Table 1.

Discovery GWAS, replication and combined meta-analysis results for MG

								Discovery			Replication			Discovery and replication
Nearest gene	Index SNP	CHR	BP (GRCh37)	A1/A2	FRQ case	FRQ control	Proxy	P	OR	SE	P-rep	OR-rep	SE-rep	P-comb	OR-comb	SE-comb
PTPN22	rs2476601b	1	114377568	A/G	0.121	0.13	same	2.77e−31	1.45965	0.0325	3.92e−14	1.311637	0.035159	3.25e−43	1.38944	0.0239
MAGI3	rs7522138d	1	114217705	A/G	0.441	0.47	same	6.77e−09	0.88462	0.0212	2.91e−02	0.957836	0.022749	3.36e−08	0.91796	0.0155
CHRNA1	rs6433501a,b	2	175616667	G/A	0.151	0.112	same	3.54e−07	1.17081	0.031	1.01e−05	1.14714	0.03172	2.69e−11	1.15917	0.0222
CTLA4	rs231779b	2	204734487	T/C	0.386	0.451	rs231770	1.24e−06	1.11149	0.0218	2.37e−05	1.09845	0.024511	6.87e−10	1.10572	0.0163
TNIP1	rs6861227a,c,d	5	150447128	G/T	0.165	0.128	same	7.44e−08	1.16754	0.0288	2.07e−02	1.075955	0.031392	3.03e−08	1.12479	0.0212
MHC	rs1264706b	6	30063652	C/G	0.129	0.072	same	1.26e−34	1.61996	0.0393	1.92e−02	1.091196	0.041711	3.44e−25	1.34528	0.0286
TBX18	rs215918	6	85513783	A/G	0.405	0.374	same	3.42e−08	0.88754	0.0216	3.30e−03	0.938976	0.02322	3.84e−09	0.91101	0.0158
RNASET2	rs2301436a,d	6	167437988	T/C	0.493	0.477	same	1.09e−07	1.11818	0.021	6.69e−03	1.05781	0.022716	2.33e−08	1.08992	0.0154
FAM76B	rs4409785b	11	95311422	C/T	0.192	0.169	same	2.73e−11	1.19494	0.0267	3.44e−03	1.08206	0.028953	1.48e−11	1.14168	0.0196
ATXN2	rs4766578a	12	111904371	T/A	0.516	0.406	same	6.72e−08	1.12345	0.0216	2.09e−04	1.08362	0.022773	2.35e−10	1.1044	0.0157
IKZF3	rs12946510	17	37912377	T/C	0.476	0.493	same	7.61e−11	1.1474	0.0211	2.38e−04	1.08288	0.022772	8.28e−13	1.11717	0.0155
TNFRSF11A	rs7239261b	18	60005046	A/C	0.457	0.436	same	3.98e−20	1.21458	0.0212	4.43e−04	1.079214	0.022905	2.46e−19	1.15016	0.0156

The table presents the results from the discovery-, replication-, and combined inverse-variance-weighted fixed-effects meta-analyses.

BP (GRCh37) Base Pair position on Genome Reference Consortium Human Build 37, CHR chromosome, comb combined meta-analysis of discovery and control GWAS results, FRQ frequency.

^aReached genome-wide significance in leave-one-out discovery GWAS.

^bPreviously published as genome-wide significant locus.

^cOnly previously reported in EOMG.

^dWould not withstand a multiple testing correction for 13 million tests (P < 3.85e⁻⁹), accounting for the leave-one-out GWAS.