Table 4. Regions of the genome showing moderate evidence of association.
| Collection | Chromosome | Region (Mb) |
SNP | Trend P value | Genotypic P value | log10(BF), additive |
log10(BF), general |
Risk allele | Minor allele | Heterozygote odds ratio |
Homozygote odds ratio |
Control MAF | Case MAF |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BD | 2p25 | 11.94-12.00 | rs4027132 | 1.31 × 10-05 | 9.68 × 10-06 | 3.07 | 2.84 | A | G | 1.39 (1.19-1.64) |
1.51 (1.27-1.79) |
0.459 | 0.414 |
| BD | 2q12 | 104.41-104.58 | rs7570682 | 3.11 × 10-06 | 1.64 × 10-05 | 3.68 | 3.23 | A | A | 1.23 (1.09-1.40) |
1.64 (1.28-2.12) |
0.214 | 0.255 |
| BD | 2q14 | 115.63-116.11 | rs1375144 | 2.43 × 10-06 | 1.31 × 10-05 | 3.80 | 2.92 | A | G | 1.32 (1.07-1.63) |
1.59 (1.29-1.96) |
0.337 | 0.291 |
| BD | 2q37 | 241.23-241.28 | rs2953145 | 1.11 × 10-05 | 6.57 × 10-06 | 3.22 | 3.50 | C | G | 1.84 (1.31-2.58) |
2.14 (1.53-2.98) |
0.226 | 0.189 |
| BD | 3p23 | 32.26-32.33 | rs4276227 | 4.57 × 10-06 | 2.62 × 10-05 | 3.52 | 3.04 | C | T | 1.20 (0.99-1.46) |
1.49 (1.23-1.81) |
0.371 | 0.326 |
| BD | 3q27 | 184.29-184.40 | rs683395 | 2.30 × 10-06 | 5.11 × 10-06 | 3.87 | 3.73 | G | G | 1.47 (1.26-1.71) |
1.30 (0.69-2.46) |
0.080 | 0.109 |
| BD | 6p21 | 42.82-42.86 | rs6458307 | 3.43 × 10-01 | 4.35 × 10-06 | 20.80 | 2.84 | T | T | 0.84 (0.75-0.96) |
1.39 (1.13-1.69) |
0.312 | 0.321 |
| BD | 8p12 | 34.22-34.61 | rs2609653 | 6.86 × 10-06 | - | 3.44 | 3.21 | C | C | 1.43 (1.19-1.71) |
3.62 (1.26-10.44) |
0.052 | 0.074 |
| BD | 9q32 | 114.31-114.39 | rs10982256 | 8.80 × 10-06 | 4.41 × 10-05 | 3.23 | 2.37 | T | C | 1.26 (1.08-1.47) |
1.47 (1.24-1.74) |
0.471 | 0.425 |
| BD | 14q22 | 57.17-57.24 | rs10134944 | 3.21 × 10-06 | 6.89 × 10-06 | 3.73 | 3.59 | T | T | 1.45 (1.24-1.68) |
1.32 (0.74-2.33) |
0.086 | 0.115 |
| BD | 14q32 | 103.43-103.62 | rs11622475 | 2.10 × 10-06 | 8.14 × 10-06 | 3.87 | 3.24 | C | T | 1.13 (0.89-1.44) |
1.47 (1.17-1.86) |
0.300 | 0.256 |
| BD | 16q12 | 51.36-51.50 | rs1344484 | 1.64 × 10-06 | 1.03 × 10-05 | 3.94 | 3.41 | T | C | 1.24 (1.03-1.48) |
1.52 (1.27-1.82) |
0.402 | 0.353 |
| BD | 20p13 | 3.70-3.73 | rs3761218 | 4.43 × 10-05 | 6.71 × 10-06 | 2.58 | 3.18 | T | C | 0.97 (0.81-1.15) |
1.31 (1.09-1.57) |
0.397 | 0.356 |
| CAD | 1q43 | 236.77-236.85 | rs17672135 | 1.04 × 10-04 | 2.35 × 10-06 | 2.36 | 3.88 | T | C | 0.70 (0.61-0.81) |
