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| Blue ticks every 10000 bases |
| even |
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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 |
| Panmask Easy 151b |
| Panmask Easy 151b Regions: High accuracy for variant calling |
| 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 V50 |
| GENCODE V50 |
| 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 V47 |
| GENCODE V47 |
| GENCODE V48 |
| GENCODE V48 |
| GENCODE V49 |
| GENCODE V49 |
| 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) |
| All GENCODE V48 |
| All GENCODE annotations from V48 (Ensembl 114) |
| All GENCODE V49 |
| All GENCODE annotations from V49 (Ensembl 115) |
| All GENCODE V50 |
| All GENCODE annotations from V50 (Ensembl 116) |
| 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 |
| NMD Escape |
| NMD Escape: Predicted regions where premature termination codons escape NMD |
| NMDetective-B PTC |
| NMDetective-B: Decision tree NMD efficiency for first out-of-frame PTC |
| NMDetective-A PTC |
| NMDetective-A: Random forest NMD efficiency for first out-of-frame PTC |
| NMDetective-B |
| NMDetective-B: Decision tree prediction of NMD efficiency (Lindeboom 2016) |
| NMDetective-A |
| NMDetective-A: Random forest prediction of NMD efficiency (Lindeboom 2016) |
| NMDetective-AI variants |
| NMDetective-AI: Per-stop-gain predictions for every codon (MANE Select only) |
| NMDetective-AI |
| NMDetective-AI: Deep-learning NMD efficiency prediction per position (MANE Select only) |
| NMD Escape RefSeq |
| NMD escape predictions: NCBI RefSeq Curated transcripts |
| NMD Escape Gencode |
| NMD escape predictions: Gencode transcripts |
| NMD Escape MANE |
| NMD escape predictions: MANE Select Plus Clinical transcripts |
| Non-canonical ORFs |
| Non-canonical Open Reading Frames |
| UTRannotator uORFs |
| ncORFs: Upstream Open Reading Frames (uORFs) from UTRannotator |
| OpenProt (MS>=2) |
| ncORFs: OpenProt - proteins with at least 2 MS peptides v2.2 |
| OpenProt |
| ncORFs: OpenProt - alternative and reference proteins v2.2 |
| nuORFdb |
| ncORFs: nuORFdb - non-canonical ORFs from nuORFdb v1.2 |
| MetamORF |
| ncORFs: MetamORF - meta-database of non-canonical ORFs |
| GENCODE Phase II ncORFs Prim |
| ncORFs: GENCODE Phase II non-canonical ORFs - primary |
| GENCODE Phase II ncORFs Compr |
| ncORFs: GENCODE Phase II non-canonical ORFs - comprehensive |
| GENCODE Phase I ncORFs |
| ncORFs: GENCODE Phase I non-canonical ORFs with Ribo-seq, peptide evidence |
| 5ULTRA uORFs |
| ncORFs: uORFs in MANE Select transcripts from 5ULTRA |
| 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 |
| 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 |
| 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) |
| 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 |
| COSMIC |
| Catalogue of Somatic Mutations in Cancer V101 |
|
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 |
| updated
Deleteriousness Predictions |
| Variant Deleteriousness / Variant Impact Prediction Scores |
| PromoterAI |
| PromoterAI Promoter Variant Impact Scores (zoom for exact score) |
| PrimateAI-3D |
| PrimateAI-3D Pathogenicity Predictions for Missense Variants |
| new
popEVE Scores |
| popEVE proteome-wide missense deleteriousness scores |
| MutScore |
