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Configure Tracks on UCSC Genome Browser: Human Jan. 2022 (T2T CHM13v2.0/hs1) (hs1)
  Tracks:    Groups:
Control track and group visibility more selectively below.
-   Hub: THP-1_su23    
0hr_chr19 0hr_chr19
0hr_hic 0hr_hic
0hr_hic_30 0hr_hic_30
0hr_occ PMA_0hr_occupancy
0hr_sen PMA_0hr_sensitivity
0hr_small PMA_0hr_small.bb
0hr_small PMA_0hr_small_RPKM
12hr_occ PMA_12hr_occupancy
12hr_sen PMA_12hr_sensitivity
12hr_small PMA_12hr_small.bb
12hr_small PMA_12hr_small_RPKM
1hr_occ PMA_1hr_occupancy
1hr_sen PMA_1hr_sensitivity
1hr_small PMA_1hr_small.bb
1hr_small PMA_1hr_small_RPKM
24hr_occ PMA_24hr_occupancy
24hr_sen PMA_24hr_sensitivity
24hr_small PMA_24hr_small.bb
24hr_small PMA_24hr_small_RPKM
48hr_occ PMA_48hr_occupancy
48hr_sen PMA_48hr_sensitivity
48hr_small PMA_48hr_small.bb
48hr_small PMA_48hr_small_RPKM
4hr_occ PMA_4hr_occupancy
4hr_sen PMA_4hr_sensitivity
4hr_small PMA_4hr_small.bb
4hr_small PMA_4hr_small_RPKM
72hr_hic 72hr_hic
72hr_hic_30 72hr_hic_30
72hr_occ PMA_72hr_occupancy
72hr_sen PMA_72hr_sensitivity
72hr_sen_alt PMA_72hr_sensitivity_alt
72hr_small PMA_72hr_small.bb
72hr_small PMA_72hr_small_RPKM
8hr_occ PMA_8hr_occupancy
8hr_sen PMA_8hr_sensitivity
8hr_small PMA_8hr_small.bb
8hr_small PMA_8hr_small_RPKM
BACH1_motif BACH1_motif
EGR2_motif EGR2_motif
FOSL2_motif FOSL2_motif
KLF6_motif KLF6_motif
macrophage_ATAC macrophage_ATAC
macrophage_ATAC_rep2 macrophage_ATAC_rep2
macrophage_CTCF macrophage_CTCF
macrophage_CTCF_rep2 macrophage_CTCF_rep2
macrophage_H3K27ac macrophage_H3K27ac
macrophage_H3K27ac_alt macrophage_H3K27ac_alt
macrophage_H3K27ac_alt_rep2 macrophage_H3K27ac_alt_rep2
macrophage_H3K27ac_rep2 macrophage_H3K27ac_rep2
macrophage_H3K27me3 macrophage_H3K27me3
macrophage_H3K27me3_rep2 macrophage_H3K27me3_rep2
macrophage_H3K4me1 macrophage_H3K4me1
macrophage_H3K4me1_rep2 macrophage_H3K4me1_rep2
macrophage_H3K4me3 macrophage_H3K4me3
macrophage_H3K4me3_rep2 macrophage_H3K4me3_rep2
macrophage_H3K9me3 macrophage_H3K9me3
macrophage_H3K9me3_rep2 macrophage_H3K9me3_rep2
macrophage_MAF macrophage_MAF
macrophage_MAF_rep2 macrophage_MAF_rep2
macrophage_PU1 macrophage_PU1
macrophage_PU1_rep2 macrophage_PU1_rep2
MAF_motif MAF_motif
monocyte_ATAC monocyte_ATAC
monocyte_ATAC_rep2 monocyte_ATAC_rep2
monocyte_CTCF monocyte_CTCF
monocyte_CTCF_rep2 monocyte_CTCF_rep2
monocyte_H3K27ac monocyte_H3K27ac
monocyte_H3K27ac_alt monocyte_H3K27ac_alt
monocyte_H3K27ac_alt_rep2 monocyte_H3K27ac_alt_rep2
monocyte_H3K27ac_rep2 monocyte_H3K27ac_rep2
monocyte_H3K27me3 monocyte_H3K27me3
monocyte_H3K27me3_rep2 monocyte_H3K27me3_rep2
monocyte_H3K4me1 monocyte_H3K4me1
monocyte_H3K4me1_rep2 monocyte_H3K4me1_rep2
monocyte_H3K4me3 monocyte_H3K4me3
