Table 2. Summary of the methods.

	Simes test	Fisher test	GATES	VEGAS	FOSCO
Source	[12]	[11]	[10]	[9]	–
Core idea	Adjust p-values by under assumption of independence	Obtain p-value based on under the assumption of independence	Adjust p-values by , where me(i) is obtained from each gene empirically	Obtain p-values base on . The distribution under the null hypothesis is obtained through Monte Carlo methods	Adjust p-values by where α is determined empirically from a random permutation
Linear regression coefficient after correction*	2.32E-04	−8.32E-03	−3.14E-04	−1.00E-04	−3.75E-04
SNPs association to genes	NCBI dbSNPs	NCBI dbSNPs	NCBI dbSNPs+5kb flanking regions	UCSG Genome Brower hg18+50 kb flanking regions	NCBI dbSNPs

Note: * Linear regression coefficient before correction β = −7.23E-03.