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LOC132089662 Neanderthal introgressed variant-containing enhancer experimental_106460 [ Homo sapiens (human) ]

Gene ID: 132089662, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089662
Gene description
Neanderthal introgressed variant-containing enhancer experimental_106460
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 the introgressed 9:119313242 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089662 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 (116550878..116551047)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (128743886..128744055)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (119313157..119313326)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene pappalysin 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:119048252-119048828 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:119048829-119049403 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:119093474-119094066 Neighboring gene PAPPA antisense RNA 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:119117289-119117861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:119157715-119158214 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:119185010-119185266 Neighboring gene PAPPA antisense RNA 1 Neighboring gene GATA motif-containing MPRA enhancer 254 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:119233104-119233695 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:119233696-119234286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:119243946-119244892 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106426 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:119301784-119302983 Neighboring gene astrotactin 2 Neighboring gene Sharpr-MPRA regulatory region 10185 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106457 Neighboring gene ASTN2 antisense RNA 1 Neighboring gene uncharacterized LOC107987014 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:119352121-119352680 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:119352681-119353238 Neighboring gene uncharacterized LOC105376240

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_230221.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    116550878..116551047
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    128743886..128744055
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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