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LOC132090735 Neanderthal introgressed variant-containing enhancer experimental_81891 [ Homo sapiens (human) ]

Gene ID: 132090735, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090735
Gene description
Neanderthal introgressed variant-containing enhancer experimental_81891
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
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 expression-modulating variant (emVar), and was validated as a functional enhancer by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells, with activity observed for the non-introgressed 5:146788696 or rs1432857 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090735 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 (147409048..147409217)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (147944826..147944995)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (146788611..146788780)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene STK32A antisense RNA 1 Neighboring gene serine/threonine kinase 32A Neighboring gene dihydropyrimidinase like 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16489 Neighboring gene NANOG hESC enhancer GRCh37_chr5:146835510-146836011 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:146935385-146935884 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:146940356-146941285 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:146946379-146947278 Neighboring gene JAKMIP2 antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:146947279-146948178 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:146948179-146949078 Neighboring gene janus kinase and microtubule interacting protein 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:147051411-147052610 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:147101014-147101804 Neighboring gene uncharacterized LOC105378218

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)

General gene information

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Other Names

  • emVar-containing allelic enhancer experimental_81891

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_231294.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    147409048..147409217
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    147944826..147944995
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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