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LOC127889662 H3K4me1 hESC enhancer GRCh37_chr18:75611971-75612487 [ Homo sapiens (human) ]

Gene ID: 127889662, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127889662
Gene description
H3K4me1 hESC enhancer GRCh37_chr18:75611971-75612487
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 region was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive 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 a silencer based on its ability to 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 LOC127889662 in Genome Data Viewer
Location:
chromosome: 18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (77900015..77900531)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (78131625..78132141)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985129 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:75465232-75465784 Neighboring gene NANOG hESC enhancer GRCh37_chr18:75474392-75475106 Neighboring gene MPRA-validated peak3188 silencer Neighboring gene VISTA enhancer hs1020 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:75535169-75536368 Neighboring gene VISTA enhancer hs1186 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:75577351-75577852 Neighboring gene RNA, 5S ribosomal pseudogene 461 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:75609611-75610121 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:75617943-75618714 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:75629975-75630209 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50500 Neighboring gene NANOG hESC enhancer GRCh37_chr18:75682747-75683315 Neighboring gene long intergenic non-protein coding RNA 1029 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:75714815-75715343 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr18:75717895-75718640 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr18:75718641-75719385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:75791151-75791652 Neighboring gene RNA, U6 small nuclear 655, pseudogene

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. 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
  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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 9567

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_139180.1 

    Range
    101..617
    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    77900015..77900531
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    78131625..78132141
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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