Table 2.
LD-independent SNPs with p-values smaller than 5 x 10−6
| Best SNP | Chr | A11 | A2 | MAF | Effect size | p-value | Variance explained (%) | Function Class | Closest protein coding gene (± 500 kb) |
|---|---|---|---|---|---|---|---|---|---|
| rs6077860+ | 20 | A | C | 0.21 | 1.27 | 4.61E-08 | 2.13 | Intronic | PSMF1 |
| rs1446965+ | 1 | A | G | 0.11 | -1.73 | 7.60E-08 | 1.95 | Downstream | APCS |
| rs72830077+ | 5 | G | A | 0.02 | 4.01 | 3.32E-07 | 1.17 | Intronic | TENM2 |
| rs6777575 | 3 | G | T | 0.34 | 1.29 | 5.21E-07 | 0.92 | Intronic | MAP3K13 |
| rs151087896 | 11 | T | TTTC | 0.23 | 1.57 | 1.08E-06 | 0.33 | Intergenic | B3GAT1 |
| rs78070351 | 20 | G | A | 0.08 | -1.72 | 1.78E-06 | 0.05 | Intronic | UQCC1 |
| rs28627209 | 18 | G | A | 0.10 | -1.82 | 2.26E-06 | 0.03 | Intronic | NFATC1 |
| rs2216360 | 3 | C | T | 0.19 | 1.26 | 3.32E-06 | 0.02 | Intronic | MECOM |
| rs17004715+ | 21 | G | A | 0.04 | 2.69 | 3.34E-06 | 0.02 | Intronic; Splice region variant | ITGB2 |
| rs7366960 | 1 | A | T | 0.42 | 1.19 | 3.84E-06 | 0.02 | Downstream | SLC27A3 |
| rs114172604 | 6 | A | G | 0.03 | 2.64 | 3.94E-06 | 0.02 | In LOC105377975 (lncRNA) | MAN1A1 |
| rs11876680 | 18 | C | A | 0.08 | -1.71 | 4.39E-06 | 0.02 | Intronic | SETBP1 |
| rs79045984+ | 15 | G | A | 0.02 | -3.68 | 4.61E-06 | 0.02 | Intronic | SCAPER |
| rs2002371 | 1 | T | C | 0.27 | -1.07 | 4.62E-06 | 0.01 | Intronic | CNIH3 |
| rs16978169 | 18 | C | T | 0.08 | -1.70 | 4.74E-06 | 0.02 | Intronic | SETBP1 |
Note: We define LD-independent SNPs as those with low LD (r2 < 0.1) to a more significantly associated SNP within a 500 kb window. +directly genotyped (all others are imputed); 1A1 is referred to as the effect allele.