Hi,

I have used plink (--assoc option) to detect the level of association between a list of snps and two quantitative traits ( list_snps~QT1, list_snps~QT2). For quality control, I have included two snps (rs123_star, rs456_star) that have been previously genotyped with TaqMan. (So if everything went well in the analysis, rs123 from the list should have around the same significance levels as rs123_star; and similarly for rs456 and rs456_star)

At a preliminary look at the top significant SNPs (sorted by F value) for each association I could observe :

Table 1 : snps~QT1 :  rs123, rs456 missing from top 40 

 Rank       id               QT1_F_value        QT2_F_value

  1.  rs123_star         3285,58              1535,86    
  6.  rs456_star           802,02                     19,27    

Table 2 : snps~QT2 :  rs456, rs456_star are missing from top 40; additionally the differences between the F values are extreme for rs123 and rs123_star.

 Rank       id               QT2_F_value        QT1_F_value

  1.  rs123_star         1535,856              3285,582

  12  rs123              470,0224              12,36226

What could be the explanation of such a huge difference in significance levels between the same SNPs ?

(the genotypes for rs123 and rs456 resulted after a GWAS (chip data); the genotypes for rs123_star and rs456_star were obtained using Taqman genotyping on the same population)