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Table 5 Summary of SNP associations with ulceration status, anatomic site, and tumor thickness

From: Melanoma risk loci as determinants of melanoma recurrence and survival

SNP Locus Gene prior GWAS associations   Ulceration status
Crude Adjusted
     MAF OR CI 95% P OR CI 95% P
rs6001027 22q13.1 PLA2G6 CM; OR = 0.83, p = 1.9e-8 0.35 0.71 0.53-0.92 0.01 0.70 0.53-0.92 0.01
rs2284063 22q13.1 PLA2G6 CM; OR = 0.83, p = 2.4e-9 0.35 0.73 0.56-0.96 0.02 0.73 0.55-0.95 0.02
rs132985 22q13.1 PLA2G6 Nevi; OR = 1.23, p = 2.6e-7 0.44 0.77 0.60-0.99 0.04 0.76 0.59-0.98 0.03
SNP Locus Gene prior GWAS Associations   Anatomic site
Crude Adjusted
     MAF OR CI 95% P OR CI 95% P
rs7279297 21q22.3 PRDM15 Tanning; β = -0.12, p = 2.7e-6 0.31 1.26 1.01-1.56 0.03 1.32 1.05-1.66 0.01
rs1028889 1p21.3 - Tanning; β = 0.10, p = 1.4e-4 0.27 0.81 0.65-0.99 0.04 0.74 0.58-0.92 0.008
rs6497287 15q13.1 HERC2 Eye color; p = 5.05e-15 0.12 0.70 0.53-0.93 0.01 0.70 0.51-0.93 0.01
rs7183877 15q13.1 HERC2 Hair; β = -.29, p = 2.0e-12 0.12 0.72 0.54-0.95 0.02 0.71 0.52-0.95 0.02
    Eye color; p = 6.18e-11        
SNP Locus Gene prior GWAS Associations   Thickness
Crude Adjusted
     MAF β Coeff. SE P β Coeff. SE P
rs966321 1p36.32 - Tanning; β = -.14, p = 1.6e-9 0.49 -0.40 0.14 0.005 -0.37 0.14 0.008
rs10861741 12q23.3 BTBD11 Hair; β = .12, p = 1.3e-4 0.15 -0.49 0.20 0.01 -0.47 0.19 0.01
  1. SNP associations with ulceration status and anatomic site were observed using an additive model logistic regression analysis. SNP associations with primary tumor thickness were observed using an additive model linear regression analysis. Both crude (unadjusted by covariates) and adjusted results are shown; adjustments included age at diagnosis, gender, and ethnicity. Associations with melanoma and melanoma related host phenotypes observed in prior GWAS studies are also listed for each SNP.