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. 2016 Sep 8;6:33090. doi: 10.1038/srep33090

Table 1. Annotation of potential regulatory SNPs in RegulomeDB Category of 1.

Chromosome: Location RefSNP1 Allele Gene Position Histone marked2 DNase eQTL Motifs altered3 Protein bound3
1:207387765 rs1346720 T/C CD55 intergenic 69 kb 3′ of C4BPA − − + − SETDB1*
1:207424726 rs7545125 A/G CD55 intergenic 70 kb 5′ of CD55 + − + −; DIx2, Foxo, Ik-2, NF-AT, NF-AT1, YY1 CEBPB*
1:207456473 rs12095015 T/C CD55 intergenic 38 kb 5′ of CD55 + + + MGA; Foxp1, Irf, SRF, Zec CDX2, JUN; CJUN
1:207470459 rs1652333 G/A CD55 intergenic 24 kb 5′ of CD55 + − + −; Ap-4, E2A, Evi-1, Mef2, Myf, RP58 MEF-2, TCF21, AP-4, TFAP4, MYF6
1:207472188 rs2802236 T/C CD55 intergenic 23 kb 5′ of CD55 + + + HOXA5(Hox-1.3); Eomes, Hoxa5, Pax5, Pax6, Zfp187 FOXA1, ESR1, EP300, GATA3*; ERALPHA-A
1:207478979 rs1572275 C/A CD55 intergenic 16 kb 5′ of CD55 + + + −; AIRE, Pou5f1 SMARCC1, RAD21*, POLR2A, CEBPB*, TAF1*, NFYB, TBP*, CHD2, TFAP2A
1:207483444 rs2564974 G/A CD55 intergenic 11 kb 5′ of CD55 + + + Irx-3, Irx3, Irx4, Irx6, TFAP4; CDP, Irx, Myb STAT1, SMARCC1, TCF7L2, SP1, EP300, TCF12, MYC, ELF1*, RCOR1, MEF2A, TEAD4, SPI1, BHLHE40, JUND*, GATA2*, TAL1*, JUN, USF1, MAX*, GATA1, POLR2A, CBX3, SIRT6*; PU1*, POL2*, BAF155*, CJUN*, CMYC*, INI1*
1:207494415 rs2564978 T/C CD55 intergenic 399 bp 5′ of CD55 + + + FXR/RXR-alpha* E2F1, MTA3, POLR2A*, SPI1, ELF1*, TAF1, CEBPB*, TBL1XR1, EP300*, TBP*, FOS, TRIM28, MYC*, STAT3*, KDM5B, ZNF143, HDAC1, MAX*, SP4, CDX2, MXI1, GATA1, STAT1, CTCF*, JUNB, PHF8, RAD21*, BACH1, TCF12, GABPB1, ZKSCAN1, IRF1, SIN3A, SETDB1, NFKB1*, HNF4A; PU1, GTF2F1, POL2S2, SMC3, CEBPB
1:207501210 rs4844592 T/A CD55 intronic + + + Srf, SPI1, SPIC; HDAC2 POLR2A*
1:207502533 rs6700168 A/C CD55 intronic + + + IRC900814 POLR2A*, NFYA, CHD2, MAX, RCOR1, SMC3, ZKSCAN1, ZNF143; POL24H8, GTF2F1, POL2B, POL2S2
1:207506328 rs10864231 T/G CD55 intronic − + + −; PL2F, Pax5 POLR2A*, TAF1; POL24H8
1:207507480 rs1507758 G/C CD55 intronic + + + −; Foxp1 POLR2A*, SETDB1*
1:207509364 rs1507760 C/T CD55 intronic + + + −; NK-kappaB POLR2A*, EBF1, CHD1, EP300, CTCF*, GATA1, RAD21*, NFKB1*, TBP, SP1, YY1, TBL1XR1, CHD2, RUNX3, BHLHE40, MXI1; POL24H8, POL2B
9:71733141 rs11145326 C/G TJP2 intergenic 3.1kb 5′ of TJP2 − − + −; MSX2, Pax6, STAT, Sox PAX6, SOX15, SOX7, SOX8
9:71770938 rs11145488 G/A TJP2 intronic + + + −; Nanog, Sox  
9:71791546 rs1538583 A/G TJP2 intronic + + + POU3F2; Foxa, Pbx3, Pou1f1, Pou3f2, STAT EBF1*, PML, NFIC
