U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC112997534 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:77702656-77703855 [ Homo sapiens (human) ]

Gene ID: 112997534, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC112997534
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:77702656-77703855
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. It 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 a functional enhancer 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 Activating non-DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). 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 histone modification. 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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (76781503..76782702)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (80122204..80123403)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (77703089..77703383)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene shroom family member 3 Neighboring gene uncharacterized LOC105377290 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:77585909-77587108 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr4:77610214-77610736 Neighboring gene SUMO2 pseudogene 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:77618582-77619300 Neighboring gene SHROOM3 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 6551 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15489 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15491 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15492 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:77707749-77708250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:77708251-77708750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:77722401-77723191 Neighboring gene uncharacterized LOC124900719 Neighboring gene putative uncharacterized protein encoded by LINC00596

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 21631
  • H3K27ac hESC enhancer GRCh37_chr4:77702895-77703854
  • Sharpr-MPRA regulatory region 8749

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_061527.2 

    Range
    101..1300
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    76781503..76782702
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    80122204..80123403
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases