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Fig. S1. Manhattan plot for p-values from single-marker drinking index analysis.

Fig. S2. Manhattan plot for p-values from single-marker alcohol dependence and abuse symptom count analysis.

Fig. S3. Quantile–quantile plot for p-values from single-marker drinking index analysis.

Fig. S4. Quantile–quantile plot for p-values from single-marker alcohol dependence and abuse symptom count analysis.

Table S1. (A) Top 10 associations of individual SNPs with alcohol use and abuse phenotypes among parents. (B) Top 10 associations of individual SNPs with alcohol use and abuse phenotypes among nonparents.

Table S2. (A) Mean cross-validated correlations between polygenic score-predicted alcohol use and abuse phenotypic values and observed phenotypic values at each of 10 p-value thresholds among parents. (B) Mean cross-validated correlations between polygenic score-predicted alcohol use and abuse phenotypic values and observed phenotypic values at each of 10 p-value thresholds among nonparents.

Table S3. (A) Estimates of explained phenotypic variance (inline image) attributable to GABA system SNPs and all available SNPs, separately for autosomal and chromosome X markers among parents. (B) Estimates of explained phenotypic variance (inline image) attributable to GABA system SNPs and all available SNPs, separately for autosomal and chromosome X markers among nonparents.

Table S4. (A) Top 10 associations with alcohol use and abuse phenotypes from gene-based tests among parents. (B) Top 10 associations with alcohol use and abuse phenotypes from gene-based tests among nonparents.

Table S5. (A) Top 10 associations with alcohol use and abuse phenotypes from “Top-SNP” gene-based tests among parents. (B) Top 10 associations with alcohol use and abuse phenotypes from “Top-SNP” gene-based tests among non-parents.

Data S1. Drinking index.

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