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LOC112163542 BRD4-independent group 4 enhancer GRCh37_chr12:129281709-129282908 [ Homo sapiens (human) ]

Gene ID: 112163542, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112163542
Gene description
BRD4-independent group 4 enhancer GRCh37_chr12:129281709-129282908
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. 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 enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 15:Elon, transcriptional elongation, stronger H3K36me3, more exonic), with weaker activity in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 15:Elon). 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 LOC112163542 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 (128797164..128798363)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (128829167..128830366)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (129282049..129282343)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene transmembrane protein 132C Neighboring gene microRNA 3612 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr12:128867427-128868398 Neighboring gene NANOG hESC enhancer GRCh37_chr12:128866078-128866579 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:128868399-128869369 Neighboring gene uncharacterized LOC124903115 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:128942780-128943732 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:128943733-128944685 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:129028409-129028584 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7326 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5087 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:129141297-129142496 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:129148562-129149148 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25284 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:129192543-129193044 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:129193045-129193544 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7327 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:129212543-129213042 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:129238411-129239610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:129271367-129271867 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7328 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7329 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:129276413-129276913 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7331 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:129286977-129287478 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:129287479-129287978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7333 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7334 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7335 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7336 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7337 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7338 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7339 Neighboring gene uncharacterized LOC124903083 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7341 Neighboring gene solute carrier family 15 member 4 Neighboring gene uncharacterized LOC124903089

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 7332
  • Sharpr-MPRA regulatory region 7648

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_056566.2 

    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
    128797164..128798363
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    128829167..128830366
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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