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. Author manuscript; available in PMC: 2019 Mar 1.
Published in final edited form as: J Invest Dermatol. 2017 Oct 17;138(3):557–561. doi: 10.1016/j.jid.2017.09.034

Table 2.

Association of 24 selected SNPs with risk of in situ and invasive cSCC

SNP_Minor Allele1 hg19 Position Gene INFO2 Control Subjects Freq. Patients P-Value4
In Situ Group Invasive Group
Freq. OR (95% CI)3 Freq. OR (95% CI)3
From genome-wide scan
rs41269979_T chr6: 32620835 HLA-DQA1, HLA-DQB1 0.88 0.15 0.12 0.71 (0.64–0.79) 0.16 0.97 (0.92–1.03) 1.85 × 10−7
From prior GWAS
rs192481803_T6 chr2: 35336564 intergenic 0.82 0.01 0.01 0.81 (0.52–1.27) 0.01 0.91 (0.69–1.19) 0.66
rs62246017_A5 chr3: 71483084 FOXP1 0.94 0.33 0.34 1.09 (1.01–1.17) 0.35 1.11 (1.07–1.17) 0.51
rs6791479_T5 chr3: 189205032 TPRG1, TP63 1.00 0.43 0.44 1.08 (1.01–1.15) 0.46 1.17 (1.12–1.22) 0.02
rs35407_A6 chr5: 33946571 SLC45A2 0.74 0.04 0.02 0.49 (0.38–0.63) 0.02 0.53 (0.46–0.62) 0.58
rs16891982_C5 chr5: 33951693 SLC45A2 1.00 0.05 0.02 0.49 (0.39–0.61) 0.02 0.52 (0.45–0.60) 0.62
rs17247181_T7 chr5: 65255672 ERBB2IP 0.99 0.10 0.10 1.03 (0.92–1.15) 0.10 1.00 (0.93–1.07) 0.60
rs12203592_T5,6 chr6: 396321 IRF4 0.99 0.16 0.23 1.45 (1.34–1.58) 0.26 1.71 (1.63–1.80) 3.94 × 10−4
rs4455710_T5 chr6: 32608858 HLA-DQA1 0.99 0.38 0.43 1.30 (1.22–1.38) 0.40 1.16 (1.11–1.21) 2.93 × 10−3
rs9689649_C7 chr6: 162101178 PARK2 0.97 0.24 0.24 0.99 (0.92–1.07) 0.23 0.98 (0.93–1.03) 0.69
rs117132860_A6 chr7: 17134708 AHR 0.70 0.02 0.02 1.04 (0.79–1.36) 0.03 1.31 (1.12–1.53) 0.13
rs9643297_G7 chr8: 134483695 ST3GAL1 0.91 0.31 0.30 0.99 (0.92–1.07) 0.30 0.99 (0.94–1.04) 0.91
rs10810657_T6 chr9: 16884586 BNC2, CNTLN 0.99 0.41 0.38 0.90 (0.84–0.97) 0.38 0.90 (0.86–0.94) 0.91
rs74664507_T5 chr9: 16913836 BNC2, CNTLN 0.95 0.44 0.41 0.89 (0.83–0.95) 0.41 0.89 (0.85–0.93) 0.92
rs57994353_C6 chr9: 139356987 SEC16A 0.78 0.26 0.29 1.20 (1.10–1.30) 0.27 1.08 (1.02–1.14) 0.03
rs1126809_A5,6 chr11: 89017961 TYR 0.98 0.27 0.32 1.21 (1.13–1.30) 0.32 1.20 (1.15–1.26) 0.92
rs74899442_C6 chr11: 115890279 CADM1, BUD13 0.76 0.004 0.004 0.99 (0.57–1.72) 0.004 0.86 (0.59–1.24) 0.66
rs1800407_T6 chr15: 28230318 OCA2 0.83 0.07 0.08 1.14 (1.00–1.30) 0.08 1.18 (1.08–1.28) 0.70
rs12916300_C5 chr15: 28410491 HERC2 1.00 0.27 0.23 0.93 (0.85–1.00) 0.22 0.85 (0.81–0.89) 0.07
rs1805007_T6 chr16: 89986117 MC1R 0.81 0.08 0.10 1.39 (1.22–1.57) 0.11 1.67 (1.55–1.80) 7.71 × 10−3
rs4268748_C5 chr16: 90026512 DEF8 0.87 0.26 0.29 1.21 (1.12–1.31) 0.32 1.44 (1.37–1.51) 1.09 × 10−4
rs8063761_T7 chr16: 90027626 DEF8 0.91 0.31 0.34 1.19 (1.11–1.28) 0.37 1.39 (1.33–1.46) 1.40 ×10−4
rs6059655_A5,6 chr20: 32665748 RALY 0.99 0.07 0.10 1.28 (1.14–1.43) 0.11 1.38 (1.28–1.47) 0.24
rs754626_G7 chr20: 36017340 SRC 0.61 0.18 0.19 1.10 (0.99–1.22) 0.18 1.01 (0.94–1.08) 0.19

Abbreviations: chr, chromosome; CI, confidence interval; cSCC, cutaneous squamous cell carcinoma; Freq., frequency; GWAS, genome-wide association study; INFO, IMPUTE-2 information measure for imputation accuracy; OR, odds ratio; SNP, single-nucleotide polymorphism.

1

Allele with frequency ≤ 0.5 in control group.

2

IMPUTE-2 information measure for imputation accuracy (Marchini and Howie, 2010).

3

OR per minor allele with 95% CI, adjusted for the first 10 principal components, sex, age, immunosuppressive status, array (European vs. non-European), and reagent type (Kit-A vs. Kit-O).

4

P for heterogeneity from test of H0: β_in situ = β_invasive. P value can reflect a statistically significant difference between the ORs, even if CIs overlap.

5

Reported by Asgari et al. (2016).

6

Reported by Chahal et al. (2016).

7

Reported by Siiskonen et al. (2016).