Table 1.
Thirty-eight genetic variants associated with type 2 diabetes (T2D) at genome-wide significance.
| Locus | Marker | Chr | Type of variant | Risk allele/ other allele |
Risk allele frequency |
OR for T2D (95% CI) |
|---|---|---|---|---|---|---|
| KCNQ1 | rs223789274 a | 11 | Intronic | C/T | 0.61b | 1.40 (1.34–1.47) |
| TCF7L2 | rs79031469 | 10 | Intronic | T/C | 0.25 | 1.37 (1.28–1.47)18 |
| DUSP9 | rs594532619 | X | 8 kb upstream | G/A | 0.12 | 1.27 (1.18–1.37) |
| CDKN2A/B | rs1081166115–17 | 9 | 125 kb upstream | T/C | 0.79 | 1.20 (1.14–1.25) |
| IRS1 | rs294364175 | 2 | 502 kb upstream | C/T | 0.61 | 1.19 (1.13–1.25) |
| IGF2BP2 | rs440296015–17 | 3 | Intronic | T/G | 0.29 | 1.17 (1.10–1.25)18 |
| FTO | rs805013615, 16 | 16 | Intronic | A/C | 0.45 | 1.15 (1.09–1.22)18 |
| KCNJ11/ABCC8 | rs5219c/rs75711012 c | 11 | Missense:Glu23Lys/Ala1369Ser | T/C | 0.50 | 1.15 (1.09–1.21)17 |
| G/T | 0.40 | |||||
| THADA | rs757859718 | 2 | Missense: Thr1187Ala | T/C | 0.92 | 1.15 (1.10–1.20) |
| CENTD2 | rs155222419 | 11 | 5′ UTR | A/C | 0.88 | 1.14 (1.11–1.17) |
| PPARG | rs180128211 | 3 | Missense: Pro12Ala | C/G | 0.92 | 1.14 (1.08–1.20)15–17 |
| HHEX | rs111187514 | 10 | 7.7 kb downstream | C/T | 0.56 | 1.13 (1.08–1.17)17 |
| NOTCH2 | rs1092393118 | 1 | Intronic | T/G | 0.11 | 1.13 (1.08–1.17) |
| WFS1 | rs180121419 | 4 | Intron-exon junction | G/A | 0.27 | 1.13 (1.07–1.18) |
| ADCY5 | rs1170806776 | 3 | Intronic | A/G | 0.78 | 1.12 (1.09–1.15) |
| CDKAL1 | rs775484015–17 | 6 | Intronic | C/G | 0.31 | 1.12 (1.08–1.16) |
| HNF1B | rs75721077, 78 | 17 | Intronic | A/G | 0.43 | 1.12 (1.07–1.18)19 |
| SLC30A8 | rs1326663414 | 8 | Missense: Arg325Trp | C/T | 0.75 | 1.12 (1.07–1.16)19 |
| CDC123/CAMK1D | rs1277979018 | 10 | Intergenic region | G/A | 0.23 | 1.11 (1.07–1.14) |
| RBMS1/ITGB6 | rs759373079 | 2 | Intronic | C/T | 0.57 | 1.11 (1.08–1.16) |
| TLE4 | rs1329213619 | 9 | 234 kb upstream | C/T | 0.93 | 1.11 (1.07–1.15) |
| HMGA2 | rs153134319 | 12 | 43 kb upstream | C/G | 0.10 | 1.10 (1.07–1.14) |
| JAZF1 | rs86474518 | 7 | Intronic | T/C | 0.52 | 1.10 (1.07–1.13) |
| ADAMTS9 | rs460710318 | 3 | 38 kb upstream | C/T | 0.81 | 1.09 (1.06–1.12) |
| MTNR1B | rs1083096376 | 11 | Intronic | G/C | 0.30 | 1.09 (1.06–1.12) |
| TSPAN8/LGR5 | rs796158118 | 12 | Intronic | C/T | 0.23 | 1.09 (1.06–1.12) |
| BCL11A | rs24302119 | 2 | 99 kb downstream | A/G | 0.46 | 1.08 (1.06–1.10) |
| KCNQ1 | rs23136219 a | 11 | Intronic | G/A | 0.52 | 1.08 (1.06–1.10) |
| ZBED3 | rs445705319 | 5 | 41 kb upstream | G/A | 0.26 | 1.08 (1.06–1.11) |
| GCK | rs460751776 | 7 | 36 kb upstream | A/G | 0.20 | 1.07 (1.05–1.10) |
| KLF14 | rs97228319 | 7 | 47 kb upstream | G/A | 0.55 | 1.07 (1.05–1.10) |
| OASL/HNF1A | rs795719719 | 12 | 20 kb downstream | T/A | 0.85 | 1.07 (1.05–1.10) |
| PRC1 | rs804268019 | 15 | Intronic | A/C | 0.22 | 1.07 (1.05–1.09) |
| PROX1 | rs34087476 | 1 | 2 kb upstream | C/T | 0.50 | 1.07 (1.05–1.09) |
| DGKB/TMEM195 | rs219134976 | 7 | Intergenic region | T/G | 0.47 | 1.06 (1.04–1.08) |
| GCKR | rs78009476 | 2 | Intronic | C/T | 0.62 | 1.06 (1.04–1.08) |
| TP53INP1 | rs89685419 | 8 | Intronic | T/C | 0.48 | 1.06 (1.04–1.09) |
| ZFAND6 | rs1163439719 | 15 | 1.5 kb downstream | G/A | 0.56 | 1.06 (1.04–1.08) |
SNPs are ordered by odds ratio (OR) for T2D. Reference for each SNP is from the original report, and OR for T2D is from that reference cited unless otherwise noted. Risk allele frequencies are from HapMap CEU unless otherwise noted. Chr, chromosome. CI, confidence interval. kb, kilobase. Adapted from Billings LK, Florez JC. Ann NY Acad Sci. 2010 Nov; 1212:59–77.
a
These SNPs are in low linkage disequilibrium (LD) in Europeans (r2 = 0.01) and likely represent independent association signals.
b
Risk allele frequency from HapMap-JPT.
c
These two SNPs are in strong LD in adjacent genes in Europeans (r2 = 0.87).