U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC128772438 melanoma risk locus-associated MPRA allelic enhancer 22:45631393 [ Homo sapiens (human) ]

Gene ID: 128772438, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC128772438
Gene description
melanoma risk locus-associated MPRA allelic enhancer 22:45631393
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, rs5766576, that is in strong linkage disequilibrium with a melanoma risk locus identified at 22q13.31 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 and UACC903 melanoma cells, where differences in transcriptional activity were observed between the reference and alternative rs5766576 alleles. This locus also represents an accessible chromatin region that was validated as an enhancer based on its ability to activate 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
See LOC128772438 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (45235240..45235589)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (45720199..45720560)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (45631121..45631470)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373064 Neighboring gene nucleoporin 50 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45586750-45587250 Neighboring gene KIAA0930 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 22:45598280 Neighboring gene microRNA 1249 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45606871-45607371 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45607503-45608052 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45608053-45608602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45619103-45619604 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45619605-45620104 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45620306-45621300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45621301-45622293 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 22:45629066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19219 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13875 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13876 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13877 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13878 Neighboring gene HNF1 motif-containing MPRA enhancer 63 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19221 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45659291-45660126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13879 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45665375-45666026 Neighboring gene ribosomal protein S10 pseudogene 31 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13880 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45686240-45686773 Neighboring gene uroplakin 3A

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 within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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 Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 19217

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_149929.2 

    Range
    101..450
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    45235240..45235589
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    45720199..45720560
    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