Identification of locally acting eQTL (referred to here as cis-acting) was performed by testing SNPs that fell within a 2.5Mb interval either side of the probe for association with expression in each cell type using linear and Spearman rank models. In this large, highly purified paired sample set we found little difference between the significance values using either approach - however, only eQTL that reached a permuted p<1×10−3 in both analyses were carried forward. We identified 82,346 eQTL (SNP-probe interactions, referred to hereafter as eSNPs) at permuted p<0.001, 32.2% of which were unique to B-cells, 45.9% to monocytes and 21.8% shared between cell types (Figure 1, Supplementary Figure 1, Supplementary Tables 1-2). This corresponded to 7468, 6831 and 1323 genes (8441, 7589 and 1466 probes) in which there was at least one cis-eSNP with permuted p<0.001 specific to B-cells, monocytes 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
