T-Trees

A novel tree-based approach for Genome-Wide Association Studies

Supplementary data

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2	Best: rs2164411 (3)	Gene	25.31-25.36Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs874401		25313931	0.1739	0.9367	0.4804	0.9782	0.00037	97
	rs4665287		25324960	0.1716	1	0.2974	0.8688	0.00032	105
	rs2164411		25364557	0.1533	1.454e-17	0.1946	0.0004458	0.003	26
4	Best: rs16837871 (9)	Gene	6.06-6.08Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7679272		6057618	0.2312	0.8982	0.7932	0.6926	0.0011	51
	rs16837871		6059184	0.1501	3.343e-26	0.2844	8.967e-25	0.012	7
	rs7664218		6060685	0.1886	0.4241	0.462	0.2432	0.0053	15
	rs7664229		6060707	0.1882	0.4237	0.5801	0.2025	0.0056	14
	rs7691494		6060721	0.1885	0.4671	0.5398	0.2127	0.0056	13
	rs6446412	C4orf50 NCBI Gene Pubmed Genecard	6079898	0.3675	1	0.72	0.4908	0.00016	147
	rs13107008	C4orf50 NCBI Gene Pubmed Genecard	6080067	0.3734	0.8085	0.9055	0.4402	0.00014	161
	rs7434820	C4orf50 NCBI Gene Pubmed Genecard	6081537	0.3297	0.9181	0.2581	0.6587	0.00011	176
	rs6826497	C4orf50 NCBI Gene Pubmed Genecard	6083331	0.3341	0.7209	0.3184	0.6761	0.00011	189
4	Best: rs13126272 (4)	Gene	186.09-186.11Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1996546	ACSL1 NCBI Gene Pubmed Genecard	186089438	0.1406	0.04634	0.4928	0.8814	0.00016	146
	rs11132255	ACSL1 NCBI Gene Pubmed Genecard	186093876	0.1623	0.2019	0.7876	0.593	0.00022	125
	rs11936062	ACSL1 NCBI Gene Pubmed Genecard SLED1 NCBI Gene Pubmed Genecard	186096519	0.1621	0.1439	0.9459	0.6093	0.00019	136
	rs13126272	ACSL1 NCBI Gene Pubmed Genecard	186107089	0.3404	4.19e-43	0.03015	3.11e-06	0.0038	18
5	Best: rs2048646 (2)	Gene	34.78-34.79Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2048646	RAI14 NCBI Gene Pubmed Genecard	34784322	0.2308	3.772e-23	0.1665	0.03838	0.0028	28
	rs334912	RAI14 NCBI Gene Pubmed Genecard	34789097	0.4568	0.3111	0.1185	0.441	0.00012	171
5	Best: rs2416472 (17)	Gene	117.00-117.07Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs397925		116998548	0.3304	0.9583	0.7095	0.1394	0.00038	96
	rs9327047		116999827	0.2337	1	0.5731	0.5898	0.00035	99
	rs434363		117000415	0.3384	0.9179	0.7746	0.1673	0.00028	111
	rs9327048		117001096	0.2326	0.8977	0.7188	0.6945	0.00042	93
	rs384890		117001576	0.3372	0.8767	0.6822	0.1355	0.00031	107
	rs371616		117001959	0.339	1	0.7437	0.1542	0.00034	100
	rs388811		117002034	0.339	0.9588	0.6829	0.1094	0.00032	103
	rs392457		117002064	0.3377	0.8769	0.7123	0.1668	0.00024	118
	rs367474		117004156	0.3407	0.836	0.7422	0.07442	0.00018	139
	rs2416472		117033845	0.313	2.209e-20	0.9345	2.058e-16	0.0067	11
	rs17411921		117033876	0.3364	1	0.3656	0.3451	0.0021	30
	rs7714451		117037818	0.2435	0.8504	0.8041	0.3581	0.00098	54
	rs7723508		117044836	0.3017	0.3839	0.9652	0.5875	9.8e-05	194
