U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC128772258 melanoma risk locus-associated MPRA allelic enhancer 3:169487501 [ Homo sapiens (human) ]

Gene ID: 128772258, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC128772258
Gene description
melanoma risk locus-associated MPRA allelic enhancer 3:169487501
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer, 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, rs9811216, that is in strong linkage disequilibrium with a melanoma risk locus identified at 3q26.2 in genome-wide association studies (GWASs), and for which the reference allele has a risk effect. A subregion 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 rs9811216 alleles. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (169769630..169769785)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (172553731..172553886)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene telomerase RNA component (TERC) promoter Neighboring gene telomerase RNA component Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 3:169486144 Neighboring gene actin related protein T3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20783 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20784 Neighboring gene tRNA-Val (anticodon AAC) 1-1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:169490847-169491350 Neighboring gene myoneurin

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
  3. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 14875

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_149749.2 

    Range
    101..256
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    169769630..169769785
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    172553731..172553886
    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