Study Report

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Basic Info

Reference	Andreassen OA, 2013 PMID: 23637625
Citation	Andreassen, O. A., W. K. Thompson, et al. (2013). "Improved detection of common variants associated with schizophrenia and bipolar disorder using pleiotropy-informed conditional false discovery rate." PLoS Genet 9(4): e1003455.
Disease Type	bipolar disorder & schizophrenia
Study Design	case-control
Study Type	GWAS
Sample Size	n= 9379 cases and n =7736 control samples in schizophrenia, and n= 6990 cases and n =4820 controls in bipolar disorder
Predominant Ethnicity

Detail Info

Sample Diagnosis	from the Psychiatric GWAS Consortium (PGC)-Schizophrenia and Bipolar Disorder Working Groups
Sample Status	The schizophrenia (SCZ) GWAS summary statistics results were obtained from the PGC Schizophrenia Work Group, which consisted of 9,394 cases with schizophrenia or schizoaffective disorder and 12,462 controls (52% screened) from a total of 17 samples from 11 countries. The bipolar disorder (BD) GWAS summary statistics results were obtained from the PGC Bipolar Disorder Working Group, which consisted of n= 16,731 participants, including 7481 cases and 9250 controls, from 11 studies from 7 countries. All cases have experienced pathologically relevant episodes of elevated mood (mania or hypomania) and meet operational criteria for a BD diagnosis. The sample consisted of BD I (84%), BD II (11%), schizoaffective disorder bipolar type (4%), and BD NOS (1%). Due to overlapping control samples in these studies, the common controls were split randomly, and divided between the two case-control analyses. All results presented here are based on these non-overlapping control samples, with n= 9379 cases and n =7736 control samples in schizophrenia, and n= 6990 cases and n =4820 controls in bipolar disorder analyses.
Technique	We applied a control method leveraging only intergenic SNPs which are likely depleted for true associations.
Statistical Method	Analyses implemented here were motivated by previously published stratified FDR methods.
Result Summary	Here, we computed conditional Q-Q curves of data from the Psychiatric Genome Consortium (SCZ; n = 9,379 cases and n = 7,736 controls; BD: n = 6,990 cases and n = 4,820 controls) to show enrichment of SNPs associated with SCZ as a function of association with BD and vice versa with a corresponding reduction in FDR. Applying the conditional FDR method, we identified 58 loci associated with SCZ and 35 loci associated with BD below the conditional FDR level of 0.05. Of these, 14 loci were associated with both SCZ and BD (conjunction FDR). Together, these findings show the feasibility of genetic pleiotropy-informed methods to improve gene discovery in SCZ and BD and indicate overlapping genetic mechanisms between these two disorders.

SNPs reported by this study for BD (count: 106)

SNP	Related Gene(s)	Allele Change	Statistical Values	Author Comments	Result Category
rs1625579	MIR137HG		Conditional FDR; SCZ loci given BD: FDR=0.011 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.10. More...	Positive
rs11205362	PRPF3	G/A	Conditional FDR; SCZ loci given BD: FDR=0.033 for SCZ and BD\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.033 for BD and SZ, Z-score=3.404 for BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.11. This SNP is with conjunction FDR<0.07 with schizophrenia and bipolar disorder considered jointly. More...	Positive
rs4650608	PTGFR IFI44L	T/C	Conditional FDR; SCZ loci given BD: FDR=0.028 for SCZ and BD\|\|Conditional FDR; BD loci given SCZ: P-value=0.001, FDR=0.64629, FDR=0.0425 for BD and SCZ\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.043 for BD and SZ, Z-score=3.289 for BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.08. This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. This SNP is with conjunction FDR<0.06 with schizophrenia and bipolar disorder considered jointly. More...	Positive
rs4907103	LPAR3		Conditional FDR; SCZ loci given BD: FDR=0.039 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.09. More...	Positive
rs10189138	VRK2		Conditional FDR; SCZ loci given BD: FDR=0.038 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.14. More...	Positive
rs11692886	SH3RF3		Conditional FDR; SCZ loci given BD: FDR=0.035 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.15. More...	Positive
rs10495658	RN7SKP168		Conditional FDR; SCZ loci given BD: FDR=0.044 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.12. More...	Positive
rs813592	GCKR FNDC4		Conditional FDR; SCZ loci given BD: FDR=0.014 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.13. More...	Positive
rs17662626			Conditional FDR; SCZ loci given BD: FDR=0.03 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.18. More...	Positive
rs2675968	C2orf82		Conditional FDR; SCZ loci given BD: FDR=0.021 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.19. More...	Positive
rs6435387	KIF5C		Conditional FDR; SCZ loci given BD: FDR=0.02 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.16. More...	Positive
rs17180327			Conditional FDR; SCZ loci given BD: FDR=0.038 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.17. More...	Positive
