SNPs significantly associated with MS lesion pathology. A. SNPs previously associated with clinical or MRI measures for disease severity. rs2234978/FAS, heterozygotes (T:C) and minor allele homozygotes (T:T) showed a higher proportion of active lesions compared to major allele homozygotes (C:C). rs11957313/KCNIP1, heterozygotes (G:A) and minor allele homozygotes (A:A) showed a lower proportion of active lesions compared to major allele homozygotes (G:G). rs8056098, minor allele homozygotes (A:A) showed a lower proportion of mixed active/inactive lesions compared to heterozygotes (G:A) and major allele homozygotes (G:G). B. SNPs located in genes previously associated with MS pathological characteristics. rs3130253/MOG, heterozygotes (G:A) showed a higher proportion of active lesions compared to major allele homozygotes (G:G). rs1064395/NCAN, heterozygotes (G:A) showed a higher incidence of cortical gray matter lesions compared to major allele homozygotes (G:G). rs5742909/CTLA4, heterozygotes (T:C) showed a higher proportion of remyelinated lesions compared to major allele homozygotes (C:C). *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001 (generalized linear models).