Table 3

Frequencies of previously detected genetic variants for RA: comparison of meta-analysis of ACPA-positive RA patients from three populations with ACPA-negative RA patients

				EIRA ACPA-positive		EIRA ACPA-negative		NARAC		WTCCC		ACPA-positive RA	ACPA-negative RA
SNP	Chromosome	Gene/loci	Minor allele^*	MAF cases	MAF controls	MAF cases	MAF controls	MAF cases	MAF controls	MAF cases	MAF controls	OR (95%CI)^*	OR (95%CI)^†
rs3890745	1p36	MMEL1-TNFRSF14	C	0.28	0.31	0.29	0.31	0.29	0.32	0.29	0.34	0.85 (0.80 to 0.91)	0.94 (0.82 to 1.09)
rs2476601	1p13	PTPN22	A	0.18	0.12	0.14	0.12	0.16	0.08	0.15	0.09	1.74 (1.59 to 1.90)	1.17 (0.96 to 1.42)
rs7574865	2q32	STAT4	T	0.24	0.22	0.26	0.22	0.25	0.23	0.23	0.21	1.12 (1.05 to 1.21)	1.23 (1.05 to 1.43)
rs3087243	2q33	CTLA4	A	0.34	0.39	0.38	0.39	0.38	0.42	0.43	0.45	0.88 (0.83 to 0.93)	0.97 (0.84 to 1.11)
rs2064476	6p21	HLA-DPB1	G	0.20	0.26	0.27	0.26	0.22	0.30	0.25	0.31	0.71 (0.66 to 0.76)	1.02 (0.88 to 1.18)
rs10499194	6q23	OLIG3,TNFAIP3	T	0.19	0.21	0.20	0.21	0.25	0.30	0.25	0.27	0.86 (0.80 to 0.92)	1.28 (1.10 to 1.50)
rs6920220	6q23	OLIG3,TNFAIP3	A	0.25	0.23	0.24	0.23	0.24	0.19	0.26	0.22	1.22 (1.14 to 1.31)	1.08 (0.93 to 1.26)
rs3807306	7q32	IRF5	G	0.45	0.49	0.41	0.49	0.48	0.50	0.46	0.50	0.87 (0.81 to 0.92)	0.72 (0.63 to 0.82)
rs2812378	9p13	CCL21	G	0.35	0.32	0.36	0.32	0.35	0.33	0.37	0.34	1.14 (1.07 to 1.21)	1.21 (1.05 to 1.39)
rs3761847	9q33	TRAF1-C5	G	0.51	0.46	0.48	0.46	0.47	0.38	0.43	0.43	1.32 (1.21 to 1.44)^‡	1.08 (0.95 to 1.23)
rs4750316	10p15	PRKCQ	C	0.17	0.21	0.19	0.21	0.18	0.19	0.16	0.20	0.83 (0.77 to 0.90)	0.87 (0.74 to 1.03)
rs1678542	12q13	KIF5A-PIP4K2C	G	0.40	0.42	0.42	0.42	0.36	0.37	0.33	0.37	0.88 (0.82 to 0.93)	0.99 (0.87 to 1.14)
rs1328674	13q14-q21	HTR2A	T	0.04	0.02	0.04	0.02	0.04	0.04	0.04	0.04	1.16 (0.99 to 1.35)	1.83 (1.25 to 2.68)
rs4810485	20q13	CD40	T	0.20	0.24	0.24	0.24	0.21	0.27	0.23	0.24	0.77 (0.69 to 0.85)^‡	0.98 (0.84 to 1.14)

Statistically significant odds ratios shown in bold.
↵* Mantel–Haenszel OR from meta-analysis of EIRA ACPA-positive RA/NARAC/WTCCC.
↵† Mantel–Haenszel OR for EIRA ACPA-negative RA.
↵‡ WTCCC excluded due to heterogeneity between ACPA positive cohorts.
ACPA, antibodies to citrullinated peptide antigens; EIRA, Swedish Epidemiological Investigation of Rheumatoid Arthritis; MAF, minor allele frequency; NARAC, North American RA Consortium; RA, rheumatoid arthritis; SNP, single nucleotide polymorphism; WTCCC, Wellcome Trust Case–Control Consortium.