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Full list of author information is available at the end of the articleBackground Genome-wide genetic analysis of gene expression [1,2] identifies expression quantitative trait loci (eQTLs) which are mainly regulatory variants associated with cis- expression of nearby genes. Discovery of eQTLs may help elucidate the genetic mechanisms underlying natural variation in gene expression [3,4]. Identifying these genetic variants may improve our understanding of molecular mechanisms of disease risk, and of potential drug targets. Human cross-tissue allele-specific expression studies indicate a significant fraction of genes are under genetic control by one or more alleles [5-7]. Strong eQTLs are often highly correlated with markers of disease and quantitative traits at loci identified in GWAS [8-13], suggesting that these eQTLs account for a significant fraction of human phenotypic variability