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LOC132089675 Neanderthal introgressed variant-containing enhancer experimental_107631 [ Homo sapiens (human) ]

Gene ID: 132089675, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089675
Gene description
Neanderthal introgressed variant-containing enhancer experimental_107631
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 9:29159034 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089675 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 (29158951..29159120)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (29172622..29172791)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (29158949..29159118)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene leucine rich repeat and Ig domain containing 2 Neighboring gene NANOG hESC enhancer GRCh37_chr9:28929045-28929614 Neighboring gene NANOG hESC enhancer GRCh37_chr9:28938893-28939474 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:28970143-28971066 Neighboring gene microRNA 876 Neighboring gene microRNA 873 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_107603 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19824 Neighboring gene NANOG hESC enhancer GRCh37_chr9:29251246-29251747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28256 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:29439922-29441121 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:29450054-29451253 Neighboring gene pyruvate dehydrogenase kinase 1 pseudogene 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:29566267-29567466 Neighboring gene uncharacterized LOC105376005

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_230234.1 

    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
    29158951..29159120
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    29172622..29172791
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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