Table 2.
Selection of risk variants in the CARe IBC chip
| Gene region | CARe SNP | Risk allele | CEU (r2)a | YRI (r2) a | MAF | OR (EA)b | p value | OR (AA) b | p value |
|---|---|---|---|---|---|---|---|---|---|
| NOTCH2 | rs835574 | T (min) | 0.9 | - | 0.13 | 1.19 | 5×10−3 | - | - |
| TCF7L2 | rs7903146 | T (min) | 1.0 | 1.00 | 0.29 | 1.40 | 2×10−14 | 1.33 | 1×10−6 |
| GCKR | rs780094 | C (maj) | 1.0 | 1.00 | 0.42 | 1.27 | 5×10−8 | 1.09 | 0.23 |
| CDKAL1 | rs7754840 | C (min) | 1.0 | - | 0.31 | 1.17 | 4×10−4 | - | - |
| GCK | rs6975024 | C (min) | 1.0 | 1.00 | 0.17 | 1.19 | 2×10−3 | 1.01 | 0.91 |
| KCNJ11 | rs5215 | C (min) | 1.0 | 1.00 | 0.37 | 1.09 | 0.06 | 0.98 | 0.85 |
| WFS1 | rs5018647 | C (maj) | 1.0 | 1.00 | 0.40 | 1.11 | 0.02 | 0.94 | 0.32 |
| HHEX | rs5015480 | C (maj) | 1.0 | - | 0.41 | 1.10 | 0.03 | - | - |
| IGF2BP2 | rs4402960 | T (min) | 1.0 | 1.00 | 0.32 | 1.20 | 3×10−5 | 1.11 | 0.06 |
| IRS1 | rs2943634 | C (maj) | 0.9 | - | 0.33 | 1.07 | 0.14 | 1.03 | 0.56 |
| KCNQ1 | rs231362 | G (maj) | 1.0 | 1.00 | 0.49 | 1.14 | 2×10−3 | 1.12 | 0.08 |
| PPARG | rs1801282 | C (maj) | 1.0 | - | 0.12 | 1.13 | 0.06 | - | - |
| SLC30A8 | rs13266634 | C (maj) | 1.0 | - | 0.32 | 1.18 | 3×10−4 | - | - |
| HNF1A | rs12427353 | G (maj) | 0.8 | - | 0.20 | 1.04 | 0.41 | - | - |
| MTNR1B | rs10830963 | G (min) | 1.0 | 1.00 | 0.26 | 1.19 | 2×10−4 | 1.06 | 0.62 |
| CDKN2A/2B | rs10811661 | T (maj) | 1.0 | - | 0.18 | 1.11 | 0.06 | - | - |
a
Linkage disequilibrium metric in the named HapMap populations for the CARe SNP correlated with the published type 2 diabetes risk allele
b
Type 2 diabetes-associated OR in CARe participants as indicated
AA, African-American; EA, European-American; MAF, minor allele frequency in CARe participants; Maj, major allele; Min, minor allele