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LOC126862181 BRD4-independent group 4 enhancer GRCh37_chr15:75090696-75091895 [ Homo sapiens (human) ]

Gene ID: 126862181, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126862181
Gene description
BRD4-independent group 4 enhancer GRCh37_chr15:75090696-75091895
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 includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA). In HCT116 colorectal carcinoma cells, a subregion 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. Another subregion was also validated as an enhancer by ChIP-STARR-seq in primed human embryonic stem cells, where it is marked by the H3K4me1 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: 15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (74798112..74799554)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (72668006..72669448)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene CYP1A2 5' regulatory region Neighboring gene cytochrome P450 family 1 subfamily A member 2 Neighboring gene dioxin-responsive -38 kb CYP1A2 enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75059675-75060452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75063617-75064332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75064333-75065046 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75066003-75066580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75070096-75070626 Neighboring gene Sharpr-MPRA regulatory region 4992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9791 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9792 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6657 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75075123-75075698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9793 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9794 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9795 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9796 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:75080141-75080318 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75084649-75085478 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75085479-75086307 Neighboring gene C-terminal Src kinase Neighboring gene microRNA 4513 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75092171-75093022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75093023-75093872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75112197-75113010 Neighboring gene lectin, mannose binding 1 like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75113011-75113824 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75114639-75115451 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:75118950-75119157 Neighboring gene uncharacterized LOC105370897 Neighboring gene complexin 3

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 9806
  • H3K4me1 hESC enhancer GRCh37_chr15:75090468-75091319

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_086679.3 

    Range
    101..1543
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    74798112..74799554
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    72668006..72669448
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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