Control track and group visibility more selectively below.
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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%) |
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 |
GRC Patch Release |
| GRCh37 alternate sequences, haplotypes and reference sequence patches |
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 |
LRG Regions |
| Locus Reference Genomic (LRG) Sequences Mapped to Feb. 2009 (GRCh37/hg19) Assembly |
Map Contigs |
| Physical Map Contigs |
Mappability |
| Mappability or Uniqueness of Reference Genome from ENCODE |
Recomb Rate |
| Recombination Rate from deCODE, Marshfield, or Genethon Maps (deCODE default) |
Short Match |
| Perfect Matches to Short Sequence (AAAAA) |
STS Markers |
| STS Markers on Genetic (blue) and Radiation Hybrid (black) Maps |
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UCSC Genes |
| UCSC Genes (RefSeq, GenBank, CCDS, Rfam, tRNAs & Comparative Genomics) |
RefSeq Genes |
| RefSeq Genes |
AceView Genes |
| AceView Gene Models With Alt-Splicing |
CCDS |
| Consensus CDS |
Ensembl Genes |
| Ensembl Genes |
EvoFold |
| EvoFold Predictions of RNA Secondary Structure |
Exoniphy |
| Exoniphy Human/Mouse/Rat/Dog |
GENCODE... |
| GENCODE Gene Annotation |
GENCODE Genes V19 |
| Gene Annotations from ENCODE/GENCODE Version 19 |
GENCODE Genes V17 |
| Gene Annotations from ENCODE/GENCODE Version 17 |
GENCODE Genes V14 |
| Gene Annotations from ENCODE/GENCODE Version 14 |
GENCODE Genes V7 |
| Gene Annotations from ENCODE/GENCODE Version 7 |
Geneid Genes |
| Geneid Gene Predictions |
Genscan Genes |
| Genscan Gene Predictions |
H-Inv 7.0 |
| H-Inv 7.0 Gene Predictions |
IKMC Genes Mapped |
| International Knockout Mouse Consortium Genes Mapped to Human Genome |
lincRNAs... |
| Human Body Map lincRNAs and TUCP Transcripts |
lincRNA RNA-Seq Reads |
| lincRNA RNA-Seq reads expression abundances |
lincRNA Transcripts |
| lincRNA and TUCP transcripts |
LRG Transcripts |
| Locus Reference Genomic (LRG) Fixed Transcript Annotations |
MGC Genes |
| Mammalian Gene Collection Full ORF mRNAs |
N-SCAN |
| N-SCAN Gene Predictions |
Old UCSC Genes |
| Previous Version of UCSC Genes |
ORFeome Clones |
| ORFeome Collaboration Gene Clones |
Other RefSeq |
| Non-Human RefSeq Genes |
Pfam in UCSC Gene |
| Pfam Domains in UCSC Genes |
Retroposed Genes |
| Retroposed Genes V5, Including Pseudogenes |
SGP Genes |
| SGP Gene Predictions Using Mouse/Human Homology |
SIB Genes |
| Swiss Institute of Bioinformatics Gene Predictions from mRNA and ESTs |
sno/miRNA |
| C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from snoRNABase and miRBase |
TransMap... |
| TransMap Alignments |
TransMap UCSC |
| TransMap UCSC Gene Mappings |
TransMap RefGene |
| TransMap RefSeq Gene Mappings |
TransMap mRNA |
| TransMap GenBank mRNA Mappings |
TransMap ESTs |
| TransMap Spliced EST Mappings |
tRNA Genes |
| Transfer RNA Genes Identified with tRNAscan-SE |
UCSC Alt Events |
| Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes |
Vega Genes |
| Vega Annotations |
Yale Pseudo60 |
| Yale Pseudogenes based on Ensembl Release 60 |
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Publications |
| Publications: Sequences in Scientific Articles |
ClinVar Variants |
| ClinVar Variants |
Coriell CNVs |
| Coriell Cell Line Copy Number Variants |
COSMIC |
| COSMIC: Catalogue Of Somatic Mutations In Cancer |
GAD View |
| Genetic Association Studies of Complex Diseases and Disorders |
GeneReviews |
| GeneReviews |
GWAS Catalog |
| NHGRI Catalog of Published Genome-Wide Association Studies |
ISCA |
| International Standards for Cytogenomic Arrays Consortium |
MGI Mouse QTL |
| MGI Mouse Quantitative Trait Loci Coarsely Mapped to Human |
RGD Human QTL |
| Human Quantitative Trait Locus from RGD |
RGD Rat QTL |
| Rat Quantitative Trait Locus from RGD Coarsely Mapped to Human |
UniProt Variants |
| UniProt/SwissProt Amino Acid Substitutions |
Web Sequences |
| DNA Sequences in Web Pages Indexed by Bing.com / Microsoft Research |
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Human mRNAs |
| Human mRNAs from GenBank |
Spliced ESTs |
| Human ESTs That Have Been Spliced |
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 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 |
