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LOC128772254 melanoma risk locus-associated MPRA allelic enhancer 2:38298139 [ Homo sapiens (human) ]

Gene ID: 128772254, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128772254
Gene description
melanoma risk locus-associated MPRA allelic enhancer 2:38298139
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, rs1800440, that is in strong linkage disequilibrium with a melanoma risk locus identified at 2p22.2 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 C283T melanocytes, where differences in transcriptional activity were observed between the reference and alternative rs1800440 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC128772254 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (38070924..38071068)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (38077810..38077954)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15600 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11365 Neighboring gene PU.1 (SPI1) induced regulator of S100A8 and S100A9 alarmin transcription 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11366 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:38168691-38169192 Neighboring gene regulator of microtubule dynamics 2 Neighboring gene RMDN2 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:38207514-38207877 Neighboring gene zinc finger protein 430 pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr2:38244929-38245461 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11367 Neighboring gene CYP1B1 promoter Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:38326323-38326823 Neighboring gene cytochrome P450 family 1 subfamily B member 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:38334037-38334776 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:38334777-38335516 Neighboring gene uncharacterized LOC107985871 Neighboring gene CYP1B1 antisense RNA 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:38373590-38374789 Neighboring gene RNA, U6 small nuclear 951, pseudogene Neighboring gene uncharacterized LOC102723739 Neighboring gene ribosomal protein L7 pseudogene 12

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_149745.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    38070924..38071068
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    38077810..38077954
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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