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Configure Tracks on UCSC Genome Browser: Human Feb. 2009 (GRCh37/hg19)
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-   FANTOM5    
FANTOM5 summary... FANTOM5 summary
     Max counts     Max counts of CAGE reads
     Total counts     Total counts of CAGE reads
     TSS peaks     FANTOM5 DPI peak, robust set
     EnhProm_Organ     enhancer - promoter correlations distances organ
     EnhProm_CellType     enhancer_promoter_correlations_distances_cell_type
     FANTOM-NET_Enhancers     FANTOM-NET Enhancers (hg19)
     Enhancers     Enhancers (hg19)
FANTOM CAT... FANTOM CAT
     FANTOM_CAT.lv4_stringent     FANTOM_CAT.lv4_stringent
     FANTOM_CAT.lv3_robust     FANTOM_CAT.lv3_robust
     FANTOM_CAT.lv2_permissive     FANTOM_CAT.lv2_permissive
     FANTOM_CAT.lv1_raw     FANTOM_CAT.lv1_raw
TSS activity(read counts) TSS activity per sample(read counts)
TSS activity(TPM) TSS activity per sample(TPM)
+   Mapping and Sequencing    
-   Genes and Gene Predictions    
UCSC Genes UCSC Genes (RefSeq, GenBank, CCDS, Rfam, tRNAs & Comparative Genomics)
updated NCBI RefSeq RefSeq gene predictions from NCBI
Other RefSeq Non-Human RefSeq Genes
AceView Genes AceView Gene Models With Alt-Splicing
AUGUSTUS AUGUSTUS ab initio gene predictions v3.1
CCDS Consensus CDS
CRISPR Targets CRISPR/Cas9 -NGG Targets, whole genome
updated Ensembl Genes Ensembl Genes
EvoFold EvoFold Predictions of RNA Secondary Structure
Exoniphy Exoniphy Human/Mouse/Rat/Dog
GENCODE... GENCODE Gene Annotation
     GENCODE Genes V7     Gene Annotations from ENCODE/GENCODE Version 7
     GENCODE Genes V14     Gene Annotations from ENCODE/GENCODE Version 14
     GENCODE Genes V17     Gene Annotations from ENCODE/GENCODE Version 17
     GENCODE Genes V19     Gene Annotations from GENCODE Version 19
     GENCODE Gene V24lift37     Gene Annotations from GENCODE Version 24lift37
     GENCODE Gene V27lift37     Gene Annotations from GENCODE Version 27lift37
     GENCODE V28lift37     GENCODE lifted annotations from V28lift37 (Ensembl 92)
     GENCODE V31lift37     GENCODE lifted annotations from V31lift37 (Ensembl 97)
     GENCODE V33lift37     GENCODE lifted annotations from V33lift37 (Ensembl 99)
     GENCODE V34lift37     GENCODE lifted annotations from V34lift37 (Ensembl 100)
Geneid Genes Geneid Gene Predictions
Genscan Genes Genscan Gene Predictions
H-Inv 7.0 H-Inv 7.0 Gene Predictions
IKMC Genes Mapped International Knockout Mouse Consortium Genes Mapped to Human Genome
lincRNAs... Human Body Map lincRNAs and TUCP Transcripts
     lincRNA Transcripts     lincRNA and TUCP transcripts
     lincRNA RNA-Seq Reads     lincRNA RNA-Seq reads expression abundances
LRG Transcripts Locus Reference Genomic (LRG) Fixed Transcript Annotations
N-SCAN N-SCAN Gene Predictions
Old UCSC Genes Previous Version of UCSC Genes
ORFeome Clones ORFeome Collaboration Gene Clones
Pfam in UCSC Gene Pfam Domains in UCSC Genes
Retroposed Genes Retroposed Genes V5, Including Pseudogenes
SGP Genes SGP Gene Predictions Using Mouse/Human Homology
SIB Genes Swiss Institute of Bioinformatics Gene Predictions from mRNA and ESTs
sno/miRNA C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from snoRNABase and miRBase
TransMap V5... TransMap Alignments Version 5
     TransMap ESTs     TransMap EST Mappings Version 5
     TransMap RNA     TransMap GenBank RNA Mappings Version 5
     TransMap RefGene     TransMap RefSeq Gene Mappings Version 5
     TransMap Ensembl     TransMap Ensembl and GENCODE Mappings Version 5
tRNA Genes Transfer RNA Genes Identified with tRNAscan-SE
UCSC Alt Events Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes
UniProt UniProt SwissProt/TrEMBL Protein Annotations
