T-Trees

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

Supplementary data

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1	Best: rs16838195 (4)	Gene	153.90-153.96Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16838099		153896615	0.07767	0.7531	0.4377	0.7578	0.00011	183
	rs1176555		153949614	0.2715	0.6015	0.01963	0.7259	0.00011	173
	rs1176559		153952042	0.0003052	1	1	0.06128	9.7e-05	197
	rs16838195		153958298	0.01009	0.6284	1	8.69e-34	0.0045	6
2	Best: rs902133 (2)	Gene	10.90-10.91Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17456162	PDIA6 NCBI Gene Pubmed Genecard	10898688	0.214	0.7852	0.6258	0.6326	0.00014	144
	rs902133		10908783	0.005956	1	1	8.407e-17	0.0009	38
2	Best: rs10460436 (2)	Gene	232.64-232.71Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10460436		232640846	0.0213	1	1	0.7749	0.00021	113
	rs12473319	DIS3L2 NCBI Gene Pubmed Genecard	232706476	0.01732	1	0.6425	0.0002331	0.00017	126
3	Best: rs1605705 (7)	Gene	7.26-7.30Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2136152	GRM7 NCBI Gene Pubmed Genecard	7257402	0.1652	0.002957	0.3341	0.02256	0.00094	33
	rs4686119	GRM7 NCBI Gene Pubmed Genecard	7257739	0.1728	0.007161	0.6196	0.01757	0.00038	76
	rs908465	GRM7 NCBI Gene Pubmed Genecard	7258715	0.1712	0.005078	0.4546	0.01172	0.00074	46
	rs1605705	GRM7 NCBI Gene Pubmed Genecard	7265044	0.1782	0.414	0.2996	0.01483	0.004	8
	rs9809928	GRM7 NCBI Gene Pubmed Genecard	7277350	0.1721	0.01139	0.2616	0.02151	0.00028	90
	rs4095095	GRM7 NCBI Gene Pubmed Genecard	7284658	0.3126	0.5678	0.01607	0.004358	9.7e-05	196
	rs1876614	GRM7 NCBI Gene Pubmed Genecard	7296289	0.1616	0.001315	0.133	0.01991	0.00038	75
3	Best: rs9856460 (4)	Gene	141.43-141.44Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4308237	CLSTN2 NCBI Gene Pubmed Genecard	141425064	0.4514	0.04888	0.9704	0.3295	0.00048	61
	rs9856460	CLSTN2 NCBI Gene Pubmed Genecard	141425151	0.4507	0.04917	0.8528	0.2808	0.0015	21
	rs2350514	CLSTN2 NCBI Gene Pubmed Genecard	141434080	0.4622	0.1315	0.5297	0.3953	0.00089	39
	rs4538338	CLSTN2 NCBI Gene Pubmed Genecard	141436333	0.4556	6.906e-08	0.58	0.1583	0.00094	34
4	Best: rs4532278 (4)	Gene	182.12-182.13Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6831911		182124306	0.1515	0.0029	0.8805	0.001472	0.00056	57
	rs4532278		182126147	0.2089	1	0.544	0.7033	0.00072	48
	rs4274891		182126371	0.2089	1	0.4728	0.7222	0.0004	73
	rs7657018		182132571	0.1389	0.2142	0.6465	0.8813	0.00045	65
5	Best: rs160619 (2)	Gene	143.36-143.37Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs160625		143356896	0.02817	0.3582	1	0.2127	0.0014	23
	rs160619		143372726	0.01407	1	0.4054	2.783e-27	0.003	11
5	Best: rs4246045 (6)	Gene	150.15-150.21Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17111367	SMIM3 NCBI Gene Pubmed Genecard	150149083	0.05138	1	0.3494	0.8884	9.4e-05	199
	rs13360680	SMIM3 NCBI Gene Pubmed Genecard	150152005	0.04215	1	0.485	0.572	0.00039	74
	rs4246045		150157290	0.1415	0.1011	5.988e-05	0.002115	0.00073	47
	rs13361189		150203580	0.07507	0.01334	0.008476	0.00129	0.00022	110
