Table 2. Identification of HNF4A and FOXA2 potential regulatory variants at lipid loci.
For each of these two transcription factors, we identified target genes in mouse livers, and then searched if the human homologs of these target genes were located within a 500 kilobase window around the 95 sentinel lipid SNPs. For the lipid loci that contain at least one target gene, we then query if the SNPs (or linkage disequilibrium proxies) overlapped with corresponding ENCODE ChIP-seq peaks and disrupted predicted binding sites. Two SNPs for each HNF4A and FOXA2 (in bold) met all these criteria.
| A-HNF4A | ||||
| Sentinel lipid SNP | Chr:Position (hg19) | HNF4A target gene(s) |
Is there a HNF4A ChIP- seq peak at the locus? |
SNPs in LD with sentinel lipid SNP that overlap with ENCODE HNF4A peaks (Do they disrupt predicted HNF4A binding sites?) |
| rs4846914 | Chr1:230,295,691 | GALNT2 | YES | rs4846913 (NO) |
| rs2144300 (NO) | ||||
| rs1260326 | Chr2:27,730,940 | FNDC4, SLC30A3 | NO | |
| rs1800562 | Chr6:26,093,141 | SLC17A3, HIST1H4D, HIST1H4F | NO | |
| rs17145738 | Chr7:72,982,874 | MLXIPL | YES | rs34060476 (NO) |
| rs2081687 | Chr8:59,388,565 | UBXN2B | NO | |
| rs11136341 | Chr8:145,043,543 | NRBP2 | NO | |
| rs7134594 | Chr12:110,000,193 | MMAB, MYO1H | YES | rs10744826 (NO) |
| rs10161126 (NO) | ||||
| rs1169288 | Chr12:121,416,650 | HNF1A | NO | |
| rs4759375 | Chr12:123,796,238 | SETD8 | YES | rs10846506 (NO) |
| rs838880 | Chr12:125,261,593 | BRI3BP | YES | rs838881 (NO) |
| rs838882 (YES) | ||||
| rs838884 (NO) | ||||
| rs16942887 | Chr16:67,928,042 | DUS2L, PSMB10 | YES | rs7188085 (NO) |
| rs2107369 (NO) | ||||
| rs8044328 (NO) | ||||
| rs4420638 | Chr19:45,422,946 | BCAM, PVRL2 | NO | |
| rs6029526 | Chr20:39,672,618 | PLCG1 | NO | |
| rs6065906 | Chr20:44,554,015 | WFDC3 | YES | rs6065905 (NO) |
| rs12185764 (YES) | ||||
| B-FOXA2 | ||||
| Sentinel lipid SNP | Chr:Position (hg19) | FOXA2 target gene(s) |
Is there a FOXA2 ENCODE peak at the locus? |
SNPs in LD with sentinel lipid SNP that overlap with ENCODE FOXA2 peaks (Do they disrupt predicted FOXA2 binding sites?) |
| rs629301 | Chr1:109,818,306 | SORT1 | YES | rs7528419 (NO) |
| rs12740374 (NO) | ||||
| rs660240 (NO) | ||||
| rs12328675 | Chr2:165,540,800 | COBLL1 | YES | rs7607980 (NO) |
| rs2290159 | Chr3:12,628,920 | PPARG | YES | rs60448371 (NO) |
| rs55762590 (NO) | ||||
| rs6450176 | Chr5:53,298,025 | ARL15 | YES | rs6889847 (NO) |
| rs6876198 (NO) | ||||
| rs3776712 (NO) | ||||
| rs1541681 (NO) | ||||
| rs1541680 (NO) | ||||
| rs3776707 (NO) | ||||
| rs3776706 (NO) | ||||
| rs3776705 (NO) | ||||
| rs3776703 (NO) | ||||
| rs3776702 (YES) | ||||
| rs1800562 | Chr6:26,093,141 | SLC17A3 | YES | rs115740542 (NO) |
| rs1169288 | Chr12:121,416,650 | P2RX7 | YES | rs6489786 (NO) |
| rs1169288 (NO) | ||||
| rs7206971 | Chr17:45,425,115 | ITGB3 | YES | rs4793978 (NO) |
| rs11079784 (NO) | ||||
| rs4129767 | Chr17:76,403,984 | BIRC5 | YES | rs4969182 (YES) |
| rs181362 | Chr22:21,932,068 | HIC2, SDF2L1 | NO | |