Trans-eQTL analysis resulted in far fewer significant associations. Using human interactome data, only 4 eSNPs survived correction for multiple testing. Furthermore, all of these eQTL had already been identified as cis acting and their presence in trans was an artifact of the genomic proximity between the respective interacting genes. Trans analysis of 50-kb window-based cis-eQTL proved to be more successful (Supplementary Table 3). A total of 291 of these also showed evidence of trans effects. Although the majority of these eSNPs were located on the same chromosome as the gene and possibly represent cis effects that extend beyond 50 kb, 9 trans-eQTL spanned different chromosomes.
