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LOC128772340 melanoma risk locus-associated MPRA allelic enhancer 9:110708974 [ Homo sapiens (human) ]

Gene ID: 128772340, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128772340
Gene description
melanoma risk locus-associated MPRA allelic enhancer 9:110708974
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, rs10979122, that is in strong linkage disequilibrium with a melanoma risk locus identified at 9q31.2 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 UACC903 melanoma cells, where differences in transcriptional activity were observed between the reference and alternative rs10979122 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC128772340 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (107946621..107946765)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (120115156..120115300)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene small EDRK-rich factor 2-like Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:110634669-110635552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28755 Neighboring gene RNA, 5S ribosomal pseudogene 293 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_104396 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 9:110702889 and 9:110702983 Neighboring gene ribosomal protein S15a pseudogene 27 Neighboring gene uncharacterized LOC107987112 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:110762694-110763893 Neighboring gene uncharacterized LOC124902243 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:110779148-110780347

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_149831.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    107946621..107946765
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    120115156..120115300
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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