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

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

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
  1. 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.
  2. Chr chromosome, GWAS genome-wide association study; mQTL DNA methylation quantitative trait loci; nsnps number of SNPs