Table 1.

Summary of Some Major Available ChromHMM Reference Models and Annotations Defined Across Multiple Cell and Tissue Types.

Model	Input Marks	Cell/Tissue Types	Assembly	# of States	Ref.	URLs
Roadmap Epigenomics Core Model	5-marks observed human data (H3K4me1, H3K4me3, H3K27me3, H3K9me3, H3K36me3)	127 diverse ones (111 Roadmap, 16 ENCODE)	hg19	15	3	http://compbio.mit.edu/roadmap https://www.encodeproject.org http://epigenomegateway.wustl.edu/ https://genome.ucsc.edu/ (Roadmap Epigenomics Integrative Analysis Hub)
Roadmap Epigenomics Expanded Model	6-marks observed human data (H3K4me1, H3K4me3, H3K27me3, H3K9me3, H3K36me3, H3K27ac)	98 diverse ones (82 Roadmap, 16 ENCODE)	hg19	18	3	http://compbio.mit.edu/roadmap https://www.encodeproject.org http://epigenomegateway.wustl.edu/ https://genome.ucsc.edu/ (Roadmap Epigenomics Integrative Analysis Hub)
Roadmap Epigenomics Imputation Based Model	12-marks imputed human data (H3K4me1, H3K4me3, H3K27me3, H3K9me3, H3K36me3, H3K27ac, H3K9ac, H4K20me1, H3K79me2, H3K4me2, H2A.Z, UW DNaseI)	127 diverse ones (111 Roadmap,16 ENCODE)	hg19	25	12	http://compbio.mit.edu/roadmap http://epigenomegateway.wustl.edu/ https://genome.ucsc.edu/ (Roadmap Epigenomics Integrative Analysis Hub)
ENCODE Integrative Analysis ChromHMM Model	14 marks observed human data (H3K4me1, H3K4me3, H3K27me3, H3K36me3, H3K27ac, H3K9ac, H4K20me1, H3K4me2, Pol2, CTCF, FAIRE-seq, UW DNaseI, Duke DNaseI, Input)	6 ENCODE Cell Types	hg19	25	11, 25	https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeAwgSegmentation&db=hg19
Ernst et al, 2011 Nature Model	10 marks observed human data (H3K4me1, H3K4me3, H3K27me3, H3K36me3, H3K27ac, H3K9ac, H4K20me1, H3K4me2, CTCF, Input)	9 ENCODE Cell Types	hg18 and hg19 liftover	15	1	https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeBroadHmm&db=hg19 https://www.encodeproject.org
Ensembl Human Models	Minimum of 6-marks observed human data (H3K4me1, H3K4me3, H3K27me3, H3K9me3, H3K36me3, and H3K27ac)	74 Cell Types from Blueprint, Roadmap Epigenomics, and ENCODE	hg38	25	14, 19	http://ensembl.org/info/genome/funcgen/regulatory_segmentation.html ftp://ftp.ensembl.org/pub/release-87/data_files/homo_sapiens/GRCh38/segmentation_file/085/
Mouse ENCODE	4-marks observed mouse and human data (H3K4me1, H3K4me3, H3K36me3, H3K27me3)	15 mouse ENCODE cell types and 6 ENCODE cell types	mm9	7	16	https://www.encodeproject.org http://main.genomebrowser.bx.psu.edu/cgibin/hgTrackUi?g=meryChromHmm7s&db=mm9