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	0.1744	0.4714	0.4804	0.847	0.00057	74
	rs4665287		25324960	0.1707	0.1896	0.2974	0.9114	0.00058	72
	rs2164411		25364557	0.1541	2.035e-10	0.1946	0.001213	0.0033	18
4	Best: rs1553460 (9)	Gene	17.73-17.90Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs9784574		17734890	0.157	0.7223	0.6287	0.508	0.00011	184
	rs1039539		17850862	0.2638	0.4471	0.3804	0.04709	0.00051	79
	rs17523800		17870443	0.3646	0.802	0.9367	0.5142	0.00079	65
	rs11938418		17871212	0.2809	0.2721	0.03268	0.5144	0.0021	25
	rs1553460		17872130	0.3134	8.847e-94	2.877e-05	1.281e-28	0.031	3
	rs1503881		17878898	0.2751	0.4608	0.3237	0.06403	0.00037	91
	rs1503882		17878953	0.2749	0.5709	0.3966	0.04121	0.00042	88
	rs4698673		17885266	0.2811	0.6961	0.5442	0.0237	0.00022	120
	rs6857578		17896563	0.2811	0.5392	0.5459	0.03404	0.00012	178
4	Best: rs13126272 (3)	Gene	186.09-186.11Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11132255	ACSL1 NCBI Gene Pubmed Genecard	186093876	0.1639	0.4997	0.7876	1	0.00015	150
	rs11936062	ACSL1 NCBI Gene Pubmed Genecard SLED1 NCBI Gene Pubmed Genecard	186096519	0.1639	0.6702	0.9459	0.9773	0.00012	170
	rs13126272	ACSL1 NCBI Gene Pubmed Genecard	186107089	0.341	2.3e-43	0.03015	1.272e-06	0.006	10
8	Best: rs17480050 (19)	Gene	19.35-19.51Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17407449	CSGALNACT1 NCBI Gene Pubmed Genecard	19348064	0.1233	0.9108	0.618	0.1347	0.00075	67
	rs13261824	CSGALNACT1 NCBI Gene Pubmed Genecard	19358192	0.4849	0.8529	0.2682	0.414	0.00017	133
	rs7002047	CSGALNACT1 NCBI Gene Pubmed Genecard	19368059	0.3474	0.3373	0.5658	0.166	0.0001	196
	rs4922040	CSGALNACT1 NCBI Gene Pubmed Genecard	19385519	0.338	0.6436	0.7083	0.2672	0.00015	149
	rs11784776	CSGALNACT1 NCBI Gene Pubmed Genecard	19396011	0.2061	0.6672	0.7795	0.5009	0.004	15
	rs4921653	CSGALNACT1 NCBI Gene Pubmed Genecard	19404133	0.4006	0.267	0.9694	0.7487	0.00026	110
	rs4921654	CSGALNACT1 NCBI Gene Pubmed Genecard	19404254	0.3996	0.2884	0.9082	0.7486	0.00031	94
	rs17479749	CSGALNACT1 NCBI Gene Pubmed Genecard	19404858	0.2079	0.9436	0.6548	0.7766	0.004	14
	rs4922048	CSGALNACT1 NCBI Gene Pubmed Genecard	19405094	0.3986	0.2876	0.7878	0.814	0.00023	113
	rs9644631	CSGALNACT1 NCBI Gene Pubmed Genecard	19415110	0.412	0.2923	0.9697	0.6398	0.0005	81
	rs4921657	CSGALNACT1 NCBI Gene Pubmed Genecard	19415147	0.4109	0.3381	0.909	0.6245	0.00054	76
	rs17480050	CSGALNACT1 NCBI Gene Pubmed Genecard	19426197	0.119	0	1	0	0.24	1
	rs2975494	CSGALNACT1 NCBI Gene Pubmed Genecard	19426611	0.1549	1	0.9415	0.0202	0.00012	177
	rs17128573	CSGALNACT1 NCBI Gene Pubmed Genecard	19434020	0.3536	0.9599	0.2392	0.3575	0.00098	57
	rs4922060	CSGALNACT1 NCBI Gene Pubmed Genecard	19452788	0.1677	0.5542	0.8447	0.3701	0.007	7
	SNP_A-1992585		19454071	0.1829	0.3806	0.7159	0.1757	0.0061	9
	rs6996732	CSGALNACT1 NCBI Gene Pubmed Genecard	19462308	0.2127	0.9448	0.7412	0.9592	0.0016	35
	rs7818368	CSGALNACT1 NCBI Gene Pubmed Genecard	19483828	0.1884	0.6523	0.9036	0.7684	0.003	20
	rs12542189	CSGALNACT1 NCBI Gene Pubmed Genecard	19509899	0.3214	0.1829	1	0.9284	0.00019	128
8	Best: rs7821190 (2)	Gene	32.03-32.03Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7821190	NRG1 NCBI Gene Pubmed Genecard	32028147	0.003658	1	1	8.108e-07	0.00027	101
