Endothelial cells (ECs) differentiate from mesodermal progenitors during vasculogenesis. By comparing changes in chromatin interactions between human umbilical vein ECs, embryonic stem cells and mesendoderm cells, we identified regions exhibiting EC-specific compartmentalization and changes in the degree of connectivity within topologically associated domains (TADs). These regions were characterized by EC-specific transcription, binding of lineage-determining transcription factors and cohesin. In addition, we identified 1200 EC-specific long-range interactions (LRIs) between TADs. Most of the LRIs were connected between regions enriched for H3K9me3 involving pericentromeric regions, suggesting their involvement in establishing compartmentalization of heterochromatin during differentiation. Second, we provide evidence that EC-specific LRIs correlate with changes in the hierarchy of chromatin aggregation. Despite these rearrangements, the majority of chromatin domains fall within a pre-established hierarchy conserved throughout differentiation. Finally, we investigated the effect of hypoxia on chromatin organization. Although hypoxia altered the expression of hundreds of genes, minimal effect on chromatin organization was seen. Nevertheless, 70% of hypoxia-inducible genes situated within a TAD bound by HIF1α suggesting that transcriptional responses to hypoxia largely depend on pre-existing chromatin organization. Collectively our results show that large structural rearrangements establish chromatin architecture required for functional endothelium and this architecture remains largely unchanged in response to hypoxia.