12:56114768 rs3138144 G/C RDH5 intronic + + + −; BCL, NRSF MYC, CEBPB, POLR2A, EP300, RUNX3, ZBTB7A, RXRA, MAZ, SMC3, CTCF*, E2F1
12:56115584 rs3138142 C/T RDH5 exon, synonymous-coding + + + Nr2f2; PLAG1*, RXRA* POLR2A
17:31184630 rs17183628 T/C MYO1D intronic + − + Zfp691, ZFP652; FXR, Pax4, VDR TEAD4
17:31187215 rs17781142 G/C MYO1D intronic + + + −; LBP-1 JUN, PML, GATA2*, POLR2A, MAX, RCOR1, CEBPB, STAT2, GATA1*, STAT5A, EBF1*, TAF7, JUND, EP300, CCNT2*, MAZ, IRF1, NFKB1, EBF1, TBL1XR1, MYC*
17:31239644 rs10512441 C/T MYO1D intergenic 15 kb 5′ of TMEM98 − + + HNF3beta; Foxa, Foxj2 EP300*, POLR2A*, CTCF*, TRIM28, FOXA2*, JUND, GATA3*, UBTF, SRF*, TAF1, YY1, ZBTB7A, ZNF143, SP1, ARID3A, HDAC2, FOXA1*, TBP*, MYC, PML, PHF8, MAZ; KAP1*, HDAC2*
18:72154930 rs747176 G/A CNDP2 intergenic 8.6 kb 5′ of CNDP2 + − + −; Mrg, Pax5, Pbx3, TAL1, Tgif1  
18:72167123 rs3764509 C/G CNDP2 5′ UTR + + + −; Pbx3 POU2F2, SIN3A*, STAT3*, STAT1*, TAF1*, USF1*, TBP, USF2, SAP30, RUNX3, BHLHE40, CTCF, E2F6*, YY1*, CEBPB*; MAX, POLR2A, POL24H8, SIN3AK20, MYC, NFKB, MXI1, ETS1
18:72167801 rs12605820 G/A CNDP2 intronic + + + Sfpi1; Foxo, HP1, Mef2, TCF12  
18:72168485 rs8084410 T/C CNDP2 intronic + + + TEF*, TEAD1, TEAD4, TEAD3; DMRT4, RFX5, TCF12 SIN3A
18:72168607 rs2303463 G/A CNDP2 exon, synonymous-coding + + + EGR2, EGR3  
18:72170298 rs4891557 C/T CNDP2 intronic + − + ESR1, EWSR1-FLI1; ERalpha-a, EWSR1-FLI1, Irf, RXRA, VDR  
18:72170396 rs4891559 G/A CNDP2 intronic + − + −; Bbx, Foxj2  
18:72174022 rs12971120 A/G CNDP2 intronic + + +    
18:72174979 rs3829640 A/G CNDP2 intronic + + + −; Bcl6b  
18:72176082 rs2278161 T/C CNDP2 exon, nonsynonymous- coding + + + −; BDP1 GATA2*, TAL1*, MYC
18:72177231 rs11151960 G/A CNDP2 intronic + + + Sox13, Zic1, Zic2; E2F, Tel2 PAX5
18:72178160 rs2278159 T/C CNDP2 exon, synonymous-coding + + + −; Maf  
18:72178299 rs2278158 G/T CNDP2 intronic + + + −; Ets, TATA  
18:72179578 rs734559 G/A CNDP2 intronic + + + Lyf-1, PTF1-beta; CEBPB, HMG-1Y, Ik-1, IK-2, NF-AT, NF-AT1, PTF1-beta, Pou5f1  
18:72182964 rs3794950 G/A CNDP2 intronic + + + −; Jundm2  

RefSNP ID = reference SNP identification number in NCBI reference assembly, eQTL = expression quantitative trait loci, DNase = deoxyribonuclease.

1GWAS significant SNPs are bolded.

2Promoter and Enhancer histone marks are included.

3Data of motif altered and protein bound are separated by semicolons: before from RegulomeDB and after from Haploreg database. The repeated sites in both databases are marked with an asterisk.