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To perform a 1‐stage meta‐analysis of genome‐wide association studies (GWAS) of multiple sclerosis (MS) susceptibility and to explore functional consequences of new susceptibility loci.

We synthesized 7 MS GWAS. Each data set was imputed using HapMap phase II, and a per single nucleotide polymorphism (SNP) meta‐analysis was performed across the 7 data sets. We explored RNA expression data using a quantitative trait analysis in peripheral blood mononuclear cells (PBMCs) of 228 subjects with demyelinating disease.

We meta‐analyzed 2,529,394 unique SNPs in 5,545 cases and 12,153 controls. We identified 3 novel susceptibility alleles: rs170934^T at 3p24.1 (odds ratio [OR], 1.17; p = 1.6 × 10⁻⁸) near EOMES, rs2150702^G in the second intron of MLANA on chromosome 9p24.1 (OR, 1.16; p = 3.3 × 10⁻⁸), and rs6718520^A in an intergenic region on chromosome 2p21 …