|
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 () |
|
|
updated
GENCODE V47 |
| GENCODE V47 |
updated
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 |
|
|
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 |
Overlaps |
| Revel: Positions with >1 score due to overlapping transcripts (mouseover for details) |
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) |
new
DECIPHER |
| DECIPHER |
DECIPHER SNVs |
| DECIPHER: Chromosomal Imbalance and Phenotype in Humans (SNVs) |
new
DECIPHER DDG2P |
| DECIPHER: Developmental Disorders panel in the Gene2Phenotype database (DDG2P) |
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 |
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 |
|
|
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 |
|
|
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 |
|
|
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 |
|
|
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 |
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 |
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 |
|
|
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 |
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 |
VISTA Enhancers |
| VISTA Enhancers |
|
|
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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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 |
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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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