7b34df1cd22e7187feff14f87d2570a9c12c71ab jnavarr5 Wed Oct 1 17:05:13 2025 -0700 Upating the include for the colorsdb.ra name change to longReadVariants.ra, refs #36440 diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra index 981e0121f95..a77b9e00c8e 100644 --- src/hg/makeDb/trackDb/human/trackDb.ra +++ src/hg/makeDb/trackDb/human/trackDb.ra @@ -1,5607 +1,5607 @@ include predictionScoresSuper.ra #PanelApp include panelApp.ra # ENCODE tracks include trackDb.encode.ra # chainNet tracks include trackDb.chainNet.ra # Neandertal tracks include trackDb.nt.ra # Denisova tracks include trackDb.denisova.ra # Genome variants aka pgSnp aka personal genomes include trackDb.pgSnp.ra # Genotype Tissue Expresssion (GTEx) include trackDb.gtex.ra # GeneHancer from Weizmann labs include trackDb.geneHancer.ra # NCBI ClinVar include clinvar.ra include clinvar.alpha.ra alpha # Dosage sensitivity map Collins 2022 include dosageSensitivityCollins2022.ra # NCBI dbVar include trackDb.dbVar.ra # ClinGen include trackDb.clinGen.ra # CIViC cancer variant interpretation include civic.ra # Genome In a Bottle include trackDb.giab.ra # CADD scores include cadd.ra include cadd1_7.ra # Revel scores include revel.ra # constraint scores include constraintSuper.ra # GenCC include genCC.ra # Splice Impact super track: spliceVarDb, spliceAi, etc include spliceImpactSuper.ra track cytoBandIdeo shortLabel Chromosome Band (Ideogram) longLabel Chromosome Bands Localized by FISH Mapping Clones (for Ideogram) group map visibility dense type bed 4 + track cytoBand shortLabel Chromosome Band longLabel Chromosome Bands Localized by FISH Mapping Clones group map visibility hide type bed 4 + track hiSeqDepth compositeTrack on shortLabel Hi Seq Depth longLabel Regions of Exceptionally High Depth of Aligned Short Reads group map visibility hide color 139,69,19 altColor 0,0,0 type bed 3 track hiSeqDepthTopPt1Pct parent hiSeqDepth shortLabel Top 0.001 Depth longLabel Top 0.001 of Read Depth Distribution priority 1 track hiSeqDepthTopPt5Pct parent hiSeqDepth shortLabel Top 0.005 Depth longLabel Top 0.005 of Read Depth Distribution priority 2 track hiSeqDepthTop1Pct parent hiSeqDepth shortLabel Top 0.01 Depth longLabel Top 0.01 of Read Depth Distribution priority 3 track hiSeqDepthTop5Pct parent hiSeqDepth shortLabel Top 0.05 Depth longLabel Top 0.05 of Read Depth Distribution priority 4 track hiSeqDepthTop10Pct parent hiSeqDepth shortLabel Top 0.10 Depth longLabel Top 0.10 of Read Depth Distribution priority 5 track lrg shortLabel LRG Regions longLabel Locus Reference Genomic (LRG) / RefSeqGene Sequences Mapped to $date Assembly group map visibility hide type bigBed 12 + noScoreFilter . urlLabel Link to LRG report: url http://ftp.ebi.ac.uk/pub/databases/lrgex/$$.xml urls hgncId="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$$" ncbiAcc="https://www.ncbi.nlm.nih.gov/nuccore/$$" baseColorDefault diffBases baseColorUseSequence lrg indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . color 72,167,38 searchIndex name,ncbiAcc track gad shortLabel GAD View longLabel Genetic Association Studies of Complex Diseases and Disorders group phenDis visibility hide color 200,0,0 type bed 4 url http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=gene= track phegeni shortLabel PheGenI SNPs longLabel NCBI Phenotype-Genotype Integrator SNPs group phenDis visibility hide color 0,100,0 type bigBed 9 + release alpha mouseOverField trait bigDataUrl /gbdb/$D/bbi/phegeni.bb urls studyId=https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$$ geneId1=https://www.ncbi.nlm.nih.gov/gene/?term=$$%5Buid%5D geneId2=https://www.ncbi.nlm.nih.gov/gene/?term=$$%5Buid%5D analysisId=https://www.ncbi.nlm.nih.gov/projects/SNP/gViewer/gView.cgi?aid=$$ catalogId=https://www.ebi.ac.uk/gwas/search?query=$$ track varsInPubs shortLabel Variants in Papers longLabel Genetic Variants mentioned in scientific publications superTrack on group phenDis type bed 3 pennantIcon Updated red ../goldenPath/newsarch.html#080125 "Added PubTator Variants Aug. 01, 2025" track mastermind shortLabel Mastermind Variants longLabel Genomenon Mastermind Variants extracted from full text publications visibility dense type bigBed 9 + urls url=$$ bigDataUrl /gbdb/$D/bbi/mastermind.bb noScoreFilter on exonNumbers off mouseOver Variant: $name
Gene: $gene
Linkout: $_mouseOver
Article count 1: $mmcnt1
Article count 2: $mmcnt2
Article count 3: $mmcnt3 itemRgb on filter.mmcnt1 0 filter.mmcnt2 0 filter.mmcnt3 0 dataVersion /gbdb/$D/bbi/mastermindRelease.txt parent varsInPubs pack maxWindowCoverage 40000 maxItems 1000000 html varsInPubs.html track avada shortLabel Avada Variants longLabel Avada Variants extracted from full text publications visibility dense type bigBed 9 + bigDataUrl /gbdb/$D/bbi/avada.bb noScoreFilter on exonNumbers off #itemRgb on dataVersion release 1 parent varsInPubs pack urls pmid="https://www.ncbi.nlm.nih.gov/pubmed/$$" doi="https://doi.org/$$" ensId="http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?g=$$" entrezs="https://www.ncbi.nlm.nih.gov/gene/$$" refSeq="https://www.ncbi.nlm.nih.gov/nuccore/$$" mouseOver Variant: $variant
Ensembl ID: $ensId
Title of Publication: $title
Reference: $ref
Authors: $authors
Pubmed ID: $pmid html varsInPubs.html track varChat shortLabel enGenome VarChat longLabel enGenome VarChat: Literature match and variant's summary visibility dense type bigBed 9 + 4 bigDataUrl /gbdb/$D/bbi/varChat.bb noScoreFilter on exonNumbers off parent varsInPubs pack maxWindowCoverage 40000 maxItems 1000000 mouseOverField _mouseOver url https://varchat.engenome.com/search?source=ucsc&text=$ urlLabel Open Variant on VarChat bedNameLabel Nucleotide Change skipFields Variant,VariantUrl,score detailsDynamicTable VariantDetails|Variant Details dataVersion /gbdb/$D/bbi/varChatVersion.txt html varChat.html track pubtator shortLabel PubTator Variants longLabel dbSNP variants and other genetic variants grounded to dbSNP by tmVar; collected by PubTator3 visibility dense type bigBed 9 + bigDataUrl /gbdb/$D/pubs2/pubtatorDbSnp.bb noScoreFilter on exonNumbers off itemRgb on parent varsInPubs pack urls pubmedIds="https://www.ncbi.nlm.nih.gov/pubmed/$$" mouseOver $name found in ${numPubmedIds} PubMed articles pennantIcon New red ../goldenPath/newsarch.html#080125 "Released Aug. 01, 2025" html varsInPubs track varaico shortLabel Varaico Variants longLabel Varaico Variants extracted from full text publications, titles, and abstracts visibility dense type bigBed 9 + bigDataUrl /gbdb/$D/bbi/varaico.bb noScoreFilter on exonNumbers off # itemRgb on dataVersion release 1 parent varsInPubs pack urls outlink="$$" selectedPmid="https://www.ncbi.nlm.nih.gov/pubmed/$$" rgene="https://www.ncbi.nlm.nih.gov/nuccore/$$" mouseOver $hgncSymbol $variantOrigStrs in: $author ($journal, $year) - $title
Number of publications: $pmidCount
Variant Effect: $variantEffect html varaico.html track caseControl compositeTrack on shortLabel Case Control longLabel Case Control Consortium group phenDis visibility hide type chromGraph minMax 0,15 linesAt 5,10 track cccTrendPvalBd parent caseControl shortLabel CCC Bipolar Dis longLabel Case Control Consortium Bipolar Disorder Trend -log10 P-value priority 1 track cccTrendPvalCad parent caseControl shortLabel CCC Coronary Art longLabel Case Control Consortium Coronary Artery Disease Trend -log10 P-value priority 2 track cccTrendPvalCd parent caseControl shortLabel CCC Crohns Dis longLabel Case Control Consortium Crohn's Disease Trend -log10 P-value priority 3 track cccTrendPvalHt parent caseControl shortLabel CCC Hypertension longLabel Case Control Consortium Hypertension Trend -log10 P-value priority 4 track cccTrendPvalRa parent caseControl shortLabel CCC Rheum Arth longLabel Case Control Consortium Rheumatoid Arthritis Trend -log10 P-value priority 5 track cccTrendPvalT1d parent caseControl shortLabel CCC T1 Diabetes longLabel Case Control Consortium Type 1 Diabetes Trend -log10 P-value priority 6 track cccTrendPvalT2d parent caseControl shortLabel CCC T2 Diabetes longLabel Case Control Consortium Type 2 Diabetes Trend -log10 P-value priority 7 track nimhBipolar compositeTrack on shortLabel NIMH Bipolar longLabel NIMH Bipolar Disease group phenDis visibility hide type chromGraph minMax 0,5 linesAt 1,3 track nimhBipolarUs parent nimhBipolar shortLabel NIMH Bipolar Us longLabel NIMH Bipolar Disorder (US) -log10 P-value priority 1 track nimhBipolarDe parent nimhBipolar shortLabel NIMH Bipolar De longLabel NIMH Bipolar Disorder (German) -log10 P-value priority 2 track gwasCatalog shortLabel GWAS Catalog longLabel NHGRI-EBI Catalog of Published Genome-Wide Association Studies url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: group phenDis visibility hide type bed 4 + snpTable snp130 snpVersion 130 color 0,90,0 track xenoRefGene override visibility hide track vegaGene shortLabel Vega Genes longLabel Vega Annotations group genes visibility hide chromosomes chr1,chr16,chr18,chr19,chr6,chr7,chr9,chr10,chr13,chr14,chr20,chr22,chrX,chrY color 0,100,180 type genePred vegaPep url http://vega.sanger.ac.uk/Homo_sapiens/geneview?transcript=$$ track vegaPseudoGene shortLabel Vega Pseudogenes longLabel Vega Annotated Pseudogenes and Immunoglobulin Segments group genes visibility hide chromosomes chr1,chr16,chr18,chr6,chr7,chr9,chr10,chr13,chr14,chr20,chr22,chrX,chrY, color 30,130,210 type genePred url http://vega.sanger.ac.uk/Homo_sapiens/geneview?transcript=$$ track sanger20 shortLabel Sanger 20 longLabel Sanger Institute Chromosome 20 Genes group genes visibility pack chromosomes chr20, color 0,100,180 type genePred track sanger22 shortLabel Sanger 22 longLabel Sanger Institute Chromosome 22 Genes group genes visibility pack chromosomes chr22, color 0,100,180 type genePred track sanger22pseudo shortLabel Sanger 22 Pseudo longLabel Sanger Center Chromosome 22 Pseudogenes group genes visibility hide chromosomes chr22, color 30,130,210 type genePred track hgIkmc shortLabel IKMC Genes Mapped longLabel International Knockout Mouse Consortium Genes Mapped to Human Genome group genes visibility hide type bed 12 noScoreFilter . itemRgb on urlLabel KOMP Data Coordination Center: url http://www.mousephenotype.org/data/genes/$$ mgiUrlLabel MGI Report: mgiUrl https://www.informatics.jax.org//marker/$$ exonNumbers off track acembly shortLabel AceView Genes longLabel AceView Gene Models With Alt-Splicing group genes visibility hide color 155,0,125 type genePred acemblyPep acemblyMrna autoTranslate 0 url https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&l=$$ itemClassTbl acemblyClass geneClasses main putative cDNA_supported gClass_main 128,0,125 gClass_putative 200,0,125 gClass_cDNA_supported 200,0,125 urlLabel AceView Gene Summary: track slamMouse shortLabel Slam Mouse longLabel Slam Gene Predictions Using Human/Mouse Homology group genes visibility hide color 100,50,0 altColor 175,150,128 type genePred track slamRat shortLabel Slam Rat longLabel Slam Gene Predictions Using Human/Rat Homology group genes visibility hide color 100,50,0 altColor 175,150,128 type genePred track exoniphy shortLabel Exoniphy longLabel Exoniphy Human/Mouse/Rat/Dog group genes visibility hide color 173,17,162 type genePred track pseudoYale shortLabel Yale Pseudo longLabel Yale Pseudogenes. group genes visibility hide color 100,50,0 altColor 255,240,200 spectrum on type genePred autoTranslate 0 url http://www.pseudogene.org/cgi-bin/display-by-acc.cgi?id=$$ track pseudoYale60 shortLabel Yale Pseudo60 longLabel Yale Pseudogenes based on Ensembl Release 60 group genes visibility hide spectrum on type genePred autoTranslate 0 geneClasses Processed Duplicated Ambiguous gClass_Processed 180,0,0 gClass_Duplicated 100,50,0 gClass_Ambiguous 100,91,191 itemClassTbl pseudoYale60Class dataVersion December 2010 urlLabel Yale pseudogene.org link: url http://tables.pseudogene.org/index.cgi?table=Human60&value=$$ searchTable pseudoYale60 searchType genePred termRegex PGOHUM[0-9]+ searchPriority 50 track luNega shortLabel UCSC Pseudo longLabel UCSC Pseudogenes group genes type bed 12 visibility hide track acescan shortLabel ACEScan longLabel ACEScan Alternative Conserved Human-Mouse Exon Predictions group genes visibility hide color 125,38,205 type genePred track HInvGeneMrna shortLabel H-Inv longLabel H-Invitational Genes mRNA Alignments group rna visibility hide color 0,100,100 type psl . track altGraphX shortLabel Alt-Splicing longLabel Alternative Splicing from ESTs/mRNAs group rna visibility hide type altGraphX track altGraphX2 shortLabel Alt-Splicing2 longLabel Alternative Splicing from ESTs/mRNAs - test take 2 group rna visibility hide type altGraphX track mgcIntrons shortLabel mgcIntronPicks longLabel Introns and Flanking Exons for RACE PCR group rna visibility hide type bed 12 . track omim shortLabel OMIM longLabel Online Mendelian Inheritance in Man url https://www.ncbi.nlm.nih.gov/omim/$$ group varRep visibility hide type bed 4 . track orthoMrna shortLabel Mouse mRNAs longLabel Mouse mRNAs Mapped from mm3 via Nets/Chains group rna color 16,107,44 visibility hide type bed 12 . track burgeRnaSeqGemMapperAlign compositeTrack on shortLabel Burge RNA-seq longLabel Burge Lab RNA-seq Aligned by GEM Mapper group expression subGroup1 view Views RawSignal=Raw_Signal Alignments=Alignments subGroup2 tissueType Tissue_Type BT474=BT474 HME=HME MB435=MB435 MCF7=MCF7 T47D=T47D adipose=Adipose brain=Brain breast=Breast colon=Colon heart=Heart liver=Liver lymphNode=LymphNode skelMuscle=SkelMuscle testes=Testes sortOrder view=+ tissueType=+ dimensions dimensionY=tissueType dragAndDrop subTracks configurable on visibility hide noInherit on type bed 12 track burgeRnaSeqGemMapperAlignViewRawSignal shortLabel All Raw Signal view RawSignal visibility full parent burgeRnaSeqGemMapperAlign color 46,0,184 type bedGraph 4 maxHeightPixels 100:24:16 windowingFunction maximum transformFunc NONE autoScale on viewLimits 0:1000 track burgeRnaSeqGemMapperAlignBrainAllRawSignal parent burgeRnaSeqGemMapperAlignViewRawSignal on shortLabel RNA-seq Brain Sig longLabel Burge Lab RNA-seq 32mer Reads from Brain, Raw Signal subGroups view=RawSignal tissueType=brain track burgeRnaSeqGemMapperAlignLiverAllRawSignal parent burgeRnaSeqGemMapperAlignViewRawSignal off shortLabel RNA-seq Liver Sig longLabel Burge Lab RNA-seq 32mer Reads from Liver, Raw Signal subGroups view=RawSignal tissueType=liver track burgeRnaSeqGemMapperAlignHeartAllRawSignal parent burgeRnaSeqGemMapperAlignViewRawSignal on shortLabel RNA-seq Heart Sig longLabel Burge Lab RNA-seq 32mer Reads from Heart, Raw Signal subGroups view=RawSignal tissueType=heart track burgeRnaSeqGemMapperAlignSkelMuscleAllRawSignal parent burgeRnaSeqGemMapperAlignViewRawSignal off shortLabel RNA-seq Muscle Sig longLabel Burge Lab RNA-seq 32mer Reads from Skeletal Muscle, Raw Signal subGroups view=RawSignal tissueType=skelMuscle track burgeRnaSeqGemMapperAlignColonAllRawSignal parent burgeRnaSeqGemMapperAlignViewRawSignal off shortLabel RNA-seq Colon Sig longLabel