T-Trees

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

Supplementary data

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1	Best: rs12134541 (3)	Gene	118.80-118.81Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12134541		118796533	0.4779	0.5563	0.8542	0.6957	0.00029	77
	rs7413837		118797124	0.4734	0.08129	0.7686	0.4305	0.00017	121
	rs11590971		118811929	0.4783	0.5869	0.8543	0.7574	0.00012	161
1	Best: rs1923496 (2)	Gene	149.24-149.24Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6694145		149237898	0.3387	0.0765	0.2367	0.6956	0.0001	177
	rs1923496		149237921	0.332	0.7544	0.2336	0.1239	0.00015	126
1	Best: rs16837761 (2)	Gene	235.59-235.59Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	SNP_A-2266855		235586135	0.1652	0.0001482	0.2787	0.3044	9e-05	193
	rs16837761		235588822	0.165	0.08796	0.3847	0.6775	0.00014	139
2	Best: rs902133 (4)	Gene	10.90-10.93Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17456162	PDIA6 NCBI Gene Pubmed Genecard	10898688	0.212	0.1676	0.6259	0.2681	0.0012	31
	rs902133		10908783	0.005918	1	1	1.413e-16	0.0052	12
	rs1106184		10914125	0.3834	0.8495	1	0.1501	0.0002	103
	rs1734370		10929308	0.2923	0.9138	0.1958	0.3898	9.2e-05	192
2	Best: rs13394205 (2)	Gene	17.91-17.91Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs13394205		17907655	0.003901	1	0.1138	6.533e-09	0.00044	60
	rs10188361		17910426	0.004601	1	1	1	0.00022	95
2	Best: rs10188442 (4)	Gene	133.02-133.02Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7355605	GPR39 NCBI Gene Pubmed Genecard	133015798	0.1998	0.7196	1	0.4551	0.00019	109
	rs4592905	GPR39 NCBI Gene Pubmed Genecard	133021241	0.1997	0.7197	1	0.4249	0.00021	96
	rs4309626	GPR39 NCBI Gene Pubmed Genecard	133021612	0.2003	0.6675	1	0.4559	0.00015	129
	rs10188442	GPR39 NCBI Gene Pubmed Genecard	133022971	0.204	0.1653	1	0.7395	0.0006	46
3	Best: rs17046143 (2)	Gene	6.84-6.85Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17046139		6844166	0.06696	0.03024	0.2582	0.1275	9.2e-05	189
	rs17046143		6848446	0.00306	1	1	3.688e-11	0.0025	20
3	Best: rs4683064 (6)	Gene	45.11-45.16Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6775113	CDCP1 NCBI Gene Pubmed Genecard	45114105	0.1677	0.3889	0.1987	0.08652	0.00016	123
	rs6779858	CDCP1 NCBI Gene Pubmed Genecard	45123678	0.4264	0.675	0.6542	0.05548	0.00018	112
	rs6778556	CDCP1 NCBI Gene Pubmed Genecard	45128426	0.194	0.2243	1	0.5845	0.0001	173
	rs7625872	CDCP1 NCBI Gene Pubmed Genecard	45132572	0.1369	0.5697	0.8758	0.7194	0.0001	180
	rs4683064	CDCP1 NCBI Gene Pubmed Genecard	45160449	0.005455	1	1	4.585e-16	0.0054	11
	rs7622796	CDCP1 NCBI Gene Pubmed Genecard	45161724	0.4899	0.3647	0.06611	0.9179	9.4e-05	188
3	Best: rs3845903 (2)	Gene	66.60-66.60Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs3845903	LRIG1 NCBI Gene Pubmed Genecard	66600360	0.005735	1	1	3.743e-09	0.0005	53
	rs9846493	LRIG1 NCBI Gene Pubmed Genecard	66600833	0.0005065	1	1	0.3918	0.00021	97
