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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