Despite the wealth of information our study provides, we acknowledge several shortcomings. First, our non–ADs were not normal controls but often had other brain pathologies. It will be necessary to seek replication of these findings or novel cisSNP/transcript associations in normal brain tissue, as well. Second, we only focused on single SNP associations. The preliminary observations from our eGWAS findings suggest that multiple independent variants may affect brain expression levels of some genes, whereas others might be under the influence of a single strong variant. Finally, like any association study, it is not clear whether the cisSNPs identified in our eGWAS are themselves the functional SNPs or simply in LD with un-genotyped regulatory variants. Future studies focusing on analysis of haplotypes, SNPxSNP interactions, novel variant discovery and functional in-vitro studies testing effects of multiple variants are required to dissect the genetic variation underlying brain gene expression levels.
