Step-wise conditional analysis.

Step-wise conditional analysis was performed for 107 SNPs in the HLA region that achieved P<10−3 in GWAS. The full analysis is shown in Table S1. Here, we show the summary results for the four SNPs that remained significant after conditioning on the other significant SNPs. For consistency, we show all odds ratios (OR) on the positive side (i.e., testing risk allele against the alternate allele). The risk allele at each SNP is shown in bold. All association tests were adjusted for age at enrollment, sex, and PC1 and PC2 (principal components that define Jewish/non-Jewish origin and the European country of ancestry). Once the four SNPs that retain conditioned P<0.05 were identified, we re-tested association of each of the SNPs with PD conditioning on the other three. We obtained P = 5×10−4 for SNP1 conditioned on SNP2 and SNP3 and SNP4, P = 5×10−4 for SNP2 conditioned on SNP1 and SNP3 and SNP4, P = 4×10−3 for SNP3 conditioned on SNP1 and SNP2 and SNP4, and P = 0.025 for SNP4 conditioned on SNP1 and SNP2 and SNP3. BP = base pair position of the SNP on chromosome 6. Minor/major allele = the two alternative nucleotides at the SNP, the one with higher frequency denoted as major allele. MAF = minor allele frequency. HWE P = P value for the test of Hardy-Weinberg Equilibrium.