Table 1. Combined analysis of association with SLE in the Swedish discovery and confirmation cohortsa.

Gene	CHR	SNPb	Basepair	Minor/major alleles	MAF cases	MAF controls	Pc	Risk allele	OR (95% CI)
IKBKE	1	rs1539243	204 714 410	T/C	0.16	0.18	0.031	C	1.19 (1.02–1.39)
IKBKE	1	rs17433930	204 719 362	G/A	0.07	0.09	0.013	A	1.33 (1.06–1.67)
TANK	2	rs3754974	161 721 201	G/A	0.05	0.04	0.0087	G	1.44 (1.09–1.89)
TANK	2	rs1267075	161 768 063	G/A	0.19	0.18	0.75	G	1.02 (0.88–1.19)
STAT1	2	rs2030171	191 577 408	A/G	0.35	0.29	1.2E−05	A	1.31 (1.16–1.49)
STAT1	2	rs16833172	191 584 314	A/G	0.04	0.03	0.015	A	1.51 (1.09–2.09)
IL8	4	rs4694178	74 831 552	C/A	0.52	0.46	5.2E−05	C	1.26 (1.12–1.42)
NRP1	10	rs734187	33 524 702	A/G	0.24	0.24	0.67	A	1.03 (0.90–1.18)
NRP1	10	rs1331314	33 564 687	G/C	0.11	0.10	0.32	G	1.11 (0.92–1.34)
NRP1	10	rs2073320	33 593 263	A/G	0.38	0.37	0.42	A	1.05 (0.93–1.18)
TRAF6	11	rs5030482	36 466 602	C/T	0.12	0.14	0.0094	T	1.25 (1.05–1.49)
TRAF6	11	rs5030472	36 470 362	T/C	0.09	0.12	0.013	C	1.28 (1.05–1.55)
STAT5B	17	rs6503691	37 647 616	T/C	0.09	0.10	0.44	C	1.08 (0.88–1.32)
PIAS4	19	rs2289863	3 979 783	C/T	0.27	0.29	0.19	T	1.09 (0.96–1.25)

Abbreviations: CI, confidence Interval; MAF, minor Allele Frequency; OR, odds ratio; SNP, single-nucleotide polymorphism.

^a826 Swedish cases and 1835 controls genotyped in the discovery and replication phases including controls genotyped on the 1M chip.

^bGenotypes for rs17433930, rs3754974, rs2030171, rs16833172, rs4694178, rs734187 and rs1331314 were imputed in the Swedish controls genotyped on the 1M chip.

^cP-values calculated using SNPtest.

P-values <0.05 are indicated in bold.