Table 3 Colocalized loci for CVDs-CeVDs-RFs triplets

From: Identification of shared genetic etiology of cardiovascular and cerebrovascular diseases through common cardiometabolic risk factors

	Loci information				Traits combination and MOLOC results					SNPs and genes annotation
No.	CHR	Band	Min pos	Max pos	CVD	CeVD	RF	PPA	Best SNP	Most severe consequence	CADD score	RegulomeDB ranking	Gene mapping by L2G	Gene mapping by V2G
1	1	1p36.22	10,763,241	10,802,977	CAD	AS	SBP	0.98	rs17035646	intron_variant	6.41	4	CASZ1	CASZ1
	1	1p36.22	10,787,538	10,802,977	CAD	AS	TG	0.97	rs880315	intron_variant	8.97	4	CASZ1	CASZ1
	1	1p36.22	10,787,538	10,873,382	CAD	AS	LDL-C	0.97	rs17035646	intron_variant	6.41	4	CASZ1	CASZ1
	1	1p36.22	10,763,241	10,802,977	CAD	AIS	SBP	0.98	rs17035646	intron_variant	6.41	4	CASZ1	CASZ1
	1	1p36.22	10,787,538	10,802,977	CAD	AIS	TG	0.97	rs17035646	intron_variant	6.41	4	CASZ1	CASZ1
	1	1p36.22	10,787,538	10,873,382	CAD	AIS	LDL-C	0.96	rs17035646	intron_variant	6.41	4	CASZ1	CASZ1
	1	1p36.22	10,771,488	10,802,468	AF	AS	SBP	1.00	rs17035646	intron_variant	6.41	4	CASZ1	CASZ1
	1	1p36.22	10,787,538	10,802,468	AF	AS	TG	1.00	rs880315	intron_variant	8.97	4	CASZ1	CASZ1
	1	1p36.22	10,787,538	10,802,468	AF	AS	LDL-C	0.99	rs880315	intron_variant	8.97	4	CASZ1	CASZ1
	1	1p36.22	10,771,488	10,802,468	AF	AIS	SBP	1.00	rs17035646	intron_variant	6.41	4	CASZ1	CASZ1
	1	1p36.22	10,787,538	10,802,468	AF	AIS	TG	0.99	rs17035646	intron_variant	6.41	4	CASZ1	CASZ1
	1	1p36.22	10,787,538	10,802,468	AF	AIS	LDL-C	0.99	rs17035646	intron_variant	6.41	4	CASZ1	CASZ1
2	6	6p21.2	36,616,698	36,659,932	HF	AS	TG	0.92	rs4151702	intron_variant	5.17	5	CDKN1A	CDKN1A
	6	6p21.2	36,616,698	36,659,932	HF	AIS	TG	0.94	rs4135240	intron_variant	7.95	2b	CDKN1A	CDKN1A
	6	6p21.2	36,613,812	36,659,932	AF	AS	TG	0.96	rs4151702	intron_variant	5.17	5	CDKN1A	CDKN1A
	6	6p21.2	36,613,812	36,659,932	AF	AIS	TG	0.95	rs4151702	intron_variant	5.17	5	CDKN1A	CDKN1A
3	7	7p21.1	18,983,174	19,064,300	CAD	AS	SBP	1.00	rs2107595	regulatory_region_variant	18.10	2b	TWIST1	TWIST1
	7	7p21.1	18,983,174	19,064,300	CAD	AIS	SBP	1.00	rs2107595	regulatory_region_variant	18.10	2b	TWIST1	TWIST1
	7	7p21.1	18,986,970	19,062,130	MI	AS	SBP	1.00	rs2107595	regulatory_region_variant	18.10	2b	TWIST1	TWIST1
	7	7p21.1	18,985,270	19,062,130	MI	AIS	SBP	1.00	rs2107595	regulatory_region_variant	18.10	2b	TWIST1	TWIST1
4	9	9p21.3	21,675,670	22,202,907	CAD	AS	LDL-C	0.84	rs2891168	intron_variant	3.47	4	CDKN2B	CDKN2B
	9	9p21.3	21,675,670	22,202,907	CAD	AIS	LDL-C	0.83	rs2891168	intron_variant	3.47	4	CDKN2B	CDKN2B
	9	9p21.3	21,683,805	22,137,685	MI	AS	LDL-C	0.83	rs2891168	intron_variant	3.47	4	CDKN2B	CDKN2B
	9	9p21.3	21,683,805	22,137,685	MI	AIS	LDL-C	0.81	rs2891168	intron_variant	3.47	4	CDKN2B	CDKN2B
	9	9p21.3	21,997,872	22,125,913	HF	AS	LDL-C	0.90	rs7859727	intron_variant	1.45	3a	CDKN2B	CDKN2B
	9	9p21.3	21,997,872	22,125,913	HF	AIS	LDL-C	0.93	rs7859727	intron_variant	1.45	3a	CDKN2B	CDKN2B
5	9	9q34.2	136,121,623	136,384,162	CAD	AS	TG	0.98	rs635634	upstream_gene_variant	2.34	4	ABO	ABO
