This repository contains the code and files used for analyses, as well as track files (compatible with the UCSC genome browser) for mSTARR-seq hg38 windows with regulatory activity, and windows with methylation-dependent regulatory activity, in all three conditions (baseline, IFNA, and dex). mSTARR-seq RNA and DNA raw sequencing data generated in this study for K562 and HepG2 cells are available in the NCBI Sequence Read Archive (SRA; BioProject accession number PRJNA922490). K562 endogenous RNA-seq data are available in the NCBI Gene Expression Omnibus (GEO series accession GSE222643). The previously published data from (Lea et al., 2018) used in this study are available in NCBI’s SRA accession number SRP120556. The sequencing data for the macrophage RNA-seq and WGBS datasets are available at the European Genome-phenome Archive (EGA) under accession numbers EGAD00001008422 and EGAD00001008359, respectively.