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LOC126859645 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:30736863-30738062 [ Homo sapiens (human) ]

Gene ID: 126859645, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126859645
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:30736863-30738062
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. This sequence was defined as a group 1 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors in HCT116 colorectal carcinoma cells, with strong dependence on P300/CBP. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells, where both are marked by the H3K27ac and H3K4me1 histone modifications. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in HepG2 liver carcinoma cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC126859645 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (30769086..30770285)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (30633420..30634619)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:30711111-30711991 Neighboring gene IER3 antisense RNA 1 Neighboring gene immediate early response 3 Neighboring gene RNA, 7SL, cytoplasmic 353, pseudogene Neighboring gene Sharpr-MPRA regulatory region 12821 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:30731545-30732332 Neighboring gene HLA complex group 20 Neighboring gene Sharpr-MPRA regulatory region 6937 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:30756540-30756717 Neighboring gene CRISPRi-validated cis-regulatory element chr6.1563 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91437 Neighboring gene Sharpr-MPRA regulatory region 6414 Neighboring gene long intergenic non-protein coding RNA 243 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:30795009-30795509 Neighboring gene Sharpr-MPRA regulatory region 12192 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:30808614-30808790 Neighboring gene long intergenic non-protein coding RNA 2570 Neighboring gene Sharpr-MPRA regulatory region 587 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:30814964-30815466

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, 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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:30736947-30737478
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:30737479-30738010
  • ReSE screen-validated silencer GRCh37_chr6:30736912-30737091

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_084146.1 

    Range
    101..1300
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    30769086..30770285
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    2248796..2249994
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    2025056..2026255
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    2079328..2080527
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    2024175..2025374
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    30633420..30634619
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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