U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC128772422 melanoma risk locus-associated MPRA allelic enhancer 19:3540539 [ Homo sapiens (human) ]

Gene ID: 128772422, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC128772422
Gene description
melanoma risk locus-associated MPRA allelic enhancer 19:3540539
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, rs12984831, that is in strong linkage disequilibrium with a melanoma risk locus identified at 19p13.3 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 UACC903 melanoma cells, where differences in transcriptional activity were observed between the reference and alternative rs12984831 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: 19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (3540469..3540613)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (3518640..3518784)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13735 Neighboring gene deoxyhypusine hydroxylase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13737 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9847 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3516112-3516938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3516939-3517763 Neighboring gene fizzy and cell division cycle 20 related 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3518044-3518846 Neighboring gene uncharacterized LOC124904617 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3520450-3521250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3539157-3540009 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 19:3542983 Neighboring gene tektin bundle interacting protein 1 Neighboring gene major facilitator superfamily domain containing 12 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 19:3550926 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9848 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9849 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9850 Neighboring gene Sharpr-MPRA regulatory region 8051 Neighboring gene uncharacterized LOC124904618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3571588-3572156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3572157-3572724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9851 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9853 Neighboring gene high mobility group 20B Neighboring gene GIPC PDZ domain containing family member 3

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_149913.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    3540469..3540613
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    3518640..3518784
    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