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LOC126863046 BRD4-independent group 4 enhancer GRCh37_chr20:49157072-49158271 [ Homo sapiens (human) ]

Gene ID: 126863046, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126863046
Gene description
BRD4-independent group 4 enhancer GRCh37_chr20:49157072-49158271
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 H3K27ac histone modification were also shown to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells. 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: 20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (50540535..50542082)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (52310192..52311739)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 10608 Neighboring gene RNA, 7SL, cytoplasmic 636, pseudogene Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:49056367-49057566 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49065061-49066026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49074250-49074778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49076728-49077228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18087 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18088 Neighboring gene cytochrome c oxidase subunit 6C pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18090 Neighboring gene Sharpr-MPRA regulatory region 4283 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49126094-49126681 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13022 Neighboring gene protein tyrosine phosphatase non-receptor type 1 Neighboring gene Sharpr-MPRA regulatory region 13607 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:49177610-49178809 Neighboring gene RNA, 7SL, cytoplasmic 672, pseudogene Neighboring gene microRNA 645

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 18092
  • H3K27ac hESC enhancer GRCh37_chr20:49157618-49158118
  • H3K27ac hESC enhancer GRCh37_chr20:49158119-49158619

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_087543.2 

    Range
    101..1648
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    50540535..50542082
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    52310192..52311739
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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