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LOC128772263 melanoma risk locus-associated MPRA allelic enhancer 5:1330840 [ Homo sapiens (human) ]

Gene ID: 128772263, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128772263
Gene description
melanoma risk locus-associated MPRA allelic enhancer 5:1330840
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, rs452384, that is in strong linkage disequilibrium with a melanoma risk locus identified at 5p15.33 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 UACC903 melanoma cells, where differences in transcriptional activity were observed between the reference and alternative rs452384 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (1330653..1330797)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (1239075..1239219)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1264322-1264939 Neighboring gene telomerase reverse transcriptase Neighboring gene Sharpr-MPRA regulatory region 13256 Neighboring gene TERT enhancer in intron 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1290609-1291360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1291361-1292111 Neighboring gene TERT 5' regulatory region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22305 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22306 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22307 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:1320136 Neighboring gene microRNA 4457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1325297-1325797 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:1327650-1328264 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:1328265-1328877 Neighboring gene CLPTM1 like Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:1341101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1357815-1358370 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1358371-1358926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1358927-1359482 Neighboring gene long intergenic non-protein coding RNA 1511 Neighboring gene MT-CO2 pseudogene 32 Neighboring gene Sharpr-MPRA regulatory region 8068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1386240-1386808 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:1404958-1406157 Neighboring gene solute carrier family 6 member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1412675-1413175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1414882-1415854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1415855-1416827 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1422785-1423310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1438947-1439628

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_149754.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    1330653..1330797
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187547.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    183212..183356 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    1239075..1239219
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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