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Configure Tracks on UCSC Genome Browser: Human Dec. 2013 (GRCh38/hg38)
  Tracks:    Groups:
Control track and group visibility more selectively below.
-   Hub: VISIONS trackHub    
human_retina_ATAC human_retina_adult_ATAC
human_retina_CREB human_retina_adult_CREB
human_retina_CRX human_retina_adult_CRX
human_retina_CTCF human_retina_adult_CTCF
human_retina_H3K27ac human_retina_adult_H3K27ac
human_retina_H3K4me2 human_retina_adult_H3K4me2
human_retina_MEF2D human_retina_adult_MEF2D
human_retina_NRL human_retina_adult_NRL
human_retina_OTX2 human_retina_adult_OTX2
human_retina_RORB human_retina_adult_RORB
N > A Impact Score N > A Predicted Impact Score
N > C Impact Scores N > C Predicted Impact Scores
N > G Impact Scores N > G Predicted Impact Scores
N > T Impact Scores N > T Predicted Impact Scores
Summed Negative Impact Scores Summed Negative Predicted Impact Scores
-   Custom Tracks    
dSVM Windows dSVM Windows
-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
p14 Fix Patches Reference Assembly Fix Patch Sequence Alignments
p14 Alt Haplotypes Reference Assembly Alternate Haplotype Sequence Alignments
Assembly Assembly from Fragments
Assembly Tracks Assembly identifiers, clones, and markers
     STS Markers     STS Markers on Genetic (blue) and Radiation Hybrid (black) Maps
     Scaffolds     GRCh38 Defined Scaffold Identifiers
     GRC Contigs     Genome Reference Consortium Contigs
     FISH Clones     Clones Placed on Cytogenetic Map Using FISH
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
Gap Gap Locations
GC Percent GC Percent in 5-Base Windows
GRC Incident GRC Incident Database
Hg19 Diff Contigs New to GRCh38/(hg38), Not Carried Forward from GRCh37/(hg19)
INSDC Accession at INSDC - International Nucleotide Sequence Database Collaboration
LiftOver & ReMap UCSC LiftOver and NCBI ReMap: Genome alignments to convert annotations to hg19
LRG Regions Locus Reference Genomic (LRG) / RefSeqGene 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
updated Problematic Regions Problematic/special genomic regions for sequencing or very variable regions
    new GIAB Problematic Regions     Difficult regions from GIAB via NCBI
     Highly Reproducible Regions     Highly Reproducible genomic regions for sequencing
     Problematic Regions     Problematic/special genomic regions for sequencing or very variable regions
Recomb Rate Recombination rate: Genetic maps from deCODE and 1000 Genomes
     Recomb. 1k Genomes     Recombination rate: 1000 Genomes, lifted from hg19 (PR Loh)
     Recomb. deCODE Dmn     Recombination rate: De-novo mutations found in deCODE samples
     Recomb. deCODE Evts     Recombination events in deCODE Genetic Map (zoom to < 10kbp to see the events)
     Recomb. deCODE Mat     Recombination rate: deCODE Genetics, maternal
     Recomb. deCODE Pat     Recombination rate: deCODE Genetics, paternal
     Recomb. deCODE Avg     Recombination rate: deCODE Genetics, average from paternal and maternal (mat for chrX)
RefSeq Acc RefSeq Accession
Restr Enzymes Restriction Enzymes from REBASE
Short Match Perfect Matches to Short Sequence ()
-   Genes and Gene Predictions    
updated GENCODE V47 GENCODE V47
NCBI RefSeq RefSeq genes from NCBI
CCDS Consensus CDS
CRISPR Targets CRISPR/Cas9 -NGG Targets, whole genome
GENCODE Archive GENCODE Archive
     GENCODE V36     GENCODE V36
     GENCODE V38     GENCODE V38
     GENCODE V39     GENCODE V39
     GENCODE V43     GENCODE V43
     GENCODE V44     GENCODE V44
     GENCODE V45     GENCODE V45
     GENCODE V46     GENCODE V46
updated GENCODE Versions Container of all new and previous GENCODE releases
     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 V30     All GENCODE annotations from V30 (Ensembl 96)
     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)
     All GENCODE V39     All GENCODE annotations from V39 (Ensembl 105)
     All GENCODE V40     All GENCODE annotations from V40 (Ensembl 106)
