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LOC128772312 melanoma risk locus-associated MPRA allelic enhancer 7:124397814 [ Homo sapiens (human) ]

Gene ID: 128772312, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128772312
Gene description
melanoma risk locus-associated MPRA allelic enhancer 7:124397814
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, rs2299902, that is in strong linkage disequilibrium with a melanoma risk locus identified at 7q31.33 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 rs2299902 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (124757688..124757832)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (126075042..126075186)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ribosomal protein S2 pseudogene 31 Neighboring gene RNA, U6 small nuclear 102, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:124371425-124371925 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:124372079-124372580 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:124374223-124374759 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18589 Neighboring gene Sharpr-MPRA regulatory region 5263 Neighboring gene G protein-coupled receptor 37 Neighboring gene long intergenic non-protein coding RNA 3043 Neighboring gene Sharpr-MPRA regulatory region 10744 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:124449868 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:124472442-124472991 Neighboring gene protection of telomeres 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:124533191-124533332 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:124542275 Neighboring gene Sharpr-MPRA regulatory region 5954

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_149803.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    124757688..124757832
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    126075042..126075186
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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