We defined a SNP as having a pleiotropic effect on two phenotypes when the P value for the O’Brien test statistic from the joint model of association of two phenotypes ( P joint ) with the SNP is at least one order of magnitude more significant than the P values ( P univariate ) for both phenotypes and the univariate P values are at least nominally significant ( P univariate < 0.05).
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Genome-wide pleiotropy analysis of neuropathological traits related to Alzheimer's disease.
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