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Table 1 Top SCZ-associated genes predicted by Sherlock integrative analysis

From: Comprehensive and integrative analyses identify TYW5 as a schizophrenia risk gene

Gene CHR BPa LBFb P valuec Supporting SNP Cis or Trans GWAS P valued eQTL P valuee FDRf
CYP21A1P 6 32146528 15.0977 3.38E-06 rs1150755 cis 1.30E-07 6.36E-09 <0.01
     rs2854275 cis 2.26E-08 1.13E-10  
C4A 6 31584437 14.9444 3.38E-06 rs3130614 cis 1.28E-08 5.65E-19 <0.01
     rs2854275 cis 2.41E-06 1.13E-10  
CSPG4P12 15 82898038 7.55567 3.38E-06 rs11635505 cis 2.57E-07 4.95E-13 <0.01
BAG6 6 31834667 7.55201 3.38E-06 rs707939 cis 4.57E-08 4.70E-13 <0.01
GLT8D1 3 52794367 7.4461 3.38E-06 rs2268023 cis 3.42E-06 3.66E-09 <0.01
PCDHA10 5 140138726 7.40982 3.38E-06 rs4451093 cis 1.28E-13 1.20E-10 <0.01
GNL3 3 52597126 7.39453 3.38E-06 rs2590838 cis 4.54E-06 8.82E-13 <0.01
TYW5 2 200598933 7.37493 3.38E-06 rs203772 cis 1.83E-08 2.74E-10 <0.01
ITIH4 3 52849336 7.35272 3.38E-06 rs6445539 cis 6.21E-09 1.17E-09 <0.01
DDAH2 6 31837338 7.34818 3.38E-06 rs707938 cis 6.04E-06 1.07E-11 <0.01
DNM1P51 15 82549305 7.3218 3.38E-06 rs12915234 cis 9.24E-13 4.34E-13 <0.01
DDHD2 8 38215456 7.30636 3.38E-06 rs6992943 cis 8.37E-07 8.02E-12 <0.01
GOLGA2P7 15 82722026 7.29214 3.38E-06 rs12906983 cis 7.03E-12 5.63E-12 <0.01
BTN3A2 6 26485364 7.17497 3.38E-06 rs9366655 cis 3.34E-14 1.34E-14 <0.01
CORO7 16 4424614 7.16594 3.38E-06 rs4785964 cis 7.76E-08 4.03E-08 <0.01
FTSJ2 7 2242519 7.11154 3.38E-06 rs7787274 cis 7.63E-07 9.36E-08 <0.01
HLA-J 6 29753592 6.93651 3.38E-06 rs3129063 cis 8.86E-06 1.70E-06 <0.01
FTCDNL1 2 200449965 6.92637 3.38E-06 rs11694369 cis 1.47E-07 8.15E-16 <0.01
ZSCAN23 6 28496744 6.84615 3.38E-06 rs2531831 cis 2.02E-06 1.78E-08 <0.01
MAPK3 16 29854171 6.73467 3.38E-06 rs11649612 cis 3.70E-06 5.00E-10 <0.01
PCDHA9 5 140228723 6.60836 3.38E-06 rs192231 cis 3.29E-07 1.10E-08 <0.01
NDUFAF7 2 37393080 6.60052 3.38E-06 rs10190959 cis 1.56E-06 1.86E-07 <0.01
ZNF204P 6 27420057 6.58274 3.38E-06 rs764284 cis 3.38E-07 1.12E-11 <0.01
  1. TYW5 was shown in bold
  2. agene locations were based on hg19
  3. bLBF logarithm of Bayes factor. The LBF score of a gene reflects the association strength between this gene and SCZ. For example, a LBF of 5.0 means that the gene is more likely to be associated with the disease (exp(5.0) = ~148 times) than no association
  4. cP value from Sherlock integrative analysis. Larger LBF corresponds to smaller P value
  5. dGWAS P value indicates the association significance between this SNP and SCZ
  6. eeQTL P value indicates the association significance between this SNP and gene expression in brain
  7. fFDR was corrected by Benjamini–Hochberg procedure