Table 2.
Six SNPs associated with MS lesion characteristics in autopsy tissue.
| SNP | Chr:Location (hg19) | Gene | Position (UCSC, hg19) | P‐value (FDR) | P‐value (post‐hoc test unadjusted) | Pathological outcome | Correlation with MS severity | cis eQTLs GTEx (FDR <0.05) |
|---|---|---|---|---|---|---|---|---|
| rs2234978 | 10:90771829 | FAS | exon 7 | 0.020 | CT vs CC (P = 0.0003) TT vs CC (P = 0.004) | Minor T allele associated with increased proportion of active lesions | Odds ratio 1.83 (TT vs CC) predicting time to EDSS6 58 | FAS and ACTA‐2 |
| rs3130253 | 6:29634012 | MOG | exon 3 | 0.020 | AG vs GG (P = 0.0001) | Minor A allele associated with increased proportion of active lesions | HLA‐A | |
| rs1064395 | 19:19361735 | NCAN | exon 15 | 0.010 | AG vs GG (P = 0.00002 ) | Minor A allele associated with increased incidence of cortical gray matter lesions | NCAN significantly upregulated (FC 2.7) in the area around mixed active/inactive lesions compared to the area around inactive lesions 33 | CILP2, HAPLN, ZNF101, LPAR2, TSSK6, TM6SF2 |
| rs11957313 | 5:169950394 | KCNIP1 | intron 1 | 0.047 | AG vs GG (P = 0.015) AA vs GG (P = 0.026) | Minor A allele associated with decrease in proportion of active lesions | Brain parenchymal volume (Log P > 5.0) 4 | C5orf58 |
| rs8056098 | 16:11138812 | CLEC16A | intron 15 | 0.047 | AA vs GG (P = 0.002) AA vs GA (P = 0.0009) | Homozygotes for minor A allele show a lower proportion of mixed active/inactive lesions | Odds ratio 0.65 (MSSS<2.5 vs >7) 6 | NA |
| rs5742909 | 2:204732347 | CTLA4 | near '5 | 0.047 | TC vs CC (P = 0.0002) | Minor T allele associated with increase in remyelinated lesions | NA |