Abstract As our understanding of the intricate mechanisms of gene regulation increases, it is apparent that traditional methods of identifying aberrant genetic mechanisms associated with complex disease, such as linkage and association studies, will not be sufficient. Additionally, the traditional paradigm that variants that lead to disease must exist within the coding region of a gene needs to be changed. One step in better modeling of disease risk and understanding disease variants lies in expanding the paradigm of complex disease study to include epigenetic influences that contribute to diseases. We hypothesize that changes in DNA methylation status of genes in endothelial cells (ECs) and smooth muscle cells (SMCs) undergoing phenotypic switching, a hallmark of atherosclerosis formation, could play a role in atherosclerosis initiation and progression. This proposal specifically seeks to create comprehensive maps of the cytosine methylated genome in (1) ECs and SMCs under a disease and (2) non-disease state influenced using a novel and validated human surrogate vascular co-culture model that can recalibrate the EC and SMC phenotype into a healthy or atheroprone phenotype outside the human body and (3) diseased and non-diseased human aorta tissue. We tackle three paradigms to demonstrate how to evaluate cytosine methylation changes, in healthy cells and tissues, in disease cells and tissues, and in early (flow phenotype) and late (lipid and plaque laden tissue) atherosclerosis. In addition, highthroughput sequencing methods and tools will be developed using these data and be made available to all scientists.