Table 3

DAS28 response data by genotype and association p values for 17 successfully genotyped SNPs in 1012 individuals

										First cohort (n=1012)
												Additive model				Dominant model^*
SNP	Gene	Chr	bp	Genotype	Count	Mean baseline DAS28	SD baseline DAS28	Mean change in DAS28	SD change in DAS28	HWE exact p value	Genotypic global p value	Global p value	Coef	Min 95	Max 95	Global p value	Coef	Min 95	Max 95
rs10865035	AFF3	2	100202166	AA	240	6.72	1.02	−2.28	1.57	0.089	0.051	0.018	−0.16	−0.29	−0.03	0.024	−0.25	−0.46	−0.03
				AG	532	6.69	0.96	−2.51	1.51
				GG	237	6.68	0.99	−2.58	1.63
rs1160542	AFF3	2	100198587	AA	247	6.70	0.97	−2.59	1.61	0.050	0.066	0.022	0.15	0.02	0.29	0.101	0.17	−0.03	0.38
				AG	530	6.69	0.96	−2.49	1.51
				GG	221	6.68	1.00	−2.25	1.56
rs7574865	STAT4	2	191672878	GG	564	6.73	0.99	−2.57	1.55	0.400	0.051	0.094	0.13	−0.02	0.28	0.028	0.20	0.02	0.39
				GT	389	6.65	0.95	−2.33	1.58
				TT	57	6.64	1.10	−2.49	1.40
rs10181656	STAT4	2	191678124	CC	563	6.73	0.99	−2.57	1.54	0.559	0.067	0.122	0.12	−0.03	0.27	0.038	0.19	0.01	0.37
				CG	389	6.65	0.95	−2.33	1.60
				GG	60	6.63	1.07	−2.50	1.37
rs231775	CTLA4	2	204440959	AA	365	6.68	1.00	−2.50	1.53	0.794	0.775	0.500	0.04	−0.09	0.17	0.484	0.07	−0.12	0.25
				AG	482	6.69	0.98	−2.44	1.52
				GG	165	6.73	0.94	−2.52	1.72
rs3087243	CTLA4	2	204447164	GG	340	6.67	0.97	−2.53	1.64	0.948	0.712	0.570	0.04	−0.09	0.17	0.427	0.08	−0.11	0.27
				GA	492	6.74	0.96	−2.46	1.49
				AA	176	6.61	1.05	−2.41	1.57
rs6822844	IL2–IL21	4	123728871	GG	725	6.69	0.95	−2.45	1.58	0.151	0.376	0.317	−0.09	−0.26	0.08	0.208	−0.13	−0.33	0.07
				GT	254	6.68	1.05	−2.52	1.50
				TT	31	7.00	0.84	−2.70	1.33
rs13192841	TNFAIP3	6	138008907	GG	577	6.66	0.98	−2.50	1.59	0.672	0.406	0.469	0.05	−0.09	0.20	0.271	0.10	−0.08	0.28
				GA	371	6.72	0.99	−2.41	1.51
				AA	64	6.77	0.92	−2.60	1.48
rs6920220	TNFAIP3	6	138048197	GG	525	6.69	0.96	−2.49	1.49	0.430	0.536	0.314	0.07	−0.07	0.22	0.265	0.10	−0.08	0.28
				GA	413	6.69	1.00	−2.44	1.61
				AA	71	6.68	1.02	−2.43	1.68
rs5029937	TNFAIP3	6	138236844	GG	900	6.67	0.98	−2.44	1.54	0.763	0.463	0.216	−0.18	−0.47	0.11	0.227	−0.18	−0.48	0.11
				GT	105	6.91	0.92	−2.73	1.64
				TT	2	7.46	0.35	−3.43	1.01
rs2812378	CCL21	9	34700260	TT	379	6.67	1.02	−2.42	1.53	0.386	0.876	0.637	−0.03	−0.17	0.10	0.609	−0.05	−0.24	0.14
				TC	490	6.70	0.95	−2.51	1.56
				CC	140	6.74	0.96	−2.48	1.62
rs10760130	TRAF1	9	122741811	AA	313	6.71	0.99	−2.39	1.58	0.798	0.457	0.981	0.00	−0.13	0.13	0.520	−0.06	−0.26	0.13
				AG	492	6.68	0.94	−2.54	1.53
				GG	200	6.71	1.07	−2.41	1.57
rs2900180	TRAF1	9	122746203	CC	425	6.73	0.98	−2.47	1.61	0.077	0.730	0.592	0.04	−0.09	0.17	0.841	0.02	−0.16	0.20
				CT	441	6.65	0.95	−2.50	1.49
				TT	146	6.70	1.05	−2.41	1.57
rs4750316	PRKCQ	10	6433266	GG	695	6.71	0.95	−2.54	1.56	0.510	0.346	0.387	0.07	−0.09	0.24	0.237	0.12	−0.08	0.31
				GC	283	6.67	1.01	−2.33	1.50
				CC	33	6.43	1.23	−2.19	1.80
rs1678542	KIF5A	12	56254982	CC	419	6.72	0.98	−2.50	1.55	0.448	0.724	0.600	0.04	−0.10	0.17	0.456	0.07	−0.11	0.25
				CG	473	6.65	0.96	−2.44	1.55
				GG	119	6.74	1.05	−2.49	1.56
rs763361	CD226	18	65682622	TT	272	6.65	1.00	−2.64	1.50	0.900	0.050	0.016	0.16	0.03	0.29	0.026	0.23	0.03	0.43
				TC	508	6.69	0.96	−2.45	1.57
				CC	232	6.75	0.98	−2.32	1.57
rs4810485	CD40	20	44181354	GG	607	6.68	0.95	−2.50	1.54	0.048	0.398	0.221	0.10	−0.06	0.27	0.325	0.09	−0.09	0.28
				GT	358	6.68	1.01	−2.40	1.56
				TT	35	6.90	0.97	−2.46	1.65

Significant p values (<0.05) are shown in bold type, italic indicates p<0.10.
↵* Results for the recessive model are not shown; only rs1160542 (AFF3) demonstrated association with treatment response under a recessive model (coef 0.23 (0.01, 0.45), p=0.037).
bp, base pairs; Chr, chromosome; Coef, coefficient for minor allele; DAS, disease activity score; HWE, Hardy–Weinberg equilibrium; SNP, single nucleotide polymorphism.