T-Trees

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

Supplementary data

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1	Best: rs11209026 (11)	Gene	67.31-67.46Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7515029		67308393	0.03583	0.527	0.1899	3.545e-10	0.0011	48
	rs4655679		67311678	0.2724	0.2114	0.2108	3.707e-08	0.00016	190
	rs17375018	IL23R NCBI Gene Pubmed Genecard	67367168	0.2825	0.09514	0.3592	1.048e-08	0.00024	148
	rs11805303	IL23R NCBI Gene Pubmed Genecard	67387537	0.345	0.3935	0.1359	3.698e-13	0.00032	117
	rs10489629	IL23R NCBI Gene Pubmed Genecard	67400370	0.4291	0.5071	0.3481	3.717e-12	0.00026	138
	SNP_A-2045577		67401629	0.3026	0.219	0.5559	6.928e-10	0.00016	195
	rs2201841	IL23R NCBI Gene Pubmed Genecard	67406223	0.3452	0.5132	0.3081	5.183e-12	0.0003	124
	rs11209026	IL23R NCBI Gene Pubmed Genecard	67417979	0.04501	1	3.526e-05	5.433e-18	0.0069	10
	rs11209033		67456521	0.351	0.3663	0.3784	1.52e-10	0.00016	191
	rs12119179		67459436	0.3508	0.3665	0.3549	5.981e-11	0.00017	180
	rs7546245		67462495	0.3479	0.4768	0.06445	4.94e-11	0.00025	146
1	Best: rs12078461 (9)	Gene	117.16-117.18Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2251406		117157407	0.03558	0.2736	0.05161	1	0.00051	94
	rs2254224	PTGFRN NCBI Gene Pubmed Genecard	117169906	0.03523	1	0.7747	0.418	0.0012	44
	rs2250865	PTGFRN NCBI Gene Pubmed Genecard	117174733	0.03802	0.5324	0.5896	0.2404	0.00061	81
	rs2250457	PTGFRN NCBI Gene Pubmed Genecard	117177807	0.03472	0.1689	0.07758	0.4479	0.0011	49
	rs943371	PTGFRN NCBI Gene Pubmed Genecard	117179732	0.03157	0.2657	0.1825	0.2199	0.00066	74
	rs2806863	PTGFRN NCBI Gene Pubmed Genecard	117181555	0.03494	1	0.2593	0.3521	0.00089	60
	rs2806864	PTGFRN NCBI Gene Pubmed Genecard	117181823	0.03462	0.1682	0.2593	0.4833	0.00095	59
	rs17036573	PTGFRN NCBI Gene Pubmed Genecard	117182536	0.03472	1	0.7721	0.4479	0.001	55
	rs12078461	PTGFRN NCBI Gene Pubmed Genecard	117184091	0.0471	2.506e-182	0.04908	7.194e-13	0.05	2
2	Best: rs2164411 (3)	Gene	25.31-25.36Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs874401		25313931	0.1724	0.3088	0.4804	0.6509	0.00022	156
	rs4665287		25324960	0.1689	0.3852	0.2974	0.4759	0.00016	196
	rs2164411		25364557	0.1554	2.852e-13	0.1946	0.00482	0.0053	13
2	Best: rs10210302 (5)	Gene	233.94-233.97Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10210302	ATG16L1 NCBI Gene Pubmed Genecard	233940839	0.4511	0.426	0.01984	1.075e-13	0.0013	41
	rs6752107	ATG16L1 NCBI Gene Pubmed Genecard	233943448	0.4512	0.4261	0.01992	1.756e-13	0.0012	42
	rs6431654	ATG16L1 NCBI Gene Pubmed Genecard	233943769	0.4503	0.4857	0.02653	1.236e-13	0.0011	53
	rs3828309	ATG16L1 NCBI Gene Pubmed Genecard	233962410	0.4515	0.5505	0.0264	5.055e-13	0.00097	58
	rs3792106	ATG16L1 NCBI Gene Pubmed Genecard	233972740	0.3964	0.1421	0.0256	1.677e-11	0.00071	70
3	Best: rs9839841 (2)	Gene	16.45-16.46Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs9839841	RFTN1 NCBI Gene Pubmed Genecard	16454562	0.1948	2.302e-06	0.5137	7.204e-13	0.0014	38
	rs9817739	RFTN1 NCBI Gene Pubmed Genecard	16455831	0.2174	0.2452	0.8312	0.1027	0.0011	52
3	Best: rs11718165 (3)	Gene	49.43-49.68Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11715915	AMT NCBI Gene Pubmed Genecard	49430334	0.3049	0.1137	0.009876	3.027e-05	0.00016	194
