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LOC132089076 Neanderthal introgressed variant-containing enhancer experimental_75752 [ Homo sapiens (human) ]

Gene ID: 132089076, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089076
Gene description
Neanderthal introgressed variant-containing enhancer experimental_75752
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 4:165648872 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089076 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (164727635..164727804)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (168075317..168075486)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (165648787..165648956)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene membrane associated ring-CH-type finger 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:165162454-165162964 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:165162965-165163475 Neighboring gene acidic nuclear phosphoprotein 32 family member C, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:165272175-165272792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:165304399-165304900 Neighboring gene MPRA-validated peak5144 silencer Neighboring gene RNA, U6 small nuclear 284, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:165597429-165597929 Neighboring gene MPRA-validated peak5145 silencer Neighboring gene CHORDC1 pseudogene 3 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:165720294-165720912 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:165720913-165721532 Neighboring gene RNA, U6 small nuclear 668, pseudogene Neighboring gene small integral membrane protein 31 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:165794162-165794662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22107 Neighboring gene apelin receptor early endogenous ligand

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_229635.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    164727635..164727804
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    168075317..168075486
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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