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LOC125418085 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:46431794-46432993 [ Homo sapiens (human) ]

Gene ID: 125418085, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125418085
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:46431794-46432993
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. 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. Two subregions marked by the H3K27ac and H3K4me1 histone modifications were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells. Another subregion was validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Nov 2022]
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Genomic context

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See LOC125418085 in Genome Data Viewer
Location:
21q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (45011879..45013933)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (43374048..43376102)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46422723-46423264 Neighboring gene long intergenic non-protein coding RNA 165 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46436709-46437209 Neighboring gene P38 inhibited cutaneous squamous cell carcinoma associated lincRNA Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46438875-46439748 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46448329-46448828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46451141-46451808 Neighboring gene uncharacterized LOC105372836 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:46470000-46471199 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46471769-46472400 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46484683-46485516 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13399 Neighboring gene signal sequence receptor subunit 4 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46513297-46513797 Neighboring gene adenosine deaminase RNA specific B1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13400 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18586 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46553428-46553928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46553929-46554429 Neighboring gene Sharpr-MPRA regulatory region 4412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46569001-46569596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46571268-46572124 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46580749-46581394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46622742-46623359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46626875-46627374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46640206-46640772

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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_chr21:46431879-46432864
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46432865-46433848
  • Sharpr-MPRA regulatory region 531

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_081111.3 

    Range
    101..2155
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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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    45011879..45013933
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    43374048..43376102
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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