Table 2.
Previously known RA risk associated SNPs in Europeans.
| SNP | GWAS Meta-Analysis | Power | ||||||
|---|---|---|---|---|---|---|---|---|
| Locus | ID | Gene(s) | Minor allele | MAF | OR (95% CI) | PGWAS | α = 10−6 | α = 5×10−8 |
| 1p36 | rs3890745* | TNFRSF14 | C | 0.32 | 0.89 (0.85,0.94) | 3.6×10−6 | 0.45 | 0.24 |
|
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| 1p13 | rs2476601 | PTPN22 | A | 0.10 | 1.94 (1.81,2.08) | 9.1×10−74 | 1 | 1 |
|
| ||||||||
| 1p13 | rs11586238 | CD2,CD58 | G | 0.24 | 1.13 (1.07,1.19) | 1.0×10−5 | 0.46 | 0.26 |
|
| ||||||||
| 1q23 | rs12746613* | FCGR2A | T | 0.12 | 1.13 (1.06,1.21) | 0.0004 | 0.11 | 0.04 |
|
| ||||||||
| 1q31 | rs10919563* | PTPRC | A | 0.13 | 0.88 (0.82,0.94) | 0.0002 | 0.10 | 0.03 |
|
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| 2p16 | rs13031237 | REL | T | 0.37 | 1.13 (1.07,1.18) | 7.9×10−7 | 0.67 | 0.45 |
|
| ||||||||
| 2q11 | rs10865035* | AFF3 | A | 0.47 | 1.12 (1.07,1.17) | 2.0×10−6 | 0.55 | 0.33 |
|
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| 2q32 | rs7574865 | STAT4 | T | 0.22 | 1.16 (1.10,1.23) | 2.9×10−7 | 0.77 | 0.58 |
|
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| 2q33 | rs1980422 | CD28 | C | 0.24 | 1.12 (1.06,1.18) | 5.2×10−5 | 0.32 | 0.15 |
|
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| 2q33 | rs3087243 | CTLA4 | A | 0.44 | 0.87 (0.83,0.91) | 1.2×10−8 | 0.89 | 0.74 |
|
| ||||||||
| 4q27 | rs6822844 | IL2,IL21 | T | 0.18 | 0.90 (0.84,0.95) | 0.0007 | 0.08 | 0.02 |
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| 6p21 | rs6910071 | HLA-DRB1 (*0401 tag) | G | 0.22 | 2.88 (2.73,3.03) | <10−299 | 1 | 1 |
|
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| 6q21 | rs548234 | PRDM1 | C | 0.33 | 1.10 (1.05,1.16) | 9.7×10−5 | 0.21 | 0.08 |
|
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| 6q23 | rs10499194 | TNFAIP3 | T | 0.27 | 0.91 (0.87,0.96) | 0.0007 | 0.11 | 0.03 |
|
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| 6q23 | rs6920220 | TNFAIP3 | A | 0.22 | 1.22 (1.16,1.29) | 8.9×10−13 | 1 | 0.99 |
|
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| 6q23 | rs5029937 | TNFAIP3 | T | 0.04 | 1.40 (1.24,1.58) | 7.5×10−8 | 0.95 | 0.86 |
|
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| 6q25 | rs394581* | TAGAP | C | 0.30 | 0.91 (0.87,0.96) | 0.0006 | 0.13 | 0.05 |
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| 8p23 | rs2736340 | BLK | T | 0.25 | 1.12 (1.07,1.18) | 1.5×10−5 | 0.34 | 0.17 |
|
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| 9p13 | rs2812378* | CCL21 | G | 0.34 | 1.10 (1.05,1.16) | 0.0001 | 0.21 | 0.09 |
|
| ||||||||
| 9q33 | rs3761847 | TRAF1,C5 | G | 0.43 | 1.13 (1.08,1.18) | 2.1×10−7 | 0.70 | 0.49 |
|
| ||||||||
| 10p15 | rs2104286 | IL2RA | C | 0.27 | 0.92 (0.87,0.97) | 0.002 | 0.05 | 0.02 |
|
| ||||||||
| 10p15 | rs4750316 | PRKCQ | C | 0.19 | 0.87 (0.82,0.92) | 2.0×10−6 | 0.41 | 0.21 |
|
| ||||||||
| 11p12 | rs540386* | TRAF6 | T | 0.14 | 0.88 (0.83,0.94) | 0.0003 | 0.13 | 0.05 |
|
| ||||||||
| 12q13 | rs1678542* | KIF5A,PIP4K2C | G | 0.38 | 0.91 (0.87,0.96) | 0.0002 | 0.20 | 0.08 |
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| ||||||||
| 20q13 | rs4810485 | CD40 | T | 0.25 | 0.85 (0.80,0.90) | 2.8×10−9 | 0.88 | 0.73 |
|
| ||||||||
| 22q12 | rs3218253* | IL2RB | A | 0.26 | 1.09 (1.03,1.15) | 0.002 | 0.07 | 0.02 |
GWAS meta-analysis results for previously known SNPs associated with RA risk among European populations. Listed are the chromosome, SNP ID, and candidate gene(s) in the region. The minor allele and frequency (positive strand in HapMap release 22, frequency in controls subjects), odds ratio (95% confidence interval), and association P-value are derived from our GWAS meta-analysis. Most SNPs have achieved P<5×10−8 in combined analysis from previous studies; those with an asterisk (*) have been validated by replication in independent samples, but may not have attained P<5×10−8 in any single study. SNPs with strong evidence of association in Asians (including PADI4, rs2240340, PGWAS = 0.01; FCRL3, rs3761959, PGWAS = 0.001; and CD244, rs3753389, PGWAS = 0.26) or suggestive evidence of association in Europeans are shown in Supplementary Table 1 online. Power was calculated based on the odds ratios from our meta-analysis at α = 10−6 (a threshold for selecting SNPs for replication in the current study) and 5×10−8 (genome-wide signicance). Details of the power calculations can be found in the Supplementary Materials online.