     All GENCODE V41     All GENCODE annotations from V41 (Ensembl 107)
     All GENCODE V42     All GENCODE annotations from V42 (Ensembl 108)
     All GENCODE V43     All GENCODE annotations from V43 (Ensembl 109)
     All GENCODE V44     All GENCODE annotations from V44 (Ensembl 110)
     All GENCODE V45     All GENCODE annotations from V45 (Ensembl 111)
     All GENCODE V46     All GENCODE annotations from V46 (Ensembl 112)
    new All GENCODE V47     All GENCODE annotations from V47 (Ensembl 113)
HGNC HUGO Gene Nomenclature
IKMC Genes Mapped International Knockout Mouse Consortium Genes Mapped to Human Genome
LRG Transcripts Locus Reference Genomic (LRG) / RefSeqGene Fixed Transcript Annotations
MANE MANE Select Plus Clinical: Representative transcript from RefSeq & GENCODE
MGC/ORFeome Genes MGC/ORFeome Full ORF mRNA Clones
     ORFeome Clones     ORFeome Collaboration Gene Clones
     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
Other RefSeq Non-Human RefSeq Genes
Pfam in GENCODE Pfam Domains in GENCODE Genes
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 Online Mendelian Inheritance in Man
     OMIM Cyto Loci     OMIM Cytogenetic Loci Phenotypes - Gene Unknown
     OMIM Genes     OMIM Gene Phenotypes - Dark Green Can Be Disease-causing
     OMIM Alleles     OMIM Allelic Variant Phenotypes
AbSplice Scores Aberrant Splicing Prediction Scores
CADD 1.6 CADD 1.6 Score for all single-basepair mutations and selected insertions/deletions
     CADD 1.6 Ins     CADD 1.6 Score: Insertions - label is length of insertion
     CADD 1.6 Del     CADD 1.6 Score: Deletions - label is length of deletion
     CADD 1.6     CADD 1.6 Score for all possible single-basepair mutations (zoom in for scores)
new CADD 1.7 CADD 1.7 Score for all single-basepair mutations and selected insertions/deletions
    new CADD 1.7 Ins     CADD 1.7 Score: Insertions - label is length of insertion
    new CADD 1.7 Del     CADD 1.7 Score: Deletions - label is length of deletion
    new CADD 1.7     CADD 1.7 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)
new ClinGen ClinGen curation activities (Dosage Sensitivity and Gene-Disease Validity)
ClinGen CNVs Clinical Genome Resource (ClinGen) CNVs
ClinVar Variants ClinVar Variants
Constraint scores Human constraint scores
     UKB Depl. Rank Score     UK Biobank / deCODE Genetics Depletion Rank Score
     HMC     HMC - Homologous Missense Constraint Score on PFAM domains
     JARVIS     JARVIS: score to prioritize non-coding regions for disease relevance
Coriell CNVs Coriell Cell Line Copy Number Variants
COSMIC Catalogue of Somatic Mutations in Cancer V98
COSMIC Regions Catalogue of Somatic Mutations in Cancer V82
COVID Data Container of SARS-CoV-2 data
     COVID Rare Harmful Var     Rare variants underlying COVID-19 severity and susceptibility from the COVID Human Genetics Effort
     COVID GWAS v3     GWAS meta-analyses from the COVID-19 Host Genetics Initiative
     COVID GWAS v4     COVID risk variants from GWAS meta-analyses by the COVID-19 Host Genetics Initiative (Rel 4, Oct 2020)
DECIPHER CNVs DECIPHER CNVs
DECIPHER SNVs DECIPHER: Chromosomal Imbalance and Phenotype in Humans (SNVs)
Development Delay Copy Number Variation Morbidity Map of Developmental Delay
Dosage Sensitivity pHaplo and pTriplo dosage sensitivity map from Collins et al 2022
GenCC GenCC: The Gene Curation Coalition Annotations
Gene Interactions Protein Interactions from Curated Databases and Text-Mining
GeneReviews GeneReviews
GWAS Catalog NHGRI-EBI Catalog of Published Genome-Wide Association Studies
HGMD public Human Gene Mutation Database - Public Version Dec 2023
LOVD Variants LOVD: Leiden Open Variation Database Public Variants
Orphanet Orphadata: Aggregated Data From Orphanet
PanelApp Genomics England PanelApp Diagnostics
REVEL Scores REVEL Pathogenicity Score for single-base coding mutations (zoom for exact score)
SNPedia SNPedia
new SpliceAI SpliceAI: Splice Variant Prediction Score
     SpliceAI indels (masked)     SpliceAI Indels (masked)