Burge Lab RNA-seq 32mer Reads from Colon, Raw Signal subGroups view=RawSignal tissueType=colon track burgeRnaSeqGemMapperAlignAdiposeAllRawSignal parent burgeRnaSeqGemMapperAlignViewRawSignal off shortLabel RNA-seq Adipose Sig longLabel Burge Lab RNA-seq 32mer Reads from Adipose, Raw Signal subGroups view=RawSignal tissueType=adipose track burgeRnaSeqGemMapperAlignTestesAllRawSignal parent burgeRnaSeqGemMapperAlignViewRawSignal off shortLabel RNA-seq Testes Sig longLabel Burge Lab RNA-seq 32mer Reads from Testes, Raw Signal subGroups view=RawSignal tissueType=testes track burgeRnaSeqGemMapperAlignLymphNodeAllRawSignal parent burgeRnaSeqGemMapperAlignViewRawSignal on shortLabel RNA-seq Lymph Node Sig longLabel Burge Lab RNA-seq 32mer Reads from Lymph Node, Raw Signal subGroups view=RawSignal tissueType=lymphNode track burgeRnaSeqGemMapperAlignBreastAllRawSignal parent burgeRnaSeqGemMapperAlignViewRawSignal on shortLabel RNA-seq Breast Sig longLabel Burge Lab RNA-seq 32mer Reads from Breast, Raw Signal subGroups view=RawSignal tissueType=breast track burgeRnaSeqGemMapperAlignBT474AllRawSignal parent burgeRnaSeqGemMapperAlignViewRawSignal off shortLabel RNA-seq BT474 Sig longLabel Burge Lab RNA-seq 32mer Reads from BT474 Breast Tumour Cell Line, Raw Signal subGroups view=RawSignal tissueType=BT474 track burgeRnaSeqGemMapperAlignHMEAllRawSignal parent burgeRnaSeqGemMapperAlignViewRawSignal off shortLabel RNA-seq HME Sig longLabel Burge Lab RNA-seq 32mer Reads from HME (Human Mammary Epithelial) Cell Line, Raw Signal subGroups view=RawSignal tissueType=HME track burgeRnaSeqGemMapperAlignMCF7AllRawSignal parent burgeRnaSeqGemMapperAlignViewRawSignal off shortLabel RNA-seq MCF7 Sig longLabel Burge Lab RNA-seq 32mer Reads from MCF-7 Breast Adenocarcinoma Cell Line, Raw Signal subGroups view=RawSignal tissueType=MCF7 track burgeRnaSeqGemMapperAlignMB435AllRawSignal parent burgeRnaSeqGemMapperAlignViewRawSignal off shortLabel RNA-seq MB435 Sig longLabel Burge Lab RNA-seq 32mer Reads from MB-435 Cell Line, Raw Signal subGroups view=RawSignal tissueType=MB435 track burgeRnaSeqGemMapperAlignT47DAllRawSignal parent burgeRnaSeqGemMapperAlignViewRawSignal off shortLabel RNA-seq T47D Sig longLabel Burge Lab RNA-seq 32mer Reads from T-47D Breast Ductal Carcinoma Cell Line, Raw Signal subGroups view=RawSignal tissueType=T47D track burgeRnaSeqGemMapperAlignViewAlignments shortLabel Alignments view Alignments visibility dense parent burgeRnaSeqGemMapperAlign color 12,12,120 type bed 12 maxWindowToDraw 50000000 track burgeRnaSeqGemMapperAlignBrain parent burgeRnaSeqGemMapperAlignViewAlignments on shortLabel RNA-seq Brain longLabel Burge Lab RNA-seq 32mer Reads from Brain subGroups view=Alignments tissueType=brain track burgeRnaSeqGemMapperAlignLiver parent burgeRnaSeqGemMapperAlignViewAlignments off shortLabel RNA-seq Liver longLabel Burge Lab RNA-seq 32mer Reads from Liver subGroups view=Alignments tissueType=liver track burgeRnaSeqGemMapperAlignHeart parent burgeRnaSeqGemMapperAlignViewAlignments off shortLabel RNA-seq Heart longLabel Burge Lab RNA-seq 32mer Reads from Heart subGroups view=Alignments tissueType=heart track burgeRnaSeqGemMapperAlignSkelMuscle parent burgeRnaSeqGemMapperAlignViewAlignments off shortLabel RNA-seq Muscle longLabel Burge Lab RNA-seq 32mer Reads from Skeletal Muscle subGroups view=Alignments tissueType=skelMuscle track burgeRnaSeqGemMapperAlignColon parent burgeRnaSeqGemMapperAlignViewAlignments off shortLabel RNA-seq Colon longLabel Burge Lab RNA-seq 32mer Reads from Colon subGroups view=Alignments tissueType=colon track burgeRnaSeqGemMapperAlignAdipose parent burgeRnaSeqGemMapperAlignViewAlignments off shortLabel RNA-seq Adipose longLabel Burge Lab RNA-seq 32mer Reads from Adipose subGroups view=Alignments tissueType=adipose track burgeRnaSeqGemMapperAlignTestes parent burgeRnaSeqGemMapperAlignViewAlignments off shortLabel RNA-seq Testes longLabel Burge Lab RNA-seq 32mer Reads from Testes subGroups view=Alignments tissueType=testes track burgeRnaSeqGemMapperAlignLymphNode parent burgeRnaSeqGemMapperAlignViewAlignments off shortLabel RNA-seq Lymph Node longLabel Burge Lab RNA-seq 32mer Reads from Lymph Node subGroups view=Alignments tissueType=lymphNode track burgeRnaSeqGemMapperAlignBreast parent burgeRnaSeqGemMapperAlignViewAlignments on shortLabel RNA-seq Breast longLabel Burge Lab RNA-seq 32mer Reads from Breast subGroups view=Alignments tissueType=breast track burgeRnaSeqGemMapperAlignBT474 parent burgeRnaSeqGemMapperAlignViewAlignments off shortLabel RNA-seq BT474 longLabel Burge Lab RNA-seq 32mer Reads from BT474 Breast Tumor Cell Line subGroups view=Alignments tissueType=BT474 track burgeRnaSeqGemMapperAlignHME parent burgeRnaSeqGemMapperAlignViewAlignments off shortLabel RNA-seq HME longLabel Burge Lab RNA-seq 32mer Reads from HME (Human Mammary Epithelial) Cell Line subGroups view=Alignments tissueType=HME track burgeRnaSeqGemMapperAlignMCF7 parent burgeRnaSeqGemMapperAlignViewAlignments off shortLabel RNA-seq MCF7 longLabel Burge Lab RNA-seq 32mer Reads from MCF-7 Breast Adenocarcinoma Cell Line subGroups view=Alignments tissueType=MCF7 track burgeRnaSeqGemMapperAlignMB435 parent burgeRnaSeqGemMapperAlignViewAlignments off shortLabel RNA-seq MB435 longLabel Burge Lab RNA-seq 32mer Reads from MB-435 Cell Line subGroups view=Alignments tissueType=MB435 track burgeRnaSeqGemMapperAlignT47D parent burgeRnaSeqGemMapperAlignViewAlignments off shortLabel RNA-seq T47D longLabel Burge Lab RNA-seq 32mer Reads from T-47D Breast Ductal Carcinoma Cell Line subGroups view=Alignments tissueType=T47D track gladHumES shortLabel Gstone Arrays longLabel Gladstone Microarray Data group expression visibility hide type expRatio expScale 4.0 expStep 0.5 expTable gladHumESExps track gnfAtlas2 shortLabel GNF Atlas 2 longLabel GNF Expression Atlas 2 group expression visibility hide type expRatio expScale 4.0 expStep 0.5 expDrawExons on expTable gnfHumanAtlas2MedianExps groupings gnfHumanAtlas2Groups track affyUcla shortLabel UCLA GeneChip longLabel UCLA Affymetrix U133 GeneChip Data group expression visibility hide type bed 15 + expTable affyUclaExps canPack off track affyUclaNorm shortLabel UCLA Tissues longLabel UCLA Affymetrix U133 GeneChip Normal Tissues group expression expScale 3.0 expStep 0.5 expTable affyUclaNormExps chip U133 visibility hide type bed 15 + track nci60 shortLabel NCI60 longLabel Microarray Experiments for NCI 60 Cell Lines group expression visibility hide type expRatio expScale 3.0 expStep 0.5 expDrawExons on groupings nci60Groups expTable nci60Exps # (expTable is obselete) track affy shortLabel GNF longLabel GNF Gene Expression Atlas Using Affymetrix GeneChips group expression visibility hide type bed 15 + expTable affyExps track affyRatio shortLabel GNF Ratio longLabel GNF Gene Expression Atlas Ratios Using Affymetrix GeneChips group expression visibility hide type expRatio expScale 3.0 expStep 0.5 expDrawExons on groupings affyRatioGroups expTable affyExps # (expTable is obselete) track humanNormal shortLabel Human Normal longLabel Expression from Normal Human Tissue group expression visibility hide type expRatio expScale 3.0 expStep 0.5 groupings humanNormalGroups expTable humanNormalExps track cghNci60 shortLabel CGH NCI60 longLabel Comparative Genomic Hybridization Experiments for NCI 60 Cell Lines group regulation visibility hide type bed 15 + track yaleBertoneTars shortLabel Bertone Yale TAR longLabel Yale Transcriptionally Active Regions (TARs) (Bertone data) group expression visibility hide color 50,100,50 url http://dart.gersteinlab.org/cgi-bin/ar/lookup.cgi?acc=$$ urlLabel Yale DART Link: type psl . track affyTranscriptome shortLabel Transcriptome longLabel Affymetrix Experimentally Derived Transcriptome group expression visibility hide color 100,50,0 altColor 0,0,255 chromosomes chr22,chr21 type sample track affyU133 shortLabel Affy U133 longLabel Alignments of Affymetrix Consensus/Exemplars from HG-U133 group expression visibility hide type psl . track affyGnf1h shortLabel Affy GNF1H longLabel Alignments of Affymetrix Consensus/Exemplars from GNF1H group expression visibility hide type psl . track affyU95 shortLabel Affy U95 longLabel Alignments of Affymetrix Consensus/Exemplars from HG-U95 group expression visibility hide type psl . track illuminaProbes shortLabel Illumina WG-6 longLabel Alignments of Illumina WG-6 3.0 Probe Set group expression visibility hide type bed 12 . pslTable illuminaProbesAlign seqTable illuminaProbesSeq track switchDbTss shortLabel SwitchGear TSS longLabel SwitchGear Genomics Transcription Start Sites group regulation visibility hide origAssembly hg17 type bed 6 + track promoterStanford shortLabel Stanford Promoters longLabel Stanford Promoters group regulation visibility hide type bed 6 . track promoterStanfordGene shortLabel Stanford Gene Model longLabel Stanford ENCODE Gene Models group regulation chromosomes chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr18,chr19,chr2,chr20,chr21,chr22,chr4,chr5,chr6,chr7,chr8,chr9,chrX visibility hide type bed 12 . track regpotent shortLabel Reg. Potential longLabel Human/Mouse Regulatory Potential Score group regulation color 100,50,0 altColor 50,150,128 visibility hide type sample 0 8 track vistaEnhancers shortLabel Vista Enhancers longLabel Vista HMR-Conserved Non-coding Human Enhancers from LBNL group regulation visibility hide color 50,70,120 type bed 5 + useScore 1 release alpha track uc16 shortLabel Ultra Conserved longLabel Ultraconserved Elements (200 bp 100% ID in Rat/Mouse/Human) group compGeno visibility hide exonArrows off color 150,0,0 type bed 4 . track ux16 shortLabel Extended Ultras longLabel Ultras Extended Until 5 Bases Below 85% in Conservation Track group compGeno visibility hide exonArrows off color 100,0,100 type bed 4 . track humMusL shortLabel Mouse Cons longLabel Human/Mouse Evolutionary Conservation Score (std units) group compGeno color 175,150,128 altColor 175,150,128 visibility hide type sample 0 8 track ecoresTetNig1 shortLabel Tetraodon Ecores longLabel Human($db)/$o_Organism ($o_date) Evolutionary Conserved Regions group compGeno visibility hide color 0,60,120 autoTranslate 0 type genePred otherDb tetNig1 track blastCe3WB shortLabel C. elegans Proteins longLabel C. elegans Proteins group genes visibility hide colorChromDefault off type psl protein pred ce3.blastWBPep01 blastRef ce3.blastWBRef01 track blastDm2FB override longLabel D. melanogaster Proteins (dm2) visibility hide track slamNonCodingMouse shortLabel Slam Non-Coding Mouse longLabel Slam Predictions of Human/Mouse Conserved Non-Coding Regions group compGeno visibility hide color 30,130,210 altColor 200,220,255 spectrum on type bed 5 . track slamNonCodingRat shortLabel Slam Non-Coding Rat longLabel Slam Predictions of Human/Rat Conserved Non-Coding Regions group compGeno visibility hide color 30,130,210 altColor 200,220,255 spectrum on type bed 5 . track chimpSimpleDiff shortLabel Chimp Diff longLabel $o_Organism ($o_date) Simple Differences in Regions of High Quality Sequence group compGeno visibility hide type bed 3 + otherDb panTro1 track snp141Common shortLabel Common SNPs(141) longLabel Simple Nucleotide Polymorphisms (dbSNP 141) Found in >= 1% of Samples group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp141Seq snpExceptionDesc snp141ExceptionDesc defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + chimpOrangMacOrthoTable snp141OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp141CodingDbSnp, track snp141Flagged shortLabel Flagged SNPs(141) longLabel Simple Nucleotide Polymorphisms (dbSNP 141) Flagged by dbSNP as Clinically Assoc group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp141Seq snpExceptionDesc snp141ExceptionDesc defaultGeneTracks knownGene type bed 6 + chimpOrangMacOrthoTable snp141OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp141CodingDbSnp, track snp141Mult shortLabel Mult. SNPs(141) longLabel Simple Nucleotide Polymorphisms (dbSNP 141) That Map to Multiple Genomic Loci group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp141Seq snpExceptionDesc snp141ExceptionDesc defaultGeneTracks knownGene defaultMaxWeight 3 maxWindowToDraw 10000000 type bed 6 + chimpOrangMacOrthoTable snp141OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp141CodingDbSnp, track snp141 shortLabel All SNPs(141) longLabel Simple Nucleotide Polymorphisms (dbSNP 141) group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + chimpOrangMacOrthoTable snp141OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp141CodingDbSnp, track snp142Common shortLabel Common SNPs(142) longLabel Simple Nucleotide Polymorphisms (dbSNP 142) Found in >= 1% of Samples group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp142Seq snpExceptionDesc snp142ExceptionDesc defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + chimpOrangMacOrthoTable snp142OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp142CodingDbSnp, html snp142Common_bugFix track snp142Flagged shortLabel Flagged SNPs(142) longLabel Simple Nucleotide Polymorphisms (dbSNP 142) Flagged by dbSNP as Clinically Assoc group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp142Seq snpExceptionDesc snp142ExceptionDesc defaultGeneTracks knownGene type bed 6 + chimpOrangMacOrthoTable snp142OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp142CodingDbSnp, html snp142Flagged_bugFix track snp142Mult shortLabel Mult. SNPs(142) longLabel Simple Nucleotide Polymorphisms (dbSNP 142) That Map to Multiple Genomic Loci group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp142Seq snpExceptionDesc snp142ExceptionDesc defaultGeneTracks knownGene defaultMaxWeight 3 maxWindowToDraw 10000000 type bed 6 + chimpOrangMacOrthoTable snp142OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp142CodingDbSnp, html snp142Mult_bugFix track snp142 shortLabel All SNPs(142) longLabel Simple Nucleotide Polymorphisms (dbSNP 142) group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + chimpOrangMacOrthoTable snp142OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp142CodingDbSnp, html snp142_bugFix track snp144Common shortLabel Common SNPs(144) longLabel Simple Nucleotide Polymorphisms (dbSNP 144) Found in >= 1% of Samples group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp144Seq snpExceptionDesc snp144ExceptionDesc defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp144OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp144CodingDbSnp, track snp144Flagged shortLabel Flagged SNPs(144) longLabel Simple Nucleotide Polymorphisms (dbSNP 144) Flagged by dbSNP as Clinically Assoc group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp144Seq snpExceptionDesc snp144ExceptionDesc defaultGeneTracks knownGene type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp144OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp144CodingDbSnp, track snp144Mult shortLabel Mult. SNPs(144) longLabel Simple Nucleotide Polymorphisms (dbSNP 144) That Map to Multiple Genomic Loci