Control track and group visibility more selectively below.
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| Andrea track |
| User Supplied Track |
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| Base Position |
| Chromosome position in bases. (Clicks here zoom in 3x) |
| 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 |
| p14
GRC Patches |
| GRC Patches: Alt Haplotypes and Fix Sequences |
| 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 |
| Problematic Regions |
| Problematic/special genomic regions for sequencing or very variable regions |
| 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 () |
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| 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 |
| 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) |
| All GENCODE V47 |
| All GENCODE annotations from V47 (Ensembl 113) |
| updated
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 |
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lincRNA TUCP |
| lincRNA and TUCP transcripts |
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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 |
| new
Pseudogenes |
| Pseudogenes and Parents |
| 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 |
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| 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 |
| AlphaMissense |
| AlphaMissense Score for all possible single-basepair mutations (zoom in for 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) |
| CADD 1.7 |
| CADD 1.7 Score for all single-basepair mutations and selected insertions/deletions |
| CADD 1.7 Ins |
| CADD 1.7 Score: Insertions - label is length of insertion |
| CADD 1.7 Del |
| CADD 1.7 Score: Deletions - label is length of deletion |
| 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
CIViC |
| CIViC - Expert & crowd-sourced cancer variant interpretation |
| 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 |
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Coriell CNVs |
| Coriell Cell Line Copy Number Variants |
| updated
COSMIC |
| Catalogue of Somatic Mutations in Cancer V101 |
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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 |
| DECIPHER |
| DECIPHER Population CNVs |
| DECIPHER: Population CNVs |
| DECIPHER SNVs |
| DECIPHER: Chromosomal Imbalance and Phenotype in Humans (SNVs) |
| DECIPHER CNVs |
| DECIPHER CNVs |
| 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 2024 |
| LOVD Variants |
| LOVD: Leiden Open Variation Database Public Variants |
| new
MITOMAP |
| MITOMAP: A human mitochondrial genome database |
| Orphanet |
| Orphadata: Aggregated Data From Orphanet |
| PanelApp |
| Genomics England PanelApp Diagnostics |
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REVEL Scores |
| REVEL Pathogenicity Score for single-base coding mutations (zoom for exact score) |
| SNPedia |
| SNPedia |
| new
Splicing Impact |
| Splicing Impact Prediction Scores and Databases |
| new
SpliceVarDB |
| SpliceVarDB: Experimentally validated splicing variants |
| SpliceAI |
| SpliceAI: Splice Variant Prediction Score |
| AbSplice Scores |
| Aberrant Splicing Prediction Scores |
| TCGA Pan-Cancer |
| TCGA Pan-Cancer mutations: 33 TCGA Cancer Projects Summary (Pan-Can 33) |
| UniProt Variants |
| UniProt/SwissProt Amino Acid Substitutions |
| updated
Variants in Papers |
| Genetic Variants mentioned in scientific publications |
| Mastermind Variants |
| Genomenon Mastermind Variants extracted from full text publications |
| new
enGenome VarChat |
| enGenome VarChat: Literature match and variant's summary |
| Avada Variants |
| Avada Variants extracted from full text publications |
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| 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 |
| gnomAD Variants |
| Genome Aggregation Database (gnomAD) Genome and Exome Variants |
| gnomAD Structural Variants |
| Genome Aggregation Database (gnomAD) - Structural Variants v4.1 |
| gnomAD Rare CNV Variants |
| Genome Aggregation Database (gnomAD) - Rare CNV variants (<1% overall site frequency) v4.1 |
| 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 |
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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 |
| gnomAD v4.1 |
| Genome Aggregation Database (gnomAD) Genome and Exome Variants v4.1 |
| Platinum Genomes |
| Platinum genome variants |
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| 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 |
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| 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 |
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| 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 |
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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 |
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| Blood (PBMC) Hao |
| Peripheral blood mononuclear cells (PBMC) from Hao et al 2020 |
| Blood PBMC Time |
| Blood PBMCs binned by time into experiment from Hao et al 2020 |
| Blood PBMC Phase |
| Blood PBMCs binned by phase of cell cycle from Hao et al 2020 |
| Blood PBMC Donor |
| Blood PBMCs binned by blood donor from Hao et al 2020 |
| Blood PBMC Cells 3 |
| Blood PBMCs binned by cell type (level 3) from Hao et al 2020 |
| Blood PBMC Cells 2 |
| Blood PBMCs binned by cell type (level 2) from Hao et al 2020 |
| Blood PBMC Cells |
| Blood (PBMCs) binned by cell type (level 1) from Hao et al 2020 |
| Colon Wang |
| Colon single cell sequencing from Wang et al 2020 |
| Colon Donor |
| Colon cells binned by organ donor from Wang et al 2020 |
| Colon Cells |
| Colon cells binned by cell type from Wang et al 2020 |
| Cortex Velmeshev |
| Cerebral cortex single cell data from Velmeshev et al 2019 |
| Cortex Sex |
| Cerebral cortex RNA binned by sex of donor from Velmeshev et al 2019 |
| Cortex Sample |
| Cerebral cortex RNA binned by biosample from Velmeshev et al 2019 |
| Cortex Donor |
| Cerebral cortex RNA binned by organ donor from Velmeshev et al 2019 |
| Cortex Diagnosis |
| Cerebral cortex RNA binned by ASD/control diagnosis from Velmeshev et al 2019 |
| Cortex Cells |
| Cerebral cortex RNA binned by cell type from Velmeshev et al 2019 |
| Cross Tissue Nuclei |
| Single Nuclei sequenced across many tissues |
| GTEx Immune Atlas |
| GTEx single nuclei immune expression |
| Cross Tissue Details |
| Cross tissue nuclei full details |
| Cross Tissue Nuclei |
| Cross tissue nuclei RNA by tissue and cell type |
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Fetal Gene Atlas |
| Fetal Gene Atlas from Cao et al 2020 |
| Fetal Sex |
| Fetal Gene Atlas binned by sex from Cao et al 2020 |
| Fetal RT Group |
| Fetal Gene Atlas binned by RT group from Cao et al 2020 |
| Fetal Organ |
| Fetal Gene Atlas binned by organ from Cao et al 2020 |
| Fetal Lineage |
| Fetal Gene Atlas binned by cell lineage and organ from Cao et al 2020 |
| Fetal Exp |
| Fetal Gene Atlas binned by experiment id from Cao et al 2020 |
| Fetal Donor ID |
| Fetal Gene Atlas binned by donor ID from Cao et al 2020 |
| Fetal Cells |
| Fetal Gene Atlas binned by cell type from Cao et al 2020 |
| Fetal Assay |
| Fetal Gene Atlas binned by assay (cell/nucleus) from Cao et al 2020 |
| Heart Cell Atlas |
| Heart single cell RNA data from https://heartcellatlas.com |
| Heart HCA Version |
| Heart cell RNA binned by 10x chemistry version from https://heartcellatlas.org |
| Heart HCA State |
| Heart cell RNA binned by cell state from https://heartcellatlas.org |
| Heart HCA Source |
| Heart cell RNA binned by source (nucleus vs whole cell) from https://heartcellatlas.org |
| Heart HCA Sex |
| Heart cell RNA binned by sex of donor from https://heartcellatlas.org |
| Heart HCA Sample |
| Heart cell RNA binned by biosample from https://heartcellatlas.org |
