Table 1 Top candidate genes for schizophrenia—CFG analysis of ISC GWAS data

DISC1, disrupted in schizophrenia 1

0.002934, rs10910616

SZ^{18, 27, 78, 79, 80, 81, 82, 83, 84, 85}

(I) Antipsychotic treatment,⁸⁶ mouse neurodevelopment⁸⁷

1q42.2 (Assoc) SZ^{22, 67, 88, 89, 90, 91, 92, 93, 94}

(I) SZ HIP²⁵

(I) SZ lymphoblasts,²⁵ PMBCs²⁶

5.0

0.001562, rs12754490

0.0001308, rs11122318

HSPA1B, heat-shock 70-kDa protein 1B

0.0009003, rs2763979

(D) PCP HIP; (D) CLZ VT⁶

(D) CLZ

6p21.33 (Assoc) SZ⁴⁴

(I) SZ⁴⁵

(I) SZ, IPS-derived neurons¹⁰

5.0

MBP, myelin basic protein

0.01002, rs12959006

(I) PCP and CLZ AMY; (D), PCP PFC,⁶ (I), SZ,⁹⁵ (D) SZ⁹⁶

(I) PCP and CLZ

18q23 (Assoc) SZ³⁷

(D) SZ³⁸

(D) SZ peripheral blood⁹⁷

5.0

0.01345, rs9967028

0.03257, rs1629089

TCF4, transcription factor 4

0.0002902, rs17594665

SZ⁹⁸

(I) PCP NAC⁶

18q21.2 (Assoc) SZ^{32, 33, 34, 35}

(I) SZ³⁶

(I) SZ, IPS-derived neurons;¹⁰ (D) delusions SZ⁷

5.0

0.01039, rs17594665

0.00126, rs1539951

MOBP, myelin-associated oligodendrocyte basic protein

0.003529, rs1708044

(I), PCP and CLZ AMY; (D), CLZ CP; (I), CLZ NAC; (D), PCP PFC; (D), CLZ VT,⁶ (I), Psychosis,⁹⁹ (I), Response to antipsychotics,¹⁰⁰ (D), SZ¹⁰¹

(I) CLZ

3p22.1 (Linkage) SZ¹⁰²

(D), SZ,³⁸ (I), SZ and substance abuse¹⁰³

(D), SZ lymphocytes¹⁰⁴

4.5

0.02583, rs1405798

0.004474, rs1538783

NCAM1, neural cell adhesion molecule 1

0.003917, rs11214441

SZ¹⁰⁵

(I) SZ⁹⁵

11q23.2 (Assoc) SZ¹⁰⁶

(I) SZ^{106, 107}

(D) SZ, IPS-derived neurons¹⁰

4.5

0.002043, rs1245133

0.001454, rs600964

NDUFV2, NADH dehydrogenase (ubiquinon) flavoprotein 2, 24kDa

0.003243, rs8084822

Response to antipsychotics¹⁰⁸

(D) PCP and CLZ

18p11.22 (Assoc) SZ¹⁰⁹

(D), SZ Striatum,¹¹⁰ (I), SZ parito-occipital cortex^{1, 10} (I), SZ¹¹¹

(I), SZ lymphocytes¹¹⁰

4.5

0.004361, rs1893144

0.0009294, rs10468792

NRCAM, neuronal cell adhesion molecule

0.006234, rs10250083

SZ¹¹²

(I) CLZ VT⁶

7q31.1 (Linkage) SZ¹¹³

(D) SZ⁴⁸

(D) SZ serum⁴⁹

4.5

0.004773, rs404287

0.002343, rs409797

RAB18, RAB18, member RAS oncogene family

0.03817, rs12261690

(I) PCP AMY; (D), PCP PFC; (D) CLZ VT⁶

(I) PCP

10p12.1 (Linkage) SZ^{114, 115, 116, 117, 118}

(D) SZ¹¹⁹

(D) SZ whole blood¹²⁰

4.5

0.01716, rs7476899

0.01231, rs11015796

ADCYAP1, adenylate cyclase-activating polypeptide 1 (pituitary)

