. 2015 Jul 22;16:89. doi: 10.1186/s12863-015-0241-9

Table 5.

Boundaries of the validated regions that are additively significant on calving interval as well as the most significant SNPs and their associated genes within these regions in discovery and validation populations

		Most strongly associated SNP in discovery						Most strongly associated SNP in validation
BTC^a	Interval (Mbp)^b	SNP	Position (bP)	-log10 (P)	Effect ± SE	MAF^c	$\frac{σ_{a}^{2}}{σ_{p}^{2}}$ (%)^d	SNP		Position (bp)	-log10 (P)	Effect ± SE	MAF	$\frac{σ_{a}^{2}}{σ_{p}^{2}}$ (%)	Genes
5	12.551 - 13.463	rs133249083	13027942	4.139	2.462 ± 0.620	0.329	0.095	rs135584613		13270757	3.229	−3.077 ± 0.893	0.325	0.140	NA
5	88.607 - 89.159	rs135833682	88822777	4.076	−2.191 ± 0.556	0.417	0.083	rs133539520		88861488	2.679	−2.784 ± 0.934	0.313	0.112	ABCC9
9	55.233 - 55.657	rs134339497	55233033	4.325	−2.364 ± 0.580	0.402	0.096	rs136630637		55637401	2.399	−2.559 ± 0.887	0.337	0.098	NA
9	57.397 - 57.735	rs137407787	57396816	4.130	−2.346 ± 0.591	0.358	0.091	rs42550144		57723628	2.408	−2.685 ± 0.929	0.290	0.100	EPHA7
9	60.121 - 60.477	rs43600502	60477358	5.195	−2.642 ± 0.584	0.352	0.114	rs133175600		60130790	2.127	2.813 ± 1.05	0.212	0.087	LOC101902479
11	20.620 – 21.274	rs133774241	20994163	4.318	−2.706 ± 0.665	0.241	0.096	rs137059194		20898669	2.410	−2.467 ± 0.8529	0.458	0.101	LOC783737
11	39.466 - 39.772	rs109315341	39466071	4.126	−2.971 ± 0.749	0.177	0.092	rs133126268		39747182	2.408	−3.706 ± 1.284	0.115	0.094	NA
11	40.896 - 41.299	rs133462686	41298588	4.491	−3.036 ± 0.729	0.182	0.098	rs109834745		40895791	2.414	3.554 ± 1.228	0.139	0.101	LOC101903002
18	4.541 - 4.810	rs109920290	4541123	4.326	2.4 ± 0.589	0.391	0.098	rs110689012		4810082	2.044	3.37 ± 1.29	0.119	0.080	NA
18	37.446 - 37.925	rs41875426	37446338	4.061	2.679 ± 0.682	0.213	0.086	rs137407722		37925382	3.142	4.111 ± 1.213	0.147	0.142	NA
18	53.789 - 54.605	rs41891477	54232476	4.180	−2.302 ± 0.576	0.399	0.091	rs109907036		54028686	3.680	4.065 ± 1.094	0.186	0.168	PRKD2 / PPP5C
18	57.109 - 58.052	rs110801791	57516245	4.675	−3.508 ± 0.824	0.136	0.103	rs41895542		57269152	2.496	3.6 ± 1.219	0.133	0.100	NA
18	61.922 - 62.150	rs133761590	62115202	4.661	2.525 ± 0.594	0.369	0.106	rs137170802		62143810	2.736	−3.018 ± 0.966	0.255	0.116	CACNG6 / VSTM1
22	4.979 - 5.598	rs41996522	5028345	6.076	−2.784 ± 0.564	0.442	0.137	rs41995585		5133660	2.168	−3.028 ± 1.117	0.168	0.086	NA
27	41.873 - 42.109	rs134294374	42079983	5.581	−2.76 ± 0.586	0.367	0.127	rs41586304		41872925	2.295	3.105 ± 1.107	0.176	0.094	NR1D2
27	43.595 - 44.261	rs110746407	43914360	6.075	−2.781 ± 0.564	0.441	0.136		rs43064076	43595406	2.873	−3.831 ± 1.192	0.146	0.123	NA
X	139.211 - 139.509	rs136627433	139508886	4.679	−2.606 ± 0.6098	0.394	0.116		rs110719178	139490243	2.320	−3.327 ± 1.175	0.163	0.101	NA

^aBTC: Bos Taurus chromosome

^bIntervals containing individually validated SNPs are in bold

^c MAF minor allele frequency

^d σ ²_a = additive variance; σ ²_p = phenotypic variance