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LOC128772252 melanoma risk locus-associated MPRA allelic enhancer 2:25787416 [ Homo sapiens (human) ]

Gene ID: 128772252, updated on 12-Sep-2024

Summary

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Gene symbol
LOC128772252
Gene description
melanoma risk locus-associated MPRA allelic enhancer 2:25787416
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, rs58031038, that is in strong linkage disequilibrium with a melanoma risk locus identified at 2p23.3 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 C283T melanocytes, where differences in transcriptional activity were observed between the reference and alternative rs58031038 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC128772252 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (25564476..25564620)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (25599776..25599920)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (25787345..25787489)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900608 Neighboring gene dystrobrevin beta Neighboring gene DTNB antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15459 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 2:25722050 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:25724405-25724507 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 2:25741070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15461 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 2:25749376 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:25757983-25758812 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 2:25761103 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:25781041-25781736 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 2:25786543 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15462 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:25827447-25827680 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 2:25873082 Neighboring gene Sharpr-MPRA regulatory region 7937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15463 Neighboring gene Sharpr-MPRA regulatory region 10860 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:25945408-25946199 Neighboring gene uncharacterized LOC105374332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25966542-25967042 Neighboring gene uncharacterized LOC124906191 Neighboring gene ASXL transcriptional regulator 2

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_149743.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    25564476..25564620
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    25599776..25599920
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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