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LOC132089799 Neanderthal introgressed variant-containing enhancer experimental_13913 [ Homo sapiens (human) ]

Gene ID: 132089799, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089799
Gene description
Neanderthal introgressed variant-containing enhancer experimental_13913
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 10:64728697 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089799 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (62968852..62969021)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (63826997..63827166)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (64728612..64728781)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2400 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2401 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:64576972-64577969 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3432 Neighboring gene early growth response 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3433 Neighboring gene uncharacterized LOC107984012 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:64684239-64684456 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_14056 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_14069 Neighboring gene MPRA-validated peak959 silencer Neighboring gene uncharacterized LOC105378328 Neighboring gene RNA, U6 small nuclear 543, pseudogene

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 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_230357.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    62968852..62969021
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    63826997..63827166
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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