Attribute List for Genome Assembly: hg17


This page summarizes the different attribute groups included in EpiGRAPH and provides references to the source from which the datasets were obtained. Further information can be obtained from the EpiGRAPH Background page and from the EpiGRAPH attribute reference sheet.



DNA_Sequence


Attributes that describe the DNA sequence itself, including base composition and oligonucleotide patterns


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
Base_compositionStrand-specific frequency of occurence for each nucleotide (A, C, G and T)Calculated directly from the DNA sequence
All_2mersFrequency of occurence separately for each oligonucleotides of size two that does not include any Ns (not strand-specific)Calculated directly from the DNA sequence
All_4mersFrequency of occurence separately for each oligonucleotides of size four that does not include any Ns (not strand-specific)Calculated directly from the DNA sequence


DNA_Structure


Attributes that describe the DNA structure (as inferred from the DNA sequence), such as distortions of the DNA helix and predicted solvent accessibility


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
Predicted_Helix_StructureHelix structure of naked DNA as predicted from octamers with known structureCalculated by a simple sliding window approach using the simulation data reported in Gardiner et al. (2003) J Mol Bioltwist
roll
tilt
rise
slide
shift
Predicted_Solvent_Accessible_SurfaceSolvent accessible surface area of naked DNA as predicted from trimers with known valuesCalculated similarly to the UCSC Genome Browser Boston University ORChID track (http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78806550&c=chr7&g=encodeBu_ORChID1)pk1_mean
pk2_mean
pk3_mean


Repetitive_DNA


Attributes that describe repetition within the DNA, including transposable elements, tandem repeats and segmental duplications


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
RepeatMaskerRepeats as detected by RepeatMasker. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=rmsk for details.UCSC Genome Browser, tables chr1_rmsk to chrY_rmskswScore
repStart
repLeft
repClass
repFamily
Simple_RepeatsTandem repeats as detected by Tandem Repeats Finder. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=simpleRepeat for details.UCSC Genome Browser, table simpleRepeatperiod
copyNum
score
entropy
Self_ChainSelf-chain alignments as detected by blastz. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=chainSelf for details.UCSC Genome Browser, tables chr1_chainSelf to chrY_chainSelfnormScore
Segmental_DupsSegmental duplications as detected by the 'fuguization' method. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=genomicSuperDups for details.UCSC Genome Browser, table genomicSuperDups


Chromosome_Organisation


Attributes that describe the large-scale functional organisation of the chromosomes, including chromosomal bands and special-interest regions


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
Chromosome_BandChromosome Bands localized by FISH mapping clones. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=cytoBand for details.UCSC Genome Browser, table cytoBandgieStain
IsoFinder_Isochore_PredictionsIsochores as detected by IsoFinder. See http://genome-test.cse.ucsc.edu/goldenPath/customTracks/hgTrackIsochores.html for details.Downloaded from UCSC Genome Browser on 31th October 2006, manually merged into one filescore
GC
Bernardi_Isochore_PredictionsIsochores as detected by Bernardi's prediction algorithm. See Costantini et al. (2006) Genome Res for details.Supplementary Table 1 from Costantini et al. (2006) Genome ResGC
dGC
GC_sd
ENCODE_RegionsTarget regions of the international ENCODE project pilot phase. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78872892&c=chr2&g=encodeRegions for details.UCSC Genome Browser, table encodeRegions


Evolutionary_History


Attributes that describe the evolutionary history of the genome, including conservation and local recombination rates


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
Recomb_RateLow-resolution recombination rates estimated from genetic maps. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=recombRate for details.UCSC Genome Browser, table recombRatedecodeAvg
decodeFemale
decodeMale
marshfieldAvg
genethonAvg
SNP_Recomb_RatesHigh-resolution recombination rates estimated from SNP data. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=snpRecombRate for details.UCSC Genome Browser, table snpRecombRateHapmapdataValue
SNP_Recomb_HotsHigh-resolution recombination hotspots estimated from SNP data. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=snpRecombHotspot for details.UCSC Genome Browser, table snpRecombHotspotHapmap
Multiz_AlignmentAlignment of 16 vertebrates, including mammalian, amphibian, bird, and fish species, with the human genome. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78778577&c=chr7&g=multiz17way for details.UCSC Genome Browser, table multiz17waySummaryscore
leftStatus
rightStatus
src
Multiz_ConservationEvolutionary conservation in 17 vertebrates, including mammalian, amphibian, bird, and fish species, based on a phylogenetic hidden Markov model (phastCons). See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78778577&c=chr7&g=multiz17way for details.UCSC Genome Browser, directory multiz17wayscore


Population_Variation


Attributes that describe the variability among today's individuals, including SNPs and microdeletions


