T-Trees

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

Supplementary data

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1	Best: rs1896250 (6)	Gene	80.57-80.57Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1365752		80568982	0.3763	0.3131	0.4782	0.5226	0.00096	65
	rs1365754		80569197	0.3834	0.2155	0.3474	0.4197	0.00025	159
	rs1896250		80569215	0.3973	6.966e-08	0.9372	8.255e-05	0.0011	54
	rs1549553		80569915	0.3764	0.3129	0.5025	0.5085	0.00028	146
	rs1549556		80570515	0.385	0.1521	0.5571	0.4437	0.00051	97
	rs1549557		80570530	0.3768	0.3129	0.6082	0.5504	0.00065	80
1	Best: rs825148 (5)	Gene	219.91-219.97Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1518038	SUSD4 NCBI Gene Pubmed Genecard	219910553	0.1048	0.5751	0.2483	0.00528	0.00064	82
	rs12074782		219946890	0.04217	1	0.6574	0.6074	0.00063	83
	rs2678370		219965833	0.04058	0.3657	0.2381	0.7139	0.0017	41
	rs2678369		219965851	0.04082	0.7674	0.2388	0.7543	0.00097	64
	rs825148		219967019	0.05298	2.41e-210	0.01382	5.213e-13	0.031	2
2	Best: rs2164411 (3)	Gene	25.31-25.36Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs874401		25313931	0.1791	0.7664	0.4804	0.1004	0.0003	133
	rs4665287		25324960	0.1758	0.7049	0.2974	0.1287	0.00022	177
	rs2164411		25364557	0.1614	3.202e-07	0.1946	0.4748	0.00042	107
2	Best: rs1870340 (3)	Gene	96.53-96.54Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12052336		96528325	0.01865	1	1	0.7032	0.00027	153
	rs1870340		96538827	0.02738	3.159e-122	0.6301	4.889e-08	0.008	16
	rs12614696		96540831	0.01957	1	0.6325	0.5511	0.0038	27
2	Best: rs935019 (4)	Gene	127.16-127.17Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs935019	GYPC NCBI Gene Pubmed Genecard	127162719	0.2605	5.856e-13	0.8874	0.009614	0.00092	66
	rs10174588		127171100	0.3401	0.298	0.8027	0.02925	0.00091	68
	rs17014263		127173698	0.09277	0.8938	0.6585	0.8308	0.00054	94
	rs7597899		127173990	0.09246	1	0.6584	0.9148	0.00037	115
2	Best: rs12694298 (2)	Gene	213.89-213.89Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16849921		213886528	0.2533	0.8622	0.002875	0.008286	0.00024	162
	rs12694298		213887413	0.1047	0.6202	0.2792	0.7589	0.00025	160
3	Best: rs804974 (3)	Gene	121.76-121.83Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs805009		121763466	0.4525	0.8551	0.7093	0.678	0.00017	196
	rs804980		121826456	0.2257	2.675e-13	0.9562	0.001511	0.0014	49
	rs804974	HGD NCBI Gene Pubmed Genecard	121834481	0.2146	0.9476	0.8676	0.1995	0.0016	43
4	Best: rs16837871 (6)	Gene	6.04-6.06Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4443226	MIR378D1 NCBI Gene Pubmed Genecard	6042701	0.3276	0.4113	0.1764	0.4655	0.00018	193
	rs7679272		6057618	0.2297	0.3671	0.7932	0.9803	0.00045	104
	rs16837871		6059184	0.1478	8.617e-23	0.2844	1.753e-28	0.011	11
	rs7664218		6060685	0.1851	0.7649	0.462	0.9153	0.0059	19
	rs7664229		6060707	0.1849	0.8227	0.5801	0.8107	0.0059	20
	rs7691494		6060721	0.1852	0.823	0.5398	0.8317	0.0086	15
4	Best: rs1553460 (9)	Gene	17.85-17.90Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1039539		17850862	0.258	0.5536	0.3804	0.7214	0.00061	86
	rs17523800		17870443	0.3665	0.09689	0.9367	0.8638	0.00042	109
