T-Trees

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

Supplementary data

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4	Best: rs1553460 (6)	Gene	17.85-17.88Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1039539		17850862	0.2588	0.9056	0.3804	0.5515	9.4e-05	125
	rs17523800		17870443	0.3702	0.2634	0.9367	0.4523	7.2e-05	162
	rs11938418		17871212	0.2799	0.4568	0.03268	0.3554	0.00038	48
	rs1553460		17872130	0.3129	2.344e-101	2.877e-05	1.784e-27	0.007	13
	rs1503881		17878898	0.2689	0.563	0.3237	0.8884	8.9e-05	138
	rs1503882		17878953	0.2682	0.5237	0.3966	0.8514	9.2e-05	128
4	Best: rs890447 (3)	Gene	139.61-139.63Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11100890	LINC00499 NCBI Gene Pubmed Genecard	139614079	0.03972	0.1105	0.237	0.4258	0.00045	43
	rs890447	LINC00499 NCBI Gene Pubmed Genecard	139618590	0.05217	2.704e-205	0.02218	2.637e-12	0.012	7
	rs12509850	LINC00499 NCBI Gene Pubmed Genecard	139628613	0.03636	0.1727	0.7972	0.7819	0.00011	113
5	Best: rs2416472 (2)	Gene	117.03-117.03Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2416472		117033845	0.3204	1.488e-24	0.9345	4.362e-10	0.0003	59
	rs17411921		117033876	0.3436	0.6882	0.3656	0.3824	8.3e-05	144
8	Best: rs17480050 (8)	Gene	19.40-19.48Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11784776	CSGALNACT1 NCBI Gene Pubmed Genecard	19396011	0.2078	0.3671	0.7795	0.8983	0.0005	41
	rs17479749	CSGALNACT1 NCBI Gene Pubmed Genecard	19404858	0.21	0.5835	0.6548	0.7402	0.00051	39
	rs17480050	CSGALNACT1 NCBI Gene Pubmed Genecard	19426197	0.1177	0	1	0	0.072	3
	rs17128573	CSGALNACT1 NCBI Gene Pubmed Genecard	19434020	0.3512	0.4848	0.2392	0.7611	6.4e-05	181
	rs4922060	CSGALNACT1 NCBI Gene Pubmed Genecard	19452788	0.1706	0.3759	0.8447	0.9561	0.0011	28
	SNP_A-1992585		19454071	0.1864	0.4497	0.7159	0.8106	0.00098	30
	rs6996732	CSGALNACT1 NCBI Gene Pubmed Genecard	19462308	0.2131	0.1544	0.7412	0.9596	0.00019	79
	rs7818368	CSGALNACT1 NCBI Gene Pubmed Genecard	19483828	0.1877	0.3712	0.9036	0.9154	0.00046	42
8	Best: rs6989092 (2)	Gene	95.06-95.06Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6989092		95058214	0.01709	1	0.7267	3.597e-35	0.0036	19
	rs16916320		95060875	0.02965	0.3997	1	0.2716	9.6e-05	124
8	Best: rs16908145 (3)	Gene	139.11-139.11Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	SNP_A-2207118		139106414	0.02162	1	0.6486	0.8869	0.00025	65
	rs16908145	FLJ45872 NCBI Gene Pubmed Genecard	139107155	0.01392	0.002711	0.4023	2.699e-21	0.0021	23
	SNP_A-4193710		139110948	0.02262	0.2534	0.6608	1	0.00027	64
10	Best: rs7906587 (16)	Gene	118.22-118.28Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7906587	PNLIPRP3 NCBI Gene Pubmed Genecard	118221656	0.0776	1.038e-285	0.00433	1.001e-28	0.022	5
	rs10787680		118236762	0.05962	0.4368	0.7322	0.255	0.00031	57
	rs6585402		118245100	0.05847	0.04312	0.2999	0.4004	0.0003	58
