346535
Merged-chr12-77801008-1	chr12	77800958	77801058	+	2.2	cIP1vsInput	Intergenic	Intergenic	390867	NM_001252616	53618	Mm.489686	NM_001252614	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding	0	0.336634
Merged-chr17-13857742-1	chr17	13857692	13857792	+	2.2	cIP1vsInput	"intron (NM_010806, intron 20 of 32)"	"intron (NM_010806, intron 20 of 32)"	-90631	NM_001122977	635895	Mm.388844	NM_001122977	ENSMUSG00000067941	Gm7168	EG635895	predicted gene 7168	protein-coding	0.01	0.316832
Merged-chr14-50286193-1	chr14	50286143	50286243	+	2.2	cIP2vsInput	Intergenic	Intergenic	-3922	NM_146665	258659	Mm.377622	NM_146665	ENSMUSG00000091873	Olfr732	MOR241-1	olfactory receptor 732	protein-coding	0	0.376238
Merged-chr3-119515584-1	chr3	119515534	119515634	+	2.2	cIP1vsInput	Intergenic	Intergenic	267804	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0	0.346535
Merged-chr4-96297022-1	chr4	96296972	96297072	+	2.2	cIP1vsInput	"intron (NM_001004141, intron 8 of 8)"	ORR1C1|LTR|ERVL-MaLR	51658	NM_001004141	100066	Mm.26915	NM_001004141	ENSMUSG00000066097	Cyp2j11	AI314783|Cyp2j11-ps	"cytochrome P450, family 2, subfamily j, polypeptide 11"	protein-coding	0	0.346535
Merged-chr18-84565938-1	chr18	84565888	84565988	+	2.2	cIP1vsInput	"intron (NM_001033341, intron 1 of 8)"	"intron (NM_001033341, intron 1 of 8)"	23566	NM_001033341	240476	Mm.329575	NM_001033341	ENSMUSG00000048410	Zfp407	6430585N13Rik|Gm333|Gm334|Gm948|ZNF407	zinc finger protein 407	protein-coding	0	0.19802
Merged-chr2-129903993-1	chr2	129903943	129904043	+	2.2	cIP2vsInput	Intergenic	Intergenic	-102534	NR_029452	654409	Mm.305555	NR_029452		4932416H05Rik	-	RIKEN cDNA 4932416H05 gene	miscRNA	0	0.425743
Merged-chr14-91241344-1	chr14	91241294	91241394	+	2.2	cIP2vsInput	Intergenic	L1MC|LINE|L1	1114453	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0.01	0.356436
Merged-chr4-155694300-1	chr4	155694250	155694350	+	2.2	cIP2vsInput	promoter-TSS (NM_178699)	promoter-TSS (NM_178699)	-42	NM_178699	230991	Mm.29083	NM_178699	ENSMUSG00000074738	B930041F14Rik	MNCb-3966	RIKEN cDNA B930041F14 gene	protein-coding	0.11	0.722772
Merged-chr1-170157189-1	chr1	170157139	170157239	+	2.2	cIP2vsInput	"intron (NM_133806, intron 4 of 10)"	"intron (NM_133806, intron 4 of 10)"	17757	NM_133806	107652	Mm.27969	XM_003689330	ENSMUSG00000026670	Uap1	AA420407|AA437972|AGX-1|AGX-2|AGX1|AgX|ESTM38|SPAG2	UDP-N-acetylglucosamine pyrophosphorylase 1	protein-coding	0.01	0.346535
Merged-chr10-74848020-1	chr10	74847970	74848070	+	2.2	cIP1vsInput	Intergenic	Intergenic	-119211	NM_010311	14687	Mm.393508	NM_010311		Gnaz	AI847979|Gz	"guanine nucleotide binding protein, alpha z subunit"	protein-coding	0.01	0.376238
Merged-chr16-16714566-1	chr16	16714516	16714616	+	2.2	cIP1vsInput	"intron (NR_045920, intron 2 of 5)"	"intron (NR_045920, intron 2 of 5)"	3555	NR_045920	74066	Mm.61161	NM_028739		4933404G15Rik	4933401J20Rik	RIKEN cDNA 4933404G15 gene	miscRNA	0	0.316832
Merged-chr14-82576533-1	chr14	82576483	82576583	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1867030	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0	0.326733
Merged-chr12-57377283-1	chr12	57377233	57377333	+	2.2	cIP2vsInput	"intron (NM_001164370, intron 8 of 9)"	"intron (NM_001164370, intron 8 of 9)"	146858	NM_001164370	73490	Mm.268180	NM_001164370	ENSMUSG00000047022	Mipol1	1700081O04Rik|6030439O22Rik|AU021838|AW536152|D12Ertd19e	mirror-image polydactyly gene 1 homolog (human)	protein-coding	0	0.326733
Merged-chr12-93068685-1	chr12	93068635	93068735	+	2.2	cIP2vsInput	Intergenic	Intergenic	-1219528	NM_011344	20338	Mm.250605	NM_001039089	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding	0.01	0.257426
Merged-chr9-29213264-1	chr9	29213214	29213314	+	2.2	cIP1vsInput	"intron (NM_172290, intron 2 of 7)"	"intron (NM_172290, intron 2 of 7)"	749865	NM_172290	235106	Mm.283138	NM_172290		Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding	0	0.326733
Merged-chr12-47805271-1	chr12	47805221	47805321	+	2.2	cIP2vsInput	Intergenic	Intergenic	496191	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0.01	0.376238
Merged-chr1-75009928-1	chr1	75009878	75009978	+	2.2	cIP2vsInput	"intron (NM_029342, intron 2 of 4)"	"intron (NM_029342, intron 2 of 4)"	36711	NM_029342	75570	Mm.442409	NM_029342		Nhej1	1700029B21Rik|XLF|cernunnos	nonhomologous end-joining factor 1	protein-coding	0	0.386139
Merged-chrX-42216256-1	chrX	42216206	42216306	+	2.2	cIP2vsInput	"intron (NM_001077712, intron 4 of 32)"	L1MB7|LINE|L1	65555	NM_021465	20843	Mm.290422	NM_001077712	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding	0.01	0.376238
Merged-chr18-85275920-1	chr18	85275870	85275970	+	2.2	cIP2vsInput	Intergenic	Intergenic	-324396	NM_025969	67105	Mm.250617	NM_025969	ENSMUSG00000024645	Timm21	1700034H14Rik|2700002I20Rik	tranlocase of inner mitochondrial membrane 21	protein-coding	0.01	0.336634
Merged-chr10-114940889-1	chr10	114940839	114940939	+	2.2	cIP1vsInput	Intergenic	Intergenic	-139519	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding	0.01	0.306931
Merged-chr2-3838113-1	chr2	3838063	3838163	+	2.2	cIP2vsInput	Intergenic	Intergenic	124655	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	"family with sequence similarity 107, member B"	protein-coding	0	0.326733
Merged-chr8-9088631-1	chr8	9088581	9088681	+	2.2	cIP2vsInput	Intergenic	Intergenic	43657	NR_045854	71249	Mm.158635	NR_045854		4933430N04Rik	-	RIKEN cDNA 4933430N04 gene	miscRNA	0	0.287129
Merged-chr17-78127385-1	chr17	78127335	78127435	+	2.2	cIP2vsInput	Intergenic	Intergenic	-72863	NM_015800	50766	Mm.311912	NM_015800	ENSMUSG00000024074	Crim1	AU015004	cysteine rich transmembrane BMP regulator 1 (chordin like)	protein-coding	0	0.326733
Merged-chr3-44090336-1	chr3	44090286	44090386	+	2.2	cIP2vsInput	Intergenic	MusHAL1|LINE|L1	1287924	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	miscRNA	0	0.376238
Merged-chr1-115135388-1	chr1	115135338	115135438	+	2.2	cIP2vsInput	Intergenic	Intergenic	-549749	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0.01	0.336634
Merged-chr14-23117888-1	chr14	23117838	23117938	+	2.2	cIP1vsInput	Intergenic	L1M4|LINE|L1	-23317	NR_033550	791307	Mm.364384	NR_033550	ENSMUSG00000068680	Gm10248	ENSMUSG00000068680	predicted gene 10248	miscRNA	0	0.287129
Merged-chr9-76669082-1	chr9	76669032	76669132	+	2.2	cIP2vsInput	Intergenic	Intergenic	-123278	NM_001045518	208994	Mm.256929	NM_001045518	ENSMUSG00000032358	Fam83b	C530008M07Rik|Gm516	"family with sequence similarity 83, member B"	protein-coding	0	0.366337
Merged-chr17-23592812-1	chr17	23592762	23592862	+	2.2	cIP2vsInput	"intron (NM_011747, intron 1 of 5)"	CpG	6675	NM_011747	22654	Mm.40326	NM_011747	ENSMUSG00000062012	Zfp13	4933429B21|AI835008|Krox-8|Rhit|Zfp-13	zinc finger protein 13	protein-coding	0.06	0.584158
Merged-chr19-43059329-1	chr19	43059279	43059379	+	2.2	cIP1vsInput	"intron (NM_001081257, intron 3 of 11)"	"intron (NM_001081257, intron 3 of 11)"	-279353	NM_019424	192236	Mm.218381	NM_019424	ENSMUSG00000025188	Hps1	6030422N11Rik|BB405864|Hps|ep	Hermansky-Pudlak syndrome 1 homolog (human)	protein-coding	0.01	0.306931
Merged-chr8-98639215-1	chr8	98639165	98639265	+	2.2	cIP1vsInput	Intergenic	L1MEf|LINE|L1	777242	NM_007667	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.316832
Merged-chr11-38168254-1	chr11	38168204	38168304	+	2.2	cIP1vsInput	Intergenic	Intergenic	351791	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0	0.336634
Merged-chr13-110044370-1	chr13	110044320	110044420	+	2.2	cIP1vsInput	Intergenic	ORR1E|LTR|ERVL-MaLR	140561	NR_035442	100316683		NR_035442		Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	miscRNA	0.01	0.356436
Merged-chr13-13867242-2	chr13	13867178	13867306	+	2.2	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	82703	NM_010317	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	"guanine nucleotide binding protein (G protein), gamma 4"	protein-coding	0	0.51938
Merged-chr6-62182049-1	chr6	62181999	62182099	+	2.2	cIP2vsInput	"intron (NM_001164316, intron 10 of 10)"	"intron (NM_001164316, intron 10 of 10)"	-1001239	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	miscRNA	0.01	0.306931
Merged-chr11-9965802-1	chr11	9965752	9965852	+	2.2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	773860	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	"ATP-binding cassette, sub-family A (ABC1), member 13"	protein-coding	0	0.287129
Merged-chr12-54323799-1	chr12	54323749	54323849	+	2.2	cIP1vsInput	Intergenic	Intergenic	67519	NR_033689	665239	Mm.26856	NR_033689		Gm7550	EG665239|Gm666	predicted gene 7550	miscRNA	0	0.356436
Merged-chr8-20346111-1	chr8	20346061	20346161	+	2.2	cIP1vsInput	"intron (NM_001177408, intron 6 of 9)"	L1VL4|LINE|L1	17091	NM_001177408	100040599	Mm.445582	NM_001177408	ENSMUSG00000074449	Gm15319	OTTMUSG00000020118	predicted gene 15319	protein-coding	0.01	0.366337
Merged-chr9-91277143-1	chr9	91277093	91277193	+	2.2	cIP1vsInput	Intergenic	Intergenic	88656	NM_009573	22771	Mm.477226	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding	0.01	0.356436
Merged-chr10-75952084-1	chr10	75952034	75952134	+	2.2	cIP2vsInput	Intergenic	Intergenic	-2430	NM_198635	333669	Mm.31077	NM_198635	ENSMUSG00000033255	Gm5134	EG333669	predicted gene 5134	protein-coding	0.01	0.316832
Merged-chr14-34008147-1	chr14	34008097	34008197	+	2.2	cIP2vsInput	Intergenic	Lx5b|LINE|L1	-29383	NM_001013777	382867	Mm.343728	NM_001013777	ENSMUSG00000044519	Zfp488	Gm1206|Znf488	zinc finger protein 488	protein-coding	0	0.356436
Merged-chr6-139131179-1	chr6	139131129	139131229	+	2.2	cIP1vsInput	Intergenic	Intergenic	191397	NR_045149	70962	Mm.410833	NR_045149		4922502N22Rik	-	RIKEN cDNA 4922502N22 gene	miscRNA	0	0.316832
Merged-chr11-68485544-1	chr11	68485494	68485594	+	2.2	cIP1vsInput	"intron (NM_177320, intron 5 of 18)"	"intron (NM_177320, intron 5 of 18)"	-17475	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	"phosphoinositide-3-kinase, regulatory subunit 6"	protein-coding	0.01	0.376238
Merged-chr3-114205346-1	chr3	114205296	114205396	+	2.2	cIP2vsInput	"intron (NM_007729, intron 58 of 66)"	"intron (NM_007729, intron 58 of 66)"	174806	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	"collagen, type XI, alpha 1"	protein-coding	0	0.326733
Merged-chr14-115462035-1	chr14	115461985	115462085	+	2.2	cIP1vsInput	"intron (NM_175500, intron 5 of 7)"	"intron (NM_175500, intron 5 of 7)"	-52483	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	miscRNA	0	0.306931
Merged-chr18-9270951-1	chr18	9270901	9271001	+	2.2	cIP2vsInput	Intergenic	Intergenic	11858	NM_153086	225152	Mm.119273	NM_153086	ENSMUSG00000036855	Gjd4	9430022F06Rik|Cx39	"gap junction protein, delta 4"	protein-coding	0.02	0.435644
Merged-chr3-135075542-1	chr3	135075492	135075592	+	2.2	cIP2vsInput	Intergenic	L1M2|LINE|L1	-137021	NM_173762	229841	Mm.161470	NM_173762	ENSMUSG00000045328	Cenpe	312kDa|AU019344|BC049989|C530022J18|CENP-E|Kif10	centromere protein E	protein-coding	0	0.356436
Merged-chr12-52335934-1	chr12	52335884	52335984	+	2.2	cIP1vsInput	Intergenic	Intergenic	-180143	NM_009706	11855	Mm.474991	NM_009706	ENSMUSG00000035133	Arhgap5	p190-B|p190B	Rho GTPase activating protein 5	protein-coding	0	0.287129
Merged-chr7-103891643-1	chr7	103891593	103891693	+	2.2	cIP1vsInput	Intergenic	L1M4|LINE|L1	2828	NM_013617	18366	Mm.377107	NM_013617	ENSMUSG00000063615	Olfr64	5'[b]2|5'beta2|MOR1-1|MOR1-2|ORL533	olfactory receptor 64	protein-coding	0	0.346535
Merged-chr10-73814421-1	chr10	73814371	73814471	+	2.2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-7446	NM_001142760	11994	Mm.338933	NM_001142735	ENSMUSG00000052613	Pcdh15	BB078305|ENSMUSG00000046980|Gm9815|Ush1f|av|nmf19	protocadherin 15	protein-coding	0	0.326733
Merged-chr1-83977893-1	chr1	83977843	83977943	+	2.2	cIP2vsInput	Intergenic	Intergenic	306752	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding	0	0.287129
Merged-chr1-48906388-1	chr1	48906338	48906438	+	2.2	cIP1vsInput	Intergenic	Intergenic	-2021135	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.287129
Merged-chr7-123074715-1	chr7	123074665	123074765	+	2.2	cIP1vsInput	Intergenic	Intergenic	-49170	NM_144925	233833	Mm.102305	NM_144925	ENSMUSG00000052707	Tnrc6a	2010321I05Rik|3110054G10Rik|AW557223|CAGH26|D130023A07Rik|GW182|Tnrc6	trinucleotide repeat containing 6a	protein-coding	0	0.277228
Merged-chr3-103227689-1	chr3	103227639	103227739	+	2.2	cIP2vsInput	Intergenic	RLTR25A|LTR|ERVK	-51604	NM_053170	94093	Mm.195036	NM_001079830	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g|ectodermin|mKIAA1113	tripartite motif-containing 33	protein-coding	0	0.356436
Merged-chr11-48771746-1	chr11	48771696	48771796	+	2.2	cIP1vsInput	Intergenic	Intergenic	-28614	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Gnb2l1	AL033335|GB-like|Gnb2-rs1|Rack1|p205	"guanine nucleotide binding protein (G protein), beta polypeptide 2 like 1"	protein-coding	0.01	0.356436
Merged-chr6-62948569-1	chr6	62948519	62948619	+	2.2	cIP2vsInput	Intergenic	ERVL-B4-int|LTR|ERVL	-308288	NM_008167	14804	Mm.447390	NM_008167		Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	"glutamate receptor, ionotropic, delta 2"	protein-coding	0	0.356436
Merged-chr15-54738803-1	chr15	54738753	54738853	+	2.2	cIP1vsInput	Intergenic	Intergenic	-7125	NM_010930	18133	Mm.5167	NM_010930	ENSMUSG00000037362	Nov	C130088N23Rik|CCN3	nephroblastoma overexpressed gene	protein-coding	0	0.386139
Merged-chr14-14346135-1	chr14	14346085	14346185	+	2.2	cIP2vsInput	promoter-TSS (NM_008369)	promoter-TSS (NM_008369)	-360	NM_008369	16188	Mm.425857	NM_008369	ENSMUSG00000068758	Il3ra	CD123|CDw123|SUT-1	"interleukin 3 receptor, alpha chain"	protein-coding	0.09	0.623762
Merged-chr19-48761851-1	chr19	48761801	48761901	+	2.2	cIP2vsInput	"intron (NM_025696, intron 17 of 26)"	"intron (NM_025696, intron 17 of 26)"	555826	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding	0	0.217822
Merged-chr1-94643393-1	chr1	94643343	94643443	+	2.2	cIP1vsInput	Intergenic	Intergenic	-154049	NR_040473	74689	Mm.399187	NR_040473		4930440C22Rik	-	RIKEN cDNA 4930440C22 gene	miscRNA	0	0.29703
Merged-chr2-74927608-1	chr2	74927558	74927658	+	2.2	cIP2vsInput	Intergenic	Intergenic	101796	NM_016804	53375	Mm.478750	NM_016804		Mtx2	1500012G02Rik	metaxin 2	protein-coding	0	0.39604
Merged-chr15-71241113-1	chr15	71241063	71241163	+	2.2	cIP2vsInput	Intergenic	Intergenic	486725	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	"family with sequence similarity 135, member B"	protein-coding	0.04	0.534653
Merged-chr1-39664778-1	chr1	39664728	39664828	+	2.2	cIP2vsInput	TTS (NM_001145660)	TTS (NM_001145660)	-13596	NM_170597	263764	Mm.122091	NM_170597	ENSMUSG00000050967	Creg2	A830098L22Rik	cellular repressor of E1A-stimulated genes 2	protein-coding	0.02	0.356436
Merged-chr3-140345909-1	chr3	140345859	140345959	+	2.2	cIP2vsInput	Intergenic	Intergenic	866446	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0	0.29703
Merged-chr4-125921904-1	chr4	125921854	125921954	+	2.2	cIP1vsInput	"non-coding (NR_015560, exon 2 of 6)"	"non-coding (NR_015560, exon 2 of 6)"	406	NR_015560	72395	Mm.112888	NR_015560	ENSMUSG00000085562	2610028E06Rik	BB043107	RIKEN cDNA 2610028E06 gene	miscRNA	0.05	0.564356
Merged-chr14-95247547-1	chr14	95247497	95247597	+	2.2	cIP1vsInput	Intergenic	Intergenic	-633719	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.326733
Merged-chrX-146124807-1	chrX	146124757	146124857	+	2.2	cIP2vsInput	Intergenic	Intergenic	-637761	NM_153319	27494	Mm.100068	NM_153319	ENSMUSG00000041688	Amot	C81439|CAG-2|D0Kist1|E230009N18Rik|Sii6|mKIAA1071	angiomotin	protein-coding	0	0.306931
Merged-chr8-102166047-1	chr8	102165997	102166097	+	2.2	cIP1vsInput	Intergenic	Intergenic	619064	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0.01	0.29703
Merged-chr1-51458847-1	chr1	51458797	51458897	+	2.2	cIP2vsInput	Intergenic	RLTR51A_Mm|LTR|ERVK?	19552	NM_028696	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a	nucleic acid binding protein 1	protein-coding	0.04	0.415842
Merged-chr18-49213025-1	chr18	49212975	49213075	+	2.2	cIP2vsInput	Intergenic	Intergenic	-310264	NR_033785	67321	Mm.245802	NR_033785		1700044K03Rik	-	RIKEN cDNA 1700044K03 gene	miscRNA	0	0.29703
Merged-chr18-51670468-1	chr18	51670418	51670518	+	2.2	cIP1vsInput	Intergenic	Intergenic	453078	NR_029788	723830		NR_029788		Mir28	Mirn28|mmu-mir-28	microRNA 28	miscRNA	0	0.227723
Merged-chr4-45297481-1	chr4	45297431	45297531	+	2.2	cIP1vsInput	"intron (NM_027266, intron 1 of 8)"	"intron (NM_027266, intron 1 of 8)"	313	NM_027266	69934	Mm.46761	NM_027266	ENSMUSG00000035601	Trmt10b	2610042J10Rik|Rg9mtd3|Rnmtd3	tRNA methyltransferase 10B	protein-coding	0.06	0.49505
Merged-chr2-41922642-1	chr2	41922592	41922692	+	2.2	cIP2vsInput	"intron (NM_053011, intron 3 of 90)"	"intron (NM_053011, intron 3 of 90)"	730956	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0	0.316832
Merged-chr14-64498853-1	chr14	64498803	64498903	+	2.2	cIP1vsInput	Intergenic	(TAGA)n|Simple_repeat|Simple_repeat	-42950	NM_026322	110265	Mm.26713	NM_001253712	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding	0	0.316832
Merged-chr10-73419351-1	chr10	73419301	73419401	+	2.2	cIP2vsInput	Intergenic	Intergenic	-332646	NR_040646	327768	Mm.417745	NR_040646		A330049N07Rik	-	RIKEN cDNA A330049N07 gene	miscRNA	0	0.326733
Merged-chr1-122519807-1	chr1	122519757	122519857	+	2.2	cIP2vsInput	Intergenic	Intergenic	-951827	NM_025860	66942	Mm.44219	NM_025860	ENSMUSG00000001674	Ddx18	2310005B10Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	protein-coding	0.03	0.316832
Merged-chr5-106251821-1	chr5	106251771	106251871	+	2.2	cIP1vsInput	Intergenic	Intergenic	206345	NM_001005477	104382	Mm.271593	NM_001005477	ENSMUSG00000034384	Barhl2	E130309B19Rik|MBH1	BarH-like 2 (Drosophila)	protein-coding	0.01	0.435644
Merged-chr3-81724647-1	chr3	81724597	81724697	+	2.2	cIP1vsInput	Intergenic	Intergenic	-207969	NM_177662	229445	Mm.254642	NM_177662	ENSMUSG00000028015	Ctso	A330105D01Rik|A430056C07|AI118514	cathepsin O	protein-coding	0	0.39604
Merged-chr1-193841162-1	chr1	193841112	193841212	+	2.2	cIP2vsInput	Intergenic	Intergenic	-333632	NR_029592	387201		NR_029592	ENSMUSG00000065533	Mir205	Mirn205|mmu-mir-205	microRNA 205	miscRNA	0	0.316832
Merged-chr3-136016890-1	chr3	136016840	136016940	+	2.2	cIP2vsInput	Intergenic	Intergenic	-176621	NR_040540	71038	Mm.410798	NR_040540		4933401H06Rik	-	RIKEN cDNA 4933401H06 gene	miscRNA	0	0.366337
Merged-chr6-97697606-1	chr6	97697556	97697656	+	2.2	cIP2vsInput	Intergenic	Charlie9|DNA|hAT-Charlie	-79949	NM_145148	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720|mKIAA1013	FERM domain containing 4B	protein-coding	0.02	0.386139
Merged-chr1-121400290-1	chr1	121400240	121400340	+	2.2	cIP1vsInput	Intergenic	Intergenic	-30777	NM_029955	70829	Mm.25788	NM_027567	ENSMUSG00000026339	Ccdc93	4633402D15Rik|9230102M16Rik	coiled-coil domain containing 93	protein-coding	0.01	0.287129
Merged-chr6-76747676-1	chr6	76747626	76747726	+	2.2	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-495041	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0	0.376238
Merged-chr5-18821484-1	chr5	18821434	18821534	+	2.2	cIP2vsInput	Intergenic	Intergenic	405071	NR_102342	70832	Mm.398993	XR_106346	ENSMUSG00000097626	4921504A21Rik	-	RIKEN cDNA 4921504A21 gene	miscRNA	0	0.346535
Merged-chr5-45153716-1	chr5	45153666	45153766	+	2.2	cIP2vsInput	Intergenic	Intergenic	187515	NR_073013	75783	Mm.218472	NR_073013		4930431F12Rik	-	RIKEN cDNA 4930431F12 gene	miscRNA	0	0.356436
Merged-chr18-17174072-1	chr18	17174022	17174122	+	2.2	cIP1vsInput	Intergenic	Intergenic	61410	NR_033607	664619	Mm.250005	NR_033607		4921533I20Rik	-	PRP18 pre-mRNA processing factor 18 homolog pseudogene	pseudo	0	0.336634
Merged-chr13-57421466-1	chr13	57421416	57421516	+	2.2	cIP1vsInput	"3' UTR (NM_001166464, exon 11 of 11)"	"3' UTR (NM_001166464, exon 11 of 11)"	486866	NM_009262	20745	Mm.379020	NM_001166463		Spock1	Spock|Ticn1|testican	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1"	protein-coding	0.01	0.386139
Merged-chr6-138515152-1	chr6	138515102	138515202	+	2.2	cIP1vsInput	"intron (NM_207222, intron 1 of 4)"	"intron (NM_207222, intron 1 of 4)"	66816	NM_207222	109593	Mm.490545	NM_207222		Lmo3	AI854781|BB106490|Rbtn-3|Rbtn3	LIM domain only 3	protein-coding	0	0.346535
Merged-chr4-34263563-1	chr4	34263513	34263613	+	2.2	cIP2vsInput	Intergenic	(TTAG)n|Simple_repeat|Simple_repeat	-213496	NM_026293	67652	Mm.55848	NM_026293	ENSMUSG00000028264	Spaca1	1700124L11Rik|4930540L03Rik	sperm acrosome associated 1	protein-coding	0.01	0.326733
Merged-chr15-65353147-1	chr15	65353097	65353197	+	2.2	cIP2vsInput	Intergenic	L1MA8|LINE|L1	-430851	NM_009623	11514	Mm.1425	NM_009623	ENSMUSG00000022376	Adcy8	AC8|AW060868	adenylate cyclase 8	protein-coding	0.01	0.287129
Merged-chr6-148484737-1	chr6	148484687	148484787	+	2.2	cIP2vsInput	Intergenic	Intergenic	-40385	NM_198967	387314	Mm.137858	NM_198967	ENSMUSG00000030306	Tmtc1	Arg99|BC023818	transmembrane and tetratricopeptide repeat containing 1	protein-coding	0.01	0.356436
Merged-chr7-55999029-1	chr7	55998979	55999079	+	2.2	cIP2vsInput	"intron (NM_153578, intron 1 of 4)"	"intron (NM_153578, intron 1 of 4)"	20544	NM_153578	233280	Mm.443911	NM_153578		Nipa1	1110027G09Rik|A830014A18Rik|FSP3|Spg6	non imprinted in Prader-Willi/Angelman syndrome 1 homolog (human)	protein-coding	0.01	0.366337
Merged-chr11-24949064-1	chr11	24949014	24949114	+	2.2	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	-218342	NR_033491	100038617	Mm.387376	NR_033491	ENSMUSG00000073103	Gm10466	ENSMUSG00000073103	predicted gene 10466	miscRNA	0	0.277228
Merged-chr3-71320477-1	chr3	71320427	71320527	+	2.2	cIP2vsInput	Intergenic	Intergenic	-513186	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	miscRNA	0	0.29703
Merged-chr4-74454299-1	chr4	74454249	74454349	+	2.2	cIP1vsInput	Intergenic	Lx3B|LINE|L1	202420	NM_144787	76804	Mm.209059	NM_001172095	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding	0	0.29703
Merged-chr5-43092928-1	chr5	43092878	43092978	+	2.2	cIP2vsInput	Intergenic	B1_Mur1|SINE|Alu	-140535	NM_175937	231207	Mm.7233	NM_001177379	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding	0	0.376238
Merged-chr2-86376504-1	chr2	86376454	86376554	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1094	NM_207563	404325	Mm.355578	NM_207563	ENSMUSG00000075187	Olfr1057	GA_x5J8B7TRQ4E-1174-939|GA_x5J8B7TY464-2-187|MOR185-11	olfactory receptor 1057	protein-coding	0.02	0.287129
Merged-chr17-88681292-1	chr17	88681242	88681342	+	2.2	cIP2vsInput	"intron (NM_023630, intron 3 of 8)"	Lx2B2|LINE|L1	12632	NM_023630	71828	Mm.61330	NM_023630	ENSMUSG00000024154	Gtf2a1l	1700011N16Rik|Alf|Gtf2a1lf	"general transcription factor IIA, 1-like"	protein-coding	0.01	0.366337
Merged-chr3-123837063-1	chr3	123837013	123837113	+	2.2	cIP2vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	-164671	NM_031186	83398	Mm.487979	NM_031186	ENSMUSG00000027977	Ndst3	4921531K01Rik|4930511P15Rik	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	protein-coding	0	0.316832
Merged-chr6-40906618-1	chr6	40906568	40906668	+	2.2	cIP2vsInput	"intron (NR_035473, intron 1 of 3)"	L1_Mus3|LINE|L1	4048	NR_035473	100316775		NR_035473		Mir1950	mmu-mir-1950	microRNA 1950	miscRNA	0	0.316832
Merged-chr9-83934067-1	chr9	83934017	83934117	+	2.2	cIP2vsInput	Intergenic	MurERV4-int|LTR|ERVK	-14714	NM_199195	12040	Mm.12819	NM_199195		Bckdhb	-	"branched chain ketoacid dehydrogenase E1, beta polypeptide"	protein-coding	0	0.39604
Merged-chr12-50127733-1	chr12	50127683	50127783	+	2.2	cIP2vsInput	Intergenic	Intergenic	521490	NM_008858	18760	Mm.133719	NM_008858	ENSMUSG00000002688	Prkd1	PKD|PKD1|Pkcm|Prkcm	protein kinase D1	protein-coding	0	0.336634
Merged-chr12-111387052-2	chr12	111386981	111387123	+	2.2	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-9334	NM_183016	217866		NM_183016	ENSMUSG00000021279	Cdc42bpb	MRCKb	CDC42 binding protein kinase beta	protein-coding	0.021127	0.671329
Merged-chr12-62918886-1	chr12	62918836	62918936	+	2.2	cIP2vsInput	Intergenic	Intergenic	1394254	NM_178714	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.01	0.306931
Merged-chr4-111323109-1	chr4	111323059	111323159	+	2.2	cIP1vsInput	"intron (NM_001048189, intron 5 of 12)"	L1_Mur2|LINE|L1	-91897	NR_033793	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding	0	0.306931
Merged-chr1-94035496-1	chr1	94035446	94035546	+	2.2	cIP2vsInput	Intergenic	Intergenic	15003	NM_173772	241159	Mm.214565	NM_173772	ENSMUSG00000034000	Neu4	9330166I04	sialidase 4	protein-coding	0.05	0.584158
Merged-chr2-56308795-1	chr2	56308745	56308845	+	2.2	cIP1vsInput	Intergenic	Intergenic	806243	NM_013613	18227	Mm.3507	NM_001139509	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	"nuclear receptor subfamily 4, group A, member 2"	protein-coding	0.02	0.306931
Merged-chr1-192566673-1	chr1	192566623	192566723	+	2.2	cIP1vsInput	"intron (NM_144881, intron 10 of 11)"	Lx2|LINE|L1	204546	NM_144881	226861	Mm.145857	NM_144881	ENSMUSG00000037375	Hhat	2810432O22Rik|AI462858|AP-2CRE|Skn|Tg(TFAP2A-cre)1Will	hedgehog acyltransferase	protein-coding	0	0.326733
Merged-chr13-39854215-1	chr13	39854165	39854265	+	2.2	cIP2vsInput	Intergenic	Intergenic	433796	NM_172143	218165	Mm.364096	NM_172143	ENSMUSG00000047094	Ofcc1	opo	orofacial cleft 1 candidate 1	protein-coding	0	0.39604
Merged-chr4-18806346-1	chr4	18806296	18806396	+	2.2	cIP2vsInput	Intergenic	Intergenic	-474504	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding	0.01	0.267327
Merged-chr7-121903209-1	chr7	121903159	121903259	+	2.2	cIP2vsInput	"intron (NR_073548, intron 4 of 12)"	LTR16A1|LTR|ERVL	38171	NR_073548	20277	Mm.7709	NM_001272023	ENSMUSG00000030873	Scnn1b	-	"sodium channel, nonvoltage-gated 1 beta"	protein-coding	0.01	0.49505
Merged-chr13-57272415-1	chr13	57272365	57272465	+	2.2	cIP2vsInput	Intergenic	Intergenic	-376827	NM_012035	26946	Mm.62409	NM_012035	ENSMUSG00000021541	Trpc7	TRP-7|TRP7|Trrp8	"transient receptor potential cation channel, subfamily C, member 7"	protein-coding	0	0.287129
Merged-chr1-31953939-1	chr1	31953889	31953989	+	2.2	cIP1vsInput	Intergenic	Intergenic	-218867	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm1	"KH domain containing, RNA binding, signal transduction associated 2"	protein-coding	0	0.336634
Merged-chr12-26415438-1	chr12	26415388	26415488	+	2.2	cIP2vsInput	promoter-TSS (NM_001081977)	promoter-TSS (NM_001081977)	-182	NM_080563	108089	Mm.214932	NM_001081977	ENSMUSG00000020642	Rnf144a	AI316797|Rnf144|UIP4|Ubce7ip4	ring finger protein 144A	protein-coding	0.01	0.633663
Merged-chr7-7171730-1	chr7	7171680	7171780	+	2.2	cIP2vsInput	"intron (NM_146179, intron 1 of 3)"	"intron (NM_146179, intron 1 of 3)"	377	NM_146179	232854	Mm.184857	NM_146179	ENSMUSG00000034538	Zfp418	A230102I05Rik	zinc finger protein 418	protein-coding	0.03	0.485149
Merged-chr3-150104831-1	chr3	150104781	150104881	+	2.2	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	830094	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	miscRNA	0	0.326733
Merged-chr4-90894732-1	chr4	90894682	90894782	+	2.2	cIP2vsInput	Intergenic	Intergenic	477323	NM_010486	15569	Mm.318042	NM_001177883	ENSMUSG00000008489	Elavl2	Hub|mel-N1	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)"	protein-coding	0	0.376238
Merged-chr2-150560790-1	chr2	150560740	150560840	+	2.2	cIP1vsInput	Intergenic	Intergenic	-9625	NM_009977	13011	Mm.12965	NM_009977	ENSMUSG00000068129	Cst7	Cmap	cystatin F (leukocystatin)	protein-coding	0	0.326733
Merged-chr13-7769939-1	chr13	7769889	7769989	+	2.2	cIP1vsInput	Intergenic	MTEa|LTR|ERVL-MaLR	-432970	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	"adenosine deaminase, RNA-specific, B2"	protein-coding	0	0.356436
Merged-chr4-7482368-1	chr4	7482318	7482418	+	2.2	cIP1vsInput	Intergenic	Intergenic	-78320	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	miscRNA	0	0.326733
Merged-chr5-62480737-1	chr5	62480687	62480787	+	2.2	cIP2vsInput	Intergenic	Intergenic	285440	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	"ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2"	protein-coding	0	0.336634
Merged-chr19-50043491-1	chr19	50043441	50043541	+	2.2	cIP2vsInput	Intergenic	Intergenic	635155	NM_001252501	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0	0.336634
Merged-chr7-102255908-1	chr7	102255858	102255958	+	2.2	cIP2vsInput	Intergenic	Intergenic	-5790	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	"ras homolog gene family, member G"	protein-coding	0	0.356436
Merged-chr8-51541966-1	chr8	51541916	51542016	+	2.2	cIP1vsInput	Intergenic	Intergenic	1173854	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0.01	0.39604
Merged-chr3-97496282-1	chr3	97496232	97496332	+	2.2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-85103	NM_146275	258272	Mm.377406	NM_146275	ENSMUSG00000051392	Olfr1402	MOR217-1	olfactory receptor 1402	protein-coding	0.01	0.316832
Merged-chr16-47470805-1	chr16	47470755	47470855	+	2.2	cIP2vsInput	Intergenic	Intergenic	-812930	NM_028610	73693	Mm.35597	NM_001018002	ENSMUSG00000058550	Dppa4	2410091M23Rik|C76608|ECAT15-1	developmental pluripotency associated 4	protein-coding	0	0.277228
Merged-chr10-96080765-1	chr10	96080715	96080815	+	2.2	cIP1vsInput	Intergenic	Intergenic	140102	NM_001001932	216238	Mm.490373	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding	0	0.386139
Merged-chr4-108813010-2	chr4	108812936	108813085	+	2.2	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	20574	NM_027453	70533	Mm.379178	NM_027453	ENSMUSG00000028568	Btf3l4	4632412E09Rik|5730434I03Rik|AI316863|AU022207|AW552446	basic transcription factor 3-like 4	protein-coding	0	0.36
Merged-chr19-26994062-1	chr19	26994012	26994112	+	2.2	cIP2vsInput	Intergenic	Intergenic	108137	NM_001033407	329047	Mm.293289	NM_001033407	ENSMUSG00000074913	Gm815	-	predicted gene 815	protein-coding	0	0.49505
Merged-chr8-83550862-1	chr8	83550812	83550912	+	2.2	cIP1vsInput	Intergenic	Intergenic	9769	NM_146270	258267	Mm.377401	NM_146270	ENSMUSG00000047286	Olfr370	MOR267-16|MOR26716	olfactory receptor 370	protein-coding	0.01	0.336634
Merged-chr4-78359840-1	chr4	78359790	78359890	+	2.2	cIP1vsInput	Intergenic	Intergenic	-147945	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0	0.366337
Merged-chr14-61988930-1	chr14	61988880	61988980	+	2.2	cIP2vsInput	Intergenic	Intergenic	304049	NM_173419	239133	Mm.127330	NM_173419	ENSMUSG00000048281	Dleu7	BC038059	"deleted in lymphocytic leukemia, 7"	protein-coding	0	0.366337
Merged-chr2-101456143-1	chr2	101456093	101456193	+	2.2	cIP2vsInput	Intergenic	Intergenic	-168605	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding	0	0.366337
Merged-chr6-16504794-1	chr6	16504744	16504844	+	2.2	cIP2vsInput	Intergenic	Intergenic	393647	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding	0	0.326733
Merged-chr16-72732356-1	chr16	72732306	72732406	+	2.2	cIP2vsInput	"intron (NM_019413, intron 1 of 28)"	"intron (NM_019413, intron 1 of 28)"	69207	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout homolog 1 (Drosophila)	protein-coding	0	0.29703
Merged-chrX-12158566-1	chrX	12158516	12158616	+	2.2	cIP2vsInput	"intron (NR_045434, intron 1 of 3)"	CpG	1780	NR_045434	72937	Mm.490017	NR_045434	ENSMUSG00000087271	2900008C10Rik	-	RIKEN cDNA 2900008C10 gene	miscRNA	0.12	0.70297
Merged-chr16-54438682-1	chr16	54438632	54438732	+	2.2	cIP2vsInput	Intergenic	Intergenic	844555	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding	0	0.306931
Merged-chr13-85538009-1	chr13	85537959	85538059	+	2.2	cIP1vsInput	Intergenic	L1MA4|LINE|L1	-248523	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding	0.02	0.386139
Merged-chrX-31133212-1	chrX	31133162	31133262	+	2.2	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-203157	NM_001243011	100042159	Mm.489579	NM_001243011	ENSMUSG00000095835	Gm3701	-	predicted gene 3701	protein-coding	0	0.346535
Merged-chr17-67513109-1	chr17	67513059	67513159	+	2.2	cIP1vsInput	Intergenic	Intergenic	119614	NM_001033340	240131	Mm.295736	NM_001033340	ENSMUSG00000073375	Lrrc30	Gm326	leucine rich repeat containing 30	protein-coding	0	0.336634
Merged-chr15-40878026-1	chr15	40877976	40878076	+	2.2	cIP2vsInput	"intron (NM_011766, intron 4 of 7)"	"intron (NM_011766, intron 4 of 7)"	222984	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	"zinc finger protein, multitype 2"	protein-coding	0.02	0.415842
Merged-chr9-38832907-1	chr9	38832857	38832957	+	2.2	cIP2vsInput	Intergenic	Intergenic	5292	NM_146816	258812	Mm.377702	NM_146816	ENSMUSG00000044798	Olfr923	MOR164-2	olfactory receptor 923	protein-coding	0	0.326733
Merged-chr18-43950675-1	chr18	43950625	43950725	+	2.2	cIP2vsInput	Intergenic	Lx8|LINE|L1	-12566	NM_001081180	72432	Mm.35369	NM_001081180	ENSMUSG00000055561	Spink5	2310065D10Rik|AV238912|LEKT1|LETK1|VAKT1	"serine peptidase inhibitor, Kazal type 5"	protein-coding	0	0.386139
Merged-chr9-101084862-1	chr9	101084812	101084912	+	2.2	cIP1vsInput	Intergenic	Intergenic	-15708	NM_001100451	77853	Mm.478345	NM_001100451		Msl2	E130103E02Rik|Msl2l1|Rnf184	male-specific lethal 2 homolog (Drosophila)	protein-coding	0	0.326733
Merged-chr6-118679275-1	chr6	118679225	118679325	+	2.2	cIP2vsInput	"intron (NM_001159533, intron 18 of 46)"	"intron (NM_001159533, intron 18 of 46)"	-117019	NM_001081112	232339	Mm.276116	NM_001081112	ENSMUSG00000007827	Ankrd26	5730521P14Rik|BC008111|mKIAA1074	ankyrin repeat domain 26	protein-coding	0.02	0.336634
Merged-chr1-65718666-1	chr1	65718616	65718716	+	2.2	cIP1vsInput	Intergenic	Lx5|LINE|L1	-207856	NM_027010	12969	Mm.275362	NM_027010	ENSMUSG00000025945	Crygf	3110001K11Rik|Cryg-2|DGcry-2|Len-2	"crystallin, gamma F"	protein-coding	0	0.326733
Merged-chr12-39168610-1	chr12	39168560	39168660	+	2.2	cIP1vsInput	Intergenic	Intergenic	384899	NM_001163154	14009	Mm.4866	NM_001163154	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant gene 1	protein-coding	0.01	0.306931
Merged-chr18-24646688-1	chr18	24646638	24646738	+	2.2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-7003	NM_026779	68591	Mm.28252	NM_026779	ENSMUSG00000039616	Mocos	1110018O12Rik|HMCS|MCS|MOS	molybdenum cofactor sulfurase	protein-coding	0	0.316832
Merged-chr18-49183407-1	chr18	49183357	49183457	+	2.2	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-339882	NR_033785	67321	Mm.245802	NR_033785		1700044K03Rik	-	RIKEN cDNA 1700044K03 gene	miscRNA	0.01	0.29703
Merged-chr17-58495300-1	chr17	58495250	58495350	+	2.2	cIP2vsInput	Intergenic	Intergenic	496075	NM_027001	69239	Mm.246732	NM_027001	ENSMUSG00000024227	2610034M16Rik	AV114557	RIKEN cDNA 2610034M16 gene	protein-coding	0.01	0.386139
Merged-chr9-106987367-1	chr9	106987317	106987417	+	2.2	cIP1vsInput	"intron (NM_153413, intron 21 of 52)"	"intron (NM_153413, intron 21 of 52)"	-95429	NM_029103	74840	Mm.29778	NM_029103	ENSMUSG00000032575	Manf	3230402M22Rik|AA407711|AA408789|AA673178|Armet|D17914|D18Mgi17	mesencephalic astrocyte-derived neurotrophic factor	protein-coding	0	0.356436
Merged-chr3-100557315-1	chr3	100557265	100557365	+	2.2	cIP2vsInput	Intergenic	MTD|LTR|ERVL-MaLR	-68123	NM_001142952	74645	Mm.226900	NM_001142952		Fam46c	4930431B09Rik|AI449797	"family with sequence similarity 46, member C"	protein-coding	0.01	0.425743
Merged-chr5-79884508-1	chr5	79884458	79884558	+	2.2	cIP1vsInput	Intergenic	ORR1D1|LTR|ERVL-MaLR	-368604	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0	0.316832
Merged-chr8-99661923-1	chr8	99661873	99661973	+	2.2	cIP1vsInput	Intergenic	Intergenic	-245466	NM_001039154	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.336634
Merged-chr6-130033314-1	chr6	130033264	130033364	+	2.2	cIP2vsInput	"intron (NM_013793, intron 6 of 7)"	L1_Mus3|LINE|L1	-6354	NM_053154	93971	Mm.14112	NM_053154		Klra19	Ly49s	"killer cell lectin-like receptor, subfamily A, member 19"	protein-coding	0	0.306931
Merged-chr11-89893711-1	chr11	89893661	89893761	+	2.2	cIP1vsInput	Intergenic	Intergenic	109183	NM_008796	18559	Mm.5062	NM_008796		Pctp	PC-TP|StarD2	phosphatidylcholine transfer protein	protein-coding	0	0.336634
Merged-chr17-52785660-1	chr17	52785610	52785710	+	2.2	cIP1vsInput	"intron (NM_001031811, intron 3 of 15)"	"intron (NM_001031811, intron 3 of 15)"	182951	NM_001031811	211468	Mm.490760	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	"potassium voltage-gated channel, subfamily H (eag-related), member 8"	protein-coding	0	0.326733
Merged-chr2-136024707-1	chr2	136024657	136024757	+	2.2	cIP2vsInput	Intergenic	Intergenic	-33220	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	"lysosomal-associated membrane protein family, member 5"	protein-coding	0.01	0.346535
Merged-chr11-100425992-1	chr11	100425942	100426042	+	2.2	cIP2vsInput	"intron (NM_026561, intron 8 of 8)"	"intron (NM_026561, intron 8 of 8)"	10298	NM_001163481	14230	Mm.3894	NM_001163481	ENSMUSG00000001555	Fkbp10	AI325255|FKBP-10|FKBP-65|FKBP65|Fkbp-rs1|Fkbp1-rs|Fkbp6|Fkbprp	FK506 binding protein 10	protein-coding	0.03	0.544554
Merged-chr5-19094233-1	chr5	19094183	19094283	+	2.2	cIP2vsInput	Intergenic	MLT1D|LTR|ERVL-MaLR	132322	NR_102342	70832	Mm.398993	XR_106346	ENSMUSG00000097626	4921504A21Rik	-	RIKEN cDNA 4921504A21 gene	miscRNA	0	0.346535
Merged-chr12-58053448-1	chr12	58053398	58053498	+	2.2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-158356	NM_009216	20605	Mm.278336	NM_009216		Sstr1	SRIF-2|SS-1-R|SS1-R|SS1R|Smstr-1|Smstr1|sst1	somatostatin receptor 1	protein-coding	0.01	0.346535
Merged-chr5-89680240-1	chr5	89680190	89680290	+	2.2	cIP1vsInput	"intron (NM_001081401, intron 21 of 21)"	(TTTTG)n|Simple_repeat|Simple_repeat	63804	NR_037571	631105	Mm.7732	NR_037571		Gm7056	Gm149	predicted gene 7056	miscRNA	0.01	0.277228
Merged-chr2-86472562-1	chr2	86472512	86472612	+	2.2	cIP1vsInput	Intergenic	Intergenic	11178	NM_146405	258400	Mm.357298	NM_146405	ENSMUSG00000075180	Olfr228	MOR189-3|Olfr228-ps1	olfactory receptor 228	protein-coding	0	0.376238
Merged-chr19-59812489-1	chr19	59812439	59812539	+	2.2	cIP1vsInput	Intergenic	Intergenic	130875	NM_001033172	74998	Mm.24167	NM_001033172	ENSMUSG00000040022	Rab11fip2	4930470G04Rik|A830046J09Rik|AW558126|Nrip11	RAB11 family interacting protein 2 (class I)	protein-coding	0.01	0.287129
Merged-chr6-92283930-1	chr6	92283880	92283980	+	2.2	cIP2vsInput	Intergenic	Intergenic	-39282	NM_009426	22044	Mm.1363	NM_009426	ENSMUSG00000005892	Trh	AI324969|AL022609	thyrotropin releasing hormone	protein-coding	0.01	0.336634
Merged-chr5-14221207-1	chr5	14221157	14221257	+	2.2	cIP2vsInput	"intron (NM_011348, intron 5 of 16)"	"intron (NM_011348, intron 5 of 16)"	195931	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	"sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E"	protein-coding	0.01	0.336634
Merged-chr7-120529919-1	chr7	120529869	120529969	+	2.2	cIP1vsInput	"intron (NR_024051, intron 22 of 29)"	L1_Mus2|LINE|L1	-67706	NR_024324	78552	Mm.289190	NR_024324	ENSMUSG00000044141	E130201H02Rik	-	Y box protein 1 pseudogene	pseudo	0	0.287129
Merged-chr2-40496065-1	chr2	40496015	40496115	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1269727	NM_024209	67857	Mm.392662	NM_024209		Ppp6c	2310003C10Rik	"protein phosphatase 6, catalytic subunit"	protein-coding	0	0.306931
Merged-chr16-74545946-1	chr16	74545896	74545996	+	2.2	cIP2vsInput	Intergenic	Intergenic	-135034	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout homolog 2 (Drosophila)	protein-coding	0.01	0.336634
Merged-chr11-24792136-1	chr11	24792086	24792186	+	2.2	cIP2vsInput	Intergenic	Intergenic	-61414	NR_033491	100038617	Mm.387376	NR_033491	ENSMUSG00000073103	Gm10466	ENSMUSG00000073103	predicted gene 10466	miscRNA	0.01	0.366337
Merged-chr4-74557650-1	chr4	74557600	74557700	+	2.2	cIP1vsInput	Intergenic	Intergenic	305771	NM_144787	76804	Mm.209059	NM_001172095	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding	0	0.326733
Merged-chr10-46285893-1	chr10	46285843	46285943	+	2.2	cIP2vsInput	Intergenic	Intergenic	41144	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0.01	0.29703
Merged-chr5-114497256-1	chr5	114497206	114497306	+	2.2	cIP1vsInput	Intergenic	(TAGA)n|Simple_repeat|Simple_repeat	52950	NM_023556	17855	Mm.28088	NM_023556	ENSMUSG00000041939	Mvk	2310010A05Rik|AI256848|AI414037|MK	mevalonate kinase	protein-coding	0	0.346535
Merged-chr9-94859892-1	chr9	94859842	94859942	+	2.2	cIP1vsInput	"intron (NM_177909, intron 6 of 15)"	MER44D|DNA|TcMar-Tigger	190000	NM_177909	331004	Mm.326125	NM_177909	ENSMUSG00000031129	Slc9a9	5730527A11Rik|9930105B05|AI854429|Nhe9	"solute carrier family 9 (sodium/hydrogen exchanger), member 9"	protein-coding	0	0.287129
Merged-chr14-66191332-1	chr14	66191282	66191382	+	2.2	cIP1vsInput	"intron (NM_172498, intron 2 of 29)"	"intron (NM_172498, intron 2 of 29)"	22220	NM_001162366	19229	Mm.21613	NM_001162365	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding	0	0.316832
Merged-chr3-38624151-1	chr3	38624101	38624201	+	2.2	cIP1vsInput	Intergenic	Intergenic	-139335	NM_001167883	99696	Mm.290937	NM_001033198	ENSMUSG00000044864	Ankrd50	AI662170|E430012K20Rik|mKIAA1223|mKIAA3019	ankyrin repeat domain 50	protein-coding	0.01	0.386139
Merged-chr5-55683831-1	chr5	55683781	55683881	+	2.2	cIP2vsInput	Intergenic	Intergenic	1333839	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0.01	0.356436
Merged-chr6-41716786-1	chr6	41716736	41716836	+	2.2	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-12461	NM_032540	23925	Mm.19958	NM_032540	ENSMUSG00000029866	Kel	CD238|Ece3	Kell blood group	protein-coding	0	0.386139
Merged-chr10-78905946-1	chr10	78905896	78905996	+	2.2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-10896	NM_001199840	259163	Mm.419145	NM_001199840	ENSMUSG00000094673	Olfr1354	EG257869|GA_x5J8B7TPDN2-1058-1265|GA_x6K02T03FR9-4826-3919|MOR139-5|MOR139-7|MOR185-8|Olfr1354-ps1|Olfr233-ps1	olfactory receptor 1354	protein-coding	0	0.306931
Merged-chr6-10014312-1	chr6	10014262	10014362	+	2.2	cIP2vsInput	Intergenic	Lx2|LINE|L1	960066	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	miscRNA	0	0.326733
Merged-chr16-39947402-1	chr16	39947352	39947452	+	2.2	cIP2vsInput	Intergenic	RLTR31B2|LTR|ERVK	1045057	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	"immunoglobulin superfamily, member 11"	protein-coding	0.01	0.356436
Merged-chrX-96037771-1	chrX	96037721	96037821	+	2.2	cIP1vsInput	Intergenic	Lx8b|LINE|L1	-58274	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding	0.02	0.376238
Merged-chr1-55513587-1	chr1	55513537	55513637	+	2.2	cIP2vsInput	"intron (NM_001114663, intron 1 of 5)"	"intron (NM_001114663, intron 1 of 5)"	107641	NM_001114663	227120	Mm.194183	NM_001114663		Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding	0	0.366337
Merged-chr1-30157496-1	chr1	30157446	30157546	+	2.2	cIP2vsInput	Intergenic	Intergenic	705760	NM_001081080	213109	Mm.486727	NM_001081080	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding	0	0.326733
Merged-chr9-101259710-1	chr9	101259660	101259760	+	2.2	cIP1vsInput	Intergenic	Intergenic	-7878	NM_001161362	235542	Mm.335386	NM_001161362	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	"protein phosphatase 2, regulatory subunit B'', alpha"	protein-coding	0	0.287129
Merged-chr15-10789755-1	chr15	10789705	10789805	+	2.2	cIP1vsInput	"non-coding (NR_045063, exon 7 of 7)"	"non-coding (NR_045063, exon 7 of 7)"	-39296	NR_040357	100502601	Mm.399434	NR_040357		Gm19276	-	"predicted gene, 19276"	miscRNA	0.01	0.376238
Merged-chr12-10161209-1	chr12	10161159	10161259	+	2.2	cIP1vsInput	Intergenic	Intergenic	-208762	NM_027588	70881	Mm.272843	NM_027588	ENSMUSG00000020622	Nt5c1b	4921514H13Rik|AIRP|CN-IB	"5'-nucleotidase, cytosolic IB"	protein-coding	0.01	0.346535
Merged-chr18-29830186-1	chr18	29830136	29830236	+	2.2	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-333770	NR_045391	78058	Mm.416952	NR_045391		4930578E11Rik	-	RIKEN cDNA 4930578E11 gene	miscRNA	0	0.366337
Merged-chr9-85267582-1	chr9	85267532	85267632	+	2.2	cIP1vsInput	Intergenic	L1ME1|LINE|L1	59542	NM_001160378	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	D930050G01Rik	"family with sequence similarity 46, member A"	protein-coding	0	0.306931
Merged-chr1-93174671-1	chr1	93174621	93174721	+	2.2	cIP1vsInput	Intergenic	Intergenic	-13723	NM_172411	71874	Mm.158766	NM_001159940	ENSMUSG00000034159	2310007B03Rik	-	RIKEN cDNA 2310007B03 gene	protein-coding	0.01	0.514851
Merged-chr9-89961227-1	chr9	89961177	89961277	+	2.2	cIP2vsInput	"intron (NM_011245, intron 5 of 26)"	(TAGA)n|Simple_repeat|Simple_repeat	51452	NM_001039655	19417	Mm.44561	NM_001039655	ENSMUSG00000032356	Rasgrf1	AI844718|CDC25|CDC25Mm|Grf1|Grfbeta|P190-A|Ras-GRF1|p190|p190RhoGEF	RAS protein-specific guanine nucleotide-releasing factor 1	protein-coding	0	0.316832
Merged-chr6-22814467-1	chr6	22814417	22814517	+	2.2	cIP1vsInput	Intergenic	Intergenic	-61035	NM_001081306	19283	Mm.41639	NM_001081306	ENSMUSG00000068748	Ptprz1	AI850339|DSD-1-PG|PTPbeta|PTPzeta|Ptprz|Ptpz|RPTPz|Rptpbeta	"protein tyrosine phosphatase, receptor type Z, polypeptide 1"	protein-coding	0	0.287129
Merged-chr11-86244284-1	chr11	86244234	86244334	+	2.2	cIP2vsInput	"intron (NM_027421, intron 8 of 24)"	"intron (NM_027421, intron 8 of 24)"	13284	NM_027421	70422	Mm.440906	NM_027421	ENSMUSG00000018068	Ints2	2810417D08Rik|AA408260|AI987735|mKIAA1287	integrator complex subunit 2	protein-coding	0	0.336634
Merged-chr6-73498703-1	chr6	73498653	73498753	+	2.2	cIP2vsInput	Intergenic	Intergenic	-29036	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0.01	0.346535
Merged-chr15-97963155-1	chr15	97963105	97963205	+	2.2	cIP2vsInput	Intergenic	MLT1J|LTR|ERVL-MaLR	-1074	NM_201359	380967	Mm.489364	NM_001252153	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding	0	0.455446
Merged-chr6-134853811-1	chr6	134853761	134853861	+	2.2	cIP1vsInput	"intron (NM_177687, intron 4 of 4)"	RSINE1|SINE|B4	23612	NM_177687	232430	Mm.267010	NM_177687		Crebl2	AI046348|B230205M03	cAMP responsive element binding protein-like 2	protein-coding	0.03	0.485149
Merged-chr2-123111646-1	chr2	123111596	123111696	+	2.2	cIP2vsInput	Intergenic	Intergenic	329647	NM_021507	59010	Mm.28986	NM_001162503	ENSMUSG00000005803	Sqrdl	0610039J17Rik|4930557M22Rik	sulfide quinone reductase-like (yeast)	protein-coding	0.01	0.29703
Merged-chr3-68281121-1	chr3	68281071	68281171	+	2.2	cIP1vsInput	"intron (NM_001113420, intron 1 of 6)"	"intron (NM_001113420, intron 1 of 6)"	-213072	NR_036665	30953	Mm.331064	NM_001113420	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding	0	0.39604
Merged-chr18-52028833-1	chr18	52028783	52028883	+	2.2	cIP2vsInput	Intergenic	Intergenic	94713	NR_029788	723830		NR_029788		Mir28	Mirn28|mmu-mir-28	microRNA 28	miscRNA	0.01	0.366337
Merged-chr4-51309005-1	chr4	51308955	51309055	+	2.2	cIP2vsInput	Intergenic	Intergenic	92327	NM_001162865	74914	Mm.159368	NM_001162865	ENSMUSG00000039555	Cylc2	4930488P18Rik	"cylicin, basic protein of sperm head cytoskeleton 2"	protein-coding	0	0.336634
Merged-chr6-83566281-1	chr6	83566231	83566331	+	2.2	cIP2vsInput	"intron (NM_024239, intron 2 of 9)"	L1M5|LINE|L1	-1758	NR_078345	100861870	Mm.461230	XR_140763		Gm21284	-	"predicted gene, 21284"	miscRNA	0	0.346535
Merged-chr1-166187660-1	chr1	166187610	166187710	+	2.2	cIP1vsInput	Intergenic	MER77|LTR|ERVL	51084	NM_175296	98558	Mm.26189	NM_175296	ENSMUSG00000040629	Mael	4933405K18Rik|AU019877	maelstrom homolog (Drosophila)	protein-coding	0.01	0.435644
Merged-chr9-26003904-1	chr9	26003854	26003954	+	2.2	cIP1vsInput	Intergenic	RMER4B|LTR|ERVK	522307	NM_026189	67484	Mm.112977	NM_026189	ENSMUSG00000036611	Eepd1	2310005P05Rik|AI481005	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding	0	0.356436
Merged-chr19-3183493-1	chr19	3183443	3183543	+	2.2	cIP2vsInput	"intron (NR_045304, intron 2 of 2)"	L1_Mur2|LINE|L1	14210	NR_045304	70011	Mm.393871	NR_045304		1700030N03Rik	1700087C08Rik	RIKEN cDNA 1700030N03 gene	miscRNA	0	0.39604
Merged-chr1-67923743-1	chr1	67923693	67923793	+	2.2	cIP2vsInput	Intergenic	Intergenic	800677	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding	0.01	0.336634
Merged-chr3-13360091-1	chr3	13360041	13360141	+	2.2	cIP2vsInput	Intergenic	Intergenic	-111564	NM_178631	76897	Mm.422625	NM_001163328	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0	0.29703
Merged-chr9-46886506-1	chr9	46886456	46886556	+	2.2	cIP2vsInput	Intergenic	L1MEc|LINE|L1	-27097	NR_015605	73040	Mm.265384	NR_015605		2900052N01Rik	AU067665	RIKEN cDNA 2900052N01 gene	miscRNA	0	0.326733
Merged-chr5-95968326-1	chr5	95968276	95968376	+	2.2	cIP1vsInput	Intergenic	L2b|LINE|L2	11387	NM_018866	55985	Mm.10116	NM_018866	ENSMUSG00000023078	Cxcl13	4631412M08Rik|ANGIE2|Angie|BCA-1|BLC|BLR1L|Scyb13	chemokine (C-X-C motif) ligand 13	protein-coding	0.01	0.326733
Merged-chr8-73911094-1	chr8	73911044	73911144	+	2.2	cIP1vsInput	Intergenic	Intergenic	-558538	NM_010687	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large	BPFD#36|Gyltl1a|Mbp-1|Mbp1|enr|fg|froggy|mKIAA0609|myd	like-glycosyltransferase	protein-coding	0	0.316832
Merged-chr6-76676303-1	chr6	76676253	76676353	+	2.2	cIP2vsInput	Intergenic	Intergenic	-566414	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0	0.415842
Merged-chr4-54258804-1	chr4	54258754	54258854	+	2.2	cIP1vsInput	Intergenic	Intergenic	432759	NM_028053	52076	Mm.27184	NM_028053	ENSMUSG00000028420	Tmem38b	1600017F22Rik|AA437809|AV051057|D4Ertd89e|TRIC-B|mg33b	transmembrane protein 38B	protein-coding	0	0.356436
Merged-chr17-21433015-1	chr17	21432965	21433065	+	2.2	cIP2vsInput	"intron (NM_011760, intron 3 of 3)"	"intron (NM_011760, intron 3 of 3)"	9788	NM_011760	22712	Mm.12916	NM_011760	ENSMUSG00000023882	Zfp54	2810034D10Rik|KRAB10|Zfp-54|Zfp76|mszf83	zinc finger protein 54	protein-coding	0	0.287129
Merged-chr3-104569248-1	chr3	104569198	104569298	+	2.2	cIP1vsInput	Intergenic	B1_Mus1|SINE|Alu	-57392	NM_001025067	269473	Mm.34855	NM_001025067	ENSMUSG00000032913	Lrig2	4632419I10Rik|BB096938	leucine-rich repeats and immunoglobulin-like domains 2	protein-coding	0.02	0.415842
Merged-chr16-82867318-1	chr16	82867268	82867368	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1503825	NR_040567	75247	Mm.417813	NR_040567		4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	miscRNA	0.01	0.306931
Merged-chr2-46581294-1	chr2	46581244	46581344	+	2.2	cIP1vsInput	Intergenic	Intergenic	884689	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	miscRNA	0	0.356436
Merged-chr6-17860167-1	chr6	17860117	17860217	+	2.2	cIP1vsInput	"intron (NM_001083315, intron 8 of 14)"	"intron (NM_001083315, intron 8 of 14)"	110951	NM_022332	64213	Mm.12051	NM_001083315	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding	0.01	0.346535
Merged-chr10-105623126-1	chr10	105623076	105623176	+	2.2	cIP2vsInput	Intergenic	Intergenic	48575	NR_038032	327812	Mm.191660	NR_038032	ENSMUSG00000085282	Gm15663	9330159K06|OTTMUSG00000025047	predicted gene 15663	miscRNA	0	0.316832
Merged-chr9-78039270-1	chr9	78039220	78039320	+	2.2	cIP2vsInput	Intergenic	Intergenic	-12688	NM_008103	14531	Mm.1400	NM_008103	ENSMUSG00000023333	Gcm1	GCMa|Gcm-rs2|Gcm1-rs1|glide	glial cells missing homolog 1 (Drosophila)	protein-coding	0.08	0.60396
Merged-chr18-50358340-1	chr18	50358290	50358390	+	2.2	cIP2vsInput	Intergenic	Intergenic	79971	NM_001004061	225497	Mm.329435	NM_001004061	ENSMUSG00000035420	Fam170a	Gm93|Znfd	"family with sequence similarity 170, member A"	protein-coding	0	0.366337
Merged-chr16-92912032-1	chr16	92911982	92912082	+	2.2	cIP1vsInput	Intergenic	Intergenic	-85966	NM_001111022	12394	Mm.470227	NM_001111021	ENSMUSG00000022952	Runx1	AI462102|AML1|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding	0.01	0.356436
Merged-chr1-133961924-1	chr1	133961874	133961974	+	2.2	cIP1vsInput	Intergenic	Intergenic	-40523	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding	0.02	0.554455
Merged-chr15-41359343-1	chr15	41359293	41359393	+	2.2	cIP1vsInput	Intergenic	Intergenic	-88139	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding	0	0.326733
Merged-chr13-18887554-1	chr13	18887504	18887604	+	2.2	cIP1vsInput	Intergenic	Intergenic	-60817	NM_175007	218038	Mm.101650	NM_175007	ENSMUSG00000021314	Amph	-	amphiphysin	protein-coding	0	0.267327
Merged-chr15-61090174-1	chr15	61090124	61090224	+	2.2	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-168904	NM_001081067	117586	Mm.291499	NM_001081067	ENSMUSG00000022347	A1bg	C44	alpha-1-B glycoprotein	protein-coding	0	0.356436
Merged-chr2-23344339-1	chr2	23344289	23344389	+	2.2	cIP2vsInput	"intron (NM_008752, intron 1 of 1)"	L1_Mur3|LINE|L1	23093	NM_008752	18232	Mm.131616	NM_008752	ENSMUSG00000069132	Nxph2	-	neurexophilin 2	protein-coding	0	0.356436
Merged-chr12-35853621-1	chr12	35853571	35853671	+	2.2	cIP1vsInput	Intergenic	Intergenic	-72000	NM_207531	403205	Mm.190508	NM_207531	ENSMUSG00000036231	Agr3	BCMP11|E030025L21Rik|Gm888	anterior gradient 3	protein-coding	0	0.336634
Merged-chr4-26443453-1	chr4	26443403	26443503	+	2.2	cIP1vsInput	Intergenic	Intergenic	-96801	NM_172865	242362	Mm.245602	NM_172865	ENSMUSG00000040520	Manea	4932703L02Rik	"mannosidase, endo-alpha"	protein-coding	0	0.386139
Merged-chr14-98391646-1	chr14	98391596	98391696	+	2.2	cIP2vsInput	Intergenic	L1MB2|LINE|L1	-222103	NM_007826	13134	Mm.320593	NM_001038610	ENSMUSG00000055639	Dach1	AI182278|Dac|Dach|E130112M23Rik	dachshund 1 (Drosophila)	protein-coding	0	0.39604
Merged-chr18-47591899-1	chr18	47591849	47591949	+	2.2	cIP2vsInput	"intron (NR_033454, intron 1 of 5)"	"intron (NR_033454, intron 1 of 5)"	54164	NR_033454	328953	Mm.246768	NR_033454		Gm5095	A730092B10	predicted gene 5095	miscRNA	0.02	0.306931
Merged-chr6-61301917-1	chr6	61301867	61301967	+	2.2	cIP1vsInput	"intron (NM_183310, intron 1 of 10)"	"intron (NM_183310, intron 1 of 10)"	-121107	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	miscRNA	0.02	0.336634
Merged-chr14-12987552-1	chr14	12987502	12987602	+	2.2	cIP1vsInput	Intergenic	L1VL1|LINE|L1	-164473	NM_012061	27062	Mm.260881	NM_001042617	ENSMUSG00000054423	Cadps	AU067781|CAPS|CAPS1|mKIAA1121	Ca2+-dependent secretion activator	protein-coding	0	0.326733
Merged-chr1-14097154-1	chr1	14097104	14097204	+	2.2	cIP1vsInput	Intergenic	Intergenic	213045	NM_001252192	14048	Mm.250185	NM_001252192	ENSMUSG00000025932	Eya1	bor	eyes absent 1 homolog (Drosophila)	protein-coding	0.01	0.346535
Merged-chr4-47718907-1	chr4	47718857	47718957	+	2.2	cIP2vsInput	Intergenic	L1MB1|LINE|L1	244246	NM_024171	66212	Mm.20188	NM_024171	ENSMUSG00000053317	Sec61b	1190006C12Rik|AI326121|AW122942	Sec61 beta subunit	protein-coding	0	0.326733
Merged-chr18-19061763-1	chr18	19061713	19061813	+	2.2	cIP2vsInput	Intergenic	MLTR25A|LTR|ERVK	940334	NM_007882	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding	0.01	0.346535
Merged-chr8-54141763-1	chr8	54141713	54141813	+	2.2	cIP2vsInput	"intron (NM_009506, intron 1 of 6)"	"intron (NM_009506, intron 1 of 6)"	64231	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding	0	0.316832
Merged-chr3-69656594-1	chr3	69656544	69656644	+	2.2	cIP1vsInput	Intergenic	Intergenic	-57733	NM_020026	26879	Mm.153710	NM_020026	ENSMUSG00000043300	B3galnt1	B3galt3|b3GT3	"UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1"	protein-coding	0	0.465347
Merged-chr6-20780861-1	chr6	20780811	20780911	+	2.2	cIP2vsInput	Intergenic	Intergenic	-435248	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	"potassium voltage-gated channel, Shal-related family, member 2"	protein-coding	0	0.376238
Merged-chr19-4962040-1	chr19	4961990	4962090	+	2.2	cIP1vsInput	promoter-TSS (NM_025553)	promoter-TSS (NM_025553)	-266	NM_025553	66419	Mm.28494	NM_025553	ENSMUSG00000024902	Mrpl11	2410001P07Rik|L11mt	mitochondrial ribosomal protein L11	protein-coding	0.05	0.554455
Merged-chr1-19499495-1	chr1	19499445	19499545	+	2.2	cIP2vsInput	Intergenic	L1M2|LINE|L1	287441	NM_001025305	21419	Mm.137021	NM_001025305	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding	0	0.29703
Merged-chr5-18939595-1	chr5	18939545	18939645	+	2.2	cIP1vsInput	Intergenic	Lx7|LINE|L1	286960	NR_102342	70832	Mm.398993	XR_106346	ENSMUSG00000097626	4921504A21Rik	-	RIKEN cDNA 4921504A21 gene	miscRNA	0.01	0.336634
Merged-chr6-23844821-1	chr6	23844771	23844871	+	2.2	cIP2vsInput	Intergenic	Intergenic	-5400	NM_001252105	320405	Mm.259632	NM_001252105	ENSMUSG00000017978	Cadps2	A230044C21Rik|Caps-2|Caps2|Cpd2	Ca2+-dependent activator protein for secretion 2	protein-coding	0	0.29703
Merged-chr9-27375669-1	chr9	27375619	27375719	+	2.2	cIP1vsInput	Intergenic	Intergenic	-21152	NM_029299	75469	Mm.45824	NM_029299	ENSMUSG00000031991	Spata19	1700001L23Rik|AV047838	spermatogenesis associated 19	protein-coding	0	0.247525
Merged-chr13-11117460-1	chr13	11117410	11117510	+	2.2	cIP1vsInput	Intergenic	Intergenic	-404592	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	"zona pellucida glycoprotein 4, pseudogene"	pseudo	0	0.336634
Merged-chr2-78378468-1	chr2	78378418	78378518	+	2.2	cIP2vsInput	Intergenic	Intergenic	140921	NM_177843	329436	Mm.235448	NM_177843		Gm14461	A830093M07|OTTMUSG00000016703	predicted gene 14461	protein-coding	0	0.336634
Merged-chr17-42008775-1	chr17	42008725	42008825	+	2.2	cIP2vsInput	Intergenic	Intergenic	-307172	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding	0	0.386139
Merged-chr14-85258841-1	chr14	85258791	85258891	+	2.2	cIP2vsInput	Intergenic	Intergenic	-782417	NR_015539	319903	Mm.440481	NR_015539		9630013A20Rik	-	RIKEN cDNA 9630013A20 gene	miscRNA	0.01	0.336634
Merged-chr2-101522120-1	chr2	101522070	101522170	+	2.2	cIP1vsInput	Intergenic	Intergenic	-102628	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding	0.02	0.326733
Merged-chr17-73384876-1	chr17	73384826	73384926	+	2.2	cIP1vsInput	"intron (NM_001033444, intron 1 of 22)"	"intron (NM_001033444, intron 1 of 22)"	14420	NM_001033444	381122	Mm.81496	NM_001033444	ENSMUSG00000043705	Capn13	CANP 13|Gm943	calpain 13	protein-coding	0	0.316832
Merged-chr11-41855377-1	chr11	41855327	41855427	+	2.2	cIP2vsInput	Intergenic	Intergenic	145337	NM_177408	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2"	protein-coding	0	0.326733
Merged-chr5-10415714-1	chr5	10415664	10415764	+	2.2	cIP2vsInput	Intergenic	Intergenic	-449315	NR_003596	623849	Mm.335888	NR_003596	ENSMUSG00000091422	Gm6455	EG623849	predicted gene 6455	pseudo	0	0.306931
Merged-chr5-44292738-1	chr5	44292688	44292788	+	2.2	cIP2vsInput	Intergenic	Lx4A|LINE|L1	-66132	NM_173764	231225	Mm.30688	NM_173764	ENSMUSG00000046985	Tapt1	4932414K18Rik	transmembrane anterior posterior transformation 1	protein-coding	0	0.356436
Merged-chr4-117705214-1	chr4	117705164	117705264	+	2.2	cIP1vsInput	Intergenic	Intergenic	-22989	NM_023178	66233	Mm.29142	NM_023178	ENSMUSG00000009640	Dmap1	1500016M21Rik|DNMAP1|DNMTAP1|Dmtap1|mKIAA1425	DNA methyltransferase 1-associated protein 1	protein-coding	0.02	0.455446
Merged-chr3-53194839-1	chr3	53194789	53194889	+	2.2	cIP1vsInput	"intron (NM_175386, intron 2 of 3)"	Charlie1|DNA|hAT-Charlie	153292	NM_175386	108927	Mm.118617	NM_175386	ENSMUSG00000048332	Lhfp	2810489O06Rik|AI194968	lipoma HMGIC fusion partner	protein-coding	0.01	0.366337
Merged-chr3-57586649-1	chr3	57586599	57586699	+	2.2	cIP2vsInput	Intergenic	Intergenic	-10739	NM_001168281	97064	Mm.405029	NM_001168281	ENSMUSG00000027803	Wwtr1	2310058J06Rik|2610021I22Rik|C78399|Taz	WW domain containing transcription regulator 1	protein-coding	0.01	0.277228
Merged-chr16-95760259-1	chr16	95760209	95760309	+	2.2	cIP1vsInput	Intergenic	Intergenic	57852	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	"E26 avian leukemia oncogene 2, 3' domain"	protein-coding	0.02	0.534653
Merged-chr2-53346686-1	chr2	53346636	53346736	+	2.2	cIP2vsInput	Intergenic	L1Md_F3|LINE|L1	154602	NM_022989	65103	Mm.37623	NM_022989	ENSMUSG00000026960	Arl6ip6	2310057C01Rik|2610529A11Rik|Aip-6	ADP-ribosylation factor-like 6 interacting protein 6	protein-coding	0	0.366337
Merged-chr9-66285455-1	chr9	66285405	66285505	+	2.2	cIP1vsInput	Intergenic	Intergenic	-64995	NM_145617	235439	Mm.244179	NM_145617	ENSMUSG00000038664	Herc1	2810449H11Rik|B230218H07|D130015N03Rik|tbl	hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1	protein-coding	0	0.39604
Merged-chr11-50827664-1	chr11	50827614	50827714	+	2.2	cIP2vsInput	promoter-TSS (NM_013922)	promoter-TSS (NM_013922)	67	NM_013922	30944	Mm.103674	NM_013922	ENSMUSG00000044807	Zfp354c	5330421P20Rik|AJ18|AW743325|Kid3|Tcf17l2|Znf354c|mKIAA4218	zinc finger protein 354C	protein-coding	0.08	0.673267
Merged-chr10-15829193-1	chr10	15829143	15829243	+	2.2	cIP2vsInput	Intergenic	Intergenic	1068904	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding	0	0.336634
Merged-chr14-25262950-1	chr14	25262900	25263000	+	2.2	cIP2vsInput	Intergenic	Intergenic	-119709	NR_045718	75862	Mm.109191	NR_045718		4930572O13Rik	-	RIKEN cDNA 4930572O13 gene	miscRNA	0	0.465347
Merged-chr11-49190558-1	chr11	49190508	49190608	+	2.2	cIP2vsInput	Intergenic	RLTR18-int|LTR|ERVK	-3469	NM_172793	237754	Mm.130787	NM_172793		Btnl9	B430208I01|Btn3|D330012D11Rik	butyrophilin-like 9	protein-coding	0.01	0.405941
Merged-chr16-51260720-1	chr16	51260670	51260770	+	2.2	cIP2vsInput	Intergenic	Intergenic	-527947	NR_028300	68190	Mm.482928	NR_028300		5330426P16Rik	-	RIKEN cDNA 5330426P16 gene	miscRNA	0	0.346535
Merged-chr2-71118233-1	chr2	71118183	71118283	+	2.2	cIP2vsInput	"exon (NM_028593, exon 1 of 4)"	"exon (NM_028593, exon 1 of 4)"	179	NM_028593	73649	Mm.45435	NM_028593	ENSMUSG00000027015	Cybrd1	2210407P13Rik|Dcytb	cytochrome b reductase 1	protein-coding	0.09	0.633663
Merged-chr1-141708611-1	chr1	141708561	141708661	+	2.2	cIP2vsInput	Intergenic	Lx7|LINE|L1	-1052209	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0	0.316832
Merged-chr3-27096711-1	chr3	27096661	27096761	+	2.2	cIP1vsInput	TTS (NM_001177625)	TTS (NM_001177625)	57143	NM_007900	13605	Mm.261453	NM_001177625	ENSMUSG00000027699	Ect2	AI528536|mKIAA4037	ect2 oncogene	protein-coding	0.01	0.277228
Merged-chr3-134559936-1	chr3	134559886	134559986	+	2.2	cIP2vsInput	Intergenic	Intergenic	-136301	NR_040600	75208	Mm.84580	NR_040600		4930539C22Rik	-	RIKEN cDNA 4930539C22 gene	miscRNA	0	0.356436
Merged-chr3-72598852-1	chr3	72598802	72598902	+	2.2	cIP2vsInput	Intergenic	Intergenic	368014	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding	0	0.346535
Merged-chr1-85148376-1	chr1	85148326	85148426	+	2.2	cIP1vsInput	Intergenic	L1Md_A|LINE|L1	-38523	NM_213615	381287	Mm.487565	NM_213615	ENSMUSG00000089844	A530032D15Rik	Gm1888	RIKEN cDNA A530032D15Rik gene	protein-coding	0	0.356436
Merged-chr11-16551394-1	chr11	16551344	16551444	+	2.2	cIP1vsInput	Intergenic	Intergenic	-42910	NM_001109971	20335	Mm.325350	NM_001109971	ENSMUSG00000078974	Sec61g	-	"SEC61, gamma subunit"	protein-coding	0	0.217822
Merged-chr3-63005711-1	chr3	63005661	63005761	+	2.2	cIP2vsInput	Intergenic	Intergenic	-290161	NM_008604	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding	0	0.376238
Merged-chr4-50138924-1	chr4	50138874	50138974	+	2.2	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-293155	NM_001276355	242443	Mm.440095	NM_001033351		Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	"glutamate receptor ionotropic, NMDA3A"	protein-coding	0	0.29703
Merged-chr7-87150105-1	chr7	87150055	87150155	+	2.2	cIP1vsInput	Intergenic	Intergenic	-96690	NM_015760	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding	0	0.267327
Merged-chr9-112892902-1	chr9	112892852	112892952	+	2.2	cIP1vsInput	Intergenic	LTR16A1|LTR|ERVL	636328	NR_033433	620760	Mm.259863	NR_015468	ENSMUSG00000087038	2900079G21Rik	C130083B14|Gm6179	RIKEN cDNA 2900079G21 gene	miscRNA	0.01	0.39604
Merged-chr2-8883675-1	chr2	8883625	8883725	+	2.2	cIP1vsInput	Intergenic	Intergenic	-305840	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	miscRNA	0.01	0.316832
Merged-chr2-14925283-1	chr2	14925233	14925333	+	2.2	cIP2vsInput	"intron (NM_023116, intron 3 of 13)"	"intron (NM_023116, intron 3 of 13)"	51627	NR_045533	12296	Mm.313930	NM_001252533	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	"calcium channel, voltage-dependent, beta 2 subunit"	protein-coding	0	0.326733
Merged-chr3-100872255-1	chr3	100872205	100872305	+	2.2	cIP2vsInput	"intron (NM_178594, intron 1 of 5)"	L1_Mur3|LINE|L1	46796	NM_178594	242122	Mm.137467	NM_178594		Vtcn1	B7h4|B7s1|B7x|BC032925	V-set domain containing T cell activation inhibitor 1	protein-coding	0	0.346535
Merged-chr10-114372744-1	chr10	114372694	114372794	+	2.2	cIP1vsInput	Intergenic	Intergenic	428626	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding	0	0.346535
Merged-chr7-55198698-1	chr7	55198648	55198748	+	2.2	cIP2vsInput	"intron (NM_178705, intron 7 of 11)"	"intron (NM_178705, intron 7 of 11)"	363453	NM_178705	233271	Mm.474990	NM_178705		Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding	0	0.29703
Merged-chr8-67431712-1	chr8	67431662	67431762	+	2.2	cIP2vsInput	Intergenic	Intergenic	-59046	NM_008673	17960	Mm.14125	NM_008673	ENSMUSG00000025588	Nat1	Nat-1	N-acetyl transferase 1	protein-coding	0	0.415842
Merged-chr5-15045395-1	chr5	15045345	15045445	+	2.2	cIP2vsInput	Intergenic	MTD|LTR|ERVL-MaLR	-12388	NM_182957	66773	Mm.368256	NM_182957	ENSMUSG00000091897	Gm17019	-	predicted gene 17019	protein-coding	0.01	0.326733
Merged-chr6-112083010-1	chr6	112082960	112083060	+	2.2	cIP2vsInput	Intergenic	Intergenic	-127698	NR_027865	67336	Mm.378014	NR_027865		1700054K19Rik	-	RIKEN cDNA 1700054K19 gene	miscRNA	0.01	0.306931
Merged-chr1-115198331-1	chr1	115198281	115198381	+	2.2	cIP2vsInput	Intergenic	MusHAL1|LINE|L1	-486806	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0	0.336634
Merged-chr4-50299359-1	chr4	50299309	50299409	+	2.2	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	-453590	NM_001276355	242443	Mm.440095	NM_001033351		Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	"glutamate receptor ionotropic, NMDA3A"	protein-coding	0	0.386139
Merged-chr6-44833378-1	chr6	44833328	44833428	+	2.2	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-226683	NM_001004357	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0	0.356436
Merged-chr2-103200110-1	chr2	103200060	103200160	+	2.2	cIP2vsInput	Intergenic	Intergenic	103086	NM_007914	13661	Mm.10724	NM_007914	ENSMUSG00000012350	Ehf	9030625L19Rik|AU019492	ets homologous factor	protein-coding	0	0.356436
Merged-chr1-67812803-1	chr1	67812753	67812853	+	2.2	cIP2vsInput	Intergenic	Intergenic	689737	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding	0	0.257426
Merged-chr3-99973110-1	chr3	99973060	99973160	+	2.2	cIP2vsInput	"intron (NM_028892, intron 4 of 48)"	"intron (NM_028892, intron 4 of 48)"	87693	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding	0	0.257426
Merged-chr9-108714284-1	chr9	108714234	108714334	+	2.2	cIP2vsInput	"exon (NM_008924, exon 2 of 11)"	"exon (NM_008924, exon 2 of 11)"	22141	NM_008924	19087	Mm.486392	NM_008924	ENSMUSG00000032601	Prkar2a	1110061A24Rik|AI317181|AI836829|RII(alpha)	"protein kinase, cAMP dependent regulatory, type II alpha"	protein-coding	0.02	0.29703
Merged-chr1-151549135-1	chr1	151549085	151549185	+	2.2	cIP1vsInput	Intergenic	Intergenic	-22238	NM_022018	63913	Mm.482559	NM_022018		Fam129a	AI256368|AU019833|Niban	"family with sequence similarity 129, member A"	protein-coding	0.01	0.336634
Merged-chr16-36150916-1	chr16	36150866	36150966	+	2.2	cIP1vsInput	Intergenic	L1VL2|LINE|L1	-5895	NM_173869	268885	Mm.187847	NM_173869	ENSMUSG00000059657	Stfa2l1	-	stefin A2 like 1	protein-coding	0	0.346535
Merged-chr18-41967464-1	chr18	41967414	41967514	+	2.2	cIP1vsInput	Intergenic	ORR1D1|LTR|ERVL-MaLR	-16270	NM_029942	77619	Mm.30649	NM_029942	ENSMUSG00000056671	Prelid2	1700003A01Rik|C330008K14Rik	PRELI domain containing 2	protein-coding	0.01	0.39604
Merged-chr15-32914024-1	chr15	32913974	32914074	+	2.2	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	-6699	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding	0	0.326733
Merged-chr18-76414583-1	chr18	76414533	76414633	+	2.2	cIP1vsInput	Intergenic	Lx7|LINE|L1	153462	NM_001252481	17126	Mm.490934	NM_001252481		Smad2	7120426M23Rik|Madh2|Madr2|Smad-2|mMad2	SMAD family member 2	protein-coding	0.01	0.29703
Merged-chr5-68560225-1	chr5	68560175	68560275	+	2.2	cIP1vsInput	Intergenic	Intergenic	528390	NM_001018019	433899	Mm.332422	NM_001018019	ENSMUSG00000068082	Grxcr1	Tg(Eno2-Gabrb3)0370Brll|pi|tde	"glutaredoxin, cysteine rich 1"	protein-coding	0	0.217822
Merged-chr15-46171686-1	chr15	46171636	46171736	+	2.2	cIP2vsInput	Intergenic	Intergenic	-152899	NR_045509	71120	Mm.158571	NR_045509		1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	miscRNA	0	0.356436
Merged-chr12-97650242-1	chr12	97650192	97650292	+	2.2	cIP2vsInput	Intergenic	Intergenic	609095	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding	0	0.287129
Merged-chr4-22341504-1	chr4	22341454	22341554	+	2.2	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-16061	NM_172988	269514	Mm.40708	NM_172988	ENSMUSG00000040410	Fbxl4	4732456I21|AI836810|FBL4|FBL5	F-box and leucine-rich repeat protein 4	protein-coding	0	0.346535
Merged-chr19-12643725-1	chr19	12643675	12643775	+	2.2	cIP1vsInput	"intron (NM_145935, intron 2 of 5)"	L1_Mus4|LINE|L1	10417	NM_145935	107146	Mm.39974	NM_145935		Glyat	A330009E03Rik|ACGNAT|AI195249|AI315345|CAT|GAT	glycine-N-acyltransferase	protein-coding	0	0.316832
Merged-chr1-8359671-1	chr1	8359621	8359721	+	2.2	cIP2vsInput	Intergenic	Intergenic	940059	NM_027671	71096	Mm.388998	NM_027671		Sntg1	4933426D16Rik|G1SYN|SYN4	"syntrophin, gamma 1"	protein-coding	0	0.326733
Merged-chr12-91203620-1	chr12	91203570	91203670	+	2.2	cIP1vsInput	"intron (NM_181815, intron 20 of 25)"	"intron (NM_181815, intron 20 of 25)"	93391	NR_030473	735273		NR_030473		Mir669c	Mirn669c|Mirn669c-1	microRNA 669c	miscRNA	0.01	0.336634
Merged-chr7-62298339-1	chr7	62298289	62298389	+	2.2	cIP1vsInput	Intergenic	Intergenic	-49938	NM_010882	17984	Mm.400253	NM_010882	ENSMUSG00000033585	Ndn	AI528698|Peg6	necdin	protein-coding	0	0.405941
Merged-chr6-123638480-1	chr6	123638430	123638530	+	2.2	cIP2vsInput	"intron (NM_001104637, intron 2 of 5)"	"intron (NM_001104637, intron 2 of 5)"	12155	NM_001104637	546913	Mm.469875	NM_001104637	ENSMUSG00000095486	Vmn2r22	EG546913	"vomeronasal 2, receptor 22"	protein-coding	0	0.277228
Merged-chr16-74548896-1	chr16	74548846	74548946	+	2.2	cIP1vsInput	Intergenic	Intergenic	-137984	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout homolog 2 (Drosophila)	protein-coding	0.01	0.366337
Merged-chr11-38489896-1	chr11	38489846	38489946	+	2.2	cIP2vsInput	Intergenic	Intergenic	30149	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0.01	0.376238
Merged-chr18-43852557-1	chr18	43852507	43852607	+	2.2	cIP1vsInput	Intergenic	Intergenic	-59679	NM_001033280	225443	Mm.100304	NM_001033280	ENSMUSG00000071858	Gm94	-	predicted gene 94	protein-coding	0	0.425743
Merged-chr1-82758748-1	chr1	82758698	82758798	+	2.2	cIP2vsInput	"intron (NM_025453, intron 3 of 3)"	"intron (NM_025453, intron 3 of 3)"	9708	NM_025453	66261	Mm.46325	NM_025453	ENSMUSG00000026149	Tm4sf20	1810018L02Rik	transmembrane 4 L six family member 20	protein-coding	0	0.316832
Merged-chr1-17264531-1	chr1	17264481	17264581	+	2.2	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	119158	NM_010267	14545	Mm.18218	NM_010267	ENSMUSG00000025777	Gdap1	-	ganglioside-induced differentiation-associated-protein 1	protein-coding	0	0.326733
Merged-chr17-51686014-1	chr17	51685964	51686064	+	2.2	cIP2vsInput	Intergenic	Lx10|LINE|L1	126040	NM_001163630	20230	Mm.311655	NM_001163630	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding	0	0.336634
Merged-chr11-117408187-1	chr11	117408137	117408237	+	2.2	cIP2vsInput	Intergenic	Intergenic	75874	NM_001113488	53860	Mm.38450	NM_001113486	ENSMUSG00000059248	9-Sep	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding	0.01	0.435644
Merged-chr15-45332175-1	chr15	45332125	45332225	+	2.2	cIP2vsInput	Intergenic	Intergenic	-217241	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	"potassium channel, subfamily V, member 1"	protein-coding	0	0.336634
Merged-chr7-63836271-1	chr7	63836221	63836321	+	2.2	cIP2vsInput	Intergenic	Lx5|LINE|L1	-80586	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding	0	0.405941
Merged-chr1-87198828-1	chr1	87198778	87198878	+	2.2	cIP2vsInput	"3' UTR (NM_021600, exon 12 of 12)"	"3' UTR (NM_021600, exon 12 of 12)"	-6983	NM_009604	11449	Mm.2810	NM_009604	ENSMUSG00000026253	Chrng	Achr-3|Acrg	"cholinergic receptor, nicotinic, gamma polypeptide"	protein-coding	0.04	0.623762
Merged-chr14-89653682-1	chr14	89653632	89653732	+	2.2	cIP2vsInput	Intergenic	Intergenic	-242542	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0	0.336634
Merged-chr11-14025906-1	chr11	14025856	14025956	+	2.2	cIP1vsInput	Intergenic	L1M4|LINE|L1	573319	NR_045918	73307	Mm.399291	NR_045918	ENSMUSG00000085561	1700046C09Rik	-	RIKEN cDNA 1700046C09 gene	miscRNA	0	0.207921
Merged-chr1-173651295-1	chr1	173651245	173651345	+	2.2	cIP2vsInput	Intergenic	RLTR33|LTR|ERVK	20436	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Pyhin1	4930422C14|AI447904|Ifi209|Ifix	"pyrin and HIN domain family, member 1"	protein-coding	0	0.39604
Merged-chr1-154649980-1	chr1	154649930	154650030	+	2.2	cIP1vsInput	"intron (NM_009782, intron 3 of 46)"	Lx3_Mus|LINE|L1	75940	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	"calcium channel, voltage-dependent, R type, alpha 1E subunit"	protein-coding	0	0.326733
Merged-chr6-35465700-1	chr6	35465650	35465750	+	2.2	cIP2vsInput	Intergenic	Intergenic	74188	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding	0	0.277228
Merged-chr8-5567729-1	chr8	5567679	5567779	+	2.2	cIP2vsInput	Intergenic	Intergenic	-462497	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.326733
Merged-chr4-22194286-1	chr4	22194236	22194336	+	2.2	cIP2vsInput	Intergenic	Intergenic	-163279	NM_172988	269514	Mm.40708	NM_172988	ENSMUSG00000040410	Fbxl4	4732456I21|AI836810|FBL4|FBL5	F-box and leucine-rich repeat protein 4	protein-coding	0.02	0.346535
Merged-chr6-79598566-1	chr6	79598516	79598616	+	2.2	cIP2vsInput	Intergenic	Intergenic	-219465	NM_001190732	100463512	Mm.461086	NM_001190732	ENSMUSG00000096887	Gm20594	Mtrnr2l	"predicted gene, 20594"	protein-coding	0.01	0.287129
Merged-chr3-39220209-1	chr3	39220159	39220259	+	2.2	cIP1vsInput	Intergenic	Intergenic	333269	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT tumor suppressor homolog 4 (Drosophila)	protein-coding	0	0.455446
Merged-chr16-78789056-1	chr16	78789006	78789106	+	2.2	cIP2vsInput	Intergenic	Intergenic	-141892	NM_139134	246048	Mm.77895	NM_139134	ENSMUSG00000022860	Chodl	3110074E07Rik|MT75|PRED12	chondrolectin	protein-coding	0.01	0.356436
Merged-chr5-76928853-1	chr5	76928803	76928903	+	2.2	cIP2vsInput	"intron (NM_172146, intron 1 of 10)"	(CAAAAA)n|Simple_repeat|Simple_repeat	-22558	NM_025939	67054	Mm.431705	NM_025939	ENSMUSG00000029247	Paics	2610511I09Rik|ADE2H1|AIRC|PAIS	"phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoribosylaminoimidazole, succinocarboxamide synthetase"	protein-coding	0.01	0.257426
Merged-chr2-81471778-1	chr2	81471728	81471828	+	2.2	cIP2vsInput	Intergenic	Intergenic	-581880	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0	0.386139
Merged-chr3-107918221-1	chr3	107918171	107918271	+	2.2	cIP2vsInput	Intergenic	B2_Mm2|SINE|B2	13524	NM_026672	68312	Mm.458189	NM_026672	ENSMUSG00000004035	Gstm7	0610005A07Rik|AI894236|Cd203c	"glutathione S-transferase, mu 7"	protein-coding	0.02	0.475248
Merged-chr14-90199349-1	chr14	90199299	90199399	+	2.2	cIP2vsInput	"intron (NR_045712, intron 5 of 8)"	"intron (NR_045712, intron 5 of 8)"	72458	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0.01	0.366337
Merged-chr14-106950842-1	chr14	106950792	106950892	+	2.2	cIP1vsInput	Intergenic	Intergenic	-464322	NR_045938	73631	Mm.48862	NR_045938		1700128A07Rik	-	RIKEN cDNA 1700128A07 gene	miscRNA	0	0.336634
Merged-chr5-88136917-1	chr5	88136867	88136967	+	2.2	cIP2vsInput	Intergenic	Intergenic	50361	NM_001252680	20600	Mm.1397	NM_001252679	ENSMUSG00000029281	Smr2	MSG2|Vcs2	submaxillary gland androgen regulated protein 2	protein-coding	0.01	0.326733
Merged-chr2-45928432-1	chr2	45928382	45928482	+	2.2	cIP2vsInput	Intergenic	Intergenic	231827	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	miscRNA	0	0.366337
Merged-chr3-123204635-1	chr3	123204585	123204685	+	2.2	cIP2vsInput	"intron (NM_080451, intron 1 of 4)"	"intron (NM_080451, intron 1 of 4)"	31514	NM_080451	118449	Mm.474733	NM_080451	ENSMUSG00000050315	Synpo2	1110069I04Rik|2310068J10Rik|9530006G20Rik|AI848603|Myo	synaptopodin 2	protein-coding	0.01	0.326733
Merged-chr18-89349262-1	chr18	89349212	89349312	+	2.2	cIP1vsInput	"intron (NM_001039173, intron 7 of 7)"	Lx7|LINE|L1	151835	NM_001039149	225825	Mm.139293	NM_001039148	ENSMUSG00000034028	Cd226	BC051526|DNAM-1|DNAM1|Pta1|TLiSA1	CD226 antigen	protein-coding	0	0.306931
Merged-chr3-104705370-1	chr3	104705320	104705420	+	2.2	cIP1vsInput	Intergenic	RLTR13D3A1|LTR|ERVK	66702	NM_009196	20501	Mm.9086	NM_009196	ENSMUSG00000032902	Slc16a1	AL022710|Mct1	"solute carrier family 16 (monocarboxylic acid transporters), member 1"	protein-coding	0.01	0.287129
Merged-chr7-51531583-1	chr7	51531533	51531633	+	2.2	cIP2vsInput	"intron (NR_073508, intron 4 of 20)"	L1_Mus2|LINE|L1	20554	NM_001271879	233246	Mm.411727	NM_001271879	ENSMUSG00000055489	Ano5	9330162L24|Gdd1|Tmem16e	anoctamin 5	protein-coding	0	0.336634
Merged-chr16-83071162-1	chr16	83071112	83071212	+	2.2	cIP2vsInput	Intergenic	Intergenic	-1299981	NR_040567	75247	Mm.417813	NR_040567		4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	miscRNA	0	0.336634
Merged-chr3-138812437-1	chr3	138812387	138812487	+	2.2	cIP2vsInput	"intron (NM_019571, intron 1 of 7)"	"intron (NM_019571, intron 1 of 7)"	70242	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|AU024142|NET-4|Tm4sf9	tetraspanin 5	protein-coding	0.01	0.346535
Merged-chr12-99451901-1	chr12	99451851	99451951	+	2.2	cIP2vsInput	Intergenic	B4|SINE|B4	-1827	NM_183186	71375	Mm.489662	NM_183186	ENSMUSG00000033713	Foxn3	5430426H20Rik|AA589593|AW556347|Ches1|Ches1l|HTLFL1	forkhead box N3	protein-coding	0.01	0.475248
Merged-chr14-68683839-1	chr14	68683789	68683889	+	2.2	cIP2vsInput	Intergenic	L1M2|LINE|L1	-27997	NM_183366	13522	Mm.117450	NM_010082	ENSMUSG00000014725	Adam28	C130072N01Rik|D430033C21Rik|Dtgn1|MDC-L|MDC-Lm|MDC-Ls|MDCL|TECADAM|eMDCII	a disintegrin and metallopeptidase domain 28	protein-coding	0	0.336634
Merged-chr9-45300568-1	chr9	45300518	45300618	+	2.2	cIP1vsInput	Intergenic	Intergenic	-18532	NM_001013373	214531	Mm.477907	NM_001013373	ENSMUSG00000037129	Tmprss13	BC010843|Tpmrss13	"transmembrane protease, serine 13"	protein-coding	0.06	0.544554
Merged-chr11-113311638-1	chr11	113311588	113311688	+	2.2	cIP1vsInput	"intron (NM_001166503, intron 6 of 9)"	"intron (NM_001166503, intron 6 of 9)"	-101969	NR_040276	319871	Mm.383743	NR_040276	ENSMUSG00000085421	4732490B19Rik	-	RIKEN cDNA 4732490B19 gene	miscRNA	0	0.366337
Merged-chr1-192317319-1	chr1	192317269	192317369	+	2.2	cIP1vsInput	"intron (NM_010600, intron 6 of 10)"	"intron (NM_010600, intron 6 of 10)"	126447	NM_010600	16510	Mm.4489	NM_001038607	ENSMUSG00000058248	Kcnh1	Kv10.1|M-eag	"potassium voltage-gated channel, subfamily H (eag-related), member 1"	protein-coding	0.01	0.346535
Merged-chr3-150957047-1	chr3	150956997	150957097	+	2.2	cIP1vsInput	Intergenic	ID4_|SINE|ID	-480835	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0	0.376238
Merged-chr1-149071211-1	chr1	149071161	149071261	+	2.2	cIP2vsInput	Intergenic	Intergenic	890073	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0.01	0.326733
Merged-chr9-92521526-1	chr9	92521476	92521576	+	2.2	cIP1vsInput	Intergenic	Intergenic	-20697	NM_011961	26432	Mm.79983	NM_001142916	ENSMUSG00000032374	Plod2	D530025C14Rik|LH2|Plod-2	"procollagen lysine, 2-oxoglutarate 5-dioxygenase 2"	protein-coding	0	0.326733
Merged-chr3-9173615-1	chr3	9173565	9173665	+	2.2	cIP1vsInput	Intergenic	Intergenic	-76952	NM_177660	229055	Mm.413596	NM_177660	ENSMUSG00000069114	Zbtb10	4832414A18|AU021107|RINZF	zinc finger and BTB domain containing 10	protein-coding	0.01	0.346535
Merged-chr4-85032186-1	chr4	85032136	85032236	+	2.2	cIP1vsInput	"intron (NM_175275, intron 12 of 25)"	L1M2|LINE|L1	147859	NM_177385	338349	Mm.440562	NM_175275	ENSMUSG00000038070	Cntln	AI448092|B430108F07Rik|D530005L17Rik	"centlein, centrosomal protein"	protein-coding	0	0.386139
Merged-chr5-83266220-1	chr5	83266170	83266270	+	2.2	cIP2vsInput	Intergenic	Intergenic	88975	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	"trans-2,3-enoyl-CoA reductase-like"	protein-coding	0	0.29703
Merged-chr1-169920193-1	chr1	169920143	169920243	+	2.2	cIP2vsInput	Intergenic	Intergenic	-8746	NM_001033185	78465	Mm.489035	NM_001033185	ENSMUSG00000070532	1700084C01Rik	-	RIKEN cDNA 1700084C01 gene	protein-coding	0.01	0.415842
Merged-chr9-16602257-1	chr9	16602207	16602307	+	2.2	cIP2vsInput	Intergenic	Intergenic	-224026	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT tumor suppressor homolog 3 (Drosophila)	protein-coding	0.01	0.326733
Merged-chr8-5543562-1	chr8	5543512	5543612	+	2.2	cIP2vsInput	Intergenic	Intergenic	-438330	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.336634
Merged-chr15-71626556-1	chr15	71626506	71626606	+	2.2	cIP2vsInput	"intron (NM_177819, intron 1 of 19)"	"intron (NM_177819, intron 1 of 19)"	101282	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	"family with sequence similarity 135, member B"	protein-coding	0.01	0.29703
Merged-chr10-73446349-1	chr10	73446299	73446399	+	2.2	cIP1vsInput	Intergenic	Intergenic	-359644	NR_040646	327768	Mm.417745	NR_040646		A330049N07Rik	-	RIKEN cDNA A330049N07 gene	miscRNA	0	0.277228
Merged-chr11-10500041-1	chr11	10499991	10500091	+	2.2	cIP2vsInput	Intergenic	Intergenic	-613975	NM_177033	319922	Mm.487612	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding	0	0.29703
Merged-chr9-116186125-1	chr9	116186075	116186175	+	2.2	cIP1vsInput	Intergenic	Intergenic	-10762	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	"transforming growth factor, beta receptor II"	protein-coding	0	0.336634
Merged-chr9-85825577-1	chr9	85825527	85825627	+	2.2	cIP1vsInput	Intergenic	L1M2|LINE|L1	-16803	NM_011627	21983	Mm.484180	NM_001164792	ENSMUSG00000035274	Tpbg	5T4|AW495680	trophoblast glycoprotein	protein-coding	0	0.326733
Merged-chr1-6089185-1	chr1	6089135	6089235	+	2.2	cIP1vsInput	Intergenic	Intergenic	-125477	NM_009826	12421	Mm.293811	NM_009826	ENSMUSG00000025907	Rb1cc1	2900055E04Rik|5930404L04Rik|Cc1|FIP200|LaXp180	RB1-inducible coiled-coil 1	protein-coding	0	0.326733
Merged-chr11-82890189-1	chr11	82890139	82890239	+	2.2	cIP2vsInput	"intron (NM_011235, intron 1 of 9)"	"intron (NM_011235, intron 1 of 9)"	426	NM_011235	19364	Mm.9286	NM_011235		Rad51d	R51H3|Rad51l3|Trad-d2|Trad-d3|Trad-d4|Trad-d6|Trad-d7	RAD51 homolog D	protein-coding	0.06	0.613861
Merged-chr9-81226977-1	chr9	81226927	81227027	+	2.2	cIP1vsInput	Intergenic	Lx2B2|LINE|L1	-404953	NR_040394	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	miscRNA	0	0.316832
Merged-chr12-61714624-1	chr12	61714574	61714674	+	2.2	cIP1vsInput	"intron (NM_178714, intron 2 of 3)"	L1_Mur1|LINE|L1	189992	NM_178714	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0	0.306931
Merged-chr2-46260717-1	chr2	46260667	46260767	+	2.2	cIP1vsInput	Intergenic	Lx8b|LINE|L1	564112	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	miscRNA	0	0.336634
Merged-chr7-34571050-1	chr7	34571000	34571100	+	2.2	cIP2vsInput	Intergenic	Intergenic	81791	NM_146188	233107	Mm.486198	NM_146188	ENSMUSG00000030499	Kctd15	BC031749	potassium channel tetramerisation domain containing 15	protein-coding	0.05	0.683168
Merged-chr1-78601486-1	chr1	78601436	78601536	+	2.2	cIP1vsInput	Intergenic	Intergenic	-56339	NM_001033606	74205	Mm.276016	NM_001033606	ENSMUSG00000032883	Acsl3	2610510B12Rik|Acs3|C85929|Facl3|Pro2194	acyl-CoA synthetase long-chain family member 3	protein-coding	0	0.326733
Merged-chr1-74321568-1	chr1	74321518	74321618	+	2.2	cIP2vsInput	"intron (NM_001039509, intron 2 of 9)"	"intron (NM_001039509, intron 2 of 9)"	-11042	NM_019999	56695	Mm.384726	NM_001039509	ENSMUSG00000026179	Pnkd	2210013N15Rik|2810403H05Rik|AI854243|Brp17|MNCb-5687|MR-1|Tahccp2	paroxysmal nonkinesiogenic dyskinesia	protein-coding	0.01	0.445545
Merged-chr16-87909497-1	chr16	87909447	87909547	+	2.2	cIP2vsInput	"intron (NM_146072, intron 15 of 16)"	(TATG)n|Simple_repeat|Simple_repeat	210543	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1	protein-coding	0	0.336634
Merged-chr18-33247977-1	chr18	33247927	33248027	+	2.2	cIP2vsInput	Intergenic	Intergenic	-34161	NM_133774	170459	Mm.393277	NM_133774		Stard4	4632419C16Rik|9030213J02Rik|AA517649|AW324468	StAR-related lipid transfer (START) domain containing 4	protein-coding	0	0.287129
Merged-chr1-177856712-1	chr1	177856662	177856762	+	2.2	cIP2vsInput	Intergenic	L2|LINE|L2	-60203	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	"adenylosuccinate synthetase, non muscle"	protein-coding	0.01	0.455446
Merged-chr17-87687832-1	chr17	87687782	87687882	+	2.2	cIP2vsInput	"intron (NM_008628, intron 6 of 15)"	"intron (NM_008628, intron 6 of 15)"	15275	NM_008628	17685	Mm.4619	NM_008628	ENSMUSG00000024151	Msh2	AI788990	mutS homolog 2 (E. coli)	protein-coding	0.01	0.326733
Merged-chr10-89946233-1	chr10	89946183	89946283	+	2.2	cIP1vsInput	"intron (NM_001128086, intron 1 of 24)"	"intron (NM_001128086, intron 1 of 24)"	72724	NM_001128086	77531	Mm.440605	NM_001128086		Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding	0	0.356436
Merged-chr12-41721721-1	chr12	41721671	41721771	+	2.2	cIP2vsInput	"intron (NM_053122, intron 2 of 2)"	"intron (NM_053122, intron 2 of 2)"	92957	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding	0	0.306931
Merged-chr12-115997399-1	chr12	115997349	115997449	+	2.2	cIP2vsInput	Intergenic	Lx8|LINE|L1	-50325	NM_001004066	56220	Mm.254997	NM_001004066	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding	0.01	0.425743
Merged-chr2-57423486-1	chr2	57423436	57423536	+	2.2	cIP2vsInput	Intergenic	Lx2B|LINE|L1	185104	NM_010274	14571	Mm.3711	NM_001145820	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	"glycerol phosphate dehydrogenase 2, mitochondrial"	protein-coding	0	0.376238
Merged-chr6-67687232-1	chr6	67687182	67687282	+	2.2	cIP2vsInput	Intergenic	Intergenic	-121533	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo	0	0.277228
Merged-chr9-61672196-1	chr9	61672146	61672246	+	2.2	cIP2vsInput	Intergenic	(TATG)n|Simple_repeat|Simple_repeat	242314	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	"ribosomal protein, large, P1"	protein-coding	0.01	0.326733
Merged-chr8-101671793-1	chr8	101671743	101671843	+	2.2	cIP1vsInput	Intergenic	Intergenic	1113318	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0	0.316832
Merged-chr5-58408043-1	chr5	58407993	58408093	+	2.2	cIP2vsInput	Intergenic	Intergenic	44955	NR_046190	78163	Mm.243828	NR_046190		4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	miscRNA	0.01	0.29703
Merged-chr17-33009338-1	chr17	33009288	33009388	+	2.2	cIP2vsInput	Intergenic	Intergenic	16199	NM_001045559	240067	Mm.246667	NM_199020	ENSMUSG00000053390	Zfp952	BC057593|C920016K16Rik	zinc finger protein 952	protein-coding	0	0.356436
Merged-chr15-54509143-1	chr15	54509093	54509193	+	2.2	cIP2vsInput	Intergenic	Intergenic	-62223	NM_178920	105853	Mm.410994	NM_178920	ENSMUSG00000024479	Mal2	AI461653	"mal, T cell differentiation protein 2"	protein-coding	0	0.336634
Merged-chr10-17315937-1	chr10	17315887	17315987	+	2.2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-220155	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0	0.316832
Merged-chr14-88501096-1	chr14	88501046	88501146	+	2.2	cIP1vsInput	Intergenic	Intergenic	-29700	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0	0.326733
Merged-chr11-117521926-1	chr11	117521876	117521976	+	2.2	cIP1vsInput	Intergenic	Intergenic	-89321	NR_015489	78403	Mm.212543	NR_015489		2900041M22Rik	-	RIKEN cDNA 2900041M22 gene	miscRNA	0.02	0.465347
Merged-chr2-82522370-1	chr2	82522320	82522420	+	2.2	cIP2vsInput	Intergenic	Intergenic	468712	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0	0.237624
Merged-chr1-46747710-1	chr1	46747660	46747760	+	2.2	cIP2vsInput	Intergenic	Intergenic	105799	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.316832
Merged-chr13-80209240-1	chr13	80209190	80209290	+	2.2	cIP2vsInput	Intergenic	Intergenic	-674182	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0	0.336634
Merged-chr17-66235409-1	chr17	66235359	66235459	+	2.2	cIP2vsInput	Intergenic	Intergenic	111889	NM_001003919	320209	Mm.259605	NM_001003919	ENSMUSG00000035842	Ddx11	4732462I11Rik|CHL1|CHLR1|KRG2|essa15a	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	protein-coding	0.07	0.594059
Merged-chr1-68423661-1	chr1	68423611	68423711	+	2.2	cIP2vsInput	"intron (NM_010154, intron 3 of 26)"	"intron (NM_010154, intron 3 of 26)"	684398	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0	0.277228
Merged-chr5-32554970-1	chr5	32554920	32555020	+	2.2	cIP2vsInput	Intergenic	MLT1A1|LTR|ERVL-MaLR	-56201	NM_001205133	22612	Mm.4558	NM_001205132	ENSMUSG00000014932	Yes1	Yes|p61-Yes	Yamaguchi sarcoma viral (v-yes) oncogene homolog 1	protein-coding	0.01	0.366337
Merged-chr2-26104898-1	chr2	26104848	26104948	+	2.2	cIP1vsInput	"intron (NM_026495, intron 1 of 5)"	"intron (NM_026495, intron 1 of 5)"	-12502	NM_001037098	67991	Mm.131074	NM_001037098	ENSMUSG00000026932	Nacc2	0610020I02Rik|AI448087|Btbd14a|C030048H19Rik	"nucleus accumbens associated 2, BEN and BTB (POZ) domain containing"	protein-coding	0	0.277228
Merged-chr12-30657253-1	chr12	30657203	30657303	+	2.2	cIP1vsInput	Intergenic	Intergenic	72810	NM_172049	211986	Mm.34035	NM_172049	ENSMUSG00000043061	Tmem18	BC024093	transmembrane protein 18	protein-coding	0	0.326733
Merged-chr10-125359847-1	chr10	125359797	125359897	+	2.2	cIP1vsInput	Intergenic	Intergenic	-31312	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	"solute carrier family 16 (monocarboxylic acid transporters), member 7"	protein-coding	0.01	0.405941
Merged-chr6-134409760-1	chr6	134409710	134409810	+	2.2	cIP2vsInput	"intron (NM_025778, intron 2 of 6)"	L1M2|LINE|L1	13431	NM_025778	66813	Mm.474472	NM_025778	ENSMUSG00000030200	Bcl2l14	4930452K23Rik|4933405K19Rik|9030625M01Rik|AI429211|Bclg	BCL2-like 14 (apoptosis facilitator)	protein-coding	0.01	0.326733
Merged-chr1-63583510-1	chr1	63583460	63583560	+	2.2	cIP2vsInput	"intron (NM_011780, intron 24 of 25)"	"intron (NM_011780, intron 24 of 25)"	103417	NM_001081658	241073	Mm.297680	NM_001081658	ENSMUSG00000069085	Dytn	Gm215	dystrotelin	protein-coding	0.01	0.376238
Merged-chr7-129844251-1	chr7	129844201	129844301	+	2.2	cIP1vsInput	Intergenic	HAL1|LINE|L1	-117914	NR_046077	100043150	Mm.334264	NR_046077		Gm4265	-	predicted gene 4265	miscRNA	0.02	0.366337
Merged-chr9-43284480-1	chr9	43284430	43284530	+	2.2	cIP2vsInput	Intergenic	Intergenic	24601	NM_001243261	235302	Mm.135745	NM_001243261	ENSMUSG00000095385	D630033O11Rik	Gm588	RIKEN cDNA D630033O11 gene	protein-coding	0.02	0.594059
Merged-chr16-78197576-2	chr16	78197499	78197654	+	2.2	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	57878	NR_045698	100503619	Mm.387531	NR_045698		E330011O21Rik	-	RIKEN cDNA E330011O21 gene	miscRNA	0.012903	0.358974
Merged-chr13-102056880-1	chr13	102056830	102056930	+	2.2	cIP2vsInput	Intergenic	Intergenic	-288663	NM_001077495	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	AA414921|C530050K14|PI3K|p50alpha|p55alpha|p85alpha	"phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)"	protein-coding	0	0.326733
Merged-chr2-133680497-1	chr2	133680447	133680547	+	2.2	cIP2vsInput	Intergenic	Intergenic	128338	NM_007553	12156	Mm.103205	NM_007553		Bmp2	AI467020|Bmp2a	bone morphogenetic protein 2	protein-coding	0	0.346535
Merged-chr5-44032973-1	chr5	44032923	44033023	+	2.2	cIP2vsInput	"exon (NM_008935, exon 10 of 27)"	"exon (NM_008935, exon 10 of 27)"	-51174	NM_001271616	14181	Mm.46053	NM_001271616	ENSMUSG00000048373	Fgfbp1	FGF-BP|FGF-BP1|FGFBP-1	fibroblast growth factor binding protein 1	protein-coding	0.02	0.336634
Merged-chr12-101582512-1	chr12	101582462	101582562	+	2.2	cIP2vsInput	"intron (NM_173023, intron 18 of 26)"	Lx5|LINE|L1	129061	NM_028924	74413	Mm.390521	NM_001082976	ENSMUSG00000021187	Tc2n	4933406D09Rik|Mtac2d1|Tac2-N	"tandem C2 domains, nuclear"	protein-coding	0	0.336634
Merged-chr5-40713401-1	chr5	40713351	40713451	+	2.2	cIP1vsInput	Intergenic	Intergenic	994754	NM_027295	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	"RAB28, member RAS oncogene family"	protein-coding	0.01	0.326733
Merged-chr16-88950912-1	chr16	88950862	88950962	+	2.2	cIP2vsInput	Intergenic	Intergenic	11961	NM_183296	71369	Mm.251757	NM_183296		Krtap16-3	5430404J20Rik|Krtap16-10	keratin associated protein 16-3	protein-coding	0	0.257426
Merged-chr4-54255113-1	chr4	54255063	54255163	+	2.2	cIP2vsInput	Intergenic	Intergenic	429068	NM_028053	52076	Mm.27184	NM_028053	ENSMUSG00000028420	Tmem38b	1600017F22Rik|AA437809|AV051057|D4Ertd89e|TRIC-B|mg33b	transmembrane protein 38B	protein-coding	0.01	0.326733
Merged-chr7-99793107-1	chr7	99793057	99793157	+	2.2	cIP1vsInput	Intergenic	B1_Mur1|SINE|Alu	25943	NM_146356	258353	Mm.377450	NM_146356	ENSMUSG00000073997	Olfr521	MOR101-2	olfactory receptor 521	protein-coding	0	0.405941
Merged-chr10-48734627-1	chr10	48734577	48734677	+	2.2	cIP2vsInput	Intergenic	Lx2A1|LINE|L1	361216	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	"proteasome (prosome, macropain) subunit, alpha type 6 pseudogene"	pseudo	0	0.287129
Merged-chr6-64650309-1	chr6	64650259	64650359	+	2.2	cIP1vsInput	"intron (NM_008167, intron 14 of 15)"	"intron (NM_008167, intron 14 of 15)"	-78837	NM_007500	11921	Mm.57229	NM_007500	ENSMUSG00000073043	Atoh1	Hath1|MATH-1|Math1|bHLHa14	atonal homolog 1 (Drosophila)	protein-coding	0.02	0.29703
Merged-chr3-133397614-1	chr3	133397564	133397664	+	2.2	cIP2vsInput	Intergenic	Intergenic	87498	NM_146141	74776	Mm.210305	NM_146141	ENSMUSG00000028013	Ppa2	1110013G13Rik|Sid6306	pyrophosphatase (inorganic) 2	protein-coding	0	0.306931
Merged-chr2-98474673-1	chr2	98474623	98474723	+	2.2	cIP2vsInput	Intergenic	Intergenic	1006999	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.336634
Merged-chr3-153644723-1	chr3	153644673	153644773	+	2.2	cIP2vsInput	"intron (NM_011372, intron 1 of 4)"	"intron (NM_011372, intron 1 of 4)"	80410	NM_011372	20447	Mm.440929	NM_011372		St6galnac3	Siat7c	"ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3"	protein-coding	0.01	0.415842
Merged-chr7-92630829-2	chr7	92630766	92630893	+	2.2	cIP1vsInput|cIP2vsInput	"intron (NM_028665, intron 2 of 11)"	L1ME3C|LINE|L1	6313	NM_028665	73845	Mm.73248	NM_028665	ENSMUSG00000041343	Ankrd42	4931426M20|4933417L02Rik|Ikbn	ankyrin repeat domain 42	protein-coding	0.007874	0.320312
Merged-chr5-108489972-1	chr5	108489922	108490022	+	2.2	cIP2vsInput	"intron (NM_172716, intron 8 of 10)"	MTD|LTR|ERVL-MaLR	28640	NM_172716	69587	Mm.486543	NM_172716		Pcgf3	2310035N15Rik|AI662857|D630042K08Rik|DONG1|E430039C14|RNF3A|Rnf3	polycomb group ring finger 3	protein-coding	0	0.326733
Merged-chr16-46949584-1	chr16	46949534	46949634	+	2.2	cIP2vsInput	Intergenic	Lx9|LINE|L1	-452617	NM_021497	58998	Mm.328072	NM_021495	ENSMUSG00000022656	Pvrl3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113	poliovirus receptor-related 3	protein-coding	0	0.39604
Merged-chr2-118884244-1	chr2	118884194	118884294	+	2.2	cIP2vsInput	Intergenic	Intergenic	-17371	NM_001045523	228536	Mm.330487	NM_001045523	ENSMUSG00000040007	Bahd1	AL022997|AW541238|Gm117|mKIAA0945	bromo adjacent homology domain containing 1	protein-coding	0.01	0.306931
Merged-chr8-117225379-1	chr8	117225329	117225429	+	2.2	cIP2vsInput	Intergenic	RMER5|LTR|ERV1	-31640	NM_001163262	74440	Mm.233181	NM_001163262	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding	0	0.356436
Merged-chr5-47121335-1	chr5	47121285	47121385	+	2.2	cIP2vsInput	Intergenic	RMER5|LTR|ERV1	-861820	NM_178804	20563	Mm.289739	NM_178804		Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|mKIAA4141	slit homolog 2 (Drosophila)	protein-coding	0	0.326733
Merged-chr2-146990343-1	chr2	146990293	146990393	+	2.2	cIP1vsInput	Intergenic	Intergenic	-22717	NM_011917	24128	Mm.3065	NM_011917	ENSMUSG00000027433	Xrn2	-	5'-3' exoribonuclease 2	protein-coding	0	0.405941
Merged-chr7-13956558-1	chr7	13956508	13956608	+	2.2	cIP1vsInput	"intron (NM_001101534, intron 3 of 5)"	Lx8|LINE|L1	33030	NM_001101534	434121	Mm.482762	NM_001101534	ENSMUSG00000074377	Sult2a4	EG434121|Gm5584	"sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 4"	protein-coding	0.01	0.306931
Merged-chr7-97926929-1	chr7	97926879	97926979	+	2.2	cIP2vsInput	"intron (NM_177696, intron 1 of 17)"	L1_Mur3|LINE|L1	6971	NM_177696	233537	Mm.375772	NM_177696	ENSMUSG00000035582	Gdpd4	4921513O04	glycerophosphodiester phosphodiesterase domain containing 4	protein-coding	0	0.376238
Merged-chr9-33858508-1	chr9	33858458	33858558	+	2.2	cIP2vsInput	Intergenic	L2a|LINE|L2	-183863	NR_040744	77119	Mm.367930	NR_040744		7630403G23Rik	-	RIKEN cDNA 7630403G23 gene	miscRNA	0	0.405941
Merged-chr7-83163816-1	chr7	83163766	83163866	+	2.2	cIP1vsInput	Intergenic	ORR1C2|LTR|ERVL-MaLR	-192425	NR_045855	71285	Mm.76818	NR_045855		4933430H16Rik	-	RIKEN cDNA 4933430H16 gene	miscRNA	0.01	0.405941
Merged-chr18-9667473-1	chr18	9667423	9667523	+	2.2	cIP2vsInput	Intergenic	Intergenic	-40175	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding	0	0.356436
Merged-chr2-180925477-1	chr2	180925427	180925527	+	2.2	cIP1vsInput	Intergenic	Intergenic	-3546	NM_001163247	329581	Mm.187879	NM_001163247	ENSMUSG00000038840	Birc7	E130019N06|KIAP|Livin|ML-IAP	baculoviral IAP repeat-containing 7 (livin)	protein-coding	0.01	0.425743
Merged-chr16-31080707-1	chr16	31080657	31080757	+	2.2	cIP2vsInput	"intron (NM_198626, intron 1 of 3)"	CpG	725	NM_198626	268880	Mm.286693	NM_198626	ENSMUSG00000047434	AI480653	Xxylt1	expressed sequence AI480653	protein-coding	0.07	0.60396
Merged-chr9-89521497-1	chr9	89521447	89521547	+	2.2	cIP1vsInput	Intergenic	Intergenic	101489	NM_153509	209743	Mm.458520	NM_153509	ENSMUSG00000039313	AF529169	DD1|Kiaa1024	cDNA sequence AF529169	protein-coding	0.01	0.366337
Merged-chr12-29981857-1	chr12	29981807	29981907	+	2.2	cIP1vsInput	"intron (NM_181395, intron 4 of 22)"	"intron (NM_181395, intron 4 of 22)"	43821	NM_181395	69675	Mm.251774	NM_181395	ENSMUSG00000020674	Pxdn	2310075M15Rik|C85409|E330004E07|VPO1|mKIAA0230	peroxidasin homolog (Drosophila)	protein-coding	0.01	0.485149
Merged-chr15-64532010-1	chr15	64531960	64532060	+	2.2	cIP2vsInput	Intergenic	Intergenic	-149091	NM_010026	13196	Mm.277236	NM_001276461	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	"ArfGAP with SH3 domain, ankyrin repeat and PH domain1"	protein-coding	0	0.445545
Merged-chr14-123783092-1	chr14	123783042	123783142	+	2.2	cIP1vsInput	"intron (NM_145467, intron 2 of 10)"	"intron (NM_145467, intron 2 of 10)"	122952	NM_145467	223272	Mm.383176	NM_145467		Itgbl1	B930011D01Rik	"integrin, beta-like 1"	protein-coding	0	0.287129
Merged-chr15-57555416-1	chr15	57555366	57555466	+	2.2	cIP1vsInput	Intergenic	Lx7|LINE|L1	-77791	NM_172378	210463	Mm.26555	NM_172378	ENSMUSG00000022366	Slc22a22	oat-pg	"solute carrier family 22 (organic cation transporter), member 22"	protein-coding	0	0.267327
Merged-chr1-97525327-1	chr1	97525277	97525377	+	2.2	cIP2vsInput	Intergenic	Intergenic	136691	NM_133825	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	"DNA segment, Chr 1, ERATO Doi 622, expressed"	protein-coding	0	0.356436
Merged-chr6-79181204-1	chr6	79181154	79181254	+	2.2	cIP1vsInput	Intergenic	L1M2|LINE|L1	149162	NR_040301	100504701	Mm.400420	NR_040301		Gm20362	-	"predicted gene, 20362"	miscRNA	0.01	0.316832
Merged-chr3-12634975-1	chr3	12634925	12635025	+	2.2	cIP2vsInput	Intergenic	Intergenic	-790616	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0.01	0.326733
Merged-chr6-143697639-1	chr6	143697589	143697689	+	2.2	cIP2vsInput	Intergenic	Intergenic	-46351	NR_045732	73425	Mm.417844	NR_045732	ENSMUSG00000086887	1700060C16Rik	-	RIKEN cDNA 1700060C16 gene	miscRNA	0.02	0.366337
Merged-chr3-74354048-1	chr3	74353998	74354098	+	2.2	cIP2vsInput	Intergenic	Lx6|LINE|L1	-336771	NR_040450	100504692	Mm.394454	NR_040450		Gm20356	-	"predicted gene, 20356"	miscRNA	0	0.316832
Merged-chr6-131897545-1	chr6	131897495	131897595	+	2.2	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-207482	NM_207019	387346	Mm.377908	NM_207019	ENSMUSG00000063478	Tas2r114	T2R14|Tas2r14|mGR14|mt2r46	"taste receptor, type 2, member 114"	protein-coding	0.02	0.267327
Merged-chr10-20365930-1	chr10	20365880	20365980	+	2.2	cIP1vsInput	Intergenic	AT_rich|Low_complexity|Low_complexity	18111	NM_027930	71804	Mm.262151	NM_027930	ENSMUSG00000019992	Mtfr2	2610016C23Rik|4933412C16Rik|Dufd1|Fam54a	mitochondrial fission regulator 2	protein-coding	0	0.356436
Merged-chr10-45591178-1	chr10	45591128	45591228	+	2.2	cIP2vsInput	"intron (NM_172473, intron 4 of 23)"	"intron (NM_172473, intron 4 of 23)"	13349	NM_172473	209462	Mm.458633	NM_172473	ENSMUSG00000038822	Hace1	1700042J16Rik|A730034A22Rik|BC025474	"HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1"	protein-coding	0	0.306931
Merged-chr1-62395091-1	chr1	62395041	62395141	+	2.2	cIP1vsInput	"intron (NM_001081050, intron 18 of 22)"	"intron (NM_001081050, intron 18 of 22)"	-308226	NM_001077406	18187	Mm.266341	NM_001077403	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding	0.02	0.336634
Merged-chr12-42632433-1	chr12	42632383	42632483	+	2.2	cIP2vsInput	Intergenic	Intergenic	1003669	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding	0.01	0.39604
Merged-chr3-59428347-1	chr3	59428297	59428397	+	2.2	cIP1vsInput	Intergenic	Intergenic	-84091	NM_001162884	242050	Mm.444186	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	"immunoglobulin superfamily, member 10"	protein-coding	0.01	0.356436
Merged-chr3-78919650-1	chr3	78919600	78919700	+	2.2	cIP2vsInput	Intergenic	Intergenic	226225	NM_001099624	76089	Mm.462396	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding	0.03	0.455446
Merged-chr14-81906468-1	chr14	81906418	81906518	+	2.2	cIP1vsInput	Intergenic	MERVL_2A-int|LTR|ERVL	1906166	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.356436
Merged-chr18-70302652-1	chr18	70302602	70302702	+	2.2	cIP1vsInput	Intergenic	Intergenic	-58068	NM_029346	75577	Mm.58214	NM_029346	ENSMUSG00000024512	Dynap	2310002L13Rik	dynactin associated protein	protein-coding	0.01	0.326733
Merged-chr11-37760725-1	chr11	37760675	37760775	+	2.2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	759320	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0	0.29703
Merged-chr15-49655216-1	chr15	49655166	49655266	+	2.2	cIP1vsInput	Intergenic	Intergenic	-863227	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0	0.386139
Merged-chr14-53356150-1	chr14	53356100	53356200	+	2.2	cIP2vsInput	Intergenic	Intergenic	-309790	NM_001205242	100568452	Mm.486072	NM_001205242		A430107P09Rik	Va10	RIKEN cDNA A430107P09 gene	protein-coding	0	0.29703
Merged-chr1-171793818-1	chr1	171793768	171793868	+	2.2	cIP1vsInput	"intron (NM_013730, intron 5 of 6)"	L1ME3B|LINE|L1	26686	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding	0.01	0.316832
Merged-chr19-13747800-1	chr19	13747750	13747850	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1308	NM_146990	258992	Mm.391191	NM_146990	ENSMUSG00000050865	Olfr1494	MOR266-1	olfactory receptor 1494	protein-coding	0.01	0.267327
Merged-chr15-56806941-1	chr15	56806891	56806991	+	2.2	cIP2vsInput	Intergenic	L1MA6|LINE|L1	-112395	NM_008216	15117	Mm.5148	NM_008216	ENSMUSG00000022367	Has2	-	hyaluronan synthase 2	protein-coding	0	0.425743
Merged-chr15-11672573-1	chr15	11672523	11672623	+	2.2	cIP2vsInput	Intergenic	Intergenic	233101	NM_008728	18162	Mm.25259	NM_001039181	ENSMUSG00000022206	Npr3	B430320C24Rik|C81222|NPR-C|lgj|stri	natriuretic peptide receptor 3	protein-coding	0.01	0.346535
Merged-chr7-57109640-1	chr7	57109590	57109690	+	2.2	cIP1vsInput	"intron (NM_008074, intron 3 of 9)"	"intron (NM_008074, intron 3 of 9)"	277231	NM_008074	14407	Mm.434343	NM_008074		Gabrg3	B230362M20Rik|Gabrg-3	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 3"	protein-coding	0	0.326733
Merged-chr5-64727464-1	chr5	64727414	64727514	+	2.2	cIP2vsInput	Intergenic	Intergenic	-76059	NM_008453	16599	Mm.439720	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding	0	0.306931
Merged-chr15-96499537-1	chr15	96499487	96499587	+	2.2	cIP1vsInput	Intergenic	RMER19A|LTR|ERVK	-38694	NM_028148	72193	Mm.472183	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding	0.01	0.39604
Merged-chr6-68728713-1	chr6	68728663	68728763	+	2.2	cIP2vsInput	Intergenic	Intergenic	598461	NR_004434	19783		NR_004434		Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	miscRNA	0	0.306931
Merged-chr1-20003941-1	chr1	20003891	20003991	+	2.2	cIP2vsInput	Intergenic	Intergenic	-352513	NR_045734	75028	Mm.417820	NR_045734		4930486I03Rik	-	RIKEN cDNA 4930486I03 gene	miscRNA	0.01	0.346535
Merged-chr6-124149714-1	chr6	124149664	124149764	+	2.2	cIP2vsInput	Intergenic	L1MCa|LINE|L1	82070	NM_001104642	232367	Mm.469872	NM_001104642	ENSMUSG00000072778	Vmn2r27	EG232367	"vomeronasal 2, receptor27"	protein-coding	0.01	0.326733
Merged-chr2-3246777-1	chr2	3246727	3246827	+	2.2	cIP2vsInput	Intergenic	Intergenic	-37511	NM_008708	18108	Mm.392918	NM_008708	ENSMUSG00000026643	Nmt2	A930001K02Rik|AI605445|AU044698|hNMT-2	N-myristoyltransferase 2	protein-coding	0	0.346535
Merged-chr3-13912999-1	chr3	13912949	13913049	+	2.2	cIP2vsInput	"intron (NM_178631, intron 3 of 9)"	"intron (NM_178631, intron 3 of 9)"	-33373	NM_001163329	76897	Mm.422625	NM_001163328	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0.01	0.366337
Merged-chr4-99128407-1	chr4	99128357	99128457	+	2.2	cIP1vsInput	Intergenic	Intergenic	-7492	NM_026082	67299	Mm.260623	NM_026082	ENSMUSG00000028556	Dock7	3110056M06Rik|Gm430|m|mKIAA1771	dedicator of cytokinesis 7	protein-coding	0	0.455446
Merged-chr12-64654165-1	chr12	64654115	64654215	+	2.2	cIP1vsInput	Intergenic	Intergenic	-179267	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.376238
Merged-chr19-50204880-1	chr19	50204830	50204930	+	2.2	cIP2vsInput	"intron (NM_001252501, intron 18 of 25)"	"intron (NM_001252501, intron 18 of 25)"	473766	NM_001252501	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0.02	0.356436
Merged-chr14-113544728-1	chr14	113544678	113544778	+	2.2	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-1287237	NR_045661	75822	Mm.410813	NR_045661		4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	miscRNA	0.01	0.326733
Merged-chr7-108348451-1	chr7	108348401	108348501	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1472	NM_146310	258307	Mm.377427	NM_146310	ENSMUSG00000093980	Olfr493	MOR204-35	olfactory receptor 493	protein-coding	0	0.405941
Merged-chr5-23225251-1	chr5	23225201	23225301	+	2.2	cIP2vsInput	"intron (NM_001081231, intron 3 of 3)"	"intron (NM_001081231, intron 3 of 3)"	209102	NR_040469	269630	Mm.436103	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	miscRNA	0.03	0.534653
Merged-chr2-43784860-1	chr2	43784810	43784910	+	2.2	cIP2vsInput	"intron (NM_001025377, intron 2 of 5)"	"intron (NM_001025377, intron 2 of 5)"	36033	NM_001025377	76117	Mm.217350	NM_001025377	ENSMUSG00000049744	Arhgap15	5830480G12Rik	Rho GTPase activating protein 15	protein-coding	0.02	0.306931
Merged-chr1-10898660-1	chr1	10898610	10898710	+	2.2	cIP1vsInput	Intergenic	MTE2b|LTR|ERVL-MaLR	-32786	NR_030645	100124448		NR_030645		Mir467e	Mirn467e	microRNA 467e	miscRNA	0	0.316832
Merged-chr15-14369648-1	chr15	14369598	14369698	+	2.2	cIP2vsInput	Intergenic	Intergenic	-1196009	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	K-cadherin|cad6|cadherin-6	cadherin 6	protein-coding	0	0.346535
Merged-chr3-106560848-1	chr3	106560798	106560898	+	2.2	cIP2vsInput	"intron (NM_001025582, intron 3 of 6)"	ORR1C1-int|LTR|ERVL-MaLR	13021	NM_001025582	67171	Mm.290488	NM_001025582	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding	0	0.346535
Merged-chr1-54898612-1	chr1	54898562	54898662	+	2.2	cIP2vsInput	"intron (NM_001081433, intron 1 of 27)"	"intron (NM_001081433, intron 1 of 27)"	27775	NM_001081433	329154	Mm.397910	NM_001081433	ENSMUSG00000052331	Ankrd44	4930444A19Rik|A130096K20|E130014H08Rik|PP6-ARS-B	ankyrin repeat domain 44	protein-coding	0	0.376238
Merged-chr16-66714374-1	chr16	66714324	66714424	+	2.2	cIP2vsInput	"intron (NM_001145977, intron 7 of 8)"	"intron (NM_001145977, intron 7 of 8)"	57256	NR_040512	75501	Mm.396161	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	miscRNA	0	0.346535
Merged-chr9-91654400-1	chr9	91654350	91654450	+	2.2	cIP1vsInput	Intergenic	Intergenic	285428	NM_009576	22774	Mm.434835	NM_009576		Zic4	-	zinc finger protein of the cerebellum 4	protein-coding	0	0.376238
Merged-chr10-14989044-1	chr10	14988994	14989094	+	2.2	cIP1vsInput	Intergenic	MYSERV16_I-int|LTR|ERVK	228755	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding	0	0.376238
Merged-chr7-87849299-1	chr7	87849249	87849349	+	2.2	cIP2vsInput	"intron (NM_001081414, intron 4 of 9)"	L1_Mur3|LINE|L1	265131	NM_001143834	108071	Mm.235018	NM_001033224	ENSMUSG00000049583	Grm5	6430542K11Rik|AI850523|Gprc1e|mGluR5|mGluR5b	"glutamate receptor, metabotropic 5"	protein-coding	0	0.277228
Merged-chr1-145085694-1	chr1	145085644	145085744	+	2.2	cIP2vsInput	Intergenic	RMER16B3|LTR|ERVK	-310273	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding	0	0.386139
Merged-chr7-94202333-1	chr7	94202283	94202383	+	2.2	cIP1vsInput	Intergenic	Lx9|LINE|L1	1122454	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0	0.316832
Merged-chr13-82532195-1	chr13	82532145	82532245	+	2.2	cIP1vsInput	Intergenic	Intergenic	748903	NM_007684	12626	Mm.12481	NM_007684	ENSMUSG00000021537	Cetn3	MmCEN3	centrin 3	protein-coding	0	0.326733
Merged-chr11-121702470-1	chr11	121702420	121702520	+	2.2	cIP2vsInput	promoter-TSS (NM_144797)	promoter-TSS (NM_144797)	43	NM_144797	210029	Mm.153566	NM_144797		Metrnl	9430048M07Rik|BC019776	"meteorin, glial cell differentiation regulator-like"	protein-coding	0.07	0.673267
Merged-chr3-42670436-1	chr3	42670386	42670486	+	2.2	cIP1vsInput	Intergenic	Intergenic	927818	NM_027271	73852	Mm.29006	NM_001099785	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	"DNA segment, Chr 3, ERATO Doi 751, expressed"	protein-coding	0.01	0.287129
Merged-chr9-37806116-1	chr9	37806066	37806166	+	2.2	cIP2vsInput	Intergenic	Intergenic	2227	NM_146883	258883	Mm.377734	NM_146883	ENSMUSG00000066750	Olfr876	MOR161-1	olfactory receptor 876	protein-coding	0	0.346535
Merged-chr12-82066709-1	chr12	82066659	82066759	+	2.2	cIP2vsInput	Intergenic	Intergenic	-103307	NM_001167983	217692	Mm.261333	NM_001167983	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding	0.01	0.534653
Merged-chr2-81378311-1	chr2	81378261	81378361	+	2.2	cIP2vsInput	Intergenic	L1ME1|LINE|L1	-675347	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0	0.316832
Merged-chr3-4993647-1	chr3	4993597	4993697	+	2.2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	194939	NR_045272	100503859	Mm.75172	NR_045272		1110015O18Rik	-	RIKEN cDNA 1110015O18 gene	miscRNA	0	0.316832
Merged-chr13-20292615-1	chr13	20292565	20292665	+	2.2	cIP2vsInput	"intron (NM_080288, intron 13 of 21)"	"intron (NM_080288, intron 13 of 21)"	-180375	NR_038122	140580	Mm.342392	NR_038122		Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding	0.01	0.514851
Merged-chr5-19398198-1	chr5	19398148	19398248	+	2.2	cIP2vsInput	"intron (NM_001170746, intron 1 of 22)"	"intron (NM_001170746, intron 1 of 22)"	171152	NM_001170746	50791	Mm.441283	NM_001170745	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	"membrane associated guanylate kinase, WW and PDZ domain containing 2"	protein-coding	0.01	0.376238
Merged-chr14-118551848-1	chr14	118551798	118551898	+	2.2	cIP2vsInput	"intron (NM_001033336, intron 20 of 30)"	"intron (NM_001033336, intron 20 of 30)"	125083	NM_001163675	239273	Mm.40537	NM_001033336	ENSMUSG00000032849	Abcc4	D630049P08Rik|MOATB|MRP4	"ATP-binding cassette, sub-family C (CFTR/MRP), member 4"	protein-coding	0.08	0.584158
Merged-chr1-91366345-1	chr1	91366295	91366395	+	2.2	cIP2vsInput	promoter-TSS (NM_173395)	promoter-TSS (NM_173395)	-85	NM_173395	227358	Mm.389157	NM_173395	ENSMUSG00000047443	Fam132b	4832406C22|myonectin	"family with sequence similarity 132, member B"	protein-coding	0.12	0.752475
Merged-chr4-103913500-1	chr4	103913450	103913550	+	2.2	cIP1vsInput	Intergenic	Intergenic	-454060	NM_010014	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding	0.02	0.356436
Merged-chr5-96043790-1	chr5	96043740	96043840	+	2.2	cIP2vsInput	Intergenic	Intergenic	86851	NM_018866	55985	Mm.10116	NM_018866	ENSMUSG00000023078	Cxcl13	4631412M08Rik|ANGIE2|Angie|BCA-1|BLC|BLR1L|Scyb13	chemokine (C-X-C motif) ligand 13	protein-coding	0	0.346535
Merged-chr1-21706022-1	chr1	21705972	21706072	+	2.2	cIP2vsInput	"intron (NM_023872, intron 1 of 13)"	"intron (NM_023872, intron 1 of 13)"	255920	NM_001160139	226922	Mm.403737	NM_001160139	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	"potassium voltage-gated channel, subfamily Q, member 5"	protein-coding	0.02	0.336634
Merged-chr9-12312036-1	chr9	12311986	12312086	+	2.2	cIP2vsInput	Intergenic	Lx2|LINE|L1	793819	NR_040755	78219	Mm.414868	NR_040755		4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	miscRNA	0	0.386139
Merged-chr10-15580862-1	chr10	15580812	15580912	+	2.2	cIP2vsInput	Intergenic	Lx9|LINE|L1	820573	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding	0	0.386139
Merged-chr18-45505210-1	chr18	45505160	45505260	+	2.2	cIP1vsInput	Intergenic	Intergenic	-54944	NM_080465	140492	Mm.458654	NM_080465		Kcnn2	KCa2.2|SK2|SKCA2|fri	"potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2"	protein-coding	0.01	0.336634
Merged-chr7-24316406-2	chr7	24316325	24316488	+	2.2	cIP1vsInput|cIP2vsInput	"intron (NM_009568, intron 1 of 4)"	"intron (NM_009568, intron 1 of 4)"	260	NM_009568	22756	Mm.487703	NM_001199321	ENSMUSG00000074282	Zfp94	-	zinc finger protein 94	protein-coding	0.055215	0.621951
Merged-chr5-115107652-1	chr5	115107602	115107702	+	2.2	cIP2vsInput	"intron (NM_001271590, intron 1 of 1)"	"intron (NM_001271590, intron 1 of 1)"	310	NM_001271591	100502825	Mm.361657	XM_003085347		Gm13826	OTTMUSG00000014624	predicted gene 13826	protein-coding	0	0.524752
Merged-chr8-18988928-1	chr8	18988878	18988978	+	2.2	cIP2vsInput	"intron (NM_181683, intron 1 of 1)"	"intron (NM_181683, intron 1 of 1)"	2127	NM_181683	353320	Mm.270483	NM_181683	ENSMUSG00000053695	Defb37	BD-37	defensin beta 37	protein-coding	0	0.326733
Merged-chr1-116176371-1	chr1	116176321	116176421	+	2.2	cIP1vsInput	"intron (NM_001077425, intron 8 of 23)"	L1_Mur2|LINE|L1	491234	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0	0.326733
Merged-chr2-28744248-1	chr2	28744198	28744298	+	2.2	cIP2vsInput	"intron (NM_001033874, intron 10 of 12)"	MLT1D|LTR|ERVL-MaLR	10970	NR_037271	100526498		NR_037271		Mir3088	mmu-mir-3088	microRNA 3088	miscRNA	0.01	0.524752
Merged-chr15-60416970-1	chr15	60416920	60417020	+	2.2	cIP1vsInput	Intergenic	Lx7|LINE|L1	-400352	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding	0	0.306931
Merged-chr17-22300216-1	chr17	22300166	22300266	+	2.2	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	61184	NM_176962	319615	Mm.442162	NM_176962	ENSMUSG00000033972	Zfp944	6330416L07Rik	zinc finger protein 944	protein-coding	0	0.346535
Merged-chr6-15597590-1	chr6	15597540	15597640	+	2.2	cIP1vsInput	Intergenic	Intergenic	-123071	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding	0.01	0.346535
Merged-chr6-107655837-1	chr6	107655787	107655887	+	2.2	cIP1vsInput	Intergenic	Intergenic	126111	NM_008516	16979	Mm.488119	NM_008516	ENSMUSG00000034648	Lrrn1	2810047E21Rik|NLRR-1	"leucine rich repeat protein 1, neuronal"	protein-coding	0	0.376238
Merged-chrX-122613684-1	chrX	122613634	122613734	+	2.2	cIP2vsInput	Intergenic	MurERV4_19-int|LTR|ERVK	-216299	NM_138742	54561	Mm.490573	NM_138742	ENSMUSG00000055733	Nap1l3	MB20	nucleosome assembly protein 1-like 3	protein-coding	0	0.306931
Merged-chr17-75704575-1	chr17	75704525	75704625	+	2.2	cIP2vsInput	Intergenic	Intergenic	-152629	NM_133747	72722		NM_133747	ENSMUSG00000002017	Fam98a	2810405J04Rik|AL024114	"family with sequence similarity 98, member A"	protein-coding	0	0.306931
Merged-chr6-36171050-1	chr6	36171000	36171100	+	2.2	cIP2vsInput	Intergenic	Intergenic	-217034	NM_203491	243764	Mm.448632	NM_203491		Chrm2	AChR-M2|Chrm-2|M2	"cholinergic receptor, muscarinic 2, cardiac"	protein-coding	0	0.366337
Merged-chr10-46464311-1	chr10	46464261	46464361	+	2.2	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	219562	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0.02	0.346535
Merged-chr6-9871955-1	chr6	9871905	9872005	+	2.2	cIP2vsInput	Intergenic	Intergenic	921936	NM_008751	18231	Mm.46954	NM_008751		Nxph1	C130005L03Rik	neurexophilin 1	protein-coding	0	0.29703
Merged-chr9-12228881-1	chr9	12228831	12228931	+	2.2	cIP1vsInput	Intergenic	Intergenic	876974	NR_040755	78219	Mm.414868	NR_040755		4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	miscRNA	0.01	0.257426
Merged-chr6-146162256-1	chr6	146162206	146162306	+	2.2	cIP2vsInput	"intron (NM_010586, intron 51 of 55)"	"intron (NM_010586, intron 51 of 55)"	228109	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding	0.01	0.336634
Merged-chr14-90861263-1	chr14	90861213	90861313	+	2.2	cIP2vsInput	Intergenic	Lx|LINE|L1	734372	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0.01	0.336634
Merged-chr6-11334912-1	chr6	11334862	11334962	+	2.2	cIP2vsInput	Intergenic	Intergenic	-360534	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	miscRNA	0.01	0.316832
Merged-chr14-45571996-1	chr14	45571946	45572046	+	2.2	cIP1vsInput	Intergenic	HAL1b|LINE|L1	28286	NR_045809	67651	Mm.55930	NR_045809		4930527F14Rik	-	RIKEN cDNA 4930527F14 gene	miscRNA	0	0.306931
Merged-chr7-45814140-1	chr7	45814090	45814190	+	2.2	cIP2vsInput	"5' UTR (NM_011181, exon 1 of 12)"	"5' UTR (NM_011181, exon 1 of 12)"	176	NM_011181	19158	Mm.272130	NM_001112701	ENSMUSG00000003269	Cyth2	ARNO|CLM2|Pscd2	cytohesin 2	protein-coding	0.16	0.782178
Merged-chr1-99124784-1	chr1	99124734	99124834	+	2.2	cIP2vsInput	Intergenic	Intergenic	-647981	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding	0	0.356436
Merged-chr13-36822764-1	chr13	36822714	36822814	+	2.2	cIP1vsInput	Intergenic	Intergenic	-88287	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding	0	0.277228
Merged-chr4-105150036-1	chr4	105149986	105150086	+	2.2	cIP2vsInput	Intergenic	L1M5|LINE|L1	-7311	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Ppap2b	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b	phosphatidic acid phosphatase type 2B	protein-coding	0	0.336634
Merged-chr4-68809902-1	chr4	68809852	68809952	+	2.2	cIP1vsInput	"intron (NM_019967, intron 5 of 7)"	"intron (NM_019967, intron 5 of 7)"	144495	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Dbc1	BRINP|Brinp1|Dbccr1|Fam5a	deleted in bladder cancer 1 (human)	protein-coding	0	0.405941
Merged-chr8-111338189-1	chr8	111338139	111338239	+	2.2	cIP1vsInput	promoter-TSS (NM_029005)	promoter-TSS (NM_029005)	-286	NM_029005	74568	Mm.207971	NM_029005	ENSMUSG00000012519	Mlkl	9130019I15Rik	mixed lineage kinase domain-like	protein-coding	0.06	0.584158
Merged-chr16-28148210-1	chr16	28148160	28148260	+	2.2	cIP1vsInput	Intergenic	Intergenic	297865	NM_183064	14167	Mm.7996	NM_001276419	ENSMUSG00000022523	Fgf12	AV114868|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding	0	0.326733
Merged-chr4-90328643-1	chr4	90328593	90328693	+	2.2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	32671	NR_033610	619842	Mm.484218	NR_033610	ENSMUSG00000080756	Gm12633	OTTMUSG00000007790	zinc finger protein 352 pseudogene	pseudo	0	0.346535
Merged-chr16-65657507-1	chr16	65657457	65657557	+	2.2	cIP2vsInput	Intergenic	Intergenic	-94810	NM_026879	68942	Mm.432944	NM_026879	ENSMUSG00000004843	Chmp2b	1190006E07Rik	charged multivesicular body protein 2B	protein-coding	0	0.277228
Merged-chr5-69052418-1	chr5	69052368	69052468	+	2.2	cIP2vsInput	Intergenic	Intergenic	289291	NM_175519	243043	Mm.234821	NM_175519	ENSMUSG00000037653	Kctd8	A730087N02Rik	potassium channel tetramerisation domain containing 8	protein-coding	0	0.306931
Merged-chr16-67648959-1	chr16	67648909	67649009	+	2.2	cIP2vsInput	Intergenic	Intergenic	-28051	NM_178721	239857	Mm.394300	NM_001145977	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0.01	0.356436
Merged-chr9-85309988-1	chr9	85309938	85310038	+	2.2	cIP1vsInput	Intergenic	Intergenic	17136	NM_001160378	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	D930050G01Rik	"family with sequence similarity 46, member A"	protein-coding	0	0.316832
Merged-chr1-121400532-1	chr1	121400482	121400582	+	2.2	cIP1vsInput	Intergenic	Intergenic	-30535	NM_029955	70829	Mm.25788	NM_027567	ENSMUSG00000026339	Ccdc93	4633402D15Rik|9230102M16Rik	coiled-coil domain containing 93	protein-coding	0.01	0.39604
Merged-chr5-151510884-1	chr5	151510834	151510934	+	2.2	cIP2vsInput	Intergenic	Lx9|LINE|L1	76040	NM_001102582	632671	Mm.469837	NM_001102582	ENSMUSG00000091794	Vmn2r18	EG632671|Vn2r18	"vomeronasal 2, receptor 18"	protein-coding	0	0.366337
Merged-chr8-20608670-1	chr8	20608620	20608720	+	2.2	cIP2vsInput	Intergenic	Intergenic	-6257	NM_001270553	100861668	Mm.445582	NM_001270553		Gm21119	-	"predicted gene, 21119"	protein-coding	0	0.257426
Merged-chr9-23294488-1	chr9	23294438	23294538	+	2.2	cIP1vsInput	"intron (NM_028472, intron 4 of 14)"	"intron (NM_028472, intron 4 of 14)"	71412	NM_028472	73230	Mm.335020	NM_028472	ENSMUSG00000031963	Bmper	3110056H04Rik|CV-2|Crim3|Cv2	BMP-binding endothelial regulator	protein-coding	0.01	0.356436
Merged-chr6-36354982-1	chr6	36354932	36355032	+	2.2	cIP2vsInput	"intron (NR_015589, intron 3 of 5)"	L1M5|LINE|L1	-33102	NM_203491	243764	Mm.448632	NM_203491		Chrm2	AChR-M2|Chrm-2|M2	"cholinergic receptor, muscarinic 2, cardiac"	protein-coding	0	0.29703
Merged-chr11-85438056-1	chr11	85438006	85438106	+	2.2	cIP2vsInput	"intron (NM_001166643, intron 7 of 23)"	"intron (NM_001166643, intron 7 of 23)"	84892	NM_001166643	192197	Mm.287663	NM_001166642	ENSMUSG00000059439	Bcas3	1500019F07Rik|2610028P08Rik|AU021018|BC028339|K20D4|rudhira	breast carcinoma amplified sequence 3	protein-coding	0	0.386139
Merged-chr5-134227646-1	chr5	134227596	134227696	+	2.2	cIP2vsInput	"intron (NM_010876, intron 2 of 10)"	ID_B1|SINE|B4	1979	NM_010876	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NOXO2|Ncf-1|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding	0.01	0.50495
Merged-chr4-51318967-1	chr4	51318917	51319017	+	2.2	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	102289	NM_001162865	74914	Mm.159368	NM_001162865	ENSMUSG00000039555	Cylc2	4930488P18Rik	"cylicin, basic protein of sperm head cytoskeleton 2"	protein-coding	0	0.287129
Merged-chr13-83235328-1	chr13	83235278	83235378	+	2.2	cIP1vsInput	Intergenic	MusHAL1|LINE|L1	-268706	NM_001170537	17260	Mm.487610	NM_001170537	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding	0	0.306931
Merged-chr18-83715410-1	chr18	83715360	83715460	+	2.2	cIP1vsInput	Intergenic	L1ME4a|LINE|L1	371152	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding	0.01	0.316832
Merged-chr1-117134309-1	chr1	117134259	117134359	+	2.2	cIP2vsInput	Intergenic	RMER4B|LTR|ERVK	1176823	NM_011650	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding	0	0.386139
Merged-chr2-145729090-1	chr2	145729040	145729140	+	2.2	cIP1vsInput	"intron (NR_033220, intron 2 of 3)"	"intron (NR_033220, intron 2 of 3)"	27895	NR_033220	408057	Mm.486711	NR_033220	ENSMUSG00000087594	BC039771	-	cDNA sequence BC039771	miscRNA	0	0.346535
Merged-chr3-36181450-1	chr3	36181400	36181500	+	2.2	cIP1vsInput	"intron (NM_198192, intron 4 of 5)"	"intron (NM_198192, intron 4 of 5)"	30370	NM_001101478	241944	Mm.260056	NM_001101478	ENSMUSG00000033883	D3Ertd254e	-	"DNA segment, Chr 3, ERATO Doi 254, expressed"	protein-coding	0	0.287129
Merged-chr13-84461046-1	chr13	84460996	84461096	+	2.2	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	238750	NM_175187	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding	0	0.326733
Merged-chr10-55724412-1	chr10	55724362	55724462	+	2.2	cIP1vsInput	Intergenic	Intergenic	-382505	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding	0	0.336634
Merged-chr9-16460564-1	chr9	16460514	16460614	+	2.2	cIP2vsInput	Intergenic	Intergenic	-82333	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT tumor suppressor homolog 3 (Drosophila)	protein-coding	0	0.247525
Merged-chr13-56442190-1	chr13	56442140	56442240	+	2.2	cIP1vsInput	"intron (NM_177809, intron 1 of 7)"	L1MB5|LINE|L1	3835	NM_177809	328258	Mm.482177	NM_177809		Slc25a48	AU042651|E230025K15	"solute carrier family 25, member 48"	protein-coding	0.02	0.405941
Merged-chr13-16536634-1	chr13	16536584	16536684	+	2.2	cIP1vsInput	Intergenic	Lx|LINE|L1	522159	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding	0	0.376238
Merged-chr4-84835295-1	chr4	84835245	84835345	+	2.2	cIP2vsInput	Intergenic	Intergenic	-49032	NM_175275	338349	Mm.440562	NM_175275	ENSMUSG00000038070	Cntln	AI448092|B430108F07Rik|D530005L17Rik	"centlein, centrosomal protein"	protein-coding	0.02	0.346535
Merged-chr7-91964967-1	chr7	91964917	91965017	+	2.2	cIP2vsInput	"intron (NM_011807, intron 7 of 22)"	"intron (NM_011807, intron 7 of 22)"	-97427	NM_001243046	23859	Mm.257035	NM_001243046		Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|PSD93	"discs, large homolog 2 (Drosophila)"	protein-coding	0.01	0.316832
Merged-chr10-115671375-1	chr10	115671325	115671425	+	2.2	cIP1vsInput	Intergenic	Intergenic	-83595	NM_010195	14160	Mm.42103	NM_010195	ENSMUSG00000020140	Lgr5	FEX|Gpr49	leucine rich repeat containing G protein coupled receptor 5	protein-coding	0	0.386139
Merged-chr13-9481304-1	chr13	9481254	9481354	+	2.2	cIP2vsInput	"intron (NM_001081426, intron 1 of 36)"	"intron (NM_001081426, intron 1 of 36)"	204779	NM_001081426	208440	Mm.217326	NM_172459	ENSMUSG00000048264	Dip2c	2900024P20Rik|9630044M06|mKIAA0934	DIP2 disco-interacting protein 2 homolog C (Drosophila)	protein-coding	0	0.306931
Merged-chr14-6485286-1	chr14	6485236	6485336	+	2.2	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-198036	NM_001270812	100861615	Mm.399319	NM_001270812	ENSMUSG00000079396	LOC100861615	-	alpha takusan-like	protein-coding	0	0.306931
Merged-chr3-93829814-1	chr3	93829764	93829864	+	2.2	cIP1vsInput	Intergenic	Intergenic	3794	NM_207271	399674	Mm.377923	NM_207271	ENSMUSG00000058005	Tdpoz3	-	TD and POZ domain containing 3	protein-coding	0	0.366337
Merged-chr1-148083032-1	chr1	148082982	148083082	+	2.2	cIP1vsInput	Intergenic	Intergenic	1585345	NM_001145807	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.287129
Merged-chrX-113767644-1	chrX	113767594	113767694	+	2.2	cIP2vsInput	"intron (NM_001142570, intron 7 of 11)"	ORR1E|LTR|ERVL-MaLR	469388	NM_001142570	93837	Mm.79760	NM_001142570	ENSMUSG00000025592	Dach2	9430028N04Rik	dachshund 2 (Drosophila)	protein-coding	0.01	0.29703
Merged-chr1-126317332-1	chr1	126317282	126317382	+	2.2	cIP1vsInput	"intron (NM_001081756, intron 5 of 16)"	"intron (NM_001081756, intron 5 of 16)"	175595	NM_172484	210356	Mm.377234	NM_001081756	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding	0.01	0.386139
Merged-chr6-135011714-1	chr6	135011664	135011764	+	2.2	cIP1vsInput	"exon (NM_026360, exon 1 of 12)"	"exon (NM_026360, exon 1 of 12)"	102	NM_026360	67755	Mm.166524	NM_026360	ENSMUSG00000030204	Ddx47	4930588A18Rik|C77285	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	protein-coding	0.02	0.465347
Merged-chr6-110032047-1	chr6	110031997	110032097	+	2.2	cIP2vsInput	Intergenic	Intergenic	-613551	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0.01	0.366337
Merged-chr1-33663227-1	chr1	33663177	33663277	+	2.2	cIP1vsInput	"intron (NM_008922, intron 4 of 13)"	"intron (NM_008922, intron 4 of 13)"	6531	NM_008922	19076	Mm.27705	NM_008922	ENSMUSG00000026134	Prim2	AI323589	"DNA primase, p58 subunit"	protein-coding	0	0.356436
Merged-chr12-98958676-1	chr12	98958626	98958726	+	2.2	cIP2vsInput	"intron (NM_029553, intron 7 of 13)"	"intron (NM_029553, intron 7 of 13)"	38064	NM_198311	76260	Mm.282660	NM_029553	ENSMUSG00000021013	Ttc8	0610012F22Rik|AV001447|BBS8	tetratricopeptide repeat domain 8	protein-coding	0	0.366337
Merged-chr11-31238670-1	chr11	31238620	31238720	+	2.2	cIP1vsInput	Intergenic	Lx9|LINE|L1	131391	NM_011491	20856	Mm.32506	NM_011491		Stc2	AW125853|Stc2l|mustc2	stanniocalcin 2	protein-coding	0	0.356436
Merged-chr13-17261196-1	chr13	17261146	17261246	+	2.2	cIP2vsInput	"intron (NM_138654, intron 11 of 13)"	Lx9|LINE|L1	433569	NM_138654	192136	Mm.364180	NM_138654		5033411D12Rik	D17907	RIKEN cDNA 5033411D12 gene	protein-coding	0	0.306931
Merged-chr4-18126555-1	chr4	18126505	18126605	+	2.2	cIP1vsInput	Intergenic	Intergenic	273073	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0	0.356436
Merged-chr14-35286521-1	chr14	35286471	35286571	+	2.2	cIP2vsInput	"intron (NM_008166, intron 5 of 15)"	MYSERV-int|LTR|ERVK	391912	NR_029774	723847		NR_029774		Mir346	Mirn346|mmu-mir-346	microRNA 346	miscRNA	0.01	0.366337
Merged-chr3-115002853-1	chr3	115002803	115002903	+	2.2	cIP1vsInput	"intron (NM_153458, intron 1 of 5)"	"intron (NM_153458, intron 1 of 5)"	-78112	NM_153157	229759	Mm.54183	NM_153157	ENSMUSG00000027965	Olfm3	B230206G02Rik	olfactomedin 3	protein-coding	0	0.326733
Merged-chr1-108087782-1	chr1	108087732	108087832	+	2.2	cIP2vsInput	Intergenic	Intergenic	170523	NR_102307	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0	0.326733
Merged-chr13-27171927-1	chr13	27171877	27171977	+	2.2	cIP1vsInput	Intergenic	Intergenic	15128	NM_172156	215029	Mm.461202	NM_172156	ENSMUSG00000062201	Prl3d3	PL-Ig|Plig	"prolactin family 3, subfamily d, member 3"	protein-coding	0	0.29703
Merged-chrX-169100092-1	chrX	169100042	169100142	+	2.2	cIP2vsInput	"intron (NM_178754, intron 1 of 12)"	"intron (NM_178754, intron 1 of 12)"	63463	NM_178754	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|C130038E13|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding	0.01	0.267327
Merged-chr9-67669161-1	chr9	67669111	67669211	+	2.2	cIP1vsInput	Intergenic	L1MA4|LINE|L1	-90276	NM_001081314	75697	Mm.105353	NM_001081314	ENSMUSG00000091956	C2cd4b	3300001A09Rik|Fam148b	C2 calcium-dependent domain containing 4B	protein-coding	0	0.405941
Merged-chr6-37582595-1	chr6	37582545	37582645	+	2.2	cIP1vsInput	Intergenic	ORR1A4-int|LTR|ERVL-MaLR	52422	NM_145364	208665	Mm.262635	NM_145364	ENSMUSG00000038641	Akr1d1	-	"aldo-keto reductase family 1, member D1"	protein-coding	0.01	0.346535
Merged-chr2-39331308-1	chr2	39331258	39331358	+	2.2	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-104970	NM_024209	67857	Mm.392662	NM_024209		Ppp6c	2310003C10Rik	"protein phosphatase 6, catalytic subunit"	protein-coding	0.01	0.346535
Merged-chr2-96327520-1	chr2	96327470	96327570	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1140154	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.316832
Merged-chr15-33143138-2	chr15	33143065	33143211	+	2.2	cIP1vsInput|cIP2vsInput	"intron (NM_176073, intron 1 of 7)"	ORR1F|LTR|ERVL-MaLR	60009	NM_176073	54381	Mm.158251	NM_018755	ENSMUSG00000039007	Cpq	1190003P12Rik|2610034C17Rik|Hls2|Lal-1|Pgcp	carboxypeptidase Q	protein-coding	0	0.340136
Merged-chr17-55264963-1	chr17	55264913	55265013	+	2.2	cIP2vsInput	Intergenic	Intergenic	-180754	NM_172829	240119	Mm.311687	NM_172829	ENSMUSG00000024172	St6gal2	C230064G14Rik|St6galII|mKIAA1877	"beta galactoside alpha 2,6 sialyltransferase 2"	protein-coding	0	0.306931
Merged-chr15-57206021-1	chr15	57205971	57206071	+	2.2	cIP2vsInput	Intergenic	Intergenic	271604	NM_172378	210463	Mm.26555	NM_172378	ENSMUSG00000022366	Slc22a22	oat-pg	"solute carrier family 22 (organic cation transporter), member 22"	protein-coding	0	0.326733
Merged-chr4-18728477-1	chr4	18728427	18728527	+	2.2	cIP2vsInput	Intergenic	Intergenic	-552373	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding	0	0.336634
Merged-chr1-39407484-1	chr1	39407434	39407534	+	2.2	cIP2vsInput	"intron (NM_018775, intron 2 of 19)"	"intron (NM_018775, intron 2 of 19)"	39633	NM_001252218	114641	Mm.443000	NM_001252218	ENSMUSG00000073702	Rpl31	-	ribosomal protein L31	protein-coding	0	0.316832
Merged-chr4-147437920-1	chr4	147437870	147437970	+	2.2	cIP2vsInput	"intron (NM_001039209, intron 1 of 2)"	Lx3_Mus|LINE|L1	-115357	NM_001014397	433804	Mm.332047	XM_003946328	ENSMUSG00000065999	Gm13154	OTTMUSG00000010673	predicted gene 13154	protein-coding	0	0.346535
Merged-chr15-34986925-1	chr15	34986875	34986975	+	2.2	cIP2vsInput	"intron (NM_019635, intron 8 of 10)"	Lx5c|LINE|L1	148876	NM_001271704	16539	Mm.487585	NM_001271704	ENSMUSG00000050963	Kcns2	E130006J24Rik|Kv9.2	"K+ voltage-gated channel, subfamily S, 2"	protein-coding	0	0.306931
Merged-chr6-65315755-1	chr6	65315705	65315805	+	2.2	cIP2vsInput	Intergenic	Intergenic	-65539	NM_175524	243407	Mm.389758	NM_175524	ENSMUSG00000029917	C130060K24Rik	-	RIKEN cDNA C130060K24 gene	protein-coding	0.02	0.415842
Merged-chr11-26753086-1	chr11	26753036	26753136	+	2.2	cIP1vsInput	Intergenic	Intergenic	-32022	NR_002890	654472	Mm.347777	NR_002890	ENSMUSG00000069939	Gm12070	OTTMUSG00000005300	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0.01	0.29703
Merged-chr19-40042237-1	chr19	40042187	40042287	+	2.2	cIP2vsInput	"intron (NM_206537, intron 7 of 8)"	L1_Mur2|LINE|L1	31576	NM_206537	404195	Mm.379575	NM_206537	ENSMUSG00000067225	Cyp2c54	EG404195	"cytochrome P450, family 2, subfamily c, polypeptide 54"	protein-coding	0	0.29703
Merged-chr3-11602419-1	chr3	11602369	11602469	+	2.2	cIP1vsInput	Intergenic	L1MC3|LINE|L1	241940	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.366337
Merged-chr2-127620296-1	chr2	127620246	127620346	+	2.2	cIP1vsInput	Intergenic	MT2B|LTR|ERVL	32870	NM_029963	77721	Mm.439980	NM_029963		Mrps5	1620401I16Rik|AI850294	mitochondrial ribosomal protein S5	protein-coding	0	0.39604
Merged-chr1-164524164-1	chr1	164524114	164524214	+	2.2	cIP2vsInput	Intergenic	Intergenic	-65809	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	"ATPase, Na+/K+ transporting, beta 1 polypeptide"	protein-coding	0	0.287129
Merged-chr3-42676018-1	chr3	42675968	42676068	+	2.2	cIP2vsInput	Intergenic	Intergenic	933400	NM_027271	73852	Mm.29006	NM_001099785	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	"DNA segment, Chr 3, ERATO Doi 751, expressed"	protein-coding	0	0.326733
Merged-chr1-183909841-1	chr1	183909791	183909891	+	2.2	cIP2vsInput	Intergenic	Intergenic	124157	NM_028516	73363	Mm.50115	NM_028516	ENSMUSG00000044854	1700056E22Rik	-	RIKEN cDNA 1700056E22 gene	protein-coding	0	0.346535
Merged-chr10-15580113-1	chr10	15580063	15580163	+	2.2	cIP2vsInput	Intergenic	L1M4|LINE|L1	819824	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding	0.01	0.346535
Merged-chr18-46920857-1	chr18	46920807	46920907	+	2.2	cIP2vsInput	promoter-TSS (NM_001033446)	promoter-TSS (NM_001033446)	-958	NM_001033446	381142	Mm.329423	NM_001033446	ENSMUSG00000073568	Arl14epl	Gm949	ADP-ribosylation factor-like 14 effector protein-like	protein-coding	0	0.356436
Merged-chr5-130853522-1	chr5	130853472	130853572	+	2.2	cIP2vsInput	Intergenic	Intergenic	404730	NM_021371	140904	Mm.320206	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8	calneuron 1	protein-coding	0.07	0.60396
Merged-chr10-53471472-1	chr10	53471422	53471522	+	2.2	cIP2vsInput	Intergenic	LTRIS4|LTR|ERV1	47517	NR_037973	100502868	Mm.297722	NR_037973		Gm20597	B230314j19	"predicted gene, 20597"	miscRNA	0	0.405941
Merged-chr16-85208583-1	chr16	85208533	85208633	+	2.2	cIP1vsInput	Intergenic	Intergenic	-34876	NM_001198823	11820	Mm.490986	NM_001198823	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding	0	0.29703
Merged-chr3-59666372-1	chr3	59666322	59666422	+	2.2	cIP1vsInput	Intergenic	Intergenic	-63414	NM_001101531	433597	Mm.297801	NM_001101531	ENSMUSG00000090527	Gm5538	-	predicted gene 5538	protein-coding	0	0.29703
Merged-chr1-142620479-1	chr1	142620429	142620529	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1020218	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0	0.267327
Merged-chr16-45692663-1	chr16	45692613	45692713	+	2.2	cIP2vsInput	"intron (NM_172455, intron 1 of 17)"	"intron (NM_172455, intron 1 of 17)"	995	NM_172455	208171	Mm.186306	NM_172455	ENSMUSG00000033177	Tmprss7	B230219I23Rik|Gm1748	transmembrane serine protease 7	protein-coding	0	0.336634
Merged-chr5-60717942-1	chr5	60717892	60717992	+	2.2	cIP2vsInput	Intergenic	Intergenic	-731940	NR_040682	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0	0.356436
Merged-chr11-10207903-1	chr11	10207853	10207953	+	2.2	cIP1vsInput	Intergenic	Lx3A|LINE|L1	-906113	NM_177033	319922	Mm.487612	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding	0	0.306931
Merged-chr19-30933875-1	chr19	30933825	30933925	+	2.2	cIP2vsInput	"intron (NM_001013833, intron 4 of 17)"	"intron (NM_001013833, intron 4 of 17)"	-2913	NR_033643	625995	Mm.490410	NR_033643		Gm6642	EG625995	ubiquitin-like 5 pseudogene	pseudo	0	0.356436
Merged-chr18-36902705-1	chr18	36902655	36902755	+	2.2	cIP1vsInput	Intergenic	Intergenic	-17600	NR_076393	627427		NR_076393		Gm6756	EG627427	3-phosphoglycerate dehydrogenase pseudogene	pseudo	0	0.326733
Merged-chr13-23271577-1	chr13	23271527	23271627	+	2.2	cIP1vsInput	Intergenic	L1M3|LINE|L1	-6773	NR_046038	74061	Mm.399501	NR_046038	ENSMUSG00000085122	4933404K08Rik	-	RIKEN cDNA 4933404K08 gene	miscRNA	0	0.346535
Merged-chr2-139161924-1	chr2	139161874	139161974	+	2.2	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-331996	NM_175467	228677	Mm.100450	NM_175467	ENSMUSG00000039092	Sptlc3	C130053K05Rik	"serine palmitoyltransferase, long chain base subunit 3"	protein-coding	0	0.277228
Merged-chr5-136083969-1	chr5	136083919	136084019	+	2.2	cIP2vsInput	promoter-TSS (NM_133914)	promoter-TSS (NM_133914)	53	NM_001039103	54153	Mm.290655	NM_001039103	ENSMUSG00000004952	Rasa4	AA793972|AW112107|BB079060|CAPRI|GAPL|mKIAA0538	RAS p21 protein activator 4	protein-coding	0.07	0.742574
Merged-chr1-165894100-1	chr1	165894050	165894150	+	2.2	cIP1vsInput	"intron (NM_198934, intron 12 of 16)"	"intron (NM_198934, intron 12 of 16)"	40848	NM_198933	18986	Mm.245261	NM_011137	ENSMUSG00000026565	Pou2f1	2810482H01Rik|NF-A1|Oct-1|Oct1|Otf-1|Otf1	"POU domain, class 2, transcription factor 1"	protein-coding	0	0.376238
Merged-chr9-80386852-1	chr9	80386802	80386902	+	2.2	cIP2vsInput	"intron (NM_022016, intron 8 of 16)"	"intron (NM_022016, intron 8 of 16)"	78586	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding	0.01	0.306931
Merged-chr4-69439777-1	chr4	69439727	69439827	+	2.2	cIP2vsInput	Intergenic	Lx4A|LINE|L1	-485380	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Dbc1	BRINP|Brinp1|Dbccr1|Fam5a	deleted in bladder cancer 1 (human)	protein-coding	0.01	0.336634
Merged-chr1-143473107-1	chr1	143473057	143473157	+	2.2	cIP2vsInput	Intergenic	Lx7|LINE|L1	-167590	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0	0.405941
Merged-chr14-89184021-1	chr14	89183971	89184071	+	2.2	cIP1vsInput	Intergenic	Intergenic	-712203	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0	0.336634
Merged-chr17-5026238-1	chr17	5026188	5026288	+	2.2	cIP1vsInput	"intron (NM_001085355, intron 1 of 19)"	"intron (NM_001085355, intron 1 of 19)"	31164	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding	0	0.346535
Merged-chr3-61060943-1	chr3	61060893	61060993	+	2.2	cIP2vsInput	Intergenic	Lx5c|LINE|L1	58148	NM_008772	18441	Mm.281452	NM_008772	ENSMUSG00000027765	P2ry1	P2Y1	"purinergic receptor P2Y, G-protein coupled 1"	protein-coding	0	0.316832
Merged-chr1-79474636-1	chr1	79474586	79474686	+	2.2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-34546	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding	0	0.277228
Merged-chr6-19274441-1	chr6	19274391	19274491	+	2.2	cIP1vsInput	Intergenic	Intergenic	408123	NM_001167757	75196	Mm.67665	NM_001167757	ENSMUSG00000029517	Ankrd7	4930532L20Rik|AV278427	ankyrin repeat domain 7	protein-coding	0	0.306931
Merged-chr4-71926208-1	chr4	71926158	71926258	+	2.2	cIP1vsInput	Intergenic	Lx5c|LINE|L1	274711	NM_011599	21885	Mm.399716	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg1|Tle4l	"transducin-like enhancer of split 1, homolog of Drosophila E(spl)"	protein-coding	0	0.287129
Merged-chr3-14063588-1	chr3	14063538	14063638	+	2.2	cIP1vsInput	"intron (NM_178631, intron 4 of 9)"	"intron (NM_178631, intron 4 of 9)"	117216	NM_001163330	76897	Mm.422625	NM_001163328	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0	0.405941
Merged-chr15-87624079-1	chr15	87624029	87624129	+	2.2	cIP2vsInput	"intron (NM_001252310, intron 1 of 3)"	CpG	-1151	NM_134096	106014	Mm.244319	NM_001252310	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	"family with sequence similarity 19, member A5"	protein-coding	0.07	0.693069
Merged-chr2-122393361-1	chr2	122393311	122393411	+	2.2	cIP2vsInput	Intergenic	Intergenic	-24443	NM_001013829	435684	Mm.458215	NM_001013829	ENSMUSG00000033256	Shf	-	Src homology 2 domain containing F	protein-coding	0	0.277228
Merged-chr9-80324283-1	chr9	80324233	80324333	+	2.2	cIP2vsInput	"intron (NM_022016, intron 14 of 16)"	"intron (NM_022016, intron 14 of 16)"	141155	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding	0	0.376238
Merged-chr14-11412509-1	chr14	11412459	11412559	+	2.2	cIP2vsInput	Intergenic	Lx2B|LINE|L1	-141044	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	"protein tyrosine phosphatase, receptor type, G"	protein-coding	0	0.336634
Merged-chr11-34845580-1	chr11	34845530	34845630	+	2.2	cIP2vsInput	Intergenic	Intergenic	-11939	NM_027411	70385	Mm.194368	NM_027411	ENSMUSG00000069910	Spdl1	1700018I02Rik|2600001J17Rik|2810049B11Rik|AA409762|Ccdc99	spindle apparatus coiled-coil protein 1	protein-coding	0.01	0.49505
Merged-chr3-106823578-1	chr3	106823528	106823628	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1021	NM_146489	258482	Mm.377527	NM_146489	ENSMUSG00000043529	Olfr266	MOR122-2	olfactory receptor 266	protein-coding	0	0.336634
Merged-chr5-69266962-1	chr5	69266912	69267012	+	2.2	cIP1vsInput	"intron (NM_175519, intron 1 of 1)"	"intron (NM_175519, intron 1 of 1)"	74747	NM_175519	243043	Mm.234821	NM_175519	ENSMUSG00000037653	Kctd8	A730087N02Rik	potassium channel tetramerisation domain containing 8	protein-coding	0	0.326733
Merged-chr6-87505627-1	chr6	87505577	87505677	+	2.2	cIP2vsInput	"intron (NM_001037727, intron 1 of 10)"	"intron (NM_001037727, intron 1 of 10)"	-9327	NM_175476	232201	Mm.119564	NM_001037727	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding	0	0.316832
Merged-chr2-24254821-1	chr2	24254771	24254871	+	2.2	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	-22133	NM_001146088	54450	Mm.29261	NM_001146087	ENSMUSG00000026983	Il1f5	AI413231|Fil1delta|IL36RN|Il-1h3|Il1hy1	"interleukin 1 family, member 5 (delta)"	protein-coding	0.01	0.29703
Merged-chr8-82893245-1	chr8	82893195	82893295	+	2.2	cIP1vsInput	"intron (NM_177378, intron 1 of 6)"	"intron (NM_177378, intron 1 of 6)"	29889	NM_177378	330812	Mm.66737	NM_177378	ENSMUSG00000047747	Rnf150	A630007N06Rik|C030044C12Rik|Greul5|mKIAA1214	ring finger protein 150	protein-coding	0.01	0.366337
Merged-chr14-94995946-1	chr14	94995896	94995996	+	2.2	cIP1vsInput	Intergenic	Intergenic	-885320	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.356436
Merged-chr4-105436861-1	chr4	105436811	105436911	+	2.2	cIP2vsInput	Intergenic	Intergenic	279514	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Ppap2b	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b	phosphatidic acid phosphatase type 2B	protein-coding	0.01	0.346535
Merged-chr3-86731964-1	chr3	86731914	86732014	+	2.2	cIP1vsInput	"intron (NM_001077687, intron 48 of 50)"	"intron (NM_001077687, intron 48 of 50)"	-183681	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding	0	0.326733
Merged-chr5-10143425-1	chr5	10143375	10143475	+	2.2	cIP1vsInput	Intergenic	Intergenic	-418073	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	"glutamate receptor, metabotropic 3"	protein-coding	0	0.326733
Merged-chr1-95507540-1	chr1	95507490	95507590	+	2.2	cIP2vsInput	Intergenic	Intergenic	160054	NM_009183	20452	Mm.306228	NM_001159745	ENSMUSG00000040710	St8sia4	PST|PST-1|ST8SiaIV|Siat8d	"ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4"	protein-coding	0	0.336634
Merged-chr3-79673794-1	chr3	79673744	79673844	+	2.2	cIP1vsInput	"intron (NM_212452, intron 5 of 17)"	CYRA11_Mm|Unknown|Y-chromosome	44715	NM_029482	75939	Mm.221520	NM_029482	ENSMUSG00000027811	4930579G24Rik	-	RIKEN cDNA 4930579G24 gene	protein-coding	0	0.336634
Merged-chr18-81928264-1	chr18	81928214	81928314	+	2.2	cIP1vsInput	Intergenic	Intergenic	63816	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	miscRNA	0.02	0.574257
Merged-chr17-59868480-1	chr17	59868430	59868530	+	2.2	cIP1vsInput	Intergenic	Intergenic	-855158	NM_026497	67993	Mm.36507	NM_026497		Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0.01	0.316832
Merged-chr9-28146383-1	chr9	28146333	28146433	+	2.2	cIP2vsInput	"intron (NM_177906, intron 1 of 7)"	"intron (NM_177906, intron 1 of 7)"	355114	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding	0	0.356436
Merged-chr2-78432450-1	chr2	78432400	78432500	+	2.2	cIP2vsInput	Intergenic	MLT1D|LTR|ERVL-MaLR	194903	NM_177843	329436	Mm.235448	NM_177843		Gm14461	A830093M07|OTTMUSG00000016703	predicted gene 14461	protein-coding	0	0.326733
Merged-chr1-102384418-1	chr1	102384368	102384468	+	2.2	cIP2vsInput	Intergenic	MMERVK9E_I-int|LTR|ERVK	1228650	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.306931
Merged-chr14-40076909-1	chr14	40076859	40076959	+	2.2	cIP1vsInput	Intergenic	Intergenic	421246	NR_045936	73591	Mm.65499	NR_045936		1700109I08Rik	-	RIKEN cDNA 1700109I08 gene	miscRNA	0.02	0.376238
Merged-chr6-75613645-1	chr6	75613595	75613695	+	2.2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-1629072	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0.01	0.346535
Merged-chr8-43586581-1	chr8	43586531	43586631	+	2.2	cIP2vsInput	Intergenic	Intergenic	-9874	NM_010085	13525	Mm.334510	NM_010085	ENSMUSG00000048516	Adam26a	Adam26|Dtgn4	a disintegrin and metallopeptidase domain 26A (testase 3)	protein-coding	0	0.356436
Merged-chrX-114701787-1	chrX	114701737	114701837	+	2.2	cIP1vsInput	Intergenic	Intergenic	-203225	NM_001276396	237009	Mm.302216	NM_207241	ENSMUSG00000050435	Ube2dnl1	Ube2dnl	ubiquitin-conjugating enzyme E2D N-terminal like 1	protein-coding	0	0.356436
Merged-chr8-82474066-1	chr8	82474016	82474116	+	2.2	cIP2vsInput	Intergenic	Intergenic	-71480	NM_008357	16168	Mm.490053	NM_001254747		Il15	AI503618|IL-15	interleukin 15	protein-coding	0	0.29703
Merged-chr14-87980452-1	chr14	87980402	87980502	+	2.2	cIP2vsInput	Intergenic	Intergenic	490944	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0	0.29703
Merged-chr11-40715420-1	chr11	40715370	40715470	+	2.2	cIP2vsInput	"intron (NM_013552, intron 8 of 17)"	"intron (NM_013552, intron 8 of 17)"	18017	NM_013552	15366	Mm.116997	NM_013552	ENSMUSG00000020330	Hmmr	AA386826|CD168|Rhamm	hyaluronan mediated motility receptor (RHAMM)	protein-coding	0	0.326733
Merged-chr15-35803412-1	chr15	35803362	35803462	+	2.2	cIP2vsInput	"intron (NM_177151, intron 39 of 61)"	Lx|LINE|L1	134834	NM_053071	12864	Mm.548	NM_053071	ENSMUSG00000014313	Cox6c	-	cytochrome c oxidase subunit VIc	protein-coding	0	0.366337
Merged-chrX-150577327-1	chrX	150577277	150577377	+	2.2	cIP2vsInput	"intron (NM_029943, intron 5 of 5)"	Lx7|LINE|L1	10822	NM_029943	77622	Mm.440275	NM_029943	ENSMUSG00000025269	Apex2	C430040P13Rik|ape2	apurinic/apyrimidinic endonuclease 2	protein-coding	0	0.316832
Merged-chr5-54387048-1	chr5	54386998	54387098	+	2.2	cIP2vsInput	Intergenic	Lx|LINE|L1	37056	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0	0.356436
Merged-chr1-137717700-1	chr1	137717650	137717750	+	2.2	cIP2vsInput	Intergenic	Intergenic	-248755	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mmu-mir-213	microRNA 181a-1	miscRNA	0.01	0.29703
Merged-chr10-42612909-1	chr10	42612859	42612959	+	2.2	cIP1vsInput	Intergenic	Intergenic	-29321	NM_152229	21907	Mm.287100	NM_152229	ENSMUSG00000019803	Nr2e1	Mtl1|Mtll|TLL|Tlx|XTLL|fierce|frc|tailless	"nuclear receptor subfamily 2, group E, member 1"	protein-coding	0	0.346535
Merged-chr8-35654555-1	chr8	35654505	35654605	+	2.2	cIP2vsInput	"intron (NM_001081279, intron 1 of 2)"	"intron (NM_001081279, intron 1 of 2)"	-65535	NR_040376	100504714	Mm.381744	NR_040376	ENSMUSG00000097357	Gm16793	-	"predicted gene, 16793"	miscRNA	0.02	0.485149
Merged-chr18-9170134-1	chr18	9170084	9170184	+	2.2	cIP2vsInput	Intergenic	ORR1B1-int|LTR|ERVL-MaLR	-42722	NM_008058	14370	Mm.184289	NM_008058	ENSMUSG00000036904	Fzd8	Fz8	frizzled homolog 8 (Drosophila)	protein-coding	0	0.405941
Merged-chr16-70889418-1	chr16	70889368	70889468	+	2.2	cIP2vsInput	Intergenic	Intergenic	-241658	NR_040561	70972	Mm.399391	NR_040561		4931420L22Rik	-	RIKEN cDNA 4931420L22 gene	miscRNA	0.01	0.287129
Merged-chr1-149311181-1	chr1	149311131	149311231	+	2.2	cIP2vsInput	Intergenic	Intergenic	650103	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0	0.326733
Merged-chr7-69347887-1	chr7	69347837	69347937	+	2.2	cIP2vsInput	Intergenic	Intergenic	-148207	NR_045940	73796	Mm.410832	NR_045940		4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	miscRNA	0.01	0.415842
Merged-chr3-10091100-1	chr3	10091050	10091150	+	2.2	cIP1vsInput	"intron (NR_045710, intron 1 of 1)"	"intron (NR_045710, intron 1 of 1)"	2823	NR_045710	100041480	Mm.455632	NR_045710	ENSMUSG00000049230	Gm9833	ENSMUSG00000049230	"myelin basic protein expression factor 2, repressor pseudogene"	pseudo	0.01	0.247525
Merged-chr1-40559155-1	chr1	40559105	40559205	+	2.2	cIP2vsInput	Intergenic	Intergenic	-21072	NM_177084	110895	Mm.108602	NM_177084	ENSMUSG00000026065	Slc9a4	AW990558|D730009J23Rik|NHE4	"solute carrier family 9 (sodium/hydrogen exchanger), member 4"	protein-coding	0	0.316832
Merged-chr2-111153584-1	chr2	111153534	111153634	+	2.2	cIP2vsInput	Intergenic	Intergenic	76016	NM_026248	67575	Mm.84331	NM_026248	ENSMUSG00000027157	4930430A15Rik	-	RIKEN cDNA 4930430A15 gene	protein-coding	0	0.267327
Merged-chr18-51603361-1	chr18	51603311	51603411	+	2.2	cIP2vsInput	Intergenic	Intergenic	485463	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding	0	0.306931
Merged-chr3-137759526-1	chr3	137759476	137759576	+	2.2	cIP1vsInput	Intergenic	MTC|LTR|ERVL-MaLR	-105073	NM_016750	51788	Mm.489602	NM_016750	ENSMUSG00000037894	H2afz	H2A.Z	"H2A histone family, member Z"	protein-coding	0	0.326733
Merged-chr5-85974692-1	chr5	85974642	85974742	+	2.2	cIP1vsInput	Intergenic	Intergenic	90891	NM_007683	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	Cenpc	centromere protein C1	protein-coding	0	0.306931
Merged-chr14-112843839-1	chr14	112843789	112843889	+	2.2	cIP2vsInput	Intergenic	Tigger19a|DNA|TcMar-Tigger	822409	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0	0.316832
Merged-chrX-83554765-1	chrX	83554715	83554815	+	2.2	cIP1vsInput	"intron (NM_007868, intron 7 of 78)"	Lx9|LINE|L1	-66841	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding	0	0.227723
Merged-chr14-71017887-1	chr14	71017837	71017937	+	2.2	cIP2vsInput	Intergenic	L1M5|LINE|L1	127757	NM_008115	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding	0.01	0.316832
Merged-chr12-32704410-1	chr12	32704360	32704460	+	2.2	cIP2vsInput	Intergenic	MTD|LTR|ERVL-MaLR	-115925	NM_021524	59027		NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding	0	0.336634
Merged-chr9-115391512-1	chr9	115391462	115391562	+	2.2	cIP1vsInput	Intergenic	Intergenic	55351	NR_040730	73856	Mm.399156	NR_040730		4930428G15Rik	-	RIKEN cDNA 4930428G15 gene	miscRNA	0	0.49505
Merged-chr13-46161852-1	chr13	46161802	46161902	+	2.2	cIP2vsInput	Intergenic	Intergenic	-111869	NM_001005422	380842	Mm.188108	NM_001005422	ENSMUSG00000063529	Stmnd1	Gm1574	stathmin domain containing 1	protein-coding	0.02	0.455446
Merged-chr16-60767559-1	chr16	60767509	60767609	+	2.2	cIP1vsInput	Intergenic	Intergenic	-162028	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0.01	0.267327
Merged-chr8-14175939-1	chr8	14175889	14175989	+	2.2	cIP2vsInput	"intron (NM_001145965, intron 1 of 14)"	L1_Mur2|LINE|L1	80064	NM_172910	244310	Mm.404697	NM_001145965	ENSMUSG00000047495	Dlgap2	6430596N04Rik|DAP2|Sapap2	"discs, large (Drosophila) homolog-associated protein 2"	protein-coding	0	0.287129
Merged-chr1-98495924-1	chr1	98495874	98495974	+	2.2	cIP2vsInput	"intron (NM_027584, intron 9 of 13)"	(TTG)n|Simple_repeat|Simple_repeat	74800	NM_027584	70866	Mm.389164	NM_001164233	ENSMUSG00000026336	Slco6d1	4921511I05Rik	"solute carrier organic anion transporter family, member 6d1"	protein-coding	0	0.316832
Merged-chr17-18185892-1	chr17	18185842	18185942	+	2.2	cIP1vsInput	TTS (NM_001104541)	TTS (NM_001104541)	33962	NM_001104541	627111	Mm.469863	NM_001104541	ENSMUSG00000091350	Vmn2r92	EG627111	"vomeronasal 2, receptor 92"	protein-coding	0	0.346535
Merged-chr4-50330326-1	chr4	50330276	50330376	+	2.2	cIP1vsInput	Intergenic	MTE2b|LTR|ERVL-MaLR	-484557	NM_001276355	242443	Mm.440095	NM_001033351		Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	"glutamate receptor ionotropic, NMDA3A"	protein-coding	0	0.316832
Merged-chr4-62943694-1	chr4	62943644	62943744	+	2.2	cIP2vsInput	Intergenic	Intergenic	-21880	NM_028326	72701	Mm.482416	NM_028326	ENSMUSG00000028358	Zfp618	2810031P15Rik|2810040O04Rik|AI415580|AI505139|D430033D05Rik|Nedd10|Znf618|bM257P7.1	zinc finger protein 618	protein-coding	0.01	0.415842
Merged-chr10-72432838-1	chr10	72432788	72432888	+	2.2	cIP1vsInput	Intergenic	Intergenic	-222057	NM_025635	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding	0.01	0.356436
Merged-chr12-102722991-1	chr12	102722941	102723041	+	2.2	cIP2vsInput	Intergenic	Intergenic	-18122	NM_172584	217837	Mm.488700	NM_172584	ENSMUSG00000057963	Itpk1	BC031182	"inositol 1,3,4-triphosphate 5/6 kinase"	protein-coding	0.03	0.336634
Merged-chr15-47021600-1	chr15	47021550	47021650	+	2.2	cIP2vsInput	Intergenic	L1VL4|LINE|L1	398295	NR_045811	75281	Mm.159487	NR_045811		4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	miscRNA	0	0.316832
Merged-chr13-92941423-1	chr13	92941373	92941473	+	2.2	cIP2vsInput	Intergenic	L1M4|LINE|L1	96636	NM_001162945	382793	Mm.296770	NM_001162945	ENSMUSG00000021704	Mtx3	4930470O13Rik|AA409304|AI853833|AU067765|EG624619|Gm1194|Gm6514	metaxin 3	protein-coding	0	0.316832
Merged-chr14-30849173-1	chr14	30849123	30849223	+	2.2	cIP1vsInput	"intron (NM_028839, intron 1 of 7)"	ORR1A3-int|LTR|ERVL-MaLR	23579	NM_028839	69179	Mm.143025	NM_028839	ENSMUSG00000006526	Tmem110	1810038N08Rik|2310014H19Rik|AW554125	transmembrane protein 110	protein-coding	0.01	0.29703
Merged-chr6-93743840-1	chr6	93743790	93743890	+	2.2	cIP1vsInput	"intron (NM_001083321, intron 11 of 21)"	"intron (NM_001083321, intron 11 of 21)"	169714	NM_001083321	14924	Mm.217216	NM_001029850	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	"membrane associated guanylate kinase, WW and PDZ domain containing 1"	protein-coding	0	0.326733
Merged-chr1-175115426-1	chr1	175115376	175115476	+	2.2	cIP1vsInput	"intron (NM_001199003, intron 9 of 17)"	Lx4A|LINE|L1	-193607	NM_011825	23893	Mm.25760	NM_011825	ENSMUSG00000050069	Grem2	Gremlin2|Prdc	"gremlin 2 homolog, cysteine knot superfamily (Xenopus laevis)"	protein-coding	0.01	0.346535
Merged-chr17-58800860-1	chr17	58800810	58800910	+	2.2	cIP1vsInput	Intergenic	RLTR17D_Mm|LTR|ERVK	190515	NM_027001	69239	Mm.246732	NM_027001	ENSMUSG00000024227	2610034M16Rik	AV114557	RIKEN cDNA 2610034M16 gene	protein-coding	0	0.29703
Merged-chr8-80343258-1	chr8	80343208	80343308	+	2.2	cIP1vsInput	Intergenic	BLACKJACK|DNA|hAT-Blackjack	-150787	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding	0	0.366337
Merged-chr12-37074705-1	chr12	37074655	37074755	+	2.2	cIP2vsInput	Intergenic	Intergenic	-33841	NM_008584	17286	Mm.341398	NM_008584		Meox2	AI528662|Gax|Mox-2|Mox2	mesenchyme homeobox 2	protein-coding	0.02	0.336634
Merged-chr17-54883997-1	chr17	54883947	54884047	+	2.2	cIP1vsInput	Intergenic	L1MA6|LINE|L1	-513923	NR_045825	69418	Mm.391004	NR_045825		1700025K24Rik	-	RIKEN cDNA 1700025K24 gene	miscRNA	0	0.306931
Merged-chr4-4904002-1	chr4	4903952	4904052	+	2.2	cIP1vsInput	Intergenic	ETnERV2-int|LTR|ERVK	-110696	NM_177730	242291	Mm.369779	NM_177730		Impad1	1110001C20Rik|AA408880|AI451589|AL022796|B230207P20|Jaws|gPAPP	inositol monophosphatase domain containing 1	protein-coding	0.01	0.316832
Merged-chr11-25927532-1	chr11	25927482	25927582	+	2.2	cIP1vsInput	"intron (NR_027973, intron 2 of 5)"	"intron (NR_027973, intron 2 of 5)"	283044	NR_027973	70626	Mm.379180	NR_027973		5730522E02Rik	-	RIKEN cDNA 5730522E02 gene	miscRNA	0	0.247525
Merged-chr4-133619580-1	chr4	133619530	133619630	+	2.2	cIP1vsInput	"intron (NM_001017968, intron 2 of 7)"	"intron (NM_001017968, intron 2 of 7)"	13849	NM_001017968	503610	Mm.331948	NM_001017968		Zdhhc18	-	"zinc finger, DHHC domain containing 18"	protein-coding	0	0.336634
Merged-chr14-57308977-1	chr14	57308927	57309027	+	2.2	cIP1vsInput	"intron (NM_030004, intron 4 of 7)"	Lx9|LINE|L1	89506	NM_030004	68631	Mm.25539	NM_030004	ENSMUSG00000021947	Cryl1	1110025H08Rik|A230106J09Rik|C85932|gul3dh	"crystallin, lambda 1"	protein-coding	0.01	0.465347
Merged-chr16-13760451-1	chr16	13760401	13760501	+	2.2	cIP1vsInput	Intergenic	(CAATA)n|Simple_repeat|Simple_repeat	-20248	NM_001039521	106298	Mm.490362	NM_001039521	ENSMUSG00000022682	Rrn3	AL023001|E130302O19Rik|R75565|TIF-1A|Tif1a	RRN3 RNA polymerase I transcription factor homolog (yeast)	protein-coding	0	0.29703
Merged-chr1-55489081-1	chr1	55489031	55489131	+	2.2	cIP2vsInput	"intron (NM_001114663, intron 1 of 5)"	"intron (NM_001114663, intron 1 of 5)"	83135	NM_001114663	227120	Mm.194183	NM_001114663		Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding	0	0.356436
Merged-chr4-38339280-1	chr4	38339230	38339330	+	2.2	cIP1vsInput	Intergenic	Lx2|LINE|L1	-1111013	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding	0	0.346535
Merged-chr3-139289262-1	chr3	139289212	139289312	+	2.2	cIP2vsInput	"intron (NM_198659, intron 6 of 13)"	"intron (NM_198659, intron 6 of 13)"	83369	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding	0	0.316832
Merged-chr2-140884797-1	chr2	140884747	140884847	+	2.2	cIP2vsInput	"intron (NM_001013802, intron 4 of 18)"	"intron (NM_001013802, intron 4 of 18)"	-213321	NM_178382	71436	Mm.426781	NM_001172160	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0	0.237624
Merged-chr9-38450287-1	chr9	38450237	38450337	+	2.2	cIP1vsInput	TTS (NM_146802)	TTS (NM_146802)	1495	NM_146802	258798	Mm.377696	NM_146802	ENSMUSG00000049334	Olfr902	MOR169-1	olfactory receptor 902	protein-coding	0.01	0.415842
Merged-chr7-72806682-1	chr7	72806632	72806732	+	2.2	cIP2vsInput	Intergenic	Intergenic	295386	NR_046024	625243	Mm.261798	NR_046024		Gm6567	-	predicted gene 6567	miscRNA	0.02	0.277228
Merged-chr4-35284678-1	chr4	35284628	35284728	+	2.2	cIP1vsInput	Intergenic	Zaphod|DNA|hAT-Tip100	-58798	NM_001081343	73205	Mm.331544	NM_001081343	ENSMUSG00000028300	3110043O21Rik	AI840585	RIKEN cDNA 3110043O21 gene	protein-coding	0	0.376238
Merged-chr7-87158738-1	chr7	87158688	87158788	+	2.2	cIP2vsInput	Intergenic	Intergenic	-88057	NM_015760	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding	0.01	0.316832
Merged-chr6-19083052-1	chr6	19083002	19083102	+	2.2	cIP2vsInput	Intergenic	MER92-int|LTR|ERV1	216734	NM_001167757	75196	Mm.67665	NM_001167757	ENSMUSG00000029517	Ankrd7	4930532L20Rik|AV278427	ankyrin repeat domain 7	protein-coding	0	0.287129
Merged-chr17-74694348-1	chr17	74694298	74694398	+	2.2	cIP2vsInput	"intron (NM_007566, intron 70 of 72)"	"intron (NM_007566, intron 70 of 72)"	-23402	NM_152817	74196	Mm.209503	NM_152817	ENSMUSG00000024078	Ttc27	2610511O17Rik	tetratricopeptide repeat domain 27	protein-coding	0	0.306931
Merged-chr14-84551353-1	chr14	84551303	84551403	+	2.2	cIP2vsInput	Intergenic	Intergenic	-74929	NR_015539	319903	Mm.440481	NR_015539		9630013A20Rik	-	RIKEN cDNA 9630013A20 gene	miscRNA	0	0.306931
Merged-chrX-38564579-1	chrX	38564529	38564629	+	2.2	cIP2vsInput	"intron (NM_028288, intron 3 of 22)"	"intron (NM_028288, intron 3 of 22)"	11617	NM_028288	72584	Mm.327675	NM_001110142		Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding	0.01	0.653465
Merged-chr15-48633840-1	chr15	48633790	48633890	+	2.2	cIP1vsInput	"intron (NM_001081391, intron 2 of 70)"	MTE2a|LTR|ERVL-MaLR	158149	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0.01	0.336634
Merged-chr5-85508270-1	chr5	85508220	85508320	+	2.2	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	557313	NM_007683	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	Cenpc	centromere protein C1	protein-coding	0.01	0.336634
Merged-chr5-62917857-1	chr5	62917807	62917907	+	2.2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	104034	NM_001170705	100322896	Mm.479821	NM_001170705	ENSMUSG00000090326	Gm17384	Dthd1	"predicted gene, 17384"	protein-coding	0	0.376238
Merged-chr1-70978749-1	chr1	70978699	70978799	+	2.2	cIP2vsInput	Intergenic	Intergenic	124223	NM_007525	12021	Mm.490738	NM_007525	ENSMUSG00000026196	Bard1	ENSMUSG00000060893|ENSMUSG00000073653	BRCA1 associated RING domain 1	protein-coding	0	0.287129
Merged-chr8-101719190-1	chr8	101719140	101719240	+	2.2	cIP2vsInput	Intergenic	Intergenic	1065921	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0	0.336634
Merged-chr5-117712465-1	chr5	117712415	117712515	+	2.2	cIP2vsInput	"intron (NM_001114545, intron 14 of 19)"	"intron (NM_001114545, intron 14 of 19)"	-154654	NM_008712	18125	Mm.442195	NM_008712	ENSMUSG00000029361	Nos1	2310005C01Rik|NO|NOS-I|Nos-1|bNOS|nNOS	"nitric oxide synthase 1, neuronal"	protein-coding	0.01	0.356436
Merged-chr14-8840457-1	chr14	8840407	8840507	+	2.2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	174067	NR_045968	74859	Mm.84041	NR_045968	ENSMUSG00000097898	4930455B14Rik	1700027C12Rik	RIKEN cDNA 4930455B14 gene	miscRNA	0	0.336634
Merged-chr4-34338425-1	chr4	34338375	34338475	+	2.2	cIP1vsInput	Intergenic	Intergenic	-212190	NM_001007589	433693	Mm.399624	NM_026019	ENSMUSG00000028291	Akirin2	2700059D21Rik|AA114675|AA522011|AU019887|Akirin-2	akirin 2	protein-coding	0.01	0.306931
Merged-chr16-51052675-1	chr16	51052625	51052725	+	2.2	cIP1vsInput	Intergenic	Intergenic	-319902	NR_028300	68190	Mm.482928	NR_028300		5330426P16Rik	-	RIKEN cDNA 5330426P16 gene	miscRNA	0.01	0.386139
Merged-chr3-72697399-1	chr3	72697349	72697449	+	2.2	cIP1vsInput	Intergenic	Intergenic	269467	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding	0	0.316832
Merged-chr8-43400432-1	chr8	43400382	43400482	+	2.2	cIP1vsInput	Intergenic	Intergenic	-93423	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding	0.01	0.277228
Merged-chr1-104646522-1	chr1	104646472	104646572	+	2.2	cIP1vsInput	Intergenic	Intergenic	-122297	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0	0.336634
Merged-chr7-120158932-1	chr7	120158882	120158982	+	2.2	cIP2vsInput	Intergenic	Intergenic	-13642	NM_011775	22787	Mm.6510	NM_011775	ENSMUSG00000030911	Zp2	Zp-2	zona pellucida glycoprotein 2	protein-coding	0	0.376238
Merged-chr4-20862210-1	chr4	20862160	20862260	+	2.2	cIP1vsInput	Intergenic	Intergenic	-83542	NM_172987	269513		NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding	0	0.316832
Merged-chr3-61186680-1	chr3	61186630	61186730	+	2.2	cIP1vsInput	Intergenic	Intergenic	-177827	NM_028712	74012	Mm.477648	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	"RAP2B, member of RAS oncogene family"	protein-coding	0	0.346535
Merged-chr9-102733038-1	chr9	102732988	102733088	+	2.2	cIP2vsInput	"3' UTR (NM_019764, exon 10 of 10)"	"3' UTR (NM_019764, exon 10 of 10)"	-6610	NR_033301	434510	Mm.387937	NR_033301	ENSMUSG00000093812	Gm5627	EG434510	predicted gene 5627	miscRNA	0.01	0.356436
Merged-chr3-93858991-1	chr3	93858941	93859041	+	2.2	cIP2vsInput	Intergenic	Intergenic	32971	NM_207271	399674	Mm.377923	NM_207271	ENSMUSG00000058005	Tdpoz3	-	TD and POZ domain containing 3	protein-coding	0.03	0.544554
Merged-chr3-123394002-1	chr3	123393952	123394052	+	2.2	cIP1vsInput	Intergenic	Intergenic	-8012	NM_201638	210529	Mm.260039	NM_201638	ENSMUSG00000028114	Mettl14	G430022H21Rik|mKIAA1627	methyltransferase like 14	protein-coding	0	0.306931
Merged-chr4-37988372-1	chr4	37988322	37988422	+	2.2	cIP2vsInput	Intergenic	Intergenic	-1036628	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0	0.306931
Merged-chr12-117671854-1	chr12	117671804	117671904	+	2.2	cIP1vsInput	"intron (NM_175930, intron 11 of 27)"	"intron (NM_175930, intron 11 of 27)"	155375	NM_175930	217944	Mm.227642	NM_175930	ENSMUSG00000041992	Rapgef5	4932413M22|C86120|D030051B22Rik|GFR|Mrgef|mKIAA0277|mmr-gef	Rap guanine nucleotide exchange factor (GEF) 5	protein-coding	0.01	0.366337
Merged-chr15-21042060-1	chr15	21042010	21042110	+	2.2	cIP1vsInput	Intergenic	Intergenic	-69392	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding	0	0.386139
Merged-chr18-79157908-1	chr18	79157858	79157958	+	2.2	cIP2vsInput	Intergenic	Intergenic	-48517	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding	0.01	0.326733
Merged-chr2-18014010-1	chr2	18013960	18014060	+	2.2	cIP1vsInput	Intergenic	MTD|LTR|ERVL-MaLR	-13239	NR_028378	100034739	Mm.401643	NR_028378		Gm17762	-	"predicted gene, 17762"	miscRNA	0	0.475248
Merged-chr10-66459444-1	chr10	66459394	66459494	+	2.2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-335380	NR_038039	69433	Mm.23366	NR_038039		1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	miscRNA	0	0.326733
Merged-chr6-140301504-1	chr6	140301454	140301554	+	2.2	cIP1vsInput	Intergenic	Intergenic	-122595	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	"pleckstrin homology domain containing, family A member 5"	protein-coding	0	0.356436
Merged-chrX-108820038-1	chrX	108819988	108820088	+	2.2	cIP2vsInput	"intron (NM_001081477, intron 6 of 40)"	L1ME2z|LINE|L1	14317	NM_001081477	382236	Mm.426127	NM_001081477		Brwd3	Brodl|D030064D06Rik|Gm596	bromodomain and WD repeat domain containing 3	protein-coding	0.01	0.336634
Merged-chr10-23653851-1	chr10	23653801	23653901	+	2.2	cIP1vsInput	Intergenic	Lx|LINE|L1	131600	NR_037680	100529074	Mm.371846	NR_037680		Snora33	ACA33|MBI-42	"small nucleolar RNA, H/ACA box 33"	snoRNA	0	0.415842
Merged-chr17-52028990-1	chr17	52028940	52029040	+	2.2	cIP2vsInput	Intergenic	Intergenic	146263	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	"predicted gene, 20098"	miscRNA	0	0.306931
Merged-chr1-67380175-1	chr1	67380125	67380225	+	2.2	cIP1vsInput	Intergenic	RMER3D-int|LTR|ERVK	257109	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding	0	0.336634
Merged-chr18-40979543-1	chr18	40979493	40979593	+	2.2	cIP2vsInput	Intergenic	Intergenic	721182	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding	0	0.287129
Merged-chr13-76172436-1	chr13	76172386	76172486	+	2.2	cIP2vsInput	"intron (NM_001081352, intron 38 of 43)"	L1MC|LINE|L1	73702	NM_001081352	218343	Mm.277964	NM_001081352	ENSMUSG00000033991	Ttc37	mKIAA0372	tetratricopeptide repeat domain 37	protein-coding	0	0.346535
Merged-chr17-29603398-1	chr17	29603348	29603448	+	2.2	cIP1vsInput	"intron (NM_198647, intron 12 of 12)"	"intron (NM_198647, intron 12 of 12)"	-7093	NR_045447	74092	Mm.396264	NR_045447	ENSMUSG00000089900	0610038L08Rik	-	RIKEN cDNA 0610038L08 gene	miscRNA	0.03	0.475248
Merged-chr13-30993721-1	chr13	30993671	30993771	+	2.2	cIP2vsInput	Intergenic	A-rich|Low_complexity|Low_complexity	-19674	NM_025588	66482	Mm.293510	NM_025588	ENSMUSG00000021357	Exoc2	2410030I24Rik|AI648199|Sec5|Sec5l1	exocyst complex component 2	protein-coding	0	0.346535
Merged-chr1-118261149-1	chr1	118261099	118261199	+	2.2	cIP1vsInput	Intergenic	Intergenic	49983	NM_011650	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding	0	0.336634
Merged-chr11-28302957-1	chr11	28302907	28303007	+	2.2	cIP2vsInput	Intergenic	Intergenic	281339	NM_001166661	216613	Mm.93759	NM_001166661	ENSMUSG00000032878	Ccdc85a	E030025D05Rik	coiled-coil domain containing 85A	protein-coding	0	0.326733
Merged-chr3-86129699-1	chr3	86129649	86129749	+	2.2	cIP2vsInput	"3' UTR (NM_001082414, exon 15 of 15)"	"3' UTR (NM_001082414, exon 15 of 15)"	9159	NR_004417	19870		NR_004417		Snord73a	Rnu73a|U73a	"small nucleolar RNA, C/D box U73A"	snoRNA	0.01	0.336634
Merged-chr5-43808006-1	chr5	43807956	43808056	+	2.2	cIP2vsInput	Intergenic	CpG	-10887	NM_009763	12182	Mm.246332	NM_009763	ENSMUSG00000029082	Bst1	114/A10|A530073F09|BP-3|Bp3|Bsta1|CD157|Ly65	bone marrow stromal cell antigen 1	protein-coding	0.08	0.653465
Merged-chr10-64693569-1	chr10	64693519	64693619	+	2.2	cIP2vsInput	"intron (NM_001164519, intron 8 of 12)"	"intron (NM_001164519, intron 8 of 12)"	-603314	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding	0	0.346535
Merged-chr3-27348273-1	chr3	27348223	27348323	+	2.2	cIP1vsInput	Intergenic	Intergenic	-23078	NM_177330	208188	Mm.194721	NM_177330	ENSMUSG00000051136	Ghsr	C530020I22Rik	growth hormone secretagogue receptor	protein-coding	0	0.336634
Merged-chr6-79095769-1	chr6	79095719	79095819	+	2.2	cIP1vsInput	Intergenic	Intergenic	63727	NR_040301	100504701	Mm.400420	NR_040301		Gm20362	-	"predicted gene, 20362"	miscRNA	0	0.346535
Merged-chr2-100044826-1	chr2	100044776	100044876	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1579922	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding	0	0.316832
Merged-chr7-121007156-1	chr7	121007106	121007206	+	2.2	cIP1vsInput	"intron (NM_028955, intron 7 of 7)"	"intron (NM_028955, intron 7 of 7)"	24647	NM_028955	74466	Mm.189707	NM_028955	ENSMUSG00000030877	4933427G17Rik	-	RIKEN cDNA 4933427G17 gene	protein-coding	0.01	0.306931
Merged-chr9-52386157-1	chr9	52386107	52386207	+	2.2	cIP2vsInput	Intergenic	Intergenic	-218046	NM_001162921	244871	Mm.390172	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding	0	0.29703
Merged-chr4-9246995-1	chr4	9246945	9247045	+	2.2	cIP2vsInput	Intergenic	Intergenic	-22322	NM_028940	74438	Mm.473368	NM_028940	ENSMUSG00000041216	Clvs1	4933402J24Rik|Clvl1|Rlbp1l1	clavesin 1	protein-coding	0.02	0.316832
Merged-chr16-18066285-1	chr16	18066235	18066335	+	2.2	cIP2vsInput	"intron (NM_010047, intron 2 of 5)"	"intron (NM_010047, intron 2 of 5)"	13425	NM_010047	13353	Mm.27155	NM_010047	ENSMUSG00000003531	Dgcr6	AU044152	DiGeorge syndrome critical region gene 6	protein-coding	0.04	0.564356
Merged-chr11-86830604-1	chr11	86830554	86830654	+	2.2	cIP2vsInput	Intergenic	Intergenic	-22944	NM_026191	67487	Mm.260627	NM_026191	ENSMUSG00000018425	Dhx40	2410016C14Rik|ARG147|DDX40|PAD	DEAH (Asp-Glu-Ala-His) box polypeptide 40	protein-coding	0.01	0.326733
Merged-chr17-42795317-1	chr17	42795267	42795367	+	2.2	cIP1vsInput	"3' UTR (NM_009847, exon 18 of 18)"	"3' UTR (NM_009847, exon 18 of 18)"	-53138	NM_001033493	435529	Mm.136350	NM_001033493	ENSMUSG00000057899	Gpr111	PGR20	G protein-coupled receptor 111	protein-coding	0.01	0.316832
Merged-chr9-24173471-1	chr9	24173421	24173521	+	2.2	cIP2vsInput	"intron (NM_175678, intron 3 of 9)"	"intron (NM_175678, intron 3 of 9)"	75453	NM_175678	319239	Mm.130824	NM_175678	ENSMUSG00000043659	Npsr1	9330128H10Rik|GPRA|Gpr154|MVTR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0	0.306931
Merged-chr6-129765682-1	chr6	129765632	129765732	+	2.2	cIP2vsInput	TTS (NM_001014997)	TTS (NM_001014997)	10167	NM_001014997	232415	Mm.290598	NM_001014997	ENSMUSG00000071158	Gm156	Klrh1	predicted gene 156	protein-coding	0	0.356436
Merged-chr2-126983834-1	chr2	126983784	126983884	+	2.2	cIP1vsInput	Intergenic	Intergenic	-24877	NM_175550	108011	Mm.134045	NM_175550		Ap4e1	2310033A20Rik|9930028M04Rik|AV087807	"adaptor-related protein complex AP-4, epsilon 1"	protein-coding	0	0.346535
Merged-chr1-27146736-1	chr1	27146686	27146786	+	2.2	cIP2vsInput	Intergenic	Intergenic	-459276	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding	0	0.277228
Merged-chr2-167833759-1	chr2	167833709	167833809	+	2.2	cIP1vsInput	Intergenic	Intergenic	-98568	NM_011201	19246	Mm.277916	NM_011201	ENSMUSG00000027540	Ptpn1	PTP-1B|PTP-HA2|PTP1B	"protein tyrosine phosphatase, non-receptor type 1"	protein-coding	0.07	0.544554
Merged-chr1-98323830-1	chr1	98323780	98323880	+	2.2	cIP1vsInput	Intergenic	Intergenic	-97294	NM_001164233	70866	Mm.389164	NM_001164233	ENSMUSG00000026336	Slco6d1	4921511I05Rik	"solute carrier organic anion transporter family, member 6d1"	protein-coding	0	0.287129
Merged-chr6-27196011-1	chr6	27195961	27196061	+	2.2	cIP1vsInput	Intergenic	ORR1E-int|LTR|ERVL-MaLR	740739	NR_030420	735266		NR_030420		Mir592	Mirn592|mir-592|mmu-mir-592	microRNA 592	miscRNA	0	0.29703
Merged-chrX-13702034-1	chrX	13701984	13702084	+	2.2	cIP1vsInput	"intron (NM_009806, intron 3 of 24)"	"intron (NM_009806, intron 3 of 24)"	40671	NM_175669	319200	Mm.383294	NM_175669	ENSMUSG00000047678	Gpr82	-	G protein-coupled receptor 82	protein-coding	0	0.386139
Merged-chr12-24788540-1	chr12	24788490	24788590	+	2.2	cIP1vsInput	Intergenic	L1MEi|LINE|L1	-43059	NM_026037	67216	Mm.167671	NM_001083341	ENSMUSG00000020646	Mboat2	2810049G06Rik|AU022889|AW547221|LPCAT4|Moact2|Oact2	membrane bound O-acyltransferase domain containing 2	protein-coding	0	0.29703
Merged-chr1-32025130-1	chr1	32025080	32025180	+	2.2	cIP2vsInput	Intergenic	Intergenic	-147676	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm1	"KH domain containing, RNA binding, signal transduction associated 2"	protein-coding	0	0.306931
Merged-chr14-92770155-1	chr14	92770105	92770205	+	2.2	cIP1vsInput	Intergenic	Intergenic	1118733	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.326733
Merged-chr15-11347667-1	chr15	11347617	11347717	+	2.2	cIP1vsInput	TTS (NM_175501)	TTS (NM_175501)	51991	NM_033074	110960	Mm.286061	NM_033074	ENSMUSG00000022241	Tars	D15Wsu59e|ThrRS	threonyl-tRNA synthetase	protein-coding	0	0.336634
Merged-chr6-44874617-1	chr6	44874567	44874667	+	2.2	cIP2vsInput	Intergenic	L1M4|LINE|L1	-185444	NM_001004357	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0	0.346535
Merged-chr13-111207169-1	chr13	111207119	111207219	+	2.2	cIP2vsInput	Intergenic	Intergenic	22262	NR_045908	73129	Mm.417826	NR_045908		3110015C05Rik	-	RIKEN cDNA 3110015C05 gene	miscRNA	0.01	0.455446
Merged-chr14-67211911-1	chr14	67211861	67211961	+	2.2	cIP2vsInput	Intergenic	Intergenic	-21381	NM_010095	13592	Mm.319947	NM_001276387	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding	0.02	0.524752
Merged-chr11-23601246-1	chr11	23601196	23601296	+	2.2	cIP1vsInput	"intron (NM_027860, intron 12 of 21)"	L1_Mus3|LINE|L1	32385	NM_027860	71675	Mm.48031	NM_027860	ENSMUSG00000042208	0610010F05Rik	Kiaa1841|mKIAA1841	RIKEN cDNA 0610010F05 gene	protein-coding	0	0.376238
Merged-chr3-126903869-1	chr3	126903819	126903919	+	2.2	cIP1vsInput	Intergenic	Intergenic	39517	NM_001034168	109676	Mm.484610	NM_001034168	ENSMUSG00000032826	Ank2	AI835472|AW491075|Ank-2	"ankyrin 2, brain"	protein-coding	0.01	0.346535
Merged-chr6-64654774-1	chr6	64654724	64654824	+	2.2	cIP1vsInput	"intron (NM_008167, intron 14 of 15)"	ETnERV3-int|LTR|ERVK	-74372	NM_007500	11921	Mm.57229	NM_007500	ENSMUSG00000073043	Atoh1	Hath1|MATH-1|Math1|bHLHa14	atonal homolog 1 (Drosophila)	protein-coding	0	0.366337
Merged-chr2-53424062-1	chr2	53424012	53424112	+	2.2	cIP2vsInput	Intergenic	Intergenic	231978	NM_022989	65103	Mm.37623	NM_022989	ENSMUSG00000026960	Arl6ip6	2310057C01Rik|2610529A11Rik|Aip-6	ADP-ribosylation factor-like 6 interacting protein 6	protein-coding	0	0.306931
Merged-chr3-85245286-1	chr3	85245236	85245336	+	2.2	cIP1vsInput	Intergenic	(ATG)n|Simple_repeat|Simple_repeat	-72233	NR_040542	73283	Mm.489084	NR_040542		1700036G14Rik	-	RIKEN cDNA 1700036G14 gene	miscRNA	0	0.445545
Merged-chr10-113772536-1	chr10	113772486	113772586	+	2.2	cIP2vsInput	Intergenic	Intergenic	185958	NR_035418	100316831		NR_035418		Mir669h	Mirn669h|mmu-mir-669h	microRNA 669h	miscRNA	0	0.336634
Merged-chr9-22613107-1	chr9	22613057	22613157	+	2.2	cIP1vsInput	"intron (NM_181316, intron 9 of 21)"	"intron (NM_181316, intron 9 of 21)"	137392	NM_178415	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding	0	0.356436
Merged-chr1-170202721-1	chr1	170202671	170202771	+	2.2	cIP1vsInput	"intron (NM_010633, intron 7 of 7)"	Charlie2a|DNA|hAT-Charlie	12672	NM_010633	16589	Mm.389214	NM_010633		Uhmk1	4732477C12Rik|4930500M09Rik|AA673513|AI449218|AU021979|KIS|Kist|P-CIP2	U2AF homology motif (UHM) kinase 1	protein-coding	0	0.306931
Merged-chr18-27597147-1	chr18	27597097	27597197	+	2.2	cIP1vsInput	Intergenic	Intergenic	-963017	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	miscRNA	0	0.356436
Merged-chr17-9589995-1	chr17	9589945	9590045	+	2.2	cIP1vsInput	Intergenic	Intergenic	79709	NM_001163836	67543	Mm.26987	NM_026226	ENSMUSG00000046173	Pabpc6	4932702K14Rik|AI428050|Pabpc3	"poly(A) binding protein, cytoplasmic 6"	protein-coding	0	0.346535
Merged-chr12-64422562-1	chr12	64422512	64422612	+	2.2	cIP2vsInput	Intergenic	Intergenic	52336	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0.01	0.326733
Merged-chr1-148373549-1	chr1	148373499	148373599	+	2.2	cIP2vsInput	Intergenic	Intergenic	1587735	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0	0.386139
Merged-chr17-52401772-1	chr17	52401722	52401822	+	2.2	cIP1vsInput	Intergenic	Lx|LINE|L1	-200937	NM_001031811	211468	Mm.490760	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	"potassium voltage-gated channel, subfamily H (eag-related), member 8"	protein-coding	0	0.405941
Merged-chr6-130562324-1	chr6	130562274	130562374	+	2.2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-175450	NM_016659	16627	Mm.333431	NM_016659	ENSMUSG00000079853	Klra1	A1|Klra22|Ly49a|Ly49o<129>|Ly49v	"killer cell lectin-like receptor, subfamily A, member 1"	protein-coding	0	0.326733
Merged-chr1-144923437-1	chr1	144923387	144923487	+	2.2	cIP1vsInput	Intergenic	Intergenic	-148016	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding	0.01	0.39604
Merged-chr3-80749989-1	chr3	80749939	80750039	+	2.2	cIP1vsInput	"intron (NM_001039195, intron 2 of 12)"	"intron (NM_001039195, intron 2 of 12)"	52802	NM_013540	14800	Mm.220224	NM_001039195	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	"glutamate receptor, ionotropic, AMPA2 (alpha 2)"	protein-coding	0	0.39604
Merged-chr1-146472141-1	chr1	146472091	146472191	+	2.2	cIP1vsInput	Intergenic	Intergenic	-23525	NM_153539	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.346535
Merged-chr12-6865206-1	chr12	6865156	6865256	+	2.2	cIP2vsInput	Intergenic	Intergenic	515124	NR_045045	73575	Mm.179463	NR_045045		1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	miscRNA	0	0.29703
Merged-chr3-74183603-1	chr3	74183553	74183653	+	2.2	cIP1vsInput	Intergenic	Intergenic	-166326	NR_040450	100504692	Mm.394454	NR_040450		Gm20356	-	"predicted gene, 20356"	miscRNA	0	0.326733
Merged-chr6-55734435-1	chr6	55734385	55734485	+	2.2	cIP2vsInput	Intergenic	L1MDa|LINE|L1	49864	NR_046071	100041339	Mm.403680	NR_046071		Gm3279	-	predicted gene 3279	miscRNA	0	0.336634
Merged-chr10-7589819-1	chr10	7589769	7589869	+	2.2	cIP2vsInput	promoter-TSS (NM_172784)	promoter-TSS (NM_172784)	19	NM_172784	237253	Mm.206759	NM_172784	ENSMUSG00000019796	Lrp11	1700034J19Rik|6330533B21|9830160H19Rik	low density lipoprotein receptor-related protein 11	protein-coding	0.16	0.762376
Merged-chrY-7011568-1	chrY	7011518	7011618	+	2.2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	156209	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.356436
Merged-chr11-73382042-1	chr11	73381992	73382092	+	2.2	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	10796	NM_146922	258924	Mm.236410	NM_001172686	ENSMUSG00000063881	Olfr376	MOR135-12	olfactory receptor 376	protein-coding	0	0.326733
Merged-chr2-41573069-1	chr2	41573019	41573119	+	2.2	cIP1vsInput	"intron (NM_053011, intron 7 of 90)"	"intron (NM_053011, intron 7 of 90)"	1080529	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0.01	0.316832
Merged-chr6-131333462-1	chr6	131333412	131333512	+	2.2	cIP2vsInput	Intergenic	MYSERV-int|LTR|ERVK	-19635	NM_172891	243659	Mm.20114	NM_172891	ENSMUSG00000032899	Styk1	9130025L13|AI326477|Nok	serine/threonine/tyrosine kinase 1	protein-coding	0.01	0.316832
Merged-chr17-59746297-1	chr17	59746247	59746347	+	2.2	cIP2vsInput	Intergenic	Intergenic	-732975	NM_026497	67993	Mm.36507	NM_026497		Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0	0.29703
Merged-chr11-22304614-1	chr11	22304564	22304664	+	2.2	cIP2vsInput	Intergenic	B1F|SINE|Alu	-17819	NM_001252515	216565	Mm.281732	NM_001252515	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding	0.01	0.376238
Merged-chr14-73869872-1	chr14	73869822	73869922	+	2.2	cIP2vsInput	Intergenic	Intergenic	317086	NM_011506	20916	Mm.38951	NM_011506	ENSMUSG00000022110	Sucla2	4930547K18Rik	"succinate-Coenzyme A ligase, ADP-forming, beta subunit"	protein-coding	0	0.366337
Merged-chr10-124513726-1	chr10	124513676	124513776	+	2.2	cIP1vsInput	"intron (NR_028310, intron 3 of 3)"	"intron (NR_028310, intron 3 of 3)"	44652	NR_028310	75030	Mm.159403	NR_028310		4930503E24Rik	-	"eukaryotic translation initiation factor 3, subunit I pseudogene"	pseudo	0.01	0.316832
Merged-chr16-58106003-1	chr16	58105953	58106053	+	2.2	cIP2vsInput	Intergenic	Intergenic	-302532	NM_028523	73379	Mm.373589	NM_028523	ENSMUSG00000035107	Dcbld2	1700055P21Rik|AW146002|CLCP1|Esdn	"discoidin, CUB and LCCL domain containing 2"	protein-coding	0	0.336634
Merged-chrX-129791987-1	chrX	129791937	129792037	+	2.2	cIP1vsInput	"intron (NM_172493, intron 1 of 26)"	"intron (NM_172493, intron 1 of 26)"	42245	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diap2	Dia3|Diaph2|Drf2|E430022I22Rik	diaphanous homolog 2 (Drosophila)	protein-coding	0	0.326733
Merged-chr15-77608754-1	chr15	77608704	77608804	+	2.2	cIP1vsInput	Intergenic	RLTR17D_Mm|LTR|ERVK	-10214	NR_033577	666661	Mm.390818	NR_033577		Gm8221	-	apolipoprotein L 7c pseudogene	pseudo	0.01	0.306931
Merged-chr12-58917157-1	chr12	58917107	58917207	+	2.2	cIP1vsInput	Intergenic	Intergenic	94860	NM_009147	20334	Mm.209207	NM_009147	ENSMUSG00000020986	Sec23a	Msec23|Sec23r	SEC23A (S. cerevisiae)	protein-coding	0.02	0.336634
Merged-chr19-43339059-1	chr19	43339009	43339109	+	2.2	cIP2vsInput	"intron (NM_001081257, intron 2 of 11)"	Lx|LINE|L1	49296	NM_001081257	545291	Mm.442200	NM_001081257	ENSMUSG00000074852	Hpse2	Gm968|Hpa2	heparanase 2	protein-coding	0	0.346535
Merged-chr11-117547849-1	chr11	117547799	117547899	+	2.2	cIP1vsInput	Intergenic	Intergenic	-63398	NR_015489	78403	Mm.212543	NR_015489		2900041M22Rik	-	RIKEN cDNA 2900041M22 gene	miscRNA	0.01	0.366337
Merged-chr6-5256418-1	chr6	5256368	5256468	+	2.2	cIP2vsInput	promoter-TSS (NM_173006)	promoter-TSS (NM_173006)	-185	NM_173006	269823	Mm.9122	NM_173006	ENSMUSG00000029759	Pon3	2810004E20|AI786302	paraoxonase 3	protein-coding	0.01	0.50495
Merged-chr2-140135146-1	chr2	140135096	140135196	+	2.2	cIP2vsInput	"intron (NM_001081090, intron 10 of 13)"	L1_Rod|LINE|L1	35412	NM_001081090	66580	Mm.21228	NM_001081090	ENSMUSG00000045624	Esf1	2610101J03Rik|ABTAP|AW545818|C79684	"ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)"	protein-coding	0	0.316832
Merged-chr10-61211908-1	chr10	61211858	61211958	+	2.2	cIP1vsInput	"intron (NM_001081127, intron 14 of 21)"	"intron (NM_001081127, intron 14 of 21)"	36646	NM_023064	65971	Mm.30227	NM_001017407	ENSMUSG00000020096	Tbata	1700021K02Rik|AI428928|Spatial|Titest	"thymus, brain and testes associated"	protein-coding	0.07	0.554455
Merged-chr12-87314280-1	chr12	87314230	87314330	+	2.2	cIP2vsInput	"intron (NM_011479, intron 9 of 11)"	PB1D10|SINE|Alu	47552	NM_146036	217737	Mm.22626	NM_146036	ENSMUSG00000021037	Ahsa1	BC023857|p38	"AHA1, activator of heat shock protein ATPase 1"	protein-coding	0.02	0.346535
Merged-chr10-77535154-1	chr10	77535104	77535204	+	2.2	cIP2vsInput	"intron (NM_008404, intron 1 of 15)"	"intron (NM_008404, intron 1 of 15)"	4806	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding	0.03	0.376238
Merged-chr8-87709886-1	chr8	87709836	87709936	+	2.2	cIP1vsInput	"intron (NM_033327, intron 5 of 7)"	"intron (NM_033327, intron 5 of 7)"	145979	NM_177901	330820	Mm.212913	NM_177901		4933402J07Rik	-	RIKEN cDNA 4933402J07 gene	protein-coding	0	0.514851
Merged-chr10-43255140-1	chr10	43255090	43255190	+	2.2	cIP1vsInput	"intron (NM_001168289, intron 1 of 7)"	"intron (NM_001168289, intron 1 of 7)"	33654	NM_001168289	71365	Mm.490430	NM_001168289	ENSMUSG00000038240	Pdss2	5430420P03Rik|Gm60|Plmp|kd|mDLP1	"prenyl (solanesyl) diphosphate synthase, subunit 2"	protein-coding	0.01	0.257426
Merged-chr5-50791781-1	chr5	50791731	50791831	+	2.2	cIP1vsInput	Intergenic	Intergenic	640448	NR_040696	73965	Mm.243823	NR_040696		4930448I18Rik	-	RIKEN cDNA 4930448I18 gene	miscRNA	0	0.29703
Merged-chr11-112716877-1	chr11	112716827	112716927	+	2.2	cIP2vsInput	Intergenic	Intergenic	-5521	NR_024085	217294	Mm.297761	NM_146031	ENSMUSG00000041674	BC006965	-	cDNA sequence BC006965	miscRNA	0.01	0.415842
Merged-chr18-44786459-1	chr18	44786409	44786509	+	2.2	cIP2vsInput	"intron (NM_001085373, intron 1 of 18)"	"intron (NM_001085373, intron 1 of 18)"	25723	NM_001085373	328949	Mm.427116	NM_001033406	ENSMUSG00000071856	Mcc	D18Ertd451e|E330037C19	mutated in colorectal cancers	protein-coding	0.01	0.277228
Merged-chr3-14164920-1	chr3	14164870	14164970	+	2.2	cIP1vsInput	"intron (NM_178631, intron 9 of 9)"	"intron (NM_178631, intron 9 of 9)"	-198197	NR_033591	622229	Mm.486084	NR_033591		Gm6300	EG622229	"solute carrier family 7 (cationic amino acid transporter, y+ system), member pseudogene"	pseudo	0	0.287129
Merged-chr10-37773479-1	chr10	37773429	37773529	+	2.2	cIP1vsInput	Intergenic	Intergenic	-634553	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding	0	0.39604
Merged-chr12-105266168-1	chr12	105266118	105266218	+	2.2	cIP2vsInput	Intergenic	Intergenic	-43431	NM_009337	21432	Mm.18154	NM_009337	ENSMUSG00000041359	Tcl1	Tcl1a	T cell lymphoma breakpoint 1	protein-coding	0	0.336634
Merged-chr18-58323805-1	chr18	58323755	58323855	+	2.2	cIP1vsInput	Intergenic	Intergenic	-113879	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding	0	0.29703
Merged-chr1-45480652-1	chr1	45480602	45480702	+	2.2	cIP1vsInput	"intron (NM_007737, intron 1 of 53)"	"intron (NM_007737, intron 1 of 53)"	22630	NM_007737	12832	Mm.10299	NM_007737	ENSMUSG00000026042	Col5a2	1110014L14Rik|D230017N05	"collagen, type V, alpha 2"	protein-coding	0	0.316832
Merged-chr14-109514101-1	chr14	109514051	109514151	+	2.2	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	53871	NR_039542	100628607		NR_039542	ENSMUSG00000092639	Mir3964	mmu-mir-3964|mu-mir-3964	microRNA 3964	miscRNA	0	0.29703
Merged-chr4-117257480-1	chr4	117257430	117257530	+	2.2	cIP1vsInput	"intron (NM_026837, intron 1 of 2)"	"intron (NM_026837, intron 1 of 2)"	5491	NM_026837	68777	Mm.331805	NM_026837	ENSMUSG00000048772	Tmem53	1110038M16Rik|1500001P22Rik|1700012A05Rik	transmembrane protein 53	protein-coding	0	0.247525
Merged-chr9-111357242-1	chr9	111357192	111357292	+	2.2	cIP1vsInput	"intron (NM_001164659, intron 8 of 21)"	"intron (NM_001164659, intron 8 of 21)"	45503	NM_001164659	320429	Mm.270754	NM_001164659	ENSMUSG00000062296	Trank1	A230061D21Rik|C030048J01Rik|Gm187|Lba1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding	0	0.257426
Merged-chr18-75174971-1	chr18	75174921	75175021	+	2.2	cIP2vsInput	"intron (NM_027727, intron 13 of 16)"	"intron (NM_027727, intron 13 of 16)"	122346	NR_045394	100503117	Mm.399752	NR_045393		2010010A06Rik	5033420E22Rik	RIKEN cDNA 2010010A06 gene	miscRNA	0	0.356436
Merged-chr13-118592984-1	chr13	118592934	118593034	+	2.2	cIP2vsInput	Intergenic	Intergenic	36816	NR_045982	75890	Mm.141235	NR_045982		1700003P14Rik	1700030O10Rik|4930584L06Rik	RIKEN cDNA 1700003P14 gene	miscRNA	0	0.336634
Merged-chr8-9485283-1	chr8	9485233	9485333	+	2.2	cIP2vsInput	"intron (NM_173446, intron 1 of 2)"	"intron (NM_173446, intron 1 of 2)"	285740	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	"family with sequence similarity 155, member A"	protein-coding	0.02	0.306931
Merged-chr6-52073777-1	chr6	52073727	52073827	+	2.2	cIP2vsInput	Intergenic	HAL1|LINE|L1	-61228	NM_018773	54353	Mm.392558	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding	0	0.277228
Merged-chr1-148230251-1	chr1	148230201	148230301	+	2.2	cIP2vsInput	Intergenic	Intergenic	1731033	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0	0.267327
Merged-chr15-4759586-1	chr15	4759536	4759636	+	2.2	cIP2vsInput	"intron (NM_016704, intron 6 of 15)"	"intron (NM_016704, intron 6 of 15)"	32376	NM_016704	12274	Mm.20247	NM_016704	ENSMUSG00000022181	C6	AW111623	complement component 6	protein-coding	0	0.415842
Merged-chr8-31557834-1	chr8	31557784	31557884	+	2.2	cIP1vsInput	Intergenic	L1ME3G|LINE|L1	190085	NR_046272	74517	Mm.390001	NR_046272		7420700N18Rik	-	RIKEN cDNA 7420700N18 gene	miscRNA	0	0.366337
Merged-chr13-64392434-1	chr13	64392384	64392484	+	2.2	cIP2vsInput	Intergenic	L1MA7|LINE|L1	-22128	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding	0.01	0.336634
Merged-chr3-118705203-1	chr3	118705153	118705253	+	2.2	cIP1vsInput	"intron (NM_170778, intron 3 of 22)"	MTB|LTR|ERVL-MaLR	143025	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding	0	0.425743
Merged-chr11-28458161-1	chr11	28458111	28458211	+	2.2	cIP1vsInput	"intron (NM_181577, intron 2 of 4)"	"intron (NM_181577, intron 2 of 4)"	126135	NM_001166661	216613	Mm.93759	NM_001166661	ENSMUSG00000032878	Ccdc85a	E030025D05Rik	coiled-coil domain containing 85A	protein-coding	0.01	0.366337
Merged-chr10-72226762-1	chr10	72226712	72226812	+	2.2	cIP1vsInput	Intergenic	Intergenic	-246072	NR_003644	108950	Mm.212793	NR_003644	ENSMUSG00000043859	1700049L16Rik	-	hematological and neurological expressed 1-like pseudogene	pseudo	0	0.356436
Merged-chr5-73452734-1	chr5	73452684	73452784	+	2.2	cIP2vsInput	"intron (NM_181323, intron 15 of 15)"	L1M3e|LINE|L1	-28321	NM_001190734	100737	Mm.220312	NM_001190733	ENSMUSG00000051674	Dcun1d4	AI836376	"DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)"	protein-coding	0	0.386139
Merged-chr8-123414592-1	chr8	123414542	123414642	+	2.2	cIP1vsInput	"intron (NM_023279, intron 1 of 3)"	"intron (NM_023279, intron 1 of 3)"	3028	NM_023279	22152	Mm.40068	NM_023279	ENSMUSG00000062380	Tubb3	3200002H15Rik|M(beta)3|M(beta)6	"tubulin, beta 3 class III"	protein-coding	0.01	0.257426
Merged-chr11-18296478-1	chr11	18296428	18296528	+	2.2	cIP1vsInput	Intergenic	Intergenic	-342603	NM_026576	68145	Mm.178684	NM_026576	ENSMUSG00000016984	Etaa1	5730466H23Rik|AA672646	Ewing's tumor-associated antigen 1	protein-coding	0	0.445545
Merged-chr15-60198642-1	chr15	60198592	60198692	+	2.2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-182024	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding	0.01	0.287129
Merged-chr12-38607252-1	chr12	38607202	38607302	+	2.2	cIP2vsInput	"intron (NM_178681, intron 24 of 24)"	"intron (NM_178681, intron 24 of 24)"	7269	NR_045943	73867	Mm.78933	NR_045943		4930428E07Rik	-	RIKEN cDNA 4930428E07 gene	miscRNA	0	0.277228
Merged-chr13-83921836-1	chr13	83921786	83921886	+	2.2	cIP2vsInput	"intron (NR_036594, intron 2 of 2)"	L1_Mur3|LINE|L1	30628	NR_036594	72677	Mm.245636	NR_036594		2810049E08Rik	-	RIKEN cDNA 2810049E08 gene	miscRNA	0.01	0.336634
Merged-chr18-66011468-1	chr18	66011418	66011518	+	2.2	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-8833	NM_001172062	70361	Mm.449042	NM_001172062	ENSMUSG00000041891	Lman1	2610020P13Rik|AI326273|AU043785|C730041J05|ERGIC53|F5F8D|MCFD1|MR60|P58|gp58	"lectin, mannose-binding, 1"	protein-coding	0	0.346535
Merged-chr6-111164411-1	chr6	111164361	111164461	+	2.2	cIP1vsInput	"intron (NM_177328, intron 4 of 9)"	L1_Mur3|LINE|L1	518813	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0.02	0.346535
Merged-chr16-78490674-1	chr16	78490624	78490724	+	2.2	cIP2vsInput	Intergenic	Intergenic	-69642	NR_040569	75818	Mm.410817	NR_040569		4930478L05Rik	-	RIKEN cDNA 4930478L05 gene	miscRNA	0.01	0.465347
Merged-chr17-3066059-1	chr17	3066009	3066109	+	2.2	cIP2vsInput	"intron (NR_003519, intron 7 of 7)"	ETnERV3-int|LTR|ERVK	18124	NR_003519	328734	Mm.335641	NR_003519		Pisd-ps2	D030013I16Rik	"phosphatidylserine decarboxylase, pseudogene 2"	pseudo	0.01	0.336634
Merged-chr4-29743635-1	chr4	29743585	29743685	+	2.2	cIP2vsInput	Intergenic	Intergenic	-920961	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	miscRNA	0	0.277228
Merged-chr18-19552402-1	chr18	19552352	19552452	+	2.2	cIP2vsInput	Intergenic	Intergenic	449695	NM_007882	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding	0	0.277228
Merged-chr1-21370280-1	chr1	21370230	21370330	+	2.2	cIP1vsInput	TTS (NM_001033904)	TTS (NM_001033904)	1949	NM_001033904	433278	Mm.484599	NM_001033904		Khdc1c	Khdc1b	KH domain containing 1C	protein-coding	0	0.356436
Merged-chr9-50333353-1	chr9	50333303	50333403	+	2.2	cIP2vsInput	Intergenic	L1ME1|LINE|L1	-161172	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	1600029D21Rik	0610037B23Rik|AA407923|AU043048|PLET1	RIKEN cDNA 1600029D21 gene	protein-coding	0.01	0.326733
Merged-chr17-58977343-1	chr17	58977293	58977393	+	2.2	cIP2vsInput	"intron (NM_027001, intron 2 of 12)"	"intron (NM_027001, intron 2 of 12)"	14032	NM_027001	69239	Mm.246732	NM_027001	ENSMUSG00000024227	2610034M16Rik	AV114557	RIKEN cDNA 2610034M16 gene	protein-coding	0.01	0.386139
Merged-chr16-40220724-1	chr16	40220674	40220774	+	2.2	cIP2vsInput	Intergenic	Intergenic	-1312618	NM_175548	268890	Mm.473653	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding	0	0.336634
Merged-chr4-88822888-1	chr4	88822838	88822938	+	2.2	cIP1vsInput	Intergenic	Intergenic	2969	NM_008333	15964	Mm.377087	NM_008333	ENSMUSG00000070906	Ifna11	IFN-[a]11	interferon alpha 11	protein-coding	0.01	0.356436
Merged-chr13-17838887-1	chr13	17838837	17838937	+	2.2	cIP2vsInput	Intergenic	Intergenic	-33790	NM_027118	69562	Mm.193924	NM_001081058	ENSMUSG00000041297	Cdk13	2310015O17Rik|Cdc2l5	cyclin-dependent kinase 13	protein-coding	0.01	0.346535
Merged-chr15-79927818-1	chr15	79927768	79927868	+	2.2	cIP2vsInput	"intron (NM_144811, intron 2 of 6)"	CpG	4828	NM_144811	52609	Mm.323442	NM_144811	ENSMUSG00000053411	Cbx7	1600014J01Rik|AI851678|D15Ertd417e	chromobox 7	protein-coding	0.09	0.633663
Merged-chr3-15846331-1	chr3	15846281	15846381	+	2.2	cIP1vsInput	"intron (NM_001173459, intron 1 of 5)"	Lx2|LINE|L1	2156	NM_001173459	100038947	Mm.490172	XM_003946334	ENSMUSG00000074677	LOC100038947	-	signal-regulatory protein beta 1-like	protein-coding	0	0.356436
Merged-chr6-11100310-1	chr6	11100260	11100360	+	2.2	cIP1vsInput	Intergenic	Lx8|LINE|L1	-125932	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	miscRNA	0.01	0.237624
Merged-chr1-147836295-1	chr1	147836245	147836345	+	2.2	cIP1vsInput	Intergenic	L1M4|LINE|L1	1338608	NM_001145807	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.29703
Merged-chr1-114821509-1	chr1	114821459	114821559	+	2.2	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-863628	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0	0.326733
Merged-chr4-129350844-1	chr4	129350794	129350894	+	2.2	cIP2vsInput	Intergenic	B3|SINE|B2	14818	NM_025970	67106	Mm.36575	NM_025970		Zbtb8os	2010001H09Rik|2310028N13Rik|AI851226|Arch|Archm	zinc finger and BTB domain containing 8 opposite strand	protein-coding	0	0.544554
Merged-chr12-67775315-1	chr12	67775265	67775365	+	2.2	cIP1vsInput	Intergenic	Intergenic	-106044	NR_033146	100316870	Mm.379794	NR_033146		Gm17821	-	DDB1 and CUL4 associated factor 5 pseudogene	pseudo	0.01	0.356436
Merged-chrX-14303529-1	chrX	14303479	14303579	+	2.2	cIP1vsInput	Intergenic	MERVL_2A-int|LTR|ERVL	92381	NM_001034100	385328	Mm.275681	NM_001034100	ENSMUSG00000061065	Gm5382	EG385328	predicted gene 5382	protein-coding	0	0.386139
Merged-chr14-106661476-1	chr14	106661426	106661526	+	2.2	cIP1vsInput	Intergenic	Intergenic	-174956	NR_045938	73631	Mm.48862	NR_045938		1700128A07Rik	-	RIKEN cDNA 1700128A07 gene	miscRNA	0	0.257426
Merged-chr7-27526589-1	chr7	27526539	27526639	+	2.2	cIP1vsInput	"intron (NM_001033315, intron 1 of 3)"	"intron (NM_001033315, intron 1 of 3)"	3328	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding	0.01	0.445545
Merged-chr15-35736888-1	chr15	35736838	35736938	+	2.2	cIP2vsInput	"intron (NM_177151, intron 34 of 61)"	L1VL2|LINE|L1	-75841	NR_030606	100124469		NR_030606	ENSMUSG00000077890	Mir875	Mirn875|mmu-mir-875	microRNA 875	miscRNA	0.01	0.336634
Merged-chr2-50738157-1	chr2	50738107	50738207	+	2.2	cIP1vsInput	Intergenic	Intergenic	-171527	NR_033595	227885	Mm.301654	NR_033595	ENSMUSG00000083270	Gm13498	OTTMUSG00000012426	"heat shock protein 90 alpha (cytosolic), class B member 1 pseudogene"	pseudo	0.03	0.346535
Merged-chr15-71447781-1	chr15	71447731	71447831	+	2.2	cIP1vsInput	"intron (NM_177819, intron 19 of 19)"	"intron (NM_177819, intron 19 of 19)"	280057	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	"family with sequence similarity 135, member B"	protein-coding	0	0.316832
Merged-chr6-47226624-1	chr6	47226574	47226674	+	2.2	cIP2vsInput	"intron (NM_001004357, intron 21 of 23)"	"intron (NM_001004357, intron 21 of 23)"	-17772	NM_025771	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0	0.29703
Merged-chr12-13862791-1	chr12	13862741	13862841	+	2.2	cIP1vsInput	Intergenic	Intergenic	289247	NM_029007	105005	Mm.227253	NM_029007	ENSMUSG00000020607	Fam84a	2310003N02Rik|4731402F03Rik|AW125753|Nse1	"family with sequence similarity 84, member A"	protein-coding	0	0.346535
Merged-chr3-83161015-1	chr3	83160965	83161065	+	2.2	cIP2vsInput	Intergenic	Intergenic	105477	NM_016784	53317	Mm.286349	NM_016784	ENSMUSG00000027998	Plrg1	AA958940|C80566|Tango4	"pleiotropic regulator 1, PRL1 homolog (Arabidopsis)"	protein-coding	0	0.366337
Merged-chr6-20721761-1	chr6	20721711	20721811	+	2.2	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	-494348	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	"potassium voltage-gated channel, Shal-related family, member 2"	protein-coding	0	0.326733
Merged-chr13-64826396-1	chr13	64826346	64826446	+	2.2	cIP2vsInput	"intron (NM_001081129, intron 3 of 23)"	Helitron1Na_Mam|RC|Helitron	77492	NM_001081129	238680	Mm.390590	NM_001081129	ENSMUSG00000033063	Cntnap3	-	contactin associated protein-like 3	protein-coding	0	0.336634
Merged-chr1-149187033-1	chr1	149186983	149187083	+	2.2	cIP2vsInput	Intergenic	Intergenic	774251	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0	0.366337
Merged-chr7-93643779-1	chr7	93643729	93643829	+	2.2	cIP1vsInput	Intergenic	MLT1A0|LTR|ERVL-MaLR	563900	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0	0.316832
Merged-chr10-34469454-1	chr10	34469404	34469504	+	2.2	cIP1vsInput	Intergenic	Intergenic	-13946	NM_001159544	14302	Mm.332432	NM_001159544	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding	0	0.29703
Merged-chrX-7713460-1	chrX	7713410	7713510	+	2.2	cIP2vsInput	Intergenic	Intergenic	-8789	NM_172372	54636	Mm.305725	NM_172372	ENSMUSG00000039382	Wdr45	C79260|DXImx38e|JM5|Sfc19|Wdrx1	WD repeat domain 45	protein-coding	0	0.326733
Merged-chr4-5267185-1	chr4	5267135	5267235	+	2.2	cIP1vsInput	Intergenic	Intergenic	-365143	NR_038183	73872	Mm.427301	NR_038183	ENSMUSG00000086066	4930423M02Rik	-	RIKEN cDNA 4930423M02 gene	miscRNA	0.01	0.287129
Merged-chr17-89087176-1	chr17	89087126	89087226	+	2.2	cIP1vsInput	"intron (NM_013523, intron 2 of 9)"	"intron (NM_013523, intron 2 of 9)"	113499	NM_013523	14309	Mm.57155	NM_013523	ENSMUSG00000032937	Fshr	-	follicle stimulating hormone receptor	protein-coding	0	0.366337
Merged-chr6-58058824-1	chr6	58058774	58058874	+	2.2	cIP2vsInput	Intergenic	MurERV4_19-int|LTR|ERVK	-49622	NM_134172	171190	Mm.377170	NM_134172	ENSMUSG00000048697	Vmn1r26	V1rc17	vomeronasal 1 receptor 26	protein-coding	0	0.306931
Merged-chr18-73122195-1	chr18	73122145	73122245	+	2.2	cIP2vsInput	Intergenic	Intergenic	-450510	NM_001039214	240396	Mm.436942	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 homolog C (C. elegans)	protein-coding	0.02	0.39604
Merged-chr14-123814187-1	chr14	123814137	123814237	+	2.2	cIP1vsInput	"intron (NM_145467, intron 2 of 10)"	"intron (NM_145467, intron 2 of 10)"	154047	NM_145467	223272	Mm.383176	NM_145467		Itgbl1	B930011D01Rik	"integrin, beta-like 1"	protein-coding	0	0.287129
Merged-chr14-40034061-1	chr14	40034011	40034111	+	2.2	cIP2vsInput	Intergenic	Intergenic	378398	NR_045936	73591	Mm.65499	NR_045936		1700109I08Rik	-	RIKEN cDNA 1700109I08 gene	miscRNA	0	0.336634
Merged-chr1-49545007-1	chr1	49544957	49545057	+	2.2	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	-1382516	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.326733
Merged-chr6-104999297-1	chr6	104999247	104999347	+	2.2	cIP2vsInput	Intergenic	Intergenic	493371	NR_040297	100503536	Mm.366960	NR_040297		Gm19757	-	"predicted gene, 19757"	miscRNA	0	0.346535
Merged-chr6-127165453-1	chr6	127165403	127165503	+	2.2	cIP2vsInput	"intron (NR_040275, intron 1 of 1)"	L1M4|LINE|L1	-14405	NM_009829	12444	Mm.333406	NM_009829	ENSMUSG00000000184	Ccnd2	2600016F06Rik|AI256817|BF642806|C86853|Vin-1|Vin1|cD2	cyclin D2	protein-coding	0	0.336634
Merged-chr6-74452224-1	chr6	74452174	74452274	+	2.2	cIP1vsInput	Intergenic	Intergenic	-982557	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0.01	0.376238
Merged-chr9-85029675-1	chr9	85029625	85029725	+	2.2	cIP2vsInput	Intergenic	MYSERV6-int|LTR|ERVK	255277	NR_040739	75253	Mm.401984	NR_040739		4930554C24Rik	-	RIKEN cDNA 4930554C24 gene	miscRNA	0	0.336634
Merged-chr8-99743222-1	chr8	99743172	99743272	+	2.2	cIP2vsInput	Intergenic	Intergenic	-326765	NM_001039154	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.29703
Merged-chr10-64701331-1	chr10	64701281	64701381	+	2.2	cIP2vsInput	"intron (NM_001164519, intron 8 of 12)"	"intron (NM_001164519, intron 8 of 12)"	-611076	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding	0	0.247525
Merged-chr15-102003102-1	chr15	102003052	102003152	+	2.2	cIP2vsInput	"intron (NM_031170, intron 1 of 8)"	"intron (NM_031170, intron 1 of 8)"	1240	NM_031170	16691	Mm.358618	NM_031170	ENSMUSG00000049382	Krt8	AA960620|AL022697|AU019895|Card2|EndoA|K8|Krt-2.8|Krt2-8	keratin 8	protein-coding	0.05	0.643564
Merged-chr5-54821271-1	chr5	54821221	54821321	+	2.2	cIP1vsInput	Intergenic	Intergenic	471279	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0	0.277228
Merged-chr6-142335448-1	chr6	142335398	142335498	+	2.2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-10249	NM_183165	232491	Mm.490474	NM_183165		Pyroxd1	-	pyridine nucleotide-disulphide oxidoreductase domain 1	protein-coding	0.01	0.326733
Merged-chr1-102130873-1	chr1	102130823	102130923	+	2.2	cIP1vsInput	Intergenic	Intergenic	975105	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.366337
Merged-chr4-14793692-1	chr4	14793642	14793742	+	2.2	cIP1vsInput	"intron (NM_028499, intron 1 of 7)"	L1_Mur1|LINE|L1	2360	NM_028499	73314	Mm.52613	NM_028499	ENSMUSG00000023151	Lrrc69	1700034K16Rik	leucine rich repeat containing 69	protein-coding	0	0.326733
Merged-chr17-36826872-1	chr17	36826822	36826922	+	2.2	cIP2vsInput	Intergenic	Intergenic	-10269	NM_001025599	22670	Mm.34587	NM_030698	ENSMUSG00000024457	Trim26	AI462198|Zfp173|Zfp1736	tripartite motif-containing 26	protein-coding	0	0.326733
Merged-chr10-52955862-1	chr10	52955812	52955912	+	2.2	cIP2vsInput	"intron (NM_178675, intron 2 of 7)"	"intron (NM_178675, intron 2 of 7)"	265361	NM_178675	215085	Mm.338690	NM_178675	ENSMUSG00000038602	Slc35f1	Duf6|E130016L02	"solute carrier family 35, member F1"	protein-coding	0	0.336634
Merged-chr8-26169651-1	chr8	26169601	26169701	+	2.2	cIP1vsInput	Intergenic	Intergenic	11482	NM_199042	73754	Mm.383241	NM_199042		Thap1	4833431A01Rik|AW490810	"THAP domain containing, apoptosis associated protein 1"	protein-coding	0.01	0.356436
Merged-chr7-124277310-1	chr7	124277260	124277360	+	2.2	cIP1vsInput	"intron (NM_001252072, intron 1 of 1)"	"intron (NM_001252072, intron 1 of 1)"	294129	NM_001252072	628779	Mm.40210	NM_001252072	ENSMUSG00000078591	Hs3st4	EG628779|Gm6915	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	protein-coding	0	0.306931
Merged-chr14-32580230-1	chr14	32580180	32580280	+	2.2	cIP2vsInput	"3' UTR (NM_001081221, exon 21 of 21)"	"3' UTR (NM_001081221, exon 21 of 21)"	-19697	NM_001001796	107751	Mm.119274	NM_001001796	ENSMUSG00000041730	Prrxl1	Drg11|Drgx	paired related homeobox protein-like 1	protein-coding	0	0.287129
Merged-chr17-51453331-1	chr17	51453281	51453381	+	2.2	cIP2vsInput	"intron (NR_037260, intron 3 of 4)"	L1_Mur2|LINE|L1	-5062	NR_046166	328837	Mm.236143	NR_046166		C330011F03Rik	C330011F03	RIKEN cDNA C330011F03 gene	miscRNA	0	0.336634
Merged-chr6-31137013-1	chr6	31136963	31137063	+	2.2	cIP1vsInput	Intergenic	Intergenic	-73920	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1	microRNA 29b-1	miscRNA	0.01	0.485149
Merged-chr6-12502787-1	chr6	12502737	12502837	+	2.2	cIP1vsInput	"intron (NM_001164805, intron 3 of 26)"	"intron (NM_001164805, intron 3 of 26)"	246466	NM_001164805	330267	Mm.400067	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	"thrombospondin, type I, domain containing 7A"	protein-coding	0	0.366337
Merged-chr4-11923313-1	chr4	11923263	11923363	+	2.2	cIP1vsInput	Intergenic	Intergenic	42400	NM_001098231	381511	Mm.331489	NM_001033453	ENSMUSG00000049225	Pdp1	Gm1024|Ppm2c	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding	0.01	0.386139
Merged-chr13-16191805-1	chr13	16191755	16191855	+	2.2	cIP1vsInput	Intergenic	Intergenic	177330	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding	0	0.336634
Merged-chr3-22466604-1	chr3	22466554	22466654	+	2.2	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	215234	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	miscRNA	0	0.336634
Merged-chr2-86552248-1	chr2	86552198	86552298	+	2.2	cIP2vsInput	TTS (NM_146409)	TTS (NM_146409)	5890	NM_146409	258404	Mm.271334	NM_146409	ENSMUSG00000075178	Olfr1080	MOR192-1	olfactory receptor 1080	protein-coding	0	0.346535
Merged-chr6-13001451-1	chr6	13001401	13001501	+	2.2	cIP2vsInput	Intergenic	Intergenic	-68308	NM_027992	71900	Mm.27742	NM_027992	ENSMUSG00000029571	Tmem106b	2310036D22Rik|5830455K21Rik|6430519M21Rik|AI428776|AI661344	transmembrane protein 106B	protein-coding	0	0.336634
Merged-chr8-39925178-1	chr8	39925128	39925228	+	2.2	cIP2vsInput	"intron (NR_035426, intron 3 of 5)"	ORR1B2-int|LTR|ERVL-MaLR	-282500	NM_001113326	20288	Mm.239291	NM_001113326	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding	0	0.366337
Merged-chr10-13755778-1	chr10	13755728	13755828	+	2.2	cIP1vsInput	"intron (NM_025446, intron 3 of 5)"	"intron (NM_025446, intron 3 of 5)"	113052	NM_025446	66253	Mm.45755	NM_025446		Aig1	1500031O19Rik|AV064870|AW413422|CGI-103	androgen-induced 1	protein-coding	0	0.376238
Merged-chr14-78659312-1	chr14	78659262	78659362	+	2.2	cIP2vsInput	"intron (NM_001081336, intron 1 of 28)"	"intron (NM_001081336, intron 1 of 28)"	-30022	NR_045588	380921	Mm.379505	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16	"diacylglycerol kinase, eta"	protein-coding	0.01	0.465347
Merged-chr3-124570887-1	chr3	124570837	124570937	+	2.2	cIP2vsInput	"intron (NR_015460, intron 3 of 3)"	"intron (NR_015460, intron 3 of 3)"	10204	NR_015460	384775	Mm.489851	NR_015460	ENSMUSG00000039174	1700003H04Rik	4930538K10Rik|4933400D22Rik	RIKEN cDNA 1700003H04 gene	miscRNA	0	0.306931
Merged-chr7-52225298-1	chr7	52225248	52225348	+	2.2	cIP1vsInput	Intergenic	Intergenic	-209582	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding	0	0.356436
Merged-chr14-87482168-1	chr14	87482118	87482218	+	2.2	cIP2vsInput	"intron (NM_172605, intron 7 of 13)"	"intron (NM_172605, intron 7 of 13)"	65585	NM_001253755	219249	Mm.35168	NM_001253755	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding	0	0.267327
Merged-chr7-85172354-1	chr7	85172304	85172404	+	2.2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-16452	NM_001102579	620672	Mm.469836	NM_001102579	ENSMUSG00000095664	Vmn2r67	EG620672	"vomeronasal 2, receptor 67"	protein-coding	0.01	0.386139
Merged-chr7-55058109-1	chr7	55058059	55058159	+	2.2	cIP1vsInput	"exon (NM_178705, exon 3 of 12)"	"exon (NM_178705, exon 3 of 12)"	222864	NM_178705	233271	Mm.474990	NM_178705		Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding	0.01	0.39604
Merged-chr15-32920899-1	chr15	32920849	32920949	+	2.2	cIP2vsInput	"5' UTR (NM_008304, exon 1 of 5)"	"5' UTR (NM_008304, exon 1 of 5)"	176	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding	0.11	0.594059
Merged-chr6-17359257-1	chr6	17359207	17359307	+	2.2	cIP1vsInput	Intergenic	Intergenic	51617	NM_001243064	12389	Mm.28278	NM_001243064	ENSMUSG00000007655	Cav1	Cav|Cav-1	"caveolin 1, caveolae protein"	protein-coding	0	0.207921
Merged-chr14-82202588-1	chr14	82202538	82202638	+	2.2	cIP2vsInput	Intergenic	Lx8b|LINE|L1	2202286	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.29703
Merged-chr5-137584254-1	chr5	137584204	137584304	+	2.2	cIP2vsInput	"intron (NM_015799, intron 19 of 19)"	"intron (NM_015799, intron 19 of 19)"	14403	NM_015799	50765	Mm.21757	NM_015799	ENSMUSG00000029716	Tfr2	Trfr2	transferrin receptor 2	protein-coding	0	0.465347
Merged-chr14-69995313-1	chr14	69995263	69995363	+	2.2	cIP2vsInput	"intron (NM_028560, intron 4 of 6)"	"intron (NM_028560, intron 4 of 6)"	-82132	NM_018781	13655	Mm.440893	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding	0.03	0.633663
Merged-chr4-59058322-1	chr4	59058272	59058372	+	2.2	cIP2vsInput	Intergenic	Intergenic	23166	NM_025277	14700	Mm.41780	NM_025277	ENSMUSG00000038607	Gng10	AV006524	"guanine nucleotide binding protein (G protein), gamma 10"	protein-coding	0	0.346535
Merged-chr11-40355871-1	chr11	40355821	40355921	+	2.2	cIP1vsInput	Intergenic	Intergenic	336811	NM_134017	108645	Mm.293771	NM_001199274	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	"methionine adenosyltransferase II, beta"	protein-coding	0.01	0.445545
Merged-chrX-161868054-1	chrX	161868004	161868104	+	2.2	cIP2vsInput	"intron (NM_001081052, intron 3 of 7)"	L1ME4a|LINE|L1	150501	NM_198409	24004	Mm.328503	NM_001103367	ENSMUSG00000043518	Rai2	3f8	retinoic acid induced 2	protein-coding	0	0.336634
Merged-chr6-86041632-1	chr6	86041582	86041682	+	2.2	cIP1vsInput	"intron (NM_001271858, intron 1 of 15)"	"intron (NM_001271858, intron 1 of 15)"	12951	NM_001271860	11519	Mm.104155	NM_001271857	ENSMUSG00000030000	Add2	2900072M03Rik|add97	adducin 2 (beta)	protein-coding	0	0.465347
Merged-chr8-71611172-1	chr8	71611122	71611222	+	2.2	cIP2vsInput	"5' UTR (NM_146211, exon 1 of 12)"	"5' UTR (NM_146211, exon 1 of 12)"	148	NM_146211	234407	Mm.334606	NM_146211	ENSMUSG00000034807	Glt25d1	2810024B22Rik	glycosyltransferase 25 domain containing 1	protein-coding	0.16	0.70297
Merged-chr9-31882723-1	chr9	31882673	31882773	+	2.2	cIP1vsInput	"intron (NM_013800, intron 1 of 3)"	HAL1|LINE|L1	30562	NM_013800	12023	Mm.261044	NM_013800	ENSMUSG00000032033	Barx2	2310006E12Rik|Barx2b	BarH-like homeobox 2	protein-coding	0	0.287129
Merged-chr2-108776835-1	chr2	108776785	108776885	+	2.2	cIP2vsInput	Intergenic	Intergenic	501455	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding	0	0.346535
Merged-chr1-113397528-1	chr1	113397478	113397578	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1532610	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik	dermatan sulfate epimerase-like	protein-coding	0	0.29703
Merged-chr14-91266255-1	chr14	91266205	91266305	+	2.2	cIP2vsInput	Intergenic	Intergenic	1139364	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0	0.316832
Merged-chr19-29685612-1	chr19	29685562	29685662	+	2.2	cIP1vsInput	Intergenic	RLTR16|LTR|ERVK	-12329	NM_029993	77836	Mm.138437	NM_029993		Mlana	A930034P04Rik|Mart1	melan-A	protein-coding	0.02	0.524752
Merged-chr8-104400180-1	chr8	104400130	104400230	+	2.2	cIP1vsInput	Intergenic	Intergenic	-4373	NM_153582	97487	Mm.29658	NM_153582	ENSMUSG00000096188	Cmtm4	Cklfsf4|D19397|ENSMUSG00000051554|Gm9853	CKLF-like MARVEL transmembrane domain containing 4	protein-coding	0.01	0.445545
Merged-chr11-77816325-1	chr11	77816275	77816375	+	2.2	cIP1vsInput	"intron (NM_011586, intron 1 of 39)"	"intron (NM_011586, intron 1 of 39)"	39060	NM_011586	360013	Mm.476162	NM_011586	ENSMUSG00000000631	Myo18a	MyoPDZ|MysPDZ	myosin XVIIIA	protein-coding	0.01	0.386139
Merged-chrX-41350644-1	chrX	41350594	41350694	+	2.2	cIP2vsInput	Intergenic	L2|LINE|L2	-50660	NM_016886	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3|mKIAA4184	"glutamate receptor, ionotropic, AMPA3 (alpha 3)"	protein-coding	0	0.386139
Merged-chr2-43401218-1	chr2	43401168	43401268	+	2.2	cIP1vsInput	Intergenic	Intergenic	-154111	NM_027552	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding	0	0.267327
Merged-chr1-115226350-1	chr1	115226300	115226400	+	2.2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-458787	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0	0.316832
Merged-chr7-85427854-1	chr7	85427804	85427904	+	2.2	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-12178	NM_001105182	330581	Mm.469909	NM_001105182	ENSMUSG00000091006	Vmn2r69	-	"vomeronasal 2, receptor 69"	protein-coding	0	0.366337
Merged-chr1-70459468-1	chr1	70459418	70459518	+	2.2	cIP1vsInput	"intron (NM_025728, intron 5 of 7)"	"intron (NM_025728, intron 5 of 7)"	-266247	NM_177164	320460	Mm.360649	NM_177164	ENSMUSG00000045648	Vwc2l	A830006F12Rik|Brl	von Willebrand factor C domain-containing protein 2-like	protein-coding	0	0.455446
Merged-chr15-22805006-1	chr15	22804956	22805056	+	2.2	cIP2vsInput	Intergenic	Intergenic	-90022	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding	0	0.336634
Merged-chr14-53578784-1	chr14	53578734	53578834	+	2.2	cIP2vsInput	Intergenic	Intergenic	-87156	NM_001205242	100568452	Mm.486072	NM_001205242		A430107P09Rik	Va10	RIKEN cDNA A430107P09 gene	protein-coding	0.01	0.326733
Merged-chr19-41317837-1	chr19	41317787	41317887	+	2.2	cIP2vsInput	"intron (NM_031376, intron 8 of 16)"	"intron (NM_031376, intron 8 of 16)"	-53833	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding	0.02	0.544554
Merged-chr18-25298365-1	chr18	25298315	25298415	+	2.2	cIP1vsInput	"intron (NM_001033532, intron 6 of 10)"	"intron (NM_001033532, intron 6 of 10)"	129345	NM_001033532	225289	Mm.391081	NM_001033532	ENSMUSG00000033632	AW554918	4921538P22|AI461742|Kiaa1328|mKIAA1328	expressed sequence AW554918	protein-coding	0.01	0.267327
Merged-chr13-64801473-1	chr13	64801423	64801523	+	2.2	cIP2vsInput	"intron (NM_001081129, intron 3 of 23)"	"intron (NM_001081129, intron 3 of 23)"	102415	NM_001081129	238680	Mm.390590	NM_001081129	ENSMUSG00000033063	Cntnap3	-	contactin associated protein-like 3	protein-coding	0	0.346535
Merged-chr10-78534481-1	chr10	78534431	78534531	+	2.2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-40019	NM_173751	216136	Mm.2644	NM_173751	ENSMUSG00000032763	Ilvbl	5830463I21|AI415009	ilvB (bacterial acetolactate synthase)-like	protein-coding	0	0.316832
Merged-chr9-94791305-1	chr9	94791255	94791355	+	2.2	cIP1vsInput	"intron (NM_177909, intron 4 of 15)"	"intron (NM_177909, intron 4 of 15)"	121413	NM_177909	331004	Mm.326125	NM_177909	ENSMUSG00000031129	Slc9a9	5730527A11Rik|9930105B05|AI854429|Nhe9	"solute carrier family 9 (sodium/hydrogen exchanger), member 9"	protein-coding	0.01	0.29703
Merged-chr13-84105103-1	chr13	84105053	84105153	+	2.2	cIP1vsInput	Intergenic	Intergenic	-117193	NR_029418	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding	0	0.247525
Merged-chr5-77217219-1	chr5	77217169	77217269	+	2.2	cIP1vsInput	Intergenic	Lx8|LINE|L1	-5766	NM_183284	69982	Mm.46106	NM_183284	ENSMUSG00000053030	Spink2	1700007F22Rik|AV038945|HUSI-II	"serine peptidase inhibitor, Kazal type 2"	protein-coding	0.01	0.445545
Merged-chr6-74199155-1	chr6	74199105	74199205	+	2.2	cIP1vsInput	Intergenic	Intergenic	-729488	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.346535
Merged-chr5-133301650-1	chr5	133301600	133301700	+	2.2	cIP1vsInput	Intergenic	Intergenic	-759307	NM_177047	319974	Mm.488992	NM_177047		Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding	0	0.336634
Merged-chr8-96572734-1	chr8	96572684	96572784	+	2.2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-26761	NR_039538	100628567		NR_039538		Mir28c	mmu-mir-28c	microRNA 28c	miscRNA	0	0.346535
Merged-chrX-88918269-1	chrX	88918219	88918319	+	2.2	cIP2vsInput	Intergenic	Intergenic	-158716	NR_037313	100499530		NR_037313	ENSMUSG00000084559	Mir1906-2	mmu-mir-1906-2	microRNA 1906-2	miscRNA	0.01	0.326733
Merged-chr4-15900301-1	chr4	15900251	15900351	+	2.2	cIP1vsInput	"intron (NM_009788, intron 6 of 10)"	"intron (NM_009788, intron 6 of 10)"	19037	NM_009788	12307	Mm.277665	NM_009788		Calb1	Brain-2|CB|Calb|Calb-1	calbindin 1	protein-coding	0	0.336634
Merged-chr16-87578565-1	chr16	87578515	87578615	+	2.2	cIP1vsInput	"intron (NM_144854, intron 3 of 4)"	"intron (NM_144854, intron 3 of 4)"	25235	NM_144854	224419	Mm.194466	NM_144854	ENSMUSG00000025610	Map3k7cl	C21orf7|ORF63|Tak1l	Map3k7 C-terminal like	protein-coding	0	0.346535
Merged-chrY-10060666-1	chrY	10060616	10060716	+	2.2	cIP1vsInput	Intergenic	ORR1D1|LTR|ERVL-MaLR	1137182	NM_001199331	100040022	Mm.485767	NM_001199331	ENSMUSG00000095172	Gm20822	-	"predicted gene, 20822"	protein-coding	0.02	0.39604
Merged-chr8-5967669-1	chr8	5967619	5967719	+	2.2	cIP2vsInput	Intergenic	Intergenic	-862437	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.316832
Merged-chr6-108562188-1	chr6	108562138	108562238	+	2.2	cIP2vsInput	Intergenic	L1M5|LINE|L1	60979	NR_040757	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	miscRNA	0	0.306931
Merged-chr12-47651545-1	chr12	47651495	47651595	+	2.2	cIP1vsInput	Intergenic	Intergenic	649917	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0	0.247525
Merged-chr9-15672819-1	chr9	15672769	15672869	+	2.2	cIP1vsInput	Intergenic	Intergenic	-36950	NM_172289	234967	Mm.138815	NM_172289	ENSMUSG00000043885	Slc36a4	6330573I15Rik|PAT4	"solute carrier family 36 (proton/amino acid symporter), member 4"	protein-coding	0.01	0.336634
Merged-chr8-63021580-1	chr8	63021530	63021630	+	2.2	cIP2vsInput	"intron (NM_001252620, intron 3 of 11)"	"intron (NM_001252620, intron 3 of 11)"	70235	NM_023689	72902	Mm.334552	NM_001252620	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3"	protein-coding	0	0.356436
Merged-chr9-62147775-1	chr9	62147725	62147825	+	2.2	cIP2vsInput	Intergenic	Intergenic	-25181	NR_039595	100628602		NR_039595	ENSMUSG00000092696	Mir5133	mmu-mir-5133|mu-mir-5133	microRNA 5133	miscRNA	0.01	0.29703
Merged-chr6-110672867-1	chr6	110672817	110672917	+	2.2	cIP2vsInput	"intron (NM_177328, intron 1 of 9)"	"intron (NM_177328, intron 1 of 9)"	27269	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0.01	0.326733
Merged-chr9-81096740-1	chr9	81096690	81096790	+	2.2	cIP2vsInput	Intergenic	Intergenic	-535190	NR_040394	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	miscRNA	0.01	0.346535
Merged-chr6-143308472-1	chr6	143308422	143308522	+	2.2	cIP2vsInput	Intergenic	Intergenic	62584	NR_027803	52285	Mm.354898	NM_001033129		D6Ertd474e	1700001I24Rik|AU023129	"DNA segment, Chr 6, ERATO Doi 474, expressed"	miscRNA	0	0.376238
Merged-chr17-25405309-1	chr17	25405259	25405359	+	2.2	cIP2vsInput	"intron (NM_021415, intron 2 of 34)"	"intron (NM_021415, intron 2 of 34)"	28474	NM_021415	58226	Mm.268378	NM_001163691	ENSMUSG00000024112	Cacna1h	Cav3.2|MNCb-1209|alpha13.2	"calcium channel, voltage-dependent, T type, alpha 1H subunit"	protein-coding	0.02	0.742574
Merged-chrX-73787028-1	chrX	73786978	73787078	+	2.2	cIP2vsInput	promoter-TSS (NM_008323)	promoter-TSS (NM_008323)	0	NM_001166480	20832	Mm.831	NM_001166480	ENSMUSG00000002014	Ssr4	AW743063|C78062|Trap	"signal sequence receptor, delta"	protein-coding	0.06	0.643564
Merged-chr1-29233890-1	chr1	29233840	29233940	+	2.2	cIP2vsInput	Intergenic	Intergenic	-453638	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0	0.287129
Merged-chr2-133899001-1	chr2	133898951	133899051	+	2.2	cIP2vsInput	Intergenic	Intergenic	346842	NM_007553	12156	Mm.103205	NM_007553		Bmp2	AI467020|Bmp2a	bone morphogenetic protein 2	protein-coding	0	0.336634
Merged-chr9-11616955-1	chr9	11616905	11617005	+	2.2	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	-712180	NM_001170787	244682	Mm.490683	NM_001033359	ENSMUSG00000039488	Cntn5	6720426O10Rik|A830025P08Rik|Gm507|NB-2	contactin 5	protein-coding	0	0.376238
Merged-chr13-68028085-1	chr13	68028035	68028135	+	2.2	cIP1vsInput	Intergenic	Intergenic	164759	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding	0.01	0.316832
Merged-chr16-55863599-2	chr16	55863542	55863657	+	2.2	cIP1vsInput|cIP2vsInput	"intron (NM_001134457, intron 3 of 5)"	"intron (NM_001134457, intron 3 of 5)"	-24958	NM_001159395	80859	Mm.247272	NM_001159394	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	"nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta"	protein-coding	0.026087	0.491379
Merged-chrX-9908790-1	chrX	9908740	9908840	+	2.2	cIP2vsInput	"intron (NM_177704, intron 2 of 16)"	Lx6|LINE|L1	23168	NM_177704	236643	Mm.246606	NM_177704	ENSMUSG00000054453	Sytl5	ENSMUSG00000054453|slp5	synaptotagmin-like 5	protein-coding	0	0.316832
Merged-chr13-87485525-1	chr13	87485475	87485575	+	2.2	cIP2vsInput	Intergenic	L1MC1|LINE|L1	-1335947	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0.01	0.29703
Merged-chr1-78982205-1	chr1	78982155	78982255	+	2.2	cIP1vsInput	Intergenic	L1ME3|LINE|L1	165256	NM_021342	57814	Mm.24386	NM_021342	ENSMUSG00000047330	Kcne4	AW487937|MiRP3	"potassium voltage-gated channel, Isk-related subfamily, gene 4"	protein-coding	0.01	0.386139
Merged-chr8-116465274-1	chr8	116465224	116465324	+	2.2	cIP1vsInput	Intergenic	Intergenic	-39741	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding	0.01	0.376238
Merged-chr10-92621855-1	chr10	92621805	92621905	+	2.2	cIP1vsInput	Intergenic	Intergenic	100563	NM_008682	17997	Mm.2998	NM_008682	ENSMUSG00000019988	Nedd1	-	"neural precursor cell expressed, developmentally down-regulated gene 1"	protein-coding	0.01	0.356436
Merged-chr13-48464271-1	chr13	48464221	48464321	+	2.2	cIP2vsInput	Intergenic	Intergenic	49139	NM_001164575	67911	Mm.251375	NM_001164575	ENSMUSG00000050954	Zfp169	1700025J14Rik|4930429A13Rik|BE688704	zinc finger protein 169	protein-coding	0.01	0.465347
Merged-chr4-131253621-1	chr4	131253571	131253671	+	2.2	cIP1vsInput	Intergenic	Intergenic	309236	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	"matrilin 1, cartilage matrix protein"	protein-coding	0.01	0.50495
Merged-chr18-55850264-1	chr18	55850214	55850314	+	2.2	cIP1vsInput	Intergenic	Intergenic	-581868	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding	0	0.247525
Merged-chr13-51717248-1	chr13	51717198	51717298	+	2.2	cIP1vsInput	"intron (NM_013660, intron 6 of 15)"	"intron (NM_013660, intron 6 of 15)"	65534	NM_029279	75420	Mm.275981	NM_029279	ENSMUSG00000035139	Secisbp2	2210413N07Rik|2810012K13Rik|SBP2	SECIS binding protein 2	protein-coding	0.03	0.663366
Merged-chr2-131345348-1	chr2	131345298	131345398	+	2.2	cIP1vsInput	"intron (NM_178607, intron 1 of 5)"	"intron (NM_178607, intron 1 of 5)"	7544	NM_178607	51902	Mm.477523	NM_178607	ENSMUSG00000048911	Rnf24	2810473M14Rik|4930505A13Rik|AI317164|C86507|D2Ertd504e	ring finger protein 24	protein-coding	0.01	0.386139
Merged-chr7-27850617-1	chr7	27850567	27850667	+	2.2	cIP1vsInput	"intron (NM_011762, intron 4 of 4)"	Lx5|LINE|L1	-9968	NM_001024726	545938	Mm.458180	NM_001024726		Zfp607	4732475C15Rik	zinc finger proten 607	protein-coding	0	0.366337
Merged-chr7-93797612-1	chr7	93797562	93797662	+	2.2	cIP1vsInput	Intergenic	L1MEg|LINE|L1	717733	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0	0.227723
Merged-chr14-81521263-1	chr14	81521213	81521313	+	2.2	cIP1vsInput	Intergenic	Lx8|LINE|L1	1520961	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.29703
Merged-chr8-42256520-1	chr8	42256470	42256570	+	2.2	cIP1vsInput	Intergenic	RLTR21|LTR|ERVK	429253	NR_045497	69966	Mm.416903	NR_045497		2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	miscRNA	0.01	0.376238
Merged-chr2-174110505-1	chr2	174110455	174110555	+	2.2	cIP2vsInput	"exon (NM_213733, exon 1 of 12)"	"exon (NM_213733, exon 1 of 12)"	154	NM_213733	228961	Mm.295629	NM_213733	ENSMUSG00000039263	Npepl1	BC023239|C85514|mKIAA1974	aminopeptidase-like 1	protein-coding	0.1	0.752475
Merged-chr17-76384656-1	chr17	76384606	76384706	+	2.2	cIP2vsInput	Intergenic	Intergenic	523633	NR_033456	100043885	Mm.127562	NR_033456		Gm4710	-	predicted gene 4710	miscRNA	0	0.29703
Merged-chr6-74666982-1	chr6	74666932	74667032	+	2.2	cIP2vsInput	Intergenic	Intergenic	-1197315	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.356436
Merged-chr10-122410697-1	chr10	122410647	122410747	+	2.2	cIP1vsInput	Intergenic	ORR1D1-int|LTR|ERVL-MaLR	-37802	NM_016847	54140	Mm.4351	NM_016847	ENSMUSG00000020123	Avpr1a	AVPR|Avpr1|V1a|V1aR	arginine vasopressin receptor 1A	protein-coding	0.01	0.306931
Merged-chr1-153425148-1	chr1	153425098	153425198	+	2.2	cIP2vsInput	promoter-TSS (NM_001033162)	promoter-TSS (NM_001033162)	-61	NM_001033162	71836	Mm.49460	NM_001033162	ENSMUSG00000042708	Shcbp1l	1700012A16Rik	Shc SH2-domain binding protein 1-like	protein-coding	0.13	0.732673
Merged-chr17-60553654-1	chr17	60553604	60553704	+	2.2	cIP1vsInput	Intergenic	Lx3_Mus|LINE|L1	-764098	NR_030569	100124495		NR_030569		Mir466g	Mirn466g	microRNA 466g	miscRNA	0	0.366337
Merged-chr10-64830714-1	chr10	64830664	64830764	+	2.2	cIP2vsInput	"intron (NM_001164519, intron 8 of 12)"	"intron (NM_001164519, intron 8 of 12)"	-740459	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding	0	0.287129
Merged-chr4-79240181-1	chr4	79240131	79240231	+	2.2	cIP2vsInput	Intergenic	PB1D11|SINE|Alu	-1028286	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0.01	0.346535
Merged-chr16-64652216-1	chr16	64652166	64652266	+	2.2	cIP1vsInput	Intergenic	Intergenic	118723	NM_026273	67609	Mm.212157	NM_026273		4930453N24Rik	AI649104	RIKEN cDNA 4930453N24 gene	protein-coding	0	0.316832
Merged-chr14-111408418-1	chr14	111408368	111408468	+	2.2	cIP1vsInput	Intergenic	Intergenic	-266697	NM_198865	75409	Mm.417152	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	"SLIT and NTRK-like family, member 5"	protein-coding	0	0.316832
Merged-chr13-31103156-1	chr13	31103106	31103206	+	2.2	cIP2vsInput	Intergenic	Intergenic	-129109	NM_025588	66482	Mm.293510	NM_025588	ENSMUSG00000021357	Exoc2	2410030I24Rik|AI648199|Sec5|Sec5l1	exocyst complex component 2	protein-coding	0.01	0.326733
Merged-chr17-52189660-1	chr17	52189610	52189710	+	2.2	cIP1vsInput	Intergenic	B3|SINE|B2	306933	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	"predicted gene, 20098"	miscRNA	0.01	0.425743
Merged-chr4-89103724-1	chr4	89103674	89103774	+	2.2	cIP1vsInput	Intergenic	Intergenic	-33646	NM_024433	66902	Mm.28500	NM_024433	ENSMUSG00000062937	Mtap	1300019I21Rik|MSAP	methylthioadenosine phosphorylase	protein-coding	0	0.346535
Merged-chr17-78749172-1	chr17	78749122	78749222	+	2.2	cIP1vsInput	Intergenic	Intergenic	-12612	NM_011500	268980	Mm.486430	NM_011500		Strn	AU022939|D130055P19	"striatin, calmodulin binding protein"	protein-coding	0	0.267327
Merged-chr2-18908963-1	chr2	18908913	18909013	+	2.2	cIP1vsInput	"intron (NM_008845, intron 1 of 9)"	"intron (NM_008845, intron 1 of 9)"	89158	NM_008845	18718	Mm.313977	NM_008845	ENSMUSG00000026737	Pip4k2a	AW742916|Pip5k2a	"phosphatidylinositol-5-phosphate 4-kinase, type II, alpha"	protein-coding	0	0.316832
Merged-chr13-53947306-1	chr13	53947256	53947356	+	2.2	cIP1vsInput	Intergenic	Intergenic	108352	NM_010076	13488	Mm.54161	NM_010076	ENSMUSG00000021478	Drd1a	C030036C15Rik|Drd-1|Drd1|Gpcr15	dopamine receptor D1A	protein-coding	0.02	0.405941
Merged-chr1-149670462-1	chr1	149670412	149670512	+	2.2	cIP2vsInput	Intergenic	Intergenic	290822	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0.02	0.346535
Merged-chr2-125415139-1	chr2	125415089	125415189	+	2.2	cIP1vsInput	"intron (NM_007993, intron 6 of 65)"	"intron (NM_007993, intron 6 of 65)"	91299	NM_007993	14118	Mm.271644	NM_007993	ENSMUSG00000027204	Fbn1	AI536462|B430209H23|Fib-1|Tsk	fibrillin 1	protein-coding	0	0.257426
Merged-chr12-101488389-1	chr12	101488339	101488439	+	2.2	cIP2vsInput	"intron (NM_173023, intron 10 of 26)"	MYSERV16_I-int|LTR|ERVK	83716	NM_173023	271036	Mm.84218	NM_173023	ENSMUSG00000047014	Catsperb	4931410B03|4932415G16Rik	catsper channel auxiliary subunit beta	protein-coding	0.01	0.356436
Merged-chr18-43619982-1	chr18	43619932	43620032	+	2.2	cIP1vsInput	"intron (NM_001163637, intron 1 of 21)"	"intron (NM_001163637, intron 1 of 21)"	67791	NM_001163637	76217	Mm.134602	NM_001163637	ENSMUSG00000024502	Jakmip2	6430702L21Rik|AI850334|D930046L20Rik	janus kinase and microtubule interacting protein 2	protein-coding	0	0.346535
Merged-chr15-95263062-1	chr15	95263012	95263112	+	2.2	cIP2vsInput	"intron (NM_016743, intron 16 of 20)"	"intron (NM_016743, intron 16 of 20)"	-113744	NR_015482	100043315	Mm.159041	NR_015482		LOC100043315	-	uncharacterized LOC100043315	miscRNA	0	0.346535
Merged-chr6-60471265-1	chr6	60471215	60471315	+	2.2	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	-67558	NR_015565	208079	Mm.490691	NR_015565		A530053G22Rik	-	RIKEN cDNA A530053G22 gene	miscRNA	0	0.326733
Merged-chr15-36191670-1	chr15	36191620	36191720	+	2.2	cIP2vsInput	"intron (NM_012031, intron 6 of 18)"	"intron (NM_012031, intron 6 of 18)"	12140	NM_012031	26942		NM_012031	ENSMUSG00000037617	Spag1	tpis	sperm associated antigen 1	protein-coding	0.01	0.336634
Merged-chr18-14034101-1	chr18	14034051	14034151	+	2.2	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-61368	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding	0.01	0.356436
Merged-chr3-4412723-1	chr3	4412673	4412773	+	2.2	cIP2vsInput	Intergenic	Intergenic	-385985	NR_045272	100503859	Mm.75172	NR_045272		1110015O18Rik	-	RIKEN cDNA 1110015O18 gene	miscRNA	0	0.247525
Merged-chr5-114467691-1	chr5	114467641	114467741	+	2.2	cIP1vsInput	Intergenic	Intergenic	23385	NM_023556	17855	Mm.28088	NM_023556	ENSMUSG00000041939	Mvk	2310010A05Rik|AI256848|AI414037|MK	mevalonate kinase	protein-coding	0.02	0.455446
Merged-chr1-113400142-1	chr1	113400092	113400192	+	2.2	cIP2vsInput	Intergenic	MER58A|DNA|hAT-Charlie	-1535224	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik	dermatan sulfate epimerase-like	protein-coding	0	0.326733
Merged-chr1-121430874-1	chr1	121430824	121430924	+	2.2	cIP1vsInput	promoter-TSS (NM_029955)	promoter-TSS (NM_029955)	-193	NM_029955	70829	Mm.25788	NM_027567	ENSMUSG00000026339	Ccdc93	4633402D15Rik|9230102M16Rik	coiled-coil domain containing 93	protein-coding	0	0.237624
Merged-chr6-75602189-1	chr6	75602139	75602239	+	2.2	cIP2vsInput	Intergenic	Intergenic	-1640528	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0	0.316832
Merged-chr4-79806010-1	chr4	79805960	79806060	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1028220	NM_031202	22178	Mm.412291	NM_031202	ENSMUSG00000005994	Tyrp1	TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding	0	0.326733
Merged-chr13-25091817-1	chr13	25091767	25091867	+	2.2	cIP2vsInput	"intron (NM_001195617, intron 2 of 7)"	"intron (NM_001195617, intron 2 of 7)"	35813	NM_177577	195208	Mm.284719	NM_001195617	ENSMUSG00000035910	Dcdc2a	AW492955|Dcdc2|RU2	doublecortin domain containing 2a	protein-coding	0	0.306931
Merged-chr16-83670688-1	chr16	83670638	83670738	+	2.2	cIP1vsInput	Intergenic	Intergenic	-700455	NR_040567	75247	Mm.417813	NR_040567		4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	miscRNA	0	0.376238
Merged-chr6-57067773-1	chr6	57067723	57067823	+	2.2	cIP1vsInput	Intergenic	Intergenic	-3122	NM_134185	171203	Mm.377181	NM_134185	ENSMUSG00000091541	Vmn1r9	V1rc30	vomeronasal 1 receptor 9	protein-coding	0	0.257426
Merged-chr15-101421061-1	chr15	101421011	101421111	+	2.2	cIP2vsInput	"intron (NM_033073, intron 6 of 8)"	"intron (NM_033073, intron 6 of 8)"	8658	NM_033073	110310	Mm.486285	NM_033073		Krt7	D15Wsu77e|K7|Krt2-7	keratin 7	protein-coding	0.02	0.564356
Merged-chr12-14612699-1	chr12	14612649	14612749	+	2.2	cIP1vsInput	Intergenic	Intergenic	351165	NR_045003	791361	Mm.217963	NR_045003		Gm16497	ENSMUSG00000066623	predicted gene 16497	miscRNA	0.01	0.316832
Merged-chr4-25303858-1	chr4	25303808	25303908	+	2.2	cIP2vsInput	Intergenic	Charlie1b|DNA|hAT-Charlie	-22037	NM_026194	67490	Mm.226295	NM_026194	ENSMUSG00000040359	Ufl1	1810074P20Rik|AI429228|Kiaa0776|Maxer|Rcad|mKIAA0776	UFM1 specific ligase 1	protein-coding	0	0.366337
Merged-chr15-36210126-1	chr15	36210076	36210176	+	2.2	cIP1vsInput	"intron (NM_012031, intron 10 of 18)"	"intron (NM_012031, intron 10 of 18)"	30596	NM_012031	26942		NM_012031	ENSMUSG00000037617	Spag1	tpis	sperm associated antigen 1	protein-coding	0.01	0.336634
Merged-chr4-20984588-1	chr4	20984538	20984638	+	2.2	cIP1vsInput	Intergenic	Intergenic	-205920	NM_172987	269513		NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding	0	0.207921
Merged-chr11-10258213-1	chr11	10258163	10258263	+	2.2	cIP2vsInput	Intergenic	Intergenic	-855803	NM_177033	319922	Mm.487612	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding	0	0.316832
Merged-chr7-24299657-1	chr7	24299607	24299707	+	2.2	cIP2vsInput	promoter-TSS (NM_009561)	promoter-TSS (NM_009561)	-108	NM_009561	22719	Mm.12832	NM_009561	ENSMUSG00000050605	Zfp61	-	zinc finger protein 61	protein-coding	0.08	0.574257
Merged-chr14-24351057-1	chr14	24351007	24351107	+	2.2	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	57693	NM_001033214	105418	Mm.2077	NM_001033214	ENSMUSG00000038925	E330034G19Rik	AA415275	RIKEN cDNA E330034G19 gene	protein-coding	0.01	0.376238
Merged-chr1-148452161-1	chr1	148452111	148452211	+	2.2	cIP1vsInput	Intergenic	Intergenic	1509123	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0	0.316832
Merged-chr4-111524957-1	chr4	111524907	111525007	+	2.2	cIP1vsInput	"intron (NM_001048189, intron 6 of 12)"	"intron (NM_001048189, intron 6 of 12)"	109951	NM_026279	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding	0.01	0.346535
Merged-chr9-112428312-1	chr9	112428262	112428362	+	2.2	cIP2vsInput	Intergenic	Intergenic	171738	NR_033433	620760	Mm.259863	NR_015468	ENSMUSG00000087038	2900079G21Rik	C130083B14|Gm6179	RIKEN cDNA 2900079G21 gene	miscRNA	0	0.336634
Merged-chr1-61510641-1	chr1	61510591	61510691	+	2.2	cIP1vsInput	Intergenic	Lx2B|LINE|L1	-128183	NM_001081050	72823	Mm.441881	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta|RP23-20G7.1	par-3 partitioning defective 3 homolog B (C. elegans)	protein-coding	0.01	0.326733
Merged-chr5-83617225-1	chr5	83617175	83617275	+	2.2	cIP1vsInput	Intergenic	Intergenic	-262030	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	"trans-2,3-enoyl-CoA reductase-like"	protein-coding	0.01	0.316832
Merged-chr10-15245894-1	chr10	15245844	15245944	+	2.2	cIP2vsInput	Intergenic	ORR1F|LTR|ERVL-MaLR	485605	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding	0.01	0.316832
Merged-chr16-47151130-1	chr16	47151080	47151180	+	2.2	cIP2vsInput	Intergenic	LTR40b|LTR|ERVL	-654163	NM_021497	58998	Mm.328072	NM_021495	ENSMUSG00000022656	Pvrl3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113	poliovirus receptor-related 3	protein-coding	0	0.366337
Merged-chr14-82064057-1	chr14	82064007	82064107	+	2.2	cIP1vsInput	Intergenic	Intergenic	2063755	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.227723
Merged-chr6-57353089-1	chr6	57353039	57353139	+	2.2	cIP2vsInput	Intergenic	L1VL2|LINE|L1	8289	NM_134171	171189	Mm.377169	NM_134171	ENSMUSG00000093411	Vmn1r17	V1rc16	vomeronasal 1 receptor 17	protein-coding	0	0.306931
Merged-chr1-156336779-1	chr1	156336729	156336829	+	2.2	cIP1vsInput	Intergenic	Intergenic	26044	NM_130456	170484	Mm.289099	NM_130456	ENSMUSG00000026602	Nphs2	AI790225|PDCN|SRN1	"nephrosis 2 homolog, podocin (human)"	protein-coding	0.01	0.376238
Merged-chr18-15603294-1	chr18	15603244	15603344	+	2.2	cIP1vsInput	"intron (NM_199055, intron 2 of 3)"	L1MB2|LINE|L1	114752	NM_199055	71367	Mm.329304	NM_199055	ENSMUSG00000047161	Chst9	5430438D01Rik	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	protein-coding	0.01	0.386139
Merged-chr16-26832755-1	chr16	26832705	26832805	+	2.2	cIP2vsInput	Intergenic	Intergenic	157219	NM_001013761	239789	Mm.326909	NM_001013761	ENSMUSG00000068428	Gmnc	Gemc1|Gm1778|Gm606	geminin coiled-coil domain containing	protein-coding	0.01	0.386139
Merged-chr6-9856924-1	chr6	9856874	9856974	+	2.2	cIP2vsInput	Intergenic	Lx6|LINE|L1	906905	NM_008751	18231	Mm.46954	NM_008751		Nxph1	C130005L03Rik	neurexophilin 1	protein-coding	0	0.306931
Merged-chr1-9426919-1	chr1	9426869	9426969	+	2.2	cIP1vsInput	Intergenic	ERVB4_1B-I_MM-int|LTR|ERVK	-118489	NM_021511	59014	Mm.29061	NM_021511	ENSMUSG00000061024	Rrs1	5730466A07Rik|AA415037|D1Ertd701e|Rrr	RRS1 ribosome biogenesis regulator homolog (S. cerevisiae)	protein-coding	0	0.326733
Merged-chr15-65456393-1	chr15	65456343	65456443	+	2.2	cIP2vsInput	Intergenic	Intergenic	-330648	NM_133766	76740	Mm.260647	NM_133766	ENSMUSG00000015002	Efr3a	A130089M23Rik|BB071175|C76891|C920006C10Rik|D030063F01Rik|mKIAA0143	EFR3 homolog A (S. cerevisiae)	protein-coding	0	0.336634
Merged-chr10-36911904-1	chr10	36911854	36911954	+	2.2	cIP2vsInput	Intergenic	Intergenic	-62640	NM_008229	15182	Mm.19806	NM_008229	ENSMUSG00000019777	Hdac2	D10Wsu179e|YAF1|Yy1bp|mRPD3	histone deacetylase 2	protein-coding	0	0.346535
Merged-chr4-131420449-1	chr4	131420399	131420499	+	2.2	cIP1vsInput	Intergenic	L1ME1|LINE|L1	417829	NM_011214	19273	Mm.4860	NM_001083119	ENSMUSG00000028909	Ptpru	Ftp-1|PCP-2|PTP|PTP-lambda|PTPlambda|Pcp2|Ptpf|Ptprl|R-PTP-U|R-PTP-psi|RPTPlambda	"protein tyrosine phosphatase, receptor type, U"	protein-coding	0	0.326733
Merged-chr6-148641629-1	chr6	148641579	148641679	+	2.2	cIP1vsInput	Intergenic	Intergenic	-27320	NR_045867	622319	Mm.491049	NM_001037912	ENSMUSG00000070995	Gm6313	EG622319	predicted gene 6313	miscRNA	0.02	0.39604
Merged-chr3-92199478-1	chr3	92199428	92199528	+	2.2	cIP2vsInput	Intergenic	Intergenic	-16357	NM_001164787	100303744	Mm.429851	NM_001164787	ENSMUSG00000068893	Sprr2a2	-	small proline-rich protein 2A2	protein-coding	0	0.306931
Merged-chr5-28422889-1	chr5	28422839	28422939	+	2.2	cIP1vsInput	Intergenic	MTE-int|LTR|ERVL-MaLR	-44095	NR_015562	654796	Mm.403014	NR_015562	ENSMUSG00000097726	9530036O11Rik	-	RIKEN cDNA 9530036O11Rik	miscRNA	0.02	0.50495
Merged-chr9-73923437-1	chr9	73923387	73923487	+	2.2	cIP1vsInput	"intron (NM_001081153, intron 1 of 30)"	"intron (NM_001081153, intron 1 of 30)"	10130	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|AU019458|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C (C. elegans)	protein-coding	0.01	0.336634
Merged-chr1-59623299-1	chr1	59623249	59623349	+	2.2	cIP2vsInput	"intron (NM_001013771, intron 13 of 19)"	"intron (NM_001013771, intron 13 of 19)"	47535	NM_009460	22218	Mm.362118	NM_009460	ENSMUSG00000026021	Sumo1	GMP1|PIC1|SENTRIN|SMT3|SMT3H3|SMTP3|SUMO-1|Smt3C|Ubl1	SMT3 suppressor of mif two 3 homolog 1 (yeast)	protein-coding	0.01	0.29703
Merged-chr4-80248100-1	chr4	80248050	80248150	+	2.2	cIP2vsInput	Intergenic	Intergenic	-586130	NM_031202	22178	Mm.412291	NM_031202	ENSMUSG00000005994	Tyrp1	TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding	0	0.346535
Merged-chr13-34372839-1	chr13	34372789	34372889	+	2.2	cIP2vsInput	Intergenic	Intergenic	-27657	NM_001033167	73102	Mm.23932	NM_001033167	ENSMUSG00000038267	Slc22a23	3110004L20Rik	"solute carrier family 22, member 23"	protein-coding	0.02	0.39604
Merged-chr16-89676212-1	chr16	89676162	89676262	+	2.2	cIP1vsInput	Intergenic	Intergenic	-105029	NM_001113406	16693	Mm.310906	NM_001113406	ENSMUSG00000091212	Krtap11-1	AA162070|AA589467|AV018433|Hacl1|KAP11.1|PRED29	keratin associated protein 11-1	protein-coding	0	0.336634
Merged-chr12-63199799-1	chr12	63199749	63199849	+	2.2	cIP2vsInput	Intergenic	Lx9|LINE|L1	1275099	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.346535
Merged-chr6-71087036-1	chr6	71086986	71087086	+	2.2	cIP1vsInput	Intergenic	Lx7|LINE|L1	57340	NM_001033929	232078	Mm.37547	NM_001033929	ENSMUSG00000054474	Thnsl2	BC051244|TSH2	threonine synthase-like 2 (bacterial)	protein-coding	0	0.435644
Merged-chr13-92309690-1	chr13	92309640	92309740	+	2.2	cIP2vsInput	"intron (NM_010829, intron 9 of 23)"	"intron (NM_010829, intron 9 of 23)"	-45093	NM_010049	13361	Mm.23695	NM_010049	ENSMUSG00000021707	Dhfr	8430436I03Rik|AA607882|AI662710|AW555094	dihydrofolate reductase	protein-coding	0.01	0.306931
Merged-chr13-85331533-1	chr13	85331483	85331583	+	2.2	cIP1vsInput	Intergenic	Intergenic	-42047	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding	0.01	0.29703
Merged-chr9-59299963-1	chr9	59299913	59300013	+	2.2	cIP1vsInput	"intron (NM_028121, intron 2 of 6)"	"intron (NM_028121, intron 2 of 6)"	8391	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding	0	0.346535
Merged-chr11-9619746-1	chr11	9619696	9619796	+	2.2	cIP1vsInput	"intron (NM_178259, intron 56 of 61)"	"intron (NM_178259, intron 56 of 61)"	427804	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	"ATP-binding cassette, sub-family A (ABC1), member 13"	protein-coding	0	0.287129
Merged-chr5-85853303-1	chr5	85853253	85853353	+	2.2	cIP1vsInput	Intergenic	Intergenic	212280	NM_007683	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	Cenpc	centromere protein C1	protein-coding	0	0.316832
Merged-chr8-78395679-1	chr8	78395629	78395729	+	2.2	cIP1vsInput	Intergenic	L1ME1|LINE|L1	40973	NM_138944	18997	Mm.234261	NM_138944	ENSMUSG00000031688	Pou4f2	Brn-3.2|Brn-3b|Brn3b|Pou4f-rs1|mBrn3-3R	"POU domain, class 4, transcription factor 2"	protein-coding	0	0.316832
Merged-chr4-93611422-1	chr4	93611372	93611472	+	2.2	cIP1vsInput	Intergenic	Intergenic	-275911	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding	0.01	0.366337
Merged-chr9-110155606-1	chr9	110155556	110155656	+	2.2	cIP1vsInput	"intron (NM_009211, intron 6 of 27)"	"intron (NM_009211, intron 6 of 27)"	23582	NM_009211	20588	Mm.85410	NM_009211	ENSMUSG00000032481	Smarcc1	AI115498|BAF155|Rsc8|SRG3	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1"	protein-coding	0	0.277228
Merged-chr2-116330781-1	chr2	116330731	116330831	+	2.2	cIP1vsInput	Intergenic	Intergenic	-254685	NR_033447	69974	Mm.440293	NR_033447		2810405F15Rik	-	RIKEN cDNA 2810405F15 gene	miscRNA	0	0.336634
Merged-chr4-66664900-1	chr4	66664850	66664950	+	2.2	cIP2vsInput	Intergenic	L1MDa|LINE|L1	-162911	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding	0	0.366337
Merged-chr6-54215626-1	chr6	54215576	54215676	+	2.2	cIP1vsInput	"intron (NM_001163640, intron 3 of 12)"	"intron (NM_001163640, intron 3 of 12)"	-57196	NM_023543	69993	Mm.448157	NM_001163640	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin (chimaerin) 2	protein-coding	0	0.257426
Merged-chr16-51096547-1	chr16	51096497	51096597	+	2.2	cIP1vsInput	Intergenic	Intergenic	-363774	NR_028300	68190	Mm.482928	NR_028300		5330426P16Rik	-	RIKEN cDNA 5330426P16 gene	miscRNA	0	0.306931
Merged-chr15-91594996-1	chr15	91594946	91595046	+	2.2	cIP1vsInput	Intergenic	Intergenic	-21735	NM_001033633	239606	Mm.360596	NM_001033633	ENSMUSG00000036298	Slc2a13	6530403A04|A630029G22Rik|AI505012|Gm308	"solute carrier family 2 (facilitated glucose transporter), member 13"	protein-coding	0.01	0.267327
Merged-chr4-74783045-1	chr4	74782995	74783095	+	2.2	cIP2vsInput	Intergenic	Intergenic	495241	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	3110001D03Rik	1700027K24Rik	RIKEN cDNA 3110001D03 gene	protein-coding	0	0.346535
Merged-chr1-114481151-1	chr1	114481101	114481201	+	2.2	cIP2vsInput	Intergenic	Intergenic	-1203986	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0	0.29703
Merged-chr17-27989975-1	chr17	27989925	27990025	+	2.2	cIP2vsInput	"intron (NM_181413, intron 9 of 24)"	"intron (NM_181413, intron 9 of 24)"	80635	NM_181413	224650	Mm.32556	NM_181413	ENSMUSG00000024219	Anks1	Anks1a|mKIAA0229	ankyrin repeat and SAM domain containing 1	protein-coding	0.03	0.564356
Merged-chr6-91722572-1	chr6	91722522	91722622	+	2.2	cIP1vsInput	"intron (NM_009320, intron 2 of 14)"	"intron (NM_009320, intron 2 of 14)"	38505	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	"solute carrier family 6 (neurotransmitter transporter, taurine), member 6"	protein-coding	0.01	0.485149
Merged-chr3-36906192-1	chr3	36906142	36906242	+	2.2	cIP2vsInput	"intron (NM_172679, intron 13 of 85)"	"intron (NM_172679, intron 13 of 85)"	43086	NM_172679	229227	Mm.207907	NM_172679	ENSMUSG00000037270	4932438A13Rik	4732443H21|B830039D19Rik|D630029K19Rik|FSA|Kiaa1109|RP23-243E17.1|Tweek	RIKEN cDNA 4932438A13 gene	protein-coding	0.01	0.316832
Merged-chr18-38049184-1	chr18	38049134	38049234	+	2.2	cIP1vsInput	Intergenic	Intergenic	-50215	NM_001205336	106952	Mm.247642	NM_001205336	ENSMUSG00000024451	Arap3	Centd3|Drag1|E030006K04Rik|cnt-d3	"ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3"	protein-coding	0	0.356436
Merged-chr8-6309905-1	chr8	6309855	6309955	+	2.2	cIP2vsInput	Intergenic	Intergenic	-1204673	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.336634
Merged-chr14-14190818-1	chr14	14190768	14190868	+	2.2	cIP2vsInput	Intergenic	L1VL2|LINE|L1	-14738	NM_146392	258387	Mm.377472	NM_146392	ENSMUSG00000052417	Olfr720	MOR274-2	olfactory receptor 720	protein-coding	0	0.356436
Merged-chr8-32483395-1	chr8	32483345	32483445	+	2.2	cIP1vsInput	Intergenic	L1_Mus4|LINE|L1	331500	NR_046039	666589	Mm.367675	NR_046039		Gm8179	EG666589	predicted gene 8179	miscRNA	0.01	0.346535
Merged-chr16-26563796-1	chr16	26563746	26563846	+	2.2	cIP2vsInput	Intergenic	Intergenic	-17909	NM_001159318	16180	Mm.253424	NM_001159317	ENSMUSG00000022514	Il1rap	6430709H04Rik|AI255955|AV239853|IL-1RAcP	interleukin 1 receptor accessory protein	protein-coding	0	0.336634
Merged-chr6-62732486-1	chr6	62732436	62732536	+	2.2	cIP1vsInput	Intergenic	Intergenic	-524371	NM_008167	14804	Mm.447390	NM_008167		Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	"glutamate receptor, ionotropic, delta 2"	protein-coding	0	0.336634
Merged-chr8-97841200-1	chr8	97841150	97841250	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1295227	NR_039538	100628567		NR_039538		Mir28c	mmu-mir-28c	microRNA 28c	miscRNA	0	0.316832
Merged-chr7-125972335-1	chr7	125972285	125972385	+	2.2	cIP2vsInput	"intron (NM_001101488, intron 2 of 6)"	"intron (NM_001101488, intron 2 of 6)"	110076	NM_001101488	269994	Mm.39599	NM_001101488	ENSMUSG00000046182	Gsg1l	AI852434|C230098I05Rik|G630023A01Rik|Gm637|g1l	GSG1-like	protein-coding	0.03	0.584158
Merged-chr17-87637419-1	chr17	87637369	87637469	+	2.2	cIP1vsInput	"intron (NM_008532, intron 2 of 9)"	"intron (NM_008532, intron 2 of 9)"	1440	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding	0.03	0.326733
Merged-chr7-51716358-1	chr7	51716308	51716408	+	2.2	cIP2vsInput	Intergenic	Intergenic	94528	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	"solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6"	protein-coding	0	0.336634
Merged-chr8-76199561-1	chr8	76199511	76199611	+	2.2	cIP2vsInput	Intergenic	Intergenic	700612	NR_028579	100039211	Mm.367571	NR_028579	ENSMUSG00000074235	Gm10649	ENSMUSG00000074235	predicted gene 10649	miscRNA	0	0.356436
Merged-chr1-153180928-1	chr1	153180878	153180978	+	2.2	cIP1vsInput	"intron (NM_008485, intron 2 of 23)"	"intron (NM_008485, intron 2 of 23)"	5519	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	"laminin, gamma 2"	protein-coding	0.01	0.445545
Merged-chr2-104953342-1	chr2	104953292	104953392	+	2.2	cIP2vsInput	"intron (NM_177600, intron 9 of 17)"	"intron (NM_177600, intron 9 of 17)"	63685	NM_145380	98221	Mm.379278	NM_145380	ENSMUSG00000027170	Eif3m	Ga17|Pcid1|Tango7	"eukaryotic translation initiation factor 3, subunit M"	protein-coding	0	0.306931
Merged-chr12-47775646-1	chr12	47775596	47775696	+	2.2	cIP1vsInput	Intergenic	L1M4|LINE|L1	525816	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0.01	0.287129
Merged-chrX-39845911-1	chrX	39845861	39845961	+	2.2	cIP1vsInput	Intergenic	Lx|LINE|L1	17693	NM_001191032	100504400	Mm.373409	NM_001191032	ENSMUSG00000095240	Cypt14	-	cysteine-rich perinuclear theca 14	protein-coding	0	0.356436
Merged-chr15-54147111-1	chr15	54147061	54147161	+	2.2	cIP1vsInput	Intergenic	L1_Mus4|LINE|L1	131373	NM_008764	18383	Mm.15383	NM_008764	ENSMUSG00000063727	Tnfrsf11b	OCIF|Opg|TR1	"tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)"	protein-coding	0	0.366337
Merged-chr1-49066317-1	chr1	49066267	49066367	+	2.2	cIP2vsInput	Intergenic	Intergenic	-1861206	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.277228
Merged-chr15-82305576-1	chr15	82305526	82305626	+	2.2	cIP1vsInput	"intron (NM_029066, intron 1 of 5)"	B1_Mur4|SINE|Alu	6592	NM_029066	74716	Mm.159315	NM_029066	ENSMUSG00000022455	Wbp2nl	4930521I23Rik|PAWP	WBP2 N-terminal like	protein-coding	0.03	0.485149
Merged-chr2-109425090-1	chr2	109425040	109425140	+	2.2	cIP2vsInput	Intergenic	Lx5|LINE|L1	144352	NM_139303	228421	Mm.274086	NM_139303	ENSMUSG00000027115	Kif18a	AU024633|B130001M12Rik	kinesin family member 18A	protein-coding	0	0.326733
Merged-chrY-6479566-1	chrY	6479516	6479616	+	2.2	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	688211	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.39604
Merged-chr2-42468024-1	chr2	42467974	42468074	+	2.2	cIP2vsInput	"intron (NM_053011, intron 1 of 90)"	"intron (NM_053011, intron 1 of 90)"	185574	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0	0.277228
Merged-chr15-68266537-1	chr15	68266487	68266587	+	2.2	cIP2vsInput	Intergenic	Intergenic	-7681	NM_198644	380993	Mm.309526	NM_001145888	ENSMUSG00000022335	Zfat	Gm922|Zfat1|Zfp406	zinc finger and AT hook domain containing	protein-coding	0	0.326733
Merged-chrX-12140587-1	chrX	12140537	12140637	+	2.2	cIP2vsInput	"intron (NR_045434, intron 1 of 3)"	CpG	19759	NR_045434	72937	Mm.490017	NR_045434	ENSMUSG00000087271	2900008C10Rik	-	RIKEN cDNA 2900008C10 gene	miscRNA	0.07	0.653465
Merged-chr12-91477362-1	chr12	91477312	91477412	+	2.2	cIP2vsInput	"intron (NM_001113404, intron 1 of 8)"	"intron (NM_001113404, intron 1 of 8)"	76369	NM_011648	22095	Mm.173847	NM_001113404	ENSMUSG00000020963	Tshr	AI481368|hypothroid|hyt|pet	thyroid stimulating hormone receptor	protein-coding	0	0.336634
Merged-chr1-170638320-1	chr1	170638270	170638370	+	2.2	cIP2vsInput	Intergenic	Intergenic	-6212	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding	0	0.306931
Merged-chr11-102070613-1	chr11	102070563	102070663	+	2.2	cIP2vsInput	"intron (NM_016695, intron 3 of 12)"	"intron (NM_016695, intron 3 of 12)"	17902	NM_016695	50997	Mm.36242	NM_016695	ENSMUSG00000017314	Mpp2	D11Bwg0652e|Dlg2|Dlgh2|Pals4	"membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)"	protein-coding	0.09	0.712871
Merged-chr16-30626986-1	chr16	30626936	30627036	+	2.2	cIP2vsInput	"intron (NR_035427, intron 4 of 5)"	"intron (NR_035427, intron 4 of 5)"	27263	NM_177632	224093	Mm.28244	NM_177632	ENSMUSG00000046546	Fam43a	Tuf1	"family with sequence similarity 43, member A"	protein-coding	0	0.366337
Merged-chr5-26639747-1	chr5	26639697	26639797	+	2.2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-146433	NR_029445	75942	Mm.50087	NR_029445		4930584F24Rik	1700001J09Rik|4930522C06Rik	RIKEN cDNA 4930584F24 gene	miscRNA	0.01	0.346535
Merged-chr14-95176361-1	chr14	95176311	95176411	+	2.2	cIP2vsInput	Intergenic	RMER6D|LTR|ERVK	-704905	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.346535
Merged-chr19-13638882-1	chr19	13638832	13638932	+	2.2	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	5769	NM_146635	258628	Mm.271478	NM_146635	ENSMUSG00000045678	Olfr1489	MOR202-19	olfactory receptor 1489	protein-coding	0	0.316832
Merged-chr13-87659603-1	chr13	87659553	87659653	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1161869	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0	0.306931
Merged-chr2-110404594-1	chr2	110404544	110404644	+	2.2	cIP1vsInput	Intergenic	MT2B1|LTR|ERVL	-41601	NM_026271	67606	Mm.291809	NM_026271	ENSMUSG00000074971	Fibin	1110018M03Rik	fin bud initiation factor homolog (zebrafish)	protein-coding	0	0.326733
Merged-chr10-16196103-1	chr10	16196053	16196153	+	2.2	cIP1vsInput	Intergenic	Intergenic	899679	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0	0.29703
Merged-chr2-39626696-1	chr2	39626646	39626746	+	2.2	cIP1vsInput	Intergenic	Lx|LINE|L1	-400358	NM_024209	67857	Mm.392662	NM_024209		Ppp6c	2310003C10Rik	"protein phosphatase 6, catalytic subunit"	protein-coding	0	0.316832
Merged-chr13-111993349-1	chr13	111993299	111993399	+	2.2	cIP2vsInput	Intergenic	Intergenic	-184366	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding	0	0.386139
Merged-chr11-89848852-1	chr11	89848802	89848902	+	2.2	cIP1vsInput	Intergenic	Intergenic	154042	NM_008796	18559	Mm.5062	NM_008796		Pctp	PC-TP|StarD2	phosphatidylcholine transfer protein	protein-coding	0.01	0.316832
Merged-chr18-11507953-1	chr18	11507903	11508003	+	2.2	cIP2vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	-125323	NM_001252495	225182	Mm.154275	NM_175458	ENSMUSG00000041238	Rbbp8	9930104E21Rik|CtIP|RBBP-8|RIM|SAE2	retinoblastoma binding protein 8	protein-coding	0.02	0.29703
Merged-chr4-52269405-1	chr4	52269355	52269455	+	2.2	cIP2vsInput	Intergenic	L1M2|LINE|L1	169559	NR_045175	72648	Mm.391869	NR_045175	ENSMUSG00000085763	2700081L22Rik	-	RIKEN cDNA 2700081L22 gene	miscRNA	0.01	0.316832
Merged-chr19-47486062-1	chr19	47486012	47486112	+	2.2	cIP1vsInput	Intergenic	MLT1B|LTR|ERVL-MaLR	-21651	NM_008018	14218	Mm.127560	NM_177833	ENSMUSG00000053617	Sh3pxd2a	2310014D11Rik|AA589508|AI256723|AI413738|C230050L11|EG329070|Fish|Gm5098|Sh3md1|TSK5|Tks5	SH3 and PX domains 2A	protein-coding	0.01	0.534653
Merged-chr6-41211169-1	chr6	41211119	41211219	+	2.2	cIP2vsInput	Intergenic	Intergenic	-91103	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding	0	0.336634
Merged-chr17-19666724-1	chr17	19666674	19666774	+	2.2	cIP1vsInput	"intron (NM_001104564, intron 1 of 5)"	"intron (NM_001104564, intron 1 of 5)"	6325	NM_001104564	224572	Mm.469856	NM_001104564	ENSMUSG00000095961	Vmn2r102	EG224572	"vomeronasal 2, receptor 102"	protein-coding	0	0.386139
Merged-chr4-50226876-1	chr4	50226826	50226926	+	2.2	cIP2vsInput	Intergenic	Intergenic	-381107	NM_001276355	242443	Mm.440095	NM_001033351		Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	"glutamate receptor ionotropic, NMDA3A"	protein-coding	0	0.346535
Merged-chr9-84865441-1	chr9	84865391	84865491	+	2.2	cIP1vsInput	Intergenic	L1M2|LINE|L1	91043	NR_040739	75253	Mm.401984	NR_040739		4930554C24Rik	-	RIKEN cDNA 4930554C24 gene	miscRNA	0	0.356436
Merged-chr8-5429598-1	chr8	5429548	5429648	+	2.2	cIP2vsInput	Intergenic	Intergenic	-324366	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.267327
Merged-chrX-52570970-1	chrX	52570920	52571020	+	2.2	cIP2vsInput	"intron (NM_016697, intron 2 of 7)"	"intron (NM_016697, intron 2 of 7)"	-4873	NR_045367	100504594	Mm.447008	NR_045367	ENSMUSG00000055110	A630012P03Rik	-	RIKEN cDNA A630012P03 gene	miscRNA	0	0.316832
Merged-chr14-9203098-1	chr14	9203048	9203148	+	2.2	cIP1vsInput	Intergenic	RMER5|LTR|ERV1	536708	NR_045968	74859	Mm.84041	NR_045968	ENSMUSG00000097898	4930455B14Rik	1700027C12Rik	RIKEN cDNA 4930455B14 gene	miscRNA	0	0.356436
Merged-chr1-48437870-1	chr1	48437820	48437920	+	2.2	cIP2vsInput	Intergenic	Intergenic	-1584361	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.316832
Merged-chr2-136822958-1	chr2	136822908	136823008	+	2.2	cIP2vsInput	Intergenic	Intergenic	-68260	NM_028201	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding	0.01	0.386139
Merged-chr10-101635852-1	chr10	101635802	101635902	+	2.2	cIP1vsInput	Intergenic	Lx4A|LINE|L1	-45635	NM_001205098	67569	Mm.403713	NM_001162368	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"	protein-coding	0.01	0.336634
Merged-chr6-110450561-1	chr6	110450511	110450611	+	2.2	cIP1vsInput	Intergenic	Intergenic	-195037	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0.01	0.306931
Merged-chr3-20567397-1	chr3	20567347	20567447	+	2.2	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-200220	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	"angiotensin II receptor, type 1b"	protein-coding	0	0.316832
Merged-chr8-59237562-1	chr8	59237512	59237612	+	2.2	cIP1vsInput	Intergenic	Intergenic	325807	NM_173411	234290	Mm.39244	NM_173411	ENSMUSG00000049946	BC030500	-	cDNA sequence BC030500	protein-coding	0	0.29703
Merged-chr1-102339950-1	chr1	102339900	102340000	+	2.2	cIP1vsInput	Intergenic	RLTR15|LTR|ERVK	1184182	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.405941
Merged-chr17-14217404-1	chr17	14217354	14217454	+	2.2	cIP2vsInput	Intergenic	Intergenic	-13573	NM_172826	240025	Mm.79993	NM_172826	ENSMUSG00000048826	Dact2	2900084M21Rik|A630024E20|Dpr2|Frd2|dapper2	"dapper homolog 2, antagonist of beta-catenin (xenopus)"	protein-coding	0	0.336634
Merged-chrX-43259078-1	chrX	43259028	43259128	+	2.2	cIP1vsInput	"intron (NM_011855, intron 1 of 32)"	"intron (NM_011855, intron 1 of 32)"	15708	NM_011855	23963	Mm.327698	NM_011855	ENSMUSG00000016150	Tenm1	Odz1|Odz2|TCAP-1|Ten-m1	teneurin transmembrane protein 1	protein-coding	0	0.346535
Merged-chr15-56359016-1	chr15	56358966	56359066	+	2.2	cIP1vsInput	Intergenic	Intergenic	-330928	NR_002874	594843	Mm.484850	NR_002874	ENSMUSG00000086541	Has2as	EG594843|Hasnt	HAS2 antisense RNA (non-protein coding)	miscRNA	0	0.326733
Merged-chr2-81870499-1	chr2	81870449	81870549	+	2.2	cIP2vsInput	Intergenic	Intergenic	-183159	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0	0.356436
Merged-chr8-72239672-1	chr8	72239622	72239722	+	2.2	cIP2vsInput	promoter-TSS (NM_007456)	promoter-TSS (NM_007456)	-460	NM_007456	11767	Mm.290086	NM_007456	ENSMUSG00000003033	Ap1m1	AA408894|AP47|Adtm1A|Cltnm|[m]1A|mu1A	"adaptor-related protein complex AP-1, mu subunit 1"	protein-coding	0.04	0.514851
Merged-chr2-16012221-1	chr2	16012171	16012271	+	2.2	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-344101	NM_026162	67448	Mm.394655	NM_026162		Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding	0	0.29703
Merged-chr14-104343418-1	chr14	104343368	104343468	+	2.2	cIP1vsInput	Intergenic	L1MA10|LINE|L1	124581	NM_011143	18996	Mm.246550	NM_011143	ENSMUSG00000048349	Pou4f1	Brn-3|Brn-3.0|Brn3|Brn3.0|Brn3a|E130119J07Rik	"POU domain, class 4, transcription factor 1"	protein-coding	0.01	0.386139
Merged-chr6-25045716-1	chr6	25045666	25045766	+	2.2	cIP1vsInput	Intergenic	Intergenic	-89591	NM_177013	319832	Mm.127446	NM_177013	ENSMUSG00000048022	Tmem229a	6332401O19Rik	transmembrane protein 229A	protein-coding	0	0.356436
Merged-chr1-20036424-1	chr1	20036374	20036474	+	2.2	cIP2vsInput	Intergenic	Intergenic	-320030	NR_045734	75028	Mm.417820	NR_045734		4930486I03Rik	-	RIKEN cDNA 4930486I03 gene	miscRNA	0	0.306931
Merged-chr1-9453001-1	chr1	9452951	9453051	+	2.2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-92407	NM_021511	59014	Mm.29061	NM_021511	ENSMUSG00000061024	Rrs1	5730466A07Rik|AA415037|D1Ertd701e|Rrr	RRS1 ribosome biogenesis regulator homolog (S. cerevisiae)	protein-coding	0.01	0.346535
Merged-chr3-111874391-1	chr3	111874341	111874441	+	2.2	cIP2vsInput	Intergenic	Intergenic	-7512	NR_045362	625585	Mm.389497	NR_045362		Gm6602	-	predicted gene 6602	miscRNA	0	0.306931
Merged-chr12-4133420-1	chr12	4133370	4133470	+	2.2	cIP2vsInput	promoter-TSS (NM_001159537)	promoter-TSS (NM_001159537)	23	NM_001159537	104111	Mm.489807	NM_001159536	ENSMUSG00000020654	Adcy3	AC3|mKIAA0511	adenylate cyclase 3	protein-coding	0.11	0.712871
Merged-chrX-84038059-1	chrX	84038009	84038109	+	2.2	cIP2vsInput	"intron (NM_007868, intron 44 of 78)"	"intron (NM_007868, intron 44 of 78)"	-550135	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding	0	0.277228
Merged-chr12-15826546-1	chr12	15826496	15826596	+	2.2	cIP2vsInput	Intergenic	Intergenic	-9761	NM_144551	217410	Mm.266679	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles homolog 2 (Drosophila)	protein-coding	0	0.346535
Merged-chr8-86835049-1	chr8	86834999	86835099	+	2.2	cIP2vsInput	Intergenic	Intergenic	50209	NM_030563	80750	Mm.428374	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding	0.01	0.49505
Merged-chr15-46254712-1	chr15	46254662	46254762	+	2.2	cIP1vsInput	Intergenic	Intergenic	-69873	NR_045509	71120	Mm.158571	NR_045509		1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	miscRNA	0	0.336634
Merged-chr10-82135703-1	chr10	82135653	82135753	+	2.2	cIP2vsInput	"intron (NM_001163064, intron 1 of 3)"	L1_Mus3|LINE|L1	7690	NM_001163064	216177	Mm.482395	NM_001163064		AU041133	-	expressed sequence AU041133	protein-coding	0	0.386139
Merged-chr8-15505143-1	chr8	15505093	15505193	+	2.2	cIP2vsInput	Intergenic	MLTR14|LTR|ERV1	447490	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding	0.01	0.475248
Merged-chr12-26160415-1	chr12	26160365	26160465	+	2.2	cIP1vsInput	Intergenic	(ATATG)n|Simple_repeat|Simple_repeat	-50852	NR_046278	74930	Mm.398932	NR_046278		4930480M12Rik	-	RIKEN cDNA 4930480M12 gene	miscRNA	0.01	0.217822
Merged-chr4-94130884-1	chr4	94130834	94130934	+	2.2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	425912	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0	0.336634
Merged-chr1-50885864-1	chr1	50885814	50885914	+	2.2	cIP1vsInput	Intergenic	Intergenic	-41659	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.366337
Merged-chr5-121497932-1	chr5	121497882	121497982	+	2.2	cIP1vsInput	Intergenic	Intergenic	5048	NM_172125	280667	Mm.444773	NM_172125	ENSMUSG00000062438	Adam1b	Adam1|Ftna	a disintegrin and metallopeptidase domain 1b	protein-coding	0	0.306931
Merged-chr10-66168844-1	chr10	66168794	66168894	+	2.2	cIP1vsInput	Intergenic	MIRc|SINE|MIR	-44780	NR_038039	69433	Mm.23366	NR_038039		1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	miscRNA	0	0.346535
Merged-chr7-19768446-1	chr7	19768396	19768496	+	2.2	cIP2vsInput	"intron (NM_020486, intron 2 of 14)"	"intron (NM_020486, intron 2 of 14)"	2086	NM_020486	57278	Mm.29236	NM_020486	ENSMUSG00000002980	Bcam	1200005K12Rik|B-CAM|Gplu|Lu	basal cell adhesion molecule	protein-coding	0.05	0.643564
Merged-chrX-134883466-1	chrX	134883416	134883516	+	2.2	cIP2vsInput	Intergenic	Intergenic	-74245	NM_001166398	67416	Mm.285969	NM_001166397	ENSMUSG00000033436	Armcx2	3230401N03Rik|AI043003|ALEX2	"armadillo repeat containing, X-linked 2"	protein-coding	0.01	0.356436
Merged-chr8-91539144-1	chr8	91539094	91539194	+	2.2	cIP1vsInput	"intron (NM_011936, intron 8 of 8)"	"intron (NM_011936, intron 8 of 8)"	225619	NM_011936	26383	Mm.4375	NM_011936	ENSMUSG00000055932	Fto	AW743446|mKIAA1752	fat mass and obesity associated	protein-coding	0.01	0.336634
Merged-chr5-15525740-1	chr5	15525690	15525790	+	2.2	cIP1vsInput	Intergenic	Intergenic	-93359	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4d	protein-coding	0.01	0.455446
Merged-chr5-15881867-1	chr5	15881817	15881917	+	2.2	cIP1vsInput	"intron (NR_045974, intron 1 of 5)"	L1MC4|LINE|L1	1899	NR_045974	75058	Mm.183467	NR_045974		4930519H02Rik	-	RIKEN cDNA 4930519H02 gene	miscRNA	0	0.29703
Merged-chrX-151169549-1	chrX	151169499	151169599	+	2.2	cIP2vsInput	Intergenic	CpG	-28529	NM_001271679	279561	Mm.441474	XR_141418		Wnk3	Prkwnk3|Wnk3-ps	WNK lysine deficient protein kinase 3	protein-coding	0.13	0.732673
Merged-chr11-4348434-1	chr11	4348384	4348484	+	2.2	cIP1vsInput	"intron (NM_029458, intron 10 of 10)"	B3A|SINE|B2	81339	NM_001039537	16878	Mm.4964	NM_001039537	ENSMUSG00000034394	Lif	-	leukemia inhibitory factor	protein-coding	0.03	0.435644
Merged-chr7-84962884-1	chr7	84962834	84962934	+	2.2	cIP2vsInput	"intron (NM_001105180, intron 1 of 5)"	"intron (NM_001105180, intron 1 of 5)"	1125	NM_001105180	100009609	Mm.389926	NM_001105180	ENSMUSG00000066372	Vmn2r65	ENSMUSG00000070600|V2ro	"vomeronasal 2, receptor 65"	protein-coding	0	0.306931
Merged-chr10-6885429-1	chr10	6885379	6885479	+	2.2	cIP2vsInput	TTS (NM_001170800)	TTS (NM_001170800)	95036	NM_001170800	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding	0	0.277228
Merged-chr13-105902334-1	chr13	105902284	105902384	+	2.2	cIP1vsInput	Intergenic	Intergenic	458641	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0	0.316832
Merged-chr9-47699415-1	chr9	47699365	47699465	+	2.2	cIP2vsInput	"intron (NM_001025600, intron 1 of 8)"	"intron (NM_001025600, intron 1 of 8)"	118793	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	miscRNA	0.02	0.306931
Merged-chr1-108672429-1	chr1	108672379	108672479	+	2.2	cIP2vsInput	Intergenic	Lx5b|LINE|L1	755170	NR_102307	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0	0.316832
Merged-chr10-64489104-1	chr10	64489054	64489154	+	2.2	cIP2vsInput	"intron (NM_001164519, intron 6 of 12)"	"intron (NM_001164519, intron 6 of 12)"	-398849	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding	0	0.316832
Merged-chr10-56590898-1	chr10	56590848	56590948	+	2.2	cIP1vsInput	Intergenic	Intergenic	213598	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	"gap junction protein, alpha 1"	protein-coding	0	0.257426
Merged-chr17-29078360-1	chr17	29078310	29078410	+	2.2	cIP1vsInput	"intron (NR_036469, intron 1 of 1)"	"intron (NR_036469, intron 1 of 1)"	601	NR_036469	100504267	Mm.438550	NR_036469	ENSMUSG00000085912	Trp53cor1	Gm16197|OTTMUSG00000031656	tumor protein p53 pathway corepressor 1	miscRNA	0.05	0.633663
Merged-chr10-14605850-1	chr10	14605800	14605900	+	2.2	cIP2vsInput	Intergenic	RMER15-int|LTR|ERVL	-60814	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Gpr126	1190004A11Rik|AI449247|AW045736|DREG|Gm222	G protein-coupled receptor 126	protein-coding	0.01	0.39604
Merged-chr8-59344761-1	chr8	59344711	59344811	+	2.2	cIP1vsInput	Intergenic	Intergenic	433006	NM_173411	234290	Mm.39244	NM_173411	ENSMUSG00000049946	BC030500	-	cDNA sequence BC030500	protein-coding	0	0.346535
Merged-chr10-72202821-1	chr10	72202771	72202871	+	2.2	cIP2vsInput	Intergenic	Intergenic	-222131	NR_003644	108950	Mm.212793	NR_003644	ENSMUSG00000043859	1700049L16Rik	-	hematological and neurological expressed 1-like pseudogene	pseudo	0.02	0.29703
Merged-chr11-24387420-1	chr11	24387370	24387470	+	2.2	cIP2vsInput	Intergenic	Intergenic	-94489	NR_045857	71316	Mm.79162	NR_045857	ENSMUSG00000086892	4933430M04Rik	-	RIKEN cDNA 4933430M04 gene	miscRNA	0	0.346535
Merged-chr9-114326717-1	chr9	114326667	114326767	+	2.2	cIP2vsInput	Intergenic	Intergenic	-3418	NM_007535	12046	Mm.378887	NM_007535	ENSMUSG00000053820	Bcl2a1c	A1-c	B cell leukemia/lymphoma 2 related protein A1c	protein-coding	0	0.346535
Merged-chr8-67053245-1	chr8	67053195	67053295	+	2.2	cIP2vsInput	Intergenic	Intergenic	193028	NM_001163564	234344	Mm.334561	NM_001163564	ENSMUSG00000014907	Naf1	Gm174	nuclear assembly factor 1 homolog (S. cerevisiae)	protein-coding	0	0.306931
Merged-chr7-19068733-1	chr7	19068683	19068783	+	2.2	cIP1vsInput	"intron (NM_001159671, intron 4 of 4)"	"intron (NM_001159671, intron 4 of 4)"	-7467	NM_010058	13401	Mm.2852	NM_010058	ENSMUSG00000030410	Dmwd	DMR-N9|Dm9	dystrophia myotonica-containing WD repeat motif	protein-coding	0	0.237624
Merged-chr3-97469782-1	chr3	97469732	97469832	+	2.2	cIP2vsInput	Intergenic	Intergenic	-58603	NM_146275	258272	Mm.377406	NM_146275	ENSMUSG00000051392	Olfr1402	MOR217-1	olfactory receptor 1402	protein-coding	0	0.316832
Merged-chr15-45788660-1	chr15	45788610	45788710	+	2.2	cIP2vsInput	Intergenic	B4|SINE|B4	-535925	NR_045509	71120	Mm.158571	NR_045509		1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	miscRNA	0	0.465347
Merged-chr1-69818435-1	chr1	69818385	69818485	+	2.2	cIP2vsInput	Intergenic	Intergenic	-8535	NM_029160	66722	Mm.440554	NM_001271533	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding	0	0.306931
Merged-chrX-23409167-1	chrX	23409117	23409217	+	2.2	cIP1vsInput	Intergenic	Intergenic	-44114	NM_026167	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik|mKIAA1309	kelch-like 13	protein-coding	0	0.326733
Merged-chr19-41455849-1	chr19	41455799	41455899	+	2.2	cIP2vsInput	Intergenic	Intergenic	-70779	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding	0.02	0.455446
Merged-chr1-161170517-1	chr1	161170467	161170567	+	2.2	cIP2vsInput	TTS (NM_028664)	TTS (NM_028664)	-11203	NM_001195189	100502590	Mm.449990	NM_001195189		4930469G21Rik	-	RIKEN cDNA 4930469G21 gene	protein-coding	0.03	0.316832
Merged-chr6-40750760-1	chr6	40750710	40750810	+	2.2	cIP1vsInput	"intron (NM_001171003, intron 33 of 47)"	"intron (NM_001171003, intron 33 of 47)"	121929	NM_001171003	232714	Mm.33401	NM_001171003	ENSMUSG00000068587	Mgam	6030407P20Rik|MGA	maltase-glucoamylase	protein-coding	0.01	0.346535
Merged-chr19-53881094-1	chr19	53881044	53881144	+	2.2	cIP1vsInput	Intergenic	Intergenic	-11137	NM_011050	18569	Mm.1605	NM_001168491	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding	0.01	0.366337
Merged-chr12-97873294-1	chr12	97873244	97873344	+	2.2	cIP2vsInput	Intergenic	Intergenic	386043	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding	0.02	0.445545
Merged-chr7-95117319-1	chr7	95117269	95117369	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1093318	NM_011858	23966	Mm.391678	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding	0	0.316832
Merged-chr5-55846873-1	chr5	55846823	55846923	+	2.2	cIP2vsInput	Intergenic	Intergenic	1496881	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0	0.336634
Merged-chr19-34605596-1	chr19	34605546	34605646	+	2.2	cIP1vsInput	Intergenic	Intergenic	-2361	NM_001005858	667370	Mm.271850	NM_001005858	ENSMUSG00000062488	I830012O16Rik	-	RIKEN cDNA I830012O16 gene	protein-coding	0	0.455446
Merged-chr19-8845020-1	chr19	8844970	8845070	+	2.2	cIP2vsInput	"intron (NM_008144, intron 3 of 10)"	B1_Mus2|SINE|Alu	5692	NM_008144	14705	Mm.345134	NM_001136064	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Bernardinelli-Seip congenital lipodystrophy 2 homolog (human)	protein-coding	0.01	0.415842
Merged-chr10-72951053-1	chr10	72951003	72951103	+	2.2	cIP2vsInput	Intergenic	Intergenic	135652	NR_040646	327768	Mm.417745	NR_040646		A330049N07Rik	-	RIKEN cDNA A330049N07 gene	miscRNA	0.01	0.386139
Merged-chr8-18094977-1	chr8	18094927	18095027	+	2.2	cIP2vsInput	Intergenic	RMER4B|LTR|ERVK	-500196	NM_173189	244329	Mm.235296	NM_173189	ENSMUSG00000039842	Mcph1	5430437K10Rik|BRIT1|D030046N04Rik|MCT	"microcephaly, primary autosomal recessive 1"	protein-coding	0	0.366337
Merged-chr7-86102552-1	chr7	86102502	86102602	+	2.2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	69172	NM_001102578	546981	Mm.469835	NM_001102578	ENSMUSG00000090436	Vmn2r75	EG546981	"vomeronasal 2, receptor 75"	protein-coding	0	0.336634
Merged-chr17-45555721-1	chr17	45555671	45555771	+	2.2	cIP1vsInput	promoter-TSS (NM_008690)	promoter-TSS (NM_008690)	5	NM_008690	18037	Mm.57043	NM_008690	ENSMUSG00000023947	Nfkbie	IKBE	"nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, epsilon"	protein-coding	0.08	0.683168
Merged-chr14-80022462-1	chr14	80022412	80022512	+	2.2	cIP2vsInput	TTS (NM_001030294)	TTS (NM_001030294)	22160	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.356436
Merged-chr1-29432922-1	chr1	29432872	29432972	+	2.2	cIP1vsInput	Intergenic	Intergenic	-652670	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0.01	0.376238
Merged-chr5-7636398-1	chr5	7636348	7636448	+	2.2	cIP2vsInput	Intergenic	Lx3C|LINE|L1	-292020	NM_001163223	207618	Mm.478808	NM_001163223	ENSMUSG00000092094	Zfp804b	Gm441	zinc finger protein 804B	protein-coding	0.01	0.39604
Merged-chr6-91978831-1	chr6	91978781	91978881	+	2.2	cIP2vsInput	Intergenic	CpG	-8279	NM_172731	232237	Mm.295740	NM_172731	ENSMUSG00000034037	Fgd5	C330025N11Rik|ZFYVE23|mFLJ00274	"FYVE, RhoGEF and PH domain containing 5"	protein-coding	0.13	0.762376
Merged-chr5-8030004-1	chr5	8029954	8030054	+	2.2	cIP1vsInput	Intergenic	RLTR22_Mur|LTR|ERVK	-16076	NM_025618	109552	Mm.96211	NM_001080974	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding	0	0.306931
Merged-chr18-55571444-1	chr18	55571394	55571494	+	2.2	cIP2vsInput	Intergenic	Intergenic	-581264	NM_175751	269023	Mm.471753	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding	0.01	0.376238
Merged-chr15-8538346-1	chr15	8538296	8538396	+	2.2	cIP2vsInput	Intergenic	MLT1B|LTR|ERVL-MaLR	-93883	NM_201232	71175	Mm.440537	NM_027707	ENSMUSG00000022141	Nipbl	4921518A06Rik|4933421G18Rik|C79399|Idn3	Nipped-B homolog (Drosophila)	protein-coding	0.01	0.346535
Merged-chr1-169143379-1	chr1	169143329	169143429	+	2.2	cIP1vsInput	Intergenic	Intergenic	388085	NM_023284	66977	Mm.151315	NM_023284	ENSMUSG00000026683	Nuf2	2410003C07Rik|AU044112|C85691|Cdca1|NUF2R	"NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"	protein-coding	0	0.366337
Merged-chr10-73646387-1	chr10	73646337	73646437	+	2.2	cIP2vsInput	Intergenic	Intergenic	-175480	NM_001142760	11994	Mm.338933	NM_001142735	ENSMUSG00000052613	Pcdh15	BB078305|ENSMUSG00000046980|Gm9815|Ush1f|av|nmf19	protocadherin 15	protein-coding	0	0.326733
Merged-chr6-68014033-1	chr6	68013983	68014083	+	2.2	cIP1vsInput	Intergenic	L1_Mur1|LINE|L1	-448334	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo	0	0.29703
Merged-chr14-82575967-1	chr14	82575917	82576017	+	2.2	cIP1vsInput	Intergenic	MusHAL1|LINE|L1	-1867596	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0.01	0.257426
Merged-chr3-45881235-1	chr3	45881185	45881285	+	2.2	cIP1vsInput	Intergenic	Intergenic	-441926	NR_040594	72274	Mm.396202	NR_040594		1700027H10Rik	-	RIKEN cDNA 1700027H10 gene	miscRNA	0	0.376238
Merged-chr13-20233439-1	chr13	20233389	20233489	+	2.2	cIP1vsInput	"intron (NM_080288, intron 4 of 21)"	"intron (NM_080288, intron 4 of 21)"	142932	NM_080288	140580	Mm.342392	NR_038122		Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding	0.01	0.39604
Merged-chr2-98179825-1	chr2	98179775	98179875	+	2.2	cIP2vsInput	Intergenic	Intergenic	712151	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.29703
Merged-chr17-5549897-1	chr17	5549847	5549947	+	2.2	cIP2vsInput	"intron (NM_146073, intron 1 of 8)"	L2a|LINE|L2	57297	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	"zinc finger, DHHC domain containing 14"	protein-coding	0	0.326733
Merged-chr3-151489333-1	chr3	151489283	151489383	+	2.2	cIP1vsInput	"intron (NM_133222, intron 2 of 15)"	"intron (NM_133222, intron 2 of 15)"	51451	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0	0.306931
Merged-chr3-99672439-1	chr3	99672389	99672489	+	2.2	cIP1vsInput	Intergenic	Lx5c|LINE|L1	-212978	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding	0	0.366337
Merged-chr5-10207703-1	chr5	10207653	10207753	+	2.2	cIP2vsInput	Intergenic	Intergenic	-482351	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	"glutamate receptor, metabotropic 3"	protein-coding	0	0.29703
Merged-chr15-5749619-1	chr15	5749569	5749669	+	2.2	cIP2vsInput	Intergenic	L1M2|LINE|L1	253301	NR_045274	71432	Mm.291087	NR_045274		5430437J10Rik	-	RIKEN cDNA 5430437J10 gene	miscRNA	0	0.326733
Merged-chr14-6908681-1	chr14	6908631	6908731	+	2.2	cIP1vsInput	Intergenic	Intergenic	118768	NM_001164727	100038847	Mm.483675	NM_001164727	ENSMUSG00000093985	Gm10406	ENSMUSG00000072735	predicted gene 10406	protein-coding	0.01	0.376238
Merged-chr6-102171416-1	chr6	102171366	102171466	+	2.2	cIP1vsInput	"intron (NM_008779, intron 19 of 21)"	"intron (NM_008779, intron 19 of 21)"	293251	NM_008779	18488	Mm.435479	NM_008779	ENSMUSG00000030075	Cntn3	Pang	contactin 3	protein-coding	0	0.287129
Merged-chr2-129731367-1	chr2	129731317	129731417	+	2.2	cIP1vsInput	Intergenic	Intergenic	-41499	NM_018863	18610	Mm.6239	NM_018863		Pdyn	Dyn	prodynorphin	protein-coding	0.01	0.316832
Merged-chr1-48154294-1	chr1	48154244	48154344	+	2.2	cIP1vsInput	Intergenic	Intergenic	-1300785	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.336634
Merged-chr4-20854260-1	chr4	20854210	20854310	+	2.2	cIP1vsInput	Intergenic	L1M5|LINE|L1	-75592	NM_172987	269513		NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding	0	0.29703
Merged-chr6-119451997-1	chr6	119451947	119452047	+	2.2	cIP1vsInput	"intron (NM_009525, intron 1 of 4)"	"intron (NM_009525, intron 1 of 4)"	-2611	NM_001271757	22419	Mm.321818	NM_001271757	ENSMUSG00000030170	Wnt5b	AW545702|Wnt-5b	wingless-related MMTV integration site 5B	protein-coding	0.03	0.465347
Merged-chr13-42899091-1	chr13	42899041	42899141	+	2.2	cIP2vsInput	"intron (NM_001005740, intron 1 of 12)"	"intron (NM_001005740, intron 1 of 12)"	189510	NM_001005740	218194	Mm.160124	NM_001005740	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding	0.01	0.277228
Merged-chr2-58076410-1	chr2	58076360	58076460	+	2.2	cIP1vsInput	Intergenic	RMER12C|LTR|ERVK	-23658	NM_029972	77767	Mm.91712	NM_029972	ENSMUSG00000026830	Ermn	A330104H05Rik|AI854460|ermin|mKIAA1189	"ermin, ERM-like protein"	protein-coding	0	0.306931
Merged-chr10-78826387-1	chr10	78826337	78826437	+	2.2	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	21526	NM_146308	258305	Mm.377425	NM_146308	ENSMUSG00000051190	Olfr1356	MOR142-1|MOR142-2_p	olfactory receptor 1356	protein-coding	0	0.29703
Merged-chr7-39919028-1	chr7	39918978	39919078	+	2.2	cIP2vsInput	Intergenic	Intergenic	401262	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding	0	0.366337
Merged-chr3-6670613-1	chr3	6670563	6670663	+	2.2	cIP1vsInput	Intergenic	Intergenic	-50170	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding	0.01	0.405941
Merged-chr16-33301943-1	chr16	33301893	33301993	+	2.2	cIP1vsInput	Intergenic	Intergenic	50487	NM_080557	69150	Mm.396285	NM_080557	ENSMUSG00000022808	Snx4	1810036H14Rik|AI037066	sorting nexin 4	protein-coding	0	0.514851
Merged-chr14-106944296-1	chr14	106944246	106944346	+	2.2	cIP1vsInput	Intergenic	Intergenic	-457776	NR_045938	73631	Mm.48862	NR_045938		1700128A07Rik	-	RIKEN cDNA 1700128A07 gene	miscRNA	0	0.366337
Merged-chr14-39866269-1	chr14	39866219	39866319	+	2.2	cIP1vsInput	Intergenic	Lx8b|LINE|L1	210606	NR_045936	73591	Mm.65499	NR_045936		1700109I08Rik	-	RIKEN cDNA 1700109I08 gene	miscRNA	0.01	0.29703
Merged-chr11-47980271-1	chr11	47980221	47980321	+	2.2	cIP1vsInput	Intergenic	Intergenic	-600969	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	"sarcoglycan, delta (dystrophin-associated glycoprotein)"	protein-coding	0.01	0.356436
Merged-chr7-113806050-1	chr7	113806000	113806100	+	2.2	cIP1vsInput	"intron (NM_145584, intron 2 of 15)"	Lx6|LINE|L1	40052	NM_145584	233744	Mm.334160	NM_145584	ENSMUSG00000038156	Spon1	AI666765|AW455831|BC020531|D330035F22Rik|FSP	"spondin 1, (f-spondin) extracellular matrix protein"	protein-coding	0	0.376238
Merged-chr4-15744641-1	chr4	15744591	15744691	+	2.2	cIP1vsInput	Intergenic	MLTR18B_MM|LTR|ERVK	-136623	NM_009788	12307	Mm.277665	NM_009788		Calb1	Brain-2|CB|Calb|Calb-1	calbindin 1	protein-coding	0	0.376238
Merged-chr5-7326170-1	chr5	7326120	7326220	+	2.2	cIP1vsInput	"intron (NM_001163223, intron 1 of 3)"	"intron (NM_001163223, intron 1 of 3)"	18208	NM_001163223	207618	Mm.478808	NM_001163223	ENSMUSG00000092094	Zfp804b	Gm441	zinc finger protein 804B	protein-coding	0.01	0.277228
Merged-chr7-108410768-1	chr7	108410718	108410818	+	2.2	cIP2vsInput	Intergenic	Intergenic	-11805	NM_146738	258733	Mm.377663	NM_146738	ENSMUSG00000095239	Olfr497	MOR204-9	olfactory receptor 497	protein-coding	0	0.306931
Merged-chr10-18562867-1	chr10	18562817	18562917	+	2.2	cIP1vsInput	Intergenic	Intergenic	-16791	NM_019487	56016	Mm.35551	NM_019487	ENSMUSG00000019853	Hebp2	SOUL	heme binding protein 2	protein-coding	0.02	0.39604
Merged-chr12-109250408-1	chr12	109250358	109250458	+	2.2	cIP1vsInput	Intergenic	Lx2B2|LINE|L1	-182191	NM_001163175	380785	Mm.342085	NM_001163175	ENSMUSG00000040867	Begain	BM948371|Gm897	brain-enriched guanylate kinase-associated	protein-coding	0	0.326733
Merged-chr19-26619441-1	chr19	26619391	26619491	+	2.2	cIP1vsInput	"intron (NM_011416, intron 1 of 32)"	"intron (NM_011416, intron 1 of 32)"	14281	NM_011416	67155	Mm.313303	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2"	protein-coding	0	0.346535
Merged-chr5-59617097-1	chr5	59617047	59617147	+	2.2	cIP1vsInput	Intergenic	Intergenic	368905	NR_040683	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0	0.267327
Merged-chr17-68570839-1	chr17	68570789	68570889	+	2.2	cIP1vsInput	"intron (NM_177278, intron 13 of 20)"	"intron (NM_177278, intron 13 of 20)"	-266297	NM_001206661	622645	Mm.86422	NM_001206661	ENSMUSG00000095407	Tmem200c	EG622645|Gm6338	transmembrane protein 200C	protein-coding	0.01	0.316832
Merged-chr1-85112384-1	chr1	85112334	85112434	+	2.2	cIP1vsInput	Intergenic	Intergenic	-2531	NM_213615	381287	Mm.487565	NM_213615	ENSMUSG00000089844	A530032D15Rik	Gm1888	RIKEN cDNA A530032D15Rik gene	protein-coding	0.02	0.366337
Merged-chr7-24547276-1	chr7	24547226	24547326	+	2.2	cIP2vsInput	"5' UTR (NM_009532, exon 1 of 17)"	"5' UTR (NM_009532, exon 1 of 17)"	126	NM_009532	22594	Mm.4347	NM_009532	ENSMUSG00000051768	Xrcc1	Xrcc-1	X-ray repair complementing defective repair in Chinese hamster cells 1	protein-coding	0.08	0.683168
Merged-chr9-27610305-1	chr9	27610255	27610355	+	2.2	cIP1vsInput	Intergenic	L1M2|LINE|L1	-180964	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding	0	0.306931
Merged-chr9-60399888-1	chr9	60399838	60399938	+	2.2	cIP1vsInput	"intron (NM_001040426, intron 4 of 17)"	"intron (NM_001040426, intron 4 of 17)"	111147	NM_001040426	207596	Mm.379523	NM_001040426	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	"thrombospondin, type I, domain containing 4"	protein-coding	0.02	0.623762
Merged-chr8-38018992-1	chr8	38018942	38019042	+	2.2	cIP1vsInput	"intron (NM_145841, intron 1 of 7)"	"intron (NM_145841, intron 1 of 7)"	233210	NR_029884	723860		NR_029884		Mir383	Mirn383|mmu-mir-383	microRNA 383	miscRNA	0.01	0.336634
Merged-chr3-18479914-1	chr3	18479864	18479964	+	2.2	cIP2vsInput	"intron (NR_040544, intron 1 of 3)"	"intron (NR_040544, intron 1 of 3)"	563	NR_040544	73959	Mm.60616	NR_040544		4930433B08Rik	-	RIKEN cDNA 4930433B08 gene	miscRNA	0.01	0.346535
Merged-chr14-53781432-1	chr14	53781382	53781482	+	2.2	cIP2vsInput	Intergenic	Intergenic	115492	NM_001205242	100568452	Mm.486072	NM_001205242		A430107P09Rik	Va10	RIKEN cDNA A430107P09 gene	protein-coding	0	0.326733
Merged-chr1-117219068-1	chr1	117219018	117219118	+	2.2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	1092064	NM_011650	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding	0	0.346535
Merged-chr15-4974904-1	chr15	4974854	4974954	+	2.2	cIP1vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	76167	NM_001166066	223825	Mm.159281	NM_001166066	ENSMUSG00000022155	Mroh2b	4930455B06Rik|Heatr7b2	maestro heat-like repeat family member 2B	protein-coding	0.01	0.336634
Merged-chr4-110664652-1	chr4	110664602	110664702	+	2.2	cIP2vsInput	"intron (NM_001048189, intron 3 of 12)"	"intron (NM_001048189, intron 3 of 12)"	266861	NM_030231	78933	Mm.435620	NM_001048189	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding	0	0.346535
Merged-chr8-125102340-1	chr8	125102290	125102390	+	2.2	cIP1vsInput	"intron (NM_174854, intron 3 of 12)"	"intron (NM_174854, intron 3 of 12)"	48145	NM_174854	244667	Mm.233504	NM_170596	ENSMUSG00000043051	Disc1	-	disrupted in schizophrenia 1	protein-coding	0.02	0.465347
Merged-chr12-108957135-1	chr12	108957085	108957185	+	2.2	cIP1vsInput	"intron (NM_177602, intron 2 of 6)"	L1MA4|LINE|L1	62863	NM_177602	212198	Mm.342082	NM_177602	ENSMUSG00000040877	Wdr25	B930090D16Rik	WD repeat domain 25	protein-coding	0.01	0.376238
Merged-chr12-33035364-1	chr12	33035314	33035414	+	2.2	cIP1vsInput	"intron (NM_001024478, intron 18 of 19)"	"intron (NM_001024478, intron 18 of 19)"	57511	NM_001024478	68764	Mm.447248	NM_001024478	ENSMUSG00000035860	Cdhr3	1110049B09Rik|BB172694|Cdh28	cadherin-related family member 3	protein-coding	0	0.425743
Merged-chr2-81060648-1	chr2	81060598	81060698	+	2.2	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	421384	NM_001190179	69482	Mm.29200	NM_001190179		Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding	0	0.346535
Merged-chr8-37088064-1	chr8	37088014	37088114	+	2.2	cIP1vsInput	Intergenic	Intergenic	94489	NM_001039220	621080	Mm.373292	NM_001039220	ENSMUSG00000074384	AI429214	-	expressed sequence AI429214	protein-coding	0.01	0.356436
Merged-chr4-40229208-1	chr4	40229158	40229258	+	2.2	cIP2vsInput	"intron (NM_172689, intron 3 of 17)"	"intron (NM_172689, intron 3 of 17)"	10617	NM_172689	230073	Mm.86382	NM_172689		Ddx58	6430573D20Rik|C330021E21|RIG-I|RLR-1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	protein-coding	0.01	0.366337
Merged-chr3-159103519-1	chr3	159103469	159103569	+	2.2	cIP2vsInput	"intron (NR_040750, intron 2 of 4)"	Lx|LINE|L1	27155	NR_040750	624759	Mm.491054	NR_040750		Gm20752	-	"predicted gene, 20752"	miscRNA	0	0.336634
Merged-chr18-38006141-1	chr18	38006091	38006191	+	2.2	cIP2vsInput	Intergenic	Intergenic	-7172	NM_001205336	106952	Mm.247642	NM_001205336	ENSMUSG00000024451	Arap3	Centd3|Drag1|E030006K04Rik|cnt-d3	"ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3"	protein-coding	0	0.554455
Merged-chr3-36425101-1	chr3	36425051	36425151	+	2.2	cIP1vsInput	Intergenic	Intergenic	50786	NM_009673	11747	Mm.1620	NM_009673	ENSMUSG00000027712	Anxa5	Anx5|R74653	annexin A5	protein-coding	0	0.287129
Merged-chr11-57419596-1	chr11	57419546	57419646	+	2.2	cIP2vsInput	Intergenic	Intergenic	99048	NM_001168667	67726	Mm.25632	NM_001168667	ENSMUSG00000020523	Fam114a2	1810073G14Rik|9030624B09Rik	"family with sequence similarity 114, member A2"	protein-coding	0.01	0.366337
Merged-chr8-110727002-1	chr8	110726952	110727052	+	2.2	cIP2vsInput	"intron (NM_198625, intron 3 of 13)"	"intron (NM_198625, intron 3 of 13)"	5518	NM_198625	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding	0.06	0.673267
Merged-chr15-9907204-1	chr15	9907154	9907254	+	2.2	cIP2vsInput	Intergenic	Intergenic	-158398	NM_177123	320277	Mm.127822	NM_177123		Spef2	C230086A09Rik	sperm flagellar 2	protein-coding	0.01	0.316832
Merged-chr17-21691401-1	chr17	21691351	21691451	+	2.2	cIP2vsInput	"non-coding (NR_045766, exon 1 of 1)"	"non-coding (NR_045766, exon 1 of 1)"	1189	NR_045766	100310809	Mm.463100	NR_045766		Gm10509	ENSMUSG00000073448	zinc finger protein 51 pseudogene	pseudo	0	0.356436
Merged-chr3-36736447-1	chr3	36736397	36736497	+	2.2	cIP1vsInput	Intergenic	ID_B1|SINE|B4	-46280	NM_019510	22065	Mm.74363	NM_019510	ENSMUSG00000027716	Trpc3	Mwk|Trcp3|Trp3|Trrp3	"transient receptor potential cation channel, subfamily C, member 3"	protein-coding	0.01	0.465347
Merged-chr16-59349312-1	chr16	59349262	59349362	+	2.2	cIP1vsInput	Intergenic	Intergenic	-3613	NM_146991	258993	Mm.377781	NM_146991	ENSMUSG00000066257	Olfr206	MOR182-4	olfactory receptor 206	protein-coding	0.01	0.366337
Merged-chr1-58248019-1	chr1	58247969	58248069	+	2.2	cIP1vsInput	"intron (NM_023631, intron 19 of 34)"	"intron (NM_023631, intron 19 of 34)"	-30307	NM_001008419	213043	Mm.414292	NM_001008419	ENSMUSG00000079554	Aox3l1	Aoh3	aldehyde oxidase 3-like 1	protein-coding	0.01	0.39604
Merged-chr1-92647945-1	chr1	92647895	92647995	+	2.2	cIP1vsInput	"intron (NM_153114, intron 1 of 4)"	"intron (NM_153114, intron 1 of 4)"	896	NM_153114	260301	Mm.219545	NM_153114	ENSMUSG00000044055	Otos	OTOSP	otospiralin	protein-coding	0.03	0.564356
Merged-chr4-66569194-1	chr4	66569144	66569244	+	2.2	cIP2vsInput	Intergenic	Lx3_Mus|LINE|L1	-164711	NM_207109	56079	Mm.445312	NM_019514	ENSMUSG00000028373	Astn2	1d8|Astnl|bM452J22.1	astrotactin 2	protein-coding	0	0.366337
Merged-chr2-49440065-1	chr2	49440015	49440115	+	2.2	cIP1vsInput	Intergenic	MYSERV-int|LTR|ERVK	-11421	NM_172663	227867	Mm.29167	NM_172663	ENSMUSG00000069495	Epc2	5830499L14|D2Ertd694e	enhancer of polycomb homolog 2 (Drosophila)	protein-coding	0	0.306931
Merged-chr8-20122510-2	chr8	20122460	20122560	+	2.2	cIP1vsInput|cIP2vsInput	Intergenic	CpG	174922	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo	0.13	0.742574
Merged-chr17-53661887-1	chr17	53661837	53661937	+	2.2	cIP2vsInput	"intron (NM_001190846, intron 13 of 17)"	"intron (NM_001190846, intron 13 of 17)"	27428	NM_028232	72415	Mm.153202	NM_028232	ENSMUSG00000023940	Sgol1	3300001M08Rik|C81037|Sgo1	shugoshin-like 1 (S. pombe)	protein-coding	0.01	0.376238
Merged-chr17-5406379-1	chr17	5406329	5406429	+	2.2	cIP2vsInput	Intergenic	Intergenic	12388	NM_175349	106557	Mm.432764	NM_175349		Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding	0	0.326733
Merged-chr8-47021037-1	chr8	47020987	47021087	+	2.2	cIP1vsInput	"intron (NM_177304, intron 1 of 7)"	"intron (NM_177304, intron 1 of 7)"	34112	NM_177304	320981	Mm.211429	NM_177304	ENSMUSG00000038173	Enpp6	4833421B01Rik|B830047L21Rik|D8Ertd514e|E-NPP 6|Npp6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding	0	0.376238
Merged-chr18-22287899-1	chr18	22287849	22287949	+	2.2	cIP1vsInput	Intergenic	Intergenic	-57190	NM_001167777	211961	Mm.392310	NM_001167777	ENSMUSG00000045215	Asxl3	C230079D11Rik|D430002O22Rik|D930044O18Rik|Gm329|Gm945	additional sex combs like 3 (Drosophila)	protein-coding	0	0.326733
Merged-chr1-109210639-1	chr1	109210589	109210689	+	2.2	cIP2vsInput	Intergenic	Intergenic	-773098	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.306931
Merged-chr9-82672004-1	chr9	82671954	82672054	+	2.2	cIP1vsInput	Intergenic	L1M2|LINE|L1	-157802	NM_001168240	65099	Mm.41415	NM_001168240	ENSMUSG00000032251	Irak1bp1	4921528N06Rik|AI851240|Aabp3|Aip70|Simpl	interleukin-1 receptor-associated kinase 1 binding protein 1	protein-coding	0	0.267327
Merged-chr6-70768906-1	chr6	70768856	70768956	+	2.2	cIP2vsInput	"intron (NM_009075, intron 8 of 8)"	"intron (NM_009075, intron 8 of 8)"	23269	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding	0.01	0.49505
Merged-chr5-148793478-1	chr5	148793428	148793528	+	2.2	cIP2vsInput	Intergenic	Intergenic	51638	NR_028285	70138	Mm.417834	NR_028285	ENSMUSG00000086494	2210417A02Rik	AV081004	RIKEN cDNA 2210417A02 gene	miscRNA	0.01	0.316832
Merged-chr19-60143686-1	chr19	60143636	60143736	+	2.2	cIP2vsInput	promoter-TSS (NR_026942)	promoter-TSS (NR_026942)	-989	NR_026942	107376	Mm.245813	NR_026942	ENSMUSG00000053117	E330013P04Rik	9930018I18Rik|AW492152	RIKEN cDNA E330013P04 gene	miscRNA	0	0.346535
Merged-chr15-60143109-1	chr15	60143059	60143159	+	2.2	cIP1vsInput	Intergenic	Intergenic	-126491	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding	0.01	0.207921
Merged-chr18-20350631-1	chr18	20350581	20350681	+	2.2	cIP1vsInput	Intergenic	Intergenic	-26204	NM_181682	225256	Mm.355485	NM_181682	ENSMUSG00000061928	Dsg1b	Dsg5	desmoglein 1 beta	protein-coding	0.01	0.415842
Merged-chr6-7238894-1	chr6	7238844	7238944	+	2.2	cIP1vsInput	Intergenic	Intergenic	282876	NM_001077713	71238	Mm.490412	NM_001077713		Acn9	0610005M07Rik|4933430A16Rik	ACN9 homolog (S. cerevisiae)	protein-coding	0	0.346535
Merged-chr8-97062892-1	chr8	97062842	97062942	+	2.2	cIP2vsInput	Intergenic	Intergenic	-516919	NR_039538	100628567		NR_039538		Mir28c	mmu-mir-28c	microRNA 28c	miscRNA	0.01	0.366337
Merged-chr7-53807466-1	chr7	53807416	53807516	+	2.2	cIP2vsInput	Intergenic	Intergenic	-1027779	NM_178705	233271	Mm.474990	NM_178705		Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding	0	0.326733
Merged-chr13-87237303-1	chr13	87237253	87237353	+	2.2	cIP1vsInput	Intergenic	ORR1D1-int|LTR|ERVL-MaLR	-1190508	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0	0.39604
Merged-chr3-125155014-1	chr3	125154964	125155064	+	2.2	cIP1vsInput	Intergenic	MYSERV6-int|LTR|ERVK	-249077	NM_022565	64580	Mm.444289	NM_022565	ENSMUSG00000027971	Ndst4	4930439H17Rik	N-deacetylase/N-sulfotransferase (heparin glucosaminyl) 4	protein-coding	0	0.287129
Merged-chr12-52075872-1	chr12	52075822	52075922	+	2.2	cIP2vsInput	Intergenic	Intergenic	-21874	NM_029760	76826	Mm.244781	NM_029760		Nubpl	2410170E07Rik	nucleotide binding protein-like	protein-coding	0.01	0.366337
Merged-chr16-42935526-1	chr16	42935476	42935576	+	2.2	cIP1vsInput	Intergenic	Intergenic	-20054	NR_002445	170658	Mm.375824	NR_002445	ENSMUSG00000081824	BC002163	-	NADH dehydrogenase Fe-S protein 5 pseudogene	pseudo	0	0.306931
Merged-chr3-150923316-1	chr3	150923266	150923366	+	2.2	cIP1vsInput	Intergenic	Intergenic	-514566	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0	0.267327
Merged-chr5-96175852-1	chr5	96175802	96175902	+	2.2	cIP1vsInput	Intergenic	Intergenic	-13862	NM_144910	231464	Mm.384746	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	"CCR4-NOT transcription complex, subunit 6-like"	protein-coding	0.01	0.316832
Merged-chr9-84497241-1	chr9	84497191	84497291	+	2.2	cIP1vsInput	Intergenic	Intergenic	-277157	NR_040739	75253	Mm.401984	NR_040739		4930554C24Rik	-	RIKEN cDNA 4930554C24 gene	miscRNA	0.01	0.306931
Merged-chr1-123229738-1	chr1	123229688	123229788	+	2.2	cIP2vsInput	Intergenic	Intergenic	815821	NM_199021	269109	Mm.483255	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding	0	0.366337
Merged-chr4-22330852-1	chr4	22330802	22330902	+	2.2	cIP2vsInput	Intergenic	Lx6|LINE|L1	-26713	NM_172988	269514	Mm.40708	NM_172988	ENSMUSG00000040410	Fbxl4	4732456I21|AI836810|FBL4|FBL5	F-box and leucine-rich repeat protein 4	protein-coding	0	0.306931
Merged-chr12-35481248-1	chr12	35481198	35481298	+	2.2	cIP1vsInput	Intergenic	Intergenic	53741	NM_013464	11622	Mm.341377	NM_013464	ENSMUSG00000019256	Ahr	Ah|Ahh|Ahre|In|bHLHe76	aryl-hydrocarbon receptor	protein-coding	0	0.386139
Merged-chr4-49986796-1	chr4	49986746	49986846	+	2.2	cIP2vsInput	Intergenic	RMER16C|LTR|ERVK	-141027	NM_001276355	242443	Mm.440095	NM_001033351		Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	"glutamate receptor ionotropic, NMDA3A"	protein-coding	0	0.376238
Merged-chr13-109364039-1	chr13	109363989	109364089	+	2.2	cIP1vsInput	"intron (NM_011056, intron 3 of 16)"	"intron (NM_011056, intron 3 of 16)"	39295	NR_030644	100124489		NR_030644		Mir582	Mirn582|mmu-mir-582	microRNA 582	miscRNA	0	0.316832
Merged-chrX-111433679-1	chrX	111433629	111433729	+	2.2	cIP2vsInput	"intron (NM_025949, intron 8 of 24)"	"intron (NM_025949, intron 8 of 24)"	104266	NM_025949	67071	Mm.37617	NM_025949	ENSMUSG00000025665	Rps6ka6	2610524K04Rik|RSK4	ribosomal protein S6 kinase polypeptide 6	protein-coding	0	0.316832
Merged-chr15-58561694-1	chr15	58561644	58561744	+	2.2	cIP2vsInput	Intergenic	Intergenic	146226	NM_145959	210998	Mm.3224	NM_145959	ENSMUSG00000037119	D15Ertd621e	AV220772|BC033609|Fam91a1|SKIN|mKIAA0493	"DNA segment, Chr 15, ERATO Doi 621, expressed"	protein-coding	0.02	0.415842
Merged-chr5-54819162-1	chr5	54819112	54819212	+	2.2	cIP2vsInput	Intergenic	L1MB3|LINE|L1	469170	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0.01	0.306931
Merged-chr3-140415960-1	chr3	140415910	140416010	+	2.2	cIP2vsInput	Intergenic	Intergenic	796395	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0	0.346535
Merged-chr17-66960133-1	chr17	66960083	66960183	+	2.2	cIP1vsInput	"intron (NM_008984, intron 7 of 30)"	"intron (NM_008984, intron 7 of 30)"	-365511	NM_028998	74556	Mm.218634	NM_028998	ENSMUSG00000024105	Themis3	9130404H23Rik	thymocyte selection associated family member 3	protein-coding	0	0.326733
Merged-chr16-87784818-1	chr16	87784768	87784868	+	2.2	cIP2vsInput	Intergenic	MTE2a|LTR|ERVL-MaLR	85864	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1	protein-coding	0.02	0.485149
Merged-chr13-104709577-1	chr13	104709527	104709627	+	2.2	cIP1vsInput	"intron (NM_026072, intron 11 of 13)"	"intron (NM_026072, intron 11 of 13)"	107376	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	protein-coding	0.01	0.386139
Merged-chr4-124944572-1	chr4	124944522	124944622	+	2.2	cIP2vsInput	TTS (NM_177573)	TTS (NM_177573)	7524	NM_177573	194268	Mm.266907	NM_177573		9930104L06Rik	-	RIKEN cDNA 9930104L06 gene	protein-coding	0	0.306931
Merged-chr9-38493146-1	chr9	38493096	38493196	+	2.2	cIP1vsInput	Intergenic	Intergenic	5115	NM_146803	258799	Mm.390171	NM_146803	ENSMUSG00000039962	Olfr906	MOR167-2	olfactory receptor 906	protein-coding	0	0.277228
Merged-chr11-121841755-1	chr11	121841705	121841805	+	2.2	cIP2vsInput	"exon (NM_029049, exon 4 of 4)"	"exon (NM_029049, exon 4 of 4)"	11537	NM_029049	74675	Mm.61213	NM_029049	ENSMUSG00000039198	Ptchd3	4930451E13Rik|4933440L20Rik|RNDEu-3	patched domain containing 3	protein-coding	0.01	0.425743
Merged-chr5-61025430-1	chr5	61025380	61025480	+	2.2	cIP2vsInput	Intergenic	Lx5|LINE|L1	-783413	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding	0	0.326733
Merged-chr10-104993867-1	chr10	104993817	104993917	+	2.2	cIP1vsInput	Intergenic	Intergenic	580612	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding	0.01	0.336634
Merged-chr2-81476381-1	chr2	81476331	81476431	+	2.2	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	-577277	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0	0.316832
Merged-chr9-23830919-1	chr9	23830869	23830969	+	2.2	cIP2vsInput	Intergenic	L1M2|LINE|L1	-267099	NM_175678	319239	Mm.130824	NM_175678	ENSMUSG00000043659	Npsr1	9330128H10Rik|GPRA|Gpr154|MVTR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0	0.287129
Merged-chr19-59893697-1	chr19	59893647	59893747	+	2.2	cIP2vsInput	Intergenic	Intergenic	49667	NM_001033172	74998	Mm.24167	NM_001033172	ENSMUSG00000040022	Rab11fip2	4930470G04Rik|A830046J09Rik|AW558126|Nrip11	RAB11 family interacting protein 2 (class I)	protein-coding	0.01	0.346535
Merged-chr6-23745067-1	chr6	23745017	23745117	+	2.2	cIP2vsInput	"intron (NM_001252105, intron 1 of 28)"	L1MEj|LINE|L1	-89931	NM_027754	71300	Mm.443309	NM_027754	ENSMUSG00000078179	Rnf148	4933432M07Rik|Greul3	ring finger protein 148	protein-coding	0	0.356436
Merged-chr12-77888058-1	chr12	77888008	77888108	+	2.2	cIP2vsInput	Intergenic	L1ME3A|LINE|L1	-338597	NM_172952	268566	Mm.453131	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding	0	0.356436
Merged-chr15-44114292-1	chr15	44114242	44114342	+	2.2	cIP2vsInput	Intergenic	Intergenic	-81843	NM_013696	22045	Mm.309350	NM_013696	ENSMUSG00000038760	Trhr	TRH-R1	thyrotropin releasing hormone receptor	protein-coding	0	0.29703
Merged-chr1-148421353-1	chr1	148421303	148421403	+	2.2	cIP1vsInput	Intergenic	Intergenic	1539931	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0	0.39604
Merged-chr8-34300501-1	chr8	34300451	34300551	+	2.2	cIP2vsInput	Intergenic	Intergenic	145938	NM_026432	67887	Mm.290353	NM_026432	ENSMUSG00000031532	Tmem66	1810045K07Rik|SARAF	transmembrane protein 66	protein-coding	0.01	0.445545
Merged-chr11-14727290-1	chr11	14727240	14727340	+	2.2	cIP1vsInput	Intergenic	MTD|LTR|ERVL-MaLR	128050	NM_001164166	432536	Mm.33646	NR_002893		Pom121l12	1700054H16Rik	POM121 membrane glycoprotein-like 12	protein-coding	0	0.405941
Merged-chr1-61608688-1	chr1	61608638	61608738	+	2.2	cIP1vsInput	Intergenic	MIRb|SINE|MIR	-30136	NM_001081050	72823	Mm.441881	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta|RP23-20G7.1	par-3 partitioning defective 3 homolog B (C. elegans)	protein-coding	0.01	0.346535
Merged-chr16-33898689-1	chr16	33898639	33898739	+	2.2	cIP1vsInput	"intron (NM_010580, intron 5 of 14)"	"intron (NM_010580, intron 5 of 14)"	68314	NM_009471	22247	Mm.466951	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding	0.01	0.455446
Merged-chr11-65623190-1	chr11	65623140	65623240	+	2.2	cIP2vsInput	Intergenic	L1MB3|LINE|L1	111642	NR_030417	791070		NR_030417		Mir744	Mirn744|mir-744|mmu-mir-744	microRNA 744	miscRNA	0	0.306931
Merged-chr19-28104902-1	chr19	28104852	28104952	+	2.2	cIP2vsInput	Intergenic	Intergenic	-93736	NM_011265	19726	Mm.313321	NM_001166414	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	"regulatory factor X, 3 (influences HLA class II expression)"	protein-coding	0.01	0.376238
Merged-chr18-87042178-1	chr18	87042128	87042228	+	2.2	cIP1vsInput	Intergenic	Intergenic	329130	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding	0.02	0.29703
Merged-chr6-78959286-1	chr6	78959236	78959336	+	2.2	cIP2vsInput	Intergenic	Intergenic	-72756	NR_040302	100504701	Mm.400420	NR_040301		Gm20362	-	"predicted gene, 20362"	miscRNA	0	0.326733
Merged-chr3-109063372-1	chr3	109063322	109063422	+	2.2	cIP2vsInput	Intergenic	Intergenic	-17127	NM_029054	74686	Mm.307948	NM_029054	ENSMUSG00000027880	Slc25a54	4930443G12Rik|SCaMC-1like	"solute carrier family 25, member 54"	protein-coding	0.01	0.326733
Merged-chr13-85763885-1	chr13	85763835	85763935	+	2.2	cIP2vsInput	Intergenic	Intergenic	282910	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0	0.405941
Merged-chr10-64738467-1	chr10	64738417	64738517	+	2.2	cIP2vsInput	"intron (NM_001164519, intron 8 of 12)"	"intron (NM_001164519, intron 8 of 12)"	-648212	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding	0.01	0.287129
Merged-chr12-63506890-1	chr12	63506840	63506940	+	2.2	cIP2vsInput	Intergenic	RMER15|LTR|ERVL	968008	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0.01	0.326733
Merged-chr10-100854162-1	chr10	100854112	100854212	+	2.2	cIP1vsInput	Intergenic	Intergenic	261776	NM_001081246	66605	Mm.72646	NM_001081246	ENSMUSG00000056912	1700017N19Rik	-	RIKEN cDNA 1700017N19 gene	protein-coding	0	0.376238
Merged-chr9-39744050-1	chr9	39744000	39744100	+	2.2	cIP1vsInput	Intergenic	Intergenic	-6338	NM_001011826	258086	Mm.377345	NM_001011826	ENSMUSG00000055820	Olfr967	MOR171-30P	olfactory receptor 967	protein-coding	0	0.247525
Merged-chr5-72989773-1	chr5	72989723	72989823	+	2.2	cIP2vsInput	Intergenic	Intergenic	-17131	NM_173403	231290	Mm.253661	NM_173403		Slc10a4	E130304D01	"solute carrier family 10 (sodium/bile acid cotransporter family), member 4"	protein-coding	0.01	0.356436
Merged-chr17-29647107-1	chr17	29647057	29647157	+	2.2	cIP1vsInput	Intergenic	Intergenic	-13494	NM_028791	74157	Mm.475060	NM_028791		Ftsjd2	1300018I05Rik|AI451264|MTr1|mKIAA0082	FtsJ methyltransferase domain containing 2	protein-coding	0	0.534653
Merged-chr17-61879331-1	chr17	61879281	61879381	+	2.2	cIP2vsInput	Intergenic	Intergenic	561579	NR_030569	100124495		NR_030569		Mir466g	Mirn466g	microRNA 466g	miscRNA	0.01	0.306931
Merged-chr18-37100311-1	chr18	37100261	37100361	+	2.2	cIP1vsInput	"intron (NM_001003671, intron 1 of 3)"	L1_Mur3|LINE|L1	10175	NM_001003671	353236	Mm.308500	NM_001003671	ENSMUSG00000007440	Pcdhac1	CNRc1	"protocadherin alpha subfamily C, 1"	protein-coding	0	0.29703
Merged-chr10-95883277-1	chr10	95883227	95883327	+	2.2	cIP2vsInput	Intergenic	Intergenic	-57386	NM_001001932	216238	Mm.490373	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding	0	0.326733
Merged-chr10-123700288-1	chr10	123700238	123700338	+	2.2	cIP2vsInput	"intron (NM_001252387, intron 2 of 4)"	L1MA8|LINE|L1	436212	NM_001252387	268354	Mm.51939	NM_001252387	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	"family with sequence similarity 19, member A2"	protein-coding	0	0.356436
Merged-chr5-70701975-1	chr5	70701925	70702025	+	2.2	cIP1vsInput	Intergenic	Intergenic	140642	NM_010252	14405	Mm.255292	NM_010252	ENSMUSG00000001260	Gabrg1	GabaA|GabaA/BZ	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1"	protein-coding	0	0.356436
Merged-chr10-6190423-1	chr10	6190373	6190473	+	2.2	cIP1vsInput	Intergenic	Intergenic	-268023	NM_019958	56533	Mm.44606	NM_001161822	ENSMUSG00000019775	Rgs17	6430507P11Rik|Rgsz2	regulator of G-protein signaling 17	protein-coding	0.01	0.366337
Merged-chr16-78544370-1	chr16	78544320	78544420	+	2.2	cIP1vsInput	"3' UTR (NM_001252439, exon 5 of 5)"	"3' UTR (NM_001252439, exon 5 of 5)"	-15946	NR_040569	75818	Mm.410817	NR_040569		4930478L05Rik	-	RIKEN cDNA 4930478L05 gene	miscRNA	0.01	0.336634
Merged-chr17-55672919-1	chr17	55672869	55672969	+	2.2	cIP2vsInput	"intron (NM_028370, intron 9 of 16)"	"intron (NM_028370, intron 9 of 16)"	39709	NM_028370	72836	Mm.448349	NM_028370	ENSMUSG00000024174	Pot1b	2810458H16Rik	protection of telomeres 1B	protein-coding	0.01	0.386139
Merged-chr15-18934715-1	chr15	18934665	18934765	+	2.2	cIP2vsInput	"intron (NM_009865, intron 2 of 11)"	"intron (NM_009865, intron 2 of 11)"	114386	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0	0.316832
Merged-chr3-78729401-1	chr3	78729351	78729451	+	2.2	cIP1vsInput	Intergenic	L1MDa|LINE|L1	416474	NM_001099624	76089	Mm.462396	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding	0	0.306931
Merged-chr2-146307952-1	chr2	146307902	146308002	+	2.2	cIP2vsInput	"intron (NM_001033348, intron 38 of 40)"	"intron (NM_001033348, intron 38 of 40)"	48666	NR_040619	77806	Mm.392819	NR_040619	ENSMUSG00000085958	A930019D19Rik	-	RIKEN cDNA A930019D19 gene	miscRNA	0.01	0.326733
Merged-chr18-85685963-1	chr18	85685913	85686013	+	2.2	cIP1vsInput	Intergenic	Intergenic	-708989	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding	0	0.29703
Merged-chr4-13364370-1	chr4	13364320	13364420	+	2.2	cIP1vsInput	Intergenic	Intergenic	-378932	NM_001111026	12395	Mm.470961	NM_001111026	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	"runt-related transcription factor 1; translocated to, 1 (cyclin D-related)"	protein-coding	0.01	0.366337
Merged-chr13-85608849-1	chr13	85608799	85608899	+	2.2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-319363	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding	0.01	0.277228
Merged-chr16-93132365-1	chr16	93132315	93132415	+	2.2	cIP1vsInput	Intergenic	Intergenic	220824	NR_040486	69857	Mm.81192	NR_040486		1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	miscRNA	0	0.336634
Merged-chr11-31092753-1	chr11	31092703	31092803	+	2.2	cIP1vsInput	"intron (NM_023906, intron 9 of 9)"	"intron (NM_023906, intron 9 of 9)"	-106388	NM_026527	68044	Mm.32656	NM_026527	ENSMUSG00000020309	Chac2	2510006C20Rik	"ChaC, cation transport regulator 2"	protein-coding	0	0.316832
Merged-chr16-54760408-1	chr16	54760358	54760458	+	2.2	cIP1vsInput	Intergenic	Intergenic	522829	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding	0	0.366337
Merged-chr5-83830830-1	chr5	83830780	83830880	+	2.2	cIP1vsInput	Intergenic	Lx8|LINE|L1	-475635	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	"trans-2,3-enoyl-CoA reductase-like"	protein-coding	0	0.376238
Merged-chr16-40062654-1	chr16	40062604	40062704	+	2.2	cIP1vsInput	Intergenic	Intergenic	1160309	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	"immunoglobulin superfamily, member 11"	protein-coding	0	0.306931
Merged-chr6-77118063-1	chr6	77118013	77118113	+	2.2	cIP2vsInput	"intron (NM_009819, intron 8 of 18)"	"intron (NM_009819, intron 8 of 18)"	-124654	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0	0.366337
Merged-chr5-127902782-1	chr5	127902732	127902832	+	2.2	cIP2vsInput	"intron (NM_172885, intron 4 of 8)"	"intron (NM_172885, intron 4 of 8)"	270520	NM_177005	319804	Mm.237888	NM_177005		Glt1d1	5730455A04Rik	glycosyltransferase 1 domain containing 1	protein-coding	0.01	0.366337
Merged-chr14-78094484-1	chr14	78094434	78094534	+	2.2	cIP1vsInput	Intergenic	Lx9|LINE|L1	-5477	NM_177629	219170	Mm.320428	NM_177629	ENSMUSG00000045655	Fam216b	9330158N17|AU021034	"family with sequence similarity 216, member B"	protein-coding	0	0.29703
Merged-chr15-8936141-1	chr15	8936091	8936191	+	2.2	cIP1vsInput	Intergenic	MIRb|SINE|MIR	-119541	NM_198024	223332	Mm.418007	NM_198024		Ranbp3l	C130037N17Rik	RAN binding protein 3-like	protein-coding	0	0.336634
Merged-chr18-50276964-1	chr18	50276914	50277014	+	2.2	cIP2vsInput	Intergenic	Intergenic	-1405	NM_001004061	225497	Mm.329435	NM_001004061	ENSMUSG00000035420	Fam170a	Gm93|Znfd	"family with sequence similarity 170, member A"	protein-coding	0	0.316832
Merged-chr5-59345985-1	chr5	59345935	59346035	+	2.2	cIP2vsInput	Intergenic	Intergenic	640017	NR_040683	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0.01	0.316832
Merged-chr3-59382291-1	chr3	59382241	59382341	+	2.2	cIP1vsInput	Intergenic	Intergenic	-38035	NM_001162884	242050	Mm.444186	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	"immunoglobulin superfamily, member 10"	protein-coding	0	0.306931
Merged-chr12-60733406-1	chr12	60733356	60733456	+	2.2	cIP1vsInput	Intergenic	Intergenic	788414	NR_045049	100504101	Mm.235026	NR_045049		Gm20063	-	"predicted gene, 20063"	miscRNA	0	0.29703
Merged-chr14-120014133-1	chr14	120014083	120014183	+	2.2	cIP2vsInput	Intergenic	Intergenic	28302	NM_001001490	239283	Mm.138520	NM_001001490	ENSMUSG00000044819	Oxgr1	Gm299|Gpr80|Gpr99|P2Y15	oxoglutarate (alpha-ketoglutarate) receptor 1	protein-coding	0.01	0.336634
Merged-chr7-138940359-1	chr7	138940309	138940409	+	2.2	cIP2vsInput	Intergenic	Intergenic	-30853	NM_009760	12176	Mm.378890	NM_009760	ENSMUSG00000078566	Bnip3	Nip3	BCL2/adenovirus E1B interacting protein 3	protein-coding	0.05	0.60396
Merged-chr7-103840583-1	chr7	103840533	103840633	+	2.2	cIP1vsInput	promoter-TSS (NM_001127686)	promoter-TSS (NM_001127686)	-62	NM_001127686	436003	Mm.475617	XM_003946245		Hbb-bh2	EG436003|Gm5736	"hemoglobin beta, bh2"	protein-coding	0	0.376238
Merged-chr13-104665331-1	chr13	104665281	104665381	+	2.2	cIP1vsInput	"intron (NM_026072, intron 11 of 13)"	"intron (NM_026072, intron 11 of 13)"	151622	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	protein-coding	0	0.376238
Merged-chr7-95947865-1	chr7	95947815	95947915	+	2.2	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-262772	NM_011858	23966	Mm.391678	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding	0.01	0.306931
Merged-chrX-83263610-1	chrX	83263560	83263660	+	2.2	cIP2vsInput	"intron (NM_007868, intron 2 of 78)"	"intron (NM_007868, intron 2 of 78)"	224314	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding	0.02	0.336634
Merged-chrX-63272846-1	chrX	63272796	63272896	+	2.2	cIP1vsInput	Intergenic	Intergenic	-745835	NR_045442	75545	Mm.391270	NR_045442	ENSMUSG00000085757	1700019B21Rik	-	RIKEN cDNA 1700019B21 gene	miscRNA	0	0.336634
Merged-chr13-115884009-1	chr13	115883959	115884059	+	2.2	cIP2vsInput	Intergenic	Intergenic	425679	NM_021459	16392	Mm.42242	NM_021459	ENSMUSG00000042258	Isl1	-	"ISL1 transcription factor, LIM/homeodomain"	protein-coding	0	0.29703
Merged-chr4-151774834-1	chr4	151774784	151774884	+	2.2	cIP2vsInput	"intron (NM_001081557, intron 3 of 23)"	"intron (NM_001081557, intron 3 of 23)"	86934	NM_001195565	100072	Mm.318846	NM_001166021	ENSMUSG00000014592	Camta1	1810059M14Rik|2310058O09Rik|AI316882|AW987475|mKIAA0833	calmodulin binding transcription activator 1	protein-coding	0	0.316832
Merged-chr4-14636218-1	chr4	14636168	14636268	+	2.2	cIP2vsInput	Intergenic	Intergenic	-14440	NM_145947	208890	Mm.483839	NM_145947		Slc26a7	-	"solute carrier family 26, member 7"	protein-coding	0	0.316832
Merged-chr1-135314116-1	chr1	135314066	135314166	+	2.2	cIP1vsInput	promoter-TSS (NM_011590)	promoter-TSS (NM_011590)	-379	NM_011590	21854	Mm.2368	NM_011590	ENSMUSG00000062580	Timm17a	17kDa|mTim17a	translocase of inner mitochondrial membrane 17a	protein-coding	0.02	0.376238
Merged-chr8-49765495-1	chr8	49765445	49765545	+	2.2	cIP2vsInput	Intergenic	Intergenic	-602617	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0.02	0.39604
Merged-chr3-48413439-1	chr3	48413389	48413489	+	2.2	cIP2vsInput	Intergenic	Intergenic	195661	NR_003617	66332	Mm.46124	NR_003617		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo	0	0.29703
Merged-chr4-108742415-1	chr4	108742365	108742465	+	2.2	cIP2vsInput	"intron (NM_001254730, intron 3 of 3)"	L1MB7|LINE|L1	-18539	NM_183300	230597	Mm.196776	NM_183300	ENSMUSG00000034557	Zfyve9	E030027L17|Madhip|NSP|SARA|SMADIP	"zinc finger, FYVE domain containing 9"	protein-coding	0	0.306931
Merged-chr16-83892513-1	chr16	83892463	83892563	+	2.2	cIP1vsInput	Intergenic	Lx5|LINE|L1	-478630	NR_040567	75247	Mm.417813	NR_040567		4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	miscRNA	0	0.376238
Merged-chr5-52867138-1	chr5	52867088	52867188	+	2.2	cIP1vsInput	TTS (NM_024213)	TTS (NM_024213)	33003	NM_024213	52206	Mm.272568	NM_024213		Anapc4	2610306D21Rik|APC4|D5Ertd249e	anaphase promoting complex subunit 4	protein-coding	0.01	0.287129
Merged-chr2-126462670-1	chr2	126462620	126462720	+	2.2	cIP2vsInput	"exon (NM_001080944, exon 4 of 28)"	"exon (NM_001080944, exon 4 of 28)"	28883	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	"ATPase, class I, type 8B, member 4"	protein-coding	0.03	0.356436
Merged-chr17-68998900-1	chr17	68998850	68998950	+	2.2	cIP1vsInput	Intergenic	Intergenic	-157910	NM_013813	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb4.1l3	4.1B|DAL1P|Dal1|Epb41l3|NBL3	erythrocyte protein band 4.1-like 3	protein-coding	0	0.356436
Merged-chr18-76378949-1	chr18	76378899	76378999	+	2.2	cIP2vsInput	Intergenic	Intergenic	117828	NM_001252481	17126	Mm.490934	NM_001252481		Smad2	7120426M23Rik|Madh2|Madr2|Smad-2|mMad2	SMAD family member 2	protein-coding	0.19	0.831683
Merged-chr1-146195605-1	chr1	146195555	146195655	+	2.2	cIP2vsInput	Intergenic	Intergenic	-300061	NM_153539	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.326733
Merged-chr4-24326614-1	chr4	24326564	24326664	+	2.2	cIP1vsInput	Intergenic	Lx3C|LINE|L1	-169848	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	"MMS22-like, DNA repair protein"	protein-coding	0	0.326733
Merged-chr2-97316321-1	chr2	97316271	97316371	+	2.2	cIP2vsInput	Intergenic	Intergenic	-151353	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.316832
Merged-chr3-59883145-1	chr3	59883095	59883195	+	2.2	cIP1vsInput	Intergenic	Intergenic	22094	NM_001243003	666803	Mm.389443	NM_001243003	ENSMUSG00000095522	Gm8298	EG666803	predicted gene 8298	protein-coding	0.01	0.29703
Merged-chr9-51360609-1	chr9	51360559	51360659	+	2.2	cIP1vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	-31692	NM_027217	69809	Mm.75315	NM_027217	ENSMUSG00000036027	1810046K07Rik	-	RIKEN cDNA 1810046K07 gene	protein-coding	0.01	0.277228
Merged-chr16-72767515-1	chr16	72767465	72767565	+	2.2	cIP1vsInput	"intron (NM_019413, intron 2 of 28)"	"intron (NM_019413, intron 2 of 28)"	104366	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout homolog 1 (Drosophila)	protein-coding	0	0.326733
Merged-chr5-98474513-1	chr5	98474463	98474563	+	2.2	cIP2vsInput	"intron (NM_001024614, intron 2 of 5)"	"intron (NM_001024614, intron 2 of 5)"	1151	NR_030484	735265		NR_030484		Mir703	Mirn703|mmu-mir-703	microRNA 703	miscRNA	0	0.376238
Merged-chr8-20417742-1	chr8	20417692	20417792	+	2.2	cIP1vsInput	"intron (NR_028428, intron 1 of 5)"	"intron (NR_028428, intron 1 of 5)"	7072	NR_028428	381598	Mm.483074	NM_001024708	ENSMUSG00000071793	2610005L07Rik	2810038F24Rik|6720476A01Rik	cadherin 11 pseudogene	pseudo	0	0.306931
Merged-chr12-74671811-1	chr12	74671761	74671861	+	2.2	cIP1vsInput	Intergenic	Intergenic	374337	NM_198866	386753	Mm.395044	NM_198866	ENSMUSG00000029878	Dbpht2	Spot2	DNA binding protein with his-thr domain	protein-coding	0	0.376238
Merged-chr4-28099657-1	chr4	28099607	28099707	+	2.2	cIP2vsInput	Intergenic	RMER6C|LTR|ERVK	-713488	NM_001122889	13841	Mm.257266	NM_001122889	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding	0	0.39604
Merged-chr9-80398386-1	chr9	80398336	80398436	+	2.2	cIP2vsInput	"exon (NM_022016, exon 6 of 17)"	"exon (NM_022016, exon 6 of 17)"	67052	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding	0	0.49505
Merged-chr1-30076291-1	chr1	30076241	30076341	+	2.2	cIP1vsInput	Intergenic	Intergenic	786965	NM_001081080	213109	Mm.486727	NM_001081080	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding	0	0.267327
Merged-chr18-3644385-1	chr18	3644335	3644435	+	2.2	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	136428	NM_026505	68010	Mm.284863	NM_026505	ENSMUSG00000024232	Bambi	2610003H06Rik	BMP and activin membrane-bound inhibitor	protein-coding	0	0.386139
Merged-chr15-87625850-1	chr15	87625800	87625900	+	2.2	cIP2vsInput	"intron (NM_134096, intron 1 of 3)"	"intron (NM_134096, intron 1 of 3)"	620	NM_134096	106014	Mm.244319	NM_001252310	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	"family with sequence similarity 19, member A5"	protein-coding	0.04	0.623762
Merged-chr14-74836609-1	chr14	74836559	74836659	+	2.2	cIP2vsInput	"intron (NM_001033439, intron 2 of 19)"	Lx7|LINE|L1	104264	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|sid478	esterase D/formylglutathione hydrolase	protein-coding	0	0.336634
Merged-chr1-109734673-1	chr1	109734623	109734723	+	2.2	cIP2vsInput	Intergenic	Lx|LINE|L1	-249064	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.366337
Merged-chr2-96902089-1	chr2	96902039	96902139	+	2.2	cIP2vsInput	Intergenic	Intergenic	-565585	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.326733
Merged-chr14-107129320-1	chr14	107129270	107129370	+	2.2	cIP2vsInput	Intergenic	Intergenic	-642800	NR_045938	73631	Mm.48862	NR_045938		1700128A07Rik	-	RIKEN cDNA 1700128A07 gene	miscRNA	0	0.366337
Merged-chr5-151686824-1	chr5	151686774	151686874	+	2.2	cIP2vsInput	Intergenic	Intergenic	-35616	NM_027009	69263	Mm.12553	NM_027009	ENSMUSG00000033970	Rfc3	2810416I22Rik|38kDa|AU022547|Recc3	replication factor C (activator 1) 3	protein-coding	0.03	0.465347
Merged-chr8-15027995-1	chr8	15027945	15028045	+	2.2	cIP2vsInput	"exon (NM_029116, exon 2 of 2)"	"exon (NM_029116, exon 2 of 2)"	16970	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding	0.12	0.712871
Merged-chr9-35957030-1	chr9	35956980	35957080	+	2.2	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-107150	NR_030730	100041605	Mm.99350	NR_030730		Gm3428	-	predicted gene 3428	miscRNA	0	0.346535
Merged-chr13-65904596-1	chr13	65904546	65904646	+	2.2	cIP2vsInput	Intergenic	MurSatRep1|Unknown|Unknown	-208857	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding	0.01	0.257426
Merged-chr16-15765464-1	chr16	15765414	15765514	+	2.2	cIP1vsInput	"intron (NM_011159, intron 54 of 85)"	Lx8|LINE|L1	97858	NM_029354	72083	Mm.22351	NM_029354	ENSMUSG00000022671	Mzt2	2410018G20Rik|2610001E06Rik|Fam128|Fam128b	mitotic spindle organizing protein 2	protein-coding	0.01	0.465347
Merged-chr1-87520441-1	chr1	87520391	87520491	+	2.2	cIP2vsInput	"intron (NM_001111314, intron 3 of 14)"	"intron (NM_001111314, intron 3 of 14)"	-10079	NM_019867	53972	Mm.435439	NM_001111314	ENSMUSG00000026259	Ngef	Tims2|ephexin	neuronal guanine nucleotide exchange factor	protein-coding	0	0.336634
Merged-chr16-26120965-1	chr16	26120915	26121015	+	2.2	cIP1vsInput	Intergenic	Intergenic	-15181	NM_173379	210530		NM_173379		Leprel1	4832416N06|AW553532|Mlat4|P3H2	leprecan-like 1	protein-coding	0.02	0.336634
Merged-chr17-68053643-1	chr17	68053593	68053693	+	2.2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-49535	NM_172964	268970	Mm.9935	NM_172964	ENSMUSG00000024043	Arhgap28	AU044757|AW550892|E130310N06	Rho GTPase activating protein 28	protein-coding	0	0.336634
Merged-chr2-24016063-1	chr2	24016013	24016113	+	2.2	cIP2vsInput	"intron (NM_080462, intron 4 of 6)"	RMER3D-int|LTR|ERVK	33316	NM_080462	140483	Mm.33120	NM_080462	ENSMUSG00000026986	Hnmt	1500031F01Rik|AI788969	histamine N-methyltransferase	protein-coding	0.01	0.376238
Merged-chr2-78321180-1	chr2	78321130	78321230	+	2.2	cIP1vsInput	Intergenic	Intergenic	83633	NM_177843	329436	Mm.235448	NM_177843		Gm14461	A830093M07|OTTMUSG00000016703	predicted gene 14461	protein-coding	0	0.326733
Merged-chr3-123274478-1	chr3	123274428	123274528	+	2.2	cIP2vsInput	"intron (NM_027135, intron 2 of 22)"	"intron (NM_027135, intron 2 of 22)"	6982	NM_027135	69608	Mm.29293	NM_027135	ENSMUSG00000039234	Sec24d	2310020L09Rik|Gm1349	"Sec24 related gene family, member D (S. cerevisiae)"	protein-coding	0.01	0.435644
Merged-chr10-29867988-1	chr10	29867938	29868038	+	2.2	cIP1vsInput	Intergenic	L1MEf|LINE|L1	-332121	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3 homolog (Xenopus laevis)	protein-coding	0	0.277228
Merged-chr12-105980509-1	chr12	105980459	105980559	+	2.2	cIP2vsInput	Intergenic	ORR1F|LTR|ERVL-MaLR	-29754	NM_011705	22367	Mm.2981	NM_001029843	ENSMUSG00000021115	Vrk1	51PK	vaccinia related kinase 1	protein-coding	0.02	0.415842
Merged-chr2-172136105-1	chr2	172136055	172136155	+	2.2	cIP1vsInput	Intergenic	(GAAA)n|Simple_repeat|Simple_repeat	-92639	NM_175631	228942	Mm.40555	NM_175631	ENSMUSG00000067578	Cbln4	AI848962	cerebellin 4 precursor protein	protein-coding	0	0.29703
Merged-chr7-10448754-1	chr7	10448704	10448804	+	2.2	cIP1vsInput	TTS (NM_134229)	TTS (NM_134229)	1965	NM_134229	171263	Mm.377216	NM_134229	ENSMUSG00000046716	Vmn1r67	V1re10	vomeronasal 1 receptor 67	protein-coding	0	0.306931
Merged-chr10-57410290-1	chr10	57410240	57410340	+	2.2	cIP2vsInput	Intergenic	Intergenic	76063	NR_045353	74928	Mm.416643	NR_045353	ENSMUSG00000097370	4930467K11Rik	-	RIKEN cDNA 4930467K11 gene	miscRNA	0	0.346535
Merged-chr9-75607641-1	chr9	75607591	75607691	+	2.2	cIP1vsInput	"intron (NM_016711, intron 1 of 9)"	MER2|DNA|TcMar-Tigger	3684	NM_016711	50876	Mm.291880	NM_001038710	ENSMUSG00000032186	Tmod2	N-Tmod|NTMOD	tropomodulin 2	protein-coding	0.03	0.425743
Merged-chr3-126111513-1	chr3	126111463	126111563	+	2.2	cIP1vsInput	Intergenic	Lx3_Mus|LINE|L1	-172963	NM_011674	22239	Mm.306021	NM_011674	ENSMUSG00000032854	Ugt8a	AI850488|AW455908|Cgt|Ugt8|mCerGT	UDP galactosyltransferase 8A	protein-coding	0	0.405941
Merged-chr6-110086315-1	chr6	110086265	110086365	+	2.2	cIP1vsInput	Intergenic	Intergenic	-559283	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0	0.287129
Merged-chr2-94994984-1	chr2	94994934	94995034	+	2.2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-556837	NM_007466	11800	Mm.486651	NM_007466	ENSMUSG00000027193	Api5	AAC-11|AI196452	apoptosis inhibitor 5	protein-coding	0	0.356436
Merged-chr10-46920113-1	chr10	46920063	46920163	+	2.2	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	675364	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0	0.316832
Merged-chr9-39055320-1	chr9	39055270	39055370	+	2.2	cIP1vsInput	Intergenic	Intergenic	5344	NM_146439	258431	Mm.271359	NM_146439	ENSMUSG00000094182	Olfr937	MOR171-24	olfactory receptor 937	protein-coding	0	0.237624
Merged-chr4-48784502-1	chr4	48784452	48784552	+	2.2	cIP1vsInput	Intergenic	Lx8|LINE|L1	120988	NM_026509	68016	Mm.133444	NM_026509	ENSMUSG00000028348	Murc	2310039E09Rik	muscle-related coiled-coil protein	protein-coding	0	0.356436
Merged-chr2-51475874-1	chr2	51475824	51475924	+	2.2	cIP2vsInput	Intergenic	Intergenic	-151637	NM_199158	387511	Mm.377918	NM_199158	ENSMUSG00000056115	Tas2r134	T2R134|Tas2r34	"taste receptor, type 2, member 134"	protein-coding	0.02	0.435644
Merged-chr1-192779370-1	chr1	192779320	192779420	+	2.2	cIP1vsInput	Intergenic	Intergenic	-8151	NM_144881	226861	Mm.145857	NM_144881	ENSMUSG00000037375	Hhat	2810432O22Rik|AI462858|AP-2CRE|Skn|Tg(TFAP2A-cre)1Will	hedgehog acyltransferase	protein-coding	0.01	0.485149
Merged-chr7-55062309-1	chr7	55062259	55062359	+	2.2	cIP2vsInput	"intron (NM_178705, intron 3 of 11)"	"intron (NM_178705, intron 3 of 11)"	227064	NM_178705	233271	Mm.474990	NM_178705		Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding	0	0.386139
Merged-chr14-94162602-1	chr14	94162552	94162652	+	2.2	cIP2vsInput	Intergenic	Intergenic	-271933	NM_001271798	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.356436
Merged-chr19-54620093-1	chr19	54620043	54620143	+	2.2	cIP1vsInput	Intergenic	Intergenic	479354	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	"glycerol-3-phosphate acyltransferase, mitochondrial"	protein-coding	0	0.316832
Merged-chr12-6947104-1	chr12	6947054	6947154	+	2.2	cIP1vsInput	Intergenic	Intergenic	433226	NR_045045	73575	Mm.179463	NR_045045		1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	miscRNA	0	0.366337
Merged-chr8-119425328-1	chr8	119425278	119425378	+	2.2	cIP1vsInput	Intergenic	A-rich|Low_complexity|Low_complexity	-11834	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding	0	0.267327
Merged-chr14-106895092-1	chr14	106895042	106895142	+	2.2	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-408572	NR_045938	73631	Mm.48862	NR_045938		1700128A07Rik	-	RIKEN cDNA 1700128A07 gene	miscRNA	0.01	0.346535
Merged-chr16-12060693-1	chr16	12060643	12060743	+	2.2	cIP2vsInput	"intron (NM_001174086, intron 2 of 3)"	MIRb|SINE|MIR	76580	NM_001174086	72555	Mm.310139	NM_001174086		Shisa9	2700045P11Rik|Ckamp44	shisa homolog 9 (Xenopus laevis)	protein-coding	0	0.237624
Merged-chr15-54062743-1	chr15	54062693	54062793	+	2.2	cIP1vsInput	Intergenic	Intergenic	-160307	NM_177225	320679	Mm.442455	NM_177225	ENSMUSG00000058656	Samd12	A830094I09Rik	sterile alpha motif domain containing 12	protein-coding	0	0.39604
Merged-chr17-93386705-1	chr17	93386655	93386755	+	2.2	cIP2vsInput	Intergenic	Intergenic	187283	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0	0.336634
Merged-chr15-16222041-1	chr15	16221991	16222091	+	2.2	cIP1vsInput	Intergenic	Intergenic	-556060	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0	0.257426
Merged-chr6-141453214-1	chr6	141453164	141453264	+	2.2	cIP2vsInput	"intron (NM_018779, intron 2 of 15)"	"intron (NM_018779, intron 2 of 15)"	-71172	NM_001177772	58807	Mm.284495	NM_001177772	ENSMUSG00000030235	Slco1c1	OATP-14|OATP-F|Oatp2|Oatpf|Slc21a14	"solute carrier organic anion transporter family, member 1c1"	protein-coding	0	0.336634
Merged-chr15-33948356-1	chr15	33948306	33948406	+	2.2	cIP2vsInput	Intergenic	L1VL2|LINE|L1	-134363	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding	0	0.376238
Merged-chr17-68541410-1	chr17	68541360	68541460	+	2.2	cIP1vsInput	"intron (NM_177278, intron 12 of 20)"	L1_Mus3|LINE|L1	267613	NM_177278	320858	Mm.137356	NM_177278		L3mbtl4	A730037L19Rik|D930040M24Rik	l(3)mbt-like 4 (Drosophila)	protein-coding	0	0.237624
Merged-chr10-33664349-1	chr10	33664299	33664399	+	2.2	cIP1vsInput	Intergenic	Intergenic	-39749	NM_175448	215890	Mm.417656	NM_175448	ENSMUSG00000019785	Clvs2	A330019N05Rik|Rlbp1l2	clavesin 2	protein-coding	0	0.29703
Merged-chr5-79222335-1	chr5	79222285	79222385	+	2.2	cIP2vsInput	"intron (NR_035474, intron 3 of 4)"	L2|LINE|L2	293569	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0	0.346535
Merged-chr14-84934541-1	chr14	84934491	84934591	+	2.2	cIP1vsInput	Intergenic	Intergenic	-458117	NR_015539	319903	Mm.440481	NR_015539		9630013A20Rik	-	RIKEN cDNA 9630013A20 gene	miscRNA	0.01	0.217822
Merged-chr2-54819344-1	chr2	54819294	54819394	+	2.2	cIP2vsInput	"intron (NM_173030, intron 4 of 12)"	MERVL_2A-int|LTR|ERVL	382957	NM_173030	271786	Mm.330227	NM_173030	ENSMUSG00000060988	Galnt13	A230002A12|A230020F20|BB182356	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13	protein-coding	0	0.326733
Merged-chr10-34951744-1	chr10	34951694	34951794	+	2.2	cIP2vsInput	Intergenic	Intergenic	468344	NM_010237	14302	Mm.332432	NM_001159544	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding	0	0.346535
Merged-chr4-102923871-1	chr4	102923821	102923921	+	2.2	cIP2vsInput	"intron (NM_144906, intron 15 of 23)"	"intron (NM_144906, intron 15 of 23)"	-62508	NM_026100	67344	Mm.111346	NM_001163767	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding	0	0.435644
Merged-chr2-96550796-2	chr2	96550740	96550853	+	2.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-916878	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.324561
Merged-chr6-137465513-2	chr6	137465461	137465566	+	2.15	cIP1vsInput|cIP2vsInput	TTS (NM_011216)	TTS (NM_011216)	54382	NM_001271589	13860	Mm.235346	NM_001271587	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding	0	0.584906
Merged-chr9-107521802-2	chr9	107521726	107521878	+	2.15	cIP1vsInput|cIP2vsInput	"intron (NM_001174047, intron 23 of 38)"	RLTR17B_Mm|LTR|ERVK	-12143	NM_019704	56395	Mm.260153	NM_019704	ENSMUSG00000010045	Tmem115	C78915|Pl6|Pp6	transmembrane protein 115	protein-coding	0.039474	0.522876
Merged-chr3-63006200-2	chr3	63006124	63006276	+	2.15	cIP1vsInput|cIP2vsInput	Intergenic	L1MA8|LINE|L1	-289672	NM_008604	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding	0	0.313725
Merged-chrY-6694769-2	chrY	6694677	6694861	+	2.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	473008	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01087	0.356757
Merged-chr19-23056996-2	chr19	23056899	23057094	+	2.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-84230	NM_010638	16601	Mm.392684	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding	0.046154	0.52551
Merged-chr12-20249728-2	chr12	20249654	20249803	+	2.15	cIP1vsInput|cIP2vsInput	Intergenic	RLTR11A2|LTR|ERVK	566051	NR_015521	69513	Mm.273972	NR_015521		1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	miscRNA	0.006711	0.273333
Merged-chr5-62434587-2	chr5	62434529	62434646	+	2.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	331590	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	"ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2"	protein-coding	0.008547	0.313559
Merged-chr3-67330891-2	chr3	67330826	67330956	+	2.15	cIP1vsInput|cIP2vsInput	"intron (NM_025822, intron 7 of 9)"	"intron (NM_025822, intron 7 of 9)"	-43206	NM_010801	17349	Mm.10414	NM_001039543	ENSMUSG00000048416	Mlf1	HLS7	myeloid leukemia factor 1	protein-coding	0	0.374046
Merged-chr14-88593049-2	chr14	88592979	88593119	+	2.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-121653	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0	0.283688
Merged-chr6-118179840-2	chr6	118179788	118179892	+	2.15	cIP1vsInput|cIP2vsInput	"intron (NM_001080780, intron 4 of 18)"	"intron (NM_001080780, intron 4 of 18)"	17904	NM_009050	19713	Mm.57199	NM_001080780	ENSMUSG00000030110	Ret	PTC|RET51|RET9|c-Ret	ret proto-oncogene	protein-coding	0.009615	0.590476
Merged-chrY-6463678-2	chrY	6463620	6463737	+	2.15	cIP1vsInput|cIP2vsInput	Intergenic	YREP_Mm|Unknown|Unknown	704099	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.305085
Merged-chr8-19720732-2	chr8	19720680	19720784	+	2.15	cIP1vsInput|cIP2vsInput	Intergenic	L1VL4|LINE|L1	-8844	NM_001270553	100861668	Mm.445582	NM_001270553		Gm21119	-	"predicted gene, 21119"	protein-coding	0	0.371429
Merged-chr4-55240657-2	chr4	55240591	55240724	+	2.15	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-109385	NM_009011	19359	Mm.196846	NM_009011	ENSMUSG00000028426	Rad23b	0610007D13Rik|AV001138|HR23B|mHR23B|p58	RAD23b homolog (S. cerevisiae)	protein-coding	0.022556	0.544776
Merged-chr3-77241946-2	chr3	77241896	77241996	+	2.15	cIP1vsInput|cIP2vsInput	Intergenic	Lx6|LINE|L1	1166363	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.306931
Merged-chr8-19733206-1	chr8	19733156	19733256	+	2.1	cIP2vsInput	"intron (NM_001270553, intron 2 of 9).2"	MTD|LTR|ERVL-MaLR	3630	NM_001039553	626415	Mm.425517	NM_001039553		4930467E23Rik	ENSMUSG00000074453|OTTMUSG00000018948|TSAP	RIKEN cDNA 4930467E23 gene	protein-coding	0	0.346535
Merged-chr2-64518113-1	chr2	64518063	64518163	+	2.1	cIP1vsInput	Intergenic	Intergenic	-420075	NM_001267847	60344	Mm.483676	NM_001267846	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding	0	0.316832
Merged-chrX-141528529-1	chrX	141528479	141528579	+	2.1	cIP1vsInput	"intron (NM_001163155, intron 1 of 50)"	L1M5|LINE|L1	53110	NM_001163155	12830	Mm.286892	NM_001163155	ENSMUSG00000031274	Col4a5	-	"collagen, type IV, alpha 5"	protein-coding	0	0.287129
Merged-chr4-83502238-1	chr4	83502188	83502288	+	2.1	cIP1vsInput	Intergenic	L1MDa|LINE|L1	-15848	NM_133948	101739	Mm.448301	NM_133948	ENSMUSG00000028484	Psip1	AA408851|AU015605|Dfs70|Ledgfa|Ledgfb|Psip2	PC4 and SFRS1 interacting protein 1	protein-coding	0	0.376238
Merged-chr3-72136951-1	chr3	72136901	72137001	+	2.1	cIP1vsInput	Intergenic	Intergenic	829915	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding	0.01	0.336634
Merged-chr3-135613281-1	chr3	135613231	135613331	+	2.1	cIP2vsInput	"intron (NM_008689, intron 11 of 24)"	L1_Mur2|LINE|L1	78266	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	"nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105"	protein-coding	0	0.346535
Merged-chr1-106449547-1	chr1	106449497	106449597	+	2.1	cIP1vsInput	Intergenic	Intergenic	264743	NM_009741	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding	0.01	0.316832
Merged-chr7-6545861-1	chr7	6545811	6545911	+	2.1	cIP1vsInput	Intergenic	Intergenic	-24132	NM_146389	258384	Mm.271316	NM_146389	ENSMUSG00000056696	Olfr1350	MOR222-3	olfactory receptor 1350	protein-coding	0	0.425743
Merged-chr10-111966096-1	chr10	111966046	111966146	+	2.1	cIP1vsInput	Intergenic	Intergenic	-6599	NM_178610	52705	Mm.34606	NM_178610	ENSMUSG00000063334	Krr1	2610511F02Rik|AI255219|AI428520|D10Ertd773e|Hrb2	"KRR1, small subunit (SSU) processome component, homolog (yeast)"	protein-coding	0.01	0.29703
Merged-chr13-71801878-1	chr13	71801828	71801928	+	2.1	cIP1vsInput	Intergenic	Intergenic	161845	NM_010573	16371	Mm.316056	NM_010573	ENSMUSG00000060969	Irx1	-	Iroquois related homeobox 1 (Drosophila)	protein-coding	0	0.376238
Merged-chr4-7172194-1	chr4	7172144	7172244	+	2.1	cIP2vsInput	Intergenic	Intergenic	-181471	NM_145711	252838	Mm.488241	NM_145711		Tox	1700007F02Rik	thymocyte selection-associated high mobility group box	protein-coding	0.01	0.336634
Merged-chr15-42392095-1	chr15	42392045	42392145	+	2.1	cIP2vsInput	Intergenic	Intergenic	284700	NM_009640	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding	0	0.306931
Merged-chr15-65194230-1	chr15	65194180	65194280	+	2.1	cIP2vsInput	Intergenic	Intergenic	-271934	NM_009623	11514	Mm.1425	NM_009623	ENSMUSG00000022376	Adcy8	AC8|AW060868	adenylate cyclase 8	protein-coding	0.01	0.346535
Merged-chr16-74614417-1	chr16	74614367	74614467	+	2.1	cIP2vsInput	Intergenic	Intergenic	-203505	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout homolog 2 (Drosophila)	protein-coding	0.01	0.376238
Merged-chr6-73701067-1	chr6	73701017	73701117	+	2.1	cIP1vsInput	Intergenic	Intergenic	-231400	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.346535
Merged-chr8-114156396-1	chr8	114156346	114156446	+	2.1	cIP2vsInput	Intergenic	Intergenic	22817	NM_024437	67528	Mm.27889	NM_024437	ENSMUSG00000031767	Nudt7	1300007B24Rik|2210404C19Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 7	protein-coding	0.01	0.524752
Merged-chr10-126283914-1	chr10	126283864	126283964	+	2.1	cIP1vsInput	Intergenic	Intergenic	317695	NM_177152	320398	Mm.275586	NM_177152	ENSMUSG00000020105	Lrig3	9030421L11Rik|9130004I02Rik|9430095K15Rik|mKIAA3016	leucine-rich repeats and immunoglobulin-like domains 3	protein-coding	0	0.356436
Merged-chr16-58945008-1	chr16	58944958	58945058	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-16364	NM_146999	259001	Mm.223388	NM_146999	ENSMUSG00000090951	Olfr181	MOR184-4	olfactory receptor 181	protein-coding	0	0.346535
Merged-chr4-23529101-1	chr4	23529051	23529151	+	2.1	cIP2vsInput	Intergenic	Intergenic	-967361	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	"MMS22-like, DNA repair protein"	protein-coding	0	0.39604
Merged-chr12-65914920-1	chr12	65914870	65914970	+	2.1	cIP1vsInput	Intergenic	Intergenic	369481	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding	0	0.366337
Merged-chr5-48676775-1	chr5	48676725	48676825	+	2.1	cIP2vsInput	"intron (NM_001199244, intron 1 of 7)"	MER47B|DNA|TcMar-Tigger	-77093	NM_001199245	80334	Mm.160172	NM_001199242	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding	0.01	0.316832
Merged-chr1-124515916-1	chr1	124515866	124515966	+	2.1	cIP1vsInput	Intergenic	Intergenic	-470357	NM_199021	269109	Mm.483255	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding	0	0.267327
Merged-chr6-16591600-1	chr6	16591550	16591650	+	2.1	cIP2vsInput	Intergenic	Intergenic	306841	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding	0	0.326733
Merged-chr1-116684938-1	chr1	116684888	116684988	+	2.1	cIP2vsInput	Intergenic	Lx9|LINE|L1	999801	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0.01	0.366337
Merged-chr7-30422303-1	chr7	30422253	30422353	+	2.1	cIP2vsInput	Intergenic	CpG	-1001	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	"nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta"	protein-coding	0.16	0.732673
Merged-chr12-98804497-1	chr12	98804447	98804547	+	2.1	cIP2vsInput	"intron (NM_001081191, intron 33 of 43)"	Cheshire|DNA|hAT-Charlie	33475	NM_001160108	75553	Mm.25549	NM_001008506	ENSMUSG00000021012	Zc3h14	1010001P15Rik|1700016A15Rik|2700069A02Rik|AU014748	zinc finger CCCH type containing 14	protein-coding	0.02	0.465347
Merged-chr19-31240064-1	chr19	31240014	31240114	+	2.1	cIP1vsInput	"intron (NM_001013833, intron 3 of 17)"	"intron (NM_001013833, intron 3 of 17)"	-23668	NR_002849	78103	Mm.445198	NR_002849		8430431K14Rik	-	RIKEN cDNA 8430431K14 gene	miscRNA	0	0.336634
Merged-chr8-58299191-1	chr8	58299141	58299241	+	2.1	cIP1vsInput	"intron (NM_175032, intron 4 of 11)"	"intron (NM_175032, intron 4 of 11)"	401605	NM_001177534	100271928	Mm.484123	NM_001177534		Gm15881	OTTMUSG00000027193	predicted gene 15881	protein-coding	0	0.267327
Merged-chr2-99191871-1	chr2	99191821	99191921	+	2.1	cIP1vsInput	Intergenic	Intergenic	1724197	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.376238
Merged-chr6-6737968-1	chr6	6737918	6738018	+	2.1	cIP2vsInput	Intergenic	L1MC|LINE|L1	-125366	NM_010057	13396	Mm.439763	NM_010057	ENSMUSG00000029754	Dlx6	-	distal-less homeobox 6	protein-coding	0	0.366337
Merged-chr14-109783516-1	chr14	109783466	109783566	+	2.1	cIP1vsInput	Intergenic	Lx5|LINE|L1	323286	NR_039542	100628607		NR_039542	ENSMUSG00000092639	Mir3964	mmu-mir-3964|mu-mir-3964	microRNA 3964	miscRNA	0	0.29703
Merged-chr13-70032716-1	chr13	70032666	70032766	+	2.1	cIP1vsInput	Intergenic	Intergenic	-4368	NR_045965	74280	Mm.273343	NR_045965		1700084F23Rik	1700003E18Rik|4930589D02Rik	RIKEN cDNA 1700084F23 gene	miscRNA	0	0.277228
Merged-chr16-15430395-1	chr16	15430345	15430445	+	2.1	cIP1vsInput	Intergenic	Intergenic	164123	NM_001159351	70620	Mm.390775	NM_001159351		Ube2v2	1110021H13Rik|4632410D19Rik|5730524P06Rik|6820402M05|AI848315|C81524|MMS2	ubiquitin-conjugating enzyme E2 variant 2	protein-coding	0	0.415842
Merged-chr1-58513853-1	chr1	58513803	58513903	+	2.1	cIP1vsInput	Intergenic	RMER16-int|LTR|ERVK	-8744	NM_008765	18393	Mm.3411	NM_001025378	ENSMUSG00000026037	Orc2	AU041563|Orc2l	"origin recognition complex, subunit 2"	protein-coding	0.01	0.326733
Merged-chr9-12504478-1	chr9	12504428	12504528	+	2.1	cIP1vsInput	Intergenic	Intergenic	601377	NR_040755	78219	Mm.414868	NR_040755		4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	miscRNA	0	0.287129
Merged-chr4-96146186-1	chr4	96146136	96146236	+	2.1	cIP2vsInput	Intergenic	Lx5|LINE|L1	-5034	NM_001100182	242546	Mm.302562	NM_001100182	ENSMUSG00000081225	Cyp2j12	BB197342|Cyp2j12-ps|OTTMUSG00000007939	"cytochrome P450, family 2, subfamily j, polypeptide 12"	protein-coding	0	0.356436
Merged-chr5-82931327-1	chr5	82931277	82931377	+	2.1	cIP2vsInput	Intergenic	Intergenic	-132262	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mmu-mir-1187	microRNA 1187	miscRNA	0	0.326733
Merged-chr18-50087607-1	chr18	50087557	50087657	+	2.1	cIP1vsInput	"intron (NM_134131, intron 1 of 1)"	L2|LINE|L2	34325	NM_134131	106869	Mm.27740	NM_001177759	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2	"tumor necrosis factor, alpha-induced protein 8"	protein-coding	0.05	0.514851
Merged-chr7-108720754-1	chr7	108720704	108720804	+	2.1	cIP1vsInput	Intergenic	Lx|LINE|L1	7399	NM_146724	258719	Mm.377653	NM_146724	ENSMUSG00000056946	Olfr512	MOR268-3	olfactory receptor 512	protein-coding	0	0.336634
Merged-chr3-10873284-1	chr3	10873234	10873334	+	2.1	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-433160	NM_001127191	74718	Mm.440548	NM_001127191	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding	0.01	0.366337
Merged-chr13-80395380-1	chr13	80395330	80395430	+	2.1	cIP2vsInput	Intergenic	Intergenic	-488042	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0	0.336634
Merged-chr1-21034682-1	chr1	21034632	21034732	+	2.1	cIP1vsInput	"intron (NM_177409, intron 2 of 10)"	L1MA4|LINE|L1	44543	NM_177409	170829	Mm.273241	NM_177409		Tram2	C330003D03Rik	translocating chain-associating membrane protein 2	protein-coding	0	0.356436
Merged-chr3-111981940-1	chr3	111981890	111981990	+	2.1	cIP2vsInput	"intron (NR_045362, intron 2 of 3)"	"intron (NR_045362, intron 2 of 3)"	100037	NR_045362	625585	Mm.389497	NR_045362		Gm6602	-	predicted gene 6602	miscRNA	0.01	0.287129
Merged-chr11-37830299-1	chr11	37830249	37830349	+	2.1	cIP1vsInput	Intergenic	Intergenic	689746	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0	0.316832
Merged-chr18-14451066-1	chr18	14451016	14451116	+	2.1	cIP1vsInput	Intergenic	L1_Mus4|LINE|L1	218760	NR_045373	74529	Mm.400519	NR_045373		8430422H06Rik	-	RIKEN cDNA 8430422H06 gene	miscRNA	0	0.326733
Merged-chr13-118846185-1	chr13	118846135	118846235	+	2.1	cIP1vsInput	Intergenic	L1MA4A|LINE|L1	131486	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding	0	0.455446
Merged-chr11-81588822-1	chr11	81588772	81588872	+	2.1	cIP2vsInput	"intron (NM_001034013, intron 1 of 9)"	"intron (NM_001034013, intron 1 of 9)"	-15283	NM_001033765	237880	Mm.435528	NM_001033765		1700071K01Rik	-	RIKEN cDNA 1700071K01 gene	protein-coding	0.04	0.613861
Merged-chr1-116690067-1	chr1	116690017	116690117	+	2.1	cIP2vsInput	Intergenic	Intergenic	1004930	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0	0.306931
Merged-chr2-52509217-1	chr2	52509167	52509267	+	2.1	cIP2vsInput	"intron (NM_001037099, intron 2 of 13)"	"intron (NM_001037099, intron 2 of 13)"	49350	NM_146123	12298	Mm.330223	NM_001037099	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lethargic|lh	"calcium channel, voltage-dependent, beta 4 subunit"	protein-coding	0	0.366337
Merged-chr10-50398800-1	chr10	50398750	50398850	+	2.1	cIP1vsInput	Intergenic	Intergenic	-193869	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0	0.386139
Merged-chr4-127244380-1	chr4	127244330	127244430	+	2.1	cIP2vsInput	"intron (NM_030252, intron 1 of 1)"	"intron (NM_030252, intron 1 of 1)"	596	NM_030252	80284	Mm.139607	NM_030252	ENSMUSG00000042380	Smim12	BC003266	small integral membrane protein 12	protein-coding	0.02	0.425743
Merged-chr5-25137899-1	chr5	25137849	25137949	+	2.1	cIP1vsInput	Intergenic	Lx6|LINE|L1	36924	NR_027851	67261	Mm.461781	NM_026059	ENSMUSG00000043833	2900005J15Rik	-	RIKEN cDNA 2900005J15 gene	miscRNA	0	0.326733
Merged-chr2-80918586-1	chr2	80918536	80918636	+	2.1	cIP2vsInput	Intergenic	Intergenic	279322	NM_001190179	69482	Mm.29200	NM_001190179		Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding	0	0.316832
Merged-chr12-48346492-1	chr12	48346442	48346542	+	2.1	cIP1vsInput	Intergenic	Intergenic	-45030	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0	0.336634
Merged-chr17-91184580-1	chr17	91184530	91184630	+	2.1	cIP1vsInput	Intergenic	Intergenic	-91778	NM_020252	18189	Mm.312068	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0	0.237624
Merged-chr1-160421165-1	chr1	160421115	160421215	+	2.1	cIP2vsInput	"intron (NM_013862, intron 17 of 20)"	"intron (NM_013862, intron 17 of 20)"	-69594	NM_001038621	29809	Mm.25833	NM_001038621	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding	0.01	0.386139
Merged-chr4-80449644-1	chr4	80449594	80449694	+	2.1	cIP2vsInput	Intergenic	Intergenic	-384586	NM_031202	22178	Mm.412291	NM_031202	ENSMUSG00000005994	Tyrp1	TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding	0	0.316832
Merged-chr14-49890822-1	chr14	49890772	49890872	+	2.1	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	11119	NM_146494	258487	Mm.270514	NM_146494	ENSMUSG00000048933	Olfr722	MOR241-3	olfactory receptor 722	protein-coding	0	0.346535
Merged-chrX-139433295-1	chrX	139433245	139433345	+	2.1	cIP2vsInput	Intergenic	Intergenic	-47072	NM_175326	102871	Mm.26565	NM_175326	ENSMUSG00000042498	D330045A20Rik	AI132325	RIKEN cDNA D330045A20 gene	protein-coding	0.01	0.356436
Merged-chr16-13657404-1	chr16	13657354	13657454	+	2.1	cIP2vsInput	"intron (NM_028761, intron 5 of 23)"	B2_Mm2|SINE|B2	10766	NM_028761	74108	Mm.182350	NM_028761	ENSMUSG00000022685	Parn	1200003I18Rik|DAN	poly(A)-specific ribonuclease (deadenylation nuclease)	protein-coding	0.01	0.415842
Merged-chrX-129395721-1	chrX	129395671	129395771	+	2.1	cIP2vsInput	Intergenic	Intergenic	344197	NR_045441	75274	Mm.108718	NR_045441	ENSMUSG00000086244	4930558G05Rik	-	RIKEN cDNA 4930558G05 gene	miscRNA	0	0.306931
Merged-chr16-80855547-1	chr16	80855497	80855597	+	2.1	cIP1vsInput	Intergenic	MTEb|LTR|ERVL-MaLR	-345150	NM_001113208	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.326733
Merged-chr4-9156721-1	chr4	9156671	9156771	+	2.1	cIP1vsInput	Intergenic	Lx8|LINE|L1	-112596	NM_028940	74438	Mm.473368	NM_028940	ENSMUSG00000041216	Clvs1	4933402J24Rik|Clvl1|Rlbp1l1	clavesin 1	protein-coding	0	0.445545
Merged-chr10-87596666-1	chr10	87596616	87596716	+	2.1	cIP1vsInput	Intergenic	Intergenic	74871	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding	0	0.465347
Merged-chrY-6464273-1	chrY	6464223	6464323	+	2.1	cIP1vsInput	Intergenic	YREP_Mm|Unknown|Unknown	703504	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.386139
Merged-chr9-34953228-1	chr9	34953178	34953278	+	2.1	cIP1vsInput	"intron (NM_001190911, intron 4 of 16)"	"intron (NM_001190911, intron 4 of 16)"	-163500	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	miscRNA	0.01	0.445545
Merged-chr3-112813809-1	chr3	112813759	112813859	+	2.1	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	342918	NM_001190404	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding	0.03	0.356436
Merged-chr5-134276155-1	chr5	134276105	134276205	+	2.1	cIP2vsInput	"intron (NM_001080749, intron 9 of 32)"	"intron (NM_001080749, intron 9 of 32)"	38591	NM_001080748	14886	Mm.412191	NM_001080746	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding	0.01	0.346535
Merged-chr18-89639208-1	chr18	89639158	89639258	+	2.1	cIP2vsInput	"intron (NM_001039173, intron 1 of 7)"	"intron (NM_001039173, intron 1 of 7)"	129928	NM_001039173	623279	Mm.447164	NM_001039173		Dok6	Dok-6	docking protein 6	protein-coding	0	0.287129
Merged-chr1-54250279-1	chr1	54250229	54250329	+	2.1	cIP2vsInput	promoter-TSS (NM_030025)	promoter-TSS (NM_030025)	-404	NM_030025	78016	Mm.67455	NM_030025	ENSMUSG00000025983	Ccdc150	4930511H11Rik	coiled-coil domain containing 150	protein-coding	0.04	0.49505
Merged-chr14-71960649-1	chr14	71960599	71960699	+	2.1	cIP2vsInput	Intergenic	Intergenic	103940	NR_046274	74667	Mm.159286	NR_046274		4930434J06Rik	-	RIKEN cDNA 4930434J06 gene	miscRNA	0	0.346535
Merged-chr3-134968423-1	chr3	134968373	134968473	+	2.1	cIP1vsInput	Intergenic	Intergenic	139416	NM_021382	21338	Mm.103810	NM_021382	ENSMUSG00000028172	Tacr3	Nk3r|Nkr|Tac3r	tachykinin receptor 3	protein-coding	0.01	0.316832
Merged-chrX-62386307-1	chrX	62386257	62386357	+	2.1	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	99165	NM_001199996	74437	Mm.85792	NM_001199996	ENSMUSG00000045330	4933402E13Rik	-	RIKEN cDNA 4933402E13 gene	protein-coding	0	0.326733
Merged-chr12-67697245-1	chr12	67697195	67697295	+	2.1	cIP2vsInput	Intergenic	Intergenic	-27974	NR_033146	100316870	Mm.379794	NR_033146		Gm17821	-	DDB1 and CUL4 associated factor 5 pseudogene	pseudo	0	0.306931
Merged-chr4-94159133-1	chr4	94159083	94159183	+	2.1	cIP2vsInput	Intergenic	Intergenic	397663	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.01	0.346535
Merged-chr7-18873235-1	chr7	18873185	18873285	+	2.1	cIP2vsInput	Intergenic	Intergenic	-11455	NM_009402	21946	Mm.21855	NM_009402	ENSMUSG00000030413	Pglyrp1	PGRP|PGRP-S|Pglyrp|Tag7|Tasg7|Tnfsf3l	peptidoglycan recognition protein 1	protein-coding	0.02	0.435644
Merged-chr8-7550805-1	chr8	7550755	7550855	+	2.1	cIP2vsInput	Intergenic	Intergenic	1109968	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding	0.02	0.336634
Merged-chr11-92394906-1	chr11	92394856	92394956	+	2.1	cIP1vsInput	Intergenic	Lx9|LINE|L1	-704384	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding	0	0.29703
Merged-chr3-44533922-1	chr3	44533872	44533972	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	844338	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	miscRNA	0	0.39604
Merged-chr14-15514629-1	chr14	15514579	15514679	+	2.1	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	-75642	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding	0	0.316832
Merged-chr14-96029440-1	chr14	96029390	96029490	+	2.1	cIP1vsInput	Intergenic	Intergenic	148174	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.346535
Merged-chr2-67577131-1	chr2	67577081	67577181	+	2.1	cIP2vsInput	Intergenic	Intergenic	131129	NM_001024618	241431	Mm.261043	NM_001024618	ENSMUSG00000027022	Xirp2	2310003D02Rik|2310008C07Rik|A530024P18Rik|AI452089|Cmya3|Gm352|Xin2	xin actin-binding repeat containing 2	protein-coding	0.02	0.29703
Merged-chr8-63020818-1	chr8	63020768	63020868	+	2.1	cIP1vsInput	"intron (NM_001252620, intron 3 of 11)"	"intron (NM_001252620, intron 3 of 11)"	69473	NM_023689	72902	Mm.334552	NM_001252620	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3"	protein-coding	0	0.267327
Merged-chr9-37818818-1	chr9	37818768	37818868	+	2.1	cIP2vsInput	Intergenic	Lx5|LINE|L1	14929	NM_146883	258883	Mm.377734	NM_146883	ENSMUSG00000066750	Olfr876	MOR161-1	olfactory receptor 876	protein-coding	0	0.356436
Merged-chr18-17889692-1	chr18	17889642	17889742	+	2.1	cIP2vsInput	Intergenic	Intergenic	-308702	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	miscRNA	0	0.435644
Merged-chr14-53724577-1	chr14	53724527	53724627	+	2.1	cIP1vsInput	Intergenic	Lx8|LINE|L1	58637	NM_001205242	100568452	Mm.486072	NM_001205242		A430107P09Rik	Va10	RIKEN cDNA A430107P09 gene	protein-coding	0	0.366337
Merged-chrX-107154274-1	chrX	107154224	107154324	+	2.1	cIP1vsInput	"intron (NM_175442, intron 1 of 1)"	L1MD2|LINE|L1	4659	NM_175442	213438	Mm.265244	NM_001122595	ENSMUSG00000054293	A630033H20Rik	AI662791|P2ry10	RIKEN cDNA A630033H20 gene	protein-coding	0	0.306931
Merged-chr10-103992895-1	chr10	103992845	103992945	+	2.1	cIP1vsInput	Intergenic	Intergenic	-150092	NM_001177535	100043292	Mm.339215	NM_001177535	ENSMUSG00000090854	Gm4340	-	predicted gene 4340	protein-coding	0.01	0.306931
Merged-chr12-6210182-1	chr12	6210132	6210232	+	2.1	cIP2vsInput	Intergenic	Intergenic	833680	NR_015579	72669	Mm.10434	NR_015579		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	miscRNA	0.01	0.326733
Merged-chr9-60653214-1	chr9	60653164	60653264	+	2.1	cIP2vsInput	"intron (NM_001146047, intron 8 of 16)"	"intron (NM_001146047, intron 8 of 16)"	34320	NM_001146047	102747	Mm.269413	NM_001146046	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding	0	0.376238
Merged-chr6-109210239-1	chr6	109210189	109210289	+	2.1	cIP2vsInput	Intergenic	Intergenic	381598	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	"ER degradation enhancer, mannosidase alpha-like 1"	protein-coding	0	0.386139
Merged-chr4-10099392-1	chr4	10099342	10099442	+	2.1	cIP1vsInput	Intergenic	Lx6|LINE|L1	-181995	NR_004448	74662	Mm.483401	NR_004448		4930448K20Rik	1700009K09Rik	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0	0.326733
Merged-chr17-36061605-1	chr17	36061555	36061655	+	2.1	cIP1vsInput	Intergenic	Intergenic	-3234	NM_001199967	100529082	Mm.484916	NM_001199967	ENSMUSG00000079492	Gm11127	ENSMUSG00000079492	predicted gene 11127	protein-coding	0	0.514851
Merged-chr14-92208233-1	chr14	92208183	92208283	+	2.1	cIP1vsInput	Intergenic	Intergenic	1680655	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0.01	0.326733
Merged-chr12-12099301-1	chr12	12099251	12099351	+	2.1	cIP2vsInput	Intergenic	Intergenic	-162838	NM_029758	76820	Mm.440802	NM_001146119	ENSMUSG00000020589	Fam49a	2410157M17Rik|9630047E15|D12Ertd553e	"family with sequence similarity 49, member A"	protein-coding	0	0.287129
Merged-chr9-5080286-1	chr9	5080236	5080336	+	2.1	cIP1vsInput	Intergenic	L1VL4|LINE|L1	-218231	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding	0.01	0.316832
Merged-chr14-31488735-1	chr14	31488685	31488785	+	2.1	cIP1vsInput	"intron (NM_025907, intron 3 of 5)"	L1M5|LINE|L1	6242	NM_025907	67011	Mm.291731	NM_025907		Mettl6	1600013P15Rik|AI467521|AU020711	methyltransferase like 6	protein-coding	0	0.306931
Merged-chr9-16733920-1	chr9	16733870	16733970	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-355689	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT tumor suppressor homolog 3 (Drosophila)	protein-coding	0	0.336634
Merged-chr8-71835565-1	chr8	71835515	71835615	+	2.1	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-46503	NM_145624	236193	Mm.290790	NM_145624		Zfp709	BC021921|GIOT-4|HIT-40	zinc finger protein 709	protein-coding	0	0.376238
Merged-chr3-15057859-1	chr3	15057809	15057909	+	2.1	cIP2vsInput	Intergenic	MMERVK9C_I-int|LTR|ERVK	86658	NR_040550	77127	Mm.195792	NR_040549		A930001A20Rik	-	RIKEN cDNA A930001A20 gene	miscRNA	0.01	0.277228
Merged-chr3-133496692-1	chr3	133496642	133496742	+	2.1	cIP1vsInput	"intron (NM_001040400, intron 2 of 10)"	L1_Rod|LINE|L1	47698	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding	0.01	0.336634
Merged-chr19-12519233-1	chr19	12519183	12519283	+	2.1	cIP2vsInput	Intergenic	Intergenic	-17237	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4 homolog (Drosophila)	protein-coding	0.01	0.425743
Merged-chr9-8017723-1	chr9	8017673	8017773	+	2.1	cIP2vsInput	Intergenic	Intergenic	-13127	NM_009534	22601	Mm.486262	NM_001171147	ENSMUSG00000053110	Yap1	AI325207|Yap|Yap65|Yki|Yorkie	yes-associated protein 1	protein-coding	0.04	0.633663
Merged-chr11-93113010-1	chr11	93112960	93113060	+	2.1	cIP1vsInput	"intron (NM_028296, intron 1 of 8)"	"intron (NM_028296, intron 1 of 8)"	13720	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding	0.02	0.415842
Merged-chr12-91144829-1	chr12	91144779	91144879	+	2.1	cIP1vsInput	"intron (NM_181815, intron 20 of 25)"	"intron (NM_181815, intron 20 of 25)"	34600	NR_030473	735273		NR_030473		Mir669c	Mirn669c|Mirn669c-1	microRNA 669c	miscRNA	0	0.217822
Merged-chr15-28120842-1	chr15	28120792	28120892	+	2.1	cIP1vsInput	Intergenic	L1ME2z|LINE|L1	-82924	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnahc5	AU022615|Dnah5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	"dynein, axonemal, heavy chain 5"	protein-coding	0.01	0.376238
Merged-chr14-83065430-1	chr14	83065380	83065480	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1378133	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0	0.316832
Merged-chr19-4743377-1	chr19	4743327	4743427	+	2.1	cIP1vsInput	"intron (NM_021287, intron 20 of 36)"	"intron (NM_021287, intron 20 of 36)"	-13148	NM_025717	66704	Mm.396734	NM_025717	ENSMUSG00000033760	Rbm4b	4921506I22Rik|AI504630|AI506404|Lark2	RNA binding motif protein 4B	protein-coding	0	0.326733
Merged-chr6-138392767-1	chr6	138392717	138392817	+	2.1	cIP2vsInput	"intron (NM_207222, intron 3 of 4)"	"intron (NM_207222, intron 3 of 4)"	189201	NM_207222	109593	Mm.490545	NM_207222		Lmo3	AI854781|BB106490|Rbtn-3|Rbtn3	LIM domain only 3	protein-coding	0.01	0.336634
Merged-chr8-117404054-1	chr8	117404004	117404104	+	2.1	cIP1vsInput	"intron (NM_001163262, intron 3 of 20)"	"intron (NM_001163262, intron 3 of 20)"	54884	NM_028941	74440	Mm.233181	NM_001163262	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding	0.02	0.564356
Merged-chr5-41511376-1	chr5	41511326	41511426	+	2.1	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	196779	NM_027295	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	"RAB28, member RAS oncogene family"	protein-coding	0.01	0.29703
Merged-chr6-104781440-1	chr6	104781390	104781490	+	2.1	cIP1vsInput	"intron (NM_017383, intron 11 of 22)"	"intron (NM_017383, intron 11 of 22)"	288396	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding	0	0.277228
Merged-chr9-122269055-1	chr9	122269005	122269105	+	2.1	cIP1vsInput	"intron (NM_133979, intron 4 of 12)"	"intron (NM_133979, intron 4 of 12)"	25368	NM_001271873	102566	Mm.474116	NM_001271873	ENSMUSG00000037949	Ano10	AI604832|Tmem16k	anoctamin 10	protein-coding	0.01	0.336634
Merged-chr4-29502987-1	chr4	29502937	29503037	+	2.1	cIP1vsInput	Intergenic	Intergenic	689842	NM_010141	13841	Mm.257266	NM_001122889	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding	0	0.405941
Merged-chr2-86570121-1	chr2	86570071	86570171	+	2.1	cIP1vsInput	Intergenic	Intergenic	-11983	NM_146409	258404	Mm.271334	NM_146409	ENSMUSG00000075178	Olfr1080	MOR192-1	olfactory receptor 1080	protein-coding	0	0.326733
Merged-chr2-5328044-1	chr2	5327994	5328094	+	2.1	cIP1vsInput	"intron (NM_177343, intron 6 of 10)"	"intron (NM_177343, intron 6 of 10)"	-51346	NR_030601	100124465		NR_030601		Mir466d	Mirn466d	microRNA 466d	miscRNA	0.01	0.445545
Merged-chr17-67368610-1	chr17	67368560	67368660	+	2.1	cIP1vsInput	Intergenic	Intergenic	-14151	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	"protein tyrosine phosphatase, receptor type, M"	protein-coding	0	0.277228
Merged-chr13-118109232-1	chr13	118109182	118109282	+	2.1	cIP1vsInput	Intergenic	Intergenic	278020	NM_021556	59054	Mm.143810	NM_021556	ENSMUSG00000021731	Mrps30	2610020A16Rik|AA968347|PAP|Pdcd9	mitochondrial ribosomal protein S30	protein-coding	0.01	0.306931
Merged-chr2-89799355-1	chr2	89799305	89799405	+	2.1	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-10005	NM_146476	258468	Mm.314870	NM_146476	ENSMUSG00000075074	Olfr1254	MOR231-13	olfactory receptor 1254	protein-coding	0.01	0.356436
Merged-chr14-51746009-1	chr14	51745959	51746059	+	2.1	cIP2vsInput	Intergenic	L1Md_T|LINE|L1	27581	NM_177544	219033	Mm.343899	NM_177544	ENSMUSG00000060615	Ang4	Rnase5d	"angiogenin, ribonuclease A family, member 4"	protein-coding	0	0.356436
Merged-chr14-96387081-1	chr14	96387031	96387131	+	2.1	cIP1vsInput	"intron (NM_053105, intron 1 of 10)"	"intron (NM_053105, intron 1 of 10)"	131953	NM_053105	93688	Mm.308735	NM_053105	ENSMUSG00000022076	Klhl1	mKIAA1490	kelch-like 1	protein-coding	0	0.267327
Merged-chr6-104523217-1	chr6	104523167	104523267	+	2.1	cIP2vsInput	"intron (NM_017383, intron 1 of 22)"	"intron (NM_017383, intron 1 of 22)"	30173	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding	0.01	0.287129
Merged-chr11-11247781-1	chr11	11247731	11247831	+	2.1	cIP2vsInput	"intron (NM_177033, intron 3 of 3)"	"intron (NM_177033, intron 3 of 3)"	133765	NM_177033	319922	Mm.487612	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding	0	0.336634
Merged-chr16-35030291-1	chr16	35030241	35030341	+	2.1	cIP2vsInput	"intron (NM_023587, intron 2 of 6)"	"intron (NM_023587, intron 2 of 6)"	7870	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Ptplb	6330408J20Rik|AI255777|AI481689|HACD2	"protein tyrosine phosphatase-like (proline instead of catalytic arginine), member b"	protein-coding	0.01	0.316832
Merged-chrX-134059112-2	chrX	134059026	134059199	+	2.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_133196)	promoter-TSS (NM_133196)	-237	NM_133196	108062	Mm.67938	NM_133196	ENSMUSG00000031256	Cstf2	64kDa|C630034J23Rik|Cstf64	"cleavage stimulation factor, 3' pre-RNA subunit 2"	protein-coding	0.080925	0.672414
Merged-chr2-87062169-1	chr2	87062119	87062219	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	10054	NM_146844	258841	Mm.223265	NM_146844	ENSMUSG00000075163	Olfr1107	MOR172-2	olfactory receptor 1107	protein-coding	0	0.326733
Merged-chr4-124277186-1	chr4	124277136	124277236	+	2.1	cIP2vsInput	Intergenic	Intergenic	208773	NR_040774	78460	Mm.452060	NR_040774		1700057H15Rik	-	RIKEN cDNA 1700057H15 gene	miscRNA	0.05	0.564356
Merged-chr7-66006285-1	chr7	66006235	66006335	+	2.1	cIP1vsInput	"intron (NM_011048, intron 13 of 21)"	"intron (NM_011048, intron 13 of 21)"	-54051	NM_021336	68981	Mm.22362	NM_021336	ENSMUSG00000030512	Snrpa1	1500015N06Rik	small nuclear ribonucleoprotein polypeptide A'	protein-coding	0.02	0.29703
Merged-chr1-135644744-1	chr1	135644694	135644794	+	2.1	cIP2vsInput	Intergenic	Intergenic	-59389	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding	0	0.326733
Merged-chr6-139558134-1	chr6	139558084	139558184	+	2.1	cIP1vsInput	Intergenic	Intergenic	-56225	NM_001128090	632971	Mm.475610	NM_001128090	ENSMUSG00000092164	Rergl	EG632971	RERG/RAS-like	protein-coding	0.01	0.316832
Merged-chr11-20278062-1	chr11	20278012	20278112	+	2.1	cIP1vsInput	Intergenic	Intergenic	-28638	NM_172260	216543	Mm.260314	NM_172260	ENSMUSG00000044066	Cep68	6030463E10Rik|AI481761|BC027174|Kiaa0582	centrosomal protein 68	protein-coding	0	0.326733
Merged-chr7-105188708-1	chr7	105188658	105188758	+	2.1	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	-7397	NM_001011857	258160	Mm.377366	NM_001011857	ENSMUSG00000047794	Olfr685	MOR37-1	olfactory receptor 685	protein-coding	0.01	0.425743
Merged-chr12-58729020-1	chr12	58728970	58729070	+	2.1	cIP2vsInput	Intergenic	Intergenic	282997	NM_009147	20334	Mm.209207	NM_009147	ENSMUSG00000020986	Sec23a	Msec23|Sec23r	SEC23A (S. cerevisiae)	protein-coding	0	0.306931
Merged-chr13-29295044-1	chr13	29294994	29295094	+	2.1	cIP1vsInput	Intergenic	L1M3|LINE|L1	278789	NR_045075	77920	Mm.197051	NR_045073	ENSMUSG00000086363	A330102I10Rik	-	RIKEN cDNA A330102I10 gene	miscRNA	0.01	0.316832
Merged-chrX-89510869-1	chrX	89510819	89510919	+	2.1	cIP1vsInput	Intergenic	Intergenic	-101180	NM_008821	18630	Mm.3086	NM_008821	ENSMUSG00000035395	Pet2	PC231|PC326|Pex3	plasmacytoma expressed transcript 2	protein-coding	0	0.29703
Merged-chr5-35524016-1	chr5	35523966	35524066	+	2.1	cIP1vsInput	"intron (NM_153107, intron 1 of 10)"	"intron (NM_153107, intron 1 of 10)"	1610	NM_153107	242939	Mm.108557	NM_153107	ENSMUSG00000036596	Cpz	AV136066	carboxypeptidase Z	protein-coding	0.03	0.60396
Merged-chr5-82627336-1	chr5	82627286	82627386	+	2.1	cIP1vsInput	Intergenic	RMER6-int|LTR|ERVK	171729	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mmu-mir-1187	microRNA 1187	miscRNA	0	0.29703
Merged-chr1-8705246-1	chr1	8705196	8705296	+	2.1	cIP2vsInput	"intron (NM_027671, intron 6 of 20)"	L1_Rod|LINE|L1	594484	NM_027671	71096	Mm.388998	NM_027671		Sntg1	4933426D16Rik|G1SYN|SYN4	"syntrophin, gamma 1"	protein-coding	0	0.336634
Merged-chr11-38778720-1	chr11	38778670	38778770	+	2.1	cIP1vsInput	Intergenic	Intergenic	-258675	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0	0.326733
Merged-chr15-18838799-1	chr15	18838749	18838849	+	2.1	cIP1vsInput	"intron (NM_009865, intron 1 of 11)"	"intron (NM_009865, intron 1 of 11)"	18470	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0	0.306931
Merged-chr15-50128006-1	chr15	50127956	50128056	+	2.1	cIP1vsInput	Intergenic	Intergenic	761108	NR_035444	100316685		NR_035444	ENSMUSG00000084458	Mir1907	Mirn1907|mmu-mir-1907	microRNA 1907	miscRNA	0	0.336634
Merged-chr13-110734757-1	chr13	110734707	110734807	+	2.1	cIP2vsInput	Intergenic	Intergenic	339713	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding	0	0.277228
Merged-chr9-77781753-1	chr9	77781703	77781803	+	2.1	cIP2vsInput	"intron (NM_010295, intron 6 of 15)"	"intron (NM_010295, intron 6 of 15)"	27218	NM_010295	14629	Mm.89888	NM_010295	ENSMUSG00000032350	Gclc	D9Wsu168e|GLCL-H|Ggcs-hs|Glclc	"glutamate-cysteine ligase, catalytic subunit"	protein-coding	0.01	0.326733
Merged-chr16-86419505-1	chr16	86419455	86419555	+	2.1	cIP1vsInput	Intergenic	Intergenic	-518380	NM_011782	23794	Mm.437478	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|AI481094|ASMP-2	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"	protein-coding	0.01	0.277228
Merged-chr12-28138522-1	chr12	28138472	28138572	+	2.1	cIP1vsInput	Intergenic	Intergenic	409815	NM_001177964	68511	Mm.310284	NM_001177964		Dcdc2c	1110015M06Rik	doublecortin domain containing 2C	protein-coding	0	0.356436
Merged-chr15-34558022-1	chr15	34557972	34558072	+	2.1	cIP1vsInput	Intergenic	Lx2|LINE|L1	62711	NM_152894	67724	Mm.248779	NM_026340	ENSMUSG00000022325	Pop1	4932434G09Rik	"processing of precursor 1, ribonuclease P/MRP family, (S. cerevisiae)"	protein-coding	0	0.29703
Merged-chr3-141663026-1	chr3	141662976	141663076	+	2.1	cIP1vsInput	"intron (NM_009472, intron 1 of 15)"	"intron (NM_009472, intron 1 of 15)"	197462	NM_009472	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	6030473H24|AI047720|B130051O18Rik|Unc5h3|rcm	unc-5 homolog C (C. elegans)	protein-coding	0.01	0.405941
Merged-chr14-43050132-1	chr14	43050082	43050182	+	2.1	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	-34556	NM_001244671	100042055	Mm.429109	NM_001244671	ENSMUSG00000095226	Gm10377	ENSMUSG00000072606	predicted gene 10377	protein-coding	0.01	0.376238
Merged-chr6-133332800-1	chr6	133332750	133332850	+	2.1	cIP2vsInput	Intergenic	Intergenic	40584	NM_027784	232426	Mm.158689	NM_027784	ENSMUSG00000055594	5530400C23Rik	GRP	RIKEN cDNA 5530400C23 gene	protein-coding	0	0.306931
Merged-chr5-21520856-1	chr5	21520806	21520906	+	2.1	cIP2vsInput	"intron (NM_001199632, intron 17 of 20)"	"intron (NM_001199632, intron 17 of 20)"	-22671	NM_028977	74511	Mm.439963	NM_028977	ENSMUSG00000039883	Lrrc17	37kDa|4833425M04Rik|6130400C22Rik|P37nb	leucine rich repeat containing 17	protein-coding	0.02	0.514851
Merged-chr14-95126724-1	chr14	95126674	95126774	+	2.1	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-754542	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.306931
Merged-chr2-33659253-1	chr2	33659203	33659303	+	2.1	cIP2vsInput	Intergenic	Intergenic	18060	NR_046275	100504399	Mm.72070	NM_177842		C130021I20Rik	-	Riken cDNA C130021I20 gene	miscRNA	0.01	0.386139
Merged-chr11-104957873-1	chr11	104957823	104957923	+	2.1	cIP2vsInput	Intergenic	Intergenic	-134346	NM_001081046	70894	Mm.87320	NM_001081046	ENSMUSG00000020690	Efcab3	4921510J17Rik	EF-hand calcium binding domain 3	protein-coding	0	0.336634
Merged-chr7-109916315-1	chr7	109916265	109916365	+	2.1	cIP1vsInput	"intron (NM_021494, intron 9 of 22)"	"intron (NM_021494, intron 9 of 22)"	44107	NM_021494	19347	Mm.21904	NM_021494	ENSMUSG00000035901	Dennd5a	1500012B19Rik|AJ245569|AW496491|ORF37|Rab6ip1|mKIAA1091	DENN/MADD domain containing 5A	protein-coding	0.01	0.435644
Merged-chr17-46636478-1	chr17	46636428	46636528	+	2.1	cIP1vsInput	"intron (NM_029091, intron 8 of 15)"	"intron (NM_029091, intron 8 of 15)"	-6974	NM_175168	71461	Mm.181833	NM_175168	ENSMUSG00000023972	Ptk7	8430404F20Rik|chz|mPTK7/CCK4	PTK7 protein tyrosine kinase 7	protein-coding	0.02	0.564356
Merged-chr5-53355201-1	chr5	53355151	53355251	+	2.1	cIP2vsInput	Intergenic	Intergenic	88095	NM_001145433	66278	Mm.442576	NM_001145433		Smim20	1110067B18Rik|1810013D10Rik|N28078	small integral membrane protein 20	protein-coding	0.03	0.633663
Merged-chr15-45474744-1	chr15	45474694	45474794	+	2.1	cIP2vsInput	Intergenic	Intergenic	-359810	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	"potassium channel, subfamily V, member 1"	protein-coding	0	0.29703
Merged-chr7-69594968-1	chr7	69594918	69595018	+	2.1	cIP2vsInput	Intergenic	Intergenic	98874	NR_045940	73796	Mm.410832	NR_045940		4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	miscRNA	0.01	0.306931
Merged-chr9-58762027-1	chr9	58761977	58762077	+	2.1	cIP2vsInput	Intergenic	Intergenic	-20468	NM_028598	73673	Mm.205196	NM_028598	ENSMUSG00000074269	2410076I21Rik	4930527A11Rik	RIKEN cDNA 2410076I21 gene	protein-coding	0.02	0.435644
Merged-chr4-36299758-1	chr4	36299708	36299808	+	2.1	cIP2vsInput	"intron (NM_001165999, intron 3 of 7)"	"intron (NM_001165999, intron 3 of 7)"	345695	NR_030545	100124458		NR_030545	ENSMUSG00000077851	Mir876	Mirn876|mmu-mir-876	microRNA 876	miscRNA	0	0.326733
Merged-chr10-74621732-1	chr10	74621682	74621782	+	2.1	cIP1vsInput	"intron (NM_001142736, intron 29 of 32)"	"intron (NM_001142736, intron 29 of 32)"	-345499	NM_010311	14687	Mm.393508	NM_010311		Gnaz	AI847979|Gz	"guanine nucleotide binding protein, alpha z subunit"	protein-coding	0	0.336634
Merged-chr2-68748041-1	chr2	68747991	68748091	+	2.1	cIP1vsInput	"intron (NM_183113, intron 28 of 28)"	"intron (NM_183113, intron 28 of 28)"	90157	NM_183113	75721	Mm.65456	NM_183113	ENSMUSG00000079324	4932414N04Rik	-	RIKEN cDNA 4932414N04 gene	protein-coding	0	0.356436
Merged-chr7-83903982-1	chr7	83903932	83904032	+	2.1	cIP1vsInput	Intergenic	Intergenic	11982	NM_023403	67943	Mm.117365	NM_023403	ENSMUSG00000038503	Mesdc2	2210015O11Rik|AW537813|mKIAA0081|mesd|msd	mesoderm development candidate 2	protein-coding	0	0.29703
Merged-chr11-90330440-1	chr11	90330390	90330490	+	2.1	cIP1vsInput	Intergenic	Zaphod3|DNA|hAT-Tip100	60477	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding	0	0.376238
Merged-chr6-82797835-1	chr6	82797785	82797885	+	2.1	cIP2vsInput	Intergenic	Intergenic	-23381	NM_013820	15277	Mm.469167	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding	0	0.39604
Merged-chr13-87906464-1	chr13	87906414	87906514	+	2.1	cIP1vsInput	Intergenic	Intergenic	-915008	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0.01	0.29703
Merged-chr12-14802324-1	chr12	14802274	14802374	+	2.1	cIP1vsInput	Intergenic	Intergenic	248065	NR_045960	73972	Mm.107680	NR_045960		4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	miscRNA	0	0.29703
Merged-chr1-96136686-1	chr1	96136636	96136736	+	2.1	cIP1vsInput	Intergenic	Intergenic	-114928	NR_040467	73454	Mm.396229	NR_040467		1700063A18Rik	-	RIKEN cDNA 1700063A18 gene	miscRNA	0	0.326733
Merged-chr2-23720474-1	chr2	23720424	23720524	+	2.1	cIP1vsInput	Intergenic	Intergenic	-148370	NM_001165997	76857	Mm.480695	NM_001165997		Spopl	4921517N04Rik|AU014935|BB233739|E430033K04Rik	speckle-type POZ protein-like	protein-coding	0	0.277228
Merged-chr17-54609270-1	chr17	54609220	54609320	+	2.1	cIP1vsInput	Intergenic	Intergenic	-239196	NR_045825	69418	Mm.391004	NR_045825		1700025K24Rik	-	RIKEN cDNA 1700025K24 gene	miscRNA	0	0.29703
Merged-chr11-37703645-1	chr11	37703595	37703695	+	2.1	cIP1vsInput	Intergenic	MLT1C|LTR|ERVL-MaLR	-759402	NM_011856	23964	Mm.445432	NM_011856	ENSMUSG00000049336	Tenm2	2610040L17Rik|9330187F13Rik|D3Bwg1534e|Odz2|Odz3|Ten-m2|mKIAA1127	teneurin transmembrane protein 2	protein-coding	0	0.356436
Merged-chr9-77699105-2	chr9	77699052	77699158	+	2.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-55430	NM_010295	14629	Mm.89888	NM_010295	ENSMUSG00000032350	Gclc	D9Wsu168e|GLCL-H|Ggcs-hs|Glclc	"glutamate-cysteine ligase, catalytic subunit"	protein-coding	0	0.364486
Merged-chrX-145398920-1	chrX	145398870	145398970	+	2.1	cIP2vsInput	Intergenic	Intergenic	-50026	NM_178358	237091	Mm.135547	NM_178358	ENSMUSG00000041700	Lhfpl1	Lhfp	lipoma HMGIC fusion partner-like 1	protein-coding	0	0.346535
Merged-chr18-18541176-1	chr18	18541126	18541226	+	2.1	cIP2vsInput	Intergenic	Intergenic	-960186	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	miscRNA	0	0.29703
Merged-chr12-97441639-1	chr12	97441589	97441689	+	2.1	cIP2vsInput	Intergenic	MER53|DNA|hAT	817698	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding	0	0.247525
Merged-chr11-74197218-1	chr11	74197168	74197268	+	2.1	cIP1vsInput	TTS (NM_207622)	TTS (NM_207622)	1713	NM_207622	404316	Mm.246537	NM_207622	ENSMUSG00000070378	Olfr403	IA7|MOR125-5_p|Olfr43	olfactory receptor 403	protein-coding	0	0.366337
Merged-chr19-55151017-1	chr19	55150967	55151067	+	2.1	cIP2vsInput	Intergenic	Intergenic	-29868	NM_009348	21684	Mm.42139	NM_009348	ENSMUSG00000024979	Tectb	Tctnb	tectorin beta	protein-coding	0	0.336634
Merged-chr10-10964571-1	chr10	10964521	10964621	+	2.1	cIP1vsInput	"intron (NM_001114333, intron 2 of 9)"	MIR|SINE|MIR	117760	NM_001114333	14816	Mm.482986	NM_001114333	ENSMUSG00000019828	Grm1	4930455H15Rik|ENSMUSG00000075319|Gm10828|Gprc1a|mGluR1|nmf373|rcw|wobl	"glutamate receptor, metabotropic 1"	protein-coding	0.01	0.366337
Merged-chr1-188678622-1	chr1	188678572	188678672	+	2.1	cIP1vsInput	"intron (NM_021408, intron 37 of 70)"	"intron (NM_021408, intron 37 of 70)"	329218	NM_172650	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding	0	0.287129
Merged-chr7-96992116-1	chr7	96992066	96992166	+	2.1	cIP1vsInput	"intron (NM_153591, intron 5 of 13)"	"intron (NM_153591, intron 5 of 13)"	40589	NM_153591	244141	Mm.274864	NM_153591	ENSMUSG00000018995	Nars2	AI875199	asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)	protein-coding	0.01	0.485149
Merged-chr1-152981217-1	chr1	152981167	152981267	+	2.1	cIP2vsInput	"intron (NM_175460, intron 1 of 10)"	"intron (NM_175460, intron 1 of 10)"	26116	NM_175460	226518	Mm.40548	NM_175460	ENSMUSG00000042751	Nmnat2	AI843915|D030041I09Rik|PNAT1|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding	0	0.277228
Merged-chr18-6098150-1	chr18	6098100	6098200	+	2.1	cIP1vsInput	"intron (NM_001039692, intron 3 of 18)"	"intron (NM_001039692, intron 3 of 18)"	37948	NM_029277	75415	Mm.239675	NM_001039692	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding	0	0.316832
Merged-chr8-51124554-1	chr8	51124504	51124604	+	2.1	cIP2vsInput	Intergenic	Intergenic	756442	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0.02	0.376238
Merged-chr3-44653426-1	chr3	44653376	44653476	+	2.1	cIP2vsInput	Intergenic	Lx7|LINE|L1	724834	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	miscRNA	0	0.306931
Merged-chr10-48046429-1	chr10	48046379	48046479	+	2.1	cIP2vsInput	Intergenic	Intergenic	1049414	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	"proteasome (prosome, macropain) subunit, alpha type 6 pseudogene"	pseudo	0	0.287129
Merged-chr8-23721876-1	chr8	23721826	23721926	+	2.1	cIP2vsInput	"intron (NM_177086, intron 1 of 6)"	Charlie1a|DNA|hAT-Charlie	52215	NM_177086	320158	Mm.121274	NM_001277239	ENSMUSG00000037492	Zmat4	9630048M01Rik	"zinc finger, matrin type 4"	protein-coding	0	0.356436
Merged-chr12-83346188-1	chr12	83346138	83346238	+	2.1	cIP1vsInput	"intron (NM_001267625, intron 3 of 10)"	"intron (NM_001267625, intron 3 of 10)"	141548	NM_001267626	70127	Mm.403230	NM_001267625	ENSMUSG00000021221	Dpf3	2810403B03Rik|6530402L11Rik|BAF45C|C78788|CERD4|cer-d4	"D4, zinc and double PHD fingers, family 3"	protein-coding	0.01	0.277228
Merged-chr1-21204806-1	chr1	21204756	21204856	+	2.1	cIP2vsInput	Intergenic	Intergenic	-13825	NM_029398	75712	Mm.441478	NM_029398	ENSMUSG00000025933	Tmem14a	5730496E24Rik|C85783|PTD011	transmembrane protein 14A	protein-coding	0	0.336634
Merged-chr4-3814979-1	chr4	3814929	3815029	+	2.1	cIP1vsInput	Intergenic	RLTR45-int|LTR|ERVK	20621	NM_026147	67427	Mm.473992	NM_026147		Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding	0.01	0.435644
Merged-chr1-6485513-1	chr1	6485463	6485563	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1718	NM_001244693	240690	Mm.234612	NM_001244692	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding	0	0.376238
Merged-chr5-89316447-1	chr5	89316397	89316497	+	2.1	cIP2vsInput	Intergenic	Lx5b|LINE|L1	141451	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding	0.01	0.287129
Merged-chr14-47441194-1	chr14	47441144	47441244	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-22787	NM_144553	218977	Mm.240543	NM_001145949	ENSMUSG00000037544	Dlgap5	C77459|C86398|Dap-5|Dlg7|Hurp|mKIAA0008	"discs, large (Drosophila) homolog-associated protein 5"	protein-coding	0	0.356436
Merged-chrX-117201212-1	chrX	117201162	117201262	+	2.1	cIP2vsInput	Intergenic	MTE2a|LTR|ERVL-MaLR	186455	NM_001102665	100039319	Mm.469831	NM_001102665		Gm14920	ENSMUSG00000067441|Gm1539|H2A.Bbd1|OTTMUSG00000018481	predicted pseudogene 14920	protein-coding	0	0.336634
Merged-chr12-34902111-1	chr12	34902061	34902161	+	2.1	cIP1vsInput	"intron (NM_001271386, intron 2 of 27)"	MLT1E1A|LTR|ERVL-MaLR	14984	NM_001271386	79221	Mm.483009	NM_001271386	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding	0.01	0.415842
Merged-chr3-54936024-1	chr3	54935974	54936074	+	2.1	cIP1vsInput	Intergenic	Intergenic	-20137	NM_177854	329641	Mm.51187	NM_177854	ENSMUSG00000056306	Sertm1	6030405A18Rik	serine rich and transmembrane domain containing 1	protein-coding	0.01	0.267327
Merged-chr13-91178120-1	chr13	91178070	91178170	+	2.1	cIP2vsInput	"intron (NM_025770, intron 2 of 7)"	"intron (NM_025770, intron 2 of 7)"	45867	NM_025770	66795	Mm.235385	NM_025770	ENSMUSG00000021619	Atg10	5330424L23Rik|5430428K15Rik|AI852123|APG10|Agp10|Apg10l|Apg10p|Atg10l	autophagy related 10	protein-coding	0	0.287129
Merged-chr6-105816533-1	chr6	105816483	105816583	+	2.1	cIP1vsInput	"intron (NM_001109749, intron 1 of 25)"	"intron (NM_001109749, intron 1 of 25)"	138788	NM_173004	269784	Mm.321683	NM_001109749	ENSMUSG00000064293	Cntn4	9630050B05|Axcam|BIG-2	contactin 4	protein-coding	0	0.336634
Merged-chr5-120116506-1	chr5	120116456	120116556	+	2.1	cIP1vsInput	promoter-TSS (NM_028762)	promoter-TSS (NM_028762)	-7	NM_028762	74111	Mm.41022	NM_028762		Rbm19	1200009A02Rik|AV302714|NPO	RNA binding motif protein 19	protein-coding	0.11	0.653465
Merged-chr13-19200522-1	chr13	19200472	19200572	+	2.1	cIP2vsInput	Intergenic	MMERVK9C_I-int|LTR|ERVK	195230	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding	0.01	0.326733
Merged-chrY-88979060-1	chrY	88979010	88979110	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1806382	NM_133362	170942	Mm.391385	XM_003946384	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding	0.01	0.465347
Merged-chr1-135773321-1	chr1	135773271	135773371	+	2.1	cIP2vsInput	Intergenic	Intergenic	7236	NM_013750	27280	Mm.34346	NM_013750	ENSMUSG00000041801	Phlda3	Tih1	"pleckstrin homology-like domain, family A, member 3"	protein-coding	0	0.514851
Merged-chr7-63386603-1	chr7	63386553	63386653	+	2.1	cIP2vsInput	Intergenic	Intergenic	-58169	NM_130880	170711	Mm.156872	NM_130880	ENSMUSG00000033510	Otud7a	AJ430384|Otud7	OTU domain containing 7A	protein-coding	0	0.29703
Merged-chr19-14946354-1	chr19	14946304	14946404	+	2.1	cIP2vsInput	Intergenic	Intergenic	-348371	NM_011600	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333	"transducin-like enhancer of split 4, homolog of Drosophila E(spl)"	protein-coding	0	0.316832
Merged-chr19-27281398-1	chr19	27281348	27281448	+	2.1	cIP1vsInput	Intergenic	Intergenic	-41221	NM_183179	240595	Mm.269759	NM_183179	ENSMUSG00000047298	Kcnv2	KV11.1	"potassium channel, subfamily V, member 2"	protein-coding	0	0.316832
Merged-chr11-9728989-1	chr11	9728939	9729039	+	2.1	cIP1vsInput	Intergenic	Intergenic	537047	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	"ATP-binding cassette, sub-family A (ABC1), member 13"	protein-coding	0	0.336634
Merged-chr10-101601616-1	chr10	101601566	101601666	+	2.1	cIP1vsInput	Intergenic	Intergenic	-79871	NM_001205098	67569	Mm.403713	NM_001162368	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"	protein-coding	0	0.316832
Merged-chr12-30817474-1	chr12	30817424	30817524	+	2.1	cIP2vsInput	Intergenic	Intergenic	-66850	NM_001159743	100294583	Mm.399726	NM_001159743	ENSMUSG00000054204	Fam150b	6230419C23Rik	"family with sequence similarity 150, member B"	protein-coding	0.01	0.336634
Merged-chr2-71400905-1	chr2	71400855	71400955	+	2.1	cIP1vsInput	"intron (NM_026115, intron 2 of 10)"	RLTR42-int|LTR|ERVK	11645	NM_026115	107435		NM_026115	ENSMUSG00000027018	Hat1	2410071B14Rik|AA536933|Hat-1|KAT1	histone aminotransferase 1	protein-coding	0	0.306931
Merged-chr16-64803566-1	chr16	64803516	64803616	+	2.1	cIP1vsInput	Intergenic	Intergenic	-17245	NM_028059	72020	Mm.25960	NM_028059	ENSMUSG00000047141	Zfp654	1600021C16Rik|1810008K20Rik|Znf654	zinc finger protein 654	protein-coding	0	0.376238
Merged-chr6-130670976-1	chr6	130670926	130671026	+	2.1	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	-284102	NM_016659	16627	Mm.333431	NM_016659	ENSMUSG00000079853	Klra1	A1|Klra22|Ly49a|Ly49o<129>|Ly49v	"killer cell lectin-like receptor, subfamily A, member 1"	protein-coding	0	0.366337
Merged-chr2-181715022-1	chr2	181714972	181715072	+	2.1	cIP2vsInput	promoter-TSS (NM_001252565)	promoter-TSS (NM_001252565)	6	NR_045542	18389	Mm.285075	NM_001252565	ENSMUSG00000027584	Oprl1	KOR-3|KOR3|LC132|MOR-C|ORGC|ORL1|Oprl|XOR1|morc	opioid receptor-like 1	protein-coding	0.04	0.613861
Merged-chr2-34975488-1	chr2	34975438	34975538	+	2.1	cIP1vsInput	Intergenic	Intergenic	-13716	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding	0	0.445545
Merged-chr17-59774598-1	chr17	59774548	59774648	+	2.1	cIP2vsInput	Intergenic	Intergenic	-761276	NM_026497	67993	Mm.36507	NM_026497		Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0.02	0.306931
Merged-chr2-43309408-1	chr2	43309358	43309458	+	2.1	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-245921	NM_027552	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding	0.01	0.346535
Merged-chr12-14838416-1	chr12	14838366	14838466	+	2.1	cIP2vsInput	Intergenic	Intergenic	211973	NR_045960	73972	Mm.107680	NR_045960		4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	miscRNA	0.02	0.346535
Merged-chr3-5129792-1	chr3	5129742	5129842	+	2.1	cIP1vsInput	Intergenic	RMER3D-int|LTR|ERVK	-88762	NM_030708	80892	Mm.41522	NM_030708	ENSMUSG00000025255	Zfhx4	A930021B15|C130041O22Rik|Zfh-4|Zfh4	zinc finger homeodomain 4	protein-coding	0.01	0.326733
Merged-chr14-124747338-1	chr14	124747288	124747388	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-70211	NM_207667	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding	0	0.287129
Merged-chr8-81237684-1	chr8	81237634	81237734	+	2.1	cIP1vsInput	Intergenic	Intergenic	-222778	NM_027554	74841	Mm.246018	NM_027554	ENSMUSG00000038250	Usp38	4631402N15Rik|4833420O05Rik|AA536967|AU044701|AW544820|mKIAA1891	ubiquitin specific peptidase 38	protein-coding	0	0.356436
Merged-chr1-95841773-1	chr1	95841723	95841823	+	2.1	cIP2vsInput	Intergenic	RSINE1|SINE|B4	-125255	NR_040479	75381	Mm.417807	NR_040479		4930598F16Rik	-	RIKEN cDNA 4930598F16 gene	miscRNA	0	0.39604
Merged-chr13-23321351-1	chr13	23321301	23321401	+	2.1	cIP2vsInput	Intergenic	Intergenic	43001	NR_046038	74061	Mm.399501	NR_046038	ENSMUSG00000085122	4933404K08Rik	-	RIKEN cDNA 4933404K08 gene	miscRNA	0	0.376238
Merged-chr6-36580216-1	chr6	36580166	36580266	+	2.1	cIP2vsInput	Intergenic	B4A|SINE|B4	158474	NR_030524	735279		NR_030524	ENSMUSG00000070075	Mir490	Mirn490|mmu-mir-490	microRNA 490	miscRNA	0	0.465347
Merged-chr5-44357502-1	chr5	44357452	44357552	+	2.1	cIP2vsInput	Intergenic	Intergenic	-130896	NM_173764	231225	Mm.30688	NM_173764	ENSMUSG00000046985	Tapt1	4932414K18Rik	transmembrane anterior posterior transformation 1	protein-coding	0	0.376238
Merged-chr3-108061610-1	chr3	108061560	108061660	+	2.1	cIP2vsInput	Intergenic	Intergenic	-16751	NM_001160411	14865	Mm.31203	NM_001160411	ENSMUSG00000027890	Gstm4	1110004G14Rik|GSTM7-7|Gstb-4|Gstb4	"glutathione S-transferase, mu 4"	protein-coding	0.03	0.425743
Merged-chr12-33539340-1	chr12	33539290	33539390	+	2.1	cIP2vsInput	Intergenic	Intergenic	109716	NM_172253	28071	Mm.413045	NM_172253	ENSMUSG00000020561	Twistnb	2410173G11|2810024J17Rik|D16Wsu83e	TWIST neighbor	protein-coding	0	0.29703
Merged-chr6-6942552-1	chr6	6942502	6942602	+	2.1	cIP2vsInput	Intergenic	RLTR28|LTR|ERVL	-13466	NM_001077713	71238	Mm.490412	NM_001077713		Acn9	0610005M07Rik|4933430A16Rik	ACN9 homolog (S. cerevisiae)	protein-coding	0.03	0.49505
Merged-chr3-63492969-1	chr3	63492919	63493019	+	2.1	cIP1vsInput	Intergenic	Intergenic	197097	NM_008604	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding	0	0.257426
Merged-chr2-155812014-1	chr2	155811964	155812064	+	2.1	cIP1vsInput	"intron (NM_010808, intron 6 of 8)"	"intron (NM_010808, intron 6 of 8)"	7189	NR_015528	613262	Mm.330707	NR_015528	ENSMUSG00000074649	BC029722	-	cDNA sequence BC029722	miscRNA	0	0.455446
Merged-chr15-62657313-1	chr15	62657263	62657363	+	2.1	cIP2vsInput	Intergenic	Intergenic	-437862	NR_003523	67552	Mm.484027	NR_003523		H2afy3	4933432H23Rik	"H2A histone family, member Y3"	pseudo	0	0.356436
Merged-chr7-53599996-1	chr7	53599946	53600046	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1235249	NM_178705	233271	Mm.474990	NM_178705		Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding	0	0.306931
Merged-chr1-121005704-1	chr1	121005654	121005754	+	2.1	cIP2vsInput	Intergenic	Intergenic	-81701	NR_038008	98452	Mm.489010	NR_038008	ENSMUSG00000097881	B230209K01Rik	AI848258|Gm818	RIKEN cDNA B230209K01 gene	miscRNA	0	0.336634
Merged-chr13-105506846-1	chr13	105506796	105506896	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	63153	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0	0.336634
Merged-chr4-124600524-1	chr4	124600474	124600574	+	2.1	cIP1vsInput	Intergenic	Intergenic	31345	NR_045819	108809	Mm.250313	NR_045819		4933407E24Rik	-	RIKEN cDNA 4933407E24 gene	miscRNA	0	0.336634
Merged-chr9-28330294-1	chr9	28330244	28330344	+	2.1	cIP2vsInput	"intron (NM_177906, intron 1 of 7)"	"intron (NM_177906, intron 1 of 7)"	539025	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding	0	0.366337
Merged-chr2-150835546-1	chr2	150835496	150835596	+	2.1	cIP1vsInput	"intron (NM_024465, intron 10 of 12)"	"intron (NM_024465, intron 10 of 12)"	48750	NM_153781	110078	Mm.222584	NM_153781	ENSMUSG00000033059	Pygb	-	brain glycogen phosphorylase	protein-coding	0	0.306931
Merged-chr4-141751807-1	chr4	141751757	141751857	+	2.1	cIP1vsInput	"intron (NM_001081408, intron 2 of 6)"	PB1|SINE|Alu	5132	NM_001081408	75986	Mm.30032	NM_001081408	ENSMUSG00000040706	Agmat	5033405N08Rik	agmatine ureohydrolase (agmatinase)	protein-coding	0.01	0.405941
Merged-chr14-117341244-1	chr14	117341194	117341294	+	2.1	cIP1vsInput	"intron (NM_001079844, intron 2 of 9)"	"intron (NM_001079844, intron 2 of 9)"	415929	NM_011821	23888	Mm.440025	NM_001079844	ENSMUSG00000058571	Gpc6	6720429C22Rik|AI480529	glypican 6	protein-coding	0.01	0.346535
Merged-chr13-30501951-1	chr13	30501901	30502001	+	2.1	cIP1vsInput	Intergenic	Intergenic	43365	NM_025710	66694	Mm.181933	NM_025710	ENSMUSG00000038462	Uqcrfs1	4430402G14Rik|AI875505	"ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1"	protein-coding	0.01	0.287129
Merged-chr9-50305295-1	chr9	50305245	50305345	+	2.1	cIP2vsInput	Intergenic	MTEa|LTR|ERVL-MaLR	-189230	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	1600029D21Rik	0610037B23Rik|AA407923|AU043048|PLET1	RIKEN cDNA 1600029D21 gene	protein-coding	0.01	0.376238
Merged-chr10-16314096-1	chr10	16314046	16314146	+	2.1	cIP1vsInput	Intergenic	Intergenic	781686	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0	0.247525
Merged-chr19-34017685-1	chr19	34017635	34017735	+	2.1	cIP2vsInput	"intron (NM_001205349, intron 1 of 9)"	L1_Rod|LINE|L1	9431	NM_001205349	240633	Mm.58924	NM_001205349	ENSMUSG00000024771	Lipk	9930115F20|BC055815|Lipl2	"lipase, family member K"	protein-coding	0	0.386139
Merged-chr4-141420060-1	chr4	141420010	141420110	+	2.1	cIP1vsInput	promoter-TSS (NM_013868)	promoter-TSS (NM_013868)	-719	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	"heat shock protein family, member 7 (cardiovascular)"	protein-coding	0.04	0.653465
Merged-chr12-96707533-1	chr12	96707483	96707583	+	2.1	cIP1vsInput	Intergenic	Intergenic	-660311	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0	0.316832
Merged-chr4-20351481-1	chr4	20351431	20351531	+	2.1	cIP2vsInput	"intron (NM_172987, intron 3 of 4)"	MER44B|DNA|TcMar-Tigger	309429	NM_010281	14590	Mm.20461	NM_010281		Ggh	gamma-GH	gamma-glutamyl hydrolase	protein-coding	0	0.29703
Merged-chr14-96280523-2	chr14	96280429	96280617	+	2.1	cIP1vsInput|cIP2vsInput	"intron (NM_053105, intron 4 of 10)"	"intron (NM_053105, intron 4 of 10)"	238511	NM_053105	93688	Mm.308735	NM_053105	ENSMUSG00000022076	Klhl1	mKIAA1490	kelch-like 1	protein-coding	0.005319	0.333333
Merged-chr10-87154223-1	chr10	87154173	87154273	+	2.1	cIP1vsInput	"intron (NM_029685, intron 3 of 5)"	"intron (NM_029685, intron 3 of 5)"	96177	NM_029685	76640	Mm.78423	NM_029685	ENSMUSG00000047129	1700113H08Rik	-	RIKEN cDNA 1700113H08 gene	protein-coding	0.02	0.415842
Merged-chr3-139280118-1	chr3	139280068	139280168	+	2.1	cIP1vsInput	"intron (NM_198659, intron 6 of 13)"	ORR1C1-int|LTR|ERVL-MaLR	74225	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding	0	0.336634
Merged-chr6-94395051-1	chr6	94395001	94395101	+	2.1	cIP1vsInput	Intergenic	Intergenic	-105263	NM_026255	67582	Mm.280725	NM_026255	ENSMUSG00000045100	Slc25a26	4930433D19Rik|4933433F13Rik|AW557176|D6Bwg0781e|Slc25a6	"solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 26"	protein-coding	0.03	0.435644
Merged-chr8-86300639-1	chr8	86300589	86300689	+	2.1	cIP2vsInput	Intergenic	RMER6B|LTR|ERVK	265951	NM_172912	244562	Mm.67485	NM_172912	ENSMUSG00000036872	Abcc12	4930467B22Rik|MRP9	"ATP-binding cassette, sub-family C (CFTR/MRP), member 12"	protein-coding	0	0.386139
Merged-chr15-50570926-1	chr15	50570876	50570976	+	2.1	cIP2vsInput	Intergenic	Intergenic	318188	NR_035444	100316685		NR_035444	ENSMUSG00000084458	Mir1907	Mirn1907|mmu-mir-1907	microRNA 1907	miscRNA	0	0.39604
Merged-chr15-89137645-1	chr15	89137595	89137695	+	2.1	cIP2vsInput	"intron (NM_013871, intron 2 of 11)"	"intron (NM_013871, intron 2 of 11)"	3058	NM_013871	29857	Mm.38343	NM_013871	ENSMUSG00000022610	Mapk12	AW123708|Erk6|P38gamma|Prkm12|Sapk3	mitogen-activated protein kinase 12	protein-coding	0.02	0.613861
Merged-chr14-89262937-1	chr14	89262887	89262987	+	2.1	cIP1vsInput	Intergenic	Lx|LINE|L1	-633287	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0	0.366337
Merged-chr13-86177437-1	chr13	86177387	86177487	+	2.1	cIP1vsInput	Intergenic	Lx8b|LINE|L1	-130642	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0.01	0.366337
Merged-chr11-121204098-1	chr11	121204048	121204148	+	2.1	cIP1vsInput	promoter-TSS (NM_001001333)	promoter-TSS (NM_001001333)	-335	NM_001001333	238023	Mm.275130	NM_001001333	ENSMUSG00000039307	Hexdc	BC069960	"hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing"	protein-coding	0.03	0.554455
Merged-chr3-154103659-1	chr3	154103609	154103709	+	2.1	cIP2vsInput	"intron (NM_001081263, intron 1 of 21)"	"intron (NM_001081263, intron 1 of 21)"	130223	NM_001081263	242259	Mm.239962	NM_001081263	ENSMUSG00000028360	Slc44a5	AA117069|Gm422	"solute carrier family 44, member 5"	protein-coding	0	0.306931
Merged-chr2-99468649-1	chr2	99468599	99468699	+	2.1	cIP1vsInput	Intergenic	Intergenic	2000975	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.346535
Merged-chr9-16196482-1	chr9	16196432	16196532	+	2.1	cIP2vsInput	"intron (NM_001080814, intron 2 of 24)"	"intron (NM_001080814, intron 2 of 24)"	181749	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT tumor suppressor homolog 3 (Drosophila)	protein-coding	0	0.316832
Merged-chr15-22859364-1	chr15	22859314	22859414	+	2.1	cIP1vsInput	Intergenic	Intergenic	-144380	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding	0	0.346535
Merged-chr16-54558057-1	chr16	54558007	54558107	+	2.1	cIP1vsInput	Intergenic	L1ME4b|LINE|L1	725180	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding	0	0.247525
Merged-chr2-23375460-1	chr2	23375410	23375510	+	2.1	cIP1vsInput	"intron (NM_008752, intron 1 of 1)"	Lx2|LINE|L1	54214	NM_008752	18232	Mm.131616	NM_008752	ENSMUSG00000069132	Nxph2	-	neurexophilin 2	protein-coding	0	0.346535
Merged-chr16-32118502-1	chr16	32118452	32118552	+	2.1	cIP1vsInput	Intergenic	Intergenic	18700	NM_025892	66994	Mm.22990	NM_025892	ENSMUSG00000035790	Cep19	1500031L02Rik|AI428934|AL022620	centrosomal protein 19	protein-coding	0.01	0.346535
Merged-chr9-48231326-1	chr9	48231276	48231376	+	2.1	cIP1vsInput	Intergenic	Intergenic	109572	NM_030069	78252	Mm.31626	NM_030069	ENSMUSG00000032028	Nxpe2	4432416J03Rik|AI323362|Fam55b	"neurexophilin and PC-esterase domain family, member 2"	protein-coding	0.01	0.316832
Merged-chr8-15663066-1	chr8	15663016	15663116	+	2.1	cIP1vsInput	Intergenic	Intergenic	505772	NR_037214	100526464		NR_037214		Mir3106	mmu-mir-3106	microRNA 3106	miscRNA	0	0.455446
Merged-chr18-20821567-1	chr18	20821517	20821617	+	2.1	cIP1vsInput	"intron (NM_177038, intron 26 of 28)"	"intron (NM_177038, intron 26 of 28)"	74511	NM_177038	75964	Mm.273769	NM_029491	ENSMUSG00000033382	Trappc8	5033403J15Rik|AI845423|D030074E01Rik|Trs85|mKIAA1012	trafficking protein particle complex 8	protein-coding	0	0.29703
Merged-chr4-138922223-1	chr4	138922173	138922273	+	2.1	cIP2vsInput	Intergenic	Intergenic	-8276	NM_028453	73162	Mm.307701	NM_028453	ENSMUSG00000041161	Otud3	3110030K17Rik	OTU domain containing 3	protein-coding	0.06	0.643564
Merged-chr15-23946121-1	chr15	23946071	23946171	+	2.1	cIP1vsInput	Intergenic	Lx2|LINE|L1	909658	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l	cadherin 18	protein-coding	0	0.336634
Merged-chr1-113115091-1	chr1	113115041	113115141	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1250173	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik	dermatan sulfate epimerase-like	protein-coding	0	0.356436
Merged-chr4-71538350-1	chr4	71538300	71538400	+	2.1	cIP2vsInput	Intergenic	Intergenic	662569	NM_011599	21885	Mm.399716	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg1|Tle4l	"transducin-like enhancer of split 1, homolog of Drosophila E(spl)"	protein-coding	0	0.356436
Merged-chr1-14457453-1	chr1	14457403	14457503	+	2.1	cIP1vsInput	Intergenic	Intergenic	-147254	NM_010164	14048	Mm.250185	NM_001252192	ENSMUSG00000025932	Eya1	bor	eyes absent 1 homolog (Drosophila)	protein-coding	0	0.287129
Merged-chr1-91494711-1	chr1	91494661	91494761	+	2.1	cIP2vsInput	promoter-TSS (NM_028718)	promoter-TSS (NM_028718)	43	NM_028718	74019	Mm.318430	NM_028718	ENSMUSG00000034292	Traf3ip1	3930402D05Rik|AU041749|MIP-T3	TRAF3 interacting protein 1	protein-coding	0.19	0.811881
Merged-chr10-61518876-1	chr10	61518826	61518926	+	2.1	cIP1vsInput	"intron (NM_153542, intron 2 of 4)"	ORR1B1|LTR|ERVL-MaLR	43043	NM_153542	216011	Mm.136116	NM_153542	ENSMUSG00000037151	Lrrc20	BC036304	leucine rich repeat containing 20	protein-coding	0.02	0.564356
Merged-chr5-59727507-1	chr5	59727457	59727557	+	2.1	cIP1vsInput	Intergenic	Intergenic	258495	NR_040683	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0.01	0.376238
Merged-chr12-77518633-1	chr12	77518583	77518683	+	2.1	cIP1vsInput	Intergenic	Intergenic	108492	NM_001252616	53618	Mm.489686	NM_001252614	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding	0	0.356436
Merged-chr2-172121557-1	chr2	172121507	172121607	+	2.1	cIP1vsInput	Intergenic	L1MEc|LINE|L1	-78091	NM_175631	228942	Mm.40555	NM_175631	ENSMUSG00000067578	Cbln4	AI848962	cerebellin 4 precursor protein	protein-coding	0.03	0.405941
Merged-chr17-31920562-1	chr17	31920512	31920612	+	2.1	cIP1vsInput	Intergenic	Intergenic	-64770	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding	0.02	0.534653
Merged-chr9-82171355-1	chr9	82171305	82171405	+	2.1	cIP1vsInput	Intergenic	L1M3b|LINE|L1	307611	NM_175213	75033	Mm.457083	NM_175213	ENSMUSG00000043289	Mei4	4930486G11Rik	"meiosis-specific, MEI4 homolog (S. cerevisiae)"	protein-coding	0	0.376238
Merged-chr16-89293395-1	chr16	89293345	89293445	+	2.1	cIP2vsInput	Intergenic	L1M3|LINE|L1	87534	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding	0	0.376238
Merged-chr16-54508851-1	chr16	54508801	54508901	+	2.1	cIP1vsInput	Intergenic	Intergenic	774386	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding	0	0.257426
Merged-chr7-76456582-1	chr7	76456532	76456632	+	2.1	cIP2vsInput	"intron (NM_001199224, intron 17 of 22)"	Lx8|LINE|L1	226695	NM_001199224	244071	Mm.322829	NM_001199224		Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding	0	0.277228
Merged-chr1-66184311-1	chr1	66184261	66184361	+	2.1	cIP1vsInput	"intron (NM_001039934, intron 1 of 14)"	"intron (NM_001039934, intron 1 of 14)"	8982	NM_001039934	17756	Mm.256966	NM_001039934	ENSMUSG00000015222	Map2	MAP-2|Mtap-2|Mtap2	microtubule-associated protein 2	protein-coding	0	0.326733
Merged-chr3-118711936-1	chr3	118711886	118711986	+	2.1	cIP1vsInput	"intron (NM_170778, intron 3 of 22)"	"intron (NM_170778, intron 3 of 22)"	149758	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding	0.01	0.326733
Merged-chr8-80078056-1	chr8	80078006	80078106	+	2.1	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-20048	NM_020259	15245	Mm.254493	NM_020259		Hhip	Hhip1	Hedgehog-interacting protein	protein-coding	0.01	0.346535
Merged-chr4-117189036-1	chr4	117188986	117189086	+	2.1	cIP1vsInput	Intergenic	Intergenic	-6412	NM_134471	73804	Mm.247651	NM_134471	ENSMUSG00000028678	Kif2c	4930402F02Rik|ESTM5|Knsl6|MCAK|X83316	kinesin family member 2C	protein-coding	0.02	0.465347
Merged-chr3-158656875-1	chr3	158656825	158656925	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-94654	NM_001081358	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding	0	0.326733
Merged-chr14-60115684-1	chr14	60115634	60115734	+	2.1	cIP2vsInput	Intergenic	(CAAA)n|Simple_repeat|Simple_repeat	-28850	NM_015803	50769	Mm.319599	NM_015803	ENSMUSG00000021983	Atp8a2	AI415030|Atpc1b|Ib	"ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"	protein-coding	0	0.287129
Merged-chr5-11890640-1	chr5	11890590	11890690	+	2.1	cIP1vsInput	Intergenic	Intergenic	-27403	NM_001177510	545732	Mm.389066	NM_001177510	ENSMUSG00000067848	4933402N22Rik	-	RIKEN cDNA 4933402N22 gene	protein-coding	0	0.267327
Merged-chr15-6010290-1	chr15	6010240	6010340	+	2.1	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-289499	NM_001008702	13132	Mm.240830	NM_001008702	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	"disabled 2, mitogen-responsive phosphoprotein"	protein-coding	0.01	0.346535
Merged-chr12-73743928-1	chr12	73743878	73743978	+	2.1	cIP1vsInput	"intron (NM_008856, intron 10 of 13)"	"intron (NM_008856, intron 10 of 13)"	158887	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	"protein kinase C, eta"	protein-coding	0.01	0.415842
Merged-chr16-39033782-1	chr16	39033732	39033832	+	2.1	cIP1vsInput	Intergenic	Intergenic	131437	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	"immunoglobulin superfamily, member 11"	protein-coding	0.01	0.326733
Merged-chr1-194089964-1	chr1	194089914	194090014	+	2.1	cIP1vsInput	Intergenic	Intergenic	132795	NR_040477	74942	Mm.60689	NR_040477		4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	miscRNA	0	0.346535
Merged-chr5-25129564-1	chr5	25129514	25129614	+	2.1	cIP1vsInput	Intergenic	Lx6|LINE|L1	28589	NR_027851	67261	Mm.461781	NM_026059	ENSMUSG00000043833	2900005J15Rik	-	RIKEN cDNA 2900005J15 gene	miscRNA	0	0.346535
Merged-chr18-78776740-1	chr18	78776690	78776790	+	2.1	cIP1vsInput	"intron (NM_053099, intron 5 of 5)"	L3|LINE|CR1	-179790	NM_030683	27411	Mm.44158	NM_001110273	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	"solute carrier family 14 (urea transporter), member 2"	protein-coding	0	0.346535
Merged-chr14-120819283-1	chr14	120819233	120819333	+	2.1	cIP1vsInput	Intergenic	Lx4A|LINE|L1	-91911	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding	0.01	0.336634
Merged-chr16-73382043-1	chr16	73381993	73382093	+	2.1	cIP2vsInput	Intergenic	Intergenic	718894	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout homolog 1 (Drosophila)	protein-coding	0.01	0.356436
Merged-chr11-40240910-1	chr11	40240860	40240960	+	2.1	cIP1vsInput	Intergenic	Cheshire|DNA|hAT-Charlie	451772	NM_134017	108645	Mm.293771	NM_001199274	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	"methionine adenosyltransferase II, beta"	protein-coding	0	0.386139
Merged-chr10-80371783-1	chr10	80371733	80371833	+	2.1	cIP1vsInput	Intergenic	ZP3AR|Satellite|Satellite	-2146	NR_038088	100568459		NR_038088		Bc1	Gm24367	brain cytoplasmic RNA 1	miscRNA	0.01	0.584158
Merged-chr1-66798369-1	chr1	66798319	66798419	+	2.1	cIP1vsInput	"intron (NM_177645, intron 2 of 13)"	Lx7|LINE|L1	19226	NM_177645	68691	Mm.482481	NM_001122738	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding	0	0.306931
Merged-chr11-13871143-1	chr11	13871093	13871193	+	2.1	cIP2vsInput	Intergenic	Intergenic	728082	NR_045918	73307	Mm.399291	NR_045918	ENSMUSG00000085561	1700046C09Rik	-	RIKEN cDNA 1700046C09 gene	miscRNA	0	0.287129
Merged-chr14-116355746-1	chr14	116355696	116355796	+	2.1	cIP2vsInput	"intron (NM_175500, intron 7 of 7)"	L1MCa|LINE|L1	-569569	NM_001079844	23888	Mm.440025	NM_001079844	ENSMUSG00000058571	Gpc6	6720429C22Rik|AI480529	glypican 6	protein-coding	0	0.326733
Merged-chr2-87789720-1	chr2	87789670	87789770	+	2.1	cIP2vsInput	Intergenic	Intergenic	7184	NM_146646	258640	Mm.377607	NM_146646	ENSMUSG00000068816	Olfr152	MOR181-1|Olfr4-1|V1	olfactory receptor 152	protein-coding	0.01	0.287129
Merged-chr3-139404328-1	chr3	139404278	139404378	+	2.1	cIP2vsInput	"intron (NM_198659, intron 10 of 13)"	"intron (NM_198659, intron 10 of 13)"	198435	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding	0.01	0.316832
Merged-chr10-130110728-1	chr10	130110678	130110778	+	2.1	cIP1vsInput	Intergenic	Lx4A|LINE|L1	2060	NM_146673	258668	Mm.377630	NM_146673	ENSMUSG00000096747	Olfr823	MOR210-4	olfactory receptor 823	protein-coding	0	0.524752
Merged-chr18-40766567-1	chr18	40766517	40766617	+	2.1	cIP1vsInput	Intergenic	L1_Mus4|LINE|L1	508206	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding	0.01	0.29703
Merged-chr18-89163550-1	chr18	89163500	89163600	+	2.1	cIP2vsInput	Intergenic	Intergenic	-33877	NM_178687	225825	Mm.139293	NM_001039148	ENSMUSG00000034028	Cd226	BC051526|DNAM-1|DNAM1|Pta1|TLiSA1	CD226 antigen	protein-coding	0	0.386139
Merged-chr5-26667246-1	chr5	26667196	26667296	+	2.1	cIP1vsInput	Intergenic	L1VL2|LINE|L1	-150111	NM_010075	13483	Mm.42078	NM_001136060	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding	0	0.29703
Merged-chr1-144870815-1	chr1	144870765	144870865	+	2.1	cIP1vsInput	Intergenic	Intergenic	-95394	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding	0	0.346535
Merged-chr9-90884224-1	chr9	90884174	90884274	+	2.1	cIP1vsInput	Intergenic	Intergenic	481575	NM_009573	22771	Mm.477226	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding	0.01	0.326733
Merged-chr5-103356226-1	chr5	103356176	103356276	+	2.1	cIP2vsInput	Intergenic	Intergenic	-57197	NR_040699	74624	Mm.389662	NR_040699		4930429D17Rik	-	RIKEN cDNA 4930429D17 gene	miscRNA	0.01	0.326733
Merged-chr1-101206130-1	chr1	101206080	101206180	+	2.1	cIP1vsInput	Intergenic	Lx3_Mus|LINE|L1	50362	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.405941
Merged-chr16-54123958-1	chr16	54123908	54124008	+	2.1	cIP2vsInput	Intergenic	Intergenic	1159279	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding	0	0.356436
Merged-chr6-147441007-1	chr6	147440957	147441057	+	2.1	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-34864	NM_025911	67015	Mm.209774	NM_025911	ENSMUSG00000030301	Ccdc91	1700086G08Rik|1810060J02Rik|AU045683|AW555238|p56	coiled-coil domain containing 91	protein-coding	0	0.366337
Merged-chr1-33124939-1	chr1	33124889	33124989	+	2.1	cIP1vsInput	Intergenic	Intergenic	544819	NM_008922	19076	Mm.27705	NM_008922	ENSMUSG00000026134	Prim2	AI323589	"DNA primase, p58 subunit"	protein-coding	0	0.29703
Merged-chr4-53676477-1	chr4	53676427	53676527	+	2.1	cIP2vsInput	"intron (NM_001195284, intron 6 of 12)"	L1MC|LINE|L1	-37705	NM_139309	246179	Mm.247210	NM_139309	ENSMUSG00000028414	Fktn	D830030O17Rik|Fcmd	fukutin	protein-coding	0	0.316832
Merged-chr7-90508523-1	chr7	90508473	90508573	+	2.1	cIP1vsInput	Intergenic	Intergenic	-32528	NM_026734	68472	Mm.289791	NM_026734		Tmem126b	1110001A23Rik	transmembrane protein 126B	protein-coding	0	0.277228
Merged-chr16-6497611-1	chr16	6497561	6497661	+	2.1	cIP1vsInput	"intron (NM_021477, intron 3 of 16)"	"intron (NM_021477, intron 3 of 16)"	522024	NR_045799	68238	Mm.434605	NR_045799		1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	miscRNA	0	0.336634
Merged-chr17-17910092-1	chr17	17910042	17910142	+	2.1	cIP2vsInput	Intergenic	CpG	22268	NM_008039	14289		NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding	0.06	0.594059
Merged-chr3-74958436-1	chr3	74958386	74958486	+	2.1	cIP1vsInput	Intergenic	MYSERV6-int|LTR|ERVK	185287	NM_172515	213234	Mm.80075	NM_172515	ENSMUSG00000034151	Zbbx	4931432L23	"zinc finger, B-box domain containing"	protein-coding	0.01	0.326733
Merged-chr8-97285849-1	chr8	97285799	97285899	+	2.1	cIP2vsInput	Intergenic	Intergenic	-739876	NR_039538	100628567		NR_039538		Mir28c	mmu-mir-28c	microRNA 28c	miscRNA	0.01	0.306931
Merged-chr13-74692374-1	chr13	74692324	74692424	+	2.1	cIP2vsInput	TTS (NM_030711)	TTS (NM_030711)	52502	NM_030711	80898	Mm.83526	NM_030711	ENSMUSG00000021583	Erap1	Arts1|ERAAP|PILSA|PILSAP	endoplasmic reticulum aminopeptidase 1	protein-coding	0	0.227723
Merged-chr4-96638857-1	chr4	96638807	96638907	+	2.1	cIP1vsInput	"intron (NM_010007, intron 5 of 8)"	"intron (NM_010007, intron 5 of 8)"	25262	NM_010007	13109	Mm.12838	NM_010007		Cyp2j5	-	"cytochrome P450, family 2, subfamily j, polypeptide 5"	protein-coding	0	0.326733
Merged-chr3-16027574-1	chr3	16027524	16027624	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-21242	NM_001081687	381484	Mm.217376	NM_001081687	ENSMUSG00000078780	Gm5150	-	predicted gene 5150	protein-coding	0.01	0.326733
Merged-chr4-21702312-1	chr4	21702262	21702362	+	2.1	cIP2vsInput	Intergenic	Intergenic	-16349	NM_001080771	230025	Mm.208541	NM_001080771	ENSMUSG00000040478	Prdm13	-	PR domain containing 13	protein-coding	0	0.346535
Merged-chr17-88287699-1	chr17	88287649	88287749	+	2.1	cIP1vsInput	Intergenic	L1MEj|LINE|L1	-153013	NM_180974	14236	Mm.393597	NM_180974	ENSMUSG00000034998	Foxn2	3230402J05Rik|6030465J18Rik|Fkh19|Foxn1|HTLF	forkhead box N2	protein-coding	0	0.39604
Merged-chr6-5530293-1	chr6	5530243	5530343	+	2.1	cIP2vsInput	Intergenic	Intergenic	-34015	NM_013743	27273	Mm.235547	NM_013743	ENSMUSG00000019577	Pdk4	AV005916	"pyruvate dehydrogenase kinase, isoenzyme 4"	protein-coding	0	0.336634
Merged-chr13-52436265-1	chr13	52436215	52436315	+	2.1	cIP2vsInput	Intergenic	Intergenic	94571	NM_001024474	68203	Mm.29362	NM_001024474	ENSMUSG00000047842	Diras2	2900052J15Rik|AI414999	"DIRAS family, GTP-binding RAS-like 2"	protein-coding	0	0.544554
Merged-chr2-53601970-1	chr2	53601920	53602020	+	2.1	cIP1vsInput	Intergenic	Intergenic	409886	NM_022989	65103	Mm.37623	NM_022989	ENSMUSG00000026960	Arl6ip6	2310057C01Rik|2610529A11Rik|Aip-6	ADP-ribosylation factor-like 6 interacting protein 6	protein-coding	0	0.326733
Merged-chr17-39746296-1	chr17	39746246	39746346	+	2.1	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-96701	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA	0	0.336634
Merged-chr3-20812752-1	chr3	20812702	20812802	+	2.1	cIP2vsInput	Intergenic	Intergenic	-445575	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	"angiotensin II receptor, type 1b"	protein-coding	0	0.306931
Merged-chr5-75310272-1	chr5	75310222	75310322	+	2.1	cIP1vsInput	Intergenic	T-rich|Low_complexity|Low_complexity	154106	NM_001083316	18595	Mm.221403	NM_001083316	ENSMUSG00000029231	Pdgfra	AI115593|CD140a|Pdgfr-2	"platelet derived growth factor receptor, alpha polypeptide"	protein-coding	0.01	0.217822
Merged-chr11-56371043-1	chr11	56370993	56371093	+	2.1	cIP2vsInput	Intergenic	L1MDa|LINE|L1	-330056	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding	0.01	0.356436
Merged-chr8-66650529-1	chr8	66650479	66650579	+	2.1	cIP1vsInput	Intergenic	Lx2B|LINE|L1	37565	NM_016708	18168	Mm.10685	NM_016708	ENSMUSG00000044014	Npy5r	NPY5-R|NPYY5-R|Y5R	neuropeptide Y receptor Y5	protein-coding	0	0.346535
Merged-chr1-108778965-1	chr1	108778915	108779015	+	2.1	cIP2vsInput	Intergenic	Intergenic	861706	NR_102307	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0	0.287129
Merged-chr9-106429420-1	chr9	106429370	106429470	+	2.1	cIP2vsInput	promoter-TSS (NM_009082)	promoter-TSS (NM_009082)	-119	NM_009082	19944	Mm.431965	NM_009082	ENSMUSG00000048758	Rpl29	Rpl43	ribosomal protein L29	protein-coding	0.04	0.574257
Merged-chr13-4923271-1	chr13	4923221	4923321	+	2.1	cIP1vsInput	Intergenic	Intergenic	-314107	NM_018859	56043	Mm.251908	NM_018859	ENSMUSG00000045410	Akr1e1	1810061I10Rik|Akr1e2	"aldo-keto reductase family 1, member E1"	protein-coding	0	0.306931
Merged-chr4-22914837-1	chr4	22914787	22914887	+	2.1	cIP1vsInput	Intergenic	Intergenic	-426471	NM_008899	18992	Mm.487875	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	"POU domain, class 3, transcription factor 2"	protein-coding	0	0.277228
Merged-chr18-87594184-1	chr18	87594134	87594234	+	2.1	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	881136	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding	0	0.326733
Merged-chr8-96827943-1	chr8	96827893	96827993	+	2.1	cIP2vsInput	Intergenic	L1MB7|LINE|L1	-281970	NR_039538	100628567		NR_039538		Mir28c	mmu-mir-28c	microRNA 28c	miscRNA	0	0.346535
Merged-chr11-62189082-1	chr11	62189032	62189132	+	2.1	cIP1vsInput	"intron (NM_001029936, intron 10 of 12)"	"intron (NM_001029936, intron 10 of 12)"	-59902	NM_007413	11541	Mm.40740	NM_007413	ENSMUSG00000018500	Adora2b	A2BAR|A2BR|A2b|AA2BR|AI480866|AI605384	adenosine A2b receptor	protein-coding	0	0.267327
Merged-chr3-45093799-1	chr3	45093749	45093849	+	2.1	cIP2vsInput	Intergenic	Intergenic	284461	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	miscRNA	0	0.316832
Merged-chr2-77721825-1	chr2	77721775	77721875	+	2.1	cIP2vsInput	"intron (NM_178723, intron 1 of 9)"	"intron (NM_178723, intron 1 of 9)"	-18553	NM_001113399	241494	Mm.490320	NM_001113399	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding	0	0.306931
Merged-chr2-52274833-1	chr2	52274783	52274883	+	2.1	cIP2vsInput	"intron (NM_010889, intron 46 of 156)"	"intron (NM_010889, intron 46 of 156)"	-16169	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	miscRNA	0	0.306931
Merged-chr15-79647384-1	chr15	79647334	79647434	+	2.1	cIP1vsInput	"intron (NM_029407, intron 3 of 17)"	B4|SINE|B4	11572	NM_029407	75729	Mm.78946	NM_029407	ENSMUSG00000042564	Fam227a	4933432B09Rik	"family with sequence similarity 227, member A"	protein-coding	0	0.425743
Merged-chr4-23436531-1	chr4	23436481	23436581	+	2.1	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-948165	NM_008899	18992	Mm.487875	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	"POU domain, class 3, transcription factor 2"	protein-coding	0	0.306931
Merged-chr6-126175846-1	chr6	126175796	126175896	+	2.1	cIP2vsInput	Intergenic	L1MEg|LINE|L1	-9102	NM_008742	18205	Mm.267570	NM_001164034	ENSMUSG00000049107	Ntf3	AI316846|AI835689|Nt3|Ntf-3	neurotrophin 3	protein-coding	0	0.326733
Merged-chr16-87384770-1	chr16	87384720	87384820	+	2.1	cIP1vsInput	"intron (NM_001081068, intron 25 of 29)"	Lx7|LINE|L1	30585	NM_026366	67768	Mm.296532	NM_001159331	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding	0	0.356436
Merged-chr11-98644128-1	chr11	98644078	98644178	+	2.1	cIP1vsInput	Intergenic	MMERVK9C_I-int|LTR|ERVK	-2631	NM_029727	76758	Mm.159149	NM_029727	ENSMUSG00000017211	Gsdma2	2200001G21Rik|2210006M16Rik|2210009F20Rik|2210411P14Rik|Gsdm2|Gsdml2	gasdermin A2	protein-coding	0	0.306931
Merged-chr3-75344275-1	chr3	75344225	75344325	+	2.1	cIP1vsInput	Intergenic	Lx2B2|LINE|L1	-74197	NM_026460	67931	Mm.259446	NM_026460	ENSMUSG00000034139	Serpini2	Spi14	"serine (or cysteine) peptidase inhibitor, clade I, member 2"	protein-coding	0	0.356436
Merged-chr3-67407300-1	chr3	67407250	67407350	+	2.1	cIP2vsInput	Intergenic	Intergenic	-22815	NM_138591	28030	Mm.122466	NM_138591		Gfm1	AW545374|D3Wsu133e|Gfm	"G elongation factor, mitochondrial 1"	protein-coding	0	0.306931
Merged-chr3-60873214-1	chr3	60873164	60873264	+	2.1	cIP1vsInput	Intergenic	Intergenic	-129581	NM_008772	18441	Mm.281452	NM_008772	ENSMUSG00000027765	P2ry1	P2Y1	"purinergic receptor P2Y, G-protein coupled 1"	protein-coding	0	0.257426
Merged-chr16-9704763-1	chr16	9704713	9704813	+	2.1	cIP1vsInput	"intron (NM_008170, intron 3 of 11)"	L1ME3|LINE|L1	287770	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	"glutamate receptor, ionotropic, NMDA2A (epsilon 1)"	protein-coding	0	0.277228
Merged-chr2-43154035-1	chr2	43153985	43154085	+	2.1	cIP2vsInput	Intergenic	Intergenic	-401294	NM_027552	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding	0.01	0.336634
Merged-chr4-97185359-1	chr4	97185309	97185409	+	2.1	cIP2vsInput	Intergenic	Intergenic	-396584	NM_001122952	18027	Mm.409646	NM_001122952	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|NF1-A|NF1A	nuclear factor I/A	protein-coding	0.01	0.366337
Merged-chr9-108661688-1	chr9	108661638	108661738	+	2.1	cIP2vsInput	promoter-TSS (NM_020520)	promoter-TSS (NM_020520)	-410	NM_020520	57279	Mm.29666	NM_020520	ENSMUSG00000032602	Slc25a20	1110007P09Rik|C78826|Cact|mCAC	"solute carrier family 25 (mitochondrial carnitine/acylcarnitine translocase), member 20"	protein-coding	0	0.346535
Merged-chr13-109761083-1	chr13	109761033	109761133	+	2.1	cIP1vsInput	"intron (NM_011056, intron 5 of 16)"	"intron (NM_011056, intron 5 of 16)"	-142726	NR_035442	100316683		NR_035442		Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	miscRNA	0.02	0.376238
Merged-chr2-28622828-1	chr2	28622778	28622878	+	2.1	cIP1vsInput	promoter-TSS (NM_001160406)	promoter-TSS (NM_001160406)	-846	NM_001160406	14582	Mm.373385	NM_001160406	ENSMUSG00000026815	Gfi1b	Gfi-1B	growth factor independent 1B	protein-coding	0.01	0.544554
Merged-chr7-103658290-1	chr7	103658240	103658340	+	2.1	cIP1vsInput	Intergenic	Intergenic	3028	NM_147122	259126	Mm.377863	NM_147122	ENSMUSG00000055124	Olfr623	MOR1-4	olfactory receptor 623	protein-coding	0	0.267327
Merged-chr2-98758044-1	chr2	98757994	98758094	+	2.1	cIP1vsInput	Intergenic	L1VL4|LINE|L1	1290370	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.336634
Merged-chr1-92648990-1	chr1	92648940	92649040	+	2.1	cIP2vsInput	promoter-TSS (NM_153114)	promoter-TSS (NM_153114)	-149	NM_153114	260301	Mm.219545	NM_153114	ENSMUSG00000044055	Otos	OTOSP	otospiralin	protein-coding	0.01	0.554455
Merged-chr16-75309999-1	chr16	75309949	75310049	+	2.1	cIP1vsInput	Intergenic	Intergenic	257683	NM_177142	320355	Mm.99517	NM_001252513		Lipi	D930038D03Rik|lpd1	"lipase, member I"	protein-coding	0.01	0.277228
Merged-chr15-49220309-1	chr15	49220259	49220359	+	2.1	cIP1vsInput	Intergenic	Intergenic	-428320	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0	0.326733
Merged-chr7-85626977-1	chr7	85626927	85627027	+	2.1	cIP1vsInput	Intergenic	Intergenic	11515	NM_001105184	233445	Mm.389930	NM_001105184	ENSMUSG00000091205	Vmn2r71	EG233445	"vomeronasal 2, receptor 71"	protein-coding	0	0.326733
Merged-chr10-65138152-1	chr10	65138102	65138202	+	2.1	cIP2vsInput	Intergenic	Intergenic	985912	NR_038039	69433	Mm.23366	NR_038039		1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	miscRNA	0.01	0.356436
Merged-chr1-117200887-1	chr1	117200837	117200937	+	2.1	cIP1vsInput	Intergenic	RMER20A|LTR|ERVK	1110245	NM_011650	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding	0	0.445545
Merged-chr19-38018231-1	chr19	38018181	38018281	+	2.1	cIP1vsInput	"intron (NM_001099634, intron 3 of 52)"	RMER12|LTR|ERVK	25346	NM_001099634	226101	Mm.34674	NM_001099634	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding	0	0.376238
Merged-chrX-128232026-1	chrX	128231976	128232076	+	2.1	cIP2vsInput	Intergenic	Intergenic	-819498	NR_045441	75274	Mm.108718	NR_045441	ENSMUSG00000086244	4930558G05Rik	-	RIKEN cDNA 4930558G05 gene	miscRNA	0	0.29703
Merged-chr6-142163597-1	chr6	142163547	142163647	+	2.1	cIP1vsInput	"intron (NM_023718, intron 1 of 14)"	RLTR25A|LTR|ERVK	22552	NM_023718	28254	Mm.38953	NM_023718	ENSMUSG00000079262	Slco1a6	4930422F19Rik|AI790453|Oatp-5|Oatp5|Slc21a13	"solute carrier organic anion transporter family, member 1a6"	protein-coding	0.01	0.386139
Merged-chr6-53399032-1	chr6	53398982	53399082	+	2.1	cIP2vsInput	Intergenic	Intergenic	111737	NR_015553	320189		NR_015553		9430076C15Rik	-	RIKEN cDNA 9430076C15 gene	miscRNA	0.02	0.405941
Merged-chr9-113594809-1	chr9	113594759	113594859	+	2.1	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-7657	NR_040760	102688	Mm.394901	NR_040760		AU023762	-	expressed sequence AU023762	miscRNA	0	0.306931
Merged-chr3-158339294-1	chr3	158339244	158339344	+	2.1	cIP2vsInput	"intron (NM_001081358, intron 4 of 27)"	L1_Mur3|LINE|L1	222927	NM_001081358	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding	0.01	0.336634
Merged-chr2-32411771-1	chr2	32411721	32411821	+	2.1	cIP1vsInput	Intergenic	Intergenic	15881	NM_133783	96979	Mm.28048	NM_133783	ENSMUSG00000026820	Ptges2	0610038H10Rik|C79137|Gbf1|Mpges2|Pges2	prostaglandin E synthase 2	protein-coding	0.02	0.425743
Merged-chr8-37734395-1	chr8	37734345	37734445	+	2.1	cIP1vsInput	"intron (NM_145841, intron 2 of 7)"	"intron (NM_145841, intron 2 of 7)"	517807	NR_029884	723860		NR_029884		Mir383	Mirn383|mmu-mir-383	microRNA 383	miscRNA	0	0.316832
Merged-chr14-23901763-1	chr14	23901713	23901813	+	2.1	cIP2vsInput	"intron (NM_001253368, intron 1 of 28)"	"intron (NM_001253368, intron 1 of 28)"	102442	NM_001253375	16531	Mm.486347	NM_001253358	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	"potassium large conductance calcium-activated channel, subfamily M, alpha member 1"	protein-coding	0.01	0.425743
Merged-chr3-56865418-1	chr3	56865368	56865468	+	2.1	cIP1vsInput	Intergenic	Intergenic	436501	NM_008536	17112	Mm.856	NM_008536	ENSMUSG00000027800	Tm4sf1	L6|M3s1	transmembrane 4 superfamily member 1	protein-coding	0.01	0.316832
Merged-chr10-64830051-1	chr10	64830001	64830101	+	2.1	cIP1vsInput	"intron (NM_001164519, intron 8 of 12)"	"intron (NM_001164519, intron 8 of 12)"	-739796	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding	0.01	0.336634
Merged-chr3-117195752-1	chr3	117195702	117195802	+	2.1	cIP1vsInput	Intergenic	Intergenic	-117987	NR_038029	433646	Mm.158997	NR_038029	ENSMUSG00000028009	1700061I17Rik	-	RIKEN cDNA 1700061I17 gene	miscRNA	0	0.386139
Merged-chr2-152708157-1	chr2	152708107	152708207	+	2.1	cIP1vsInput	"3' UTR (NM_001159551, exon 13 of 13)"	"3' UTR (NM_001159551, exon 13 of 13)"	21009	NM_025543	66405	Mm.440291	NM_025543	ENSMUSG00000042814	Mcts2	2400002F11Rik|RP23-35I8.12	malignant T cell amplified sequence 2	protein-coding	0.03	0.514851
Merged-chr2-33366190-1	chr2	33366140	33366240	+	2.1	cIP2vsInput	"intron (NM_175211, intron 1 of 19)"	"intron (NM_175211, intron 1 of 19)"	5288	NM_175211	241308	Mm.274249	NM_175211	ENSMUSG00000038831	Ralgps1	5830418G11Rik|AI853783|AI854138|RALGEF2|RALGPS1A|RalGEF 2|mKIAA0351	Ral GEF with PH domain and SH3 binding motif 1	protein-coding	0.02	0.386139
Merged-chr17-38159295-1	chr17	38159245	38159345	+	2.1	cIP2vsInput	Intergenic	L1VL4|LINE|L1	10705	NM_146831	258828	Mm.390995	NM_146831	ENSMUSG00000063240	Olfr133	MOR256-6	olfactory receptor 133	protein-coding	0	0.306931
Merged-chr6-70125119-1	chr6	70125069	70125169	+	2.1	cIP1vsInput	Intergenic	Lx2|LINE|L1	667056	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding	0.02	0.326733
Merged-chr3-77423921-1	chr3	77423871	77423971	+	2.1	cIP2vsInput	Intergenic	Intergenic	1348338	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.336634
Merged-chr1-77110852-1	chr1	77110802	77110902	+	2.1	cIP2vsInput	Intergenic	Intergenic	404236	NM_007936	13838	Mm.400747	NM_007936	ENSMUSG00000026235	Epha4	2900005C20Rik|AI385584|Cek8|Hek8|Sek|Sek1|Tyro1|rb	Eph receptor A4	protein-coding	0.02	0.336634
Merged-chr5-59565867-1	chr5	59565817	59565917	+	2.1	cIP1vsInput	Intergenic	Lx3_Mus|LINE|L1	420135	NR_040683	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0	0.574257
Merged-chr5-140884246-1	chr5	140884196	140884296	+	2.1	cIP2vsInput	"intron (NM_175362, intron 17 of 24)"	"intron (NM_175362, intron 17 of 24)"	-53815	NM_010302	14673	Mm.370185	NM_010302		Gna12	AI414047|AI504261|Galpha12	"guanine nucleotide binding protein, alpha 12"	protein-coding	0	0.386139
Merged-chr4-127170086-1	chr4	127170036	127170136	+	2.1	cIP1vsInput	"intron (NM_198618, intron 1 of 11)"	"intron (NM_198618, intron 1 of 11)"	815	NM_198618	242667	Mm.331885	NM_198618	ENSMUSG00000042388	Dlgap3	BC058433|DAP-3|DAP3|Prpl8|Sapap3	"discs, large (Drosophila) homolog-associated protein 3"	protein-coding	0.04	0.594059
Merged-chr12-48234516-1	chr12	48234466	48234566	+	2.1	cIP2vsInput	"intron (NR_039586, intron 1 of 2)"	"intron (NR_039586, intron 1 of 2)"	66946	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0.01	0.386139
Merged-chr18-27736947-1	chr18	27736897	27736997	+	2.1	cIP1vsInput	Intergenic	Intergenic	-823217	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	miscRNA	0	0.277228
Merged-chr6-42536522-1	chr6	42536472	42536572	+	2.1	cIP2vsInput	Intergenic	Intergenic	2498	NM_001081301	546896	Mm.439626	NM_001081301	ENSMUSG00000071494	Olfr455	EG546896|MOR0-17_p|MOR0-2P|MORO-2|Olfr455-ps1	olfactory receptor 455	protein-coding	0	0.39604
Merged-chr9-13135150-1	chr9	13135100	13135200	+	2.1	cIP1vsInput	Intergenic	Intergenic	-29295	NR_040755	78219	Mm.414868	NR_040755		4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	miscRNA	0	0.306931
Merged-chr10-101197953-1	chr10	101197903	101198003	+	2.1	cIP1vsInput	Intergenic	Intergenic	-483534	NM_001205098	67569	Mm.403713	NM_001162368	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"	protein-coding	0	0.336634
Merged-chr1-123297236-1	chr1	123297186	123297286	+	2.1	cIP1vsInput	Intergenic	Intergenic	748323	NM_199021	269109	Mm.483255	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding	0.01	0.336634
Merged-chr10-72037762-1	chr10	72037712	72037812	+	2.1	cIP1vsInput	Intergenic	Intergenic	-57072	NR_003644	108950	Mm.212793	NR_003644	ENSMUSG00000043859	1700049L16Rik	-	hematological and neurological expressed 1-like pseudogene	pseudo	0.01	0.336634
Merged-chr15-98857305-1	chr15	98857255	98857355	+	2.1	cIP1vsInput	"intron (NM_001033276, intron 19 of 54)"	"intron (NM_001033276, intron 19 of 54)"	13900	NM_001033276	381022	Mm.264889	NM_001033388	ENSMUSG00000048154	Mll2	ALR|BC032281|BC058659|C430014K11Rik|KMT2B|KMT2D|Mll4	myeloid/lymphoid or mixed-lineage leukemia 2	protein-coding	0.01	0.425743
Merged-chr9-74345727-1	chr9	74345677	74345777	+	2.1	cIP1vsInput	Intergenic	Intergenic	235393	NM_001033500	546144	Mm.335289	NM_177908	ENSMUSG00000044976	Wdr72	AW558070|D230040E23	WD repeat domain 72	protein-coding	0	0.405941
Merged-chr5-86411280-1	chr5	86411230	86411330	+	2.1	cIP1vsInput	"3' UTR (NM_001033233, exon 9 of 9)"	"3' UTR (NM_001033233, exon 9 of 9)"	-37893	NM_145561	231382	Mm.240139	NM_145561		Tmprss11d	AST|AsP|BC020151	"transmembrane protease, serine 11d"	protein-coding	0.01	0.29703
Merged-chr16-35757222-1	chr16	35757172	35757272	+	2.1	cIP2vsInput	"intron (NM_153550, intron 1 of 8)"	L1MEc|LINE|L1	12134	NM_153550	224132		NM_153550	ENSMUSG00000022848	Dirc2	RCC4	disrupted in renal carcinoma 2 (human)	protein-coding	0.01	0.326733
Merged-chr12-34124215-1	chr12	34124165	34124265	+	2.1	cIP1vsInput	"intron (NM_001271386, intron 24 of 27)"	"intron (NM_001271386, intron 24 of 27)"	166544	NM_011658	22160	Mm.3280	NM_011658	ENSMUSG00000035799	Twist1	AA960487|M-Twist|Pde|Ska10|Ska<m10Jus>|Twist|bHLHa38|pdt	twist basic helix-loop-helix transcription factor 1	protein-coding	0	0.336634
Merged-chr13-108630602-1	chr13	108630552	108630652	+	2.1	cIP1vsInput	Intergenic	Intergenic	-23575	NM_011056	238871	Mm.434429	NM_011056		Pde4d	9630011N22Rik|Dpde3	"phosphodiesterase 4D, cAMP specific"	protein-coding	0	0.326733
Merged-chr2-179174145-1	chr2	179174095	179174195	+	2.1	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-240791	NM_026596	68175	Mm.158187	NM_026596		4930591A17Rik	-	RIKEN cDNA 4930591A17 gene	protein-coding	0.01	0.316832
Merged-chr12-84051585-1	chr12	84051535	84051635	+	2.1	cIP1vsInput	promoter-TSS (NM_134246)	promoter-TSS (NM_134246)	-566	NM_134246	171281	Mm.482217	NM_134246	ENSMUSG00000021228	Acot3	AW108394|PTE-Ia|Pte2a	acyl-CoA thioesterase 3	protein-coding	0.01	0.39604
Merged-chr14-108106694-1	chr14	108106644	108106744	+	2.1	cIP1vsInput	Intergenic	Intergenic	807545	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	"SLIT and NTRK-like family, member 1"	protein-coding	0.01	0.316832
Merged-chr12-98178541-1	chr12	98178491	98178591	+	2.1	cIP1vsInput	Intergenic	Intergenic	80796	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding	0	0.415842
Merged-chr3-53472501-1	chr3	53472451	53472551	+	2.1	cIP1vsInput	"intron (NM_173382, intron 6 of 12)"	MLT1F|LTR|ERVL-MaLR	8684	NM_173382	212127	Mm.218697	NM_173382	ENSMUSG00000049504	Proser1	2810046L04Rik|9330161F11	proline and serine rich 1	protein-coding	0.01	0.257426
Merged-chr11-92912899-1	chr11	92912849	92912949	+	2.1	cIP1vsInput	Intergenic	Intergenic	-186391	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding	0	0.316832
Merged-chr1-103899324-1	chr1	103899274	103899374	+	2.1	cIP1vsInput	Intergenic	Intergenic	-869495	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0.01	0.366337
Merged-chr6-130563701-2	chr6	130563641	130563761	+	2.1	cIP1vsInput|cIP2vsInput	Intergenic	B4|SINE|B4	-176827	NM_016659	16627	Mm.333431	NM_016659	ENSMUSG00000079853	Klra1	A1|Klra22|Ly49a|Ly49o<129>|Ly49v	"killer cell lectin-like receptor, subfamily A, member 1"	protein-coding	0	0.347107
Merged-chr10-72363282-1	chr10	72363232	72363332	+	2.1	cIP1vsInput	Intergenic	Intergenic	-291613	NM_025635	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding	0	0.356436
Merged-chr18-30927106-1	chr18	30927056	30927156	+	2.1	cIP2vsInput	Intergenic	Intergenic	390022	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding	0	0.316832
Merged-chr8-5513412-1	chr8	5513362	5513462	+	2.1	cIP2vsInput	Intergenic	Intergenic	-408180	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.336634
Merged-chr6-21877952-1	chr6	21877902	21878002	+	2.1	cIP1vsInput	Intergenic	MER53|DNA|hAT	-25437	NM_173007	269831	Mm.21950	NM_173007	ENSMUSG00000029669	Tspan12	9030619E17|AI426782|AI663988|AW111457|Tm4sf12	tetraspanin 12	protein-coding	0	0.316832
Merged-chr16-86554205-1	chr16	86554155	86554255	+	2.1	cIP2vsInput	Intergenic	Lx3_Mus|LINE|L1	-653080	NM_011782	23794	Mm.437478	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|AI481094|ASMP-2	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"	protein-coding	0.01	0.455446
Merged-chr16-58258992-1	chr16	58258942	58259042	+	2.1	cIP1vsInput	Intergenic	Intergenic	-149543	NM_028523	73379	Mm.373589	NM_028523	ENSMUSG00000035107	Dcbld2	1700055P21Rik|AW146002|CLCP1|Esdn	"discoidin, CUB and LCCL domain containing 2"	protein-coding	0.01	0.267327
Merged-chr4-62573498-1	chr4	62573448	62573548	+	2.1	cIP1vsInput	"intron (NM_019492, intron 2 of 19)"	L1M5|LINE|L1	13651	NM_019492	50780	Mm.286753	NM_001081650	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding	0.01	0.336634
Merged-chr17-22659115-1	chr17	22659065	22659165	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	57967	NM_001104575	628185	Mm.390947	NM_001104575	ENSMUSG00000094921	Vmn2r112	EG628185|V2rp1	"vomeronasal 2, receptor 112"	protein-coding	0.01	0.366337
Merged-chr8-7586524-1	chr8	7586474	7586574	+	2.1	cIP1vsInput	Intergenic	Intergenic	1074249	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding	0	0.29703
Merged-chr1-147838605-1	chr1	147838555	147838655	+	2.1	cIP2vsInput	Intergenic	Intergenic	1340918	NM_001145807	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.326733
Merged-chr17-91898454-1	chr17	91898404	91898504	+	2.1	cIP2vsInput	Intergenic	Intergenic	-805652	NM_020252	18189	Mm.312068	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0	0.316832
Merged-chr13-81242306-1	chr13	81242256	81242356	+	2.1	cIP1vsInput	"intron (NM_054053, intron 85 of 89)"	"intron (NM_054053, intron 85 of 89)"	278232	NR_015587	319983	Mm.343027	NR_015587	ENSMUSG00000097098	9330111N05Rik	-	RIKEN cDNA 9330111N05 gene	miscRNA	0.01	0.346535
Merged-chr4-38010845-1	chr4	38010795	38010895	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-1059101	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0	0.356436
Merged-chr17-60403868-1	chr17	60403818	60403918	+	2.1	cIP2vsInput	Intergenic	Intergenic	-913884	NR_030569	100124495		NR_030569		Mir466g	Mirn466g	microRNA 466g	miscRNA	0	0.29703
Merged-chr8-46305847-1	chr8	46305797	46305897	+	2.1	cIP2vsInput	Intergenic	Intergenic	-11176	NM_173789	234219	Mm.145631	NM_173789	ENSMUSG00000047171	Helt	A830086M02|Hesl|Mgn|megane	helt bHLH transcription factor	protein-coding	0.03	0.465347
Merged-chr1-44496221-1	chr1	44496171	44496271	+	2.1	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-55450	NM_028450	70676	Mm.133132	NM_027506	ENSMUSG00000056870	Gulp1	3110030A04Rik|5730529O06Rik|CED-6|Ced6|GULP|Gulp-2	"GULP, engulfment adaptor PTB domain containing 1"	protein-coding	0.01	0.366337
Merged-chr1-194152487-1	chr1	194152437	194152537	+	2.1	cIP2vsInput	Intergenic	Intergenic	70272	NR_040477	74942	Mm.60689	NR_040477		4930503O07Rik	-	RIKEN cDNA 4930503O07 gene	miscRNA	0	0.49505
Merged-chr2-170071563-1	chr2	170071513	170071613	+	2.1	cIP2vsInput	promoter-TSS (NR_033634)	promoter-TSS (NR_033634)	-785	NR_033632	100043910	Mm.468546	NR_033632	ENSMUSG00000097065	A630075F10Rik	4831414D02|Gm4722	RIKEN cDNA A630075F10 gene	miscRNA	0.01	0.405941
Merged-chr3-22679465-1	chr3	22679415	22679515	+	2.1	cIP1vsInput	Intergenic	Lx10|LINE|L1	428095	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	miscRNA	0	0.336634
Merged-chr15-5086379-1	chr15	5086329	5086429	+	2.1	cIP1vsInput	Intergenic	Intergenic	22154	NM_001163138	239319	Mm.31252	NM_001163138		Card6	D730008L15	"caspase recruitment domain family, member 6"	protein-coding	0.01	0.386139
Merged-chr1-147327355-1	chr1	147327305	147327405	+	2.1	cIP1vsInput	Intergenic	Intergenic	829668	NM_001145807	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.267327
Merged-chr8-82600547-1	chr8	82600497	82600597	+	2.1	cIP1vsInput	Intergenic	Intergenic	173579	NM_145600	30932	Mm.269248	NM_145600	ENSMUSG00000031711	Zfp330	BC008086|Noa36|Znf330	zinc finger protein 330	protein-coding	0	0.366337
Merged-chr1-172910151-1	chr1	172910101	172910201	+	2.1	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-15097	NM_011318	20219	Mm.330510	NM_011318	ENSMUSG00000026542	Apcs	Sap	serum amyloid P-component	protein-coding	0	0.287129
Merged-chr15-14508616-1	chr15	14508566	14508666	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1334977	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	K-cadherin|cad6|cadherin-6	cadherin 6	protein-coding	0.01	0.306931
Merged-chr2-98759109-1	chr2	98759059	98759159	+	2.1	cIP1vsInput	Intergenic	L1VL4|LINE|L1	1291435	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.366337
Merged-chr2-158864056-1	chr2	158864006	158864106	+	2.1	cIP1vsInput	Intergenic	Intergenic	69236	NM_145742	71715	Mm.315652	NM_145742	ENSMUSG00000027655	Dhx35	1200009D07Rik|Ddx35	DEAH (Asp-Glu-Ala-His) box polypeptide 35	protein-coding	0.03	0.594059
Merged-chr12-10160774-1	chr12	10160724	10160824	+	2.1	cIP2vsInput	Intergenic	Intergenic	-209197	NM_027588	70881	Mm.272843	NM_027588	ENSMUSG00000020622	Nt5c1b	4921514H13Rik|AIRP|CN-IB	"5'-nucleotidase, cytosolic IB"	protein-coding	0.01	0.287129
Merged-chr1-4332719-1	chr1	4332669	4332769	+	2.1	cIP2vsInput	"intron (NM_001195662, intron 3 of 3)"	"intron (NM_001195662, intron 3 of 3)"	27595	NM_011283	19888	Mm.294263	NM_001195662	ENSMUSG00000025900	Rp1	Dcdc3|Orp1|Rp1h|mG145	retinitis pigmentosa 1 (human)	protein-coding	0	0.346535
Merged-chr10-58604039-1	chr10	58603989	58604089	+	2.1	cIP1vsInput	"intron (NM_010100, intron 11 of 11)"	L1MD1|LINE|L1	71657	NM_010100	13608	Mm.174523	NM_010100	ENSMUSG00000003227	Edar	ED1R|ED3|ED5|EDA-A1R|EDA3|dl	ectodysplasin-A receptor	protein-coding	0	0.405941
Merged-chr3-125804355-1	chr3	125804305	125804405	+	2.1	cIP1vsInput	Intergenic	Intergenic	134195	NM_011674	22239	Mm.306021	NM_011674	ENSMUSG00000032854	Ugt8a	AI850488|AW455908|Cgt|Ugt8|mCerGT	UDP galactosyltransferase 8A	protein-coding	0.01	0.366337
Merged-chr8-73432570-1	chr8	73432520	73432620	+	2.1	cIP1vsInput	Intergenic	Intergenic	-80014	NM_010687	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large	BPFD#36|Gyltl1a|Mbp-1|Mbp1|enr|fg|froggy|mKIAA0609|myd	like-glycosyltransferase	protein-coding	0	0.287129
Merged-chr13-82558926-1	chr13	82558876	82558976	+	2.1	cIP1vsInput	Intergenic	Intergenic	775634	NM_007684	12626	Mm.12481	NM_007684	ENSMUSG00000021537	Cetn3	MmCEN3	centrin 3	protein-coding	0	0.247525
Merged-chrX-64698785-1	chrX	64698735	64698835	+	2.1	cIP2vsInput	Intergenic	MIR|SINE|MIR	-348859	NM_027302	70062	Mm.45791	NM_027302	ENSMUSG00000031181	Ctag2	1700030B21Rik	cancer/testis antigen 2	protein-coding	0	0.306931
Merged-chr14-12224420-1	chr14	12224370	12224470	+	2.1	cIP2vsInput	"intron (NM_008981, intron 26 of 29)"	"intron (NM_008981, intron 26 of 29)"	-59789	NM_146051	218734	Mm.44068	NM_146051	ENSMUSG00000033111	3830406C13Rik	3110059I09Rik|AV167947	RIKEN cDNA 3830406C13 gene	protein-coding	0	0.326733
Merged-chr9-26919676-1	chr9	26919626	26919726	+	2.1	cIP1vsInput	"intron (NM_001177509, intron 3 of 20)"	"intron (NM_001177509, intron 3 of 20)"	3405	NM_001177509	382064	Mm.335028	NM_001177509	ENSMUSG00000079644	Gm1110	-	predicted gene 1110	protein-coding	0	0.287129
Merged-chr13-42814788-1	chr13	42814738	42814838	+	2.1	cIP1vsInput	"intron (NM_001005740, intron 1 of 12)"	B4A|SINE|B4	105207	NM_001005740	218194	Mm.160124	NM_001005740	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding	0.01	0.50495
Merged-chr14-99820849-1	chr14	99820799	99820899	+	2.1	cIP1vsInput	Intergenic	Intergenic	328947	NM_010636	16597	Mm.458816	NM_010636		Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding	0	0.445545
Merged-chr6-97496466-1	chr6	97496416	97496516	+	2.1	cIP2vsInput	"intron (NM_145148, intron 2 of 23)"	MIRc|SINE|MIR	121191	NM_145148	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720|mKIAA1013	FERM domain containing 4B	protein-coding	0	0.376238
Merged-chr6-85663495-1	chr6	85663445	85663545	+	2.1	cIP2vsInput	"intron (NM_145223, intron 14 of 22)"	L1_Mur2|LINE|L1	45066	NM_001253910	100043497	Mm.440772	NM_001253910	ENSMUSG00000089694	Gm4477	-	predicted gene 4477	protein-coding	0	0.336634
Merged-chr5-42864915-1	chr5	42864865	42864965	+	2.1	cIP2vsInput	Intergenic	Intergenic	-368548	NM_175937	231207	Mm.7233	NM_001177379	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding	0.02	0.356436
Merged-chr12-116187140-1	chr12	116187090	116187190	+	2.1	cIP1vsInput	Intergenic	Lx6|LINE|L1	75885	NM_146039	217935	Mm.31382	NM_146039	ENSMUSG00000042050	Wdr60	D430033N04Rik	WD repeat domain 60	protein-coding	0.01	0.356436
Merged-chr7-95466864-1	chr7	95466814	95466914	+	2.1	cIP1vsInput	Intergenic	Intergenic	-743773	NM_011858	23966	Mm.391678	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding	0.02	0.366337
Merged-chr13-106044391-1	chr13	106044341	106044441	+	2.1	cIP1vsInput	Intergenic	L1MC1|LINE|L1	600698	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0	0.316832
Merged-chr4-26950670-1	chr4	26950620	26950720	+	2.1	cIP2vsInput	Intergenic	HAL1|LINE|L1	-245221	NR_040656	75360	Mm.67233	NR_040656	ENSMUSG00000086257	4930548K13Rik	-	RIKEN cDNA 4930548K13 gene	miscRNA	0	0.326733
Merged-chr9-27198591-1	chr9	27198541	27198641	+	2.1	cIP2vsInput	Intergenic	Intergenic	-43170	NM_023277	83964	Mm.28770	NM_023277	ENSMUSG00000031990	Jam3	1110002N23Rik|JAM-3|JAM-C|Jcam3	junction adhesion molecule 3	protein-coding	0	0.247525
Merged-chr2-177272059-1	chr2	177272009	177272109	+	2.1	cIP1vsInput	Intergenic	Intergenic	-192683	NM_001177568	628308	Mm.460436	NM_001177568		Gm14420	OTTMUSG00000016588	predicted gene 14420	protein-coding	0	0.475248
Merged-chr9-62449621-1	chr9	62449571	62449671	+	2.1	cIP2vsInput	"intron (NM_175484, intron 3 of 11)"	RLTR21|LTR|ERVK	87423	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	"coronin, actin binding protein, 2B"	protein-coding	0.01	0.316832
Merged-chr12-16282549-1	chr12	16282499	16282599	+	2.1	cIP2vsInput	Intergenic	L1M4|LINE|L1	307221	NM_015763	14245	Mm.153625	NM_001130412	ENSMUSG00000020593	Lpin1	4631420P06|Kiaa0188|Lipin1|fld|mKIAA0188	lipin 1	protein-coding	0	0.376238
Merged-chr7-44798281-1	chr7	44798231	44798331	+	2.1	cIP2vsInput	Intergenic	ETnERV3-int|LTR|ERVK	17377	NM_030693	107503	Mm.389890	NM_030693	ENSMUSG00000038539	Atf5	AFTA|Atf7|Atfx|ODA-10	activating transcription factor 5	protein-coding	0	0.336634
Merged-chrX-7574070-2	chrX	7573975	7574165	+	2.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_138605)	promoter-TSS (NM_138605)	50	NM_138605	54646	Mm.148163	NM_138605	ENSMUSG00000039556	Ppp1r3f	DXImx48e|R3F|RF3|Sfc15	"protein phosphatase 1, regulatory (inhibitor) subunit 3F"	protein-coding	0.121053	0.748691
Merged-chr4-154200628-1	chr4	154200578	154200678	+	2.1	cIP2vsInput	"intron (NM_001162977, intron 3 of 36)"	"intron (NM_001162977, intron 3 of 36)"	29915	NM_001162977	230971	Mm.275216	NM_172273	ENSMUSG00000057751	Megf6	2600001P17Rik|Egfl3	multiple EGF-like-domains 6	protein-coding	0.02	0.594059
Merged-chr1-70050400-1	chr1	70050350	70050450	+	2.1	cIP2vsInput	"intron (NM_025728, intron 2 of 7)"	"intron (NM_025728, intron 2 of 7)"	98785	NM_025728	66722	Mm.440554	NM_001271533	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding	0	0.326733
Merged-chr1-140778862-1	chr1	140778812	140778912	+	2.1	cIP2vsInput	Intergenic	Intergenic	-122460	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0.01	0.306931
Merged-chr16-54748143-1	chr16	54748093	54748193	+	2.1	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	535094	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding	0	0.316832
Merged-chr18-55843841-1	chr18	55843791	55843891	+	2.1	cIP2vsInput	Intergenic	Intergenic	-588291	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding	0	0.356436
Merged-chr14-108618702-1	chr14	108618652	108618752	+	2.1	cIP1vsInput	Intergenic	Intergenic	295537	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	"SLIT and NTRK-like family, member 1"	protein-coding	0	0.326733
Merged-chr11-18462663-1	chr11	18462613	18462713	+	2.1	cIP1vsInput	Intergenic	ORR1A3-int|LTR|ERVL-MaLR	-508788	NM_026576	68145	Mm.178684	NM_026576	ENSMUSG00000016984	Etaa1	5730466H23Rik|AA672646	Ewing's tumor-associated antigen 1	protein-coding	0	0.366337
Merged-chr6-49632660-1	chr6	49632610	49632710	+	2.1	cIP1vsInput	Intergenic	Intergenic	-190069	NM_023456	109648	Mm.154796	NM_023456	ENSMUSG00000029819	Npy	0710005A05Rik	neuropeptide Y	protein-coding	0	0.336634
Merged-chr5-130324137-1	chr5	130324087	130324187	+	2.1	cIP1vsInput	"intron (NM_001015876, intron 13 of 15)"	"intron (NM_001015876, intron 13 of 15)"	-45321	NM_181045	140904	Mm.320206	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8	calneuron 1	protein-coding	0.02	0.29703
Merged-chr19-50095231-1	chr19	50095181	50095281	+	2.1	cIP1vsInput	Intergenic	MER126|DNA|DNA	583415	NM_001252501	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0.01	0.257426
Merged-chr12-45181770-1	chr12	45181720	45181820	+	2.1	cIP2vsInput	Intergenic	Intergenic	-107287	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding	0	0.39604
Merged-chr2-10958585-1	chr2	10958535	10958635	+	2.1	cIP1vsInput	Intergenic	Intergenic	-213797	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	"protein kinase C, theta"	protein-coding	0	0.316832
Merged-chr3-157115508-1	chr3	157115458	157115558	+	2.1	cIP2vsInput	"intron (NM_001039094, intron 4 of 6)"	"intron (NM_001039094, intron 4 of 6)"	-418889	NM_017381	53861	Mm.259036	NM_017381	ENSMUSG00000028180	Zranb2	AI227013|Zfp265|Zis|Znf265	"zinc finger, RAN-binding domain containing 2"	protein-coding	0.01	0.485149
Merged-chr19-61010650-1	chr19	61010600	61010700	+	2.1	cIP1vsInput	"intron (NM_018869, intron 2 of 15)"	"intron (NM_018869, intron 2 of 15)"	120901	NM_018869	14773	Mm.279400	NM_018869	ENSMUSG00000003228	Grk5	Gprk5	G protein-coupled receptor kinase 5	protein-coding	0	0.366337
Merged-chr8-88804666-1	chr8	88804616	88804716	+	2.1	cIP2vsInput	Intergenic	Intergenic	107638	NM_001128171	74256	Mm.490395	NM_001128170	ENSMUSG00000036712	Cyld	2010013M14Rik|2900009M21Rik|C130039D01Rik|CDMT|CYLD1|EAC|mKIAA0849	cylindromatosis (turban tumor syndrome)	protein-coding	0	0.316832
Merged-chr2-136964315-1	chr2	136964265	136964365	+	2.1	cIP1vsInput	"intron (NM_001038641, intron 2 of 7)"	L1M2a|LINE|L1	64964	NM_001038641	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding	0	0.316832
Merged-chr3-15553949-1	chr3	15553899	15553999	+	2.1	cIP1vsInput	"intron (NM_001173460, intron 1 of 5)"	L1_Mur2|LINE|L1	21116	NM_001173460	668101	Mm.423523	NM_001173460	ENSMUSG00000095028	Sirpb1b	-	signal-regulatory protein beta 1B	protein-coding	0	0.316832
Merged-chr7-83592033-1	chr7	83591983	83592083	+	2.1	cIP2vsInput	"intron (NM_177695, intron 3 of 22)"	"intron (NM_177695, intron 3 of 22)"	7102	NM_177695	233424	Mm.486619	NM_177695		Tmc3	9030203A06	transmembrane channel-like gene family 3	protein-coding	0	0.39604
Merged-chr7-127615400-1	chr7	127615350	127615450	+	2.1	cIP1vsInput	promoter-TSS (NM_177226)	promoter-TSS (NM_177226)	-967	NM_177226	320683	Mm.490212	NM_177226	ENSMUSG00000045639	Zfp629	9330199A09Rik|Znf629	zinc finger protein 629	protein-coding	0.03	0.594059
Merged-chr2-40243289-1	chr2	40243239	40243339	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1016951	NM_024209	67857	Mm.392662	NM_024209		Ppp6c	2310003C10Rik	"protein phosphatase 6, catalytic subunit"	protein-coding	0.01	0.336634
Merged-chr3-43765373-1	chr3	43765323	43765423	+	2.1	cIP1vsInput	Intergenic	L1_Mur1|LINE|L1	1612887	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	miscRNA	0	0.366337
Merged-chr8-51705017-1	chr8	51704967	51705067	+	2.1	cIP2vsInput	Intergenic	Intergenic	1336905	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.366337
Merged-chr6-92113469-1	chr6	92113419	92113519	+	2.1	cIP1vsInput	"intron (NM_011630, intron 1 of 14)"	"intron (NM_011630, intron 1 of 14)"	22051	NM_011630	22026	Mm.442385	NM_011630	ENSMUSG00000005893	Nr2c2	TAK1|Tr4|mKIAA4145	"nuclear receptor subfamily 2, group C, member 2"	protein-coding	0.02	0.405941
Merged-chr10-80602796-1	chr10	80602746	80602846	+	2.1	cIP1vsInput	promoter-TSS (NM_019575)	promoter-TSS (NM_019575)	-84	NM_001100606	100113398	Mm.273170	NM_001100606	ENSMUSG00000035370	Adat3	A430024H01Rik	"adenosine deaminase, tRNA-specific 3"	protein-coding	0.07	0.574257
Merged-chr11-53917293-1	chr11	53917243	53917343	+	2.1	cIP1vsInput	Intergenic	Intergenic	-25590	NM_011396	20520	Mm.42253	NM_011396	ENSMUSG00000018900	Slc22a5	Lstpl|Octn2|jvs	"solute carrier family 22 (organic cation transporter), member 5"	protein-coding	0.01	0.386139
Merged-chr19-44582808-1	chr19	44582758	44582858	+	2.1	cIP2vsInput	Intergenic	Intergenic	19954	NM_176958	319594	Mm.145278	NM_176958	ENSMUSG00000036450	Hif1an	2310046M24Rik|A830014H24Rik|FIH1	"hypoxia-inducible factor 1, alpha subunit inhibitor"	protein-coding	0.03	0.643564
Merged-chr13-88381045-1	chr13	88380995	88381095	+	2.1	cIP2vsInput	Intergenic	Intergenic	-440427	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0	0.366337
Merged-chr5-145683591-1	chr5	145683541	145683641	+	2.1	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	36545	NM_017396	53973	Mm.379071	XM_003946424	ENSMUSG00000075551	Cyp3a41a	Cyp3a41	"cytochrome P450, family 3, subfamily a, polypeptide 41A"	protein-coding	0.01	0.326733
Merged-chr18-65645994-1	chr18	65645944	65646044	+	2.1	cIP2vsInput	"intron (NM_207255, intron 3 of 5)"	"intron (NM_207255, intron 3 of 5)"	-52274	NM_177028	319888	Mm.183576	NM_177028	ENSMUSG00000046610	Oacyl	5330437I02Rik|Acyl3	O-acyltransferase like	protein-coding	0	0.336634
Merged-chr13-86791623-1	chr13	86791573	86791673	+	2.1	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-744828	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0.02	0.386139
Merged-chr11-10153639-1	chr11	10153589	10153689	+	2.1	cIP1vsInput	Intergenic	Intergenic	-960377	NM_177033	319922	Mm.487612	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding	0	0.336634
Merged-chr2-8917947-1	chr2	8917897	8917997	+	2.1	cIP1vsInput	Intergenic	Lx8b|LINE|L1	-271568	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	miscRNA	0.01	0.405941
Merged-chr1-101260052-1	chr1	101260002	101260102	+	2.1	cIP2vsInput	Intergenic	Intergenic	104284	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.366337
Merged-chr14-20947684-1	chr14	20947634	20947734	+	2.1	cIP1vsInput	"intron (NM_009502, intron 1 of 20)"	"intron (NM_009502, intron 1 of 20)"	18251	NM_009502	22330	Mm.279361	NM_009502	ENSMUSG00000021823	Vcl	9430097D22|AA571387|AI462105|AW545629	vinculin	protein-coding	0.01	0.346535
Merged-chr1-24417314-1	chr1	24417264	24417364	+	2.1	cIP2vsInput	"intron (NM_007733, intron 14 of 50)"	"intron (NM_007733, intron 14 of 50)"	170123	NM_007733	12823	Mm.329196	NM_007733		Col19a1	-	"collagen, type XIX, alpha 1"	protein-coding	0	0.336634
Merged-chr1-51258265-1	chr1	51258215	51258315	+	2.1	cIP1vsInput	"intron (NR_045151, intron 3 of 4)"	"intron (NR_045151, intron 3 of 4)"	-30861	NM_138741	20324	Mm.398690	NM_138741	ENSMUSG00000045954	Sdpr	-	serum deprivation response	protein-coding	0.01	0.366337
Merged-chrX-104302712-1	chrX	104302662	104302762	+	2.1	cIP1vsInput	"intron (NM_009592, intron 8 of 15)"	"intron (NM_009592, intron 8 of 15)"	-101595	NM_001077354	245555	Mm.381907	NM_001077354	ENSMUSG00000046449	C77370	A230051P11|C77386|Kiaa2022|Xpn|mKIAA2022	expressed sequence C77370	protein-coding	0	0.29703
Merged-chr1-47063221-1	chr1	47063171	47063271	+	2.1	cIP1vsInput	Intergenic	Lx2B|LINE|L1	-209712	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0.01	0.376238
Merged-chr7-24783332-1	chr7	24783282	24783382	+	2.1	cIP2vsInput	"intron (NM_007675, intron 3 of 3)"	"intron (NM_007675, intron 3 of 3)"	6128	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding	0	0.356436
Merged-chr15-55984882-1	chr15	55984832	55984932	+	2.1	cIP1vsInput	Intergenic	Intergenic	-77933	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	"syntrophin, basic 1"	protein-coding	0.01	0.336634
Merged-chr5-57001187-1	chr5	57001137	57001237	+	2.1	cIP1vsInput	Intergenic	Intergenic	716732	NR_015588	319216	Mm.446765	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	miscRNA	0	0.287129
Merged-chr1-93235799-1	chr1	93235749	93235849	+	2.1	cIP2vsInput	promoter-TSS (NM_172463)	promoter-TSS (NM_172463)	-98	NM_172463	208777	Mm.271897	NM_172463		Sned1	6720455I24Rik|AI197264|AI642697|D430044C15Rik|SST3|Snep	"sushi, nidogen and EGF-like domains 1"	protein-coding	0.09	0.683168
Merged-chr1-14337945-1	chr1	14337895	14337995	+	2.1	cIP2vsInput	Intergenic	MIR|SINE|MIR	-27746	NM_010164	14048	Mm.250185	NM_001252192	ENSMUSG00000025932	Eya1	bor	eyes absent 1 homolog (Drosophila)	protein-coding	0	0.287129
Merged-chr13-60070758-1	chr13	60070708	60070808	+	2.1	cIP2vsInput	"intron (NR_046142, intron 1 of 2)"	PB1D10|SINE|Alu	41047	NR_046142	328263	Mm.123405	NR_046142		A530065N20Rik	A530065N20	RIKEN cDNA A530046M15 gene	miscRNA	0.02	0.465347
Merged-chr2-88445341-1	chr2	88445291	88445391	+	2.1	cIP1vsInput	TTS (NM_001011535)	TTS (NM_001011535)	3780	NM_001011535	258167	Mm.223246	NM_001011535	ENSMUSG00000075124	Olfr1182	MOR225-7P|MOR225-8P|Olfr1536-ps1	olfactory receptor 1182	protein-coding	0	0.287129
Merged-chr15-72281377-1	chr15	72281327	72281427	+	2.1	cIP1vsInput	Intergenic	Lx5|LINE|L1	-247150	NM_027174	69700	Mm.322500	NM_027174		Col22a1	2310067L16Rik|C80743	"collagen, type XXII, alpha 1"	protein-coding	0	0.29703
Merged-chr2-15435765-1	chr2	15435715	15435815	+	2.1	cIP1vsInput	Intergenic	Intergenic	380403	NM_029466	75869	Mm.174068	NM_029466		Arl5b	4930587A11Rik|AW146430|Arl8	ADP-ribosylation factor-like 5B	protein-coding	0	0.277228
Merged-chr4-23362001-1	chr4	23361951	23362051	+	2.1	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-873635	NM_008899	18992	Mm.487875	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	"POU domain, class 3, transcription factor 2"	protein-coding	0	0.277228
Merged-chr2-133264055-1	chr2	133264005	133264105	+	2.1	cIP1vsInput	Intergenic	L1MA5A|LINE|L1	-288104	NM_007553	12156	Mm.103205	NM_007553		Bmp2	AI467020|Bmp2a	bone morphogenetic protein 2	protein-coding	0	0.376238
Merged-chr7-62069129-1	chr7	62069079	62069179	+	2.1	cIP2vsInput	Intergenic	Intergenic	-22881	NR_037288	100526527		NR_037288	ENSMUSG00000093108	Mir344f	mmu-mir-344f	microRNA Mir344f	miscRNA	0	0.336634
Merged-chr14-92958133-1	chr14	92958083	92958183	+	2.1	cIP1vsInput	Intergenic	Intergenic	930755	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.336634
Merged-chr4-48785079-1	chr4	48785029	48785129	+	2.1	cIP1vsInput	Intergenic	Intergenic	121565	NM_026509	68016	Mm.133444	NM_026509	ENSMUSG00000028348	Murc	2310039E09Rik	muscle-related coiled-coil protein	protein-coding	0	0.316832
Merged-chr7-99282913-1	chr7	99282863	99282963	+	2.1	cIP1vsInput	"intron (NM_001048167, intron 1 of 2)"	"intron (NM_001048167, intron 1 of 2)"	14567	NM_001043355	17760	Mm.154087	NM_001043355	ENSMUSG00000055407	Map6	2810411E12Rik|Map-6|Mtap6|STOP	microtubule-associated protein 6	protein-coding	0.03	0.415842
Merged-chr15-51486621-1	chr15	51486571	51486671	+	2.1	cIP1vsInput	Intergenic	Intergenic	-91011	NR_045092	100502643	Mm.131987	NR_045092		Gm19303	-	"predicted gene, 19303"	miscRNA	0	0.336634
Merged-chr18-28170075-1	chr18	28170025	28170125	+	2.1	cIP1vsInput	Intergenic	MYSERV-int|LTR|ERVK	-390089	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	miscRNA	0	0.39604
Merged-chr17-70179028-1	chr17	70178978	70179078	+	2.1	cIP1vsInput	Intergenic	Intergenic	-245764	NM_177639	224997	Mm.367369	NM_001128180	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	"discs, large (Drosophila) homolog-associated protein 1"	protein-coding	0	0.326733
Merged-chr16-69357627-1	chr16	69357577	69357677	+	2.1	cIP2vsInput	Intergenic	L1VL2|LINE|L1	506117	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding	0	0.277228
Merged-chr14-93799552-1	chr14	93799502	93799602	+	2.1	cIP2vsInput	"intron (NM_001081377, intron 1 of 3)"	"intron (NM_001081377, intron 1 of 3)"	89336	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.326733
Merged-chr17-50084388-1	chr17	50084338	50084438	+	2.1	cIP1vsInput	"intron (NM_181397, intron 4 of 9)"	"intron (NM_181397, intron 4 of 9)"	106109	NM_181397	76438	Mm.41854	NM_181397		Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding	0.01	0.336634
Merged-chr15-42205124-1	chr15	42205074	42205174	+	2.1	cIP1vsInput	Intergenic	Intergenic	-335404	NM_175456	223513	Mm.148913	NM_175456	ENSMUSG00000042895	Abra	C130068O12Rik|STARS	actin-binding Rho activating protein	protein-coding	0	0.316832
Merged-chr1-61277649-1	chr1	61277599	61277699	+	2.1	cIP1vsInput	Intergenic	Intergenic	-100783	NR_040483	77341	Mm.402964	NR_040483	ENSMUSG00000085447	9530026F06Rik	-	RIKEN cDNA 9530026F06 gene	miscRNA	0.01	0.306931
Merged-chr18-26774515-1	chr18	26774465	26774565	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1020532	NM_001174074	108013	Mm.266435	NM_001146292	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	"CUGBP, Elav-like family member 4"	protein-coding	0	0.29703
Merged-chr3-133969916-1	chr3	133969866	133969966	+	2.1	cIP1vsInput	Intergenic	Intergenic	-266579	NM_001004367	319478	Mm.487501	NM_001004367	ENSMUSG00000044365	Cxxc4	9330210J02Rik|C030003J12Rik|Idax	CXXC finger 4	protein-coding	0	0.277228
Merged-chr6-102200300-1	chr6	102200250	102200350	+	2.1	cIP2vsInput	"intron (NM_008779, intron 17 of 21)"	"intron (NM_008779, intron 17 of 21)"	264367	NM_008779	18488	Mm.435479	NM_008779	ENSMUSG00000030075	Cntn3	Pang	contactin 3	protein-coding	0.01	0.336634
Merged-chr11-87843008-1	chr11	87842958	87843058	+	2.1	cIP1vsInput	Intergenic	RLTR13C3|LTR|ERVK	-10217	NM_001039684	380718	Mm.24404	NM_001039684	ENSMUSG00000034121	Mks1	AK190930|B8d3	"Meckel syndrome, type 1"	protein-coding	0.01	0.39604
Merged-chr18-22821237-1	chr18	22821187	22821287	+	2.1	cIP2vsInput	"intron (NM_199024, intron 6 of 9)"	"intron (NM_199024, intron 6 of 9)"	217426	NM_001161483	319211	Mm.209896	NM_001161483	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding	0	0.356436
Merged-chr4-6495306-1	chr4	6495256	6495356	+	2.1	cIP1vsInput	Intergenic	RMER3D-int|LTR|ERVK	-41035	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding	0.04	0.445545
Merged-chr1-31611059-1	chr1	31611009	31611109	+	2.1	cIP1vsInput	Intergenic	Intergenic	346212	NR_015347	226957	Mm.25966	NR_015347		Gm4850	EG226957	THO complex 4 pseudogene	pseudo	0.01	0.277228
Merged-chr3-82288769-2	chr3	82288701	82288837	+	2.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-69303	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding	0.007353	0.335766
Merged-chr7-123691150-1	chr7	123691100	123691200	+	2.1	cIP2vsInput	Intergenic	MIR|SINE|MIR	-190701	NM_001081329	210162	Mm.135397	NM_001081329	ENSMUSG00000030757	Zkscan2	9430065N20Rik|AW493225|Zfp694	zinc finger with KRAB and SCAN domains 2	protein-coding	0	0.366337
Merged-chr5-70500421-1	chr5	70500371	70500471	+	2.1	cIP1vsInput	Intergenic	Intergenic	342196	NM_010252	14405	Mm.255292	NM_010252	ENSMUSG00000001260	Gabrg1	GabaA|GabaA/BZ	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1"	protein-coding	0	0.29703
Merged-chr3-157604702-1	chr3	157604652	157604752	+	2.1	cIP2vsInput	"intron (NM_011196, intron 1 of 2)"	"intron (NM_011196, intron 1 of 2)"	37810	NM_011196	19218	Mm.30424	NM_011196	ENSMUSG00000040016	Ptger3	EP3|Pgerep3|Ptgerep3	prostaglandin E receptor 3 (subtype EP3)	protein-coding	0	0.39604
Merged-chr13-69209882-1	chr13	69209832	69209932	+	2.1	cIP1vsInput	Intergenic	Intergenic	-210341	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding	0	0.405941
Merged-chr11-107639684-1	chr11	107639634	107639734	+	2.1	cIP1vsInput	"intron (NM_198298, intron 20 of 31)"	Lx9|LINE|L1	76792	NM_007582	12299	Mm.57093	NM_007582	ENSMUSG00000020722	Cacng1	-	"calcium channel, voltage-dependent, gamma subunit 1"	protein-coding	0	0.366337
Merged-chr2-54752415-1	chr2	54752365	54752465	+	2.1	cIP1vsInput	"intron (NM_173030, intron 4 of 12)"	Lx9|LINE|L1	316028	NM_173030	271786	Mm.330227	NM_173030	ENSMUSG00000060988	Galnt13	A230002A12|A230020F20|BB182356	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13	protein-coding	0	0.366337
Merged-chr9-93849313-1	chr9	93849263	93849363	+	2.1	cIP1vsInput	Intergenic	L1MC4a|LINE|L1	688768	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49	RIKEN cDNA 1190002N15 gene	protein-coding	0.01	0.29703
Merged-chr7-41488103-1	chr7	41488053	41488153	+	2.1	cIP1vsInput	"intron (NM_001033530, intron 1 of 3)"	L1_Mur2|LINE|L1	11787	NM_001033530	101835	Mm.370336	NM_001033530	ENSMUSG00000074166	AW146154	AI451288	expressed sequence AW146154	protein-coding	0	0.306931
Merged-chr15-29173065-1	chr15	29173015	29173115	+	2.1	cIP1vsInput	Intergenic	Lx7|LINE|L1	969299	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnahc5	AU022615|Dnah5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	"dynein, axonemal, heavy chain 5"	protein-coding	0	0.336634
Merged-chr12-55856929-1	chr12	55856879	55856979	+	2.1	cIP1vsInput	"intron (NM_001037756, intron 4 of 9)"	RLTR13D3|LTR|ERVK	20563	NM_001037756	52592	Mm.24761	NM_001037756	ENSMUSG00000012076	Brms1l	0710008O11Rik|AI159718|BRMS1|D12Ertd407e	breast cancer metastasis-suppressor 1-like	protein-coding	0	0.445545
Merged-chr18-20170481-1	chr18	20170431	20170531	+	2.1	cIP1vsInput	Intergenic	L1_Mus4|LINE|L1	-55708	NM_013504	13505	Mm.33740	NM_013504	ENSMUSG00000044322	Dsc1	Dsc1a|Dsc1b	desmocollin 1	protein-coding	0	0.346535
Merged-chr7-62216790-1	chr7	62216740	62216840	+	2.1	cIP2vsInput	Intergenic	Intergenic	-131487	NM_010882	17984	Mm.400253	NM_010882	ENSMUSG00000033585	Ndn	AI528698|Peg6	necdin	protein-coding	0	0.287129
Merged-chr8-49118890-1	chr8	49118840	49118940	+	2.1	cIP2vsInput	Intergenic	L1M2|LINE|L1	-444200	NM_011857	23965	Mm.42191	NM_001145937	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding	0	0.306931
Merged-chr12-97556431-1	chr12	97556381	97556481	+	2.1	cIP1vsInput	Intergenic	Intergenic	702906	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding	0	0.39604
Merged-chr14-48382588-1	chr14	48382538	48382638	+	2.1	cIP1vsInput	Intergenic	Intergenic	-63764	NM_172600	218989	Mm.85211	NM_172600	ENSMUSG00000036339	Tmem260	5930435P15|6720456H20Rik	transmembrane protein 260	protein-coding	0.01	0.336634
Merged-chr2-111381093-1	chr2	111381043	111381143	+	2.1	cIP1vsInput	Intergenic	L1MA4|LINE|L1	2091	NM_146381	258379	Mm.377467	NM_146381	ENSMUSG00000050781	Olfr1284	MOR245-13	olfactory receptor 1284	protein-coding	0.01	0.306931
Merged-chr17-54738907-1	chr17	54738857	54738957	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-368833	NR_045825	69418	Mm.391004	NR_045825		1700025K24Rik	-	RIKEN cDNA 1700025K24 gene	miscRNA	0	0.366337
Merged-chr10-83226100-1	chr10	83226050	83226150	+	2.1	cIP1vsInput	Intergenic	Intergenic	111717	NM_177388	338365	Mm.67073	NM_177388	ENSMUSG00000034591	Slc41a2	A230035L05Rik|SLC41A1-L1	"solute carrier family 41, member 2"	protein-coding	0.02	0.425743
Merged-chr19-42936308-1	chr19	42936258	42936358	+	2.1	cIP1vsInput	"intron (NM_001081257, intron 6 of 11)"	"intron (NM_001081257, intron 6 of 11)"	-156332	NM_019424	192236	Mm.218381	NM_019424	ENSMUSG00000025188	Hps1	6030422N11Rik|BB405864|Hps|ep	Hermansky-Pudlak syndrome 1 homolog (human)	protein-coding	0	0.287129
Merged-chr4-39261151-1	chr4	39261101	39261201	+	2.1	cIP1vsInput	Intergenic	MTEa|LTR|ERVL-MaLR	-189142	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding	0	0.29703
Merged-chr6-50230508-1	chr6	50230458	50230558	+	2.1	cIP1vsInput	"intron (NM_018769, intron 3 of 9)"	L1MB3|LINE|L1	31261	NM_018769	54722	Mm.248361	NM_018769	ENSMUSG00000029821	Dfna5	2310037D07Rik|4932441K13Rik|Dfna5h|EG14210|Fin15	"deafness, autosomal dominant 5 (human)"	protein-coding	0	0.316832
Merged-chr8-51464783-1	chr8	51464733	51464833	+	2.1	cIP2vsInput	Intergenic	Intergenic	1096671	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.287129
Merged-chr9-13112818-1	chr9	13112768	13112868	+	2.1	cIP1vsInput	Intergenic	L1M5|LINE|L1	-6963	NR_040755	78219	Mm.414868	NR_040755		4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	miscRNA	0	0.287129
Merged-chr16-88592060-1	chr16	88592010	88592110	+	2.1	cIP2vsInput	Intergenic	Intergenic	20219	NM_001163141	239932	Mm.120273	NM_001163141	ENSMUSG00000050239	Krtap24-1	Gm312	keratin associated protein 24-1	protein-coding	0	0.29703
Merged-chr14-73930265-1	chr14	73930215	73930315	+	2.1	cIP1vsInput	Intergenic	Lx5c|LINE|L1	377479	NM_011506	20916	Mm.38951	NM_011506	ENSMUSG00000022110	Sucla2	4930547K18Rik	"succinate-Coenzyme A ligase, ADP-forming, beta subunit"	protein-coding	0	0.267327
Merged-chr3-86328693-1	chr3	86328643	86328743	+	2.1	cIP1vsInput	"intron (NM_001077687, intron 22 of 50)"	"intron (NM_001077687, intron 22 of 50)"	104003	NM_001077687	80877	Mm.439825	NM_001077687	ENSMUSG00000028080	Lrba	C80285|D3Ertd775e|Lab300|Lba	LPS-responsive beige-like anchor	protein-coding	0.01	0.326733
Merged-chr4-26033211-1	chr4	26033161	26033261	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-233208	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding	0.01	0.316832
Merged-chr9-24600683-1	chr9	24600633	24600733	+	2.1	cIP1vsInput	"intron (NM_001166207, intron 16 of 21)"	L1_Mur2|LINE|L1	-24502	NM_173412	235067	Mm.437189	NM_173412	ENSMUSG00000047995	Cypt4	1700009B20Rik|Ckt1r2	cysteine-rich perinuclear theca 4	protein-coding	0	0.306931
Merged-chr13-71255908-1	chr13	71255858	71255958	+	2.1	cIP2vsInput	Intergenic	Intergenic	372960	NM_029873	77166	Mm.159859	NM_029873	ENSMUSG00000021600	8030423J24Rik	-	RIKEN cDNA 8030423J24 gene	protein-coding	0	0.316832
Merged-chr11-25112815-1	chr11	25112765	25112865	+	2.1	cIP2vsInput	Intergenic	Intergenic	-213292	NR_045853	71234	Mm.158627	NR_045853	ENSMUSG00000033015	4933427E13Rik	-	RIKEN cDNA 4933427E13 gene	miscRNA	0	0.316832
Merged-chr5-92475174-1	chr5	92475124	92475224	+	2.1	cIP1vsInput	"intron (NM_007644, intron 2 of 11)"	"intron (NM_007644, intron 2 of 11)"	30434	NM_007644	12492	Mm.297964	NM_007644	ENSMUSG00000029426	Scarb2	9330185J12Rik|Cd36l2|LGP85|LIMP-2|MLGP85	"scavenger receptor class B, member 2"	protein-coding	0	0.405941
Merged-chr5-26778081-1	chr5	26778031	26778131	+	2.1	cIP2vsInput	Intergenic	Lx8|LINE|L1	-39276	NM_010075	13483	Mm.42078	NM_001136060	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding	0	0.425743
Merged-chr16-73797228-1	chr16	73797178	73797278	+	2.1	cIP1vsInput	Intergenic	Intergenic	544839	NR_030464	751561		NR_030464		Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	miscRNA	0	0.316832
Merged-chr13-77010991-1	chr13	77010941	77011041	+	2.1	cIP1vsInput	"intron (NM_030174, intron 17 of 20)"	L1_Mur2|LINE|L1	124477	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Ankrd32	2700017A04Rik|AW545819|Brctd1|Brctx|C730024G01Rik	ankyrin repeat domain 32	protein-coding	0	0.326733
Merged-chr18-28452509-1	chr18	28452459	28452559	+	2.1	cIP2vsInput	Intergenic	Intergenic	-107655	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	miscRNA	0	0.405941
Merged-chr10-128509493-1	chr10	128509443	128509543	+	2.1	cIP1vsInput	TTS (NM_011843)	TTS (NM_011843)	-10808	NM_172259	216459	Mm.291688	NM_172259	ENSMUSG00000039824	Myl6b	5730437E04Rik|BC037527|MLC1SA	"myosin, light polypeptide 6B"	protein-coding	0.02	0.544554
Merged-chr7-94134801-1	chr7	94134751	94134851	+	2.1	cIP1vsInput	Intergenic	Intergenic	1054922	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0	0.336634
Merged-chr10-47533739-1	chr10	47533689	47533789	+	2.1	cIP1vsInput	Intergenic	Lx9|LINE|L1	1288990	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0	0.326733
Merged-chrX-10173936-1	chrX	10173886	10173986	+	2.1	cIP1vsInput	"intron (NM_001177952, intron 13 of 16)"	"intron (NM_001177952, intron 13 of 16)"	42517	NM_001177952	19893	Mm.247556	NM_001177950	ENSMUSG00000031174	Rpgr	Rp3h	retinitis pigmentosa GTPase regulator	protein-coding	0.01	0.316832
Merged-chr7-24237579-1	chr7	24237529	24237629	+	2.1	cIP1vsInput	promoter-TSS (NM_020262)	promoter-TSS (NM_020262)	19	NM_020262	56869	Mm.103751	NM_020262		Zfp109	-	zinc finger protein 109	protein-coding	0.08	0.712871
Merged-chr17-6801217-1	chr17	6801167	6801267	+	2.1	cIP2vsInput	Intergenic	RSINE1|SINE|B4	-18437	NM_009510	22350	Mm.471952	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding	0	0.425743
Merged-chr8-42446188-1	chr8	42446138	42446238	+	2.1	cIP1vsInput	Intergenic	Intergenic	618921	NR_045497	69966	Mm.416903	NR_045497		2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	miscRNA	0	0.29703
Merged-chr4-118181351-1	chr4	118181301	118181401	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1308	NM_172382	230674	Mm.234234	NM_001161823	ENSMUSG00000033326	Kdm4a	D4Ertd222e|JHDM3A|Jmjd2|Jmjd2a|mKIAA0677	lysine (K)-specific demethylase 4A	protein-coding	0	0.366337
Merged-chr3-35188151-1	chr3	35188101	35188201	+	2.1	cIP2vsInput	Intergenic	Intergenic	-471489	NR_038348	100041108	Mm.484676	NR_038347		Gm3143	-	predicted gene 3143	miscRNA	0	0.336634
Merged-chr16-60782997-1	chr16	60782947	60783047	+	2.1	cIP2vsInput	Intergenic	Intergenic	-177466	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0	0.326733
Merged-chr8-19971330-1	chr8	19971280	19971380	+	2.1	cIP1vsInput	"intron (NM_001270553, intron 6 of 9).2"	"intron (NM_001270553, intron 6 of 9).2"	241754	NM_001039553	626415	Mm.425517	NM_001039553		4930467E23Rik	ENSMUSG00000074453|OTTMUSG00000018948|TSAP	RIKEN cDNA 4930467E23 gene	protein-coding	0	0.376238
Merged-chr2-145588384-1	chr2	145588334	145588434	+	2.1	cIP2vsInput	"intron (NM_053195, intron 7 of 16)"	"intron (NM_053195, intron 7 of 16)"	-33402	NM_001037929	627302	Mm.445953	NM_001037929		Gm14092	OTTMUSG00000015643	predicted gene 14092	protein-coding	0.03	0.425743
Merged-chr3-13804038-1	chr3	13803988	13804088	+	2.1	cIP2vsInput	"intron (NM_178631, intron 3 of 9)"	"intron (NM_178631, intron 3 of 9)"	-142334	NM_001163329	76897	Mm.422625	NM_001163328	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0	0.336634
Merged-chr9-28190306-1	chr9	28190256	28190356	+	2.1	cIP1vsInput	"intron (NM_177906, intron 1 of 7)"	"intron (NM_177906, intron 1 of 7)"	399037	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding	0.01	0.316832
Merged-chr14-86083765-1	chr14	86083715	86083815	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-162205	NR_040457	75155	Mm.399239	NR_040457		4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	miscRNA	0	0.326733
Merged-chr17-20621358-1	chr17	20621308	20621408	+	2.1	cIP1vsInput	Intergenic	Lx4B|LINE|L1	3519	NM_008040	14290	Mm.455334	NM_008040	ENSMUSG00000060701	Fpr-rs3	-	"formyl peptide receptor, related sequence 3"	protein-coding	0	0.336634
Merged-chr1-12534866-1	chr1	12534816	12534916	+	2.1	cIP1vsInput	Intergenic	L1_Mus4|LINE|L1	-132697	NR_045297	329096	Mm.417782	NR_045297	ENSMUSG00000097171	Gm17644	4932411L15	"predicted gene, 17644"	miscRNA	0	0.326733
Merged-chr11-55404622-1	chr11	55404572	55404672	+	2.1	cIP1vsInput	"intron (NM_009242, intron 5 of 9)"	RSINE1|SINE|B4	15458	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	AA517111|BM-40	secreted acidic cysteine rich glycoprotein	protein-coding	0	0.514851
Merged-chr11-5478967-1	chr11	5478917	5479017	+	2.1	cIP1vsInput	Intergenic	RSINE1|SINE|B4	-34120	NM_001080924	407821	Mm.216313	NM_001080924	ENSMUSG00000041961	Znrf3	AA591877|BC019575|Gm1167	zinc and ring finger 3	protein-coding	0.03	0.49505
Merged-chr15-88934379-1	chr15	88934329	88934429	+	2.1	cIP2vsInput	"intron (NM_172818, intron 4 of 11)"	"intron (NM_172818, intron 4 of 11)"	20039	NM_172818	239591	Mm.479911	NM_172818	ENSMUSG00000022388	Ttll8	1700019P01Rik|4933401B17	"tubulin tyrosine ligase-like family, member 8"	protein-coding	0.02	0.50495
Merged-chr2-112093701-1	chr2	112093651	112093751	+	2.1	cIP1vsInput	Intergenic	L1MA9|LINE|L1	-1002	NM_146450	258442	Mm.377505	NM_146450	ENSMUSG00000074945	Olfr1314	MOR245-2	olfactory receptor 1314	protein-coding	0	0.386139
Merged-chr11-45504057-1	chr11	45504007	45504107	+	2.1	cIP2vsInput	Intergenic	Intergenic	-304026	NR_045876	100009664	Mm.415439	NR_045876		F630206G17Rik	-	RIKEN cDNA F630206G17 gene	miscRNA	0.01	0.366337
Merged-chr7-100685696-1	chr7	100685646	100685746	+	2.1	cIP1vsInput	Intergenic	Intergenic	-21006	NM_178764	319604	Mm.260362	NM_178764	ENSMUSG00000029461	Fam168a	2610030B18Rik|B930006L02Rik|mKIAA0280	"family with sequence similarity 168, member A"	protein-coding	0.02	0.435644
Merged-chr12-6557028-1	chr12	6556978	6557078	+	2.1	cIP1vsInput	Intergenic	Lx|LINE|L1	823302	NR_045045	73575	Mm.179463	NR_045045		1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	miscRNA	0.01	0.306931
Merged-chr10-86794781-1	chr10	86794731	86794831	+	2.1	cIP1vsInput	"intron (NM_175331, intron 1 of 13)"	"intron (NM_175331, intron 1 of 13)"	15776	NM_175331	103466	Mm.200446	NM_175331	ENSMUSG00000054027	Nt5dc3	AU040402|AW540062|C630002B14Rik|TU12B1-TY	5'-nucleotidase domain containing 3	protein-coding	0.01	0.356436
Merged-chr5-61853284-1	chr5	61853234	61853334	+	2.1	cIP2vsInput	Intergenic	Intergenic	44441	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding	0.01	0.336634
Merged-chr4-99705582-1	chr4	99705532	99705632	+	2.1	cIP1vsInput	Intergenic	Intergenic	-10048	NM_001081264	320438	Mm.32408	NM_001081264	ENSMUSG00000073792	Alg6	E230028F23Rik	"asparagine-linked glycosylation 6 (alpha-1,3,-glucosyltransferase)"	protein-coding	0	0.435644
Merged-chr14-103998588-1	chr14	103998538	103998638	+	2.1	cIP2vsInput	"intron (NR_045953, intron 1 of 2)"	"intron (NR_045953, intron 1 of 2)"	28554	NR_045953	73877	Mm.399172	NR_045953		4930432J09Rik	-	RIKEN cDNA 4930432J09 gene	miscRNA	0.01	0.29703
Merged-chr3-158899527-1	chr3	158899477	158899577	+	2.1	cIP1vsInput	Intergenic	Intergenic	-176837	NR_040750	624759	Mm.491054	NR_040750		Gm20752	-	"predicted gene, 20752"	miscRNA	0	0.346535
Merged-chr13-8882305-1	chr13	8882255	8882355	+	2.1	cIP1vsInput	Intergenic	Intergenic	-3301	NM_145360	319554	Mm.29847	NM_145360	ENSMUSG00000058258	Idi1	4832416K17Rik	isopentenyl-diphosphate delta isomerase	protein-coding	0	0.306931
Merged-chr5-109003450-1	chr5	109003400	109003500	+	2.1	cIP1vsInput	"exon (NM_009491, exon 2 of 6)"	"exon (NM_009491, exon 2 of 6)"	2986	NM_009491	22307	Mm.261598	NM_009491	ENSMUSG00000067010	Vmn2r10	V2r16|VR16	"vomeronasal 2, receptor 10"	protein-coding	0	0.336634
Merged-chr16-11940555-1	chr16	11940505	11940605	+	2.1	cIP1vsInput	Intergenic	Intergenic	-31132	NM_146067	223978	Mm.442728	NM_146067	ENSMUSG00000065979	Cpped1	C530044N13Rik	calcineurin-like phosphoesterase domain containing 1	protein-coding	0	0.376238
Merged-chr13-69740064-1	chr13	69740014	69740114	+	2.1	cIP1vsInput	promoter-TSS (NM_001145162)	promoter-TSS (NM_001145162)	-167	NM_001145162	76980	Mm.23960	NM_001145162	ENSMUSG00000052981	Ube2ql1	3110006E14Rik	ubiquitin-conjugating enzyme E2Q family-like 1	protein-coding	0.08	0.673267
Merged-chr8-9809884-1	chr8	9809834	9809934	+	2.1	cIP2vsInput	Intergenic	Intergenic	-38861	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	"family with sequence similarity 155, member A"	protein-coding	0.03	0.158416
Merged-chr18-72584071-1	chr18	72584021	72584121	+	2.1	cIP2vsInput	Intergenic	L1MA8|LINE|L1	-233002	NM_007831	13176	Mm.167882	NM_007831		Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding	0	0.356436
Merged-chr10-56729995-1	chr10	56729945	56730045	+	2.1	cIP2vsInput	Intergenic	Intergenic	352695	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	"gap junction protein, alpha 1"	protein-coding	0.02	0.326733
Merged-chr18-10356127-1	chr18	10356077	10356177	+	2.1	cIP1vsInput	"intron (NM_001083628, intron 1 of 32)"	"intron (NM_001083628, intron 1 of 32)"	30948	NM_001083628	381157	Mm.261535	NM_001083628	ENSMUSG00000042942	Greb1l	mKIAA4095	growth regulation by estrogen in breast cancer-like	protein-coding	0	0.336634
Merged-chr12-48346886-1	chr12	48346836	48346936	+	2.1	cIP1vsInput	Intergenic	Intergenic	-45424	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0	0.316832
Merged-chr4-35874617-1	chr4	35874567	35874667	+	2.1	cIP1vsInput	"intron (NM_001166000, intron 8 of 8)"	"intron (NM_001166000, intron 8 of 8)"	-29413	NM_001166001	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0	0.29703
Merged-chr7-128814491-1	chr7	128814441	128814541	+	2.1	cIP2vsInput	Intergenic	Intergenic	69621	NM_001029982	207352	Mm.297105	NM_001029982	ENSMUSG00000055319	Sec23ip	D7Ertd373e|p125	Sec23 interacting protein	protein-coding	0.01	0.574257
Merged-chr19-52984101-1	chr19	52984051	52984151	+	2.1	cIP1vsInput	Intergenic	RLTR22_Mur|LTR|ERVK	54553	NM_133216	170750	Mm.99776	NM_133216	ENSMUSG00000025027	Xpnpep1	D230045I08Rik|sAMP	"X-prolyl aminopeptidase (aminopeptidase P) 1, soluble"	protein-coding	0	0.346535
Merged-chr13-6765682-1	chr13	6765632	6765732	+	2.1	cIP1vsInput	Intergenic	MER2|DNA|TcMar-Tigger	-116958	NM_019703	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|PFK-C	"phosphofructokinase, platelet"	protein-coding	0	0.306931
Merged-chrX-84827083-1	chrX	84827033	84827133	+	2.1	cIP1vsInput	"intron (NM_007868, intron 59 of 78)"	"intron (NM_007868, intron 59 of 78)"	-422594	NM_028046	71996	Mm.20201	NM_028046	ENSMUSG00000035491	1600014K23Rik	AI324104	RIKEN cDNA 1600014K23 gene	protein-coding	0	0.306931
Merged-chrX-106910619-1	chrX	106910569	106910669	+	2.1	cIP2vsInput	Intergenic	Intergenic	-10006	NM_175271	78134	Mm.90147	NM_175271	ENSMUSG00000049929	Lpar4	5730485F04Rik|Gpr23|LPA4|p2y9	lysophosphatidic acid receptor 4	protein-coding	0	0.267327
Merged-chr12-59040346-1	chr12	59040296	59040396	+	2.1	cIP2vsInput	Intergenic	U2|snRNA|snRNA	21115	NM_030057	78232	Mm.290070	NM_030057	ENSMUSG00000020993	Trappc6b	5830498C14Rik|C79212	trafficking protein particle complex 6B	protein-coding	0.03	0.485149
Merged-chr17-18179202-1	chr17	18179152	18179252	+	2.1	cIP1vsInput	"intron (NM_001104541, intron 5 of 5)"	L1Md_A|LINE|L1	27272	NM_001104541	627111	Mm.469863	NM_001104541	ENSMUSG00000091350	Vmn2r92	EG627111	"vomeronasal 2, receptor 92"	protein-coding	0	0.287129
Merged-chr9-42508065-1	chr9	42508015	42508115	+	2.1	cIP2vsInput	Intergenic	Intergenic	-35839	NM_173038	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding	0.01	0.29703
Merged-chr14-104062877-1	chr14	104062827	104062927	+	2.1	cIP1vsInput	Intergenic	Intergenic	-35735	NR_045953	73877	Mm.399172	NR_045953		4930432J09Rik	-	RIKEN cDNA 4930432J09 gene	miscRNA	0.01	0.336634
Merged-chr5-33782766-1	chr5	33782716	33782816	+	2.1	cIP2vsInput	promoter-TSS (NM_019694)	promoter-TSS (NM_019694)	-62	NM_019694	56384	Mm.260538	NM_019694		Letm1	-	leucine zipper-EF-hand containing transmembrane protein 1	protein-coding	0.11	0.752475
Merged-chr11-119206748-1	chr11	119206698	119206798	+	2.1	cIP2vsInput	"intron (NM_172443, intron 3 of 11)"	"intron (NM_172443, intron 3 of 11)"	21751	NM_172443	207592	Mm.205263	NM_172443	ENSMUSG00000039976	Tbc1d16	B930087K01|BC026530|Tcd1d16	"TBC1 domain family, member 16"	protein-coding	0.01	0.594059
Merged-chr17-40604794-1	chr17	40604744	40604844	+	2.1	cIP1vsInput	Intergenic	L1M2|LINE|L1	6200	NM_001177583	100126777	Mm.471590	NM_001177583	ENSMUSG00000095540	Gm20580	Esp4	"predicted gene, 20580"	protein-coding	0.01	0.326733
Merged-chr3-42980651-1	chr3	42980601	42980701	+	2.1	cIP2vsInput	Intergenic	Intergenic	1238033	NM_027271	73852	Mm.29006	NM_001099785	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	"DNA segment, Chr 3, ERATO Doi 751, expressed"	protein-coding	0	0.336634
Merged-chr19-25031306-1	chr19	25031256	25031356	+	2.1	cIP2vsInput	"intron (NM_028785, intron 1 of 47)"	"intron (NM_028785, intron 1 of 47)"	31777	NM_028785	76088	Mm.102485	NM_175233	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding	0	0.376238
Merged-chr7-92711611-1	chr7	92711561	92711661	+	2.1	cIP2vsInput	Intergenic	L1M5|LINE|L1	29848	NR_015510	666737	Mm.490939	NR_015510		4632427E13Rik	AU015482	RIKEN cDNA 4632427E13 gene	miscRNA	0.01	0.336634
Merged-chr5-143341380-1	chr5	143341330	143341430	+	2.1	cIP1vsInput	Intergenic	RMER16-int|LTR|ERVK	12072	NR_027874	67672	Mm.30983	NR_027874	ENSMUSG00000089889	0610040B10Rik	-	RIKEN cDNA 0610040B10 gene	miscRNA	0.01	0.336634
Merged-chr8-38269478-1	chr8	38269428	38269528	+	2.1	cIP2vsInput	"intron (NM_145841, intron 1 of 7)"	Lx8|LINE|L1	-17276	NR_029884	723860		NR_029884		Mir383	Mirn383|mmu-mir-383	microRNA 383	miscRNA	0	0.316832
Merged-chr3-50661823-1	chr3	50661773	50661873	+	2.1	cIP1vsInput	Intergenic	Intergenic	-218210	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	"solute carrier family 7 (cationic amino acid transporter, y+ system), member 11"	protein-coding	0.01	0.306931
Merged-chr1-48982767-1	chr1	48982717	48982817	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1944756	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.306931
Merged-chr15-55593266-1	chr15	55593216	55593316	+	2.1	cIP1vsInput	"intron (NM_001168250, intron 13 of 16)"	"intron (NM_001168250, intron 13 of 16)"	35858	NM_001168250	105837	Mm.390829	NM_001168250	ENSMUSG00000022369	Mtbp	AI429604|MDM2BP	"Mdm2, transformed 3T3 cell double minute p53 binding protein"	protein-coding	0	0.277228
Merged-chr17-92982875-1	chr17	92982825	92982925	+	2.1	cIP1vsInput	Intergenic	Intergenic	-216547	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0	0.346535
Merged-chr7-86149974-1	chr7	86149924	86150024	+	2.1	cIP1vsInput	"intron (NM_001102578, intron 5 of 5)"	Lx9|LINE|L1	21750	NM_001102578	546981	Mm.469835	NM_001102578	ENSMUSG00000090436	Vmn2r75	EG546981	"vomeronasal 2, receptor 75"	protein-coding	0	0.277228
Merged-chr14-93929467-1	chr14	93929417	93929517	+	2.1	cIP1vsInput	Intergenic	Intergenic	-38798	NM_001271798	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.386139
Merged-chr11-28663628-1	chr11	28663578	28663678	+	2.1	cIP2vsInput	Intergenic	Intergenic	-17936	NR_045906	72818	Mm.410846	NR_045906	ENSMUSG00000084966	2810471M01Rik	-	RIKEN cDNA 2810471M01 gene	miscRNA	0	0.306931
Merged-chr8-50179843-1	chr8	50179793	50179893	+	2.1	cIP1vsInput	Intergenic	Intergenic	-188269	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.237624
Merged-chr4-151427627-1	chr4	151427577	151427677	+	2.1	cIP1vsInput	"intron (NM_001081557, intron 5 of 23)"	L1M4b|LINE|L1	-369674	NM_009498	22319	Mm.273930	NM_009498	ENSMUSG00000028955	Vamp3	D130027G05Rik|VAMP-3|ceb	vesicle-associated membrane protein 3	protein-coding	0	0.366337
Merged-chr8-38841124-1	chr8	38841074	38841174	+	2.1	cIP2vsInput	Intergenic	Intergenic	-164743	NM_030254	80286	Mm.272722	NM_030254		Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding	0	0.306931
Merged-chr1-19453167-1	chr1	19453117	19453217	+	2.1	cIP1vsInput	Intergenic	Intergenic	241113	NM_001025305	21419	Mm.137021	NM_001025305	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding	0	0.366337
Merged-chr14-94461549-1	chr14	94461499	94461599	+	2.1	cIP2vsInput	Intergenic	Intergenic	-570880	NM_001271798	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0.01	0.336634
Merged-chr17-37496241-1	chr17	37496191	37496291	+	2.1	cIP1vsInput	"intron (NM_146328, intron 1 of 1)"	"intron (NM_146328, intron 1 of 1)"	3773	NM_146328	258325	Mm.484339	NM_146328	ENSMUSG00000090894	Olfr110	MOR249-2	olfactory receptor 110	protein-coding	0	0.306931
Merged-chr1-123863883-1	chr1	123863833	123863933	+	2.1	cIP2vsInput	"intron (NM_199021, intron 2 of 25)"	L1_Mur1|LINE|L1	181676	NM_199021	269109	Mm.483255	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding	0.02	0.316832
Merged-chr1-81818342-1	chr1	81818292	81818392	+	2.1	cIP2vsInput	Intergenic	Intergenic	473097	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding	0	0.386139
Merged-chr18-31382111-1	chr18	31382061	31382161	+	2.1	cIP1vsInput	Intergenic	Intergenic	-64983	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding	0.02	0.435644
Merged-chr3-112339018-1	chr3	112338968	112339068	+	2.1	cIP2vsInput	Intergenic	Intergenic	457115	NR_045362	625585	Mm.389497	NR_045362		Gm6602	-	predicted gene 6602	miscRNA	0.01	0.316832
Merged-chr6-71167109-1	chr6	71167059	71167159	+	2.1	cIP1vsInput	Intergenic	Intergenic	-22733	NM_178413	232078	Mm.37547	NM_001033929	ENSMUSG00000054474	Thnsl2	BC051244|TSH2	threonine synthase-like 2 (bacterial)	protein-coding	0.01	0.356436
Merged-chr12-61320373-1	chr12	61320323	61320423	+	2.1	cIP1vsInput	Intergenic	Tigger17b|DNA|TcMar-Tigger	201447	NR_045049	100504101	Mm.235026	NR_045049		Gm20063	-	"predicted gene, 20063"	miscRNA	0	0.29703
Merged-chr10-90337046-1	chr10	90336996	90337096	+	2.1	cIP1vsInput	"intron (NM_001128086, intron 11 of 24)"	"intron (NM_001128086, intron 11 of 24)"	-238681	NM_001177397	77531	Mm.440605	NM_001128086		Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding	0	0.227723
Merged-chr14-53848560-1	chr14	53848510	53848610	+	2.1	cIP2vsInput	Intergenic	Intergenic	182620	NM_001205242	100568452	Mm.486072	NM_001205242		A430107P09Rik	Va10	RIKEN cDNA A430107P09 gene	protein-coding	0	0.356436
Merged-chr1-117882571-1	chr1	117882521	117882621	+	2.1	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	428561	NM_011650	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding	0	0.336634
Merged-chr4-93035654-1	chr4	93035604	93035704	+	2.1	cIP1vsInput	Intergenic	Intergenic	299857	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding	0	0.316832
Merged-chr9-6738686-1	chr9	6738636	6738736	+	2.1	cIP1vsInput	Intergenic	Intergenic	438360	NM_029851	110350	Mm.237596	NM_029851	ENSMUSG00000047193	Dync2h1	4432416O06Rik|AI448217|D030010H02Rik|D330044F14Rik|DHC1b|DHC2|Dnchc2|b2b414Clo|mKIAA1997	dynein cytoplasmic 2 heavy chain 1	protein-coding	0	0.346535
Merged-chr11-74161258-1	chr11	74161208	74161308	+	2.1	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	6102	NM_146708	258703	Mm.377644	NM_146708	ENSMUSG00000070379	Olfr402	MOR255-4	olfactory receptor 402	protein-coding	0	0.346535
Merged-chr14-117086982-1	chr14	117086932	117087032	+	2.1	cIP2vsInput	"intron (NM_001079844, intron 1 of 9)"	"intron (NM_001079844, intron 1 of 9)"	161667	NM_011821	23888	Mm.440025	NM_001079844	ENSMUSG00000058571	Gpc6	6720429C22Rik|AI480529	glypican 6	protein-coding	0	0.386139
Merged-chr14-32438243-1	chr14	32438193	32438293	+	2.1	cIP2vsInput	"intron (NM_009891, intron 8 of 15)"	"intron (NM_009891, intron 8 of 15)"	26607	NM_021712	20508	Mm.190503	NM_021712		Slc18a3	VAChT|VAT	"solute carrier family 18 (vesicular monoamine), member 3"	protein-coding	0.01	0.326733
Merged-chr9-5395134-1	chr9	5395084	5395184	+	2.1	cIP2vsInput	Intergenic	Intergenic	49658	NM_009808	12364	Mm.42163	NM_009808	ENSMUSG00000025887	Casp12	-	caspase 12	protein-coding	0	0.336634
Merged-chr3-31818621-1	chr3	31818571	31818671	+	2.1	cIP2vsInput	Intergenic	Intergenic	-84082	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	"potassium large conductance calcium-activated channel, subfamily M, beta member 2"	protein-coding	0	0.326733
Merged-chr15-98048454-1	chr15	98048404	98048504	+	2.1	cIP1vsInput	"intron (NM_144851, intron 13 of 17)"	"intron (NM_144851, intron 13 of 17)"	-43730	NM_001113515	12824	Mm.2423	NM_001113515	ENSMUSG00000022483	Col2a1	Col2|Col2a|Col2a-1|Del1|Dmm|Lpk|M100856|Rgsc856	"collagen, type II, alpha 1"	protein-coding	0.02	0.386139
Merged-chr17-50956152-1	chr17	50956102	50956202	+	2.1	cIP2vsInput	"intron (NM_028162, intron 8 of 21)"	"intron (NM_028162, intron 8 of 21)"	-191744	NR_035408	735256		NR_035408		Mir669a-1	Mir669a-1a|Mirn669a-1|Mirn669a-1a|mir-669a-1	microRNA 669a-1	miscRNA	0.01	0.306931
Merged-chr1-46616809-1	chr1	46616759	46616859	+	2.1	cIP1vsInput	Intergenic	Intergenic	236700	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0.01	0.465347
Merged-chr1-32015109-1	chr1	32015059	32015159	+	2.1	cIP2vsInput	Intergenic	L1M2|LINE|L1	-157697	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm1	"KH domain containing, RNA binding, signal transduction associated 2"	protein-coding	0	0.306931
Merged-chr15-5466014-1	chr15	5465964	5466064	+	2.1	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-30304	NR_045274	71432	Mm.291087	NR_045274		5430437J10Rik	-	RIKEN cDNA 5430437J10 gene	miscRNA	0	0.267327
Merged-chr11-27743040-1	chr11	27742990	27743090	+	2.1	cIP2vsInput	Intergenic	MER58A|DNA|hAT-Charlie	841256	NM_001166661	216613	Mm.93759	NM_001166661	ENSMUSG00000032878	Ccdc85a	E030025D05Rik	coiled-coil domain containing 85A	protein-coding	0.01	0.386139
Merged-chr2-162657032-1	chr2	162656982	162657082	+	2.1	cIP1vsInput	"intron (NM_021464, intron 1 of 29)"	"intron (NM_021464, intron 1 of 29)"	4115	NM_021464	19281	Mm.381206	NM_021464	ENSMUSG00000053141	Ptprt	RPTP-rfo|RPTPrho|mKIAA0283	"protein tyrosine phosphatase, receptor type, T"	protein-coding	0.01	0.455446
Merged-chr4-16876291-1	chr4	16876241	16876341	+	2.1	cIP1vsInput	Intergenic	Intergenic	712181	NR_045765	100415915	Mm.387180	NR_045765	ENSMUSG00000085112	A530072M11Rik	-	RIKEN cDNA gene A530072M11	miscRNA	0.01	0.207921
Merged-chr18-29946853-1	chr18	29946803	29946903	+	2.1	cIP1vsInput	Intergenic	Intergenic	-326043	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	"phosphoinositide-3-kinase, class 3"	protein-coding	0	0.326733
Merged-chr10-118520267-1	chr10	118520217	118520317	+	2.1	cIP2vsInput	Intergenic	Intergenic	79220	NM_008337	15978	Mm.240327	NM_008337	ENSMUSG00000055170	Ifng	IFN-g|Ifg	interferon gamma	protein-coding	0	0.306931
Merged-chr8-98203021-1	chr8	98202971	98203071	+	2.1	cIP2vsInput	Intergenic	Intergenic	1213436	NM_007667	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0.02	0.336634
Merged-chr1-7188319-1	chr1	7188269	7188369	+	2.1	cIP2vsInput	Intergenic	Intergenic	99399	NM_183028	319263		NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0	0.29703
Merged-chr13-75012487-1	chr13	75012437	75012537	+	2.1	cIP1vsInput	Intergenic	Intergenic	-77500	NM_013628	18548	Mm.1333	NM_013628	ENSMUSG00000021587	Pcsk1	Nec-1|Nec1|PC1|PC3|Phpp-1|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0.01	0.277228
Merged-chr8-65399597-1	chr8	65399547	65399647	+	2.1	cIP2vsInput	Intergenic	Intergenic	-218443	NM_001166372	72925	Mm.380457	NM_001166372	ENSMUSG00000036469	1-Mar	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding	0.01	0.277228
Merged-chr18-72849845-1	chr18	72849795	72849895	+	2.1	cIP2vsInput	Intergenic	Intergenic	-498776	NM_007831	13176	Mm.167882	NM_007831		Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding	0	0.316832
Merged-chr11-7776607-1	chr11	7776557	7776657	+	2.1	cIP1vsInput	Intergenic	Lx2B|LINE|L1	-562684	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding	0	0.346535
Merged-chr6-42936263-1	chr6	42936213	42936313	+	2.1	cIP1vsInput	Intergenic	Intergenic	9030	NM_146295	258292	Mm.333032	NM_146295	ENSMUSG00000073111	Olfr446	MOR261-12	olfactory receptor 446	protein-coding	0	0.207921
Merged-chr14-112084062-1	chr14	112084012	112084112	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	62632	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0	0.316832
Merged-chr2-95858253-1	chr2	95858203	95858303	+	2.1	cIP1vsInput	Intergenic	B3|SINE|B2	-1420106	NM_007466	11800	Mm.486651	NM_007466	ENSMUSG00000027193	Api5	AAC-11|AI196452	apoptosis inhibitor 5	protein-coding	0	0.415842
Merged-chr7-106549443-1	chr7	106549393	106549493	+	2.1	cIP1vsInput	Intergenic	Intergenic	95202	NM_001277179	434223	Mm.334112	XM_001000891		Gm1966	-	predicted gene 1966	protein-coding	0	0.356436
Merged-chr11-99732617-1	chr11	99732567	99732667	+	2.1	cIP2vsInput	Intergenic	RMER12B|LTR|ERVK	40296	NM_001126322	100040276	Mm.475095	NM_001126322	ENSMUSG00000078668	Gm11595	OTTMUSG00000002543	predicted gene 11595	protein-coding	0.01	0.306931
Merged-chr2-95534894-1	chr2	95534844	95534944	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1096747	NM_007466	11800	Mm.486651	NM_007466	ENSMUSG00000027193	Api5	AAC-11|AI196452	apoptosis inhibitor 5	protein-coding	0	0.29703
Merged-chr11-54586406-1	chr11	54586356	54586456	+	2.1	cIP1vsInput	"intron (NM_001252494, intron 6 of 28)"	L1ME1|LINE|L1	-9740	NM_001252498	192786	Mm.254404	NM_001252494	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding	0.01	0.316832
Merged-chr8-34639148-1	chr8	34639098	34639198	+	2.1	cIP1vsInput	"intron (NR_040706, intron 1 of 4)"	"intron (NR_040706, intron 1 of 4)"	1168	NR_040706	330734	Mm.149998	NR_040706		B930018H19Rik	B930018H19	RIKEN cDNA B930018H19 gene	miscRNA	0.02	0.376238
Merged-chr14-86917632-1	chr14	86917582	86917682	+	2.1	cIP1vsInput	"intron (NM_019670, intron 18 of 27)"	"intron (NM_019670, intron 18 of 27)"	223482	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diap3	4930417P13Rik|Dia2|Diaph3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous homolog 3 (Drosophila)	protein-coding	0	0.336634
Merged-chr3-111123499-1	chr3	111123449	111123549	+	2.1	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-758404	NR_045362	625585	Mm.389497	NR_045362		Gm6602	-	predicted gene 6602	miscRNA	0.01	0.336634
Merged-chr1-123002553-1	chr1	123002503	123002603	+	2.1	cIP1vsInput	Intergenic	Intergenic	1043006	NM_199021	269109	Mm.483255	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding	0.01	0.326733
Merged-chr17-55362264-1	chr17	55362214	55362314	+	2.1	cIP1vsInput	Intergenic	MLTR18B_MM|LTR|ERVK	-83453	NM_172829	240119	Mm.311687	NM_172829	ENSMUSG00000024172	St6gal2	C230064G14Rik|St6galII|mKIAA1877	"beta galactoside alpha 2,6 sialyltransferase 2"	protein-coding	0	0.376238
Merged-chr19-18461770-1	chr19	18461720	18461820	+	2.1	cIP1vsInput	Intergenic	Intergenic	170043	NM_017375	20409	Mm.172222	NM_017375		Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding	0	0.346535
Merged-chr3-17111124-1	chr3	17111074	17111174	+	2.1	cIP2vsInput	Intergenic	Intergenic	-678797	NR_033490	70441	Mm.458192	NR_033490		2610100L16Rik	100040120|Gm2612	RIKEN cDNA 2610100L16 gene	miscRNA	0	0.326733
Merged-chr17-20413334-1	chr17	20413284	20413384	+	2.1	cIP1vsInput	Intergenic	Intergenic	-5829	NM_001166735	665525	Mm.480265	NM_001166735	ENSMUSG00000091151	Vmn1r224	EG665525|Gm7673	vomeronasal 1 receptor 224	protein-coding	0.01	0.366337
Merged-chr17-11095478-1	chr17	11095428	11095528	+	2.1	cIP2vsInput	"intron (NM_016694, intron 2 of 11)"	"intron (NM_016694, intron 2 of 11)"	255094	NM_016694	50873	Mm.311110	NM_016694		Park2	PRKN	"Parkinson disease (autosomal recessive, juvenile) 2, parkin"	protein-coding	0.01	0.267327
Merged-chr2-51960951-1	chr2	51960901	51961001	+	2.1	cIP1vsInput	"intron (NM_019401, intron 1 of 7)"	"intron (NM_019401, intron 1 of 7)"	12257	NM_001141949	64685	Mm.7491	NM_001141948	ENSMUSG00000026946	Nmi	-	N-myc (and STAT) interactor	protein-coding	0.01	0.346535
Merged-chr1-7685147-1	chr1	7685097	7685197	+	2.1	cIP1vsInput	Intergenic	Intergenic	596227	NM_183028	319263		NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0	0.356436
Merged-chr8-28527602-1	chr8	28527552	28527652	+	2.1	cIP2vsInput	Intergenic	L1M5|LINE|L1	-442749	NR_033590	666422	Mm.484413	NR_033590		Gm8096	EG666422	3-phosphoglycerate dehydrogenase pseudogene	pseudo	0	0.257426
Merged-chr14-39596735-1	chr14	39596685	39596785	+	2.1	cIP1vsInput	Intergenic	Intergenic	-58928	NR_045936	73591	Mm.65499	NR_045936		1700109I08Rik	-	RIKEN cDNA 1700109I08 gene	miscRNA	0	0.316832
Merged-chr10-50276693-1	chr10	50276643	50276743	+	2.1	cIP1vsInput	Intergenic	Intergenic	-315976	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0	0.326733
Merged-chr2-158340304-1	chr2	158340254	158340354	+	2.1	cIP2vsInput	Intergenic	Intergenic	21205	NR_015463	68108	Mm.119198	NR_015463		9430008C03Rik	-	RIKEN cDNA 9430008C03 gene	miscRNA	0	0.346535
Merged-chr5-7266338-1	chr5	7266288	7266388	+	2.1	cIP2vsInput	"intron (NM_001163223, intron 1 of 3)"	L1_Mur3|LINE|L1	-37826	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding	0.01	0.39604
Merged-chr1-166661197-1	chr1	166661147	166661247	+	2.1	cIP1vsInput	TTS (NM_172844)	TTS (NM_172844)	-13504	NM_001164312	226604	Mm.330032	NM_001164312	ENSMUSG00000051081	Gm4847	EG226604|Fmo12	predicted gene 4847	protein-coding	0.01	0.316832
Merged-chr8-53276490-1	chr8	53276440	53276540	+	2.1	cIP2vsInput	Intergenic	Intergenic	-235212	NM_001205054	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding	0	0.336634
Merged-chr5-58410385-1	chr5	58410335	58410435	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	42613	NR_046190	78163	Mm.243828	NR_046190		4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	miscRNA	0	0.277228
Merged-chrX-63115577-1	chrX	63115527	63115627	+	2.1	cIP2vsInput	Intergenic	Intergenic	-588566	NR_045442	75545	Mm.391270	NR_045442	ENSMUSG00000085757	1700019B21Rik	-	RIKEN cDNA 1700019B21 gene	miscRNA	0	0.29703
Merged-chr12-98639040-1	chr12	98638990	98639090	+	2.1	cIP1vsInput	"intron (NM_178914, intron 4 of 11)"	L1M3|LINE|L1	10856	NM_178914	104871	Mm.210053	NM_178914	ENSMUSG00000021007	Spata7	AI661438|B230306G18Rik|HSD3	spermatogenesis associated 7	protein-coding	0	0.316832
Merged-chrX-91007339-1	chrX	91007289	91007389	+	2.1	cIP2vsInput	Intergenic	Intergenic	115197	NM_001101450	212952	Mm.477436	NM_001101450	ENSMUSG00000091497	Gm44	-	predicted gene 44	protein-coding	0	0.376238
Merged-chr6-109765166-1	chr6	109765116	109765216	+	2.1	cIP1vsInput	Intergenic	RMER30|DNA|hAT-Charlie	-880432	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0	0.29703
Merged-chr12-65204011-1	chr12	65203961	65204061	+	2.1	cIP2vsInput	Intergenic	Intergenic	-21506	NM_027614	70948	Mm.219475	NM_027614	ENSMUSG00000035560	Wdr20b	4921538B03Rik|4930427E19Rik|Wdr20	WD repeat domain 20b	protein-coding	0.01	0.386139
Merged-chr10-43533620-1	chr10	43533570	43533670	+	2.1	cIP1vsInput	"intron (NM_026411, intron 1 of 3)"	B1F2|SINE|Alu	7374	NM_026411	67851	Mm.209953	NM_026411	ENSMUSG00000019797	1700021F05Rik	-	RIKEN cDNA 1700021F05 gene	protein-coding	0.01	0.544554
Merged-chr2-24583173-1	chr2	24583123	24583223	+	2.1	cIP1vsInput	Intergenic	RMER16-int|LTR|ERVK	-107574	NM_011040	18510	Mm.2533	NM_011040	ENSMUSG00000026976	Pax8	Pax-8	paired box gene 8	protein-coding	0	0.326733
Merged-chr5-4734583-1	chr5	4734533	4734633	+	2.1	cIP2vsInput	Intergenic	Intergenic	23633	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled homolog 1 (Drosophila)	protein-coding	0.01	0.356436
Merged-chr3-144975547-1	chr3	144975497	144975597	+	2.1	cIP2vsInput	promoter-TSS (NM_207208)	promoter-TSS (NM_207208)	-502	NM_207208	99663	Mm.442050	NM_207208	ENSMUSG00000068547	Clca6	9130020L07Rik|AI504701|Clca4	chloride channel calcium activated 6	protein-coding	0.03	0.376238
Merged-chr10-12997141-1	chr10	12997091	12997191	+	2.1	cIP2vsInput	Intergenic	Intergenic	-11309	NM_175102	66125	Mm.402225	NM_175102	ENSMUSG00000078348	Sf3b5	10kDa|1110005L13Rik|AU043053|Sf3b10	"splicing factor 3b, subunit 5"	protein-coding	0.05	0.366337
Merged-chr11-12970973-1	chr11	12970923	12971023	+	2.1	cIP1vsInput	Intergenic	Intergenic	-506013	NM_172496	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	4732460E13|C530045F18Rik|mKIAA0633	cordon-bleu	protein-coding	0	0.306931
Merged-chr15-16460303-1	chr15	16460253	16460353	+	2.1	cIP1vsInput	Intergenic	Intergenic	-317798	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0.01	0.356436
Merged-chr6-48670646-1	chr6	48670596	48670696	+	2.1	cIP1vsInput	Intergenic	Intergenic	-5489	NM_174960	317758	Mm.116971	NM_174960	ENSMUSG00000051124	Gimap9	A630002K24|BB145400	"GTPase, IMAP family member 9"	protein-coding	0	0.405941
Merged-chr3-37213446-1	chr3	37213396	37213496	+	2.1	cIP1vsInput	Intergenic	Intergenic	19172	NM_021782	60505	Mm.157689	NM_021782	ENSMUSG00000027718	Il21	-	interleukin 21	protein-coding	0	0.326733
Merged-chr12-116080532-1	chr12	116080482	116080582	+	2.1	cIP1vsInput	"intron (NM_009511, intron 2 of 12)"	"intron (NM_009511, intron 2 of 12)"	2806	NM_009511	22355	Mm.395245	XM_003946399	ENSMUSG00000011171	Vipr2	VPAC2|VPAC2R|Vip2	vasoactive intestinal peptide receptor 2	protein-coding	0	0.316832
Merged-chr13-67388906-1	chr13	67388856	67388956	+	2.1	cIP2vsInput	TTS (NM_001080941)	TTS (NM_001080941)	10861	NM_001080941	72807	Mm.303790	NM_001080941	ENSMUSG00000078994	Zfp429	2810487A22Rik|AI929863|Rsl2	zinc finger protein 429	protein-coding	0.03	0.39604
Merged-chr15-60526792-1	chr15	60526742	60526842	+	2.1	cIP1vsInput	Intergenic	Intergenic	-296173	NR_030696	320469	Mm.230853	NM_177166	ENSMUSG00000097493	9930014A18Rik	-	RIKEN cDNA 9930014A18 gene	miscRNA	0.01	0.306931
Merged-chrX-141688737-1	chrX	141688687	141688787	+	2.1	cIP1vsInput	"3' UTR (NM_007736, exon 52 of 52)"	"3' UTR (NM_007736, exon 52 of 52)"	36480	NM_010572	16370	Mm.261591	NM_010572	ENSMUSG00000054667	Irs4	IRS-4	insulin receptor substrate 4	protein-coding	0.01	0.29703
Merged-chr14-120052597-1	chr14	120052547	120052647	+	2.1	cIP2vsInput	Intergenic	Lx8|LINE|L1	-10162	NM_001001490	239283	Mm.138520	NM_001001490	ENSMUSG00000044819	Oxgr1	Gm299|Gpr80|Gpr99|P2Y15	oxoglutarate (alpha-ketoglutarate) receptor 1	protein-coding	0	0.326733
Merged-chr9-77160334-1	chr9	77160284	77160384	+	2.1	cIP2vsInput	"intron (NM_027150, intron 7 of 7)"	"intron (NM_027150, intron 7 of 7)"	-114553	NM_012033	26944	Mm.23199	NM_012033	ENSMUSG00000032357	Tinag	AI452335|TIN-ag	tubulointerstitial nephritis antigen	protein-coding	0	0.356436
Merged-chr13-25350516-1	chr13	25350466	25350566	+	2.1	cIP2vsInput	Intergenic	L1MD|LINE|L1	-80520	NM_009513	22360	Mm.4766	NM_009513	ENSMUSG00000048978	Nrsn1	Neurensin-1|Neuro-p24|Vmp	neurensin 1	protein-coding	0.01	0.29703
Merged-chr7-129867633-2	chr7	129867545	129867722	+	2.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-94532	NR_046077	100043150	Mm.334264	NR_046077		Gm4265	-	predicted gene 4265	miscRNA	0.00565	0.331461
Merged-chr15-51520024-1	chr15	51519974	51520074	+	2.1	cIP2vsInput	Intergenic	Intergenic	-124414	NR_045092	100502643	Mm.131987	NR_045092		Gm19303	-	"predicted gene, 19303"	miscRNA	0.01	0.336634
Merged-chr11-56333552-1	chr11	56333502	56333602	+	2.1	cIP2vsInput	Intergenic	Intergenic	-292565	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding	0	0.336634
Merged-chr11-28525068-1	chr11	28525018	28525118	+	2.1	cIP1vsInput	"intron (NM_181577, intron 2 of 4)"	"intron (NM_181577, intron 2 of 4)"	59228	NM_001166661	216613	Mm.93759	NM_001166661	ENSMUSG00000032878	Ccdc85a	E030025D05Rik	coiled-coil domain containing 85A	protein-coding	0	0.306931
Merged-chr12-48380646-1	chr12	48380596	48380696	+	2.1	cIP1vsInput	Intergenic	Intergenic	-79184	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0	0.316832
Merged-chr8-28384348-1	chr8	28384298	28384398	+	2.1	cIP2vsInput	Intergenic	Intergenic	-299495	NR_033590	666422	Mm.484413	NR_033590		Gm8096	EG666422	3-phosphoglycerate dehydrogenase pseudogene	pseudo	0	0.346535
Merged-chr10-71479975-1	chr10	71479925	71480025	+	2.1	cIP1vsInput	Intergenic	Intergenic	132182	NM_027184	69718	Mm.245867	NM_027184	ENSMUSG00000060733	Ipmk	2410017C19Rik|AA408208|Impk	inositol polyphosphate multikinase	protein-coding	0.01	0.346535
Merged-chr11-61418529-1	chr11	61418479	61418579	+	2.1	cIP2vsInput	Intergenic	MTD|LTR|ERVL-MaLR	35357	NM_009548	22671	Mm.89201	NM_009548	ENSMUSG00000010086	Rnf112	AI854096|R75574|ZNF179|Zfp179|bfp	ring finger protein 112	protein-coding	0	0.415842
Merged-chr8-31520434-1	chr8	31520384	31520484	+	2.1	cIP1vsInput	Intergenic	Intergenic	152685	NR_046272	74517	Mm.390001	NR_046272		7420700N18Rik	-	RIKEN cDNA 7420700N18 gene	miscRNA	0	0.29703
Merged-chr7-122421062-1	chr7	122421012	122421112	+	2.1	cIP1vsInput	"intron (NM_008855, intron 2 of 16)"	"intron (NM_008855, intron 2 of 16)"	131937	NM_008855	18751	Mm.446371	NM_008855		Prkcb	A130082F03Rik|PKC-Beta|Pkcb|Prkcb1|Prkcb2	"protein kinase C, beta"	protein-coding	0.02	0.376238
Merged-chr3-129798884-2	chr3	129798827	129798941	+	2.1	cIP1vsInput|cIP2vsInput	"intron (NM_001205102, intron 2 of 3)"	"intron (NM_001205102, intron 2 of 3)"	5146	NM_001205102	242235	Mm.302549	NM_001205102	ENSMUSG00000093865	Lrit3	Gm421	"leucine-rich repeat, immunoglobulin-like and transmembrane domains 3"	protein-coding	0.008772	0.426087
Merged-chr3-29601533-1	chr3	29601483	29601583	+	2.1	cIP1vsInput	"intron (NM_001167748, intron 6 of 12)"	"intron (NM_001167748, intron 6 of 12)"	184710	NR_030422	791072		NR_030422		Mir551b	Mirn551b|mir-551b	microRNA 551b	miscRNA	0.01	0.287129
Merged-chr13-28088321-1	chr13	28088271	28088371	+	2.1	cIP1vsInput	Intergenic	Intergenic	-54163	NM_023746	28078	Mm.155058	NM_023746	ENSMUSG00000017064	Prl5a1	1600013P04Rik|D13Wsu14e|PLP-L|Prlpl|RP23-231P12.2	"prolactin family 5, subfamily a, member 1"	protein-coding	0.01	0.336634
Merged-chr6-8936787-1	chr6	8936737	8936837	+	2.1	cIP1vsInput	Intergenic	Intergenic	-13232	NM_008751	18231	Mm.46954	NM_008751		Nxph1	C130005L03Rik	neurexophilin 1	protein-coding	0	0.29703
Merged-chr16-67383021-1	chr16	67382971	67383071	+	2.1	cIP2vsInput	"intron (NM_178721, intron 1 of 9)"	"intron (NM_178721, intron 1 of 9)"	237887	NM_001145977	239857	Mm.394300	NM_001145977	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0	0.306931
Merged-chr1-119913397-1	chr1	119913347	119913447	+	2.1	cIP1vsInput	promoter-TSS (NM_175106)	promoter-TSS (NM_175106)	-229	NM_175106	66343	Mm.49942	NM_175106	ENSMUSG00000036975	Tmem177	2300008B03Rik	transmembrane protein 177	protein-coding	0.09	0.60396
Merged-chr17-41977386-1	chr17	41977336	41977436	+	2.1	cIP1vsInput	Intergenic	MLTR25C|LTR|ERVK	-338561	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding	0.01	0.366337
Merged-chr10-47692080-1	chr10	47692030	47692130	+	2.1	cIP1vsInput	Intergenic	ORR1C2|LTR|ERVL-MaLR	1403763	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	"proteasome (prosome, macropain) subunit, alpha type 6 pseudogene"	pseudo	0	0.316832
Merged-chr19-5002314-1	chr19	5002264	5002364	+	2.1	cIP2vsInput	Intergenic	Intergenic	-12343	NM_153553	225872	Mm.287867	NM_153553	ENSMUSG00000045903	Npas4	LE-PAS|Nxf	neuronal PAS domain protein 4	protein-coding	0.09	0.594059
Merged-chr1-55270822-1	chr1	55270772	55270872	+	2.1	cIP1vsInput	Intergenic	Intergenic	33645	NM_175439	212679	Mm.19223	NM_175439	ENSMUSG00000046994	Mars2	C730026E21Rik|MetRS	methionine-tRNA synthetase 2 (mitochondrial)	protein-coding	0.01	0.425743
Merged-chr7-56668824-1	chr7	56668774	56668874	+	2.1	cIP1vsInput	Intergenic	Intergenic	429053	NM_021879	18431	Mm.137052	NM_021879	ENSMUSG00000030450	Oca2	D7H15S12|D7Icr28RN|D7Nic1|p	oculocutaneous albinism II	protein-coding	0	0.326733
Merged-chr14-54800627-1	chr14	54800577	54800677	+	2.1	cIP1vsInput	Intergenic	RLTR17D_Mm|LTR|ERVK	-18741	NM_016972	50934	Mm.276831	NM_016972	ENSMUSG00000022180	Slc7a8	AA408822|LAT2	"solute carrier family 7 (cationic amino acid transporter, y+ system), member 8"	protein-coding	0	0.445545
Merged-chr11-101395179-1	chr11	101395129	101395229	+	2.1	cIP2vsInput	Intergenic	Intergenic	22254	NM_144829	69684	Mm.146283	NM_144829	ENSMUSG00000075528	Aarsd1	1110069E20Rik|2310044P18Rik|AA589600|AlaX|AlaXp-II	alanyl-tRNA synthetase domain containing 1	protein-coding	0	0.415842
Merged-chr8-94200009-1	chr8	94199959	94200059	+	2.1	cIP1vsInput	Intergenic	Intergenic	-14592	NM_172410	71805	Mm.458170	NM_172410	ENSMUSG00000032939	Nup93	2410008G02Rik	nucleoporin 93	protein-coding	0.01	0.356436
Merged-chr8-55670852-1	chr8	55670802	55670902	+	2.1	cIP1vsInput	Intergenic	Lx6|LINE|L1	236112	NM_175939	244486	Mm.67684	NM_175939	ENSMUSG00000046258	Adam29	-	a disintegrin and metallopeptidase domain 29	protein-coding	0.01	0.287129
Merged-chr4-20235365-1	chr4	20235315	20235415	+	2.1	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	193313	NM_010281	14590	Mm.20461	NM_010281		Ggh	gamma-GH	gamma-glutamyl hydrolase	protein-coding	0	0.306931
Merged-chr5-89411044-1	chr5	89410994	89411094	+	2.1	cIP1vsInput	Intergenic	Intergenic	46854	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding	0	0.29703
Merged-chr18-9178498-1	chr18	9178448	9178548	+	2.1	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-34358	NM_008058	14370	Mm.184289	NM_008058	ENSMUSG00000036904	Fzd8	Fz8	frizzled homolog 8 (Drosophila)	protein-coding	0	0.316832
Merged-chr14-109672889-1	chr14	109672839	109672939	+	2.1	cIP1vsInput	Intergenic	L1VL4|LINE|L1	212659	NR_039542	100628607		NR_039542	ENSMUSG00000092639	Mir3964	mmu-mir-3964|mu-mir-3964	microRNA 3964	miscRNA	0.01	0.356436
Merged-chr18-39584799-1	chr18	39584749	39584849	+	2.1	cIP2vsInput	Intergenic	L1MB3|LINE|L1	-97554	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	"nuclear receptor subfamily 3, group C, member 1"	protein-coding	0	0.386139
Merged-chr13-41123752-1	chr13	41123702	41123802	+	2.1	cIP1vsInput	Intergenic	Intergenic	-13764	NM_008104	107889	Mm.1399	NM_008104	ENSMUSG00000021362	Gcm2	Gcm-rs1|Gcm1|Gcm1-rs2	glial cells missing homolog 2 (Drosophila)	protein-coding	0	0.326733
Merged-chr3-43534896-1	chr3	43534846	43534946	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	1792278	NM_027271	73852	Mm.29006	NM_001099785	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	"DNA segment, Chr 3, ERATO Doi 751, expressed"	protein-coding	0.01	0.326733
Merged-chr2-18459688-1	chr2	18459638	18459738	+	2.1	cIP1vsInput	Intergenic	MMERVK9C_I-int|LTR|ERVK	-66858	NM_007869	13418	Mm.246674	NM_001190817	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	"DnaJ (Hsp40) homolog, subfamily C, member 1"	protein-coding	0.01	0.316832
Merged-chr13-17926796-1	chr13	17926746	17926846	+	2.1	cIP1vsInput	"intron (NM_019491, intron 1 of 4)"	"intron (NM_019491, intron 1 of 4)"	17421	NM_019491	56044	Mm.27348	NM_019491	ENSMUSG00000008859	Rala	3010001O15Rik|AW322615|Ral|Rasl1	v-ral simian leukemia viral oncogene homolog A (ras related)	protein-coding	0	0.366337
Merged-chr16-48201576-1	chr16	48201526	48201626	+	2.1	cIP2vsInput	Intergenic	Intergenic	-82159	NM_028610	73693	Mm.35597	NM_001018002	ENSMUSG00000058550	Dppa4	2410091M23Rik|C76608|ECAT15-1	developmental pluripotency associated 4	protein-coding	0	0.336634
Merged-chr1-19937038-1	chr1	19936988	19937088	+	2.1	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	-419416	NR_045734	75028	Mm.417820	NR_045734		4930486I03Rik	-	RIKEN cDNA 4930486I03 gene	miscRNA	0.01	0.366337
Merged-chr18-6576234-1	chr18	6576184	6576284	+	2.1	cIP1vsInput	Intergenic	RMER16-int|LTR|ERVK	-27399	NM_027598	70901	Mm.158484	NM_027598	ENSMUSG00000039540	4921524L21Rik	-	RIKEN cDNA 4921524L21 gene	protein-coding	0	0.257426
Merged-chr3-31934465-1	chr3	31934415	31934515	+	2.1	cIP2vsInput	"intron (NM_028231, intron 2 of 5)"	"intron (NM_028231, intron 2 of 5)"	31762	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	"potassium large conductance calcium-activated channel, subfamily M, beta member 2"	protein-coding	0.01	0.50495
Merged-chr11-28879223-1	chr11	28879173	28879273	+	2.1	cIP1vsInput	"intron (NM_146015, intron 4 of 10)"	"intron (NM_146015, intron 4 of 10)"	26018	NM_146015	216616	Mm.44176	NM_146015	ENSMUSG00000020467	Efemp1	-	epidermal growth factor-containing fibulin-like extracellular matrix protein 1	protein-coding	0	0.287129
Merged-chr6-147520724-1	chr6	147520674	147520774	+	2.1	cIP2vsInput	"intron (NM_025911, intron 3 of 12)"	MT2B1|LTR|ERVL	44853	NM_025911	67015	Mm.209774	NM_025911	ENSMUSG00000030301	Ccdc91	1700086G08Rik|1810060J02Rik|AU045683|AW555238|p56	coiled-coil domain containing 91	protein-coding	0.02	0.49505
Merged-chr14-26798881-1	chr14	26798831	26798931	+	2.1	cIP2vsInput	Intergenic	Intergenic	-95723	NM_001170748	142687	Mm.138259	NM_001170748	ENSMUSG00000021898	Asb14	Asb-14	ankyrin repeat and SOCS box-containing 14	protein-coding	0.02	0.356436
Merged-chr1-128956629-1	chr1	128956579	128956679	+	2.1	cIP1vsInput	Intergenic	Intergenic	-316675	NM_172485	210417	Mm.380518	NM_172485	ENSMUSG00000042581	Thsd7b	1700074E13Rik|B930082A18|D130067I03Rik	"thrombospondin, type I, domain containing 7B"	protein-coding	0.01	0.346535
Merged-chr8-23573719-1	chr8	23573669	23573769	+	2.1	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-95942	NM_001277239	320158	Mm.121274	NM_001277239	ENSMUSG00000037492	Zmat4	9630048M01Rik	"zinc finger, matrin type 4"	protein-coding	0	0.346535
Merged-chr6-75179013-1	chr6	75178963	75179063	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1709346	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.405941
Merged-chr3-38662915-1	chr3	38662865	38662965	+	2.1	cIP1vsInput	Intergenic	Intergenic	-178099	NM_001167883	99696	Mm.290937	NM_001033198	ENSMUSG00000044864	Ankrd50	AI662170|E430012K20Rik|mKIAA1223|mKIAA3019	ankyrin repeat domain 50	protein-coding	0.01	0.306931
Merged-chr4-14248336-1	chr4	14248286	14248386	+	2.1	cIP1vsInput	Intergenic	Intergenic	373442	NM_145947	208890	Mm.483839	NM_145947		Slc26a7	-	"solute carrier family 26, member 7"	protein-coding	0	0.336634
Merged-chr19-35546134-1	chr19	35546084	35546184	+	2.1	cIP2vsInput	Intergenic	Intergenic	511226	NM_008315	15566	Mm.254266	NM_008315	ENSMUSG00000024798	Htr7	5-HT7	5-hydroxytryptamine (serotonin) receptor 7	protein-coding	0	0.336634
Merged-chr4-36282972-1	chr4	36282922	36283022	+	2.1	cIP1vsInput	"intron (NM_001165999, intron 3 of 7)"	"intron (NM_001165999, intron 3 of 7)"	362481	NR_030545	100124458		NR_030545	ENSMUSG00000077851	Mir876	Mirn876|mmu-mir-876	microRNA 876	miscRNA	0	0.346535
Merged-chr9-77085216-1	chr9	77085166	77085266	+	2.1	cIP2vsInput	Intergenic	Intergenic	-39435	NM_012033	26944	Mm.23199	NM_012033	ENSMUSG00000032357	Tinag	AI452335|TIN-ag	tubulointerstitial nephritis antigen	protein-coding	0.01	0.336634
Merged-chr5-72053071-1	chr5	72053021	72053121	+	2.1	cIP1vsInput	"intron (NM_008069, intron 5 of 8)"	"intron (NM_008069, intron 5 of 8)"	115112	NM_178599	27784	Mm.44223	NM_178599	ENSMUSG00000029213	Commd8	C77770|D5Buc26e	COMM domain containing 8	protein-coding	0.01	0.376238
Merged-chr8-30395562-1	chr8	30395512	30395612	+	2.1	cIP1vsInput	Intergenic	Intergenic	-172833	NR_045856	71314	Mm.158666	NR_045856	ENSMUSG00000097044	4933433F19Rik	-	RIKEN cDNA 4933433F19 gene	miscRNA	0	0.415842
Merged-chr11-22522445-1	chr11	22522395	22522495	+	2.1	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	10162	NM_153596	103765	Mm.221274	NM_153596	ENSMUSG00000049904	Tmem17	AI503894|AW049890	transmembrane protein 17	protein-coding	0.01	0.316832
Merged-chr2-12493490-1	chr2	12493440	12493540	+	2.1	cIP1vsInput	Intergenic	Intergenic	-74030	NM_024185	66960	Mm.34059	NM_024185	ENSMUSG00000026767	Fam188a	1810041E18Rik|2310047O13Rik|5830410F13Rik|AI447827|AW111958	"family with sequence similarity 188, member A"	protein-coding	0	0.326733
Merged-chr13-52658597-1	chr13	52658547	52658647	+	2.1	cIP2vsInput	Intergenic	Intergenic	61715	NM_011518	20963	Mm.375031	NM_001198977	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding	0.02	0.49505
Merged-chr2-118245445-1	chr2	118245395	118245495	+	2.1	cIP1vsInput	"intron (NM_027759, intron 5 of 10)"	"intron (NM_027759, intron 5 of 10)"	11521	NM_027759	71313	Mm.85046	NM_027759	ENSMUSG00000027344	Fsip1	1700012M13Rik|4933432K11Rik	fibrous sheath-interacting protein 1	protein-coding	0.01	0.29703
Merged-chr2-55908553-1	chr2	55908503	55908603	+	2.1	cIP2vsInput	Intergenic	Lx9|LINE|L1	471397	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK1|Kcnf3|Kir3.1	"potassium inwardly-rectifying channel, subfamily J, member 3"	protein-coding	0	0.326733
Merged-chr1-149471921-1	chr1	149471871	149471971	+	2.1	cIP1vsInput	Intergenic	Intergenic	489363	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0	0.287129
Merged-chr3-59881577-1	chr3	59881527	59881627	+	2.1	cIP1vsInput	Intergenic	Intergenic	20526	NM_001243003	666803	Mm.389443	NM_001243003	ENSMUSG00000095522	Gm8298	EG666803	predicted gene 8298	protein-coding	0	0.287129
Merged-chrX-113165296-1	chrX	113165246	113165346	+	2.1	cIP2vsInput	"intron (NM_018818, intron 1 of 14)"	Lx5|LINE|L1	20219	NM_018818	12662	Mm.257316	XM_003689460	ENSMUSG00000025531	Chm	Rep-1	choroidermia	protein-coding	0	0.287129
Merged-chr1-45105504-1	chr1	45105454	45105554	+	2.1	cIP2vsInput	Intergenic	Intergenic	-206034	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|MMS10-W|Ms10w|mKIAA4231	"collagen, type III, alpha 1"	protein-coding	0	0.376238
Merged-chr4-40166683-1	chr4	40166633	40166733	+	2.1	cIP2vsInput	"intron (NM_007386, intron 3 of 20)"	L1_Mm|LINE|L1	23418	NM_007386	11428	Mm.331547	NM_007386	ENSMUSG00000028405	Aco1	AI256519|Aco-1|Irebp|Irp1	aconitase 1	protein-coding	0	0.356436
Merged-chr11-70309564-1	chr11	70309514	70309614	+	2.1	cIP2vsInput	Intergenic	Intergenic	12954	NM_145684	11685	Mm.274093	NM_145684	ENSMUSG00000018907	Alox12e	8-LOX|AW259591|Alox12-ps1|Alox12-ps2|Aloxe|e-LOX1	"arachidonate lipoxygenase, epidermal"	protein-coding	0.02	0.425743
Merged-chr4-98798032-1	chr4	98797982	98798082	+	2.1	cIP2vsInput	"non-coding (NR_040437, exon 3 of 3)"	"non-coding (NR_040437, exon 3 of 3)"	4264	NR_040437	399570	Mm.71924	NR_040437	ENSMUSG00000085843	A730085A09Rik	-	RIKEN cDNA A730085A09 gene	miscRNA	0	0.326733
Merged-chr2-99843434-1	chr2	99843384	99843484	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1781314	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding	0	0.306931
Merged-chr2-123442050-1	chr2	123442000	123442100	+	2.1	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	660051	NM_021507	59010	Mm.28986	NM_001162503	ENSMUSG00000005803	Sqrdl	0610039J17Rik|4930557M22Rik	sulfide quinone reductase-like (yeast)	protein-coding	0.02	0.356436
Merged-chr9-5640560-1	chr9	5640510	5640610	+	2.1	cIP1vsInput	Intergenic	MLT1H|LTR|ERVL-MaLR	295084	NM_009808	12364	Mm.42163	NM_009808	ENSMUSG00000025887	Casp12	-	caspase 12	protein-coding	0	0.306931
Merged-chr5-151360696-1	chr5	151360646	151360746	+	2.1	cIP2vsInput	Intergenic	Intergenic	-7979	NR_045700	625175	Mm.443286	NR_045699	ENSMUSG00000097321	1700028E10Rik	A630054D14|Gm6561	RIKEN cDNA 1700028E10 gene	miscRNA	0	0.415842
Merged-chr9-30058125-1	chr9	30058075	30058175	+	2.1	cIP2vsInput	Intergenic	Intergenic	-94996	NM_172290	235106	Mm.283138	NM_172290		Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding	0.01	0.425743
Merged-chrY-6075555-1	chrY	6075505	6075605	+	2.1	cIP1vsInput	Intergenic	YREP_Mm|Unknown|Unknown	1092222	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.287129
Merged-chr3-70943349-1	chr3	70943299	70943399	+	2.1	cIP2vsInput	Intergenic	Intergenic	-136058	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	miscRNA	0	0.306931
Merged-chr4-94339625-1	chr4	94339575	94339675	+	2.1	cIP2vsInput	Intergenic	Intergenic	217171	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0	0.356436
Merged-chr11-92484556-1	chr11	92484506	92484606	+	2.1	cIP1vsInput	Intergenic	Intergenic	-614734	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding	0.01	0.366337
Merged-chr11-15987302-1	chr11	15987252	15987352	+	2.1	cIP2vsInput	Intergenic	Intergenic	-270422	NM_145967	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	9330184N17Rik|BC027127|Vstm2	V-set and transmembrane domain containing 2A	protein-coding	0	0.336634
Merged-chr14-95918809-1	chr14	95918759	95918859	+	2.1	cIP2vsInput	Intergenic	Intergenic	37543	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.366337
Merged-chrX-97027239-1	chrX	97027189	97027289	+	2.1	cIP1vsInput	Intergenic	Intergenic	-45357	NM_001033361	245526	Mm.336164	NM_001033361	ENSMUSG00000031212	Pgr15l	-	G protein-coupled receptor 15-like	protein-coding	0	0.39604
Merged-chr6-64011744-1	chr6	64011694	64011794	+	2.1	cIP1vsInput	"intron (NM_008167, intron 4 of 15)"	ORR1B1-int|LTR|ERVL-MaLR	-717402	NM_007500	11921	Mm.57229	NM_007500	ENSMUSG00000073043	Atoh1	Hath1|MATH-1|Math1|bHLHa14	atonal homolog 1 (Drosophila)	protein-coding	0	0.306931
Merged-chr3-26096088-1	chr3	26096038	26096138	+	2.1	cIP1vsInput	"intron (NM_138666, intron 3 of 7)"	"intron (NM_138666, intron 3 of 7)"	57219	NM_001163387	192167	Mm.316080	NM_001163387	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|mKIAA1070	neuroligin 1	protein-coding	0.01	0.29703
Merged-chr11-97685769-1	chr11	97685719	97685819	+	2.1	cIP2vsInput	promoter-TSS (NM_001085500)	promoter-TSS (NM_001085500)	-183	NM_001085500	217149	Mm.29659	NM_001085500	ENSMUSG00000078695	Cisd3	Mel-13|Mel13	CDGSH iron sulfur domain 3	protein-coding	0.14	0.762376
Merged-chr1-69985798-1	chr1	69985748	69985848	+	2.1	cIP1vsInput	"intron (NM_025728, intron 1 of 7)"	Lx4A|LINE|L1	34183	NM_025728	66722	Mm.440554	NM_001271533	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding	0.01	0.316832
Merged-chr8-106038242-1	chr8	106038192	106038292	+	2.1	cIP1vsInput	"intron (NM_025518, intron 7 of 15)"	"intron (NM_025518, intron 7 of 15)"	-21361	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	"nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3"	protein-coding	0.01	0.316832
Merged-chr5-13913825-1	chr5	13913775	13913875	+	2.1	cIP2vsInput	Intergenic	Intergenic	-111451	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	"sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E"	protein-coding	0	0.336634
Merged-chr13-47417103-1	chr13	47417053	47417153	+	2.1	cIP1vsInput	Intergenic	Intergenic	223100	NM_001170643	218215	Mm.287609	NM_001170643	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding	0	0.405941
Merged-chr3-61243875-1	chr3	61243825	61243925	+	2.1	cIP1vsInput	Intergenic	Intergenic	-120632	NM_028712	74012	Mm.477648	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	"RAP2B, member of RAS oncogene family"	protein-coding	0	0.287129
Merged-chrX-131451795-1	chrX	131451745	131451845	+	2.1	cIP2vsInput	Intergenic	Intergenic	1702053	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diap2	Dia3|Diaph2|Drf2|E430022I22Rik	diaphanous homolog 2 (Drosophila)	protein-coding	0	0.356436
Merged-chrX-108526192-1	chrX	108526142	108526242	+	2.1	cIP1vsInput	Intergenic	L1VL2|LINE|L1	308163	NM_001081477	382236	Mm.426127	NM_001081477		Brwd3	Brodl|D030064D06Rik|Gm596	bromodomain and WD repeat domain containing 3	protein-coding	0	0.366337
Merged-chr3-20411244-1	chr3	20411194	20411294	+	2.1	cIP1vsInput	Intergenic	Intergenic	-44067	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	"angiotensin II receptor, type 1b"	protein-coding	0.02	0.346535
Merged-chr2-89513591-1	chr2	89513541	89513641	+	2.1	cIP1vsInput	Intergenic	Lx3C|LINE|L1	14817	NM_146969	258971	Mm.389308	NM_146969	ENSMUSG00000075084	Olfr1243	MOR231-4	olfactory receptor 1243	protein-coding	0	0.306931
Merged-chr5-150823467-1	chr5	150823417	150823517	+	2.1	cIP2vsInput	Intergenic	Intergenic	-129140	NM_013823	16591	Mm.6500	NM_013823	ENSMUSG00000058488	Kl	alpha-kl	klotho	protein-coding	0	0.366337
Merged-chr5-17029262-1	chr5	17029212	17029312	+	2.1	cIP1vsInput	Intergenic	Intergenic	-446860	NM_027609	70935	Mm.332225	NM_027609	ENSMUSG00000058643	Speer4f	4922502J04Rik|SPEER-4F	spermatogenesis associated glutamate (E)-rich protein 4f	protein-coding	0	0.356436
Merged-chr3-7821822-1	chr3	7821772	7821872	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	133065	NR_040587	75476	Mm.396221	NR_040587		1700010I02Rik	-	RIKEN cDNA 1700010I02 gene	miscRNA	0	0.29703
Merged-chr10-66039276-1	chr10	66039226	66039326	+	2.1	cIP1vsInput	Intergenic	Intergenic	84788	NR_038039	69433	Mm.23366	NR_038039		1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	miscRNA	0.01	0.366337
Merged-chr4-7542661-1	chr4	7542611	7542711	+	2.1	cIP2vsInput	Intergenic	Intergenic	-18027	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	miscRNA	0	0.316832
Merged-chr3-21199628-1	chr3	21199578	21199678	+	2.1	cIP1vsInput	Intergenic	L1VL4|LINE|L1	-832451	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	"angiotensin II receptor, type 1b"	protein-coding	0	0.356436
Merged-chr9-38144994-1	chr9	38144944	38145044	+	2.1	cIP1vsInput	TTS (NM_146481)	TTS (NM_146481)	1857	NM_146481	258474	Mm.377521	NM_146481	ENSMUSG00000096409	Olfr890	MOR162-3	olfactory receptor 890	protein-coding	0	0.306931
Merged-chr15-17511481-1	chr15	17511431	17511531	+	2.1	cIP1vsInput	Intergenic	Intergenic	733380	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0	0.257426
Merged-chr1-110556756-1	chr1	110556706	110556806	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	420616	NM_001081386	227485	Mm.322070	NM_001081386	ENSMUSG00000047216	Cdh19	-	"cadherin 19, type 2"	protein-coding	0	0.366337
Merged-chr3-37158225-1	chr3	37158175	37158275	+	2.1	cIP1vsInput	Intergenic	Intergenic	-32271	NM_008366	16183	Mm.14190	NM_008366	ENSMUSG00000027720	Il2	Il-2	interleukin 2	protein-coding	0.01	0.366337
Merged-chr11-38224656-1	chr11	38224606	38224706	+	2.1	cIP2vsInput	Intergenic	Intergenic	295389	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0.01	0.336634
Merged-chr3-101845576-1	chr3	101845526	101845626	+	2.1	cIP1vsInput	Intergenic	Intergenic	-9353	NM_172295	242125	Mm.32900	NM_172295	ENSMUSG00000044313	Mab21l3	-	mab-21-like 3 (C. elegans)	protein-coding	0.01	0.514851
Merged-chr5-90975699-1	chr5	90975649	90975749	+	2.1	cIP1vsInput	"intron (NM_026788, intron 6 of 7)"	"intron (NM_026788, intron 6 of 7)"	44503	NM_026788	665563	Mm.153030	NM_026788	ENSMUSG00000029376	Mthfd2l	1110019K23Rik|C630010D07Rik	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like	protein-coding	0	0.336634
Merged-chr2-34834008-1	chr2	34833958	34834058	+	2.1	cIP1vsInput	Intergenic	RMER1B|Other|Other	-7773	NM_001164772	30050	Mm.4465	NM_001164768	ENSMUSG00000035949	Fbxw2	2700071L08Rik|FBW2|Fwd2|MD6	F-box and WD-40 domain protein 2	protein-coding	0.02	0.386139
Merged-chrX-63311230-1	chrX	63311180	63311280	+	2.1	cIP1vsInput	Intergenic	Lx4A|LINE|L1	-784219	NR_045442	75545	Mm.391270	NR_045442	ENSMUSG00000085757	1700019B21Rik	-	RIKEN cDNA 1700019B21 gene	miscRNA	0	0.316832
Merged-chr9-56119317-1	chr9	56119267	56119367	+	2.1	cIP1vsInput	"intron (NM_011193, intron 3 of 14)"	"intron (NM_011193, intron 3 of 14)"	29341	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding	0.02	0.554455
Merged-chr5-95922912-1	chr5	95922862	95922962	+	2.1	cIP2vsInput	Intergenic	Intergenic	-34027	NM_018866	55985	Mm.10116	NM_018866	ENSMUSG00000023078	Cxcl13	4631412M08Rik|ANGIE2|Angie|BCA-1|BLC|BLR1L|Scyb13	chemokine (C-X-C motif) ligand 13	protein-coding	0	0.277228
Merged-chr5-21412554-1	chr5	21412504	21412604	+	2.1	cIP1vsInput	"intron (NM_029195, intron 1 of 18)"	"intron (NM_029195, intron 1 of 18)"	12123	NM_029195	75172	Mm.426695	NM_029195	ENSMUSG00000064280	Ccdc146	4930528G09Rik|mKIAA1505	coiled-coil domain containing 146	protein-coding	0.01	0.336634
Merged-chr19-39077360-1	chr19	39077310	39077410	+	2.1	cIP2vsInput	"intron (NM_028191, intron 5 of 8)"	Lx2|LINE|L1	16354	NM_028191	72303	Mm.482578	NM_028191	ENSMUSG00000067231	Cyp2c65	2210009K14Rik	"cytochrome P450, family 2, subfamily c, polypeptide 65"	protein-coding	0	0.356436
Merged-chr2-82681060-1	chr2	82681010	82681110	+	2.1	cIP1vsInput	Intergenic	Intergenic	627402	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0	0.29703
Merged-chr1-49402461-1	chr1	49402411	49402511	+	2.1	cIP1vsInput	Intergenic	L1MA5|LINE|L1	-1525062	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.247525
Merged-chr5-55760793-1	chr5	55760743	55760843	+	2.1	cIP1vsInput	Intergenic	ORR1D1|LTR|ERVL-MaLR	1410801	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0	0.425743
Merged-chr9-53717719-1	chr9	53717669	53717769	+	2.1	cIP1vsInput	Intergenic	Intergenic	-11487	NM_175562	270160	Mm.290285	NM_175562	ENSMUSG00000055069	Rab39	C230094F14Rik|Rab39a	"RAB39, member RAS oncogene family"	protein-coding	0	0.336634
Merged-chr8-60220478-1	chr8	60220428	60220528	+	2.1	cIP1vsInput	Intergenic	Intergenic	-285646	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|mKat-2	aminoadipate aminotransferase	protein-coding	0.02	0.277228
Merged-chr8-103630656-1	chr8	103630606	103630706	+	2.1	cIP2vsInput	"intron (NR_045730, intron 1 of 4)"	L1M4|LINE|L1	26857	NR_045730	71058	Mm.67707	NR_045730		4933400L20Rik	-	RIKEN cDNA 4933400L20 gene	miscRNA	0.01	0.356436
Merged-chr1-92405491-1	chr1	92405441	92405541	+	2.1	cIP1vsInput	Intergenic	Intergenic	68267	NM_024197	67273	Mm.248778	NM_024197		Ndufa10	2900053E13Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 10	protein-coding	0	0.366337
Merged-chr10-121161337-1	chr10	121161287	121161387	+	2.1	cIP1vsInput	Intergenic	Intergenic	127333	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding	0.02	0.50495
Merged-chr14-116041572-1	chr14	116041522	116041622	+	2.1	cIP1vsInput	"intron (NM_175500, intron 7 of 7)"	"intron (NM_175500, intron 7 of 7)"	-632020	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	miscRNA	0	0.227723
Merged-chr14-6800445-1	chr14	6800395	6800495	+	2.1	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	227004	NM_001164727	100038847	Mm.483675	NM_001164727	ENSMUSG00000093985	Gm10406	ENSMUSG00000072735	predicted gene 10406	protein-coding	0	0.445545
Merged-chrX-100067598-1	chrX	100067548	100067648	+	2.1	cIP2vsInput	"intron (NM_001177940, intron 1 of 6)"	L1_Mur3|LINE|L1	91992	NM_001177943	13607	Mm.328086	NM_001177937	ENSMUSG00000059327	Eda	EDA1|Ed1|Eda-A1|Eda-A2|HED|Ta|XLHED|tabby	ectodysplasin-A	protein-coding	0	0.326733
Merged-chr13-106143472-1	chr13	106143422	106143522	+	2.1	cIP2vsInput	Intergenic	L1MB7|LINE|L1	699779	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0.01	0.366337
Merged-chr14-110601954-1	chr14	110601904	110602004	+	2.1	cIP1vsInput	Intergenic	Intergenic	153195	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	"SLIT and NTRK-like family, member 6"	protein-coding	0	0.277228
Merged-chr2-109391243-1	chr2	109391193	109391293	+	2.1	cIP2vsInput	Intergenic	Intergenic	110505	NM_139303	228421	Mm.274086	NM_139303	ENSMUSG00000027115	Kif18a	AU024633|B130001M12Rik	kinesin family member 18A	protein-coding	0.01	0.425743
Merged-chr5-27511921-1	chr5	27511871	27511971	+	2.1	cIP1vsInput	"intron (NM_001136060, intron 5 of 25)"	L1Md_F2|LINE|L1	-10529	NM_028561	73526	Mm.389608	NM_028561	ENSMUSG00000048703	Speer4b	1700081O22Rik|SPEER-4B	spermatogenesis associated glutamate (E)-rich protein 4b	protein-coding	0.01	0.376238
Merged-chrX-140255818-1	chrX	140255768	140255868	+	2.1	cIP2vsInput	Intergenic	L1ME1|LINE|L1	-55130	NR_037208	100499512		NR_037208	ENSMUSG00000093102	Mir3475	mmu-mir-3475	microRNA 3475	miscRNA	0.03	0.435644
Merged-chr10-58431132-1	chr10	58431082	58431182	+	2.1	cIP2vsInput	Intergenic	B1_Mm|SINE|Alu	-15720	NM_011240	19386	Mm.485644	NM_011240	ENSMUSG00000003226	Ranbp2	A430087B05Rik|AI256741|NUP358	RAN binding protein 2	protein-coding	0.02	0.435644
Merged-chr14-56304412-1	chr14	56304362	56304462	+	2.1	cIP2vsInput	Intergenic	Intergenic	-42152	NM_013542	14939	Mm.14874	NM_013542	ENSMUSG00000015437	Gzmb	AI553453|CCP-1/C11|CCP1|Ctla-1|Ctla1|GZB	granzyme B	protein-coding	0.02	0.49505
Merged-chr19-40064168-1	chr19	40064118	40064218	+	2.1	cIP2vsInput	"intron (NM_206537, intron 5 of 8)"	L1MB7|LINE|L1	9645	NM_206537	404195	Mm.379575	NM_206537	ENSMUSG00000067225	Cyp2c54	EG404195	"cytochrome P450, family 2, subfamily c, polypeptide 54"	protein-coding	0.02	0.376238
Merged-chr1-11862442-1	chr1	11862392	11862492	+	2.1	cIP1vsInput	"intron (NM_177173, intron 10 of 13)"	"intron (NM_177173, intron 10 of 13)"	448337	NM_001160371	320492	Mm.52021	NM_001160369	ENSMUSG00000057715	A830018L16Rik	-	RIKEN cDNA A830018L16 gene	protein-coding	0	0.29703
Merged-chr1-112401444-1	chr1	112401394	112401494	+	2.1	cIP2vsInput	Intergenic	Intergenic	-536526	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik	dermatan sulfate epimerase-like	protein-coding	0	0.356436
Merged-chr14-84228364-1	chr14	84228314	84228414	+	2.1	cIP2vsInput	Intergenic	Intergenic	-215199	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0	0.336634
Merged-chr11-40923052-1	chr11	40923002	40923102	+	2.1	cIP1vsInput	Intergenic	Intergenic	-167766	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding	0	0.366337
Merged-chr3-60239087-1	chr3	60239037	60239137	+	2.1	cIP2vsInput	Intergenic	Lx7|LINE|L1	157218	NM_032400	84112	Mm.125110	NM_032400	ENSMUSG00000027762	Sucnr1	Gpr91	succinate receptor 1	protein-coding	0.01	0.336634
Merged-chr5-98860588-1	chr5	98860538	98860638	+	2.1	cIP1vsInput	"intron (NM_173404, intron 1 of 2)"	"intron (NM_173404, intron 1 of 2)"	6149	NM_173404	110075	Mm.209571	NM_173404	ENSMUSG00000029335	Bmp3	9130206H07|9530029I04Rik	bone morphogenetic protein 3	protein-coding	0	0.455446
Merged-chr1-172787184-1	chr1	172787134	172787234	+	2.1	cIP1vsInput	Intergenic	Charlie21a|DNA|hAT-Charlie	89128	NM_007768	12944	Mm.28767	NM_007768	ENSMUSG00000037942	Crp	AI255847	"C-reactive protein, pentraxin-related"	protein-coding	0	0.336634
Merged-chr19-41335632-1	chr19	41335582	41335682	+	2.1	cIP2vsInput	"intron (NM_031376, intron 2 of 16)"	L1MB7|LINE|L1	49438	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding	0	0.346535
Merged-chr7-27929384-1	chr7	27929334	27929434	+	2.1	cIP1vsInput	promoter-TSS (NM_028538)	promoter-TSS (NM_028538)	46	NM_028538	73430	Mm.379224	NM_028538	ENSMUSG00000070709	1700049G17Rik	AV321011|BB026409	RIKEN cDNA 1700049G17 gene	protein-coding	0.06	0.544554
Merged-chr14-35767051-1	chr14	35767001	35767101	+	2.1	cIP2vsInput	Intergenic	Intergenic	44927	NM_001033766	239036	Mm.239970	NM_001033766	ENSMUSG00000041068	4930596D02Rik	-	RIKEN cDNA 4930596D02 gene	protein-coding	0	0.326733
Merged-chr19-8373275-1	chr19	8373225	8373325	+	2.1	cIP1vsInput	"intron (NM_177002, intron 4 of 9)"	"intron (NM_177002, intron 4 of 9)"	31830	NM_177002	319800	Mm.426083	NM_177002	ENSMUSG00000052562	Slc22a30	AA986766|C730048C13Rik|UST1R	"solute carrier family 22, member 30"	protein-coding	0.01	0.356436
Merged-chr4-23115771-1	chr4	23115721	23115821	+	2.1	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-627405	NM_008899	18992	Mm.487875	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	"POU domain, class 3, transcription factor 2"	protein-coding	0	0.336634
Merged-chr13-6891151-1	chr13	6891101	6891201	+	2.1	cIP2vsInput	Intergenic	Intergenic	-242427	NM_019703	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|PFK-C	"phosphofructokinase, platelet"	protein-coding	0.01	0.336634
Merged-chr4-78159880-1	chr4	78159830	78159930	+	2.1	cIP1vsInput	"intron (NM_011211, intron 1 of 39)"	L1M2|LINE|L1	52015	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0.01	0.306931
Merged-chr1-143717433-1	chr1	143717383	143717483	+	2.1	cIP1vsInput	Intergenic	Intergenic	-14749	NM_145991	214498	Mm.398849	NM_145991		Cdc73	8430414L16Rik|BC027756|C130030P16Rik|C81219|Hrpt2	"cell division cycle 73, Paf1/RNA polymerase II complex component"	protein-coding	0	0.435644
Merged-chr15-76879259-1	chr15	76879209	76879309	+	2.1	cIP1vsInput	promoter-TSS (NM_145916)	promoter-TSS (NM_145916)	-17	NM_145916	223669	Mm.38948	NM_145916	ENSMUSG00000033669	Zfp7	KRAB20|KRAB7|Krox-2|Zfp-7|Zfp65|Zfp80|Zfp86-rs1|mszf73-2	zinc finger protein 7	protein-coding	0.09	0.663366
Merged-chr2-12266132-1	chr2	12266082	12266182	+	2.1	cIP2vsInput	"intron (NM_001001309, intron 2 of 29)"	Lx9|LINE|L1	-35114	NR_040353	338535	Mm.483275	NR_040353		E030013I19Rik	-	RIKEN cDNA E030013I19 gene	miscRNA	0	0.326733
Merged-chr17-30868103-1	chr17	30868053	30868153	+	2.1	cIP1vsInput	"intron (NM_013811, intron 91 of 92)"	B3|SINE|B2	-33764	NM_021332	14652	Mm.390969	NM_021332	ENSMUSG00000024027	Glp1r	GLP-1R|GLP1Rc	glucagon-like peptide 1 receptor	protein-coding	0.01	0.485149
Merged-chr7-27860479-1	chr7	27860429	27860529	+	2.1	cIP1vsInput	promoter-TSS (NM_001024726)	promoter-TSS (NM_001024726)	-106	NM_001024726	545938	Mm.458180	NM_001024726		Zfp607	4732475C15Rik	zinc finger proten 607	protein-coding	0.02	0.524752
Merged-chr8-49840850-1	chr8	49840800	49840900	+	2.1	cIP2vsInput	Intergenic	Intergenic	-527262	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.316832
Merged-chr3-122653840-1	chr3	122653790	122653890	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-34173	NM_153118	214459	Mm.470230	NM_001114665	ENSMUSG00000039735	Fnbp1l	2610318I01Rik|AW548221|TOCA1	formin binding protein 1-like	protein-coding	0	0.29703
Merged-chr9-90189285-1	chr9	90189235	90189335	+	2.1	cIP2vsInput	"intron (NM_001003911, intron 13 of 23)"	"intron (NM_001003911, intron 13 of 23)"	26307	NM_001003911	108153	Mm.102141	NM_001003911	ENSMUSG00000032363	Adamts7	ADAM-TS7|ADAMTS7B	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 7"	protein-coding	0.01	0.405941
Merged-chr19-13962574-1	chr19	13962524	13962624	+	2.1	cIP1vsInput	Intergenic	MYSERV6-int|LTR|ERVK	43552	NM_001011850	258151	Mm.377361	NM_001011850	ENSMUSG00000062314	Olfr1505	MOR211-4P	olfactory receptor 1505	protein-coding	0	0.366337
Merged-chr11-43275192-1	chr11	43275142	43275242	+	2.1	cIP2vsInput	Intergenic	Lx9|LINE|L1	99269	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	miscRNA	0.01	0.376238
Merged-chr15-43750304-1	chr15	43750254	43750354	+	2.1	cIP2vsInput	Intergenic	MIRb|SINE|MIR	119725	NM_175502	239408	Mm.461451	NM_175502	ENSMUSG00000054409	Tmem74	AA549547|B230382K22Rik	transmembrane protein 74	protein-coding	0.01	0.336634
Merged-chr13-85332602-1	chr13	85332552	85332652	+	2.1	cIP1vsInput	Intergenic	MLT1B|LTR|ERVL-MaLR	-43116	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding	0	0.316832
Merged-chr18-75805818-1	chr18	75805768	75805868	+	2.1	cIP1vsInput	Intergenic	Intergenic	-14360	NM_145356	207259	Mm.159332	NM_145356	ENSMUSG00000044646	Zbtb7c	B230208J24Rik|Kr-pok|Zbtb36	zinc finger and BTB domain containing 7C	protein-coding	0.01	0.415842
Merged-chr4-26084988-1	chr4	26084938	26085038	+	2.1	cIP1vsInput	Intergenic	L1M5|LINE|L1	261664	NM_172865	242362	Mm.245602	NM_172865	ENSMUSG00000040520	Manea	4932703L02Rik	"mannosidase, endo-alpha"	protein-coding	0	0.316832
Merged-chr13-21025318-1	chr13	21025268	21025368	+	2.1	cIP1vsInput	Intergenic	Intergenic	47981	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding	0.01	0.376238
Merged-chr6-42833825-1	chr6	42833775	42833875	+	2.1	cIP2vsInput	Intergenic	Intergenic	-4058	NM_147064	259067	Mm.451673	NM_147064	ENSMUSG00000049168	Olfr449	MOR103-1	olfactory receptor 449	protein-coding	0	0.386139
Merged-chr10-73325213-1	chr10	73325163	73325263	+	2.1	cIP2vsInput	Intergenic	Intergenic	-238508	NR_040646	327768	Mm.417745	NR_040646		A330049N07Rik	-	RIKEN cDNA A330049N07 gene	miscRNA	0	0.326733
Merged-chr9-80526565-1	chr9	80526515	80526615	+	2.1	cIP1vsInput	Intergenic	L1MA9|LINE|L1	-61127	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding	0	0.306931
Merged-chr9-56278990-1	chr9	56278940	56279040	+	2.1	cIP1vsInput	"intron (NM_172924, intron 3 of 6)"	"intron (NM_172924, intron 3 of 6)"	-117920	NM_019793	56434	Mm.393554	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding	0	0.39604
Merged-chr6-109242291-1	chr6	109242241	109242341	+	2.1	cIP2vsInput	Intergenic	Intergenic	413650	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	"ER degradation enhancer, mannosidase alpha-like 1"	protein-coding	0	0.356436
Merged-chr18-33111662-1	chr18	33111612	33111712	+	2.1	cIP1vsInput	"intron (NM_009793, intron 4 of 10)"	"intron (NM_009793, intron 4 of 10)"	102154	NM_133774	170459	Mm.393277	NM_133774		Stard4	4632419C16Rik|9030213J02Rik|AA517649|AW324468	StAR-related lipid transfer (START) domain containing 4	protein-coding	0.02	0.415842
Merged-chr1-10935223-1	chr1	10935173	10935273	+	2.1	cIP1vsInput	Intergenic	Intergenic	-58242	NM_029525	109294	Mm.123247	XM_003946036	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	"phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2"	protein-coding	0	0.306931
Merged-chr9-114978336-1	chr9	114978286	114978386	+	2.1	cIP2vsInput	Intergenic	CpG	-44349	NM_175380	333433	Mm.38198	NM_175380	ENSMUSG00000050627	Gpd1l	2210409H23Rik|D9Ertd660e	glycerol-3-phosphate dehydrogenase 1-like	protein-coding	0.06	0.683168
Merged-chr4-11180988-1	chr4	11180938	11181038	+	2.1	cIP1vsInput	Intergenic	MMERGLN-int|LTR|ERV1	-10366	NM_001037134	12448	Mm.35867	NM_001037134	ENSMUSG00000028212	Ccne2	-	cyclin E2	protein-coding	0.01	0.445545
Merged-chr17-58513229-1	chr17	58513179	58513279	+	2.1	cIP1vsInput	Intergenic	Intergenic	478146	NM_027001	69239	Mm.246732	NM_027001	ENSMUSG00000024227	2610034M16Rik	AV114557	RIKEN cDNA 2610034M16 gene	protein-coding	0	0.336634
Merged-chr9-77976066-1	chr9	77976016	77976116	+	2.1	cIP1vsInput	"intron (NM_134255, intron 4 of 7)"	"intron (NM_134255, intron 4 of 7)"	58701	NM_134255	68801	Mm.475262	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	"ELOVL family member 5, elongation of long chain fatty acids (yeast)"	protein-coding	0.02	0.376238
Merged-chrX-110694409-1	chrX	110694359	110694459	+	2.1	cIP2vsInput	Intergenic	Intergenic	-120056	NM_008901	18994	Mm.405149	NM_008901	ENSMUSG00000056854	Pou3f4	Brn-4|Brn4|OTF-9|Otf9|Slf|oct-9	"POU domain, class 3, transcription factor 4"	protein-coding	0.01	0.247525
Merged-chr10-97345315-1	chr10	97345265	97345365	+	2.1	cIP2vsInput	Intergenic	Intergenic	-78163	NR_039547	100628616		NR_039547		Mir3966	mmu-mir-3966|mu-mir-3966	microRNA 3966	miscRNA	0.03	0.346535
Merged-chr4-94923946-2	chr4	94923866	94924027	+	2.1	cIP1vsInput|cIP2vsInput	"intron (NM_027089, intron 5 of 7)"	Tigger17c|DNA|TcMar-Tigger	4864	NM_027089	67753	Mm.25097	NM_027089	ENSMUSG00000028575	Eqtn	1700028B15Rik|4930579C15Rik|Afaf|C81058|Eqtl|Eqts|equatorin	"equatorin, sperm acrosome associated"	protein-coding	0.006211	0.345679
Merged-chr2-143791550-1	chr2	143791500	143791600	+	2.1	cIP2vsInput	"intron (NM_008792, intron 8 of 11)"	"intron (NM_008792, intron 8 of 11)"	-2364	NR_040625	378775	Mm.441313	NR_040625	ENSMUSG00000087115	Gm12360	9430032N09Rik|OTTMUSG00000006467	predicted gene 12360	miscRNA	0	0.336634
Merged-chr3-116778161-1	chr3	116778111	116778211	+	2.1	cIP2vsInput	"intron (NM_001081326, intron 20 of 33)"	"intron (NM_001081326, intron 20 of 33)"	30005	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	"amylo-1,6-glucosidase, 4-alpha-glucanotransferase"	protein-coding	0	0.336634
Merged-chr1-103573481-1	chr1	103573431	103573531	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1195338	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0	0.336634
Merged-chr12-43326786-1	chr12	43326736	43326836	+	2.1	cIP2vsInput	Intergenic	Intergenic	883282	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	"DnaJ (Hsp40) homolog, subfamily B, member 9"	protein-coding	0	0.336634
Merged-chr1-147514975-1	chr1	147514925	147515025	+	2.1	cIP1vsInput	Intergenic	Intergenic	1017288	NM_001145807	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.29703
Merged-chr5-59222465-1	chr5	59222415	59222515	+	2.1	cIP1vsInput	Intergenic	Intergenic	763537	NR_040683	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0	0.316832
Merged-chr1-141337217-1	chr1	141337167	141337267	+	2.1	cIP2vsInput	Intergenic	Lx9|LINE|L1	-680815	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0	0.336634
Merged-chr12-14951371-1	chr12	14951321	14951421	+	2.1	cIP1vsInput	Intergenic	L1M2|LINE|L1	99018	NR_045960	73972	Mm.107680	NR_045960		4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	miscRNA	0.02	0.366337
Merged-chr12-60256455-1	chr12	60256405	60256505	+	2.1	cIP2vsInput	Intergenic	T-rich|Low_complexity|Low_complexity	-1036972	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding	0.01	0.386139
Merged-chrX-58821510-1	chrX	58821460	58821560	+	2.1	cIP2vsInput	Intergenic	Intergenic	-89951	NM_023774	75352	Mm.60906	NM_023774	ENSMUSG00000046180	4930550L24Rik	mage-k1	RIKEN cDNA 4930550L24 gene	protein-coding	0.01	0.356436
Merged-chr18-6041049-1	chr18	6040999	6041099	+	2.1	cIP1vsInput	"intron (NM_001039692, intron 10 of 18)"	"intron (NM_001039692, intron 10 of 18)"	95049	NM_029277	75415	Mm.239675	NM_001039692	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding	0	0.316832
Merged-chr4-84599433-1	chr4	84599383	84599483	+	2.1	cIP2vsInput	"intron (NM_172870, intron 1 of 5)"	"intron (NM_172870, intron 1 of 5)"	75653	NM_172870	242509	Mm.190774	NM_172870		Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding	0	0.346535
Merged-chr13-68581625-1	chr13	68581575	68581675	+	2.1	cIP1vsInput	promoter-TSS (NM_027123)	promoter-TSS (NM_027123)	496	NM_172480	210009	Mm.205514	NM_172480	ENSMUSG00000034617	Mtrr	4732420G08|MSR	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	protein-coding	0.03	0.445545
Merged-chr11-88147670-1	chr11	88147620	88147720	+	2.1	cIP1vsInput	"intron (NM_198013, intron 1 of 10)"	L1MB4|LINE|L1	-21895	NM_001172099	103841	Mm.374846	NM_001172099	ENSMUSG00000018378	Cuedc1	AI841487|C330016O16Rik	CUE domain containing 1	protein-coding	0.02	0.465347
Merged-chr3-83177937-1	chr3	83177887	83177987	+	2.1	cIP1vsInput	Intergenic	Intergenic	122399	NM_016784	53317	Mm.286349	NM_016784	ENSMUSG00000027998	Plrg1	AA958940|C80566|Tango4	"pleiotropic regulator 1, PRL1 homolog (Arabidopsis)"	protein-coding	0	0.336634
Merged-chr13-112796690-1	chr13	112796640	112796740	+	2.1	cIP1vsInput	Intergenic	RSINE1|SINE|B4	-4102	NM_008247	19012	Mm.317186	NM_008247	ENSMUSG00000021759	Ppap2a	Hic53|Hpic53|LPP-1|LPP1|mPAP	phosphatidic acid phosphatase type 2A	protein-coding	0.01	0.415842
Merged-chr5-50493447-1	chr5	50493397	50493497	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	342114	NR_040696	73965	Mm.243823	NR_040696		4930448I18Rik	-	RIKEN cDNA 4930448I18 gene	miscRNA	0.01	0.366337
Merged-chr16-75788542-1	chr16	75788492	75788592	+	2.1	cIP2vsInput	Intergenic	Intergenic	-21724	NM_030201	110920	Mm.26704	NM_030201	ENSMUSG00000032932	Hspa13	1600002I10Rik|AV006182|B230217N24Rik|Stch	"heat shock protein 70 family, member 13"	protein-coding	0	0.306931
Merged-chr11-18454760-1	chr11	18454710	18454810	+	2.1	cIP1vsInput	Intergenic	ORR1D2-int|LTR|ERVL-MaLR	-500885	NM_026576	68145	Mm.178684	NM_026576	ENSMUSG00000016984	Etaa1	5730466H23Rik|AA672646	Ewing's tumor-associated antigen 1	protein-coding	0	0.346535
Merged-chr11-70266431-1	chr11	70266381	70266481	+	2.1	cIP2vsInput	Intergenic	Intergenic	-11090	NM_007440	11684	Mm.12286	NM_007440	ENSMUSG00000000320	Alox12	9930022G08Rik|Alox12p|P-12LO	arachidonate 12-lipoxygenase	protein-coding	0	0.544554
Merged-chrX-62857172-1	chrX	62857122	62857222	+	2.1	cIP1vsInput	Intergenic	Lx9|LINE|L1	-330161	NR_045442	75545	Mm.391270	NR_045442	ENSMUSG00000085757	1700019B21Rik	-	RIKEN cDNA 1700019B21 gene	miscRNA	0.01	0.316832
Merged-chr8-48935707-1	chr8	48935657	48935757	+	2.1	cIP1vsInput	Intergenic	Intergenic	-261017	NM_011857	23965	Mm.42191	NM_001145937	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding	0	0.287129
Merged-chr9-85561055-1	chr9	85561005	85561105	+	2.1	cIP1vsInput	Intergenic	Intergenic	188279	NM_001081282	108837	Mm.487092	NM_175371	ENSMUSG00000035941	Ibtk	5430411K16Rik|AA409502|BTKI|mKIAA1417	inhibitor of Bruton agammaglobulinemia tyrosine kinase	protein-coding	0	0.326733
Merged-chr2-77664453-1	chr2	77664403	77664503	+	2.1	cIP1vsInput	"intron (NM_178723, intron 3 of 9)"	"intron (NM_178723, intron 3 of 9)"	38819	NM_001113399	241494	Mm.490320	NM_001113399	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding	0.01	0.316832
Merged-chr7-103831753-1	chr7	103831703	103831803	+	2.1	cIP2vsInput	Intergenic	Intergenic	-3825	NM_001201391	100503605	Mm.288567	NM_001201391		Beta-s	Hbbt1|Hbbt2	hemoglobin subunit beta-1-like	protein-coding	0.01	0.376238
Merged-chr1-116614737-1	chr1	116614687	116614787	+	2.1	cIP1vsInput	Intergenic	Intergenic	929600	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0	0.405941
Merged-chr6-55152936-1	chr6	55152886	55152986	+	2.1	cIP2vsInput	Intergenic	Intergenic	-19964	NM_009953	12922	Mm.236081	NM_009953	ENSMUSG00000003476	Crhr2	CRF-R2|CRFR2alpha|CRFR2beta|Crfr2	corticotropin releasing hormone receptor 2	protein-coding	0	0.366337
Merged-chr14-33923289-1	chr14	33923239	33923339	+	2.1	cIP2vsInput	promoter-TSS (NM_145741)	promoter-TSS (NM_145741)	-298	NM_145741	14560	Mm.432071	NM_145741	ENSMUSG00000021943	Gdf10	Bmp3b	growth differentiation factor 10	protein-coding	0.07	0.70297
Merged-chr13-105825522-1	chr13	105825472	105825572	+	2.1	cIP2vsInput	Intergenic	Intergenic	381829	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0.02	0.287129
Merged-chr1-127518694-1	chr1	127518644	127518744	+	2.1	cIP2vsInput	"intron (NM_028135, intron 5 of 7)"	"intron (NM_028135, intron 5 of 7)"	159327	NM_028135	72160	Mm.281287	NM_028135	ENSMUSG00000026347	Tmem163	2610024A01Rik|SV31	transmembrane protein 163	protein-coding	0	0.316832
Merged-chr9-95150784-1	chr9	95150734	95150834	+	2.1	cIP1vsInput	"intron (NM_177909, intron 14 of 15)"	"intron (NM_177909, intron 14 of 15)"	256486	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding	0.02	0.475248
Merged-chr3-76099452-1	chr3	76099402	76099502	+	2.1	cIP1vsInput	"intron (NM_001253719, intron 1 of 15)"	"intron (NM_001253719, intron 1 of 15)"	23869	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0.02	0.346535
Merged-chr11-18611854-1	chr11	18611804	18611904	+	2.1	cIP1vsInput	Intergenic	Intergenic	407115	NM_001193271	17268	Mm.445192	NM_001193271	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding	0	0.237624
Merged-chr4-51295258-1	chr4	51295208	51295308	+	2.1	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	78580	NM_001162865	74914	Mm.159368	NM_001162865	ENSMUSG00000039555	Cylc2	4930488P18Rik	"cylicin, basic protein of sperm head cytoskeleton 2"	protein-coding	0	0.29703
Merged-chr3-151167620-1	chr3	151167570	151167670	+	2.1	cIP2vsInput	Intergenic	Intergenic	-270262	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0.01	0.356436
Merged-chr11-8136469-1	chr11	8136419	8136519	+	2.1	cIP1vsInput	Intergenic	Intergenic	528066	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding	0	0.316832
Merged-chr8-6415691-1	chr8	6415641	6415741	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1310459	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.306931
Merged-chr15-91471514-1	chr15	91471464	91471564	+	2.1	cIP1vsInput	"intron (NM_001033633, intron 3 of 9)"	ORR1D1|LTR|ERVL-MaLR	101747	NM_001033633	239606	Mm.360596	NM_001033633	ENSMUSG00000036298	Slc2a13	6530403A04|A630029G22Rik|AI505012|Gm308	"solute carrier family 2 (facilitated glucose transporter), member 13"	protein-coding	0.01	0.386139
Merged-chr10-85948378-1	chr10	85948328	85948428	+	2.1	cIP2vsInput	"intron (NM_145422, intron 5 of 11)"	"intron (NM_145422, intron 5 of 11)"	9415	NM_145422	28088	Mm.9257	NM_145422	ENSMUSG00000001783	D10Wsu52e	AI255213|AI463255|FAAP|HSPC117	"DNA segment, Chr 10, Wayne State University 52, expressed"	protein-coding	0	0.316832
Merged-chr13-16725145-1	chr13	16725095	16725195	+	2.1	cIP1vsInput	Intergenic	Intergenic	710670	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding	0.01	0.376238
Merged-chr12-33375927-1	chr12	33375877	33375977	+	2.1	cIP1vsInput	Intergenic	Intergenic	-18927	NM_029152	75040	Mm.156068	NM_029152	ENSMUSG00000020562	Efcab10	4930504H06Rik	EF-hand calcium binding domain 10	protein-coding	0	0.386139
Merged-chr9-74676586-1	chr9	74676536	74676636	+	2.1	cIP1vsInput	Intergenic	L1MC5a|LINE|L1	-171851	NR_045284	100503019	Mm.482658	NR_045284	ENSMUSG00000066477	Gm16551	-	predicted gene 16551	miscRNA	0	0.346535
Merged-chr6-111043228-1	chr6	111043178	111043278	+	2.1	cIP2vsInput	"intron (NM_177328, intron 2 of 9)"	MIR|SINE|MIR	397630	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0	0.336634
Merged-chr2-144917295-1	chr2	144917245	144917345	+	2.1	cIP1vsInput	Intergenic	Intergenic	93629	NM_025490	66328	Mm.490926	NM_025490	ENSMUSG00000027431	Scp2d1	1700010M22Rik	SCP2 sterol-binding domain containing 1	protein-coding	0	0.306931
Merged-chr5-8134620-1	chr5	8134570	8134670	+	2.1	cIP2vsInput	"intron (NM_001007220, intron 16 of 28)"	"intron (NM_001007220, intron 16 of 28)"	78078	NM_001080974	109552	Mm.96211	NM_001080974	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding	0	0.386139
Merged-chr10-88865489-1	chr10	88865439	88865539	+	2.1	cIP2vsInput	Intergenic	Intergenic	-20503	NM_145423	216225	Mm.77381	NM_145423	ENSMUSG00000020062	Slc5a8	Ait|SMCT	"solute carrier family 5 (iodide transporter), member 8"	protein-coding	0	0.306931
Merged-chr14-36448124-1	chr14	36448074	36448174	+	2.1	cIP2vsInput	Intergenic	Intergenic	353159	NM_175008	218921	Mm.212464	NM_175008	ENSMUSG00000096405	4930474N05Rik	-	RIKEN cDNA 4930474N05 gene	protein-coding	0.01	0.336634
Merged-chr5-55034440-1	chr5	55034390	55034490	+	2.1	cIP2vsInput	Intergenic	Intergenic	684448	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0	0.306931
Merged-chr5-147769445-1	chr5	147769395	147769495	+	2.1	cIP2vsInput	Intergenic	Intergenic	-43457	NM_010228	14254	Mm.389712	NM_010228	ENSMUSG00000029648	Flt1	AI323757|Flt-1|VEGFR-1|VEGFR1|sFlt1	FMS-like tyrosine kinase 1	protein-coding	0	0.306931
Merged-chr12-20272113-1	chr12	20272063	20272163	+	2.1	cIP1vsInput	Intergenic	B1_Mm|SINE|Alu	543666	NR_015521	69513	Mm.273972	NR_015521		1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	miscRNA	0	0.366337
Merged-chr11-10013059-1	chr11	10013009	10013109	+	2.1	cIP2vsInput	Intergenic	Intergenic	821117	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	"ATP-binding cassette, sub-family A (ABC1), member 13"	protein-coding	0	0.306931
Merged-chr2-10531064-1	chr2	10531014	10531114	+	2.1	cIP2vsInput	"intron (NM_177386, intron 13 of 22)"	"intron (NM_177386, intron 13 of 22)"	13460	NR_035417	100316668		NR_035417		Mir669i	Mirn669i|mmu-mir-669i	microRNA 669i	miscRNA	0.01	0.29703
Merged-chr12-108835986-1	chr12	108835936	108836036	+	2.1	cIP2vsInput	promoter-TSS (NM_181328)	promoter-TSS (NM_181328)	-110	NM_181328	214663	Mm.266264	NM_181328	ENSMUSG00000021265	Slc25a29	C030003J19Rik|CACL|mCACL	"solute carrier family 25 (mitochondrial carrier, palmitoylcarnitine transporter), member 29"	protein-coding	0.12	0.752475
Merged-chr1-163259015-1	chr1	163258965	163259065	+	2.1	cIP2vsInput	"intron (NM_001025570, intron 2 of 2)"	MIRb|SINE|MIR	54635	NM_011127	18933	Mm.288642	NM_001025570	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding	0	0.29703
Merged-chr3-57755162-1	chr3	57755112	57755212	+	2.1	cIP2vsInput	"intron (NM_011883, intron 1 of 8)"	"intron (NM_011883, intron 1 of 8)"	19096	NM_001113413	24017	Mm.274360	NM_001113413	ENSMUSG00000036503	Rnf13	2010001H16Rik|Rzf	ring finger protein 13	protein-coding	0	0.366337
Merged-chr15-16107017-1	chr15	16106967	16107067	+	2.1	cIP1vsInput	Intergenic	Intergenic	-671084	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0	0.267327
Merged-chr13-108026040-1	chr13	108025990	108026090	+	2.1	cIP1vsInput	Intergenic	Intergenic	-18434	NM_001048250	75616	Mm.29464	NM_001048250		Smim15	2810008M24Rik	small integral membrane protein 15	protein-coding	0.01	0.514851
Merged-chr3-150747316-1	chr3	150747266	150747366	+	2.1	cIP1vsInput	Intergenic	Intergenic	-690566	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0	0.316832
Merged-chr10-73611872-1	chr10	73611822	73611922	+	2.1	cIP2vsInput	Intergenic	Intergenic	-209995	NM_001142760	11994	Mm.338933	NM_001142735	ENSMUSG00000052613	Pcdh15	BB078305|ENSMUSG00000046980|Gm9815|Ush1f|av|nmf19	protocadherin 15	protein-coding	0.01	0.346535
Merged-chr8-109325380-1	chr8	109325330	109325430	+	2.1	cIP1vsInput	Intergenic	Intergenic	15528	NR_002928	384864	Mm.390083	NR_002928		Gm1943	-	WD repeat domain 70 pseudogene	pseudo	0.03	0.485149
Merged-chrX-130888394-1	chrX	130888344	130888444	+	2.1	cIP2vsInput	Intergenic	L1VL4|LINE|L1	1138652	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diap2	Dia3|Diaph2|Drf2|E430022I22Rik	diaphanous homolog 2 (Drosophila)	protein-coding	0	0.316832
Merged-chr6-122457595-1	chr6	122457545	122457645	+	2.1	cIP2vsInput	"intron (NM_027664, intron 5 of 5)"	"intron (NM_027664, intron 5 of 5)"	28710	NM_027664	108653	Mm.277939	NM_027664	ENSMUSG00000040649	Rimklb	4931417E21Rik|4933426K21Rik|AA097693|AI325948|AU015629|Naags	ribosomal modification protein rimK-like family member B	protein-coding	0	0.386139
Merged-chr1-179161717-1	chr1	179161667	179161767	+	2.1	cIP2vsInput	"intron (NM_027188, intron 5 of 11)"	"intron (NM_027188, intron 5 of 11)"	356286	NM_027188	69726	Mm.222338	NM_027188		Smyd3	2410008A19Rik|Zmynd1	SET and MYND domain containing 3	protein-coding	0.01	0.356436
Merged-chr2-156585030-1	chr2	156584980	156585080	+	2.1	cIP2vsInput	Intergenic	Intergenic	28392	NR_040372	100504350	Mm.94426	NR_040372	ENSMUSG00000086118	Gm14169	OTTMUSG00000015869	predicted gene 14169	miscRNA	0.05	0.60396
Merged-chr14-81862611-1	chr14	81862561	81862661	+	2.1	cIP2vsInput	Intergenic	Intergenic	1862309	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.316832
Merged-chr14-34896484-1	chr14	34896434	34896534	+	2.1	cIP2vsInput	"intron (NM_008166, intron 2 of 15)"	CpG	1875	NR_029774	723847		NR_029774		Mir346	Mirn346|mmu-mir-346	microRNA 346	miscRNA	0.12	0.70297
Merged-chr19-51786033-1	chr19	51785983	51786083	+	2.1	cIP1vsInput	Intergenic	Intergenic	-478290	NM_008386	16333	Mm.46269	NM_008386	ENSMUSG00000035804	Ins1	Ins-1|Ins2-rs1	insulin I	protein-coding	0.01	0.366337
Merged-chr12-84063805-1	chr12	84063755	84063855	+	2.1	cIP2vsInput	Intergenic	Intergenic	-5520	NM_145444	217698	Mm.484019	NM_145444	ENSMUSG00000042540	Acot5	BC016076|PTE-Ic	acyl-CoA thioesterase 5	protein-coding	0.01	0.376238
Merged-chr4-79295053-1	chr4	79295003	79295103	+	2.1	cIP2vsInput	Intergenic	Lx7|LINE|L1	-1083158	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0	0.306931
Merged-chr14-89605384-1	chr14	89605334	89605434	+	2.1	cIP2vsInput	Intergenic	Intergenic	-290840	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0	0.306931
Merged-chr6-3836919-1	chr6	3836869	3836969	+	2.1	cIP1vsInput	Intergenic	Intergenic	-72206	NM_007588	12311	Mm.4642	NM_001042725	ENSMUSG00000023964	Calcr	Clr	calcitonin receptor	protein-coding	0	0.267327
Merged-chr3-19000043-1	chr3	18999993	19000093	+	2.1	cIP2vsInput	Intergenic	Intergenic	163022	NM_028840	74252	Mm.316007	XM_003689346	ENSMUSG00000027599	Armc1	2310016N05Rik|2900046P06Rik|3110009G21Rik|AA409258|AW048872|Arcp|C330014L16Rik	armadillo repeat containing 1	protein-coding	0	0.356436
Merged-chr6-148561816-1	chr6	148561766	148561866	+	2.1	cIP2vsInput	Intergenic	(TTGG)n|Simple_repeat|Simple_repeat	52493	NR_045867	622319	Mm.491049	NM_001037912	ENSMUSG00000070995	Gm6313	EG622319	predicted gene 6313	miscRNA	0	0.366337
Merged-chr2-43019309-1	chr2	43019259	43019359	+	2.1	cIP2vsInput	Intergenic	L1MA6|LINE|L1	-365711	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0	0.346535
Merged-chr3-50093074-1	chr3	50093024	50093124	+	2.1	cIP2vsInput	Intergenic	Intergenic	-335758	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding	0.01	0.316832
Merged-chr12-10360724-1	chr12	10360674	10360774	+	2.1	cIP2vsInput	Intergenic	Intergenic	-9247	NM_027588	70881	Mm.272843	NM_027588	ENSMUSG00000020622	Nt5c1b	4921514H13Rik|AIRP|CN-IB	"5'-nucleotidase, cytosolic IB"	protein-coding	0	0.435644
Merged-chr3-93315445-1	chr3	93315395	93315495	+	2.1	cIP2vsInput	Intergenic	Intergenic	-4304	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|AV011854|S100a18|S100a18-ps1	hornerin	protein-coding	0.01	0.306931
Merged-chr18-67921738-1	chr18	67921688	67921788	+	2.1	cIP1vsInput	Intergenic	Lx9|LINE|L1	-11519	NM_172631	52662	Mm.440183	NM_172631	ENSMUSG00000024544	Ldlrad4	8230401C20Rik|A430083H02|A430108L08Rik|C18orf1|D18Ertd653e|D330030L18Rik	low density lipoprotein receptor class A domain containing 4	protein-coding	0.03	0.415842
Merged-chr5-109532586-1	chr5	109532536	109532636	+	2.1	cIP1vsInput	Intergenic	Intergenic	26407	NM_016715	57914	Mm.35771	NM_001164735	ENSMUSG00000033467	Crlf2	CRLM2|Ly114|Tpte2|Tslpr	cytokine receptor-like factor 2	protein-coding	0	0.326733
Merged-chr17-6655421-1	chr17	6655371	6655471	+	2.1	cIP2vsInput	"intron (NM_001166627, intron 1 of 4).2"	CpG	410	NM_001166630	100040563	Mm.458102	NM_001166630		Dynlt1c	100040603|Dynlt1d	dynein light chain Tctex-type 1C	protein-coding	0.14	0.663366
Merged-chr16-19254335-1	chr16	19254285	19254385	+	2.1	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	32406	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding	0.01	0.366337
Merged-chr13-100527739-1	chr13	100527689	100527789	+	2.1	cIP1vsInput	"intron (NM_008756, intron 4 of 8)"	"intron (NM_008756, intron 4 of 8)"	24759	NM_008756	18260	Mm.4807	NM_008756	ENSMUSG00000021638	Ocln	AI503564|Ocl	occludin	protein-coding	0	0.376238
Merged-chr3-10496385-1	chr3	10496335	10496435	+	2.1	cIP2vsInput	Intergenic	Lx6|LINE|L1	-56261	NM_001127191	74718	Mm.440548	NM_001127191	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding	0	0.316832
Merged-chr11-27006549-1	chr11	27006499	27006599	+	2.1	cIP1vsInput	Intergenic	Intergenic	221441	NR_002890	654472	Mm.347777	NR_002890	ENSMUSG00000069939	Gm12070	OTTMUSG00000005300	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0	0.29703
Merged-chr18-58851863-1	chr18	58851813	58851913	+	2.1	cIP1vsInput	"intron (NM_175506, intron 2 of 22)"	"intron (NM_175506, intron 2 of 22)"	15099	NM_175506	240322	Mm.71963	NM_175506	ENSMUSG00000053441	Adamts19	4831407I23Rik|AU015154|D230034E10Rik	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 19"	protein-coding	0	0.287129
Merged-chr2-29157647-1	chr2	29157597	29157697	+	2.1	cIP2vsInput	"intron (NM_198033, intron 13 of 25)"	"intron (NM_198033, intron 13 of 25)"	32655	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding	0	0.39604
Merged-chr3-86489111-1	chr3	86489061	86489161	+	2.1	cIP1vsInput	"intron (NM_001077687, intron 37 of 50)"	L1ME1|LINE|L1	59172	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding	0.01	0.346535
Merged-chr10-47731717-1	chr10	47731667	47731767	+	2.1	cIP1vsInput	Intergenic	L1M2|LINE|L1	1364126	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	"proteasome (prosome, macropain) subunit, alpha type 6 pseudogene"	pseudo	0	0.366337
Merged-chr10-87691106-1	chr10	87691056	87691156	+	2.1	cIP2vsInput	Intergenic	Intergenic	-167950	NM_001111275	16000	Mm.268521	NM_001111274	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding	0	0.346535
Merged-chrX-92422100-1	chrX	92422050	92422150	+	2.1	cIP2vsInput	"intron (NM_173783, intron 3 of 4)"	"intron (NM_173783, intron 3 of 4)"	-67849	NM_001034103	546347	Mm.380183	NM_001034103	ENSMUSG00000071726	Gm5941	EG546347	predicted gene 5941	protein-coding	0	0.316832
Merged-chr18-25816988-1	chr18	25816938	25817038	+	2.1	cIP1vsInput	Intergenic	Intergenic	-63005	NM_001174074	108013	Mm.266435	NM_001146292	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	"CUGBP, Elav-like family member 4"	protein-coding	0.01	0.386139
Merged-chrX-41315072-1	chrX	41315022	41315122	+	2.1	cIP2vsInput	Intergenic	Intergenic	-86232	NM_016886	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3|mKIAA4184	"glutamate receptor, ionotropic, AMPA3 (alpha 3)"	protein-coding	0	0.346535
Merged-chr11-81303566-1	chr11	81303516	81303616	+	2.1	cIP2vsInput	"intron (NM_001034013, intron 1 of 9)"	"intron (NM_001034013, intron 1 of 9)"	-150663	NM_007384	11418	Mm.234998	NM_001034013	ENSMUSG00000020704	Asic2	ACIC2|Accn1|BNC1|BNaC1|BNaC1a|Mdeg	acid-sensing (proton-gated) ion channel 2	protein-coding	0.01	0.326733
Merged-chr18-88843400-1	chr18	88843350	88843450	+	2.1	cIP2vsInput	Intergenic	Lx3C|LINE|L1	50807	NM_018821	54607	Mm.476577	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding	0.01	0.336634
Merged-chr3-113791572-1	chr3	113791522	113791622	+	2.1	cIP2vsInput	Intergenic	Intergenic	-161423	NM_001038696	67225	Mm.316928	NM_001038696	ENSMUSG00000027981	Rnpc3	2810441O16Rik|AI447568|C030014B17Rik	"RNA-binding region (RNP1, RRM) containing 3"	protein-coding	0	0.336634
Merged-chr19-9501696-1	chr19	9501646	9501746	+	2.1	cIP1vsInput	Intergenic	L1VL4|LINE|L1	57552	NR_073559	619371	Mm.391205	NM_001030317		Stxbp3b	Munc18c(L)|Stxbp3-1	syntaxin-binding protein 3B	pseudo	0	0.336634
Merged-chr14-18090068-1	chr14	18090018	18090118	+	2.1	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	108424	NM_009380	21834	Mm.32563	NM_001113417	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding	0.01	0.316832
Merged-chr2-84908641-1	chr2	84908591	84908691	+	2.1	cIP2vsInput	Intergenic	L1MC1|LINE|L1	-21949	NM_199223	269295	Mm.389289	NM_199223	ENSMUSG00000050896	Rtn4rl2	Ngr2|Ngrh1|Ngrl3	reticulon 4 receptor-like 2	protein-coding	0	0.306931
Merged-chr12-66069253-1	chr12	66069203	66069303	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	215148	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding	0	0.366337
Merged-chr1-92611462-1	chr1	92611412	92611512	+	2.1	cIP1vsInput	Intergenic	Intergenic	3623	NM_146491	258484	Mm.377528	NM_146491		Olfr1410	MOR208-2	olfactory receptor 1410	protein-coding	0	0.277228
Merged-chr17-54814997-1	chr17	54814947	54815047	+	2.1	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-444923	NR_045825	69418	Mm.391004	NR_045825		1700025K24Rik	-	RIKEN cDNA 1700025K24 gene	miscRNA	0	0.386139
Merged-chr8-37887641-1	chr8	37887591	37887691	+	2.1	cIP1vsInput	"intron (NM_145841, intron 2 of 7)"	"intron (NM_145841, intron 2 of 7)"	364561	NR_029884	723860		NR_029884		Mir383	Mirn383|mmu-mir-383	microRNA 383	miscRNA	0	0.326733
Merged-chr2-139530252-1	chr2	139530202	139530302	+	2.1	cIP1vsInput	"intron (NM_175467, intron 2 of 12)"	L1M4b|LINE|L1	36332	NM_175467	228677	Mm.100450	NM_175467	ENSMUSG00000039092	Sptlc3	C130053K05Rik	"serine palmitoyltransferase, long chain base subunit 3"	protein-coding	0	0.356436
Merged-chr3-156039574-1	chr3	156039524	156039624	+	2.1	cIP2vsInput	Intergenic	Intergenic	63220	NR_040553	329780	Mm.119000	NR_040553		9330178D15Rik	9330178D15	RIKEN cDNA 9330178D15 gene	miscRNA	0	0.316832
Merged-chr6-10708006-1	chr6	10707956	10708056	+	2.1	cIP2vsInput	Intergenic	Intergenic	266372	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	miscRNA	0	0.326733
Merged-chr7-94278882-1	chr7	94278832	94278932	+	2.1	cIP1vsInput	Intergenic	Intergenic	1199003	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0.01	0.346535
Merged-chr18-59271611-1	chr18	59271561	59271661	+	2.1	cIP2vsInput	"intron (NM_001081328, intron 2 of 2)"	"intron (NM_001081328, intron 2 of 2)"	96271	NM_001081328	78923	Mm.485185	NM_001081328		Chsy3	4833446K15Rik|AI662215	chondroitin sulfate synthase 3	protein-coding	0	0.376238
Merged-chr11-15698021-1	chr11	15697971	15698071	+	2.1	cIP1vsInput	Intergenic	Intergenic	-559703	NM_145967	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	9330184N17Rik|BC027127|Vstm2	V-set and transmembrane domain containing 2A	protein-coding	0.01	0.29703
Merged-chr14-113973621-1	chr14	113973571	113973671	+	2.1	cIP2vsInput	Intergenic	Intergenic	-858344	NR_045661	75822	Mm.410813	NR_045661		4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	miscRNA	0.01	0.346535
Merged-chr8-23779305-1	chr8	23779255	23779355	+	2.1	cIP1vsInput	"intron (NM_177086, intron 2 of 6)"	L1M5|LINE|L1	109644	NM_177086	320158	Mm.121274	NM_001277239	ENSMUSG00000037492	Zmat4	9630048M01Rik	"zinc finger, matrin type 4"	protein-coding	0	0.366337
Merged-chr1-68197361-1	chr1	68197311	68197411	+	2.1	cIP1vsInput	"intron (NM_010154, intron 20 of 26)"	"intron (NM_010154, intron 20 of 26)"	910698	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0.01	0.326733
Merged-chr11-59525480-1	chr11	59525430	59525530	+	2.1	cIP1vsInput	Intergenic	Intergenic	-17206	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	"NLR family, pyrin domain containing 3"	protein-coding	0.05	0.534653
Merged-chr6-47847924-1	chr6	47847874	47847974	+	2.1	cIP2vsInput	"intron (NM_027477, intron 2 of 5)"	"intron (NM_027477, intron 2 of 5)"	12263	NM_027477	272347	Mm.395440	NM_027477	ENSMUSG00000062519	Zfp398	5730513I23Rik|6430539K21	zinc finger protein 398	protein-coding	0	0.316832
Merged-chr16-5455214-1	chr16	5455164	5455264	+	2.1	cIP1vsInput	Intergenic	B4|SINE|B4	-199258	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Fam86	5730409G15Rik|Fam86a	family with sequence similarity 86	protein-coding	0.03	0.534653
Merged-chr16-61150864-1	chr16	61150814	61150914	+	2.1	cIP2vsInput	Intergenic	ETnERV3-int|LTR|ERVK	-545333	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0	0.356436
Merged-chr18-79672445-1	chr18	79672395	79672495	+	2.1	cIP1vsInput	Intergenic	Intergenic	-374450	NM_053117	93737	Mm.24678	NM_053117	ENSMUSG00000056214	Pard6g	2410049N21Rik|Par6a	par-6 partitioning defective 6 homolog gamma (C. elegans)	protein-coding	0	0.435644
Merged-chr17-50424813-1	chr17	50424763	50424863	+	2.1	cIP2vsInput	Intergenic	RLTR19-int|LTR|ERVK	-84734	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding	0	0.455446
Merged-chr17-10947374-1	chr17	10947324	10947424	+	2.1	cIP2vsInput	"intron (NM_016694, intron 1 of 11)"	"intron (NM_016694, intron 1 of 11)"	106990	NM_016694	50873	Mm.311110	NM_016694		Park2	PRKN	"Parkinson disease (autosomal recessive, juvenile) 2, parkin"	protein-coding	0.01	0.356436
Merged-chr3-91488757-1	chr3	91488707	91488807	+	2.1	cIP2vsInput	Intergenic	Intergenic	-397952	NM_001101461	229550	Mm.98335	NM_001101461	ENSMUSG00000091175	9130204L05Rik	Gm127	RIKEN cDNA 9130204L05 gene	protein-coding	0	0.336634
Merged-chr2-146208761-1	chr2	146208711	146208811	+	2.1	cIP2vsInput	Intergenic	L1MB5|LINE|L1	-13236	NM_016889	53626	Mm.379070	NM_016889	ENSMUSG00000068154	Insm1	IA-1	insulinoma-associated 1	protein-coding	0	0.336634
Merged-chr11-86074954-1	chr11	86074904	86075004	+	2.1	cIP2vsInput	"intron (NM_178309, intron 17 of 19)"	"intron (NM_178309, intron 17 of 19)"	-50604	NR_046030	629393	Mm.372867	NR_046030		Gm20759	-	"predicted gene, 20759"	miscRNA	0.01	0.376238
Merged-chr5-5722161-1	chr5	5722111	5722211	+	2.1	cIP1vsInput	Intergenic	Intergenic	27156	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding	0.01	0.346535
Merged-chr2-83812474-1	chr2	83812424	83812524	+	2.1	cIP1vsInput	promoter-TSS (NM_175514)	promoter-TSS (NM_175514)	-254	NM_175514	241520	Mm.436122	NM_175514		Fam171b	D430039N05Rik	"family with sequence similarity 171, member B"	protein-coding	0.02	0.524752
Merged-chr18-29708350-1	chr18	29708300	29708400	+	2.1	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	-211934	NR_045391	78058	Mm.416952	NR_045391		4930578E11Rik	-	RIKEN cDNA 4930578E11 gene	miscRNA	0.01	0.356436
Merged-chr13-39528067-1	chr13	39528017	39528117	+	2.1	cIP1vsInput	Intergenic	Intergenic	-567192	NM_001170431	108652	Mm.255506	NM_001170430	ENSMUSG00000021432	Slc35b3	4921526O06Rik|AI428480|CGI-19|PABST2|PAPST2	"solute carrier family 35, member B3"	protein-coding	0	0.287129
Merged-chr7-12321242-1	chr7	12321192	12321292	+	2.1	cIP1vsInput	TTS (NM_134209)	TTS (NM_134209)	886	NM_134209	171243	Mm.377199	NM_134209	ENSMUSG00000066804	Vmn1r83	V1rg8	vomeronasal 1 receptor 83	protein-coding	0	0.39604
Merged-chr14-84155351-1	chr14	84155301	84155401	+	2.1	cIP1vsInput	Intergenic	Intergenic	-288212	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0	0.366337
Merged-chr6-75395185-1	chr6	75395135	75395235	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1847532	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0	0.356436
Merged-chr3-159574887-1	chr3	159574837	159574937	+	2.1	cIP1vsInput	Intergenic	Lx|LINE|L1	-24294	NM_029987	19892	Mm.131708	NM_029987	ENSMUSG00000028174	Rpe65	65kDa|A930029L06Rik|LCA2|Mord1|RP20|rd12	retinal pigment epithelium 65	protein-coding	0.01	0.326733
Merged-chr15-29165335-1	chr15	29165285	29165385	+	2.1	cIP2vsInput	Intergenic	Intergenic	961569	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnahc5	AU022615|Dnah5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	"dynein, axonemal, heavy chain 5"	protein-coding	0	0.247525
Merged-chr19-13758776-1	chr19	13758726	13758826	+	2.1	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-9568	NM_146344	258341	Mm.377442	NM_146344	ENSMUSG00000047207	Olfr1495	MOR266-9	olfactory receptor 1495	protein-coding	0	0.306931
Merged-chr1-81635725-1	chr1	81635675	81635775	+	2.1	cIP1vsInput	Intergenic	Intergenic	558408	NM_172849	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding	0	0.326733
Merged-chr17-23924494-1	chr17	23924444	23924544	+	2.1	cIP1vsInput	Intergenic	Intergenic	7036	NM_001077633	620253	Mm.390964	XM_003945992	ENSMUSG00000057417	Dcpp3	Dcpp-3|EG620253|SPT-3	demilune cell and parotid protein 3	protein-coding	0.01	0.534653
Merged-chr2-49303932-1	chr2	49303882	49303982	+	2.1	cIP2vsInput	"intron (NM_029924, intron 15 of 16)"	"intron (NM_029924, intron 15 of 16)"	-147554	NM_172663	227867	Mm.29167	NM_172663	ENSMUSG00000069495	Epc2	5830499L14|D2Ertd694e	enhancer of polycomb homolog 2 (Drosophila)	protein-coding	0	0.277228
Merged-chr14-89271177-1	chr14	89271127	89271227	+	2.1	cIP1vsInput	Intergenic	Intergenic	-625047	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0	0.227723
Merged-chr17-54707418-1	chr17	54707368	54707468	+	2.1	cIP1vsInput	Intergenic	Intergenic	-337344	NR_045825	69418	Mm.391004	NR_045825		1700025K24Rik	-	RIKEN cDNA 1700025K24 gene	miscRNA	0	0.287129
Merged-chr4-92401094-1	chr4	92401044	92401144	+	2.1	cIP2vsInput	Intergenic	Intergenic	-253873	NM_027034	69314	Mm.55891	NM_027034	ENSMUSG00000028533	Izumo3	1700011H22Rik	IZUMO family member 3	protein-coding	0	0.306931
Merged-chr14-64555064-1	chr14	64555014	64555114	+	2.1	cIP2vsInput	Intergenic	ID_B1|SINE|B4	-33051	NR_040709	268755	Mm.194050	NR_040709		A930011O12Rik	Rncr3	RIKEN cDNA A930011O12 gene	miscRNA	0	0.39604
Merged-chr10-105996703-1	chr10	105996653	105996753	+	2.1	cIP2vsInput	Intergenic	Intergenic	155224	NM_025602	52713	Mm.339224	NM_025602		Ccdc59	2300004H16Rik|D10Ertd718e	coiled-coil domain containing 59	protein-coding	0	0.386139
Merged-chr4-90793174-1	chr4	90793124	90793224	+	2.1	cIP2vsInput	Intergenic	Lx10|LINE|L1	-431860	NR_033610	619842	Mm.484218	NR_033610	ENSMUSG00000080756	Gm12633	OTTMUSG00000007790	zinc finger protein 352 pseudogene	pseudo	0	0.356436
Merged-chr4-90457302-1	chr4	90457252	90457352	+	2.1	cIP2vsInput	Intergenic	MTE-int|LTR|ERVL-MaLR	-95988	NR_033610	619842	Mm.484218	NR_033610	ENSMUSG00000080756	Gm12633	OTTMUSG00000007790	zinc finger protein 352 pseudogene	pseudo	0	0.306931
Merged-chr4-4571460-1	chr4	4571410	4571510	+	2.1	cIP2vsInput	Intergenic	L1MEc|LINE|L1	221846	NM_177730	242291	Mm.369779	NM_177730		Impad1	1110001C20Rik|AA408880|AI451589|AL022796|B230207P20|Jaws|gPAPP	inositol monophosphatase domain containing 1	protein-coding	0.01	0.346535
Merged-chr1-80747592-1	chr1	80747542	80747642	+	2.1	cIP1vsInput	"intron (NM_175291, intron 1 of 55)"	"intron (NM_175291, intron 1 of 55)"	10961	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding	0	0.316832
Merged-chr12-11907037-1	chr12	11906987	11907087	+	2.1	cIP2vsInput	Intergenic	Intergenic	-24138	NR_003964	627110	Mm.194735	NR_003964		Tubb2a-ps2	C79445	"tubulin, beta 2a, pseudogene 2"	pseudo	0.01	0.306931
Merged-chr6-11000270-1	chr6	11000220	11000320	+	2.1	cIP2vsInput	Intergenic	Lx7|LINE|L1	-25892	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	miscRNA	0	0.336634
Merged-chr12-60271162-1	chr12	60271112	60271212	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1051679	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding	0	0.326733
Merged-chr8-55798351-1	chr8	55798301	55798401	+	2.1	cIP2vsInput	Intergenic	Intergenic	108613	NM_175939	244486	Mm.67684	NM_175939	ENSMUSG00000046258	Adam29	-	a disintegrin and metallopeptidase domain 29	protein-coding	0	0.316832
Merged-chr7-83821926-1	chr7	83821876	83821976	+	2.1	cIP2vsInput	Intergenic	Intergenic	-27087	NM_029335	75556	Mm.17649	NM_029335	ENSMUSG00000011154	1700026D08Rik	AW047638|AW551802	RIKEN cDNA 1700026D08 gene	protein-coding	0	0.445545
Merged-chr3-28990705-1	chr3	28990655	28990755	+	2.1	cIP2vsInput	Intergenic	Intergenic	-91872	NM_001167748	75740	Mm.330948	NM_001167748	ENSMUSG00000063600	Egfem1	6130401L20Rik|Efcab11	EGF-like and EMI domain containing 1	protein-coding	0	0.346535
Merged-chr6-130059628-1	chr6	130059578	130059678	+	2.1	cIP2vsInput	"exon (NM_013793, exon 4 of 8)"	"exon (NM_013793, exon 4 of 8)"	5674	NM_001039118	654450	Mm.333431	NM_001039118		Klra33	-	killer cell lectin-like receptor subfamily A member 33	protein-coding	0.01	0.366337
Merged-chr2-118779746-1	chr2	118779696	118779796	+	2.1	cIP2vsInput	promoter-TSS (NM_170593)	promoter-TSS (NM_170593)	27	NM_170593	214240	Mm.221499	NM_170593	ENSMUSG00000040035	Disp2	AI840597|B230210L08Rik|DispB|mKIAA1742	dispatched homolog 2 (Drosophila)	protein-coding	0.1	0.70297
Merged-chr11-108578418-1	chr11	108578368	108578468	+	2.1	cIP2vsInput	"intron (NM_029606, intron 19 of 27)"	L1_Mus1|LINE|L1	-104191	NM_145688	76380	Mm.344071	NM_029586	ENSMUSG00000020728	Cep112	1700001M19Rik|1700029K01Rik|8430407H02Rik|AV043680|AV207351|Ccdc46|Macoco	centrosomal protein 112	protein-coding	0.01	0.376238
Merged-chr6-141132515-1	chr6	141132465	141132565	+	2.1	cIP1vsInput	Intergenic	Intergenic	-116754	NM_018779	54611	Mm.485878	NM_018779	ENSMUSG00000041741	Pde3a	A930022O17Rik|C87899	"phosphodiesterase 3A, cGMP inhibited"	protein-coding	0	0.336634
Merged-chr8-39723698-1	chr8	39723648	39723748	+	2.1	cIP1vsInput	"intron (NR_035426, intron 3 of 5)"	"intron (NR_035426, intron 3 of 5)"	-81020	NM_001113326	20288	Mm.239291	NM_001113326	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding	0	0.277228
Merged-chr6-112508021-1	chr6	112507971	112508071	+	2.1	cIP1vsInput	Intergenic	L1M3a|LINE|L1	-18213	NM_001081147	18430	Mm.333310	NM_001081147	ENSMUSG00000049112	Oxtr	OTR	oxytocin receptor	protein-coding	0.01	0.336634
Merged-chr1-110549310-1	chr1	110549260	110549360	+	2.1	cIP1vsInput	Intergenic	MTE2a|LTR|ERVL-MaLR	428062	NM_001081386	227485	Mm.322070	NM_001081386	ENSMUSG00000047216	Cdh19	-	"cadherin 19, type 2"	protein-coding	0	0.336634
Merged-chr18-61904579-1	chr18	61904529	61904629	+	2.1	cIP1vsInput	"intron (NM_198649, intron 1 of 22)"	MIR|SINE|MIR	7245	NM_198649	319713		NM_001164491	ENSMUSG00000032735	Ablim3	AW990719|D930036B08Rik	"actin binding LIM protein family, member 3"	protein-coding	0	0.386139
Merged-chr12-32239111-1	chr12	32239061	32239161	+	2.1	cIP1vsInput	Intergenic	ORR1A2|LTR|ERVL-MaLR	-30462	NM_001146200	30955	Mm.404021	NM_001146200	ENSMUSG00000020573	Pik3cg	5830428L06Rik|PI3Kgamma|p110gamma	"phosphoinositide-3-kinase, catalytic, gamma polypeptide"	protein-coding	0	0.405941
Merged-chr7-140377022-1	chr7	140376972	140377072	+	2.1	cIP1vsInput	Intergenic	RLTR14_RN|LTR|ERV1	-3414	NM_146519	258512	Mm.377545	NM_146519	ENSMUSG00000060974	Olfr530	MOR252-2	olfactory receptor 530	protein-coding	0	0.39604
Merged-chrX-135705279-1	chrX	135705229	135705329	+	2.1	cIP1vsInput	Intergenic	RLTR14|LTR|ERV1	-11489	NM_027952	71841	Mm.371643	NM_027952	ENSMUSG00000058252	1700008I05Rik	C77164|TCP11	RIKEN cDNA 1700008I05 gene	protein-coding	0	0.366337
Merged-chr14-78932895-1	chr14	78932845	78932945	+	2.1	cIP1vsInput	"intron (NM_173758, intron 5 of 25)"	"intron (NM_173758, intron 5 of 25)"	83717	NM_173758	219189	Mm.159651	NM_027906	ENSMUSG00000058997	Vwa8	1300010F03Rik|4932416F07Rik|AI957255|Kiaa0564|mKIAA0564	von Willebrand factor A domain containing 8	protein-coding	0	0.336634
Merged-chr1-5935558-1	chr1	5935508	5935608	+	2.1	cIP1vsInput	Intergenic	MusHAL1|LINE|L1	-18160	NM_010342	226304	Mm.291110	NM_010342	ENSMUSG00000033774	Npbwr1	Gpr7|Nbpwr1	neuropeptides B/W receptor 1	protein-coding	0	0.356436
Merged-chr17-90829827-1	chr17	90829777	90829877	+	2.1	cIP1vsInput	"intron (NM_020252, intron 4 of 22)"	L1_Mus2|LINE|L1	-31342	NR_045463	78800	Mm.410772	NR_045463	ENSMUSG00000090160	4930480K15Rik	-	RIKEN cDNA 4930480K15 gene	miscRNA	0.01	0.39604
Merged-chr5-121512591-1	chr5	121512541	121512641	+	2.1	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	9104	NM_172126	280668	Mm.1453	NM_172126	ENSMUSG00000072647	Adam1a	Adam1|Ftna	a disintegrin and metallopeptidase domain 1a	protein-coding	0.01	0.356436
Merged-chr5-62104907-1	chr5	62104857	62104957	+	2.1	cIP1vsInput	Intergenic	Intergenic	296064	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding	0	0.267327
Merged-chr8-48086533-1	chr8	48086483	48086583	+	2.1	cIP1vsInput	Intergenic	Intergenic	-12559	NM_001161516	320685	Mm.121549	NM_001161515	ENSMUSG00000031562	Dctd	6030466N05Rik	dCMP deaminase	protein-coding	0	0.366337
Merged-chr11-87471652-1	chr11	87471602	87471702	+	2.1	cIP1vsInput	"intron (NM_031386, intron 2 of 30)"	"intron (NM_031386, intron 2 of 30)"	44061	NM_001199293	83560	Mm.440758	NM_001199293	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding	0.01	0.247525
Merged-chr1-137754284-1	chr1	137754234	137754334	+	2.1	cIP1vsInput	Intergenic	Intergenic	-212171	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mmu-mir-213	microRNA 181a-1	miscRNA	0	0.326733
Merged-chr18-88608155-1	chr18	88608105	88608205	+	2.1	cIP2vsInput	Intergenic	Intergenic	286052	NM_018821	54607	Mm.476577	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding	0.01	0.356436
Merged-chr3-106872136-1	chr3	106872086	106872186	+	2.1	cIP2vsInput	Intergenic	Lx5b|LINE|L1	-49579	NM_146489	258482	Mm.377527	NM_146489	ENSMUSG00000043529	Olfr266	MOR122-2	olfactory receptor 266	protein-coding	0	0.316832
Merged-chr6-23508427-1	chr6	23508377	23508477	+	2.1	cIP2vsInput	"intron (NM_001252105, intron 7 of 28)"	"intron (NM_001252105, intron 7 of 28)"	141878	NM_198251	386611	Mm.436547	NM_198251	ENSMUSG00000051956	Rnf133	Greul2	ring finger protein 133	protein-coding	0.01	0.326733
Merged-chr18-48766771-1	chr18	48766721	48766821	+	2.1	cIP1vsInput	Intergenic	Intergenic	721436	NM_001025388	433182	Mm.372357	NM_001025388	ENSMUSG00000059040	Gm5506	EG433182|Eno1	predicted gene 5506	protein-coding	0.01	0.306931
Merged-chr2-100082037-1	chr2	100081987	100082087	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1542711	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding	0	0.306931
Merged-chr5-119155675-1	chr5	119155625	119155725	+	2.1	cIP1vsInput	Intergenic	MTE-int|LTR|ERVL-MaLR	44343	NR_046033	665194	Mm.491047	NR_046033		Gm7538	EG665194	predicted gene 7538	miscRNA	0	0.39604
Merged-chrY-6912483-1	chrY	6912433	6912533	+	2.1	cIP1vsInput	Intergenic	C573_MM|Other|Other	255294	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.356436
Merged-chr15-17310779-1	chr15	17310729	17310829	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	532678	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0.02	0.346535
Merged-chr16-33175595-1	chr16	33175545	33175645	+	2.1	cIP1vsInput	Intergenic	ORR1D1|LTR|ERVL-MaLR	-9476	NM_176840	106326	Mm.486405	NM_176840	ENSMUSG00000022807	Osbpl11	9430097N02Rik|AI132306|AU019795|ORP-11	oxysterol binding protein-like 11	protein-coding	0.01	0.514851
Merged-chr3-117021391-1	chr3	117021341	117021441	+	2.1	cIP1vsInput	Intergenic	Intergenic	-52439	NM_023245	114301	Mm.253736	NM_023245	ENSMUSG00000033377	Palmd	4631423C22Rik|PALML	palmdelphin	protein-coding	0	0.326733
Merged-chrX-47561369-1	chrX	47561319	47561419	+	2.1	cIP1vsInput	Intergenic	MLT1J|LTR|ERVL-MaLR	331183	NM_053123	93761	Mm.229151	NM_053123	ENSMUSG00000031099	Smarca1	5730494M04Rik|Snf2l	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1"	protein-coding	0	0.336634
Merged-chr7-36958599-1	chr7	36958549	36958649	+	2.1	cIP2vsInput	Intergenic	Intergenic	260481	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding	0.03	0.485149
Merged-chrX-93632177-1	chrX	93632127	93632227	+	2.1	cIP2vsInput	promoter-TSS (NM_008892)	promoter-TSS (NM_008892)	-22	NM_008892	18968	Mm.1923	NM_008892	ENSMUSG00000006678	Pola1	AW321876|Pola	"polymerase (DNA directed), alpha 1"	protein-coding	0.1	0.623762