3	Best: rs16858040 (3)	Gene	147.40-147.40Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16858032	PLSCR4 NCBI Gene Pubmed Genecard	147400873	0.004053	1	1	0.3334	0.00022	93
	rs16858035	PLSCR4 NCBI Gene Pubmed Genecard	147401964	0.004053	1	1	0.5193	0.00017	118
	rs16858040	PLSCR4 NCBI Gene Pubmed Genecard	147402096	0.002349	1	1	1.939e-08	0.00077	38
4	Best: rs615604 (3)	Gene	23.64-23.67Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10517032		23644651	0.06236	0.2674	0.0002599	0.3275	0.00013	149
	rs13119672		23660732	0.1372	0.02946	0.2162	1.688e-05	0.001	34
	rs615604		23665037	0.1553	0.161	0.73	0.4955	0.0034	15
4	Best: rs7666328 (6)	Gene	116.10-116.16Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4512014		116098512	0.01262	1	1	0.0004013	0.00032	73
	rs9999383	NDST4 NCBI Gene Pubmed Genecard	116138939	0.06074	0.152	0.5297	0.5184	0.0004	66
	rs7666328	NDST4 NCBI Gene Pubmed Genecard	116140909	0.0377	0.08569	0.002822	2.598e-14	0.0026	19
	rs9991654	NDST4 NCBI Gene Pubmed Genecard	116148684	0.1196	1	0.724	0.4468	0.00023	90
	rs10005762	NDST4 NCBI Gene Pubmed Genecard	116154592	0.118	0.917	0.3194	0.1908	0.00014	133
	rs7668760	NDST4 NCBI Gene Pubmed Genecard	116159126	0.1199	1	1	0.3752	0.00019	106
5	Best: rs12515142 (3)	Gene	36.46-36.46Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16903012		36457368	0.1979	0.7238	0.1473	0.7763	0.0001	175
	rs7735940		36459688	0.2408	0.09901	0.2159	0.1288	0.00015	130
	rs12515142		36462168	0.1398	0.6304	0.5986	0.4061	0.00022	92
6	Best: rs9357438 (6)	Gene	9.59-9.62Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2876167		9589358	0.3962	0.108	1	0.9496	0.00015	128
	rs9369420		9594453	0.2394	0.7576	0.6496	0.7539	0.00012	158
	rs1003063		9595662	0.04459	0.2736	0.08538	0.9206	0.00047	56
	rs9357438		9600144	0.04301	0.04685	0.04368	0.6477	0.0058	10
	rs9357440		9600379	0.0487	0.003836	0.00629	0.004517	0.0018	23
	rs9296475		9616633	0.44	0.2706	0.5032	0.9339	0.00023	89
6	Best: rs2621382 (4)	Gene	32.86-32.87Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17429127		32859592	0.06519	0.4377	0.05541	0.4046	0.00024	88
	rs9276712		32867230	0.06449	0.1143	0.2334	0.4257	0.00054	51
	rs2621382		32868423	0.4477	0.3355	0.8533	0.2145	0.00058	48
	rs2157082		32868692	0.423	1.024e-05	0.0003954	0.004056	0.00048	55
8	Best: rs2604383 (3)	Gene	15.70-15.70Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2604383		15700499	0.02748	0.1683	0.4055	0.001172	0.00014	138
	rs2721243		15702701	0.04167	0.2764	0.6281	0.2795	0.00011	172
	rs10091618		15703445	0.03955	0.1291	1	0.7507	9e-05	194
8	Best: rs2469997 (4)	Gene	120.42-120.43Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2469997		120422448	0.1865	0.3351	0.9035	0.7915	0.0012	30
	rs6469823		120423165	0.1818	0.8764	0.7613	0.2858	0.00016	125
	rs2447179		120424956	0.182	0.8767	0.8084	0.2743	0.00016	124
	rs2447178		120425369	0.1819	0.8764	0.8084	0.2741	0.00018	114
