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Configure Tracks on UCSC Genome Browser: Human Mar. 2006 (NCBI36/hg18)
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-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Alt Haplotypes Alternate Haplotypes to Reference Sequence Correspondence
Assembly Assembly from Fragments
BAC End Pairs BAC End Pairs
BU ORChID ENCODE Boston Univ (Tullius Lab) ORChID Predicted DNA Cleavage Sites
Chromosome Band Chromosome Bands Localized by FISH Mapping Clones
Coverage Clone Coverage
deCODE Recomb deCODE Recombination maps, 10Kb bin size, October 2010
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
Hg19 Diff Contigs dropped or changed from NCBI build 36(hg18) to GRCh37(hg19)
Hi Seq Depth Regions of Exceptionally High Depth of Aligned Short Reads
Map Contigs Physical Map Contigs
Mappability Mappability or Uniqueness of Reference Genome
Recomb Rate Recombination Rate from deCODE, Marshfield, or Genethon Maps (deCODE default)
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
-   Phenotype and Disease Associations    
ClinGen CNVs Clinical Genome Resource (ClinGen) CNVs
DECIPHER CNVs DECIPHER: Chromosomal Imbalance and Phenotype in Humans (CNVs)
GAD View Genetic Association Studies of Complex Diseases and Disorders
GeneReviews GeneReviews
GWAS Catalog NHGRI-EBI Catalog of Published Genome-Wide Association Studies
MGI Mouse QTL MGI Mouse Quantitative Trait Loci Coarsely Mapped to Human
OMIM Alleles OMIM Allelic Variants
OMIM Genes OMIM Genes - Dark Green Can Be Disease-causing
OMIM Pheno Loci OMIM Phenotypes - Gene Unknown
R-DMR Reprogrammed Differentially Methylated Regions
RGD Human QTL Human Quantitative Trait Locus from RGD
RGD Rat QTL Rat Quantitative Trait Locus from RGD Coarsely Mapped to Human
-   Genes and Gene Predictions    
UCSC Genes UCSC Genes (RefSeq, GenBank, tRNAs & Comparative Genomics)
RefSeq Genes RefSeq Genes
Other RefSeq Non-Human RefSeq Genes
ACEScan ACEScan Alternative Conserved Human-Mouse Exon Predictions
AceView Genes AceView Gene Models With Alt-Splicing
Augustus Augustus Gene Predictions
CCDS Consensus CDS
Ensembl Genes Ensembl Genes
EvoFold EvoFold Predictions of RNA Secondary Structure
EvoFold v.2 EvoFold v.2 Predictions of RNA Secondary Structure
Exoniphy Exoniphy Human/Mouse/Rat/Dog
Gencode Genes ENCODE Gencode Gene Annotations
Geneid Genes Geneid Gene Predictions
Genscan Genes Genscan Gene Predictions
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
Pfam in UCSC Gene Pfam Domains in UCSC Genes
Pos Sel Genes Positively Selected Genes (6 species)
RNA Genes Non-coding RNA Genes (dark) and Pseudogenes (light)
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
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
-   mRNA and EST    
Human mRNAs Human mRNAs from GenBank
Spliced ESTs Human ESTs That Have Been Spliced
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
SIB Alt-Splicing Alternative Splicing Graph from Swiss Institute of Bioinformatics
UniGene UniGene Alignments
-   Expression    
Affy Exon... Affymetrix All Exon Microarrays
     Affy Exon Probes     Affymetrix Exon Array 1.0: Probesets
     Affy Exon Tissues     Affymetrix Exon Array 1.0: Normal Tissues
Affy GNF1H Alignments of Affymetrix Consensus/Exemplars from GNF1H
