Table 2. Top associations between single risk alleles and subphenotypes.

PHENOTYPE*	SNP	GENE	Unadjusted p†	FDR‡ p	OR† (95% CI)
anti-dsDNA antibodies	rs7574865	STAT4	4.40E–05	0.00097	1.40 (1.19–1.64)
anti–dsDNA antibodies	rs2187668	HLA-DR3	0.00090	0.0099	1.37 (1.14–1.65)
renal disorder	rs2187668	HLA-DR3	0.00060	0.013	1.37 (1.14–1.64)
anti-dsDNA antibodies	rs5754217	UBE2L3	0.0033	0.020	1.31 (1.09–1.56)
anti-dsDNA antibodies	rs9888739	ITGAM	0.0037	0.020	1.32 (1.09–1.59)
age at diagnosis<34 years	rs7574865	STAT4	0.0013	0.029	1.27 (1.01–1.47)
immunologic disorder	rs4963128	KIAA1542	0.0019	0.036	0.79 (0.68–0.92)
immunologic disorder	rs9462015	UHRF1BP1	0.0033	0.036	1.25 (1.08–1.44)
arthritis	rs9888739	ITGAM	0.0017	0.038	0.72 (0.59–0.88)

*anti-dsDNA positivity defined by presence of any positive test versus presence of all negative tests; renal disorder, immunologic disorder, and arthritis defined as in the 1987 ACR criteria [13], [14].

†: Logistic regression adjusted for PC1-PC4, parent study, disease duration, and gender.

‡: 5% False Discovery Rate by Benjamin-Hochberg method [16].