**This repository contains data associated with the paper: Freire-Pritchett\* / Schoenfelder\* et al. Global rewiring of cis-regulatory units upon lineage commitment of human embryonic stem cells.** The description of individual folders and files is given below. All genomic coordinates are for the GRCh37 assembly. **CHiCAGO objects** The PCHi-C data in the form of objects produced by the Chicago R package, saved as rds archives. **ChromHMM output files** Dense segmentation files produced by ChromHMM algorithm saved in bed format (these files provide a dense view of the segmentation in a single track with states being differentiated solely by color). State number and classification: 1 – Polycomb; 2 – Background; 3 – Poised; 4 – Mixed; 5 – Background; 6 – Background; 7 – Active; 8 – Active; 9 – Intermediate; 10 – Active; 11 – Mixed; 12 – Active; 13 – Active; 14 – Active; 15 – Poised; 16 – Poised. Please note that the label annotations for the data released here (as above) do not match those shown in Figure 1 - figure supplement 3A in the paper. We apologise for the confusion.