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LOC126860241 MED14-independent group 3 enhancer GRCh37_chr7:155274926-155276125 [ Homo sapiens (human) ]

Gene ID: 126860241, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126860241
Gene description
MED14-independent group 3 enhancer GRCh37_chr7:155274926-155276125
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 was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) 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 naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. 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: 7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (155482231..155483430)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (156662827..156664026)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene EN2 divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr7:155233227-155233442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:155246511-155247036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155247037-155247562 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:155249486-155250477 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:155262299-155262494 Neighboring gene VISTA enhancer hs1418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155277075-155277575 Neighboring gene engrailed homeobox 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:155282581-155283314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18847 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:155286713-155287262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155290079-155290782 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18848 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:155301523-155302370 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr7:155302371-155303216 Neighboring gene canopy FGF signaling regulator 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155334782-155335582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155340869-155341370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155382158-155382978 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155386984-155387730 Neighboring gene Sharpr-MPRA regulatory region 10004 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:155436294-155437248 Neighboring gene RBM33 divergent transcript

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 26897
  • H3K4me1 hESC enhancer GRCh37_chr7:155275204-155275704

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_084742.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    155482231..155483430
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    156662827..156664026
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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