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LOC132090879 Neanderthal introgressed variant-containing enhancer experimental_39776 [ Homo sapiens (human) ]

Gene ID: 132090879, updated on 14-Oct-2023

Summary

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Gene symbol
LOC132090879
Gene description
Neanderthal introgressed variant-containing enhancer experimental_39776
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
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 expression-modulating variant (emVar), and was validated as a functional enhancer by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 15:53847667 or rs76695954 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090879 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (53555385..53555554)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (51364971..51365140)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107983981 Neighboring gene long intergenic non-protein coding RNA 2490 Neighboring gene Sharpr-MPRA regulatory region 13260 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:53599743-53600942 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:53604840-53605570 Neighboring gene uncharacterized LOC105370826 Neighboring gene NANOG hESC enhancer GRCh37_chr15:53740354-53740863 Neighboring gene WD repeat domain 72 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:53917398-53918006 Neighboring gene RNA, U2 small nuclear 53, pseudogene Neighboring gene RNA, U6 small nuclear 449, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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

General gene information

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Other Names

  • emVar-containing allelic enhancer experimental_39776

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_231438.1 

    Range
    101..270
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    53555385..53555554
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    51364971..51365140
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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