group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp144Seq snpExceptionDesc snp144ExceptionDesc defaultGeneTracks knownGene defaultMaxWeight 3 maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp144OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp144CodingDbSnp, track snp144 shortLabel All SNPs(144) longLabel Simple Nucleotide Polymorphisms (dbSNP 144) group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp144OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp144CodingDbSnp, track snp146Common shortLabel Common SNPs(146) longLabel Simple Nucleotide Polymorphisms (dbSNP 146) Found in >= 1% of Samples group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp146Seq snpExceptionDesc snp146ExceptionDesc defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp146OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp146CodingDbSnp, track snp146Flagged shortLabel Flagged SNPs(146) longLabel Simple Nucleotide Polymorphisms (dbSNP 146) Flagged by dbSNP as Clinically Assoc group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp146Seq snpExceptionDesc snp146ExceptionDesc defaultGeneTracks knownGene type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp146OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp146CodingDbSnp, track snp146Mult shortLabel Mult. SNPs(146) longLabel Simple Nucleotide Polymorphisms (dbSNP 146) That Map to Multiple Genomic Loci group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp146Seq snpExceptionDesc snp146ExceptionDesc defaultGeneTracks knownGene defaultMaxWeight 3 maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp146OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp146CodingDbSnp, track snp146 shortLabel All SNPs(146) longLabel Simple Nucleotide Polymorphisms (dbSNP 146) group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp146OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp146CodingDbSnp, track snp147Common shortLabel Common SNPs(147) longLabel Simple Nucleotide Polymorphisms (dbSNP 147) Found in >= 1% of Samples group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp147Seq snpExceptionDesc snp147ExceptionDesc defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp147OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp147CodingDbSnp, track snp147Flagged shortLabel Flagged SNPs(147) longLabel Simple Nucleotide Polymorphisms (dbSNP 147) Flagged by dbSNP as Clinically Assoc group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp147Seq snpExceptionDesc snp147ExceptionDesc defaultGeneTracks knownGene type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp147OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp147CodingDbSnp, track snp147Mult shortLabel Mult. SNPs(147) longLabel Simple Nucleotide Polymorphisms (dbSNP 147) That Map to Multiple Genomic Loci group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp147Seq snpExceptionDesc snp147ExceptionDesc defaultGeneTracks knownGene defaultMaxWeight 3 maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp147OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp147CodingDbSnp, track snp147 shortLabel All SNPs(147) longLabel Simple Nucleotide Polymorphisms (dbSNP 147) group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp147OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp147CodingDbSnp, track snp149Common shortLabel Common SNPs(149) longLabel Simple Nucleotide Polymorphisms (dbSNP 149) Found in >= 1% of Samples group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp149Seq snpExceptionDesc snp149ExceptionDesc defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp149OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp149CodingDbSnp, track snp149Flagged shortLabel Flagged SNPs(149) longLabel Simple Nucleotide Polymorphisms (dbSNP 149) Flagged by dbSNP as Clinically Assoc group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp149Seq snpExceptionDesc snp149ExceptionDesc defaultGeneTracks knownGene type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp149OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp149CodingDbSnp, track snp149Mult shortLabel Mult. SNPs(149) longLabel Simple Nucleotide Polymorphisms (dbSNP 149) That Map to Multiple Genomic Loci group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp149Seq snpExceptionDesc snp149ExceptionDesc defaultGeneTracks knownGene defaultMaxWeight 3 maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp149OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp149CodingDbSnp, track snp149 shortLabel All SNPs(149) longLabel Simple Nucleotide Polymorphisms (dbSNP 149) group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp149OrthoPt4Pa2Rm3 chimpDb panTro4 orangDb ponAbe2 macaqueDb rheMac3 hapmapPhase III codingAnnotations snp149CodingDbSnp, track snp150Common shortLabel Common SNPs(150) longLabel Simple Nucleotide Polymorphisms (dbSNP 150) Found in >= 1% of Samples group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp150Seq snpExceptionDesc snp150ExceptionDesc defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp150OrthoPt5Pa2Rm8 chimpDb panTro5 orangDb ponAbe2 macaqueDb rheMac8 hapmapPhase III codingAnnotations snp150CodingDbSnp, track snp150Flagged shortLabel Flagged SNPs(150) longLabel Simple Nucleotide Polymorphisms (dbSNP 150) Flagged by dbSNP as Clinically Assoc group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp150Seq snpExceptionDesc snp150ExceptionDesc defaultGeneTracks knownGene type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp150OrthoPt5Pa2Rm8 chimpDb panTro5 orangDb ponAbe2 macaqueDb rheMac8 hapmapPhase III codingAnnotations snp150CodingDbSnp, track snp150Mult shortLabel Mult. SNPs(150) longLabel Simple Nucleotide Polymorphisms (dbSNP 150) That Map to Multiple Genomic Loci group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp150Seq snpExceptionDesc snp150ExceptionDesc defaultGeneTracks knownGene defaultMaxWeight 3 maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp150OrthoPt5Pa2Rm8 chimpDb panTro5 orangDb ponAbe2 macaqueDb rheMac8 hapmapPhase III codingAnnotations snp150CodingDbSnp, track snp150 shortLabel All SNPs(150) longLabel Simple Nucleotide Polymorphisms (dbSNP 150) group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp150OrthoPt5Pa2Rm8 chimpDb panTro5 orangDb ponAbe2 macaqueDb rheMac8 hapmapPhase III codingAnnotations snp150CodingDbSnp, track snp151Common shortLabel Common SNPs(151) longLabel Simple Nucleotide Polymorphisms (dbSNP 151) Found in >= 1% of Samples group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp151Seq snpExceptionDesc snp151ExceptionDesc defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp151OrthoPt5Pa2Rm8 chimpDb panTro5 orangDb ponAbe2 macaqueDb rheMac8 hapmapPhase III codingAnnotations snp151CodingDbSnp, track snp151Flagged shortLabel Flagged SNPs(151) longLabel Simple Nucleotide Polymorphisms (dbSNP 151) Flagged by dbSNP as Clinically Assoc group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp151Seq snpExceptionDesc snp151ExceptionDesc defaultGeneTracks knownGene type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp151OrthoPt5Pa2Rm8 chimpDb panTro5 orangDb ponAbe2 macaqueDb rheMac8 hapmapPhase III codingAnnotations snp151CodingDbSnp, track snp151Mult shortLabel Mult. SNPs(151) longLabel Simple Nucleotide Polymorphisms (dbSNP 151) That Map to Multiple Genomic Loci group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp151Seq snpExceptionDesc snp151ExceptionDesc defaultGeneTracks knownGene defaultMaxWeight 3 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp151OrthoPt5Pa2Rm8 chimpDb panTro5 orangDb ponAbe2 macaqueDb rheMac8 hapmapPhase III codingAnnotations snp151CodingDbSnp, track snp151 shortLabel All SNPs(151) longLabel Simple Nucleotide Polymorphisms (dbSNP 151) group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp151OrthoPt5Pa2Rm8 chimpDb panTro5 orangDb ponAbe2 macaqueDb rheMac8 hapmapPhase III codingAnnotations snp151CodingDbSnp, track dbSnp153Composite compositeTrack on shortLabel dbSNP 153 longLabel Short Genetic Variants from dbSNP release 153 type bed 3 group varRep visibility hide url https://www.ncbi.nlm.nih.gov/snp/$$ urlLabel dbSNP: subGroup1 view Views variants=Variants errs=Mapping_Errors maxWindowCoverage 4000000 priority 1 track dbSnp153ViewVariants view variants parent dbSnp153Composite shortLabel Variants visibility dense type bigDbSnp detailsTabUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp153Details.tab.gz freqSourceOrder 1000Genomes,GnomAD_exomes,TOPMED,ExAC,PAGE_STUDY,GnomAD,GoESP,Estonian,ALSPAC,TWINSUK,NorthernSweden,Vietnamese classFilterValues snv,mnv,ins,del,delins,identity classFilterType multipleListOr showCfg on ucscNotesFilterValues \ altIsAmbiguous|Alternate allele contains IUPAC ambiguous base(s),\ classMismatch|Variant class/type is inconsistent with allele sizes,\ clinvar|Present in ClinVar,\ clinvarBenign|ClinVar significance of benign and/or likely benign,\ clinvarConflicting|ClinVar includes both benign and pathogenic reports,\ clinvarPathogenic|ClinVar significance of pathogenic and/or likely pathogenic,\ clusterError|Overlaps a variant with the same type/class and position,\ commonAll|MAF >= 1% in all projects that report frequencies,\ commonSome|MAF >= 1% in at least one project that reports frequencies,\ diffMajor|Different projects report different major alleles,\ freqIncomplete|Frequency reported with incomplete allele data,\ freqIsAmbiguous|Frequency reported for allele with IUPAC ambiguous base(s),\ freqNotMapped|Frequency reported on different assembly but not mapped by dbSNP,\ freqNotRefAlt|Reference genome allele is not major allele in at least one project,\ multiMap|Variant is placed in more than one genomic position,\ otherMapErr|Another mapping of this variant has illegal coords (indel mapping error?),\ overlapDiffClass|Variant overlaps other variant(s) of different type/class,\ overlapSameClass|Variant overlaps other variant(s) of same type/class but different position,\ rareAll|MAF < 1% in all projects that report frequencies (or no frequency data),\ rareSome|MAF < 1% in at least one project that reports frequencies,\ refIsAmbiguous|Reference genome allele contains IUPAC ambiguous base(s),\ refIsMinor|Reference genome allele is minor allele in at least one project that reports frequencies,\ refIsRare|Reference genome allele frequency is <1% in at least one project,\ refIsSingleton|Reference genome frequency is 0 in all projects that report frequencies,\ refMismatch|Reference allele mismatches reference genome sequence,\ revStrand|Variant maps to opposite strand relative to dbSNP's preferred top-level placement #' ucscNotesFilterType multipleListOr maxFuncImpactFilterLabel Greatest functional impact on gene maxFuncImpactFilterValues 0|(not annotated),\ 865|frameshift,\ 1587|stop_gained,\ 1574|splice_acceptor_variant,\ 1575|splice_donor_variant,\ 1821|inframe_insertion,\ 1583|missense_variant,\ 1590|terminator_codon_variant,\ 1819|synonymous_variant,\ 1580|coding_sequence_variant,\ 1623|5_prime_UTR_variant,\ 1624|3_prime_UTR_variant,\ 1619|nc_transcript_variant,\ 2153|genic_upstream_transcript_variant,\ 1986|upstream_transcript_variant,\ 2152|genic_downstream_transcript_variant,\ 1987|downstream_transcript_variant,\ 1627|intron_variant maxFuncImpactFilterType multipleListOr track dbSnp153Common parent dbSnp153ViewVariants on subGroups view=variants shortLabel Common dbSNP(153) longLabel Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants from dbSNP Release 153 bigDataUrl /gbdb/$D/snp/dbSnp153Common.bb defaultGeneTracks knownGene priority 1 track dbSnp153ClinVar parent dbSnp153ViewVariants off subGroups view=variants shortLabel dbSNP(153) in ClinVar longLabel Short Genetic Variants from dbSNP Release 153 Included in ClinVar bigDataUrl /gbdb/$D/snp/dbSnp153ClinVar.bb defaultGeneTracks knownGene priority 2 track dbSnp153Mult parent dbSnp153ViewVariants off subGroups view=variants shortLabel dbSNP(153) Mult. longLabel Short Genetic Variants from dbSNP Release 153 that Map to Multiple Genomic Loci bigDataUrl /gbdb/$D/snp/dbSnp153Mult.bb defaultGeneTracks knownGene priority 3 track dbSnp153 parent dbSnp153ViewVariants off subGroups view=variants shortLabel All dbSNP(153) longLabel All Short Genetic Variants from dbSNP Release 153 bigDataUrl /gbdb/$D/snp/dbSnp153.bb maxWindowToDraw 1000000 defaultGeneTracks knownGene priority 4 tableBrowser noGenome track dbSnp153ViewErrs parent dbSnp153Composite view errs shortLabel Mapping Errors visibility dense track dbSnp153BadCoords parent dbSnp153ViewErrs off subGroups view=errs shortLabel Map Err dbSnp(153) longLabel Mappings with Inconsistent Coordinates from dbSNP 153 bigDataUrl /gbdb/$D/snp/dbSnp153BadCoords.bb type bigBed 4 color 100,100,100 priority 5 track dbSnp155Composite compositeTrack on shortLabel dbSNP 155 longLabel Short Genetic Variants from dbSNP release 155 type bed 3 group varRep visibility pack url https://www.ncbi.nlm.nih.gov/snp/$$ urlLabel dbSNP: subGroup1 view Views variants=Variants errs=Mapping_Errors maxWindowCoverage 4000000 priority 0.8 track dbSnp155ViewVariants view variants parent dbSnp155Composite shortLabel Variants visibility dense type bigDbSnp detailsTabUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp155Details.tab.gz freqSourceOrder 1000Genomes,dbGaP_PopFreq,TOPMED,KOREAN,SGDP_PRJ,Qatari,NorthernSweden,Siberian,TWINSUK,TOMMO,ALSPAC,GENOME_DK,GnomAD,GoNL,Estonian,Vietnamese,Korea1K,HapMap,PRJEB36033,HGDP_Stanford,Daghestan,PAGE_STUDY,Chileans,MGP,PRJEB37584,GoESP,ExAC,GnomAD_exomes,FINRISK,PharmGKB,PRJEB37766 classFilterValues snv,mnv,ins,del,delins,identity classFilterType multipleListOr ucscNotesFilterValues \ altIsAmbiguous|Alternate allele contains IUPAC ambiguous base(s),\ classMismatch|Variant class/type is inconsistent with allele sizes,\ clinvar|Present in ClinVar,\ clinvarBenign|ClinVar significance of benign and/or likely benign,\ clinvarConflicting|ClinVar includes both benign and pathogenic reports,\ clinvarPathogenic|ClinVar significance of pathogenic and/or likely pathogenic,\ clusterError|Overlaps a variant with the same type/class and position,\ commonAll|MAF >= 1% in all projects that report frequencies,\ commonSome|MAF >= 1% in at least one project that reports frequencies,\ diffMajor|Different projects report different major alleles,\ freqIncomplete|Frequency reported with incomplete allele data,\ freqIsAmbiguous|Frequency reported for allele with IUPAC ambiguous base(s),\ freqNotMapped|Frequency reported on different assembly but not mapped by dbSNP,\ freqNotRefAlt|Reference genome allele is not major allele in at least one project,\ multiMap|Variant is placed in more than one genomic position,\ otherMapErr|Another mapping of this variant has illegal coords (indel mapping error?),\ overlapDiffClass|Variant overlaps other variant(s) of different type/class,\ overlapSameClass|Variant overlaps other variant(s) of same type/class but different position,\ rareAll|MAF < 1% in all projects that report frequencies (or no frequency data),\ rareSome|MAF < 1% in at least one project