1.32 (0.79-2.22) |
0.134 | 0.108 |
| CAD | 5q21 | 99.98-100.11 | rs383830 | 5.72 × 10-06 | 1.34 × 10-05 | 3.49 | 3.26 | T | A | 1.60 (1.16-2.21) |
1.92 (1.40-2.63) |
0.220 | 0.182 |
| CAD | 6q25 | 151.34-151.42 | rs6922269 | 6.33 × 10-06 | 1.50 × 10-05 | 3.38 | 3.14 | A | A | 1.17 (1.04-1.32) |
1.65 (1.32-2.06) |
0.253 | 0.294 |
| CAD | 16q23 | 81.72-81.79 | rs8055236 | 9.73 × 10-06 | 5.60 × 10-06 | 3.28 | 3.59 | G | T | 1.91 (1.33-2.74) |
2.23 (1.56-3.17) |
0.198 | 0.162 |
| CAD | 19q12 | 34.74-34.78 | rs7250581 | 9.12 × 10-06 | 2.50 × 10-05 | 3.30 | 2.87 | G | A | 1.06 (0.79-1.43) |
1.40 (1.05-1.86) |
0.220 | 0.182 |
| CAD | 22q12 | 25.01-25.06 | rs688034 | 6.90 × 10-06 | 3.75 × 10-06 | 3.33 | 3.15 | T | T | 1.11 (0.98-1.25) |
1.62 (1.34-1.95) |
0. × 10 | 0.355 |
| CD | 1q24 | 169.53-169.67 | rs12037606 | 1.79 × 10-06 | 1.09 × 10-05 | 3.89 | 3.35 | A | A | 1.22 (1.07-1.40) |
1.52 (1.28-1.82) |
0.388 | 0.438 |
| CD | 5q23 | 131.40-131.90 | rs6596075 | 5.40 × 10-07 | 3.19 × 10-06 | 4.54 | 4.01 | C | G | 1.55 (1.00-2.39) |
2.06 (1.35-3.14) |
0.166 | 0.127 |
| CD | 6p22 | 20.83-20.85 | rs6908425 | 5.13 × 10-06 | 1.10 × 10-05 | 3.55 | 3.38 | C | T | 1.63 (1.18-2.25) |
1.95 (1.43-2.67) |
0.230 | 0.190 |
| CD | 6p21 | 32.79-32.91 | rs9469220 | 8.65 × 10-07 | 2.28 × 10-06 | 4.19 | 3.92 | A | A | 1.14 (0.98-1.32) |
1.52 (1.28-1.79) |
0.481 | 0.534 |
| CD | 6q23 | 138.06-138.17 | rs7753394 | 4.42 × 10-06 | 2.59 × 10-05 | 3.52 | 2.99 | C | C | 1.21 (1.04-1.40) |
1.48 (1.25-1.76) |
0.482 | 0.531 |
| CD | 7q36 | 147.62-147.70 | rs7807268 | 6.89 × 10-06 | 4.42 × 10-06 | 3.33 | 3.58 | G | G | 1.38 (1.20-1.60) |
1.47 (1.24-1.74) |
0.462 | 0.509 |
| CD | 10p15 | 38.52-38.57 | rs6601764 | 2.56 × 10-06 | 8.95 × 10-06 | 3.74 | 3.01 | C | C | 1.16 (1.01-1.33) |
1.52 (1.28-1.80) |
0.408 | 0.458 |
| CD | 19q13 | 50.89-51.07 | rs8111071 | 6.14 × 10-06 | 1.75 × 10-05 | 3.48 | 3.29 | G | G | 1.47 (1.25-1.73) |
1.28 (0.56-2.88) |
0.070 | 0.096 |
| HT | 1q43 | 235.67-235.79 | rs2820037 | 5.76 × 10-05 | 7.66 × 10-07 | 2.54 | 3.99 | T | T | 1.54 (1.03-2.31) |
1.09 (0.74-1.62) |
0.141 | 0.171 |
| HT | 8q24 | 140.17-140.35 | rs6997709 | 7.88 × 10-06 | 4.36 × 10-05 | 3.32 | 2.60 | G | T | 1.20 (0.94-1.52) |
1.49 (1.18-1.89) |
0.285 | 0.244 |
