Although only a fraction of the CD45+ cells have a B-cell immunophenotype28, clear enrichment of RUNX1 and ETV6-RUNX1 was observed across the peaks identified in BCP-ALL (Supplementary Figs. 1c and 2d) and the combined RUNX1 and ETV6-RUNX1 peaks from the CD45+ cells were enriched for RUNX and ETS motifs (Supplementary Fig. 2e), indicating overlap between the regulatory programs in these experimental systems. Here, RUNX1 is linked to acute lymphoblastic leukemia.