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LOC128772382 melanoma risk locus-associated MPRA allelic enhancer 12:96243941 [ Homo sapiens (human) ]

Gene ID: 128772382, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128772382
Gene description
melanoma risk locus-associated MPRA allelic enhancer 12:96243941
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, rs11108303, that is in strong linkage disequilibrium with a melanoma risk locus identified at 12q23.1 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 rs11108303 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC128772382 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (95850091..95850235)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (95826512..95826656)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 247, pseudogene Neighboring gene SNRPF divergent transcript Neighboring gene long intergenic non-protein coding RNA 2410 Neighboring gene MPRA-validated peak1901 silencer Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 12:96244864 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 12:96249988 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:96252439-96253054 Neighboring gene small nuclear ribonucleoprotein polypeptide F Neighboring gene coiled-coil domain containing 38 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:96301545-96302055 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:96302056-96302565 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:96322471-96322972

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_149873.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    95850091..95850235
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    95826512..95826656
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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