Table 2. deltaSVM predicted causal autoimmune SNPs.

Scoring autoimmune GWAS loci with deltaSVM trained on Th1 yields predictions for high confidence causal SNPs.

Disease	Lead SNP	Predicted SNP	CHR	Lead SNP Position	Predicted SNP Position	Distance	Nearset Gene	|deltaSVM|	Ref.
VIT	rs853308	rs860475	chr8	133929917	133929799	−118	TG	16.797	29
VIT	rs16872571	rs4697651	chr4	10726853	10721433	−5420	.	13.978	29
T1D	rs7020673	rs4380994	chr9	4291747	4282536	−9211	GLIS3	13.591	30
CRO	rs6908425	rs7748720	chr6	20728731	20689945	−38786	CDKAL1	13.177	31,32
MS	rs1782645	rs1250568	chr10	81048611	81045280	−3331	ZMIZ1	11.039	33
CEL	rs1250552	rs1250568	chr10	81058027	81045280	−12747	ZMIZ1	11.039	34
CRO	rs10801047	rs6665749	chr1	191559356	191577594	18238	.	10.646	35
CRO	rs2797685	rs2797685	chr1	7879063	7879063	0	PER3	10.411	31
Allergy	rs962993-T	rs962993	chr10	9053132	9053132	0	.	10.008	36
PBC	rs10931468	rs3771317	chr2	191538562	191543962	5400	NAB1	9.999	37
CEL	rs7753008	rs72928038	chr6	90809639	90976768	167129	BACH2	9.787	38
RA	rs72928038	rs72928038	chr6	90976768	90976768	0	BACH2	9.787	39, 40, 33
ATD
MS
MS	rs564976	rs485789	chr3	159729059	159730148	1089	AK097161	8.782
MS	rs733724	rs733724	chr6	105223864	105223864	0	HACE1	7.360	41
PBC	rs3024921	rs3024921	chr2	191943272	191943272	0	STAT4	6.931	42