	rs11949556		150209994	0.1204	0.3133	0.4709	0.03353	0.00059	52
	rs6893009		150213497	0.1196	0.1862	0.4139	0.03295	0.00032	84
6	Best: rs6457617 (79)	Gene	31.73-32.80Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs805297	APOM NCBI Gene Pubmed Genecard	31730585	0.322	0.3349	0.3672	1.471e-23	0.0002	116
	rs707974	C6orf47 NCBI Gene Pubmed Genecard GPANK1 NCBI Gene Pubmed Genecard	31737478	0.1428	0.1406	0.0329	3.357e-27	0.00058	53
	rs2075800	HSPA1L NCBI Gene Pubmed Genecard	31885925	0.3576	0.5772	0.07243	1.494e-32	0.00058	54
	rs2072633	CFB NCBI Gene Pubmed Genecard RDBP NCBI Gene Pubmed Genecard	32027557	0.4172	0.4856	0.0005212	9.44e-27	0.00027	97
	rs17421624	TNXB NCBI Gene Pubmed Genecard	32174155	0.3481	0.6415	0.06068	6.441e-35	0.00083	44
	rs9296009		32222493	0.277	0.6176	0.3249	8.797e-39	0.0012	28
	rs206015	NOTCH4 NCBI Gene Pubmed Genecard	32290737	0.1505	0.8784	0.8715	5.851e-12	0.00028	92
	rs438475	NOTCH4 NCBI Gene Pubmed Genecard	32294223	0.1706	0.5556	0.4033	8.746e-06	0.00014	146
	SNP_A-2064274		32300414	0.04176	0.6353	0.004361	3.68e-11	0.00018	123
	rs3134926		32308125	0.2544	0.721	0.8242	4.923e-25	0.0009	37
	rs9267954		32321030	0.3251	0.03798	0.09683	2.193e-41	0.00093	35
	rs1265777	C6orf10 NCBI Gene Pubmed Genecard	32381136	0.4432	0.01048	0.6425	6.974e-46	0.00052	59
	rs574710	C6orf10 NCBI Gene Pubmed Genecard	32396168	0.4451	0.005334	0.7283	4.005e-45	0.00085	43
	rs539703	C6orf10 NCBI Gene Pubmed Genecard	32396440	0.4429	0.005414	0.536	2.956e-45	0.0004	71
	rs12524063	C6orf10 NCBI Gene Pubmed Genecard	32405288	0.1009	0.141	0.7459	0.001812	0.00038	77
	rs3132959	C6orf10 NCBI Gene Pubmed Genecard	32406920	0.2008	0.1211	0.03745	1.425e-28	0.00033	83
	rs926591	C6orf10 NCBI Gene Pubmed Genecard	32413668	0.4432	0.007118	0.6427	2.961e-45	0.00057	55
	rs9368716	C6orf10 NCBI Gene Pubmed Genecard	32414068	0.4939	0.03986	0.3552	1.04e-26	0.00011	187
	rs4959093	C6orf10 NCBI Gene Pubmed Genecard	32421075	0.443	0.006194	0.6426	1.204e-44	0.0013	27
	rs910049	C6orf10 NCBI Gene Pubmed Genecard	32423705	0.2052	0.009674	0.0001615	4.37e-28	0.00017	125
	rs2894249	C6orf10 NCBI Gene Pubmed Genecard	32433813	0.1968	0.1143	0.3487	2.288e-26	0.00011	175
	rs3129932	C6orf10 NCBI Gene Pubmed Genecard	32444105	0.2005	0.1443	0.04217	9.171e-29	0.00026	100
	rs3129933	C6orf10 NCBI Gene Pubmed Genecard	32444139	0.1691	0.008723	0.1172	3.67e-09	0.0001	191
	rs3129934	C6orf10 NCBI Gene Pubmed Genecard	32444165	0.1402	0.07095	0.05096	4.017e-16	0.0001	189
	rs9268402	C6orf10 NCBI Gene Pubmed Genecard	32449331	0.4343	0.4734	0.8547	1.409e-61	0.003	12
	rs9391858	C6orf10 NCBI Gene Pubmed Genecard	32449376	0.1641	0.9392	0.2866	0.0001055	0.00021	115
	rs9268403	C6orf10 NCBI Gene Pubmed Genecard	32449451	0.3687	0.09106	0.4642	1.826e-55	0.0011	30
	rs12201454		32451664	0.3687	0.1099	0.4379	4.669e-56	0.00078	45
	rs9268429		32453030	0.3754	0.008078	0.00122	3.946e-54	0.00057	56
	rs12528797		32453064	0.1246	0.005402	0.4619	4.229e-06	0.00034	79
	rs7757831		32453161	0.023	0.3714	0.07818	4.55e-05	0.00017	127