	rs6585406		118245287	0.05724	0.0009619	0.007612	0.3255	0.00041	44
	rs11197703		118245329	0.05998	0.6983	1	0.3363	0.0003	60
	rs2420296		118248953	0.05721	0.0009614	0.0001286	0.3038	0.00035	51
	rs10736256		118254226	0.05918	0.698	0.8623	0.2894	0.00024	67
	rs11197713		118254822	0.05925	1	0.8627	0.2903	0.00028	63
	rs10787687		118254911	0.06	0.6987	1	0.2948	0.00033	54
	rs4570504		118255066	0.05977	0.4357	1	0.3578	0.00029	61
	rs4751990		118260772	0.06684	0.3701	0.652	0.6181	0.00019	80
	rs10787704		118268518	0.05994	0.6983	0.8669	0.3367	0.00034	53
	rs10510021		118268635	0.06013	0.4357	0.7368	0.4582	0.00032	55
	rs10749223		118269047	0.06019	1	0.7342	0.2953	0.00032	56
	rs2420287		118273902	0.06833	0.8632	0.7651	0.3881	0.0002	74
	rs10885981		118276595	0.06076	0.5715	1	0.2408	0.00028	62
11	Best: rs2241572 (2)	Gene	129.30-129.32Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2241572	PRDM10 NCBI Gene Pubmed Genecard	129298658	0.3438	1.84499999999018e-313	1	0	0.33	1
	rs3734068	PRDM10 NCBI Gene Pubmed Genecard	129320230	0.05985	0.8458	0.6135	0.315	0.0059	15
16	Best: rs11640295 (5)	Gene	11.28-11.31Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1559394	PRM2 NCBI Gene Pubmed Genecard	11276706	0.2678	0.3572	0.08828	0.4395	6.3e-05	183
	rs181694		11292330	0.2163	0.1194	0.9568	0.7056	7.3e-05	159
	rs11640295		11298229	0.2835	2.709e-40	0.000145	5.067e-09	0.0009	32
	rs2867936		11306199	0.2154	0.07582	0.6629	0.7419	6.2e-05	187
	rs12927773		11311464	0.1912	0.3307	0.9529	0.4446	6e-05	198
17	Best: rs3785579 (9)	Gene	62.46-62.65Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs9892020		62460904	0.151	0.04652	0.0001116	0.4867	0.0058	16
	rs4790993		62465677	0.3048	0.562	0.4015	0.0615	0.0005	40
	rs2159210		62466422	0.2381	0.5312	0.9593	0.8455	0.007	12
	rs3785579	CACNG1 NCBI Gene Pubmed Genecard	62472963	0.2768	0	0.02123	0	0.21	2
	rs7217216	HELZ NCBI Gene Pubmed Genecard	62500117	0.2124	0.74	1	0.1282	0.00054	38
	rs10491170	HELZ NCBI Gene Pubmed Genecard	62512481	0.2123	0.74	1	0.1282	0.00057	36
	rs8066806	HELZ NCBI Gene Pubmed Genecard	62629181	0.1675	0.9375	0.6814	0.04219	0.00065	33
	rs8080100	HELZ NCBI Gene Pubmed Genecard	62642504	0.1527	0.4433	0.2431	0.1756	0.0011	27
	rs16960718	HELZ NCBI Gene Pubmed Genecard	62647612	0.1526	0.4439	0.5107	0.1493	0.00092	31
18	Best: rs1595963 (2)	Gene	25.70-25.71Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16947249		25701439	0.03157	1	1	0.314	0.00012	107
	rs1595963		25714346	0.03915	1.616e-184	0.2715	2.068e-14	0.0093	10
18	Best: rs4799934 (5)	Gene	33.34-33.36Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	SNP_A-1817219		33339731	0.05487	0.2823	0.4616	0.4644	0.00038	47
	rs1786811	CELF4 NCBI Gene Pubmed Genecard	33340772	0.06211	0.8508	0.2584	0.4649	0.00057	37
	rs1786776	CELF4 NCBI Gene Pubmed Genecard	33341455	0.06466	0.4621	0.352	0.7042	0.00058	35
