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LOC132089744 Neanderthal introgressed variant-containing enhancer experimental_10254 [ Homo sapiens (human) ]

Gene ID: 132089744, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089744
Gene description
Neanderthal introgressed variant-containing enhancer experimental_10254
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 10:121617389 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089744 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 (119857792..119857961)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (120755349..120755518)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (121617304..121617473)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene inositol polyphosphate-5-phosphatase F Neighboring gene RNA, 7SL, cytoplasmic 846, pseudogene Neighboring gene Sharpr-MPRA regulatory region 8600 Neighboring gene uncharacterized LOC105378513 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2882 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2883 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_10180 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_10184 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:121575109-121575271 Neighboring gene phosphatase and actin regulator 2 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:121610009-121610508 Neighboring gene minichromosome maintenance complex binding protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4133 Neighboring gene NANOG hESC enhancer GRCh37_chr10:121648618-121649156 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:121650957-121651468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:121651469-121651979 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:121651980-121652490 Neighboring gene SEC23 interacting protein Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_10320 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_10351 Neighboring gene microRNA 4682

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_230302.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    119857792..119857961
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    120755349..120755518
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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