Although many cisSNP effects can be detected in many different tissue types and disease conditions as shown here and by others [12], [20], there conceivably exist expression variants which exert their effects in a tissue or disease-specific manner. For example in the eQTL comparing blood and adipose tissue, Emilsson et al. [20] also found that more transcripts from adipose tissue had significant correlations with obesity-related traits. In reality, both scenarios may be at play, such that some expression variants have more ubiquitous effects, whereas others may need tissue/cell/region/disease specific factors to exert their influence on gene expression. Indeed, many of the CNS disease related cisSNP associations in our brain eGWAS could not be identified in our comparison to a liver eGWAS [23] or an existing database for a LCL eGWAS [12], suggesting that disease-relevant tissue may be necessary to detect effects of certain cisSNPs, and highlighting the value of this brain eGWAS for CNS traits/conditions.
