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					Supplementary Table 1: Stage 1 GWAS Samples - Ascertainment, Phenotyping, and Demographics.
                                                                     Cases                                                                                                                                      Controls

                     Years                                          Record                                                Age at                                                                                                                     Age at
                     Collecte                                                               Diagnostic                    Enrollmen Age at         Family        Years                                                                               Enrollmen
Collection           d          Ascertainment          Instruments Review Exclusions        Criteria   Diagnosis          t         Onset          History       Collected   Ascertainment         Instruments Exclusions                   Screened t
                     1990-      inpatients,                                                                                                                      2004-       birth cohort, blood                                                     median 44-
Cardiff UK           2003       outpatients            PSE, SCAN    yes      SIP, GMC       DSM-IV      SZ                44.8 (13.1) 23.8 (7.9)    26%          2005        donors                none         none                        no       45
                     2001-      inpatients,                                                                                           14.6                       2004-                                          any non-negative
CATIE                2005       outpatients            SCID         yes      SA, MR, Cog DSM-IV         SZ                41.3 (11.4) (11.0)     n.a.            2007        online panel          CIDI-SF      psychosis screen            yes      41.5 (11.3)
                                                                                                                                                                                                   brief
ISC -                1997-      inpatients,            SCID,                                DSM-IV,                                   23.9                       2001-                             questionnair
Aberdeen             2006       outpatients            OPCRIT       yes      SA, Cog        ICD-10      SZ                40.0 (13.5) (10.0)          30%        2006        general practice      e            MMI (or FHx thereof), Rx    yes      41.0 (15.0)
                                inpatients,
                     1999-      outpatients, ≥1 SZ                                                                                                               2004-       GenOutpt, staff;                 known psychiatric
ISC - Cardiff        2005       hospitalization        SCAN         yes      IQ<70          DSM-IV      SZ                36.8 (10.5) 24.5 (7.2)      18%        2005        govt                none         treatment                     no       49.1 (15.5)
                     2000-      inpatients,            SCID,                                DSM-IV,                                                              2004-                                        chronic medications or
ISC - Dublin         2005       outpatients            OPCRIT       yes      SIP, GMC       ICD-10      SZ                45.4 (11.7) 24.7 (7.2) n.a.            2005        blood donors        not screened illness                       no       n.a.
ISC -                1986-      inpatients,                                                                                                                      1994-                                        chronic medications or
Edinburgh            2006       outpatients            SADS-L       yes      IQ<70          DSM-IV      SZ                42.2 (13.5) 24.3 (8.3)      28%        2006        blood donors, staff not screened illness                       no       43.5 (18.5)
                                                                                                                                                                             blood donors,
                                                                             SIP, SA                                                                                         staff, university
                     1983-                                                   bipolar, LD,                                                                        1994-       students, general
ISC - London         2006       ICD-10 SZ patients     SADS-L       yes      HI             RDC         SZ                45.3 (14.8) 23.6 (7.4)      19%        2006        practice              SADS-L         SIP, SA bipolar, LD, HI   yes      38.1 (15.4)
                                                       DIGS, SIS,
                                                       SANS,                                                                                                                 brochures to
                     1995-      families with SZ or    SAPS,                 IQ<70,                     SZ or SA                                                 1995-       community
ISC - Portugal       2002       bipolar disorder       OPCRIT       yes      SIPS, HI       DSM-IV      depressed         39.9 (14.7) 23.2 (7.3)      19%        2002        organizations         DIGS           MMI (or FHx thereof)      yes      41.5 (13.5)


                                                                                                                                                                                                   medical
                                                                                                                                                                                                   record
                                                                                                                                                                                                   review and
                                                                                                                                                                                                   brief
                                                                                                                                                                                                   interview
                                ≥2 SZ                                                                                                                                                              confirmation
                     2005-      hospitalizations (ICD-                                                                                33.4                       2005-       national hospital     of lack of    hospitalization for SZ,
ISC - SW1            2009       8, 9, or 10)           clinical exam yes     bipolar        DSM-IV      SZ                52.0 (11.5) (10.1)         9.5%        2009        registry              SZ or bipolar SA, bipolar                yes      50.1 (12.1)


                                                                                                                                                                                                   medical
                                                                                                                                                                                                   record
                                                                                                                                                                                                   review and
                                                                                                                                                                                                   brief
                                                                                                                                                                                                   interview
                                ≥2 SZ                                                                                                                                                              confirmation
                     2005-      hospitalizations (ICD-                                                                                34.0                       2005-       national hospital     of lack of    hospitalization for SZ,
ISC - SW2            2009       8, 9, or 10)           clinical exam yes     bipolar     DSM-IV         SZ                55.8 (12.8) (11.3)         6.4%        2009        registry              SZ or bipolar SA, bipolar                yes      54.4 (11.9)
                                inpatients,                                  SIP, GMC, >
                     1989-      outpatients, ads,                            moderate                   SZ or SA (10%                                            2004-                             CIDI-SF,      any non-negative
MGS                  2008       support groups         DIGS          yes     MR          DSM-IV         SA)               43.0 (11.6) 21.4 (7.0)      29%        2007        online panel          screening ?'s psychosis screen           yes      50.6 (16.4)
                                                                                                                                                                             population-based      brief
SGENE -              1992-      consecutive            SCID, SADS-           SIP, HI,                                                                            2003-       epidemiological       questionnair
Bonn                 2002       inpatients             L, OPCRIT   yes       GMC            DSM-IV      SZ                34.1 (11.0) 21.9 (6.5)      30%        2009        studies               e             none                       no       50.4 (11.4)
                                                                                                                                                                          national blood
                                                                                                                                                                          donor corps &
                                inpatients and                               known                                                                                        randomly drawn
                                outpatients through                          organic                                                                                      from national
SGENE -              2003-      national psychiatric                         psychiatric                                                                                  biobank population                      apparent behavioral
Copenhagen           2009       biobank                OPCRIT       yes      disorders      ICD-10      SZ or SA          41.3 (12.7) 26.7 (9.3)      11%            2005 cohort             observation          abnormality               yes      42.3 (11.7)



                                                                                                                                                                                                   several
                                                                                                                                                                                                   screenings
                                                                                                                                                                             randomly selected     (e.g., SCID,
                                                                                                                                                                             from same region      FHAM,
                                                                                                                                                                             as cases by using     MMST,        HI, MR, LD, substance
SGENE -              1997-      inpatients,                                  HI, ND, SIP,                                                                        1997-       government            neurological abuse, psychotic disorder
Munich               2010       outpatients            SCID         yes      GMC, MR      DSM-IV        SZ                37.9 (11.7) 23.6 (8.6)      30%        2010        database              examination) or ND (or FHx thereof)    yes        51.3 (15.8)