     SpliceAI SNVs (masked)     SpliceAI SNVs (masked)
     SpliceAI indels     SpliceAI Indels (unmasked)
     SpliceAI SNVs     SpliceAI SNVs (unmasked)
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
     Avada Variants     Avada Variants extracted from full text publications
-   Human Pangenome - HPRC    
Multiple Alignment Multiple Alignment on 90 human genome assemblies
Pairwise Alignments Human Genomes, Chain/Net pairwise alignments, as mapped by the HPRC project
Rearrangements Rearrangements including indels, inversions, and duplications
Short Variants Short Variants
     HPRC Variants > 3bp     HPRC VCF variants filtered for items size > 3bp
     HPRC Variants <= 3bp     HPRC VCF variants filtered for items size <= 3bp
     HPRC All Variants     HPRC variants decomposed from hprc-v1.0-mc.grch38.vcfbub.a100k.wave.vcf.gz (Liao et al 2023), no size filtering
-   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
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
Single Cell Expression Single cell RNA expression levels cell types from many organs
+   Single Cell RNA-seq    
-   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)
FANTOM5 FANTOM5: Mapped transcription start sites (TSS) and their usage
     TSS activity (TPM)     FANTOM5: TSS activity per sample (TPM)
     TSS activity - read counts     FANTOM5: TSS activity per sample read counts
     Max counts of CAGE reads     FANTOM5: Max counts of CAGE reads
     Total counts of CAGE reads     FANTOM5: Total counts of CAGE reads
     TSS peaks     FANTOM5: DPI peak, robust set
GeneHancer GeneHancer Regulatory Elements and Gene Interactions
GTEx cis-eQTLs GTEx fine-mapped cis-eQTLs
Hi-C and Micro-C Comparison of Micro-C and In situ Hi-C protocols in H1-hESC and HFFc6
JASPAR Transcription Factors JASPAR Transcription Factor Binding Site Database
ORegAnno Regulatory elements from ORegAnno
RefSeq Func Elems NCBI RefSeq Functional Elements
ReMap ChIP-seq ReMap Atlas of Regulatory Regions
VISTA Enhancers VISTA Enhancers
-   Comparative Genomics    
Conservation Vertebrate Multiz Alignment & Conservation (100 Species)
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
Cactus 447-way Cactus Alignment & Conservation on 447 mammal species, including Zoonomia genomes
CHM13 alignments CHM13 (GCA_009914755.4) v1_nfLO liftOver alignments
Multiz 470-way Multiz Alignment & Conservation (470 mammals)
-   Variation    
dbSNP 155 Short Genetic Variants from dbSNP release 155
1000 Genomes 1000 Genomes Phase 3
     1000G Ph3 Vars     1000 Genomes Phase 3 Integrated Variant Calls from IGSR: SNVs and Indels
     1000 Genomes Trios     Thousand Genomes Project Family VCF Trios
Array Probesets Microarray Probesets
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
     dbSNP 153     Short Genetic Variants from dbSNP release 153
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
new gnomAD Variants Genome Aggregation Database (gnomAD) Genome and Exome Variants
    new gnomAD Structural Variants     Genome Aggregation Database (gnomAD) - Structural Variants v4.1
    new gnomAD Rare CNV Variants     Genome Aggregation Database (gnomAD) - Rare CNV variants (<1% overall site frequency) v4.1
    new gnomAD Constraint Metrics     Genome Aggregation Database (gnomAD) Predicted Constraint Metrics (LOEUF, pLI, and Z-scores)
     gnomAD Mut Constraint     Gnocchi: Genome Aggregation Database (gnomAD) non-coding constraint of haploinsufficient variation, includes chrX
     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
    new gnomAD v4.1     Genome Aggregation Database (gnomAD) Genome and Exome Variants v4.1
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
NuMTs Sequence Nuclear mitochondrial DNA segments
RepeatMasker Viz. Detailed Visualization of RepeatMasker Annotations
Segmental Dups Duplications of >1000 Bases of Non-RepeatMasked Sequence
Self Alignment Human Chained Self Alignments
Simple Repeats Simple Tandem Repeats by TRF
WM + SDust Genomic Intervals Masked by WindowMasker + SDust