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LOC127817142 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:5855412-5856004 [ Homo sapiens (human) ]

Gene ID: 127817142, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127817142
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:5855412-5856004
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 includes an enhancer that was validated 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, Jun 2023]
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Genomic context

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See LOC127817142 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (5813395..5814041)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (5817156..5817802)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (5855358..5856004)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene GDP dissociation inhibitor 2 Neighboring gene MPRA-validated peak855 silencer Neighboring gene nuclear receptor binding factor 2 pseudogene 5 Neighboring gene uncharacterized LOC124902367 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:5854819-5855411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2928 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2929 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2930 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2938 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2939 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_13451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2940 Neighboring gene MPRA-validated peak856 silencer Neighboring gene tRNA-Val (anticodon TAC) 3-1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2941 Neighboring gene ribosomal protein L12 pseudogene 28 Neighboring gene ankyrin repeat domain 16

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 2087
  • ATAC-STARR-seq lymphoblastoid silent region 2088

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_118625.2 

    Range
    101..747
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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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    5813395..5814041
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    5817156..5817802
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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