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 50% of the variance in expression of 14, 37 and 61 genes respectively. Using further RNA purified from randomly selected individuals within the cohort we were able to replicate the cellular specificity for selected genes by real-time PCR (n=14-29 homozygous individuals per gene) (Supplementary Figure 3). When RNA from crude PBMCs from the same individuals was analysed however, the signal was frequently absent (Supplementary Figure 3b,d,i), supporting the importance of cell purification in the identification of subtle primary cell-specific eQTL.
