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LOC126807225 MED14-independent group 3 enhancer GRCh37_chr4:180385948-180387147 [ Homo sapiens (human) ]

Gene ID: 126807225, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126807225
Gene description
MED14-independent group 3 enhancer GRCh37_chr4:180385948-180387147
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 region includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay. In HCT116 colorectal carcinoma cells, a subregion 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. Another subregion was also validated as an enhancer by ChIP-STARR-seq in primed human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors and is marked by the H3K27ac histone modification. [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC126807225 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (179464794..179466049)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (182806421..182807676)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORD65 Neighboring gene NANOG hESC enhancer GRCh37_chr4:179674014-179674924 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76488 Neighboring gene uncharacterized LOC105377563 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:179838787-179839346 Neighboring gene MPRA-validated peak5156 silencer Neighboring gene MPRA-validated peak5157 silencer Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:180086998-180087709 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:180087710-180088420 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:180091265-180091975 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76514 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76540 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:180630948-180631634 Neighboring gene NANOG hESC enhancer GRCh37_chr4:180647508-180648029 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15820 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22172 Neighboring gene uncharacterized LOC124900818 Neighboring gene uncharacterized LOC124900623 Neighboring gene uncharacterized LOC124900819

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. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:180386615-180387203

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_083546.2 

    Range
    101..1356
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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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    179464794..179466049
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    182806421..182807676
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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