We next evaluated linkage disequilibrium with the widely-studied SNP rs1799971 (r2 values shown in Figure S5 and D’ values shown in Figure S6). Rs3778150 and rs1799971 had r2=0 and D’=0.05 in the AFR panel. In the EUR panel, rs3778150 and rs1799971 had D’=1; the rs3778150 minor allele (C, frequency=15%) occurring on the same haplotype background with the rs1799971 major allele (A, frequency=84%) but a weak r2 value (r2=0.03) reflecting the discrepant allele frequencies.