	rs1526882		117054771	0.07527	0.07498	0.8004	0.0907	0.00026	114
	rs17346822		117058221	0.09689	0.07025	0.3607	0.06805	0.00071	68
	rs6421871		117068096	0.09852	0.1277	1	0.04722	0.0007	69
	rs17142889		117068908	0.1345	0.6834	0.9383	0.1711	0.00083	62
6	Best: rs9465871 (2)	Gene	20.75-20.83Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs9348440	CDKAL1 NCBI Gene Pubmed Genecard	20749315	0.1368	0.04388	0.06399	9.7e-05	0.00015	151
	rs9465871	CDKAL1 NCBI Gene Pubmed Genecard	20825234	0.1943	0.229	0.04364	1.38e-06	0.00015	150
6	Best: rs3777582 (8)	Gene	46.01-46.03Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs946226	CLIC5 NCBI Gene Pubmed Genecard	46006171	0.02348	0.6241	1	1	0.00043	90
	rs12055836	CLIC5 NCBI Gene Pubmed Genecard	46007801	0.02408	0.3065	0.08571	1	0.00042	92
	rs3822887	CLIC5 NCBI Gene Pubmed Genecard	46016169	0.03285	0.2682	1	0.9536	0.00086	60
	rs3777576	CLIC5 NCBI Gene Pubmed Genecard	46016309	0.0314	0.7203	0.7549	0.6763	0.00064	73
	rs949678	CLIC5 NCBI Gene Pubmed Genecard	46020959	0.02603	0.638	0.003196	1	0.0004	94
	rs3777582	CLIC5 NCBI Gene Pubmed Genecard	46022006	0.08189	4.399e-295	0.0001294	6.762e-30	0.071	2
	rs3777583	CLIC5 NCBI Gene Pubmed Genecard	46022068	0.09784	0.1378	0.3877	0.1526	0.00024	119
	rs4236089	CLIC5 NCBI Gene Pubmed Genecard	46034552	0.09109	0.1109	0.1074	0.2343	0.00014	156
6	Best: rs10499044 (2)	Gene	107.25-107.26Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10499044		107247988	0.0991	3.753e-13	0.001966	7.063e-22	0.0062	12
	rs2798360		107255166	0.145	0.9264	0.9404	0.9528	0.00055	83
7	Best: rs1477523 (6)	Gene	136.22-136.37Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs324571	LOC349160 NCBI Gene Pubmed Genecard	136222708	0.05503	0.008535	0.8632	0.2747	0.00014	159
	rs324572	LOC349160 NCBI Gene Pubmed Genecard	136222827	0.05281	0.008421	0.0003267	0.6422	9.9e-05	193
	rs11560399	LOC349160 NCBI Gene Pubmed Genecard	136258088	0.04972	0.1236	0.7055	0.2327	0.0006	78
	rs1477523	LOC349160 NCBI Gene Pubmed Genecard	136262393	0.05342	2.972e-189	0.00595	3.576e-08	0.033	5
	rs17168987	PTN NCBI Gene Pubmed Genecard	136369221	0.03981	1	0.6256	0.7105	0.00019	137
	rs12668115	PTN NCBI Gene Pubmed Genecard	136369293	0.03942	0.3641	0.3249	1	0.00022	124
8	Best: rs2517202 (2)	Gene	17.51-17.52Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2517202	PDGFRL NCBI Gene Pubmed Genecard	17512131	0.006119	1	1	2.208e-08	0.00059	79
	rs13439798	PDGFRL NCBI Gene Pubmed Genecard	17524548	0.009998	1	1	0.2524	0.00012	174
8	Best: rs17480050 (19)	Gene	19.35-19.53Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17407449	CSGALNACT1 NCBI Gene Pubmed Genecard	19348064	0.1237	0.06181	0.618	0.1855	0.00031	108
	rs13261824	CSGALNACT1 NCBI Gene Pubmed Genecard	19358192	0.4777	0.2703	0.2682	0.009987	0.00011	177
