Control track and group visibility more selectively below.
|
|
|---|
| Raw_4C_seq_reads_8_donors |
| Raw_4C_seq_reads_8_donors |
|
|
|
|
|---|
| 05_MseI_1701_N701_S505_L1_L2-MseI-windows-counts-bedtools.bg.sorted |
| 05_MseI_1701_N701_S505_L1_L2-MseI-windows-counts-bedtools.bg.sorted |
| 11_MseI_1802_N702_S505_L1_L2-MseI-windows-counts-bedtools.bg.sorted |
| 11_MseI_1802_N702_S505_L1_L2-MseI-windows-counts-bedtools.bg.sorted |
| 17_MseI_1806_N703_S505_L1_L2-MseI-windows-counts-bedtools.bg.sorted |
| 17_MseI_1806_N703_S505_L1_L2-MseI-windows-counts-bedtools.bg.sorted |
| 23_MseI_1811_N704_S505_L1_L2-MseI-windows-counts-bedtools.bg.sorted |
| 23_MseI_1811_N704_S505_L1_L2-MseI-windows-counts-bedtools.bg.sorted |
| 29_MseI_1819_N705_S505_L1_L2-MseI-windows-counts-bedtools.bg.sorted |
| 29_MseI_1819_N705_S505_L1_L2-MseI-windows-counts-bedtools.bg.sorted |
| 35_MseI_1823_N706_S505_L1_L2-MseI-windows-counts-bedtools.bg.sorted |
| 35_MseI_1823_N706_S505_L1_L2-MseI-windows-counts-bedtools.bg.sorted |
| 41_MseI_1978_N707_S505_L1_L2-MseI-windows-counts-bedtools.bg.sorted |
| 41_MseI_1978_N707_S505_L1_L2-MseI-windows-counts-bedtools.bg.sorted |
| 47_MseI_2004_N708_S505_L1_L2-MseI-windows-counts-bedtools.bg.sorted |
| 47_MseI_2004_N708_S505_L1_L2-MseI-windows-counts-bedtools.bg.sorted |
| All_nonrisk_bedtools.bg |
| All_nonrisk_bedtools.bg |
| All_risk_bedtools.bg |
| All_risk_bedtools.bg |
|
|
|
|
|---|
| Base Position |
| Chromosome position in bases. (Clicks here zoom in 3x) |
| Assembly |
| Assembly from Fragments |
| BAC End Pairs |
| BAC End Pairs |
| BU ORChID |
| ORChID Predicted DNA Cleavage Sites from ENCODE/Boston Univ (Tullius lab) |
| Chromosome Band |
| Chromosome Bands Localized by FISH Mapping Clones |
deCODE Recomb |
| deCODE Recombination maps, 10Kb bin size, October 2010 |
| ENCODE Pilot |
| Regions Used for ENCODE Pilot Project (1%) |
| Exome Probesets |
| Exome Capture Probesets and Targeted Region |
|
FISH Clones |
| Clones Placed on Cytogenetic Map Using FISH |
|
Fosmid End Pairs |
| Fosmid End Pairs |
| Gap |
| Gap Locations |
| GC Percent |
| GC Percent in 5-Base Windows |
| GRC Incident |
| GRC Incident Database |
| GRC Map Contigs |
| Genome Reference Consortium Map Contigs |
| p14
GRC Patches |
| GRC Patches: Alt Haplotypes and Fix Sequences |
| Hg18 Diff |
| Contigs New to GRCh37/(hg19), Not Carried Forward from NCBI Build 36(hg18) |
| Hg38 Diff |
| Contigs Dropped or Changed from GRCh37(hg19) to GRCh38(hg38) |
| Hi Seq Depth |
| Regions of Exceptionally High Depth of Aligned Short Reads |
| INSDC |
| Accession at INSDC - International Nucleotide Sequence Database Collaboration |
| liftOver & ReMap |
| UCSC LiftOver and NCBI ReMap: Genome alignments to convert annotations to hg38 |
| LRG Regions |
| Locus Reference Genomic (LRG) / RefSeqGene Sequences Mapped to Feb. 2009 (GRCh37/hg19) Assembly |
| Map Contigs |
| Physical Map Contigs |
| Mappability |
| Mappability or Uniqueness of Reference Genome from ENCODE |
| Problematic Regions |
| Problematic Regions for NGS or Sanger sequencing or very variable regions |
