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LOC132090778 Neanderthal introgressed variant-containing enhancer experimental_98599 [ Homo sapiens (human) ]

Gene ID: 132090778, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090778
Gene description
Neanderthal introgressed variant-containing enhancer experimental_98599
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
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 expression-modulating variant (emVar), and was validated as a functional enhancer by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 7:38522986 or rs1558617 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090778 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 (38483301..38483470)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (38639881..38640050)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (38522901..38523070)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene T cell receptor gamma locus Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25869 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25870 Neighboring gene T cell receptor gamma locus antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25871 Neighboring gene Sharpr-MPRA regulatory region 15414 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98536 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25872 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98538 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_98539 and experimental_98540 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98545 Neighboring gene T cell receptor gamma variable 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98547 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98548 Neighboring gene T cell receptor gamma variable 1 (non-functional) Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98550 Neighboring gene amphiphysin Neighboring gene ReSE screen-validated silencer GRCh37_chr7:38473600-38473818 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98556 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98558 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98567 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25873 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98573 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98575/98576 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98581 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98586 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98589 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98595 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98607 Neighboring gene RNA, 7SL, cytoplasmic 83, pseudogene Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr7:38629347-38629908 Neighboring gene keratin 8 pseudogene 20

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)

General gene information

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Other Names

  • emVar-containing allelic enhancer experimental_98599

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_231337.1 

    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
    38483301..38483470
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    38639881..38640050
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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