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LOC132090316 Neanderthal introgressed variant-containing enhancer experimental_40151 [ Homo sapiens (human) ]

Gene ID: 132090316, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090316
Gene description
Neanderthal introgressed variant-containing enhancer experimental_40151
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 15:55364293 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090316 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 (55072010..55072179)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (52875519..52875688)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (55364208..55364377)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene unc-13 homolog C Neighboring gene intraflagellar transport 80 homolog (Chlamydomonas) pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_39945 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_39975 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 74 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40016 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40047 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6452 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:54886172-54887371 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:54897116-54897693 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40093 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40111 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40127 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40125 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:55282569-55283080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:55283081-55283592 Neighboring gene uncharacterized LOC105370829 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:55356487-55357068 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:55435814-55435975 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:55488259-55489150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9439 Neighboring gene Sharpr-MPRA regulatory region 6285 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6453 Neighboring gene ribosomal L24 domain containing 1 Neighboring gene RAB27A, member RAS oncogene family

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_230874.1 

    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
    55072010..55072179
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    52875519..52875688
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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