8	Best: rs1372662 (10)	Gene	135.58-135.67Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6421008	ZFAT NCBI Gene Pubmed Genecard	135581827	0.05382	0.1631	0.8609	0.3617	0.00042	63
	rs7386230	ZFAT NCBI Gene Pubmed Genecard	135595641	0.1104	0.09785	0.5191	0.4905	9e-05	195
	rs6578234	ZFAT NCBI Gene Pubmed Genecard	135635545	0.3333	0.5754	0.4086	0.9304	0.00045	58
	rs7827545	ZFAT NCBI Gene Pubmed Genecard	135635749	0.3217	4.033e-05	0.3015	0.006298	0.0028	18
	rs1372662	ZFAT NCBI Gene Pubmed Genecard	135636228	0.3328	0.6846	0.3422	0.8785	0.0075	7
	rs6578237	ZFAT NCBI Gene Pubmed Genecard	135638540	0.3324	0.6817	0.2806	0.7918	0.0012	28
	rs7846013	ZFAT NCBI Gene Pubmed Genecard	135639149	0.3308	0.4139	0.3845	0.9825	0.002	22
	rs7007819	ZFAT NCBI Gene Pubmed Genecard	135644921	0.3592	0.1664	0.8121	0.3034	0.00036	68
	rs6983560	ZFAT NCBI Gene Pubmed Genecard	135653735	0.2413	0.398	0.1869	0.156	0.0011	32
	rs16905189	ZFAT NCBI Gene Pubmed Genecard	135667314	0.3606	0.8843	0.2799	0.145	0.00017	116
9	Best: rs2458879 (10)	Gene	117.77-117.81Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1271480		117768477	0.4322	0.1986	0.05154	0.2447	0.00031	76
	rs643215		117777505	0.4335	0.2918	0.05154	0.2532	0.00018	115
	rs2466429		117780847	0.4291	0.5486	0.003318	0.2262	0.00022	94
	rs2458879		117783588	0.3856	0.388	0.847	0.4464	0.0091	5
	rs488101		117787179	0.3633	5.561e-06	0.5866	4.696e-07	0.0038	14
	rs16906491		117799130	0.005371	1	1	0.5766	0.00041	64
	rs2151370		117804641	0.3789	0.8846	0.7863	0.2109	0.0029	17
	rs2151369		117804765	0.1811	0.05594	0.5788	0.8937	0.00013	142
	rs2151368		117804779	0.1815	0.09167	0.5381	0.8307	9.7e-05	185
	rs2780244		117808231	0.3812	0.6991	0.5872	0.2695	0.0012	29
10	Best: rs2601749 (4)	Gene	14.82-14.82Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1955196	FAM107B NCBI Gene Pubmed Genecard	14820745	0.4078	0.6749	0.8789	0.3145	0.00017	119
	rs7075577	FAM107B NCBI Gene Pubmed Genecard	14821059	0.3825	0.07044	1	0.3738	0.00013	150
	rs2601751	FAM107B NCBI Gene Pubmed Genecard	14821179	0.4075	0.7799	0.9393	0.2411	0.00013	148
	rs2601749	FAM107B NCBI Gene Pubmed Genecard	14821336	0.4013	0.7795	0.01153	0.03485	0.00024	87
10	Best: rs3122348 (15)	Gene	30.97-31.06Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs3122344		30969266	0.2527	0.5911	0.6973	0.8312	0.00028	81
	SNP_A-2100739		30990735	0.08045	0.2412	0.7978	0.241	0.0074	8
	rs3122348	LOC645954 NCBI Gene Pubmed Genecard	30991151	0.03374	4.725e-06	1	6.122e-96	0.055	1
	rs7083541	LOC645954 NCBI Gene Pubmed Genecard	30997484	0.489	0.1893	0.6073	0.2749	0.00049	54
	rs11008174	LOC645954 NCBI Gene Pubmed Genecard	31010206	0.2486	0.5797	1	0.3056	0.00015	127
	rs4749580	LOC645954 NCBI Gene Pubmed Genecard	31014180	0.4169	0.6078	0.6244	0.3581	0.00034	71
	rs16930315	LOC645954 NCBI Gene Pubmed Genecard	31017645	0.1085	0.7261	0.5706	0.9472	0.00021	101
	rs7078126	LOC645954 NCBI Gene Pubmed Genecard	31024312	0.07923	0.7591	1	0.849	0.022	3
	rs7093972	LOC645954 NCBI Gene Pubmed Genecard	31024349	0.07818	0.6394	0.523	0.8782	0.0097	4