Merged-chr5-62982740-1	chr5	62982690	62982790	+	2.1	cIP2vsInput	Intergenic	Intergenic	168917	NM_001170705	100322896	Mm.479821	NM_001170705	ENSMUSG00000090326	Gm17384	Dthd1	"predicted gene, 17384"	protein-coding	0	0.316832
Merged-chr16-7242384-1	chr16	7242334	7242434	+	2.1	cIP2vsInput	"intron (NM_021477, intron 6 of 16)"	"intron (NM_021477, intron 6 of 16)"	172549	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	"RNA binding protein, fox-1 homolog (C. elegans) 1"	protein-coding	0	0.336634
Merged-chr3-12281202-1	chr3	12281152	12281252	+	2.1	cIP1vsInput	Intergenic	Lx|LINE|L1	-436843	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.29703
Merged-chr5-5537389-1	chr5	5537339	5537439	+	2.1	cIP1vsInput	TTS (NM_153116)	TTS (NM_153116)	22112	NM_153116	207704	Mm.323984	NM_153116	ENSMUSG00000040464	Gtpbp10	4930545J22Rik|BC034507	GTP-binding protein 10 (putative)	protein-coding	0.01	0.405941
Merged-chr6-28981329-2	chr6	28981265	28981393	+	2.1	cIP1vsInput|cIP2vsInput	Intergenic	CpG	-41290	NR_029567	387237		NR_029567	ENSMUSG00000065469	Mir129-1	Mirn129-1|Mirn129b|miR-129b	microRNA 129-1	miscRNA	0.09375	0.635659
Merged-chr3-8957706-1	chr3	8957656	8957756	+	2.1	cIP1vsInput	"intron (NM_001025264, intron 1 of 6)"	"intron (NM_001025264, intron 1 of 6)"	6348	NM_001025262	21985	Mm.371590	NM_001025261	ENSMUSG00000027506	Tpd52	AI043038|mD52	tumor protein D52	protein-coding	0	0.29703
Merged-chr12-7046885-1	chr12	7046835	7046935	+	2.1	cIP2vsInput	Intergenic	Intergenic	333445	NR_045045	73575	Mm.179463	NR_045045		1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	miscRNA	0.01	0.346535
Merged-chr1-167959007-1	chr1	167958957	167959057	+	2.1	cIP2vsInput	Intergenic	Intergenic	269449	NM_033652	110648	Mm.330081	NM_033652	ENSMUSG00000026686	Lmx1a	Lmx1.1|dr|dreher|sst	LIM homeobox transcription factor 1 alpha	protein-coding	0.01	0.316832
Merged-chr3-113113685-1	chr3	113113635	113113735	+	2.1	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	43042	NM_001190404	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding	0.01	0.475248
Merged-chrX-58714136-1	chrX	58714086	58714186	+	2.1	cIP1vsInput	Intergenic	Lx9|LINE|L1	-197325	NM_023774	75352	Mm.60906	NM_023774	ENSMUSG00000046180	4930550L24Rik	mage-k1	RIKEN cDNA 4930550L24 gene	protein-coding	0	0.425743
Merged-chr18-77096854-1	chr18	77096804	77096904	+	2.1	cIP1vsInput	"intron (NM_001164170, intron 1 of 12)"	"intron (NM_001164170, intron 1 of 12)"	31174	NM_001164168	17344	Mm.6370	NM_001164167	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding	0	0.306931
Merged-chr2-57552500-1	chr2	57552450	57552550	+	2.1	cIP2vsInput	Intergenic	Intergenic	314118	NM_010274	14571	Mm.3711	NM_001145820	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	"glycerol phosphate dehydrogenase 2, mitochondrial"	protein-coding	0	0.326733
Merged-chr1-140745833-1	chr1	140745783	140745883	+	2.1	cIP2vsInput	Intergenic	Intergenic	-89431	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0.01	0.316832
Merged-chr9-24146451-1	chr9	24146401	24146501	+	2.1	cIP2vsInput	"intron (NM_175678, intron 3 of 9)"	MER34A|LTR|ERV1	48433	NM_175678	319239	Mm.130824	NM_175678	ENSMUSG00000043659	Npsr1	9330128H10Rik|GPRA|Gpr154|MVTR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0	0.316832
Merged-chr4-37680443-1	chr4	37680393	37680493	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-728699	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0	0.336634
Merged-chr4-33622952-1	chr4	33622902	33623002	+	2.1	cIP1vsInput	Intergenic	L1MD|LINE|L1	-301680	NM_007726	12801	Mm.7992	NM_007726	ENSMUSG00000044288	Cnr1	CB-R|CB1|CB1R	cannabinoid receptor 1 (brain)	protein-coding	0.02	0.336634
Merged-chr9-93721781-1	chr9	93721731	93721831	+	2.1	cIP2vsInput	Intergenic	Intergenic	-716048	NR_040756	78349	Mm.52612	NR_040756		1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	miscRNA	0	0.336634
Merged-chr4-151335728-1	chr4	151335678	151335778	+	2.1	cIP2vsInput	"intron (NM_001081557, intron 5 of 23)"	UCON18|Unknown|Unknown	-277775	NM_009498	22319	Mm.273930	NM_009498	ENSMUSG00000028955	Vamp3	D130027G05Rik|VAMP-3|ceb	vesicle-associated membrane protein 3	protein-coding	0.02	0.366337
Merged-chr1-48808380-1	chr1	48808330	48808430	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1954871	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.287129
Merged-chr2-78093919-1	chr2	78093869	78093969	+	2.1	cIP2vsInput	Intergenic	Intergenic	-143628	NM_177843	329436	Mm.235448	NM_177843		Gm14461	A830093M07|OTTMUSG00000016703	predicted gene 14461	protein-coding	0	0.306931
Merged-chr2-123783836-1	chr2	123783786	123783886	+	2.1	cIP2vsInput	Intergenic	Intergenic	346120	NR_040611	74702	Mm.410814	NR_040611	ENSMUSG00000085496	4930517E11Rik	-	RIKEN cDNA 4930517E11 gene	miscRNA	0	0.257426
Merged-chr10-52670788-1	chr10	52670738	52670838	+	2.1	cIP1vsInput	Intergenic	(GA)n|Simple_repeat|Simple_repeat	-19713	NM_178675	215085	Mm.338690	NM_178675	ENSMUSG00000038602	Slc35f1	Duf6|E130016L02	"solute carrier family 35, member F1"	protein-coding	0	0.405941
Merged-chr8-35080781-1	chr8	35080731	35080831	+	2.1	cIP2vsInput	Intergenic	B3|SINE|B2	-115091	NM_175091	21951	Mm.88364	NM_175091	ENSMUSG00000031529	Tnks	4930554K12Rik|AI662855|ARTD5|C86528|D130072O21Rik|TANK1|mTNKS1	"tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase"	protein-coding	0.01	0.445545
Merged-chr3-6441023-1	chr3	6440973	6441073	+	2.1	cIP1vsInput	Intergenic	Intergenic	179420	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding	0	0.306931
Merged-chr1-65673053-1	chr1	65673003	65673103	+	2.1	cIP2vsInput	Intergenic	MYSERV-int|LTR|ERVK	-253469	NM_027010	12969	Mm.275362	NM_027010	ENSMUSG00000025945	Crygf	3110001K11Rik|Cryg-2|DGcry-2|Len-2	"crystallin, gamma F"	protein-coding	0.01	0.336634
Merged-chr18-30705179-1	chr18	30705129	30705229	+	2.1	cIP1vsInput	Intergenic	B3|SINE|B2	432283	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	"phosphoinositide-3-kinase, class 3"	protein-coding	0	0.29703
Merged-chr5-86321815-1	chr5	86321765	86321865	+	2.1	cIP1vsInput	"intron (NM_145561, intron 7 of 9)"	Lx4A|LINE|L1	-32507	NM_001030297	435845	Mm.359654	NM_001030297	ENSMUSG00000061184	Tmprss11c	Tmprss13	"transmembrane protease, serine 11c"	protein-coding	0	0.386139
Merged-chr12-17452402-1	chr12	17452352	17452452	+	2.1	cIP2vsInput	Intergenic	Intergenic	-92471	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	"ornithine decarboxylase, structural 1"	protein-coding	0.01	0.50495
Merged-chr1-79284042-1	chr1	79283992	79284092	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	156048	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding	0.01	0.306931
Merged-chr8-18096851-1	chr8	18096801	18096901	+	2.1	cIP2vsInput	Intergenic	Intergenic	-498322	NM_173189	244329	Mm.235296	NM_173189	ENSMUSG00000039842	Mcph1	5430437K10Rik|BRIT1|D030046N04Rik|MCT	"microcephaly, primary autosomal recessive 1"	protein-coding	0	0.316832
Merged-chr8-47002692-1	chr8	47002642	47002742	+	2.1	cIP2vsInput	"intron (NM_177304, intron 1 of 7)"	L1M4|LINE|L1	15767	NM_177304	320981	Mm.211429	NM_177304	ENSMUSG00000038173	Enpp6	4833421B01Rik|B830047L21Rik|D8Ertd514e|E-NPP 6|Npp6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding	0.01	0.405941
Merged-chr7-93762839-1	chr7	93762789	93762889	+	2.1	cIP2vsInput	Intergenic	Intergenic	682960	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0	0.316832
Merged-chr13-50958343-1	chr13	50958293	50958393	+	2.1	cIP2vsInput	Intergenic	Intergenic	142384	NR_029463	77428	Mm.405630	NR_029463		9430083A17Rik	-	RIKEN cDNA 9430083A17 gene	miscRNA	0.02	0.50495
Merged-chr14-8356025-1	chr14	8355975	8356075	+	2.1	cIP2vsInput	"intron (NM_146050, intron 6 of 9)"	"intron (NM_146050, intron 6 of 9)"	22738	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding	0.02	0.50495
Merged-chr12-46168406-1	chr12	46168356	46168456	+	2.1	cIP2vsInput	Intergenic	RMER3D-int|LTR|ERVK	650369	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding	0	0.366337
Merged-chr14-86918030-1	chr14	86917980	86918080	+	2.1	cIP2vsInput	"intron (NM_019670, intron 18 of 27)"	"intron (NM_019670, intron 18 of 27)"	223084	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diap3	4930417P13Rik|Dia2|Diaph3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous homolog 3 (Drosophila)	protein-coding	0	0.346535
Merged-chr16-85061116-1	chr16	85061066	85061166	+	2.1	cIP1vsInput	"intron (NM_001198824, intron 5 of 16)"	"intron (NM_001198824, intron 5 of 16)"	88905	NR_045889	100038614	Mm.441351	NR_045889		Gm10791	ENSMUSG00000074933	predicted gene 10791	miscRNA	0	0.376238
Merged-chr1-145007349-1	chr1	145007299	145007399	+	2.1	cIP2vsInput	Intergenic	Intergenic	-231928	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding	0	0.29703
Merged-chr17-82159177-1	chr17	82159127	82159227	+	2.1	cIP2vsInput	Intergenic	Intergenic	-420800	NM_011406	20541	Mm.489060	NM_001112798		Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	"solute carrier family 8 (sodium/calcium exchanger), member 1"	protein-coding	0	0.366337
Merged-chr2-132349256-1	chr2	132349206	132349306	+	2.1	cIP1vsInput	Intergenic	Intergenic	36191	NM_144944	246313	Mm.283777	NM_144944	ENSMUSG00000050558	Prokr2	B830005M06Rik|EG-VEGRF2|Gpcr73l1|Gpr73l1|PKR2	prokineticin receptor 2	protein-coding	0	0.336634
Merged-chr15-15552440-1	chr15	15552390	15552490	+	2.1	cIP1vsInput	Intergenic	Lx9|LINE|L1	-1225661	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0	0.306931
Merged-chr8-54283294-1	chr8	54283244	54283344	+	2.1	cIP1vsInput	Intergenic	Intergenic	205762	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding	0	0.425743
Merged-chr9-81525083-1	chr9	81525033	81525133	+	2.1	cIP2vsInput	Intergenic	Intergenic	-106847	NR_040394	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	miscRNA	0.01	0.386139
Merged-chr5-63739262-1	chr5	63739212	63739312	+	2.1	cIP1vsInput	"intron (NM_177006, intron 2 of 6)"	"intron (NM_177006, intron 2 of 6)"	-73233	NM_029554	76261	Mm.38143	NM_029554	ENSMUSG00000060512	0610040J01Rik	AI662686	RIKEN cDNA 0610040J01 gene	protein-coding	0	0.316832
Merged-chr19-21357544-1	chr19	21357494	21357594	+	2.1	cIP1vsInput	Intergenic	RSINE1|SINE|B4	85266	NM_009551	22682	Mm.379919	NM_009551		Zfand5	2310057A04Rik|5830475F03Rik|AA415485|Za20d2|Zfp216	"zinc finger, AN1-type domain 5"	protein-coding	0	0.346535
Merged-chr6-139505393-1	chr6	139505343	139505443	+	2.1	cIP1vsInput	Intergenic	ID4_|SINE|ID	-3484	NM_001128090	632971	Mm.475610	NM_001128090	ENSMUSG00000092164	Rergl	EG632971	RERG/RAS-like	protein-coding	0	0.405941
Merged-chr1-40130443-1	chr1	40130393	40130493	+	2.1	cIP2vsInput	Intergenic	Intergenic	-44592	NR_037980	100047133	Mm.447052	NR_037980	ENSMUSG00000097899	Gm16894	-	"predicted gene, 16894"	miscRNA	0	0.405941
Merged-chr6-138555438-1	chr6	138555388	138555488	+	2.1	cIP1vsInput	"intron (NM_207222, intron 1 of 4)"	"intron (NM_207222, intron 1 of 4)"	26530	NM_207222	109593	Mm.490545	NM_207222		Lmo3	AI854781|BB106490|Rbtn-3|Rbtn3	LIM domain only 3	protein-coding	0.02	0.326733
Merged-chr1-63658514-1	chr1	63658464	63658564	+	2.1	cIP2vsInput	"intron (NM_001081658, intron 10 of 14)"	Lx8|LINE|L1	28413	NM_001081658	241073	Mm.297680	NM_001081658	ENSMUSG00000069085	Dytn	Gm215	dystrotelin	protein-coding	0.03	0.60396
Merged-chr6-105036341-1	chr6	105036291	105036391	+	2.1	cIP1vsInput	Intergenic	Intergenic	456327	NR_040297	100503536	Mm.366960	NR_040297		Gm19757	-	"predicted gene, 19757"	miscRNA	0	0.306931
Merged-chr18-16315775-1	chr18	16315725	16315825	+	2.1	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	493274	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-cadherin|Ncad	cadherin 2	protein-coding	0.01	0.336634
Merged-chr18-23369586-1	chr18	23369536	23369636	+	2.1	cIP2vsInput	Intergenic	Intergenic	-45829	NM_010087	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|A0|Dtn|a-DB-1|adbn	dystrobrevin alpha	protein-coding	0	0.316832
Merged-chr9-15476872-1	chr9	15476822	15476922	+	2.1	cIP1vsInput	Intergenic	Intergenic	-28623	NM_133214	170748	Mm.86572	NM_133214	ENSMUSG00000058173	Smco4	Fn5	single-pass membrane protein with coiled-coil domains 4	protein-coding	0.01	0.425743
Merged-chr3-105308188-1	chr3	105308138	105308238	+	2.1	cIP2vsInput	Intergenic	Intergenic	-144142	NM_001039347	56543	Mm.44530	NM_001039347	ENSMUSG00000040896	Kcnd3	AW045978|Kncd3|Kv4.3	"potassium voltage-gated channel, Shal-related family, member 3"	protein-coding	0.02	0.39604
Merged-chr9-83454652-1	chr9	83454602	83454702	+	2.1	cIP2vsInput	Intergenic	Intergenic	-13525	NM_029434	75782	Mm.199698	NM_027448	ENSMUSG00000032258	Lca5	4930431B11Rik|5730406O13Rik|AV274874|ORF64	Leber congenital amaurosis 5 (human)	protein-coding	0	0.29703
Merged-chr4-71970772-1	chr4	71970722	71970822	+	2.1	cIP1vsInput	Intergenic	Intergenic	230147	NM_011599	21885	Mm.399716	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg1|Tle4l	"transducin-like enhancer of split 1, homolog of Drosophila E(spl)"	protein-coding	0	0.336634
Merged-chr9-53994625-1	chr9	53994575	53994675	+	2.1	cIP2vsInput	Intergenic	(CCCTAA)n|Simple_repeat|Simple_repeat	-19324	NM_177769	270162	Mm.259791	NM_177769	ENSMUSG00000041986	Elmod1	4831417L10|AI428506|AI834991	ELMO/CED-12 domain containing 1	protein-coding	0.01	0.376238
Merged-chr14-86974530-1	chr14	86974480	86974580	+	2.1	cIP2vsInput	"intron (NM_019670, intron 14 of 27)"	"intron (NM_019670, intron 14 of 27)"	166584	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diap3	4930417P13Rik|Dia2|Diaph3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous homolog 3 (Drosophila)	protein-coding	0.01	0.326733
Merged-chr16-35030863-1	chr16	35030813	35030913	+	2.1	cIP2vsInput	"intron (NM_023587, intron 2 of 6)"	"intron (NM_023587, intron 2 of 6)"	8442	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Ptplb	6330408J20Rik|AI255777|AI481689|HACD2	"protein tyrosine phosphatase-like (proline instead of catalytic arginine), member b"	protein-coding	0.01	0.346535
Merged-chr3-42963266-1	chr3	42963216	42963316	+	2.1	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	1220648	NM_027271	73852	Mm.29006	NM_001099785	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	"DNA segment, Chr 3, ERATO Doi 751, expressed"	protein-coding	0	0.346535
Merged-chr17-19214952-1	chr17	19214902	19215002	+	2.1	cIP2vsInput	Intergenic	L1VL2|LINE|L1	-147183	NM_001104551	665376	Mm.469859	NM_001104551	ENSMUSG00000090304	Vmn2r99	EG665376	"vomeronasal 2, receptor 99"	protein-coding	0	0.326733
Merged-chr3-140143332-1	chr3	140143282	140143382	+	2.1	cIP2vsInput	Intergenic	Intergenic	937439	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding	0	0.39604
Merged-chr7-67471844-1	chr7	67471794	67471894	+	2.1	cIP2vsInput	Intergenic	Intergenic	-98986	NM_001033713	17258	Mm.426509	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding	0	0.39604
Merged-chr4-39356905-1	chr4	39356855	39356955	+	2.1	cIP1vsInput	Intergenic	Intergenic	-93388	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding	0	0.405941
Merged-chr1-30678111-1	chr1	30678061	30678161	+	2.1	cIP1vsInput	Intergenic	RLTR15|LTR|ERVK	185145	NM_001081080	213109	Mm.486727	NM_001081080	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding	0.03	0.415842
Merged-chr1-116690500-1	chr1	116690450	116690550	+	2.1	cIP1vsInput	Intergenic	Intergenic	1005363	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0	0.267327
Merged-chr6-11899606-1	chr6	11899556	11899656	+	2.1	cIP2vsInput	TTS (NM_010886)	TTS (NM_010886)	7840	NM_010886	17992	Mm.415865	NM_010886	ENSMUSG00000029632	Ndufa4	MLRQ	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4"	protein-coding	0	0.29703
Merged-chr18-30833058-1	chr18	30833008	30833108	+	2.1	cIP1vsInput	Intergenic	Lx7|LINE|L1	484070	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding	0	0.326733
Merged-chr19-18262685-1	chr19	18262635	18262735	+	2.1	cIP1vsInput	Intergenic	Lx9|LINE|L1	369128	NM_017375	20409	Mm.172222	NM_017375		Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding	0	0.316832
Merged-chr13-76569138-1	chr13	76569088	76569188	+	2.1	cIP1vsInput	"intron (NM_030174, intron 1 of 20)"	"intron (NM_030174, intron 1 of 20)"	184177	NM_030174	78771	Mm.316249	NM_030174		Mctp1	2810465F10Rik	"multiple C2 domains, transmembrane 1"	protein-coding	0	0.29703
Merged-chr13-59318110-1	chr13	59318060	59318160	+	2.1	cIP1vsInput	Intergenic	Intergenic	239209	NM_001048008	67269	Mm.153008	NM_001048008	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|BB114605|CCP1|Nna1|mKIAA1035|nmf243|pcd	ATP/GTP binding protein 1	protein-coding	0.02	0.316832
Merged-chrX-138986142-1	chrX	138986092	138986192	+	2.1	cIP2vsInput	"intron (NM_013724, intron 18 of 27)"	"intron (NM_013724, intron 18 of 27)"	71712	NM_013724	27206	Mm.482319	NM_013724	ENSMUSG00000052854	Nrk	AA407323|AA409510|AI225895|AV168563|AW538185|Nesk	Nik related kinase	protein-coding	0	0.29703
Merged-chr12-48389230-1	chr12	48389180	48389280	+	2.1	cIP1vsInput	Intergenic	Intergenic	-87768	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0	0.346535
Merged-chr13-15924125-1	chr13	15924075	15924175	+	2.1	cIP1vsInput	Intergenic	(TTTG)n|Simple_repeat|Simple_repeat	-90350	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding	0	0.267327
Merged-chrX-93531683-1	chrX	93531633	93531733	+	2.1	cIP1vsInput	"intron (NM_008892, intron 26 of 36)"	L1MB2|LINE|L1	100472	NM_008892	18968	Mm.1923	NM_008892	ENSMUSG00000006678	Pola1	AW321876|Pola	"polymerase (DNA directed), alpha 1"	protein-coding	0	0.346535
Merged-chr8-82453201-1	chr8	82453151	82453251	+	2.1	cIP1vsInput	Intergenic	Lx10|LINE|L1	-50615	NM_008357	16168	Mm.490053	NM_001254747		Il15	AI503618|IL-15	interleukin 15	protein-coding	0	0.415842
Merged-chr5-139358973-1	chr5	139358923	139359023	+	2.1	cIP1vsInput	TTS (NM_028469)	TTS (NM_028469)	6356	NM_001160265	545817	Mm.482474	NM_001160265	ENSMUSG00000029541	Cyp2w1	Gm455	"cytochrome P450, family 2, subfamily w, polypeptide 1"	protein-coding	0.01	0.594059
Merged-chr6-104542544-1	chr6	104542494	104542594	+	2.1	cIP1vsInput	"intron (NM_017383, intron 1 of 22)"	L1M5|LINE|L1	49500	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding	0	0.287129
Merged-chr3-113902326-1	chr3	113902276	113902376	+	2.1	cIP2vsInput	Intergenic	Intergenic	-128214	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	"collagen, type XI, alpha 1"	protein-coding	0.01	0.316832
Merged-chr3-76637222-1	chr3	76637172	76637272	+	2.1	cIP2vsInput	"intron (NM_178673, intron 12 of 15)"	"intron (NM_178673, intron 12 of 15)"	561639	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.356436
Merged-chr15-42411045-1	chr15	42410995	42411095	+	2.1	cIP2vsInput	Intergenic	Intergenic	265750	NM_009640	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding	0.02	0.326733
Merged-chr9-3312942-1	chr9	3312892	3312992	+	2.1	cIP2vsInput	Intergenic	MusHAL1|LINE|L1	-22289	NM_026303	67667	Mm.440994	NM_026303		Alkbh8	4930562C03Rik|8030431D03Rik|9430088N01Rik|Abh8	"alkB, alkylation repair homolog 8 (E. coli)"	protein-coding	0	0.346535
Merged-chr17-70475515-1	chr17	70475465	70475565	+	2.1	cIP1vsInput	"intron (NM_027712, intron 1 of 9)"	"intron (NM_027712, intron 1 of 9)"	-46595	NM_001128180	224997	Mm.367369	NM_001128180	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	"discs, large (Drosophila) homolog-associated protein 1"	protein-coding	0	0.326733
Merged-chr8-56185481-1	chr8	56185431	56185531	+	2.1	cIP1vsInput	Intergenic	Lx7|LINE|L1	-109071	NM_008278	15446	Mm.18832	NM_008278	ENSMUSG00000031613	Hpgd	15-PGDH|AV026552	hydroxyprostaglandin dehydrogenase 15 (NAD)	protein-coding	0.01	0.376238
Merged-chr5-70181625-1	chr5	70181575	70181675	+	2.1	cIP1vsInput	Intergenic	Intergenic	-589340	NM_001038015	67980	Mm.33830	NM_001038015	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding	0.01	0.306931
Merged-chr19-51288226-1	chr19	51288176	51288276	+	2.1	cIP1vsInput	Intergenic	Intergenic	-609580	NM_021377	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0	0.326733
Merged-chr12-42180994-1	chr12	42180944	42181044	+	2.1	cIP1vsInput	Intergenic	Intergenic	552230	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding	0	0.326733
Merged-chr13-78065897-1	chr13	78065847	78065947	+	2.1	cIP1vsInput	"intron (NM_138312, intron 10 of 10)"	"intron (NM_138312, intron 10 of 10)"	40995	NM_029315	75507	Mm.443255	NM_029315		Pou5f2	1700013G10Rik|SPRM-1|Sprm1	"POU domain class 5, transcription factor 2"	protein-coding	0	0.306931
Merged-chr5-3858746-1	chr5	3858696	3858796	+	2.1	cIP1vsInput	"exon (NM_172879, exon 3 of 6)"	"exon (NM_172879, exon 3 of 6)"	13573	NM_172879	242838	Mm.482273	NM_172879	ENSMUSG00000040367	Lrrd1	4932412H11Rik	leucine rich repeats and death domain containing 1	protein-coding	0.01	0.366337
Merged-chr12-78331776-1	chr12	78331726	78331826	+	2.1	cIP1vsInput	"intron (NM_145965, intron 1 of 22)"	B1_Mur2|SINE|Alu	105121	NM_145965	268566	Mm.453131	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding	0.01	0.376238
Merged-chr2-11572088-1	chr2	11572038	11572138	+	2.1	cIP2vsInput	Intergenic	Intergenic	-18159	NM_001177758	170768		NM_172976	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	"6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3"	protein-coding	0.01	0.425743
Merged-chr17-67191036-1	chr17	67190986	67191086	+	2.1	cIP2vsInput	"intron (NM_008984, intron 2 of 30)"	"intron (NM_008984, intron 2 of 30)"	163423	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	"protein tyrosine phosphatase, receptor type, M"	protein-coding	0	0.49505
Merged-chr8-81848278-1	chr8	81848228	81848328	+	2.1	cIP2vsInput	"intron (NM_001024617, intron 5 of 22)"	"intron (NM_001024617, intron 5 of 22)"	133078	NM_001024617	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	"inositol polyphosphate-4-phosphatase, type II"	protein-coding	0	0.346535
Merged-chr1-124266906-1	chr1	124266856	124266956	+	2.1	cIP1vsInput	Intergenic	MTEb|LTR|ERVL-MaLR	-221347	NM_199021	269109	Mm.483255	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding	0	0.316832
Merged-chr16-45684851-1	chr16	45684801	45684901	+	2.1	cIP2vsInput	"intron (NM_172455, intron 3 of 17)"	"intron (NM_172455, intron 3 of 17)"	8807	NM_172455	208171	Mm.186306	NM_172455	ENSMUSG00000033177	Tmprss7	B230219I23Rik|Gm1748	transmembrane serine protease 7	protein-coding	0.02	0.326733
Merged-chr11-52209716-1	chr11	52209666	52209766	+	2.1	cIP1vsInput	Intergenic	Intergenic	4271	NM_207253	276865	Mm.377871	NM_207253	ENSMUSG00000060170	Olfr1371	GA_x6K02T2QP88-3214035-3214970|MOR256-58	olfactory receptor 1371	protein-coding	0	0.267327
Merged-chrX-124112899-1	chrX	124112849	124112949	+	2.1	cIP2vsInput	Intergenic	Intergenic	23011	NM_001100616	100038941	Mm.388852	NM_001100616	ENSMUSG00000072049	Vmn2r121	EG625699	"vomeronasal 2, receptor 121"	protein-coding	0	0.356436
Merged-chr3-56913010-1	chr3	56912960	56913060	+	2.1	cIP1vsInput	Intergenic	Lx5c|LINE|L1	388909	NM_008536	17112	Mm.856	NM_008536	ENSMUSG00000027800	Tm4sf1	L6|M3s1	transmembrane 4 superfamily member 1	protein-coding	0	0.306931
Merged-chr17-6600469-1	chr17	6600419	6600519	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1202	NM_001166627	100040531	Mm.458208	NM_001199947	ENSMUSG00000095677	Dynlt1f	100040631|Dynlt1e	dynein light chain Tctex-type 1F	protein-coding	0.02	0.405941
Merged-chr9-82660444-1	chr9	82660394	82660494	+	2.1	cIP1vsInput	Intergenic	Lx8b|LINE|L1	-169362	NM_001168240	65099	Mm.41415	NM_001168240	ENSMUSG00000032251	Irak1bp1	4921528N06Rik|AI851240|Aabp3|Aip70|Simpl	interleukin-1 receptor-associated kinase 1 binding protein 1	protein-coding	0.01	0.326733
Merged-chr6-42489416-1	chr6	42489366	42489466	+	2.1	cIP1vsInput	Intergenic	Intergenic	-2202	NM_001011528	259144	Mm.377865	NM_001011528	ENSMUSG00000090631	Olfr456	MOR257-7P	olfactory receptor 456	protein-coding	0.02	0.405941
Merged-chr2-118945736-1	chr2	118945686	118945786	+	2.1	cIP1vsInput	Intergenic	Ricksha_0|DNA|MULE-MuDR	19239	NM_028117	72136	Mm.490292	NM_028117	ENSMUSG00000074916	Chst14	2600016L03Rik|D4ST-1|D4st1	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 14	protein-coding	0	0.316832
Merged-chr10-62500674-1	chr10	62500624	62500724	+	2.1	cIP1vsInput	"intron (NM_011157, intron 1 of 2)"	MER33|DNA|hAT-Charlie	7081	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding	0.01	0.306931
Merged-chr10-129718520-1	chr10	129718470	129718570	+	2.1	cIP1vsInput	Intergenic	Intergenic	5022	NM_146555	258548	Mm.391456	NM_146555	ENSMUSG00000096858	Olfr805	MOR110-4	olfactory receptor 805	protein-coding	0	0.326733
Merged-chr15-70749496-1	chr15	70749446	70749546	+	2.1	cIP1vsInput	Intergenic	(CACCAT)n|Simple_repeat|Simple_repeat	825263	NR_045071	100503580	Mm.404646	NR_045071		Gm19782	-	"predicted gene, 19782"	miscRNA	0.01	0.455446
Merged-chr3-147554843-1	chr3	147554793	147554893	+	2.1	cIP2vsInput	Intergenic	Intergenic	702476	NM_027594	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|Ttll7s	"tubulin tyrosine ligase-like family, member 7"	protein-coding	0.01	0.287129
Merged-chr16-51571972-1	chr16	51571922	51572022	+	2.1	cIP1vsInput	Intergenic	Intergenic	-459577	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding	0	0.326733
Merged-chr2-105857463-1	chr2	105857413	105857513	+	2.1	cIP1vsInput	"intron (NM_023876, intron 3 of 9)"	"intron (NM_023876, intron 3 of 9)"	47037	NM_023876	77766	Mm.33870	NM_023876		Elp4	A330107A17Rik|Paxneb	elongation protein 4 homolog (S. cerevisiae)	protein-coding	0.01	0.316832
Merged-chr2-124050280-1	chr2	124050230	124050330	+	2.1	cIP1vsInput	Intergenic	L1MCa|LINE|L1	79676	NR_040611	74702	Mm.410814	NR_040611	ENSMUSG00000085496	4930517E11Rik	-	RIKEN cDNA 4930517E11 gene	miscRNA	0	0.356436
Merged-chr12-90436005-1	chr12	90435955	90436055	+	2.1	cIP1vsInput	Intergenic	Intergenic	302433	NM_010050	13371	Mm.408815	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	"deiodinase, iodothyronine, type II"	protein-coding	0	0.29703
Merged-chr5-38782053-1	chr5	38782003	38782103	+	2.1	cIP1vsInput	"intron (NM_013748, intron 4 of 18)"	"intron (NM_013748, intron 4 of 18)"	94640	NM_013748	27278	Mm.440845	NM_013748	ENSMUSG00000039315	Clnk	MIST	cytokine-dependent hematopoietic cell linker	protein-coding	0	0.445545
Merged-chr2-133123390-1	chr2	133123340	133123440	+	2.1	cIP1vsInput	Intergenic	ORR1F|LTR|ERVL-MaLR	-177354	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family homolog 1 (Drosophila)	protein-coding	0.01	0.366337
Merged-chr8-72798484-1	chr8	72798434	72798534	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	36604	NM_007975	14065	Mm.12948	NM_007975	ENSMUSG00000050147	F2rl3	PAR4	coagulation factor II (thrombin) receptor-like 3	protein-coding	0	0.366337
Merged-chr1-188566247-1	chr1	188566197	188566297	+	2.1	cIP1vsInput	"intron (NM_021408, intron 29 of 70)"	"intron (NM_021408, intron 29 of 70)"	303409	NM_021408	22283	Mm.331238	NM_021408	ENSMUSG00000026609	Ush2a	A930011D15Rik|A930037M10Rik|Gm676|Gm983|Mush2a|Usherin	"Usher syndrome 2A (autosomal recessive, mild)"	protein-coding	0	0.29703
Merged-chr10-10021180-1	chr10	10021130	10021230	+	2.1	cIP1vsInput	Intergenic	Intergenic	-120140	NM_001081344	78808	Mm.331751	NM_030191	ENSMUSG00000019790	Stxbp5	0710001E20Rik|4930565N16Rik|AW742610|LGL3|mKIAA1006	syntaxin binding protein 5 (tomosyn)	protein-coding	0	0.405941
Merged-chr13-53430424-1	chr13	53430374	53430474	+	2.1	cIP2vsInput	"intron (NR_037991, intron 4 of 7)"	"intron (NR_037991, intron 4 of 7)"	36735	NR_037991	100040421	Mm.83967	NR_037991		Gm2762	1700025I17Rik	predicted gene 2762	miscRNA	0.01	0.336634
Merged-chr3-157320759-1	chr3	157320709	157320809	+	2.1	cIP1vsInput	Intergenic	Intergenic	-213638	NM_017381	53861	Mm.259036	NM_017381	ENSMUSG00000028180	Zranb2	AI227013|Zfp265|Zis|Znf265	"zinc finger, RAN-binding domain containing 2"	protein-coding	0	0.326733
Merged-chr12-110771511-1	chr12	110771461	110771561	+	2.1	cIP2vsInput	"intron (NM_027149, intron 1 of 2)"	"intron (NM_027149, intron 1 of 2)"	33562	NM_027149	69641	Mm.435546	NM_027149	ENSMUSG00000037957	Wdr20a	2310040A13Rik|AI549910|WDR20	WD repeat domain 20A	protein-coding	0	0.336634
Merged-chr11-84642562-1	chr11	84642512	84642612	+	2.1	cIP2vsInput	Intergenic	CpG	77870	NR_046197	78471	Mm.47152	NR_046197	ENSMUSG00000085044	1700109G15Rik	-	RIKEN cDNA 1700109G15 gene	miscRNA	0.13	0.693069
Merged-chr2-20810344-1	chr2	20810294	20810394	+	2.1	cIP2vsInput	"3' UTR (NM_029895, exon 19 of 19)"	"3' UTR (NM_029895, exon 19 of 19)"	157377	NM_001081364	71435	Mm.465492	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding	0.01	0.336634
Merged-chr1-142130022-1	chr1	142129972	142130072	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1473620	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0	0.316832
Merged-chr16-25219410-1	chr16	25219360	25219460	+	2.1	cIP1vsInput	Intergenic	Intergenic	-67407	NM_175165	71338	Mm.126851	NM_175165	ENSMUSG00000048399	Tprg	5430420C16Rik|Tprg1	transformation related protein 63 regulated	protein-coding	0	0.376238
Merged-chr19-5433717-1	chr19	5433667	5433767	+	2.1	cIP2vsInput	Intergenic	Intergenic	8573	NM_134149	107242	Mm.329658	NM_001256515	ENSMUSG00000047423	AI837181	Bles03|N28173	expressed sequence AI837181	protein-coding	0.03	0.653465
Merged-chr8-41417186-2	chr8	41417130	41417243	+	2.1	cIP1vsInput|cIP2vsInput	promoter-TSS (NM_013522)	promoter-TSS (NM_013522)	-68	NM_013522	14300	Mm.217312	NM_013522	ENSMUSG00000031590	Frg1	-	FSHD region gene 1	protein-coding	0.088496	0.596491
Merged-chr2-47568063-1	chr2	47568013	47568113	+	2.1	cIP2vsInput	Intergenic	MIR|SINE|MIR	-1246046	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding	0	0.316832
Merged-chr6-46697634-1	chr6	46697584	46697684	+	2.1	cIP2vsInput	"intron (NM_001004357, intron 13 of 23)"	L1ME2z|LINE|L1	-546762	NM_025771	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0	0.287129
Merged-chr14-89952942-1	chr14	89952892	89952992	+	2.1	cIP2vsInput	Intergenic	Lx3C|LINE|L1	56718	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0	0.50495
Merged-chr19-27549524-1	chr19	27549474	27549574	+	2.1	cIP2vsInput	Intergenic	L1MB2|LINE|L1	119487	NR_027987	107372	Mm.17942	NM_175354		C030016D13Rik	AW413347	RIKEN cDNA C030016D13 gene	miscRNA	0	0.316832
Merged-chr3-29416738-1	chr3	29416688	29416788	+	2.1	cIP1vsInput	promoter-TSS (NR_030422)	promoter-TSS (NR_030422)	-85	NR_030422	791072		NR_030422		Mir551b	Mirn551b|mir-551b	microRNA 551b	miscRNA	0.01	0.376238
Merged-chr8-84947366-1	chr8	84947316	84947416	+	2.1	cIP2vsInput	"intron (NM_144929, intron 1 of 5)"	"intron (NM_144929, intron 1 of 5)"	375	NM_144929	234542	Mm.461701	NM_144929	ENSMUSG00000048617	Rtbdn	A330096I21Rik|BC022744|Rtbnd	retbindin	protein-coding	0.05	0.544554
Merged-chr9-106134361-1	chr9	106134311	106134411	+	2.1	cIP1vsInput	Intergenic	Intergenic	-19763	NR_029549	387153		NR_029549	ENSMUSG00000065407	Mir135a-1	Mir135a01|Mirn135|Mirn135a-1	microRNA 135a-1	miscRNA	0.01	0.237624
Merged-chr12-30991148-1	chr12	30991098	30991198	+	2.1	cIP2vsInput	Intergenic	Intergenic	79479	NM_013709	24057	Mm.218624	NM_013709	ENSMUSG00000020669	Sh3yl1	AI314953|Ray|YSC84	Sh3 domain YSC-like 1	protein-coding	0	0.346535
Merged-chr12-15674695-1	chr12	15674645	15674745	+	2.1	cIP2vsInput	Intergenic	Intergenic	142090	NM_144551	217410	Mm.266679	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles homolog 2 (Drosophila)	protein-coding	0.01	0.316832
Merged-chr1-58810030-1	chr1	58809980	58810080	+	2.1	cIP2vsInput	"intron (NM_001080126, intron 1 of 8)"	L1_Mur2|LINE|L1	7528	NM_001080126	12370	Mm.336851	NM_001080126	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding	0.01	0.336634
Merged-chr1-109055530-1	chr1	109055480	109055580	+	2.1	cIP2vsInput	Intergenic	MYSERV16_I-int|LTR|ERVK	-928207	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.326733
Merged-chr5-6928775-1	chr5	6928725	6928825	+	2.1	cIP2vsInput	"intron (NM_001163223, intron 1 of 3)"	"intron (NM_001163223, intron 1 of 3)"	-375389	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding	0	0.267327
Merged-chr9-4224042-1	chr9	4223992	4224092	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	85452	NM_026276	67618	Mm.33970	NM_026276	ENSMUSG00000025894	Aasdhppt	2010309J24Rik|2810407B07Rik|AASD-PPT|CGI-80|LYS2|LYS5	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	protein-coding	0.01	0.366337
Merged-chr2-86412361-1	chr2	86412311	86412411	+	2.1	cIP1vsInput	TTS (NM_207134)	TTS (NM_207134)	1689	NM_207134	259022	Mm.377793	NM_207134	ENSMUSG00000075185	Olfr1061	MOR188-1|MOR188-7|MOR188-9|Olfr1515	olfactory receptor 1061	protein-coding	0	0.287129
Merged-chr4-53085465-1	chr4	53085415	53085515	+	2.1	cIP1vsInput	"intron (NM_013454, intron 12 of 49)"	"intron (NM_013454, intron 12 of 49)"	73541	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding	0.02	0.386139
Merged-chr3-4214126-1	chr3	4214076	4214176	+	2.1	cIP1vsInput	Intergenic	Intergenic	-584582	NR_045272	100503859	Mm.75172	NR_045272		1110015O18Rik	-	RIKEN cDNA 1110015O18 gene	miscRNA	0	0.376238
Merged-chr11-26452860-1	chr11	26452810	26452910	+	2.1	cIP1vsInput	"intron (NR_102382, intron 7 of 11)"	"intron (NR_102382, intron 7 of 11)"	65776	NR_102382	67030	Mm.18875	NM_001277273		Fancl	2010322C19Rik|AW554273|B230118H11Rik|Phf9|Pog|gcd	"Fanconi anemia, complementation group L"	protein-coding	0	0.366337
Merged-chr15-33556963-1	chr15	33556913	33557013	+	2.1	cIP1vsInput	"intron (NM_018755, intron 8 of 8)"	"intron (NM_018755, intron 8 of 8)"	96473	NR_045070	75880	Mm.396109	NR_045070		4930592A05Rik	-	RIKEN cDNA 4930592A05 gene	miscRNA	0	0.326733
Merged-chr1-26020588-1	chr1	26020538	26020638	+	2.1	cIP1vsInput	Intergenic	Intergenic	-190881	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Bai3	A830096D10Rik	brain-specific angiogenesis inhibitor 3	protein-coding	0	0.356436
Merged-chr1-67338496-1	chr1	67338446	67338546	+	2.1	cIP1vsInput	Intergenic	RLTR17B_Mm|LTR|ERVK	215430	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding	0	0.267327
Merged-chr13-12944924-2	chr13	12944848	12945001	+	2.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	60406	NM_031191	18811	Mm.88796	NM_031191	ENSMUSG00000079092	Prl2c2	MRP-1|PLF-1|Plf|Plf1	"prolactin family 2, subfamily c, member 2"	protein-coding	0	0.331169
Merged-chr8-50449180-1	chr8	50449130	50449230	+	2.1	cIP1vsInput	Intergenic	MTB|LTR|ERVL-MaLR	81068	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.475248
Merged-chr14-96735194-1	chr14	96735144	96735244	+	2.1	cIP2vsInput	Intergenic	Intergenic	-216160	NM_053105	93688	Mm.308735	NM_053105	ENSMUSG00000022076	Klhl1	mKIAA1490	kelch-like 1	protein-coding	0	0.346535
Merged-chr11-55943367-1	chr11	55943317	55943417	+	2.1	cIP2vsInput	Intergenic	Intergenic	97620	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding	0.01	0.346535
Merged-chr6-91607678-1	chr6	91607628	91607728	+	2.1	cIP1vsInput	Intergenic	MTC|LTR|ERVL-MaLR	-76389	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	"solute carrier family 6 (neurotransmitter transporter, taurine), member 6"	protein-coding	0.02	0.455446
Merged-chr10-26408423-1	chr10	26408373	26408473	+	2.1	cIP2vsInput	Intergenic	L1M2|LINE|L1	-33238	NM_172787	237339	Mm.338439	NM_172787	ENSMUSG00000039089	L3mbtl3	AI481284|MBT-1	l(3)mbt-like 3 (Drosophila)	protein-coding	0	0.336634
Merged-chr11-54186158-1	chr11	54186108	54186208	+	2.1	cIP2vsInput	"intron (NR_045506, intron 2 of 2)"	L1M4|LINE|L1	27130	NR_045506	71056	Mm.56332	NR_045506	ENSMUSG00000086209	4933405E24Rik	-	RIKEN cDNA 4933405E24 gene	miscRNA	0.01	0.366337
Merged-chr2-34390463-1	chr2	34390413	34390513	+	2.1	cIP1vsInput	Intergenic	Intergenic	-18427	NM_016768	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding	0	0.336634
Merged-chr1-74533458-1	chr1	74533408	74533508	+	2.1	cIP2vsInput	"intron (NM_176972, intron 1 of 25)"	"intron (NM_176972, intron 1 of 25)"	-9431	NM_001081456	18802	Mm.290731	NM_001081456	ENSMUSG00000026173	Plcd4	4921507K24Rik	"phospholipase C, delta 4"	protein-coding	0	0.39604
Merged-chr14-86634839-1	chr14	86634789	86634889	+	2.1	cIP2vsInput	Intergenic	L1MEd|LINE|L1	388869	NR_040457	75155	Mm.399239	NR_040457		4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	miscRNA	0	0.287129
Merged-chr1-66970391-1	chr1	66970341	66970441	+	2.1	cIP1vsInput	Intergenic	L1VL4|LINE|L1	-25335	NM_021285	17901	Mm.1000	NM_001113387	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	"myosin, light polypeptide 1"	protein-coding	0.02	0.306931
Merged-chr15-15842189-1	chr15	15842139	15842239	+	2.1	cIP1vsInput	Intergenic	Intergenic	-935912	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0	0.326733
Merged-chr18-15668903-1	chr18	15668853	15668953	+	2.1	cIP2vsInput	"intron (NM_199055, intron 1 of 3)"	"intron (NM_199055, intron 1 of 3)"	49143	NM_199055	71367	Mm.329304	NM_199055	ENSMUSG00000047161	Chst9	5430438D01Rik	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	protein-coding	0.01	0.29703
Merged-chr13-88043065-1	chr13	88043015	88043115	+	2.1	cIP1vsInput	Intergenic	Intergenic	-778407	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0.01	0.247525
Merged-chr9-94839186-1	chr9	94839136	94839236	+	2.1	cIP1vsInput	"intron (NM_177909, intron 5 of 15)"	"intron (NM_177909, intron 5 of 15)"	169294	NM_177909	331004	Mm.326125	NM_177909	ENSMUSG00000031129	Slc9a9	5730527A11Rik|9930105B05|AI854429|Nhe9	"solute carrier family 9 (sodium/hydrogen exchanger), member 9"	protein-coding	0	0.306931
Merged-chr6-97665699-1	chr6	97665649	97665749	+	2.1	cIP2vsInput	Intergenic	Intergenic	-48042	NM_145148	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720|mKIAA1013	FERM domain containing 4B	protein-coding	0	0.356436
Merged-chr15-18276711-1	chr15	18276661	18276761	+	2.1	cIP2vsInput	"intron (NR_045711, intron 6 of 11)"	"intron (NR_045711, intron 6 of 11)"	92916	NR_045711	70886	Mm.399021	NR_045711		4921515E04Rik	-	RIKEN cDNA 4921515E04 gene	miscRNA	0	0.326733
Merged-chr1-108357290-1	chr1	108357240	108357340	+	2.1	cIP1vsInput	Intergenic	Intergenic	440031	NR_102307	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0	0.326733
Merged-chr1-25659690-1	chr1	25659640	25659740	+	2.1	cIP1vsInput	"intron (NM_175642, intron 2 of 30)"	"intron (NM_175642, intron 2 of 30)"	170017	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Bai3	A830096D10Rik	brain-specific angiogenesis inhibitor 3	protein-coding	0	0.336634
Merged-chr11-60448199-1	chr11	60448149	60448249	+	2.1	cIP1vsInput	Intergenic	Intergenic	-6418	NM_021354	13495	Mm.41803	XM_003945908	ENSMUSG00000020537	Drg2	AI255295|AI461605	developmentally regulated GTP binding protein 2	protein-coding	0.01	0.29703
Merged-chr10-57765535-1	chr10	57765485	57765585	+	2.1	cIP1vsInput	Intergenic	B1_Mur3|SINE|Alu	-19388	NM_021272	12140	Mm.3644	NM_021272	ENSMUSG00000019874	Fabp7	B-FABP|BFABP|Blbp|MRG	"fatty acid binding protein 7, brain"	protein-coding	0.01	0.524752
Merged-chr2-13179665-1	chr2	13179615	13179715	+	2.1	cIP1vsInput	"intron (NM_009105, intron 7 of 8)"	"intron (NM_009105, intron 7 of 8)"	91613	NM_009105	20163	Mm.905	NM_009105	ENSMUSG00000026727	Rsu1	RsuI|rsp-1	Ras suppressor protein 1	protein-coding	0	0.306931
Merged-chr16-79652605-1	chr16	79652555	79652655	+	2.1	cIP1vsInput	Intergenic	Intergenic	-561508	NM_008941	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	"transmembrane protease, serine 15"	protein-coding	0	0.326733
Merged-chrY-41271803-1	chrY	41271753	41271853	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1658520	NR_038299	100041346	Mm.490246	NR_038299		Gm20871	-	Sycp3 like Y-linked pseudogene	pseudo	0.01	0.326733
Merged-chr8-108056714-1	chr8	108056664	108056764	+	2.1	cIP1vsInput	Intergenic	Intergenic	-468232	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	"proteasome (prosome, macropain) 26S subunit, non-ATPase, 7"	protein-coding	0.03	0.60396
Merged-chr15-35177764-1	chr15	35177714	35177814	+	2.1	cIP2vsInput	Intergenic	Lx|LINE|L1	-21958	NM_019635	56274	Mm.262330	NM_019635	ENSMUSG00000022329	Stk3	0610042I06Rik|MST|Mst2|Mst3|Ste20|mess1	serine/threonine kinase 3	protein-coding	0	0.316832
Merged-chr5-52762264-1	chr5	52762214	52762314	+	2.1	cIP2vsInput	"intron (NM_028744, intron 8 of 9)"	"intron (NM_028744, intron 8 of 9)"	20690	NM_025951	67073	Mm.248647	NM_025951	ENSMUSG00000029186	Pi4k2b	2610042N09Rik|4933409G22Rik	phosphatidylinositol 4-kinase type 2 beta	protein-coding	0	0.306931
Merged-chr1-27499317-1	chr1	27499267	27499367	+	2.1	cIP1vsInput	Intergenic	Intergenic	-811857	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding	0	0.326733
Merged-chr17-75736226-1	chr17	75736176	75736276	+	2.1	cIP2vsInput	Intergenic	RMER19A|LTR|ERVK	-124797	NR_033456	100043885	Mm.127562	NR_033456		Gm4710	-	predicted gene 4710	miscRNA	0.01	0.306931
Merged-chr15-83205060-1	chr15	83205010	83205110	+	2.1	cIP2vsInput	Intergenic	Intergenic	-32852	NM_029787	109754	Mm.22560	NM_029787	ENSMUSG00000018042	Cyb5r3	0610016L08Rik|2500002N19Rik|C85115|Dia-1|Dia1|WU:AL591952.1-001|WU:AL591952.1-002|WU:AL591952.1-003|WU:Cyb5r3	cytochrome b5 reductase 3	protein-coding	0	0.534653
Merged-chr5-97233737-1	chr5	97233687	97233787	+	2.1	cIP2vsInput	Intergenic	Intergenic	-122141	NM_198422	231474	Mm.332505	NM_198422	ENSMUSG00000055725	Paqr3	6330415A20Rik|AY424292|RKTG	progestin and adipoQ receptor family member III	protein-coding	0.01	0.346535
Merged-chr4-84147615-1	chr4	84147565	84147665	+	2.1	cIP2vsInput	Intergenic	Intergenic	527471	NM_172870	242509	Mm.190774	NM_172870		Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding	0	0.366337
Merged-chr2-122206198-1	chr2	122206148	122206248	+	2.1	cIP2vsInput	"3' UTR (NM_028914, exon 7 of 7)"	"3' UTR (NM_028914, exon 7 of 7)"	19926	NM_028914	74401	Mm.374834	NM_028914	ENSMUSG00000027229	4933406J08Rik	-	RIKEN cDNA 4933406J08 gene	protein-coding	0	0.247525
Merged-chr5-9636840-1	chr5	9636790	9636890	+	2.1	cIP2vsInput	"intron (NM_181850, intron 1 of 5)"	"intron (NM_181850, intron 1 of 5)"	88512	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	"glutamate receptor, metabotropic 3"	protein-coding	0.03	0.346535
Merged-chr11-20188414-1	chr11	20188364	20188464	+	2.1	cIP2vsInput	Intergenic	MER110A|LTR|ERV1	-13188	NM_008996	19324	Mm.271944	NM_008996	ENSMUSG00000020149	Rab1	Gtbp|Rab-1|Rab1A|Ypt1|mKIAA3012	"RAB1, member RAS oncogene family"	protein-coding	0	0.336634
Merged-chr12-6963642-1	chr12	6963592	6963692	+	2.1	cIP2vsInput	Intergenic	Intergenic	416688	NR_045045	73575	Mm.179463	NR_045045		1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	miscRNA	0	0.287129
Merged-chr3-128550352-1	chr3	128550302	128550402	+	2.1	cIP1vsInput	Intergenic	Intergenic	-318747	NR_045704	402774	Mm.209170	NR_045704		D030025E07Rik	-	RIKEN cDNA D030025E07 gene	miscRNA	0	0.386139
Merged-chr1-29249266-1	chr1	29249216	29249316	+	2.1	cIP1vsInput	Intergenic	Intergenic	-469014	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0	0.217822
Merged-chr2-36021760-2	chr2	36021669	36021852	+	2.1	cIP1vsInput|cIP2vsInput	Intergenic	(CA)n|Simple_repeat|Simple_repeat	27532	NM_026703	68375	Mm.19834	NM_026703	ENSMUSG00000026895	Ndufa8	0610033L03Rik|AW261656	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 8"	protein-coding	0.081967	0.565217
Merged-chr11-51318426-1	chr11	51318376	51318476	+	2.1	cIP1vsInput	"intron (NM_153393, intron 2 of 28)"	"intron (NM_153393, intron 2 of 28)"	28506	NM_153393	237759	Mm.154093	NM_153393	ENSMUSG00000063564	Col23a1	2810458L13Rik|AI429655	"collagen, type XXIII, alpha 1"	protein-coding	0	0.316832
Merged-chr11-73548168-1	chr11	73548118	73548218	+	2.1	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	-30971	NM_146443	258435	Mm.377500	NM_146443	ENSMUSG00000095312	Olfr382	MOR135-14	olfactory receptor 382	protein-coding	0	0.366337
Merged-chr3-12008992-1	chr3	12008942	12009042	+	2.1	cIP1vsInput	Intergenic	Intergenic	-164633	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.277228
Merged-chr4-134487171-1	chr4	134487121	134487221	+	2.1	cIP2vsInput	Intergenic	RLTR49|LTR|ERVK	-9807	NM_027995	71904	Mm.142343	NM_027995	ENSMUSG00000037348	Paqr7	2310021M12Rik|AV001994|BB007237|Mpra|PGLP|mPR	progestin and adipoQ receptor family member VII	protein-coding	0.02	0.326733
Merged-chr2-113293475-1	chr2	113293425	113293525	+	2.1	cIP1vsInput	"intron (NM_029232, intron 9 of 11)"	L1ME3|LINE|L1	7743	NM_029232	75275	Mm.159484	NM_029232	ENSMUSG00000041255	Tmco5b	4930563P21Rik	transmembrane and coiled-coil domains 5B	protein-coding	0	0.277228
Merged-chr2-11346906-1	chr2	11346856	11346956	+	2.1	cIP2vsInput	"intron (NR_040615, intron 2 of 2)"	"intron (NR_040615, intron 2 of 2)"	7417	NR_040369	100503147	Mm.91961	NR_040369		Gm13293	OTTMUSG00000011311	predicted gene 13293	miscRNA	0	0.366337
Merged-chr4-66953821-1	chr4	66953771	66953871	+	2.1	cIP2vsInput	Intergenic	Intergenic	126010	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding	0	0.346535
Merged-chr14-49350768-1	chr14	49350718	49350818	+	2.1	cIP1vsInput	"intron (NM_029238, intron 1 of 7)"	"intron (NM_029238, intron 1 of 7)"	-105340	NM_025956	67082	Mm.87439	NM_025956	ENSMUSG00000021850	1700011H14Rik	-	RIKEN cDNA 1700011H14 gene	protein-coding	0.01	0.366337
Merged-chr14-57551751-1	chr14	57551701	57551801	+	2.1	cIP1vsInput	"intron (NM_026526, intron 3 of 4)"	"intron (NM_026526, intron 3 of 4)"	19818	NM_026526	68043	Mm.45225	NM_026526	ENSMUSG00000021951	N6amt2	2510005D08Rik|AW045965|Ayu21-96|Gt(pU21)96Imeg|GtAyu21-96	N-6 adenine-specific DNA methyltransferase 2 (putative)	protein-coding	0.01	0.366337
Merged-chr16-9704655-1	chr16	9704605	9704705	+	2.1	cIP2vsInput	"intron (NM_008170, intron 3 of 11)"	L1ME3|LINE|L1	287878	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	"glutamate receptor, ionotropic, NMDA2A (epsilon 1)"	protein-coding	0	0.277228
Merged-chr16-56752369-1	chr16	56752319	56752419	+	2.1	cIP1vsInput	"exon (NM_172825, exon 9 of 16)"	"exon (NM_172825, exon 9 of 16)"	-34919	NM_001252443	21787	Mm.489792	NM_001252443	ENSMUSG00000022757	Tfg	AI173908	Trk-fused gene	protein-coding	0.02	0.29703
Merged-chr14-99209209-1	chr14	99209159	99209259	+	2.1	cIP1vsInput	"intron (NM_029320, intron 14 of 17)"	"intron (NM_029320, intron 14 of 17)"	-89482	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding	0.01	0.356436
Merged-chr6-25616804-1	chr6	25616754	25616854	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	73176	NM_010338	14763	Mm.409670	NM_010338		Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding	0	0.326733
Merged-chr14-119967454-1	chr14	119967404	119967504	+	2.1	cIP2vsInput	Intergenic	MER96B|DNA|hAT-Tip100	74981	NM_001001490	239283	Mm.138520	NM_001001490	ENSMUSG00000044819	Oxgr1	Gm299|Gpr80|Gpr99|P2Y15	oxoglutarate (alpha-ketoglutarate) receptor 1	protein-coding	0.04	0.405941
Merged-chr13-87447614-1	chr13	87447564	87447664	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1373858	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0	0.326733
Merged-chr7-60307114-1	chr7	60307064	60307164	+	2.1	cIP2vsInput	Intergenic	Intergenic	-166895	NM_001082962	20646	Mm.274995	NM_001082961	ENSMUSG00000000948	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding	0	0.336634
Merged-chr7-81971822-1	chr7	81971772	81971872	+	2.1	cIP2vsInput	"intron (NM_007562, intron 4 of 4)"	"intron (NM_007562, intron 4 of 4)"	20477	NM_007562	12173	Mm.243802	NM_007562	ENSMUSG00000025105	Bnc1	AI047752|AW546376|Bnc	basonuclin 1	protein-coding	0	0.366337
Merged-chr10-70296316-1	chr10	70296266	70296366	+	2.1	cIP1vsInput	Intergenic	Intergenic	51040	NM_025807	66859	Mm.19325	NM_025807	ENSMUSG00000037762	Slc16a9	1200003C15Rik|4930425B13Rik|AI552636	"solute carrier family 16 (monocarboxylic acid transporters), member 9"	protein-coding	0.01	0.376238
Merged-chr13-7544096-1	chr13	7544046	7544146	+	2.1	cIP1vsInput	Intergenic	Intergenic	-658813	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	"adenosine deaminase, RNA-specific, B2"	protein-coding	0	0.346535
Merged-chr13-59850065-1	chr13	59850015	59850115	+	2.1	cIP2vsInput	Intergenic	Intergenic	-26918	NM_153538	214290	Mm.233082	NM_153538	ENSMUSG00000035248	Zcchc6	6030448M23Rik|AA420405	"zinc finger, CCHC domain containing 6"	protein-coding	0.01	0.366337
Merged-chr4-4398772-1	chr4	4398722	4398822	+	2.1	cIP1vsInput	Intergenic	Intergenic	-260327	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding	0	0.336634
Merged-chr14-19368846-1	chr14	19368796	19368896	+	2.1	cIP1vsInput	Intergenic	MLT1K|LTR|ERVL-MaLR	233741	NM_001024706	432825	Mm.443243	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding	0.01	0.435644
Merged-chr19-38395915-1	chr19	38395865	38395965	+	2.1	cIP2vsInput	promoter-TSS (NM_175507)	promoter-TSS (NM_175507)	-65	NM_175507	240660	Mm.262085	NM_175507	ENSMUSG00000044026	Slc35g1	AA590464|D330039I19Rik|Tmem20	"solute carrier family 35, member G1"	protein-coding	0.11	0.782178
Merged-chr1-77583421-1	chr1	77583371	77583471	+	2.1	cIP1vsInput	Intergenic	Intergenic	-68333	NM_007936	13838	Mm.400747	NM_007936	ENSMUSG00000026235	Epha4	2900005C20Rik|AI385584|Cek8|Hek8|Sek|Sek1|Tyro1|rb	Eph receptor A4	protein-coding	0.01	0.376238
Merged-chr4-36837067-1	chr4	36837017	36837117	+	2.1	cIP1vsInput	"intron (NM_001165999, intron 1 of 7)"	"intron (NM_001165999, intron 1 of 7)"	114677	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0	0.326733
Merged-chr13-40360857-1	chr13	40360807	40360907	+	2.1	cIP1vsInput	Intergenic	RMER17B|LTR|ERVK	-72846	NM_172143	218165	Mm.364096	NM_172143	ENSMUSG00000047094	Ofcc1	opo	orofacial cleft 1 candidate 1	protein-coding	0.01	0.564356
Merged-chr10-79469675-1	chr10	79469625	79469725	+	2.1	cIP1vsInput	"intron (NM_001104537, intron 1 of 5)"	"intron (NM_001104537, intron 1 of 5)"	717	NM_001104537	625029	Mm.469865	NM_001104537	ENSMUSG00000091381	Vmn2r83	EG625029	"vomeronasal 2, receptor 83"	protein-coding	0	0.29703
Merged-chr1-102649842-1	chr1	102649792	102649892	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	1494074	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.316832
Merged-chr4-73503748-1	chr4	73503698	73503798	+	2.1	cIP1vsInput	Intergenic	Intergenic	-98676	NM_001013393	433719	Mm.348294	NM_001013393	ENSMUSG00000066137	Gm11487	OTTMUSG00000001246	predicted gene 11487	protein-coding	0	0.326733
Merged-chr16-27139238-1	chr16	27139188	27139288	+	2.1	cIP1vsInput	Intergenic	Intergenic	-149264	NM_001013761	239789	Mm.326909	NM_001013761	ENSMUSG00000068428	Gmnc	Gemc1|Gm1778|Gm606	geminin coiled-coil domain containing	protein-coding	0	0.39604
Merged-chr14-91156876-1	chr14	91156826	91156926	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	1029985	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0	0.316832
Merged-chr1-135225408-1	chr1	135225358	135225458	+	2.1	cIP1vsInput	Intergenic	Intergenic	33064	NM_001163131	13710	Mm.441439	NM_001163131	ENSMUSG00000003051	Elf3	ESE-1|ESX|jen	E74-like factor 3	protein-coding	0	0.564356
Merged-chr14-112778916-1	chr14	112778866	112778966	+	2.1	cIP1vsInput	Intergenic	Intergenic	757486	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0.01	0.287129
Merged-chr1-176358174-1	chr1	176358124	176358224	+	2.1	cIP1vsInput	Intergenic	Intergenic	-82862	NM_176916	319455	Mm.338001	NM_001195816	ENSMUSG00000055214	Pld5	B230365F16Rik	"phospholipase D family, member 5"	protein-coding	0.02	0.356436
Merged-chr1-85317020-1	chr1	85316970	85317070	+	2.1	cIP2vsInput	Intergenic	Intergenic	-46454	NM_001037909	620078	Mm.461248	NM_001037909	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding	0.03	0.336634
Merged-chr4-48243746-1	chr4	48243696	48243796	+	2.1	cIP1vsInput	"intron (NM_029572, intron 1 of 11)"	"intron (NM_029572, intron 1 of 11)"	35843	NM_029572	76299	Mm.317701	NM_029572	ENSMUSG00000028343	Erp44	1110001E24Rik|AI849526|AL033348|Txndc4	endoplasmic reticulum protein 44	protein-coding	0	0.257426
Merged-chr10-57097612-1	chr10	57097562	57097662	+	2.1	cIP1vsInput	Intergenic	Charlie1a|DNA|hAT-Charlie	388741	NR_045353	74928	Mm.416643	NR_045353	ENSMUSG00000097370	4930467K11Rik	-	RIKEN cDNA 4930467K11 gene	miscRNA	0	0.316832
Merged-chr2-109439671-1	chr2	109439621	109439721	+	2.1	cIP1vsInput	Intergenic	Lx8b|LINE|L1	158933	NM_139303	228421	Mm.274086	NM_139303	ENSMUSG00000027115	Kif18a	AU024633|B130001M12Rik	kinesin family member 18A	protein-coding	0	0.316832
Merged-chr4-13926903-1	chr4	13926853	13926953	+	2.1	cIP2vsInput	Intergenic	Intergenic	142121	NM_009822	12395	Mm.470961	NM_001111026	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	"runt-related transcription factor 1; translocated to, 1 (cyclin D-related)"	protein-coding	0.01	0.366337
Merged-chr2-47067006-1	chr2	47066956	47067056	+	2.1	cIP2vsInput	Intergenic	L1M5|LINE|L1	1370401	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	miscRNA	0.01	0.356436
Merged-chr1-187082981-1	chr1	187082931	187083031	+	2.1	cIP1vsInput	"intron (NM_028848, intron 9 of 9)"	"intron (NM_028848, intron 9 of 9)"	-42157	NR_040554	69308	Mm.490882	NR_040554		1700007P06Rik	-	RIKEN cDNA 1700007P06 gene	miscRNA	0	0.425743
Merged-chr2-102583764-1	chr2	102583714	102583814	+	2.1	cIP1vsInput	"intron (NM_173749, intron 2 of 10)"	L1MC5a|LINE|L1	33743	NM_173749	210622	Mm.431895	NM_173749	ENSMUSG00000027188	Pamr1	5930437L24|E430002G05Rik|Ramp	peptidase domain containing associated with muscle regeneration 1	protein-coding	0.03	0.376238
Merged-chr1-115554633-1	chr1	115554583	115554683	+	2.1	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-130504	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0	0.326733
Merged-chr3-159435050-1	chr3	159435000	159435100	+	2.1	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-60383	NM_001172092	76131	Mm.371655	NM_001172092	ENSMUSG00000028175	Depdc1a	5830484J08Rik|Depdc1	DEP domain containing 1a	protein-coding	0	0.376238
Merged-chr8-98560965-1	chr8	98560915	98561015	+	2.1	cIP2vsInput	Intergenic	Lx5c|LINE|L1	855492	NM_007667	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.29703
Merged-chr5-84813696-1	chr5	84813646	84813746	+	2.1	cIP2vsInput	Intergenic	Intergenic	-396314	NM_007937	13839	Mm.438006	NM_007937		Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding	0	0.29703
Merged-chrX-132814894-1	chrX	132814844	132814944	+	2.1	cIP1vsInput	Intergenic	L1MCb|LINE|L1	874099	NM_001105245	279653	Mm.39738	NM_001105245	ENSMUSG00000051323	Pcdh19	B530002L05Rik|Gm717|mKIAA1313	protocadherin 19	protein-coding	0	0.306931
Merged-chrX-83809190-1	chrX	83809140	83809240	+	2.1	cIP2vsInput	"intron (NM_007868, intron 25 of 78)"	"intron (NM_007868, intron 25 of 78)"	-321266	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding	0	0.257426
Merged-chr6-78633592-1	chr6	78633542	78633642	+	2.1	cIP1vsInput	Intergenic	A-rich|Low_complexity|Low_complexity	-164718	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515	regenerating islet-derived 3 gamma	protein-coding	0	0.306931
Merged-chr13-14969014-1	chr13	14968964	14969064	+	2.1	cIP1vsInput	Intergenic	Intergenic	338756	NM_134067	105351	Mm.41450	NM_001104646	ENSMUSG00000039182	AW209491	-	expressed sequence AW209491	protein-coding	0	0.326733
Merged-chrX-120310001-1	chrX	120309951	120310051	+	2.1	cIP1vsInput	"intron (NR_073452, intron 1 of 6)"	"intron (NR_073452, intron 1 of 6)"	19674	NR_073451	245578	Mm.490224	NM_001271809		Pcdh11x	PCDHX|PCDHX11|Pcdh11	protocadherin 11 X-linked	protein-coding	0	0.346535
Merged-chr12-98158666-1	chr12	98158616	98158716	+	2.1	cIP1vsInput	Intergenic	Intergenic	100671	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding	0	0.346535
Merged-chr19-60369388-1	chr19	60369338	60369438	+	2.1	cIP2vsInput	Intergenic	Intergenic	98916	NM_201615	226278	Mm.377241	NM_201615	ENSMUSG00000045052	Prlhr	Gm339|Gpr10|Gr3|Prrpr	prolactin releasing hormone receptor	protein-coding	0	0.346535
Merged-chr4-54677473-1	chr4	54677423	54677523	+	2.1	cIP1vsInput	Intergenic	Lx5c|LINE|L1	-270472	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding	0	0.326733
Merged-chr13-43546746-1	chr13	43546696	43546796	+	2.1	cIP2vsInput	"intron (NM_001081059, intron 6 of 8)"	"intron (NM_001081059, intron 6 of 8)"	13445	NM_001081059	76137	Mm.426290	NM_001081059	ENSMUSG00000021371	Mcur1	6230416A05Rik|AU015498|AV136929|AW554392|C88263|Ccdc90a	mitochondrial calcium uniporter regulator 1	protein-coding	0	0.287129
Merged-chr3-112366394-1	chr3	112366344	112366444	+	2.1	cIP2vsInput	Intergenic	Intergenic	484491	NR_045362	625585	Mm.389497	NR_045362		Gm6602	-	predicted gene 6602	miscRNA	0.01	0.306931
Merged-chr14-24717202-1	chr14	24717152	24717252	+	2.1	cIP1vsInput	Intergenic	MIR|SINE|MIR	226521	NM_011297	20088	Mm.16775	NM_011297	ENSMUSG00000025290	Rps24	-	ribosomal protein S24	protein-coding	0	0.485149
Merged-chr6-73432683-1	chr6	73432633	73432733	+	2.1	cIP1vsInput	Intergenic	Intergenic	36984	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.29703
Merged-chr7-88097414-1	chr7	88097364	88097464	+	2.1	cIP1vsInput	"intron (NM_001081414, intron 9 of 9)"	"intron (NM_001081414, intron 9 of 9)"	-180679	NM_009982	13032	Mm.322945	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|DPP1|DPPI	cathepsin C	protein-coding	0	0.346535
Merged-chr1-143085707-1	chr1	143085657	143085757	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-554990	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0	0.39604
Merged-chr4-16377933-2	chr4	16377873	16377993	+	2.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	213823	NR_045765	100415915	Mm.387180	NR_045765	ENSMUSG00000085112	A530072M11Rik	-	RIKEN cDNA gene A530072M11	miscRNA	0	0.280992
Merged-chr17-37715860-1	chr17	37715810	37715910	+	2.1	cIP2vsInput	Intergenic	Intergenic	-10139	NM_146631	258624	Mm.272073	NM_146631	ENSMUSG00000063994	Olfr120	MOR263-3	olfactory receptor 120	protein-coding	0	0.356436
Merged-chr15-70417555-1	chr15	70417505	70417605	+	2.1	cIP2vsInput	Intergenic	Intergenic	493322	NR_045071	100503580	Mm.404646	NR_045071		Gm19782	-	"predicted gene, 19782"	miscRNA	0	0.326733
Merged-chr8-80635144-1	chr8	80635094	80635194	+	2.1	cIP1vsInput	"intron (NM_001167898, intron 2 of 7)"	"intron (NM_001167898, intron 2 of 7)"	24105	NM_001167898	333315	Mm.134296	NM_001167898	ENSMUSG00000042353	Frem3	Gm795|NV2	Fras1 related extracellular matrix protein 3	protein-coding	0	0.316832
Merged-chr1-23358422-1	chr1	23358372	23358472	+	2.1	cIP2vsInput	Intergenic	Intergenic	24753	NM_001081079	70155	Mm.28013	NM_001081079	ENSMUSG00000026158	Ogfrl1	2210417C17Rik	opioid growth factor receptor-like 1	protein-coding	0.01	0.346535
Merged-chr6-53183986-1	chr6	53183936	53184036	+	2.1	cIP1vsInput	Intergenic	L1VL4|LINE|L1	-37178	NR_073371	231989	Mm.372520	XM_001473662		Gm4872	D430007I03	predicted gene 4872	miscRNA	0	0.306931
Merged-chr17-39704683-1	chr17	39704633	39704733	+	2.1	cIP1vsInput	Intergenic	Intergenic	63726	NM_001244651	668200	Mm.464782	NM_001244651	ENSMUSG00000095104	Gm9041	EG668200|Esp16	predicted gene 9041	protein-coding	0	0.326733
Merged-chrY-6485014-1	chrY	6484964	6485064	+	2.1	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	682763	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.366337
Merged-chr15-29236638-1	chr15	29236588	29236688	+	2.1	cIP1vsInput	Intergenic	Intergenic	-935955	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	"catenin (cadherin associated protein), delta 2"	protein-coding	0	0.356436
Merged-chrX-114366386-1	chrX	114366336	114366436	+	2.1	cIP1vsInput	Intergenic	L1_Mur1|LINE|L1	-108134	NM_172781	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding	0	0.326733
Merged-chrX-64685120-1	chrX	64685070	64685170	+	2.1	cIP1vsInput	Intergenic	Intergenic	-362524	NM_027302	70062	Mm.45791	NM_027302	ENSMUSG00000031181	Ctag2	1700030B21Rik	cancer/testis antigen 2	protein-coding	0.01	0.267327
Merged-chr4-98533596-1	chr4	98533546	98533646	+	2.1	cIP1vsInput	"intron (NM_172696, intron 25 of 43)"	"intron (NM_172696, intron 25 of 43)"	-13038	NM_007704	12695	Mm.90218	NM_001005784	ENSMUSG00000061859	Inadl	Cipp|Patj	InaD-like (Drosophila)	protein-coding	0	0.534653
Merged-chr14-118837535-1	chr14	118837485	118837585	+	2.1	cIP1vsInput	"intron (NM_001160097, intron 1 of 3)"	"intron (NM_001160097, intron 1 of 3)"	-17415	NM_021386	58187	Mm.390755	NM_001160096	ENSMUSG00000022132	Cldn10	6720456I16Rik|Cldn10a|Cldn10b|D14Ertd728e	claudin 10	protein-coding	0	0.346535
Merged-chr3-6387712-1	chr3	6387662	6387762	+	2.1	cIP2vsInput	Intergenic	Intergenic	232731	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding	0	0.267327
Merged-chr13-47691297-1	chr13	47691247	47691347	+	2.1	cIP2vsInput	Intergenic	Intergenic	-219138	NR_045156	619327	Mm.412752	NR_045156		G630093K05Rik	-	RIKEN cDNA G630093K05 gene	miscRNA	0.01	0.49505
Merged-chr16-68303718-1	chr16	68303668	68303768	+	2.1	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-682810	NM_178721	239857	Mm.394300	NM_001145977	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0	0.287129
Merged-chr17-20661011-1	chr17	20660961	20661061	+	2.1	cIP2vsInput	Intergenic	Intergenic	-26497	NM_134191	171225	Mm.377184	NM_134191	ENSMUSG00000042848	Vmn1r226	V1re2	vomeronasal 1 receptor 226	protein-coding	0	0.336634
Merged-chr5-80480118-1	chr5	80480068	80480168	+	2.1	cIP2vsInput	Intergenic	Intergenic	-541475	NM_198702	319387	Mm.461016	NM_198702	ENSMUSG00000037605	Lphn3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|mKIAA0768	latrophilin 3	protein-coding	0	0.336634
Merged-chr10-3271679-1	chr10	3271629	3271729	+	2.1	cIP2vsInput	Intergenic	Intergenic	-3908	NM_001204916	670558	Mm.398582	NM_001204916		H60c	4632413I24Rik|Gm9491	histocompatibility 60c	protein-coding	0	0.287129
Merged-chr10-121421030-1	chr10	121420980	121421080	+	2.1	cIP1vsInput	"intron (NM_138956, intron 1 of 4)"	MIRb|SINE|MIR	55220	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding	0.03	0.475248
Merged-chr2-36579467-1	chr2	36579417	36579517	+	2.1	cIP1vsInput	Intergenic	Lx2|LINE|L1	10867	NM_146628	258621	Mm.377598	NM_146628	ENSMUSG00000096822	Olfr344	MOR136-12	olfactory receptor 344	protein-coding	0	0.356436
Merged-chr3-13962291-1	chr3	13962241	13962341	+	2.1	cIP1vsInput	"intron (NM_001163329, intron 1 of 7)"	L1M2|LINE|L1	15919	NM_001163330	76897	Mm.422625	NM_001163328	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0.02	0.376238
Merged-chr1-32136688-1	chr1	32136638	32136738	+	2.1	cIP2vsInput	Intergenic	Intergenic	-36118	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm1	"KH domain containing, RNA binding, signal transduction associated 2"	protein-coding	0.01	0.306931
Merged-chr6-60093099-1	chr6	60093049	60093149	+	2.1	cIP1vsInput	Intergenic	B4A|SINE|B4	310608	NR_015565	208079	Mm.490691	NR_015565		A530053G22Rik	-	RIKEN cDNA A530053G22 gene	miscRNA	0	0.306931
Merged-chr2-83882820-1	chr2	83882770	83882870	+	2.1	cIP1vsInput	Intergenic	Intergenic	58406	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding	0	0.29703
Merged-chr9-52559423-1	chr9	52559373	52559473	+	2.1	cIP2vsInput	Intergenic	Intergenic	120006	NM_178906	330941	Mm.335160	NM_177907	ENSMUSG00000078307	AI593442	E130102D23	expressed sequence AI593442	protein-coding	0	0.326733
Merged-chr4-108870536-1	chr4	108870486	108870586	+	2.1	cIP1vsInput	Intergenic	Intergenic	-8534	NM_023537	69908	Mm.41580	NM_023537	ENSMUSG00000003411	Rab3b	2610528C18Rik	"RAB3B, member RAS oncogene family"	protein-coding	0.02	0.326733
Merged-chr19-22444416-1	chr19	22444366	22444466	+	2.1	cIP1vsInput	"intron (NM_001035242, intron 1 of 24)"	MTD|LTR|ERVL-MaLR	-3792	NM_177341	226025	Mm.440339	NM_001035239	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	"transient receptor potential cation channel, subfamily M, member 3"	protein-coding	0	0.425743
Merged-chr17-39716108-1	chr17	39716058	39716158	+	2.1	cIP1vsInput	Intergenic	Intergenic	75151	NM_001244651	668200	Mm.464782	NM_001244651	ENSMUSG00000095104	Gm9041	EG668200|Esp16	predicted gene 9041	protein-coding	0.01	0.415842
Merged-chr9-61011627-1	chr9	61011577	61011677	+	2.1	cIP2vsInput	Intergenic	L1M2|LINE|L1	-5442	NR_040767	330956	Mm.207985	NR_040767		Gm5122	A430102L10	predicted gene 5122	miscRNA	0.02	0.445545
Merged-chr7-104344048-1	chr7	104343998	104344098	+	2.1	cIP1vsInput	"intron (NM_001146007, intron 4 of 7)"	B3|SINE|B2	9301	NM_175677	319236	Mm.425502	NM_001146007	ENSMUSG00000057143	Trim12c	9230105E10Rik|Trim12-2	tripartite motif-containing 12C	protein-coding	0.01	0.485149
Merged-chr11-98607071-1	chr11	98607021	98607121	+	2.1	cIP1vsInput	Intergenic	Intergenic	8780	NM_001195544	192852	Mm.342821	NM_001195544		Gm12	-	predicted gene 12	protein-coding	0.02	0.435644
Merged-chr11-100027091-1	chr11	100027041	100027141	+	2.1	cIP1vsInput	"intron (NM_013570, intron 2 of 6)"	"intron (NM_013570, intron 2 of 6)"	2777	NM_013570	16671	Mm.439738	NM_013570	ENSMUSG00000057723	Krt33b	Ha3|Ha4|Krt1-3|mHa3	keratin 33B	protein-coding	0	0.257426
Merged-chr2-104701368-1	chr2	104701318	104701418	+	2.1	cIP1vsInput	"intron (NM_177190, intron 2 of 9)"	"intron (NM_177190, intron 2 of 9)"	10794	NM_177190	320554	Mm.249065	NM_177190	ENSMUSG00000027175	Tcp11l1	C130096D04Rik	t-complex 11 like 1	protein-coding	0	0.336634
Merged-chr7-18021233-1	chr7	18021183	18021283	+	2.1	cIP2vsInput	Intergenic	Intergenic	11344	NM_028171	69785	Mm.46086	NM_027210	ENSMUSG00000057195	Ceacam13	1600012K03Rik|1600025J19Rik	carcinoembryonic antigen-related cell adhesion molecule 13	protein-coding	0	0.356436
Merged-chr19-11798713-1	chr19	11798663	11798763	+	2.1	cIP1vsInput	"intron (NM_001025307, intron 2 of 10)"	RLTR21|LTR|ERVK	20180	NM_011502	20908	Mm.272264	NM_001025308	ENSMUSG00000041488	Stx3	AA960228|AV006285|AW536415|Syn-3	syntaxin 3	protein-coding	0	0.247525
Merged-chr10-32686870-1	chr10	32686820	32686920	+	2.1	cIP1vsInput	"intron (NM_001013411, intron 1 of 6)"	B2_Mm2|SINE|B2	203045	NM_001013411	432450	Mm.49665	NM_001013411		Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding	0	0.415842
Merged-chr9-6739417-1	chr9	6739367	6739467	+	2.1	cIP1vsInput	Intergenic	(TGAA)n|Simple_repeat|Simple_repeat	437629	NM_029851	110350	Mm.237596	NM_029851	ENSMUSG00000047193	Dync2h1	4432416O06Rik|AI448217|D030010H02Rik|D330044F14Rik|DHC1b|DHC2|Dnchc2|b2b414Clo|mKIAA1997	dynein cytoplasmic 2 heavy chain 1	protein-coding	0.01	0.29703
Merged-chr5-67267556-1	chr5	67267506	67267606	+	2.1	cIP1vsInput	"intron (NM_030108, intron 5 of 8)"	"intron (NM_030108, intron 5 of 8)"	6904	NM_030108	67878	Mm.23217	NM_028975	ENSMUSG00000037720	Tmem33	1110006G02Rik|1600019D15Rik|2410089A21Rik|2700052H22Rik|5430406L04Rik|AA388285|AI314185|AI426615|db83	transmembrane protein 33	protein-coding	0.01	0.287129
Merged-chr16-53114664-1	chr16	53114614	53114714	+	2.1	cIP1vsInput	Intergenic	Intergenic	-298920	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	miscRNA	0.01	0.386139
Merged-chr5-17220589-1	chr5	17220539	17220639	+	2.1	cIP1vsInput	Intergenic	Intergenic	-255533	NM_027609	70935	Mm.332225	NM_027609	ENSMUSG00000058643	Speer4f	4922502J04Rik|SPEER-4F	spermatogenesis associated glutamate (E)-rich protein 4f	protein-coding	0.01	0.287129
Merged-chr1-58764981-1	chr1	58764931	58765031	+	2.1	cIP2vsInput	Intergenic	MMERVK9E_I-int|LTR|ERVK	-30393	NM_009812	12370	Mm.336851	NM_001080126	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding	0.02	0.366337
Merged-chr2-13910861-1	chr2	13910811	13910911	+	2.1	cIP2vsInput	Intergenic	Intergenic	-117341	NM_145838	241230	Mm.393036	NM_145838		St8sia6	1700007J08Rik|AI314453|AI875066|ST8SiaVI|Siat8f	"ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6"	protein-coding	0	0.366337
Merged-chr9-4500883-1	chr9	4500833	4500933	+	2.1	cIP1vsInput	"intron (NM_019691, intron 9 of 16)"	RCHARR1|DNA|hAT-Charlie	117346	NM_145609	78100	Mm.206549	NM_145609	ENSMUSG00000041124	Msantd4	8430410K20Rik|Mysantd4	Myb/SANT-like DNA-binding domain containing 4 with coiled-coils	protein-coding	0	0.306931
Merged-chr16-32689923-1	chr16	32689873	32689973	+	2.1	cIP2vsInput	Intergenic	Intergenic	-21726	NR_033493	675921	Mm.404316	NR_033493	ENSMUSG00000075265	Gm10818	ENSMUSG00000075265	predicted gene 10818	miscRNA	0.01	0.475248
Merged-chr9-91792411-1	chr9	91792361	91792461	+	2.1	cIP1vsInput	Intergenic	Intergenic	-400525	NM_001195693	100504689	Mm.464262	NM_001195693	ENSMUSG00000095654	Plscr5	331000	"phospholipid scramblase family, member 5"	protein-coding	0.01	0.326733
Merged-chr5-97782454-1	chr5	97782404	97782504	+	2.1	cIP2vsInput	Intergenic	Lx7|LINE|L1	248508	NM_133738	71914	Mm.24842	NM_133738		Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding	0.02	0.366337
Merged-chr18-82733466-1	chr18	82733416	82733516	+	2.1	cIP1vsInput	Intergenic	Intergenic	13185	NR_039572	100628586		NR_039572	ENSMUSG00000092638	Mir5112	mmu-mir-5112|mu-mir-5112	microRNA 5112	miscRNA	0	0.326733
Merged-chr12-43700931-1	chr12	43700881	43700981	+	2.1	cIP2vsInput	Intergenic	Intergenic	509137	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	"DnaJ (Hsp40) homolog, subfamily B, member 9"	protein-coding	0	0.316832
Merged-chr18-18644292-1	chr18	18644242	18644342	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1063302	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	miscRNA	0	0.316832
Merged-chr14-55497492-1	chr14	55497442	55497542	+	2.1	cIP1vsInput	"intron (NM_001024645, intron 17 of 39)"	"intron (NM_001024645, intron 17 of 39)"	6399	NM_001024645	268747	Mm.151577	NM_001024645	ENSMUSG00000022211	Lrrc16b	mFLJ00240	leucine rich repeat containing 16B	protein-coding	0.01	0.60396
Merged-chr14-90378299-1	chr14	90378249	90378349	+	2.1	cIP1vsInput	Intergenic	ORR1C2|LTR|ERVL-MaLR	251408	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0.02	0.376238
Merged-chr1-96772878-1	chr1	96772828	96772928	+	2.1	cIP1vsInput	Intergenic	Intergenic	99293	NM_172658	227394	Mm.11662	NM_172658	ENSMUSG00000040693	Slco4c1	9530051F04|C330017E21Rik|OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20|oatp-R	"solute carrier organic anion transporter family, member 4C1"	protein-coding	0.01	0.277228
Merged-chr1-32360049-1	chr1	32359999	32360099	+	2.1	cIP1vsInput	"intron (NM_133235, intron 3 of 8)"	"intron (NM_133235, intron 3 of 8)"	160950	NM_001199956	408192	Mm.485769	NM_001199956	ENSMUSG00000049830	Gm9839	ENSMUSG00000049830|Senp15	predicted gene 9839	protein-coding	0	0.277228
Merged-chr7-57926603-1	chr7	57926553	57926653	+	2.1	cIP1vsInput	Intergenic	L1Md_Gf|LINE|L1	335430	NM_008071	14402	Mm.8004	NM_001038701	ENSMUSG00000033676	Gabrb3	A230092K12Rik|AW049585|Cp1|Gabrb-3|beta3	"gamma-aminobutyric acid (GABA) A receptor, subunit beta 3"	protein-coding	0	0.316832
Merged-chr5-6377525-1	chr5	6377475	6377575	+	2.1	cIP1vsInput	Intergenic	RMER15|LTR|ERVL	-628208	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding	0	0.346535
Merged-chr11-34849134-1	chr11	34849084	34849184	+	2.1	cIP2vsInput	Intergenic	Intergenic	-15493	NM_027411	70385	Mm.194368	NM_027411	ENSMUSG00000069910	Spdl1	1700018I02Rik|2600001J17Rik|2810049B11Rik|AA409762|Ccdc99	spindle apparatus coiled-coil protein 1	protein-coding	0.01	0.386139
Merged-chr17-71764515-1	chr17	71764465	71764565	+	2.1	cIP2vsInput	Intergenic	RLTR22_Mur|LTR|ERVK	-5176	NR_073185	78785	Mm.196382	NM_001271483	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	"CAP-GLY domain containing linker protein family, member 4"	protein-coding	0	0.316832
Merged-chr5-87438875-1	chr5	87438825	87438925	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-14672	NM_133894	100559	Mm.212589	NM_133894	ENSMUSG00000061906	Ugt2b38	9430041C03Rik|AA986709	"UDP glucuronosyltransferase 2 family, polypeptide B38"	protein-coding	0.01	0.306931
Merged-chr3-126513293-1	chr3	126513243	126513343	+	2.1	cIP1vsInput	Intergenic	Lx5c|LINE|L1	-83680	NM_001025438	108058	Mm.255822	NM_001025438	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|[d]-CaMKII|mKIAA4163	"calcium/calmodulin-dependent protein kinase II, delta"	protein-coding	0.01	0.554455
Merged-chr18-4194615-1	chr18	4194565	4194665	+	2.1	cIP1vsInput	Intergenic	Intergenic	28783	NM_026092	67328	Mm.158148	NM_026092	ENSMUSG00000024233	Lyzl1	1700038F02Rik|Lyc2	lysozyme-like 1	protein-coding	0	0.455446
Merged-chr8-55932801-1	chr8	55932751	55932851	+	2.1	cIP2vsInput	Intergenic	L1MB8|LINE|L1	-8024	NM_080438	110304	Mm.307061	NM_080438		Glra3	-	"glycine receptor, alpha 3 subunit"	protein-coding	0	0.29703
Merged-chr8-5378664-1	chr8	5378614	5378714	+	2.1	cIP1vsInput	Intergenic	Intergenic	-273432	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0.01	0.346535
Merged-chr17-19152469-1	chr17	19152419	19152519	+	2.1	cIP2vsInput	Intergenic	Intergenic	98976	NM_001104550	224552	Mm.469860	NM_001104550	ENSMUSG00000096717	Vmn2r98	EG224552	"vomeronasal 2, receptor 98"	protein-coding	0.01	0.306931
Merged-chr8-100246721-1	chr8	100246671	100246771	+	2.1	cIP2vsInput	Intergenic	Intergenic	-830264	NM_001039154	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.316832
Merged-chr1-102556811-1	chr1	102556761	102556861	+	2.1	cIP2vsInput	Intergenic	ORR1E|LTR|ERVL-MaLR	1401043	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.326733
Merged-chr2-38658645-1	chr2	38658595	38658695	+	2.1	cIP1vsInput	Intergenic	Intergenic	-14739	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	"proteasome (prosome, macropain) subunit, beta type 7"	protein-coding	0.11	0.693069
Merged-chr6-147666198-1	chr6	147666148	147666248	+	2.1	cIP1vsInput	Intergenic	Intergenic	-24043	NR_033636	100039727	Mm.396220	NR_033636	ENSMUSG00000085077	1700049E15Rik	Gm15761|OTTMUSG00000026044	RIKEN cDNA 1700049E15 gene	miscRNA	0	0.386139
Merged-chr11-76827914-1	chr11	76827864	76827964	+	2.1	cIP1vsInput	"intron (NM_007754, intron 2 of 20)"	"intron (NM_007754, intron 2 of 20)"	19094	NM_007754	12874	Mm.276736	NM_007754	ENSMUSG00000020841	Cpd	AA960140|AW322530|D830034L15Rik	carboxypeptidase D	protein-coding	0	0.19802
Merged-chr12-96861908-1	chr12	96861858	96861958	+	2.1	cIP1vsInput	Intergenic	Intergenic	-814686	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0	0.247525
Merged-chr11-103566475-1	chr11	103566425	103566525	+	2.1	cIP1vsInput	"intron (NM_001033434, intron 7 of 13)"	MYSERV6-int|LTR|ERVK	48264	NM_001033434	380730	Mm.380214	NM_001033434	ENSMUSG00000034239	Gm884	-	predicted gene 884	protein-coding	0	0.336634
Merged-chrX-119703049-1	chrX	119702999	119703099	+	2.1	cIP1vsInput	Intergenic	Intergenic	-224147	NM_053114	93728	Mm.125979	NM_053114	ENSMUSG00000034732	Pabpc5	C820015E17	"poly(A) binding protein, cytoplasmic 5"	protein-coding	0.02	0.336634
Merged-chr9-52816417-1	chr9	52816367	52816467	+	2.1	cIP2vsInput	Intergenic	Intergenic	136554	NR_045333	382139	Mm.335162	NR_045333		Gm1715	-	predicted gene 1715	miscRNA	0.02	0.356436
Merged-chr2-141605327-1	chr2	141605277	141605377	+	2.1	cIP1vsInput	"intron (NM_001013802, intron 6 of 18)"	"intron (NM_001013802, intron 6 of 18)"	-933851	NM_178382	71436	Mm.426781	NM_001172160	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0	0.257426
Merged-chr16-29145450-1	chr16	29145400	29145500	+	2.1	cIP1vsInput	Intergenic	Intergenic	-64245	NM_013751	27281	Mm.103650	NM_013751	ENSMUSG00000022525	Hrasls	2810012B06Rik|A-C1|HRSL1|Hrasrs	HRAS-like suppressor	protein-coding	0.01	0.366337
Merged-chr12-57220903-1	chr12	57220853	57220953	+	2.1	cIP2vsInput	Intergenic	L2|LINE|L2	-9509	NM_001037746	328099	Mm.268180	NM_001037746		Prps1l3	AU021838|AW536152|Gm5081	phosphoribosyl pyrophosphate synthetase 1-like 3	protein-coding	0	0.346535
Merged-chr4-19476098-1	chr4	19476048	19476148	+	2.1	cIP1vsInput	"intron (NM_013927, intron 14 of 17)"	L1_Mus1|LINE|L1	94006	NM_027769	70568	Mm.38390	NM_027769	ENSMUSG00000028228	Cpne3	5430428M23Rik|5730450C07Rik|C85108|CPN3	copine III	protein-coding	0	0.326733
Merged-chr14-46133433-1	chr14	46133383	46133483	+	2.1	cIP2vsInput	Intergenic	Lx7|LINE|L1	49406	NR_002875	218963	Mm.282093	NR_002875		Gm1821	-	ubiquitin pseudogene	pseudo	0.01	0.366337
Merged-chr18-64830989-1	chr18	64830939	64831039	+	2.1	cIP2vsInput	Intergenic	L1ME3Cz|LINE|L1	-56767	NM_001114386	83814	Mm.98668	NM_001114386	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	"neural precursor cell expressed, developmentally down-regulated gene 4-like"	protein-coding	0.01	0.376238
Merged-chr15-54214948-1	chr15	54214898	54214998	+	2.1	cIP1vsInput	Intergenic	Intergenic	63536	NM_008764	18383	Mm.15383	NM_008764	ENSMUSG00000063727	Tnfrsf11b	OCIF|Opg|TR1	"tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)"	protein-coding	0.01	0.306931
Merged-chr14-54401784-1	chr14	54401734	54401834	+	2.1	cIP2vsInput	"intron (NM_011405, intron 4 of 11)"	RLTR17D_Mm|LTR|ERVK	7688	NM_001253680	20540	Mm.489701	NM_001253679	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	"solute carrier family 7 (cationic amino acid transporter, y+ system), member 7"	protein-coding	0.01	0.326733
Merged-chr9-25828559-1	chr9	25828509	25828609	+	2.1	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	346962	NM_026189	67484	Mm.112977	NM_026189	ENSMUSG00000036611	Eepd1	2310005P05Rik|AI481005	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding	0	0.29703
Merged-chr13-12491371-1	chr13	12491321	12491421	+	2.1	cIP1vsInput	"intron (NM_133643, intron 4 of 5)"	L1M3|LINE|L1	29079	NM_133643	171211	Mm.159671	NM_133643	ENSMUSG00000095105	Edaradd	1810032E07Rik|5830469M23Rik|A630043P06|cr	EDAR (ectodysplasin-A receptor)-associated death domain	protein-coding	0	0.29703
Merged-chr1-188379036-1	chr1	188378986	188379086	+	2.1	cIP1vsInput	"exon (NM_021408, exon 9 of 71)"	"exon (NM_021408, exon 9 of 71)"	116198	NM_021408	22283	Mm.331238	NM_021408	ENSMUSG00000026609	Ush2a	A930011D15Rik|A930037M10Rik|Gm676|Gm983|Mush2a|Usherin	"Usher syndrome 2A (autosomal recessive, mild)"	protein-coding	0.02	0.584158
Merged-chr3-16763875-1	chr3	16763825	16763925	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	580692	NM_001145919	229096	Mm.23834	NM_001145919	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding	0	0.336634
Merged-chr6-22133299-1	chr6	22133249	22133349	+	2.1	cIP1vsInput	"intron (NM_001081351, intron 11 of 21)"	"intron (NM_001081351, intron 11 of 21)"	147389	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding	0	0.336634
Merged-chr11-20013917-1	chr11	20013867	20013967	+	2.1	cIP1vsInput	"intron (NM_033523, intron 4 of 5)"	ORR1D2|LTR|ERVL-MaLR	89475	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	"sprouty-related, EVH1 domain containing 2"	protein-coding	0	0.346535
Merged-chr15-16417303-1	chr15	16417253	16417353	+	2.1	cIP2vsInput	Intergenic	Intergenic	-360798	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0	0.356436
Merged-chr15-10162616-1	chr15	10162566	10162666	+	2.1	cIP1vsInput	Intergenic	Intergenic	-14622	NM_011169	19116	Mm.442446	NR_045590	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding	0	0.386139
Merged-chr5-61807955-1	chr5	61807905	61808005	+	2.1	cIP1vsInput	promoter-TSS (NM_019468)	promoter-TSS (NM_019468)	-888	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding	0	0.386139
Merged-chr5-78969636-1	chr5	78969586	78969686	+	2.1	cIP2vsInput	"intron (NR_035474, intron 3 of 4)"	"intron (NR_035474, intron 3 of 4)"	546268	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0	0.336634
Merged-chr3-73549710-1	chr3	73549660	73549760	+	2.1	cIP2vsInput	"intron (NR_040557, intron 2 of 4)"	"intron (NR_040557, intron 2 of 4)"	-68059	NR_040547	74693	Mm.292227	NR_040547		4930509J09Rik	-	RIKEN cDNA 4930509J09 gene	miscRNA	0	0.207921
Merged-chr3-107940829-1	chr3	107940779	107940879	+	2.1	cIP1vsInput	"intron (NM_008184, intron 7 of 7)"	MIRb|SINE|MIR	2920	NM_008184	14867	Mm.458154	NM_008184	ENSMUSG00000068762	Gstm6	-	"glutathione S-transferase, mu 6"	protein-coding	0.04	0.485149
Merged-chr4-52063089-1	chr4	52063039	52063139	+	2.1	cIP2vsInput	Intergenic	Intergenic	-11979	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	miscRNA	0.01	0.326733
Merged-chr3-136475322-1	chr3	136475272	136475372	+	2.1	cIP1vsInput	Intergenic	Intergenic	-25973	NR_040592	70055	Mm.261063	NR_040592		1700030L20Rik	-	RIKEN cDNA 1700030L20 gene	miscRNA	0.04	0.485149
Merged-chr6-77247983-1	chr6	77247933	77248033	+	2.1	cIP1vsInput	"intron (NM_009819, intron 7 of 18)"	"intron (NM_009819, intron 7 of 18)"	5266	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0.01	0.356436
Merged-chr1-26136127-1	chr1	26136077	26136177	+	2.1	cIP1vsInput	Intergenic	Intergenic	-306420	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Bai3	A830096D10Rik	brain-specific angiogenesis inhibitor 3	protein-coding	0.01	0.356436
Merged-chr4-26503675-1	chr4	26503625	26503725	+	2.1	cIP2vsInput	Intergenic	Intergenic	-157023	NM_172865	242362	Mm.245602	NM_172865	ENSMUSG00000040520	Manea	4932703L02Rik	"mannosidase, endo-alpha"	protein-coding	0	0.257426
Merged-chr5-70421657-1	chr5	70421607	70421707	+	2.1	cIP1vsInput	Intergenic	Lx2B2|LINE|L1	420960	NM_010252	14405	Mm.255292	NM_010252	ENSMUSG00000001260	Gabrg1	GabaA|GabaA/BZ	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1"	protein-coding	0	0.306931
Merged-chrX-169856658-1	chrX	169856608	169856708	+	2.1	cIP2vsInput	"intron (NM_010797, intron 1 of 9)"	"intron (NM_010797, intron 1 of 9)"	-22964	NM_183151	17318	Mm.34441	NM_010797	ENSMUSG00000035299	Mid1	61B3-R|DXHXS1141|Fxy|Trim18	midline 1	protein-coding	0	0.267327
Merged-chr13-68801544-1	chr13	68801494	68801594	+	2.1	cIP2vsInput	"intron (NM_153534, intron 3 of 24)"	"intron (NM_153534, intron 3 of 24)"	197997	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding	0.01	0.356436
Merged-chr14-37263746-1	chr14	37263696	37263796	+	2.1	cIP1vsInput	Intergenic	Intergenic	-128424	NM_078478	66092	Mm.486242	NM_001199122	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010	growth hormone inducible transmembrane protein	protein-coding	0	0.356436
Merged-chr18-31195567-1	chr18	31195517	31195617	+	2.1	cIP2vsInput	"intron (NM_009065, intron 3 of 4)"	"intron (NM_009065, intron 3 of 4)"	121561	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding	0	0.366337
Merged-chr2-49383261-1	chr2	49383211	49383311	+	2.1	cIP2vsInput	Intergenic	Lx6|LINE|L1	-68225	NM_172663	227867	Mm.29167	NM_172663	ENSMUSG00000069495	Epc2	5830499L14|D2Ertd694e	enhancer of polycomb homolog 2 (Drosophila)	protein-coding	0	0.376238
Merged-chr19-35749089-1	chr19	35749039	35749139	+	2.1	cIP1vsInput	Intergenic	Intergenic	308271	NM_008315	15566	Mm.254266	NM_008315	ENSMUSG00000024798	Htr7	5-HT7	5-hydroxytryptamine (serotonin) receptor 7	protein-coding	0	0.247525
Merged-chr2-156906676-1	chr2	156906626	156906726	+	2.1	cIP1vsInput	Intergenic	Intergenic	-19598	NM_029983	77799	Mm.387161	NM_029983	ENSMUSG00000027636	Sla2	A930009E21Rik|AI430952|SLAP-2|SLAP2	Src-like-adaptor 2	protein-coding	0.02	0.356436
Merged-chrX-31247591-1	chrX	31247541	31247641	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-88778	NM_001243011	100042159	Mm.489579	NM_001243011	ENSMUSG00000095835	Gm3701	-	predicted gene 3701	protein-coding	0.01	0.425743
Merged-chr13-23025809-1	chr13	23025759	23025859	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-8529	NM_134214	171248	Mm.377204	NM_134214	ENSMUSG00000061829	Vmn1r214	V1rh5	vomeronasal 1 receptor 214	protein-coding	0	0.267327
Merged-chr10-118839065-1	chr10	118839015	118839115	+	2.1	cIP2vsInput	Intergenic	Intergenic	29838	NM_001014390	69181	Mm.458174	NM_001014390	ENSMUSG00000028630	Dyrk2	1810038L18Rik	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	protein-coding	0	0.316832
Merged-chr19-21246680-1	chr19	21246630	21246730	+	2.1	cIP1vsInput	Intergenic	BC1_Mm|scRNA|scRNA	-25598	NM_009551	22682	Mm.379919	NM_009551		Zfand5	2310057A04Rik|5830475F03Rik|AA415485|Za20d2|Zfp216	"zinc finger, AN1-type domain 5"	protein-coding	0	0.257426
Merged-chr10-110637342-1	chr10	110637292	110637392	+	2.1	cIP1vsInput	Intergenic	Intergenic	36692	NR_028438	109335	Mm.367727	NR_028438		9230102K24Rik	-	RIKEN cDNA 9230102K24 gene	miscRNA	0	0.376238
Merged-chr6-67713535-1	chr6	67713485	67713585	+	2.1	cIP2vsInput	Intergenic	MTE-int|LTR|ERVL-MaLR	-147836	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo	0.01	0.316832
Merged-chr7-6679418-1	chr7	6679368	6679468	+	2.1	cIP2vsInput	"intron (NM_011769, intron 7 of 7)"	MLT1A0|LTR|ERVL-MaLR	17014	NM_011769	22776	Mm.89976	NM_011769	ENSMUSG00000002266	Zim1	-	"zinc finger, imprinted 1"	protein-coding	0.01	0.405941
Merged-chr1-10808980-1	chr1	10808930	10809030	+	2.1	cIP2vsInput	"intron (NR_030645, intron 2 of 3)"	Lx6|LINE|L1	56894	NR_030645	100124448		NR_030645		Mir467e	Mirn467e	microRNA 467e	miscRNA	0.01	0.336634
Merged-chrX-108099250-1	chrX	108099200	108099300	+	2.1	cIP1vsInput	Intergenic	Intergenic	-150814	NM_001033252	213450	Mm.300779	NM_001033252	ENSMUSG00000073006	Gm732	-	predicted gene 732	protein-coding	0.01	0.326733
Merged-chr4-31007150-1	chr4	31007100	31007200	+	2.1	cIP2vsInput	Intergenic	MTEb|LTR|ERVL-MaLR	342554	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	miscRNA	0	0.306931
Merged-chr19-9426312-1	chr19	9426262	9426362	+	2.1	cIP1vsInput	Intergenic	MMERVK9C_I-int|LTR|ERVK	132936	NR_073559	619371	Mm.391205	NM_001030317		Stxbp3b	Munc18c(L)|Stxbp3-1	syntaxin-binding protein 3B	pseudo	0.01	0.326733
Merged-chr5-19173601-1	chr5	19173551	19173651	+	2.1	cIP1vsInput	Intergenic	Intergenic	52954	NR_102342	70832	Mm.398993	XR_106346	ENSMUSG00000097626	4921504A21Rik	-	RIKEN cDNA 4921504A21 gene	miscRNA	0	0.306931
Merged-chr8-69790374-1	chr8	69790324	69790424	+	2.1	cIP1vsInput	promoter-TSS (NM_133224)	promoter-TSS (NM_133224)	-789	NM_133224	170759	Mm.186066	NM_133224	ENSMUSG00000031862	Atp13a1	Atp13a|Cgi152|catp	ATPase type 13A1	protein-coding	0.02	0.405941
Merged-chr17-49653943-1	chr17	49653893	49653993	+	2.1	cIP1vsInput	"intron (NM_177052, intron 3 of 22)"	L1_Mus3|LINE|L1	38771	NM_177052	319991	Mm.441340	NM_177052	ENSMUSG00000023999	Kif6	D130004B10Rik|D130084M03Rik	kinesin family member 6	protein-coding	0.02	0.316832
Merged-chr2-37057347-1	chr2	37057297	37057397	+	2.1	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	-10960	NM_146622	258615	Mm.271468	NM_146622	ENSMUSG00000083361	Olfr360	MOR159-1	olfactory receptor 360	protein-coding	0	0.356436
Merged-chr11-27924610-1	chr11	27924560	27924660	+	2.1	cIP1vsInput	Intergenic	MT2C_Mm|LTR|ERVL	659686	NM_001166661	216613	Mm.93759	NM_001166661	ENSMUSG00000032878	Ccdc85a	E030025D05Rik	coiled-coil domain containing 85A	protein-coding	0	0.366337
Merged-chr3-130135782-1	chr3	130135732	130135832	+	2.1	cIP1vsInput	Intergenic	MIR|SINE|MIR	-45063	NM_029838	77018	Mm.91728	NM_001244952	ENSMUSG00000058897	Col25a1	2700062B08Rik|CLAC-P	"collagen, type XXV, alpha 1"	protein-coding	0	0.405941
Merged-chr4-106288611-1	chr4	106288561	106288661	+	2.1	cIP1vsInput	Intergenic	L2|LINE|L2	-27602	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding	0	0.39604
Merged-chr14-52453491-1	chr14	52453441	52453541	+	2.1	cIP1vsInput	Intergenic	MT2A|LTR|ERVL	3098	NM_020514	57271	Mm.88824	NM_020514	ENSMUSG00000035626	Olfr1509	MOR244-3|Mor83|Or83	olfactory receptor 1509	protein-coding	0	0.455446
Merged-chr11-24937894-1	chr11	24937844	24937944	+	2.1	cIP2vsInput	Intergenic	Intergenic	-207172	NR_033491	100038617	Mm.387376	NR_033491	ENSMUSG00000073103	Gm10466	ENSMUSG00000073103	predicted gene 10466	miscRNA	0.01	0.366337
Merged-chr14-92444268-1	chr14	92444218	92444318	+	2.1	cIP2vsInput	Intergenic	Intergenic	1444620	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0.01	0.287129
Merged-chr12-67787445-1	chr12	67787395	67787495	+	2.1	cIP2vsInput	Intergenic	L1M2|LINE|L1	-118174	NR_033146	100316870	Mm.379794	NR_033146		Gm17821	-	DDB1 and CUL4 associated factor 5 pseudogene	pseudo	0	0.336634
Merged-chr14-65666305-1	chr14	65666255	65666355	+	2.1	cIP1vsInput	promoter-TSS (NM_028903)	promoter-TSS (NM_028903)	-98	NM_028903	71145	Mm.83840	NM_001168318	ENSMUSG00000022032	Scara5	4932433F15Rik|4933425F03Rik|AV278087|Tesr	"scavenger receptor class A, member 5 (putative)"	protein-coding	0.01	0.514851
Merged-chr4-36133112-1	chr4	36133062	36133162	+	2.1	cIP1vsInput	"intron (NM_001166000, intron 5 of 8)"	"intron (NM_001166000, intron 5 of 8)"	-287908	NM_001166001	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0	0.316832
Merged-chr8-114167380-1	chr8	114167330	114167430	+	2.1	cIP1vsInput	Intergenic	Intergenic	33801	NM_024437	67528	Mm.27889	NM_024437	ENSMUSG00000031767	Nudt7	1300007B24Rik|2210404C19Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 7	protein-coding	0.01	0.326733
Merged-chr5-8826889-1	chr5	8826839	8826939	+	2.1	cIP1vsInput	"intron (NM_011075, intron 15 of 27)"	MTD|LTR|ERVL-MaLR	28742	NM_011075	18669	Mm.389059	NM_011075	ENSMUSG00000028970	Abcb1b	Abcb1|Mdr1|Mdr1b|Pgy-1|Pgy1|mdr	"ATP-binding cassette, sub-family B (MDR/TAP), member 1B"	protein-coding	0.01	0.49505
Merged-chr10-25980769-1	chr10	25980719	25980819	+	2.1	cIP1vsInput	Intergenic	Intergenic	-86264	NR_030449	751520		NR_030449	ENSMUSG00000076253	Mir680-3	Mirn680-3	microRNA 680-3	miscRNA	0.02	0.287129
Merged-chr15-100978097-1	chr15	100978047	100978147	+	2.1	cIP1vsInput	"intron (NM_011323, intron 10 of 25)"	"intron (NM_011323, intron 10 of 25)"	41826	NM_011323	20273	Mm.385012	NM_001077499	ENSMUSG00000023033	Scn8a	AI853486|C630029C19Rik|NaCh6|Nav1.6|dmu|med|mnd-2|mnd2|nmf2|nmf335|nmf58|nur14|seal	"sodium channel, voltage-gated, type VIII, alpha"	protein-coding	0	0.326733
Merged-chr14-18745443-1	chr14	18745393	18745493	+	2.1	cIP2vsInput	"intron (NM_144839, intron 3 of 5)"	"intron (NM_144839, intron 3 of 5)"	148184	NM_144839	218793	Mm.23551	NM_144839	ENSMUSG00000058317	Ube2e2	BC016265	ubiquitin-conjugating enzyme E2E 2	protein-coding	0	0.336634
Merged-chr17-64901470-1	chr17	64901420	64901520	+	2.1	cIP1vsInput	Intergenic	Intergenic	299821	NM_008549	17158	Mm.2433	NM_008549	ENSMUSG00000024085	Man2a1	Mana-2|Mana2|Map-2	"mannosidase 2, alpha 1"	protein-coding	0.01	0.376238
Merged-chr18-71847776-1	chr18	71847726	71847826	+	2.1	cIP2vsInput	"intron (NM_007831, intron 2 of 28)"	"intron (NM_007831, intron 2 of 28)"	503293	NM_007831	13176	Mm.167882	NM_007831		Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding	0.01	0.346535
Merged-chr1-195307615-1	chr1	195307565	195307665	+	2.1	cIP2vsInput	Intergenic	Intergenic	-130900	NM_007758	12902	Mm.235387	NM_007758	ENSMUSG00000026616	Cr2	C3DR|CD21|CD35|Cr-1|Cr-2|Cr1	complement receptor 2	protein-coding	0	0.356436
Merged-chrX-23230268-1	chrX	23230218	23230318	+	2.1	cIP2vsInput	"intron (NM_026167, intron 7 of 8)"	"intron (NM_026167, intron 7 of 8)"	134785	NM_026167	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik|mKIAA1309	kelch-like 13	protein-coding	0	0.316832
Merged-chr3-60865949-1	chr3	60865899	60865999	+	2.1	cIP1vsInput	Intergenic	Intergenic	-136846	NM_008772	18441	Mm.281452	NM_008772	ENSMUSG00000027765	P2ry1	P2Y1	"purinergic receptor P2Y, G-protein coupled 1"	protein-coding	0.02	0.376238
Merged-chr3-48500983-1	chr3	48500933	48501033	+	2.1	cIP2vsInput	Intergenic	L1VL2|LINE|L1	108117	NR_003617	66332	Mm.46124	NR_003617		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo	0	0.316832
Merged-chr13-68901797-1	chr13	68901747	68901847	+	2.1	cIP1vsInput	"intron (NM_153534, intron 2 of 24)"	L1M2|LINE|L1	97744	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding	0.01	0.287129
Merged-chr5-71737486-1	chr5	71737436	71737536	+	2.1	cIP2vsInput	"intron (NM_008069, intron 3 of 8)"	L1_Mus1|LINE|L1	37470	NM_008069	14400	Mm.38567	NM_008069		Gabrb1	AW061132|B230208N19Rik|Gabrb-1	"gamma-aminobutyric acid (GABA) A receptor, subunit beta 1"	protein-coding	0	0.287129
Merged-chr14-16928670-1	chr14	16928620	16928720	+	2.1	cIP2vsInput	Intergenic	Intergenic	-353460	NM_011243	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2|RARbeta2	"retinoic acid receptor, beta"	protein-coding	0	0.277228
Merged-chr9-8466326-1	chr9	8466276	8466376	+	2.1	cIP1vsInput	Intergenic	Intergenic	-77816	NM_013838	22068	Mm.325086	NM_013838	ENSMUSG00000031997	Trpc6	AV025995|LLHWJM002|LLHWJM003|LLHWJM004|TRP-6|Trrp6|mtrp6	"transient receptor potential cation channel, subfamily C, member 6"	protein-coding	0.01	0.306931
Merged-chr6-75615917-1	chr6	75615867	75615967	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1626800	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0.01	0.336634
Merged-chr12-42927319-1	chr12	42927269	42927369	+	2.1	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	1282749	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	"DnaJ (Hsp40) homolog, subfamily B, member 9"	protein-coding	0	0.336634
Merged-chr14-96123562-1	chr14	96123512	96123612	+	2.1	cIP2vsInput	"intron (NM_053105, intron 9 of 10)"	"intron (NM_053105, intron 9 of 10)"	242296	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.29703
Merged-chr1-154698053-1	chr1	154698003	154698103	+	2.1	cIP1vsInput	"intron (NM_009782, intron 3 of 46)"	"intron (NM_009782, intron 3 of 46)"	27867	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	"calcium channel, voltage-dependent, R type, alpha 1E subunit"	protein-coding	0.01	0.366337
Merged-chrX-85597607-1	chrX	85597557	85597657	+	2.1	cIP1vsInput	"intron (NM_025729, intron 2 of 8)"	"intron (NM_025729, intron 2 of 8)"	23585	NM_025729	66724	Mm.119646	NM_025729	ENSMUSG00000035476	Tab3	4921526G09Rik|Map3k7ip3|mKIAA4135	TGF-beta activated kinase 1/MAP3K7 binding protein 3	protein-coding	0.01	0.346535
Merged-chr8-126780659-1	chr8	126780609	126780709	+	2.1	cIP1vsInput	Intergenic	Lx8b|LINE|L1	-58859	NR_037297	100526512		NR_037297	ENSMUSG00000092794	Mir3110	mmu-mir-3110	microRNA 3110	miscRNA	0	0.29703
Merged-chr9-93129145-1	chr9	93129095	93129195	+	2.1	cIP2vsInput	Intergenic	Intergenic	-123412	NR_040756	78349	Mm.52612	NR_040756		1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	miscRNA	0	0.29703
Merged-chr18-15740679-1	chr18	15740629	15740729	+	2.1	cIP1vsInput	Intergenic	Intergenic	-22633	NM_199055	71367	Mm.329304	NM_199055	ENSMUSG00000047161	Chst9	5430438D01Rik	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	protein-coding	0	0.346535
Merged-chr6-73908457-1	chr6	73908407	73908507	+	2.1	cIP2vsInput	Intergenic	MTC|LTR|ERVL-MaLR	-438790	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.415842
Merged-chr5-22623274-1	chr5	22623224	22623324	+	2.1	cIP1vsInput	Intergenic	RMER6-int|LTR|ERVK	72861	NR_102315	320719	Mm.459265	XR_106347	ENSMUSG00000097207	6030443J06Rik	1700030G06Rik	RIKEN cDNA 6030443J06 gene	miscRNA	0	0.425743
Merged-chr16-86338814-1	chr16	86338764	86338864	+	2.1	cIP1vsInput	Intergenic	Intergenic	-437689	NM_011782	23794	Mm.437478	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|AI481094|ASMP-2	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"	protein-coding	0	0.316832
Merged-chr1-85171234-1	chr1	85171184	85171284	+	2.1	cIP1vsInput	Intergenic	Intergenic	-28377	NM_001081746	665378	Mm.449722	NM_001081746		Gm7609	EG665378	predicted pseudogene 7609	protein-coding	0	0.425743
Merged-chr16-68914474-1	chr16	68914424	68914524	+	2.1	cIP2vsInput	Intergenic	Intergenic	949270	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding	0.01	0.287129
Merged-chr8-96199826-1	chr8	96199776	96199876	+	2.1	cIP2vsInput	Intergenic	Intergenic	236282	NR_037310	100499527		NR_037310	ENSMUSG00000093084	Mir1186b	mmu-mir-1186b	microRNA 1186b	miscRNA	0.01	0.29703
Merged-chr10-79811643-1	chr10	79811593	79811693	+	2.1	cIP1vsInput	"intron (NM_023128, intron 5 of 8)"	"intron (NM_023128, intron 5 of 8)"	-9378	NM_030218	78906	Mm.33087	NM_030218	ENSMUSG00000035852	9130017N09Rik	-	RIKEN cDNA 9130017N09 gene	protein-coding	0.01	0.366337
Merged-chr10-112865867-1	chr10	112865817	112865917	+	2.1	cIP2vsInput	Intergenic	Intergenic	63159	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132|ENSMUSG00000074747	ataxin 7-like 3B	protein-coding	0	0.29703
Merged-chr5-42915152-1	chr5	42915102	42915202	+	2.1	cIP1vsInput	Intergenic	Intergenic	-318311	NM_175937	231207	Mm.7233	NM_001177379	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding	0	0.39604
Merged-chr3-79009397-1	chr3	79009347	79009447	+	2.1	cIP2vsInput	Intergenic	Lx6|LINE|L1	136478	NM_001099624	76089	Mm.462396	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding	0	0.29703
Merged-chr8-3314244-1	chr8	3314194	3314294	+	2.1	cIP1vsInput	Intergenic	Intergenic	-34627	NM_010568	16337	Mm.268003	NM_010568		Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding	0.02	0.425743
Merged-chr14-40595347-1	chr14	40595297	40595397	+	2.1	cIP2vsInput	Intergenic	Intergenic	297618	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding	0	0.336634
Merged-chr10-4866677-1	chr10	4866627	4866727	+	2.1	cIP1vsInput	"intron (NM_007956, intron 5 of 8)"	"intron (NM_007956, intron 5 of 8)"	202386	NM_022027	64009	Mm.331626	NM_001079686	ENSMUSG00000019769	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756	"spectrin repeat containing, nuclear envelope 1"	protein-coding	0	0.356436
Merged-chr8-84250301-1	chr8	84250251	84250351	+	2.1	cIP1vsInput	promoter-TSS (NM_001007571)	promoter-TSS (NM_001007571)	-540	NM_001007571	101966	Mm.200723	NM_001007571	ENSMUSG00000019362	D8Ertd738e	AA589584	"DNA segment, Chr 8, ERATO Doi 738, expressed"	protein-coding	0.01	0.376238
Merged-chr13-56337066-1	chr13	56337016	56337116	+	2.1	cIP1vsInput	Intergenic	Intergenic	-25834	NR_046061	100038494	Mm.370447	NR_046061		Gm10782	ENSMUSG00000074885	predicted gene 10782	miscRNA	0.01	0.376238
Merged-chr2-98439274-1	chr2	98439224	98439324	+	2.1	cIP2vsInput	Intergenic	Intergenic	971600	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.346535
Merged-chr7-80387955-1	chr7	80387905	80388005	+	2.1	cIP1vsInput	promoter-TSS (NM_010194)	promoter-TSS (NM_010194)	-9	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding	0.04	0.633663
Merged-chr11-99126705-1	chr11	99126655	99126755	+	2.1	cIP1vsInput	Intergenic	Intergenic	28372	NM_007719	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding	0.01	0.584158
Merged-chr6-10501317-1	chr6	10501267	10501367	+	2.1	cIP1vsInput	Intergenic	Lx10|LINE|L1	473061	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	miscRNA	0	0.336634
Merged-chr1-8758252-1	chr1	8758202	8758302	+	2.1	cIP1vsInput	"intron (NM_027671, intron 6 of 20)"	"intron (NM_027671, intron 6 of 20)"	541478	NM_027671	71096	Mm.388998	NM_027671		Sntg1	4933426D16Rik|G1SYN|SYN4	"syntrophin, gamma 1"	protein-coding	0	0.326733
Merged-chr5-86971527-1	chr5	86971477	86971577	+	2.1	cIP1vsInput	Intergenic	Intergenic	-29333	NM_172881	243085	Mm.312095	NM_172881		Ugt2b35	C730031G17	"UDP glucuronosyltransferase 2 family, polypeptide B35"	protein-coding	0.01	0.415842
Merged-chr6-121536480-1	chr6	121536430	121536530	+	2.1	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-62802	NM_001033354	243621	Mm.299442	NM_001033354	ENSMUSG00000040797	Iqsec3	AK122446|BRAG3|mKIAA1110|synarfGEF	IQ motif and Sec7 domain 3	protein-coding	0	0.376238
Merged-chr11-84911041-1	chr11	84910991	84911091	+	2.1	cIP1vsInput	TTS (NM_025414)	TTS (NM_025414)	5315	NM_001005223	448850	Mm.379733	NM_001005223	ENSMUSG00000020526	Znhit3	Myohd1|Trip3	"zinc finger, HIT type 3"	protein-coding	0	0.316832
Merged-chr6-13207873-1	chr6	13207823	13207923	+	2.1	cIP1vsInput	"intron (NM_001013757, intron 4 of 11)"	"intron (NM_001013757, intron 4 of 11)"	17092	NM_001013757	232585	Mm.389082	NM_001013757	ENSMUSG00000079679	Vwde	Gm467	von Willebrand factor D and EGF domains	protein-coding	0	0.346535
Merged-chr12-49313425-1	chr12	49313375	49313475	+	2.1	cIP1vsInput	Intergenic	L1Md_F3|LINE|L1	-69458	NM_001160112	15228	Mm.4704	NM_001160112	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding	0	0.326733
Merged-chr4-54707428-1	chr4	54707378	54707478	+	2.1	cIP2vsInput	Intergenic	L1MC4|LINE|L1	-240517	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding	0.03	0.326733
Merged-chr14-27243505-1	chr14	27243455	27243555	+	2.1	cIP1vsInput	"intron (NM_027871, intron 1 of 10)"	"intron (NM_027871, intron 1 of 10)"	5466	NM_027871	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding	0	0.356436
Merged-chr2-97848892-1	chr2	97848842	97848942	+	2.1	cIP1vsInput	Intergenic	Intergenic	381218	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.306931
Merged-chr1-46393816-1	chr1	46393766	46393866	+	2.1	cIP2vsInput	Intergenic	Intergenic	327078	NM_001160386	227058	Mm.296880	NM_001160386	ENSMUSG00000041144	Dnahc7b	Gm107	"dynein, axonemal, heavy chain 7B"	protein-coding	0	0.336634
Merged-chr14-18064986-1	chr14	18064936	18065036	+	2.1	cIP2vsInput	Intergenic	Lx6|LINE|L1	83342	NM_009380	21834	Mm.32563	NM_001113417	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding	0	0.306931
Merged-chr14-13626063-1	chr14	13626013	13626113	+	2.1	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-44813	NM_177624	218739	Mm.39919	NM_177624	ENSMUSG00000044772	Sntn	A430083B19Rik	"sentan, cilia apical structure protein"	protein-coding	0	0.356436
Merged-chr6-135217670-1	chr6	135217620	135217720	+	2.1	cIP1vsInput	"intron (NM_028982, intron 4 of 12)"	"intron (NM_028982, intron 4 of 12)"	19683	NM_028982	74525	Mm.34182	NM_028982	ENSMUSG00000030207	8430419L09Rik	Kiaa1467|mKIAA1467	RIKEN cDNA 8430419L09 gene	protein-coding	0	0.415842
Merged-chr12-93203638-1	chr12	93203588	93203688	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1354481	NM_011344	20338	Mm.250605	NM_001039089	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding	0	0.306931
Merged-chr19-35797694-1	chr19	35797644	35797744	+	2.1	cIP1vsInput	Intergenic	Intergenic	259666	NM_008315	15566	Mm.254266	NM_008315	ENSMUSG00000024798	Htr7	5-HT7	5-hydroxytryptamine (serotonin) receptor 7	protein-coding	0.01	0.326733
Merged-chr11-58509476-1	chr11	58509426	58509526	+	2.1	cIP1vsInput	Intergenic	Intergenic	-6922	NM_001011861	100502887	Mm.378539	XM_003945906	ENSMUSG00000058807	Olfr331	MOR275-4	olfactory receptor 331	protein-coding	0	0.267327
Merged-chr3-128449233-1	chr3	128449183	128449283	+	2.1	cIP2vsInput	Intergenic	Intergenic	-217628	NR_045704	402774	Mm.209170	NR_045704		D030025E07Rik	-	RIKEN cDNA D030025E07 gene	miscRNA	0	0.366337
Merged-chr3-25708614-1	chr3	25708564	25708664	+	2.1	cIP2vsInput	"intron (NM_001163387, intron 3 of 5)"	"intron (NM_001163387, intron 3 of 5)"	444693	NM_001163387	192167	Mm.316080	NM_001163387	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|mKIAA1070	neuroligin 1	protein-coding	0.01	0.366337
Merged-chr14-33808800-1	chr14	33808750	33808850	+	2.1	cIP1vsInput	Intergenic	MER121|DNA|TcMar?	-114787	NM_145741	14560	Mm.432071	NM_145741	ENSMUSG00000021943	Gdf10	Bmp3b	growth differentiation factor 10	protein-coding	0.03	0.485149
Merged-chr13-72265589-1	chr13	72265539	72265639	+	2.1	cIP1vsInput	Intergenic	Intergenic	-301866	NM_010573	16371	Mm.316056	NM_010573	ENSMUSG00000060969	Irx1	-	Iroquois related homeobox 1 (Drosophila)	protein-coding	0.01	0.336634
Merged-chr10-124833013-1	chr10	124832963	124833063	+	2.1	cIP2vsInput	Intergenic	Intergenic	363939	NR_028310	75030	Mm.159403	NR_028310		4930503E24Rik	-	"eukaryotic translation initiation factor 3, subunit I pseudogene"	pseudo	0.01	0.316832
Merged-chr10-104643555-1	chr10	104643505	104643605	+	2.1	cIP2vsInput	Intergenic	RLTR12A|LTR|ERVK	449513	NM_001270900	667692		NM_001270900	ENSMUSG00000097878	Gm8764	EG667692	predicted gene 8764	protein-coding	0.01	0.366337
Merged-chr5-17907867-1	chr5	17907817	17907917	+	2.1	cIP1vsInput	Intergenic	Intergenic	-18908	NM_001159558	12491	Mm.406799	NM_001159555	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding	0	0.346535
Merged-chr12-25988581-1	chr12	25988531	25988631	+	2.1	cIP2vsInput	Intergenic	Intergenic	-222686	NR_046278	74930	Mm.398932	NR_046278		4930480M12Rik	-	RIKEN cDNA 4930480M12 gene	miscRNA	0	0.376238
Merged-chr9-19260673-1	chr9	19260623	19260723	+	2.1	cIP1vsInput	Intergenic	Lx3B|LINE|L1	-11210	NM_146567	258560	Mm.377569	NM_146567	ENSMUSG00000048391	Olfr843	MOR155-2	olfactory receptor 843	protein-coding	0	0.306931
Merged-chr14-88318057-1	chr14	88318007	88318107	+	2.1	cIP2vsInput	Intergenic	Intergenic	153339	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0	0.306931
Merged-chr17-5748546-1	chr17	5748496	5748596	+	2.1	cIP1vsInput	"intron (NM_146073, intron 8 of 8)"	"intron (NM_146073, intron 8 of 8)"	-50111	NR_045081	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	miscRNA	0	0.29703
Merged-chr1-65391050-1	chr1	65391000	65391100	+	2.1	cIP1vsInput	Intergenic	Intergenic	79793	NM_139270	213527	Mm.294225	NM_139270	ENSMUSG00000025946	Pth2r	Pthr2	parathyroid hormone 2 receptor	protein-coding	0	0.287129
Merged-chr3-102826843-1	chr3	102826793	102826893	+	2.1	cIP2vsInput	"intron (NM_011516, intron 30 of 32)"	"intron (NM_011516, intron 30 of 32)"	-44129	NM_001165940	22094	Mm.110730	NM_001165939	ENSMUSG00000027857	Tshb	-	"thyroid stimulating hormone, beta subunit"	protein-coding	0	0.326733
Merged-chr9-107080012-1	chr9	107079962	107080062	+	2.1	cIP1vsInput	"intron (NM_153413, intron 6 of 52)"	"intron (NM_153413, intron 6 of 52)"	-112795	NR_102273	100417434		NR_102273		AA543401	Mycs-like	"myc-like oncogene, s-myc protein pseudogene"	pseudo	0	0.316832
Merged-chr10-103703507-1	chr10	103703457	103703557	+	2.1	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	335699	NM_175328	103098	Mm.458408	NM_001252330	ENSMUSG00000019894	Slc6a15	AA536730|AI326450|AI326451|v7-3	"solute carrier family 6 (neurotransmitter transporter), member 15"	protein-coding	0.01	0.336634
Merged-chr17-61719521-1	chr17	61719471	61719571	+	2.1	cIP1vsInput	Intergenic	Intergenic	401769	NR_030569	100124495		NR_030569		Mir466g	Mirn466g	microRNA 466g	miscRNA	0	0.366337
Merged-chr6-83891310-1	chr6	83891260	83891360	+	2.1	cIP1vsInput	Intergenic	Intergenic	-23043	NM_001166371	18139	Mm.132392	NM_001166371	ENSMUSG00000030016	Zfml	AI323587|Np220|Znf638|mNP220	"zinc finger, matrin-like"	protein-coding	0.01	0.356436
Merged-chr19-49667443-1	chr19	49667393	49667493	+	2.1	cIP1vsInput	Intergenic	Intergenic	1011203	NM_001252501	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0	0.376238
Merged-chr2-89401077-1	chr2	89401027	89401127	+	2.1	cIP2vsInput	Intergenic	RLTR22_Mur|LTR|ERVK	6000	NM_146790	258786	Mm.377690	NM_146790	ENSMUSG00000075089	Olfr1238	MOR231-11	olfactory receptor 1238	protein-coding	0	0.366337
Merged-chr14-7867080-1	chr14	7867030	7867130	+	2.1	cIP1vsInput	"intron (NM_134080, intron 1 of 45)"	"intron (NM_134080, intron 1 of 45)"	49123	NM_134080	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016	"filamin, beta"	protein-coding	0	0.455446
Merged-chr13-15278072-1	chr13	15278022	15278122	+	2.1	cIP1vsInput	Intergenic	Intergenic	-185651	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding	0	0.356436
Merged-chr7-97911767-1	chr7	97911717	97911817	+	2.1	cIP2vsInput	"3' UTR (NM_011035, exon 15 of 15)"	"3' UTR (NM_011035, exon 15 of 15)"	-8191	NM_177696	233537	Mm.375772	NM_177696	ENSMUSG00000035582	Gdpd4	4921513O04	glycerophosphodiester phosphodiesterase domain containing 4	protein-coding	0.01	0.435644
Merged-chr10-16323439-1	chr10	16323389	16323489	+	2.1	cIP1vsInput	Intergenic	Lx5|LINE|L1	772343	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0	0.306931
Merged-chr1-25273309-1	chr1	25273259	25273359	+	2.1	cIP1vsInput	"intron (NM_175642, intron 16 of 30)"	"intron (NM_175642, intron 16 of 30)"	4645	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	"predicted gene, 20172"	protein-coding	0.01	0.356436
Merged-chr1-31831863-1	chr1	31831813	31831913	+	2.1	cIP1vsInput	Intergenic	L1ME1|LINE|L1	-340943	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm1	"KH domain containing, RNA binding, signal transduction associated 2"	protein-coding	0	0.217822
Merged-chr15-60502548-1	chr15	60502498	60502598	+	2.1	cIP2vsInput	Intergenic	Intergenic	-320417	NR_030696	320469	Mm.230853	NM_177166	ENSMUSG00000097493	9930014A18Rik	-	RIKEN cDNA 9930014A18 gene	miscRNA	0.01	0.316832
Merged-chr17-87172245-1	chr17	87172195	87172295	+	2.1	cIP2vsInput	Intergenic	Intergenic	22697	NR_046016	399626	Mm.396062	NR_046016		C330024C12Rik	-	RIKEN cDNA C330024C12 gene	miscRNA	0	0.336634
Merged-chr9-33173732-1	chr9	33173682	33173782	+	2.1	cIP1vsInput	Intergenic	Intergenic	477690	NM_001038642	23871	Mm.292415	NM_001038642	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1	"E26 avian leukemia oncogene 1, 5' domain"	protein-coding	0.01	0.346535
Merged-chr10-7295222-1	chr10	7295172	7295272	+	2.1	cIP2vsInput	Intergenic	Charlie1b|DNA|hAT-Charlie	-82985	NM_172546	215748	Mm.37984	NM_172546	ENSMUSG00000015202	Cnksr3	6820402C05|BC024086|Magi1	Cnksr family member 3	protein-coding	0	0.455446
Merged-chr11-52522350-1	chr11	52522300	52522400	+	2.1	cIP2vsInput	Intergenic	Intergenic	125922	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding	0	0.366337
Merged-chr18-20389742-1	chr18	20389692	20389792	+	2.1	cIP1vsInput	"intron (NM_181682, intron 3 of 14)"	"intron (NM_181682, intron 3 of 14)"	12907	NM_181682	225256	Mm.355485	NM_181682	ENSMUSG00000061928	Dsg1b	Dsg5	desmoglein 1 beta	protein-coding	0	0.217822
Merged-chrX-83728549-1	chrX	83728499	83728599	+	2.1	cIP1vsInput	"intron (NM_007868, intron 16 of 78)"	"intron (NM_007868, intron 16 of 78)"	-240625	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding	0.01	0.356436
Merged-chr15-70727435-1	chr15	70727385	70727485	+	2.1	cIP2vsInput	Intergenic	Intergenic	803202	NR_045071	100503580	Mm.404646	NR_045071		Gm19782	-	"predicted gene, 19782"	miscRNA	0	0.29703
Merged-chr3-20640938-1	chr3	20640888	20640988	+	2.1	cIP1vsInput	Intergenic	Intergenic	-273761	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	"angiotensin II receptor, type 1b"	protein-coding	0	0.326733
Merged-chr4-26753440-1	chr4	26753390	26753490	+	2.1	cIP2vsInput	Intergenic	Intergenic	-47991	NR_040656	75360	Mm.67233	NR_040656	ENSMUSG00000086257	4930548K13Rik	-	RIKEN cDNA 4930548K13 gene	miscRNA	0	0.306931
Merged-chr17-89789231-1	chr17	89789181	89789281	+	2.1	cIP1vsInput	Intergenic	Intergenic	409990	NR_045952	100043904	Mm.396198	NR_045952		Gm4719	-	predicted gene 4719	miscRNA	0	0.287129
Merged-chr7-71641272-1	chr7	71641222	71641322	+	2.1	cIP1vsInput	Intergenic	Intergenic	665323	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	"multiple C2 domains, transmembrane 2"	protein-coding	0.01	0.386139
Merged-chr14-87735902-1	chr14	87735852	87735952	+	2.1	cIP1vsInput	Intergenic	Intergenic	319319	NM_001253755	219249	Mm.35168	NM_001253755	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding	0.01	0.376238
Merged-chr10-15087192-1	chr10	15087142	15087242	+	2.1	cIP2vsInput	Intergenic	Intergenic	326903	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding	0.01	0.366337
Merged-chr12-45205074-1	chr12	45205024	45205124	+	2.1	cIP1vsInput	Intergenic	Lx5b|LINE|L1	-130591	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding	0.01	0.316832
Merged-chrX-42692392-1	chrX	42692342	42692442	+	2.1	cIP2vsInput	"intron (NM_011855, intron 17 of 32)"	"intron (NM_011855, intron 17 of 32)"	189784	NM_011364	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain protein 1A	protein-coding	0.01	0.346535
Merged-chr8-7874642-1	chr8	7874592	7874692	+	2.1	cIP2vsInput	Intergenic	Intergenic	786131	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding	0	0.445545
Merged-chr13-33691934-1	chr13	33691884	33691984	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	30529	NM_001076790	238568	Mm.249698	NM_001076790	ENSMUSG00000047889	Serpinb6d	Gm11390|OTTMUSG00000000712|SPI3D	"serine (or cysteine) peptidase inhibitor, clade B, member 6d"	protein-coding	0	0.29703
Merged-chr17-82890984-1	chr17	82890934	82891034	+	2.1	cIP2vsInput	Intergenic	Intergenic	187241	NR_045094	100503434	Mm.187281	NR_045094		Gm19689	-	"predicted gene, 19689"	miscRNA	0.01	0.376238
Merged-chr18-22105848-1	chr18	22105798	22105898	+	2.1	cIP2vsInput	"intron (NM_027616, intron 10 of 22)"	"intron (NM_027616, intron 10 of 22)"	65548	NM_027616	70950	Mm.235716	NM_027616	ENSMUSG00000024306	Ccdc178	4921528I01Rik	coiled coil domain containing 178	protein-coding	0	0.346535
Merged-chr16-68250363-1	chr16	68250313	68250413	+	2.1	cIP1vsInput	Intergenic	Intergenic	-629455	NM_178721	239857	Mm.394300	NM_001145977	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0.01	0.29703
Merged-chr18-65840488-1	chr18	65840438	65840538	+	2.1	cIP1vsInput	Intergenic	Intergenic	-33006	NM_175012	225642	Mm.20298	NM_175012	ENSMUSG00000024517	Grp	BLP	gastrin releasing peptide	protein-coding	0.01	0.445545
Merged-chr7-42360715-1	chr7	42360665	42360765	+	2.1	cIP2vsInput	Intergenic	L1VL1|LINE|L1	69654	NR_028441	628490	Mm.246518	NR_028441	ENSMUSG00000070621	Vmn2r-ps60	Casr-rs4|Gprc2a-rs4	"vomeronasal 2, receptor, pseudogene 60"	pseudo	0	0.386139
Merged-chr4-86997235-1	chr4	86997185	86997285	+	2.1	cIP1vsInput	"intron (NM_001110240, intron 8 of 9)"	"intron (NM_001110240, intron 8 of 9)"	122821	NM_139306	230379	Mm.458684	NM_139306	ENSMUSG00000038007	Acer2	2410116I05Rik|Asah3l|CRG-L1|maCER2	alkaline ceramidase 2	protein-coding	0	0.376238
Merged-chr10-5351065-1	chr10	5351015	5351115	+	2.1	cIP2vsInput	"intron (NM_153399, intron 22 of 31)"	"intron (NM_153399, intron 22 of 31)"	-156358	NM_001079686	64009	Mm.331626	NM_001079686	ENSMUSG00000019769	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756	"spectrin repeat containing, nuclear envelope 1"	protein-coding	0.01	0.356436
Merged-chr5-41239671-1	chr5	41239621	41239721	+	2.1	cIP1vsInput	Intergenic	Intergenic	468484	NM_027295	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	"RAB28, member RAS oncogene family"	protein-coding	0	0.326733
Merged-chrX-70200958-1	chrX	70200908	70201008	+	2.1	cIP2vsInput	Intergenic	L1MC5|LINE|L1	-57370	NR_033213	74305	Mm.410860	NR_033213		1700111N16Rik	-	RIKEN cDNA 1700111N16 gene	miscRNA	0	0.287129
Merged-chr8-88094172-1	chr8	88094122	88094222	+	2.1	cIP1vsInput	Intergenic	Intergenic	-24587	NM_029074	382030	Mm.216574	NM_029074	ENSMUSG00000036810	Cnep1r1	5033428A16Rik|NEP1-R1|Tmem188	CTD nuclear envelope phosphatase 1 regulatory subunit 1	protein-coding	0.01	0.306931
Merged-chr18-87279150-1	chr18	87279100	87279200	+	2.1	cIP2vsInput	Intergenic	Intergenic	566102	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding	0.01	0.366337
Merged-chr1-143585234-1	chr1	143585184	143585284	+	2.1	cIP2vsInput	Intergenic	Intergenic	-55463	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0	0.29703
Merged-chr2-40104944-1	chr2	40104894	40104994	+	2.1	cIP1vsInput	Intergenic	Intergenic	-878606	NM_024209	67857	Mm.392662	NM_024209		Ppp6c	2310003C10Rik	"protein phosphatase 6, catalytic subunit"	protein-coding	0	0.336634
Merged-chr13-93103379-1	chr13	93103329	93103429	+	2.1	cIP2vsInput	"intron (NM_023821, intron 1 of 12)"	L1MEg|LINE|L1	8546	NR_046182	408254	Mm.474857	NR_046182		A630019I02Rik	-	RIKEN cDNA A630019I02 gene	miscRNA	0	0.336634
Merged-chr10-18732432-1	chr10	18732382	18732482	+	2.1	cIP1vsInput	"intron (NM_001033258, intron 2 of 33)"	Charlie2b|DNA|hAT-Charlie	11326	NM_001033258	215821	Mm.428163	NM_001033258	ENSMUSG00000019852	D10Bwg1379e	9630004D11|Arfgef3|B930094H20Rik|mKIAA1244	"DNA segment, Chr 10, Brigham & Women's Genetics 1379 expressed"	protein-coding	0.01	0.376238
Merged-chr18-66834473-1	chr18	66834423	66834523	+	2.1	cIP2vsInput	Intergenic	Intergenic	26014	NM_016977	17202	Mm.229447	NM_016977	ENSMUSG00000047259	Mc4r	Mc4-r	melanocortin 4 receptor	protein-coding	0.01	0.336634
Merged-chr8-8797473-1	chr8	8797423	8797523	+	2.1	cIP2vsInput	Intergenic	Intergenic	-106936	NM_176849	234023	Mm.251655	NM_176849	ENSMUSG00000040459	Arglu1	9430010O03Rik|C130008N12	arginine and glutamate rich 1	protein-coding	0.01	0.356436
Merged-chr1-15054565-1	chr1	15054515	15054615	+	2.1	cIP2vsInput	Intergenic	Intergenic	-135703	NM_177781	277328	Mm.186329	NM_177781	ENSMUSG00000032769	Trpa1	Anktm1	"transient receptor potential cation channel, subfamily A, member 1"	protein-coding	0.01	0.356436
Merged-chr3-70472873-1	chr3	70472823	70472923	+	2.1	cIP1vsInput	Intergenic	Intergenic	334418	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	miscRNA	0	0.356436
Merged-chr6-143564885-1	chr6	143564835	143564935	+	2.1	cIP1vsInput	Intergenic	Intergenic	86403	NR_045732	73425	Mm.417844	NR_045732	ENSMUSG00000086887	1700060C16Rik	-	RIKEN cDNA 1700060C16 gene	miscRNA	0	0.287129
Merged-chr8-63467982-1	chr8	63467932	63468032	+	2.1	cIP1vsInput	Intergenic	Intergenic	484188	NM_001195687	244495	Mm.485331	NM_001195687	ENSMUSG00000094443	Gm4975	EG244495|Sgo2B	predicted gene 4975	protein-coding	0	0.29703
Merged-chr12-51496462-1	chr12	51496412	51496512	+	2.1	cIP1vsInput	Intergenic	Intergenic	-96879	NM_007728	12810	Mm.21325	NM_001198835	ENSMUSG00000020953	Coch	AW122937|Coch-5B2|D12H14S564E	coagulation factor C homolog (Limulus polyphemus)	protein-coding	0.02	0.316832
Merged-chr8-36347005-1	chr8	36346955	36347055	+	2.1	cIP1vsInput	Intergenic	Intergenic	-97489	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding	0	0.306931
Merged-chr19-11892743-1	chr19	11892693	11892793	+	2.1	cIP2vsInput	Intergenic	Intergenic	-3280	NM_146410	258405	Mm.358933	NM_146410	ENSMUSG00000060878	Olfr1420	MOR266-4	olfactory receptor 1420	protein-coding	0	0.366337
Merged-chr1-29402782-1	chr1	29402732	29402832	+	2.1	cIP1vsInput	Intergenic	Intergenic	-622530	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0	0.316832
Merged-chr4-74130822-1	chr4	74130772	74130872	+	2.1	cIP2vsInput	"intron (NM_172869, intron 5 of 13)"	"intron (NM_172869, intron 5 of 13)"	-111675	NM_001172095	76804	Mm.209059	NM_001172095	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding	0.01	0.356436
Merged-chr16-64301249-1	chr16	64301199	64301299	+	2.1	cIP2vsInput	Intergenic	ID_B1|SINE|B4	177885	NM_173861	224291	Mm.246580	NM_173861	ENSMUSG00000068167	Csnka2ip	Ckt2	"casein kinase 2, alpha prime interacting protein"	protein-coding	0.01	0.524752
Merged-chr2-42959305-1	chr2	42959255	42959355	+	2.1	cIP2vsInput	Intergenic	Lx3B|LINE|L1	-305707	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0	0.356436
Merged-chr4-71075994-1	chr4	71075944	71076044	+	2.1	cIP2vsInput	Intergenic	Intergenic	-541066	NM_172694	230316	Mm.251188	NM_172694		Megf9	4933405H16Rik|9630025C07|Egfl5|mKIAA0818	multiple EGF-like-domains 9	protein-coding	0.01	0.336634
Merged-chr1-161641584-1	chr1	161641534	161641634	+	2.1	cIP1vsInput	Intergenic	Intergenic	146911	NM_001205243	14103	Mm.3355	NM_001205243	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|gld	"Fas ligand (TNF superfamily, member 6)"	protein-coding	0.03	0.326733
Merged-chr3-50011168-1	chr3	50011118	50011218	+	2.1	cIP2vsInput	Intergenic	Intergenic	-253852	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding	0.01	0.336634
Merged-chr10-100212379-1	chr10	100212329	100212429	+	2.1	cIP2vsInput	Intergenic	Intergenic	-123297	NM_001166636	100043247	Mm.478257	NM_001166636	ENSMUSG00000096640	Gm4312	-	predicted gene 4312	protein-coding	0	0.306931
Merged-chr14-88439590-1	chr14	88439540	88439640	+	2.1	cIP1vsInput	Intergenic	Lx7|LINE|L1	31806	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0.01	0.326733
Merged-chrX-128670329-1	chrX	128670279	128670379	+	2.1	cIP1vsInput	Intergenic	Intergenic	-381195	NR_045441	75274	Mm.108718	NR_045441	ENSMUSG00000086244	4930558G05Rik	-	RIKEN cDNA 4930558G05 gene	miscRNA	0	0.356436
Merged-chr6-123933611-1	chr6	123933561	123933661	+	2.1	cIP2vsInput	Intergenic	Intergenic	-80421	NM_001104641	545874	Mm.484595	NM_001104641	ENSMUSG00000094672	Vmn2r25	EG545874	"vomeronasal 2, receptor 25"	protein-coding	0	0.326733
Merged-chr9-101346135-1	chr9	101346085	101346185	+	2.1	cIP2vsInput	Intergenic	L1MA5|LINE|L1	-94303	NM_001161362	235542	Mm.335386	NM_001161362	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	"protein phosphatase 2, regulatory subunit B'', alpha"	protein-coding	0.01	0.425743
Merged-chr16-83003492-1	chr16	83003442	83003542	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1367651	NR_040567	75247	Mm.417813	NR_040567		4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	miscRNA	0	0.287129
Merged-chr8-27827875-1	chr8	27827825	27827925	+	2.1	cIP1vsInput	Intergenic	Lx4B|LINE|L1	256978	NR_033590	666422	Mm.484413	NR_033590		Gm8096	EG666422	3-phosphoglycerate dehydrogenase pseudogene	pseudo	0	0.287129
Merged-chr1-140914398-1	chr1	140914348	140914448	+	2.1	cIP1vsInput	Intergenic	Intergenic	-257996	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0	0.326733
Merged-chr17-42010306-1	chr17	42010256	42010356	+	2.1	cIP2vsInput	Intergenic	Intergenic	-305641	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding	0	0.316832
Merged-chr3-42979104-1	chr3	42979054	42979154	+	2.1	cIP2vsInput	Intergenic	Intergenic	1236486	NM_027271	73852	Mm.29006	NM_001099785	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	"DNA segment, Chr 3, ERATO Doi 751, expressed"	protein-coding	0.01	0.366337
Merged-chr1-102710156-1	chr1	102710106	102710206	+	2.1	cIP1vsInput	Intergenic	Intergenic	1554388	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.336634
Merged-chr1-185393308-1	chr1	185393258	185393358	+	2.1	cIP1vsInput	"intron (NM_029735, intron 12 of 31)"	"intron (NM_029735, intron 12 of 31)"	30213	NM_029735	107508	Mm.490980	NM_029735	ENSMUSG00000026615	Eprs	2410081F06Rik|3010002K18Rik|C79379|Qprs	glutamyl-prolyl-tRNA synthetase	protein-coding	0.01	0.316832
Merged-chr10-21103394-1	chr10	21103344	21103444	+	2.1	cIP1vsInput	Intergenic	RMER17C-int|LTR|ERVK	57590	NM_001198914	17863	Mm.52109	NM_033597	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding	0.01	0.336634
Merged-chr1-157101942-1	chr1	157101892	157101992	+	2.1	cIP2vsInput	"intron (NM_028540, intron 5 of 8)"	L1ME4a|LINE|L1	6703	NM_028540	73435	Mm.116705	NM_028540	ENSMUSG00000026592	Tex35	1700057K13Rik	testis expressed 35	protein-coding	0	0.346535
Merged-chr8-90616807-1	chr8	90616757	90616857	+	2.1	cIP2vsInput	Intergenic	Intergenic	-212028	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding	0.01	0.356436
Merged-chr15-31865349-1	chr15	31865299	31865399	+	2.1	cIP1vsInput	Intergenic	L1M2|LINE|L1	263233	NM_026546	68073	Mm.119185	NM_026546	ENSMUSG00000039065	Fam173b	A930016P21Rik|AA987072	"family with sequence similarity 173, member B"	protein-coding	0.01	0.326733
Merged-chr8-127535933-1	chr8	127535883	127535983	+	2.1	cIP2vsInput	"intron (NM_033620, intron 22 of 24)"	"intron (NM_033620, intron 22 of 24)"	236281	NM_001013580	93742	Mm.299254	NM_001013580	ENSMUSG00000025812	Pard3	AA960621|AI256638|ASIP|D8Ertd580e|PAR-3|Par3|Pard3a	par-3 (partitioning defective 3) homolog (C. elegans)	protein-coding	0	0.267327
Merged-chr1-152475001-1	chr1	152474951	152475051	+	2.1	cIP1vsInput	"intron (NM_177756, intron 4 of 11)"	"intron (NM_177756, intron 4 of 11)"	75134	NM_177756	269132	Mm.23782	NM_177756	ENSMUSG00000032649	Colgalt2	AI427652|D730024P12|Glt25d2	collagen beta(1-O)galactosyltransferase 2	protein-coding	0	0.277228
Merged-chr2-12655208-1	chr2	12655158	12655258	+	2.1	cIP2vsInput	Intergenic	Intergenic	-235748	NM_024185	66960	Mm.34059	NM_024185	ENSMUSG00000026767	Fam188a	1810041E18Rik|2310047O13Rik|5830410F13Rik|AI447827|AW111958	"family with sequence similarity 188, member A"	protein-coding	0	0.386139
Merged-chr14-86614961-1	chr14	86614911	86615011	+	2.1	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	368991	NR_040457	75155	Mm.399239	NR_040457		4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	miscRNA	0.02	0.326733
Merged-chr9-36231144-1	chr9	36231094	36231194	+	2.1	cIP1vsInput	Intergenic	RLTR21|LTR|ERVK	-95514	NR_030729	100041618	Mm.484847	NR_030729		Gm3434	-	predicted gene 3434	miscRNA	0	0.316832
Merged-chr3-131237777-1	chr3	131237727	131237827	+	2.1	cIP2vsInput	"intron (NM_008212, intron 6 of 7)"	"intron (NM_008212, intron 6 of 7)"	34260	NM_008212	15107	Mm.260164	NM_008212	ENSMUSG00000027984	Hadh	AA409008|AU019341|AW742602|Hadhsc|Schad	hydroxyacyl-Coenzyme A dehydrogenase	protein-coding	0	0.376238
Merged-chr13-87176462-1	chr13	87176412	87176512	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-1129667	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0	0.326733
Merged-chr1-173560166-1	chr1	173560116	173560216	+	2.1	cIP2vsInput	Intergenic	Lx7|LINE|L1	-24209	NM_001024721	545384	Mm.371698	NM_001024721		BC094916	Ifi214|p214	cDNA sequence BC094916	protein-coding	0	0.287129
Merged-chr7-69460101-1	chr7	69460051	69460151	+	2.1	cIP1vsInput	Intergenic	Intergenic	-35993	NR_045940	73796	Mm.410832	NR_045940		4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	miscRNA	0	0.356436
Merged-chr5-109745690-1	chr5	109745640	109745740	+	2.1	cIP1vsInput	Intergenic	Intergenic	88452	NR_027964	667213	Mm.454429	NR_027964		Gm10416	EG667213|ENSMUSG00000072761	zinc finger protein pseudogene	pseudo	0	0.287129
Merged-chr14-30562279-1	chr14	30562229	30562329	+	2.1	cIP2vsInput	"intron (NM_009388, intron 4 of 13)"	MER99|DNA|hAT?	-9870	NR_037237	100526475		NR_037237		Mir3076	mmu-mir-3076	microRNA 3076	miscRNA	0.01	0.306931
Merged-chr1-15182594-1	chr1	15182544	15182644	+	2.1	cIP2vsInput	Intergenic	Lx5b|LINE|L1	-129858	NM_001098528	98741	Mm.156081	NM_001033195		Kcnb2	9630047L19Rik|BB130875|Kv2.2	"potassium voltage gated channel, Shab-related subfamily, member 2"	protein-coding	0	0.366337
Merged-chr3-143134573-1	chr3	143134523	143134623	+	2.1	cIP2vsInput	Intergenic	Intergenic	-108482	NR_040551	320072	Mm.136397	NR_040551		A830019L24Rik	-	RIKEN cDNA A830019L24 gene	miscRNA	0.01	0.376238
Merged-chr8-24858495-1	chr8	24858445	24858545	+	2.1	cIP1vsInput	"intron (NM_153397, intron 19 of 21)"	L1_Mus4|LINE|L1	-34126	NM_001272059	11499	Mm.143889	NM_001272057	ENSMUSG00000031554	Adam5	tMDC II|tMDCII	a disintegrin and metallopeptidase domain 5	protein-coding	0.01	0.356436
Merged-chr11-26434815-1	chr11	26434765	26434865	+	2.1	cIP1vsInput	"intron (NR_102382, intron 7 of 11)"	"intron (NR_102382, intron 7 of 11)"	47731	NR_102382	67030	Mm.18875	NM_001277273		Fancl	2010322C19Rik|AW554273|B230118H11Rik|Phf9|Pog|gcd	"Fanconi anemia, complementation group L"	protein-coding	0	0.316832
Merged-chr16-78637066-1	chr16	78637016	78637116	+	2.1	cIP1vsInput	Intergenic	Intergenic	-60378	NM_025967	67102	Mm.37332	NM_001252438		D16Ertd472e	1700010I10Rik|2310009O17Rik|E330003K22Rik|Eurl	"DNA segment, Chr 16, ERATO Doi 472, expressed"	protein-coding	0	0.346535
Merged-chr19-51944080-1	chr19	51944030	51944130	+	2.1	cIP2vsInput	Intergenic	Lx5|LINE|L1	-320243	NM_008386	16333	Mm.46269	NM_008386	ENSMUSG00000035804	Ins1	Ins-1|Ins2-rs1	insulin I	protein-coding	0	0.326733
Merged-chr3-115869685-1	chr3	115869635	115869735	+	2.1	cIP1vsInput	Intergenic	Intergenic	18374	NR_027894	68161	Mm.392043	NR_015487		A930005H10Rik	-	RIKEN cDNA A930005H10 gene	miscRNA	0	0.267327
Merged-chr18-23723843-1	chr18	23723793	23723893	+	2.1	cIP1vsInput	Intergenic	Lx5|LINE|L1	-28490	NM_001162942	212307	Mm.132237	NM_001162941	ENSMUSG00000024277	Mapre2	AI314113|C820009F03Rik|D18Abb1e|EB1|EB2|RP1	"microtubule-associated protein, RP/EB family, member 2"	protein-coding	0	0.316832
Merged-chr3-82468340-1	chr3	82468290	82468390	+	2.1	cIP2vsInput	Intergenic	Intergenic	79745	NM_008731	18167	Mm.1433	NM_001205099	ENSMUSG00000028004	Npy2r	NPY2-R	neuropeptide Y receptor Y2	protein-coding	0	0.455446
Merged-chr6-138355626-1	chr6	138355576	138355676	+	2.1	cIP1vsInput	Intergenic	RSINE1|SINE|B4	215089	NM_019946	56615	Mm.14796	NM_019946	ENSMUSG00000008540	Mgst1	1500002K10Rik|Gst	microsomal glutathione S-transferase 1	protein-coding	0	0.445545
Merged-chr6-107388309-1	chr6	107388259	107388359	+	2.1	cIP1vsInput	Intergenic	Intergenic	-141417	NM_008516	16979	Mm.488119	NM_008516	ENSMUSG00000034648	Lrrn1	2810047E21Rik|NLRR-1	"leucine rich repeat protein 1, neuronal"	protein-coding	0.01	0.326733
Merged-chrX-163676885-1	chrX	163676835	163676935	+	2.1	cIP1vsInput	Intergenic	Intergenic	84444	NR_003640	74264	Mm.39304	NR_003640	ENSMUSG00000083695	1700045I19Rik	AI853461	ring finger protein 138 pseudogene	pseudo	0.01	0.306931
Merged-chr6-57216193-1	chr6	57216143	57216243	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	6335	NM_053235	113862	Mm.431976	NM_053235	ENSMUSG00000064259	Vmn1r13	V1rc5	vomeronasal 1 receptor 13	protein-coding	0	0.316832
Merged-chr1-106978709-1	chr1	106978659	106978759	+	2.1	cIP2vsInput	Intergenic	RLTR49|LTR|ERVK	-2275	NM_172852	241196	Mm.110886	NM_172852	ENSMUSG00000048775	Serpinb13	5430417G24|HUR7|HURPIN|PI13|headpin	"serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 13"	protein-coding	0	0.356436
Merged-chr12-27218080-1	chr12	27218030	27218130	+	2.1	cIP1vsInput	Intergenic	Intergenic	-57564	NR_045870	636791	Mm.423496	NM_001039248		Gm9866	EG636791|ENSMUSG00000052076	predicted gene 9866	miscRNA	0	0.326733
Merged-chr7-55074389-1	chr7	55074339	55074439	+	2.1	cIP2vsInput	"intron (NM_178705, intron 4 of 11)"	"intron (NM_178705, intron 4 of 11)"	239144	NM_178705	233271	Mm.474990	NM_178705		Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding	0.01	0.376238
Merged-chr7-87610067-1	chr7	87610017	87610117	+	2.1	cIP2vsInput	"intron (NM_001081414, intron 3 of 9)"	"intron (NM_001081414, intron 3 of 9)"	25899	NM_001143834	108071	Mm.235018	NM_001033224	ENSMUSG00000049583	Grm5	6430542K11Rik|AI850523|Gprc1e|mGluR5|mGluR5b	"glutamate receptor, metabotropic 5"	protein-coding	0.02	0.376238
Merged-chr3-29822502-1	chr3	29822452	29822552	+	2.1	cIP2vsInput	Intergenic	Intergenic	190702	NM_007963	14013	Mm.426829	NM_021442	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding	0.01	0.316832
Merged-chr11-18376995-1	chr11	18376945	18377045	+	2.1	cIP1vsInput	Intergenic	Intergenic	-423120	NM_026576	68145	Mm.178684	NM_026576	ENSMUSG00000016984	Etaa1	5730466H23Rik|AA672646	Ewing's tumor-associated antigen 1	protein-coding	0.01	0.356436
Merged-chr6-18062490-1	chr6	18062440	18062540	+	2.1	cIP1vsInput	"intron (NM_023729, intron 10 of 12)"	"intron (NM_023729, intron 10 of 12)"	-32045	NM_023653	22413	Mm.33653	NM_023653	ENSMUSG00000010797	Wnt2	2610510E18Rik|Int1l1|Irp|Mirp|Wnt-2|Wnt2a	wingless-related MMTV integration site 2	protein-coding	0	0.29703
Merged-chr4-17139207-1	chr4	17139157	17139257	+	2.1	cIP2vsInput	Intergenic	LTR40b|LTR|ERVL	-714275	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0.04	0.29703
Merged-chr4-27326898-1	chr4	27326848	27326948	+	2.1	cIP1vsInput	Intergenic	Intergenic	-621449	NR_040656	75360	Mm.67233	NR_040656	ENSMUSG00000086257	4930548K13Rik	-	RIKEN cDNA 4930548K13 gene	miscRNA	0	0.277228
Merged-chr14-10993995-1	chr14	10993945	10994045	+	2.1	cIP2vsInput	"intron (NM_010210, intron 2 of 8)"	Lx|LINE|L1	168037	NM_010210	14198	Mm.441926	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding	0	0.306931
Merged-chr5-69941741-1	chr5	69941691	69941791	+	2.1	cIP1vsInput	Intergenic	Intergenic	-349456	NM_001038015	67980	Mm.33830	NM_001038015	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding	0	0.287129
Merged-chr10-102401636-1	chr10	102401586	102401686	+	2.1	cIP2vsInput	Intergenic	Intergenic	27199	NM_026243	67569	Mm.403713	NM_001162368	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"	protein-coding	0	0.356436
Merged-chr14-111386396-1	chr14	111386346	111386446	+	2.1	cIP1vsInput	Intergenic	Lx7|LINE|L1	-288719	NM_198865	75409	Mm.417152	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	"SLIT and NTRK-like family, member 5"	protein-coding	0.01	0.336634
Merged-chr17-67922244-1	chr17	67922194	67922294	+	2.1	cIP2vsInput	"intron (NM_172964, intron 1 of 17)"	"intron (NM_172964, intron 1 of 17)"	81864	NM_172964	268970	Mm.9935	NM_172964	ENSMUSG00000024043	Arhgap28	AU044757|AW550892|E130310N06	Rho GTPase activating protein 28	protein-coding	0.01	0.336634
Merged-chr2-139041675-1	chr2	139041625	139041725	+	2.1	cIP2vsInput	Intergenic	MLT1C|LTR|ERVL-MaLR	221746	NR_035477	100316816		NR_035477	ENSMUSG00000088983	Mir1952	mmu-mir-1952	microRNA 1952	miscRNA	0	0.376238
Merged-chr19-32827112-1	chr19	32827062	32827162	+	2.1	cIP2vsInput	TTS (NM_008960)	TTS (NM_008960)	69535	NM_008960	19211	Mm.245395	NM_177096	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding	0	0.346535
Merged-chr16-70721251-1	chr16	70721201	70721301	+	2.1	cIP1vsInput	Intergenic	Intergenic	104826	NR_040474	52645	Mm.188475	NR_040474		D16Ertd519e	-	"DNA segment, Chr 16, ERATO Doi 519, expressed"	miscRNA	0	0.277228
Merged-chr2-157943521-1	chr2	157943471	157943571	+	2.1	cIP2vsInput	"intron (NM_198627, intron 3 of 3)"	"intron (NM_198627, intron 3 of 3)"	28868	NM_198627	277432	Mm.441156	NM_198627	ENSMUSG00000037843	Vstm2l	Gm691	V-set and transmembrane domain containing 2-like	protein-coding	0.04	0.574257
Merged-chr17-94387366-1	chr17	94387316	94387416	+	2.1	cIP1vsInput	Intergenic	Lx|LINE|L1	362526	NM_176917	76781	Mm.486648	NM_176917	ENSMUSG00000055660	Mettl4	2410198H06Rik|A730091E08Rik|AV296509|HsT661	methyltransferase like 4	protein-coding	0.01	0.356436
Merged-chr3-64014484-1	chr3	64014434	64014534	+	2.1	cIP1vsInput	"intron (NM_001033300, intron 14 of 15)"	"intron (NM_001033300, intron 14 of 15)"	38341	NM_001033300	229363	Mm.490620	NM_001033300		Gmps	AA591640|AI047208	guanine monophosphate synthetase	protein-coding	0	0.29703
Merged-chr10-63784784-1	chr10	63784734	63784834	+	2.1	cIP1vsInput	"intron (NM_001164376, intron 5 of 17)"	"intron (NM_001164376, intron 5 of 17)"	-36271	NM_001164519	216033	Mm.444692	NM_001164376	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	"catenin (cadherin associated protein), alpha 3"	protein-coding	0	0.336634
Merged-chr6-65508627-1	chr6	65508577	65508677	+	2.1	cIP1vsInput	Intergenic	Intergenic	-81771	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding	0	0.386139
Merged-chr13-21476828-1	chr13	21476778	21476878	+	2.1	cIP2vsInput	Intergenic	L1MC5a|LINE|L1	-2021	NM_001039115	544922	Mm.441300	NM_001039115	ENSMUSG00000054931	Zkscan4	AI841875|Gm11272|OTTMUSG00000000421	zinc finger with KRAB and SCAN domains 4	protein-coding	0	0.316832
Merged-chr16-93710968-1	chr16	93710918	93711018	+	2.1	cIP1vsInput	promoter-TSS (NM_026700)	promoter-TSS (NM_026700)	-939	NM_026700	70028	Mm.23230	NM_026700	ENSMUSG00000022946	Dopey2	0610038M01Rik|2610510B01Rik|AI503246|C21orf5|mKIAA0933	dopey family member 2	protein-coding	0.02	0.386139
Merged-chr5-85689748-1	chr5	85689698	85689798	+	2.1	cIP1vsInput	Intergenic	Intergenic	375835	NM_007683	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	Cenpc	centromere protein C1	protein-coding	0.01	0.346535
Merged-chr4-38160703-1	chr4	38160653	38160753	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-1208959	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.01	0.326733
Merged-chr2-33723730-1	chr2	33723680	33723780	+	2.1	cIP1vsInput	Intergenic	Intergenic	-82086	NR_045729	320482	Mm.442057	NR_045729	ENSMUSG00000086484	Nron	A630071L07Rik|Gm24353	"non-protein coding RNA, repressor of NFAT"	miscRNA	0.02	0.29703
Merged-chr14-80811499-1	chr14	80811449	80811549	+	2.1	cIP1vsInput	Intergenic	Intergenic	811197	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.356436
Merged-chr2-70558313-1	chr2	70558263	70558363	+	2.1	cIP2vsInput	"intron (NR_040496, intron 1 of 2)"	"intron (NR_040496, intron 1 of 2)"	-3851	NM_008077	14415	Mm.272120	NM_008077	ENSMUSG00000070880	Gad1	EP10|GAD25|GAD44|GAD67|Gad-1	glutamate decarboxylase 1	protein-coding	0.01	0.554455
Merged-chr1-46104642-1	chr1	46104592	46104692	+	2.1	cIP2vsInput	"intron (NM_001160386, intron 8 of 65)"	L1_Mur2|LINE|L1	37904	NM_001160386	227058	Mm.296880	NM_001160386	ENSMUSG00000041144	Dnahc7b	Gm107	"dynein, axonemal, heavy chain 7B"	protein-coding	0.03	0.346535
Merged-chr9-17936226-1	chr9	17936176	17936276	+	2.1	cIP2vsInput	Intergenic	Lx|LINE|L1	-356041	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	"cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1"	protein-coding	0	0.346535
Merged-chr17-35021345-1	chr17	35021295	35021395	+	2.1	cIP2vsInput	"intron (NM_138582, intron 8 of 16)"	"intron (NM_138582, intron 8 of 16)"	4766	NM_138582	27762	Mm.390966	NM_138582	ENSMUSG00000007030	Vwa7	C6orf27|D17H6S56E-3|G7c|NG37	von Willebrand factor A domain containing 7	protein-coding	0.01	0.633663
Merged-chr17-3912178-1	chr17	3912128	3912228	+	2.1	cIP1vsInput	Intergenic	Intergenic	170817	NR_045764	75815	Mm.183387	NR_045764		4930470H14Rik	-	RIKEN cDNA 4930470H14 gene	miscRNA	0	0.346535
Merged-chr10-109712887-1	chr10	109712837	109712937	+	2.1	cIP2vsInput	"intron (NM_001081035, intron 29 of 38)"	"intron (NM_001081035, intron 29 of 38)"	287332	NM_001081035	260315	Mm.461280	NM_001081035	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding	0	0.326733
Merged-chr10-46760448-1	chr10	46760398	46760498	+	2.1	cIP1vsInput	Intergenic	Intergenic	515699	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0	0.346535
Merged-chr8-31361586-1	chr8	31361536	31361636	+	2.1	cIP2vsInput	Intergenic	L1_Mm|LINE|L1	-6163	NR_046272	74517	Mm.390001	NR_046272		7420700N18Rik	-	RIKEN cDNA 7420700N18 gene	miscRNA	0	0.306931
Merged-chrX-116213423-1	chrX	116213373	116213473	+	2.1	cIP1vsInput	Intergenic	Intergenic	-235521	NM_001033471	382239	Mm.336224	NM_001033471	ENSMUSG00000072995	Cpxcr1	Gm1143	"CPX chromosome region, candidate 1"	protein-coding	0.01	0.356436
Merged-chr8-113297731-1	chr8	113297681	113297781	+	2.1	cIP2vsInput	Intergenic	Intergenic	230469	NR_033584	791378	Mm.350576	NR_033584		Gm10280	ENSMUSG00000069883	predicted gene 10280	miscRNA	0	0.386139
Merged-chr16-79485865-1	chr16	79485815	79485915	+	2.1	cIP1vsInput	Intergenic	Intergenic	-394768	NM_008941	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	"transmembrane protease, serine 15"	protein-coding	0	0.267327
Merged-chr3-60664296-1	chr3	60664246	60664346	+	2.1	cIP1vsInput	Intergenic	Intergenic	163044	NM_001253708	56758	Mm.255723	NM_001253708	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding	0	0.257426
Merged-chr12-59432338-1	chr12	59432288	59432388	+	2.1	cIP1vsInput	Intergenic	Intergenic	-212855	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding	0	0.247525
Merged-chr12-15315398-1	chr12	15315348	15315448	+	2.1	cIP2vsInput	Intergenic	Intergenic	-265009	NR_045960	73972	Mm.107680	NR_045960		4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	miscRNA	0.02	0.356436
Merged-chr9-83186686-1	chr9	83186636	83186736	+	2.1	cIP2vsInput	Intergenic	L1MB7|LINE|L1	-40079	NM_026122	94353	Mm.244426	NM_026122	ENSMUSG00000066456	Hmgn3	1110002A15Rik|6330514M13Rik|BB071015|TRIP7	high mobility group nucleosomal binding domain 3	protein-coding	0	0.336634
Merged-chr14-51259848-1	chr14	51259798	51259898	+	2.1	cIP1vsInput	Intergenic	ID4|SINE|ID	-3736	NM_053113	93726	Mm.153688	NM_053113	ENSMUSG00000047222	Ear11	-	"eosinophil-associated, ribonuclease A family, member 11"	protein-coding	0.01	0.435644
Merged-chr12-95411304-1	chr12	95411254	95411354	+	2.1	cIP2vsInput	Intergenic	Intergenic	-280922	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0.02	0.346535
Merged-chr6-139615740-1	chr6	139615690	139615790	+	2.1	cIP1vsInput	Intergenic	Intergenic	-100119	NM_207683	18705	Mm.391538	NM_207683	ENSMUSG00000030228	Pik3c2g	C80387|PI3K-C2-gamma	"phosphatidylinositol 3-kinase, C2 domain containing, gamma polypeptide"	protein-coding	0	0.316832
Merged-chr9-82464599-1	chr9	82464549	82464649	+	2.1	cIP1vsInput	Intergenic	Intergenic	-365207	NM_001168240	65099	Mm.41415	NM_001168240	ENSMUSG00000032251	Irak1bp1	4921528N06Rik|AI851240|Aabp3|Aip70|Simpl	interleukin-1 receptor-associated kinase 1 binding protein 1	protein-coding	0	0.366337
Merged-chr11-7478245-1	chr11	7478195	7478295	+	2.1	cIP2vsInput	Intergenic	L1MA6|LINE|L1	-264322	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding	0.01	0.366337
Merged-chr14-15139635-1	chr14	15139585	15139685	+	2.1	cIP1vsInput	Intergenic	Lx6|LINE|L1	299352	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding	0	0.346535
Merged-chr3-16895554-1	chr3	16895504	16895604	+	2.1	cIP1vsInput	Intergenic	Intergenic	712371	NM_001145919	229096	Mm.23834	NM_001145919	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding	0	0.316832
Merged-chr6-98271342-1	chr6	98271292	98271392	+	2.1	cIP2vsInput	"intron (NM_001128092, intron 2 of 3)"	"intron (NM_001128092, intron 2 of 3)"	71412	NM_001128092	330390	Mm.484161	NM_001128092	ENSMUSG00000090667	Gm765	-	predicted gene 765	protein-coding	0.01	0.356436
Merged-chr10-104615728-1	chr10	104615678	104615778	+	2.1	cIP1vsInput	Intergenic	L1MC1|LINE|L1	421686	NM_001270900	667692		NM_001270900	ENSMUSG00000097878	Gm8764	EG667692	predicted gene 8764	protein-coding	0	0.257426
Merged-chr14-94804649-1	chr14	94804599	94804699	+	2.1	cIP2vsInput	Intergenic	Intergenic	-913980	NM_001271798	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0.03	0.306931
Merged-chr3-59876766-1	chr3	59876716	59876816	+	2.1	cIP2vsInput	"exon (NM_001243003, exon 5 of 5)"	"exon (NM_001243003, exon 5 of 5)"	15715	NM_001243003	666803	Mm.389443	NM_001243003	ENSMUSG00000095522	Gm8298	EG666803	predicted gene 8298	protein-coding	0	0.376238
Merged-chr3-92717588-1	chr3	92717538	92717638	+	2.1	cIP1vsInput	Intergenic	RMER12C|LTR|ERVK	2762	NM_026394	67828	Mm.158176	NM_026394	ENSMUSG00000042124	Lce1f	1110055J05Rik	late cornified envelope 1F	protein-coding	0.01	0.356436
Merged-chr17-12654230-1	chr17	12654180	12654280	+	2.1	cIP1vsInput	"intron (NM_009202, intron 8 of 10)"	"intron (NM_009202, intron 8 of 10)"	21608	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	"solute carrier family 22 (organic cation transporter), member 1"	protein-coding	0.02	0.435644
Merged-chr8-5607110-1	chr8	5607060	5607160	+	2.1	cIP1vsInput	Intergenic	Lx4A|LINE|L1	-501878	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.336634
Merged-chrX-137871721-1	chrX	137871671	137871771	+	2.1	cIP1vsInput	"intron (NM_030688, intron 2 of 10)"	(TA)n|Simple_repeat|Simple_repeat	300172	NM_030688	60367	Mm.328321	NM_030688	ENSMUSG00000059203	Il1rapl2	-	interleukin 1 receptor accessory protein-like 2	protein-coding	0	0.207921
Merged-chr14-11088758-1	chr14	11088708	11088808	+	2.1	cIP2vsInput	"intron (NM_010210, intron 2 of 8)"	"intron (NM_010210, intron 2 of 8)"	73274	NM_010210	14198	Mm.441926	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding	0.01	0.316832
Merged-chr16-82700572-1	chr16	82700522	82700622	+	2.1	cIP1vsInput	Intergenic	Intergenic	1499875	NM_010954	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.316832
Merged-chr14-62208023-1	chr14	62207973	62208073	+	2.1	cIP2vsInput	Intergenic	L1M5|LINE|L1	84956	NM_173419	239133	Mm.127330	NM_173419	ENSMUSG00000048281	Dleu7	BC038059	"deleted in lymphocytic leukemia, 7"	protein-coding	0.01	0.356436
Merged-chr5-129846484-1	chr5	129846434	129846534	+	2.1	cIP1vsInput	promoter-TSS (NM_026445)	promoter-TSS (NM_026445)	-506	NM_026445	67902	Mm.103546	XM_003689383	ENSMUSG00000025538	Sumf2	2610040F05Rik	sulfatase modifying factor 2	protein-coding	0.01	0.465347
Merged-chr17-82152026-1	chr17	82151976	82152076	+	2.1	cIP2vsInput	Intergenic	Intergenic	-413649	NM_011406	20541	Mm.489060	NM_001112798		Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	"solute carrier family 8 (sodium/calcium exchanger), member 1"	protein-coding	0.01	0.326733
Merged-chr6-135602242-1	chr6	135602192	135602292	+	2.1	cIP2vsInput	Intergenic	L1M3|LINE|L1	239311	NM_010128	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding	0.01	0.356436
Merged-chr14-17065060-1	chr14	17065010	17065110	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-489850	NM_011243	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2|RARbeta2	"retinoic acid receptor, beta"	protein-coding	0	0.306931
Merged-chr9-80652217-1	chr9	80652167	80652267	+	2.1	cIP1vsInput	Intergenic	Intergenic	-186779	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding	0	0.356436
Merged-chr14-106542654-1	chr14	106542604	106542704	+	2.1	cIP1vsInput	Intergenic	Intergenic	-56134	NR_045938	73631	Mm.48862	NR_045938		1700128A07Rik	-	RIKEN cDNA 1700128A07 gene	miscRNA	0	0.267327
Merged-chr1-115098035-1	chr1	115097985	115098085	+	2.1	cIP2vsInput	Intergenic	Lx5|LINE|L1	-587102	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0	0.356436
Merged-chr7-53815941-1	chr7	53815891	53815991	+	2.1	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	-1019304	NM_178705	233271	Mm.474990	NM_178705		Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding	0	0.326733
Merged-chr17-89330342-1	chr17	89330292	89330392	+	2.1	cIP2vsInput	Intergenic	Intergenic	10115	NR_045432	71052	Mm.399489	NR_045432		4933400B14Rik	-	RIKEN cDNA 4933400B14 gene	miscRNA	0	0.376238
Merged-chr4-51008670-1	chr4	51008620	51008720	+	2.1	cIP2vsInput	Intergenic	L1MC|LINE|L1	-208008	NM_001162865	74914	Mm.159368	NM_001162865	ENSMUSG00000039555	Cylc2	4930488P18Rik	"cylicin, basic protein of sperm head cytoskeleton 2"	protein-coding	0	0.29703
Merged-chr10-102900002-1	chr10	102899952	102900052	+	2.1	cIP1vsInput	Intergenic	Intergenic	128775	NM_172553	216285	Mm.19287	NM_172553	ENSMUSG00000036602	Alx1	AI314867|C130005I02|Cart1	ALX homeobox 1	protein-coding	0	0.316832
Merged-chr10-105003455-1	chr10	105003405	105003505	+	2.1	cIP1vsInput	Intergenic	Intergenic	571024	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding	0.01	0.346535
Merged-chr10-6741184-1	chr10	6741134	6741234	+	2.1	cIP1vsInput	Intergenic	MTA_Mm|LTR|ERVL-MaLR	-47417	NM_001039652	18390	Mm.439715	NM_011013	ENSMUSG00000000766	Oprm1	M-OR-1|MOP-R|MOR-1|MOR-1O|Oprm|mor|muOR	"opioid receptor, mu 1"	protein-coding	0	0.435644
Merged-chr5-89322028-1	chr5	89321978	89322078	+	2.1	cIP1vsInput	Intergenic	Intergenic	135870	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding	0	0.366337
Merged-chr6-143953477-1	chr6	143953427	143953527	+	2.1	cIP2vsInput	"intron (NM_001243163, intron 7 of 13)"	"intron (NM_001243163, intron 7 of 13)"	256091	NM_001113559	20678	Mm.1752	NM_001113559	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY-box containing gene 5	protein-coding	0.02	0.366337
Merged-chr8-67195718-1	chr8	67195668	67195768	+	2.1	cIP2vsInput	Intergenic	Intergenic	-295040	NM_008673	17960	Mm.14125	NM_008673	ENSMUSG00000025588	Nat1	Nat-1	N-acetyl transferase 1	protein-coding	0	0.386139
Merged-chr12-98983640-1	chr12	98983590	98983690	+	2.1	cIP1vsInput	TTS (NM_198311)	TTS (NM_198311)	63028	NM_198311	76260	Mm.282660	NM_029553	ENSMUSG00000021013	Ttc8	0610012F22Rik|AV001447|BBS8	tetratricopeptide repeat domain 8	protein-coding	0.02	0.267327
Merged-chr16-5765535-1	chr16	5765485	5765585	+	2.1	cIP2vsInput	Intergenic	Intergenic	-119258	NM_021477	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	"RNA binding protein, fox-1 homolog (C. elegans) 1"	protein-coding	0	0.336634
Merged-chr5-8076664-1	chr5	8076614	8076714	+	2.1	cIP2vsInput	"3' UTR (NM_001098225, exon 30 of 30)"	"3' UTR (NM_001098225, exon 30 of 30)"	20122	NM_001080974	109552	Mm.96211	NM_001080974	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding	0.01	0.405941
Merged-chrX-31246876-1	chrX	31246826	31246926	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-89493	NM_001243011	100042159	Mm.489579	NM_001243011	ENSMUSG00000095835	Gm3701	-	predicted gene 3701	protein-coding	0	0.346535
Merged-chr12-67719575-1	chr12	67719525	67719625	+	2.1	cIP2vsInput	Intergenic	Intergenic	-50304	NR_033146	100316870	Mm.379794	NR_033146		Gm17821	-	DDB1 and CUL4 associated factor 5 pseudogene	pseudo	0	0.356436
Merged-chr4-20842342-1	chr4	20842292	20842392	+	2.1	cIP2vsInput	Intergenic	Intergenic	-63674	NM_172987	269513		NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding	0	0.386139
Merged-chr10-44078134-1	chr10	44078084	44078184	+	2.1	cIP2vsInput	Intergenic	Intergenic	-73288	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding	0.01	0.326733
Merged-chr11-88987057-1	chr11	88987007	88987107	+	2.1	cIP1vsInput	"intron (NM_016706, intron 5 of 6)"	"intron (NM_016706, intron 5 of 6)"	-12346	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding	0	0.287129
Merged-chr2-163968642-1	chr2	163968592	163968692	+	2.1	cIP1vsInput	Intergenic	Intergenic	-26555	NM_018753	54401	Mm.34319	NM_018753	ENSMUSG00000018326	Ywhab	1300003C17Rik	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide"	protein-coding	0	0.366337
Merged-chr1-154076786-1	chr1	154076736	154076836	+	2.1	cIP1vsInput	Intergenic	Intergenic	-124401	NM_001204908	100503355	Mm.484410	NM_001204908	ENSMUSG00000066797	Zfp648	ENSMUSG00000066797|Gm10178|Gm203	zinc finger protein 648	protein-coding	0.01	0.366337
Merged-chr15-58659051-1	chr15	58659001	58659101	+	2.1	cIP1vsInput	Intergenic	MIRc|SINE|MIR	164376	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding	0	0.356436
Merged-chr3-134679258-1	chr3	134679208	134679308	+	2.1	cIP1vsInput	Intergenic	Tigger1|DNA|TcMar-Tigger	-149749	NM_021382	21338	Mm.103810	NM_021382	ENSMUSG00000028172	Tacr3	Nk3r|Nkr|Tac3r	tachykinin receptor 3	protein-coding	0	0.376238
Merged-chr2-51849910-1	chr2	51849860	51849960	+	2.1	cIP2vsInput	Intergenic	Intergenic	84734	NM_001141982	71684	Mm.28309	NM_001141981	ENSMUSG00000036249	Rbm43	0610033I05Rik	RNA binding motif protein 43	protein-coding	0	0.316832
Merged-chrX-107578766-1	chrX	107578716	107578816	+	2.1	cIP2vsInput	Intergenic	Lx8b|LINE|L1	36184	NR_033580	71011	Mm.307348	NR_033580	ENSMUSG00000055700	4933401B06Rik	-	GLE1 RNA export mediator pseudogene	pseudo	0	0.376238
Merged-chr6-63216097-1	chr6	63216047	63216147	+	2.1	cIP1vsInput	Intergenic	Intergenic	-40760	NM_008167	14804	Mm.447390	NM_008167		Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	"glutamate receptor, ionotropic, delta 2"	protein-coding	0.02	0.306931
Merged-chr3-133882303-1	chr3	133882253	133882353	+	2.1	cIP2vsInput	Intergenic	Intergenic	-337913	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding	0	0.356436
Merged-chr17-55672751-1	chr17	55672701	55672801	+	2.1	cIP1vsInput	"intron (NM_028370, intron 10 of 16)"	"intron (NM_028370, intron 10 of 16)"	39877	NM_028370	72836	Mm.448349	NM_028370	ENSMUSG00000024174	Pot1b	2810458H16Rik	protection of telomeres 1B	protein-coding	0.02	0.386139
Merged-chr3-149246557-1	chr3	149246507	149246607	+	2.1	cIP2vsInput	Intergenic	Intergenic	-28180	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	miscRNA	0	0.336634
Merged-chr5-98528625-1	chr5	98528575	98528675	+	2.1	cIP1vsInput	"intron (NM_001024614, intron 3 of 5)"	"intron (NM_001024614, intron 3 of 5)"	-52961	NR_030484	735265		NR_030484		Mir703	Mirn703|mmu-mir-703	microRNA 703	miscRNA	0.03	0.336634
Merged-chr3-13233910-1	chr3	13233860	13233960	+	2.1	cIP1vsInput	Intergenic	RLTR21|LTR|ERVK	-237745	NM_178631	76897	Mm.422625	NM_001163328	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0	0.29703
Merged-chr14-53367763-1	chr14	53367713	53367813	+	2.1	cIP1vsInput	Intergenic	Intergenic	-298177	NM_001205242	100568452	Mm.486072	NM_001205242		A430107P09Rik	Va10	RIKEN cDNA A430107P09 gene	protein-coding	0	0.336634
Merged-chr3-140873062-1	chr3	140873012	140873112	+	2.1	cIP1vsInput	Intergenic	Intergenic	339293	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0	0.29703
Merged-chr3-148693034-1	chr3	148692984	148693084	+	2.1	cIP2vsInput	Intergenic	Intergenic	261601	NM_001081298	99633	Mm.462301	NM_001081298	ENSMUSG00000028184	Lphn2	AI450192|Gm619|Lec1|Lphh1|mKIAA0786	latrophilin 2	protein-coding	0	0.485149
Merged-chr9-89897606-2	chr9	89897530	89897682	+	2.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-12169	NM_011245	19417	Mm.44561	NM_001039655	ENSMUSG00000032356	Rasgrf1	AI844718|CDC25|CDC25Mm|Grf1|Grfbeta|P190-A|Ras-GRF1|p190|p190RhoGEF	RAS protein-specific guanine nucleotide-releasing factor 1	protein-coding	0.013158	0.30719
Merged-chr2-91371268-1	chr2	91371218	91371318	+	2.1	cIP1vsInput	"intron (NM_175123, intron 3 of 8)"	"intron (NM_175123, intron 3 of 8)"	73374	NM_175123	228356	Mm.386861	NM_175123	ENSMUSG00000040591	1110051M20Rik	AI586322	RIKEN cDNA 1110051M20 gene	protein-coding	0	0.326733
Merged-chr3-159155090-1	chr3	159155040	159155140	+	2.1	cIP1vsInput	"intron (NR_040750, intron 2 of 4)"	Lx3A|LINE|L1	78726	NR_040750	624759	Mm.491054	NR_040750		Gm20752	-	"predicted gene, 20752"	miscRNA	0	0.29703
Merged-chr3-118263358-1	chr3	118263308	118263408	+	2.1	cIP1vsInput	Intergenic	Intergenic	-170499	NR_029551	387155		NR_029551		Mir137	Mirn137|mmu-mir-137	microRNA 137	miscRNA	0	0.366337
Merged-chr2-85787563-1	chr2	85787513	85787613	+	2.1	cIP1vsInput	Intergenic	Intergenic	2089	NM_146571	258564	Mm.223093	NM_146571	ENSMUSG00000033850	Olfr1015	MOR213-3	olfactory receptor 1015	protein-coding	0	0.29703
Merged-chr4-55801542-1	chr4	55801492	55801592	+	2.1	cIP1vsInput	Intergenic	Intergenic	-269067	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding	0	0.346535
Merged-chr1-168513686-1	chr1	168513636	168513736	+	2.1	cIP1vsInput	Intergenic	Intergenic	-81428	NM_008783	18514	Mm.440114	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|AI848790|AU015730|D230003C07Rik|Pbx-1|Pbx1a|Pbx1b	pre B cell leukemia homeobox 1	protein-coding	0	0.405941
Merged-chr7-11815841-1	chr7	11815791	11815891	+	2.1	cIP1vsInput	Intergenic	RMER16-int|LTR|ERVK	-30934	NM_134206	171240	Mm.377196	NM_134206	ENSMUSG00000047655	Vmn1r74	V1rg5	vomeronasal 1 receptor 74	protein-coding	0	0.346535
Merged-chr16-51195061-1	chr16	51195011	51195111	+	2.1	cIP2vsInput	Intergenic	Intergenic	-462288	NR_028300	68190	Mm.482928	NR_028300		5330426P16Rik	-	RIKEN cDNA 5330426P16 gene	miscRNA	0	0.277228
Merged-chr17-79191978-1	chr17	79191928	79192028	+	2.1	cIP1vsInput	Intergenic	Intergenic	140072	NM_027455	70536	Mm.293870	NM_027455	ENSMUSG00000024084	Qpct	5730422A13Rik	glutaminyl-peptide cyclotransferase (glutaminyl cyclase)	protein-coding	0.01	0.39604
Merged-chr17-32965789-1	chr17	32965739	32965839	+	2.1	cIP2vsInput	promoter-TSS (NR_033585)	promoter-TSS (NR_033585)	-42	NM_153063	224691	Mm.328953	NM_153063	ENSMUSG00000053600	Zfp472	KRIM-1|Krim-1A|Krim-1B|Krim1	zinc finger protein 472	protein-coding	0.03	0.554455
Merged-chr16-68914755-1	chr16	68914705	68914805	+	2.1	cIP1vsInput	Intergenic	Intergenic	948989	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding	0	0.306931
Merged-chr5-72549767-1	chr5	72549717	72549817	+	2.1	cIP2vsInput	"intron (NM_133921, intron 5 of 22)"	"intron (NM_133921, intron 5 of 22)"	9878	NM_133921	100978	Mm.462187	NM_133921	ENSMUSG00000072889	Nfxl1	1700012H24Rik|AW538212|D430033A06Rik|DNABF|GCF|Gm1058|TCF9	"nuclear transcription factor, X-box binding-like 1"	protein-coding	0	0.326733
Merged-chr1-74068929-1	chr1	74068879	74068979	+	2.1	cIP2vsInput	"intron (NM_027884, intron 2 of 34)"	CpG-274	55518	NM_027884	21961	Mm.309975	NM_177169	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding	0.07	0.732673
Merged-chr14-91987597-1	chr14	91987547	91987647	+	2.1	cIP1vsInput	Intergenic	Intergenic	1860706	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0.01	0.29703
Merged-chr5-88947945-1	chr5	88947895	88947995	+	2.1	cIP1vsInput	"intron (NM_001197147, intron 2 of 25)"	"intron (NM_001197147, intron 2 of 25)"	60685	NM_018760	54403	Mm.41044	NM_001136260	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	"solute carrier family 4 (anion exchanger), member 4"	protein-coding	0	0.356436
Merged-chr7-109765034-1	chr7	109764984	109765084	+	2.1	cIP1vsInput	"intron (NM_020610, intron 3 of 6)"	"intron (NM_020610, intron 3 of 6)"	-12771	NM_020050	56786	Mm.240668	NM_020050	ENSMUSG00000031021	Tmem9b	2310004K06Rik|AW539847|D7H11orf15|ICRFP703B1614Q5.3	"TMEM9 domain family, member B"	protein-coding	0	0.366337
Merged-chr3-87461656-1	chr3	87461606	87461706	+	2.1	cIP1vsInput	"intron (NM_001113238, intron 11 of 11)"	"intron (NM_001113238, intron 11 of 11)"	25874	NM_001113238	329693	Mm.331122	NM_001113238		Fcrl5	Fcrh3|mBXMH2	Fc receptor-like 5	protein-coding	0.01	0.29703
Merged-chr13-27762829-1	chr13	27762779	27762879	+	2.1	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	17975	NM_026206	67505	Mm.49048	NM_026206	ENSMUSG00000060738	Prl7c1	1600017N11Rik|PLP-O|Prlpo|Prplo	"prolactin family 7, subfamily c, member 1"	protein-coding	0.01	0.29703
Merged-chr1-31832199-1	chr1	31832149	31832249	+	2.1	cIP1vsInput	Intergenic	L1ME1|LINE|L1	-340607	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm1	"KH domain containing, RNA binding, signal transduction associated 2"	protein-coding	0.01	0.306931
Merged-chr9-93410065-1	chr9	93410015	93410115	+	2.1	cIP2vsInput	Intergenic	L1MA6|LINE|L1	-404332	NR_040756	78349	Mm.52612	NR_040756		1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	miscRNA	0.01	0.356436
Merged-chr2-54194902-1	chr2	54194852	54194952	+	2.1	cIP2vsInput	Intergenic	Intergenic	-109350	NM_023396	67874	Mm.27086	NM_023396	ENSMUSG00000075334	Rprm	2410012A13Rik|Reprimo	"reprimo, TP53 dependent G2 arrest mediator candidate"	protein-coding	0	0.316832
Merged-chr10-100917645-1	chr10	100917595	100917695	+	2.1	cIP1vsInput	Intergenic	Intergenic	325259	NM_001081246	66605	Mm.72646	NM_001081246	ENSMUSG00000056912	1700017N19Rik	-	RIKEN cDNA 1700017N19 gene	protein-coding	0	0.356436
Merged-chrX-59458017-1	chrX	59457967	59458067	+	2.1	cIP1vsInput	Intergenic	Lx5|LINE|L1	-323581	NM_010200	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding	0	0.287129
Merged-chr18-90209884-1	chr18	90209834	90209934	+	2.1	cIP1vsInput	Intergenic	Intergenic	-300270	NM_198295	67988	Mm.268041	NM_198295	ENSMUSG00000024614	Tmx3	6430411B10Rik|A730024F05Rik|AV259382|Txndc10|mKIAA1830	thioredoxin-related transmembrane protein 3	protein-coding	0	0.336634
Merged-chr2-104510836-1	chr2	104510786	104510886	+	2.1	cIP1vsInput	Intergenic	L1MC2|LINE|L1	-16347	NM_001145824	15259	Mm.257925	NM_001145824	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY	homeodomain interacting protein kinase 3	protein-coding	0.01	0.336634
Merged-chr13-71096241-1	chr13	71096191	71096291	+	2.1	cIP1vsInput	Intergenic	Intergenic	213293	NM_029873	77166	Mm.159859	NM_029873	ENSMUSG00000021600	8030423J24Rik	-	RIKEN cDNA 8030423J24 gene	protein-coding	0.01	0.366337
Merged-chr8-102820307-1	chr8	102820257	102820357	+	2.1	cIP1vsInput	Intergenic	MER136|DNA|DNA	-35196	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0	0.287129
Merged-chr8-38738652-1	chr8	38738602	38738702	+	2.1	cIP1vsInput	Intergenic	Intergenic	-77144	NM_145841	244431	Mm.210388	NM_145841	ENSMUSG00000039539	Sgcz	C230085N17Rik	sarcoglycan zeta	protein-coding	0	0.326733
Merged-chr8-13252780-1	chr8	13252730	13252830	+	2.1	cIP1vsInput	"intron (NM_172750, intron 1 of 6)"	"intron (NM_172750, intron 1 of 6)"	1382	NM_172750	234072	Mm.132785	NM_172750	ENSMUSG00000031448	Adprhl1	Arh2|D330008N11Rik	ADP-ribosylhydrolase like 1	protein-coding	0.03	0.415842
Merged-chr6-44773485-1	chr6	44773435	44773535	+	2.1	cIP1vsInput	Intergenic	Intergenic	-286576	NM_001004357	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0.02	0.277228
Merged-chr4-133449626-1	chr4	133449576	133449676	+	2.1	cIP1vsInput	Intergenic	Intergenic	-30507	NM_175307	100342	Mm.204656	NM_175307	ENSMUSG00000046694	Fam46b	4732473B16Rik|AU045678|AU046069	"family with sequence similarity 46, member B"	protein-coding	0.02	0.475248
Merged-chr14-88072727-1	chr14	88072677	88072777	+	2.1	cIP1vsInput	Intergenic	L1M2|LINE|L1	398669	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0	0.247525
Merged-chr5-39914957-1	chr5	39914907	39915007	+	2.1	cIP1vsInput	Intergenic	L1MC1|LINE|L1	-270326	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding	0	0.39604
Merged-chr17-3759024-1	chr17	3758974	3759074	+	2.1	cIP1vsInput	Intergenic	Intergenic	-62763	NM_198958	224480	Mm.328756	NM_198958	ENSMUSG00000023802	Nox3	GP91-3|het|nmf250	NADPH oxidase 3	protein-coding	0	0.326733
Merged-chr3-11961053-1	chr3	11961003	11961103	+	2.1	cIP1vsInput	Intergenic	RLTR19-int|LTR|ERVK	-116694	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0.01	0.326733
Merged-chr16-39656276-1	chr16	39656226	39656326	+	2.1	cIP2vsInput	Intergenic	Intergenic	753931	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	"immunoglobulin superfamily, member 11"	protein-coding	0	0.257426
Merged-chr4-72968559-1	chr4	72968509	72968609	+	2.1	cIP1vsInput	Intergenic	ORR1E-int|LTR|ERVL-MaLR	-115925	NM_001199270	353204	Mm.317892	NM_001199270	ENSMUSG00000059343	Aldoart1	4921524E03Rik|Aldo1-ps|Aldo1-ps2|Aldoa-ps2	aldolase 1 A retrogene 1	protein-coding	0	0.346535
Merged-chr18-7162971-1	chr18	7162921	7163021	+	2.1	cIP2vsInput	"intron (NM_001081393, intron 18 of 20)"	L1VL4|LINE|L1	134930	NM_001081393	74934	Mm.107918	NM_001081393	ENSMUSG00000061802	Armc4	4930463I21Rik	armadillo repeat containing 4	protein-coding	0.01	0.386139
Merged-chr2-99635871-1	chr2	99635821	99635921	+	2.1	cIP1vsInput	Intergenic	Lx8|LINE|L1	-1988877	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding	0	0.336634
Merged-chr19-15608633-1	chr19	15608583	15608683	+	2.1	cIP2vsInput	Intergenic	Intergenic	315989	NM_001205339	107272	Mm.470456	NM_001205339	ENSMUSG00000024640	Psat1	D8Ertd814e|EPIP|PSA|Psat	phosphoserine aminotransferase 1	protein-coding	0	0.316832
Merged-chr2-16078605-1	chr2	16078555	16078655	+	2.1	cIP2vsInput	Intergenic	L1MA5|LINE|L1	-277717	NM_026162	67448	Mm.394655	NM_026162		Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding	0.01	0.336634
Merged-chr1-65545898-1	chr1	65545848	65545948	+	2.1	cIP1vsInput	Intergenic	Intergenic	234641	NM_139270	213527	Mm.294225	NM_139270	ENSMUSG00000025946	Pth2r	Pthr2	parathyroid hormone 2 receptor	protein-coding	0.02	0.435644
Merged-chr3-99702770-1	chr3	99702720	99702820	+	2.1	cIP1vsInput	Intergenic	L1MEd|LINE|L1	-182647	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding	0.01	0.316832
Merged-chr4-3864425-1	chr4	3864375	3864475	+	2.1	cIP2vsInput	Intergenic	Intergenic	7680	NM_020021	17451	Mm.459300	NM_020021	ENSMUSG00000078365	Mos	c-mos	Moloney sarcoma oncogene	protein-coding	0	0.336634
Merged-chr5-61023689-1	chr5	61023639	61023739	+	2.1	cIP2vsInput	Intergenic	Lx5|LINE|L1	-785154	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding	0	0.316832
Merged-chr4-73159891-1	chr4	73159841	73159941	+	2.1	cIP2vsInput	Intergenic	Intergenic	245181	NM_001013393	433719	Mm.348294	NM_001013393	ENSMUSG00000066137	Gm11487	OTTMUSG00000001246	predicted gene 11487	protein-coding	0	0.346535
Merged-chr10-23213306-1	chr10	23213256	23213356	+	2.1	cIP2vsInput	"intron (NM_010167, intron 3 of 18)"	"intron (NM_010167, intron 3 of 18)"	136597	NM_010167	14051	Mm.446298	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	eyes absent 4 homolog (Drosophila)	protein-coding	0	0.306931
Merged-chr7-79591577-1	chr7	79591527	79591627	+	2.1	cIP1vsInput	Intergenic	Intergenic	26080	NM_019799	56315	Mm.10909	NM_019799	ENSMUSG00000030549	Rhcg	BB065800	Rhesus blood group-associated C glycoprotein	protein-coding	0.01	0.554455
Merged-chr9-81463233-1	chr9	81463183	81463283	+	2.1	cIP2vsInput	Intergenic	Intergenic	-168697	NR_040394	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	miscRNA	0	0.316832
Merged-chrX-51648786-1	chrX	51648736	51648836	+	2.1	cIP2vsInput	"intron (NM_001077202, intron 2 of 4)"	"intron (NM_001077202, intron 2 of 4)"	31691	NM_015819	50786	Mm.252561	NM_001077202	ENSMUSG00000062184	Hs6st2	6OST2	heparan sulfate 6-O-sulfotransferase 2	protein-coding	0.01	0.306931
Merged-chr2-111756467-1	chr2	111756417	111756517	+	2.1	cIP1vsInput	Intergenic	Intergenic	2216	NM_146887	258889	Mm.473590	NM_146887	ENSMUSG00000057149	Olfr1301	MOR248-5	olfactory receptor 1301	protein-coding	0	0.237624
Merged-chr1-146872248-1	chr1	146872198	146872298	+	2.1	cIP1vsInput	"intron (NM_153539, intron 7 of 7)"	"intron (NM_153539, intron 7 of 7)"	374561	NM_001145807	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.356436
Merged-chr1-9378188-1	chr1	9378138	9378238	+	2.1	cIP1vsInput	Intergenic	Lx8|LINE|L1	-78458	NM_027671	71096	Mm.388998	NM_027671		Sntg1	4933426D16Rik|G1SYN|SYN4	"syntrophin, gamma 1"	protein-coding	0.01	0.336634
Merged-chr8-64578331-1	chr8	64578281	64578381	+	2.1	cIP1vsInput	Intergenic	B3A|SINE|B2	-63890	NR_030491	735270		NR_030491	ENSMUSG00000076042	Mir710	Mirn710|mmu-mir-710	microRNA 710	miscRNA	0.03	0.485149
Merged-chr1-167990350-1	chr1	167990300	167990400	+	2.1	cIP1vsInput	Intergenic	Lx7|LINE|L1	300792	NM_033652	110648	Mm.330081	NM_033652	ENSMUSG00000026686	Lmx1a	Lmx1.1|dr|dreher|sst	LIM homeobox transcription factor 1 alpha	protein-coding	0.01	0.336634
Merged-chr4-23520514-1	chr4	23520464	23520564	+	2.1	cIP1vsInput	Intergenic	Lx8b|LINE|L1	-975948	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	"MMS22-like, DNA repair protein"	protein-coding	0.01	0.336634
Merged-chr18-18833672-1	chr18	18833622	18833722	+	2.1	cIP1vsInput	Intergenic	RLTR45-int|LTR|ERVK	1168425	NM_007882	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding	0	0.237624
Merged-chr16-89059972-1	chr16	89059922	89060022	+	2.1	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	4030	NM_001276278	68637	Mm.384089	XM_003945561		1110025L11Rik	-	RIKEN cDNA 1110025L11 gene	protein-coding	0	0.346535
Merged-chr6-24873490-1	chr6	24873440	24873540	+	2.1	cIP1vsInput	"intron (NM_028957, intron 1 of 3)"	L1_Mus2|LINE|L1	15493	NM_028957	74468	Mm.251601	NM_028957	ENSMUSG00000029678	Hyal5	4933439A12Rik	hyaluronoglucosaminidase 5	protein-coding	0	0.326733
Merged-chr2-86046053-1	chr2	86046003	86046103	+	2.1	cIP1vsInput	promoter-TSS (NM_001011872)	promoter-TSS (NM_001011872)	-391	NM_001011872	258216	Mm.330363	NM_001011872	ENSMUSG00000060422	Olfr1034	MOR227-8P|MOR245-14P|Olfr1533-ps1	olfactory receptor 1034	protein-coding	0	0.326733
Merged-chr17-52109618-1	chr17	52109568	52109668	+	2.1	cIP1vsInput	Intergenic	Intergenic	226891	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	"predicted gene, 20098"	miscRNA	0	0.306931
Merged-chr7-62649467-1	chr7	62649417	62649517	+	2.1	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	-184957	NM_013788	27412	Mm.422745	NM_013788	ENSMUSG00000070526	Peg12	Frat3	paternally expressed 12	protein-coding	0.01	0.326733
Merged-chr10-26735912-1	chr10	26735862	26735962	+	2.1	cIP1vsInput	Intergenic	Lx9|LINE|L1	-36600	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding	0.01	0.356436
Merged-chr6-75051280-2	chr6	75051207	75051354	+	2.1	cIP1vsInput|cIP2vsInput	Intergenic	RMER15|LTR|ERVL	-1581613	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.324324
Merged-chr7-136582869-1	chr7	136582819	136582919	+	2.1	cIP1vsInput	Intergenic	Intergenic	127735	NR_046021	621677	Mm.207290	NR_046021		Gm6249	EG621677	predicted gene 6249	miscRNA	0.02	0.405941
Merged-chr12-59798150-1	chr12	59798100	59798200	+	2.1	cIP2vsInput	Intergenic	Intergenic	-578667	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding	0	0.316832
Merged-chr13-77563268-1	chr13	77563218	77563318	+	2.1	cIP1vsInput	"intron (NM_001145676, intron 19 of 19)"	Lx9|LINE|L1	-145422	NM_001163420	68675	Mm.343005	NM_001163419	ENSMUSG00000064138	Fam172a	1110033M05Rik|2610318O14Rik|53-E6|9430037D06Rik|AF064782|pEN87	"family with sequence similarity 172, member A"	protein-coding	0	0.415842
Merged-chr4-79577865-1	chr4	79577815	79577915	+	2.1	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-1256365	NM_031202	22178	Mm.412291	NM_031202	ENSMUSG00000005994	Tyrp1	TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding	0.01	0.346535
Merged-chr14-66883612-1	chr14	66883562	66883662	+	2.1	cIP1vsInput	Intergenic	Intergenic	14762	NM_001034881	432870	Mm.425890	NM_001034881	ENSMUSG00000075553	Gm5464	EG432870	predicted gene 5464	protein-coding	0	0.534653
Merged-chr6-53490385-1	chr6	53490335	53490435	+	2.1	cIP2vsInput	Intergenic	Intergenic	-82989	NM_172728	231991	Mm.321138	NM_172728	ENSMUSG00000053007	Creb5	Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding	0	0.29703
Merged-chr12-7503744-1	chr12	7503694	7503794	+	2.1	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-123414	NR_045045	73575	Mm.179463	NR_045045		1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	miscRNA	0	0.376238
Merged-chr9-51815073-1	chr9	51815023	51815123	+	2.1	cIP2vsInput	"intron (NM_175535, intron 2 of 14)"	"intron (NM_175535, intron 2 of 14)"	49721	NM_175535	244867	Mm.443529	NM_175535	ENSMUSG00000053199	Arhgap20	6530403F17Rik|A530023E23Rik|mKIAA1391	Rho GTPase activating protein 20	protein-coding	0.02	0.356436
Merged-chr1-91723817-1	chr1	91723767	91723867	+	2.1	cIP1vsInput	Intergenic	Lx6|LINE|L1	-77660	NM_007855	13345	Mm.9474	NM_007855	ENSMUSG00000007805	Twist2	Dermo1|bHLHa39	twist basic helix-loop-helix transcription factor 2	protein-coding	0.01	0.346535
Merged-chr4-77597903-1	chr4	77597853	77597953	+	2.1	cIP1vsInput	"intron (NM_011211, intron 3 of 39)"	L1_Mus4|LINE|L1	613992	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0	0.316832
Merged-chr6-27957409-1	chr6	27957359	27957459	+	2.1	cIP2vsInput	"intron (NM_008174, intron 3 of 10)"	"intron (NM_008174, intron 3 of 10)"	-20659	NR_030420	735266		NR_030420		Mir592	Mirn592|mir-592|mmu-mir-592	microRNA 592	miscRNA	0.02	0.386139
Merged-chr16-44069066-1	chr16	44069016	44069116	+	2.1	cIP1vsInput	Intergenic	Intergenic	-41121	NM_001172107	207798	Mm.19316	NM_001172107	ENSMUSG00000036292	Gramd1c	4921521N14Rik	GRAM domain containing 1C	protein-coding	0.02	0.376238
Merged-chr12-91400180-1	chr12	91400130	91400230	+	2.1	cIP2vsInput	promoter-TSS (NM_011648)	promoter-TSS (NM_011648)	-813	NM_001113404	22095	Mm.173847	NM_001113404	ENSMUSG00000020963	Tshr	AI481368|hypothroid|hyt|pet	thyroid stimulating hormone receptor	protein-coding	0.01	0.405941
Merged-chr13-51403319-1	chr13	51403269	51403369	+	2.1	cIP1vsInput	Intergenic	Lx8|LINE|L1	-5299	NM_010101	13610	Mm.136736	NM_010101	ENSMUSG00000067586	S1pr3	AI132464|Edg3|Lpb3|S1p3	sphingosine-1-phosphate receptor 3	protein-coding	0.01	0.376238
Merged-chr2-158681333-1	chr2	158681283	158681383	+	2.1	cIP1vsInput	"intron (NM_001159662, intron 1 of 10)"	"intron (NM_001159662, intron 1 of 10)"	14198	NM_001159662	228852	Mm.150540	NM_001159662	ENSMUSG00000037754	Ppp1r16b	ANKRD4|C130078N17Rik|TIMAP|Wdt4	"protein phosphatase 1, regulatory (inhibitor) subunit 16B"	protein-coding	0	0.39604
Merged-chr8-102342111-1	chr8	102342061	102342161	+	2.1	cIP2vsInput	Intergenic	Intergenic	443000	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0	0.356436
Merged-chr2-64202074-1	chr2	64202024	64202124	+	2.1	cIP2vsInput	Intergenic	Intergenic	-104036	NM_001267847	60344	Mm.483676	NM_001267846	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding	0.01	0.376238
Merged-chr2-67219887-1	chr2	67219837	67219937	+	2.1	cIP2vsInput	Intergenic	L1VL2|LINE|L1	46053	NM_001033477	383709	Mm.244520	NM_001033477		Gm1322	-	predicted gene 1322	protein-coding	0.01	0.346535
Merged-chr9-27663174-1	chr9	27663124	27663224	+	2.1	cIP2vsInput	Intergenic	Intergenic	-128095	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding	0.01	0.346535
Merged-chr1-52416247-1	chr1	52416197	52416297	+	2.1	cIP2vsInput	Intergenic	L1VL4|LINE|L1	84201	NM_008667	17936	Mm.25903	NM_008667		Nab1	-	Ngfi-A binding protein 1	protein-coding	0	0.287129
Merged-chr2-81689523-1	chr2	81689473	81689573	+	2.1	cIP2vsInput	Intergenic	Intergenic	-364135	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0	0.287129
Merged-chr14-71129904-1	chr14	71129854	71129954	+	2.1	cIP1vsInput	Intergenic	Intergenic	-121369	NR_046075	100043132	Mm.399336	NR_046075		Gm4251	-	predicted gene 4251	miscRNA	0	0.524752
Merged-chr16-61187896-1	chr16	61187846	61187946	+	2.1	cIP2vsInput	Intergenic	Intergenic	-582365	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0.01	0.346535
Merged-chr10-112905957-1	chr10	112905907	112906007	+	2.1	cIP1vsInput	Intergenic	Intergenic	23069	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132|ENSMUSG00000074747	ataxin 7-like 3B	protein-coding	0	0.39604
Merged-chr5-126733686-1	chr5	126733636	126733736	+	2.1	cIP2vsInput	Intergenic	Intergenic	-297103	NR_040685	71247	Mm.399586	NR_040685		4933438B17Rik	-	RIKEN cDNA 4933438B17 gene	miscRNA	0.03	0.623762
Merged-chr1-17318974-1	chr1	17318924	17319024	+	2.1	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	173601	NM_010267	14545	Mm.18218	NM_010267	ENSMUSG00000025777	Gdap1	-	ganglioside-induced differentiation-associated-protein 1	protein-coding	0	0.356436
Merged-chr18-16375936-1	chr18	16375886	16375986	+	2.1	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	433113	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-cadherin|Ncad	cadherin 2	protein-coding	0	0.326733
Merged-chr16-29137063-1	chr16	29137013	29137113	+	2.1	cIP1vsInput	Intergenic	Intergenic	-72632	NM_013751	27281	Mm.103650	NM_013751	ENSMUSG00000022525	Hrasls	2810012B06Rik|A-C1|HRSL1|Hrasrs	HRAS-like suppressor	protein-coding	0.01	0.336634
Merged-chr10-63771223-1	chr10	63771173	63771273	+	2.1	cIP1vsInput	"intron (NM_001164376, intron 5 of 17)"	L1MB8|LINE|L1	-49832	NM_001164519	216033	Mm.444692	NM_001164376	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	"catenin (cadherin associated protein), alpha 3"	protein-coding	0.01	0.356436
Merged-chr6-107120848-1	chr6	107120798	107120898	+	2.1	cIP2vsInput	Intergenic	Lx2B2|LINE|L1	-320761	NM_175357	58799	Mm.290085	NM_021449		Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding	0.01	0.356436
Merged-chrX-139219255-1	chrX	139219205	139219305	+	2.1	cIP1vsInput	"intron (NM_001164632, intron 2 of 4)"	"intron (NM_001164632, intron 2 of 4)"	2089	NM_001164632	245631	Mm.131001	NM_001164630	ENSMUSG00000042515	Mum1l1	9430086K21Rik	melanoma associated antigen (mutated) 1-like 1	protein-coding	0.01	0.366337
Merged-chr7-93977909-1	chr7	93977859	93977959	+	2.1	cIP2vsInput	Intergenic	Lx4B|LINE|L1	898030	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0	0.287129
Merged-chr10-16770657-1	chr10	16770607	16770707	+	2.1	cIP2vsInput	Intergenic	Intergenic	325125	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0	0.316832
Merged-chr8-64461910-1	chr8	64461860	64461960	+	2.1	cIP1vsInput	Intergenic	Intergenic	52531	NR_030491	735270		NR_030491	ENSMUSG00000076042	Mir710	Mirn710|mmu-mir-710	microRNA 710	miscRNA	0	0.386139
Merged-chr9-108170697-1	chr9	108170647	108170747	+	2.1	cIP1vsInput	"intron (NM_007567, intron 1 of 11)"	"intron (NM_007567, intron 1 of 11)"	19686	NM_007567	12217	Mm.20425	NM_007567	ENSMUSG00000032589	Bsn	-	bassoon	protein-coding	0.02	0.475248
Merged-chr1-163708221-1	chr1	163708171	163708271	+	2.1	cIP1vsInput	"intron (NM_001143956, intron 2 of 3)"	"intron (NM_001143956, intron 2 of 3)"	17011	NM_001143956	240879	Mm.484621	NM_001143956		Mettl11b	Gm207|NTM1B	methyltransferase like 11B	protein-coding	0	0.336634
Merged-chr2-177369899-1	chr2	177369849	177369949	+	2.1	cIP1vsInput	Intergenic	RMER6BA|LTR|ERVK	-94843	NM_001177568	628308	Mm.460436	NM_001177568		Gm14420	OTTMUSG00000016588	predicted gene 14420	protein-coding	0	0.366337
Merged-chr8-51493137-1	chr8	51493087	51493187	+	2.1	cIP1vsInput	Intergenic	Lx3_Mus|LINE|L1	1125025	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.386139
Merged-chr4-148585706-1	chr4	148585656	148585756	+	2.1	cIP1vsInput	Intergenic	RLTR19-int|LTR|ERVK	-5807	NM_009272	20810	Mm.10	NM_009272	ENSMUSG00000006442	Srm	AA407669|SpdST|SpdSy	spermidine synthase	protein-coding	0	0.29703
Merged-chr7-105662925-1	chr7	105662875	105662975	+	2.1	cIP2vsInput	Intergenic	Lx|LINE|L1	22385	NM_019502	14356	Mm.220330	NM_019502		Timm10b	Fxc1|Tim10b|Tim9b	translocase of inner mitochondrial membrane 10B	protein-coding	0	0.316832
Merged-chr2-27289455-1	chr2	27289405	27289505	+	2.1	cIP1vsInput	"intron (NM_009500, intron 11 of 27)"	"intron (NM_009500, intron 11 of 27)"	-42152	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding	0.03	0.524752
Merged-chr3-77855366-1	chr3	77855316	77855416	+	2.1	cIP1vsInput	Intergenic	Intergenic	1290509	NM_001099624	76089	Mm.462396	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding	0	0.415842
Merged-chr4-3975621-1	chr4	3975571	3975671	+	2.1	cIP2vsInput	Intergenic	Intergenic	36707	NM_001190322	66433	Mm.27406	NM_001190322	ENSMUSG00000042198	Chchd7	1810049H20Rik	coiled-coil-helix-coiled-coil-helix domain containing 7	protein-coding	0	0.39604
Merged-chr18-8216703-1	chr18	8216653	8216753	+	2.1	cIP1vsInput	Intergenic	Intergenic	347506	NM_153085	225131	Mm.204524	NM_001146298	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding	0	0.336634
Merged-chr14-109096597-1	chr14	109096547	109096647	+	2.1	cIP2vsInput	Intergenic	Intergenic	-182358	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	"SLIT and NTRK-like family, member 1"	protein-coding	0.02	0.336634
Merged-chr1-75834101-1	chr1	75834051	75834151	+	2.1	cIP1vsInput	Intergenic	Intergenic	287835	NM_009208	20536	Mm.5053	NM_009208		Slc4a3	A930038D23Rik|Ae3	"solute carrier family 4 (anion exchanger), member 3"	protein-coding	0	0.376238
Merged-chr16-65753110-1	chr16	65753060	65753160	+	2.1	cIP2vsInput	Intergenic	Intergenic	-62523	NM_028572	73569	Mm.482366	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like 3 (Drosophila)	protein-coding	0	0.366337
Merged-chr13-100126652-1	chr13	100126602	100126702	+	2.1	cIP1vsInput	"exon (NM_011420, exon 2 of 9)"	"exon (NM_011420, exon 2 of 9)"	1797	NM_011420	20595	Mm.2025	NM_001252629	ENSMUSG00000021645	Smn1	AI849087|Gemin1|Smn	survival motor neuron 1	protein-coding	0	0.326733
Merged-chr1-110342877-1	chr1	110342827	110342927	+	2.1	cIP1vsInput	Intergenic	L1_Mur1|LINE|L1	359140	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.326733
Merged-chr4-8164538-1	chr4	8164488	8164588	+	2.1	cIP1vsInput	"intron (NM_007592, intron 8 of 8)"	"intron (NM_007592, intron 8 of 8)"	74503	NM_007592	12319	Mm.119320	NM_007592		Car8	AW546993|Ca8|Cals|Cals1|Carp|wdl	carbonic anhydrase 8	protein-coding	0	0.277228
Merged-chr14-87836204-1	chr14	87836154	87836254	+	2.1	cIP1vsInput	Intergenic	L1MA7|LINE|L1	419621	NM_001253755	219249	Mm.35168	NM_001253755	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding	0	0.257426
Merged-chrX-13208284-1	chrX	13208234	13208334	+	2.1	cIP2vsInput	Intergenic	Intergenic	27999	NR_045430	72122	Mm.75434	NR_045429		2010308F09Rik	-	RIKEN cDNA 2010308F09 gene	miscRNA	0.05	0.564356
Merged-chr15-26531836-1	chr15	26531786	26531886	+	2.1	cIP2vsInput	Intergenic	MTEa|LTR|ERVL-MaLR	222764	NM_177597	211147	Mm.54257	NM_177597	ENSMUSG00000022269	11-Mar	9630025C22	membrane-associated ring finger (C3HC4) 11	protein-coding	0	0.366337
Merged-chr7-88808331-1	chr7	88808281	88808381	+	2.1	cIP2vsInput	Intergenic	Intergenic	378058	NM_028238	72433	Mm.276669	NM_028238	ENSMUSG00000030559	Rab38	2310011F14Rik|AU043391|cht	"RAB38, member of RAS oncogene family"	protein-coding	0	0.356436
Merged-chr14-45735861-1	chr14	45735811	45735911	+	2.1	cIP1vsInput	Intergenic	ID|SINE|ID	-77718	NM_001042719	114874	Mm.459394	NM_001039106	ENSMUSG00000037697	Ddhd1	4921528E07Rik|9630061G18Rik|C85251|mKIAA1705	DDHD domain containing 1	protein-coding	0	0.415842
Merged-chr10-26549148-1	chr10	26549098	26549198	+	2.1	cIP1vsInput	Intergenic	Intergenic	125503	NR_033633	667572	Mm.482728	NR_033633		Gm8709	EG667572	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0	0.326733
Merged-chrX-121519848-1	chrX	121519798	121519898	+	2.1	cIP1vsInput	Intergenic	Intergenic	877537	NM_138742	54561	Mm.490573	NM_138742	ENSMUSG00000055733	Nap1l3	MB20	nucleosome assembly protein 1-like 3	protein-coding	0	0.287129
Merged-chr2-12169233-1	chr2	12169183	12169283	+	2.1	cIP2vsInput	"intron (NM_001001309, intron 23 of 29)"	"intron (NM_001001309, intron 23 of 29)"	-132013	NR_040353	338535	Mm.483275	NR_040353		E030013I19Rik	-	RIKEN cDNA E030013I19 gene	miscRNA	0	0.356436
Merged-chr7-14628508-1	chr7	14628458	14628558	+	2.1	cIP1vsInput	Intergenic	Lx3A|LINE|L1	-5442	NR_045119	100417675	Mm.372763	NR_045119		Nlrp5-ps	Gm18756	"NLR family, pyrin domain containing 5, pseudogene"	pseudo	0	0.306931
Merged-chr8-34485052-1	chr8	34485002	34485102	+	2.1	cIP1vsInput	Intergenic	Intergenic	155264	NR_040706	330734	Mm.149998	NR_040706		B930018H19Rik	B930018H19	RIKEN cDNA B930018H19 gene	miscRNA	0.01	0.455446
Merged-chr12-26657742-1	chr12	26657692	26657792	+	2.1	cIP1vsInput	Intergenic	L1M3|LINE|L1	188527	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	"cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial"	protein-coding	0	0.257426
Merged-chr1-46603302-1	chr1	46603252	46603352	+	2.1	cIP1vsInput	Intergenic	Intergenic	250207	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.257426
Merged-chrX-141417414-1	chrX	141417364	141417464	+	2.1	cIP1vsInput	"intron (NM_053185, intron 2 of 44)"	Tigger1|DNA|TcMar-Tigger	56662	NM_053185	94216	Mm.155586	NM_053185	ENSMUSG00000031273	Col4a6	BB116301	"collagen, type IV, alpha 6"	protein-coding	0	0.277228
Merged-chr4-30623083-1	chr4	30623033	30623133	+	2.1	cIP1vsInput	Intergenic	Lx7|LINE|L1	-41513	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	miscRNA	0	0.287129
Merged-chr1-146290335-1	chr1	146290285	146290385	+	2.1	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	-205331	NM_153539	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0.01	0.346535
Merged-chr7-62337197-1	chr7	62337147	62337247	+	2.1	cIP2vsInput	Intergenic	RLTR17B_Mm|LTR|ERVK	-11080	NM_010882	17984	Mm.400253	NM_010882	ENSMUSG00000033585	Ndn	AI528698|Peg6	necdin	protein-coding	0	0.356436
Merged-chr5-90588074-1	chr5	90588024	90588124	+	2.1	cIP1vsInput	"intron (NM_001252661, intron 12 of 13)"	"intron (NM_001252661, intron 12 of 13)"	26865	NM_001252661	622307	Mm.389654	NM_001252661	ENSMUSG00000070690	5830473C10Rik	Arg|Gm17754	RIKEN cDNA 5830473C10 gene	protein-coding	0	0.39604
Merged-chr18-50383031-1	chr18	50382981	50383081	+	2.1	cIP1vsInput	Intergenic	Intergenic	104662	NM_001004061	225497	Mm.329435	NM_001004061	ENSMUSG00000035420	Fam170a	Gm93|Znfd	"family with sequence similarity 170, member A"	protein-coding	0	0.326733
Merged-chr10-25038359-1	chr10	25038309	25038409	+	2.1	cIP1vsInput	Intergenic	Intergenic	-110889	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	"arginase, liver"	protein-coding	0	0.277228
Merged-chr1-173302594-1	chr1	173302544	173302644	+	2.1	cIP2vsInput	Intergenic	Intergenic	-24838	NM_001205011	100504232	Mm.482546	NM_001205011	ENSMUSG00000079180	Mptx2	ENSMUSG00000079180|Gm11062	mucosal pentraxin 2	protein-coding	0	0.336634
Merged-chr16-6480387-1	chr16	6480337	6480437	+	2.1	cIP1vsInput	"intron (NM_021477, intron 2 of 16)"	"intron (NM_021477, intron 2 of 16)"	504800	NR_045799	68238	Mm.434605	NR_045799		1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	miscRNA	0.01	0.326733
Merged-chr15-9927149-1	chr15	9927099	9927199	+	2.1	cIP1vsInput	Intergenic	L1M2|LINE|L1	-178343	NM_177123	320277	Mm.127822	NM_177123		Spef2	C230086A09Rik	sperm flagellar 2	protein-coding	0	0.277228
Merged-chr3-15314334-1	chr3	15314284	15314384	+	2.1	cIP1vsInput	"intron (NM_001076679, intron 2 of 2)"	L1_Mus3|LINE|L1	17968	NM_001076679	751864	Mm.431296	NM_001076679	ENSMUSG00000078783	Gm9733	-	predicted gene 9733	protein-coding	0.01	0.287129
Merged-chr1-174196369-1	chr1	174196319	174196419	+	2.1	cIP1vsInput	"intron (NM_011465, intron 15 of 51)"	"intron (NM_011465, intron 15 of 51)"	23593	NM_011465	20739	Mm.200611	NM_011465	ENSMUSG00000026532	Spta1	AF093576|AI451697|Spna-1|Spna1|ha|ihj|nmf4|sph	"spectrin alpha, erythrocytic 1"	protein-coding	0	0.207921
Merged-chr5-34742518-1	chr5	34742468	34742568	+	2.1	cIP1vsInput	"intron (NM_019497, intron 11 of 15)"	L1_Mur3|LINE|L1	-19222	NM_010414	15194	Mm.209071	NM_010414	ENSMUSG00000029104	Htt	AI256365|C430023I11Rik|Hd|Hdh|IT15	huntingtin	protein-coding	0	0.287129
Merged-chr3-139582032-1	chr3	139581982	139582082	+	2.1	cIP2vsInput	"intron (NM_198659, intron 12 of 13)"	"intron (NM_198659, intron 12 of 13)"	376139	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding	0	0.257426
Merged-chr3-156716637-1	chr3	156716587	156716687	+	2.1	cIP1vsInput	"intron (NM_001039094, intron 1 of 6)"	"intron (NM_001039094, intron 1 of 6)"	154678	NM_177274	320840	Mm.317293	NM_001039094	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra|mKIAA3001	neuronal growth regulator 1	protein-coding	0	0.336634
Merged-chrX-94212757-1	chrX	94212707	94212807	+	2.1	cIP2vsInput	promoter-TSS (NM_012010)	promoter-TSS (NM_012010)	-106	NM_012010	26905	Mm.218851	NM_012010	ENSMUSG00000035150	Eif2s3x	AA409828|AA547477|AI314668|Eif-2gx	"eukaryotic translation initiation factor 2, subunit 3, structural gene X-linked"	protein-coding	0.07	0.544554
Merged-chr17-46762510-1	chr17	46762460	46762560	+	2.1	cIP1vsInput	"intron (NM_011195, intron 1 of 3)"	"intron (NM_011195, intron 1 of 3)"	1202	NM_011195	19208	Mm.215173	NM_011195		Ptcra	gp33|pT-alpha|pT-alpha-TCR|pT[a]|pTa|pTalpha	pre T cell antigen receptor alpha	protein-coding	0	0.405941
Merged-chr4-18340676-1	chr4	18340626	18340726	+	2.1	cIP1vsInput	Intergenic	L1_Mur1|LINE|L1	487194	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0	0.39604
Merged-chr1-171301601-1	chr1	171301551	171301651	+	2.1	cIP1vsInput	Intergenic	RMER16-int|LTR|ERVK	-6619	NM_025388	66155	Mm.2815	NM_025388	ENSMUSG00000062963	Ufc1	1110021H02Rik|AA062310|ESTM29	ubiquitin-fold modifier conjugating enzyme 1	protein-coding	0	0.376238
Merged-chr12-74774186-1	chr12	74774136	74774236	+	2.1	cIP1vsInput	Intergenic	Lx2|LINE|L1	403146	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	"potassium voltage-gated channel, subfamily H (eag-related), member 5"	protein-coding	0	0.336634
Merged-chr10-46441855-1	chr10	46441805	46441905	+	2.1	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	197106	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0.01	0.39604
Merged-chr3-121690915-1	chr3	121690865	121690965	+	2.1	cIP1vsInput	Intergenic	Intergenic	20152	NM_001033814	619318	Mm.371258	NM_001033814		4930432M17Rik	-	RIKEN cDNA 4930432M17 gene	protein-coding	0.01	0.366337
Merged-chr7-130597256-1	chr7	130597206	130597306	+	2.1	cIP1vsInput	"intron (NM_001004468, intron 1 of 21)"	"intron (NM_001004468, intron 1 of 21)"	19772	NM_206856	57752	Mm.86322	NM_001004468	ENSMUSG00000030852	Tacc2	mKIAA4180	"transforming, acidic coiled-coil containing protein 2"	protein-coding	0.01	0.405941
Merged-chr1-167859442-1	chr1	167859392	167859492	+	2.1	cIP1vsInput	Intergenic	Charlie1|DNA|hAT-Charlie	169884	NM_033652	110648	Mm.330081	NM_033652	ENSMUSG00000026686	Lmx1a	Lmx1.1|dr|dreher|sst	LIM homeobox transcription factor 1 alpha	protein-coding	0.01	0.346535
Merged-chr9-57629552-1	chr9	57629502	57629602	+	2.1	cIP1vsInput	"intron (NM_007783, intron 5 of 12)"	"intron (NM_007783, intron 5 of 12)"	-8778	NM_199222	235416	Mm.295630	NM_199222	ENSMUSG00000056271	Lman1l	BC020188|slamp	"lectin, mannose-binding 1 like"	protein-coding	0	0.554455
Merged-chr6-116706404-1	chr6	116706354	116706454	+	2.1	cIP1vsInput	"intron (NM_178768, intron 1 of 4)"	Lx8b|LINE|L1	10354	NM_178768	319776	Mm.133120	NM_178768	ENSMUSG00000048108	Tmem72	C230095G01Rik	transmembrane protein 72	protein-coding	0	0.326733
Merged-chr7-61397794-1	chr7	61397744	61397844	+	2.1	cIP1vsInput	Intergenic	Intergenic	217533	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	miscRNA	0	0.257426
Merged-chr1-66880291-1	chr1	66880241	66880341	+	2.1	cIP1vsInput	Intergenic	RLTR22_Mur|LTR|ERVK	-16982	NM_007381	11363	Mm.2445	NM_007381	ENSMUSG00000026003	Acadl	AA960361|AU018452|C79855|LCAD	"acyl-Coenzyme A dehydrogenase, long-chain"	protein-coding	0	0.336634
Merged-chr6-130788973-2	chr6	130788914	130789033	+	2.1	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-402099	NM_016659	16627	Mm.333431	NM_016659	ENSMUSG00000079853	Klra1	A1|Klra22|Ly49a|Ly49o<129>|Ly49v	"killer cell lectin-like receptor, subfamily A, member 1"	protein-coding	0.008403	0.333333
Merged-chr3-43017971-1	chr3	43017921	43018021	+	2.1	cIP2vsInput	Intergenic	Intergenic	1275353	NM_027271	73852	Mm.29006	NM_001099785	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	"DNA segment, Chr 3, ERATO Doi 751, expressed"	protein-coding	0	0.287129
Merged-chr12-103643755-1	chr12	103643705	103643805	+	2.1	cIP1vsInput	Intergenic	Intergenic	-12350	NM_144834	217847	Mm.29094	NM_144834	ENSMUSG00000061947	Serpina10	PZI|ZPI	"serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10"	protein-coding	0	0.29703
Merged-chr9-99681318-1	chr9	99681268	99681368	+	2.1	cIP1vsInput	Intergenic	Intergenic	28745	NM_019815	56492	Mm.386784	NM_001194921		Cldn18	-	claudin 18	protein-coding	0	0.277228
Merged-chr1-146195496-1	chr1	146195446	146195546	+	2.1	cIP1vsInput	Intergenic	Intergenic	-300170	NM_153539	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0.01	0.346535
Merged-chr19-49453589-1	chr19	49453539	49453639	+	2.1	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	1225057	NM_001252501	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0.01	0.366337
Merged-chr9-20149018-1	chr9	20148968	20149068	+	2.1	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	19898	NM_146557	258550	Mm.334988	NM_146557	ENSMUSG00000058491	Olfr869	MOR145-6	olfactory receptor 869	protein-coding	0	0.346535
Merged-chr3-138264895-1	chr3	138264845	138264945	+	2.1	cIP1vsInput	Intergenic	Intergenic	-12750	NM_007409	11522	Mm.412004	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding	0.01	0.39604
Merged-chrX-33930032-1	chrX	33929982	33930082	+	2.1	cIP1vsInput	Intergenic	Intergenic	-227683	NM_001145038	100040732	Mm.465135	NM_001145038	ENSMUSG00000078324	Gm2933	-	predicted gene 2933	protein-coding	0	0.336634
Merged-chr2-94524852-1	chr2	94524802	94524902	+	2.1	cIP1vsInput	Intergenic	Intergenic	-86705	NM_007466	11800	Mm.486651	NM_007466	ENSMUSG00000027193	Api5	AAC-11|AI196452	apoptosis inhibitor 5	protein-coding	0.02	0.356436
Merged-chrX-35899689-1	chrX	35899639	35899739	+	2.1	cIP2vsInput	"intron (NM_001009947, intron 1 of 52)"	"intron (NM_001009947, intron 1 of 52)"	10857	NM_001009947	75974	Mm.32873	NM_177745	ENSMUSG00000031093	Dock11	5033414A21Rik|8030476J24|Zizimin2|sph238	dedicator of cytokinesis 11	protein-coding	0.01	0.445545
Merged-chr2-3552510-1	chr2	3552460	3552560	+	2.1	cIP1vsInput	Intergenic	L1VL4|LINE|L1	29209	NR_030565	100124474		NR_030565		Mir466b-3	Mirn466b-3	microRNA 466b-3	miscRNA	0	0.277228
Merged-chr4-18945897-1	chr4	18945847	18945947	+	2.1	cIP2vsInput	Intergenic	Intergenic	-334953	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding	0	0.415842
Merged-chr10-104227048-1	chr10	104226998	104227098	+	2.1	cIP2vsInput	Intergenic	Intergenic	33006	NM_001270900	667692		NM_001270900	ENSMUSG00000097878	Gm8764	EG667692	predicted gene 8764	protein-coding	0.01	0.316832
Merged-chr9-6638888-1	chr9	6638838	6638938	+	2.1	cIP1vsInput	Intergenic	Intergenic	-372341	NM_027942	71829	Mm.141452	NM_027942	ENSMUSG00000047619	Ddi1	1700011N24Rik	"DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)"	protein-coding	0.01	0.386139
Merged-chr8-75316034-1	chr8	75315984	75316084	+	2.1	cIP1vsInput	Intergenic	L1MB5|LINE|L1	102090	NM_029182	75141	Mm.179267	NM_029182	ENSMUSG00000034472	Rasd2	4930526B11Rik|AU045414|Rhes|TEM-2|TEM2	"RASD family, member 2"	protein-coding	0	0.366337
Merged-chr9-91025232-1	chr9	91025182	91025282	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	340567	NM_009573	22771	Mm.477226	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding	0	0.366337
Merged-chr6-110319482-1	chr6	110319432	110319532	+	2.1	cIP2vsInput	Intergenic	Intergenic	-326116	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0	0.356436
Merged-chr3-86241882-1	chr3	86241832	86241932	+	2.1	cIP2vsInput	"intron (NM_001077687, intron 2 of 50)"	ID_B1|SINE|B4	17192	NM_001077687	80877	Mm.439825	NM_001077687	ENSMUSG00000028080	Lrba	C80285|D3Ertd775e|Lab300|Lba	LPS-responsive beige-like anchor	protein-coding	0	0.405941
Merged-chr18-43348149-1	chr18	43348099	43348199	+	2.1	cIP1vsInput	"intron (NM_001136086, intron 6 of 13)"	Lx9|LINE|L1	25123	NM_001136086	22240	Mm.428551	NM_001136086	ENSMUSG00000024501	Dpysl3	CRMP-4|TUC4|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding	0	0.465347
Merged-chr5-87312711-1	chr5	87312661	87312761	+	2.1	cIP2vsInput	Intergenic	Intergenic	24484	NM_028094	72094	Mm.482739	NM_028094	ENSMUSG00000035780	Ugt2a3	2010321J07Rik	"UDP glucuronosyltransferase 2 family, polypeptide A3"	protein-coding	0	0.346535
Merged-chr4-16068015-1	chr4	16067965	16068065	+	2.1	cIP2vsInput	Intergenic	Intergenic	-54138	NM_145950	209212	Mm.46455	NM_145950	ENSMUSG00000041153	Osgin2	BC010311|C230027H09Rik	oxidative stress induced growth inhibitor family member 2	protein-coding	0	0.346535
Merged-chr13-40793642-1	chr13	40793592	40793692	+	2.1	cIP1vsInput	Intergenic	Intergenic	-59819	NM_011547	21418	Mm.85544	NM_001122948	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap2|Ap2tf|Tcfap2a	"transcription factor AP-2, alpha"	protein-coding	0	0.336634
Merged-chr4-17227175-1	chr4	17227125	17227225	+	2.1	cIP2vsInput	Intergenic	Intergenic	-626307	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0	0.316832
