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    LOC128781585 melanoma risk locus-associated MPRA allelic enhancer 12:13073965 [ Homo sapiens (human) ]

    Gene ID: 128781585, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC128781585
    Gene description
    melanoma risk locus-associated MPRA allelic enhancer 12:13073965
    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 sequence includes a genetic variant, rs1684353, that is in strong linkage disequilibrium with a melanoma risk locus identified at 12p13.1 in genome-wide association studies (GWASs), and for which the reference allele has a protective effect. This region was validated as a functional enhancer by massively parallel reporter assays (MPRAs) in C283T melanocytes, where differences in transcriptional activity were observed between the reference and alternative rs1684353 alleles. [provided by RefSeq, Mar 2023]
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    Genomic context

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    See LOC128781585 in Genome Data Viewer
    Location:
    chromosome: 12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (12920959..12921103)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (12794568..12794712)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (13073893..13074037)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902881 Neighboring gene RPL13AP20-GPRC5A intergenic CAGE-defined mid-level expression enhancer Neighboring gene G protein-coupled receptor class C group 5 member A Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 12:13058787 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 12:13059781 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 12:13075202 Neighboring gene microRNA 614 Neighboring gene GPRC5D and HEBP1 antisense RNA 1 Neighboring gene G protein-coupled receptor class C group 5 member D Neighboring gene small nucleolar RNA SNORD88

    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. Massively parallel reporter assays and variant scoring identified functional variants and target genes for melanoma loci and highlighted cell-type specificity. Long E, et al. Am J Hum Genet, 2022 Dec 1. PMID 36423637, Free PMC Article
    2. Genome-wide association meta-analyses combining multiple risk phenotypes provide insights into the genetic architecture of cutaneous melanoma susceptibility. Landi MT, et al. Nat Genet, 2020 May. PMID 32341527, 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_149935.1 

      Range
      101..245
      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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      12920959..12921103
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      12794568..12794712
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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