Table 3 Joint testing pairs of cis-SNPs improves the number of eQTL detected at FDR 5% by 10.7%
FDR1%2%3%4%5%10%15%20%25%
Marg452849365240545856416432707276008123
Joint488453765726601562487206794786259277
New5976987818509081113126314311565
LM276303334358381473566634701
  • Many of the new genes (row “New”) discovered using the joint test appear to be linkage masked (row “LM”), with correlation between the significant SNP pair >0.2.