T-Trees

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

Supplementary data

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1	Best: rs6679677 (2)	Gene	113.89-114.02Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1230666	MAGI3 NCBI Gene Pubmed Genecard	113885452	0.1696	0.1706	0.5488	1.294e-17	0.001	61
	rs6679677		114015850	0.1238	0.05009	0.241	5.471e-26	0.0036	27
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	0.0001	181
	rs160619		143372726	0.01407	1	0.4054	2.783e-27	0.011	6
6	Best: rs6457620 (94)	Gene	31.70-32.82Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2736172	PRRC2A NCBI Gene Pubmed Genecard SNORA38 NCBI Gene Pubmed Genecard	31698877	0.3823	0.3088	0.1829	8.868e-18	0.00011	176
	rs3130048	BAG6 NCBI Gene Pubmed Genecard	31721718	0.2582	0.0001805	0.407	1.023e-05	0.00011	169
	rs805297	APOM NCBI Gene Pubmed Genecard	31730585	0.322	0.3349	0.3672	1.471e-23	0.00044	75
	rs707974	C6orf47 NCBI Gene Pubmed Genecard GPANK1 NCBI Gene Pubmed Genecard	31737478	0.1428	0.1406	0.0329	3.357e-27	0.0022	39
	rs2075800	HSPA1L NCBI Gene Pubmed Genecard	31885925	0.3576	0.5772	0.07243	1.494e-32	0.0012	56
	rs644045		31991936	0.3374	0.1629	0.004705	3.83e-19	0.00028	90
	rs541862	CFB NCBI Gene Pubmed Genecard	32024930	0.07737	1	0.3237	3.779e-13	0.00023	105
	rs2072633	CFB NCBI Gene Pubmed Genecard RDBP NCBI Gene Pubmed Genecard	32027557	0.4172	0.4856	0.0005212	9.44e-27	0.00089	66
	rs550513	RDBP NCBI Gene Pubmed Genecard	32028666	0.07874	1	0.4565	5.938e-14	0.00027	94
	rs406936	SKIV2L NCBI Gene Pubmed Genecard	32041140	0.1132	1	0.3697	3.415e-10	9.8e-05	189
	rs17421624	TNXB NCBI Gene Pubmed Genecard	32174155	0.3481	0.6415	0.06068	6.441e-35	0.0013	52
	rs9296009		32222493	0.277	0.6176	0.3249	8.797e-39	0.0017	48
	rs3130348	AGPAT1 NCBI Gene Pubmed Genecard	32248255	0.2104	0.3929	0.2145	7.502e-10	0.0001	185
	rs3130284	AGPAT1 NCBI Gene Pubmed Genecard	32248465	0.2096	0.4384	0.2549	9.612e-10	0.0001	179
	rs206015	NOTCH4 NCBI Gene Pubmed Genecard	32290737	0.1505	0.8784	0.8715	5.851e-12	0.00016	123
	SNP_A-2064274		32300414	0.04176	0.6353	0.004361	3.68e-11	0.00021	110
	rs3134926		32308125	0.2544	0.721	0.8242	4.923e-25	0.0024	38
	rs427037		32320242	0.1698	0.7797	0.8098	2.183e-09	0.0001	180
	rs9267954		32321030	0.3251	0.03798	0.09683	2.193e-41	0.0019	44
	rs3115576		32324828	0.4494	0.01086	0.14	2.278e-21	0.00022	108
	rs6936204		32325070	0.319	0.5557	0.0167	3.922e-24	0.00043	76
	rs9267971		32325163	0.4492	0.01082	0.1503	3.864e-21	0.00023	102
	rs3130311		32325345	0.4495	0.01086	0.1398	2.726e-21	0.00027	95
	rs7767325		32341864	0.2119	0.01409	0.1874	4.823e-14	0.00013	138
	rs3132928		32341993	0.2113	0.01711	0.2039	6.453e-14	0.00013	141
	rs3115560		32344120	0.2124	0.01321	0.1393	1.142e-13	0.00012	157
	rs1265777	C6orf10 NCBI Gene Pubmed Genecard	32381136	0.4432	0.01048	0.6425	6.974e-46	0.0028	34
	rs9268230	C6orf10 NCBI Gene Pubmed Genecard	32395545	0.2981	4.093e-05	0.03595	6.416e-14	0.00057	71
	rs574710	C6orf10 NCBI Gene Pubmed Genecard	32396168	0.4451	0.005334	0.7283	4.005e-45	0.0035	28
