T-Trees

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

Supplementary data

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1	Best: rs2789336 (4)	Gene	18.82-18.84Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs626600		18823131	0.2252	0.07526	0.176	0.4018	7.9e-05	187
	rs851113		18825256	0.2272	0.06631	0.1616	0.4303	7.4e-05	199
	rs2743213		18829665	0.001321	1	1	0.1533	0.00011	135
	rs2789336		18836715	0.006416	1	1	2.34e-11	0.0015	23
1	Best: rs12031413 (6)	Gene	30.67-30.68Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6692098		30667189	0.1971	0.1322	0.1515	0.01598	0.00018	98
	rs900963		30668443	0.003354	1	1	0.2111	0.00026	75
	rs4949613		30675196	0.001117	1	1	0.5434	8.3e-05	181
	rs16833853		30676115	0.04383	0.4119	0.02825	0.9598	0.00015	105
	rs12031413		30680719	0.004206	1	1	2.767e-15	0.0052	7
	rs262609		30684820	0.2531	0.5449	0.8471	0.5067	0.00021	84
1	Best: rs1208054 (4)	Gene	86.93-86.98Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12097397		86927375	0.007534	1	1	0.472	0.00012	133
	rs166412		86954083	0.1293	0.6334	0.6732	0.053	0.00092	30
	rs691531		86957299	0.2001	0.001028	1	0.01509	0.0015	22
	rs1208054		86983009	0.2197	0.6509	0.549	0.1412	0.0037	10
1	Best: rs275145 (9)	Gene	164.79-164.87Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs275145	GPR161 NCBI Gene Pubmed Genecard	164789060	0.003889	1	1	3.017e-16	0.0065	5
	rs6427119	GPR161 NCBI Gene Pubmed Genecard	164805803	0.3335	0.3839	0.6212	0.6937	0.00032	67
	rs10918827	GPR161 NCBI Gene Pubmed Genecard	164808702	0.3366	0.5748	0.6824	0.5705	0.0002	88
	rs16828104	GPR161 NCBI Gene Pubmed Genecard	164822557	0.1757	0.8233	0.9475	0.01073	0.00031	69
	rs10489208	GPR161 NCBI Gene Pubmed Genecard	164826367	0.09015	1	0.6377	0.02341	0.00023	80
	rs11805261	GPR161 NCBI Gene Pubmed Genecard	164826919	0.07847	0.7591	0.05276	0.6731	0.00011	137
	rs1543358		164863250	0.2947	0.6663	0.3073	0.3544	8.3e-05	180
	rs7517978		164869703	0.2628	0.1646	1	0.4538	0.00011	143
	rs12097383		164869742	0.0809	0.888	0.4331	0.02582	0.00028	73
1	Best: rs2300564 (3)	Gene	165.12-165.12Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12691501	LOC100505918 NCBI Gene Pubmed Genecard	165121575	0.3803	0.9226	0.1985	0.2583	0.00016	101
	rs2300564	LOC100505918 NCBI Gene Pubmed Genecard	165122725	0.4047	0.4523	0.6212	0.9833	0.00021	83
	rs858111	LOC100505918 NCBI Gene Pubmed Genecard	165123510	0.4953	0.7163	0.34	0.7411	0.00011	146
2	Best: rs1453783 (6)	Gene	5.37-5.39Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10929488		5367555	0.3904	0.599	0.2195	0.3639	0.00055	43
	rs1540555		5368091	0.000609	1	1	0.03886	0.00011	145
	rs1453783		5368662	0.3744	0.4996	0.01623	0.305	0.001	26
	rs6728135		5374777	0.3913	0.5971	0.1448	0.2358	0.00039	56
	rs10929491		5376586	0.3924	0.39	0.2063	0.3215	0.00018	96
