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LOC132089873 Neanderthal introgressed variant-containing enhancer experimental_17841 [ Homo sapiens (human) ]

Gene ID: 132089873, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089873
Gene description
Neanderthal introgressed variant-containing enhancer experimental_17841
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 10:88191307 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089873 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (86431465..86431634)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (87311997..87312166)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (88191222..88191391)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene glutamate ionotropic receptor delta type subunit 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88024064-88024564 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_17795 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88051161-88051975 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88051976-88052790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88057946-88058446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88089455-88090419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88091551-88092052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88092053-88092552 Neighboring gene microRNA 346 Neighboring gene Sharpr-MPRA regulatory region 9256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88122633-88123146 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88123147-88123660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2556 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2557 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2558 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2559 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88136831-88137373 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2563 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3683 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3684 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88159531-88160524 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88160525-88161518 Neighboring gene uncharacterized LOC124902473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88162319-88162871 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3688 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3689 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:88183258-88184012 Neighboring gene Sharpr-MPRA regulatory region 10398 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:88221644-88222250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88263469-88263969 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2569 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2570 Neighboring gene RNA, U6 small nuclear 780, pseudogene Neighboring gene WAPL cohesin release factor Neighboring gene WAPL divergent transcript

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_230431.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    86431465..86431634
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    87311997..87312166
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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