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LOC128772336 melanoma risk locus-associated MPRA allelic enhancer 9:21805208 [ Homo sapiens (human) ]

Gene ID: 128772336, updated on 12-Sep-2024

Summary

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Gene symbol
LOC128772336
Gene description
melanoma risk locus-associated MPRA allelic enhancer 9:21805208
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, rs80138396, that is in strong linkage disequilibrium with a melanoma risk locus identified at 9p21.3 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 rs80138396 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC128772336 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (21805137..21805281)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (21819367..21819513)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (21805136..21805280)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3 histone pseudogene 30 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:21684484-21685683 Neighboring gene uncharacterized LOC107987026 Neighboring gene RNA, 7SL, cytoplasmic 151, pseudogene Neighboring gene KH-type splicing regulatory protein pseudogene 1 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 9:21720826 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 9:21760452 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:21801514-21802144 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19809 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:21802145-21802773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28241 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:21832108-21833307 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28243 Neighboring gene tubulin beta 8 class VIII pseudogene 1 Neighboring gene methylthioadenosine phosphorylase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19810 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 9:21959860 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 9:21962977 Neighboring gene CDKN2A antisense RNA 1 Neighboring gene cyclin dependent kinase inhibitor 2A

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

See Variation Viewer (GRCh37.p13)

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_149827.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    21805137..21805281
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    21819367..21819513
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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