Additional file 2: Supplementary Table 1. Number of SNPs included in each JIA PRS generated using different SNP P value thresholds. Supplementary Table 2. SNPs included in the JIA PRS with the SNP P value threshold of <1.00E-5. SE, standard error; SNP, single nucleotide polymorphism. Supplementary Table 3. Data inclusion and data losses for the ALSPAC cohort and associated cardiovascular phenotypes. Outlying data was defined as those greater than three times the interquartile range. To maintain data anonymity, any cell containing a value less than 5 (including 0) has been replaced with <5. Apo-AI, apolioprotein-AI; Apo-B, apolipoprotein-B; BMI, body mass index; BP, Blood pressure; cIMT, carotid intima-media thickness; hsCRP, high sensitivity C-reactive protein; FMI, fat mass index; HOMA2_IR, Homeostasis Model Assessment 2 insulin reistance index; HDL, high density lipoprotein cholesterol; LDL, low density lipoprotein cholesterol; LVMI, left ventricular mass index. Supplementary Table 4. Assocations between JIA PRS generated using SNPs with the P value <5e-5, and positive and negative control outcomes. Pseudo R2 is used to evaulate the gooness of fit. CI, confidence interval; JIA, JIA; OR, odds ratio; PRS, polygenic risk score. Supplementary Table 5. Assocations between JIA PRS generated using SNPs with the P value <5e-5 and continous cardiovascular outcomes. *adjusted for 10 ancestry informed principal components and sex. Outcomes with P<0.05 are italicised. R2 is the proportion of the variance in the outcome which can be explained by the JIA PRS. Apo-AI, apolioprotein-AI; Apo-B, apolipoprotein-B; BMI, body mass index; BP, Blood pressure; CI, confidence interval; cIMT, carotid intima-media thickness; hsCRP, high sensitivity C-reactive protein; FMI, fat mass index; HOMA2_IR, Homeostasis Model Assessment 2 insulin reistance index; HDL, high density lipoprotein cholesterol; JIA, juvenile idiopathic arthritis; LDL, low density lipoprotein cholesterol; LVMI, left ventricular mass index; PRS, polygenic risk score. Supplementary Table 6. Assocations between JIA PRS generated using SNPs with the P value <5e-5 and dichotomous cardiovascular outcomes. *adjusted for 10 ancestry informed principal components and sex. Outcomes with P<0.05 are italicised. Pseudo R2 is used to evaulate the gooness of fit. BP, blood pressure; CI, confidence interval; JIA, juvenile idiopathic arthritis; OR, odds ratio. Supplementary Table 7. Assocations between JIA PRS generated using SNPs with the P value <1e-5 and cardiovascular outcomes in the main analysis, sensitivity analysis 1 (exclusion of MHSCregion SNP) and sensitivity analysis 2 (exclusion of participants with autoimmune disease). All estimates are adjusted for 10 ancestry informed principal components and sex. Outcomes with P <0.05 are italicised. *For dichotomous outcomes, OR (95% CI) are reported. R2 is the proportion of the variance in the outcome which can be explained by the JIA PRS. ^for dichotomous outcomes, pseudo R2 is reported. Pseudo R2 is used to evaulate the gooness of fit. Apo-AI, apolioprotein-AI; Apo-B, apolipoprotein-B; BMI, body mass index; BP, Blood pressure; CI, confidence interval; cIMT, carotid intima-media thickness; hsCRP, high sensitivity C-reactive protein; FMI, fat mass index; HOMA2_IR, Homeostasis Model Assessment 2 insulin reistance index; HDL, high density lipoprotein cholesterol; JIA, juvenile idiopathic arthritis; LDL, low density lipoprotein cholesterol; LVMI, left ventricular mass index; PRS, polygenic risk score. Supplementary Table 8. Assocations between JIA PRS generated using SNPs with the P value <5e-5 and cardiovascular outcomes from age 7 years to age 24 years for participants who attended the Focus24+ clinic. ^For measures which are not continuous N (%) is reported and participants with missing data are excluded from the denominator. *variable not calculated for earlier time points due to the different clinical thresholds by age. Apo-AI, apolioprotein-AI; Apo-B, apolipoprotein-B; BMI, body mass index; BP, Blood pressure; cIMT, carotid intima-media thickness; hsCRP, high sensitivity C-reactive protein; FMI, fat mass index; HOMA2_IR, Homeostasis Model Assessment 2 insulin reistance index; HDL, high density lipoprotein cholesterol; LDL, low density lipoprotein cholesterol; LVMI, left ventricular mass index. Supplementary Table 9. Assocations between JIA PRS generated using SNPs with the P value <5e-5 and cardiovascular outcomes from age 7 years to age 24 years. *adjusted for 10 ancestry informed principal components and sex. Outcomes with P<0.05 are italicised. R2 is the proportion of the variance in the outcome which can be explained by the JIA PRS. BMI, body mass index; BP, Blood pressure; CI, confidence interval; hsCRP, high sensitivity C-reactive protein; FMI, fat mass index; HOMA2_IR, Homeostasis Model Assessment 2 insulin reistance index; IA, juvenile idiopathic arthritis; PRS, polygenic risk score. Supplementary Table 10. Assocations between JIA PRS generated using SNPs with the P value <5e-5 and cardiovascular outcomes from age 7 years to age 24 years for Focus24+ participants who attended a) any earlier clinic and b) every earlier clinic. All estiamtes are adjusted for 10 ancestry informed principal components and sex. R2 is the proportion of the variance in the outcome which can be explained by the JIA PRS. Sample size varies by outcome due to missing data. BMI, body mass index; BP, Blood pressure; CI, confidence interval; hsCRP, high sensitivity C-reactive protein; FMI, fat mass index; HOMA2_IR, Homeostasis Model Assessment 2 insulin reistance index; IA, juvenile idiopathic arthritis; PRS, polygenic risk score.

Genetics, Juvenile idiopathic arthritis, Cardiovascular, ALSPAC