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LOC126861355 BRD4-independent group 4 enhancer GRCh37_chr11:117738498-117739697 [ Homo sapiens (human) ]

Gene ID: 126861355, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126861355
Gene description
BRD4-independent group 4 enhancer GRCh37_chr11:117738498-117739697
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. 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 naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K4me1 histone modification. [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (117867783..117869291)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (117884182..117885690)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117690567-117691301 Neighboring gene FXYD6-FXYD2 readthrough Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117692983-117693536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117695199-117695752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117695753-117696305 Neighboring gene FXYD domain containing ion transport regulator 2 Neighboring gene FXYD6 antisense RNA 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:117712427-117713626 Neighboring gene FXYD domain containing ion transport regulator 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117726457-117726957 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:117740007-117740526 Neighboring gene Sharpr-MPRA regulatory region 1172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117778029-117778529 Neighboring gene transmembrane serine protease 13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117784655-117785647 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5577 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:117802800-117803339 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117803340-117803878 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_19102 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:117843533-117843947 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_19132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5579 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5580 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_19171 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117869597-117870098 Neighboring gene interleukin 10 receptor subunit alpha

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. 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

  • NANOG-H3K4me1 hESC enhancer GRCh37_chr11:117739486-117740006

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_085854.2 

    Range
    101..1609
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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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    117867783..117869291
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    117884182..117885690
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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