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LOC124629374 BRD4-independent group 4 enhancer GRCh37_chr12:56731981-56733180 [ Homo sapiens (human) ]

Gene ID: 124629374, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124629374
Gene description
BRD4-independent group 4 enhancer GRCh37_chr12:56731981-56733180
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 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 4 enhancer that depends on the BRD2, P300/CBP, MED14 and CDK7 cofactors, but it has limited or no dependence on the BRD4 bromodomain protein. A subregion was also validated as a functional repressive element 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 Repressive non-DNase unmatched - State 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). 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]
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Genomic context

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See LOC124629374 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (56338197..56339396)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (56305843..56307042)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene CNPY2 antisense RNA 1 Neighboring gene canopy FGF signaling regulator 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:56709757-56710345 Neighboring gene MPRA-validated peak1742 silencer Neighboring gene poly(A) specific ribonuclease subunit PAN2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6491 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:56730556-56731403 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29688 Neighboring gene interleukin 23 subunit alpha Neighboring gene signal transducer and activator of transcription 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4558 Neighboring gene RNA, U7 small nuclear 40 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6495 Neighboring gene apolipoprotein F

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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 6492
  • Sharpr-MPRA regulatory region 7971

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_079744.2 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    56338197..56339396
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    56305843..56307042
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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