Results from genome-wide association studies (GWAS) have established an important role for common non-coding genetic variation in complex diseases [1, 2]. These associations are likely to reflect variants that influence gene expression, through effects on RNA transcription, splicing, or stability. By combining genome-wide genotyping with transcriptome profiling, variants associated with altered gene expression can be mapped on a genomic scale as expression quantitative trait loci (eQTL) [3, 4]. Although eQTL are often shared between tissues, they can also operate in a tissue-specific manner [4–6], as a result of cellular differences in the expression of the trans-regulators that interact with these loci [7], as well as in the epigenetic modification and accessibility of the regulatory elements in which they are located [8, 9].