	rs1786768	CELF4 NCBI Gene Pubmed Genecard	33347744	0.06442	0.7148	1	0.3747	0.0004	46
	rs4799934	CELF4 NCBI Gene Pubmed Genecard	33357665	0.07764	4.831e-288	0.002834	1.895e-26	0.022	4
19	Best: rs11671119 (3)	Gene	19.15-19.21Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11671119	MEF2BNB-MEF2B NCBI Gene Pubmed Genecard	19147077	0.04508	2.632e-201	0.1124	9.267e-18	0.011	8
	rs11668677	NCAN NCBI Gene Pubmed Genecard	19202446	0.03193	0.2604	0.07384	1	7.2e-05	161
	rs11672216	NCAN NCBI Gene Pubmed Genecard	19205579	0.03342	0.2788	0.7702	0.8176	9.3e-05	126
22	Best: rs4819660 (2)	Gene	16.89-16.89Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4819660	FLJ41941 NCBI Gene Pubmed Genecard	16893188	0.2329	8.455e-78	6.853e-07	5.103e-09	0.0023	21
	rs4819661	FLJ41941 NCBI Gene Pubmed Genecard	16893383	0.2106	0.4808	0.372	0.3407	7.6e-05	150
23	Best: rs311152 (2)	Gene	2.68-2.75Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs311152		2683671	0.3549	0.9199	0.5993	1.133e-14	0.00023	70
	rs4892897	GYG2 NCBI Gene Pubmed Genecard	2753421	0.3414	0.3625	0.2742	0.2447	6.3e-05	182
23	Best: rs4826780 (4)	Gene	5.25-5.36Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4826780		5251391	0.4299	0.6803	0.4292	0.01586	9.3e-05	127
	rs5916081		5265446	0.4277	0.539	0.6342	0.01588	6.7e-05	176
	rs4826690		5278423	0.2345	0.05166	0.7661	0.007687	7.6e-05	149
	rs7058159		5356400	0.3064	0.09787	0.9041	0.2778	7.4e-05	156
23	Best: rs6530079 (7)	Gene	6.69-7.14Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6639703		6687431	0.225	0.8977	0.05094	0.0396	7.5e-05	152
	rs6638643		6726195	0.233	0.5199	0.07689	0.02113	6.8e-05	172
	rs6530012		6738677	0.2547	0.1477	0.1304	0.01464	6.1e-05	193
	rs5934286		6790430	0.2836	0.4931	0.7976	0.01046	7e-05	166
	rs941172	HDHD1 NCBI Gene Pubmed Genecard	6926340	0.2433	1	0.9437	0.02687	6.2e-05	186
	rs2024159	STS NCBI Gene Pubmed Genecard	7025948	0.3016	0.3672	0.71	0.01104	6.9e-05	168
	rs6530079		7136817	0.2724	0.5477	0.4364	0.001509	9.8e-05	121
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	0.2676	0.2055	0.3219	0.156	9.1e-05	134
	rs5979435	ARHGAP6 NCBI Gene Pubmed Genecard	11391705	0.1882	0.0179	0.2967	0.01397	9.9e-05	116
23	Best: rs4240155 (4)	Gene	14.73-14.78Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6527137		14734842	0.4958	0.06978	0.756	0.01117	0.00012	109
	rs11094668		14759628	0.4922	0.1309	0.8763	0.006069	9.9e-05	117
	rs5978704		14763020	0.4921	0.1294	0.7559	0.004441	8.9e-05	136
	rs4240155		14781196	0.4938	0.06978	0.7168	0.008323	0.00014	94
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	0.1688	0.1714	0.02833	0.00014	98
	rs6629114	TMEM27 NCBI Gene Pubmed Genecard	15427789	0.185	0.2353	0.1535	0.05547	9.9e-05	118
23	Best: rs12688591 (5)	Gene	21.73-21.77Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2238962	SMS NCBI Gene Pubmed Genecard	21733540	0.2439	0.5951	0.5783	0.2327	6e-05	196