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
SNPsCompilation of single nucleotide polymorphisms from the dbSNP database. http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=snp125 for details.UCSC Genome Browser, table snp125class
func


Genes


Attributes that describe the distribution of known and predicted protein-coding genes, pseudogenes and non-coding genes within the genome


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
CCDSHigh-confidence gene annotations from the Consensus Coding DNA Sequence (CCDS) project. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=ccdsGene for details.UCSC Genome Browser, table ccdsGene
Known_GenesKnown protein-coding genes based on protein data from UniProt (SWISS-PROT and TrEMBL) and on mRNA data from the NCBI reference sequences collection (RefSeq) and GenBank. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=knownGene for details.UCSC Genome Browser, table knownGene
RefSeq_GenesKnown protein-coding genes taken from the NCBI mRNA reference sequences collection (RefSeq). See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=refGene for details.UCSC Genome Browser, table refGene
Vega_GenesHigh-confidence manual gene annotations from the Vertebrate Genome Annotation (VEGA) database. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=vegaGene for details.UCSC Genome Browser, table vegaGene
Vega_PseudogenesHigh-confidence manual pseudogene annotations from the Vertebrate Genome Annotation (VEGA) database. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=vegaPseudoGene for details.UCSC Genome Browser, table vegaPseudoGene
Yale_PseudoPseudogene annotation based on computational predictions. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=pseudoYale for detailsUCSC Genome Browser, table pseudoYale
EvoFoldRNA secondary structure predictions made with the EvoFold program, a comparative method that used multiple-sequence alignments for identifying conserved functional RNA structures. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=evofold for detailsUCSC Genome Browser, table evofoldscore
sno_miRNAAnnotation of four different types of non-coding RNAs, based on several public databases. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=wgRna for detailsUCSC Genome Browser, table wgRnatype


Regulatory_Regions


Attributes that describe putative regulatory regions and functional elements in the genome


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
TFBS_ConservedAnnotation of TRANSFAC-predicted transcription factor binding sites conserved in the human/mouse/rat alignment. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=tfbsConsSites for details.UCSC Genome Browser, table tfbsConsSiteszScore
name
TScanS_miRNAAnnotation of microRNA regulatory targets predicted by TargetScanS. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=targetScanS for details.UCSC Genome Browser, table targetScanSscore
PicTar_miRNAMicroRNA target sites in 3' UTRs as predicted by PicTar, based on the RefSeq annotation of 3' UTRs. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=picTar for details.UCSC Genome Browser, table picTarMiRNA5Wayscore
CpG_IslandsCpG islands according to a UCSC Genome Browser detection algorithm. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=cpgIslandExt for details.UCSC Genome Browser, table cpgIslandExtperGc
obsExp
GGM_CpG_IslandsCpG islands as calculated by the CpG Island Searcher script with the Gardiner-Garden criteria on the repeat-masked genomeC Bock et al. (2007) "CpG island mapping by epigenome prediction". http://neighborhood.bioinf.mpi-inf.mpg.de/CpG_islands_revisited/GC
ObsExp
Length
Bona_Fide_CpG_IslandsCpG island strength predictions and maps of predicted bona fide CpG islands according to three different thresholds (sensitive, balanced and specific, respectively)C Bock et al. (2007) "CpG island mapping by epigenome prediction". http://neighborhood.bioinf.mpi-inf.mpg.de/CpG_islands_revisited/CombinedEpigeneticScore
OptimizedScore
isCGI_sensitive
isCGI_balanced
isCGI_specific


Transcriptome


Attributes that describe the transcriptional activity, including non-genic transcription and promoter activity


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
GNF_Atlas_2Gen expression data from the GNF Gene Expression Atlas for 79 individual samples grouped into 28 tissue types. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=gnfAtlas2 for detailsUCSC Genome Browser, table gnfAtlas2 with significant post-processingadrenalgland
Appendix
bonemarrow
fetalbrain
fetalliver
fetallung
heart
kidney
liver
lung
OlfactoryBulb
Ovary
pancreas
pituitary
placenta
Pons
Prostate
salivarygland
Skeletal_Muscle
skin
SmoothMuscle
spinalcord
testis
thymus
tongue
Tonsil
trachea
Uterus
type
Human_mRNAsAnnotation of alignments between human mRNAs in GenBank and the genome. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=mrna for detailsUCSC Genome Browser, table all_mrna
Spliced_ESTsAnnotation of alignments between human spliced ESTs in GenBank and the genome. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=intronEst for detailsUCSC Genome Browser, tables chr*_intronEst
Human_ESTsAnnotation of alignments between human ESTs in GenBank and the genome. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=est for detailsUCSC Genome Browser, table all_est
RIKEN_CAGE_TagsTranscription initiation events detected by 5' cap analysis gene expression (CAGE). See http://fantom.gsc.riken.go.jp/ for details.extracted from the CAGE Promoter Special from the FANTOM3 website at http://fantom.gsc.riken.go.jp/cage_tags
RIKEN_CAGE_ClustersClusters of transcription initiation events detected by 5' cap analysis gene expression (CAGE). See http://fantom.gsc.riken.go.jp/ for details.extracted from the CAGE Promoter Special from the FANTOM3 website at http://fantom.gsc.riken.go.jp/CTSSs
cage_tags
class
Affy_Txn_Phase2Transcriptome data from Affymetrix high-resolution tiling arrays for the ten chromosomes 6, 7, 13, 14, 19, 20, 21, 22, X, and Y. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=affyTxnPhase2 for detailsUCSC Genome Browser, tables *TnFgtype


