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LOC132088915 Neanderthal introgressed variant-containing enhancer experimental_67503 [ Homo sapiens (human) ]

Gene ID: 132088915, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132088915
Gene description
Neanderthal introgressed variant-containing enhancer experimental_67503
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 3:194803130 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132088915 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 (195082316..195082485)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (197779968..197780137)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (194803045..194803214)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194707036-194707536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194708829-194709329 Neighboring gene uncharacterized LOC105374295 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194751125-194752122 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194752123-194753121 Neighboring gene Sharpr-MPRA regulatory region 6289 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194781985-194782758 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:194789061-194790260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194793833-194794333 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194799753-194800269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21037 Neighboring gene xyloside xylosyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21040 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:194815702-194816901 Neighboring gene XXYLT1 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:194823367-194824566 Neighboring gene uncharacterized LOC124909476 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15030

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_229474.1 

    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
    195082316..195082485
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    197779968..197780137
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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