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LOC132088964 Neanderthal introgressed variant-containing enhancer experimental_69934 [ Homo sapiens (human) ]

Gene ID: 132088964, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132088964
Gene description
Neanderthal introgressed variant-containing enhancer experimental_69934
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 3:3547473 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132088964 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (3505704..3505873)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (3501557..3501726)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (3547388..3547557)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14009 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:3168955-3169685 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19345 Neighboring gene tRNA nucleotidyl transferase 1 Neighboring gene cereblon Neighboring gene ReSE screen-validated silencer GRCh37_chr3:3310572-3310785 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69928 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69968 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:3600748-3601947 Neighboring gene uncharacterized LOC100130207 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14011 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14012 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14013 Neighboring gene Sharpr-MPRA regulatory region 107 Neighboring gene leucine rich repeat neuronal 1 Neighboring gene polyribonucleotide nucleotidyltransferase 1 pseudogene 1

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_229523.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    3505704..3505873
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    3501557..3501726
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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