| Recomb Rate |
| Recombination Rate from deCODE, Marshfield, or Genethon Maps (deCODE default) |
| RefSeq Acc |
| RefSeq Accession |
| Restr Enzymes |
| Restriction Enzymes from REBASE |
| Short Match |
| Perfect Matches to Short Sequence () |
| STS Markers |
| STS Markers on Genetic (blue) and Radiation Hybrid (black) Maps |
|
|
|
|
|---|
| GENCODE V47lift37 |
| GENCODE V47lift37 |
| NCBI RefSeq |
| RefSeq genes from NCBI |
| Genes Archive |
| Previous versions of GENCODE/UCSC Genes (knownGene) |
| UCSC Genes 2013 |
| Legacy UCSC Genes track (knownGene) from 2013 |
| GENCODE V47lift37 |
| GENCODE V47lift37 |
| GENCODE V45lift37 |
| GENCODE V45lift37 |
| CCDS |
| Consensus CDS |
| CRISPR Targets |
| CRISPR/Cas9 -NGG Targets, whole genome |
| Ensembl Genes |
| Ensembl Genes |
EvoFold |
| EvoFold Predictions of RNA Secondary Structure |
| Exoniphy |
| Exoniphy Human/Mouse/Rat/Dog |
| GENCODE Versions |
| Container of all new and previous GENCODE releases |
| GENCODE Genes V7 |
| Gene Annotations from ENCODE/GENCODE Version 7 |
| GENCODE Genes V14 |
| Gene Annotations from ENCODE/GENCODE Version 14 |
| GENCODE Genes V17 |
| Gene Annotations from ENCODE/GENCODE Version 17 |
| GENCODE Genes V19 |
| Gene Annotations from GENCODE Version 19 |
| GENCODE Gene V24lift37 |
| Gene Annotations from GENCODE Version 24lift37 |
| GENCODE Gene V27lift37 |
| Gene Annotations from GENCODE Version 27lift37 |
| GENCODE V28lift37 |
| GENCODE lifted annotations from V28lift37 (Ensembl 92) |
| GENCODE V31lift37 |
| GENCODE lifted annotations from V31lift37 (Ensembl 97) |
| GENCODE V33lift37 |
| GENCODE lifted annotations from V33lift37 (Ensembl 99) |
| GENCODE V34lift37 |
| GENCODE lifted annotations from V34lift37 (Ensembl 100) |
| GENCODE V35lift37 |
| GENCODE lifted annotations from V35lift37 (Ensembl 101) |
| GENCODE V36lift37 |
| GENCODE lifted annotations from V36lift37 (Ensembl 102) |
| GENCODE V37lift37 |
| GENCODE lifted annotations from V37lift37 (Ensembl 103) |
| GENCODE V38lift37 |
| GENCODE lifted annotations from V38lift37 (Ensembl 104) |
| GENCODE V39lift37 |
| GENCODE lifted annotations from V39lift37 (Ensembl 105) |
| GENCODE V40lift37 |
| GENCODE lifted annotations from V40lift37 (Ensembl 106) |
| GENCODE V41lift37 |
| GENCODE lifted annotations from V41lift37 (Ensembl 107) |
| GENCODE V42lift37 |
| GENCODE lifted annotations from V42lift37 (Ensembl 108) |
| GENCODE V43lift37 |
| GENCODE lifted annotations from V43lift37 (Ensembl 109) |
| GENCODE V44lift37 |
| GENCODE lifted annotations from V44lift37 (Ensembl 110) |
| GENCODE V45lift37 |
| GENCODE lifted annotations from V45lift37 (Ensembl 111) |
| GENCODE V46lift37 |
| GENCODE lifted annotations from V46lift37 (Ensembl 112) |
| GENCODE V47lift37 |
| GENCODE lifted annotations from V47lift37 (Ensembl 113) |
| H-Inv 7.0 |
| H-Inv 7.0 Gene Predictions |
| updated
HGNC |
| HUGO Gene Nomenclature |
| IKMC Genes Mapped |
| International Knockout Mouse Consortium Genes Mapped to Human Genome |
| lincRNAs |
| Human Body Map lincRNAs and TUCP Transcripts |
