Table 1.
Meta-analysis results for psoriasis loci. For known loci, the most significant SNP within 500kb (3Mb for MHC region) of the previously published SNP is shown. rs34536443 was the most strongly associated SNP in the TYK2 region, but found to be independent of the previously published SNP (rs12720356). ‘GWAS P value’: P value from the meta-analysis of the 3 GWAS datasets. ‘Immunochip P value’: the result of the meta-analysis of the two Immunochip datasets. ‘Combined P-value’: the P-value from the meta-analysis including all 5 datasets, RAF: Risk allele frequency, ‘Notable genes’: genes most likely to have an effect on the development of psoriasis.
| SNP | Chr. | Position (bp) | GWAS P-value (meta) | Immunochip p-value (meta) | Combined P-value | Risk/ Non-risk allele | RAF (Case) | RAF (Ctrls) | ORa (meta) | Notable genes | No. of genes +/− 500kb |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Known Loci | |||||||||||
| rs7552167 | 1 | 24,518,643 | 2.3×10−5 | 8.4×10−8 | 8.5×10−12 | G/A | 0.878 | 0.858 | 1.21 | IL28RA | 26 |
| rs9988642 | 1 | 67,726,104 | 2.5×10−13 | 3.5×10−15 | 1.1×10−26 | T/C | 0.952 | 0.929 | 1.52 | IL23R | 17 |
| rs6677595 | 1 | 152,590,187 | 8.1×10−15 | 2.7×10−20 | 2.1×10−33 | T/C | 0.689 | 0.640 | 1.26 | LCE3B, LCE3D | 43 |
| rs62149416 | 2 | 61,083,506 | 3.4×10−10 | 3.2×10−9 | 1.8×10−17 | T/C | 0.671 | 0.635 | 1.17 | FLJ16341, REL | 9 |
| rs17716942 | 2 | 163,260,691 | 4.1×10−9 | 1.0×10−10 | 3.3×10−18 | T/C | 0.891 | 0.863 | 1.27 | KCNH7, IFIH1 | 7 |
| rs27432 | 5 | 96,119,273 | 4.4×10−8 | 7.5×10−14 | 1.9×10−20 | A/G | 0.309 | 0.274 | 1.20 | ERAP1 | 7 |
| rs1295685 | 5 | 131,996,445 | 8.5×10−6 | 6.7×10−6 | 3.4×10−10 | G/A | 0.807 | 0.798 | 1.18 | IL13, IL4 | 21 |
| rs2233278 | 5 | 150,467,189 | 4.9×10−17 | 5.2×10−27 | 2.2×10−42 | C/G | 0.090 | 0.058 | 1.59 | TNIP1 | 17 |
| rs12188300 | 5 | 158,829,527 | 7.5×10−23 | 3.3×10−32 | 3.2×10−53 | T/A | 0.132 | 0.095 | 1.58 | IL12B | 5 |
| rs4406273 | 6 | 31,266,090 | 5.3×10−300 | 3.6×10−427 | 4.5×10−723 | A/G | 0.259 | 0.092 | 4.32 | HLA-B, HLA-C | 56 |
| rs33980500 | 6 | 111,913,262 | 4.3×10−20 | 7.6×10−27 | 4.2×10−45 | T/C | 0.108 | 0.074 | 1.52 | TRAF3IP2 | 8 |
| rs582757 | 6 | 138,197,824 | 2.0×10−14 | 3.7×10−13 | 2.2×10−25 | C/T | 0.315 | 0.273 | 1.23 | TNFAIP3 | 5 |
| rs1250546 | 10 | 81,032,532 | 5.1×10−4 | 3.2×10−4 | 6.8×10−7 | A/G | 0.605 | 0.579 | 1.10 | ZMIZ1 | 9 |
| rs645078 | 11 | 64,135,298 | 4.7×10−3 | 1.5×10−4 | 2.2×10−6 | A/C | 0.626 | 0.609 | 1.09 | RPS6KA4, PRDX5 | 36 |
