Single locus analysis of the two MS-associated SNPs and the two T1D-associated SNPs in a DNA collection of up to 1,303 MS parent-child trios with MS from the USA, 2,440 MS cases from the USA, 6,425 T1D cases from GB and 9,407 healthy controls from the USA and GB.

Note that for rs2104286 and rs41295061 in the MS collection, we included previously published genotyping data (USA trios, US MS cases, US controls, GB cases; [6]). For rs41295061 and rs11594656 in the T1D collection, we included previously published genotyping data (GB cases and controls; [8]. We assumed a model of multiplicative effects when it was not significantly different from the full genotype model (P>0.05). For rs2104286, we used the full genotype model in the USA case-control collection, as it was significantly different from the multiplicative model (P = 6.57×10−3). Combined P values for the USA and GB case-control were stratified by population (note that for population stratification, a 2-df test was used for rs2104286 as there was a significant difference between 1-df and 2-df tests, P = 3.85×10−3). T, transmitted; NT, not transmitted; MAF, minor allele frequency in unaffected parents or control subjects; RR, relative risk of minor allele; OR, odds ratio of minor allele; 95% c.i. = 95% confidence interval.