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Configure Tracks on UCSC Genome Browser: Human Dec. 2013 (GRCh38/hg38)
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-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Alt Map... GRCh38 Haplotype to Reference Sequence Mapping Correspondence
     Alt Map     GRCh38 Alignments to the Alternate Sequences/Haplotypes
     Haplotypes     GRCh38 Haplotype to Reference Sequence Mapping Correspondence
Assembly Assembly from Fragments
Centromeres Centromere Locations
Chromosome Band Chromosome Bands Localized by FISH Mapping Clones
Clone Ends Mapping of clone libraries end placements
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
GRC Patch Release GRCh38 patch release 9, alternate sequences and reference sequence patches
Hg19 Diff Contigs New to GRCh38/(hg38), Not Carried Forward from GRCh37/(hg19)
INSDC Accession at INSDC - International Nucleotide Sequence Database Collaboration
LRG Regions Locus Reference Genomic (LRG) Sequences Mapped to Dec. 2013 (GRCh38/hg38) Assembly
Restr Enzymes Restriction Enzymes from REBASE
Scaffolds GRCh38 Defined Scaffold Identifiers
Short Match Perfect Matches to Short Sequence (TATAWAAR)
STS Markers STS Markers on Genetic (blue) and Radiation Hybrid (black) Maps
-   Genes and Gene Predictions    
GENCODE v24 GENCODE v24 Comprehensive Transcript Set (only Basic displayed by default)
NCBI RefSeq RefSeq gene predictions from NCBI
All GENCODE... All GENCODE transcripts include comprehensive set and previous versions
     All GENCODE V26     All GENCODE annotations from V26 (Ensembl 88)
     All GENCODE V24     All GENCODE transcripts including comprehensive set V24
     All GENCODE V23     All GENCODE transcripts including comprehensive set V23
     All GENCODE V22     All GENCODE transcripts including comprehensive set V22
     GENCODE V20 (Ensembl 76)     Gene Annotations from GENCODE Version 20 (Ensembl 76)
AUGUSTUS AUGUSTUS ab initio gene predictions v3.1
CCDS Consensus CDS
CRISPR... CRISPR/Cas9 Sp. Pyog. target sites
     CRISPR Regions     Genome regions processed to find CRISPR/Cas9 target sites (exons +/- 200 bp)
     CRISPR Targets     CRISPR/Cas9 -NGG Targets
Geneid Genes Geneid Gene Predictions
Genscan Genes Genscan Gene Predictions
IKMC Genes Mapped International Knockout Mouse Consortium Genes Mapped to Human Genome
LRG Transcripts Locus Reference Genomic (LRG) Fixed Transcript Annotations
MGC Genes Mammalian Gene Collection Full ORF mRNAs
Non-coding RNA... RNA sequences that do not code for a protein
     lincRNA RNA-Seq     lincRNA RNA-Seq reads expression abundances
     lincRNA TUCP     lincRNA and TUCP transcripts
     sno/miRNA     C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from snoRNABase and miRBase
     tRNA Genes     Transfer RNA Genes Identified with tRNAscan-SE
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
RetroGenes V9 Retroposed Genes V9, Including Pseudogenes
SGP Genes SGP Gene Predictions Using Mouse/Human Homology
SIB Genes Swiss Institute of Bioinformatics Gene Predictions from mRNA and ESTs
TransMap... TransMap Alignments Version 4
     TransMap Ensembl     TransMap Ensembl Mappings Version 4
     TransMap RefGene     TransMap RefSeq Gene Mappings Version 4
     TransMap RNA     TransMap GenBank RNA Mappings Version 4
     TransMap ESTs     TransMap EST Mappings Version 4
UCSC Alt Events Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes
UniProt UniProt/SwissProt Annotations
-   Phenotype and Literature    
OMIM Alleles OMIM Allelic Variants
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
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
OMIM Genes OMIM Genes - Dark Green Can Be Disease-causing
OMIM Pheno Loci OMIM Phenotypes - Gene Unknown
UniProt Variants UniProt/SwissProt Amino Acid Substitutions
-   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 Expression in 53 tissues from GTEx RNA-seq of 8555 samples (570 donors)
Affy GNF1H Alignments of Affymetrix Consensus/Exemplars from GNF1H
Affy U133 Alignments of Affymetrix Consensus/Exemplars from HG-U133
Affy U95 Alignments of Affymetrix Consensus/Exemplars from HG-U95
GNF Atlas 2 GNF Expression Atlas 2
GWIPS-viz Riboseq Ribosome Profiling from GWIPS-viz
-   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 Regulatory Elements) on 7 cell lines from ENCODE
     DNase Clusters     DNase I Hypersensitivity Peak Clusters from ENCODE (95 cell types)
     DNase Signal     DNase I Hypersensitivity Signal Colored by Similarity from ENCODE
     DNase HS     DNase I Hypersensitivity in 95 cell types from ENCODE
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)
ORegAnno Regulatory elements from ORegAnno
-   Comparative Genomics    
Conservation Vertebrate Multiz Alignment & Conservation (100 Species)
Cons 7 Verts Multiz Alignment & Conservation (7 Species)
Cons 20 Mammals Primates Multiz Alignment & Conservation (20 Species)
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    
Common SNPs(147) Simple Nucleotide Polymorphisms (dbSNP 147) Found in >= 1% of Samples
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)
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
DGV Struct Var Database of Genomic Variants: Structural Variation (CNV, Inversion, In/del)
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
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(141) Simple Nucleotide Polymorphisms (dbSNP 141) That Map to Multiple Genomic Loci
-   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