Merged-chr9-119425444-1	chr9	119425394	119425494	+	2.1	cIP2vsInput	"intron (NM_007397, intron 1 of 9)"	"intron (NM_007397, intron 1 of 9)"	-19479	NM_001172136	208194	Mm.101578	NM_001172136	ENSMUSG00000042787	Exog	AW557704|ENGL-B|ENGL-a|Endogl1|Endogl2|Engl|Engla|Englb	"endo/exonuclease (5'-3'), endonuclease G-like"	protein-coding	0.01	0.633663
Merged-chr15-9264669-1	chr15	9264619	9264719	+	2.1	cIP1vsInput	Intergenic	L1VL2|LINE|L1	-15160	NM_207216	105887	Mm.482274	NM_207216	ENSMUSG00000072664	Ugt3a1	AI746432	"UDP glycosyltransferases 3 family, polypeptide A1"	protein-coding	0	0.306931
Merged-chr10-48824759-1	chr10	48824709	48824809	+	2.1	cIP1vsInput	Intergenic	Lx5|LINE|L1	271084	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	"proteasome (prosome, macropain) subunit, alpha type 6 pseudogene"	pseudo	0	0.366337
Merged-chrX-64875494-1	chrX	64875444	64875544	+	2.1	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-172150	NM_027302	70062	Mm.45791	NM_027302	ENSMUSG00000031181	Ctag2	1700030B21Rik	cancer/testis antigen 2	protein-coding	0	0.29703
Merged-chr19-7827125-1	chr19	7827075	7827175	+	2.1	cIP1vsInput	Intergenic	Intergenic	-24458	NM_146232	236149	Mm.207060	NM_146232	ENSMUSG00000053303	Slc22a26	-	"solute carrier family 22 (organic cation transporter), member 26"	protein-coding	0	0.39604
Merged-chr18-59450891-1	chr18	59450841	59450941	+	2.1	cIP1vsInput	Intergenic	Intergenic	275551	NM_001081328	78923	Mm.485185	NM_001081328		Chsy3	4833446K15Rik|AI662215	chondroitin sulfate synthase 3	protein-coding	0	0.336634
Merged-chr12-76856186-1	chr12	76856136	76856236	+	2.1	cIP2vsInput	"intron (NM_145927, intron 1 of 11)"	B3|SINE|B2	18719	NM_145927	110606	Mm.151174	NM_145927	ENSMUSG00000033373	Fntb	2010013E13Rik|AA409500	"farnesyltransferase, CAAX box, beta"	protein-coding	0	0.425743
Merged-chrY-10413504-1	chrY	10413454	10413554	+	2.1	cIP1vsInput	Intergenic	Intergenic	784344	NM_001199331	100040022	Mm.485767	NM_001199331	ENSMUSG00000095172	Gm20822	-	"predicted gene, 20822"	protein-coding	0	0.376238
Merged-chr1-25743012-1	chr1	25742962	25743062	+	2.1	cIP2vsInput	"intron (NM_175642, intron 2 of 30)"	"intron (NM_175642, intron 2 of 30)"	86695	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Bai3	A830096D10Rik	brain-specific angiogenesis inhibitor 3	protein-coding	0	0.326733
Merged-chr15-52325321-1	chr15	52325271	52325371	+	2.1	cIP1vsInput	"intron (NM_172816, intron 4 of 7)"	"intron (NM_172816, intron 4 of 7)"	29768	NM_172816	239436	Mm.208831	NM_172816	ENSMUSG00000022315	Slc30a8	C820002P14Rik|ZnT-8|ZnT8	"solute carrier family 30 (zinc transporter), member 8"	protein-coding	0	0.346535
Merged-chr18-51615909-1	chr18	51615859	51615959	+	2.1	cIP1vsInput	Intergenic	Intergenic	498011	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding	0.01	0.306931
Merged-chr1-62938331-1	chr1	62938281	62938381	+	2.1	cIP2vsInput	Intergenic	Intergenic	-143599	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	miscRNA	0.01	0.356436
Merged-chr7-37527809-1	chr7	37527759	37527859	+	2.1	cIP1vsInput	"intron (NM_172385, intron 4 of 5)"	"intron (NM_172385, intron 4 of 5)"	241943	NM_172385	243937	Mm.388121	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding	0	0.267327
Merged-chr12-35283452-1	chr12	35283402	35283502	+	2.1	cIP2vsInput	Intergenic	Intergenic	236263	NM_001014973	217463	Mm.213991	NM_001014973	ENSMUSG00000020590	Snx13	Rgs-px1|mKIAA0713	sorting nexin 13	protein-coding	0	0.386139
Merged-chr17-76283355-1	chr17	76283305	76283405	+	2.1	cIP1vsInput	Intergenic	Intergenic	422332	NR_033456	100043885	Mm.127562	NR_033456		Gm4710	-	predicted gene 4710	miscRNA	0	0.366337
Merged-chr5-9803721-1	chr5	9803671	9803771	+	2.1	cIP1vsInput	Intergenic	Intergenic	-78369	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	"glutamate receptor, metabotropic 3"	protein-coding	0	0.326733
Merged-chr5-126502278-1	chr5	126502228	126502328	+	2.1	cIP2vsInput	Intergenic	Intergenic	-528511	NR_040685	71247	Mm.399586	NR_040685		4933438B17Rik	-	RIKEN cDNA 4933438B17 gene	miscRNA	0	0.306931
Merged-chr11-113471879-1	chr11	113471829	113471929	+	2.1	cIP1vsInput	"intron (NM_001166503, intron 4 of 9)"	"intron (NM_001166503, intron 4 of 9)"	93936	NM_001166503	69806	Mm.341021	NM_001166503	ENSMUSG00000041654	Slc39a11	1810074D23Rik	"solute carrier family 39 (metal ion transporter), member 11"	protein-coding	0.03	0.50495
Merged-chr10-46908904-1	chr10	46908854	46908954	+	2.1	cIP1vsInput	Intergenic	Intergenic	664155	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0	0.306931
Merged-chr5-87050036-1	chr5	87049986	87050086	+	2.1	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	42519	NM_001029867	231396	Mm.439851	NM_001029867	ENSMUSG00000070704	Ugt2b36	-	"UDP glucuronosyltransferase 2 family, polypeptide B36"	protein-coding	0.01	0.306931
Merged-chr13-9882847-1	chr13	9882797	9882897	+	2.1	cIP2vsInput	"intron (NM_033269, intron 4 of 4)"	"intron (NM_033269, intron 4 of 4)"	-117533	NM_144516	66505	Mm.397307	NM_001199141	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	"zinc finger, MYND domain containing 11"	protein-coding	0.04	0.455446
Merged-chr16-53989438-1	chr16	53989388	53989488	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1173694	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	miscRNA	0	0.376238
Merged-chr11-94630167-1	chr11	94630117	94630217	+	2.1	cIP1vsInput	"intron (NM_133807, intron 1 of 6)"	CpG	343	NM_133807	98238	Mm.172720	NM_133807	ENSMUSG00000020869	Lrrc59	AA959742|C78668	leucine rich repeat containing 59	protein-coding	0.08	0.623762
Merged-chr1-34371681-1	chr1	34371631	34371731	+	2.1	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	61518	NR_039562	100628580		NR_039562	ENSMUSG00000092852	Mir5103	mmu-mir-5103|mu-mir-5103	microRNA 5103	miscRNA	0.01	0.366337
Merged-chr7-84952966-1	chr7	84952916	84953016	+	2.1	cIP1vsInput	"intron (NM_001105180, intron 1 of 5)"	Lx3B|LINE|L1	11043	NM_001105180	100009609	Mm.389926	NM_001105180	ENSMUSG00000066372	Vmn2r65	ENSMUSG00000070600|V2ro	"vomeronasal 2, receptor 65"	protein-coding	0	0.336634
Merged-chr14-79996482-1	chr14	79996432	79996532	+	2.1	cIP2vsInput	Intergenic	Intergenic	-3820	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.356436
Merged-chr14-82691641-1	chr14	82691591	82691691	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1751922	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0	0.29703
Merged-chr6-68007992-1	chr6	68007942	68008042	+	2.1	cIP1vsInput	Intergenic	Intergenic	-442293	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo	0	0.326733
Merged-chrX-15698777-1	chrX	15698727	15698827	+	2.1	cIP2vsInput	Intergenic	L1MA5|LINE|L1	-587288	NR_033171	67395	Mm.50369	NM_026128	ENSMUSG00000045217	Ppp1r2-ps9	4930403L05Rik	"protein phosphatase 1, regulatory (inhibitor) subunit 2, pseudogene 9"	pseudo	0.01	0.346535
Merged-chr5-82626251-1	chr5	82626201	82626301	+	2.1	cIP1vsInput	Intergenic	RMER6-int|LTR|ERVK	172814	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mmu-mir-1187	microRNA 1187	miscRNA	0	0.386139
Merged-chr2-98438464-1	chr2	98438414	98438514	+	2.1	cIP1vsInput	Intergenic	Intergenic	970790	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.356436
Merged-chr4-43241570-1	chr4	43241520	43241620	+	2.1	cIP1vsInput	"intron (NM_001081413, intron 21 of 39)"	"intron (NM_001081413, intron 21 of 39)"	-25589	NM_177195	320571	Mm.74465	NM_177195	ENSMUSG00000028457	Atp8b5	4930417M19Rik|Feta	"ATPase, class I, type 8B, member 5"	protein-coding	0	0.29703
Merged-chr12-93447622-1	chr12	93447572	93447672	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1598465	NM_011344	20338	Mm.250605	NM_001039089	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding	0	0.287129
Merged-chr6-109238320-1	chr6	109238270	109238370	+	2.1	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	409679	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	"ER degradation enhancer, mannosidase alpha-like 1"	protein-coding	0	0.346535
Merged-chr10-15582368-1	chr10	15582318	15582418	+	2.1	cIP2vsInput	Intergenic	Intergenic	822079	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding	0	0.356436
Merged-chr3-36026114-1	chr3	36026064	36026164	+	2.1	cIP1vsInput	"intron (NM_178418, intron 5 of 11)"	"intron (NM_178418, intron 5 of 11)"	-25436	NM_023644	72039	Mm.249016	NM_023644	ENSMUSG00000027709	Mccc1	1810045E08Rik|2310058B18Rik|MCCalpha|Mcca|R75106	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)	protein-coding	0	0.326733
Merged-chr13-38681967-1	chr13	38681917	38682017	+	2.1	cIP2vsInput	Intergenic	Intergenic	-22939	NM_025380	66143	Mm.490319	NM_025380	ENSMUSG00000001707	Eef1e1	1110003A02Rik	eukaryotic translation elongation factor 1 epsilon 1	protein-coding	0.01	0.336634
Merged-chr15-53811293-1	chr15	53811243	53811343	+	2.1	cIP1vsInput	"intron (NM_177225, intron 2 of 4)"	"intron (NM_177225, intron 2 of 4)"	91143	NM_177225	320679	Mm.442455	NM_177225	ENSMUSG00000058656	Samd12	A830094I09Rik	sterile alpha motif domain containing 12	protein-coding	0	0.356436
Merged-chr15-60406976-1	chr15	60406926	60407026	+	2.1	cIP1vsInput	Intergenic	Intergenic	-390358	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding	0	0.356436
Merged-chr5-102283092-1	chr5	102283042	102283142	+	2.1	cIP2vsInput	Intergenic	Lx2B|LINE|L1	-198299	NM_146161	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding	0	0.316832
Merged-chr4-67863602-1	chr4	67863552	67863652	+	2.1	cIP2vsInput	Intergenic	Intergenic	1035791	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding	0.01	0.366337
Merged-chr19-33501470-1	chr19	33501420	33501520	+	2.1	cIP1vsInput	Intergenic	Intergenic	88841	NM_001013770	381236	Mm.329814	NM_001013770	ENSMUSG00000024766	Lipo1	AI747699	"lipase, member O1"	protein-coding	0.01	0.29703
Merged-chr8-111439143-1	chr8	111439093	111439193	+	2.1	cIP1vsInput	Intergenic	MTE2b|LTR|ERVL-MaLR	-45322	NM_178086	338521	Mm.41083	NM_178086	ENSMUSG00000033579	Fa2h	FAAH|Faxdc1|G630055L08Rik	fatty acid 2-hydroxylase	protein-coding	0	0.544554
Merged-chr3-79411583-1	chr3	79411533	79411633	+	2.1	cIP2vsInput	"intron (NM_001142953, intron 2 of 4)"	"intron (NM_001142953, intron 2 of 4)"	66207	NM_001142953	100233207	Mm.373801	NM_001142953	ENSMUSG00000091685	Gm17359	-	"predicted gene, 17359"	protein-coding	0	0.336634
Merged-chr7-52941977-1	chr7	52941927	52942027	+	2.1	cIP1vsInput	Intergenic	Intergenic	-926261	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding	0	0.306931
Merged-chr3-76953030-1	chr3	76952980	76953080	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	877447	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.257426
Merged-chr6-14625232-1	chr6	14625182	14625282	+	2.1	cIP1vsInput	Intergenic	Intergenic	130042	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	"protein phosphatase 1, regulatory (inhibitor) subunit 3A"	protein-coding	0	0.346535
Merged-chr11-51681673-1	chr11	51681623	51681723	+	2.1	cIP2vsInput	Intergenic	Intergenic	6961	NM_025319	66050	Mm.35693	NM_025319	ENSMUSG00000007777	0610009B22Rik	-	RIKEN cDNA 0610009B22 gene	protein-coding	0.01	0.356436
Merged-chr17-90189143-1	chr17	90189093	90189193	+	2.1	cIP2vsInput	"intron (NM_020252, intron 19 of 22)"	L1VL2|LINE|L1	-672026	NR_045463	78800	Mm.410772	NR_045463	ENSMUSG00000090160	4930480K15Rik	-	RIKEN cDNA 4930480K15 gene	miscRNA	0	0.336634
Merged-chrY-5988454-1	chrY	5988404	5988504	+	2.1	cIP2vsInput	Intergenic	Intergenic	1179323	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.425743
Merged-chr1-158124424-1	chr1	158124374	158124474	+	2.1	cIP1vsInput	Intergenic	Intergenic	231836	NM_207583	240843	Mm.329579	NM_207583	ENSMUSG00000004031	Fam5b	6430517E21Rik|BB361039|mKIAA1747	"family with sequence similarity 5, member B"	protein-coding	0.01	0.405941
Merged-chr19-22431885-1	chr19	22431835	22431935	+	2.1	cIP2vsInput	"intron (NM_001035242, intron 1 of 24)"	"intron (NM_001035242, intron 1 of 24)"	-16323	NM_177341	226025	Mm.440339	NM_001035239	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	"transient receptor potential cation channel, subfamily M, member 3"	protein-coding	0	0.366337
Merged-chr3-23919621-1	chr3	23919571	23919671	+	2.1	cIP2vsInput	Intergenic	Intergenic	1668251	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	miscRNA	0	0.346535
Merged-chr3-101326527-1	chr3	101326477	101326577	+	2.1	cIP1vsInput	Intergenic	Arthur1B|DNA|hAT-Tip100	-38588	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding	0	0.405941
Merged-chr4-106413374-1	chr4	106413324	106413424	+	2.1	cIP2vsInput	"intron (NM_183225, intron 52 of 67)"	"intron (NM_183225, intron 52 of 67)"	50951	NM_153565	100102	Mm.133268	NM_153565	ENSMUSG00000044254	Pcsk9	AI415265|AI747682|FH3|HCHOLA3|Narc1|PC9	proprotein convertase subtilisin/kexin type 9	protein-coding	0	0.336634
Merged-chr4-93577934-1	chr4	93577884	93577984	+	2.1	cIP1vsInput	Intergenic	Intergenic	-242423	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding	0	0.29703
Merged-chr5-18109931-1	chr5	18109881	18109981	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	147361	NM_001081143	242851	Mm.332230	NM_001081143	ENSMUSG00000028777	Gnat3	Ggust|Gtn	"guanine nucleotide binding protein, alpha transducing 3"	protein-coding	0	0.29703
Merged-chr1-66552878-1	chr1	66552828	66552928	+	2.1	cIP2vsInput	"intron (NM_175510, intron 21 of 64)"	"intron (NM_175510, intron 21 of 64)"	84431	NM_175510	329178	Mm.44798	NM_175510	ENSMUSG00000055567	Unc80	C030018G13Rik|C230061B10Rik|UNC-80	unc-80 homolog (C. elegans)	protein-coding	0.01	0.405941
Merged-chr10-30812107-1	chr10	30812057	30812157	+	2.1	cIP1vsInput	Intergenic	Intergenic	-9000	NM_172495	211329	Mm.297903	NM_001111267	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding	0	0.346535
Merged-chr3-72518437-1	chr3	72518387	72518487	+	2.1	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	448429	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding	0	0.306931
Merged-chr1-97647592-1	chr1	97647542	97647642	+	2.1	cIP1vsInput	"intron (NM_133825, intron 2 of 2)"	"intron (NM_133825, intron 2 of 2)"	14426	NM_133825	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	"DNA segment, Chr 1, ERATO Doi 622, expressed"	protein-coding	0	0.306931
Merged-chr10-103664297-1	chr10	103664247	103664347	+	2.1	cIP1vsInput	Intergenic	Intergenic	296489	NM_175328	103098	Mm.458408	NM_001252330	ENSMUSG00000019894	Slc6a15	AA536730|AI326450|AI326451|v7-3	"solute carrier family 6 (neurotransmitter transporter), member 15"	protein-coding	0	0.306931
Merged-chr7-86255710-1	chr7	86255660	86255760	+	2.1	cIP2vsInput	Intergenic	Lx4A|LINE|L1	-9509	NM_001102580	675969	Mm.469834	NM_001102580	ENSMUSG00000091239	Vmn2r76	-	"vomeronasal 2, receptor 76"	protein-coding	0.01	0.346535
Merged-chr16-67442213-1	chr16	67442163	67442263	+	2.1	cIP2vsInput	"intron (NM_178721, intron 1 of 9)"	"intron (NM_178721, intron 1 of 9)"	178695	NM_001145977	239857	Mm.394300	NM_001145977	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0	0.287129
Merged-chr5-55100913-1	chr5	55100863	55100963	+	2.1	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	750921	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0	0.356436
Merged-chr2-150201825-1	chr2	150201775	150201875	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-16274	NM_001142411	245174	Mm.378428	NM_001142411		Zfp937	EG245174|Gm4979|ZIPO-I	zinc finger protein 937	protein-coding	0	0.306931
Merged-chr5-12516335-1	chr5	12516285	12516385	+	2.1	cIP1vsInput	"intron (NM_028882, intron 7 of 17)"	"intron (NM_028882, intron 7 of 17)"	133169	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	"sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D"	protein-coding	0	0.366337
Merged-chr1-102530965-1	chr1	102530915	102531015	+	2.1	cIP2vsInput	Intergenic	Intergenic	1375197	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.287129
Merged-chr6-78362514-1	chr6	78362464	78362564	+	2.1	cIP1vsInput	Intergenic	Intergenic	-8371	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding	0	0.39604
Merged-chrX-150477975-1	chrX	150477925	150478025	+	2.1	cIP1vsInput	Intergenic	Intergenic	-18825	NM_001164683	382245	Mm.277309	NM_001164683	ENSMUSG00000041353	Tmem29	2700081K05Rik|6330540D07Rik|CXorf44-like	transmembrane protein 29	protein-coding	0.01	0.405941
Merged-chr3-159189679-1	chr3	159189629	159189729	+	2.1	cIP1vsInput	"intron (NR_040750, intron 2 of 4)"	L1Md_F2|LINE|L1	113315	NR_040750	624759	Mm.491054	NR_040750		Gm20752	-	"predicted gene, 20752"	miscRNA	0	0.316832
Merged-chr5-129769591-1	chr5	129769541	129769641	+	2.1	cIP1vsInput	"intron (NM_133900, intron 5 of 7)"	"intron (NM_133900, intron 5 of 7)"	17662	NM_133900	100678	Mm.271784	NM_133900	ENSMUSG00000029446	Psph	AI480570|PSP|PSPase	phosphoserine phosphatase	protein-coding	0.01	0.346535
Merged-chr17-21819821-1	chr17	21819771	21819871	+	2.1	cIP1vsInput	"exon (NM_029281, exon 5 of 5)"	"exon (NM_029281, exon 5 of 5)"	25938	NM_029281	75424	Mm.271252	NM_029281	ENSMUSG00000069743	Zfp820	2610036F08Rik	zinc finger protein 820	protein-coding	0	0.316832
Merged-chr3-62293360-1	chr3	62293310	62293410	+	2.1	cIP1vsInput	Intergenic	Lx5|LINE|L1	-45417	NM_001081295	622434		NM_001081295	ENSMUSG00000036885	Arhgef26	4631416L12Rik|8430436L14Rik|AI303572|AW491953|SGEF	Rho guanine nucleotide exchange factor (GEF) 26	protein-coding	0	0.306931
Merged-chr3-140234004-1	chr3	140233954	140234054	+	2.1	cIP2vsInput	Intergenic	Intergenic	978351	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0.01	0.415842
Merged-chr14-17990538-1	chr14	17990488	17990588	+	2.1	cIP1vsInput	"intron (NM_009380, intron 1 of 6)"	"intron (NM_009380, intron 1 of 6)"	8894	NM_009380	21834	Mm.32563	NM_001113417	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding	0.01	0.366337
Merged-chr15-68697903-1	chr15	68697853	68697953	+	2.1	cIP2vsInput	Intergenic	Intergenic	-230517	NM_010158	13992	Mm.17964	NM_010158	ENSMUSG00000022332	Khdrbs3	Etle|SLM-2|Slm2|T-STAR	"KH domain containing, RNA binding, signal transduction associated 3"	protein-coding	0	0.376238
Merged-chr2-20478591-1	chr2	20478541	20478641	+	2.1	cIP2vsInput	"intron (NM_001081006, intron 2 of 21)"	"intron (NM_001081006, intron 2 of 21)"	-31456	NM_029895	208618	Mm.237935	NM_001081006	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding	0.01	0.366337
Merged-chr5-19646877-1	chr5	19646827	19646927	+	2.1	cIP2vsInput	"intron (NM_001170746, intron 1 of 22)"	L1_Mur2|LINE|L1	-260641	NM_001170745	50791	Mm.441283	NM_001170745	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	"membrane associated guanylate kinase, WW and PDZ domain containing 2"	protein-coding	0	0.29703
Merged-chr3-5595335-1	chr3	5595285	5595385	+	2.1	cIP2vsInput	Intergenic	Intergenic	-19087	NM_001163305	19302	Mm.132336	NM_001163304	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding	0.01	0.386139
Merged-chr10-107197998-1	chr10	107197948	107198048	+	2.1	cIP2vsInput	Intergenic	Intergenic	-73833	NM_001039354	108030	Mm.268025	NM_001033223	ENSMUSG00000019906	Lin7a	AI848705|LIN-7A|MALS-1|TIP-33|Veli|Veli1	lin-7 homolog A (C. elegans)	protein-coding	0	0.306931
Merged-chr6-147912963-1	chr6	147912913	147913013	+	2.1	cIP1vsInput	Intergenic	Intergenic	-134453	NM_178797	330450	Mm.475174	NM_178797	ENSMUSG00000030303	Far2	A230046P18|AW048109|BC055759|Mlstd1	fatty acyl CoA reductase 2	protein-coding	0	0.366337
Merged-chr15-44321512-1	chr15	44321462	44321562	+	2.1	cIP1vsInput	Intergenic	Charlie2a|DNA|hAT-Charlie	-106599	NM_175009	223527	Mm.490404	NM_175009	ENSMUSG00000022338	Eny2	1810057B09Rik|6720481I12|DC6|Ey2	enhancer of yellow 2 homolog (Drosophila)	protein-coding	0	0.326733
Merged-chr6-75019624-1	chr6	75019574	75019674	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1549957	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0.01	0.336634
Merged-chr9-60541531-1	chr9	60541481	60541581	+	2.1	cIP1vsInput	"intron (NR_040463, intron 2 of 4)"	"intron (NR_040463, intron 2 of 4)"	4351	NR_040464	100504561	Mm.410770	NR_040463		9230112J17Rik	-	RIKEN cDNA 9230112J17 gene	miscRNA	0	0.356436
Merged-chr1-181291470-1	chr1	181291420	181291520	+	2.1	cIP1vsInput	Intergenic	Intergenic	-61158	NM_028408	72978	Mm.338083	NM_001160211	ENSMUSG00000026514	Cnih3	2900075G08Rik	cornichon homolog 3 (Drosophila)	protein-coding	0.01	0.376238
Merged-chr18-31257285-1	chr18	31257235	31257335	+	2.1	cIP2vsInput	"intron (NM_009065, intron 1 of 4)"	"intron (NM_009065, intron 1 of 4)"	59843	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding	0	0.346535
Merged-chr16-78997704-1	chr16	78997654	78997754	+	2.1	cIP1vsInput	"intron (NM_178855, intron 18 of 26)"	"intron (NM_178855, intron 18 of 26)"	66756	NM_139134	246048	Mm.77895	NM_139134	ENSMUSG00000022860	Chodl	3110074E07Rik|MT75|PRED12	chondrolectin	protein-coding	0.01	0.326733
Merged-chr13-67191798-1	chr13	67191748	67191848	+	2.1	cIP1vsInput	Intergenic	MTE2b|LTR|ERVL-MaLR	-2708	NM_001048204	218311	Mm.82396	NM_183156	ENSMUSG00000051037	Zfp455	3732412P20Rik|Rslcan-10	zinc finger protein 455	protein-coding	0	0.316832
Merged-chr15-15430890-1	chr15	15430840	15430940	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1347211	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0.01	0.336634
Merged-chrX-157844372-1	chrX	157844322	157844422	+	2.1	cIP1vsInput	"intron (NM_177751, intron 20 of 21)"	"intron (NM_177751, intron 20 of 21)"	25937	NM_001081667	245683	Mm.295846	NM_001081667	ENSMUSG00000047485	Klhl34	Gm388	kelch-like 34	protein-coding	0.01	0.316832
Merged-chr1-33830952-1	chr1	33830902	33831002	+	2.1	cIP1vsInput	Intergenic	RLTR9A3A|LTR|ERVK	7962	NM_001161816	433287	Mm.383632	NM_001161816		Gm15455	AA692849|OTTMUSG00000022109	predicted gene 15455	protein-coding	0.02	0.50495
Merged-chr19-50259192-1	chr19	50259142	50259242	+	2.1	cIP1vsInput	"intron (NM_001252501, intron 8 of 25)"	"intron (NM_001252501, intron 8 of 25)"	419454	NM_001252501	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0.02	0.435644
Merged-chr17-6629818-1	chr17	6629768	6629868	+	2.1	cIP1vsInput	Intergenic	Intergenic	-8893	NR_028305	100040525	Mm.472852	NR_028305		Tmem181c-ps	100040596|ENSMUSG00000079729|ENSMUSG00000079731|Tmem181d-ps	"transmembrane protein 181C, pseudogene"	pseudo	0.03	0.376238
Merged-chrX-105869871-1	chrX	105869821	105869921	+	2.1	cIP1vsInput	"intron (NM_009530, intron 9 of 34)"	B1F1|SINE|Alu	59501	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked homolog (human)	protein-coding	0	0.405941
Merged-chr8-104669648-1	chr8	104669598	104669698	+	2.1	cIP2vsInput	Intergenic	Lx6|LINE|L1	-27920	NM_026753	68523	Mm.279	NM_026753	ENSMUSG00000031879	Fam96b	1110019N10Rik	"family with sequence similarity 96, member B"	protein-coding	0	0.346535
Merged-chr1-8761784-1	chr1	8761734	8761834	+	2.1	cIP2vsInput	"intron (NM_027671, intron 6 of 20)"	Lx5c|LINE|L1	537946	NM_027671	71096	Mm.388998	NM_027671		Sntg1	4933426D16Rik|G1SYN|SYN4	"syntrophin, gamma 1"	protein-coding	0	0.336634
Merged-chr12-115497479-1	chr12	115497429	115497529	+	2.1	cIP2vsInput	Intergenic	Intergenic	-550245	NM_001004066	56220	Mm.254997	NM_001004066	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding	0.01	0.39604
Merged-chr1-81190532-1	chr1	81190482	81190582	+	2.1	cIP2vsInput	"intron (NM_172849, intron 2 of 4)"	"intron (NM_172849, intron 2 of 4)"	113215	NM_172849	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding	0	0.366337
Merged-chr18-13384139-1	chr18	13384089	13384189	+	2.1	cIP1vsInput	Intergenic	Intergenic	377149	NM_153087	225192	Mm.207073	NM_153087	ENSMUSG00000037346	Hrh4	AXOR35|BG26|GPCR105|GPRv53|H4|H4R|HH4R	histamine receptor H4	protein-coding	0	0.287129
Merged-chr4-98632618-1	chr4	98632568	98632668	+	2.1	cIP1vsInput	"intron (NM_001005787, intron 5 of 15)"	"intron (NM_001005787, intron 5 of 15)"	85984	NM_001005787	12695	Mm.90218	NM_001005784	ENSMUSG00000061859	Inadl	Cipp|Patj	InaD-like (Drosophila)	protein-coding	0.01	0.356436
Merged-chr5-136136121-1	chr5	136136071	136136171	+	2.1	cIP2vsInput	promoter-TSS (NM_027891)	promoter-TSS (NM_027891)	-47	NM_027891	71735	Mm.425292	NM_027891	ENSMUSG00000029703	Lrwd1	1200011O22Rik|AU042569|AW548074|Orca	leucine-rich repeats and WD repeat domain containing 1	protein-coding	0.09	0.623762
Merged-chr6-113193912-1	chr6	113193862	113193962	+	2.1	cIP1vsInput	"exon (NM_177763, exon 2 of 4)"	"exon (NM_177763, exon 2 of 4)"	1472	NM_177763	269788	Mm.37943	NM_177763	ENSMUSG00000042873	Lhfpl4	1190004M23Rik|AI604880|B230384L07|mKIAA4027	lipoma HMGIC fusion partner-like protein 4	protein-coding	0.07	0.564356
Merged-chr13-85416708-1	chr13	85416658	85416758	+	2.1	cIP1vsInput	Intergenic	Intergenic	-127222	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding	0.01	0.39604
Merged-chrX-36817331-1	chrX	36817281	36817381	+	2.1	cIP1vsInput	Intergenic	Intergenic	21679	NM_007451	11740	Mm.371544	NM_007451	ENSMUSG00000016319	Slc25a5	Ant2	"solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 5"	protein-coding	0	0.534653
Merged-chr9-45146207-1	chr9	45146157	45146257	+	2.1	cIP2vsInput	"intron (NM_001013390, intron 1 of 4)"	"intron (NM_001013390, intron 1 of 4)"	7165	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	"sodium channel, type IV, beta"	protein-coding	0.03	0.584158
Merged-chr16-39769192-1	chr16	39769142	39769242	+	2.1	cIP1vsInput	Intergenic	Intergenic	866847	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	"immunoglobulin superfamily, member 11"	protein-coding	0	0.356436
Merged-chr3-111873668-1	chr3	111873618	111873718	+	2.1	cIP1vsInput	Intergenic	Intergenic	-8235	NR_045362	625585	Mm.389497	NR_045362		Gm6602	-	predicted gene 6602	miscRNA	0	0.267327
Merged-chr1-135670576-1	chr1	135670526	135670626	+	2.1	cIP2vsInput	Intergenic	Intergenic	-58621	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding	0.04	0.633663
Merged-chr3-34342437-1	chr3	34342387	34342487	+	2.1	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	-217944	NR_015580	320478	Mm.444063	NR_015580		Sox2ot	B230215L15Rik	SOX2 overlapping transcript (non-protein coding)	miscRNA	0	0.336634
Merged-chr4-89916926-1	chr4	89916876	89916976	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	228728	NM_175647	242523	Mm.130167	NM_175647	ENSMUSG00000043753	Dmrta1	Dmrt4	doublesex and mab-3 related transcription factor like family A1	protein-coding	0	0.376238
Merged-chr1-193475003-1	chr1	193474953	193475053	+	2.1	cIP1vsInput	Intergenic	Intergenic	32527	NR_029592	387201		NR_029592	ENSMUSG00000065533	Mir205	Mirn205|mmu-mir-205	microRNA 205	miscRNA	0	0.336634
Merged-chr8-32947280-1	chr8	32947230	32947330	+	2.1	cIP1vsInput	"intron (NM_001177589, intron 1 of 3)"	"intron (NM_001177589, intron 1 of 3)"	2746	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding	0.01	0.316832
Merged-chr13-78310479-1	chr13	78310429	78310529	+	2.1	cIP1vsInput	Intergenic	L1M3|LINE|L1	-111497	NM_010151	13865	Mm.439653	NM_010151		Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR3|Erbal3|SVP44|Tcfcoup1	"nuclear receptor subfamily 2, group F, member 1"	protein-coding	0	0.306931
Merged-chr7-101412848-1	chr7	101412798	101412898	+	2.1	cIP1vsInput	TTS (NM_027180)	TTS (NM_027180)	-8843	NM_001008548	207728	Mm.247564	NM_001008548	ENSMUSG00000030653	Pde2a	CGS-PDE|cGSPDE	"phosphodiesterase 2A, cGMP-stimulated"	protein-coding	0	0.534653
Merged-chr10-103802749-1	chr10	103802699	103802799	+	2.1	cIP2vsInput	Intergenic	RLTR15|LTR|ERVK	-340238	NM_001177535	100043292	Mm.339215	NM_001177535	ENSMUSG00000090854	Gm4340	-	predicted gene 4340	protein-coding	0.02	0.287129
Merged-chr15-18134499-1	chr15	18134449	18134549	+	2.1	cIP1vsInput	"intron (NR_045711, intron 9 of 11)"	"intron (NR_045711, intron 9 of 11)"	235128	NR_045711	70886	Mm.399021	NR_045711		4921515E04Rik	-	RIKEN cDNA 4921515E04 gene	miscRNA	0	0.287129
Merged-chr3-119411143-1	chr3	119411093	119411193	+	2.1	cIP1vsInput	"intron (NM_170778, intron 20 of 22)"	"intron (NM_170778, intron 20 of 22)"	372245	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.01	0.445545
Merged-chr13-17466688-1	chr13	17466638	17466738	+	2.1	cIP1vsInput	"intron (NM_138654, intron 8 of 13)"	Lx9|LINE|L1	228077	NM_138654	192136	Mm.364180	NM_138654		5033411D12Rik	D17907	RIKEN cDNA 5033411D12 gene	protein-coding	0	0.287129
Merged-chr8-107529624-1	chr8	107529574	107529674	+	2.1	cIP1vsInput	"intron (NM_025830, intron 8 of 23)"	"intron (NM_025830, intron 8 of 23)"	-21620	NR_029553	387158		NR_029553		Mir140	Mirn140|mmu-mir-140	microRNA 140	miscRNA	0.01	0.336634
Merged-chr18-58612299-1	chr18	58612249	58612349	+	2.1	cIP2vsInput	"exon (NM_001081072, exon 10 of 10)"	"exon (NM_001081072, exon 10 of 10)"	-47183	NM_025478	66307	Mm.182574	NM_025478	ENSMUSG00000024601	Isoc1	2610034N03Rik	isochorismatase domain containing 1	protein-coding	0.02	0.326733
Merged-chr8-98144675-1	chr8	98144625	98144725	+	2.1	cIP1vsInput	Intergenic	Intergenic	1271782	NM_007667	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.247525
Merged-chr11-69444577-1	chr11	69444527	69444627	+	2.1	cIP2vsInput	"intron (NM_001081330, intron 63 of 85)"	ORR1C2|LTR|ERVL-MaLR	-30902	NM_001017426	216850	Mm.472522	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding	0	0.306931
Merged-chr2-83305663-1	chr2	83305613	83305713	+	2.1	cIP1vsInput	Intergenic	Intergenic	-338915	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding	0	0.356436
Merged-chr11-41167327-1	chr11	41167277	41167377	+	2.1	cIP2vsInput	Intergenic	Intergenic	-412041	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding	0	0.316832
Merged-chr4-60508522-1	chr4	60508472	60508572	+	2.1	cIP1vsInput	Intergenic	RMER16-int|LTR|ERVK	-6562	NM_001163010	17840	Mm.482072	NM_001163010	ENSMUSG00000078683	Mup1	Ltn-1|Lvtn-1|Mup-1|Mup-a|Mup10|Mup7|Up-1	major urinary protein 1	protein-coding	0.02	0.366337
Merged-chr4-24688051-1	chr4	24688001	24688101	+	2.1	cIP1vsInput	"intron (NM_001033531, intron 4 of 9)"	"intron (NM_001033531, intron 4 of 9)"	163035	NM_001163020	212390	Mm.412074	NM_001033531	ENSMUSG00000040387	Klhl32	6430524H05Rik|D4Ertd389e|Gm1356|mKIAA1900	kelch-like 32	protein-coding	0.01	0.326733
Merged-chr18-16865111-1	chr18	16865061	16865161	+	2.1	cIP1vsInput	Intergenic	Intergenic	48704	NR_045399	328906	Mm.136064	NR_045399	ENSMUSG00000086095	Gm15328	D830029L11|OTTMUSG00000020196	predicted gene 15328	miscRNA	0	0.237624
Merged-chr1-7767879-1	chr1	7767829	7767929	+	2.1	cIP2vsInput	Intergenic	Intergenic	678959	NM_183028	319263		NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0	0.326733
Merged-chr4-25169787-1	chr4	25169737	25169837	+	2.1	cIP1vsInput	Intergenic	Intergenic	73089	NM_021318	57756	Mm.87325	NM_021318	ENSMUSG00000028259	Fhl5	1700027G07Rik|Act	four and a half LIM domains 5	protein-coding	0	0.376238
Merged-chr12-64402515-1	chr12	64402465	64402565	+	2.1	cIP2vsInput	Intergenic	Intergenic	72383	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.376238
Merged-chrX-11028254-1	chrX	11028204	11028304	+	2.1	cIP2vsInput	Intergenic	L1M4c|LINE|L1	-271003	NM_001111037	100042922	Mm.374311	NM_001111037	ENSMUSG00000095208	Gm14483	OTTMUSG00000016789	predicted gene 14483	protein-coding	0.01	0.287129
Merged-chr4-57184690-1	chr4	57184640	57184740	+	2.1	cIP1vsInput	Intergenic	PB1D10|SINE|Alu	12619	NR_040669	329851	Mm.392470	NR_040669	ENSMUSG00000085967	Gm12530	D730003B17|OTTMUSG00000007337	predicted gene 12530	miscRNA	0.01	0.445545
Merged-chr5-32600978-1	chr5	32600928	32601028	+	2.1	cIP1vsInput	Intergenic	Intergenic	-10193	NM_001205133	22612	Mm.4558	NM_001205132	ENSMUSG00000014932	Yes1	Yes|p61-Yes	Yamaguchi sarcoma viral (v-yes) oncogene homolog 1	protein-coding	0	0.376238
Merged-chr10-5084291-1	chr10	5084241	5084341	+	2.1	cIP2vsInput	"intron (NM_001079686, intron 36 of 54)"	"intron (NM_001079686, intron 36 of 54)"	-15228	NM_022027	64009	Mm.331626	NM_001079686	ENSMUSG00000019769	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756	"spectrin repeat containing, nuclear envelope 1"	protein-coding	0	0.306931
Merged-chr14-82804617-1	chr14	82804567	82804667	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1638946	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0	0.306931
Merged-chr18-68597571-1	chr18	68597521	68597621	+	2.1	cIP2vsInput	Intergenic	Intergenic	-168251	NM_001271716	17200	Mm.426053	NM_001271716	ENSMUSG00000045569	Mc2r	ACTH-R|ACTHR|MC2-R	melanocortin 2 receptor	protein-coding	0.02	0.386139
Merged-chr1-153557466-1	chr1	153557416	153557516	+	2.1	cIP2vsInput	Intergenic	Intergenic	-7752	NM_028749	74091	Mm.24887	NM_028749	ENSMUSG00000042684	Npl	0610033B02Rik	N-acetylneuraminate pyruvate lyase	protein-coding	0	0.465347
Merged-chr5-37605801-1	chr5	37605751	37605851	+	2.1	cIP1vsInput	"intron (NM_022416, intron 3 of 11)"	L1_Mur3|LINE|L1	111352	NM_022416	64293	Mm.103714	NM_022416	ENSMUSG00000029123	Stk32b	2510009F08Rik|STKG6|Stk32|YANK2	serine/threonine kinase 32B	protein-coding	0	0.346535
Merged-chr1-68633035-1	chr1	68632985	68633085	+	2.1	cIP1vsInput	"intron (NM_010154, intron 2 of 26)"	"intron (NM_010154, intron 2 of 26)"	475024	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0	0.306931
Merged-chr17-17205412-1	chr17	17205362	17205462	+	2.1	cIP2vsInput	Intergenic	MurSatRep1|Unknown|Unknown	84029	NM_011765	22759	Mm.436633	NM_011765	ENSMUSG00000095990	Zfp97	NGD16-4	zinc finger protein 97	protein-coding	0	0.386139
Merged-chr6-141625439-1	chr6	141625389	141625489	+	2.1	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-4079	NM_020495	28253	Mm.272223	NM_020495	ENSMUSG00000030236	Slco1b2	7330442B20Rik|OATP-C|OATP2|Oatp1b2|Oatp4|Slc21a10|Slc21a6|lst-1|mlst-1	"solute carrier organic anion transporter family, member 1b2"	protein-coding	0	0.326733
Merged-chr3-18073280-1	chr3	18073230	18073330	+	2.1	cIP2vsInput	"intron (NM_007825, intron 5 of 5)"	"intron (NM_007825, intron 5 of 5)"	18955	NM_021560	59058	Mm.149938	NM_021560	ENSMUSG00000025128	Bhlhe22	Beta3|Bhlhb5	"basic helix-loop-helix family, member e22"	protein-coding	0	0.386139
Merged-chr14-120123683-1	chr14	120123633	120123733	+	2.1	cIP2vsInput	Intergenic	L1ME1|LINE|L1	-81248	NM_001001490	239283	Mm.138520	NM_001001490	ENSMUSG00000044819	Oxgr1	Gm299|Gpr80|Gpr99|P2Y15	oxoglutarate (alpha-ketoglutarate) receptor 1	protein-coding	0.01	0.316832
Merged-chr18-19552141-1	chr18	19552091	19552191	+	2.1	cIP2vsInput	Intergenic	Intergenic	449956	NM_007882	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding	0.01	0.455446
Merged-chr1-112984733-1	chr1	112984683	112984783	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1119815	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik	dermatan sulfate epimerase-like	protein-coding	0	0.356436
Merged-chr1-164745157-1	chr1	164745107	164745207	+	2.1	cIP2vsInput	Intergenic	Intergenic	-51575	NM_019759	56429	Mm.28935	NM_019759	ENSMUSG00000026574	Dpt	1810032B19Rik|5033416F05Rik|EQ-1|Eq1	dermatopontin	protein-coding	0	0.455446
Merged-chr3-134293146-1	chr3	134293096	134293196	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-52563	NR_035435	100316832		NR_035435	ENSMUSG00000084564	Mir1895	Mirn1895|mmu-mir-1895	microRNA 1895	miscRNA	0.01	0.316832
Merged-chr3-155323335-1	chr3	155323285	155323385	+	2.1	cIP1vsInput	Intergenic	L2c|LINE|L2	229901	NM_028938	74435	Mm.195711	NM_028938	ENSMUSG00000028182	Lrriq3	4930438B07Rik|4930511J15Rik|4933403H06Rik|BB020367|Lrrc44	leucine-rich repeats and IQ motif containing 3	protein-coding	0	0.346535
Merged-chr6-43945296-1	chr6	43945246	43945346	+	2.1	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-279121	NM_013861	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding	0.01	0.356436
Merged-chr1-93113577-1	chr1	93113527	93113627	+	2.1	cIP1vsInput	Intergenic	Intergenic	-11712	NM_001110315	16560	Mm.276408	NM_001110315	ENSMUSG00000014602	Kif1a	ATSV|C630002N23Rik|Gm1626|Kns1	kinesin family member 1A	protein-coding	0	0.366337
Merged-chr4-136416358-1	chr4	136416308	136416408	+	2.1	cIP2vsInput	Intergenic	Intergenic	-7166	NM_008309	15552	Mm.40573	NM_008309	ENSMUSG00000070687	Htr1d	AI853647|Gpcr14|Htr1db	5-hydroxytryptamine (serotonin) receptor 1D	protein-coding	0.04	0.544554
Merged-chr10-22155226-1	chr10	22155176	22155276	+	2.1	cIP1vsInput	Intergenic	Intergenic	-3383	NM_009016	19368	Mm.458004	NM_009016		Raet1a	RAE-1alpha|Rae1alpha|Raet1	"retinoic acid early transcript 1, alpha"	protein-coding	0.01	0.336634
Merged-chr10-59197740-1	chr10	59197690	59197790	+	2.1	cIP1vsInput	"intron (NM_001024910, intron 1 of 9)"	"intron (NM_001024910, intron 1 of 9)"	24107	NM_001024911	103080	Mm.397041	NM_001024910	ENSMUSG00000019917	10-Sep	4921515A04Rik|9430099J10Rik|AA408298|AI874685	septin 10	protein-coding	0	0.257426
Merged-chr4-5546138-1	chr4	5546088	5546188	+	2.1	cIP2vsInput	Intergenic	Intergenic	-86190	NR_038183	73872	Mm.427301	NR_038183	ENSMUSG00000086066	4930423M02Rik	-	RIKEN cDNA 4930423M02 gene	miscRNA	0.01	0.366337
Merged-chr10-115969251-1	chr10	115969201	115969301	+	2.1	cIP1vsInput	Intergenic	Intergenic	-49112	NM_011217	19279	Mm.336316	NM_001161837	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	"protein tyrosine phosphatase, receptor type, R"	protein-coding	0	0.366337
Merged-chr3-74843281-1	chr3	74843231	74843331	+	2.1	cIP2vsInput	Intergenic	Intergenic	300442	NM_172515	213234	Mm.80075	NM_172515	ENSMUSG00000034151	Zbbx	4931432L23	"zinc finger, B-box domain containing"	protein-coding	0.03	0.346535
Merged-chr3-106043897-1	chr3	106043847	106043947	+	2.1	cIP1vsInput	Intergenic	Intergenic	-29251	NM_001200028	100503311	Mm.386825	NM_001200028	ENSMUSG00000010136	Pifo	1700027A23Rik	primary cilia formation	protein-coding	0	0.29703
Merged-chr6-60211650-1	chr6	60211600	60211700	+	2.1	cIP1vsInput	Intergenic	L1VL4|LINE|L1	192057	NR_015565	208079	Mm.490691	NR_015565		A530053G22Rik	-	RIKEN cDNA A530053G22 gene	miscRNA	0	0.306931
Merged-chr10-55583913-1	chr10	55583863	55583963	+	2.1	cIP1vsInput	Intergenic	Intergenic	-523004	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding	0	0.405941
Merged-chr13-16000208-1	chr13	16000158	16000258	+	2.1	cIP1vsInput	Intergenic	L1VL2|LINE|L1	-14267	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding	0	0.29703
Merged-chr1-174109154-1	chr1	174109104	174109204	+	2.1	cIP2vsInput	Intergenic	Intergenic	8860	NM_001005520	404222	Mm.457873	NM_001005520	ENSMUSG00000046486	Olfr231	MOR105-4|Olfr231-ps1|Olfr244|Olfr244-ps1|Olfr425|Olfr425-ps1	olfactory receptor 231	protein-coding	0	0.29703
Merged-chr17-30630028-1	chr17	30629978	30630078	+	2.1	cIP1vsInput	"intron (NM_013811, intron 1 of 92)"	"intron (NM_013811, intron 1 of 92)"	3092	NM_013811	13417	Mm.446558	NM_013811	ENSMUSG00000033826	Dnahc8	ATPase|Hst6.7b|P1-Loop	"dynein, axonemal, heavy chain 8"	protein-coding	0	0.267327
Merged-chr10-56263977-1	chr10	56263927	56264027	+	2.1	cIP1vsInput	Intergenic	Intergenic	-35288	NM_001033385	544696	Mm.411188	NM_001033385	ENSMUSG00000038122	D630037F22Rik	Bromi	RIKEN cDNA D630037F22 gene	protein-coding	0	0.29703
Merged-chr17-42221281-1	chr17	42221231	42221331	+	2.1	cIP1vsInput	Intergenic	Intergenic	-94666	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding	0	0.336634
Merged-chr10-78185015-1	chr10	78184965	78185065	+	2.1	cIP2vsInput	"intron (NM_029546, intron 1 of 20)"	CpG	134	NM_029546	110816	Mm.103522	XM_003946427	ENSMUSG00000032834	Pwp2	6530411D08Rik|Pwp2h|wdp103	PWP2 periodic tryptophan protein homolog (yeast)	protein-coding	0.11	0.683168
Merged-chr2-32382026-1	chr2	32381976	32382076	+	2.1	cIP1vsInput	promoter-TSS (NM_198001)	promoter-TSS (NM_198001)	-111	NM_198001	73737	Mm.27608	NM_198001	ENSMUSG00000039195	1110008P14Rik	C79326|RP23-161B9.10	RIKEN cDNA 1110008P14 gene	protein-coding	0.1	0.70297
Merged-chr4-89622458-1	chr4	89622408	89622508	+	2.1	cIP1vsInput	Intergenic	Intergenic	-65740	NM_175647	242523	Mm.130167	NM_175647	ENSMUSG00000043753	Dmrta1	Dmrt4	doublesex and mab-3 related transcription factor like family A1	protein-coding	0	0.257426
Merged-chr9-92870911-1	chr9	92870861	92870961	+	2.1	cIP1vsInput	Intergenic	Intergenic	134822	NR_040756	78349	Mm.52612	NR_040756		1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	miscRNA	0	0.336634
Merged-chr5-35793112-1	chr5	35793062	35793162	+	2.1	cIP2vsInput	"intron (NM_001177700, intron 1 of 16)"	"intron (NM_001177700, intron 1 of 16)"	35232	NM_177678	231148	Mm.254446	NM_001177696	ENSMUSG00000029095	Ablim2	AI606905|C230091L11	actin-binding LIM protein 2	protein-coding	0.02	0.485149
Merged-chr6-7574765-1	chr6	7574715	7574815	+	2.1	cIP1vsInput	Intergenic	Lx2|LINE|L1	19694	NM_009311	21333	Mm.410823	NM_009311	ENSMUSG00000061762	Tac1	4930528L02Rik|NK-1|NK1|Nkna|PPT-A|PPTA|SP	tachykinin 1	protein-coding	0	0.39604
Merged-chr1-179182933-1	chr1	179182883	179182983	+	2.1	cIP1vsInput	"intron (NM_027188, intron 5 of 11)"	"intron (NM_027188, intron 5 of 11)"	335070	NM_027188	69726	Mm.222338	NM_027188		Smyd3	2410008A19Rik|Zmynd1	SET and MYND domain containing 3	protein-coding	0.01	0.346535
Merged-chr7-120485585-1	chr7	120485535	120485635	+	2.1	cIP1vsInput	"intron (NR_024051, intron 15 of 29)"	Lx8b|LINE|L1	63884	NR_024051	233810	Mm.334203	NM_207130	ENSMUSG00000051900	Abca16	AY243472	"ATP-binding cassette, sub-family A (ABC1), member 16"	protein-coding	0.01	0.306931
Merged-chr13-65339854-1	chr13	65339804	65339904	+	2.1	cIP1vsInput	Intergenic	MurSatRep1|Unknown|Unknown	61000	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding	0.01	0.326733
Merged-chr8-32565798-1	chr8	32565748	32565848	+	2.1	cIP1vsInput	Intergenic	Intergenic	384228	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding	0	0.277228
Merged-chr11-29668611-1	chr11	29668561	29668661	+	2.1	cIP1vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	-24287	NM_194053	68585	Mm.488364	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding	0.01	0.336634
Merged-chr1-35288769-1	chr1	35288719	35288819	+	2.1	cIP1vsInput	Intergenic	L1MD2|LINE|L1	438810	NM_145516	226971	Mm.292751	NM_145516	ENSMUSG00000026123	Plekhb2	2310009M15Rik|AU018239|Evt2|Phdc|evt-2	"pleckstrin homology domain containing, family B (evectins) member 2"	protein-coding	0	0.29703
Merged-chr10-46986843-1	chr10	46986793	46986893	+	2.1	cIP1vsInput	Intergenic	MTD|LTR|ERVL-MaLR	742094	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0.01	0.316832
Merged-chr5-110149093-1	chr5	110149043	110149143	+	2.1	cIP1vsInput	"intron (NM_172717, intron 7 of 17)"	"intron (NM_172717, intron 7 of 17)"	13253	NM_172717	231600	Mm.30264	NM_172717	ENSMUSG00000014668	Chfr	5730484M20Rik|C230082M18|RNF116	checkpoint with forkhead and ring finger domains	protein-coding	0	0.247525
Merged-chr6-97740266-1	chr6	97740216	97740316	+	2.1	cIP2vsInput	Intergenic	Intergenic	-66792	NM_001113198	17342	Mm.454504	NM_001113198	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding	0.02	0.366337
Merged-chr4-102045885-1	chr4	102045835	102045935	+	2.1	cIP2vsInput	Intergenic	Intergenic	59045	NM_001085520	381536	Mm.297685	NM_001085520		Gm12789	OTTMUSG00000008445	predicted gene 12789	protein-coding	0	0.356436
Merged-chr13-98168572-1	chr13	98168522	98168622	+	2.1	cIP1vsInput	"intron (NM_012026, intron 1 of 35)"	"intron (NM_012026, intron 1 of 35)"	37593	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding	0	0.356436
Merged-chr1-22706600-1	chr1	22706550	22706650	+	2.1	cIP1vsInput	"intron (NM_001012623, intron 2 of 14).2"	MER63D|DNA|hAT-Blackjack	99124	NM_001012625	116837	Mm.461684	NM_001012623		Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding	0	0.356436
Merged-chrX-52165432-1	chrX	52165382	52165482	+	2.1	cIP2vsInput	promoter-TSS (NM_008150)	promoter-TSS (NM_008150)	-509	NM_008150	14735	Mm.478164	NM_008150	ENSMUSG00000031119	Gpc4	9530073D23Rik|AF311610|AI385680|AI661372|K-glypican	glypican 4	protein-coding	0.08	0.732673
Merged-chr5-56199839-1	chr5	56199789	56199889	+	2.1	cIP1vsInput	Intergenic	L1_Mus4|LINE|L1	1518080	NR_015588	319216	Mm.446765	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	miscRNA	0	0.336634
Merged-chr7-23327623-1	chr7	23327573	23327673	+	2.1	cIP1vsInput	"intron (NM_001004194, intron 2 of 8)"	ETnERV3-int|LTR|ERVK	26431	NM_001004194	446099	Mm.442342	NM_001004194	ENSMUSG00000045693	Nlrp4e	4930406H16Rik|Nalp-epsilon|Nalp4e|Nlrp4	"NLR family, pyrin domain containing 4E"	protein-coding	0	0.277228
Merged-chr5-126668951-1	chr5	126668901	126669001	+	2.1	cIP2vsInput	Intergenic	Intergenic	-361838	NR_040685	71247	Mm.399586	NR_040685		4933438B17Rik	-	RIKEN cDNA 4933438B17 gene	miscRNA	0.01	0.445545
Merged-chr14-19021579-1	chr14	19021529	19021629	+	2.1	cIP2vsInput	Intergenic	Intergenic	-127952	NM_144839	218793	Mm.23551	NM_144839	ENSMUSG00000058317	Ube2e2	BC016265	ubiquitin-conjugating enzyme E2E 2	protein-coding	0	0.366337
Merged-chr7-124800161-1	chr7	124800111	124800211	+	2.1	cIP2vsInput	Intergenic	L1M5|LINE|L1	-91226	NR_045907	73076	Mm.417827	NR_045907	ENSMUSG00000086254	3100003L05Rik	-	RIKEN cDNA 3100003L05 gene	miscRNA	0	0.326733
Merged-chr18-51406006-1	chr18	51405956	51406056	+	2.1	cIP1vsInput	Intergenic	Intergenic	288108	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding	0	0.29703
Merged-chr8-71415230-1	chr8	71415180	71415280	+	2.1	cIP1vsInput	Intergenic	RMER4A|LTR|ERVK	9218	NM_172756	234396	Mm.216549	NM_172756	ENSMUSG00000046295	Ankle1	8430438L13Rik|Ankrd41|C430003I23|Lem3	ankyrin repeat and LEM domain containing 1	protein-coding	0.01	0.346535
Merged-chr1-35254625-1	chr1	35254575	35254675	+	2.1	cIP1vsInput	Intergenic	Lx5b|LINE|L1	404666	NM_145516	226971	Mm.292751	NM_145516	ENSMUSG00000026123	Plekhb2	2310009M15Rik|AU018239|Evt2|Phdc|evt-2	"pleckstrin homology domain containing, family B (evectins) member 2"	protein-coding	0	0.316832
Merged-chr3-76927859-1	chr3	76927809	76927909	+	2.1	cIP1vsInput	Intergenic	Intergenic	852276	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.29703
Merged-chr4-17596546-1	chr4	17596496	17596596	+	2.1	cIP2vsInput	Intergenic	MLT1A1|LTR|ERVL-MaLR	-256936	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0	0.356436
Merged-chr2-22332775-1	chr2	22332725	22332825	+	2.1	cIP1vsInput	"intron (NM_148413, intron 11 of 19)"	"intron (NM_148413, intron 11 of 19)"	105272	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding	0.01	0.346535
Merged-chr6-80829617-1	chr6	80829567	80829667	+	2.1	cIP2vsInput	Intergenic	Intergenic	809974	NM_178731	243499	Mm.483425	NM_001134743	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding	0	0.336634
Merged-chrX-66036135-1	chrX	66036085	66036185	+	2.1	cIP2vsInput	Intergenic	Intergenic	-613183	NM_001161431	245450	Mm.403134	NM_001161431	ENSMUSG00000036790	Slitrk2	A930040J07	"SLIT and NTRK-like family, member 2"	protein-coding	0	0.316832
Merged-chr3-5877343-1	chr3	5877293	5877393	+	2.1	cIP2vsInput	Intergenic	L1VL2|LINE|L1	-301095	NM_001163305	19302	Mm.132336	NM_001163304	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding	0	0.336634
Merged-chr17-78486551-1	chr17	78486501	78486601	+	2.1	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	-21512	NM_001197028	74199	Mm.292983	NM_001197028	ENSMUSG00000024076	Vit	1700052E02Rik|1700110E08Rik|2810429K11Rik	vitrin	protein-coding	0	0.336634
Merged-chr2-137021200-1	chr2	137021150	137021250	+	2.1	cIP1vsInput	"intron (NM_001038641, intron 4 of 7)"	"intron (NM_001038641, intron 4 of 7)"	95320	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding	0	0.356436
Merged-chr1-55813216-1	chr1	55813166	55813266	+	2.1	cIP1vsInput	Intergenic	HAL1ME|LINE|L1	-118025	NR_045837	329159	Mm.98697	NR_045837		9130227L01Rik	-	RIKEN cDNA 9130227L01 gene	miscRNA	0	0.326733
Merged-chr15-89804797-1	chr15	89804747	89804847	+	2.1	cIP1vsInput	"intron (NM_018803, intron 3 of 6)"	"intron (NM_018803, intron 3 of 6)"	37063	NM_018803	54526	Mm.261601	NM_018803	ENSMUSG00000063260	Syt10	-	synaptotagmin X	protein-coding	0.02	0.366337
Merged-chr9-23666080-1	chr9	23666030	23666130	+	2.1	cIP2vsInput	Intergenic	MTEa|LTR|ERVL-MaLR	-431938	NM_175678	319239	Mm.130824	NM_175678	ENSMUSG00000043659	Npsr1	9330128H10Rik|GPRA|Gpr154|MVTR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0	0.326733
Merged-chr2-124354624-1	chr2	124354574	124354674	+	2.1	cIP1vsInput	Intergenic	Intergenic	-132266	NR_040612	75946	Mm.415059	NR_040612	ENSMUSG00000086954	4930583P06Rik	-	RIKEN cDNA 4930583P06 gene	miscRNA	0.01	0.405941
Merged-chr10-34627659-1	chr10	34627609	34627709	+	2.1	cIP2vsInput	Intergenic	Lx|LINE|L1	144259	NM_010237	14302	Mm.332432	NM_001159544	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding	0	0.306931
Merged-chr9-12201430-1	chr9	12201380	12201480	+	2.1	cIP1vsInput	Intergenic	Intergenic	904425	NR_040755	78219	Mm.414868	NR_040755		4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	miscRNA	0	0.316832
Merged-chr7-136837950-1	chr7	136837900	136838000	+	2.1	cIP1vsInput	Intergenic	Intergenic	-56661	NM_008598	17314	Mm.440219	NM_008598	ENSMUSG00000054612	Mgmt	AGT|AI267024|Agat	O-6-methylguanine-DNA methyltransferase	protein-coding	0	0.455446
Merged-chr2-57598320-1	chr2	57598270	57598370	+	2.1	cIP1vsInput	Intergenic	Intergenic	359938	NM_010274	14571	Mm.3711	NM_001145820	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	"glycerol phosphate dehydrogenase 2, mitochondrial"	protein-coding	0	0.306931
Merged-chr14-95968031-1	chr14	95967981	95968081	+	2.1	cIP1vsInput	Intergenic	Intergenic	86765	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.336634
Merged-chr1-81019209-1	chr1	81019159	81019259	+	2.1	cIP2vsInput	Intergenic	L1ME1|LINE|L1	-58108	NM_172849	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding	0	0.29703
Merged-chr14-50088010-1	chr14	50087960	50088060	+	2.1	cIP1vsInput	Intergenic	Intergenic	-3331	NM_146316	258313	Mm.463727	NM_146316	ENSMUSG00000060523	Olfr726	MOR246-4	olfactory receptor 726	protein-coding	0	0.29703
Merged-chr1-135653115-1	chr1	135653065	135653165	+	2.1	cIP1vsInput	Intergenic	RMER6C|LTR|ERVK	-67760	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding	0.01	0.455446
Merged-chr12-44457426-1	chr12	44457376	44457476	+	2.1	cIP2vsInput	"intron (NM_176930, intron 3 of 30)"	"intron (NM_176930, intron 3 of 30)"	128541	NM_001146031	319504	Mm.208439	NM_001146031	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuron-glia-CAM-related cell adhesion molecule	protein-coding	0	0.336634
Merged-chr8-57595544-1	chr8	57595494	57595594	+	2.1	cIP1vsInput	"intron (NM_001167981, intron 1 of 11)"	"intron (NM_001167981, intron 1 of 11)"	-56209	NR_040698	100502619	Mm.393851	NR_040698		AW046200	-	expressed sequence AW046200	miscRNA	0.03	0.445545
Merged-chr5-38998880-1	chr5	38998830	38998930	+	2.1	cIP1vsInput	Intergenic	Intergenic	-122187	NM_013748	27278	Mm.440845	NM_013748	ENSMUSG00000039315	Clnk	MIST	cytokine-dependent hematopoietic cell linker	protein-coding	0	0.336634
Merged-chr12-119818060-1	chr12	119818010	119818110	+	2.1	cIP1vsInput	Intergenic	Intergenic	-127902	NM_001160385	217951	Mm.387395	NM_001160385	ENSMUSG00000048004	Tmem196	Gm528	transmembrane protein 196	protein-coding	0.01	0.316832
Merged-chr5-40814764-1	chr5	40814714	40814814	+	2.1	cIP2vsInput	Intergenic	Intergenic	893391	NM_027295	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	"RAB28, member RAS oncogene family"	protein-coding	0.01	0.306931
Merged-chr2-88389523-1	chr2	88389473	88389573	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1726	NM_001011868	258203	Mm.376126	NM_001011868	ENSMUSG00000056995	Olfr1178	MOR225-6P	olfactory receptor 1178	protein-coding	0.02	0.316832
Merged-chr2-56820913-1	chr2	56820863	56820963	+	2.1	cIP1vsInput	Intergenic	Intergenic	294125	NM_013613	18227	Mm.3507	NM_001139509	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	"nuclear receptor subfamily 4, group A, member 2"	protein-coding	0.01	0.346535
Merged-chrX-57041055-1	chrX	57041005	57041105	+	2.1	cIP1vsInput	Intergenic	Intergenic	-2019	NM_009766	12209	Mm.10687	NM_009766	ENSMUSG00000031130	Brs3	BRS-3	bombesin-like receptor 3	protein-coding	0.02	0.386139
Merged-chr4-8113781-1	chr4	8113731	8113831	+	2.1	cIP1vsInput	Intergenic	Intergenic	125260	NM_007592	12319	Mm.119320	NM_007592		Car8	AW546993|Ca8|Cals|Cals1|Carp|wdl	carbonic anhydrase 8	protein-coding	0.01	0.514851
Merged-chr3-55548148-1	chr3	55548098	55548198	+	2.1	cIP1vsInput	Intergenic	Intergenic	86390	NM_001195540	13175	Mm.472264	NM_001111051	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding	0	0.326733
Merged-chr5-79170000-1	chr5	79169950	79170050	+	2.1	cIP2vsInput	"intron (NR_035474, intron 3 of 4)"	"intron (NR_035474, intron 3 of 4)"	345904	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0	0.336634
Merged-chr4-51021990-1	chr4	51021940	51022040	+	2.1	cIP1vsInput	Intergenic	L1MA6|LINE|L1	-194688	NM_001162865	74914	Mm.159368	NM_001162865	ENSMUSG00000039555	Cylc2	4930488P18Rik	"cylicin, basic protein of sperm head cytoskeleton 2"	protein-coding	0	0.346535
Merged-chr6-8545517-1	chr6	8545467	8545567	+	2.1	cIP1vsInput	"intron (NM_133236, intron 2 of 7)"	"intron (NM_133236, intron 2 of 7)"	35921	NM_133236	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding	0.01	0.267327
Merged-chr16-18212194-1	chr16	18212144	18212244	+	2.1	cIP2vsInput	"intron (NR_015575, intron 1 of 2)"	"intron (NR_015575, intron 1 of 2)"	1339	NR_027843	66779	Mm.387525	NR_015575		4933432I09Rik	-	RIKEN cDNA 4933432I09 gene	miscRNA	0.01	0.465347
Merged-chr1-190542534-1	chr1	190542484	190542584	+	2.1	cIP1vsInput	Intergenic	Intergenic	369236	NM_178775	320119	Mm.220912	NM_178775	ENSMUSG00000089872	Rps6kc1	AA682037|B130003F20Rik|C80612|Rpk118	ribosomal protein S6 kinase polypeptide 1	protein-coding	0	0.336634
Merged-chr15-29837671-1	chr15	29837621	29837721	+	2.1	cIP2vsInput	Intergenic	Intergenic	-334922	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	"catenin (cadherin associated protein), delta 2"	protein-coding	0.01	0.356436
Merged-chr5-85026246-1	chr5	85026196	85026296	+	2.1	cIP1vsInput	Intergenic	Intergenic	-608864	NM_007937	13839	Mm.438006	NM_007937		Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding	0	0.326733
Merged-chr10-8628873-1	chr10	8628823	8628923	+	2.1	cIP1vsInput	Intergenic	Intergenic	-110048	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding	0.04	0.336634
Merged-chr11-25688069-1	chr11	25688019	25688119	+	2.1	cIP1vsInput	"intron (NR_027973, intron 2 of 5)"	RCHARR1|DNA|hAT-Charlie	361962	NR_045853	71234	Mm.158627	NR_045853	ENSMUSG00000033015	4933427E13Rik	-	RIKEN cDNA 4933427E13 gene	miscRNA	0	0.287129
Merged-chr4-27212429-1	chr4	27212379	27212479	+	2.1	cIP1vsInput	Intergenic	Intergenic	-506980	NR_040656	75360	Mm.67233	NR_040656	ENSMUSG00000086257	4930548K13Rik	-	RIKEN cDNA 4930548K13 gene	miscRNA	0	0.326733
Merged-chr15-4557166-1	chr15	4557116	4557216	+	2.1	cIP1vsInput	"intron (NM_177355, intron 2 of 2)"	"intron (NM_177355, intron 2 of 2)"	-170044	NM_016704	12274	Mm.20247	NM_016704	ENSMUSG00000022181	C6	AW111623	complement component 6	protein-coding	0.01	0.356436
Merged-chrX-9272546-1	chrX	9272496	9272596	+	2.1	cIP2vsInput	promoter-TSS (NM_023500)	promoter-TSS (NM_023500)	-238	NM_023500	22439	Mm.56468	NM_023500	ENSMUSG00000015342	Xk	1810038K19Rik|XRG1|Xkh	Kell blood group precursor (McLeod phenotype) homolog	protein-coding	0.04	0.653465
Merged-chr9-90497360-1	chr9	90497310	90497410	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-226591	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	"TBC1 domain family, member 2B"	protein-coding	0	0.306931
Merged-chr1-154112109-1	chr1	154112059	154112159	+	2.1	cIP2vsInput	Intergenic	Intergenic	-89078	NM_001204908	100503355	Mm.484410	NM_001204908	ENSMUSG00000066797	Zfp648	ENSMUSG00000066797|Gm10178|Gm203	zinc finger protein 648	protein-coding	0	0.366337
Merged-chr6-76437195-1	chr6	76437145	76437245	+	2.1	cIP2vsInput	Intergenic	Intergenic	-805522	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0	0.326733
Merged-chr3-150720023-1	chr3	150719973	150720073	+	2.1	cIP2vsInput	Intergenic	Intergenic	-717859	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0	0.306931
Merged-chr1-163096840-1	chr1	163096790	163096890	+	2.1	cIP2vsInput	Intergenic	Intergenic	-11170	NM_030071	78258	Mm.78368	NM_030071	ENSMUSG00000071890	Mroh9	4921528O07Rik|Armc11	maestro heat-like repeat family member 9	protein-coding	0	0.326733
Merged-chr16-44919416-1	chr16	44919366	44919466	+	2.1	cIP1vsInput	Intergenic	MusHAL1|LINE|L1	-24262	NM_027578	74603	Mm.297337	NM_001128132	ENSMUSG00000036172	Cd200r3	4733401I18Rik|4833409J19Rik|AI505817|BB106877|mCD200RLb	CD200 receptor 3	protein-coding	0	0.386139
Merged-chr7-29933516-1	chr7	29933466	29933566	+	2.1	cIP1vsInput	"3' UTR (NM_178384, exon 5 of 5)"	"3' UTR (NM_178384, exon 5 of 5)"	18377	NM_178384	72723	Mm.371648	NM_178384	ENSMUSG00000059975	Zfp74	2810054M15Rik|KRAB8|Zfp66|Znf569|mszf21|mszf77	zinc finger protein 74	protein-coding	0	0.306931
Merged-chr8-20899019-1	chr8	20898969	20899069	+	2.1	cIP1vsInput	Intergenic	Intergenic	2954	NM_001177471	100504014	Mm.490239	NM_001177471	ENSMUSG00000082976	Gm15056	Defb52|OTTMUSG00000018888	predicted gene 15056	protein-coding	0	0.326733
Merged-chr12-60433679-1	chr12	60433629	60433729	+	2.1	cIP1vsInput	Intergenic	Intergenic	1088141	NR_045049	100504101	Mm.235026	NR_045049		Gm20063	-	"predicted gene, 20063"	miscRNA	0	0.336634
Merged-chr16-26711497-1	chr16	26711447	26711547	+	2.1	cIP2vsInput	"intron (NM_001159318, intron 9 of 10)"	"intron (NM_001159318, intron 9 of 10)"	129792	NM_008364	16180	Mm.253424	NM_001159317	ENSMUSG00000022514	Il1rap	6430709H04Rik|AI255955|AV239853|IL-1RAcP	interleukin 1 receptor accessory protein	protein-coding	0	0.336634
Merged-chr6-135377776-1	chr6	135377726	135377826	+	2.1	cIP1vsInput	"intron (NM_010128, intron 2 of 4)"	"intron (NM_010128, intron 2 of 4)"	14845	NM_010128	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding	0.02	0.39604
Merged-chr10-123707513-1	chr10	123707463	123707563	+	2.1	cIP1vsInput	"intron (NM_001252387, intron 4 of 4)"	"intron (NM_001252387, intron 4 of 4)"	443437	NM_001252387	268354	Mm.51939	NM_001252387	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	"family with sequence similarity 19, member A2"	protein-coding	0	0.326733
Merged-chr5-90931177-1	chr5	90931127	90931227	+	2.1	cIP1vsInput	promoter-TSS (NM_026788)	promoter-TSS (NM_026788)	-19	NM_026788	665563	Mm.153030	NM_026788	ENSMUSG00000029376	Mthfd2l	1110019K23Rik|C630010D07Rik	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like	protein-coding	0.11	0.732673
Merged-chr6-116447511-1	chr6	116447461	116447561	+	2.1	cIP2vsInput	"intron (NM_009662, intron 3 of 13)"	L1MB8|LINE|L1	13667	NM_009662	11689	Mm.41072	NM_009662	ENSMUSG00000025701	Alox5	5-LO|5-LOX|5LO|5LX|AI850497|F730011J02	arachidonate 5-lipoxygenase	protein-coding	0.01	0.29703
Merged-chr8-56441202-1	chr8	56441152	56441252	+	2.1	cIP1vsInput	Intergenic	Intergenic	109364	NM_001009951	382010	Mm.425534	NM_001009951	ENSMUSG00000038215	Cep44	4933440G23Rik|mKIAA1712	centrosomal protein 44	protein-coding	0	0.326733
Merged-chr2-84561861-1	chr2	84561811	84561911	+	2.1	cIP2vsInput	Intergenic	Intergenic	-54988	NR_046046	672763	Mm.491046	NR_046046	ENSMUSG00000087362	Gm13710	OTTMUSG00000013441	predicted gene 13710	miscRNA	0	0.425743
Merged-chr7-46784943-1	chr7	46784893	46784993	+	2.1	cIP1vsInput	"intron (NM_001005247, intron 6 of 22)"	"intron (NM_001005247, intron 6 of 22)"	10938	NM_001005248	246694	Mm.379442	NM_178742	ENSMUSG00000014418	Hps5	AI646796|AL022647|C85120|haze|hz|maroon|mr|ru-2|ru2	Hermansky-Pudlak syndrome 5 homolog (human)	protein-coding	0	0.386139
Merged-chr4-25401159-1	chr4	25401109	25401209	+	2.1	cIP2vsInput	Intergenic	Intergenic	-119338	NM_026194	67490	Mm.226295	NM_026194	ENSMUSG00000040359	Ufl1	1810074P20Rik|AI429228|Kiaa0776|Maxer|Rcad|mKIAA0776	UFM1 specific ligase 1	protein-coding	0	0.405941
Merged-chr17-93675682-1	chr17	93675632	93675732	+	2.1	cIP1vsInput	Intergenic	MTE2b|LTR|ERVL-MaLR	476260	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0.01	0.386139
Merged-chr15-21789982-1	chr15	21789932	21790032	+	2.1	cIP2vsInput	Intergenic	Lx3C|LINE|L1	678530	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding	0	0.336634
Merged-chr1-153091374-1	chr1	153091324	153091424	+	2.1	cIP2vsInput	"intron (NM_175460, intron 7 of 10)"	"intron (NM_175460, intron 7 of 10)"	95073	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	"laminin, gamma 2"	protein-coding	0.02	0.455446
Merged-chr13-83204203-1	chr13	83204153	83204253	+	2.1	cIP2vsInput	Intergenic	Lx10|LINE|L1	-299831	NM_001170537	17260	Mm.487610	NM_001170537	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding	0	0.326733
Merged-chr7-132646056-1	chr7	132646006	132646106	+	2.1	cIP2vsInput	"intron (NM_029609, intron 5 of 6)"	L1ME3E|LINE|L1	35413	NM_029609	76429	Mm.276721	NM_029609	ENSMUSG00000030946	Lhpp	2310007H09Rik	phospholysine phosphohistidine inorganic pyrophosphate phosphatase	protein-coding	0	0.316832
Merged-chr5-59714076-1	chr5	59714026	59714126	+	2.1	cIP1vsInput	Intergenic	Intergenic	271926	NR_040683	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0	0.29703
Merged-chr1-141279264-1	chr1	141279214	141279314	+	2.1	cIP1vsInput	Intergenic	Intergenic	-622862	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0.02	0.366337
Merged-chr11-10059256-1	chr11	10059206	10059306	+	2.1	cIP2vsInput	Intergenic	Intergenic	867314	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	"ATP-binding cassette, sub-family A (ABC1), member 13"	protein-coding	0.01	0.306931
Merged-chr11-27349064-1	chr11	27349014	27349114	+	2.1	cIP1vsInput	Intergenic	Intergenic	563956	NR_002890	654472	Mm.347777	NR_002890	ENSMUSG00000069939	Gm12070	OTTMUSG00000005300	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0	0.336634
Merged-chr17-23165248-1	chr17	23165198	23165298	+	2.1	cIP1vsInput	Intergenic	MT2B1|LTR|ERVL	27980	NM_009555	22700	Mm.486936	NM_009555	ENSMUSG00000002617	Zfp40	CTfin12|Zfp-40	zinc finger protein 40	protein-coding	0	0.336634
Merged-chr1-151138808-1	chr1	151138758	151138858	+	2.1	cIP2vsInput	"intron (NR_038011, intron 1 of 6)"	"intron (NR_038011, intron 1 of 6)"	774	NR_038011	402734	Mm.337666	NR_038011		C730036E19Rik	-	RIKEN cDNA C730036E19 gene	miscRNA	0.01	0.316832
Merged-chr7-50621079-1	chr7	50621029	50621129	+	2.1	cIP2vsInput	"intron (NM_001037906, intron 14 of 19)"	L1_Mur3|LINE|L1	21889	NM_172901	243996	Mm.443270	NM_172901		4933405O20Rik	AV046776	RIKEN cDNA 4933405O20 gene	protein-coding	0	0.316832
Merged-chrX-58500096-1	chrX	58500046	58500146	+	2.1	cIP1vsInput	Intergenic	Intergenic	-411365	NM_023774	75352	Mm.60906	NM_023774	ENSMUSG00000046180	4930550L24Rik	mage-k1	RIKEN cDNA 4930550L24 gene	protein-coding	0	0.277228
Merged-chr2-30161910-1	chr2	30161860	30161960	+	2.1	cIP1vsInput	Intergenic	Intergenic	-9614	NM_007931	13804	Mm.474473	NM_007931	ENSMUSG00000015337	Endog	-	endonuclease G	protein-coding	0	0.257426
Merged-chr16-27822046-1	chr16	27821996	27822096	+	2.1	cIP2vsInput	Intergenic	L1MC2|LINE|L1	-27884	NR_033475	100038623	Mm.387135	NR_033475		Gm10823	ENSMUSG00000075290	predicted gene 10823	miscRNA	0.01	0.346535
Merged-chr19-42387603-1	chr19	42387553	42387653	+	2.1	cIP1vsInput	"intron (NM_145123, intron 2 of 14)"	L1ME4a|LINE|L1	44180	NM_145123	72832	Mm.313558	NM_145123	ENSMUSG00000042401	Crtac1	2810454P21Rik|AW047536|Crtac1B|Lotus	cartilage acidic protein 1	protein-coding	0	0.287129
Merged-chr5-44273191-1	chr5	44273141	44273241	+	2.1	cIP1vsInput	Intergenic	Intergenic	-46585	NM_173764	231225	Mm.30688	NM_173764	ENSMUSG00000046985	Tapt1	4932414K18Rik	transmembrane anterior posterior transformation 1	protein-coding	0	0.336634
Merged-chr1-33727531-1	chr1	33727481	33727581	+	2.1	cIP1vsInput	"intron (NM_001159729, intron 4 of 7)"	"intron (NM_001159729, intron 4 of 7)"	7112	NM_001159729	19335	Mm.86744	NM_001159729	ENSMUSG00000004768	Rab23	AW545388|opb|opb2	"RAB23, member RAS oncogene family"	protein-coding	0.01	0.455446
Merged-chr14-96348575-1	chr14	96348525	96348625	+	2.1	cIP2vsInput	"intron (NM_053105, intron 3 of 10)"	X9_LINE|LINE|L1?	170459	NM_053105	93688	Mm.308735	NM_053105	ENSMUSG00000022076	Klhl1	mKIAA1490	kelch-like 1	protein-coding	0.01	0.376238
Merged-chr3-30696585-1	chr3	30696535	30696635	+	2.1	cIP2vsInput	Intergenic	Intergenic	-48767	NM_027941	71827	Mm.45373	NM_027941	ENSMUSG00000027702	Lrrc34	1700007J06Rik|SPATA34	leucine rich repeat containing 34	protein-coding	0	0.405941
Merged-chr16-83146542-1	chr16	83146492	83146592	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1224601	NR_040567	75247	Mm.417813	NR_040567		4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	miscRNA	0	0.336634
Merged-chr12-119496399-1	chr12	119496349	119496449	+	2.1	cIP1vsInput	Intergenic	Intergenic	52989	NM_001163136	238455	Mm.31376	NM_001163136	ENSMUSG00000041886	Macc1	4732474O15Rik|Gm267	metastasis associated in colon cancer 1	protein-coding	0	0.316832
Merged-chr13-119105562-1	chr13	119105512	119105612	+	2.1	cIP2vsInput	Intergenic	Lx9|LINE|L1	303449	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding	0	0.277228
Merged-chr14-75031759-1	chr14	75031709	75031809	+	2.1	cIP2vsInput	"intron (NM_198642, intron 1 of 13)"	"intron (NM_198642, intron 1 of 13)"	15732	NM_198642	271221	Mm.320280	NM_198642	ENSMUSG00000034959	5031414D18Rik	Gm744|Gm911|Kiaa0226l	RIKEN cDNA 5031414D18 gene	protein-coding	0	0.267327
Merged-chr11-31592714-1	chr11	31592664	31592764	+	2.1	cIP1vsInput	Intergenic	Intergenic	79148	NM_001024919	69556	Mm.34183	NM_001024919	ENSMUSG00000044502	Bod1	2310022M17Rik|BOD2.1|Fam44b	biorientation of chromosomes in cell division 1	protein-coding	0	0.445545
Merged-chr3-4023061-1	chr3	4023011	4023111	+	2.1	cIP1vsInput	Intergenic	L1VL4|LINE|L1	515031	NM_013920	30942	Mm.330897	NM_013920		Hnf4g	NR2A2	"hepatocyte nuclear factor 4, gamma"	protein-coding	0	0.306931
Merged-chr8-67033248-1	chr8	67033198	67033298	+	2.1	cIP1vsInput	Intergenic	Intergenic	173031	NM_001163564	234344	Mm.334561	NM_001163564	ENSMUSG00000014907	Naf1	Gm174	nuclear assembly factor 1 homolog (S. cerevisiae)	protein-coding	0	0.277228
Merged-chr9-8450232-1	chr9	8450182	8450282	+	2.1	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-93910	NM_013838	22068	Mm.325086	NM_013838	ENSMUSG00000031997	Trpc6	AV025995|LLHWJM002|LLHWJM003|LLHWJM004|TRP-6|Trrp6|mtrp6	"transient receptor potential cation channel, subfamily C, member 6"	protein-coding	0	0.306931
Merged-chr8-8708050-1	chr8	8708000	8708100	+	2.1	cIP1vsInput	Intergenic	ORR1D2|LTR|ERVL-MaLR	-17513	NM_176849	234023	Mm.251655	NM_176849	ENSMUSG00000040459	Arglu1	9430010O03Rik|C130008N12	arginine and glutamate rich 1	protein-coding	0	0.485149
Merged-chr12-49190865-1	chr12	49190815	49190915	+	2.1	cIP1vsInput	Intergenic	Intergenic	-192018	NM_001160112	15228	Mm.4704	NM_001160112	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding	0.01	0.316832
Merged-chr13-11359098-1	chr13	11359048	11359148	+	2.1	cIP1vsInput	Intergenic	L1MB8|LINE|L1	-162954	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	"zona pellucida glycoprotein 4, pseudogene"	pseudo	0	0.257426
Merged-chr13-65622173-1	chr13	65622123	65622223	+	2.1	cIP2vsInput	Intergenic	Intergenic	343319	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding	0.01	0.356436
Merged-chr5-40468894-1	chr5	40468844	40468944	+	2.1	cIP1vsInput	Intergenic	Intergenic	-824263	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding	0	0.287129
Merged-chr9-19183678-1	chr9	19183628	19183728	+	2.1	cIP2vsInput	Intergenic	Intergenic	46750	NM_146565	258558	Mm.377567	NM_146565		Olfr837	MOR152-2	olfactory receptor 837	protein-coding	0	0.306931
Merged-chr3-111802655-1	chr3	111802605	111802705	+	2.1	cIP1vsInput	Intergenic	Intergenic	-79248	NR_045362	625585	Mm.389497	NR_045362		Gm6602	-	predicted gene 6602	miscRNA	0	0.316832
Merged-chr17-78855352-1	chr17	78855302	78855402	+	2.1	cIP2vsInput	"exon (NM_011163, exon 15 of 16)"	"exon (NM_011163, exon 15 of 16)"	-2808	NR_003363	625054	Mm.311918	NR_003363		Gm6548	EG625054	eukaryotic translation elongation factor 1 alpha 1 pseudogene	pseudo	0.03	0.336634
Merged-chr19-15192117-1	chr19	15192067	15192167	+	2.1	cIP2vsInput	Intergenic	Intergenic	-594134	NM_011600	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333	"transducin-like enhancer of split 4, homolog of Drosophila E(spl)"	protein-coding	0.02	0.336634
Merged-chr2-51521002-1	chr2	51520952	51521052	+	2.1	cIP1vsInput	Intergenic	Intergenic	-106509	NM_199158	387511	Mm.377918	NM_199158	ENSMUSG00000056115	Tas2r134	T2R134|Tas2r34	"taste receptor, type 2, member 134"	protein-coding	0	0.336634
Merged-chr15-37373150-1	chr15	37373100	37373200	+	2.1	cIP1vsInput	"intron (NM_001170868, intron 2 of 3)"	MYSERV6-int|LTR|ERVK	-52404	NM_029113	74892	Mm.107630	NM_029113	ENSMUSG00000022288	4930447A16Rik	-	RIKEN cDNA 4930447A16 gene	protein-coding	0	0.29703
Merged-chr5-17907567-1	chr5	17907517	17907617	+	2.1	cIP1vsInput	Intergenic	Intergenic	-18608	NM_001159558	12491	Mm.406799	NM_001159555	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding	0	0.356436
Merged-chr1-150307978-1	chr1	150307928	150308028	+	2.1	cIP1vsInput	Intergenic	Intergenic	-11439	NM_024458	20028	Mm.440883	NM_001159730	ENSMUSG00000006007	Pdc	Rpr-1|Rpr1	phosducin	protein-coding	0.01	0.316832
Merged-chr18-79626952-1	chr18	79626902	79627002	+	2.1	cIP1vsInput	Intergenic	Intergenic	-419943	NM_053117	93737	Mm.24678	NM_053117	ENSMUSG00000056214	Pard6g	2410049N21Rik|Par6a	par-6 partitioning defective 6 homolog gamma (C. elegans)	protein-coding	0	0.326733
Merged-chr12-14356079-1	chr12	14356029	14356129	+	2.1	cIP1vsInput	Intergenic	Intergenic	94545	NR_045003	791361	Mm.217963	NR_045003		Gm16497	ENSMUSG00000066623	predicted gene 16497	miscRNA	0	0.356436
Merged-chr2-54666150-1	chr2	54666100	54666200	+	2.1	cIP1vsInput	"intron (NM_173030, intron 3 of 12)"	"intron (NM_173030, intron 3 of 12)"	229763	NM_173030	271786	Mm.330227	NM_173030	ENSMUSG00000060988	Galnt13	A230002A12|A230020F20|BB182356	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13	protein-coding	0	0.316832
Merged-chr10-104969043-1	chr10	104968993	104969093	+	2.1	cIP1vsInput	Intergenic	Intergenic	605436	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding	0	0.306931
Merged-chr13-115473382-1	chr13	115473332	115473432	+	2.1	cIP2vsInput	Intergenic	Intergenic	-371418	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding	0	0.356436
Merged-chr13-5903230-1	chr13	5903180	5903280	+	2.1	cIP2vsInput	Intergenic	Intergenic	41741	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding	0	0.306931
Merged-chrX-157975782-1	chrX	157975732	157975832	+	2.1	cIP2vsInput	"intron (NM_177751, intron 4 of 21)"	MLT1I|LTR|ERVL-MaLR	67328	NM_177751	245684	Mm.197074	NM_177751	ENSMUSG00000025658	Cnksr2	C030004A01|Cnk2|Ksr2|mKIAA0902	connector enhancer of kinase suppressor of Ras 2	protein-coding	0	0.306931
Merged-chr9-39838380-1	chr9	39838330	39838430	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1056	NM_146614	258607	Mm.377589	NM_146614	ENSMUSG00000093934	Olfr971	MOR171-13	olfactory receptor 971	protein-coding	0.01	0.336634
Merged-chr19-45531791-1	chr19	45531741	45531841	+	2.1	cIP2vsInput	"3' UTR (NM_001037758, exon 15 of 15)"	"3' UTR (NM_001037758, exon 15 of 15)"	28752	NM_020032	56626	Mm.46509	NM_020032	ENSMUSG00000025218	Poll	1110003P06Rik|AV007317	"polymerase (DNA directed), lambda"	protein-coding	0.03	0.574257
Merged-chr13-105532310-1	chr13	105532260	105532360	+	2.1	cIP2vsInput	Intergenic	MER92B|LTR|ERV1	88617	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0	0.336634
Merged-chr6-80156728-1	chr6	80156678	80156778	+	2.1	cIP1vsInput	Intergenic	L1MA6|LINE|L1	137085	NM_178731	243499	Mm.483425	NM_001134743	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding	0	0.29703
Merged-chr5-39080575-1	chr5	39080525	39080625	+	2.1	cIP2vsInput	Intergenic	Intergenic	-203882	NM_013748	27278	Mm.440845	NM_013748	ENSMUSG00000039315	Clnk	MIST	cytokine-dependent hematopoietic cell linker	protein-coding	0	0.316832
Merged-chr13-77425068-1	chr13	77425018	77425118	+	2.1	cIP1vsInput	"intron (NM_001145676, intron 19 of 19)"	"intron (NM_001145676, intron 19 of 19)"	-283622	NM_001163420	68675	Mm.343005	NM_001163419	ENSMUSG00000064138	Fam172a	1110033M05Rik|2610318O14Rik|53-E6|9430037D06Rik|AF064782|pEN87	"family with sequence similarity 172, member A"	protein-coding	0	0.306931
Merged-chr1-30233865-1	chr1	30233815	30233915	+	2.1	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	629391	NM_001081080	213109	Mm.486727	NM_001081080	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding	0	0.336634
Merged-chrX-77538315-1	chrX	77538265	77538365	+	2.1	cIP1vsInput	"intron (NM_020601, intron 1 of 15)"	"intron (NM_020601, intron 1 of 15)"	27088	NM_020601	21372	Mm.258476	NM_020601		Tbl1x	5330429M20|Tbl1	transducin (beta)-like 1 X-linked	protein-coding	0.01	0.267327
Merged-chr2-99923008-1	chr2	99922958	99923058	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1701740	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding	0	0.316832
Merged-chr17-85757002-1	chr17	85756952	85757052	+	2.1	cIP2vsInput	Intergenic	L1ME2|LINE|L1	-68748	NM_011380	20472	Mm.5039	NM_011380	ENSMUSG00000024134	Six2	-	sine oculis-related homeobox 2	protein-coding	0	0.326733
Merged-chr8-40688136-1	chr8	40688086	40688186	+	2.1	cIP1vsInput	Intergenic	Lx5|LINE|L1	13042	NM_010086	13526	Mm.67403	NM_010086	ENSMUSG00000046723	Adam24	Dtgn5	a disintegrin and metallopeptidase domain 24 (testase 1)	protein-coding	0	0.29703
Merged-chr19-58904350-1	chr19	58904300	58904400	+	2.1	cIP1vsInput	Intergenic	Intergenic	7409	NR_037247	100526480		NR_037247	ENSMUSG00000092813	Mir3086	mmu-mir-3086	microRNA 3086	miscRNA	0.01	0.415842
Merged-chr14-61708245-1	chr14	61708195	61708295	+	2.1	cIP1vsInput	Intergenic	Intergenic	-25872	NR_028264	668253	Mm.483605	NR_028264		Dleu2	1810047A16Rik|4932411A06Rik|7730401J12Rik|AI197277|AI788824|Alt1|Gm9069|Leu2	"deleted in lymphocytic leukemia, 2"	miscRNA	0	0.346535
Merged-chr17-92620062-1	chr17	92620012	92620112	+	2.1	cIP1vsInput	Intergenic	Intergenic	-579360	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0	0.277228
Merged-chr10-13036981-1	chr10	13036931	13037031	+	2.1	cIP1vsInput	Intergenic	RMER15|LTR|ERVL	28531	NM_175102	66125	Mm.402225	NM_175102	ENSMUSG00000078348	Sf3b5	10kDa|1110005L13Rik|AU043053|Sf3b10	"splicing factor 3b, subunit 5"	protein-coding	0	0.415842
Merged-chr4-38411175-1	chr4	38411125	38411225	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1039118	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding	0	0.326733
Merged-chr1-158654397-1	chr1	158654347	158654447	+	2.1	cIP1vsInput	"intron (NM_001205204, intron 16 of 22)"	"intron (NM_001205204, intron 16 of 22)"	148772	NR_030441	735253		NR_030441		Mir488	Mirn488|mmu-mir-488	microRNA 488	miscRNA	0.01	0.415842
Merged-chr13-13538882-1	chr13	13538832	13538932	+	2.1	cIP2vsInput	Intergenic	Intergenic	-51527	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding	0.01	0.544554
Merged-chr10-10034731-1	chr10	10034681	10034781	+	2.1	cIP2vsInput	Intergenic	Lx|LINE|L1	-133691	NM_001081344	78808	Mm.331751	NM_030191	ENSMUSG00000019790	Stxbp5	0710001E20Rik|4930565N16Rik|AW742610|LGL3|mKIAA1006	syntaxin binding protein 5 (tomosyn)	protein-coding	0	0.316832
Merged-chr3-122154905-1	chr3	122154855	122154955	+	2.1	cIP2vsInput	"intron (NM_007378, intron 36 of 49)"	"intron (NM_007378, intron 36 of 49)"	-90652	NM_008129	14630	Mm.292676	NM_008129		Gclm	AI649393|Gcmc|Glclr	"glutamate-cysteine ligase, modifier subunit"	protein-coding	0.01	0.475248
Merged-chr3-12414826-1	chr3	12414776	12414876	+	2.1	cIP1vsInput	Intergenic	Lx6|LINE|L1	-570467	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.326733
Merged-chr19-54750727-1	chr19	54750677	54750777	+	2.1	cIP1vsInput	Intergenic	Intergenic	348720	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	"glycerol-3-phosphate acyltransferase, mitochondrial"	protein-coding	0	0.267327
Merged-chr5-3796540-1	chr5	3796490	3796590	+	2.1	cIP1vsInput	"intron (NM_001003909, intron 1 of 19)"	"intron (NM_001003909, intron 1 of 19)"	6569	NM_001003909	70797	Mm.130148	NM_001003909	ENSMUSG00000040351	Ankib1	2310061P20Rik|4631416I11Rik|AW494740|C80642|mKIAA1386	ankyrin repeat and IBR domain containing 1	protein-coding	0	0.336634
Merged-chr6-130107505-1	chr6	130107455	130107555	+	2.1	cIP1vsInput	"intron (NM_053152, intron 3 of 5)"	L1_Mus3|LINE|L1	22330	NM_010650	16639	Mm.439698	NM_001101620	ENSMUSG00000089727	Klra8	Cmv-1|Cmv1|Ly49h|Ly49u<129>	"killer cell lectin-like receptor, subfamily A, member 8"	protein-coding	0	0.316832
Merged-chr13-11039459-1	chr13	11039409	11039509	+	2.1	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-482593	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	"zona pellucida glycoprotein 4, pseudogene"	pseudo	0.01	0.366337
Merged-chr18-60423690-1	chr18	60423640	60423740	+	2.1	cIP1vsInput	Intergenic	MLTR13|LTR|ERVK	47661	NM_001146275	60440	Mm.261140	NM_001146275	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding	0	0.316832
Merged-chr19-50477823-1	chr19	50477773	50477873	+	2.1	cIP1vsInput	"intron (NM_001252501, intron 1 of 25)"	"intron (NM_001252501, intron 1 of 25)"	200823	NM_001252501	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0.04	0.435644
Merged-chr5-63046346-1	chr5	63046296	63046396	+	2.1	cIP2vsInput	Intergenic	Intergenic	232523	NM_001170705	100322896	Mm.479821	NM_001170705	ENSMUSG00000090326	Gm17384	Dthd1	"predicted gene, 17384"	protein-coding	0.01	0.326733
Merged-chrX-168442804-1	chrX	168442754	168442854	+	2.1	cIP1vsInput	"intron (NM_001033330, intron 3 of 19)"	B4|SINE|B4	134429	NM_001033330	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1	FERM and PDZ domain containing 4	protein-coding	0.01	0.366337
Merged-chr5-16733083-1	chr5	16733033	16733133	+	2.1	cIP1vsInput	Intergenic	Intergenic	179533	NM_010427	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF/HGF	hepatocyte growth factor	protein-coding	0.01	0.39604
Merged-chr17-89715238-1	chr17	89715188	89715288	+	2.1	cIP2vsInput	Intergenic	Intergenic	335997	NR_045952	100043904	Mm.396198	NR_045952		Gm4719	-	predicted gene 4719	miscRNA	0	0.306931
Merged-chr2-81075713-1	chr2	81075663	81075763	+	2.1	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	436449	NM_001190179	69482	Mm.29200	NM_001190179		Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding	0	0.356436
Merged-chr17-19833777-1	chr17	19833727	19833827	+	2.1	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	60414	NM_001104565	627636	Mm.469855	NM_001104565	ENSMUSG00000091771	Vmn2r103	EG627636|Vmn103	"vomeronasal 2, receptor 103"	protein-coding	0	0.316832
Merged-chr2-101376367-1	chr2	101376317	101376417	+	2.1	cIP2vsInput	Intergenic	Intergenic	-248381	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding	0	0.366337
Merged-chr12-88185457-1	chr12	88185407	88185507	+	2.1	cIP1vsInput	Intergenic	RLTR22_Mur|LTR|ERVK	-3563	NM_001105254	100039315	Mm.426539	NM_001105254	ENSMUSG00000066027	Gm10436	ENSMUSG00000072907	predicted gene 10436	protein-coding	0	0.346535
Merged-chr5-81852958-1	chr5	81852908	81853008	+	2.1	cIP1vsInput	Intergenic	RLTR13C1|LTR|ERVK	831365	NM_198702	319387	Mm.461016	NM_198702	ENSMUSG00000037605	Lphn3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|mKIAA0768	latrophilin 3	protein-coding	0	0.405941
Merged-chr10-25068718-1	chr10	25068668	25068768	+	2.1	cIP2vsInput	Intergenic	Intergenic	-141248	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	"arginase, liver"	protein-coding	0	0.366337
Merged-chr5-59318110-1	chr5	59318060	59318160	+	2.1	cIP1vsInput	Intergenic	Intergenic	667892	NR_040683	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0	0.336634
Merged-chr13-22066509-1	chr13	22066459	22066559	+	2.1	cIP2vsInput	Intergenic	MYSERV16_I-int|LTR|ERVK	-21369	NM_145850	252912	Mm.377269	NM_145850	ENSMUSG00000069299	Vmn1r188	V1rh17	vomeronasal 1 receptor 188	protein-coding	0.01	0.485149
Merged-chr2-120027353-1	chr2	120027303	120027403	+	2.1	cIP1vsInput	promoter-TSS (NM_001114637)	promoter-TSS (NM_001114637)	-130	NM_001114637	433466	Mm.482417	NM_001114637	ENSMUSG00000033852	Jmjd7	-	jumonji domain containing 7	protein-coding	0.05	0.445545
Merged-chr8-117085673-1	chr8	117085623	117085723	+	2.1	cIP2vsInput	Intergenic	Intergenic	-3224	NM_029686	76645	Mm.159753	NM_029686	ENSMUSG00000034416	Pkd1l2	1700126L06Rik	polycystic kidney disease 1 like 2	protein-coding	0.02	0.564356
Merged-chr13-49802960-1	chr13	49802910	49803010	+	2.1	cIP1vsInput	Intergenic	Intergenic	120830	NM_172015	105148	Mm.21118	NM_172015	ENSMUSG00000037851	Iars	2510016L12Rik|AI327140|AU044614|E430001P04Rik|ILRS	isoleucine-tRNA synthetase	protein-coding	0.01	0.405941
Merged-chr10-55652397-1	chr10	55652347	55652447	+	2.1	cIP2vsInput	Intergenic	Intergenic	-454520	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding	0	0.29703
Merged-chr5-123906760-1	chr5	123906710	123906810	+	2.1	cIP1vsInput	promoter-TSS (NM_026603)	promoter-TSS (NM_026603)	-515	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding	0.02	0.356436
Merged-chr17-19169442-1	chr17	19169392	19169492	+	2.1	cIP2vsInput	Intergenic	Lx2|LINE|L1	115949	NM_001104550	224552	Mm.469860	NM_001104550	ENSMUSG00000096717	Vmn2r98	EG224552	"vomeronasal 2, receptor 98"	protein-coding	0.01	0.326733
Merged-chr8-123292562-1	chr8	123292512	123292612	+	2.1	cIP1vsInput	"intron (NM_016925, intron 20 of 42)"	"intron (NM_016925, intron 20 of 42)"	26014	NM_016925	14087	Mm.444516	NM_016925	ENSMUSG00000032815	Fanca	AW208693|FACA	"Fanconi anemia, complementation group A"	protein-coding	0.01	0.386139
Merged-chr18-28449454-1	chr18	28449404	28449504	+	2.1	cIP2vsInput	Intergenic	Intergenic	-110710	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	miscRNA	0	0.29703
Merged-chr4-31989104-1	chr4	31989054	31989154	+	2.1	cIP2vsInput	"intron (NM_009316, intron 8 of 16)"	"intron (NM_009316, intron 8 of 16)"	24997	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding	0	0.336634
Merged-chr18-47784947-1	chr18	47784897	47784997	+	2.1	cIP1vsInput	Intergenic	Intergenic	-137894	NR_045404	414127	Mm.450768	NR_045404		G630055G22Rik	-	RIKEN cDNA G630055G22 gene	miscRNA	0.01	0.316832
Merged-chr6-42877633-1	chr6	42877583	42877683	+	2.1	cIP1vsInput	Intergenic	Intergenic	-18820	NM_146273	258270	Mm.377404	NM_146273	ENSMUSG00000043119	Olfr448	MOR261-13	olfactory receptor 448	protein-coding	0.01	0.326733
Merged-chr18-55307861-1	chr18	55307811	55307911	+	2.1	cIP1vsInput	Intergenic	B3|SINE|B2	-317681	NM_175751	269023	Mm.471753	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding	0.01	0.435644
Merged-chr6-8031262-1	chr6	8031212	8031312	+	2.1	cIP2vsInput	"intron (NM_001037865, intron 27 of 34)"	"intron (NM_001037865, intron 27 of 34)"	161355	NM_001037865	213945	Mm.297404	NM_001037865	ENSMUSG00000068794	Col28a1	Col28|Gm466	"collagen, type XXVIII, alpha 1"	protein-coding	0	0.356436
Merged-chr9-100224146-1	chr9	100224096	100224196	+	2.1	cIP1vsInput	Intergenic	L1M5|LINE|L1	201846	NR_040763	108970	Mm.390215	NR_040763		4930519F24Rik	-	RIKEN cDNA 4930519F24 gene	miscRNA	0	0.336634
Merged-chr9-98471420-1	chr9	98471370	98471470	+	2.1	cIP1vsInput	Intergenic	Intergenic	-19117	NM_009034	19660	Mm.12825	NM_009034	ENSMUSG00000032454	Rbp2	Crbp-2|CrbpII|Rbp-2	"retinol binding protein 2, cellular"	protein-coding	0	0.277228
Merged-chr4-33119632-1	chr4	33119582	33119682	+	2.1	cIP2vsInput	Intergenic	MYSERV6-int|LTR|ERVK	-12924	NM_008075	14408	Mm.14116	NM_008075	ENSMUSG00000028280	Gabrr1	GABA-C	"gamma-aminobutyric acid (GABA) C receptor, subunit rho 1"	protein-coding	0	0.39604
Merged-chr3-6675951-1	chr3	6675901	6676001	+	2.1	cIP1vsInput	Intergenic	Intergenic	-55508	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding	0	0.346535
Merged-chr3-43307721-1	chr3	43307671	43307771	+	2.1	cIP1vsInput	Intergenic	Intergenic	1565103	NM_027271	73852	Mm.29006	NM_001099785	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	"DNA segment, Chr 3, ERATO Doi 751, expressed"	protein-coding	0.02	0.306931
Merged-chr12-112941978-1	chr12	112941928	112942028	+	2.1	cIP2vsInput	"intron (NM_025399, intron 1 of 4)"	CpG	140	NM_025399	66174	Mm.7070	NM_025399	ENSMUSG00000002804	Nudt14	1110030M18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 14	protein-coding	0.14	0.762376
Merged-chr1-140784557-1	chr1	140784507	140784607	+	2.1	cIP1vsInput	Intergenic	Intergenic	-128155	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0.01	0.306931
Merged-chr16-46904053-1	chr16	46904003	46904103	+	2.1	cIP2vsInput	Intergenic	Intergenic	-407086	NM_021497	58998	Mm.328072	NM_021495	ENSMUSG00000022656	Pvrl3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113	poliovirus receptor-related 3	protein-coding	0	0.306931
Merged-chr5-60123579-1	chr5	60123529	60123629	+	2.1	cIP2vsInput	Intergenic	Intergenic	-137577	NR_040682	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0.01	0.366337
Merged-chr12-95948600-1	chr12	95948550	95948650	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	98622	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0.01	0.356436
Merged-chr8-20518666-1	chr8	20518616	20518716	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-93852	NR_028428	381598	Mm.483074	NM_001024708	ENSMUSG00000071793	2610005L07Rik	2810038F24Rik|6720476A01Rik	cadherin 11 pseudogene	pseudo	0.01	0.356436
Merged-chr12-45163445-1	chr12	45163395	45163495	+	2.1	cIP1vsInput	Intergenic	Intergenic	-88962	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding	0.03	0.524752
Merged-chr4-51693703-1	chr4	51693653	51693753	+	2.1	cIP2vsInput	Intergenic	Charlie1a|DNA|hAT-Charlie	357407	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	miscRNA	0	0.277228
Merged-chr18-87647559-1	chr18	87647509	87647609	+	2.1	cIP2vsInput	Intergenic	Lx9|LINE|L1	934511	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding	0.01	0.316832
Merged-chr17-3188192-1	chr17	3188142	3188242	+	2.1	cIP1vsInput	"intron (NM_134123, intron 15 of 19)"	"intron (NM_134123, intron 15 of 19)"	73220	NM_134123	106583	Mm.486401	NM_134123		Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding	0	0.346535
Merged-chr3-44032091-1	chr3	44032041	44032141	+	2.1	cIP2vsInput	Intergenic	Intergenic	1346169	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	miscRNA	0	0.326733
Merged-chr5-20163406-1	chr5	20163356	20163456	+	2.1	cIP1vsInput	"intron (NM_015823, intron 2 of 21)"	MER5A1|DNA|hAT-Charlie	255888	NM_015823	50791	Mm.441283	NM_001170745	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	"membrane associated guanylate kinase, WW and PDZ domain containing 2"	protein-coding	0	0.346535
Merged-chr16-71855409-1	chr16	71855359	71855459	+	2.1	cIP2vsInput	Intergenic	Intergenic	605505	NR_040576	78221	Mm.399298	NR_040576		4930567J20Rik	-	RIKEN cDNA 4930567J20 gene	miscRNA	0	0.386139
Merged-chr6-123927366-1	chr6	123927316	123927416	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-74176	NM_001104641	545874	Mm.484595	NM_001104641	ENSMUSG00000094672	Vmn2r25	EG545874	"vomeronasal 2, receptor 25"	protein-coding	0.01	0.346535
Merged-chr2-51848920-1	chr2	51848870	51848970	+	2.1	cIP2vsInput	Intergenic	Intergenic	85724	NM_001141982	71684	Mm.28309	NM_001141981	ENSMUSG00000036249	Rbm43	0610033I05Rik	RNA binding motif protein 43	protein-coding	0	0.346535
Merged-chr1-86774002-1	chr1	86773952	86774052	+	2.1	cIP2vsInput	"intron (NM_153530, intron 5 of 20)"	"intron (NM_153530, intron 5 of 20)"	70198	NM_001172157	208718	Mm.389152	NM_001172157	ENSMUSG00000053333	Dis3l2	4930429A22Rik|8030493P09Rik	DIS3 mitotic control homolog (S. cerevisiae)-like 2	protein-coding	0	0.287129
Merged-chr4-17569061-1	chr4	17569011	17569111	+	2.1	cIP2vsInput	Intergenic	Intergenic	-284421	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0	0.356436
Merged-chr17-4697907-1	chr17	4697857	4697957	+	2.1	cIP1vsInput	Intergenic	L1VL4|LINE|L1	-297167	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding	0	0.29703
Merged-chr2-153714436-1	chr2	153714386	153714486	+	2.1	cIP1vsInput	Intergenic	Intergenic	-26851	NM_007896	13589	Mm.143877	NM_007896	ENSMUSG00000027479	Mapre1	5530600P05Rik|AI462499|AI504412|AW260097|BIM1p|D2Ertd459e|Eb1	"microtubule-associated protein, RP/EB family, member 1"	protein-coding	0	0.257426
Merged-chr19-40092024-1	chr19	40091974	40092074	+	2.1	cIP2vsInput	"3' UTR (NM_001167877, exon 4 of 4)"	"3' UTR (NM_001167877, exon 4 of 4)"	2345	NM_001167877	107141	Mm.474575	NM_001167875	ENSMUSG00000054827	Cyp2c50	AI266900	"cytochrome P450, family 2, subfamily c, polypeptide 50"	protein-coding	0	0.306931
Merged-chr16-25812609-1	chr16	25812559	25812659	+	2.1	cIP2vsInput	"intron (NM_001127265, intron 1 of 8)"	"intron (NM_001127265, intron 1 of 8)"	10693	NM_001127264	22061	Mm.20894	NM_001127259	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding	0	0.366337
Merged-chr19-9168971-1	chr19	9168921	9169021	+	2.1	cIP1vsInput	Intergenic	MurERV4-int|LTR|ERVK	-33405	NM_025610	66514	Mm.272847	NM_025610		Asrgl1	2410004D18Rik|ALP|ALP1|AU040643|AW060375	asparaginase like 1	protein-coding	0.01	0.326733
Merged-chr14-92077860-1	chr14	92077810	92077910	+	2.1	cIP2vsInput	Intergenic	Intergenic	1811028	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.306931
Merged-chr1-29847535-1	chr1	29847485	29847585	+	2.1	cIP2vsInput	Intergenic	Intergenic	1015721	NM_001081080	213109	Mm.486727	NM_001081080	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding	0.02	0.356436
Merged-chr12-112693275-1	chr12	112693225	112693325	+	2.1	cIP2vsInput	Intergenic	Intergenic	14435	NM_001100460	382639	Mm.11350	NM_001100460	ENSMUSG00000037638	Zbtb42	EG382639|Gm5188|simiRP58	zinc finger and BTB domain containing 42	protein-coding	0.01	0.584158
Merged-chr16-30252267-1	chr16	30252217	30252317	+	2.1	cIP1vsInput	Intergenic	Intergenic	15265	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	"carboxypeptidase N, polypeptide 2"	protein-coding	0.07	0.60396
Merged-chr15-18832166-1	chr15	18832116	18832216	+	2.1	cIP1vsInput	"intron (NM_009865, intron 1 of 11)"	"intron (NM_009865, intron 1 of 11)"	11837	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0.02	0.326733
Merged-chr10-75621281-1	chr10	75621231	75621331	+	2.1	cIP1vsInput	Intergenic	Intergenic	22727	NM_001162913	71733	Mm.247956	NM_001162913	ENSMUSG00000006342	Susd2	1200011D11Rik	sushi domain containing 2	protein-coding	0	0.336634
Merged-chr1-108191073-1	chr1	108191023	108191123	+	2.1	cIP1vsInput	Intergenic	Intergenic	273814	NR_102307	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0	0.356436
Merged-chr19-23337537-1	chr19	23337487	23337587	+	2.1	cIP2vsInput	"intron (NM_174857, intron 9 of 13)"	"intron (NM_174857, intron 9 of 13)"	-63640	NM_001252684	226026	Mm.23267	NM_001252684	ENSMUSG00000024943	Smc5	MLZ-453|SMC-5|Smc5l1|mKIAA0594|mSMC5	structural maintenance of chromosomes 5	protein-coding	0.01	0.306931
Merged-chr19-40233369-1	chr19	40233319	40233419	+	2.1	cIP1vsInput	"intron (NM_016861, intron 4 of 6)"	"intron (NM_016861, intron 4 of 6)"	38247	NM_016861	54132	Mm.5567	NM_016861	ENSMUSG00000055044	Pdlim1	Clim1|mClim1	PDZ and LIM domain 1 (elfin)	protein-coding	0	0.277228
Merged-chr16-10411708-1	chr16	10411658	10411758	+	2.1	cIP2vsInput	promoter-TSS (NM_011955)	promoter-TSS (NM_011955)	-230	NM_011955	26425	Mm.325732	NM_011955	ENSMUSG00000022503	Nubp1	-	nucleotide binding protein 1	protein-coding	0.02	0.415842
Merged-chr14-83863724-1	chr14	83863674	83863774	+	2.1	cIP2vsInput	Intergenic	Intergenic	-579839	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0.01	0.306931
Merged-chrX-79730782-1	chrX	79730732	79730832	+	2.1	cIP1vsInput	Intergenic	Intergenic	-59347	NM_028025	71967	Mm.379207	NM_001113734	ENSMUSG00000046942	Mageb16	2410003J06Rik	"melanoma antigen family B, 16"	protein-coding	0	0.316832
Merged-chr17-83164971-1	chr17	83164921	83165021	+	2.1	cIP2vsInput	Intergenic	Intergenic	-50312	NM_134117	106522	Mm.311974	NM_134117	ENSMUSG00000024247	Pkdcc	AI115348|AW548124|Adtk1|ESTM17|MAd1|Sgk493|Vlk|X83346	"protein kinase domain containing, cytoplasmic"	protein-coding	0.02	0.544554
Merged-chr12-90530937-1	chr12	90530887	90530987	+	2.1	cIP2vsInput	Intergenic	Intergenic	207501	NM_010050	13371	Mm.408815	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	"deiodinase, iodothyronine, type II"	protein-coding	0	0.326733
Merged-chr15-25058477-1	chr15	25058427	25058527	+	2.1	cIP1vsInput	Intergenic	Intergenic	355287	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	"brain abundant, membrane attached signal protein 1"	protein-coding	0	0.287129
Merged-chr4-140684894-1	chr4	140684844	140684944	+	2.1	cIP2vsInput	Intergenic	Intergenic	-16579	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding	0.01	0.376238
Merged-chr2-122048911-1	chr2	122048861	122048961	+	2.1	cIP1vsInput	"intron (NM_001256055, intron 5 of 7)"	MTD|LTR|ERVL-MaLR	20288	NM_144545	78655	Mm.458184	NM_144545		Eif3j1	1810016I04Rik|2700079K05Rik|AA409117|AA409446|C78575|Eif3j|Eif3j-1|Eif3j-2|Eif3j2|Eif3s1|eIF3-alpha|eIF3-p35|eIF3j-A|eIF3j-B	"eukaryotic translation initiation factor 3, subunit J1"	protein-coding	0	0.336634
Merged-chr16-67639498-1	chr16	67639448	67639548	+	2.1	cIP1vsInput	Intergenic	Intergenic	-18590	NM_178721	239857	Mm.394300	NM_001145977	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0	0.277228
Merged-chr3-113842253-1	chr3	113842203	113842303	+	2.1	cIP2vsInput	Intergenic	Intergenic	-188287	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	"collagen, type XI, alpha 1"	protein-coding	0.01	0.287129
Merged-chr1-97390178-1	chr1	97390128	97390228	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-261875	NM_028942	74441	Mm.60362	NM_028942	ENSMUSG00000026331	Slco6c1	4933404A18Rik|C79179	"solute carrier organic anion transporter family, member 6c1"	protein-coding	0.01	0.326733
Merged-chr17-70838721-1	chr17	70838671	70838771	+	2.1	cIP2vsInput	Intergenic	Intergenic	8056	NM_001164077	21815	Mm.101034	NM_001164074	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding	0	0.39604
Merged-chr1-178427171-1	chr1	178427121	178427221	+	2.1	cIP2vsInput	"intron (NM_026626, intron 1 of 6)"	"intron (NM_026626, intron 1 of 6)"	21290	NM_026626	68226	Mm.252132	NM_026626	ENSMUSG00000026495	Efcab2	1700073K01Rik|D830011E08Rik	EF-hand calcium binding domain 2	protein-coding	0	0.287129
Merged-chr17-40356535-1	chr17	40356485	40356585	+	2.1	cIP2vsInput	Intergenic	Lx4A|LINE|L1	-37328	NM_009638	11571	Mm.16781	NM_009638	ENSMUSG00000025431	Crisp1	AW324342|Aeg1|CRISP-1	cysteine-rich secretory protein 1	protein-coding	0.01	0.336634
Merged-chr17-82203108-1	chr17	82203058	82203158	+	2.1	cIP2vsInput	Intergenic	Intergenic	-464731	NM_011406	20541	Mm.489060	NM_001112798		Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	"solute carrier family 8 (sodium/calcium exchanger), member 1"	protein-coding	0.01	0.356436
Merged-chrX-75171771-1	chrX	75171721	75171821	+	2.1	cIP1vsInput	TTS (NM_001161373)	TTS (NM_001161373)	-8020	NM_001033786	434800	Mm.460747	NM_001033786	ENSMUSG00000073094	Smim9	4930428E23Rik	small integral membrane protein 9	protein-coding	0	0.306931
Merged-chrX-101954411-1	chrX	101954361	101954461	+	2.1	cIP2vsInput	"intron (NM_001163610, intron 1 of 7)"	"intron (NM_001163610, intron 1 of 7)"	105026	NM_001163610	100042480	Mm.232	NM_001163610	ENSMUSG00000079481	Nhsl2	1110062M06Rik|6430511F03|AI225852|AW488865|EG621083|ENSMUSG00000073037|Gm10456	NHS-like 2	protein-coding	0.07	0.673267
Merged-chr2-87093128-1	chr2	87093078	87093178	+	2.1	cIP2vsInput	"exon (NM_146766, exon 1 of 1)"	"exon (NM_146766, exon 1 of 1)"	267	NM_146766	258762	Mm.377678	NM_146766	ENSMUSG00000075161	Olfr1109	MOR172-5	olfactory receptor 1109	protein-coding	0.01	0.366337
Merged-chr6-88293859-1	chr6	88293809	88293909	+	2.1	cIP1vsInput	"intron (NM_023060, intron 5 of 6)"	"intron (NM_023060, intron 5 of 6)"	71591	NM_019964	56691	Mm.272871	NM_019964	ENSMUSG00000048206	Dnajb8	1700016F14Rik|1700031F10Rik|AI326313|mDj6	"DnaJ (Hsp40) homolog, subfamily B, member 8"	protein-coding	0	0.326733
Merged-chr6-139944056-1	chr6	139944006	139944106	+	2.1	cIP1vsInput	"intron (NM_207683, intron 22 of 23)"	"intron (NM_207683, intron 22 of 23)"	97361	NM_054066	114875	Mm.50808	NM_054066	ENSMUSG00000030230	Plcz1	1700041H07Rik|PLCzeta	"phospholipase C, zeta 1"	protein-coding	0	0.247525
Merged-chr1-55920620-1	chr1	55920570	55920670	+	2.1	cIP1vsInput	Intergenic	Intergenic	-10621	NR_045837	329159	Mm.98697	NR_045837		9130227L01Rik	-	RIKEN cDNA 9130227L01 gene	miscRNA	0	0.356436
Merged-chr8-3548217-1	chr8	3548167	3548267	+	2.1	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	-19781	NM_001024728	546049	Mm.428003	NM_001024728	ENSMUSG00000065952	C330021F23Rik	2610027C06Rik|Rps23r1|Rps23rg1	RIKEN cDNA C330021F23 gene	protein-coding	0.01	0.39604
Merged-chr9-116993193-1	chr9	116993143	116993243	+	2.1	cIP1vsInput	"intron (NM_001172126, intron 3 of 12)"	"intron (NM_001172126, intron 3 of 12)"	259290	NM_001172123	207181	Mm.326411	NM_001172121	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	"RNA binding motif, single stranded interacting protein"	protein-coding	0	0.336634
Merged-chr2-142329758-1	chr2	142329708	142329808	+	2.1	cIP2vsInput	"intron (NM_001013802, intron 16 of 18)"	"intron (NM_001013802, intron 16 of 18)"	571706	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding	0	0.326733
Merged-chr5-79296948-1	chr5	79296898	79296998	+	2.1	cIP2vsInput	"intron (NR_035474, intron 2 of 4)"	"intron (NR_035474, intron 2 of 4)"	218956	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0.01	0.326733
Merged-chr15-10834901-1	chr15	10834851	10834951	+	2.1	cIP1vsInput	Intergenic	B1F|SINE|Alu	5850	NR_040357	100502601	Mm.399434	NR_040357		Gm19276	-	"predicted gene, 19276"	miscRNA	0	0.455446
Merged-chr13-84512136-1	chr13	84512086	84512186	+	2.1	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	289840	NM_175187	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding	0.01	0.356436
Merged-chr1-5759618-1	chr1	5759568	5759668	+	2.1	cIP1vsInput	Intergenic	Intergenic	157780	NM_010342	226304	Mm.291110	NM_010342	ENSMUSG00000033774	Npbwr1	Gpr7|Nbpwr1	neuropeptides B/W receptor 1	protein-coding	0.01	0.326733
Merged-chr16-18333175-1	chr16	18333125	18333225	+	2.1	cIP2vsInput	"intron (NM_138583, intron 1 of 8)"	MTEa|LTR|ERVL-MaLR	-5710	NR_029571	387180		NR_029571	ENSMUSG00000065464	Mir185	Mirn185|mmu-mir-185	microRNA 185	miscRNA	0	0.326733
Merged-chr18-18561558-1	chr18	18561508	18561608	+	2.1	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-980568	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	miscRNA	0	0.346535
Merged-chr17-42039968-1	chr17	42039918	42040018	+	2.1	cIP1vsInput	Intergenic	Intergenic	-275979	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding	0.01	0.366337
Merged-chr7-13335509-1	chr7	13335459	13335559	+	2.1	cIP1vsInput	"intron (NM_001004762, intron 4 of 15)"	"intron (NM_001004762, intron 4 of 15)"	6187	NM_001004762	232889	Mm.223639	NM_001004762	ENSMUSG00000033847	Pla2g4c	D7Ertd445e	"phospholipase A2, group IVC (cytosolic, calcium-independent)"	protein-coding	0.02	0.405941
Merged-chrX-106219699-1	chrX	106219649	106219749	+	2.1	cIP2vsInput	"5' UTR (NM_001001176, exon 1 of 7)"	"5' UTR (NM_001001176, exon 1 of 7)"	143	NM_001001176	407786	Mm.19440	NM_001001176	ENSMUSG00000047242	Taf9b	BC066223|Taf9l	"TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor"	protein-coding	0.07	0.693069
Merged-chr10-42384437-1	chr10	42384387	42384487	+	2.1	cIP2vsInput	"intron (NM_145743, intron 7 of 12)"	"intron (NM_145743, intron 7 of 12)"	94128	NM_145743	215951	Mm.89646	NM_145743	ENSMUSG00000038302	Lace1	CG8520	lactation elevated 1	protein-coding	0	0.29703
Merged-chr1-33108031-1	chr1	33107981	33108081	+	2.1	cIP1vsInput	Intergenic	Intergenic	-560738	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding	0.01	0.277228
Merged-chr13-87451035-1	chr13	87450985	87451085	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1370437	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0.01	0.29703
Merged-chr7-116934961-1	chr7	116934911	116935011	+	2.1	cIP1vsInput	Intergenic	Intergenic	430592	NM_001130479	53322	Mm.9901	NM_016773	ENSMUSG00000030659	Nucb2	AI607786|Calnuc|Nefa|Nesfatin-1	nucleobindin 2	protein-coding	0.01	0.425743
Merged-chr16-58987557-1	chr16	58987507	58987607	+	2.1	cIP2vsInput	Intergenic	Lx7|LINE|L1	-7847	NM_146485	258478	Mm.271400	NM_146485	ENSMUSG00000062105	Olfr183	MOR183-2	olfactory receptor 183	protein-coding	0	0.306931
Merged-chr4-68122000-1	chr4	68121950	68122050	+	2.1	cIP1vsInput	Intergenic	Intergenic	832397	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Dbc1	BRINP|Brinp1|Dbccr1|Fam5a	deleted in bladder cancer 1 (human)	protein-coding	0	0.336634
Merged-chr17-12020643-1	chr17	12020593	12020693	+	2.1	cIP1vsInput	"intron (NM_016694, intron 10 of 11)"	MYSERV16_I-int|LTR|ERVK	-98641	NM_026644	68262	Mm.258300	NM_026644	ENSMUSG00000023827	Agpat4	1500003P24Rik	"1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)"	protein-coding	0.01	0.415842
Merged-chr12-63226808-1	chr12	63226758	63226858	+	2.1	cIP2vsInput	Intergenic	Intergenic	1248090	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.277228
Merged-chr11-89336931-1	chr11	89336881	89336981	+	2.1	cIP2vsInput	Intergenic	ERVL-int|LTR|ERVL	-34372	NM_008711	18121	Mm.135266	NM_008711	ENSMUSG00000048616	Nog	-	noggin	protein-coding	0.01	0.316832
Merged-chr3-157993027-1	chr3	157992977	157993077	+	2.1	cIP1vsInput	"intron (NM_001013806, intron 8 of 12)"	"intron (NM_001013806, intron 8 of 12)"	30395	NM_026989	69207	Mm.223946	NM_001093752	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding	0	0.376238
Merged-chr12-62586664-1	chr12	62586614	62586714	+	2.1	cIP1vsInput	Intergenic	Intergenic	1062032	NM_178714	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0	0.346535
Merged-chr15-92789874-1	chr15	92789824	92789924	+	2.1	cIP1vsInput	Intergenic	Intergenic	192765	NM_001164594	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding	0.02	0.376238
Merged-chr10-6200538-1	chr10	6200488	6200588	+	2.1	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	-278138	NM_019958	56533	Mm.44606	NM_001161822	ENSMUSG00000019775	Rgs17	6430507P11Rik|Rgsz2	regulator of G-protein signaling 17	protein-coding	0	0.336634
Merged-chrX-72448013-1	chrX	72447963	72448063	+	2.1	cIP1vsInput	"intron (NM_008067, intron 8 of 9)"	L1MEg|LINE|L1	-61155	NM_001085506	236852	Mm.115316	NM_001085506	ENSMUSG00000043453	Magea10	-	"melanoma antigen family A, 10"	protein-coding	0.02	0.336634
Merged-chr4-27627837-1	chr4	27627787	27627887	+	2.1	cIP1vsInput	Intergenic	Intergenic	-922388	NR_040656	75360	Mm.67233	NR_040656	ENSMUSG00000086257	4930548K13Rik	-	RIKEN cDNA 4930548K13 gene	miscRNA	0.01	0.306931
Merged-chr19-50015610-1	chr19	50015560	50015660	+	2.1	cIP2vsInput	Intergenic	Intergenic	663036	NM_001252501	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0	0.316832
Merged-chr3-11393648-1	chr3	11393598	11393698	+	2.1	cIP2vsInput	Intergenic	Intergenic	450711	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.29703
Merged-chr17-42887278-1	chr17	42887228	42887328	+	2.1	cIP1vsInput	Intergenic	Intergenic	-10854	NM_009847	12488	Mm.218637	NM_009847	ENSMUSG00000061665	Cd2ap	AL024079|C78928|METS-1|Mets1	CD2-associated protein	protein-coding	0.02	0.356436
Merged-chr10-8482106-1	chr10	8482056	8482156	+	2.1	cIP1vsInput	"intron (NM_177387, intron 1 of 7)"	"intron (NM_177387, intron 1 of 7)"	36719	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding	0	0.39604
Merged-chr17-10827205-1	chr17	10827155	10827255	+	2.1	cIP2vsInput	"intron (NM_027032, intron 1 of 4)"	L1_Mus2|LINE|L1	12986	NM_027032	69310	Mm.18889	NM_027032	ENSMUSG00000037196	Pacrg	1700008H23Rik	PARK2 co-regulated	protein-coding	0	0.267327
Merged-chr17-17346338-1	chr17	17346288	17346388	+	2.1	cIP1vsInput	Intergenic	L1VL2|LINE|L1	-27994	NM_025934	67045	Mm.35117	NM_025934	ENSMUSG00000023846	Riok2	2010110K24Rik|2410085M17Rik	RIO kinase 2 (yeast)	protein-coding	0.01	0.326733
Merged-chr10-6183667-1	chr10	6183617	6183717	+	2.1	cIP2vsInput	Intergenic	Intergenic	-261267	NM_019958	56533	Mm.44606	NM_001161822	ENSMUSG00000019775	Rgs17	6430507P11Rik|Rgsz2	regulator of G-protein signaling 17	protein-coding	0	0.366337
Merged-chr2-23438284-1	chr2	23438234	23438334	+	2.1	cIP2vsInput	Intergenic	Intergenic	117038	NM_008752	18232	Mm.131616	NM_008752	ENSMUSG00000069132	Nxph2	-	neurexophilin 2	protein-coding	0	0.405941
Merged-chr1-68135584-1	chr1	68135534	68135634	+	2.1	cIP1vsInput	"intron (NM_010154, intron 20 of 26)"	MER5A|DNA|hAT-Charlie	972475	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0.01	0.316832
Merged-chr1-28297582-1	chr1	28297532	28297632	+	2.1	cIP1vsInput	Intergenic	Intergenic	482670	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0.01	0.326733
Merged-chr14-24311294-1	chr14	24311244	24311344	+	2.1	cIP1vsInput	Intergenic	Intergenic	17930	NM_001033214	105418	Mm.2077	NM_001033214	ENSMUSG00000038925	E330034G19Rik	AA415275	RIKEN cDNA E330034G19 gene	protein-coding	0	0.485149
Merged-chr3-16048247-1	chr3	16048197	16048297	+	2.1	cIP1vsInput	Intergenic	B1_Mur2|SINE|Alu	-41915	NM_001081687	381484	Mm.217376	NM_001081687	ENSMUSG00000078780	Gm5150	-	predicted gene 5150	protein-coding	0	0.366337
Merged-chr2-65480029-1	chr2	65479979	65480079	+	2.1	cIP2vsInput	"intron (NM_018732, intron 20 of 26)"	"intron (NM_018732, intron 20 of 26)"	87463	NM_018732	20269	Mm.330256	NM_018732	ENSMUSG00000057182	Scn3a	Gm1000|Nav1.3	"sodium channel, voltage-gated, type III, alpha"	protein-coding	0	0.316832
Merged-chr3-159455957-1	chr3	159455907	159456007	+	2.1	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-39476	NM_001172092	76131	Mm.371655	NM_001172092	ENSMUSG00000028175	Depdc1a	5830484J08Rik|Depdc1	DEP domain containing 1a	protein-coding	0	0.336634
Merged-chr1-113876287-1	chr1	113876237	113876337	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1808850	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0	0.326733
Merged-chr10-100146303-1	chr10	100146253	100146353	+	2.1	cIP2vsInput	Intergenic	Intergenic	130479	NM_013598	17311	Mm.45124	NM_013598	ENSMUSG00000019966	Kitl	Clo|Con|Gb|Kitlg|Mgf|SCF|SF|SLF|Sl|blz|contrasted	kit ligand	protein-coding	0	0.346535
Merged-chr6-13713405-1	chr6	13713355	13713455	+	2.1	cIP1vsInput	Intergenic	Intergenic	-35439	NM_175312	101148	Mm.354863	NM_175312	ENSMUSG00000042742	B630005N14Rik	AI666701	RIKEN cDNA B630005N14 gene	protein-coding	0	0.336634
Merged-chr2-64208165-1	chr2	64208115	64208215	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-110127	NM_001267847	60344	Mm.483676	NM_001267846	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding	0	0.29703
Merged-chr16-9881466-1	chr16	9881416	9881516	+	2.1	cIP2vsInput	"intron (NM_008170, intron 1 of 11)"	RLTR17D_Mm|LTR|ERVK	111067	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	"glutamate receptor, ionotropic, NMDA2A (epsilon 1)"	protein-coding	0	0.326733
Merged-chr14-23280986-1	chr14	23280936	23281036	+	2.1	cIP2vsInput	Intergenic	RMER6A|LTR|ERVK	-186415	NR_033550	791307	Mm.364384	NR_033550	ENSMUSG00000068680	Gm10248	ENSMUSG00000068680	predicted gene 10248	miscRNA	0	0.346535
Merged-chr8-73615956-1	chr8	73615906	73616006	+	2.1	cIP2vsInput	Intergenic	L2a|LINE|L2	-263400	NM_010687	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large	BPFD#36|Gyltl1a|Mbp-1|Mbp1|enr|fg|froggy|mKIAA0609|myd	like-glycosyltransferase	protein-coding	0	0.346535
Merged-chr8-78178283-1	chr8	78178233	78178333	+	2.1	cIP1vsInput	Intergenic	L1ME2|LINE|L1	-35059	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding	0.01	0.415842
Merged-chr1-98560396-1	chr1	98560346	98560446	+	2.1	cIP1vsInput	Intergenic	RMER16-int|LTR|ERVK	139272	NM_027584	70866	Mm.389164	NM_001164233	ENSMUSG00000026336	Slco6d1	4921511I05Rik	"solute carrier organic anion transporter family, member 6d1"	protein-coding	0	0.277228
Merged-chr2-126404669-1	chr2	126404619	126404719	+	2.1	cIP1vsInput	"intron (NM_001080944, intron 11 of 27)"	"intron (NM_001080944, intron 11 of 27)"	86884	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	"ATPase, class I, type 8B, member 4"	protein-coding	0.01	0.356436
Merged-chr12-7496891-1	chr12	7496841	7496941	+	2.1	cIP1vsInput	Intergenic	Intergenic	-116561	NR_045045	73575	Mm.179463	NR_045045		1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	miscRNA	0	0.356436
Merged-chr9-12197847-1	chr9	12197797	12197897	+	2.1	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	908008	NR_040755	78219	Mm.414868	NR_040755		4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	miscRNA	0	0.336634
Merged-chr7-133444627-1	chr7	133444577	133444677	+	2.1	cIP2vsInput	Intergenic	Intergenic	157488	NM_028654	73808	Mm.159067	NM_028654	ENSMUSG00000030976	Tex36	4930404H21Rik	testis expressed 36	protein-coding	0	0.316832
Merged-chr14-46180005-1	chr14	46179955	46180055	+	2.1	cIP1vsInput	Intergenic	HAL1b|LINE|L1	95978	NR_002875	218963	Mm.282093	NR_002875		Gm1821	-	ubiquitin pseudogene	pseudo	0	0.277228
Merged-chr14-61787318-1	chr14	61787268	61787368	+	2.1	cIP1vsInput	Intergenic	Intergenic	-104945	NR_028264	668253	Mm.483605	NR_028264		Dleu2	1810047A16Rik|4932411A06Rik|7730401J12Rik|AI197277|AI788824|Alt1|Gm9069|Leu2	"deleted in lymphocytic leukemia, 2"	miscRNA	0	0.237624
Merged-chr11-34921307-1	chr11	34921257	34921357	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-87666	NM_027411	70385	Mm.194368	NM_027411	ENSMUSG00000069910	Spdl1	1700018I02Rik|2600001J17Rik|2810049B11Rik|AA409762|Ccdc99	spindle apparatus coiled-coil protein 1	protein-coding	0	0.336634
Merged-chr5-97462703-1	chr5	97462653	97462753	+	2.1	cIP2vsInput	"intron (NR_045981, intron 3 of 7)"	"intron (NR_045981, intron 3 of 7)"	-5695	NM_010294	14626	Mm.61206	NM_010294	ENSMUSG00000050553	Gk2	GKTA|Gk-rs2	glycerol kinase 2	protein-coding	0	0.366337
Merged-chr12-67747841-1	chr12	67747791	67747891	+	2.1	cIP1vsInput	Intergenic	Lx3C|LINE|L1	-78570	NR_033146	100316870	Mm.379794	NR_033146		Gm17821	-	DDB1 and CUL4 associated factor 5 pseudogene	pseudo	0	0.316832
Merged-chr19-35000317-1	chr19	35000267	35000367	+	2.1	cIP1vsInput	Intergenic	Intergenic	77959	NM_183046	240641	Mm.278471	NM_183046	ENSMUSG00000024795	Kif20b	B130024C23|C330014J10Rik|Mphosph1	kinesin family member 20B	protein-coding	0	0.376238
Merged-chr18-41238848-1	chr18	41238798	41238898	+	2.1	cIP1vsInput	Intergenic	B4|SINE|B4	712346	NM_029942	77619	Mm.30649	NM_029942	ENSMUSG00000056671	Prelid2	1700003A01Rik|C330008K14Rik	PRELI domain containing 2	protein-coding	0	0.277228
Merged-chr4-78683792-1	chr4	78683742	78683842	+	2.1	cIP1vsInput	Intergenic	Intergenic	-471897	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0	0.316832
Merged-chr14-102426778-1	chr14	102426728	102426828	+	2.1	cIP2vsInput	Intergenic	Intergenic	555854	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mmu-mir-5130|mu-mir-5130	microRNA 5130	miscRNA	0	0.316832
Merged-chr1-27324580-1	chr1	27324530	27324630	+	2.1	cIP1vsInput	Intergenic	Intergenic	-637120	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding	0	0.346535
Merged-chr1-17380787-1	chr1	17380737	17380837	+	2.1	cIP1vsInput	Intergenic	Intergenic	-221114	NM_053191	94227	Mm.442452	NM_053191	ENSMUSG00000067780	Pi15	P24TI|P25TI|PI-15|SugarCrisp	peptidase inhibitor 15	protein-coding	0	0.326733
Merged-chr4-5105456-1	chr4	5105406	5105506	+	2.1	cIP1vsInput	Intergenic	Lx4B|LINE|L1	-312150	NM_177730	242291	Mm.369779	NM_177730		Impad1	1110001C20Rik|AA408880|AI451589|AL022796|B230207P20|Jaws|gPAPP	inositol monophosphatase domain containing 1	protein-coding	0	0.366337
Merged-chr13-27456123-1	chr13	27456073	27456173	+	2.1	cIP1vsInput	Intergenic	Intergenic	-17435	NM_001271378	19112	Mm.142728	NM_001271378	ENSMUSG00000021345	Prl8a6	PLP-C1|PLP-Ca|PLP-calpha|Prlpc|Prlpc1	"prolactin family 8, subfamily a, member 6"	protein-coding	0	0.247525
Merged-chr16-79842556-1	chr16	79842506	79842606	+	2.1	cIP1vsInput	Intergenic	L1MC1|LINE|L1	-751459	NM_008941	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	"transmembrane protease, serine 15"	protein-coding	0.01	0.356436
Merged-chr18-45043516-1	chr18	45043466	45043566	+	2.1	cIP1vsInput	Intergenic	L1ME1|LINE|L1	214851	NM_001163013	240255	Mm.244482	NM_001163013	ENSMUSG00000034653	Ythdc2	3010002F02Rik|BC037178	YTH domain containing 2	protein-coding	0	0.336634
Merged-chr13-46383749-1	chr13	46383699	46383799	+	2.1	cIP1vsInput	Intergenic	Intergenic	-34551	NM_001081425	666794	Mm.38269	NM_001081425	ENSMUSG00000038132	Rbm24	6330546B05Rik|AI606861	RNA binding motif protein 24	protein-coding	0.01	0.277228
Merged-chr4-74001338-1	chr4	74001288	74001388	+	2.1	cIP1vsInput	Intergenic	Intergenic	-12265	NM_172869	242506	Mm.221597	NM_001163732	ENSMUSG00000049122	Frmd3	4.1O|9430066I12Rik|EPB41L4O|P410	FERM domain containing 3	protein-coding	0.01	0.346535
Merged-chr17-34960015-1	chr17	34959965	34960065	+	2.1	cIP1vsInput	promoter-TSS (NM_010478)	promoter-TSS (NM_010478)	-777	NM_010478	15511	Mm.372314	NM_010478	ENSMUSG00000090877	Hspa1b	Hsp70|Hsp70-1|Hsp70.1|hsp68	heat shock protein 1B	protein-coding	0.03	0.554455
Merged-chr13-8131339-1	chr13	8131289	8131389	+	2.1	cIP2vsInput	Intergenic	Intergenic	-71570	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	"adenosine deaminase, RNA-specific, B2"	protein-coding	0.01	0.376238
Merged-chr10-102810603-1	chr10	102810553	102810653	+	2.1	cIP1vsInput	Intergenic	Lx9|LINE|L1	218174	NM_172553	216285	Mm.19287	NM_172553	ENSMUSG00000036602	Alx1	AI314867|C130005I02|Cart1	ALX homeobox 1	protein-coding	0	0.356436
Merged-chr14-82577075-1	chr14	82577025	82577125	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-1866488	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0.01	0.376238
Merged-chr14-106891495-1	chr14	106891445	106891545	+	2.1	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-404975	NR_045938	73631	Mm.48862	NR_045938		1700128A07Rik	-	RIKEN cDNA 1700128A07 gene	miscRNA	0	0.306931
Merged-chr15-53521337-1	chr15	53521287	53521387	+	2.1	cIP1vsInput	"intron (NM_177225, intron 4 of 4)"	"intron (NM_177225, intron 4 of 4)"	-175154	NM_010162	14042	Mm.309395	NM_010162		Ext1	AA409028	exostoses (multiple) 1	protein-coding	0	0.29703
Merged-chrX-84088435-1	chrX	84088385	84088485	+	2.1	cIP2vsInput	"intron (NM_007868, intron 44 of 78)"	"intron (NM_007868, intron 44 of 78)"	-600511	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding	0.01	0.336634
Merged-chr1-98774786-1	chr1	98774736	98774836	+	2.1	cIP2vsInput	Intergenic	Lx4A|LINE|L1	353662	NM_027584	70866	Mm.389164	NM_001164233	ENSMUSG00000026336	Slco6d1	4921511I05Rik	"solute carrier organic anion transporter family, member 6d1"	protein-coding	0	0.336634
Merged-chr9-123799366-1	chr9	123799316	123799416	+	2.1	cIP2vsInput	"intron (NM_148925, intron 16 of 18)"	"intron (NM_148925, intron 16 of 18)"	-7111	NM_030712	80901	Mm.124289	NM_030712	ENSMUSG00000048521	Cxcr6	BB217514|BONZO|STRL33	chemokine (C-X-C motif) receptor 6	protein-coding	0	0.376238
Merged-chr4-155410108-1	chr4	155410058	155410158	+	2.1	cIP1vsInput	"intron (NR_102283, intron 4 of 4)"	"intron (NR_102283, intron 4 of 4)"	918	NM_001166029	544678	Mm.472798	NM_001166029	ENSMUSG00000042233	2010015L04Rik	A530045M11	RIKEN cDNA 2010015L04 gene	protein-coding	0.03	0.445545
Merged-chr9-39518304-1	chr9	39518254	39518354	+	2.1	cIP2vsInput	Intergenic	Intergenic	-6586	NM_146745	258740	Mm.223173	NM_146745	ENSMUSG00000095322	Olfr957	MOR171-12	olfactory receptor 957	protein-coding	0.01	0.376238
Merged-chr14-82907772-1	chr14	82907722	82907822	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1535791	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0.01	0.29703
Merged-chr12-35130079-1	chr12	35130029	35130129	+	2.1	cIP2vsInput	"intron (NM_001014973, intron 20 of 25)"	"intron (NM_001014973, intron 20 of 25)"	82890	NM_001014973	217463	Mm.213991	NM_001014973	ENSMUSG00000020590	Snx13	Rgs-px1|mKIAA0713	sorting nexin 13	protein-coding	0.01	0.336634
Merged-chr6-123698645-1	chr6	123698595	123698695	+	2.1	cIP2vsInput	Intergenic	MMERVK9C_I-int|LTR|ERVK	-4176	NM_001104638	435916	Mm.469874	NM_001104638	ENSMUSG00000091620	Vmn2r23	EG435916	"vomeronasal 2, receptor 23"	protein-coding	0	0.277228
Merged-chr3-47973024-1	chr3	47972974	47973074	+	2.1	cIP1vsInput	Intergenic	Intergenic	53735	NR_040408	666202	Mm.465057	NR_040408		Gm7977	EG666202	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide pseudogene"	pseudo	0	0.287129
Merged-chr3-54931108-1	chr3	54931058	54931158	+	2.1	cIP1vsInput	Intergenic	Charlie1a|DNA|hAT-Charlie	-15221	NM_177854	329641	Mm.51187	NM_177854	ENSMUSG00000056306	Sertm1	6030405A18Rik	serine rich and transmembrane domain containing 1	protein-coding	0	0.29703
Merged-chr4-90108887-1	chr4	90108837	90108937	+	2.1	cIP2vsInput	Intergenic	Intergenic	-109933	NM_153102	236537	Mm.214642	NM_153102	ENSMUSG00000070902	Zfp352	2czf48	zinc finger protein 352	protein-coding	0	0.29703
Merged-chr11-86429311-1	chr11	86429261	86429361	+	2.1	cIP1vsInput	"intron (NR_030571, intron 1 of 2)"	"intron (NR_030571, intron 1 of 2)"	13467	NR_030571	100124487		NR_030571		Mir467c	Mirn467c	microRNA 467c	miscRNA	0.01	0.346535
Merged-chr1-48642057-1	chr1	48642007	48642107	+	2.1	cIP2vsInput	Intergenic	L1Md_F3|LINE|L1	-1788548	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.366337
Merged-chr3-58248777-1	chr3	58248727	58248827	+	2.1	cIP1vsInput	Intergenic	Intergenic	-84970	NR_040538	67850	Mm.416968	NR_040538		1700007F19Rik	-	RIKEN cDNA 1700007F19 gene	miscRNA	0	0.376238
Merged-chr5-76274873-1	chr5	76274823	76274923	+	2.1	cIP1vsInput	"intron (NM_007715, intron 2 of 22)"	"intron (NM_007715, intron 2 of 22)"	29675	NM_007715	12753	Mm.392894	NM_007715	ENSMUSG00000029238	Clock	5330400M04Rik|KAT13D|bHLHe8|mKIAA0334	circadian locomotor output cycles kaput	protein-coding	0	0.267327
Merged-chr3-25730804-1	chr3	25730754	25730854	+	2.1	cIP1vsInput	"intron (NM_001163387, intron 3 of 5)"	"intron (NM_001163387, intron 3 of 5)"	422503	NM_001163387	192167	Mm.316080	NM_001163387	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|mKIAA1070	neuroligin 1	protein-coding	0.01	0.336634
Merged-chr9-3752775-1	chr9	3752725	3752825	+	2.1	cIP1vsInput	"intron (NM_001033322, intron 4 of 7)"	"intron (NM_001033322, intron 4 of 7)"	220426	NM_001033322	234889	Mm.91240	NM_001033322		Gucy1a2	6330407I18Rik|A230060L24Rik	"guanylate cyclase 1, soluble, alpha 2"	protein-coding	0	0.336634
Merged-chr15-19481178-1	chr15	19481128	19481228	+	2.1	cIP1vsInput	Intergenic	Intergenic	660849	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0	0.366337
Merged-chr9-21533555-1	chr9	21533505	21533605	+	2.1	cIP1vsInput	"intron (NM_206536, intron 2 of 5)"	(TTTTTG)n|Simple_repeat|Simple_repeat	7378	NM_001198794	382062	Mm.325205	NM_001198794	ENSMUSG00000057191	AB124611	Gm1706	cDNA sequence AB124611	protein-coding	0	0.277228
Merged-chr3-120623825-1	chr3	120623775	120623875	+	2.1	cIP1vsInput	Intergenic	Lx6|LINE|L1	547870	NM_028456	66568	Mm.263163	NM_025637	ENSMUSG00000028133	Rwdd3	2510027J23Rik|3110037C01Rik|AI035684|AI662458|X2CR1	RWD domain containing 3	protein-coding	0	0.346535
Merged-chr15-83822630-1	chr15	83822580	83822680	+	2.1	cIP1vsInput	"intron (NM_172610, intron 3 of 6)"	L1M2|LINE|L1	42607	NM_172610	223726	Mm.36395	NM_172610	ENSMUSG00000041708	Mpped1	6230403M19|AW456965|D15Bwg0669e	metallophosphoesterase domain containing 1	protein-coding	0.01	0.316832
Merged-chr4-127173687-1	chr4	127173637	127173737	+	2.1	cIP2vsInput	"intron (NM_198618, intron 1 of 11)"	"intron (NM_198618, intron 1 of 11)"	4416	NM_198618	242667	Mm.331885	NM_198618	ENSMUSG00000042388	Dlgap3	BC058433|DAP-3|DAP3|Prpl8|Sapap3	"discs, large (Drosophila) homolog-associated protein 3"	protein-coding	0.03	0.643564
Merged-chr1-101529855-1	chr1	101529805	101529905	+	2.1	cIP2vsInput	Intergenic	Intergenic	374087	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.306931
Merged-chr5-119513193-1	chr5	119513143	119513243	+	2.1	cIP1vsInput	Intergenic	L1ME4a|LINE|L1	67165	NR_045702	100993	Mm.381453	NR_045702		AW549542	-	expressed sequence AW549542	miscRNA	0.01	0.217822
Merged-chr16-52915787-1	chr16	52915737	52915837	+	2.1	cIP1vsInput	Intergenic	MTE-int|LTR|ERVL-MaLR	-100043	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	miscRNA	0	0.366337
Merged-chr16-14243953-1	chr16	14243903	14244003	+	2.1	cIP1vsInput	"intron (NM_013607, intron 8 of 41)"	ID_B1|SINE|B4	47455	NM_013607	17880	Mm.250705	NM_001161775	ENSMUSG00000018830	Myh11	AV071570|SM1|SM2|smMHC	"myosin, heavy polypeptide 11, smooth muscle"	protein-coding	0	0.386139
Merged-chr4-145214619-1	chr4	145214569	145214669	+	2.1	cIP1vsInput	"3' UTR (NM_011610, exon 10 of 10)"	"3' UTR (NM_011610, exon 10 of 10)"	-19614	NM_001276465	230895	Mm.476856	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13 D (yeast)	protein-coding	0.03	0.584158
Merged-chr6-142055333-1	chr6	142055283	142055383	+	2.1	cIP1vsInput	Intergenic	Lx3_Mus|LINE|L1	-46588	NM_001081318	625716	Mm.295865	NM_001081318	ENSMUSG00000079263	Gm6614	EG625716	predicted gene 6614	protein-coding	0	0.287129
Merged-chr10-17051253-1	chr10	17051203	17051303	+	2.1	cIP1vsInput	"intron (NR_038020, intron 1 of 8)"	L1_Mus1|LINE|L1	44529	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0	0.425743
Merged-chrX-135742408-1	chrX	135742358	135742458	+	2.1	cIP2vsInput	promoter-TSS (NM_001004359)	promoter-TSS (NM_001004359)	-284	NM_001004359	67298	Mm.271980	NM_001004359	ENSMUSG00000043384	Gprasp1	2210415K24Rik|3110031O14Rik|C87852|GASP|GASP1	G protein-coupled receptor associated sorting protein 1	protein-coding	0.06	0.50495
Merged-chr10-64769738-1	chr10	64769688	64769788	+	2.1	cIP2vsInput	"intron (NM_001164519, intron 8 of 12)"	L1_Mus3|LINE|L1	-679483	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding	0	0.326733
Merged-chr1-121114666-1	chr1	121114616	121114716	+	2.1	cIP1vsInput	"intron (NR_038008, intron 3 of 4)"	RMER15|LTR|ERVL	27261	NR_038008	98452	Mm.489010	NR_038008	ENSMUSG00000097881	B230209K01Rik	AI848258|Gm818	RIKEN cDNA B230209K01 gene	miscRNA	0	0.425743
Merged-chr14-38163977-1	chr14	38163927	38164027	+	2.1	cIP2vsInput	Intergenic	Intergenic	-734325	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	4930529F24Rik	-	RIKEN cDNA 4930529F24 gene	miscRNA	0	0.356436
Merged-chr19-15254173-1	chr19	15254123	15254223	+	2.1	cIP2vsInput	Intergenic	Intergenic	-656190	NM_011600	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333	"transducin-like enhancer of split 4, homolog of Drosophila E(spl)"	protein-coding	0	0.356436
Merged-chr2-32003278-1	chr2	32003228	32003328	+	2.1	cIP1vsInput	"intron (NM_172268, intron 16 of 35)"	"intron (NM_172268, intron 16 of 35)"	28828	NM_172268	227720	Mm.289686	NM_172268	ENSMUSG00000001855	Nup214	BC039282|CAN|D2H9S46E	nucleoporin 214	protein-coding	0	0.336634
Merged-chr18-88320562-1	chr18	88320512	88320612	+	2.1	cIP1vsInput	Intergenic	Lx9|LINE|L1	573645	NM_018821	54607	Mm.476577	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding	0	0.336634
Merged-chr17-69035426-1	chr17	69035376	69035476	+	2.1	cIP1vsInput	Intergenic	Intergenic	-121384	NM_013813	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb4.1l3	4.1B|DAL1P|Dal1|Epb41l3|NBL3	erythrocyte protein band 4.1-like 3	protein-coding	0	0.29703
Merged-chr1-98611218-1	chr1	98611168	98611268	+	2.1	cIP1vsInput	Intergenic	Intergenic	190094	NM_027584	70866	Mm.389164	NM_001164233	ENSMUSG00000026336	Slco6d1	4921511I05Rik	"solute carrier organic anion transporter family, member 6d1"	protein-coding	0	0.306931
Merged-chr4-40468494-1	chr4	40468444	40468544	+	2.1	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-3686	NM_177175	320500	Mm.156365	NM_001166009	ENSMUSG00000046593	Tmem215	A930001M12Rik	transmembrane protein 215	protein-coding	0	0.326733
Merged-chr18-17713722-1	chr18	17713672	17713772	+	2.1	cIP1vsInput	Intergenic	Intergenic	-132732	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	miscRNA	0	0.257426
Merged-chr1-153556890-1	chr1	153556840	153556940	+	2.1	cIP2vsInput	Intergenic	Intergenic	-7176	NM_028749	74091	Mm.24887	NM_028749	ENSMUSG00000042684	Npl	0610033B02Rik	N-acetylneuraminate pyruvate lyase	protein-coding	0.01	0.376238
Merged-chr13-112593347-1	chr13	112593297	112593397	+	2.1	cIP1vsInput	Intergenic	Intergenic	-12685	NM_139299	218624	Mm.380801	NM_139299	ENSMUSG00000050377	Il31ra	CRL3|GLM-R|GPL|Glmr|NR10	interleukin 31 receptor A	protein-coding	0	0.316832
Merged-chr4-37115563-1	chr4	37115513	37115613	+	2.1	cIP1vsInput	Intergenic	L1MD|LINE|L1	-163819	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0	0.356436
Merged-chr9-86535931-1	chr9	86535881	86535981	+	2.1	cIP2vsInput	"exon (NM_177208, exon 28 of 39)"	"exon (NM_177208, exon 28 of 39)"	35911	NM_001163746	109785	Mm.390201	NM_001163746	ENSMUSG00000056131	Pgm3	2810473H05Rik|Agm1|BB187688|C77933|PAGM|Pgm-3	phosphoglucomutase 3	protein-coding	0	0.336634
Merged-chr18-7314511-1	chr18	7314461	7314561	+	2.1	cIP1vsInput	Intergenic	L1_Mus4|LINE|L1	-16610	NM_001081393	74934	Mm.107918	NM_001081393	ENSMUSG00000061802	Armc4	4930463I21Rik	armadillo repeat containing 4	protein-coding	0	0.346535
Merged-chrX-59578883-1	chrX	59578833	59578933	+	2.1	cIP1vsInput	Intergenic	Intergenic	-420581	NM_007979	14071	Mm.391283	NM_007979	ENSMUSG00000031138	F9	AW111646|Cf-9|Cf9	coagulation factor IX	protein-coding	0	0.326733
Merged-chr12-90763304-1	chr12	90763254	90763354	+	2.1	cIP2vsInput	Intergenic	MER21C|LTR|ERVL	-24866	NM_010050	13371	Mm.408815	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	"deiodinase, iodothyronine, type II"	protein-coding	0	0.326733
Merged-chr2-127190613-1	chr2	127190563	127190663	+	2.1	cIP1vsInput	"intron (NM_198630, intron 1 of 1)"	RLTR13D3A1|LTR|ERVK	17667	NM_198630	329509	Mm.120738	NM_198630	ENSMUSG00000044145	1810024B03Rik	-	RIKEN cDNA 1810024B03 gene	protein-coding	0	0.306931
Merged-chr5-78829092-1	chr5	78829042	78829142	+	2.1	cIP1vsInput	Intergenic	Lx7|LINE|L1	686812	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0	0.386139
Merged-chr18-73623181-1	chr18	73623131	73623231	+	2.1	cIP2vsInput	Intergenic	CpG	50476	NM_001039214	240396	Mm.436942	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 homolog C (C. elegans)	protein-coding	0.16	0.772277
Merged-chr6-37765737-1	chr6	37765687	37765787	+	2.1	cIP2vsInput	Intergenic	MurERV4-int|LTR|ERVK	-105074	NM_001272064	21848	Mm.41063	NM_001272064	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding	0.02	0.346535
Merged-chr14-95713216-1	chr14	95713166	95713266	+	2.1	cIP1vsInput	Intergenic	Intergenic	-168050	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.316832
Merged-chr11-26300853-1	chr11	26300803	26300903	+	2.1	cIP1vsInput	Intergenic	Intergenic	-86231	NM_025923	67030	Mm.18875	NM_001277273		Fancl	2010322C19Rik|AW554273|B230118H11Rik|Phf9|Pog|gcd	"Fanconi anemia, complementation group L"	protein-coding	0.01	0.29703
Merged-chr8-37242888-1	chr8	37242838	37242938	+	2.1	cIP1vsInput	Intergenic	Intergenic	249313	NM_001039220	621080	Mm.373292	NM_001039220	ENSMUSG00000074384	AI429214	-	expressed sequence AI429214	protein-coding	0	0.29703
Merged-chr9-65128280-1	chr9	65128230	65128330	+	2.1	cIP2vsInput	"intron (NM_020043, intron 10 of 19)"	"intron (NM_020043, intron 10 of 19)"	-12909	NM_008988	19289	Mm.453118	NM_008988	ENSMUSG00000032394	Igdcc3	2810401C09Rik|AI851425|Punc|WI-14920	"immunoglobulin superfamily, DCC subclass, member 3"	protein-coding	0.1	0.683168
Merged-chr5-63766862-1	chr5	63766812	63766912	+	2.1	cIP2vsInput	"intron (NM_177006, intron 3 of 6)"	"intron (NM_177006, intron 3 of 6)"	-45633	NM_029554	76261	Mm.38143	NM_029554	ENSMUSG00000060512	0610040J01Rik	AI662686	RIKEN cDNA 0610040J01 gene	protein-coding	0	0.336634
Merged-chr3-8958400-1	chr3	8958350	8958450	+	2.1	cIP2vsInput	"intron (NM_001025264, intron 1 of 6)"	"intron (NM_001025264, intron 1 of 6)"	5654	NM_001025262	21985	Mm.371590	NM_001025261	ENSMUSG00000027506	Tpd52	AI043038|mD52	tumor protein D52	protein-coding	0	0.267327
Merged-chr2-47680973-1	chr2	47680923	47681023	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1133136	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding	0.01	0.326733
Merged-chr6-79100973-1	chr6	79100923	79101023	+	2.1	cIP1vsInput	Intergenic	RLTR17B_Mm|LTR|ERVK	68931	NR_040301	100504701	Mm.400420	NR_040301		Gm20362	-	"predicted gene, 20362"	miscRNA	0	0.287129
Merged-chr1-45518421-1	chr1	45518371	45518471	+	2.1	cIP1vsInput	Intergenic	Intergenic	-15139	NM_007737	12832	Mm.10299	NM_007737	ENSMUSG00000026042	Col5a2	1110014L14Rik|D230017N05	"collagen, type V, alpha 2"	protein-coding	0	0.257426
Merged-chr7-97893749-1	chr7	97893699	97893799	+	2.1	cIP2vsInput	"intron (NM_011035, intron 8 of 14)"	"intron (NM_011035, intron 8 of 14)"	-26209	NM_177696	233537	Mm.375772	NM_177696	ENSMUSG00000035582	Gdpd4	4921513O04	glycerophosphodiester phosphodiesterase domain containing 4	protein-coding	0	0.366337
Merged-chr3-112890712-1	chr3	112890662	112890762	+	2.1	cIP1vsInput	Intergenic	MTEb|LTR|ERVL-MaLR	266015	NM_001190404	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding	0	0.39604
Merged-chrX-75618934-1	chrX	75618884	75618984	+	2.1	cIP2vsInput	Intergenic	Lx7|LINE|L1	-40730	NM_175122	67790	Mm.45148	NM_175122	ENSMUSG00000031202	Rab39b	6330580M05Rik	"RAB39B, member RAS oncogene family"	protein-coding	0	0.376238
Merged-chr4-51012098-1	chr4	51012048	51012148	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-204580	NM_001162865	74914	Mm.159368	NM_001162865	ENSMUSG00000039555	Cylc2	4930488P18Rik	"cylicin, basic protein of sperm head cytoskeleton 2"	protein-coding	0.01	0.39604
Merged-chr2-99213488-1	chr2	99213438	99213538	+	2.1	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	1745814	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.386139
Merged-chr10-109595716-1	chr10	109595666	109595766	+	2.1	cIP2vsInput	Intergenic	Intergenic	404503	NM_001081035	260315	Mm.461280	NM_001081035	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding	0	0.267327
Merged-chr3-53769988-1	chr3	53769938	53770038	+	2.1	cIP2vsInput	Intergenic	Intergenic	93819	NM_026435	67890	Mm.23067	NM_026435		Ufm1	1810045K17Rik|AI132708|AI463323|ENSMUSG00000074598|Gm10726	ubiquitin-fold modifier 1	protein-coding	0	0.366337
Merged-chr2-161812191-1	chr2	161812141	161812241	+	2.1	cIP1vsInput	"intron (NM_021464, intron 9 of 29)"	"intron (NM_021464, intron 9 of 29)"	-578622	NR_040617	77645	Mm.447752	NR_040617	ENSMUSG00000084919	C330008G21Rik	-	RIKEN cDNA C330008G21 gene	miscRNA	0	0.455446
Merged-chr1-89094323-1	chr1	89094273	89094373	+	2.1	cIP1vsInput	"intron (NM_133816, intron 1 of 5)"	"intron (NM_133816, intron 1 of 5)"	23861	NM_133816	98402	Mm.170983	NM_133816		Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding	0.02	0.455446
Merged-chr6-112459322-1	chr6	112459272	112459372	+	2.1	cIP2vsInput	promoter-TSS (NM_007617)	promoter-TSS (NM_007617)	-183	NM_007617	12391	Mm.3924	NM_007617	ENSMUSG00000062694	Cav3	AI385751|Cav-3|M-cav|M-caveolin|caveolin-3	caveolin 3	protein-coding	0	0.49505
Merged-chr6-91497464-1	chr6	91497414	91497514	+	2.1	cIP1vsInput	"intron (NM_009531, intron 10 of 15)"	"intron (NM_009531, intron 10 of 15)"	18424	NM_009531	22591	Mm.2806	NM_009531	ENSMUSG00000030094	Xpc	-	"xeroderma pigmentosum, complementation group C"	protein-coding	0	0.326733
Merged-chr3-58194232-1	chr3	58194182	58194282	+	2.1	cIP1vsInput	Intergenic	L1M2|LINE|L1	-30425	NR_040538	67850	Mm.416968	NR_040538		1700007F19Rik	-	RIKEN cDNA 1700007F19 gene	miscRNA	0	0.237624
Merged-chr2-111035135-1	chr2	111035085	111035185	+	2.1	cIP2vsInput	Intergenic	MTE2a|LTR|ERVL-MaLR	-84891	NM_001128103	228432	Mm.483325	NM_001128103	ENSMUSG00000074968	Ano3	AI838058|B230324K02Rik|Tmem16c	anoctamin 3	protein-coding	0	0.386139
Merged-chr2-160107110-1	chr2	160107060	160107160	+	2.1	cIP1vsInput	Intergenic	L1MA4|LINE|L1	90457	NR_040499	71613	Mm.98139	NR_040499	ENSMUSG00000086653	9130015L21Rik	-	RIKEN cDNA 9130015L21 gene	miscRNA	0	0.356436
Merged-chr10-7231625-1	chr10	7231575	7231675	+	2.1	cIP1vsInput	Intergenic	Intergenic	-19388	NM_172546	215748	Mm.37984	NM_172546	ENSMUSG00000015202	Cnksr3	6820402C05|BC024086|Magi1	Cnksr family member 3	protein-coding	0	0.356436
Merged-chr5-131702083-1	chr5	131702033	131702133	+	2.1	cIP1vsInput	"intron (NM_177047, intron 5 of 18)"	"intron (NM_177047, intron 5 of 18)"	-178186	NR_040704	75369	Mm.389696	NR_040704		4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	miscRNA	0	0.306931
Merged-chr2-144730314-1	chr2	144730264	144730364	+	2.1	cIP1vsInput	"intron (NM_025314, intron 4 of 5)"	L1MB8|LINE|L1	-93352	NM_025490	66328	Mm.490926	NM_025490	ENSMUSG00000027431	Scp2d1	1700010M22Rik	SCP2 sterol-binding domain containing 1	protein-coding	0.02	0.435644
Merged-chrY-7016115-1	chrY	7016065	7016165	+	2.1	cIP1vsInput	Intergenic	Intergenic	151662	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.386139
Merged-chr3-38409094-1	chr3	38409044	38409144	+	2.1	cIP1vsInput	Intergenic	Intergenic	75722	NM_001167883	99696	Mm.290937	NM_001033198	ENSMUSG00000044864	Ankrd50	AI662170|E430012K20Rik|mKIAA1223|mKIAA3019	ankyrin repeat domain 50	protein-coding	0	0.326733
Merged-chr11-54260909-1	chr11	54260859	54260959	+	2.1	cIP2vsInput	Intergenic	Lx7|LINE|L1	6370	NM_010556	16187	Mm.983	NM_010556		Il3	BPA|Csfmu|HCGF|Il-3|MCGF|PSF	interleukin 3	protein-coding	0	0.356436
Merged-chr8-116079795-1	chr8	116079745	116079845	+	2.1	cIP1vsInput	Intergenic	Intergenic	-372901	NM_001025577	17132	Mm.488377	NM_001025577		Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma (v-maf) AS42 oncogene homolog	protein-coding	0	0.39604
Merged-chr9-97965883-1	chr9	97965833	97965933	+	2.1	cIP1vsInput	"intron (NM_022319, intron 1 of 17)"	L1ME4a|LINE|L1	67284	NM_022319	64085	Mm.440903	NM_022319	ENSMUSG00000032452	Clstn2	2900042C18Rik|AI448973|CSTN2|Cs2|Cst-2|mKIAA4134	calsyntenin 2	protein-coding	0	0.306931
Merged-chr15-37222038-1	chr15	37221988	37222088	+	2.1	cIP2vsInput	Intergenic	Intergenic	-10998	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3	grainyhead-like 2 (Drosophila)	protein-coding	0.01	0.485149
Merged-chr9-84704605-1	chr9	84704555	84704655	+	2.1	cIP1vsInput	Intergenic	Lx|LINE|L1	-69793	NR_040739	75253	Mm.401984	NR_040739		4930554C24Rik	-	RIKEN cDNA 4930554C24 gene	miscRNA	0	0.475248
Merged-chr18-25445326-1	chr18	25445276	25445376	+	2.1	cIP1vsInput	"intron (NM_001033532, intron 10 of 10)"	"intron (NM_001033532, intron 10 of 10)"	276306	NM_001033532	225289	Mm.391081	NM_001033532	ENSMUSG00000033632	AW554918	4921538P22|AI461742|Kiaa1328|mKIAA1328	expressed sequence AW554918	protein-coding	0	0.326733
Merged-chr3-118481252-1	chr3	118481202	118481302	+	2.1	cIP1vsInput	Intergenic	Intergenic	47395	NR_029551	387155		NR_029551		Mir137	Mirn137|mmu-mir-137	microRNA 137	miscRNA	0.01	0.287129
Merged-chr4-118490118-1	chr4	118490068	118490168	+	2.1	cIP2vsInput	promoter-TSS (NM_011587)	promoter-TSS (NM_011587)	-269	NM_011587	21846	Mm.4345	NM_011587	ENSMUSG00000033191	Tie1	D430008P04Rik|TIE|tie-1	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	protein-coding	0.02	0.60396
Merged-chr4-61917005-1	chr4	61916955	61917055	+	2.1	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-81825	NM_008649	17844	Mm.445286	XM_003689354	ENSMUSG00000058523	Mup5	Mup18	major urinary protein 5	protein-coding	0	0.356436
Merged-chr9-75971133-1	chr9	75971083	75971183	+	2.1	cIP2vsInput	Intergenic	Intergenic	-43844	NM_173731	208982	Mm.82306	NM_173731	ENSMUSG00000007908	Hmgcll1	BC037381	3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1	protein-coding	0	0.336634
Merged-chr2-57578611-1	chr2	57578561	57578661	+	2.1	cIP1vsInput	Intergenic	Intergenic	340229	NM_010274	14571	Mm.3711	NM_001145820	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	"glycerol phosphate dehydrogenase 2, mitochondrial"	protein-coding	0.01	0.415842
Merged-chr14-11955940-1	chr14	11955890	11955990	+	2.1	cIP2vsInput	"intron (NM_008981, intron 3 of 29)"	"intron (NM_008981, intron 3 of 29)"	-328269	NM_146051	218734	Mm.44068	NM_146051	ENSMUSG00000033111	3830406C13Rik	3110059I09Rik|AV167947	RIKEN cDNA 3830406C13 gene	protein-coding	0	0.356436
Merged-chr16-15607012-1	chr16	15606962	15607062	+	2.1	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-12494	NM_023585	70620	Mm.390775	NM_001159351		Ube2v2	1110021H13Rik|4632410D19Rik|5730524P06Rik|6820402M05|AI848315|C81524|MMS2	ubiquitin-conjugating enzyme E2 variant 2	protein-coding	0.01	0.346535
Merged-chr18-27556636-1	chr18	27556586	27556686	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1003528	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	miscRNA	0	0.267327
Merged-chr12-104375509-1	chr12	104375459	104375559	+	2.1	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-11655	NM_009253	20717	Mm.482078	NM_009253	ENSMUSG00000079012	Serpina3m	3e46|AI195004|MMCM7|MMSPi2.4|Spi-2l|Spi-2rs1|Spi2-rs1|Spi2.4|spi2	"serine (or cysteine) peptidase inhibitor, clade A, member 3M"	protein-coding	0.01	0.356436
Merged-chr9-118003885-1	chr9	118003835	118003935	+	2.1	cIP2vsInput	Intergenic	Intergenic	-36614	NM_001048146	27215	Mm.92705	NM_001048146	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding	0	0.247525
Merged-chr2-80225677-1	chr2	80225627	80225727	+	2.1	cIP1vsInput	Intergenic	Intergenic	-66793	NM_177256	320769	Mm.60992	NR_033713	ENSMUSG00000050114	Prdx6b	1-cysPrx-P1|4930414C22Rik|Aop2-rs1|Prdx5-rs1|Prdx6-ps1|Prdx6-rs1|Prdx6-rs1-ps	peroxiredoxin 6B	protein-coding	0	0.405941
Merged-chr16-97451540-1	chr16	97451490	97451590	+	2.1	cIP1vsInput	"non-coding (NR_003520, exon 7 of 9)"	"non-coding (NR_003520, exon 7 of 9)"	11365	NM_010846	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	myxovirus (influenza virus) resistance 1	protein-coding	0.01	0.316832
Merged-chr7-140839160-1	chr7	140839110	140839210	+	2.1	cIP1vsInput	"intron (NR_045717, intron 3 of 3)"	"intron (NR_045717, intron 3 of 3)"	3664	NM_029821	76974	Mm.272359	NM_029821		1190003J15Rik	2810420C16Rik|Urah	RIKEN cDNA 1190003J15 gene	protein-coding	0.01	0.574257
Merged-chr6-36355632-1	chr6	36355582	36355682	+	2.1	cIP1vsInput	"intron (NR_015589, intron 3 of 5)"	"intron (NR_015589, intron 3 of 5)"	-32452	NM_203491	243764	Mm.448632	NM_203491		Chrm2	AChR-M2|Chrm-2|M2	"cholinergic receptor, muscarinic 2, cardiac"	protein-coding	0	0.386139
Merged-chr3-150957675-1	chr3	150957625	150957725	+	2.1	cIP2vsInput	Intergenic	Intergenic	-480207	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0	0.336634
Merged-chr19-61164838-1	chr19	61164788	61164888	+	2.1	cIP1vsInput	Intergenic	Intergenic	11471	NM_001177513	633057	Mm.426097	NM_001177513	ENSMUSG00000094649	Gm7102	EG633057	predicted gene 7102	protein-coding	0.01	0.306931
Merged-chr15-89623491-1	chr15	89623441	89623541	+	2.1	cIP2vsInput	Intergenic	B3|SINE|B2	-31568	NM_026817	68708	Mm.23258	NM_026817	ENSMUSG00000022621	Rabl2	1110031N17Rik|AW549303|Rabl2a	"RAB, member of RAS oncogene family-like 2"	protein-coding	0.02	0.50495
Merged-chr5-123228344-1	chr5	123228294	123228394	+	2.1	cIP1vsInput	"exon (NM_026000, exon 1 of 6)"	"exon (NM_026000, exon 1 of 6)"	154	NM_026000	67151	Mm.278997	NM_026000	ENSMUSG00000029440	Psmd9	1500011J20Rik|2610202L11Rik|Bridge-1|P27	"proteasome (prosome, macropain) 26S subunit, non-ATPase, 9"	protein-coding	0.14	0.673267
Merged-chr14-112095016-1	chr14	112094966	112095066	+	2.1	cIP1vsInput	Intergenic	Charlie1a|DNA|hAT-Charlie	73586	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0.01	0.287129
Merged-chr14-47454681-1	chr14	47454631	47454731	+	2.1	cIP2vsInput	Intergenic	B3|SINE|B2	-17880	NR_027414	78938	Mm.11935	NM_001146085	ENSMUSG00000037536	Fbxo34	2900057B08Rik|5830426G16Rik	F-box protein 34	protein-coding	0.01	0.465347
Merged-chr1-182192173-1	chr1	182192123	182192223	+	2.1	cIP2vsInput	Intergenic	Intergenic	-34075	NM_001166728	625823	Mm.479992	NM_001166728		Vmn1r1	EG625823|Gm6628	vomeronasal 1 receptor 1	protein-coding	0.01	0.356436
Merged-chr11-47058101-1	chr11	47058051	47058151	+	2.1	cIP1vsInput	"intron (NM_011891, intron 6 of 7)"	"intron (NM_011891, intron 6 of 7)"	247302	NM_178759	276891	Mm.69002	NM_178759	ENSMUSG00000055546	Timd4	B430010N18Rik|TIM-4|Tim4	T cell immunoglobulin and mucin domain containing 4	protein-coding	0.01	0.267327
Merged-chr19-18639723-1	chr19	18639673	18639773	+	2.1	cIP2vsInput	"intron (NM_145497, intron 3 of 8)"	"intron (NM_145497, intron 3 of 8)"	7707	NM_145497	225994	Mm.211595	NM_145497	ENSMUSG00000037847	Nmrk1	AA408380|D630020N23Rik|Nrk1	nicotinamide riboside kinase 1	protein-coding	0	0.455446
Merged-chr16-10248823-1	chr16	10248773	10248873	+	2.1	cIP2vsInput	Intergenic	ID4_|SINE|ID	55917	NM_029253	75329	Mm.108729	NM_029253	ENSMUSG00000039200	Atf7ip2	4930558K11Rik|BC018510|Get-1|PSM2	activating transcription factor 7 interacting protein 2	protein-coding	0	0.366337
Merged-chrX-106595504-1	chrX	106595454	106595554	+	2.1	cIP2vsInput	"intron (NM_001033541, intron 1 of 3)"	"intron (NM_001033541, intron 1 of 3)"	7958	NM_021476	58861	Mm.287166	NM_021476		Cysltr1	BB147369|CysLT1R|Cyslt1	cysteinyl leukotriene receptor 1	protein-coding	0	0.356436
Merged-chr17-83262765-1	chr17	83262715	83262815	+	2.1	cIP1vsInput	Intergenic	Intergenic	47482	NM_134117	106522	Mm.311974	NM_134117	ENSMUSG00000024247	Pkdcc	AI115348|AW548124|Adtk1|ESTM17|MAd1|Sgk493|Vlk|X83346	"protein kinase domain containing, cytoplasmic"	protein-coding	0	0.326733
Merged-chr6-79291985-1	chr6	79291935	79292035	+	2.1	cIP1vsInput	Intergenic	Intergenic	259943	NR_040301	100504701	Mm.400420	NR_040301		Gm20362	-	"predicted gene, 20362"	miscRNA	0	0.267327
Merged-chr5-112414003-1	chr5	112413953	112414053	+	2.1	cIP2vsInput	Intergenic	Intergenic	-21790	NM_028386	72898	Mm.397047	NM_028386	ENSMUSG00000029348	Asphd2	2900006N09Rik|9230106G13Rik	aspartate beta-hydroxylase domain containing 2	protein-coding	0.01	0.376238
Merged-chr10-12318882-1	chr10	12318832	12318932	+	2.1	cIP1vsInput	Intergenic	Intergenic	542853	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding	0	0.29703
Merged-chr6-103246252-1	chr6	103246202	103246302	+	2.1	cIP2vsInput	Intergenic	Intergenic	-264624	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule with homology to L1CAM	protein-coding	0.01	0.346535
Merged-chr3-140643301-1	chr3	140643251	140643351	+	2.1	cIP2vsInput	Intergenic	Intergenic	569054	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0.01	0.386139
Merged-chr3-11422932-1	chr3	11422882	11422982	+	2.1	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	421427	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.29703
Merged-chr9-16638183-1	chr9	16638133	16638233	+	2.1	cIP1vsInput	Intergenic	Intergenic	-259952	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT tumor suppressor homolog 3 (Drosophila)	protein-coding	0	0.316832
Merged-chr14-82894129-1	chr14	82894079	82894179	+	2.1	cIP2vsInput	Intergenic	Intergenic	-1549434	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0	0.356436
Merged-chr14-90792411-1	chr14	90792361	90792461	+	2.1	cIP1vsInput	Intergenic	Intergenic	665520	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0	0.316832
Merged-chr15-65915532-1	chr15	65915482	65915582	+	2.1	cIP2vsInput	Intergenic	Intergenic	-3245	NM_010953	18256	Mm.41776	NM_010953	ENSMUSG00000015001	Oc90	Ocn-95|PLA2L|Pla2ll|oc95	otoconin 90	protein-coding	0	0.356436
Merged-chr15-46260768-1	chr15	46260718	46260818	+	2.1	cIP1vsInput	Intergenic	Intergenic	-63817	NR_045509	71120	Mm.158571	NR_045509		1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	miscRNA	0.01	0.29703
Merged-chr12-64610578-1	chr12	64610528	64610628	+	2.1	cIP1vsInput	Intergenic	Intergenic	-135680	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.346535
Merged-chr12-51296930-1	chr12	51296880	51296980	+	2.1	cIP1vsInput	Intergenic	L1M5|LINE|L1	-51300	NM_001167964	217558	Mm.253264	NM_001015099	ENSMUSG00000035293	G2e3	6030408C04Rik|9030416F18|AW046379|D930034K21Rik|mKIAA1333	G2/M-phase specific E3 ubiquitin ligase	protein-coding	0	0.267327
Merged-chr10-40044383-1	chr10	40044333	40044433	+	2.1	cIP1vsInput	"intron (NM_001114332, intron 4 of 5)"	"intron (NM_001114332, intron 4 of 5)"	-19115	NM_144821	215929	Mm.483536	NM_144821	ENSMUSG00000038522	AI317395	AI482555|Naglt1a	expressed sequence AI317395	protein-coding	0.01	0.405941
Merged-chr8-8810871-1	chr8	8810821	8810921	+	2.1	cIP2vsInput	Intergenic	Intergenic	-120334	NM_176849	234023	Mm.251655	NM_176849	ENSMUSG00000040459	Arglu1	9430010O03Rik|C130008N12	arginine and glutamate rich 1	protein-coding	0	0.346535
Merged-chr14-70466392-1	chr14	70466342	70466442	+	2.1	cIP2vsInput	"intron (NM_145981, intron 4 of 4)"	"intron (NM_145981, intron 4 of 4)"	8875	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding	0.04	0.554455
Merged-chr4-4386573-1	chr4	4386523	4386623	+	2.1	cIP1vsInput	Intergenic	Intergenic	-248128	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding	0	0.29703
Merged-chr2-39268589-1	chr2	39268539	39268639	+	2.1	cIP2vsInput	Intergenic	Intergenic	-42251	NM_024209	67857	Mm.392662	NM_024209		Ppp6c	2310003C10Rik	"protein phosphatase 6, catalytic subunit"	protein-coding	0	0.415842
Merged-chr3-65309521-1	chr3	65309471	65309571	+	2.1	cIP1vsInput	"intron (NM_010597, intron 7 of 13)"	"intron (NM_010597, intron 7 of 13)"	39908	NR_040390	319798	Mm.445698	NR_040390		A730090N16Rik	-	RIKEN cDNA A730090N16 gene	miscRNA	0.01	0.29703
Merged-chr15-90023268-1	chr15	90023218	90023318	+	2.1	cIP2vsInput	Intergenic	BLACKJACK|DNA|hAT-Blackjack	-181408	NM_018803	54526	Mm.261601	NM_018803	ENSMUSG00000063260	Syt10	-	synaptotagmin X	protein-coding	0	0.366337
Merged-chr5-69981857-1	chr5	69981807	69981907	+	2.1	cIP1vsInput	Intergenic	Intergenic	-389572	NM_001038015	67980	Mm.33830	NM_001038015	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding	0	0.386139
Merged-chr17-19995837-1	chr17	19995787	19995887	+	2.1	cIP2vsInput	Intergenic	Intergenic	52368	NM_001104566	22313	Mm.379039	NM_001104566	ENSMUSG00000090315	Vmn2r104	V2r7	"vomeronasal 2, receptor 104"	protein-coding	0	0.346535
Merged-chr1-138858713-1	chr1	138858663	138858763	+	2.1	cIP1vsInput	Intergenic	Intergenic	-1859	NM_001081226	69549	Mm.487694	NM_001081226	ENSMUSG00000079283	2310009B15Rik	-	RIKEN cDNA 2310009B15 gene	protein-coding	0	0.435644
Merged-chrX-120292887-1	chrX	120292837	120292937	+	2.1	cIP2vsInput	"intron (NR_073452, intron 1 of 6)"	CpG	2560	NR_073451	245578	Mm.490224	NM_001271809		Pcdh11x	PCDHX|PCDHX11|Pcdh11	protocadherin 11 X-linked	protein-coding	0.1	0.643564
Merged-chr17-67254348-1	chr17	67254298	67254398	+	2.1	cIP2vsInput	"intron (NM_008984, intron 1 of 30)"	RLTR40|LTR|ERVK	100111	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	"protein tyrosine phosphatase, receptor type, M"	protein-coding	0	0.366337
Merged-chr9-10288855-2	chr9	10288778	10288932	+	2.05	cIP1vsInput|cIP2vsInput	"intron (NM_001170787, intron 3 of 24)"	"intron (NM_001170787, intron 3 of 24)"	615871	NM_001033359	244682	Mm.490683	NM_001033359	ENSMUSG00000039488	Cntn5	6720426O10Rik|A830025P08Rik|Gm507|NB-2	contactin 5	protein-coding	0	0.335484
Merged-chr3-13973445-2	chr3	13973352	13973538	+	2.05	cIP1vsInput|cIP2vsInput	"intron (NM_001163329, intron 1 of 7)"	"intron (NM_001163329, intron 1 of 7)"	27073	NM_001163330	76897	Mm.422625	NM_001163328	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0.005376	0.299465
Merged-chr1-104724136-2	chr1	104724075	104724197	+	2.05	cIP1vsInput|cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-44683	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0	0.341463
Merged-chr4-78379175-2	chr4	78379086	78379264	+	2.05	cIP1vsInput|cIP2vsInput	Intergenic	Lx3C|LINE|L1	-167280	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0	0.340782
Merged-chr2-114945697-2	chr2	114945636	114945758	+	2.05	cIP1vsInput|cIP2vsInput	Intergenic	L1MC1|LINE|L1	-290769	NM_025675	66632	Mm.117809	NM_025675	ENSMUSG00000057147	Atpbd4	5730421E18Rik	ATP binding domain 4	protein-coding	0	0.349593
Merged-chr7-134098806-2	chr7	134098723	134098890	+	2.05	cIP1vsInput|cIP2vsInput	"intron (NM_007400, intron 3 of 22)"	"intron (NM_007400, intron 3 of 22)"	126291	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna|mKIAA4001	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding	0.005988	0.321429
Merged-chr18-44989114-2	chr18	44989047	44989182	+	2.05	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	160449	NM_001163013	240255	Mm.244482	NM_001163013	ENSMUSG00000034653	Ythdc2	3010002F02Rik|BC037178	YTH domain containing 2	protein-coding	0	0.308824
Merged-chr14-65026281-2	chr14	65026220	65026343	+	2.05	cIP1vsInput|cIP2vsInput	"intron (NM_153414, intron 10 of 16)"	"intron (NM_153414, intron 10 of 16)"	71825	NM_018788	54616	Mm.103748	NM_018788	ENSMUSG00000021978	Extl3	2900009G18Rik|AU040105|Ext1l|mKIAA0519	exostoses (multiple)-like 3	protein-coding	0	0.41129
Merged-chr13-105959687-2	chr13	105959606	105959769	+	2.05	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	515994	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0	0.329268
Merged-chr1-18522983-1	chr1	18522933	18523033	+	2	cIP2vsInput	Intergenic	Lx9|LINE|L1	-257845	NM_001040027	654464	Mm.99530	NM_001040027		Gm15386	BD-17|Defb17|OTTMUSG00000020946|OTTMUSG00000020948	predicted gene 15386	protein-coding	0	0.435644
Merged-chr9-4950427-1	chr9	4950377	4950477	+	2	cIP2vsInput	Intergenic	Intergenic	-154193	NM_019691	14802	Mm.209263	NM_001113180	ENSMUSG00000025892	Gria4	GluA4|GluR-D|Glur-4|Glur4|Gluralpha4|spkw1	"glutamate receptor, ionotropic, AMPA4 (alpha 4)"	protein-coding	0	0.336634
Merged-chr7-81753330-1	chr7	81753280	81753380	+	2	cIP2vsInput	Intergenic	Intergenic	-9623	NM_025997	67148	Mm.241472	NM_025997	ENSMUSG00000038646	Fam103a1	2410047I02Rik|2610204K14Rik|RAM	"family with sequence similarity 103, member A1"	protein-coding	0	0.336634
Merged-chr12-100502923-1	chr12	100502873	100502973	+	2	cIP2vsInput	"intron (NM_001033213, intron 1 of 19)"	"intron (NM_001033213, intron 1 of 19)"	17899	NM_001033213	104718	Mm.295441	NM_001033213	ENSMUSG00000033530	Ttc7b	AA408451|Ttc7l1	tetratricopeptide repeat domain 7B	protein-coding	0	0.564356
Merged-chr12-30069036-1	chr12	30068986	30069086	+	2	cIP2vsInput	"intron (NM_009417, intron 16 of 16)"	RLTR19-int|LTR|ERVK	63573	NM_009417	22018	Mm.4991	NM_009417	ENSMUSG00000020673	Tpo	-	thyroid peroxidase	protein-coding	0.01	0.326733
Merged-chr1-141268779-1	chr1	141268729	141268829	+	2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-612377	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0	0.316832
Merged-chr2-101391743-1	chr2	101391693	101391793	+	2	cIP2vsInput	Intergenic	Lx2B|LINE|L1	-233005	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding	0	0.336634
Merged-chr10-36668201-1	chr10	36668151	36668251	+	2	cIP2vsInput	"intron (NM_001081208, intron 2 of 3)"	"intron (NM_001081208, intron 2 of 3)"	161394	NM_001253356	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0	0.336634
Merged-chr11-49364151-1	chr11	49364101	49364201	+	2	cIP2vsInput	Intergenic	Intergenic	23617	NM_147065	259068	Mm.377819	NM_147065	ENSMUSG00000045421	Olfr1390	MOR256-2	olfactory receptor 1390	protein-coding	0	0.346535
Merged-chr2-123959259-1	chr2	123959209	123959309	+	2	cIP1vsInput	Intergenic	Intergenic	170697	NR_040611	74702	Mm.410814	NR_040611	ENSMUSG00000085496	4930517E11Rik	-	RIKEN cDNA 4930517E11 gene	miscRNA	0	0.306931
Merged-chr13-104858361-1	chr13	104858311	104858411	+	2	cIP2vsInput	"exon (NM_029984, exon 2 of 3)"	"exon (NM_029984, exon 2 of 3)"	5532	NM_029984	77803	Mm.159995	NM_029984	ENSMUSG00000042655	Fam159b	A930021C24Rik	"family with sequence similarity 159, member B"	protein-coding	0	0.39604
Merged-chr12-96505763-1	chr12	96505713	96505813	+	2	cIP2vsInput	Intergenic	Lx10|LINE|L1	-458541	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0	0.346535
Merged-chr3-93062612-1	chr3	93062562	93062662	+	2	cIP2vsInput	Intergenic	Intergenic	-6211	NM_001034860	229571	Mm.331194	NM_001034860		Gm4858	EG229571	predicted gene 4858	protein-coding	0	0.415842
Merged-chr5-104561861-1	chr5	104561811	104561911	+	2	cIP2vsInput	Intergenic	Intergenic	36126	NR_030673	100662	Mm.319836	NR_030673	ENSMUSG00000097392	D930016D06Rik	100041172|1110004B06Rik|AI451450|Gm3179	RIKEN cDNA D930016D06 gene	miscRNA	0	0.39604
Merged-chrX-132081931-1	chrX	132081881	132081981	+	2	cIP2vsInput	Intergenic	Lx3_Mus|LINE|L1	1607062	NM_001105245	279653	Mm.39738	NM_001105245	ENSMUSG00000051323	Pcdh19	B530002L05Rik|Gm717|mKIAA1313	protocadherin 19	protein-coding	0	0.346535
Merged-chr5-78390460-1	chr5	78390410	78390510	+	2	cIP2vsInput	Intergenic	Intergenic	-878712	NR_027806	231332	Mm.373616	NM_001010832		Pea15b	-	phosphoprotein enriched in astrocytes 15B	pseudo	0.01	0.326733
Merged-chr18-69850868-1	chr18	69850818	69850918	+	2	cIP2vsInput	Intergenic	Intergenic	-74691	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding	0	0.386139
Merged-chr5-40333402-1	chr5	40333352	40333452	+	2	cIP2vsInput	Intergenic	Intergenic	-688771	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding	0	0.306931
Merged-chrX-156184911-1	chrX	156184861	156184961	+	2	cIP1vsInput	Intergenic	Intergenic	-354572	NR_033598	74941	Mm.484588	NR_033598		4930503H13Rik	-	gem (nuclear organelle) associated protein 8 pseudogene	pseudo	0	0.316832
Merged-chr8-64608365-1	chr8	64608315	64608415	+	2	cIP2vsInput	"intron (NM_013494, intron 5 of 8)"	"intron (NM_013494, intron 5 of 8)"	84675	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|R74677|fat	carboxypeptidase E	protein-coding	0	0.356436
Merged-chr6-134969050-1	chr6	134969000	134969100	+	2	cIP1vsInput	Intergenic	Intergenic	-12951	NM_001109914	381823	Mm.296104	NM_001109914	ENSMUSG00000090698	Apold1	Gm1075	apolipoprotein L domain containing 1	protein-coding	0	0.376238
Merged-chr11-19823926-1	chr11	19823876	19823976	+	2	cIP2vsInput	Intergenic	Lx7|LINE|L1	-100516	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	"sprouty-related, EVH1 domain containing 2"	protein-coding	0.01	0.386139
Merged-chr18-28278303-1	chr18	28278253	28278353	+	2	cIP2vsInput	Intergenic	Intergenic	-281861	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	miscRNA	0	0.287129
Merged-chr3-158109686-1	chr3	158109636	158109736	+	2	cIP2vsInput	"intron (NM_001081358, intron 26 of 27)"	"intron (NM_001081358, intron 26 of 27)"	72983	NM_024194	67144	Mm.358704	NM_024194	ENSMUSG00000063052	Lrrc40	2610040E16Rik|AI837674	leucine rich repeat containing 40	protein-coding	0	0.306931
Merged-chr9-68181012-1	chr9	68180962	68181062	+	2	cIP2vsInput	Intergenic	Lx5b|LINE|L1	-155298	NR_045745	434412	Mm.490707	NR_045745		Gm20745	-	"predicted gene, 20745"	miscRNA	0	0.39604
Merged-chr13-27113234-1	chr13	27113184	27113284	+	2	cIP2vsInput	Intergenic	Lx8|LINE|L1	-8470	NM_172155	215028	Mm.458451	NM_172155	ENSMUSG00000062737	Prl3d2	PL-Ib|Plib	"prolactin family 3, subfamily d, member 1"	protein-coding	0	0.346535
Merged-chr2-104112190-1	chr2	104112140	104112240	+	2	cIP1vsInput	"intron (NM_001111060, intron 4 of 4)"	"intron (NM_001111060, intron 4 of 4)"	-10579	NM_026634	68243	Mm.158191	NM_026634	ENSMUSG00000032671	A930018P22Rik	-	RIKEN cDNA A930018P22 gene	protein-coding	0.01	0.316832
Merged-chr6-135998710-1	chr6	135998660	135998760	+	2	cIP1vsInput	"intron (NM_008171, intron 4 of 14)"	"intron (NM_008171, intron 4 of 14)"	174801	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	"glutamate receptor, ionotropic, NMDA2B (epsilon 2)"	protein-coding	0	0.386139
Merged-chr13-99647811-1	chr13	99647761	99647861	+	2	cIP2vsInput	Intergenic	RMER1A|Other|Other	-131209	NM_008634	17755	Mm.474896	NM_008634	ENSMUSG00000052727	Map1b	A230055D22|AI843217|LC1|MAP5|Mtap-5|Mtap1b|Mtap5	microtubule-associated protein 1B	protein-coding	0.02	0.584158
Merged-chr6-149583889-1	chr6	149583839	149583939	+	2	cIP2vsInput	Intergenic	MMSAT4|Satellite|Satellite	175003	NM_009753	12121	Mm.260763	NM_001112796		Bicd1	B830009D06Rik|mKIAA4125	bicaudal D homolog 1 (Drosophila)	protein-coding	0	0.316832
Merged-chr4-46569849-1	chr4	46569799	46569899	+	2	cIP2vsInput	"intron (NM_001164804, intron 1 of 11)"	"intron (NM_001164804, intron 1 of 11)"	-3409	NM_178893	107684	Mm.485361	NM_001164804	ENSMUSG00000028337	Coro2a	9030208C03Rik|AI563590|IR10	"coronin, actin binding protein 2A"	protein-coding	0.01	0.514851
Merged-chr4-64815306-1	chr4	64815256	64815356	+	2	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-308868	NM_021362	18491	Mm.317854	NM_021362	ENSMUSG00000028370	Pappa	8430414N03Rik|IGFBP-4ase|PAG1|PAPP-A	pregnancy-associated plasma protein A	protein-coding	0	0.366337
Merged-chr18-87951620-1	chr18	87951570	87951670	+	2	cIP1vsInput	Intergenic	Intergenic	942587	NM_018821	54607	Mm.476577	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding	0	0.267327
Merged-chr15-28551714-1	chr15	28551664	28551764	+	2	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	347948	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnahc5	AU022615|Dnah5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	"dynein, axonemal, heavy chain 5"	protein-coding	0	0.366337
Merged-chr7-27850000-1	chr7	27849950	27850050	+	2	cIP2vsInput	"intron (NM_011762, intron 4 of 4)"	Lx5|LINE|L1	-10585	NM_001024726	545938	Mm.458180	NM_001024726		Zfp607	4732475C15Rik	zinc finger proten 607	protein-coding	0.01	0.336634
Merged-chr8-34429542-1	chr8	34429492	34429592	+	2	cIP2vsInput	Intergenic	Intergenic	210774	NR_040706	330734	Mm.149998	NR_040706		B930018H19Rik	B930018H19	RIKEN cDNA B930018H19 gene	miscRNA	0.01	0.465347
Merged-chr2-102783879-1	chr2	102783829	102783929	+	2	cIP2vsInput	"3' UTR (NM_001077514, exon 11 of 11)"	"3' UTR (NM_001077514, exon 11 of 11)"	77441	NM_001077515	20511	Mm.371582	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	"solute carrier family 1 (glial high affinity glutamate transporter), member 2"	protein-coding	0	0.445545
Merged-chr16-10252262-1	chr16	10252212	10252312	+	2	cIP2vsInput	Intergenic	Intergenic	59356	NM_029253	75329	Mm.108729	NM_029253	ENSMUSG00000039200	Atf7ip2	4930558K11Rik|BC018510|Get-1|PSM2	activating transcription factor 7 interacting protein 2	protein-coding	0	0.366337
Merged-chr5-109386650-1	chr5	109386600	109386700	+	2	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-33363	NM_001104628	384221	Mm.469879	NM_001104628	ENSMUSG00000091879	Vmn2r17	EG384221	"vomeronasal 2, receptor 17"	protein-coding	0.01	0.336634
Merged-chr3-102864451-1	chr3	102864401	102864501	+	2	cIP2vsInput	"intron (NM_011516, intron 24 of 32)"	"intron (NM_011516, intron 24 of 32)"	71649	NM_011516	20957	Mm.243849	NM_011516	ENSMUSG00000027855	Sycp1	SCP1	synaptonemal complex protein 1	protein-coding	0	0.306931
Merged-chr3-80940898-1	chr3	80940848	80940948	+	2	cIP2vsInput	Intergenic	Intergenic	-27274	NM_010298	14658	Mm.275639	NM_010298	ENSMUSG00000028020	Glrb	AI853901|Glyrb|spa|spastic	"glycine receptor, beta subunit"	protein-coding	0	0.316832
Merged-chr6-81296269-1	chr6	81296219	81296319	+	2	cIP2vsInput	Intergenic	Lx6|LINE|L1	600407	NR_030151	723871		NR_030151		Mir468	Mirn468|mmu-mir-468	microRNA 468	miscRNA	0	0.336634
Merged-chr12-72311928-1	chr12	72311878	72311978	+	2	cIP2vsInput	"intron (NM_153457, intron 1 of 8)"	Ricksha_a|DNA|MULE-MuDR	-75204	NM_001007596	104001	Mm.221275	NM_001007596	ENSMUSG00000021087	Rtn1	0710005K15Rik|4930441F12Rik|Nsp|R75279|Rtn1-a|Rtn1-b|Rtn1-c	reticulon 1	protein-coding	0.01	0.29703
Merged-chr3-155152684-1	chr3	155152634	155152734	+	2	cIP2vsInput	"intron (NM_028938, intron 5 of 7)"	"intron (NM_028938, intron 5 of 7)"	59250	NM_028938	74435	Mm.195711	NM_028938	ENSMUSG00000028182	Lrriq3	4930438B07Rik|4930511J15Rik|4933403H06Rik|BB020367|Lrrc44	leucine-rich repeats and IQ motif containing 3	protein-coding	0	0.287129
Merged-chr15-14542604-1	chr15	14542554	14542654	+	2	cIP2vsInput	Intergenic	Intergenic	-1368965	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	K-cadherin|cad6|cadherin-6	cadherin 6	protein-coding	0.02	0.316832
Merged-chr7-85234357-1	chr7	85234307	85234407	+	2	cIP2vsInput	"intron (NM_001105181, intron 2 of 5)"	"intron (NM_001105181, intron 2 of 5)"	3347	NM_001105181	620697	Mm.389945	NM_001105181	ENSMUSG00000096861	Vmn2r68	EG620697|Vmn2r68-ps	"vomeronasal 2, receptor 68"	protein-coding	0	0.306931
Merged-chr14-115630557-1	chr14	115630507	115630607	+	2	cIP2vsInput	"intron (NM_175500, intron 6 of 7)"	L1M4a1|LINE|L1	-221005	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	miscRNA	0	0.415842
Merged-chr3-102400587-1	chr3	102400537	102400637	+	2	cIP2vsInput	Intergenic	Intergenic	-69341	NM_001112698	18049	Mm.1259	NM_001112698	ENSMUSG00000027859	Ngf	Ngfb	nerve growth factor	protein-coding	0	0.306931
Merged-chr10-30303401-1	chr10	30303351	30303451	+	2	cIP2vsInput	Intergenic	MMERVK9E_I-int|LTR|ERVK	-102861	NM_001109747	66311	Mm.251779	NM_001109747	ENSMUSG00000075266	Cenpw	2610036L11Rik|Cug2	centromere protein W	protein-coding	0.01	0.316832
Merged-chr9-48549009-1	chr9	48548959	48549059	+	2	cIP1vsInput	Intergenic	L1MC2|LINE|L1	53666	NM_001004191	434402	Mm.386950	NM_001004191	ENSMUSG00000042293	Gm5617	EG434402	predicted gene 5617	protein-coding	0.02	0.316832
Merged-chr4-82748595-1	chr4	82748545	82748645	+	2	cIP2vsInput	Intergenic	Lx|LINE|L1	111066	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	"zinc finger, DHHC domain containing 21"	protein-coding	0.01	0.366337
Merged-chr11-24348024-1	chr11	24347974	24348074	+	2	cIP2vsInput	Intergenic	Intergenic	-133885	NR_045857	71316	Mm.79162	NR_045857	ENSMUSG00000086892	4933430M04Rik	-	RIKEN cDNA 4933430M04 gene	miscRNA	0	0.29703
Merged-chr17-47024593-1	chr17	47024543	47024643	+	2	cIP2vsInput	Intergenic	MYSERV6-int|LTR|ERVK	-14061	NM_001177374	224826	Mm.28234	NM_001177374	ENSMUSG00000023977	Ubr2	9930021A08Rik|AI462103|AW540746|E130209G04Rik|mKIAA0349	ubiquitin protein ligase E3 component n-recognin 2	protein-coding	0.01	0.326733
Merged-chr13-76515709-1	chr13	76515659	76515759	+	2	cIP2vsInput	"intron (NM_030174, intron 1 of 20)"	"intron (NM_030174, intron 1 of 20)"	130748	NM_030174	78771	Mm.316249	NM_030174		Mctp1	2810465F10Rik	"multiple C2 domains, transmembrane 1"	protein-coding	0	0.336634
Merged-chr14-36104210-1	chr14	36104160	36104260	+	2	cIP2vsInput	Intergenic	Intergenic	9245	NM_175008	218921	Mm.212464	NM_175008	ENSMUSG00000096405	4930474N05Rik	-	RIKEN cDNA 4930474N05 gene	protein-coding	0	0.366337
Merged-chr14-92328493-1	chr14	92328443	92328543	+	2	cIP2vsInput	Intergenic	L1M3|LINE|L1	1560395	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0.02	0.306931
Merged-chr5-79018748-1	chr5	79018698	79018798	+	2	cIP2vsInput	"intron (NR_035474, intron 3 of 4)"	"intron (NR_035474, intron 3 of 4)"	497156	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0	0.356436
Merged-chr2-64580052-1	chr2	64580002	64580102	+	2	cIP2vsInput	Intergenic	L1M4b|LINE|L1	442714	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding	0.01	0.316832
Merged-chr6-132333754-1	chr6	132333704	132333804	+	2	cIP2vsInput	"intron (NM_053251, intron 4 of 6)"	"intron (NM_053251, intron 4 of 6)"	-19011	NM_001024705	381832	Mm.441627	XM_003946205	ENSMUSG00000052262	Prpmp5	MP5	proline-rich protein MP5	protein-coding	0	0.326733
Merged-chr8-100683370-1	chr8	100683320	100683420	+	2	cIP2vsInput	Intergenic	Intergenic	-1266913	NM_001039154	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.316832
Merged-chr3-68282145-1	chr3	68282095	68282195	+	2	cIP2vsInput	"intron (NM_001113420, intron 1 of 6)"	L1MA6|LINE|L1	-212048	NR_036665	30953	Mm.331064	NM_001113420	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding	0	0.346535
Merged-chr13-91325993-1	chr13	91325943	91326043	+	2	cIP2vsInput	Intergenic	Intergenic	62092	NR_045161	320297	Mm.375866	NR_045161	ENSMUSG00000097182	A830009L08Rik	-	RIKEN cDNA A830009L08 gene	miscRNA	0	0.326733
Merged-chr6-22551043-1	chr6	22550993	22551093	+	2	cIP2vsInput	Intergenic	Intergenic	-194962	NM_138587	27999	Mm.490307	NM_138587	ENSMUSG00000029672	Fam3c	D6Wsu176e|Ilei	"family with sequence similarity 3, member C"	protein-coding	0.03	0.415842
Merged-chr13-84868413-1	chr13	84868363	84868463	+	2	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-321064	NM_023243	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding	0.01	0.316832
Merged-chr8-53939673-1	chr8	53939623	53939723	+	2	cIP2vsInput	Intergenic	Intergenic	-137859	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding	0.01	0.356436
Merged-chr10-31737806-1	chr10	31737756	31737856	+	2	cIP2vsInput	"intron (NM_001013411, intron 5 of 6)"	"intron (NM_001013411, intron 5 of 6)"	-128081	NM_001146349	268291	Mm.295212	NM_001146349		Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding	0.02	0.277228
Merged-chrX-69325504-1	chrX	69325454	69325554	+	2	cIP2vsInput	Intergenic	Intergenic	-34827	NM_008032	14266	Mm.466576	NM_008032	ENSMUSG00000031189	Aff2	FMR2P|Fmr2|Ox19|Oxh	"AF4/FMR2 family, member 2"	protein-coding	0	0.316832
Merged-chr13-50360383-1	chr13	50360333	50360433	+	2	cIP2vsInput	Intergenic	Intergenic	-57494	NM_175401	109082	Mm.18638	NM_175401	ENSMUSG00000037816	Fbxw17	1110064L07Rik|C85886	F-box and WD-40 domain protein 17	protein-coding	0	0.267327
Merged-chr13-75202757-1	chr13	75202707	75202807	+	2	cIP1vsInput	Intergenic	Intergenic	112770	NM_013628	18548	Mm.1333	NM_013628	ENSMUSG00000021587	Pcsk1	Nec-1|Nec1|PC1|PC3|Phpp-1|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0.01	0.316832
Merged-chr10-11847449-1	chr10	11847399	11847499	+	2	cIP2vsInput	Intergenic	L3b|LINE|CR1	504004	NM_010146	13853	Mm.89946	NM_010146		Epm2a	"TG-B|Tg(TcraK,TcrbK)TG-BFlv"	"epilepsy, progressive myoclonic epilepsy, type 2 gene alpha"	protein-coding	0.01	0.366337
Merged-chr11-28138122-1	chr11	28138072	28138172	+	2	cIP2vsInput	Intergenic	Intergenic	446174	NM_001166661	216613	Mm.93759	NM_001166661	ENSMUSG00000032878	Ccdc85a	E030025D05Rik	coiled-coil domain containing 85A	protein-coding	0	0.277228
Merged-chr7-53221575-1	chr7	53221525	53221625	+	2	cIP1vsInput	Intergenic	Intergenic	-1205859	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding	0	0.29703
Merged-chr2-180104567-1	chr2	180104517	180104617	+	2	cIP2vsInput	promoter-TSS (NM_133849)	promoter-TSS (NM_133849)	-160	NM_133849	99296	Mm.285360	NM_133849	ENSMUSG00000039059	Hrh3	AW049250|H3R|HH3R	histamine receptor H3	protein-coding	0.18	0.811881
Merged-chr8-50127178-1	chr8	50127128	50127228	+	2	cIP2vsInput	Intergenic	Intergenic	-240934	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.227723
Merged-chr17-39195765-1	chr17	39195715	39195815	+	2	cIP2vsInput	Intergenic	Intergenic	-118728	NM_001177582	100126779	Mm.471589	NM_001177582	ENSMUSG00000096697	Gm20581	Esp23	"predicted gene, 20581"	protein-coding	0	0.386139
Merged-chr2-98438913-1	chr2	98438863	98438963	+	2	cIP2vsInput	Intergenic	Intergenic	971239	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.326733
Merged-chr18-8353171-1	chr18	8353121	8353221	+	2	cIP1vsInput	Intergenic	L1_Mus1|LINE|L1	483974	NM_153085	225131	Mm.204524	NM_001146298	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding	0	0.346535
Merged-chr18-74150480-1	chr18	74150430	74150530	+	2	cIP2vsInput	Intergenic	Intergenic	57338	NM_001164355	66468	Mm.283406	NM_001164355	ENSMUSG00000036223	Ska1	2810433K01Rik|AV117428	spindle and kinetochore associated complex subunit 1	protein-coding	0	0.346535
Merged-chr9-90326103-1	chr9	90326053	90326153	+	2	cIP2vsInput	Intergenic	Intergenic	-55334	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	"TBC1 domain family, member 2B"	protein-coding	0	0.267327
Merged-chr3-20446840-1	chr3	20446790	20446890	+	2	cIP1vsInput	Intergenic	L1_Mur1|LINE|L1	-79663	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	"angiotensin II receptor, type 1b"	protein-coding	0	0.336634
Merged-chrX-128155495-1	chrX	128155445	128155545	+	2	cIP2vsInput	Intergenic	L1MB3|LINE|L1	761202	NR_003646	245598	Mm.72281	NR_003646	ENSMUSG00000049815	4921511C20Rik	Gm383	high density lipoprotein (HDL) binding protein pseudogene	pseudo	0	0.376238
Merged-chr4-49781763-1	chr4	49781713	49781813	+	2	cIP2vsInput	"intron (NM_001276355, intron 2 of 8)"	"intron (NM_001276355, intron 2 of 8)"	64006	NM_001033351	242443	Mm.440095	NM_001033351		Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	"glutamate receptor ionotropic, NMDA3A"	protein-coding	0	0.29703
Merged-chr3-156494651-1	chr3	156494601	156494701	+	2	cIP1vsInput	Intergenic	Intergenic	67036	NR_040398	329782	Mm.183459	NR_040398	ENSMUSG00000085084	4930570G19Rik	C630015G22	RIKEN cDNA 4930570G19 gene	miscRNA	0	0.386139
Merged-chr10-74526520-1	chr10	74526470	74526570	+	2	cIP1vsInput	"intron (NM_001142736, intron 25 of 32)"	L1_Mur1|LINE|L1	-440711	NM_010311	14687	Mm.393508	NM_010311		Gnaz	AI847979|Gz	"guanine nucleotide binding protein, alpha z subunit"	protein-coding	0	0.356436
Merged-chr8-29875069-1	chr8	29875019	29875119	+	2	cIP2vsInput	Intergenic	Intergenic	-655433	NM_153135	210801	Mm.248433	NM_153135	ENSMUSG00000063626	Unc5d	D930029E11Rik|Unc5h4|mKIAA1777	unc-5 homolog D (C. elegans)	protein-coding	0	0.29703
Merged-chr1-29613943-1	chr1	29613893	29613993	+	2	cIP1vsInput	Intergenic	Intergenic	-833691	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0.01	0.316832
Merged-chr18-51160811-1	chr18	51160761	51160861	+	2	cIP2vsInput	"intron (NM_001081224, intron 1 of 1)"	"intron (NM_001081224, intron 1 of 1)"	42913	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding	0.01	0.376238
Merged-chr10-47027231-1	chr10	47027181	47027281	+	2	cIP2vsInput	Intergenic	Intergenic	782482	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0	0.316832
Merged-chr8-60347166-1	chr8	60347116	60347216	+	2	cIP2vsInput	Intergenic	Intergenic	-158958	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|mKat-2	aminoadipate aminotransferase	protein-coding	0	0.326733
Merged-chr16-31897100-1	chr16	31897050	31897150	+	2	cIP2vsInput	"intron (NM_013900, intron 15 of 15)"	"intron (NM_013900, intron 15 of 15)"	18290	NM_013900	30060	Mm.30988	NM_013900	ENSMUSG00000022780	Mfi2	CD228|MTf	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	protein-coding	0.04	0.673267
Merged-chr10-52607009-1	chr10	52606959	52607059	+	2	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-61270	NR_037920	22639	Mm.490597	NM_009540	ENSMUSG00000049576	Zfa-ps	Zfa|Zfx	"zinc finger protein, autosomal, pseudogene"	pseudo	0.01	0.29703
Merged-chr4-36545744-1	chr4	36545694	36545794	+	2	cIP1vsInput	"intron (NM_001166000, intron 1 of 8)"	L2|LINE|L2	99709	NR_030545	100124458		NR_030545	ENSMUSG00000077851	Mir876	Mirn876|mmu-mir-876	microRNA 876	miscRNA	0	0.366337
Merged-chr8-39303522-1	chr8	39303472	39303572	+	2	cIP2vsInput	"intron (NR_044988, intron 1 of 3)"	"intron (NR_044988, intron 1 of 3)"	5542	NR_044988	621335	Mm.208080	NR_044988		Gm6213	EG621335	predicted gene 6213	miscRNA	0.01	0.366337
Merged-chr17-73680228-1	chr17	73680178	73680278	+	2	cIP2vsInput	"intron (NM_027864, intron 1 of 14)"	L1M5|LINE|L1	30223	NM_027864	71685	Mm.271953	NM_027864	ENSMUSG00000024064	Galnt14	0610033M06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14	protein-coding	0	0.386139
Merged-chr14-37352755-1	chr14	37352705	37352805	+	2	cIP1vsInput	Intergenic	Intergenic	-217433	NM_078478	66092	Mm.486242	NM_001199122	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010	growth hormone inducible transmembrane protein	protein-coding	0	0.455446
Merged-chr9-93244972-1	chr9	93244922	93245022	+	2	cIP2vsInput	Intergenic	Intergenic	-239239	NR_040756	78349	Mm.52612	NR_040756		1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	miscRNA	0	0.386139
Merged-chr10-70072408-1	chr10	70072358	70072458	+	2	cIP1vsInput	Intergenic	Intergenic	-24713	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding	0.01	0.465347
Merged-chr16-68632985-1	chr16	68632935	68633035	+	2	cIP2vsInput	Intergenic	RLTR24|LTR|ERV1	-1012077	NM_178721	239857	Mm.394300	NM_001145977	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding	0	0.366337
Merged-chr18-86230965-1	chr18	86230915	86231015	+	2	cIP2vsInput	Intergenic	Lx10|LINE|L1	-163987	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding	0	0.386139
Merged-chr1-42163100-1	chr1	42163050	42163150	+	2	cIP2vsInput	Intergenic	Intergenic	531725	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	2610017I09Rik	-	RIKEN cDNA 2610017I09 gene	miscRNA	0	0.326733
Merged-chr16-86179153-1	chr16	86179103	86179203	+	2	cIP2vsInput	Intergenic	Intergenic	-278028	NM_011782	23794	Mm.437478	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|AI481094|ASMP-2	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"	protein-coding	0	0.287129
Merged-chr11-119849767-1	chr11	119849717	119849817	+	2	cIP1vsInput	"intron (NM_028898, intron 16 of 33)"	Lx4A|LINE|L1	-15402	NR_045312	319454	Mm.442144	NR_045312	ENSMUSG00000085081	A430071A18Rik	-	RIKEN cDNA A430071A18 gene	miscRNA	0	0.346535
Merged-chr5-146330738-1	chr5	146330688	146330788	+	2	cIP2vsInput	Intergenic	Intergenic	-54268	NM_145155	245880	Mm.472750	NM_145155		Wasf3	Scar3|Wave3	"WAS protein family, member 3"	protein-coding	0.01	0.326733
Merged-chr1-48717532-1	chr1	48717482	48717582	+	2	cIP1vsInput	Intergenic	Intergenic	-1864023	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.267327
Merged-chr14-50299950-1	chr14	50299900	50300000	+	2	cIP2vsInput	promoter-TSS (NM_146663)	promoter-TSS (NM_146663)	-620	NM_146663	258657	Mm.377620	NM_146663	ENSMUSG00000090874	Olfr733	MOR241-2	olfactory receptor 733	protein-coding	0	0.376238
Merged-chr3-83852624-1	chr3	83852574	83852674	+	2	cIP2vsInput	Intergenic	MYSERV16_I-int|LTR|ERVK	-11016	NM_011905	24088	Mm.87596	NM_011905	ENSMUSG00000027995	Tlr2	Ly105	toll-like receptor 2	protein-coding	0	0.326733
Merged-chr8-3568205-1	chr8	3568155	3568255	+	2	cIP2vsInput	"intron (NM_001024728, intron 1 of 5)"	B1_Mur2|SINE|Alu	207	NM_001024728	546049	Mm.428003	NM_001024728	ENSMUSG00000065952	C330021F23Rik	2610027C06Rik|Rps23r1|Rps23rg1	RIKEN cDNA C330021F23 gene	protein-coding	0.02	0.485149
Merged-chr14-83815442-1	chr14	83815392	83815492	+	2	cIP2vsInput	Intergenic	Intergenic	-628121	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0.01	0.346535
Merged-chr10-98005181-1	chr10	98005131	98005231	+	2	cIP2vsInput	Intergenic	Lx7|LINE|L1	-38091	NR_033537	100038699	Mm.467933	NR_033537		Gm10754	ENSMUSG00000074776	predicted gene 10754	miscRNA	0	0.316832
Merged-chr6-138530014-1	chr6	138529964	138530064	+	2	cIP2vsInput	"intron (NM_207222, intron 1 of 4)"	RLTR13D2|LTR|ERVK	51954	NM_207222	109593	Mm.490545	NM_207222		Lmo3	AI854781|BB106490|Rbtn-3|Rbtn3	LIM domain only 3	protein-coding	0	0.356436
Merged-chrX-118804494-1	chrX	118804444	118804544	+	2	cIP1vsInput	Intergenic	Intergenic	-323757	NM_001142750	100039551	Mm.423457	NM_001142750	ENSMUSG00000063242	Tgif2lx2	-	"TGFB-induced factor homeobox 2-like, X-linked 2"	protein-coding	0.01	0.306931
Merged-chr6-148685189-1	chr6	148685139	148685239	+	2	cIP1vsInput	Intergenic	Intergenic	-70880	NR_045867	622319	Mm.491049	NM_001037912	ENSMUSG00000070995	Gm6313	EG622319	predicted gene 6313	miscRNA	0	0.29703
Merged-chr14-38618520-1	chr14	38618470	38618570	+	2	cIP2vsInput	"intron (NM_001190188, intron 3 of 8)"	"intron (NM_001190188, intron 3 of 8)"	-279782	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	4930529F24Rik	-	RIKEN cDNA 4930529F24 gene	miscRNA	0.01	0.376238
Merged-chr1-157634237-1	chr1	157634187	157634287	+	2	cIP2vsInput	Intergenic	Intergenic	108067	NM_001159986	89867	Mm.87114	NM_001159986	ENSMUSG00000026589	Sec16b	Lztr2|Rgpr|Rgpr-p117	SEC16 homolog B (S. cerevisiae)	protein-coding	0	0.326733
Merged-chr15-26911979-1	chr15	26911929	26912029	+	2	cIP2vsInput	Intergenic	L2|LINE|L2	-16415	NM_176959	448987	Mm.253378	NM_176959		Fbxl7	AL023057|D230018M15Rik|FBL7|Fbl6	F-box and leucine-rich repeat protein 7	protein-coding	0.01	0.376238
Merged-chr6-140883000-1	chr6	140882950	140883050	+	2	cIP2vsInput	Intergenic	Intergenic	258702	NM_009637	11569	Mm.479349	NM_001005605	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding	0.02	0.336634
Merged-chr18-64217073-1	chr18	64217023	64217123	+	2	cIP2vsInput	"intron (NR_045366, intron 2 of 5)"	L1MA5A|LINE|L1	-37286	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	"ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3"	protein-coding	0	0.405941
Merged-chr4-105061728-1	chr4	105061678	105061778	+	2	cIP2vsInput	"intron (NM_178143, intron 2 of 8)"	L2|LINE|L2	48170	NM_178143	108079	Mm.48638	NM_178143	ENSMUSG00000028518	Prkaa2	2310008I11Rik|A830082D05|AMPKalpha2	"protein kinase, AMP-activated, alpha 2 catalytic subunit"	protein-coding	0	0.346535
Merged-chr2-143372036-1	chr2	143371986	143372086	+	2	cIP1vsInput	Intergenic	Intergenic	-174097	NM_008792	18549	Mm.447466	NM_008792	ENSMUSG00000027419	Pcsk2	6330411F23Rik|AI839700|Nec-2|Nec2|PC2|Phpp-2|SPC2	proprotein convertase subtilisin/kexin type 2	protein-coding	0	0.29703
Merged-chr6-79023818-1	chr6	79023768	79023868	+	2	cIP2vsInput	Intergenic	Intergenic	-8224	NR_040302	100504701	Mm.400420	NR_040301		Gm20362	-	"predicted gene, 20362"	miscRNA	0.01	0.346535
Merged-chr11-32619766-1	chr11	32619716	32619816	+	2	cIP2vsInput	"intron (NM_009288, intron 18 of 18)"	"intron (NM_009288, intron 18 of 18)"	-22789	NM_001271348	103583	Mm.474118	NM_001271347	ENSMUSG00000020271	Fbxw11	2310065A07Rik|AA536858|BTRC2|BTRCP2|Fbxw1b|HOS	F-box and WD-40 domain protein 11	protein-coding	0.02	0.534653
Merged-chr15-96913282-1	chr15	96913232	96913332	+	2	cIP2vsInput	Intergenic	B4A|SINE|B4	142674	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	"solute carrier family 38, member 4"	protein-coding	0	0.475248
Merged-chr3-129669008-1	chr3	129668958	129669058	+	2	cIP2vsInput	Intergenic	RLTR45-int|LTR|ERVK	-84750	NR_040589	319224	Mm.477035	NR_040589		6330410L21Rik	-	RIKEN cDNA 6330410L21 gene	miscRNA	0.02	0.316832
Merged-chr4-37691623-1	chr4	37691573	37691673	+	2	cIP2vsInput	Intergenic	Intergenic	-739879	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0	0.227723
Merged-chr1-154226015-1	chr1	154225965	154226065	+	2	cIP2vsInput	Intergenic	Intergenic	24828	NM_001204908	100503355	Mm.484410	NM_001204908	ENSMUSG00000066797	Zfp648	ENSMUSG00000066797|Gm10178|Gm203	zinc finger protein 648	protein-coding	0	0.346535
Merged-chrX-86965029-1	chrX	86964979	86965079	+	2	cIP2vsInput	"intron (NM_001160403, intron 6 of 10)"	RLTR42-int|LTR|ERVK	-610035	NR_036689	245502	Mm.490821	NR_036689		Gm41	-	"melanoma antigen, family B, 4 pseudogene"	pseudo	0	0.356436
Merged-chr5-148186691-1	chr5	148186641	148186741	+	2	cIP2vsInput	"intron (NM_029920, intron 4 of 14)"	"intron (NM_029920, intron 4 of 14)"	213213	NM_007513	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	"solute carrier family 7 (cationic amino acid transporter, y+ system), member 1"	protein-coding	0	0.346535
Merged-chr15-70435014-1	chr15	70434964	70435064	+	2	cIP1vsInput	Intergenic	Intergenic	510781	NR_045071	100503580	Mm.404646	NR_045071		Gm19782	-	"predicted gene, 19782"	miscRNA	0	0.356436
Merged-chr7-117544553-1	chr7	117544503	117544603	+	2	cIP1vsInput	"intron (NM_175645, intron 2 of 11)"	"intron (NM_175645, intron 2 of 11)"	163574	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding	0	0.435644
Merged-chr7-85714202-1	chr7	85714152	85714252	+	2	cIP2vsInput	Intergenic	Intergenic	40779	NM_001105185	244114	Mm.469907	NM_001105185	ENSMUSG00000051877	Vmn2r72	EG244114|Vmn2r72-ps	"vomeronasal 2, receptor 72"	protein-coding	0	0.356436
Merged-chr10-55169488-1	chr10	55169438	55169538	+	2	cIP2vsInput	Intergenic	Intergenic	-937429	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding	0.01	0.346535
Merged-chr5-87547270-1	chr5	87547220	87547320	+	2	cIP2vsInput	Intergenic	Intergenic	-9075	NM_019878	56362	Mm.23502	NM_019878	ENSMUSG00000029269	Sult1b1	ST1B1|St2b2	"sulfotransferase family 1B, member 1"	protein-coding	0	0.326733
Merged-chrX-82961247-1	chrX	82961197	82961297	+	2	cIP2vsInput	"intron (NM_007868, intron 1 of 78)"	"intron (NM_007868, intron 1 of 78)"	12377	NM_007868	13405	Mm.416750	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|mdx|pke	"dystrophin, muscular dystrophy"	protein-coding	0	0.306931
Merged-chr3-135030477-1	chr3	135030427	135030527	+	2	cIP2vsInput	Intergenic	Intergenic	-182086	NM_173762	229841	Mm.161470	NM_173762	ENSMUSG00000045328	Cenpe	312kDa|AU019344|BC049989|C530022J18|CENP-E|Kif10	centromere protein E	protein-coding	0.01	0.425743
Merged-chr16-56543776-1	chr16	56543726	56543826	+	2	cIP2vsInput	"intron (NM_001014399, intron 2 of 27)"	"intron (NM_001014399, intron 2 of 27)"	65930	NM_001014424	320712	Mm.209236	NM_001014399	ENSMUSG00000035258	Abi3bp	5033411B22Rik|AI506287|BG172926|D930038M13Rik|TARSH|eratin	"ABI gene family, member 3 (NESH) binding protein"	protein-coding	0	0.366337
Merged-chr2-58242018-1	chr2	58241968	58242068	+	2	cIP2vsInput	Intergenic	Intergenic	-34761	NR_040365	100502932	Mm.417207	NR_040365	ENSMUSG00000086995	Gm13544	OTTMUSG00000012672	predicted gene 13544	miscRNA	0	0.306931
Merged-chr15-23549010-1	chr15	23548960	23549060	+	2	cIP1vsInput	Intergenic	Intergenic	512547	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l	cadherin 18	protein-coding	0	0.257426
Merged-chr2-143234439-1	chr2	143234389	143234489	+	2	cIP2vsInput	Intergenic	Intergenic	155947	NM_020595	57329	Mm.157751	NM_020595	ENSMUSG00000027416	Otor	CDRAP|Fdp|MIA|MIAL	otoraplin	protein-coding	0.01	0.386139
Merged-chr10-65443387-1	chr10	65443337	65443437	+	2	cIP1vsInput	Intergenic	Intergenic	680677	NR_038039	69433	Mm.23366	NR_038039		1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	miscRNA	0	0.326733
Merged-chr9-81829361-1	chr9	81829311	81829411	+	2	cIP2vsInput	Intergenic	Intergenic	-34383	NM_175213	75033	Mm.457083	NM_175213	ENSMUSG00000043289	Mei4	4930486G11Rik	"meiosis-specific, MEI4 homolog (S. cerevisiae)"	protein-coding	0	0.306931
Merged-chrX-81907014-1	chrX	81906964	81907064	+	2	cIP2vsInput	Intergenic	Intergenic	-448892	NM_173435	245492	Mm.109633	NM_173435	ENSMUSG00000060673	4930595M18Rik	-	RIKEN cDNA 4930595M18 gene	protein-coding	0	0.277228
Merged-chrX-119950822-1	chrX	119950772	119950872	+	2	cIP2vsInput	Intergenic	L1MC1|LINE|L1	23626	NM_053114	93728	Mm.125979	NM_053114	ENSMUSG00000034732	Pabpc5	C820015E17	"poly(A) binding protein, cytoplasmic 5"	protein-coding	0	0.287129
Merged-chr16-86350686-1	chr16	86350636	86350736	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-449561	NM_011782	23794	Mm.437478	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|AI481094|ASMP-2	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"	protein-coding	0	0.336634
Merged-chr1-3957136-1	chr1	3957086	3957186	+	2	cIP2vsInput	Intergenic	Lx4A|LINE|L1	-285638	NM_001011874	497097	Mm.489375	NM_001011874		Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X Kell blood group precursor related family member 4	protein-coding	0	0.306931
Merged-chr4-93622005-1	chr4	93621955	93622055	+	2	cIP2vsInput	Intergenic	Intergenic	-286494	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding	0.01	0.29703
Merged-chr3-8398892-1	chr3	8398842	8398942	+	2	cIP2vsInput	Intergenic	Intergenic	64206	NR_033512	620966	Mm.301719	NR_033512		Gm6194	1700003N22Rik|EG620966	transmembrane protein 189 pseudogene	pseudo	0.01	0.326733
Merged-chr1-57711907-1	chr1	57711857	57711957	+	2	cIP2vsInput	Intergenic	Intergenic	-62954	NM_144882	67198	Mm.159989	NM_001164566	ENSMUSG00000038305	Spats2l	2810022L02Rik|A230104H11Rik|AA987173|AI480531|AI842453|AW413586	"spermatogenesis associated, serine-rich 2-like"	protein-coding	0	0.366337
Merged-chr9-73597014-1	chr9	73596964	73597064	+	2	cIP2vsInput	"intron (NM_001081153, intron 17 of 30)"	"intron (NM_001081153, intron 17 of 30)"	336553	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|AU019458|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C (C. elegans)	protein-coding	0	0.247525
Merged-chr10-15060416-1	chr10	15060366	15060466	+	2	cIP2vsInput	Intergenic	Intergenic	300127	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding	0	0.346535
Merged-chr6-18144091-1	chr6	18144041	18144141	+	2	cIP2vsInput	Intergenic	Intergenic	-26596	NM_021050	12638	Mm.15621	NM_021050	ENSMUSG00000041301	Cftr	AW495489|Abcc7	cystic fibrosis transmembrane conductance regulator	protein-coding	0	0.316832
Merged-chr6-76725097-1	chr6	76725047	76725147	+	2	cIP2vsInput	Intergenic	Intergenic	-517620	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0.01	0.336634
Merged-chr3-129141355-1	chr3	129141305	129141405	+	2	cIP2vsInput	Intergenic	Intergenic	-58563	NM_011098	18741	Mm.246804	NM_001042502	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1a|Brx1b|Munc30|Otlx2|Pitx2a|Pitx2b|Pitx2c|Pitx2cbeta|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding	0	0.287129
Merged-chr7-53027276-1	chr7	53027226	53027326	+	2	cIP2vsInput	Intergenic	Intergenic	-1011560	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding	0	0.346535
Merged-chr4-16620223-1	chr4	16620173	16620273	+	2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	456113	NR_045765	100415915	Mm.387180	NR_045765	ENSMUSG00000085112	A530072M11Rik	-	RIKEN cDNA gene A530072M11	miscRNA	0	0.386139
Merged-chr2-113727779-1	chr2	113727729	113727829	+	2	cIP1vsInput	Intergenic	Intergenic	-19229	NR_040614	75166	Mm.410811	NR_040614	ENSMUSG00000084798	4930533B01Rik	-	RIKEN cDNA 4930533B01 gene	miscRNA	0	0.277228
Merged-chr4-78827739-1	chr4	78827689	78827789	+	2	cIP2vsInput	Intergenic	Intergenic	-615844	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0	0.386139
Merged-chr14-81971430-1	chr14	81971380	81971480	+	2	cIP2vsInput	Intergenic	Intergenic	1971128	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.326733
Merged-chr9-8679189-1	chr9	8679139	8679239	+	2	cIP2vsInput	"intron (NM_013838, intron 11 of 12)"	"intron (NM_013838, intron 11 of 12)"	135047	NM_013838	22068	Mm.325086	NM_013838	ENSMUSG00000031997	Trpc6	AV025995|LLHWJM002|LLHWJM003|LLHWJM004|TRP-6|Trrp6|mtrp6	"transient receptor potential cation channel, subfamily C, member 6"	protein-coding	0	0.336634
Merged-chr1-146452371-1	chr1	146452321	146452421	+	2	cIP2vsInput	Intergenic	Intergenic	-43295	NM_153539	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0.01	0.326733
Merged-chr6-124047225-1	chr6	124047175	124047275	+	2	cIP2vsInput	"intron (NM_019917, intron 3 of 5)"	L1MCa|LINE|L1	22467	NM_019917	56552	Mm.23795	NM_019917	ENSMUSG00000096630	Vmn2r26	V2R1|V2r1b	"vomeronasal 2, receptor 26"	protein-coding	0	0.326733
Merged-chr2-46298334-1	chr2	46298284	46298384	+	2	cIP2vsInput	Intergenic	Intergenic	601729	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	miscRNA	0	0.306931
Merged-chr8-29869298-1	chr8	29869248	29869348	+	2	cIP2vsInput	Intergenic	Lx9|LINE|L1	-649662	NM_153135	210801	Mm.248433	NM_153135	ENSMUSG00000063626	Unc5d	D930029E11Rik|Unc5h4|mKIAA1777	unc-5 homolog D (C. elegans)	protein-coding	0.01	0.336634
Merged-chr9-85625436-1	chr9	85625386	85625486	+	2	cIP1vsInput	Intergenic	MER74A|LTR|ERVL	123898	NM_001081282	108837	Mm.487092	NM_175371	ENSMUSG00000035941	Ibtk	5430411K16Rik|AA409502|BTKI|mKIAA1417	inhibitor of Bruton agammaglobulinemia tyrosine kinase	protein-coding	0	0.336634
Merged-chr3-92391435-1	chr3	92391385	92391485	+	2	cIP2vsInput	Intergenic	Intergenic	5750	NM_011474	20762	Mm.10693	NM_011474	ENSMUSG00000046259	Sprr2h	AI661967	small proline-rich protein 2H	protein-coding	0	0.326733
Merged-chr15-14941418-1	chr15	14941368	14941468	+	2	cIP1vsInput	Intergenic	MYSERV6-int|LTR|ERVK	-1767779	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	K-cadherin|cad6|cadherin-6	cadherin 6	protein-coding	0	0.267327
Merged-chr7-86085129-1	chr7	86085079	86085179	+	2	cIP2vsInput	Intergenic	Intergenic	86595	NM_001102578	546981	Mm.469835	NM_001102578	ENSMUSG00000090436	Vmn2r75	EG546981	"vomeronasal 2, receptor 75"	protein-coding	0	0.316832
Merged-chr12-78699065-1	chr12	78699015	78699115	+	2	cIP2vsInput	"intron (NM_027597, intron 1 of 7)"	"intron (NM_027597, intron 1 of 7)"	7530	NM_029069	70897	Mm.56514	NM_027597	ENSMUSG00000056987	Fam71d	4921509E07Rik|4930516C23Rik|GARI-L2	"family with sequence similarity 71, member D"	protein-coding	0.01	0.366337
Merged-chr11-12701625-1	chr11	12701575	12701675	+	2	cIP2vsInput	Intergenic	Intergenic	-236665	NM_172496	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	4732460E13|C530045F18Rik|mKIAA0633	cordon-bleu	protein-coding	0	0.316832
Merged-chr2-74021190-1	chr2	74021140	74021240	+	2	cIP2vsInput	Intergenic	Intergenic	-109896	NM_175015	228033	Mm.2966	NM_175015	ENSMUSG00000018770	Atp5g3	6030447M23	"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9)"	protein-coding	0.02	0.306931
Merged-chr12-51052098-1	chr12	51052048	51052148	+	2	cIP1vsInput	Intergenic	MIRb|SINE|MIR	-296132	NM_001167964	217558	Mm.253264	NM_001015099	ENSMUSG00000035293	G2e3	6030408C04Rik|9030416F18|AW046379|D930034K21Rik|mKIAA1333	G2/M-phase specific E3 ubiquitin ligase	protein-coding	0.01	0.386139
Merged-chr3-4245096-1	chr3	4245046	4245146	+	2	cIP2vsInput	Intergenic	Lx|LINE|L1	-553612	NR_045272	100503859	Mm.75172	NR_045272		1110015O18Rik	-	RIKEN cDNA 1110015O18 gene	miscRNA	0.01	0.346535
Merged-chr2-66921877-1	chr2	66921827	66921927	+	2	cIP2vsInput	Intergenic	Intergenic	-136967	NM_009135	20272	Mm.38127	NM_009135	ENSMUSG00000034810	Scn7a	1110034K09Rik|AI642000|NaG|Nav2|Nav2.3|Nax|Scn6a	"sodium channel, voltage-gated, type VII, alpha"	protein-coding	0	0.39604
Merged-chr9-110248995-1	chr9	110248945	110249045	+	2	cIP1vsInput	"intron (NM_013884, intron 2 of 4)"	B1_Mur1|SINE|Alu	5212	NM_001166273	29873	Mm.38496	NM_001166273	ENSMUSG00000032482	Cspg5	Caleb|Ngc	chondroitin sulfate proteoglycan 5	protein-coding	0.01	0.49505
Merged-chr18-46288804-1	chr18	46288754	46288854	+	2	cIP2vsInput	"intron (NM_001160399, intron 6 of 9)"	"intron (NM_001160399, intron 6 of 9)"	-7954	NM_172627	225467	Mm.393044	NM_172627	ENSMUSG00000024477	Pggt1b	2010207C17Rik|2610100E13|AI451237|AI551093|BGG1|GGT1	"protein geranylgeranyltransferase type I, beta subunit"	protein-coding	0	0.336634
Merged-chrX-87570709-1	chrX	87570659	87570759	+	2	cIP2vsInput	"intron (NM_001160403, intron 2 of 10)"	"intron (NM_001160403, intron 2 of 10)"	544914	NM_001160403	331461	Mm.426143	NM_001160403		Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding	0	0.306931
Merged-chr14-37930438-1	chr14	37930388	37930488	+	2	cIP1vsInput	Intergenic	Intergenic	-795116	NM_078478	66092	Mm.486242	NM_001199122	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010	growth hormone inducible transmembrane protein	protein-coding	0	0.366337
Merged-chr13-15102250-1	chr13	15102200	15102300	+	2	cIP2vsInput	Intergenic	Intergenic	-361473	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding	0	0.306931
Merged-chr4-25179946-1	chr4	25179896	25179996	+	2	cIP2vsInput	Intergenic	Intergenic	62930	NM_021318	57756	Mm.87325	NM_021318	ENSMUSG00000028259	Fhl5	1700027G07Rik|Act	four and a half LIM domains 5	protein-coding	0	0.366337
Merged-chr10-71108216-1	chr10	71108166	71108266	+	2	cIP2vsInput	"intron (NM_031397, intron 1 of 20)"	"intron (NM_031397, intron 1 of 20)"	51418	NM_031397	83675	Mm.458090	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	bicaudal C homolog 1 (Drosophila)	protein-coding	0.01	0.336634
Merged-chr5-35189426-1	chr5	35189376	35189476	+	2	cIP2vsInput	Intergenic	Intergenic	-83729	NM_013587	16976	Mm.277661	NM_013587	ENSMUSG00000029103	Lrpap1	AA617339|AI790446|AU042172|C77774|HBP44|RAP	low density lipoprotein receptor-related protein associated protein 1	protein-coding	0.01	0.534653
Merged-chr6-39759404-1	chr6	39759354	39759454	+	2	cIP1vsInput	Intergenic	RMER17C-int|LTR|ERVK	-33941	NM_139294	109880	Mm.489691	NM_139294	ENSMUSG00000002413	Braf	9930012E13Rik|AA120551|AA387315|AA473386|B-raf|Braf-2|Braf2|C230098H17|C87398|D6Ertd631e	Braf transforming gene	protein-coding	0.01	0.336634
Merged-chr4-140180090-1	chr4	140180040	140180140	+	2	cIP2vsInput	"intron (NM_198610, intron 1 of 9)"	"intron (NM_198610, intron 1 of 9)"	66721	NM_198610	230868	Mm.298731	NM_198610	ENSMUSG00000040972	Igsf21	BC055811|Gm141	"immunoglobulin superfamily, member 21"	protein-coding	0	0.534653
Merged-chr2-100391530-1	chr2	100391480	100391580	+	2	cIP1vsInput	Intergenic	Intergenic	-1233218	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding	0	0.316832
Merged-chr2-61004883-1	chr2	61004833	61004933	+	2	cIP2vsInput	Intergenic	Intergenic	-29732	NR_045335	100038493	Mm.388076	NR_045335	ENSMUSG00000075325	Gm13582	ENSMUSG00000075325|OTTMUSG00000012844	predicted gene 13582	miscRNA	0	0.39604
