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LOC132090827 Neanderthal introgressed variant-containing enhancer experimental_10489 [ Homo sapiens (human) ]

Gene ID: 132090827, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090827
Gene description
Neanderthal introgressed variant-containing enhancer experimental_10489
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 both the introgressed and non-introgressed 10:122724865 or rs55853266 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090827 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (120965267..120965436)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (121861460..121861629)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (122724780..122724949)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2930 Neighboring gene WDR11 divergent transcript Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:122558239-122558907 Neighboring gene H3K27ac hESC enhancers GRCh37_chr10:122610516-122611060 and GRCh37_chr10:122611061-122611604 Neighboring gene WD repeat domain 11 Neighboring gene uncharacterized LOC105378519 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:122669667-122670866 Neighboring gene Sharpr-MPRA regulatory region 5528 Neighboring gene uncharacterized LOC105378520 Neighboring gene uncharacterized LOC105378521 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:122784424-122784924 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:122784925-122785425

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_10489

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_231386.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    120965267..120965436
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    121861460..121861629
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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