We next sought to investigate whether the observed methQTLs and eQTLs represent individual loci where the underlying variant influences both CpG methylation and gene expression. These data revealed that in general, there was little co-association between methQTLs and eQTLs. Of the SNP, CpG and mRNA combinations considered (see Materials and Methods), 4.8% (average across tissues) were significant as both a methQTL and eQTL; this includes 2.6% (average of 13 sites per tissue) of CpG methylation sites where a significant methQTL is present and 8.2% (average of 11 transcripts per tissue) of mRNA transcripts that have a significant eQTL.