                                                                                                                                                                                                                  HI, ND, MR,
                                                                                                                                                                                                                  SZ/bipolar/depression (or
                                                                                                                                                                             random from                          FHx thereof),
                                                                                                        SZ,                                                                  comprehensive                        hypothyroidism,
                                                                                                        schizophreniform                                                     national database                    uncontrolled
SGENE -              2003-      inpatients,                                                              (6%), or SA                                             2004-       from same region      interview,     hypertension, diabetes,
TOP3                 2008       outpatients            SCID         yes      IQ<70          DSM-IV      (17%)            34.1 (10.2) 24.9 (8.9) n.a.             2008        as cases              PRIME-MD       significant substance use yes      35.3 (10.0)
                                                                                                                                                                             ads and primary
                                                                                                                                                                             care physician
                                                                                > moderate                                                                                   referrals, drawn
SGENE -            1995-       inpatients,                                      MR, SIP,                                                                          1995-      from the same                     > moderate MR, FHx of
UCLA               2003        outpatients              CASH            yes     GMC           DSM-IV        SZ                 34.8 (13.9) 26.3 (9.3) n.a.        2003       region as cases     CASH          MMI                        yes        31.6 (11.2)
                                                                                                            SZ,                                                              ads, from same      SCID-NP
                   1999-       inpatients,                                                                  schizophreniform                                      1999-      community as        and urine     Axis I Disorder (or FHx
Zucker Hillside 2006           outpatients              SCID            yes     IQ<70, GMC DSM-IV           , or SA            38.8 (10.4) 21.7 (5.9)     30% 2006           cases               drug screen thereof), Rx                 yes        47.9 (18.4)
Notes: Year collected refers to the calendar years during which subjects were collected. Age data is provided as mean years (standard deviation). Age at onset is usually age at illness onset, though occasionally is age at first psychiatric contact or age     .
at impairment (see text). Family History % refers to the proportion of cases with known family history of psychosis (largely SZ) though in some instances this information was not available (n.a.); please note that except for one family sample (Multicenter-   .
Pedigree), all other samples are case-control samples that contain only unrelated cases and unrelated controls (except for Iceland which has some related individuals but these are controlled for with genomic control).                                          .
Abbreviations: Collection names as in Table 1. PSE = Present State Examination [64]; SCAN = Schedules for Clinical Assessment in Neuropsychiatry [65]; SCID = Structured Clinical Interview for DSM-IV [66-68]; OPCRIT = Operational Criteria                      .
Checklist [69]; SADS-L = Schedule for Affective Disorders and Schizophrenia–Lifetime version [70-71]; DIGS = Diagnostic Interview for Genetic Studies [72]; SIS = Kendler's Structured Interview for Schizotypy [73]; SANS = Schedule for the Assessment           .
of Negative Symptoms [74]; SAPS = Schedule for the Assessment of Positive Symptoms; CASH = comprehensive assessment of symptoms and history [27]; DIP = Diagnostic Interview for Psychosis [75]; FHAM = Family History Assessment Module
                                                                                                                                                                                                                                                                   .
[76]; MMSE = Mini Mental Status Exam [77-78]; DSM = Diagnostic and Statistical Manual of Mental Disorders [15-79]; ICD = International Classification of Diseases [80-83]; RDC = Research Diagnostic Criteria [84]; MINI = Mini International                      .
Neuropsychiatric Interview [85]; SZ = schizophrenia; SA = schizoaffective disorder; SIP = substance-induced psychosis (includes active/recent significant substance use); GMC = psychosis due to general medical condition; MR = mental retardation;               .
Cog = other cognitive disorders; IQ = intelligence quotient; LD = learning disability; HI = head injury (with various durations of loss of consciousness specified); ND = neurological disease; ECT = electroconvulsive therapy; GenOutpt = general (non-          .
psychiatric) outpatients; staff refers to hospital staff; govt refers to government sources such as Drivers LIcense applicants; CIDI-SF = Composite International Diagnostic Interview – Short Form [86-88]; PRIME-MD = Primary Care Evaluation of Mental
                                                                                                                                                             .
                 .
Supplementary Table 2: Stage 2 Replication Samples - Ascertainment, Phenotyping, and Demographics.
                                                                              Cases                                                                                                                                         Controls
                                                                     Recor                                                                             Family
                        Years                                        d                                                          Age at                                 Years                                                                                          Age at
                        Collecte                                     Revie                            Diagnosti                 Enrollmen Age at       Histor          Collecte                                  Instrument                                           Enrollmen
Collection              d        Ascertainment           Instruments w           Exclusions           c Criteria Diagnosis      t         Onset        y               d            Ascertainment                s              Exclusions                   Screened t
                                                                                 site-specific, but
                                                                                 generally
                                                                                 excluding
                                                                                 individuals
                                                                                 believed to have
                                 pedigrees with SZ in    various                 ND, GMC, or
Multicenter-            1983-    multiple family         structured              SIP causes of                                               23.7
Pedigree                2003     members                 interviews     yes      psychosis            DSM-III-R SZ or SA        n.a.         (7.5)       100%          n.a.        n.a.                          n.a.           n.a.                         n.a.     n.a.
                                 national newborn                                                                                                                                  national newborn
                                 biobank & psychiatric                                                                                       18.9                                  biobank & psychiatric         clinical
SGENE - Aarhus              2008 registry                clinical exam no        none                 ICD-10     SZ             18.9 (2.8)   (2.8)            8%              2008 registry                      exam           SZ                           yes      18.9 (2.8)
                                                                                 known organic
                                 psychiatric                                     psychiatric
                        1994-    depatments, twin                                disorders, drug      DSM-IV,                                24.4                      2001-                                     questionnair chronic medications,
SGENE - Aarhus          2005     studies                 SCAN           yes      dependency           ICD-10     SZ             26.4 (7.0)   (6.1)     n.a.            2003         medical students             e            chronic illness                no       22.0 (n.a.)

                        2004-                            clinical                other psychotic                 SZ or SA                   24.1                       2004-        spouses of patients with
SGENE - Belgium         2008     inpatients, outpatients diagnosis      yes      conditions           DSM-IV     (22%)          34.8 (11.4) (6.6)      n.a.            2008         neurological disorders       observation    neurological disorder        no       51.0 (n.a.)

                                 inpatients and                                                                                                                                    national blood donor
                                 outpatients through                             known organic                                                                                     corps & randomly drawn
SGENE -                 2003-    national psychiatric                            psychiatric                                                26.7                                   from national biobank                        apparent behavioral
Copenhagen              2009     biobank                 OPCRIT         yes      disorders            ICD-10     SZ or SA       41.3 (12.7) (9.3)         11%                 2005 population cohort             observation    abnormality                  yes      42.3 (11.7)
                                                                                                                                                                                    drawn from deCODE
                                                                                                                                                                                    Genetics case and
                                                                                                                                                                                    control programs,
                                                                                                                                                                                    unselected except for
                                                                                                                                                                                    not including those in
                        1990-                                                                                                               24.0                       1996-        SZ or bipolar case                          already known research
SGENE - Iceland         2008     inpatients, outpatients SADS-L         yes      MR                   RDC        SZ             45.7 (15.4) (7.1)         50%          2010         groups already               none           diagnoses of SZ, bipolar   no         62.1 (18.1)
                        1990-    family, twin, & genetic SADS-L,                 SIP, GMC, HI,                                              22.3                       1990-        family, twin, & genetic                     MMI (or FHx thereof), SIP,
SGENE - England         2008     studies                 SCAN           yes      ND                   ICD-10     SZ             n.a         (5.3)      n.a.            2008         studies                      FIGS           ND                         yes        n.a



                                                                                                                                                                                   derived from a nationally
                                                                                                                                                                                   representative Health
                                                                                                                                                                                   2000 suvey (N=8028);
                                                                                                                                                                                   sex and age (± 5 years)
                                                                                                                 SZ (87.4%),                                                       matched to cases, with
                                                                                                                 SA (8.7%),                                                        prioritization for those
                                                                                                                 schizophrenifor                                                   with neuropsychological
                                 families with SZ-       SCID-I,                                                 m (1.3%),                                                         testing and from the
                                 spectrum disorders,     SCID-II,                                                other           born                                              isolate and its
                        1998-    hospitalization         SANS,                                                   psychotic       between   22.5                                    neighboring                   SCID-I or      lifetime history of any               20-70
SGENE - Helsinki        2003     between 1969-1998       SAPS           yes      none                 DSM-IV     disorder (3.8%) 1940-1974 (5.6)         100%                 2000 municipalities                CIDI           psychotic disorders          yes      years old



