Variants in LD with a causal variant show elevated test statistics in association analysis proportional to the LD (measured by r2) with the causal variant1–3. The more genetic variation an index variant tags, the higher the probability that this index variant will tag a causal variant. In contrast, inflation from cryptic relatedness within or between cohorts4,5,6 or population stratification purely from genetic drift will not correlate with LD Score.
