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LOC132090808 Neanderthal introgressed variant-containing enhancer experimental_12499 [ Homo sapiens (human) ]

Gene ID: 132090808, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090808
Gene description
Neanderthal introgressed variant-containing enhancer experimental_12499
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 10:44337849 or rs76720082 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090808 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 (43842316..43842485)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (44723160..44723329)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (44337764..44337933)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378275 Neighboring gene long intergenic non-protein coding RNA 2658 Neighboring gene heterogeneous nuclear ribonucleoprotein A3 pseudogene 1 Neighboring gene MPRA-validated peak936 silencer Neighboring gene long intergenic non-protein coding RNA 619 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:44358448-44358948 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:44358949-44359449 Neighboring gene long intergenic non-protein coding RNA 840 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_12564 Neighboring gene Sharpr-MPRA regulatory region 2960 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_12586 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:44372279-44372466

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_12499

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_231367.1 

    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
    43842316..43842485
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    44723160..44723329
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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