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LOC128772431 melanoma risk locus-associated MPRA allelic enhancer 22:38600595 [ Homo sapiens (human) ]

Gene ID: 128772431, updated on 12-Sep-2024

Summary

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Gene symbol
LOC128772431
Gene description
melanoma risk locus-associated MPRA allelic enhancer 22:38600595
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, rs2267374, that is in strong linkage disequilibrium with a melanoma risk locus identified at 22q13.1 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 C283T melanocytes and UACC903 melanoma cells, where differences in transcriptional activity were observed between the reference and alternative rs2267374 alleles. [provided by RefSeq, Mar 2023]
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Genomic context

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See LOC128772431 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (38204516..38204660)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (38668868..38669012)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (38600523..38600667)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:38482017-38482796 Neighboring gene BAR/IMD domain containing adaptor protein 2 like 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38494339-38494893 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:38510521-38511423 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38518609-38519118 Neighboring gene phospholipase A2 group VI Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38538756-38539256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18993 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38559728-38560228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38560229-38560729 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 22:38561911 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 22:38570189 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 22:38572440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18996 Neighboring gene Sharpr-MPRA regulatory region 6169 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 22:38580917 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18999 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13708 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13710 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 22:38603571 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 22:38607237 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 22:38607534 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 22:38608227 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38609813-38610394 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13712 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:38614213-38615412 Neighboring gene MAF bZIP transcription factor F Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38618750-38619250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38620666-38621166 Neighboring gene transmembrane protein 184B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:38624990-38625720 Neighboring gene TMEM184B antisense RNA 1 Neighboring gene small nucleolar RNA, H/ACA box 92 Neighboring gene RNA, 7SL, cytoplasmic 704, 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)

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_149922.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    38204516..38204660
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    38668868..38669012
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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