| HT | 12p12 | 24.86-24.95 | rs7961152 | 7.39 × 10-06 | 3.03 × 10-05 | 3.29 | 2.51 | A | A | 1.16 (1.01-1.32) |
1.47 (1.25-1.74) |
0.415 | 0.461 |
| HT | 12q23 | 100.52-100.58 | rs11110912 | 9.18 × 10-06 | 1.94 × 10-05 | 3.27 | 3.11 | G | G | 1.33 (1.18-1.51) |
1.34 (0.96-1.86) |
0.165 | 0.200 |
| HT | 13q21 | 66.90-67.04 | rs1937506 | 9.23 × 10-06 | 4.53 × 10-05 | 3.25 | 2.85 | G | A | 1.33 (1.04-1.69) |
1.60 (1.26-2.02) |
0.289 | 0.248 |
| HT | 15q26 | 94.60-94.67 | rs2398162 | 7.85 × 10-06 | 5.67 × 10-06 | 3.33 | 3.40 | A | G | 0.97 (0.76-1.25) |
1.31 (1.03-1.67) |
0.258 | 0.218 |
| RA | 1p36 | 2.44-2.77 | rs6684865 | 5.37 × 10-06 | 3.14 × 10-05 | 3.47 | 2.97 | G | A | 1.27 (1.02-1.56) |
1.54 (1.25-1.90) |
0.338 | 0.294 |
| RA | 1p31 | 80.16-80.36 | rs11162922 | 1.80 × 10-06 | - | 4.11 | 3.80 | A | G | 1.27 (0.41-4.01) |
2.00 (0.64-6.20) |
0.072 | 0.048 |
| RA | 4p15 | 24.99-25.13 | rs3816587 | 7.65 × 10-03 | 9.25 × 10-06 | 0.50 | 2.64 | C | C | 0.91 (0.80-1.04) |
1.35 (1.14-1.59) |
0.406 | 0.434 |
| RA | 6q23 | 138.00-138.06 | rs6920220 | 4.99 × 10-06 | 1.58 × 10-05 | 3.49 | 3.17 | A | A | 1.20 (1.06-1.36) |
1.72 (1.33-2.22) |
0.223 | 0.263 |
| RA | 7q32 | 130.80-130.84 | rs11761231 | 1.74 × 10-06 | 2.65 × 10-06 | 3.92 | 3.42 | C | T | 1.44 (1.19-1.75) |
1.64 (1.35-1.99) |
0.375 | 0.327 |
| RA | 10p15 | 6.07-6.16 | rs2104286 | 7.02 × 10-06 | 2.52 × 10-05 | 3.37 | 2.57 | T | C | 1.41 (1.10-1.81) |
1.68 (1.31-2.14) |
0.286 | 0.244 |
| RA | 13q12 | 19.845-19.855 | rs9550642 | 8.44 × 10-06 | 3.90 × 10-05 | 3.35 | 3.02 | A | A | 1.34 (1.15-1.56) |
2.23 (1.21-4.13) |
0.084 | 0.112 |
| RA | 21q22 | 41.430-41.465 | rs2837960 | 3.45 × 10-02 | 1.68 × 10-06 | 0.05 | 2.70 | G | G | 0.95 (0.83-1.08) |
2.30 (1.64-3.23) |
0.171 | 0.188 |
| RA | 22q13 | 35.870-35.885 | rs743777 | 7.92 × 10-06 | 1.15 × 10-06 | 3.29 | 3.52 | G | G | 1.09 (0.97-1.24) |
1.72 (1.40-2.11) |
0.292 | 0.336 |
| T1D | 1q42 | 221.92-222.17 | rs2639703 | 8.46 × 10-06 | 1.74 × 10-05 | 3.25 | 3.06 | C | C | 1.15 (1.02-1.30) |
1.61 (1.31-1.99) |
0.276 | 0.318 |
| T1D | 4q27 | 123.02-123.92 | rs17388568 | 5.01 × 10-07 | 3.27 × 10-06 | 4.42 | 3.89 | A | A | 1.26 (1.11-1.42) |
1.58 (1.27-1.95) |
0.260 | 0.307 |
| T1D | 5q14 | 86.20-86.50 | rs2544677 | 8.23 × 10-06 | 4.43 × 10-05 | 3.32 | 2.70 | C | G | 1.34 (1.00-1.79) |
1.65 (1.24-2.18) |
0.242 | 0.204 |
