. Author manuscript; available in PMC: 2012 Jul 1.

Published in final edited form as: J Hum Genet. 2011 Jun 2;56(7):496–502. doi: 10.1038/jhg.2011.48

Table 6.

Frequency of 33 SNPs spanning PTEN in 2 GWAS studies

			CGEMS (650 aggressive/527 non-aggressive)					GASP2 (637 aggressive/863 non-aggressive)

SNP	Position	Minor allele	F_A^▲	F_U^▲	P^a	OR^a	Status	F_A^▲	F_U^▲	P^a	OR^a	Status
rs3781195	89 632 589	G	0.03	0.03	0.82	1.06	Imputed	0.02	0.02	0.84	0.95	Imputed
rs1234220	89 635 453	G	0.11	0.10	0.70	1.06	Original	0.11	0.09	0.15	1.19	Imputed
rs11202596	89 637 134	A	0.09	0.08	0.58	1.09	Original	0.04	0.05	0.44	0.85	Imputed
rs1234219	89 639 557	G	0.08	0.07	0.47	1.13	Imputed	0.07	0.06	0.26	1.20	Imputed
rs7069904	89 639 818	A	0.03	0.02	0.41	1.27	Imputed	0.01	0.00	0.21	1.91	Imputed
rs1234218	89 640 739	T	0.07	0.07	0.69	1.07	Imputed	0.07	0.06	0.30	1.17	Imputed
rs1903858	89 643 666	G	0.32	0.30	0.26	1.11	Imputed	0.27	0.28	0.66	0.96	Imputed
rs2299939	89 647 130	A	0.19	0.20	0.49	0.93	Original	0.08	0.09	0.19	0.80	Imputed
rs1234225	89 663 549	T	0.36	0.33	0.10	1.16	Imputed	0.33	0.33	0.72	1.03	Imputed
rs12569998	89 664 137	G	0.14	0.14	0.95	0.99	Imputed	0.13	0.13	0.56	0.94	Original
rs1234224	89 665 276	G	0.36	0.33	0.10	1.16	Imputed	0.33	0.33	0.72	1.03	Imputed
rs1234223	89 665 570	C	0.10	0.10	0.68	1.06	Imputed	0.11	0.09	0.15	1.19	Imputed
rs17106896	89 667 087	T	0.05	0.04	0.19	1.30	Imputed	0.01	0.01	0.32	1.58	Imputed
rs1676759	89 668 276	G	0.03	0.03	0.98	1.01	Imputed	0.01	0.01	0.96	1.02	Imputed
rs11202600	89 672 813	C	0.07	0.07	0.69	1.07	Imputed	0.09	0.07	0.06	1.29	Original
rs10490920	89 675 623	C	0.14	0.14	0.95	0.99	Imputed	0.12	0.13	0.48	0.93	Imputed
rs1234213	89 679 301	A	0.36	0.33	0.09	1.16	Imputed	0.33	0.33	0.75	1.03	Imputed
rs7078674	89 687 333	0	0.00	0.00	NA	NA	Imputed	0.00	0.00	NA	NA	Imputed
rs12357281	89 690 651	C	0.09	0.08	0.64	1.07	Imputed	0.04	0.05	0.38	0.84	Imputed
rs2299941	89 694 699	G	0.14	0.14	0.98	1.00	Imputed	0.12	0.13	0.41	0.91	Imputed
rs2735343	89 695 409	C	0.36	0.33	0.11	1.15	Imputed	0.33	0.33	0.79	1.02	Imputed
rs2248293	89 697 245	C	0.36	0.33	0.11	1.15	Original	0.30	0.30	0.75	0.97	Imputed
rs17562384	89 699 396	C	0.19	0.20	0.47	0.93	Imputed	0.08	0.09	0.17	0.79	Imputed
rs2673832	89 702 453	G	0.11	0.10	0.44	1.11	Original	0.02	0.02	0.38	0.76	Imputed
rs12572106	89 706 087	C	0.14	0.14	0.98	1.00	Imputed	0.12	0.13	0.48	0.93	Imputed
rs17431184	89 710 231	C	0.19	0.20	0.47	0.93	Imputed	0.08	0.10	0.15	0.78	Imputed
rs2736627	89 711 074	C	0.09	0.09	0.64	1.07	Imputed	0.02	0.02	0.38	0.76	Imputed
rs926091	89 711 392	T	0.14	0.14	0.98	1.00	Imputed	0.12	0.13	0.48	0.93	Imputed
rs532678	89 713 322	T	0.36	0.33	0.11	1.15	Imputed	0.33	0.33	0.80	1.02	Imputed
rs11202607	89 717 394	T	0.07	0.07	0.67	1.07	Original	0.07	0.06	0.31	1.17	Imputed
rs478839	89 721 850	G	0.39	0.42	0.25	0.91	Original	0.38	0.38	0.92	0.99	Imputed
rs17346680	89 727 081	A	0.04	0.04	0.98	1.00	Imputed	0.07	0.06	0.20	1.22	Original
rs10509532	89 727 534	T	0.14	0.14	0.91	0.99	Original	0.12	0.13	0.48	0.93	Original

Abbreviations: CGEMS, cancer genetic markers of susceptibility; GWAS, whole genome-wide association study; OR, odds ratio; SNPs, single nucleotide polymorphisms.

P and OR are calculated based on an unconditional logistic regression with adjustment for age and geographic region, assuming an additive model of inheritance.

^▲

F_A, frequency in aggressive cases; F_U, frequency in non-aggressive cases.