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LOC132090897 Neanderthal introgressed variant-containing enhancer experimental_47861 [ Homo sapiens (human) ]

Gene ID: 132090897, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090897
Gene description
Neanderthal introgressed variant-containing enhancer experimental_47861
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 introgressed 18:4206116 or rs145932302 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090897 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 (4206031..4206200)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (4365957..4366126)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (4206031..4206200)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene DLG associated protein 1 Neighboring gene DLGAP1 antisense RNA 4 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr18:4017491-4018172 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene 66 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:4117736-4118323 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:4118324-4118910 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:4119078-4119849 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:4124501-4125480 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:4125481-4126460 Neighboring gene uncharacterized LOC124904239 Neighboring gene Sharpr-MPRA regulatory region 11006 Neighboring gene NANOG hESC enhancer GRCh37_chr18:4195745-4196246 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47879 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:4233399-4234316 Neighboring gene DLGAP1 antisense RNA 5 Neighboring gene Sharpr-MPRA regulatory region 437 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:4407683-4407856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9259 Neighboring gene elongin C pseudogene 27

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_47861

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_231456.1 

    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
    4206031..4206200
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    4365957..4366126
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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