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LOC106799846 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:3791796-3792995 [ Homo sapiens (human) ]

Gene ID: 106799846, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106799846
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:3791796-3792995
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 region, which is poorly conserved between human and mouse at the sequence level, overlaps the non-coding gene LINC01730 on chromosome 20. A 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. An overlapping subregion was also shown to function as an enhancer in human Jurkat T cells, where its chromatin structure represents a histone acetylation island in human T cells based on the diacetylation of histone H3 at lysines 9 and 14. Another subregion was shown to be an enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Dec 2022]
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Genomic context

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Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (3811149..3812516)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (3842084..3843451)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (3792104..3793163)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3766083-3766793 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3766794-3767503 Neighboring gene centromere protein B Neighboring gene cell division cycle 25B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3775953-3776684 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12630 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:3777341-3777548 Neighboring gene Sharpr-MPRA regulatory region 3723 Neighboring gene Sharpr-MPRA regulatory region 8683 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:3782484-3783683 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3787799-3788390 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3788391-3788981 Neighboring gene long intergenic non-protein coding RNA 1730 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12631 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:3800994-3801697 Neighboring gene adaptor related protein complex 5 subunit sigma 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:3811623-3812123 Neighboring gene NFE2L2 motif-containing MPRA enhancer 155/156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17487 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12633 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:3831491-3831992 Neighboring gene mitochondrial antiviral signaling protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3838319-3838818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3846659-3847160

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. Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. Roh TY, et al. Genome Res, 2007 Jan. PMID 17135569, Free PMC Article
  2. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Roh TY, et al. Genes Dev, 2005 Mar 1. PMID 15706033, Free PMC Article
  3. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  4. 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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3792566-3793115
  • non-conserved AI 110
  • nonconserved acetylation island sequence 110 enhancer

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_046147.2 

    Range
    101..1468
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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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    3811149..3812516
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    3842084..3843451
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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