| lincRNA Transcripts |
| lincRNA and TUCP transcripts |
| lincRNA RNA-Seq Reads |
| lincRNA RNA-Seq reads expression abundances |
| LRG Transcripts |
| Locus Reference Genomic (LRG) / RefSeqGene Fixed Transcript Annotations |
| MGC/ORFeome Genes |
| MGC/ORFeome Full ORF mRNA Clones |
| ORFeome Clones |
| ORFeome Collaboration Gene Clones |
| MGC Genes |
| Mammalian Gene Collection Full ORF mRNAs |
| Other RefSeq |
| Non-Human RefSeq Genes |
| Pfam in UCSC Gene |
| Pfam Domains in UCSC 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 |
| N-SCAN |
| N-SCAN Gene Predictions |
| Genscan Genes |
| Genscan Gene Predictions |
| Geneid Genes |
| Geneid Gene Predictions |
| AUGUSTUS |
| AUGUSTUS ab initio gene predictions v3.1 |
| AceView Genes |
| AceView Gene Models With Alt-Splicing |
| Retroposed Genes |
| Retroposed Genes V5, Including Pseudogenes |
| sno/miRNA |
| C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from snoRNABase and miRBase |
| 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 |
| tRNA Genes |
| Transfer RNA Genes Identified with tRNAscan-SE |
| UCSC Alt Events |
| Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes |
| UniProt |
| UniProt SwissProt/TrEMBL Protein Annotations |
| Vega Genes |
| Vega Annotations |
| Yale Pseudo60 |
| Yale Pseudogenes based on Ensembl Release 60 |
|
|
|
|
|---|
| 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 |
| Publications |
| Publications: Sequences in Scientific Articles |
| 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) |
| 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 |
| MTR All Data |
| MTR - Missense Tolerance Ratio Scores all annotations |
| MTR Scores |
| MTR - Missense Tolerance Ratio Scores by base |
| MetaDome All Data |
| MetaDome - Tolerance Landscape score all annotations |
| MetaDome |
| MetaDome - Tolerance Landscape 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 |
| new
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 SNVs (not updated anymore - use the hg38 track) |
|
DECIPHER CNVs |
| DECIPHER CNVs (not updated anymore - use the hg38 track) |
| Deleteriousness Predictions |
| Variant Deleteriousness / Variant Impact Prediction Scores |
| BayesDel |
| BayesDel - deleteriousness meta-score |
| Development Delay |
| Copy Number Variation Morbidity Map of Developmental Delay |
| Dosage Sensitivity |
| pHaplo and pTriplo dosage sensitivity map from Collins et al 2022 |
| GAD View |
| Genetic Association Studies of Complex Diseases and Disorders |
| 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 |
| Haploinsufficiency |
| Haploinsufficiency predictions for genes from DECIPHER |
| HGMD public |
| Human Gene Mutation Database - Public Version Dec 2024 |
| Lens Patents |
| Lens PatSeq Patent Document Sequences |
| LOVD Variants |
| LOVD: Leiden Open Variation Database Public Variants |
|
MGI Mouse QTL |
| MGI Mouse Quantitative Trait Loci Coarsely Mapped to Human |
| new
MITOMAP |
| MITOMAP: A human mitochondrial genome database |
| Orphanet |
| Orphadata: Aggregated Data From Orphanet |
