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LOC132090765 Neanderthal introgressed variant-containing enhancer experimental_88787 [ Homo sapiens (human) ]

Gene ID: 132090765, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090765
Gene description
Neanderthal introgressed variant-containing enhancer experimental_88787
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 6:121415301 or rs76392801 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090765 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (121094070..121094239)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (122281196..122281365)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (121415216..121415385)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene COX6A1 pseudogene 3 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:121251634-121252404 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:121252405-121253175 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:121253176-121253945 Neighboring gene uncharacterized LOC105377977 Neighboring gene TBC1 domain family member 32 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88931 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_89007 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_89060 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_89073 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_89101 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_89176 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17513 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25019 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:121697099-121697600 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:121697601-121698100 Neighboring gene RNA, U6 small nuclear 1286, pseudogene Neighboring gene ribosomal protein S15a pseudogene 21

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_88787

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_231324.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    121094070..121094239
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    122281196..122281365
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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