The overlap between meQTLs and eQTLs. (a) QQ-plot describing the eQTL association P-values in 180 cis-meQTL SNPs (red) and in eight samples of SNPs that match the cis-meQTL SNPs for minor allele frequency and distance-to-probe distributions (black). (b) Association signals in 508 FDR 10% eQTLs before and after regressing out gene-specific methylation. In black are 439 eQTLs that overlap across the two phenotypes, in red are 45 eQTLs present before methylation regressions, and in blue are 24 eQTLs present after regressing out methylation. The flat lines (green) correspond to the FDR 10% eQTL threshold.