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LOC128772276 melanoma risk locus-associated MPRA allelic enhancer 6:21163919 [ Homo sapiens (human) ]

Gene ID: 128772276, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128772276
Gene description
melanoma risk locus-associated MPRA allelic enhancer 6:21163919
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, rs6914598, that is in strong linkage disequilibrium with a melanoma risk locus identified at 6p22.3 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 rs6914598 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (21163616..21163760)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (21035744..21035888)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene CDK5 regulatory subunit associated protein 1 like 1 Neighboring gene RNA, U6 small nuclear 150, pseudogene Neighboring gene uncharacterized LOC105374966 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:21150224 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 6:21164131 and 6:21164145 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:21166705 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24135 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:21186041-21186767 Neighboring gene NANOG hESC enhancer GRCh37_chr6:21223372-21223889 Neighboring gene uncharacterized LOC107986578 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:21230452-21231651 Neighboring gene Sharpr-MPRA regulatory region 5810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24137 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:21263602-21264102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:21275814-21276318 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:21276319-21276823 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21327213-21328056 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21361231-21362046 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:21362047-21362861 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21367138-21367689 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21367690-21368242 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21368243-21368793 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21393485-21394340 Neighboring gene MPRA-validated peak5728 silencer Neighboring gene long intergenic non-protein coding RNA 581

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_149767.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    21163616..21163760
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    21035744..21035888
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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