Table 1 summarizes the information on eQTLs for SNPs (with MAF>0.05) on high throughput platforms, associated with traits in the GWAS catalog, and associated with phenotypes selected to represent those for which lymphoblastoid cell lines (LCLs) might be expected to be a poor proxy for the human tissues most relevant for disease (neurological/psychiatric phenotypes, cancers) and those for which LCLs might be expected to be a good proxy for the human tissues most relevant to disease (autoimmune disorders). As is apparent from the table, neurological and psychiatric phenotypes as well as cancers (regardless of tumor site) showed levels of enrichment similar to those observed for the overall trait-associated SNP set, although as expected, autoimmune disorders showed somewhat greater levels of enrichment. Division of the GWAS catalog SNPs into those identified through studies on autoimmune disorders and those identified through studies on other complex traits reveals that the apparent enrichment of eQTLs (defined at a threshold of p<10−6) detected through studies on LCLs is indeed significantly greater (p = 0.00011) for SNPs identified through studies in autoimmune disorders than for SNPs identified through studies of other traits.