| T1D | 5q31 | 132.64-132.67 | rs17166496 | 6.06 × 10-01 | 5.20 × 10-06 | 20.97 | 3.25 | C | G | 0.77 (0.68-0.87) |
1.09 (0.92-1.29) |
0.391 | 0.386 |
| T1D | 10p15 | 6.07-6.18 | rs2104286 | 7.96 × 10-06 | 4.32 × 10-05 | 3.31 | 2.88 | T | C | 1.30 (1.02-1.65) |
1.57 (1.25-1.99) |
0.286 | 0.245 |
| T1D | 12p13 | 9.71-9.80 | rs11052552 | 1.02 × 10-04 | 7.24 × 10-07 | 2.22 | 3.80 | G | T | 1.49 (1.28-1.73) |
1.43 (1.21-1.69) |
0.486 | 0.446 |
| T1D | 18p11 | 12.76-12.91 | rs2542151 | 1.89 × 10-06 | 1.16 × 10-05 | 3.91 | 3.52 | G | G | 1.30 (1.15-1.47) |
1.62 (1.17-2.24) |
0.163 | 0.201 |
| T2D | 1p31 | 66.04-66.36 | rs4655595 | 2.68 × 10-06 | 1.33 × 10-05 | 3.81 | 3.47 | G | G | 1.37 (1.17-1.59) |
2.33 (1.23-4.42) |
0.080 | 0.108 |
| T2D | 2q24 | 160.90-161.17 | rs6718526 | 2.40 × 10-06 | 1.16 × 10-05 | 3.86 | 3.35 | C | T | 1.49 (1.05-2.11) |
1.86 (1.32-2.63) |
0.209 | 0.171 |
| T2D | 3p14 | 55.24-55.32 | rs358806 | 4.77 × 10-01 | 3.05 × 10-06 | 20.83 | 2.72 | A | A | 0.86 (0.75-0.97) |
1.78 (1.34-2.36) |
0.198 | 0.204 |
| T2D | 4q27 | 122.92-123.02 | rs7659604 | 2.1 × 10-02 | 9.42 × 10-06 | 0.13 | 2.74 | T | T | 1.35 (1.19-1.54) |
1.09 (0.91-1.30) |
0.380 | 0.403 |
| T2D | 10q11 | 43.43-43.63 | rs9326506 | 7.78 × 10-06 | 2.99 × 10-05 | 3.27 | 2.92 | C | C | 1.28 (1.11-1.48) |
1.46 (1.24-1.72) |
0.492 | 0.538 |
| T2D | 12q13 | 49.50-49.87 | rs12304921 | 5.37 × 10-02 | 7.07 × 10-06 | 20.09 | 2.68 | G | G | 2.50 (1.53-4.09) |
1.94 (1.20-3.15) |
0.145 | 0.159 |
| T2D | 12q15 | 69.58-69.96 | rs1495377 | 1.31 × 10-06 | 6.52 × 10-06 | 4.01 | 3.15 | G | G | 1.28 (1.11-1.49) |
1.51 (1.28-1.78) |
0.497 | 0.547 |
| T2D | 15q24 | 72.24-72.50 | rs2930291 | 7.72 × 10-06 | 4.40 × 10-05 | 3.30 | 2.42 | G | A | 1.25 (1.04-1.51) |
1.50 (1.24-1.82) |
0.377 | 0.332 |
| T2D | 15q25 | 78.12-78.36 | rs2903265 | 9.57 × 10-06 | 4.98 × 10-05 | 3.24 | 2.53 | G | A | 1.18 (0.93-1.49) |
1.47 (1.17-1.86) |
0.284 | 0.243 |
Regions with at least one SNP with a P value of greater than 5 × 10-7 and less than 1 × 10-5 for either the trend or the genotypic test. Columns as for Table 3. Cluster plots for each SNP have been inspected visually. Positions are in NCBI build-35 coordinates. Genotypic P values were not calculated for SNPs with the lowest MAFs owing to low numbers of rare-allele homozygotes and sensitivity to genotype calling errors.