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LOC112543434 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:7038146-7039345 [ Homo sapiens (human) ]

Gene ID: 112543434, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112543434
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:7038146-7039345
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 marked by the H3K4me1 histone modification were also shown to be active enhancers by ChIP-STARR-seq in naive human embryonic stem cells. 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 non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). The same subregion also displayed weak activation by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 12:CtcfO). [provided by RefSeq, Nov 2022]
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Genomic context

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Location:
18p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (7038101..7039346)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (7198624..7199869)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (7038309..7038603)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 916, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:6951323-6951880 Neighboring gene uncharacterized LOC101927188 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:6958646-6959845 Neighboring gene laminin subunit alpha 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr18:7034687-7035886 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:7043747-7043948 Neighboring gene SLC25A51 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:7158211-7158711 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:7203119-7203796 Neighboring gene leucine rich repeat containing 30

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

  • H3K4me1 hESC enhancer GRCh37_chr18:7038100-7038600
  • H3K4me1 hESC enhancer GRCh37_chr18:7038601-7039101
  • Sharpr-MPRA regulatory region 1572

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_057385.3 

    Range
    101..1346
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    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    7038101..7039346
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    7198624..7199869
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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