	rs11938418		17871212	0.2839	0.9115	0.03268	0.9088	0.0011	58
	rs1553460		17872130	0.3102	1.415e-94	2.877e-05	2.415e-24	0.012	8
	rs1503880		17878437	0.2783	0.9544	0.339	0.2787	0.0018	39
	rs1503881		17878898	0.2723	0.195	0.3237	0.2757	0.0021	38
	rs1503882		17878953	0.2718	0.1762	0.3966	0.2364	0.0013	52
	rs4698673		17885266	0.276	0.1446	0.5442	0.3793	0.00086	71
	rs6857578		17896563	0.2783	0.2021	0.5459	0.1813	0.00053	95
4	Best: rs615604 (3)	Gene	23.66-23.67Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs13119672		23660732	0.1364	0.02805	0.2414	8.542e-06	0.00041	110
	rs615604		23665037	0.1547	0.1571	0.8345	0.4239	0.0008	74
	rs582804		23668742	0.1542	0.157	0.9443	0.4571	0.00037	116
4	Best: rs6840033 (8)	Gene	141.58-141.62Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs868653	LOC100129858 NCBI Gene Pubmed Genecard SCOC NCBI Gene Pubmed Genecard	141577389	0.08771	0.164	0.09089	0.3549	0.0004	112
	rs883455	LOC100129858 NCBI Gene Pubmed Genecard SCOC NCBI Gene Pubmed Genecard	141582852	0.07441	0.7398	0.595	0.7829	0.00034	125
	rs6840033	LOC100129858 NCBI Gene Pubmed Genecard SCOC NCBI Gene Pubmed Genecard	141586466	0.2063	4.642e-19	0.9156	2.345e-11	0.0032	31
	rs7678137	LOC100129858 NCBI Gene Pubmed Genecard SCOC NCBI Gene Pubmed Genecard	141594739	0.07444	0.2306	0.06637	0.4085	0.00018	192
	rs6825404	LOC100129858 NCBI Gene Pubmed Genecard SCOC NCBI Gene Pubmed Genecard	141605361	0.1182	0.08176	0.8598	0.9236	0.00076	76
	rs10519535	LOC100129858 NCBI Gene Pubmed Genecard SCOC NCBI Gene Pubmed Genecard	141607267	0.09924	0.03706	0.6119	0.5571	0.00023	171
	rs12509386	LOC100129858 NCBI Gene Pubmed Genecard SCOC NCBI Gene Pubmed Genecard	141611515	0.1118	0.2054	1	0.7932	0.0009	70
	rs16998462	LOC100129858 NCBI Gene Pubmed Genecard SCOC NCBI Gene Pubmed Genecard	141622476	0.1122	0.1344	1	0.7683	0.00047	99
6	Best: rs4072775 (4)	Gene	18.17-18.19Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12527940		18165784	0.3201	0.9577	0.7693	0.04881	0.00017	195
	rs10456820		18180845	0.2083	0.571	0.2888	0.3408	0.00059	88
	rs4072775		18188230	0.3476	3.025e-07	2.709e-06	0.09051	0.0012	53
	rs16870039		18188344	0.1885	3.727e-08	0.0717	7.673e-06	0.00065	81
6	Best: rs6903505 (2)	Gene	91.73-91.73Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7775358		91726062	0.4249	0.0004301	0.9088	0.02327	0.00017	194
	rs6903505		91728665	0.4049	0.373	0.7591	0.7684	0.00023	167
6	Best: rs4131463 (5)	Gene	99.33-99.36Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7772259		99326572	0.06345	0.02082	0.5326	1	0.00029	143
	rs10499023		99333450	0.2622	0.4742	0.9249	0.1885	0.00025	158
	rs12661050		99340992	0.3727	0.4973	0.09727	0.9829	0.00023	168
	rs4839985		99354647	0.3248	0.7564	0.9665	0.8599	0.0003	134
	rs4131463		99364552	0.0497	5.27e-202	0.1821	7.382e-14	0.028	3
6	Best: rs10499044 (3)	Gene	107.25-107.26Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6940205		107247939	0.2265	0.1412	0.5957	0.4896	0.0002	186
	rs10499044		107247988	0.1045	2.371e-18	0.001966	6.596e-13	0.0015	47
	rs2798360		107255166	0.1461	0.1762	0.9404	0.6596	0.001	59
