and shared by both cell types, respectively (a full description of associations at different significance thresholds is given in Supplementary Table 3). Comparative analysis of this dataset demonstrated a high concordance of eSNPs identified here that were shared between cell types and those previously identified in primary cell eQTL analysis10,14. This degree of commonality was not so clearly demonstrable upon analysis of LCLs15, possibly reflective of intrinsic differences between primary and cultured cells (Supplementary Figure 2). Cell specific eSNPs may exist secondary to cell-specific function of genetic variants, or alternatively when transcript expression is restricted to one cell type only. In order to identify eSNPs formed due to cell specific functional variants we defined genes expressed at similar levels across cell types but which demonstrated robust cell-specific effects. Even after excluding genes whose mean log2 expression across the cohort differed in magnitude by >0.5 between cell types, we identified 70149 cis-eSNPs in almost identical proportions by cell type. In general, whilst cell-specific eQTLs were observed more frequently, they tended to have smaller effect sizes than those shared between cells (median r2 5.1%, 5.5% and 9.8% for B-cell-specific, monocyte-specific and shared respectively) with 54, 107 and 351 eSNPs explaining more than
