ABSTRACT. Tissue-specific expression quantitative trait loci (eQTLs) are always linked to specific diseases. In this study, we focused on eQTLs common to multiple tissues and explored their functional mechanisms in disease for the first time. We found 11 common eQTL genes among multiple tissues. Five genes were validated through a genome-wide association study, 3 genes were validated using the Online Mendelian Inheritance in Man database, and the others were validated through text mining. Most of these disorders were related to the systemic immune system. In functional analyses using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes, these common eQTL genes were enriched in biological processes and pathways mostly related to the 6547 ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 12 (4): 6546-6553 (2013) Common eQTLs related to the immune system immunity. Therefore, we believe that these common eQTL genes are related to immune system.