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LOC113839553 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:38047203-38048402 [ Homo sapiens (human) ]

Gene ID: 113839553, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113839553
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:38047203-38048402
Gene type
biological region
Feature type(s)
regulatory: enhancer
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. The major subregion 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, where it 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. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in naive human embryonic stem cells, where both are associated with the OCT4 and NANOG transcription factors and are marked by the H3K27ac histone modification, and one is additionally marked by H3K4me1. An overlapping 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 non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Nov 2022]
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Genomic context

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See LOC113839553 in Genome Data Viewer
Location:
9p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (38046942..38048929)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (38070870..38072857)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (38047849..38048143)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 25 member 51 Neighboring gene phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19914 Neighboring gene thioredoxin related transmembrane protein 2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28405 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:37923197-37923808 Neighboring gene RNA, U7 small nuclear 124 pseudogene Neighboring gene SH2 domain containing adaptor protein B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:37951849-37952348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:37997675-37998176 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28408 Neighboring gene Sharpr-MPRA regulatory region 5136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38008584-38009525 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38010092-38010724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19915 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38016883-38017646 Neighboring gene Sharpr-MPRA regulatory region 2787 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38021463-38021972 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38026045-38026553 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38026554-38027063 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38027064-38027572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38027573-38028081 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:38028793-38028962 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:38030139-38030638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:38032069-38032570 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38037811-38038416 Neighboring gene VISTA enhancer hs2062 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:38048927-38049920 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:38058891-38060090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38067661-38068464 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19917 Neighboring gene uncharacterized LOC105376039 Neighboring gene Sharpr-MPRA regulatory region 13386 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28411 Neighboring gene U8 small nucleolar RNA

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
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:38047933-38048926
  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:38046939-38047932
  • Sharpr-MPRA regulatory region 8558

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_063162.3 

    Range
    101..2088
    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
    38046942..38048929
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    38070870..38072857
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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