Table 3.

Overall joint probabilities from non-HLA (6p21) genomic regions suggestive of genetic association

Gene	SNP	Chr	Position (Mb)	MAF (affected women)	MAF (controls)	Minor allele	Set 1 P	Set 2 P	Set 3 P	Set 4 P	Overall joint P	OR	95% CI
NMNAT2	rs2022013	1q25.3	181.620476	0.3797	0.4197	G	0.27761	0.00061	0.04818	0.00002	1.08E-07	0.85	0.79–0.9
-	rs2431697	5q33.3	159.812556	0.3848	0.4342	C	0.00180	0.05430	0.00093	0.01260	1.00E-10	0.82	0.77–0.87
-	rs6568431	6q21	106.695499	0.4237	0.3812	A	0.00066	0.01535	0.00797	0.26498	1.74E-08	1.19	1.12–1.27
ATG5	rs573775	6q21	106.871559	0.3178	0.281	T	0.03760	0.00005	0.00427	0.95153	1.36E-07	1.19	1.12–1.27
ICA1	rs10156091	7p21.3	8.153619	0.1198	0.0969	A	0.03768	0.00003	0.03378	0.10622	1.90E-07	1.32	1.19–1.47
TNPO3	rs10239340	7q32.1	128.455746	0.324	0.3842	T	0.04340	3.73E-07	7.42E-06	0.10424	6.98E-16	0.77	0.73–0.82
-	rs6601327	8p23.1	9.432942	0.4039	0.3649	C	0.00059	0.06181	0.38560	0.01097	1.99E-07	1.18	1.11–1.25
XKR6	rs6985109	8p23.1	10.798995	0.5138	0.462	G	0.00123	0.09025	0.00082	0.00430	2.51E-11	1.23	1.16–1.3
XKR6	rs4240671	8p23.1	10.805158	0.4499	0.4947	A	0.34769	0.12244	0.00552	0.00347	6.60E-09	0.75	0.68–0.83
XKR6	rs11783247	8p23.1	10.826285	0.5099	0.4627	C	0.00469	0.10787	0.00150	0.02095	8.00E-10	1.21	1.14–1.28
XKR6	rs6984496	8p23.1	10.833503	0.5078	0.4588	C	0.00164	0.13155	0.00066	0.02292	2.00E-10	1.22	1.14–1.29
C8orf12	rs7836059	8p23.1	11.309574	0.439	0.4871	T	0.00606	0.08327	0.01088	0.00647	4.00E-10	0.82	0.78–0.88
BLK	rs2248932	8p23.1	11.429059	0.3928	0.3475	T	0.00751	0.45841	0.06147	0.00001	7.00E-10	1.22	1.14–1.3
-	rs10903340	8p21.1	11.487996	0.4593	0.4193	C	0.00346	0.31025	0.07304	0.02869	1.46E-07	1.18	1.11–1.25
LYN	rs7829816	8q12	57.011940	0.1844	0.2159	C	0.52653	0.00187	0.00016	0.95150	5.40E-09	0.77	0.70–0.84
LYN	rs2667978	8q12	57.060505	0.19	0.2244	C	0.00021	0.02071	0.00701	0.51240	5.10E-08	0.81	0.76–0.88
UBE2L3	rs5754217	22q11.21	20.269675	0.2287	0.1953	A	0.01589	0.00187	0.20201	0.01842	7.53E-08	1.22	1.14–1.32
SCUBE1	rs2071725	22q13.2	41.939704	0.1176	0.1453	A	0.00255	0.01762	0.00015	0.84821	1.21E-07	0.78	0.72–0.86

Listed are SNP_s that exceed P < 2 × 10⁻⁷ in the overall joint analysis but not P < 0.05 in each individual set, in contrast to Table 1. The additive model is presented unless the test for lack of fit to an additive model was significant (P < 0.05), as for rs7829816 and rs1015609 (dominant). Chr, chromosome; MAF, minor allele frequency. Odds ratio (OR) is shown with 95% confidence interval (CI) boundaries. Positions are from build 35 throughout.