Table 1

Association results for the 46 novel susceptibility loci for systemic lupus erythematosus

Region	CHR	Position	Variant	EA	NEA	EAF	OR	SE	P value	I²	P_Het	N	Nearest gene
1	1	117 043 302	rs9651076	A	G	0.431	1.117	0.015	3.26E−13	10.7	0.347	208 370	CD58
2	1	157 108 159	rs116785379	C	G	0.107	1.211	0.024	6.68E−16	43.7	0.114	208 370	ETV3
7	1	201 979 455	rs3806357	A	G	0.251	1.106	0.017	4.25E−09	0.0	0.672	208 370	ELF3
9	2	7 573 079	rs75362385	T	G	0.321	0.887	0.017	8.40E−13	68.3	0.007	208 370	LOC100506274
14	2	111 877 174	rs73954925	C	G	0.878	1.169	0.024	5.11E−11	56.4	0.043	208 370	BCL2L11
18	2	198 929 806	rs7572733	T	C	0.260	1.143	0.017	1.25E−14	0.0	0.647	208 370	PLCL1
20	3	28 072 086	rs438613	T	C	0.588	0.920	0.014	7.52E−09	69.4	0.006	208 370	LINC01980
21	3	72 225 916	rs7637844	A	C	0.871	0.877	0.023	1.28E−08	0.0	0.906	208 370	LINC00870
25	4	2 700 844	rs231694	T	C	0.380	1.111	0.018	9.71E−09	23.7	0.269	57 253	FAM193A
26	4	40 307 587	rs113284964	G	GCTTC	0.371	1.134	0.015	1.35E−16	67.2	0.009	208 370	LINC02265
27	4	79 644 279	rs6533951	A	G	0.350	1.111	0.016	1.25E−10	61.4	0.024	208 370	LINC01094
28	4	84 146 996	rs6841907	T	C	0.729	0.906	0.016	1.10E−09	43.5	0.115	208 370	COQ2
31	4	109 061 618	rs58107865	C	G	0.227	0.802	0.021	6.57E−25	1.1	0.409	208 370	LEF1
34	5	131 120 338	rs370449198	A	AC	0.922	0.721	0.060	4.41E−08	0.0	0.408	187 562	FNIP1
35	5	131 829 578	rs2549002	A	C	0.682	0.905	0.016	2.40E−10	20.6	0.279	208 370	IRF1
40	6	243 302	rs9503037	A	G	0.693	0.881	0.016	1.36E−15	42.3	0.123	208 370	LOC285766
43	6	36 715 031	rs34868004	CA	C	0.225	1.104	0.017	4.46E−09	40.7	0.134	208 370	CPNE5
46	6	116 690 849	rs9488914	T	C	0.920	0.862	0.026	1.14E−08	65.3	0.013	208 370	DSE
48	6	154 570 651	rs9322454	A	G	0.659	1.090	0.015	2.42E−08	0.0	0.430	208 370	IPCEF1
54	8	71 330 166	rs142937720	A	AAGTGGCC	0.383	0.894	0.016	2.27E−12	67.9	0.008	208 370	NCOA2
55	8	72 894 959	rs17374162	A	G	0.411	0.917	0.015	3.02E−09	35.7	0.169	208 370	MSC-AS1
56	8	129 425 593	rs16902895	A	G	0.678	1.122	0.016	1.48E−13	0.0	0.801	208 370	LINC00824
58	9	21 267 087	rs7858766	T	C	0.538	1.139	0.016	2.25E−15	0.0	0.825	208 370	IFNA22P
59	10	5 910 746	rs77448389	A	G	0.913	0.855	0.025	7.30E−10	0.0	0.584	208 370	ANKRD16
62	10	64 411 288	rs10995261	T	C	0.240	0.909	0.017	2.57E−08	43.9	0.113	208 370	ZNF365
63	10	73 466 709	rs10823829	T	C	0.718	0.910	0.016	1.05E−09	0.0	0.771	208 370	CDH23
64	10	105 677 911	rs111447985	A	C	0.073	1.172	0.028	1.72E−08	0.0	0.526	208 370	STN1
65	10	112 664 114	rs58164562	T	C	0.748	0.892	0.016	3.14E−12	33.3	0.186	208 370	BBIP1
66	11	4 113 200	rs3750996	A	G	0.834	1.167	0.022	1.89E−12	0.0	0.522	208 370	STIM1
67	11	18 362 382	rs77885959	T	G	0.978	1.694	0.062	3.16E−17	0.0	0.511	204 433	GTF2H1
74	12	4 140 876	rs2540119	T	C	0.544	1.086	0.015	3.51E−08	44.9	0.106	208 370	PARP11
77	12	103 916 080	rs6539078	T	C	0.591	0.894	0.015	9.49E−14	0.0	0.916	208 370	LOC105369945
79	12	121 368 518	rs3999421	A	T	0.506	0.910	0.016	1.29E−09	47.3	0.091	208 370	XLOC_009911
81	12	133 040 182	rs200521476	G	GCATCAC	0.812	0.875	0.023	5.66E−09	26.7	0.235	208 370	FBRSL1
86	15	101 529 012	rs35985016	A	G	0.930	0.843	0.030	1.95E−08	0.0	0.897	204 433	LRRK1
90	16	50 089 207	rs11288784	G	GT	0.365	0.902	0.016	2.38E−10	0.0	0.664	208 370	HEATR3
93	16	79 745 672	rs11376510	G	GT	0.737	0.898	0.017	2.23E−10	0.0	0.719	208 370	MAFTRR
95	17	7 240 391	rs61759532	T	C	0.076	1.235	0.032	2.79E−11	24.9	0.247	208 370	ACAP1
97	17	47 468 020	rs2671655	T	C	0.651	1.087	0.015	4.60E−08	0.0	0.756	208 370	LOC10272459
98	17	76 373 179	rs113417153	T	C	0.193	0.893	0.020	1.90E−08	2.1	0.403	208 370	PGS1
100	18	77 386 912	rs118075465	A	G	0.147	1.140	0.020	1.16E−10	0.0	0.543	208 370	LOC284241
101	19	948 532	rs2238577	T	C	0.455	0.885	0.016	1.83E−14	60.8	0.026	208 370	ARID3A
102	19	6 697 088	rs5826945	A	T	0.929	0.836	0.028	9.67E−11	50.0	0.075	208 370	C3
105	19	33 072 768	rs12461589	T	C	0.248	0.898	0.017	5.00E−10	0.0	0.510	208 370	PDCD5
106	19	49 851 746	rs33974425	CCAGCTGCAT	C	0.702	1.120	0.016	4.40E−12	42.6	0.121	208 370	TEAD2
108	22	18 649 356	rs4819670	T	C	0.210	1.151	0.022	5.53E−11	0.0	0.650	208 370	USP18

CHR, chromosome; EA, effect allele; EAF, effect allele frequency; I², genetic heterogeneity I² statistics at scale of 0% to 100%; N, study sample size; NEA, non-effect allele; OR, Odds ratio; P_Het, P-values for the χ² test of genetic heterogeneity; Region, unique ID for genomic region; ;SE, Standard error of odds ratio.