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LOC126860945 BRD4-independent group 4 enhancer GRCh37_chr10:64414839-64416038 [ Homo sapiens (human) ]

Gene ID: 126860945, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126860945
Gene description
BRD4-independent group 4 enhancer GRCh37_chr10:64414839-64416038
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 three accessible chromatin subregions that were validated as enhancers based on their 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. Another subregion containing a Neanderthal adaptively introgressed genetic variant was also validated as an enhancer by MPRAs in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 10:64415184 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC126860945 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (62655079..62656278)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (63512904..63514103)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC283045 Neighboring gene RNA, 7SL, cytoplasmic 591, pseudogene Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:64143375-64144574 Neighboring gene zinc finger protein 365 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:64224563-64225064 Neighboring gene NANOG hESC enhancer GRCh37_chr10:64242262-64242794 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_13640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3417 Neighboring gene uncharacterized LOC105378327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3422 Neighboring gene talanin Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_13669 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_13680 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3424 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_13703 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_13720/13722 and experimental_13723 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:64437081-64437582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:64437583-64438082 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3428 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_13731 Neighboring gene aldehyde dehydrogenase 7 family member A1 pseudogene 4 Neighboring gene uncharacterized LOC124902437

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. 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

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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

  • ATAC-STARR-seq lymphoblastoid active region 3425
  • ATAC-STARR-seq lymphoblastoid active region 3426
  • ATAC-STARR-seq lymphoblastoid active region 3427
  • Neanderthal introgressed variant-containing enhancer experimental_13694

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_085444.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    62655079..62656278
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    63512904..63514103
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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