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LOC132089955 Neanderthal introgressed variant-containing enhancer experimental_22479 [ Homo sapiens (human) ]

Gene ID: 132089955, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089955
Gene description
Neanderthal introgressed variant-containing enhancer experimental_22479
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 11:99964302 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089955 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (100093485..100093654)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (100102745..100102914)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (99964217..99964386)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22004 Neighboring gene contactin 5 Neighboring gene RN7SK pseudogene 53 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22054 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22152 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22162 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22201 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22214 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:99195590-99196789 Neighboring gene NANOG hESC enhancer GRCh37_chr11:99289721-99290406 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:99293814-99294789 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22279 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:99454493-99454616 Neighboring gene uncharacterized LOC107984431 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:99796493-99797261 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22387 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22407 Neighboring gene Sharpr-MPRA regulatory region 1581 Neighboring gene uncharacterized LOC105369456 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22485 Neighboring gene NANOG hESC enhancer GRCh37_chr11:99976083-99977077 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:100199299-100200498 Neighboring gene replication protein A2 pseudogene 3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:100421613-100422390 Neighboring gene Sharpr-MPRA regulatory region 9794 Neighboring gene RNA, 7SL, cytoplasmic 222, 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 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_230513.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    100093485..100093654
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    100102745..100102914
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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