Extended Data Fig. 5: ASM-QTLs dominate in correlations between MDSs and mRNA.
From: The correlation between CpG methylation and gene expression is driven by sequence variants
(a) Example of an association found between expression of VAMP5-201 (ENST00000306384), y-axis, and 5-mCpG haplotype rates, x-axis, of an MDS (chr2:85584168-85584976) located within the CpG island promoter of the TSS; that is, an example of CpG island promoter methylation. (b) The fraction of variance in VAMP5-201 mRNA isoform expression explained by (top) ASM-QTL found in association with the MDS (middle) CpG methylation of the MDS and (bottom) CpG methylation of the MDS after correction for the ASM-QTL. This same association between MDS at chr2:85584168-85584976 and mRNA expression of VAMP5-201 is then shown separately on (c) the reference- and (d) the alternative alleles of ASM-QTL chr2:85580659:IG.0:0, respectively. Least squares regression line is shown within each of three scatter plots, in blue colour, and the estimated regression coefficient and their 95% confidence intervals are shown at the bottom, along with the corresponding two-sided P-values.
