In summary, the PASSPORT-seq assay is a powerful tool that bridges bioinformatic predictions and high-throughput mechanistic investigation of functional genetic variants that affect miRNA–mRNA interactions. Future efforts will be aimed toward further increasing the capacity of the assay and identifying translational effects. This assay also has the potential to be modified to be applicable to genetic variants in other functional genomic regions such as promoters and splice junctions. Collectively, these assays will be key to elucidating the mechanisms underlying the genetic contribution to the inter-individual phenotypic variability.