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    LOC128772296 melanoma risk locus-associated MPRA allelic enhancer 6:90866227 [ Homo sapiens (human) ]

    Gene ID: 128772296, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC128772296
    Gene description
    melanoma risk locus-associated MPRA allelic enhancer 6:90866227
    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, rs7774138, that is in strong linkage disequilibrium with a melanoma risk locus identified at 6q15 in genome-wide association studies (GWASs), and for which the reference allele has a risk 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 rs7774138 alleles. [provided by RefSeq, Mar 2023]
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    Genomic context

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    Location:
    chromosome: 6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (90156436..90156580)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (91368138..91368282)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak5956 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:90620440-90621084 Neighboring gene Sharpr-MPRA regulatory region 14578 Neighboring gene gap junction protein alpha 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:90644322-90644822 Neighboring gene BTB domain and CNC homolog 2 Neighboring gene RN7SK pseudogene 110 Neighboring gene Sharpr-MPRA regulatory region 1684 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:90866333-90867532 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:90883525 Neighboring gene uncharacterized LOC105377890 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:90894000-90895199 Neighboring gene Sharpr-MPRA regulatory region 6453 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:90927428-90928086 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:90931785-90932984 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:90941289 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24833 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:90981657 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:90982387 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:90995265-90995765 Neighboring gene uncharacterized LOC124901361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24834

    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

    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_149787.1 

      Range
      101..245
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      90156436..90156580
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      91368138..91368282
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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