Table 2.
New loci identified in this study
| RAFc | Discovery sample | Replication sample | Combined | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Chr | rsID | Positiona | Gene of interest (#)b |
Risk allele |
cases | controls | P scan | OR (95% CI) | P repl | OR (95% CI) | P comb |
| 1p36 | rs4649203 | 24392507 | IL28RA (2) | A | 0.77 | 0.73 | 6.46×10−06 | 1.22 (1.12-1.32) | 1.36×10−03 | 1.13 (1.05-1.22) | 6.89×10−08 |
| 2p16 | rs702873 | 60935046 | REL (5) | G | 0.62 | 0.56 | 1.32×10−07 | 1.23 (1.14-1.32) | 1.41×10−03 | 1.12 (1.04-1.20) | 3.59×10−09 |
| 2q24 | rs17716942 | 162968937 | IFIH1 (5) | A | 0.90 | 0.86 | 4.05×10−08 | 1.38 (1.23-1.54) | 3.82×10−07 | 1.29 (1.17-1.43) | 1.06×10−13 |
| 3p24 | rs6809854d | 18759427 | None | G | 0.23 | 0.19 | 3.09×10−06 | 1.24 (1.14-1.36) | 4.92×10−03 | 1.14 (1.04-1.26) | 1.12×10−07 |
| 5q15 | rs27524 | 96127700 | ERAP1 (2) | A | 0.40 | 0.36 | 6.81×10−10 | 1.27 (1.18-1.38) | 7.96×10−04 | 1.13 (1.05-1.22) | 2.56×10−11 |
| 6q21 | rs240993e | 111780407 | TRAF3IP2 (4) | A | 0.30 | 0.25 | 8.71×10−13 | 1.36 (1.25-1.48) | 3.37×10−09 | 1.25 (1.16-1.34) | 5.29×10−20 |
| rs458017ef | 111802784 | G | 0.09 | 0.06 | 8.11×10−11 | 1.62 (1.40-1.88) | 9.59×10−08 | 1.37 (1.22-1.54) | 2.16×10−16 | ||
| 14q13 | rs8016947 | 34902417 | NFKBIA (1) | C | 0.61 | 0.57 | 4.26×10−06 | 1.19 (1.11-1.29) | 7.89×10−07 | 1.19 (1.11-1.27) | 1.52×10−11 |
| 19p13 | rs12720356g | 10330975 | TYK2 (9) | A | 0.93 | 0.90 | 9.25×10−06 | 1.34 (1.18-1.52) | 8.82×10−07 | 1.40 (1.23-1.61) | 4.04×10−11 |
| rs280519g | 10333933 | A | 0.51 | 0.47 | 8.51×10−07 | 1.20 (1.12-1.30) | 5.93×10−04 | 1.13 (1.05-1.21) | 4.42×10−09 | ||
Evidence for association at loci reported in this study
NCBI human genome build 36 coordinates
The number in brackets shows the number of genes between recombination hotspots
Risk Allele Frequency
This SNP failed Sequenom genotyping so replication genotyping for this locus is at rs7428395 r2=0.97 calculated from 58C (HapMap CEU r2=1)
Separate signals within the same locus, where the marginal P values and OR are reported. For further discussion and details of joint models, see text.
This SNP failed Sequenom genotyping so replication genotyping for this locus is at rs465969 r2=0.73 calculated from 58C (HapMap CEU r2=0.82).
Separate signals within the same locus, where the marginal P values and OR are reported. For further discussion and details of joint models, see text.