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LOC112163607 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:53692451-53693650 [ Homo sapiens (human) ]

Gene ID: 112163607, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112163607
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:53692451-53693650
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 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 both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). This locus also includes four 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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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (53298667..53299919)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (53264378..53265630)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (53693289..53693583)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6405 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:53645725-53646396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6406 Neighboring gene major facilitator superfamily domain containing 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6407 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:53670028-53670528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:53670529-53671029 Neighboring gene extra spindle pole bodies like 1, separase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:53684247-53684748 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:53689034-53690233 Neighboring gene prefoldin subunit 5 Neighboring gene MYG1 exonuclease Neighboring gene aladin WD repeat nucleoporin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6414 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:53717573-53718306 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:53721571-53722293 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:53722294-53723015 Neighboring gene Sp7 transcription factor

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

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 6410
  • ATAC-STARR-seq lymphoblastoid active region 6411
  • ATAC-STARR-seq lymphoblastoid active region 6412
  • ATAC-STARR-seq lymphoblastoid active region 6413
  • Sharpr-MPRA regulatory region 12

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_056588.3 

    Range
    101..1353
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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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    53298667..53299919
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791795.1 Reference GRCh38.p14 PATCHES

    Range
    22427..23678
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    53264378..53265630
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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