T-Trees

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

Supplementary data

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10	Best: rs3122348 (6)	Gene	30.99-31.06Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	SNP_A-2100739		30990735	0.07869	0.02921	0.7977	0.6736	0.0066	3
	rs3122348	LOC645954 NCBI Gene Pubmed Genecard	30991151	0.03151	2.849e-05	1	5.572e-88	0.087	1
	rs7078126	LOC645954 NCBI Gene Pubmed Genecard	31024312	0.07803	0.6296	1	0.7583	0.0043	4
	rs7093972	LOC645954 NCBI Gene Pubmed Genecard	31024349	0.07753	0.4234	0.523	0.9385	0.0041	5
	rs3858241	LOC645954 NCBI Gene Pubmed Genecard	31041299	0.06498	0.8515	0.02187	0.9333	0.0031	6
	rs1494134		31057878	0.145	0.925	0.4684	0.2297	0.00028	95
23	Best: rs16983713 (7)	Gene	5.25-5.43Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4826780		5251391	0.4295	0.7589	0.6012	0.0153	0.0002	157
	rs4826690		5278423	0.2349	0.03848	0.7684	0.0051	0.00034	67
	rs16983713		5278919	0.2344	0.05206	0.8829	0.006159	0.00038	57
	rs7058159		5356400	0.3067	0.07657	0.858	0.293	0.00022	132
	rs12394831		5423057	0.2805	1	1	0.2087	0.00019	186
	rs9698745		5423410	0.285	0.8098	0.5767	0.296	0.00019	184
	rs7051992		5425745	0.2849	0.8098	0.5768	0.2964	0.0002	167
23	Best: rs941172 (8)	Gene	6.69-7.22Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6638634		6687308	0.2192	0.7876	0.1067	0.05821	0.0002	171
	rs6639703		6687431	0.2252	0.8979	0.07355	0.04714	0.0002	166
	rs6638643		6726195	0.2333	0.5207	0.09314	0.02761	0.00023	127
	rs6530012		6738677	0.2552	0.1868	0.1719	0.01523	0.00025	118
	rs5934286		6790430	0.2841	0.425	0.7994	0.01008	0.00019	191
	rs941172	HDHD1 NCBI Gene Pubmed Genecard	6926340	0.244	0.899	0.9442	0.02574	0.00029	87
	rs2024159	STS NCBI Gene Pubmed Genecard	7025948	0.3019	0.2642	0.7581	0.01148	0.00022	136
	rs6639846		7221058	0.218	0.1354	0.9398	0.1225	0.00025	121
23	Best: rs17269753 (2)	Gene	8.82-8.83Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17269753		8824586	0.224	0.1558	0.6379	0.01704	0.00025	120
	rs10126241		8827607	0.2354	0.2201	0.8221	0.02249	0.00022	135
23	Best: rs5979435 (2)	Gene	11.37-11.39Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5933905	ARHGAP6 NCBI Gene Pubmed Genecard	11366712	0.2681	0.1671	0.328	0.1422	0.00029	88
	rs5979435	ARHGAP6 NCBI Gene Pubmed Genecard	11391705	0.1887	0.02697	0.4405	0.01595	0.00048	44
23	Best: rs5978704 (6)	Gene	14.72-14.85Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5980078		14722059	0.4675	0.2305	0.8768	0.01636	0.00034	66
	rs6527137		14734842	0.4959	0.05739	0.8776	0.009302	0.00055	37
	rs11094668		14759628	0.4924	0.1315	1	0.004635	0.00051	39
	rs5978704		14763020	0.4924	0.1082	0.8775	0.00365	0.00082	18
	rs4240155		14781196	0.4939	0.05739	0.8372	0.006892	0.00055	36
	rs5978707		14849016	0.4942	0.04479	0.5038	0.05573	0.00019	182
23	Best: SNP_A-1907375 (2)	Gene	15.42-15.43Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	SNP_A-1907375		15418427	0.1822	0.1745	0.2411	0.03744	0.00039	55
	rs6629114	TMEM27 NCBI Gene Pubmed Genecard	15427789	0.1849	0.3084	0.1875	0.07093	0.00033	71
23	Best: rs12688591 (5)	Gene	21.73-21.76Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2238962	SMS NCBI Gene Pubmed Genecard	21733540	0.2445	0.5965	0.891	0.3134	0.0002	164
	rs2283723	SMS NCBI Gene Pubmed Genecard	21740152	0.3214	0.4207	0.1801	0.3259	0.00034	69
	rs12688591	SMS NCBI Gene Pubmed Genecard	21743104	0.296	0.627	0.08807	0.219	0.0005	42
	rs3747276	SMS NCBI Gene Pubmed Genecard	21745121	0.3284	0.1349	0.5234	0.4937	0.00027	104
	rs10521911	SMS NCBI Gene Pubmed Genecard	21761456	0.1806	0.7139	0.7338	0.185	0.00049	43
23	Best: rs12216932 (4)	Gene	21.92-22.02Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5904508	PHEX NCBI Gene Pubmed Genecard	21922488	0.424	0.01884	0.2931	0.03446	0.00029	92
	rs5904513	PHEX NCBI Gene Pubmed Genecard	21990451	0.3548	0.09445	0.09183	0.174	0.00022	133
