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LOC126859711 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:74289636-74290835 [ Homo sapiens (human) ]

Gene ID: 126859711, updated on 12-Sep-2024

Summary

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Gene symbol
LOC126859711
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:74289636-74290835
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 (MPRA). 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 primed human embryonic stem cells, where both are associated with the OCT4 and NANOG transcription factors and are marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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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See LOC126859711 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (73579754..73581441)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (74756803..74758487)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (74289477..74291164)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:74229093-74229915 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74229916-74230737 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74230738-74231560 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17336 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17337 Neighboring gene EEF1A1 antisense RNA 1 Neighboring gene eukaryotic translation elongation factor 1 alpha 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24751 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24752 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:74273247-74273796 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74275447-74275996 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74285738-74286453 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74291165-74292007 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94401 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94402 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94403 Neighboring gene solute carrier family 17 member 5 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94405 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:74329139-74329367 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:74333473-74333650 Neighboring gene ribosomal protein S27 pseudogene 15 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94408 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94411 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94412 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94413 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94414 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94416 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17338 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24754 Neighboring gene Sharpr-MPRA regulatory region 11313 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24755 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74405769-74406483 Neighboring gene CD109 antisense RNA 1 Neighboring gene CD109 molecule

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 within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 24753
  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74289477-74290320
  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74290321-74291164

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_084212.2 

    Range
    101..1788
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    73579754..73581441
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    74756803..74758487
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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