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LOC132089642 Neanderthal introgressed variant-containing enhancer experimental_105469 [ Homo sapiens (human) ]

Gene ID: 132089642, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089642
Gene description
Neanderthal introgressed variant-containing enhancer experimental_105469
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 9:113694568 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089642 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (110932203..110932372)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (123103865..123104034)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (113694483..113694652)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene muscle associated receptor tyrosine kinase Neighboring gene uncharacterized LOC107987115 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:113544666-113545865 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:113553096-113553668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28787 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28788 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_105418 Neighboring gene lysophosphatidic acid receptor 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_105435 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_105449 Neighboring gene RNA, U6 small nuclear 432, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28791 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:113715081-113715580 Neighboring gene uncharacterized LOC124902248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20176 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28792 Neighboring gene RNY4 pseudogene 18

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_230201.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    110932203..110932372
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    123103865..123104034
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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