	rs10437404	LOC645954 NCBI Gene Pubmed Genecard	31037243	0.3487	0.3408	0.1374	0.3532	0.00044	59
	rs16930258	LOC645954 NCBI Gene Pubmed Genecard	31037513	0.08511	0.1682	0.2567	0.1612	0.00029	80
	rs7910154	LOC645954 NCBI Gene Pubmed Genecard	31040399	0.1357	0.6948	0.5372	0.4891	0.00013	151
	rs10763821	LOC645954 NCBI Gene Pubmed Genecard	31040907	0.1372	0.5571	0.4444	0.419	0.00014	134
	rs3858241	LOC645954 NCBI Gene Pubmed Genecard	31041299	0.06603	1	0.02188	0.5615	0.0042	13
	rs1494134		31057878	0.1468	0.463	0.4684	0.5415	0.00034	70
10	Best: rs11005510 (10)	Gene	58.18-58.29Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11005491		58177677	0.08391	1	0.002518	0.8818	0.00011	166
	rs11005493		58178940	0.09669	0.6962	0.02805	0.8074	0.00065	45
	rs11005494		58179408	0.3148	0.464	0.007322	0.8593	9.9e-05	182
	rs11005497		58179944	0.09678	0.7926	0.03679	0.7019	0.00032	74
	rs1915936		58202771	0.08881	0.4798	0.1751	0.8282	0.0018	24
	rs11005510		58202995	0.01019	1	1	1.273e-20	0.0076	6
	rs10509061		58211893	0.4682	0.4958	0.6065	0.6207	0.00014	135
	rs7069529		58221174	0.447	0.7489	0.1469	0.2455	9.7e-05	184
	rs1925315		58261483	0.05435	0.08575	0.2741	0.586	0.00017	120
	rs1608110		58285889	0.0415	0.1809	0.08828	0.1634	0.00045	57
10	Best: rs16909905 (2)	Gene	58.39-58.41Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2393191		58394623	0.01562	0.3097	0.571	0.2463	0.00066	43
	rs16909905		58410545	0.01198	1	0.3529	0.9247	0.00067	42
10	Best: rs7918047 (2)	Gene	131.97-132.00Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7080464		131974739	0.03085	0.04696	0.4053	5.071e-08	0.001	35
	rs7918047		132001099	0.05836	0.09054	0.4042	0.8607	0.0017	25
11	Best: rs16916476 (5)	Gene	27.01-27.04Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10501072		27008990	0.2507	0.3385	0.7306	0.5842	0.00019	110
	rs10501074		27009369	0.416	0.02558	0.7906	0.5299	9.8e-05	183
	rs16916476	BBOX1 NCBI Gene Pubmed Genecard	27019064	0.004885	1	1	9.293e-17	0.0066	9
	rs7119888	BBOX1 NCBI Gene Pubmed Genecard	27035886	0.3583	0.2426	0.6299	0.1832	0.00011	170
	rs11029818	BBOX1 NCBI Gene Pubmed Genecard	27039881	0.0007097	1	1	1	0.00042	62
16	Best: rs6499937 (4)	Gene	56.73-56.75Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1006438		56730104	0.06616	0.8587	1	0.6489	0.00018	113
	rs4784901	CSNK2A2 NCBI Gene Pubmed Genecard	56751827	0.1711	0.6871	0.7002	0.6037	0.00054	52
	rs6499937	CSNK2A2 NCBI Gene Pubmed Genecard	56753662	0.005612	1	1	1.295e-08	0.001	33
	rs7185886	CSNK2A2 NCBI Gene Pubmed Genecard	56754237	0.01176	1	0.3445	0.924	0.0007	41
16	Best: rs2133803 (4)	Gene	59.66-59.67Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4785146		59658897	0.408	0.4798	0.6497	0.3349	0.00012	157
	rs12935144		59665165	0.406	0.8503	0.2689	0.4742	0.00012	159
	rs8062408		59665530	0.1355	0.5134	0.8714	0.1019	0.00015	131
	rs2133803		59665671	0.4591	0.6171	0.1195	0.1419	0.00019	108
