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LOC128772228 melanoma risk locus-associated MPRA allelic enhancer 1:150937329 [ Homo sapiens (human) ]

Gene ID: 128772228, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128772228
Gene description
melanoma risk locus-associated MPRA allelic enhancer 1:150937329
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, rs4451553, that is in strong linkage disequilibrium with a melanoma risk locus identified at 1q21.3 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 UACC903 melanoma cells, where differences in transcriptional activity were observed between the reference and alternative rs4451553 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC128772228 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (150964781..150964925)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (150088480..150088624)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985204 Neighboring gene cortexin domain containing 2 Neighboring gene CYCS pseudogene 51 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150887442 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150889489 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150889877 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150891209 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150903234 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150907955 Neighboring gene SET domain bifurcated histone lysine methyltransferase 1 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150908639 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150910911 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150913142 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150916657 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150922512 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150937964 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:150945529-150946460 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150946490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1307 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1308 Neighboring gene ceramide synthase 2 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr1:150949461-150949964 and GRCh37_chr1:150949965-150950466 Neighboring gene uncharacterized LOC105371438 Neighboring gene annexin A9

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_149719.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    150964781..150964925
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    150088480..150088624
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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