Annotation description and citation 

Human (hg19) probe annotations 

	LECIFScore_HumanMouse_KwonErnst2021NatureCommunications
		description: score that quantifies conservation at the functional genomics level between human and mouse learned from thousands of functional genomic annotations
		citation: https://www.nature.com/articles/s41467-021-22653-8
		webpage: https://github.com/ernstlab/LECIF

	CNEPScore_GrujicEtAl2020NatureCommunications
		description: score of evidence that each base of the genome is in a constrained non-exonic base based on large-scale collections of human epigenomic and transcription factor binding data
		citation: https://www.nature.com/articles/s41467-020-19962-9
		webpage: https://github.com/ernstlab/CNEP

	CSS-CNEPScore_GrujicEtAl2020NatureCommunications
		description: expected CNEP score based on ConsHMM conservation state annotation and overlapping constrained element annotations 
		citation: https://www.nature.com/articles/s41467-020-19962-9
		webpage: https://github.com/ernstlab/CNEP

	PhastConsScore_SiepelEtAl2005GenomeResearch
		description: sequence constraint score based on 100-way vertebrate sequence alignment
		citation: https://genome.cshlp.org/content/15/8/1034.long
		species list: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons100way/README.txt
		
	PhastConsPlacentalScore_SiepelEtAl2005GenomeResearch
		description: sequence constraint score based on 46-way placental mammal sequence alignment
		citation: https://genome.cshlp.org/content/15/8/1034.long
		species list: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/README.txt

	PhyloPScore_Pollard2009GenomeResearch
		description: sequence constraint score based on 100-way vertebrate sequence alignment
		citation: https://genome.cshlp.org/content/20/1/110.long
		species list: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phyloP100way/README.txt
		
	PhyloPPlacentalScore_Pollard2009GenomeResearch
		description: sequence constraint score based on 46-way placental mammal sequence alignment
		citation: https://genome.cshlp.org/content/20/1/110.long
		species list: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phyloP46way/README.txt

	ConsHMMState_Multiz100way_ArnesonErnst2019CommunicationsBiology
		description: 100 ConsHMM conservation states that capture combinatorial and spatial patterns in 100-way vertebrate sequence alignment with human as the reference
		citation: https://www.nature.com/articles/s42003-019-0488-1
		webpage: http://www.biolchem.ucla.edu/labs/ernst/ConsHMMAtlas/
		note: see 'ConsHMMState_Multiz100way_ArnesonErnst2019CommunicationsBiology_SupplementaryData1.xlsx' for state description

	ChromHMMState_FullStack100State_VuErnst2022GenomeBiology
		description: 100 ChromHMM chromatin states from a full-stack model learned from over 1000 datasets from more than 100 cell types
		citation: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02572-z
		webpage: https://github.com/ernstlab/full_stack_ChromHMM_annotations	

	ChromHMMState_Roadmap5Mark127Epigenome15State_ErnstKellis2012NatureMethods_RoadmapEpigenomicsConsortium2015Nature
		description: 15 ChromHMM chromatin states learned from 5 marks for 127 epigenomes 
		citation: https://www.nature.com/articles/nmeth.1906, https://www.nature.com/articles/nature14248
		ChromHMM webpage: http://compbio.mit.edu/ChromHMM/
		Roadmap Epigenomics Consortium webpage: https://egg2.wustl.edu/roadmap/web_portal/chr_state_learning.html#core_15state

	ChromHMMState_Roadmap6Mark98Epigenome18State_ErnstKellis2012NatureMethods_RoadmapEpigenomicsConsortium2015Nature
		description: 18 ChromHMM chromatin states learned from 6 marks for 98 epigenomes
		citation: https://www.nature.com/articles/nmeth.1906, https://www.nature.com/articles/nature14248
		ChromHMM webpage: http://compbio.mit.edu/ChromHMM/
		Roadmap Epigenomics Consortium webpage: https://egg2.wustl.edu/roadmap/web_portal/chr_state_learning.html#exp_18state

	ChromHMMState_Roadmap12Mark127Epigenome25State_ErnstKellis2012NatureMethods_RoadmapEpigenomicsConsortium2015Nature
		description: 25 ChromHMM chromatin states learned from 12 marks for 127 epigenomes based on imputed data
		citation: https://www.nature.com/articles/nmeth.1906, https://www.nature.com/articles/nature14248
		ChromHMM webpage: http://compbio.mit.edu/ChromHMM/
		Roadmap Epigenomics Consortium webpage: https://egg2.wustl.edu/roadmap/web_portal/imputed.html#chr_imp


Mouse (mm10) probe annotations

	LECIFScore_HumanMouse_KwonErnst2021NatureCommunications
		description: score that quantifies conservation at the functional genomics level between human and mouse learned from thousands of functional genomic annotations
		citation: https://www.nature.com/articles/s41467-021-22653-8
		webpage: https://github.com/ernstlab/LECIF

	PhastConsScore_SiepelEtAl2005GenomeResearch
		description: sequence constraint score based on 60-way vertebrate sequence alignment
		citation: https://genome.cshlp.org/content/15/8/1034.long
		species list: http://hgdownload.cse.ucsc.edu/goldenPath/mm10/phastCons60way/README.txt
		
	PhastConsPlacentalScore_SiepelEtAl2005GenomeResearch
		description: sequence constraint score based on 60-way placental mammal sequence alignment
		citation: https://genome.cshlp.org/content/15/8/1034.long
		species list: http://hgdownload.cse.ucsc.edu/goldenPath/mm10/phastCons60way/README.txt

	PhyloPScore_Pollard2009GenomeResearch
		description: sequence constraint score based on 60-way vertebrate sequence alignment
		citation: https://genome.cshlp.org/content/20/1/110.long
		species list: http://hgdownload.cse.ucsc.edu/goldenPath/mm10/phyloP60way/README.txt
		
	PhyloPPlacentalScore_Pollard2009GenomeResearch
		description: sequence constraint score based on 60-way placental mammal sequence alignment
		citation: https://genome.cshlp.org/content/20/1/110.long
		species list: http://hgdownload.cse.ucsc.edu/goldenPath/mm10/phyloP60way/README.txt
		
	ConsHMMState_Multiz60way_ArnesonEtAl2020NARGenomBioinform
		description: 60 ConsHMM conservation states that capture combinatorial and spatial patterns in 60-way vertebrate sequence alignment with mouse as the reference
		citation: https://academic.oup.com/nargab/article/2/4/lqaa104/6040971
		webpage: http://www.biolchem.ucla.edu/labs/ernst/ConsHMMAtlas/

	ChromHMMState_ENCODE_GorkinEtAl2020Nature
		description: 15 ChromHMM chromatin state learned from 8 marks for 66 tissues during mouse embryonic development 
		citation: https://www.nature.com/articles/s41586-020-2093-3
		webpage with state description: http://enhancer.sdsc.edu/enhancer_export/ENCODE/chromHMM/readme
		
		
Contact Soo Bin Kwon (skwon94@ucla.edu) or Jason Ernst (jason.ernst@ucla.edu) for more information.