Merged-chr1-32819523-1	chr1	32819473	32819573	+	2	cIP2vsInput	Intergenic	(TTTG)n|Simple_repeat|Simple_repeat	-272230	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding	0	0.356436
Merged-chr13-119239541-1	chr13	119239491	119239591	+	2	cIP2vsInput	Intergenic	Intergenic	169470	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding	0	0.405941
Merged-chr18-89679598-1	chr18	89679548	89679648	+	2	cIP1vsInput	"intron (NM_001039173, intron 1 of 7)"	L1_Mur2|LINE|L1	89538	NM_001039173	623279	Mm.447164	NM_001039173		Dok6	Dok-6	docking protein 6	protein-coding	0	0.346535
Merged-chr19-49007791-1	chr19	49007741	49007841	+	2	cIP2vsInput	Intergenic	Intergenic	801766	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding	0	0.39604
Merged-chr7-42434232-1	chr7	42434182	42434282	+	2	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-3863	NR_028441	628490	Mm.246518	NR_028441	ENSMUSG00000070621	Vmn2r-ps60	Casr-rs4|Gprc2a-rs4	"vomeronasal 2, receptor, pseudogene 60"	pseudo	0	0.346535
Merged-chr1-179524312-1	chr1	179524262	179524362	+	2	cIP2vsInput	Intergenic	Intergenic	-6309	NM_027188	69726	Mm.222338	NM_027188		Smyd3	2410008A19Rik|Zmynd1	SET and MYND domain containing 3	protein-coding	0	0.346535
Merged-chr10-113922045-1	chr10	113921995	113922095	+	2	cIP2vsInput	Intergenic	Intergenic	335467	NR_035418	100316831		NR_035418		Mir669h	Mirn669h|mmu-mir-669h	microRNA 669h	miscRNA	0	0.29703
Merged-chr1-31954220-1	chr1	31954170	31954270	+	2	cIP1vsInput	Intergenic	Intergenic	-218586	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm1	"KH domain containing, RNA binding, signal transduction associated 2"	protein-coding	0	0.306931
Merged-chr14-6257598-1	chr14	6257548	6257648	+	2	cIP2vsInput	Intergenic	Intergenic	29652	NM_001270812	100861615	Mm.399319	NM_001270812	ENSMUSG00000079396	LOC100861615	-	alpha takusan-like	protein-coding	0.01	0.356436
Merged-chr15-25117884-1	chr15	25117834	25117934	+	2	cIP2vsInput	Intergenic	Intergenic	295880	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	"brain abundant, membrane attached signal protein 1"	protein-coding	0	0.366337
Merged-chr3-76479065-1	chr3	76479015	76479115	+	2	cIP1vsInput	"intron (NM_178673, intron 6 of 15)"	"intron (NM_178673, intron 6 of 15)"	403482	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.316832
Merged-chr1-139639512-1	chr1	139639462	139639562	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-79290	NM_015780	50702	Mm.220362	NM_015780	ENSMUSG00000057037	Cfhr1	AI194696|CFHRB|Cfhl1	complement factor H-related 1	protein-coding	0	0.267327
Merged-chr15-52322993-1	chr15	52322943	52323043	+	2	cIP2vsInput	"intron (NM_172816, intron 4 of 7)"	"intron (NM_172816, intron 4 of 7)"	27440	NM_172816	239436	Mm.208831	NM_172816	ENSMUSG00000022315	Slc30a8	C820002P14Rik|ZnT-8|ZnT8	"solute carrier family 30 (zinc transporter), member 8"	protein-coding	0	0.346535
Merged-chr13-18772157-1	chr13	18772107	18772207	+	2	cIP2vsInput	"intron (NM_172120, intron 4 of 28)"	"intron (NM_172120, intron 4 of 28)"	54865	NM_172120	218035	Mm.27389	NM_172120	ENSMUSG00000041236	Vps41	AI317346|Vam2|mVam2	vacuolar protein sorting 41 (yeast)	protein-coding	0.01	0.29703
Merged-chrX-31204650-1	chrX	31204600	31204700	+	2	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-131719	NM_001243011	100042159	Mm.489579	NM_001243011	ENSMUSG00000095835	Gm3701	-	predicted gene 3701	protein-coding	0	0.306931
Merged-chr17-69713645-1	chr17	69713595	69713695	+	2	cIP1vsInput	Intergenic	Intergenic	274319	NM_001145192	320722	Mm.400254	NM_001145192	ENSMUSG00000091636	A330050F15Rik	-	RIKEN cDNA A330050F15 gene	protein-coding	0.01	0.316832
Merged-chr8-121736373-1	chr8	121736323	121736423	+	2	cIP2vsInput	"intron (NM_020605, intron 1 of 4)"	"intron (NM_020605, intron 1 of 4)"	5814	NM_020605	57340	Mm.306870	NM_020605	ENSMUSG00000025318	Jph3	JP-3|Jp3	junctophilin 3	protein-coding	0.03	0.544554
Merged-chr10-29882291-1	chr10	29882241	29882341	+	2	cIP2vsInput	Intergenic	Intergenic	318249	NM_001109747	66311	Mm.251779	NM_001109747	ENSMUSG00000075266	Cenpw	2610036L11Rik|Cug2	centromere protein W	protein-coding	0	0.316832
Merged-chr12-43326393-1	chr12	43326343	43326443	+	2	cIP1vsInput	Intergenic	Intergenic	883675	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	"DnaJ (Hsp40) homolog, subfamily B, member 9"	protein-coding	0	0.316832
Merged-chr7-79649003-1	chr7	79648953	79649053	+	2	cIP2vsInput	Intergenic	Intergenic	-11193	NM_029835	77011	Mm.28132	NM_029835	ENSMUSG00000046591	Ticrr	5730590G19Rik|BC028450|Lrrk1	TOPBP1-interacting checkpoint and replication regulator	protein-coding	0.01	0.415842
Merged-chr17-41461014-1	chr17	41460964	41461064	+	2	cIP2vsInput	Intergenic	L1MB8|LINE|L1	526329	NM_008650	17850	Mm.259884	NM_008650	ENSMUSG00000023921	Mut	D230010K02Rik|Mcm	methylmalonyl-Coenzyme A mutase	protein-coding	0	0.346535
Merged-chr5-91065575-1	chr5	91065525	91065625	+	2	cIP1vsInput	Intergenic	Intergenic	-9042	NM_007950	13874	Mm.4791	NM_007950	ENSMUSG00000029377	Ereg	EPR	epiregulin	protein-coding	0.01	0.346535
Merged-chr15-42886186-1	chr15	42886136	42886236	+	2	cIP2vsInput	Intergenic	Intergenic	-209391	NM_009640	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding	0.01	0.346535
Merged-chr7-19939725-1	chr7	19939675	19939775	+	2	cIP1vsInput	"intron (NM_027308, intron 3 of 4)"	RLTR26B_MM|LTR|ERVK	11018	NM_027308	70080	Mm.98583	NM_027308	ENSMUSG00000040498	Igsf23	2210010C17Rik	"immunoglobulin superfamily, member 23"	protein-coding	0	0.524752
Merged-chr10-70216587-1	chr10	70216537	70216637	+	2	cIP2vsInput	"intron (NR_038041, intron 1 of 2)"	"intron (NR_038041, intron 1 of 2)"	11920	NR_038041	69563	Mm.64672	NR_038041	ENSMUSG00000019933	2310015B20Rik	-	RIKEN cDNA 2310015B20 gene	miscRNA	0	0.306931
Merged-chr7-52479612-1	chr7	52479562	52479662	+	2	cIP2vsInput	Intergenic	Intergenic	-463896	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding	0	0.405941
Merged-chrX-10502425-1	chrX	10502375	10502475	+	2	cIP1vsInput	"intron (NM_019634, intron 1 of 7)"	"intron (NM_019634, intron 1 of 7)"	17309	NM_019634	21912	Mm.18590	NM_019634	ENSMUSG00000058254	Tspan7	1200014P11Rik|A15|AI323365|Cd231|Mxs1|PE31|R74651|TALLA|Tm4sf2	tetraspanin 7	protein-coding	0.01	0.326733
Merged-chr9-84668994-1	chr9	84668944	84669044	+	2	cIP1vsInput	Intergenic	Intergenic	-105404	NR_040739	75253	Mm.401984	NR_040739		4930554C24Rik	-	RIKEN cDNA 4930554C24 gene	miscRNA	0.01	0.336634
Merged-chr4-51792202-1	chr4	51792152	51792252	+	2	cIP2vsInput	Intergenic	Intergenic	258908	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	miscRNA	0	0.306931
Merged-chr13-12966812-1	chr13	12966762	12966862	+	2	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	38518	NM_031191	18811	Mm.88796	NM_031191	ENSMUSG00000079092	Prl2c2	MRP-1|PLF-1|Plf|Plf1	"prolactin family 2, subfamily c, member 2"	protein-coding	0.01	0.267327
Merged-chr10-91981985-1	chr10	91981935	91982035	+	2	cIP2vsInput	Intergenic	Intergenic	90200	NR_029812	723955		NR_029812	ENSMUSG00000065524	Mir135a-2	Mirn135a-2	microRNA 135a-2	miscRNA	0	0.346535
Merged-chr6-61985575-1	chr6	61985525	61985625	+	2	cIP2vsInput	"intron (NM_001164316, intron 10 of 10)"	"intron (NM_001164316, intron 10 of 10)"	-804765	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	miscRNA	0	0.405941
Merged-chr3-140126277-1	chr3	140126227	140126327	+	2	cIP2vsInput	Intergenic	Lx8|LINE|L1	920384	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding	0	0.386139
Merged-chr3-98906467-1	chr3	98906417	98906517	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-13237	NM_019545	56185	Mm.281874	NM_019545	ENSMUSG00000027870	Hao2	AI325478|Hao-2|Hao3|Haox3	hydroxyacid oxidase 2	protein-coding	0	0.356436
Merged-chr13-84215687-1	chr13	84215637	84215737	+	2	cIP2vsInput	Intergenic	Intergenic	-6609	NR_029418	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding	0.01	0.316832
Merged-chr9-3808429-1	chr9	3808379	3808479	+	2	cIP1vsInput	"intron (NM_001033322, intron 6 of 7)"	L1_Mur1|LINE|L1	276080	NM_001033322	234889	Mm.91240	NM_001033322		Gucy1a2	6330407I18Rik|A230060L24Rik	"guanylate cyclase 1, soluble, alpha 2"	protein-coding	0	0.415842
Merged-chr3-71522488-1	chr3	71522438	71522538	+	2	cIP2vsInput	Intergenic	Intergenic	-715197	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	miscRNA	0	0.306931
Merged-chr9-22613241-1	chr9	22613191	22613291	+	2	cIP2vsInput	"intron (NM_181316, intron 9 of 21)"	"intron (NM_181316, intron 9 of 21)"	137526	NM_178415	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding	0	0.39604
Merged-chr11-40239507-1	chr11	40239457	40239557	+	2	cIP2vsInput	Intergenic	Cheshire|DNA|hAT-Charlie	453175	NM_134017	108645	Mm.293771	NM_001199274	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	"methionine adenosyltransferase II, beta"	protein-coding	0.01	0.366337
Merged-chr10-65529421-1	chr10	65529371	65529471	+	2	cIP2vsInput	Intergenic	Intergenic	594643	NR_038039	69433	Mm.23366	NR_038039		1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	miscRNA	0.02	0.415842
Merged-chr1-141771505-1	chr1	141771455	141771555	+	2	cIP2vsInput	Intergenic	Intergenic	-1115103	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0	0.306931
Merged-chr7-70022354-1	chr7	70022304	70022404	+	2	cIP2vsInput	Intergenic	Intergenic	338239	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	"nuclear receptor subfamily 2, group F, member 2"	protein-coding	0	0.336634
Merged-chr2-102056802-1	chr2	102056752	102056852	+	2	cIP2vsInput	"intron (NM_178886, intron 4 of 5)"	"intron (NM_178886, intron 4 of 5)"	129575	NM_178886	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding	0	0.326733
Merged-chr18-24416509-1	chr18	24416459	24416559	+	2	cIP2vsInput	Intergenic	Intergenic	12661	NR_029573	387182		NR_029573	ENSMUSG00000065532	Mir187	Mirn187|mmu-mir-187	microRNA 187	miscRNA	0.01	0.326733
Merged-chr17-35185663-1	chr17	35185613	35185713	+	2	cIP1vsInput	"intron (NM_010734, intron 3 of 3)"	B4A|SINE|B4	2777	NM_010734	16988	Mm.19379	NM_010734	ENSMUSG00000073412	Lst1	B144	leukocyte specific transcript 1	protein-coding	0	0.594059
Merged-chr14-37402223-1	chr14	37402173	37402273	+	2	cIP1vsInput	Intergenic	L1MEf|LINE|L1	-266901	NM_078478	66092	Mm.486242	NM_001199122	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010	growth hormone inducible transmembrane protein	protein-coding	0.01	0.326733
Merged-chr12-67815794-1	chr12	67815744	67815844	+	2	cIP2vsInput	Intergenic	Intergenic	-146523	NR_033146	100316870	Mm.379794	NR_033146		Gm17821	-	DDB1 and CUL4 associated factor 5 pseudogene	pseudo	0	0.316832
Merged-chr4-37401553-1	chr4	37401503	37401603	+	2	cIP2vsInput	Intergenic	Intergenic	-449809	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0	0.316832
Merged-chr9-116560434-1	chr9	116560384	116560484	+	2	cIP2vsInput	Intergenic	Intergenic	-385071	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	"transforming growth factor, beta receptor II"	protein-coding	0	0.39604
Merged-chr18-30776797-1	chr18	30776747	30776847	+	2	cIP2vsInput	Intergenic	Intergenic	503901	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	"phosphoinositide-3-kinase, class 3"	protein-coding	0.01	0.306931
Merged-chr4-68407368-1	chr4	68407318	68407418	+	2	cIP2vsInput	Intergenic	L1MA5|LINE|L1	547029	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Dbc1	BRINP|Brinp1|Dbccr1|Fam5a	deleted in bladder cancer 1 (human)	protein-coding	0.02	0.316832
Merged-chr6-65510624-1	chr6	65510574	65510674	+	2	cIP2vsInput	Intergenic	Intergenic	-79774	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding	0	0.386139
Merged-chr10-38257794-1	chr10	38257744	38257844	+	2	cIP2vsInput	Intergenic	PB1D10|SINE|Alu	563985	NM_001177783	215919	Mm.294313	NM_001177783	ENSMUSG00000094311	Rfpl4b	100040915|Gm3037|Gm62	ret finger protein-like 4B	protein-coding	0	0.356436
Merged-chr2-156065330-1	chr2	156065280	156065380	+	2	cIP2vsInput	"5' UTR (NM_139151, exon 1 of 12)"	"5' UTR (NM_139151, exon 1 of 12)"	117	NM_139151	245865	Mm.330713	NM_139151	ENSMUSG00000038180	Spag4	1700041K21Rik|MNCb-0953|Sun4|mKIAA4118	sperm associated antigen 4	protein-coding	0.1	0.722772
Merged-chr1-116746188-1	chr1	116746138	116746238	+	2	cIP2vsInput	Intergenic	MMSAT4|Satellite|Satellite	1061051	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0.01	0.346535
Merged-chr6-22788168-1	chr6	22788118	22788218	+	2	cIP2vsInput	Intergenic	Intergenic	-87334	NM_001081306	19283	Mm.41639	NM_001081306	ENSMUSG00000068748	Ptprz1	AI850339|DSD-1-PG|PTPbeta|PTPzeta|Ptprz|Ptpz|RPTPz|Rptpbeta	"protein tyrosine phosphatase, receptor type Z, polypeptide 1"	protein-coding	0.01	0.356436
Merged-chr12-114404359-1	chr12	114404309	114404409	+	2	cIP2vsInput	Intergenic	Intergenic	860451	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding	0.01	0.435644
Merged-chr14-101133704-1	chr14	101133654	101133754	+	2	cIP2vsInput	Intergenic	L1MD3|LINE|L1	66365	NM_029680	76627	Mm.31415	NM_029680	ENSMUSG00000042888	1700110M21Rik	-	RIKEN cDNA 1700110M21 gene	protein-coding	0	0.29703
Merged-chr18-29469148-1	chr18	29469098	29469198	+	2	cIP2vsInput	"intron (NR_045391, intron 2 of 7)"	"intron (NR_045391, intron 2 of 7)"	26948	NR_045395	78199	Mm.243850	NR_045395		4930527G23Rik	-	RIKEN cDNA 4930527G23 gene	miscRNA	0.02	0.386139
Merged-chr12-3531219-1	chr12	3531169	3531269	+	2	cIP1vsInput	Intergenic	ETnERV2-int|LTR|ERVK	-41172	NM_001162465	13528	Mm.286202	NM_001162465	ENSMUSG00000071454	Dtnb	-	"dystrobrevin, beta"	protein-coding	0.01	0.346535
Merged-chr2-37269477-1	chr2	37269427	37269527	+	2	cIP2vsInput	"intron (NM_001081010, intron 1 of 1)"	"intron (NM_001081010, intron 1 of 1)"	2526	NM_001081010	545417	Mm.379955	NM_001081010		Olfr367-ps	EG545417|MOR128-1|ORL1283|OTTMUSG00000012147|Olfr367	"olfactory receptor 367, pseudogene"	protein-coding	0	0.386139
Merged-chr18-43471578-1	chr18	43471528	43471628	+	2	cIP1vsInput	Intergenic	Intergenic	-78247	NM_009468	22240	Mm.428551	NM_001136086	ENSMUSG00000024501	Dpysl3	CRMP-4|TUC4|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding	0	0.326733
Merged-chr12-9656826-1	chr12	9656776	9656876	+	2	cIP2vsInput	Intergenic	Intergenic	82384	NM_011859	23967	Mm.45055	NM_011859	ENSMUSG00000048387	Osr1	Odd1|Osr	odd-skipped related 1 (Drosophila)	protein-coding	0	0.435644
Merged-chr8-31471177-1	chr8	31471127	31471227	+	2	cIP2vsInput	Intergenic	Intergenic	103428	NR_046272	74517	Mm.390001	NR_046272		7420700N18Rik	-	RIKEN cDNA 7420700N18 gene	miscRNA	0	0.326733
Merged-chr2-52009449-1	chr2	52009399	52009499	+	2	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-28664	NM_009398	21930	Mm.3509	NM_009398	ENSMUSG00000053475	Tnfaip6	TSG-6|Tnfip6|Tsg6	tumor necrosis factor alpha induced protein 6	protein-coding	0	0.326733
Merged-chr3-35420625-1	chr3	35420575	35420675	+	2	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	245538	NR_040748	625963	Mm.251506	NR_040748		Gm6639	-	predicted gene 6639	miscRNA	0.01	0.316832
Merged-chr19-15162965-1	chr19	15162915	15163015	+	2	cIP2vsInput	Intergenic	L1MA5|LINE|L1	-564982	NM_011600	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333	"transducin-like enhancer of split 4, homolog of Drosophila E(spl)"	protein-coding	0	0.277228
Merged-chr17-42320794-1	chr17	42320744	42320844	+	2	cIP2vsInput	"intron (NM_028474, intron 2 of 3)"	"intron (NM_028474, intron 2 of 3)"	4847	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding	0	0.376238
Merged-chr1-58227775-1	chr1	58227725	58227825	+	2	cIP2vsInput	"intron (NM_023631, intron 6 of 34)"	ID_B1|SINE|B4	17378	NM_023631	71872	Mm.244525	NM_023631	ENSMUSG00000038242	Aox4	2310003G12Rik|Aoh2	aldehyde oxidase 4	protein-coding	0	0.465347
Merged-chr14-53549305-1	chr14	53549255	53549355	+	2	cIP1vsInput	Intergenic	MYSERV16_I-int|LTR|ERVK	-116635	NM_001205242	100568452	Mm.486072	NM_001205242		A430107P09Rik	Va10	RIKEN cDNA A430107P09 gene	protein-coding	0	0.306931
Merged-chr3-128641212-1	chr3	128641162	128641262	+	2	cIP2vsInput	Intergenic	L1M2|LINE|L1	-409607	NR_045704	402774	Mm.209170	NR_045704		D030025E07Rik	-	RIKEN cDNA D030025E07 gene	miscRNA	0	0.316832
Merged-chr17-61214203-1	chr17	61214153	61214253	+	2	cIP2vsInput	Intergenic	Intergenic	-103549	NR_030569	100124495		NR_030569		Mir466g	Mirn466g	microRNA 466g	miscRNA	0.01	0.326733
Merged-chr13-64573253-1	chr13	64573203	64573303	+	2	cIP2vsInput	Intergenic	B3A|SINE|B2	-75461	NM_001195435	68880	Mm.390594	NM_001195435	ENSMUSG00000096537	1190003K10Rik	-	RIKEN cDNA 1190003K10 gene	protein-coding	0	0.445545
Merged-chr5-46771455-1	chr5	46771405	46771505	+	2	cIP2vsInput	Intergenic	Intergenic	-913915	NM_001163073	209707	Mm.71498	NM_001163073	ENSMUSG00000015882	Lcorl	Mlr1	ligand dependent nuclear receptor corepressor-like	protein-coding	0	0.39604
Merged-chr19-8186024-1	chr19	8185974	8186074	+	2	cIP2vsInput	"intron (NM_172776, intron 5 of 9)"	L1_Mus1|LINE|L1	32815	NM_172776	236293	Mm.440581	NM_172776	ENSMUSG00000075044	Slc22a29	D630002G06Rik	solute carrier family 22. member 29	protein-coding	0	0.336634
Merged-chr17-59675012-1	chr17	59674962	59675062	+	2	cIP2vsInput	Intergenic	Intergenic	-661690	NM_026497	67993	Mm.36507	NM_026497		Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0	0.287129
Merged-chr10-27362703-1	chr10	27362653	27362753	+	2	cIP2vsInput	"intron (NM_008481, intron 7 of 63)"	"intron (NM_008481, intron 7 of 63)"	254239	NM_008481	16773	Mm.256087	NM_008481	ENSMUSG00000019899	Lama2	5830440B04|dy|mKIAA4087|mer|merosin	"laminin, alpha 2"	protein-coding	0	0.336634
Merged-chr15-19143686-1	chr15	19143636	19143736	+	2	cIP2vsInput	Intergenic	Intergenic	323357	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0.01	0.386139
Merged-chr3-136572084-1	chr3	136572034	136572134	+	2	cIP2vsInput	Intergenic	Intergenic	-98686	NM_008913	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|AI841391|AW413465|CN|Caln|Calna|CnA	"protein phosphatase 3, catalytic subunit, alpha isoform"	protein-coding	0	0.336634
Merged-chr16-65182044-1	chr16	65181994	65182094	+	2	cIP2vsInput	Intergenic	Intergenic	-76260	NM_008310	15557	Mm.5040	NM_008310	ENSMUSG00000050783	Htr1f	Htr1eb	5-hydroxytryptamine (serotonin) receptor 1F	protein-coding	0	0.376238
Merged-chr5-89322502-1	chr5	89322452	89322552	+	2	cIP2vsInput	Intergenic	Intergenic	135396	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding	0.01	0.346535
Merged-chr16-62972166-1	chr16	62972116	62972216	+	2	cIP2vsInput	Intergenic	Intergenic	117832	NM_011173	19128	Mm.127156	NM_011173	ENSMUSG00000022912	Pros1	AW214361	protein S (alpha)	protein-coding	0.01	0.326733
Merged-chrX-96174538-1	chrX	96174488	96174588	+	2	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-65388	NR_030718	100038363	Mm.30815	NR_030718	ENSMUSG00000078122	F630028O10Rik	ENSMUSG00000065522|Gm14924|OTTMUSG00000018496	RIKEN cDNA F630028O10 gene	miscRNA	0	0.356436
Merged-chr2-91101665-1	chr2	91101615	91101715	+	2	cIP2vsInput	"intron (NM_011355, intron 2 of 4)"	"intron (NM_011355, intron 2 of 4)"	4868	NM_011355	20375	Mm.1302	NM_011355		Sfpi1	Dis-1|Dis1|PU.1|Sfpi-1|Spi-1|Spi1|Tcfpu1|Tfpu.1	SFFV proviral integration 1	protein-coding	0.02	0.49505
Merged-chr17-78779583-1	chr17	78779533	78779633	+	2	cIP2vsInput	"intron (NM_001081179, intron 26 of 35)"	Lx|LINE|L1	-43023	NM_011500	268980	Mm.486430	NM_011500		Strn	AU022939|D130055P19	"striatin, calmodulin binding protein"	protein-coding	0.01	0.336634
Merged-chr3-139176087-1	chr3	139176037	139176137	+	2	cIP2vsInput	Intergenic	Intergenic	-29806	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding	0	0.287129
Merged-chr14-114274155-1	chr14	114274105	114274205	+	2	cIP2vsInput	Intergenic	Lx5b|LINE|L1	-557810	NR_045661	75822	Mm.410813	NR_045661		4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	miscRNA	0	0.336634
Merged-chr6-102781444-1	chr6	102781394	102781494	+	2	cIP2vsInput	Intergenic	Intergenic	-316777	NM_008779	18488	Mm.435479	NM_008779	ENSMUSG00000030075	Cntn3	Pang	contactin 3	protein-coding	0	0.316832
Merged-chr3-8983938-1	chr3	8983888	8983988	+	2	cIP2vsInput	"intron (NM_001025264, intron 1 of 6)"	"intron (NM_001025264, intron 1 of 6)"	-19884	NM_001025261	21985	Mm.371590	NM_001025261	ENSMUSG00000027506	Tpd52	AI043038|mD52	tumor protein D52	protein-coding	0	0.346535
Merged-chr10-15563663-1	chr10	15563613	15563713	+	2	cIP2vsInput	Intergenic	Intergenic	803374	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding	0	0.346535
Merged-chr17-49936184-1	chr17	49936134	49936234	+	2	cIP1vsInput	Intergenic	ID_B1|SINE|B4	254313	NM_181397	76438	Mm.41854	NM_181397		Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding	0.01	0.415842
Merged-chr17-21650033-1	chr17	21649983	21650083	+	2	cIP2vsInput	promoter-TSS (NM_001166497)	promoter-TSS (NM_001166497)	-578	NM_001166497	73229	Mm.296733	NM_001166497		3110052M02Rik	mszf57|mszf71	RIKEN cDNA 3110052M02 gene	protein-coding	0.01	0.356436
Merged-chr19-39674886-1	chr19	39674836	39674936	+	2	cIP2vsInput	Intergenic	Intergenic	-25844	NM_001024719	545288	Mm.297048	NM_001024719	ENSMUSG00000062624	Cyp2c67	C730004C24Rik	"cytochrome P450, family 2, subfamily c, polypeptide 67"	protein-coding	0.01	0.336634
Merged-chr2-163592403-1	chr2	163592353	163592453	+	2	cIP1vsInput	Intergenic	Intergenic	-9911	NM_181734	76080	Mm.89828	NM_029512	ENSMUSG00000017679	Ttpal	3110080A02Rik|5830472M02Rik	tocopherol (alpha) transfer protein-like	protein-coding	0	0.29703
Merged-chr1-146189307-1	chr1	146189257	146189357	+	2	cIP2vsInput	Intergenic	Intergenic	-306359	NM_153539	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0.01	0.386139
Merged-chr14-61101827-1	chr14	61101777	61101877	+	2	cIP1vsInput	Intergenic	L1MB7|LINE|L1	-36630	NM_172809	50720	Mm.446687	NM_172809	ENSMUSG00000048279	Sacs	A230052M14|DNAJC29|E130115J16Rik|mKIAA0730	sacsin	protein-coding	0.01	0.326733
Merged-chr8-25477385-1	chr8	25477335	25477435	+	2	cIP2vsInput	Intergenic	ORR1C1|LTR|ERVL-MaLR	-41387	NM_001079909	14182	Mm.265716	NM_001079908	ENSMUSG00000031565	Fgfr1	AW208770|Eask|FLG|Fgfr-1|Flt-2|Hspy	fibroblast growth factor receptor 1	protein-coding	0	0.356436
Merged-chr6-145262471-1	chr6	145262421	145262521	+	2	cIP2vsInput	Intergenic	Intergenic	11919	NR_045598	100039495	Mm.121014	NR_045598	ENSMUSG00000086013	Gm15706	OTTMUSG00000025463	predicted gene 15706	miscRNA	0	0.346535
Merged-chr3-113927946-1	chr3	113927896	113927996	+	2	cIP2vsInput	Intergenic	Intergenic	-102594	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	"collagen, type XI, alpha 1"	protein-coding	0.01	0.346535
Merged-chr11-56666532-1	chr11	56666482	56666582	+	2	cIP2vsInput	Intergenic	Intergenic	-345086	NM_001113325	14799	Mm.4920	NM_001113325	ENSMUSG00000020524	Gria1	2900051M01Rik|Glr-1|Glr1|GluA1|GluR-A|GluRA|Glur-1|Glur1|HIPA1|gluR-K1	"glutamate receptor, ionotropic, AMPA1 (alpha 1)"	protein-coding	0.01	0.356436
Merged-chr15-33605748-1	chr15	33605698	33605798	+	2	cIP2vsInput	"intron (NR_045070, intron 5 of 5)"	L1M4|LINE|L1	47688	NR_045070	75880	Mm.396109	NR_045070		4930592A05Rik	-	RIKEN cDNA 4930592A05 gene	miscRNA	0	0.356436
Merged-chr3-126174224-1	chr3	126174174	126174274	+	2	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-189628	NM_173451	271970	Mm.317021	NM_173451	ENSMUSG00000046561	Arsj	9330196J05Rik|D830047F08	arylsulfatase J	protein-coding	0.01	0.306931
Merged-chr6-66787277-1	chr6	66787227	66787327	+	2	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-10147	NM_134168	171186	Mm.377167	NM_134168	ENSMUSG00000093632	Vmn1r38	V1rc13	vomeronasal 1 receptor 38	protein-coding	0	0.356436
Merged-chr3-36715251-1	chr3	36715201	36715301	+	2	cIP2vsInput	Intergenic	Intergenic	-25084	NM_019510	22065	Mm.74363	NM_019510	ENSMUSG00000027716	Trpc3	Mwk|Trcp3|Trp3|Trrp3	"transient receptor potential cation channel, subfamily C, member 3"	protein-coding	0	0.356436
Merged-chr5-56848882-1	chr5	56848832	56848932	+	2	cIP1vsInput	Intergenic	Intergenic	869037	NR_015588	319216	Mm.446765	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	miscRNA	0	0.346535
Merged-chr2-56774901-1	chr2	56774851	56774951	+	2	cIP2vsInput	Intergenic	Intergenic	340137	NM_013613	18227	Mm.3507	NM_001139509	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	"nuclear receptor subfamily 4, group A, member 2"	protein-coding	0	0.306931
Merged-chr17-19187115-1	chr17	19187065	19187165	+	2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	133622	NM_001104550	224552	Mm.469860	NM_001104550	ENSMUSG00000096717	Vmn2r98	EG224552	"vomeronasal 2, receptor 98"	protein-coding	0	0.287129
Merged-chr9-16829612-1	chr9	16829562	16829662	+	2	cIP2vsInput	Intergenic	Intergenic	-451381	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT tumor suppressor homolog 3 (Drosophila)	protein-coding	0	0.39604
Merged-chr9-119623898-1	chr9	119623848	119623948	+	2	cIP1vsInput	"intron (NM_001205321, intron 22 of 27)"	"intron (NM_001205321, intron 22 of 27)"	-44882	NM_021544	20271	Mm.103584	NM_001253860	ENSMUSG00000032511	Scn5a	Nav1.5|Nav1.5c|SkM1|SkM2|mH1	"sodium channel, voltage-gated, type V, alpha"	protein-coding	0.01	0.49505
Merged-chr5-87729179-1	chr5	87729129	87729229	+	2	cIP2vsInput	Intergenic	Intergenic	-29758	NM_009972	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding	0	0.247525
Merged-chr17-22209083-1	chr17	22209033	22209133	+	2	cIP2vsInput	"intron (NM_001205095, intron 2 of 4)"	"intron (NM_001205095, intron 2 of 4)"	16531	NM_001205095	240038	Mm.227945	NM_001205095	ENSMUSG00000096433	Gm4944	EG240038	predicted gene 4944	protein-coding	0	0.366337
Merged-chr13-62832730-1	chr13	62832680	62832780	+	2	cIP2vsInput	Intergenic	Intergenic	25640	NM_007994	14120	Mm.391871	NM_007994	ENSMUSG00000021456	Fbp2	Fbp-1|Fbp1|Rae-30	fructose bisphosphatase 2	protein-coding	0.01	0.316832
Merged-chr11-73399204-1	chr11	73399154	73399254	+	2	cIP2vsInput	"intron (NM_146921, intron 1 of 2)"	"intron (NM_146921, intron 1 of 2)"	291	NM_146921	258923	Mm.246523	NM_146921	ENSMUSG00000069823	Olfr1	I54|MOR135-13	olfactory receptor 1	protein-coding	0	0.326733
Merged-chr19-60748143-1	chr19	60748093	60748193	+	2	cIP2vsInput	Intergenic	L1ME3B|LINE|L1	-7844	NM_178421	332397	Mm.186390	NM_178421	ENSMUSG00000072437	Nanos1	-	nanos homolog 1 (Drosophila)	protein-coding	0	0.366337
Merged-chrX-39099360-1	chrX	39099310	39099410	+	2	cIP2vsInput	Intergenic	Intergenic	-246906	NM_001177380	78631	Mm.243738	NM_001177380	ENSMUSG00000079619	Cypt15	1700085A12Rik	cysteine-rich perinuclear theca 15	protein-coding	0.01	0.316832
Merged-chr9-119814406-1	chr9	119814356	119814456	+	2	cIP2vsInput	"intron (NM_011887, intron 4 of 26)"	"intron (NM_011887, intron 4 of 26)"	11050	NM_011887	24046	Mm.89981	NM_011887	ENSMUSG00000034115	Scn11a	NSS2|NaN|NaT|SNS2	"sodium channel, voltage-gated, type XI, alpha"	protein-coding	0	0.326733
Merged-chr7-135334560-1	chr7	135334510	135334610	+	2	cIP1vsInput	Intergenic	Intergenic	65941	NM_001163611	100043254	Mm.192092	NM_001163611	ENSMUSG00000073804	Nps	ENSMUSG00000073804	neuropeptide S	protein-coding	0.02	0.405941
Merged-chr1-76744104-1	chr1	76744054	76744154	+	2	cIP2vsInput	Intergenic	Intergenic	254971	NR_038013	620079	Mm.378379	NR_038012		Gm17751	-	"predicted gene, 17751"	miscRNA	0	0.306931
Merged-chr2-82878273-1	chr2	82878223	82878323	+	2	cIP2vsInput	Intergenic	Intergenic	-766305	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding	0	0.306931
Merged-chr3-59651794-1	chr3	59651744	59651844	+	2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-77992	NM_001101531	433597	Mm.297801	NM_001101531	ENSMUSG00000090527	Gm5538	-	predicted gene 5538	protein-coding	0	0.376238
Merged-chr3-150480179-1	chr3	150480129	150480229	+	2	cIP2vsInput	Intergenic	Intergenic	-957703	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Eltd1	1110033N21Rik|ETL1|Etl	"EGF, latrophilin seven transmembrane domain containing 1"	protein-coding	0	0.346535
Merged-chr4-33818539-1	chr4	33818489	33818589	+	2	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	-106093	NM_007726	12801	Mm.7992	NM_007726	ENSMUSG00000044288	Cnr1	CB-R|CB1|CB1R	cannabinoid receptor 1 (brain)	protein-coding	0	0.306931
Merged-chr14-93913549-1	chr14	93913499	93913599	+	2	cIP2vsInput	Intergenic	Intergenic	-22880	NM_001271798	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.326733
Merged-chr18-87476918-1	chr18	87476868	87476968	+	2	cIP2vsInput	Intergenic	Intergenic	763870	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding	0	0.386139
Merged-chr12-67522954-1	chr12	67522904	67523004	+	2	cIP2vsInput	Intergenic	Intergenic	146317	NR_033146	100316870	Mm.379794	NR_033146		Gm17821	-	DDB1 and CUL4 associated factor 5 pseudogene	pseudo	0	0.326733
Merged-chrX-151472085-1	chrX	151472035	151472135	+	2	cIP1vsInput	"3' UTR (NM_198105, exon 16 of 16)"	"3' UTR (NM_198105, exon 16 of 16)"	-48587	NM_177201	320595	Mm.17156	NM_001113354	ENSMUSG00000041229	Phf8	9830141C09Rik|mKIAA1111	PHD finger protein 8	protein-coding	0	0.39604
Merged-chr3-14299027-1	chr3	14298977	14299077	+	2	cIP2vsInput	Intergenic	Lx2A|LINE|L1	-64090	NR_033591	622229	Mm.486084	NR_033591		Gm6300	EG622229	"solute carrier family 7 (cationic amino acid transporter, y+ system), member pseudogene"	pseudo	0	0.336634
Merged-chr3-73426175-1	chr3	73426125	73426225	+	2	cIP2vsInput	"intron (NR_040547, intron 2 of 7)"	MTE2b|LTR|ERVL-MaLR	55476	NR_040547	74693	Mm.292227	NR_040547		4930509J09Rik	-	RIKEN cDNA 4930509J09 gene	miscRNA	0	0.326733
Merged-chr6-80644009-1	chr6	80643959	80644059	+	2	cIP2vsInput	Intergenic	MYSERV16_I-int|LTR|ERVK	624366	NM_178731	243499	Mm.483425	NM_001134743	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding	0	0.29703
Merged-chr4-18945516-1	chr4	18945466	18945566	+	2	cIP2vsInput	Intergenic	Intergenic	-335334	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding	0	0.316832
Merged-chr7-53223280-1	chr7	53223230	53223330	+	2	cIP2vsInput	Intergenic	Lx8|LINE|L1	-1207564	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding	0.01	0.366337
Merged-chr14-107626336-1	chr14	107626286	107626386	+	2	cIP1vsInput	Intergenic	Intergenic	-1139816	NR_045938	73631	Mm.48862	NR_045938		1700128A07Rik	-	RIKEN cDNA 1700128A07 gene	miscRNA	0	0.29703
Merged-chr6-63243693-1	chr6	63243643	63243743	+	2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-13164	NM_008167	14804	Mm.447390	NM_008167		Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	"glutamate receptor, ionotropic, delta 2"	protein-coding	0	0.336634
Merged-chr8-80919922-1	chr8	80919872	80919972	+	2	cIP2vsInput	Intergenic	Intergenic	-39443	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding	0.01	0.306931
Merged-chr11-62669246-1	chr11	62669196	62669296	+	2	cIP2vsInput	Intergenic	Intergenic	20582	NM_175002	216829	Mm.486481	NM_175002		Mmgt2	AI852046	membrane magnesium transporter 2	protein-coding	0	0.39604
Merged-chr3-126859678-1	chr3	126859628	126859728	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	83708	NM_001034168	109676	Mm.484610	NM_001034168	ENSMUSG00000032826	Ank2	AI835472|AW491075|Ank-2	"ankyrin 2, brain"	protein-coding	0.01	0.336634
Merged-chr5-26953955-1	chr5	26953905	26954005	+	2	cIP2vsInput	"intron (NM_001198886, intron 1 of 25)"	MLT2D|LTR|ERVL	49177	NM_001198886	13483	Mm.42078	NM_001136060	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding	0	0.356436
Merged-chr7-52458232-1	chr7	52458182	52458282	+	2	cIP2vsInput	Intergenic	L1MA6|LINE|L1	-442516	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding	0	0.366337
Merged-chr10-68013899-1	chr10	68013849	68013949	+	2	cIP2vsInput	"intron (NM_001081346, intron 6 of 12)"	"intron (NM_001081346, intron 6 of 12)"	34301	NM_001081346	170799	Mm.209844	NM_001081346	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding	0.07	0.584158
Merged-chr19-43905955-1	chr19	43905905	43906005	+	2	cIP2vsInput	"intron (NM_028029, intron 3 of 15)"	"intron (NM_028029, intron 3 of 15)"	34243	NM_028029	71972	Mm.426081	NM_028029		Dnmbp	2410003L07Rik|2410003M15Rik|TUBA	dynamin binding protein	protein-coding	0.01	0.346535
Merged-chr9-84642438-1	chr9	84642388	84642488	+	2	cIP2vsInput	Intergenic	Intergenic	-131960	NR_040739	75253	Mm.401984	NR_040739		4930554C24Rik	-	RIKEN cDNA 4930554C24 gene	miscRNA	0	0.29703
Merged-chr7-51194641-1	chr7	51194591	51194691	+	2	cIP2vsInput	Intergenic	Intergenic	-316388	NR_073508	233246	Mm.411727	NM_001271879	ENSMUSG00000055489	Ano5	9330162L24|Gdd1|Tmem16e	anoctamin 5	protein-coding	0	0.386139
Merged-chr7-16262912-1	chr7	16262862	16262962	+	2	cIP2vsInput	Intergenic	ID_B1|SINE|B4	-3372	NM_007577	12273	Mm.247623	NM_001173550	ENSMUSG00000049130	C5ar1	C5aR|C5r1|Cd88|D7Msu1	complement component 5a receptor 1	protein-coding	0.01	0.49505
Merged-chr8-59274951-1	chr8	59274901	59275001	+	2	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	363196	NM_173411	234290	Mm.39244	NM_173411	ENSMUSG00000049946	BC030500	-	cDNA sequence BC030500	protein-coding	0	0.326733
Merged-chr6-107598364-1	chr6	107598314	107598414	+	2	cIP2vsInput	Intergenic	Intergenic	68638	NM_008516	16979	Mm.488119	NM_008516	ENSMUSG00000034648	Lrrn1	2810047E21Rik|NLRR-1	"leucine rich repeat protein 1, neuronal"	protein-coding	0	0.277228
Merged-chr6-84720969-1	chr6	84720919	84721019	+	2	cIP2vsInput	"intron (NM_177077, intron 20 of 21)"	MurERV4-int|LTR|ERVK	-127061	NM_001177713	232174	Mm.255246	NM_001177713	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	"cytochrome P450, family 26, subfamily b, polypeptide 1"	protein-coding	0	0.316832
Merged-chr1-181016555-1	chr1	181016505	181016605	+	2	cIP2vsInput	"intron (NM_010145, intron 1 of 8)"	"intron (NM_010145, intron 1 of 8)"	940	NM_010145	13849	Mm.9075	NM_010145	ENSMUSG00000038776	Ephx1	AI195553|Eph-1|Eph1|mEH	"epoxide hydrolase 1, microsomal"	protein-coding	0.03	0.554455
Merged-chr17-40313323-1	chr17	40313273	40313373	+	2	cIP1vsInput	"intron (NM_009638, intron 1 of 7)"	"intron (NM_009638, intron 1 of 7)"	5884	NM_009638	11571	Mm.16781	NM_009638	ENSMUSG00000025431	Crisp1	AW324342|Aeg1|CRISP-1	cysteine-rich secretory protein 1	protein-coding	0	0.346535
Merged-chrX-118556889-1	chrX	118556839	118556939	+	2	cIP2vsInput	Intergenic	Intergenic	-76152	NM_001142750	100039551	Mm.423457	NM_001142750	ENSMUSG00000063242	Tgif2lx2	-	"TGFB-induced factor homeobox 2-like, X-linked 2"	protein-coding	0	0.316832
Merged-chr13-10613095-1	chr13	10613045	10613145	+	2	cIP2vsInput	Intergenic	Intergenic	-252292	NM_033269	12671	Mm.342315	NM_033269		Chrm3	Chrm-3|M3|M3R	"cholinergic receptor, muscarinic 3, cardiac"	protein-coding	0	0.326733
Merged-chr15-56941197-1	chr15	56941147	56941247	+	2	cIP1vsInput	Intergenic	Intergenic	-246651	NM_008216	15117	Mm.5148	NM_008216	ENSMUSG00000022367	Has2	-	hyaluronan synthase 2	protein-coding	0	0.445545
Merged-chr8-31965550-1	chr8	31965500	31965600	+	2	cIP2vsInput	Intergenic	Intergenic	-47347	NM_178591	211323	Mm.460675	NM_178591	ENSMUSG00000062991	Nrg1	6030402G23Rik|ARIA|D230005F13Rik|GGF|GGFII|HRG|HRGalpha|Hgl|NDF|SMDF	neuregulin 1	protein-coding	0	0.29703
Merged-chr2-88278134-1	chr2	88278084	88278184	+	2	cIP2vsInput	Intergenic	Intergenic	-3087	NM_207566	404329	Mm.377943	NM_207566	ENSMUSG00000075132	Olfr1173	-	olfactory receptor 1173	protein-coding	0.01	0.29703
Merged-chr12-112130763-1	chr12	112130713	112130813	+	2	cIP2vsInput	promoter-TSS (NR_029590)	promoter-TSS (NR_029590)	-117	NR_029590	387199		NR_029590	ENSMUSG00000065574	Mir203	Mirn203|mmu-mir-203	microRNA 203	miscRNA	0.17	0.772277
Merged-chrX-121720762-1	chrX	121720712	121720812	+	2	cIP1vsInput	Intergenic	Lx2|LINE|L1	676623	NM_138742	54561	Mm.490573	NM_138742	ENSMUSG00000055733	Nap1l3	MB20	nucleosome assembly protein 1-like 3	protein-coding	0	0.326733
Merged-chr17-42239678-1	chr17	42239628	42239728	+	2	cIP2vsInput	Intergenic	L1MA4|LINE|L1	-76269	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding	0	0.386139
Merged-chrX-51149154-1	chrX	51149104	51149204	+	2	cIP2vsInput	"intron (NM_134163, intron 2 of 7)"	"intron (NM_134163, intron 2 of 7)"	56678	NM_134163	171170	Mm.295324	NM_134163		Mbnl3	A530038J18Rik|AI661274|CHCR|E430034C16Rik|MBLX|MBLX39|MBXL	muscleblind-like 3 (Drosophila)	protein-coding	0.02	0.386139
Merged-chr18-59598970-1	chr18	59598920	59599020	+	2	cIP2vsInput	Intergenic	Intergenic	423630	NM_001081328	78923	Mm.485185	NM_001081328		Chsy3	4833446K15Rik|AI662215	chondroitin sulfate synthase 3	protein-coding	0	0.336634
Merged-chrX-50761238-1	chrX	50761188	50761288	+	2	cIP2vsInput	Intergenic	Intergenic	-80198	NM_133729	70415	Mm.391246	NM_133729		2610018G03Rik	Mst4	RIKEN cDNA 2610018G03 gene	protein-coding	0	0.316832
Merged-chr4-73504811-1	chr4	73504761	73504861	+	2	cIP1vsInput	Intergenic	Intergenic	-99739	NM_001013393	433719	Mm.348294	NM_001013393	ENSMUSG00000066137	Gm11487	OTTMUSG00000001246	predicted gene 11487	protein-coding	0.01	0.346535
Merged-chr3-45736664-1	chr3	45736614	45736714	+	2	cIP2vsInput	Intergenic	Lx7|LINE|L1	-297355	NR_040594	72274	Mm.396202	NR_040594		1700027H10Rik	-	RIKEN cDNA 1700027H10 gene	miscRNA	0	0.326733
Merged-chr14-70377995-1	chr14	70377945	70378045	+	2	cIP2vsInput	"intron (NM_021308, intron 20 of 22)"	"intron (NM_021308, intron 20 of 22)"	-26571	NM_001135151	213053	Mm.270647	NM_001135151	ENSMUSG00000022094	Slc39a14	BC021530|G630015O18Rik|Zip14|fad123	"solute carrier family 39 (zinc transporter), member 14"	protein-coding	0	0.346535
Merged-chr5-59447006-1	chr5	59446956	59447056	+	2	cIP1vsInput	Intergenic	Intergenic	538996	NR_040683	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0	0.237624
Merged-chr11-13249462-1	chr11	13249412	13249512	+	2	cIP1vsInput	Intergenic	MIR|SINE|MIR	-784502	NM_172496	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	4732460E13|C530045F18Rik|mKIAA0633	cordon-bleu	protein-coding	0	0.356436
Merged-chr3-128787039-1	chr3	128786989	128787089	+	2	cIP2vsInput	Intergenic	Intergenic	-412879	NM_011098	18741	Mm.246804	NM_001042502	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1a|Brx1b|Munc30|Otlx2|Pitx2a|Pitx2b|Pitx2c|Pitx2cbeta|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding	0	0.316832
Merged-chr12-64610432-1	chr12	64610382	64610482	+	2	cIP2vsInput	Intergenic	Intergenic	-135534	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0.01	0.366337
Merged-chr1-93272727-1	chr1	93272677	93272777	+	2	cIP2vsInput	"intron (NM_172463, intron 12 of 30)"	"intron (NM_172463, intron 12 of 30)"	33143	NM_178051	69821	Mm.52809	NM_178051		Mterfd2	1810059A23Rik|4933412H03Rik|Mterf4	MTERF domain containing 2	protein-coding	0.06	0.60396
Merged-chr17-77843308-1	chr17	77843258	77843358	+	2	cIP1vsInput	Intergenic	Intergenic	-356940	NM_015800	50766	Mm.311912	NM_015800	ENSMUSG00000024074	Crim1	AU015004	cysteine rich transmembrane BMP regulator 1 (chordin like)	protein-coding	0.01	0.316832
Merged-chr13-118133998-1	chr13	118133948	118134048	+	2	cIP2vsInput	Intergenic	Intergenic	253254	NM_021556	59054	Mm.143810	NM_021556	ENSMUSG00000021731	Mrps30	2610020A16Rik|AA968347|PAP|Pdcd9	mitochondrial ribosomal protein S30	protein-coding	0	0.356436
Merged-chr13-115582555-1	chr13	115582505	115582605	+	2	cIP2vsInput	Intergenic	Intergenic	-480591	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding	0.01	0.346535
Merged-chr19-17521096-1	chr19	17521046	17521146	+	2	cIP2vsInput	"intron (NM_001190483, intron 21 of 37)"	Lx8|LINE|L1	127053	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding	0.01	0.346535
Merged-chr4-34018716-1	chr4	34018666	34018766	+	2	cIP2vsInput	Intergenic	Intergenic	31351	NM_026293	67652	Mm.55848	NM_026293	ENSMUSG00000028264	Spaca1	1700124L11Rik|4930540L03Rik	sperm acrosome associated 1	protein-coding	0	0.346535
Merged-chr11-25479537-1	chr11	25479487	25479587	+	2	cIP2vsInput	Intergenic	Intergenic	153430	NR_045853	71234	Mm.158627	NR_045853	ENSMUSG00000033015	4933427E13Rik	-	RIKEN cDNA 4933427E13 gene	miscRNA	0	0.376238
Merged-chr18-7733677-1	chr18	7733627	7733727	+	2	cIP2vsInput	Intergenic	ORR1A2-int|LTR|ERVL-MaLR	-106814	NM_001161620	75739	Mm.133293	NM_001081287	ENSMUSG00000057440	Mpp7	1110068J02Rik|2810038M04Rik|5430426E14Rik|AI415104|Gm955	"membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)"	protein-coding	0.01	0.376238
Merged-chr9-6022883-1	chr9	6022833	6022933	+	2	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-145729	NM_027924	71785	Mm.390122	NM_027924	ENSMUSG00000032006	Pdgfd	1110003I09Rik	"platelet-derived growth factor, D polypeptide"	protein-coding	0	0.356436
Merged-chr7-94290146-1	chr7	94290096	94290196	+	2	cIP2vsInput	Intergenic	Lx9|LINE|L1	1210267	NM_021427	58238	Mm.473915	NM_021427		Fam181b	A830059I20Rik|AB041569	"family with sequence similarity 181, member B"	protein-coding	0	0.356436
Merged-chr7-87661090-1	chr7	87661040	87661140	+	2	cIP2vsInput	"intron (NM_001081414, intron 3 of 9)"	Lx10|LINE|L1	76922	NM_001143834	108071	Mm.235018	NM_001033224	ENSMUSG00000049583	Grm5	6430542K11Rik|AI850523|Gprc1e|mGluR5|mGluR5b	"glutamate receptor, metabotropic 5"	protein-coding	0	0.366337
Merged-chr3-48816394-1	chr3	48816344	48816444	+	2	cIP2vsInput	Intergenic	Intergenic	-207294	NR_003617	66332	Mm.46124	NR_003617		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo	0.01	0.326733
Merged-chr17-50768780-1	chr17	50768730	50768830	+	2	cIP2vsInput	"intron (NM_028162, intron 18 of 21)"	"intron (NM_028162, intron 18 of 21)"	259233	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding	0	0.336634
Merged-chr15-69516798-1	chr15	69516748	69516848	+	2	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	-407435	NR_045071	100503580	Mm.404646	NR_045071		Gm19782	-	"predicted gene, 19782"	miscRNA	0	0.316832
Merged-chr6-141353886-1	chr6	141353836	141353936	+	2	cIP2vsInput	"intron (NM_018779, intron 1 of 15)"	"intron (NM_018779, intron 1 of 15)"	13333	NR_033555	100093700	Mm.483778	NR_033555		Gm10400	ENSMUSG00000072690	predicted gene 10400	miscRNA	0	0.29703
Merged-chr3-73602148-1	chr3	73602098	73602198	+	2	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	106267	NM_009738	12038	Mm.250719	NM_009738	ENSMUSG00000027792	Bche	C730038G20Rik	butyrylcholinesterase	protein-coding	0	0.356436
Merged-chr1-5363538-1	chr1	5363488	5363588	+	2	cIP2vsInput	Intergenic	Intergenic	-224955	NM_011011	18387	Mm.7977	NM_001204371	ENSMUSG00000025905	Oprk1	K-OR-1|KOR|KOR-1|MSL-1|Oprk2|R21	"opioid receptor, kappa 1"	protein-coding	0	0.435644
Merged-chr5-16714637-1	chr5	16714587	16714687	+	2	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	161087	NM_010427	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF/HGF	hepatocyte growth factor	protein-coding	0	0.29703
Merged-chr12-37213879-1	chr12	37213829	37213929	+	2	cIP2vsInput	Intergenic	RMER1C|Other|Other	-27760	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding	0	0.326733
Merged-chr5-27608624-1	chr5	27608574	27608674	+	2	cIP1vsInput	"intron (NM_001136060, intron 8 of 25)"	Lx2|LINE|L1	-107232	NM_028561	73526	Mm.389608	NM_028561	ENSMUSG00000048703	Speer4b	1700081O22Rik|SPEER-4B	spermatogenesis associated glutamate (E)-rich protein 4b	protein-coding	0.01	0.346535
Merged-chr14-14044667-1	chr14	14044617	14044717	+	2	cIP2vsInput	"intron (NM_139227, intron 3 of 11)"	"intron (NM_139227, intron 3 of 11)"	32176	NM_139227	246103	Mm.133625	NM_139227	ENSMUSG00000021738	Atxn7	A430107N12Rik|AI627028|Sca7|ataxin-7	ataxin 7	protein-coding	0	0.346535
Merged-chr2-3114749-1	chr2	3114699	3114799	+	2	cIP2vsInput	Intergenic	Intergenic	-3639	NM_001081161	269233	Mm.23044	NM_001081161		Fam171a1	9630050M13Rik|AA409679	"family with sequence similarity 171, member A1"	protein-coding	0.02	0.336634
Merged-chr12-64540893-1	chr12	64540843	64540943	+	2	cIP2vsInput	Intergenic	Intergenic	-65995	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.277228
Merged-chr12-27441020-1	chr12	27440970	27441070	+	2	cIP2vsInput	Intergenic	Intergenic	-98302	NM_009234	20666	Mm.466344	NM_009234		Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY-box containing gene 11	protein-coding	0.01	0.326733
Merged-chr15-48119794-1	chr15	48119744	48119844	+	2	cIP2vsInput	"intron (NM_001081391, intron 13 of 70)"	L1MC1|LINE|L1	672195	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0	0.336634
Merged-chr2-73596994-1	chr2	73596944	73597044	+	2	cIP2vsInput	"non-coding (NR_040623, exon 1 of 4)"	"non-coding (NR_040623, exon 1 of 4)"	468	NR_040623	329427	Mm.257073	NR_040623	ENSMUSG00000086544	Gm13704	OTTMUSG00000013429	predicted gene 13704	miscRNA	0.03	0.60396
Merged-chr13-47033319-1	chr13	47033269	47033369	+	2	cIP2vsInput	"intron (NM_016785, intron 5 of 8)"	RMER4B|LTR|ERVK	9898	NM_016785	22017	Mm.10169	NM_016785		Tpmt	AW106912	thiopurine methyltransferase	protein-coding	0	0.465347
Merged-chr10-26112609-1	chr10	26112559	26112659	+	2	cIP1vsInput	Intergenic	Lx|LINE|L1	-33557	NM_029881	77220	Mm.266260	NM_029881	ENSMUSG00000049420	Tmem200a	C030003D03Rik	transmembrane protein 200A	protein-coding	0	0.346535
Merged-chr6-75076956-1	chr6	75076906	75077006	+	2	cIP2vsInput	Intergenic	Intergenic	-1607289	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.346535
Merged-chr17-22461061-1	chr17	22461011	22461111	+	2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	36793	NM_198003	74149	Mm.30767	NM_198003	ENSMUSG00000071266	Zfp946	1300003B13Rik	zinc finger protein 946	protein-coding	0	0.346535
Merged-chr8-38287013-1	chr8	38286963	38287063	+	2	cIP2vsInput	"intron (NM_145841, intron 1 of 7)"	"intron (NM_145841, intron 1 of 7)"	-34811	NR_029884	723860		NR_029884		Mir383	Mirn383|mmu-mir-383	microRNA 383	miscRNA	0	0.366337
Merged-chr6-137665717-1	chr6	137665667	137665767	+	2	cIP2vsInput	Intergenic	Intergenic	-16432	NM_007945	13860	Mm.235346	NM_001271587	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding	0	0.415842
Merged-chr3-134389887-1	chr3	134389837	134389937	+	2	cIP1vsInput	Intergenic	Intergenic	33748	NR_040600	75208	Mm.84580	NR_040600		4930539C22Rik	-	RIKEN cDNA 4930539C22 gene	miscRNA	0.01	0.336634
Merged-chr6-33752074-1	chr6	33752024	33752124	+	2	cIP2vsInput	"intron (NM_009148, intron 10 of 17)"	"intron (NM_009148, intron 10 of 17)"	-277374	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding	0.01	0.336634
Merged-chr10-19077328-1	chr10	19077278	19077378	+	2	cIP2vsInput	Intergenic	Intergenic	-61918	NM_009397	21929	Mm.116683	NM_001166402	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	"tumor necrosis factor, alpha-induced protein 3"	protein-coding	0	0.336634
Merged-chr15-50425403-1	chr15	50425353	50425453	+	2	cIP2vsInput	Intergenic	Intergenic	463711	NR_035444	100316685		NR_035444	ENSMUSG00000084458	Mir1907	Mirn1907|mmu-mir-1907	microRNA 1907	miscRNA	0	0.346535
Merged-chr4-96182902-1	chr4	96182852	96182952	+	2	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-41750	NM_001100182	242546	Mm.302562	NM_001100182	ENSMUSG00000081225	Cyp2j12	BB197342|Cyp2j12-ps|OTTMUSG00000007939	"cytochrome P450, family 2, subfamily j, polypeptide 12"	protein-coding	0	0.336634
Merged-chrX-133117098-1	chrX	133117048	133117148	+	2	cIP2vsInput	Intergenic	Intergenic	571895	NM_001105245	279653	Mm.39738	NM_001105245	ENSMUSG00000051323	Pcdh19	B530002L05Rik|Gm717|mKIAA1313	protocadherin 19	protein-coding	0.01	0.356436
Merged-chr16-80203562-1	chr16	80203512	80203612	+	2	cIP2vsInput	Intergenic	Intergenic	-997135	NM_001113208	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.29703
Merged-chr9-111685638-1	chr9	111685588	111685688	+	2	cIP2vsInput	"intron (NM_016853, intron 1 of 10)"	"intron (NM_016853, intron 1 of 10)"	4578	NM_016853	20840	Mm.1414	NM_016853	ENSMUSG00000032502	Stac	-	src homology three (SH3) and cysteine rich domain	protein-coding	0	0.326733
Merged-chr1-67877125-1	chr1	67877075	67877175	+	2	cIP2vsInput	Intergenic	L1MEc|LINE|L1	754059	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding	0	0.247525
Merged-chr13-61348691-1	chr13	61348641	61348741	+	2	cIP2vsInput	Intergenic	MusHAL1|LINE|L1	9479	NM_019539	56092	Mm.3692	NM_019539	ENSMUSG00000021440	Cts7	AA408230|AA408952|CTS1|Epcs24|Epcs71	cathepsin 7	protein-coding	0	0.29703
Merged-chr2-73223379-1	chr2	73223329	73223429	+	2	cIP2vsInput	Intergenic	MTC|LTR|ERVL-MaLR	-8932	NM_025942	67059	Mm.22661	NM_025942	ENSMUSG00000027108	Ola1	2510025G09Rik|2810405J23Rik|2810409H07Rik|Gtpbp9|PTD004	Obg-like ATPase 1	protein-coding	0.01	0.356436
Merged-chr10-71923321-1	chr10	71923271	71923371	+	2	cIP2vsInput	Intergenic	Intergenic	57369	NR_003644	108950	Mm.212793	NR_003644	ENSMUSG00000043859	1700049L16Rik	-	hematological and neurological expressed 1-like pseudogene	pseudo	0	0.306931
Merged-chr11-103508787-1	chr11	103508737	103508837	+	2	cIP1vsInput	Intergenic	RSINE1|SINE|B4	-96123	NM_183034	353047	Mm.383308	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	"pleckstrin homology domain containing, family M (with RUN domain) member 1"	protein-coding	0.01	0.435644
Merged-chr8-126075884-1	chr8	126075834	126075934	+	2	cIP2vsInput	Intergenic	Lx4B|LINE|L1	80782	NM_008430	16525	Mm.10800	NM_008430	ENSMUSG00000033998	Kcnk1	AI788889|TWIK-1	"potassium channel, subfamily K, member 1"	protein-coding	0	0.287129
Merged-chr6-74376016-1	chr6	74375966	74376066	+	2	cIP2vsInput	Intergenic	Intergenic	-906349	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.316832
Merged-chr2-55143935-1	chr2	55143885	55143985	+	2	cIP2vsInput	Intergenic	Intergenic	-293221	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK1|Kcnf3|Kir3.1	"potassium inwardly-rectifying channel, subfamily J, member 3"	protein-coding	0.01	0.29703
Merged-chr8-23991982-1	chr8	23991932	23992032	+	2	cIP2vsInput	"intron (NM_177086, intron 5 of 6)"	"intron (NM_177086, intron 5 of 6)"	322321	NM_177086	320158	Mm.121274	NM_001277239	ENSMUSG00000037492	Zmat4	9630048M01Rik	"zinc finger, matrin type 4"	protein-coding	0	0.356436
Merged-chr12-30382682-1	chr12	30382632	30382732	+	2	cIP2vsInput	Intergenic	Lx4A|LINE|L1	-9307	NM_172951	268534	Mm.279765	NM_172951	ENSMUSG00000020672	Sntg2	2210008K22Rik|9530013L23|BB121248	"syntrophin, gamma 2"	protein-coding	0.01	0.336634
Merged-chr13-12964293-1	chr13	12964243	12964343	+	2	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	41037	NM_031191	18811	Mm.88796	NM_031191	ENSMUSG00000079092	Prl2c2	MRP-1|PLF-1|Plf|Plf1	"prolactin family 2, subfamily c, member 2"	protein-coding	0.01	0.475248
Merged-chrX-120564290-1	chrX	120564240	120564340	+	2	cIP1vsInput	"intron (NR_073452, intron 3 of 6)"	"intron (NR_073452, intron 3 of 6)"	273963	NR_073451	245578	Mm.490224	NM_001271809		Pcdh11x	PCDHX|PCDHX11|Pcdh11	protocadherin 11 X-linked	protein-coding	0	0.306931
Merged-chr2-47938948-1	chr2	47938898	47938998	+	2	cIP2vsInput	Intergenic	B3A|SINE|B2	-875161	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding	0	0.366337
Merged-chr15-80160788-1	chr15	80160738	80160838	+	2	cIP2vsInput	"3' UTR (NM_025609, exon 11 of 11)"	"3' UTR (NM_025609, exon 11 of 11)"	-12933	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding	0.01	0.50495
Merged-chr8-4725819-1	chr8	4725769	4725869	+	2	cIP2vsInput	Intergenic	MurSatRep1|Unknown|Unknown	53715	NM_011369	20419	Mm.37801	NM_011369	ENSMUSG00000022322	Shcbp1	mPAL	Shc SH2-domain binding protein 1	protein-coding	0.01	0.29703
Merged-chr13-64955703-1	chr13	64955653	64955753	+	2	cIP2vsInput	Intergenic	Intergenic	38297	NM_030047	78124	Mm.342895	NM_030047	ENSMUSG00000056223	Spata31	4930458L03Rik|Aep1|Fam75a|Spata31a|Vad1.3	spermatogenesis associated 31	protein-coding	0	0.336634
Merged-chr5-59012315-1	chr5	59012265	59012365	+	2	cIP2vsInput	Intergenic	Intergenic	-559317	NR_046190	78163	Mm.243828	NR_046190		4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	miscRNA	0.01	0.336634
Merged-chr12-55089732-1	chr12	55089682	55089782	+	2	cIP2vsInput	"intron (NM_011899, intron 2 of 15)"	"intron (NM_011899, intron 2 of 15)"	9236	NM_011899	24067	Mm.471968	NM_011899		Srp54a	54kDa|Srp54	signal recognition particle 54A	protein-coding	0	0.346535
Merged-chr10-57630176-1	chr10	57630126	57630226	+	2	cIP2vsInput	Intergenic	Intergenic	-1805	NM_008863	18768	Mm.262135	NM_001039050	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	"protein kinase inhibitor beta, cAMP dependent, testis specific"	protein-coding	0.01	0.346535
Merged-chr8-19688267-1	chr8	19688217	19688317	+	2	cIP2vsInput	Intergenic	Lx7|LINE|L1	-41309	NM_001270553	100861668	Mm.445582	NM_001270553		Gm21119	-	"predicted gene, 21119"	protein-coding	0.01	0.346535
Merged-chr1-160822598-1	chr1	160822548	160822648	+	2	cIP1vsInput	Intergenic	Intergenic	-29660	NM_013862	29809	Mm.25833	NM_001038621	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding	0	0.316832
Merged-chr12-41362573-1	chr12	41362523	41362623	+	2	cIP2vsInput	Intergenic	Lx5c|LINE|L1	123484	NM_001271708	16981	Mm.39913	NM_001271708	ENSMUSG00000036295	Lrrn3	NLRR-3	"leucine rich repeat protein 3, neuronal"	protein-coding	0	0.346535
Merged-chr3-17127076-1	chr3	17127026	17127126	+	2	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-662845	NR_033490	70441	Mm.458192	NR_033490		2610100L16Rik	100040120|Gm2612	RIKEN cDNA 2610100L16 gene	miscRNA	0.01	0.356436
Merged-chr14-77046308-1	chr14	77046258	77046358	+	2	cIP2vsInput	"intron (NM_175369, intron 1 of 5)"	L1Md_F2|LINE|L1	9536	NM_175369	108811	Mm.102168	NM_175369	ENSMUSG00000034795	Ccdc122	4933415L06Rik	coiled-coil domain containing 122	protein-coding	0	0.306931
Merged-chr12-98324460-1	chr12	98324410	98324510	+	2	cIP1vsInput	Intergenic	Intergenic	55825	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding	0	0.29703
Merged-chr16-60950900-1	chr16	60950850	60950950	+	2	cIP2vsInput	Intergenic	Intergenic	-345369	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0.01	0.356436
Merged-chr9-15916398-1	chr9	15916348	15916448	+	2	cIP2vsInput	"intron (NM_001080814, intron 24 of 24)"	"intron (NM_001080814, intron 24 of 24)"	-41842	NM_145712	244701	Mm.222631	NM_145712	ENSMUSG00000050901	Mtnr1b	Mel-1B-R|Mel1b|Mt2	melatonin receptor 1B	protein-coding	0	0.287129
Merged-chr17-41583230-1	chr17	41583180	41583280	+	2	cIP1vsInput	Intergenic	ORR1C1-int|LTR|ERVL-MaLR	648545	NM_008650	17850	Mm.259884	NM_008650	ENSMUSG00000023921	Mut	D230010K02Rik|Mcm	methylmalonyl-Coenzyme A mutase	protein-coding	0.02	0.336634
Merged-chr3-139256805-1	chr3	139256755	139256855	+	2	cIP2vsInput	"intron (NM_198659, intron 6 of 13)"	"intron (NM_198659, intron 6 of 13)"	50912	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding	0	0.29703
Merged-chr3-124962971-1	chr3	124962921	124963021	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-381880	NR_015460	384775	Mm.489851	NR_015460	ENSMUSG00000039174	1700003H04Rik	4930538K10Rik|4933400D22Rik	RIKEN cDNA 1700003H04 gene	miscRNA	0.02	0.306931
Merged-chr14-107033154-1	chr14	107033104	107033204	+	2	cIP2vsInput	Intergenic	Intergenic	-546634	NR_045938	73631	Mm.48862	NR_045938		1700128A07Rik	-	RIKEN cDNA 1700128A07 gene	miscRNA	0	0.346535
Merged-chr1-108779927-1	chr1	108779877	108779977	+	2	cIP2vsInput	Intergenic	Intergenic	862668	NR_102307	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0	0.376238
Merged-chr13-75022009-1	chr13	75021959	75022059	+	2	cIP2vsInput	Intergenic	Lx3_Mus|LINE|L1	-67978	NM_013628	18548	Mm.1333	NM_013628	ENSMUSG00000021587	Pcsk1	Nec-1|Nec1|PC1|PC3|Phpp-1|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0	0.346535
Merged-chr11-10758374-1	chr11	10758324	10758424	+	2	cIP2vsInput	Intergenic	Intergenic	-355642	NM_177033	319922	Mm.487612	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding	0.02	0.455446
Merged-chr1-148840763-1	chr1	148840713	148840813	+	2	cIP1vsInput	Intergenic	Intergenic	1120521	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0.01	0.267327
Merged-chr15-25227274-1	chr15	25227224	25227324	+	2	cIP2vsInput	Intergenic	Intergenic	186490	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	"brain abundant, membrane attached signal protein 1"	protein-coding	0	0.326733
Merged-chr3-69143264-1	chr3	69143214	69143314	+	2	cIP1vsInput	"intron (NM_001243000, intron 1 of 2)"	"intron (NM_001243000, intron 1 of 2)"	12031	NM_001243000	381452	Mm.331067	NM_001243000	ENSMUSG00000094763	Gm1647	-	predicted gene 1647	protein-coding	0	0.287129
Merged-chr17-38514719-1	chr17	38514669	38514769	+	2	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-39473	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Gm20410	Esp34	predicted gene 20410	protein-coding	0	0.445545
Merged-chr9-19308591-1	chr9	19308541	19308641	+	2	cIP2vsInput	Intergenic	Intergenic	-29868	NM_207145	258249	Mm.377393	NM_207145	ENSMUSG00000061614	Olfr845	GA_x5J8B7W6RL5-13522154-13521822|MOR150-1|MOR150-1P|MOR150-2|Olfr1522-ps1	olfactory receptor 845	protein-coding	0	0.356436
Merged-chr8-30726966-1	chr8	30726916	30727016	+	2	cIP1vsInput	Intergenic	HERV16-int|LTR|ERVL	158571	NR_045856	71314	Mm.158666	NR_045856	ENSMUSG00000097044	4933433F19Rik	-	RIKEN cDNA 4933433F19 gene	miscRNA	0	0.386139
Merged-chr6-77055143-1	chr6	77055093	77055193	+	2	cIP1vsInput	"intron (NM_009819, intron 9 of 18)"	"intron (NM_009819, intron 9 of 18)"	-187574	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0	0.316832
Merged-chr14-98478307-1	chr14	98478257	98478357	+	2	cIP2vsInput	Intergenic	Intergenic	-308764	NM_007826	13134	Mm.320593	NM_001038610	ENSMUSG00000055639	Dach1	AI182278|Dac|Dach|E130112M23Rik	dachshund 1 (Drosophila)	protein-coding	0	0.356436
Merged-chr4-137662873-1	chr4	137662823	137662923	+	2	cIP2vsInput	Intergenic	Intergenic	-1853	NM_029563	110351	Mm.180763	NM_001081155	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|Rap1ga1	Rap1 GTPase-activating protein	protein-coding	0.01	0.574257
Merged-chr12-96503291-1	chr12	96503241	96503341	+	2	cIP2vsInput	Intergenic	Intergenic	-456069	NM_027076	69423	Mm.46121	NM_027076	ENSMUSG00000059695	1700019M22Rik	-	RIKEN cDNA 1700019M22 gene	protein-coding	0.01	0.326733
Merged-chr5-83558099-1	chr5	83558049	83558149	+	2	cIP2vsInput	Intergenic	Intergenic	-202904	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	"trans-2,3-enoyl-CoA reductase-like"	protein-coding	0	0.326733
Merged-chrX-120781457-1	chrX	120781407	120781507	+	2	cIP2vsInput	"intron (NM_001271810, intron 5 of 5)"	"intron (NM_001271810, intron 5 of 5)"	491130	NR_073451	245578	Mm.490224	NM_001271809		Pcdh11x	PCDHX|PCDHX11|Pcdh11	protocadherin 11 X-linked	protein-coding	0.02	0.346535
Merged-chr1-148054669-1	chr1	148054619	148054719	+	2	cIP2vsInput	Intergenic	Intergenic	1556982	NM_001145807	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.336634
Merged-chr3-17988253-1	chr3	17988203	17988303	+	2	cIP1vsInput	Intergenic	Intergenic	39809	NM_029289	75439	Mm.27023	NM_029289	ENSMUSG00000027564	Cypt12	1700001F04Rik|AV209098	cysteine-rich perinuclear theca 12	protein-coding	0	0.257426
Merged-chr8-89124234-1	chr8	89124184	89124284	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-80072	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding	0.01	0.366337
Merged-chr6-9898631-1	chr6	9898581	9898681	+	2	cIP2vsInput	Intergenic	(CA)n|Simple_repeat|Simple_repeat	948612	NM_008751	18231	Mm.46954	NM_008751		Nxph1	C130005L03Rik	neurexophilin 1	protein-coding	0	0.386139
Merged-chr13-9888051-1	chr13	9888001	9888101	+	2	cIP2vsInput	"intron (NM_033269, intron 4 of 4)"	"intron (NM_033269, intron 4 of 4)"	-122737	NM_144516	66505	Mm.397307	NM_001199141	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	"zinc finger, MYND domain containing 11"	protein-coding	0.01	0.435644
Merged-chrX-36796461-1	chrX	36796411	36796511	+	2	cIP2vsInput	"intron (NM_007451, intron 1 of 3)"	"intron (NM_007451, intron 1 of 3)"	809	NM_007451	11740	Mm.371544	NM_007451	ENSMUSG00000016319	Slc25a5	Ant2	"solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 5"	protein-coding	0.07	0.633663
Merged-chr3-15254752-1	chr3	15254702	15254802	+	2	cIP2vsInput	Intergenic	MYSERV16_I-int|LTR|ERVK	77550	NM_001076679	751864	Mm.431296	NM_001076679	ENSMUSG00000078783	Gm9733	-	predicted gene 9733	protein-coding	0.01	0.415842
Merged-chr16-87051499-1	chr16	87051449	87051549	+	2	cIP2vsInput	Intergenic	Intergenic	-302686	NM_001159331	67768	Mm.296532	NM_001159331	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding	0	0.336634
Merged-chr1-101865270-1	chr1	101865220	101865320	+	2	cIP2vsInput	Intergenic	Intergenic	709502	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0.01	0.346535
Merged-chr12-64456687-1	chr12	64456637	64456737	+	2	cIP2vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	18211	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.306931
Merged-chr5-46056581-1	chr5	46056531	46056631	+	2	cIP2vsInput	Intergenic	Intergenic	-199041	NM_001163073	209707	Mm.71498	NM_001163073	ENSMUSG00000015882	Lcorl	Mlr1	ligand dependent nuclear receptor corepressor-like	protein-coding	0	0.306931
Merged-chr2-41440747-1	chr2	41440697	41440797	+	2	cIP2vsInput	"intron (NM_053011, intron 17 of 90)"	"intron (NM_053011, intron 17 of 90)"	1212851	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0	0.326733
Merged-chr9-46480357-1	chr9	46480307	46480407	+	2	cIP2vsInput	Intergenic	Intergenic	-160371	NM_183104	74361	Mm.159169	NM_183104	ENSMUSG00000056617	4931429L15Rik	-	RIKEN cDNA 4931429L15 gene	protein-coding	0.03	0.50495
Merged-chr13-23168332-1	chr13	23168282	23168382	+	2	cIP2vsInput	Intergenic	MusHAL1|LINE|L1	5689	NM_134238	171272	Mm.377224	NM_134238	ENSMUSG00000061376	Vmn1r219	V1rh13	vomeronasal 1 receptor 219	protein-coding	0.01	0.316832
Merged-chr10-32963652-1	chr10	32963602	32963702	+	2	cIP1vsInput	Intergenic	RLTR33|LTR|ERVK	-73737	NM_001025286	432450	Mm.49665	NM_001013411		Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding	0	0.326733
Merged-chr5-5895006-1	chr5	5894956	5895056	+	2	cIP1vsInput	Intergenic	Intergenic	-145689	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding	0.01	0.29703
Merged-chr17-33321670-1	chr17	33321620	33321720	+	2	cIP1vsInput	Intergenic	L1_Mus4|LINE|L1	32126	NM_001142957	100043468	Mm.276296	NM_001142957		Zfp955b	A430003O12Rik|C430039G02Rik|C530035A18Rik|Gm4455|Zfp883b	zinc finger protein 955B	protein-coding	0.01	0.326733
Merged-chr10-54970924-1	chr10	54970874	54970974	+	2	cIP2vsInput	Intergenic	RLTR11B|LTR|ERVK	895002	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	"predicted gene, 16998"	miscRNA	0	0.346535
Merged-chr9-105521425-1	chr9	105521375	105521475	+	2	cIP2vsInput	promoter-TSS (NM_001253831)	promoter-TSS (NM_001253831)	-168	NM_001253831	235574	Mm.489853	NM_001253831	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	"ATPase, Ca++-sequestering"	protein-coding	0.03	0.514851
Merged-chr13-19333323-1	chr13	19333273	19333373	+	2	cIP2vsInput	Intergenic	Intergenic	62429	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding	0	0.257426
Merged-chr19-40199938-1	chr19	40199888	40199988	+	2	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-12652	NM_145499	226105	Mm.29119	NM_145499	ENSMUSG00000060613	Cyp2c70	-	"cytochrome P450, family 2, subfamily c, polypeptide 70"	protein-coding	0	0.326733
Merged-chr10-76140378-1	chr10	76140328	76140428	+	2	cIP1vsInput	Intergenic	Intergenic	-7073	NM_133184	64452	Mm.154797	NM_133184	ENSMUSG00000020229	Slc5a4a	SGLT3-a	"solute carrier family 5, member 4a"	protein-coding	0	0.346535
Merged-chr18-52377421-1	chr18	52377371	52377471	+	2	cIP1vsInput	Intergenic	Intergenic	45885	NM_026286	67634	Mm.179144	NM_026286	ENSMUSG00000024510	Ftmt	4930447C24Rik|FerH|Fth3|MtF	ferritin mitochondrial	protein-coding	0	0.267327
Merged-chr3-99954880-1	chr3	99954830	99954930	+	2	cIP2vsInput	"intron (NM_028892, intron 3 of 48)"	"intron (NM_028892, intron 3 of 48)"	69463	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding	0	0.29703
Merged-chr3-17227525-1	chr3	17227475	17227575	+	2	cIP2vsInput	Intergenic	Lx5|LINE|L1	-562396	NR_033490	70441	Mm.458192	NR_033490		2610100L16Rik	100040120|Gm2612	RIKEN cDNA 2610100L16 gene	miscRNA	0.01	0.366337
Merged-chr3-73623162-1	chr3	73623112	73623212	+	2	cIP1vsInput	Intergenic	Intergenic	85253	NM_009738	12038	Mm.250719	NM_009738	ENSMUSG00000027792	Bche	C730038G20Rik	butyrylcholinesterase	protein-coding	0.01	0.316832
Merged-chr1-183691668-1	chr1	183691618	183691718	+	2	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	273165	NM_030175	78772	Mm.29003	NM_030175	ENSMUSG00000053461	Hhipl2	4930507C10Rik|AW208802	hedgehog interacting protein-like 2	protein-coding	0.01	0.277228
Merged-chr7-28446643-1	chr7	28446593	28446693	+	2	cIP2vsInput	"3' UTR (NM_022024, exon 7 of 7)"	"3' UTR (NM_022024, exon 7 of 7)"	-5342	NM_030562	80749	Mm.483073	NM_001141921		Lrfn1	BC004018|SALM2|Semo1	leucine rich repeat and fibronectin type III domain containing 1	protein-coding	0.04	0.564356
Merged-chr12-20247776-1	chr12	20247726	20247826	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	568003	NR_015521	69513	Mm.273972	NR_015521		1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	miscRNA	0	0.326733
Merged-chr13-98192582-1	chr13	98192532	98192632	+	2	cIP2vsInput	"intron (NM_012026, intron 1 of 35)"	"intron (NM_012026, intron 1 of 35)"	13583	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding	0.03	0.554455
Merged-chr6-41611467-1	chr6	41611417	41611517	+	2	cIP2vsInput	"intron (NM_001146351, intron 1 of 17)"	"intron (NM_001146351, intron 1 of 17)"	5985	NM_007680	13848	Mm.271976	NM_001146351	ENSMUSG00000029869	Ephb6	Cekl|Mep	Eph receptor B6	protein-coding	0	0.336634
Merged-chr6-92675045-1	chr6	92674995	92675095	+	2	cIP2vsInput	"intron (NM_001081146, intron 2 of 8)"	"intron (NM_001081146, intron 2 of 8)"	31139	NM_001081146	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle homolog 2 (Drosophila)	protein-coding	0.01	0.316832
Merged-chr6-41447810-1	chr6	41447760	41447860	+	2	cIP2vsInput	Intergenic	Intergenic	-1713	NM_001103153	100040233	Mm.297485	NM_001103153	ENSMUSG00000071517	Gm10334	ENSMUSG00000071517	predicted gene 10334	protein-coding	0.01	0.356436
Merged-chr14-34711171-1	chr14	34711121	34711221	+	2	cIP2vsInput	"intron (NM_001004436, intron 4 of 18)"	B3|SINE|B2	37243	NM_001004436	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapal	2410073G16|A530089A20Rik|BC037674|FOE|mKIAA0261|mWAPL	wings apart-like homolog (Drosophila)	protein-coding	0.01	0.435644
Merged-chr9-35709498-1	chr9	35709448	35709548	+	2	cIP1vsInput	Intergenic	Lx3A|LINE|L1	-22127	NM_001199953	100312987	Mm.445254	NM_001167677	ENSMUSG00000091215	Gm17252	Pate	"predicted gene, 17252"	protein-coding	0	0.306931
Merged-chr1-46369073-1	chr1	46369023	46369123	+	2	cIP2vsInput	"intron (NM_001160386, intron 65 of 65)"	"intron (NM_001160386, intron 65 of 65)"	302335	NM_001160386	227058	Mm.296880	NM_001160386	ENSMUSG00000041144	Dnahc7b	Gm107	"dynein, axonemal, heavy chain 7B"	protein-coding	0	0.336634
Merged-chr10-26747736-1	chr10	26747686	26747786	+	2	cIP2vsInput	Intergenic	Intergenic	-24776	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding	0	0.287129
Merged-chr13-16392926-1	chr13	16392876	16392976	+	2	cIP2vsInput	Intergenic	MER58A|DNA|hAT-Charlie	378451	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding	0.01	0.316832
Merged-chr2-104872038-1	chr2	104871988	104872088	+	2	cIP2vsInput	Intergenic	B1F|SINE|Alu	-14286	NM_177600	211936	Mm.416538	NM_177600	ENSMUSG00000045106	Ccdc73	2210415I11Rik|4931417A20|AV080665|BC095976	coiled-coil domain containing 73	protein-coding	0.01	0.455446
Merged-chr8-21092555-1	chr8	21092505	21092605	+	2	cIP2vsInput	Intergenic	B1_Mus1|SINE|Alu	3495	NM_001177482	634825	Mm.429748	NM_001177482		Gm14851	CRS1C-2|OTTMUSG00000018260	predicted gene 14851	protein-coding	0.01	0.465347
Merged-chr13-62016071-1	chr13	62016021	62016121	+	2	cIP2vsInput	Intergenic	Intergenic	-113819	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 80	protein-coding	0.06	0.60396
Merged-chr3-16105923-1	chr3	16105873	16105973	+	2	cIP2vsInput	Intergenic	Intergenic	-77260	NR_027375	229096	Mm.23834	NM_001145919	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding	0	0.405941
Merged-chr16-84238812-1	chr16	84238762	84238862	+	2	cIP2vsInput	Intergenic	Intergenic	-132331	NR_040567	75247	Mm.417813	NR_040567		4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	miscRNA	0	0.39604
Merged-chr7-85646746-1	chr7	85646696	85646796	+	2	cIP2vsInput	Intergenic	Lx2|LINE|L1	31284	NM_001105184	233445	Mm.389930	NM_001105184	ENSMUSG00000091205	Vmn2r71	EG233445	"vomeronasal 2, receptor 71"	protein-coding	0.01	0.405941
Merged-chr9-76449611-1	chr9	76449561	76449661	+	2	cIP2vsInput	Intergenic	Intergenic	96193	NM_001045518	208994	Mm.256929	NM_001045518	ENSMUSG00000032358	Fam83b	C530008M07Rik|Gm516	"family with sequence similarity 83, member B"	protein-coding	0.01	0.376238
Merged-chr8-110266659-1	chr8	110266609	110266709	+	2	cIP2vsInput	promoter-TSS (NM_172916)	promoter-TSS (NM_172916)	-318	NM_172916	244653	Mm.488112	NM_172916	ENSMUSG00000059854	Hydin	1700034M11Rik|4930545D19Rik|4932703P14|A830061H17|AC069308.21gm4|hy-3|hy3|hyrh	"HYDIN, axonemal central pair apparatus protein"	protein-coding	0	0.50495
Merged-chr17-60079473-1	chr17	60079423	60079523	+	2	cIP1vsInput	Intergenic	Intergenic	-1066151	NM_026497	67993	Mm.36507	NM_026497		Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0	0.29703
Merged-chr12-84784688-1	chr12	84784638	84784738	+	2	cIP2vsInput	"intron (NM_013589, intron 34 of 34)"	"intron (NM_013589, intron 34 of 34)"	11418	NM_028863	74316	Mm.25719	NM_028863	ENSMUSG00000021241	Isca2	0710001C05Rik|5730594E03Rik|Hbld1	iron-sulfur cluster assembly 2 homolog (S. cerevisiae)	protein-coding	0.05	0.623762
Merged-chr6-143818583-1	chr6	143818533	143818633	+	2	cIP2vsInput	Intergenic	Intergenic	-167295	NR_045732	73425	Mm.417844	NR_045732	ENSMUSG00000086887	1700060C16Rik	-	RIKEN cDNA 1700060C16 gene	miscRNA	0	0.326733
Merged-chr4-107447634-1	chr4	107447584	107447684	+	2	cIP2vsInput	"intron (NM_147221, intron 2 of 10)"	"intron (NM_147221, intron 2 of 10)"	12915	NM_147221	230587	Mm.331757	NM_147221	ENSMUSG00000034762	Glis1	Gli5|Gli6|GliH1	GLIS family zinc finger 1	protein-coding	0.02	0.29703
Merged-chr4-31197434-1	chr4	31197384	31197484	+	2	cIP1vsInput	Intergenic	Intergenic	532838	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	miscRNA	0.01	0.306931
Merged-chr8-41216373-1	chr8	41216323	41216423	+	2	cIP2vsInput	Intergenic	Intergenic	-1217	NM_145594	234199	Mm.277955	NM_145594	ENSMUSG00000031594	Fgl1	Mfire1	fibrinogen-like protein 1	protein-coding	0.01	0.376238
Merged-chr4-14626112-1	chr4	14626062	14626162	+	2	cIP1vsInput	Intergenic	Intergenic	-4334	NM_145947	208890	Mm.483839	NM_145947		Slc26a7	-	"solute carrier family 26, member 7"	protein-coding	0	0.326733
Merged-chr15-19073785-1	chr15	19073735	19073835	+	2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	253456	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0	0.326733
Merged-chr13-19872388-1	chr13	19872338	19872438	+	2	cIP2vsInput	Intergenic	Lx2B2|LINE|L1	-48131	NM_181754	353346	Mm.239268	NM_181754	ENSMUSG00000053101	Gpr141	PGR13	G protein-coupled receptor 141	protein-coding	0	0.366337
Merged-chr8-55814125-1	chr8	55814075	55814175	+	2	cIP2vsInput	Intergenic	Intergenic	92839	NM_175939	244486	Mm.67684	NM_175939	ENSMUSG00000046258	Adam29	-	a disintegrin and metallopeptidase domain 29	protein-coding	0.01	0.277228
Merged-chr2-81314104-1	chr2	81314054	81314154	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	674840	NM_001190179	69482	Mm.29200	NM_001190179		Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding	0	0.336634
Merged-chr6-20383734-1	chr6	20383684	20383784	+	2	cIP2vsInput	Intergenic	Intergenic	-832375	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	"potassium voltage-gated channel, Shal-related family, member 2"	protein-coding	0	0.29703
Merged-chr10-116876746-1	chr10	116876696	116876796	+	2	cIP1vsInput	"intron (NM_001033333, intron 1 of 24)"	MTD|LTR|ERVL-MaLR	20133	NM_001033333	237558	Mm.336386	NM_001033333	ENSMUSG00000034057	Myrfl	Gm239	myelin regulatory factor-like	protein-coding	0	0.465347
Merged-chr14-88724472-1	chr14	88724422	88724522	+	2	cIP2vsInput	Intergenic	Intergenic	-253076	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0	0.29703
Merged-chr7-63339389-1	chr7	63339339	63339439	+	2	cIP2vsInput	Intergenic	Intergenic	-105383	NM_130880	170711	Mm.156872	NM_130880	ENSMUSG00000033510	Otud7a	AJ430384|Otud7	OTU domain containing 7A	protein-coding	0	0.346535
Merged-chr7-5637778-1	chr7	5637728	5637828	+	2	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-26465	NM_001166733	636731	Mm.479999	NM_001166733	ENSMUSG00000094313	Vmn1r61	Gm7186	vomeronasal 1 receptor 61	protein-coding	0	0.39604
Merged-chrX-98724219-1	chrX	98724169	98724269	+	2	cIP2vsInput	"intron (NM_052976, intron 7 of 24)"	L1_Rod|LINE|L1	166766	NM_052976	94190	Mm.254336	NM_052976		Ophn1	C130037N19Rik	oligophrenin 1	protein-coding	0	0.346535
Merged-chr1-102471886-1	chr1	102471836	102471936	+	2	cIP2vsInput	Intergenic	Intergenic	1316118	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.336634
Merged-chr3-157809756-1	chr3	157809706	157809806	+	2	cIP2vsInput	Intergenic	Intergenic	115307	NM_145953	107869	Mm.28301	NM_145953	ENSMUSG00000028179	Cth	0610010I13Rik|AI314617|BC019483|CSE|Cys3	cystathionase (cystathionine gamma-lyase)	protein-coding	0	0.405941
Merged-chrX-61837045-1	chrX	61836995	61837095	+	2	cIP2vsInput	Intergenic	L1MA4A|LINE|L1	127429	NM_001018087	434784	Mm.23468	NM_001018087	ENSMUSG00000057615	Ldoc1	Gm366|Mar7|Mart7	"leucine zipper, down-regulated in cancer 1"	protein-coding	0.01	0.306931
Merged-chr3-37877115-1	chr3	37877065	37877165	+	2	cIP1vsInput	Intergenic	Intergenic	-21698	NR_040559	626410	Mm.389417	NR_040559		Gm20755	-	"predicted gene, 20755"	miscRNA	0	0.306931
Merged-chr10-85220948-1	chr10	85220898	85220998	+	2	cIP2vsInput	Intergenic	Intergenic	-35894	NM_007771	12952	Mm.26237	NM_007771	ENSMUSG00000020038	Cry1	AU020726|AU021000|Phll1	cryptochrome 1 (photolyase-like)	protein-coding	0.01	0.336634
Merged-chr3-5888080-1	chr3	5888030	5888130	+	2	cIP2vsInput	Intergenic	Intergenic	-311832	NM_001163305	19302	Mm.132336	NM_001163304	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding	0.01	0.316832
Merged-chr14-48491007-1	chr14	48490957	48491057	+	2	cIP1vsInput	"intron (NM_172600, intron 10 of 15)"	L1MA4|LINE|L1	44655	NM_172600	218989	Mm.85211	NM_172600	ENSMUSG00000036339	Tmem260	5930435P15|6720456H20Rik	transmembrane protein 260	protein-coding	0	0.267327
Merged-chr4-110025696-1	chr4	110025646	110025746	+	2	cIP2vsInput	Intergenic	Intergenic	47671	NM_172296	242620	Mm.32825	NM_172296	ENSMUSG00000047143	Dmrta2	Dmrt5	doublesex and mab-3 related transcription factor like family A2	protein-coding	0	0.316832
Merged-chr14-111076362-1	chr14	111076312	111076412	+	2	cIP2vsInput	Intergenic	Intergenic	-321213	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	"SLIT and NTRK-like family, member 6"	protein-coding	0	0.356436
Merged-chr3-140510374-1	chr3	140510324	140510424	+	2	cIP2vsInput	Intergenic	Intergenic	701981	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding	0	0.346535
Merged-chr1-101663931-1	chr1	101663881	101663981	+	2	cIP1vsInput	Intergenic	Intergenic	508163	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0.01	0.346535
Merged-chr11-25183053-1	chr11	25183003	25183103	+	2	cIP2vsInput	Intergenic	Intergenic	-143054	NR_045853	71234	Mm.158627	NR_045853	ENSMUSG00000033015	4933427E13Rik	-	RIKEN cDNA 4933427E13 gene	miscRNA	0	0.316832
Merged-chr4-4222147-1	chr4	4222097	4222197	+	2	cIP2vsInput	Intergenic	Intergenic	-83702	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding	0.01	0.356436
Merged-chr4-69307987-1	chr4	69307937	69308037	+	2	cIP2vsInput	Intergenic	Intergenic	-353590	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Dbc1	BRINP|Brinp1|Dbccr1|Fam5a	deleted in bladder cancer 1 (human)	protein-coding	0.01	0.336634
Merged-chr1-99408548-1	chr1	99408498	99408598	+	2	cIP2vsInput	Intergenic	Intergenic	-364217	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding	0	0.356436
Merged-chrX-17141984-1	chrX	17141934	17142034	+	2	cIP2vsInput	"intron (NM_028916, intron 14 of 14)"	"intron (NM_028916, intron 14 of 14)"	177384	NM_028916	74405	Mm.248531	NM_028916	ENSMUSG00000025038	Efhc2	4933407D04Rik|mRib72-2	EF-hand domain (C-terminal) containing 2	protein-coding	0	0.366337
Merged-chr6-59224992-1	chr6	59224942	59225042	+	2	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	16122	NM_001081145	68140	Mm.25843	NM_001081145	ENSMUSG00000049232	Tigd2	3632410O17Rik	tigger transposable element derived 2	protein-coding	0.01	0.356436
Merged-chr9-18889912-1	chr9	18889862	18889962	+	2	cIP2vsInput	Intergenic	Intergenic	14583	NM_146566	258559	Mm.377568	NM_146566	ENSMUSG00000062868	Olfr830	MOR152-1	olfactory receptor 830	protein-coding	0	0.356436
Merged-chr19-14270067-1	chr19	14270017	14270117	+	2	cIP2vsInput	Intergenic	Lx8b|LINE|L1	168439	NR_003027	19862		NR_003027	ENSMUSG00000095132	Rnu6	-	U6 small nuclear RNA	snRNA	0	0.415842
Merged-chr6-34137906-1	chr6	34137856	34137956	+	2	cIP2vsInput	Intergenic	Intergenic	39148	NM_021435	58246	Mm.245527	NM_021435		Slc35b4	4930474D06Rik|AB041549|AW494345	"solute carrier family 35, member B4"	protein-coding	0.01	0.336634
Merged-chr5-107669647-1	chr5	107669597	107669697	+	2	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	33833	NR_045871	654809	Mm.399159	NR_045871		4930428O21Rik	-	RIKEN cDNA 4930428O21 gene	miscRNA	0	0.356436
Merged-chr13-87844254-1	chr13	87844204	87844304	+	2	cIP2vsInput	Intergenic	Lx|LINE|L1	-977218	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0	0.29703
Merged-chr8-113934550-1	chr8	113934500	113934600	+	2	cIP2vsInput	Intergenic	MTD|LTR|ERVL-MaLR	-85711	NM_172466	208936	Mm.167471	NM_172466		Adamts18	9630038L21|ADAMTS21|E130314N14Rik	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 18"	protein-coding	0	0.29703
Merged-chr3-38688019-1	chr3	38687969	38688069	+	2	cIP2vsInput	Intergenic	Intergenic	-198921	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT tumor suppressor homolog 4 (Drosophila)	protein-coding	0	0.316832
Merged-chr14-112646888-1	chr14	112646838	112646938	+	2	cIP1vsInput	Intergenic	MIR|SINE|MIR	625458	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0	0.346535
Merged-chr15-19304785-1	chr15	19304735	19304835	+	2	cIP2vsInput	Intergenic	Intergenic	484456	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0	0.376238
Merged-chr8-19913479-2	chr8	19913422	19913537	+	2	cIP1vsInput|cIP2vsInput	"intron (NM_001270553, intron 6 of 9).2"	L1_Mur2|LINE|L1	183903	NM_001039553	626415	Mm.425517	NM_001039553		4930467E23Rik	ENSMUSG00000074453|OTTMUSG00000018948|TSAP	RIKEN cDNA 4930467E23 gene	protein-coding	0.008696	0.396552
Merged-chr2-174354776-1	chr2	174354726	174354826	+	2	cIP1vsInput	Intergenic	Intergenic	24687	NM_001077510	14683	Mm.125770	NM_001077507	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gsa|Nesp|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH	"GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus"	protein-coding	0	0.267327
Merged-chr10-115029093-1	chr10	115029043	115029143	+	2	cIP2vsInput	Intergenic	Intergenic	155929	NM_173391	216343	Mm.31597	NM_173391	ENSMUSG00000006764	Tph2	AU043594|Ntph	tryptophan hydroxylase 2	protein-coding	0	0.326733
Merged-chr5-15672066-1	chr5	15672016	15672116	+	2	cIP1vsInput	Intergenic	(TAA)n|Simple_repeat|Simple_repeat	-8644	NR_001585	75858	Mm.359463	NR_001585	ENSMUSG00000089871	Speer7-ps1	4930568L21Rik|SPEER-7|Speer7-ps	"spermatogenesis associated glutamate (E)-rich protein 7, pseudogene 1"	pseudo	0	0.237624
Merged-chr16-26315652-1	chr16	26315602	26315702	+	2	cIP2vsInput	Intergenic	Charlie1|DNA|hAT-Charlie	56187	NM_016674	12737	Mm.289441	NM_016674	ENSMUSG00000022512	Cldn1	AI596271	claudin 1	protein-coding	0	0.346535
Merged-chr2-110853374-1	chr2	110853324	110853424	+	2	cIP1vsInput	"intron (NM_001128103, intron 4 of 26)"	"intron (NM_001128103, intron 4 of 26)"	96870	NM_001128103	228432	Mm.483325	NM_001128103	ENSMUSG00000074968	Ano3	AI838058|B230324K02Rik|Tmem16c	anoctamin 3	protein-coding	0	0.316832
Merged-chr8-102497988-1	chr8	102497938	102498038	+	2	cIP2vsInput	Intergenic	Intergenic	287123	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0.01	0.326733
Merged-chr17-76734744-1	chr17	76734694	76734794	+	2	cIP2vsInput	Intergenic	Intergenic	873721	NR_033456	100043885	Mm.127562	NR_033456		Gm4710	-	predicted gene 4710	miscRNA	0	0.336634
Merged-chr13-114502937-1	chr13	114502887	114502987	+	2	cIP2vsInput	Intergenic	Intergenic	-44207	NM_008046	14313	Mm.4913	NM_008046	ENSMUSG00000021765	Fst	AL033346	follistatin	protein-coding	0.01	0.405941
Merged-chr2-178822633-1	chr2	178822583	178822683	+	2	cIP2vsInput	Intergenic	RMER3D-int|LTR|ERVK	392026	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding	0	0.336634
Merged-chr6-43024729-1	chr6	43024679	43024779	+	2	cIP2vsInput	Intergenic	Intergenic	69229	NM_146656	258650	Mm.377613	NM_146656	ENSMUSG00000073110	Olfr444	MOR261-2	olfactory receptor 444	protein-coding	0	0.306931
Merged-chr1-68609919-1	chr1	68609869	68609969	+	2	cIP1vsInput	"intron (NM_010154, intron 2 of 26)"	"intron (NM_010154, intron 2 of 26)"	498140	NM_010154	13869	Mm.442420	NM_010154		Erbb4	Her4|c-erbB-4	v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)	protein-coding	0	0.217822
Merged-chr7-117184023-1	chr7	117183973	117184073	+	2	cIP2vsInput	Intergenic	Intergenic	-196956	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding	0	0.306931
Merged-chr6-73541720-1	chr6	73541670	73541770	+	2	cIP2vsInput	Intergenic	Intergenic	-72053	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.306931
Merged-chr4-66712415-1	chr4	66712365	66712465	+	2	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	-115396	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding	0	0.346535
Merged-chr1-27761478-1	chr1	27761428	27761528	+	2	cIP2vsInput	Intergenic	Intergenic	1018774	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0	0.306931
Merged-chr2-11408565-1	chr2	11408515	11408615	+	2	cIP2vsInput	Intergenic	Intergenic	-10065	NR_040615	77543	Mm.490670	NR_040615		8030442B05Rik	-	RIKEN cDNA 8030442B05 gene	miscRNA	0.01	0.425743
Merged-chr6-117052544-1	chr6	117052494	117052594	+	2	cIP2vsInput	Intergenic	Intergenic	-115991	NM_001012477	20315	Mm.303231	NM_001012477	ENSMUSG00000061353	Cxcl12	AI174028|Pbsf|Scyb12|Sdf1|Sdf1a|Sdf1b|Tlsf|Tlsfa|Tlsfb|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding	0	0.346535
Merged-chr2-40942685-1	chr2	40942635	40942735	+	2	cIP2vsInput	"intron (NM_053011, intron 43 of 90)"	"intron (NM_053011, intron 43 of 90)"	1710913	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0.01	0.326733
Merged-chr5-112282872-1	chr5	112282822	112282922	+	2	cIP2vsInput	"intron (NM_009419, intron 1 of 6)"	"intron (NM_009419, intron 1 of 6)"	6165	NM_009419	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding	0.02	0.405941
Merged-chr16-77153303-1	chr16	77153253	77153353	+	2	cIP2vsInput	Intergenic	MER21B|LTR|ERVL	139234	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding	0	0.336634
Merged-chr14-89580948-1	chr14	89580898	89580998	+	2	cIP2vsInput	Intergenic	Intergenic	-315276	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0	0.316832
Merged-chr1-109884288-1	chr1	109884238	109884338	+	2	cIP2vsInput	Intergenic	Lx|LINE|L1	-99449	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.356436
Merged-chr17-92514220-1	chr17	92514170	92514270	+	2	cIP2vsInput	Intergenic	Intergenic	-685202	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0	0.29703
Merged-chr17-39403759-1	chr17	39403709	39403809	+	2	cIP2vsInput	Intergenic	Lx5|LINE|L1	-2600	NM_001244763	100126774	Mm.350534	NM_001244763	ENSMUSG00000094024	Gm20579	Esp18	"predicted gene, 20579"	protein-coding	0	0.306931
Merged-chr15-18771524-1	chr15	18771474	18771574	+	2	cIP2vsInput	Intergenic	Intergenic	-48805	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0	0.29703
Merged-chr3-102982805-1	chr3	102982755	102982855	+	2	cIP2vsInput	Intergenic	Intergenic	-12935	NM_025679	66641	Mm.208619	NM_025679	ENSMUSG00000027854	Sike1	2810005O12Rik|5730470L24Rik|AI450236|AI839862|Sike|Sikeb	suppressor of IKBKE 1	protein-coding	0	0.306931
Merged-chr10-18220596-1	chr10	18220546	18220646	+	2	cIP2vsInput	"intron (NM_144820, intron 3 of 5)"	"intron (NM_144820, intron 3 of 5)"	-9706	NM_001195036	100045792	Mm.380617	NM_001195036	ENSMUSG00000071392	Ect2l	C330021H03Rik|ENSMUSG00000071392|Gm10331	epithelial cell transforming sequence 2 oncogene-like	protein-coding	0	0.316832
Merged-chr3-133824901-1	chr3	133824851	133824951	+	2	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-280511	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding	0	0.336634
Merged-chr11-69209960-1	chr11	69209910	69210010	+	2	cIP2vsInput	Intergenic	MYSERV16_I-int|LTR|ERVK	-12117	NM_009661	11688	Mm.289672	NM_009661	ENSMUSG00000020891	Alox8	15-LOX-2|15-LOX-B|8-LOX|8S-LOX|Alox15b	arachidonate 8-lipoxygenase	protein-coding	0	0.277228
Merged-chrX-68164499-1	chrX	68164449	68164549	+	2	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-154320	NR_030575	100124449		NR_030575		Mir509	Mirn509|mmu-mir-509	microRNA 509	miscRNA	0	0.356436
Merged-chr6-74858087-1	chr6	74858037	74858137	+	2	cIP2vsInput	Intergenic	Intergenic	-1388420	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.356436
Merged-chr1-52974411-1	chr1	52974361	52974461	+	2	cIP1vsInput	Intergenic	Intergenic	-21571	NM_144953	67080	Mm.236287	NM_144953		1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding	0	0.386139
Merged-chr16-73557178-1	chr16	73557128	73557228	+	2	cIP2vsInput	Intergenic	Intergenic	784889	NR_030464	751561		NR_030464		Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	miscRNA	0.01	0.356436
Merged-chr13-76174311-1	chr13	76174261	76174361	+	2	cIP1vsInput	"intron (NM_001081352, intron 39 of 43)"	"intron (NM_001081352, intron 39 of 43)"	75577	NM_001081352	218343	Mm.277964	NM_001081352	ENSMUSG00000033991	Ttc37	mKIAA0372	tetratricopeptide repeat domain 37	protein-coding	0.01	0.306931
Merged-chr7-130368960-1	chr7	130368910	130369010	+	2	cIP2vsInput	Intergenic	Intergenic	-102152	NM_201601	14183	Mm.16340	NM_010207	ENSMUSG00000030849	Fgfr2	AU043015|AW556123|Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFR|KGFRTr|svs	fibroblast growth factor receptor 2	protein-coding	0.02	0.50495
Merged-chr1-185969781-1	chr1	185969731	185969831	+	2	cIP2vsInput	"intron (NR_030555, intron 5 of 6)"	"intron (NR_030555, intron 5 of 6)"	147529	NM_146106	226791	Mm.257116	NM_146106	ENSMUSG00000039246	Lyplal1	BC027340|Q96AVO	lysophospholipase-like 1	protein-coding	0	0.366337
Merged-chr2-123083659-1	chr2	123083609	123083709	+	2	cIP2vsInput	Intergenic	L1VL2|LINE|L1	301660	NM_021507	59010	Mm.28986	NM_001162503	ENSMUSG00000005803	Sqrdl	0610039J17Rik|4930557M22Rik	sulfide quinone reductase-like (yeast)	protein-coding	0	0.336634
Merged-chr7-86063411-1	chr7	86063361	86063461	+	2	cIP2vsInput	Intergenic	Intergenic	-101929	NM_001105187	546980	Mm.469905	NM_001105187	ENSMUSG00000090774	Vmn2r74	EG546980	"vomeronasal 2, receptor 74"	protein-coding	0	0.316832
Merged-chr1-99359188-1	chr1	99359138	99359238	+	2	cIP2vsInput	Intergenic	Intergenic	-413577	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding	0	0.306931
Merged-chr4-127375543-1	chr4	127375493	127375593	+	2	cIP1vsInput	Intergenic	Intergenic	-17379	NM_010291	14622	Mm.26859	NM_010291	ENSMUSG00000042357	Gjb5	Cnx31.1|Cx31.1|Gjb-5	"gap junction protein, beta 5"	protein-coding	0	0.405941
Merged-chr2-127399519-1	chr2	127399469	127399569	+	2	cIP2vsInput	Intergenic	ID_B1|SINE|B4	-25680	NM_001081089	215456	Mm.440454	NM_001081089	ENSMUSG00000046338	Gpat2	A530057A03Rik|Gm116|xGPAT1	"glycerol-3-phosphate acyltransferase 2, mitochondrial"	protein-coding	0.01	0.425743
Merged-chr15-10814767-1	chr15	10814717	10814817	+	2	cIP2vsInput	Intergenic	Intergenic	-14284	NR_040357	100502601	Mm.399434	NR_040357		Gm19276	-	"predicted gene, 19276"	miscRNA	0.01	0.445545
Merged-chr9-123861681-1	chr9	123861631	123861731	+	2	cIP2vsInput	"intron (NM_011798, intron 1 of 1)"	"intron (NM_011798, intron 1 of 1)"	348	NM_011798	23832	Mm.390241	NM_011798		Xcr1	Ccxcr1|Gpr5|mXcr1	chemokine (C motif) receptor 1	protein-coding	0	0.287129
Merged-chr13-67675829-1	chr13	67675779	67675879	+	2	cIP2vsInput	"intron (NM_001001187, intron 1 of 3)"	L1_Rod|LINE|L1	7683	NM_001001187	408068	Mm.435551	NM_175676	ENSMUSG00000048280	Zfp738	3830402I07Rik|6720487G11Rik	zinc finger protein 738	protein-coding	0	0.306931
Merged-chr1-8530550-1	chr1	8530500	8530600	+	2	cIP2vsInput	"intron (NM_027671, intron 15 of 20)"	Lx7|LINE|L1	769180	NM_027671	71096	Mm.388998	NM_027671		Sntg1	4933426D16Rik|G1SYN|SYN4	"syntrophin, gamma 1"	protein-coding	0	0.346535
Merged-chr3-139264231-1	chr3	139264181	139264281	+	2	cIP2vsInput	"intron (NM_198659, intron 6 of 13)"	"intron (NM_198659, intron 6 of 13)"	58338	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding	0	0.277228
Merged-chr14-53637282-1	chr14	53637232	53637332	+	2	cIP1vsInput	Intergenic	Lx9|LINE|L1	-28658	NM_001205242	100568452	Mm.486072	NM_001205242		A430107P09Rik	Va10	RIKEN cDNA A430107P09 gene	protein-coding	0.02	0.336634
Merged-chr17-35897298-1	chr17	35897248	35897348	+	2	cIP2vsInput	promoter-TSS (NM_001033630)	promoter-TSS (NM_001033630)	80	NM_001033630	69662	Mm.260159	NM_001033630	ENSMUSG00000050705	2310061I04Rik	-	RIKEN cDNA 2310061I04 gene	protein-coding	0.16	0.732673
Merged-chrX-146264778-1	chrX	146264728	146264828	+	2	cIP2vsInput	Intergenic	Intergenic	-697735	NM_008312	15560	Mm.439670	NM_008312	ENSMUSG00000041380	Htr2c	5-HT2C|5-HT2cR|5-HTR2C|5HT1c|Htr1c|SR1	5-hydroxytryptamine (serotonin) receptor 2C	protein-coding	0.01	0.376238
Merged-chr1-14949314-1	chr1	14949264	14949364	+	2	cIP2vsInput	Intergenic	L1MA5|LINE|L1	-30452	NM_177781	277328	Mm.186329	NM_177781	ENSMUSG00000032769	Trpa1	Anktm1	"transient receptor potential cation channel, subfamily A, member 1"	protein-coding	0	0.39604
Merged-chr8-72444000-1	chr8	72443950	72444050	+	2	cIP1vsInput	promoter-TSS (NM_028500)	promoter-TSS (NM_028500)	120	NM_028170	72254	Mm.275872	NM_028170	ENSMUSG00000052794	1700030K09Rik	-	RIKEN cDNA 1700030K09 gene	protein-coding	0.04	0.584158
Merged-chr18-56502751-1	chr18	56502701	56502801	+	2	cIP2vsInput	"3' UTR (NM_026240, exon 14 of 14)"	"3' UTR (NM_026240, exon 14 of 14)"	59547	NM_138600	110695	Mm.30250	NM_001127338		Aldh7a1	Atq1|D18Wsu181e	"aldehyde dehydrogenase family 7, member A1"	protein-coding	0.04	0.594059
Merged-chr10-57458573-1	chr10	57458523	57458623	+	2	cIP1vsInput	Intergenic	Lx2B|LINE|L1	27780	NR_045353	74928	Mm.416643	NR_045353	ENSMUSG00000097370	4930467K11Rik	-	RIKEN cDNA 4930467K11 gene	miscRNA	0	0.346535
Merged-chr8-62546142-1	chr8	62546092	62546192	+	2	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-405090	NM_001252620	72902	Mm.334552	NM_001252620	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3"	protein-coding	0	0.326733
Merged-chr1-98918465-1	chr1	98918415	98918515	+	2	cIP2vsInput	Intergenic	Intergenic	497341	NM_027584	70866	Mm.389164	NM_001164233	ENSMUSG00000026336	Slco6d1	4921511I05Rik	"solute carrier organic anion transporter family, member 6d1"	protein-coding	0	0.316832
Merged-chr7-72419498-1	chr7	72419448	72419548	+	2	cIP2vsInput	Intergenic	Intergenic	-112903	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	"multiple C2 domains, transmembrane 2"	protein-coding	0.01	0.356436
Merged-chr5-116289686-1	chr5	116289636	116289736	+	2	cIP2vsInput	promoter-TSS (NM_177759)	promoter-TSS (NM_177759)	-701	NM_177759	269693	Mm.10946	NM_177759		Ccdc60	AU018954|C130098D09	coiled-coil domain containing 60	protein-coding	0.02	0.485149
Merged-chr7-11607951-1	chr7	11607901	11608001	+	2	cIP2vsInput	Intergenic	Intergenic	62568	NM_145843	252905	Mm.377264	NM_145843	ENSMUSG00000095430	Vmn1r72	V1rg1	vomeronasal 1 receptor 72	protein-coding	0	0.326733
Merged-chr2-96935841-1	chr2	96935791	96935891	+	2	cIP1vsInput	Intergenic	Intergenic	-531833	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0.01	0.39604
Merged-chr2-48597209-1	chr2	48597159	48597259	+	2	cIP2vsInput	Intergenic	Intergenic	-216900	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding	0	0.336634
Merged-chr16-15673904-1	chr16	15673854	15673954	+	2	cIP2vsInput	"intron (NM_011159, intron 16 of 85)"	"intron (NM_011159, intron 16 of 85)"	36038	NM_011159	19090	Mm.71	NM_011159	ENSMUSG00000022672	Prkdc	AI326420|AU019811|DNA-PKcs|DNAPDcs|DNAPK|DNPK1|DOXNPH|HYRC1|XRCC7|dxnph|p460|scid|slip	"protein kinase, DNA activated, catalytic polypeptide"	protein-coding	0	0.316832
Merged-chr7-60860402-1	chr7	60860352	60860452	+	2	cIP2vsInput	Intergenic	Intergenic	-720183	NM_001082962	20646	Mm.274995	NM_001082961	ENSMUSG00000000948	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding	0	0.326733
Merged-chrX-111403436-1	chrX	111403386	111403486	+	2	cIP2vsInput	"intron (NM_025949, intron 21 of 24)"	"intron (NM_025949, intron 21 of 24)"	134509	NM_025949	67071	Mm.37617	NM_025949	ENSMUSG00000025665	Rps6ka6	2610524K04Rik|RSK4	ribosomal protein S6 kinase polypeptide 6	protein-coding	0	0.386139
Merged-chr7-107540508-1	chr7	107540458	107540558	+	2	cIP2vsInput	"intron (NM_021889, intron 6 of 6)"	"intron (NM_021889, intron 6 of 6)"	-26925	NM_172907	244198	Mm.77425	NM_172907	ENSMUSG00000051041	Olfml1	6720478C22|AV321997|BC047207|MVAL564|ONT2|mONT2	olfactomedin-like 1	protein-coding	0	0.386139
Merged-chr9-38148407-1	chr9	38148357	38148457	+	2	cIP2vsInput	Intergenic	Intergenic	5270	NM_146481	258474	Mm.377521	NM_146481	ENSMUSG00000096409	Olfr890	MOR162-3	olfactory receptor 890	protein-coding	0	0.316832
Merged-chr11-38774112-1	chr11	38774062	38774162	+	2	cIP2vsInput	Intergenic	Intergenic	-254067	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0.01	0.306931
Merged-chr14-72067425-1	chr14	72067375	72067475	+	2	cIP2vsInput	Intergenic	Intergenic	210716	NR_046274	74667	Mm.159286	NR_046274		4930434J06Rik	-	RIKEN cDNA 4930434J06 gene	miscRNA	0.01	0.366337
Merged-chr10-81016857-1	chr10	81016807	81016907	+	2	cIP2vsInput	Intergenic	Intergenic	-1932	NM_010319	14708	Mm.222496	NM_001038655	ENSMUSG00000048240	Gng7	AI840417	"guanine nucleotide binding protein (G protein), gamma 7"	protein-coding	0.03	0.673267
Merged-chr7-92548696-1	chr7	92548646	92548746	+	2	cIP2vsInput	Intergenic	Intergenic	-12453	NM_025515	66365	Mm.21173	NM_001162918	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding	0	0.376238
Merged-chr1-59147312-1	chr1	59147262	59147362	+	2	cIP2vsInput	"intron (NM_001164682, intron 8 of 22)"	MYSERV16_I-int|LTR|ERVK	14324	NM_145143	227157	Mm.474049	NM_001164682	ENSMUSG00000079550	Mpp4	Dlg6	"membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4)"	protein-coding	0	0.336634
Merged-chr3-158343301-1	chr3	158343251	158343351	+	2	cIP1vsInput	"intron (NM_001081358, intron 4 of 27)"	"intron (NM_001081358, intron 4 of 27)"	218920	NM_001081358	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding	0	0.29703
Merged-chr5-58002527-1	chr5	58002477	58002577	+	2	cIP2vsInput	"intron (NM_001122758, intron 2 of 2)"	"intron (NM_001122758, intron 2 of 2)"	284506	NM_018764	54216	Mm.397491	NM_001122758	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding	0.01	0.316832
Merged-chr1-92641856-1	chr1	92641806	92641906	+	2	cIP2vsInput	promoter-TSS (NR_028108)	promoter-TSS (NR_028108)	92	NR_028108	66915	Mm.30179	NM_001163425	ENSMUSG00000073616	Myeov2	1110002M09Rik	myeloma overexpressed 2	protein-coding	0.09	0.732673
Merged-chr12-58052840-1	chr12	58052790	58052890	+	2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-158964	NM_009216	20605	Mm.278336	NM_009216		Sstr1	SRIF-2|SS-1-R|SS1-R|SS1R|Smstr-1|Smstr1|sst1	somatostatin receptor 1	protein-coding	0.01	0.326733
Merged-chr9-82564269-1	chr9	82564219	82564319	+	2	cIP1vsInput	Intergenic	Intergenic	-265537	NM_001168240	65099	Mm.41415	NM_001168240	ENSMUSG00000032251	Irak1bp1	4921528N06Rik|AI851240|Aabp3|Aip70|Simpl	interleukin-1 receptor-associated kinase 1 binding protein 1	protein-coding	0	0.29703
Merged-chr14-92594295-1	chr14	92594245	92594345	+	2	cIP2vsInput	Intergenic	Intergenic	1294593	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.336634
Merged-chr10-12161038-1	chr10	12160988	12161088	+	2	cIP2vsInput	Intergenic	Lx|LINE|L1	700697	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding	0	0.346535
Merged-chr14-53342143-1	chr14	53342093	53342193	+	2	cIP2vsInput	Intergenic	Intergenic	-323797	NM_001205242	100568452	Mm.486072	NM_001205242		A430107P09Rik	Va10	RIKEN cDNA A430107P09 gene	protein-coding	0.01	0.287129
Merged-chr12-108757542-1	chr12	108757492	108757592	+	2	cIP1vsInput	Intergenic	Intergenic	-35769	NM_009537	22632	Mm.458511	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding	0	0.366337
Merged-chr13-68637736-1	chr13	68637686	68637786	+	2	cIP2vsInput	"intron (NM_153534, intron 22 of 24)"	"intron (NM_153534, intron 22 of 24)"	40297	NM_027035	69315	Mm.272795	NM_027035	ENSMUSG00000021534	1700001L19Rik	-	RIKEN cDNA 1700001L19 gene	protein-coding	0	0.306931
Merged-chr9-55953730-1	chr9	55953680	55953780	+	2	cIP2vsInput	Intergenic	Intergenic	-15615	NM_001081341	244891	Mm.86588	NM_001081341	ENSMUSG00000034007	Scaper	C430017I08|D530014O03Rik|Zfp291	S phase cyclin A-associated protein in the ER	protein-coding	0	0.366337
Merged-chr8-92266013-1	chr8	92265963	92266063	+	2	cIP2vsInput	Intergenic	Intergenic	90107	NR_033641	71296	Mm.86664	NR_033641	ENSMUSG00000031736	4933436C20Rik	-	RIKEN cDNA 4933436C20 gene	miscRNA	0.03	0.455446
Merged-chr18-37446640-1	chr18	37446590	37446690	+	2	cIP2vsInput	TTS (NM_053138)	TTS (NM_053138)	-1017	NM_053139	93885	Mm.196699	NM_053139	ENSMUSG00000044043	Pcdhb14	2210006M07Rik|Pcdhb17|PcdhbN	protocadherin beta 14	protein-coding	0	0.287129
Merged-chr3-155773956-1	chr3	155773906	155774006	+	2	cIP1vsInput	Intergenic	Intergenic	-202398	NR_040553	329780	Mm.119000	NR_040553		9330178D15Rik	9330178D15	RIKEN cDNA 9330178D15 gene	miscRNA	0	0.326733
Merged-chr12-10742450-1	chr12	10742400	10742500	+	2	cIP1vsInput	Intergenic	Intergenic	-305363	NR_045860	71457	Mm.95280	NR_045860		7420701I03Rik	-	RIKEN cDNA 7420701I03 gene	miscRNA	0	0.336634
Merged-chr1-142091961-1	chr1	142091911	142092011	+	2	cIP1vsInput	Intergenic	RLTR18B|LTR|ERVK	-1435559	NR_040604	75910	Mm.491057	NR_040604		4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	miscRNA	0.01	0.29703
Merged-chrX-118645304-1	chrX	118645254	118645354	+	2	cIP2vsInput	Intergenic	Lx8|LINE|L1	-164567	NM_001142750	100039551	Mm.423457	NM_001142750	ENSMUSG00000063242	Tgif2lx2	-	"TGFB-induced factor homeobox 2-like, X-linked 2"	protein-coding	0	0.376238
Merged-chr13-114907498-1	chr13	114907448	114907548	+	2	cIP2vsInput	"intron (NM_008396, intron 1 of 29)"	"intron (NM_008396, intron 1 of 29)"	24543	NM_008396	16398	Mm.5007	NM_008396	ENSMUSG00000015533	Itga2	CD49B|DX5	integrin alpha 2	protein-coding	0	0.425743
Merged-chr14-105042503-1	chr14	105042453	105042553	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	72173	NR_040628	100502987	Mm.474826	NR_040628		Gm17066	-	predicted gene 17066	miscRNA	0	0.316832
Merged-chr13-78049851-1	chr13	78049801	78049901	+	2	cIP2vsInput	"intron (NM_138312, intron 10 of 10)"	"intron (NM_138312, intron 10 of 10)"	24949	NM_029315	75507	Mm.443255	NM_029315		Pou5f2	1700013G10Rik|SPRM-1|Sprm1	"POU domain class 5, transcription factor 2"	protein-coding	0	0.346535
Merged-chr5-61539700-1	chr5	61539650	61539750	+	2	cIP2vsInput	Intergenic	Intergenic	-269143	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding	0.01	0.287129
Merged-chr7-6940635-1	chr7	6940585	6940685	+	2	cIP2vsInput	"intron (NM_021323, intron 5 of 7)"	"intron (NM_021323, intron 5 of 7)"	36027	NR_036631	116811	Mm.381671	NR_036631		Zim3	1700128I23Rik	"zinc finger, imprinted 3"	miscRNA	0.02	0.306931
Merged-chr17-44925106-1	chr17	44925056	44925156	+	2	cIP2vsInput	"intron (NM_178652, intron 3 of 11)"	Tigger7|DNA|TcMar-Tigger	-44221	NM_029257	75341	Mm.386821	XM_001003502		4930564C03Rik	-	RIKEN cDNA 4930564C03 gene	protein-coding	0	0.326733
Merged-chr13-75445095-1	chr13	75445045	75445145	+	2	cIP2vsInput	Intergenic	Intergenic	-199951	NR_030451	751556		NR_030451	ENSMUSG00000076236	Mir682	Mirn682|mir-682|mmu-mir-682	microRNA 682	miscRNA	0	0.39604
Merged-chr13-27108635-1	chr13	27108585	27108685	+	2	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-13069	NM_172155	215028	Mm.458451	NM_172155	ENSMUSG00000062737	Prl3d2	PL-Ib|Plib	"prolactin family 3, subfamily d, member 1"	protein-coding	0.01	0.267327
Merged-chr2-43448510-1	chr2	43448460	43448560	+	2	cIP2vsInput	Intergenic	ORR1D2|LTR|ERVL-MaLR	-106819	NM_027552	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding	0.02	0.326733
Merged-chr17-51940971-1	chr17	51940921	51941021	+	2	cIP2vsInput	"intron (NR_045095, intron 2 of 2)"	"intron (NR_045095, intron 2 of 2)"	58244	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	"predicted gene, 20098"	miscRNA	0.01	0.386139
Merged-chr8-51612897-1	chr8	51612847	51612947	+	2	cIP2vsInput	Intergenic	MLT1E-int|LTR|ERVL-MaLR	1244785	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.306931
Merged-chr13-57867700-1	chr13	57867650	57867750	+	2	cIP2vsInput	"intron (NM_001166466, intron 2 of 11)"	"intron (NM_001166466, intron 2 of 11)"	40632	NM_009262	20745	Mm.379020	NM_001166463		Spock1	Spock|Ticn1|testican	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1"	protein-coding	0.03	0.534653
Merged-chr7-43785178-1	chr7	43785128	43785228	+	2	cIP2vsInput	"3' UTR (NM_133712, exon 6 of 6)"	"3' UTR (NM_133712, exon 6 of 6)"	4124	NM_133712	69540	Mm.46421	NM_133712	ENSMUSG00000030693	Klk10	2300002A13Rik|NES1|PRSSL1	kallikrein related-peptidase 10	protein-coding	0	0.50495
Merged-chr1-192203745-1	chr1	192203695	192203795	+	2	cIP2vsInput	"intron (NM_001038607, intron 1 of 10)"	"intron (NM_001038607, intron 1 of 10)"	12873	NM_010600	16510	Mm.4489	NM_001038607	ENSMUSG00000058248	Kcnh1	Kv10.1|M-eag	"potassium voltage-gated channel, subfamily H (eag-related), member 1"	protein-coding	0.01	0.445545
Merged-chr14-81340100-1	chr14	81340050	81340150	+	2	cIP2vsInput	Intergenic	Intergenic	1339798	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.29703
Merged-chr1-18921642-1	chr1	18921592	18921692	+	2	cIP2vsInput	Intergenic	Intergenic	-181380	NM_153154	226896	Mm.244858	NM_153154	ENSMUSG00000042596	Tfap2d	Tcfap2d	"transcription factor AP-2, delta"	protein-coding	0	0.336634
Merged-chr14-75938191-1	chr14	75938141	75938241	+	2	cIP1vsInput	"intron (NM_026816, intron 5 of 7)"	"intron (NM_026816, intron 5 of 7)"	-16812	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding	0	0.316832
Merged-chr18-60299736-1	chr18	60299686	60299786	+	2	cIP2vsInput	"intron (NM_001101475, intron 1 of 1)"	"intron (NM_001101475, intron 1 of 1)"	6356	NM_001101475	240328	Mm.329461	NM_001101475	ENSMUSG00000090942	F830016B08Rik	Ifgga4	RIKEN cDNA F830016B08 gene	protein-coding	0	0.346535
Merged-chr3-21692850-1	chr3	21692800	21692900	+	2	cIP2vsInput	Intergenic	Intergenic	-383802	NM_030732	81004	Mm.446265	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding	0.01	0.336634
Merged-chr2-88611976-1	chr2	88611926	88612026	+	2	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	20170	NM_146772	258768	Mm.377683	NM_146772	ENSMUSG00000068808	Olfr1189	MOR237-2	olfactory receptor 1189	protein-coding	0.01	0.326733
Merged-chr3-104980685-1	chr3	104980635	104980735	+	2	cIP2vsInput	Intergenic	MYSERV6-int|LTR|ERVK	-18976	NM_009520	22414	Mm.10740	NM_009520	ENSMUSG00000027840	Wnt2b	Wnt13	wingless related MMTV integration site 2b	protein-coding	0	0.267327
Merged-chr14-124610575-1	chr14	124610525	124610625	+	2	cIP2vsInput	"intron (NM_207667, intron 1 of 4)"	"intron (NM_207667, intron 1 of 4)"	66552	NM_207667	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding	0.02	0.39604
Merged-chr16-61180313-1	chr16	61180263	61180363	+	2	cIP1vsInput	Intergenic	LTR72_RN|LTR|ERV1	-574782	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0	0.336634
Merged-chr13-7985332-1	chr13	7985282	7985382	+	2	cIP2vsInput	Intergenic	L1_Mm|LINE|L1	-217577	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	"adenosine deaminase, RNA-specific, B2"	protein-coding	0.01	0.356436
Merged-chr14-106293503-1	chr14	106293453	106293553	+	2	cIP2vsInput	Intergenic	Intergenic	187305	NR_073203	212085	Mm.452063	NM_198601	ENSMUSG00000022113	Trim52	4921513B05Rik	tripartite motif-containing 52	protein-coding	0	0.346535
Merged-chr1-170378095-1	chr1	170378045	170378145	+	2	cIP2vsInput	"intron (NM_001109985, intron 3 of 9)"	L1MDa|LINE|L1	69234	NM_001039593	76925	Mm.33631	NM_001039593	ENSMUSG00000042800	1700015E13Rik	-	RIKEN cDNA 1700015E13 gene	protein-coding	0	0.366337
Merged-chr9-93292545-1	chr9	93292495	93292595	+	2	cIP2vsInput	Intergenic	Intergenic	-286812	NR_040756	78349	Mm.52612	NR_040756		1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	miscRNA	0	0.29703
Merged-chr6-57226888-1	chr6	57226838	57226938	+	2	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-6551	NM_053237	113864	Mm.431974	NM_053237		Vmn1r14	V1rc7	vomeronasal 1 receptor 14	protein-coding	0	0.366337
Merged-chr4-14248182-1	chr4	14248132	14248232	+	2	cIP2vsInput	Intergenic	Intergenic	373596	NM_145947	208890	Mm.483839	NM_145947		Slc26a7	-	"solute carrier family 26, member 7"	protein-coding	0	0.287129
Merged-chr14-84812835-1	chr14	84812785	84812885	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-336411	NR_015539	319903	Mm.440481	NR_015539		9630013A20Rik	-	RIKEN cDNA 9630013A20 gene	miscRNA	0	0.356436
Merged-chr8-68636937-1	chr8	68636887	68636987	+	2	cIP2vsInput	"intron (NM_001252623, intron 3 of 10)"	"intron (NM_001252623, intron 3 of 10)"	98209	NM_001252623	234356	Mm.489712	NM_001252623	ENSMUSG00000036356	Csgalnact1	4732435N03Rik|CSGalNAcT-1	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.01	0.356436
Merged-chr16-47172792-1	chr16	47172742	47172842	+	2	cIP2vsInput	Intergenic	Intergenic	-675825	NM_021497	58998	Mm.328072	NM_021495	ENSMUSG00000022656	Pvrl3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113	poliovirus receptor-related 3	protein-coding	0	0.376238
Merged-chr3-59306361-1	chr3	59306311	59306411	+	2	cIP2vsInput	"intron (NM_177855, intron 42 of 43)"	"intron (NM_177855, intron 42 of 43)"	37895	NM_001162884	242050	Mm.444186	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	"immunoglobulin superfamily, member 10"	protein-coding	0.01	0.366337
Merged-chr3-67292576-1	chr3	67292526	67292626	+	2	cIP2vsInput	"intron (NM_025822, intron 7 of 9)"	"intron (NM_025822, intron 7 of 9)"	-81521	NM_010801	17349	Mm.10414	NM_001039543	ENSMUSG00000048416	Mlf1	HLS7	myeloid leukemia factor 1	protein-coding	0	0.287129
Merged-chr1-102726507-1	chr1	102726457	102726557	+	2	cIP2vsInput	Intergenic	B4|SINE|B4	1570739	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.336634
Merged-chrX-169767262-1	chrX	169767212	169767312	+	2	cIP1vsInput	"intron (NM_010797, intron 1 of 9)"	"intron (NM_010797, intron 1 of 9)"	12373	NR_003635	66747		NR_003635	ENSMUSG00000055357	4933400A11Rik	-	"capping protein (actin filament) muscle Z-line, alpha 1 pseudogene"	pseudo	0	0.376238
Merged-chr14-34025454-1	chr14	34025404	34025504	+	2	cIP2vsInput	Intergenic	L1VL2|LINE|L1	-15624	NM_001034880	432838	Mm.318383	NM_001034880	ENSMUSG00000072624	Gm5460	EG432838	predicted gene 5460	protein-coding	0	0.346535
Merged-chrX-73914874-1	chrX	73914824	73914924	+	2	cIP2vsInput	Intergenic	Intergenic	-3576	NM_001162424	171207	Mm.482337	NM_001162423	ENSMUSG00000031389	Arhgap4	A130009C12Rik|A530015A20Rik|Rgc1|c1|mKIAA0131	Rho GTPase activating protein 4	protein-coding	0.03	0.613861
Merged-chr1-54964017-1	chr1	54963967	54964067	+	2	cIP2vsInput	Intergenic	Intergenic	-37630	NM_001081433	329154	Mm.397910	NM_001081433	ENSMUSG00000052331	Ankrd44	4930444A19Rik|A130096K20|E130014H08Rik|PP6-ARS-B	ankyrin repeat domain 44	protein-coding	0	0.336634
Merged-chr1-133039616-1	chr1	133039566	133039666	+	2	cIP2vsInput	Intergenic	Intergenic	-6396	NM_001099276	240752	Mm.387308	NM_001099276	ENSMUSG00000026447	Pik3c2b	C330011J12Rik|Gm199|PI3K-C2beta|PI3KC2beta	"phosphoinositide-3-kinase, class 2, beta polypeptide"	protein-coding	0	0.435644
Merged-chr1-78790128-1	chr1	78790078	78790178	+	2	cIP2vsInput	Intergenic	Intergenic	-26821	NM_021342	57814	Mm.24386	NM_021342	ENSMUSG00000047330	Kcne4	AW487937|MiRP3	"potassium voltage-gated channel, Isk-related subfamily, gene 4"	protein-coding	0	0.346535
Merged-chr6-101829164-1	chr6	101829114	101829214	+	2	cIP2vsInput	Intergenic	L1MEc|LINE|L1	54915	NR_027989	207157	Mm.57632	NM_177579		Gm9871	0610005I04|EG207157|ENSMUSG00000052236	predicted gene 9871	miscRNA	0	0.336634
Merged-chr9-29914635-1	chr9	29914585	29914685	+	2	cIP2vsInput	"intron (NM_172290, intron 1 of 7)"	"intron (NM_172290, intron 1 of 7)"	48494	NM_172290	235106	Mm.283138	NM_172290		Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding	0	0.306931
Merged-chr15-34635646-1	chr15	34635596	34635696	+	2	cIP2vsInput	"intron (NM_145469, intron 3 of 10)"	"intron (NM_145469, intron 3 of 10)"	-39427	NR_045883	71637	Mm.410827	NR_045883		4930413F20Rik	-	RIKEN cDNA 4930413F20 gene	miscRNA	0	0.287129
Merged-chr8-81552700-1	chr8	81552650	81552750	+	2	cIP1vsInput	Intergenic	L1_Mm|LINE|L1	-162500	NM_001024617	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	"inositol polyphosphate-4-phosphatase, type II"	protein-coding	0.01	0.326733
Merged-chr13-102471174-1	chr13	102471124	102471224	+	2	cIP2vsInput	Intergenic	Intergenic	-222384	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding	0	0.336634
Merged-chr4-115910694-1	chr4	115910644	115910744	+	2	cIP2vsInput	Intergenic	B4|SINE|B4	26294	NM_001039124	654462	Mm.388913	NM_001039124	ENSMUSG00000073774	Kncn	Kino|L5	kinocilin	protein-coding	0	0.465347
Merged-chr4-39825314-1	chr4	39825264	39825364	+	2	cIP1vsInput	Intergenic	RMER12B|LTR|ERVK	-317951	NM_007386	11428	Mm.331547	NM_007386	ENSMUSG00000028405	Aco1	AI256519|Aco-1|Irebp|Irp1	aconitase 1	protein-coding	0.01	0.316832
Merged-chr10-53193215-1	chr10	53193165	53193265	+	2	cIP2vsInput	Intergenic	L1Md_F|LINE|L1	-87055	NR_038015	100502820	Mm.55827	NR_038015		Gm19395	-	"predicted gene, 19395"	miscRNA	0.01	0.346535
Merged-chr5-110959647-1	chr5	110959597	110959697	+	2	cIP1vsInput	"intron (NM_001267622, intron 2 of 22)"	"intron (NM_001267622, intron 2 of 22)"	-44497	NR_030482	735278		NR_030482		Mir701	Mirn701|mmu-mir-701	microRNA 701	miscRNA	0	0.366337
Merged-chr1-7044303-1	chr1	7044253	7044353	+	2	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-44617	NM_183028	319263		NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.02	0.386139
Merged-chr10-129891637-1	chr10	129891587	129891687	+	2	cIP2vsInput	Intergenic	L1VL4|LINE|L1	11089	NM_146670	258665	Mm.377627	NM_146670	ENSMUSG00000061961	Olfr815	MOR113-3	olfactory receptor 815	protein-coding	0	0.346535
Merged-chr7-128208250-1	chr7	128208200	128208300	+	2	cIP2vsInput	Intergenic	Intergenic	-1884	NM_009943	12862	Mm.43824	NM_009943	ENSMUSG00000030785	Cox6a2	CoxVIaH|VIaH	cytochrome c oxidase subunit VIa polypeptide 2	protein-coding	0	0.425743
Merged-chr10-114849940-1	chr10	114849890	114849990	+	2	cIP2vsInput	Intergenic	Intergenic	-48570	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding	0	0.366337
Merged-chr8-63709278-1	chr8	63709228	63709328	+	2	cIP2vsInput	Intergenic	MYSERV-int|LTR|ERVK	242892	NM_001195687	244495	Mm.485331	NM_001195687	ENSMUSG00000094443	Gm4975	EG244495|Sgo2B	predicted gene 4975	protein-coding	0	0.346535
Merged-chr12-112412609-1	chr12	112412559	112412659	+	2	cIP2vsInput	"intron (NR_036459, intron 3 of 3)"	"intron (NR_036459, intron 3 of 3)"	10589	NR_036459	100504733	Mm.255309	NM_176956		A730018C14Rik	-	RIKEN cDNA A730018C14 gene	miscRNA	0	0.376238
Merged-chr16-85247450-1	chr16	85247400	85247500	+	2	cIP2vsInput	Intergenic	Intergenic	-73743	NM_001198823	11820	Mm.490986	NM_001198823	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding	0	0.415842
Merged-chr2-149092560-1	chr2	149092510	149092610	+	2	cIP2vsInput	Intergenic	Intergenic	-217092	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding	0	0.366337
Merged-chr1-96105495-1	chr1	96105445	96105545	+	2	cIP2vsInput	Intergenic	Intergenic	-83737	NR_040467	73454	Mm.396229	NR_040467		1700063A18Rik	-	RIKEN cDNA 1700063A18 gene	miscRNA	0	0.366337
Merged-chr10-50816024-1	chr10	50815974	50816074	+	2	cIP2vsInput	"intron (NM_198007, intron 36 of 41)"	"intron (NM_198007, intron 36 of 41)"	-79627	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding	0.01	0.366337
Merged-chrX-116751093-1	chrX	116751043	116751143	+	2	cIP1vsInput	Intergenic	L1VL4|LINE|L1	-263664	NM_001102665	100039319	Mm.469831	NM_001102665		Gm14920	ENSMUSG00000067441|Gm1539|H2A.Bbd1|OTTMUSG00000018481	predicted pseudogene 14920	protein-coding	0.01	0.306931
Merged-chr5-4944135-1	chr5	4944085	4944185	+	2	cIP2vsInput	"intron (NM_011074, intron 11 of 14)"	"intron (NM_011074, intron 11 of 14)"	-185919	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled homolog 1 (Drosophila)	protein-coding	0	0.29703
Merged-chr8-111418616-1	chr8	111418566	111418666	+	2	cIP2vsInput	Intergenic	L1M4|LINE|L1	-24795	NM_178086	338521	Mm.41083	NM_178086	ENSMUSG00000033579	Fa2h	FAAH|Faxdc1|G630055L08Rik	fatty acid 2-hydroxylase	protein-coding	0.01	0.366337
Merged-chr2-89878198-1	chr2	89878148	89878248	+	2	cIP2vsInput	Intergenic	Intergenic	-2630	NM_146982	258984	Mm.389309	NM_146982	ENSMUSG00000049057	Olfr1257	MOR232-1	olfactory receptor 1257	protein-coding	0.01	0.356436
Merged-chr14-95838648-1	chr14	95838598	95838698	+	2	cIP1vsInput	Intergenic	Intergenic	-42618	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.306931
Merged-chr7-60244438-1	chr7	60244388	60244488	+	2	cIP1vsInput	Intergenic	Intergenic	-104219	NM_001082962	20646	Mm.274995	NM_001082961	ENSMUSG00000000948	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding	0.1	0.663366
Merged-chr13-34955820-1	chr13	34955770	34955870	+	2	cIP2vsInput	"intron (NM_026947, intron 4 of 8)"	MER2|DNA|TcMar-Tigger	7989	NM_026947	69123	Mm.482475	NM_026947	ENSMUSG00000021416	Eci3	1810022C23Rik|Kseg2	enoyl-Coenzyme A delta isomerase 3	protein-coding	0	0.316832
Merged-chr18-10686526-1	chr18	10686476	10686576	+	2	cIP1vsInput	"intron (NM_134130, intron 3 of 8)"	MYSERV16_I-int|LTR|ERVK	20170	NM_134130	106861	Mm.273108	NM_134130	ENSMUSG00000002475	Abhd3	AA675331|LABH3	abhydrolase domain containing 3	protein-coding	0	0.356436
Merged-chr12-62822536-1	chr12	62822486	62822586	+	2	cIP2vsInput	Intergenic	Lx7|LINE|L1	1297904	NM_178714	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.01	0.326733
Merged-chr1-195143917-1	chr1	195143867	195143967	+	2	cIP2vsInput	"intron (NM_007758, intron 17 of 18)"	"intron (NM_007758, intron 17 of 18)"	-12347	NM_013499	12946	Mm.301652	NM_013499	ENSMUSG00000016481	Cr1l	Crry|Mcp|mCRY	complement component (3b/4b) receptor 1-like	protein-coding	0	0.376238
Merged-chr9-101761706-1	chr9	101761656	101761756	+	2	cIP2vsInput	Intergenic	RLTR19-int|LTR|ERVK	-509874	NM_001161362	235542	Mm.335386	NM_001161362	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	"protein phosphatase 2, regulatory subunit B'', alpha"	protein-coding	0	0.326733
Merged-chr6-39067422-1	chr6	39067372	39067472	+	2	cIP2vsInput	"intron (NR_040523, intron 1 of 3)"	"intron (NR_040523, intron 1 of 3)"	164	NR_040523	69986	Mm.490941	NR_040523		1700025N23Rik	-	RIKEN cDNA 1700025N23 gene	miscRNA	0.03	0.60396
Merged-chr12-97563765-1	chr12	97563715	97563815	+	2	cIP1vsInput	Intergenic	Intergenic	695572	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding	0	0.425743
Merged-chr1-3299461-1	chr1	3299411	3299511	+	2	cIP2vsInput	"intron (NM_001011874, intron 2 of 2)"	L1M4a1|LINE|L1	372037	NM_001011874	497097	Mm.489375	NM_001011874		Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X Kell blood group precursor related family member 4	protein-coding	0	0.386139
Merged-chr5-10838218-1	chr5	10838168	10838268	+	2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-26811	NR_003596	623849	Mm.335888	NR_003596	ENSMUSG00000091422	Gm6455	EG623849	predicted gene 6455	pseudo	0.02	0.376238
Merged-chr8-34633151-1	chr8	34633101	34633201	+	2	cIP2vsInput	"intron (NR_040706, intron 1 of 4)"	L1_Mus4|LINE|L1	7165	NR_040706	330734	Mm.149998	NR_040706		B930018H19Rik	B930018H19	RIKEN cDNA B930018H19 gene	miscRNA	0	0.306931
Merged-chr10-6105454-1	chr10	6105404	6105504	+	2	cIP2vsInput	Intergenic	Intergenic	-183054	NM_019958	56533	Mm.44606	NM_001161822	ENSMUSG00000019775	Rgs17	6430507P11Rik|Rgsz2	regulator of G-protein signaling 17	protein-coding	0.01	0.366337
Merged-chr7-134985275-1	chr7	134985225	134985325	+	2	cIP2vsInput	"intron (NM_001033420, intron 27 of 51)"	"intron (NM_001033420, intron 27 of 51)"	-46845	NM_001143802	627214	Mm.323610	NM_001143802	ENSMUSG00000073805	Fam196a	B830028B13Rik	"family with sequence similarity 196, member A"	protein-coding	0.02	0.29703
Merged-chr3-93859587-1	chr3	93859537	93859637	+	2	cIP2vsInput	Intergenic	MMERVK9C_I-int|LTR|ERVK	33567	NM_207271	399674	Mm.377923	NM_207271	ENSMUSG00000058005	Tdpoz3	-	TD and POZ domain containing 3	protein-coding	0	0.287129
Merged-chr14-121579087-1	chr14	121579037	121579137	+	2	cIP2vsInput	"intron (NM_001081039, intron 43 of 53)"	"intron (NM_001081039, intron 43 of 53)"	-73833	NM_053079	56643	Mm.155618	NM_053079	ENSMUSG00000025557	Slc15a1	D630032F02|PECT1|PEPT1	"solute carrier family 15 (oligopeptide transporter), member 1"	protein-coding	0	0.326733
Merged-chr18-24720046-1	chr18	24719996	24720096	+	2	cIP2vsInput	"intron (NM_175276, intron 1 of 26)"	"intron (NM_175276, intron 1 of 26)"	10601	NM_175276	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding	0.01	0.366337
Merged-chr3-53285888-1	chr3	53285838	53285938	+	2	cIP2vsInput	Intergenic	L1M2|LINE|L1	177370	NM_172501	212114	Mm.85744	NM_172501		Nhlrc3	4833441N19|8030451K01Rik|mKIAA4083	NHL repeat containing 3	protein-coding	0.01	0.316832
Merged-chr10-71401488-1	chr10	71401438	71401538	+	2	cIP2vsInput	Intergenic	Intergenic	53695	NM_027184	69718	Mm.245867	NM_027184	ENSMUSG00000060733	Ipmk	2410017C19Rik|AA408208|Impk	inositol polyphosphate multikinase	protein-coding	0	0.39604
Merged-chr2-95800035-1	chr2	95799985	95800085	+	2	cIP2vsInput	Intergenic	Intergenic	-1361888	NM_007466	11800	Mm.486651	NM_007466	ENSMUSG00000027193	Api5	AAC-11|AI196452	apoptosis inhibitor 5	protein-coding	0	0.346535
Merged-chr8-21793024-1	chr8	21792974	21793074	+	2	cIP1vsInput	"intron (NM_007843, intron 1 of 1)"	"intron (NM_007843, intron 1 of 1)"	16469	NM_007843	13214	Mm.431316	NM_007843	ENSMUSG00000044748	Defb1	AW260221|BD-1	defensin beta 1	protein-coding	0	0.29703
Merged-chr4-98904993-1	chr4	98904943	98905043	+	2	cIP1vsInput	Intergenic	Intergenic	-18817	NM_146144	230484	Mm.371692	NM_146144	ENSMUSG00000028560	Usp1	-	ubiquitin specific peptidase 1	protein-coding	0	0.237624
Merged-chr1-107069459-1	chr1	107069409	107069509	+	2	cIP1vsInput	Intergenic	Intergenic	14021	NM_201376	394252	Mm.352392	NM_201376	ENSMUSG00000058017	Serpinb3d	Serpinb3l1	"serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 3D"	protein-coding	0	0.346535
Merged-chr15-5678558-1	chr15	5678508	5678608	+	2	cIP2vsInput	Intergenic	L1M2|LINE|L1	182240	NR_045274	71432	Mm.291087	NR_045274		5430437J10Rik	-	RIKEN cDNA 5430437J10 gene	miscRNA	0	0.445545
Merged-chr9-58775393-1	chr9	58775343	58775443	+	2	cIP2vsInput	Intergenic	L1ME3A|LINE|L1	-33834	NM_028598	73673	Mm.205196	NM_028598	ENSMUSG00000074269	2410076I21Rik	4930527A11Rik	RIKEN cDNA 2410076I21 gene	protein-coding	0	0.346535
Merged-chrX-106885570-1	chrX	106885520	106885620	+	2	cIP2vsInput	Intergenic	Intergenic	-35055	NM_175271	78134	Mm.90147	NM_175271	ENSMUSG00000049929	Lpar4	5730485F04Rik|Gpr23|LPA4|p2y9	lysophosphatidic acid receptor 4	protein-coding	0	0.326733
Merged-chr4-81861340-1	chr4	81861290	81861390	+	2	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-204040	NR_040659	545641	Mm.216028	NR_040659	ENSMUSG00000085022	Gm5860	EG545641	predicted gene 5860	miscRNA	0.02	0.326733
Merged-chr3-93275859-1	chr3	93275809	93275909	+	2	cIP2vsInput	Intergenic	L1MEd|LINE|L1	-43890	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|AV011854|S100a18|S100a18-ps1	hornerin	protein-coding	0	0.29703
Merged-chr11-18251655-1	chr11	18251605	18251705	+	2	cIP2vsInput	Intergenic	Intergenic	-297780	NM_026576	68145	Mm.178684	NM_026576	ENSMUSG00000016984	Etaa1	5730466H23Rik|AA672646	Ewing's tumor-associated antigen 1	protein-coding	0	0.336634
Merged-chr5-55223783-1	chr5	55223733	55223833	+	2	cIP2vsInput	Intergenic	Intergenic	873791	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0.01	0.247525
Merged-chr1-138312546-1	chr1	138312496	138312596	+	2	cIP2vsInput	Intergenic	Intergenic	38808	NM_177397	338375	Mm.114424	NM_177397	ENSMUSG00000026394	Atp6v1g3	-	"ATPase, H+ transporting, lysosomal V1 subunit G3"	protein-coding	0	0.356436
Merged-chr9-74564043-1	chr9	74563993	74564093	+	2	cIP2vsInput	Intergenic	Intergenic	-284394	NR_045284	100503019	Mm.482658	NR_045284	ENSMUSG00000066477	Gm16551	-	predicted gene 16551	miscRNA	0.02	0.376238
Merged-chr7-126728536-1	chr7	126728486	126728586	+	2	cIP2vsInput	Intergenic	Lx7|LINE|L1	-23782	NM_009898	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	"coronin, actin binding protein 1A"	protein-coding	0.01	0.316832
Merged-chr1-13450129-1	chr1	13450079	13450179	+	2	cIP2vsInput	Intergenic	Intergenic	-76046	NM_008678	17978	Mm.2537	NM_001077695	ENSMUSG00000005886	Ncoa2	9530095N19|D1Ertd433e|GRIP-1|Grip1|KAT13C|SRC-2|TIF-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding	0	0.306931
Merged-chr18-50378500-1	chr18	50378450	50378550	+	2	cIP2vsInput	Intergenic	Intergenic	100131	NM_001004061	225497	Mm.329435	NM_001004061	ENSMUSG00000035420	Fam170a	Gm93|Znfd	"family with sequence similarity 170, member A"	protein-coding	0	0.356436
Merged-chr6-107223851-1	chr6	107223801	107223901	+	2	cIP2vsInput	Intergenic	Intergenic	-305875	NM_008516	16979	Mm.488119	NM_008516	ENSMUSG00000034648	Lrrn1	2810047E21Rik|NLRR-1	"leucine rich repeat protein 1, neuronal"	protein-coding	0	0.336634
Merged-chr15-50078787-1	chr15	50078737	50078837	+	2	cIP1vsInput	Intergenic	Intergenic	810327	NR_035444	100316685		NR_035444	ENSMUSG00000084458	Mir1907	Mirn1907|mmu-mir-1907	microRNA 1907	miscRNA	0.01	0.336634
Merged-chr1-97060144-1	chr1	97060094	97060194	+	2	cIP2vsInput	"intron (NM_028942, intron 13 of 13)"	"intron (NM_028942, intron 13 of 13)"	-62584	NM_001039475	67854	Mm.263706	NM_026413	ENSMUSG00000045463	Slco6b1	1700022M03Rik	"solute carrier organic anion transporter family, member 6b1"	protein-coding	0	0.336634
Merged-chr17-62312124-1	chr17	62312074	62312174	+	2	cIP2vsInput	Intergenic	Intergenic	569193	NM_207654	13640	Mm.401670	NM_010109		Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding	0.02	0.306931
Merged-chrX-124110376-1	chrX	124110326	124110426	+	2	cIP1vsInput	Intergenic	Intergenic	25534	NM_001100616	100038941	Mm.388852	NM_001100616	ENSMUSG00000072049	Vmn2r121	EG625699	"vomeronasal 2, receptor 121"	protein-coding	0	0.29703
Merged-chr14-112373944-1	chr14	112373894	112373994	+	2	cIP2vsInput	Intergenic	Intergenic	352514	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0.01	0.316832
Merged-chr15-18113381-1	chr15	18113331	18113431	+	2	cIP2vsInput	"intron (NR_045711, intron 9 of 11)"	"intron (NR_045711, intron 9 of 11)"	256246	NR_045711	70886	Mm.399021	NR_045711		4921515E04Rik	-	RIKEN cDNA 4921515E04 gene	miscRNA	0	0.237624
Merged-chr8-44868716-1	chr8	44868666	44868766	+	2	cIP2vsInput	Intergenic	B4|SINE|B4	-81492	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT tumor suppressor homolog 1 (Drosophila)	protein-coding	0	0.366337
Merged-chr2-72035861-1	chr2	72035811	72035911	+	2	cIP2vsInput	"intron (NM_001204165, intron 3 of 30)"	"intron (NM_001204165, intron 3 of 30)"	-18756	NM_001204166	56508	Mm.196153	NM_001204165	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding	0.02	0.554455
Merged-chr7-110331162-1	chr7	110331112	110331212	+	2	cIP2vsInput	"intron (NM_177324, intron 31 of 40)"	"intron (NM_177324, intron 31 of 40)"	109459	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding	0	0.386139
Merged-chr12-19201575-1	chr12	19201525	19201625	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	687065	NM_001201330	236366	Mm.352227	NM_001033157		5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding	0	0.346535
Merged-chr5-14907653-2	chr5	14907603	14907703	+	2	cIP1vsInput|cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	7236	NM_198666	381714	Mm.368256	NM_198666	ENSMUSG00000033219	Gm9758	ENSMUSG00000033219	predicted gene 9758	protein-coding	0	0.386139
Merged-chr8-66451792-1	chr8	66451742	66451842	+	2	cIP2vsInput	"intron (NM_001166372, intron 6 of 7)"	"intron (NM_001166372, intron 6 of 7)"	34715	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16 homolog (S. cerevisiae)	protein-coding	0	0.316832
Merged-chr3-61996617-1	chr3	61996567	61996667	+	2	cIP2vsInput	Intergenic	Intergenic	-342160	NM_001081295	622434		NM_001081295	ENSMUSG00000036885	Arhgef26	4631416L12Rik|8430436L14Rik|AI303572|AW491953|SGEF	Rho guanine nucleotide exchange factor (GEF) 26	protein-coding	0.01	0.376238
Merged-chr6-8101511-1	chr6	8101461	8101561	+	2	cIP2vsInput	"intron (NM_001037865, intron 15 of 34)"	"intron (NM_001037865, intron 15 of 34)"	91106	NM_001037865	213945	Mm.297404	NM_001037865	ENSMUSG00000068794	Col28a1	Col28|Gm466	"collagen, type XXVIII, alpha 1"	protein-coding	0	0.376238
Merged-chr17-60160958-1	chr17	60160908	60161008	+	2	cIP2vsInput	Intergenic	Intergenic	-1147636	NM_026497	67993	Mm.36507	NM_026497		Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0.02	0.346535
Merged-chr3-95411341-1	chr3	95411291	95411391	+	2	cIP2vsInput	Intergenic	Intergenic	-8500	NR_015490	67654	Mm.75066	NR_015490		4930558C23Rik	-	RIKEN cDNA 4930558C23 gene	miscRNA	0.01	0.326733
Merged-chr3-86049788-1	chr3	86049738	86049838	+	2	cIP2vsInput	Intergenic	Intergenic	-34646	NM_001082414	27059	Mm.2454	NM_012059	ENSMUSG00000028082	Sh3d19	AW011754|Kryn	SH3 domain protein D19	protein-coding	0.01	0.326733
Merged-chr10-44033116-1	chr10	44033066	44033166	+	2	cIP1vsInput	Intergenic	L1MB8|LINE|L1	-28270	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding	0.01	0.415842
Merged-chr6-62817616-1	chr6	62817566	62817666	+	2	cIP1vsInput	Intergenic	Intergenic	-439241	NM_008167	14804	Mm.447390	NM_008167		Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	"glutamate receptor, ionotropic, delta 2"	protein-coding	0.02	0.376238
Merged-chr8-114080958-1	chr8	114080908	114081008	+	2	cIP2vsInput	Intergenic	Intergenic	-52621	NM_024446	67528	Mm.27889	NM_024437	ENSMUSG00000031767	Nudt7	1300007B24Rik|2210404C19Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 7	protein-coding	0.01	0.386139
Merged-chr18-23303941-1	chr18	23303891	23303991	+	2	cIP2vsInput	Intergenic	Intergenic	-111474	NM_010087	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|A0|Dtn|a-DB-1|adbn	dystrobrevin alpha	protein-coding	0	0.326733
Merged-chr8-72094303-1	chr8	72094253	72094353	+	2	cIP1vsInput	Intergenic	RLTR19-int|LTR|ERVK	-5459	NM_146539	258532	Mm.377557	NM_146539	ENSMUSG00000061561	Olfr373	MOR282-2	olfactory receptor 373	protein-coding	0	0.376238
Merged-chr3-125017019-1	chr3	125016969	125017069	+	2	cIP2vsInput	Intergenic	Intergenic	-387072	NM_022565	64580	Mm.444289	NM_022565	ENSMUSG00000027971	Ndst4	4930439H17Rik	N-deacetylase/N-sulfotransferase (heparin glucosaminyl) 4	protein-coding	0.01	0.257426
Merged-chr14-85407536-1	chr14	85407486	85407586	+	2	cIP2vsInput	Intergenic	Intergenic	-838434	NR_040457	75155	Mm.399239	NR_040457		4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	miscRNA	0	0.326733
Merged-chr17-52929717-1	chr17	52929667	52929767	+	2	cIP2vsInput	"intron (NM_001031811, intron 11 of 15)"	L1_Mus4|LINE|L1	327008	NM_001031811	211468	Mm.490760	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	"potassium voltage-gated channel, subfamily H (eag-related), member 8"	protein-coding	0.01	0.376238
Merged-chr5-40089150-1	chr5	40089100	40089200	+	2	cIP2vsInput	Intergenic	Lx2B2|LINE|L1	-444519	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding	0.02	0.39604
Merged-chr12-84757174-1	chr12	84757124	84757224	+	2	cIP2vsInput	"exon (NM_023409, exon 4 of 4)"	"exon (NM_023409, exon 4 of 4)"	15938	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann Pick type C2	protein-coding	0	0.415842
Merged-chrX-96363307-1	chrX	96363257	96363357	+	2	cIP2vsInput	Intergenic	Intergenic	-6067	NM_172931	245525	Mm.166749	NM_172931	ENSMUSG00000045802	Hsf3	B230358A15Rik|HSF 3|HSTF 3|mHSF3	heat shock transcription factor 3	protein-coding	0	0.287129
Merged-chr17-92291168-1	chr17	92291118	92291218	+	2	cIP2vsInput	Intergenic	Lx7|LINE|L1	-908254	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0	0.356436
Merged-chr18-50324535-1	chr18	50324485	50324585	+	2	cIP1vsInput	Intergenic	Intergenic	46166	NM_001004061	225497	Mm.329435	NM_001004061	ENSMUSG00000035420	Fam170a	Gm93|Znfd	"family with sequence similarity 170, member A"	protein-coding	0.01	0.247525
Merged-chr1-46152626-1	chr1	46152576	46152676	+	2	cIP2vsInput	"intron (NM_001160386, intron 20 of 65)"	ETnERV2-int|LTR|ERVK	85888	NM_001160386	227058	Mm.296880	NM_001160386	ENSMUSG00000041144	Dnahc7b	Gm107	"dynein, axonemal, heavy chain 7B"	protein-coding	0	0.346535
Merged-chr12-65844750-1	chr12	65844700	65844800	+	2	cIP2vsInput	Intergenic	Intergenic	439651	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding	0.01	0.306931
Merged-chr7-40105197-1	chr7	40105147	40105247	+	2	cIP2vsInput	Intergenic	L1M4|LINE|L1	-569540	NR_045504	71029	Mm.399496	NR_045504		4933402C06Rik	-	RIKEN cDNA 4933402C06 gene	miscRNA	0	0.316832
Merged-chr4-38844691-1	chr4	38844641	38844741	+	2	cIP2vsInput	Intergenic	L1Md_F3|LINE|L1	-605602	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding	0	0.386139
Merged-chr9-35355708-1	chr9	35355658	35355758	+	2	cIP2vsInput	Intergenic	MER2|DNA|TcMar-Tigger	74603	NR_040715	71133	Mm.158577	NR_040715		4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	miscRNA	0	0.306931
Merged-chr5-54280739-1	chr5	54280689	54280789	+	2	cIP2vsInput	Intergenic	URR1B|DNA|hAT-Charlie	-69253	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0.01	0.356436
Merged-chr12-6913154-1	chr12	6913104	6913204	+	2	cIP2vsInput	Intergenic	Intergenic	467176	NR_045045	73575	Mm.179463	NR_045045		1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	miscRNA	0.01	0.346535
Merged-chr2-143260329-1	chr2	143260279	143260379	+	2	cIP2vsInput	Intergenic	Intergenic	181837	NM_020595	57329	Mm.157751	NM_020595	ENSMUSG00000027416	Otor	CDRAP|Fdp|MIA|MIAL	otoraplin	protein-coding	0	0.386139
Merged-chr8-37925693-1	chr8	37925643	37925743	+	2	cIP1vsInput	"intron (NM_145841, intron 2 of 7)"	"intron (NM_145841, intron 2 of 7)"	326509	NR_029884	723860		NR_029884		Mir383	Mirn383|mmu-mir-383	microRNA 383	miscRNA	0	0.326733
Merged-chr1-120073491-1	chr1	120073441	120073541	+	2	cIP2vsInput	"intron (NM_019432, intron 1 of 1)"	"intron (NM_019432, intron 1 of 1)"	289	NM_019432	170706	Mm.24750	NM_019432		Tmem37	AI173373|AW540203|Pr|Pr1	transmembrane protein 37	protein-coding	0.03	0.564356
Merged-chr1-131639904-1	chr1	131639854	131639954	+	2	cIP2vsInput	"intron (NM_007799, intron 1 of 9)"	Zaphod2|DNA|hAT-Tip100	1590	NM_007799	13034	Mm.230249	NM_007799	ENSMUSG00000004552	Ctse	A430072O03Rik|C920004C08Rik|CE|CatE	cathepsin E	protein-coding	0	0.306931
Merged-chr4-70649373-1	chr4	70649323	70649423	+	2	cIP2vsInput	Intergenic	Intergenic	-114445	NM_172694	230316	Mm.251188	NM_172694		Megf9	4933405H16Rik|9630025C07|Egfl5|mKIAA0818	multiple EGF-like-domains 9	protein-coding	0	0.326733
Merged-chr11-65852525-1	chr11	65852475	65852575	+	2	cIP1vsInput	"intron (NM_001099633, intron 63 of 68)"	"intron (NM_001099633, intron 63 of 68)"	45281	NM_026107	52712	Mm.340052	NM_026107	ENSMUSG00000018347	Zkscan6	1700128E15Rik|D11Ertd714e|KOX11|Zfp535|Znf18	zinc finger with KRAB and SCAN domains 6	protein-coding	0	0.425743
Merged-chr12-34134186-1	chr12	34134136	34134236	+	2	cIP2vsInput	"intron (NM_001271386, intron 24 of 27)"	"intron (NM_001271386, intron 24 of 27)"	176515	NM_011658	22160	Mm.3280	NM_011658	ENSMUSG00000035799	Twist1	AA960487|M-Twist|Pde|Ska10|Ska<m10Jus>|Twist|bHLHa38|pdt	twist basic helix-loop-helix transcription factor 1	protein-coding	0	0.29703
Merged-chr1-30700244-1	chr1	30700194	30700294	+	2	cIP2vsInput	Intergenic	Intergenic	163012	NM_001081080	213109	Mm.486727	NM_001081080	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding	0.01	0.247525
Merged-chr8-40064642-1	chr8	40064592	40064692	+	2	cIP1vsInput	"intron (NR_035426, intron 3 of 5)"	"intron (NR_035426, intron 3 of 5)"	163145	NR_035426	100316806		NR_035426		Mir669e	Mirn669e|mmu-mir-669e	microRNA 669e	miscRNA	0	0.237624
Merged-chr10-35873902-1	chr10	35873852	35873952	+	2	cIP2vsInput	Intergenic	Intergenic	-632905	NM_001253355	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0	0.316832
Merged-chr1-149037309-1	chr1	149037259	149037359	+	2	cIP2vsInput	Intergenic	Intergenic	923975	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0.01	0.287129
Merged-chr11-15674684-1	chr11	15674634	15674734	+	2	cIP2vsInput	Intergenic	Lx5b|LINE|L1	-583040	NM_145967	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	9330184N17Rik|BC027127|Vstm2	V-set and transmembrane domain containing 2A	protein-coding	0	0.405941
Merged-chr7-95438572-1	chr7	95438522	95438622	+	2	cIP2vsInput	Intergenic	Intergenic	-772065	NM_011858	23966	Mm.391678	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding	0	0.306931
Merged-chr12-113903886-1	chr12	113903836	113903936	+	2	cIP1vsInput	Intergenic	Lx|LINE|L1	359978	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding	0	0.326733
Merged-chr9-104998555-1	chr9	104998505	104998605	+	2	cIP2vsInput	"intron (NM_028719, intron 10 of 15)"	L1ME4c|LINE|L1	-54713	NM_053159	94062	Mm.29746	NM_053159	ENSMUSG00000032563	Mrpl3	2010320L16Rik|5930422H18Rik|AA407889	mitochondrial ribosomal protein L3	protein-coding	0	0.346535
Merged-chr6-122376563-1	chr6	122376513	122376613	+	2	cIP2vsInput	Intergenic	RMER6D|LTR|ERVK	-36336	NM_001271579	13619	Mm.6822	NM_001042623	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding	0	0.326733
Merged-chr11-56354257-1	chr11	56354207	56354307	+	2	cIP2vsInput	Intergenic	Intergenic	-313270	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding	0	0.376238
Merged-chr17-36188515-1	chr17	36188465	36188565	+	2	cIP2vsInput	"intron (NM_008208, intron 3 of 5)"	"intron (NM_008208, intron 3 of 5)"	1636	NM_008208	15043	Mm.426002	NM_001030310	ENSMUSG00000054128	H2-T3	H-2T3|H2-Tw3|TL	"histocompatibility 2, T region locus 3"	protein-coding	0.01	0.326733
Merged-chr18-62832294-1	chr18	62832244	62832344	+	2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-75947	NR_037693	78449	Mm.262195	NR_037693	ENSMUSG00000041789	2700046A07Rik	A330042I05Rik	RIKEN cDNA 2700046A07 gene	miscRNA	0.01	0.376238
Merged-chr6-55740552-1	chr6	55740502	55740602	+	2	cIP2vsInput	Intergenic	Tigger5|DNA|TcMar-Tigger	55981	NR_046071	100041339	Mm.403680	NR_046071		Gm3279	-	predicted gene 3279	miscRNA	0	0.326733
Merged-chr1-31495632-1	chr1	31495582	31495682	+	2	cIP2vsInput	Intergenic	Intergenic	230785	NR_015347	226957	Mm.25966	NR_015347		Gm4850	EG226957	THO complex 4 pseudogene	pseudo	0	0.356436
Merged-chr11-27303007-1	chr11	27302957	27303057	+	2	cIP2vsInput	Intergenic	Intergenic	517899	NR_002890	654472	Mm.347777	NR_002890	ENSMUSG00000069939	Gm12070	OTTMUSG00000005300	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0	0.366337
Merged-chr8-81550730-1	chr8	81550680	81550780	+	2	cIP2vsInput	Intergenic	Lx5b|LINE|L1	-164470	NM_001024617	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	"inositol polyphosphate-4-phosphatase, type II"	protein-coding	0	0.316832
Merged-chr6-75453493-1	chr6	75453443	75453543	+	2	cIP2vsInput	Intergenic	RMER6C|LTR|ERVK	-1789224	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0	0.366337
Merged-chr18-28154535-1	chr18	28154485	28154585	+	2	cIP2vsInput	Intergenic	Intergenic	-405629	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	miscRNA	0	0.366337
Merged-chr9-47998094-1	chr9	47998044	47998144	+	2	cIP1vsInput	Intergenic	Intergenic	-179886	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	miscRNA	0	0.326733
Merged-chr15-67594548-1	chr15	67594498	67594598	+	2	cIP2vsInput	Intergenic	Intergenic	367779	NR_045140	69334	Mm.63770	NR_045140		1700012I11Rik	-	RIKEN cDNA 1700012I11 gene	miscRNA	0	0.326733
Merged-chr10-106117175-1	chr10	106117125	106117225	+	2	cIP2vsInput	Intergenic	Intergenic	275696	NM_025602	52713	Mm.339224	NM_025602		Ccdc59	2300004H16Rik|D10Ertd718e	coiled-coil domain containing 59	protein-coding	0	0.267327
Merged-chr8-69388448-1	chr8	69388398	69388498	+	2	cIP2vsInput	"intron (NR_038043, intron 1 of 5)"	Lx5|LINE|L1	7096	NR_038044	378466	Mm.37846	NM_194351		Gm10033	9330175B10Rik|ENSMUSG00000057924|ENSMUSG00000071083|Gm10311	predicted gene 10033	miscRNA	0.01	0.425743
Merged-chr3-26343251-1	chr3	26343201	26343301	+	2	cIP2vsInput	Intergenic	MTEb|LTR|ERVL-MaLR	-11342	NM_138666	192167	Mm.316080	NM_001163387	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|mKIAA1070	neuroligin 1	protein-coding	0	0.405941
Merged-chr16-12503860-1	chr16	12503810	12503910	+	2	cIP1vsInput	Intergenic	Lx6|LINE|L1	-307530	NR_040507	75493	Mm.396146	NR_040507		1700003L19Rik	-	RIKEN cDNA 1700003L19 gene	miscRNA	0	0.366337
Merged-chr7-75158473-1	chr7	75158423	75158523	+	2	cIP2vsInput	"intron (NM_153579, intron 2 of 12)"	L1M2|LINE|L1	149913	NM_001109753	64176	Mm.273082	NM_001109753	ENSMUSG00000053025	Sv2b	A830038F04Rik|AI850768|mKIAA0735	synaptic vesicle glycoprotein 2 b	protein-coding	0	0.346535
Merged-chr4-147826795-1	chr4	147826745	147826845	+	2	cIP2vsInput	"exon (NM_198619, exon 4 of 4)"	"exon (NM_198619, exon 4 of 4)"	-4593	NR_033639	277692	Mm.474523	NR_033639	ENSMUSG00000080059	Rps19-ps3	BE292558|Gm13143|OTTMUSG00000010662|Rps19-ps	"ribosomal protein S19, pseudogene 3"	pseudo	0	0.336634
Merged-chr17-37776133-1	chr17	37776083	37776183	+	2	cIP2vsInput	Intergenic	Intergenic	7491	NM_146288	258285	Mm.419238	NM_146288	ENSMUSG00000083947	Olfr122	MOR263-10	olfactory receptor 122	protein-coding	0	0.277228
Merged-chr16-79441400-1	chr16	79441350	79441450	+	2	cIP2vsInput	Intergenic	Intergenic	-350303	NM_008941	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	"transmembrane protease, serine 15"	protein-coding	0.01	0.346535
Merged-chr6-130798754-1	chr6	130798704	130798804	+	2	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-411880	NM_016659	16627	Mm.333431	NM_016659	ENSMUSG00000079853	Klra1	A1|Klra22|Ly49a|Ly49o<129>|Ly49v	"killer cell lectin-like receptor, subfamily A, member 1"	protein-coding	0	0.306931
Merged-chr7-123663138-1	chr7	123663088	123663188	+	2	cIP2vsInput	Intergenic	Intergenic	-162689	NM_001081329	210162	Mm.135397	NM_001081329	ENSMUSG00000030757	Zkscan2	9430065N20Rik|AW493225|Zfp694	zinc finger with KRAB and SCAN domains 2	protein-coding	0.02	0.326733
Merged-chrX-118846433-1	chrX	118846383	118846483	+	2	cIP2vsInput	Intergenic	Intergenic	-365696	NM_001142750	100039551	Mm.423457	NM_001142750	ENSMUSG00000063242	Tgif2lx2	-	"TGFB-induced factor homeobox 2-like, X-linked 2"	protein-coding	0.01	0.316832
Merged-chr17-38675794-1	chr17	38675744	38675844	+	2	cIP1vsInput	Intergenic	MTC-int|LTR|ERVL-MaLR	36347	NM_001177586	100126768	Mm.471528	NM_001177586	ENSMUSG00000092342	Gm20516	Esp31	predicted gene 20516	protein-coding	0	0.326733
Merged-chr4-141248100-1	chr4	141248050	141248150	+	2	cIP2vsInput	"exon (NM_172520, exon 7 of 17)"	"exon (NM_172520, exon 7 of 17)"	5216	NM_172520	213649	Mm.134460	NM_172520	ENSMUSG00000028919	Arhgef19	6030432F23|6430573B13Rik|WGEF	Rho guanine nucleotide exchange factor (GEF) 19	protein-coding	0.09	0.712871
Merged-chr1-96732349-1	chr1	96732299	96732399	+	2	cIP2vsInput	Intergenic	RLTR40|LTR|ERVK	-69776	NR_040478	75159	Mm.243854	NR_040478		4930533P14Rik	-	RIKEN cDNA 4930533P14 gene	miscRNA	0	0.247525
Merged-chr5-79289672-1	chr5	79289622	79289722	+	2	cIP2vsInput	"intron (NR_035474, intron 2 of 4)"	"intron (NR_035474, intron 2 of 4)"	226232	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0.01	0.277228
Merged-chr12-97907072-1	chr12	97907022	97907122	+	2	cIP2vsInput	Intergenic	Intergenic	352265	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding	0.01	0.405941
Merged-chr3-136314807-1	chr3	136314757	136314857	+	2	cIP2vsInput	"intron (NM_001033350, intron 1 of 16)"	"intron (NM_001033350, intron 1 of 16)"	11239	NM_001033350	242248	Mm.30832	NM_001033350	ENSMUSG00000037922	Bank1	A530094C12Rik|AI451642|AVIEF|BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0	0.39604
Merged-chr2-18561478-1	chr2	18561428	18561528	+	2	cIP2vsInput	Intergenic	L1VL2|LINE|L1	-110984	NM_147778	12238	Mm.249586	NM_147778	ENSMUSG00000051154	Commd3	AW550818|Bup|D2Ertd542e	COMM domain containing 3	protein-coding	0	0.29703
Merged-chr17-61940705-1	chr17	61940655	61940755	+	2	cIP2vsInput	Intergenic	L1MD|LINE|L1	622953	NR_030569	100124495		NR_030569		Mir466g	Mirn466g	microRNA 466g	miscRNA	0.01	0.316832
Merged-chr17-20522250-1	chr17	20522200	20522300	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	19951	NM_134194	171228	Mm.377186	NM_134194	ENSMUSG00000043537	Vmn1r225	V1re5	vomeronasal 1 receptor 225	protein-coding	0	0.316832
Merged-chr6-32319132-1	chr6	32319082	32319182	+	2	cIP2vsInput	"intron (NM_175750, intron 3 of 31)"	MTC|LTR|ERVL-MaLR	-192009	NR_040277	319849	Mm.440860	NR_040277	ENSMUSG00000086763	B230378P21Rik	-	RIKEN cDNA B230378P21 gene	miscRNA	0	0.49505
Merged-chr5-49382843-1	chr5	49382793	49382893	+	2	cIP2vsInput	Intergenic	MER90|LTR|ERV1	-97184	NM_001199244	80334	Mm.160172	NM_001199242	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding	0	0.336634
Merged-chr3-7556581-1	chr3	7556531	7556631	+	2	cIP2vsInput	Intergenic	Lx|LINE|L1	53155	NM_173181	67306	Mm.332366	NM_173181	ENSMUSG00000043542	Zc2hc1a	3110050N22Rik|AI790358|AU023959|Fam164a	"zinc finger, C2HC-type containing 1A"	protein-coding	0.01	0.366337
Merged-chrY-6399349-1	chrY	6399299	6399399	+	2	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	768428	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.39604
Merged-chr9-81673479-1	chr9	81673429	81673529	+	2	cIP1vsInput	Intergenic	L1MA6|LINE|L1	-40927	NM_010482	15551	Mm.445308	NM_010482	ENSMUSG00000049511	Htr1b	-	5-hydroxytryptamine (serotonin) receptor 1B	protein-coding	0	0.336634
Merged-chr10-101604197-1	chr10	101604147	101604247	+	2	cIP2vsInput	Intergenic	Intergenic	-77290	NM_001205098	67569	Mm.403713	NM_001162368	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"	protein-coding	0	0.316832
Merged-chr2-99754962-1	chr2	99754912	99755012	+	2	cIP2vsInput	Intergenic	Intergenic	-1869786	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding	0	0.326733
Merged-chr12-39627299-1	chr12	39627249	39627349	+	2	cIP2vsInput	Intergenic	Intergenic	410077	NM_007487	11861	Mm.12723	NM_001039515	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding	0	0.346535
Merged-chr18-14406267-1	chr18	14406217	14406317	+	2	cIP2vsInput	Intergenic	Intergenic	173961	NR_045373	74529	Mm.400519	NR_045373		8430422H06Rik	-	RIKEN cDNA 8430422H06 gene	miscRNA	0	0.306931
Merged-chr8-53729788-1	chr8	53729738	53729838	+	2	cIP2vsInput	Intergenic	Intergenic	-90723	NM_146208	234258	Mm.281749	NM_146208	ENSMUSG00000039396	Neil3	AI449477|BC034753|C85903	nei like 3 (E. coli)	protein-coding	0.01	0.356436
Merged-chr3-77570092-1	chr3	77570042	77570142	+	2	cIP2vsInput	Intergenic	Intergenic	1494509	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0.01	0.366337
Merged-chr12-38480812-1	chr12	38480762	38480862	+	2	cIP2vsInput	"intron (NM_178681, intron 22 of 24)"	ORR1G|LTR|ERVL-MaLR	133709	NR_045943	73867	Mm.78933	NR_045943		4930428E07Rik	-	RIKEN cDNA 4930428E07 gene	miscRNA	0	0.366337
Merged-chr13-119025336-1	chr13	119025286	119025386	+	2	cIP1vsInput	Intergenic	Intergenic	310637	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding	0	0.316832
Merged-chrY-10354984-1	chrY	10354934	10355034	+	2	cIP2vsInput	Intergenic	RLTR6-int|LTR|ERV1	842864	NM_001199331	100040022	Mm.485767	NM_001199331	ENSMUSG00000095172	Gm20822	-	"predicted gene, 20822"	protein-coding	0	0.366337
Merged-chr5-21710957-1	chr5	21710907	21711007	+	2	cIP2vsInput	Intergenic	Intergenic	-9612	NM_178728	242864	Mm.153292	NM_178728	ENSMUSG00000044968	Napepld	A530089G06|Mbldc1|NAPE-PLD	N-acyl phosphatidylethanolamine phospholipase D	protein-coding	0	0.29703
Merged-chr13-100916851-1	chr13	100916801	100916901	+	2	cIP2vsInput	Intergenic	Intergenic	-83424	NM_022885	69048	Mm.402215	NM_022885	ENSMUSG00000021629	Slc30a5	1810010K08Rik|AF233321|ZNT5|ZTL1|ZnT-5|Zntl1	"solute carrier family 30 (zinc transporter), member 5"	protein-coding	0	0.356436
Merged-chr10-100754649-1	chr10	100754599	100754699	+	2	cIP2vsInput	Intergenic	Intergenic	162263	NM_001081246	66605	Mm.72646	NM_001081246	ENSMUSG00000056912	1700017N19Rik	-	RIKEN cDNA 1700017N19 gene	protein-coding	0.01	0.326733
Merged-chr3-24957249-1	chr3	24957199	24957299	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	1196058	NM_001163387	192167	Mm.316080	NM_001163387	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|mKIAA1070	neuroligin 1	protein-coding	0	0.29703
Merged-chr13-92080835-1	chr13	92080785	92080885	+	2	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	-92793	NM_009027	19418	Mm.248630	NM_009027		Rasgrf2	6330417G04Rik|AW048350|Grf2|Ras-GRF2	RAS protein-specific guanine nucleotide-releasing factor 2	protein-coding	0	0.366337
Merged-chr18-40668369-1	chr18	40668319	40668419	+	2	cIP2vsInput	Intergenic	Intergenic	410008	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding	0.01	0.356436
Merged-chr2-92801727-1	chr2	92801677	92801777	+	2	cIP2vsInput	Intergenic	Intergenic	-113374	NM_030725	80976	Mm.33490	NM_030725	ENSMUSG00000027220	Syt13	5730409J20Rik|AI549909|mKIAA1427	synaptotagmin XIII	protein-coding	0	0.336634
Merged-chr10-45735761-1	chr10	45735711	45735811	+	2	cIP1vsInput	Intergenic	Lx6|LINE|L1	-71943	NR_040624	320363	Mm.123343	NR_040624		D030045P18Rik	-	RIKEN cDNA D030045P18 gene	miscRNA	0	0.336634
Merged-chr14-97361226-1	chr14	97361176	97361276	+	2	cIP1vsInput	Intergenic	Lx8|LINE|L1	808317	NM_001038610	13134	Mm.320593	NM_001038610	ENSMUSG00000055639	Dach1	AI182278|Dac|Dach|E130112M23Rik	dachshund 1 (Drosophila)	protein-coding	0	0.376238
Merged-chr3-132961895-1	chr3	132961845	132961945	+	2	cIP2vsInput	Intergenic	Intergenic	-11604	NM_033525	114249	Mm.279310	NM_001029836	ENSMUSG00000040998	Npnt	1110009H02Rik|AA682063|AI314031|Nctn|POEM	nephronectin	protein-coding	0	0.326733
Merged-chr14-30888478-1	chr14	30888428	30888528	+	2	cIP1vsInput	"intron (NM_018746, intron 2 of 22)"	"intron (NM_018746, intron 2 of 22)"	1986	NM_018746	16427	Mm.34819	NM_001159299	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4	"inter alpha-trypsin inhibitor, heavy chain 4"	protein-coding	0.02	0.524752
Merged-chr1-149491543-1	chr1	149491493	149491593	+	2	cIP2vsInput	Intergenic	Lx8|LINE|L1	469741	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2alpha	"phospholipase A2, group IVA (cytosolic, calcium-dependent)"	protein-coding	0.01	0.376238
Merged-chr7-87150242-1	chr7	87150192	87150292	+	2	cIP2vsInput	Intergenic	Intergenic	-96553	NM_015760	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding	0.01	0.29703
Merged-chr6-141788592-1	chr6	141788542	141788642	+	2	cIP2vsInput	Intergenic	Intergenic	67579	NM_030687	28250	Mm.255586	NM_030687	ENSMUSG00000030237	Slco1a4	AI785519|Oatp1a4|Oatp2|Slc21a5	"solute carrier organic anion transporter family, member 1a4"	protein-coding	0	0.346535
Merged-chr15-20392702-1	chr15	20392652	20392752	+	2	cIP2vsInput	Intergenic	Intergenic	274048	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding	0.01	0.366337
Merged-chr3-61668929-1	chr3	61668879	61668979	+	2	cIP1vsInput	Intergenic	Intergenic	304422	NM_028712	74012	Mm.477648	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	"RAP2B, member of RAS oncogene family"	protein-coding	0	0.316832
Merged-chr15-57635972-1	chr15	57635922	57636022	+	2	cIP2vsInput	Intergenic	L1ME1|LINE|L1	-58695	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding	0.01	0.356436
Merged-chr12-47300619-1	chr12	47300569	47300669	+	2	cIP2vsInput	Intergenic	Lx6|LINE|L1	-481844	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding	0	0.326733
Merged-chr5-8547529-1	chr5	8547479	8547579	+	2	cIP2vsInput	"intron (NM_198620, intron 6 of 9)"	"intron (NM_198620, intron 6 of 9)"	75423	NM_198620	242819	Mm.332192	NM_198620	ENSMUSG00000040570	Rundc3b	Gm440	RUN domain containing 3B	protein-coding	0.01	0.277228
Merged-chr15-91610026-1	chr15	91609976	91610076	+	2	cIP1vsInput	Intergenic	Intergenic	-36765	NM_001033633	239606	Mm.360596	NM_001033633	ENSMUSG00000036298	Slc2a13	6530403A04|A630029G22Rik|AI505012|Gm308	"solute carrier family 2 (facilitated glucose transporter), member 13"	protein-coding	0.01	0.306931
Merged-chr6-75959478-1	chr6	75959428	75959528	+	2	cIP2vsInput	Intergenic	Intergenic	-1283239	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0.02	0.376238
Merged-chr12-37961192-1	chr12	37961142	37961242	+	2	cIP1vsInput	"intron (NM_178681, intron 1 of 24)"	"intron (NM_178681, intron 1 of 24)"	80487	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	"diacylglycerol kinase, beta"	protein-coding	0.01	0.336634
Merged-chr11-14924959-1	chr11	14924909	14925009	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	325719	NM_001164166	432536	Mm.33646	NR_002893		Pom121l12	1700054H16Rik	POM121 membrane glycoprotein-like 12	protein-coding	0	0.405941
Merged-chr3-78331586-1	chr3	78331536	78331636	+	2	cIP2vsInput	Intergenic	Lx8b|LINE|L1	814289	NM_001099624	76089	Mm.462396	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding	0	0.415842
Merged-chr13-65341633-1	chr13	65341583	65341683	+	2	cIP1vsInput	Intergenic	MurSatRep1|Unknown|Unknown	62779	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding	0	0.277228
Merged-chr14-50080044-1	chr14	50079994	50080094	+	2	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	4635	NM_146316	258313	Mm.463727	NM_146316	ENSMUSG00000060523	Olfr726	MOR246-4	olfactory receptor 726	protein-coding	0	0.346535
Merged-chr14-14576157-1	chr14	14576107	14576207	+	2	cIP2vsInput	Intergenic	MLTR18B_MM|LTR|ERVK	-126868	NM_001033270	218756	Mm.258893	NM_001033270	ENSMUSG00000021733	Slc4a7	C330023F04|E430014N10Rik|NBC3|NBCn1|NBCn1-G	"solute carrier family 4, sodium bicarbonate cotransporter, member 7"	protein-coding	0	0.356436
Merged-chr17-80358307-1	chr17	80358257	80358357	+	2	cIP1vsInput	"intron (NM_001145452, intron 8 of 17)"	RLTR17D_Mm|LTR|ERVK	15235	NR_028385	791338	Mm.204722	NR_028385		Gm10190	ENSMUSG00000066938	predicted gene 10190	miscRNA	0.02	0.316832
Merged-chr12-49614769-1	chr12	49614719	49614819	+	2	cIP2vsInput	Intergenic	Intergenic	-133907	NR_045472	69054	Mm.417838	NR_045472		1810007C17Rik	-	RIKEN cDNA 1810007C17 gene	miscRNA	0	0.326733
Merged-chr9-95023088-1	chr9	95023038	95023138	+	2	cIP1vsInput	"intron (NM_177909, intron 11 of 15)"	"intron (NM_177909, intron 11 of 15)"	353196	NM_177909	331004	Mm.326125	NM_177909	ENSMUSG00000031129	Slc9a9	5730527A11Rik|9930105B05|AI854429|Nhe9	"solute carrier family 9 (sodium/hydrogen exchanger), member 9"	protein-coding	0	0.356436
Merged-chr9-115391086-1	chr9	115391036	115391136	+	2	cIP2vsInput	Intergenic	Intergenic	54925	NR_040730	73856	Mm.399156	NR_040730		4930428G15Rik	-	RIKEN cDNA 4930428G15 gene	miscRNA	0.01	0.574257
Merged-chr1-49545702-1	chr1	49545652	49545752	+	2	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	-1381821	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.356436
Merged-chrX-20921191-1	chrX	20921141	20921241	+	2	cIP2vsInput	promoter-TSS (NM_013680)	promoter-TSS (NM_013680)	-273	NM_013680	20964	Mm.439844	NM_001110780	ENSMUSG00000037217	Syn1	Syn-1	synapsin I	protein-coding	0.09	0.693069
Merged-chr10-47915537-1	chr10	47915487	47915587	+	2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	1180306	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	"proteasome (prosome, macropain) subunit, alpha type 6 pseudogene"	pseudo	0	0.346535
Merged-chr7-52518271-1	chr7	52518221	52518321	+	2	cIP2vsInput	Intergenic	Intergenic	-502555	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding	0	0.29703
Merged-chrX-75062701-1	chrX	75062651	75062751	+	2	cIP2vsInput	"intron (NM_181584, intron 1 of 9)"	"intron (NM_181584, intron 1 of 9)"	22204	NM_181584	210710	Mm.267056	NM_181584	ENSMUSG00000032750	Gab3	5930433H21Rik	growth factor receptor bound protein 2-associated protein 3	protein-coding	0	0.316832
Merged-chr15-94407181-1	chr15	94407131	94407231	+	2	cIP2vsInput	Intergenic	Intergenic	-2831	NM_001164786	223838	Mm.214132	NM_001164785	ENSMUSG00000022449	Adamts20	Adamst20|bt	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 20"	protein-coding	0	0.346535
Merged-chr14-91182202-1	chr14	91182152	91182252	+	2	cIP1vsInput	Intergenic	L1M4|LINE|L1	1055311	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0	0.316832
Merged-chr2-82730321-1	chr2	82730271	82730371	+	2	cIP2vsInput	Intergenic	Intergenic	676663	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0	0.277228
Merged-chr5-116485816-1	chr5	116485766	116485866	+	2	cIP2vsInput	"intron (NM_026886, intron 1 of 12)"	"intron (NM_026886, intron 1 of 12)"	47094	NR_015595	76798	Mm.444322	NR_015595	ENSMUSG00000086219	2410137F16Rik	-	RIKEN cDNA 2410137F16 gene	miscRNA	0.02	0.50495
Merged-chr14-65556539-1	chr14	65556489	65556589	+	2	cIP2vsInput	"intron (NR_045599, intron 10 of 14)"	"intron (NR_045599, intron 10 of 14)"	36573	NM_001253812	74195	Mm.474894	NM_001253812	ENSMUSG00000022031	Elp3	2610507P14Rik|KAT9	elongator acetyltransferase complex subunit 3	protein-coding	0.02	0.356436
Merged-chr4-18353084-1	chr4	18353034	18353134	+	2	cIP2vsInput	Intergenic	ORR1D2|LTR|ERVL-MaLR	499602	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding	0.01	0.386139
Merged-chr18-41630283-1	chr18	41630233	41630333	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	320911	NM_029942	77619	Mm.30649	NM_029942	ENSMUSG00000056671	Prelid2	1700003A01Rik|C330008K14Rik	PRELI domain containing 2	protein-coding	0	0.316832
Merged-chr2-16901534-1	chr2	16901484	16901584	+	2	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	112192	NR_040632	75069	Mm.399263	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	miscRNA	0.01	0.346535
Merged-chr5-109477863-1	chr5	109477813	109477913	+	2	cIP2vsInput	Intergenic	MurSatRep1|Unknown|Unknown	57850	NM_001104628	384221	Mm.469879	NM_001104628	ENSMUSG00000091879	Vmn2r17	EG384221	"vomeronasal 2, receptor 17"	protein-coding	0	0.356436
Merged-chr1-38856812-1	chr1	38856762	38856862	+	2	cIP2vsInput	Intergenic	Intergenic	-35597	NM_001029878	381338	Mm.487137	NM_001029878	ENSMUSG00000048814	Lonrf2	2900060P06Rik|AI851349	LON peptidase N-terminal domain and ring finger 2	protein-coding	0	0.237624
Merged-chrX-62431811-1	chrX	62431761	62431861	+	2	cIP2vsInput	Intergenic	Intergenic	84258	NR_045443	75545	Mm.391270	NR_045442	ENSMUSG00000085757	1700019B21Rik	-	RIKEN cDNA 1700019B21 gene	miscRNA	0.01	0.326733
Merged-chrX-7402683-1	chrX	7402633	7402733	+	2	cIP2vsInput	Intergenic	Lx8|LINE|L1	18364	NR_027925	68355	Mm.45111	NR_027924		2010204K13Rik	0610010M13Rik|Cip7	RIKEN cDNA 2010204K13 gene	miscRNA	0.01	0.287129
Merged-chr14-84217253-1	chr14	84217203	84217303	+	2	cIP1vsInput	Intergenic	Intergenic	-226310	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0.01	0.316832
Merged-chr1-33684469-1	chr1	33684419	33684519	+	2	cIP2vsInput	Intergenic	Intergenic	14645	NR_033199	67503	Mm.87069	NM_026204	ENSMUSG00000044744	1700001G17Rik	-	RIKEN cDNA 1700001G17 gene	miscRNA	0	0.376238
Merged-chr10-79310030-1	chr10	79309980	79310080	+	2	cIP2vsInput	Intergenic	Lx8|LINE|L1	-46561	NM_001101572	624845	Mm.469866	NM_001101572	ENSMUSG00000091468	Vmn2r82	EG624845	"vomeronasal 2, receptor 82"	protein-coding	0	0.405941
Merged-chr6-90063695-1	chr6	90063645	90063745	+	2	cIP2vsInput	Intergenic	Intergenic	9323	NM_011911	24112	Mm.89985	NM_011911	ENSMUSG00000095932	Vmn1r49	V1r5|V1rb2|VRi2	"vomeronasal 1, receptor 49"	protein-coding	0	0.326733
Merged-chr18-29605165-1	chr18	29605115	29605215	+	2	cIP2vsInput	Intergenic	Intergenic	-108749	NR_045391	78058	Mm.416952	NR_045391		4930578E11Rik	-	RIKEN cDNA 4930578E11 gene	miscRNA	0	0.376238
Merged-chr4-137844811-1	chr4	137844761	137844861	+	2	cIP1vsInput	Intergenic	Intergenic	-17426	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding	0.01	0.49505
Merged-chr9-48362334-2	chr9	48362281	48362387	+	2	cIP1vsInput|cIP2vsInput	"intron (NM_172921, intron 1 of 8)"	"intron (NM_172921, intron 1 of 8)"	293	NM_172921	244853	Mm.489737	NM_172921	ENSMUSG00000044229	Nxpe4	C130036J11|D930028F11Rik|Fam55d	"neurexophilin and PC-esterase domain family, member 4"	protein-coding	0.018868	0.504673
Merged-chr1-95963430-1	chr1	95963380	95963480	+	2	cIP2vsInput	Intergenic	Intergenic	58328	NR_040467	73454	Mm.396229	NR_040467		1700063A18Rik	-	RIKEN cDNA 1700063A18 gene	miscRNA	0	0.29703
Merged-chr1-102486703-1	chr1	102486653	102486753	+	2	cIP2vsInput	Intergenic	Lx3A|LINE|L1	1330935	NR_037989	100504525	Mm.87065	NR_037989		Gm20268	-	"predicted gene, 20268"	miscRNA	0	0.336634
Merged-chr3-139403332-1	chr3	139403282	139403382	+	2	cIP2vsInput	"intron (NM_198659, intron 10 of 13)"	MT2B|LTR|ERVL	197439	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding	0.01	0.376238
Merged-chr1-105192432-1	chr1	105192382	105192482	+	2	cIP1vsInput	Intergenic	Intergenic	164278	NM_178779	320311	Mm.389162	NM_001160368	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding	0	0.336634
Merged-chr14-104783063-1	chr14	104783013	104783113	+	2	cIP1vsInput	"intron (NR_015593, intron 2 of 5)"	"intron (NR_015593, intron 2 of 5)"	143916	NR_015593	320249	Mm.490936	NR_015593		D130009I18Rik	-	RIKEN cDNA D130009I18 gene	miscRNA	0	0.39604
Merged-chr8-96415032-1	chr8	96414982	96415082	+	2	cIP1vsInput	Intergenic	Intergenic	130941	NR_039538	100628567		NR_039538		Mir28c	mmu-mir-28c	microRNA 28c	miscRNA	0	0.356436
Merged-chr2-146798714-1	chr2	146798664	146798764	+	2	cIP2vsInput	Intergenic	Lx4B|LINE|L1	-57175	NM_001033298	228730	Mm.292352	NM_001033298	ENSMUSG00000074749	Plk1s1	Gm114|Ncrna00153	polo-like kinase 1 substrate 1	protein-coding	0	0.366337
Merged-chr12-37948803-1	chr12	37948753	37948853	+	2	cIP2vsInput	"intron (NM_178681, intron 1 of 24)"	"intron (NM_178681, intron 1 of 24)"	68098	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	"diacylglycerol kinase, beta"	protein-coding	0	0.29703
Merged-chr8-39984492-1	chr8	39984442	39984542	+	2	cIP1vsInput	"intron (NR_035426, intron 3 of 5)"	"intron (NR_035426, intron 3 of 5)"	243295	NR_035426	100316806		NR_035426		Mir669e	Mirn669e|mmu-mir-669e	microRNA 669e	miscRNA	0.01	0.277228
Merged-chr2-109495993-1	chr2	109495943	109496043	+	2	cIP2vsInput	Intergenic	MIRb|SINE|MIR	-178707	NM_007540	12064	Mm.1442	NM_001048139	ENSMUSG00000048482	Bdnf	-	brain derived neurotrophic factor	protein-coding	0	0.346535
Merged-chr16-98077252-1	chr16	98077202	98077302	+	2	cIP2vsInput	"intron (NR_015491, intron 1 of 4)"	"intron (NR_015491, intron 1 of 4)"	5187	NR_015491	320586	Mm.442230	NR_015491		A630089N07Rik	-	RIKEN cDNA A630089N07 gene	miscRNA	0.01	0.356436
Merged-chr16-20979728-1	chr16	20979678	20979778	+	2	cIP2vsInput	Intergenic	ETnERV2-int|LTR|ERVK	174216	NM_025634	66561	Mm.422867	NM_025634		2310042E22Rik	-	RIKEN cDNA 2310042E22 gene	protein-coding	0	0.376238
Merged-chr1-108741651-1	chr1	108741601	108741701	+	2	cIP1vsInput	Intergenic	Intergenic	824392	NR_102307	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0	0.346535
Merged-chr13-21684721-1	chr13	21684671	21684771	+	2	cIP2vsInput	Intergenic	Intergenic	-9741	NM_146543	258536	Mm.223076	NM_146543	ENSMUSG00000094398	Olfr1360	MOR256-10|MOR256-35	olfactory receptor 1360	protein-coding	0.01	0.316832
Merged-chr1-146026491-1	chr1	146026441	146026541	+	2	cIP1vsInput	Intergenic	Intergenic	-469175	NM_153539	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.247525
Merged-chr6-43588949-1	chr6	43588899	43588999	+	2	cIP2vsInput	"intron (NM_013861, intron 3 of 8)"	"intron (NM_013861, intron 3 of 8)"	77226	NM_013861	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding	0	0.39604
Merged-chrX-45225156-1	chrX	45225106	45225206	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	134252	NM_026841	68800	Mm.336041	NM_026841	ENSMUSG00000037086	1110059M19Rik	-	RIKEN cDNA 1110059M19 gene	protein-coding	0	0.306931
Merged-chr2-177841227-1	chr2	177841177	177841277	+	2	cIP1vsInput	promoter-TSS (NM_001024849)	promoter-TSS (NM_001024849)	-909	NM_001024849	329575	Mm.425123	NM_001024849		Gm14325	OTTMUSG00000016325	predicted gene 14325	protein-coding	0	0.316832
Merged-chr15-70346631-1	chr15	70346581	70346681	+	2	cIP2vsInput	Intergenic	Intergenic	422398	NR_045071	100503580	Mm.404646	NR_045071		Gm19782	-	"predicted gene, 19782"	miscRNA	0	0.326733
Merged-chr16-19893623-1	chr16	19893573	19893673	+	2	cIP2vsInput	Intergenic	Intergenic	-9349	NR_015488	68162	Mm.35159	NR_015488		A930003A15Rik	AI853191	RIKEN cDNA A930003A15 gene	miscRNA	0	0.356436
Merged-chr1-32975163-1	chr1	32975113	32975213	+	2	cIP1vsInput	Intergenic	Intergenic	-427870	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding	0	0.356436
Merged-chr11-15592605-1	chr11	15592555	15592655	+	2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-665119	NM_145967	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	9330184N17Rik|BC027127|Vstm2	V-set and transmembrane domain containing 2A	protein-coding	0	0.386139
Merged-chr4-115137990-1	chr4	115137940	115138040	+	2	cIP2vsInput	Intergenic	Intergenic	-4013	NM_001003947	81906	Mm.215544	NM_001003947	ENSMUSG00000047155	Cyp4x1	A230025G20|CYPIVX1|CYP_a|Cyp4a28-ps	"cytochrome P450, family 4, subfamily x, polypeptide 1"	protein-coding	0.01	0.316832
Merged-chrX-116275034-1	chrX	116274984	116275084	+	2	cIP2vsInput	Intergenic	Intergenic	-173910	NM_001033471	382239	Mm.336224	NM_001033471	ENSMUSG00000072995	Cpxcr1	Gm1143	"CPX chromosome region, candidate 1"	protein-coding	0	0.306931
Merged-chr6-147197391-1	chr6	147197341	147197441	+	2	cIP2vsInput	"intron (NR_033640, intron 2 of 2)"	MTD|LTR|ERVL-MaLR	17150	NR_033640	100039641	Mm.170402	NR_033640	ENSMUSG00000085600	E330012B07Rik	Gm15768|OTTMUSG00000026071	RIKEN cDNA E330012B07 gene	miscRNA	0	0.376238
Merged-chr8-42848190-1	chr8	42848140	42848240	+	2	cIP2vsInput	Intergenic	Intergenic	293296	NM_177742	244448	Mm.64542	NM_177742	ENSMUSG00000031651	Triml1	4933403D14|BC050188	tripartite motif family-like 1	protein-coding	0.01	0.336634
Merged-chr4-83929355-1	chr4	83929305	83929405	+	2	cIP2vsInput	Intergenic	ID_B1|SINE|B4	403810	NM_001081012	320226	Mm.180032	NM_001081012	ENSMUSG00000052407	Ccdc171	4930418J05Rik|4930473A06Rik|A330015D16Rik	coiled-coil domain containing 171	protein-coding	0.01	0.39604
Merged-chr15-5692701-1	chr15	5692651	5692751	+	2	cIP2vsInput	Intergenic	Lx7|LINE|L1	196383	NR_045274	71432	Mm.291087	NR_045274		5430437J10Rik	-	RIKEN cDNA 5430437J10 gene	miscRNA	0	0.336634
Merged-chr3-82795145-1	chr3	82795095	82795195	+	2	cIP2vsInput	Intergenic	Intergenic	81338	NM_001277170	633285	Mm.265114	NM_001146328	ENSMUSG00000033882	Rbm46	EG633285|ENSMUSG00000033882|Gm761	RNA binding motif protein 46	protein-coding	0	0.267327
Merged-chr16-37800728-1	chr16	37800678	37800778	+	2	cIP2vsInput	"intron (NM_008047, intron 2 of 10)"	"intron (NM_008047, intron 2 of 10)"	23673	NM_008047	14314	Mm.182434	NM_008047	ENSMUSG00000022816	Fstl1	AI316791|AW107808|Fstl|TSC-36	follistatin-like 1	protein-coding	0	0.316832
Merged-chr12-34982301-1	chr12	34982251	34982351	+	2	cIP2vsInput	Intergenic	Intergenic	-2460	NM_029294	75456	Mm.79179	NM_029294	ENSMUSG00000092305	Prps1l1	1700011K15Rik	phosphoribosyl pyrophosphate synthetase 1-like 1	protein-coding	0	0.366337
Merged-chr9-89530246-1	chr9	89530196	89530296	+	2	cIP1vsInput	Intergenic	LTR33A_|LTR|ERVL	92740	NM_153509	209743	Mm.458520	NM_153509	ENSMUSG00000039313	AF529169	DD1|Kiaa1024	cDNA sequence AF529169	protein-coding	0	0.386139
Merged-chr1-86138200-1	chr1	86138150	86138250	+	2	cIP2vsInput	"intron (NM_027357, intron 24 of 24)"	RSINE1|SINE|B4	-16580	NM_030184	78795	Mm.379264	NM_027456	ENSMUSG00000062590	Armc9	3830422A13Rik|4831423D23Rik|4930438O05Rik|5730415N24Rik	armadillo repeat containing 9	protein-coding	0	0.415842
Merged-chr10-14811411-1	chr10	14811361	14811461	+	2	cIP2vsInput	Intergenic	RLTR12H|LTR|ERVK	51122	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding	0.01	0.386139
Merged-chr13-87245455-1	chr13	87245405	87245505	+	2	cIP2vsInput	Intergenic	Intergenic	-1198660	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0	0.316832
Merged-chr2-111049392-1	chr2	111049342	111049442	+	2	cIP2vsInput	Intergenic	Intergenic	-99148	NM_001128103	228432	Mm.483325	NM_001128103	ENSMUSG00000074968	Ano3	AI838058|B230324K02Rik|Tmem16c	anoctamin 3	protein-coding	0	0.316832
Merged-chr10-89787194-1	chr10	89787144	89787244	+	2	cIP2vsInput	"exon (NM_029166, exon 8 of 21)"	"exon (NM_029166, exon 8 of 21)"	42203	NM_029166	75089	Mm.446134	NM_029166	ENSMUSG00000019951	Uhrf1bp1l	2010319N22Rik|4930506D01Rik|AA589495|C80672|E030041M21Rik|mKIAA0701	UHRF1 (ICBP90) binding protein 1-like	protein-coding	0.01	0.465347
Merged-chr1-99027738-1	chr1	99027688	99027788	+	2	cIP2vsInput	Intergenic	MTE2b|LTR|ERVL-MaLR	606614	NM_027584	70866	Mm.389164	NM_001164233	ENSMUSG00000026336	Slco6d1	4921511I05Rik	"solute carrier organic anion transporter family, member 6d1"	protein-coding	0	0.326733
Merged-chr13-87709734-1	chr13	87709684	87709784	+	2	cIP2vsInput	Intergenic	Intergenic	-1111738	NM_010103	13612	Mm.125580	NM_001037987	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding	0.01	0.336634
Merged-chr3-77241128-1	chr3	77241078	77241178	+	2	cIP2vsInput	Intergenic	Lx6|LINE|L1	1165545	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.316832
Merged-chr1-168622196-1	chr1	168622146	168622246	+	2	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-189938	NM_008783	18514	Mm.440114	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|AI848790|AU015730|D230003C07Rik|Pbx-1|Pbx1a|Pbx1b	pre B cell leukemia homeobox 1	protein-coding	0	0.306931
Merged-chr4-71237517-1	chr4	71237467	71237567	+	2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-702589	NM_172694	230316	Mm.251188	NM_172694		Megf9	4933405H16Rik|9630025C07|Egfl5|mKIAA0818	multiple EGF-like-domains 9	protein-coding	0.01	0.356436
Merged-chr12-67708510-1	chr12	67708460	67708560	+	2	cIP2vsInput	Intergenic	Intergenic	-39239	NR_033146	100316870	Mm.379794	NR_033146		Gm17821	-	DDB1 and CUL4 associated factor 5 pseudogene	pseudo	0	0.306931
Merged-chr3-130501702-1	chr3	130501652	130501752	+	2	cIP2vsInput	"intron (NM_001244952, intron 12 of 35)"	"intron (NM_001244952, intron 12 of 35)"	-115746	NM_001163587	71760	Mm.29125	NM_001163587	ENSMUSG00000019232	Agxt2l1	1300019H02Rik|AI195447	alanine-glyoxylate aminotransferase 2-like 1	protein-coding	0	0.316832
Merged-chr14-82954022-1	chr14	82953972	82954072	+	2	cIP2vsInput	Intergenic	Intergenic	-1489541	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0	0.29703
Merged-chr9-10584241-1	chr9	10584191	10584291	+	2	cIP2vsInput	"intron (NM_001033359, intron 2 of 20)"	L1VL4|LINE|L1	320485	NM_001033359	244682	Mm.490683	NM_001033359	ENSMUSG00000039488	Cntn5	6720426O10Rik|A830025P08Rik|Gm507|NB-2	contactin 5	protein-coding	0.01	0.356436
Merged-chr1-28810067-1	chr1	28810017	28810117	+	2	cIP2vsInput	Intergenic	Intergenic	-29815	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0	0.356436
Merged-chr1-85110280-1	chr1	85110230	85110330	+	2	cIP1vsInput	promoter-TSS (NM_213615)	promoter-TSS (NM_213615)	-427	NM_213615	381287	Mm.487565	NM_213615	ENSMUSG00000089844	A530032D15Rik	Gm1888	RIKEN cDNA A530032D15Rik gene	protein-coding	0.01	0.50495
Merged-chr10-52567685-1	chr10	52567635	52567735	+	2	cIP2vsInput	Intergenic	MLT1D|LTR|ERVL-MaLR	-21946	NR_037920	22639	Mm.490597	NM_009540	ENSMUSG00000049576	Zfa-ps	Zfa|Zfx	"zinc finger protein, autosomal, pseudogene"	pseudo	0.02	0.435644
Merged-chr17-19820334-1	chr17	19820284	19820384	+	2	cIP2vsInput	Intergenic	Intergenic	46971	NM_001104565	627636	Mm.469855	NM_001104565	ENSMUSG00000091771	Vmn2r103	EG627636|Vmn103	"vomeronasal 2, receptor 103"	protein-coding	0	0.326733
Merged-chr19-61297124-1	chr19	61297074	61297174	+	2	cIP1vsInput	Intergenic	MMSAT4|Satellite|Satellite	-68706	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	"colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)"	protein-coding	0.01	0.326733
Merged-chr13-74456346-1	chr13	74456296	74456396	+	2	cIP2vsInput	Intergenic	Intergenic	37604	NM_146231	235956	Mm.296909	NM_146231		Zfp825	-	zinc finger protein 825	protein-coding	0	0.336634
Merged-chr1-191165325-1	chr1	191165275	191165375	+	2	cIP2vsInput	promoter-TSS (NM_001109759)	promoter-TSS (NM_001109759)	-508	NM_001109759	619288	Mm.61148	NM_001109759	ENSMUSG00000091017	Fam71a	4933417M04Rik|GARI-L4	"family with sequence similarity 71, member A"	protein-coding	0.01	0.326733
Merged-chr15-65240511-1	chr15	65240461	65240561	+	2	cIP2vsInput	Intergenic	Lx6|LINE|L1	-318215	NM_009623	11514	Mm.1425	NM_009623	ENSMUSG00000022376	Adcy8	AC8|AW060868	adenylate cyclase 8	protein-coding	0	0.316832
Merged-chr15-9532769-1	chr15	9532719	9532819	+	2	cIP2vsInput	Intergenic	MIR3|SINE|MIR	-2893	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding	0	0.376238
Merged-chr1-13957520-1	chr1	13957470	13957570	+	2	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-170591	NR_004447	433273	Mm.363045	NR_004447	ENSMUSG00000097711	Gm5523	EG433273	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0	0.326733
Merged-chr6-26942789-1	chr6	26942739	26942839	+	2	cIP2vsInput	Intergenic	Lx8b|LINE|L1	993961	NR_030420	735266		NR_030420		Mir592	Mirn592|mir-592|mmu-mir-592	microRNA 592	miscRNA	0.01	0.326733
Merged-chr12-65530784-1	chr12	65530734	65530834	+	2	cIP2vsInput	Intergenic	Intergenic	305267	NM_027614	70948	Mm.219475	NM_027614	ENSMUSG00000035560	Wdr20b	4921538B03Rik|4930427E19Rik|Wdr20	WD repeat domain 20b	protein-coding	0.01	0.39604
Merged-chr12-95084726-1	chr12	95084676	95084776	+	2	cIP2vsInput	Intergenic	Intergenic	-607500	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0.01	0.346535
Merged-chr1-174715352-2	chr1	174715263	174715442	+	2	cIP1vsInput|cIP2vsInput	"intron (NM_019445, intron 13 of 17)"	"intron (NM_019445, intron 13 of 17)"	206467	NM_011825	23893	Mm.25760	NM_011825	ENSMUSG00000050069	Grem2	Gremlin2|Prdc	"gremlin 2 homolog, cysteine knot superfamily (Xenopus laevis)"	protein-coding	0.005587	0.283333
Merged-chr10-47633933-1	chr10	47633883	47633983	+	2	cIP1vsInput	Intergenic	Intergenic	1389184	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0	0.346535
Merged-chr9-10708322-1	chr9	10708272	10708372	+	2	cIP2vsInput	"intron (NM_001033359, intron 1 of 20)"	"intron (NM_001033359, intron 1 of 20)"	196404	NM_001033359	244682	Mm.490683	NM_001033359	ENSMUSG00000039488	Cntn5	6720426O10Rik|A830025P08Rik|Gm507|NB-2	contactin 5	protein-coding	0	0.306931
Merged-chr11-48639179-1	chr11	48639129	48639229	+	2	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-161181	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Gnb2l1	AL033335|GB-like|Gnb2-rs1|Rack1|p205	"guanine nucleotide binding protein (G protein), beta polypeptide 2 like 1"	protein-coding	0	0.346535
Merged-chr1-47723321-1	chr1	47723271	47723371	+	2	cIP2vsInput	Intergenic	Intergenic	-869812	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.346535
Merged-chr1-99410716-2	chr1	99410647	99410786	+	2	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-362049	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding	0	0.278571
Merged-chr6-124794631-1	chr6	124794581	124794681	+	2	cIP2vsInput	Intergenic	MYSERV-int|LTR|ERVK	-14310	NM_013539	14794	Mm.261906	NM_013539	ENSMUSG00000038451	Spsb2	AI461677|C9|Grcc9|SSB2	splA/ryanodine receptor domain and SOCS box containing 2	protein-coding	0	0.29703
Merged-chr13-11337988-1	chr13	11337938	11338038	+	2	cIP1vsInput	Intergenic	Intergenic	-184064	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	"zona pellucida glycoprotein 4, pseudogene"	pseudo	0.01	0.287129
Merged-chr19-60260423-1	chr19	60260373	60260473	+	2	cIP2vsInput	Intergenic	Intergenic	-33726	NM_029648	76539	Mm.290183	NM_029648	ENSMUSG00000057858	D19Ertd737e	2310065H12Rik|2610015K05Rik|Fam204a	"DNA segment, Chr 19, ERATO Doi 737, expressed"	protein-coding	0	0.326733
Merged-chr3-102932677-1	chr3	102932627	102932727	+	2	cIP2vsInput	"exon (NM_011516, exon 6 of 33)"	"exon (NM_011516, exon 6 of 33)"	3423	NM_011516	20957	Mm.243849	NM_011516	ENSMUSG00000027855	Sycp1	SCP1	synaptonemal complex protein 1	protein-coding	0.01	0.366337
Merged-chr3-75850575-1	chr3	75850525	75850625	+	2	cIP2vsInput	Intergenic	Intergenic	106256	NM_175193	73124	Mm.249232	NM_175193	ENSMUSG00000034109	Golim4	3110027H23Rik|GIMPC|GPP130|Golph4|P138	golgi integral membrane protein 4	protein-coding	0	0.316832
Merged-chr11-96488774-1	chr11	96488724	96488824	+	2	cIP2vsInput	"intron (NM_001033186, intron 1 of 12)"	"intron (NM_001033186, intron 1 of 12)"	24183	NM_001177898	78473	Mm.446811	NM_001033186		Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding	0.01	0.366337
Merged-chr12-74818257-1	chr12	74818207	74818307	+	2	cIP2vsInput	Intergenic	Charlie7|DNA|hAT-Charlie	359075	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	"potassium voltage-gated channel, subfamily H (eag-related), member 5"	protein-coding	0.01	0.267327
Merged-chrX-120932307-1	chrX	120932257	120932357	+	2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	641980	NR_073451	245578	Mm.490224	NM_001271809		Pcdh11x	PCDHX|PCDHX11|Pcdh11	protocadherin 11 X-linked	protein-coding	0	0.346535
Merged-chr7-62744814-1	chr7	62744764	62744864	+	2	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	-280304	NM_013788	27412	Mm.422745	NM_013788	ENSMUSG00000070526	Peg12	Frat3	paternally expressed 12	protein-coding	0.01	0.346535
Merged-chr10-130127360-1	chr10	130127310	130127410	+	2	cIP2vsInput	promoter-TSS (NM_146674)	promoter-TSS (NM_146674)	-305	NM_146674	258669	Mm.377631	NM_146674	ENSMUSG00000095804	Olfr824	MOR210-3	olfactory receptor 824	protein-coding	0	0.306931
Merged-chr6-139715707-1	chr6	139715657	139715757	+	2	cIP2vsInput	promoter-TSS (NM_207683)	promoter-TSS (NM_207683)	-152	NM_207683	18705	Mm.391538	NM_207683	ENSMUSG00000030228	Pik3c2g	C80387|PI3K-C2-gamma	"phosphatidylinositol 3-kinase, C2 domain containing, gamma polypeptide"	protein-coding	0.01	0.356436
Merged-chr5-59985076-1	chr5	59985026	59985126	+	2	cIP2vsInput	"intron (NR_040682, intron 1 of 4)"	Lx10|LINE|L1	926	NR_040683	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0	0.356436
Merged-chr11-27293132-1	chr11	27293082	27293182	+	2	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	508024	NR_002890	654472	Mm.347777	NR_002890	ENSMUSG00000069939	Gm12070	OTTMUSG00000005300	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0	0.376238
Merged-chr1-55600523-1	chr1	55600473	55600573	+	2	cIP2vsInput	"intron (NM_001114663, intron 1 of 5)"	"intron (NM_001114663, intron 1 of 5)"	194577	NM_001114663	227120	Mm.194183	NM_001114663		Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding	0	0.386139
Merged-chr14-84573423-1	chr14	84573373	84573473	+	2	cIP2vsInput	Intergenic	Intergenic	-96999	NR_015539	319903	Mm.440481	NR_015539		9630013A20Rik	-	RIKEN cDNA 9630013A20 gene	miscRNA	0.01	0.386139
Merged-chr2-110866732-1	chr2	110866682	110866782	+	2	cIP2vsInput	"intron (NM_001128103, intron 3 of 26)"	"intron (NM_001128103, intron 3 of 26)"	83512	NM_001128103	228432	Mm.483325	NM_001128103	ENSMUSG00000074968	Ano3	AI838058|B230324K02Rik|Tmem16c	anoctamin 3	protein-coding	0.01	0.29703
Merged-chr14-111337865-1	chr14	111337815	111337915	+	2	cIP1vsInput	Intergenic	Intergenic	-337250	NM_198865	75409	Mm.417152	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	"SLIT and NTRK-like family, member 5"	protein-coding	0.02	0.277228
Merged-chr4-79949040-1	chr4	79948990	79949090	+	2	cIP2vsInput	Intergenic	Intergenic	-885190	NM_031202	22178	Mm.412291	NM_031202	ENSMUSG00000005994	Tyrp1	TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding	0	0.287129
Merged-chr10-36139628-1	chr10	36139578	36139678	+	2	cIP2vsInput	Intergenic	Intergenic	-367179	NM_001253355	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0	0.376238
Merged-chr4-19061023-1	chr4	19060973	19061073	+	2	cIP2vsInput	Intergenic	Lx3_Mus|LINE|L1	-219827	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding	0	0.316832
Merged-chr9-4225426-1	chr9	4225376	4225476	+	2	cIP2vsInput	Intergenic	Intergenic	84068	NM_026276	67618	Mm.33970	NM_026276	ENSMUSG00000025894	Aasdhppt	2010309J24Rik|2810407B07Rik|AASD-PPT|CGI-80|LYS2|LYS5	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	protein-coding	0	0.39604
Merged-chr19-34130056-1	chr19	34130006	34130106	+	2	cIP1vsInput	"intron (NM_024204, intron 2 of 5)"	"intron (NM_024204, intron 2 of 5)"	29113	NM_023903	78753	Mm.195937	NM_023903	ENSMUSG00000056078	Lipm	4632427C23Rik|AW227514|Lipl3	"lipase, family member M"	protein-coding	0	0.306931
Merged-chr16-56340339-1	chr16	56340289	56340389	+	2	cIP2vsInput	Intergenic	Intergenic	136026	NM_174876	224224	Mm.151998	NM_174876	ENSMUSG00000035270	Impg2	IPM200|PG10.2|Rsbp|Spacrcan	interphotoreceptor matrix proteoglycan 2	protein-coding	0	0.376238
Merged-chrX-129275437-1	chrX	129275387	129275487	+	2	cIP2vsInput	Intergenic	MIR|SINE|MIR	223913	NR_045441	75274	Mm.108718	NR_045441	ENSMUSG00000086244	4930558G05Rik	-	RIKEN cDNA 4930558G05 gene	miscRNA	0	0.316832
Merged-chrX-63987535-1	chrX	63987485	63987585	+	2	cIP2vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	164663	NM_001177377	627470	Mm.233605	NM_001177377	ENSMUSG00000079579	Gm6760	EG627470	predicted gene 6760	protein-coding	0	0.326733
Merged-chr3-23269866-1	chr3	23269816	23269916	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	1018496	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	miscRNA	0.01	0.326733
Merged-chrX-38765178-1	chrX	38765128	38765228	+	2	cIP2vsInput	Intergenic	Looper|DNA|PiggyBac	-7602	NM_183126	77883	Mm.113311	NM_183126	ENSMUSG00000051361	6030498E09Rik	-	RIKEN cDNA 6030498E09 gene	protein-coding	0	0.29703
Merged-chr5-84728702-1	chr5	84728652	84728752	+	2	cIP2vsInput	Intergenic	Intergenic	-311320	NM_007937	13839	Mm.438006	NM_007937		Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding	0	0.287129
Merged-chr9-5852045-1	chr9	5851995	5852095	+	2	cIP2vsInput	Intergenic	Lx2|LINE|L1	-316567	NM_027924	71785	Mm.390122	NM_027924	ENSMUSG00000032006	Pdgfd	1110003I09Rik	"platelet-derived growth factor, D polypeptide"	protein-coding	0	0.386139
Merged-chr14-39308665-1	chr14	39308615	39308715	+	2	cIP1vsInput	"intron (NM_001190187, intron 1 of 9)"	Lx3_Mus|LINE|L1	164423	NM_001190187	18183	Mm.258705	NM_001190187	ENSMUSG00000041014	Nrg3	ska	neuregulin 3	protein-coding	0.01	0.425743
Merged-chr8-99071746-1	chr8	99071696	99071796	+	2	cIP2vsInput	"intron (NM_001039154, intron 10 of 12)"	Lx6|LINE|L1	344711	NM_007667	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.277228
Merged-chr3-102884440-1	chr3	102884390	102884490	+	2	cIP1vsInput	"intron (NM_011516, intron 20 of 32)"	Lx3_Mus|LINE|L1	51660	NM_011516	20957	Mm.243849	NM_011516	ENSMUSG00000027855	Sycp1	SCP1	synaptonemal complex protein 1	protein-coding	0.01	0.376238
Merged-chr4-52859917-1	chr4	52859867	52859967	+	2	cIP2vsInput	Intergenic	Intergenic	-3406	NM_146824	258821	Mm.297704	NM_146824	ENSMUSG00000049648	Olfr273	MOR262-8	olfactory receptor 273	protein-coding	0.01	0.29703
Merged-chr17-20167454-1	chr17	20167404	20167504	+	2	cIP1vsInput	Intergenic	Intergenic	15643	NM_177316	321020	Mm.377882	NM_177316	ENSMUSG00000071275	Fpr-rs6	-	"formyl peptide receptor, related sequence 6"	protein-coding	0	0.277228
Merged-chrX-90268792-1	chrX	90268742	90268842	+	2	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-335940	NM_001033880	245511	Mm.391261	NR_003621	ENSMUSG00000035387	4930415L06Rik	Smek3p	RIKEN cDNA 4930415L06 gene	protein-coding	0	0.277228
Merged-chr10-46910007-1	chr10	46909957	46910057	+	2	cIP2vsInput	Intergenic	L1M2|LINE|L1	665258	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0.01	0.326733
Merged-chr7-136883945-1	chr7	136883895	136883995	+	2	cIP2vsInput	Intergenic	Intergenic	-10666	NM_008598	17314	Mm.440219	NM_008598	ENSMUSG00000054612	Mgmt	AGT|AI267024|Agat	O-6-methylguanine-DNA methyltransferase	protein-coding	0.01	0.356436
Merged-chr2-51892647-1	chr2	51892597	51892697	+	2	cIP2vsInput	Intergenic	Intergenic	41997	NM_001141982	71684	Mm.28309	NM_001141981	ENSMUSG00000036249	Rbm43	0610033I05Rik	RNA binding motif protein 43	protein-coding	0	0.346535
Merged-chr5-148587746-1	chr5	148587696	148587796	+	2	cIP2vsInput	Intergenic	MER2|DNA|TcMar-Tigger	-34958	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding	0	0.29703
Merged-chr15-46015559-1	chr15	46015509	46015609	+	2	cIP2vsInput	Intergenic	MMERVK9E_I-int|LTR|ERVK	-309026	NR_045509	71120	Mm.158571	NR_045509		1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	miscRNA	0.01	0.366337
Merged-chr1-47252388-1	chr1	47252338	47252438	+	2	cIP2vsInput	Intergenic	Lx6|LINE|L1	-398879	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.29703
Merged-chr17-23232153-1	chr17	23232103	23232203	+	2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-38925	NM_009555	22700	Mm.486936	NM_009555	ENSMUSG00000002617	Zfp40	CTfin12|Zfp-40	zinc finger protein 40	protein-coding	0	0.346535
Merged-chr18-13632401-1	chr18	13632351	13632451	+	2	cIP2vsInput	Intergenic	Intergenic	340332	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding	0	0.39604
Merged-chr5-30201782-1	chr5	30201732	30201832	+	2	cIP2vsInput	"intron (NM_001014394, intron 5 of 13)"	"intron (NM_001014394, intron 5 of 13)"	3940	NM_001014394	381628	Mm.291148	NM_001014394	ENSMUSG00000067642	Gpr113	Gm1041|Pgr23	G protein-coupled receptor 113	protein-coding	0.01	0.514851
Merged-chr5-60738416-1	chr5	60738366	60738466	+	2	cIP2vsInput	Intergenic	Intergenic	-752414	NR_040682	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0	0.287129
Merged-chr13-73646889-1	chr13	73646839	73646939	+	2	cIP2vsInput	"intron (NM_009354, intron 13 of 15)"	"intron (NM_009354, intron 13 of 15)"	19888	NM_009354	21752	Mm.10109	NM_009354	ENSMUSG00000021611	Tert	EST2|TCS1|TP2|TR|TRT	telomerase reverse transcriptase	protein-coding	0.03	0.613861
Merged-chr19-22414534-1	chr19	22414484	22414584	+	2	cIP2vsInput	"intron (NM_001035242, intron 1 of 24)"	"intron (NM_001035242, intron 1 of 24)"	-33674	NM_177341	226025	Mm.440339	NM_001035239	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	"transient receptor potential cation channel, subfamily M, member 3"	protein-coding	0	0.356436
Merged-chr8-71931916-1	chr8	71931866	71931966	+	2	cIP2vsInput	"intron (NM_133358, intron 3 of 3)"	"intron (NM_133358, intron 3 of 3)"	9091	NM_133358	170938	Mm.480419	NM_133358	ENSMUSG00000066880	Zfp617	Zfps11-6	zinc finger protein 617	protein-coding	0.01	0.306931
Merged-chr2-21411304-1	chr2	21411254	21411354	+	2	cIP2vsInput	"intron (NM_001004761, intron 2 of 10)"	"intron (NM_001004761, intron 2 of 10)"	43737	NM_001004761	241263	Mm.166647	NM_175706	ENSMUSG00000045967	Gpr158	5330427M13Rik|mKIAA1136	G protein-coupled receptor 158	protein-coding	0	0.356436
Merged-chr5-45406186-1	chr5	45406136	45406236	+	2	cIP1vsInput	Intergenic	MIRb|SINE|MIR	44043	NM_024236	110391	Mm.30204	NM_024236	ENSMUSG00000015806	Qdpr	2610008L04Rik|D5Ertd371e|Dhpr|PKU2	quinoid dihydropteridine reductase	protein-coding	0.01	0.445545
Merged-chr6-37545398-1	chr6	37545348	37545448	+	2	cIP1vsInput	"intron (NM_145364, intron 3 of 8)"	MLTR18C_MM|LTR|ERVK	15225	NM_145364	208665	Mm.262635	NM_145364	ENSMUSG00000038641	Akr1d1	-	"aldo-keto reductase family 1, member D1"	protein-coding	0	0.306931
Merged-chr4-29566635-1	chr4	29566585	29566685	+	2	cIP2vsInput	Intergenic	L2|LINE|L2	753490	NM_010141	13841	Mm.257266	NM_001122889	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding	0.01	0.346535
Merged-chr1-109108311-1	chr1	109108261	109108361	+	2	cIP1vsInput	Intergenic	Intergenic	-875426	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.39604
Merged-chr15-39277392-1	chr15	39277342	39277442	+	2	cIP2vsInput	"intron (NM_053271, intron 3 of 26)"	"intron (NM_053271, intron 3 of 26)"	79106	NM_053271	116838	Mm.309296	NM_001256382		Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding	0	0.306931
Merged-chr14-94451423-1	chr14	94451373	94451473	+	2	cIP2vsInput	Intergenic	Intergenic	-560754	NM_001271798	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.29703
Merged-chr2-109565079-1	chr2	109565029	109565129	+	2	cIP1vsInput	Intergenic	Intergenic	-109621	NM_007540	12064	Mm.1442	NM_001048139	ENSMUSG00000048482	Bdnf	-	brain derived neurotrophic factor	protein-coding	0	0.326733
Merged-chr10-79223555-1	chr10	79223505	79223605	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-24222	NM_175936	216144	Mm.246574	NM_175936	ENSMUSG00000055515	Vmn2r81	EC1-V2R|EC1-VR2|V2rf2	"vomeronasal 2, receptor 81"	protein-coding	0.01	0.29703
Merged-chr1-48471298-1	chr1	48471248	48471348	+	2	cIP1vsInput	Intergenic	MIR|SINE|MIR	-1617789	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.326733
Merged-chr2-100881424-1	chr2	100881374	100881474	+	2	cIP2vsInput	Intergenic	Intergenic	-743324	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding	0	0.39604
Merged-chr3-140171969-1	chr3	140171919	140172019	+	2	cIP2vsInput	Intergenic	Intergenic	966076	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding	0	0.316832
Merged-chr4-85456624-1	chr4	85456574	85456674	+	2	cIP1vsInput	Intergenic	Intergenic	251168	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding	0	0.445545
Merged-chr1-17199695-1	chr1	17199645	17199745	+	2	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	54322	NM_010267	14545	Mm.18218	NM_010267	ENSMUSG00000025777	Gdap1	-	ganglioside-induced differentiation-associated-protein 1	protein-coding	0	0.366337
Merged-chr14-51440767-1	chr14	51440717	51440817	+	2	cIP2vsInput	Intergenic	Intergenic	-11195	NM_009487	22301	Mm.482572	NM_009486	ENSMUSG00000070448	Vmn2r89	V2r10|V2r11	"vomeronasal 2, receptor 89"	protein-coding	0	0.267327
Merged-chr17-85633761-1	chr17	85633711	85633811	+	2	cIP2vsInput	Intergenic	(A)n|Simple_repeat|Simple_repeat	12927	NM_011381	20473	Mm.391586	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding	0.02	0.415842
Merged-chr16-65039941-1	chr16	65039891	65039991	+	2	cIP1vsInput	"intron (NM_008310, intron 2 of 2)"	"intron (NM_008310, intron 2 of 2)"	65843	NM_008310	15557	Mm.5040	NM_008310	ENSMUSG00000050783	Htr1f	Htr1eb	5-hydroxytryptamine (serotonin) receptor 1F	protein-coding	0.01	0.29703
Merged-chr9-4271752-1	chr9	4271702	4271802	+	2	cIP2vsInput	Intergenic	Intergenic	37742	NM_026276	67618	Mm.33970	NM_026276	ENSMUSG00000025894	Aasdhppt	2010309J24Rik|2810407B07Rik|AASD-PPT|CGI-80|LYS2|LYS5	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	protein-coding	0.01	0.306931
Merged-chr3-59068563-1	chr3	59068513	59068613	+	2	cIP2vsInput	"intron (NM_177855, intron 5 of 43)"	"intron (NM_177855, intron 5 of 43)"	33258	NM_173398	229323	Mm.123648	NM_173398	ENSMUSG00000050075	Gpr171	A630006E05|F730001G15Rik|H963	G protein-coupled receptor 171	protein-coding	0	0.336634
Merged-chr8-37062672-2	chr8	37062622	37062723	+	2	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	69097	NM_001039220	621080	Mm.373292	NM_001039220	ENSMUSG00000074384	AI429214	-	expressed sequence AI429214	protein-coding	0	0.343137
Merged-chr5-147380138-1	chr5	147380088	147380188	+	2	cIP2vsInput	"intron (NM_010229, intron 2 of 23)"	RLTR11A2|LTR|ERVK	20351	NM_010229	14255	Mm.194	NM_010229	ENSMUSG00000042817	Flt3	B230315G04|CD135|Flk-2|Flk2|Flt-3|Ly72|wmfl	FMS-like tyrosine kinase 3	protein-coding	0	0.366337
Merged-chr15-19282332-1	chr15	19282282	19282382	+	2	cIP2vsInput	Intergenic	Intergenic	462003	NM_009865	320873	Mm.446240	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding	0	0.336634
Merged-chr6-67979933-1	chr6	67979883	67979983	+	2	cIP2vsInput	Intergenic	ETnERV2-int|LTR|ERVK	-414234	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo	0	0.287129
Merged-chr7-24227523-1	chr7	24227473	24227573	+	2	cIP2vsInput	TTS (NM_020262)	TTS (NM_020262)	10075	NM_020262	56869	Mm.103751	NM_020262		Zfp109	-	zinc finger protein 109	protein-coding	0.01	0.316832
Merged-chr7-10637626-1	chr7	10637576	10637676	+	2	cIP2vsInput	Intergenic	Intergenic	4039	NM_134228	171262	Mm.222634	NM_134228	ENSMUSG00000045340	Vmn1r70	V1rd2|V1rl1	vomeronasal 1 receptor 70	protein-coding	0	0.336634
Merged-chr17-65142793-1	chr17	65142743	65142843	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	397989	NM_001008973	381107	Mm.141275	NM_001008973	ENSMUSG00000045036	Tmem232	E130009J12Rik|Gm940|Tes13-L|Tes13-S	transmembrane protein 232	protein-coding	0.01	0.356436
Merged-chr13-8009123-1	chr13	8009073	8009173	+	2	cIP1vsInput	Intergenic	Intergenic	-193786	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	"adenosine deaminase, RNA-specific, B2"	protein-coding	0	0.445545
Merged-chr7-62497840-1	chr7	62497790	62497890	+	2	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-33330	NM_013788	27412	Mm.422745	NM_013788	ENSMUSG00000070526	Peg12	Frat3	paternally expressed 12	protein-coding	0.02	0.366337
Merged-chr10-52534661-1	chr10	52534611	52534711	+	2	cIP2vsInput	Intergenic	Intergenic	11078	NR_037920	22639	Mm.490597	NM_009540	ENSMUSG00000049576	Zfa-ps	Zfa|Zfx	"zinc finger protein, autosomal, pseudogene"	pseudo	0.02	0.316832
Merged-chr17-71755398-1	chr17	71755348	71755448	+	2	cIP2vsInput	Intergenic	Intergenic	-2513	NM_146082	225004	Mm.134151	NM_146082	ENSMUSG00000044375	BC027072	-	cDNA sequence BC027072	protein-coding	0	0.326733
Merged-chr13-20964803-1	chr13	20964753	20964853	+	2	cIP2vsInput	"intron (NM_012054, intron 12 of 20)"	"intron (NM_012054, intron 12 of 20)"	108496	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding	0	0.257426
Merged-chr1-113409737-1	chr1	113409687	113409787	+	2	cIP2vsInput	Intergenic	Lx5|LINE|L1	-1544819	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik	dermatan sulfate epimerase-like	protein-coding	0.01	0.386139
Merged-chr6-139155611-1	chr6	139155561	139155661	+	2	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	166965	NR_045149	70962	Mm.410833	NR_045149		4922502N22Rik	-	RIKEN cDNA 4922502N22 gene	miscRNA	0.01	0.287129
Merged-chr11-91735543-1	chr11	91735493	91735593	+	2	cIP2vsInput	Intergenic	Intergenic	-157988	NM_028547	73470	Mm.67677	NM_028547	ENSMUSG00000046755	Kif2b	1700063D03Rik	kinesin family member 2B	protein-coding	0.01	0.267327
Merged-chr18-89789933-1	chr18	89789883	89789983	+	2	cIP2vsInput	Intergenic	RMER5|LTR|ERV1	-20797	NM_001039173	623279	Mm.447164	NM_001039173		Dok6	Dok-6	docking protein 6	protein-coding	0.01	0.336634
Merged-chr1-110343058-1	chr1	110343008	110343108	+	2	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	359321	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.316832
Merged-chr6-105845740-1	chr6	105845690	105845790	+	2	cIP2vsInput	"intron (NM_001109749, intron 2 of 25)"	"intron (NM_001109749, intron 2 of 25)"	167995	NM_173004	269784	Mm.321683	NM_001109749	ENSMUSG00000064293	Cntn4	9630050B05|Axcam|BIG-2	contactin 4	protein-coding	0	0.336634
Merged-chr19-50456622-1	chr19	50456572	50456672	+	2	cIP2vsInput	"intron (NM_001252501, intron 2 of 25)"	"intron (NM_001252501, intron 2 of 25)"	222024	NM_001252501	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0	0.316832
Merged-chr19-17409613-2	chr19	17409523	17409704	+	2	cIP1vsInput|cIP2vsInput	Intergenic	MER45A|DNA|hAT-Tip100	15570	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding	0.01105	0.461538
Merged-chr2-96708194-1	chr2	96708144	96708244	+	2	cIP2vsInput	Intergenic	Intergenic	-759480	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0.01	0.356436
Merged-chr11-104673072-1	chr11	104673022	104673122	+	2	cIP2vsInput	Intergenic	Intergenic	65072	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding	0.01	0.326733
