Table 3.

List of genes with associations (P<0.001) in all MSSS analyses^a

Locus	Chr	Median MSSS (≤5 vs >5)			Extreme MSSS (<2.5 vs ≥7)			Continuous MSSS
		SNP	OR	P-value	SNP	OR	P-value	SNP	β	P-value
AGBL4	1	rs12127450	0.65	0.00049	rs12127450	0.53	0.00028	rs12127450	−0.54	8.8×10−5
NTNG1	1	rs17505688	1.80	0.00091	rs17505688	2.24	0.00086	rs17505688	0.75	0.00023
PTGER3	1	rs17541777	0.64	0.00031	rs5673	2.02	0.00091	rs17541777	−0.52	0.00018
ASXL2	2	rs10178552	0.71	0.00014	rs10178552	0.58	1.0×10−5	rs10178552	−0.41	4.8×10−5
LHCGR	2	rs13019537	0.61	0.00012	rs17398267	0.57	0.00016	rs13019537	−0.49	0.00052
MYT1L	2	rs13387792	0.60	0.00040	rs13387792	0.45	0.00020	rs13387792	−0.61	5.4×10−5
PPARGC1A	4	rs8192678	1.40	0.00026	rs8192678	1.72	5.9×10−5	rs8192678	0.37	0.00022
TRIM2	4	rs12644284	0.69	0.00056	rs12644284	0.49	3.9×10−5	rs12644284	−0.49	3.9×10−5
CTNND2	5	rs11750073	1.58	0.00025	rs11750073	1.99	6.5×10−5	rs11750073	0.52	0.00023
ARID1B	6	rs7744583	1.37	0.00061	rs7744583	1.59	0.00054	rs7744583	0.36	0.00030
POPDC3	6	rs11962089	0.55	5.9×10−5	rs11962089	0.45	0.00016	rs11962089	−0.69	8.3×10−6
LOC100289506	7	rs758944	1.37	0.00090	rs7789940	1.87	6.0×10−6	rs758944	0.48	7.9×10−6
NPSR1	7	rs2530548	0.75	0.00045	rs12111597	0.56	0.000842	rs17170015	−0.48	4.7×10−5
RELN	7	rs626065	0.76	0.00096	rs10487166	0.45	5.3×10−5	rs517761	−0.36	0.00012
YWHAG	7	rs11765693	1.37	0.00087	rs17149161	1.87	5.8×10−6	rs7779014	0.48	8.0×10−6
INTS10	8	rs7812549	0.66	0.00095	rs7812549	0.54	0.00055	rs7812549	−0.5	0.00017
ZFPM2	8	rs10505082	0.62	2.5×10−5	rs10505082	0.58	0.00067	rs16873632	−0.65	0.00011
PTPRD	9	rs10977017	1.67	1.0×10−5	rs10958932	0.65	0.00092	rs10977017	0.57	1.5×10−5
TBC1D2	9	rs10985528	0.58	0.00038	rs12352986	0.44	0.00057	rs10985528	−0.56	0.00038
CAMK1D	10	rs2399849	1.58	0.00027	rs2999981	5.36	0.00019	rs2399849	0.50	0.00049
DOCK1	10	rs2766051	1.68	0.00054	rs2050305	1.81	0.00023	rs2766051	0.65	0.00015
OR6T1	11	rs1476203	0.65	4.4×10−5	rs1476202	0.6	0.00068	rs1476203	−0.41	0.00025
KDM2B	12	rs7134248	0.73	0.00041	rs7134248	0.66	0.00067	rs7134248	−0.37	0.00017
FAM189A1	15	rs7167473	0.74	0.00053	rs11634779	0.58	0.00031	rs7167473	−0.36	0.00021
CLEC16A	16	rs8056098	0.74	0.00055	rs8056098	0.65	0.00053	rs7186166	−0.44	0.00034
GRIN2A	16	rs1448239	1.65	3.0×10−5	rs1448239	1.89	0.00020	rs1448239	0.56	3.2×10−5
ACCN1	17	rs9892479	2.20	0.00099	rs9892479	2.95	0.00082	rs9892479	0.99	0.00043
DTD1	20	rs4814783	0.70	0.00097	rs6075409	1.70	0.00062	rs6075409	0.43	0.00046
CERK	22	rs9616098	3.56	0.00035	rs9616098	5.92	7.2×10−5	rs9616098	1.55	0.00023

Abbreviations: Chr, chromosome; MSSS, multiple sclerosis severity score; OR, odds ratio; SNP, single-nucleotide polymorphism.

^aGenes with only one significant SNP association (P<0.05) were excluded. For each meta-analysis, the most significantly associated SNP variant is reported for each gene.