Table 2.

Modelling analysis results for single-nucleotide polymorphisms (SNP) showing genome-wide significant association in previous genome-wide association studies from the Psychiatric Genome-Wide Association Study Consortium

	Chromosome	Base-pair position*	Nearest gene	Alleles	Frequency†	p value	Best-fit model (BIC)‡
Bipolar disorder 7
rs937l601	6	152832266	SYNE1	T/G	0·346	4·27×10−9	BPD
rs10994397	10	61949130	ANK3	T/C	0·065	7·08×10−9	BPD
rs4765914§,¶	12	2290157	CACNA1C	T/C	0·204	1·52×10−8	BPD, MDD, schizophrenia
rs12576775	11	78754841	ODZ4	G/A	0·175	4·40×10−8	BPD
Schizophrenia 6
rs2021722	6	30282110	MHC	C/T	0·789	2·18×10−12	Schizophrenia
rs1625579	1	98275522	MIR137	T/G	0·801	1·59×10−11	ASD, schizophrenia
rs12966547§	18	50903015	CCDC68	G/A	0·588	2·60×10−10	BPD, MDD, schizophrenia
rs7914558§	10	104765898	CNNM2	G/A	0·587	1·82×10−9	MDD, schizophrenia
rs11191580§	10	104896201	NT5C2	T/C	0·911	1·11×10−8	Five disorder
rs7004633	8	89829427	MMP16	G/A	0·184	2·75×10−8	Schizophrenia
rs10503253	8	4168252	CSMD1	A/C	0·193	4·14×10−8	Schizophrenia
rs17662626§	2	193692866	PCGEM1	A/G	0·915	4·65×10−8	ASD, schizophrenia
rs548181	11	124966919	STT3A	G/A	0·884	8·87×10−7	Schizophrenia
rs17512836	18	51345959	TCF4	C/T	0·027	1·05×10−6	ASD, schizophrenia

Peak SNPs in associated region after clumping. BIC=Bayesian information criteria. BPD=bipolar disorder. MDD=major depressive disorder. ASD=autism spectrum disorders.

^*Detected with University of California Santa Cruz Genome Browser (version hg18).

^†Risk allele frequency in controls.

^‡Best-fit multinomial logistic model by BIC (appendix pp 46-50 [bipolar disorder] and 51-61 [schizophrenia] provide a comparison of BIC and Akaike information criteria across models).

^§The BIC for the best and second best models do not differ significantly (ie, greater than 2 as previously suggested²⁶).

^¶rs4765914 is a proxy SNP for rs4765913 based on linkage disequilibrium (481 base pairs away, r²=0·874).