Table 2a.

Statistically significant associations at gene level for age at menarche.

Group	Gene	Chr.	SNP	Function	Position (bp)a	Major, Minor alleles	MAFb	Betac	s.e.	Raw p-valued	Adjusted p-valuee	Imputation quality (NHS/WGHS)	Other statistically significant SNPs in high linkage disequilibrium with the listed SNP (pairwise r2>0.8)
1	FSHB	11	rs555621	5′-UTR	30193120	T,C	0.41	0.059	0.016	0.00018	0.0011	1.00/0.97	rs601681, rs622356, rs639403, rs609896, rs1716022, rs560078, rs6169, rs506197, rs615577, rs618611, rs590833, rs489096, rs572883, rs543401, rs595496, rs518357, rs601640
			rs11031010	5′-UTR	30196754	C,A	0.15	0.079	0.023	0.00061	0.0037	0.99/0.87
			rs1782507	5′-UTR	30200444	G,T	0.35	0.046	0.016	0.0035	0.021	1.00/1.00
	LHCGR	2	rs4953616	Intronic	48853079	C,T	0.28	−0.065	0.017	0.00010	0.0060	1.00/1.00	rs4318432, rs6737881
			rs6729809	Intronic	48850313	T,C	0.33	0.063	0.017	0.00017	0.0099	0.98/0.95
			rs7579411	Intronic	48850007	C,T	0.43	0.058	0.016	0.00022	0.013	1.00/1.00	rs4574159
			rs4374421	Intronic	48847043	T,C	0.32	0.060	0.017	0.00030	0.017	1.00/1.00
	POMC	2	rs2164808	3′-UTR	25288827	C,T	0.45	0.046	0.016	0.0034	0.038	0.98/0.98
			rs7589318	3′-UTR	25290023	G,A	0.32	0.048	0.017	0.0042	0.047	0.98/0.97
	UGT2B4	4	rs2013573	Intronic	70535238	T,C	0.21	0.060	0.019	0.0012	0.019	1.00/1.00
			rs13111134	Intronic	70535571	A,G	0.28	0.055	0.018	0.0026	0.042	0.95/0.87
2	GHRH	20	rs1073768	3′-UTR	35310424	T,C	0.43	−0.046	0.016	0.0032	0.045	1.00/1.00
4	CD40LG	X	rs5930973	Intronic	135457668	G,A	0.06	0.101	0.031	0.0013	0.0067	1.00/0.99
			rs3092921	3′-UTR	135468520	T,C	0.09	0.074	0.028	0.0074	0.037	1.00/0.98
6	FGFR1	8	rs2288696	Intronic	38405382	A,G	0.22	−0.058	0.019	0.0016	0.033	1.00/0.99
	KISS1	1	rs7538038	Intronic	200892683	A,G	0.27	−0.061	0.018	0.00090	0.012	0.92/0.92	rs12097666, rs4951316, rs11240695, rs2510, rs4951319
	NKX2-1	14	rs999460	3′-UTR	36054262	C,T	0.36	0.046	0.016	0.0039	0.039	1.00/1.00

^aPositions based on NCBI build 35;

^bMinor allele frequency among combined samples of the NHS and the WGHS;

^cThe regression parameter beta refers to the mean change in age at menarche or age at natural menopause per copy of the SNP minor allele;

^dThe unadjusted p-values are from linear regression with additive genetic coding;

^eThe p values are adjusted for multiple comparisons in each gene using the estimated effective number of independent markers. UTR, untranslated region.