COUP-TFII is a modulator of cell-type-specific genetic programs based on genomic localization maps.

•The cistrome of COUP-TFII shows cell-type specific distribution in three cell lines.•The vast majority of shared COUP-TFII binding sites are located with CTCF in promoter-associated regions.•Cell-type-specific COUP-TFII co-occupied with master transcription factors in enhancer regions.•Shared COUP-TFII binding events can be found in VEGFA genes in three different cell lines.