Table 5. Comparison of risk allele frequencies between the control groups from the Pakistani studies and between the combined total of the Pakistani control groups and NPHSII.

Gene/Locus	SNP	RAF Islamabad Controls	RAF Lahore Controls	p-value	RAF NPSHII(95% CI)	p-value
MIA3	rs17465367	0.64(0.59–0.69)	0.63(0.58–0.67)	0.68	0.71(0.69–0.72)	3.42x10-5
9p21	rs10757274	0.44(0.40–0.49)	0.46(0.42–0.51)	0.60	0.48(0.47–0.50)	3.16x10-3
DAB2IP	rs7025486	0.31 (0.26–0.35)	0.32(0.27–0.36)	0.84	0.26(0.17–0.24)	4.70x10-4
CXCL12	rs1746048	0.65 (0.61–0.70)	0.64(0.59–0.68)	0.65	0.86(0.85–0.87)	<2.20x10-16
SMAD3	rs17228212	0.19 (0.15–0.22)	0.18(0.14–0.21)	0.76	0.31(0.30–0.32)	4.88x10-14
MRAS	rs9818870	0.10 (0.07–0.13)	0.09(0.06–0.12)	0.75	0.16(0.15–0.17)	2.61x10-6
SORT1	rs599839	0.72 (0.68–0.77)	0.74(0.70–0.79)	0.55	0.78(0.77–0.79)	2.03x10-3
ACE	rs4341	0.41 (0.36–0.45)	0.47(0.43–0.52)	0.05	0.52(0.50–0.53)	3.09x10-5
NOS3	rs1799983	0.16 (0.13–0.20)	0.18(0.15–0.22)	0.51	0.33(0.32–0.35)	<2.20x10-16
APOA5	rs662799	0.15 (0.12–0.18)	0.17(0.13–0.20)	0.60	0.06(0.05–0.07)	<2.20x10-16
APOB	rs1042031	0.15 (0.12–0.19)	0.13(0.09–0.16)	0.24	0.18(0.17–0.19)	9.75x10-3
CETP	rs708272	0.55 (0.50–0.60)	0.56(0.51–0.61)	0.83	0.56(0.55–0.58)	0.62
LPA	rs3789220	0.01 (0–0.02)	0.003(0–0.01)	0.81	0.02(0.01–0.02)	0.02
LPA	rs10455872	0.01 (0–0.03)	0.01(0.00–0.03)	1	0.07(0.07–0.08)	1.06x10-10
PCSK9	rs11591147	1.00	0.995 (0.00–0.01)	0.50	0.99 (0.99–0.99)	0.07
APOE	rs429358	0.09 (0.06–0.11)	0.11 (0.08–0.14)	0.52	0.17 (0.16–0.18)	1.60x10-9
APOE	rs7412	0.96 (0.94–0.98)	0.96 (0.94–0.98)	1	0.91 (0.90–0.92)	2.69x10-6
LPL	rs328	0.92 (0.89–0.94)	0.91 (0.89–0.94)	0.98	0.90 (0.89–0.91)	0.12
LPL	rs1801177	0.01 (0–0.02)	0	0.14	0.01 (0.01–0.02)	0.04

Comparisons were performed using tests of proportion. RAF = Risk Allele Frequency, CI = Confidence Interval.