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LOC132090873 Neanderthal introgressed variant-containing enhancer experimental_36905 [ Homo sapiens (human) ]

Gene ID: 132090873, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090873
Gene description
Neanderthal introgressed variant-containing enhancer experimental_36905
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 14:78947863 or rs17107727 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090873 in Genome Data Viewer
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (78481435..78481604)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (72690064..72690233)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (78947778..78947947)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene tRNA suppressor (anticodon CTA) 3-1 Neighboring gene ribosomal protein S26 pseudogene 48 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:78793548-78794747 Neighboring gene neurexin 3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_36858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8817 Neighboring gene MPRA-validated peak2214 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5982 Neighboring gene Sharpr-MPRA regulatory region 7209 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_36943 Neighboring gene uncharacterized LOC105370589 Neighboring gene MPRA-validated peak2216 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:79358917-79359500 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:79359501-79360083 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:79400229-79400386 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:79451802-79452322 Neighboring gene uncharacterized LOC124903353

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_36905

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_231432.1 

    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    78481435..78481604
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    72690064..72690233
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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