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LOC127460059 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:103424099-103424877 [ Homo sapiens (human) ]

Gene ID: 127460059, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127460059
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:103424099-103424877
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 primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes two accessible chromatin subregions that were validated as silencers based on their 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 LOC127460059 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (102411871..102412649)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (103537782..103538560)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (103424099..103424877)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27748 Neighboring gene SUMO2 pseudogene 19 Neighboring gene UBR5 divergent transcript Neighboring gene ubiquitin protein ligase E3 component n-recognin 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27749 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27750 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:103329370-103329870 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr8:103335870-103336617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27751 Neighboring gene uncharacterized LOC124902086 Neighboring gene Sharpr-MPRA regulatory region 4694 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27753 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:103423320-103424098 Neighboring gene uncharacterized LOC105375683 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27755 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27757 Neighboring gene RNA, U6atac small nuclear 8, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:103446806-103447531 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:103447532-103448256 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:103449587-103450136 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:103450137-103450684 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 14

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 within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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

Variation

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See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 19438
  • ATAC-STARR-seq lymphoblastoid silent region 19439

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_114828.1 

    Range
    101..879
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    102411871..102412649
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    103537782..103538560
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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