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LOC132089505 Neanderthal introgressed variant-containing enhancer experimental_100118 [ Homo sapiens (human) ]

Gene ID: 132089505, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089505
Gene description
Neanderthal introgressed variant-containing enhancer experimental_100118
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 the non-introgressed 7:80383025 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089505 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 (80753624..80753793)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (82004958..82005127)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (80382940..80383109)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901685 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:80157849-80158348 Neighboring gene NANOG hESC enhancer GRCh37_chr7:80162485-80162986 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:80163190-80164389 Neighboring gene CD36 molecule (CD36 blood group) Neighboring gene Sharpr-MPRA regulatory region 7331 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:80393335-80394071 Neighboring gene uncharacterized LOC124901686 Neighboring gene semaphorin 3C Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:80512613-80513812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26210 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18334 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:80627598-80627796 Neighboring gene NANOG hESC enhancer GRCh37_chr7:80642207-80642710 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:80703763-80704962 Neighboring gene HNF1 motif-containing MPRA enhancer 195 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:80809759-80810307 Neighboring gene voltage dependent anion channel 3 pseudogene

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_230064.1 

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

    Range
    80753624..80753793
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    82004958..82005127
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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