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LOC132090780 Neanderthal introgressed variant-containing enhancer experimental_99465 [ Homo sapiens (human) ]

Gene ID: 132090780, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090780
Gene description
Neanderthal introgressed variant-containing enhancer experimental_99465
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 the introgressed 7:50730961 or rs3819431 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090780 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 (50663179..50663348)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (50824352..50824521)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (50730876..50731045)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene dopa decarboxylase Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:50598907-50600106 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:50602470-50603669 Neighboring gene DDC antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:50637965-50638490 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_99443 Neighboring gene growth factor receptor bound protein 10 Neighboring gene uncharacterized LOC124901632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:50720584-50721214 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_99457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:50736937-50737438 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:50737439-50737938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:50782907-50783422 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_99483 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:50836560-50837139 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:50837140-50837720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:50875755-50876262 Neighboring gene Sharpr-MPRA regulatory region 14531 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:50894096-50895295 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:50905976-50907175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:50920730-50921230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:50921231-50921731 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:50935547-50936047 Neighboring gene ribosomal protein L39 pseudogene 23 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:50954893-50955392 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:50966118-50966911 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:50966912-50967704 Neighboring gene MPRA-validated peak6518 silencer Neighboring gene small nucleolar RNA SNORA4

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_99465

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_231339.1 

    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
    50663179..50663348
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    50824352..50824521
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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