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LOC126859801 MED14-independent group 3 enhancer GRCh37_chr6:135921214-135922413 [ Homo sapiens (human) ]

Gene ID: 126859801, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126859801
Gene description
MED14-independent group 3 enhancer GRCh37_chr6:135921214-135922413
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 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, 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. A subregion was also validated as an enhancer by ChIP-STARR-seq in primed human embryonic stem cells, where it is marked by the H3K27ac histone modification. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in K562 erythroleukemia cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC126859801 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (135600076..135601275)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (136788342..136789541)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated MYB cis-regulatory element XLOC_042889 Neighboring gene uncharacterized LOC124901407 Neighboring gene Sharpr-MPRA regulatory region 12318 Neighboring gene Abelson helper integration site 1 Neighboring gene beta-transducin repeat containing E3 ubiquitin protein ligase pseudogene 1 Neighboring gene MPRA-validated peak6137 silencer Neighboring gene MPRA-validated peak6138 silencer Neighboring gene MPRA-validated peak6140 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17569 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17570 Neighboring gene AHI1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17571 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene 73 Neighboring gene long intergenic non-protein coding RNA 2524

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, 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

  • H3K27ac hESC enhancer GRCh37_chr6:135921449-135921948
  • ReSE screen-validated silencer GRCh37_chr6:135921745-135921942

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_084302.1 

    Range
    101..1300
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    135600076..135601275
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    136788342..136789541
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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