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Table 6 False positive rates (type I error) estimation in % for different LD patterns and pruning levels

From: Confounding of linkage disequilibrium patterns in large scale DNA based gene-gene interaction studies

LD LD block settings:
pruning A B C D
unpruned < 1% < 1% < 1% < 1%
LD (r2) 0:75 < 1% < 1% < 1% < 1%
LD (r2) 0:60 < 1% < 1% < 1% < 1%
LD (r2) 0:50 < 1% < 1% < 1% < 1%
LD (r2) 0:20 < 1% < 1% < 1% < 1%
  1. Null data with no disease association to the investigated pair of SNPs as disease susceptibility loci