Table 2.

Allelic association analysis in patients with primary Sjögren’s syndrome compared with healthy controls

Variant	Position	Gene/region	P-value	Conditional P-value	OR (95% CI)	RAF, cases/controls	Minor/major alleles	snpEff annotation [19]
All cases vs controlsa
rs6933289	chr6:32604551	HLA-DQA1	1.4 × 10−46	—	3.88 (3.22, 4.66)	0.31/0.13	T/C	Upstream
rs3099839	chr6:31430065	HCP5	1.6 × 10−43	2.4 × 10−6b	3.75 (3.11, 4.52)	0.30/0.11	T/C	Upstream
rs4919321	chr10:101230461	GOT1	1.1 × 10−6	—	1.43 (1.23, 1.64)	0.73/0.67	C/G	Intergenic
rs6630	chr19:4090422	MAP2K2	1.7 × 10−6	—	1.82 (1.43, 2.33)	0.94/0.88	T/G	3′ UTR
rs11761199	chr7:128581835	IRF5	1.8 × 10−6	—	1.39 (1.22, 1.61)	0.55/0.47	A/G	Intronic
rs7197	chr6:32412580	HLA-DRA	9.2 × 10−5	1.6 × 10−13c	1.34 (1.16, 1.55)	0.27/0.23	T/C	3′ UTR
SSA/SSB antibody positive cases vs controlsa
rs6933289	chr6:32604551	HLA-DQA1	2.2 × 10−62	—	6.10 (4.93, 7.54)	0.37/0.13	T/C	Upstream
rs2523607	chr6:31322790	HLA-B	5.3 × 10−58	6.8 × 10−07b	5.27 (4.30, 6.45)	0.36/0.12	A/T	Upstream
rs7197	chr6:32412580	HLA-DRA	5.2 × 10−8	2.6 × 10−25c	1.56 (1.33, 1.84)	0.30/0.23	T/C	3′ UTR
rs3823536	chr7:128579666	IRF5	7.4 × 10−8	—	1.52 (1.30, 1.79)	0.57/0.47	G/A	Upstream
rs4919321	chr10:101230461	GOT1	2.4 × 10−6	—	1.47 (1.25, 1.72)	0.73/0.67	C/G	Intergenic

Independent signals with uncorrected or conditional P-values exceeding a suggestive significance threshold of P < 1 × 10⁻⁵ are shown. The risk allele is marked in bold.

^aAll cases n = 918, SSA and/or SSB antibody positive cases n = 663, controls n = 1264.

^bAnalysis passing suggestive significance threshold with rs6933289 and rs7197 as covariates.

^cAnalysis passing suggestive significance threshold with rs6933289 as covariate. Chr, chromosome, OR, odds ratio; RAF, risk allele frequency; UTR, untranslated region.