Extended Data Fig. 6: Enrichment of meQTL SNPs and CPGs for association with gene expression.

Sentinel meQTL SNPs and CpGs are enriched for association with gene expression in cis and trans (SNPs) and only in cis (CpGs). Panel a: Results are presented as the proportion of SNPs that are observed to be associated with gene expression in cis (top row) or in trans (bottom row), stratified by proximity between SNP and CpG for the respective SNP-CpG pair (cis, long-range cis and trans from left to right). Panel b: Similarly, results are presented as the proportion of CpGs that are observed to be associated with gene expression in cis (top row) or in trans (bottom row), stratified by proximity between SNP and CpG for the respective SNP-CpG pair (cis, long-range cis and trans from left to right). Both panels: In each plot, the observed proportion (yellow boxplots) is compared to the proportion expected under the null hypothesis based on permutation testing (blue boxplots, see Methods). Inset in each figure is the P-value for comparison between observed and expected proportions (t-test). Boxplots show medians (center lines), first and third quartiles (lower and upper box limits, respectively), 1.5-fold interquartile ranges (whisker extents) and outliers (black circles). Proportions were calculated based on 100 sets of permutations with 1,000 SNPs (Panel A) or 1,000 CpGs (Panel B) in each permutation.