We calculated LD scores using LDSC v1
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0.0 in 1 centiMorgan windows around 13,307,412 non-singleton variants genotyped in 379 European individuals (CEU, FIN, GBR, IBS and TSI populations) in the phase 1 integrated release of the 1,000 Genomes Project 35 . For regression http://www.datingranking.net/local-hookup/honolulu/ weights 13 , we restricted LD score calculation to SNPs included in both the GWAS sumap phase 3; for rg estimation in pairs of traits this was the intersection of SNPs for both traits and HapMap. Because population structure and confounding were highly controlled in the ALS summary statistics by the use of mixed linear model association tests, we constrained the LD score regression intercept to 1 for hS 2 estimation in ALS, and we also estimated hS 2 with a free intercept. For hS 2 estimation in all other traits and for rg estimation the intercept was a free parameter. We also estimated rg using ALS meta-analysis results 7 with free and constrained intercepts and with permuted data conserving population structure.
