@article {Pierce094656, author = {Brandon L. Pierce and Lin Tong and Maria Argos and Farzana Jasmine and Muhammad Rakibuz-Zaman and Golam Sarwar and Md. Tariqul Islam and Hasan Shahriar and Tariqul Islam and Mahfuzar Rahman and Md. Yunus and Muhammad G. Kibriya and Lin S. Chen and Habibul Ahsan}, title = {Co-occurring eQTLs and mQTLs: detecting shared causal variants and shared biological mechanisms}, elocation-id = {094656}, year = {2016}, doi = {10.1101/094656}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Inherited genetic variation impacts local gene expression and DNA methylation in humans. Expression and methylation quantitative trait loci (cis-eQTLs and cis-mQTLs) often occur at the same genomic location, suggesting a common causal variant and shared mechanism. Using DNA and RNA from peripheral blood of Bangladeshi individuals, we use {\textquotedblleft}co-localization{\textquotedblright} methods to identify 3,695 eQTL-mQTL pairs that are likely to share a causal variant. Using partial correlation analysis and mediation analysis, we identify \>500 pairs with evidence of a causal relationships between expression and methylation (i.e., shared mechanism) with many additional pairs that we are underpowered to detect. These co-localized pairs are enriched for SNPs showing opposite effects on expression and methylation, although a many affect multiple CpGs in opposite directions. Evidence of shared SNP-age interaction also supports shared mechanisms for two eQTL-mQTL pairs. This work demonstrates the pervasiveness of co-regulated expression and methylation traits in the human genome. This approach can be applied to other types of molecular QTLs to enhance our understanding of regulatory mechanisms.}, URL = {https://www.biorxiv.org/content/early/2016/12/15/094656}, eprint = {https://www.biorxiv.org/content/early/2016/12/15/094656.full.pdf}, journal = {bioRxiv} }