Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease

Ronald, James; Rajagopalan, Ramakrishnan; Ranchalis, Jane E; Marshall, Julieann K; Hatsukami, Thomas S; Heagerty, Patrick J; Jarvik, Gail P

doi:10.1186/1476-511X-8-52

Lipids in Health and Disease

Table 2 SNPs analyzed in the CLEAR study.

From: Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease

SNP	Chr	Base Pair	Nearby Gene(s)	Minor (Major) Allele	Change in HDL/LDL per copy of minor allele (mg/dL)	Genotyped/Imputation Accuracy^f
rs11206510^ab	1	55268627	PCSK9	C (T)	-2.8 LDL	0.55
rs11591147^cd	1	55278235	PCSK9	T (G)	-16.4 LDL	Genotyped
rs12740374^a	1	109619113	CELSR2-PSRC1-SORT1	T (G)	-7.1 LDL	0.97^g
rs646776^de	1	109620053	CELSR2-PSRC1-SORT1	G (A)	-4.8 LDL	Genotyped
rs4846914^ad	1	228362314	GALNT2	G (A)	-0.7 HDL	Genotyped
rs6754295^e	2	21059688	APOB	C (A)	0.9 HDL	Genotyped
rs693^bcde	2	21085700	APOB	G (A)	-3.0 LDL	Genotyped
rs7575840^c	2	21126995	APOB	T (G)	3.7 LDL	Genotyped
rs515135^a	2	21139562	APOB	T (C)	-4.9 LDL	0.90
rs6756629^e	2	43918594	ABCG5	A (G)	-4.8 LDL	Genotyped
rs6544713^a	2	43927385	ABCG8	T (C)	4.6 LDL	1.00
rs12654264^cd	5	74684359	HMGCR	T (A)	2.7 LDL	Genotyped
rs3846662^e	5	74686840	HMGCR	G (A)	2.4 LDL	Genotyped
rs3846663^a	5	74691482	HMGCR	T (C)	2.1 LDL	0.97^h
rs1501908^a	5	156330747	TIMD4-HAVCR1	G (C)	-2.1 LDL	0.11
rs12670798^c	7	21573877	DNAH11	G (A)	2.7 LDL	0.18
rs328^cd	8	19864004	LPL	G (C)	2.9 HDL	Genotyped
rs10096633^e	8	19875201	LPL	A (G)	1.9 HDL	0.94ⁱ
rs12678919^a	8	19888502	LPL	G (A)	3.2 HDL	0.94ⁱ
rs2083637^e	8	19909455	LPL	G (A)	1.5 HDL	0.45
rs471364^a	9	15279578	TCC39B	C (T)	-1.1 HDL	No genotyped SNPs within 200 kb
rs3890182^cd	9	106687476	ABCA1	A (G)	-1.1 HDL	Genotyped
rs3905000^e	9	106696891	ABCA1	A (G)	-1.6 HDL	0.98^j
rs1883025^a	9	106704122	ABCA1	T (C)	-1.1 HDL	Genotyped
rs7395662^e	11	48475469	MADD-FOLH1	A (G)	1.0 HDL	No genotyped SNPs within 200 kb
rs174547^a	11	61327359	FADS1-FADS2-FADS3	C (T)	-1.2 HDL	1.00
rs174570^e	11	61353788	FADS1-FADS2-FADS3	A (G)	-3.4 LDL	Genotyped
rs964184^a	11	116154127	APOA1-APOC3-APOA4-APOA5	G (C)	-2.3 HDL	1.00
rs2338104^ab	12	108379551	MMAB-MVK	C (G)	-1.0 HDL	Genotyped
rs2650000^a	12	119873345	HNF1A	A (C)	2.1 LDL	0.98
rs10468017^a	15	56465804	LIPC	T (C)	1.4 HDL	0.029
rs1532085^e	15	56470658	LIPC	A (G)	1.8 HDL	0.17
rs1800588^cd	15	56510967	LIPC	T (C)	1.4 HDL	Genotyped
rs173539^a	16	55545545	CETP	T (C)	3.4 HDL	1.00
rs1800775^cd	16	55552737	CETP	A (C)	2.5 HDL	Genotyped
rs1532624^e	16	55562980	CETP	A (C)	2.9 HDL	Genotyped
rs2271293^ae	16	66459571	LCAT-CTCF-PRMT8	A (G)	1.8 HDL	0.98
rs4939883^ae	18	45421212	LIPG	A (G)	-1.4 HDL	0.92
rs2967605^a	19	8375738	ANGPTL4	T (C)	-1.6 HDL	0.76
rs1529729^c	19	11024562	LDLR	C (T)	1.9 LDL	Genotyped
rs6511720^abc	19	11063306	LDLR	T (G)	-4.6 LDL	Genotyped
rs2228671^e	19	11071912	LDLR	A (G)	-4.2 LDL	Genotyped
rs688^c	19	11227602	LDLR	T (C)	1.4 LDL	Genotyped
rs10401969^a	19	19268718	NCAN-CILP2-PBX4	C (T)	-1.5 LDL	0.22
rs16996148^bd	19	19519472	NCAN-CILP2-PBX4	T (G)	-3.1 LDL	Genotyped
rs157580^e	19	50087106	TOMM40-APOE	G (A)	-3.4 LDL	Genotyped
rs2075650^e	19	50087459	TOMM40-APOE	G (A)	4.9 LDL	Genotyped
rs4420638^abc	19	50114786	APOE	G (A)	8.9 LDL	0.81
rs6102059^a	20	38662198	MAFB	T (C)	-1.8 LDL	-0.074
rs1800961^a	20	42475778	HNF4A	T (C)	-2.6 HDL	Genotyped
rs7679^a	20	44009909	PLTP	C (T)	-1.0 HDL	Genotyped

The estimated changes in HDL or LDL per copy of the minor allele are based on effects reported in ^aKathiresan et al[14], ^bWiller CJ et al[15], ^cKathiresan et al[12], ^dKathiresan et al[13], and ^eAulchenko et al[11]. ^fOnly SNPs with estimated imputation accuracies of >90% were included in downstream analyses. ^gExcluded from downstream analyses due to r² = 1.00 with rs646776. ^hExcluded due to r² = 0.99 with rs12654264. ⁱExcluded due to r² = 0.93 and 0.95 with rs328. ^jExcluded due to r² = 0.96 with rs3890182.

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ISSN: 1476-511X

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