	rs3752433	PHEX NCBI Gene Pubmed Genecard	21999377	0.3287	0.1354	0.08102	0.1287	0.0003	83
	rs12216932	PHEX NCBI Gene Pubmed Genecard	22022503	0.3743	0.2414	0.08864	0.01907	0.00059	30
23	Best: rs17312220 (2)	Gene	24.04-24.23Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17312220		24038623	0.02086	0.2151	1	0.07416	0.0004	51
	rs17217563		24233307	0.3044	0.426	1	0.01364	0.00018	193
23	Best: rs5944611 (6)	Gene	26.41-26.86Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5943949		26410699	0.3225	0.3006	0.5927	0.1729	0.00018	199
	rs5944611		26583141	0.3293	0.142	0.215	0.03923	0.00068	24
	rs1842186		26663640	0.3288	0.1709	0.1745	0.05068	0.00055	35
	rs6526585		26748338	0.3031	0.01855	0.6649	0.1079	0.00032	75
	rs6526586		26748991	0.3081	0.02693	0.5419	0.1361	0.00025	117
	rs1898741		26863297	0.2873	0.4045	0.443	0.06729	0.00028	100
23	Best: rs17315366 (2)	Gene	30.75-30.78Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5927652		30749906	0.4924	0.8412	0.165	0.0133	0.00026	113
	rs17315366		30778255	0.09807	0.788	1	0.02879	0.00036	63
23	Best: rs2057142 (2)	Gene	33.06-33.15Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5928224	DMD NCBI Gene Pubmed Genecard	33064527	0.348	0.16	1	0.09181	0.00021	146
	rs2057142		33154631	0.3937	0.3026	0.03956	0.03442	0.00033	73
23	Best: rs3128091 (5)	Gene	34.69-34.98Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17319056		34693776	0.2519	0.3438	0.531	0.08283	0.0002	165
	rs3128091		34770391	0.2123	0.7577	0.5822	0.03676	0.0003	81
	rs12846686		34813547	0.1704	0.5911	0.2185	0.02754	0.00019	174
	rs11798320		34965178	0.1722	0.846	0.7847	0.1658	0.00026	107
	rs11795655		34979596	0.1727	0.5623	0.5271	0.3283	0.00019	190
23	Best: rs3002415 (2)	Gene	39.46-39.47Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs3002422		39460022	0.4824	0.4247	0.9589	0.002204	0.00032	74
	rs3002415		39466715	0.3012	0.5589	0.9509	0.007625	0.00084	17
23	Best: rs11091213 (3)	Gene	47.36-47.47Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1997638		47361269	0.2258	0.4958	0.3389	0.1703	0.00019	179
	rs5953113	ZNF81 NCBI Gene Pubmed Genecard	47461227	0.4554	0.271	0.1326	0.06165	0.00019	183
	rs11091213	ZNF81 NCBI Gene Pubmed Genecard	47465469	0.456	0.2698	0.08696	0.0773	0.00021	148
23	Best: rs443731 (4)	Gene	67.85-68.12Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs241393		67848063	0.4385	0.3624	0.6757	0.02663	0.00027	101
	rs443731		67856344	0.4228	0.1075	0.6733	0.006233	0.00058	33
	rs241388		67872999	0.418	0.1031	0.2886	0.008127	0.00045	48
	rs5981167		68117480	0.2482	0.324	0.0291	0.6159	0.00034	68
23	Best: rs5936814 (5)	Gene	68.97-68.98Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5936809	EDA NCBI Gene Pubmed Genecard	68968019	0.3515	0.276	0.3946	0.005974	0.0004	52
	rs5936811	EDA NCBI Gene Pubmed Genecard	68974251	0.3396	0.3719	0.3242	0.01307	0.00033	70
	rs17216448	EDA NCBI Gene Pubmed Genecard	68975685	0.3807	0.1355	0.5843	0.0009851	0.00047	47
	rs5936814	EDA NCBI Gene Pubmed Genecard	68980230	0.3878	0.7531	0.4462	0.002409	0.00081	20
	rs6625553	EDA NCBI Gene Pubmed Genecard	68980582	0.3863	0.9149	0.1881	0.00288	0.0005	41
23	Best: rs2038452 (5)	Gene	90.18-90.20Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2038452		90181597	0.2292	0.6765	0.3765	0.06899	0.00027	106
	rs5941840		90183030	0.2292	0.6765	0.3767	0.06888	0.00025	119
	rs5941853		90197403	0.2793	0.9006	0.09724	0.32	0.00022	140
	rs1474970		90200834	0.3124	0.3436	0.7201	0.2835	0.00019	180
	rs17246141		90201446	0.3653	0.2365	0.7815	0.2665	0.00019	181
23	Best: rs2808726 (2)	Gene	95.09-95.14Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2808726		95093032	0.1241	0.3324	0.7395	0.5364	0.00028	94
	rs5949779		95135596	0.3047	0.05576	0.5121	0.1658	0.00022	134
23	Best: rs5921205 (3)	Gene	97.74-97.85Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2335828		97740166	0.4549	0.2254	0.1078	0.2292	0.0002	170
	rs241863		97781312	0.4817	0.05523	0.08652	0.3437	0.00023	130
