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LOC132090288 Neanderthal introgressed variant-containing enhancer experimental_38563 [ Homo sapiens (human) ]

Gene ID: 132090288, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090288
Gene description
Neanderthal introgressed variant-containing enhancer experimental_38563
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 14:88421619 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090288 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 (87955190..87955359)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (82175837..82176006)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (88421534..88421703)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2296 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:87896478-87897677 Neighboring gene long intergenic non-protein coding RNA 2330 Neighboring gene NANOG hESC enhancer GRCh37_chr14:88228569-88229110 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:88263144-88263835 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:88296681-88297225 Neighboring gene Sharpr-MPRA regulatory region 1922 Neighboring gene uncharacterized LOC124903355 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_38584 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_38590 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5988 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:88459339-88459839 Neighboring gene shieldin complex subunit 2 pseudogene 2 Neighboring gene galactosylceramidase Neighboring gene RNA, U6 small nuclear 835, 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_230846.1 

    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
    87955190..87955359
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    82175837..82176006
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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