	rs16878694	NRG1 NCBI Gene Pubmed Genecard	32030847	0.001148	1	1	2.979e-05	0.00011	180
8	Best: rs1909936 (2)	Gene	82.41-82.41Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1909935		82407915	0.02144	1	0.6289	0.1696	0.00029	97
	rs1909936		82408006	0.01823	2.399e-40	0.629	0.1539	0.0029	21
10	Best: rs12355606 (3)	Gene	18.53-18.55Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10828308	CACNB2 NCBI Gene Pubmed Genecard	18534882	0.009393	1	1	0.1026	0.00018	131
	rs12355606	CACNB2 NCBI Gene Pubmed Genecard	18537827	0.006391	1	1	8.349e-12	0.0041	13
	rs10508559	CACNB2 NCBI Gene Pubmed Genecard	18545319	0.009057	1	1	0.03523	0.0001	194
11	Best: rs17116117 (5)	Gene	113.31-113.31Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17116117	HTR3B NCBI Gene Pubmed Genecard	113306801	0.04118	0.1197	0.116	8.539e-10	0.00088	61
	rs17116145	HTR3B NCBI Gene Pubmed Genecard	113309536	0.02727	1	0.5202	0.03917	0.00013	168
	rs1176741	HTR3B NCBI Gene Pubmed Genecard	113312525	0.02895	0.6266	0.1192	0.04583	0.00013	164
	rs1176739	HTR3B NCBI Gene Pubmed Genecard	113313027	0.02968	0.3476	0.3693	0.07359	0.00012	174
	rs1176738	HTR3B NCBI Gene Pubmed Genecard	113313305	0.02907	0.6279	0.1193	0.05362	0.00014	153
15	Best: rs12050604 (28)	Gene	40.73-41.32Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs9920163	STARD9 NCBI Gene Pubmed Genecard	40729673	0.2138	0.6927	0.9098	0.008499	0.00043	86
	rs16957020	STARD9 NCBI Gene Pubmed Genecard	40751718	0.2139	0.7922	0.6103	0.009863	0.00046	83
	rs2136899	STARD9 NCBI Gene Pubmed Genecard	40777678	0.189	0.9422	0.7114	0.05434	0.00021	122
	rs8034447		40801457	0.2045	0.785	1	0.0256	0.00016	140
	rs16957091	CDAN1 NCBI Gene Pubmed Genecard	40804718	0.2302	0.9008	0.8719	0.003631	0.00045	85
	rs7175582	TTBK2 NCBI Gene Pubmed Genecard	40826355	0.2163	0.6479	1	0.01027	0.0005	80
	rs7166775	TTBK2 NCBI Gene Pubmed Genecard	40829982	0.2345	0.7118	0.9577	0.002791	0.0008	64
	rs7182141	TTBK2 NCBI Gene Pubmed Genecard	40849840	0.2286	0.7532	0.8295	0.007106	0.00048	82
	rs9920935	TTBK2 NCBI Gene Pubmed Genecard	40862494	0.2027	0.2785	0.2564	0.6208	0.00013	162
	rs16957168	TTBK2 NCBI Gene Pubmed Genecard	40877812	0.1871	0.6627	1	0.02101	0.00069	69
	rs10467975	TTBK2 NCBI Gene Pubmed Genecard	40884944	0.09372	0.8846	1	0.1139	0.0012	52
	rs10518779	TTBK2 NCBI Gene Pubmed Genecard	40915917	0.1864	0.5067	0.95	0.04872	0.00076	66
	rs16957244	TTBK2 NCBI Gene Pubmed Genecard	40953321	0.1161	0.907	0.6594	0.2958	0.0018	28
	rs8036096	TTBK2 NCBI Gene Pubmed Genecard	40958312	0.3072	0.7888	0.8608	0.1528	0.0015	44
	rs1381855	UBR1 NCBI Gene Pubmed Genecard	41051297	0.3078	0.707	0.7934	0.2764	0.0014	45
	rs6416436	UBR1 NCBI Gene Pubmed Genecard	41075511	0.1164	0.7256	0.3795	0.2531	0.0017	31
	rs4923955	UBR1 NCBI Gene Pubmed Genecard	41082380	0.1168	0.7255	0.4854	0.2153	0.0016	39
	rs1037990	UBR1 NCBI Gene Pubmed Genecard	41086979	0.1162	0.6425	0.6593	0.3114	0.0017	34
	rs8027733	UBR1 NCBI Gene Pubmed Genecard	41101610	0.118	0.9087	0.3388	0.3471	0.0013	49
	rs6493076	UBR1 NCBI Gene Pubmed Genecard	41105432	0.1165	0.8165	0.5383	0.3118	0.0016	41
	rs4923956	UBR1 NCBI Gene Pubmed Genecard	41125944	0.3061	1	0.8607	0.3262	0.0013	47
	rs12050604	UBR1 NCBI Gene Pubmed Genecard	41144698	0.2741	1.41e-19	0.9648	4.19e-11	0.0041	12
