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LOC128772392 melanoma risk locus-associated MPRA allelic enhancer 13:113539894 [ Homo sapiens (human) ]

Gene ID: 128772392, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128772392
Gene description
melanoma risk locus-associated MPRA allelic enhancer 13:113539894
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, rs1046793, that is in strong linkage disequilibrium with a melanoma risk locus identified at 13q34 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 and UACC903 melanoma cells, where differences in transcriptional activity were observed between the reference and alternative rs1046793 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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Location:
chromosome: 13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (112885508..112885652)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (112135481..112135627)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ATPase phospholipid transporting 11A Neighboring gene uncharacterized LOC124903253 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113430716-113431329 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:113432945-113433094 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113434144-113435009 Neighboring gene uncharacterized LOC124903252 Neighboring gene NANOG hESC enhancer GRCh37_chr13:113444396-113445115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8035 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113460948-113461629 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113462993-113463672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113505150-113505650 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:113526644-113527843 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:113529546-113529735 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 13:113533651 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 13:113534907 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 13:113536132 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 13:113537448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113540393-113540968 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 13:113543499 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113546091-113546840 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113552283-113552788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113556232-113557108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113557109-113557983 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113559740-113560614 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113560615-113561488 Neighboring gene uncharacterized LOC124903214 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113583655-113584497 Neighboring gene MCF.2 cell line derived transforming sequence like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5536 Neighboring gene Sharpr-MPRA regulatory region 2656 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113607452-113608169 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113610492-113611232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113611233-113611972 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113611973-113612713 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113615435-113616158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113617605-113618326 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113622683-113623202 Neighboring gene MCF2L antisense RNA 1

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_149883.1 

    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    112885508..112885652
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    112135481..112135627
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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