| MutScore: Variant clustering in 3D protein structures |
| new
EVE Scores |
| EVE missense variant effect scores |
| new
ClinPred |
| ClinPred Pathogenicity Score for missense variants (zoom for exact score) |
| new
AlphaGenome |
| AlphaGenome Variant Impact (AVI) score for all single-base substitutions |
| Development Delay |
| Copy Number Variation Morbidity Map of Developmental Delay |
| Dosage Sensitivity |
| pHaplo and pTriplo dosage sensitivity map from Collins et al 2022 |
| G2P Project |
| Gene2Phenotype Project |
| 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 2025 |
| Human Gene Mutation Database - Public Version 2025 |
| LOVD Variants |
| LOVD: Leiden Open Variation Database Public Variants |
| MITOMAP |
| MITOMAP: A human mitochondrial genome database |
| Orphanet |
| Orphadata: Aggregated Data From Orphanet |
| PanelApp |
| Genomics England and Australia PanelApp Diagnostics |
|
REVEL Scores |
| REVEL Pathogenicity Score for single-base coding mutations (zoom for exact score) |
| SNPedia |
| SNPedia |
| Splicing Impact |
| Splicing Impact Prediction Scores and Databases |
| SpliceVarDB |
| SpliceVarDB: Experimentally validated splicing variants |
| AbSplice Scores |
| Aberrant Splicing Prediction Scores |
| SpliceAI Wildtype |
| SpliceAI Wildtype: Splicing of the reference genome sequence |
| SpliceAI Variants |
| SpliceAI: Splice Variant Prediction Score |
| 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 |
| Varaico Variants (suppl) |
| Varaico Variants extracted from Supplementary Data |
| Varaico Variants |
| Varaico Variants extracted from full text publications, titles, and abstracts |
| PubTator Variants |
| dbSNP variants and other genetic variants grounded to dbSNP by tmVar; collected by PubTator3 |
| enGenome VarChat |
| enGenome VarChat: Literature match and variant's summary |
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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 |
| Ancient Hominids |
| Ancient Hominid DNA Variants |
| Arcseqhub Neanderthal |
| Ancient Hominids: Arcseqhub Neanderthal VCF Variants |
| Arcseqhub Denisovan |
| Ancient Hominids: Arcseqhub Denisovan VCF Variants |
| Array Probesets |
| Microarray Probesets and OGM sites |
| 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 Struct Var |
| NCBI dbVar Structural Variants |
| dbVar Somatic SV |
| NCBI dbVar Somatic Structural Variants |
| dbVar Other SV |
| NCBI dbVar Other Structural Variants |
| 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 |
| updated
gnomAD |
| Genome Aggregation Database (gnomAD) |
| gnomAD Structural Variants |
| Genome Aggregation Database (gnomAD) - Structural Variants v4.1 |
| gnomAD STR |
| Genome Aggregation Database (gnomAD) - Short Tandem Repeat Genotypes at Disease-Associated Loci |
| gnomAD Rare CNV Variants |
| Genome Aggregation Database (gnomAD) - Rare CNV variants (<1% overall site frequency) v4.1 |
| gnomAD pext |
| Genome Aggregation Database (gnomAD) Proportion Expression Across Transcript Scores (pext) |
| new
gnomAD MPC overlaps |
| gnomAD MPC v4.1.1 - variants scored against multiple transcripts |
| new
gnomAD MPC |
| gnomAD Missense Deleteriousness Prediction by Constraint (MPC) v4.1.1 |
| updated
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 v3 Genome Coverage |
| Genome Aggregation Database (gnomAD) Genome Sample Coverage v3.0.1 |
