Table 4.
Strong two-SNP associations with T1D
| SNP1 | Pos1 | Pval1 | Gene | SNP2 | Pos2 | Pval2 | Gene | JointP |
|---|---|---|---|---|---|---|---|---|
| rs7525703 | chr1: 143 | 2e–2 | PRKAB2 | rs2077749 | chr1: 143 | 3e–6 | PRKAB2 | 2e–12 |
| rs6809441 | chr3: 41 | 4e–2 | ULK4 | N/A | chr3: 41 | 7e–2 | ULK4 | 5e–11 |
| rs330483 | chr4: 176 | 4e–6 | ADAM29 | rs330504 | chr4: 176 | 1e–1 | ADAM29 | 2e–11 |
| rs6906469 | chr6: 10 | 1e–3 | DFCC1 | rs659964* | chr12: 111 | 2e–6 | ACAD10 | 4e–11 |
| rs3132676* | chr6: 30 | 1e–5 | TRIM40 | rs9376523 | chr6: 141 | 6e–4 | TXLNB | 3e–11 |
| rs9296661 | chr6: 52 | 4e–4 | PKHD1 | rs1265566* | chr12: 110 | 1e–6 | CUTL2 | 5e–11 |
| rs13340508 | chr7: 75 | 9e–3 | CCL24 | rs17361077 | chr7: 75 | 4e–5 | CCL24 | 6e–12 |
| rs4838140 | chr9: 124 | 2e–5 | NEK6 | rs7860360 | chr9: 125 | 6e–4 | SCAI | 4e–10 |
| rs11104868 | chr12: 87 | 1e–4 | KITLG | rs7961663* | chr12: 110 | 3e–6 | CUTL2 | 1e–11 |
| rs1958305 | chr14: 23 | 5e–5 | DHRS2 | rs12100601 | chr14: 23 | 2e–2 | DHRS2 | 0 |
| rs7262414 | chr20: 40 | 2e–5 | PTPRT | rs2867064 | chr20: 40 | 7e–2 | PTPRT | 0 |
Pairs of SNPs showing strong joint T1D associations (p-value < 5e–10) by B-stat. If multiple SNP pairs are located around the same loci, only one pair is shown. Pval1, Pval2, JointP represent nominal p-values of SNP1, SNP2, and their joint associations, respectively.
*
SNP lies in known regions in T1Dbase.