Table 3. Genome-wide significant loci outside the MHC region and the top variant within the MHC region.
Bold font in the left half of the table indicates novel loci, whereas bold font in the right half indicates variants that replicated in Sardinians. All P values shown are two-sided. Gene names of known loci are as listed by Sawcer et al. (3). C, chromosome. For additional details, see table S4.
| Variant | C | MA | Gene | MAF DE | OR (CI) DE1 + DE2 | P DE1 + DE2 | P Sardinia | OR (CI) DE + Sardinia | P DE + Sardinia |
| rs10797431 | 1 | T | MMEL1 | 34.1 | 0.84 (0.80–0.89) | 1.81 × 10−10 | |||
| rs6689470 | 1 | A | EVI5 | 14.2 | 1.24 (1.16–1.33) | 3.93 × 10−10 | |||
| rs2300747 | 1 | G | CD58 | 12.4 | 0.75 (0.69–0.81) | 1.74 × 10−12 | |||
| rs7535818 | 1 | G | RGS1 | 19.2 | 0.76 (0.71–0.82) | 1.51 × 10−15 | |||
| rs2681424 | 3 | C | CD86 | 49.7 | 0.86 (0.82–0.90) | 9.51 × 10−10 | |||
| rs6859219 | 5 | A | ANKRD55 | 22.2 | 0.84 (0.79–0.89) | 8.06 × 10−9 | |||
| rs3104373 | 6 | T | HLA-DRB1 | 13.6 | 2.90 (2.72–3.09) | 1.34 × 10−234 | |||
| rs4364506 | 6 | A | L3MBTL3 | 26.4 | 0.84 (0.80–0.89) | 4.06 × 10−9 | 0.83 | 0.89 (0.85–0.93) | 1.99 × 10−6 |
| rs2182410 | 10 | T | IL2RA | 38.1 | 0.84 (0.79–0.88) | 1.15 × 10−11 | |||
| rs1891621 | 10 | G | Intergenic | 46.7 | 0.87 (0.83–0.91) | 2.94 × 10−8 | |||
| rs1800693 | 12 | C | TNFRSF1A | 42.1 | 1.17 (1.11–1.23) | 1.06 × 10−9 | |||
| rs2812197 | 13 | T | DLEU1 | 38.4 | 0.86 (0.82–0.91) | 9.95 × 10−9 | 6.86 × 10−3 | 0.87 (0.83–0.91) | 2.83 × 10−10 |
| rs6498168 | 16 | T | CLEC16A | 35.5 | 1.23 (1.17–1.29) | 1.98 × 10−15 | |||
| rs34286592 | 16 | T | MAZ | 14.2 | 1.21 (1.13–1.30) | 4.58 × 10−8 | 0.44 | 1.16 (1.09–1.23) | 4.79 × 10-7 |
| rs4925166 | 17 | T | SHMT1 | 34.5 | 0.85 (0.81–0.90) | 2.69 × 10−9 | 5.63 × 10−4 | 0.86 (0.82–0.90) | 7.40 × 10−12 |
| rs2836425 | 21 | T | ERG | 12.7 | 1.22 (1.14–1.31) | 2.84 × 10−8 | 0.35 | 1.18 (1.11–1.25) | 1.54 × 10−7 |