	rs539703	C6orf10 NCBI Gene Pubmed Genecard	32396440	0.4429	0.005414	0.536	2.956e-45	0.0028	35
	rs3132959	C6orf10 NCBI Gene Pubmed Genecard	32406920	0.2008	0.1211	0.03745	1.425e-28	0.002	43
	rs926591	C6orf10 NCBI Gene Pubmed Genecard	32413668	0.4432	0.007118	0.6427	2.961e-45	0.0033	30
	rs3129900	C6orf10 NCBI Gene Pubmed Genecard	32413957	0.1399	0.09045	0.06866	9.991e-16	0.00018	119
	rs9368716	C6orf10 NCBI Gene Pubmed Genecard	32414068	0.4939	0.03986	0.3552	1.04e-26	0.0005	74
	rs4959093	C6orf10 NCBI Gene Pubmed Genecard	32421075	0.443	0.006194	0.6426	1.204e-44	0.0032	32
	rs910049	C6orf10 NCBI Gene Pubmed Genecard	32423705	0.2052	0.009674	0.0001615	4.37e-28	0.0019	45
	rs2894249	C6orf10 NCBI Gene Pubmed Genecard	32433813	0.1968	0.1143	0.3487	2.288e-26	0.0017	47
	rs3129932	C6orf10 NCBI Gene Pubmed Genecard	32444105	0.2005	0.1443	0.04217	9.171e-29	0.0021	42
	rs3129934	C6orf10 NCBI Gene Pubmed Genecard	32444165	0.1402	0.07095	0.05096	4.017e-16	0.00022	106
	rs9268402	C6orf10 NCBI Gene Pubmed Genecard	32449331	0.4343	0.4734	0.8547	1.409e-61	0.0072	12
	rs9391858	C6orf10 NCBI Gene Pubmed Genecard	32449376	0.1641	0.9392	0.2866	0.0001055	0.0002	113
	rs9268403	C6orf10 NCBI Gene Pubmed Genecard	32449451	0.3687	0.09106	0.4642	1.826e-55	0.0048	20
	rs12201454		32451664	0.3687	0.1099	0.4379	4.669e-56	0.005	18
	rs9268429		32453030	0.3754	0.008078	0.00122	3.946e-54	0.0044	23
	rs12528797		32453064	0.1246	0.005402	0.4619	4.229e-06	0.00033	83
	rs6930777		32459544	0.124	0.007507	0.2634	1.154e-06	0.00042	78
	rs2076533	BTNL2 NCBI Gene Pubmed Genecard	32471505	0.4836	0.8847	0.7952	3.592e-65	0.0076	11
	rs2076530	BTNL2 NCBI Gene Pubmed Genecard	32471794	0.4784	0.9227	0.9411	7.233e-63	0.0065	14
	rs9268480	BTNL2 NCBI Gene Pubmed Genecard	32471822	0.3688	0.1098	0.4383	2.773e-55	0.0046	21
	rs10947260	BTNL2 NCBI Gene Pubmed Genecard	32481163	0.05237	1	0.01913	5.707e-10	0.00012	150
	rs3806156	BTNL2 NCBI Gene Pubmed Genecard	32481676	0.4249	0.2197	0.9687	5.662e-37	0.0021	41
	rs3763307	BTNL2 NCBI Gene Pubmed Genecard	32482600	0.369	0.1001	0.4134	7.417e-56	0.0049	19
	rs3763308	BTNL2 NCBI Gene Pubmed Genecard	32482618	0.03011	1	0.6102	3.137e-08	0.00011	165
	rs3135377		32493377	0.1893	0.641	1	1.706e-22	0.00094	63
	rs9268557		32497283	0.4478	0.2885	0.6597	2.362e-67	0.008	10
	rs9268560		32497490	0.4118	0.04098	0.9414	4.842e-70	0.01	7
	rs3135363		32497626	0.2305	0.6397	0.2042	1.243e-24	0.00092	64
	rs9268645	HLA-DRA NCBI Gene Pubmed Genecard	32516505	0.4321	0.2745	0.6106	3.375e-46	0.0025	37
	rs3135393	HLA-DRA NCBI Gene Pubmed Genecard	32516820	0.1605	0.9159	0.06781	1.41e-16	0.00012	158
	rs3177928	HLA-DRA NCBI Gene Pubmed Genecard	32520413	0.1607	0.8165	0.5617	5.624e-05	0.00013	145
	rs7194	HLA-DRA NCBI Gene Pubmed Genecard	32520458	0.3395	0.6724	0.8483	7.25e-52	0.004	26
	rs1051336	HLA-DRA NCBI Gene Pubmed Genecard	32520570	0.1613	0.6751	0.7618	2.121e-16	0.00013	139
	rs9268853		32537621	0.4276	0.255	0.937	2.202e-52	0.0041	24
	rs9268856		32537697	0.2164	0.3984	0.8082	4.137e-28	0.0012	58
