Table 2 Results of GWAS on 25,826 structural variants (AF > 0.1%) across 42 quantitative phenotypes

Chrom	Start	End	Size	Type	Phenotype	P value	Gene(s)	Beta	AF	Tagging SNP
3	133,503,766	133,505,083	1317	DEL	Total iron binding capacity	6.55E-111	SRPRB/TF	0.41	0.32	rs1830084
3	133,503,766	133,505,083	1317	DEL	Unsaturated iron-binding capacity	4.23E-58	SRPRB/TF	0.29	0.32	rs1830084
4	9,952,309	9,952,540	231	DEL	Uric acid	3.38E-18	SLC2A9	−0.14	0.52	rs998676
8	145,958,042	145,958,453	411	DEL	Amino alanatransferase serum levels	8.71E-11	ZNF251	−1.00	0.00	NA
12	9,557,847	9,558,660	813	DEL	Prothrombin time	1.50E-10	LOC728715	0.13	0.24	NA
2	234,543,315	234,544,978	1663	DEL	Bilirubin	3.65E-10	UGT1A8	0.28	0.04	NA
16	89,646,237	89,646,704	467	DEL	Prothrombin time	1.16E-09	CPNE7	0.16	0.11	NA
10	127,190,797	127,201,222	10,425	DUP	Folate	1.76E-09	−	0.22	0.07	NA
17	77,995,566	77,998,870	3304	DUP	Fibrinogen	1.98E-09	TBC1D16	−0.23	0.04	NA
13	113,499,466	113,500,108	642	DEL	Prothrombin time	2.02E-09	ATP11A	−0.16	0.13	NA
17	77,998,102	77,998,534	432	DUP	Prothrombin time	2.27E-09	TBC1D16	0.08	0.52	NA
12	9,557,787	9,558,661	874	DEL	Prothrombin time	4.03E-09	LOC728715	−0.12	0.19	NA
12	39,860,052	39,860,299	247	INV	Folate	5.00E-09	−	0.29	0.19	NA
4	163,578,584	163,579,619	1035	INV	Prothrombin time	7.04E-09	−	0.25	0.04	NA
16	89,974,223	89,975,006	783	DEL	Potassium	9.47E-09	TCF25	0.46	0.01	NA
21	32,114,209	32,114,891	682	DUP	Prothrombin time	1.12E-08	−	0.08	0.31	NA
12	9,557,787	9,558,661	874	DEL	Folate	2.98E-08	LOC728715	0.12	0.19	NA

List of common and rare SVs with allele frequency (AF) greater than 0.1% and size up to two megabases (2 Mb), and summarizes associations of deletions, duplications, and inversions with the analysed traits. The table contains 17 significant associations (p < 4.6 × 10⁻⁸; 0.05 / [25,826 SVs × 42 clinical traits]), involving 15 SVs distributed across ten chromosomes and nine clinical traits.

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