7	Best: rs1528356 (14)	Gene	120.71-120.72Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1919096		120707046	0.05549	1	1	0.4704	0.00047	100
	rs1919095		120707076	0.05482	0.654	0.861	0.525	0.00042	108
	rs2896304		120708523	0.05576	1	0.8638	0.417	0.00061	87
	rs4727930		120708949	0.05516	1	1	0.4417	0.00026	155
	rs10229163		120712149	0.05462	0.1677	0.5996	0.3877	0.00024	161
	rs10261636		120712512	0.04951	0.3176	0.03192	0.5022	0.00022	173
	rs4451245		120715189	0.05543	1	1	0.4704	0.0004	111
	rs1528358		120715223	0.05627	0.654	0.6151	0.2433	0.0047	24
	rs1528356		120715406	0.06613	7.097e-264	0.004003	3.198e-22	0.038	1
	rs1534528		120715973	0.05716	1	0.7434	0.1071	0.0015	45
	rs7793149		120716897	0.05523	1	1	0.4427	0.00055	93
	rs4731018		120717374	0.05517	1	0.8612	0.5874	0.00029	141
	rs4731020		120717469	0.05125	0.02079	0.002834	0.2595	0.0017	40
	rs10235141		120720024	0.05504	1	1	0.4147	0.00032	130
8	Best: rs7837736 (6)	Gene	15.34-15.37Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7837736		15341074	0.1218	2.916e-75	0.1452	1.345e-102	0.026	4
	rs1908465		15352804	0.2839	0.03695	0.5201	0.1759	0.0074	17
	rs7833963		15354189	0.04657	0.04943	0.001786	0.2803	0.00032	129
	rs10098376		15356646	0.0615	0.6788	0.7547	0.3211	0.00019	189
	rs17576874		15367926	0.2038	0.1693	0.002803	0.4419	0.0002	185
	rs17576922		15368930	0.1964	0.1577	0.002574	0.4352	0.00021	179
8	Best: rs3018857 (2)	Gene	95.09-95.09Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2978169		95092674	0.07874	0.1152	0.3971	0.002227	0.00029	139
	rs3018857		95093002	0.06524	0.8464	0.6568	0.4029	0.00056	92
8	Best: rs7012271 (2)	Gene	114.39-114.43Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7012271	CSMD3 NCBI Gene Pubmed Genecard	114386848	0.3159	0.9167	0.9319	0.9116	0.00062	85
	rs4437686	CSMD3 NCBI Gene Pubmed Genecard	114426589	0.3254	0.06122	0.7636	0.02899	0.00017	199
8	Best: rs2469997 (2)	Gene	120.42-120.42Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2469997		120422448	0.1866	0.2659	0.8546	0.7703	0.00077	75
	rs6469823		120423165	0.1815	1	0.7135	0.2837	0.00019	190
8	Best: rs1372662 (7)	Gene	135.63-135.65Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6988000	ZFAT NCBI Gene Pubmed Genecard	135628716	0.2412	0.8547	0.08362	0.3587	0.00069	78
	rs6578234	ZFAT NCBI Gene Pubmed Genecard	135635545	0.3332	0.5069	0.3825	0.9301	0.00029	136
	rs7827545	ZFAT NCBI Gene Pubmed Genecard	135635749	0.3218	1.923e-05	0.2795	0.006527	0.0017	42
	rs1372662	ZFAT NCBI Gene Pubmed Genecard	135636228	0.3329	0.5758	0.3388	0.8609	0.0048	23
	rs6578237	ZFAT NCBI Gene Pubmed Genecard	135638540	0.3325	0.572	0.2775	0.8081	0.00053	96
	rs7846013	ZFAT NCBI Gene Pubmed Genecard	135639149	0.3309	0.3064	0.3379	1	0.00091	69
	rs6983560	ZFAT NCBI Gene Pubmed Genecard	135653735	0.2408	0.4301	0.1675	0.184	0.00038	113
9	Best: rs17797701 (4)	Gene	1.79-1.81Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17724676		1789272	0.02169	1	0.07245	0.1786	0.0026	36
	rs4142985		1809662	0.0217	1	0.6695	0.2287	0.0011	57
	rs1556412		1813898	0.02153	1	0.4036	0.3547	0.0035	29
	rs17797701		1814888	0.01434	1.99e-09	0.4026	1.43e-20	0.0066	18
