Novel risk genes identified in a genome-wide association study for coronary artery disease in patients with type 1 diabetes

Charmet, Romain; Duffy, Seamus; Keshavarzi, Sareh; Gyorgy, Beata; Marre, Michel; Rossing, Peter; McKnight, Amy Jayne; Maxwell, Alexander P.; Ahluwalia, Tarun veer Singh; Paterson, Andrew D.; Trégouët, David-Alexandre; Hadjadj, Samy

doi:10.1186/s12933-018-0705-0

Cardiovascular Diabetology

Table 2 Replication of CAD SNPs previously identified in the general population

From: Novel risk genes identified in a genome-wide association study for coronary artery disease in patients with type 1 diabetes

SNP	CHR	BP	Locus	Published GWAS results			Discovery GWAS in T1D patients
SNP	CHR	BP	Locus	EA^a	EAF^b	OR^c	EAF^d	OR^e	[95% CI]	P^f	Direction^g	Power^h
rs11206510	1	55496039	PCSK9	T/C	0.848	1.08	0.815	1.08	[0.883–1.324]	0.223	−++	0.150
rs9970807	1	56965664	PPAP2B	C/T	0.915	1.13	0.906	1.21	[0.904–1.625]	0.098	+++	0.380
rs7528419	1	109817192	SORT1	A/G	0.786	1.12	0.784	1.11	[0.918–1.348]	0.138	+++	0.260
rs11810571	1	151762308	TDRKH	G/C	0.849	1.06	0.854	1.05	[0.836–1.316]	0.339	−+−	0.080
rs1892094	1	169094459	ATP1B1	T/C	0.500	0.96	0.529	1.08	[0.919–1.266]	0.822	−++	0.200
rs6700559	1	200646073	DDX59	T/C	0.470	0.96	0.460	1.15	[0.982–1.338]	0.958	+−+	0.520
rs2820315	1	201872264	LMOD1	T/C	0.300	1.05	0.298	0.97	[0.820–0.156]	0.618	−++	0.060
rs17464857	1	222762709	MIA3	T/G	0.861	1.06	0.842	1.12	[0.901–1.405]	0.148	+++	0.250
rs16986953	2	19942473	AK097927	A/G	0.105	1.09	0.075	1.07	[0.799–1.450]	0.314	+++	0.080
rs7567217	2	21303470	APOB	T/C	0.860	1.07	0.858	1.02	[0.811–1.297]	0.415	−+	0.060
rs7568458	2	85788175	GGCX	A/T	0.449	1.06	0.460	1.06	[0.904–1.247]	0.232	+−+	0.140
rs17678683	2	145286559	ZEB2	G/T	0.088	1.10	0.079	1.23	[0.900–1.692]	0.095	+−	0.390
rs2252641	2	145801461	ZEB2	C/T	0.475	1.03	0.450	1.01	[0.867–1.186]	0.430	++−	0.050
rs1250229	2	216304384	FN1	T/C	0.256	1.07	0.260	0.88	[0.730–1.060]	0.911	−	0.390
rs2571445	2	218683154	TNS1	A/G	0.390	1.04	0.388	1.05	[0.894–1.234]	0.275	+−+	0.110
rs1801251	2	233633460	KCNJ13	A/G	0.350	1.05	0.344	1.15	[0.975–1.352]	0.049	++−	0.490
rs7623687	3	49448566	RHOA	A/C	0.855	1.08	0.864	0.96	[0.756–1.212]	0.626	+++	0.060
rs142695226	3	124475201	ITGB5	G/T	0.138	1.07	0.152	0.95	[0.754–1.195]	0.672	−+−	0.090
rs201477372	3	138099161	MRAS	TTTC/T	0.163	1.08	0.155	1.02	[0.829–1.264]	0.411	−+−	0.060