                                                                                                                                                                                   derived from a nationally
                                                                                                                                                                                   representative Health
                                                                                                                                                                                   2000 suvey (N=8028);
                                                                                                                                                                                   sex and age (± 5 years)
                                                                                                                                                                                   matched to cases, with
                                                                                                                                                                                   prioritization for those
                                                                                                                                                                                   with neuropsychological
                                 families with SZ-       SCID-I,                                                                                                                   testing and from the
                                 spectrum disorders,     SCID-II,                                                               born                                               isolate and its
SGENE -                 1998-    hospitalization         SANS,                                                                  between   22.5                                     neighboring                   SCID-I or      lifetime history of any               20-70
Kuusamo                 2003     between 1969-1998       SAPS           yes      none                 DSM-IV     SZ             1940-1974 (5.6)          100%                 2000 municipalities                CIDI           psychotic disorders          yes      years old
                                                                                 severe                                                                                                                          medical
                                                                                 disorganization,                                                                                                                records,
                        2005-                                                    HI, MR, ND,                                                28.6                       2005-        GenOutpt, university         clinical
SGENE - Hungary         2007     inpatients, outpatients MINI           yes      SIPS, SA             DSM-IV     SZ             37.6 (11.6) (9.7)      n.a.            2007         staff                        examination    psychiatric disorders        yes      39.8 (15.0)
                        1997-    South Verona case                                                                                          27.0                                                                 SCID-NP;       psychotic disorders (or
SGENE - Italy           2004     registry                SCAN           yes      LD, MR, Cog          ICD-10     SZ             40.2 (13.3) (8.8)             5%              2004 blood donors                  FIGS           FHx thereof)                 yes      38.6 (11.6)


                                                                                                                                                                                                            several
                                                                                                                                                                                                            screenings
                                                                                                                                                                                                            (e.g., SCID,
                                                                                                                                                                                                            FHAM,
                                                                                                                                                                                    randomly selected from  MMST,
                                                                                                                                                                                    same region as cases by neurological HI, MR, LD, substance
                        1997-                                                    HI, ND, SIP,                                               23.6                       1997-        using government                     abuse, psychotic disorder
SGENE - Munich          2010     inpatients, outpatients SCID           yes      GMC, MR              DSM-IV     SZ             37.9 (11.7) (8.6)         30%          2010         database                examination) or ND (or FHx thereof)              yes      51.3 (15.8)

                                                                                                                                                                                                             several
                                                                                                                                                                                                             screenings
                                                                                                                                                                                                             (e.g., SCID,
                                                                                                                                                                                                             FHAM,
                                                                                                                                                                                    randomly selected from   MMST,
                                                                                                                                                                                    same region as cases by neurological HI, MR, LD, substance
                        1997-                                                    HI, ND, SIP,                                               23.6                       1997-        using government                      abuse, psychotic disorder
SGENE - Munich          2010     inpatients, outpatients SCID           yes      GMC, MR              DSM-IV     SZ             37.9 (11.7) (8.6)         30%          2010         database                 examination) or ND (or FHx thereof)             yes      51.3 (15.8)
                                                                                                                                                                                    students, researchers
                                                                                                                                                                                    and their spouses,
                        1994-                                                                                                               25.4                       1994-        hospital staff, friends,
SGENE - Russia          2008     outpatients             MINI           yes      SIPS/GMC, ND         DSM-IV    SZ              44.0 (11.9) (8.7)         16%          2008         blood donors             MMPI, SPQ MMPI>80, SPQ>40                       yes      44.1 (19.5)
                                                                                                                SZ,
                                                                                                                schizophrenifor                                                     population registry,
                        1991-                                                                         DSM-III-  m (3%), or SA               24.6                       1991-        previous controls in
SGENE - Sweden          2003     outpatients             interviews     yes      none                 R, DSM-IV (10%)           43.6 (14.2) (6.8)         16%          2003         psychiatry research          SCID           SZ                           yes      40.5 (9.8)
                                                                                                                                                                                                                 medical
                                                                                                                                                                                                                 record
                                                                                                                                                                                                                 review and
                                                                                                                                                                                                                 brief
                                                                                                                                                                                                                 interview
                                                                                                                                                                                                                 confirmation
                                                                                                                                                                                                                  of lack of
                        2005-    ≥2 SZ hospitalizations                                                                                     31.3                       2005-                                     SZ or        hospitalization for SZ, SA,
SW3                     2009     (ICD-8, 9, or 10)      clinical exam yes        bipolar              DSM-IV     SZ             53.2 (11.6) (9.4)             8%       2009         national hospital registry   bipolar      bipolar                     yes         56.3 (12.1)
                                                                                                                                                                                                                 medical
                                                                                                                                                                                                                 record
                                                                                                                                                                                                                 review and
                                                                                                                                                                                                                 brief
                                                                                                                                                                                                                 interview
                                                                                                                                                                                                                 confirmation
                                                                                                                                                                                                                  of lack of
                        2005-    ≥2 SZ hospitalizations                                                                                     31.4                       2005-                                     SZ or        hospitalization for SZ, SA,
SW4                     2009     (ICD-8, 9, or 10)      clinical exam yes        bipolar              DSM-IV     SZ             54.2 (11.9) (9.7)         10%          2009         national hospital registry   bipolar      bipolar                     yes         57.1 (11.8)
                                                                                                                                                                       ASRB:
                                                                                                                                                                       2006-
                                                                                                                                                                       2009;                                     ASRB: DIP;     ASRB: hospitalization or
                        ASRB:                                                                                                                 ASRB:                    BPS:                                      BPS: DIP;      treatment for SZ or
                        2006-                                                                                                    ASRB:        23.7                     1997-                                     OHBDC:         bipolar (or FHx thereof);       ASRB:
                        2009;                                           ASRB:                                                    39.5         (6.9);    ASRB:          1998;                                     brief          BPS: lifetime ever history      37.4
                        BPS:     inpatients,                            yes;     IQ<70, HI, SIP,     DSM-III-                    (11.1);      BPS:      31%;           OHBDC:                                    screening      of psychosis; OHBDC:            (13.1);
                        1997-    outpatients, ads,                      BPS:     GMC, ND,            R, DSM-                     BPS: 41.6 22.5         BPS:           2001-                                     questionnair   current medications for         BPS: 42.0
UQ and ASRB             1998     support groups           DIP           no       recent ECT          IV, ICD-10 SZ or SA         (12.3)       (7.1)     28%            2002    ads, blood donors                 e              any condition       yes         (13.1)
                                                                                                                 SZ,
                                                          SCID,                                                  schizophrenifor
ISGC and               1999-                              SADS-L,                                                m (0.2%), or                 23.8                  2005-                                not           chronic medications,
WTCCC2                 2008       inpatients, outpatients SCAN          yes       SIP, GMC           DSM-IV      SA (17%)        42.4 (11.3) (8.1)      n..a.       2006       blood donors              screened      chronic illness              no          n.a.
Notes: Year collected refers to the calendar years during which subjects were collected. Age data is provided as mean years (standard deviation). Age at onset is usually age at illness onset, though occasionally is age at first psychiatric contact or age at                   .
impairment (see text). For the SGENE - Belgium sample, age at onset and ascertainment are tabulated for the SZ cases, these values for the SA cases are 26.0 (8.7) and 40.7 (11.0), respectively. For the UQ/ASRB sample, some items have information tabulated                     .
separately for Australian Schizophrenia Research Bank (ASRB), Brisbane Psychosis Study (BPS), and/or Oxfordshire Healthy Blood Donor Controls (OHBDC) components. Family History % refers to the proportion of cases with known family history of psychosis                         .
(largely SZ) though in some instances this information was not available (n.a.); please note that except for one family sample (Multicenter-Pedigree), all other samples are case-control samples that contain only unrelated cases and unrelated controls (except for              .
Iceland which has some related individuals but these are controlled for with genomic control).                                                                                                                                                                                      .
Abbreviations: Collection names as in Table 1. PSE = Present State Examination [64]; SCAN = Schedules for Clinical Assessment in Neuropsychiatry [65]; SCID = Structured Clinical Interview for DSM-IV [66-68]; OPCRIT = Operational Criteria Checklist [69];                       .
SADS-L = Schedule for Affective Disorders and Schizophrenia–Lifetime version [70-71]; DIGS = Diagnostic Interview for Genetic Studies [72]; SIS = Kendler's Structured Interview for Schizotypy [73]; SANS = Schedule for the Assessment of Negative Symptoms                       .
[74]; SAPS = Schedule for the Assessment of Positive Symptoms; CASH = comprehensive assessment of symptoms and history [27]; DIP = Diagnostic Interview for Psychosis [75]; FHAM = Family History Assessment Module [76]; MMSE = Mini Mental Status Exam                            .
[77-78]; DSM = Diagnostic and Statistical Manual of Mental Disorders [15-79]; ICD = International Classification of Diseases [80-83]; RDC = Research Diagnostic Criteria [84]; MINI = Mini International Neuropsychiatric Interview [85]; SZ = schizophrenia; SA =                  .
schizoaffective disorder; SIP = substance-induced psychosis (includes active/recent significant substance use); GMC = psychosis due to general medical condition; MR = mental retardation; Cog = other cognitive disorders; IQ = intelligence quotient; LD = learning               .
disability; HI = head injury (with various durations of loss of consciousness specified); ND = neurological disease; ECT = electroconvulsive therapy; GenOutpt = general (non-psychiatric) outpatients; staff refers to hospital staff; govt refers to government sources           .

