Other e- or sQTLs that overlapped with associations in genome-wide association studies were found for SNPs previously implicated in ankylosing sponylitis, asthma, celiac disease, Crohn disease, HDL cholesterol, lupus, multiple sclerosis rheumatoid arthritis, and type 1 diabetes. It is unclear why the majority of the splicing/expression associations we have found are for SNPs originally implicated in autoimmune diseases. Although this result could reflect a particular importance of splicing variation in autoimmunity, two other possibilities seem more plausible. First, the imbalance could be the result of a methodological bias in evaluating a tissue type clearly relevant to immune system function (PBMCs). While brain tissue was included, little progress has been made identifying common variants that influence brain-specific phenotypes in genome-wide studies. Interestingly, for each e- or sQTL the association in the immune system relevant PBMCs in all cases was stronger compared to that observed in the brain tissue samples (Table 3), which argues for the importance of assessing expression and splicing effects in tissue types most relevant to the disease under study.