Epigenome_and_Chromatin_Structure


Attributes that describe the chromatin structure and epigenetic modifications, including histone modifications and protein binding


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
NHGRI_DNaseI_MPSS_SitesDNaseI sensitivity measured by Massively Parallel Signature Sequencing (MPSS). See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=nhgriDnaseHs for details.UCSC Genome Browser, table nhgriDnaseHs
GIS_p53_5FU_HCT116Genome-wide p53 binding sites as determined by chromatin immunoprecipitation (ChIP) and paired-end di-tag (PET) sequencing. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=encodeGisChipPet for details.UCSC Genome Browser, tables encodeGisChipPet
LI_Ng_TAF1_IMR90Genome-wide analysis of likely TAF1 binding sites in fibroblastoid (IMR90) cells as assayed by ChIP/chip using a NimbleGen microarray. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=encodeUcsdNgChip for details.UCSC Genome Browser, tables encodeUcsdNgChipKnownSites and encodeUcsdNgChipNovelSites
DNA_Methylation_BrainRestriction enzyme digestion and direct sequencing of 3073 unmethylated domains and 2565 methylated domains from human brain DNA. See http://epigenomics.cu-genome.org/html/meth_landscape/ for details.Rollins et al. (2005) Genome ResearchCpG_richness
Methylation


ENCODE_Transcriptome


Attributes that describe the transcriptome of the ENCODE regions in high detail, including tiling array data and RT-PCR


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
Known_Pred_RNAKnown and predicted non-protein-coding RNA genes and pseudogenes. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78872892&c=chr2&g=encodeRna for details.UCSC Genome Browser ENCODE data, table encodeRnascore
source
GIS_PET_RNAAnnotation of full-length mRNA transcripts determined by paired-end ditag (PET) sequencing. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78872892&c=chr2&g=encodeGisRnaPet for details.UCSC Genome Browser ENCODE data, table encodeGisRnaPet*
Affy_Transfrags_normalTranscriptome data from Affymetrix high-resolution tiling arrays for the ENCODE region. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78872892&c=chr2&g=encodeAffyRnaTransfrags for detailsUCSC Genome Browser ENCODE data, tables encodeAffyRna*
Affy_Transfrags_stimulatedTranscriptome data from Affymetrix high-resolution tiling arrays for the ENCODE region. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78872892&c=chr2&g=encodeAffyRnaTransfrags for detailsUCSC Genome Browser ENCODE data, tables encodeAffyRnaHl60Sites*time
Yale_Transfrags_hematopoieticTranscriptome data for differentiation of hematopoietic cells, measured by Affymetrix high-resolution tiling arrays for the ENCODE region. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78875894&c=chr2&g=encodeYaleAffyRNATars for detailsUCSC Genome Browser ENCODE data, tables encodeYale*Tars


ENCODE_Epigenome_and_Chromatin_Structure


Attributes that describe the epigenome of the ENCODE regions in high detail, including histone modifications and chromatin structure


