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LOC126860795 MED14-independent group 3 enhancer GRCh37_chr9:139444236-139445435 [ Homo sapiens (human) ]

Gene ID: 126860795, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126860795
Gene description
MED14-independent group 3 enhancer GRCh37_chr9:139444236-139445435
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). 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 both are associated with the NANOG transcription factor and are 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: 9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (136549641..136551464)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (148781500..148783323)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene notch receptor 1 Neighboring gene uncharacterized LOC124902310 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139420763-139421634 Neighboring gene microRNA 4673 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29311 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20525 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139433302-139433969 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139434130-139434814 Neighboring gene Sharpr-MPRA regulatory region 6589 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139436183-139436865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20527 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20528 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20529 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139441357-139442268 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29316 Neighboring gene microRNA 4674 Neighboring gene NOTCH1 associated lncRNA in T cell acute lymphoblastic leukemia 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139458066-139458926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139458927-139459788 Neighboring gene VISTA enhancer hs2207 Neighboring gene uncharacterized LOC124902311 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29317 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139473242-139473768 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139479375-139480026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139493297-139493830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139494899-139495430 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139495673-139496524 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:139499139-139499319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139499925-139500774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139501625-139502474 Neighboring gene Sharpr-MPRA regulatory region 9516 Neighboring gene long intergenic non-protein coding RNA 1451

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 29315
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139444093-139445004
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139445005-139445916

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_085294.2 

    Range
    101..1924
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    136549641..136551464
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    148781500..148783323
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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