A genome-wide linkage and association study using COGA data

BMC Genomic Data

Table 2 The most significant SNPs identified by FBAT. Empirical variance was used to estimate the p-value.

Chrom	SNP	position (cM)	freq	p value of (HWE)	No. of fam	S^a	E(S)^b	Var(S)^c	Z^d	p-value^e
1	tsc0616094	68.9	0.868	1.0	41	221	202.4	26.6	3.6	0.000305
1	tsc0668988	99.4887	0.37	0.39	55	121	146.7	55.2	-3.5	0.000552
1	tsc1177811	105.535	0.318	0.13	53	83	105.4	43.5	-3.4	0.000682
3 ^f	tsc0515272	164.236	0.876	0.02	45	248	223.4	29.6	4.5	0.000006
4	tsc0571248	172.977	0.223	0.26	54	79	102.2	49.6	-3.3	0.000988
5	tsc0158479	95.668	0.063	0.50	35	27	43.9	20.6	-3.7	0.000198
6	tsc1175206	127.576	0.675	0.59	59	279	252.9	52.6	3.6	0.000327
6	tsc0608218	146.124	0.184	0.61	48	63	81.7	31.4	-3.3	0.000839
9	tsc0048697	13.7398	0.342	0.87	54	113	135.5	46.2	-3.3	0.000935
11	tsc0569292	6.78451	0.788	0.02	40	191	173	27.3	3.5	0.00055
11	tsc0919042	81.1855	0.15	0.75	49	65	88.5	44.7	-3.5	0.000444
13	tsc0271621	60.1748	0.173	0.59	46	55	81.3	59.5	-3.4	0.000659
13	tsc0056748	73.9934	0.191	1.0	42	28	49.4	28.1	-4.0	0.000053
14	tsc0902508	81.2799	0.14	0.39	40	46	64.9	30.7	-3.4	0.000639
15	tsc0058074	49.9916	0.556	0.89	75	300	331.9	86.3	-3.4	0.000599
16	tsc1750530	59.8297	0.107	0.02	46	44	69.7	45.8	-3.8	0.000147
19	tsc0061923	66.8126	0.885	1.0	26	145	161.1	21.6	-3.5	0.000512
19	tsc0598556	102.054	0.664	0.26	63	335	304.3	73.9	3.6	0.000347
20	tsc0060446	35.4473	0.2	1.0	63	90	118.4	43.2	-4.3	0.000015
7	tsc0331830^g	33.9373	0.113	1.0	39	59	74.2	31.5	-2.7	0.0067
7	tsc0593964^g	42.6174	0.629	0.53	70	332	305.8	79.2	2.9	0.00328
7	tsc0042959^g	44.4931	0.136	0.47	49	57	77.9	50.7	-2.9	0.003313
7	tsc0051325^g	44.5631	0.749	0.58	61	284	309.8	79.5	-2.8	0.003754
7	tsc0797235^g	122.213	0.897	0.71	37	231	214.6	37.6	2.7	0.007624

^a Observed FBAT statistic based on a linear combination of offspring genotypes and traits.
^b Estimated mean of S.
^c Estimated variance of S.
^d Z score defined by (S - E(S))/.
^e No multiple comparison was corrected.
^f Bold text indicates that the SNP achieves genome-wide significance.
^g These SNPs listed because of linkage evidence observed on chromosome 7.

ISSN: 2730-6844