Table 3.

Genotype-based associations with RA (case-control comparison, reference is major allele homozygote)

	PedGenie 2.1
	NARAC Study 1a				NARAC Study 2b			Meta-analysis			Previously publishedc
PTPN22	Genotyped	OR	95% CI	p-trende	OR	95% CI	p-trende	OR	95% CI	p-trendf	OR	95% CI	p-trend
rs3789604	AC	0.94	0.69–1.26		1.16	0.93–1.46		1.07	0.91–1.26		1.15	0.93–1.42
	CC	1.68	0.83–3.38	0.39	1.25	0.70–2.21	0.18	1.43	0.93–2.18	0.12	1.78	1.13–2.79	0.014
rs1217413	TC	1.44	1.11–1.87		1.34	1.08–1.66		1.38	1.17–1.63
	CC	1.71	1.06–2.75	0.003	1.52	1.00–2.31	0.002	1.59	1.14–2.22	<0.001
rs1217388	TC	1.49	1.14–1.93		1.30	1.05–1.61		1.37	1.15–1.63
	CC	1.30	0.78–2.17	0.017	1.27	0.86–1.87	0.026	1.28	0.94–1.74	0.003
ss38346943	TC	0.32	0.15–0.69		0.88	0.48–1.61		0.61	0.39–0.95
	CC	--	--	--	--	--	--	--	--	--
rs1310182	CT	1.55	1.13–2.13		1.39	1.11–1.73		1.45	1.20–1.75		1.22	0.98–1.77
	TT	1.57	1.07–2.30	0.011	1.62	1.18–2.22	<0.01	1.60	1.25–2.03	<0.001	1.32	0.97–1.54	0.052
rs2476601	CT	1.92	1.41–2.60		2.36	1.84–3.04		2.18	1.80–2.65		2.19	1.73–2.78
(R620W)	TT	1.96	0.74–5.21	<0.001	2.91	1.26–6.74	<0.001	2.53	1.32–4.84	<0.001	2.90	1.37–6.18	<0.001
rs12730735	AG	1.00	0.75–1.31		1.10	0.89–1.36		1.06	0.89–1.25
	GG	0.48	0.29–0.80	0.08	0.56	0.37–0.83	0.14	0.53	0.39–0.72	0.024
rs12760457	AG	1.01	0.75–1.36		1.09	0.87–1.37		1.06	0.89–1.26
	GG	0.48	0.28–0.82	0.09	0.55	0.37–0.82	0.14	0.52	0.38–0.72	0.023
rs2488458	GA	1.51	1.15–1.97		1.33	1.07–1.66		1.40	1.18–1.67
	AA	1.27	0.79–2.05	0.014	1.20	0.81–1.78	0.037	1.23	0.91–1.67	0.003
rs1217414	CT	1.02	0.77–1.35		0.85	0.69–1.04		0.91	0.78–1.06
	TT	0.60	0.34–1.03	0.20	0.70	0.46–1.06	0.053	0.65	0.46–0.92	0.018

^aProblem 2 data, 446 family cases and 103 family controls in 202 affected NARAC pedigrees, 664 independent NYC controls; excludes Plenge et al. [6] samples.

^bProblem 2 data, samples in Plenge et al. [6] candidate gene file, 839 family cases in 463 pedigrees and 854 independent NYC controls.

^cCarlton et al. [5] sample set 2, 661 random independent cases from NARAC pedigrees and 1322 NYC controls; adjusted for R620W or rs3789604 (R620W).

^dMinor allele heterozygote and homozygote genotypes according to Carlton et al. [5] Table 1.

^eEmpirical confidence intervals and chi-square p-values, 1000 simulations; p < 0.05 in bold.

^fEmpirical confidence intervals and CMH chi-square trend test p-values, 1000 simulations; p < 0.05 in bold.