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LOC126860956 MED14-independent group 3 enhancer GRCh37_chr10:75503472-75504671 [ Homo sapiens (human) ]

Gene ID: 126860956, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126860956
Gene description
MED14-independent group 3 enhancer GRCh37_chr10:75503472-75504671
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). This sequence was defined as a group 3 enhancer that depends on the BRD2, BRD4, P300/CBP and CDK7 cofactors in HCT116 colorectal carcinoma cells, but it has limited or no dependence on the MED14 core Mediator complex subunit. Two subregions marked by the H3K27ac histone modification were also shown to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells. 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: 10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (73743714..73744913)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (74615130..74616329)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene BMS1P4-AGAP5 readthrough Neighboring gene BMS1 pseudogene 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:75468020-75468273 Neighboring gene RNA, 5S ribosomal pseudogene 320 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3568 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:75491691-75492411 Neighboring gene glutamate dehydrogenase 1 pseudogene 3 Neighboring gene dual specificity phosphatase 8 pseudogene 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:75500671-75501238 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:75501239-75501806 Neighboring gene uncharacterized LOC124902453 Neighboring gene SEC24 homolog C, COPII coat complex component Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3570 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3571 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2487 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:75532921-75533451 Neighboring gene uncharacterized LOC107984243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3574 Neighboring gene fucosyltransferase 11

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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 3569
  • H3K27ac hESC enhancer GRCh37_chr10:75503511-75504078
  • H3K27ac hESC enhancer GRCh37_chr10:75504079-75504645

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_085455.1 

    Range
    101..1300
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    73743714..73744913
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    74615130..74616329
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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