In this study we illustrate that eQTL analysis of expression data obtained from highly purified primary cells enriches eQTL identification and reveals underlying cellular specific complexity not appreciable from mixed tissue. It is clear that whilst many eQTL with large effect sizes are shared across cells, the majority of eQTL in primary tissue are cell-specific. The degree to which a single variant can associate with the expression of different genes in monocytes and B-cells is particularly striking. It is probable that analysis of further divergent primary cell populations will increase the number of examples of such cell-specific eQTL. The delineation of cell-directional eQTLs is also of importance; in the case of those observed with SELL, which encodes a membrane protein involved in cellular recruitment to areas of inflammation, the intriguing possibility is raised that a polymorphism may influence the predominant cell subset recruited.