UniGene |
| UniGene Alignments |
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Affy Exon Array |
| Affymetrix Human Exon Array Probes and Probesets |
Affy GNF1H |
| Alignments of Affymetrix Consensus/Exemplars from GNF1H |
Affy RNA Loc |
| RNA Subcellular Localization by Tiling Microarray from ENCODE Affymetrix/CSHL |
Affy U133 |
| Alignments of Affymetrix Consensus/Exemplars from HG-U133 |
Affy U133Plus2 |
| Alignments of Affymetrix Consensus/Exemplars from HG-U133 Plus 2.0 |
Affy U95 |
| Alignments of Affymetrix Consensus/Exemplars from HG-U95 |
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 |
Duke Affy Exon |
| Affymetrix Exon Array from ENCODE/Duke |
UW Affy Exon |
| Affymetrix Exon Array from ENCODE/University of Washington |
ENC ProtGeno... |
| ENCODE Proteogenomics |
UNC/BSU ProtGenc |
| Proteogenomics Hg19 and GENCODE Mapping from ENCODE/Univ. North Carolina/Boise State Univ. |
UNC/BSU ProtGeno |
| Proteogenomics Hg19 Mapping from ENCODE/Univ. North Carolina/Boise State Univ. |
ENC RNA-seq... |
| ENCODE RNA-seq |
Caltech RNA-seq |
| RNA-seq from ENCODE/Caltech |
CSHL Long RNA-seq |
| Long RNA-seq from ENCODE/Cold Spring Harbor Lab |
GIS RNA-seq |
| RNA-seq from ENCODE/Genome Institute of Singapore |
HAIB RNA-seq |
| RNA-seq from ENCODE/HAIB |
SYDH RNA-seq |
| RNA-seq from ENCODE/Stanford/Yale/USC/Harvard |
GIS RNA PET |
| RNA Sub-cellular Localization by Paired-end diTag Sequencing from ENCODE/GIS |
GNF Atlas 2 |
| GNF Expression Atlas 2 |
Illumina WG-6 |
| Alignments of Illumina WG-6 3.0 Probe Set |
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 |
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ENCODE Regulation... |
| Integrated Regulation from ENCODE |
Transcription |
| Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE |
Layered H3K4Me1 |
| H3K4Me1 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 H3K27Ac |
| H3K27Ac Mark (Often Found Near Active Regulatory Elements) on 7 cell lines from ENCODE |
DNase Clusters |
| Digital DNaseI Hypersensitivity Clusters in 125 cell types from ENCODE |
DNase Clusters V1 |
| Digital DNaseI Hypersensitivity Clusters in 74 cell types (2 reps) from ENCODE |
Txn Factor ChIP |
| Transcription Factor ChIP-seq (161 factors) from ENCODE with Factorbook Motifs |
Txn Fac ChIP V2 |
| Transcription Factor ChIP-seq from ENCODE V2 |
CD34 DnaseI |
| Eur. Inst. Oncology/J. C. Venter Inst. Nuclease Accessible Sites |
CpG Islands... |
| CpG Islands (Islands < 300 Bases are Light Green) |
CpG Islands |
| CpG Islands (Islands < 300 Bases are Light Green) |
Unmasked CpG |
| CpG Islands on All Sequence (Islands < 300 Bases are Light Green) |
ENC Chromatin... |
| ENCODE Chromatin Interactions |
GIS ChIA-PET |
| Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan |
UMass 5C |
| Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass. |
UW 5C | Downloads | Chromatin Interactions by 5C from ENCODE/University of Washington |
ENC DNA Methyl... |
| ENCODE DNA Methylation |
HAIB Methyl RRBS |
| DNA Methylation by Reduced Representation Bisulfite Seq from ENCODE/HudsonAlpha |
HAIB Methyl450 |
| CpG Methylation by Methyl 450K Bead Arrays from ENCODE/HAIB |
ENC DNase/FAIRE... |
| ENCODE Open Chromatin by DNaseI HS and FAIRE |
Uniform DNaseI HS |
| DNaseI Hypersensitivity Uniform Peaks from ENCODE/Analysis |
Open Chrom Synth |
| DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom(Duke/UNC/UTA) |
Duke DNaseI HS |
| Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University) |
UNC FAIRE |
| Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill) |
UW DNaseI DGF |
| DNaseI Digital Genomic Footprinting from ENCODE/University of Washington |
UW DNaseI HS |
| DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington |
ENC Histone... |
| ENCODE Histone Modification |
Broad ChromHMM |
| Chromatin State Segmentation by HMM from ENCODE/Broad |
Broad Histone |
| Histone Modifications by ChIP-seq from ENCODE/Broad Institute |
SYDH Histone |
| Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard |
UW Histone |
| Histone Modifications by ChIP-seq from ENCODE/University of Washington |
ENC RNA Binding... |
| ENCODE RNA Binding Proteins |
SUNY RIP GeneST |
