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LOC132090558 Neanderthal introgressed variant-containing enhancer experimental_51865 [ Homo sapiens (human) ]

Gene ID: 132090558, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090558
Gene description
Neanderthal introgressed variant-containing enhancer experimental_51865
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 genetic variant, and was validated as an enhancer by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 19:56638845 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090558 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (56127391..56127560)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (59226226..59226393)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (56638760..56638929)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 787 Neighboring gene uncharacterized LOC124904773 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56626767-56627443 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56628849-56629564 Neighboring gene Sharpr-MPRA regulatory region 1998 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:56632431-56633146 Neighboring gene uncharacterized LOC124904772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56640200-56640700 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56640701-56641201 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51899 Neighboring gene zinc finger protein 444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15116 Neighboring gene MPRA-validated peak3570 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15117 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56686512-56687062 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:56687063-56687613 Neighboring gene galanin like peptide

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)

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_231116.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    56127391..56127560
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    59226226..59226393
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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