Rare variant analysis of blood pressure phenotypes in the Genetic Analysis Workshop 18 whole genome sequencing data using sequence kernel association test

Table 3 Causal genes with empirical power over 0.2 using any weighting scheme

Causal Genes	Number of SNPs		Number of causal SNPs¹		Total % variance explained²	All			Rare
	All	Rare	All	Rare		Equal	M-B	Default	Equal	M-B	Default
DBP
MAP4	542	392	6	5	0.04826	0.30	0.27	0.07	0.09	0.06	0.07
FLT3	639	308	4	2	0.01053	0.33	0.26	0.04	0.06	0.04	0.04
DHX8	142	89	2	2	0.00007	0.25	0.23	0.06	0.09	0.04	0.05
FGR	92	78	2	1	0.00006	0.33	0.12	0.16	0.18	0.11	0.16
TXNIP	9	6	1	1	<1.0E-5	0.09	0.16	0.25	0.33	0.21	0.29
GLUL	44	24	2	2	0.00012	0.07	0.12	0.28	0.12	0.24	0.28
PDCD6IP	359	215	4	2	0.00058	0.04	0.06	0.29	0.15	0.33	0.30
DGKE	136	71	1	0	0.00005	0.02	0.05	0.23	0.05	0.28	0.25
PTTG1IP	174	116	2	2	0.00005	0.04	0.09	0.15	0.20	0.13	0.15
EPHA2	133	93	1	1	0.00021	0.03	0.17	0.11	0.03	0.20	0.10
SBP
MAP4	542	392	7	5	0.05824	0.27	0.27	0.14	0.17	0.09	0.14
FLT3	639	308	4	2	0.00841	0.20	0.18	0.04	0.04	0.03	0.03
DHX8	142	89	2	2	0.00002	0.25	0.25	0.02	0.10	0.03	0.03
S100A6	14	11	2	2	0.00003	0.27	0.09	0.06	0.05	0.05	0.05
KRT23	79	31	2	1	0.00016	0.24	0.24	0.04	0.03	0.02	0.02
TXNIP	9	6	1	1	<1.0E-5	0.09	0.14	0.20	0.26	0.14	0.22
GLUL	44	24	2	2	0.00006	0.04	0.09	0.27	0.11	0.22	0.28
PDCD6IP	359	215	4	2	0.00027	0.04	0.08	0.33	0.17	0.36	0.33
SCAP	114	83	1	1	0.00003	0.06	0.17	0.40	0.39	0.24	0.36
EPHA2	133	93	1	1	0.00018	0.04	0.27	0.21	0.10	0.34	0.22

¹Number of causal single-nucleotide polymorphisms (SNPs) is computed based on the used annotation file (not based on the answers).
²Total % variance explained is computed by adding the percent variance explained by each SNP based on the used annotation file (not based on the answers).
Bolded text indicates the empirical power greater than 0.2.
DBP, diastolic blood pressure; M-B, Madsen-Browning; SBP, systolic blood pressure.

ISSN: 1753-6561