Table 3.
SNP | Associated genes | Location in gene | ATAC-seq peak cell type-specificity | Preferential mRNA expression | TF binding sites [19] |
---|---|---|---|---|---|
Type 2 diabetes mellitus | |||||
rs7732130a | TCF7L2 | Intron | Endocrine cells | Same | NKX6.1, NKX2.2, FOXA2, MAFB |
rs7732130a | ZBED3-AS1 | Intron | Endocrine cells | β-cells | NKX2.2 |
rs1169288 | HNF1A | 5’ UTR | Endocrine cells | Same | NKX2.2, FOXA2 |
rs1800574 | HNF1A | 5′ UTR | Endocrine cells | Same | NKX2.2, FOXA2 |
rs5215 | KCNJ11 | 5′ UTR | Endocrine cells | β-cells | FOXA2 |
rs17066842 | MC4R | n/a (5′) | Endocrine cells | Same | NKX2.2 |
rs13266634 | SLC30A8 | Intron | Endocrine cells | Same | NKX2.2, FOXA2 |
rs11708067a | ADCY5 | Intron | α-cells | Same | none |
rs10811660a | CDKN2A-CDKN2B | n/a (5′) | α-cells | Same | MAFB, FOXA2 |
rs10757283 | CDKN2A-CDKN2B | n/a (5′) | α-cells | Same | MAFB, FOXA2 |
rs2237895 | KCNQ1 | Intron | α-cells | Same | NKX2.2, FOXA2 |
rs74046911 | KCNQ1 | Intron | α-cells | Same | NKX2.2, FOXA2 |
rs458069 | KCNQ1 | Intron | α-cells | Same | NKX2.2, FOXA2 |
Type 1 diabetes mellitus | |||||
rs11755527 | BACH2 | Intron | Endocrine cells | Same | None |
rs10517086 | none | n/a | Endocrine cells | n/a | None |
TF: transcription factor; UTR: untranslated region; n/a: not applicable.
Located within ATAC-seq peak region. Other SNPs are located within 1,000 bp of ATAC-seq peak region and TF binding sites.