Mixture SNPs effect on phenotype in genome-wide association studies

BMC Genomics

Table 6 The Framingham Heart Study: PVE Estimation Using Proportion of SNPs Based on P-value Threshold ^a

	P-value <0.1^bc	P-value <0.01^bc	P-value <0.001^bc	P-value <0.0001^bc
	(s.e.)	(s.e.)	(s.e.)	(s.e.)
Number of SNPs	2690	561	145	45
Genetic Variance	4.45 (0.34)	3.34 (0.37)	2.08 (0.38)	0.86 (0.31)
Error Variance	20.66 (0.34)	22.31 (0.35)	24.06 (0.38)	25.25 (0.39)
Total Variance	25.11 (0.45)	25.65 (0.50)	26.14 (0.53)	26.11 (0.50)
PVE	0.18 ^d (0.06)	0.13 ^d (0.04)	0.08 ^d (0.03)	0.03 ^d (0.01)
	P-value <0 . 00001 ^bc	P-value <0 . 000001 ^bc	P-value <0 . 0000001 ^bc
	(s.e.)	(s.e.)	(s.e.)
Number of SNPs	21	10	7
Genetic Variance	0.43 (0.21)	0.43 (0.28)	0.25 (0.22)
Error Variance	25.48 (0.40)	25.60 (0.40)	25.73 (0.40)
Total Variance	25.91 (0.45)	26.03 (0.49)	25.97 (0.46)
PVE	0.02 ^d (0.01)	0.02 ^d (0.01)	0.01 ^d (0.01)

^aThe analysis in the table is carried out using the GCTA software developed by [3]. ^bP-value is obtained by regressing BMI on each single SNP. ^cValues in the parenthesis are standard errors. ^dPVE decreases from 18 % to 1 % as a smaller group of SNPs are included in the analysis.

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