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LOC126863250 BRD4-independent group 4 enhancer GRCh37_chrX:46404230-46405429 [ Homo sapiens (human) ]

Gene ID: 126863250, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126863250
Gene description
BRD4-independent group 4 enhancer GRCh37_chrX:46404230-46405429
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]
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Genomic context

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See LOC126863250 in Genome Data Viewer
Location:
chromosome: X
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (46544795..46545994)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (45951763..45952962)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene KRAB box domain containing 4 Neighboring gene VEZT pseudogene 1 Neighboring gene zinc finger protein 674 Neighboring gene U6 spliceosomal RNA Neighboring gene RNA, U6 small nuclear 50, pseudogene Neighboring gene ZNF674 antisense RNA 1 (head to head) Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:46411040-46411938 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29571 Neighboring gene marker of proliferation Ki-67 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20790 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20791 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:46447043-46447647 Neighboring gene carbohydrate sulfotransferase 7 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:46447648-46448251

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 29570

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_087746.1 

    Range
    101..1300
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    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    46544795..46545994
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    45951763..45952962
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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