. Author manuscript; available in PMC: 2023 Oct 26.

Published in final edited form as: Nat Genet. 2023 Sep 28;55(10):1651–1664. doi: 10.1038/s41588-023-01518-4

Table 1 |.

Novel and known independent lead SNPs associated with coronary artery calcification

rsID	Chr	Pos (hg19)	Effect/ Other allele	EAF	Effect	SE	P _meta	I ²	P _het	Nearest gene(s)	Annotation

*Novel loci for coronary artery calcification quantity*

rs3844006	6	132,095,002	T/C	0.221	−0.114	0.020	7.56E-09	0.5	0.453	miR-548h-5 (dist: 18,309 bp), ENPP3 (dist.: 26,449 bp), ENPP1 (dist.: 34,154 bp)	intergenic
rs2854746	7	45,960,645	C/G	0.414	0.110	0.018	5.33E-10	0	0.760	IGFBP3	missense
rs10899970	10	44,515,716	A/G	0.474	0.095	0.017	2.91E-08	0	0.940	AL512640.1 (dist.:14,271 bp), CXCL12 (dist: 366,225 bp)	intergenic
rs9633535	10	63,836,088	T/C	0.371	0.098	0.018	2.57E-08	4	0.407	ARID5B	intronic
rs10762577	10	75,917,431	A/G	0.258	−0.107	0.019	4.09E-08	0	0.683	ADK	intronic
rs11063120	12	4,486,618	A/G	0.303	−0.133	0.022	2.78E-09	56	0.001	FGF23	intronic
rs9515203	13	111,049,623	T/C	0.732	0.123	0.022	1.43E-08	0	0.744	COL4A1 (dist: 90,119 bp), COL4A2 (dist: -91,464 bp)	intronic
rs7182103	15	79,123,946	T/G	0.575	0.112	0.017	1.62E-11	4.1	0.405	ADAMTS7 (dist.: -20,140 bp), MORF4L1 (dist.: 21,117 bp)	intronic

*Known loci for coronary artery calcification quantity*

rs10456561	6	12,887,465	A/G	0.036	0.375	0.069	4.76E-08	14.7	0.292	PHACTR1	intronic
rs35355695	6	12,891,103	T/G	0.256	−0.115	0.020	4.87E-09	5.2	0.390	PHACTR1	intronic
rs9349379	6	12,903,957	A/G	0.623	−0.218	0.020	6.11E-29	18	0.234	PHACTR1	intronic
rs10811650	9	22,067,593	A/G	0.619	−0.195	0.018	2.15E-27	53.2	0.003	CDKN2B-AS1	ncRNA intronic
rs72652478	9	22,102,043	C/G	0.957	−0.479	0.081	3.82E-09	0	0.983	CDKN2B-AS1	ncRNA intronic
rs62555371	9	22,107,238	A/T	0.866	0.270	0.032	5.49E-17	20.9	0.190	CDKN2B-AS1	ncRNA intronic
rs4977575	9	22,124,744	C/G	0.455	−0.264	0.018	7.49E-47	45	0.012	CDKN2B-AS1 (dist.: -3,651 bp), CDKN2B (dist: 115,440 bp)	intergenic
rs7412	19	45,412,079	T/C	0.090	−0.313	0.039	4.42E-16	0	0.657	APOE	missense

Top lead SNP in genomic risk loci associated with coronary artery calcification quantity at a significance level of P < 5 × 10⁻⁸ for the combined-ancestry meta-analysis (up to 35,776 individuals from 22 studies). SNP effect sizes (Beta) and two-sided P−values (P_META) were derived from weighted Z−scores in fixed effects model and central association P−values determined from chi-square test statistics. rsID, rsID of the lead SNP. Lead SNP chromosome (Chr) and position (Pos) are provided in hg19/b37 and hg38. Effect/Other allele indicates the effect and other (non-effect) allele. EAF, effect allele frequency. Effect, effect size. SE, standard error of the effect. P_meta, P−value of association of the lead SNP with CAC after multi-ancestry meta-analysis. I², heterogeneity statistic indicating the variation between CAC quantity across the studies, expressed as a percent. P_het, P−value of the heterogeneity test; P > 0.05 is indicative of study homogeneity for a given SNP. Nearest gene(s), nearest gene upstream or downstream and nearest protein-coding gene(s) to lead SNP, with distance to canonical TSS for intergenic SNPs or intronic with equidistant protein-coding genes. Annotation, functional annotation of lead SNP.

Reported is either the gene that overlaps with the SNP or the nearest gene(s) up- and downstream of the sentinel variant (separated by a comma).

SNP rs4977575 and rs10811650 reside 57,151 bp apart (r² = 0.116, D′ = 0.643).

SNP rs4977575 and rs62555371 reside 17,506 bp apart (r² = 0.076, D′ = 0.983).

SNP rs9349379 and rs35355695 reside 12,854 bp apart (r² = 0.088, D′ = 0.988).

SNP rs9349379 and rs10456561 reside 16,492 bp apart (r² = 0.027, D′ = 0.981).