	rs9268858		32537736	0.4279	0.1867	0.9685	1.727e-52	0.0041	25
	rs9268861		32537872	0.1815	0.7082	0.5398	1.05e-16	0.00029	88
	rs9268862		32538145	0.2155	0.2719	0.9609	2.077e-26	0.0008	68
	rs4428528		32538340	0.1904	0.01531	6.914e-05	5.919e-22	0.00029	89
	rs7766843		32538707	0.2167	0.313	0.9227	5.918e-28	0.0014	51
	rs7746922		32538953	0.2245	0.01023	1.338e-05	1.256e-31	0.0012	57
	rs7747521		32539083	0.2161	0.3132	0.9612	2.053e-27	0.001	60
	rs9268877		32539125	0.3549	0.6744	0.2936	9.637e-11	0.00028	93
	rs9268878		32539270	0.2168	0.3547	0.8462	1.049e-27	0.0012	55
	rs9269186	HLA-DRB3 NCBI Gene Pubmed Genecard	32556394	0.2146	0.8651	0.4067	6.653e-28	0.00099	62
	rs9270986		32682038	0.1295	0.06667	0.0861	7.916e-16	0.00022	107
	rs615672	LOC100507709 NCBI Gene Pubmed Genecard LOC100507714 NCBI Gene Pubmed Genecard	32682149	0.2903	0.1528	0.9013	8.276e-30	0.0016	49
	rs9271208		32686981	0.2354	0.3485	0.4763	9.068e-14	0.00038	80
	rs4530903		32689867	0.1215	0.01194	1	7.961e-08	0.00055	73
	rs9271850		32703038	0.2712	0.4193	6.921e-05	9.951e-46	0.0045	22
	rs3129768		32703061	0.1506	0.1008	0.1654	1.018e-20	0.0004	79
	rs9272219		32710247	0.2227	0.5272	0.7719	3.63e-21	0.00091	65
	rs9272346	HLA-DQA1 NCBI Gene Pubmed Genecard	32712350	0.3572	0.05634	0.7869	1.681e-14	0.0002	114
	rs7775228		32766057	0.1057	0.8644	0.1001	7.637e-20	0.0018	46
	rs6457617		32771829	0.4336	0.5981	0.533	2.101e-83	0.013	5
	rs6457620		32771977	0.4331	0.5619	0.5331	1.526e-83	0.014	3
	rs2647015		32772071	0.08806	0.6908	0.01512	8.099e-15	0.0012	54
	rs2647046		32776314	0.3428	0.4659	0.285	3.058e-55	0.0053	17
	rs2858308		32777978	0.08797	1	0.02477	1.459e-14	0.0013	53
	rs9275418		32778222	0.3077	0.1058	0.4651	1.55e-50	0.006	15
	rs9275523		32782972	0.2913	0.1361	0.678	4.414e-60	0.009	8
	rs9275572		32786977	0.359	1	1	3.437e-63	0.007	13
	rs3916765		32793528	0.1475	0.2313	0.1444	1.127e-18	0.00036	81
	rs2227127	HLA-DQA2 NCBI Gene Pubmed Genecard	32819760	0.4025	0.613	0.2397	3.564e-13	9.8e-05	191
	rs9276448		32823607	0.06546	0.0003608	0.1818	5.045e-06	0.00011	164
10	Best: rs3122348 (6)	Gene	30.99-31.06Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	SNP_A-2100739		30990735	0.07531	0.3013	0.7977	0.2569	0.006	16
	rs3122348	LOC645954 NCBI Gene Pubmed Genecard	30991151	0.0289	0.0001649	1	3.637e-78	0.052	1
	rs7078126	LOC645954 NCBI Gene Pubmed Genecard	31024312	0.07512	0.8597	1	0.09223	0.0032	31
	rs7093972	LOC645954 NCBI Gene Pubmed Genecard	31024349	0.07392	0.37	0.523	0.06957	0.0033	29
	rs3858241	LOC645954 NCBI Gene Pubmed Genecard	31041299	0.06328	0.3159	0.02187	0.4709	0.0025	36
	rs1494134		31057878	0.1442	0.3376	0.4684	0.134	0.00012	160
23	Best: rs5982644 (2)	Gene	3.02-3.02Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5983012	ARSF NCBI Gene Pubmed Genecard	3021746	0.0821	0.07119	0.3892	0.3842	0.00011	163
	rs5982644	ARSF NCBI Gene Pubmed Genecard	3021766	0.08197	0.07128	0.3892	0.3615	0.00014	137
23	Best: rs16985421 (2)	Gene	9.08-9.08Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16985418		9076420	0.189	0.5494	0.01144	0.684	0.00011	175
