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LOC128779116 melanoma risk locus-associated MPRA allelic enhancer 16:82156398 [ Homo sapiens (human) ]

Gene ID: 128779116, updated on 12-Sep-2024

Summary

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Gene symbol
LOC128779116
Gene description
melanoma risk locus-associated MPRA allelic enhancer 16:82156398
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, rs12922879, that is in strong linkage disequilibrium with a melanoma risk locus identified at 16q23.3 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 rs12922879 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC128779116 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 (82122721..82122865)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (88186458..88186602)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (82156326..82156470)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene MT-CYB pseudogene 28 Neighboring gene MT-ND6 pseudogene 28 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:82167193 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:82173035-82173622 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:82185320 Neighboring gene M-phase phosphoprotein 6 Neighboring gene Sharpr-MPRA regulatory region 8727 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:82194405 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:82196808 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:82199461 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:82199598 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:82203758 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7765 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:82215972 Neighboring gene RN7SK pseudogene 190

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 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_149931.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    82122721..82122865
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    88186458..88186602
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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