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LOC128772366 melanoma risk locus-associated MPRA allelic enhancer 11:120249395 [ Homo sapiens (human) ]

Gene ID: 128772366, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128772366
Gene description
melanoma risk locus-associated MPRA allelic enhancer 11:120249395
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, rs11600723, that is in strong linkage disequilibrium with a melanoma risk locus identified at 11q23.3 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 rs11600723 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC128772366 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (120378614..120378758)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (120402374..120402518)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369531 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:120146894-120147083 Neighboring gene POU class 2 homeobox 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120177487-120177989 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120176405-120176922 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_19560 and experimental_19565 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120184592 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:120193421-120193580 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3990 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3989 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120195689 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3991 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:120224214-120224428 Neighboring gene Rho guanine nucleotide exchange factor 12 Neighboring gene TLC domain containing 5 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120288060 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120305787 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120306759 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120313899 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120345004 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120350393 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120356317 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5637 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3993 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:120386966-120387568 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:120387569-120388170 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120402421-120402957 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120418648-120419393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:120435257-120435837 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:120435838-120436417 Neighboring gene uncharacterized LOC107984400 Neighboring gene glutamate ionotropic receptor kainate type subunit 4 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:120479691-120480414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120480713-120481226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5639 Neighboring gene elongin C pseudogene 22

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_149857.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    120378614..120378758
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    120402374..120402518
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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