that reports frequencies,\ refIsAmbiguous|Reference genome allele contains IUPAC ambiguous base(s),\ refIsMinor|Reference genome allele is minor allele in at least one project that reports frequencies,\ refIsRare|Reference genome allele frequency is <1% in at least one project,\ refIsSingleton|Reference genome frequency is 0 in all projects that report frequencies,\ refMismatch|Reference allele mismatches reference genome sequence,\ revStrand|Variant maps to opposite strand relative to dbSNP's preferred top-level placement #' ucscNotesFilterType multipleListOr maxFuncImpactFilterLabel Greatest functional impact on gene maxFuncImpactFilterValues 0|(not annotated),\ 1589|frameshift,\ 1587|stop_gained,\ 1574|splice_acceptor_variant,\ 1575|splice_donor_variant,\ 1821|inframe_insertion,\ 1583|missense_variant,\ 1590|terminator_codon_variant,\ 1819|synonymous_variant,\ 1580|coding_sequence_variant,\ 1623|5_prime_UTR_variant,\ 1624|3_prime_UTR_variant,\ 1619|nc_transcript_variant,\ 2|genic_upstream_transcript_variant,\ 1986|upstream_transcript_variant,\ 2152|genic_downstream_transcript_variant,\ 1987|downstream_transcript_variant,\ 1627|intron_variant maxFuncImpactFilterType multipleListOr track dbSnp155Common parent dbSnp155ViewVariants on subGroups view=variants shortLabel Common dbSNP(155) longLabel Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants from dbSNP Release 155 defaultGeneTracks knownGene bigDataUrl /gbdb/$D/snp/dbSnp155Common.bb showCfg on priority 1 track dbSnp155ClinVar parent dbSnp155ViewVariants off subGroups view=variants shortLabel ClinVar dbSNP(155) longLabel Short Genetic Variants from dbSNP Release 155 Included in ClinVar defaultGeneTracks knownGene bigDataUrl /gbdb/$D/snp/dbSnp155ClinVar.bb priority 2 track dbSnp155Mult parent dbSnp155ViewVariants off subGroups view=variants shortLabel Mult. dbSNP(155) longLabel Short Genetic Variants from dbSNP Release 155 that Map to Multiple Genomic Loci defaultGeneTracks knownGene bigDataUrl /gbdb/$D/snp/dbSnp155Mult.bb priority 3 track dbSnp155 parent dbSnp155ViewVariants off subGroups view=variants shortLabel All dbSNP(155) longLabel All Short Genetic Variants from dbSNP Release 155 defaultGeneTracks knownGene bigDataUrl /gbdb/$D/snp/dbSnp155.bb maxWindowToDraw 1000000 priority 4 tableBrowser noGenome track dbSnp155ViewErrs parent dbSnp155Composite view errs shortLabel Mapping Errors visibility dense track dbSnp155BadCoords parent dbSnp155ViewErrs off subGroups view=errs shortLabel Map Err dbSnp(155) longLabel Mappings with Inconsistent Coordinates from dbSNP 155 bigDataUrl /gbdb/$D/snp/dbSnp155BadCoords.bb type bigBed 4 color 100,100,100 priority 5 track hgdpGeo shortLabel HGDP Allele Freq longLabel Human Genome Diversity Project SNP Population Allele Frequencies group varRep visibility hide url http://hgdp.uchicago.edu/cgi-bin/gbrowse/HGDP/?name=$$ urlLabel HGDP Selection Browser: type bed 4 + track hgdpFst shortLabel HGDP Smoothd FST longLabel Human Genome Diversity Project Smoothed Relative FST (Fixation Index) group varRep visibility hide chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22, viewLimits 0:5 minLimit 0 maxLimit 6 autoScale Off maxHeightPixels 100:20:10 type bedGraph 4 track hgdpHzy compositeTrack on shortLabel HGDP Hetrzygsty longLabel Human Genome Diversity Project Smoothed Expected Heterozygosity on 7 Continents group varRep visibility hide chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22, viewLimits 0:0.25 minLimit 0 maxLimit 0.25 autoScale Off maxHeightPixels 100:20:10 type bedGraph 4 track hgdpHzyAfrica parent hgdpHzy shortLabel Hetzgty Africa longLabel Human Genome Diversity Proj Smoothd Expec Heterozygosity (Africa) color 224, 0, 0 priority 1 track hgdpHzyBantu parent hgdpHzy shortLabel Hetzgty Bantu longLabel Human Genome Diversity Proj Smoothd Expec Heterozygosity (Bantu pops. in Africa) color 224, 0, 0 priority 2 track hgdpHzyMideast parent hgdpHzy shortLabel Hetzgty Mideast longLabel Human Genome Diversity Proj Smoothd Expec Heterozygosity (Mideast) color 0,0,200 priority 3 track hgdpHzyEurope parent hgdpHzy shortLabel Hetzgty Europe longLabel Human Genome Diversity Proj Smoothd Expec Heterozygosity (Europe) color 240,144,0 priority 4 track hgdpHzySAsia parent hgdpHzy shortLabel Hetzgty S. Asia longLabel Human Genome Diversity Proj Smoothd Expec Heterozygosity (S. Asia) color 0,0,0 priority 5 track hgdpHzyEAsia parent hgdpHzy shortLabel Hetzgty E. Asia longLabel Human Genome Diversity Proj Smoothd Expec Heterozygosity (E. Asia) color 0,200,0 priority 6 track hgdpHzyOceania parent hgdpHzy shortLabel Hetzgty Oceania longLabel Human Genome Diversity Proj Smoothd Expec Heterozygosity (Oceania) color 0,200,200 priority 7 track hgdpHzyAmericas parent hgdpHzy shortLabel Hetzgty Americas longLabel Human Genome Diversity Proj Smoothd Expec Heterozygosity (Americas) color 224,192,0 priority 8 track hgdpIhs compositeTrack on shortLabel HGDP iHS longLabel Human Genome Diversity Project Integrated Haplotype Score on 7 Continents group varRep visibility hide chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX viewLimits 0:5 minLimit 0 maxLimit 6 autoScale Off maxHeightPixels 100:20:10 type bedGraph 4 track hgdpIhsBantu parent hgdpIhs shortLabel iHS Bantu longLabel Human Genome Diversity Project iHS (Bantu populations in Africa) color 224, 0, 0 priority 1 track hgdpIhsMideast parent hgdpIhs shortLabel iHS Mideast longLabel Human Genome Diversity Project iHS (Mideast) color 0,0,200 priority 2 track hgdpIhsEurope parent hgdpIhs shortLabel iHS Europe longLabel Human Genome Diversity Project iHS (Europe) color 240,144,0 priority 3 track hgdpIhsSAsia parent hgdpIhs shortLabel iHS S. Asia longLabel Human Genome Diversity Project iHS (South Asia) color 0,0,0 priority 4 track hgdpIhsEAsia parent hgdpIhs shortLabel iHS E. Asia longLabel Human Genome Diversity Project iHS (East Asia) color 0,200,0 priority 5 track hgdpIhsOceania parent hgdpIhs shortLabel iHS Oceania longLabel Human Genome Diversity Project iHS (Oceania) color 0,200,200 priority 6 track hgdpIhsAmericas parent hgdpIhs shortLabel iHS Americas longLabel Human Genome Diversity Project iHS (Americas) color 224,192,0 priority 7 track hgdpXpehh compositeTrack on shortLabel HGDP XP-EHH longLabel Human Genome Diversity Proj Cross-Pop Ext Haplo Homzgty (XP-EHH) on 7 Continents group varRep visibility hide chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22, viewLimits 0:5 minLimit 0 maxLimit 7 autoScale Off maxHeightPixels 100:20:10 type bedGraph 4 track hgdpXpehhBantu parent hgdpXpehh shortLabel XP-EHH Bantu longLabel Human Genome Diversity Project XP-EHH (Bantu populations in Africa) color 224, 0, 0 priority 1 track hgdpXpehhMideast parent hgdpXpehh shortLabel XP-EHH Mideast longLabel Human Genome Diversity Project XP-EHH (Mideast) color 0,0,200 priority 2 track hgdpXpehhEurope parent hgdpXpehh shortLabel XP-EHH Europe longLabel Human Genome Diversity Project XP-EHH (Europe) color 240,144,0 priority 3 track hgdpXpehhSAsia parent hgdpXpehh shortLabel XP-EHH S. Asia longLabel Human Genome Diversity Project XP-EHH (South Asia) color 0,0,0 priority 4 track hgdpXpehhEAsia parent hgdpXpehh shortLabel XP-EHH E. Asia longLabel Human Genome Diversity Project XP-EHH (East Asia) color 0,200,0 priority 5 track hgdpXpehhOceania parent hgdpXpehh shortLabel XP-EHH Oceania longLabel Human Genome Diversity Project XP-EHH (Oceania) color 0,200,200 priority 6 track hgdpXpehhAmericas parent hgdpXpehh shortLabel XP-EHH Americas longLabel Human Genome Diversity Project XP-EHH (Americas) color 224,192,0 priority 7 track protVarPos shortLabel UniProt Variants longLabel UniProt Variants group varRep visibility hide color 0,200,0 type bed 4 + track gvPos release alpha shortLabel Locus Variants longLabel Compilation of $Organism Variants from LSDBs group varRep visibility hide color 150,0,150 type bed 4 + track gvPos release beta,public html gvPosOld shortLabel Locus Variants longLabel Compilation of $Organism Variants from LSDBs group varRep visibility hide color 150,0,150 type bed 4 + track dgv shortLabel DGV Beta (old) longLabel Database of Genomic Variants: Obsolete, here for QA comparison group varRep visibility hide itemRgb on type bed 9 + noScoreFilter . exonArrows off urlLabel DGV Browser and Report: url http://dgv.tcag.ca/dgv/app/variant?id=$$&ref=$D dataVersion beta (Nov. 23, 2012) release alpha track dgvPlus compositeTrack on shortLabel DGV Struct Var longLabel Database of Genomic Variants: Structural Variation (CNV, Inversion, In/del) group varRep visibility hide itemRgb on type bed 9 + noScoreFilter . exonArrows off exonNumbers off urlLabel DGV Browser and Report: url http://dgv.tcag.ca/dgv/app/variant?id=$$&ref=$D coriellUrlBase http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref= dataVersion 2020-02-25 track dgvMerged parent dgvPlus shortLabel DGV Struct Var longLabel Database of Genomic Variants: Structural Var Regions (CNV, Inversion, In/del) priority 1 mouseOver ID: $name
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Type: $varType track dgvSupporting parent dgvPlus shortLabel DGV Supp Var longLabel Database of Genomic Variants: Supporting Structural Var (CNV, Inversion, In/del) priority 2 mouseOver ID: $name
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pop=ChbJpt track covMask1kGPilotLowCovYriDepth parent covMask1kGPilotLowCovDepth shortLabel Depth YRI longLabel Coverage Analysis from the 1000 Genomes Project Pilot Phase: Abnormal Depth, YRI subGroups view=Depth pop=Yri track covMask1kGPilotLowCovMapQ view MapQ shortLabel Map Qual Failure visibility hide parent covMask1kGPilotLowCov color 224,108,108 track covMask1kGPilotLowCovCeuMapQ parent covMask1kGPilotLowCovMapQ shortLabel Map Qual CEU longLabel Coverage Analysis from the 1000 Genomes Project Pilot Phase: Mapping Quality Failure, CEU subGroups view=MapQ pop=Ceu track covMask1kGPilotLowCovChbJptMapQ parent covMask1kGPilotLowCovMapQ shortLabel Map Qual CHB/JPT longLabel Coverage Analysis from the 1000 Genomes Project Pilot Phase: Mapping Quality Failure, CHB/JPT subGroups view=MapQ pop=ChbJpt track covMask1kGPilotLowCovYriMapQ parent covMask1kGPilotLowCovMapQ shortLabel Map Qual YRI longLabel Coverage Analysis from the 1000 Genomes Project Pilot Phase: Mapping Quality Failure, YRI 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group varRep chromosomes chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9 type bigWig 0 1000 autoScale off viewLimits 0:20 maxHeightPixels 128:40:11 track tgpRecombRateCeu subTrack tgpRecombRate shortLabel 1000G Recomb CEU longLabel 1000 Genomes Pilot Project Recombination Rates (CEU) type bigWig 0.0 108.0 track tgpRecombRateChbJpt subTrack tgpRecombRate shortLabel 1000GRecmb CHBJPT longLabel 1000 Genomes Pilot Project Recombination Rates (CHB+JPT) type bigWig 0.0 97.0 track tgpRecombRateYri subTrack tgpRecombRate shortLabel 1000G Recomb YRI longLabel 1000 Genomes Pilot Project Recombination Rates (YRI) type bigWig 0.0 62.0 track tgpRecombRateAvg subTrack tgpRecombRate shortLabel 1000G Recomb AVG longLabel 1000 Genomes Pilot Project Recombination Rates (average) type bigWig 0.0 108.0 track tgpRecombAvgMap subTrack tgpRecombRate shortLabel 1000G Genetic Map longLabel 1000 Genomes Pilot Project Average Genetic Map Position (cM) type bigWig 0.0 286.788605 viewLimits 0:286.788605 autoScale on track kiddEichlerDisc compositeTrack on shortLabel HGSV Discordant longLabel HGSV Discordant Clone End Alignments group varRep visibility hide itemRgb on type bed 12 urlLabel Clone Summary (Eichler Lab Browser): url http://mrhgsv.gs.washington.edu/cgi-bin/hgc?i=$$&c=$S&l=$[&r=$]&db=$D&position=$S:$[-$] ncbiAccXref kiddEichlerToNcbi pairedEndUrlFormat https://www.ncbi.nlm.nih.gov/Traces/trace.cgi?&cmd=retrieve&val=CENTER_NAME%%3D'ABC'%%20and%%20LIBRARY_ID%%3D'%s'%%20and%%20TRACE_NAME%%3D'%s'&retrieve=Submit track kiddEichlerDiscAbc14 parent kiddEichlerDisc shortLabel Discordant ABC14 longLabel HGSV Individual ABC14 (CEPH) Discordant Clone End Alignments priority 1 track kiddEichlerDiscAbc13 parent kiddEichlerDisc shortLabel Discordant ABC13 longLabel HGSV Individual ABC13 (Yoruba) Discordant Clone End Alignments priority 2 track kiddEichlerDiscAbc12 parent kiddEichlerDisc shortLabel Discordant ABC12 longLabel 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Alignments priority 9 track kiddEichlerValid compositeTrack on shortLabel HGSV Validated longLabel HGSV Validated Sites of Structural Variation group varRep visibility hide itemRgb on noScoreFilter . type bed 9 track kiddEichlerValidAbc14 parent kiddEichlerValid shortLabel Validated ABC14 longLabel HGSV Individual ABC14 (CEPH) Validated Sites of Structural Variation priority 1 track kiddEichlerValidAbc13 parent kiddEichlerValid shortLabel Validated ABC13 longLabel HGSV Individual ABC13 (Yoruba) Validated Sites of Structural Variation priority 2 track kiddEichlerValidAbc12 parent kiddEichlerValid shortLabel Validated ABC12 longLabel HGSV Individual ABC12 (CEPH) Validated Sites of Structural Variation priority 3 track kiddEichlerValidAbc11 parent kiddEichlerValid shortLabel Validated ABC11 longLabel HGSV Individual ABC11 (China) Validated Sites of Structural Variation priority 4 track kiddEichlerValidAbc10 parent kiddEichlerValid shortLabel Validated ABC10 longLabel HGSV Individual ABC10 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[a-z0-9.-]+(_[a-z0-9]+)? searchName hgIkmcPrefix searchTable hgIkmc searchType bed searchMethod prefix searchPriority 5 termRegex [a-z0-9.-]+ dontCheck [a-z0-9.