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Configure Tracks on UCSC Genome Browser: Human Feb. 2009 (GRCh37/hg19)
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-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Assembly Assembly from Fragments
BAC End Pairs BAC End Pairs
BU ORChID ORChID Predicted DNA Cleavage Sites from ENCODE/Boston Univ (Tullius lab)
Chromosome Band Chromosome Bands Localized by FISH Mapping Clones
deCODE Recomb deCODE Recombination maps, 10Kb bin size, October 2010
ENCODE Pilot Regions Used for ENCODE Pilot Project (1%)
FISH Clones Clones Placed on Cytogenetic Map Using FISH
Fosmid End Pairs Fosmid End Pairs
Gap Gap Locations
GC Percent GC Percent in 5-Base Windows
GRC Incident GRC Incident Database
GRC Map Contigs Genome Reference Consortium Map Contigs
GRC Patch Release GRCh37 alternate sequences, haplotypes and reference sequence patches
Hg18 Diff Contigs New to GRCh37/(hg19), Not Carried Forward from NCBI Build 36(hg18)
Hg38 Diff Contigs Dropped or Changed from GRCh37(hg19) to GRCh38(hg38)
Hi Seq Depth Regions of Exceptionally High Depth of Aligned Short Reads
INSDC Accession at INSDC - International Nucleotide Sequence Database Collaboration
LRG Regions Locus Reference Genomic (LRG) Sequences Mapped to Feb. 2009 (GRCh37/hg19) Assembly
Map Contigs Physical Map Contigs
Mappability Mappability or Uniqueness of Reference Genome from ENCODE
Recomb Rate Recombination Rate from deCODE, Marshfield, or Genethon Maps (deCODE default)
Short Match Perfect Matches to Short Sequence (AAAAA)
STS Markers STS Markers on Genetic (blue) and Radiation Hybrid (black) Maps
-   Genes and Gene Predictions    
UCSC Genes UCSC Genes (RefSeq, GenBank, CCDS, Rfam, tRNAs & Comparative Genomics)
RefSeq Genes RefSeq Genes
AceView Genes AceView Gene Models With Alt-Splicing
CCDS Consensus CDS
Ensembl Genes Ensembl Genes
EvoFold EvoFold Predictions of RNA Secondary Structure
Exoniphy Exoniphy Human/Mouse/Rat/Dog
GENCODE... GENCODE Gene Annotation
     GENCODE Genes V19     Gene Annotations from ENCODE/GENCODE Version 19
     GENCODE Genes V17     Gene Annotations from ENCODE/GENCODE Version 17
     GENCODE Genes V14     Gene Annotations from ENCODE/GENCODE Version 14
     GENCODE Genes V7     Gene Annotations from ENCODE/GENCODE Version 7
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 RNA-Seq Reads     lincRNA RNA-Seq reads expression abundances
     lincRNA Transcripts     lincRNA and TUCP transcripts
LRG Transcripts Locus Reference Genomic (LRG) Fixed Transcript Annotations
MGC Genes Mammalian Gene Collection Full ORF mRNAs
N-SCAN N-SCAN Gene Predictions
Old UCSC Genes Previous Version of UCSC Genes
ORFeome Clones ORFeome Collaboration Gene Clones
Other RefSeq Non-Human RefSeq Genes
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... TransMap Alignments
     TransMap UCSC     TransMap UCSC Gene Mappings
     TransMap RefGene     TransMap RefSeq Gene Mappings
     TransMap mRNA     TransMap GenBank mRNA Mappings
     TransMap ESTs     TransMap Spliced EST Mappings
tRNA Genes Transfer RNA Genes Identified with tRNAscan-SE
UCSC Alt Events Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes
Vega Genes Vega Annotations
Yale Pseudo60 Yale Pseudogenes based on Ensembl Release 60
-   Phenotype and Literature    
Publications Publications: Sequences in Scientific Articles
ClinVar Variants ClinVar Variants
Coriell CNVs Coriell Cell Line Copy Number Variants
COSMIC COSMIC: Catalogue Of Somatic Mutations In Cancer
GAD View Genetic Association Studies of Complex Diseases and Disorders
GeneReviews GeneReviews
GWAS Catalog NHGRI Catalog of Published Genome-Wide Association Studies
ISCA International Standards for Cytogenomic Arrays Consortium
MGI Mouse QTL MGI Mouse Quantitative Trait Loci Coarsely Mapped to Human
RGD Human QTL Human Quantitative Trait Locus from RGD
RGD Rat QTL Rat Quantitative Trait Locus from RGD Coarsely Mapped to Human
UniProt Variants UniProt/SwissProt Amino Acid Substitutions
Web Sequences DNA Sequences in Web Pages Indexed by Bing.com / Microsoft Research
-   mRNA and EST    
Human mRNAs Human mRNAs from GenBank
Spliced ESTs Human ESTs That Have Been Spliced
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
UniGene UniGene Alignments
-   Expression    
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 U133 Alignments of Affymetrix Consensus/Exemplars from HG-U133
Affy U133Plus2 Alignments of Affymetrix Consensus/Exemplars from HG-U133 Plus 2.0
Affy U95 Alignments of Affymetrix Consensus/Exemplars from HG-U95
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
     Duke Affy Exon     Affymetrix Exon Array from ENCODE/Duke
     UW Affy Exon     Affymetrix Exon Array from ENCODE/University of Washington
ENC ProtGeno... ENCODE Proteogenomics
     UNC/BSU ProtGenc     Proteogenomics Hg19 and GENCODE Mapping from ENCODE/Univ. North Carolina/Boise State Univ.
