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LOC126806956 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:4764243-4765442 [ Homo sapiens (human) ]

Gene ID: 126806956, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126806956
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:4764243-4765442
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 region includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA). The major subregion had activity 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 were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells, where both are associated with the NANOG transcription factor and are marked by the H3K27ac and H3K4me1 histone modifications. 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 LOC126806956 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (4762516..4764044)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (4732111..4733639)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900165 Neighboring gene STX18 antisense RNA 1 (head to head) Neighboring gene long intergenic non-protein coding RNA 3091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15215 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:4584074-4584574 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:4611951-4612940 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:4641873-4642792 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:4643711-4644628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:4652800-4653697 Neighboring gene NFE2L2 motif-containing MPRA enhancer 85 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:4666938-4667438 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:4668341-4668936 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15216 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:4672506-4673099 Neighboring gene small nucleolar RNA, C/D box 162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21231 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:4760651-4761066 Neighboring gene uncharacterized LOC101928279 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:4782258-4783457 Neighboring gene Sharpr-MPRA regulatory region 11147 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:4853897-4854854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:4854855-4855811 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15217 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15218 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15219 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:4864037-4864708 Neighboring gene long intergenic non-protein coding RNA 1396 Neighboring gene msh homeobox 1

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. 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
  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

  • ATAC-STARR-seq lymphoblastoid active region 21232
  • ATAC-STARR-seq lymphoblastoid active region 21233
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:4764697-4765233
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:4765234-4765771

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_083277.2 

    Range
    101..1629
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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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    4762516..4764044
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    4732111..4733639
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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