Configure Image
 
image width:pixels
label area width:characters
text size:
font:
style:
Display chromosome ideogram above main graphic
Show light blue vertical guidelines, or light red vertical window separators in multi-region view
Display labels to the left of items in tracks
Display description above each track
Show track controls under main graphic
Next/previous item navigation
Next/previous exon navigation
Show exon numbers
Enable highlight with drag-and-select (if unchecked, drag-and-select always zooms to selection)

Configure Tracks on UCSC Genome Browser: Human Dec. 2013 (GRCh38/hg38)
  Tracks:    Groups:
Control track and group visibility more selectively below.
-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
p13 updated Fix Patches Reference Assembly Fix Patch Sequence Alignments
p13 updated Alt Haplotypes Reference Assembly Alternate Haplotype Sequence Alignments
Assembly Assembly from Fragments
Centromeres Centromere Locations
Chromosome Band Chromosome Bands Localized by FISH Mapping Clones
Clone Ends Mapping of clone libraries end placements
Exome Probesets Exome Capture Probesets and Targeted Region
FISH Clones Clones Placed on Cytogenetic Map Using FISH
Gap Gap Locations
GC Percent GC Percent in 5-Base Windows
GRC Contigs Genome Reference Consortium Contigs
GRC Incident GRC Incident Database
Hg19 Diff Contigs New to GRCh38/(hg38), Not Carried Forward from GRCh37/(hg19)
Hg19 Mapping Hg19 Mappings: UCSC LiftOver and NCBI ReMap
INSDC Accession at INSDC - International Nucleotide Sequence Database Collaboration
LRG Regions Locus Reference Genomic (LRG) Sequences Mapped to Dec. 2013 (GRCh38/hg38) Assembly
Mappability Hoffman Lab Umap and Bismap Mappability
     Umap     Single-read and multi-read mappability by Umap
     Bismap     Single-read and multi-read mappability after bisulfite conversion
RefSeq Acc RefSeq Accession
Restr Enzymes Restriction Enzymes from REBASE
Scaffolds GRCh38 Defined Scaffold Identifiers
Short Match Perfect Matches to Short Sequence ()
STS Markers STS Markers on Genetic (blue) and Radiation Hybrid (black) Maps
-   Genes and Gene Predictions    
GENCODE V38 GENCODE V38
NCBI RefSeq RefSeq genes from NCBI
All GENCODE All GENCODE transcripts, including comprehensive set and previous version
     GENCODE V20 (Ensembl 76)     Gene Annotations from GENCODE Version 20 (Ensembl 76)
     All GENCODE V22     All GENCODE transcripts including comprehensive set V22
     All GENCODE V23     All GENCODE transcripts including comprehensive set V23
     All GENCODE V24     All GENCODE transcripts including comprehensive set V24
     All GENCODE V25     All GENCODE transcripts including comprehensive set V25
     All GENCODE V26     All GENCODE annotations from V26 (Ensembl 88)
     All GENCODE V27     All GENCODE annotations from V27 (Ensembl 90)
     All GENCODE V28     All GENCODE annotations from V28 (Ensembl 92)
     All GENCODE V29     All GENCODE annotations from V29 (Ensembl 94)
     All GENCODE V31     All GENCODE annotations from V31 (Ensembl 97)
     All GENCODE V32     All GENCODE annotations from V32 (Ensembl 98)
     All GENCODE V33     All GENCODE annotations from V33 (Ensembl 99)
     All GENCODE V34     All GENCODE annotations from V34 (Ensembl 100)
     All GENCODE V35     All GENCODE annotations from V35 (Ensembl 101)
     All GENCODE V36     All GENCODE annotations from V36 (Ensembl 102)
     All GENCODE V37     All GENCODE annotations from V37 (Ensembl 103)
     All GENCODE V38     All GENCODE annotations from V38 (Ensembl 104)
CCDS Consensus CDS
CRISPR Targets CRISPR/Cas9 -NGG Targets, whole genome
IKMC Genes Mapped International Knockout Mouse Consortium Genes Mapped to Human Genome
LRG Transcripts Locus Reference Genomic (LRG) Fixed Transcript Annotations
updated MANE select v0.95 NCBI RefSeq and Ensembl transcripts from the MANE Project (v0.95)
MGC Genes Mammalian Gene Collection Full ORF mRNAs
Non-coding RNA RNA sequences that do not code for a protein
     tRNA Genes     Transfer RNA Genes Identified with tRNAscan-SE
     sno/miRNA     C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from snoRNABase and miRBase
     lincRNA TUCP     lincRNA and TUCP transcripts
     lincRNA RNA-Seq     lincRNA RNA-Seq reads expression abundances
Old UCSC Genes Previous Version of UCSC Genes
ORFeome Clones ORFeome Collaboration Gene Clones
Other RefSeq Non-Human RefSeq Genes
Pfam in GENCODE Pfam Domains in GENCODE Genes
new Prediction Archive Gene Prediction Archive
     SIB Genes     Swiss Institute of Bioinformatics Gene Predictions from mRNA and ESTs
     SGP Genes     SGP Gene Predictions Using Mouse/Human Homology
     Genscan Genes     Genscan Gene Predictions
     Geneid Genes     Geneid Gene Predictions
     AUGUSTUS     AUGUSTUS ab initio gene predictions v3.1
RetroGenes V9 Retroposed Genes V9, Including Pseudogenes
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
UCSC Alt Events Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes
UniProt UniProt SwissProt/TrEMBL Protein Annotations
-   Phenotype and Literature    
OMIM Alleles OMIM Allelic Variant Phenotypes
CADD CADD 1.6 Score for all single-basepair mutations and selected insertions/deletions
     Insertions     CADD 1.6 Score: Insertions - label is length of insertion
     Deletions     CADD 1.6 Score: Deletions - label is length of deletion
     CADD     CADD 1.6 Score for all possible single-basepair mutations (zoom in for scores)
Cancer Gene Expr Gene Expression in 33 TCGA Cancer Tissues (GENCODE v23)
     Cancer Transc Expr     Transcript-level Expression in 33 TCGA Cancer Tissues (GENCODE v23)
     Cancer Gene Expr     Gene Expression in 33 TCGA Cancer Tissues (GENCODE v23)
ClinGen ClinGen curation activities (Dosage Sensitivity and Gene-Disease Validity)
deprecated 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
Development Delay Copy Number Variation Morbidity Map of Developmental Delay
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
LOVD Variants Leiden Open Variation Database Public Variants
OMIM Cyto Loci OMIM Cytogenetic Loci Phenotypes - Gene Unknown
OMIM Genes OMIM Gene Phenotypes - Dark Green Can Be Disease-causing
new REVEL Scores REVEL Pathegenicity Score for single-base coding mutations (zoom for exact score)
SNPedia SNPedia
TCGA Pan-Cancer TCGA Pan-Cancer mutations: 33 TCGA Cancer Projects Summary (Pan-Can 33)
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
-   COVID-19    
COVID GWAS v4 COVID risk variants from GWAS meta-analyses by the COVID-19 Host Genetics Initiative (Rel 4, Oct 2020)
COVID GWAS v3 GWAS meta-analyses from the COVID-19 Host Genetics Initiative
Rare Harmful Vars Rare variants underlying COVID-19 severity and susceptibility from the COVID Human Genetics Effort
-   mRNA and EST    
Human ESTs Human ESTs Including Unspliced
Human mRNAs Human mRNAs from GenBank
Other ESTs Non-Human ESTs from GenBank
Other mRNAs Non-Human mRNAs from GenBank
SIB Alt-Splicing Alternative Splicing Graph from Swiss Institute of Bioinformatics
Spliced ESTs Human ESTs That Have Been Spliced
-   Expression    
GTEx Gene V8 Gene Expression in 54 tissues from GTEx RNA-seq of 17382 samples, 948 donors (V8, Aug 2019)
GTEx RNA-Seq Coverage GTEx V8 RNA-Seq Read Coverage by Tissue
new Affy Archive Affymetrix Archive
     Affy U95     Alignments of Affymetrix Consensus/Exemplars from HG-U95
     Affy U133     Alignments of Affymetrix Consensus/Exemplars from HG-U133
     Affy GNF1H     Alignments of Affymetrix Consensus/Exemplars from GNF1H
EPDnew Promoters Promoters from EPDnew
GNF Atlas 2 GNF Expression Atlas 2
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
GWIPS-viz Riboseq Ribosome Profiling from GWIPS-viz
miRNA Tissue Atlas Tissue-Specific microRNA Expression from Two Individuals
-   Regulation    
ENCODE cCREs ENCODE Candidate Cis-Regulatory Elements (cCREs) combined from all cell types
ENCODE Regulation Integrated Regulation from ENCODE
     TF ChIP     Transcription Factor ChIP-seq Peaks (340 factors in 129 cell types) from ENCODE 3
     TF Clusters     Transcription Factor ChIP-seq Clusters (340 factors, 129 cell types) from ENCODE 3
     DNase HS     DNase I Hypersensitivity in 95 cell types from ENCODE
     DNase Signal     DNase I Hypersensitivity Signal Colored by Similarity from ENCODE
     DNase Clusters     DNase I Hypersensitivity Peak Clusters from ENCODE (95 cell types)
     Layered H3K27Ac     H3K27Ac 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 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
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)
GeneHancer GeneHancer Regulatory Elements and Gene Interactions
GTEx cis-eQTLs GTEx High-Confidence cis-eQTLs from CAVIAR
Hi-C and Micro-C Comparison of Micro-C and In situ Hi-C protocols in H1-hESC and HFFc6
new JASPAR Transcription Factors JASPAR Transcription Factor Binding Site Database
ORegAnno Regulatory elements from ORegAnno
RefSeq Func Elems NCBI RefSeq Functional Elements
-   Comparative Genomics    
Conservation Vertebrate Multiz Alignment & Conservation (100 Species)
new Cactus 241-way Cactus Alignment & Conservation of Zoonomia Placental Mammals (241 Species)
Cons 30 Primates Mammals Multiz Alignment & Conservation (27 primates)
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
-   Variation    
dbSNP 153 Short Genetic Variants from dbSNP release 153
new 1000G Archive 1000 Genomes Archive
     1000G Ph3 Vars     1000 Genomes Phase 3 Integrated Variant Calls from IGSR: SNVs and Indels
     1000 Genomes Trios     Thousand Genomes Project Family VCF Trios
dbSNP Archive dbSNP Track Archive
     All SNPs(141)     Simple Nucleotide Polymorphisms (dbSNP 141)
     Common SNPs(141)     Simple Nucleotide Polymorphisms (dbSNP 141) Found in >= 1% of Samples
     Flagged SNPs(141)     Simple Nucleotide Polymorphisms (dbSNP 141) Flagged by dbSNP as Clinically Assoc
     Mult. SNPs(141)     Simple Nucleotide Polymorphisms (dbSNP 141) That Map to Multiple Genomic Loci
     All SNPs(142)     Simple Nucleotide Polymorphisms (dbSNP 142)
     Common SNPs(142)     Simple Nucleotide Polymorphisms (dbSNP 142) Found in >= 1% of Samples
     Flagged SNPs(142)     Simple Nucleotide Polymorphisms (dbSNP 142) Flagged by dbSNP as Clinically Assoc
     Mult. SNPs(142)     Simple Nucleotide Polymorphisms (dbSNP 142) That Map to Multiple Genomic Loci
     All SNPs(144)     Simple Nucleotide Polymorphisms (dbSNP 144)
     Common SNPs(144)     Simple Nucleotide Polymorphisms (dbSNP 144) Found in >= 1% of Samples
     Flagged SNPs(144)     Simple Nucleotide Polymorphisms (dbSNP 144) Flagged by dbSNP as Clinically Assoc
     Mult. SNPs(144)     Simple Nucleotide Polymorphisms (dbSNP 144) That Map to Multiple Genomic Loci
     All SNPs(146)     Simple Nucleotide Polymorphisms (dbSNP 146)
     Common SNPs(146)     Simple Nucleotide Polymorphisms (dbSNP 146) Found in >= 1% of Samples
     Flagged SNPs(146)     Simple Nucleotide Polymorphisms (dbSNP 146) Flagged by dbSNP as Clinically Assoc
     Mult. SNPs(146)     Simple Nucleotide Polymorphisms (dbSNP 146) That Map to Multiple Genomic Loci
     All SNPs(147)     Simple Nucleotide Polymorphisms (dbSNP 147)
     Common SNPs(147)     Simple Nucleotide Polymorphisms (dbSNP 147) Found in >= 1% of Samples
     Flagged SNPs(147)     Simple Nucleotide Polymorphisms (dbSNP 147) Flagged by dbSNP as Clinically Assoc
     Mult. SNPs(147)     Simple Nucleotide Polymorphisms (dbSNP 147) That Map to Multiple Genomic Loci
     Flagged SNPs(150)     Simple Nucleotide Polymorphisms (dbSNP 150) Flagged by dbSNP as Clinically Assoc
     Common SNPs(150)     Simple Nucleotide Polymorphisms (dbSNP 150) Found in >= 1% of Samples
     All SNPs(150)     Simple Nucleotide Polymorphisms (dbSNP 150)
     Mult. SNPs(150)     Simple Nucleotide Polymorphisms (dbSNP 150) That Map to Multiple Genomic Loci
     Mult. SNPs(151)     Simple Nucleotide Polymorphisms (dbSNP 151) That Map to Multiple Genomic Loci
     Flagged SNPs(151)     Simple Nucleotide Polymorphisms (dbSNP 151) Flagged by dbSNP as Clinically Assoc
     All SNPs(151)     Simple Nucleotide Polymorphisms (dbSNP 151)
     Common SNPs(151)     Simple Nucleotide Polymorphisms (dbSNP 151) Found in >= 1% of Samples
dbVar Common Struct Var NCBI Curated Common Structural Variants from dbVar
     dbVar Conflict SV     NCBI dbVar Curated Conflict Variants
     dbVar Common SV     NCBI dbVar Curated Common Structural Variants
DGV Struct Var Database of Genomic Variants: Structural Variation (CNV, Inversion, In/del)
Genome In a Bottle Genome In a Bottle Structural Variants and Trios
gnomAD Variants Genome Aggregation Database (gnomAD) Genome and Exome Variants
     gnomAD v2     Genome Aggregation Database (gnomAD) Genome and Exome Variants v2.1
     gnomAD v3     Genome Aggregation Database (gnomAD) Genome Variants v3
     gnomAD v3.1     Genome Aggregation Database (gnomAD) Genome Variants v3.1
     gnomAD v3.1.1     Genome Aggregation Database (gnomAD) Genome Variants v3.1.1
Platinum Genomes Platinum genome variants
-   Repeats    
RepeatMasker Repeating Elements by RepeatMasker
Interrupted Rpts Fragments of Interrupted Repeats Joined by RepeatMasker ID
Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
RepeatMasker Viz. Detailed Visualization of RepeatMasker Annotations
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