	rs11718165	BSN NCBI Gene Pubmed Genecard	49671801	0.2945	0.0157	0.01605	2.214e-06	0.00042	102
	rs9858542	BSN NCBI Gene Pubmed Genecard	49676987	0.3	0.004937	0.1859	7.587e-07	0.00025	145
4	Best: rs157613 (14)	Gene	16.37-16.48Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16893807	LDB2 NCBI Gene Pubmed Genecard	16372861	0.06366	0.3764	1	0.09621	0.00017	183
	rs283027	LDB2 NCBI Gene Pubmed Genecard	16430132	0.09554	0.4506	0.9187	0.03828	0.001	54
	rs157631	LDB2 NCBI Gene Pubmed Genecard	16431157	0.08319	1	0.348	0.1636	0.0011	50
	rs284208	LDB2 NCBI Gene Pubmed Genecard	16432194	0.07871	0.5827	0.8073	0.03751	0.0019	31
	rs284210	LDB2 NCBI Gene Pubmed Genecard	16433085	0.08162	0.7306	0.2849	0.1012	0.0016	35
	rs189988	LDB2 NCBI Gene Pubmed Genecard	16446504	0.07623	0.7144	0.801	0.1261	0.0017	33
	rs207683	LDB2 NCBI Gene Pubmed Genecard	16448574	0.07654	0.4647	0.6145	0.1267	0.0021	25
	rs207684	LDB2 NCBI Gene Pubmed Genecard	16449488	0.07696	0.7144	0.7087	0.08472	0.0019	29
	rs150260	LDB2 NCBI Gene Pubmed Genecard	16453444	0.06963	1	0.7848	0.09318	0.0029	20
	rs157613	LDB2 NCBI Gene Pubmed Genecard	16454556	0.08214	3.158e-253	3.956e-06	1.132e-14	0.09	1
	rs157611	LDB2 NCBI Gene Pubmed Genecard	16457449	0.08712	0.6258	1	0.08136	0.0011	51
	rs287961	LDB2 NCBI Gene Pubmed Genecard	16466584	0.07958	1	1	0.04845	0.0019	27
	rs158278	LDB2 NCBI Gene Pubmed Genecard	16477310	0.08572	0.5036	1	0.02438	0.0013	40
	rs150261	LDB2 NCBI Gene Pubmed Genecard	16484771	0.07785	1	1	0.01194	0.0023	24
4	Best: rs1553460 (16)	Gene	17.73-17.93Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs9784574		17734890	0.1593	0.929	0.6287	0.9302	0.00019	171
	rs1039539		17850862	0.2596	0.2913	0.3804	0.403	0.00088	62
	rs17523800		17870443	0.3641	0.9585	0.9367	0.4112	0.001	56
	rs11938418		17871212	0.2851	0.5213	0.03268	0.6361	0.002	26
	rs1553460		17872130	0.315	5.835e-93	2.877e-05	1.594e-31	0.041	4
	rs1503881		17878898	0.2713	0.6323	0.3237	0.4004	0.00079	66
	rs1503882		17878953	0.2707	0.6751	0.3966	0.3608	0.00071	71
	rs4698673		17885266	0.2749	0.721	0.5442	0.5492	0.0006	83
	rs6857578		17896563	0.2755	0.5129	0.5459	0.5498	0.00052	92
	rs6835889		17896783	0.2583	0.5369	0.9613	0.4944	0.00033	115
	rs2320566		17908729	0.2591	0.5379	0.8846	0.4348	0.00025	143
	rs7679575		17911601	0.2601	0.5798	0.9615	0.4651	0.00028	133
	rs2080231		17912133	0.2607	0.6222	0.5284	0.3157	0.00028	131
	rs1503865		17913113	0.2655	0.8083	0.7746	0.4243	0.00027	135
	rs6811915		17919583	0.2699	0.8564	0.3708	0.5795	0.00037	110
	rs1503890		17925211	0.2731	0.5907	0.8516	0.4717	0.00026	137
4	Best: rs17035797 (3)	Gene	158.43-158.43Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17035797	GLRB NCBI Gene Pubmed Genecard	158430043	0.07442	1.375e-10	0.9056	1.286e-09	0.00052	93
	rs17035810	GLRB NCBI Gene Pubmed Genecard	158432108	0.0891	0.1425	0.9091	0.9104	0.00019	170
	rs17035814	GLRB NCBI Gene Pubmed Genecard	158432547	0.08857	0.1051	0.6444	0.735	0.00017	186
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	0.1633	0.9299	0.7876	0.8397	0.00017	184
	rs11936062	ACSL1 NCBI Gene Pubmed Genecard SLED1 NCBI Gene Pubmed Genecard	186096519	0.163	0.8596	0.9459	0.7936	0.00016	193