	rs5921205		97847262	0.2867	0.5471	0.2614	0.2839	0.00026	109
23	Best: rs12841456 (2)	Gene	99.55-99.71Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12841456		99553718	0.3903	0.6725	0.6254	0.07077	0.00021	143
	rs877358	SRPX2 NCBI Gene Pubmed Genecard	99709176	0.124	0.03749	0.6247	0.1523	0.00021	144
23	Best: rs1338512 (2)	Gene	116.77-116.78Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1338512		116765946	0.2923	0.1482	0.3206	0.08246	0.00024	126
	rs6645968		116776263	0.2888	0.2762	0.4525	0.07207	0.00021	149
23	Best: rs5910392 (2)	Gene	117.52-117.56Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5910392	DOCK11 NCBI Gene Pubmed Genecard	117515258	0.1454	0.5425	0.1721	0.03007	0.00093	15
	rs1287171	DOCK11 NCBI Gene Pubmed Genecard	117560510	0.1767	0.4725	0.4646	0.1224	0.00024	125
23	Best: rs3101156 (2)	Gene	124.24-124.26Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs3126330		124242122	0.4085	0.6865	0.8725	0.002862	0.00042	49
	rs3101156		124258625	0.4036	0.417	0.9571	0.00116	0.00081	19
23	Best: rs204359 (2)	Gene	125.62-125.93Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12834033		125619096	0.09193	1	1	0.201	0.00027	103
	rs204359		125925433	0.06747	0.08713	1	0.1848	0.00031	79
23	Best: rs6529475 (5)	Gene	129.75-130.23Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2864894	ENOX2 NCBI Gene Pubmed Genecard	129754301	0.2108	0.8831	0.8145	0.02866	0.00042	50
	rs6529475		130156854	0.1798	0.1308	0.1181	0.1111	0.0013	11
	rs4639666		130156931	0.1248	0.06975	0.09087	0.1137	0.00061	29
	rs7882682		130189739	0.1802	0.342	0.1179	0.2455	0.00073	21
	rs17000451		130227181	0.1248	0.03447	0.2198	0.0972	0.00023	129
23	Best: rs5933109 (5)	Gene	130.80-131.03Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs202765		130797177	0.2429	0.1572	0.3167	0.01246	0.00029	89
	rs1569893		130865872	0.2406	0.2419	0.8841	0.01658	0.00019	189
	rs5933079	FRMD7 NCBI Gene Pubmed Genecard	130976861	0.3019	0.1561	0.1526	0.3742	0.00026	112
	rs5933091		131003642	0.3021	0.197	0.172	0.3896	0.00031	78
	rs5933109		131031301	0.2477	0.465	0.3109	0.04477	0.00047	46
23	Best: SNP_A-2065339 (2)	Gene	135.09-135.14Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1040649		135090882	0.4495	1	0.4327	0.01963	0.00019	176
	SNP_A-2065339		135137064	0.2828	0.4091	1	0.02264	0.00024	122
23	Best: rs1342044 (2)	Gene	136.57-136.64Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs697833		136567072	0.2304	0.8858	0.9411	0.1301	0.00019	175
	rs1342044		136635466	0.2205	1	0.4958	0.07954	0.00048	45
23	Best: rs5965859 (2)	Gene	144.27-144.28Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5965859		144274410	0.4405	0.004436	0.2504	0.1366	0.00036	64
	rs5919854		144279499	0.4401	0.001487	0.4315	0.1493	0.00025	115
23	Best: rs1076616 (2)	Gene	146.37-146.39Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17273952		146374566	0.09129	0.241	0.7725	0.9647	0.00033	72
	rs1076616		146388887	0.09039	0.4079	0.8828	0.7897	0.00037	60
23	Best: rs241127 (3)	Gene	147.39-147.47Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5936220	AFF2 NCBI Gene Pubmed Genecard	147389782	0.212	0.6541	0.7554	0.09213	0.0002	156
	rs241109	AFF2 NCBI Gene Pubmed Genecard	147450011	0.2151	0.4637	0.8177	0.05821	0.00021	152
	rs241127	AFF2 NCBI Gene Pubmed Genecard	147468299	0.2171	0.5544	0.5934	0.05911	0.00026	110
23	Best: rs12845940 (2)	Gene	149.86-149.86Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12845940		149858263	0.3932	0.7513	0.5131	0.0202	0.00039	56
	rs4828789		149862821	0.391	1	0.7005	0.02132	0.00038	58
23	Best: SNP_A-1999621 (3)	Gene	151.10-151.16Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11094561	GABRA3 NCBI Gene Pubmed Genecard	151098668	0.1459	0.2517	0.1391	0.07103	0.00028	98
	SNP_A-1999621		151116918	0.1052	0.054	0.04449	0.01794	0.0004	53
	rs1492293	GABRA3 NCBI Gene Pubmed Genecard	151163320	0.1448	0.3297	0.09031	0.07616	0.0003	82