Table 1.

Association results on top 96 SNPs.

Chromosome	SNP	Position	MAF	P-Value HWE	Allele	P-value^# discovery	P-value^# validation	P-value joint^#
1	rs201171	6573680	0.14	0.62	T/C	6.74E-05	0.72	1.49E-02
1	rs4394668	12593816	0.21	1	C/T	4.89E-06	2.78E-02	1.31E-05
1	rs4618985	12593911	0.27	0.94	C/A	2.04E-05	2.67E-02	4.71E-05
1	rs1831870	57399791	0.45	1	C/T	3.27E-05	0.69	1.18E-02
1	rs155288	57405075	0.45	0.95	T/C	2.84E-05	0.63	9.28E-03
1	rs5008948	80011986	0.29	0.02	C/T	6.11E-05	0.69	0.05
1	rs12024204	80015589	0.45	0.91	A/G	2.50E-05	0.83	0.04
1	rs11162822	80018536	0.26	0.03	C/T	8.78E-05	*0.72*	*0.14*
1	rs6424674	80047434	0.47	1	G/A	3.97E-05	0.81	0.07
1	rs10493644	80056276	0.43	0.72	A/C	7.03E-05	0.91	0.06
1	rs17425287	80058999	0.46	0.95	T/C	2.40E-05	0.8	0.06
1	rs7523086	1.16E+08	0.38	0.19	A/G	7.27E-05	0.02	1
1	rs16833075	2.34E+08	0.16	0.75	G/T	6.81E-05	0.44	7.15E-03
2	rs492780	44997398	0.05	0.01	C/T	8.78E-05	*0.34*	*7.81E-03*
2	rs1467068	60716378	0.32	0.74	T/C	3.35E-05	*0.11*	*0.51*
2	rs6732653	60717337	0.32	0.79	A/G	3.50E-05	*0.11*	*0.51*
2	rs1866206	60720330	0.32	0.69	T/C	4.92E-05	0.11	0.54
2	rs4852531	79903226	0.45	0.2	C/T	5.93E-05	0.26	2.63E-03
2	rs11679682	1.74E+08	0.23	0.25	C/T	7.80E-05	0.78	0.03
2	rs11689493	1.74E+08	0.38	0.95	C/T	4.31E-05	0.39	5.59E-03
2	rs4129081	1.91E+08	0.26	0.82	A/C	3.56E-05	0.71	0.07
2	rs6707773	1.91E+08	0.26	0.71	T/C	7.44E-05	0.68	0.09
2	rs13019278	1.91E+08	0.26	0.76	A/G	8.14E-05	*0.9*	*4.85E-02*
2	rs12622496	1.91E+08	0.25	0.64	C/T	9.66E-06	0.97	2.18E-02
2	rs3731723	2.31E+08	0.41	0.04	T/C	3.20E-05	0.07	4.08E-04
2	rs722555	2.31E+08	0.41	0.06	G/A	2.59E-05	0.09	*4.10E-04*
2	rs6436915	2.31E+08	0.44	0.51	T/G	1.67E-05	0.14	5.51E-04
3	rs2279977	3389586	0.45	0.52	C/A	7.52E-05	*0.48*	*5.13E-03*
3	rs9822786	1.13E+08	0.08	1.27E-03	T/G	2.98E-07	*0.46*	*0.45*
3	rs12491012	1.55E+08	0.1	0.76	A/G	5.44E-05	0.25	4.21E-03
3	rs1811763	1.74E+08	0.14	0.33	A/G	1.65E-05	0.31	1.66E-03
5	rs1896731	25934777	0.36	1	C/T	7.67E-05	8.00E-03	1.90E-05
5	rs10038113	25938099	0.41	0.23	C/T	2.75E-05	3.28E-03	3.40E-06
5	rs11739167	25945521	0.45	0.6	T/C	1.79E-05	1.98E-02	3.05E-05
5	rs7447989	25950789	0.38	0.66	G/A	3.29E-05	0.16	1.07E-03
5	rs6873221	25964323	0.45	0.45	A/G	5.07E-06	*9.06E-03*	*5.90E-06*
5	rs12187724	25970827	0.38	0.66	C/A	4.78E-05	*0.08*	*5.02E-04*
5	rs1423435	37940845	0.47	0.86	T/C	5.70E-05	0.68	1.47E-02
5	rs12153325	51897032	0.45	0.27	C/T	3.89E-05	*0.58*	*8.10E-03*
5	rs10461556	51907079	0.45	0.32	T/C	8.76E-06	0.45	2.63E-03
5	rs350436	51932211	0.46	0.27	C/T	5.31E-05	0.6	9.84E-03
5	rs830907	51940364	0.45	0.27	T/C	7.48E-05	0.6	0.01
5	rs315717	1.7E+08	0.48	0.73	T/C	3.06E-05	0.94	0.05
5	rs3804254	1.7E+08	0.48	0.64	T/C	4.24E-05	*0.9*	*4.38E-02*
6	rs2317222	778579	0.19	0.51	G/A	9.97E-05	0.57	1.60E-02
6	rs1936022	72723073	0.4	0.01	T/C	7.10E-05	*0.19*	*0.38*
6	rs6907646	72736738	0.39	0.03	A/G	9.20E-05	*0.15*	*0.47*
6	rs12529724	91590812	0.25	0.14	A/G	1.64E-05	0.9	2.36E-02
6	rs1504279	91596967	0.3	0.13	G/A	1.19E-06	*0.6*	*4.35E-03*
6	rs1504281	91597253	0.43	0.31	T/C	8.03E-05	0.51	1.13E-02
6	rs2799644	96464883	0.34	0.52	T/C	5.90E-05	0.73	0.11
7	rs320813	9751778	0.35	0.9	T/C	7.23E-05	0.59	1.27E-02