                    .                                                                                                                                              .
Supplementary Table 3: Stage 1 Sample QC.



                                 Cases      Cases                          Controls Controls
                                 After      After                           After      After
                      Cases      QC         QC        Cases     Controls QC           QC
Collection            Submitted Filter 1 Filter 2 Analyzed Submitted Filter 1 Filter 2
Stage 1: GWAS - European ancestry samples
Cardiff UK                   479      476        472        472     2,938      2,936     2,934
CATIE                        417      410        402        402       411        391        207
ISC - Aberdeen               720      720        720        720       702        699        698
ISC - Cardiff                528      527        527        527       611        609        609
ISC - Dublin                 275      272        270        270       866        860        860
ISC - Edinburgh              369      368        368        368       287        284        284
ISC - London                 523      521        518        518       505        494        491
ISC - Portugal               347      346        346        346       216        216        215
ISC - SW1                    170      168        168        168       170        167        167
ISC - SW2                    390      390        390        390       230        229        229
MGS                        2,681    2,681      2,679      2,679     2,653      2,653     2,484
SGENE - Bonn                 479      479        474        474     1,310      1,305     1,304
SGENE - Copenhagen           492      491        482        482       468        458        457
SGENE - Munich               437      437        434        434       351        351        351
SGENE - TOP3                 278      248        248        248       394        369        351
SGENE - UCLA                 715      705        704        704       643        637        631
Zucker Hillside              233      192        192        192       250        190        190
Grand totals
GWAS                       9,533    9,431      9,394      9,394    13,005    12,848 12,462
Stage 1 describes the 17 samples which provided full GWAS genotyping data. QC sample filter 1 is the removal o
QC sample filter 2 is the removal of one of each pair of samples shown to be identical (unintended duplicates) or c
Lambda1000 (pre-QC) are on genotyped SNPs without covariates; the corresponding post-QC values are on the a
"post-QC, imput, & covar" values are on the analyzed samples and analyzed SNPs (genotped and imputed) incorp
1.229 and lambda1000 = 1.021.
Abbreviations: GWAS = genome-wide association study; QC = quality control; SGENE = Schizophrenia Genetics C
Organized Psychoses Research 3; UCLA = University of California at Los Angeles; SW1 = Sweden 1; SW2 = Swe
Multicenter Pedigree study, cases indicates the number of families; CATIE = Clinical Antipsychotic Trials of Interve
Irish Schizophrenia Genomics Consortium
                                                                                                  Lambda
                                                                Lambda                            1000
            Controls                                            (post-          Lambda            (post-
                                  SNPs                   Lambda QC,    Lambda 1000                QC,
            Analyze     SNPs      analyze       Lambda (post- imput, & 1000     (post-            imput, &
            d           submitted d             (pre-QC) QC)    covar) (pre-QC) QC)               covar)

               2,934      371,438    ######        1.085    1.081      1.055     1.103    1.099      1.068
                 207      447,544    ######        1.091    1.085      1.008     1.220    1.212      1.029
                 698      369,998    ######        1.088    1.082      1.079     1.124    1.116      1.111
                 609      681,054    ######        1.017    1.017      1.033     1.030    1.030      1.058
                 860      680,931    ######        1.014    1.016      1.028     1.034    1.039      1.068
                 284      683,732    ######        1.035    1.039      1.036     1.108    1.122      1.112
                 491      298,972    ######        1.039    1.022      1.013     1.076    1.043      1.026
                 215      368,394    ######        1.057    1.049      1.065     1.214    1.184      1.245
                 167      369,016    ######        1.014    1.014      1.022     1.082    1.084      1.131
                 229      681,932    ######        1.053    1.051      1.059     1.183    1.177      1.204
               2,484      655,360    ######        1.139    1.139      1.076     1.052    1.052      1.029
               1,304      498,027    ######        1.056    1.055      1.044     1.080    1.078      1.063
                 457      539,454    ######        1.042    1.044      1.026     1.088    1.093      1.055
                 351      295,628    ######        1.055    1.055      1.017     1.141    1.141      1.044
                 351      754,746    ######        1.123    1.076      0.998     1.377    1.256      0.993
                 631      518,915    ######        1.030    1.030      1.027     1.044    1.045      1.041
                 190      387,462    ######        1.065    1.073      1.037     1.269    1.382      1.194

               12,462
sample filter 1 is the removal of samples with >2% missing genotypes (I.e., <98% genotyping completion).
al (unintended duplicates) or closely related to each other (cryptic relatives). Lambda (pre-QC) and
 g post-QC values are on the analyzed samples and analyzed SNPs (genotped); and the corresponding
 genotped and imputed) incorporating covariates. The post-QC entire stage 1 analyzed sample lambda =

NE = Schizophrenia Genetics Consortium; ISC = International Schizophrenia Consortium; TOP3 = Thematic
SW1 = Sweden 1; SW2 = Sweden 2; WTCCC = Wellcome Trust case Control Consortium; for the
 Antipsychotic Trials of Intervention Effectiveness; MGS = Molecular Genetics of Schizophrenia; ISGC =
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Supplementary Table 4: Genomic Regions Containing ≥1SNP with p <1E-05 for Stage 1
Association.

                              Stage 1
                                                                Frequenc Frequenc
                              p -value
SNP       Chr   bp                       OR      95% CI Alleles y Cases    y Controls Info ngt
rs2252865   1     8,345,263   4.90E-06    1.10   1.06-1.14 TC         0.35       0.34 1.01     0
rs1009080   1    30,204,147   5.84E-06    1.11   1.06-1.15 GA         0.31       0.29 1.00   17
rs1625579   1    98,275,522   5.72E-07    1.14   1.08-1.19 TG         0.82       0.80 0.99     3
rs6703335   1    #########    3.26E-06    1.10   1.06-1.14 GA         0.59       0.56 0.99   11
rs2272417   2    27,560,144   7.05E-06    1.10   1.05-1.14 CT         0.42       0.40 0.94     4
rs11682175 2     57,841,097   4.07E-06    1.10   1.06-1.14 CT         0.49       0.47 0.93     5
rs17180327 2     #########    6.80E-07    1.12   1.07-1.15 GA         0.37       0.35 0.94     4
rs17662626 2     #########    3.09E-06    1.22   1.13-1.30 AG         0.92       0.91 0.77     4
rs2675968   2    #########    2.58E-06    1.11   1.06-1.15 TC         0.33       0.30 0.99   13
rs13025591 2     #########    1.07E-06    1.11   1.06-1.14 CA         0.42       0.39 0.98     6
rs4624519   3    36,837,984   6.26E-06    1.10   1.05-1.14 TC         0.38       0.35 0.99   13
rs2239547   3    52,830,269   2.25E-06    1.12   1.07-1.16 TC         0.74       0.72 0.99     0
rs11130874 3     62,039,809   2.09E-07    1.14   1.09-1.19 AG         0.81       0.79 0.99     4
rs1879248   3    #########    1.27E-06    1.13   1.07-1.17 TC         0.75       0.73 0.88     0
rs12485391 3     #########    5.74E-06    1.16   1.09-1.22 CA         0.88       0.87 0.91     6
rs12522297 5     #########    7.24E-06    1.14   1.08-1.19 GA         0.84       0.82 0.93     7
rs1433019   5    #########    3.09E-06    1.13   1.07-1.17 AC         0.80       0.78 1.00   17
rs9379780   6    25,815,150   3.02E-07    1.12   1.07-1.15 AG         0.63       0.60 0.98     3
rs198817    6    26,234,503   3.66E-07    1.11   1.07-1.15 GA         0.55       0.53 0.99     0
rs13218591 6     26,484,811   6.64E-06    1.11   1.06-1.15 TC         0.72       0.70 1.00     0
rs3800316   6    27,364,081   1.57E-08    1.14   1.09-1.19 AC         0.75       0.73 0.98     1
rs17693963 6     27,818,144   1.56E-10    1.25   1.18-1.32 AC         0.91       0.89 1.01     4
rs1339898   6    28,503,485   2.71E-08    1.14   1.09-1.18 CT         0.71       0.68 0.94     0
rs3130827   6    29,338,662   3.20E-06    1.10   1.06-1.14 CT         0.66       0.64 1.02     4
rs2021722   6    30,282,110   4.30E-11    1.19   1.13-1.23 CT         0.81       0.78 1.00     0
rs2429657   6    30,579,499   4.67E-06    1.12   1.07-1.16 GA         0.25       0.23 0.95     4
rs1064627   6    30,806,520   8.39E-07    1.14   1.09-1.19 AG         0.83       0.81 0.99     0
rs1265099   6    31,213,392   3.19E-06    1.10   1.06-1.14 AG         0.60       0.57 0.96     4
rs3094604   6    31,542,090   7.16E-06    1.13   1.07-1.18 AG         0.84       0.82 0.97     0
rs707938    6    31,837,338   2.62E-06    1.11   1.06-1.15 AG         0.70       0.68 0.95     1
rs9268856   6    32,537,697   8.64E-08    1.14   1.08-1.18 CA         0.76       0.74 1.00   11
rs9272105   6    32,707,977   1.27E-08    1.13   1.08-1.16 GA         0.48       0.47 0.99     1
rs7762279   6    32,863,268   3.35E-08    1.21   1.14-1.28 TC         0.90       0.88 0.93     4
rs7383287   6    32,891,064   5.15E-06    1.13   1.07-1.17 AG         0.80       0.78 0.94     4
rs9276933   6    33,038,773   2.76E-06    1.19   1.11-1.25 TC         0.90       0.88 0.84     1
rs9462875   6    43,276,095   1.46E-06    1.15   1.09-1.21 AG         0.84       0.82 0.90     7
rs10226475 7      2,192,688   5.06E-08    1.12   1.08-1.16 AG         0.64       0.61 1.00   12
rs4719530   7     2,419,150   9.55E-06    1.15   1.08-1.21 TC         0.13       0.11 1.00   13
rs12699131 7     71,389,252   5.16E-06    1.10   1.05-1.13 AG         0.49       0.47 1.00   13
rs4415249        7 ######### 4.18E-06 1.14 1.08-1.20 CA                        0.86       0.85 1.00 12
rs10503253 8 4,168,252 3.84E-07 1.14 1.09-1.19 AC                              0.21       0.19 0.96   4
rs10503256 8 4,201,587 1.97E-07 1.12 1.07-1.15 AG                              0.37       0.35 1.00 16
rs500115         8 8,672,925 5.78E-06 1.15 1.09-1.21 TC                        0.87       0.86 0.95   4
rs12234997 8 9,275,118 3.06E-06 1.11 1.06-1.14 AG                              0.46       0.43 0.93   3
rs2162119        8 64,998,535 9.75E-06 1.10 1.05-1.13 CT                       0.49       0.46 0.99   0
rs7004633        8 89,829,427 1.45E-08 1.17 1.11-1.21 GA                       0.20       0.18 0.93   4
rs10098073 8 ######### 5.42E-06 1.10 1.05-1.13 AC                              0.50       0.47 0.99 13
rs12352353 9 4,733,341 6.57E-07 1.16 1.10-1.22 AG                              0.86       0.85 0.94   5
rs41441548 10 34,190,827 2.66E-06 1.25 1.15-1.33 AG                            0.08       0.07 0.70   5
rs16915157 10 62,016,644 4.44E-06 1.13 1.07-1.17 TC                            0.21       0.19 0.98 13
rs7914558 10 ######### 1.58E-07 1.12 1.07-1.15 GA                              0.61       0.59 1.00   0
rs11191580 10 ######### 2.23E-08 1.23 1.15-1.29 TC                             0.92       0.91 1.02 11
rs11191732 10 ######### 2.26E-07 1.14 1.09-1.19 AG                             0.22       0.20 0.97   3
rs1025641 10 ######### 8.28E-07 1.12 1.07-1.16 TC                              0.69       0.67 0.97   4
rs4356203 11 17,116,724 1.91E-06 1.10 1.06-1.14 GA                             0.43       0.41 1.00   6
rs7938219 11 29,159,016 5.73E-06 1.16 1.09-1.22 AG                             0.13       0.11 0.96   2
rs2509843 11 97,630,614 1.10E-06 1.11 1.06-1.15 GA                             0.41       0.39 0.95   3
rs11220082 11 ######### 2.57E-07 1.11 1.07-1.15 TC                             0.55       0.53 1.00   0
rs548181        11 ######### 2.91E-08 1.20 1.13-1.26 GA                        0.90       0.88 0.97   0
rs10894294 11 ######### 6.50E-06 1.10 1.05-1.13 CA                             0.51       0.48 0.98   6
rs7972947 12 2,040,694 7.77E-07 1.16 1.09-1.21 CA                              0.79       0.78 0.73   3
rs4765905 12 2,219,845 8.92E-07 1.11 1.07-1.15 CG                              0.35       0.33 1.00 12
rs10135277 14 34,892,982 5.11E-07 1.11 1.06-1.15 CT                            0.60       0.57 1.01 13
rs1869901 15 38,382,919 3.49E-07 1.11 1.07-1.15 GA                             0.42       0.39 0.98   4
rs4775413 15 59,627,395 4.01E-06 1.10 1.06-1.14 TC                             0.56       0.54 0.97   6
rs1078163 15 86,269,935 5.14E-06 1.14 1.08-1.19 CT                             0.17       0.15 1.00 16
rs16957445 18 49,657,366 8.16E-06 1.11 1.06-1.15 CT                            0.72       0.70 0.99   6
rs12966547 18 50,903,015 1.00E-06 1.11 1.06-1.14 GA                            0.61       0.58 0.99   0
rs17512836 18 51,345,959 2.35E-08 1.41 1.28-1.52 CT                            0.04       0.02 0.98   0
rs16997475 21 26,430,592 9.56E-06 1.21 1.12-1.29 AG                            0.07       0.06 0.92   0
rs2833899 21 32,855,134 4.08E-06 1.13 1.08-1.18 TC                             0.83       0.82 0.99   1
rs7289747 22 18,290,716 9.67E-06 1.20 1.11-1.27 CA                             0.07       0.06 1.01 17
rs9621795 22 32,601,782 6.59E-06 1.11 1.06-1.15 AG                             0.57       0.55 0.76   1
rs5758209 22 39,791,811 8.39E-06 1.10 1.05-1.13 TG                             0.52       0.50 0.95   0
Notes: Each SNP listed is the most associated SNP in an LD-defined interval - additional SNPs with
p<1E-05 with r^2>0.20 to a listed SNP are not shown; SNPs with Info <0.60 are not listed either.
