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LOC132089543 Neanderthal introgressed variant-containing enhancer experimental_99082 [ Homo sapiens (human) ]

Gene ID: 132089543, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089543
Gene description
Neanderthal introgressed variant-containing enhancer experimental_99082
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 7:43648480 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089543 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (43608796..43608965)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (43766851..43767020)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (43648395..43648564)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 Neighboring gene uncharacterized LOC102724903 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:43343825-43344325 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98938 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:43416277-43416776 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:43507100-43507600 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:43593671-43594870 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18123 Neighboring gene lncRNA upregulator of antiviral response interferon signaling Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:43616728-43617927 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25911 Neighboring gene Sharpr-MPRA regulatory region 11578 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:43688133-43688994 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:43686409-43687270 Neighboring gene Sharpr-MPRA regulatory region 11574 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25913 Neighboring gene serine/threonine kinase 17a Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:43691438-43692181 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18125 Neighboring gene NFE2L2 motif-containing MPRA enhancer 272 Neighboring gene cytochrome c oxidase assembly factor 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:43768408-43769137 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:43769138-43769866 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25915 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:43789665-43790184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:43789145-43789664 Neighboring gene uncharacterized LOC107986727 Neighboring gene CRISPRi-validated cis-regulatory element chr7.1855 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25917 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25918 Neighboring gene Sharpr-MPRA regulatory region 4653 Neighboring gene biliverdin reductase A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18128 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_99190 Neighboring gene URGCP-MRPS24 readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18129 Neighboring gene mitochondrial ribosomal protein S24

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 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_230102.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    43608796..43608965
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    43766851..43767020
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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