	rs13126272	ACSL1 NCBI Gene Pubmed Genecard	186107089	0.3377	5.003e-58	0.03015	3.653e-05	0.0062	11
5	Best: rs17234657 (9)	Gene	40.37-40.52Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1186661		40367121	0.1325	0.3797	0.002757	1.548e-12	0.00062	79
	rs16869934		40433109	0.2672	0.2206	0.7542	1.523e-11	0.00018	175
	rs17234657		40437266	0.1455	0.4183	0.3518	2.369e-13	0.00072	68
	rs9292777		40473705	0.3665	0.124	0.3337	7.534e-13	0.00025	142
	rs10213846		40478626	0.2993	0.3793	0.556	1.776e-12	0.00018	177
	rs11957215		40481438	0.2998	0.4515	0.556	1.277e-12	0.00018	179
	rs4957295		40483754	0.3012	0.2608	0.5856	1.879e-12	0.00019	172
	rs4957297		40490831	0.2996	0.2586	0.5845	2.45e-12	0.0002	163
	rs6871834		40515944	0.2966	0.1658	0.6726	4.268e-12	0.00019	167
5	Best: rs2416472 (16)	Gene	117.00-117.07Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs397925		116998548	0.3358	0.1793	0.7095	0.9279	0.0004	104
	rs9327047		116999827	0.2357	0.3191	0.5731	1	0.00041	103
	rs434363		117000415	0.3441	0.5598	0.7746	0.9462	0.00046	98
	rs9327048		117001096	0.2339	0.423	0.7188	0.9799	0.00053	91
	rs384890		117001576	0.3431	0.3391	0.6822	0.982	0.00035	112
	rs371616		117001959	0.3451	0.4276	0.7437	0.8927	0.00048	96
	rs388811		117002034	0.3449	0.4576	0.6829	0.9283	0.00038	109
	rs392457		117002064	0.3436	0.4266	0.7123	0.9104	0.00048	97
	rs367474		117004156	0.3469	0.3669	0.7422	0.8213	0.00025	144
	rs2416472		117033845	0.3189	2.397e-17	0.9345	7.193e-12	0.0046	14
	rs17411921		117033876	0.3391	0.2187	0.3656	0.7865	0.0018	32
	rs7714451		117037818	0.2481	0.6101	0.8041	0.6924	0.0011	47
	rs1526882		117054771	0.07739	0.3889	0.8004	0.4718	0.00029	126
	rs17346822		117058221	0.09942	0.4093	0.3607	0.4321	0.00055	89
	rs6421871		117068096	0.1007	0.4076	1	0.2558	0.00064	77
	rs17142889		117068908	0.1372	0.4119	0.9383	0.6637	0.00089	61
6	Best: rs17083420 (3)	Gene	121.66-121.68Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17083385	C6orf170 NCBI Gene Pubmed Genecard	121660900	0.01185	1	0.3563	0.6933	0.00027	136
	rs17083389	C6orf170 NCBI Gene Pubmed Genecard	121662173	0.01185	1	0.3485	0.8437	0.00022	157
	rs17083420	C6orf170 NCBI Gene Pubmed Genecard	121683273	0.008823	3.453e-11	1	7.683e-07	0.0015	36
9	Best: rs302925 (13)	Gene	132.51-132.60Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7037273	DDX31 NCBI Gene Pubmed Genecard	132509241	0.11	0.5429	0.3451	0.8644	0.00024	149
	rs11243840	DDX31 NCBI Gene Pubmed Genecard	132510911	0.1084	1	0.7738	0.9452	0.00031	121
	rs7034065	DDX31 NCBI Gene Pubmed Genecard	132525974	0.1043	0.7059	0.07922	0.3932	0.00022	153
	rs10512415	DDX31 NCBI Gene Pubmed Genecard	132554633	0.1008	0.6868	0.6087	0.8579	0.00025	147
	rs4498679	DDX31 NCBI Gene Pubmed Genecard	132566094	0.1091	1	0.3431	0.9727	0.0002	161
	rs96153	GTF3C4 NCBI Gene Pubmed Genecard	132579647	0.4034	0.8817	0.701	0.7938	0.00025	141
	rs455764	GTF3C4 NCBI Gene Pubmed Genecard	132586345	0.4044	0.921	0.8181	0.7606	0.00022	152
	rs444197	GTF3C4 NCBI Gene Pubmed Genecard	132588057	0.4045	0.921	0.7884	0.7939	0.0003	125
	rs10901198	GTF3C4 NCBI Gene Pubmed Genecard	132588803	0.1189	0.9098	0.4786	0.7918	0.00028	130