	rs2283723	SMS NCBI Gene Pubmed Genecard	21740152	0.3205	0.3572	0.1118	0.2968	0.0001	115
	rs12688591	SMS NCBI Gene Pubmed Genecard	21743104	0.295	0.6265	0.04843	0.1684	0.00017	84
	rs10521911	SMS NCBI Gene Pubmed Genecard	21761456	0.1797	0.7133	0.9313	0.1332	0.00013	103
	rs5951678	SMS NCBI Gene Pubmed Genecard	21768641	0.2208	0.6161	0.6529	0.7067	9.1e-05	133
23	Best: rs12216932 (3)	Gene	21.92-22.02Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5904508	PHEX NCBI Gene Pubmed Genecard	21922488	0.4233	0.01789	0.2893	0.05505	6.1e-05	191
	rs3752433	PHEX NCBI Gene Pubmed Genecard	21999377	0.3288	0.1347	0.06037	0.1138	8.3e-05	143
	rs12216932	PHEX NCBI Gene Pubmed Genecard	22022503	0.3747	0.2401	0.07607	0.016	0.00016	88
23	Best: rs3935727 (2)	Gene	22.49-22.49Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5970861	LOC100873065 NCBI Gene Pubmed Genecard	22493408	0.4867	0.84	0.1194	0.1369	6.7e-05	174
	rs3935727	LOC100873065 NCBI Gene Pubmed Genecard	22493774	0.4373	0.4737	0.1011	0.04395	0.00012	106
23	Best: rs5944611 (3)	Gene	26.58-26.75Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5944611		26583141	0.3302	0.172	0.2348	0.0359	0.00017	83
	rs1842186		26663640	0.3297	0.206	0.2115	0.0496	0.00014	97
	rs6526586		26748991	0.3097	0.02762	0.5811	0.1577	6.5e-05	180
23	Best: rs17315366 (2)	Gene	30.75-30.78Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5927652		30749906	0.49	0.9196	0.07775	0.01028	8.1e-05	145
	rs17315366		30778255	0.09913	0.7888	1	0.04858	8.7e-05	140
23	Best: rs3002415 (2)	Gene	39.46-39.47Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs3002422		39460022	0.4838	0.4844	1	0.003749	7.6e-05	151
	rs3002415		39466715	0.3026	0.5581	0.7574	0.01111	0.00023	69
23	Best: rs5953113 (4)	Gene	47.39-47.47Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4824635		47391945	0.416	0.9183	0.07736	0.1013	6e-05	195
	rs1207489		47450026	0.4714	0.6165	0.1594	0.04244	6.2e-05	188
	rs5953113	ZNF81 NCBI Gene Pubmed Genecard	47461227	0.4558	0.3166	0.1166	0.04474	9.2e-05	130
	rs11091213	ZNF81 NCBI Gene Pubmed Genecard	47465469	0.4565	0.3154	0.07525	0.05687	9.2e-05	131
23	Best: rs241388 (5)	Gene	67.85-68.29Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs241393		67848063	0.4375	0.2653	0.792	0.02582	9.7e-05	123
	rs443731		67856344	0.422	0.0854	0.8316	0.005963	0.00015	90
	rs241388		67872999	0.4171	0.0664	0.4532	0.007779	0.00018	81
	rs5981167		68117480	0.2479	0.3226	0.03956	0.6996	7.1e-05	163
	rs5981203		68287509	0.293	0.001877	0.01448	0.01463	6.9e-05	170
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	0.3511	0.3241	0.3304	0.003436	0.00012	105
	rs5936811	EDA NCBI Gene Pubmed Genecard	68974251	0.3393	0.4317	0.2919	0.009219	0.00011	111
	rs17216448	EDA NCBI Gene Pubmed Genecard	68975685	0.3812	0.1347	0.5811	0.00112	0.00015	92
