Combined analysis of methQTLs and eQTLs did not reveal a simple relationship between genetically influenced DNA methylation and expression. QTLs that influenced both DNA methylation and expression levels of a physically close transcript were identified, these were in the minority; for the most part strong methQTLs were not also QTLs for expression. It is plausible that this observation reflects a genuine biological disconnect between CpG methylation and gene expression. Alternatively, this may be a result of poor power within the series to detect such effects or, as discussed below, a consequence of differences in cellularity confounding our results. Notably, when analyzing joint methQTL-eQTLs where the methylation site in question resided in a CpG island, the classical inverse relationship between CpG methylation and expression was clearly observed.
