Table 2.

Analysis of Baseline CD4 Count Conditional on Genetic Markers, Adjusted by Age, Race, Study

Gene	SNP	Age X Genotype Interaction	Age Group	Level	Count	Adjusted Analysis			P-value cut off under FDR control at 0.1	Significant Controlling for FDR at 0.1
						Slope (LCI, UCI)	P-value	Multivariate Wald Test P-value
HLA	HLA_A-24 alleles	0.3208	All	Absence	919	1419(1267,1571)		0.043	0.010	-
				Presence	106	−130(−256,−4)	0.043
HLA	HLA_A-68 alleles	0.0496	(0, 2]	Absence	408	1436(1190,1681)		0.036	0.009	-
				Presence	64	−224(−434,−14)	0.036
HLA	HLA_B-27/57 alleles	0.0152	(0, 2]	Absence	432	1344(1081,1608)		0.025	0.008	-
				Presence	39	380(48,712)	0.025
HLA	HLA_DRB1*7 alleles	0.2431	All	Absence	829	1362(1207,1517)		0.020	0.007	-
				Presence	189	152(24,280)	0.020
IRGM	IRGM_313-C/T	0.0267	(0, 2]	C/C	218	1403(1156,1649)		0.017	0.006	-
				C/T	190	89(−98,276)	0.353
				T/T	70	470(148,792)	0.004
CCR5	CCR5_wt/delta32	0.0829	(0, 2]	wt/wt	448	1355(1097,1612)		0.016	0.005	-
				wt/D32	23	482(89,876)	0.016
APOBEC3G	APOBEC3G_197193-T/C	0.0533	(0, 2]	T/T	416	1434(1189,1678)		0.016	0.004	-
				C/C+T/C	61	−270(−490,−51)	0.016
HLA	HLA_Cw-1 alleles	0.0436	(2, 18]	Absence	523	657(538,776)		0.014	0.003	-
				Presence	29	−162(−291,−32)	0.014
MBL2	MBL2_A/O	0.0250	(2, 18]	A/A	308	646(527,765)		0.007	0.002	-
				A/O	220	−32(−103,40)	0.384
				O/O	36	229(69,389)	0.005
HLA	HLA_DRB1*3 alleles	0.0243	(0, 2]	Absence	368	1483(1229,1736)		0.007	0.001	-
				Presence	103	−269(−463,−75)	0.007

Note: This table only includes the SNPs with multivariate Wald test nominal p-value <0.05. P-values are compared to the corresponding cut off values and p-values that are less than the cut off value are considered as significant under the FDR control at the pre-specified level.

-: Not significant at FDR=0.1