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LOC132090898 Neanderthal introgressed variant-containing enhancer experimental_47746 [ Homo sapiens (human) ]

Gene ID: 132090898, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090898
Gene description
Neanderthal introgressed variant-containing enhancer experimental_47746
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 the non-introgressed 18:11657835 or rs17514586 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090898 in Genome Data Viewer
Location:
chromosome: 18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (11657751..11657920)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (11820100..11820269)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (11657750..11657919)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene nuclear pore complex interacting protein family member B1, pseudogene Neighboring gene microRNA 7153 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:11689154-11689654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:11696745-11697246 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:11714059-11714618 Neighboring gene G protein subunit alpha L Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:11732672-11733280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:11737507-11738276 Neighboring gene ASNS pseudogene 6 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:11775153-11775652 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:11796263-11796399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13096 Neighboring gene Sharpr-MPRA regulatory region 95 Neighboring gene charged multivesicular body protein 1B

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_47746

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_231457.1 

    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    11657751..11657920
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    11820100..11820269
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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