	rs6709704		5389548	0.2424	0.494	0.8427	0.5479	0.00018	93
2	Best: rs902133 (3)	Gene	10.90-10.91Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17456162	PDIA6 NCBI Gene Pubmed Genecard	10898688	0.2163	0.2056	0.6258	0.861	0.001	28
	rs12623588		10908210	0.296	0.1174	0.1216	0.5127	0.00018	95
	rs902133		10908783	0.004703	1	1	2.823e-12	0.0035	11
2	Best: rs903228 (3)	Gene	53.60-53.61Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6705121		53599909	0.03705	0.07171	0.05209	0.3257	0.0002	85
	rs903228		53603700	0.05832	0.7283	0.5606	3.286e-05	0.00027	74
	rs17044786		53612155	0.03604	0.7669	0.04863	0.136	8.5e-05	173
3	Best: rs10510375 (6)	Gene	7.92-7.93Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7644574		7917241	0.1417	0.05669	0.7567	0.172	0.00018	94
	rs7652461		7917292	0.1415	0.03705	0.6425	0.1823	0.00016	102
	rs7644832		7917456	0.1416	0.0577	0.9386	0.2039	0.00014	108
	rs17742449		7925948	0.1415	0.05779	0.8167	0.1933	7.8e-05	193
	rs1488487		7926021	0.156	0.01904	0.02206	0.7548	0.00011	134
	rs10510375		7927250	0.004191	1	1	4.469e-07	0.00058	41
3	Best: rs3845903 (2)	Gene	66.59-66.60Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs9870850	LRIG1 NCBI Gene Pubmed Genecard	66586348	0.0005075	1	1	0.3905	0.00011	144
	rs3845903	LRIG1 NCBI Gene Pubmed Genecard	66600360	0.005538	1	1	4.544e-11	0.001	27
3	Best: rs10513440 (2)	Gene	154.52-154.56Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10513440		154523522	0.2006	0.3875	0.002706	0.0003721	0.00017	100
	rs16822557		154563412	0.000913	1	1	0.0002372	0.0001	148
3	Best: rs9858104 (5)	Gene	163.64-163.70Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11924705		163644318	0.4273	0.2405	3.435e-05	0.005139	0.00042	53
	rs6789378		163650098	0.4193	0.4267	0.476	0.1275	0.00043	52
	rs9858104		163658445	0.4206	0.2616	0.3887	0.1496	0.0005	48
	rs7434223		163666164	0.4187	0.6057	0.5734	0.1674	0.00018	97
	rs1382203		163701551	0.4875	0.1595	0.9414	0.3321	0.00019	92
4	Best: rs6826705 (4)	Gene	1.11-1.12Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6826705		1112464	0.2981	0.2302	0.1609	0.8211	0.0011	25
	rs6853712		1116157	0.1779	0.3182	0.9498	0.6863	0.0001	149
	rs2127908		1118755	0.306	0.5987	0.2761	0.1798	0.00033	63
	rs4974627		1119805	0.3064	0.5285	0.2763	0.195	0.00011	140
4	Best: rs10517298 (3)	Gene	33.74-33.78Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10517298		33736984	0.08957	0.2764	0.4885	0.4232	0.00017	99
	rs16988170		33768963	0.09471	0.2896	0.6687	0.9719	8.7e-05	169
	rs13142173		33776530	0.09389	0.2267	0.6682	0.8596	0.00011	136
4	Best: rs7666328 (2)	Gene	116.14-116.14Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs9999383	NDST4 NCBI Gene Pubmed Genecard	116138939	0.06313	0.3465	0.5297	0.582	8.1e-05	186
	rs7666328	NDST4 NCBI Gene Pubmed Genecard	116140909	0.03332	0.1799	0.002817	2.484e-07	0.00032	66