	rs6930777		32459544	0.124	0.007507	0.2634	1.154e-06	0.00013	147
	rs2076533	BTNL2 NCBI Gene Pubmed Genecard	32471505	0.4836	0.8847	0.7952	3.592e-65	0.0032	10
	rs2076530	BTNL2 NCBI Gene Pubmed Genecard	32471794	0.4784	0.9227	0.9411	7.233e-63	0.0014	24
	rs9268480	BTNL2 NCBI Gene Pubmed Genecard	32471822	0.3688	0.1098	0.4383	2.773e-55	0.001	32
	rs10947260	BTNL2 NCBI Gene Pubmed Genecard	32481163	0.05237	1	0.01913	5.707e-10	0.00031	86
	rs10947261	BTNL2 NCBI Gene Pubmed Genecard	32481210	0.05644	0.5403	0.03931	2.926e-09	0.00024	103
	rs3806156	BTNL2 NCBI Gene Pubmed Genecard	32481676	0.4249	0.2197	0.9687	5.662e-37	0.00028	91
	rs3763307	BTNL2 NCBI Gene Pubmed Genecard	32482600	0.369	0.1001	0.4134	7.417e-56	0.004	9
	rs3763308	BTNL2 NCBI Gene Pubmed Genecard	32482618	0.03011	1	0.6102	3.137e-08	0.00011	180
	rs9268541		32492505	0.0462	0.7205	0.07867	1.27e-07	0.00011	172
	rs3135377		32493377	0.1893	0.641	1	1.706e-22	0.0016	20
	rs9268557		32497283	0.4478	0.2885	0.6597	2.362e-67	0.0023	15
	rs9268560		32497490	0.4118	0.04098	0.9414	4.842e-70	0.0044	7
	rs3135363		32497626	0.2305	0.6397	0.2042	1.243e-24	0.00085	42
	rs9268645	HLA-DRA NCBI Gene Pubmed Genecard	32516505	0.4321	0.2745	0.6106	3.375e-46	0.0026	14
	rs3177928	HLA-DRA NCBI Gene Pubmed Genecard	32520413	0.1607	0.8165	0.5617	5.624e-05	0.00065	49
	rs7194	HLA-DRA NCBI Gene Pubmed Genecard	32520458	0.3395	0.6724	0.8483	7.25e-52	0.0017	19
	rs9268831		32535726	0.4732	0.09225	0.1425	2.781e-20	0.00046	63
	rs9268853		32537621	0.4276	0.255	0.937	2.202e-52	0.0013	26
	rs9268858		32537736	0.4279	0.1867	0.9685	1.727e-52	0.0012	29
	rs7746922		32538953	0.2245	0.01023	1.338e-05	1.256e-31	0.00034	80
	rs7747521		32539083	0.2161	0.3132	0.9612	2.053e-27	0.00011	186
	rs9268877		32539125	0.3549	0.6744	0.2936	9.637e-11	0.00023	107
	rs9268878		32539270	0.2168	0.3547	0.8462	1.049e-27	0.00011	179
	rs9269186	HLA-DRB3 NCBI Gene Pubmed Genecard	32556394	0.2146	0.8651	0.4067	6.653e-28	0.00011	185
	rs9270986		32682038	0.1295	0.06667	0.0861	7.916e-16	0.001	31
	rs615672	LOC100507709 NCBI Gene Pubmed Genecard LOC100507714 NCBI Gene Pubmed Genecard	32682149	0.2903	0.1528	0.9013	8.276e-30	0.00037	78
	rs9271208		32686981	0.2354	0.3485	0.4763	9.068e-14	0.00015	141
	rs4530903		32689867	0.1215	0.01194	1	7.961e-08	0.00015	138
	rs9271850		32703038	0.2712	0.4193	6.921e-05	9.951e-46	0.0029	13
	rs3129768		32703061	0.1506	0.1008	0.1654	1.018e-20	0.00018	122
	rs9272219		32710247	0.2227	0.5272	0.7719	3.63e-21	0.0017	18
	rs9272346	HLA-DQA1 NCBI Gene Pubmed Genecard	32712350	0.3572	0.05634	0.7869	1.681e-14	0.00016	130
	rs9273363		32734250	0.3291	0.7315	0.6336	8.128e-11	0.0002	117
	rs9275134		32758590	0.2626	0.7024	0.4837	2.861e-09	0.00013	152
	rs7775228		32766057	0.1057	0.8644	0.1001	7.637e-20	0.00034	81
	rs9469220		32766288	0.4975	0.3386	0.8543	6.703e-05	0.00021	112
	rs6457617		32771829	0.4336	0.5981	0.533	2.101e-83	0.0092	4
	rs6457620		32771977	0.4331	0.5619	0.5331	1.526e-83	0.0067	5
	rs2647015		32772071	0.08806	0.6908	0.01512	8.099e-15	0.00015	137
