Common Regulatory Variation Impacts Gene Expression in a Cell Type–Dependent Manner

Tissue-Specific Control The effect of genetic variation on gene expression and phenotype among individuals is largely unknown. Dimas et al. (p. 1246, published online 30 July 2009) show that in humans there are several genes whose allelic expression varies in a tissue-specific manner and are apparently controlled by cis elements. Up to 80% of variants seem to have tissue-specific functions when compared in fibroblasts, as well as B cells and T cells. This variation among regulatory variants correlated with transcript complexity, which suggests that some of the observed regulatory variation is due to genotype-specific use of transcripts and transcription start sites. Genetic variation in regulatory elements among humans affects gene expression in a tissue-specific manner. Studies correlating genetic variation to gene expression facilitate the interpretation of common human phenotypes and disease. As functional variants may be operating in a tissue-dependent manner, we performed gene expression profiling and association with genetic variants (single-nucleotide polymorphisms) on three cell types of 75 individuals. We detected cell type–specific genetic effects, with 69 to 80% of regulatory variants operating in a cell type–specific manner, and identified multiple expressive quantitative trait loci (eQTLs) per gene, unique or shared among cell types and positively correlated with the number of transcripts per gene. Cell type–specific eQTLs were found at larger distances from genes and at lower effect size, similar to known enhancers. These data suggest that the complete regulatory variant repertoire can only be uncovered in the context of cell-type specificity.