Transcription and chromatin regulators, and histone modifications play essential roles in gene expression regulation.We have created CistromeMap as a web server to provide a comprehensive knowledgebase of all of the publicly available ChIP-Seq and DNase-Seq data in mouse and human.In total, CistromeMap contains 2711 ChIP-Seq datasets for transcription and chromatin regulators, 2355 for histone modifications and variants, 412 DNase-Seq, and 996 control datasets.We systematically annotated the following metadata for each sample: cell line/ population, cell type, tissue origin, strain (for mouse), disease state, factor name, PubMed ID (for published data), data source, reference, and last author.Based on the original literature and online information about official gene symbol, cell line and tissue origin, we created our own ontology for better annotation and organization.Among transcription and chromatin regulators, POLR2A, CTCF, ESR1, RELA, and EP300 are the most often profiled ChIP-Seq factors.For histone marks, H3K4me3, H3K27me3, H3K4me1, H3K36me3 and H3K9me3 ChIP-Seq are the most common, which together accounts for over 70% of all of the histone ChIP-Seq data.More details of the above statistics are available at http://cistrome.dfci.harvard.edu/pc/dcstats/, and will be automatically updated as more ChIP-Seq and DNase-Seq data become available .