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LOC121740638 BRD4-independent group 4 enhancer GRCh37_chr6:10403277-10404476 [ Homo sapiens (human) ]

Gene ID: 121740638, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121740638
Gene description
BRD4-independent group 4 enhancer GRCh37_chr6:10403277-10404476
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. A subregion 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. An overlapping subregion was also validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). Another 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 two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or repress 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 LOC121740638 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (10403044..10404863)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (10270774..10272593)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (10404389..10404683)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RPL7L1 pseudogene 20 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:10390646-10391250 Neighboring gene uncharacterized LOC124901485 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:10399255-10399797 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:10399798-10400339 Neighboring gene transcription factor AP-2 alpha Neighboring gene TFAP2A antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16900 Neighboring gene TFAP2A antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:10414531-10415188 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:10415189-10415848 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:10416507-10417164 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:10417165-10417822 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:10419141-10419798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16901 Neighboring gene uncharacterized LOC107986564 Neighboring gene long intergenic non-protein coding RNA 518

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  3. 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
  4. 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 23966
  • ATAC-STARR-seq lymphoblastoid silent region 16899
  • H3K27ac hESC enhancer GRCh37_chr6:10404479-10405096
  • Sharpr-MPRA regulatory region 6139

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_075700.3 

    Range
    101..1920
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    10403044..10404863
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    10270774..10272593
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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