Association analysis of HDL-C levels with rs9930761T>C and rs5883C>T, with and without adjusting for upstream SNP rs247616C>T, in the Whitehall II Study.

Minor allele frequency (MAF) was 6.7% for rs9930761, 5.5% for rs5883, and 33.6% for rs247616. Linkage disequilibrium (LD) for rs247616–rs9930761 is R2 = 0.035 and D′ = 0.962 (haplotype frequencies are (versus expected under linkage equilibrium) TC 0.001 (0.023), CC 0.067 (0.044), TT 0.337 (0.315), and CT 0.595 (0.618). Note that the minor alleles rarely occur together (TC 0.001), indicating a strong negative LD between rs9930761/rs5883 and rs247616, requiring HDL-C versus rs9930761/rs5883 analysis conditional on rs247616. For all SNPs see Supporting Information Table S4.