not inherently evident whether the unaffected or affected tissue regions would be most suitable for eQTL studies. Whereas unaffected regions would have the advantage of minimizing confounding on expression measurements from pathology (such as inflammation and cell death), affected regions may be more relevant for disease-associated eQTL mapping. The substantial overlap in significant cisSNP associations between different brain regions and disease types in our study implies that sample size may be the most critical element of successful eQTL mapping. In other words, analysis of expression data collected in different tissue regions and diseases, provided there is careful statistical control, could greatly enhance power to detect eQTLs. Nevertheless, there may be important eQTLs that are specific to brain region and disease.