	rs5936814	EDA NCBI Gene Pubmed Genecard	68980230	0.3869	0.8332	0.3227	0.001457	0.00017	85
	rs6625553	EDA NCBI Gene Pubmed Genecard	68980582	0.3853	1	0.121	0.001906	0.00013	101
23	Best: rs2808726 (2)	Gene	95.09-95.14Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2808726		95093032	0.1227	0.3318	0.5723	0.507	9e-05	135
	rs5949779		95135596	0.3032	0.07201	0.5862	0.125	7.5e-05	153
23	Best: rs1338512 (2)	Gene	116.77-116.78Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1338512		116765946	0.2921	0.1477	0.1882	0.0631	0.00011	110
	rs6645968		116776263	0.2886	0.2754	0.2824	0.05468	7.7e-05	148
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	0.1455	0.544	0.1714	0.03216	0.00024	66
	rs1287171	DOCK11 NCBI Gene Pubmed Genecard	117560510	0.1769	0.4755	0.4638	0.1289	7.1e-05	164
23	Best: rs3101156 (2)	Gene	124.24-124.26Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs3126330		124242122	0.409	0.6847	0.9142	0.003504	0.00011	112
	rs3101156		124258625	0.4042	0.3607	1	0.001573	0.00021	73
23	Best: rs7473865 (2)	Gene	125.62-125.64Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12834033		125619096	0.09249	1	1	0.2159	6.6e-05	178
	rs7473865		125644343	0.04799	0.006388	0.456	7.43e-10	0.0004	45
23	Best: rs6529475 (4)	Gene	129.75-130.19Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2864894	ENOX2 NCBI Gene Pubmed Genecard	129754301	0.2116	1	0.7532	0.02589	0.00013	100
	rs6529475		130156854	0.1794	0.1281	0.1571	0.08859	0.00035	49
	rs4639666		130156931	0.1244	0.04099	0.1396	0.07413	0.00016	89
	rs7882682		130189739	0.1797	0.338	0.1342	0.2166	0.00019	77
23	Best: rs5933109 (3)	Gene	130.80-131.03Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs202765		130797177	0.2424	0.12	0.3114	0.01412	6.7e-05	175
	rs5933079	FRMD7 NCBI Gene Pubmed Genecard	130976861	0.3033	0.1522	0.1346	0.5214	7.4e-05	157
	rs5933109		131031301	0.2494	0.4664	0.2477	0.07589	0.00011	114
23	Best: rs5965859 (2)	Gene	144.27-144.28Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5965859		144274410	0.4402	0.002236	0.2057	0.1415	6.6e-05	177
	rs5919854		144279499	0.4398	0.0006975	0.3679	0.1547	5.9e-05	200
23	Best: rs1076616 (2)	Gene	146.37-146.39Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17273952		146374566	0.09021	0.2264	0.6589	0.8934	6.3e-05	184
	rs1076616		146388887	0.08932	0.4018	0.7641	0.8223	7.5e-05	155
23	Best: rs12845940 (2)	Gene	149.86-149.86Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12845940		149858263	0.393	0.8319	0.5094	0.01697	8.9e-05	137
	rs4828789		149862821	0.3906	1	0.6579	0.01925	6.3e-05	185
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	0.1471	0.1866	0.1142	0.0706	9.2e-05	132
	SNP_A-1999621		151116918	0.1062	0.05534	0.04443	0.0159	0.00012	104
	rs1492293	GABRA3 NCBI Gene Pubmed Genecard	151163320	0.1458	0.2476	0.0732	0.08145	9.2e-05	129