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LOC132089028 Neanderthal introgressed variant-containing enhancer experimental_73994 [ Homo sapiens (human) ]

Gene ID: 132089028, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089028
Gene description
Neanderthal introgressed variant-containing enhancer experimental_73994
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 4:129336481 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089028 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (128415241..128415410)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (131719365..131719534)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (129336396..129336565)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene La ribonucleoprotein 1B Neighboring gene FOSL1 pseudogene 1 Neighboring gene NANOG hESC enhancer GRCh37_chr4:129186588-129187089 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:129197563-129197760 Neighboring gene Sharpr-MPRA regulatory region 13521 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15683 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15684 Neighboring gene Sharpr-MPRA regulatory region 12082 Neighboring gene progesterone receptor membrane component 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:129242766-129243328 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:129271007-129271585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:129271620-129272158 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:129283869-129284407 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:129308825-129310024 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73985 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129337187-129337688 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129337689-129338188 Neighboring gene long intergenic non-protein coding RNA 2615 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:129390695-129391894 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15685 Neighboring gene NFE2L2 motif-containing MPRA enhancer 199 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:129456135-129456788 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:129456789-129457442 Neighboring gene uncharacterized LOC101927259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21891

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_229587.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    128415241..128415410
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    131719365..131719534
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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