Many variants clustered as defined by r2> 0.8 within the genes but the proportion of clusters containing SNPs with p<.05 remained quite similar with SNAP analyses in both CEU and YPI populations (data not shown). Of the variants with linkage disequilibrium data available in SNAP for the CEU population, 27 SNPs in GABRA2 broke down into 10 clusters of which 5 clusters had SNPs with p<.05 (50%), 24 SNPs in BDNF broke down into 9 clusters of which 4 clusters had SNPs with p<.05 (44%), and 6 SNPs in HTR1A broke down into 3 clusters of which 1 cluster had SNPs with p<.05 (33%). Generally fewer SNPs clustered in the YRI population than in the CEU population but the proportion of clusters containing SNPs with p<.05 was comparable between the two populations. In the YRI population, 25 SNPs in GABRA2 broke down into 16 clusters of which 12 clusters had SNPs with p<.05 (75%), 25 SNPs in BDNF broke down into 19 clusters of which 10 clusters had SNPs with p<.05 (53%), and 9 SNPs in HTR1A broke down into 5 clusters of which 2 cluster had SNPs with p<.05 (40%).