	rs6998060	CSGALNACT1 NCBI Gene Pubmed Genecard	19368021	0.3408	0.4443	0.5948	0.5844	0.0001	191
	rs4922040	CSGALNACT1 NCBI Gene Pubmed Genecard	19385519	0.3324	0.1965	0.7083	0.7407	0.0001	190
	rs11784776	CSGALNACT1 NCBI Gene Pubmed Genecard	19396011	0.2037	0.1939	0.7795	0.1642	0.0032	23
	rs4921654	CSGALNACT1 NCBI Gene Pubmed Genecard	19404254	0.3983	0.2723	0.9082	0.5113	0.00011	185
	rs17479749	CSGALNACT1 NCBI Gene Pubmed Genecard	19404858	0.2043	0.2211	0.6548	0.1727	0.0033	21
	rs4922048	CSGALNACT1 NCBI Gene Pubmed Genecard	19405094	0.3973	0.3641	0.7878	0.5671	0.00011	186
	rs9644631	CSGALNACT1 NCBI Gene Pubmed Genecard	19415110	0.4087	0.2543	0.9697	0.198	0.00029	110
	rs4921657	CSGALNACT1 NCBI Gene Pubmed Genecard	19415147	0.4076	0.2954	0.909	0.1904	0.00025	117
	rs17480050	CSGALNACT1 NCBI Gene Pubmed Genecard	19426197	0.1142	0	1	0	0.18	1
	rs17128573	CSGALNACT1 NCBI Gene Pubmed Genecard	19434020	0.3432	0.8774	0.2392	0.08402	0.0011	49
	rs10503652	CSGALNACT1 NCBI Gene Pubmed Genecard	19434179	0.1496	0.861	0.9412	0.3519	9.6e-05	195
	rs4922060	CSGALNACT1 NCBI Gene Pubmed Genecard	19452788	0.1643	0.5416	0.8447	0.04379	0.0051	16
	SNP_A-1992585		19454071	0.1802	0.3719	0.7159	0.02677	0.0046	17
	rs6996732	CSGALNACT1 NCBI Gene Pubmed Genecard	19462308	0.2085	0.322	0.7412	0.1929	0.0012	48
	rs7818368	CSGALNACT1 NCBI Gene Pubmed Genecard	19483828	0.1835	0.9379	0.9036	0.228	0.0028	27
	rs12542189	CSGALNACT1 NCBI Gene Pubmed Genecard	19509899	0.3156	0.485	1	0.1078	0.00035	98
	rs7846346	CSGALNACT1 NCBI Gene Pubmed Genecard	19529918	0.3189	0.5565	0.6142	0.07869	0.0002	133
9	Best: rs488101 (2)	Gene	117.69-117.79Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11793751		117693568	0.1416	0.2995	0.2894	0.9053	9.6e-05	196
	rs488101		117787179	0.3644	3.774e-08	0.6116	6.925e-07	0.00021	128
10	Best: rs7077039 (9)	Gene	114.74-114.80Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4074720	TCF7L2 NCBI Gene Pubmed Genecard	114738487	0.4907	0.8907	0.2816	6.164e-11	0.00011	178
	rs7901695	TCF7L2 NCBI Gene Pubmed Genecard	114744078	0.3487	0.5029	0.2352	1.217e-12	0.00022	123
	rs4506565	TCF7L2 NCBI Gene Pubmed Genecard	114746031	0.3516	0.4738	0.3117	9.839e-13	0.00023	122
	rs4132670	TCF7L2 NCBI Gene Pubmed Genecard	114757761	0.3517	0.4444	0.2927	3.459e-12	0.00019	135
	rs10787472	TCF7L2 NCBI Gene Pubmed Genecard	114771287	0.4912	0.9269	0.2205	2.622e-11	0.00015	152
	rs7077039	TCF7L2 NCBI Gene Pubmed Genecard	114779067	0.4836	1	0.1349	4.204e-12	0.00026	113
	rs11196205	TCF7L2 NCBI Gene Pubmed Genecard	114797037	0.4941	0.7138	0.1943	8.182e-11	0.00018	140
	rs10885409	TCF7L2 NCBI Gene Pubmed Genecard	114798062	0.4935	0.7483	0.2211	1.075e-10	0.00016	145
	rs11196208	TCF7L2 NCBI Gene Pubmed Genecard	114801306	0.4926	0.927	0.2823	7.199e-11	0.00013	163