Affy RNA Loc ENCODE Affymetrix/CSHL Subcellular RNA Localization by Tiling Array
Affy Txn... Affy Transcriptome Phase 3
     Affy Tx lRNA Reg     Affymetrix Transcriptome Phase 3 Long RNA Fragments
     Affy Tx lRNA Sig     Affymetrix Transcriptome Phase 3 Long RNA Signal
     Affy Tx sRNA Reg     Affymetrix Transcriptome Phase 3 Short RNA Fragments
     Affy Tx sRNA Sig     Affymetrix Transcriptome Phase 3 Short RNA Signal
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
B-Cell Transcriptome B-Cell Transcriptome (RNA-Seq)
Bertone Yale TAR Yale Transcriptionally Active Regions (TARs) (Bertone data)
Burge RNA-seq Burge Lab RNA-seq Aligned by GEM Mapper
Caltech RNA-seq ENCODE Caltech RNA-seq
CSHL Long RNA-seq ENCODE Cold Spring Harbor Labs Long RNA-seq
CSHL Sm RNA-seq ENCODE Cold Spring Harbor Labs Small RNA-seq
Duke Affy Exon ENCODE Duke Affy All-Exon Arrays
GIS PET Loc ENCODE GIS Subcellular RNA Localization by Paired End diTag Sequencing
GIS PET RNA Gene Identification Signature Paired-End Tags of PolyA+ RNA
GIS RNA-seq ENCODE Genome Institute of Singapore RNA-seq
GNF Atlas 2 GNF Expression Atlas 2
GNF Ratio GNF Gene Expression Atlas Ratios Using Affymetrix GeneChips
Helicos RNA-seq ENCODE Helicos RNA-seq
HudsonAlpha RNA-seq ENCODE HudsonAlpha RNA-seq
Illumina WG-6 Alignments of Illumina WG-6 3.0 Probe Set
RIKEN CAGE Loc ENCODE RIKEN RNA Subcellular Localization by CAGE Tags
Sestan Brain Sestan Lab Human Brain Atlas Microarrays
UW Affy Exon ENCODE UW Affy All-Exon Arrays
-   Regulation    
ENCODE Regulation... ENCODE Integrated Regulation
     Transcription     ENCODE Transcription Levels Assayed by RNA-seq on 6 Cell Lines
     Layered H3K4Me1     ENCODE Enhancer- and Promoter-Associated Histone Mark (H3K4Me1) on 8 Cell Lines
     Enhanced H3K27Ac     ENCODE Enhancer- and Promoter-Associated Histone Mark (H3K27Ac) on 8 Cell Lines
     Layered H3K4Me3     ENCODE Promoter-Associated Histone Mark (H3K4Me3) on 9 Cell Lines
     DNase Clusters     ENCODE Digital DNaseI Hypersensitivity Clusters
     Txn Factor ChIP     ENCODE Transcription Factor ChIP-seq
7X Reg Potential ESPERR Regulatory Potential (7 Species)
Broad ChromHMM ENCODE Chromatin State Segmentation by HMM from Broad Institute, MIT and MGH
Broad Histone ENCODE Histone Modifications by Broad Institute ChIP-seq
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)
EIO/JCVI NAS Eur. Inst. Oncology/J. C. Venter Inst. Nuclease Accessible Sites
Eponine TSS Eponine Predicted Transcription Start Sites
FirstEF FirstEF: First-Exon and Promoter Prediction
FOX2 CLIP-seq FOX2 Adaptor-trimmed CLIP-seq reads
HAIB Methyl-seq ENCODE HudsonAlpha Methyl-seq
HAIB Methyl27 ENCODE HudsonAlpha CpG Methylation by Illumina Methyl27
LI/UCSD TAF1... Ludwig Institute/UC San Diego TAF1 Binding in Fibroblasts
     LI TAF1 Signal     Ludwig Institute NimbleGen ChIP-chip Signal: TAF1 antibody, IMR90 cells
     LI TAF1 Sites     Ludwig Institute NimbleGen ChIP-chip Sites: TAF1 antibody, IMR90 cells
     LI TAF1 Valid     Ludwig Institute ChIP-chip Validation: TAF1 in IMR90 cells
NHGRI Bi-Pro ENCODE NHGRI Elnitski Bidirectional Promoters
NHGRI NRE ENCODE NHGRI Elnitski Negative Regulatory Elements
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)
Nucleosome Occupancy... UW Predicted Nucleosome Occupancy