| PanelApp |
| Genomics England PanelApp Diagnostics |
| Polygenic Risk Scores |
| Polygenic Risk Scores |
| PRS eMERGE |
| Polygenic Risk Scores from NHGRI Electronic Medical Records and Genomics (eMERGE) project |
| REVEL Scores |
| REVEL Pathogenicity Score for single-base coding mutations (zoom for exact score) |
|
RGD Human QTL |
| Human Quantitative Trait Locus from RGD |
|
RGD Rat QTL |
| Rat Quantitative Trait Locus from RGD Coarsely Mapped to Human |
| SNPedia |
| SNPedia |
| new
Splicing Impact |
| Splicing Impact Prediction Scores and Databases |
| SpliceAI |
| SpliceAI: Splice Variant Prediction Score |
| AbSplice Scores |
| Aberrant Splicing Prediction Scores |
| 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 |
| Web Sequences |
| DNA Sequences in Web Pages Indexed by Bing.com / Microsoft Research |
|
|
|
|
|---|
| dbSNP 155 |
| Short Genetic Variants from dbSNP release 155 |
| 1000G Archive |
| 1000 Genomes Archive |
| 1000G Ph3 Vars |
| 1000 Genomes Phase 3 Integrated Variant Calls: SNVs, Indels, SVs |
| 1000G Ph3 Accsbl |
| 1000 Genomes Project Phase 3 Paired-end Accessible Regions |
| 1000G Ph1 Vars |
| 1000 Genomes Phase 1 Integrated Variant Calls: SNVs, Indels, SVs |
| 1000G Ph1 Accsbl |
| 1000 Genomes Project Phase 1 Paired-end Accessible Regions |
| Array Probesets |
| Microarray Probesets |
| dbSNP Archive |
| dbSNP Track Archive |
| Mult. SNPs(138) |
| Simple Nucleotide Polymorphisms (dbSNP 138) That Map to Multiple Genomic Loci |
| Flagged SNPs(138) |
| Simple Nucleotide Polymorphisms (dbSNP 138) Flagged as Clinically Assoc |
| Common SNPs(138) |
| Simple Nucleotide Polymorphisms (dbSNP 138) Found in >= 1% of Samples |
| All SNPs(138) |
| Simple Nucleotide Polymorphisms (dbSNP 138) |
| Flagged SNPs(141) |
| Simple Nucleotide Polymorphisms (dbSNP 141) Flagged by dbSNP as Clinically Assoc |
| Common SNPs(141) |
| Simple Nucleotide Polymorphisms (dbSNP 141) Found in >= 1% of Samples |
| All SNPs(141) |
| Simple Nucleotide Polymorphisms (dbSNP 141) |
| Mult. SNPs(142) |
| Simple Nucleotide Polymorphisms (dbSNP 142) That Map to Multiple Genomic Loci |
| Flagged SNPs(142) |
| Simple Nucleotide Polymorphisms (dbSNP 142) Flagged by dbSNP as Clinically Assoc |
| Common SNPs(142) |
| Simple Nucleotide Polymorphisms (dbSNP 142) Found in >= 1% of Samples |
| All SNPs(142) |
| Simple Nucleotide Polymorphisms (dbSNP 142) |
| Mult. SNPs(144) |
| Simple Nucleotide Polymorphisms (dbSNP 144) That Map to Multiple Genomic Loci |
| Flagged SNPs(144) |
| Simple Nucleotide Polymorphisms (dbSNP 144) Flagged by dbSNP as Clinically Assoc |
| Common SNPs(144) |
| Simple Nucleotide Polymorphisms (dbSNP 144) Found in >= 1% of Samples |
| All SNPs(144) |
| Simple Nucleotide Polymorphisms (dbSNP 144) |
| Mult. SNPs(146) |
| Simple Nucleotide Polymorphisms (dbSNP 146) That Map to Multiple Genomic Loci |
| Flagged SNPs(146) |
| Simple Nucleotide Polymorphisms (dbSNP 146) Flagged by dbSNP as Clinically Assoc |
| Common SNPs(146) |
| Simple Nucleotide Polymorphisms (dbSNP 146) Found in >= 1% of Samples |
| All SNPs(146) |