17	Best: rs1873598 (3)	Gene	70.50-70.58Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1873598	CDR2L NCBI Gene Pubmed Genecard	70504641	0.001834	1	1	5.417e-08	0.00066	44
	rs4789124	CDR2L NCBI Gene Pubmed Genecard	70506972	0.003548	1	1	0.731	0.00035	69
	rs6501756	LOC100996374 NCBI Gene Pubmed Genecard	70582337	0.03232	0.03981	0.5199	0.08077	0.00011	164
19	Best: rs12980129 (2)	Gene	22.69-22.70Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16999569		22694550	0.02625	0.7175	0.4054	0.00998	0.00011	168
	rs12980129		22700751	0.0277	0.5143	1	0.0003348	0.00014	136
20	Best: rs200759 (2)	Gene	15.55-15.55Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs200752	MACROD2 NCBI Gene Pubmed Genecard	15547531	0.1158	0.6024	0.3028	0.03071	0.00011	162
	rs200759	MACROD2 NCBI Gene Pubmed Genecard	15554421	0.113	0.823	0.1692	0.871	0.00042	61
22	Best: rs10212068 (8)	Gene	35.92-35.99Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16997923		35923326	0.001733	1	1	0.323	0.00022	91
	rs69264	SSTR3 NCBI Gene Pubmed Genecard	35928450	0.197	0.1682	0.4554	0.4689	0.00021	100
	rs4821602	SSTR3 NCBI Gene Pubmed Genecard	35933689	0.4937	0.892	0.7973	0.7731	0.00027	83
	rs13053175		35937809	0.4367	0.1965	0.7377	0.3397	0.00029	79
	rs1476002	RAC2 NCBI Gene Pubmed Genecard	35955288	0.1188	0.01775	2.898e-05	0.7987	0.00011	171
	rs6000632		35968615	0.2593	0.4375	0.5669	0.7228	0.00018	111
	rs10212068		35969121	0.02785	1	0.002604	7.425e-62	0.031	2
	rs5750402		35985788	0.1739	0.1084	0.8959	0.1343	0.0006	47
23	Best: SNP_A-1998393 (2)	Gene	24.36-24.44Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6526393	PCYT1B NCBI Gene Pubmed Genecard	24355404	0.01625	1	0.3149	0.7827	0.00013	147
	SNP_A-1998393		24435950	0.01139	0.0004369	0.05584	3.782e-07	0.00081	37
23	Best: rs5951179 (8)	Gene	70.86-70.96Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6625898		70861066	0.04722	1	0.2286	0.04832	0.00025	85
	rs6525524		70877954	0.04115	1	1	0.04641	0.00032	75
	rs6525525		70877990	0.04104	0.6796	1	0.06894	0.0002	105
	rs11094231		70885810	0.06505	0.661	0.8265	0.1709	0.00013	144
	rs6624585	NHSL2 NCBI Gene Pubmed Genecard	70943258	0.07536	0.4339	1	0.2519	0.00011	165
	rs5951180	NHSL2 NCBI Gene Pubmed Genecard	70946225	0.1203	0.4216	0.05262	0.943	0.00033	72
	rs5951179	NHSL2 NCBI Gene Pubmed Genecard	70949622	0.04122	0.2565	0.7934	0.0002621	0.0034	16
	rs7878231	NHSL2 NCBI Gene Pubmed Genecard	70961868	0.04442	1	0.7859	0.1585	0.002	21
23	Best: rs5938070 (5)	Gene	74.40-74.45Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2367177	ZDHHC15 NCBI Gene Pubmed Genecard	74400509	0.02463	0.3386	0.304	0.02334	0.00013	145
	rs2146767	ZDHHC15 NCBI Gene Pubmed Genecard	74420469	0.02662	1	0.6329	0.001825	0.00074	40
	rs4892579	ZDHHC15 NCBI Gene Pubmed Genecard	74428079	0.02725	0.372	0.6376	0.003325	0.00076	39
	rs4892583	ZDHHC15 NCBI Gene Pubmed Genecard	74448870	0.027	0.3596	1	0.003164	0.00013	146
	rs5938070	ZDHHC15 NCBI Gene Pubmed Genecard	74450099	0.02472	1	0.6378	8.33e-07	0.0015	26