. 2007 Dec 18;1(Suppl 1):S12. doi: 10.1186/1753-6561-1-s1-s12

Table 2.

Allele-based associations with RA (case-control comparison, odds ratios (ORs) estimated for minor allele)

	PedGenie 2.1

	NARAC Study 1^a				NARAC Study 2^b				Meta-analysis			Previously published^c,d

PTPN22	MAF^e	OR	95% CI	p^f	MAF^e	OR	95% CI	p^f	OR	95% CI	p^g	OR	95% CI	p^h
Rs3789604	0.182	1.11	0.88–1.41	0.36	0.175	1.15	0.95–1.39	0.17	1.13	0.98–1.32	0.10	1.15	0.97–1.35	0.11
Rs3811021	0.182	1.11	0.88–1.40	0.38	0.176	1.14	0.95–1.37	0.17	1.13	0.97–1.31	0.11	1.15	0.97–1.36	0.10
rs1217413	0.210	1.38	1.13–1.70	0.003	0.230	1.28	1.07–1.53	0.002	1.32	1.16–1.51	<0.001	1.37	1.18–1.60	<0.001
ss38346942	0.015	1.21	0.61–2.37	0.59	0.012	1.22	0.65–2.27	0.56	1.21	0.75–1.97	0.42	1.03	0.59–1.79	1.00
rs1217388	0.246	1.29	1.04–1.59	0.017	0.260	1.20	1.01–1.42	0.028	1.23	1.07–1.42	0.003	1.28	1.11–1.49	0.001
ss38346943	0.031	0.32	0.16–0.67	0.001	0.023	0.84	0.47–1.48	0.55	0.60	0.39–0.92	0.020	0.63	0.40–1.01	0.05
rs1310182	0.430	1.28	1.06–1.56	0.008	0.435	1.28	1.09–1.49	0.001	1.28	1.13–1.45	<0.001	1.35	1.18–1.54	<0.001
ss38346944	0.029	1.14	0.65–1.99	0.63	0.019	1.37	0.84–2.22	0.24	1.26	0.85–1.85	0.24	1.29	0.87–1.93	0.21

rs2476601	0.087	1.79	1.39–2.30	<0.001	0.085	2.19	1.75–2.74	<0.001	2.03	1.70–2.42	<0.001	1.93	1.58–2.37	<0.001
(R620W)												2.184	1.76–2.70	<0.001

rs12730735	0.292	0.83	0.68–1.01	0.07	0.295	0.89	0.76–1.04	0.14	0.86	0.76–0.98	0.025	0.81	0.70–0.94	0.006
rs11102685	0.076	1.21	0.87–1.77	0.26	0.078	1.20	0.93–1.55	0.19	1.20	0.98–1.49	0.09	1.27	1.01–1.60	0.040
rs12760457	0.291	0.83	0.68–1.02	0.09	0.296	0.88	0.74–1.05	0.14	0.86	0.76–0.98	0.022	0.82	0.71–0.96	0.010
rs2488458	0.246	1.29	1.05–1.58	0.014	0.260	1.20	1.01–1.41	0.037	1.23	1.08–1.41	0.003	1.27	1.10–1.48	0.002
rs1217414	0.282	0.88	0.70–1.10	0.20	0.270	0.84	0.72–0.99	0.06	0.86	0.76–0.97	0.018	0.84	0.72–0.98	0.020

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

^bProblem 2, 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 randomly selected independent cases from NARAC pedigrees and 1322 independent NYC controls).

^dPlenge et al. [6] second collection; 840 family cases (NARAC) and 867 independent NYC controls: R620W SNP only.

^eMinor allele frequency in controls.

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

^gEmpirical confidence intervals and CMH chi-square general association test, 1000 simulations; p < 0.05 in bold.

^hFisher's exact chi-square test; p < 0.05 in bold.