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LOC128772322 melanoma risk locus-associated MPRA allelic enhancer 7:130757740 [ Homo sapiens (human) ]

Gene ID: 128772322, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128772322
Gene description
melanoma risk locus-associated MPRA allelic enhancer 7:130757740
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, rs10954299, that is in strong linkage disequilibrium with a melanoma risk locus identified at 7q32.3 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 rs10954299 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC128772322 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (131072909..131073053)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (132390433..132390577)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA, p53 induced transcript Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:130597482-130598681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18651 Neighboring gene long intergenic non-protein coding RNA 513 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:130635654-130635822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26659 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:130644756-130645955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26664 Neighboring gene Sharpr-MPRA regulatory region 13565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26667 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130729465 Neighboring gene Sharpr-MPRA regulatory region 6658 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130743720 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130743868 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 7:130744026 and 7:130744055 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130746088 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130750088 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130751320 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130751957 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130754812 Neighboring gene RNA, U6 small nuclear 1010, pseudogene Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130758576 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130763709 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:130775512-130776367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18655 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18656 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:130792685-130793536 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18657 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18658 Neighboring gene MKLN1 intron CAGE-defined mid-level expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18660 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:130848608-130849807 Neighboring gene muskelin 1 Neighboring gene MPRA-validated peak6722 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:130872973-130874172 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:130875573-130876331 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130880490 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130888388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26673 Neighboring gene MPRA-validated peak6724 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26675 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:130929013-130929606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:130930791-130931382 Neighboring gene ribosomal protein L27 pseudogene 11 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:131012400-131012976 Neighboring gene MKLN1 antisense RNA

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_149813.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    131072909..131073053
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    132390433..132390577
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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