	rs787240	GTF3C4 NCBI Gene Pubmed Genecard	132589693	0.4048	0.9605	0.8782	0.7773	0.00025	140
	rs567423	GTF3C4 NCBI Gene Pubmed Genecard	132591324	0.4043	0.8427	0.6179	0.8106	0.00022	158
	rs2772006		132596942	0.4048	1	0.8181	0.7773	0.00032	116
	rs302925		132602950	0.4753	4.665e-20	0.55	6.324e-06	0.0012	45
10	Best: rs7067790 (3)	Gene	125.67-125.67Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs769282		125666695	0.4153	0.6572	0.494	0.7947	0.0025	22
	rs7067790		125667027	0.391	4.183e-22	0.3557	1.101e-07	0.0078	9
	rs17680424		125667065	0.4107	0.6565	0.7031	0.9827	0.0034	18
11	Best: rs17116117 (17)	Gene	113.02-113.31Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17610557		113018709	0.1269	0.006757	0.3389	0.01123	0.00027	134
	rs17532157		113021980	0.1258	0.006766	0.1074	0.01706	0.00026	139
	rs17532479		113028191	0.127	0.00676	0.4256	0.01124	0.00032	118
	rs11606746		113042520	0.1246	0.01561	0.8071	0.009078	0.00028	129
	rs17611093		113053519	0.1255	0.004272	0.1696	0.01827	0.00023	150
	rs11604887		113108019	0.1207	0.0269	0.868	0.01154	0.00044	99
	rs17541153	ZW10 NCBI Gene Pubmed Genecard	113120832	0.1193	0.02694	0.2357	0.02956	0.00039	106
	rs1633550	USP28 NCBI Gene Pubmed Genecard	113174415	0.1228	0.03043	0.8693	0.02269	0.00056	86
	rs1633548	USP28 NCBI Gene Pubmed Genecard	113176716	0.1219	0.007761	0.5062	0.03357	0.00042	101
	rs2513574	USP28 NCBI Gene Pubmed Genecard	113186515	0.1218	0.004699	0.804	0.01149	0.00055	87
	rs2519200	USP28 NCBI Gene Pubmed Genecard	113190019	0.2377	0.03424	0.8808	0.05645	0.0003	123
	rs17116117	HTR3B NCBI Gene Pubmed Genecard	113306801	0.04869	0.0002921	0.116	1.03e-23	0.011	8
	rs17116145	HTR3B NCBI Gene Pubmed Genecard	113309536	0.02901	0.6371	0.5202	0.4452	0.00049	95
	rs1176741	HTR3B NCBI Gene Pubmed Genecard	113312525	0.03034	0.6448	0.1192	0.3501	0.00055	88
	rs1176740	HTR3B NCBI Gene Pubmed Genecard	113312606	0.03063	1	0.1206	0.4204	0.0006	82
	rs1176739	HTR3B NCBI Gene Pubmed Genecard	113313027	0.03086	1	0.3693	0.3544	0.00061	80
	rs1176738	HTR3B NCBI Gene Pubmed Genecard	113313305	0.03035	0.6448	0.1193	0.3501	0.0007	73
14	Best: rs234202 (6)	Gene	97.06-97.07Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7152926		97061670	0.01249	1	0.3325	0.4417	0.0002	165
	rs11850997		97064772	0.01239	1	1	0.2879	0.00029	128
	rs11846702		97064817	0.01249	1	0.3327	0.4418	0.00019	173
	rs234202		97066758	0.007656	1	1	1.208e-09	0.0014	37
	rs234205		97068179	0.01228	1	1	0.333	0.00031	120
	rs234206		97068727	0.01276	1	0.3415	0.3911	0.00015	199
16	Best: rs4471699 (3)	Gene	30.23-30.29Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4471699	LOC595101 NCBI Gene Pubmed Genecard	30227808	0.4485	2.313e-49	0.6026	4.639e-20	0.033	5
	rs11644392	LOC595101 NCBI Gene Pubmed Genecard	30235818	0.484	0.6991	0.6828	0.2196	0.013	7
	rs11863150	MYLPF NCBI Gene Pubmed Genecard	30293004	0.3655	0.6073	0.4977	0.6412	0.0041	15
16	Best: rs2076756 (3)	Gene	49.30-49.31Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17221417	NOD2 NCBI Gene Pubmed Genecard	49297083	0.313	0.01632	0.2236	4.587e-12	0.0003	122
	rs2066843	NOD2 NCBI Gene Pubmed Genecard	49302700	0.2851	0.001976	0.3607	5.456e-13	0.00064	76
	rs2076756	NOD2 NCBI Gene Pubmed Genecard	49314382	0.27	0.004606	0.7621	3.002e-15	0.0014	39