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LOC126805925 MED14-independent group 3 enhancer GRCh37_chr1:174817888-174819087 [ Homo sapiens (human) ]

Gene ID: 126805925, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126805925
Gene description
MED14-independent group 3 enhancer GRCh37_chr1:174817888-174819087
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. The major subregion had activity in HCT116 colorectal carcinoma cells, where it 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. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells, where those are marked by the H3K27ac and H3K4me1 histone modifications and associated with the NANOG transcription factor. [provided by RefSeq, Oct 2022]
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Genomic context

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Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (174848438..174849949)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (174201142..174202653)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RAB GTPase activating protein 1 like Neighboring gene ReSE screen-validated silencer GRCh37_chr1:174472688-174472877 Neighboring gene G protein-coupled receptor 52 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:174564621-174565222 Neighboring gene Sharpr-MPRA regulatory region 10542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2123 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2124 Neighboring gene BANF1 pseudogene 4 Neighboring gene NADH:ubiquinone oxidoreductase complex assembly factor 4 pseudogene 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:174871033-174871534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2125 Neighboring gene RABGAP1L antisense RNA 1 Neighboring gene ribosomal protein S26 pseudogene 12

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

  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:174817576-174818166
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:174818167-174818757

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_082249.2 

    Range
    101..1612
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    174848438..174849949
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    174201142..174202653
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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