Replicability analysis in genome-wide association studies via Cartesian hidden Markov models

BMC Bioinformatics

Table 1 Results of repfdr and repLIS procedure when top k=500

SNP ID	Chr	repfdr ranks	repLIS ranks	repfdr values	repLIS values
rs7570682	2	−	35	1	3.7e-2
rs1375144	2	−	24	1	3.1e-2
rs2953145	2	−	25	1	3.2e-2
rs4276227^s	3	105	64	6.4e-3	4.5e-2
rs683395^s	3	99	51	6.1e-3	4.3e-2
rs10982256	9	−	305	1	7.9e-2
rs1344484	16	49	15	1.9e-3	2.3e-2
rs420259	16	255	115	1.5e-2	5.4e-2
rs3761218	20	233	−	1.4e-2	9.9e-1

^s The SNPs that are only identified by [28] and others are simultaneously identified by [29]. ’ −’ denotes a relevant SNP non-identified by the corresponding procedure. There is a significant improvement of rankings for most of these SNPs with replicated associations when conducting repLIS procedure

ISSN: 1471-2105