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LOC121725167 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:197121050-197122249 [ Homo sapiens (human) ]

Gene ID: 121725167, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121725167
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:197121050-197122249
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 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 (MPRA) 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. A subregion was also validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). Another subregion was also validated as an enhancer by ChIP-STARR-seq in primed human embryonic stem cells, where it is marked by the H3K4me1 histone modification. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their 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 LOC121725167 in Genome Data Viewer
Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (197394070..197395378)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (200120878..200122186)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (197121569..197121863)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101926923 Neighboring gene uncharacterized LOC124906373 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:197090769-197091337 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:197104842-197105355 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:197105356-197105868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21108 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:197136564-197137763 Neighboring gene NANOG hESC enhancer GRCh37_chr3:197144782-197145297 Neighboring gene uncharacterized LOC105374308 Neighboring gene MPRA-validated peak4993 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr3:197189524-197189726 Neighboring gene uncharacterized LOC105374309 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:197205169-197206368

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

  • ATAC-STARR-seq lymphoblastoid active region 21109
  • ATAC-STARR-seq lymphoblastoid active region 21110
  • H3K4me1 hESC enhancer GRCh37_chr3:197120941-197121442
  • Sharpr-MPRA regulatory region 14311

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_075637.3 

    Range
    101..1409
    Download
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    197394070..197395378
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    200120878..200122186
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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