We show that numerous cis-eQTLs can be identified through an expression analysis of peripheral blood RNA. We also show many of these are only detectable in peripheral blood RNA, and not in EBV-transformed B cell lines. Through a meta-analysis of these two datasets we identified numerous additional cis-eQTLs. We show that for some cis-eQTLs genetic variation does not lead to overall gene expression changes, but rather leads to shifts in the types of different splice isoforms that are produced. The complex nature of genotypic effects on gene expression limits our ability to fully elucidate the effect on RNA expression level or sequence and combined with the significant multiple testing problems prevented the accurate identification of trans effects.
