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LOC132089256 Neanderthal introgressed variant-containing enhancer experimental_85179 [ Homo sapiens (human) ]

Gene ID: 132089256, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089256
Gene description
Neanderthal introgressed variant-containing enhancer experimental_85179
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 both the introgressed and non-introgressed 5:42290564 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089256 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (42290377..42290546)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (42545852..42546021)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (42290479..42290648)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak5238 silencer Neighboring gene F-box protein 4 Neighboring gene methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase pseudogene 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:42078724-42079249 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:42090075-42091274 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85089 Neighboring gene long intergenic non-protein coding RNA 2996 Neighboring gene NANOG hESC enhancer GRCh37_chr5:42225166-42225693 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85146 Neighboring gene NANOG hESC enhancer GRCh37_chr5:42288621-42289193 Neighboring gene GHR upstream promoter region module A Neighboring gene zinc finger protein 35 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:42508817-42509317 Neighboring gene SERPINE1 mRNA binding protein 1 pseudogene 6 Neighboring gene growth hormone receptor Neighboring gene GHR downstream promoter region module B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:42756975-42757476 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:42757477-42757976 Neighboring gene coiled-coil domain containing 152 Neighboring gene selenoprotein P

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_229815.1 

    Range
    101..270
    Download
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    42290377..42290546
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    42545852..42546021
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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