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LOC126860731 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:114803347-114804546 [ Homo sapiens (human) ]

Gene ID: 126860731, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126860731
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:114803347-114804546
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 region includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay. The major subregion had activity 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 marked by the H3K27ac and H3K4me1 histone modifications and one is additionally associated with the NANOG transcription factor. [provided by RefSeq, Nov 2022]
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Genomic context

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See LOC126860731 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (112041032..112042310)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (124212431..124213709)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 710, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28806 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28807 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28809 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28813 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28814 Neighboring gene long intergenic non-protein coding RNA 2977 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28815 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28817 Neighboring gene sushi domain containing 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28819 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:114854003-114854649 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106106 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:114860013-114860932 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:114860933-114861851 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:114882774-114883345 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:114906608-114907807 Neighboring gene RNA, U6 small nuclear 855, pseudogene Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:114928255-114928756 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:114928757-114929256 Neighboring gene ribosomal protein L29 pseudogene 20

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. 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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:114803312-114803951
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:114803952-114804590

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_085231.2 

    Range
    101..1379
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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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    112041032..112042310
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    124212431..124213709
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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