| Simple Nucleotide Polymorphisms (dbSNP 146) |
| Mult. SNPs(147) |
| Simple Nucleotide Polymorphisms (dbSNP 147) That Map to Multiple Genomic Loci |
| Flagged SNPs(147) |
| Simple Nucleotide Polymorphisms (dbSNP 147) Flagged by dbSNP as Clinically Assoc |
| Common SNPs(147) |
| Simple Nucleotide Polymorphisms (dbSNP 147) Found in >= 1% of Samples |
| All SNPs(147) |
| Simple Nucleotide Polymorphisms (dbSNP 147) |
| Mult. SNPs(150) |
| Simple Nucleotide Polymorphisms (dbSNP 150) 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(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 |
| new
denovo-db |
| denovo-db v.1.6.1 |
| DGV Struct Var |
| Database of Genomic Variants: Structural Variation (CNV, Inversion, In/del) |
| EVS Variants |
| NHLBI GO Exome Sequencing Project (ESP) - Variants from 6,503 Exomes |
| ExAC |
| Exome Aggregation Consortium (ExAC) Variants and Calling Regions |
| Genome In a Bottle |
| Genome In a Bottle Structural Variants and Trios |
|
Genome Variants |
| Personal Genome Variants |
| GIS DNA PET |
| ENCODE Genome Institute of Singapore DNA Paired-End Ditags |
| gnomAD |
| Genome Aggregation Database (gnomAD) - Variants, Coverage, and Constraint |
| gnomAD Structural Variants |
| Genome Aggregation Database (gnomAD) - Structural Variants |
| gnomAD pext |
| gnomAD Proportion Expression Across Transcript Scores (pext) |
| gnomAD Genomes Variants |
| Genome Aggregation Database (gnomAD) Genome Variants v2.1.1 |
| gnomAD Exomes Variants |
| Genome Aggregation Database (gnomAD) Exome Variants v2.1.1 |
| gnomAD Coverage |
| Genome Aggregation Database (gnomAD) - Genome and Exome Sample Coverage |
| gnomAD Constraint Metrics |
| Genome Aggregation Database (gnomAD) - Predicted Constraint Metrics (pLI and Z-scores) |
| HAIB Genotype |
| Genotype (CNV and SNP) by Illumina 1MDuo and CBS from ENCODE/HudsonAlpha |
|
HapMap SNPs |
| HapMap SNPs (rel27, merged Phase II + Phase III genotypes) |
| HGDP Allele Freq |
| Human Genome Diversity Project SNP Population Allele Frequencies |
| Platinum Genomes |
| Platinum genome variants |
|
|
|
|
|---|
|
CGAP SAGE |
| CGAP Long SAGE |
| Gene Bounds |
| Gene Boundaries as Defined by RNA and Spliced EST Clusters |
|
H-Inv |
| H-Invitational Genes mRNA Alignments |
| Human ESTs |
| Human ESTs Including Unspliced |
| Human mRNAs |
| Human mRNAs from GenBank |
| Human RNA Editing |
| Human RNA Editing from the DAtabase of RNa EDiting |
| Other ESTs |
| Non-Human ESTs from GenBank |
| Other mRNAs |
| Non-Human mRNAs from GenBank |
|
Poly(A) |
| Poly(A) Sites, Both Reported and Predicted |
| PolyA-Seq |
| Poly(A)-sequencing from Merck Research Laboratories |
| SIB Alt-Splicing |
| Alternative Splicing Graph from Swiss Institute of Bioinformatics |
| Spliced ESTs |
| Human ESTs That Have Been Spliced |
| UniGene |
| UniGene Alignments |
|
|
|
|
|---|
| GTEx Gene V8 |
| Gene Expression in 54 tissues from GTEx RNA-seq of 17382 samples, 948 donors (V8, Aug 2019) |
| Allen Brain |
| Allen Brain Atlas Probes |
| Burge RNA-seq |
| Burge Lab RNA-seq Aligned by GEM Mapper |
