Table 2.

Association results for selected SNPs in the discovery cohort and replication cohort and all cases and controls combined

SNP	CHR	BP (hg19)	A1	F_A	F_U	A2	P-Discovery	OR-Discovery	F_A	F_U	P-Replication	OR-Replication	P-meta	OR-Meta	Gene	Region
rs12995389	2	6485953	A	0.31	0.41	G	8.04 × 10−8	0.66	0.38	0.40	0.464	0.91	2.35 × 10−7	0.72	LOC400940;LINC01247	intergenic
rs9287675	2	6494761	A	0.24	0.32	G	5.03 × 10−7	0.66	0.30	0.31	0.817	0.97	3.37 × 10−6	0.73	LOC400940;LINC01247	intergenic
rs7598285	2	6505563	G	0.21	0.32	A	2.70 × 10−12	0.55	0.30	0.30	0.891	0.98	1.69 × 10−10	0.65	LINC01247	downstream
rs10519086	2	67262646	G	0.02	0.08	T	5.61 × 10−11	0.18	0.07	0.09	0.164	0.72	6.82 × 10−11	0.42	LINC01799;LINC01828	intergenic
rs72809129	2	77475663	A	0.24	0.35	C	6.97 × 10−10	0.59	0.43	0.47	0.268	0.87	1.42 × 10−9	0.67	LRRTM4	intronic
rs7422259	2	167377995	T	0.04	0.11	G	1.11 × 10−9	0.37	0.10	0.14	0.076	0.71	3.60 × 10−10	0.49	SCN7A;XIRP2	intergenic
rs4959041	6	30077967	C	0.25	0.27	T	6.90 × 10−6	0.92	0.23	0.25	0.279	0.86	5.88 × 10−6	0.91	TRIM31-AS1	ncRNA_intronic
rs9261445	6	30094788	T	0.23	0.26	G	4.37 × 10−7	0.86	0.23	0.25	0.298	0.86	5.30 × 10−7	0.86	TRIM31-AS1;TRIM40	intergenic
rs9261453	6	30099948	G	0.24	0.26	A	5.65 × 10−6	0.91	0.23	0.24	0.540	0.91	1.25 × 10−5	0.91	TRIM31-AS1;TRIM40	intergenic
rs9261484	6	30108683	T	0.26	0.29	C	7.14 × 10−6	0.89	0.24	0.26	0.492	0.91	1.33 × 10−5	0.89	TRIM40	intronic
rs9261496	6	30111014	T	0.25	0.26	C	7.88 × 10−6	0.91	0.22	0.25	0.410	0.89	1.11 × 10−5	0.91	TRIM40	intronic
rs9261502	6	30111610	T	0.24	0.26	A	4.51 × 10−6	0.91	0.22	0.24	0.568	0.92	1.11 × 10−5	0.91	TRIM40	intronic
rs9261521	6	30117773	T	0.22	0.25	C	2.61 × 10−8	0.81	0.24	0.25	0.860	0.97	3.17 × 10−7	0.85	TRIM40;TRIM10	intergenic
rs2069837	7	22768027	G	0.09	0.20	A	9.73 × 10−15	0.41	0.18	0.24	8.89 × 10−3	0.67	4.64 × 10−16	0.49	IL6	intronic
rs17158686	7	83794756	G	0.11	0.18	T	2.38 × 10−7	0.54	0.16	0.20	0.072	0.75	4.99 × 10−8	0.61	SEMA3A	intronic

CHR chromosome, BP base-pair position (hg19), A1 Minor allele code, A2 major allele code, F_A frequency of this allele in cases, F_U frequency of this allele in controls, P logistic p value for association test, OR estimated odds ratio (for A1, i.e. A2 is reference), P-meta p value for METAL combined analysis