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LOC132090919 Neanderthal introgressed variant-containing enhancer experimental_62654 [ Homo sapiens (human) ]

Gene ID: 132090919, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090919
Gene description
Neanderthal introgressed variant-containing enhancer experimental_62654
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 22:20759405 or rs77462388 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090919 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (20405030..20405199)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (20809331..20809500)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (20759320..20759489)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905153 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:20708428-20708649 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:20715037-20715538 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:20715539-20716038 Neighboring gene ubiquitin specific peptidase 41, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62637 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:20747551-20748540 Neighboring gene zinc finger protein 74 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62657 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:20764690-20764912 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62670 Neighboring gene RNA, U6 small nuclear 225, pseudogene Neighboring gene VISTA enhancer hs1620 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:20783264-20783430 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:20784487-20785326 Neighboring gene scavenger receptor class F member 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_62654

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_231478.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    20405030..20405199
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    20809331..20809500
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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