Table 2.

Cross-trait meta-analysis of type 2 diabetes/glycaemic traits and PCOS

SNP	CHR	BP	A1	A2	EAF	Beta_PCOS	Beta_trait	pPCOS	psingle trait	pCPASSOC	Genes within clumping ranges
T2DM and PCOS
rs8050136	16	53816275	A	C	0.41	0.15	0.12	4.50×10–6	7.60×10–74	1.95×10–85	FTO
rs9675376	18	57969244	A	G	0.3	0.13	0.04	2.40×10–4	3.90×10–9	4.47×10–10
rs72753599	1	214180519	T	C	0.2	–0.14	–0.06	6.00×10–4	1.60×10–12	3.94×10–13	PROX1
rs10938398	4	45186139	A	G	0.42	0.11	0.04	8.80×10–4	4.90×10–12	1.02×10–12
T2DMadjBMI and PCOS
rs9930501	16	53830452	A	G	0.55	–0.14	–0.05	5.30×10–6	6.00×10–13	6.07×10–15	FTO
rs1509097a	2	165737931	T	C	0.5	–0.13	–0.04	5.20×10–5	5.30×10–7	3.34×10–8	SLC38A11
rs2238689	19	46178661	T	C	0.57	0.11	–0.07	5.40×10–4	1.40×10–21	9.67×10–24	EML2, FBXO46, GIPR, MIR642A, MIR642B, QPCTL, SNRPD2
rs72753599	1	214180519	T	C	0.2	–0.14	–0.07	6.00×10–4	1.60×10–12	6.26×10–14	PROX1
rs3934729a	3	123019763	T	C	0.61	–0.11	0.04	7.40×10–4	1.60×10–7	1.44×10–8	ADCY5, SEC22A
FGadjBMI and PCOS
rs72753599	1	214180519	T	C	0.2	–0.14	–0.01	6.00×10–4	5.06×10–12	1.62×10–12	PROX1
rs9844212	3	123021870	C	G	0.59	–0.11	0.01	6.00×10–4	7.35×10–13	4.41×10–13	ADCY5, SEC22A
rs6485690	11	46798631	A	G	0.34	–0.11	0.01	9.40×10–4	4.60×10–9	1.06×10–10	ARFGAP2, ARHGAP1, ATG13, C11orf49 (CSTPP1), CKAP5, DDB2, F2, LRP4, LRP4-AS1, MIR5582, MIR6745, PACSIN3, SNORD67, ZNF408
FIadjBMI and PCOS
rs745379a	8	11615695	A	G	0.48	–0.12	–0.01	3.40×10–4	8.26×10–6	1.49×10–9	C8orf49 (LINC02905), FDFT1, GATA4, LINC00208, NEIL2
rs3813583a	16	79755080	A	C	0.62	0.12	0.01	4.80×10–4	1.88×10–4	2.64×10–8
rs4135247a	3	12396588	A	G	0.56	–0.11	–0.01	6.00×10–4	1.49×10–6	6.02×10–9	PPARG
HbA1c and PCOS
rs8047587a	16	53798622	T	G	0.45	0.14	0.01	6.80×10–6	1.87×10–5	2.87×10–10	FTO
rs1265564	12	111708458	A	C	0.58	0.13	0.01	1.60×10–4	5.62×10–12	2.91×10–13	ACAD10, ATXN2, BRAP, CUX2, FAM109A (PHETA1), MIR6760, SH2B3
rs2238689a	19	46178661	T	C	0.57	0.11	–0.01	5.40×10–4	1.45×10–6	1.12×10–8	GIPR, MIR642A, MIR642B
rs4731113	7	123283949	T	C	0.97	0.31	0.02	8.00×10–4	4.90×10–8	3.28×10–9	LMOD2, WASL

SNPs with p_CPASSOC <5×10^–8 and p_{single trait} <1×10^–3 are presented

^aNovel SNPs, defined as shared SNPs that are neither driven by a single trait nor in LD with index SNPs identified in single-trait GWASs (LD r²<0.2)

A1, effect allele; A2, alternative allele; Beta, effect allele beta coefficient; BP, physical position of SNP (base pairs); CHR, chromosome; EAF: effect allele frequency; p_CPASSOC, p value for cross-phenotype association; p_PCOS, p value for PCOS; p_{single trait}, p value for each individual trait; T2DM, type 2 diabetes mellitus