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LOC121366024 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:126840763-126841962 [ Homo sapiens (human) ]

Gene ID: 121366024, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121366024
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:126840763-126841962
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay in HCT116 colorectal carcinoma cells. This sequence was defined as a group 1 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on P300/CBP. A subregion was also validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). The same subregion also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 21:Repr, strong Polycomb repression). [provided by RefSeq, Aug 2022]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (124078484..124079683)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (136276382..136277581)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (126840969..126841263)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:126769682-126770393 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:126770394-126771104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20255 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:126774959-126775531 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:126775532-126776104 Neighboring gene LHX2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:126792309-126793096 Neighboring gene uncharacterized LOC107987037 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:126803186-126803720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:126803721-126804253 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:126807814-126808609 Neighboring gene LIM homeobox 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28957 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:126893859-126894071 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28958 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28959 Neighboring gene Sharpr-MPRA regulatory region 10969 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:126905749-126906322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:126906323-126906898 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:126906899-126907472 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28962 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:126964420-126964620 Neighboring gene NFE2L2 motif-containing MPRA enhancer 159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28964 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127004798-127005314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127005315-127005831 Neighboring gene Sharpr-MPRA regulatory region 14990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28973 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20260 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20261 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:127020845-127021790 Neighboring gene uncharacterized LOC124902268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127026232-127026845 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20262 Neighboring gene uncharacterized LOC613206 Neighboring gene NIMA related kinase 6

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  2. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 10835

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_074374.2 

    Range
    101..1300
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    124078484..124079683
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    136276382..136277581
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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