Endothelial cell morphology and gene expression are driven by shear stress. Disturbed flow causes constitutive endothelial activation resulting in chronic, non-resolving, and pathological inflammation underlying human CAD. Human CAD is a complex disease that is strongly influenced by heredity. It is unclear how genetic variation can mediate shear stress response in human endothelium. In this work I demonstrate that mechanosensitive enhancers transcriptionally regulate many flow-sensitive genes in human endothelial cells using fine mapping strategies, epigenomic profiling of histone proteins, chromatin accessibility, gene expression, genome editing, and other functional assays. First, I found that a human polymorphism associated human cardiovascular disease predisposition, rs17114036, to be located within an endothelial-specific enhancer that is selectively activated by unidirectional flow. CRISPR-Cas9-based genome editing functionally demonstrates that removing this rs17114036-containing region decreases PLPP3 under unidirectional flow and results in a pro-inflammatory, athero-relevant phenotype. Next, to systematically investigate all genomic flow-sensitive cis-regulatory elements, I performed differential bioinformatics analyses on RNA and ATAC-seq data from endothelial cells subjected to unidirectional and disturbed flow to identify thousands of genes and nucleosome-free clusters that are significantly regulated by flow. Lastly, I integrated this data with promoter capture Hi-C from endothelial cells to directly link regulatory elements with its target gene to probe the gene-regulatory changes that occur in response to flow. I further discovered that many of these elements harbor hundreds of polymorphisms from the GWAS catalog, associating mechanosensitive enhancers with many human cardiovascular phenotypes. Taken together this work finds networks of genes, sets of gene regulatory elements, and human polymorphisms related to human cardiovascular traits. These results demonstrate that human genetic variation mediates endothelial mechanotransduction mechanisms and that these thousands of gene-regulatory elements influence human cardiovascular disease predisposition and traits.