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LOC128772356 melanoma risk locus-associated MPRA allelic enhancer 11:108140516 [ Homo sapiens (human) ]

Gene ID: 128772356, updated on 12-Sep-2024

Summary

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Gene symbol
LOC128772356
Gene description
melanoma risk locus-associated MPRA allelic enhancer 11:108140516
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, rs3092991, that is in strong linkage disequilibrium with a melanoma risk locus identified at 11q22.3 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 rs3092991 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC128772356 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (108269717..108269861)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (108277239..108277383)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (108140444..108140588)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr11:107991956-107992494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5482 Neighboring gene MPRA-validated peak1447 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr11:108021496-108021664 Neighboring gene acetyl-CoA acetyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3877 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108047982 Neighboring gene nuclear protein, coactivator of histone transcription Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108089151 Neighboring gene NANOG hESC enhancer GRCh37_chr11:108089784-108090285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5484 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5487 Neighboring gene MPRA-validated peak1450 silencer Neighboring gene MPRA-validated peak1449 silencer Neighboring gene ATM serine/threonine kinase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:108147863-108148662 Neighboring gene chromosome 11 open reading frame 65 Neighboring gene MPRA-validated peak1451 silencer Neighboring gene MPRA-validated peak1452 silencer Neighboring gene MPRA-validated peak1453 silencer Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108273376 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108294773 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108301322 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108309656 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108323261 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108333620 Neighboring gene Sharpr-MPRA regulatory region 13200 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:108337475-108338327 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108344264 Neighboring gene uncharacterized LOC124902749 Neighboring gene protein O-glucosyltransferase 3

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_149847.1 

    Range
    101..245
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    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    108269717..108269861
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    108277239..108277383
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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