Vega Genes Vega Annotations
Yale Pseudo60 Yale Pseudogenes based on Ensembl Release 60
-   Phenotype and Literature    
Publications Publications: Sequences in Scientific Articles
ClinGen CNVs Clinical Genome Resource (ClinGen) CNVs
ClinVar Variants ClinVar Variants
Coriell CNVs Coriell Cell Line Copy Number Variants
COSMIC Regions Catalogue of Somatic Mutations in Cancer V82
DECIPHER CNVs DECIPHER: Chromosomal Imbalance and Phenotype in Humans (CNVs)
DECIPHER SNVs DECIPHER: Chromosomal Imbalance and Phenotype in Humans (SNVs)
Development Delay Copy Number Variation Morbidity Map of Developmental Delay
GAD View Genetic Association Studies of Complex Diseases and Disorders
Gene Interactions Protein Interactions from Curated Databases and Text-Mining
GeneReviews GeneReviews
GWAS Catalog NHGRI-EBI Catalog of Published Genome-Wide Association Studies
HGMD Variants Human Gene Mutation Database Public Variants
Lens Patents Lens PatSeq Patent Document Sequences
LOVD Variants Leiden Open Variation Database Public Variants
MGI Mouse QTL MGI Mouse Quantitative Trait Loci Coarsely Mapped to Human
OMIM Alleles OMIM Allelic Variant Phenotypes
OMIM Cyto Loci OMIM Cytogenetic Loci Phenotypes - Gene Unknown
OMIM Genes OMIM Gene Phenotypes - Dark Green Can Be Disease-causing
RGD Human QTL Human Quantitative Trait Locus from RGD
RGD Rat QTL Rat Quantitative Trait Locus from RGD Coarsely Mapped to Human
SNPedia SNPedia
UniProt Variants UniProt/SwissProt Amino Acid Substitutions
Variants in Papers... Genetic Variants mentioned in scientific publications
     Mastermind Variants     Genomenon Mastermind Variants extracted from full text publications
     Avada Variants     Avada Variants extracted from full text publications
Web Sequences DNA Sequences in Web Pages Indexed by Bing.com / Microsoft Research
-   mRNA and EST    
Human mRNAs Human mRNAs from GenBank
CGAP SAGE CGAP Long SAGE
Gene Bounds Gene Boundaries as Defined by RNA and Spliced EST Clusters
H-Inv H-Invitational Genes mRNA Alignments
Human ESTs Human ESTs Including Unspliced
Human RNA Editing Human RNA Editing from the DAtabase of RNa EDiting
Other ESTs Non-Human ESTs from GenBank
Other mRNAs Non-Human mRNAs from GenBank
Poly(A) Poly(A) Sites, Both Reported and Predicted
PolyA-Seq Poly(A)-sequencing from Merck Research Laboratories
SIB Alt-Splicing Alternative Splicing Graph from Swiss Institute of Bioinformatics
Spliced ESTs Human ESTs That Have Been Spliced
UniGene UniGene Alignments
-   Expression    
GTEx Gene Gene Expression in 53 tissues from GTEx RNA-seq of 8555 samples (570 donors)
GTEx Transcript Transcript Expression in 53 tissues from GTEx RNA-seq of 8555 samples/570 donors
Affy Exon Array Affymetrix Human Exon Array Probes and Probesets
Affy GNF1H Alignments of Affymetrix Consensus/Exemplars from GNF1H
Affy RNA Loc RNA Subcellular Localization by Tiling Microarray from ENCODE Affymetrix/CSHL
Affy U95 Alignments of Affymetrix Consensus/Exemplars from HG-U95
Affy U133 Alignments of Affymetrix Consensus/Exemplars from HG-U133
Affy U133Plus2 Alignments of Affymetrix Consensus/Exemplars from HG-U133 Plus 2.0
Allen Brain Allen Brain Atlas Probes
Burge RNA-seq Burge Lab RNA-seq Aligned by GEM Mapper
CSHL Small RNA-seq Small RNA-seq from ENCODE/Cold Spring Harbor Lab
ENC Exon Array... ENCODE Exon Array
     UW Affy Exon     Affymetrix Exon Array from ENCODE/University of Washington
     Duke Affy Exon     Affymetrix Exon Array from ENCODE/Duke
new GTEx Gene V8 Gene Expression in 54 tissues from GTEx RNA-seq of 17382 samples, 948 donors (V8, Aug 2019)
ENC ProtGeno... ENCODE Proteogenomics
     UNC/BSU ProtGeno     Proteogenomics Hg19 Mapping from ENCODE/Univ. North Carolina/Boise State Univ.