     Nucl Occ: A375     UW Predicted Nucleosome Occupancy - A375
     Nucl Occ: Dennis     UW Predicted Nucleosome Occupancy - Dennis
     Nucl Occ: MEC     UW Predicted Nucleosome Occupancy - MEC
Open Chromatin ENCODE Open Chromatin, Duke/UNC/UT
ORegAnno Regulatory elements from ORegAnno
SUNY RBP ENCODE SUNY Albany RNA Binding Proteins by RIP-chip
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
Uppsala ChIP... Uppsala University ChIP-chip
     UU ChIP Signal     Uppsala University ChIP-chip Signal
     UU ChIP Sites     Uppsala University ChIP-chip Sites
UW DNase DGF ENCODE Univ. Washington Digital DNase Genomic Footprinting
UW DNaseI HS ENCODE Univ. Washington DNaseI Hypersensitivity by Digital DNaseI
UW Histone ENCODE Histone Modifications by Univ. Washington ChIP-seq
Vista Enhancers Vista HMR-Conserved Non-coding Human Enhancers from LBNL
Yale TFBS ENCODE Transcription Factor Binding Sites by ChIP-seq from Yale/UC-Davis/Harvard
-   Comparative Genomics    
Conservation Vertebrate Multiz Alignment & Conservation (44 Species)
17-Way Cons Vertebrate Multiz Alignment & Conservation (17 Species)
17-Way Most Cons PhastCons Conserved Elements, 17-way Vertebrate Multiz Alignment
28-Way Base Cons Basewise Conservation by PhyloP for 28-Species Multiz Align.
28-Way Cons Vertebrate Multiz Alignment & PhastCons Conservation (28 Species)
28-Way Most Cons PhastCons Conserved Elements, 28-way Vertebrate Multiz Alignment
Cons Indels MmCf Indel-based Conservation for human hg18, mouse mm8 and dog canFam2
Evo Cpg Weizmann Evolutionary CpG Islands
phastBias gBGC phastBias gBGC predictions
Chimp Chain/Net Chimp (Mar. 2006 (CGSC 2.1/panTro2)), Chain and Net Alignments
Orangutan Chain/Net Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)), Chain and Net Alignments
Rhesus Chain/Net Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)), Chain and Net Alignments
Marmoset Chain/Net Marmoset (June 2007 (WUGSC 2.0.2/calJac1)), Chain and Net Alignments
Guinea pig Chain/Net Guinea pig (Feb. 2008 (Broad/cavPor3)), Chain and Net Alignments
Rat Chain/Net Rat (Nov. 2004 (Baylor 3.4/rn4)), Chain and Net Alignments
Mouse Chain/Net Mouse (July 2007 (NCBI37/mm9)), Chain and Net Alignments
Dog Chain/Net Dog (May 2005 (Broad/canFam2)), Chain and Net Alignments
Cat Chain/Net Cat (Mar. 2006 (Broad/felCat3)), Chain and Net Alignments
Horse Chain/Net Horse (Jan. 2007 (Broad/equCab1)), Chain and Net Alignments
bosTau4 Chain/Net Cow (Oct. 2007 (Baylor 4.0/bosTau4)), Chain and Net Alignments
Tenrec Chain/Net Tenrec (July 2005 (Broad/echTel1)), Chain and Net Alignments
Opossum Chain/Net Opossum (Jan. 2006 (Broad/monDom4)), Chain and Net Alignments
Platypus Chain/Net Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)), Chain and Net Alignments
Lizard Chain/Net Lizard (Feb. 2007 (Broad/anoCar1)), Chain and Net Alignments
Chicken Chain/Net Chicken (May 2006 (WUGSC 2.1/galGal3)), Chain and Net Alignments
Zebra finch Chain/Net Zebra finch (Jul. 2008 (WUGSC 3.2.4/taeGut1)), Chain and Net Alignments
xenTro2 Chain/Net X. tropicalis (Aug. 2005 (JGI 4.1/xenTro2)), Chain and Net Alignments
Zebrafish Chain/Net Zebrafish (July 2007 (Zv7/danRer5)), Chain and Net Alignments
Stickleback Chain/Net Stickleback (Feb. 2006 (Broad/gasAcu1)), Chain and Net Alignments
