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LOC132090864 Neanderthal introgressed variant-containing enhancer experimental_33339 [ Homo sapiens (human) ]

Gene ID: 132090864, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090864
Gene description
Neanderthal introgressed variant-containing enhancer experimental_33339
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 introgressed 13:77928997 or rs17763409 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090864 in Genome Data Viewer
Location:
chromosome: 13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (77354777..77354946)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (76578630..76578799)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (77928912..77929081)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene MYC binding protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5419 Neighboring gene uncharacterized LOC127898562 Neighboring gene uncharacterized LOC107984564 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7842 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7843 Neighboring gene Sharpr-MPRA regulatory region 1150 Neighboring gene uncharacterized LOC124903185 Neighboring gene uncharacterized LOC124903186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7845

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_33339

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_231423.1 

    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    77354777..77354946
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    76578630..76578799
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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