	9	9q34.2	136,121,623	136,384,162	CAD	AS	HDL-C	0.99	rs635634	upstream_gene_variant	2.34	4	ABO	ABO
	9	9q34.2	136,121,623	136,384,162	CAD	AIS	TG	0.98	rs635634	upstream_gene_variant	2.34	4	ABO	ABO
	9	9q34.2	136121623	136384162	CAD	AIS	HDL-C	0.99	rs635634	upstream_gene_variant	2.34	4	ABO	ABO
	9	9q34.2	136,128,259	136,541,229	MI	AS	TG	0.98	rs635634	upstream_gene_variant	2.34	4	ABO	ABO
	9	9q34.2	136,042,324	136,541,229	MI	AS	HDL-C	0.99	rs635634	upstream_gene_variant	2.34	4	ABO	ABO
	9	9q34.2	136,128,259	136,541,229	MI	AIS	TG	0.98	rs635634	upstream_gene_variant	2.34	4	ABO	ABO
	9	9q34.2	136,042,324	136,541,229	MI	AIS	LDL-C	0.80	rs2519093	intron_variant	7.47	4	ABO	ABO
	9	9q34.2	136,042,324	136,541,229	MI	AIS	HDL-C	0.99	rs635634	upstream_gene_variant	2.34	4	ABO	ABO
	9	9q34.2	136,137,065	136,155,000	HF	AS	SBP	0.81	rs635634	upstream_gene_variant	2.34	4	ABO	ABO
	9	9q34.2	136,137,065	136,296,530	HF	AS	TG	0.92	rs635634	upstream_gene_variant	2.34	4	ABO	ABO
	9	9q34.2	136,137,065	136,296,530	HF	AS	HDL-C	0.95	rs635634	upstream_gene_variant	2.34	4	ABO	ABO
	9	9q34.2	136,137,065	136,155,000	HF	AIS	SBP	0.82	rs635634	upstream_gene_variant	2.34	4	ABO	ABO
	9	9q34.2	136137065	136,296,530	HF	AIS	TG	0.96	rs532436	intron_variant	3.46	3a	ABO	ABO
	9	9q34.2	136,137,065	136,155,444	HF	AIS	LDL-C	0.82	rs2519093	intron_variant	7.47	4	ABO	ABO
	9	9q34.2	136,137,065	136,296,530	HF	AIS	HDL-C	0.96	rs532436	intron_variant	3.46	3a	ABO	ABO
6	11	11p15.4	9,750,757	9,822,520	MI	AIS	SBP	0.87	rs360153	non_coding_transcript_exon_variant	0.73	4	SWAP70	SWAP70
7	12	12q24.12	111,281,636	113,235,279	CAD	AS	SBP	0.96	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111,281,636	113,486,539	CAD	AS	LDL-C	0.98	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111,281,636	113,486,539	CAD	AS	HDL-C	0.98	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111,281,636	113,235,279	CAD	AIS	SBP	0.97	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111,281,636	113,486,539	CAD	AIS	LDL-C	0.98	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111,281,636	113,486,539	CAD	AIS	HDL-C	0.98	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111,359,712	113,112,650	MI	AS	SBP	0.95	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111,359,712	113,030,227	MI	AS	LDL-C	0.97	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111359712	113,030,227	MI	AS	HDL-C	0.97	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111,359,712	113,112,650	MI	AIS	SBP	0.96	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111,359,712	113,030,227	MI	AIS	LDL-C	0.97	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111359712	113,030,227	MI	AIS	HDL-C	0.97	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111426615	113,024,793	HF	AS	SBP	0.95	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111,426,615	113,024,793	HF	AS	LDL-C	0.97	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111,426,615	112,985,328	HF	AS	HDL-C	0.97	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111,426,615	113,024,793	HF	AIS	SBP	0.97	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111,426,615	113,024,793	HF	AIS	LDL-C	0.98	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
