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LOC132089518 Neanderthal introgressed variant-containing enhancer experimental_97964 [ Homo sapiens (human) ]

Gene ID: 132089518, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089518
Gene description
Neanderthal introgressed variant-containing enhancer experimental_97964
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 contains a Neanderthal adaptively introgressed genetic variant, and was validated as an enhancer by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 7:157309001 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089518 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (157516222..157516391)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (158704809..158704978)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (157308916..157309085)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927914 Neighboring gene Sharpr-MPRA regulatory region 4962 Neighboring gene MPRA-validated peak6872 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26930 Neighboring gene uncharacterized LOC105375610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:157305630-157306130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:157306131-157306631 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:157307834-157308764 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:157313607-157314110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:157314111-157314614 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:157355168-157356367 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:157357033-157358232 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:157387093-157388292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:157388362-157388862 Neighboring gene uncharacterized LOC105375615 Neighboring gene protein tyrosine phosphatase receptor type N2 Neighboring gene microRNA 153-2

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. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. Jagoda E, et al. Mol Biol Evol, 2022 Jan 7. PMID 34662402, 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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

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_230077.1 

    Range
    101..270
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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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    157516222..157516391
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    158704809..158704978
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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