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LOC126862694 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:9017064-9018263 [ Homo sapiens (human) ]

Gene ID: 126862694, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126862694
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:9017064-9018263
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 region includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA). In HCT116 colorectal carcinoma cells, a subregion 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. Another subregion was also validated as an enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes three accessible chromatin subregions, two of which were validated as enhancers and one as a silencer based on their ability to activate or repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (9016517..9018265)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (9179941..9181689)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8690155-8691020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9273 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9274 Neighboring gene NANOG hESC enhancer GRCh37_chr18:8708630-8709131 Neighboring gene TOMM20 pseudogene 3 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr18:8724358-8724941 Neighboring gene gastric cancer associated transcript 2 Neighboring gene Sharpr-MPRA regulatory region 10096 Neighboring gene microtubule crosslinking factor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8766085-8766684 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8766685-8767282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8771566-8772066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8772067-8772567 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8790509-8791032 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:8800176-8801375 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8818635-8819136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8829938-8830461 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8830462-8830984 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8844937-8845437 Neighboring gene MPRA-validated peak3053 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8948615-8949387 Neighboring gene NANOG hESC enhancer GRCh37_chr18:8977106-8977637 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13063 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8990234-8990766 Neighboring gene NANOG hESC enhancer GRCh37_chr18:8997551-8998052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:9022070-9022745 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:9037094-9037241 Neighboring gene ribosomal protein S4X pseudogene 19 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9276 Neighboring gene uncharacterized LOC124904243

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 13064
  • ATAC-STARR-seq lymphoblastoid active region 13065
  • ATAC-STARR-seq lymphoblastoid silent region 9275
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:9016515-9017339

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_087191.2 

    Range
    101..1849
    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    9016517..9018265
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    9179941..9181689
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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