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LOC126862936 MED14-independent group 3 enhancer GRCh37_chr19:56602588-56603787 [ Homo sapiens (human) ]

Gene ID: 126862936, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126862936
Gene description
MED14-independent group 3 enhancer GRCh37_chr19:56602588-56603787
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 marked by the H3K27ac and H3K4me1 histone modifications were also shown to be active enhancers by ChIP-STARR-seq in naive human embryonic stem cells. [provided by RefSeq, Nov 2022]
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Genomic context

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See LOC126862936 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (56091219..56092435)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (59190072..59191288)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene NLR family pyrin domain containing 5 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:56537936-56539135 Neighboring gene long intergenic non-protein coding RNA 1864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11062 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15111 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11063 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56596377-56596878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56596879-56597378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:56597714-56598313 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51805 Neighboring gene zinc finger protein 787 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15112 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:56622697-56623374 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15113 Neighboring gene uncharacterized LOC124904773 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56626767-56627443 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56628849-56629564 Neighboring gene Sharpr-MPRA regulatory region 1998 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:56632431-56633146 Neighboring gene uncharacterized LOC124904772

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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:56602793-56603298
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:56603299-56603804

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_087433.2 

    Range
    101..1317
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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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    56091219..56092435
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    59190072..59191288
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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