Table 1.

Top SNPs identified by Random Forests in MS case-control dataset

Chr	SNP	Gene	MAF	RF Rank	CHISQ	P-Value
6	rs3129900	C6orf10	0.17	1	272.2	3.75 * 10-61
6	rs3129934	C6orf10	0.17	2	274.4	1.28 * 10-61
6	rs9270986	HLA Tag SNP	0.17	3	274.6	1.14 * 10-61
6	rs3129768	HLA-DQA* (70 bp)	0.20	4	238.9	3.14 * 10-53
6	rs2647046	HLA-DQA2* (8.5 kb)	0.39	5	113.9	1.38 * 10-26
6	rs3129932	C6orf10	0.23	6	219.8	1.02 * 10-49
6	rs9275572	HLA-DQA2* (2.1 kb)	0.42	7	101.5	7.24 * 10-24
6	rs3131294	NOTCH4	0.14	8	215.4	9.26 * 10-49
6	rs910049	C6orf10	0.24	9	222.2	2.98 * 10-50
6	rs2894249	C6orf10	0.23	10	220.7	6.28 * 10-50
6	rs3135377	HLA-DRA* (80.6 kb)	0.21	11	217.9	2.60 * 10-49
6	rs9469220	HLA-DQA2* (18.5 kb)	0.50	12	99.2	2.28 * 10-23
6	rs7194	HLA-DRA	0.40	13	129.7	4.69 * 10-30
6	rs6457620	HLA-DQB1* (137.5 kb)	0.49	14	96.03	1.13 * 10-22
6	rs3130287	TNXB	0.15	15	181.2	2.72 * 10-41
6	rs6457617	HLA-DQB1 (137.4 kb)	0.49	16	96.03	1.13 * 10-22
6	rs6936204	C6orf10* (14.6 kb)	0.36	17	113.3	1.83 * 10-26
12	rs1805755	M6PR	¡ .01	18	73.42	1.05 * 10-17
12	rs1716167	MPHOSPH9	0.21	19	22.38	2.23 * 10-6
7	rs17708673	C7orf25 (106.2 kb)	0.16	20	6.357	1.17 * 10-2
6	rs9268877	HLA-DRA* (126.3 kb)	0.42	21	74.57	5.85 * 10-18
6	rs9276440	HLA-DQA2	0.45	22	83.75	5.63 * 10-20
6	rs2621383	HLA-DOB* (825.5 kb)	0.37	23	82.72	9.44 * 10-20
22	rs80515	FAM19A5* (1.4 mb)	0.10	24	3.751	5.28 * 10-2
20	rs2425754	CDH22* (580.3 kb)	0.15	25	4.193	4.06 * 10-2

The top 25 SNPs from RF analysis of the whole dataset are shown above. Most of the top SNPs are on chromosome 6p within the HLA region. 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.