U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    LOC126859567 BRD4-independent group 4 enhancer GRCh37_chr6:5581546-5582745 [ Homo sapiens (human) ]

    Gene ID: 126859567, updated on 10-Oct-2023

    Summary

    Go to the top of the page Help
    Gene symbol
    LOC126859567
    Gene description
    BRD4-independent group 4 enhancer GRCh37_chr6:5581546-5582745
    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 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. 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
    Location:
    chromosome: 6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (5581313..5582512)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (5450599..5451798)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene LYRM4 antisense RNA 1 Neighboring gene LYR motif containing 4 Neighboring gene uncharacterized LOC124901249 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23902 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16874 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23903 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23904 Neighboring gene Sharpr-MPRA regulatory region 4425 Neighboring gene phenylalanyl-tRNA synthetase 2, mitochondrial Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:5368745-5369944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23906 Neighboring gene NANOG hESC enhancer GRCh37_chr6:5412113-5412622 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:5438556-5439472 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:5439473-5440389 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5456946-5457932 Neighboring gene FARS2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23907 Neighboring gene MPRA-validated peak5636 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23908 Neighboring gene NANOG hESC enhancer GRCh37_chr6:5529614-5530223 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:5541695-5542894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23910 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 37 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:5639236-5640099 Neighboring gene uncharacterized LOC101927950 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:5665450-5666649 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:5672975-5673971

    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

    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 23909

    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_084068.1 

      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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      5581313..5582512
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      5450599..5451798
      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