5	Best: rs153822 (2)	Gene	14.68-14.70Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs153822		14680833	0.04874	0.1528	0.01355	0.5033	0.00012	127
	rs152718		14702033	0.0007123	1	1	0.01755	8.8e-05	165
6	Best: rs17429127 (10)	Gene	32.85-32.87Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2857210		32849720	0.325	0.6066	0.4771	0.8603	8.9e-05	164
	rs2621416		32849846	0.2481	0.9033	0.8821	0.7014	8.4e-05	175
	rs17429127		32859592	0.06683	0.715	0.05534	1	0.0029	13
	rs9276712		32867230	0.06652	0.7156	0.2332	0.8686	0.00034	61
	rs2621384		32867251	0.388	0.3167	0.9692	0.9663	0.0009	31
	rs2857161		32867275	0.3831	0.3153	0.969	0.783	0.0001	151
	rs2621383		32867313	0.3864	0.166	0.7861	0.7667	7.6e-05	196
	rs2621382		32868423	0.452	0.5518	0.8245	0.8198	0.00032	68
	rs2157082		32868692	0.4413	0.5525	0.000395	0.115	0.0021	16
	rs2857154		32870594	0.3855	0.8853	0.8461	0.8984	0.00063	39
7	Best: rs7792409 (4)	Gene	47.52-47.52Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7791862		47516496	0.2231	0.5666	0.3576	0.04159	0.00036	59
	rs7792409		47516602	0.2196	0.745	0.3576	0.3193	0.00064	38
	rs7792551		47516674	0.2196	0.6041	0.3295	0.2629	0.00026	76
	rs7792432		47516725	0.2201	0.5596	0.7048	0.2848	9.7e-05	156
7	Best: rs11575518 (2)	Gene	50.31-50.31Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11575535	DDC NCBI Gene Pubmed Genecard	50306203	0.01814	0.3266	1	0.02911	7.9e-05	190
	rs11575518	DDC NCBI Gene Pubmed Genecard	50309890	0.01506	1	1	0.6724	8.4e-05	177
8	Best: rs16878847 (3)	Gene	32.07-32.09Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2045796	NRG1 NCBI Gene Pubmed Genecard	32068589	0.2966	0.4127	0.7263	0.604	0.00011	147
	rs9297186	NRG1 NCBI Gene Pubmed Genecard	32079918	0.08926	0.3266	0.6517	0.9712	0.00011	142
	rs16878847	NRG1 NCBI Gene Pubmed Genecard	32091161	0.002246	1	1	1.463e-09	0.0015	21
8	Best: rs7826024 (2)	Gene	37.16-37.16Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	SNP_A-1901278		37157665	0.005208	1	1	0.0001281	0.00041	54
	rs7826024		37164161	0.005381	1	1	0.1614	0.00046	50
8	Best: rs1372662 (12)	Gene	135.58-135.65Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7831961	ZFAT NCBI Gene Pubmed Genecard	135576242	0.2976	0.1018	0.6303	0.6356	0.00014	106
	rs6421008	ZFAT NCBI Gene Pubmed Genecard	135581827	0.05377	0.3456	0.8609	0.338	0.00086	32
	rs7386230	ZFAT NCBI Gene Pubmed Genecard	135595641	0.1083	0.8055	0.5199	0.1116	8.3e-05	179
	rs6988000	ZFAT NCBI Gene Pubmed Genecard	135628716	0.2406	0.3265	0.08562	0.4697	0.0022	15
	rs6578234	ZFAT NCBI Gene Pubmed Genecard	135635545	0.3333	0.7204	0.3858	0.8955	0.0019	18
	rs7827545	ZFAT NCBI Gene Pubmed Genecard	135635749	0.32	1.249e-05	0.2828	0.001082	0.0038	9
	rs1372662	ZFAT NCBI Gene Pubmed Genecard	135636228	0.3319	0.6828	0.3219	0.9303	0.0089	4