     UNC/BSU ProtGeno     Proteogenomics Hg19 Mapping from ENCODE/Univ. North Carolina/Boise State Univ.
ENC RNA-seq... ENCODE RNA-seq
     Caltech RNA-seq     RNA-seq from ENCODE/Caltech
     CSHL Long RNA-seq     Long RNA-seq from ENCODE/Cold Spring Harbor Lab
     GIS RNA-seq     RNA-seq from ENCODE/Genome Institute of Singapore
     HAIB RNA-seq     RNA-seq from ENCODE/HAIB
     SYDH RNA-seq     RNA-seq from ENCODE/Stanford/Yale/USC/Harvard
GIS RNA PET RNA Sub-cellular Localization by Paired-end diTag Sequencing from ENCODE/GIS
GNF Atlas 2 GNF Expression Atlas 2
Illumina WG-6 Alignments of Illumina WG-6 3.0 Probe Set
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
-   Regulation    
ENCODE Regulation... Integrated Regulation from ENCODE
     Transcription     Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE
     Layered H3K4Me1     H3K4Me1 Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE
     Layered H3K4Me3     H3K4Me3 Mark (Often Found Near Promoters) on 7 cell lines from ENCODE
     Layered H3K27Ac     H3K27Ac Mark (Often Found Near Active Regulatory Elements) on 7 cell lines from ENCODE
     DNase Clusters     Digital DNaseI Hypersensitivity Clusters in 125 cell types from ENCODE
     DNase Clusters V1     Digital DNaseI Hypersensitivity Clusters in 74 cell types (2 reps) from ENCODE
     Txn Factor ChIP     Transcription Factor ChIP-seq (161 factors) from ENCODE with Factorbook Motifs
     Txn Fac ChIP V2     Transcription Factor ChIP-seq from ENCODE V2
CD34 DnaseI Eur. Inst. Oncology/J. C. Venter Inst. Nuclease Accessible Sites
CpG Islands... CpG Islands (Islands < 300 Bases are Light Green)
     CpG Islands     CpG Islands (Islands < 300 Bases are Light Green)
     Unmasked CpG     CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
ENC Chromatin... ENCODE Chromatin Interactions
     GIS ChIA-PET     Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan
     UMass 5C     Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass.
