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LOC127827538 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:50053149-50053658 [ Homo sapiens (human) ]

Gene ID: 127827538, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127827538
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:50053149-50053658
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 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 an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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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Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (49586059..49586940)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (43784311..43785192)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:50020527-50021112 Neighboring gene RNA, 5S ribosomal pseudogene 384 Neighboring gene ribosomal protein S29 Neighboring gene ribosomal protein L32 pseudogene 29 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8309 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:50049568-50050079 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:50050080-50050590 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:50050591-50051102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8310 Neighboring gene RNA component of signal recognition particle 7SL1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8312 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8313 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8314 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:50065755-50066525 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5696 Neighboring gene ras homolog family member Q pseudogene 1 Neighboring gene leucine rich repeat protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8317 Neighboring gene ribosomal protein L36a like

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 active region 8311

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_129041.2 

    Range
    101..982
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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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    49586059..49586940
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    43784311..43785192
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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