Stage 1 is discovery GWAS sample. Alleles are listed with risk allele first; frequency (in Stage 1
cases, and Stage 1 controls, respectively) and OR (odds ratio, and their 95% CI, confidence interval)
refer to the risk allele. Bolding of p-values indicates p<5E-08. Info is the imputation confidence
reported by Beagle. Ngt is the number of the 17 Stage 1 samples that were directly genotyped (i.e.,
not imputed). bp is the base position (HG18). Genes are those in the LD-defined region.
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Supplementary Table 5. Conditional Analyses.
                                                  Conditional bp
           Best p - Best SNP         Conditiona SNP            apart    Conditional
Best SNP value      position    Chr l SNP         position     (hg18)    p -value
Discovery (Stage 1) Scan
rs7972947 ######      2,040,694 12 rs4765905        2,219,845 ######         5.19E-06
rs11191580 ###### ######### 10 rs2296569           ######### 69,700          3.92E-05
rs10226475 ######     2,192,688    7 rs1010302      2,381,093 ######         1.90E-04
rs17512836 ###### 51,345,959 18 rs587136           51,376,047 30,088         5.43E-04
rs10503256 ######     4,201,587    8 rs4875334      4,166,391 35,196         6.52E-04
rs548181 ###### ######### 11 rs11220082 ######### ######                     9.76E-04
rs11191732 ###### ######### 10 rs10748844 #########               6,591      1.14E-03
rs10135277 ###### 34,892,982 14 rs10872893 34,985,695 92,713                 5.32E-03
rs12352353 ######     4,733,341    9 rs12685759     4,685,004 48,337         5.96E-03
rs7004633 ###### 89,829,427        8 rs1498539     89,912,936 83,509         8.05E-03
rs1869901 ###### 38,382,919 15 rs537455            38,195,116 ######         1.70E-02
rs1025641 ###### ######### 10 rs4362070            ######### ######          2.47E-02
rs1625579 ###### 98,275,522        1 rs11165922 98,109,411 ######            4.22E-02
rs11130874 ###### 62,039,809       3 rs2291540     62,238,087 ######         6.24E-02
rs17180327 ###### #########        2 rs2679339     ######### ######          6.36E-02
100 permutations (the 52 with >=1 region with a p <1E-06 are tabulated for each region)
                                              Conditional bp
          Best p - Best SNP        Conditiona SNP         apart  Conditional batra
Best SNP value     position    Chr l SNP      position    (hg18) p -value     #
rs289101 ###### 60,463,417 15 rs12915440 60,549,510 86,093           3.01E-05   12
rs8035991 ###### 24,170,042 15 rs11858514 24,234,989 64,947          7.92E-05   25
rs4886554 ###### 76,131,977 15 rs8032467       75,943,293 ######     1.50E-04    5
rs1869340 ###### 74,955,684      2 rs363640    74,755,736 ######     3.51E-04   49
rs233379 ###### 13,634,311       5 rs1354191   13,776,956 ######     5.38E-04   18
rs16956732 ###### 65,157,292 16 rs4258603      65,264,053 ######     6.36E-04   27
rs10155413 ###### #########      4 rs1456266   ######### 34,601      1.24E-03   93
rs11060225 ###### ######### 12 rs11837776 ######### ######           1.35E-03   54
rs7550768 ###### 11,602,870      1 rs2745292   11,523,641 79,229     1.37E-03   35
rs16973319 ###### 80,120,223 15 rs2665086      80,172,913 52,690     1.39E-03   50
rs12965304 ###### 55,239,043 18 rs9966402      55,302,830 63,787     1.44E-03   22
rs313327 ###### ######### 12 rs10861228 ######### 79,079             1.47E-03   27
rs4939821 ###### 44,625,991 18 rs1316889       44,602,332 23,659     1.57E-03   61
rs10750489 ###### ######### 11 rs1086213       ######### ######      1.72E-03    3
rs17077971 ###### 63,608,819 18 rs2448763      63,479,042 ######     1.87E-03   45
rs17153249 ###### ######### 10 rs1025512       ######### 50,841      2.02E-03   88
rs10976131 ######    7,216,519   9 rs10481608   7,379,305 ######     2.14E-03   27
rs302099 ###### 83,152,069       7 rs2158725   83,135,177 16,892     2.37E-03   19
rs17067182 ######    3,574,226   8 rs6999415    3,377,552 ######     2.68E-03   79
rs17793145 ###### 13,154,016     8 rs4831429   13,330,455 ######     2.89E-03   81
rs10973441 ###### 37,612,777           9 rs1571234     37,476,603 ######         2.95E-03      79
rs2898002 ###### 45,762,494 12 rs854895                45,766,825     4,331      3.09E-03      84
rs12526618 ###### #########            6 rs7761155     ######### ######          3.09E-03      33
rs6017203 ###### 41,906,637 20 rs6031159               41,893,832 12,805         3.26E-03      23
rs7639990 ###### #########             3 rs16857326 ######### ######             3.71E-03      50
rs13008971 ######        8,897,923     2 rs10189304     8,746,096 ######         4.01E-03      61
rs1885487 ######         7,613,922     6 rs752479       7,684,378 70,456         4.22E-03        1
rs2277940 ###### #########             5 rs3805433     ######### 26,003          4.23E-03      12
rs12374311 ###### #########            4 rs1874347     #########      1,158      4.35E-03      17
rs7738608 ###### 16,492,644            6 rs421172      16,509,776 17,132         5.09E-03        5
rs12732868 ######        5,234,497     1 rs6703948      5,213,305 21,192         5.98E-03      20
rs3783853 ###### 88,873,022 14 rs17778186 88,712,343 ######                      6.54E-03      43
rs3820422 ###### #########             1 rs11590996 ######### 62,623             7.00E-03      48
rs6681578 ###### 64,786,174            1 rs1436753     64,869,851 83,677         8.62E-03      86
rs10970384 ######        3,148,247     9 rs7046265      3,053,752 94,495         8.64E-03      69
rs11747553 ###### 54,805,177           5 rs6866871     54,951,687 ######         8.72E-03      47
rs6013210 ###### 49,599,041 20 rs6013171               49,442,958 ######         1.08E-02      62
rs1321501 ###### 88,733,318            6 rs6454648     88,543,052 ######         1.09E-02      77
rs7732249 ###### 59,402,026            5 rs1546364     59,229,581 ######         1.27E-02      65
rs6567206 ###### 57,156,811 18 rs9783862               57,350,414 ######         1.57E-02      39
rs6517861 ###### 19,520,287 21 rs17720336 19,356,709 ######                      1.67E-02      56
rs8091331 ######         7,382,667 18 rs10502357        7,579,318 ######         1.72E-02      52
rs1353920 ###### #########             5 rs1353919     ######### 31,709          1.82E-02      93
rs10791946 ###### 67,344,588 11 rs11603033 67,205,316 ######                     2.18E-02      35
rs4597986 ###### 29,830,144            5 rs6876965     29,792,295 37,849         2.28E-02      97
rs4759511 ###### ######### 12 rs12425018 ######### 57,938                        2.42E-02      98
rs2650618 ###### 18,763,800 16 rs2641889               18,714,812 48,988         2.60E-02      44
rs7964041 ###### ######### 12 rs10850376 ######### ######                        3.54E-02      70
rs16902273 ###### 91,087,683           8 rs4961182     91,279,648 ######         3.88E-02      24
rs7550594 ###### 50,663,681            1 rs3862266     50,595,022 68,659         5.27E-02      44
rs4552479 ###### 11,379,994            4 rs13132638 11,186,017 ######            5.63E-02      82
rs13096071 ###### #########            3 rs1351833     ######### 95,546          6.45E-02      37
Note: After the conditional analyses described above, these regions gave the clearest indication     .
for one or more independent signals. Best SNP is the one with the lowest p -value tagging the        .
LD region; second best SNP is the SNP (after conditioning on the best SNP) in the LD region          .
with the lowest p -value. The batra number refers to the permutation (1-100) tabulated.              .
                                                                                                     .
Supplementary Table 6: Association Results for SNPs advanced to Stage 2.

