File S1 - Evidence of Gene−Environment Interaction for Two Genes on Chromosome 4 and Environmental Tobacco Smoke in Controlling the Risk of Nonsyndromic Cleft Palate

Supporting information. Figure S1.1: Manhattan plot with P values from likelihood ratio tests with 1 degree of freedom testing for GxSmoking interaction among 272 European CP trios. Figure S1.2 Manhattan plot with P values from likelihood ratio tests with 1 degree of freedom testing for GxAlcohol consumption interaction among 272 European CP trios. Figure S1.3 Manhattan plot with P values from likelihood ratio tests with 1 degree of freedom testing for GxMultivitamin supplementation consumption interaction among 272 European CP trios. Figure S2: Q-Q plot with P values from likelihood ratio tests with 1 degree of freedom testing for GxETS interaction among 259 Asian CP trios (492,698 SNPs were left in Asian trios after quality control). The gray shaded region indicates 95% confidence band for order statistics. The numbers on the top axis indicate the respective locations for (ordered) expected –log10 p-values. (e.g., the number 1 (10) indicates the expected value, on the –log10 scale, for the minimum (i.e. the tenth smallest) p-value). Figure S3.1 LD plots for SLC2A9 among 259 Asian CP trios. Black squares represent r2 = 1; gray squares represent 02<1; white squares represent r2 = 0. Figure S3.2 LD plots for WDR1 among 259 Asian CP trios. Black squares represent r2 = 1; gray squares represent 02<1; white squares represent r2 = 0. Figure S4: P values from likelihood ratio test with 1 degree of freedom testing for GxETS interaction after including the imputed SNPs among Asian CP trios. Circles represent imputed genotypes using 1000 Genomes as a reference population and squares represent observed SNPs. Table S1.
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