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LOC126860242 MED14-independent group 3 enhancer GRCh37_chr7:155534138-155535337 [ Homo sapiens (human) ]

Gene ID: 126860242, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126860242
Gene description
MED14-independent group 3 enhancer GRCh37_chr7:155534138-155535337
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. 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 (155741444..155742643)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (156922467..156923666)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes 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 H3K4me1 hESC enhancer GRCh37_chr7:155334782-155335582 Neighboring gene canopy FGF signaling regulator 1 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 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26899 Neighboring gene RNA binding motif protein 33 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:155520719-155521219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26901 Neighboring gene VISTA enhancer hs1268 Neighboring gene Sharpr-MPRA regulatory region 9615 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26902 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:155561116-155561309 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:155567610-155568809 Neighboring gene Sharpr-MPRA regulatory region 3765 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155574696-155575231 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155575232-155575766 Neighboring gene MPRA-validated peak6863 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26903 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:155597860-155598829 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:155598830-155599798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155607457-155608100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155608399-155608900 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:155628074-155629066 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:155632935-155634134 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:155638472-155638619 Neighboring gene MPRA-validated peak6864 silencer Neighboring gene sonic hedgehog signaling molecule Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:155661375-155662574 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26904 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:155678617-155679816 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:155743904-155745103 Neighboring gene uncharacterized LOC124901788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155745489-155745989 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:155747182-155747910

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

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 26900

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_084743.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    155741444..155742643
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    156922467..156923666
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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