11	Best: rs11042656 (5)	Gene	10.16-10.19Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12286927	SBF2 NCBI Gene Pubmed Genecard	10161787	0.05873	0.8478	0.00128	0.1126	0.002	35
	rs12288200	SBF2 NCBI Gene Pubmed Genecard	10167703	0.054	0.003602	0.004318	0.4892	0.002	34
	rs16907568	SBF2 NCBI Gene Pubmed Genecard	10168778	0.05916	0.696	0.000869	0.3549	0.0022	29
	rs11042656	SBF2 NCBI Gene Pubmed Genecard	10171031	0.07577	8.284e-274	0.0005072	8.384e-26	0.061	4
	rs1822295	SBF2 NCBI Gene Pubmed Genecard	10189732	0.05709	0.6948	0.002827	0.0959	0.0018	36
11	Best: rs10501796 (3)	Gene	92.07-92.09Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4122086	FAT3 NCBI Gene Pubmed Genecard	92070494	0.00885	1	1	0.5084	0.00014	157
	rs10501795	FAT3 NCBI Gene Pubmed Genecard	92087066	0.008745	1	1	0.5041	0.00015	149
	rs10501796	FAT3 NCBI Gene Pubmed Genecard	92092804	0.005181	1	1	1.233e-08	0.00084	61
11	Best: rs17116117 (19)	Gene	113.02-113.31Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17610557		113018709	0.1336	0.3747	0.3389	1	0.00021	127
	rs17532157		113021980	0.1323	0.4271	0.1074	0.9512	0.00027	112
	rs17532479		113028191	0.1339	0.3774	0.4256	0.9514	0.00023	120
	rs11606746		113042520	0.1318	0.227	0.8071	0.926	0.00021	130
	rs17611093		113053519	0.1314	0.6167	0.1696	0.9265	0.00031	106
	rs11604887		113108019	0.127	0.06307	0.868	0.9503	0.00038	95
	rs17541153	ZW10 NCBI Gene Pubmed Genecard	113120832	0.1253	0.12	0.2357	0.9002	0.0003	109
	rs1633550	USP28 NCBI Gene Pubmed Genecard	113174415	0.1294	0.06917	0.8693	0.8288	0.00043	91
	rs1633548	USP28 NCBI Gene Pubmed Genecard	113176716	0.1278	0.4734	0.5062	0.9009	0.0005	85
	rs1713671	USP28 NCBI Gene Pubmed Genecard	113180048	0.4167	0.6381	0.1031	0.6136	0.00017	143
	rs2513574	USP28 NCBI Gene Pubmed Genecard	113186515	0.127	0.463	0.804	0.6168	0.00045	88
	rs2519200	USP28 NCBI Gene Pubmed Genecard	113190019	0.2477	0.09148	0.8808	0.3365	0.00022	126
	rs4936283	USP28 NCBI Gene Pubmed Genecard	113218600	0.4599	0.3575	0.3933	0.3077	9.5e-05	198
	rs17116117	HTR3B NCBI Gene Pubmed Genecard	113306801	0.05261	8.317e-05	0.116	3.41e-31	0.012	8
	rs17116145	HTR3B NCBI Gene Pubmed Genecard	113309536	0.02942	0.4026	0.5202	0.6673	0.00056	82
	rs1176741	HTR3B NCBI Gene Pubmed Genecard	113312525	0.03099	1	0.1192	0.6752	0.00079	63
	rs1176740	HTR3B NCBI Gene Pubmed Genecard	113312606	0.03117	1	0.1206	0.6763	0.00062	74
	rs1176739	HTR3B NCBI Gene Pubmed Genecard	113313027	0.0317	0.7045	0.3693	0.7673	0.00067	71
	rs1176738	HTR3B NCBI Gene Pubmed Genecard	113313305	0.03111	1	0.1193	0.7199	0.0007	70
12	Best: rs10492267 (3)	Gene	96.85-96.93Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10860262		96851491	0.04229	0.7793	0.3501	0.7181	0.0033	20
	rs10492267		96851806	0.02589	6.375e-08	0.8032	8.527e-30	0.012	6
	rs2192796		96927337	0.05695	1	0.72	0.2828	0.00043	89
