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LOC126859846 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:158183852-158185051 [ Homo sapiens (human) ]

Gene ID: 126859846, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126859846
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:158183852-158185051
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 region includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA). In HCT116 colorectal carcinoma cells, a subregion 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. Another subregion was also validated as an enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or repress 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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Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (157762391..157764061)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (159004415..159006085)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene zinc finger DHHC-type palmitoyltransferase 14 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157951781-157952686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157952687-157953591 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157954158-157954658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157954659-157955159 Neighboring gene MPRA-validated peak6260 silencer Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157973253-157974075 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157977751-157978536 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157982847-157983820 Neighboring gene microRNA 3692 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157993864-157994596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158014227-158014728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158014729-158015228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158037061-158037562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158037563-158038062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158066653-158067153 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:158069048-158070247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158090399-158091006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158091007-158091612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158109923-158110424 Neighboring gene uncharacterized LOC107986663 Neighboring gene NANOG hESC enhancer GRCh37_chr6:158127150-158127715 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:158131630-158132829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158134197-158134698 Neighboring gene uncharacterized LOC124901555 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158134699-158135198 Neighboring gene NANOG hESC enhancer GRCh37_chr6:158152966-158153487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158153745-158154270 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158162257-158162797 Neighboring gene Sharpr-MPRA regulatory region 4686 Neighboring gene Sharpr-MPRA regulatory region 7014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25338 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17727 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25339 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:158251124-158251862 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25340 Neighboring gene Sharpr-MPRA regulatory region 12251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25341 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17728 Neighboring gene sorting nexin 9 Neighboring gene Sharpr-MPRA regulatory region 15079 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17729 Neighboring gene SNX9 antisense RNA 1 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 26

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 25337
  • ATAC-STARR-seq lymphoblastoid silent region 17726
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158183423-158184350

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_084347.3 

    Range
    101..1771
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    157762391..157764061
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    159004415..159006085
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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