0.002876, rs9954574

SZ¹²¹

(I) CLZ NAC; (D) CLZ VT ⁶

18p11.32 (Assoc) SZ^{121, 122}

(D) SZ¹¹⁹

4.0

0.02558, rs1394890

0.005448, rs16953183

ALDH1A1, aldehyde dehydrogenase 1 family, member A1

0.02526, rs11143438

(I) PCP and CLZ AMY; (D), PCP and CLZ NAC,⁶ (I) Psychosis⁹⁹

(I) PCP

(D) SZ,^{111, 123} (I) SZ¹²⁴

(I) SZ, fibroblasts¹²⁵

4.0

0.01389, rs7028573

0.01285, rs11999628

ANK3, ankyrin 3, node of Ranvier (ankyrin G)

0.001727, rs4948256

(D) PCP AMY; (I), PCP CP;v(D), PCP NAC; (I), CLZ VT⁶

10q21.2 (Assoc) SZ^{48, 126}

(D) SZ⁴⁸

(I), SZ IPS-derived neurons¹⁰

4.0

0.006456, rs10509133

0.005837, rs7906905

BDNF, brain-derived neurotrophic factor

0.001666, rs10742178

(I) SZ,^{127, 128, 129} (I) PCP in rats, ¹³⁰ (I) MK-801 in rats¹³¹

11p14.1 (Assoc) SZ^{132, 133, 134, 135}

(D) SZ^{136, 137, 138}

(D) SZ serum,^{49, 139, 140, 141} (D) leukocytes psychosis¹⁴²

4.0

0.005507, rs2131060

CD9, CD9 molecule

0.0455, rs3181291

(I) PCP AMY; (D), PCP PFC; (I), PCP VT⁶

(I) PCP and CLZ

(D) SZ¹⁴³

(D) SZ IPS-derived neurons¹⁰

4.0

0.01167, rs2268014

0.04739, rs7342306

CNR1, cannabinoid receptor 1 (brain)

0.002567, rs1324073

SZ¹⁴⁴

(D) PCP and CLZ VT,⁶ (D) response to antipsychotics¹⁰⁰

6q15 (Assoc), SZ^{50, 51}

(D) SZ⁵²

4.0

0.001542, rs9451023

0.002128, rs873413

COMT, catechol-O-methyltransferase

0.04098, rs1544325

SZ^{145, 146}

(I), CLZ VT⁶, (D), SZ¹⁴⁷

22q11.21 (Assoc) SZ¹⁴⁸

(I), SZ¹⁴⁹

4.0

0.01457, rs1544325

CPLX2, complexin 2

0.04338, rs10213927

SZ¹⁵⁰

(D), PCP and CLZ VT,⁶ (D), SZ¹²⁷

5q35.2, (Assoc), SZ¹⁵¹

(D), SZ^{136, 152, 153}

4.0

0.01658, rs6887620

DRD2, dopamine receptor D2

0.01151, rs12791990

(D), PCP and CLZ PFC,⁶ (D), SZ¹⁵⁴

11q23.2 (Assoc), SZ^{155, 156}

(D) SZ^{136, 157, 158}

(D) SZ delusions⁷

4.0

0.007265, rs4938021

0.01096, rs17529477

DTNBP1, dystrobrevin binding protein 1

0.002634, rs12209943

SZ^{159, 160, 161, 162}

6p22.3 (Assoc) SZ^{163, 164, 165, 166, 167, 168}

(D), SZ^{169, 170, 171, 172}

(D) Lymphocytes¹⁷³

4.0

0.009146, rs9477021

0.0001501, rs16876575

FABP7, fatty acid–binding protein 7, brain

0.01053, rs9490546

SZ¹⁷⁴

(I), CLZ NAC; (I), PCP and CLZ PFC⁶

6q22.31 (Assoc), SZ¹⁷⁴

(I), SZ¹⁷⁴

4.0

GABRB3, gamma-aminobutyric acid (GABA) A receptor, β3

0.004635, rs8037461

(I), PCP AMY; (D), PCP HIP; (D), PCP PFC⁶

15q12 (Assoc) SZ¹⁷⁵

(I) SZ,¹⁷⁶ (D) SZ¹⁷⁷

(I), SZ serum¹⁷⁸

4.0

0.01579, rs12904865

0.0009769, rs4906835

GAD1, glutamate decarboxylase 1 (brain, 67 kDa)

0.03907, rs16859026

(I), PCP AMY,⁶ (D), SZ,^{127, 128} (I), SZ¹⁷⁶

(I), CLZ

2q31.1 (Assoc), SZ¹⁷⁹

(D), SZ,^{136, 176, 177, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191} (I), SZ¹⁹²

4.0

0.008447, rs10191129

0.01776, rs2883888

GNB1L, guanine nucleotide–binding protein (G-protein), β-polypeptide 1-like

0.03659, rs17745302

Impaired PPI¹⁹³

(I), Chronic haloperidol,¹⁹⁴ (D), SZ¹⁴⁷

22q11.21 (Assoc), SZ¹⁹⁵

(D), SZ ¹⁹⁴

4.0

GRIA1, glutamate receptor, ionotropic, AMPA 1

0.0008031, rs2962816

SZ¹⁹⁶

(D), PCP and CLZ AMY,⁶ (I), response to antipsychotics,¹⁰⁰ (D), response to PCP¹⁹⁷

5q33.2 (Assoc), SZ ^{198, 199}

(D), SZ^{200, 201}, (I), SZ^{181, 202, 203}

4.0

0.00659, rs10044974

0.006037, rs498660

GRIA4, glutamate receptor, ionotrophic, AMPA 4

0.02792, rs649098

Cognition (impaired PPI)²⁰⁴

(I), PCP and CLZ AMY,⁶ (D), SZ²⁰⁵

11q22.3 (Assoc), SZ²⁰⁶

(D), SZ,^{119, 207} (I), SZ²⁰²

4.0

0.001526, rs7116118

0.00343, rs2277280

GRIN2B, glutamate receptor, ionotropic, N-methyl D-aspartate 2B

0.001569, rs4363703

SZ ²⁰⁸

(D), CLZ AMY; (I), CLZ VT,⁶ MK-801-treated rats,²⁰⁹ (D), response to antipsychotics,¹⁰⁰ (D), SZ,¹⁷⁶