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
Affy_SitesChIP-on-Chip of several histone modifications and DNA-binding proteins in retinoic-acid stimulated HL-60 cells harvested after 0, 2, 8, and 32 hours. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=encodeAffyChIpHl60Sites for details.UCSC Genome Browser ENCODE data, tables encodeAffyChIpHl60Sites*chromMod
time
GIS_STAT1_HeLaSTAT1 binding sites as determined by chromatin immunoprecipitation (ChIP) and paired-end di-tag (PET) sequencing. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=encodeGisChipPetStat1 for details.UCSC Genome Browser ENCODE data, tables encodeGisChipPetStat1*state
LI_ChIP_VariousAnalysis of initiation-complex form of RNA polymerase II (Pol2), TATA-associated factor (TAF1), acetylated histone H3 (H3ac), lysine-4-dimethylated H3 (H3K4me2), suppressor of zeste 12 protein homolog (SUZ12), and lysine-27-tri-methylated H3 (H3K27me3) in several cell lines. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=encodeLIChIP for details.UCSC Genome Browser ENCODE data, tables encodeUcsdChip* (excluding encodeUcsdChipHeLaH3H4*)dataValue
chromMod
LI_gIF_ChIPAnalysis of H3K4me2, H3K4me3, H3ac, H4ac, STAT1, RNA polymerase II and TAF1 in interferon-gamma-induced and control cells. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=encodeLIChIPgIF for details.UCSC Genome Browser ENCODE data, tables encodeUcsdChipHeLaH3H4*dataValue
chromMod
state
LI_Ng_gIF_ChIPAnalysis of dimethylated K4 histone H3 (HK4me2 or diMeH3K4), trimethylated K4 histone H3 (H3K4me3 or triMeH3K4), RNA polymerase II, acetylated histone H3 (H3ac or AcH3), acetylated histone H4 (H4ac or AcH3) and STAT1 in interferon-gamma-induced and control cells, using NimbleGen arrays. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=encodeUcsdNgGif for details.UCSC Genome Browser ENCODE data, tables encodeUcsdNgHeLa*dataValue
chromMod
state
Sanger_ChIPChIP-on-Chip analysis of histone modifications H3K4me1, H3K4me2, H3K4me3, H3ac, and H4ac. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=encodeSangerChip for details.UCSC Genome Browser ENCODE data, tables encodeSangerChip* but not encodeSangerChipCenter* or encodeSangerChipHit*score
chromMod
Stanf_ChIPChIP-on-Chip analysis of Sp1 and Sp3 binding. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=encodeStanfordChip for details.UCSC Genome Browser ENCODE data, tables encodeStanfordChip* but not encodeStanfordChipSmoothed*dataValue
chromMod
UCD_Ng_ChIPChIP-on-Chip analysis of E2F1 and C-Myc binding. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=encodeUCDavisChip for details.UCSC Genome Browser ENCODE data, tables encodeUCDavis*chromMod
UT_Austin_ChIPChIP-on-Chip analysis of E2F4 and C-Myc binding. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=encodeUtexChip for details.UCSC Genome Browser ENCODE data, tables encodeUtexChip*dataValue
chromMod
Uppsala_ChIPChIP-on-Chip analysis of HNF-3b, HNF-4a and USF-1 binding as well as of H3ac. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=encodeUppsalaChip for details.UCSC Genome Browser ENCODE data, tables encodeUppsalaChip* but not encodeUppsalaChip*But*dataValue
chromMod
Yale_ChIP_SitesChIP-on-Chip analysis of binding. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78602259&c=chr7&g=encodeYaleChipSites for details.UCSC Genome Browser ENCODE data, tables encodeYaleChipSites*floatScore
chromMod
Stanf_MethDNA methylation profile as determined by digestion with a cocktail of six methyl-sensitive restriction enzymes. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=encodeStanfordMeth for details.UCSC Genome Browser ENCODE data, tables encodeStanfordMeth*dataValue
UNC_FAIREEnrichment for nucleosome-depleted regions as detected by the Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) protocol. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=encodeUncFaire for details.UCSC Genome Browser ENCODE data, tables encodeUncFaireSignal and encodeUncFairePeaksdataValue
UVa_DNA_Rep_TimingReplication timing as determined in synchronized HeLa cells. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=encodeUvaDnaRep for details.UCSC Genome Browser ENCODE data, tables encodeUvaDnaRep*time
UVa_DNA_Rep_OriginsReplication origins as determined in synchronized HeLa cells. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=encodeUvaDnaRepOrigins for details.UCSC Genome Browser ENCODE data, tables encodeUvaDnaRepOrigins*type
UW_Reg_DNaseI_QCP_ScoresDNaseI hypersensitive sites determined by quantitative chromatin profiling (QCP). See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=encodeRegulomeProb for details.UCSC Genome Browser ENCODE data, tables encodeRegulomeDnase*dataValue
UW_Reg_DNaseI_Array_ScoresDNaseI sensitivity measured by tiling array hybridization. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=encodeRegulomeDnaseArray for details.UCSC Genome Browser ENCODE data, table encodeRegulomeDnaseGM06990SensdataValue
UW_Reg_DNaseI_Array_SitesDNaseI sensitivity measured by tiling array hybridization. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=encodeRegulomeDnaseArray for details.UCSC Genome Browser ENCODE data, table encodeRegulomeDnaseGM06990SensfloatScore
NHGRI_DNaseI_Array_SitesDNaseI sensitivity measured by tiling array hybridization. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78858929&c=chr2&g=encodeNhgriDukeDnaseHs for details.UCSC Genome Browser ENCODE data, tables encodeNhgriDnaseHsChip*pValue