| gnomAD v4 Exome Coverage |
| Genome Aggregation Database (gnomAD) Exome Sample Coverage v4.0 |
|
gnomAD v2 |
| Genome Aggregation Database (gnomAD) Genome and Exome Variants v2.1 |
| gnomAD v3 |
| Genome Aggregation Database (gnomAD) Genome Variants v3 |
| Deprecated: gnomAD v3.1 |
| Deprecated: Genome Aggregation Database (gnomAD) Genome Variants v3.1 |
| gnomAD v3.1.1 |
| Genome Aggregation Database (gnomAD) Genome Variants v3.1.1 |
| updated
gnomAD v4.1.1 |
| Genome Aggregation Database (gnomAD) Genome and Exome Variants v4.1.1 |
| new
Long-read SVs |
| Structural Variants from Long-read Sequencing |
| SVatalog 101 SVs |
| Structural Variants from 101 SVatalog samples (cystic fibrosis; Chirmade et al. 2026) |
| GA4K 502 SVs |
| Structural Variants from 502 GA4K samples (Children's Mercy, pediatric rare disease; PacBio HiFi) |
| Arab APR 53 SVs |
| Structural Variants from 53 Arab Pangenome Reference samples (UAE-resident; HiFi + ONT) |
| ToMMo 333 SVs |
| Structural Variants from 333 Japanese samples (ToMMo, 111 trios) |
| CPC 58 SVs |
| Structural Variants from 58 Chinese Pangenome Consortium samples (CPC-only; HiFi) |
| Han 945 SVs |
| Structural Variants from 945 Han Chinese samples (long-read) |
| deCODE 3622 SVs |
| Structural Variants from 3,622 deCODE samples (Icelandic; Oxford Nanopore) |
| CARD 351 SVs |
| Structural Variants from 351 NIH CARD brain samples (ONT; NABEC + HBCC) |
| HGSVC2 32 SVs |
| Structural Variants from 32 HGSVC2 assemblies (freeze 4; Ebert et al. 2021) |
| HGSVC3 65 SVs |
| Structural Variants from 65 HGSVC3 assemblies (diverse ancestry; HiFi + ONT) |
| HPRC v2.1 233 SVs |
| Structural Variants from 233 HPRC v2.1 assemblies (minigraph-cactus pangenome graph) |
| 1KG Boehringer ONT SVs |
| Structural Variants from 888 1000 Genomes samples (Boehringer ONT; Noyvert et al. 2025) |
| 1KG UW ONT SVs |
| Structural Variants from 100 1000 Genomes samples (University of Washington ONT; Gustafson et al. 2024) |
| 1KG Vienna ONT SVs |
| Structural Variants from 1,019 1000 Genomes samples (Vienna ONT; Schloissnig et al. 2025) |
| 1KG Lin 1218 SVs |
| Structural Variants from 1,218 1000 Genomes samples (long-read merge; Lin et al.) |
| AoU 1027 SVs |
| Structural Variants from 1,027 All of Us samples (PacBio HiFi) |
| CoLoRSdb 1427 SVs |
| Structural Variants from 1,427 CoLoRSdb samples (Consortium of Long-Read Sequencing, PacBio HiFi) |
| All LR SVs merged |
| All long-read SVs merged across subtracks by exact position, with per-database AC |
| new
Mobile Element Insertions |
| Mobile Element Insertions (polymorphic) |
| SweGen 1000 MEIs |
| Mobile element insertions in 1,000 SweGen Swedish samples (MELT, lifted from GRCh37) |
| HMEID 5675 MEIs |
| Mobile element insertions in 5,675 NyuWa + 1000 Genomes samples (HMEID v1.1) |
| HGSVC3 65 MEIs |
| Mobile element insertions in 65 HGSVC3 long-read assembled samples |
| euL1db Ref L1HS |
| euL1db: L1-HS copies present in the reference genome (Mir 2015) |
| euL1db Insertions |
| euL1db: curated L1-HS insertion polymorphisms (Mir 2015) |
| Phased Variants |
| Phased Variants from various sequencing projects |
| gnomAD HGDP+1000G 4k WGS |
| Phased Variants: gnomAD HGDP + 1000 genomes callset - 4094 whole genomes, 80 populations |
| Simons Genome Diversity Project 0.3k WGS |
