Table 1.

Results of Meta-analysis and Replication on the Identified Loci Associated with SLE

SNP	Chr	Risk Allele	Gene	p Value						OR	phet
				META	HK Rep	AH Rep 1	Thai	AH Rep 2	Combined
Loci with Genome-wide Significance
rs6705628	2p13	C	TET3	2.6 × 10−8	0.04	1.0 × 10−4	0.11	1.3 × 10−5	6.9 × 10−17	0.75	0.43
rs4852324	2p13	T	TET3	4.8 × 10−9	0.33	1.4 × 10−5	0.12	4.4 × 10−3	5.7 × 10−14	0.79	0.05
rs6804441	3q13	A	CD80	1.5 × 10−5	0.02	0.02	0.06	6.1 × 10−12	2.5 × 10−16	0.79	0.01
rs4948496	10q21	C	ARID5B	2.4 × 10−4	5.7 × 10−3	0.03	1.8 × 10−5	0.01	5.1 × 10−11	0.85	0.15
rs12822507	12p13	A	CREBL2	1.5 × 10−4	0.12	0.09	0.99	8.0 × 10−5	2.2 × 10−8	0.86	0.39
rs10845606	12p13	C	GPR19	1.1 × 10−5	0.16	1.8 × 10−7	0.05	5.8 × 10−7	3.8 × 10−17	0.79	0.18
rs34330	12p13	C	CDKN1B	2.3 × 10−4	5.6 × 10−3	1.5 × 10−3	0.02	9.0 × 10−4	4.8 × 10−12	0.84	0.60
rs4622329	12q23	A	DRAM1	9.5 × 10−5	0.68	1.5 × 10−6	9.6 × 10−5	0.02	9.4 × 10−12	0.84	0.02
Loci with Suggestive Significance
rs10911390	1q31	T	APOBEC4	1.5 × 10−4	0.14	0.20	0.31	0.06	6.4 × 10−6	1.13	0.75
rs1393820	2p13	G	C1D	3.9 × 10−5	0.26	0.13	0.09	0.63	9.1 × 10−5	0.82	0.12
rs515983	2q22	T	TMEM163	5.9 × 10−5	0.05	0.06	0.30	0.72	8.2 × 10−5	0.87	0.09
rs11717455	3p22	T	SCN10A	2.4 × 10−5	0.02	0.86	0.23	0.07	6.9 × 10−6	0.71	0.10
rs2023532	4q24	C	UBE2D3	2.3 × 10−4	0.29	0.01	0.22	0.60	1.1 × 10−5	0.80	0.30
rs2367894	5p13	G	FYB	1.3 × 10−4	0.50	0.01	0.65	0.60	4.0 × 10−5	0.84	0.20
rs12529935	6q15	C	BACH2	8.6 × 10−5	0.79	0.03	0.27	0.12	9.3 × 10−6	0.74	0.55
rs6957263	7q22	T	PUS7	1.3 × 10−4	0.01	0.11	0.17	0.09	2.0 × 10−5	0.80	0.03
rs2252996	10q22	A	SLC29A3	5.3 × 10−4	0.06	0.36	0.91	8.5 × 10−4	3.1 × 10−6	0.82	0.31
rs4910907	11p15	G	RRM1	1.6 × 10−6	0.44	0.16	0.22	0.32	6.5 × 10−5	1.07	0.02
rs12917712	16p11	T	SEZ6L2	8.6 × 10−6	0.03	0.03	0.68	0.84	7.1 × 10−6	1.07	0.19
rs12461589	19q12	C	PDCD5	2.0 × 10−5	0.10	0.67	0.05	0.25	7.8 × 10−5	0.83	0.04
rs2303745	19p13.1	A	DDA1	1.5 × 10−4	0.04	0.09	0.07	0.38	1.1 × 10−6	1.07	0.50
rs13333054	16q24	T	IRF8a	6.9 × 10−4	3.0 × 10−4	0.12	0.12	N/A	4.6 × 10−5	1.06	0.02
rs2785197	11p13	C	CD44a	7.7 × 10−4	0.75	3.4 × 10−3	0.98	2.6 × 10−4	1.9 × 10−7	0.81	0.18

The following abbreviations are used: chr, chromosome; META, results from the meta-analysis of the Hong Kong and Anhui GWASs; HK Rep, Hong Kong replication panel; AH Rep 1, Anhui replication panel 1; Thai, Thailand replication panel; AH Rep 2, Anhui replication panel 2; combined, p values from a combined analysis of the results from the two GWASs and the four replication panels with the use of the Cochran-Mantel-Haenszel test of disease association conditional on SNP-frequency differences among different panels; OR, odds ratio from the combined analysis; and p_het, p values of the homogeneity test of ORs from the six different panels with the use of the Breslow-Day test.

^aPreviously reported loci.