| CSHL Small RNA-seq |
| Small RNA-seq from ENCODE/Cold Spring Harbor Lab |
| ENC Exon Array |
| ENCODE Exon Array |
| UW Affy Exon |
| Affymetrix Exon Array from ENCODE/University of Washington |
| Duke Affy Exon |
| Affymetrix Exon Array from ENCODE/Duke |
| ENC ProtGeno |
| ENCODE Proteogenomics |
| UNC/BSU ProtGeno |
| Proteogenomics Hg19 Mapping from ENCODE/Univ. North Carolina/Boise State Univ. |
| UNC/BSU ProtGenc |
| Proteogenomics Hg19 and GENCODE Mapping from ENCODE/Univ. North Carolina/Boise State Univ. |
| ENC RNA-seq |
| ENCODE RNA-seq |
| SYDH RNA-seq |
| RNA-seq from ENCODE/Stanford/Yale/USC/Harvard |
| HAIB RNA-seq |
| RNA-seq from ENCODE/HAIB |
| GIS RNA-seq |
| RNA-seq from ENCODE/Genome Institute of Singapore |
| CSHL Long RNA-seq |
| Long RNA-seq from ENCODE/Cold Spring Harbor Lab |
| Caltech RNA-seq |
| RNA-seq from ENCODE/Caltech |
| EPDnew Promoters |
| Promoters from EPDnew human version 006 |
| Affy Archive |
| Affymetrix Archive |
| Affy U133Plus2 |
| Alignments of Affymetrix Consensus/Exemplars from HG-U133 Plus 2.0 |
| Affy U133 |
| Alignments of Affymetrix Consensus/Exemplars from HG-U133 |
| Affy U95 |
| Alignments of Affymetrix Consensus/Exemplars from HG-U95 |
| Affy RNA Loc |
| RNA Subcellular Localization by Tiling Microarray from ENCODE Affymetrix/CSHL |
| Affy GNF1H |
| Alignments of Affymetrix Consensus/Exemplars from GNF1H |
| Affy Exon Array |
| Affymetrix Human Exon Array Probes and Probesets |
| GIS RNA PET |
| RNA Sub-cellular Localization by Paired-end diTag Sequencing from ENCODE/GIS |
| 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 |
|
Illumina WG-6 |
| Alignments of Illumina WG-6 3.0 Probe Set |
| PeptideAtlas |
| Peptide sequences identified from MS spectra of 971 samples by PeptideAtlas |
| qPCR Primers |
| Human (hg19) Whole Transcriptome qPCR Primers |
| RIKEN CAGE Loc |
| RNA Subcellular CAGE Localization from ENCODE/RIKEN |
|
Sestan Brain |
| Sestan Lab Human Brain Atlas Microarrays |
|
|
|
|
|---|
| ENCODE Regulation |
| Integrated Regulation from ENCODE |
| Txn Fac ChIP V2 |
| Transcription Factor ChIP-seq from ENCODE (V2) |
| Txn Factor ChIP |
| Transcription Factor ChIP-seq Clusters (161 factors) from ENCODE with Factorbook Motifs |
| Txn Factr ChIP E3 |
| Transcription Factor ChIP-seq Clusters (338 factors, 130 cell types) from ENCODE 3 |
| DNase Clusters |
| DNaseI Hypersensitivity Clusters in 125 cell types from ENCODE (V3) |
| Layered H3K27Ac |
| H3K27Ac Mark (Often Found Near Active 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 |
|
CD34 DnaseI |
| Eur. Inst. Oncology/J. C. Venter Inst. Nuclease Accessible Sites |
| 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) |
| ENC Chromatin |
| ENCODE Chromatin Interactions |
| UW 5C | Downloads | Chromatin Interactions by 5C from ENCODE/University of Washington |
| UMass 5C |
| Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass. |
GIS ChIA-PET |
| Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan |
| ENC DNA Methyl |
| ENCODE DNA Methylation |
| HAIB Methyl450 |