| Heart HCA Region |
| Heart cell RNA binned by region of collection from https://heartcellatlas.org |
| Heart HCA Donor |
| Heart cell RNA binned by organ donor from https://heartcellatlas.org |
| Heart HCA Cells |
| Heart cell RNA binned by cell type from https://heartcellatlas.org |
| Heart HCA Age |
| Heart cell RNA binned by age group of donor from https://heartcellatlas.org |
| Ileum Wang |
| Ileum single cell sequencing from Wang et al 2020 |
| Ileum Donor |
| Ileum cells binned by organ donor from Wang et al 2020 |
| Ileum Cells |
| Ileum cells binned by cell type from Wang et al 2020 |
| Kidney Stewart |
| Kidney single cell data from Stewart et al 2019 |
| Kidney Project |
| Kidney RNA binned by project from Stewart et al 2019 |
| Kidney Experiment |
| Kidney RNA binned by Experiment from Stewart et al 2019 |
| Kidney Details |
| Kidney RNA binned by detailed cell type from Stewart et al 2019 |
| Kidney Compartment |
| Kidney RNA binned by compartment from Stewart et al 2019 |
| Kidney Cells |
| Kidney RNA binned by merged cell type from Stewart et al 2019 |
| Kidney Broad CT |
| Kidney RNA binned by broad cell type from Stewart et al 2019 |
| Liver MacParland |
| Liver single cell sequencing from MacParland et al 2018 |
| Liver Donor |
| Liver cells binned by organ donor from MacParland et al 2018 |
| Liver Cells |
| Liver cells binned by cell type from MacParland et al 2018 |
| Liver Broad |
| Liver cells binned by broad cell type from MacParland et al 2018 |
| Lung Travaglini |
| Lung cells from from Travaglini et al 2020 |
| Lung Sample FACS |
| Lung cells FACS method binned by sample from Travaglini et al 2020 |
| Lung Sample |
| Lung cells 10x method binned by sample from Travaglini et al 2020 |
| Lung Organ FACS |
| Lung cells FACS method binned by organ from Travaglini et al 2020 |
| Lung Organ |
| Lung cells 10x method binned by organ from Travaglini et al 2020 |
| Lung Mag Sel |
| Lung cells 10x method binned by magnetic.selection from Travaglini et al 2020 |
| Lung Locat FACS |
| Lung cells FACS method binned by location from Travaglini et al 2020 |
| Lung Locat |
| Lung cells 10x method binned by location from Travaglini et al 2020 |
| Lung Label FACS |
| Lung cells FACS method binned by label from Travaglini et al 2020 |
| Lung Half Det FACS |
| Lung cells FACS method binned by merged cell type from Travaglini et al 2020 |
| Lung Half Det |
| Lung cells 10x method binned by halfway detailed cell type from Travaglini et al 2020 |
| Lung Gating FACS |
| Lung cells FACS method binned by gating from Travaglini et al 2020 |
| Lung Donor FACS |
| Lung cells FACS method binned by organ donor from Travaglini et al 2020 |
| Lung Donor |
| Lung cells 10x method binned by organ donor from Travaglini et al 2020 |
| Lung Detail FACS |
| Lung cells FACS method binned by detailed cell type from Travaglini et al 2020 |
| Lung Detail |
| Lung cells 10x method binned by detailed cell type from Travaglini et al 2020 |
| Lung Compart FACS |
| Lung cells FACS method binned by compartment from Travaglini et al 2020 |
| Lung Compart |
| Lung cells 10x method binned by compartment from Travaglini et al 2020 |
| Lung Cells FACS |
| Lung cells FACS method binned by merged cell type from Travaglini et al 2020 |
| Lung Cells |
| Lung cells 10x method binned by merged cell type from Travaglini et al 2020 |
| Muscle De Micheli |
| Muscle single cell data from De Micheli et al 2020 |
| Muscle Sample |
| Muscle RNA binned by biosample from De Micheli et al 2020 |
| Muscle Cells |
| Muscle RNA binned by cell type from De Micheli et al 2020 |
| Pancreas Baron |
| Pancreas single cell sequencing from Baron et al 2016 |
| Pancreas Donor |
| Pancreas cells binned by organ donor from Baron et al 2016 |
| Pancreas Details |
| Pancreas cells binned by detailed cell type from Baron et al 2016 |
| Pancreas Cells |
| Pancreas cells binned by cell type from Baron et al 2016 |