16	Best: rs9889057 (2)	Gene	58.89-58.90Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs9889057		58890875	0.36	3.844e-32	0.1044	3.94e-05	0.00097	55
	rs10500428		58896364	0.3513	0.1607	0.2247	0.862	0.00072	67
21	Best: rs226261 (17)	Gene	26.95-27.00Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2830320		26947555	0.192	1	0.7661	0.937	0.0017	37
	rs2174536		26947727	0.1922	1	0.6346	0.979	0.0017	38
	rs458076		26947782	0.4461	1	0.9702	0.7702	0.0013	45
	rs2830322		26948370	0.1911	0.9411	0.5511	0.979	0.0014	43
	rs996632		26952709	0.1851	0.364	0.7593	0.9574	0.0014	44
	rs226261		26953847	0.3736	1.103e-53	0.9032	6.753e-08	0.01	9
	rs756166		26953857	0.192	0.8832	0.677	0.979	0.002	31
	rs11088006		26954058	0.1911	0.9411	0.4743	1	0.0016	40
	rs2830380		26979808	0.3455	0.3114	1	0.6469	0.0011	50
	rs2830385		26981436	0.2942	0.5488	0.03555	0.4251	0.00066	72
	rs2830389		26982303	0.2938	0.5498	0.04896	0.387	0.0006	76
	rs2830395		26985677	0.4498	0.853	0.7941	0.4772	0.00073	65
	rs2212809		26986061	0.4402	0.8531	0.8222	0.9168	0.0012	47
	rs2830414		26994734	0.3453	0.4467	0.9028	0.5852	0.0011	52
	rs3017533		26995179	0.3608	0.5855	0.7189	0.7953	0.00021	129
	rs2830418		27001505	0.08104	0.01098	0.06489	0.5943	0.00047	87
	rs2830419		27002006	0.3369	0.7968	0.9344	0.4548	0.00097	57
22	Best: rs11705626 (10)	Gene	23.76-23.88Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11705626	KIAA1671 NCBI Gene Pubmed Genecard	23760513	0.08137	8.083e-28	0.05827	1.059e-96	0.063	3
	rs9624709	KIAA1671 NCBI Gene Pubmed Genecard	23769428	0.1516	0.6477	0.2319	0.2136	0.0031	24
	rs742169	KIAA1671 NCBI Gene Pubmed Genecard	23773158	0.1527	0.5853	0.1577	0.2968	0.0034	19
	rs742170	KIAA1671 NCBI Gene Pubmed Genecard	23773207	0.1502	0.4623	0.2017	0.2453	0.0032	22
	rs6004418	KIAA1671 NCBI Gene Pubmed Genecard	23789619	0.2274	0.8443	0.7535	0.6375	0.00012	170
	rs17668150	KIAA1671 NCBI Gene Pubmed Genecard	23793384	0.1566	0.08184	0.8345	0.8416	0.0013	46
	rs17668511	KIAA1671 NCBI Gene Pubmed Genecard	23814598	0.1042	0.1107	0.3685	0.8914	0.002	32
	rs4476445	KIAA1671 NCBI Gene Pubmed Genecard	23855556	0.1106	0.643	0.03026	1	0.0015	42
	rs9612876	KIAA1671 NCBI Gene Pubmed Genecard	23869541	0.1147	0.3703	0.4637	0.8448	0.0016	41
	rs9608373	KIAA1671 NCBI Gene Pubmed Genecard	23882188	0.1153	0.05741	0.928	1	0.002	33
23	Best: rs5988334 (2)	Gene	0.49-0.64Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6645017		494871	0.4674	0.863	0.4545	0.0003295	0.00012	173
	rs5988334		635819	0.2158	0.003418	0.002057	3.314e-06	0.00032	104
23	Best: rs6654309 (2)	Gene	134.83-134.83Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6654309	SLC9A6 NCBI Gene Pubmed Genecard	134830202	0.03289	0.3922	0.2621	0.003847	0.003	25
	rs12689820	SLC9A6 NCBI Gene Pubmed Genecard	134832528	0.03702	0.6321	0.2589	0.3319	9.9e-05	192