Using single-SNP testing, the UKPDC and WTCCC2 (2011) found evidence for an association with Parkinson’s disease in the 4q22 region with the lowest P-value at rs356220. A conditional analysis on rs356220 revealed a second SNP rs7687945 with P-value 3×10−5 that in the single-SNP testing had only a modest P-value of 0.13. These two SNPs are in low Linkage Disequilibrium (LD) (r2=0.168 in the original data) but the LD was sufficient enough to mask the effect of rs7687945 in single-SNP testing. This complex pattern of association was replicated in an independent French dataset (UKPDC and WTCCC2, 2011).