| Phased Variants: Simons Genome Diversity Project - 279 samples, unmixed populations |
| Human Genome Diversity Project, 1k WGS |
| Phased Variants: Human Genome Diversity Project (HGDP) - 1043 samples, isolated populations |
| Mexico Biobank, 6k Array |
| Phased Variants: Mexico Biobank 6k Array |
| Platinum Genomes |
| Platinum genome variants |
| new
SNV Frequencies |
| SNV Frequencies from various cohorts or national projects |
| Canada HostSeq 10.5k WGS |
| SNV Frequencies: gnomAD-Canada HostSeq - 10,487 WGS, Canadian COVID-19 cohort |
| UK Biobank 361k imputed |
| SNV Frequencies: UK Biobank Genotypes - 361k White British, Neale Lab Round 2 imputed |
| Taiwan TPMI Axiom array |
| SNV Frequencies: Taiwan Precision Medicine Initiative - Axiom TPM1 chip, Han Chinese |
| Sweden SweGen 1k WGS |
| SNV Frequencies: Sweden SweGen - 1k WGS |
| SVatalog 101 WGS |
| SNV Frequencies: GWAS SVatalog - 101 samples, 10X Genomics linked-read SNPs |
| Singapore NPM 9.7k WGS |
| SNV Frequencies: NPM Singapore - 9,770 WGS samples |
| SGDP 279 WGS |
| SNV Frequencies: Simons Genome Diversity Project - 279 WGS, 142 populations |
| SFARI SPARK 140k WES |
| SNV Frequencies: SFARI SPARK - 140k WES |
| SFARI SPARK iWGS v1.1 Pilot |
| SNV Frequencies: SFARI SPARK iWGS v1.1 Pilot - 12,519 WGS |
| SCHEMA 121k WES Sz |
| SNV Frequencies: SCHEMA Schizophrenia Exome Meta-Analysis - WES 24k cases, 97k controls |
| Saudi Genome 302 WGS |
| SNV Frequencies: Saudi Genome Project - 302 WGS samples |
| NHLBI TOPMed 10 151k WGS |
| SNV Frequencies: NHLBI TOPMed - 151k WGS |
| Netherlands GoNL 498 WGS |
| SNV Frequencies: Genome of the Netherlands - 250 Dutch trios |
| NCBI ALFA 408k mixed |
| SNV Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array, 163M variants |
| Mexico Biobank 6k Array |
| SNV Frequencies: Mexico Biobank - 6,011 individuals, genotyping array |
| Korea KOVA 5.3k mixed |
| SNV Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.4k WES |
| Japan ToMMo 61k WGS |
| SNV Frequencies: Japan 61k - ToMMo SNV+Indels |
| India IndiGenomes 1k WGS |
| SNV Frequencies: IndiGenomes India - 1,029 samples |
| India GenomeIndia 9.7k WGS |
| SNV Frequencies: GenomeIndia - 9,768 WGS, 83 populations (Bhattacharyya 2025) |
| HRC 30k WGS |
| SNV Frequencies: Haplotype Reference Consortium - 30k WGS (excl. 1000 Genomes) |
| GREGoR R4 3.6k WGS |
| SNV Frequencies: GREGoR Consortium - Release 4, 3,624 WGS samples, rare disease families |
| gnomAD HGDP+1kG 4k WGS |
| SNV Frequencies: gnomAD HGDP + 1000 Genomes - 4,094 WGS, 80 populations |
| GenomeAsia 1.7k SNVs |
| SNV Frequencies: GenomeAsia Pilot - Substitutions |
| GenomeAsia 1.7k Indels |
| SNV Frequencies: GenomeAsia Pilot - Indels |
| GA4K 552 PacBio LR |
| SNV Frequencies: GA4K Children's Mercy - 552 PacBio HiFi WGS, pediatric RD |
| FinnGen R12 500k imputed |
| SNV Frequencies: Finland FinnGen - 500k samples, arrays, imputation used 8.5k WGS |
| CoLoRSdb 1k LR SNV/Ind |
| SNV Frequencies: CoLoRSdb v1.2.0 - 1,027 PacBio HiFi WGS, SNV/indel callset |
| China WBBC 4.5k WGS |
| SNV Frequencies: Westlake BioBank for Chinese - 4,480 WGS, 4 regional Han groups |
| China ChinaMAP 10.5k WGS |
| SNV Frequencies: ChinaMAP phase 1 - 10,588 WGS at ~40x, Chinese natural population |
| Brazil ABraOM 1k WGS |
| SNV Frequencies: ABraOM Brazil - 1,171 unrelated individuals |
| Australia MGRB 4k WGS |
