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LOC128772387 melanoma risk locus-associated MPRA allelic enhancer 12:116744946 [ Homo sapiens (human) ]

Gene ID: 128772387, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128772387
Gene description
melanoma risk locus-associated MPRA allelic enhancer 12:116744946
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, rs76530201, that is in strong linkage disequilibrium with a melanoma risk locus identified at 12q24.21 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 rs76530201 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC128772387 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 (116307069..116307213)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (116288086..116288230)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene mediator complex subunit 13L Neighboring gene NANOG hESC enhancer GRCh37_chr12:116591702-116592247 Neighboring gene microRNA 620 Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 18 Neighboring gene Sharpr-MPRA regulatory region 4680 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 12:116675052 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4899 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7091 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7092 Neighboring gene uncharacterized LOC105370005 Neighboring gene Sharpr-MPRA regulatory region 4817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4901 Neighboring gene CRISPRi-validated cis-regulatory element chr12.3954 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:116806721-116807222 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:116820714-116821390 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:116864663-116865210 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:116865211-116865757 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:116865758-116866304 Neighboring gene microRNA 4472-2

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_149878.1 

    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
    116307069..116307213
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    116288086..116288230
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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