monocyte_H3K4me3_rep2 monocyte_H3K4me3_rep2
monocyte_H3K9me3 monocyte_H3K9me3
monocyte_H3K9me3_rep2 monocyte_H3K9me3_rep2
monocyte_MAF monocyte_MAF
monocyte_MAF_rep2 monocyte_MAF_rep2
PAX5_motif PAX5_motif
PU1_motif PU1_motif
TAF1_motif TAF1_motif
ZN770_motif ZN770_motif
-   Hub: THP-1_public    
0hr_distribution PMA_0hr_distribution
0hr_sensitivity PMA_0hr_sensitivity
12hr_distribution PMA_12hr_distribution
12hr_sensitivity PMA_12hr_sensitivity
1hr_distribution PMA_1hr_distribution
1hr_sensitivity PMA_1hr_sensitivity
24hr_distribution PMA_24hr_distribution
24hr_sensitivity PMA_24hr_sensitivity
48hr_distribution PMA_48hr_distribution
48hr_sensitivity PMA_48hr_sensitivity
4hr_distribution PMA_4hr_distribution
4hr_sensitivity PMA_4hr_sensitivity
72hr_distribution PMA_72hr_distribution
72hr_sensitivity PMA_72hr_sensitivity
8hr_distribution PMA_8hr_distribution
8hr_sensitivity PMA_8hr_sensitivity
-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
CenSat Annotation Centromeric Satellite Annotation
CHM13 unique CHM13 unique in comparison to GRCh38/hg38 and GRCh37/hg19
rDNA models Consensus rDNA models
Assembly Assembly from NCBI Genbank Sequences
GC Percent GC Percent in 5-Base Windows
Human liftOver LiftOver alignments from CHM13 to hg19/hg38 and HG002 with two different pipelines
Mappability Single-read and multi-read mappability by Umap
Microsatellites Microsatellite repeats
new Problematic Regions Difficult regions from GIAB via NCBI
Restr Enzymes Restriction Enzymes from REBASE
Short Match Perfect Matches to Short Sequence ()
-   Genes and Gene Predictions    
CAT/Liftoff Genes CAT + Liftoff Gene Annotations
NCBI RefSeq RefSeq gene predictions from NCBI
CRISPR Targets CRISPR/Cas9 -NGG Targets, whole genome
-   Phenotype and Literature    
ClinVar Variants ClinVar Variants 20220313 (lifted)
GWAS Variants GWAS Variants 2022-03-08 (lifted)
-   mRNA and EST    
CHM13 PROseq CHM13 PROseq stranded with unique genome-wide kmer filtering
CHM13 RNA-Seq CHM13 RNA-Seq (paired-end) unique genome-wide kmer filtering (unstranded)
RefSeq mRNAs RefSeq mRNAs mapped to this assembly
-   Expression and Regulation    
CpG Islands CpG Islands (Islands < 300 Bases are Light Green)
T2T Encode T2T Encode Reanalysis
-   Comparative Genomics    
Cactus Alignment Cactus Alignment
Primate Chain/Net Primate chain alignments to target sequence: hs1
-   Variation and Repeats    
dbSNP 155 dbSNP 155 (lifted)
RepeatMasker RepeatMasker Repetitive Elements
SEDEF Segmental Dups SEDEF Segmental Duplications
Simple Repeats Simple Tandem Repeats by TRF
WM + SDust Genomic Intervals Masked by WindowMasker + SDust
SGDP copy number SGDP copy number estimates
SGDP copy number subset SGDP copy number estimates subset