Merged-chr11-20455150-1	chr11	20455100	20455200	+	2	cIP2vsInput	Intergenic	Intergenic	-88103	NM_021372	58172	Mm.339676	NM_001038625	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding	0.07	0.693069
Merged-chr14-6984197-1	chr14	6984147	6984247	+	2	cIP2vsInput	Intergenic	Intergenic	43252	NM_001164727	100038847	Mm.483675	NM_001164727	ENSMUSG00000093985	Gm10406	ENSMUSG00000072735	predicted gene 10406	protein-coding	0	0.267327
Merged-chr15-6693117-1	chr15	6693067	6693167	+	2	cIP2vsInput	Intergenic	L1ME1|LINE|L1	-15264	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	"RPTOR independent companion of MTOR, complex 2"	protein-coding	0.01	0.346535
Merged-chrX-156648277-1	chrX	156648227	156648327	+	2	cIP1vsInput	Intergenic	Intergenic	108794	NR_033598	74941	Mm.484588	NR_033598		4930503H13Rik	-	gem (nuclear organelle) associated protein 8 pseudogene	pseudo	0.01	0.287129
Merged-chr2-67161636-1	chr2	67161586	67161686	+	2	cIP2vsInput	Intergenic	Intergenic	-12198	NM_001033477	383709	Mm.244520	NM_001033477		Gm1322	-	predicted gene 1322	protein-coding	0	0.29703
Merged-chr11-31341870-1	chr11	31341820	31341920	+	2	cIP1vsInput	Intergenic	L1M2|LINE|L1	28191	NM_011491	20856	Mm.32506	NM_011491		Stc2	AW125853|Stc2l|mustc2	stanniocalcin 2	protein-coding	0	0.336634
Merged-chr6-14476088-1	chr6	14476038	14476138	+	2	cIP2vsInput	Intergenic	Intergenic	279186	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	"protein phosphatase 1, regulatory (inhibitor) subunit 3A"	protein-coding	0.01	0.306931
Merged-chr3-59458754-1	chr3	59458704	59458804	+	2	cIP2vsInput	Intergenic	Intergenic	-114498	NM_001162884	242050	Mm.444186	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	"immunoglobulin superfamily, member 10"	protein-coding	0	0.336634
Merged-chr9-65367787-1	chr9	65367737	65367837	+	2	cIP2vsInput	"intron (NM_001111145, intron 1 of 6)"	"intron (NM_001111145, intron 1 of 6)"	6727	NM_001111145	208080	Mm.291862	NM_001111145	ENSMUSG00000086228	Gm514	-	predicted gene 514	protein-coding	0.01	0.346535
Merged-chr11-29756522-1	chr11	29756472	29756572	+	2	cIP2vsInput	"intron (NM_146016, intron 32 of 41)"	"intron (NM_146016, intron 32 of 41)"	37959	NM_024226	68585	Mm.488364	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding	0	0.455446
Merged-chr8-29621116-1	chr8	29621066	29621166	+	2	cIP1vsInput	Intergenic	Intergenic	-401480	NM_153135	210801	Mm.248433	NM_153135	ENSMUSG00000063626	Unc5d	D930029E11Rik|Unc5h4|mKIAA1777	unc-5 homolog D (C. elegans)	protein-coding	0.01	0.386139
Merged-chr5-48669329-1	chr5	48669279	48669379	+	2	cIP2vsInput	"intron (NM_001199244, intron 1 of 7)"	"intron (NM_001199244, intron 1 of 7)"	-69647	NM_001199245	80334	Mm.160172	NM_001199242	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding	0.01	0.356436
Merged-chr1-104556119-1	chr1	104556069	104556169	+	2	cIP2vsInput	Intergenic	Intergenic	-212700	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0	0.346535
Merged-chr2-40351889-1	chr2	40351839	40351939	+	2	cIP2vsInput	Intergenic	Intergenic	-1125551	NM_024209	67857	Mm.392662	NM_024209		Ppp6c	2310003C10Rik	"protein phosphatase 6, catalytic subunit"	protein-coding	0	0.336634
Merged-chr6-90328027-1	chr6	90327977	90328077	+	2	cIP2vsInput	Intergenic	Intergenic	-2842	NM_027928	71797	Mm.49071	NM_027928	ENSMUSG00000056643	Chst13	1110067M19Rik|C4ST-3	carbohydrate (chondroitin 4) sulfotransferase 13	protein-coding	0	0.405941
Merged-chr5-132088616-1	chr5	132088566	132088666	+	2	cIP2vsInput	"intron (NM_177047, intron 2 of 18)"	"intron (NM_177047, intron 2 of 18)"	208347	NR_040704	75369	Mm.389696	NR_040704		4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	miscRNA	0.02	0.29703
Merged-chr16-19505421-1	chr16	19505371	19505471	+	2	cIP2vsInput	Intergenic	Lx7|LINE|L1	10213	NM_146935	258937	Mm.377757	NM_146935	ENSMUSG00000045341	Olfr167	MOR272-1	olfactory receptor 167	protein-coding	0	0.366337
Merged-chr14-84888555-1	chr14	84888505	84888605	+	2	cIP2vsInput	Intergenic	Intergenic	-412131	NR_015539	319903	Mm.440481	NR_015539		9630013A20Rik	-	RIKEN cDNA 9630013A20 gene	miscRNA	0	0.326733
Merged-chr6-87399171-1	chr6	87399121	87399221	+	2	cIP2vsInput	Intergenic	Intergenic	-10236	NM_026860	68888	Mm.46387	NM_026860	ENSMUSG00000030048	Gkn3	1190003M12Rik	gastrokine 3	protein-coding	0	0.346535
Merged-chr12-39243563-1	chr12	39243513	39243613	+	2	cIP2vsInput	Intergenic	Intergenic	459852	NM_001163154	14009	Mm.4866	NM_001163154	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant gene 1	protein-coding	0	0.257426
Merged-chr5-54554995-1	chr5	54554945	54555045	+	2	cIP1vsInput	Intergenic	Intergenic	205003	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0.01	0.346535
Merged-chr4-111276747-1	chr4	111276697	111276797	+	2	cIP2vsInput	"intron (NM_001048189, intron 5 of 12)"	"intron (NM_001048189, intron 5 of 12)"	-138259	NR_033793	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding	0	0.29703
Merged-chr19-18233360-1	chr19	18233310	18233410	+	2	cIP1vsInput	Intergenic	RLTR20A3_MM|LTR|ERVK	-395728	NM_001190483	18552	Mm.3401	NM_001163144	ENSMUSG00000024713	Pcsk5	PC5|PC5/6A|PC5A|PC6|SPC6|b2b585Clo	proprotein convertase subtilisin/kexin type 5	protein-coding	0	0.386139
Merged-chr6-130971779-1	chr6	130971729	130971829	+	2	cIP2vsInput	Intergenic	Lx3_Mus|LINE|L1	275583	NM_001170851	16633	Mm.4783	NM_001170851	ENSMUSG00000030187	Klra2	Klra30|Ly49b	"killer cell lectin-like receptor, subfamily A, member 2"	protein-coding	0	0.346535
Merged-chr12-30326354-1	chr12	30326304	30326404	+	2	cIP2vsInput	"intron (NM_172951, intron 1 of 16)"	"intron (NM_172951, intron 1 of 16)"	47021	NM_172951	268534	Mm.279765	NM_172951	ENSMUSG00000020672	Sntg2	2210008K22Rik|9530013L23|BB121248	"syntrophin, gamma 2"	protein-coding	0	0.39604
Merged-chr8-67183400-1	chr8	67183350	67183450	+	2	cIP2vsInput	Intergenic	Intergenic	-307358	NM_008673	17960	Mm.14125	NM_008673	ENSMUSG00000025588	Nat1	Nat-1	N-acetyl transferase 1	protein-coding	0	0.376238
Merged-chr13-67663931-1	chr13	67663881	67663981	+	2	cIP2vsInput	Intergenic	L1VL4|LINE|L1	19581	NM_001001187	408068	Mm.435551	NM_175676	ENSMUSG00000048280	Zfp738	3830402I07Rik|6720487G11Rik	zinc finger protein 738	protein-coding	0	0.316832
Merged-chr2-88356593-1	chr2	88356543	88356643	+	2	cIP1vsInput	Intergenic	Intergenic	17026	NM_146771	258767	Mm.377682	NM_146771	ENSMUSG00000050023	Olfr1176	MOR174-5	olfactory receptor 1176	protein-coding	0	0.346535
Merged-chr15-52973285-1	chr15	52973235	52973335	+	2	cIP2vsInput	Intergenic	Intergenic	260840	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding	0	0.336634
Merged-chr11-17506212-1	chr11	17506162	17506262	+	2	cIP1vsInput	Intergenic	Charlie12|DNA|hAT-Charlie	248594	NM_020558	57316	Mm.287982	NM_020558	ENSMUSG00000000581	C1d	1110036E10Rik|AI875855|SUN-CoR	C1D nuclear receptor co-repressor	protein-coding	0	0.376238
Merged-chr17-10891244-1	chr17	10891194	10891294	+	2	cIP2vsInput	"intron (NM_016694, intron 1 of 11)"	"intron (NM_016694, intron 1 of 11)"	50860	NM_016694	50873	Mm.311110	NM_016694		Park2	PRKN	"Parkinson disease (autosomal recessive, juvenile) 2, parkin"	protein-coding	0	0.326733
Merged-chr2-92592612-1	chr2	92592562	92592662	+	2	cIP2vsInput	Intergenic	Intergenic	-7095	NM_023850	76969	Mm.38021	NM_023850	ENSMUSG00000027221	Chst1	2610008E20Rik|AW125896|C6ST|GST-1|Gst1|KSGAL6ST	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	protein-coding	0	0.336634
Merged-chr5-82836022-1	chr5	82835972	82836072	+	2	cIP2vsInput	Intergenic	Intergenic	-36957	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mmu-mir-1187	microRNA 1187	miscRNA	0.01	0.306931
Merged-chr3-124030343-1	chr3	124030293	124030393	+	2	cIP1vsInput	Intergenic	Intergenic	-290694	NM_146140	229801	Mm.165810	NM_146140	ENSMUSG00000044528	Tram1l1	A830091N21Rik	translocation associated membrane protein 1-like 1	protein-coding	0.01	0.306931
Merged-chrX-137912456-1	chrX	137912406	137912506	+	2	cIP2vsInput	"intron (NM_030688, intron 2 of 10)"	L1MC|LINE|L1	297124	NM_026469	67944	Mm.443280	NM_026469	ENSMUSG00000071686	Tex13a	1700025D03Rik	testis expressed 13A	protein-coding	0	0.316832
Merged-chr3-68121491-1	chr3	68121441	68121541	+	2	cIP1vsInput	"intron (NM_001113420, intron 1 of 6)"	"intron (NM_001113420, intron 1 of 6)"	56689	NM_001113420	30953	Mm.331064	NM_001113420	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding	0.01	0.49505
Merged-chr2-112716819-1	chr2	112716769	112716869	+	2	cIP2vsInput	"intron (NM_177652, intron 65 of 103)"	"intron (NM_177652, intron 65 of 103)"	157137	NM_001165935	74268	Mm.436657	NM_001165935		Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	"apoptosis, caspase activation inhibitor"	protein-coding	0	0.336634
Merged-chr14-49525320-1	chr14	49525270	49525370	+	2	cIP2vsInput	"intron (NM_029238, intron 1 of 7)"	"intron (NM_029238, intron 1 of 7)"	517	NM_029238	75288	Mm.78738	NM_029238	ENSMUSG00000021852	Slc35f4	4930550L21Rik	"solute carrier family 35, member F4"	protein-coding	0.05	0.623762
Merged-chr1-24417052-1	chr1	24417002	24417102	+	2	cIP1vsInput	"intron (NM_007733, intron 14 of 50)"	"intron (NM_007733, intron 14 of 50)"	170385	NM_007733	12823	Mm.329196	NM_007733		Col19a1	-	"collagen, type XIX, alpha 1"	protein-coding	0.01	0.356436
Merged-chr16-59841829-1	chr16	59841779	59841879	+	2	cIP2vsInput	"intron (NM_007938, intron 11 of 17)"	"intron (NM_007938, intron 11 of 17)"	-202490	NM_019665	56297	Mm.392505	NM_019665	ENSMUSG00000022722	Arl6	1110018H24Rik|2210411E14Rik|BBS3	ADP-ribosylation factor-like 6	protein-coding	0.01	0.326733
Merged-chr15-91762733-1	chr15	91762683	91762783	+	2	cIP2vsInput	"intron (NM_025730, intron 33 of 50)"	L1_Rod|LINE|L1	-75593	NM_207243	239611	Mm.486225	NM_207243		Muc19	MUC-19	mucin 19	protein-coding	0.02	0.306931
Merged-chr4-67338176-1	chr4	67338126	67338226	+	2	cIP2vsInput	Intergenic	Intergenic	510365	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding	0	0.346535
Merged-chr4-121546515-1	chr4	121546465	121546565	+	2	cIP1vsInput	Intergenic	Intergenic	75610	NM_001099309	666927	Mm.465133	NM_001099309		Gm12887	OTTMUSG00000008910	predicted gene 12887	protein-coding	0.01	0.29703
Merged-chr3-5825930-1	chr3	5825880	5825980	+	2	cIP2vsInput	Intergenic	Intergenic	-249682	NM_001163305	19302	Mm.132336	NM_001163304	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding	0	0.267327
Merged-chr3-13091569-1	chr3	13091519	13091619	+	2	cIP2vsInput	Intergenic	Intergenic	-380086	NM_178631	76897	Mm.422625	NM_001163328	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0	0.336634
Merged-chr9-94315511-1	chr9	94315461	94315561	+	2	cIP2vsInput	Intergenic	Intergenic	222570	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49	RIKEN cDNA 1190002N15 gene	protein-coding	0	0.316832
Merged-chr11-59864802-1	chr11	59864752	59864852	+	2	cIP2vsInput	"intron (NM_134029, intron 3 of 4)"	L1M4|LINE|L1	16729	NM_134029	103850	Mm.41761	NM_134029	ENSMUSG00000032615	Nt5m	2010013E09Rik|AI846937|dNT-2	"5',3'-nucleotidase, mitochondrial"	protein-coding	0	0.366337
Merged-chr6-95236801-1	chr6	95236751	95236851	+	2	cIP2vsInput	Intergenic	RLTR40|LTR|ERVK	97192	NR_033559	414067	Mm.355990	NR_033559	ENSMUSG00000068180	AY512915	-	cDNA sequence AY512915	miscRNA	0	0.326733
Merged-chr11-105114102-1	chr11	105114052	105114152	+	2	cIP1vsInput	"intron (NM_001081046, intron 9 of 9)"	"intron (NM_001081046, intron 9 of 9)"	-12323	NM_172567	52686	Mm.270091	NM_172567		Mettl2	2810438F06Rik|AW493404|C130031G21Rik|D11Ertd768e|METL|PSENIP1	methyltransferase like 2	protein-coding	0	0.376238
Merged-chr14-98547507-1	chr14	98547457	98547557	+	2	cIP1vsInput	Intergenic	Lx9|LINE|L1	-377964	NM_007826	13134	Mm.320593	NM_001038610	ENSMUSG00000055639	Dach1	AI182278|Dac|Dach|E130112M23Rik	dachshund 1 (Drosophila)	protein-coding	0	0.356436
Merged-chr4-8039127-1	chr4	8039077	8039177	+	2	cIP2vsInput	Intergenic	Intergenic	199914	NM_007592	12319	Mm.119320	NM_007592		Car8	AW546993|Ca8|Cals|Cals1|Carp|wdl	carbonic anhydrase 8	protein-coding	0	0.247525
Merged-chr2-140465591-1	chr2	140465541	140465641	+	2	cIP2vsInput	"intron (NM_001013802, intron 3 of 18)"	MIRb|SINE|MIR	70156	NM_028387	72899	Mm.229466	NM_001013802	ENSMUSG00000068205	Macrod2	1110033L15Rik|2610107G07Rik|2900006F19Rik	MACRO domain containing 2	protein-coding	0	0.29703
Merged-chr4-147489197-1	chr4	147489147	147489247	+	2	cIP2vsInput	"intron (NM_001039209, intron 1 of 2)"	RMER16-int|LTR|ERVK	-64080	NM_001014397	433804	Mm.332047	XM_003946328	ENSMUSG00000065999	Gm13154	OTTMUSG00000010673	predicted gene 13154	protein-coding	0.01	0.326733
Merged-chr7-96992396-1	chr7	96992346	96992446	+	2	cIP2vsInput	"intron (NM_153591, intron 5 of 13)"	"intron (NM_153591, intron 5 of 13)"	40869	NM_153591	244141	Mm.274864	NM_153591	ENSMUSG00000018995	Nars2	AI875199	asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)	protein-coding	0	0.29703
Merged-chr12-97907557-1	chr12	97907507	97907607	+	2	cIP2vsInput	Intergenic	MER2|DNA|TcMar-Tigger	351780	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding	0	0.306931
Merged-chr10-66124712-1	chr10	66124662	66124762	+	2	cIP2vsInput	promoter-TSS (NR_038039)	promoter-TSS (NR_038039)	-648	NR_038039	69433	Mm.23366	NR_038039		1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	miscRNA	0	0.346535
Merged-chr4-142797095-1	chr4	142797045	142797145	+	2	cIP2vsInput	Intergenic	Intergenic	415614	NM_001081355	110593	Mm.332020	NM_001081355	ENSMUSG00000057637	Prdm2	4833427P12Rik|E330024L24Rik|Gm1033|Gm19732|KMT8|Riz|Riz1|Znfpr1c1	"PR domain containing 2, with ZNF domain"	protein-coding	0	0.287129
Merged-chr18-87760940-1	chr18	87760890	87760990	+	2	cIP2vsInput	Intergenic	Intergenic	1047892	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding	0	0.207921
Merged-chr7-108390700-1	chr7	108390650	108390750	+	2	cIP2vsInput	Intergenic	Lx9|LINE|L1	-4422	NM_146364	258361	Mm.223052	NM_146364	ENSMUSG00000094104	Olfr495	MOR204-37	olfactory receptor 495	protein-coding	0	0.29703
Merged-chr8-10151635-1	chr8	10151585	10151685	+	2	cIP2vsInput	Intergenic	Intergenic	-2288	NM_001081397	244281	Mm.422761	NM_001081397	ENSMUSG00000039057	Myo16	C230040D10Rik|Gm1105|NYAP3|mKIAA0865	myosin XVI	protein-coding	0	0.39604
Merged-chr8-74184531-1	chr8	74184481	74184581	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-688643	NM_027837	71597	Mm.158735	NM_027837		Isx	9130012O13Rik|Pix-1	intestine specific homeobox	protein-coding	0	0.316832
Merged-chr1-145589509-1	chr1	145589459	145589559	+	2	cIP1vsInput	Intergenic	Intergenic	-814088	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding	0	0.346535
Merged-chr15-28536248-1	chr15	28536198	28536298	+	2	cIP2vsInput	Intergenic	Intergenic	332482	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnahc5	AU022615|Dnah5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	"dynein, axonemal, heavy chain 5"	protein-coding	0	0.346535
Merged-chr16-8654776-1	chr16	8654726	8654826	+	2	cIP1vsInput	"intron (NM_016881, intron 7 of 8)"	PB1D10|SINE|Alu	17069	NM_016881	54128	Mm.9699	NM_016881	ENSMUSG00000022711	Pmm2	AI585868|C86848	phosphomannomutase 2	protein-coding	0.01	0.49505
Merged-chr12-32403538-1	chr12	32403488	32403588	+	2	cIP2vsInput	Intergenic	Intergenic	24749	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding	0	0.29703
Merged-chr10-50857215-1	chr10	50857165	50857265	+	2	cIP2vsInput	Intergenic	Intergenic	-38436	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding	0.01	0.336634
Merged-chr2-96076085-1	chr2	96076035	96076135	+	2	cIP2vsInput	Intergenic	Intergenic	-1391589	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.29703
Merged-chrX-71492591-1	chrX	71492541	71492641	+	2	cIP2vsInput	"5' UTR (NM_138309, exon 1 of 9)"	"5' UTR (NM_138309, exon 1 of 9)"	258	NM_138309	171486	Mm.283879	NM_001199349	ENSMUSG00000035776	Cd99l2	AW548191|Mic2l1|Xap89	CD99 antigen-like 2	protein-coding	0.06	0.663366
Merged-chr16-33307246-1	chr16	33307196	33307296	+	2	cIP2vsInput	Intergenic	Intergenic	55790	NM_080557	69150	Mm.396285	NM_080557	ENSMUSG00000022808	Snx4	1810036H14Rik|AI037066	sorting nexin 4	protein-coding	0	0.326733
Merged-chr8-89524220-1	chr8	89524170	89524270	+	2	cIP1vsInput	Intergenic	Intergenic	-480058	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding	0	0.415842
Merged-chr8-101983338-1	chr8	101983288	101983388	+	2	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	801773	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0	0.356436
Merged-chr7-90782117-1	chr7	90782067	90782167	+	2	cIP2vsInput	Intergenic	Intergenic	-306122	NM_026734	68472	Mm.289791	NM_026734		Tmem126b	1110001A23Rik	transmembrane protein 126B	protein-coding	0	0.326733
Merged-chr5-70785837-1	chr5	70785787	70785887	+	2	cIP2vsInput	"intron (NM_010252, intron 3 of 8)"	"intron (NM_010252, intron 3 of 8)"	56780	NM_010252	14405	Mm.255292	NM_010252	ENSMUSG00000001260	Gabrg1	GabaA|GabaA/BZ	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1"	protein-coding	0	0.267327
Merged-chr13-89213478-1	chr13	89213428	89213528	+	2	cIP2vsInput	"intron (NM_001037987, intron 9 of 10)"	(CA)n|Simple_repeat|Simple_repeat	-327158	NM_013500	12950	Mm.266790	NM_013500	ENSMUSG00000021613	Hapln1	BB099155|CLP|Crtl1|Crtl1l|LP|LP-1	hyaluronan and proteoglycan link protein 1	protein-coding	0	0.366337
Merged-chr9-109759229-1	chr9	109759179	109759279	+	2	cIP1vsInput	Intergenic	RMER16-int|LTR|ERVK	-13140	NM_198674	382109	Mm.246849	NM_198674	ENSMUSG00000059547	Fbxw26	EG382109|Gm5163	F-box and WD-40 domain protein 26	protein-coding	0	0.287129
Merged-chr2-157242590-1	chr2	157242540	157242640	+	2	cIP2vsInput	"intron (NM_001039557, intron 8 of 24)"	"intron (NM_001039557, intron 8 of 24)"	-36508	NM_019642	20014	Mm.22130	NM_019642	ENSMUSG00000027642	Rpn2	1300012C06Rik|AV261018|Rpn-2	ribophorin II	protein-coding	0	0.405941
Merged-chr13-5451383-1	chr13	5451333	5451433	+	2	cIP2vsInput	Intergenic	Intergenic	406709	NR_045891	71867	Mm.179181	NR_045891		1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	miscRNA	0.01	0.346535
Merged-chr14-38135512-1	chr14	38135462	38135562	+	2	cIP1vsInput	Intergenic	Lx3_Mus|LINE|L1	-762790	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	4930529F24Rik	-	RIKEN cDNA 4930529F24 gene	miscRNA	0	0.316832
Merged-chr5-88034238-1	chr5	88034188	88034288	+	2	cIP2vsInput	Intergenic	Intergenic	31713	NM_011422	20599	Mm.482945	NM_011423	ENSMUSG00000029280	Smr3a	AA589601|MSG1|MSG3|Smr1|Smr3	submaxillary gland androgen regulated protein 3A	protein-coding	0	0.336634
Merged-chr3-131885966-1	chr3	131885916	131886016	+	2	cIP2vsInput	Intergenic	Intergenic	-199326	NM_020265	56811	Mm.103593	NM_020265	ENSMUSG00000028031	Dkk2	-	dickkopf homolog 2 (Xenopus laevis)	protein-coding	0.01	0.356436
Merged-chr2-22099088-1	chr2	22099038	22099138	+	2	cIP2vsInput	Intergenic	Lx9|LINE|L1	-128415	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding	0	0.336634
Merged-chr11-20455553-1	chr11	20455503	20455603	+	2	cIP2vsInput	Intergenic	Intergenic	-87700	NM_021372	58172	Mm.339676	NM_001038625	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding	0.02	0.435644
Merged-chr4-93458459-1	chr4	93458409	93458509	+	2	cIP1vsInput	Intergenic	Intergenic	-122948	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding	0.01	0.257426
Merged-chr2-170873749-1	chr2	170873699	170873799	+	2	cIP2vsInput	"intron (NM_029761, intron 7 of 7)"	"intron (NM_029761, intron 7 of 7)"	141942	NM_001163686	76829	Mm.41633	NM_001163686	ENSMUSG00000027560	Dok5	2700055C10Rik	docking protein 5	protein-coding	0.03	0.435644
Merged-chr5-5605186-1	chr5	5605136	5605236	+	2	cIP2vsInput	"intron (NM_172447, intron 13 of 22)"	L1_Mur2|LINE|L1	31387	NR_033499	667705	Mm.376656	NR_033499	ENSMUSG00000073234	Gm8773	EG667705	predicted gene 8773	miscRNA	0	0.346535
Merged-chr4-27441425-1	chr4	27441375	27441475	+	2	cIP2vsInput	Intergenic	Lx9|LINE|L1	-735976	NR_040656	75360	Mm.67233	NR_040656	ENSMUSG00000086257	4930548K13Rik	-	RIKEN cDNA 4930548K13 gene	miscRNA	0	0.316832
Merged-chr9-59186278-1	chr9	59186228	59186328	+	2	cIP2vsInput	Intergenic	Intergenic	-105294	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding	0.01	0.336634
Merged-chr6-132609893-1	chr6	132609843	132609943	+	2	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	13947	NM_031499	83380	Mm.484054	NM_031499	ENSMUSG00000058295	Prp2	MP14	proline rich protein 2	protein-coding	0	0.336634
Merged-chr14-89202321-1	chr14	89202271	89202371	+	2	cIP2vsInput	Intergenic	Intergenic	-693903	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0	0.356436
Merged-chr14-34699865-1	chr14	34699815	34699915	+	2	cIP2vsInput	"intron (NM_001004436, intron 4 of 18)"	Charlie1a|DNA|hAT-Charlie	25937	NM_001004436	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapal	2410073G16|A530089A20Rik|BC037674|FOE|mKIAA0261|mWAPL	wings apart-like homolog (Drosophila)	protein-coding	0	0.316832
Merged-chr14-53601000-1	chr14	53600950	53601050	+	2	cIP1vsInput	Intergenic	Intergenic	-64940	NM_001205242	100568452	Mm.486072	NM_001205242		A430107P09Rik	Va10	RIKEN cDNA A430107P09 gene	protein-coding	0	0.336634
Merged-chr11-10380995-1	chr11	10380945	10381045	+	2	cIP2vsInput	Intergenic	RMER30|DNA|hAT-Charlie	-733021	NM_177033	319922	Mm.487612	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding	0	0.366337
Merged-chr11-81665558-1	chr11	81665508	81665608	+	2	cIP2vsInput	"intron (NM_001034013, intron 1 of 9)"	(TAGA)n|Simple_repeat|Simple_repeat	-92019	NM_001033765	237880	Mm.435528	NM_001033765		1700071K01Rik	-	RIKEN cDNA 1700071K01 gene	protein-coding	0	0.366337
Merged-chr5-71768404-1	chr5	71768354	71768454	+	2	cIP2vsInput	"intron (NM_008069, intron 3 of 8)"	"intron (NM_008069, intron 3 of 8)"	68388	NM_008069	14400	Mm.38567	NM_008069		Gabrb1	AW061132|B230208N19Rik|Gabrb-1	"gamma-aminobutyric acid (GABA) A receptor, subunit beta 1"	protein-coding	0	0.366337
Merged-chr7-82577553-1	chr7	82577503	82577603	+	2	cIP2vsInput	"intron (NM_001190374, intron 22 of 29)"	"intron (NM_001190374, intron 22 of 29)"	70975	NM_177894	330577	Mm.222812	NM_177894	ENSMUSG00000038570	Fam154b	1700129I04Rik|D030069K18	"family with sequence similarity 154, member B"	protein-coding	0	0.326733
Merged-chr5-71121898-1	chr5	71121848	71121948	+	2	cIP2vsInput	Intergenic	Intergenic	-26049	NM_008066	14395	Mm.5304	NM_008066	ENSMUSG00000000560	Gabra2	C630048P16Rik|Gabra-2	"gamma-aminobutyric acid (GABA) A receptor, subunit alpha 2"	protein-coding	0	0.366337
Merged-chr13-101371755-1	chr13	101371705	101371805	+	2	cIP2vsInput	Intergenic	Intergenic	25825	NR_046187	78136	Mm.399065	NR_046187		4922502H24Rik	-	RIKEN cDNA 4922502H24 gene	miscRNA	0	0.336634
Merged-chrX-39061366-1	chrX	39061316	39061416	+	2	cIP2vsInput	Intergenic	Intergenic	-284900	NM_001177380	78631	Mm.243738	NM_001177380	ENSMUSG00000079619	Cypt15	1700085A12Rik	cysteine-rich perinuclear theca 15	protein-coding	0.01	0.346535
Merged-chr12-44370918-1	chr12	44370868	44370968	+	2	cIP2vsInput	"intron (NM_176930, intron 1 of 30)"	"intron (NM_176930, intron 1 of 30)"	42033	NM_001146031	319504	Mm.208439	NM_001146031	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuron-glia-CAM-related cell adhesion molecule	protein-coding	0	0.366337
Merged-chr1-103887870-1	chr1	103887820	103887920	+	2	cIP2vsInput	Intergenic	Intergenic	-880949	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0	0.247525
Merged-chrX-166964157-1	chrX	166964107	166964207	+	2	cIP2vsInput	Intergenic	Intergenic	106213	NM_001101606	667794	Mm.302232	NM_001101606		Gm8817	EG667794	predicted gene 8817	protein-coding	0.01	0.29703
Merged-chr11-13631192-1	chr11	13631142	13631242	+	2	cIP2vsInput	Intergenic	Intergenic	968033	NR_045918	73307	Mm.399291	NR_045918	ENSMUSG00000085561	1700046C09Rik	-	RIKEN cDNA 1700046C09 gene	miscRNA	0.01	0.376238
Merged-chr5-16901349-1	chr5	16901299	16901399	+	2	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	347799	NM_010427	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF/HGF	hepatocyte growth factor	protein-coding	0	0.366337
Merged-chr12-46108150-1	chr12	46108100	46108200	+	2	cIP2vsInput	Intergenic	L1M5|LINE|L1	710625	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding	0	0.257426
Merged-chr5-68059021-1	chr5	68058971	68059071	+	2	cIP2vsInput	"intron (NM_001018019, intron 1 of 3)"	"intron (NM_001018019, intron 1 of 3)"	27186	NM_001018019	433899	Mm.332422	NM_001018019	ENSMUSG00000068082	Grxcr1	Tg(Eno2-Gabrb3)0370Brll|pi|tde	"glutaredoxin, cysteine rich 1"	protein-coding	0	0.405941
Merged-chr1-122398213-1	chr1	122398163	122398263	+	2	cIP2vsInput	Intergenic	MTE2a|LTR|ERVL-MaLR	-830233	NM_025860	66942	Mm.44219	NM_025860	ENSMUSG00000001674	Ddx18	2310005B10Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	protein-coding	0	0.376238
Merged-chr4-65893996-1	chr4	65893946	65894046	+	2	cIP2vsInput	"intron (NM_019514, intron 9 of 21)"	L1MC4|LINE|L1	289010	NM_001161782	69807	Mm.22786	NM_001161782	ENSMUSG00000051675	Trim32	1810045E12Rik|3f3|BBS11|Zfp117	tripartite motif-containing 32	protein-coding	0.01	0.316832
Merged-chr2-123650218-1	chr2	123650168	123650268	+	2	cIP2vsInput	Intergenic	Intergenic	479738	NR_040611	74702	Mm.410814	NR_040611	ENSMUSG00000085496	4930517E11Rik	-	RIKEN cDNA 4930517E11 gene	miscRNA	0.01	0.316832
Merged-chr7-3904632-1	chr7	3904582	3904682	+	2	cIP2vsInput	"intron (NM_011087, intron 1 of 9)"	L1VL2|LINE|L1	-6512	NM_011094	18730	Mm.482470	NM_011094		Pira7	16M2	paired-Ig-like receptor A7	protein-coding	0	0.29703
Merged-chr9-68132654-1	chr9	68132604	68132704	+	2	cIP2vsInput	Intergenic	Intergenic	-106940	NR_045745	434412	Mm.490707	NR_045745		Gm20745	-	"predicted gene, 20745"	miscRNA	0	0.356436
Merged-chr10-11391850-1	chr10	11391800	11391900	+	2	cIP2vsInput	"intron (NM_010146, intron 2 of 3)"	"intron (NM_010146, intron 2 of 3)"	48405	NM_010146	13853	Mm.89946	NM_010146		Epm2a	"TG-B|Tg(TcraK,TcrbK)TG-BFlv"	"epilepsy, progressive myoclonic epilepsy, type 2 gene alpha"	protein-coding	0	0.188119
Merged-chr3-121005330-1	chr3	121005280	121005380	+	2	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	166365	NM_028456	66568	Mm.263163	NM_025637	ENSMUSG00000028133	Rwdd3	2510027J23Rik|3110037C01Rik|AI035684|AI662458|X2CR1	RWD domain containing 3	protein-coding	0	0.39604
Merged-chr11-119253442-1	chr11	119253392	119253492	+	2	cIP2vsInput	"intron (NM_175430, intron 14 of 18)"	"intron (NM_175430, intron 14 of 18)"	-14525	NM_001159324	14387	Mm.4793	NM_001159324	ENSMUSG00000025579	Gaa	E430018M07Rik	"glucosidase, alpha, acid"	protein-coding	0.1	0.683168
Merged-chr4-130225615-1	chr4	130225565	130225665	+	2	cIP2vsInput	Intergenic	Intergenic	-3320	NM_001034872	332942	Mm.387701	NM_001034872	ENSMUSG00000023120	Gm853	OTTMUSG00000009560	predicted gene 853	protein-coding	0	0.336634
Merged-chr13-4868289-1	chr13	4868239	4868339	+	2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-259125	NM_018859	56043	Mm.251908	NM_018859	ENSMUSG00000045410	Akr1e1	1810061I10Rik|Akr1e2	"aldo-keto reductase family 1, member E1"	protein-coding	0	0.267327
Merged-chr19-12387704-1	chr19	12387654	12387754	+	2	cIP2vsInput	"intron (NR_030566, intron 3 of 3)"	"intron (NR_030566, intron 3 of 3)"	-6561	NM_146684	258679	Mm.271520	NM_146684	ENSMUSG00000046650	Olfr1440	MOR215-1	olfactory receptor 1440	protein-coding	0.01	0.405941
Merged-chr5-33996567-1	chr5	33996517	33996617	+	2	cIP2vsInput	"5' UTR (NM_001001985, exon 1 of 3)"	"5' UTR (NM_001001985, exon 1 of 3)"	583	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding	0.09	0.712871
Merged-chr14-59164159-1	chr14	59164109	59164209	+	2	cIP2vsInput	"intron (NM_001004158, intron 1 of 1)"	Lx7|LINE|L1	14590	NM_001004158	380907	Mm.81009	NM_001004158	ENSMUSG00000053868	Gm5142	EG380907	predicted gene 5142	protein-coding	0.01	0.366337
Merged-chr14-57232395-1	chr14	57232345	57232445	+	2	cIP2vsInput	Intergenic	Intergenic	-98784	NM_001010937	14623	Mm.25652	NM_008128	ENSMUSG00000040055	Gjb6	AA958971|Cx30|D14Bwg0506e	"gap junction protein, beta 6"	protein-coding	0	0.336634
Merged-chr10-26091007-1	chr10	26090957	26091057	+	2	cIP2vsInput	Intergenic	Lx7|LINE|L1	-11955	NM_029881	77220	Mm.266260	NM_029881	ENSMUSG00000049420	Tmem200a	C030003D03Rik	transmembrane protein 200A	protein-coding	0	0.356436
Merged-chrX-97280141-1	chrX	97280091	97280191	+	2	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	97068	NM_001161432	245527	Mm.189270	NM_001161432	ENSMUSG00000034457	Eda2r	9430060M22Rik|TNFRSF27|Xedar	ectodysplasin A2 receptor	protein-coding	0	0.287129
Merged-chr13-91846780-1	chr13	91846730	91846830	+	2	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	30105	NM_198415	76722	Mm.316438	NM_198415	ENSMUSG00000021622	Ckmt2	2300008A19Rik|ScCKmit	"creatine kinase, mitochondrial 2"	protein-coding	0	0.326733
Merged-chr5-119036474-1	chr5	119036424	119036524	+	2	cIP1vsInput	Intergenic	MTC-int|LTR|ERVL-MaLR	-71762	NR_040693	73477	Mm.410863	NR_040693		1700081H04Rik	-	RIKEN cDNA 1700081H04 gene	miscRNA	0.01	0.465347
Merged-chrX-17168812-1	chrX	17168762	17168862	+	2	cIP2vsInput	"intron (NM_028916, intron 11 of 14)"	"intron (NM_028916, intron 11 of 14)"	150556	NM_028916	74405	Mm.248531	NM_028916	ENSMUSG00000025038	Efhc2	4933407D04Rik|mRib72-2	EF-hand domain (C-terminal) containing 2	protein-coding	0	0.326733
Merged-chr5-133051286-1	chr5	133051236	133051336	+	2	cIP2vsInput	Intergenic	Intergenic	-508943	NM_177047	319974	Mm.488992	NM_177047		Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding	0.01	0.386139
Merged-chr1-178211118-1	chr1	178211068	178211168	+	2	cIP1vsInput	"intron (NM_024282, intron 1 of 4)"	"intron (NM_024282, intron 1 of 4)"	23701	NM_024282	78825	Mm.440132	NM_024282	ENSMUSG00000026502	Desi2	5830417C01Rik|DeSI-2|Fam152a|Pppde1	desumoylating isopeptidase 2	protein-coding	0	0.287129
Merged-chr14-112625943-1	chr14	112625893	112625993	+	2	cIP1vsInput	Intergenic	Intergenic	604513	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0	0.277228
Merged-chrY-7047499-1	chrY	7047449	7047549	+	2	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	120278	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.306931
Merged-chr1-144781136-1	chr1	144781086	144781186	+	2	cIP1vsInput	Intergenic	Intergenic	-5715	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding	0	0.366337
Merged-chr13-112598367-1	chr13	112598317	112598417	+	2	cIP1vsInput	TTS (NM_010029)	TTS (NM_010029)	-17705	NM_139299	218624	Mm.380801	NM_139299	ENSMUSG00000050377	Il31ra	CRL3|GLM-R|GPL|Glmr|NR10	interleukin 31 receptor A	protein-coding	0	0.316832
Merged-chr1-105106323-1	chr1	105106273	105106373	+	2	cIP1vsInput	Intergenic	Intergenic	250387	NM_178779	320311	Mm.389162	NM_001160368	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding	0.01	0.306931
Merged-chr9-24264920-1	chr9	24264870	24264970	+	2	cIP2vsInput	"intron (NM_175678, intron 4 of 9)"	L1MA8|LINE|L1	166902	NM_175678	319239	Mm.130824	NM_175678	ENSMUSG00000043659	Npsr1	9330128H10Rik|GPRA|Gpr154|MVTR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0	0.356436
Merged-chr1-195217362-1	chr1	195217312	195217412	+	2	cIP2vsInput	Intergenic	Intergenic	-40647	NM_007758	12902	Mm.235387	NM_007758	ENSMUSG00000026616	Cr2	C3DR|CD21|CD35|Cr-1|Cr-2|Cr1	complement receptor 2	protein-coding	0	0.346535
Merged-chr1-119708120-1	chr1	119708070	119708170	+	2	cIP2vsInput	"intron (NM_019933, intron 13 of 26)"	"intron (NM_019933, intron 13 of 26)"	-59120	NM_145506	226352	Mm.253156	NM_001113416	ENSMUSG00000026383	Epb4.1l5	1700030C16Rik|AL022914|BE37|E230025E14Rik|Epb41l5|Lulu1|NBL5	erythrocyte protein band 4.1-like 5	protein-coding	0	0.247525
Merged-chr14-13390935-1	chr14	13390885	13390985	+	2	cIP1vsInput	"intron (NM_028052, intron 2 of 5)"	L1MD|LINE|L1	-63023	NM_001163032	72003	Mm.317515	NM_001163032	ENSMUSG00000056296	Synpr	1500003F20Rik|SPO	synaptoporin	protein-coding	0.01	0.366337
Merged-chr14-12823669-1	chr14	12823619	12823719	+	2	cIP2vsInput	promoter-TSS (NM_012061)	promoter-TSS (NM_012061)	-590	NM_012061	27062	Mm.260881	NM_001042617	ENSMUSG00000054423	Cadps	AU067781|CAPS|CAPS1|mKIAA1121	Ca2+-dependent secretion activator	protein-coding	0.03	0.376238
Merged-chr4-98276504-1	chr4	98276454	98276554	+	2	cIP2vsInput	Intergenic	Intergenic	106761	NM_053157	94043	Mm.331719	NM_053157	ENSMUSG00000028563	Tm2d1	2310026L18Rik|AA990549|Bbp	TM2 domain containing 1	protein-coding	0.01	0.356436
Merged-chr17-93938298-1	chr17	93938248	93938348	+	2	cIP2vsInput	Intergenic	Intergenic	738876	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0	0.336634
Merged-chr16-27599708-1	chr16	27599658	27599758	+	2	cIP2vsInput	Intergenic	Intergenic	210731	NM_026202	67501	Mm.258985	NM_001025615	ENSMUSG00000038127	Ccdc50	2610529H08Rik|5730448P06Rik|AW048328|AW546090|C3orf6|D16Bwg1543e	coiled-coil domain containing 50	protein-coding	0.01	0.336634
Merged-chr18-39911507-1	chr18	39911457	39911557	+	2	cIP2vsInput	Intergenic	Intergenic	138010	NM_011033	18459	Mm.9493	NM_011033	ENSMUSG00000051732	Pabpc2	Pabp|Pabp+|Pabp2	"poly(A) binding protein, cytoplasmic 2"	protein-coding	0	0.306931
Merged-chr1-103159576-1	chr1	103159526	103159626	+	2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-1609243	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0	0.356436
Merged-chr4-73303809-1	chr4	73303759	73303859	+	2	cIP2vsInput	Intergenic	Intergenic	101263	NM_001013393	433719	Mm.348294	NM_001013393	ENSMUSG00000066137	Gm11487	OTTMUSG00000001246	predicted gene 11487	protein-coding	0	0.29703
Merged-chr18-5799521-1	chr18	5799471	5799571	+	2	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-207084	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	miscRNA	0	0.405941
Merged-chr12-117671624-1	chr12	117671574	117671674	+	2	cIP2vsInput	"intron (NM_175930, intron 11 of 27)"	"intron (NM_175930, intron 11 of 27)"	155145	NM_175930	217944	Mm.227642	NM_175930	ENSMUSG00000041992	Rapgef5	4932413M22|C86120|D030051B22Rik|GFR|Mrgef|mKIAA0277|mmr-gef	Rap guanine nucleotide exchange factor (GEF) 5	protein-coding	0	0.287129
Merged-chrX-74023845-1	chrX	74023795	74023895	+	2	cIP2vsInput	promoter-TSS (NR_030758)	promoter-TSS (NR_030758)	73	NM_001177975	16179	Mm.38241	NM_001177973	ENSMUSG00000031392	Irak1	AA408924|IRAK|IRAK-1|IRAK1-S|Il1rak|Plpk|mPLK	interleukin-1 receptor-associated kinase 1	protein-coding	0.15	0.762376
Merged-chr2-111362662-1	chr2	111362612	111362712	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-5972	NM_207236	228443	Mm.377244	NM_207236	ENSMUSG00000064266	Olfr1283	GA_x6K02T2Q125-72420217-72421134|MOR248-19	olfactory receptor 1283	protein-coding	0	0.326733
Merged-chr6-76213304-1	chr6	76213254	76213354	+	2	cIP1vsInput	Intergenic	L1_Mur2|LINE|L1	-1029413	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0	0.336634
Merged-chrX-110265241-1	chrX	110265191	110265291	+	2	cIP2vsInput	Intergenic	Intergenic	-107512	NR_033597	634340	Mm.66709	NR_033597	ENSMUSG00000082853	Gm7134	EG634340	kinesin family member 18B pseudogene	pseudo	0.01	0.336634
Merged-chr6-53138243-1	chr6	53138193	53138293	+	2	cIP2vsInput	Intergenic	Intergenic	-69619	NM_173406	231986	Mm.386865	NM_001168277		Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding	0	0.425743
Merged-chr1-166428897-1	chr1	166428847	166428947	+	2	cIP2vsInput	Intergenic	L1M2|LINE|L1	-19069	NM_001142948	71592	Mm.192094	NM_001142948	ENSMUSG00000040596	Pogk	9130401E23Rik|BASS2|mKIAA1513	pogo transposable element with KRAB domain	protein-coding	0	0.376238
Merged-chr17-19529296-1	chr17	19529246	19529346	+	2	cIP2vsInput	"intron (NM_001104562, intron 5 of 5)"	L1_Mur2|LINE|L1	24485	NM_001104562	627537	Mm.469858	NM_001104562	ENSMUSG00000091859	Vmn2r100	EG627537	"vomeronasal 2, receptor 100"	protein-coding	0	0.306931
Merged-chr12-50135844-1	chr12	50135794	50135894	+	2	cIP2vsInput	Intergenic	L1MC1|LINE|L1	513379	NM_008858	18760	Mm.133719	NM_008858	ENSMUSG00000002688	Prkd1	PKD|PKD1|Pkcm|Prkcm	protein kinase D1	protein-coding	0	0.376238
Merged-chr3-113968242-1	chr3	113968192	113968292	+	2	cIP1vsInput	Intergenic	L1MD2|LINE|L1	-62298	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	"collagen, type XI, alpha 1"	protein-coding	0	0.29703
Merged-chr16-52703996-1	chr16	52703946	52704046	+	2	cIP2vsInput	Intergenic	Lx8b|LINE|L1	111748	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	miscRNA	0	0.356436
Merged-chr19-20291400-1	chr19	20291350	20291450	+	2	cIP1vsInput	Intergenic	ORR1C1|LTR|ERVL-MaLR	99271	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding	0	0.316832
Merged-chr1-69705017-1	chr1	69704967	69705067	+	2	cIP2vsInput	Intergenic	Intergenic	-19057	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding	0	0.277228
Merged-chr17-25906123-1	chr17	25906073	25906173	+	2	cIP2vsInput	"intron (NM_139154, intron 2 of 6)"	"intron (NM_139154, intron 2 of 6)"	-3896	NR_028042	100043160	Mm.482893	NR_028042		Gm10012	ENSMUSG00000056875	"cytochrome c oxidase, subunit VIIc pseudogene"	pseudo	0	0.356436
Merged-chr16-10259659-1	chr16	10259609	10259709	+	2	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	54309	NM_007929	13731	Mm.246009	NM_007929	ENSMUSG00000022505	Emp2	XMP	epithelial membrane protein 2	protein-coding	0.01	0.356436
Merged-chr5-148564728-1	chr5	148564678	148564778	+	2	cIP2vsInput	Intergenic	Intergenic	-11940	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding	0.01	0.336634
Merged-chr2-114514989-1	chr2	114514939	114515039	+	2	cIP2vsInput	Intergenic	Intergenic	139939	NM_025675	66632	Mm.117809	NM_025675	ENSMUSG00000057147	Atpbd4	5730421E18Rik	ATP binding domain 4	protein-coding	0	0.287129
Merged-chr11-105968465-1	chr11	105968415	105968515	+	2	cIP2vsInput	"intron (NM_207624, intron 1 of 24)"	"intron (NM_207624, intron 1 of 24)"	520	NM_207624	11421	Mm.754	NM_009598	ENSMUSG00000020681	Ace	AW208573|CD143	angiotensin I converting enzyme (peptidyl-dipeptidase A) 1	protein-coding	0.04	0.584158
Merged-chr15-17567979-1	chr15	17567929	17568029	+	2	cIP2vsInput	Intergenic	MTE2b|LTR|ERVL-MaLR	789878	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0	0.306931
Merged-chr15-18496037-1	chr15	18495987	18496087	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-126410	NR_045711	70886	Mm.399021	NR_045711		4921515E04Rik	-	RIKEN cDNA 4921515E04 gene	miscRNA	0	0.287129
Merged-chrX-75615584-1	chrX	75615534	75615634	+	2	cIP2vsInput	Intergenic	L1MD1|LINE|L1	-37380	NM_175122	67790	Mm.45148	NM_175122	ENSMUSG00000031202	Rab39b	6330580M05Rik	"RAB39B, member RAS oncogene family"	protein-coding	0	0.287129
Merged-chr1-126335606-1	chr1	126335556	126335656	+	2	cIP2vsInput	"intron (NM_001081756, intron 5 of 16)"	"intron (NM_001081756, intron 5 of 16)"	157321	NM_172484	210356	Mm.377234	NM_001081756	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding	0.01	0.326733
Merged-chr4-36332242-1	chr4	36332192	36332292	+	2	cIP1vsInput	"intron (NM_001165999, intron 3 of 7)"	"intron (NM_001165999, intron 3 of 7)"	313211	NR_030545	100124458		NR_030545	ENSMUSG00000077851	Mir876	Mirn876|mmu-mir-876	microRNA 876	miscRNA	0	0.277228
Merged-chr15-29292080-1	chr15	29292030	29292130	+	2	cIP1vsInput	Intergenic	L1VL2|LINE|L1	-880513	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	"catenin (cadherin associated protein), delta 2"	protein-coding	0	0.336634
Merged-chrX-77571227-1	chrX	77571177	77571277	+	2	cIP1vsInput	"intron (NM_020601, intron 1 of 15)"	"intron (NM_020601, intron 1 of 15)"	60000	NM_020601	21372	Mm.258476	NM_020601		Tbl1x	5330429M20|Tbl1	transducin (beta)-like 1 X-linked	protein-coding	0	0.366337
Merged-chr18-22255053-1	chr18	22255003	22255103	+	2	cIP1vsInput	Intergenic	Intergenic	-83657	NM_027616	70950	Mm.235716	NM_027616	ENSMUSG00000024306	Ccdc178	4921528I01Rik	coiled coil domain containing 178	protein-coding	0	0.356436
Merged-chr7-122263805-1	chr7	122263755	122263855	+	2	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-25320	NM_008855	18751	Mm.446371	NM_008855		Prkcb	A130082F03Rik|PKC-Beta|Pkcb|Prkcb1|Prkcb2	"protein kinase C, beta"	protein-coding	0	0.29703
Merged-chr2-98382528-1	chr2	98382478	98382578	+	2	cIP2vsInput	Intergenic	MYSERV6-int|LTR|ERVK	914854	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.306931
Merged-chr8-35174008-1	chr8	35173958	35174058	+	2	cIP2vsInput	Intergenic	Intergenic	-201733	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	"protein phosphatase 1, regulatory (inhibitor) subunit 3B"	protein-coding	0.01	0.366337
Merged-chr5-79207932-1	chr5	79207882	79207982	+	2	cIP2vsInput	"intron (NR_035474, intron 3 of 4)"	"intron (NR_035474, intron 3 of 4)"	307972	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0	0.267327
Merged-chr18-89416578-1	chr18	89416528	89416628	+	2	cIP2vsInput	"intron (NM_001039173, intron 6 of 7)"	"intron (NM_001039173, intron 6 of 7)"	219151	NM_001039149	225825	Mm.139293	NM_001039148	ENSMUSG00000034028	Cd226	BC051526|DNAM-1|DNAM1|Pta1|TLiSA1	CD226 antigen	protein-coding	0.01	0.346535
Merged-chr10-49485805-1	chr10	49485755	49485855	+	2	cIP2vsInput	"intron (NM_010349, intron 7 of 17)"	"intron (NM_010349, intron 7 of 17)"	302949	NM_010349	14806	Mm.332838	NM_001111268	ENSMUSG00000056073	Grik2	AW124492|GluK2|Glur-6|Glur6|Glurbeta2	"glutamate receptor, ionotropic, kainate 2 (beta 2)"	protein-coding	0.01	0.376238
Merged-chr15-73003403-1	chr15	73003353	73003453	+	2	cIP2vsInput	"intron (NM_029640, intron 7 of 21)"	"intron (NM_029640, intron 7 of 21)"	52409	NM_029640	76510	Mm.158902	NM_001164641	ENSMUSG00000047921	Trappc9	1810044A24Rik|2900005P22Rik|4632408O18Rik|Ibp|Nibp|TRS130|mKIAA1882	trafficking protein particle complex 9	protein-coding	0	0.50495
Merged-chr4-135067286-1	chr4	135067236	135067336	+	2	cIP2vsInput	Intergenic	Intergenic	-53359	NM_019732	12399	Mm.378894	NM_019732	ENSMUSG00000070691	Runx3	AML2|Cbfa3|Pebp2a3	runt related transcription factor 3	protein-coding	0.02	0.544554
Merged-chr6-68262815-1	chr6	68262765	68262865	+	2	cIP1vsInput	Intergenic	Lx5|LINE|L1	-697116	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo	0.01	0.326733
Merged-chr3-72171698-1	chr3	72171648	72171748	+	2	cIP2vsInput	Intergenic	B4A|SINE|B4	795168	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding	0.02	0.356436
Merged-chr2-10760355-1	chr2	10760305	10760405	+	2	cIP2vsInput	Intergenic	Intergenic	242751	NR_035417	100316668		NR_035417		Mir669i	Mirn669i|mmu-mir-669i	microRNA 669i	miscRNA	0	0.336634
Merged-chr8-17972489-1	chr8	17972439	17972539	+	2	cIP2vsInput	Intergenic	MLT2B2|LTR|ERVL	-437104	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding	0.01	0.346535
Merged-chr13-40249818-1	chr13	40249768	40249868	+	2	cIP2vsInput	"intron (NM_172143, intron 5 of 18)"	"intron (NM_172143, intron 5 of 18)"	38193	NM_172143	218165	Mm.364096	NM_172143	ENSMUSG00000047094	Ofcc1	opo	orofacial cleft 1 candidate 1	protein-coding	0	0.376238
Merged-chrX-138841785-1	chrX	138841735	138841835	+	2	cIP2vsInput	"intron (NM_030688, intron 10 of 10)"	"intron (NM_030688, intron 10 of 10)"	-72645	NM_013724	27206	Mm.482319	NM_013724	ENSMUSG00000052854	Nrk	AA407323|AA409510|AI225895|AV168563|AW538185|Nesk	Nik related kinase	protein-coding	0	0.326733
Merged-chr17-47131459-1	chr17	47131409	47131509	+	2	cIP2vsInput	Intergenic	Intergenic	-9483	NM_001097623	224829	Mm.260989	NM_001097623	ENSMUSG00000064043	Trerf1	9430096I18Rik|AI429294|B830015H24|RAPA|Trep-132|Trep132	transcriptional regulating factor 1	protein-coding	0	0.326733
Merged-chr17-24506767-1	chr17	24506717	24506817	+	2	cIP2vsInput	"exon (NM_027937, exon 19 of 20)"	"exon (NM_027937, exon 19 of 20)"	17984	NM_027937	268932		NM_027937	ENSMUSG00000033597	Caskin1	3300002N10Rik|C130061I24|C630036E02Rik|mKIAA1306	CASK interacting protein 1	protein-coding	0.07	0.693069
Merged-chr4-32088074-1	chr4	32088024	32088124	+	2	cIP1vsInput	Intergenic	Intergenic	123967	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding	0	0.306931
Merged-chr1-9278061-1	chr1	9278011	9278111	+	2	cIP2vsInput	"intron (NM_027671, intron 1 of 20)"	"intron (NM_027671, intron 1 of 20)"	21669	NM_027671	71096	Mm.388998	NM_027671		Sntg1	4933426D16Rik|G1SYN|SYN4	"syntrophin, gamma 1"	protein-coding	0.01	0.316832
Merged-chr7-41007999-1	chr7	41007949	41008049	+	2	cIP2vsInput	Intergenic	Lx6|LINE|L1	20390	NM_207248	243944	Mm.333806	NM_207248	ENSMUSG00000091692	4930433I11Rik	Gm481	RIKEN cDNA 4930433I11 gene	protein-coding	0	0.356436
Merged-chr13-6492542-1	chr13	6492492	6492592	+	2	cIP2vsInput	Intergenic	Intergenic	-55615	NM_145131	69617	Mm.41933	NM_145131	ENSMUSG00000021193	Pitrm1	2310012C15Rik|AA410010|MP-1|MP1|Ntup1|PreP|mKIAA1104	pitrilysin metallepetidase 1	protein-coding	0	0.336634
Merged-chr15-60346738-1	chr15	60346688	60346788	+	2	cIP2vsInput	Intergenic	Intergenic	-330120	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding	0	0.326733
Merged-chr1-52974799-1	chr1	52974749	52974849	+	2	cIP2vsInput	Intergenic	Intergenic	-21959	NM_144953	67080	Mm.236287	NM_144953		1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding	0	0.316832
Merged-chr3-49472422-1	chr3	49472372	49472472	+	2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	284894	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding	0	0.336634
Merged-chr1-186867355-1	chr1	186867305	186867405	+	2	cIP1vsInput	Intergenic	L1M4b|LINE|L1	-100061	NM_033077	110957	Mm.108054	NM_033077	ENSMUSG00000039224	D1Pas1	Pl10	"DNA segment, Chr 1, Pasteur Institute 1"	protein-coding	0	0.326733
Merged-chr2-152586896-1	chr2	152586846	152586946	+	2	cIP2vsInput	Intergenic	MLTR31FA_MM|LTR|ERVK	-6584	NM_145157	246700	Mm.82820	NM_145157	ENSMUSG00000050645	Defb19	BD-19|Defb24|Tdl|mBD-19	defensin beta 19	protein-coding	0	0.277228
Merged-chr18-87848857-1	chr18	87848807	87848907	+	2	cIP2vsInput	Intergenic	L1MD2|LINE|L1	1045350	NM_018821	54607	Mm.476577	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding	0	0.316832
Merged-chr19-6341138-1	chr19	6341088	6341188	+	2	cIP2vsInput	promoter-TSS (NM_009006)	promoter-TSS (NM_009006)	-112	NM_009006	26412	Mm.25860	NM_009006		Map4k2	AI385662|BL44|GCK|Rab8ip	mitogen-activated protein kinase kinase kinase kinase 2	protein-coding	0.13	0.841584
Merged-chr8-6265170-1	chr8	6265120	6265220	+	2	cIP2vsInput	Intergenic	Intergenic	-1159938	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0.01	0.356436
Merged-chr8-109323800-1	chr8	109323750	109323850	+	2	cIP2vsInput	Intergenic	Intergenic	17108	NR_002928	384864	Mm.390083	NR_002928		Gm1943	-	WD repeat domain 70 pseudogene	pseudo	0.01	0.316832
Merged-chr3-50762541-1	chr3	50762491	50762591	+	2	cIP2vsInput	Intergenic	Intergenic	-318928	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	"solute carrier family 7 (cationic amino acid transporter, y+ system), member 11"	protein-coding	0	0.326733
Merged-chr2-68778127-1	chr2	68778077	68778177	+	2	cIP2vsInput	Intergenic	Intergenic	-83430	NM_172856	241447	Mm.393211	NM_172856		Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding	0	0.346535
Merged-chr3-29726285-1	chr3	29726235	29726335	+	2	cIP2vsInput	Intergenic	Intergenic	286919	NM_007963	14013	Mm.426829	NM_021442	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding	0.02	0.435644
Merged-chr16-79045499-1	chr16	79045449	79045549	+	2	cIP2vsInput	"intron (NM_178855, intron 10 of 26)"	Lx|LINE|L1	45598	NM_178855	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	"transmembrane protease, serine 15"	protein-coding	0	0.29703
Merged-chr5-41951542-1	chr5	41951492	41951592	+	2	cIP2vsInput	Intergenic	Intergenic	-107227	NM_001081422	665775	Mm.158726	NM_001081422	ENSMUSG00000061755	Bod1l	A230054D04Rik|AI853319|FAM44A|mKIAA1327	biorientation of chromosomes in cell division 1-like	protein-coding	0	0.29703
Merged-chr16-9898521-1	chr16	9898471	9898571	+	2	cIP2vsInput	"intron (NM_008170, intron 1 of 11)"	L1MB5|LINE|L1	94012	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	"glutamate receptor, ionotropic, NMDA2A (epsilon 1)"	protein-coding	0	0.346535
Merged-chr17-18265066-1	chr17	18265016	18265116	+	2	cIP2vsInput	"intron (NM_001104543, intron 1 of 5)"	RLTR22_Mur|LTR|ERVK	12500	NM_001104543	665227	Mm.469861	NM_001104543	ENSMUSG00000090417	Vmn2r94	EG665227	"vomeronasal 2, receptor 94"	protein-coding	0.01	0.376238
Merged-chr3-20538225-1	chr3	20538175	20538275	+	2	cIP1vsInput	Intergenic	RMER16-int|LTR|ERVK	-171048	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	"angiotensin II receptor, type 1b"	protein-coding	0.01	0.29703
Merged-chrX-7789463-1	chrX	7789413	7789513	+	2	cIP2vsInput	promoter-TSS (NM_207670)	promoter-TSS (NM_207670)	-532	NM_207670	54645	Mm.194811	NM_207670	ENSMUSG00000031153	Gripap1	AI854681|DXImx47e|GRASP-1|Sfc10|mKIAA1167	GRIP1 associated protein 1	protein-coding	0.02	0.306931
Merged-chr13-52155360-1	chr13	52155310	52155410	+	2	cIP2vsInput	Intergenic	Intergenic	58619	NR_045061	74050	Mm.84860	NR_045061		4921525O09Rik	-	RIKEN cDNA 4921525O09 gene	miscRNA	0	0.49505
Merged-chr3-25626539-1	chr3	25626489	25626589	+	2	cIP2vsInput	"intron (NM_001163387, intron 3 of 5)"	"intron (NM_001163387, intron 3 of 5)"	526768	NM_001163387	192167	Mm.316080	NM_001163387	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|mKIAA1070	neuroligin 1	protein-coding	0	0.316832
Merged-chr16-86073347-1	chr16	86073297	86073397	+	2	cIP1vsInput	Intergenic	Intergenic	-172222	NM_011782	23794	Mm.437478	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|AI481094|ASMP-2	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"	protein-coding	0.01	0.356436
Merged-chr9-18663743-1	chr9	18663693	18663793	+	2	cIP2vsInput	Intergenic	T-rich|Low_complexity|Low_complexity	91890	NM_146606	18322	Mm.246530	NM_146606	ENSMUSG00000054141	Olfr24	MOR132-1|MTPCR51	olfactory receptor 24	protein-coding	0	0.336634
Merged-chr6-54699722-1	chr6	54699672	54699772	+	2	cIP2vsInput	"3' UTR (NM_026629, exon 3 of 3)"	"3' UTR (NM_026629, exon 3 of 3)"	17950	NM_026629	68235	Mm.233860	NM_026629	ENSMUSG00000038065	2410066E13Rik	AI448550|B230212L03Rik	RIKEN cDNA 2410066E13 gene	protein-coding	0.06	0.554455
Merged-chr10-44190829-1	chr10	44190779	44190879	+	2	cIP2vsInput	"intron (NR_001582, intron 2 of 6)"	L1_Mus3|LINE|L1	20382	NR_001582	70365	Mm.87073	NR_001582		Speer5-ps1	1700007C10Rik|SPEER-5|Speer5-ps	"spermatogenesis associated glutamate (E)-rich protein 5, pseudogene 1"	pseudo	0	0.287129
Merged-chr7-66981155-1	chr7	66981105	66981205	+	2	cIP1vsInput	"intron (NM_001033877, intron 8 of 22)"	"intron (NM_001033877, intron 8 of 22)"	141420	NM_001033877	233332	Mm.445763	NM_001033877	ENSMUSG00000058145	Adamts17	AU023434	"a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 17"	protein-coding	0	0.316832
Merged-chr9-35620897-1	chr9	35620847	35620947	+	2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-9012	NM_020264	56872	Mm.390143	NM_020264	ENSMUSG00000032099	Pate4	9530004K16Rik|Pate-B|Svs7	prostate and testis expressed 4	protein-coding	0	0.405941
Merged-chr11-104195678-1	chr11	104195628	104195728	+	2	cIP2vsInput	Intergenic	MIRb|SINE|MIR	9351	NM_199019	237958	Mm.117063	NM_001082535	ENSMUSG00000049506	Sppl2c	4933407P14Rik|IMP5	signal peptide peptidase 2C	protein-coding	0.03	0.49505
Merged-chr9-115878298-1	chr9	115878248	115878348	+	2	cIP2vsInput	Intergenic	Lx4A|LINE|L1	-31157	NM_028638	73748	Mm.485018	NM_028638	ENSMUSG00000056880	Gadl1	1110027M19Rik	glutamate decarboxylase-like 1	protein-coding	0	0.386139
Merged-chr14-71687247-1	chr14	71687197	71687297	+	2	cIP1vsInput	Intergenic	ORR1E|LTR|ERVL-MaLR	-169462	NR_046274	74667	Mm.159286	NR_046274		4930434J06Rik	-	RIKEN cDNA 4930434J06 gene	miscRNA	0	0.366337
Merged-chr9-34228549-1	chr9	34228499	34228599	+	2	cIP2vsInput	Intergenic	Lx7|LINE|L1	186178	NR_040744	77119	Mm.367930	NR_040744		7630403G23Rik	-	RIKEN cDNA 7630403G23 gene	miscRNA	0	0.336634
Merged-chr15-9496043-1	chr15	9495993	9496093	+	2	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	33833	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding	0	0.306931
Merged-chr9-91032893-1	chr9	91032843	91032943	+	2	cIP2vsInput	Intergenic	RMER1C|Other|Other	332906	NM_009573	22771	Mm.477226	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding	0.01	0.455446
Merged-chr5-57481756-1	chr5	57481706	57481806	+	2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	236163	NR_015588	319216	Mm.446765	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	miscRNA	0.01	0.316832
Merged-chr15-52837169-1	chr15	52837119	52837219	+	2	cIP2vsInput	Intergenic	Intergenic	124724	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding	0	0.356436
Merged-chr4-19384965-1	chr4	19384915	19385015	+	2	cIP2vsInput	"intron (NM_013927, intron 8 of 17)"	L1_Mus2|LINE|L1	104115	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding	0	0.336634
Merged-chr14-114113652-1	chr14	114113602	114113702	+	2	cIP2vsInput	Intergenic	Intergenic	-718313	NR_045661	75822	Mm.410813	NR_045661		4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	miscRNA	0	0.326733
Merged-chr8-20371993-1	chr8	20371943	20372043	+	2	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-8791	NM_001177408	100040599	Mm.445582	NM_001177408	ENSMUSG00000074449	Gm15319	OTTMUSG00000020118	predicted gene 15319	protein-coding	0	0.316832
Merged-chr9-121605214-1	chr9	121605164	121605264	+	2	cIP2vsInput	"intron (NR_040740, intron 3 of 3)"	"intron (NR_040740, intron 3 of 3)"	18194	NR_040740	75384	Mm.445955	NR_040740	ENSMUSG00000084995	4930596M17Rik	4930589B17Rik	RIKEN cDNA 4930596M17 gene	miscRNA	0	0.39604
Merged-chr9-13991308-1	chr9	13991258	13991358	+	2	cIP2vsInput	Intergenic	L3|LINE|CR1	163581	NM_176836	72826	Mm.246174	NM_176836	ENSMUSG00000037808	Fam76b	2810485I05Rik|C78303	"family with sequence similarity 76, member B"	protein-coding	0.02	0.316832
Merged-chr2-22135561-1	chr2	22135511	22135611	+	2	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	-91942	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding	0.01	0.435644
Merged-chr16-63915358-1	chr16	63915308	63915408	+	2	cIP1vsInput	Intergenic	Intergenic	-51201	NM_010140	13837	Mm.1977	NM_010140		Epha3	AW492086|Cek4|ETK1|End3|Hek|Hek4|Mek4|Tyro4	Eph receptor A3	protein-coding	0	0.247525
Merged-chr6-137478237-1	chr6	137478187	137478287	+	2	cIP2vsInput	"3' UTR (NM_001271595, exon 21 of 21)"	"3' UTR (NM_001271595, exon 21 of 21)"	41658	NM_001271589	13860	Mm.235346	NM_001271587	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding	0.02	0.366337
Merged-chr16-44340261-1	chr16	44340211	44340311	+	2	cIP1vsInput	Intergenic	Intergenic	-7140	NM_144550	212514	Mm.483587	NM_144550	ENSMUSG00000043065	Spice1	Ccdc52|D16Ertd480e	spindle and centriole associated protein 1	protein-coding	0.01	0.366337
Merged-chr3-143334880-1	chr3	143334830	143334930	+	2	cIP2vsInput	Intergenic	Intergenic	91825	NR_040551	320072	Mm.136397	NR_040551		A830019L24Rik	-	RIKEN cDNA A830019L24 gene	miscRNA	0	0.455446
Merged-chr2-88960928-1	chr2	88960878	88960978	+	2	cIP2vsInput	Intergenic	Intergenic	2460	NM_207140	258241	Mm.377387	NM_207140	ENSMUSG00000048226	Olfr1212	MOR233-17|MOR233-20	olfactory receptor 1212	protein-coding	0.01	0.346535
Merged-chr8-95967181-1	chr8	95967131	95967231	+	2	cIP2vsInput	Intergenic	Intergenic	3637	NR_037310	100499527		NR_037310	ENSMUSG00000093084	Mir1186b	mmu-mir-1186b	microRNA 1186b	miscRNA	0	0.306931
Merged-chr1-174263811-1	chr1	174263761	174263861	+	2	cIP2vsInput	Intergenic	Lx2B|LINE|L1	-12835	NM_146715	258710	Mm.377647	NM_146715	ENSMUSG00000050788	Olfr419	MOR267-6	olfactory receptor 419	protein-coding	0	0.366337
Merged-chr6-82482473-1	chr6	82482423	82482523	+	2	cIP2vsInput	"intron (NM_009313, intron 2 of 5)"	BLACKJACK|DNA|hAT-Blackjack	79998	NM_009313	21336	Mm.8055	NM_009313	ENSMUSG00000030043	Tacr1	Nk1r|Spr|Tac1r	tachykinin receptor 1	protein-coding	0	0.287129
Merged-chr6-149221501-1	chr6	149221451	149221551	+	2	cIP2vsInput	Intergenic	RLTR30|LTR|ERV1	-32789	NM_001113424	232566	Mm.209147	NM_001113424		Amn1	5830467E07Rik|A230083D09|C730024G19Rik	antagonist of mitotic exit network 1	protein-coding	0	0.425743
Merged-chr7-127727736-1	chr7	127727686	127727786	+	2	cIP1vsInput	Intergenic	Intergenic	-2120	NM_198858	244218	Mm.249829	NM_198858		Ctf2	Gm494|NP	cardiotrophin 2	protein-coding	0	0.425743
Merged-chr9-20878535-1	chr9	20878485	20878585	+	2	cIP2vsInput	"exon (NM_145154, exon 2 of 6)"	"exon (NM_145154, exon 2 of 6)"	1175	NM_145154	70726	Mm.34019	NM_145154	ENSMUSG00000038742	Angptl6	6330404E11Rik|AGF|ARP3|Arp5	angiopoietin-like 6	protein-coding	0.1	0.663366
Merged-chr3-89203071-1	chr3	89203021	89203121	+	2	cIP2vsInput	"5' UTR (NM_001077411, exon 1 of 11)"	"5' UTR (NM_001077411, exon 1 of 11)"	131	NM_008094	14466	Mm.5031	NM_008094	ENSMUSG00000028048	Gba	GBA1|GC|GCase|GLUC|betaGC	"glucosidase, beta, acid"	protein-coding	0.02	0.49505
Merged-chr7-26622980-1	chr7	26622930	26623030	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-10902	NM_134231	171265	Mm.377217	NM_134231	ENSMUSG00000091924	Vmn1r185	V1re12	vomeronasal 1 receptor 185	protein-coding	0	0.336634
Merged-chr16-46246852-1	chr16	46246802	46246902	+	2	cIP1vsInput	Intergenic	Intergenic	-126604	NM_032465	84544	Mm.29204	NM_032465	ENSMUSG00000022657	Cd96	1700109I12Rik|Tactile	CD96 antigen	protein-coding	0	0.346535
Merged-chr1-25500560-1	chr1	25500510	25500610	+	2	cIP2vsInput	"intron (NM_175642, intron 9 of 30)"	"intron (NM_175642, intron 9 of 30)"	-222606	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	"predicted gene, 20172"	protein-coding	0	0.316832
Merged-chr7-45162153-1	chr7	45162103	45162203	+	2	cIP2vsInput	Intergenic	Intergenic	-1768	NM_182993	72961	Mm.255631	NM_182993	ENSMUSG00000070570	Slc17a7	2900052E22Rik|AI851913|Vglut1	"solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7"	protein-coding	0.02	0.534653
Merged-chr8-30174193-1	chr8	30174143	30174243	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-394202	NR_045856	71314	Mm.158666	NR_045856	ENSMUSG00000097044	4933433F19Rik	-	RIKEN cDNA 4933433F19 gene	miscRNA	0	0.29703
Merged-chr14-124431823-1	chr14	124431773	124431873	+	2	cIP1vsInput	"intron (NM_207667, intron 1 of 4)"	"intron (NM_207667, intron 1 of 4)"	-239277	NM_010201	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding	0	0.287129
Merged-chr10-104773570-1	chr10	104773520	104773620	+	2	cIP2vsInput	Intergenic	Intergenic	579528	NM_001270900	667692		NM_001270900	ENSMUSG00000097878	Gm8764	EG667692	predicted gene 8764	protein-coding	0.01	0.316832
Merged-chr1-144863107-1	chr1	144863057	144863157	+	2	cIP2vsInput	Intergenic	Intergenic	-87686	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding	0	0.386139
Merged-chr6-48602094-1	chr6	48602044	48602144	+	2	cIP2vsInput	Intergenic	CpG	8211	NM_001079904	58887	Mm.219183	NM_001079901	ENSMUSG00000052751	Repin1	AI425994|Ap4|E430037F08Rik|Zfp-464|Zfp464	replication initiator 1	protein-coding	0.05	0.584158
Merged-chr3-49550688-1	chr3	49550638	49550738	+	2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	206628	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding	0	0.356436
Merged-chr11-83740332-1	chr11	83740282	83740382	+	2	cIP2vsInput	Intergenic	ORR1F|LTR|ERVL-MaLR	-6608	NM_183249	66107	Mm.902	NM_183249	ENSMUSG00000051748	1100001G20Rik	Wdnm1-like	RIKEN cDNA 1100001G20 gene	protein-coding	0	0.485149
Merged-chr8-60706106-1	chr8	60706056	60706156	+	2	cIP2vsInput	Intergenic	Intergenic	50549	NM_001177882	71306	Mm.23242	NM_001177881	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding	0	0.356436
Merged-chr6-143612254-1	chr6	143612204	143612304	+	2	cIP2vsInput	"intron (NR_045732, intron 4 of 4)"	"intron (NR_045732, intron 4 of 4)"	39034	NR_045732	73425	Mm.417844	NR_045732	ENSMUSG00000086887	1700060C16Rik	-	RIKEN cDNA 1700060C16 gene	miscRNA	0	0.247525
Merged-chr4-81892927-1	chr4	81892877	81892977	+	2	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-172453	NR_040659	545641	Mm.216028	NR_040659	ENSMUSG00000085022	Gm5860	EG545641	predicted gene 5860	miscRNA	0.01	0.29703
Merged-chr6-46524909-1	chr6	46524859	46524959	+	2	cIP2vsInput	"intron (NM_001004357, intron 13 of 23)"	"intron (NM_001004357, intron 13 of 23)"	-719487	NM_025771	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0	0.316832
Merged-chr1-70242901-1	chr1	70242851	70242951	+	2	cIP1vsInput	"intron (NM_025728, intron 2 of 7)"	"intron (NM_025728, intron 2 of 7)"	291286	NM_025728	66722	Mm.440554	NM_001271533	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding	0	0.346535
Merged-chr11-83048881-1	chr11	83048831	83048931	+	2	cIP2vsInput	Intergenic	L1VL2|LINE|L1	-8348	NR_073524	237887	Mm.341645	NM_181542	ENSMUSG00000072621	Slfn10-ps	Slfn10|mFLJ00257	"schlafen 10, pseudogene"	pseudo	0	0.356436
Merged-chr5-18295184-1	chr5	18295134	18295234	+	2	cIP2vsInput	"intron (NM_010305, intron 3 of 7)"	"intron (NM_010305, intron 3 of 7)"	65229	NM_010305	14677	Mm.254629	NM_010305	ENSMUSG00000057614	Gnai1	AU046200|Gialpha1|Gnai-1	"guanine nucleotide binding protein (G protein), alpha inhibiting 1"	protein-coding	0.01	0.326733
Merged-chr4-24663830-1	chr4	24663780	24663880	+	2	cIP2vsInput	"intron (NM_001033531, intron 5 of 9)"	"intron (NM_001033531, intron 5 of 9)"	167368	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	"MMS22-like, DNA repair protein"	protein-coding	0	0.316832
Merged-chr4-15235971-1	chr4	15235921	15236021	+	2	cIP2vsInput	Intergenic	Intergenic	-29849	NM_181401	100201	Mm.394111	NM_181401	ENSMUSG00000043252	Tmem64	9630015D15Rik|AI790744|AV300874	transmembrane protein 64	protein-coding	0.02	0.326733
Merged-chr16-81856134-1	chr16	81856084	81856184	+	2	cIP2vsInput	Intergenic	Intergenic	655437	NM_010954	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.405941
Merged-chr8-108795664-1	chr8	108795614	108795714	+	2	cIP2vsInput	"intron (NM_007496, intron 2 of 9)"	"intron (NM_007496, intron 2 of 9)"	81020	NM_007496	11906	Mm.477670	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding	0.01	0.356436
Merged-chr16-39348814-1	chr16	39348764	39348864	+	2	cIP2vsInput	Intergenic	MLT1H|LTR|ERVL-MaLR	446469	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	"immunoglobulin superfamily, member 11"	protein-coding	0.02	0.376238
Merged-chr5-82491656-1	chr5	82491606	82491706	+	2	cIP1vsInput	Intergenic	Intergenic	307409	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mmu-mir-1187	microRNA 1187	miscRNA	0	0.287129
Merged-chr14-117035689-1	chr14	117035639	117035739	+	2	cIP1vsInput	"intron (NM_001079844, intron 1 of 9)"	L1MD|LINE|L1	110374	NM_011821	23888	Mm.440025	NM_001079844	ENSMUSG00000058571	Gpc6	6720429C22Rik|AI480529	glypican 6	protein-coding	0.02	0.316832
Merged-chr4-118196313-1	chr4	118196263	118196363	+	2	cIP2vsInput	Intergenic	Intergenic	-16270	NM_172382	230674	Mm.234234	NM_001161823	ENSMUSG00000033326	Kdm4a	D4Ertd222e|JHDM3A|Jmjd2|Jmjd2a|mKIAA0677	lysine (K)-specific demethylase 4A	protein-coding	0.03	0.524752
Merged-chr4-102041397-1	chr4	102041347	102041447	+	2	cIP2vsInput	Intergenic	Intergenic	54557	NM_001085520	381536	Mm.297685	NM_001085520		Gm12789	OTTMUSG00000008445	predicted gene 12789	protein-coding	0.02	0.376238
Merged-chr8-41961355-1	chr8	41961305	41961405	+	2	cIP2vsInput	"intron (NR_045497, intron 3 of 5)"	MLT2D|LTR|ERVL	134088	NR_045497	69966	Mm.416903	NR_045497		2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	miscRNA	0.01	0.425743
Merged-chr19-11104192-1	chr19	11104142	11104242	+	2	cIP1vsInput	"intron (NM_027058, intron 5 of 6)"	MLT1C-int|LTR|ERVL-MaLR	-23089	NM_022430	64381	Mm.34460	NM_022430	ENSMUSG00000024730	Ms4a8a	2010004L09Rik|AI481240|CD20L5|Ms4a8	"membrane-spanning 4-domains, subfamily A, member 8A"	protein-coding	0	0.356436
Merged-chr3-92939762-1	chr3	92939712	92939812	+	2	cIP2vsInput	Intergenic	Intergenic	-4724	NM_033175	94060	Mm.301748	NM_033175	ENSMUSG00000045475	Lce3c	2300007B01Rik|AV076207|Eig3|Sprrl1	late cornified envelope 3C	protein-coding	0	0.336634
Merged-chr5-13058144-1	chr5	13058094	13058194	+	2	cIP1vsInput	Intergenic	Intergenic	-338640	NM_001243072	20346	Mm.483774	NM_001243072	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	"sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A"	protein-coding	0	0.277228
Merged-chr13-74550942-1	chr13	74550892	74550992	+	2	cIP1vsInput	Intergenic	Intergenic	-56992	NM_146231	235956	Mm.296909	NM_146231		Zfp825	-	zinc finger protein 825	protein-coding	0.01	0.376238
Merged-chr12-18244861-1	chr12	18244811	18244911	+	2	cIP2vsInput	Intergenic	Intergenic	-269649	NM_001033157	236366	Mm.352227	NM_001033157		5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding	0	0.306931
Merged-chr14-82605783-1	chr14	82605733	82605833	+	2	cIP2vsInput	Intergenic	Intergenic	-1837780	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0.01	0.326733
Merged-chr1-107265522-1	chr1	107265472	107265572	+	2	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	12849	NM_201363	381286	Mm.337362	NM_201363	ENSMUSG00000073601	Serpinb3c	1110001H02Rik|1110013A16Rik|Scca2|Serpinb4	"serine (or cysteine) peptidase inhibitor, clade B, member 3C"	protein-coding	0.01	0.336634
Merged-chr7-88827389-1	chr7	88827339	88827439	+	2	cIP2vsInput	Intergenic	L1MDa|LINE|L1	397116	NM_028238	72433	Mm.276669	NM_028238	ENSMUSG00000030559	Rab38	2310011F14Rik|AU043391|cht	"RAB38, member of RAS oncogene family"	protein-coding	0	0.306931
Merged-chr16-4805202-1	chr16	4805152	4805252	+	2	cIP2vsInput	Intergenic	ERVB4_1B-I_MM-int|LTR|ERVK	-15267	NM_025670	66626	Mm.443028	NM_025670	ENSMUSG00000004071	Cdip1	2700048O17Rik|5730403B10Rik|AU018521|AW742692|CDIP	cell death inducing Trp53 target 1	protein-coding	0.02	0.435644
Merged-chr15-103514426-1	chr15	103514376	103514476	+	2	cIP2vsInput	"intron (NM_008800, intron 2 of 15)"	"intron (NM_008800, intron 2 of 15)"	11128	NM_008800	18574	Mm.390792	NM_008800	ENSMUSG00000022489	Pde1b	63kDa|Pde1b1	"phosphodiesterase 1B, Ca2+-calmodulin dependent"	protein-coding	0.01	0.49505
Merged-chr1-184409533-1	chr1	184409483	184409583	+	2	cIP2vsInput	Intergenic	(ATATG)n|Simple_repeat|Simple_repeat	148158	NR_040472	73590	Mm.82792	NR_040472		1700112H15Rik	-	RIKEN cDNA 1700112H15 gene	miscRNA	0.01	0.366337
Merged-chr4-90511028-1	chr4	90510978	90511078	+	2	cIP2vsInput	Intergenic	Intergenic	-149714	NR_033610	619842	Mm.484218	NR_033610	ENSMUSG00000080756	Gm12633	OTTMUSG00000007790	zinc finger protein 352 pseudogene	pseudo	0	0.336634
Merged-chr1-112814031-1	chr1	112813981	112814081	+	2	cIP2vsInput	Intergenic	MLTR14|LTR|ERV1	-949113	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik	dermatan sulfate epimerase-like	protein-coding	0	0.405941
Merged-chr2-112745341-1	chr2	112745291	112745391	+	2	cIP1vsInput	"intron (NM_177652, intron 60 of 103)"	Lx4A|LINE|L1	185659	NM_001165935	74268	Mm.436657	NM_001165935		Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	"apoptosis, caspase activation inhibitor"	protein-coding	0	0.376238
Merged-chr16-88204709-1	chr16	88204659	88204759	+	2	cIP1vsInput	"intron (NM_146072, intron 1 of 16)"	"intron (NM_146072, intron 1 of 16)"	85549	NM_146072	14805	Mm.5134	NM_010348		Grik1	A830007B11Rik|D16Ium24|D16Ium24e|GluK1|GluK5|Glur-5|Glur5|Glurbeta1	"glutamate receptor, ionotropic, kainate 1"	protein-coding	0.01	0.39604
Merged-chr6-3399325-1	chr6	3399275	3399375	+	2	cIP2vsInput	"5' UTR (NM_010156, exon 1 of 2)"	"5' UTR (NM_010156, exon 1 of 2)"	246	NM_010156	209086	Mm.196013	NM_177590		Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding	0.01	0.277228
Merged-chr3-26553683-1	chr3	26553633	26553733	+	2	cIP2vsInput	Intergenic	Intergenic	-83948	NM_029150	70862	Mm.330943	NM_027583	ENSMUSG00000039335	Spata16	4921511F01Rik|4930503K02Rik|Nyd-sp12	spermatogenesis associated 16	protein-coding	0	0.287129
Merged-chr17-22646550-1	chr17	22646500	22646600	+	2	cIP2vsInput	Intergenic	Intergenic	45402	NM_001104575	628185	Mm.390947	NM_001104575	ENSMUSG00000094921	Vmn2r112	EG628185|V2rp1	"vomeronasal 2, receptor 112"	protein-coding	0	0.316832
Merged-chrX-80781600-1	chrX	80781550	80781650	+	2	cIP2vsInput	Intergenic	Lx7|LINE|L1	-289044	NM_138751	192216	Mm.490421	NM_138751	ENSMUSG00000025666	Tmem47	3010015F07Rik|AI115536|BCMP1|Tm4sf10	transmembrane protein 47	protein-coding	0.01	0.336634
Merged-chr2-81507120-1	chr2	81507070	81507170	+	2	cIP2vsInput	Intergenic	Intergenic	-546538	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0	0.29703
Merged-chr17-76130586-1	chr17	76130536	76130636	+	2	cIP1vsInput	Intergenic	Lx3_Mus|LINE|L1	269563	NR_033456	100043885	Mm.127562	NR_033456		Gm4710	-	predicted gene 4710	miscRNA	0	0.336634
Merged-chr12-17904283-1	chr12	17904233	17904333	+	2	cIP2vsInput	Intergenic	MMSAT4|Satellite|Satellite	213469	NM_016677	53602	Mm.489835	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding	0	0.306931
Merged-chr3-64547985-1	chr3	64547935	64548035	+	2	cIP2vsInput	"intron (NM_001104619, intron 2 of 4)"	"intron (NM_001104619, intron 2 of 4)"	11833	NM_001104619	667069	Mm.484956	NM_001104619	ENSMUSG00000090581	Vmn2r6	EG620718|EG667069	"vomeronasal 2, receptor 6"	protein-coding	0	0.326733
Merged-chr8-17279269-1	chr8	17279219	17279319	+	2	cIP1vsInput	"intron (NM_053171, intron 1 of 69)"	"intron (NM_053171, intron 1 of 69)"	256116	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding	0	0.277228
Merged-chr9-90041593-1	chr9	90041543	90041643	+	2	cIP2vsInput	Intergenic	Intergenic	-12674	NM_007801	13036	Mm.2277	NM_007801	ENSMUSG00000032359	Ctsh	AL022844	cathepsin H	protein-coding	0	0.346535
Merged-chr2-96827508-1	chr2	96827458	96827558	+	2	cIP2vsInput	Intergenic	MIR|SINE|MIR	-640166	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.316832
Merged-chr17-55333196-1	chr17	55333146	55333246	+	2	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-112521	NM_172829	240119	Mm.311687	NM_172829	ENSMUSG00000024172	St6gal2	C230064G14Rik|St6galII|mKIAA1877	"beta galactoside alpha 2,6 sialyltransferase 2"	protein-coding	0	0.287129
Merged-chr7-96465144-1	chr7	96465094	96465194	+	2	cIP2vsInput	"intron (NM_011858, intron 3 of 32)"	RCHARR1|DNA|hAT-Charlie	-123180	NR_046043	670727	Mm.421352	NR_046043	ENSMUSG00000085751	Gm15412	OTTMUSG00000021245	predicted gene 15412	miscRNA	0	0.366337
Merged-chr6-106277069-1	chr6	106277019	106277119	+	2	cIP2vsInput	"intron (NM_001109749, intron 5 of 25)"	"intron (NM_001109749, intron 5 of 25)"	158304	NM_001109751	269784	Mm.321683	NM_001109749	ENSMUSG00000064293	Cntn4	9630050B05|Axcam|BIG-2	contactin 4	protein-coding	0.02	0.366337
Merged-chr6-81695451-1	chr6	81695401	81695501	+	2	cIP2vsInput	Intergenic	Intergenic	201225	NR_030151	723871		NR_030151		Mir468	Mirn468|mmu-mir-468	microRNA 468	miscRNA	0	0.356436
Merged-chr1-67668198-1	chr1	67668148	67668248	+	2	cIP2vsInput	Intergenic	Intergenic	545132	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding	0.01	0.346535
Merged-chr5-138300491-1	chr5	138300441	138300541	+	2	cIP2vsInput	"intron (NM_016964, intron 21 of 33)"	"intron (NM_016964, intron 21 of 33)"	19982	NM_016964	50878	Mm.285609	NM_016964	ENSMUSG00000036928	Stag3	SA-2	stromal antigen 3	protein-coding	0.01	0.376238
Merged-chr18-73227320-1	chr18	73227270	73227370	+	2	cIP2vsInput	Intergenic	Intergenic	-345385	NM_001039214	240396	Mm.436942	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 homolog C (C. elegans)	protein-coding	0.02	0.316832
Merged-chr17-76367050-1	chr17	76367000	76367100	+	2	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	506027	NR_033456	100043885	Mm.127562	NR_033456		Gm4710	-	predicted gene 4710	miscRNA	0.01	0.316832
Merged-chr3-23845562-1	chr3	23845512	23845612	+	2	cIP2vsInput	Intergenic	Intergenic	1594192	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	miscRNA	0	0.326733
Merged-chr6-23901376-1	chr6	23901326	23901426	+	2	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-61955	NM_001252105	320405	Mm.259632	NM_001252105	ENSMUSG00000017978	Cadps2	A230044C21Rik|Caps-2|Caps2|Cpd2	Ca2+-dependent activator protein for secretion 2	protein-coding	0	0.366337
Merged-chr6-58815763-1	chr6	58815713	58815813	+	2	cIP1vsInput	Intergenic	Intergenic	-17937	NM_028705	73998	Mm.191892	NM_028705	ENSMUSG00000029804	Herc3	5730409F18Rik|AI646603|mKIAA0032	hect domain and RLD 3	protein-coding	0.02	0.267327
Merged-chr8-50762205-1	chr8	50762155	50762255	+	2	cIP2vsInput	Intergenic	Intergenic	394093	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.29703
Merged-chr16-63119612-1	chr16	63119562	63119662	+	2	cIP2vsInput	Intergenic	Intergenic	265278	NM_011173	19128	Mm.127156	NM_011173	ENSMUSG00000022912	Pros1	AW214361	protein S (alpha)	protein-coding	0	0.326733
Merged-chr2-89152431-1	chr2	89152381	89152481	+	2	cIP2vsInput	Intergenic	Lx8|LINE|L1	-1095	NM_146892	258894	Mm.330379	NM_146892	ENSMUSG00000075100	Olfr1223	MOR233-10	olfactory receptor 1223	protein-coding	0	0.356436
Merged-chr6-137505637-1	chr6	137505587	137505687	+	2	cIP2vsInput	"intron (NM_001271589, intron 7 of 13)"	"intron (NM_001271589, intron 7 of 13)"	14258	NM_001271589	13860	Mm.235346	NM_001271587	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding	0	0.425743
Merged-chr1-4272802-1	chr1	4272752	4272852	+	2	cIP2vsInput	Intergenic	Intergenic	87512	NM_011283	19888	Mm.294263	NM_001195662	ENSMUSG00000025900	Rp1	Dcdc3|Orp1|Rp1h|mG145	retinitis pigmentosa 1 (human)	protein-coding	0	0.326733
Merged-chr3-127671527-1	chr3	127671477	127671577	+	2	cIP2vsInput	"intron (NM_027808, intron 13 of 13)"	"intron (NM_027808, intron 13 of 13)"	38382	NM_009718	11924	Mm.42017	NM_009718	ENSMUSG00000027967	Neurog2	Atoh4|Math4A|bHLHa8|ngn-2|ngn2	neurogenin 2	protein-coding	0.01	0.376238
Merged-chr11-10195917-1	chr11	10195867	10195967	+	2	cIP1vsInput	Intergenic	Intergenic	-918099	NM_177033	319922	Mm.487612	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding	0	0.326733
Merged-chr10-105911281-1	chr10	105911231	105911331	+	2	cIP2vsInput	Intergenic	Intergenic	69802	NM_025602	52713	Mm.339224	NM_025602		Ccdc59	2300004H16Rik|D10Ertd718e	coiled-coil domain containing 59	protein-coding	0	0.326733
Merged-chr4-7829738-1	chr4	7829688	7829788	+	2	cIP1vsInput	Intergenic	Intergenic	269050	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	miscRNA	0.01	0.277228
Merged-chr15-37894719-1	chr15	37894669	37894769	+	2	cIP2vsInput	Intergenic	MYSERV6-int|LTR|ERVK	66336	NM_199476	382985	Mm.24738	NM_199476	ENSMUSG00000022292	Rrm2b	p53R2	ribonucleotide reductase M2 B (TP53 inducible)	protein-coding	0	0.316832
Merged-chr1-123511452-1	chr1	123511402	123511502	+	2	cIP1vsInput	"intron (NM_199021, intron 5 of 25)"	"intron (NM_199021, intron 5 of 25)"	534107	NM_199021	269109	Mm.483255	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding	0	0.336634
Merged-chr1-116960332-1	chr1	116960282	116960382	+	2	cIP2vsInput	Intergenic	Intergenic	1275195	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0.01	0.356436
Merged-chr10-114424188-1	chr10	114424138	114424238	+	2	cIP2vsInput	"intron (NM_146241, intron 15 of 18)"	L1_Mus3|LINE|L1	377182	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding	0	0.39604
Merged-chr13-72419851-2	chr13	72419796	72419907	+	2	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	208713	NR_030701	328287	Mm.235072	NR_030701		Gm20554	D430050G20	"predicted gene, 20554"	miscRNA	0.018018	0.5
Merged-chr10-118968631-1	chr10	118968581	118968681	+	2	cIP2vsInput	Intergenic	ORR1D1|LTR|ERVL-MaLR	-99728	NM_001014390	69181	Mm.458174	NM_001014390	ENSMUSG00000028630	Dyrk2	1810038L18Rik	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	protein-coding	0	0.336634
Merged-chr17-91534020-1	chr17	91533970	91534070	+	2	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-441218	NM_020252	18189	Mm.312068	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0	0.366337
Merged-chr9-112490592-1	chr9	112490542	112490642	+	2	cIP2vsInput	Intergenic	Intergenic	234018	NR_033433	620760	Mm.259863	NR_015468	ENSMUSG00000087038	2900079G21Rik	C130083B14|Gm6179	RIKEN cDNA 2900079G21 gene	miscRNA	0.01	0.336634
Merged-chr15-38360987-1	chr15	38360937	38361037	+	2	cIP1vsInput	Intergenic	RMER6C|LTR|ERVK	-60280	NM_013692	21847	Mm.4292	NM_013692	ENSMUSG00000037465	Klf10	AI115143|EGR[a]|Egral|Gdnfif|Tieg|Tieg1|mGIF	Kruppel-like factor 10	protein-coding	0	0.39604
Merged-chr18-19303964-1	chr18	19303914	19304014	+	2	cIP2vsInput	Intergenic	Intergenic	698133	NM_007882	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding	0	0.326733
Merged-chr5-113471695-1	chr5	113471645	113471745	+	2	cIP2vsInput	Intergenic	Tigger17c|DNA|TcMar-Tigger	-78725	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding	0.01	0.386139
Merged-chr18-10279891-1	chr18	10279841	10279941	+	2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-45288	NM_001083628	381157	Mm.261535	NM_001083628	ENSMUSG00000042942	Greb1l	mKIAA4095	growth regulation by estrogen in breast cancer-like	protein-coding	0	0.356436
Merged-chr16-26217270-1	chr16	26217220	26217320	+	2	cIP1vsInput	Intergenic	L1M2|LINE|L1	-111486	NM_173379	210530		NM_173379		Leprel1	4832416N06|AW553532|Mlat4|P3H2	leprecan-like 1	protein-coding	0	0.326733
Merged-chr17-42101352-1	chr17	42101302	42101402	+	2	cIP2vsInput	Intergenic	Intergenic	-214595	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding	0.01	0.29703
Merged-chr2-137354048-1	chr2	137353998	137354098	+	2	cIP2vsInput	Intergenic	Intergenic	-237528	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding	0	0.455446
Merged-chr9-38470286-1	chr9	38470236	38470336	+	2	cIP2vsInput	Intergenic	Intergenic	-2463	NM_146804	258800	Mm.377697	NM_146804	ENSMUSG00000096794	Olfr905	MOR167-1	olfactory receptor 905	protein-coding	0.01	0.316832
Merged-chr1-63595911-1	chr1	63595861	63595961	+	2	cIP2vsInput	"3' UTR (NM_011780, exon 26 of 26)"	"3' UTR (NM_011780, exon 26 of 26)"	91016	NM_001081658	241073	Mm.297680	NM_001081658	ENSMUSG00000069085	Dytn	Gm215	dystrotelin	protein-coding	0	0.287129
Merged-chr13-81081048-1	chr13	81080998	81081098	+	2	cIP2vsInput	Intergenic	Intergenic	116974	NR_015587	319983	Mm.343027	NR_015587	ENSMUSG00000097098	9330111N05Rik	-	RIKEN cDNA 9330111N05 gene	miscRNA	0.01	0.306931
Merged-chr14-51498226-1	chr14	51498176	51498276	+	2	cIP1vsInput	Intergenic	Intergenic	46263	NM_009486	22301	Mm.482572	NM_009486	ENSMUSG00000070448	Vmn2r89	V2r10|V2r11	"vomeronasal 2, receptor 89"	protein-coding	0.02	0.326733
Merged-chr1-74196165-1	chr1	74196115	74196215	+	2	cIP2vsInput	Intergenic	B3|SINE|B2	-1534	NM_178241	227288	Mm.337035	NM_178241	ENSMUSG00000048480	Cxcr1	Il8ra	chemokine (C-X-C motif) receptor 1	protein-coding	0.02	0.564356
Merged-chr9-91804179-1	chr9	91804129	91804229	+	2	cIP2vsInput	Intergenic	Intergenic	-388757	NM_001195693	100504689	Mm.464262	NM_001195693	ENSMUSG00000095654	Plscr5	331000	"phospholipid scramblase family, member 5"	protein-coding	0	0.316832
Merged-chr7-140042015-1	chr7	140041965	140042065	+	2	cIP1vsInput	Intergenic	L1M2|LINE|L1	5624	NM_027201	69752	Mm.200818	NM_027201	ENSMUSG00000025470	Zfp511	2410004P19Rik|C86579|Znf511	zinc finger protein 511	protein-coding	0	0.316832
Merged-chr3-73276987-1	chr3	73276937	73277037	+	2	cIP2vsInput	"intron (NR_040557, intron 2 of 4)"	"intron (NR_040557, intron 2 of 4)"	204664	NR_040547	74693	Mm.292227	NR_040547		4930509J09Rik	-	RIKEN cDNA 4930509J09 gene	miscRNA	0	0.336634
Merged-chr2-92028642-1	chr2	92028592	92028692	+	2	cIP2vsInput	Intergenic	Intergenic	-4472	NM_011957	26427	Mm.10353	NM_011957	ENSMUSG00000027230	Creb3l1	Oasis	cAMP responsive element binding protein 3-like 1	protein-coding	0.01	0.574257
Merged-chr2-155663715-1	chr2	155663665	155663765	+	2	cIP2vsInput	"exon (NM_001163452, exon 6 of 19)"	"exon (NM_001163452, exon 6 of 19)"	28669	NM_019828	56407	Mm.469980	NM_001163452	ENSMUSG00000038324	Trpc4ap	4833429F06Rik|D2Ertd113e|Trrp4ap|mFLJ00177|truss	"transient receptor potential cation channel, subfamily C, member 4 associated protein"	protein-coding	0.01	0.356436
Merged-chr6-104702384-2	chr6	104702291	104702478	+	2	cIP1vsInput|cIP2vsInput	"intron (NM_017383, intron 5 of 22)"	"intron (NM_017383, intron 5 of 22)"	209340	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding	0.010695	0.335106
Merged-chr18-89870089-1	chr18	89870039	89870139	+	2	cIP2vsInput	Intergenic	Intergenic	-100953	NM_001039173	623279	Mm.447164	NM_001039173		Dok6	Dok-6	docking protein 6	protein-coding	0	0.346535
Merged-chr2-14724194-1	chr2	14724144	14724244	+	2	cIP2vsInput	"intron (NM_023116, intron 2 of 13)"	"intron (NM_023116, intron 2 of 13)"	3552	NR_028497	625342	Mm.484784	NR_028497		Gm13315	OTTMUSG00000011384	lactate dehydrogenase A pseudogene	pseudo	0	0.415842
Merged-chr3-49831737-1	chr3	49831687	49831787	+	2	cIP2vsInput	Intergenic	Intergenic	-74421	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding	0	0.326733
Merged-chr15-21826789-1	chr15	21826739	21826839	+	2	cIP2vsInput	Intergenic	Intergenic	715337	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding	0	0.336634
Merged-chr10-89383986-1	chr10	89383936	89384036	+	2	cIP2vsInput	Intergenic	Intergenic	59981	NM_001079876	237436	Mm.11982	NM_001033331	ENSMUSG00000074802	Gas2l3	8430435B07Rik|Gm240	growth arrest-specific 2 like 3	protein-coding	0.01	0.336634
Merged-chr5-21223374-1	chr5	21223324	21223424	+	2	cIP2vsInput	"intron (NM_175437, intron 8 of 30)"	L1ME3G|LINE|L1	37107	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Pion	A530088I07Rik|GSAP	pigeon homolog (Drosophila)	protein-coding	0	0.306931
Merged-chr12-32726585-1	chr12	32726535	32726635	+	2	cIP1vsInput	Intergenic	B4A|SINE|B4	-93750	NM_021524	59027		NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding	0	0.465347
Merged-chr7-36974847-1	chr7	36974797	36974897	+	2	cIP2vsInput	Intergenic	Intergenic	276729	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding	0.01	0.50495
Merged-chr17-57929619-1	chr17	57929569	57929669	+	2	cIP2vsInput	"intron (NM_001081653, intron 3 of 23)"	"intron (NM_001081653, intron 3 of 23)"	160049	NM_001081653	620292	Mm.391030	NM_001081653	ENSMUSG00000038048	Cntnap5c	Caspr5-3|EG620292|Gm325	contactin associated protein-like 5C	protein-coding	0	0.29703
Merged-chr17-63135568-1	chr17	63135518	63135618	+	2	cIP2vsInput	"intron (NM_015794, intron 7 of 8)"	"intron (NM_015794, intron 7 of 8)"	-254251	NM_010109	13640	Mm.401670	NM_010109		Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding	0	0.326733
Merged-chrX-137646780-1	chrX	137646730	137646830	+	2	cIP2vsInput	"intron (NM_030688, intron 1 of 10)"	"intron (NM_030688, intron 1 of 10)"	75231	NM_030688	60367	Mm.328321	NM_030688	ENSMUSG00000059203	Il1rapl2	-	interleukin 1 receptor accessory protein-like 2	protein-coding	0	0.366337
Merged-chr2-141767200-1	chr2	141767150	141767250	+	2	cIP2vsInput	"intron (NM_001013802, intron 7 of 18)"	"intron (NM_001013802, intron 7 of 18)"	-1095724	NM_178382	71436	Mm.426781	NM_001172160	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding	0	0.336634
Merged-chr4-6096571-1	chr4	6096521	6096621	+	2	cIP2vsInput	Intergenic	Intergenic	-94534	NM_026534	68053	Mm.427021	NM_026534		Ubxn2b	3110003A22Rik|6430407D20Rik|AI451665|p37	UBX domain protein 2B	protein-coding	0	0.306931
Merged-chr3-108069766-1	chr3	108069716	108069816	+	2	cIP2vsInput	Intergenic	ORSL-2b|DNA|hAT-Tip100	16861	NM_028779	109674	Mm.274335	NM_028779	ENSMUSG00000027889	Ampd2	1200014F01Rik|AI552571|Ampd-2	adenosine monophosphate deaminase 2	protein-coding	0.04	0.594059
Merged-chr11-20086591-1	chr11	20086541	20086641	+	2	cIP2vsInput	"intron (NM_146243, intron 4 of 8)"	"intron (NM_146243, intron 4 of 8)"	26360	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding	0	0.435644
Merged-chr6-56985252-1	chr6	56985202	56985302	+	2	cIP2vsInput	promoter-TSS (NM_134174)	promoter-TSS (NM_134174)	-90	NM_134174	171192	Mm.377172	NM_134174	ENSMUSG00000090346	Vmn1r5	V1rc19	vomeronasal 1 receptor 5	protein-coding	0	0.227723
Merged-chr2-178048399-1	chr2	178048349	178048449	+	2	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	25115	NM_001177399	626848	Mm.422604	XM_003946452		Etohi1	-	ethanol induced 1	protein-coding	0	0.336634
Merged-chr1-143322061-1	chr1	143322011	143322111	+	2	cIP2vsInput	Intergenic	Intergenic	-318636	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2"	protein-coding	0	0.415842
Merged-chr11-9224094-1	chr11	9224044	9224144	+	2	cIP2vsInput	"intron (NM_178259, intron 3 of 61)"	Lx7|LINE|L1	32152	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	"ATP-binding cassette, sub-family A (ABC1), member 13"	protein-coding	0	0.326733
Merged-chr18-23062286-1	chr18	23062236	23062336	+	2	cIP1vsInput	Intergenic	L1MCb|LINE|L1	-20633	NM_199024	319211	Mm.209896	NM_001161483	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding	0	0.356436
Merged-chr1-129887816-1	chr1	129887766	129887866	+	2	cIP2vsInput	"intron (NM_172485, intron 12 of 27)"	"intron (NM_172485, intron 12 of 27)"	535183	NM_007827	13137	Mm.436759	NM_007827	ENSMUSG00000026401	Daf2	AI323748|Cd55b|Daf|Daf-TM|TM-DAF	decay accelerating factor 2	protein-coding	0	0.316832
Merged-chr6-19252811-1	chr6	19252761	19252861	+	2	cIP2vsInput	Intergenic	Intergenic	386493	NM_001167757	75196	Mm.67665	NM_001167757	ENSMUSG00000029517	Ankrd7	4930532L20Rik|AV278427	ankyrin repeat domain 7	protein-coding	0	0.277228
Merged-chr12-41576614-1	chr12	41576564	41576664	+	2	cIP2vsInput	Intergenic	L1MB2|LINE|L1	-52150	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding	0	0.277228
Merged-chr8-88811201-1	chr8	88811151	88811251	+	2	cIP2vsInput	Intergenic	Lx7|LINE|L1	114173	NM_001128171	74256	Mm.490395	NM_001128170	ENSMUSG00000036712	Cyld	2010013M14Rik|2900009M21Rik|C130039D01Rik|CDMT|CYLD1|EAC|mKIAA0849	cylindromatosis (turban tumor syndrome)	protein-coding	0.02	0.326733
Merged-chr19-44162341-1	chr19	44162291	44162391	+	2	cIP2vsInput	"intron (NM_181422, intron 2 of 14)"	"intron (NM_181422, intron 2 of 14)"	-15895	NM_028607	73689	Mm.124685	NM_028607	ENSMUSG00000057506	Bloc1s2a	2410089B13Rik|BLOS2|Bloc1s2	"biogenesis of lysosome-related organelles complex-1, subunit 2A"	protein-coding	0.01	0.316832
Merged-chr6-36943744-1	chr6	36943694	36943794	+	2	cIP1vsInput	"intron (NM_001081206, intron 22 of 33)"	"intron (NM_001081206, intron 22 of 33)"	-132383	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding	0.01	0.257426
Merged-chr4-124938127-1	chr4	124938077	124938177	+	2	cIP1vsInput	"intron (NM_177573, intron 1 of 4)"	"intron (NM_177573, intron 1 of 4)"	1079	NM_177573	194268	Mm.266907	NM_177573		9930104L06Rik	-	RIKEN cDNA 9930104L06 gene	protein-coding	0	0.386139
Merged-chr12-92897046-1	chr12	92896996	92897096	+	2	cIP1vsInput	Intergenic	Intergenic	-1047889	NM_011344	20338	Mm.250605	NM_001039089	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding	0	0.336634
Merged-chr6-7794455-1	chr6	7794405	7794505	+	2	cIP2vsInput	Intergenic	Intergenic	-50769	NM_052993	94192	Mm.482425	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	"core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1"	protein-coding	0	0.346535
Merged-chr13-78705102-1	chr13	78705052	78705152	+	2	cIP2vsInput	Intergenic	Intergenic	-506120	NM_010151	13865	Mm.439653	NM_010151		Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR3|Erbal3|SVP44|Tcfcoup1	"nuclear receptor subfamily 2, group F, member 1"	protein-coding	0	0.346535
Merged-chr3-5904735-1	chr3	5904685	5904785	+	2	cIP2vsInput	Intergenic	Intergenic	-328487	NM_001163305	19302	Mm.132336	NM_001163304	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding	0	0.376238
Merged-chrX-162775947-1	chrX	162775897	162775997	+	2	cIP2vsInput	"intron (NM_009031, intron 10 of 11)"	"intron (NM_009031, intron 10 of 11)"	15575	NM_009031	245688	Mm.486181	NM_009031	ENSMUSG00000031353	Rbbp7	AA409861|AI173248|AU019541|BB114024|mRbAp46	retinoblastoma binding protein 7	protein-coding	0	0.336634
Merged-chr2-87152626-1	chr2	87152576	87152676	+	2	cIP2vsInput	Intergenic	Intergenic	-1967	NM_146593	258586	Mm.223113	NM_146593	ENSMUSG00000075158	Olfr1111	MOR181-2	olfactory receptor 1111	protein-coding	0	0.356436
Merged-chr3-90703739-1	chr3	90703689	90703789	+	2	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	-8048	NM_009114	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding	0	0.247525
Merged-chr6-74625540-1	chr6	74625490	74625590	+	2	cIP2vsInput	Intergenic	Intergenic	-1155873	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0	0.287129
Merged-chrX-139020368-1	chrX	139020318	139020418	+	2	cIP1vsInput	Intergenic	L1MCa|LINE|L1	64868	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	"serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7"	protein-coding	0.01	0.306931
Merged-chr2-60383835-1	chr2	60383785	60383885	+	2	cIP2vsInput	promoter-TSS (NM_013825)	promoter-TSS (NM_013825)	-604	NM_013825	17076	Mm.2074	NM_013825	ENSMUSG00000026980	Ly75	CD205|DEC-205|DEC205	lymphocyte antigen 75	protein-coding	0.01	0.336634
Merged-chr11-40230437-1	chr11	40230387	40230487	+	2	cIP2vsInput	Intergenic	(TTTTG)n|Simple_repeat|Simple_repeat	462245	NM_134017	108645	Mm.293771	NM_001199274	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	"methionine adenosyltransferase II, beta"	protein-coding	0	0.287129
Merged-chr6-13034611-1	chr6	13034561	13034661	+	2	cIP2vsInput	Intergenic	Intergenic	-35148	NM_027992	71900	Mm.27742	NM_027992	ENSMUSG00000029571	Tmem106b	2310036D22Rik|5830455K21Rik|6430519M21Rik|AI428776|AI661344	transmembrane protein 106B	protein-coding	0	0.29703
Merged-chr2-18986679-1	chr2	18986629	18986729	+	2	cIP2vsInput	"intron (NM_008845, intron 1 of 9)"	MER47B|DNA|TcMar-Tigger	11442	NM_008845	18718	Mm.313977	NM_008845	ENSMUSG00000026737	Pip4k2a	AW742916|Pip5k2a	"phosphatidylinositol-5-phosphate 4-kinase, type II, alpha"	protein-coding	0	0.336634
Merged-chr2-3090726-1	chr2	3090676	3090776	+	2	cIP1vsInput	Intergenic	Intergenic	-27662	NM_001081161	269233	Mm.23044	NM_001081161		Fam171a1	9630050M13Rik|AA409679	"family with sequence similarity 171, member A1"	protein-coding	0	0.336634
Merged-chr14-84347613-1	chr14	84347563	84347663	+	2	cIP2vsInput	Intergenic	Intergenic	-95950	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0	0.316832
Merged-chr13-100345765-1	chr13	100345715	100345815	+	2	cIP2vsInput	Intergenic	Intergenic	-28077	NM_021545	53880	Mm.218759	NM_021545		Naip7	Birc1g|Naip-rs4B|Naip6	"NLR family, apoptosis inhibitory protein 7"	protein-coding	0	0.267327
Merged-chr8-45442262-1	chr8	45442212	45442312	+	2	cIP1vsInput	Intergenic	Intergenic	-31723	NM_126166	142980	Mm.33874	NM_126166	ENSMUSG00000031639	Tlr3	AI957183	toll-like receptor 3	protein-coding	0	0.29703
Merged-chr8-37863035-1	chr8	37862985	37863085	+	2	cIP2vsInput	"intron (NM_145841, intron 2 of 7)"	RLTR31B_Mm|LTR|ERVK	389167	NR_029884	723860		NR_029884		Mir383	Mirn383|mmu-mir-383	microRNA 383	miscRNA	0.01	0.465347
Merged-chr4-40446112-1	chr4	40446062	40446162	+	2	cIP2vsInput	Intergenic	Intergenic	-26068	NM_177175	320500	Mm.156365	NM_001166009	ENSMUSG00000046593	Tmem215	A930001M12Rik	transmembrane protein 215	protein-coding	0.01	0.376238
Merged-chr8-73464195-1	chr8	73464145	73464245	+	2	cIP1vsInput	Intergenic	Intergenic	-111639	NM_010687	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large	BPFD#36|Gyltl1a|Mbp-1|Mbp1|enr|fg|froggy|mKIAA0609|myd	like-glycosyltransferase	protein-coding	0	0.346535
Merged-chr5-12490943-1	chr5	12490893	12490993	+	2	cIP2vsInput	"intron (NM_028882, intron 4 of 17)"	"intron (NM_028882, intron 4 of 17)"	107777	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	"sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D"	protein-coding	0	0.356436
Merged-chr19-19585627-1	chr19	19585577	19585677	+	2	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-474431	NM_001043354	225998		NM_001043354	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta	RAR-related orphan receptor beta	protein-coding	0.01	0.356436
Merged-chr8-55067764-1	chr8	55067714	55067814	+	2	cIP2vsInput	Intergenic	Intergenic	113036	NM_001253756	234267	Mm.241700	NM_001253754	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding	0	0.29703
Merged-chr4-25237537-1	chr4	25237487	25237587	+	2	cIP2vsInput	"intron (NM_021318, intron 1 of 5)"	"intron (NM_021318, intron 1 of 5)"	5339	NM_021318	57756	Mm.87325	NM_021318	ENSMUSG00000028259	Fhl5	1700027G07Rik|Act	four and a half LIM domains 5	protein-coding	0.01	0.346535
Merged-chr18-35065965-1	chr18	35065915	35066015	+	2	cIP2vsInput	Intergenic	RMER6C|LTR|ERVK	-52947	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	"catenin (cadherin associated protein), alpha 1"	protein-coding	0.02	0.425743
Merged-chr9-124151342-1	chr9	124151292	124151392	+	2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	29799	NM_009917	12774	Mm.14302	NM_009917	ENSMUSG00000079227	Ccr5	AM4-7|CD195|Cmkbr5	chemokine (C-C motif) receptor 5	protein-coding	0.01	0.326733
Merged-chr5-109883981-1	chr5	109883931	109884031	+	2	cIP2vsInput	Intergenic	PB1D10|SINE|Alu	-49582	NR_040366	100642166		NR_040366	ENSMUSG00000090015	Gm15446	OTTMUSG00000022004	predicted gene 15446	miscRNA	0	0.415842
Merged-chr5-14144911-1	chr5	14144861	14144961	+	2	cIP2vsInput	"intron (NM_011348, intron 2 of 16)"	"intron (NM_011348, intron 2 of 16)"	119635	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	"sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E"	protein-coding	0	0.326733
Merged-chr1-96568134-1	chr1	96568084	96568184	+	2	cIP2vsInput	Intergenic	Intergenic	94439	NR_040478	75159	Mm.243854	NR_040478		4930533P14Rik	-	RIKEN cDNA 4930533P14 gene	miscRNA	0	0.287129
Merged-chr13-112383734-1	chr13	112383684	112383784	+	2	cIP2vsInput	"3' UTR (NM_001168403, exon 12 of 12)"	"3' UTR (NM_001168403, exon 12 of 12)"	-80336	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding	0.01	0.346535
Merged-chr9-55115993-1	chr9	55115943	55116043	+	2	cIP1vsInput	Intergenic	Intergenic	-33376	NM_180600	109161	Mm.207894	NM_180600	ENSMUSG00000032307	Ube2q2	3010021M21Rik	ubiquitin-conjugating enzyme E2Q (putative) 2	protein-coding	0	0.346535
Merged-chr1-60706606-1	chr1	60706556	60706656	+	2	cIP1vsInput	Intergenic	Intergenic	-39782	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding	0	0.386139
Merged-chr10-50806496-1	chr10	50806446	50806546	+	2	cIP2vsInput	"intron (NM_198007, intron 36 of 41)"	"intron (NM_198007, intron 36 of 41)"	-89155	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding	0	0.386139
Merged-chr1-56063248-1	chr1	56063198	56063298	+	2	cIP2vsInput	Intergenic	L1MEc|LINE|L1	132007	NR_045837	329159	Mm.98697	NR_045837		9130227L01Rik	-	RIKEN cDNA 9130227L01 gene	miscRNA	0	0.336634
Merged-chr16-7431724-1	chr16	7431674	7431774	+	2	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	361889	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	"RNA binding protein, fox-1 homolog (C. elegans) 1"	protein-coding	0	0.326733
Merged-chr2-57684490-1	chr2	57684440	57684540	+	2	cIP2vsInput	Intergenic	Intergenic	-313665	NM_172855	241391	Mm.484118	NM_172855	ENSMUSG00000026828	Galnt5	4832424J23	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5	protein-coding	0	0.346535
Merged-chr2-168981506-1	chr2	168981456	168981556	+	2	cIP2vsInput	Intergenic	Intergenic	3237	NR_040326	75508	Mm.271256	NR_040326	ENSMUSG00000086348	1700017J07Rik	-	RIKEN cDNA 1700017J07 gene	miscRNA	0.02	0.465347
Merged-chr11-107849564-1	chr11	107849514	107849614	+	2	cIP2vsInput	Intergenic	Intergenic	-55100	NM_019431	54377	Mm.103724	NM_019431		Cacng4	AI413107|AW491861	"calcium channel, voltage-dependent, gamma subunit 4"	protein-coding	0	0.386139
Merged-chr19-58027964-1	chr19	58027914	58028014	+	2	cIP2vsInput	"intron (NM_181415, intron 27 of 28)"	L1_Mur3|LINE|L1	-268240	NR_040449	791347	Mm.452208	NR_040449		Gm10007	ENSMUSG00000056739	predicted gene 10007	miscRNA	0	0.366337
Merged-chr12-10181626-1	chr12	10181576	10181676	+	2	cIP2vsInput	Intergenic	Intergenic	-188345	NM_027588	70881	Mm.272843	NM_027588	ENSMUSG00000020622	Nt5c1b	4921514H13Rik|AIRP|CN-IB	"5'-nucleotidase, cytosolic IB"	protein-coding	0	0.336634
Merged-chr13-66497331-1	chr13	66497281	66497381	+	2	cIP2vsInput	Intergenic	Intergenic	-56213	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding	0	0.247525
Merged-chr16-65753869-2	chr16	65753816	65753922	+	1.95	cIP1vsInput|cIP2vsInput	Intergenic	Intergenic	-61764	NM_028572	73569	Mm.482366	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like 3 (Drosophila)	protein-coding	0	0.28972
Merged-chr4-18805971-1	chr4	18805921	18806021	+	1.9	cIP2vsInput	Intergenic	MusHAL1|LINE|L1	-474879	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding	0	0.29703
Merged-chr5-148003865-1	chr5	148003815	148003915	+	1.9	cIP2vsInput	"intron (NM_029920, intron 1 of 14)"	"intron (NM_029920, intron 1 of 14)"	46545	NM_029920	77521	Mm.244177	NM_029920	ENSMUSG00000029651	Mtus2	5730592G18Rik|A730013O20Rik|AU067634|C130038G02Rik|Cazip|Gm763|mKIAA0774	microtubule associated tumor suppressor candidate 2	protein-coding	0.01	0.405941
Merged-chr15-52252877-1	chr15	52252827	52252927	+	1.9	cIP2vsInput	Intergenic	Intergenic	-42676	NM_172816	239436	Mm.208831	NM_172816	ENSMUSG00000022315	Slc30a8	C820002P14Rik|ZnT-8|ZnT8	"solute carrier family 30 (zinc transporter), member 8"	protein-coding	0.01	0.287129
Merged-chr4-49013909-1	chr4	49013859	49013959	+	1.9	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-45553	NM_178756	272031	Mm.299460	NM_178756	ENSMUSG00000063446	E130309F12Rik	Lppr1|PRG-3|mKIAA4247	RIKEN cDNA E130309F12 gene	protein-coding	0	0.346535
Merged-chr2-34383074-1	chr2	34383024	34383124	+	1.9	cIP1vsInput	Intergenic	Intergenic	-11038	NM_016768	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding	0.02	0.415842
Merged-chrX-169452296-1	chrX	169452246	169452346	+	1.9	cIP2vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	-131953	NM_008222	15159	Mm.284033	NM_008222	ENSMUSG00000031352	Hccs	-	holocytochrome c synthetase	protein-coding	0.01	0.287129
Merged-chr16-31815983-1	chr16	31815933	31816033	+	1.9	cIP2vsInput	"intron (NM_001252433, intron 13 of 24)"	"intron (NM_001252433, intron 13 of 24)"	61633	NM_001252436	13383	Mm.382	NM_001252433	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	"discs, large homolog 1 (Drosophila)"	protein-coding	0	0.326733
Merged-chr2-170905834-1	chr2	170905784	170905884	+	1.9	cIP2vsInput	Intergenic	Intergenic	174027	NM_001163686	76829	Mm.41633	NM_001163686	ENSMUSG00000027560	Dok5	2700055C10Rik	docking protein 5	protein-coding	0	0.366337
Merged-chr5-3892434-1	chr5	3892384	3892484	+	1.9	cIP2vsInput	"intron (NM_172135, intron 1 of 1)"	"intron (NM_172135, intron 1 of 1)"	1499	NM_001013023	545725	Mm.489094	NM_001013023	ENSMUSG00000040429	Mterf	4931431L11Rik|9230106K09Rik|Mterf1	mitochondrial transcription termination factor	protein-coding	0.01	0.386139
Merged-chr18-85058045-1	chr18	85057995	85058095	+	1.9	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-106521	NM_025969	67105	Mm.250617	NM_025969	ENSMUSG00000024645	Timm21	1700034H14Rik|2700002I20Rik	tranlocase of inner mitochondrial membrane 21	protein-coding	0	0.346535
Merged-chr8-62156090-1	chr8	62156040	62156140	+	1.9	cIP1vsInput	Intergenic	Intergenic	-32972	NM_011922	26359	Mm.42179	NM_001136089	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding	0	0.376238
Merged-chr12-104159088-1	chr12	104159038	104159138	+	1.9	cIP1vsInput	Intergenic	MERVL_2A-int|LTR|ERVL	-5216	NM_008458	16625	Mm.422814	NM_008458		Serpina3c	1A1|Kalbp|Klkbp|spi2	"serine (or cysteine) peptidase inhibitor, clade A, member 3C"	protein-coding	0.01	0.346535
Merged-chr2-80260081-1	chr2	80260031	80260131	+	1.9	cIP2vsInput	Intergenic	ORR1B1-int|LTR|ERVL-MaLR	-32389	NM_177256	320769	Mm.60992	NR_033713	ENSMUSG00000050114	Prdx6b	1-cysPrx-P1|4930414C22Rik|Aop2-rs1|Prdx5-rs1|Prdx6-ps1|Prdx6-rs1|Prdx6-rs1-ps	peroxiredoxin 6B	protein-coding	0	0.316832
Merged-chr17-4282441-1	chr17	4282391	4282491	+	1.9	cIP2vsInput	Intergenic	Intergenic	-160339	NR_045462	78043	Mm.460785	NR_045462		4930548J01Rik	1700113K09Rik	RIKEN cDNA 4930548J01 gene	miscRNA	0	0.376238
Merged-chr4-38304030-1	chr4	38303980	38304080	+	1.9	cIP2vsInput	Intergenic	Intergenic	-1146263	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding	0.01	0.247525
Merged-chr14-34792281-1	chr14	34792231	34792331	+	1.9	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-27855	NM_008166	14803	Mm.413604	NM_008166		Grid1	GluD1|GluRdelta1	"glutamate receptor, ionotropic, delta 1"	protein-coding	0	0.376238
Merged-chr3-42061910-1	chr3	42061860	42061960	+	1.9	cIP2vsInput	Intergenic	Intergenic	319292	NM_027271	73852	Mm.29006	NM_001099785	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	"DNA segment, Chr 3, ERATO Doi 751, expressed"	protein-coding	0	0.39604
Merged-chr10-130417396-1	chr10	130417346	130417446	+	1.9	cIP2vsInput	TTS (NM_001102602)	TTS (NM_001102602)	12216	NM_001102602	623734	Mm.469840	NM_001102602	ENSMUSG00000092048	Vmn2r85	EG623734	"vomeronasal 2, receptor 85"	protein-coding	0.01	0.326733
Merged-chr4-121663113-1	chr4	121663063	121663163	+	1.9	cIP1vsInput	Intergenic	ID_B1|SINE|B4	-40988	NM_001099309	666927	Mm.465133	NM_001099309		Gm12887	OTTMUSG00000008910	predicted gene 12887	protein-coding	0	0.39604
Merged-chr9-17392600-1	chr9	17392550	17392650	+	1.9	cIP2vsInput	Intergenic	Intergenic	-899667	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	"cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1"	protein-coding	0	0.306931
Merged-chr12-50253763-1	chr12	50253713	50253813	+	1.9	cIP2vsInput	Intergenic	Intergenic	395460	NM_008858	18760	Mm.133719	NM_008858	ENSMUSG00000002688	Prkd1	PKD|PKD1|Pkcm|Prkcm	protein kinase D1	protein-coding	0	0.267327
Merged-chr17-48708369-1	chr17	48708319	48708419	+	1.9	cIP2vsInput	Intergenic	Intergenic	-224213	NM_027452	70530	Mm.133607	NM_027452	ENSMUSG00000040490	Lrfn2	5730420O05Rik|SALM1|mKIAA1246	leucine rich repeat and fibronectin type III domain containing 2	protein-coding	0	0.326733
Merged-chr18-87531614-1	chr18	87531564	87531664	+	1.9	cIP2vsInput	Intergenic	Intergenic	818566	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding	0	0.316832
Merged-chr5-39946397-1	chr5	39946347	39946447	+	1.9	cIP2vsInput	Intergenic	Intergenic	-301766	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding	0	0.326733
Merged-chr4-85888933-1	chr4	85888883	85888983	+	1.9	cIP2vsInput	Intergenic	Intergenic	-164982	NM_029967	77739	Mm.331690	NM_029967	ENSMUSG00000066113	Adamtsl1	5930437A14Rik|6720426B09Rik|ADAMTSL-1	ADAMTS-like 1	protein-coding	0	0.326733
Merged-chr11-103081000-1	chr11	103080950	103081050	+	1.9	cIP2vsInput	"intron (NM_152813, intron 1 of 14)"	"intron (NM_152813, intron 1 of 14)"	20658	NM_152813	72469	Mm.264743	NM_152813	ENSMUSG00000020937	Plcd3	2610205J15Rik|mKIAA1964	"phospholipase C, delta 3"	protein-coding	0.02	0.50495
Merged-chr11-30307402-1	chr11	30307352	30307452	+	1.9	cIP2vsInput	Intergenic	Intergenic	-87630	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	"spectrin beta, non-erythrocytic 1"	protein-coding	0	0.376238
Merged-chrX-103529377-1	chrX	103529327	103529427	+	1.9	cIP2vsInput	Intergenic	Intergenic	-16123	NR_033398	668415	Mm.483779	NR_033398		Gm9159	EG668415	predicted gene 9159	pseudo	0.12	0.693069
Merged-chr8-63227984-1	chr8	63227934	63228034	+	1.9	cIP2vsInput	"intron (NM_001252620, intron 6 of 11)"	"intron (NM_001252620, intron 6 of 11)"	276639	NM_023689	72902	Mm.334552	NM_001252620	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3"	protein-coding	0	0.356436
Merged-chr11-40450560-1	chr11	40450510	40450610	+	1.9	cIP2vsInput	Intergenic	L2a|LINE|L2	242122	NM_134017	108645	Mm.293771	NM_001199274	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	"methionine adenosyltransferase II, beta"	protein-coding	0	0.326733
Merged-chr6-58344339-1	chr6	58344289	58344389	+	1.9	cIP1vsInput	Intergenic	L1_Mur1|LINE|L1	37042	NM_053232	113859	Mm.377156	NM_053232	ENSMUSG00000091734	Vmn1r29	V1rc2	vomeronasal 1 receptor 29	protein-coding	0	0.346535
Merged-chr2-137405713-1	chr2	137405663	137405763	+	1.9	cIP1vsInput	Intergenic	URR1B|DNA|hAT-Charlie	-289193	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding	0.01	0.306931
Merged-chr5-65906949-1	chr5	65906899	65906999	+	1.9	cIP2vsInput	Intergenic	Intergenic	43380	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	"ras homolog gene family, member H"	protein-coding	0	0.435644
Merged-chr1-17970472-1	chr1	17970422	17970522	+	1.9	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	166579	NM_030033	78081	Mm.319913	NM_030033	ENSMUSG00000025774	Crisp4	9230112K08Rik	cysteine-rich secretory protein 4	protein-coding	0	0.277228
Merged-chr9-85097512-1	chr9	85097462	85097562	+	1.9	cIP2vsInput	Intergenic	Intergenic	229612	NM_001160378	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	D930050G01Rik	"family with sequence similarity 46, member A"	protein-coding	0.01	0.336634
Merged-chr9-19585309-1	chr9	19585259	19585359	+	1.9	cIP2vsInput	"exon (NM_146524, exon 1 of 1)"	"exon (NM_146524, exon 1 of 1)"	798	NM_146524	258517	Mm.377548	NM_146524	ENSMUSG00000043087	Olfr855	MOR148-1	olfactory receptor 855	protein-coding	0.01	0.455446
Merged-chr10-107975505-1	chr10	107975455	107975555	+	1.9	cIP2vsInput	Intergenic	Intergenic	-63371	NM_001177567	628870	Mm.336090	NM_001177567	ENSMUSG00000091455	Otogl	EG628870|Gm6924	otogelin-like	protein-coding	0	0.336634
Merged-chr3-120936256-1	chr3	120936206	120936306	+	1.9	cIP2vsInput	Intergenic	Intergenic	235439	NM_028456	66568	Mm.263163	NM_025637	ENSMUSG00000028133	Rwdd3	2510027J23Rik|3110037C01Rik|AI035684|AI662458|X2CR1	RWD domain containing 3	protein-coding	0	0.356436
Merged-chr4-47892967-1	chr4	47892917	47893017	+	1.9	cIP2vsInput	Intergenic	Intergenic	-158281	NM_015743	18124	Mm.487935	NM_015743		Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	"nuclear receptor subfamily 4, group A, member 3"	protein-coding	0.01	0.336634
Merged-chr12-71597027-1	chr12	71596977	71597077	+	1.9	cIP2vsInput	Intergenic	Intergenic	56420	NR_045941	73815	Mm.416916	NR_045941		4930404H11Rik	-	RIKEN cDNA 4930404H11 gene	miscRNA	0	0.376238
Merged-chr11-9001690-1	chr11	9001640	9001740	+	1.9	cIP2vsInput	"intron (NM_008316, intron 5 of 7)"	"intron (NM_008316, intron 5 of 7)"	9447	NM_008316	15574	Mm.42201	NM_008316	ENSMUSG00000020413	Hus1	mHus1	Hus1 homolog (S. pombe)	protein-coding	0	0.39604
Merged-chr17-35178682-1	chr17	35178632	35178732	+	1.9	cIP2vsInput	Intergenic	Intergenic	-2681	NM_019467	11629	Mm.10747	NM_019467	ENSMUSG00000024397	Aif1	AI607846|AIF-1|D17H6S50E|G1|Iba1	allograft inflammatory factor 1	protein-coding	0.02	0.60396
Merged-chr14-89475962-1	chr14	89475912	89476012	+	1.9	cIP2vsInput	Intergenic	Intergenic	-420262	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0	0.29703
Merged-chr10-109314639-1	chr10	109314589	109314689	+	1.9	cIP2vsInput	Intergenic	Intergenic	-303664	NM_001252341	20979	Mm.489829	NM_001252341	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding	0	0.336634
Merged-chr6-59789586-1	chr6	59789536	59789636	+	1.9	cIP1vsInput	Intergenic	Intergenic	-363296	NM_183183	243385	Mm.485751	NM_183183	ENSMUSG00000045441	Gprin3	C030038J10Rik|C730021L23	GPRIN family member 3	protein-coding	0.01	0.257426
Merged-chr13-115631080-1	chr13	115631030	115631130	+	1.9	cIP2vsInput	Intergenic	Intergenic	-529116	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding	0.01	0.356436
Merged-chr7-53436392-1	chr7	53436342	53436442	+	1.9	cIP2vsInput	Intergenic	Intergenic	-1398853	NM_178705	233271	Mm.474990	NM_178705		Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding	0	0.316832
Merged-chr16-22373386-1	chr16	22373336	22373436	+	1.9	cIP2vsInput	Intergenic	Intergenic	66184	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant gene 5	protein-coding	0	0.405941
Merged-chr1-182607895-1	chr1	182607845	182607945	+	1.9	cIP2vsInput	"intron (NM_130890, intron 10 of 20)"	"intron (NM_130890, intron 10 of 20)"	42888	NM_130890	170725	Mm.189201	NM_001145806	ENSMUSG00000038599	Capn8	nCL-2|nCL-2'	calpain 8	protein-coding	0.01	0.336634
Merged-chr18-83940285-1	chr18	83940235	83940335	+	1.9	cIP2vsInput	Intergenic	Intergenic	146277	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding	0	0.326733
Merged-chr15-14107155-1	chr15	14107105	14107205	+	1.9	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-933516	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	K-cadherin|cad6|cadherin-6	cadherin 6	protein-coding	0	0.287129
Merged-chr11-45201117-1	chr11	45201067	45201167	+	1.9	cIP2vsInput	Intergenic	Intergenic	-84189	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	OTTMUSG00000005475	predicted gene 12159	miscRNA	0	0.356436
Merged-chr15-15994500-1	chr15	15994450	15994550	+	1.9	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-783601	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0	0.356436
Merged-chr15-70909501-1	chr15	70909451	70909551	+	1.9	cIP2vsInput	Intergenic	Intergenic	818337	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	"family with sequence similarity 135, member B"	protein-coding	0	0.306931
Merged-chr14-39828735-1	chr14	39828685	39828785	+	1.9	cIP2vsInput	Intergenic	Intergenic	173072	NR_045936	73591	Mm.65499	NR_045936		1700109I08Rik	-	RIKEN cDNA 1700109I08 gene	miscRNA	0	0.356436
Merged-chr16-39554112-1	chr16	39554062	39554162	+	1.9	cIP2vsInput	Intergenic	Lx5b|LINE|L1	651767	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	"immunoglobulin superfamily, member 11"	protein-coding	0	0.376238
Merged-chr1-115607139-1	chr1	115607089	115607189	+	1.9	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-77998	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0	0.39604
Merged-chr5-54989166-1	chr5	54989116	54989216	+	1.9	cIP2vsInput	Intergenic	Lx4A|LINE|L1	639174	NR_038045	330086	Mm.254449	NM_177871		Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	miscRNA	0	0.316832
Merged-chrX-128030439-1	chrX	128030389	128030489	+	1.9	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	636146	NR_003646	245598	Mm.72281	NR_003646	ENSMUSG00000049815	4921511C20Rik	Gm383	high density lipoprotein (HDL) binding protein pseudogene	pseudo	0	0.356436
Merged-chr10-66159281-1	chr10	66159231	66159331	+	1.9	cIP2vsInput	Intergenic	RLTR15|LTR|ERVK	-35217	NR_038039	69433	Mm.23366	NR_038039		1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	miscRNA	0.01	0.326733
Merged-chr2-77608169-1	chr2	77608119	77608219	+	1.9	cIP2vsInput	"intron (NM_178723, intron 3 of 9)"	"intron (NM_178723, intron 3 of 9)"	-88503	NM_001113400	241494	Mm.490320	NM_001113399	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding	0	0.405941
Merged-chr6-62522552-1	chr6	62522502	62522602	+	1.9	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-734305	NM_008167	14804	Mm.447390	NM_008167		Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	"glutamate receptor, ionotropic, delta 2"	protein-coding	0.01	0.376238
Merged-chr4-55317560-1	chr4	55317510	55317610	+	1.9	cIP2vsInput	Intergenic	MIRb|SINE|MIR	-32482	NM_009011	19359	Mm.196846	NM_009011	ENSMUSG00000028426	Rad23b	0610007D13Rik|AV001138|HR23B|mHR23B|p58	RAD23b homolog (S. cerevisiae)	protein-coding	0	0.346535
Merged-chr18-41693672-1	chr18	41693622	41693722	+	1.9	cIP2vsInput	Intergenic	Intergenic	257522	NM_029942	77619	Mm.30649	NM_029942	ENSMUSG00000056671	Prelid2	1700003A01Rik|C330008K14Rik	PRELI domain containing 2	protein-coding	0	0.29703
Merged-chr14-15595363-1	chr14	15595313	15595413	+	1.9	cIP2vsInput	Intergenic	L1Md_F3|LINE|L1	-156376	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding	0	0.316832
Merged-chr12-42630577-1	chr12	42630527	42630627	+	1.9	cIP1vsInput	Intergenic	Intergenic	1001813	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding	0.01	0.356436
Merged-chr4-12374822-1	chr4	12374772	12374872	+	1.9	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-202807	NM_026558	68099	Mm.25340	NM_026558	ENSMUSG00000028218	Fam92a	6720467C03Rik|Fam92a1	"family with sequence similarity 92, member A"	protein-coding	0.01	0.376238
Merged-chr2-77598381-1	chr2	77598331	77598431	+	1.9	cIP2vsInput	"intron (NM_178723, intron 3 of 9)"	"intron (NM_178723, intron 3 of 9)"	-78715	NM_001113400	241494	Mm.490320	NM_001113399	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding	0	0.326733
Merged-chr5-128681312-1	chr5	128681262	128681362	+	1.9	cIP2vsInput	Intergenic	Intergenic	-54934	NM_021311	57749	Mm.272720	NM_021311	ENSMUSG00000029423	Piwil1	MIWI	piwi-like RNA-mediated gene silencing 1	protein-coding	0	0.336634
Merged-chr9-82853242-1	chr9	82853192	82853292	+	1.9	cIP1vsInput	Intergenic	B3|SINE|B2	23436	NM_022986	65099	Mm.41415	NM_001168240	ENSMUSG00000032251	Irak1bp1	4921528N06Rik|AI851240|Aabp3|Aip70|Simpl	interleukin-1 receptor-associated kinase 1 binding protein 1	protein-coding	0	0.336634
Merged-chr4-145328305-1	chr4	145328255	145328355	+	1.9	cIP2vsInput	Intergenic	MYSERV6-int|LTR|ERVK	-13158	NM_009401	21941	Mm.12810	NM_009401		Tnfrsf8	Cd30|D1S166E|Ki|Ki-1	"tumor necrosis factor receptor superfamily, member 8"	protein-coding	0	0.346535
Merged-chr1-103454244-1	chr1	103454194	103454294	+	1.9	cIP2vsInput	Intergenic	Lx4A|LINE|L1	-1314575	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0	0.336634
Merged-chr7-13108390-1	chr7	13108340	13108440	+	1.9	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-5443	NM_001167536	100312473	Mm.480296	NM_001167536	ENSMUSG00000070816	Vmn1r86	ENSMUSG00000070816|Gm10301	vomeronasal 1 receptor 86	protein-coding	0.02	0.277228
Merged-chr9-39941241-1	chr9	39941191	39941291	+	1.9	cIP2vsInput	Intergenic	Intergenic	-1021	NM_147107	259111	Mm.223481	NM_147107	ENSMUSG00000051493	Olfr974	MOR171-1	olfactory receptor 974	protein-coding	0	0.336634
Merged-chr2-157585456-1	chr2	157585406	157585506	+	1.9	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-19095	NM_016916	53619	Mm.490288	NM_016916	ENSMUSG00000067787	Blcap	AI462828|Bc10	bladder cancer associated protein homolog (human)	protein-coding	0	0.346535
Merged-chr12-10049865-1	chr12	10049815	10049915	+	1.9	cIP2vsInput	Intergenic	Intergenic	-320106	NM_027588	70881	Mm.272843	NM_027588	ENSMUSG00000020622	Nt5c1b	4921514H13Rik|AIRP|CN-IB	"5'-nucleotidase, cytosolic IB"	protein-coding	0	0.316832
Merged-chr10-93723802-1	chr10	93723752	93723852	+	1.9	cIP2vsInput	"intron (NM_021320, intron 5 of 9)"	"intron (NM_021320, intron 5 of 9)"	-40480	NR_038017	100504069	Mm.391412	NR_038017	ENSMUSG00000085723	Gm15915	OTTMUSG00000027787	predicted gene 15915	miscRNA	0.01	0.346535
Merged-chr3-53764398-1	chr3	53764348	53764448	+	1.9	cIP2vsInput	Intergenic	Intergenic	99409	NM_026435	67890	Mm.23067	NM_026435		Ufm1	1810045K17Rik|AI132708|AI463323|ENSMUSG00000074598|Gm10726	ubiquitin-fold modifier 1	protein-coding	0.01	0.405941
Merged-chr12-71111050-1	chr12	71111000	71111100	+	1.9	cIP2vsInput	promoter-TSS (NM_029227)	promoter-TSS (NM_029227)	-378	NM_029227	75266	Mm.402075	NM_029227	ENSMUSG00000021078	Tomm20l	4930553D19Rik	translocase of outer mitochondrial membrane 20 homolog (yeast)-like	protein-coding	0.02	0.316832
Merged-chr9-50453648-1	chr9	50453598	50453698	+	1.9	cIP2vsInput	Intergenic	Intergenic	-40877	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	1600029D21Rik	0610037B23Rik|AA407923|AU043048|PLET1	RIKEN cDNA 1600029D21 gene	protein-coding	0	0.346535
Merged-chr4-7548537-1	chr4	7548487	7548587	+	1.9	cIP2vsInput	Intergenic	Intergenic	-12151	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	miscRNA	0	0.39604
Merged-chr3-49829360-1	chr3	49829310	49829410	+	1.9	cIP1vsInput	Intergenic	Intergenic	-72044	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding	0	0.207921
Merged-chr1-71153251-1	chr1	71153201	71153301	+	1.9	cIP1vsInput	Intergenic	Intergenic	-50279	NM_007525	12021	Mm.490738	NM_007525	ENSMUSG00000026196	Bard1	ENSMUSG00000060893|ENSMUSG00000073653	BRCA1 associated RING domain 1	protein-coding	0.01	0.306931
Merged-chr4-21495330-1	chr4	21495280	21495380	+	1.9	cIP2vsInput	Intergenic	Intergenic	190633	NM_001080771	230025	Mm.208541	NM_001080771	ENSMUSG00000040478	Prdm13	-	PR domain containing 13	protein-coding	0	0.316832
Merged-chr17-94490520-1	chr17	94490470	94490570	+	1.9	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	259372	NM_176917	76781	Mm.486648	NM_176917	ENSMUSG00000055660	Mettl4	2410198H06Rik|A730091E08Rik|AV296509|HsT661	methyltransferase like 4	protein-coding	0	0.29703
Merged-chr9-81413426-1	chr9	81413376	81413476	+	1.9	cIP2vsInput	Intergenic	Intergenic	-218504	NR_040394	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	miscRNA	0	0.316832
Merged-chr7-58563480-1	chr7	58563430	58563530	+	1.9	cIP2vsInput	Intergenic	Intergenic	-94722	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	"ATPase, class V, type 10A"	protein-coding	0	0.356436
Merged-chr1-99577816-1	chr1	99577766	99577866	+	1.9	cIP2vsInput	Intergenic	Intergenic	-194949	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding	0.01	0.316832
Merged-chr17-58489622-1	chr17	58489572	58489672	+	1.9	cIP2vsInput	Intergenic	L1ME4c|LINE|L1	501753	NM_027001	69239	Mm.246732	NM_027001	ENSMUSG00000024227	2610034M16Rik	AV114557	RIKEN cDNA 2610034M16 gene	protein-coding	0	0.39604
Merged-chr17-54567656-1	chr17	54567606	54567706	+	1.9	cIP2vsInput	Intergenic	Intergenic	-197582	NR_045825	69418	Mm.391004	NR_045825		1700025K24Rik	-	RIKEN cDNA 1700025K24 gene	miscRNA	0.01	0.39604
Merged-chr14-95061598-1	chr14	95061548	95061648	+	1.9	cIP2vsInput	Intergenic	Intergenic	-819668	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.29703
Merged-chr12-62943913-1	chr12	62943863	62943963	+	1.9	cIP2vsInput	Intergenic	Intergenic	1419281	NM_178714	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0	0.346535
Merged-chr14-118959971-1	chr14	118959921	118960021	+	1.9	cIP2vsInput	"intron (NM_008929, intron 3 of 11)"	"intron (NM_008929, intron 3 of 11)"	22039	NM_008929	100037258	Mm.12616	NM_008929	ENSMUSG00000022136	Dnajc3	AA408985|AU067833|Dnajc3a|Dnajc3b|Prkri|mp58|p58|p58IPK	"DnaJ (Hsp40) homolog, subfamily C, member 3"	protein-coding	0.01	0.346535
Merged-chr7-127337966-1	chr7	127337916	127338016	+	1.9	cIP2vsInput	Intergenic	MER2|DNA|TcMar-Tigger	7348	NM_146202	233890	Mm.23031	NM_146202	ENSMUSG00000047371	Zfp768	BC026432|Znf768	zinc finger protein 768	protein-coding	0.01	0.425743
Merged-chr6-12947955-1	chr6	12947905	12948005	+	1.9	cIP2vsInput	Intergenic	L1MC|LINE|L1	-121804	NM_027992	71900	Mm.27742	NM_027992	ENSMUSG00000029571	Tmem106b	2310036D22Rik|5830455K21Rik|6430519M21Rik|AI428776|AI661344	transmembrane protein 106B	protein-coding	0.01	0.306931
Merged-chr12-108306600-1	chr12	108306550	108306650	+	1.9	cIP2vsInput	"exon (NM_001044380, exon 1 of 9)"	"exon (NM_001044380, exon 1 of 9)"	330	NM_001044380	214305	Mm.36423	NM_001044380	ENSMUSG00000021260	Hhipl1	1600002O04Rik|AK129450|mKIAA1822	hedgehog interacting protein-like 1	protein-coding	0.14	0.742574
Merged-chr3-25257392-1	chr3	25257342	25257442	+	1.9	cIP2vsInput	Intergenic	Intergenic	895915	NM_001163387	192167	Mm.316080	NM_001163387	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|mKIAA1070	neuroligin 1	protein-coding	0	0.336634
Merged-chr4-70733670-1	chr4	70733620	70733720	+	1.9	cIP2vsInput	Intergenic	Intergenic	-198742	NM_172694	230316	Mm.251188	NM_172694		Megf9	4933405H16Rik|9630025C07|Egfl5|mKIAA0818	multiple EGF-like-domains 9	protein-coding	0	0.326733
Merged-chr16-85655976-1	chr16	85655926	85656026	+	1.9	cIP2vsInput	Intergenic	RLTR25B|LTR|ERVK	-105603	NM_144853	224405		NM_144853		Cyyr1	-	cysteine and tyrosine-rich protein 1	protein-coding	0	0.356436
Merged-chrX-20417100-1	chrX	20417050	20417150	+	1.9	cIP2vsInput	Intergenic	L1MDa|LINE|L1	-43427	NM_199317	382207	Mm.281517	NM_199317	ENSMUSG00000037315	Phf16	5730598B06|AI851988|AW544806|Jade3|mKIAA0215	PHD finger protein 16	protein-coding	0	0.346535
Merged-chr1-86339330-1	chr1	86339280	86339380	+	1.9	cIP2vsInput	Intergenic	ID_B1|SINE|B4	11955	NR_028478	100303740		NR_028478		Snora75	MBI-55	"small nucleolar RNA, H/ACA box 75"	snoRNA	0.01	0.514851
Merged-chr4-72084561-1	chr4	72084511	72084611	+	1.9	cIP2vsInput	Intergenic	Charlie7|DNA|hAT-Charlie	116358	NM_011599	21885	Mm.399716	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg1|Tle4l	"transducin-like enhancer of split 1, homolog of Drosophila E(spl)"	protein-coding	0	0.336634
Merged-chr15-31955973-1	chr15	31955923	31956023	+	1.9	cIP2vsInput	Intergenic	Intergenic	-221316	NM_020503	57254	Mm.377133	NM_020503	ENSMUSG00000045267	Tas2r119	T2r19|Tas2r19|mGR19|mt2r19	"taste receptor, type 2, member 119"	protein-coding	0.01	0.326733
Merged-chr3-112769224-1	chr3	112769174	112769274	+	1.9	cIP2vsInput	Intergenic	Intergenic	387503	NM_001190404	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding	0	0.336634
Merged-chr10-129299940-1	chr10	129299890	129299990	+	1.9	cIP2vsInput	Intergenic	Intergenic	-21685	NM_146284	258281	Mm.377412	NM_146284	ENSMUSG00000049573	Olfr780	MOR114-12	olfactory receptor 780	protein-coding	0.01	0.366337
Merged-chr7-12465515-1	chr7	12465465	12465565	+	1.9	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-12790	NM_001039951	67370	Mm.98929	NM_001039951	ENSMUSG00000030386	Zfp606	2410022M24Rik|AW494727	zinc finger protein 606	protein-coding	0	0.316832
Merged-chr9-121402973-1	chr9	121402923	121403023	+	1.9	cIP2vsInput	"intron (NM_175114, intron 2 of 15)"	"intron (NM_175114, intron 2 of 15)"	36015	NM_175114	67095	Mm.305318	NM_175114	ENSMUSG00000032536	Trak1	2310001H13Rik|AI413908|AI467545|hyrt|mKIAA1042	"trafficking protein, kinesin binding 1"	protein-coding	0.01	0.316832
Merged-chr9-39044511-1	chr9	39044461	39044561	+	1.9	cIP2vsInput	Intergenic	Lx|LINE|L1	3038	NM_207139	100503486	Mm.482069	NM_207139	ENSMUSG00000095194	Olfr936	EG628171|MOR171-37	olfactory receptor 936	protein-coding	0	0.366337
Merged-chr13-8760176-1	chr13	8760126	8760226	+	1.9	cIP2vsInput	"3' UTR (NM_052977, exon 10 of 10)"	"3' UTR (NM_052977, exon 10 of 10)"	110866	NM_001039389	207615	Mm.284654	NM_001039388	ENSMUSG00000021147	Wdr37	3110035P10Rik|4933417A01Rik|6430603N07|AI481191|mKIAA0982	WD repeat domain 37	protein-coding	0	0.356436
Merged-chr5-10115572-1	chr5	10115522	10115622	+	1.9	cIP2vsInput	Intergenic	Intergenic	-390220	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	"glutamate receptor, metabotropic 3"	protein-coding	0	0.376238
Merged-chr1-25319220-1	chr1	25319170	25319270	+	1.9	cIP2vsInput	"intron (NM_175642, intron 16 of 30)"	"intron (NM_175642, intron 16 of 30)"	-41266	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	"predicted gene, 20172"	protein-coding	0.02	0.336634
Merged-chr1-111226836-1	chr1	111226786	111226886	+	1.9	cIP2vsInput	Intergenic	ORR1D2|LTR|ERVL-MaLR	-249464	NM_001081386	227485	Mm.322070	NM_001081386	ENSMUSG00000047216	Cdh19	-	"cadherin 19, type 2"	protein-coding	0.01	0.346535
Merged-chr7-104244558-1	chr7	104244508	104244608	+	1.9	cIP2vsInput	"5' UTR (NM_030684, exon 1 of 8)"	"5' UTR (NM_030684, exon 1 of 8)"	101	NM_030684	94094	Mm.326945	NM_030684	ENSMUSG00000056144	Trim34a	Trim34|Trim34-1	tripartite motif-containing 34A	protein-coding	0.02	0.564356
Merged-chr18-56535426-1	chr18	56535376	56535476	+	1.9	cIP2vsInput	"intron (NM_001127338, intron 13 of 19)"	PB1D10|SINE|Alu	26872	NM_138600	110695	Mm.30250	NM_001127338		Aldh7a1	Atq1|D18Wsu181e	"aldehyde dehydrogenase family 7, member A1"	protein-coding	0.01	0.366337
Merged-chr3-111909492-1	chr3	111909442	111909542	+	1.9	cIP2vsInput	"intron (NR_045362, intron 1 of 3)"	"intron (NR_045362, intron 1 of 3)"	27589	NR_045362	625585	Mm.389497	NR_045362		Gm6602	-	predicted gene 6602	miscRNA	0	0.356436
Merged-chr12-50783273-1	chr12	50783223	50783323	+	1.9	cIP2vsInput	Intergenic	Lx9|LINE|L1	-134050	NM_008858	18760	Mm.133719	NM_008858	ENSMUSG00000002688	Prkd1	PKD|PKD1|Pkcm|Prkcm	protein kinase D1	protein-coding	0	0.29703
Merged-chr8-61006229-1	chr8	61006179	61006279	+	1.9	cIP2vsInput	"intron (NM_175089, intron 1 of 32)"	"intron (NM_175089, intron 1 of 32)"	13009	NM_175089	18004	Mm.486881	NM_175089		Nek1	D8Ertd790e|kat	NIMA (never in mitosis gene a)-related expressed kinase 1	protein-coding	0	0.356436
Merged-chr17-92257248-1	chr17	92257198	92257298	+	1.9	cIP2vsInput	Intergenic	L1MEb|LINE|L1	-942174	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0	0.267327
Merged-chr16-53836320-1	chr16	53836270	53836370	+	1.9	cIP1vsInput	Intergenic	Intergenic	-1020576	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	miscRNA	0.01	0.346535
Merged-chr1-109571594-1	chr1	109571544	109571644	+	1.9	cIP1vsInput	Intergenic	Intergenic	-412143	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.376238
Merged-chr14-21741977-1	chr14	21741927	21742027	+	1.9	cIP2vsInput	"intron (NM_001007268, intron 5 of 7)"	"intron (NM_001007268, intron 5 of 7)"	902	NM_013849	27389	Mm.390674	NM_001007268	ENSMUSG00000021768	Dusp13	Gm1203|LMW-DSP6|MDSP|TMDP|TS-DSP6	dual specificity phosphatase 13	protein-coding	0.02	0.554455
Merged-chr17-61083283-1	chr17	61083233	61083333	+	1.9	cIP2vsInput	Intergenic	Intergenic	-234469	NR_030569	100124495		NR_030569		Mir466g	Mirn466g	microRNA 466g	miscRNA	0	0.366337
Merged-chr13-109946192-1	chr13	109946142	109946242	+	1.9	cIP2vsInput	"intron (NM_011056, intron 13 of 16)"	"intron (NM_011056, intron 13 of 16)"	42383	NR_035442	100316683		NR_035442		Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	miscRNA	0.01	0.445545
Merged-chr19-11030189-1	chr19	11030139	11030239	+	1.9	cIP2vsInput	Intergenic	MusHAL1|LINE|L1	-12226	NM_001251849	76002	Mm.139320	NM_001251849	ENSMUSG00000094584	Ms4a18	5033428B15Rik	"membrane-spanning 4-domains, subfamily A, member 18"	protein-coding	0.01	0.316832
Merged-chr17-4636875-1	chr17	4636825	4636925	+	1.9	cIP2vsInput	Intergenic	Intergenic	-358199	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding	0.01	0.475248
Merged-chr12-21111885-1	chr12	21111835	21111935	+	1.9	cIP2vsInput	"5' UTR (NM_001098168, exon 1 of 28)"	"5' UTR (NM_001098168, exon 1 of 28)"	129	NM_001135192	211914	Mm.358946	NM_001004364	ENSMUSG00000052632	Asap2	6530401G17Rik|Ddef2|Gm1523|Gm592|PAG3|PAP	"ArfGAP with SH3 domain, ankyrin repeat and PH domain 2"	protein-coding	0.15	0.811881
Merged-chr3-12513982-1	chr3	12513932	12514032	+	1.9	cIP2vsInput	Intergenic	Lx6|LINE|L1	-669623	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.29703
Merged-chr17-55190813-1	chr17	55190763	55190863	+	1.9	cIP2vsInput	Intergenic	MYSERV16_I-int|LTR|ERVK	-254904	NM_172829	240119	Mm.311687	NM_172829	ENSMUSG00000024172	St6gal2	C230064G14Rik|St6galII|mKIAA1877	"beta galactoside alpha 2,6 sialyltransferase 2"	protein-coding	0	0.356436
Merged-chr10-3224419-1	chr10	3224369	3224469	+	1.9	cIP2vsInput	Intergenic	L1VL1|LINE|L1	43352	NM_001204916	670558	Mm.398582	NM_001204916		H60c	4632413I24Rik|Gm9491	histocompatibility 60c	protein-coding	0	0.326733
Merged-chr11-92974301-1	chr11	92974251	92974351	+	1.9	cIP2vsInput	Intergenic	Intergenic	-124989	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding	0	0.445545
Merged-chr1-49636100-1	chr1	49636050	49636150	+	1.9	cIP2vsInput	Intergenic	Intergenic	-1291423	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.316832
Merged-chr18-17113884-1	chr18	17113834	17113934	+	1.9	cIP2vsInput	Intergenic	Intergenic	121598	NR_033607	664619	Mm.250005	NR_033607		4921533I20Rik	-	PRP18 pre-mRNA processing factor 18 homolog pseudogene	pseudo	0	0.326733
Merged-chr7-14282939-1	chr7	14282889	14282989	+	1.9	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-28069	NM_001081325	629219	Mm.439627	NM_001081325	ENSMUSG00000070810	Sult2a6	EG629219|Gm6957	"sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 6"	protein-coding	0	0.346535
Merged-chr12-47720127-1	chr12	47720077	47720177	+	1.9	cIP2vsInput	Intergenic	MTD|LTR|ERVL-MaLR	581335	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0	0.326733
Merged-chr8-4526256-1	chr8	4526206	4526306	+	1.9	cIP2vsInput	TTS (NM_026058)	TTS (NM_026058)	32851	NM_026058	67260	Mm.35511	NM_026058	ENSMUSG00000008206	Cers4	2900019C14Rik|Lass4|Trh1	ceramide synthase 4	protein-coding	0	0.277228
Merged-chr11-81687347-1	chr11	81687297	81687397	+	1.9	cIP2vsInput	"intron (NM_001034013, intron 1 of 9)"	"intron (NM_001034013, intron 1 of 9)"	-113808	NM_001033765	237880	Mm.435528	NM_001033765		1700071K01Rik	-	RIKEN cDNA 1700071K01 gene	protein-coding	0	0.336634
Merged-chr1-20610228-1	chr1	20610178	20610278	+	1.9	cIP2vsInput	"intron (NM_153179, intron 4 of 66)"	L1_Mur3|LINE|L1	7829	NM_153179	241035	Mm.249253	NM_153179	ENSMUSG00000043760	Pkhd1	AI118496|AI182499|FPC|Tigm1	polycystic kidney and hepatic disease 1	protein-coding	0.02	0.39604
Merged-chr5-28421873-1	chr5	28421823	28421923	+	1.9	cIP2vsInput	Intergenic	Intergenic	-45111	NR_015562	654796	Mm.403014	NR_015562	ENSMUSG00000097726	9530036O11Rik	-	RIKEN cDNA 9530036O11Rik	miscRNA	0	0.306931
Merged-chr19-13779343-1	chr19	13779293	13779393	+	1.9	cIP2vsInput	Intergenic	Intergenic	-1205	NM_146989	258991	Mm.377780	NM_146989	ENSMUSG00000048356	Olfr1496	MOR127-1	olfactory receptor 1496	protein-coding	0	0.405941
Merged-chr8-127906767-1	chr8	127906717	127906817	+	1.9	cIP1vsInput	Intergenic	Intergenic	-452306	NM_008737	18186	Mm.271745	NM_008737	ENSMUSG00000025810	Nrp1	C530029I03|NP-1|NPN-1|Npn1|Nrp	neuropilin 1	protein-coding	0	0.425743
Merged-chr11-42035387-1	chr11	42035337	42035437	+	1.9	cIP2vsInput	Intergenic	Lx3_Mus|LINE|L1	-34673	NM_008073	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2"	protein-coding	0	0.346535
Merged-chr17-43883116-1	chr17	43883066	43883166	+	1.9	cIP2vsInput	"intron (NM_207649, intron 2 of 4)"	"intron (NM_207649, intron 2 of 4)"	-70075	NM_030598	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding	0	0.39604
Merged-chr16-60375360-1	chr16	60375310	60375410	+	1.9	cIP2vsInput	"intron (NM_007938, intron 3 of 17)"	"intron (NM_007938, intron 3 of 17)"	230171	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0	0.386139
Merged-chr5-109335171-1	chr5	109335121	109335221	+	1.9	cIP2vsInput	"intron (NM_001104627, intron 1 of 5)"	"intron (NM_001104627, intron 1 of 5)"	4790	NM_001104627	384220	Mm.469880	NM_001104627	ENSMUSG00000092080	Vmn2r16	EG384220	"vomeronasal 2, receptor 16"	protein-coding	0	0.376238
Merged-chr4-78444035-1	chr4	78443985	78444085	+	1.9	cIP2vsInput	Intergenic	L1Md_T|LINE|L1	-232140	NM_011211	19266	Mm.489057	XR_107614	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	"protein tyrosine phosphatase, receptor type, D"	protein-coding	0	0.29703
Merged-chr8-71829443-1	chr8	71829393	71829493	+	1.9	cIP2vsInput	Intergenic	Intergenic	-52625	NM_145624	236193	Mm.290790	NM_145624		Zfp709	BC021921|GIOT-4|HIT-40	zinc finger protein 709	protein-coding	0	0.465347
Merged-chr3-111799293-1	chr3	111799243	111799343	+	1.9	cIP2vsInput	Intergenic	Intergenic	-82610	NR_045362	625585	Mm.389497	NR_045362		Gm6602	-	predicted gene 6602	miscRNA	0	0.336634
Merged-chr10-22543131-1	chr10	22543081	22543181	+	1.9	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-101880	NM_178934	353169	Mm.473705	NM_178934	ENSMUSG00000037490	Slc2a12	GLUT-12|Glut12	"solute carrier family 2 (facilitated glucose transporter), member 12"	protein-coding	0	0.336634
Merged-chr6-12153675-1	chr6	12153625	12153725	+	1.9	cIP2vsInput	Intergenic	LTRIS5|LTR|ERV1	-44095	NR_003631	625347	Mm.389084	NR_003631	ENSMUSG00000057223	Gm6578	EG625347	mitochondrial ribosomal protein L32 pseudogene	pseudo	0	0.356436
Merged-chr11-33896562-1	chr11	33896512	33896612	+	1.9	cIP2vsInput	"intron (NM_001190886, intron 1 of 7)"	"intron (NM_001190886, intron 1 of 7)"	-52977	NM_001190885	70357	Mm.252514	NM_001190885	ENSMUSG00000053519	Kcnip1	2900046L02Rik|3202002F18Rik|AI842357|AW494471|KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding	0.01	0.336634
Merged-chr10-36782307-1	chr10	36782257	36782357	+	1.9	cIP2vsInput	"intron (NM_001253355, intron 4 of 5)"	L1_Mus2|LINE|L1	-192237	NM_008229	15182	Mm.19806	NM_008229	ENSMUSG00000019777	Hdac2	D10Wsu179e|YAF1|Yy1bp|mRPD3	histone deacetylase 2	protein-coding	0	0.336634
Merged-chr1-114233411-1	chr1	114233361	114233461	+	1.9	cIP2vsInput	Intergenic	Intergenic	-1451726	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0.01	0.356436
Merged-chr8-59698260-1	chr8	59698210	59698310	+	1.9	cIP2vsInput	Intergenic	Lx3C|LINE|L1	786505	NM_173411	234290	Mm.39244	NM_173411	ENSMUSG00000049946	BC030500	-	cDNA sequence BC030500	protein-coding	0.01	0.306931
Merged-chr14-85147592-1	chr14	85147542	85147642	+	1.9	cIP2vsInput	Intergenic	MIR|SINE|MIR	-671168	NR_015539	319903	Mm.440481	NR_015539		9630013A20Rik	-	RIKEN cDNA 9630013A20 gene	miscRNA	0	0.346535
Merged-chr14-96438322-1	chr14	96438272	96438372	+	1.9	cIP2vsInput	"intron (NM_053105, intron 1 of 10)"	L1M2|LINE|L1	80712	NM_053105	93688	Mm.308735	NM_053105	ENSMUSG00000022076	Klhl1	mKIAA1490	kelch-like 1	protein-coding	0	0.29703
Merged-chrX-122010761-1	chrX	122010711	122010811	+	1.9	cIP2vsInput	Intergenic	Lx8|LINE|L1	386624	NM_138742	54561	Mm.490573	NM_138742	ENSMUSG00000055733	Nap1l3	MB20	nucleosome assembly protein 1-like 3	protein-coding	0	0.346535
Merged-chr12-28501055-1	chr12	28501005	28501105	+	1.9	cIP2vsInput	"intron (NM_001177964, intron 8 of 8)"	Charlie1a|DNA|hAT-Charlie	47282	NM_001177964	68511	Mm.310284	NM_001177964		Dcdc2c	1110015M06Rik	doublecortin domain containing 2C	protein-coding	0	0.346535
Merged-chr4-111203993-1	chr4	111203943	111204043	+	1.9	cIP2vsInput	"intron (NM_001048189, intron 5 of 12)"	"intron (NM_001048189, intron 5 of 12)"	-211013	NR_033793	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding	0.01	0.326733
Merged-chr16-93731097-1	chr16	93731047	93731147	+	1.9	cIP2vsInput	"intron (NM_027293, intron 2 of 36)"	"intron (NM_027293, intron 2 of 36)"	19190	NM_027293	70028	Mm.23230	NM_026700	ENSMUSG00000022946	Dopey2	0610038M01Rik|2610510B01Rik|AI503246|C21orf5|mKIAA0933	dopey family member 2	protein-coding	0.03	0.475248
Merged-chr5-45301830-1	chr5	45301780	45301880	+	1.9	cIP2vsInput	Intergenic	Intergenic	148399	NM_024236	110391	Mm.30204	NM_024236	ENSMUSG00000015806	Qdpr	2610008L04Rik|D5Ertd371e|Dhpr|PKU2	quinoid dihydropteridine reductase	protein-coding	0	0.405941
Merged-chr6-91450989-1	chr6	91450939	91451039	+	1.9	cIP2vsInput	Intergenic	MYSERV-int|LTR|ERVK	10002	NR_038153	69798	Mm.229265	NR_038153		1810044D09Rik	-	RIKEN cDNA 1810044D09 gene	miscRNA	0	0.306931
Merged-chr10-52601572-1	chr10	52601522	52601622	+	1.9	cIP1vsInput	Intergenic	L1_Mus3|LINE|L1	-55833	NR_037920	22639	Mm.490597	NM_009540	ENSMUSG00000049576	Zfa-ps	Zfa|Zfx	"zinc finger protein, autosomal, pseudogene"	pseudo	0.02	0.376238
Merged-chr14-16088941-1	chr14	16088891	16088991	+	1.9	cIP1vsInput	Intergenic	L1_Mus2|LINE|L1	-160373	NM_021504	59007	Mm.258381	NM_021504	ENSMUSG00000021785	Ngly1	1110002C09Rik|PNGase|Png1	N-glycanase 1	protein-coding	0	0.336634
Merged-chr17-52684775-1	chr17	52684725	52684825	+	1.9	cIP2vsInput	"intron (NM_001031811, intron 1 of 15)"	"intron (NM_001031811, intron 1 of 15)"	82066	NM_001031811	211468	Mm.490760	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	"potassium voltage-gated channel, subfamily H (eag-related), member 8"	protein-coding	0	0.326733
Merged-chr3-78850222-1	chr3	78850172	78850272	+	1.9	cIP2vsInput	Intergenic	Intergenic	295653	NM_001099624	76089	Mm.462396	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding	0	0.326733
Merged-chr7-76733814-1	chr7	76733764	76733864	+	1.9	cIP2vsInput	"intron (NM_001199224, intron 20 of 22)"	L1M4a2|LINE|L1	503927	NM_001199224	244071	Mm.322829	NM_001199224		Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding	0	0.346535
Merged-chr1-48117648-1	chr1	48117598	48117698	+	1.9	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-1264139	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.326733
Merged-chr1-53241289-1	chr1	53241239	53241339	+	1.9	cIP2vsInput	"intron (NM_153556, intron 5 of 12)"	L1_Mus3|LINE|L1	-53672	NM_027070	69397	Mm.307084	NM_027070	ENSMUSG00000060715	1700019A02Rik	-	RIKEN cDNA 1700019A02 gene	protein-coding	0.01	0.346535
Merged-chr15-29294855-1	chr15	29294805	29294905	+	1.9	cIP2vsInput	Intergenic	Intergenic	-877738	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	"catenin (cadherin associated protein), delta 2"	protein-coding	0	0.366337
Merged-chr3-29616304-1	chr3	29616254	29616354	+	1.9	cIP2vsInput	"intron (NM_001167748, intron 6 of 12)"	L1_Mus2|LINE|L1	199481	NR_030422	791072		NR_030422		Mir551b	Mirn551b|mir-551b	microRNA 551b	miscRNA	0	0.316832
Merged-chr4-18665016-1	chr4	18664966	18665066	+	1.9	cIP2vsInput	Intergenic	Intergenic	-615834	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding	0	0.366337
Merged-chr17-54172325-1	chr17	54172275	54172375	+	1.9	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	126709	NM_022025	63993	Mm.155241	NM_022025	ENSMUSG00000023945	Slc5a7	CHT1	"solute carrier family 5 (choline transporter), member 7"	protein-coding	0	0.336634
Merged-chr15-17918085-1	chr15	17918035	17918135	+	1.9	cIP1vsInput	Intergenic	MTE2a|LTR|ERVL-MaLR	451542	NR_045711	70886	Mm.399021	NR_045711		4921515E04Rik	-	RIKEN cDNA 4921515E04 gene	miscRNA	0	0.346535
Merged-chr7-97148734-1	chr7	97148684	97148784	+	1.9	cIP1vsInput	"intron (NM_001162477, intron 1 of 9)"	L1MB3|LINE|L1	66983	NM_010248	14389	Mm.42033	NM_001162477	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding	0	0.29703
Merged-chr5-98202918-1	chr5	98202868	98202968	+	1.9	cIP2vsInput	Intergenic	Intergenic	22049	NM_029947	77630	Mm.332511	NM_029947	ENSMUSG00000035456	Prdm8	4930565F05Rik|PFM5	PR domain containing 8	protein-coding	0	0.386139
Merged-chr1-98362943-1	chr1	98362893	98362993	+	1.9	cIP2vsInput	Intergenic	Intergenic	-58181	NM_001164233	70866	Mm.389164	NM_001164233	ENSMUSG00000026336	Slco6d1	4921511I05Rik	"solute carrier organic anion transporter family, member 6d1"	protein-coding	0	0.287129
Merged-chr1-21339023-1	chr1	21338973	21339073	+	1.9	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-10654	NM_183322	368204	Mm.26006	NM_183322	ENSMUSG00000067750	Khdc1a	AU014713|C88118|Ndg1	KH domain containing 1A	protein-coding	0	0.336634
Merged-chr15-24273326-1	chr15	24273276	24273376	+	1.9	cIP2vsInput	Intergenic	Lx6|LINE|L1	1140438	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	"brain abundant, membrane attached signal protein 1"	protein-coding	0	0.326733
Merged-chr3-23909494-1	chr3	23909444	23909544	+	1.9	cIP1vsInput	Intergenic	Intergenic	1658124	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	miscRNA	0	0.356436
Merged-chr5-147937724-1	chr5	147937674	147937774	+	1.9	cIP1vsInput	Intergenic	RMER15|LTR|ERVL	-19596	NM_029920	77521	Mm.244177	NM_029920	ENSMUSG00000029651	Mtus2	5730592G18Rik|A730013O20Rik|AU067634|C130038G02Rik|Cazip|Gm763|mKIAA0774	microtubule associated tumor suppressor candidate 2	protein-coding	0.01	0.39604
Merged-chr15-51438631-1	chr15	51438581	51438681	+	1.9	cIP2vsInput	Intergenic	Intergenic	-43021	NR_045092	100502643	Mm.131987	NR_045092		Gm19303	-	"predicted gene, 19303"	miscRNA	0	0.326733
Merged-chrX-108418615-1	chrX	108418565	108418665	+	1.9	cIP1vsInput	Intergenic	Lx5b|LINE|L1	415740	NM_001081477	382236	Mm.426127	NM_001081477		Brwd3	Brodl|D030064D06Rik|Gm596	bromodomain and WD repeat domain containing 3	protein-coding	0	0.336634
Merged-chr9-51335575-1	chr9	51335525	51335625	+	1.9	cIP2vsInput	Intergenic	Intergenic	-6658	NM_027217	69809	Mm.75315	NM_027217	ENSMUSG00000036027	1810046K07Rik	-	RIKEN cDNA 1810046K07 gene	protein-coding	0.01	0.455446
Merged-chr5-143758107-1	chr5	143758057	143758157	+	1.9	cIP2vsInput	promoter-TSS (NR_015486)	promoter-TSS (NR_015486)	-247	NR_015486	320064	Mm.394666	NR_015486		D130017N08Rik	1700012G11Rik	RIKEN cDNA D130017N08 gene	miscRNA	0.04	0.574257
Merged-chr17-11913218-1	chr17	11913168	11913268	+	1.9	cIP2vsInput	"intron (NM_016694, intron 9 of 11)"	"intron (NM_016694, intron 9 of 11)"	-30029	NR_045808	52027	Mm.442257	NR_045808		D17Ertd648e	-	"DNA segment, Chr 17, ERATO Doi 648, expressed"	miscRNA	0.04	0.50495
Merged-chr1-45196740-1	chr1	45196690	45196790	+	1.9	cIP2vsInput	Intergenic	Intergenic	-114798	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|MMS10-W|Ms10w|mKIAA4231	"collagen, type III, alpha 1"	protein-coding	0	0.376238
Merged-chr14-89826941-1	chr14	89826891	89826991	+	1.9	cIP2vsInput	Intergenic	Intergenic	-69283	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0	0.326733
Merged-chr6-66832804-1	chr6	66832754	66832854	+	1.9	cIP1vsInput	Intergenic	L1_Rod|LINE|L1	-27472	NM_001166720	546903	Mm.484975	NM_001166720		Vmn1r39	EG546903|Gm5993	vomeronasal 1 receptor 39	protein-coding	0	0.306931
Merged-chr11-14079896-1	chr11	14079846	14079946	+	1.9	cIP2vsInput	Intergenic	Intergenic	519329	NR_045918	73307	Mm.399291	NR_045918	ENSMUSG00000085561	1700046C09Rik	-	RIKEN cDNA 1700046C09 gene	miscRNA	0.01	0.257426
Merged-chr10-68247741-1	chr10	68247691	68247791	+	1.9	cIP2vsInput	"intron (NM_023598, intron 2 of 9)"	"intron (NM_023598, intron 2 of 9)"	30985	NM_023598	71371		NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding	0.01	0.356436
Merged-chr12-57371033-1	chr12	57370983	57371083	+	1.9	cIP2vsInput	"intron (NM_001164370, intron 8 of 9)"	L1_Mur3|LINE|L1	140608	NM_001164370	73490	Mm.268180	NM_001164370	ENSMUSG00000047022	Mipol1	1700081O04Rik|6030439O22Rik|AU021838|AW536152|D12Ertd19e	mirror-image polydactyly gene 1 homolog (human)	protein-coding	0.01	0.287129
Merged-chr3-34678498-1	chr3	34678448	34678548	+	1.9	cIP2vsInput	TTS (NR_015580)	TTS (NR_015580)	28493	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY-box containing gene 2	protein-coding	0.01	0.336634
Merged-chr18-21269293-1	chr18	21269243	21269343	+	1.9	cIP2vsInput	"intron (NM_001033445, intron 1 of 5)"	"intron (NM_001033445, intron 1 of 5)"	30846	NM_001033445	381126	Mm.312276	NM_001033445	ENSMUSG00000042680	Garem	C86169|Fam59a|Gm944|mKIAA4238	"GRB2 associated, regulator of MAPK1"	protein-coding	0	0.29703
Merged-chr5-96272664-1	chr5	96272614	96272714	+	1.9	cIP2vsInput	Intergenic	(TTTG)n|Simple_repeat|Simple_repeat	62549	NM_053158	94061	Mm.295499	NM_001039084	ENSMUSG00000029486	Mrpl1	2410002L03Rik|5830418D04Rik|AI462572	mitochondrial ribosomal protein L1	protein-coding	0	0.306931
Merged-chr14-112447389-1	chr14	112447339	112447439	+	1.9	cIP2vsInput	Intergenic	Intergenic	425959	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0	0.277228
Merged-chr10-62112205-1	chr10	62112155	62112255	+	1.9	cIP2vsInput	Intergenic	Intergenic	-1192	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding	0.01	0.356436
Merged-chrX-106596813-1	chrX	106596763	106596863	+	1.9	cIP2vsInput	"intron (NM_001033541, intron 1 of 3)"	"intron (NM_001033541, intron 1 of 3)"	6649	NM_021476	58861	Mm.287166	NM_021476		Cysltr1	BB147369|CysLT1R|Cyslt1	cysteinyl leukotriene receptor 1	protein-coding	0.01	0.346535
Merged-chr15-89965145-1	chr15	89965095	89965195	+	1.9	cIP2vsInput	Intergenic	Intergenic	-123285	NM_018803	54526	Mm.261601	NM_018803	ENSMUSG00000063260	Syt10	-	synaptotagmin X	protein-coding	0	0.277228
Merged-chr2-124898444-1	chr2	124898394	124898494	+	1.9	cIP2vsInput	Intergenic	Intergenic	-169683	NM_175034	317750	Mm.330538	NM_175034	ENSMUSG00000035183	Slc24a5	F630045L20Rik|JSX|NCKX5|NCX5	"solute carrier family 24, member 5"	protein-coding	0	0.405941
Merged-chr17-31686404-1	chr17	31686354	31686454	+	1.9	cIP2vsInput	Intergenic	Intergenic	8459	NM_013501	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	AI323437|Acry-1|Crya-1|Crya1|DAcry-1|lop18	"crystallin, alpha A"	protein-coding	0.01	0.633663
Merged-chr9-73687885-1	chr9	73687835	73687935	+	1.9	cIP2vsInput	"intron (NM_001081153, intron 11 of 30)"	"intron (NM_001081153, intron 11 of 30)"	245682	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|AU019458|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C (C. elegans)	protein-coding	0	0.316832
Merged-chr2-17315210-1	chr2	17315160	17315260	+	1.9	cIP2vsInput	Intergenic	L1MD1|LINE|L1	-301484	NR_040632	75069	Mm.399263	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	miscRNA	0.01	0.336634
Merged-chr17-35590821-1	chr17	35590771	35590871	+	1.9	cIP2vsInput	Intergenic	Intergenic	23336	NM_175148	69542	Mm.265291	NM_175148	ENSMUSG00000039269	2300002M23Rik	Stg|emprin	RIKEN cDNA 2300002M23 gene	protein-coding	0.03	0.50495
Merged-chr14-95583714-1	chr14	95583664	95583764	+	1.9	cIP2vsInput	Intergenic	Intergenic	-297552	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0	0.29703
Merged-chr4-45941893-1	chr4	45941843	45941943	+	1.9	cIP2vsInput	"exon (NM_198660, exon 32 of 38)"	"exon (NM_198660, exon 32 of 38)"	-45569	NM_146142	100121	Mm.275413	NM_146142	ENSMUSG00000035517	Tdrd7	5730495N10Rik|AI447470|PCTAIRE2BP	tudor domain containing 7	protein-coding	0.06	0.564356
Merged-chr1-186844001-1	chr1	186843951	186844051	+	1.9	cIP2vsInput	Intergenic	Intergenic	-94643	NM_026041	67223	Mm.289841	NM_026041	ENSMUSG00000001305	Rrp15	2810430M08Rik|5430437H21Rik	ribosomal RNA processing 15 homolog (S. cerevisiae)	protein-coding	0	0.267327
Merged-chr3-72283884-1	chr3	72283834	72283934	+	1.9	cIP2vsInput	Intergenic	L1MA4A|LINE|L1	682982	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding	0	0.326733
Merged-chr6-108863404-1	chr6	108863354	108863454	+	1.9	cIP2vsInput	Intergenic	RLTR25B|LTR|ERVK	34763	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	"ER degradation enhancer, mannosidase alpha-like 1"	protein-coding	0	0.435644
Merged-chr9-62585604-1	chr9	62585554	62585654	+	1.9	cIP1vsInput	Intergenic	Intergenic	-48560	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	"coronin, actin binding protein, 2B"	protein-coding	0.01	0.376238
Merged-chr8-74458821-1	chr8	74458771	74458871	+	1.9	cIP2vsInput	Intergenic	Intergenic	-414353	NM_027837	71597	Mm.158735	NM_027837		Isx	9130012O13Rik|Pix-1	intestine specific homeobox	protein-coding	0	0.287129
Merged-chr19-19499225-1	chr19	19499175	19499275	+	1.9	cIP2vsInput	Intergenic	Intergenic	-388029	NM_001043354	225998		NM_001043354	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta	RAR-related orphan receptor beta	protein-coding	0.01	0.316832
Merged-chr10-97536236-1	chr10	97536186	97536286	+	1.9	cIP2vsInput	Intergenic	Intergenic	-29265	NM_008524	17022	Mm.18888	NM_008524	ENSMUSG00000036446	Lum	Ldc|SLRR2D	lumican	protein-coding	0.01	0.386139
Merged-chr9-62438916-1	chr9	62438866	62438966	+	1.9	cIP2vsInput	"intron (NM_175484, intron 3 of 11)"	"intron (NM_175484, intron 3 of 11)"	97573	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	"acidic (leucine-rich) nuclear phosphoprotein 32 family, member A"	protein-coding	0.01	0.524752
Merged-chr3-156293415-1	chr3	156293365	156293465	+	1.9	cIP2vsInput	Intergenic	Intergenic	268272	NR_040398	329782	Mm.183459	NR_040398	ENSMUSG00000085084	4930570G19Rik	C630015G22	RIKEN cDNA 4930570G19 gene	miscRNA	0	0.326733
Merged-chr4-98886146-1	chr4	98886096	98886196	+	1.9	cIP2vsInput	Intergenic	Intergenic	-37664	NM_146144	230484	Mm.371692	NM_146144	ENSMUSG00000028560	Usp1	-	ubiquitin specific peptidase 1	protein-coding	0	0.336634
Merged-chr9-22854887-1	chr9	22854837	22854937	+	1.9	cIP2vsInput	"intron (NM_181316, intron 20 of 21)"	L1_Mus3|LINE|L1	-368189	NM_028472	73230	Mm.335020	NM_028472	ENSMUSG00000031963	Bmper	3110056H04Rik|CV-2|Crim3|Cv2	BMP-binding endothelial regulator	protein-coding	0	0.376238
Merged-chr14-115879565-1	chr14	115879515	115879615	+	1.9	cIP2vsInput	"intron (NM_175500, intron 7 of 7)"	"intron (NM_175500, intron 7 of 7)"	-470013	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	miscRNA	0	0.366337
Merged-chr14-123783260-1	chr14	123783210	123783310	+	1.9	cIP2vsInput	"intron (NM_145467, intron 2 of 10)"	"intron (NM_145467, intron 2 of 10)"	123120	NM_145467	223272	Mm.383176	NM_145467		Itgbl1	B930011D01Rik	"integrin, beta-like 1"	protein-coding	0	0.326733
Merged-chr3-77183686-1	chr3	77183636	77183736	+	1.9	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	1108103	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.356436
Merged-chr2-154327716-1	chr2	154327666	154327766	+	1.9	cIP2vsInput	Intergenic	Intergenic	20472	NM_001025574	433492	Mm.330682	NM_001025574	ENSMUSG00000067996	Bpifb9b	5430413K10Rik|AI413838|OTTMUSG00000015915|Rp23-154j12.5	"BPI fold containing family B, member 9B"	protein-coding	0	0.316832
Merged-chr13-12797648-1	chr13	12797598	12797698	+	1.9	cIP2vsInput	"intron (NM_011118, intron 1 of 4)"	"intron (NM_011118, intron 1 of 4)"	2410	NM_011954	26421	Mm.457984	NM_011954		Prl2c4	MRP-3|Mrpplf3|PLF-3|mrp/plf3	"prolactin family 2, subfamily c, member 4"	protein-coding	0.01	0.465347
Merged-chr2-45931831-1	chr2	45931781	45931881	+	1.9	cIP2vsInput	Intergenic	LTR73|LTR|ERV1	235226	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	miscRNA	0.01	0.346535
Merged-chr12-65903216-1	chr12	65903166	65903266	+	1.9	cIP1vsInput	Intergenic	Intergenic	381185	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding	0.01	0.29703
Merged-chr16-79416895-1	chr16	79416845	79416945	+	1.9	cIP2vsInput	Intergenic	Intergenic	-325798	NM_008941	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	"transmembrane protease, serine 15"	protein-coding	0	0.287129
Merged-chr9-102763836-1	chr9	102763786	102763886	+	1.9	cIP2vsInput	Intergenic	Intergenic	24188	NR_033301	434510	Mm.387937	NR_033301	ENSMUSG00000093812	Gm5627	EG434510	predicted gene 5627	miscRNA	0.03	0.524752
Merged-chr10-88593653-1	chr10	88593603	88593703	+	1.9	cIP2vsInput	"intron (NM_001252372, intron 1 of 28)"	"intron (NM_001252372, intron 1 of 28)"	11499	NM_001252372	109272	Mm.147208	NM_001252372	ENSMUSG00000020061	Mybpc1	8030451F13Rik	"myosin binding protein C, slow-type"	protein-coding	0	0.356436
Merged-chr12-42301594-1	chr12	42301544	42301644	+	1.9	cIP2vsInput	Intergenic	Intergenic	672830	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding	0	0.326733
Merged-chr1-25482442-1	chr1	25482392	25482492	+	1.9	cIP2vsInput	"intron (NM_175642, intron 10 of 30)"	"intron (NM_175642, intron 10 of 30)"	-204488	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	"predicted gene, 20172"	protein-coding	0	0.306931
Merged-chr3-77337323-1	chr3	77337273	77337373	+	1.9	cIP2vsInput	Intergenic	Intergenic	1261740	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.277228
Merged-chr2-57439958-1	chr2	57439908	57440008	+	1.9	cIP2vsInput	Intergenic	Intergenic	201576	NM_010274	14571	Mm.3711	NM_001145820	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	"glycerol phosphate dehydrogenase 2, mitochondrial"	protein-coding	0.02	0.277228
Merged-chr7-27132787-1	chr7	27132737	27132837	+	1.9	cIP2vsInput	"intron (NM_007817, intron 9 of 9)"	"intron (NM_007817, intron 9 of 9)"	12832	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	"cytochrome P450, family 2, subfamily f, polypeptide 2"	protein-coding	0.03	0.564356
Merged-chr12-107863882-1	chr12	107863832	107863932	+	1.9	cIP2vsInput	Intergenic	Intergenic	-128394	NR_045973	74968	Mm.359821	NR_045973	ENSMUSG00000085641	4930465M20Rik	4930431H15Rik	RIKEN cDNA 4930465M20 gene	miscRNA	0.02	0.455446
Merged-chr14-51266465-1	chr14	51266415	51266515	+	1.9	cIP1vsInput	Intergenic	Intergenic	-10353	NM_053113	93726	Mm.153688	NM_053113	ENSMUSG00000047222	Ear11	-	"eosinophil-associated, ribonuclease A family, member 11"	protein-coding	0.02	0.554455
Merged-chr4-54695000-1	chr4	54694950	54695050	+	1.9	cIP2vsInput	Intergenic	Intergenic	-252945	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding	0	0.306931
Merged-chr15-92005467-1	chr15	92005417	92005517	+	1.9	cIP2vsInput	Intergenic	Intergenic	-45698	NM_001159648	12805	Mm.470343	NM_001159647	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam	contactin 1	protein-coding	0.01	0.386139
Merged-chr8-32571046-1	chr8	32570996	32571096	+	1.9	cIP2vsInput	Intergenic	L1MEg1|LINE|L1	378980	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding	0	0.257426
Merged-chr4-88781568-1	chr4	88781518	88781618	+	1.9	cIP2vsInput	promoter-TSS (NM_197889)	promoter-TSS (NM_197889)	-563	NM_197889	319146	Mm.368232	NM_197889	ENSMUSG00000096854	Ifnz	6030405N23Rik|BGIF|ENSMUSG00000073810|Lmtn	interferon zeta	protein-coding	0.03	0.39604
Merged-chr6-50058091-1	chr6	50058041	50058141	+	1.9	cIP2vsInput	Intergenic	Intergenic	-52150	NM_019939	56524	Mm.463873	NM_001164734	ENSMUSG00000038388	Mpp6	P55t|Pals2	"membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)"	protein-coding	0.02	0.326733
Merged-chr3-119207539-1	chr3	119207489	119207589	+	1.9	cIP2vsInput	"intron (NM_170778, intron 18 of 22)"	"intron (NM_170778, intron 18 of 22)"	575849	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0	0.366337
Merged-chr12-61133116-1	chr12	61133066	61133166	+	1.9	cIP2vsInput	Intergenic	Intergenic	388704	NR_045049	100504101	Mm.235026	NR_045049		Gm20063	-	"predicted gene, 20063"	miscRNA	0.01	0.336634
Merged-chr11-32183390-1	chr11	32183340	32183440	+	1.9	cIP2vsInput	Intergenic	B3|SINE|B2	16889	NM_001134458	16199	Mm.384	NM_001134458		Il9r	-	interleukin 9 receptor	protein-coding	0	0.485149
Merged-chr5-33063458-1	chr5	33063408	33063508	+	1.9	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-40761	NM_019810	20537	Mm.25237	NM_019810	ENSMUSG00000011034	Slc5a1	Sglt1	"solute carrier family 5 (sodium/glucose cotransporter), member 1"	protein-coding	0.01	0.306931
Merged-chr13-60783138-1	chr13	60783088	60783188	+	1.9	cIP2vsInput	"intron (NM_199148, intron 6 of 7)"	"intron (NM_199148, intron 6 of 7)"	3226	NM_199148	218275	Mm.222427	NM_199148	ENSMUSG00000042243	BC051665	-	cDNA sequence BC051665	protein-coding	0.02	0.277228
Merged-chr2-86475219-1	chr2	86475169	86475269	+	1.9	cIP2vsInput	Intergenic	Intergenic	8521	NM_146405	258400	Mm.357298	NM_146405	ENSMUSG00000075180	Olfr228	MOR189-3|Olfr228-ps1	olfactory receptor 228	protein-coding	0.01	0.287129
Merged-chr7-76911661-1	chr7	76911611	76911711	+	1.9	cIP2vsInput	"intron (NM_001199224, intron 22 of 22)"	"intron (NM_001199224, intron 22 of 22)"	681774	NM_001199224	244071	Mm.322829	NM_001199224		Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding	0	0.346535
Merged-chr13-64358482-1	chr13	64358432	64358532	+	1.9	cIP2vsInput	Intergenic	Intergenic	11824	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding	0.01	0.425743
Merged-chr13-8271036-1	chr13	8270986	8271086	+	1.9	cIP2vsInput	"intron (NM_052977, intron 1 of 9)"	"intron (NM_052977, intron 1 of 9)"	68127	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	"adenosine deaminase, RNA-specific, B2"	protein-coding	0	0.346535
Merged-chr17-19060517-1	chr17	19060467	19060567	+	1.9	cIP2vsInput	"intron (NM_001104550, intron 1 of 5)"	"intron (NM_001104550, intron 1 of 5)"	7024	NM_001104550	224552	Mm.469860	NM_001104550	ENSMUSG00000096717	Vmn2r98	EG224552	"vomeronasal 2, receptor 98"	protein-coding	0.01	0.316832
Merged-chr4-94566899-1	chr4	94566849	94566949	+	1.9	cIP2vsInput	"3' UTR (NM_172695, exon 14 of 14)"	"3' UTR (NM_172695, exon 14 of 14)"	-10103	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0	0.29703
Merged-chr7-86753823-1	chr7	86753773	86753873	+	1.9	cIP2vsInput	"intron (NM_016770, intron 7 of 18)"	L1_Mur2|LINE|L1	22041	NM_016770	53320	Mm.269137	NM_001159706	ENSMUSG00000001773	Folh1	GCP2|mopsm	folate hydrolase 1	protein-coding	0	0.306931
Merged-chr5-59493348-1	chr5	59493298	59493398	+	1.9	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	492654	NR_040683	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0.01	0.346535
Merged-chr6-64061778-1	chr6	64061728	64061828	+	1.9	cIP2vsInput	"intron (NM_008167, intron 5 of 15)"	"intron (NM_008167, intron 5 of 15)"	-667368	NM_007500	11921	Mm.57229	NM_007500	ENSMUSG00000073043	Atoh1	Hath1|MATH-1|Math1|bHLHa14	atonal homolog 1 (Drosophila)	protein-coding	0	0.336634
Merged-chr7-141925129-1	chr7	141925079	141925179	+	1.9	cIP2vsInput	Intergenic	Intergenic	-22723	NM_023764	54473	Mm.103551	NM_023764	ENSMUSG00000025139	Tollip	4930403G24Rik|4931428G15Rik	toll interacting protein	protein-coding	0.05	0.663366
Merged-chr15-74955919-1	chr15	74955869	74955969	+	1.9	cIP2vsInput	"intron (NM_001164039, intron 2 of 4)"	"intron (NM_001164039, intron 2 of 4)"	813	NM_001164040	17069	Mm.788	NM_001164036	ENSMUSG00000022587	Ly6e	9804|Ly67|RIG-E|Sca-2|TSA-1|Tsa1	"lymphocyte antigen 6 complex, locus E"	protein-coding	0.03	0.643564
Merged-chr13-60575977-1	chr13	60575927	60576027	+	1.9	cIP2vsInput	Intergenic	Intergenic	-25970	NM_029653	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	2310039H24Rik|2810425C21Rik|AI642003|D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding	0	0.386139
Merged-chr8-51842849-1	chr8	51842799	51842899	+	1.9	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	1474737	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.346535
Merged-chr8-68669105-1	chr8	68669055	68669155	+	1.9	cIP2vsInput	"intron (NM_172753, intron 1 of 9)"	"intron (NM_172753, intron 1 of 9)"	66041	NM_001252623	234356	Mm.489712	NM_001252623	ENSMUSG00000036356	Csgalnact1	4732435N03Rik|CSGalNAcT-1	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0	0.316832
Merged-chr17-38999294-1	chr17	38999244	38999344	+	1.9	cIP2vsInput	Intergenic	Intergenic	-37401	NM_001256050	100126776	Mm.471588	NM_001256050		Gm21947	Esp24	"predicted gene, 21947"	protein-coding	0	0.356436
Merged-chr3-92803211-1	chr3	92803161	92803261	+	1.9	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	4680	NM_001254760	631101	Mm.250525	NM_001254760	ENSMUSG00000095870	Lce1k	Gm7055|Sprrl6	late cornified envelope 1K	protein-coding	0	0.306931
Merged-chr11-71575716-1	chr11	71575666	71575766	+	1.9	cIP2vsInput	Intergenic	MER44B|DNA|TcMar-Tigger	-174987	NM_177618	216881	Mm.48648	NM_177618	ENSMUSG00000020811	Wscd1	mKIAA0523	WSC domain containing 1	protein-coding	0.01	0.356436
Merged-chr2-171192234-1	chr2	171192184	171192284	+	1.9	cIP2vsInput	Intergenic	Intergenic	460427	NM_001163686	76829	Mm.41633	NM_001163686	ENSMUSG00000027560	Dok5	2700055C10Rik	docking protein 5	protein-coding	0	0.366337
Merged-chr3-49457042-1	chr3	49456992	49457092	+	1.9	cIP1vsInput	Intergenic	Intergenic	300274	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding	0	0.257426
Merged-chr2-81858657-1	chr2	81858607	81858707	+	1.9	cIP2vsInput	Intergenic	Intergenic	-195001	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0.02	0.356436
Merged-chr16-82344666-1	chr16	82344616	82344716	+	1.9	cIP2vsInput	Intergenic	Intergenic	1143969	NM_010954	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.306931
Merged-chr15-42643077-1	chr15	42643027	42643127	+	1.9	cIP2vsInput	"intron (NM_009640, intron 1 of 8)"	"intron (NM_009640, intron 1 of 8)"	33718	NM_009640	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding	0.01	0.316832
Merged-chr1-86773244-1	chr1	86773194	86773294	+	1.9	cIP1vsInput	"intron (NM_153530, intron 5 of 20)"	"intron (NM_153530, intron 5 of 20)"	69440	NM_001172157	208718	Mm.389152	NM_001172157	ENSMUSG00000053333	Dis3l2	4930429A22Rik|8030493P09Rik	DIS3 mitotic control homolog (S. cerevisiae)-like 2	protein-coding	0	0.386139
Merged-chr2-110756710-1	chr2	110756660	110756760	+	1.9	cIP1vsInput	"intron (NM_001128103, intron 12 of 26)"	"intron (NM_001128103, intron 12 of 26)"	35102	NM_172979	269328	Mm.32566	NM_172979		Muc15	4732460E09|D730046L02Rik	mucin 15	protein-coding	0	0.287129
Merged-chr17-39476098-1	chr17	39476048	39476148	+	1.9	cIP2vsInput	Intergenic	L1_Mm|LINE|L1	-60044	NM_001255977	100043300	Mm.27927	NM_001255977	ENSMUSG00000096345	Gm4345	Esp16	predicted gene 4345	protein-coding	0	0.326733
Merged-chr16-19410511-1	chr16	19410461	19410561	+	1.9	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-2494	NM_146466	258458	Mm.377512	NM_146466	ENSMUSG00000050158	Olfr165	MOR279-1	olfactory receptor 165	protein-coding	0	0.326733
Merged-chr3-145054109-1	chr3	145054059	145054159	+	1.9	cIP2vsInput	Intergenic	Intergenic	-21333	NM_017474	23844	Mm.33483	NM_017474	ENSMUSG00000028255	Clca3	Clca1|Clca2|gob-5|gob5	chloride channel calcium activated 3	protein-coding	0	0.376238
Merged-chr18-21852964-1	chr18	21852914	21853014	+	1.9	cIP2vsInput	"intron (NM_027616, intron 21 of 22)"	"intron (NM_027616, intron 21 of 22)"	-200596	NM_001081403	225266	Mm.436836	NM_001081403	ENSMUSG00000042514	Klhl14	6330403N15Rik|AI785250|printor	kelch-like 14	protein-coding	0	0.326733
Merged-chr17-88896712-1	chr17	88896662	88896762	+	1.9	cIP2vsInput	Intergenic	Lx3B|LINE|L1	-104736	NM_013582	16867	Mm.1644	NM_013582	ENSMUSG00000024107	Lhcgr	Gpcr19-rs1|LH-R|Lhr	luteinizing hormone/choriogonadotropin receptor	protein-coding	0	0.366337
Merged-chr2-50986840-1	chr2	50986790	50986890	+	1.9	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	77156	NR_033595	227885	Mm.301654	NR_033595	ENSMUSG00000083270	Gm13498	OTTMUSG00000012426	"heat shock protein 90 alpha (cytosolic), class B member 1 pseudogene"	pseudo	0	0.306931
Merged-chr3-106998997-1	chr3	106998947	106999047	+	1.9	cIP2vsInput	Intergenic	Intergenic	-37165	NM_008418	16491	Mm.30640	NM_008418	ENSMUSG00000047959	Kcna3	Kca1-3|Kv1.3|Mk-3	"potassium voltage-gated channel, shaker-related subfamily, member 3"	protein-coding	0	0.326733
Merged-chr5-60727995-1	chr5	60727945	60728045	+	1.9	cIP1vsInput	Intergenic	Intergenic	-741993	NR_040682	71057	Mm.50817	NR_040682		4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	miscRNA	0.01	0.376238
Merged-chr14-82701579-1	chr14	82701529	82701629	+	1.9	cIP2vsInput	Intergenic	Intergenic	-1741984	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding	0	0.29703
Merged-chr6-109843611-1	chr6	109843561	109843661	+	1.9	cIP2vsInput	Intergenic	Lx7|LINE|L1	-801987	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0	0.257426
Merged-chr11-34768570-1	chr11	34768520	34768620	+	1.9	cIP2vsInput	"intron (NM_033374, intron 1 of 51)"	L1MB5|LINE|L1	15335	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding	0	0.346535
Merged-chr12-38987448-1	chr12	38987398	38987498	+	1.9	cIP2vsInput	Intergenic	ORR1B2|LTR|ERVL-MaLR	203737	NM_001163154	14009	Mm.4866	NM_001163154	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant gene 1	protein-coding	0	0.49505
Merged-chr10-29088275-1	chr10	29088225	29088325	+	1.9	cIP2vsInput	Intergenic	Intergenic	-55721	NM_026138	67412	Mm.390264	NM_026138	ENSMUSG00000038916	Soga3	6330407J23Rik	SOGA family member 3	protein-coding	0.01	0.316832
Merged-chr4-93122598-1	chr4	93122548	93122648	+	1.9	cIP2vsInput	Intergenic	Intergenic	212913	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding	0	0.29703
Merged-chr8-96894720-1	chr8	96894670	96894770	+	1.9	cIP2vsInput	Intergenic	Intergenic	-348747	NR_039538	100628567		NR_039538		Mir28c	mmu-mir-28c	microRNA 28c	miscRNA	0.01	0.316832
Merged-chr10-54347141-1	chr10	54347091	54347191	+	1.9	cIP2vsInput	Intergenic	Intergenic	271219	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	"predicted gene, 16998"	miscRNA	0	0.277228
Merged-chr3-137555886-1	chr3	137555836	137555936	+	1.9	cIP2vsInput	Intergenic	Intergenic	-3264	NM_177665	229862	Mm.246591	NM_177665	ENSMUSG00000055138	Gm4861	9230109N16|EG229862	predicted gene 4861	protein-coding	0	0.306931
Merged-chr7-60851392-1	chr7	60851342	60851442	+	1.9	cIP2vsInput	Intergenic	Intergenic	-711173	NM_001082962	20646	Mm.274995	NM_001082961	ENSMUSG00000000948	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding	0	0.306931
Merged-chr2-104952218-1	chr2	104952168	104952268	+	1.9	cIP2vsInput	"intron (NM_177600, intron 9 of 17)"	"intron (NM_177600, intron 9 of 17)"	64809	NM_145380	98221	Mm.379278	NM_145380	ENSMUSG00000027170	Eif3m	Ga17|Pcid1|Tango7	"eukaryotic translation initiation factor 3, subunit M"	protein-coding	0.01	0.306931
Merged-chr1-113329342-1	chr1	113329292	113329392	+	1.9	cIP1vsInput	Intergenic	L1MA6|LINE|L1	-1464424	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik	dermatan sulfate epimerase-like	protein-coding	0.01	0.316832
Merged-chr12-11516538-1	chr12	11516488	11516588	+	1.9	cIP2vsInput	Intergenic	Intergenic	60459	NM_001111118	209550	Mm.341257	NM_001111118	ENSMUSG00000086022	Rad51ap2	EG209550	RAD51 associated protein 2	protein-coding	0	0.336634
Merged-chr2-86518113-1	chr2	86518063	86518163	+	1.9	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	9652	NM_146406	258401	Mm.377483	NM_146406	ENSMUSG00000060742	Olfr1076	MOR189-2	olfactory receptor 1076	protein-coding	0	0.316832
Merged-chr4-39282170-1	chr4	39282120	39282220	+	1.9	cIP2vsInput	Intergenic	Intergenic	-168123	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding	0	0.356436
Merged-chr3-76895705-1	chr3	76895655	76895755	+	1.9	cIP2vsInput	Intergenic	Lx2|LINE|L1	820122	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.346535
Merged-chr6-68622428-1	chr6	68622378	68622478	+	1.9	cIP2vsInput	Intergenic	Lx2A1|LINE|L1	704746	NR_004434	19783		NR_004434		Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	miscRNA	0	0.336634
Merged-chr14-48502257-1	chr14	48502207	48502307	+	1.9	cIP2vsInput	"intron (NM_172600, intron 12 of 15)"	"intron (NM_172600, intron 12 of 15)"	55905	NM_172600	218989	Mm.85211	NM_172600	ENSMUSG00000036339	Tmem260	5930435P15|6720456H20Rik	transmembrane protein 260	protein-coding	0.01	0.326733
Merged-chr18-41581864-1	chr18	41581814	41581914	+	1.9	cIP2vsInput	Intergenic	Intergenic	369330	NM_029942	77619	Mm.30649	NM_029942	ENSMUSG00000056671	Prelid2	1700003A01Rik|C330008K14Rik	PRELI domain containing 2	protein-coding	0	0.29703
Merged-chr18-26669123-1	chr18	26669073	26669173	+	1.9	cIP2vsInput	Intergenic	Intergenic	-915140	NM_001174074	108013	Mm.266435	NM_001146292	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	"CUGBP, Elav-like family member 4"	protein-coding	0.01	0.277228
Merged-chr7-90287212-1	chr7	90287162	90287262	+	1.9	cIP2vsInput	Intergenic	Intergenic	-21780	NM_183293	75338	Mm.487222	NM_029256	ENSMUSG00000030617	Ccdc83	4930549K11Rik|4930554C01Rik|4932423M01Rik	coiled-coil domain containing 83	protein-coding	0.01	0.376238
Merged-chr17-40587563-1	chr17	40587513	40587613	+	1.9	cIP2vsInput	Intergenic	L1MC1|LINE|L1	-11031	NM_001177583	100126777	Mm.471590	NM_001177583	ENSMUSG00000095540	Gm20580	Esp4	"predicted gene, 20580"	protein-coding	0	0.336634
Merged-chr10-74699954-1	chr10	74699904	74700004	+	1.9	cIP2vsInput	Intergenic	RMER6C|LTR|ERVK	-267277	NM_010311	14687	Mm.393508	NM_010311		Gnaz	AI847979|Gz	"guanine nucleotide binding protein, alpha z subunit"	protein-coding	0	0.366337
Merged-chr4-120682263-1	chr4	120682213	120682313	+	1.9	cIP1vsInput	Intergenic	Intergenic	15700	NM_019563	56222	Mm.272646	NM_019563	ENSMUSG00000070803	Cited4	MRG-2|Mrg2	"Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 4"	protein-coding	0.03	0.485149
Merged-chr14-114748065-1	chr14	114748015	114748115	+	1.9	cIP2vsInput	Intergenic	Intergenic	-83900	NR_045661	75822	Mm.410813	NR_045661		4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	miscRNA	0.01	0.336634
Merged-chr7-87413448-1	chr7	87413398	87413498	+	1.9	cIP2vsInput	Intergenic	Intergenic	79963	NM_011661	22173	Mm.238127	NM_011661	ENSMUSG00000004651	Tyr	albino|c|skc35	tyrosinase	protein-coding	0	0.326733
Merged-chr15-34643340-1	chr15	34643290	34643390	+	1.9	cIP1vsInput	"intron (NM_145469, intron 3 of 10)"	L1VL4|LINE|L1	-31733	NR_045883	71637	Mm.410827	NR_045883		4930413F20Rik	-	RIKEN cDNA 4930413F20 gene	miscRNA	0	0.29703
Merged-chr13-9846958-1	chr13	9846908	9847008	+	1.9	cIP2vsInput	Intergenic	Intergenic	-81644	NM_144516	66505	Mm.397307	NM_001199141	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	"zinc finger, MYND domain containing 11"	protein-coding	0.02	0.49505
Merged-chr13-5124805-1	chr13	5124755	5124855	+	1.9	cIP2vsInput	Intergenic	Intergenic	-515641	NM_018859	56043	Mm.251908	NM_018859	ENSMUSG00000045410	Akr1e1	1810061I10Rik|Akr1e2	"aldo-keto reductase family 1, member E1"	protein-coding	0	0.386139
Merged-chr1-75263160-1	chr1	75263110	75263210	+	1.9	cIP2vsInput	"intron (NM_008985, intron 1 of 22)"	"intron (NM_008985, intron 1 of 22)"	1048	NM_008985	19275	Mm.2902	NM_008985	ENSMUSG00000026204	Ptprn	IA-2|mIA-A|mKIAA4064	"protein tyrosine phosphatase, receptor type, N"	protein-coding	0.05	0.584158
Merged-chr4-147185669-1	chr4	147185619	147185719	+	1.9	cIP1vsInput	"intron (NM_001039209, intron 1 of 2)"	ERVB4_1B-I_MM-int|LTR|ERVK	9803	NM_001039209	195531	Mm.489132	NM_001039209	ENSMUSG00000078496	Gm13152	OTTMUSG00000010671	predicted gene 13152	protein-coding	0	0.366337
Merged-chr8-54250616-1	chr8	54250566	54250666	+	1.9	cIP2vsInput	Intergenic	Lx5|LINE|L1	173084	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding	0	0.386139
Merged-chr8-74159129-1	chr8	74159079	74159179	+	1.9	cIP2vsInput	Intergenic	MIR|SINE|MIR	-714045	NM_027837	71597	Mm.158735	NM_027837		Isx	9130012O13Rik|Pix-1	intestine specific homeobox	protein-coding	0	0.326733
Merged-chr11-17280229-1	chr11	17280179	17280279	+	1.9	cIP2vsInput	Intergenic	ID_B1|SINE|B4	22611	NM_020558	57316	Mm.287982	NM_020558	ENSMUSG00000000581	C1d	1110036E10Rik|AI875855|SUN-CoR	C1D nuclear receptor co-repressor	protein-coding	0.01	0.465347
Merged-chr7-111680288-1	chr7	111680238	111680338	+	1.9	cIP2vsInput	"intron (NM_173739, intron 1 of 10)"	B3|SINE|B2	99689	NM_173739	233733	Mm.323322	NM_173739	ENSMUSG00000038296	Galnt18	2900011G21Rik|BC024988|Galntl4	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18	protein-coding	0	0.49505
Merged-chr10-79455722-1	chr10	79455672	79455772	+	1.9	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-13236	NM_001104537	625029	Mm.469865	NM_001104537	ENSMUSG00000091381	Vmn2r83	EG625029	"vomeronasal 2, receptor 83"	protein-coding	0	0.336634
Merged-chrX-93676038-1	chrX	93675988	93676088	+	1.9	cIP2vsInput	"intron (NM_211138, intron 1 of 7)"	"intron (NM_211138, intron 1 of 7)"	926	NM_211138	236899	Mm.166467	NM_177546	ENSMUSG00000035246	Pcyt1b	AW045697|CTTbeta	"phosphate cytidylyltransferase 1, choline, beta isoform"	protein-coding	0.04	0.435644
Merged-chr3-112968889-1	chr3	112968839	112968939	+	1.9	cIP2vsInput	Intergenic	Intergenic	187838	NM_001190404	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding	0	0.326733
Merged-chr6-83880124-1	chr6	83880074	83880174	+	1.9	cIP2vsInput	Intergenic	Intergenic	-34229	NM_001166371	18139	Mm.132392	NM_001166371	ENSMUSG00000030016	Zfml	AI323587|Np220|Znf638|mNP220	"zinc finger, matrin-like"	protein-coding	0.01	0.346535
Merged-chr13-6492863-1	chr13	6492813	6492913	+	1.9	cIP2vsInput	Intergenic	Intergenic	-55294	NM_145131	69617	Mm.41933	NM_145131	ENSMUSG00000021193	Pitrm1	2310012C15Rik|AA410010|MP-1|MP1|Ntup1|PreP|mKIAA1104	pitrilysin metallepetidase 1	protein-coding	0	0.386139
Merged-chr7-102664961-1	chr7	102664911	102665011	+	1.9	cIP2vsInput	Intergenic	Intergenic	-4940	NM_146754	258749	Mm.377671	NM_146754	ENSMUSG00000073969	Olfr556	MOR41-1	olfactory receptor 556	protein-coding	0	0.346535
Merged-chrX-131382672-1	chrX	131382622	131382722	+	1.9	cIP2vsInput	Intergenic	L1M4c|LINE|L1	1632930	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diap2	Dia3|Diaph2|Drf2|E430022I22Rik	diaphanous homolog 2 (Drosophila)	protein-coding	0.01	0.366337
Merged-chr11-64567597-1	chr11	64567547	64567647	+	1.9	cIP2vsInput	Intergenic	L1MA6|LINE|L1	-130923	NR_028445	654805	Mm.436132	NR_028445		F930015N05Rik	-	RIKEN cDNA F930015N05 gene	miscRNA	0	0.346535
Merged-chr10-46813112-1	chr10	46813062	46813162	+	1.9	cIP2vsInput	Intergenic	Intergenic	568363	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0	0.336634
Merged-chr2-147158029-1	chr2	147157979	147158079	+	1.9	cIP2vsInput	Intergenic	L1MCa|LINE|L1	-26054	NR_030769	100313531	Mm.405189	NR_030769	ENSMUSG00000086509	Nkx2-2as	Gm14112|OTTMUSG00000015691	"NK2 transcription factor related, locus 2 (Drosophila), antisense"	miscRNA	0	0.306931
Merged-chr2-17068613-1	chr2	17068563	17068663	+	1.9	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	-54887	NR_040632	75069	Mm.399263	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	miscRNA	0.01	0.346535
Merged-chr3-39875293-1	chr3	39875243	39875343	+	1.9	cIP2vsInput	Intergenic	Intergenic	647619	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	miscRNA	0.01	0.415842
Merged-chr13-31649238-1	chr13	31649188	31649288	+	1.9	cIP2vsInput	Intergenic	Intergenic	23422	NM_010225	14238	Mm.125548	NM_010225	ENSMUSG00000038402	Foxf2	FREAC2|Fkh20|LUN	forkhead box F2	protein-coding	0.01	0.326733
Merged-chr15-19859283-1	chr15	19859233	19859333	+	1.9	cIP2vsInput	Intergenic	Intergenic	807467	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding	0.01	0.336634
Merged-chr3-143682323-1	chr3	143682273	143682373	+	1.9	cIP2vsInput	"intron (NR_040405, intron 1 of 2)"	L1MEf|LINE|L1	29820	NR_040405	621809	Mm.360134	NR_040405		Gm6260	EG621809	predicted gene 6260	miscRNA	0.01	0.326733
Merged-chr7-12041599-1	chr7	12041549	12041649	+	1.9	cIP2vsInput	"exon (NM_001166731, exon 1 of 1)"	"exon (NM_001166731, exon 1 of 1)"	300	NM_001166731	628946	Mm.484974	NM_001166731	ENSMUSG00000095864	Vmn1r77	Gm6935	vomeronasal 1 receptor 77	protein-coding	0.01	0.366337
Merged-chr4-46580134-1	chr4	46580084	46580184	+	1.9	cIP2vsInput	"intron (NM_001164804, intron 1 of 11)"	MMTV-int|LTR|ERVK	-13694	NM_178893	107684	Mm.485361	NM_001164804	ENSMUSG00000028337	Coro2a	9030208C03Rik|AI563590|IR10	"coronin, actin binding protein 2A"	protein-coding	0.01	0.366337
Merged-chr2-40489720-1	chr2	40489670	40489770	+	1.9	cIP2vsInput	Intergenic	RLTR42-int|LTR|ERVK	-1263382	NM_024209	67857	Mm.392662	NM_024209		Ppp6c	2310003C10Rik	"protein phosphatase 6, catalytic subunit"	protein-coding	0	0.29703
Merged-chr4-74497300-1	chr4	74497250	74497350	+	1.9	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	245421	NM_144787	76804	Mm.209059	NM_001172095	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding	0	0.29703
Merged-chr1-137718269-1	chr1	137718219	137718319	+	1.9	cIP2vsInput	Intergenic	Intergenic	-248186	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mmu-mir-213	microRNA 181a-1	miscRNA	0.01	0.346535
Merged-chr16-12437441-1	chr16	12437391	12437491	+	1.9	cIP2vsInput	Intergenic	Intergenic	-373949	NR_040507	75493	Mm.396146	NR_040507		1700003L19Rik	-	RIKEN cDNA 1700003L19 gene	miscRNA	0.01	0.29703
Merged-chr13-15157358-1	chr13	15157308	15157408	+	1.9	cIP1vsInput	Intergenic	RMER1B|Other|Other	-306365	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding	0.01	0.455446
Merged-chr15-44135906-1	chr15	44135856	44135956	+	1.9	cIP2vsInput	Intergenic	Intergenic	-60229	NM_013696	22045	Mm.309350	NM_013696	ENSMUSG00000038760	Trhr	TRH-R1	thyrotropin releasing hormone receptor	protein-coding	0	0.366337
Merged-chrX-83956816-1	chrX	83956766	83956866	+	1.9	cIP2vsInput	"intron (NM_007868, intron 42 of 78)"	"intron (NM_007868, intron 42 of 78)"	-468892	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding	0.01	0.277228
Merged-chr13-15892687-1	chr13	15892637	15892737	+	1.9	cIP1vsInput	Intergenic	Lx8b|LINE|L1	85444	NR_046131	328190	Mm.446957	NR_046131		A530046M15Rik	A530046M15	RIKEN cDNA A530046M15 gene	miscRNA	0.01	0.405941
Merged-chr4-126732717-1	chr4	126732667	126732767	+	1.9	cIP2vsInput	"intron (NM_198960, intron 3 of 6)"	CpG	3552	NM_198960	332937	Mm.331881	NM_198960	ENSMUSG00000042477	Tfap2e	AI505200|AP-2e|Tcfap2e	"transcription factor AP-2, epsilon"	protein-coding	0.04	0.455446
Merged-chr1-107803306-1	chr1	107803256	107803356	+	1.9	cIP2vsInput	Intergenic	Lx7|LINE|L1	-113953	NR_102306	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0	0.376238
Merged-chr9-113506344-1	chr9	113506294	113506394	+	1.9	cIP2vsInput	"intron (NR_040760, intron 2 of 4)"	MIR|SINE|MIR	80808	NR_040760	102688	Mm.394901	NR_040760		AU023762	-	expressed sequence AU023762	miscRNA	0	0.356436
Merged-chr17-60301912-1	chr17	60301862	60301962	+	1.9	cIP1vsInput	Intergenic	Intergenic	-1015840	NR_030569	100124495		NR_030569		Mir466g	Mirn466g	microRNA 466g	miscRNA	0.01	0.277228
Merged-chr5-40333175-1	chr5	40333125	40333225	+	1.9	cIP1vsInput	Intergenic	Intergenic	-688544	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding	0.01	0.356436
Merged-chr3-4000032-1	chr3	3999982	4000082	+	1.9	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	492002	NM_013920	30942	Mm.330897	NM_013920		Hnf4g	NR2A2	"hepatocyte nuclear factor 4, gamma"	protein-coding	0	0.336634
Merged-chr16-23087591-1	chr16	23087541	23087641	+	1.9	cIP2vsInput	Intergenic	Intergenic	-19888	NM_001123038	13682	Mm.260084	NM_001123037	ENSMUSG00000022884	Eif4a2	4833432N07Rik|BM-010|Ddx2b|Eif4	eukaryotic translation initiation factor 4A2	protein-coding	0.01	0.356436
Merged-chr1-98879836-1	chr1	98879786	98879886	+	1.9	cIP2vsInput	Intergenic	Intergenic	458712	NM_027584	70866	Mm.389164	NM_001164233	ENSMUSG00000026336	Slco6d1	4921511I05Rik	"solute carrier organic anion transporter family, member 6d1"	protein-coding	0	0.326733
Merged-chr6-89427253-1	chr6	89427203	89427303	+	1.9	cIP2vsInput	"intron (NM_001167736, intron 4 of 6)"	"intron (NM_001167736, intron 4 of 6)"	-64640	NM_008881	18844	Mm.3789	NM_008881	ENSMUSG00000030084	Plxna1	2600013D04Rik|NOV|PlexA1|Plxn1|mKIAA4053	plexin A1	protein-coding	0.01	0.455446
Merged-chr4-122590872-1	chr4	122590822	122590922	+	1.9	cIP2vsInput	Intergenic	Intergenic	-98387	NM_023865	77432	Mm.157655	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding	0	0.316832
Merged-chr10-124472312-1	chr10	124472262	124472362	+	1.9	cIP2vsInput	"intron (NR_028310, intron 1 of 3)"	L1MA5|LINE|L1	3238	NR_028310	75030	Mm.159403	NR_028310		4930503E24Rik	-	"eukaryotic translation initiation factor 3, subunit I pseudogene"	pseudo	0	0.425743
Merged-chr3-26582042-1	chr3	26581992	26582092	+	1.9	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-55589	NM_029150	70862	Mm.330943	NM_027583	ENSMUSG00000039335	Spata16	4921511F01Rik|4930503K02Rik|Nyd-sp12	spermatogenesis associated 16	protein-coding	0	0.336634
Merged-chr6-102082493-1	chr6	102082443	102082543	+	1.9	cIP2vsInput	Intergenic	Intergenic	308244	NR_027989	207157	Mm.57632	NM_177579		Gm9871	0610005I04|EG207157|ENSMUSG00000052236	predicted gene 9871	miscRNA	0.02	0.405941
Merged-chr5-132586606-1	chr5	132586556	132586656	+	1.9	cIP2vsInput	Intergenic	Intergenic	-44263	NM_177047	319974	Mm.488992	NM_177047		Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding	0	0.366337
Merged-chr9-107361128-1	chr9	107361078	107361178	+	1.9	cIP2vsInput	Intergenic	Intergenic	20488	NM_175486	235599	Mm.71039	NM_175486	ENSMUSG00000037977	6430571L13Rik	-	RIKEN cDNA 6430571L13 gene	protein-coding	0	0.544554
Merged-chr7-37601791-1	chr7	37601741	37601841	+	1.9	cIP2vsInput	"intron (NM_172385, intron 3 of 5)"	"intron (NM_172385, intron 3 of 5)"	167961	NM_172385	243937	Mm.388121	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding	0	0.356436
Merged-chr8-39222684-1	chr8	39222634	39222734	+	1.9	cIP2vsInput	Intergenic	Lx4A|LINE|L1	-75296	NR_044988	621335	Mm.208080	NR_044988		Gm6213	EG621335	predicted gene 6213	miscRNA	0	0.336634
Merged-chr13-86595534-1	chr13	86595484	86595584	+	1.9	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-548739	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0	0.336634
Merged-chr14-21357983-1	chr14	21357933	21358033	+	1.9	cIP2vsInput	"intron (NM_134079, intron 7 of 10)"	"intron (NM_134079, intron 7 of 10)"	-141787	NM_001205241	54169	Mm.248967	NM_001205241	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding	0	0.336634
Merged-chr13-5248558-1	chr13	5248508	5248608	+	1.9	cIP2vsInput	Intergenic	Intergenic	609534	NR_045891	71867	Mm.179181	NR_045891		1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	miscRNA	0	0.356436
Merged-chr1-80993519-1	chr1	80993469	80993569	+	1.9	cIP1vsInput	Intergenic	Intergenic	-83798	NM_172849	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding	0	0.376238
Merged-chr8-37074090-1	chr8	37074040	37074140	+	1.9	cIP1vsInput	Intergenic	Intergenic	80515	NM_001039220	621080	Mm.373292	NM_001039220	ENSMUSG00000074384	AI429214	-	expressed sequence AI429214	protein-coding	0	0.336634
Merged-chr10-52546805-1	chr10	52546755	52546855	+	1.9	cIP2vsInput	Intergenic	MMERVK9E_I-int|LTR|ERVK	-1066	NR_037920	22639	Mm.490597	NM_009540	ENSMUSG00000049576	Zfa-ps	Zfa|Zfx	"zinc finger protein, autosomal, pseudogene"	pseudo	0	0.386139
Merged-chr6-25156388-1	chr6	25156338	25156438	+	1.9	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-200263	NM_177013	319832	Mm.127446	NM_177013	ENSMUSG00000048022	Tmem229a	6332401O19Rik	transmembrane protein 229A	protein-coding	0	0.287129
Merged-chr13-118521446-1	chr13	118521396	118521496	+	1.9	cIP2vsInput	Intergenic	MusHAL1|LINE|L1	-34722	NR_045982	75890	Mm.141235	NR_045982		1700003P14Rik	1700030O10Rik|4930584L06Rik	RIKEN cDNA 1700003P14 gene	miscRNA	0	0.326733
Merged-chr6-59469625-1	chr6	59469575	59469675	+	1.9	cIP2vsInput	Intergenic	BC1_Mm|scRNA|scRNA	-43335	NM_183183	243385	Mm.485751	NM_183183	ENSMUSG00000045441	Gprin3	C030038J10Rik|C730021L23	GPRIN family member 3	protein-coding	0	0.346535
Merged-chr18-8137058-1	chr18	8137008	8137108	+	1.9	cIP2vsInput	Intergenic	RLTR13D6|LTR|ERVK	267861	NM_153085	225131	Mm.204524	NM_001146298	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding	0.01	0.405941
Merged-chr4-51997261-1	chr4	51997211	51997311	+	1.9	cIP2vsInput	"intron (NR_040668, intron 2 of 2)"	"intron (NR_040668, intron 2 of 2)"	53849	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	miscRNA	0	0.316832
Merged-chr15-89323327-1	chr15	89323277	89323377	+	1.9	cIP2vsInput	"exon (NM_182928, exon 2 of 3)"	"exon (NM_182928, exon 2 of 3)"	355	NM_182928	223780	Mm.210541	NM_182928	ENSMUSG00000054136	Adm2	Am2|IMD|Imdn	adrenomedullin 2	protein-coding	0.05	0.653465
Merged-chr10-28931136-1	chr10	28931086	28931186	+	1.9	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-7629	NR_033601	114676	Mm.484516	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo	0.01	0.356436
Merged-chr7-25593778-1	chr7	25593728	25593828	+	1.9	cIP1vsInput	Intergenic	MYSERV-int|LTR|ERVK	22114	NM_001039243	632778	Mm.423112	NM_001039243	ENSMUSG00000074261	Gm7092	EG632778|Kseg1	predicted gene 7092	protein-coding	0	0.336634
Merged-chr11-55852287-1	chr11	55852237	55852337	+	1.9	cIP2vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	188700	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding	0	0.316832
Merged-chr6-80859691-1	chr6	80859641	80859741	+	1.9	cIP2vsInput	Intergenic	Intergenic	840048	NM_178731	243499	Mm.483425	NM_001134743	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding	0	0.29703
Merged-chr4-138615176-1	chr4	138615126	138615226	+	1.9	cIP2vsInput	"intron (NM_029401, intron 1 of 21)"	L1M2|LINE|L1	8816	NM_029401	75718	Mm.251530	NM_029401		Vwa5b1	4931403E03Rik	von Willebrand factor A domain containing 5B1	protein-coding	0	0.386139
Merged-chr14-89252158-1	chr14	89252108	89252208	+	1.9	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-644066	NR_002862	328451	Mm.320571	NR_002862		Gm5088	EG328451|Pabpc4l	"poly(A)-binding protein, cytoplasmic pseudogene"	pseudo	0	0.316832
Merged-chr18-89378607-1	chr18	89378557	89378657	+	1.9	cIP2vsInput	"intron (NM_001039173, intron 7 of 7)"	"intron (NM_001039173, intron 7 of 7)"	181180	NM_001039149	225825	Mm.139293	NM_001039148	ENSMUSG00000034028	Cd226	BC051526|DNAM-1|DNAM1|Pta1|TLiSA1	CD226 antigen	protein-coding	0	0.287129
Merged-chr14-119233625-1	chr14	119233575	119233675	+	1.9	cIP2vsInput	"intron (NM_015820, intron 1 of 1)"	"intron (NM_015820, intron 1 of 1)"	95360	NM_015820	50787	Mm.445777	NM_015820		Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding	0	0.306931
Merged-chr10-101316851-1	chr10	101316801	101316901	+	1.9	cIP2vsInput	Intergenic	Intergenic	-364636	NM_001205098	67569	Mm.403713	NM_001162368	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"	protein-coding	0.02	0.346535
Merged-chr2-123542730-1	chr2	123542680	123542780	+	1.9	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	587226	NR_040611	74702	Mm.410814	NR_040611	ENSMUSG00000085496	4930517E11Rik	-	RIKEN cDNA 4930517E11 gene	miscRNA	0	0.29703
Merged-chr3-18359415-1	chr3	18359365	18359465	+	1.9	cIP2vsInput	Intergenic	Intergenic	-116077	NM_007825	13123	Mm.316000	NM_007825	ENSMUSG00000039519	Cyp7b1	AW261589|D3Ertd552e|hct-1	"cytochrome P450, family 7, subfamily b, polypeptide 1"	protein-coding	0	0.306931
Merged-chr15-54994714-1	chr15	54994664	54994764	+	1.9	cIP2vsInput	Intergenic	L1MB8|LINE|L1	-74568	NM_015744	18606	Mm.250256	NM_001136077	ENSMUSG00000022425	Enpp2	ATX|Npps2|PD-Ialpha|Pdnp2	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding	0.01	0.405941
Merged-chr5-8333111-1	chr5	8333061	8333161	+	1.9	cIP2vsInput	"intron (NM_001007220, intron 2 of 28)"	"intron (NM_001007220, intron 2 of 28)"	34970	NM_001007221	11496	Mm.275895	NM_001007220	ENSMUSG00000040537	Adam22	2900022I03Rik|AI854032|MDC2	a disintegrin and metallopeptidase domain 22	protein-coding	0	0.346535
Merged-chr2-147931944-1	chr2	147931894	147931994	+	1.9	cIP2vsInput	Intergenic	Intergenic	115025	NM_010446	15376	Mm.938	NM_010446	ENSMUSG00000037025	Foxa2	HNF3-beta|HNF3beta|Hnf-3b|Hnf3b|Tcf-3b|Tcf3b	forkhead box A2	protein-coding	0	0.346535
Merged-chr3-88771848-1	chr3	88771798	88771898	+	1.9	cIP2vsInput	"intron (NM_018804, intron 1 of 3)"	"intron (NM_018804, intron 1 of 3)"	751	NM_018804	229521	Mm.379376	NM_018804	ENSMUSG00000068923	Syt11	1500004A13Rik|3632445O20Rik|5430404N14Rik|6530420C11Rik|AI851970	synaptotagmin XI	protein-coding	0.01	0.594059
Merged-chr1-133546030-1	chr1	133545980	133546080	+	1.9	cIP2vsInput	Intergenic	Intergenic	64250	NM_009227	20643	Mm.249110	NM_009227	ENSMUSG00000090553	Snrpe	AL022645|C76690|SME	small nuclear ribonucleoprotein E	protein-coding	0.01	0.306931
Merged-chr10-63559068-1	chr10	63559018	63559118	+	1.9	cIP2vsInput	"intron (NM_001164376, intron 3 of 17)"	MamRep605|LTR?|LTR?	101557	NM_001164376	216033	Mm.444692	NM_001164376	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	"catenin (cadherin associated protein), alpha 3"	protein-coding	0.02	0.336634
Merged-chrX-138684344-1	chrX	138684294	138684394	+	1.9	cIP2vsInput	"intron (NM_030688, intron 6 of 10)"	L1M2|LINE|L1	-230086	NM_013724	27206	Mm.482319	NM_013724	ENSMUSG00000052854	Nrk	AA407323|AA409510|AI225895|AV168563|AW538185|Nesk	Nik related kinase	protein-coding	0	0.386139
Merged-chr6-139626843-1	chr6	139626793	139626893	+	1.9	cIP2vsInput	Intergenic	Intergenic	-89016	NM_207683	18705	Mm.391538	NM_207683	ENSMUSG00000030228	Pik3c2g	C80387|PI3K-C2-gamma	"phosphatidylinositol 3-kinase, C2 domain containing, gamma polypeptide"	protein-coding	0.01	0.356436
Merged-chr2-66018449-1	chr2	66018399	66018499	+	1.9	cIP2vsInput	"intron (NM_178634, intron 4 of 5)"	"intron (NM_178634, intron 4 of 5)"	106344	NM_015736	14425	Mm.439760	NM_015736	ENSMUSG00000026994	Galnt3	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3	protein-coding	0	0.29703
Merged-chr8-76238461-1	chr8	76238411	76238511	+	1.9	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	661712	NR_028579	100039211	Mm.367571	NR_028579	ENSMUSG00000074235	Gm10649	ENSMUSG00000074235	predicted gene 10649	miscRNA	0.01	0.346535
Merged-chr3-47942990-1	chr3	47942940	47943040	+	1.9	cIP2vsInput	Intergenic	Intergenic	83769	NR_040408	666202	Mm.465057	NR_040408		Gm7977	EG666202	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide pseudogene"	pseudo	0.01	0.316832
Merged-chr5-101601148-1	chr5	101601098	101601198	+	1.9	cIP2vsInput	Intergenic	Intergenic	63563	NM_144955	18096	Mm.193072	NM_144955		Nkx6-1	NKX6A|Nkx6.1	NK6 homeobox 1	protein-coding	0.01	0.405941
Merged-chr15-16571601-1	chr15	16571551	16571651	+	1.9	cIP2vsInput	Intergenic	Intergenic	-206500	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0	0.316832
Merged-chr8-15397791-1	chr8	15397741	15397841	+	1.9	cIP2vsInput	Intergenic	Intergenic	340138	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding	0.03	0.336634
Merged-chr4-28753989-1	chr4	28753939	28754039	+	1.9	cIP2vsInput	Intergenic	MER5A|DNA|hAT-Charlie	-59156	NM_001122889	13841	Mm.257266	NM_001122889	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding	0	0.415842
Merged-chr12-119343638-1	chr12	119343588	119343688	+	1.9	cIP2vsInput	Intergenic	Intergenic	-99772	NM_001163136	238455	Mm.31376	NM_001163136	ENSMUSG00000041886	Macc1	4732474O15Rik|Gm267	metastasis associated in colon cancer 1	protein-coding	0.01	0.39604
Merged-chr7-60501745-1	chr7	60501695	60501795	+	1.9	cIP2vsInput	Intergenic	Intergenic	-361526	NM_001082962	20646	Mm.274995	NM_001082961	ENSMUSG00000000948	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding	0	0.376238
Merged-chr2-127171649-1	chr2	127171599	127171699	+	1.9	cIP2vsInput	Intergenic	Lx2B2|LINE|L1	-28192	NM_001163527	73338	Mm.57559	NM_001163527		Itpripl1	1700041B20Rik	"inositol 1,4,5-triphosphate receptor interacting protein-like 1"	protein-coding	0	0.405941
Merged-chr5-73868114-1	chr5	73868064	73868164	+	1.9	cIP2vsInput	Intergenic	RMER17C-int|LTR|ERVK	200297	NM_177561	69727	Mm.48795	NM_177561		Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding	0	0.287129
Merged-chr15-86047361-1	chr15	86047311	86047411	+	1.9	cIP2vsInput	Intergenic	Lx7|LINE|L1	-10334	NM_172611	223752	Mm.24442	NM_001205353	ENSMUSG00000035900	Gramd4	9930016O13	GRAM domain containing 4	protein-coding	0	0.346535
Merged-chr1-3614638-1	chr1	3614588	3614688	+	1.9	cIP2vsInput	"intron (NM_001011874, intron 1 of 2)"	L1Md_F3|LINE|L1	56860	NM_001011874	497097	Mm.489375	NM_001011874		Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X Kell blood group precursor related family member 4	protein-coding	0	0.336634
Merged-chr17-37314886-1	chr17	37314836	37314936	+	1.9	cIP2vsInput	promoter-TSS (NM_207673)	promoter-TSS (NM_207673)	-449	NM_001011721	258218	Mm.377381	NM_001011721	ENSMUSG00000091531	Olfr102	MOR250-4	olfactory receptor 102	protein-coding	0	0.326733
Merged-chr10-125483966-1	chr10	125483916	125484016	+	1.9	cIP2vsInput	Intergenic	Intergenic	-155431	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	"solute carrier family 16 (monocarboxylic acid transporters), member 7"	protein-coding	0.01	0.326733
Merged-chr12-117393133-1	chr12	117393083	117393183	+	1.9	cIP2vsInput	Intergenic	Intergenic	-56121	NR_044987	432713	Mm.459210	NR_044987		Gm5441	-	predicted gene 5441	miscRNA	0.03	0.425743
Merged-chr2-154697743-1	chr2	154697693	154697793	+	1.9	cIP2vsInput	Intergenic	ORR1A2-int|LTR|ERVL-MaLR	40717	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding	0.01	0.336634
Merged-chr4-21460238-1	chr4	21460188	21460288	+	1.9	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	225725	NM_001080771	230025	Mm.208541	NM_001080771	ENSMUSG00000040478	Prdm13	-	PR domain containing 13	protein-coding	0.01	0.326733
Merged-chr16-76179369-1	chr16	76179319	76179419	+	1.9	cIP1vsInput	Intergenic	Intergenic	56756	NR_040575	78215	Mm.243885	NR_040575		4930578N18Rik	-	RIKEN cDNA 4930578N18 gene	miscRNA	0	0.376238
Merged-chr17-27520790-1	chr17	27520740	27520840	+	1.9	cIP2vsInput	Intergenic	CpG	-17486	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	"glutamate receptor, metabotropic 4"	protein-coding	0.16	0.772277
Merged-chr1-135334966-1	chr1	135334916	135335016	+	1.9	cIP1vsInput	"intron (NM_053106, intron 1 of 2)"	"intron (NM_053106, intron 1 of 2)"	10153	NM_053106	93689	Mm.180124	NM_053106	ENSMUSG00000048096	Lmod1	9530015K06Rik|SM-Lmod	leiomodin 1 (smooth muscle)	protein-coding	0	0.326733
Merged-chr13-65570635-1	chr13	65570585	65570685	+	1.9	cIP1vsInput	Intergenic	L1Md_F2|LINE|L1	291781	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding	0.01	0.415842
Merged-chr14-54298085-1	chr14	54298035	54298135	+	1.9	cIP2vsInput	Intergenic	ORR1C1|LTR|ERVL-MaLR	-15160	NM_010991	18348	Mm.436623	NM_010991	ENSMUSG00000048153	Olfr49	IC6|MOR1181	olfactory receptor 49	protein-coding	0	0.425743
Merged-chr14-113089251-1	chr14	113089201	113089301	+	1.9	cIP2vsInput	Intergenic	RMER12|LTR|ERVK	1067821	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0	0.336634
Merged-chr16-80313672-1	chr16	80313622	80313722	+	1.9	cIP2vsInput	Intergenic	Intergenic	-887025	NM_001113208	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.29703
Merged-chr10-35686278-1	chr10	35686228	35686328	+	1.9	cIP2vsInput	Intergenic	RMER3D-int|LTR|ERVK	-820529	NM_001253355	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0	0.366337
Merged-chr2-32260159-1	chr2	32260109	32260209	+	1.9	cIP2vsInput	promoter-TSS (NM_011675)	promoter-TSS (NM_011675)	-54	NM_011675	22245	Mm.425076	NM_011675	ENSMUSG00000002550	Uck1	URK1|Umpk	uridine-cytidine kinase 1	protein-coding	0.07	0.653465
Merged-chr3-31836785-1	chr3	31836735	31836835	+	1.9	cIP2vsInput	Intergenic	RLTR42-int|LTR|ERVK	-65918	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	"potassium large conductance calcium-activated channel, subfamily M, beta member 2"	protein-coding	0	0.287129