-]+_[a-z0-9]+ track affy500K shortLabel Affy 500K longLabel Affy GeneChip Mapping 500K Array group varRep visibility hide type bed 6 + url https://www.affymetrix.com/LinkServlet?probeset=$$ track chimpParalogy shortLabel Chimp Seg Dups longLabel Chimp Segmental Duplications group varRep visibility hide type bed 3 . track chainSelfTestSwap shortLabel Test Self Chain R Swapped longLabel Test Chained Self-Alignments Swapped group x visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain hg38 otherDb hg38 chainNormScoreAvailable on track chainSelfTest shortLabel Test Self Chain longLabel Test Chained Self-Alignments group x visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain hg38 otherDb hg38 chainNormScoreAvailable on track chainSelf shortLabel Self Alignment longLabel Self-Alignment: Chained alignment of the human genome to itself group rep visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain hg16 otherDb hg16 track gbDnaBigChain shortLabel GenBank Chains longLabel GenBank DNA Sequences >5kbp Chained group x visibility hide color 100,50,0 altColor 255,240,200 type chain genbank iframeUrl https://www.ncbi.nlm.nih.gov/nuccore/$$ iframeOptions height='600' width='1024' idInUrlSql SELECT qName from gbDnaBigChain where id=%-s track gbSmall shortLabel GenBank Small longLabel GenBank Short DNA Sequences <5kbp group x visibility hide color 100,50,0 altColor 255,240,200 type psl iframeUrl https://www.ncbi.nlm.nih.gov/nuccore/$$ iframeOptions height='600' width='1024' #idInUrlSql SELECT qName from gbDnaBigChain where id=%-s track affyTranscription shortLabel Transcription longLabel Affy. SK-N-AS Transcript Abundance group expression visibility hide autoScale Off color 175,150,128 altColor 255,128,0 maxHeightPixels 128:36:16 graphTypeDefault Bar gridDefault OFF chromosomes chr6,chr7,chr13,chr14,chr19,chr20,chr21,chr22,chrX,chrY viewLimits 0:150 type wig 0 4396.07 wigColorBy affyTransfrags track affyTxnPhase2b shortLabel Affy Txn Phase2 longLabel Affymetrix Transcriptome Project Phase 2 compositeTrack on #compositeTrack on smart visibility hide group expression type bed 3 subGroup1 view Views frag=Transfrags tome=Transcriptome subGroup2 cell Cell_Line A375=A375 FHS=FHs738Lu HEPG2P=HepG2+ HEPG2m=HepG2- \ JURKAT=Jurkat NCCIT=NCCIT PC3=PC3 SKNAS=SK-N-AS U87=U87 subGroup3 loc Localization CYTO=Cytosolic NUC=Nuclear dimensions dimensionY=loc dimensionX=cell chromosomes chr6,chr7,chr13,chr14,chr19,chr20,chr21,chr22,chrX,chrY centerLabelsDense on sortOrder cell=+ loc=+ view=+ html affyTxnPhase2 track affyTxnPhase2Tome shortLabel Transcriptome view tome visibility dense parent affyTxnPhase2b viewUi on type wig 0 1000 viewLimits 0:150 autoScale Off maxHeightPixels 100:30:10 canPack off graphTypeDefault Bar gridDefault OFF color 175,150,128 altColor 255,128,0 track A375CytosolicPolyAPlusTxn shortLabel A375 Txn longLabel A375 Cytosolic polyA+, Affy Transcriptome type wig 0 5251.55 viewLimits 0:272 wigColorBy A375CytosolicPolyAPlusTnFg parent affyTxnPhase2Tome subGroups view=tome cell=A375 loc=CYTO track FHs738LuCytosolicPolyAPlusTxn shortLabel FHs738Lu Txn longLabel FHs738Lu Cytosolic polyA+, Affy Transcriptome type wig 0 5451.35 viewLimits 0:287 wigColorBy FHs738LuCytosolicPolyAPlusTnFg parent affyTxnPhase2Tome subGroups view=tome cell=FHS loc=CYTO track HepG2CytosolicPolyAPlusTxn shortLabel HepG2+ Cyto Txn longLabel HepG2 Cytosolic polyA+, Affy Transcriptome type wig 0 6183.74 viewLimits 0:282 wigColorBy HepG2CytosolicPolyAPlusTnFg parent affyTxnPhase2Tome subGroups view=tome cell=HEPG2P loc=CYTO track HepG2NuclearPolyAPlusTxn shortLabel HepG2+ Nuc Txn longLabel HepG2 Nuclear polyA+, Affy Transcriptome type wig 0 4206.84 viewLimits 0:214 wigColorBy HepG2NuclearPolyAPlusTnFg parent affyTxnPhase2Tome subGroups view=tome cell=HEPG2P loc=NUC track HepG2CytosolicPolyAMinusTxn shortLabel HepG2- Cyto Txn longLabel HepG2 Cytosolic polyA-, Affy Transcriptome type wig 0 3571.88 viewLimits 0:85 wigColorBy HepG2CytosolicPolyAMinusTnFg parent affyTxnPhase2Tome subGroups view=tome cell=HEPG2m loc=CYTO track HepG2NuclearPolyAMinusTxn shortLabel HepG2- Nuc Txn longLabel HepG2 Nuclear polyA-, Affy Transcriptome type wig 0 2656.57 viewLimits 0:94 wigColorBy HepG2NuclearPolyAMinusTnFg parent affyTxnPhase2Tome subGroups view=tome cell=HEPG2m loc=NUC track JurkatCytosolicPolyAPlusTxn shortLabel Jurkat Txn longLabel Jurkat Cytosolic polyA+, Affy Transcriptome type wig 0 5203.76 viewLimits 0:253 wigColorBy JurkatCytosolicPolyAPlusTnFg parent affyTxnPhase2Tome subGroups view=tome cell=JURKAT loc=CYTO track NCCITCytosolicPolyAPlusTxn shortLabel NCCIT Txn longLabel NCCIT Cytosolic polyA+, Affy Transcriptome type wig 0 6320.77 viewLimits 0:308 wigColorBy NCCITCytosolicPolyAPlusTnFg parent affyTxnPhase2Tome subGroups view=tome cell=NCCIT loc=CYTO track PC3CytosolicPolyAPlusTxn shortLabel PC3 Txn longLabel PC3 Cytosolic polyA+, Affy Transcriptome type wig 0 2993.96 viewLimits 0:198 wigColorBy PC3CytosolicPolyAPlusTnFg parent affyTxnPhase2Tome subGroups view=tome cell=PC3 loc=CYTO track SKNASCytosolicPolyAPlusTxn shortLabel SK-N-AS Txn longLabel SK-N-AS Cytosolic polyA+, Affy Transcriptome type wig 0 4395.02 viewLimits 0:224 wigColorBy SKNASCytosolicPolyAPlusTnFg parent affyTxnPhase2Tome subGroups view=tome cell=SKNAS loc=CYTO track U87CytosolicPolyAPlusTxn shortLabel U87 Txn longLabel U87 Cytosolic polyA+, Affy Transcriptome type wig 0 5939.33 viewLimits 0:221 wigColorBy U87CytosolicPolyAPlusTnFg parent affyTxnPhase2Tome subGroups view=tome cell=U87 loc=CYTO track affyTxnPhase2Frag shortLabel Transfrags view frag visibility pack parent affyTxnPhase2b type bed 4 + color 35,35,175 altColor 160,160,188 track A375CytosolicPolyAPlusTnFg shortLabel A375 TnFg longLabel A375 Cytosolic polyA+, Affy Transfrags parent affyTxnPhase2Frag subGroups view=frag cell=A375 loc=CYTO track FHs738LuCytosolicPolyAPlusTnFg shortLabel FHs738Lu TnFg longLabel FHs738Lu Cytosolic polyA+, Affy Transfrags parent affyTxnPhase2Frag subGroups view=frag cell=FHS loc=CYTO track HepG2CytosolicPolyAPlusTnFg shortLabel HepG2+ Cyto TnFg longLabel HepG2 Cytosolic polyA+, Affy Transfrags parent affyTxnPhase2Frag subGroups view=frag cell=HEPG2P loc=CYTO track HepG2NuclearPolyAPlusTnFg shortLabel HepG2+ Nuc TnFg longLabel HepG2 Nuclear polyA+, Affy Transfrags parent affyTxnPhase2Frag subGroups view=frag cell=HEPG2P loc=NUC track HepG2CytosolicPolyAMinusTnFg shortLabel HepG2- Cyto TnFg longLabel HepG2 Cytosolic polyA-, Affy Transfrags parent affyTxnPhase2Frag subGroups view=frag cell=HEPG2m loc=CYTO track HepG2NuclearPolyAMinusTnFg shortLabel HepG2- Nuc TnFg longLabel HepG2 Nuclear polyA-, Affy Transfrags parent affyTxnPhase2Frag subGroups view=frag cell=HEPG2m loc=NUC track JurkatCytosolicPolyAPlusTnFg shortLabel Jurkat TnFg longLabel Jurkat Cytosolic polyA+, Affy Transfrags parent affyTxnPhase2Frag subGroups view=frag cell=JURKAT loc=CYTO track NCCITCytosolicPolyAPlusTnFg shortLabel NCCIT TnFg longLabel NCCIT Cytosolic polyA+, Affy Transfrags parent affyTxnPhase2Frag subGroups view=frag cell=NCCIT loc=CYTO track PC3CytosolicPolyAPlusTnFg shortLabel PC3 TnFg longLabel PC3 Cytosolic polyA+, Affy Transfrags parent affyTxnPhase2Frag subGroups view=frag cell=PC3 loc=CYTO track SKNASCytosolicPolyAPlusTnFg shortLabel SK-N-AS TnFg longLabel SK-N-AS Cytosolic polyA+, Affy Transfrags parent affyTxnPhase2Frag subGroups view=frag cell=SKNAS loc=CYTO track U87CytosolicPolyAPlusTnFg shortLabel U87 TnFg longLabel U87 Cytosolic polyA+, Affy Transfrags parent affyTxnPhase2Frag subGroups view=frag cell=U87 loc=CYTO track affyU133Plus2 shortLabel Affy U133Plus2 longLabel Alignments of Affymetrix Consensus/Exemplars from HG-U133 Plus 2.0 group expression visibility hide type psl . track nhgriDnaseHs shortLabel NHGRI DNaseI-HS longLabel NHGRI DNaseI-Hypersensitive Sites group regulation visibility hide type bed 5 . useScore 1 origAssembly hg16 track eioJcviNAS compositeTrack on shortLabel EIO/JCVI NAS longLabel Eur. Inst. Oncology/J. C. Venter Inst. Nuclease Accessible Sites group regulation visibility hide type bed 3 . track eioJcviNASNeg parent eioJcviNAS shortLabel EIO/JCVI CD34- NAS longLabel CD34- cells Nuclease Accessible Sites priority 2 color 100,30,250 track eioJcviNASPos parent eioJcviNAS shortLabel EIO/JCVI CD34+ NAS longLabel CD34+ cells Nuclease Accessible Sites priority 1 color 100,30,150 # explicitly give this a priority >100, so it doesn't precede # the others in this group, which are assigned pri=100, and alpha sorted by short label track regPotential7X shortLabel 7X Reg Potential longLabel ESPERR Regulatory Potential (7 Species) group regulation visibility hide autoScale Off maxHeightPixels 128:36:16 graphTypeDefault Bar gridDefault OFF color 0,128,255 altColor 255,128,0 viewLimits 0.0:0.10 windowingFunction mean spanList 1 type wig 0.0 1.0 track blastDm1FB override longLabel D. melanogaster Proteins visibility hide track chainFr1ProtEx shortLabel chainFr1ProtEx longLabel chainFr1ProtEx group x visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain fr1 otherDb fr1 track webbNonExonic shortLabel NonExonic longLabel Putative Non-Exonic Regions Conserved with Chicken group x visibility hide color 0,60,120 altColor 255,220,100 spectrum on type bed 6 . track pHMM_5_WayTop1 shortLabel 1% Conserved longLabel Top 1 % of Human/Chimp/Mouse/Rat/Chicken PhyloHMM Cons group x visibility hide type bed 5 . track pHMM_5_WayTop01 shortLabel 0.1% Conserved longLabel Top 0.1 % of Human/Chimp/Mouse/Rat/Chicken PhyloHMM Cons group x visibility hide type bed 5 . track chainFr1Ex shortLabel chainFr1Ex longLabel chainFr1Ex group x priority 125 visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain fr1 otherDb fr1 track chainFr1MergeEx shortLabel chainFr1MergeEx longLabel chainFr1MergeEx group x priority 125 visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain fr1 otherDb fr1 track chainCi1ProtEx shortLabel chainCi1ProtEx longLabel chainCi1ProtEx group x priority 125 visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain ci1 otherDb ci1 track chainGalGal2Ex shortLabel chainGalGal2Ex longLabel chainGalGal2Ex group x priority 125 visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain galGal2 otherDb galGal2 track chainGalGal2MergeEx shortLabel chainGalGal2MergeEx longLabel chainGalGal2MergeEx group x priority 125 visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain galGal2 otherDb galGal2 track chainGalGal2ProtEx shortLabel chainGalGal2ProtEx longLabel chainGalGal2ProtEx group x priority 125 visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain galGal2 otherDb galGal2 track tblastFr1 shortLabel tblastFr1 longLabel Fugu (Aug. 2003/fr1) Best tblastn Hit/hg16 knownGene Exon group x spectrum on visibility hide type psl xeno track tblastGalGal2 shortLabel tblastGalGal2 longLabel $o_Organism ($o_date) tblastn Hit/hg16 knownGene Exon group x spectrum on visibility hide type psl xeno otherDb galGal1 track unAnnotated shortLabel unAnnotated longLabel Regions Not Annotated as Genes/mRNAs/ESTs/CpG/Repeats/Gaps group x visibility hide color 20,0,50 type bed 4 . track fosmidDiscordant shortLabel Fosmid Discordants longLabel Fosmid Discordants group varRep visibility dense type bed 4 . track evofold shortLabel EvoFold longLabel EvoFold Predictions of RNA Secondary Structure group genes visibility hide color 20,90,0 type bed 6 + mafTrack mzPt1Mm3Rn3Gg2_pHMM track wgRnaOld release alpha shortLabel sno/miRNA Old longLabel C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from snoRNABase and miRBase (Old Track) group genes visibility hide color 200,80,0 type bed 8 + urlLabel Laboratoire de Biologie Moléculaire Eucaryote: url http://www-snorna.biotoul.fr/plus.php?id=$$ url2Label miRBase: #url2 http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$$ url2 http://www.mirbase.org/cgi-bin/query.pl?terms=$$ track wgRna shortLabel sno/miRNA longLabel C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from snoRNABase and miRBase group genes visibility hide color 200,80,0 type bed 8 + noScoreFilter . urlLabel Laboratoire de Biologie Moleculaire Eucaryote: url http://www-snorna.biotoul.fr/plus.php?id=$$ url2Label miRBase: #url2 http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$$ url2 http://www.mirbase.org/cgi-bin/query.pl?terms=$$ dataVersion miRBase Release 13.0 (March 2009) and snoRNABase Version 3 track lrgTranscriptAli shortLabel LRG Transcripts longLabel Locus Reference Genomic (LRG) / RefSeqGene Fixed Transcript Annotations group genes visibility hide type bigPsl html lrgTranscriptAli #mouseOver ${name}: ${ncbiTranscript} ${ensemblTranscript} ${ncbiProtein} ${ensemblProtein} ${geneName} skipFields mouseOver exonNumbers on skipEmptyFields on urls ncbiTranscript=https://www.ncbi.nlm.nih.gov/nuccore/$$ ensemblTranscript=http://www.ensembl.org/Multi/Search/Results?site=ensembl_all;q=$$ ncbiProtein=https://www.ncbi.nlm.nih.gov/protein/$$ ensemblProtein=http://www.ensembl.org/Multi/Search/Results?site=ensembl_all;q=$$ altColor 127,127,127 baseColorDefault genomicCodons baseColorUseSequence lfExtra indelDoubleInsert on indelPolyA on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 color 54,125,29 urlLabel Link to LRG transcript url http://ftp.ebi.ac.uk/pub/databases/lrgex/$<_lrgParent>.xml#transcripts_anchor bigDataUrl /gbdb/$D/bbi/lrgBigPsl.bb searchIndex name track affyHuEx1 shortLabel Affy HuEx 1.0 longLabel Affymetrix Human Exon 1.0 Probe Sets group expression visibility hide url http://www.affymetrix.com/analysis/netaffx/exon/probe_set.affx?pk=1:$$ urlLabel Netaffx Link: useScore 1 type bed 6 . track affyHumanExon shortLabel Affy All Exon longLabel Affymetrix All Exon Chips group expression visibility hide type expRatio expScale 4.0 expStep 0.5 expProbeTable affyHumanExonProbeAnnot expTable affyHumanExonExps groupings affyHumanExonGroups # Affy Exon supertrack track affyAllExonSuper override group expression track affyExonTissues override group expression track affyAllExonProbes override group expression track sestanBrainAtlas shortLabel Sestan Brain longLabel Sestan Lab Human Brain Atlas Microarrays group expression visibility hide type expRatio expScale 3.0 expStep 0.5 expTable sestanBrainAtlasExps groupings sestanBrainAtlasGroups track xTBAmaf shortLabel xTBAmaf longLabel xTBAmaf group x visibility hide type wigMaf speciesGroups primate placental mammal vertebrate sGroup_primate panTro1 baboon rheMac1 marmoset galago sGroup_placental rn3 mm6 rabbit cow canFam1 rfbat hedgehog armadillo elephant tenrec sGroup_mammal monDom1 platypus sGroup_vertebrate galGal2 xenTro1 danRer2 tetNig1 fr1 # speciesGroups primate placental mammal vertebrate # sGroup_primate chimp baboon marmoset galago # sGroup_placental rat mouse cow dog armadillo # sGroup_mammal platypus # sGroup_vertebrate chicken irows on summary xTBAmafSum track brMaf shortLabel brMaf longLabel brMaf group x visibility hide type wigMaf #speciesOrder chimp baboon marmoset galago rat mouse cow dog armadillo platypus chicken speciesGroups primate placental mammal vertebrate sGroup_primate chimp baboon macaque marmoset galago sGroup_placental rat mouse rabbit cow dog rfbat hedgehog armadillo elephant tenrec sGroup_mammal monodelphis platypus sGroup_vertebrate chicken xenopus zebrafish tetraodon fugu irows on summary brMafSum track snpRecombRate compositeTrack on shortLabel SNP Recomb Rates longLabel Recombination Rates from SNP Genotyping group varRep visibility hide type bedGraph 4 viewLimits 0:16 minLimit 0 maxLimit 100 autoScale Off maxHeightPixels 64:32:16 origAssembly hg16 chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr18,chr19,chr20,chr21,chr22,chrX track snpRecombRateHapmap parent snpRecombRate shortLabel HapMap Phase I longLabel Oxford Recombination Rates from HapMap Phase I Release 16c.1 priority 1 track snpRecombRateHapmapPhase2 parent snpRecombRate shortLabel HapMap Phase II longLabel Oxford Recombination Rates from HapMap Phase II Release 21 priority 2 track snpRecombRatePerlegen parent snpRecombRate shortLabel Perlegen longLabel Oxford Recombination Rates from Perlegen Data priority 3 track hapmapLdPh compositeTrack on shortLabel HapMap LD Phased longLabel HapMap Linkage Disequilibrium - Phase II - from Phased Genotypes group varRep visibility hide canPack off chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22 dataVersion HapMap release 22 type ld2 track hapmapLdPhYri parent hapmapLdPh shortLabel Phased YRI longLabel Linkage Disequilibrium for the Yoruba (YRI) from Phased Genotypes priority 1 track hapmapLdPhCeu