SNP-SNP interactions dominate the genetic architecture of candidate genes associated with left ventricular mass in african-americans of the GENOA study

Table 3 Detailed results for the ten most significant SNP-SNP interaction models.

SNP 1	SNP 2	DF* for Interaction Test	Interaction P-value in full sample	Model P-value in full sample	Interaction q-value in full sample	CV* R² in full sample	Interaction P-value (Sample 1)	Interaction P-value (Sample 2)
rs35314437	rs7552841	2	1.78 × 10^-7	3.88 × 10^-8	0.0142	0.0165	0.0202	4.21 × 10^-6
rs257376	rs5267	3	1.33 × 10^-6	9.11 × 10^-8	0.0218	0.0031	0.0965	0.0442
rs2229169	rs6664855	4	2.45 × 10^-7	1.19 × 10^-7	0.0142	0.0094	0.0004	0.0028
rs10482839	rs7552841	3	2.13 × 10^-6	2.78 × 10^-7	0.0256	0.0143	0.0276	3.96 × 10^-5
rs17876148	rs12971616	4	4.35 × 10^-8	3.14 × 10^-7	0.0139	0.0151	1.85 × 10^-7	0.0389
rs936211	rs521898	2	1.17 × 10^-6	1.07 × 10^-6	0.0211	0.0115	0.0663	0.0023
rs6745660	rs12460421	4	0.0002	1.09 × 10^-6	0.2247	0.0158	0.0856	0.0054
rs945032	rs12028945	4	6.45 × 10^-6	1.11 × 10^-6	0.0385	0.0103	0.0028	0.0011
rs17876144	rs12971616	4	7.29 × 10^-8	1.14 × 10^-6	0.0139	0.012	2.73 × 10^-6	0.0341
rs35314437	rs4846052	1	1.73 × 10^-7	1.15 × 10^-6	0.0142	0.0177	0.0021	4.14 × 10^-5

Table 3 outlines the detailed association and multiple testing results for the top ten SNP-SNP interactions passing all three multiple testing criteria. "Interaction p-values" are from an up to 4 degree of freedom likelihood ratio test (depending on number of genotype classes represented in GENOA sample), "model p-value" column is from the likelihood ratio for the model including main effects and interactions compared to a null model (up to 8 degrees of freedom), q-value was assessed from the "interaction p-value", CV R² is the difference in CV R² when the interaction terms are included in the CV process compared to only main effects of SNPs, and the final two columns are the interaction p-values for the internal replication subset samples. These ten models were used in the multivariable model building process with the bold rows indicating interactions included in final model.
*DF = degrees of freedom, CV = cross-validation

ISSN: 1471-2350