Merged-chr18-15725997-1	chr18	15725947	15726047	+	1.9	cIP2vsInput	Intergenic	Intergenic	-7951	NM_199055	71367	Mm.329304	NM_199055	ENSMUSG00000047161	Chst9	5430438D01Rik	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	protein-coding	0	0.346535
Merged-chr7-54003355-1	chr7	54003305	54003405	+	1.9	cIP2vsInput	Intergenic	ORR1D2|LTR|ERVL-MaLR	-831890	NM_178705	233271	Mm.474990	NM_178705		Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding	0	0.39604
Merged-chr12-118023712-1	chr12	118023662	118023762	+	1.9	cIP2vsInput	"intron (NM_010060, intron 45 of 81)"	"intron (NM_010060, intron 45 of 81)"	175331	NM_010060	13411	Mm.390540	NM_010060	ENSMUSG00000018581	Dnahc11	b2b1203Clo|b2b1279Clo|b2b1289Clo|b2b1727Clo|b2b598Clo|iv|lrd	"dynein, axonemal, heavy chain 11"	protein-coding	0.01	0.475248
Merged-chr2-146721658-1	chr2	146721608	146721708	+	1.9	cIP2vsInput	Intergenic	Intergenic	-134231	NM_001033298	228730	Mm.292352	NM_001033298	ENSMUSG00000074749	Plk1s1	Gm114|Ncrna00153	polo-like kinase 1 substrate 1	protein-coding	0	0.425743
Merged-chr6-42491756-1	chr6	42491706	42491806	+	1.9	cIP2vsInput	Intergenic	Intergenic	-4542	NM_001011528	259144	Mm.377865	NM_001011528	ENSMUSG00000090631	Olfr456	MOR257-7P	olfactory receptor 456	protein-coding	0.01	0.356436
Merged-chr14-109109641-1	chr14	109109591	109109691	+	1.9	cIP2vsInput	Intergenic	Lx8|LINE|L1	-195402	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	"SLIT and NTRK-like family, member 1"	protein-coding	0	0.435644
Merged-chr14-37447508-1	chr14	37447458	37447558	+	1.9	cIP2vsInput	Intergenic	Intergenic	-312186	NM_078478	66092	Mm.486242	NM_001199122	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010	growth hormone inducible transmembrane protein	protein-coding	0	0.326733
Merged-chr7-107864467-1	chr7	107864417	107864517	+	1.9	cIP2vsInput	Intergenic	Intergenic	-18736	NM_146425	258417	Mm.377488	NM_146425	ENSMUSG00000094289	Olfr470	MOR204-22	olfactory receptor 470	protein-coding	0.01	0.316832
Merged-chr5-93344023-1	chr5	93343973	93344073	+	1.9	cIP1vsInput	Intergenic	Intergenic	76450	NM_007635	12452	Mm.3527	NM_007635	ENSMUSG00000029385	Ccng2	-	cyclin G2	protein-coding	0	0.336634
Merged-chr4-130274471-1	chr4	130274421	130274521	+	1.9	cIP2vsInput	"intron (NM_172702, intron 1 of 9)"	"intron (NM_172702, intron 1 of 9)"	749	NM_001253386	230779	Mm.45132	NM_001253386	ENSMUSG00000023232	Serinc2	2310004K20Rik|AW121759|FKSG84|TDE2|Tde2l	serine incorporator 2	protein-coding	0.04	0.613861
Merged-chr19-26397664-2	chr19	26397582	26397747	+	1.9	cIP1vsInput|cIP2vsInput	Intergenic	Lx6|LINE|L1	-207496	NM_011416	67155	Mm.313303	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2"	protein-coding	0.006061	0.36747
Merged-chr1-44834503-1	chr1	44834453	44834553	+	1.9	cIP2vsInput	Intergenic	Intergenic	-89554	NR_040602	75066	Mm.416932	NR_040602		4930521E06Rik	-	RIKEN cDNA 4930521E06 gene	miscRNA	0.01	0.29703
Merged-chr10-29879821-1	chr10	29879771	29879871	+	1.9	cIP2vsInput	Intergenic	Intergenic	320719	NM_001109747	66311	Mm.251779	NM_001109747	ENSMUSG00000075266	Cenpw	2610036L11Rik|Cug2	centromere protein W	protein-coding	0.02	0.326733
Merged-chr17-89805172-1	chr17	89805122	89805222	+	1.9	cIP2vsInput	Intergenic	Intergenic	425931	NR_045952	100043904	Mm.396198	NR_045952		Gm4719	-	predicted gene 4719	miscRNA	0	0.435644
Merged-chrX-162829395-1	chrX	162829345	162829445	+	1.9	cIP2vsInput	promoter-TSS (NM_178935)	promoter-TSS (NM_178935)	4	NM_178935	353170	Mm.371732	NM_178935	ENSMUSG00000038344	Txlng	4932441K18Rik|Fiat|Lrp	taxilin gamma	protein-coding	0.06	0.633663
Merged-chr14-55551318-1	chr14	55551268	55551368	+	1.9	cIP2vsInput	Intergenic	Intergenic	-8711	NR_037572	28199	Mm.488383	NM_001199009	ENSMUSG00000022214	Dcaf11	0710008A13Rik|C76035|D14Ucla1|Dacf11|GLO14|Wdr23	DDB1 and CUL4 associated factor 11	protein-coding	0.01	0.415842
Merged-chr14-16827528-1	chr14	16827478	16827578	+	1.9	cIP2vsInput	Intergenic	Intergenic	-252318	NM_011243	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2|RARbeta2	"retinoic acid receptor, beta"	protein-coding	0	0.306931
Merged-chr1-117961532-1	chr1	117961482	117961582	+	1.9	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	349600	NM_011650	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding	0.01	0.356436
Merged-chr9-79534018-1	chr9	79533968	79534068	+	1.9	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-14716	NR_045336	100038575	Mm.367838	NR_045336		Gm10635	ENSMUSG00000074174	predicted gene 10635	miscRNA	0.01	0.336634
Merged-chr13-76004234-1	chr13	76004184	76004284	+	1.9	cIP2vsInput	"intron (NM_001131068, intron 3 of 3)"	"intron (NM_001131068, intron 3 of 3)"	14328	NM_178916	218341	Mm.266515	NM_001131068	ENSMUSG00000043190	Rfesd	AI256775|D030068K09	Rieske (Fe-S) domain containing	protein-coding	0.01	0.277228
Merged-chr8-5215328-1	chr8	5215278	5215378	+	1.9	cIP2vsInput	Intergenic	L1VL2|LINE|L1	-110096	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.29703
Merged-chr1-7038251-1	chr1	7038201	7038301	+	1.9	cIP2vsInput	Intergenic	Intergenic	-50669	NM_183028	319263		NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0	0.306931
Merged-chrY-90733038-1	chrY	90732988	90733088	+	1.9	cIP2vsInput	Intergenic	L1_Mm|LINE|L1	-52404	NM_133362	170942	Mm.391385	XM_003946384	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding	0.04	0.386139
Merged-chr5-14355227-1	chr5	14355177	14355277	+	1.9	cIP2vsInput	Intergenic	Lx3B|LINE|L1	-159691	NM_011995	26875	Mm.146275	NM_001110796	ENSMUSG00000061601	Pclo	Acz|Pico|mKIAA0559	piccolo (presynaptic cytomatrix protein)	protein-coding	0	0.356436
Merged-chrX-69867536-1	chrX	69867486	69867586	+	1.9	cIP2vsInput	"intron (NM_008032, intron 19 of 19)"	"intron (NM_008032, intron 19 of 19)"	-77745	NM_029316	75509	Mm.233475	NM_029316	ENSMUSG00000059690	1700020N15Rik	-	RIKEN cDNA 1700020N15 gene	protein-coding	0	0.346535
Merged-chr7-12266890-1	chr7	12266840	12266940	+	1.9	cIP2vsInput	Intergenic	L1MB2|LINE|L1	-6211	NM_134210	171244	Mm.377200	NM_134210	ENSMUSG00000094078	Vmn1r81	V1rg9	vomeronasal 1 receptor 81	protein-coding	0	0.336634
Merged-chr6-136968937-1	chr6	136968887	136968987	+	1.9	cIP2vsInput	Intergenic	Intergenic	14414	NM_023898	78600	Mm.290622	NM_023898		Pde6h	A930033D18Rik|PDEgamma	"phosphodiesterase 6H, cGMP-specific, cone, gamma"	protein-coding	0	0.277228
Merged-chr19-54338850-1	chr19	54338800	54338900	+	1.9	cIP2vsInput	Intergenic	MIRb|SINE|MIR	293668	NM_007417	11551	Mm.489007	NM_007417	ENSMUSG00000033717	Adra2a	AW122659|Adra-2|Adra-2a|alpha(2A)AR|alpha2-C10|alpha2A|alpha2A-AR	"adrenergic receptor, alpha 2a"	protein-coding	0	0.475248
Merged-chr6-45679015-1	chr6	45678965	45679065	+	1.9	cIP2vsInput	"intron (NM_001004357, intron 2 of 23)"	"intron (NM_001004357, intron 2 of 23)"	618954	NM_001004357	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0	0.346535
Merged-chr17-76203857-1	chr17	76203807	76203907	+	1.9	cIP2vsInput	Intergenic	Intergenic	342834	NR_033456	100043885	Mm.127562	NR_033456		Gm4710	-	predicted gene 4710	miscRNA	0	0.287129
Merged-chr14-49528820-1	chr14	49528770	49528870	+	1.9	cIP1vsInput	Intergenic	Intergenic	-2983	NM_029238	75288	Mm.78738	NM_029238	ENSMUSG00000021852	Slc35f4	4930550L21Rik	"solute carrier family 35, member F4"	protein-coding	0	0.386139
Merged-chr16-65016185-1	chr16	65016135	65016235	+	1.9	cIP2vsInput	"intron (NM_008310, intron 2 of 2)"	"intron (NM_008310, intron 2 of 2)"	89599	NM_008310	15557	Mm.5040	NM_008310	ENSMUSG00000050783	Htr1f	Htr1eb	5-hydroxytryptamine (serotonin) receptor 1F	protein-coding	0	0.306931
Merged-chr10-52092875-1	chr10	52092825	52092925	+	1.9	cIP2vsInput	"intron (NM_011282, intron 31 of 43)"	"intron (NM_011282, intron 31 of 43)"	70189	NM_153786	215031	Mm.87237	NM_153786	ENSMUSG00000049641	Vgll2	C130057C21Rik|VITO-1|Vito1	vestigial like 2 homolog (Drosophila)	protein-coding	0	0.336634
Merged-chr8-65995643-1	chr8	65995593	65995693	+	1.9	cIP2vsInput	"intron (NM_175188, intron 3 of 7)"	"intron (NM_175188, intron 3 of 7)"	377118	NM_175188	72925	Mm.380457	NM_001166372	ENSMUSG00000036469	1-Mar	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding	0	0.316832
Merged-chr2-25064881-1	chr2	25064831	25064931	+	1.9	cIP2vsInput	Intergenic	ORR1B1-int|LTR|ERVL-MaLR	10502	NM_001177655	56876	Mm.42956	NM_001039386	ENSMUSG00000006476	Nsmf	Jacob|Nelf	NMDA receptor synaptonuclear signaling and neuronal migration factor	protein-coding	0	0.405941
Merged-chr10-63735678-1	chr10	63735628	63735728	+	1.9	cIP2vsInput	"intron (NM_001164376, intron 5 of 17)"	"intron (NM_001164376, intron 5 of 17)"	-85377	NM_001164519	216033	Mm.444692	NM_001164376	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	"catenin (cadherin associated protein), alpha 3"	protein-coding	0	0.346535
Merged-chr16-47408531-1	chr16	47408481	47408581	+	1.9	cIP2vsInput	Intergenic	L1ME3A|LINE|L1	-875204	NM_028610	73693	Mm.35597	NM_001018002	ENSMUSG00000058550	Dppa4	2410091M23Rik|C76608|ECAT15-1	developmental pluripotency associated 4	protein-coding	0.01	0.316832
Merged-chr14-51441878-1	chr14	51441828	51441928	+	1.9	cIP1vsInput	Intergenic	Intergenic	-10084	NM_009487	22301	Mm.482572	NM_009486	ENSMUSG00000070448	Vmn2r89	V2r10|V2r11	"vomeronasal 2, receptor 89"	protein-coding	0	0.29703
Merged-chr12-84986567-1	chr12	84986517	84986617	+	1.9	cIP2vsInput	Intergenic	B1_Mus1|SINE|Alu	-9754	NM_178363	56531	Mm.153183	NM_178363	ENSMUSG00000021244	Ylpm1	A930013E17Rik|ZAP|Zap3	YLP motif containing 1	protein-coding	0.02	0.50495
Merged-chr6-5702120-1	chr6	5702070	5702170	+	1.9	cIP2vsInput	Intergenic	L1M2|LINE|L1	-23519	NM_001191023	13426	Mm.20893	NM_001191023	ENSMUSG00000029757	Dync1i1	DH IC-1|DHIC-1|DIC|Dncic1|IC74	dynein cytoplasmic 1 intermediate chain 1	protein-coding	0	0.415842
Merged-chr16-9648597-1	chr16	9648547	9648647	+	1.9	cIP2vsInput	"intron (NM_008170, intron 8 of 11)"	"intron (NM_008170, intron 8 of 11)"	343936	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	"glutamate receptor, ionotropic, NMDA2A (epsilon 1)"	protein-coding	0	0.326733
Merged-chr11-16323580-1	chr11	16323530	16323630	+	1.9	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	65856	NM_145967	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	9330184N17Rik|BC027127|Vstm2	V-set and transmembrane domain containing 2A	protein-coding	0	0.386139
Merged-chr7-85206819-1	chr7	85206769	85206869	+	1.9	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	30885	NM_001105181	620697	Mm.389945	NM_001105181	ENSMUSG00000096861	Vmn2r68	EG620697|Vmn2r68-ps	"vomeronasal 2, receptor 68"	protein-coding	0.02	0.356436
Merged-chr2-9039090-1	chr2	9039040	9039140	+	1.9	cIP2vsInput	Intergenic	Intergenic	-150425	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	miscRNA	0	0.346535
Merged-chr4-12230990-1	chr4	12230940	12231040	+	1.9	cIP2vsInput	Intergenic	Intergenic	-58975	NM_026558	68099	Mm.25340	NM_026558	ENSMUSG00000028218	Fam92a	6720467C03Rik|Fam92a1	"family with sequence similarity 92, member A"	protein-coding	0	0.306931
Merged-chr16-55764528-1	chr16	55764478	55764578	+	1.9	cIP2vsInput	Intergenic	Lx7|LINE|L1	57610	NM_001159394	80859	Mm.247272	NM_001159394	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	"nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta"	protein-coding	0	0.386139
Merged-chr16-15870262-1	chr16	15870212	15870312	+	1.9	cIP2vsInput	Intergenic	Intergenic	-6940	NM_029354	72083	Mm.22351	NM_029354	ENSMUSG00000022671	Mzt2	2410018G20Rik|2610001E06Rik|Fam128|Fam128b	mitotic spindle organizing protein 2	protein-coding	0.01	0.346535
Merged-chr18-25876076-1	chr18	25876026	25876126	+	1.9	cIP2vsInput	Intergenic	MER33|DNA|hAT-Charlie	-122093	NM_001174074	108013	Mm.266435	NM_001146292	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	"CUGBP, Elav-like family member 4"	protein-coding	0.01	0.346535
Merged-chr3-128627448-1	chr3	128627398	128627498	+	1.9	cIP2vsInput	Intergenic	Intergenic	-395843	NR_045704	402774	Mm.209170	NR_045704		D030025E07Rik	-	RIKEN cDNA D030025E07 gene	miscRNA	0.01	0.326733
Merged-chr15-92842994-1	chr15	92842944	92843044	+	1.9	cIP2vsInput	Intergenic	Intergenic	245885	NM_001164594	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding	0	0.326733
Merged-chr10-54910827-1	chr10	54910777	54910877	+	1.9	cIP1vsInput	Intergenic	L1MC3|LINE|L1	834905	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	"predicted gene, 16998"	miscRNA	0.01	0.277228
Merged-chr1-51175977-1	chr1	51175927	51176027	+	1.9	cIP2vsInput	"intron (NM_019790, intron 7 of 9)"	"intron (NM_019790, intron 7 of 9)"	-113149	NM_138741	20324	Mm.398690	NM_138741	ENSMUSG00000045954	Sdpr	-	serum deprivation response	protein-coding	0	0.376238
Merged-chr2-88855613-1	chr2	88855563	88855663	+	1.9	cIP2vsInput	Intergenic	Intergenic	3661	NM_146463	258455	Mm.377509	NM_146463	ENSMUSG00000061798	Olfr1204	MOR232-6	olfactory receptor 1204	protein-coding	0.01	0.316832
Merged-chr11-48525693-1	chr11	48525643	48525743	+	1.9	cIP2vsInput	Intergenic	Intergenic	-274667	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Gnb2l1	AL033335|GB-like|Gnb2-rs1|Rack1|p205	"guanine nucleotide binding protein (G protein), beta polypeptide 2 like 1"	protein-coding	0.03	0.39604
Merged-chr8-117397494-1	chr8	117397444	117397544	+	1.9	cIP2vsInput	"intron (NM_001163262, intron 3 of 20)"	L1MB3|LINE|L1	48324	NM_028941	74440	Mm.233181	NM_001163262	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding	0	0.435644
Merged-chr13-4088246-1	chr13	4088196	4088296	+	1.9	cIP2vsInput	"intron (NM_134072, intron 8 of 8)"	"intron (NM_134072, intron 8 of 8)"	28655	NM_134072	105387	Mm.342256	NM_134072	ENSMUSG00000033715	Akr1c14	9030611N15Rik|AW557061	"aldo-keto reductase family 1, member C14"	protein-coding	0	0.356436
Merged-chr16-76916598-1	chr16	76916548	76916648	+	1.9	cIP2vsInput	Intergenic	Intergenic	94283	NR_040573	76601	Mm.396217	NR_040573		1700041M19Rik	-	RIKEN cDNA 1700041M19 gene	miscRNA	0	0.346535
Merged-chr17-53162380-1	chr17	53162330	53162430	+	1.9	cIP1vsInput	Intergenic	Lx5c|LINE|L1	300941	NM_172497	211482	Mm.60887	NM_172497	ENSMUSG00000023931	Efhb	4921525D22Rik	"EF hand domain family, member B"	protein-coding	0	0.336634
Merged-chr2-40496484-1	chr2	40496434	40496534	+	1.9	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-1270146	NM_024209	67857	Mm.392662	NM_024209		Ppp6c	2310003C10Rik	"protein phosphatase 6, catalytic subunit"	protein-coding	0.02	0.366337
Merged-chr1-166215216-1	chr1	166215166	166215266	+	1.9	cIP2vsInput	"intron (NM_175296, intron 8 of 11)"	"intron (NM_175296, intron 8 of 11)"	23528	NM_175296	98558	Mm.26189	NM_175296	ENSMUSG00000040629	Mael	4933405K18Rik|AU019877	maelstrom homolog (Drosophila)	protein-coding	0	0.346535
Merged-chr12-67673391-1	chr12	67673341	67673441	+	1.9	cIP2vsInput	Intergenic	Intergenic	-4120	NR_033146	100316870	Mm.379794	NR_033146		Gm17821	-	DDB1 and CUL4 associated factor 5 pseudogene	pseudo	0	0.316832
Merged-chr12-94097107-1	chr12	94097057	94097157	+	1.9	cIP2vsInput	Intergenic	ORR1E|LTR|ERVL-MaLR	-1595119	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0	0.366337
Merged-chr13-64736710-1	chr13	64736660	64736760	+	1.9	cIP1vsInput	TTS (NM_001081129)	TTS (NM_001081129)	167178	NM_001081129	238680	Mm.390590	NM_001081129	ENSMUSG00000033063	Cntnap3	-	contactin associated protein-like 3	protein-coding	0	0.306931
Merged-chr7-78896054-1	chr7	78896004	78896104	+	1.9	cIP2vsInput	"intron (NM_001162939, intron 1 of 3)"	CpG	127	NM_001162939	68048	Mm.34109	NM_001162939	ENSMUSG00000030609	Aen	2700083B06Rik|Isg20l1	apoptosis enhancing nuclease	protein-coding	0.09	0.663366
Merged-chr5-24540781-1	chr5	24540731	24540831	+	1.9	cIP2vsInput	promoter-TSS (NM_080444)	promoter-TSS (NM_080444)	-333	NM_080444	117590	Mm.207071	NM_080444	ENSMUSG00000038204	Asb10	Asb-10|BB137407	ankyrin repeat and SOCS box-containing 10	protein-coding	0.04	0.643564
Merged-chr8-55060430-1	chr8	55060380	55060480	+	1.9	cIP1vsInput	"3' UTR (NM_001253754, exon 7 of 7)"	"3' UTR (NM_001253754, exon 7 of 7)"	105702	NM_001253756	234267	Mm.241700	NM_001253754	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding	0.01	0.366337
Merged-chr4-96213729-1	chr4	96213679	96213779	+	1.9	cIP2vsInput	Intergenic	ORR1E-int|LTR|ERVL-MaLR	-72577	NM_001100182	242546	Mm.302562	NM_001100182	ENSMUSG00000081225	Cyp2j12	BB197342|Cyp2j12-ps|OTTMUSG00000007939	"cytochrome P450, family 2, subfamily j, polypeptide 12"	protein-coding	0	0.29703
Merged-chr2-66706042-1	chr2	66705992	66706092	+	1.9	cIP2vsInput	"intron (NM_009135, intron 10 of 24)"	"intron (NM_009135, intron 10 of 24)"	-71090	NM_018852	20274	Mm.440889	NM_018852	ENSMUSG00000075316	Scn9a	Nav1.7|PN1|mKIAA4197	"sodium channel, voltage-gated, type IX, alpha"	protein-coding	0	0.336634
Merged-chr14-92956187-1	chr14	92956137	92956237	+	1.9	cIP2vsInput	Intergenic	L1MA6|LINE|L1	932701	NM_001271800	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.287129
Merged-chr6-124129602-1	chr6	124129552	124129652	+	1.9	cIP2vsInput	Intergenic	L2a|LINE|L2	102182	NM_001104642	232367	Mm.469872	NM_001104642	ENSMUSG00000072778	Vmn2r27	EG232367	"vomeronasal 2, receptor27"	protein-coding	0	0.316832
Merged-chr10-35938908-1	chr10	35938858	35938958	+	1.9	cIP2vsInput	Intergenic	Intergenic	-567899	NM_001253355	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding	0	0.376238
Merged-chr3-114244154-1	chr3	114244104	114244204	+	1.9	cIP2vsInput	Intergenic	Intergenic	213614	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	"collagen, type XI, alpha 1"	protein-coding	0	0.366337
Merged-chr17-46830174-1	chr17	46830124	46830224	+	1.9	cIP2vsInput	"intron (NM_001100452, intron 1 of 10)"	"intron (NM_001100452, intron 1 of 10)"	1239	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding	0.02	0.376238
Merged-chr16-93424492-1	chr16	93424442	93424542	+	1.9	cIP2vsInput	"intron (NR_040494, intron 1 of 2)"	"intron (NR_040494, intron 1 of 2)"	34380	NR_040494	72264	Mm.396204	NR_040494		1700029J03Rik	-	RIKEN cDNA 1700029J03 gene	miscRNA	0	0.316832
Merged-chr3-83664287-1	chr3	83664237	83664337	+	1.9	cIP2vsInput	Intergenic	Intergenic	-90169	NR_036591	69460	Mm.389464	NR_036591		1700028M03Rik	-	RIKEN cDNA 1700028M03 gene	miscRNA	0	0.316832
Merged-chr11-58847292-1	chr11	58847242	58847342	+	1.9	cIP2vsInput	Intergenic	CpG	6176	NM_146537	258530	Mm.377556	NM_146537	ENSMUSG00000094805	Olfr311	MOR222-1	olfactory receptor 311	protein-coding	0.07	0.633663
Merged-chr12-26546536-1	chr12	26546486	26546586	+	1.9	cIP2vsInput	Intergenic	Intergenic	77321	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	"cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial"	protein-coding	0.03	0.554455
Merged-chr15-13843602-1	chr15	13843552	13843652	+	1.9	cIP2vsInput	Intergenic	Intergenic	-669963	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	K-cadherin|cad6|cadherin-6	cadherin 6	protein-coding	0	0.306931
Merged-chr4-43406394-1	chr4	43406344	43406444	+	1.9	cIP2vsInput	promoter-TSS (NM_199057)	promoter-TSS (NM_199057)	-180	NM_199057	100213	Mm.235730	NM_001037709	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding	0.04	0.60396
Merged-chr8-60380477-1	chr8	60380427	60380527	+	1.9	cIP2vsInput	Intergenic	Intergenic	-125647	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|mKat-2	aminoadipate aminotransferase	protein-coding	0	0.356436
Merged-chr14-91034244-1	chr14	91034194	91034294	+	1.9	cIP2vsInput	Intergenic	Intergenic	907353	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0	0.326733
Merged-chr1-28981361-1	chr1	28981311	28981411	+	1.9	cIP2vsInput	Intergenic	Intergenic	-201109	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0	0.346535
Merged-chr1-15224323-1	chr1	15224273	15224373	+	1.9	cIP2vsInput	Intergenic	Intergenic	-88129	NM_001098528	98741	Mm.156081	NM_001033195		Kcnb2	9630047L19Rik|BB130875|Kv2.2	"potassium voltage gated channel, Shab-related subfamily, member 2"	protein-coding	0.02	0.306931
Merged-chr5-108688853-1	chr5	108688803	108688903	+	1.9	cIP2vsInput	Intergenic	ORR1D2-int|LTR|ERVL-MaLR	-5376	NM_001164259	116701	Mm.35691	NM_001164259	ENSMUSG00000008090	Fgfrl1	FGFR5|FGFR5beta|FGFR5gamma	fibroblast growth factor receptor-like 1	protein-coding	0	0.386139
Merged-chr1-40202642-1	chr1	40202592	40202692	+	1.9	cIP2vsInput	Intergenic	Intergenic	-22438	NM_008362	16177	Mm.896	NM_001123382	ENSMUSG00000026072	Il1r1	CD121a|CD121b|IL-iR|Il1r-1	"interleukin 1 receptor, type I"	protein-coding	0	0.306931
Merged-chr9-40071325-1	chr9	40071275	40071375	+	1.9	cIP2vsInput	Intergenic	Intergenic	-2972	NM_146854	258853	Mm.377721	NM_146854	ENSMUSG00000049010	Olfr982	MOR223-4	olfactory receptor 982	protein-coding	0	0.336634
Merged-chr3-123940464-1	chr3	123940414	123940514	+	1.9	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-268072	NM_031186	83398	Mm.487979	NM_031186	ENSMUSG00000027977	Ndst3	4921531K01Rik|4930511P15Rik	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	protein-coding	0	0.336634
Merged-chr18-8720696-1	chr18	8720646	8720746	+	1.9	cIP2vsInput	Intergenic	Intergenic	-492160	NM_008058	14370	Mm.184289	NM_008058	ENSMUSG00000036904	Fzd8	Fz8	frizzled homolog 8 (Drosophila)	protein-coding	0	0.366337
Merged-chr17-41315479-1	chr17	41315429	41315529	+	1.9	cIP2vsInput	Intergenic	MTC|LTR|ERVL-MaLR	380794	NM_008650	17850	Mm.259884	NM_008650	ENSMUSG00000023921	Mut	D230010K02Rik|Mcm	methylmalonyl-Coenzyme A mutase	protein-coding	0	0.336634
Merged-chr4-26050853-1	chr4	26050803	26050903	+	1.9	cIP1vsInput	Intergenic	Lx5c|LINE|L1	-250850	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding	0	0.336634
Merged-chr14-108960702-1	chr14	108960652	108960752	+	1.9	cIP2vsInput	Intergenic	Intergenic	-46463	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	"SLIT and NTRK-like family, member 1"	protein-coding	0	0.29703
Merged-chr19-11625150-1	chr19	11625100	11625200	+	1.9	cIP2vsInput	Intergenic	Intergenic	-1431	NM_013516	14126	Mm.329735	NM_001276328	ENSMUSG00000024680	Ms4a2	FcRB|Fce1b|Fcer1b|Fcrbeta|Ms4a1|fcERI	"membrane-spanning 4-domains, subfamily A, member 2"	protein-coding	0	0.326733
Merged-chr4-112769427-1	chr4	112769377	112769477	+	1.9	cIP2vsInput	"intron (NM_177668, intron 1 of 6)"	"intron (NM_177668, intron 1 of 6)"	5434	NM_177668	230613	Mm.122553	NM_177668		Skint10	A030001H23Rik|Gm570	selection and upkeep of intraepithelial T cells 10	protein-coding	0	0.326733
Merged-chr13-21593172-1	chr13	21593122	21593222	+	1.9	cIP2vsInput	Intergenic	Intergenic	-18718	NM_146540	258533	Mm.271445	NM_146540	ENSMUSG00000046016	Olfr1364	MOR256-13	olfactory receptor 1364	protein-coding	0	0.247525
Merged-chr1-176598461-1	chr1	176598411	176598511	+	1.9	cIP2vsInput	Intergenic	Intergenic	173962	NR_029775	723921		NR_029775		Mir350	Mirn350|mmu-mir-350	microRNA 350	miscRNA	0	0.29703
Merged-chr1-33575028-1	chr1	33574978	33575078	+	1.9	cIP2vsInput	"intron (NM_008922, intron 7 of 13)"	L1_Mur3|LINE|L1	94730	NM_008922	19076	Mm.27705	NM_008922	ENSMUSG00000026134	Prim2	AI323589	"DNA primase, p58 subunit"	protein-coding	0.01	0.326733
Merged-chrX-162214371-1	chrX	162214321	162214421	+	1.9	cIP2vsInput	Intergenic	Intergenic	-54581	NM_001081052	195727	Mm.336313	NM_001081052	ENSMUSG00000059493	Nhs	Gm389|Gm48|Nhs1|Xcat	Nance-Horan syndrome (human)	protein-coding	0	0.346535
Merged-chr2-177265074-1	chr2	177265024	177265124	+	1.9	cIP2vsInput	Intergenic	MMSAT4|Satellite|Satellite	-199668	NM_001177568	628308	Mm.460436	NM_001177568		Gm14420	OTTMUSG00000016588	predicted gene 14420	protein-coding	0.01	0.386139
Merged-chr3-78189283-1	chr3	78189233	78189333	+	1.9	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	956592	NM_001099624	76089	Mm.462396	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding	0.02	0.326733
Merged-chr17-5812238-1	chr17	5812188	5812288	+	1.9	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	12748	NR_045080	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	miscRNA	0	0.39604
Merged-chr11-42074813-1	chr11	42074763	42074863	+	1.9	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-74099	NM_008073	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2"	protein-coding	0	0.356436
Merged-chr6-127587502-1	chr6	127587452	127587552	+	1.9	cIP2vsInput	"intron (NM_001033464, intron 1 of 6)"	RCHARR1|DNA|hAT-Charlie	9527	NM_001033464	381812	Mm.296093	NM_001033464	ENSMUSG00000061414	Efcab4b	Gm1073|Gm462	EF-hand calcium binding domain 4B	protein-coding	0	0.306931
Merged-chrX-128031121-1	chrX	128031071	128031171	+	1.9	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	636828	NR_003646	245598	Mm.72281	NR_003646	ENSMUSG00000049815	4921511C20Rik	Gm383	high density lipoprotein (HDL) binding protein pseudogene	pseudo	0.01	0.376238
Merged-chrX-138486551-1	chrX	138486501	138486601	+	1.9	cIP2vsInput	"intron (NM_030688, intron 5 of 10)"	B1F1|SINE|Alu	-276971	NM_026469	67944	Mm.443280	NM_026469	ENSMUSG00000071686	Tex13a	1700025D03Rik	testis expressed 13A	protein-coding	0.01	0.326733
Merged-chr4-65447050-1	chr4	65447000	65447100	+	1.9	cIP2vsInput	"intron (NM_019514, intron 18 of 21)"	"intron (NM_019514, intron 18 of 21)"	-157936	NM_053084	69807	Mm.22786	NM_001161782	ENSMUSG00000051675	Trim32	1810045E12Rik|3f3|BBS11|Zfp117	tripartite motif-containing 32	protein-coding	0.02	0.445545
Merged-chr4-145516355-1	chr4	145516305	145516405	+	1.9	cIP1vsInput	Intergenic	Intergenic	52145	NR_002888	545700	Mm.389595	NR_002888	ENSMUSG00000052912	Smarca5-ps	9230115A19Rik|OTTMUSG00000011029	"SWI/SNF related, matrix associated, actin depenent ragulator of chromatin, subfamily a, member 5, pseudogene"	pseudo	0.01	0.445545
Merged-chr2-39973779-1	chr2	39973729	39973829	+	1.9	cIP2vsInput	Intergenic	Intergenic	-747441	NM_024209	67857	Mm.392662	NM_024209		Ppp6c	2310003C10Rik	"protein phosphatase 6, catalytic subunit"	protein-coding	0	0.336634
Merged-chr7-86973870-1	chr7	86973820	86973920	+	1.9	cIP2vsInput	Intergenic	L1_Mus1|LINE|L1	-22595	NM_001105190	621430	Mm.469903	NM_001105190	ENSMUSG00000090362	Vmn2r79	EG621430	"vomeronasal 2, receptor 79"	protein-coding	0.01	0.346535
Merged-chr14-53750710-1	chr14	53750660	53750760	+	1.9	cIP1vsInput	Intergenic	Intergenic	84770	NM_001205242	100568452	Mm.486072	NM_001205242		A430107P09Rik	Va10	RIKEN cDNA A430107P09 gene	protein-coding	0	0.277228
Merged-chr14-51441402-1	chr14	51441352	51441452	+	1.9	cIP2vsInput	Intergenic	Intergenic	-10560	NM_009487	22301	Mm.482572	NM_009486	ENSMUSG00000070448	Vmn2r89	V2r10|V2r11	"vomeronasal 2, receptor 89"	protein-coding	0	0.29703
Merged-chr3-71396534-1	chr3	71396484	71396584	+	1.9	cIP2vsInput	Intergenic	Intergenic	-589243	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	miscRNA	0	0.306931
Merged-chr2-149692615-1	chr2	149692565	149692665	+	1.9	cIP1vsInput	Intergenic	ERVL-B4-int|LTR|ERVL	-138168	NM_001085521	433485	Mm.330649	NM_001085521	ENSMUSG00000074736	Syndig1	AW123113|DSPC2|Gm14134|H2C20orf39|OTTMUSG00000015750|Tmem90b	synapse differentiation inducing 1	protein-coding	0	0.366337
Merged-chr4-96295190-1	chr4	96295140	96295240	+	1.9	cIP2vsInput	"intron (NM_001004141, intron 8 of 8)"	"intron (NM_001004141, intron 8 of 8)"	53490	NM_001004141	100066	Mm.26915	NM_001004141	ENSMUSG00000066097	Cyp2j11	AI314783|Cyp2j11-ps	"cytochrome P450, family 2, subfamily j, polypeptide 11"	protein-coding	0.01	0.336634
Merged-chr1-26037190-1	chr1	26037140	26037240	+	1.9	cIP1vsInput	Intergenic	L1_Mur1|LINE|L1	-207483	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Bai3	A830096D10Rik	brain-specific angiogenesis inhibitor 3	protein-coding	0	0.336634
Merged-chr7-86428177-1	chr7	86428127	86428227	+	1.9	cIP2vsInput	Intergenic	RLTR11B|LTR|ERVK	24328	NM_212436	257958	Mm.419223	NM_212436	ENSMUSG00000061549	Olfr301	MOR211-8P|MOR221-1P|MOR221-4|Olfr1531-ps1	olfactory receptor 301	protein-coding	0	0.316832
Merged-chr16-79577350-1	chr16	79577300	79577400	+	1.9	cIP2vsInput	Intergenic	Intergenic	-486253	NM_008941	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	"transmembrane protease, serine 15"	protein-coding	0	0.39604
Merged-chr3-111143730-1	chr3	111143680	111143780	+	1.9	cIP2vsInput	Intergenic	Intergenic	-738173	NR_045362	625585	Mm.389497	NR_045362		Gm6602	-	predicted gene 6602	miscRNA	0	0.29703
Merged-chr8-71845689-1	chr8	71845639	71845739	+	1.9	cIP2vsInput	Intergenic	Intergenic	-36379	NM_145624	236193	Mm.290790	NM_145624		Zfp709	BC021921|GIOT-4|HIT-40	zinc finger protein 709	protein-coding	0.01	0.316832
Merged-chr10-47323164-1	chr10	47323114	47323214	+	1.9	cIP2vsInput	Intergenic	Intergenic	1078415	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0	0.306931
Merged-chr10-58904668-1	chr10	58904618	58904718	+	1.9	cIP2vsInput	"intron (NM_172788, intron 1 of 9)"	"intron (NM_172788, intron 1 of 9)"	91309	NM_172788	237353	Mm.410104	NM_172788	ENSMUSG00000037990	Sh3rf3	4831416G18Rik|Igfbp5-ip|Sh3md4|Sh3rf31	SH3 domain containing ring finger 3	protein-coding	0	0.316832
Merged-chr16-79942177-1	chr16	79942127	79942227	+	1.9	cIP2vsInput	Intergenic	RLTR17B_Mm|LTR|ERVK	-851080	NM_008941	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	"transmembrane protease, serine 15"	protein-coding	0	0.316832
Merged-chr1-55393362-1	chr1	55393312	55393412	+	1.9	cIP1vsInput	Intergenic	Intergenic	-12584	NM_001114663	227120	Mm.194183	NM_001114663		Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding	0	0.346535
Merged-chr12-67179384-1	chr12	67179334	67179434	+	1.9	cIP2vsInput	"intron (NM_207010, intron 1 of 15)"	"intron (NM_207010, intron 1 of 15)"	43165	NM_001193266	320772	Mm.227680	NM_001193266		Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding	0	0.267327
Merged-chr6-57857567-1	chr6	57857517	57857617	+	1.9	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-13110	NM_134183	171201	Mm.377179	NM_134183	ENSMUSG00000058588	Vmn1r21	V1rc28	vomeronasal 1 receptor 21	protein-coding	0	0.306931
Merged-chr6-143654895-1	chr6	143654845	143654945	+	1.9	cIP2vsInput	Intergenic	Intergenic	-3607	NR_045732	73425	Mm.417844	NR_045732	ENSMUSG00000086887	1700060C16Rik	-	RIKEN cDNA 1700060C16 gene	miscRNA	0.01	0.29703
Merged-chr15-14834672-1	chr15	14834622	14834722	+	1.9	cIP2vsInput	Intergenic	Intergenic	-1661033	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	K-cadherin|cad6|cadherin-6	cadherin 6	protein-coding	0	0.336634
Merged-chr16-53199882-1	chr16	53199832	53199932	+	1.9	cIP2vsInput	Intergenic	Lx9|LINE|L1	-384138	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	miscRNA	0	0.29703
Merged-chr5-27288514-1	chr5	27288464	27288564	+	1.9	cIP2vsInput	"intron (NM_001136060, intron 1 of 25)"	"intron (NM_001136060, intron 1 of 25)"	26579	NM_001136060	13483	Mm.42078	NM_001136060	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding	0	0.356436
Merged-chr8-114205451-1	chr8	114205401	114205501	+	1.9	cIP2vsInput	promoter-TSS (NM_173016)	promoter-TSS (NM_173016)	-189	NM_173016	270097	Mm.334825	NM_173016	ENSMUSG00000046844	Vat1l	9430073I07|AI427515|mKIAA1576	vesicle amine transport protein 1 homolog-like (T. californica)	protein-coding	0	0.366337
Merged-chr9-105934697-1	chr9	105934647	105934747	+	1.9	cIP2vsInput	"intron (NM_001167923, intron 5 of 40)"	(TTCA)n|Simple_repeat|Simple_repeat	25946	NM_001167923	665033	Mm.39826	NM_001167923	ENSMUSG00000091345	Col6a5	Col29a1|EG665033|Gm7455	"collagen, type VI, alpha 5"	protein-coding	0	0.316832
Merged-chr5-57691192-1	chr5	57691142	57691242	+	1.9	cIP2vsInput	"intron (NR_015588, intron 2 of 4)"	"intron (NR_015588, intron 2 of 4)"	26727	NR_015588	319216	Mm.446765	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	miscRNA	0	0.237624
Merged-chr3-16669117-1	chr3	16669067	16669167	+	1.9	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	485934	NM_001145919	229096	Mm.23834	NM_001145919	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding	0	0.366337
Merged-chr15-73981928-1	chr15	73981878	73981978	+	1.9	cIP2vsInput	Intergenic	Intergenic	-142257	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding	0.01	0.49505
Merged-chr9-56589753-1	chr9	56589703	56589803	+	1.9	cIP2vsInput	Intergenic	Intergenic	95500	NM_181074	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding	0.01	0.524752
Merged-chr7-91637303-1	chr7	91637253	91637353	+	1.9	cIP2vsInput	"intron (NM_011807, intron 2 of 22)"	"intron (NM_011807, intron 2 of 22)"	-425091	NM_001243046	23859	Mm.257035	NM_001243046		Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|PSD93	"discs, large homolog 2 (Drosophila)"	protein-coding	0	0.316832
Merged-chr13-4432622-1	chr13	4432572	4432672	+	1.9	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-1721	NM_030611	83702	Mm.196666	NM_030611	ENSMUSG00000021210	Akr1c6	3alpha-HSD|Akr1c1|Hsd17b5	"aldo-keto reductase family 1, member C6"	protein-coding	0	0.336634
Merged-chr3-44856568-1	chr3	44856518	44856618	+	1.9	cIP2vsInput	Intergenic	Intergenic	521692	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	miscRNA	0.01	0.316832
Merged-chr12-61265308-1	chr12	61265258	61265358	+	1.9	cIP2vsInput	Intergenic	Intergenic	256512	NR_045049	100504101	Mm.235026	NR_045049		Gm20063	-	"predicted gene, 20063"	miscRNA	0	0.326733
Merged-chrX-14591961-1	chrX	14591911	14592011	+	1.9	cIP2vsInput	Intergenic	L1MA8|LINE|L1	380813	NM_001034100	385328	Mm.275681	NM_001034100	ENSMUSG00000061065	Gm5382	EG385328	predicted gene 5382	protein-coding	0.01	0.29703
Merged-chr10-106204808-1	chr10	106204758	106204858	+	1.9	cIP2vsInput	Intergenic	Intergenic	-265502	NM_177373	327814	Mm.391424	NM_001205341	ENSMUSG00000053825	Ppfia2	5330438O12|B230207K17Rik|E130120L08Rik|mKIAA4112	"protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2"	protein-coding	0.01	0.346535
Merged-chr9-98339297-1	chr9	98339247	98339347	+	1.9	cIP2vsInput	"intron (NM_144533, intron 1 of 4)"	"intron (NM_144533, intron 1 of 4)"	42714	NM_144533	74080	Mm.294082	NM_144533	ENSMUSG00000032456	Nmnat3	4933408N02Rik|PNAT3	nicotinamide nucleotide adenylyltransferase 3	protein-coding	0.03	0.415842
Merged-chr6-20025223-1	chr6	20025173	20025273	+	1.9	cIP2vsInput	Intergenic	Intergenic	1158905	NM_001167757	75196	Mm.67665	NM_001167757	ENSMUSG00000029517	Ankrd7	4930532L20Rik|AV278427	ankyrin repeat domain 7	protein-coding	0	0.287129
Merged-chr17-69655277-1	chr17	69655227	69655327	+	1.9	cIP2vsInput	Intergenic	Intergenic	215951	NM_001145192	320722	Mm.400254	NM_001145192	ENSMUSG00000091636	A330050F15Rik	-	RIKEN cDNA A330050F15 gene	protein-coding	0	0.267327
Merged-chr9-90924640-1	chr9	90924590	90924690	+	1.9	cIP2vsInput	Intergenic	Intergenic	441159	NM_009573	22771	Mm.477226	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding	0	0.366337
Merged-chr4-141021069-1	chr4	141021019	141021119	+	1.9	cIP2vsInput	"intron (NM_001145958, intron 29 of 35)"	"intron (NM_001145958, intron 29 of 35)"	10432	NM_008546	17150	Mm.7386	NM_001161799	ENSMUSG00000060572	Mfap2	AI893631|Magp|Magp1	microfibrillar-associated protein 2	protein-coding	0	0.623762
Merged-chr4-5198212-1	chr4	5198162	5198262	+	1.9	cIP2vsInput	Intergenic	RLTR40|LTR|ERVK	-404906	NM_177730	242291	Mm.369779	NM_177730		Impad1	1110001C20Rik|AA408880|AI451589|AL022796|B230207P20|Jaws|gPAPP	inositol monophosphatase domain containing 1	protein-coding	0.01	0.39604
Merged-chr17-88143528-1	chr17	88143478	88143578	+	1.9	cIP2vsInput	Intergenic	Intergenic	18016	NM_001190356	225058	Mm.312053	NM_001190356		Gm4832	EG225058	predicted gene 4832	protein-coding	0.01	0.39604
Merged-chrX-120178799-1	chrX	120178749	120178849	+	1.9	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-111528	NM_001271809	245578	Mm.490224	NM_001271809		Pcdh11x	PCDHX|PCDHX11|Pcdh11	protocadherin 11 X-linked	protein-coding	0	0.316832
Merged-chr1-186111298-1	chr1	186111248	186111348	+	1.9	cIP2vsInput	"intron (NM_146106, intron 2 of 4)"	"intron (NM_146106, intron 2 of 4)"	6012	NM_146106	226791	Mm.257116	NM_146106	ENSMUSG00000039246	Lyplal1	BC027340|Q96AVO	lysophospholipase-like 1	protein-coding	0	0.366337
Merged-chr2-148995546-1	chr2	148995496	148995596	+	1.9	cIP2vsInput	Intergenic	Intergenic	-120078	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding	0.01	0.277228
Merged-chr15-71050704-1	chr15	71050654	71050754	+	1.9	cIP2vsInput	Intergenic	Intergenic	677134	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	"family with sequence similarity 135, member B"	protein-coding	0	0.316832
Merged-chr3-11994865-1	chr3	11994815	11994915	+	1.9	cIP2vsInput	Intergenic	Intergenic	-150506	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.29703
Merged-chr7-86231625-1	chr7	86231575	86231675	+	1.9	cIP2vsInput	"intron (NM_001102580, intron 1 of 5)"	"intron (NM_001102580, intron 1 of 5)"	14576	NM_001102580	675969	Mm.469834	NM_001102580	ENSMUSG00000091239	Vmn2r76	-	"vomeronasal 2, receptor 76"	protein-coding	0	0.346535
Merged-chr3-47859941-1	chr3	47859891	47859991	+	1.9	cIP2vsInput	Intergenic	Lx3B|LINE|L1	166818	NR_040408	666202	Mm.465057	NR_040408		Gm7977	EG666202	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide pseudogene"	pseudo	0	0.326733
Merged-chr1-137351347-1	chr1	137351297	137351397	+	1.9	cIP2vsInput	Intergenic	Intergenic	-390899	NM_030676	26424	Mm.16794	NM_001159769	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	"nuclear receptor subfamily 5, group A, member 2"	protein-coding	0	0.326733
Merged-chr14-85174560-1	chr14	85174510	85174610	+	1.9	cIP2vsInput	Intergenic	Intergenic	-698136	NR_015539	319903	Mm.440481	NR_015539		9630013A20Rik	-	RIKEN cDNA 9630013A20 gene	miscRNA	0.01	0.29703
Merged-chr11-67127656-1	chr11	67127606	67127706	+	1.9	cIP1vsInput	Intergenic	Lx7|LINE|L1	-7576	NR_038055	74184	Mm.162554	NR_038055	ENSMUSG00000087410	2310065F04Rik	-	RIKEN cDNA 2310065F04 gene	miscRNA	0	0.50495
Merged-chr10-87999141-1	chr10	87999091	87999191	+	1.9	cIP2vsInput	Intergenic	Intergenic	32470	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	"thymidylate synthase, pseudogene"	pseudo	0.01	0.336634
Merged-chr1-111712083-1	chr1	111712033	111712133	+	1.9	cIP2vsInput	Intergenic	Lx9|LINE|L1	152835	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik	dermatan sulfate epimerase-like	protein-coding	0.01	0.376238
Merged-chr6-75776311-1	chr6	75776261	75776361	+	1.9	cIP2vsInput	Intergenic	Intergenic	-1466406	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding	0	0.336634
Merged-chr9-18171659-1	chr9	18171609	18171709	+	1.9	cIP2vsInput	Intergenic	RMER5|LTR|ERV1	-120608	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	"cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1"	protein-coding	0	0.336634
Merged-chr1-136802174-1	chr1	136802124	136802224	+	1.9	cIP2vsInput	Intergenic	Intergenic	105963	NR_037986	100503474	Mm.428276	NR_037986		Gm16880	-	"predicted gene, 16880"	miscRNA	0.01	0.336634
Merged-chr13-27592252-1	chr13	27592202	27592302	+	1.9	cIP2vsInput	Intergenic	Intergenic	-10081	NM_028477	73244	Mm.215193	NM_028477	ENSMUSG00000019756	Prl8a1	1600017L04Rik|3830403L08Rik|PLP-Cd|Plpcd|Prlpc4	"prolactin family 8, subfamily a, member 1"	protein-coding	0	0.267327
Merged-chr13-113754307-1	chr13	113754257	113754357	+	1.9	cIP2vsInput	Intergenic	Intergenic	-40201	NM_172595	218639	Mm.79837	NM_172595	ENSMUSG00000042348	Arl15	A430036I03|Arfrp2|C230032K13Rik	ADP-ribosylation factor-like 15	protein-coding	0.01	0.277228
Merged-chr4-92339577-1	chr4	92339527	92339627	+	1.9	cIP2vsInput	Intergenic	Intergenic	-192356	NM_027034	69314	Mm.55891	NM_027034	ENSMUSG00000028533	Izumo3	1700011H22Rik	IZUMO family member 3	protein-coding	0	0.306931
Merged-chr2-80375936-1	chr2	80375886	80375986	+	1.9	cIP2vsInput	Intergenic	Lx8|LINE|L1	-15428	NR_040370	100503167	Mm.265892	NR_040370		Gm13752	OTTMUSG00000013925	predicted gene 13752	miscRNA	0	0.366337
Merged-chr15-43981510-1	chr15	43981460	43981560	+	1.9	cIP1vsInput	Intergenic	Intergenic	-111481	NM_175502	239408	Mm.461451	NM_175502	ENSMUSG00000054409	Tmem74	AA549547|B230382K22Rik	transmembrane protein 74	protein-coding	0	0.277228
Merged-chr5-109846032-1	chr5	109845982	109846082	+	1.9	cIP2vsInput	Intergenic	MurSatRep1|Unknown|Unknown	-11890	NR_027964	667213	Mm.454429	NR_027964		Gm10416	EG667213|ENSMUSG00000072761	zinc finger protein pseudogene	pseudo	0	0.306931
Merged-chr3-152685077-1	chr3	152685027	152685127	+	1.9	cIP2vsInput	Intergenic	L1VL2|LINE|L1	-16937	NM_001081277	229949	Mm.207057	NM_001081277	ENSMUSG00000039058	Ak5	-	adenylate kinase 5	protein-coding	0.01	0.346535
Merged-chr13-3960144-1	chr13	3960094	3960194	+	1.9	cIP2vsInput	Intergenic	RLTR14-int|LTR|ERV1	-14795	NM_031250	83428	Mm.313662	NM_031250	ENSMUSG00000044988	Ucn3	-	urocortin 3	protein-coding	0	0.267327
Merged-chr8-30190320-1	chr8	30190270	30190370	+	1.9	cIP2vsInput	Intergenic	Intergenic	-378075	NR_045856	71314	Mm.158666	NR_045856	ENSMUSG00000097044	4933433F19Rik	-	RIKEN cDNA 4933433F19 gene	miscRNA	0	0.316832
Merged-chr3-14204175-1	chr3	14204125	14204225	+	1.9	cIP2vsInput	Intergenic	Intergenic	-158942	NR_033591	622229	Mm.486084	NR_033591		Gm6300	EG622229	"solute carrier family 7 (cationic amino acid transporter, y+ system), member pseudogene"	pseudo	0.01	0.376238
Merged-chr9-12436762-1	chr9	12436712	12436812	+	1.9	cIP2vsInput	Intergenic	Intergenic	669093	NR_040755	78219	Mm.414868	NR_040755		4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	miscRNA	0	0.316832
Merged-chr19-47595723-1	chr19	47595673	47595773	+	1.9	cIP2vsInput	"intron (NM_001164639, intron 1 of 17)"	L1MB3|LINE|L1	15704	NM_001164639	20874	Mm.281011	NM_001164639	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding	0	0.326733
Merged-chr13-85045981-1	chr13	85045931	85046031	+	1.9	cIP2vsInput	Intergenic	Lx3B|LINE|L1	-143496	NM_023243	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding	0	0.346535
Merged-chr12-67983085-1	chr12	67983035	67983135	+	1.9	cIP2vsInput	Intergenic	Intergenic	-313814	NR_033146	100316870	Mm.379794	NR_033146		Gm17821	-	DDB1 and CUL4 associated factor 5 pseudogene	pseudo	0	0.326733
Merged-chr8-98453971-1	chr8	98453921	98454021	+	1.9	cIP2vsInput	Intergenic	MIR|SINE|MIR	962486	NM_007667	12564	Mm.441131	NM_001039154	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding	0	0.326733
Merged-chr7-102783401-1	chr7	102783351	102783451	+	1.9	cIP2vsInput	Intergenic	Intergenic	8875	NM_147092	259096	Mm.377839	NM_147092	ENSMUSG00000073966	Olfr561	MOR14-2	olfactory receptor 561	protein-coding	0	0.316832
Merged-chr15-81848456-1	chr15	81848406	81848506	+	1.9	cIP2vsInput	"3' UTR (NM_020507, exon 2 of 2)"	"3' UTR (NM_020507, exon 2 of 2)"	9870	NM_020507	57259	Mm.323595	NM_020507	ENSMUSG00000048546	Tob2	2900090N22Rik|4930545K18Rik|AV071822|mKIAA1663	"transducer of ERBB2, 2"	protein-coding	0.05	0.524752
Merged-chr6-12919734-1	chr6	12919684	12919784	+	1.9	cIP2vsInput	Intergenic	Intergenic	-150025	NM_027992	71900	Mm.27742	NM_027992	ENSMUSG00000029571	Tmem106b	2310036D22Rik|5830455K21Rik|6430519M21Rik|AI428776|AI661344	transmembrane protein 106B	protein-coding	0.01	0.386139
Merged-chr9-27952794-1	chr9	27952744	27952844	+	1.9	cIP2vsInput	"intron (NM_177906, intron 1 of 7)"	L1M5|LINE|L1	161525	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding	0.02	0.366337
Merged-chr5-101378952-1	chr5	101378902	101379002	+	1.9	cIP2vsInput	Intergenic	Intergenic	285759	NM_144955	18096	Mm.193072	NM_144955		Nkx6-1	NKX6A|Nkx6.1	NK6 homeobox 1	protein-coding	0	0.316832
Merged-chrX-122044465-1	chrX	122044415	122044515	+	1.9	cIP2vsInput	Intergenic	Intergenic	352920	NM_138742	54561	Mm.490573	NM_138742	ENSMUSG00000055733	Nap1l3	MB20	nucleosome assembly protein 1-like 3	protein-coding	0	0.356436
Merged-chr17-43421284-1	chr17	43421234	43421334	+	1.9	cIP2vsInput	"intron (NM_001081178, intron 3 of 20)"	LTR106_Mam|LTR|LTR	31818	NM_001081178	224792	Mm.23478	NM_001081178	ENSMUSG00000056492	Gpr116	8430401C09Rik|9330185D23|AI528491|mKIAA0758	G protein-coupled receptor 116	protein-coding	0.01	0.366337
Merged-chr12-93232212-1	chr12	93232162	93232262	+	1.9	cIP2vsInput	Intergenic	Intergenic	-1383055	NM_011344	20338	Mm.250605	NM_001039089	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding	0	0.356436
Merged-chr2-129513212-1	chr2	129513162	129513262	+	1.9	cIP2vsInput	"intron (NM_177653, intron 1 of 6)"	"intron (NM_177653, intron 1 of 6)"	23390	NM_177653	228592	Mm.452175	NM_177653	ENSMUSG00000043727	F830045P16Rik	Sirpb3	RIKEN cDNA F830045P16 gene	protein-coding	0.02	0.29703
Merged-chr2-105949747-1	chr2	105949697	105949797	+	1.9	cIP2vsInput	"intron (NM_028260, intron 5 of 6)"	"intron (NM_028260, intron 5 of 6)"	45109	NM_028260	66541	Mm.272253	NM_028260	ENSMUSG00000042670	Immp1l	1500034J20Rik|2610528O17Rik|AU042386	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding	0	0.326733
Merged-chr8-9915093-1	chr8	9915043	9915143	+	1.9	cIP2vsInput	Intergenic	Intergenic	61230	NM_176953	319583	Mm.80584	NM_176953	ENSMUSG00000049717	Lig4	5830471N16Rik|tiny	"ligase IV, DNA, ATP-dependent"	protein-coding	0.01	0.326733
Merged-chr12-90071736-1	chr12	90071686	90071786	+	1.9	cIP2vsInput	"intron (NM_001252074, intron 2 of 6)"	"intron (NM_001252074, intron 2 of 6)"	259253	NM_001252074	18191	Mm.487864	NM_001198587	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding	0	0.326733
Merged-chr8-17386450-1	chr8	17386400	17386500	+	1.9	cIP2vsInput	"intron (NM_053171, intron 1 of 69)"	Lx8b|LINE|L1	148935	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding	0	0.366337
Merged-chrX-65871793-1	chrX	65871743	65871843	+	1.9	cIP1vsInput	Intergenic	Lx2|LINE|L1	-777525	NM_001161431	245450	Mm.403134	NM_001161431	ENSMUSG00000036790	Slitrk2	A930040J07	"SLIT and NTRK-like family, member 2"	protein-coding	0	0.336634
Merged-chr1-17531069-1	chr1	17531019	17531119	+	1.9	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-70832	NM_053191	94227	Mm.442452	NM_053191	ENSMUSG00000067780	Pi15	P24TI|P25TI|PI-15|SugarCrisp	peptidase inhibitor 15	protein-coding	0	0.376238
Merged-chr10-97176477-1	chr10	97176427	97176527	+	1.9	cIP2vsInput	Intergenic	Intergenic	140709	NR_045358	75301	Mm.108650	NR_045358		4930556N09Rik	-	RIKEN cDNA 4930556N09 gene	miscRNA	0.01	0.277228
Merged-chrX-127972322-1	chrX	127972272	127972372	+	1.9	cIP2vsInput	Intergenic	Intergenic	578029	NR_003646	245598	Mm.72281	NR_003646	ENSMUSG00000049815	4921511C20Rik	Gm383	high density lipoprotein (HDL) binding protein pseudogene	pseudo	0.01	0.29703
Merged-chr14-60015964-1	chr14	60015914	60016014	+	1.9	cIP2vsInput	"intron (NM_015803, intron 17 of 35)"	"intron (NM_015803, intron 17 of 35)"	70870	NM_015803	50769	Mm.319599	NM_015803	ENSMUSG00000021983	Atp8a2	AI415030|Atpc1b|Ib	"ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"	protein-coding	0.01	0.356436
Merged-chr13-26617216-1	chr13	26617166	26617266	+	1.9	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	152949	NM_008232	15192	Mm.7411	NM_008232	ENSMUSG00000045835	Hdgfl1	4921520N01Rik|HRP-1|Hdgfrp1|Pwwp1	hepatoma derived growth factor-like 1	protein-coding	0	0.316832
Merged-chr16-80273916-1	chr16	80273866	80273966	+	1.9	cIP2vsInput	Intergenic	Intergenic	-926781	NM_001113208	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0.01	0.287129
Merged-chr1-55494560-1	chr1	55494510	55494610	+	1.9	cIP2vsInput	"intron (NM_001114663, intron 1 of 5)"	"intron (NM_001114663, intron 1 of 5)"	88614	NM_001114663	227120	Mm.194183	NM_001114663		Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding	0.01	0.277228
Merged-chr17-81998484-1	chr17	81998434	81998534	+	1.9	cIP2vsInput	Intergenic	Intergenic	-260107	NM_011406	20541	Mm.489060	NM_001112798		Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	"solute carrier family 8 (sodium/calcium exchanger), member 1"	protein-coding	0	0.346535
Merged-chrX-139866554-1	chrX	139866504	139866604	+	1.9	cIP2vsInput	"intron (NM_001193309, intron 2 of 16)"	"intron (NM_001193309, intron 2 of 16)"	5100	NM_029413	75746		NM_001193309	ENSMUSG00000031434	Morc4	1600017G11Rik|5630401M14Rik|AA117449|Zcwcc2	microrchidia 4	protein-coding	0	0.356436
Merged-chr4-96661104-1	chr4	96661054	96661154	+	1.9	cIP2vsInput	"intron (NM_010007, intron 2 of 8)"	"intron (NM_010007, intron 2 of 8)"	3015	NM_010007	13109	Mm.12838	NM_010007		Cyp2j5	-	"cytochrome P450, family 2, subfamily j, polypeptide 5"	protein-coding	0.02	0.386139
Merged-chr11-13871487-1	chr11	13871437	13871537	+	1.9	cIP2vsInput	Intergenic	Intergenic	727738	NR_045918	73307	Mm.399291	NR_045918	ENSMUSG00000085561	1700046C09Rik	-	RIKEN cDNA 1700046C09 gene	miscRNA	0	0.346535
Merged-chr11-113423162-1	chr11	113423112	113423212	+	1.9	cIP2vsInput	"intron (NM_027216, intron 5 of 9)"	"intron (NM_027216, intron 5 of 9)"	142653	NM_001166503	69806	Mm.341021	NM_001166503	ENSMUSG00000041654	Slc39a11	1810074D23Rik	"solute carrier family 39 (metal ion transporter), member 11"	protein-coding	0.02	0.39604
Merged-chr18-20301206-1	chr18	20301156	20301256	+	1.9	cIP2vsInput	Intergenic	Intergenic	-9667	NM_010079	13510	Mm.37953	NM_010079	ENSMUSG00000069441	Dsg1a	BB010119|Dsg1	desmoglein 1 alpha	protein-coding	0	0.277228
Merged-chr8-4566448-1	chr8	4566398	4566498	+	1.9	cIP2vsInput	Intergenic	ID_B1|SINE|B4	-46722	NM_145591	233987	Mm.102799	NM_145591		Zfp958	-	zinc finger protein 958	protein-coding	0	0.405941
Merged-chr13-17970329-1	chr13	17970279	17970379	+	1.9	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	23022	NM_025904	67008	Mm.252918	NM_025904	ENSMUSG00000075054	Yae1d1	1600012F09Rik	Yae1 domain containing 1	protein-coding	0	0.366337
Merged-chr5-62333233-1	chr5	62333183	62333283	+	1.9	cIP2vsInput	Intergenic	Intergenic	432944	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	"ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2"	protein-coding	0	0.346535
Merged-chr14-90217591-1	chr14	90217541	90217641	+	1.9	cIP2vsInput	"intron (NR_045712, intron 5 of 8)"	Charlie6|DNA|hAT-Charlie	90700	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0	0.316832
Merged-chr12-39959880-1	chr12	39959830	39959930	+	1.9	cIP2vsInput	Intergenic	Intergenic	77496	NM_007487	11861	Mm.12723	NM_001039515	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding	0.01	0.306931
Merged-chr18-21612296-1	chr18	21612246	21612346	+	1.9	cIP2vsInput	"intron (NM_001081403, intron 2 of 7)"	"intron (NM_001081403, intron 2 of 7)"	-39269	NM_001271580	74644	Mm.329311	XR_168573		4930426D05Rik	-	RIKEN cDNA 4930426D05 gene	protein-coding	0.01	0.306931
Merged-chr5-139630817-1	chr5	139630767	139630867	+	1.9	cIP1vsInput	Intergenic	Intergenic	86919	NM_013702	22255	Mm.42190	NM_013702	ENSMUSG00000029546	Uncx	Chx4|Uncx4.1	UNC homeobox	protein-coding	0	0.257426
Merged-chr17-82463114-1	chr17	82463064	82463164	+	1.9	cIP1vsInput	Intergenic	Intergenic	615111	NR_045094	100503434	Mm.187281	NR_045094		Gm19689	-	"predicted gene, 19689"	miscRNA	0	0.336634
Merged-chr3-120103867-1	chr3	120103817	120103917	+	1.9	cIP2vsInput	Intergenic	L1M5|LINE|L1	-320479	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0	0.257426
Merged-chr19-39254214-1	chr19	39254164	39254264	+	1.9	cIP1vsInput	"intron (NR_033614, intron 6 of 8)"	"intron (NR_033614, intron 6 of 8)"	24960	NR_033614	638988	Mm.483843	NR_033614	ENSMUSG00000093610	Cyp2c53-ps	Cyp2c53|EG638988	"cytochrome P450, family 2, subfamily c, polypeptide 53-ps"	pseudo	0.01	0.306931
Merged-chr5-7951347-1	chr5	7951297	7951397	+	1.9	cIP2vsInput	Intergenic	Intergenic	-9125	NM_054098	117167	Mm.31403	NM_054098	ENSMUSG00000012428	Steap4	1110021O17Rik|AI481214|Tiarp|Tnfaip9	STEAP family member 4	protein-coding	0	0.405941
Merged-chrX-160520600-1	chrX	160520550	160520650	+	1.9	cIP1vsInput	"intron (NM_001177879, intron 2 of 33)"	"intron (NM_001177879, intron 2 of 33)"	18166	NM_001177878	110094	Mm.350712	NM_001177878	ENSMUSG00000031295	Phka2	6330505C01Rik|D330034O08|Phk	phosphorylase kinase alpha 2	protein-coding	0.01	0.445545
Merged-chr15-6190699-1	chr15	6190649	6190749	+	1.9	cIP2vsInput	Intergenic	MTD|LTR|ERVL-MaLR	-109090	NM_001008702	13132	Mm.240830	NM_001008702	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	"disabled 2, mitogen-responsive phosphoprotein"	protein-coding	0	0.386139
Merged-chr14-51495684-1	chr14	51495634	51495734	+	1.9	cIP2vsInput	Intergenic	(TTTG)n|Simple_repeat|Simple_repeat	43721	NM_009486	22301	Mm.482572	NM_009486	ENSMUSG00000070448	Vmn2r89	V2r10|V2r11	"vomeronasal 2, receptor 89"	protein-coding	0	0.237624
Merged-chr14-123710121-1	chr14	123710071	123710171	+	1.9	cIP2vsInput	"intron (NM_145467, intron 2 of 10)"	"intron (NM_145467, intron 2 of 10)"	49981	NM_145467	223272	Mm.383176	NM_145467		Itgbl1	B930011D01Rik	"integrin, beta-like 1"	protein-coding	0.04	0.316832
Merged-chr3-48350221-1	chr3	48350171	48350271	+	1.9	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	258879	NR_003617	66332	Mm.46124	NR_003617		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo	0	0.306931
Merged-chr2-86266825-1	chr2	86266775	86266875	+	1.9	cIP1vsInput	Intergenic	Intergenic	9660	NM_207562	404324	Mm.377277	NM_207562	ENSMUSG00000075193	Olfr1051	GA_x5J8B7W3KVV-25848-25992|MOR187-5	olfactory receptor 1051	protein-coding	0	0.267327
Merged-chr13-108789088-1	chr13	108789038	108789138	+	1.9	cIP2vsInput	"intron (NM_011056, intron 1 of 16)"	L1M4b|LINE|L1	134911	NM_011056	238871	Mm.434429	NM_011056		Pde4d	9630011N22Rik|Dpde3	"phosphodiesterase 4D, cAMP specific"	protein-coding	0	0.336634
Merged-chr10-114678766-1	chr10	114678716	114678816	+	1.9	cIP2vsInput	"intron (NM_146241, intron 3 of 18)"	"intron (NM_146241, intron 3 of 18)"	122604	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding	0	0.336634
Merged-chr1-49403626-1	chr1	49403576	49403676	+	1.9	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-1523897	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.326733
Merged-chr13-95120819-1	chr13	95120769	95120869	+	1.9	cIP2vsInput	"intron (NM_001170669, intron 2 of 18)"	"intron (NM_001170669, intron 2 of 18)"	102231	NM_001170669	218461	Mm.100167	NM_001170669	ENSMUSG00000021684	Pde8b	B230331L10Rik|C030047E14Rik	phosphodiesterase 8B	protein-coding	0	0.366337
Merged-chr10-90455613-1	chr10	90455563	90455663	+	1.9	cIP2vsInput	"intron (NM_001128086, intron 12 of 24)"	"intron (NM_001128086, intron 12 of 24)"	-120114	NM_001177397	77531	Mm.440605	NM_001128086		Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding	0	0.316832
Merged-chr6-105311246-1	chr6	105311196	105311296	+	1.9	cIP2vsInput	Intergenic	Lx2|LINE|L1	181422	NR_040297	100503536	Mm.366960	NR_040297		Gm19757	-	"predicted gene, 19757"	miscRNA	0	0.306931
Merged-chr12-99975533-1	chr12	99975483	99975583	+	1.9	cIP2vsInput	"intron (NM_001164426, intron 2 of 2)"	L1M4|LINE|L1	11034	NM_001164427	217826	Mm.312335	NM_001164426	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	"potassium channel, subfamily K, member 13"	protein-coding	0	0.376238
Merged-chr4-26240295-1	chr4	26240245	26240345	+	1.9	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	106357	NM_172865	242362	Mm.245602	NM_172865	ENSMUSG00000040520	Manea	4932703L02Rik	"mannosidase, endo-alpha"	protein-coding	0	0.346535
Merged-chr1-97004467-1	chr1	97004417	97004517	+	1.9	cIP2vsInput	Intergenic	B4A|SINE|B4	-6907	NM_001039475	67854	Mm.263706	NM_026413	ENSMUSG00000045463	Slco6b1	1700022M03Rik	"solute carrier organic anion transporter family, member 6b1"	protein-coding	0.01	0.415842
Merged-chr11-62887340-1	chr11	62887290	62887390	+	1.9	cIP2vsInput	"intron (NM_026210, intron 5 of 6)"	"intron (NM_026210, intron 5 of 6)"	7850	NM_026210	67510	Mm.9806	NM_026210	ENSMUSG00000014177	Tvp23b	1810036I24Rik|Fam18b|Fam18b1	trans-golgi network vesicle protein 23B	protein-coding	0	0.435644
Merged-chr8-32696528-1	chr8	32696478	32696578	+	1.9	cIP2vsInput	Intergenic	Intergenic	253498	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding	0.01	0.29703
Merged-chr8-65249827-1	chr8	65249777	65249877	+	1.9	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-120290	NR_033217	407795	Mm.387876	NR_033217		BC030870	-	cDNA sequence BC030870	miscRNA	0.01	0.306931
Merged-chr10-42399523-1	chr10	42399473	42399573	+	1.9	cIP2vsInput	"intron (NM_145743, intron 7 of 12)"	"intron (NM_145743, intron 7 of 12)"	79042	NM_145743	215951	Mm.89646	NM_145743	ENSMUSG00000038302	Lace1	CG8520	lactation elevated 1	protein-coding	0	0.237624
Merged-chr5-24652204-1	chr5	24652154	24652254	+	1.9	cIP2vsInput	Intergenic	Intergenic	6751	NR_003953	72252	Mm.87446	NR_003953		1700022A21Rik	-	glycerol-3-phosphate dehydrogenase 1-like pseudogene	pseudo	0.08	0.574257
Merged-chr3-138265356-1	chr3	138265306	138265406	+	1.9	cIP2vsInput	Intergenic	L1MCc|LINE|L1	-12289	NM_007409	11522	Mm.412004	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding	0.01	0.336634
Merged-chr5-7664096-1	chr5	7664046	7664146	+	1.9	cIP2vsInput	Intergenic	Intergenic	-296376	NM_054098	117167	Mm.31403	NM_054098	ENSMUSG00000012428	Steap4	1110021O17Rik|AI481214|Tiarp|Tnfaip9	STEAP family member 4	protein-coding	0.01	0.346535
Merged-chr3-47368498-1	chr3	47368448	47368548	+	1.9	cIP2vsInput	Intergenic	Intergenic	658261	NR_040408	666202	Mm.465057	NR_040408		Gm7977	EG666202	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide pseudogene"	pseudo	0	0.326733
Merged-chr12-47298660-1	chr12	47298610	47298710	+	1.9	cIP2vsInput	Intergenic	Lx6|LINE|L1	-479885	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding	0.01	0.326733
Merged-chr2-140233652-1	chr2	140233602	140233702	+	1.9	cIP2vsInput	"intron (NM_001033296, intron 18 of 19)"	L1VL2|LINE|L1	63006	NM_027093	69487	Mm.287921	NM_027093		Ndufaf5	2310003L22Rik	"NADH dehydrogenase (ubiquinone) complex I, assembly factor 5"	protein-coding	0	0.376238
Merged-chr8-84937365-1	chr8	84937315	84937415	+	1.9	cIP2vsInput	promoter-TSS (NM_019945)	promoter-TSS (NM_019945)	-12	NM_019945	56527	Mm.154614	NM_019945	ENSMUSG00000053693	Mast1	9430008B02Rik|SAST|SAST170	microtubule associated serine/threonine kinase 1	protein-coding	0.09	0.772277
Merged-chr17-53240697-1	chr17	53240647	53240747	+	1.9	cIP2vsInput	Intergenic	Intergenic	222624	NM_172497	211482	Mm.60887	NM_172497	ENSMUSG00000023931	Efhb	4921525D22Rik	"EF hand domain family, member B"	protein-coding	0	0.247525
Merged-chr14-80743557-1	chr14	80743507	80743607	+	1.9	cIP2vsInput	Intergenic	Intergenic	743255	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0	0.29703
Merged-chr10-66777645-1	chr10	66777595	66777695	+	1.9	cIP2vsInput	Intergenic	Intergenic	319343	NM_001204915	28193	Mm.41272	NM_001204915	ENSMUSG00000019873	Reep3	D10Ucla1	receptor accessory protein 3	protein-coding	0.02	0.326733
Merged-chr6-124095308-1	chr6	124095258	124095358	+	1.9	cIP2vsInput	Intergenic	Intergenic	70550	NM_019917	56552	Mm.23795	NM_019917	ENSMUSG00000096630	Vmn2r26	V2R1|V2r1b	"vomeronasal 2, receptor 26"	protein-coding	0	0.376238
Merged-chr6-44721950-1	chr6	44721900	44722000	+	1.9	cIP1vsInput	Intergenic	Intergenic	-338111	NM_001004357	66797	Mm.440084	NM_001004357	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding	0	0.336634
Merged-chr10-103565737-1	chr10	103565687	103565787	+	1.9	cIP2vsInput	Intergenic	Intergenic	197929	NM_175328	103098	Mm.458408	NM_001252330	ENSMUSG00000019894	Slc6a15	AA536730|AI326450|AI326451|v7-3	"solute carrier family 6 (neurotransmitter transporter), member 15"	protein-coding	0	0.287129
Merged-chr6-110340804-1	chr6	110340754	110340854	+	1.9	cIP1vsInput	Intergenic	Intergenic	-304794	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0	0.346535
Merged-chr5-86316312-1	chr5	86316262	86316362	+	1.9	cIP2vsInput	"intron (NM_145561, intron 7 of 9)"	L1_Mus1|LINE|L1	-27004	NM_001030297	435845	Mm.359654	NM_001030297	ENSMUSG00000061184	Tmprss11c	Tmprss13	"transmembrane protease, serine 11c"	protein-coding	0.01	0.336634
Merged-chr9-83515551-1	chr9	83515501	83515601	+	1.9	cIP2vsInput	Intergenic	Intergenic	-32787	NM_172507	212531	Mm.100125	NM_172507	ENSMUSG00000032261	Sh3bgrl2	A930014C21Rik|AA408038|B930089I21	SH3 domain binding glutamic acid-rich protein like 2	protein-coding	0	0.356436
Merged-chr4-88259167-1	chr4	88259117	88259217	+	1.9	cIP2vsInput	"intron (NM_001081184, intron 15 of 43)"	"intron (NM_001081184, intron 15 of 43)"	137127	NR_030478	735282		NR_030478		Mir491	Mirn491|mmu-mir-491	microRNA 491	miscRNA	0	0.287129
Merged-chr17-21225999-1	chr17	21225949	21226049	+	1.9	cIP2vsInput	Intergenic	Intergenic	-2827	NM_134198	171232	Mm.377189	NM_134198	ENSMUSG00000057203	Vmn1r234	V1rf1	vomeronasal 1 receptor 234	protein-coding	0	0.316832
Merged-chr12-84134264-1	chr12	84134214	84134314	+	1.9	cIP2vsInput	"intron (NM_028821, intron 5 of 7)"	"intron (NM_028821, intron 5 of 7)"	14225	NM_027438	70481	Mm.444348	NM_027438	ENSMUSG00000054383	Pnma1	5730402C15Rik	paraneoplastic antigen MA1	protein-coding	0.01	0.475248
Merged-chr9-81056704-1	chr9	81056654	81056754	+	1.9	cIP2vsInput	Intergenic	Intergenic	-575226	NR_040394	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	miscRNA	0	0.306931
Merged-chr1-54032567-1	chr1	54032517	54032617	+	1.9	cIP2vsInput	"intron (NM_001001883, intron 2 of 28)"	Lx9|LINE|L1	162467	NM_001001883	329152	Mm.447527	NM_001001883	ENSMUSG00000042807	Hecw2	A730039N16Rik|D030049F17Rik|Gm971|Nedl2|mKIAA1301	"HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2"	protein-coding	0	0.29703
Merged-chr3-47662324-1	chr3	47662274	47662374	+	1.9	cIP2vsInput	Intergenic	Intergenic	364435	NR_040408	666202	Mm.465057	NR_040408		Gm7977	EG666202	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide pseudogene"	pseudo	0	0.39604
Merged-chr1-103245932-1	chr1	103245882	103245982	+	1.9	cIP2vsInput	Intergenic	Intergenic	-1522887	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0	0.287129
Merged-chr4-156103541-1	chr4	156103491	156103591	+	1.9	cIP2vsInput	Intergenic	MLTR11B|LTR|ERVK	-6457	NM_177205	230996	Mm.318925	NM_145557	ENSMUSG00000059939	9430015G10Rik	-	RIKEN cDNA 9430015G10 gene	protein-coding	0.01	0.435644
Merged-chr11-32578153-1	chr11	32578103	32578203	+	1.9	cIP2vsInput	"intron (NM_009288, intron 4 of 18)"	"intron (NM_009288, intron 4 of 18)"	44887	NM_009288	20868	Mm.8235	NM_009288	ENSMUSG00000020272	Stk10	Gek1|Lok|mKIAA4026	serine/threonine kinase 10	protein-coding	0	0.405941
Merged-chr2-146691006-1	chr2	146690956	146691056	+	1.9	cIP2vsInput	Intergenic	Intergenic	148075	NR_040502	74065	Mm.399508	NR_040502	ENSMUSG00000085796	4933406D12Rik	-	RIKEN cDNA 4933406D12 gene	miscRNA	0	0.376238
Merged-chr7-55313351-1	chr7	55313301	55313401	+	1.9	cIP1vsInput	Intergenic	Intergenic	-454827	NM_178706	233274	Mm.44425	NM_178706	ENSMUSG00000051504	Siglech	6430529G09Rik|Siglec-H	sialic acid binding Ig-like lectin H	protein-coding	0	0.316832
Merged-chr14-41424201-1	chr14	41424151	41424251	+	1.9	cIP2vsInput	Intergenic	Intergenic	-239003	NM_009160	20390	Mm.1321	NM_009160	ENSMUSG00000021795	Sftpd	AI573415|SP-D|Sftp4	surfactant associated protein D	protein-coding	0.02	0.465347
Merged-chr13-25409583-1	chr13	25409533	25409633	+	1.9	cIP2vsInput	Intergenic	Intergenic	-139587	NM_009513	22360	Mm.4766	NM_009513	ENSMUSG00000048978	Nrsn1	Neurensin-1|Neuro-p24|Vmp	neurensin 1	protein-coding	0	0.306931
Merged-chrX-83012198-1	chrX	83012148	83012248	+	1.9	cIP2vsInput	"intron (NM_007868, intron 1 of 78)"	"intron (NM_007868, intron 1 of 78)"	63328	NM_007868	13405	Mm.416750	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|mdx|pke	"dystrophin, muscular dystrophy"	protein-coding	0.02	0.346535
Merged-chr14-88672130-1	chr14	88672080	88672180	+	1.9	cIP2vsInput	Intergenic	Intergenic	-200734	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0	0.316832
Merged-chr2-57767609-1	chr2	57767559	57767659	+	1.9	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-230546	NM_172855	241391	Mm.484118	NM_172855	ENSMUSG00000026828	Galnt5	4832424J23	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5	protein-coding	0	0.306931
Merged-chr18-90093899-1	chr18	90093849	90093949	+	1.9	cIP2vsInput	Intergenic	Intergenic	-324763	NM_001039173	623279	Mm.447164	NM_001039173		Dok6	Dok-6	docking protein 6	protein-coding	0	0.267327
Merged-chr6-102379438-1	chr6	102379388	102379488	+	1.9	cIP1vsInput	"intron (NM_008779, intron 3 of 21)"	L1MD|LINE|L1	85229	NM_008779	18488	Mm.435479	NM_008779	ENSMUSG00000030075	Cntn3	Pang	contactin 3	protein-coding	0	0.336634
Merged-chr3-115432588-1	chr3	115432538	115432638	+	1.9	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	282467	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding	0	0.326733
Merged-chr17-77248314-1	chr17	77248264	77248364	+	1.9	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-951934	NM_015800	50766	Mm.311912	NM_015800	ENSMUSG00000024074	Crim1	AU015004	cysteine rich transmembrane BMP regulator 1 (chordin like)	protein-coding	0	0.346535
Merged-chr5-149772514-1	chr5	149772464	149772564	+	1.9	cIP2vsInput	Intergenic	Intergenic	39237	NR_077242	100861794	Mm.402054	XR_141480		Gm21221	-	"predicted gene, 21221"	miscRNA	0	0.455446
Merged-chr14-113078868-1	chr14	113078818	113078918	+	1.9	cIP2vsInput	Intergenic	Intergenic	1057438	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0.01	0.336634
Merged-chr6-35806365-1	chr6	35806315	35806415	+	1.9	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-266477	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding	0	0.346535
Merged-chr9-121985294-1	chr9	121985244	121985344	+	1.9	cIP1vsInput	"intron (NM_153540, intron 1 of 1)"	"intron (NM_153540, intron 1 of 1)"	10732	NM_153540	215494	Mm.402151	NM_153540	ENSMUSG00000066235	Gtdc2	Ago61|C85492	glycosyltransferase-like domain containing 2	protein-coding	0.01	0.534653
Merged-chr2-3904440-1	chr2	3904390	3904490	+	1.9	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	190982	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	"family with sequence similarity 107, member B"	protein-coding	0.01	0.306931
Merged-chr4-38060385-1	chr4	38060335	38060435	+	1.9	cIP2vsInput	Intergenic	B1_Mur4|SINE|Alu	-1108641	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0.01	0.415842
Merged-chr1-127897791-1	chr1	127897741	127897841	+	1.9	cIP2vsInput	"intron (NM_178690, intron 5 of 23)"	"intron (NM_178690, intron 5 of 23)"	29018	NM_178690	226407	Mm.489713	NM_178690	ENSMUSG00000036104	Rab3gap1	1700003B17Rik|4732493F09Rik|AL117896|Rab3gap|p130	RAB3 GTPase activating protein subunit 1	protein-coding	0	0.39604
Merged-chr4-110621696-1	chr4	110621646	110621746	+	1.9	cIP2vsInput	"intron (NM_001048189, intron 3 of 12)"	L1MEc|LINE|L1	223905	NM_030231	78933	Mm.435620	NM_001048189	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding	0	0.306931
Merged-chr3-111475847-1	chr3	111475797	111475897	+	1.9	cIP2vsInput	Intergenic	Intergenic	-406056	NR_045362	625585	Mm.389497	NR_045362		Gm6602	-	predicted gene 6602	miscRNA	0	0.316832
Merged-chrX-150967334-1	chrX	150967284	150967384	+	1.9	cIP2vsInput	Intergenic	Intergenic	49959	NM_001168600	237107	Mm.45987	NM_001168600	ENSMUSG00000025266	Gnl3l	BC020354	guanine nucleotide binding protein-like 3 (nucleolar)-like	protein-coding	0	0.346535
Merged-chr3-103217193-1	chr3	103217143	103217243	+	1.9	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	45482	NM_026602	68183	Mm.104919	NM_026602	ENSMUSG00000005687	Bcas2	6430539P16Rik|AI132645|C76366|C80030	breast carcinoma amplified sequence 2	protein-coding	0.01	0.326733
Merged-chr6-133755303-1	chr6	133755253	133755353	+	1.9	cIP2vsInput	Intergenic	RSINE1|SINE|B4	12100	NM_001177652	545886	Mm.449716	NM_001177652		Gm5886	EG545886|smarp	predicted gene 5886	protein-coding	0	0.435644
Merged-chr3-76956052-1	chr3	76956002	76956102	+	1.9	cIP2vsInput	Intergenic	Intergenic	880469	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0	0.316832
Merged-chr3-82290471-1	chr3	82290421	82290521	+	1.9	cIP2vsInput	Intergenic	Intergenic	-67601	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding	0.01	0.326733
Merged-chr19-60828411-1	chr19	60828361	60828461	+	1.9	cIP1vsInput	"intron (NM_001167829, intron 6 of 8)"	"intron (NM_001167829, intron 6 of 8)"	16841	NM_001167829	67894		NM_001167829	ENSMUSG00000024993	Fam45a	1810055E12Rik	"family with sequence similarity 45, member A"	protein-coding	0	0.356436
Merged-chr6-70812108-1	chr6	70812058	70812158	+	1.9	cIP2vsInput	Intergenic	Intergenic	-19933	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding	0.01	0.445545
Merged-chr6-3786380-1	chr6	3786330	3786430	+	1.9	cIP2vsInput	Intergenic	Intergenic	-21667	NM_007588	12311	Mm.4642	NM_001042725	ENSMUSG00000023964	Calcr	Clr	calcitonin receptor	protein-coding	0	0.356436
Merged-chr6-20123965-1	chr6	20123915	20124015	+	1.9	cIP2vsInput	Intergenic	Intergenic	-1092144	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	"potassium voltage-gated channel, Shal-related family, member 2"	protein-coding	0	0.356436
Merged-chr18-52402758-1	chr18	52402708	52402808	+	1.9	cIP2vsInput	Intergenic	Intergenic	-62935	NM_026040	67222	Mm.100617	XM_003946020	ENSMUSG00000024528	Srfbp1	2810036K01Rik|p49/STRAP	serum response factor binding protein 1	protein-coding	0.04	0.415842
Merged-chr13-33714065-1	chr13	33714015	33714115	+	1.9	cIP2vsInput	Intergenic	Intergenic	52660	NM_001076790	238568	Mm.249698	NM_001076790	ENSMUSG00000047889	Serpinb6d	Gm11390|OTTMUSG00000000712|SPI3D	"serine (or cysteine) peptidase inhibitor, clade B, member 6d"	protein-coding	0	0.386139
Merged-chr16-80795118-1	chr16	80795068	80795168	+	1.9	cIP2vsInput	Intergenic	Intergenic	-405579	NM_001113208	17968	Mm.433941	NM_001113208	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding	0	0.29703
Merged-chr7-41488374-1	chr7	41488324	41488424	+	1.9	cIP2vsInput	"intron (NM_001033530, intron 1 of 3)"	L1_Mur2|LINE|L1	11516	NM_001033530	101835	Mm.370336	NM_001033530	ENSMUSG00000074166	AW146154	AI451288	expressed sequence AW146154	protein-coding	0.01	0.316832
Merged-chr11-63005305-1	chr11	63005255	63005355	+	1.9	cIP2vsInput	Intergenic	Intergenic	54112	NM_025496	66338	Mm.46166	NM_025496	ENSMUSG00000042200	Cdrt4	1700019I23Rik	CMT1A duplicated region transcript 4	protein-coding	0	0.514851
Merged-chr14-117369237-1	chr14	117369187	117369287	+	1.9	cIP2vsInput	"intron (NM_001079844, intron 2 of 9)"	"intron (NM_001079844, intron 2 of 9)"	443922	NM_011821	23888	Mm.440025	NM_001079844	ENSMUSG00000058571	Gpc6	6720429C22Rik|AI480529	glypican 6	protein-coding	0	0.465347
Merged-chr9-9611604-1	chr9	9611554	9611654	+	1.9	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-372591	NM_027823	71544	Mm.334955	NM_027823	ENSMUSG00000050730	Arhgap42	9030420J04Rik|BE136619	Rho GTPase activating protein 42	protein-coding	0	0.336634
Merged-chr2-143717519-1	chr2	143717469	143717569	+	1.9	cIP2vsInput	"intron (NM_008792, intron 5 of 11)"	L1M5|LINE|L1	71667	NR_040625	378775	Mm.441313	NR_040625	ENSMUSG00000087115	Gm12360	9430032N09Rik|OTTMUSG00000006467	predicted gene 12360	miscRNA	0	0.306931
Merged-chr1-4936238-1	chr1	4936188	4936288	+	1.9	cIP2vsInput	"intron (NM_001177795, intron 2 of 5)"	"intron (NM_001177795, intron 2 of 5)"	77910	NM_001159751	21399	Mm.207263	NM_001159750	ENSMUSG00000033813	Tcea1	S-II	transcription elongation factor A (SII) 1	protein-coding	0.01	0.435644
Merged-chr7-35441255-1	chr7	35441205	35441305	+	1.9	cIP2vsInput	Intergenic	RLTR17D_Mm|LTR|ERVK	-7837	NM_001199015	30962	Mm.45874	NM_001199015	ENSMUSG00000030492	Slc7a9	CSNU3	"solute carrier family 7 (cationic amino acid transporter, y+ system), member 9"	protein-coding	0	0.326733
Merged-chr5-71046375-1	chr5	71046325	71046425	+	1.9	cIP2vsInput	"intron (NM_008066, intron 3 of 9)"	L1M2|LINE|L1	49474	NM_008066	14395	Mm.5304	NM_008066	ENSMUSG00000000560	Gabra2	C630048P16Rik|Gabra-2	"gamma-aminobutyric acid (GABA) A receptor, subunit alpha 2"	protein-coding	0	0.346535
Merged-chr8-119604786-1	chr8	119604736	119604836	+	1.9	cIP2vsInput	"intron (NM_021441, intron 1 of 14)"	"intron (NM_021441, intron 1 of 14)"	454	NM_021441	21341	Mm.475128	NM_021441	ENSMUSG00000031832	Taf1c	Tafi95|mTAFI95	"TATA box binding protein (Tbp)-associated factor, RNA polymerase I, C"	protein-coding	0.03	0.574257
Merged-chr6-132130103-1	chr6	132130053	132130153	+	1.9	cIP2vsInput	"intron (NM_053251, intron 5 of 6)"	(TTTTG)n|Simple_repeat|Simple_repeat	80418	NM_198669	381833	Mm.7982	NM_198669	ENSMUSG00000067543	Prb1	BC011176|Prpg2	proline-rich protein BstNI subfamily 1	protein-coding	0	0.29703
Merged-chr2-154308739-1	chr2	154308689	154308789	+	1.9	cIP1vsInput	"intron (NM_001025574, intron 1 of 14)"	"intron (NM_001025574, intron 1 of 14)"	1495	NM_001025574	433492	Mm.330682	NM_001025574	ENSMUSG00000067996	Bpifb9b	5430413K10Rik|AI413838|OTTMUSG00000015915|Rp23-154j12.5	"BPI fold containing family B, member 9B"	protein-coding	0.01	0.445545
Merged-chrX-104224199-1	chrX	104224149	104224249	+	1.9	cIP2vsInput	Intergenic	Lx7|LINE|L1	-23082	NM_001077354	245555	Mm.381907	NM_001077354	ENSMUSG00000046449	C77370	A230051P11|C77386|Kiaa2022|Xpn|mKIAA2022	expressed sequence C77370	protein-coding	0	0.376238
Merged-chr8-6794086-1	chr8	6794036	6794136	+	1.9	cIP2vsInput	Intergenic	Intergenic	-1688854	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	ASBT|ISBT	"solute carrier family 10, member 2"	protein-coding	0	0.346535
Merged-chr19-11842907-1	chr19	11842857	11842957	+	1.9	cIP2vsInput	Intergenic	RLTR40|LTR|ERVK	13044	NM_001011524	258227	Mm.377385	NM_001011524	ENSMUSG00000060556	Olfr1418	MOR266-5	olfactory receptor 1418	protein-coding	0	0.405941
Merged-chr11-14924773-1	chr11	14924723	14924823	+	1.9	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	325533	NM_001164166	432536	Mm.33646	NR_002893		Pom121l12	1700054H16Rik	POM121 membrane glycoprotein-like 12	protein-coding	0	0.336634
Merged-chr5-70960118-1	chr5	70960068	70960168	+	1.9	cIP2vsInput	TTS (NM_008066)	TTS (NM_008066)	-117501	NM_010252	14405	Mm.255292	NM_010252	ENSMUSG00000001260	Gabrg1	GabaA|GabaA/BZ	"gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1"	protein-coding	0.01	0.287129
Merged-chr3-104979569-1	chr3	104979519	104979619	+	1.9	cIP1vsInput	Intergenic	MYSERV6-int|LTR|ERVK	-17860	NM_009520	22414	Mm.10740	NM_009520	ENSMUSG00000027840	Wnt2b	Wnt13	wingless related MMTV integration site 2b	protein-coding	0	0.336634
Merged-chr14-80053154-1	chr14	80053104	80053204	+	1.9	cIP2vsInput	Intergenic	Intergenic	52852	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding	0.01	0.39604
Merged-chr5-36989419-1	chr5	36989369	36989469	+	1.9	cIP2vsInput	promoter-TSS (NM_011716)	promoter-TSS (NM_011716)	-437	NM_011716	22393	Mm.20916	NM_011716	ENSMUSG00000039474	Wfs1	AI481085|wolframin	Wolfram syndrome 1 homolog (human)	protein-coding	0.07	0.514851
Merged-chr16-46751951-1	chr16	46751901	46752001	+	1.9	cIP2vsInput	Intergenic	Intergenic	-254984	NM_021497	58998	Mm.328072	NM_021495	ENSMUSG00000022656	Pvrl3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113	poliovirus receptor-related 3	protein-coding	0.01	0.306931
Merged-chr4-74840226-1	chr4	74840176	74840276	+	1.9	cIP2vsInput	Intergenic	Intergenic	438060	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	3110001D03Rik	1700027K24Rik	RIKEN cDNA 3110001D03 gene	protein-coding	0	0.326733
Merged-chrX-166518335-1	chrX	166518285	166518385	+	1.9	cIP2vsInput	Intergenic	Intergenic	-7857	NM_001007577	245695	Mm.336318	NM_001007577	ENSMUSG00000051224	Tceanc	A630018P17Rik|Gm390	transcription elongation factor A (SII) N-terminal and central domain containing	protein-coding	0.03	0.287129
Merged-chr6-120978503-1	chr6	120978453	120978553	+	1.9	cIP2vsInput	"intron (NM_001270475, intron 20 of 31)"	ID_B1|SINE|B4	-61683	NM_007544	12122	Mm.235081	NM_007544	ENSMUSG00000004446	Bid	2700049M22Rik|AI875481|AU022477	BH3 interacting domain death agonist	protein-coding	0.04	0.534653
Merged-chr17-87376335-1	chr17	87376285	87376385	+	1.9	cIP2vsInput	"intron (NM_028639, intron 19 of 19)"	"intron (NM_028639, intron 19 of 19)"	51406	NM_029298	75467	Mm.50108	NM_029298	ENSMUSG00000036557	1700011E24Rik	-	RIKEN cDNA 1700011E24 gene	protein-coding	0.03	0.574257
Merged-chr1-120340588-1	chr1	120340538	120340638	+	1.9	cIP2vsInput	promoter-TSS (NM_207233)	promoter-TSS (NM_207233)	6	NM_207233	226359	Mm.337409	NM_207233	ENSMUSG00000036907	C1ql2	BC040774|CTRP10	"complement component 1, q subcomponent-like 2"	protein-coding	0.09	0.673267
Merged-chr10-4925319-1	chr10	4925269	4925369	+	1.9	cIP2vsInput	"intron (NM_007956, intron 5 of 8)"	"intron (NM_007956, intron 5 of 8)"	143744	NM_022027	64009	Mm.331626	NM_001079686	ENSMUSG00000019769	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756	"spectrin repeat containing, nuclear envelope 1"	protein-coding	0	0.336634
Merged-chr14-15682436-1	chr14	15682386	15682486	+	1.9	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-243449	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding	0	0.277228
Merged-chr3-117594108-1	chr3	117594058	117594158	+	1.9	cIP2vsInput	"intron (NM_029425, intron 1 of 5)"	"intron (NM_029425, intron 1 of 5)"	18647	NM_029425	75769	Mm.72187	NM_029425	ENSMUSG00000033342	4833424O15Rik	Lppr5|PRG-5|Pap2d	RIKEN cDNA 4833424O15 gene	protein-coding	0	0.366337
Merged-chr9-108478832-1	chr9	108478782	108478882	+	1.9	cIP2vsInput	Intergenic	Intergenic	-1030	NM_008483	16779	Mm.425599	NM_008483	ENSMUSG00000052911	Lamb2	AW211941|Lamb-2|Lams	"laminin, beta 2"	protein-coding	0.03	0.544554
Merged-chr4-103720461-1	chr4	103720411	103720511	+	1.9	cIP2vsInput	Intergenic	Intergenic	337961	NR_040673	622167	Mm.244115	NR_040673	ENSMUSG00000086136	Gm12718	OTTMUSG00000008109	predicted gene 12718	miscRNA	0	0.376238
Merged-chr10-47861128-1	chr10	47861078	47861178	+	1.9	cIP2vsInput	Intergenic	Intergenic	1234715	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	"proteasome (prosome, macropain) subunit, alpha type 6 pseudogene"	pseudo	0	0.326733
Merged-chr5-80027005-1	chr5	80026955	80027055	+	1.9	cIP2vsInput	Intergenic	Intergenic	-511101	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0	0.366337
Merged-chr3-49277291-1	chr3	49277241	49277341	+	1.9	cIP2vsInput	Intergenic	Intergenic	480025	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding	0.01	0.405941
Merged-chr10-31978340-1	chr10	31978290	31978390	+	1.9	cIP2vsInput	"intron (NM_001013411, intron 3 of 6)"	"intron (NM_001013411, intron 3 of 6)"	-368615	NM_001146349	268291	Mm.295212	NM_001146349		Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding	0.01	0.356436
Merged-chr14-91343665-1	chr14	91343615	91343715	+	1.9	cIP2vsInput	Intergenic	Intergenic	1216774	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0	0.287129
Merged-chr19-49871498-1	chr19	49871448	49871548	+	1.9	cIP2vsInput	Intergenic	Intergenic	807148	NM_001252501	58178	Mm.313672	NM_001252501	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	VPS10 domain receptor protein SORCS 1	protein-coding	0	0.247525
Merged-chr1-109011771-1	chr1	109011721	109011821	+	1.9	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-971966	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0.01	0.316832
Merged-chr19-25784402-1	chr19	25784352	25784452	+	1.9	cIP2vsInput	Intergenic	Intergenic	111991	NM_145831	226049	Mm.275572	NM_145831	ENSMUSG00000048138	Dmrt2	Terra	doublesex and mab-3 related transcription factor 2	protein-coding	0	0.376238
Merged-chr4-14366102-1	chr4	14366052	14366152	+	1.9	cIP2vsInput	Intergenic	Intergenic	255676	NM_145947	208890	Mm.483839	NM_145947		Slc26a7	-	"solute carrier family 26, member 7"	protein-coding	0	0.405941
Merged-chr17-69959285-1	chr17	69959235	69959335	+	1.9	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	-465507	NM_177639	224997	Mm.367369	NM_001128180	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	"discs, large (Drosophila) homolog-associated protein 1"	protein-coding	0	0.346535
Merged-chr4-69110171-1	chr4	69110121	69110221	+	1.9	cIP2vsInput	Intergenic	Intergenic	-155774	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Dbc1	BRINP|Brinp1|Dbccr1|Fam5a	deleted in bladder cancer 1 (human)	protein-coding	0	0.346535
Merged-chr19-51692550-1	chr19	51692500	51692600	+	1.9	cIP2vsInput	Intergenic	Intergenic	-571773	NM_008386	16333	Mm.46269	NM_008386	ENSMUSG00000035804	Ins1	Ins-1|Ins2-rs1	insulin I	protein-coding	0	0.386139
Merged-chr15-52020770-1	chr15	52020720	52020820	+	1.9	cIP2vsInput	Intergenic	Intergenic	-19337	NM_175503	239435	Mm.24204	NM_175503	ENSMUSG00000068522	Aard	A5D3|AV328152	alanine and arginine rich domain containing protein	protein-coding	0.02	0.465347
Merged-chr8-38103573-1	chr8	38103523	38103623	+	1.9	cIP1vsInput	"intron (NM_145841, intron 1 of 7)"	"intron (NM_145841, intron 1 of 7)"	148629	NR_029884	723860		NR_029884		Mir383	Mirn383|mmu-mir-383	microRNA 383	miscRNA	0	0.287129
Merged-chr15-13879271-1	chr15	13879221	13879321	+	1.9	cIP2vsInput	Intergenic	RCHARR1|DNA|hAT-Charlie	-705632	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	K-cadherin|cad6|cadherin-6	cadherin 6	protein-coding	0	0.257426
Merged-chr18-81166561-1	chr18	81166511	81166611	+	1.9	cIP1vsInput	Intergenic	Intergenic	-179983	NM_178280	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	sal-like 3 (Drosophila)	protein-coding	0.01	0.366337
Merged-chr4-25131507-1	chr4	25131457	25131557	+	1.9	cIP2vsInput	Intergenic	L1VL4|LINE|L1	111369	NM_021318	57756	Mm.87325	NM_021318	ENSMUSG00000028259	Fhl5	1700027G07Rik|Act	four and a half LIM domains 5	protein-coding	0.01	0.326733
Merged-chr2-43199778-1	chr2	43199728	43199828	+	1.9	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-355551	NM_027552	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding	0	0.336634
Merged-chr14-94088754-1	chr14	94088704	94088804	+	1.9	cIP2vsInput	Intergenic	Kanga1a|DNA|TcMar-Tc2	-198085	NM_001271798	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0	0.356436
Merged-chrX-150724042-1	chrX	150723992	150724092	+	1.9	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-66606	NM_001002272	56191	Mm.3597	NM_207679	ENSMUSG00000025272	Tro	AA409408|Maged3|Maged3l|Tnn|Trol|magphinin	trophinin	protein-coding	0	0.306931
Merged-chr16-47178891-1	chr16	47178841	47178941	+	1.9	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-681924	NM_021497	58998	Mm.328072	NM_021495	ENSMUSG00000022656	Pvrl3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113	poliovirus receptor-related 3	protein-coding	0	0.356436
Merged-chr14-123056003-1	chr14	123055953	123056053	+	1.9	cIP1vsInput	Intergenic	Intergenic	-72742	NM_028651	70551	Mm.271988	NM_028651	ENSMUSG00000041594	Tmtc4	4930403J22Rik|5730419O14Rik	transmembrane and tetratricopeptide repeat containing 4	protein-coding	0	0.316832
Merged-chrX-97829975-1	chrX	97829925	97830025	+	1.9	cIP2vsInput	Intergenic	L1M2|LINE|L1	-319775	NM_013476	11835	Mm.439657	NM_013476		Ar	AW320017|Tfm	androgen receptor	protein-coding	0	0.336634
Merged-chr8-55837147-1	chr8	55837097	55837197	+	1.8	cIP2vsInput	Intergenic	RMER6C|LTR|ERVK	69817	NM_175939	244486	Mm.67684	NM_175939	ENSMUSG00000046258	Adam29	-	a disintegrin and metallopeptidase domain 29	protein-coding	0	0.39604
Merged-chr9-52442044-1	chr9	52441994	52442094	+	1.8	cIP2vsInput	Intergenic	Intergenic	237385	NM_178906	330941	Mm.335160	NM_177907	ENSMUSG00000078307	AI593442	E130102D23	expressed sequence AI593442	protein-coding	0	0.356436
Merged-chr15-33804418-1	chr15	33804368	33804468	+	1.8	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	-116535	NM_001085421	239364	Mm.60794	NM_001085421	ENSMUSG00000038984	Tspyl5	6330530B20|E130308C19Rik	"testis-specific protein, Y-encoded-like 5"	protein-coding	0	0.356436
Merged-chr13-53052376-1	chr13	53052326	53052426	+	1.8	cIP2vsInput	Intergenic	MLTR18_MM|LTR|ERVK	-71337	NM_017373	18030	Mm.136604	NM_017373	ENSMUSG00000056749	Nfil3	AV225605|E4BP4	"nuclear factor, interleukin 3, regulated"	protein-coding	0.03	0.425743
Merged-chr6-122201236-1	chr6	122201186	122201286	+	1.8	cIP2vsInput	"intron (NR_027619, intron 7 of 35)"	L1_Mus2|LINE|L1	25183	NR_027619	17835	Mm.422976	NR_027619		Mug-ps1	Mug3	"murinoglobulin, pseudogene 1"	pseudo	0	0.356436
Merged-chr12-92140988-1	chr12	92140938	92141038	+	1.8	cIP2vsInput	Intergenic	Intergenic	-291831	NM_011344	20338	Mm.250605	NM_001039089	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding	0.02	0.287129
Merged-chr3-18926377-1	chr3	18926327	18926427	+	1.8	cIP2vsInput	Intergenic	Lx7|LINE|L1	236688	NM_028840	74252	Mm.316007	XM_003689346	ENSMUSG00000027599	Armc1	2310016N05Rik|2900046P06Rik|3110009G21Rik|AA409258|AW048872|Arcp|C330014L16Rik	armadillo repeat containing 1	protein-coding	0	0.267327
Merged-chr8-57865809-1	chr8	57865759	57865859	+	1.8	cIP2vsInput	"intron (NM_175032, intron 7 of 11)"	"intron (NM_175032, intron 7 of 11)"	-212754	NM_144731	108150	Mm.62886	NM_001167981	ENSMUSG00000031608	Galnt7	AI225872	UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.01	0.415842
Merged-chr6-12899635-1	chr6	12899585	12899685	+	1.8	cIP2vsInput	Intergenic	Intergenic	-150382	NM_001164805	330267	Mm.400067	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	"thrombospondin, type I, domain containing 7A"	protein-coding	0	0.316832
Merged-chr18-53437703-1	chr18	53437653	53437753	+	1.8	cIP2vsInput	Intergenic	Lx8b|LINE|L1	-19696	NM_008908	19038	Mm.4587	NM_008908	ENSMUSG00000024538	Ppic	CyP-20c	peptidylprolyl isomerase C	protein-coding	0.01	0.49505
Merged-chr5-82045082-1	chr5	82045032	82045132	+	1.8	cIP2vsInput	Intergenic	Intergenic	753983	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mmu-mir-1187	microRNA 1187	miscRNA	0.01	0.336634
Merged-chr3-13748403-1	chr3	13748353	13748453	+	1.8	cIP2vsInput	"intron (NM_178631, intron 2 of 9)"	"intron (NM_178631, intron 2 of 9)"	-95538	NR_040598	75203	Mm.490940	NR_040598		4930539N22Rik	-	RIKEN cDNA 4930539N22 gene	miscRNA	0	0.326733
Merged-chr2-114180368-1	chr2	114180318	114180418	+	1.8	cIP2vsInput	Intergenic	Lx5b|LINE|L1	-5029	NM_009702	11834	Mm.2545	NM_009702	ENSMUSG00000040383	Aqr	AW495846|mKIAA0560	aquarius	protein-coding	0	0.326733
Merged-chr3-63593722-1	chr3	63593672	63593772	+	1.8	cIP2vsInput	Intergenic	Intergenic	257269	NM_001177733	269437	Mm.316391	NM_001177732	ENSMUSG00000036834	Plch1	BC042549|PLCeta1|Plcl3	"phospholipase C, eta 1"	protein-coding	0	0.405941
Merged-chr8-46349775-1	chr8	46349725	46349825	+	1.8	cIP2vsInput	Intergenic	IAPEz-int|LTR|ERVK	-55104	NM_173789	234219	Mm.145631	NM_173789	ENSMUSG00000047171	Helt	A830086M02|Hesl|Mgn|megane	helt bHLH transcription factor	protein-coding	0.01	0.326733
Merged-chr9-12289618-1	chr9	12289568	12289668	+	1.8	cIP2vsInput	Intergenic	Intergenic	816237	NR_040755	78219	Mm.414868	NR_040755		4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	miscRNA	0	0.306931
Merged-chr6-14468746-1	chr6	14468696	14468796	+	1.8	cIP2vsInput	Intergenic	Intergenic	286528	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	"protein phosphatase 1, regulatory (inhibitor) subunit 3A"	protein-coding	0	0.366337
Merged-chr18-45180771-1	chr18	45180721	45180821	+	1.8	cIP2vsInput	Intergenic	L1ME3A|LINE|L1	352106	NM_001163013	240255	Mm.244482	NM_001163013	ENSMUSG00000034653	Ythdc2	3010002F02Rik|BC037178	YTH domain containing 2	protein-coding	0	0.336634
Merged-chr5-123883721-1	chr5	123883671	123883771	+	1.8	cIP2vsInput	Intergenic	Intergenic	-3701	NM_175520	243270	Mm.33362	NM_175520	ENSMUSG00000049241	Gpr81	Hcar1	G protein-coupled receptor 81	protein-coding	0	0.316832
Merged-chr5-124992583-1	chr5	124992533	124992633	+	1.8	cIP2vsInput	Intergenic	Intergenic	-10892	NM_028443	73121	Mm.296138	NM_028443	ENSMUSG00000037962	Fam101a	3110032G18Rik|cfm|cfm2	"family with sequence similarity 101, member A"	protein-coding	0.02	0.405941
Merged-chr1-48462056-1	chr1	48462006	48462106	+	1.8	cIP2vsInput	Intergenic	Lx8|LINE|L1	-1608547	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	"solute carrier family 39 (zinc transporter), member 10"	protein-coding	0	0.336634
Merged-chr5-120746576-1	chr5	120746526	120746626	+	1.8	cIP2vsInput	"intron (NM_145227, intron 2 of 10)"	"intron (NM_145227, intron 2 of 10)"	3272	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding	0.02	0.326733
Merged-chr7-139188328-1	chr7	139188278	139188378	+	1.8	cIP2vsInput	"exon (NM_021302, exon 1 of 12)"	"exon (NM_021302, exon 1 of 12)"	166	NM_021302	57740	Mm.65336	NM_001162540	ENSMUSG00000015981	Stk32c	PKE|Pkek|YANK3	serine/threonine kinase 32C	protein-coding	0.15	0.792079
Merged-chr3-10902217-1	chr3	10902167	10902267	+	1.8	cIP2vsInput	Intergenic	Intergenic	-462093	NM_001127191	74718	Mm.440548	NM_001127191	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding	0.01	0.376238
Merged-chr13-62097279-1	chr13	62097229	62097329	+	1.8	cIP2vsInput	Intergenic	Intergenic	-32611	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 80	protein-coding	0.01	0.336634
Merged-chr5-74497409-1	chr5	74497359	74497459	+	1.8	cIP2vsInput	"intron (NM_001114660, intron 2 of 8)"	"intron (NM_001114660, intron 2 of 8)"	34340	NM_178672	212986	Mm.134147	NM_001114660	ENSMUSG00000062110	Scfd2	9330137G15|E430013M20Rik|STXBP1L1	Sec1 family domain containing 2	protein-coding	0.01	0.277228
Merged-chr3-71367139-1	chr3	71367089	71367189	+	1.8	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-559848	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	miscRNA	0	0.316832
Merged-chr6-26967880-1	chr6	26967830	26967930	+	1.8	cIP2vsInput	Intergenic	Intergenic	968870	NR_030420	735266		NR_030420		Mir592	Mirn592|mir-592|mmu-mir-592	microRNA 592	miscRNA	0.02	0.346535
Merged-chr6-107466330-1	chr6	107466280	107466380	+	1.8	cIP2vsInput	Intergenic	Intergenic	-63396	NM_008516	16979	Mm.488119	NM_008516	ENSMUSG00000034648	Lrrn1	2810047E21Rik|NLRR-1	"leucine rich repeat protein 1, neuronal"	protein-coding	0	0.346535
Merged-chr1-174262004-1	chr1	174261954	174262054	+	1.8	cIP2vsInput	Intergenic	Lx2B|LINE|L1	-11028	NM_146715	258710	Mm.377647	NM_146715	ENSMUSG00000050788	Olfr419	MOR267-6	olfactory receptor 419	protein-coding	0	0.29703
Merged-chr3-22697397-1	chr3	22697347	22697447	+	1.8	cIP2vsInput	Intergenic	A-rich|Low_complexity|Low_complexity	446027	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	miscRNA	0.01	0.326733
Merged-chr1-58652541-1	chr1	58652491	58652591	+	1.8	cIP2vsInput	promoter-TSS (NR_045007)	promoter-TSS (NR_045007)	-100	NR_045007	100504501	Mm.440933	NR_045007		Gm20257	-	caspase 8 pseudogene	pseudo	0.02	0.594059
Merged-chr2-69319501-1	chr2	69319451	69319551	+	1.8	cIP2vsInput	"intron (NM_021022, intron 5 of 27)"	L1MB7|LINE|L1	23115	NM_021022	27413	Mm.439855	NM_021022	ENSMUSG00000027048	Abcb11	ABC16|Bsep|Lith1|PFIC2|PGY4|SPGP	"ATP-binding cassette, sub-family B (MDR/TAP), member 11"	protein-coding	0.01	0.29703
Merged-chr12-61075614-1	chr12	61075564	61075664	+	1.8	cIP2vsInput	Intergenic	Intergenic	446206	NR_045049	100504101	Mm.235026	NR_045049		Gm20063	-	"predicted gene, 20063"	miscRNA	0	0.29703
Merged-chr3-114975591-1	chr3	114975541	114975641	+	1.8	cIP2vsInput	"intron (NM_153458, intron 1 of 5)"	"intron (NM_153458, intron 1 of 5)"	71228	NM_153458	229759	Mm.54183	NM_153157	ENSMUSG00000027965	Olfm3	B230206G02Rik	olfactomedin 3	protein-coding	0	0.405941
Merged-chr2-3214146-1	chr2	3214096	3214196	+	1.8	cIP2vsInput	"intron (NM_001081161, intron 5 of 7)"	"intron (NM_001081161, intron 5 of 7)"	-70142	NM_008708	18108	Mm.392918	NM_008708	ENSMUSG00000026643	Nmt2	A930001K02Rik|AI605445|AU044698|hNMT-2	N-myristoyltransferase 2	protein-coding	0	0.346535
Merged-chr5-41858708-1	chr5	41858658	41858758	+	1.8	cIP2vsInput	Intergenic	Intergenic	-14393	NM_001081422	665775	Mm.158726	NM_001081422	ENSMUSG00000061755	Bod1l	A230054D04Rik|AI853319|FAM44A|mKIAA1327	biorientation of chromosomes in cell division 1-like	protein-coding	0	0.257426
Merged-chr10-22121258-1	chr10	22121208	22121308	+	1.8	cIP1vsInput	"intron (NM_001254744, intron 1 of 1)"	Lx5c|LINE|L1	28012	NM_001254744	319887	Mm.418291	NM_001254744	ENSMUSG00000055657	E030030I06Rik	-	RIKEN cDNA E030030I06 gene	protein-coding	0	0.356436
Merged-chr19-14226289-1	chr19	14226239	14226339	+	1.8	cIP2vsInput	Intergenic	Intergenic	212217	NR_003027	19862		NR_003027	ENSMUSG00000095132	Rnu6	-	U6 small nuclear RNA	snRNA	0	0.29703
Merged-chr15-64873962-1	chr15	64873912	64874012	+	1.8	cIP2vsInput	"intron (NM_009623, intron 1 of 17)"	L1_Mus4|LINE|L1	48334	NM_009623	11514	Mm.1425	NM_009623	ENSMUSG00000022376	Adcy8	AC8|AW060868	adenylate cyclase 8	protein-coding	0	0.346535
Merged-chr5-57563166-1	chr5	57563116	57563216	+	1.8	cIP2vsInput	Intergenic	Intergenic	154753	NR_015588	319216	Mm.446765	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	miscRNA	0.01	0.277228
Merged-chr15-17809994-1	chr15	17809944	17810044	+	1.8	cIP2vsInput	Intergenic	Intergenic	559633	NR_045711	70886	Mm.399021	NR_045711		4921515E04Rik	-	RIKEN cDNA 4921515E04 gene	miscRNA	0.01	0.306931
Merged-chr4-61578357-1	chr4	61578307	61578407	+	1.8	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	17468	NM_001134644	100048885	Mm.422695	NM_001134644		Gm2083	-	major urinary protein LOC100048885	protein-coding	0.01	0.465347
Merged-chr17-19101135-1	chr17	19101085	19101185	+	1.8	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	47642	NM_001104550	224552	Mm.469860	NM_001104550	ENSMUSG00000096717	Vmn2r98	EG224552	"vomeronasal 2, receptor 98"	protein-coding	0	0.316832
Merged-chr4-110476752-1	chr4	110476702	110476802	+	1.8	cIP2vsInput	"intron (NM_001048189, intron 1 of 12)"	"intron (NM_001048189, intron 1 of 12)"	78961	NM_030231	78933	Mm.435620	NM_001048189	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding	0.01	0.366337
Merged-chr13-5102643-1	chr13	5102593	5102693	+	1.8	cIP2vsInput	Intergenic	Intergenic	-493479	NM_018859	56043	Mm.251908	NM_018859	ENSMUSG00000045410	Akr1e1	1810061I10Rik|Akr1e2	"aldo-keto reductase family 1, member E1"	protein-coding	0	0.316832
Merged-chr3-59652868-1	chr3	59652818	59652918	+	1.8	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-76918	NM_001101531	433597	Mm.297801	NM_001101531	ENSMUSG00000090527	Gm5538	-	predicted gene 5538	protein-coding	0	0.356436
Merged-chr7-35141827-1	chr7	35141777	35141877	+	1.8	cIP2vsInput	Intergenic	Intergenic	22534	NM_007678	12606	Mm.349667	NM_007678	ENSMUSG00000034957	Cebpa	C/ebpalpha|CBF-A|Cebp	"CCAAT/enhancer binding protein (C/EBP), alpha"	protein-coding	0.02	0.554455
Merged-chr19-39178026-1	chr19	39177976	39178076	+	1.8	cIP2vsInput	"intron (NM_001011707, intron 7 of 8)"	"intron (NM_001011707, intron 7 of 8)"	-51228	NR_033614	638988	Mm.483843	NR_033614	ENSMUSG00000093610	Cyp2c53-ps	Cyp2c53|EG638988	"cytochrome P450, family 2, subfamily c, polypeptide 53-ps"	pseudo	0.01	0.356436
Merged-chr13-65585339-1	chr13	65585289	65585389	+	1.8	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	306485	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding	0	0.366337
Merged-chr17-68587655-1	chr17	68587605	68587705	+	1.8	cIP2vsInput	"intron (NM_177278, intron 14 of 20)"	"intron (NM_177278, intron 14 of 20)"	-249481	NM_001206661	622645	Mm.86422	NM_001206661	ENSMUSG00000095407	Tmem200c	EG622645|Gm6338	transmembrane protein 200C	protein-coding	0	0.316832
Merged-chr1-113148242-1	chr1	113148192	113148292	+	1.8	cIP2vsInput	Intergenic	Lx2|LINE|L1	-1283324	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik	dermatan sulfate epimerase-like	protein-coding	0	0.346535
Merged-chr3-46647940-1	chr3	46647890	46647990	+	1.8	cIP1vsInput	Intergenic	Intergenic	-199999	NM_001101479	241989	Mm.475785	NM_001101479	ENSMUSG00000090919	Pabpc4l	C330050A14Rik|EG241989	"poly(A) binding protein, cytoplasmic 4-like"	protein-coding	0	0.29703
Merged-chr16-53885543-1	chr16	53885493	53885593	+	1.8	cIP2vsInput	Intergenic	Intergenic	-1069799	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	miscRNA	0	0.366337
Merged-chr1-173182215-1	chr1	173182165	173182265	+	1.8	cIP2vsInput	Intergenic	Intergenic	2289	NM_146763	258758	Mm.223190	NM_146763	ENSMUSG00000058981	Olfr1406	MOR267-5	olfactory receptor 1406	protein-coding	0	0.237624
Merged-chr18-45016001-1	chr18	45015951	45016051	+	1.8	cIP2vsInput	Intergenic	Intergenic	187336	NM_001163013	240255	Mm.244482	NM_001163013	ENSMUSG00000034653	Ythdc2	3010002F02Rik|BC037178	YTH domain containing 2	protein-coding	0.03	0.514851
Merged-chr10-112329930-1	chr10	112329880	112329980	+	1.8	cIP2vsInput	"intron (NM_001025581, intron 2 of 4)"	Lx6|LINE|L1	58807	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	"potassium voltage gated channel, Shaw-related subfamily, member 2"	protein-coding	0	0.326733
Merged-chr8-33335504-1	chr8	33335454	33335554	+	1.8	cIP2vsInput	"intron (NM_001122822, intron 6 of 33)"	"intron (NM_001122822, intron 6 of 33)"	50023	NM_001122822	22427	Mm.228805	XM_003946269	ENSMUSG00000031583	Wrn	AI846146	Werner syndrome homolog (human)	protein-coding	0	0.336634
Merged-chrX-58842912-1	chrX	58842862	58842962	+	1.8	cIP2vsInput	Intergenic	Intergenic	-68549	NM_023774	75352	Mm.60906	NM_023774	ENSMUSG00000046180	4930550L24Rik	mage-k1	RIKEN cDNA 4930550L24 gene	protein-coding	0	0.287129
Merged-chr8-21955336-1	chr8	21955286	21955386	+	1.8	cIP2vsInput	Intergenic	MER31A|LTR|ERV1	-3378	NM_001081662	97476	Mm.297693	NM_001081662	ENSMUSG00000079112	C86695	-	expressed sequence C86695	protein-coding	0	0.386139
Merged-chr10-26646621-1	chr10	26646571	26646671	+	1.8	cIP2vsInput	Intergenic	MusHAL1|LINE|L1	28030	NR_033633	667572	Mm.482728	NR_033633		Gm8709	EG667572	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo	0	0.336634
Merged-chr2-84152395-1	chr2	84152345	84152445	+	1.8	cIP2vsInput	Intergenic	Intergenic	-211169	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding	0	0.346535
Merged-chr19-60341831-1	chr19	60341781	60341881	+	1.8	cIP2vsInput	Intergenic	Intergenic	-115134	NM_029648	76539	Mm.290183	NM_029648	ENSMUSG00000057858	D19Ertd737e	2310065H12Rik|2610015K05Rik|Fam204a	"DNA segment, Chr 19, ERATO Doi 737, expressed"	protein-coding	0	0.287129
Merged-chr9-68379469-1	chr9	68379419	68379519	+	1.8	cIP2vsInput	Intergenic	Intergenic	140731	NR_040737	74951	Mm.60678	NR_040737		4930502A04Rik	-	RIKEN cDNA 4930502A04 gene	miscRNA	0.01	0.356436
Merged-chr17-53125722-1	chr17	53125672	53125772	+	1.8	cIP2vsInput	Intergenic	Lx3B|LINE|L1	337599	NM_172497	211482	Mm.60887	NM_172497	ENSMUSG00000023931	Efhb	4921525D22Rik	"EF hand domain family, member B"	protein-coding	0	0.336634
Merged-chr15-15547313-1	chr15	15547263	15547363	+	1.8	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-1230788	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0.01	0.316832
Merged-chr13-118520900-1	chr13	118520850	118520950	+	1.8	cIP2vsInput	Intergenic	MusHAL1|LINE|L1	-35268	NR_045982	75890	Mm.141235	NR_045982		1700003P14Rik	1700030O10Rik|4930584L06Rik	RIKEN cDNA 1700003P14 gene	miscRNA	0	0.326733
Merged-chr7-10226016-1	chr7	10225966	10226066	+	1.8	cIP2vsInput	Intergenic	Intergenic	49335	NM_134230	171264	Mm.222637	NM_134230	ENSMUSG00000043066	Vmn1r66	S67|V1re11|V1re3	vomeronasal 1 receptor 66	protein-coding	0	0.405941
Merged-chrX-23703747-1	chrX	23703697	23703797	+	1.8	cIP2vsInput	"intron (NM_175180, intron 1 of 19)"	L1MA6|LINE|L1	10630	NM_175180	72404	Mm.423	NM_175180	ENSMUSG00000036769	Wdr44	2610034K17Rik|9130203L06|RAB11BP|RPH11	WD repeat domain 44	protein-coding	0	0.346535
Merged-chr15-10026672-1	chr15	10026622	10026722	+	1.8	cIP2vsInput	Intergenic	Intergenic	-150566	NM_011169	19116	Mm.442446	NR_045590	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding	0	0.366337
Merged-chr7-98771339-1	chr7	98771289	98771389	+	1.8	cIP2vsInput	Intergenic	Intergenic	-67506	NM_009519	22411	Mm.22182	NM_009519		Wnt11	-	wingless-related MMTV integration site 11	protein-coding	0.02	0.574257
Merged-chr5-69064366-1	chr5	69064316	69064416	+	1.8	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	277343	NM_175519	243043	Mm.234821	NM_175519	ENSMUSG00000037653	Kctd8	A730087N02Rik	potassium channel tetramerisation domain containing 8	protein-coding	0.01	0.346535
Merged-chr10-51125284-1	chr10	51125234	51125334	+	1.8	cIP2vsInput	Intergenic	Intergenic	229633	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding	0.01	0.356436
Merged-chr1-127890500-1	chr1	127890450	127890550	+	1.8	cIP2vsInput	"intron (NM_178690, intron 4 of 23)"	"intron (NM_178690, intron 4 of 23)"	21727	NM_178690	226407	Mm.489713	NM_178690	ENSMUSG00000036104	Rab3gap1	1700003B17Rik|4732493F09Rik|AL117896|Rab3gap|p130	RAB3 GTPase activating protein subunit 1	protein-coding	0	0.306931
Merged-chr13-67638025-1	chr13	67637975	67638075	+	1.8	cIP2vsInput	promoter-TSS (NM_183146)	promoter-TSS (NM_183146)	-272	NM_183146	212281	Mm.342918	NM_183146	ENSMUSG00000021510	A530054K11Rik	Rslcan3	RIKEN cDNA A530054K11 gene	protein-coding	0.02	0.376238
Merged-chr12-33497913-1	chr12	33497863	33497963	+	1.8	cIP2vsInput	Intergenic	Intergenic	68289	NM_172253	28071	Mm.413045	NM_172253	ENSMUSG00000020561	Twistnb	2410173G11|2810024J17Rik|D16Wsu83e	TWIST neighbor	protein-coding	0.01	0.376238
Merged-chr19-11565606-1	chr19	11565556	11565656	+	1.8	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	28757	NM_025658	66607	Mm.441056	NM_025658	ENSMUSG00000024678	Ms4a4d	2210417J23Rik	"membrane-spanning 4-domains, subfamily A, member 4D"	protein-coding	0	0.336634
Merged-chr15-37477131-1	chr15	37477081	37477181	+	1.8	cIP2vsInput	"intron (NM_134094, intron 4 of 6)"	"intron (NM_134094, intron 4 of 6)"	-17749	NM_001170868	52589	Mm.472945	NM_001170866	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding	0.03	0.376238
Merged-chr17-42504913-1	chr17	42504863	42504963	+	1.8	cIP2vsInput	"3' UTR (NM_028474, exon 4 of 4)"	"3' UTR (NM_028474, exon 4 of 4)"	106400	NM_181753	353344	Mm.184937	NM_181753	ENSMUSG00000043972	Opn5	Gpr136|Neuropsin|PGR12|TMEM13	opsin 5	protein-coding	0.01	0.356436
Merged-chrX-46269468-1	chrX	46269418	46269518	+	1.8	cIP2vsInput	"intron (NR_045440, intron 2 of 2)"	"intron (NR_045440, intron 2 of 2)"	59443	NR_045440	75133	Mm.417818	NR_045440	ENSMUSG00000085157	4930515L19Rik	-	RIKEN cDNA 4930515L19 gene	miscRNA	0	0.346535
Merged-chr5-56282994-1	chr5	56282944	56283044	+	1.8	cIP2vsInput	Intergenic	Intergenic	1434925	NR_015588	319216	Mm.446765	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	miscRNA	0	0.316832
Merged-chr12-63841036-1	chr12	63840986	63841086	+	1.8	cIP2vsInput	Intergenic	Intergenic	633862	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding	0	0.326733
Merged-chr8-29283491-1	chr8	29283441	29283541	+	1.8	cIP2vsInput	Intergenic	Intergenic	-63855	NM_153135	210801	Mm.248433	NM_153135	ENSMUSG00000063626	Unc5d	D930029E11Rik|Unc5h4|mKIAA1777	unc-5 homolog D (C. elegans)	protein-coding	0	0.336634
Merged-chr1-162337716-1	chr1	162337666	162337766	+	1.8	cIP2vsInput	"intron (NM_001038619, intron 4 of 20)"	"intron (NM_001038619, intron 4 of 20)"	114348	NR_029796	387210		NR_029796	ENSMUSG00000065516	Mir214	Mirn214|mmu-mir-214	microRNA 214	miscRNA	0	0.29703
Merged-chr6-68548657-1	chr6	68548607	68548707	+	1.8	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	778517	NR_004434	19783		NR_004434		Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	miscRNA	0	0.356436
Merged-chr7-123740611-1	chr7	123740561	123740661	+	1.8	cIP2vsInput	Intergenic	Intergenic	-240162	NM_001081329	210162	Mm.135397	NM_001081329	ENSMUSG00000030757	Zkscan2	9430065N20Rik|AW493225|Zfp694	zinc finger with KRAB and SCAN domains 2	protein-coding	0	0.366337
Merged-chr11-112375036-1	chr11	112374986	112375086	+	1.8	cIP2vsInput	Intergenic	Intergenic	336320	NR_024085	217294	Mm.297761	NM_146031	ENSMUSG00000041674	BC006965	-	cDNA sequence BC006965	miscRNA	0	0.336634
Merged-chrY-2752596-1	chrY	2752546	2752646	+	1.8	cIP2vsInput	Intergenic	Intergenic	-31922	NM_001177569	547210	Mm.484980	NM_001177569	ENSMUSG00000094881	Gm6026	H2al2y	predicted gene 6026	protein-coding	0	0.287129
Merged-chr1-103583344-1	chr1	103583294	103583394	+	1.8	cIP2vsInput	Intergenic	Intergenic	-1185475	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding	0.01	0.326733
Merged-chr16-89236651-1	chr16	89236601	89236701	+	1.8	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	30790	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding	0.01	0.39604
Merged-chr19-21452431-1	chr19	21452381	21452481	+	1.8	cIP2vsInput	"intron (NM_010266, intron 1 of 13)"	"intron (NM_010266, intron 1 of 13)"	20230	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581	guanine deaminase	protein-coding	0.02	0.306931
Merged-chr19-38514207-1	chr19	38514157	38514257	+	1.8	cIP2vsInput	Intergenic	Intergenic	-9990	NM_019588	74055	Mm.34031	NM_019588	ENSMUSG00000024998	Plce1	4933403A21Rik|PLCepsilon|Plce|mKIAA1516	"phospholipase C, epsilon 1"	protein-coding	0	0.277228
Merged-chr3-24981638-1	chr3	24981588	24981688	+	1.8	cIP2vsInput	Intergenic	Intergenic	1171669	NM_001163387	192167	Mm.316080	NM_001163387	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|mKIAA1070	neuroligin 1	protein-coding	0	0.356436
Merged-chr1-96163527-1	chr1	96163477	96163577	+	1.8	cIP2vsInput	Intergenic	Lx7|LINE|L1	-141769	NR_040467	73454	Mm.396229	NR_040467		1700063A18Rik	-	RIKEN cDNA 1700063A18 gene	miscRNA	0.01	0.356436
Merged-chrX-69463827-1	chrX	69463777	69463877	+	1.8	cIP2vsInput	"intron (NM_008032, intron 1 of 19)"	"intron (NM_008032, intron 1 of 19)"	103496	NM_008032	14266	Mm.466576	NM_008032	ENSMUSG00000031189	Aff2	FMR2P|Fmr2|Ox19|Oxh	"AF4/FMR2 family, member 2"	protein-coding	0.01	0.336634
Merged-chrX-119359593-1	chrX	119359543	119359643	+	1.8	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-567603	NM_053114	93728	Mm.125979	NM_053114	ENSMUSG00000034732	Pabpc5	C820015E17	"poly(A) binding protein, cytoplasmic 5"	protein-coding	0	0.326733
Merged-chr14-14300731-1	chr14	14300681	14300781	+	1.8	cIP1vsInput	Intergenic	L1_Mur3|LINE|L1	-27382	NM_147027	18330	Mm.484338	NM_147027	ENSMUSG00000072707	Olfr31	MOR274-1|MTPCR53	olfactory receptor 31	protein-coding	0	0.277228
Merged-chr9-39458516-1	chr9	39458466	39458566	+	1.8	cIP2vsInput	Intergenic	Intergenic	-2917	NM_146331	258328	Mm.377437	NM_146331	ENSMUSG00000094745	Olfr954	MOR171-42|MOR171-53	olfactory receptor 954	protein-coding	0.01	0.336634
Merged-chr2-179726940-1	chr2	179726890	179726990	+	1.8	cIP2vsInput	"intron (NM_009867, intron 2 of 15)"	"intron (NM_009867, intron 2 of 15)"	249706	NM_001081092	228980	Mm.235542	NM_001081092	ENSMUSG00000039117	Taf4a	135kDa|AI450312|TAFII130|TAFII135|Taf2c1	"TAF4A RNA polymerase II, TATA box binding protein (TBP)-associated factor"	protein-coding	0	0.366337
Merged-chrX-39635829-1	chrX	39635779	39635879	+	1.8	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	227775	NM_001191032	100504400	Mm.373409	NM_001191032	ENSMUSG00000095240	Cypt14	-	cysteine-rich perinuclear theca 14	protein-coding	0	0.376238
Merged-chr8-43310798-1	chr8	43310748	43310848	+	1.8	cIP2vsInput	Intergenic	Intergenic	-3789	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding	0	0.356436
Merged-chrX-108058294-1	chrX	108058244	108058344	+	1.8	cIP2vsInput	Intergenic	Charlie2b|DNA|hAT-Charlie	-109858	NM_001033252	213450	Mm.300779	NM_001033252	ENSMUSG00000073006	Gm732	-	predicted gene 732	protein-coding	0	0.366337
Merged-chr6-102346026-1	chr6	102345976	102346076	+	1.8	cIP2vsInput	"intron (NM_008779, intron 3 of 21)"	"intron (NM_008779, intron 3 of 21)"	118641	NM_008779	18488	Mm.435479	NM_008779	ENSMUSG00000030075	Cntn3	Pang	contactin 3	protein-coding	0	0.326733
Merged-chr8-71943936-1	chr8	71943886	71943986	+	1.8	cIP2vsInput	Intergenic	Intergenic	-7130	NM_001164581	234413	Mm.334607	NM_001164581	ENSMUSG00000052446	Zfp961	A230105L22Rik|BC065788|mszf37|mszf55-2	zinc finger protein 961	protein-coding	0.01	0.346535
Merged-chr3-111829604-1	chr3	111829554	111829654	+	1.8	cIP2vsInput	Intergenic	Intergenic	-52299	NR_045362	625585	Mm.389497	NR_045362		Gm6602	-	predicted gene 6602	miscRNA	0	0.405941
Merged-chr5-38910675-1	chr5	38910625	38910725	+	1.8	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-33982	NM_013748	27278	Mm.440845	NM_013748	ENSMUSG00000039315	Clnk	MIST	cytokine-dependent hematopoietic cell linker	protein-coding	0	0.386139
Merged-chr9-122907718-1	chr9	122907668	122907768	+	1.8	cIP2vsInput	Intergenic	Intergenic	-15360	NM_009544	22646	Mm.290595	NM_009544	ENSMUSG00000057895	Zfp105	AW557864	zinc finger protein 105	protein-coding	0.01	0.316832
Merged-chr10-48041499-1	chr10	48041449	48041549	+	1.8	cIP2vsInput	Intergenic	ORR1C1|LTR|ERVL-MaLR	1054344	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	"proteasome (prosome, macropain) subunit, alpha type 6 pseudogene"	pseudo	0	0.346535
Merged-chr15-52836516-1	chr15	52836466	52836566	+	1.8	cIP2vsInput	Intergenic	Intergenic	124071	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding	0	0.346535
Merged-chr16-7614958-1	chr16	7614908	7615008	+	1.8	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	545123	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	"RNA binding protein, fox-1 homolog (C. elegans) 1"	protein-coding	0	0.366337
Merged-chrY-6477649-1	chrY	6477599	6477699	+	1.8	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	690128	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.326733
Merged-chr6-111311980-1	chr6	111311930	111312030	+	1.8	cIP2vsInput	"intron (NM_177328, intron 7 of 9)"	"intron (NM_177328, intron 7 of 9)"	666382	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|mGluR7	"glutamate receptor, metabotropic 7"	protein-coding	0.01	0.336634
Merged-chr14-53573215-1	chr14	53573165	53573265	+	1.8	cIP2vsInput	Intergenic	ETnERV2-int|LTR|ERVK	-92725	NM_001205242	100568452	Mm.486072	NM_001205242		A430107P09Rik	Va10	RIKEN cDNA A430107P09 gene	protein-coding	0	0.346535
Merged-chr1-145442274-1	chr1	145442224	145442324	+	1.8	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-666853	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding	0	0.306931
Merged-chrX-165516926-1	chrX	165516876	165516976	+	1.8	cIP2vsInput	Intergenic	L1MA4A|LINE|L1	-189945	NM_183427	237213	Mm.113877	NM_183427	ENSMUSG00000018589	Glra2	-	"glycine receptor, alpha 2 subunit"	protein-coding	0.01	0.346535
Merged-chr14-96860296-1	chr14	96860246	96860346	+	1.8	cIP2vsInput	Intergenic	Intergenic	-341262	NM_053105	93688	Mm.308735	NM_053105	ENSMUSG00000022076	Klhl1	mKIAA1490	kelch-like 1	protein-coding	0.01	0.356436
Merged-chr2-177370299-1	chr2	177370249	177370349	+	1.8	cIP2vsInput	Intergenic	ORR1D1|LTR|ERVL-MaLR	-94443	NM_001177568	628308	Mm.460436	NM_001177568		Gm14420	OTTMUSG00000016588	predicted gene 14420	protein-coding	0	0.29703
Merged-chr6-36712875-1	chr6	36712825	36712925	+	1.8	cIP1vsInput	Intergenic	Intergenic	98486	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding	0.01	0.445545
Merged-chr10-34672717-1	chr10	34672667	34672767	+	1.8	cIP2vsInput	Intergenic	Intergenic	189317	NM_010237	14302	Mm.332432	NM_001159544	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding	0.01	0.376238
Merged-chr17-91954005-1	chr17	91953955	91954055	+	1.8	cIP2vsInput	Intergenic	Intergenic	-861203	NM_020252	18189	Mm.312068	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0	0.237624
Merged-chr6-78516583-1	chr6	78516533	78516633	+	1.8	cIP2vsInput	Intergenic	Intergenic	-47709	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515	regenerating islet-derived 3 gamma	protein-coding	0	0.326733
Merged-chr15-49837548-1	chr15	49837498	49837598	+	1.8	cIP2vsInput	Intergenic	Intergenic	-1045559	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding	0.02	0.306931
Merged-chr14-107488937-1	chr14	107488887	107488987	+	1.8	cIP2vsInput	Intergenic	MTEa-int|LTR|ERVL-MaLR	-1002417	NR_045938	73631	Mm.48862	NR_045938		1700128A07Rik	-	RIKEN cDNA 1700128A07 gene	miscRNA	0	0.336634
Merged-chr3-76690248-1	chr3	76690198	76690298	+	1.8	cIP2vsInput	"intron (NM_178673, intron 15 of 15)"	"intron (NM_178673, intron 15 of 15)"	614665	NM_001253719	213262	Mm.379337	NM_001253719	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding	0.01	0.306931
Merged-chrX-139444119-1	chrX	139444069	139444169	+	1.8	cIP2vsInput	Intergenic	Intergenic	-36248	NM_175326	102871	Mm.26565	NM_175326	ENSMUSG00000042498	D330045A20Rik	AI132325	RIKEN cDNA D330045A20 gene	protein-coding	0	0.287129
Merged-chr12-6685925-1	chr12	6685875	6685975	+	1.8	cIP2vsInput	Intergenic	Intergenic	694405	NR_045045	73575	Mm.179463	NR_045045		1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	miscRNA	0.02	0.376238
Merged-chr14-6938706-1	chr14	6938656	6938756	+	1.8	cIP2vsInput	Intergenic	B1_Mm|SINE|Alu	88743	NM_001164727	100038847	Mm.483675	NM_001164727	ENSMUSG00000093985	Gm10406	ENSMUSG00000072735	predicted gene 10406	protein-coding	0.01	0.524752
Merged-chr15-16085977-1	chr15	16085927	16086027	+	1.8	cIP2vsInput	Intergenic	Intergenic	-692124	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding	0	0.29703
Merged-chr9-63242799-1	chr9	63242749	63242849	+	1.8	cIP2vsInput	"intron (NM_011840, intron 16 of 21)"	"intron (NM_011840, intron 16 of 21)"	-93838	NM_001163758	207667	Mm.447200	NM_001163755	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding	0.01	0.346535
Merged-chrX-59101476-1	chrX	59101426	59101526	+	1.8	cIP2vsInput	"intron (NM_010200, intron 3 of 4)"	L2|LINE|L2	-3740	NR_030574	100124476		NR_030574		Mir504	Mirn504|mmu-mir-504	microRNA 504	miscRNA	0.01	0.336634
Merged-chr19-41722381-1	chr19	41722331	41722431	+	1.8	cIP2vsInput	"intron (NM_015748, intron 3 of 36)"	B1_Mur3|SINE|Alu	21475	NM_015748	20562	Mm.40322	NM_015748	ENSMUSG00000025020	Slit1	Slil1|mKIAA0813	slit homolog 1 (Drosophila)	protein-coding	0	0.49505
Merged-chr4-155361629-1	chr4	155361579	155361679	+	1.8	cIP2vsInput	promoter-TSS (NM_008860)	promoter-TSS (NM_008860)	-238	NM_008860	18762	Mm.28561	NM_001039079	ENSMUSG00000029053	Prkcz	AI098070|C80388|Pkcz|R74924|aPKCzeta|zetaPKC	"protein kinase C, zeta"	protein-coding	0.12	0.712871
Merged-chr2-149059338-1	chr2	149059288	149059388	+	1.8	cIP2vsInput	Intergenic	Intergenic	-183870	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding	0	0.306931
Merged-chrX-106933120-1	chrX	106933070	106933170	+	1.8	cIP2vsInput	"3' UTR (NM_175271, exon 3 of 3)"	"3' UTR (NM_175271, exon 3 of 3)"	12495	NM_175271	78134	Mm.90147	NM_175271	ENSMUSG00000049929	Lpar4	5730485F04Rik|Gpr23|LPA4|p2y9	lysophosphatidic acid receptor 4	protein-coding	0	0.227723
Merged-chr1-113588151-1	chr1	113588101	113588201	+	1.8	cIP2vsInput	Intergenic	Intergenic	-1723233	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik	dermatan sulfate epimerase-like	protein-coding	0.01	0.346535
Merged-chr6-13777845-1	chr6	13777795	13777895	+	1.8	cIP2vsInput	Intergenic	Intergenic	62003	NM_145066	64450	Mm.487258	NM_145066	ENSMUSG00000048216	Gpr85	2900026B03Rik	G protein-coupled receptor 85	protein-coding	0	0.306931
Merged-chrX-14784112-1	chrX	14784062	14784162	+	1.8	cIP2vsInput	Intergenic	Intergenic	327377	NR_033171	67395	Mm.50369	NM_026128	ENSMUSG00000045217	Ppp1r2-ps9	4930403L05Rik	"protein phosphatase 1, regulatory (inhibitor) subunit 2, pseudogene 9"	pseudo	0	0.29703
Merged-chr8-57065850-1	chr8	57065800	57065900	+	1.8	cIP2vsInput	Intergenic	Intergenic	-255133	NM_010402	15111	Mm.430844	NM_010402	ENSMUSG00000038193	Hand2	AI225906|AI661148|Ehand2|Hed|Th2|Thing2|bHLHa26|dHAND	heart and neural crest derivatives expressed transcript 2	protein-coding	0	0.356436
Merged-chr13-105951794-1	chr13	105951744	105951844	+	1.8	cIP2vsInput	Intergenic	MLT1D|LTR|ERVL-MaLR	508101	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding	0	0.346535
Merged-chr2-67117408-1	chr2	67117358	67117458	+	1.8	cIP2vsInput	Intergenic	Intergenic	-56426	NM_001033477	383709	Mm.244520	NM_001033477		Gm1322	-	predicted gene 1322	protein-coding	0	0.386139
Merged-chr1-146095750-1	chr1	146095700	146095800	+	1.8	cIP2vsInput	Intergenic	L1MC3|LINE|L1	-399916	NM_153539	215378	Mm.441817	NM_001145807	ENSMUSG00000035131	Fam5c	B830045N13Rik	"family with sequence similarity 5, member C"	protein-coding	0	0.326733
Merged-chrX-98343880-1	chrX	98343830	98343930	+	1.8	cIP2vsInput	Intergenic	Intergenic	194130	NM_013476	11835	Mm.439657	NM_013476		Ar	AW320017|Tfm	androgen receptor	protein-coding	0	0.336634
Merged-chr5-16911357-1	chr5	16911307	16911407	+	1.8	cIP2vsInput	Intergenic	Intergenic	357807	NM_010427	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF/HGF	hepatocyte growth factor	protein-coding	0	0.346535
Merged-chr7-116160546-1	chr7	116160496	116160596	+	1.8	cIP2vsInput	"intron (NM_172743, intron 8 of 24)"	L1MA7|LINE|L1	29295	NM_172743	233765	Mm.3741	NM_172743	ENSMUSG00000045659	Plekha7	A430081P20Rik|AI414265	"pleckstrin homology domain containing, family A member 7"	protein-coding	0	0.386139
Merged-chr3-12229052-1	chr3	12229002	12229102	+	1.8	cIP2vsInput	Intergenic	Intergenic	-384693	NR_040751	100038545	Mm.388494	NR_040751		Gm10745	ENSMUSG00000074696	predicted gene 10745	miscRNA	0	0.376238
Merged-chr17-28666678-1	chr17	28666628	28666728	+	1.8	cIP2vsInput	Intergenic	GA-rich|Low_complexity|Low_complexity	-24664	NM_001168508	26416	Mm.311337	NM_001168508	ENSMUSG00000053436	Mapk14	CSBP2|Crk1|Csbp1|Mxi2|PRKM14|PRKM15|p38|p38-alpha|p38MAPK|p38a|p38alpha	mitogen-activated protein kinase 14	protein-coding	0	0.326733
Merged-chr14-87191612-1	chr14	87191562	87191662	+	1.8	cIP2vsInput	Intergenic	Intergenic	-50498	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diap3	4930417P13Rik|Dia2|Diaph3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous homolog 3 (Drosophila)	protein-coding	0	0.277228
Merged-chr4-37350296-1	chr4	37350246	37350346	+	1.8	cIP2vsInput	Intergenic	Intergenic	-398552	NM_001165999	242384	Mm.132507	NM_001165999	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding	0	0.356436
Merged-chr5-104254276-1	chr5	104254226	104254326	+	1.8	cIP2vsInput	Intergenic	Intergenic	-45011	NM_008318	15891	Mm.4987	XM_003689386	ENSMUSG00000029306	Ibsp	BSP|BSP II|BSPII|Bsp2	integrin binding sialoprotein	protein-coding	0.01	0.336634
Merged-chr5-13877143-1	chr5	13877093	13877193	+	1.8	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	85524	NM_027650	71026	Mm.158536	NM_027650	ENSMUSG00000067855	Speer3	4933405P08Rik|SPEER-3	spermatogenesis associated glutamate (E)-rich protein 3	protein-coding	0	0.29703
Merged-chr2-8375355-1	chr2	8375305	8375405	+	1.8	cIP2vsInput	Intergenic	Intergenic	-814160	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	miscRNA	0	0.306931
Merged-chr10-16024315-1	chr10	16024265	16024365	+	1.8	cIP2vsInput	Intergenic	Intergenic	1071467	NR_038020	100504235	Mm.84044	NR_038020		Gm20125	-	"predicted gene, 20125"	miscRNA	0.01	0.366337
Merged-chr11-9805710-1	chr11	9805660	9805760	+	1.8	cIP2vsInput	Intergenic	Lx5b|LINE|L1	613768	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	"ATP-binding cassette, sub-family A (ABC1), member 13"	protein-coding	0	0.29703
Merged-chr1-108432778-1	chr1	108432728	108432828	+	1.8	cIP2vsInput	Intergenic	Lx7|LINE|L1	515519	NR_102307	319596	Mm.136054	NR_102306		D830032E09Rik	-	RIKEN cDNA D830032E09 gene	miscRNA	0.01	0.376238
Merged-chrY-6896739-1	chrY	6896689	6896789	+	1.8	cIP2vsInput	Intergenic	Lx3A|LINE|L1	271038	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0	0.405941
Merged-chrX-169703581-1	chrX	169703531	169703631	+	1.8	cIP1vsInput	"intron (NM_010797, intron 1 of 9)"	MLT1E1|LTR|ERVL-MaLR	18334	NM_010797	17318	Mm.34441	NM_010797	ENSMUSG00000035299	Mid1	61B3-R|DXHXS1141|Fxy|Trim18	midline 1	protein-coding	0	0.346535
Merged-chr1-98419860-1	chr1	98419810	98419910	+	1.8	cIP2vsInput	Intergenic	Intergenic	-1264	NM_001164233	70866	Mm.389164	NM_001164233	ENSMUSG00000026336	Slco6d1	4921511I05Rik	"solute carrier organic anion transporter family, member 6d1"	protein-coding	0	0.336634
Merged-chr14-11266159-1	chr14	11266109	11266209	+	1.8	cIP2vsInput	Intergenic	Intergenic	-104127	NM_010210	14198	Mm.441926	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding	0	0.306931
Merged-chr3-147774374-1	chr3	147774324	147774424	+	1.8	cIP2vsInput	Intergenic	Intergenic	922007	NM_027594	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|Ttll7s	"tubulin tyrosine ligase-like family, member 7"	protein-coding	0	0.306931
Merged-chr4-54820838-1	chr4	54820788	54820888	+	1.8	cIP2vsInput	Intergenic	L1M2|LINE|L1	-127107	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding	0.01	0.336634
Merged-chr12-80416945-1	chr12	80416895	80416995	+	1.8	cIP1vsInput	"intron (NM_177267, intron 1 of 8)"	Charlie1a|DNA|hAT-Charlie	19656	NM_177267	320808	Mm.447547	NM_177267	ENSMUSG00000049106	Dcaf5	9430020B07Rik|AI325023|AI430035|AI848110|AW124614|BCRG2|BCRP2|Wdr22	DDB1 and CUL4 associated factor 5	protein-coding	0.01	0.336634
Merged-chr17-92817361-1	chr17	92817311	92817411	+	1.8	cIP2vsInput	Intergenic	Intergenic	-382061	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0	0.554455
Merged-chr16-26228837-1	chr16	26228787	26228887	+	1.8	cIP2vsInput	Intergenic	Intergenic	-123053	NM_173379	210530		NM_173379		Leprel1	4832416N06|AW553532|Mlat4|P3H2	leprecan-like 1	protein-coding	0	0.346535
Merged-chr14-88813266-1	chr14	88813216	88813316	+	1.8	cIP2vsInput	Intergenic	Intergenic	-341870	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding	0	0.306931
Merged-chr10-97861671-1	chr10	97861621	97861721	+	1.8	cIP1vsInput	"intron (NR_033537, intron 2 of 4)"	MTD-int|LTR|ERVL-MaLR	105419	NR_033537	100038699	Mm.467933	NR_033537		Gm10754	ENSMUSG00000074776	predicted gene 10754	miscRNA	0.01	0.346535
Merged-chr6-30995757-1	chr6	30995707	30995807	+	1.8	cIP2vsInput	Intergenic	ORR1B1-int|LTR|ERVL-MaLR	-36767	NM_001135093	619665	Mm.204671	NM_001135093	ENSMUSG00000073209	Klf14	5330411L03Rik|AL022736|BTEB5	Kruppel-like factor 14	protein-coding	0	0.29703
Merged-chr16-45751396-1	chr16	45751346	45751446	+	1.8	cIP2vsInput	"exon (NM_153412, exon 16 of 18)"	"exon (NM_153412, exon 16 of 18)"	-8441	NM_172511	213012	Mm.247453	NM_001272070		Abhd10	-	abhydrolase domain containing 10	protein-coding	0.05	0.405941
Merged-chr14-11230830-1	chr14	11230780	11230880	+	1.8	cIP2vsInput	Intergenic	Intergenic	-68798	NM_010210	14198	Mm.441926	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding	0	0.306931
Merged-chr13-62049423-1	chr13	62049373	62049473	+	1.8	cIP2vsInput	Intergenic	MMSAT4|Satellite|Satellite	-80467	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 80	protein-coding	0	0.356436
Merged-chr10-50219639-1	chr10	50219589	50219689	+	1.8	cIP2vsInput	Intergenic	Intergenic	-373030	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.01	0.287129
Merged-chr8-51849635-1	chr8	51849585	51849685	+	1.8	cIP2vsInput	Intergenic	Lx9|LINE|L1	1481523	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.386139
Merged-chr18-85706693-1	chr18	85706643	85706743	+	1.8	cIP2vsInput	Intergenic	Intergenic	-688259	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding	0	0.316832
Merged-chr1-144320434-1	chr1	144320384	144320484	+	1.8	cIP2vsInput	Intergenic	Intergenic	-71330	NM_015811	50778	Mm.103701	NM_015811	ENSMUSG00000026358	Rgs1	BL34	regulator of G-protein signaling 1	protein-coding	0	0.29703
Merged-chr3-19858372-1	chr3	19858322	19858422	+	1.8	cIP2vsInput	Intergenic	(TTCA)n|Simple_repeat|Simple_repeat	-36499	NR_027985	70808	Mm.487101	NR_027985		4632415L05Rik	AI662792	RRS1 ribosome biogenesis regulator homolog pseudogene	pseudo	0	0.356436
Merged-chr15-13916814-1	chr15	13916764	13916864	+	1.8	cIP2vsInput	Intergenic	AT_rich|Low_complexity|Low_complexity	-743175	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	K-cadherin|cad6|cadherin-6	cadherin 6	protein-coding	0	0.19802
Merged-chr16-66138591-1	chr16	66138541	66138641	+	1.8	cIP2vsInput	Intergenic	Intergenic	322958	NM_028572	73569	Mm.482366	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like 3 (Drosophila)	protein-coding	0.01	0.386139
Merged-chr8-42485814-1	chr8	42485764	42485864	+	1.8	cIP2vsInput	Intergenic	Intergenic	655672	NM_177742	244448	Mm.64542	NM_177742	ENSMUSG00000031651	Triml1	4933403D14|BC050188	tripartite motif family-like 1	protein-coding	0	0.346535
Merged-chr2-111647773-1	chr2	111647723	111647823	+	1.8	cIP1vsInput	Intergenic	Intergenic	-1778	NM_146886	258888	Mm.377735	NM_146886	ENSMUSG00000096853	Olfr1298	MOR248-6	olfactory receptor 1298	protein-coding	0	0.29703
Merged-chr6-11972063-1	chr6	11972013	11972113	+	1.8	cIP2vsInput	"intron (NM_001168382, intron 7 of 17)"	L1_Mus1|LINE|L1	46182	NM_001168382	75725	Mm.212411	NM_001168382	ENSMUSG00000029629	Phf14	1110001C23Rik|4932409F11Rik|5730446A07Rik|AA623952|AV297001|mKIAA0783	PHD finger protein 14	protein-coding	0	0.366337
Merged-chrX-33063047-1	chrX	33062997	33063097	+	1.8	cIP2vsInput	Intergenic	L1VL4|LINE|L1	6761	NR_040388	100040552	Mm.416917	NR_040388		Gm2837	-	"spindlin family, member 2 pseudogene"	pseudo	0	0.306931
Merged-chr3-7695192-1	chr3	7695142	7695242	+	1.8	cIP2vsInput	Intergenic	Intergenic	-81765	NM_008371	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding	0	0.356436
Merged-chrX-156277678-1	chrX	156277628	156277728	+	1.8	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-261805	NR_033598	74941	Mm.484588	NR_033598		4930503H13Rik	-	gem (nuclear organelle) associated protein 8 pseudogene	pseudo	0.01	0.336634
Merged-chr15-56936714-1	chr15	56936664	56936764	+	1.8	cIP2vsInput	Intergenic	Intergenic	-242168	NM_008216	15117	Mm.5148	NM_008216	ENSMUSG00000022367	Has2	-	hyaluronan synthase 2	protein-coding	0	0.386139
Merged-chr17-91637980-1	chr17	91637930	91638030	+	1.8	cIP2vsInput	Intergenic	Intergenic	-545178	NM_020252	18189	Mm.312068	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding	0	0.376238
Merged-chrX-131544624-1	chrX	131544574	131544674	+	1.8	cIP2vsInput	Intergenic	L1M4|LINE|L1	1794882	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diap2	Dia3|Diaph2|Drf2|E430022I22Rik	diaphanous homolog 2 (Drosophila)	protein-coding	0	0.336634
Merged-chr1-184201748-1	chr1	184201698	184201798	+	1.8	cIP2vsInput	Intergenic	Intergenic	167287	NM_022019	63953	Mm.404024	NM_022019	ENSMUSG00000039384	Dusp10	2610306G15Rik|AI158871|MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0	0.257426
Merged-chrX-64788964-1	chrX	64788914	64789014	+	1.8	cIP2vsInput	Intergenic	Intergenic	-258680	NM_027302	70062	Mm.45791	NM_027302	ENSMUSG00000031181	Ctag2	1700030B21Rik	cancer/testis antigen 2	protein-coding	0	0.287129
Merged-chr14-112494360-1	chr14	112494310	112494410	+	1.8	cIP2vsInput	Intergenic	Lx2B2|LINE|L1	472930	NR_030150	723922		NR_030150		Mir466	Mirn466|mmu-mir-466	microRNA 466	miscRNA	0.01	0.306931
Merged-chrX-116877266-1	chrX	116877216	116877316	+	1.8	cIP2vsInput	Intergenic	Intergenic	-137491	NM_001102665	100039319	Mm.469831	NM_001102665		Gm14920	ENSMUSG00000067441|Gm1539|H2A.Bbd1|OTTMUSG00000018481	predicted pseudogene 14920	protein-coding	0	0.306931
Merged-chr12-48378542-1	chr12	48378492	48378592	+	1.8	cIP2vsInput	Intergenic	B2_Mm2|SINE|B2	-77080	NR_039586	100628593		NR_039586		Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	miscRNA	0	0.415842
Merged-chr16-76498432-1	chr16	76498382	76498482	+	1.8	cIP2vsInput	Intergenic	MIRb|SINE|MIR	-125383	NM_173440	268903	Mm.455873	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding	0	0.306931
Merged-chr5-58314482-1	chr5	58314432	58314532	+	1.8	cIP1vsInput	Intergenic	Intergenic	138516	NR_046190	78163	Mm.243828	NR_046190		4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	miscRNA	0	0.366337
Merged-chr12-29049169-1	chr12	29049119	29049219	+	1.8	cIP2vsInput	Intergenic	Intergenic	297341	NM_201357	380752	Mm.273724	NM_201357	ENSMUSG00000036613	Tssc1	D12Ertd604e	tumor suppressing subtransferable candidate 1	protein-coding	0.02	0.485149
Merged-chr9-91711746-1	chr9	91711696	91711796	+	1.8	cIP2vsInput	Intergenic	Intergenic	342774	NM_009576	22774	Mm.434835	NM_009576		Zic4	-	zinc finger protein of the cerebellum 4	protein-coding	0.01	0.306931
Merged-chr9-6116686-1	chr9	6116636	6116736	+	1.8	cIP2vsInput	Intergenic	Intergenic	-51926	NM_027924	71785	Mm.390122	NM_027924	ENSMUSG00000032006	Pdgfd	1110003I09Rik	"platelet-derived growth factor, D polypeptide"	protein-coding	0	0.366337
Merged-chr8-39738098-1	chr8	39738048	39738148	+	1.8	cIP2vsInput	"intron (NR_035426, intron 3 of 5)"	ORR1G|LTR|ERVL-MaLR	-95420	NM_001113326	20288	Mm.239291	NM_001113326	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding	0	0.316832
Merged-chr1-67863270-1	chr1	67863220	67863320	+	1.8	cIP2vsInput	Intergenic	Intergenic	740204	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding	0	0.306931
Merged-chr9-119226109-1	chr9	119226059	119226159	+	1.8	cIP2vsInput	"intron (NR_033303, intron 2 of 5)"	ETnERV2-int|LTR|ERVK	5583	NR_033303	109280	Mm.261557	NM_175420	ENSMUSG00000092212	Slc22a13b-ps	9330176C04Rik|Slc22a13b	"solute carrier family 22 (organic cation transporter), member 13b, pseudogene"	pseudo	0	0.326733
Merged-chr14-58244066-1	chr14	58244016	58244116	+	1.8	cIP2vsInput	Intergenic	L1MA4|LINE|L1	171380	NM_013518	14180	Mm.8846	NM_013518		Fgf9	Eks	fibroblast growth factor 9	protein-coding	0	0.306931
Merged-chr9-89926746-1	chr9	89926696	89926796	+	1.8	cIP2vsInput	"intron (NM_011245, intron 2 of 26)"	"intron (NM_011245, intron 2 of 26)"	16971	NM_001039655	19417	Mm.44561	NM_001039655	ENSMUSG00000032356	Rasgrf1	AI844718|CDC25|CDC25Mm|Grf1|Grfbeta|P190-A|Ras-GRF1|p190|p190RhoGEF	RAS protein-specific guanine nucleotide-releasing factor 1	protein-coding	0.02	0.336634
Merged-chr1-172700617-1	chr1	172700567	172700667	+	1.8	cIP2vsInput	TTS (NM_007768)	TTS (NM_007768)	2561	NM_007768	12944	Mm.28767	NM_007768	ENSMUSG00000037942	Crp	AI255847	"C-reactive protein, pentraxin-related"	protein-coding	0	0.386139
Merged-chr8-57042830-1	chr8	57042780	57042880	+	1.8	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-278153	NM_010402	15111	Mm.430844	NM_010402	ENSMUSG00000038193	Hand2	AI225906|AI661148|Ehand2|Hed|Th2|Thing2|bHLHa26|dHAND	heart and neural crest derivatives expressed transcript 2	protein-coding	0	0.316832
Merged-chr1-50120599-1	chr1	50120549	50120649	+	1.8	cIP2vsInput	Intergenic	Intergenic	-806924	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.356436
Merged-chr2-22108415-1	chr2	22108365	22108465	+	1.8	cIP2vsInput	Intergenic	Lx7|LINE|L1	-119088	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding	0	0.346535
Merged-chrX-99310859-1	chrX	99310809	99310909	+	1.8	cIP2vsInput	Intergenic	Lx4B|LINE|L1	132938	NR_033544	100038584	Mm.368385	NR_033544	ENSMUSG00000073051	Gm14812	ENSMUSG00000073051|OTTMUSG00000018066	predicted gene 14812	miscRNA	0	0.366337
Merged-chr5-98286247-1	chr5	98286197	98286297	+	1.8	cIP2vsInput	Intergenic	Intergenic	32063	NM_010203	14176	Mm.5055	NM_001277268	ENSMUSG00000029337	Fgf5	Fgf-5|HBGF-5|angora|go	fibroblast growth factor 5	protein-coding	0.01	0.39604
Merged-chr1-26998179-1	chr1	26998129	26998229	+	1.8	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-310719	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding	0	0.306931
Merged-chr6-9516123-1	chr6	9516073	9516173	+	1.8	cIP2vsInput	Intergenic	L1VL1|LINE|L1	566104	NM_008751	18231	Mm.46954	NM_008751		Nxph1	C130005L03Rik	neurexophilin 1	protein-coding	0.01	0.326733
Merged-chr3-3412344-1	chr3	3412294	3412394	+	1.8	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-95686	NM_013920	30942	Mm.330897	NM_013920		Hnf4g	NR2A2	"hepatocyte nuclear factor 4, gamma"	protein-coding	0	0.306931
Merged-chr4-111841312-1	chr4	111841262	111841362	+	1.8	cIP2vsInput	Intergenic	Intergenic	61484	NM_145551	230612	Mm.26630	NM_145551	ENSMUSG00000028544	Slc5a9	AI159731|SGLT4	"solute carrier family 5 (sodium/glucose cotransporter), member 9"	protein-coding	0.02	0.326733
Merged-chr1-29472910-1	chr1	29472860	29472960	+	1.8	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-692658	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding	0	0.366337
Merged-chr1-9173034-1	chr1	9172984	9173084	+	1.8	cIP2vsInput	"intron (NM_027671, intron 2 of 20)"	"intron (NM_027671, intron 2 of 20)"	126696	NM_027671	71096	Mm.388998	NM_027671		Sntg1	4933426D16Rik|G1SYN|SYN4	"syntrophin, gamma 1"	protein-coding	0	0.29703
Merged-chr2-174091336-1	chr2	174091286	174091386	+	1.8	cIP2vsInput	"intron (NM_001102423, intron 2 of 7)"	"intron (NM_001102423, intron 2 of 7)"	14285	NM_001102423	228960	Mm.277977	NM_001102423	ENSMUSG00000027522	Stx16	4930401D03|5430410K23Rik|6330500A18Rik|AI648908|AW553605|Syn16	syntaxin 16	protein-coding	0.01	0.405941
Merged-chr4-115323549-1	chr4	115323499	115323599	+	1.8	cIP2vsInput	"intron (NM_177406, intron 4 of 11)"	L1_Mur3|LINE|L1	24503	NM_177406	277753	Mm.276106	NM_177406	ENSMUSG00000066071	Cyp4a12a	BC025936|Cyp4a12	"cytochrome P450, family 4, subfamily a, polypeptide 12a"	protein-coding	0.01	0.366337
Merged-chr15-18128975-1	chr15	18128925	18129025	+	1.8	cIP2vsInput	"intron (NR_045711, intron 9 of 11)"	"intron (NR_045711, intron 9 of 11)"	240652	NR_045711	70886	Mm.399021	NR_045711		4921515E04Rik	-	RIKEN cDNA 4921515E04 gene	miscRNA	0	0.306931
Merged-chr7-118822411-1	chr7	118822361	118822461	+	1.8	cIP2vsInput	"intron (NM_027815, intron 26 of 30)"	Lx8|LINE|L1	33202	NM_001168220	66356	Mm.482278	NM_001168218	ENSMUSG00000030980	Knop1	2310008H09Rik|Tsg118	lysine rich nucleolar protein 1	protein-coding	0.01	0.39604
Merged-chrX-139874867-1	chrX	139874817	139874917	+	1.8	cIP2vsInput	Intergenic	Intergenic	-3213	NM_001193309	75746		NM_001193309	ENSMUSG00000031434	Morc4	1600017G11Rik|5630401M14Rik|AA117449|Zcwcc2	microrchidia 4	protein-coding	0	0.306931
Merged-chr14-39665288-1	chr14	39665238	39665338	+	1.8	cIP2vsInput	"intron (NR_045936, intron 2 of 3)"	"intron (NR_045936, intron 2 of 3)"	9625	NR_045936	73591	Mm.65499	NR_045936		1700109I08Rik	-	RIKEN cDNA 1700109I08 gene	miscRNA	0	0.316832
Merged-chr2-76144295-1	chr2	76144245	76144345	+	1.8	cIP2vsInput	"intron (NM_001081033, intron 6 of 19)"	Lx9|LINE|L1	-162328	NM_030188	78802	Mm.282339	NM_030188	ENSMUSG00000075271	Ttc30a1	4930506L13Rik	tetratricopeptide repeat domain 30A1	protein-coding	0	0.386139
Merged-chr8-62394579-1	chr8	62394529	62394629	+	1.8	cIP2vsInput	Intergenic	Intergenic	-271461	NM_011922	26359	Mm.42179	NM_001136089	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding	0	0.346535
Merged-chr2-127453695-1	chr2	127453645	127453745	+	1.8	cIP2vsInput	Intergenic	Intergenic	-9130	NM_029629	68126	Mm.288676	NM_029629	ENSMUSG00000027371	Fahd2a	1500003K14Rik|B430104H02Rik|Cgi-105|Fahd2	fumarylacetoacetate hydrolase domain containing 2A	protein-coding	0	0.475248
Merged-chrX-57467223-1	chrX	57467173	57467273	+	1.8	cIP2vsInput	"intron (NM_001128625, intron 14 of 16)"	"intron (NM_001128625, intron 14 of 16)"	36534	NM_001033360	245424	Mm.336070	NM_001033360	ENSMUSG00000036357	Gpr101	GPCR6|Gm365	G protein-coupled receptor 101	protein-coding	0.01	0.29703
Merged-chr15-92560348-1	chr15	92560298	92560398	+	1.8	cIP2vsInput	"intron (NM_001164593, intron 3 of 9)"	"intron (NM_001164593, intron 3 of 9)"	-36761	NM_001164594	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding	0.01	0.356436
Merged-chr17-15601884-1	chr17	15601834	15601934	+	1.8	cIP2vsInput	Intergenic	Intergenic	-29904	NR_045431	71008	Mm.399492	NR_045431		4933401D09Rik	-	RIKEN cDNA 4933401D09 gene	miscRNA	0	0.336634
Merged-chrX-123103938-1	chrX	123103888	123103988	+	1.8	cIP2vsInput	"intron (NM_028426, intron 1 of 3)"	MMERVK10C-int|LTR|ERVK	379	NM_028426	73061	Mm.292979	NM_028426		3110007F17Rik	-	RIKEN cDNA 3110007F17 gene	protein-coding	0.08	0.544554
Merged-chr5-5868796-1	chr5	5868746	5868846	+	1.8	cIP2vsInput	Intergenic	Intergenic	-119479	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding	0.01	0.306931
Merged-chr2-81759168-1	chr2	81759118	81759218	+	1.8	cIP2vsInput	Intergenic	Intergenic	-294490	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding	0	0.29703
Merged-chrX-117837154-1	chrX	117837104	117837204	+	1.8	cIP2vsInput	Intergenic	Intergenic	-590073	NM_001142750	100039551	Mm.423457	NM_001142750	ENSMUSG00000063242	Tgif2lx2	-	"TGFB-induced factor homeobox 2-like, X-linked 2"	protein-coding	0	0.287129
Merged-chr14-95900660-1	chr14	95900610	95900710	+	1.8	cIP2vsInput	Intergenic	Intergenic	19394	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding	0.01	0.29703
Merged-chrX-137180243-1	chrX	137180193	137180293	+	1.8	cIP2vsInput	Intergenic	Intergenic	-59917	NM_007957	13984	Mm.8017	NM_007957	ENSMUSG00000023443	Esx1	Spx1	"extraembryonic, spermatogenesis, homeobox 1"	protein-coding	0	0.29703
Merged-chr2-36368410-1	chr2	36368360	36368460	+	1.8	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-8368	NM_146947	258949	Mm.377765	NM_146947	ENSMUSG00000068950	Olfr338	MOR136-5	olfactory receptor 338	protein-coding	0	0.306931
Merged-chr9-23666659-1	chr9	23666609	23666709	+	1.8	cIP2vsInput	Intergenic	Intergenic	-431359	NM_175678	319239	Mm.130824	NM_175678	ENSMUSG00000043659	Npsr1	9330128H10Rik|GPRA|Gpr154|MVTR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0	0.29703
Merged-chr17-59560776-1	chr17	59560726	59560826	+	1.8	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-547454	NM_026497	67993	Mm.36507	NM_026497		Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding	0	0.336634
Merged-chr5-38841876-1	chr5	38841826	38841926	+	1.8	cIP2vsInput	"intron (NM_013748, intron 2 of 18)"	"intron (NM_013748, intron 2 of 18)"	34817	NM_013748	27278	Mm.440845	NM_013748	ENSMUSG00000039315	Clnk	MIST	cytokine-dependent hematopoietic cell linker	protein-coding	0	0.326733
Merged-chr10-116031839-1	chr10	116031789	116031889	+	1.8	cIP2vsInput	"intron (NM_011217, intron 1 of 13)"	"intron (NM_011217, intron 1 of 13)"	13476	NM_011217	19279	Mm.336316	NM_001161837	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	"protein tyrosine phosphatase, receptor type, R"	protein-coding	0	0.326733
Merged-chr18-73405416-1	chr18	73405366	73405466	+	1.8	cIP2vsInput	Intergenic	Intergenic	-167289	NM_001039214	240396	Mm.436942	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 homolog C (C. elegans)	protein-coding	0.01	0.356436
Merged-chr8-49979311-1	chr8	49979261	49979361	+	1.8	cIP2vsInput	Intergenic	Lx7|LINE|L1	-388801	NR_046067	100039954	Mm.400419	NR_046067		Gm2516	-	predicted gene 2516	miscRNA	0	0.29703
Merged-chr15-28760952-1	chr15	28760902	28761002	+	1.8	cIP2vsInput	Intergenic	Intergenic	557186	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnahc5	AU022615|Dnah5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	"dynein, axonemal, heavy chain 5"	protein-coding	0	0.326733
Merged-chr15-70363219-1	chr15	70363169	70363269	+	1.8	cIP1vsInput	Intergenic	Intergenic	438986	NR_045071	100503580	Mm.404646	NR_045071		Gm19782	-	"predicted gene, 19782"	miscRNA	0	0.326733
Merged-chr13-52712200-1	chr13	52712150	52712250	+	1.8	cIP2vsInput	Intergenic	Intergenic	45005	NR_027893	105404	Mm.184173	NR_027893		BB123696	-	expressed sequence BB123696	miscRNA	0.01	0.524752
Merged-chrX-89332882-1	chrX	89332832	89332932	+	1.8	cIP2vsInput	Intergenic	Intergenic	76807	NM_008821	18630	Mm.3086	NM_008821	ENSMUSG00000035395	Pet2	PC231|PC326|Pex3	plasmacytoma expressed transcript 2	protein-coding	0	0.306931
Merged-chr10-11472979-1	chr10	11472929	11473029	+	1.8	cIP2vsInput	Intergenic	RMER17C-int|LTR|ERVK	129534	NM_010146	13853	Mm.89946	NM_010146		Epm2a	"TG-B|Tg(TcraK,TcrbK)TG-BFlv"	"epilepsy, progressive myoclonic epilepsy, type 2 gene alpha"	protein-coding	0.01	0.316832
Merged-chr12-12148377-1	chr12	12148327	12148427	+	1.8	cIP2vsInput	Intergenic	Intergenic	-113762	NM_029758	76820	Mm.440802	NM_001146119	ENSMUSG00000020589	Fam49a	2410157M17Rik|9630047E15|D12Ertd553e	"family with sequence similarity 49, member A"	protein-coding	0	0.376238
Merged-chr7-89748601-1	chr7	89748551	89748651	+	1.8	cIP2vsInput	"intron (NM_181407, intron 3 of 13)"	"intron (NM_181407, intron 3 of 13)"	115783	NM_181407	109264	Mm.334011	NM_181407	ENSMUSG00000030621	Me3	1700020C08Rik|B230207H15Rik	"malic enzyme 3, NADP(+)-dependent, mitochondrial"	protein-coding	0.02	0.485149
Merged-chr9-18197417-1	chr9	18197367	18197467	+	1.8	cIP2vsInput	Intergenic	Intergenic	-94850	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	"cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1"	protein-coding	0	0.29703
Merged-chr11-18178154-1	chr11	18178104	18178204	+	1.8	cIP2vsInput	Intergenic	L1VL4|LINE|L1	-224279	NM_026576	68145	Mm.178684	NM_026576	ENSMUSG00000016984	Etaa1	5730466H23Rik|AA672646	Ewing's tumor-associated antigen 1	protein-coding	0.01	0.29703
Merged-chr1-55363404-1	chr1	55363354	55363454	+	1.8	cIP2vsInput	promoter-TSS (NM_001113367)	promoter-TSS (NM_001113367)	65	NM_029267	75388	Mm.483408	NM_001113367	ENSMUSG00000025977	Boll	4930554P13Rik|4930597B14Rik	"bol, boule-like (Drosophila)"	protein-coding	0.17	0.752475
Merged-chrX-130714498-1	chrX	130714448	130714548	+	1.8	cIP2vsInput	Intergenic	Lx|LINE|L1	964756	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diap2	Dia3|Diaph2|Drf2|E430022I22Rik	diaphanous homolog 2 (Drosophila)	protein-coding	0	0.336634
Merged-chr6-89704451-1	chr6	89704401	89704501	+	1.8	cIP2vsInput	Intergenic	Lx|LINE|L1	-9752	NM_053228	113855	Mm.377152	NM_053228	ENSMUSG00000096051	Vmn1r40	V1rb7	vomeronasal 1 receptor 40	protein-coding	0	0.336634
Merged-chr1-111698959-1	chr1	111698909	111699009	+	1.8	cIP2vsInput	Intergenic	Intergenic	165959	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik	dermatan sulfate epimerase-like	protein-coding	0	0.346535
Merged-chr2-98088416-1	chr2	98088366	98088466	+	1.8	cIP2vsInput	Intergenic	Intergenic	620742	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.316832
Merged-chr1-49300202-1	chr1	49300152	49300252	+	1.8	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-1627321	NM_019790	56363	Mm.445120	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding	0	0.326733
Merged-chr12-27816096-1	chr12	27816046	27816146	+	1.8	cIP2vsInput	Intergenic	Lx2B2|LINE|L1	-473378	NM_009234	20666	Mm.466344	NM_009234		Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY-box containing gene 11	protein-coding	0	0.376238
Merged-chr17-60798716-1	chr17	60798666	60798766	+	1.8	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-519036	NR_030569	100124495		NR_030569		Mir466g	Mirn466g	microRNA 466g	miscRNA	0	0.376238
Merged-chr11-54585022-1	chr11	54584972	54585072	+	1.8	cIP2vsInput	"intron (NM_001252494, intron 6 of 28)"	B1_Mur1|SINE|Alu	-11124	NM_001252498	192786	Mm.254404	NM_001252494	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding	0	0.336634
Merged-chr7-23981980-1	chr7	23981930	23982030	+	1.8	cIP2vsInput	Intergenic	Intergenic	-1981	NM_207546	404289	Mm.279185	NM_207546	ENSMUSG00000057946	Vmn1r181	V1rd20	vomeronasal 1 receptor 181	protein-coding	0	0.316832
Merged-chr2-98948966-1	chr2	98948916	98949016	+	1.8	cIP2vsInput	Intergenic	Intergenic	1481292	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.267327
Merged-chr2-89070562-1	chr2	89070512	89070612	+	1.8	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	4527	NM_146899	258901	Mm.377742	NM_146899	ENSMUSG00000075104	Olfr1219	MOR233-6	olfactory receptor 1219	protein-coding	0	0.346535
Merged-chr8-77864002-1	chr8	77863952	77864052	+	1.8	cIP2vsInput	Intergenic	Intergenic	-139550	NM_010332	13617	Mm.392296	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding	0	0.39604
Merged-chr3-19444186-1	chr3	19444136	19444236	+	1.8	cIP2vsInput	Intergenic	L1_Rod|LINE|L1	-64409	NM_001163536	66326	Mm.45615	NM_001163536	ENSMUSG00000027606	Dnajc5b	1700008A05Rik	"DnaJ (Hsp40) homolog, subfamily C, member 5 beta"	protein-coding	0	0.267327
Merged-chr4-56562298-1	chr4	56562248	56562348	+	1.8	cIP2vsInput	Intergenic	Lx5|LINE|L1	179127	NM_025271	11471	Mm.251434	NM_025271	ENSMUSG00000070980	Actl7b	Tact1	actin-like 7b	protein-coding	0	0.376238
Merged-chr3-104114962-1	chr3	104114912	104115012	+	1.8	cIP2vsInput	"intron (NM_133853, intron 1 of 21)"	"intron (NM_133853, intron 1 of 21)"	105444	NM_133853	99470	Mm.264849	NM_001159354	ENSMUSG00000052539	Magi3	4732496O19Rik|6530407C02Rik|AA407180|AI120132|mKIAA1634	"membrane associated guanylate kinase, WW and PDZ domain containing 3"	protein-coding	0	0.227723
Merged-chr10-24559467-1	chr10	24559417	24559517	+	1.8	cIP2vsInput	Intergenic	Intergenic	-35975	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding	0	0.287129
Merged-chr8-75254295-1	chr8	75254245	75254345	+	1.8	cIP1vsInput	Intergenic	Intergenic	40351	NM_029182	75141	Mm.179267	NM_029182	ENSMUSG00000034472	Rasd2	4930526B11Rik|AU045414|Rhes|TEM-2|TEM2	"RASD family, member 2"	protein-coding	0	0.415842
Merged-chr9-90645944-1	chr9	90645894	90645994	+	1.8	cIP2vsInput	Intergenic	Lx5b|LINE|L1	-375175	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	"TBC1 domain family, member 2B"	protein-coding	0	0.336634
Merged-chrX-115588629-1	chrX	115588579	115588679	+	1.8	cIP2vsInput	Intergenic	Intergenic	681047	NM_001081661	75097	Mm.50414	NM_001081661	ENSMUSG00000047079	Ube2dnl2	4930524E20Rik	ubiquitin-conjugating enzyme E2D N-terminal like 2	protein-coding	0	0.306931
Merged-chr19-51777229-1	chr19	51777179	51777279	+	1.8	cIP2vsInput	Intergenic	Intergenic	-487094	NM_008386	16333	Mm.46269	NM_008386	ENSMUSG00000035804	Ins1	Ins-1|Ins2-rs1	insulin I	protein-coding	0	0.356436
Merged-chrX-146205036-1	chrX	146204986	146205086	+	1.8	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-717990	NM_153319	27494	Mm.100068	NM_153319	ENSMUSG00000041688	Amot	C81439|CAG-2|D0Kist1|E230009N18Rik|Sii6|mKIAA1071	angiomotin	protein-coding	0.02	0.346535
Merged-chrX-41818232-1	chrX	41818182	41818282	+	1.8	cIP2vsInput	"intron (NM_001033422, intron 30 of 38)"	L1MA4|LINE|L1	93669	NM_001033422	331401	Mm.259498	NM_001033422	ENSMUSG00000037475	Thoc2	6330441O12Rik|D130005M13Rik|Gm1139|Gm1793|Tho2	THO complex 2	protein-coding	0	0.326733
Merged-chr15-90535267-1	chr15	90535217	90535317	+	1.8	cIP2vsInput	"intron (NM_025815, intron 13 of 19)"	"intron (NM_025815, intron 13 of 19)"	144121	NM_025815	66871	Mm.290991	NM_001033851	ENSMUSG00000052560	Cpne8	1200003E11Rik|1500031E20Rik	copine VIII	protein-coding	0	0.405941
Merged-chr1-111000653-1	chr1	111000603	111000703	+	1.8	cIP2vsInput	Intergenic	Intergenic	-23281	NM_001081386	227485	Mm.322070	NM_001081386	ENSMUSG00000047216	Cdh19	-	"cadherin 19, type 2"	protein-coding	0	0.336634
Merged-chr1-130855792-1	chr1	130855742	130855842	+	1.8	cIP2vsInput	Intergenic	Intergenic	-9985	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Faim3	1810037B05Rik|FcmuR|Toso	Fas apoptotic inhibitory molecule 3	protein-coding	0	0.366337
Merged-chr16-48062339-1	chr16	48062289	48062389	+	1.8	cIP2vsInput	Intergenic	Intergenic	-221396	NM_028610	73693	Mm.35597	NM_001018002	ENSMUSG00000058550	Dppa4	2410091M23Rik|C76608|ECAT15-1	developmental pluripotency associated 4	protein-coding	0.01	0.405941
Merged-chr3-133273034-1	chr3	133272984	133273084	+	1.8	cIP2vsInput	Intergenic	L1MC|LINE|L1	-37082	NM_146141	74776	Mm.210305	NM_146141	ENSMUSG00000028013	Ppa2	1110013G13Rik|Sid6306	pyrophosphatase (inorganic) 2	protein-coding	0.01	0.316832
Merged-chr18-87271120-1	chr18	87271070	87271170	+	1.8	cIP2vsInput	Intergenic	L1ME1|LINE|L1	558072	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding	0	0.326733
Merged-chrY-6088006-1	chrY	6087956	6088056	+	1.8	cIP2vsInput	Intergenic	ORR1C2|LTR|ERVL-MaLR	1079771	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	"predicted gene, 20826"	protein-coding	0.01	0.39604
Merged-chr2-126144858-1	chr2	126144808	126144908	+	1.8	cIP1vsInput	"intron (NM_029455, intron 2 of 16)"	"intron (NM_029455, intron 2 of 16)"	7146	NM_029455	75823	Mm.444732	NM_029455	ENSMUSG00000027209	Fam227b	4930525F21Rik	"family with sequence similarity 227, member B"	protein-coding	0	0.336634
Merged-chr7-19790242-1	chr7	19790192	19790292	+	1.8	cIP2vsInput	"intron (NM_023224, intron 5 of 11)"	"intron (NM_023224, intron 5 of 11)"	6567	NM_001161844	80794	Mm.81698	NM_001161844	ENSMUSG00000040525	Cblc	2310076I21Rik|2310079L19Rik|Cbl3	Casitas B-lineage lymphoma c	protein-coding	0.06	0.633663
Merged-chr13-66797773-1	chr13	66797723	66797823	+	1.8	cIP2vsInput	Intergenic	Lx4B|LINE|L1	107577	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding	0.01	0.49505
Merged-chr11-32298790-1	chr11	32298740	32298840	+	1.8	cIP2vsInput	Intergenic	Intergenic	-1279	NM_175000	216635	Mm.338482	NM_175000	ENSMUSG00000020295	Hbq1a	A230090E05Rik|Gm876|Hbq1|Hbqt2	"hemoglobin, theta 1A"	protein-coding	0	0.425743
Merged-chr6-105250324-1	chr6	105250274	105250374	+	1.8	cIP2vsInput	Intergenic	Intergenic	242344	NR_040297	100503536	Mm.366960	NR_040297		Gm19757	-	"predicted gene, 19757"	miscRNA	0	0.326733
Merged-chr6-3795881-1	chr6	3795831	3795931	+	1.8	cIP2vsInput	Intergenic	MLT1F1|LTR|ERVL-MaLR	-31168	NM_007588	12311	Mm.4642	NM_001042725	ENSMUSG00000023964	Calcr	Clr	calcitonin receptor	protein-coding	0	0.326733
Merged-chr14-75236257-1	chr14	75236207	75236307	+	1.8	cIP2vsInput	"intron (NR_030568, intron 2 of 3)"	"intron (NR_030568, intron 2 of 3)"	-6030	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding	0.03	0.326733
Merged-chr4-14986649-1	chr4	14986599	14986699	+	1.8	cIP2vsInput	"intron (NM_178617, intron 7 of 12)"	"intron (NM_178617, intron 7 of 12)"	56008	NM_001243100	100038514	Mm.331495	NM_001243100		Gm11837	OTTMUSG00000004551	predicted gene 11837	protein-coding	0	0.306931
Merged-chr12-62957059-1	chr12	62957009	62957109	+	1.8	cIP2vsInput	Intergenic	Lx3A|LINE|L1	1432427	NM_178714	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0	0.326733
Merged-chr4-66908399-1	chr4	66908349	66908449	+	1.8	cIP2vsInput	Intergenic	Intergenic	80588	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding	0	0.346535
Merged-chr16-72025012-1	chr16	72024962	72025062	+	1.8	cIP2vsInput	Intergenic	Intergenic	-638137	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout homolog 1 (Drosophila)	protein-coding	0	0.29703
Merged-chr4-71703490-1	chr4	71703440	71703540	+	1.8	cIP2vsInput	Intergenic	Intergenic	497429	NM_011599	21885	Mm.399716	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg1|Tle4l	"transducin-like enhancer of split 1, homolog of Drosophila E(spl)"	protein-coding	0.02	0.366337
Merged-chr9-105520530-1	chr9	105520480	105520580	+	1.8	cIP2vsInput	"intron (NM_001253831, intron 1 of 26)"	"intron (NM_001253831, intron 1 of 26)"	727	NM_001253831	235574	Mm.489853	NM_001253831	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	"ATPase, Ca++-sequestering"	protein-coding	0	0.346535
Merged-chr17-38869329-1	chr17	38869279	38869379	+	1.8	cIP2vsInput	Intergenic	Lx5|LINE|L1	-167366	NM_001256050	100126776	Mm.471588	NM_001256050		Gm21947	Esp24	"predicted gene, 21947"	protein-coding	0	0.336634
Merged-chr3-114480735-1	chr3	114480685	114480785	+	1.8	cIP2vsInput	Intergenic	Intergenic	-382518	NR_030469	735255		NR_030469		Mir669b	Mirn669b	microRNA 669b	miscRNA	0.01	0.316832
Merged-chr1-53235272-1	chr1	53235222	53235322	+	1.8	cIP2vsInput	"intron (NM_153556, intron 5 of 12)"	L1VL4|LINE|L1	-47655	NM_027070	69397	Mm.307084	NM_027070	ENSMUSG00000060715	1700019A02Rik	-	RIKEN cDNA 1700019A02 gene	protein-coding	0.01	0.376238
Merged-chr4-133103795-1	chr4	133103745	133103845	+	1.8	cIP2vsInput	Intergenic	Intergenic	-26838	NM_153423	242687	Mm.23566	NM_153423		Wasf2	AW742646|D4Ertd13e|WAVE2	"WAS protein family, member 2"	protein-coding	0.04	0.613861
Merged-chr7-40126157-1	chr7	40126107	40126207	+	1.8	cIP2vsInput	Intergenic	L1MA4|LINE|L1	-548580	NR_045504	71029	Mm.399496	NR_045504		4933402C06Rik	-	RIKEN cDNA 4933402C06 gene	miscRNA	0	0.29703
Merged-chr15-20647636-1	chr15	20647586	20647686	+	1.8	cIP2vsInput	Intergenic	Intergenic	19114	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding	0	0.316832
Merged-chr17-20992017-1	chr17	20991967	20992067	+	1.8	cIP2vsInput	Intergenic	Intergenic	2669	NM_134202	171236	Mm.377192	NM_134202	ENSMUSG00000045575	Vmn1r233	V1rf5	vomeronasal 1 receptor 233	protein-coding	0.01	0.356436
Merged-chr1-110237038-1	chr1	110236988	110237088	+	1.8	cIP2vsInput	Intergenic	L1_Mur1|LINE|L1	253301	NM_172853	241201	Mm.487119	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	"cadherin 7, type 2"	protein-coding	0	0.306931
Merged-chr1-79795269-1	chr1	79795219	79795319	+	1.8	cIP2vsInput	"intron (NM_009255, intron 8 of 8)"	MER3|DNA|hAT-Charlie	19251	NM_001081210	69163	Mm.238455	NM_001081210	ENSMUSG00000026248	Mrpl44	1810030E18Rik|5730593H20Rik|AI463302	mitochondrial ribosomal protein L44	protein-coding	0.01	0.386139
Merged-chr3-128699972-1	chr3	128699922	128700022	+	1.8	cIP2vsInput	Intergenic	Intergenic	-468367	NR_045704	402774	Mm.209170	NR_045704		D030025E07Rik	-	RIKEN cDNA D030025E07 gene	miscRNA	0.01	0.346535
Merged-chr8-59832710-1	chr8	59832660	59832760	+	1.8	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-673414	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|mKat-2	aminoadipate aminotransferase	protein-coding	0	0.306931
Merged-chr8-104207879-1	chr8	104207829	104207929	+	1.8	cIP2vsInput	"intron (NM_001141924, intron 2 of 4)"	L1M4b|LINE|L1	37366	NM_001141925	65115	Mm.41849	NM_001141922	ENSMUSG00000031872	Bean1	Bean	"brain expressed, associated with Nedd4, 1"	protein-coding	0	0.376238
Merged-chr5-126392306-1	chr5	126392256	126392356	+	1.8	cIP2vsInput	Intergenic	Intergenic	-638483	NR_040685	71247	Mm.399586	NR_040685		4933438B17Rik	-	RIKEN cDNA 4933438B17 gene	miscRNA	0	0.306931
Merged-chr14-37992976-1	chr14	37992926	37993026	+	1.8	cIP2vsInput	Intergenic	Intergenic	-857654	NM_078478	66092	Mm.486242	NM_001199122	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010	growth hormone inducible transmembrane protein	protein-coding	0	0.356436
Merged-chr8-43906615-1	chr8	43906565	43906665	+	1.8	cIP2vsInput	Intergenic	Intergenic	-207124	NM_001079931	384814	Mm.383288	NM_001079931		Gm5347	EG384814	predicted gene 5347	protein-coding	0	0.336634
Merged-chr12-74619212-1	chr12	74619162	74619262	+	1.8	cIP1vsInput	Intergenic	MYSERV6-int|LTR|ERVK	321738	NM_198866	386753	Mm.395044	NM_198866	ENSMUSG00000029878	Dbpht2	Spot2	DNA binding protein with his-thr domain	protein-coding	0	0.29703
Merged-chr3-139703233-1	chr3	139703183	139703283	+	1.8	cIP2vsInput	"intron (NM_198659, intron 13 of 13)"	"intron (NM_198659, intron 13 of 13)"	497340	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding	0.03	0.376238
Merged-chr7-104771612-1	chr7	104771562	104771662	+	1.8	cIP2vsInput	"intron (NM_001256973, intron 1 of 2)"	"intron (NM_001256973, intron 1 of 2)"	5858	NM_001256973	625530	Mm.14130	NM_001256973		Usp17le	DUB-3|Dub3|Dub6|EG625530|Gm6596|USP17|Usp17l2	ubiquitin specific peptidase 17-like E	protein-coding	0	0.346535
Merged-chrX-114446868-1	chrX	114446818	114446918	+	1.8	cIP2vsInput	Intergenic	Lx8|LINE|L1	-27652	NM_172781	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding	0	0.39604
Merged-chr17-33323326-1	chr17	33323276	33323376	+	1.8	cIP2vsInput	Intergenic	L1_Mus4|LINE|L1	33782	NM_001142957	100043468	Mm.276296	NM_001142957		Zfp955b	A430003O12Rik|C430039G02Rik|C530035A18Rik|Gm4455|Zfp883b	zinc finger protein 955B	protein-coding	0.02	0.336634
Merged-chr14-74450990-1	chr14	74450940	74451040	+	1.8	cIP2vsInput	Intergenic	Intergenic	95463	NR_046059	74425	Mm.399498	NR_046059		4933402J15Rik	-	RIKEN cDNA 4933402J15 gene	miscRNA	0.01	0.376238
Merged-chr13-70982560-1	chr13	70982510	70982610	+	1.8	cIP2vsInput	Intergenic	Intergenic	99612	NM_029873	77166	Mm.159859	NM_029873	ENSMUSG00000021600	8030423J24Rik	-	RIKEN cDNA 8030423J24 gene	protein-coding	0	0.287129
Merged-chr13-16939454-1	chr13	16939404	16939504	+	1.8	cIP2vsInput	"intron (NM_138654, intron 13 of 13)"	"intron (NM_138654, intron 13 of 13)"	755311	NM_138654	192136	Mm.364180	NM_138654		5033411D12Rik	D17907	RIKEN cDNA 5033411D12 gene	protein-coding	0.01	0.356436
Merged-chr13-86274491-1	chr13	86274441	86274541	+	1.8	cIP2vsInput	Intergenic	L1_Mus3|LINE|L1	-227696	NM_007749	12867	Mm.378898	NM_007749		Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding	0	0.326733
Merged-chr1-187551665-1	chr1	187551615	187551715	+	1.8	cIP2vsInput	Intergenic	Intergenic	-57341	NM_001243792	26381	Mm.421613	NM_001243792	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding	0.02	0.356436
Merged-chr6-144823799-1	chr6	144823749	144823849	+	1.8	cIP2vsInput	Intergenic	Intergenic	150931	NR_040519	66760	Mm.233631	NR_040519	ENSMUSG00000085785	4933425H06Rik	-	RIKEN cDNA 4933425H06 gene	miscRNA	0.02	0.386139
Merged-chr4-47943850-1	chr4	47943800	47943900	+	1.8	cIP2vsInput	Intergenic	Intergenic	-107398	NM_015743	18124	Mm.487935	NM_015743		Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	"nuclear receptor subfamily 4, group A, member 3"	protein-coding	0	0.346535
Merged-chr5-79560920-1	chr5	79560870	79560970	+	1.8	cIP2vsInput	Intergenic	Intergenic	-45016	NR_035474	100316701		NR_035474		Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	miscRNA	0.01	0.346535
Merged-chrX-157460813-1	chrX	157460763	157460863	+	1.8	cIP2vsInput	"intron (NM_009214, intron 6 of 10)"	"intron (NM_009214, intron 6 of 10)"	31233	NM_009214	20603	Mm.18652	NM_009214	ENSMUSG00000071708	Sms	AI427066|Gy|SPMSY|SpmST|gyro	spermine synthase	protein-coding	0	0.39604
Merged-chr13-79260707-1	chr13	79260657	79260757	+	1.8	cIP2vsInput	Intergenic	Intergenic	-1061725	NM_010151	13865	Mm.439653	NM_010151		Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR3|Erbal3|SVP44|Tcfcoup1	"nuclear receptor subfamily 2, group F, member 1"	protein-coding	0	0.386139
Merged-chr1-95774476-1	chr1	95774426	95774526	+	1.8	cIP2vsInput	Intergenic	Intergenic	-57958	NR_040479	75381	Mm.417807	NR_040479		4930598F16Rik	-	RIKEN cDNA 4930598F16 gene	miscRNA	0	0.267327
Merged-chr18-21475846-1	chr18	21475796	21475896	+	1.8	cIP2vsInput	Intergenic	MER2|DNA|TcMar-Tigger	-175707	NM_001033445	381126	Mm.312276	NM_001033445	ENSMUSG00000042680	Garem	C86169|Fam59a|Gm944|mKIAA4238	"GRB2 associated, regulator of MAPK1"	protein-coding	0	0.39604
Merged-chr3-18379371-1	chr3	18379321	18379421	+	1.8	cIP2vsInput	Intergenic	Intergenic	101106	NR_040544	73959	Mm.60616	NR_040544		4930433B08Rik	-	RIKEN cDNA 4930433B08 gene	miscRNA	0.01	0.306931
Merged-chr3-92350861-1	chr3	92350811	92350911	+	1.8	cIP2vsInput	Intergenic	L1MA6|LINE|L1	-1282	NM_011471	20759	Mm.261596	NM_011471	ENSMUSG00000055030	Sprr2e	-	small proline-rich protein 2E	protein-coding	0	0.316832
Merged-chr13-66494257-1	chr13	66494207	66494307	+	1.8	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-53139	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding	0	0.267327
Merged-chr1-114174646-1	chr1	114174596	114174696	+	1.8	cIP2vsInput	Intergenic	MYSERV16_I-int|LTR|ERVK	-1510491	NM_001077425	636808	Mm.337385	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding	0	0.376238
Merged-chr6-145994070-1	chr6	145994020	145994120	+	1.8	cIP2vsInput	Intergenic	MLT1B|LTR|ERVL-MaLR	59923	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding	0	0.485149
Merged-chr13-64455448-1	chr13	64455398	64455498	+	1.8	cIP2vsInput	Intergenic	Intergenic	22895	NM_053180	105278	Mm.74982	NM_053180	ENSMUSG00000021483	Cdk20	4932702G04Rik|AU019450|AW558027|CDCH|Ccrk|PNQLARE|p42	cyclin-dependent kinase 20	protein-coding	0	0.326733
Merged-chr11-38900080-1	chr11	38900030	38900130	+	1.8	cIP2vsInput	Intergenic	Intergenic	-380035	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	OTTMUSG00000005424	predicted gene 12130	miscRNA	0	0.366337
Merged-chr2-89096340-1	chr2	89096290	89096390	+	1.8	cIP2vsInput	TTS (NM_146900)	TTS (NM_146900)	1623	NM_146900	258902	Mm.223312	NM_146900	ENSMUSG00000075103	Olfr1220	MOR2335	olfactory receptor 1220	protein-coding	0	0.267327
Merged-chr3-113841501-1	chr3	113841451	113841551	+	1.8	cIP2vsInput	Intergenic	Intergenic	-189039	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	"collagen, type XI, alpha 1"	protein-coding	0.02	0.376238
Merged-chr10-123798367-1	chr10	123798317	123798417	+	1.8	cIP2vsInput	Intergenic	Intergenic	534291	NM_001252387	268354	Mm.51939	NM_001252387	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	"family with sequence similarity 19, member A2"	protein-coding	0	0.306931
Merged-chr4-74001237-1	chr4	74001187	74001287	+	1.8	cIP2vsInput	Intergenic	Intergenic	-12366	NM_172869	242506	Mm.221597	NM_001163732	ENSMUSG00000049122	Frmd3	4.1O|9430066I12Rik|EPB41L4O|P410	FERM domain containing 3	protein-coding	0	0.336634
Merged-chr14-47597551-1	chr14	47597501	47597601	+	1.8	cIP2vsInput	Intergenic	Intergenic	-29117	NM_172599	100504663	Mm.470462	NM_172599	ENSMUSG00000037526	Atg14	4832427M01|Atg14L|D14Ertd114e|D14Ertd436e	autophagy related 14	protein-coding	0	0.415842
Merged-chr5-93361275-1	chr5	93361225	93361325	+	1.8	cIP2vsInput	Intergenic	MYSERV16_I-int|LTR|ERVK	93702	NM_007635	12452	Mm.3527	NM_007635	ENSMUSG00000029385	Ccng2	-	cyclin G2	protein-coding	0.01	0.366337
Merged-chr4-147465384-1	chr4	147465334	147465434	+	1.8	cIP2vsInput	"intron (NM_001039209, intron 1 of 2)"	Lx3C|LINE|L1	-87893	NM_001014397	433804	Mm.332047	XM_003946328	ENSMUSG00000065999	Gm13154	OTTMUSG00000010673	predicted gene 13154	protein-coding	0	0.356436
Merged-chr4-136957031-1	chr4	136956981	136957081	+	1.8	cIP2vsInput	promoter-TSS (NM_007939)	promoter-TSS (NM_007939)	-215	NM_007939	13842	Mm.1390	NM_007939	ENSMUSG00000028661	Epha8	AW047546|Eek|Hek3|mKIAA1459	Eph receptor A8	protein-coding	0.15	0.772277
Merged-chr15-35216141-1	chr15	35216091	35216191	+	1.8	cIP1vsInput	Intergenic	L1MB7|LINE|L1	-60335	NM_019635	56274	Mm.262330	NM_019635	ENSMUSG00000022329	Stk3	0610042I06Rik|MST|Mst2|Mst3|Ste20|mess1	serine/threonine kinase 3	protein-coding	0	0.306931
Merged-chr16-48007597-1	chr16	48007547	48007647	+	1.8	cIP2vsInput	Intergenic	(TTTG)n|Simple_repeat|Simple_repeat	-276138	NM_028610	73693	Mm.35597	NM_001018002	ENSMUSG00000058550	Dppa4	2410091M23Rik|C76608|ECAT15-1	developmental pluripotency associated 4	protein-coding	0	0.326733
Merged-chr2-55392311-1	chr2	55392261	55392361	+	1.8	cIP2vsInput	Intergenic	Lx10|LINE|L1	-44845	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK1|Kcnf3|Kir3.1	"potassium inwardly-rectifying channel, subfamily J, member 3"	protein-coding	0	0.366337
Merged-chr7-94820244-1	chr7	94820194	94820294	+	1.8	cIP1vsInput	Intergenic	Intergenic	-1390393	NM_011858	23966	Mm.391678	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding	0	0.29703
Merged-chr1-70637988-1	chr1	70637938	70638038	+	1.8	cIP2vsInput	"intron (NM_025728, intron 7 of 7)"	"intron (NM_025728, intron 7 of 7)"	-87727	NM_177164	320460	Mm.360649	NM_177164	ENSMUSG00000045648	Vwc2l	A830006F12Rik|Brl	von Willebrand factor C domain-containing protein 2-like	protein-coding	0	0.29703
Merged-chr3-102692066-1	chr3	102692016	102692116	+	1.8	cIP2vsInput	Intergenic	Intergenic	-42704	NM_027533	70747		NM_001243132	ENSMUSG00000027858	Tspan2	6330415F13Rik|B230119D02Rik|tspan-2	tetraspanin 2	protein-coding	0.01	0.49505
Merged-chr6-80847323-1	chr6	80847273	80847373	+	1.8	cIP2vsInput	Intergenic	Intergenic	827680	NM_178731	243499	Mm.483425	NM_001134743	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding	0.01	0.29703
Merged-chr17-16740141-1	chr17	16740091	16740191	+	1.8	cIP2vsInput	Intergenic	Intergenic	-323962	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding	0	0.29703
Merged-chr4-90580189-1	chr4	90580139	90580239	+	1.8	cIP2vsInput	Intergenic	Intergenic	-218875	NR_033610	619842	Mm.484218	NR_033610	ENSMUSG00000080756	Gm12633	OTTMUSG00000007790	zinc finger protein 352 pseudogene	pseudo	0	0.326733
Merged-chr3-38220924-1	chr3	38220874	38220974	+	1.8	cIP2vsInput	Intergenic	Intergenic	-12805	NR_040541	71342	Mm.410782	NR_040541		5430434I15Rik	-	RIKEN cDNA 5430434I15 gene	miscRNA	0.01	0.29703
Merged-chr7-86412205-1	chr7	86412155	86412255	+	1.8	cIP2vsInput	"intron (NM_212436, intron 2 of 2)"	"intron (NM_212436, intron 2 of 2)"	8356	NM_212436	257958	Mm.419223	NM_212436	ENSMUSG00000061549	Olfr301	MOR211-8P|MOR221-1P|MOR221-4|Olfr1531-ps1	olfactory receptor 301	protein-coding	0	0.316832
Merged-chr17-38986560-1	chr17	38986510	38986610	+	1.8	cIP1vsInput	Intergenic	L1VL2|LINE|L1	-50135	NM_001256050	100126776	Mm.471588	NM_001256050		Gm21947	Esp24	"predicted gene, 21947"	protein-coding	0.01	0.277228
Merged-chr2-87158527-1	chr2	87158477	87158577	+	1.8	cIP2vsInput	Intergenic	Intergenic	-7868	NM_146593	258586	Mm.223113	NM_146593	ENSMUSG00000075158	Olfr1111	MOR181-2	olfactory receptor 1111	protein-coding	0	0.346535
Merged-chr5-14314153-1	chr5	14314103	14314203	+	1.8	cIP2vsInput	Intergenic	Intergenic	-200765	NM_011995	26875	Mm.146275	NM_001110796	ENSMUSG00000061601	Pclo	Acz|Pico|mKIAA0559	piccolo (presynaptic cytomatrix protein)	protein-coding	0	0.316832
Merged-chr13-22131777-1	chr13	22131727	22131827	+	1.8	cIP2vsInput	Intergenic	RMER16-int|LTR|ERVK	-29112	NM_145844	252906	Mm.377265	NM_145844	ENSMUSG00000061222	Vmn1r189	V1rh2	vomeronasal 1 receptor 189	protein-coding	0	0.316832
Merged-chr19-33881351-1	chr19	33881301	33881401	+	1.8	cIP2vsInput	Intergenic	Intergenic	-79897	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	"lipase, gastric"	protein-coding	0	0.29703
Merged-chr4-112775560-1	chr4	112775510	112775610	+	1.8	cIP2vsInput	promoter-TSS (NM_177668)	promoter-TSS (NM_177668)	-699	NM_177668	230613	Mm.122553	NM_177668		Skint10	A030001H23Rik|Gm570	selection and upkeep of intraepithelial T cells 10	protein-coding	0	0.356436
Merged-chr8-23866366-1	chr8	23866316	23866416	+	1.8	cIP2vsInput	"intron (NM_001277239, intron 4 of 7)"	"intron (NM_001277239, intron 4 of 7)"	196705	NM_177086	320158	Mm.121274	NM_001277239	ENSMUSG00000037492	Zmat4	9630048M01Rik	"zinc finger, matrin type 4"	protein-coding	0	0.29703
Merged-chr13-76289217-1	chr13	76289167	76289267	+	1.8	cIP2vsInput	Intergenic	MurERV4_19-int|LTR|ERVK	-95744	NM_030174	78771	Mm.316249	NM_030174		Mctp1	2810465F10Rik	"multiple C2 domains, transmembrane 1"	protein-coding	0	0.336634
Merged-chr7-91741305-1	chr7	91741255	91741355	+	1.8	cIP2vsInput	"intron (NM_011807, intron 3 of 22)"	"intron (NM_011807, intron 3 of 22)"	-321089	NM_001243046	23859	Mm.257035	NM_001243046		Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|PSD93	"discs, large homolog 2 (Drosophila)"	protein-coding	0.01	0.287129
Merged-chr2-148630308-1	chr2	148630258	148630358	+	1.8	cIP2vsInput	Intergenic	Tigger7|DNA|TcMar-Tigger	-42307	NM_019761	56488	Mm.34663	NM_001110159	ENSMUSG00000036992	Nxt1	1110001N02Rik	NTF2-related export protein 1	protein-coding	0	0.326733
Merged-chr4-12686103-1	chr4	12686053	12686153	+	1.8	cIP2vsInput	Intergenic	Intergenic	-220734	NM_173746	208820	Mm.12057	NM_001171801		Triqk	C130086A10|Gm11818|OTTMUSG00000004461	triple QxxK/R motif containing	protein-coding	0.02	0.336634
Merged-chr2-99624298-1	chr2	99624248	99624348	+	1.8	cIP2vsInput	Intergenic	Charlie16a|DNA|hAT-Charlie	-2000450	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding	0	0.425743
Merged-chr2-40591149-1	chr2	40591099	40591199	+	1.8	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-1364811	NM_024209	67857	Mm.392662	NM_024209		Ppp6c	2310003C10Rik	"protein phosphatase 6, catalytic subunit"	protein-coding	0	0.247525
Merged-chr17-52753060-1	chr17	52753010	52753110	+	1.8	cIP2vsInput	"intron (NM_001031811, intron 2 of 15)"	"intron (NM_001031811, intron 2 of 15)"	150351	NM_001031811	211468	Mm.490760	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	"potassium voltage-gated channel, subfamily H (eag-related), member 8"	protein-coding	0.01	0.326733
Merged-chr1-52597834-1	chr1	52597784	52597884	+	1.8	cIP2vsInput	Intergenic	Intergenic	-32871	NR_024590	227094	Mm.83541	NM_172654	ENSMUSG00000043015	Tmem194b	5330401P04Rik|9830163O08	transmembrane protein 194B	protein-coding	0	0.415842
Merged-chr6-66777348-1	chr6	66777298	66777398	+	1.8	cIP2vsInput	promoter-TSS (NM_134168)	promoter-TSS (NM_134168)	-218	NM_134168	171186	Mm.377167	NM_134168	ENSMUSG00000093632	Vmn1r38	V1rc13	vomeronasal 1 receptor 38	protein-coding	0	0.326733
Merged-chr4-21418406-1	chr4	21418356	21418456	+	1.8	cIP2vsInput	Intergenic	Intergenic	267557	NM_001080771	230025	Mm.208541	NM_001080771	ENSMUSG00000040478	Prdm13	-	PR domain containing 13	protein-coding	0.01	0.356436
Merged-chr3-113722530-1	chr3	113722480	113722580	+	1.8	cIP2vsInput	Intergenic	L1VL2|LINE|L1	-92381	NM_001038696	67225	Mm.316928	NM_001038696	ENSMUSG00000027981	Rnpc3	2810441O16Rik|AI447568|C030014B17Rik	"RNA-binding region (RNP1, RRM) containing 3"	protein-coding	0.01	0.316832
Merged-chr17-39542943-1	chr17	39542893	39542993	+	1.8	cIP2vsInput	Intergenic	Intergenic	6801	NM_001255977	100043300	Mm.27927	NM_001255977	ENSMUSG00000096345	Gm4345	Esp16	predicted gene 4345	protein-coding	0	0.316832
Merged-chr19-21351327-1	chr19	21351277	21351377	+	1.8	cIP2vsInput	Intergenic	Intergenic	79049	NM_009551	22682	Mm.379919	NM_009551		Zfand5	2310057A04Rik|5830475F03Rik|AA415485|Za20d2|Zfp216	"zinc finger, AN1-type domain 5"	protein-coding	0.01	0.415842
Merged-chr9-81437827-1	chr9	81437777	81437877	+	1.8	cIP2vsInput	Intergenic	Intergenic	-194103	NR_040394	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	miscRNA	0	0.336634
Merged-chr3-113001197-1	chr3	113001147	113001247	+	1.8	cIP2vsInput	Intergenic	Intergenic	155530	NM_001190404	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding	0	0.326733
Merged-chrX-62426357-1	chrX	62426307	62426407	+	1.8	cIP2vsInput	Intergenic	Intergenic	89712	NR_045443	75545	Mm.391270	NR_045442	ENSMUSG00000085757	1700019B21Rik	-	RIKEN cDNA 1700019B21 gene	miscRNA	0.01	0.306931
Merged-chrX-42052813-1	chrX	42052763	42052863	+	1.8	cIP2vsInput	Intergenic	Intergenic	-15023	NM_009688	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA|mXIAP	X-linked inhibitor of apoptosis	protein-coding	0.01	0.415842
Merged-chr13-11530023-1	chr13	11529973	11530073	+	1.8	cIP2vsInput	Intergenic	Intergenic	7971	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	"zona pellucida glycoprotein 4, pseudogene"	pseudo	0.01	0.29703
Merged-chr3-20908603-1	chr3	20908553	20908653	+	1.8	cIP2vsInput	Intergenic	B4A|SINE|B4	-541426	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	"angiotensin II receptor, type 1b"	protein-coding	0	0.386139
Merged-chr5-46392615-1	chr5	46392565	46392665	+	1.8	cIP2vsInput	Intergenic	Intergenic	-535075	NM_001163073	209707	Mm.71498	NM_001163073	ENSMUSG00000015882	Lcorl	Mlr1	ligand dependent nuclear receptor corepressor-like	protein-coding	0	0.29703
Merged-chr1-23594173-1	chr1	23594123	23594223	+	1.8	cIP2vsInput	Intergenic	Intergenic	-167753	NM_172124	280645	Mm.471661	NM_172124		B3gat2	GlcAT-S|Glcats	"beta-1,3-glucuronyltransferase 2 (glucuronosyltransferase S)"	protein-coding	0.02	0.366337
Merged-chr18-9011222-1	chr18	9011172	9011272	+	1.8	cIP2vsInput	Intergenic	Intergenic	-201634	NM_008058	14370	Mm.184289	NM_008058	ENSMUSG00000036904	Fzd8	Fz8	frizzled homolog 8 (Drosophila)	protein-coding	0	0.356436
Merged-chr10-78094684-1	chr10	78094634	78094734	+	1.8	cIP2vsInput	Intergenic	Intergenic	25316	NM_015790	50723	Mm.17819	NM_015790	ENSMUSG00000000732	Icosl	AU044799|B7-H2|B7RP-1|B7h|BG071784|GI50|GL50|GL50-B|ICOS-L|Icoslg|LICOS|Ly115l|mKIAA0653	icos ligand	protein-coding	0	0.346535
Merged-chr7-60967112-1	chr7	60967062	60967162	+	1.8	cIP2vsInput	Intergenic	Intergenic	648215	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	miscRNA	0	0.316832
Merged-chr4-103338965-1	chr4	103338915	103339015	+	1.8	cIP2vsInput	"intron (NM_025909, intron 7 of 8)"	L1M5|LINE|L1	25119	NM_025909	67013	Mm.30021	NM_025909	ENSMUSG00000035069	Oma1	2010001O09Rik|MPRP-1|ZMPOMA1	"OMA1 homolog, zinc metallopeptidase (S. cerevisiae)"	protein-coding	0	0.227723
Merged-chr12-60011137-1	chr12	60011087	60011187	+	1.8	cIP2vsInput	Intergenic	Intergenic	-791654	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding	0	0.29703
Merged-chr10-130324927-1	chr10	130324877	130324977	+	1.8	cIP2vsInput	"intron (NM_183264, intron 1 of 8)"	"intron (NM_183264, intron 1 of 8)"	2075	NM_183264	67596	Mm.131264	NM_183264	ENSMUSG00000034833	Tespa1	5830405N20Rik|A430001F24Rik|AI450549	"thymocyte expressed, positive selection associated 1"	protein-coding	0	0.356436
Merged-chr12-76733384-1	chr12	76733334	76733434	+	1.8	cIP2vsInput	Intergenic	Intergenic	-22837	NM_013675	20741	Mm.32881	NM_013675	ENSMUSG00000021061	Sptb	AI842465|D330027P03Rik|Gm1301|Spnb-1|Spnb1|ja|jaundiced|mKIAA4219	"spectrin beta, erythrocytic"	protein-coding	0	0.366337
Merged-chr13-75039860-1	chr13	75039810	75039910	+	1.8	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	-50127	NM_013628	18548	Mm.1333	NM_013628	ENSMUSG00000021587	Pcsk1	Nec-1|Nec1|PC1|PC3|Phpp-1|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0.01	0.356436
Merged-chr1-117304566-1	chr1	117304516	117304616	+	1.8	cIP2vsInput	Intergenic	Intergenic	1006566	NM_011650	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding	0.01	0.306931
Merged-chr7-143757181-1	chr7	143757131	143757231	+	1.8	cIP2vsInput	Intergenic	Intergenic	9812	NM_203492	381974	Mm.297839	NM_203492	ENSMUSG00000050276	Mrgprg	Gm1098|Mrgg	"MAS-related GPR, member G"	protein-coding	0.06	0.623762
Merged-chr6-73916109-1	chr6	73916059	73916159	+	1.8	cIP2vsInput	Intergenic	Intergenic	-446442	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding	0.01	0.405941
Merged-chr10-29184115-1	chr10	29184065	29184165	+	1.8	cIP2vsInput	"intron (NM_026138, intron 5 of 6)"	Lx|LINE|L1	-27528	NM_001162537	212448	Mm.379334	NM_001162537	ENSMUSG00000004360	9330159F19Rik	-	RIKEN cDNA 9330159F19 gene	protein-coding	0	0.29703
Merged-chr14-62457597-1	chr14	62457547	62457647	+	1.8	cIP2vsInput	Intergenic	Intergenic	-1308	NM_172810	239134	Mm.236557	NM_001204340	ENSMUSG00000021933	Gucy1b2	B930025B03|GC-SB2	"guanylate cyclase 1, soluble, beta 2"	protein-coding	0.06	0.544554
Merged-chr6-9288182-1	chr6	9288132	9288232	+	1.8	cIP2vsInput	Intergenic	L1M5|LINE|L1	338163	NM_008751	18231	Mm.46954	NM_008751		Nxph1	C130005L03Rik	neurexophilin 1	protein-coding	0	0.306931
Merged-chr1-32316130-1	chr1	32316080	32316180	+	1.8	cIP2vsInput	"intron (NM_133235, intron 2 of 8)"	"intron (NM_133235, intron 2 of 8)"	143324	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm1	"KH domain containing, RNA binding, signal transduction associated 2"	protein-coding	0.01	0.287129
Merged-chr7-41493607-1	chr7	41493557	41493657	+	1.8	cIP2vsInput	"intron (NM_001033530, intron 1 of 3)"	Lx3A|LINE|L1	6283	NM_001033530	101835	Mm.370336	NM_001033530	ENSMUSG00000074166	AW146154	AI451288	expressed sequence AW146154	protein-coding	0	0.306931
Merged-chr1-61462661-1	chr1	61462611	61462711	+	1.8	cIP2vsInput	Intergenic	MLT1A1|LTR|ERVL-MaLR	84229	NR_040483	77341	Mm.402964	NR_040483	ENSMUSG00000085447	9530026F06Rik	-	RIKEN cDNA 9530026F06 gene	miscRNA	0	0.316832
Merged-chr11-12658640-1	chr11	12658590	12658690	+	1.8	cIP2vsInput	Intergenic	MTD|LTR|ERVL-MaLR	-193680	NM_172496	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	4732460E13|C530045F18Rik|mKIAA0633	cordon-bleu	protein-coding	0	0.346535
Merged-chr17-79531668-1	chr17	79531618	79531718	+	1.8	cIP2vsInput	Intergenic	Lx8|LINE|L1	-21182	NR_033462	100038718	Mm.414347	NR_033462		Gm10494	ENSMUSG00000073373	predicted gene 10494	miscRNA	0.02	0.366337
Merged-chrX-108753644-1	chrX	108753594	108753694	+	1.8	cIP2vsInput	"intron (NM_001081477, intron 36 of 40)"	"intron (NM_001081477, intron 36 of 40)"	80711	NM_001081477	382236	Mm.426127	NM_001081477		Brwd3	Brodl|D030064D06Rik|Gm596	bromodomain and WD repeat domain containing 3	protein-coding	0.01	0.346535
Merged-chr9-23511696-1	chr9	23511646	23511746	+	1.8	cIP2vsInput	Intergenic	L1VL2|LINE|L1	288620	NM_028472	73230	Mm.335020	NM_028472	ENSMUSG00000031963	Bmper	3110056H04Rik|CV-2|Crim3|Cv2	BMP-binding endothelial regulator	protein-coding	0	0.346535
Merged-chr6-83215468-1	chr6	83215418	83215518	+	1.8	cIP2vsInput	Intergenic	Intergenic	-21907	NM_001166067	232156	Mm.333189	NM_001166067	ENSMUSG00000068323	Slc4a5	C330006M16|C330016K18Rik	"solute carrier family 4, sodium bicarbonate cotransporter, member 5"	protein-coding	0.01	0.643564
Merged-chr17-9584575-1	chr17	9584525	9584625	+	1.8	cIP2vsInput	Intergenic	Intergenic	85129	NM_001163836	67543	Mm.26987	NM_026226	ENSMUSG00000046173	Pabpc6	4932702K14Rik|AI428050|Pabpc3	"poly(A) binding protein, cytoplasmic 6"	protein-coding	0	0.336634
Merged-chr10-57208971-1	chr10	57208921	57209021	+	1.8	cIP2vsInput	Intergenic	Intergenic	277382	NR_045353	74928	Mm.416643	NR_045353	ENSMUSG00000097370	4930467K11Rik	-	RIKEN cDNA 4930467K11 gene	miscRNA	0	0.366337
Merged-chrX-83290556-1	chrX	83290506	83290606	+	1.8	cIP2vsInput	"intron (NM_007868, intron 2 of 78)"	L1_Mur3|LINE|L1	197368	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding	0	0.366337
Merged-chr6-104818534-1	chr6	104818484	104818584	+	1.8	cIP2vsInput	"intron (NM_017383, intron 12 of 22)"	"intron (NM_017383, intron 12 of 22)"	325490	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding	0	0.237624
Merged-chr3-13267220-1	chr3	13267170	13267270	+	1.8	cIP2vsInput	Intergenic	Intergenic	-204435	NM_178631	76897	Mm.422625	NM_001163328	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0	0.366337
Merged-chr15-46351692-1	chr15	46351642	46351742	+	1.8	cIP1vsInput	"intron (NR_045509, intron 2 of 3)"	L1_Mur1|LINE|L1	27107	NR_045509	71120	Mm.158571	NR_045509		1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	miscRNA	0	0.316832
Merged-chr12-95255674-1	chr12	95255624	95255724	+	1.8	cIP2vsInput	Intergenic	Intergenic	-436552	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0	0.316832
Merged-chr3-135960251-1	chr3	135960201	135960301	+	1.8	cIP2vsInput	Intergenic	Intergenic	-119982	NR_040540	71038	Mm.410798	NR_040540		4933401H06Rik	-	RIKEN cDNA 4933401H06 gene	miscRNA	0.01	0.326733
Merged-chr8-101381976-1	chr8	101381926	101382026	+	1.8	cIP2vsInput	Intergenic	Intergenic	1403135	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11	cadherin 11	protein-coding	0	0.247525
Merged-chr4-26793143-1	chr4	26793093	26793193	+	1.8	cIP2vsInput	Intergenic	Intergenic	-87694	NR_040656	75360	Mm.67233	NR_040656	ENSMUSG00000086257	4930548K13Rik	-	RIKEN cDNA 4930548K13 gene	miscRNA	0.01	0.316832
Merged-chr12-38275580-1	chr12	38275530	38275630	+	1.8	cIP2vsInput	"intron (NM_178681, intron 19 of 24)"	L1_Rod|LINE|L1	160449	NR_037267	100526539		NR_037267		Mir467a-10	mmu-mir-467a-10	microRNA 467a-10	miscRNA	0	0.277228
Merged-chr17-49143040-1	chr17	49142990	49143090	+	1.8	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-29507	NR_038144	69311	Mm.46140	NR_038141		1700008K24Rik	-	RIKEN cDNA 1700008K24 gene	miscRNA	0	0.326733
Merged-chr5-62545249-1	chr5	62545199	62545299	+	1.8	cIP2vsInput	Intergenic	Intergenic	220928	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	"ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2"	protein-coding	0	0.376238
Merged-chr19-58009338-1	chr19	58009288	58009388	+	1.8	cIP2vsInput	"intron (NM_181415, intron 27 of 28)"	L1MEf|LINE|L1	-286866	NR_040449	791347	Mm.452208	NR_040449		Gm10007	ENSMUSG00000056739	predicted gene 10007	miscRNA	0	0.306931
Merged-chr18-76596643-1	chr18	76596593	76596693	+	1.8	cIP2vsInput	Intergenic	Intergenic	-259762	NM_001109743	664805	Mm.329543	NM_001109743	ENSMUSG00000091519	Skor2	Corl2|EG664805|Fussel18|Gm7348	SKI family transcriptional corepressor 2	protein-coding	0.02	0.356436
Merged-chr4-21290263-1	chr4	21290213	21290313	+	1.8	cIP1vsInput	Intergenic	Intergenic	395700	NM_001080771	230025	Mm.208541	NM_001080771	ENSMUSG00000040478	Prdm13	-	PR domain containing 13	protein-coding	0	0.306931
Merged-chr16-61149471-1	chr16	61149421	61149521	+	1.8	cIP2vsInput	Intergenic	Lx5b|LINE|L1	-543940	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding	0	0.346535
Merged-chr13-84502344-1	chr13	84502294	84502394	+	1.8	cIP2vsInput	Intergenic	Lx8|LINE|L1	280048	NM_175187	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding	0	0.366337
Merged-chrX-40074274-1	chrX	40074224	40074324	+	1.8	cIP2vsInput	Intergenic	Intergenic	-210670	NM_001191032	100504400	Mm.373409	NM_001191032	ENSMUSG00000095240	Cypt14	-	cysteine-rich perinuclear theca 14	protein-coding	0	0.336634
Merged-chr12-14510734-1	chr12	14510684	14510784	+	1.8	cIP2vsInput	Intergenic	L1_Mus2|LINE|L1	249200	NR_045003	791361	Mm.217963	NR_045003		Gm16497	ENSMUSG00000066623	predicted gene 16497	miscRNA	0	0.326733
Merged-chr3-36111070-1	chr3	36111020	36111120	+	1.8	cIP2vsInput	Intergenic	L1_Mur2|LINE|L1	-40010	NM_001101478	241944	Mm.260056	NM_001101478	ENSMUSG00000033883	D3Ertd254e	-	"DNA segment, Chr 3, ERATO Doi 254, expressed"	protein-coding	0	0.336634
Merged-chr16-48820984-1	chr16	48820934	48821034	+	1.8	cIP2vsInput	Intergenic	Intergenic	4128	NM_023881	57263	Mm.21123	NM_023881	ENSMUSG00000022650	Retnlb	9030012B21Rik|Fizz2|RELMbeta|Relmb|Xcp3	resistin like beta	protein-coding	0	0.356436
Merged-chr9-93375937-1	chr9	93375887	93375987	+	1.8	cIP2vsInput	Intergenic	Intergenic	-370204	NR_040756	78349	Mm.52612	NR_040756		1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	miscRNA	0.01	0.435644
Merged-chrX-107327690-1	chrX	107327640	107327740	+	1.8	cIP2vsInput	Intergenic	Intergenic	43344	NM_001177782	213439	Mm.383562	NM_001033251	ENSMUSG00000073008	Gpr174	Gm376	G protein-coupled receptor 174	protein-coding	0	0.29703
Merged-chr6-66076812-1	chr6	66076762	66076862	+	1.8	cIP2vsInput	Intergenic	Intergenic	124241	NM_001161773	67653	Mm.389756	NR_003637	ENSMUSG00000036463	4930544G11Rik	-	RIKEN cDNA 4930544G11 gene	protein-coding	0.02	0.336634
Merged-chrX-105070234-1	chrX	105070184	105070284	+	1.8	cIP2vsInput	promoter-TSS (NR_015467)	promoter-TSS (NR_015467)	-110	NR_015467	71445	Mm.242968	NR_015467	ENSMUSG00000087174	5530601H04Rik	AI835882	RIKEN cDNA 5530601H04 gene	miscRNA	0.05	0.49505
Merged-chr10-113960026-1	chr10	113959976	113960076	+	1.8	cIP2vsInput	Intergenic	Intergenic	373448	NR_035418	100316831		NR_035418		Mir669h	Mirn669h|mmu-mir-669h	microRNA 669h	miscRNA	0.01	0.257426
Merged-chr7-107096768-1	chr7	107096718	107096818	+	1.8	cIP2vsInput	promoter-TSS (NM_020598)	promoter-TSS (NM_020598)	-699	NM_020598	18314	Mm.103814	NM_020598	ENSMUSG00000073897	Olfr17	MOR263-5|P2	olfactory receptor 17	protein-coding	0.01	0.356436
Merged-chr19-8209813-1	chr19	8209763	8209863	+	1.8	cIP2vsInput	"intron (NM_172776, intron 2 of 9)"	L1_Mus1|LINE|L1	9026	NM_172776	236293	Mm.440581	NM_172776	ENSMUSG00000075044	Slc22a29	D630002G06Rik	solute carrier family 22. member 29	protein-coding	0	0.326733
Merged-chr2-17316043-1	chr2	17315993	17316093	+	1.8	cIP2vsInput	Intergenic	Intergenic	-302317	NR_040632	75069	Mm.399263	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	miscRNA	0	0.336634
Merged-chr9-36365507-1	chr9	36365457	36365557	+	1.8	cIP2vsInput	Intergenic	Intergenic	-66377	NM_001167586	639025	Mm.386535	NM_001167586	ENSMUSG00000023093	Gm7257	EG639025|Pate-q	predicted gene 7257	protein-coding	0	0.386139
Merged-chr2-42205348-1	chr2	42205298	42205398	+	1.8	cIP2vsInput	"intron (NM_053011, intron 2 of 90)"	"intron (NM_053011, intron 2 of 90)"	448250	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding	0	0.237624
Merged-chr8-68653827-1	chr8	68653777	68653877	+	1.8	cIP2vsInput	"intron (NM_172753, intron 1 of 9)"	"intron (NM_172753, intron 1 of 9)"	81319	NM_001252623	234356	Mm.489712	NM_001252623	ENSMUSG00000036356	Csgalnact1	4732435N03Rik|CSGalNAcT-1	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0	0.316832
Merged-chrX-82342926-1	chrX	82342876	82342976	+	1.8	cIP2vsInput	Intergenic	Lx5b|LINE|L1	-605944	NM_007868	13405	Mm.416750	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|mdx|pke	"dystrophin, muscular dystrophy"	protein-coding	0	0.336634
Merged-chr14-91817667-1	chr14	91817617	91817717	+	1.8	cIP2vsInput	Intergenic	Lx2|LINE|L1	1690776	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	miscRNA	0	0.39604
Merged-chr9-81903531-1	chr9	81903481	81903581	+	1.8	cIP2vsInput	"intron (NM_175213, intron 2 of 4)"	"intron (NM_175213, intron 2 of 4)"	39787	NM_175213	75033	Mm.457083	NM_175213	ENSMUSG00000043289	Mei4	4930486G11Rik	"meiosis-specific, MEI4 homolog (S. cerevisiae)"	protein-coding	0	0.316832
Merged-chr1-140014248-1	chr1	140014198	140014298	+	1.8	cIP2vsInput	Intergenic	Lx6|LINE|L1	-155549	NM_001025575	545366	Mm.439660	NM_001025575	ENSMUSG00000033898	Cfhr2	Cfhrb_4/2	complement factor H-related 2	protein-coding	0	0.29703
Merged-chr10-46805375-1	chr10	46805325	46805425	+	1.8	cIP2vsInput	Intergenic	MLTR18C_MM|LTR|ERVK	560626	NR_028276	108637		NR_028276		Snord14c	Gm23107|Rnu14|U14	"small nucleolar RNA, C/D box 14C"	snoRNA	0	0.39604
Merged-chrX-167233444-1	chrX	167233394	167233494	+	1.8	cIP2vsInput	Intergenic	Intergenic	-24226	NM_021278	19241	Mm.490263	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	"thymosin, beta 4, X chromosome"	protein-coding	0.04	0.514851
Merged-chrX-157966100-1	chrX	157966050	157966150	+	1.8	cIP2vsInput	"intron (NM_177751, intron 4 of 21)"	"intron (NM_177751, intron 4 of 21)"	77010	NM_177751	245684	Mm.197074	NM_177751	ENSMUSG00000025658	Cnksr2	C030004A01|Cnk2|Ksr2|mKIAA0902	connector enhancer of kinase suppressor of Ras 2	protein-coding	0	0.247525
Merged-chr14-52641705-1	chr14	52641655	52641755	+	1.8	cIP2vsInput	Intergenic	L1_Mur3|LINE|L1	-146010	NM_001170918	57269	Mm.88822	NM_001170918	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding	0.01	0.366337
Merged-chr6-104354125-1	chr6	104354075	104354175	+	1.8	cIP2vsInput	Intergenic	MER58A|DNA|hAT-Charlie	-138919	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding	0.01	0.326733
Merged-chr10-56263764-1	chr10	56263714	56263814	+	1.8	cIP2vsInput	Intergenic	ID_B1|SINE|B4	-35075	NM_001033385	544696	Mm.411188	NM_001033385	ENSMUSG00000038122	D630037F22Rik	Bromi	RIKEN cDNA D630037F22 gene	protein-coding	0.01	0.356436
Merged-chr5-103637621-1	chr5	103637571	103637671	+	1.8	cIP2vsInput	Intergenic	Intergenic	-8218	NM_029415	75750	Mm.7446	NM_029415	ENSMUSG00000029321	Slc10a6	8430417G17Rik|C78479|Soat	"solute carrier family 10 (sodium/bile acid cotransporter family), member 6"	protein-coding	0.01	0.366337
Merged-chr2-89507215-1	chr2	89507165	89507265	+	1.8	cIP2vsInput	Intergenic	L1Md_F2|LINE|L1	-12869	NM_146968	258970	Mm.223361	NM_146968	ENSMUSG00000075085	Olfr1242	MOR231-5	olfactory receptor 1242	protein-coding	0	0.346535
Merged-chr9-8622871-1	chr9	8622821	8622921	+	1.8	cIP2vsInput	"intron (NM_013838, intron 2 of 12)"	L1Md_F2|LINE|L1	78729	NM_013838	22068	Mm.325086	NM_013838	ENSMUSG00000031997	Trpc6	AV025995|LLHWJM002|LLHWJM003|LLHWJM004|TRP-6|Trrp6|mtrp6	"transient receptor potential cation channel, subfamily C, member 6"	protein-coding	0	0.326733
Merged-chr5-27609092-1	chr5	27609042	27609142	+	1.8	cIP2vsInput	"intron (NM_001136060, intron 8 of 25)"	Lx2|LINE|L1	-107700	NM_028561	73526	Mm.389608	NM_028561	ENSMUSG00000048703	Speer4b	1700081O22Rik|SPEER-4B	spermatogenesis associated glutamate (E)-rich protein 4b	protein-coding	0.01	0.356436
Merged-chr3-12829634-1	chr3	12829584	12829684	+	1.8	cIP2vsInput	Intergenic	Intergenic	-642021	NM_178631	76897	Mm.422625	NM_001163328	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding	0	0.326733
Merged-chr11-65071235-1	chr11	65071185	65071285	+	1.8	cIP2vsInput	"intron (NM_175003, intron 3 of 20)"	"intron (NM_175003, intron 3 of 20)"	91726	NM_001099288	216831	Mm.134338	NM_001099288	ENSMUSG00000033389	Arhgap44	6330543G20|AI840762|AU040829|AW493732|Rich2	Rho GTPase activating protein 44	protein-coding	0	0.346535
Merged-chr3-3679280-1	chr3	3679230	3679330	+	1.8	cIP2vsInput	Intergenic	Lx8|LINE|L1	171250	NM_013920	30942	Mm.330897	NM_013920		Hnf4g	NR2A2	"hepatocyte nuclear factor 4, gamma"	protein-coding	0	0.316832
Merged-chr7-51379198-1	chr7	51379148	51379248	+	1.8	cIP2vsInput	Intergenic	Intergenic	-131831	NR_073508	233246	Mm.411727	NM_001271879	ENSMUSG00000055489	Ano5	9330162L24|Gdd1|Tmem16e	anoctamin 5	protein-coding	0.01	0.306931
Merged-chr2-94706330-1	chr2	94706280	94706380	+	1.8	cIP2vsInput	Intergenic	Lx5b|LINE|L1	-268183	NM_007466	11800	Mm.486651	NM_007466	ENSMUSG00000027193	Api5	AAC-11|AI196452	apoptosis inhibitor 5	protein-coding	0.01	0.366337
Merged-chr3-29278257-1	chr3	29278207	29278307	+	1.8	cIP2vsInput	"intron (NM_001167748, intron 4 of 12)"	MTD|LTR|ERVL-MaLR	-138566	NR_030422	791072		NR_030422		Mir551b	Mirn551b|mir-551b	microRNA 551b	miscRNA	0	0.386139
Merged-chr5-82740060-1	chr5	82740010	82740110	+	1.8	cIP2vsInput	Intergenic	Intergenic	59005	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mmu-mir-1187	microRNA 1187	miscRNA	0	0.366337
Merged-chr8-52874789-1	chr8	52874739	52874839	+	1.8	cIP2vsInput	Intergenic	Intergenic	-636913	NM_001205054	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding	0	0.247525
Merged-chr3-17448205-1	chr3	17448155	17448255	+	1.8	cIP2vsInput	Intergenic	Intergenic	-341716	NR_033490	70441	Mm.458192	NR_033490		2610100L16Rik	100040120|Gm2612	RIKEN cDNA 2610100L16 gene	miscRNA	0	0.356436
Merged-chr12-72700034-1	chr12	72699984	72700084	+	1.8	cIP2vsInput	Intergenic	Intergenic	-35206	NM_025522	66375	Mm.289653	NM_025522	ENSMUSG00000021094	Dhrs7	2310016E22Rik|5730564L20Rik|AW061210|Retdsr4|Retsdr4	dehydrogenase/reductase (SDR family) member 7	protein-coding	0	0.306931
Merged-chr18-71017366-1	chr18	71017316	71017416	+	1.8	cIP2vsInput	Intergenic	L1MA6|LINE|L1	449074	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding	0.02	0.326733
Merged-chr18-28743114-1	chr18	28743064	28743164	+	1.7	cIP2vsInput	"intron (NR_045398, intron 2 of 4)"	"intron (NR_045398, intron 2 of 4)"	182950	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	miscRNA	0	0.356436
Merged-chr13-79809299-1	chr13	79809249	79809349	+	1.7	cIP1vsInput	Intergenic	Intergenic	-1074123	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding	0	0.287129
Merged-chr2-99450837-1	chr2	99450787	99450887	+	1.7	cIP2vsInput	Intergenic	L1MB5|LINE|L1	1983163	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1|mKIAA1580	leucine rich repeat containing 4C	protein-coding	0	0.356436
Merged-chr15-88779185-1	chr15	88779135	88779235	+	1.7	cIP1vsInput	"intron (NM_181412, intron 2 of 2)"	"intron (NM_181412, intron 2 of 2)"	27474	NM_181412	223773	Mm.396622	NM_181412	ENSMUSG00000034333	Zbed4	1700009F06Rik	"zinc finger, BED domain containing 4"	protein-coding	0	0.29703
Merged-chrX-122300798-1	chrX	122300748	122300848	+	1.7	cIP2vsInput	Intergenic	MMERVK9C_I-int|LTR|ERVK	96587	NM_138742	54561	Mm.490573	NM_138742	ENSMUSG00000055733	Nap1l3	MB20	nucleosome assembly protein 1-like 3	protein-coding	0	0.247525
Merged-chr6-51235587-1	chr6	51235537	51235637	+	1.7	cIP2vsInput	Intergenic	Intergenic	34323	NR_029719	387166		NR_029719	ENSMUSG00000065505	Mir148a	Mirn148|Mirn148a	microRNA 148a	miscRNA	0	0.405941
Merged-chr14-4806483-1	chr14	4806433	4806533	+	1.7	cIP2vsInput	Intergenic	B1_Mus1|SINE|Alu	-64673	NM_001242945	100041306	Mm.396155	NM_001242945	ENSMUSG00000094132	Gm3264	-	predicted gene 3264	protein-coding	0.02	0.445545
Merged-chr10-15210892-1	chr10	15210842	15210942	+	1.7	cIP2vsInput	Intergenic	Intergenic	450603	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding	0	0.356436
Merged-chr14-97345364-1	chr14	97345314	97345414	+	1.7	cIP2vsInput	Intergenic	ORR1C2|LTR|ERVL-MaLR	824179	NM_001038610	13134	Mm.320593	NM_001038610	ENSMUSG00000055639	Dach1	AI182278|Dac|Dach|E130112M23Rik	dachshund 1 (Drosophila)	protein-coding	0	0.326733
Merged-chrX-145959166-1	chrX	145959116	145959216	+	1.7	cIP2vsInput	Intergenic	Intergenic	-472120	NM_153319	27494	Mm.100068	NM_153319	ENSMUSG00000041688	Amot	C81439|CAG-2|D0Kist1|E230009N18Rik|Sii6|mKIAA1071	angiomotin	protein-coding	0	0.326733
Merged-chr14-94713359-1	chr14	94713309	94713409	+	1.7	cIP2vsInput	Intergenic	Lx5c|LINE|L1	-822690	NM_001271798	211712	Mm.458162	NM_001081377		Pcdh9	-	protocadherin 9	protein-coding	0.01	0.326733
Merged-chr9-74128090-1	chr9	74128040	74128140	+	1.7	cIP1vsInput	"intron (NM_001033500, intron 1 of 19)"	"intron (NM_001033500, intron 1 of 19)"	17756	NM_001033500	546144	Mm.335289	NM_177908	ENSMUSG00000044976	Wdr72	AW558070|D230040E23	WD repeat domain 72	protein-coding	0	0.277228
Merged-chr3-110105025-1	chr3	110104975	110105075	+	1.7	cIP2vsInput	"intron (NM_030699, intron 2 of 7)"	"intron (NM_030699, intron 2 of 7)"	38447	NM_001163348	80883	Mm.39262	NM_001163348		Ntng1	A930010C08Rik|AI853992|Lmnt1	netrin G1	protein-coding	0	0.534653
Merged-chr16-76489090-1	chr16	76489040	76489140	+	1.7	cIP2vsInput	Intergenic	Intergenic	-116041	NM_173440	268903	Mm.455873	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding	0	0.29703
Merged-chr9-5069745-1	chr9	5069695	5069795	+	1.7	cIP1vsInput	Intergenic	Lx5c|LINE|L1	-228772	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding	0	0.277228
Merged-chr4-19203059-1	chr4	19203009	19203109	+	1.7	cIP2vsInput	Intergenic	Intergenic	-77791	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding	0.01	0.287129
Merged-chr2-19590022-1	chr2	19589972	19590072	+	1.6	cIP2vsInput	Intergenic	Intergenic	-36112	NM_027600	70909	Mm.158488	NM_027600	ENSMUSG00000026734	4921504E06Rik	4921522E24Rik	RIKEN cDNA 4921504E06 gene	protein-coding	0.01	0.366337