| rs2066819 | 12 | 56,750,204 | 7.5×10−12 | 8.9×10−8 | 5.4×10−17 | C/T | 0.948 | 0.934 | 1.39 | STAT2, IL23A | 40 |
| rs8016947 | 14 | 35,832,666 | 1.4×10−9 | 1.6×10−9 | 2.5×10−17 | G/T | 0.600 | 0.564 | 1.16 | NFKBIA | 11 |
| rs12445568 | 16 | 31,004,812 | 1.2×10−6 | 1.8×10−11 | 1.2×10−16 | C/T | 0.403 | 0.368 | 1.16 | PRSS53, FBXL19 | 46 |
| rs28998802 | 17 | 26,124,908 | 3.6×10−6 | 1.7×10−11 | 3.3×10−16 | A/G | 0.170 | 0.145 | 1.22 | NOS2 | 9 |
| rs34536443 | 19 | 10,463,118 | 5.1×10−10 | 2.6×10−22 | 9.1×10−31 | G/C | 0.974 | 0.953 | 1.88 | TYK2 | 42 |
| rs1056198 | 20 | 48,556,229 | 6.2×10−9 | 1.6×10−7 | 1.5×10−14 | C/T | 0.600 | 0.573 | 1.16 | RNF114 | 11 |
| rs4821124 | 22 | 21,979,289 | 5.4×10−5 | 1.2×10−4 | 3.8×10−8 | C/T | 0.208 | 0.189 | 1.13 | UBE2L3 | 16 |
| Newly Identified Loci | |||||||||||
| rs11121129 | 1 | 8,268,095 | 7.3×10−5 | 4.6×10−5 | 1.7×10−8 | A/G | 0.308 | 0.287 | 1.13 | SLC45A1, TNFRSF9 | 15 |
| rs7536201 | 1 | 25,293,084 | 7.8×10−5 | 6.4×10−9 | 2.3×10−12 | C/T | 0.528 | 0.494 | 1.13 | RUNX3 | 18 |
| rs10865331 | 2 | 62,551,472 | 4.5×10−4 | 2.6×10−7 | 4.7×10−10 | A/G | 0.404 | 0.374 | 1.12 | B3GNT2 | 6 |
| rs9504361 | 6 | 577,820 | 5.1×10−7 | 4.2×10−6 | 2.1×10−11 | A/G | 0.574 | 0.546 | 1.12 | EXOC2, IRF4 | 5 |
| rs2451258 | 6 | 159,506,600 | 4.4×10−4 | 2.0×10−5 | 3.4×10−8 | C/T | 0.362 | 0.348 | 1.12 | TAGAP | 8 |
| rs2700987 | 7 | 37,386,237 | 3.3×10−7 | 4.6×10−4 | 4.3×10−9 | A/C | 0.591 | 0.564 | 1.11 | ELMO1 | 3 |
| rs11795343 | 9 | 32,523,737 | 2.8×10−7 | 2.1×10−5 | 8.4×10−11 | T/C | 0.628 | 0.597 | 1.11 | DDX58 | 7 |
| rs10979182 | 9 | 110,817,020 | 2.8×10−5 | 1.2×10−4 | 2.3×10−8 | A/G | 0.617 | 0.591 | 1.12 | KLF4 | 0 |
| rs4561177 | 11 | 109,962,432 | 1.1×10−4 | 1.4×10−9 | 7.7×10−13 | A/G | 0.617 | 0.581 | 1.14 | ZC3H12C | 4 |
| rs3802826 | 11 | 128,406,438 | 1.1×10−3 | 2.0×10−7 | 9.5×10−10 | A/G | 0.505 | 0.484 | 1.12 | ETS1 | 7 |
| rs367569 | 16 | 11,365,500 | 2.6×10−4 | 4.6×10−5 | 4.9×10−8 | C/T | 0.729 | 0.709 | 1.13 | PRM3, SOCS1 | 14 |
| rs963986 | 17 | 40,561,579 | 9.9×10−5 | 1.2×10−5 | 5.3×10−9 | C/G | 0.169 | 0.154 | 1.15 | PTRF, STAT3, STAT5A/B | 42 |
| rs11652075 | 17 | 78,178,893 | 1.3×10−3 | 7.0×10−6 | 3.4×10−8 | C/T | 0.530 | 0.502 | 1.11 | CARD14 | 16 |
| rs545979 | 18 | 51,819,750 | 1.4×10−6 | 2.4×10−5 | 3.5×10−10 | T/C | 0.317 | 0.291 | 1.12 | POL1, STARD6, MBD2 | 6 |
| rs892085 | 19 | 10,818,092 | 1.2×10−7 | 4.5×10−11 | 3.0×10−17 | A/G | 0.593 | 0.558 | 1.17 | ILF3,CARM1 | 37 |
a
The overall OR was calculated using the effective sample size-weighted approach.