A meta analysis of genome-wide association studies for limb bone lengths in four pig populations

Guo, Yuanmei; Hou, Lijuan; Zhang, Xufei; Huang, Min; Mao, Huirong; Chen, Hao; Ma, Junwu; Chen, Congying; Ai, Huashui; Ren, Jun; Huang, Lusheng

doi:10.1186/s12863-015-0257-1

BMC Genomic Data

Table 2 The chromosomal regions significantly associated with the limb bones lengths

From: A meta analysis of genome-wide association studies for limb bone lengths in four pig populations

Chr¹	Trait	Population	Top SNP	Position, Mb	Effect ± S.E.	P Value²	N _SNP ³
1	Scapula	Meta	ss131151852	30.72	0.186 ± 0.041	5.43 × 10⁻⁶	1
1	Scapula	Meta	ss131149408	282.04	0.171 ± 0.039	1.10 × 10⁻⁵	1
1	Tibia	Meta	ss131148700	279.60	0.136 ± 0.033	4.38 × 10⁻⁵	1
1	Tibia	Laiwu	ss107826847	280.64	0.286 ± 0.059	1.12 × 10⁻⁵	1
1	Femur	Meta	ss131151073	285.76	0.150 ± 0.034	9.68 × 10⁻⁶	1
1	Humerus	Meta	ss131151073	285.76	0.144 ± 0.031	4.11 × 10⁻⁶	2
1	Scapula	Laiwu	ss131102194	299.48	0.300 ± 0.069	2.15 × 10⁻⁵	1
2	Scapula	Meta	ss131184380	4.87	0.144 ± 0.032	6.06 × 10⁻⁶	3
3	Humerus	Sutai	ss131215509	9.48	0.344 ± 0.075	7.14 × 10⁻⁶	1
3	Ulna	Meta	ss131222600	97.95	0.138 ± 0.034	4.99 × 10⁻⁵	1
4	Scapula	Erhualian	ss131260763	42.51	0.965 ± 0.173	2.87 × 10^-7**	10
4	Tibia	Meta	ss478940901	63.32	0.162 ± 0.036	7.61 × 10⁻⁶	1
4	Humerus	Erhualian	ss478940911	65.72	0.478 ± 0.104	1.18 × 10⁻⁵	1
4	Ulna	Erhualian	ss478940911	65.72	0.648 ± 0.116	4.37 × 10^-7*	1
4	Ulna	Meta	ss131269439	81.71	0.195 ± 0.041	1.93 × 10^-6*	6
4	Femur	Meta	ss131269533	81.94	0.173 ± 0.039	8.61 × 10⁻⁶	2
4	Scapula	Meta	ss478941011	82.53	0.187 ± 0.042	7.44 × 10⁻⁶	1
4	Humerus	Meta	ss131270306	84.98	0.164 ± 0.038	1.41 × 10⁻⁵	1
7	Femur	Meta	ss131342998	33.79	0.316 ± 0.039	9.99 × 10^-16**	32
7	Humerus	Meta	ss131342998	33.79	0.261 ± 0.035	5.53 × 10^-14**	35
7	Scapula	Meta	ss131342998	33.79	0.255 ± 0.041	6.67 × 10^-10**	18
7	Tibia	Meta	ss131342998	33.79	0.317 ± 0.036	5.53 × 10^-14**	44
7	Ulna	Meta	ss131342998	33.79	0.347 ± 0.039	5.53 × 10^-14**	48
7	Femur	F₂	ss107837325	34.80	0.884 ± 0.075	1.71 × 10^-19**	109
7	Scapula	F₂	ss107837325	34.80	1.029 ± 0.091	4.85 × 10^-18**	110
7	Femur	Erhualian	ss131343870	34.84	0.557 ± 0.096	7.05 × 10^-8**	3
7	Humerus	Erhualian	ss131343870	34.84	0.553 ± 0.071	1.84 × 10^-13**	19
7	Scapula	Erhualian	ss131343870	34.84	0.605 ± 0.093	2.04 × 10^-9**	3
