Table 1. SNPs associated with MS susceptibility with genome-wide statistical significance in the merged dataset excluding all subjects who carry the HLA-DRB1*15:01 allele listed in order of highest to lowest statistical significance using the Cochran-Armitage trend test for association.

Merged Cohort HLA-DRB1*15:01(-) Subjects
				MS Associated	Trend	Odds	95% CI
SNP	Position	Class	Gene	Allele	P Values	Ratio	Lower	Upper
rs4959039	30065047	Class I	HLA-G	A	8.45×10−13	1.59	1.40	1.81
rs9393989	30148062	Class I	RNF39	A	9.84×10−13	0.63	0.56	0.72
rs9357092	30092230	Class I	HCG9	A	1.17×10−12	0.63	0.56	0.72
rs4713281	30086330	Class I	HLA-J	A	3.19×10−12	0.63	0.56	0.72
rs4713274	30045471	Class I	MICD	C	5.11×10−12	1.56	1.38	1.77
rs1736936	29902295	Class I	HCG4P8	C	2.22×10−11	0.70	0.63	0.78
rs2523822	29936638	Class I		A	2.99×10−11	1.51	1.34	1.70
rs4713270	30042675	Class I	HCG2P6	A	4.26×10−11	0.66	0.58	0.75
rs3823355	30050061	Class I	MICD	C	7.74×10−11	1.50	1.33	1.70
rs2734971	29942427	Class I	3.8–1.4	C	2.07×10−10	1.42	1.27	1.58
rs2239530	30260093	Class I	TRIM26	C	2.96×10−10	0.65	0.57	0.74
rs2523393	29813637	Class I	FLJ35429	C	6.04×10−10	0.72	0.65	0.80
rs1541268	30211372	Class I	TRIM40	C	1.40×10−9	0.66	0.58	0.76
rs2256266	29740296	Ext Cls I	MOG	A	2.67×10−9	0.66	0.58	0.76
rs2743951	29817212	Class I	FLJ35429	C	3.55×10−9	1.37	1.24	1.52
rs1611710	29936894	Class I		C	5.06×10−9	0.74	0.66	0.82
rs2517701	30033950	Class I	HLA-80	A	5.62×10−9	1.41	1.26	1.58
rs2523946	30049921	Class I	MICD	C	8.69×10−9	1.36	1.23	1.51
rs2256543	30045811	Class I	MICD	A	9.15×10−9	1.36	1.22	1.51
rs1362126	29798997	Class I	HLA-F	A	6.99×10−9	0.75	0.67	0.83