Fig. 2: Colocalized cis-mQTL effects of MS susceptibility loci.
From: Proximal and distal effects of genetic susceptibility to multiple sclerosis on the T cell epigenome
a The top 3 colocalized MS-cis-mQTL effects are illustrated (posterior probability >0.95 for colocalization between MS susceptibility and ≥ 1 cis-mQTL effect). The MS GWAS rows (blue dots) show -log(p-value) of association between SNPs and MS susceptibility in the discovery phase of the 2019 IMSGC GWAS. CpG rows (plum dots) show -log(p-value) of association between SNPs and the specified cis-CpGs methylation levels. Locations of the local CpGs measured with the Infinium MethylationEPIC kit are shown using light blue vertical lines. Gene exon/intron positions are based on Ensembl 93. Chromatin state annotations for CD4+ T cells are downloaded from the Roadmap Epigenomics Project (sample #E043). Green vertical lines represent the genomic location of the colocalized CpGs: Long vertical lines traversing all rows represent the top specified CpGs, while other vertical lines represent the additional colocalized cis-mCpGs with posterior probability >0.8. All genomic positions are in GRCh37 (hg19) coordinates. b Comparison between MS-cis-mQTL colocalization posterior probabilities using mQTL summary statistics from our study and BLUEPRINT for the available common CpGs. Vertical red line represents the threshold for high colocalization posterior probability in our study (i.e., 0.8). c The cis-mQTL, cis-eQTL, and CpG-mRNA association for the chromosome 5 top MS-cis-mQTL colocalized effect (n = 156, 36 and 36, respectively). Methylation levels are shown in M-values. Gene expression values are in TPM. Boxplot center lines represent median; the lower and upper hinges correspond to the 25th and 75th percentiles; the lower/upper whisker extends from the hinge to the smallest/largest value no further than 1.5× inter-quartile range. Error band represents 95% confidence interval.
