An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation

Table 2 Convincing co-localization of schizophrenia and DNA methylation genome-wide association study signals in blood and brain

Schizophrenia GWAS region	Probe ID	Chr	Base position	Gene annotation	Bayesian co-localization
					mQTL in blood			mQTL in brain
					nsnps	PP3 + PP4	PP4/PP3	nsnps	PP3 + PP4	PP4/PP3
108	cg00585072	5	140186983	PCDHA2;PCDHA1;PCDHA4;PCDHA3	1595	0.9982	5.340	1260	0.9983	6.058
7	cg02951883	7	2050386	MAD1L1	1808	1.0000	14.596	2144	0.9992	11.820
3	cg08772003	10	104629869	AS3MT	1994	1.0000	51.075	1316	1.0000	36.981
3	cg11784071	10	104629166	AS3MT	1994	0.9999	8.046	1315	1.0000	39.298
3	cg24592962	10	104629151	AS3MT	1994	0.9986	36.510	1315	1.0000	55.055
99	cg14258853	12	29935411	TMTC1	3551	0.9995	46.932	2598	0.9989	10.723
47	cg26732615	19	19648335	CILP2;YJEFN3	1644	1.0000	8.196	1285	0.9906	5.514

Listed are all instances where the GWAS results indicate that the same causal variant is associated with schizophrenia and DNA methylation at a specific site in both blood and brain. Bayesian co-localization analysis compared the GWAS results evaluating the evidence for five hypotheses (see Methods); convincing co-localization signs were defined as PP3 + PP4 > 0.99 and PP4/PP3 > 5. The full set of results for all genetic loci associated with schizophrenia can be found in Additional file 2: Table S12.
Chr chromosome, GWAS genome-wide association study; mQTL DNA methylation quantitative trait loci; nsnps number of SNPs

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