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LOC128781588 melanoma risk locus-associated MPRA allelic enhancers 6:32752436, 6:32752477 and 6:32752546 [ Homo sapiens (human) ]

Gene ID: 128781588, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128781588
Gene description
melanoma risk locus-associated MPRA allelic enhancers 6:32752436, 6:32752477 and 6:32752546
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 three genetic variants, rs28986383, rs13203642 and rs13203581, that are in strong linkage disequilibrium with a melanoma risk locus identified at 6p21.32 in genome-wide association studies (GWASs), and for which the reference alleles have risk effects. Three overlapping subregions were validated as functional enhancers by massively parallel reporter assays (MPRAs) in UACC903 melanoma cells, and two subregions were additionally active in C283T melanocytes. Differences in transcriptional activity were observed between the reference and alternative alleles for all three variants. [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 (32784587..32784841)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (32607009..32607263)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene microRNA 3135b Neighboring gene major histocompatibility complex, class II, DQ beta 2 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32746394 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 6:32747727 and 6:32747786 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32748021 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32748137 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32749836 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32750346 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32751751 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32752130 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32752973 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32753654 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32754294 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32754458 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32754921 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32755087 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32756916 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32762528 Neighboring gene major histocompatibility complex, class II, DO beta Neighboring gene transporter 2, ATP binding cassette subfamily B member Neighboring gene meiotic recombination hotspot TAP2

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

General gene information

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Other Names

  • melanoma risk locus-associated MPRA allelic enhancer 6:32752436
  • melanoma risk locus-associated MPRA allelic enhancer 6:32752477
  • melanoma risk locus-associated MPRA allelic enhancer 6:32752546

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_149938.1 

    Range
    101..355
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    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
    32784587..32784841
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    4029037..4029291
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    4203933..4204187
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    4083667..4083921
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    3978882..3979136
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    4184736..4184990
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    32607009..32607263
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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