Table 2.

Top SNPs identified by Random Forests in MS case-control dataset without 6p data

Chr	SNP	Gene	MAF	RF Rank	CHISQ	P-Value
12	rs1805755	M6PR	< 0.01	1	73.42	1.05 * 10-17
7	rs6467970	SEMA3A* (44.1 kb)	0.19	2	19.71	9.00 * 10-6
10	rs10823051	CTNNA3	0.16	3	17.61	2.71 * 10-5
1	rs10754012	RGS1* (3.3 mb)	0.23	4	22.24	2.41 * 10-5
12	rs1716167	MPHOSPH9	0.21	5	22.38	2.23 * 10-6
6	rs1015340	PHACTR2	0.47	6	14.86	1.16 * 10-4
10	rs7068990	PPAPDC1A* (137.6 kb)	0.23	7	17.65	2.65 * 10-5
8	rs1466526	FAM164A* (86.0 kb)	0.25	8	15.60	7.84 * 10-5
6	rs1040638	PHACTR2	0.48	9	13.82	2.01 * 10-4
7	rs16217	NPY* (292.9 kb)	0.26	10	7.14	7.53 * 10-3
12	rs1106240	PITPNM2	0.20	11	18.71	1.52 * 10-5
8	rs4739135	FAM164A* (98.8 kb)	0.19	12	16.33	5.34 * 10-5
18	rs4798684	ADCYAP1* (19.8 kb)	0.30	13	13.41	2.51 * 10-4
6	rs1015341	PHACTR2	0.47	14	14.88	1.14 * 10-4
12	rs2695478	MPHOSPH9	0.20	15	17.30	3.19 * 10-5
1	rs11800848	EVI5	0.26	16	19.04	1.28 * 10-5
9	rs6993386	IL7	0.32	17	17.95	2.27 * 10-5
6	rs6915752	PHACTR2	0.45	18	17.71	2.57 * 10-5
20	rs2223712	BTBD3* (3.6 kb)	0.19	19	11.86	5.73 * 10-4
10	rs7092549	PPAPDC1A* (140.0 kb)	0.23	20	17.06	3.62 * 10-5
6	rs9376783	PHACTR2	0.45	21	17.26	3.27 * 10-5
17	rs17652139	CCL2* (3.0 mb)	0.23	22	11.81	5.88 * 10-4
7	rs740295	MGC87402	0.31	23	7.89	4.96 * 10-3
5	rs156823	ARL15	0.47	24	12.13	4.97 * 10-4
18	rs7241142	ADCYAP1* (20.7 kb)	0.30	25	10.81	1.01 * 10-3

The top 25 SNPs from RF analysis of the dataset without chromosome 6 SNPs are shown above. The minor allele frequency (MAF) is derived from controls and the χ²-statistic is from univariate testing. *Indicates that the gene is the closest gene with distance.