Simulation of a medication and methylation effects on triglycerides in the Genetic Analysis Workshop 20

BMC Proceedings

Table 3 Five non-causal (red-herrings) CpG markers chosen to have N(0,0.4) random variability, imitating the distribution of the 5 real causative CpG markers

Methylvar	chrom	cgposition	cggene	CpGdata Partition	rsid	rsposition	rsRole	rsGene	strand_affy	allele_affy	coded_allele	noncoded_all	coded_all_freq	p_HWE	callrate	snpid
cg00703276	3	1.3E + 08	NA	3	rs2953763	131243312		NA	–	A/G	G	A	0.987211	1	0.99881	SNP_A_8675856
cg01971676	7	4.3E + 07	HECW1	8	rs6960763	43150741	intron	HECW1	+	C/T	C	T	0.550983	0.017	0.98931	SNP_A_2264336
cg11736230	14	1E + 08	PPP1R13B	43	rs2494731	104308725	intron	AKT1	+	C/G	G	C	0.677045	0.6804	0.99406	SNP_A_2232252
cg00001261	16	3463964	NA	1	rs4786421	3462304	intron	FLJ14154	+	A/G	G	A	0.690389	0.0168	1	SNP_A_4291807
cg12598270	18	3.3E + 07	ZNF396	46	rs323312	32996624	intron	KIAA1328	–	A/G	G	A	0.858364	0.154	0.99525	SNP_A_4288135

Abbreviations: Methylvar, CpG marker name; chrom, CpG marker’s chromosome; cgposition, CpG marker position in base pairs; cggene, CpG marker’s gene; CpGdata Partition, a number that refers to a simulated data partition distributed; rsid, SNP name; rsposition, SNP’s position in base pairs; rsRole, SNP’s role; rsGene, SNP’s gene name; strand_affy, +/− strand on which the SNP is located; allele_affy – the SNP’s Affymetrix array alleles; coded_allele – coded allele; noncoded_all – noncoded allele; coded_all_freq – coded allele frequency; p_HWE – p-value for testing Hardy Weinberg Equilibrium; callrate – call rate for the SNP; snpid – Affymetrix array SNP ID

ISSN: 1753-6561