implemented in SOLAR. LD was computed in SOLAR using all available information (all genotyped SNPs on all individuals). The average ratio of SNP effective number/actual number obtained from analysis of 1,989 non-overlapping bins of SNPs was used to calculate the genome-wide effective number of tests and thus the significance threshold for genome-wide association. We performed quantitative transmission disequilibrium test (implemented in SOLAR) to test for population stratification.