                                    Stage 1      Stage 1    Stage 2          Stage 2
                                    p -value    OR (95% CI) p -value        OR (95% CI)
SNP           Chr     bp
rs2252865     1p36.23   8,345,263   4.90E-06   1.10 (1.06-1.14)     0.04   1.04 (0.99-1.10)
rs1009080     1p35.2   30,204,147   5.84E-06   1.10 (1.06-1.15)     0.06   1.06 (0.98-1.13)
rs1625579     1p21.3   98,275,522   5.72E-07   1.14 (1.08-1.19) 2.65E-06   1.11 (1.07-1.16)
rs7540658     1q25.3   #########    1.46E-05   1.11 (1.06-1.16)     0.62   0.98 (0.90-1.07)
rs3818802     1q43     #########    3.81E-06   1.10 (1.06-1.14)     0.41   1.00 (0.92-1.09)
rs6703335     1q43     #########    3.26E-06   1.10 (1.06-1.14) 2.19E-03   1.08 (1.02-1.14)
rs11682175    2p16.1   57,841,097   4.07E-06   1.10 (1.06-1.14)     0.86   0.96 (0.88-1.03)
rs6435387**   2q23.1   #########    4.45E-05   1.26 (1.15-1.37)     0.85   0.82 (0.46-1.18)
rs17180327    2q31.3   #########    6.80E-07   1.11 (1.07-1.15)     0.19   1.01 (0.97-1.05)
rs17662626    2q32.3   #########    3.09E-06   1.22 (1.13-1.30) 1.70E-03   1.16 (1.06-1.27)
rs2675968     2q37.1   #########    2.58E-06   1.11 (1.06-1.15)     0.42   1.00 (0.92-1.08)
rs13025591    2q37.2   #########    1.07E-06   1.10 (1.06-1.14)     0.13   1.03 (0.97-1.08)
rs4624519     3p22.2   36,837,984   6.26E-06   1.10 (1.05-1.14) 4.33E-03   1.07 (1.02-1.13)
rs2239547     3p21.1   52,830,269   2.25E-06   1.11 (1.07-1.16) 3.15E-03   1.08 (1.02-1.14)
rs11130874    3p14.2   62,039,809   2.09E-07   1.14 (1.09-1.19)     0.12   1.03 (0.97-1.10)
rs1879248     3q26.33 #########     1.27E-06   1.12 (1.07-1.17)     0.05   1.03 (0.99-1.08)
rs4295265     4q24     #########    1.10E-05   1.10 (1.05-1.14)     0.22   1.02 (0.95-1.10)
rs7730479     5p14.3   21,955,293   1.49E-05   1.20 (1.11-1.28)     0.34   1.03 (0.86-1.21)
rs1433019     5q35.1   #########    3.09E-06   1.12 (1.07-1.17)     0.48   1.00 (0.91-1.08)
rs1324495**   6p25.2    2,616,255   4.58E-05   1.09 (1.04-1.13)     0.44   1.00 (0.89-1.12)
rs2690121**   6p22.2   25,363,256   7.34E-05   1.13 (1.07-1.19)     0.78   0.93 (0.75-1.11)
rs6900224**   6p22.2   25,545,965   8.45E-05   1.10 (1.05-1.15)     0.10   1.09 (0.95-1.22)
rs9379780     6p22.2   25,815,150   3.02E-07   1.11 (1.07-1.15)     0.17   1.02 (0.97-1.08)
rs13218591    6p22.2   26,484,811   6.64E-06   1.10 (1.06-1.15)     0.38   1.01 (0.92-1.10)
rs3800316     6p22.1   27,364,081   1.57E-08   1.14 (1.09-1.19)     0.02   1.09 (1.01-1.17)
rs17693963    6p22.1   27,818,144   1.56E-10   1.25 (1.18-1.32) 4.00E-03   1.11 (1.03-1.19)
rs1339898     6p22.1   28,503,485   2.71E-08   1.13 (1.09-1.18)     0.19   1.02 (0.96-1.08)
rs3130827     6p22.1   29,338,662   3.20E-06   1.10 (1.06-1.14)     0.04   1.06 (0.99-1.14)
rs1736915**   6p22.1   29,812,295   6.54E-05   1.09 (1.05-1.14)     0.14   1.07 (0.94-1.19)
rs2021722     6p22.1   30,282,110   4.30E-11   1.18 (1.13-1.23) 1.55E-03   1.10 (1.03-1.17)
rs2429657     6p21.33 30,579,499    4.67E-06   1.12 (1.07-1.16) 4.71E-03   1.12 (1.03-1.21)
rs1064627     6p21.33 30,806,520    8.39E-07   1.14 (1.09-1.19)     0.02   1.08 (1.00-1.16)
rs9295938**   6p21.33 31,061,084    2.04E-05   1.13 (1.07-1.19)     0.89   0.90 (0.75-1.06)
rs1265099     6p21.33 31,213,392    3.19E-06   1.10 (1.06-1.14) 2.66E-03   1.09 (1.03-1.15)
rs3094604     6p21.33 31,542,090    7.16E-06   1.13 (1.07-1.18)     0.34   1.03 (0.88-1.17)
rs707938      6p21.33 31,837,338    2.62E-06   1.11 (1.06-1.15) 8.72E-05   1.14 (1.07-1.21)
rs204989**    6p21.32 32,269,830    4.09E-05   1.11 (1.06-1.16) 2.22E-03   1.21 (1.08-1.35)
rs2050189     6p21.32 32,447,625    1.54E-05   1.14 (1.08-1.20)     0.19   1.04 (0.94-1.15)
rs9268856     6p21.32 32,537,697    8.64E-08   1.13 (1.08-1.18) 2.98E-03   1.09 (1.03-1.15)
rs9272105     6p21.32 32,707,977    1.27E-08   1.12 (1.08-1.16)     0.42   1.00 (0.94-1.06)
rs7762279     6p21.32    32,863,268   3.35E-08   1.21 (1.14-1.28)     0.10   1.06 (0.97-1.14)
rs9276933     6p21.32    33,038,773   2.76E-06   1.18 (1.11-1.25)     0.19   1.09 (0.89-1.29)
rs9462875     6p21.1     43,276,095   1.46E-06   1.15 (1.09-1.21)     0.24   1.01 (0.96-1.06)
rs10226475    7p22.3      2,192,688   5.06E-08   1.12 (1.08-1.16)     0.19   1.01 (0.97-1.05)
rs12699131    7q11.22    71,389,252   5.16E-06   1.09 (1.05-1.13)     0.03   1.05 (0.99-1.10)
rs4415249     7q33       #########    4.18E-06   1.14 (1.08-1.20)     0.64   0.98 (0.87-1.08)
rs10503253    8p23.2      4,168,252   3.84E-07   1.14 (1.09-1.19) 7.60E-03   1.08 (1.01-1.14)
rs10503256    8p23.2      4,201,587   1.97E-07   1.11 (1.07-1.15)     0.17   1.02 (0.97-1.08)
rs500115      8p23.1      8,672,925   5.78E-06   1.15 (1.09-1.21)     0.33   1.01 (0.93-1.10)
rs12234997    8p23.1      9,275,118   3.06E-06   1.10 (1.06-1.14)     0.24   1.02 (0.95-1.10)
rs7004633     8q21.3     89,829,427   1.45E-08   1.16 (1.11-1.21)     0.01   1.05 (1.01-1.10)
rs10098073    8q24.3     #########    5.42E-06   1.09 (1.05-1.13)     0.24   1.02 (0.95-1.08)
rs12352353    9p24.1      4,733,341   6.57E-07   1.16 (1.10-1.22)     0.95   0.95 (0.89-1.01)
rs6602217     10p14       6,986,269   1.82E-05   1.18 (1.10-1.26)     0.24   1.05 (0.91-1.18)
rs41441548    10p11.22   34,190,827   2.66E-06   1.24 (1.15-1.33)     0.58   0.98 (0.81-1.15)
rs16915157    10q21.2    62,016,644   4.44E-06   1.12 (1.07-1.17)     0.10   1.05 (0.97-1.13)
rs7914558     10q24.32   #########    1.58E-07   1.11 (1.07-1.15) 1.07E-03   1.08 (1.03-1.13)
rs11191580    10q24.33   #########    2.23E-08   1.22 (1.15-1.29) 5.09E-03   1.09 (1.02-1.16)
rs11191732    10q24.33   #########    2.26E-07   1.14 (1.09-1.19)     0.10   1.04 (0.97-1.10)
rs1025641     10q26.2    #########    8.28E-07   1.11 (1.07-1.16)     0.37   1.00 (0.95-1.06)
rs4356203     11p15.1    17,116,724   1.91E-06   1.10 (1.06-1.14) 6.78E-03   1.07 (1.01-1.13)
rs7938219     11p14.1    29,159,016   5.73E-06   1.15 (1.09-1.22)     0.23   1.04 (0.93-1.14)
rs2509843     11q22.1    97,630,614   1.10E-06   1.11 (1.06-1.15)     0.58   0.99 (0.94-1.04)
rs11220082    11q24.2    #########    2.57E-07   1.11 (1.07-1.15)     0.35   1.01 (0.95-1.06)
rs548181      11q24.2    #########    2.91E-08   1.20 (1.13-1.26)     0.07   1.04 (0.98-1.11)
rs10894294    11q25      #########    6.50E-06   1.09 (1.05-1.13)     0.08   1.05 (0.97-1.13)
rs7972947     12p13.33    2,040,694   7.77E-07   1.15 (1.09-1.21)     0.61   0.99 (0.94-1.04)
rs4765905     12p13.33    2,219,845   8.92E-07   1.11 (1.07-1.15)     0.07   1.04 (0.98-1.09)
rs10135277    14q13.2    34,892,982   5.11E-07   1.10 (1.06-1.15)     0.17   1.01 (0.97-1.05)
rs1869901     15q15.1    38,382,919   3.49E-07   1.11 (1.07-1.15)     0.05   1.03 (0.99-1.07)
rs4775413     15q22.2    59,627,395   4.01E-06   1.10 (1.06-1.14)     0.04   1.04 (0.99-1.09)
rs1078163     15q25.3    86,269,935   5.14E-06   1.13 (1.08-1.19)     0.73   0.97 (0.88-1.06)
rs16957445    18q21.2    49,657,366   8.16E-06   1.10 (1.06-1.15)     0.74   0.97 (0.89-1.05)
rs12966547    18q21.2    50,903,015   1.00E-06   1.10 (1.06-1.14) 2.29E-05   1.08 (1.04-1.12)
rs17512836    18q21.2    51,345,959   2.35E-08   1.40 (1.28-1.52)     0.09   1.08 (0.96-1.20)
rs7248806**   19p13.3       946,943   2.98E-05   1.14 (1.07-1.20)     0.76   0.98 (0.93-1.03)
rs8112050     19q13.11   37,323,114   1.79E-05   1.10 (1.05-1.14)     0.19   1.03 (0.95-1.11)
rs16997475    21q21.3    26,430,592   9.56E-06   1.20 (1.12-1.29)     0.40   1.01 (0.87-1.16)
rs2833899     21q22.11   32,855,134   4.08E-06   1.13 (1.08-1.18)     0.45   1.00 (0.90-1.10)
rs7289747     22q11.21   18,290,716   9.67E-06   1.19 (1.11-1.27)     0.37   1.02 (0.88-1.15)
rs5758209     22q13.2    39,791,811   8.39E-06   1.09 (1.05-1.13)     0.47   1.00 (0.92-1.08)
Notes: Listed are the 81 SNPs (selected via the same LD-region definition as in Table S5) which were followed-up
studies totalling 19 distinct case-control samples. Stage 1 is discovery GWAS sample. Stage 2 is replication sam
single-tailed weighted (1/SE) meta p -value). Combined includes Stages 1 and 2 (reported as two-tailed weighted
value). OR (odds ratio) refers to the risk allele found in Stage 1. Bolding indicates p <5E-08 for Stage 1 and Comb
indicates p <0.05 for Stage 2. Directions of association in 8 groups of replication samples: + is same direction; - is
direction; blank is data not available. Genes within the LD region are indicated. bp is the base position (HG18). W
region (22 SNPs in 6p22.2-p21.32 tabulated above), numerous Stage 2 SNPs showed strong replication: 7 of 22 S
demonstrated a directionally consistent replication at p <0.01, with 10 of 22 SNPs having p <0.05, far in excess of c
expectations.
** In an earlier analysis 8 of these 81 SNPs had p <2E-05, and are retained in this table for completeness since the
followed up.
2.