	rs17720657	UBR1 NCBI Gene Pubmed Genecard	41164896	0.1535	0.73	0.3456	0.1817	0.00027	103
	rs4924705	UBR1 NCBI Gene Pubmed Genecard	41167552	0.1886	0.3453	0.9505	0.03674	0.001	55
	rs2176870	TMEM62 NCBI Gene Pubmed Genecard	41223702	0.2214	0.8407	0.8303	0.8997	0.00015	151
	rs2899077	EPB42 NCBI Gene Pubmed Genecard	41297317	0.0972	0.5766	0.5421	0.0963	0.00081	63
	rs11070396		41310214	0.09737	0.5725	0.6131	0.06598	0.00091	60
	rs7183814	TGM5 NCBI Gene Pubmed Genecard	41316922	0.09767	0.6742	0.7615	0.09047	0.00091	59
16	Best: rs1048194 (15)	Gene	79.62-79.70Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1048194	CENPN NCBI Gene Pubmed Genecard	79622203	0.09549	2.22329540628561e-322	9.949e-06	3.663e-39	0.1	2
	rs12456	CENPN NCBI Gene Pubmed Genecard	79622560	0.07713	0.5381	0.6863	0.1822	0.0025	22
	rs2602431	ATMIN NCBI Gene Pubmed Genecard	79628198	0.1254	1	0.4438	0.4869	0.00045	84
	rs2970077	ATMIN NCBI Gene Pubmed Genecard	79632301	0.08184	0.7667	0.5265	0.3019	0.0015	43
	rs2549899	C16orf46 NCBI Gene Pubmed Genecard	79646373	0.1035	0.8094	0.2208	0.2864	0.00054	75
	rs10459871	C16orf46 NCBI Gene Pubmed Genecard	79650568	0.08389	0.4647	0.1781	0.406	0.0018	29
	rs10459872	C16orf46 NCBI Gene Pubmed Genecard	79652452	0.08552	1	0.9031	0.2409	0.0013	46
	rs16954582		79671658	0.07521	0.8708	1	0.5513	0.0018	30
	rs10514513		79671684	0.07535	0.6258	1	0.5253	0.0017	33
	rs4324141		79672326	0.07598	0.7497	1	0.4296	0.0015	42
	rs10514514	GCSH NCBI Gene Pubmed Genecard	79672774	0.07101	0.0004741	0.0004597	0.462	0.0017	32
	rs12445303	GCSH NCBI Gene Pubmed Genecard	79673074	0.07472	0.5224	0.5842	0.3006	0.0016	36
	rs8177959	GCSH NCBI Gene Pubmed Genecard	79673188	0.07554	0.7497	0.7864	0.4285	0.0016	40
	rs8043855	GCSH NCBI Gene Pubmed Genecard	79680362	0.07338	0.0001333	3.942e-06	0.261	0.0012	51
	rs2316730	PKD1L2 NCBI Gene Pubmed Genecard	79697141	0.06606	0.000252	2.577e-06	0.8659	0.0012	50
17	Best: SNP_A-1948953 (2)	Gene	17.27-17.27Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16961675	SMCR9 NCBI Gene Pubmed Genecard	17266676	0.3224	0.9145	0.3353	0.1941	0.00012	173
	SNP_A-1948953		17267088	0.2816	9.927e-24	0.005177	3.974e-05	0.0062	8
18	Best: rs1442650 (3)	Gene	38.16-38.22Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4890398	LOC284260 NCBI Gene Pubmed Genecard	38161388	0.01552	0.4329	0.4526	0.2365	0.0011	53
	rs10502785	LOC284260 NCBI Gene Pubmed Genecard	38191787	0.0194	1	0.6257	0.7042	0.00014	154
	rs1442650	LOC284260 NCBI Gene Pubmed Genecard	38224157	0.01045	1	0.5236	2.315e-13	0.003	19
23	Best: rs3928369 (5)	Gene	32.36-32.37Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs3928369	DMD NCBI Gene Pubmed Genecard	32356769	0.2413	0.01779	0.258	0.002548	0.0003	95
	rs5928022	DMD NCBI Gene Pubmed Genecard	32356784	0.2448	0.3602	0.236	0.003479	0.00026	108
	rs808547	DMD NCBI Gene Pubmed Genecard	32371695	0.1911	0.7644	0.1924	0.001343	0.00019	127
	rs808540	DMD NCBI Gene Pubmed Genecard	32374111	0.209	0.4079	0.4868	0.003754	0.00023	114
	rs808539	DMD NCBI Gene Pubmed Genecard	32374143	0.2066	0.2278	0.5874	0.005144	0.00016	144
23	Best: rs5966463 (2)	Gene	144.00-144.00Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs9306723		144002178	0.1798	0.01083	0.4932	0.02483	0.00012	169
	rs5966463		144002395	0.1801	0.005848	0.4427	0.01967	0.00016	137