parent hapmapLdPh shortLabel Phased CEU longLabel Linkage Disequilibrium for the CEPH (CEU) from Phased Genotypes priority 2 track hapmapLdPhChbJpt parent hapmapLdPh shortLabel Ph JPT+CHB longLabel LD for the Han Chinese + Japanese from Tokyo (JPT+CHB) from Phased Genotypes priority 5 track snpRecombHotspot compositeTrack on shortLabel SNP Recomb Hots longLabel Recombination Hotspots from SNP Genotyping group varRep visibility hide type bed 3 . origAssembly hg16 track snpRecombHotspotHapmap parent snpRecombHotspot shortLabel HapMap longLabel Oxford Recombination Hotspots from HapMap Phase I Release 16c.1 priority 1 track snpRecombHotspotPerlegen parent snpRecombHotspot shortLabel Perlegen longLabel Oxford Recombination Hotspots from Perlegen Data priority 2 #track perlegenRecombColdpots #shortLabel Perlegen Recomb Coldspots #longLabel Oxford Recombination Coldspots from Perlegen Data #group varRep #priority 145.6 #visibility hide #type bed 3 . #origAssembly hg16 track syntenyCow shortLabel Cow Synteny longLabel Cow Synteny Using RH Mapping group compGeno visibility hide color 0,100,0 altColor 255,240,200 type bed 6 . track syntenicNet shortLabel Syntenic Nets longLabel Syntenic Alignment Nets for Chimp, Macaque, Mouse, Rat, and Dog compositeTrack on group compGeno visibility hide spectrum on type netAlign track netSyntenyPanTro2 parent syntenicNet shortLabel $o_Organism Syn Net longLabel $o_Organism ($o_date) Syntenic Alignment Net group compGeno priority 1 visibility hide spectrum on type netAlign panTro2 chainPanTro2 otherDb panTro2 track netSyntenyPonAbe2 parent syntenicNet shortLabel $o_Organism Syn Net longLabel $o_Organism ($o_date) Syntenic Alignment Net group compGeno priority 2 visibility hide spectrum on type netAlign ponAbe2 chainPonAbe2 otherDb ponAbe2 track netSyntenyRheMac2 parent syntenicNet shortLabel $o_Organism Syn Net longLabel $o_Organism ($o_date) Syntenic Alignment Net group compGeno priority 3 visibility hide spectrum on type netAlign rheMac2 chainRheMac2 otherDb rheMac2 track netSyntenyMm8 parent syntenicNet shortLabel Mouse Syn Net longLabel $o_Organism ($o_date) Syntenic Alignment Net group compGeno priority 4 visibility hide spectrum on type netAlign mm8 chainMm8 otherDb mm8 track netSyntenyRn4 parent syntenicNet shortLabel Rat Syn Net longLabel $o_Organism ($o_date) Syntenic Alignment Net group compGeno priority 5 visibility hide spectrum on type netAlign rn4 chainRn4 otherDb rn4 track netSyntenyCanFam2 parent syntenicNet shortLabel Dog Syn Net longLabel $o_Organism ($o_date) Syntenic Alignment Net group compGeno priority 6 visibility hide spectrum on type netAlign canFam2 chainCanFam2 otherDb canFam2 track netSyntenyEquCab1 parent syntenicNet shortLabel Horse Syn Net longLabel $o_Organism ($o_date) Syntenic Alignment Net group compGeno priority 7 visibility hide spectrum on type netAlign equCab1 chainEquCab1 otherDb equCab1 track netSyntenyMonDom4 parent syntenicNet shortLabel Opossum Syn Net longLabel $o_Organism ($o_date) Syntenic Alignment Net group compGeno priority 9 visibility hide spectrum on type netAlign monDom4 chainMonDom4 otherDb monDom4 track netSyntenyBosTau2 parent syntenicNet shortLabel Cow Syn Net longLabel $o_Organism ($o_date) Syntenic Alignment Net group compGeno priority 8 visibility hide spectrum on type netAlign bosTau3 chainBosTau2 otherDb bosTau3 track stanfordChip compositeTrack on shortLabel Stanf ChIP longLabel Stanford ChIP-chip (GMO6990, HeLa, HepG2, Jurkat, K562 cells; GABP, SRF, TAF, NRST/REST ChIP) group regulation chromosomes chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX visibility hide type bedGraph 4 color 120,0,20 altColor 150,0,25 maxHeightPixels 128:16:16 autoScale off minLimit 500 maxLimit 1000 viewLimits 0:10 origAssembly hg17 dataVersion Mar 2007 track stanfordChipGMO6990GABP parent stanfordChip shortLabel Stan GMO6690 GABP longLabel Stanford ChIP-chip (GMO6990 cells, GABP ChIP) priority 1 track stanfordChipGMO6990SRF parent stanfordChip shortLabel Stan GMO6690 SRF longLabel Stanford ChIP-chip (GMO6990 cells, SRF ChIP) priority 2 track stanfordChipHepG2GABP parent stanfordChip shortLabel Stan HepG2 GABP longLabel Stanford ChIP-chip (HepG2 cells, GABP ChIP) priority 3 track stanfordChipHepG2SRF parent stanfordChip shortLabel Stan HepG2 SRF longLabel Stanford ChIP-chip (HepG2 cells, SRF ChIP) priority 4 track stanfordChipHeLaGABP parent stanfordChip shortLabel Stan HeLa GABP longLabel Stanford ChIP-chip (HeLa cells, GABP ChIP) priority 5 track stanfordChipHeLaSRF parent stanfordChip shortLabel Stan HeLa SRF longLabel Stanford ChIP-chip (HeLa cells, SRF ChIP) priority 6 track stanfordChipHeLaTAF parent stanfordChip shortLabel Stan HeLa TAF longLabel Stanford ChIP-chip (HeLa cells, TAF ChIP) priority 7 track stanfordChipK562GABP parent stanfordChip shortLabel Stan K562 GABP longLabel Stanford ChIP-chip (K562 cells, GABP ChIP) priority 8 track stanfordChipK562SRF parent stanfordChip shortLabel Stan K562 SRF longLabel Stanford ChIP-chip (K562 cells, SRF ChIP) priority 9 track stanfordChipK562TAF parent stanfordChip shortLabel Stan K562 TAF longLabel Stanford ChIP-chip (K562 cells, TAF ChIP) priority 10 track stanfordChipNRSFMono parent stanfordChip shortLabel Stan Jurkat NRSF/REST/Mono longLabel Stanford ChIP-chip (Jurkat cells, NRSF/REST/Mono ChIP) priority 11 track stanfordChipNRSFUpstate parent stanfordChip shortLabel Stan Jurkat NRSF/REST/Upstate longLabel Stanford ChIP-chip (Jurkat cells, NRSF/REST/Upstate ChIP) priority 12 track rgdQtl override shortLabel RGD Human QTL track nibbImageProbes override group expression track allenBrainAli override group expression track eponine override track cosmic shortLabel COSMIC longLabel COSMIC: Catalogue Of Somatic Mutations In Cancer group phenDis visibility hide color 200, 0, 0 type bed 4 hgsid on url http://cancer.sanger.ac.uk/cosmic/mutation/overview?id= release alpha track cosmicNew shortLabel COSMIC longLabel COSMIC: Catalogue Of Somatic Mutations In Cancer group phenDis visibility hide color 200,0,0 type bigBed 4 + url http://cancer.sanger.ac.uk/cosmic/mutation/overview?id= html cosmic track cancerMutations shortLabel Cancer mutations longLabel Cancer somatic mutations from The Cancer Genome Atlas group phenDis visibility hide color 0,0,0 type bed release alpha compositeTrack on track pancan33 shortLabel PanCan33 longLabel Cancer mutations: 33 TCGA Cancer Projects Summary (Pan-Can 33) type bigBed 12 + release alpha bigDataUrl /gbdb/$D/bbi/cancerMutations/pancan33.bb urls case_id=https://portal.gdc.cancer.gov/cases/$$ parent cancerMutations track tcgaBrca shortLabel Breast longLabel Cancer mutations: TCGA Breast Cancer type bigBed 12 + release alpha bigDataUrl /gbdb/$D/bbi/cancerMutations/BRCA.bb urls case_id=https://portal.gdc.cancer.gov/cases/$$ parent cancerMutations track lovdComp shortLabel LOVD Variants longLabel LOVD: Leiden Open Variation Database Public Variants group phenDis visibility hide compositeTrack on type bigBed 4 + tableBrowser off lovdComp html lovdComp track lovdShort shortLabel LOVD Variants < 50 bp + ins longLabel LOVD: Leiden Open Variation Database, short < 50 bp variants and insertions of any length group phenDis visibility hide urls id="https://varcache.lovd.nl/redirect/$$" noScoreFilter on bigDataUrl /gbdb/$D/lovd/lovd.$D.short.bb parent lovdComp track lovdLong type bigBed 9 + shortLabel LOVD Variants >= 50 bp longLabel LOVD: Leiden Open Variation Database Public Variants, long >= 50 bp variants group phenDis visibility hide urls id="https://varcache.lovd.nl/redirect/$$" noScoreFilter on bigDataUrl /gbdb/$D/lovd/lovd.$D.long.bb parent lovdComp mergeSpannedItems on track hgmd shortLabel HGMD public longLabel Human Gene Mutation Database - Public Version Dec 2024 group phenDis visibility hide bigDataUrl /gbdb/$D/bbi/hgmd.bb itemRgb on type bigBed 9 . url http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$P&accession=$p urlLabel Link to HGMD mouseOverField variantType tableBrowser off hgmd noScoreFilter on maxItems 1000 maxWindowCoverage 10000000 track snpedia shortLabel SNPedia longLabel SNPedia group phenDis visibility hide color 50,0,100 type bed 4 compositeTrack on track snpediaText parent snpedia shortLabel SNPedia with text longLabel SNPedia pages with manually typed text color 50,0,100 type bed 4 itemDetailsHtmlTable snpediaTextHtml url https://www.snpedia.com/index.php/$$ urlLabel Link to SNPedia page: exonNumbers off track snpediaAll parent snpedia shortLabel SNPedia all longLabel SNPedia all SNPs (including empty pages) color 50,0,100 type bigBed 9 + searchIndex name bigDataUrl /gbdb/$D/bbi/snpediaAll.bb url https://www.snpedia.com/index.php/$$ urlLabel Link to SNPedia page: mouseOverField note itemRgb on exonNumbers off searchTable snpediaAll searchMethod exact searchType bigBed termRegex rs[0-9]+ searchPriority 14 padding 50 semiShortCircuit 1 searchTable snpediaText searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 14.001 padding 50 track interactions shortLabel Gene Interactions longLabel Protein Interactions from Curated Databases and Text-Mining group phenDis visibility hide type bigBed 9 itemRgb on exonNumbers off noScoreFilter on #release alpha,beta # draw the name field directly over the feature labelOnFeature on # linkIdInName means that the first part of the "name" field (space-separated) is the ID used for the %s parameter in directUrl directUrl hgGeneGraph?db=hg19&gene=%s # split off everything after the first space for the directUrl linkout linkIdInName on # always add the hgsid to the directUrl, default is off hgsid on bigDataUrl /gbdb/$D/bbi/interactions.bb searchName cosmicId searchTable cosmic searchMethod exact searchType bed searchPriority 10 query select chrom, chromStart, chromEnd, name from %s where name like '%s%%' termRegex COSM[0-9]+ release alpha searchTable wgRnaOld searchMethod fuzzy searchType bed searchPriority 10 searchName wgRnaOldExact searchTable wgRnaOld searchMethod exact searchType bed semiShortCircuit 1 termRegex [A-Z0-9\(\)/-]+ searchPriority 20 searchTable wgRna searchMethod fuzzy searchType bed searchPriority 10 searchName agilentCgh1x1m searchTable agilentCgh1x1m searchMethod prefix searchType bed shortCircuit 1 termRegex A_1(4|6|8)_P[0-9]+ searchPriority 17.1 searchName agilentHrd1x1m searchTable agilentHrd1x1m searchMethod prefix searchType bed shortCircuit 1 termRegex A_1(4|6|8)_P[0-9]+ searchPriority 17.2 searchName agilentCghSnp2x400k searchTable agilentCghSnp2x400k searchMethod prefix searchType bed shortCircuit 1 termRegex A_(14|16|18|20)_P[0-9]+ searchPriority 17.3 searchName agilentCgh2x400k searchTable agilentCgh2x400k searchMethod prefix searchType bed shortCircuit 1 termRegex A_1(4|6|8)_P[0-9]+ searchPriority 17.4 searchName agilentCghSnp4x180k searchTable agilentCghSnp4x180k searchMethod prefix searchType bed shortCircuit 1 termRegex A_(14|16|18|20)_P[0-9]+ searchPriority 17.5 searchName agilentCgh4x180k searchTable agilentCgh4x180k searchMethod prefix searchType bed shortCircuit 1 termRegex A_1(4|6|8)_P[0-9]+ searchPriority 17.6 searchName agilentCgh8x60k searchTable agilentCgh8x60k searchMethod prefix searchType bed shortCircuit 1 termRegex A_1(4|6|8)_P[0-9]+ searchPriority 17.7 searchName agilentCgh244a searchTable agilentCgh244a searchMethod prefix searchType bed shortCircuit 1 termRegex A_1(4|6)_P[0-9]+ searchPriority 17.8 searchName agilentCgh105a searchTable agilentCgh105a searchMethod prefix searchType bed shortCircuit 1 termRegex A_1(4|6)_P[0-9]+ searchPriority 17.9 searchName agilentCgh44k searchTable agilentCgh44k searchMethod prefix searchType bed shortCircuit 1 termRegex A_14_P[0-9]+ searchPriority 17.91 searchName wgRnaExact searchTable wgRna searchMethod exact searchType bed semiShortCircuit 1 termRegex [A-Z0-9\(\)/-]+ searchPriority 20 searchTable cnpSharp searchMethod exact searchType bed termRegex (CTD|RP11).* shortCircuit 1 searchPriority 50 searchTable cnpIafrate searchMethod exact searchType bed termRegex (AC|AL|AP|CI|CT|IH|II|RP|c1|co|na).* shortCircuit 1 searchPriority 50 searchTable affyGnf searchMethod exact searchType bed termRegex HG-U95:.+ searchPriority 15 termPrefix HG-U95: searchTable affyU95 searchMethod exact searchType psl termRegex HG-U95:.+ searchPriority 15 termPrefix HG-U95: searchName affyU95NoChip searchTable affyU95 searchMethod exact searchType psl termRegex [0-9]+[[:alnum:]_]*_at searchPriority 15 searchTable affyUcla searchMethod exact searchType bed termRegex HG-U133:.+ searchPriority 16 termPrefix HG-U133: searchName affyUclaNoChip searchTable affyUcla searchMethod exact searchType bed termRegex [0-9]+[[:alnum:]_]*_at searchPriority 16 searchTable affyU133 searchMethod exact searchType psl termRegex HG-U133[A-Z]:.+ query select tName,tStart,tEnd,qName from %s where qName like '%s;' searchPriority 16 termPrefix HG- searchName affyU133NoSemiColon searchTable affyU133 searchMethod prefix searchType psl termRegex U133[A-Z]:[0-9]+[[:alnum:]_]*_at searchPriority 16 searchName affyU133NoChip searchTable affyU133 searchMethod fuzzy searchType psl termRegex [0-9]+[[:alnum:]_]*_at searchPriority 16 searchTable affyU133Plus2 searchMethod exact searchType psl termRegex HG-U133_Plus_2:.+ searchPriority 16 termPrefix HG-U133_Plus_2: searchName affyU133Plus2NoChip searchTable affyU133Plus2 searchMethod exact searchType psl termRegex [0-9]+[[:alnum:]_]*_at searchPriority 16 searchTable affyGnf1h searchMethod exact searchType psl termRegex gnf1h[0-9]+.+ searchPriority 16 searchName affy500K searchTable affy500K searchMethod exact searchType bed shortCircuit 1 termRegex (SNP_A-[0-9]+(_[0-9]+)?) searchPriority 17 padding 250 searchName yaleBertoneTars searchTable yaleBertoneTars searchMethod exact searchType psl termRegex (TAR[0-9]+) searchPriority 18 searchName miRNAPrefix searchTable miRNA searchMethod prefix searchType bed shortCircuit 1 termRegex h?sa-(mir|let)-[0-9]+[a-z]? dontCheck h?sa-(mir|let)-[0-9]+[a-z]?(-[0-9]+)? searchPriority 18 searchTable miRNA searchMethod exact searchType bed shortCircuit 1 termRegex h?sa-(mir|let)-.+ searchPriority 18.5 searchTable illuminaProbes searchType bed termRegex ILMN_[0-9]+ shortCircuit 1 searchPriority 18.7 searchTable switchDbTss searchMethod prefix searchType bed shortCircuit 1 termRegex CHR[a-zA-Z_0-9]+ searchPriority 19 searchTable uniGene_2 searchType bed termRegex Hs\.[0-9]+ searchPriority 20 searchTable uniGene_3 searchType psl termRegex Hs\.[0-9]+ searchPriority 20 searchTable HInvGeneMrna searchMethod exact searchType psl termRegex HIT[0-9]{9,9} searchPriority 50 searchTable lrg searchMethod exact searchType bigBed termRegex (LRG_[0-9]+)|(NG_[0-9]+\.[0-9]+) semiShortCircuit 1 searchPriority 49 searchTable lrgTranscriptAli searchMethod exact searchType bigBed termRegex LRG_[0-9]+t[0-9]+ semiShortCircuit 1 searchPriority 50 searchName lrgTranscriptAliNoTNum searchTable lrgTranscriptAli query select tName, tStart, tEnd, qName from %s where qName like '%st%%' termRegex LRG_[0-9]+ dontCheck LRG_[0-9]+t[0-9+] semiShortCircuit 1 searchPriority 50 searchTable acescan searchMethod fuzzy searchType genePred termRegex .