rs12493885	3	153839866	ARHGEF26	C/G	0.886	1.07	0.866	0.87	[0.691–1.089]	0.890	+−	0.260
rs17087335	4	57838583	NOA1	T/G	0.210	1.06	0.177	0.99	[0.812–1.215]	0.523	−++	0.050
rs10857147	4	81181072	FGF5	T/A	0.275	1.05	0.282	1.02	[0.855–1.215]	0.417	++−	0.060
rs7678555	4	120909501	MAD2L1	C/A	0.301	1.05	0.287	0.92	[0.770–1.100]	0.818	−+	0.200
rs4593108	4	148281001	MIR548G	C/G	0.795	1.07	0.831	0.93	[0.761–1.145]	0.743	+−	0.110
rs1878406	4	148393664	EDNRA	C/T	0.844	0.94	0.894	0.94	[0.740–1.208]	0.328	−+	0.070
rs72689147	4	156639888	GUCY1A3	G/T	0.817	1.07	0.812	1.13	[0.919–1.390]	0.122	+++	0.300
rs273909	5	131667353	SLC22A4	G/A	0.117	1.06	0.104	0.94	[0.726–1.217]	0.680	−	0.090
rs246600	5	142516897	ARHGAP26	T/C	0.480	1.05	0.486	0.98	[0.839–1.155]	0.575	−+−	0.060
rs9349379	6	12903957	PHACTR1	G/A	0.432	1.14	0.392	1.07	[0.919–1.267]	0.174	+++	0.200
rs7454157	6	12909874	PHACTR1	G/A	0.651	1.10	0.622	1.15	[0.978–1.371]	0.044	+++	0.550
rs6909752	6	22612629	HDGFL1	A/G	0.351	1.05	0.374	1.01	[0.851–1.186]	0.476	−+−	0.050
rs3130683	6	31888367	C2	T/C	0.860	1.09	0.960	0.69	[0.455–1.034]	0.964	+−	0.580
rs17609940	6	35034800	ANKS1A	G/C	0.824	1.03	0.796	1.32	[1.077–1.635]	0.004	+++	0.890
rs56336142	6	39134099	KCNK5	T/C	0.807	1.07	0.786	1.04	[0.860–1.265]	0.333	+−	0.080
rs10947789	6	39174922	KCNK5	T/C	0.775	1.05	0.753	1.07	[0.890–1.293]	0.229	+−+	0.150
rs12202017	6	134173151	TCF21	A/G	0.700	1.07	0.713	1.02	[0.856–1.215]	0.411	+−	0.060
rs12190287	6	134214525	TCF21	C/G	0.617	1.06	0.633	1.06	[0.896–1.270]	0.232	+−	0.150
rs2048327	6	160863532	SLC22A3	T/C	0.646	0.94	0.633	1.00	[0.854–1.188]	0.538	−+−	0.050
rs3798220	6	160961137	LPA	T/C	0.975	0.70	0.986	0.74	[0.397–1.393]	0.178	+−	0.140
rs55730499	6	161005610	LPA	T/C	0.056	1.37	0.079	1.22	[0.925–1.609]	0.078	+0+	0.350
rs4252185	6	161123451	PLG	C/T	0.060	1.34	0.087	1.15	[0.862–1.541]	0.168	+++	0.210
rs4252120	6	161143608	PLG	T/C	0.740	1.03	0.709	0.91	[0.766–1.084]	0.852	−+	0.240
rs2023938	7	19036775	HDAC9	T/C	0.897	0.94	0.899	0.87	[0.679–1.135]	0.161	+−	0.200
rs2107595	7	19049388	HDAC9	A/G	0.200	1.08	0.174	1.14	[0.926–1.406]	0.106	+++	0.310
rs12539895	7	107091849	COG5	C/A	0.807	1.04	0.788	1.14	[0.931–1.394]	0.101	+−+	0.350
rs10953541	7	107244545	BCAP29	C/T	0.783	1.05	0.750	1.16	[0.967–1.401]	0.054	++−	0.490
rs11556924	7	129663496	ZC3HC1	C/T	0.687	1.08	0.593	0.97	[0.832–1.147]	0.610	−+	0.060
rs10237377	7	139757136	PARP12	T/G	0.350	0.95	0.362	0.91	[0.766–1.084]	0.148	−+−	0.260
