Genome‐wide association studies (GWAS) have identified genetic variations associated with adverse drug effects in pharmacogenomics (PGx) research. However, interpreting the biological implications of these associations remains a challenge. This review highlights 2 promising post‐GWAS methods for PGx. First, we discuss the polygenic architecture of the PGx traits, especially for drug‐induced liver injury. Experimental modelling using multiple donors' human primary hepatocytes and human liver organoids demonstrated the polygenic architecture of drug‐induced liver injury susceptibility and found biological vulnerability in genetically high‐risk tissue donors. Second, we discuss the challenges of interpreting the roles of variants in noncoding regions. Beyond methods involving expression quantitative trait locus analysis and massively parallel reporter assays, we suggest the use of in silico mutagenesis through machine learning methods to understand the roles of variants in transcriptional regulation. This review underscores the importance of these post‐GWAS methods in providing critical insights into PGx, potentially facilitating drug development and personalized treatment.