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LOC132090786 Neanderthal introgressed variant-containing enhancer experimental_103338 [ Homo sapiens (human) ]

Gene ID: 132090786, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090786
Gene description
Neanderthal introgressed variant-containing enhancer experimental_103338
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 8:53207687 or rs17315309 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090786 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (52295042..52295211)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (52671094..52671263)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (53207602..53207771)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901945 Neighboring gene ST18 C2H2C-type zinc finger transcription factor Neighboring gene uncharacterized LOC101929341 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:53125987-53126195 Neighboring gene VISTA enhancer hs698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27345 Neighboring gene ribosomal protein L34 pseudogene 17 Neighboring gene MPRA-validated peak7016 silencer Neighboring gene ST18-FAM150A intergenic CAGE-defined low expression enhancer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:53458378-53459577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:53476246-53477222 Neighboring gene ALK and LTK ligand 1

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_103338

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_231345.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    52295042..52295211
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    52671094..52671263
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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