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LOC132090882 Neanderthal introgressed variant-containing enhancer experimental_40838 [ Homo sapiens (human) ]

Gene ID: 132090882, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090882
Gene description
Neanderthal introgressed variant-containing enhancer experimental_40838
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 15:70315527 or rs12441546 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090882 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 (70023103..70023272)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (67845338..67845507)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (70315442..70315611)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr15:70097321-70097517 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70106110-70106935 Neighboring gene gem nuclear organelle associated protein 8 pseudogene 1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr15:70112963-70113484 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70114007-70114528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70135718-70136359 Neighboring gene long intergenic non-protein coding RNA 593 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70142408-70142923 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:70145330-70146529 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70208404-70208905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70211725-70212348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70212349-70212971 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70235717-70236216 Neighboring gene uncharacterized LOC101929129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9666 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr15:70282987-70283875 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70292527-70293028 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:70307241-70307744 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9667 Neighboring gene uncharacterized LOC124903518 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70324572-70325184 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:70325185-70325795 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9670 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70349697-70350197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70359676-70360176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70360177-70360677 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70363742-70364242 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:70370658-70371264 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:70371265-70371871 Neighboring gene TLE family member 3, transcriptional corepressor Neighboring gene microRNA 629

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)

General gene information

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Other Names

  • emVar-containing allelic enhancer experimental_40838

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_231441.1 

    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
    70023103..70023272
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    67845338..67845507
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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