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LOC128772212 melanoma risk locus-associated MPRA allelic enhancer 1:150818234 [ Homo sapiens (human) ]

Gene ID: 128772212, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128772212
Gene description
melanoma risk locus-associated MPRA allelic enhancer 1:150818234
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, rs7514004, that is in strong linkage disequilibrium with a melanoma risk locus identified at 1q21.3 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 rs7514004 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC128772212 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (150845686..150845830)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (149969358..149969502)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150774101 Neighboring gene ubiquitin conjugating enzyme E2 D3 pseudogene 3 Neighboring gene cathepsin K Neighboring gene RNA, U6 small nuclear 1309, pseudogene Neighboring gene aryl hydrocarbon receptor nuclear translocator Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150800090 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150800655 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150808889 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:150822359-150823012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:150823013-150823665 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150825511 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150826831 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:150846639-150847140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:150847141-150847640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1306 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:150849134-150849407 Neighboring gene uncharacterized LOC107985204 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150856806 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150858571 Neighboring gene RPS27A pseudogene 6 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150864113 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150864992 Neighboring gene cortexin domain containing 2 Neighboring gene CYCS pseudogene 51

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_149703.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    150845686..150845830
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    149969358..149969502
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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