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LOC132090389 Neanderthal introgressed variant-containing enhancer experimental_43822 [ Homo sapiens (human) ]

Gene ID: 132090389, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090389
Gene description
Neanderthal introgressed variant-containing enhancer experimental_43822
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 16:58034872 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090389 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (58000883..58001052)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (63796172..63796341)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (58034787..58034956)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10918 Neighboring gene sperm microtubule inner protein 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10919 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7539 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7540 Neighboring gene Sharpr-MPRA regulatory region 3942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10920 Neighboring gene zinc finger protein 319 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:58046115-58046647 Neighboring gene U6 snRNA biogenesis phosphodiesterase 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:58046648-58047179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58058267-58058854 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58058855-58059440 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:58059673-58060222 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58060773-58061322 Neighboring gene matrix metallopeptidase 15 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:58119688-58120378 Neighboring gene TIPIN 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 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_230947.1 

    Range
    101..270
    Download
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    58000883..58001052
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    63796172..63796341
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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