Table 3.

Nominally replicated GWAS-identified single-nucleotide polymorphisms for age at menarche in East Asian women

							SGWAS (n = 8073)		Stage II (n = 5445)		Combined (n = 13,518)
Locus	SNP	Chr	Base positiona	Nearby gene	Allelesb	EAF	Beta(SE)	P	Beta(SE)	P	Beta(SE)	P_METAL	P_het
1	rs2274465	1	44121557	KDM4A	C/G	0.74	0.053 (0.031)	0.083	0.068 (0.039)	0.078	0.059 (0.024)	0.014	0.765
2	rs466639	1	165394882	RXRG	T/C	0.16	−0.063 (0.037)	0.093	−0.054 (0.044)	0.229	−0.059 (0.029)	0.040	0.874
3	rs1400974	2	199638690	SATB2	A/G	0.43	0.083 (0.028)	0.003	0.068 (0.034)	0.046	0.077 (0.021)	3.3 × 10−4	0.726
4	rs11715566	3	117562436	IGSF11	T/C	0.61	0.097 (0.028)	4.6 × 10−4	0.037 (0.034)	0.283	0.073 (0.022)	7.0 × 10−4	0.168
5	rs10938397	4	45182527	GNPDA2	A/G	0.70	0.068 (0.029)	0.021	0.033 (0.037)	0.365	0.054 (0.023)	0.018	0.464
6	rs3733631	4	104641103	TACR3	C/G	0.32	0.054 (0.029)	0.063	0.047 (0.036)	0.194	0.051 (0.022)	0.024	0.879
7	rs17171818	5	137725003	JMJD1B	T/C	0.59	−0.075 (0.027)	0.006	0.008 (0.034)	0.826	−0.043 (0.021)	0.045	0.058
81	rs2153127	6	105348544	LIM28B	T/C	0.44	0.068 (0.028)	0.013	0.056 (0.038)	0.145	0.064 (0.022)	0.004	0.791
82	rs7759938	6	105378954	LIN28B	T/C	0.70	−0.165 (0.030)	3.2 × 10−8	−0.072 (0.039)	0.064	−0.131 (0.024)	3.5 × 10−8	0.057
91	rs10816359	9	108757670	TMEM38B	T/G	0.76	0.038 (0.032)	0.229	0.088 (0.042)	0.036	0.057 (0.025)	0.026	0.346
92	rs10453225	9	108920220	TMEM38B	T/G	0.48	−0.086 (0.027)	0.001	−0.063 (0.033)	0.058	−0.077 (0.021)	2.4 × 10−4	0.589
93	rs10739221	9	109060830	TMEM38B	T/C	0.62	−0.069 (0.028)	0.015	−0.006 (0.036)	0.865	−0.045 (0.022)	0.043	0.173
10	rs10980921	9	114279912	ZNF483	T/C	0.76	−0.025 (0.032)	0.425	−0.203 (0.061)	9.2 × 10−4	−0.062 (0.028)	0.026	0.010
11	rs1874984	10	1731871	ADARB2	C/G	0.47	0.06 (0.029)	0.036	0.027 (0.035)	0.440	0.047 (0.022)	0.035	0.472
12	rs2063730	11	78048524	GAB2	A/C	0.60	−0.048 (0.028)	0.085	−0.054 (0.035)	0.120	−0.051 (0.022)	0.021	0.902
13	rs10895140	11	101436721	TRPC6	A/G	0.60	−0.028 (0.028)	0.307	−0.108 (0.034)	0.002	−0.06 (0.022)	0.005	0.070
14	rs11215400	11	115052635	CADM1	A/C	0.88	−0.055 (0.042)	0.196	−0.071 (0.045)	0.112	−0.063 (0.031)	0.042	0.785
15	rs12915845	15	89042467	DET1	T/C	0.14	−0.028 (0.039)	0.484	−0.121 (0.049)	0.014	−0.064 (0.031)	0.038	0.141
16	rs246185	16	14395432	MKL2	T/C	0.45	−0.051 (0.029)	0.077	−0.080 (0.037)	0.032	−0.062 (0.023)	0.007	0.536
17	rs1129700	16	29918034	KCTD13	T/C	0.59	0.042 (0.031)	0.168	0.154 (0.045)	5.4 × 10−4	0.078 (0.025)	0.002	0.039
18	rs12607903	18	3817134	DLGAP1	T/C	0.56	−0.075 (0.029)	0.010	−0.057 (0.037)	0.126	−0.068 (0.023)	0.003	0.706
19	rs652260	19	7900562	EVI5L	T/C	0.58	0.050 (0.028)	0.074	0.050 (0.034)	0.141	0.050 (0.021)	0.020	0.995

SNP single-nucleotide polymorphism, Chr chromosome, EAF effective allele frequency, SE standard error, P_METAL P value from meta-analysis using METAL, P_het P value from between-study heterogeneity test

1, 2, and 3 superscript numbers in the column of “Locus” indicate independent signals at the same genetic locus