*_pred\.[0-9]+ searchPriority 50 searchTable ecoresTetNig1 searchType genePred shortcircuit 1 termRegex EG3HTT[0-9]+ searchPriority 50 searchName gvNameSearch searchTable gvPos query select chrom, chromStart, chromEnd, name from %s where name = '%s' xrefTable hgFixed.gv xrefQuery select id, name from %s where name like '%%%s%%' searchMethod fuzzy padding 1000 searchPriority 51 searchName gvAliasSearch searchTable gvPos query select chrom, chromStart, chromEnd, name from %s where name = '%s' dontCheckXrefQueryFormat on xrefTable hgFixed.gvAttr xrefQuery select id, attrVal from %s where attrType = 'commonName' and attrVal like '%%%s%%' searchMethod fuzzy padding 1000 searchPriority 51 searchName hapmapSnpsCEU searchTable hapmapSnpsCEU searchMethod exact searchType bed semiShortCircuit 1 termRegex (rs[1-9][0-9]*) searchPriority 13 padding 250 searchName hapmapSnpsCHB searchTable hapmapSnpsCHB searchMethod exact searchType bed semiShortCircuit 1 termRegex (rs[1-9][0-9]*) searchPriority 13 padding 250 searchName hapmapSnpsJPT searchTable hapmapSnpsJPT searchMethod exact searchType bed semiShortCircuit 1 termRegex (rs[1-9][0-9]*) searchPriority 13 padding 250 searchName hapmapSnpsYRI searchTable hapmapSnpsYRI searchMethod exact searchType bed semiShortCircuit 1 termRegex (rs[1-9][0-9]*) searchPriority 13 padding 250 searchName hapmapAllelesChimp searchTable hapmapAllelesChimp searchMethod exact searchType bed semiShortCircuit 1 termRegex (rs[1-9][0-9]*) searchPriority 13 padding 250 searchName hapmapAllelesMacaque searchTable hapmapAllelesMacaque searchMethod exact searchType bed semiShortCircuit 1 termRegex (rs[1-9][0-9]*) searchPriority 13 padding 250 searchTable jaxQtlAsIs searchMethod exact searchType bed semiShortCircuit 1 termRegex [a-z0-9]+ searchPriority 50 searchTable jaxQtlPadded searchMethod exact searchType bed semiShortCircuit 1 termRegex [a-z0-9]+ searchPriority 50 searchTable kiddEichlerDiscAbc7 searchMethod exact query select chrom,chromStart,chromEnd,name from %s where name like "%s,%%" xrefTable kiddEichlerToNcbi xrefQuery select name, cloneAcc from %s where cloneAcc = '%s' termRegex AC[0-9]{6} searchPriority 52 searchTable kiddEichlerDiscAbc8 searchMethod exact query select chrom,chromStart,chromEnd,name from %s where name like "%s,%%" xrefTable kiddEichlerToNcbi xrefQuery select name, cloneAcc from %s where cloneAcc = '%s' termRegex AC[0-9]{6} searchPriority 52 searchTable kiddEichlerDiscAbc9 searchMethod exact query select chrom,chromStart,chromEnd,name from %s where name like "%s,%%" xrefTable kiddEichlerToNcbi xrefQuery select name, cloneAcc from %s where cloneAcc = '%s' termRegex AC[0-9]{6} searchPriority 52 searchTable kiddEichlerDiscAbc10 searchMethod exact query select chrom,chromStart,chromEnd,name from %s where name like "%s,%%" xrefTable kiddEichlerToNcbi xrefQuery select name, cloneAcc from %s where cloneAcc = '%s' termRegex AC[0-9]{6} searchPriority 52 searchTable kiddEichlerDiscAbc11 searchMethod exact query select chrom,chromStart,chromEnd,name from %s where name like "%s,%%" xrefTable kiddEichlerToNcbi xrefQuery select name, cloneAcc from %s where cloneAcc = '%s' termRegex AC[0-9]{6} searchPriority 52 searchTable kiddEichlerDiscAbc12 searchMethod exact query select chrom,chromStart,chromEnd,name from %s where name like "%s,%%" xrefTable kiddEichlerToNcbi xrefQuery select name, cloneAcc from %s where cloneAcc = '%s' termRegex AC[0-9]{6} searchPriority 52 searchTable kiddEichlerDiscAbc13 searchMethod exact query select chrom,chromStart,chromEnd,name from %s where name like "%s,%%" xrefTable kiddEichlerToNcbi xrefQuery select name, cloneAcc from %s where cloneAcc = '%s' termRegex AC[0-9]{6} searchPriority 52 searchTable kiddEichlerDiscAbc14 searchMethod exact query select chrom,chromStart,chromEnd,name from %s where name like "%s,%%" xrefTable kiddEichlerToNcbi xrefQuery select name, cloneAcc from %s where cloneAcc = '%s' termRegex AC[0-9]{6} searchPriority 52 searchTable kiddEichlerDiscG248 searchMethod exact query select chrom,chromStart,chromEnd,name from %s where name like "%s,%%" xrefTable kiddEichlerToNcbi xrefQuery select name, cloneAcc from %s where cloneAcc = '%s' termRegex AC[0-9]{6} searchPriority 52 track fox2ClipSeqComp compositeTrack on shortLabel FOX2 CLIP-seq longLabel FOX2 Adaptor-trimmed CLIP-seq reads subGroup1 view Tracks reads=Reads density=Density clusters=Clusters group regulation visibility hide type bed 3 . dataVersion January 2009 track fox2ClipSeqCompViewreads shortLabel Reads view reads visibility pack parent fox2ClipSeqComp track fox2ClipSeq parent fox2ClipSeqCompViewreads shortLabel FOX2 CLIP-seq longLabel FOX2 Adaptor-trimmed CLIP-seq Reads subGroups view=reads priority 1 type bed 9 . itemRgb on noInherit on noScoreFilter . track fox2ClipSeqCompViewdensity shortLabel Density view density visibility full parent fox2ClipSeqComp viewLimitsMax 0:2401 track fox2ClipSeqDensityForwardStrand parent fox2ClipSeqCompViewdensity shortLabel Density Forward longLabel FOX2 Adaptor-trimmed CLIP-seq Density Forward Strand subGroups view=density priority 2 type wig 0 2401 configurable on spanList 1 maxHeightPixels 128:36:16 graphTypeDefault Bar windowingFunction mean noInherit on track fox2ClipSeqDensityReverseStrand parent fox2ClipSeqCompViewdensity shortLabel Density Reverse longLabel FOX2 Adaptor-trimmed CLIP-seq Density Reverse Strand subGroups view=density priority 3 type wig 0 1406 configurable on spanList 1 maxHeightPixels 128:36:16 graphTypeDefault Bar windowingFunction mean noInherit on track fox2ClipSeqCompViewclusters shortLabel Clusters view clusters visibility pack parent fox2ClipSeqComp track fox2ClipClusters parent fox2ClipSeqCompViewclusters shortLabel FOX2 clusters longLabel FOX2 Binding Site Clusters subGroups view=clusters priority 4 type bed 4 . noInherit on noScoreFilter . searchName fox2ClipSeq searchTable fox2ClipSeq searchMethod exact searchType bed semiShortCircuit 1 termRegex ES_[0-9]+_[0-9]+ searchPriority 30 searchTable gwasCatalog searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 13 padding 250 track darned shortLabel Human RNA Editing longLabel Human RNA Editing from the DAtabase of RNa EDiting group rna visibility hide itemRgb on noScoreFilter . type bed 9 #Overrides from priority.ra # fly track chainDm2 override priority 109 track netDm2 override priority 109.1 track chainCi2 override priority 117 track netCi2 override priority 117.1 # laminB1 supertrack track laminB1Super superTrack on shortLabel NKI Nuc Lamina longLabel NKI Nuclear Lamina Associated Domains (LaminB1 DamID) group regulation track laminB1Lads superTrack laminB1Super dense shortLabel NKI LADs (Tig3) longLabel NKI LADs (Lamina Associated Domains, Tig3 cells) group regulation visibility hide color 0,0,127 type bed 3 track laminB1 superTrack laminB1Super dense shortLabel LaminB1 (Tig3) longLabel NKI LaminB1 DamID Map (log2-ratio scores, Tig3 cells) group regulation visibility hide color 0,0,127 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean smoothingWindow 2 type wig -6.602 5.678 spanList 60 viewLimits -2:2 track ucsfBrainMethyl compositeTrack on shortLabel UCSF Brain Methyl longLabel UCSF Brain DNA Methylation group regulation subGroup1 view Views COV=Raw_Signal CG=CpG_score subGroup2 sampleType Sample_Type Brain=Brain subGroup3 assayType Assay_Type MRE1=MRE-seq MRE2=MRE-seq MRE3=MRE-seq MeDIP1=MeDIP-seq MeDIP2=MeDIP-seq H3K4me3=H3K4me3_ChIP-seq RNA1=RNA-seq RNA2=RNA-seq_(SMART) dimensions sortOrder assayType=+ view=+ #dimensions dimensionX=sampleType dimensionY=assayType dividers assayType #hierachy view COV=2 CG=3 dragAndDrop subTracks visibility hide #itemRgb on type bed 3 track ucsfBrainMethylViewCOV shortLabel Raw Signal view COV minLimit 0 maxLimit 1000 viewLimits 0:100 parent ucsfBrainMethyl visibility full track ucsfChipSeqH3K4me3BrainCoverage shortLabel H3K4me3 RawSignal longLabel H3K4me3 ChIP-seq Raw Signal parent ucsfBrainMethylViewCOV subGroups view=COV sampleType=Brain assayType=H3K4me3 type bedGraph 4 noInherit on maxHeightPixels 128:32:16 yLineOnOff on color 0,200,0 altColor 200,100,0 configurable on autoScale on priority 5 track ucsfMedipSeqBrainCoverage shortLabel MeDIP RawSignal longLabel MeDIP-seq Raw Signal parent ucsfBrainMethylViewCOV subGroups view=COV sampleType=Brain assayType=MeDIP2 type bedGraph 4 noInherit on maxHeightPixels 128:32:16 yLineOnOff on color 100,0,0 altColor 200,100,0 configurable on autoScale on priority 6 track ucsfRnaSeqBrainSmartCoverage shortLabel Smart RawSignal longLabel RNA-seq Smart-Tagged Raw Signal parent ucsfBrainMethylViewCOV subGroups view=COV sampleType=Brain assayType=RNA2 type bedGraph 4 noInherit on maxHeightPixels 128:32:16 yLineOnOff on color 0,0,200 altColor 100,0,0 autoScale on configurable on priority 7 track ucsfRnaSeqBrainAllCoverage shortLabel RNA-seq RawSignal longLabel RNA-seq Raw Signal parent ucsfBrainMethylViewCOV subGroups view=COV sampleType=Brain assayType=RNA1 type bedGraph 4 noInherit on maxHeightPixels 128:32:16 yLineOnOff on color 0,0,200 altColor 100,0,0 autoScale on configurable on priority 8 track ucsfBrainMethylViewCG shortLabel CpG score view CG minLimit 0 maxLimit 1000 viewLimits 0:100 parent ucsfBrainMethyl visibility full track ucsfMedipSeqBrainCpG shortLabel MeDIP CpG longLabel MeDIP-seq CpG Score parent ucsfBrainMethylViewCG subGroups view=CG sampleType=Brain assayType=MeDIP2 type bedGraph 4 noInherit on maxHeightPixels 128:32:16 yLineOnOff on configurable on color 100,0,0 altColor 200,100,0 autoScale on priority 9 track ucsfMreSeqBrainCpG shortLabel MRE CpG longLabel MRE-seq CpG Score parent ucsfBrainMethylViewCG subGroups view=CG sampleType=Brain assayType=MRE3 type bedGraph 4 noInherit on maxHeightPixels 128:32:16 yLineOnOff on configurable on color 0,100,0 altColor 200,100,0 autoScale on priority 10 track genotypeArrays compositeTrack on shortLabel SNP Arrays longLabel SNP Genotyping Arrays group varRep visibility hide configureByPopup off type bed 4 . track snpArrayAffy6 parent genotypeArrays shortLabel Affy SNP 6.0 longLabel Affymetrix SNP 6.0 type bed 6 + priority 1 track snpArrayAffy6SV parent genotypeArrays shortLabel Affy SNP 6.0 SV longLabel Affymetrix SNP 6.0 Structural Variation type bed 6 + priority 2 track snpArrayAffy5 parent genotypeArrays off shortLabel Affy SNP 5.0 longLabel Affymetrix SNP 5.0 type bed 6 + priority 3 track snpArrayAffy250Nsp parent genotypeArrays off shortLabel Affy 250KNsp longLabel Affymetrix GeneChip Human Mapping 250K Nsp type bed 6 + priority 4 track snpArrayAffy250Sty parent genotypeArrays off shortLabel Affy 250KSty longLabel Affymetrix GeneChip Human Mapping 250K Sty type bed 6 + priority 5 track snpArrayIllumina650 parent genotypeArrays off shortLabel Illumina 650 longLabel Illumina Human Hap 650v3 type bed 6 + priority 6 track snpArrayIllumina550 parent genotypeArrays off shortLabel Illumina 550 longLabel Illumina Human Hap 550v3 type bed 6 + priority 7 track snpArrayIllumina300 parent genotypeArrays off shortLabel Illumina 300 longLabel Illumina Human Hap 300v3 type bed 6 + priority 8 track snpArrayIllumina1M parent genotypeArrays shortLabel Illumina 1M-Duo longLabel Illumina Human1M-Duo type bed 6 + priority 9 track snpArrayIlluminaHumanCytoSNP_12 parent genotypeArrays shortLabel Illumina Cyto-12 longLabel Illumina Human CytoSNP-12 type bed 6 + priority 10 track snpArrayIlluminaHuman660W_Quad parent genotypeArrays shortLabel Illumina 660W-Q longLabel Illumina Human 660W-Quad type bed 6 + priority 11 track snpArrayIlluminaHumanOmni1_Quad parent genotypeArrays shortLabel Illumina Omni1-Q longLabel Illumina Human Omni1-Quad type bed 6 + priority 12 track iscaRetrospective shortLabel ISCA Retro longLabel International Standards for Cytogenomic Arrays Consortium - Retrospective variants group varRep visibility hide type gvf noScoreFilter . release beta,public track coriellDelDup shortLabel Coriell CNVs longLabel Coriell Cell Line Copy Number Variants group phenDis visibility hide type bed 9 + itemRgb on exonArrows off scoreFilterByRange on url http://ccr.coriell.org/Sections/Search/Search.aspx?q=$$ urlLabel Coriell details: track coriellAndy shortLabel Andy's Coriell longLabel Coriell Cell Line Deletions and Duplications spectrum on origAssembly hg18 group varRep visibility hide type bedDetail 7 pennantIcon 18.jpg ../goldenPath/help/liftOver.html "lifted from hg18" track iscaComposite compositeTrack on shortLabel ClinGen CNVs longLabel Clinical Genome Resource (ClinGen) CNVs group phenDis visibility hide subGroup1 view Views cov=Coverage cnv=CNVs dose=Dose subGroup2 class Class path=Pathogenic likP=Likely_Pathogenic unc=Uncertain likB=Likely_Benign ben=Benign subGroup3 level Evidence cur=Curated sub=Submitted dimensions dimensionY=class dimensionX=level sortOrder class=+ level=+ view=+ type bed 3 pennantIcon snowflake.png /goldenPath/newsarch.html#093020b "ClinGen CNV data are now updated on ClinVar Variants track. See news archive for details." track iscaViewTotal shortLabel Coverage (Graphical) view cov visibility full parent iscaComposite viewUi on type bedGraph 4 maxHeightPixels 128:57:16 viewLimits 0:100 alwaysZero on track iscaPathGainCum parent iscaViewTotal shortLabel Path Gain longLabel ClinGen CNVs: Pathogenic Gain Coverage color 0,0,200 subGroups view=cov class=path level=sub track iscaPathLossCum parent iscaViewTotal shortLabel Path Loss longLabel ClinGen CNVs: Pathogenic Loss Coverage color 200,0,0 subGroups view=cov class=path level=sub track iscaBenignGainCum parent iscaViewTotal shortLabel Benign Gain longLabel ClinGen CNVs: Benign Gain Coverage color 0,0,200 subGroups view=cov class=ben level=sub track iscaBenignLossCum parent iscaViewTotal shortLabel Benign Loss longLabel ClinGen CNVs: Benign Loss Coverage color 200,0,0 subGroups view=cov class=ben level=sub track iscaViewDetail shortLabel CNVs view cnv visibility pack parent iscaComposite type gvf noScoreFilter . url https://www.ncbi.nlm.nih.gov/dbvar/?term=$$ urlLabel ClinGen details: track iscaCuratedPathogenic parent iscaViewDetail off shortLabel Curated Path longLabel ClinGen CNVs: Curated Pathogenic subGroups view=cnv class=path level=cur track iscaCuratedBenign parent iscaViewDetail off shortLabel Curated Ben longLabel ClinGen CNVs: Curated Benign subGroups view=cnv class=ben level=cur track iscaPathogenic parent iscaViewDetail shortLabel Pathogenic longLabel ClinGen CNVs: Pathogenic subGroups view=cnv class=path level=sub track iscaLikelyPathogenic parent iscaViewDetail off shortLabel Uncert Path longLabel ClinGen CNVs: Uncertain: Likely Pathogenic subGroups view=cnv class=likP level=sub track iscaUncertain parent iscaViewDetail off shortLabel Uncertain longLabel ClinGen CNVs: Uncertain subGroups view=cnv class=unc level=sub track iscaLikelyBenign parent iscaViewDetail off shortLabel Uncert Ben longLabel ClinGen CNVs: Uncertain: Likely Benign subGroups view=cnv class=likB level=sub track iscaBenign parent iscaViewDetail off shortLabel Benign longLabel ClinGen CNVs: Benign subGroups view=cnv class=ben level=sub track doseSensitivity parent iscaComposite view dose shortLabel ClinGen sensitivity longLabel ClinGen sensitivity composite track group phenDis visibility hide type bigBed 9 + itemRgb on track clinGenHaploInsufficiency parent doseSensitivity shortLabel Haplo Insufficiency longLabel ClinGen Haplo Insufficiency visibility dense priority 1 type bigBed 9 + bigDataUrl /gbdb/$D/doseSensitivity/clinGenHaploInsufficiency.bb mouseOverField mouseOver subGroups view=dose class=path level=cur track clinGenTriploSensitivity parent doseSensitivity shortLabel Triplo Sensitivity longLabel ClinGen Triplo Sensitivity visibility dense priority 2 type bigBed 9 + bigDataUrl /gbdb/$D/doseSensitivity/clinGenTriploSensitivity.bb mouseOverField mouseOver subGroups view=dose class=path level=cur include phastBias.ra include omim.ra include decipher.ra include ../refSeqComposite.ra searchTable ensGene searchType genePred termRegex ENS([A-Z]{3})?T[0-9]+(\.[0-9]+)? searchPriority 50 searchName ensDotPrefix searchTable ensGene query select chrom,txStart,txEnd,name from %s where name like '%s.%%' termRegex ENS([A-Z]{3})?T[0-9]+ dontCheck ENS([A-Z]{3})?T[0-9]+\.[0-9]+ searchPriority 50 searchName ensGeneGtpGene searchTable ensGene searchType genePred searchMethod prefix xrefTable ensGtp xrefQuery select transcript,gene from %s where gene like '%s%%' termRegex ENS([A-Z]{3})?G[0-9]+(\.[0-9]+)? searchPriority 50 searchName ensGeneGtpProtein searchTable ensGene searchType genePred searchMethod prefix xrefTable ensGtp xrefQuery select transcript,protein from %s where protein like '%s%%' termRegex ENS([A-Z]{3})?P[0-9]+(\.[0-9]+)? searchTable iscaRetrospective searchMethod exact searchType bed semiShortCircuit 1 termRegex [ne]ss?v[0-9]+ searchPriority 20 release beta,public searchTable iscaCuratedBenign searchMethod exact searchType bed termRegex [ne]ss?v[0-9]+ searchPriority 20 searchTable iscaBenign searchMethod exact searchType bed termRegex [ne]ss?v[0-9]+ searchPriority 20 searchTable iscaLikelyBenign searchMethod exact searchType bed termRegex [ne]ss?v[0-9]+ searchPriority 20 searchTable iscaCuratedPathogenic searchMethod exact searchType bed termRegex [ne]ss?v[0-9]+ searchPriority 20 searchTable iscaPathogenic searchMethod exact searchType bed termRegex [ne]ss?v[0-9]+ searchPriority 20 searchTable iscaLikelyPathogenic searchMethod exact searchType bed termRegex [ne]ss?v[0-9]+ searchPriority 20 searchTable iscaUncertain searchMethod exact searchType bed termRegex [ne]ss?v[0-9]+ searchPriority 20 #NumtS track track numtSeq compositeTrack on shortLabel NumtS Sequence longLabel Human NumtS mitochondrial sequence group varRep visibility hide noInherit on type bed 3 . #configurable on html numtSeq track numtS parent numtSeq shortLabel NumtS longLabel Human NumtS color 0,60,120 #itemRgb on useScore 1 #noScoreFilter . priority 1 type bed 6 . html numtSeq track numtSAssembled parent numtSeq shortLabel NumtS assembled longLabel Human NumtS Assembled color 0,60,120 priority 2 useScore 1 #noScoreFilter . type bed 12 . html numtSeq track numtSMitochondrion parent numtSeq shortLabel NumtS on mitochon longLabel Human NumtS on Mitochondrion useScore 1 #noScoreFilter . color 0,60,120 priority 3 type bed 6 . html numtSeq track numtSMitochondrionChrPlacement parent numtSeq longLabel Human NumtS on Mitochondrion with Chromosome Placement shortLabel NumtS chr colored priority 4 itemRgb on type bed 9 . html numtSeq track bamAllNumtSSorted parent numtSeq shortLabel NumtS SNPs longLabel Human NumtS on Mitochondrion SNPs priority 5 visibility pack configurable on type bam bamSkipPrintQualScore . chromosomes chrM pairEndsByName on showNames on noColorTag . bamColorMode strand bamGrayMode aliQual aliQualRange 0:255 baseColorDefault diffBases baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 100 maxWindowToDraw 1000000 track cnvDevDelay shortLabel Development Delay longLabel Copy Number Variation Morbidity Map of Developmental Delay group phenDis visibility hide #color 0,0,200 type gvf noScoreFilter . compositeTrack on track cnvDevDelayCase shortLabel Case longLabel Copy Number Variation Morbidity Map of Developmental Delay - Case parent cnvDevDelay on type gvf visibility pack priority 1 track cnvDevDelayControl shortLabel Control longLabel Copy Number Variation Morbidity Map of Developmental Delay - Control parent cnvDevDelay on type gvf visibility pack priority 2 track gwipsvizRiboseq type bigWig 0 3589344 shortLabel GWIPS-viz Riboseq longLabel Ribosome Profiling from GWIPS-viz group expression visibility hide maxHeightPixels 100:32:8 viewLimits 0:2000 autoScale off html gwipsvizRiboseq searchTable numtSMitochondrionChrPlacement searchMethod exact searchType bed semiShortCircuit 1 searchPriority 15 query select chrom, chromStart, chromEnd, name from %s where name like '%s%%' termRegex HSA_NumtS_.* searchTable numtSMitochondrion searchMethod exact searchType bed semiShortCircuit 1 searchPriority 15 query select chrom, chromStart, chromEnd, name from %s where name like '%s%%' termRegex HSA_NumtS_.* searchTable numtS searchMethod exact searchType bed semiShortCircuit 1 searchPriority 15 query select chrom, chromStart, chromEnd, name from %s where name like '%s%%' termRegex HSA_NumtS_.* searchTable numtSAssembled searchMethod exact searchType bed semiShortCircuit 1 searchPriority 15 query select chrom, chromStart, chromEnd, name from %s where name like '%s%%' termRegex HSA_NumtS_.* include decode.rmap.ra #geneReviews track track geneReviews shortLabel GeneReviews longLabel GeneReviews group phenDis visibility hide color 0, 80, 0 type bigBed 9 + bigDataUrl /gbdb/$D/geneReviews/geneReviews.bb mouseOver Gene: $name
Count: $diseaseCount
Disease(s): $diseases
html geneReviews url https://www.ncbi.nlm.nih.gov/books/NBK1116/?term=$$ noScoreFilter on searchName geneReviews searchTable geneReviews searchType bed searchPriority 50 xrefTable geneReviewsDetail xrefQuery select geneSymbol,grTitle from %s where grTitle like '%%%s%%' searchBoth on searchTable dgv searchType bed searchPriority 50 termRegex (dgv_|[en]ss?v)[0-9]+ searchTable coriellDelDup searchMethod exact searchType bed searchPriority 50 termRegex GM[0-9]+ searchTable dgvMerged searchType bed semiShortCircuit on searchPriority 50 termRegex ([en]ss?v|dgv[0-9]+[a-z]+)[0-9]+ searchTable dgvSupporting searchType bed semiShortCircuit on searchPriority 50 termRegex ([en]ss?v|dgv[0-9]+[a-z]+)[0-9]+ searchTable uc16 searchMethod exact searchType bed searchPriority 10 termRegex uc\.[0-9]+ searchTable ux16 searchMethod exact searchType bed searchPriority 10 termRegex ux\.[0-9]+ searchTable snp141Common searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9865 padding 250 searchTable snp141Flagged searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9866 padding 250 searchTable snp141Mult searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9867 padding 250 searchTable snp141 searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9868 padding 250 searchTable snp142Common searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9861 padding 250 searchTable snp142Flagged searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9862 padding 250 searchTable snp142Mult searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9863 padding 250 searchTable snp142 searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9864 padding 250 searchTable snp144Common searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9855 padding 250 searchTable snp144Flagged searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9856 padding 250 searchTable snp144Mult searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9857 padding 250 searchTable snp144 searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9858 padding 250 searchTable snp146Common searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9851 padding 250 searchTable snp146Flagged searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9852 padding 250 searchTable snp146Mult searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9853 padding 250 searchTable snp146 searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.954 padding 250 searchTable snp147Common searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9847 padding 250 searchTable snp147Flagged searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9848 padding 250 searchTable snp147Mult searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9849 padding 250 searchTable snp147 searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.953 padding 250 searchTable snp149Common searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9844 padding 250 searchTable snp149Flagged searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9845 padding 250 searchTable snp149Mult searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9846 padding 250 searchTable snp149 searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.952 padding 250 searchTable snp150Common searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9841 padding 250 searchTable snp150 searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.951 padding 250 searchTable snp150Flagged searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9842 padding 250 searchTable snp150Mult searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9843 padding 250 searchTable snp151Common searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9837 padding 250 searchTable snp151Flagged searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9838 padding 250 searchTable snp151Mult searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9839 padding 250 searchTable snp151 searchMethod exact searchType bed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.950 padding 250 searchTable dbSnp152 searchMethod exact searchType bigBed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.949 padding 100 searchTable dbSnp153Common searchMethod exact searchType bigBed shortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9450 padding 100 searchTable dbSnp153ClinVar searchMethod exact searchType bigBed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9451 padding 100 searchTable dbSnp153 searchMethod exact searchType bigBed shortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9452 padding 100 searchTable dbSnp153Mult searchMethod exact searchType bigBed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9453 padding 100 searchTable dbSnp153BadCoords searchMethod exact searchType bigBed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9454 padding 100 searchTable dbSnp155Common searchMethod exact searchType bigBed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9450 padding 100 searchTable dbSnp155ClinVar searchMethod exact searchType bigBed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9451 padding 100 searchTable dbSnp155 searchMethod exact searchType bigBed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9452 padding 100 searchTable dbSnp155Mult searchMethod exact searchType bigBed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9453 padding 100 searchTable dbSnp155BadCoords searchMethod exact searchType bigBed #semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9454 padding 100 include cloneEnd.trackDb.ra track spMut override bigDataUrl /gbdb/$D/uniprot/unipMut.bb track sgpGene override longLabel SGP Gene Predictions Using Mouse/$Organism Homology track uniprot override hideEmptySubtracks off searchTable cnvDevDelayCase semiShortCircuit 1 termRegex nssv[0-9]+ searchType bed searchPriority 50 searchTable cnvDevDelayControl semiShortCircuit 1 termRegex nssv[0-9]+ searchType bed searchPriority 50 include covidHgiGwas.ra include covidTracks.ra track orphadata bigDataUrl /gbdb/$D/bbi/orphanet/orphadata.bb shortLabel Orphanet longLabel Orphadata: Aggregated Data From Orphanet group phenDis type bigBed 9 + bedNameLabel OrphaCode url http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=$$ urlLabel OrphaNet Phenotype Link: urls ensemblID="https://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=$$" pmid="https://pubmed.ncbi.nlm.nih.gov/$$" orphaCode="http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=$$" omim="https://www.omim.org/entry/$$?search=$$&highlight=$$" hgnc="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$$" skipEmptyFields on skipFields name,score,itemRgb mouseOver Gene: $geneSymbol, Disorder: $disorder, Inheritance(s): $inheritance, Onset: $onsetList filterValues.assnType Biomarker tested in,Candidate gene tested in,Disease-causing germline mutation(s) (gain of function) in,Disease-causing germline mutation(s) (loss of function) in,Disease-causing germline mutation(s) in,Disease-causing somatic mutation(s) in,Major susceptibility factor in,Modifying germline mutation in,Part of a fusion gene in,Role in the phenotype of filterValues.inheritance Autosomal dominant,Autosomal recessive,Mitochondrial inheritance,Multigenic/multifactorial,No data available,Not applicable,Oligogenic,Semi-dominant,Unknown,X-linked dominant,X-linked recessive,Y-linked filterValues.onsetList Adolescent,Adult,All ages,Antenatal,Childhood,Elderly,Infancy,Neonatal,No data available itemRgb on track hgnc shortLabel HGNC longLabel HUGO Gene Nomenclature bigDataUrl /gbdb/$D/hgnc/hgnc.bb type bigBed 9 + labelFields symbol, geneName, name, uniprot_ids, ensembl_gene_id, ucsc_id, refseq_accession defaultLabelFields symbol mouseOver Symbol: $symbol
$name
Alias symbol: $alias_symbol
Previous symbols: $prev_symbol filterValues.locus_type Y RNA,long non-coding RNA,micro RNA,misc RNA,ribosomal RNA,small nuclear RNA,small nucleolar RNA,transfer RNA,vault RNA,T cell receptor gene,T cell receptor pseudogene,complex locus constituent,endogenous retrovirus,gene with protein product,immunoglobulin gene,immunoglobulin pseudogene,pseudogene,readthrough,unknown group genes searchIndex name searchTrix /gbdb/$D/hgnc/search.ix skipEmptyFields on itemRgb on noScoreFilter on pennantIcon Updated red ../goldenPath/newsarch.html "Updated July 31, 2025" searchTable hgnc searchMethod exact searchType bigBed searchPriority 1.02 shortCircuit 1 track ncbiRefSeqSelect parent refSeqComposite off priority 8 type genePred shortLabel RefSeq Select and MANE longLabel NCBI RefSeq Select and MANE subset: A single representative transcript trackHandler ncbiRefSeq idXref ncbiRefSeqLink mrnaAcc name color 20,20,160 baseColorUseCds given baseColorDefault genomicCodons track ncbiRefSeqHistorical parent refSeqComposite off priority 9 type genePred shortLabel RefSeq Historical longLabel NCBI RefSeq Historical Transcript Versions color 12,12,120 idXref ncbiRefSeqLinkHistorical mrnaAcc name baseColorUseCds given baseColorDefault genomicCodons searchTable ncbiRefSeqHistorical searchMethod exact searchType genePred semiShortCircuit 1 termRegex [N][MR]_[0-9]{6}[0-9]*\.[0-9]+ searchPriority 20 include alphaMissense.ra include mitoMap.ra include nmdEscape.ra alpha include exonprimers.ra alpha -include colorsDb.ra +include longReadVariants.ra