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LOC132089229 Neanderthal introgressed variant-containing enhancer experimental_83741 [ Homo sapiens (human) ]

Gene ID: 132089229, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089229
Gene description
Neanderthal introgressed variant-containing enhancer experimental_83741
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 the introgressed 5:16897018 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089229 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 (16896824..16896993)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (16835973..16836142)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (16896933..16897102)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene reticulophagy regulator 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15947 Neighboring gene RETREG1 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 7757 Neighboring gene myosin X Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:16711171-16711672 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:16718131-16718712 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:16721745-16722434 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:16741036-16741940 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:16741941-16742846 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:16755309-16755949 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:16754668-16755308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:16794335-16794862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:16794863-16795390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:16805998-16806498 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:16806499-16806999 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:16809483-16809982 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:16829693-16830613 Neighboring gene RNA, 5S ribosomal pseudogene 179 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:16897552-16898412 Neighboring gene ribosomal protein S26 pseudogene 28 Neighboring gene RNA, U6 small nuclear 660, pseudogene

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_229788.1 

    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
    16896824..16896993
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    16835973..16836142
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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