	rs2647046		32776314	0.3428	0.4659	0.285	3.058e-55	0.00024	102
	rs2858308		32777978	0.08797	1	0.02477	1.459e-14	0.00012	161
	rs9275418		32778222	0.3077	0.1058	0.4651	1.55e-50	0.00043	66
	rs9275523		32782972	0.2913	0.1361	0.678	4.414e-60	0.0015	22
	rs9275572		32786977	0.359	1	1	3.437e-63	0.00093	36
	rs6936863		32792007	0.2619	0.2784	0.1586	0.0126	0.00012	168
	rs3916765		32793528	0.1475	0.2313	0.1444	1.127e-18	0.00015	135
	rs9275765		32797302	0.2601	0.04064	0.7323	0.003811	0.00021	114
6	Best: rs2157082 (2)	Gene	32.87-32.87Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2621384		32867251	0.361	0.1297	0.9692	6.785e-12	0.00012	163
	rs2157082		32868692	0.4429	0.8904	0.000395	0.04795	0.0003	87
8	Best: rs16874204 (3)	Gene	107.27-107.29Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16874204		107271181	0.04293	0.258	0.8225	0.9189	0.0022	16
	rs16874205		107271324	0.0523	0.001105	0.06191	8.883e-09	0.00088	40
	rs1503566		107288356	0.275	0.1258	0.1811	0.6606	0.00025	101
10	Best: rs3122348 (11)	Gene	30.97-31.04Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16931816		30969354	0.03909	0.07224	0.6217	0.6318	0.00024	104
	SNP_A-2100739		30990735	0.07531	0.3013	0.7977	0.2569	0.021	2
	rs16931828	LOC645954 NCBI Gene Pubmed Genecard	30990752	0.1145	0.1206	0.2366	0.7459	0.00028	89
	rs3122348	LOC645954 NCBI Gene Pubmed Genecard	30991151	0.0289	0.0001649	1	3.637e-78	0.028	1
	rs7083541	LOC645954 NCBI Gene Pubmed Genecard	30997484	0.4827	0.7844	0.6332	0.6492	0.00053	58
	rs11008174	LOC645954 NCBI Gene Pubmed Genecard	31010206	0.2584	0.4168	1	0.08506	0.0006	51
	rs4749580	LOC645954 NCBI Gene Pubmed Genecard	31014180	0.4256	0.4312	0.6246	0.2255	0.0003	88
	rs16930315	LOC645954 NCBI Gene Pubmed Genecard	31017645	0.1078	0.05485	0.5716	0.6896	0.00016	128
	rs7078126	LOC645954 NCBI Gene Pubmed Genecard	31024312	0.07512	0.8597	1	0.09223	0.00046	64
	rs7093972	LOC645954 NCBI Gene Pubmed Genecard	31024349	0.07392	0.37	0.523	0.06957	0.00031	85
	rs3858241	LOC645954 NCBI Gene Pubmed Genecard	31041299	0.06328	0.3159	0.02187	0.4709	0.00022	111
10	Best: rs4256909 (2)	Gene	114.07-114.08Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7896275	GUCY2GP NCBI Gene Pubmed Genecard	114071985	0.08744	0.759	0.04744	0.04438	0.00043	69
	rs4256909	GUCY2GP NCBI Gene Pubmed Genecard	114083575	0.08292	0.002676	0.4488	0.0708	0.00052	60
10	Best: rs7080464 (3)	Gene	131.97-132.00Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7080464		131974739	0.01439	1	0.4053	8.352e-24	0.0019	17
	rs7080611		131974841	0.0003055	1	1	0.5658	9.4e-05	200
	rs7918047		132001099	0.0593	0.5471	0.4041	0.7932	0.00027	99
12	Best: rs6582454 (2)	Gene	42.00-42.01Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6582454		42001173	0.4637	0.3861	0.9412	0.2635	0.00015	134
	rs1995339		42005111	0.4639	0.3861	1	0.2725	0.00012	169
15	Best: rs1711029 (4)	Gene	51.49-51.49Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1996309		51491250	0.3519	0.1946	0.6015	0.9655	0.00028	94
	rs1996310		51491390	0.3319	0.09176	0.8684	0.7421	0.00012	162
