Gene expression, as an intermediate phenotype between genetic variation and higher-level phenotypes, is an important mechanism underlying disease susceptibility and drug response. Studies of the transcriptome in several tissues13 have shown that variation in gene expression is heritable32,33 and can be mapped to the genome. Particularly, eQTL mapping provides an immediate view of the effects of genetic variants on the phenotype closest to genetic variation, namely transcript abundance, and thus promises to enable the discovery of the molecular mechanisms underlying human phenotypic variation34. Furthermore, transcriptome regulation studies facilitate the consideration of thousands of gene expression phenotypes in parallel, thereby enabling a comprehensive approach to understanding the genetic basis of complex traits35. In this study, we developed a method that explicitly utilizes the wealth of regulatory information derived from transcriptome regulation studies to map trait-associated loci.
