It remains a possibility that GWAS SNPs have divergent effects between cell types. In support of this we find 4.6% of reported GWAS SNPs have cis-eQTL to differing genes in a cell type dependent manner. For example, rs10781500, a SNP associated with ulcerative colitis51 and ankylosing spondylitis52 shows contrasting cis-eQTL for three genes at 9q34.3 dependent on cell type. In B-cells the SNP associates with expression of the small nuclear RNA activating complex polypeptide gene SNAPC4 (p=3.1×10−5) while in monocytes the association is with SDCCAG3 (p=1.9×10−12) and CARD9 (p=1.0×10−24); SDCCAG3 is a poorly characterised gene encoding a molecule implicated in presentation of TNF receptor 1 on the cell surface53 while CARD9 encodes a caspase recruitment domain-containing signaling protein with a regulatory role in innate immunity and apoptosis54. Our analysis of highly purified primary cell populations also highlights that certain traits demonstrate a preponderance of cell specific eQTL, as illustrated by systemic lupus erythematosus (SLE) for B-cells, while others traits show a predominance of monocyte-specific eQTL, as seen in ulcerative colitis (UC) (Figure 6). These diseases have contrasting and complex etiologies