9	Best: rs2035783 (3)	Gene	106.56-106.56Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10816425		106557265	0.4494	0.2156	0.7939	0.9834	0.00017	197
	rs9942941		106558689	0.4498	0.17	0.7654	0.9173	0.00026	156
	rs2035783		106558834	0.4733	0.003632	0.09145	0.002985	0.00029	142
9	Best: rs2151370 (3)	Gene	117.79-117.81Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs488101		117787179	0.3637	1.715e-05	0.6116	3.04e-07	0.0011	55
	rs2151370		117804641	0.3791	0.7345	0.8454	0.187	0.0026	35
	rs2780244		117808231	0.3814	0.594	0.6395	0.2411	0.00076	77
10	Best: rs11005510 (3)	Gene	58.20-58.21Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1915936		58202771	0.08895	0.481	0.1389	0.9133	0.00024	164
	rs11005510		58202995	0.01029	1	1	1.225e-20	0.0037	28
	rs12262474		58210292	0.08963	0.007392	0.5013	0.3031	0.00023	170
10	Best: rs2393191 (2)	Gene	58.39-58.41Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2393191		58394623	0.01577	0.3108	0.5761	0.2455	0.00027	152
	rs16909905		58410545	0.01209	1	0.3568	0.9247	0.00025	157
11	Best: rs1176741 (6)	Gene	113.28-113.31Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10789970	HTR3B NCBI Gene Pubmed Genecard	113279156	0.4083	0.4541	0.9695	0.6438	0.00021	182
	rs17116117	HTR3B NCBI Gene Pubmed Genecard	113306801	0.05276	9.736e-06	0.116	1.158e-31	0.0095	14
	rs17116145	HTR3B NCBI Gene Pubmed Genecard	113309536	0.02946	0.4044	0.5202	0.7136	0.0008	73
	rs1176741	HTR3B NCBI Gene Pubmed Genecard	113312525	0.03132	0.2589	0.1192	0.8128	0.014	7
	rs1176740	HTR3B NCBI Gene Pubmed Genecard	113312606	0.03151	1	0.1206	0.8593	0.0028	33
	rs1176738	HTR3B NCBI Gene Pubmed Genecard	113313305	0.03135	0.2589	0.1193	0.8128	0.001	60
12	Best: rs10843660 (9)	Gene	30.24-30.26Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10843648		30235699	0.09824	0.8076	0.5888	0.1265	0.00035	123
	rs1485439		30236039	0.09744	1	0.5124	0.08116	0.00035	121
	rs17459648		30247482	0.1245	0.8309	0.01231	0.3318	0.00022	172
	rs10743704		30249349	0.2972	0.4792	0.402	0.7688	0.016	6
	rs10771657		30250561	0.4332	0.3825	0.4742	0.3589	0.0013	50
	rs17459885		30252146	0.1401	1	0.3133	0.4395	0.00049	98
	rs10843660		30259724	0.3795	2.737e-65	0.03536	9.177e-35	0.017	5
	rs9669515		30260529	0.2957	0.5128	0.4791	0.7514	0.0011	56
	rs1157480		30264271	0.2963	0.4119	0.3771	0.5558	0.00066	79
12	Best: rs10879068 (2)	Gene	68.67-68.67Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1688786		68666282	0.4754	3.472e-06	0.04187	0.1238	0.00028	144
	rs10879068		68667434	0.3	0.3123	0.9294	0.2236	0.00056	91
12	Best: rs16919463 (2)	Gene	124.76-124.76Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16919463		124761686	0.1175	0.8302	0.7865	0.5421	0.0015	44
	rs4765066		124763828	0.1418	0.001025	0.8641	3.702e-08	0.00083	72
13	Best: rs17667894 (6)	Gene	90.79-90.83Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7322734		90792026	0.4075	0.8521	1	0.06679	0.00018	191
	rs11842349		90793937	0.0328	0.4241	0.3918	0.3241	0.011	10
	rs4142965		90811414	0.4377	0.8189	0.9401	0.1451	0.00028	145
	rs17667894		90812310	0.02048	1	0.3776	2.821e-42	0.012	9
	rs17667973		90823894	0.03875	0.5167	0.01391	0.4218	0.00045	105
	rs17735544		90825251	0.03366	0.4349	0.09197	0.3028	0.0013	51
