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LOC127403456 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:102455480-102455980 [ Homo sapiens (human) ]

Gene ID: 127403456, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127403456
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:102455480-102455980
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 naive 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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See LOC127403456 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (103119776..103120371)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (103627878..103628473)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (102455480..102456075)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 7406 Neighboring gene uncharacterized LOC105379105 Neighboring gene eukaryotic translation initiation factor 3 subunit K pseudogene 1 Neighboring gene gypsy retrotransposon integrase 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:102454978-102455479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22859 Neighboring gene diphosphoinositol pentakisphosphate kinase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:102477431-102477932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22860 Neighboring gene uncharacterized LOC124901037 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16210 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16211 Neighboring gene macrophage immunometabolism regulator

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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 active region 22857

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_105405.2 

    Range
    101..696
    Download
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    103119776..103120371
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    103627878..103628473
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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