U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC126863088 BRD4-independent group 4 enhancer GRCh37_chr20:62495674-62496873 [ Homo sapiens (human) ]

Gene ID: 126863088, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC126863088
Gene description
BRD4-independent group 4 enhancer GRCh37_chr20:62495674-62496873
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 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 4 enhancer that depends on the BRD2, P300/CBP, MED14 and CDK7 cofactors, but it has limited or no dependence on the BRD4 bromodomain protein. A subregion was also validated as an enhancer by ChIP-STARR-seq in primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63864321..63865520)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65684164..65685363)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62475261-62475938 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62477766-62477915 Neighboring gene chromosome 20 putative open reading frame 181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18253 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62484853-62485706 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13189 Neighboring gene uncharacterized LOC112268269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18254 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62497355-62498074 Neighboring gene abhydrolase domain containing 16B Neighboring gene TPD52 like 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61287 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61295 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61302 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62517585-62517755 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62525794-62526321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13191 Neighboring gene DnaJ heat shock protein family (Hsp40) member C5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62541709-62542208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62543630-62544130 Neighboring gene RNA, U1 small nuclear 134, pseudogene Neighboring gene uncharacterized LOC124904951 Neighboring gene microRNA 941-1 Neighboring gene microRNA 941-2

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 silent region 13190
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62495913-62496633

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_087584.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    63864321..63865520
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    65684164..65685363
    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