The extent to which a particular genetic variant may demonstrate diverging effects according to cell type is unclear. Here we find many variants show multiple, cell specific actions, with 6.4% of cell specific eSNPs additionally forming eQTL to different genes in the alternative cell type (Supplementary Figure 5a). For example rs738289 and linked eSNPs in the first intron of MGAT3, a gene encoding a glycosyltransferase21, showed association with MGAT3 in B-cells (p=9.8×10−26); by contrast in monocytes this eSNP was solely associated with the neighboring gene SYNGR1 encoding expression of vesicle associated protein (p=1.2×10−17) (Figure 2c). Just as cell type may define the gene a particular variant regulates, we observe certain genes whose expression is modulated by different variants in a cell specific manner. Such examples include TSPAN3 (Supplementary Figure 5b) and AKAP7 (not shown), in keeping with the effect of regulatory genetic variants being dependent on the environment defined by the cell type.
