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Code for analysis described in our workRegional genetic correlations highlight relationships between neurodegenerative disease loci and the immune system.

Table S1. Top genome-wide significant SNPs in meta-analysis and on each independent study. Table S2. Top genome-wide significant SNPs in conditional meta-analysis and on each independent study. Table S3. Association tests conditioning for each of the lead signals in the OCA/HERC2/APBA2 region of Chromosome 15, for the Cape Verde and Cuba samples, separately. Tables S4-S5. Omnibus tests in the Cape Verde and Cuba samples separately, based on haplotypes from our lead signals (rs1448484, rs1667392, rs36194177, rs2636060). Table S6. Follow-up results of all genome-wide signals identified from our meta-analysis in an East African sample. Table S7. Follow-up of tanning response signals in our meta-analysis. Table S8. Follow-up of skin pigmentation signals identified in a recent GWAS in a large Latin American sample in our meta-analysis. (DOCX 75 kb)

Figure S1. Distribution of M-index values in the Cuban sample. Figure S2. Manhattan plot depicting the results of the GWAS for the Cuban sample. Figure S3. QQ plot from the initial GWAS for the Cuban sample. Figures S4-S7. Correlations of African individual proportions and melanin index in the different samples. Figures S8-S9. QQ plots from the initial and conditional meta-analyses. Figures S10-S17. LD (r2 and D’) among the genome-wide significant SNPs in the OCA2/HERC2/APBA2 region of chromosome 15 in the Cuba and Cape Verde samples, and in the ASW and PUR populations of the 1KGP. Figures S18-S27. Regional plots of the OCA2/HERC2/APBA2 top markers on the region of chromosome 15. (DOCX 11908 kb)

Text S1 Supplementary information on the methods followed for the datasets included in the meta-analysis (Cape Verde, SAGE II, GALA II). (DOCX 28 kb)