Table 1. Confirmed T2D susceptibility variants.
Representative SNPs are shown for each signal with ORs and 95% CIs reported (for the Cochran-Armitage 1df test) with respect to the risk allele (denoted in bold, with the ancestral allele underlined where known). SNPs selected for inclusion are those with the strongest evidence for association in the UK datasets (except in the case of TCF7L2, where, to maximize consistency across the datasets rs7901695 is presented). In the case of HHEX, the UK meta-analysis combines data from rs5015480 and rs1111875 (r2=1 in HapMap CEU). Since DGI and FUSION had not typed the identical SNPs in all samples, results shown for those studies feature the SNP generating the strongest association: in all cases these were SNPs in strong LD (minimum r2 0.95, except TCF7L2) and with consistent direction of effect with the SNP reported in the UK data (see Table S3 for details). The use of different SNPs may result in slightly different estimates of p values and OR between the three studies. Combined estimates of the ORs were calculated by weighting the logORs of each study by the inverse of their variance.
| WTCCC | Replication meta-analysis |
All UK sample meta-analysis |
DGI | FUSION | All Combined | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1924 cases | 3757 cases | 5681 cases | 6529 cases | 2376 cases | 14586 cases | ||||||||||||
| 2938 controls | 5346 controls | 8284 controls | 7252 controls | 2432 controls | 17968 controls | ||||||||||||
| rs | chr | position | A1 | A2 | Region | OR (95%Cis) |
Padd | OR (95%Cis) |
Padd | OR (95%Cis) |
Padd | OR (95%Cis) |
Padd | OR (95%Cis) |
Padd | OR (95% Cis) |
Padd |
| rs8050136 | 16 | 52373776 | A | C | FTO | 1.27 (1.16-1.37) |
2.0×10−8 | 1.22 (1.12-1.32) |
5.4×10−7 | 1.23 (1.18-1.32) |
7.3×10−14 | 1.03 (0.91-1.17) |
0.25 | 1.11 (1.02-1.20) |
0.017 | 1.17 (1.12-1.22) |
1.3×10−12 |
| rs10946398 | 6 | 20769013 | A | C | CDKAL1 | 1.20 (1.10-1.31) |
2.5×10−5 | 1.14 (1.07-1.22) |
8.4×10−5 | 1.16 (1.10-1.22) |
1.3×10−8 | 1.08 (1.03-1.14) |
2.4×10−3 | 1.12 (1.03-1.22) |
9.5×10−3 | 1.12 (1.08,1.16) |
4.1×10−11 |
| rs5015480 | 10 | 94455539 | C | T | HHEX | 1.22 (1.12-1.33) |
5.4×10−6 | - | - | ||||||||
| rs1111875 | 10 | 94452862 | C | T | HHEX | - | - | 1.08 (1.01-1.15) |
0.020 | 1.13 (1.07-1.19) |
4.6×10−6 | 1.14 (1.06-1.22) |
1.7×10−4 | 1.10 (1.01-1.19) |
0.025 | 1.13 (1.08-1.17) |
5.7×10−10 |
| rs10811661 | 9 | 22124094 | C | T | CDKN2B | 1.22 (1.09-1.37) |
7.6×10−4 | 1.18 (1.08-1.28) |
1.7×10−4 | 1.19 (1.11-1.28) |
4.9×10−7 | 1.20 (1.12-1.28) |
5.4×10−8 | 1.20 (1.07-1.36) |
2.2×10−3 | 1.20 (1.14-1.25) |
7.8−10−15 |
| rs564398 | 9 | 22019547 | C | T | CDKN2B | 1.16 (1.07-1.27) |
3.2×10−4 | 1.12 (1.05-1.19) |
8.6×10−4 | 1.13 (1.08-1.19) |
1.3×10−6 | 1.05 (0.94-1.17) |
0.5 | 1.13 (1.01-1.27) |
0.039 | 1.12 (1.07-1.17) |
1.2×10−7 |
| rs4402960 | 3 | 186994389 | G | T | IGF2BP2 | 1.15 (1.05-1.25) |
1.7×10−3 | 1.09 (1.01-1.16) |
0.018 | 1.11 (1.05-1.16) |
1.6×10−4 | 1.17 (1.11-1.23) |
1.7×10−9 | 1.18 (1.08-1.28) |
2.4×10−4 | 1.14 (1.11-1.18) |
8.6×10−16 |
| rs13266634 | 8 | 118253964 | C | T | SLC30A8 | 1.12 (1.02-1.23) |
0.020 | 1.12 (1.04-1.19) |
1.2×10−3 | 1.12 (1.05-1.18) |
7.0×10−5 | 1.07 (1.00-1.16) |
0.047 | 1.18 (1.09-1.29) |
7.0×10−5 | 1.12 (1.07-1.16) |
5.3×10−8 |
| rs7901695 | 10 | 114744078 | C | T | TCF7L2 | 1.37 (1.25-1.49) |
6.7×10−13 | - | - | - | - | 1.38 (1.31-1.46) |
2.3×10−31 | 1.34 (1.21-1.49) |
1.4×10−8 | 1.37 (1.31-1.43) |
1.0×10−48 |
| rs5215 | 11 | 17365206 | C | T | KCNJ11 | 1.15 (1.05-1.25) |
1.3×10−3 | - | - | - | - | 1.15 (1.09-1.21) |
1.0−10−7 | 1.11 (1.02-1.20) |
0.014 | 1.14 (1.10-1.19) |
5.0×10−11 |
| rs1801282 | 3 | 12368125 | C | G | PPARG | 1.23 (1.09-1.41) |
1.3×10−3 | - | - | - | - | 1.09 (1.01-1.16) |
0.019 | 1.20 (1.07-1.33) |
1.4×10−3 | 1.14 (1.08-1.20) |
1.7×10−6 |