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LOC128772394 melanoma risk locus-associated MPRA allelic enhancer 15:28365618 [ Homo sapiens (human) ]

Gene ID: 128772394, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128772394
Gene description
melanoma risk locus-associated MPRA allelic enhancer 15:28365618
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, rs12913832, that is in strong linkage disequilibrium with a melanoma risk locus identified at 15q13.1 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 rs12913832 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (28120400..28120544)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (25862896..25863040)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene gamma-aminobutyric acid type A receptor subunit gamma3 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:27585914-27587113 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:27603646-27604146 Neighboring gene serpin family E member 4, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:27657550-27658104 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:27699000-27700199 Neighboring gene Sharpr-MPRA regulatory region 4259 Neighboring gene NANOG hESC enhancer GRCh37_chr15:27757723-27758304 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:27833083-27833211 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:27883709-27884453 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:27890620-27891400 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:27931705-27932684 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:27939287-27940486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:27947009-27947605 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:27958849-27960048 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:27996457-27996958 Neighboring gene OCA2 melanosomal transmembrane protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:28115926-28116426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:28142467-28142967 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:28149284-28149784 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_39258 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_39278 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:28228378-28228878 Neighboring gene ribosomal protein L5 pseudogene 32 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:28264414-28265082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:28268807-28269306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:28343756-28344408 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:28352349-28352910 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:28352911-28353471 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:28359141-28359640 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:28377589-28378366 Neighboring gene HECT and RLD domain containing E3 ubiquitin protein ligase 2 Neighboring gene MPRA-validated peak2277 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:28526505-28527006 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:28537256-28537799 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:28563777-28564427 Neighboring gene ribosomal protein L41 pseudogene 2 Neighboring gene HERC2 pseudogene 1

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_149885.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    28120400..28120544
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332701.1 Reference GRCh38.p14 PATCHES

    Range
    253839..253983
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_187660.1 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    253839..253983
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    25862896..25863040
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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