     UNC/BSU ProtGenc     Proteogenomics Hg19 and GENCODE Mapping from ENCODE/Univ. North Carolina/Boise State Univ.
ENC RNA-seq... ENCODE RNA-seq
     SYDH RNA-seq     RNA-seq from ENCODE/Stanford/Yale/USC/Harvard
     HAIB RNA-seq     RNA-seq from ENCODE/HAIB
     GIS RNA-seq     RNA-seq from ENCODE/Genome Institute of Singapore
     CSHL Long RNA-seq     Long RNA-seq from ENCODE/Cold Spring Harbor Lab
     Caltech RNA-seq     RNA-seq from ENCODE/Caltech
GIS RNA PET RNA Sub-cellular Localization by Paired-end diTag Sequencing from ENCODE/GIS
GNF Atlas 2 GNF Expression Atlas 2
GWIPS-viz Riboseq Ribosome Profiling from GWIPS-viz
Illumina WG-6 Alignments of Illumina WG-6 3.0 Probe Set
PeptideAtlas Peptide sequences identified from MS spectra of 971 samples by PeptideAtlas
qPCR Primers Human (hg19) Whole Transcriptome qPCR Primers
RIKEN CAGE Loc RNA Subcellular CAGE Localization from ENCODE/RIKEN
Sestan Brain Sestan Lab Human Brain Atlas Microarrays
EPDnew Promoters Promoters from EPDnew human version 006
-   Regulation    
ENCODE Regulation... Integrated Regulation from ENCODE
     Txn Fac ChIP V2     Transcription Factor ChIP-seq from ENCODE (V2)
     Txn Factor ChIP     Transcription Factor ChIP-seq Clusters (161 factors) from ENCODE with Factorbook Motifs
     Txn Factr ChIP E3     Transcription Factor ChIP-seq Clusters (338 factors, 130 cell types) from ENCODE 3
     DNase Clusters     DNaseI Hypersensitivity Clusters in 125 cell types from ENCODE (V3)
     Layered H3K27Ac     H3K27Ac Mark (Often Found Near Active Regulatory Elements) on 7 cell lines from ENCODE
     Layered H3K4Me3     H3K4Me3 Mark (Often Found Near Promoters) on 7 cell lines from ENCODE
     Layered H3K4Me1     H3K4Me1 Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE
     Transcription     Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE
GeneHancer GeneHancer Regulatory Elements and Gene Interactions
GTEx Combined eQTL Combined Expression QTLs from 44 Tissues from GTEx (midpoint release, V6)
GTEx Tissue eQTL Expression QTLs in 44 tissues from GTEx (midpoint release, V6)
CD34 DnaseI Eur. Inst. Oncology/J. C. Venter Inst. Nuclease Accessible Sites
CpG Islands... CpG Islands (Islands < 300 Bases are Light Green)
     Unmasked CpG     CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
     CpG Islands     CpG Islands (Islands < 300 Bases are Light Green)
ENC Chromatin... ENCODE Chromatin Interactions
     UW 5C    DownloadsChromatin Interactions by 5C from ENCODE/University of Washington
     UMass 5C     Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass.
     GIS ChIA-PET     Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan
ENC DNA Methyl... ENCODE DNA Methylation
     HAIB Methyl450     CpG Methylation by Methyl 450K Bead Arrays from ENCODE/HAIB
     HAIB Methyl RRBS     DNA Methylation by Reduced Representation Bisulfite Seq from ENCODE/HudsonAlpha
ENC DNase/FAIRE... ENCODE Open Chromatin by DNaseI HS and FAIRE
     UW DNaseI HS     DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington
     UW DNaseI DGF     DNaseI Digital Genomic Footprinting from ENCODE/University of Washington
     UNC FAIRE     Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill)
     Duke DNaseI HS     Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University)
     Open Chrom Synth     DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom(Duke/UNC/UTA)
     Uniform DNaseI HS     DNaseI Hypersensitivity Uniform Peaks from ENCODE/Analysis
     Master DNaseI HS     DNaseI Hypersensitive Site Master List (125 cell types) from ENCODE/Analysis
ENC Histone... ENCODE Histone Modification
     UW Histone     Histone Modifications by ChIP-seq from ENCODE/University of Washington
