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LOC126805690 BRD4-independent group 4 enhancer GRCh37_chr1:33592415-33593614 [ Homo sapiens (human) ]

Gene ID: 126805690, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126805690
Gene description
BRD4-independent group 4 enhancer GRCh37_chr1:33592415-33593614
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. A subregion was also validated as an enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it is marked by the H3K27ac histone modification. 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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Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (33126814..33128013)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (32986691..32987890)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903969 Neighboring gene uncharacterized LOC105378635 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 615 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33549697-33550196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33557899-33558556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 706 Neighboring gene antizyme inhibitor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33605527-33606126 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:33606727-33607326 Neighboring gene zinc finger protein 362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33628780-33629512 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33629513-33630245 Neighboring gene tripartite motif containing 62 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7027 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7034 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 619 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 618 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7054 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7061 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33685009-33685609 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33685744-33686528 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33709758-33710342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 622 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 621 Neighboring gene Sharpr-MPRA regulatory region 4113 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33729134-33729634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33734235-33734736 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33760897-33761407 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:33764372-33764552 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33764984-33765933 Neighboring gene MPRA-validated peak168 silencer Neighboring gene alpha 1,3-galactosyltransferase 2

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
  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

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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 707
  • H3K27ac hESC enhancer GRCh37_chr1:33592681-33593184

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_082014.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    33126814..33128013
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    32986691..32987890
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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