7	rs1529001	52748818	0.06	0.02	A/G	4.30E-05	-	-
7	rs11765584	63222219	0.32	0.46	A/G	8.07E-05	0.89	4.97E-02
7	rs1529813	63255903	0.31	0.63	A/G	1.78E-05	*0.95^	*2.31E-02*
7	rs2528795	73111430	0.23	0.87	G/A	7.78E-05	*0.14^	*5.24E-05*
7	rs1000058	1.32E+08	0.08	0.11	T/G	7.11E-05	*0.17^	*0.06*
7	rs1149558	1.33E+08	0.4	0.59	C/T	5.11E-05	0.48	0.15
7	rs1130496	1.58E+08	0.43	0.18	A/G	4.70E-05	*0.89^	*3.82E-03*
8	rs12155975	18823406	0.13	0.2	T/G	1.10E-05	0.85	3.95E-02
8	rs16930253	64276820	0.07	0.67	T/G	7.96E-05	*0.51*	*0.2*
8	rs2082804	64323440	0.08	0.44	A/G	6.68E-05	0.32	0.36
8	rs4739071	64333676	0.08	0.56	C/A	8.89E-05	0.34	0.36
8	rs6991229	64348114	0.08	0.69	C/T	5.84E-05	0.28	0.36
10	rs1865641	77612829	0.17	0.47	C/A	3.50E-05	0.62	1.56E-02
10	rs1865638	77625472	0.19	0.71	T/C	4.27E-05	*0.75*	*2.37E-02*
10	rs11001685	77632360	0.19	1	C/T	2.34E-05	*0.75*	*1.93E-02*
10	rs881631	77636503	0.17	0.53	G/A	3.39E-05	0.66	1.55E-02
10	rs12245799	77637321	0.19	0.77	C/T	2.74E-05	0.77	2.26E-02
10	rs12249859	77641198	0.19	0.78	C/A	4.79E-05	*0.84*	*2.86E-02*
10	rs10748804	1.03E+08	0.45	0.86	G/A	8.07E-05	0.17	1.33E-03
10	rs7910491	1.03E+08	0.45	0.68	G/A	5.51E-05	*0.1*	*4.43E-04*
11	rs10840070	8524783	0.39	1	T/C	3.36E-05	0.67	0.1
11	rs11021927	11533125	0.33	0.02	A/C	7.03E-05	0.67	1.50E-02
11	rs9919560	11547547	0.28	0.17	A/C	1.13E-06	0.83	1.26E-02
12	rs12366827	7834103	0.43	0.11	C/T	8.79E-05	-	-
12	rs1894827	7834643	0.43	0.1	A/G	7.43E-05	0.89	0.08
12	rs11055784	7836092	0.43	0.12	G/T	6.74E-05	-	-
12	rs11055786	7836651	0.43	0.11	T/C	8.79E-05	*0.81*	*0.1*
12	rs11117003	84639343	0.36	0.75	T/G	4.57E-05	0.25	6.91E-03
12	rs10492086	1.01E+08	0.19	0.4	G/A	5.36E-05	0.08	1.85E-04
12	rs10444509	1.01E+08	0.18	0.92	C/T	3.36E-05	0.09	2.16E-04
13	rs11616562	83656026	0.06	0.05	G/A	4.51E-05	*0.84*	*3.59E-02*
13	rs7325257	87203088	0.38	0.95	T/C	6.51E-05	*0.96*	*4.85E-02*
15	rs11636552	23686048	0.15	0.2	G/T	3.27E-05	0.42	0.17
16	rs1532926	8013919	0.38	0.81	C/A	4.71E-05	0.52	1.58E-02
16	rs4456502	10257638	0.35	0.44	G/A	8.33E-05	*0.51^	*2.77E-02*
16	rs4148358	16094676	0.23	0.04	T/C	8.50E-05	0.49	0.21
17	rs891754	29834556	0.43	0.91	C/A	6.96E-05	0.59	0.12
18	rs8088001	277705	0.07	0.36	G/T	6.23E-05	0.88	0.1
18	rs547668	10466821	0.16	0.59	T/G	8.50E-05	0.09	0.8
18	rs1144093	48371078	0.23	0.5	A/G	6.34E-05	-	-
18	rs637644	61049646	0.44	0.48	C/T	1.57E-05	0.31	0.18
20	rs6049129	23723819	0.39	3.90E-03	C/T	7.18E-05	0.31	0.35
20	rs742759	47494552	0.22	0.8	A/G	1.52E-05	*0.24*	*0.26*
20	rs171415	58229934	0.13	0.25	T/G	2.03E-06	*0.27^	*1.24E-05*

MAF: minor allele frequency in discovery dataset

P-value HWE: Hardy-Weinberg Equilibrium test p-value in discovery dataset

In italic and bold are the p-values for markers not genotyped on 550K Illumina panel. Genotypes for these markers were imputed.

“-” data could not been imputed because no genotypes are available for the reference dataset.

Allele: Minor Allele/Major Allele in discovery dataset

Shaded: Marker with improved P-value in validation dataset.

The Pedigree Disequilibrium Test (PDT) was performed on all SNPs for association testing.

the imputed markers missing more than 10% of genotypes

Distance: the distance (basepair) between gene and marker