Table 2.

Rare allele frequency comparison of genotyped SNPs between the ComparED and the FAS studies

GWAS locus	Genotyped SNP	Rare allele frequency		Chi-squared	p
		ComparED Study	FAS Study
IQCJ	rs62270407	0.30	0.28	0.28	0.59
IQCJ	rs7639707	0.06	0.043	0.58	0.45
NXPH1	rs12702829	0.34	0.43	4.0	0.046
NXPH1	rs1837523	0.24	0.26	0.25	0.62
NXPH1	rs1990554	0.01	0.01	0.03	0.87
NXPH1	rs6951762a	0.14	0.16	0.23	0.63
NXPH1	rs10224945a	0.11	0.10	0.35	0.55
NXPH1	rs28473103b	0.34	0.36	0.24	0.63
NXPH1	rs28673635	0.16	0.15	0.10	0.75
NXPH1	rs293180	0.11	0.10	0.003	0.96
NXPH1	rs61569932	0.004	0.01	0.80	0.37
NXPH1	rs6463808	0.14	0.18	1.19	0.27
PHF17	rs114348423	0.008	0.02	1.52	0.22
PHF17	rs28437435a	0.16	0.35	25.65	4.1 × 10−07
PHF17	rs75007521	0.02	0.029	0.89	0.34
MYB	rs210962	0.20	0.25	1.79	0.18
MYB	rs2050017a	0.15	0.15	0.02	0.90
MYB	rs72560788	0.08	0.09	0.09	0.76
MYB	rs72974149	0.08	0.09	0.38	0.54
NELL1	rs117114492	0.02	0.02	0.05	0.83
NELL1	rs78786240	0.08	0.03	8.07	0.005
NELL1	rs1850875	0.46	0.42	0.91	0.34
NELL1	rs11025436a	0.19	0.13	3.07	0.08
SLIT2	rs143662727	0.05	0.02	3.02	0.08
SLIT2	rs16869663	0.07	0.07	0.08	0.77
SLIT2	rs1216349a	0.31	0.11	34.25	4.9 × 10−09
SLIT2	rs61790364	0.24	0.18	2.76	0.10
SLIT2	rs13137813a	0.50	0.45	1.55	0.21
SLIT2	rs73241936	0.20	0.15	1.98	0.16
SLIT2	rs76015249	0.01	0.011	0.03	0.87
SLIT2	rs10009109	0.44	0.45	0.02	0.88

^aReplacement SNP in linkage disequilibrium with a SNP of the genetic risk score constructed in the FAS Study

^bSNP not in Hardy-Weinberg equilibrium