Table 1.

SNP-based overlap analysis of OA and BMD. For each comparison, the total number of SNPs present in both datasets after LD-pruning is given, as well as the number of SNPs falling below each P-value threshold (P_t). P_perm = empirical overlap p-value obtained through permutation analysis

	Combined OA				Hip OA				Knee OA
	LSBMD		FNBMD		LSBMD		FNBMD		LSBMD		FNBMD
Total number of SNPs	75,015		75,161		74,999		75,147		75,125		75,270
Pt	SNPs	P_perm	SNPs	P_perm	SNPs	P_perm	SNPs	P_perm	SNPs	P_perm	SNPs	P_perm
0.5	28,940	8.53 × 10−2	27,599	2.74 × 10−1	28,563	1.64 × 10−1	27065	7.33 × 10−1	28,910	7.95 × 10−1	27,534	5.84 × 10−2
0.1	2,633	7.92 × 10−2	2,119	5.41 × 10−1	2,513	1.46 × 10−2	2057	1.74 × 10−1	2,620	3.67 × 10−2	2,131	2.33 × 10−1
0.05	931	1.25 × 10−2	698	2.35 × 10−1	868	1.42 × 10−2	647	2.47 × 10−1	939	8.98 × 10−4	700	3.10 × 10−2
0.04	682	2.41 × 10−3	486	2.33 × 10−1	641	6.48 × 10−4	434	4.99 × 10−1	680	4.74 × 10−4	474	1.27 × 10−1
0.03	451	1.20 × 10−3	314	6.57 × 10−2	416	1.02 × 10−3	272	4.20 × 10−1	437	2.87 × 10−3	291	3.27 × 10−1
0.02	251	1.95 × 10−3	160	1.07 × 10−1	239	6.10 × 10−5	150	6.31 × 10−2	244	1.59 × 10−3	152	3.03 × 10−1
0.01	87	2.79 × 10−2	60	5.84 × 10−2	87	2.97 × 10−4	52	4.94 × 10−2	88	3.01 × 10−3	53	2.18 × 10−1
0.005	37	6.89 × 10−3	24	2.43 × 10−2	38	3.04 × 10−4	26	6.39 × 10−4	29	1.97 × 10−1	16	6.94 × 10−1
0.001	10	3.90 × 10−5	3	4.52 × 10−2	7	1.68 × 10−3	1	1.00	6	1.12 × 10−2	4	3.39 × 10−2
5 × 10−4	4	6.81 × 10−3	0	1.00	6	5.70 × 10−5	1	5.64 × 10−2	4	4.21 × 10−3	2	7.12 × 10−2