Medaka Chain/Net Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)), Chain and Net Alignments
Fugu Chain/Net Fugu (Oct. 2004 (JGI 4.0/fr2)), Chain and Net Alignments
Tetraodon Chain/Net Tetraodon (Feb. 2004 (Genoscope 7/tetNig1)), Chain and Net Alignments
Tetraodon Ecores Human(hg18)/Tetraodon (Feb. 2004 (Genoscope 7/tetNig1)) Evolutionary Conserved Regions
Lamprey Chain/Net Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)), Chain and Net Alignments
Lancelet Chain/Net Lancelet (Mar. 2006 (JGI 1.0/braFlo1)), Chain and Net Alignments
S. purpuratus Chain/Net S. purpuratus (Sep. 2006 (Baylor 2.1/strPur2)), Chain and Net Alignments
-   Neandertal Assembly and Analysis    
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
Modern Human Seq Alignments of Sequence Reads from 5 Modern Humans
Neandertal Cntgs Neandertal Sequence Contigs Generated by Genotype Caller
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 Assembly and Analysis    
Denisova Denisova Sequence Reads
Modern Human Seq Alignments of Sequence Reads from 7 Humans
-   Variation and Repeats    
RepeatMasker Repeating Elements by RepeatMasker
SNPs (130) Simple Nucleotide Polymorphisms (dbSNP build 130)
Agilent Array Agilent Microarray Probesets
Common Cell CNV ENCODE Common Cell Type Copy Number Variation, by Illumina 1M and CBS
DGV Struct Var Database of Genomic Variants: Structural Variation (CNV, Inversion, In/del)
Exapted Repeats Repeats Exapted as Conserved Non-Exonic Elements
Genome Variants Personal Genome Variants
GIS DNA PET ENCODE Genome Institute of Singapore DNA Paired-End Ditags
HapMap LD Phased HapMap Linkage Disequilibrium - Phase II - from Phased Genotypes
HapMap SNPs HapMap SNPs (rel27, merged Phase II + Phase III genotypes)
HGDP Allele Freq Human Genome Diversity Project SNP Population Allele Frequencies
HGDP Hetrzygsty Human Genome Diversity Project Smoothed Expected Heterozygosity on 7 Continents
HGDP iHS Human Genome Diversity Project Integrated Haplotype Score on 7 Continents
HGDP Smoothd FST Human Genome Diversity Project Smoothed Relative FST (Fixation Index)
HGDP XP-EHH Human Genome Diversity Proj Cross-Pop Ext Haplo Homzgty (XP-EHH) on 7 Continents
HGSV Discordant HGSV Discordant Clone End Alignments
Interrupted Rpts Fragments of Interrupted Repeats Joined by RepeatMasker ID
Intr Rpts 3.2.7 Fragments of Interrupted Repeats Joined by RepeatMasker ID (RM version 3.2.7)
Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
NumtS Sequence Human NumtS mitochondrial sequence
RepMask 3.2.7 Repeating Elements by RepeatMasker version 3.2.7
Segmental Dups Duplications of >1000 Bases of Non-RepeatMasked Sequence
Self Chain Human Chained Self Alignments
Simple Repeats Simple Tandem Repeats by TRF
SNPs (126) Simple Nucleotide Polymorphisms (dbSNP build 126)
SNPs (128) Simple Nucleotide Polymorphisms (dbSNP build 128)
SNPs (129) Simple Nucleotide Polymorphisms (dbSNP build 129)
Structural Var Structural Variation
Tajima's D Tajima's D (from Human May 2004 assembly)
Tajima's D SNPs Tajima's D SNPs (from Human May 2004 assembly)
+   Pilot ENCODE Regions and Genes    
+   Pilot ENCODE Transcription    
+   Pilot ENCODE Chromatin Immunoprecipitation    
+   Pilot ENCODE Chromatin Structure    
+   Pilot ENCODE Comparative Genomics and Variation