| SNV Frequencies: Australia Medical Genome Reference Bank - 4,011 WGS |
| AllOfUs v7 245k WGS |
| SNV Frequencies: AllOfUs v7 - 245k WGS, local-ancestry-stratified, AC>=20 |
| 12 Afr Pops 180 WGS |
| SNV Frequencies: 180 WGS from 12 Indigenous African Populations (Fan 2023) |
| Genotyping Array Databases Combined |
| SNV Frequencies: Genotyping-array cohorts combined (TPMI, Mexico Biobank, UK Biobank imputed) |
| Disease cohorts |
| SNV Frequencies: variants in ~150,000 affected or case individuals (autism, schizophrenia, rare disease cohorts) |
| Population reference |
| SNV Frequencies: variants in ~1.5 million individuals from population cohorts and unaffected or control arms |
| Tandem Repeat Variation |
| Tandem Repeat Variation |
| WebSTR |
| WebSTR Short Tandem Repeat Loci (EnsembleTR Panel, 1000 Genomes) |
| TRExplorer |
| TRExplorer V2 Tandem Repeat Catalog |
| ToMMo 61k STR |
| ToMMo 61KJPN Short Tandem Repeat Allele Counts (Expansion Hunter) |
| STRchive |
| STRchive Disease-Associated Short Tandem Repeat Loci |
| 1KG Vienna ONT VNTR |
| 1000 Genomes Vienna ONT VNTR Allele Statistics (VAMOS, 1,019 samples, long-read) |
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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 |
| Long-read Transcripts |
| Transcripts and other data generated using long-read sequencing technology (PacBio and Oxford Nanopore) |
| ENCODE4 Transcripts |
| ENCODE4 Long Read Transcripts |
| CLS long-read RNAs |
| Capture long-seq long-read lncRNAs |
| Other ESTs |
| Non-Human ESTs from GenBank |
| Other mRNAs |
| Non-Human mRNAs from GenBank |
| PRO-cap |
| PRO-cap nascent RNA transcription start sites from ENCODE 4 |
| MCF10A PRO-cap |
| MCF10A (ENCSR799DGV) PRO-cap transcription start sites |
| K562 PRO-cap |
| K562 (ENCSR261KBX) PRO-cap transcription start sites |
| HUVEC PRO-cap |
| HUVEC (ENCSR098LLB) PRO-cap transcription start sites |
| Calu3 PRO-cap |
| Calu3 (ENCSR935RNW) PRO-cap transcription start sites |
| Caco-2 PRO-cap |
| Caco-2 (ENCSR100LIJ) PRO-cap transcription start sites |
| A673 PRO-cap |
| A673 (ENCSR046BCI) PRO-cap transcription start sites |
| ProCapNet |
| ProCapNet predicted PRO-cap |
| MCF10A Contribution |
| MCF10A (ENCSR860TYZ) ProCapNet sequence-contribution scores |
| K562 Contribution |
| K562 (ENCSR740IPL) ProCapNet sequence-contribution scores |
| HUVEC Contribution |
| HUVEC (ENCSR801ECP) ProCapNet sequence-contribution scores |
| Calu3 Contribution |
| Calu3 (ENCSR797DEF) ProCapNet sequence-contribution scores |
| Caco-2 Contribution |
| Caco-2 (ENCSR182QNJ) ProCapNet sequence-contribution scores |
| A673 Contribution |
| A673 (ENCSR072YCM) ProCapNet sequence-contribution scores |
| MCF10A Predicted |
| MCF10A (ENCSR860TYZ) ProCapNet predicted PRO-cap |
| K562 Predicted |
| K562 (ENCSR740IPL) ProCapNet predicted PRO-cap |
| HUVEC Predicted |
| HUVEC (ENCSR801ECP) ProCapNet predicted PRO-cap |
| Calu3 Predicted |
| Calu3 (ENCSR797DEF) ProCapNet predicted PRO-cap |
| Caco-2 Predicted |
| Caco-2 (ENCSR182QNJ) ProCapNet predicted PRO-cap |
| A673 Predicted |
| A673 (ENCSR072YCM) ProCapNet predicted PRO-cap |
| recount3 |
| recount3 introns |
| 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 |
|
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 |
| MaveDB Experiments |
| Heatmaps and Alignment for MaveDB |
| MaveDB Heatmaps |