	rs1711029		51491702	0.04314	0.547	0.1223	2.247e-11	0.00041	70
	rs11853116		51492626	0.3331	0.1133	1	0.8609	0.0001	190
15	Best: rs4777568 (3)	Gene	71.02-71.02Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs8034355		71018064	0.03551	0.7879	0.3322	0.0001346	0.00011	181
	rs4777568		71019278	0.02759	1	0.2906	0.8501	0.00013	154
	rs1900899		71021133	0.02778	1	0.2935	0.9001	0.00011	174
16	Best: rs4238755 (4)	Gene	51.30-51.31Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4238755		51303590	0.2566	0.636	0.1007	0.6195	0.0014	25
	rs4784244		51305748	0.4278	0.963	0.9403	0.8347	0.00027	98
	rs1420247		51305843	0.2673	0.0491	0.05409	0.001419	0.00086	41
	rs1420248		51305862	0.2855	0.6569	0.2071	0.8549	0.00043	67
22	Best: rs10212068 (9)	Gene	35.97-36.02Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10212068		35969121	0.02803	1	0.002635	1.047e-61	0.014	3
	rs5750402		35985788	0.1767	0.8817	0.8959	0.01581	0.0004	72
	rs5756581		35986936	0.1502	0.4264	0.8284	0.7726	0.00012	170
	rs4820279		35991286	0.1797	1	0.7494	0.0497	0.00027	95
	rs4821623		35993078	0.1746	0.6304	0.9	0.4147	0.00022	109
	rs2267363	CYTH4 NCBI Gene Pubmed Genecard	36001892	0.2466	0.7077	0.07917	0.1955	0.00022	108
	rs727047	CYTH4 NCBI Gene Pubmed Genecard	36002219	0.3539	0.06351	0.4022	0.331	0.0002	119
	rs727048	CYTH4 NCBI Gene Pubmed Genecard	36002392	0.247	0.3169	0.009346	0.1701	0.00016	131
	rs5756601	CYTH4 NCBI Gene Pubmed Genecard	36017438	0.434	0.7441	0.6008	0.3255	0.00018	124
23	Best: rs2521413 (3)	Gene	9.28-9.34Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2254392	TBL1X NCBI Gene Pubmed Genecard	9280457	0.4831	0.09178	0.302	0.6812	0.00011	184
	rs2521413	TBL1X NCBI Gene Pubmed Genecard	9340778	0.4011	0.8285	2.534e-05	0.01129	0.00028	93
	rs2254091	TBL1X NCBI Gene Pubmed Genecard	9344256	0.3569	0.8206	0.001543	0.1341	0.00011	188
23	Best: rs5927971 (2)	Gene	32.12-32.13Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5927971	DMD NCBI Gene Pubmed Genecard	32117965	0.4214	0.01306	0.3975	0.3543	0.00018	121
	rs1293821	DMD NCBI Gene Pubmed Genecard	32130902	0.2505	0.08777	0.05039	0.09276	0.00012	164
23	Best: rs1883678 (2)	Gene	45.31-45.31Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1883678		45308372	0.04148	0.06991	0.4803	0.8192	0.00015	139
	rs1883672		45312140	0.04266	0.3687	0.4688	0.1429	0.00014	145
23	Best: rs932574 (2)	Gene	90.14-90.14Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs932574		90137677	0.4381	0.1096	0.008915	0.6463	0.00024	105
	rs932575		90140631	0.444	0.1369	0.0217	0.5065	0.00016	132
23	Best: rs2497903 (3)	Gene	96.83-96.85Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5920956		96830492	0.4873	0.1029	0.1508	0.05883	9.7e-05	195
	rs2497903		96848708	0.4837	0.05781	0.08057	0.08324	0.00027	96
	rs5921910		96851990	0.499	0.1272	0.1988	0.3622	0.00011	177
23	Best: rs5920824 (2)	Gene	99.46-99.48Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5920824	PCDH19 NCBI Gene Pubmed Genecard	99455333	0.3849	0.124	0.03252	0.1066	0.00014	143
	rs5966698		99480848	0.406	0.2778	0.05512	0.4868	0.00012	158