Table 2.

Properties of the 18 SNPs in the APOA1/C3/A4/A5 gene cluster

Gene	DbSNP No.	SNP name	Variant type	Chromosome position (bp)	Intermarker distances (bp)	Allele	MAF	% Geno	HWE P value
APOA5	rs3135506	APOA5_S19W	Coding nonsynonymous (Trp/Ser)	116167617	–	C/G	0.068	100.0	0.493
	rs662799	APOA5_M1123	5′ Flanking	116168917	1300	G/A	0.062	99.8	0.398
APOA4	rs1263177	APOA4_A5INTER	3′ Flanking	116180028	11 111	C/T	0.353	99.7	0.107
	rs5110	APOA4_Q360H	Coding nonsynonymous (His/Gln)	116196844	16 816	T/G	0.088	99.8	0.004
	rs675	APOA4_T347S	Coding nonsynonymous (Ser/Thr)	116196885	41	A/T	0.183	99.9	0.582
	rs5104	APOA4_N147S	Coding nonsynonymous (Asn/Ser)	116197544	659	G/A	0.130	99.8	0.966
	rs5092	APOA4_T29T	Coding, synonymous	116198674	1130	G/A	0.173	99.8	0.142
	rs5090	APOA4_M35	5′ Flanking	116199265	591	C/G	0.051	100.0	0.832
APOC3	rs2542051	APOC3_M2886	5′ Flanking	116202948	3683	C/A	0.348	99.8	0.463
	rs2542052	APOC3_M640	5′ Flanking	116205194	2246	A/C	0.360	99.9	0.228
	rs2854117	APOC3_M482	5′ Flanking	116205352	158	A/G	0.250	99.8	0.469
	rs2854116	APOC3_M455	5′ Flanking	116205379	27	G/A	0.356	99.7	0.160
	rs4520	APOC3_G34G	Coding, synonymous	116206745	1366	T/C	0.262	100.0	0.393
	rs5128	APOC3_3U386	Exon, untranslated	116208850	2105	C/G	0.094	99.9	0.384
APOA1	rs670	APOA1_M75	5′ Flanking	116213623	4773	A/G	0.160	99.9	0.136
	rs613808	APOA1_M2630	5′ Flanking	116216178	2555	A/G	0.292	100.0	0.482
	rs2727784	APOA1_M2803	5′ Flanking	116216351	173	G/A	0.353	99.8	0.521
	rs11216158	APOA1_M3012	5′ Flanking	116216560	209	A/G	0.128	99.8	0.652

APOA4_Q360H (rs5110) was excluded from the association analysis because of deviation from the Hardy–Weinberg equilibrium.

Boldface indicates tag SNPs. Bold italic indicates minor alleles.

% Geno, completeness of genotyping call; Asn, asparagine; Gln, glutamine; HET, heterozygosity; His, histidine; HWE, Hardy–Weinberg equilibrium; MAF, minor allele frequency; Ser, serine; SNP, single nucleotide polymorphism; Thr, threonine; Trp, tryptophan.