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LOC132090108 Neanderthal introgressed variant-containing enhancer experimental_28494 [ Homo sapiens (human) ]

Gene ID: 132090108, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090108
Gene description
Neanderthal introgressed variant-containing enhancer experimental_28494
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 12:40812638 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090108 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (40418751..40418920)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (40370936..40371105)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (40812553..40812722)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene LRRK2 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6207 Neighboring gene long intergenic non-protein coding RNA 1779 Neighboring gene leucine rich repeat kinase 2 Neighboring gene uncharacterized LOC105369736 Neighboring gene mucin 19, oligomeric (gene/pseudogene) Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:40868238-40869437 Neighboring gene microtubule associated protein 6 pseudogene Neighboring gene MPRA-validated peak1679 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr12:40912063-40912564 Neighboring gene RNA, U6 small nuclear 713, 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_230666.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    40418751..40418920
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    40370936..40371105
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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