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LOC126861995 MED14-independent group 3 enhancer GRCh37_chr14:73524555-73525754 [ Homo sapiens (human) ]

Gene ID: 126861995, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126861995
Gene description
MED14-independent group 3 enhancer GRCh37_chr14:73524555-73525754
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 (MPRA). 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 naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. 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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Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (73057811..73059046)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (67263366..67264601)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73437151-73437652 Neighboring gene zinc finger FYVE-type containing 1 Neighboring gene MPRA-validated peak2195 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8692 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:73502840-73503013 Neighboring gene RNA, 7SL, cytoplasmic 586, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73531656-73532156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73532157-73532657 Neighboring gene RBM25 antisense RNA 1 Neighboring gene required for meiotic nuclear division 1 homolog (S. cerevisiae) pseudogene Neighboring gene RNA binding motif protein 25 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:73591861-73592400 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5904 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8694 Neighboring gene presenilin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73635088-73636024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73636025-73636961 Neighboring gene NANOG hESC enhancer GRCh37_chr14:73637234-73637812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:73651850-73652468 Neighboring gene NANOG hESC enhancer GRCh37_chr14:73689643-73690155

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. 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
  3. 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

  • ATAC-STARR-seq lymphoblastoid active region 8693
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:73524519-73525483

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_086493.2 

    Range
    101..1336
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    73057811..73059046
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    67263366..67264601
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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