     SYDH Histone     Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard
     Broad Histone     Histone Modifications by ChIP-seq from ENCODE/Broad Institute
     Broad ChromHMM     Chromatin State Segmentation by HMM from ENCODE/Broad
ENC RNA Binding... ENCODE RNA Binding Proteins
     SUNY RIP-seq     RIP-seq from ENCODE/SUNY Albany
     SUNY RIP Tiling     RNA Binding Protein Associated RNA by Tiling Array from ENCODE/SUNY Albany
     SUNY RIP GeneST     RNA Binding Protein Associated RNA by RIP-chip GeneST from ENCODE/SUNY Albany
ENC TF Binding... ENCODE Transcription Factor Binding
     UW CTCF Binding     CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington
     UTA TFBS     Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin)
     UChicago TFBS     Transcription Factor Binding Sites by Epitope-Tag from ENCODE/UChicago
     SYDH TFBS     Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard
     HAIB TFBS     Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB
     Uniform TFBS     Transcription Factor ChIP-seq Uniform Peaks from ENCODE/Analysis
     ENCODE 3 TFBS     Transcription Factor ChIP-seq Peaks (338 factors in 130 cell types) from ENCODE 3
FSU Repli-chip Replication Timing by Repli-chip from ENCODE/FSU
Genome Segments Genome Segmentations from ENCODE
NKI Nuc Lamina... NKI Nuclear Lamina Associated Domains (LaminB1 DamID)
     NKI LADs (Tig3)     NKI LADs (Lamina Associated Domains, Tig3 cells)
     LaminB1 (Tig3)     NKI LaminB1 DamID Map (log2-ratio scores, Tig3 cells)
ORegAnno Regulatory elements from ORegAnno
Rao 2014 Hi-C Hi-C on 7 cell lines from Rao 2014
Stanf Nucleosome Nucleosome Position by MNase-seq from ENCODE/Stanford/BYU
SUNY SwitchGear RNA Binding Protein Associated RNA by SwitchGear from ENCODE/SUNY Albany
SwitchGear TSS SwitchGear Genomics Transcription Start Sites
TFBS Conserved HMR Conserved Transcription Factor Binding Sites
TS miRNA sites TargetScan miRNA Regulatory Sites
UCSF Brain Methyl UCSF Brain DNA Methylation
UMMS Brain Hist Brain Histone H3K4me3 ChIP-Seq from Univ. Mass. Medical School (Akbarian/Weng)
UW Repli-seq Replication Timing by Repli-seq from ENCODE/University of Washington
Vista Enhancers Vista HMR-Conserved Non-coding Human Enhancers from LBNL
-   Comparative Genomics    
Conservation Vertebrate Multiz Alignment & Conservation (100 Species)
Cons 46-Way Vertebrate Multiz Alignment & Conservation (46 Species)
Cons Indels MmCf Indel-based Conservation for Human hg19, Mouse mm8 and Dog canFam2
Evo Cpg Weizmann Evolutionary CpG Islands
GERP GERP Scores for Mammalian Alignments
phastBias gBGC phastBias gBGC predictions
Primate Chain/Net Primate Genomes, Chain and Net Alignments
Placental Chain/Net Non-primate Placental Mammal Genomes, Chain and Net Alignments
Vertebrate Chain/Net Non-placental Vertebrate Genomes, Chain and Net Alignments
+   Neandertal Assembly and Analysis    
+   Denisova Assembly and Analysis    
-   Variation    
dbSNP 153 Short Genetic Variants from dbSNP release 153
Common SNPs(151) Simple Nucleotide Polymorphisms (dbSNP 151) Found in >= 1% of Samples
Common SNPs(150) Simple Nucleotide Polymorphisms (dbSNP 150) Found in >= 1% of Samples
Common SNPs(147) Simple Nucleotide Polymorphisms (dbSNP 147) Found in >= 1% of Samples
Common SNPs(146) Simple Nucleotide Polymorphisms (dbSNP 146) Found in >= 1% of Samples
Common SNPs(144) Simple Nucleotide Polymorphisms (dbSNP 144) Found in >= 1% of Samples
Common SNPs(142) Simple Nucleotide Polymorphisms (dbSNP 142) Found in >= 1% of Samples
Common SNPs(141) Simple Nucleotide Polymorphisms (dbSNP 141) Found in >= 1% of Samples
Common SNPs(138) Simple Nucleotide Polymorphisms (dbSNP 138) Found in >= 1% of Samples
All SNPs(151) Simple Nucleotide Polymorphisms (dbSNP 151)
All SNPs(150) Simple Nucleotide Polymorphisms (dbSNP 150)
All SNPs(147) Simple Nucleotide Polymorphisms (dbSNP 147)
All SNPs(146) Simple Nucleotide Polymorphisms (dbSNP 146)
All SNPs(144) Simple Nucleotide Polymorphisms (dbSNP 144)
All SNPs(142) Simple Nucleotide Polymorphisms (dbSNP 142)
All SNPs(141) Simple Nucleotide Polymorphisms (dbSNP 141)
All SNPs(138) Simple Nucleotide Polymorphisms (dbSNP 138)
Flagged SNPs(151) Simple Nucleotide Polymorphisms (dbSNP 151) Flagged by dbSNP as Clinically Assoc
Flagged SNPs(150) Simple Nucleotide Polymorphisms (dbSNP 150) Flagged by dbSNP as Clinically Assoc
Flagged SNPs(147) Simple Nucleotide Polymorphisms (dbSNP 147) Flagged by dbSNP as Clinically Assoc
Flagged SNPs(146) Simple Nucleotide Polymorphisms (dbSNP 146) Flagged by dbSNP as Clinically Assoc
Flagged SNPs(144) Simple Nucleotide Polymorphisms (dbSNP 144) Flagged by dbSNP as Clinically Assoc
Flagged SNPs(142) Simple Nucleotide Polymorphisms (dbSNP 142) Flagged by dbSNP as Clinically Assoc
Flagged SNPs(141) Simple Nucleotide Polymorphisms (dbSNP 141) Flagged by dbSNP as Clinically Assoc
Flagged SNPs(138) Simple Nucleotide Polymorphisms (dbSNP 138) Flagged by dbSNP as Clinically Assoc
Mult. SNPs(151) Simple Nucleotide Polymorphisms (dbSNP 151) That Map to Multiple Genomic Loci
Mult. SNPs(150) Simple Nucleotide Polymorphisms (dbSNP 150) That Map to Multiple Genomic Loci
Mult. SNPs(147) Simple Nucleotide Polymorphisms (dbSNP 147) That Map to Multiple Genomic Loci
Mult. SNPs(146) Simple Nucleotide Polymorphisms (dbSNP 146) That Map to Multiple Genomic Loci
Mult. SNPs(144) Simple Nucleotide Polymorphisms (dbSNP 144) That Map to Multiple Genomic Loci
Mult. SNPs(142) Simple Nucleotide Polymorphisms (dbSNP 142) That Map to Multiple Genomic Loci
Mult. SNPs(138) Simple Nucleotide Polymorphisms (dbSNP 138) That Map to Multiple Genomic Loci
1000G Ph1 Accsbl 1000 Genomes Project Phase 1 Paired-end Accessible Regions
1000G Ph1 Vars 1000 Genomes Phase 1 Integrated Variant Calls: SNVs, Indels, SVs
1000G Ph3 Accsbl 1000 Genomes Project Phase 3 Paired-end Accessible Regions
1000G Ph3 Vars 1000 Genomes Phase 3 Integrated Variant Calls: SNVs, Indels, SVs
DGV Struct Var Database of Genomic Variants: Structural Variation (CNV, Inversion, In/del)
EVS Variants NHLBI GO Exome Sequencing Project (ESP) - Variants from 6,503 Exomes
ExAC Exome Aggregation Consortium (ExAC) Variants and Calling Regions
Genome Variants Personal Genome Variants
GIS DNA PET ENCODE Genome Institute of Singapore DNA Paired-End Ditags
gnomAD... Genome Aggregation Database (gnomAD) - Variants, Coverage, and Constraint
     gnomAD Variants     Genome Aggregation Database (gnomAD) - Genome and Exome Variants
     gnomAD Structural Variants     Genome Aggregation Database (gnomAD) - Structural Variants
     gnomAD Coverage     Genome Aggregation Database (gnomAD) - Genome and Exome Sample Coverage
     gnomAD Constraint Metrics     Genome Aggregation Database (gnomAD) - Predicted Constraint Metrics
HAIB Genotype Genotype (CNV and SNP) by Illumina 1MDuo and CBS from ENCODE/HudsonAlpha
HapMap SNPs HapMap SNPs (rel27, merged Phase II + Phase III genotypes)
HGDP Allele Freq Human Genome Diversity Project SNP Population Allele Frequencies
Platinum Genomes Platinum genome variants
SNP/CNV Arrays Microarray Probesets
-   Repeats    
RepeatMasker Repeating Elements by RepeatMasker
Interrupted Rpts Fragments of Interrupted Repeats Joined by RepeatMasker ID
Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
NumtS Sequence Human NumtS mitochondrial sequence
Segmental Dups Duplications of >1000 Bases of Non-RepeatMasked Sequence
Self Chain Human Chained Self Alignments
Simple Repeats Simple Tandem Repeats by TRF
WM + SDust Genomic Intervals Masked by WindowMasker + SDust