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LOC132089233 Neanderthal introgressed variant-containing enhancer experimental_83940 [ Homo sapiens (human) ]

Gene ID: 132089233, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089233
Gene description
Neanderthal introgressed variant-containing enhancer experimental_83940
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 5:2180762 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089233 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 (2180563..2180732)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (2096250..2096419)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (2180677..2180846)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929081 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1889419-1890219 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1919083-1919896 Neighboring gene keratin-associated protein 5-5-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1930660-1931240 Neighboring gene uncharacterized LOC105374618 Neighboring gene meiotic recombination hotspot 5A Neighboring gene NANOG hESC enhancer GRCh37_chr5:1944459-1944980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1945776-1946394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1948847-1949348 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:1950332-1951531 Neighboring gene Sharpr-MPRA regulatory region 501 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1961828-1962566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1964219-1964719 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1973793-1974292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:2067819-2068402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:2068403-2068984 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:2075638-2076138 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:2077789-2078290 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_83860 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_83872 Neighboring gene VISTA enhancer hs633 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:2136525-2137724 Neighboring gene NANOG hESC enhancer GRCh37_chr5:2144015-2144548 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:2145193-2145694 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:2145695-2146194 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:2146889-2147388 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_83887 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:2157739-2158239 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_83908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:2175812-2176312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:2191782-2192282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:2192283-2192783 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_83970 Neighboring gene VISTA enhancer hs1327 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:2212387-2213238 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:2260271-2261061 Neighboring gene uncharacterized LOC124901166 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:2269269-2269796 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:2269797-2270323 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_83975 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:2299803-2300482 Neighboring gene uncharacterized LOC100506858

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_229792.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    2180563..2180732
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    2096250..2096419
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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