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Fig. 3 | Genome Biology

Fig. 3

From: A genomic atlas of systemic interindividual epigenetic variation in humans

Fig. 3

Evaluating associations between CoRSIV DNA methylation and neighboring genetic variation. a CoRSIV-specific P value distributions from mQTL analyses at the two most CoRSIV-dense genomic regions. At the MHC locus on chromosome 6, most CoRSIVs show mQTL; none of 10 informative CoRSIVs in the pericentromeric region on chromosome 20 show mQTL. b Summary of pair-wise analyses. Scatter plot shows correlation of interindividual differences in CoRSIV methylation vs. interindividual differences in average CoRSIV-associated SNV genotype for one pair of GTEx donors (RVPV and X261). Distribution of all such pairwise comparisons (right); average R2 = 0.61. c Heat map of published mQTL effects at 819 CoRSIVs overlapping probes on the HM450 array. Approximately 40% (white) show no evidence of mQTL. Dotted line shows location of probes within the PM20D1 CoRSIV. d Histogram of P values for the spearman correlation between methylation and read coverage within each CoRSIV. Two insets above the histogram show two scatter plots drawn from opposite ends of the histogram. The top left inset shows a strong association (P < 0.05) between average methylation in chr3_2398 CoRSIV and individual-average read depth in this region. The top right inset shows weaker association (P > 0.85) between average methylation in chr6_24299 CoRSIV and individual-average read depth in this region. e Decay curves of correlation in methylation and LD for CoRSIVs and control regions. f Histogram of CoRSIV-specific P values for the Spearman correlation analyses of methylation decay vs. LD decay. Locations of two CoRSIVs with (ITGB2) and without a significant association (AC07910.1) are indicated. g The CoRSIV at ITGB2 yielded a significant association (P < 0.05) between methylation decay and LD decay, consistent with a haplotype-effect on methylation. The scatter plot on the left (top, blue) shows all methylation R2 for pairs of bins in which one bin is within the CoRSIV and other bin is within ± 20 kb. The scatter plot on the left (bottom, red) shows LD for all pairs of SNVs. For each pair one SNV is within the CoRSIV and the other is within 20kb. On the right, the upper diagonal shows the CoRSIV (blue) in this region, and the lower diagonal shows the LD pattern in this region (1000 Genomes CEU). h In contrast, the CoRSIV at AC07910.1 showed no association between methylation decay and LD decay (P > 0.9), suggesting pure epigenetic variation

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