	rs16985421		9076849	0.1896	0.4414	0.01491	0.6215	0.00012	156
23	Best: rs7053877 (3)	Gene	9.95-10.04Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2239941	CLCN4 NCBI Gene Pubmed Genecard	9952741	0.1216	0.7026	0.2079	0.3126	9.3e-05	197
	rs5934828		10036169	0.1253	0.2733	0.1153	0.4094	0.00012	148
	rs7053877		10037101	0.1266	0.3948	0.09288	0.3923	0.00013	146
23	Best: rs11797883 (2)	Gene	12.71-12.77Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs9780736		12709095	0.2605	0.8344	0.4656	0.05825	0.00015	131
	rs11797883		12770405	0.1168	1	0.6178	0.01932	0.00043	77
23	Best: rs5934184 (5)	Gene	14.23-14.50Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16979557		14228288	0.2003	0.6734	0.8105	0.03776	0.00028	92
	rs6526752	GLRA2 NCBI Gene Pubmed Genecard	14366062	0.2939	0.948	0.2518	0.001645	0.00028	91
	rs3027386	GLRA2 NCBI Gene Pubmed Genecard	14383899	0.2859	0.9475	0.4214	0.007577	9.4e-05	195
	rs5934184	GLRA2 NCBI Gene Pubmed Genecard	14420578	0.239	0.4132	0.5792	0.004649	0.00035	82
	rs10521644	GLRA2 NCBI Gene Pubmed Genecard	14503094	0.2633	0.7825	0.08225	0.008947	0.00032	85
23	Best: rs5950315 (3)	Gene	20.21-20.40Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5950315		20207772	0.242	0.9429	1	0.1432	0.00023	104
	rs4969748		20226186	0.2525	0.9445	0.6815	0.1993	0.00015	132
	rs5990899		20398678	0.2449	0.5108	0.5771	0.05314	0.00018	118
23	Best: rs4824185 (2)	Gene	22.09-22.10Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12557389	LOC100873065 NCBI Gene Pubmed Genecard	22089627	0.2638	0.7245	0.8983	0.002286	0.00011	161
	rs4824185	LOC100873065 NCBI Gene Pubmed Genecard	22103359	0.2215	0.9378	1	0.1936	0.00013	142
23	Best: rs17273161 (3)	Gene	35.97-36.03Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12014468		35969864	0.1058	0.542	0.5879	0.006872	0.00014	136
	rs17273161		36002399	0.1036	0.5246	0.6782	0.001491	0.00016	127
	rs6527545	CXorf30 NCBI Gene Pubmed Genecard	36031799	0.1039	0.6374	0.6834	0.00282	0.00013	143
23	Best: rs5918362 (2)	Gene	41.73-42.01Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6610660		41725409	0.04543	0.1007	0.1564	0.02497	0.00011	173
	rs5918362		42012092	0.1332	0.3453	0.9148	0.02268	0.00015	130
23	Best: rs1883678 (2)	Gene	44.87-45.31Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5905953		44866886	0.3931	0.3429	0.03628	0.08341	9.5e-05	192
	rs1883678		45308372	0.04148	0.06991	0.4803	0.8192	0.00016	122
23	Best: rs6648534 (2)	Gene	122.51-122.53Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6608109	THOC2 NCBI Gene Pubmed Genecard	122507806	0.283	0.05408	0.2155	0.0359	0.00012	153
	rs6648534	THOC2 NCBI Gene Pubmed Genecard	122532366	0.2834	0.08357	0.2649	0.02778	0.00013	144
23	Best: rs1930218 (3)	Gene	135.96-135.96Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5931075		135955615	0.2396	0.08683	0.05977	0.04833	0.00031	86
	rs5931076		135955645	0.2402	0.1178	0.03102	0.06575	0.00025	97
	rs1930218		135960994	0.2409	0.1022	0.04425	0.04865	0.00033	84