15	Best: rs16971150 (2)	Gene	77.69-77.69Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16971150		77685718	0.01841	0.4576	0.6257	0.7012	0.0051	21
	rs2865199		77690427	0.01273	1	0.6257	2.347e-13	0.0027	34
16	Best: rs6499937 (3)	Gene	56.75-56.75Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4784901	CSNK2A2 NCBI Gene Pubmed Genecard	56751827	0.1715	0.6871	0.6063	0.5839	0.00029	140
	rs6499937	CSNK2A2 NCBI Gene Pubmed Genecard	56753662	0.005564	1	1	2.2e-08	0.00047	101
	rs7185886	CSNK2A2 NCBI Gene Pubmed Genecard	56754237	0.01177	1	0.3404	0.9238	0.00036	117
16	Best: rs16955238 (6)	Gene	79.96-79.98Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs8057691	GAN NCBI Gene Pubmed Genecard	79958244	0.03318	0.2592	1	0.2044	0.00029	138
	SNP_A-2162323		79970090	0.02089	1	0.4036	0.1484	0.0031	32
	rs16955238		79973192	0.02742	4.818e-114	0.6464	2.449e-05	0.01	13
	rs16955255	LOC100996430 NCBI Gene Pubmed Genecard	79977632	0.02078	1	0.4026	0.1933	0.00021	180
	rs16955259	LOC100996430 NCBI Gene Pubmed Genecard	79977690	0.02108	1	0.4036	0.1959	0.00028	148
	rs310020	LOC100996430 NCBI Gene Pubmed Genecard	79978576	0.3809	0.01908	0.103	0.01812	0.00035	120
17	Best: SNP_A-1948953 (2)	Gene	17.27-17.27Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16961675	SMCR9 NCBI Gene Pubmed Genecard	17266676	0.3221	0.5993	0.3353	0.1707	0.00043	106
	SNP_A-1948953		17267088	0.2792	2.842e-26	0.005177	2.1e-06	0.0015	46
17	Best: rs2934884 (2)	Gene	50.27-50.29Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2934884		50273901	0.1955	0.1052	0.4164	0.3475	0.00059	90
	rs12150025		50287153	0.128	9.38e-05	0.8517	6.513e-06	0.00033	126
18	Best: rs8085875 (3)	Gene	43.91-43.93Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7243021	ZBTB7C NCBI Gene Pubmed Genecard	43911981	0.3692	0.6956	0.4298	0.3801	0.00022	174
	rs8085875	ZBTB7C NCBI Gene Pubmed Genecard	43913365	0.1743	0.3524	0.7953	0.4295	0.00092	67
	rs6417101		43926817	0.1836	0.5127	0.6983	0.0006082	0.00035	122
22	Best: rs16986990 (2)	Gene	27.75-27.75Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16986990	ZNRF3 NCBI Gene Pubmed Genecard ZNRF3-AS1 NCBI Gene Pubmed Genecard	27745369	0.01535	1	1	0.5568	0.0051	22
	rs8137391	ZNRF3 NCBI Gene Pubmed Genecard ZNRF3-AS1 NCBI Gene Pubmed Genecard	27746781	0.009938	1	1	1.487e-19	0.0045	26
23	Best: rs1419930 (2)	Gene	2.58-2.58Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5939290		2576333	0.2199	0.2145	0.2376	0.4362	0.00017	200
	rs1419930		2580231	0.0499	0.5364	5.712e-19	1.215e-07	0.0046	25
23	Best: rs5951179 (2)	Gene	70.95-70.96Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5951179	NHSL2 NCBI Gene Pubmed Genecard	70949622	0.04045	0.2548	1	0.0003442	0.0014	48
	rs7878231	NHSL2 NCBI Gene Pubmed Genecard	70961868	0.0437	1	1	0.189	0.00099	62
23	Best: rs5938070 (3)	Gene	74.42-74.45Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2146767	ZDHHC15 NCBI Gene Pubmed Genecard	74420469	0.02677	1	0.6322	0.001788	0.00017	198
	rs4892579	ZDHHC15 NCBI Gene Pubmed Genecard	74428079	0.02753	0.3741	0.6395	0.002648	0.00022	178
	rs5938070	ZDHHC15 NCBI Gene Pubmed Genecard	74450099	0.02484	1	0.637	7.929e-07	0.00063	84