Chapter 10 eQTL

So far we’ve tested associations between phenotypes and SNPs (GWAS) and phenotypes and expression (TWAS). A different approach which is agnostic to phenotypes is expression QTL mapping (eQTL). Under this framework, we are interested in identifying SNP variants which are associated with the expression of a certain gene. The concept is identical to a GWAS or TWAS, however our phenotypes being tested are molecular phenotypes (gene expression values). This is particularly interesting when we think of transcriptional regulation in determining the expression of genes. In this exercise we will conduct a targeted eQTL analysis for two genes - p1 and the top hit from the TWAS analysis.