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LOC126863161 BRD4-independent group 4 enhancer GRCh37_chr22:43659412-43660611 [ Homo sapiens (human) ]

Gene ID: 126863161, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126863161
Gene description
BRD4-independent group 4 enhancer GRCh37_chr22:43659412-43660611
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). The major subregion had activity 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. Two subregions marked by the H3K4me1 histone modification were also shown to be active enhancers by ChIP-STARR-seq in naive human embryonic stem cells. This locus also includes two 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. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (43263406..43265018)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (43744300..43745912)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43564214-43565070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43565071-43565926 Neighboring gene tubulin tyrosine ligase like 12 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43581791-43582295 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13857 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13859 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43593145-43594077 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43594078-43595009 Neighboring gene signal peptide, CUB domain and EGF like domain containing 1 Neighboring gene SCUBE1 antisense RNA 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43616253-43616754 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:43621086-43621251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43621872-43622438 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43622439-43623004 Neighboring gene Sharpr-MPRA regulatory region 15411 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43634226-43634726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43634727-43635227 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:43643537-43644038 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:43647561-43647749 Neighboring gene uncharacterized LOC124905129 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43664742-43665530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43665531-43666317 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43673726-43674226 Neighboring gene SCUBE1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43678267-43678767 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43689171-43689688 Neighboring gene Sharpr-MPRA regulatory region 12495 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43696443-43696944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43696945-43697444 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43708128-43708708 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43708709-43709288 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43709955-43710456 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43724267-43725041 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43725042-43725815 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:43742520-43742665 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43765639-43766140 Neighboring gene uncharacterized LOC105373053 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43784068-43784646 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43784647-43785225

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 19189
  • ATAC-STARR-seq lymphoblastoid active region 19190
  • H3K4me1 hESC enhancer GRCh37_chr22:43660023-43660524
  • H3K4me1 hESC enhancer GRCh37_chr22:43660525-43661024

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_087657.2 

    Range
    101..1713
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    43263406..43265018
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    43744300..43745912
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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