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. Author manuscript; available in PMC: 2014 Nov 25.
Published in final edited form as: Nat Genet. 2010 May 9;42(6):508–514. doi: 10.1038/ng.582

Table 4.

Suggestive RA risk alleles.

SNP GWAS Meta-Analysis Replication Combined
ID Chr Pos (HG18) Gene(s)a Allele PGWAS OR MAF Prep. OR (95% CI) MAF Poverall Cochran Q
Major Minor Case Control Case Control P
rs7543174a 1q21 151,340,745 IL6R T C 7.9E-05 1.13 0.18 0.16 0.01 1.07 (1.01,1.13) 0.19 0.18 1.2E-05 0.06
rs840016a 1q24 164,140,328 CD247 C T 3.6E-05 0.90 0.39 0.42 0.006 0.92 (0.86,0.98) 0.38 0.40 1.6E-06 0.62
rs13119723b 4q27 123,575,918 IL2, IL21† A G 0.001 0.89 0.13 0.15 6.7E-05 0.87 (0.81,0.93) 0.15 0.17 6.8E-07 0.46
rs11594656b 10p15 6,162,015 IL2RA† T A 0.0002 0.90 0.23 0.25 0.04 0.95 (0.90,1.00) 0.24 0.25 0.0001 0.86
rs2793108b 10p11 31,419,111 ZEB1 T C 0.002 0.93 0.40 0.43 0.001 0.93 (0.89,0.98) 0.41 0.43 1.4E-05 0.73
rs3184504b 12q24 110,347,328 SH2B3 T C 0.004 0.93 0.49 0.49 0.0002 0.92 (0.88,0.96) 0.48 0.49 6.0E-06 0.08
rs7155603a 14q24 75,030,289 BATF† A G 1.0E-05 1.16 0.21 0.19 0.001 1.12 (1.04,1.20) 0.23 0.21 1.1E-07 0.74
rs8045689a 16p11 28,895,770 CD19, NFATC2IP† T C 5.3E-05 1.14 0.32 0.30 0.01 1.06 (1.01,1.12) 0.32 0.30 2.4E-05 0.35
rs2872507b 17q12 35,294,289 IKZF3† G A 4.7E-05 1.10 0.49 0.47 0.002 1.08 (1.02,1.14) 0.48 0.46 9.4E-07 0.69
rs11203203b 21q22 42,709,255 UBASH3A† G A 2.5E-05 1.11 0.39 0.37 0.02 1.07 (1.00,1.14) 0.38 0.37 3.8E-06 0.49
rs5754217b 22q11 20,264,229 UBE2L3 G T 0.0007 1.10 0.22 0.19 0.01 1.07 (1.01,1.13) 0.22 0.21 4.8E-05 0.79

GWAS, replication and combined meta-analysis results for SNPs with highly suggestive associations with RA risk (defined as P<0.05 in our replication samples). As in Table 2, listed for each SNP are the rs ID, chromosomal location and position, candidate gene(s), and major and minor alleles, GWAS and replication analysis P-value, odds ratio and case/control minor allele frequencies, and the combined analysis P-values for association and for Cochran’s Q test for heterogeneity.

a

: Selected for replication based on GRAIL Ptext score

b

: Selected for replication based on PGWAS < 0.01 and validated autoimmune disease association: rs13119723, IL2/IL21, RA and Celiac; rs11594656, IL2RA, T1D and MS; rs2793108, ZEB1, T1D; rs3184504, SH2B3, Celiac and T1D; rs2872507, IKZF3, Crohn’s; rs11203203, UBASH3A, T1D; rs5754217, UBE2L3, SLE; the ZEB1 SNP was from the May 2009 release of the online T1D database (www.T1Dbase.org).

†

Autoimmune disease associations for SNPs other than those tested for replication in the present study (see text, Fig. 2 and Supplementary Note): CD247, Crohn’s; IL2/IL21, Celiac, RA and T1D; IL2RA, MS, RA and T1D; BATF, T1D; CD19/NFATC2IP, T1D; IKZF3, T1D; UBASH3A, Crohn’s and T1.