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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)
p12 Fix Patches Reference Assembly Fix Patch Sequence Alignments
p12 Alt Haplotypes Reference Assembly Alternate Haplotype Sequence Alignments
p12 Assembly Assembly from Fragments
Centromeres Centromere Locations
p12 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
p12 Gap Gap Locations
p12 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
p12 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
     Bismap     Single-read and multi-read mappability after bisulfite conversion
     Umap     Single-read and multi-read mappability by Umap
p12 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    
p12 GENCODE v32 GENCODE v32 Comprehensive Transcript Set (only Basic displayed by default)
updated NCBI RefSeq RefSeq gene predictions from NCBI
p12 Other RefSeq Non-Human RefSeq Genes
p12 updated All GENCODE... All GENCODE transcripts, including comprehensive set and previous version
     All GENCODE V34     All GENCODE annotations from V34 (Ensembl 100)
     All GENCODE V33     All GENCODE annotations from V33 (Ensembl 99)
     All GENCODE V31     All GENCODE annotations from V31 (Ensembl 97)
     All GENCODE V29     All GENCODE annotations from V29 (Ensembl 94)
     All GENCODE V28     All GENCODE annotations from V28 (Ensembl 92)
     All GENCODE V27     All GENCODE annotations from V27 (Ensembl 90)
     All GENCODE V26     All GENCODE annotations from V26 (Ensembl 88)
     All GENCODE V25     All GENCODE transcripts including comprehensive set V25
     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)
p12 AUGUSTUS AUGUSTUS ab initio gene predictions v3.1
CCDS Consensus CDS
CRISPR Targets CRISPR/Cas9 -NGG Targets, whole genome
Geneid Genes Geneid Gene Predictions
p12 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
MANE select v0.9 NCBI RefSeq and Ensembl transcripts from the MANE Project (v0.9)
p12 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
p12 ORFeome Clones ORFeome Collaboration Gene Clones
p12 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 V5... TransMap Alignments Version 5
     TransMap Ensembl     TransMap Ensembl and GENCODE Mappings Version 5
     TransMap RefGene     TransMap RefSeq Gene Mappings Version 5
     TransMap RNA     TransMap GenBank RNA Mappings Version 5
     TransMap ESTs     TransMap EST Mappings Version 5
p12 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
Cancer Gene Expr... Gene Expression in 33 TCGA Cancer Tissues (GENCODE v23)
     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)
new 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
new COVID-19 GWAS GWAS meta-analyses from the COVID-19 Host Genetics Initiative
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
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
-   mRNA and EST    
p12 Human mRNAs Human mRNAs from GenBank
p12 Spliced ESTs Human ESTs That Have Been Spliced
p12 Human ESTs Human ESTs Including Unspliced
p12 Other ESTs Non-Human ESTs from GenBank
p12 Other mRNAs Non-Human mRNAs from GenBank
SIB Alt-Splicing Alternative Splicing Graph from Swiss Institute of Bioinformatics
-   Expression    
p12 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
GTEx Gene V8 Gene Expression in 54 tissues from GTEx RNA-seq of 17382 samples, 948 donors (V8, Aug 2019)
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
EPDnew Promoters Promoters from EPDnew
GNF Atlas 2 GNF Expression Atlas 2
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
p12 ENCODE Regulation... Integrated Regulation from ENCODE
     p12 Transcription     Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE
     p12 Layered H3K4Me1     H3K4Me1 Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE
     p12 Layered H3K4Me3     H3K4Me3 Mark (Often Found Near Promoters) on 7 cell lines from ENCODE
     p12 Layered H3K27Ac     H3K27Ac Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE
     p12 DNase Clusters     DNase I Hypersensitivity Peak Clusters from ENCODE (95 cell types)
     p12 DNase Signal     DNase I Hypersensitivity Signal Colored by Similarity from ENCODE
     p12 DNase HS     DNase I Hypersensitivity in 95 cell types from ENCODE
     TF Clusters     Transcription Factor ChIP-seq Clusters (340 factors, 129 cell types) from ENCODE 3
     TF ChIP     Transcription Factor ChIP-seq Peaks (340 factors in 129 cell types) from ENCODE 3
GeneHancer GeneHancer Regulatory Elements and Gene Interactions
p12 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)
Hi-C and Micro-C Comparison of Micro-C and In situ Hi-C protocols in H1-hESC and HFFc6
ORegAnno Regulatory elements from ORegAnno
RefSeq Func Elems NCBI RefSeq Functional Elements
-   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)
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
Common SNPs(151) Simple Nucleotide Polymorphisms (dbSNP 151) Found in >= 1% of Samples
Common SNPs(150) Simple Nucleotide Polymorphisms (dbSNP 150) Found in >= 1% of Samples
Common SNPs(147) Simple Nucleotide Polymorphisms (dbSNP 147) Found in >= 1% of Samples
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
All SNPs(151) Simple Nucleotide Polymorphisms (dbSNP 151)
All SNPs(150) Simple Nucleotide Polymorphisms (dbSNP 150)
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)
Flagged SNPs(151) Simple Nucleotide Polymorphisms (dbSNP 151) Flagged by dbSNP as Clinically Assoc
Flagged SNPs(150) Simple Nucleotide Polymorphisms (dbSNP 150) Flagged by dbSNP as Clinically Assoc
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(151) Simple Nucleotide Polymorphisms (dbSNP 151) That Map to Multiple Genomic Loci
Mult. SNPs(150) Simple Nucleotide Polymorphisms (dbSNP 150) That Map to Multiple Genomic Loci
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
new 1000 Genomes Trios Thousand Genomes Project Family VCF Trios
1000G Ph3 Vars 1000 Genomes Phase 3 Integrated Variant Calls from IGSR: SNVs and Indels
DGV Struct Var Database of Genomic Variants: Structural Variation (CNV, Inversion, In/del)
gnomAD Variants... Genome Aggregation Database (gnomAD) Genome and Exome Variants
     gnomAD v3     Genome Aggregation Database (gnomAD) Genome Variants v3
     gnomAD v2     Genome Aggregation Database (gnomAD) Genome and Exome Variants v2.1
Platinum Genomes Platinum genome variants
-   Repeats    
p12 RepeatMasker Repeating Elements by RepeatMasker
Interrupted Rpts Fragments of Interrupted Repeats Joined by RepeatMasker ID
RepeatMasker Viz. Detailed Visualization of RepeatMasker Annotations
Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
Segmental Dups Duplications of >1000 Bases of Non-RepeatMasked Sequence
Self Chain Human Chained Self Alignments
p12 Simple Repeats Simple Tandem Repeats by TRF
p12 WM + SDust Genomic Intervals Masked by WindowMasker + SDust