The protocol below describes the specific steps for performing the integrative analysis of chromatin accessibility, chromatin states, DNA looping and transcriptome across four cellular states in a murine allelic series that models the two most common mutations in acute myeloid leukemia (AML): Flt3-ITD and Npm1c, both of which are present in 15%–20% of all AML cases. Here, FLT3 is linked to acute myeloid leukemia.