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    LOC132090449 Neanderthal introgressed variant-containing enhancer experimental_46714 [ Homo sapiens (human) ]

    Gene ID: 132090449, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC132090449
    Gene description
    Neanderthal introgressed variant-containing enhancer experimental_46714
    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 16:89810628 variant alleles. [provided by RefSeq, Sep 2023]
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    Genomic context

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    See LOC132090449 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 (89744135..89744304)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (95828870..95829039)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (89810543..89810712)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11419 Neighboring gene VPS9D1 antisense RNA 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7923 Neighboring gene VPS9 domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89795065-89795636 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46690 Neighboring gene zinc finger protein 276 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46704 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46706 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46707/46708 Neighboring gene MPRA-validated peak2667 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46713 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46718 Neighboring gene FA complementation group A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11421 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:89846248-89846785 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89872952-89873474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7925 Neighboring gene Sharpr-MPRA regulatory region 3988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11422 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7927 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:89900233-89901432 Neighboring gene uncharacterized LOC124903760 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89903444-89904066 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89904067-89904688 Neighboring gene spire type actin nucleation factor 2 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:89913406 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89913685-89914304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89914305-89914923 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89920364-89920864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89920865-89921365 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11424 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11425 Neighboring gene uncharacterized LOC112268179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89938758-89939714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7928

    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_231007.1 

      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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      89744135..89744304
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      95828870..95829039
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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