U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC126862918 MED14-independent group 3 enhancer GRCh37_chr19:47287225-47288424 [ Homo sapiens (human) ]

Gene ID: 126862918, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC126862918
Gene description
MED14-independent group 3 enhancer GRCh37_chr19:47287225-47288424
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). In HCT116 colorectal carcinoma cells, a subregion 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. Another subregion was also validated as an enhancer by ChIP-STARR-seq in naive and primed human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors and is marked by the H3K27ac and H3K4me1 histone modifications. 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 LOC126862918 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (46783968..46785251)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (49609789..49611072)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene protein kinase D2 Neighboring gene uncharacterized LOC107987269 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10823 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10824 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14847 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47228602-47229146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47230777-47231320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47231865-47232408 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:47233845-47235044 Neighboring gene striatin 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10825 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10828 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10829 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10827 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10826 Neighboring gene Sharpr-MPRA regulatory region 2893 Neighboring gene fukutin related protein Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47288509-47289110 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:47289111-47289712 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10830 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10831 Neighboring gene solute carrier family 1 member 5 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47291519-47292120 Neighboring gene heterogeneous nuclear ribonucleoprotein M pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14850 Neighboring gene small NF90 (ILF3) associated RNA E

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. 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

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 14848
  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47287907-47288508

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_087415.2 

    Range
    101..1384
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    46783968..46785251
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    49609789..49611072
    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