Table 1.- Variants (SNPs) included in the PRS calculation
(Disease/Trait: Cleft_lip)
rsID	Risk allele	Effect size
rs987525	A	0.577
Effect size: LN(OR)

Table 2.- PRS Score distribution among populations and regions
(Disease/Trait: Cleft_lip)
	count	mean	sd	se	lower.ci	upper.ci
Pyrenean regions
WEST	168	0.131	0.172	0.013	0.104	0.157
SOUTH	83	0.129	0.151	0.017	0.096	0.162
EAST	146	0.128	0.176	0.015	0.100	0.157
Populations
IBS	107	0.135	0.174	0.017	0.101	0.168
PIR	397	0.129	0.169	0.008	0.113	0.146

Table 3.- Pairwise t-test for PRS score among populations and regions
(Disease/Trait: Cleft_lip)
group1	group2	n1	n2	p	p.signif	p.adj	p.adj.signif
IBS	PIR	107	397	0.768	ns	1	ns
IBS	WEST	107	168	0.838	ns	1	ns
IBS	SOUTH	107	83	0.803	ns	1	ns
IBS	EAST	107	146	0.768	ns	1	ns
WEST	SOUTH	168	83	0.933	ns	1	ns
WEST	EAST	168	146	0.914	ns	1	ns
SOUTH	EAST	83	146	0.994	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: Cleft_lip)
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	−1.600	0.110	.	white	−0.090	0.928	.	white	−1.600	0.110	.	white	0.190	0.849	.	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	0.940	0.347	.	white	−0.170	0.865	.	white	0.940	0.347	.	white	−0.550	0.582	.	white
pct25.50	0.000	1.000	.	white	0.000	1.000	.	white	0.000	1.000	.	white	0.000	1.000	.	white
pct25	−0.310	0.757	.	white	0.200	0.841	.	white	−0.310	0.757	.	white	0.440	0.660	.	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