Table 2. Summary of results for the three-stage association study.

SNP	PhysicalPositiona	AnnotatedGene	Allele(A/B)b	Stage	Case			MAF	Control			MAF	P-valuec	OR (95% CI)c
					AA	AB	BB		AA	AB	BB
rs9276370	Chr6: 32815273	HLA-DQA2	G/T	GWAS	0.003	0.137	0.860	0.072	0.020	0.260	0.720	0.150	3.57×10−5	2.25 (1.53–3.31)
				1st replication	0.006	0.1271	0.867	0.070	0.012	0.194	0.793	0.110	2.90×10−3	1.65 (1.19–2.30)
				2nd replication	0.006	0.157	0.857	0.085	0.015	0.260	0.725	0.145	2.09×10−5	1.87 (1.40–2.50)
				Combined	0.006	0.141	0.853	0.076	0.015	0.240	0.745	0.135	1.90×10−12	1.95 (1.62–2.34)
rs7756516	Chr6: 32831895	HLA-DQB2	C/T	GWAS	0.012	0.128	0.860	0.076	0.020	0.280	0.701	0.160	1.97×10−5	2.24 (1.55–3.23)
				1st replication	0.008	0.124	0.867	0.071	0.012	0.204	0.784	0.114	1.35×10−3	1.71 (1.23–2.37)
				2nd replication	0.007	0.176	0.818	0.094	0.017	0.260	0.723	0.147	3.26×10−4	1.69 (1.27–2.25)
				Combined	0.009	0.146	0.846	0.081	0.016	0.248	0.736	0.140	1.48×10−11	1.87 (1.56–2.25)
rs7453920*	Chr6: 32837990	HLA-DQB2	A/G	GWAS	0.003	0.084	0.913	0.045	0.016	0.207	0.776	0.120	9.24×10−6	2.77 (1.77–4.35)
				1st replication	0.003	0.093	0.904	0.050	0.015	0.181	0.804	0.105	1.02×10−5	2.22 (1.56–3.16)
				2nd replication	0.002	0.109	0.890	0.056	0.010	0.192	0.798	0.106	2.15×10−5	2.08 (1.48–2.91)
				Combined	0.003	0.098	0.900	0.051	0.013	0.193	0.794	0.110	6.66×10−15	2.31 (1.87–2.85)
rs9277535*	Chr6: 33162839	HLA-DPB1	A/G	GWAS	0.062	0.343	0.595	0.234	0.106	0.503	0.391	0.358	1.80×10−6	1.87 (1.45–2.42)
				1st replication	0.071	0.357	0.572	0.249	0.142	0.428	0.431	0.355	3.64×10−6	1.61 (1.32–1.98)
				2nd replication	0.076	0.372	0.553	0.262	0.125	0.431	0.443	0.341	8.72×10−5	1.47 (1.21–1.78)
				Combined	0.071	0.360	0.569	0.251	0.125	0.451	0.424	0.350	4.87×10−14	1.59 (1.41–1.79)
rs9366816*	Chr6: 33212153	HLA-DPA3	C/T	GWAS	0.393	0.442	0.165	0.386	0.188	0.566	0.247	0.470	1.07×10−6	1.80 (1.42–2.27)
				1st replication	0.353	0.456	0.191	0.419	0.247	0.531	0.222	0.488	5.45×10−3	1.31 (1.08–1.58)
				2nd replication	0.353	0.448	0.199	0.423	0.260	0.494	0.246	0.493	7.94×10−4	1.35 (1.13–1.61)
				Combined	0.361	0.450	0.189	0.414	0.235	0.526	0.239	0.498	2.58×10−10	1.43 (1.28–1.60)

*Used in risk score calculation.

^aGenome Build 36.3.

^bRisk alleles were in bold.

^cP-values, ORs and CIs were calculated based on the additive effect model with age adjustment.