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LOC132090867 Neanderthal introgressed variant-containing enhancer experimental_32244 [ Homo sapiens (human) ]

Gene ID: 132090867, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090867
Gene description
Neanderthal introgressed variant-containing enhancer experimental_32244
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 13:109060521 or rs9559326 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090867 in Genome Data Viewer
Location:
chromosome: 13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (108408088..108408257)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (107635109..107635278)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (109060436..109060605)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene TNF superfamily member 13b Neighboring gene NANOG hESC enhancer GRCh37_chr13:108978967-108979599 Neighboring gene uncharacterized LOC105370355 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32209 Neighboring gene RNA, 5S ribosomal pseudogene 39 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32236 Neighboring gene Sharpr-MPRA regulatory region 13714 Neighboring gene host cell factor C2 pseudogene 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32288 Neighboring gene myosin XVI Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32298 Neighboring gene NANOG hESC enhancer GRCh37_chr13:109270467-109270968 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:109304354-109304547 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32357 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:109487341-109487872 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7989 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32390 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:109643265-109644464 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr13:109663206-109663857 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr13:109752798-109753997 Neighboring gene MYO16 antisense RNA 2

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_32244

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_231426.1 

    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    108408088..108408257
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    107635109..107635278
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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