Table 2

OR with 95% CI and p value for association of the minor allele at every locus with anticyclic citrullinated peptide (anti-CCP) positive or anti-CCP negative rheumatoid arthritis (RA). The minor allele is defined according to the frequency in the total population, including cases and controls.

		UK anti-CCP positive RA					UK anti-CCP negative RA					Comparison
Chr.	Locus Name	OR	95% CI	p Value	N cases	N cont	OR	95% CI	p Value	N cases	N cont	ORpos/ORneg	p Value
1	CD2/CD58	1.11	1.05 to 1.18	3.68E-04	3827	11468	1.05	0.97 to 1.13	0.242	1918	11468	1.06	0.183
1	FCGR2A	1.16	1.07 to 1.25	2.28E-04	3467	11468	1.08	0.96 to 1.20	0.195	1563	11468	1.08	0.241
1	MMEL1/TNFRSF14	0.88	0.83 to 0.93	2.12E-05	3485	12394	0.97	0.89 to 1.05	0.426	1574	12394	0.91	0.045
1	PTPN22	1.91	1.77 to 2.05	3.91E-65	3813	12398	1.20	1.07 to 1.33	1.34E-03	1894	12398	1.60	7.11E-15
1	PTPRC	0.91	0.84 to 0.99	0.022	3600	11427	0.96	0.86 to 1.08	0.504	1580	11427	0.94	0.384
2	AFF3 locus 1	1.17	1.11 to 1.23	5.36E-09	3777	11832	1.05	0.98 to 1.13	0.165	1881	11832	1.11	0.008
2	AFF3 locus 2	1.17	1.09 to 1.25	2.64E-06	2378	8425	1.06	0.97 to 1.17	0.187	991	8425	1.10	0.086
2	CD28	1.18	1.12 to 1.26	3.15E-08	3826	11469	1.08	1.00 to 1.17	0.055	1912	11469	1.09	0.049
2	CTLA4	0.91	0.87 to 0.96	9.32E-04	3626	11975	0.94	0.88 to 1.02	0.121	1592	11975	0.97	0.475
2	REL	1.13	1.07 to 1.20	1.58E-05	3196	10878	1.02	0.95 to 1.11	0.554	1437	10878	1.11	0.028
2	SPRED2	0.91	0.86 to 0.97	3.69E-03	2706	9032	0.97	0.89 to 1.06	0.565	1132	9032	0.94	0.198
2	STAT4	1.13	1.06 to 1.21	1.34E-04	3401	11822	1.11	1.02 to 1.20	0.015	1824	11822	1.02	0.656
3	DNASE1L3/PXK	1.13	1.02 to 1.24	0.014	3445	11486	0.93	0.80 to 1.08	0.338	1432	11486	1.21	0.020
4	IL2/IL21	0.88	0.82 to 0.95	1.03E-03	3402	11767	0.95	0.86 to 1.04	0.264	1814	11767	0.93	0.211
4	RBPJ	1.14	1.07 to 1.21	1.98E-05	3195	10879	1.02	0.94 to 1.11	0.681	1434	10879	1.12	0.021
5	ANKRD55/IL6ST	0.85	0.78 to 0.92	9.62E-05	2377	8428	0.80	0.70 to 0.90	2.42E-04	991	8428	1.07	0.357
5	GIN1/C5orf30	0.88	0.83 to 0.94	4.86E-05	3372	11260	0.88	0.80 to 0.95	2.32E-03	1410	11260	1.01	0.835
6	CCR6	1.13	1.07 to 1.19	1.48E-05	3423	11313	0.99	0.92 to 1.07	0.851	1508	11313	1.14	0.004
6	HLA-DRB1 0401 tag	2.68	2.50 to 2.88	9.97E-169	2378	8428	1.15	1.03 to 1.28	9.55E-03	991	8428	2.33	6.30E-47
6	HLA-DRB1 SE	4.08	3.64 to 4.56	1.18E-131	2366	1352	1.28	1.14 to 1.45	5.18E-05	1315	1352	3.18	2.56E-97
6	PRDM1	1.06	1.00 to 1.12	0.041	3827	11469	1.04	0.97 to 1.12	0.275	1916	11469	1.02	0.692
6	TAGAP	0.90	0.85 to 0.95	1.57E-04	3824	11466	0.97	0.90 to 1.04	0.416	1914	11466	0.92	0.068
6	TNFAIP3 locus 1	1.29	1.21 to 1.37	3.70E-16	3659	12392	1.09	1.00 to 1.18	0.048	1862	12392	1.18	3.52E-04
6	TNFAIP3 locus 2	0.89	0.84 to 0.95	2.72E-04	3425	11923	0.93	0.85 to 1.02	0.109	1497	11923	0.96	0.383
6	TNFAIP3 locus 3	1.45	1.28 to 1.65	1.33E-08	3414	12021	0.91	0.73 to 1.13	0.374	1460	12021	1.60	7.36E-05
7	IRF5	1.12	1.02 to 1.23	0.016	2739	9043	1.09	0.95 to 1.24	0.213	1175	9043	1.03	0.696
8	BLK	1.09	1.03 to 1.16	3.77E-03	3490	11481	1.15	1.05 to 1.25	1.53E-03	1525	11481	0.95	0.332
9	CCL21 locus 1	0.92	0.85 to 1.00	0.048	3199	10878	1.01	0.91 to 1.13	0.833	1439	10878	0.91	0.145
9	CCL21 locus 2	1.13	1.07 to 1.20	7.68E-06	3642	11936	1.04	0.97 to 1.12	0.274	1855	11936	1.09	0.046
9	TRAF1/C5	1.10	1.04 to 1.16	7.54E-04	3135	11544	1.02	0.94 to 1.10	0.698	1447	11544	1.08	0.073
10	IL2RA locus 1	1.14	1.06 to 1.23	3.21E-04	1935	5477	1.07	0.96 to 1.19	0.224	808	5477	1.07	0.240
10	IL2RA locus 2	0.88	0.83 to 0.93	2.71E-05	3806	12396	0.97	0.90 to 1.05	0.450	1896	12396	0.91	0.033
10	PRKCQ	0.87	0.82 to 0.94	1.18E-04	3657	12427	0.95	0.86 to 1.04	0.281	1624	12427	0.92	0.132
11	RAG1/TRAF6	0.92	0.85 to 0.99	0.032	3440	11379	0.98	0.88 to 1.09	0.723	1556	11379	0.94	0.285
12	KIF5A/PIP4K2C	0.90	0.85 to 0.95	1.81E-04	3688	12452	0.95	0.88 to 1.02	0.135	1881	12452	0.95	0.237
20	CD40	0.89	0.84 to 0.95	4.36E-04	3640	11971	1.02	0.94 to 1.11	0.594	1858	11971	0.87	0.005
22	IL2RB	1.15	1.08 to 1.21	3.15E-06	3811	12392	1.08	1.00 to 1.16	0.057	1900	12392	1.06	0.164

N cases, cont: number of cases or controls with available genotype. Comparison ORpos/ORneg: effect size ratio between the OR in CCP-positive and CCP-negative RA, with the p value for its significance. The CI of the effect size OR is not shown to avoid overloading the table