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LOC132090339 Neanderthal introgressed variant-containing enhancer experimental_41539 [ Homo sapiens (human) ]

Gene ID: 132090339, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090339
Gene description
Neanderthal introgressed variant-containing enhancer experimental_41539
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 15:84281918 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090339 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (83613081..83613250)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (81481008..81481177)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (84281833..84282002)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370933 Neighboring gene uncharacterized LOC105370934 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:84047926-84049125 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:84052681-84053310 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:84067046-84068245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9973 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:84124682-84125286 Neighboring gene SH3 domain containing GRB2 like 3, endophilin A3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:84198348-84198848 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41536 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41540 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41541 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41543 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41546 Neighboring gene ADAMTS like 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:84361608-84362108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:84362109-84362609 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41575 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41592 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41598 Neighboring gene RNA, U6 small nuclear 401, pseudogene Neighboring gene tubulin alpha pseudogene 4

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_230897.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    83613081..83613250
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791797.1 Reference GRCh38.p14 PATCHES

    Range
    218875..219044
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    81481008..81481177
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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