	rs6578237	ZFAT NCBI Gene Pubmed Genecard	135638540	0.331	0.679	0.2627	0.8947	0.00083	34
	rs7846013	ZFAT NCBI Gene Pubmed Genecard	135639149	0.3299	0.7194	0.3625	0.8096	0.00077	36
	rs10283108	ZFAT NCBI Gene Pubmed Genecard	135644228	0.2537	0.7627	0.5001	0.5693	0.00013	113
	rs7007819	ZFAT NCBI Gene Pubmed Genecard	135644921	0.3606	0.3003	0.8122	0.4924	0.00053	46
	rs6983560	ZFAT NCBI Gene Pubmed Genecard	135653735	0.2376	0.5338	0.2042	0.7348	0.00036	58
9	Best: rs2151370 (6)	Gene	117.78-117.82Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2458879		117783588	0.3848	1	0.847	0.3513	0.00014	112
	rs488101		117787179	0.3634	4.528e-08	0.5867	6.541e-07	0.0034	12
	rs2151370		117804641	0.3767	0.6605	0.7864	0.07414	0.0063	6
	rs2780244		117808231	0.3778	0.6245	0.5873	0.04999	0.0018	19
	rs2722824		117811679	0.2723	0.0349	0.6432	0.8171	8.2e-05	182
	rs2095164		117819672	0.4231	0.7786	0.4116	0.01846	0.00077	35
10	Best: rs7082404 (2)	Gene	77.12-77.12Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7082404		77116071	0.003559	1	1	6.976e-07	0.00024	79
	rs11001473		77124024	0.0065	1	1	0.7013	0.00019	90
10	Best: rs7077039 (3)	Gene	114.74-114.78Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7901695	TCF7L2 NCBI Gene Pubmed Genecard	114744078	0.3485	0.5361	0.2389	1.744e-12	8.1e-05	184
	rs4506565	TCF7L2 NCBI Gene Pubmed Genecard	114746031	0.3515	0.4766	0.3573	1.65e-12	8.2e-05	183
	rs7077039	TCF7L2 NCBI Gene Pubmed Genecard	114779067	0.4832	1	0.1476	3.779e-12	8.5e-05	174
11	Best: rs11038203 (3)	Gene	44.89-44.89Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11038203	TSPAN18 NCBI Gene Pubmed Genecard	44887617	0.005322	1	1	3.83e-09	0.0011	24
	rs835984	TSPAN18 NCBI Gene Pubmed Genecard	44892269	0.405	0.5128	0.562	0.007731	0.0001	150
	rs17787207	TSPAN18 NCBI Gene Pubmed Genecard	44892561	0.00822	1	1	0.5687	0.00094	29
11	Best: rs10501795 (8)	Gene	92.07-92.09Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4122086	FAT3 NCBI Gene Pubmed Genecard	92070494	0.009032	1	1	0.5865	8.9e-05	163
	rs531005	FAT3 NCBI Gene Pubmed Genecard	92070845	0.4792	0.05134	0.6589	0.04772	0.00025	78
	rs1792361	FAT3 NCBI Gene Pubmed Genecard	92083573	0.3366	0.8815	0.8026	0.008299	7.6e-05	195
	rs1791552	FAT3 NCBI Gene Pubmed Genecard	92087013	0.3373	0.9211	0.9006	0.005664	0.00013	117
	rs10501795	FAT3 NCBI Gene Pubmed Genecard	92087066	0.008929	1	1	0.5119	0.0047	8
	rs1792366	FAT3 NCBI Gene Pubmed Genecard	92089015	0.4953	0.05701	0.9123	0.03933	8.5e-05	172
	rs10501796	FAT3 NCBI Gene Pubmed Genecard	92092804	0.005315	1	1	4.282e-09	0.0027	14
	rs1791571	FAT3 NCBI Gene Pubmed Genecard	92093407	0.3364	0.8428	0.9003	0.005616	0.00014	110
12	Best: rs2900385 (2)	Gene	10.27-10.28Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4764332		10272195	0.02378	1	0.2661	0.06745	0.00014	109
