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LOC132089584 Neanderthal introgressed variant-containing enhancer experimental_102562 [ Homo sapiens (human) ]

Gene ID: 132089584, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089584
Gene description
Neanderthal introgressed variant-containing enhancer experimental_102562
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 the non-introgressed 8:20278594 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089584 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 (20420998..20421167)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (20686079..20686248)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (20278509..20278678)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene LZTS1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18972 Neighboring gene leucine zipper tumor suppressor 1 Neighboring gene RNA, 5S ribosomal pseudogene 257 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:20186237-20186853 Neighboring gene uncharacterized LOC105379314 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr8:20210567-20211189 Neighboring gene NANOG hESC enhancer GRCh37_chr8:20212340-20212863 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:20241249-20241750 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:20269567-20270766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:20290912-20291613 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_102576 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:20315593-20316153 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:20316154-20316713 Neighboring gene NANOG hESC enhancer GRCh37_chr8:20350867-20351405 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:20364504-20365243 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:20365244-20365982 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:20365983-20366722 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:20367115-20367326 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_102632 Neighboring gene small nucleolar RNA, C/D box 3F Neighboring gene uncharacterized LOC105379315 Neighboring gene NANOG hESC enhancer GRCh37_chr8:20554878-20555391 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:20662002-20662502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:20662503-20663003 Neighboring gene NANOG hESC enhancer GRCh37_chr8:20676219-20676765 Neighboring gene transmembrane protein 97 pseudogene 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 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_230143.1 

    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
    20420998..20421167
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    20686079..20686248
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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