| Pancreas Batch |
| Pancreas cells binned by batch from Baron et al 2016 |
| Placenta Vento-Tormo |
| Placenta and decidua cells from from Vento-Tormo et al 2018 |
| Placenta Stage |
| Placenta and decidua cells binned by placental stage 10x from Vento-Tormo et al 2018 |
| Placenta Mat/Fet Ss2 |
| Placenta and decidua cells binned by maternal/fetal smart-seq2 from Vento-Tormo et al 2018 |
| Placenta Mat/Fet |
| Placenta and decidua cells binned by maternal/fetal 10x from Vento-Tormo et al 2018 |
| Placenta Loc Ss2 |
| Placenta and decidua cells binned by cell location smart-seq2 from Vento-Tormo et al 2018 |
| Placenta Loc |
| Placenta and decidua cells binned by cell location 10x from Vento-Tormo et al 2018 |
| Placenta Detail Ss2 |
| Placenta and decidua cells binned by detailed cell type smart-seq2 from Vento-Tormo et al 2018 |
| Placenta Detail |
| Placenta and decidua cells binned by detailed cell type 10x from Vento-Tormo et al 2018 |
| Placenta Cells Ss2 |
| Placenta and decidua cells binned by cell type smart-seq2 from Vento-Tormo et al 2018 |
| Placenta Cells |
| Placenta and decidua cells binned by cell type 10x from Vento-Tormo et al 2018 |
| Rectum Wang |
| Rectum single cell sequencing from Wang et al 2020 |
| Rectum Donor |
| Rectum cells binned by organ donor from Wang et al 2020 |
| Rectum Cells |
| Rectum cells binned by cell type from Wang et al 2020 |
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Skin Sole-Boldo |
| Skin single cell data from Sole-Boldo et al 2020 |
| Skin Donor |
| Skin single cell RNA binned by skin donor from Sole-Boldo et al 2020 |
| Skin Cell+Age |
| Skin single cell RNA binned by cell type and donor's age from Sole-Boldo et all 2020 |
| Skin Cell |
| Skin single cell RNA binned by cell type from Sole-Boldo et al 2020 |
| Skin Age |
| Skin single cell RNA binned by skin donor's age from Sole-Boldo et al 2020 |
| Tabula Sapiens |
| Tabula Sapiens single cell RNA data from many tissues |
| Tabula Tissue Cell |
| Tabula sapiens RNA by tissue and cell type |
| Tabula Details |
| Tabula sapiens full details view |
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| 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) |
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Layered H3K27Ac |
| H3K27Ac Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE |
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Layered H3K4Me3 |
| H3K4Me3 Mark (Often Found Near Promoters) on 7 cell lines from ENCODE |
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Layered H3K4Me1 |
| H3K4Me1 Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE |
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Transcription |
| Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE |
| TF rPeak Clusters |
| Transcription Factor Representative Peak (rPeak) Clusters (912 factors in 1152 biosamples) from ENCODE 4 |
| 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 |
| updated
VISTA Enhancers |
| VISTA Enhancers |
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| UCSC 100 Vertebrates |
| UCSC 100 Vertebrates - 100 vertebrate genomes aligned with MultiZ by the UCSC Browser Group |
| Zoonomia 241 Placent |
| Zoonomia Alignment - 241 Placental Mammal Genomes aligned by the Zoonomia Project with Cactus |
| UCSC 30 Primates |
| UCSC 30 Primates - 30 primate genomes aligned with MultiZ by the UCSC Browser Group |
| 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 |
| CHM13 alignments |
| CHM13 (GCA_009914755.4) v1_nfLO liftOver alignments |
| Hiller Lab 470 Mammals |
| Hiller Lab 470 Mammals - 470 mammalian genomes aligned with Multiz by Michael Hiller's Group, |
| Zoonomia+Primates 447 |
| Zoonomia+Primates 447 - 447 mammals, including 233 primates, aligned with Cactus, for Kuderna et al. 2023 |
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| 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 |
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