	12	12q24.12	111,426,615	112,985,328	HF	AIS	HDL-C	0.98	rs3184504	missense_variant	11.21	3a	SH2B3	SH2B3
8	13	13q14.13	47,067,841	47,314,172	AF	AS	SBP	0.91	rs1535791	intron_variant	17.94	6	LRCH1	LRCH1
	13	13q14.13	47,154,966	47,290,530	AF	AS	TG	0.88	rs1535791	intron_variant	17.94	6	LRCH1	LRCH1
	13	13q14.13	47,154,966	47,290,530	AF	AS	HDL-C	0.92	rs1535791	intron_variant	17.94	6	LRCH1	LRCH1
	13	13q14.13	47,154,966	47,323,718	AF	AIS	SBP	0.89	rs9534454	intron_variant	0.68	4	LRCH1	LRCH1
	13	13q14.13	47,154,966	47,323,718	AF	AIS	TG	0.87	rs4942561	intron_variant	0.68	7	LRCH1	LRCH1
	13	13q14.13	47,154,966	47,290,530	AF	AIS	HDL-C	0.90	rs4942561	intron_variant	0.68	7	LRCH1	LRCH1
9	15	15q26.1	91,392,256	91,443,059	MI	AS	SBP	0.94	rs4932373	intron_variant	4.48	4	FES	FES
	15	15q26.1	91,392,256	91,443,059	MI	AIS	SBP	0.96	rs35346340	splice_region_variant	7.74	2b	FES	FES
	15	15q26.1	91,392,256	91,443,059	MI	AIS	LDL-C	0.91	rs35346340	splice_region_variant	7.74	2b	FES	FES
10	17	17q21.31	43,463,493	45,244,074	AF	AIS	cIMT	0.99	rs76774446	intron_variant	0.35	2b	GOSR2	RPRML
11	19	19p13.2	10,396,065	11,526,765	CAD	AS	LDL-C	0.87	rs73015024	upstream_gene_variant	1.34	7	LDLR	LDLR
	19	19p13.2	10,643,471	11,526,765	CAD	AS	cIMT	0.87	rs55997232	regulatory_region_variant	6.34	4	LDLR	LDLR
	19	19p13.2	10,643,471	11,526,765	CAD	AS	cIMT	0.87	rs55997232	regulatory_region_variant	6.34	4	LDLR	LDLR
	19	19p13.2	10,643,471	11,526,765	CAD	AIS	cIMT	0.82	rs55997232	regulatory_region_variant	6.34	4	LDLR	LDLR
	19	19p13.2	10,643,471	11,526,765	CAD	AIS	cIMT	0.82	rs55997232	regulatory_region_variant	6.34	4	LDLR	LDLR
	19	19p13.2	10,593,429	11,523,844	MI	AS	LDL-C	0.85	rs73015024	upstream_gene_variant	1.34	7	LDLR	LDLR
	19	19p13.2	10,727,014	11,523,844	MI	AS	cIMT	0.86	rs112374545	intergenic_variant	1.04	6	LDLR	LDLR
	19	19p13.2	10,727,014	11,523,844	MI	AS	cIMT	0.86	rs112374545	intergenic_variant	1.04	6	LDLR	LDLR
	19	19p13.2	10,727,014	11,523,844	MI	AIS	cIMT	0.81	rs112374545	intergenic_variant	1.04	6	LDLR	LDLR
	19	19p13.2	10,727,014	11,523,844	MI	AIS	cIMT	0.81	rs112374545	intergenic_variant	1.04	6	LDLR	LDLR

This table shows the shared genetic loci and annotation for the MOLOC results. The PPA for each CVD-CeVD-RF combination was obtained for each locus, and the best colocalized SNP was further identified. Positional and functional annotations using CADD score, RegulomeDB ranking, L2G (Locus-to-Gene), and V2G (Variant-to-Gene) were performed.
MOLOC multiple-trait colocalization, PPA posterior probability of association, CVD cardiovascular disease, CeVD cerebrovascular disease, RF risk factor, CHR the number of chromosomes, Min pos the minimum position of the locus, Max pos the maximum position of the locus, PPA posterior probability of association, CADD score combined annotation dependent depletion score, L2G locus-to-gene, V2G variant-to-gene.

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Table 3 Colocalized loci for CVDs-CeVDs-RFs triplets

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