Table 1.- Variants (SNPs) included in the PRS calculation
(Disease/Trait: Cholangiocarcinoma_in_primary_sclerosing_cholangitis)
rsID Risk allele Effect size
rs7731017 C 1.571
Effect size: LN(OR)
Table 2.- PRS Score distribution among populations and regions
(Disease/Trait: Cholangiocarcinoma_in_primary_sclerosing_cholangitis)
count mean sd se lower.ci upper.ci
Pyrenean regions
WEST 168 0.033 0.157 0.012 0.009 0.057
SOUTH 83 0.019 0.121 0.013 −0.008 0.045
EAST 146 0.048 0.190 0.016 0.017 0.079
Populations
IBS 107 0.037 0.198 0.019 −0.001 0.075
PIR 397 0.036 0.164 0.008 0.019 0.052
Table 3.- Pairwise t-test for PRS score among populations and regions
(Disease/Trait: Cholangiocarcinoma_in_primary_sclerosing_cholangitis)
group1 group2 n1 n2 p p.signif p.adj p.adj.signif
IBS PIR 107 397 0.953 ns 1 ns
IBS WEST 107 168 0.848 ns 1 ns
IBS SOUTH 107 83 0.470 ns 1 ns
IBS EAST 107 146 0.584 ns 1 ns
WEST SOUTH 168 83 0.541 ns 1 ns
WEST EAST 168 146 0.410 ns 1 ns
SOUTH EAST 83 146 0.202 ns 1 ns
* p < .05, ** p < .01, *** p < .001
Table 4.- Chi-square test comparison of percentile counts on Pyrenean regions compared to Iberian peninsula population
(Disease/Trait: Cholangiocarcinoma_in_primary_sclerosing_cholangitis)
Percentile rank PIR WEST SOUTH EAST
adj.std.val p.value sig.val adj.std.val p.value sig.val adj.std.val p.value sig.val adj.std.val p.value sig.val
pct95 −0.520 0.603 . white 0.180 0.857 . white −0.520 0.603 . white 0.860 0.390 . white
pct75.95 0.000 1.000 . white 0.000 1.000 . white 0.000 1.000 . white 0.000 1.000 . white
pct50.75 0.000 1.000 . white 0.000 1.000 . white 0.000 1.000 . white 0.000 1.000 . white
pct25.50 0.000 1.000 . white 0.000 1.000 . white 0.000 1.000 . white 0.000 1.000 . white
pct25 0.520 0.603 . white −0.180 0.857 . white 0.520 0.603 . white −0.860 0.390 . white
adj.std.val: Adjusted standardized residuals value; p.value: P value; sig.val: statistical significance, * p < .05, ** p < .01, *** p < .001; red dash to bottom: lower counts than reference; green dash to up: upper counts than reference