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LOC126862353 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:53132870-53134069 [ Homo sapiens (human) ]

Gene ID: 126862353, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126862353
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:53132870-53134069
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 an enhancer that was validated 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. This locus also includes four accessible chromatin subregions, three of which were validated as enhancers and one 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: 16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (53098870..53100157)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (58896613..58897900)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene MTCH2 pseudogene 4 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:53078114-53078979 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:53089197-53089728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10831 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:53094537-53094763 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10832 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10833 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10834 Neighboring gene CHD9 neighbor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10835 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10836 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr16:53119716-53120520 Neighboring gene chromodomain helicase DNA binding protein 9 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:53125251-53125936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10841 Neighboring gene MPRA-validated peak2596 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7494 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7495 Neighboring gene Sharpr-MPRA regulatory region 10980 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr16:53241747-53242336 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr16:53242337-53242924 Neighboring gene thyroid hormone receptor interactor 13 pseudogene Neighboring gene thyroid hormone receptor interactor 13 pseudogene Neighboring gene small nucleolar RNA U13

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

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 10837
  • ATAC-STARR-seq lymphoblastoid active region 10838
  • ATAC-STARR-seq lymphoblastoid active region 10839
  • ATAC-STARR-seq lymphoblastoid silent region 7493

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_086851.2 

    Range
    101..1388
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    53098870..53100157
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    58896613..58897900
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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