Expression quantitative trait locus (eQTL) refers to a genetic variation associated with the expression of specific genes. It has been widely applied to explain the regulatory mechanisms linking genetic variations to complex traits or diseases. Several eQTLs have been identified from tissues and single cells in individuals. Furthermore, the integration of eQTL and other omics data can be used to detect novel susceptibility genes and consequently understand the dynamic regulation of trait-associated genetic variations at the system level. Here, we review the identification methods, analysis tools, research progress, and common data resources of eQTLs, as well as their role in four typical diseases. Finally, we discussed the application fields, challenges, and future development perspectives of eQTL.