Table 1. Summary of combined association results for 941 cases and 3,291 controls.

dbSNP locus	Positiona	Alleleb	Stage	Cases	Controls	P	OR (95% CI)
				EAF	EAF
rs1906953	34144424	C/T	Discovery	0.19	0.15	4.0 × 10-05	1.45 (1.21-1.73)
6p21.31			Replication	0.21	0.12	6.5 × 10-06	2.00 (1.47-2.72)
			Combined			8.0 × 10-09	1.57 (1.35-1.83)
rs7591996	6378872	A/C	Discovery	0.50	0.45	4.8 × 10-05	1.30 (1.15-1.47)
2p25.2			Replication	0.55	0.43	5.7 × 10-06	1.69 (1.35-2.13)
			Combined			1.0 × 10-08	1.39 (1.23-1.54)
rs10208273	6441445	G/A	Discovery	0.36	0.30	3.5 × 10-06	1.37 (1.2-1.56)
2p25.2			Replication	0.34	0.29	2.7 × 10-02	1.31 (1.03-1.67)
			Combined			2.9 × 10-07	1.35 (1.21-1.52)
rs17206779	64483533	T/C	Discovery	0.53	0.47	2.2 × 10-05	1.32 (1.16-1.49)
5q12.3			Replication	0.54	0.46	6.7 × 10-03	1.37 (1.09-1.72)
			Combined			5.1 × 10-07	1.33 (1.19-1.47)

The discovery stage consists of the combined scans of Stage 1A (596 cases) and Stage 1B (98 cases) for a total of 694 scanned osteosarcoma cases and 2,703 cancer-free adult controls, all of European ancestry. The independent replication set consisted of 247 osteosarcoma cases genotyped by TaqMan and 588 controls previously scanned on Illumina Omni2.5 or OmniExpress. The combined results report the data from the meta analysis of Stage 1and the TaqMan replication (941 cases and 3,291 controls).

Abbreviations: EAF, effect (coded) allele frequency; OR, odds ratio; CI, confidence interval.

^aBuild 36 position;

^bReference/Effect alleles.