T-Trees

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

Supplementary data

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1	Best: rs11209026 (10)	Gene	67.31-67.46Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7515029		67308393	0.03591	0.5289	0.19	5.012e-10	0.0017	14
	rs4655679		67311678	0.2728	0.2111	0.2108	6.104e-08	0.00021	158
	rs17375018	IL23R NCBI Gene Pubmed Genecard	67367168	0.2828	0.09486	0.3822	1.533e-08	0.00031	84
	rs11805303	IL23R NCBI Gene Pubmed Genecard	67387537	0.3442	0.545	0.1357	1.239e-12	0.00064	40
	rs10489629	IL23R NCBI Gene Pubmed Genecard	67400370	0.4296	0.5063	0.3479	8.652e-12	0.00035	74
	SNP_A-2045577		67401629	0.3029	0.2185	0.5557	1.362e-09	0.00035	73
	rs2201841	IL23R NCBI Gene Pubmed Genecard	67406223	0.3445	0.419	0.2885	1.405e-11	0.00073	35
	rs11209026	IL23R NCBI Gene Pubmed Genecard	67417979	0.0451	1	3.524e-05	8.238e-18	0.014	1
	rs11209033		67456521	0.3505	0.339	0.3563	3.334e-10	0.0003	88
	rs12119179		67459436	0.3502	0.3142	0.3547	1.546e-10	0.00051	51
2	Best: rs3755076 (2)	Gene	45.58-45.58Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4455206	SRBD1 NCBI Gene Pubmed Genecard	45580716	0.08681	0.001621	0.0775	0.6214	0.00018	195
	rs3755076	SRBD1 NCBI Gene Pubmed Genecard	45581000	0.08665	0.002645	0.006018	0.518	0.00053	48
2	Best: rs11887827 (17)	Gene	81.58-81.76Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17020238		81577055	0.152	0.1613	1	0.9523	0.00018	193
	rs17020239		81577090	0.1482	0.1543	0.9416	0.928	0.00023	133
	rs11887827		81577812	0.3109	1.536e-07	1	2.423e-08	0.0013	20
	rs12623313		81581046	0.1486	0.2162	1	1	0.00024	117
	rs10520335		81581185	0.1485	0.1559	0.9416	0.9041	0.00031	85
	rs7593114		81585945	0.326	0.9116	0.9668	0.1436	0.00023	125
	rs9646997		81586635	0.1489	0.08993	0.8838	0.8333	0.00023	124
	rs12613517	LOC100507201 NCBI Gene Pubmed Genecard	81599721	0.1488	0.1855	1	0.9043	0.00017	200
	rs11689930	LOC100507201 NCBI Gene Pubmed Genecard	81600746	0.1489	0.2564	1	0.9521	0.00022	135
	rs7575690	LOC100507201 NCBI Gene Pubmed Genecard	81601874	0.1492	0.1878	1	0.9044	0.00021	153
	rs17020333	LOC100507201 NCBI Gene Pubmed Genecard	81602132	0.1494	0.1864	0.942	0.9761	0.00024	116
	rs12468325	LOC100507201 NCBI Gene Pubmed Genecard	81602238	0.3259	0.8247	1	0.1778	0.00019	176
	rs6725541		81671346	0.2426	0.5888	0.2783	0.04063	0.00021	146
	rs7578937		81712443	0.2417	0.4155	0.299	0.04018	0.00022	141
	rs12464902		81724164	0.06435	0.2044	0.4574	0.2758	0.00052	50
	rs7607015		81724939	0.06761	0.3123	0.2548	0.3055	0.00045	56
	rs17020570		81758512	0.1311	0.4631	0.7448	0.8491	0.0002	161
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	0.4515	0.425	0.01984	2.216e-13	0.0028	6
	rs6752107	ATG16L1 NCBI Gene Pubmed Genecard	233943448	0.4516	0.3973	0.02188	3.605e-13	0.0026	8
	rs6431654	ATG16L1 NCBI Gene Pubmed Genecard	233943769	0.4508	0.4848	0.02906	2.548e-13	0.0027	7
	rs3828309	ATG16L1 NCBI Gene Pubmed Genecard	233962410	0.452	0.5175	0.02892	1.185e-12	0.0017	15
	rs3792106	ATG16L1 NCBI Gene Pubmed Genecard	233972740	0.3968	0.1417	0.02814	3.323e-11	0.0016	18
3	Best: rs11718165 (6)	Gene	49.43-49.68Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs9814873	AMT NCBI Gene Pubmed Genecard TCTA NCBI Gene Pubmed Genecard	49429116	0.3054	0.2312	0.006667	1.201e-05	0.00022	142
	rs11715915	AMT NCBI Gene Pubmed Genecard	49430334	0.305	0.1256	0.008719	2.938e-05	0.00019	178
	rs1801143	DAG1 NCBI Gene Pubmed Genecard	49545204	0.3127	0.004583	0.3299	1.14e-05	0.00026	100
	rs9827708	BSN NCBI Gene Pubmed Genecard	49624993	0.3073	0.01567	0.2256	1.954e-06	0.00034	79
	rs11718165	BSN NCBI Gene Pubmed Genecard	49671801	0.2947	0.01334	0.01604	1.7e-06	0.0012	24
	rs9858542	BSN NCBI Gene Pubmed Genecard	49676987	0.3002	0.004826	0.1858	5.775e-07	0.00078	30
4	Best: rs17045935 (2)	Gene	114.61-114.62Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17045935	ANK2 NCBI Gene Pubmed Genecard	114612173	0.09479	0.2384	0.0001068	0.05276	0.00065	39
	rs2272229	ANK2 NCBI Gene Pubmed Genecard	114618245	0.0964	0.1528	0.002778	0.09526	0.00019	168
5	Best: rs16893874 (3)	Gene	24.77-24.77Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16893872		24765763	0.008021	0.2605	1	3.176e-05	0.00027	94
	rs16893874		24766201	0.008025	0.2605	1	3.181e-05	0.00033	80
	rs1820873		24767148	0.007918	0.2507	1	4.883e-05	0.00026	99
5	Best: rs17234657 (12)	Gene	40.43-40.61Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10512734		40429362	0.2853	0.4381	0.6972	6.014e-11	0.00038	65
	rs16869934		40433109	0.267	0.3042	0.7541	1.002e-11	0.00054	47
	rs17234657		40437266	0.1455	0.4176	0.3509	1.723e-13	0.0023	10
	rs9292777		40473705	0.3663	0.1364	0.3147	5.787e-13	0.00079	29
	rs10213846		40478626	0.2989	0.4488	0.5558	8.037e-13	0.00073	34
	rs11957215		40481438	0.2994	0.5286	0.5283	5.777e-13	0.00059	43
	rs4957295		40483754	0.3008	0.3454	0.5853	7.323e-13	0.00062	41
	rs4957297		40490831	0.2991	0.3435	0.556	1.115e-12	0.00058	45
	rs4957300		40499496	0.2995	0.3456	0.6135	2.298e-12	0.0005	52
	rs6871834		40515944	0.2962	0.2281	0.6724	1.963e-12	0.0007	36
	rs1505992		40534334	0.2911	0.4481	0.01437	1.201e-09	0.00065	38
	rs10055860		40605710	0.2685	0.7378	0.05918	5.597e-09	0.00018	190
5	Best: rs17149128 (2)	Gene	121.75-121.76Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17149115	SNCAIP NCBI Gene Pubmed Genecard	121754022	0.1274	0.007881	0.01128	0.4605	0.00017	197
	rs17149128	SNCAIP NCBI Gene Pubmed Genecard	121757816	0.1218	0.01098	0.01025	0.4098	0.0002	166
5	Best: rs931058 (4)	Gene	150.21-150.31Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11957134		150211143	0.07842	0.7856	0.5529	1.098e-07	0.00024	118
	rs1000113		150220269	0.07855	0.7862	0.7665	7.256e-08	0.00023	131
	rs11747270		150239060	0.07982	0.8934	0.6593	5.415e-08	0.00036	70
	rs931058		150313891	0.0714	0.5636	1	1.533e-08	0.00058	44
6	Best: rs600382 (2)	Gene	36.54-36.64Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16888603	KCTD20 NCBI Gene Pubmed Genecard	36540683	0.001711	1	1	4.904e-05	0.00022	138
	rs600382		36637009	0.001498	1	1	2.381e-05	0.00027	95
8	Best: rs10216909 (4)	Gene	129.88-129.96Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2056312		129876753	0.004174	1	1	0.0002032	0.00021	152
	rs16903632		129895741	0.003318	1	1	0.0002341	0.00019	180
	rs10216909		129924647	0.003212	1	1	7.763e-05	0.0003	87
	rs10094461		129956367	0.003104	1	1	0.0001462	0.00025	105
10	Best: rs16919914 (2)	Gene	65.96-65.96Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16919914		65959109	0.08018	0.08798	0.0003998	0.2221	0.00052	49
	rs10509208		65959288	0.09036	0.00833	0.006474	0.8813	0.00025	112
11	Best: rs1533339 (2)	Gene	130.84-130.84Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11222657	NTM NCBI Gene Pubmed Genecard	130840786	0.005241	1	1	0.000278	0.00019	173
	rs1533339	NTM NCBI Gene Pubmed Genecard	130841983	0.005241	1	1	0.000278	0.00021	145
16	Best: rs2076756 (4)	Gene	49.30-49.32Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17221417	NOD2 NCBI Gene Pubmed Genecard	49297083	0.3128	0.01604	0.2237	6.878e-12	0.00077	32
	rs2066843	NOD2 NCBI Gene Pubmed Genecard	49302700	0.2851	0.001923	0.3608	5.959e-13	0.0021	12
	rs2076756	NOD2 NCBI Gene Pubmed Genecard	49314382	0.2699	0.004495	0.7621	3.952e-15	0.0039	4
	rs3135499	NOD2 NCBI Gene Pubmed Genecard	49323628	0.4071	0.2343	0.2568	1.137e-08	0.00018	188
23	Best: rs6522332 (2)	Gene	89.59-89.64Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6522332		89587898	0.1601	0.3096	0.5495	0.3232	0.00021	155
	rs2755536		89636970	0.1494	0.4004	1	0.2356	0.00019	183