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LOC132089172 Neanderthal introgressed variant-containing enhancer experimental_81447 [ Homo sapiens (human) ]

Gene ID: 132089172, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089172
Gene description
Neanderthal introgressed variant-containing enhancer experimental_81447
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 5:145531113 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089172 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 (146151465..146151634)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (146685755..146685924)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (145531028..145531197)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene leucyl-tRNA synthetase 1 Neighboring gene ribosomal protein L35a pseudogene 16 Neighboring gene ribosomal protein L35a pseudogene 17 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81571 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81576 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81597 Neighboring gene MPRA-validated peak5520 silencer Neighboring gene MPRA-validated peak5521 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23359 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:145562805-145563651 Neighboring gene Sharpr-MPRA regulatory region 14811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23360 Neighboring gene RBM27-POU4F3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23361 Neighboring gene Sharpr-MPRA regulatory region 15600 Neighboring gene RNA binding motif protein 27 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81701 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81715 Neighboring gene RNA, U7 small nuclear 180 pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81725 Neighboring gene MPRA-validated peak5522 silencer Neighboring gene POU class 4 homeobox 3

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_229731.1 

    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
    146151465..146151634
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    146685755..146685924
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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