| CpG Methylation by Methyl 450K Bead Arrays from ENCODE/HAIB |
| HAIB Methyl RRBS |
| DNA Methylation by Reduced Representation Bisulfite Seq from ENCODE/HudsonAlpha |
| ENC DNase/FAIRE |
| ENCODE Open Chromatin by DNaseI HS and FAIRE |
| UW DNaseI HS |
| DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington |
| UW DNaseI DGF |
| DNaseI Digital Genomic Footprinting from ENCODE/University of Washington |
| UNC FAIRE |
| Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill) |
| Duke DNaseI HS |
| Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University) |
| Open Chrom Synth |
| DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom(Duke/UNC/UTA) |
| Uniform DNaseI HS |
| DNaseI Hypersensitivity Uniform Peaks from ENCODE/Analysis |
| Master DNaseI HS |
| DNaseI Hypersensitive Site Master List (125 cell types) from ENCODE/Analysis |
| ENC Histone |
| ENCODE Histone Modification |
| UW Histone |
| Histone Modifications by ChIP-seq from ENCODE/University of Washington |
| SYDH Histone |
| Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard |
| Broad Histone |
| Histone Modifications by ChIP-seq from ENCODE/Broad Institute |
| Broad ChromHMM |
| Chromatin State Segmentation by HMM from ENCODE/Broad |
| ENC RNA Binding |
| ENCODE RNA Binding Proteins |
| SUNY RIP-seq |
| RIP-seq from ENCODE/SUNY Albany |
| SUNY RIP Tiling |
| RNA Binding Protein Associated RNA by Tiling Array from ENCODE/SUNY Albany |
| SUNY RIP GeneST |
| RNA Binding Protein Associated RNA by RIP-chip GeneST from ENCODE/SUNY Albany |
| ENC TF Binding |
| ENCODE Transcription Factor Binding |
| Uniform TFBS |
| Transcription Factor ChIP-seq Uniform Peaks from ENCODE/Analysis |
| ENCODE 3 TFBS |
| Transcription Factor ChIP-seq Peaks (338 factors in 130 cell types) from ENCODE 3 |
| UW CTCF Binding |
| CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington |
| UTA TFBS |
| Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin) |
| UChicago TFBS |
| Transcription Factor Binding Sites by Epitope-Tag from ENCODE/UChicago |
| SYDH TFBS |
| Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard |
| HAIB TFBS |
| Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB |
| 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 |
| FANTOM CAT |
| FANTOM5: atlas of human long non-coding RNAs with accurate 5' ends |
| 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 |
| Enhancer - promoter correlations distances organ |
| FANTOM5: Enhancer - promoter correlations distances organ |
| Enhancer - promoter correlations distances cell type |
| FANTOM5: Enhancer - promoter correlations distances cell type |
| FANTOM-NET Enhancers |
| FANTOM5: FANTOM-NET Enhancers |
| Enhancers |
| FANTOM5: Enhancers |
| FSU Repli-chip |
| Replication Timing by Repli-chip from ENCODE/FSU |
| GeneHancer |
| GeneHancer Regulatory Elements and Gene Interactions |
| Genome Segments |
| Genome Segmentations from ENCODE |
| GTEx Combined eQTL |
| Combined Expression QTLs from 44 Tissues from GTEx (midpoint release, V6) |
| GTEx Tissue eQTL |