7	Tibia	Erhualian	ss131343870	34.84	0.644 ± 0.073	1.05 × 10^-15**	28
7	Ulna	Erhualian	ss131343870	34.84	0.679 ± 0.078	4.51 × 10^-15**	17
7	Humerus	F₂	ss107806758	35.18	0.818 ± 0.074	1.39 × 10^-17**	102
7	Tibia	F₂	ss107806758	35.18	0.872 ± 0.073	1.68 × 10^-19**	109
7	Ulna	F₂	ss107806758	35.18	1.129 ± 0.086	3.73 × 10^-21**	108
8	Ulna	Meta	ss107904229	133.84	0.148 ± 0.036	4.23 × 10⁻⁵	1
8	Humerus	Meta	ss131065181	145.99	0.131 ± 0.032	3.86 × 10⁻⁵	1
13	Tibia	Meta	ss131486660	29.08	0.156 ± 0.037	2.58 × 10⁻⁵	1
13	Scapula	Meta	ss131483019	214.15	0.151 ± 0.038	5.62 × 10⁻⁵	1
14	Ulna	Meta	ss131520568	10.50	0.131 ± 0.032	4.79 × 10⁻⁵	1
14	Femur	Meta	ss131515687	64.87	0.179 ± 0.038	2.46 × 10^-6*	1
14	Scapula	Meta	ss131515687	64.87	0.178 ± 0.040	8.46 × 10⁻⁶	1
14	Scapula	Sutai	ss131515687	64.87	0.261 ± 0.059	2.00 × 10⁻⁵	1
14	Humerus	Meta	ss131516260	67.34	0.137 ± 0.032	1.90 × 10⁻⁵	2
14	Tibia	Meta	ss131516260	67.34	0.150 ± 0.032	2.66 × 10^-6*	3
15	Tibia	Meta	ss478943357	20.82	0.127 ± 0.029	1.45 × 10⁻⁵	1
17	Femur	Meta	ss131554491	10.79	0.126 ± 0.032	6.26 × 10⁻⁵	1
17	Ulna	Sutai	ss131542878	13.79	0.508 ± 0.103	1.97 × 10⁻⁶	8
17	Ulna	Meta	ss131546319	37.50	0.192 ± 0.045	1.93 × 10⁻⁵	1
18	Femur	Meta	ss107835048	52.79	0.147 ± 0.033	9.83 × 10⁻⁶	2
18	Tibia	Meta	ss107835048	52.79	0.135 ± 0.031	9.52 × 10⁻⁶	2
X	Humerus	Meta	ss478936157	41.48	0.113 ± 0.021	1.47 × 10^-7**	8
X	Femur	F₂	ss478944418	43.40	0.198 ± 0.028	3.73 × 10^-8**	9
X	Humerus	F₂	ss478944418	43.40	0.191 ± 0.027	9.02 × 10^-8**	16
X	Scapula	F₂	ss478944418	43.40	0.229 ± 0.034	1.81 × 10^-7**	9
X	Ulna	F₂	ss478944418	43.40	0.241 ± 0.030	4.85 × 10^-9**	16
X	Femur	Meta	ss23131102	63.65	0.133 ± 0.022	8.67 × 10^-10**	15
X	Tibia	Meta	ss23131102	63.65	0.140 ± 0.020	4.67 × 10^-12**	20
X	Ulna	Meta	ss23131102	63.65	0.129 ± 0.022	3.55 × 10^-9**	25
X	Tibia	F₂	ss23131102	63.65	0.249 ± 0.031	1.66 × 10^-9**	24
X	Ulna	Erhualian	ss478935724	102.94	0.223 ± 0.045	7.08 × 10⁻⁶	1
X	Scapula	Meta	ss131570200	107.48	0.114 ± 0.023	6.21 × 10^-7**	15

Notes: 1. Chromosome; 2. The P value was corrected by genomic control. **: 1 % genome-wide significant; *: 5 % genome-wide significant; without *: suggestive significant; 3. number of SNPs that surpass the suggestive significance level.

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