Chromatin modifications demarcate specific types of DNA including actively transcribed genes, repressed DNA, enhancer elements etc. that demarcate part of the epigenetic state controlling cell lineage decisions and functions. We developed a novel computational algorithm that analyzes chromatin in an unbiased manner across the genome to identify genes controlling cell lineage decisions in cardiovascular development. We used this algorithm to elucidate HOPX as a novel regulator of hemogenic endothelium. This approach has broad applications for understanding the genetic/epigenetic basis of developmental processes and disease etiology.