Prostate cancer (PC) is the most frequently diagnosed non-skin cancer in the world. Previous studies showed that genomic alterations represent the most common mechanism for molecular alterations that cause the development and progression of PC. This highlights the importance of identifying functional genomic variants for early detection in high-risk PC individuals. Great efforts have been done to identify common protein-coding genetic variations; however, the impact of non-coding variations including regulatory genetic variants is not still well understood. Identification of these variants and the underlying target genes will be a key step in making an efficient treatment for PC. To gain an understanding of the functional impact of genetic variants, particularly, regulatory variants in PC, we developed Annotating Genomic Variants (AGV) an integrative pipeline that used whole genome/exome sequences, GWAS SNPs, chromosome conformation capture data, and ChIP-Seq signals to investigate the potential impact of genomic variants on the underlying target genes in PC. Totally, we report 30 PC-associated genomic variants including 3 GWAS SNPs and 27 copy number variants. We then use chromosome conformation capture (Hi-C) data to identify 30 new PC-associated regulatory variants that interact with 131 coding and non-coding genes; 56 of these genes are involved in the previously known curated gene sets/pathways including Reactome and MSigDB, in which targeted treatment options are currently available. Notably, our integrative analysis reveals several non-coding RNAs including RP11-136K7.2, and RAMP2-AS1 as the potential enhancer element of protein-coding genes CDH12 and EZH1, respectively. Using whole genome sequencing and H3K27ac we then show that 30 of 646 regulatory variants identified in this study significantly altered the expression of protein-coding genes. Together, our results provide a comprehensive map of genomic variants in PC and revealed their potential contribution to prostate cancer progression and development.