Table 1. Table of association between the top SNPs with multiple phenotypes in each gene and significant (p-value < 2.7x10-07) or suggestive (p-value < 1x10-04) associations with HPO phenotypes (A1 corresponds to the effect allele).

RSID	HPO terms	Phenotype name	Genes	Ref Allele	Effect allele (A1)	Freq A1	A1 count cases	A1 count controls	N	BETA	SE	P
Marfan Syndrome
rs589668	HP0000002	Standing/sitting height ratio	FBN1	C	T	0.25	-	-	334708	4.33E-04	3.96E-05	8.30E-28
rs589668	HP0005117	Diastolic blood pressure	FBN1	C	T	0.25	-	-	329504	0.162	0.03	8.44E-09
rs589668	HP0003758	Subcutaneous adipose tissue	FBN1	C	T	0.25	-	-	329504	-0.076	0.02	2.22E-05
Alagille Syndrome
rs1051412	HP0004421	Systolic blood pressure	JAG1	A	C	0.49	-	-	334475	-0.279	0.04	6.08E-11
rs1051412	HP0001518	Small for gestational age	JAG1	A	C	0.49	-	-	192000	0.012	0.002	6.33E-09
rs1051412	HP0000518	Cataract	JAG1	A	C	0.49	18584	311632	335473	-0.039	0.01	2.85E-04
rs1051412	HP0005117	Diastolic blood pressure	JAG1	A	C	0.49	-	-	334708	0.088	0.02	3.11E-04
rs1051412	HP0003758	Subcutaneous adipose tissue	JAG1	A	C	0.49	-	-	329504	-0.053	0.02	7.22E-04
Noonan/RASopathy syndrome
rs11001221	HP0045081	Body mass index	KAT6B	A	G	0.08	-	-	333050	0.109	0.02	6.38E-08
rs11001221	HP0003758	Subcutaneous adipose tissue	KAT6B	A	G	0.08	-	-	329504	0.144	0.03	3.16E-07
rs112747606	HP0003758	Subcutaneous adipose tissue	MAP2K1	C	T	0.23	-	-	329504	-0.108	0.02	7.06E-09
rs112747606	HP0045081	Body mass index	MAP2K1	C	T	0.23	-	-	333050	-0.076	0.01	1.01E-08
rs11066309	HP0000821	Hypothyroidism	PTPN11	G	A	0.41	17599	255384	335473	0.172	0.01	8.03E-59
rs11066309	HP0005117	Diastolic blood pressure	PTPN11	G	A	0.41	-	-	334708	0.282	0.02	3.37E-30
rs11066309	HP0000002	Standing/sitting height ratio	PTPN11	G	A	0.41	-	-	332526	2.27E-04	3.48E-05	6.91E-11
rs11066309	HP0001518	Small for gestational age	PTPN11	G	A	0.41	-	-	192000	-0.014	0	2.59E-10
rs11066309	HP0004421	Systolic blood pressure	PTPN11	G	A	0.41	-	-	334475	0.255	0.04	2.71E-09
rs11066309	HP0045081	Body mass index	PTPN11	G	A	0.41	-	-	333050	-0.055	0.01	1.24E-06
rs11066309	HP0001297	Stroke	PTPN11	G	A	0.41	4774	268208	335473	0.076	0.02	8.42E-05
rs11066309	Cystatin C	Cystatin C	PTPN11	G	A	0.41	-	-	313882	0.002	4.38E-04	8.56E-05
rs2035936	HP0045081	Body mass index	RASA2	G	T	0.06	-	-	333050	0.158	0.02	1.01E-10
rs2035936	HP0003758	Subcutaneous adipose tissue	RASA2	G	T	0.06	-	-	329504	0.187	0.03	4.30E-08
rs2035936	HP0001507	Growth abnormality	RASA2	G	T	0.06	-	-	326878	0.064	0.01	7.58E-08
rs2035936	HP0001513	Obesity	RASA2	G	T	0.06	1068	36401	335473	0.12	0.03	2.32E-04
rs11917587	HP0001507	Growth abnormality	RASA2	G	A	0.43	-	-	326878	0.035	0.01	2.13E-10
rs11917587	HP0003758	Subcutaneous adipose tissue	RASA2	G	A	0.43	-	-	329504	0.099	0.02	2.42E-10
rs11917587	HP0000002	Standing/sitting height ratio	RASA2	G	A	0.43	-	-	332526	-1.49E-04	3.46E-05	1.71E-05
rs11917587	HP0045081	Body mass index	RASA2	G	A	0.43	-	-	333050	0.046	0.01	4.32E-05
rs747744665	Cystatin C	Cystatin C	SHOC2	A	C	4.53E-04	-	-	313882	0.07	0.01	1.16E-08
rs747744665	HP0012100	Creatinine	SHOC2	A	C	4.53E-04	-	-	313757	7.106	1.28	2.55E-08
rs747744665	HP0031970	Urea	SHOC2	A	C	4.53E-04	-	-	313722	0.38	0.1	9.84E-05
rs72681869	HP0005117	Diastolic blood pressure	SOS2	G	C	0.01	-	-	334708	-0.76	0.12	5.26E-11
rs72681869	HP0004421	Systolic blood pressure	SOS2	G	C	0.01	-	-	334475	-1.293	0.2	1.41E-10
rs72681869	HP0003758	Subcutaneous adipose tissue	SOS2	G	C	0.01	-	-	329504	-0.457	0.07	7.12E-10
rs72681869	HP0045081	Body mass index	SOS2	G	C	0.01	-	-	333050	-0.251	0.05	2.14E-06
rs72681869	HP0001518	Small for gestational age	SOS2	G	C	0.01	-	-	192000	0.046	0.01	3.26E-06
rs72681869	HP0000023	Inguinal hernia	SOS2	G	C	0.01	365	7034	335473	0.213	0.06	1.32E-04
rs72681869	HP0001507	Growth abnormality	SOS2	G	C	0.01	-	-	326878	-0.092	0.03	3.65E-04