| RNA Binding Protein Associated RNA by RIP-chip GeneST from ENCODE/SUNY Albany |
SUNY RIP Tiling |
| RNA Binding Protein Associated RNA by Tiling Array from ENCODE/SUNY Albany |
SUNY RIP-seq |
| RIP-seq from ENCODE/SUNY Albany |
ENC TF Binding... |
| ENCODE Transcription Factor Binding |
Uniform TFBS |
| Transcription Factor ChIP-seq Uniform Peaks from ENCODE/Analysis |
HAIB TFBS |
| Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB |
SYDH TFBS |
| Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard |
UChicago TFBS |
| Transcription Factor Binding Sites by Epitope-Tag from ENCODE/UChicago |
UTA TFBS |
| Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin) |
UW CTCF Binding |
| CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington |
FSU Repli-chip |
| Replication Timing by Repli-chip from ENCODE/FSU |
Genome Segments |
| Genome Segmentations from ENCODE |
NKI Nuc Lamina... |
| NKI Nuclear Lamina Associated Domains (LaminB1 DamID) |
LaminB1 (Tig3) |
| NKI LaminB1 DamID Map (log2-ratio scores, Tig3 cells) |
NKI LADs (Tig3) |
| NKI LADs (Lamina Associated Domains, Tig3 cells) |
ORegAnno |
| Regulatory elements from ORegAnno |
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 sites |
| TargetScan miRNA Regulatory Sites |
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 |
Vista Enhancers |
| Vista HMR-Conserved Non-coding Human Enhancers from LBNL |
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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 |
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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 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) |
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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 |
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Common SNPs(138) |
| Simple Nucleotide Polymorphisms (dbSNP 138) Found in >= 1% of Samples |
1000G Ph1 Accsbl |
| 1000 Genomes Project Phase 1 Paired-end Accessible Regions |
1000G Ph1 Vars |
| 1000 Genomes Phase 1 Integrated Variant Calls: SNVs, Indels, SVs |
All SNPs(135) |
| Simple Nucleotide Polymorphisms (dbSNP 135) |
All SNPs(137) |
| Simple Nucleotide Polymorphisms (dbSNP 137) |
All SNPs(138) |
| Simple Nucleotide Polymorphisms (dbSNP 138) |
Common SNPs(135) |
| Simple Nucleotide Polymorphisms (dbSNP 135) Found in >= 1% of Samples |
Common SNPs(137) |
| Simple Nucleotide Polymorphisms (dbSNP 137) Found in >= 1% of Samples |
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 |
Flagged SNPs(135) |
| Simple Nucleotide Polymorphisms (dbSNP 135) Flagged by dbSNP as Clinically Assoc |
Flagged SNPs(137) |
| Simple Nucleotide Polymorphisms (dbSNP 137) Flagged by dbSNP as Clinically Assoc |
Flagged SNPs(138) |
| Simple Nucleotide Polymorphisms (dbSNP 138) Flagged by dbSNP as Clinically Assoc |
Genome Variants |
| Personal Genome Variants |
GIS DNA PET |
| ENCODE Genome Institute of Singapore DNA Paired-End Ditags |
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 |
Mult. SNPs(135) |
| Simple Nucleotide Polymorphisms (dbSNP 135) That Map to Multiple Genomic Loci |
Mult. SNPs(137) |
| Simple Nucleotide Polymorphisms (dbSNP 137) That Map to Multiple Genomic Loci |
Mult. SNPs(138) |
| Simple Nucleotide Polymorphisms (dbSNP 138) That Map to Multiple Genomic Loci |
NumtS Sequence |
| Human NumtS mitochondrial sequence |
SNP/CNV Arrays |
| Microarray Probesets |
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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 |
Segmental Dups |
| Duplications of >1000 Bases of Non-RepeatMasked Sequence |
Self Chain |
| Human Chained Self Alignments |
Simple Repeats |
| Simple Tandem Repeats by TRF |
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MGW [Angstrom] |
| DNA Shape - Minor Groove Width [Angstrom] |
2nd order MGW |
| DNA Shape - 2nd Order Minor Groove Width |
ProT [Degree] |
| DNA Shape - Propeller Twist [Degree] |
2nd order ProT |
| DNA Shape - 2nd Order Propeller Twist |
Roll [Degree] |
| DNA Shape - Roll [Degree] |
2nd order Roll |
| DNA Shape - 2nd Order Roll |
HelT [Degree] |
| DNA Shape - Helix Twist [Degree] |
2nd order HelT |
| DNA Shape - 2nd Order Helix Twist |
ORChID V2 |
| OH Radical Cleavage Intensity Database (ROChID) V2 |
|