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LOC128772304 melanoma risk locus-associated MPRA allelic enhancer 7:17134708 [ Homo sapiens (human) ]

Gene ID: 128772304, updated on 12-Sep-2024

Summary

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Gene symbol
LOC128772304
Gene description
melanoma risk locus-associated MPRA allelic enhancer 7:17134708
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, rs117132860, that is in strong linkage disequilibrium with a melanoma risk locus identified at 7p21.1 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 rs117132860 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC128772304 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (17095012..17095156)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (17224636..17224780)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (17134636..17134780)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375170 Neighboring gene uncharacterized LOC124901595 Neighboring gene Sharpr-MPRA regulatory regions 10536 and 6796 Neighboring gene bromodomain and WD repeat domain containing 1 pseudogene 3 Neighboring gene uncharacterized LOC124901596 Neighboring gene uncharacterized LOC107986772 Neighboring gene uncharacterized LOC101927609 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25671 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25672 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:17273731-17274930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17983 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17984 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17985 Neighboring gene aryl hydrocarbon receptor

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

See Variation Viewer (GRCh37.p13)

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_149795.1 

    Range
    101..245
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    17095012..17095156
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    17224636..17224780
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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