Exploring the interaction between SNP genotype and postmenopausal hormone therapy effects on stroke risk

Table 2 Top ten SNPs identified by two-component test of interaction with E-alone or E+P

Rank	Rs#	Chr	Position	Allele	MAF	OR	Marginal association test P-value	HT interaction P-value	HT interaction FDR	E-alone interaction P-value	E+P interaction P-value	Gene
1	2154299	6	6231297	A/G	0.09	1.18	0.0299	0.00015	0.015	0.08111	0.00013	F13A1
2	12194855	6	6233241	G/A	0.09	1.19	0.0265	0.00026	0.015	0.10080	0.00020	F13A1
3	630431	1	55299911	G/A	0.34	0.91	0.0498	0.00068	0.025	0.01660	0.00291	PCSK9
4	568052	1	55297430	G/A	0.34	0.90	0.0450	0.00151	0.042	0.01939	0.00610	PCSK9
5	10028444	4	88654846	A/G	0.17	1.13	0.0482	0.03593	0.715	0.15318	0.03175	SPARCL1
6	1381633	4	88687876	G/A	0.23	1.12	0.0436	0.04131	0.715	0.05512	0.10068	SPARCL1
7	243842	16	54084923	C/T	0.39	0.87	0.0041	0.04671	0.715	0.02295	0.32839	MMP2
8	2817247	6	24580402	A/G	0.10	1.18	0.0227	0.05315	0.715	0.37301	0.02427	GPLD1
9	1982049	9	1.16E+08	T/G	0.36	1.10	0.0411	0.05747	0.715	0.03309	0.27896	AMBP
10	6413453	1	1.59E+08	A/G	0.11	0.86	0.0490	0.09972	0.881	0.78264	0.03322	APOA2

Rank, rank of SNPs based on HT interaction test with two degrees of freedom. Rs#, SNP identification (rs) number in dbSNP database. Chr, chromosome. Allele, minor/major allele. MAF, minor allele frequency in the study population. OR, odds ratio for increase of per minor allele. Marginal association test P-value, P-value based on test of SNP main effect assuming additive effect. HT interaction P-value: P-value based on two degrees of freedom joint test for interaction with HT. HT interaction FDR, FDR based on two degrees of freedom joint test for interaction with HT. E-alone interaction P-value, P-value based on test for interaction with E-alone. E+P interaction P-value, P-value based on test for interaction with E+P.

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