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LOC126805612 MED14-independent group 3 enhancer GRCh37_chr1:9778914-9780113 [ Homo sapiens (human) ]

Gene ID: 126805612, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126805612
Gene description
MED14-independent group 3 enhancer GRCh37_chr1:9778914-9780113
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 human embryonic stem cells. [provided by RefSeq, Oct 2022]
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Genomic context

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Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (9718285..9720237)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (9261067..9263020)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta Neighboring gene PIK3CD antisense RNA 2 Neighboring gene ribosomal protein L26 pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 229 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 136 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:9748072-9748266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9749677-9750360 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9750361-9751042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9761057-9761631 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9769519-9770216 Neighboring gene MPRA-validated peak57 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9775415-9776390 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9776391-9777366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 231 Neighboring gene uncharacterized LOC124903839 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9780296-9781272 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9781273-9782247 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:9785121-9785329 Neighboring gene calsyntenin 1 Neighboring gene MPRA-validated peak58 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9846382-9846882 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9848516-9849304 Neighboring gene Sharpr-MPRA regulatory region 8161 Neighboring gene mitotic spindle organizing protein 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 232 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9883897-9884613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 137 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9895719-9896320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9896321-9896920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9902151-9902692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9902693-9903232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9903774-9904313 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9908375-9908876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 139 Neighboring gene uncharacterized LOC105376717 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9911316-9912116 Neighboring gene catenin beta interacting protein 1

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_chr1:9778343-9779319
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9779320-9780295

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_081936.2 

    Range
    101..2053
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    9718285..9720237
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    9261067..9263020
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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