| Variant Effect Maps from MaveDB |
| MaveDB Alignments |
| MaveDB Experiment Sequence Alignments |
| 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 |
|
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 |
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| ENCODE cCREs |
| ENCODE Registry of cCREs (candidate Cis-Regulatory Elements) |
|
ENCODE3 cCREs |
| ENCODE3 Registry of candidate Cis-Regulatory Elements (cCREs) |
| ENCODE4 Core Collection |
| ENCODE4 Core Collection of 170 biosamples with sample-specific cCRE annotations & epigenomic signals |
| ENCODE4 cCREs |
| ENCODE4 Registry of candidate Cis-Regulatory Elements (cCREs) |
| new
ENCODE4 Regulation |
| Integrated Regulation from ENCODE 4 |
| TF ChIP-seq (Indiv.) |
| Peaks and signal from individual transcription factor ChIP experiments from ENCODE 4 |
| RNA-seq (Indiv.) |
| Signal from individual total RNA-seq experiments from ENCODE 4 |
| DNase/ATAC/Histone/CTCF (Indiv.) |
| Peaks and signal from individual DNase, ATAC, histone, and CTCF experiments from ENCODE 4 |
| TF rPeaks |
| Transcription factor representative peak (rPeak) clusters from ENCODE 4 |
| Transcription (Layered) |
| Strand-specific transcription signal measured by total RNA-seq, averaged by organ/tissue |
| CTCF (Layered) |
| CTCF binding signal from ChIP-seq, averaged by organ/tissue |
| H3K27ac (Layered) |
| H3K27ac signal marking active enhancers and promoters, averaged by organ/tissue |
| H3K4me3 (Layered) |
| H3K4me3 signal marking active and poised promoters, averaged by organ/tissue |
| ATAC (Layered) |
| Chromatin accessibility from ATAC-seq signal, averaged by organ/tissue |
| DNase (Layered) |
| Chromatin accessibility from DNase-seq signal, averaged by organ/tissue |
|
ENCODE3 Regulation |
| Integrated Regulation from ENCODE3 |
| 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 |
| new
Fiber-seq |
| Fiber-seq chromatin accessibility, regulatory elements and CpG methylation |
| Fiber-seq Compendium |
| Fiber-seq accessibility, FIRE peaks and CpG methylation in 41 samples |
| Fiber-seq Accessible |
| Fiber-seq percent-accessible chromatin in seven common cell lines |
| DNA Methylation |
| DNA Methylation |
| Human Methylation Atlas Signals |
| Human Methylation Atlas WGBS cell type signals |
| Human Methylation Atlas Summary |
| Human Methylation Atlas summary regions and enhancers |
| 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) |
| new
Episignatures |
| DNA methylation episignatures of rare developmental disorders |
| MethaDory |
| MethaDory: CpG probes of published DNA methylation episignatures |
| EpigenCentral |
| EpigenCentral: CpG probes of published DNA methylation signatures |
| 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 |
| MPRAs |
| Massively Parallel Reporter Assays |
| MPRAVarDB |
| MPRAs: MPRAVarDB - MPRA-tested Regulatory Variant Effects |
| MPRA Base |
| MPRAs: MPRA Base Enhancer Elements |
| ORegAnno |
| Regulatory elements from ORegAnno |
| RefSeq Func Elems |
| NCBI RefSeq Functional Elements |
| ReMap ChIP-seq |
| ReMap Atlas of Regulatory Regions |
| 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, |
| Unusually Conserved |
| Unusually Conserved Regions - Ultracons, HARs, etc. |
| 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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|