rs3918226	7	150690176	NOS3	T/C	0.060	1.14	0.088	0.90	[0.672–1.212]	0.751	−++	0.140
rs264	8	19813180	LPL	G/A	0.853	1.06	0.846	0.94	[0.756–1.168]	0.711	−+	0.100
rs2954029	8	126490972	TRIB1	A/T	0.551	1.04	0.529	1.05	[0.896–1.232]	0.269	++−	0.110
rs3217992	9	22003223	CDKN2BAS1	C/T	0.607	0.88	0.614	0.92	[0.789–1.084]	0.169	−	0.200
rs2891168	9	22098619	CDKN2BAS1	G/A	0.489	1.21	0.505	1.16	[0.993–1.362]	0.030	+++	0.6
rs2519093	9	136141870	ABO	T/C	0.191	1.08	0.186	0.98	[0.800–1.203]	0.571	−++	0.060
rs2487928	10	30323892	KIAA1462	A/G	0.418	1.06	0.458	1.08	[0.924–1.271]	0.161	−++	0.220
rs2624695	10	44549767	CXCL12	C/T	0.534	0.94	0.503	1.08	[0.926–1.270]	0.843	+++	0.220
rs501120	10	44753867	CXCL12	T/C	0.813	1.08	0.863	1.18	[0.927–1.508]	0.088	+++	0.400
rs11203043	10	90989279	LIPA	G/A	0.576	1.04	0.551	0.89	[0.764–1.052]	0.909	−	0.360
rs1412444	10	91002927	LIPA	T/C	0.369	1.07	0.326	0.94	[0.798–1.116]	0.749	−+−	0.130
rs11191416	10	104604916	CYP17A1	T/G	0.873	1.08	0.915	0.90	[0.686–1.186]	0.768	+−	0.120
rs11042937	11	10745394	MRVI1-CTR9	T/G	0.490	1.04	0.499	1.06	[0.908–1.248]	0.220	++−	0.150
rs3993105	11	13303071	ARNTL	T/C	0.704	1.05	0.693	1.03	[0.866–1.228]	0.364	−+−	0.070
rs12801636	11	65391317	PCNX3	A/G	0.230	0.95	0.225	0.98	[0.810–1.189]	0.425	+−	0.060
rs590121	11	75274150	SERPINH1	T/G	0.300	1.05	0.295	0.80	[0.669–0.961]	0.992	−	0.830
rs9319428	13	28973621	FLT1	A/G	0.314	1.04	0.289	1.03	[0.874–1.227]	0.339	−++	0.070
rs4773144	13	110960712	COL4A2	A/G	0.572	0.95	0.555	0.99	[0.850–1.172]	0.493	−++	0.050
rs11838776	13	111040681	COL4A2	A/G	0.263	1.07	0.284	1.33	[1.113–1.606]	0.001	++−	0.980
rs9515203	13	111049623	COL4A2	T/C	0.761	1.07	0.736	1.20	[0.983–1.468]	0.036	+++	0.650
rs10139550	14	100145710	HHIPL1	G/C	0.423	1.06	0.413	0.96	[0.819–1.145]	0.645	−+	0.070
rs6494488	15	65024204	RBPMS2	G/A	0.180	0.95	0.151	1.01	[0.803–1.280]	0.545	+−	0.050
rs56062135	15	67455630	SMAD3	C/T	0.790	1.07	0.758	1.07	[0.893–1.302]	0.214	++−	0.160
rs7173743	15	79141784	ADAMTS7	T/C	0.564	1.08	0.515	1.00	[0.855–1.171]	0.495	−++	0.050
rs8042271	15	89574218	ABHD2	G/A	0.900	1.10	0.947	0.93	[0.602–1.457]	0.613	−+	0.070
rs17514846	15	91416550	FURIN-FES	A/C	0.440	1.05	0.461	1.08	[0.924–1.267]	0.163	++−	0.210
rs1800775	16	56995236	CETP	C/A	0.510	1.04	0.524	0.99	[0.844–1.153]	0.568	−+−	0.050
rs1050362	16	72130815	DHX38	A/C	0.380	1.04	0.351	1.11	[0.939–1.313]	0.110	+−+	0.310
rs7500448	16	83045790	CDH13	A/G	0.752	1.06	0.755	1.09	[0.894–1.321]	0.202	+−+	0.190
rs216172	17	2126504	SMG6	C/G	0.350	1.05	0.368	1.13	[0.963–1.329]	0.067	+++	0.420
rs12936587	17	17543722	RAI1	G/A	0.611	1.03	0.542	1.00	[0.857–1.174]	0.480	−++	0.050
rs17608766	17	45013271	GOSR2	C/T	0.140	1.07	0.133	0.89	[0.705–1.121]	0.840	−	0.220
rs999474	17	46987665	UBE2Z	G/A	0.600	1.04	0.572	0.92	[0.789–1.084]	0.832	−	0.130
rs7212798	17	59013488	BCAS3	C/T	0.150	1.08	0.155	0.98	[0.786–1.221]	0.570	−++	0.060
rs1867624	17	62387091	PECAM1	C/T	0.390	0.96	0.377	1.06	[0.898–1.241]	0.744	+++	0.130
rs663129	18	57838401	U4/MC4R	A/G	0.260	1.06	0.237	1.01	[0.847–1.227]	0.418	++−	0.060
rs1122608	19	11163601	LDLR	G/T	0.770	1.07	0.756	0.87	[0.731–1.048]	0.926	+−	0.380
rs56289821	19	11188247	LDLR	G/A	0.900	1.14	0.880	1.10	[0.855–1.427]	0.223	+−+	0.170
rs12976411	19	32882020	ZNF507	A/T	0.910	1.61	0.958	0.96	[0.639–1.460]	0.564	−+	0.050
rs8108632	19	41854534	TGFB1	T/A	0.488	1.05	0.445	1.11	[0.938–1.307]	0.113	++−	0.330
rs2075650	19	45395619	TOMM40	A/G	0.865	0.93	0.869	0.74	[0.596–0.919]	0.003	−	0.870
rs445925	19	45415640	APOE/APOC1	G/A	0.902	1.09	0.893	0.87	[0.681–1.129]	0.844	++−	0.210
rs4420638	19	45422946	APOE/APOC1	G/A	0.166	1.10	0.171	1.20	[0.985–1.461]	0.034	+−+	0.530
rs1964272	19	46190268	SNRPD2	G/A	0.510	1.05	0.509	0.95	[0.805–1.113]	0.747	−+	0.110
rs867186	20	33764554	PROCR	G/A	0.110	0.93	0.094	1.26	[0.974–1.623]	0.961	+++	0.490
rs28451064	21	35593827	KCNE2	A/G	0.121	1.14	0.126	1.36	[1.066–1.751]	0.006	+−+	0.890
rs180803	22	24658858	POM121L9P	G/T	0.970	1.20	0.979	1.18	[0.510–2.743]	0.348	−++	0.120

^aEstimated allele/non estimated allele
^bAllele frequency of the estimate allele reported in [14, 24,25,26]
^cOdds ratio for CAD reported in [14, 24,25,26]
^dAllele frequency of the estimated allele in the discovery GWAS of T1D patients
^eOdds ratio for CAD [95% confidence interval] observed in the discovery GWAS of T1D patients
^fOne sided test p value of association
^gDirectionality of the effects across the contributing cohorts
^hPower estimates were provided by the CaTS program [23] and correspond to the power of our discovery GWAS to achieve 0.05 statistical significance at the observed associations based on EAF^d and OR^e under the assumption of a multiplicative model (on log-scale)

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