Table 3.

Combined phenotypes

Trait	SNP rs ID	Chr	Physical location (bp)	GEE P-value	FBAT P-value	IN/NEAR gene
3a. SNPs significant for 3 correlated phenotypes at exam 7 by either GEE or FBAT at p < 0.01
Interleukin-6, C-reactive protein and Fibrinogen	rs10511884	9	31668988	5.7*10-5	0.0065
	rs1887027	10	6153788	2.6*10-4	0.19	IL2RA, RBM17
	rs2831617	21	28481515	6.2*10-4	0.0027
	rs2831620	21	28481869	6.4*10-4	0.0022
	rs2831618	21	28481749	6.4*10-4	0.0020
	rs2044401	9	31659518	6.6*10-4	0.12
	rs1457590	3	21530978	0.0019	0.16	ZNF659
	rs6848323	4	113286305	0.0022	0.14
	rs3110134	8	60260538	0.0025	0.12
	rs2016740	4	113238018	0.0039	0.17
	rs719006	15	59210481	0.0044	0.76	RORA
	rs877936	4	113238472	0.0055	0.31
	rs1436136	4	113421130	0.0062	0.039
	rs1436336	3	106156256	0.0067	0.0040
	rs698270	3	137592210	0.0086	0.020	STAG1
	rs847428	7	16803192	0.019	0.025
	rs2359763	3	23424931	0.024	0.0025
	rs7969455	12	7757402	0.059	0.0015	DPPA3
	rs10503717	8	22634817	0.06	0.0028
	rs4899940	14	87623621	0.11	0.0019
3b. Combined phenotypes within a specific biological domain
C-reactive protein: exams 2, 5, 6, 7	rs2808629	1	156489869	6.9*10-5	4.7*10-4	NFIA, CRP
	rs2794520	1	156491889	6.1*10-5	4.85*10-4	FCER1A, CRP
	rs6563212	13	35380415	7.3*10-4	0.30	DCAMKL1
	rs11626844	14	72413330	5.1*10-3	0.17	OR10J1, DPF3
	rs9319160	13	84918646	0.002	0.09
	rs910232	1	17143820	0.002	0.01	MAGI1, PADI2
Liver function: Alkaline phosphatase; AST; ALT; GGT	rs4911146	20	32103708	0.01	8.4*10-6	ARL6IP6, RALY
	rs953402	3	5986639	0.01	9.1*10-6	FMNL2
Vitamin D, Vitamin K phylloquinone & Vitamin K % undercarboxylated osteocalcin	rs1376544	4	180293700	0.02	9.2*10-6

Chr = chromosome;

For a given SNP, all of the phenotypes either FBAT or GEE significant if FBAT < 0.01 for particular SNP;

P-values = the geometric mean of the p-value for all traits within the biomarker cluster