It is widely appreciated that LCLs are not likely to be faithful models for gene expression in all tissues. To assess whether our findings for the associated SNPs from the NHGRI catalog were driven by enrichment in a few of the diseases for which LCLs might be reasonable proxies for tissues most strongly implicated in disease, we examined separately results for all disorders for which brain is the likely focus of disease (neurological and psychiatric disorders), all cancer phenotypes, since it might be hypothesized that the most relevant tissue was the site of the original tumor, and autoimmune disorders for which LCLs are, arguably, a reasonable proxy for tissue relevant to the disease process. Results are summarized in Table 1. We also tested whether the level of enrichment for eQTLs (defined using p<10−6 in studies on the CEU) in SNPs identified in studies on autoimmune disorders was significantly different from the level of enrichment for eQTLs in SNPs identified in studies of all other disorders using a chi-square test with 1 df.
