An empirical evaluation of the common disease-common variant hypothesis

BMC Proceedings

Table 1 Comparison of SNPs linked versus those associated with 3550 phenotypes

Thresholds			SNP category^a			Minor allele frequencies			β Coefficients (for associated SNPs)
Phenotypes	Linkage (LOD)	Assoc (Z)	A	L	Number	Range	Median	Mean	Range	Median	Mean
3550	4.99	6.66	+	+	6	0.01–0.02	0.01	0.01	2.4–5.7	4.7	4.4
			+	-	221	0.01–0.5	0.01	0.03	0.36–5.5	3.8	3.5
			-	+	15970	0.01–0.5	0.24	0.25
			-	-	510738	0.01–0.5	0.23	0.25
355^b	4.03	6.32	+	+	12	0.01–0.38	0.02	0.05	0.4–5.7	3.5	3.3
			+	-	293	0.01–0.5	0.01	0.04	0.3–5.4	3.2	3.1
			-	+	19276	0.01–0.5	0.23	0.25
			-	-	507354	0.01–0.5	0.23	0.25
108^c	3.54	6.13	+	+	21	0.01–0.38	0.02	0.06	0.27–5.7	2.4	2.7
			+	-	335	0.01–0.5	0.01	0.04	0.16–5.4	3.2	3.1
			-	+	29387	0.01–0.5	0.23	0.25
			-	-	497192	0.01–0.5	0.23	0.25
3550	3.3^d	5.34^d	+	+	82	0.01–0.5	0.07	0.12	0.2–5.7	1.1	1.6
			+	-	1118	0.01–0.5	0.06	0.12	0.16–5.7	1.3	1.7
			-	+	36239	0.01–0.5	0.23	0.25
			-	-	489496	0.01–0.5	0.23	0.25

^a A denotes a significant association, L denotes a significant linkage
^b Most heritable phenotypes (10%).
^c Phenotypes with >50% heritablility.
^d Relaxed thresholds: alpha levels do not account for testing of multiple phenotypes

ISSN: 1753-6561