| Expression QTLs in 44 tissues from GTEx (midpoint release, V6) |
| JASPAR Transcription Factors |
| JASPAR Transcription Factor Binding Site Database |
|
NKI Nuc Lamina |
| NKI Nuclear Lamina Associated Domains (LaminB1 DamID) |
| NKI LADs (Tig3) |
| NKI LADs (Lamina Associated Domains, Tig3 cells) |
| LaminB1 (Tig3) |
| NKI LaminB1 DamID Map (log2-ratio scores, Tig3 cells) |
| ORegAnno |
| Regulatory elements from ORegAnno |
| Rao 2014 Hi-C |
| Hi-C on 7 cell lines from Rao 2014 |
| ReMap ChIP-seq |
| ReMap Atlas of Regulatory Regions |
| Stanf Nucleosome |
| Nucleosome Position by MNase-seq from ENCODE/Stanford/BYU |
| SUNY SwitchGear |
| RNA Binding Protein Associated RNA by SwitchGear from ENCODE/SUNY Albany |
|
SwitchGear TSS |
| SwitchGear Genomics Transcription Start Sites |
| TFBS Conserved |
| HMR Conserved Transcription Factor Binding Sites |
| TS miRNA Targets |
| TargetScan predicted microRNA target sites |
| TS miRNA v7.2 |
| Predicted microRNA Target Sites from TargetScanHuman 7.2 (March 2018) |
| TS miRNA sites |
| TargetScan miRNA Regulatory Sites (Release 5.1, April 2009) |
| UCSF Brain Methyl |
| UCSF Brain DNA Methylation |
| UMMS Brain Hist |
| Brain Histone H3K4me3 ChIP-Seq from Univ. Mass. Medical School (Akbarian/Weng) |
| UW Repli-seq |
| Replication Timing by Repli-seq from ENCODE/University of Washington |
| updated
VISTA Enhancers |
| VISTA Enhancers |
|
|
|
|
|---|
| Conservation |
| Vertebrate Multiz Alignment & Conservation (100 Species) |
| Cons 46-Way |
| Vertebrate Multiz Alignment & Conservation (46 Species) |
|
Cons Indels MmCf |
| Indel-based Conservation for Human hg19, Mouse mm8 and Dog canFam2 |
|
Evo Cpg |
| Weizmann Evolutionary CpG Islands |
| GERP |
| GERP Scores for Mammalian Alignments |
| phastBias gBGC |
| phastBias gBGC predictions |
| 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 |
|
|
|
|
|---|
|
5% Lowest S |
| Selective Sweep Scan (S): 5% Smallest S scores |
|
Cand. Gene Flow |
| Candidate Regions for Gene Flow from Neandertal to Non-African Modern Humans |
|
H-C Coding Diffs |
| Neandertal Alleles in Human/Chimp Coding Non-synonymous Differences in Human Lineage |
| Neandertal Methyl |
| Neandertal Reconstructed DNA Methylation Map |
|
Neandertal Mito |
| Neandertal Mitochondrial Sequence (Vi33.16, 2008) |
| Neandertal Seq |
| Neandertal Sequence Reads |
|
S SNPs |
| SNPS Used for Selective Sweep Scan (S) |
|
Sel Swp Scan (S) |
| Selective Sweep Scan (S) on Neandertal vs. Human Polymorphisms (Z-Score +- Variance) |
|
|
|
|
|---|
| Denisova Methyl |
| Denisova Reconstructed DNA Methylation Map |
| Denisova Seq |
| Denisova High-Coverage Sequence Reads |
| Denisova Variants |
| Variant Calls from High-Coverage Genome Sequence of an Archaic Denisovan Individual |
| Mod Hum Variants |
| Variant Calls from 11 Modern Human Genome Sequences |
| Modern Derived |
| Modern Human Derived, Denisova Ancestral |
|
|
|
|
|---|
| 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 |
| Human NumtS mitochondrial sequence |
| 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 |
|
|