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LOC128849170 melanoma risk locus-associated MPRA allelic enhancers 16:68802068 and 16:68802072 [ Homo sapiens (human) ]

Gene ID: 128849170, updated on 12-Sep-2024

Summary

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Gene symbol
LOC128849170
Gene description
melanoma risk locus-associated MPRA allelic enhancers 16:68802068 and 16:68802072
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 two genetic variants, rs8055912 and rs8056206, that are in strong linkage disequilibrium with a melanoma risk locus identified at 16q22.1 in genome-wide association studies (GWASs), and for which the reference alleles have protective effects. Two overlapping subregions were validated as functional enhancers by massively parallel reporter assays (MPRAs) in UACC903 melanoma cells, with one subregion also being active in C283T melanocytes. Differences in transcriptional activity were observed between the reference and alternative alleles for both variants. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC128849170 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (68768093..68768241)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (74564377..74564525)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (68801996..68802144)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene cadherin 3 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68733646 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:68737269-68737769 Neighboring gene Sharpr-MPRA regulatory region 3013 Neighboring gene Sharpr-MPRA regulatory region 1210 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68741769 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68744771-68745272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68745273-68745772 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68748223 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68749055 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11024 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68757572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68762277-68762796 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68766493-68767168 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68770288 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7650 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68776246 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68778919-68779504 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68780069 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68787439-68788396 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68790502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11025 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68791231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11026 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68792712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11029 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11028 Neighboring gene RNA, 5S ribosomal pseudogene 429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11027 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68799944 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68800316-68800990 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68803726 Neighboring gene Sharpr-MPRA regulatory region 4224 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68808283 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68813037-68813640 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68813641-68814242 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68814316 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68815000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11030 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68818245 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68818709 Neighboring gene cadherin 1 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68820718 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68825333-68825902 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68826109 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:68827591-68828091 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68829108-68829608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68829609-68830109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11033 Neighboring gene ferritin light chain pseudogene 14 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:68900664-68900823 Neighboring gene transport and golgi organization 6 homolog Neighboring gene MPRA-validated peak2625 silencer Neighboring gene RNA, U7 small nuclear 42 pseudogene

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)

General gene information

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Other Names

  • melanoma risk locus-associated MPRA allelic enhancer 16:68802068
  • melanoma risk locus-associated MPRA allelic enhancer 16:68802072

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_149946.1 

    Range
    101..249
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    68768093..68768241
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    74564377..74564525
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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