12p13.1 (Assoc), SZ^{155, 167}

(D), SZ,²⁰¹ (I), SZ²¹⁰

4.0

0.001427, rs1072388

0.003102, rs12826365

GRM5, glutamate receptor, metabotropic 5

0.002559, rs992259

SZ²¹¹

(D), PCP AMY, (D), PCP VT,⁶ (D), SZ¹²⁹

11q14.3 (Assoc), SZ²¹²

(D), SZ¹⁸¹

4.0

0.01842, rs170110

0.001263, rs1846475

GSN, gelsolin

0.04739, rs12376078

(I), PCP AMY, (D), CLZ CP⁶

(I) PCP and CLZ

33.2 (Assoc), SZ²¹³

(D), SZ^{111, 192143, 214}

4.0

0.002313, rs767770

0.0001564, rs4837835

HINT1, histidine triad nucleotide–binding protein 1

0.00008672, rs11242025

SZ²¹⁵

5q23.3 (Assoc), SZ, ^{216, 217}

(D), SZ²¹⁸

(I), SZ whole blood¹²⁰

4.0

0.008637, rs7734177

HTR2A, 5-hydroxytryptamine (serotonin) receptor 2A

0.02014, rs7985155

(I), Response to antipsychotics,¹⁰⁰ (D), SZ²¹⁹ (I), SZ¹⁵⁴

13q14.2 (Assoc), SZ^{155, 220}

(D), SZ^{136, 221, 222}

(D), SZ lymphocytes²²³

4.0

0.003461, rs17070879

0.002529, rs1886439

KALRN, kalirin, RhoGEF kinase

0.006285, rs3772756

(I), CLZ VT⁶

3q21.1 (Assoc), SZ²²⁴

(D), SZ²²⁵

(D), SZ IPS-derived neurons¹⁰

4.0

0.01015, rs9832419

0.009074, rs1822791

KIF2A, kinesin heavy chain member 2A

0.005374, rs6864793

(D), CLZ VT⁶

(I) PCP and CLZ

5q12.1 (Assoc), SZ²²⁶

(D), SZ¹¹⁹

4.0

0.003396, rs153864

0.005207, rs10069830

NR4A2, nuclear receptor subfamily 4, group A, member 2

0.0006887, rs12465886

SZ²²⁷

(I), PCP and CLZ HIP, (I), PCP and CLZ NAC;, (D), PCP PFC, (I), PCP and CLZ VT⁶

2q24.1 (Assoc), SZ,²²⁸

(I), SZ IPS-derived neurons ¹⁰

4.0

0.001624, rs6743834

0.004081, rs16840214

NRG1, neuregulin 1

0.001731, rs1158001

SZ^{229, 230, 231}

8p12 (Assoc), SZ^{94, 220, 232, 233, 234, 235}

(D), SZ^{38, 236, 237, 238} (I), SZ^{239, 240, 241}

(I), SZ IPS-derived neurons,¹⁰ (I), SZ, Leucocytes,²⁴² (I), SZ lymphocyte, ²⁴³ (I), SZ delusions⁷

4.0

0.00104, rs2716960

0.000006564, rs6989777

PDE4B, phosphodiesterase 4B, cAMP-specific

0.003042, rs6588193

SZ²⁴⁴

(D), PCP,⁶ (I), psychosis,²⁴⁵ (D), response to antipsychotics²⁴⁶

1p31.3 (Assoc) SZ^{234, 247, 248, 249, 250}

(D) SZ²⁴⁷

4.0

0.02102, rs11805090

0.000103, rs17417507

PRKCA, protein kinase C, alpha

0.007991, rs6504428

(I), CLZ PFC, (D), CLZ VT,⁶ (I), response to antipsychotics²⁵¹

17q24.2, (Assoc), SZ^{252, 253}

(D), SZ¹³⁶

(D), SZ IPS-derived neurons¹⁰

4.0

0.01166, rs9908814

0.0004001, rs16959057

RELN, reelin

0.01368, rs2711865

SZ²⁵⁴

(I), CLZ PFC;, (D), PCP and CLZ VT,⁶ (D), SZ^{128, 255}

7q22.1 (Assoc), SZ^{94, 155, 233, 256, 257, 258, 259}

(D), SZ^{136, 186, 187, 190, 260, 261}

4.0

0.007165, rs10227303

0.004365, rs7794418

RGS4, regulator of G-protein signaling 4

0.004835, rs4657235

SZ²⁶²

(I), PCP and CLZ AMY;, (I), CLZ HIP ;, (D), CLZ PFC;, (I), PCP and CLZ VT,⁶ (D), SZ^{263, 264}

1q23.3 (Assoc), SZ^{167, 220, 265, 266}

(D), SZ,^{45, 210, 267, 268, 269, 270, 271} (I), SZ²⁷²

4.0

0.007928, rs12403644

0.007516, rs10917637

SLC1A2, solute carrier family 1 (glial high-affinity glutamate transporter), member 2

0.02565, rs3794086

(D), CLZ AMY, (D), CLZ VT⁶

(I), CLZ

11p13 (Assoc), SZ,²⁷³

(D), SZ,¹⁵³ (I), SZ^{274, 275}

4.0

0.03109, rs3829280

0.002563, rs12270460

SNAP25, synaptosomal-associated protein, 25 kDa

0.01815, rs6032783

SZ²⁷⁶

(I), SZ^{127, 263}

20p12.2 (Assoc), SZ²⁷⁷

(D), SZ,^{181, 278, 279, 280, 281} (I), SZ^{181, 282, 283}

4.0

0.005819, rs362616

0.01192, rs362560

SYN2, synapsin II

0.003144, rs2960421

SZ^{284, 285}

(D), PCP and CLZ AMY, (D), PCP CP, (D), PCP and CLZ VT,⁶ (I), SZ,²⁰⁵ (D), SZ^{127, 263}

3p25.2 (Assoc), SZ^{151, 286, 287}

(D), SZ,^{45, 288183} (I), SZ antipsychotic, treatment¹⁰⁷

4.0

0.042, rs2618406

0.02541, rs17671592

TNIK, TRAF2 and NCK interacting kinase

0.001377, rs260769

(I), CLZ VT⁶

3q26.31 (Assoc), SZ^{9, 89, 234, 289}

(I), SZ²⁷⁸

(D), SZ lymphoblastoid cell lines²⁹⁰

4.0

0.006987, rs12639373

0.00007179, rs13065441