Table 1.- Variants (SNPs) included in the PRS calculation
(Disease/Trait: Nonsyndromic_cleft_lip_with_or_without_cleft_palate)
rsID	Risk allele	Effect size
rs227731	G	0.322
rs7078160	A	0.307
rs7590268	G	0.351
rs17760296	G	0.405
Effect size: LN(OR)

Table 2.- PRS Score distribution among populations and regions
(Disease/Trait: Nonsyndromic_cleft_lip_with_or_without_cleft_palate)
	count	mean	sd	se	lower.ci	upper.ci
Pyrenean regions
WEST	168	0.087	0.053	0.004	0.079	0.095
SOUTH	83	0.087	0.052	0.006	0.075	0.098
EAST	146	0.083	0.049	0.004	0.075	0.091
Populations
IBS	107	0.082	0.051	0.005	0.073	0.092
PIR	397	0.085	0.051	0.003	0.080	0.090

Table 3.- Pairwise t-test for PRS score among populations and regions
(Disease/Trait: Nonsyndromic_cleft_lip_with_or_without_cleft_palate)
group1	group2	n1	n2	p	p.signif	p.adj	p.adj.signif
IBS	PIR	107	397	0.567	ns	1	ns
IBS	WEST	107	168	0.475	ns	1	ns
IBS	SOUTH	107	83	0.549	ns	1	ns
IBS	EAST	107	146	0.887	ns	1	ns
WEST	SOUTH	168	83	0.997	ns	1	ns
WEST	EAST	168	146	0.535	ns	1	ns
SOUTH	EAST	83	146	0.613	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: Nonsyndromic_cleft_lip_with_or_without_cleft_palate)
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	0.370	0.711	.	white	0.410	0.682	.	white	0.370	0.711	.	white	0.410	0.682	.	white
pct75.95	0.100	0.920	.	white	1.220	0.222	.	white	0.100	0.920	.	white	−0.470	0.638	.	white
pct50.75	0.440	0.660	.	white	−1.460	0.144	.	white	0.440	0.660	.	white	0.480	0.631	.	white
pct25.50	0.600	0.549	.	white	0.530	0.596	.	white	0.600	0.549	.	white	0.460	0.646	.	white
pct25	−1.280	0.201	.	white	−0.780	0.435	.	white	−1.280	0.201	.	white	−0.680	0.497	.	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