	rs2900385		10282883	0.01934	1	0.6254	0.6002	0.00033	65
12	Best: rs10492267 (11)	Gene	96.80-96.93Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17027652		96802618	0.03899	1	0.3203	0.6301	0.002	17
	rs7308578		96811720	0.4841	0.005666	0.1745	1	0.00053	45
	rs1450063		96813260	0.1012	1	0.007158	0.3929	0.00039	55
	rs11109275		96821602	0.142	0.1908	0.04261	0.8827	9.3e-05	161
	rs7958227		96822193	0.1003	0.05215	8.717e-05	0.4101	0.00012	132
	rs1947253		96823397	0.1004	0.897	0.05773	0.4107	0.00012	126
	rs7969412		96824826	0.1751	0.8752	0.4854	0.9568	0.00033	64
	rs10860262		96851491	0.04262	0.7845	0.361	0.6833	0.018	3
	rs10492267		96851806	0.02615	9.728e-08	0.8067	7.557e-30	0.019	2
	rs10082731		96855023	0.4926	0.03721	0.07831	0.4965	0.00012	130
	rs2192796		96927337	0.05698	1	0.5975	0.3066	0.00038	57
15	Best: rs2277610 (2)	Gene	42.65-42.75Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2277610	SPG11 NCBI Gene Pubmed Genecard	42650222	0.006086	1	0.1009	1	0.00034	60
	rs10152685	PATL2 NCBI Gene Pubmed Genecard	42746404	0.00367	1	1	7.243e-06	0.00029	72
17	Best: rs7221370 (2)	Gene	14.28-14.29Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7221370		14278769	0.002889	1	1	1.387e-06	0.00056	42
	rs10221222		14290428	0.08851	1.869e-06	0.06408	0.0418	0.00034	62
18	Best: rs974676 (2)	Gene	27.45-27.45Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1791193		27451624	0.3447	0.05841	0.4664	0.3587	7.9e-05	191
	rs974676		27454722	0.3493	0.7656	0.1695	0.7954	0.00014	111
18	Best: rs7235815 (3)	Gene	41.08-41.12Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7235815	SLC14A2 NCBI Gene Pubmed Genecard	41078093	0.006761	1	1	0.003294	0.00023	81
	rs16978327	SLC14A2 NCBI Gene Pubmed Genecard	41120153	0.02306	1	0.262	0.1142	0.00019	91
	rs11082439	SLC14A2 NCBI Gene Pubmed Genecard	41124301	0.1225	0.6561	0.3226	0.07331	0.0002	87
22	Best: rs10212068 (9)	Gene	35.97-36.02Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10212068		35969121	0.02798	1	0.002635	8.474e-62	0.035	1
	rs5750402		35985788	0.1751	0.3266	0.8959	0.05705	0.00051	47
	rs5756581		35986936	0.1456	0.6378	0.8284	0.1988	0.0003	70
	rs4820279		35991286	0.1789	0.8819	0.7494	0.0854	0.00046	49
	rs4821623		35993078	0.1734	0.6856	0.9	0.221	0.00045	51
	rs2267363	CYTH4 NCBI Gene Pubmed Genecard	36001892	0.2424	1	0.07917	0.01157	0.00055	44
	rs727047	CYTH4 NCBI Gene Pubmed Genecard	36002219	0.3554	1	0.4022	0.5757	0.00013	116
	rs727048	CYTH4 NCBI Gene Pubmed Genecard	36002392	0.2422	0.846	0.009346	0.005802	0.00067	37
	rs5756601	CYTH4 NCBI Gene Pubmed Genecard	36017438	0.4333	0.7454	0.6008	0.2601	0.00014	107
23	Best: rs952836 (2)	Gene	40.10-40.10Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs952836		40100317	0.3278	0.0001587	0.06411	0.03039	0.0002	86
	rs5917359		40102759	0.3279	0.002232	0.3145	0.4871	8.7e-05	168