U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC128772426 melanoma risk locus-associated MPRA allelic enhancer 20:62320674 [ Homo sapiens (human) ]

Gene ID: 128772426, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC128772426
Gene description
melanoma risk locus-associated MPRA allelic enhancer 20:62320674
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, rs16983884, that is in strong linkage disequilibrium with a melanoma risk locus identified at 20q13.33 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 rs16983884 alleles. [provided by RefSeq, Mar 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63689249..63689393)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65503300..65503444)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62272271-62273029 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13172 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62273358-62274096 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62275446-62276015 Neighboring gene Sharpr-MPRA regulatory region 12780 Neighboring gene stathmin 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62282910-62283480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62284757-62285436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62285437-62286115 Neighboring gene RTEL1-TNFRSF6B readthrough (NMD candidate) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18241 Neighboring gene regulator of telomere elongation helicase 1 Neighboring gene uncharacterized LOC124904954 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 20:62307938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62313341-62314065 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62314792-62315516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62330893-62331773 Neighboring gene TNF receptor superfamily member 6b Neighboring gene ADP ribosylation factor related protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13177 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13178 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62339316-62340276 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62347847-62348348 Neighboring gene zinc finger CCCH-type and G-patch domain containing Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:62359961-62360460 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62363158-62363701 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62363702-62364244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18250 Neighboring gene Lck interacting transmembrane adaptor 1

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_149917.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    63689249..63689393
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    65503300..65503444
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases