Evaluation of sample size effect on the identification of haplotype blocks

Osabe, Dai; Tanahashi, Toshihito; Nomura, Kyoko; Shinohara, Shuichi; Nakamura, Naoto; Yoshikawa, Toshikazu; Shiota, Hiroshi; Keshavarz, Parvaneh; Yamaguchi, Yuka; Kunika, Kiyoshi; Moritani, Maki; Inoue, Hiroshi; Itakura, Mitsuo

doi:10.1186/1471-2105-8-200

BMC Bioinformatics

Table 1 List and information of 37 SNPs in the analyzed region on chromosome 20q11.22

From: Evaluation of sample size effect on the identification of haplotype blocks

No.	dbSNP ID	Position	No. of used samples		Minor allele frequency			P value (HWE test)			P value (association test)		Odds ratio
			Control	Case	Control	Case	Overall	Control	Case	Overall	Allele	Genotype
A001	rs819135	32,311,428	357	362	0.40	0.34	0.37	0.32	0.30	0.18	0.03	0.08	1.27
A002	rs6088466	32,377,195	358	361	0.46	0.50	0.48	0.84	0.79	0.99	0.17	0.37	1.16
A003	rs1205336	32,389,997	358	367	0.36	0.35	0.36	0.47	0.81	0.50	0.85	0.93	1.02
A004	rs3746455	32,420,877	357	367	0.36	0.35	0.35	0.72	0.87	0.72	0.86	0.98	1.02
A005	rs6058029	32,433,304	352	367	0.35	0.35	0.35	0.44	0.87	0.51	0.94	0.90	1.01
A006	rs6087579	32,448,816	354	367	0.36	0.35	0.36	0.78	0.87	0.76	0.86	0.98	1.02
A007	rs6579165	32,458,376	357	359	0.36	0.36	0.36	0.72	0.71	0.61	0.98	1.00	1.00
A008	rs4911420	32,462,315	358	365	0.36	0.35	0.35	0.80	0.84	0.75	0.74	0.95	1.04
A009	rs4277599	32,472,566	356	360	0.36	0.35	0.35	0.70	0.74	0.61	0.79	0.96	1.03
A010	rs2424992	32,475,721	354	366	0.36	0.35	0.35	0.67	0.80	0.63	0.85	0.97	1.02
A011	rs6120644	32,487,471	355	364	0.36	0.36	0.36	0.92	0.81	0.81	0.94	0.99	1.01
A012	rs3736762	32,500,997	357	361	0.36	0.36	0.36	0.72	0.87	0.71	0.96	0.99	1.01
A013	rs6059850	32,508,445	352	364	0.36	0.35	0.35	0.98	0.70	0.77	0.76	0.92	1.03
A014	rs6059856	32,521,615	355	367	0.36	0.35	0.36	0.92	0.87	0.85	0.85	0.98	1.02
A015	rs6059866	32,539,471	355	360	0.36	0.35	0.35	0.92	0.92	0.89	0.80	0.97	1.03
A016	rs6059868	32,543,121	357	366	0.36	0.35	0.35	0.72	0.91	0.75	0.85	0.97	1.02
A017	rs6088512	32,559,552	355	365	0.36	0.35	0.36	0.86	0.83	0.78	0.86	0.98	1.02
A018	rs6120669	32,568,689	356	367	0.36	0.35	0.36	0.88	0.87	0.83	0.83	0.98	1.02
A019	rs1122174	32,574,507	356	367	0.18	0.15	0.16	0.41	0.97	0.51	0.09	0.22	1.27
A020	rs6087592	32,578,164	353	367	0.35	0.36	0.35	0.66	0.96	0.79	0.87	0.92	1.02
A021	rs11167239	32,604,133	354	363	0.36	0.36	0.36	0.88	0.72	0.72	0.85	0.97	1.02
A022	rs6088527	32,619,502	354	361	0.36	0.35	0.36	0.90	0.48	0.56	0.83	0.90	1.02
A023	rs764597	32,624,886	357	365	0.36	0.36	0.36	0.89	0.65	0.67	0.92	0.97	1.01
A024	rs2889849	32,627,938	352	365	0.18	0.15	0.16	0.32	0.41	0.80	0.11	0.13	1.26
A025	rs932542	32,635,029	357	367	0.18	0.15	0.16	0.45	0.42	0.94	0.15	0.19	1.23
A026	rs2295444	32,637,544	354	360	0.36	0.35	0.36	0.93	0.47	0.65	0.73	0.80	1.04
A027	rs2378199	32,650,141	358	360	0.17	0.14	0.16	0.26	0.36	0.73	0.07	0.08	1.30
A028	rs6088536	32,652,767	358	359	0.36	0.36	0.36	0.97	0.65	0.77	0.88	0.93	1.02
A029	rs6141488	32,656,407	356	367	0.46	0.49	0.48	0.24	0.71	0.56	0.24	0.28	1.13
A030	rs6142210	32,686,673	355	361	0.46	0.49	0.48	0.26	0.56	0.70	0.28	0.27	1.12
A031	rs6088552	32,690,152	358	366	0.46	0.49	0.48	0.24	0.60	0.64	0.22	0.23	1.14
A032	rs7269596	32,692,724	352	365	0.47	0.50	0.48	0.27	0.64	0.65	0.26	0.29	1.13
A033	rs6087612	32,694,483	352	367	0.46	0.50	0.48	0.29	0.64	0.67	0.16	0.21	1.16
A034	rs4911158	32,703,173	357	363	0.46	0.50	0.48	0.31	0.56	0.74	0.18	0.22	1.15
A035	rs6087616	32,726,694	356	364	0.46	0.50	0.48	0.46	0.60	0.86	0.18	0.28	1.15
A036	rs1321306	32,730,040	353	365	0.46	0.49	0.48	0.22	0.71	0.54	0.23	0.26	1.13
A037	rs910870	32,756,554	355	360	0.25	0.23	0.24	0.56	0.64	0.93	0.31	0.45	1.13

Genome position is based on the NCBI build 35. The number of called sample is the number after excluding the undetermined sample(s) with TaqMan assay. HWE denotes Hardy-Weinberg equilibrium. 95% CI denotes 95% confidence interval. The crude odds ratio was calculated for the allele model.

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