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LOC112543433 MED14-independent group 3 enhancer GRCh37_chr18:68004081-68005280 [ Homo sapiens (human) ]

Gene ID: 112543433, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112543433
Gene description
MED14-independent group 3 enhancer GRCh37_chr18:68004081-68005280
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 in HCT116 colorectal carcinoma cells. This sequence was defined as a group 3 enhancer that depends on the BRD2, BRD4, P300/CBP and CDK7 cofactors, but it has limited or no dependence on the MED14 core Mediator complex subunit. 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 K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). The same subregion also displayed weak activation by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Aug 2022]
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Genomic context

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Location:
18q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (70336845..70338044)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (70551909..70553108)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (68004369..68004663)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985158 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:67944250-67944750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9540 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:67960199-67960375 Neighboring gene suppressor of cytokine signaling 6 Neighboring gene long intergenic non-protein coding RNA 1909 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:68015472-68016064 Neighboring gene liver cell viability associated lncRNA Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:68024559-68025758 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:68033479-68034190 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr18:68034191-68034901 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr18:68051227-68052426 Neighboring gene long intergenic non-protein coding RNA 1910 Neighboring gene LARP7 pseudogene 3

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

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

  • Sharpr-MPRA regulatory region 10196

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_057384.2 

    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    70336845..70338044
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    70551909..70553108
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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