     UW 5C    DownloadsChromatin Interactions by 5C from ENCODE/University of Washington
ENC DNA Methyl... ENCODE DNA Methylation
     HAIB Methyl RRBS     DNA Methylation by Reduced Representation Bisulfite Seq from ENCODE/HudsonAlpha
     HAIB Methyl450     CpG Methylation by Methyl 450K Bead Arrays from ENCODE/HAIB
ENC DNase/FAIRE... ENCODE Open Chromatin by DNaseI HS and FAIRE
     Uniform DNaseI HS     DNaseI Hypersensitivity Uniform Peaks from ENCODE/Analysis
     Open Chrom Synth     DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom(Duke/UNC/UTA)
     Duke DNaseI HS     Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University)
     UNC FAIRE     Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill)
     UW DNaseI DGF     DNaseI Digital Genomic Footprinting from ENCODE/University of Washington
     UW DNaseI HS     DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington
ENC Histone... ENCODE Histone Modification
     Broad ChromHMM     Chromatin State Segmentation by HMM from ENCODE/Broad
     Broad Histone     Histone Modifications by ChIP-seq from ENCODE/Broad Institute
     SYDH Histone     Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard
     UW Histone     Histone Modifications by ChIP-seq from ENCODE/University of Washington
ENC RNA Binding... ENCODE RNA Binding Proteins
     SUNY RIP GeneST     RNA Binding Protein Associated RNA by RIP-chip GeneST from ENCODE/SUNY Albany
     SUNY RIP Tiling     RNA Binding Protein Associated RNA by Tiling Array from ENCODE/SUNY Albany
     SUNY RIP-seq     RIP-seq from ENCODE/SUNY Albany
ENC TF Binding... ENCODE Transcription Factor Binding
     Uniform TFBS     Transcription Factor ChIP-seq Uniform Peaks from ENCODE/Analysis
     HAIB TFBS     Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB
     SYDH TFBS     Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard
     UChicago TFBS     Transcription Factor Binding Sites by Epitope-Tag from ENCODE/UChicago
     UTA TFBS     Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin)
     UW CTCF Binding     CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington
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)
     LaminB1 (Tig3)     NKI LaminB1 DamID Map (log2-ratio scores, Tig3 cells)
     NKI LADs (Tig3)     NKI LADs (Lamina Associated Domains, Tig3 cells)
ORegAnno Regulatory elements from ORegAnno
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    
5% Lowest S Selective Sweep Scan (S): 5% Smallest S scores
Cand. Gene Flow Candidate Regions for Gene Flow from Neandertal to Non-African Modern Humans
H-C Coding Diffs Neandertal Alleles in Human/Chimp Coding Non-synonymous Differences in Human Lineage
Neandertal Mito Neandertal Mitochondrial Sequence (Vi33.16, 2008)
Neandertal Seq Neandertal Sequence Reads
S SNPs SNPS Used for Selective Sweep Scan (S)
Sel Swp Scan (S) Selective Sweep Scan (S) on Neandertal vs. Human Polymorphisms (Z-Score +- Variance)
-   Denisova Assembly and Analysis    
Denisova Seq Denisova High-Coverage Sequence Reads
Denisova Variants Variant Calls from High-Coverage Genome Sequence of an Archaic Denisovan Individual
Mod Hum Variants Variant Calls from 11 Modern Human Genome Sequences
Modern Derived Modern Human Derived, Denisova Ancestral
-   Variation    
Common SNPs(138) Simple Nucleotide Polymorphisms (dbSNP 138) Found in >= 1% of Samples
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
All SNPs(135) Simple Nucleotide Polymorphisms (dbSNP 135)
All SNPs(137) Simple Nucleotide Polymorphisms (dbSNP 137)
All SNPs(138) Simple Nucleotide Polymorphisms (dbSNP 138)
Common SNPs(135) Simple Nucleotide Polymorphisms (dbSNP 135) Found in >= 1% of Samples
Common SNPs(137) Simple Nucleotide Polymorphisms (dbSNP 137) Found in >= 1% of Samples
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
Flagged SNPs(135) Simple Nucleotide Polymorphisms (dbSNP 135) Flagged by dbSNP as Clinically Assoc
Flagged SNPs(137) Simple Nucleotide Polymorphisms (dbSNP 137) Flagged by dbSNP as Clinically Assoc
Flagged SNPs(138) Simple Nucleotide Polymorphisms (dbSNP 138) Flagged by dbSNP as Clinically Assoc
Genome Variants Personal Genome Variants
GIS DNA PET ENCODE Genome Institute of Singapore DNA Paired-End Ditags
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
Mult. SNPs(135) Simple Nucleotide Polymorphisms (dbSNP 135) That Map to Multiple Genomic Loci
Mult. SNPs(137) Simple Nucleotide Polymorphisms (dbSNP 137) That Map to Multiple Genomic Loci
Mult. SNPs(138) Simple Nucleotide Polymorphisms (dbSNP 138) That Map to Multiple Genomic Loci
NumtS Sequence Human NumtS mitochondrial sequence
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
Segmental Dups Duplications of >1000 Bases of Non-RepeatMasked Sequence
Self Chain Human Chained Self Alignments
Simple Repeats Simple Tandem Repeats by TRF
-   DNA Shape    
MGW [Angstrom] DNA Shape - Minor Groove Width [Angstrom]
2nd order MGW DNA Shape - 2nd Order Minor Groove Width
ProT [Degree] DNA Shape - Propeller Twist [Degree]
2nd order ProT DNA Shape - 2nd Order Propeller Twist
Roll [Degree] DNA Shape - Roll [Degree]
2nd order Roll DNA Shape - 2nd Order Roll
HelT [Degree] DNA Shape - Helix Twist [Degree]
2nd order HelT DNA Shape - 2nd Order Helix Twist
ORChID V2 OH Radical Cleavage Intensity Database (ROChID) V2