rs4687657	ITIH4 MUSTN1	G/T	Conditional FDR; SCZ loci given BD: FDR=0.028 for SCZ and BD\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.028 for BD and SZ, Z-score=3.787 for BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.22. This SNP is with conjunction FDR<0.09 with schizophrenia and bipolar disorder considered jointly. More...	Positive
rs11130874	PTPRG		Conditional FDR; SCZ loci given BD: FDR=0.03 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.23. More...	Positive
rs4663627	AGAP1		Conditional FDR; SCZ loci given BD: FDR=0.033 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.20. More...	Positive
rs13072940	TRANK1		Conditional FDR; SCZ loci given BD: FDR=0.013 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.21. More...	Positive
rs4949526			Conditional FDR; SCZ loci given BD: FDR=0.035 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.07. More...	Positive
rs11579756	KAZN		Conditional FDR; SCZ loci given BD: FDR=0.037 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.06. More...	Positive
rs2252865	RERE	T/C	Conditional FDR; SCZ loci given BD: FDR=0.03 for SCZ and BD, \|\|Conditional FDR; BD loci given SCZ: P-value=0.000219, FDR=0.44657, FDR=0.01306 for BD and SCZ\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.03 for BD and SZ, Z-score=3.696 for BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.05. This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. This SNP is with conjunction FDR<0.05 with schizophrenia and bipolar disorder considered jointly. More...	Positive
rs2239037	CACNA1C		Conditional FDR; BD loci given SCZ: P-value=0.000906, FDR=0.64629, FDR=0.03928 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs10774037	CACNA1C		Conditional FDR; BD loci given SCZ: P-value=0.000000242, FDR=0.01859, FDR=0.00161 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs10883757	TRIM8	C/T	Conditional FDR; BD loci given SCZ: P-value=0.00111, FDR=0.64629, FDR=0.03991 for BD and SCZ\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.04 for BD and SZ, Z-score=3.261 for BD	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. This SNP is with conjunction FDR<0.08 with schizophrenia and bipolar disorder considered jointly. More...	Positive
rs17138230	TENM4		Conditional FDR; BD loci given SCZ: P-value=0.0000143, FDR=0.18382, FDR=0.03822 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs4390476	UBE2D3P4		Conditional FDR; BD loci given SCZ: P-value=0.000203, FDR=0.44657, FDR=0.03843 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs11160562	EML1		Conditional FDR; BD loci given SCZ: P-value=0.000693, FDR=0.60769, FDR=0.03496 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs7296288	DHH		Conditional FDR; BD loci given SCZ: P-value=0.0000288, FDR=0.20749, FDR=0.02777 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs12427050			Conditional FDR; BD loci given SCZ: P-value=0.0005, FDR=0.57626, FDR=0.04728 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs4332037	MAD1L1		Conditional FDR; BD loci given SCZ: P-value=0.0000397, FDR=0.22281, FDR=0.02918 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs6461233	MAD1L1		Conditional FDR; BD loci given SCZ: P-value=0.000519, FDR=0.57626, FDR=0.02711 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs9371601	SYNE1		Conditional FDR; BD loci given SCZ: P-value=0.0000011, FDR=0.06351, FDR=0.02196 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs3823198	RPS6KA2 FAM103A2P		Conditional FDR; BD loci given SCZ: P-value=0.0000416, FDR=0.22281, FDR=0.01779 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs7083127	CACNB2		Conditional FDR; BD loci given SCZ: P-value=0.00014, FDR=0.37364, FDR=0.02191 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs10994359	ANK3		Conditional FDR; BD loci given SCZ: P-value=0.000000000812, FDR=0.00115, FDR=0.00001 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs10277665	THSD7A		Conditional FDR; BD loci given SCZ: P-value=0.0000542, FDR=0.24328, FDR=0.01641 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs6982836	RPL31P40		Conditional FDR; BD loci given SCZ: P-value=0.0000564, FDR=0.26909, FDR=0.04168 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs281393	RASIP1 MAMSTR		Conditional FDR; BD loci given SCZ: P-value=0.0000599, FDR=0.26909, FDR=0.01293 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs3809646	VPS9D1 ZNF276 VPS9D1-AS1		Conditional FDR; BD loci given SCZ: P-value=0.000576, FDR=0.60769, FDR=0.03171 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs1424003	CDH11		Conditional FDR; BD loci given SCZ: P-value=0.0000554, FDR=0.24328, FDR=0.01641 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs11863156			Conditional FDR; BD loci given SCZ: P-value=0.0000786, FDR=0.30029, FDR=0.00865 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs1800359	ZNF276 FANCA	A/G	Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.035 for BD and SZ, Z-score=3.329 for BD	This SNP is with conjunction FDR<0.16 with schizophrenia and...... This SNP is with conjunction FDR<0.16 with schizophrenia and bipolar disorder considered jointly. More...	Positive
rs3757440	MAD1L1 FTSJ2	A/G	Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.031 for BD and SZ, Z-score=3.49 for BD	This SNP is with conjunction FDR<0.11 with schizophrenia and...... This SNP is with conjunction FDR<0.11 with schizophrenia and bipolar disorder considered jointly. More...	Positive
rs3746972	ITGB2		Conditional FDR; BD loci given SCZ: P-value=0.000142, FDR=0.41109, FDR=0.04369 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs1051168	WDR73 NMB		Conditional FDR; SCZ loci given BD:: FDR=0.033 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs1078163	NTRK3		Conditional FDR; SCZ loci given BD: FDR=0.017 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs2304634	DNAJA3		Conditional FDR; SCZ loci given BD:: FDR=0.026 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs12708772	SHISA9	C/T	Conditional FDR; SCZ loci given BD:: FDR=0.044 for SCZ and BD\|\|Conditional FDR; BD loci given SCZ: P-value=0.000989, FDR=0.64629, FDR=0.04219 for BD and SCZ\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.044 for BD and SZ, Z-score=3.294 for BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.63. This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. This SNP is with conjunction FDR<0.14 with schizophrenia and bipolar disorder considered jointly. More...	Positive
rs1502404			Conditional FDR; SCZ loci given BD:: FDR=0.04 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs724729			Conditional FDR; SCZ loci given BD:: FDR=0.038 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs1869901	PLCB2 PLCB2-AS1		Conditional FDR; SCZ loci given BD:: FDR=0.039 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs2414718			Conditional FDR; SCZ loci given BD:: FDR=0.025 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs7972947	CACNA1C		Conditional FDR; SCZ loci given BD: FDR=0.013 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs1006737	CACNA1C	A/G	Conditional FDR; SCZ loci given BD: FDR=0.022 for SCZ and BD\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.022 for BD and SZ, Z-score=4.553 for BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.61. This SNP is with conjunction FDR<0.13 with schizophrenia and bipolar disorder considered jointly. More...	Positive
rs4517638	DAOA		Conditional FDR; SCZ loci given BD: FDR=0.015 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs961196	TTC7B	C/T	Conditional FDR; SCZ loci given BD:: FDR=0.044 for SCZ and BD\|\|Conditional FDR; BD loci given SCZ: P-value=0.000296, FDR=0.50926, FDR=0.01872 for BD and SCZ\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.044 for BD and SZ, Z-score=3.618 for BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.63. This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. This SNP is with conjunction FDR<0.14 with schizophrenia and bipolar disorder considered jointly. More...	Positive
rs6591348			Conditional FDR; SCZ loci given BD: FDR=0.027 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs17126243			Conditional FDR; SCZ loci given BD: FDR=0.027 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs11222395			Conditional FDR; SCZ loci given BD: FDR=0.032 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs7106715			Conditional FDR; SCZ loci given BD: FDR=0.039 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs2535629	ITIH3		Conditional FDR; BD loci given SCZ: P-value=0.0000129, FDR=0.17896, FDR=0.00279 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs9834970	TRANK1 LRBA	C/T	Conditional FDR; BD loci given SCZ: P-value=0.00052, FDR=0.57626, FDR=0.02711 for BD and SCZ\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.027 for BD and SZ, Z-score=3.47 for BD	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. This SNP is with conjunction FDR<0.08 with schizophrenia and bipolar disorder considered jointly. More...	Positive
rs3134942	NOTCH4	G/T	Conditional FDR; BD loci given SCZ: P-value=0.00115, FDR=0.66028, FDR=0.04844 for BD and SCZ\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.048 for BD and SZ, Z-score=3.251 for BD	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. This SNP is with conjunction FDR<0.08 with schizophrenia and bipolar disorder considered jointly. More...	Positive
rs2902101	TENM2		Conditional FDR; BD loci given SCZ: P-value=0.000104, FDR=0.33589, FDR=0.0357 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs573140	SIPA1L2		Conditional FDR; BD loci given SCZ: P-value=0.00000658, FDR=0.15946, FDR=0.03009 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs7521783			Conditional FDR; BD loci given SCZ: P-value=0.000558, FDR=0.57626, FDR=0.02503 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs2271893	LMAN2L		Conditional FDR; BD loci given SCZ: P-value=0.0000185, FDR=0.18928, FDR=0.0096 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs3911862			Conditional FDR; BD loci given SCZ: P-value=0.0000565, FDR=0.26909, FDR=0.04864 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs5758209			Conditional FDR; SCZ loci given BD:: FDR=0.031 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs9621795	LARGE		Conditional FDR; SCZ loci given BD:: FDR=0.041 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs10776799	NGF		Conditional FDR; BD loci given SCZ: P-value=0.00000968, FDR=0.17368, FDR=0.02579 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive
rs28729663	RABL2B		Conditional FDR; SCZ loci given BD:: FDR=0.041 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs12966547	CCDC68		Conditional FDR; SCZ loci given BD:: FDR=0.019 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs4785714	ZNF276		Conditional FDR; SCZ loci given BD:: FDR=0.034 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs381523	PPM1F	A/G	Conditional FDR; SCZ loci given BD:: FDR=0.038 for SCZ and BD\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: P-value=0.00128, FDR=0.66028, FDR=0.04536 for BD and SCZ\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.045 for BD and SZ, Z-score=3.22 for BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.63. This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. This SNP is with conjunction FDR<0.14 with schizophrenia and bipolar disorder considered jointly. More...	Positive
rs159788		G/A	Conditional FDR; SCZ loci given BD:: FDR=0.034 for SCZ and BD\|\|Conditional FDR; BD loci given SCZ: P-value=0.000648, FDR=0.60769, FDR=0.0308 for BD and SCZ\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.034 for BD and SZ, Z-score=3.411 for BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.63. This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. This SNP is with conjunction FDR<0.14 with schizophrenia and bipolar disorder considered jointly. More...	Positive
rs502771			Conditional FDR; SCZ loci given BD: FDR=0.039 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs9276601	HLA-DQB2		Conditional FDR; SCZ loci given BD: FDR=0.015 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs9268858	HLA-DRB9		Conditional FDR; SCZ loci given BD: FDR=0.041 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs9268862	HLA-DRB9		Conditional FDR; SCZ loci given BD: FDR=0.002 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs2284178	HCP5		Conditional FDR; SCZ loci given BD: FDR=0.036 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs805294	LY6G6C C6orf25 LY6G6D		Conditional FDR; SCZ loci given BD: FDR=0.039 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs2523722	TRIM26		Conditional FDR; SCZ loci given BD: FDR=0.001 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs2596565	ZDHHC20P2 HLA-S MICA		Conditional FDR; SCZ loci given BD: FDR=0.009 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs13190937	ZSCAN23 COX11P1		Conditional FDR; SCZ loci given BD: FDR=0.033 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.30. More...	Positive
rs3130893			Conditional FDR; SCZ loci given BD: FDR=0.006 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.31. More...	Positive
rs7749823	HIST1H1E HIST1H2BD		Conditional FDR; SCZ loci given BD: FDR=0.005 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.28. More...	Positive
rs17693963			Conditional FDR; SCZ loci given BD: FDR=0.001 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.29. More...	Positive
rs9379780			Conditional FDR; SCZ loci given BD: FDR=0.024 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.26. More...	Positive
rs198829	HIST1H2BC		Conditional FDR; SCZ loci given BD: FDR=0.027 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.27. More...	Positive
rs9838229	CCDC39		Conditional FDR; SCZ loci given BD: FDR=0.045 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.24. More...	Positive
rs13150700	SORBS2		Conditional FDR; SCZ loci given BD: FDR=0.048 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.25. More...	Positive
rs676318	LRP5		Conditional FDR; SCZ loci given BD: FDR=0.023 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs4356203	PIK3C2A		Conditional FDR; SCZ loci given BD: FDR=0.029 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs11191580	NT5C2		Conditional FDR; SCZ loci given BD: FDR=0.005 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs10883817	CNNM2		Conditional FDR; SCZ loci given BD: FDR=0.02 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs2298278	SUFU		Conditional FDR; SCZ loci given BD: FDR=0.037 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs7895695	RRP12		Conditional FDR; SCZ loci given BD: FDR=0.018 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs2153522	ANK3		Conditional FDR; SCZ loci given BD: FDR=0.046 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs7084499	ANK3		Conditional FDR; SCZ loci given BD: FDR=0.04 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs6602217			Conditional FDR; SCZ loci given BD: FDR=0.015 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs2254884	ABCA1		Conditional FDR; SCZ loci given BD: FDR=0.032 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs7004633	MMP16		Conditional FDR; SCZ loci given BD: FDR=0.005 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs12543276			Conditional FDR; SCZ loci given BD: FDR=0.046 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs7787274	MAD1L1 FTSJ2		Conditional FDR; SCZ loci given BD: FDR=0.028 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs9462875	CUL9		Conditional FDR; SCZ loci given BD: FDR=0.036 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs1480380	HLA-DMA HLA-DMB		Conditional FDR; SCZ loci given BD: FDR=0.01 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive
rs7383287	HLA-DOB		Conditional FDR; SCZ loci given BD: FDR=0.019 for SCZ and BD	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More...	Positive