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LOC132089834 Neanderthal introgressed variant-containing enhancer experimental_16253 [ Homo sapiens (human) ]

Gene ID: 132089834, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089834
Gene description
Neanderthal introgressed variant-containing enhancer experimental_16253
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 non-introgressed 10:70009572 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089834 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 (68249730..68249899)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (69118900..69119069)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (70009487..70009656)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2418 Neighboring gene long intergenic non-protein coding RNA 2640 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16219 Neighboring gene atonal bHLH transcription factor 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:70010536-70011036 Neighboring gene keratin 19 pseudogene 4 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16457 Neighboring gene phenazine biosynthesis like protein domain containing Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16478 Neighboring gene MPRA-validated peak989 silencer Neighboring gene MPRA-validated peak990 silencer Neighboring gene MPRA-validated peak991 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3460 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16557 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3462 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:70091533-70092347 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:70092348-70093161 Neighboring gene heterogeneous nuclear ribonucleoprotein H3

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_230392.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    68249730..68249899
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    69118900..69119069
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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