Fig. 2: ASM-QTLs dominate in correlations found between MDSs and mRNA expression.

a, Variance in 5-mCpG rates of MDSs, one MDS from each 100 kb segment of the genome (n = 25,079 MDSs), binned by quintiles (y axis; ~5,000 MDSs per bin) and plotted against the proportion of these MDSs that have an associated ASM-QTL (x axis) according to whether the MDS is associated with mRNA expression (black) or not (red). The proportion estimates are shown as tick marks (vertical lines), and their 95% CIs are shown as horizontal lines. b, Fraction of the variance in mRNA expression explained by each of the four variables on the y axis as follows: y = ASM-QTL represents the genotype of the ASM-QTL found in association with 5-mCpG rates of MDSs; y = 5-mCpG represents the 5-mCpG rates of MDSs; y = 5-mCpG|ASM-QTL represents the 5-mCpG rates of MDSs after correction for the ASM-QTL found in association with that same MDS; y = ASM-QTL|5-mCpG represents the genotype of the ASM-QTL found in association with 5-mCpG rates of MDSs after having corrected the genotype status for the 5-mCpG rates of that same MDS. c, Fraction of the variance in 5-mCpG rates explained by each of the four variables on the y axis, where mRNA represents mRNA expression but otherwise analogous to b. In both b and c, the center line (solid black) shown in each box represents the median; box limits represent upper and lower quartiles; whiskers represent 1.5× interquartile range. r²_mRNA,5-mCpG in b is equivalent to the reversed comparison of r²_5-mCpG,mRNA in c. d, Effects of ASM-QTL genotype (G) on CpG methylation (\({\hat{\beta }}_{{\rm{GM}}}\)) and mRNA expression (\({\hat{\beta }}_{{\rm{GE}}}\)), x axis, compared with the effects of CpG methylation on mRNA expression (\({\hat{\beta }}_{{\rm{ME}}}\)), y axis. The number of datapoints in each boxplot in b and c, and in the scatter plot in d corresponds to the number of associations found between methylation and gene expression (n = 1,513).

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