Table 1.
Type 2 diabetes-associated risk allele characteristics
| SNP | Chr | Position NCBI 36.1 (bp) | No-risk allele | Risk allele | Risk allele frequencyb | Nearest gene(s) | iHS scorec | FeST global | FfST CEU-YRI | FgST CEU-JPT + CHB | FhST JPT + CHB-YRI |
|---|---|---|---|---|---|---|---|---|---|---|---|
| rs864745 | 7 | 28,147,081 | C | Ta | 0.518 | JAZF1 | −1.562 (11.7) | 0.098 (47.3) | 0.119 (35.7) | 0.160 (19.7) | 0 (93.3) |
| rs12779790 | 10 | 12,368,016 | Aa | G | 0.229 | CDC123/CAMK1D | NA | 0.051 (67.4) | 0.113 (37.1) | 0.028 (58.7) | 0.026 (71.7) |
| rs7961581 | 12 | 69,949,369 | Ta | C | 0.233 | TSPAN8/LGR5 | −0.518 (61.1) | 0 (98.3) | 0 (85.1) | 0 (88.9) | 0 (96.4) |
| rs7578597 | 2 | 43,586,327 | C | Ta | 0.917 | THADA | −0.999 (32.2) | 0.214 (18.8) | 0.126 (33.9) | 0.096 (32.7) | 0.336 (11.7) |
| rs4607103 | 3 | 64,686,944 | T | Ca | 0.808 | ADAMTS9 | 0.541 (59.5) | 0.060 (62.8) | 0.006 (80.1) | 0.103 (31.2) | 0.044 (64.2) |
| rs10923931 | 1 | 120,319,482 | Ga | T | 0.117 | NOTCH2 | 2.249 (2.3) | 0.258 (13.1) | 0.182 (23.4) | 0.069 (40.7) | 0.391 (8.2) |
| rs10946398 | 6 | 20,769,013 | A | Ca | 0.308 | CDKAL1 | −0.161 (87.5) | 0.122 (39.3) | 0.234 (16.6) | 0.009 (72.1) | 0.142 (36.2) |
| rs5015480 | 10 | 94,455,539 | T | Ca | 0.552 | HHEX/IDE | 0.479 (63.8) | 0.181 (24.7) | 0 (98.4) | 0.236 (10.7) | 0.246 (20.1) |
| rs10811661 | 9 | 22,124,094 | Ca | T | 0.792 | CDKN2A/B | 0.328 (74.7) | 0.229 (16.7) | 0.199 (20.1) | 0.088 (34.9) | 0.373 (9.3) |
| rs4402960 | 3 | 186,994,381 | Ga | T | 0.292 | IGF2BP2 | 1.641 (9.9) | 0.098 (47.3) | 0.129 (33.4) | 0 (94.3) | 0.160 (32.8) |
| rs13266634 | 8 | 118,253,964 | T | Ca | 0.75 | SLC30A8 | −1.869 (5.9) | 0.190 (22.9) | 0.123 (34.8) | 0.084 (36.2) | 0.314 (13.3) |
| rs7901695 | 10 | 114,744,078 | T | Ca | 0.28 | TCF7L2 | −0.208 (83.8) | 0.361 (5.2) | 0.111 (37.5) | 0.323 (5.2) | 0.579 (2.1) |
| rs5215 | 11 | 17,365,206 | Ta | C | 0.408 | KCNJ11 | −0.435 (66.9) | 0.191 (22.7) | 0.384 (5.9) | 0.004 (76.4) | 0.278 (16.6) |
| rs1801282 | 3 | 12,368,125 | G | Ca | 0.925 | PPARG | −0.571 (57.4) | 0.025 (80.9) | 0.065 (51.3) | 0.005 (75.9) | 0.026 (71.3) |
| rs4430796 | 17 | 33,172,153 | A | Ga | 0.533 | TCF2 | 0.849 (40.2) | 0.098 (47.2) | 0.003 (82.7) | 0.096 (32.9) | 0.160 (32.7) |
| rs10010131 | 4 | 6,343,816 | A | Ga | 0.733 | WFS1 | 1.461 (14.3) | 0.151 (31.2) | 0 (97.5) | 0.241 (10.3) | 0.246 (20.1) |
| rs2237892d | 11 | 2,796,327 | T | Ca | 0.611 | KCNQ1 | −0.618 (54.3) | 0.172 (26.5) | 0 (89.8) | 0.209 (13.4) | 0.171 (30.7) |
iHS scores and FST values are reported with their percentile rank in parentheses
aAncestral allele
bAllele frequencies taken from HapMap data release 23a/phase II Mar08, on NCBI B36 assembly, dbSNPb126, CEU population
cHaplotter—HapMap phase II data
dFor KCNQ1 the JPT + CHB population iHS score is displayed and the risk allele frequency is from JPT HapMap
e95% quantile over 2,911,292 markers is 0.365
f95% quantile over 2,859,309 markers is 0.406
g95% quantile over 2,454,054 markers is 0.327
h95% quantile over 2,817,341 markers is 0.465
NA, iHS score unavailable through Haplotter