U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC126805638 MED14-independent group 3 enhancer GRCh37_chr1:18609585-18610784 [ Homo sapiens (human) ]

Gene ID: 126805638, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC126805638
Gene description
MED14-independent group 3 enhancer GRCh37_chr1:18609585-18610784
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 marked by the H3K4me1 histone modification were also shown to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells. Another subregion was validated as a silencer that could repress activity of a super core promoter (SCP1) by STARR-seq MPRAs in K562 erythroleukemia 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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC126805638 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (18282736..18284290)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (18102912..18104466)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene immunoglobin superfamily member 21 Neighboring gene IGSF21 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:18501697-18502198 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:18502199-18502698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18525748-18526248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18526249-18526749 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:18527418-18527918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18538061-18538884 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18557491-18558139 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18575476-18575976 Neighboring gene uncharacterized LOC124903864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18606867-18607381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18607382-18607895 Neighboring gene uncharacterized LOC124903863 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18620236-18621123 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:18622899-18623785 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18624079-18624604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18626609-18627236 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:18633258-18633415 Neighboring gene Sharpr-MPRA regulatory region 11488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18672835-18673336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18673337-18673836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18709612-18710411 Neighboring gene uncharacterized LOC124903865

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Candidate silencer elements for the human and mouse genomes. Doni Jayavelu N, et al. Nat Commun, 2020 Feb 26. PMID 32103011, Free PMC Article
  2. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  3. 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
  4. 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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 281
  • H3K4me1 hESC enhancer GRCh37_chr1:18609230-18609876
  • H3K4me1 hESC enhancer GRCh37_chr1:18609877-18610523
  • MPRA-validated peak94 silencer

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_081962.2 

    Range
    101..1655
    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
    18282736..18284290
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    18102912..18104466
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases