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    LOC128772427 melanoma risk locus-associated MPRA allelic enhancer 21:42745414 [ Homo sapiens (human) ]

    Gene ID: 128772427, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC128772427
    Gene description
    melanoma risk locus-associated MPRA allelic enhancer 21:42745414
    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, rs416981, that is in strong linkage disequilibrium with a melanoma risk locus identified at 21q22.3 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 rs416981 alleles. [provided by RefSeq, Mar 2023]
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    Genomic context

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    See LOC128772427 in Genome Data Viewer
    Location:
    chromosome: 21
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (41373415..41373559)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (39762026..39762170)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:42551642-42552451 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42572358-42572858 Neighboring gene beta-secretase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42572859-42573359 Neighboring gene placenta enriched 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42594561-42595060 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:42612073-42612217 Neighboring gene NANOG hESC enhancer GRCh37_chr21:42616252-42616757 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:42646500-42647699 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42651763-42652318 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42652319-42652873 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42661864-42662364 Neighboring gene FAM3 metabolism regulating signaling molecule B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18470 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr21:42731293-42732096 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42739613-42740114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42740714-42741402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42741403-42742089 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 21:42746568 and 21:42746578 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42750497-42750998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42750999-42751498 Neighboring gene MX dynamin like GTPase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18478 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:42824122-42825321 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42830117-42830618 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18480 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18481 Neighboring gene MX dynamin like GTPase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42851654-42852154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42852155-42852655 Neighboring gene transmembrane protease serine 2 breakpoint cluster recombination region Neighboring gene transmembrane serine protease 2 Neighboring gene TMPRSS2 promoter region

    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_149918.1 

      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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      41373415..41373559
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      39762026..39762170
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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