U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC128772343 melanoma risk locus-associated MPRA allelic enhancer 11:16133413 [ Homo sapiens (human) ]

Gene ID: 128772343, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC128772343
Gene description
melanoma risk locus-associated MPRA allelic enhancer 11:16133413
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, rs4617548, that is in strong linkage disequilibrium with a melanoma risk locus identified at 11p15.2 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 UACC903 melanoma cells, where differences in transcriptional activity were observed between the reference and alternative rs4617548 alleles. [provided by RefSeq, Mar 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC128772343 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (16111795..16111939)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (16209741..16209885)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (16133341..16133485)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376572 Neighboring gene uncharacterized LOC124900593 Neighboring gene SRY-box transcription factor 6 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:16086747 Neighboring gene MPRA-validated peak1213 silencer Neighboring gene MPRA-validated peak1214 silencer Neighboring gene VISTA enhancer hs1720 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:16199331 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:16200444 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:16210951 Neighboring gene VISTA enhancer hs883 Neighboring gene VISTA enhancer hs236 Neighboring gene VISTA enhancer hs717 Neighboring gene VISTA enhancer hs1301 Neighboring gene SOX6 proximal promoter region Neighboring gene aldo-keto reductase family 1 member B1 pseudogene 3 Neighboring gene RNA, 7SL, cytoplasmic 188, pseudogene

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_149834.1 

    Range
    101..245
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    16111795..16111939
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    16209741..16209885
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases