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Configure Tracks on UCSC Genome Browser: Human Dec. 2013 (GRCh38/hg38)
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Control track and group visibility more selectively below.
-   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    
-   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    
+   Expression    
+   Single Cell RNA-seq    
+   Regulation    
+   Comparative Genomics    
-   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