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LOC128772327 melanoma risk locus-associated MPRA allelic enhancer 8:21964802 [ Homo sapiens (human) ]

Gene ID: 128772327, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128772327
Gene description
melanoma risk locus-associated MPRA allelic enhancer 8:21964802
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, rs1552286, that is in strong linkage disequilibrium with a melanoma risk locus identified at 8p21.3 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 and UACC903 melanoma cells, where differences in transcriptional activity were observed between the reference and alternative rs1552286 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (22107219..22107363)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (22381172..22381316)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs781 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:21908959-21909751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:21915443-21916404 Neighboring gene dematin actin binding protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:21917368-21918329 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18975 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:21943692-21944301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18977 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:21951526-21952026 Neighboring gene FHF complex subunit HOOK interacting protein 2B Neighboring gene ReSE screen-validated silencer GRCh37_chr8:21961808-21961955 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:21965271-21966044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18979 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:21969459-21969958 Neighboring gene nudix hydrolase 18 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:21972531-21973193 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:21977874-21978076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:21978415-21978914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:21981891-21982392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:21982393-21982892 Neighboring gene HR lysine demethylase and nuclear receptor corepressor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:21987125-21987702 Neighboring gene HR upstream open reading frame Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:21997193-21997801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:21997802-21998409 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18981 Neighboring gene receptor accessory protein 4

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_149818.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    22107219..22107363
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    22381172..22381316
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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