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LOC132090743 Neanderthal introgressed variant-containing enhancer experimental_82589 [ Homo sapiens (human) ]

Gene ID: 132090743, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090743
Gene description
Neanderthal introgressed variant-containing enhancer experimental_82589
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 5:151756636 or rs55689355 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090743 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (152376990..152377159)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (152909969..152910138)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (151756551..151756720)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1933 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:151431291-151431938 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:151431939-151432585 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:151450292-151450532 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:151456754-151457342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:151503900-151504459 Neighboring gene MPRA-validated peak5547 silencer Neighboring gene uncharacterized LOC105378236 Neighboring gene uncharacterized LOC105378237 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:151724791-151725393 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16530 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82574 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82576 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82580 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82586 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82596 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82611 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82644 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82645 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82651 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82653 Neighboring gene neuromedin U receptor 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82661 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82666 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82670/82671 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82672 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82684 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_82696 and experimental_82697 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_82718 and experimental_82721/82722 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82727 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82735 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82741 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82746 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82750 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82779 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82809 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23469 Neighboring gene ribosomal protein L36a pseudogene 20

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_82589

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_231302.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    152376990..152377159
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    152909969..152910138
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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