Genetic variants in our genome could influence the transcription or function of miRNAs, affecting miRNA-mediated gene regulation and leading to diseases. Integration of genomics and miRNA expression data enables interrogation of the genetic architecture of miRNAs, and provides valuable resources for future studies on clinical significance of miRNAs in human disease. Here, we present the results of our genome-wide association studies on over 2000 extracellular miRNAs circulating in plasma measured by RNA-sequencing in the Rotterdam Study (Phase 1). We report both cis and trans  miRNA-expression quantitative trait loci (miRNA-eQTLs) at the nominal significance level (p-value < 0.05) and those passing the significance threshold of 1e-5, also the SNPs that have been replicated across two independent cohorts (see Ref below). The consequences of perturbation in miRNA transcription on a wide range of clinical conditions were also systematically investigated in phenome-wide association studies (PheWAS), with their causality tested using Mendelian randomization (MR) in the UK Biobank. Moreover, our colocalisation studies have highlighted several miRNA-eQTLs overlapping with gene expression, protein, and metabolite-QTLs and with disease-associated variants reported in previous GWAS studies (see the disease association and omics integration parts).