     Consistency Combined      Combined
      of direction p -value    OR (95% CI)

       + +- -++    3.16E-06   1.08 (1.04-1.11)
       + - -++     2.52E-06   1.09 (1.05-1.13)
      +-++++-+     1.59E-11   1.12 (1.09-1.16)
          + ---    3.23E-04   1.08 (1.03-1.12)
         - -++     2.44E-05   1.08 (1.04-1.11)
      + ++ -++     5.47E-08   1.09 (1.06-1.13)
         - ++-     5.29E-04   1.06 (1.02-1.10)
            --     3.40E-04   1.21 (1.11-1.32)
       -++++-+     4.80E-05   1.06 (1.03-1.09)
      + -+ +++     4.65E-08   1.20 (1.13-1.26)
         - +++     2.59E-05   1.08 (1.04-1.12)
      - ++ +++     5.92E-06   1.07 (1.04-1.11)
         -+ +-+    2.14E-07   1.09 (1.05-1.12)
      + ++ +++     6.02E-08   1.10 (1.06-1.14)
       + ++ +--    1.71E-06   1.10 (1.06-1.14)
      -+-+++-+     6.86E-06   1.07 (1.04-1.11)
         - +-+     2.90E-05   1.08 (1.04-1.12)
          + +-     4.26E-05   1.17 (1.09-1.24)
          - +--    4.28E-05   1.09 (1.05-1.13)
             +     1.05E-04   1.08 (1.04-1.12)
              -    4.79E-04   1.11 (1.05-1.16)
             +     3.72E-05   1.10 (1.05-1.14)
        ++ ++-     2.34E-06   1.08 (1.05-1.11)
          + ---    3.12E-05   1.08 (1.04-1.12)
        ++ -++     2.19E-09   1.13 (1.09-1.17)
      + ++ +++     4.03E-11   1.19 (1.14-1.24)
         +- -++    7.48E-07   1.09 (1.05-1.13)
         + -++     9.23E-07   1.09 (1.05-1.13)
             +     3.73E-05   1.09 (1.05-1.13)
      + ++ -++     2.18E-12   1.15 (1.11-1.19)
        + +++      1.40E-07   1.12 (1.07-1.16)
       - + +++     2.05E-07   1.12 (1.08-1.16)
              -    3.95E-04   1.10 (1.04-1.15)
        ++ ++      6.03E-08   1.10 (1.06-1.13)
             +     1.34E-05   1.12 (1.06-1.17)
      + + +++      2.12E-09   1.12 (1.08-1.15)
             +     1.28E-06   1.12 (1.07-1.17)
       - + ++      2.89E-05   1.11 (1.06-1.17)
        ++ -++     2.75E-09   1.12 (1.08-1.15)
       + +- +--    1.42E-06   1.08 (1.05-1.11)
    -+ -++    2.52E-07   1.15 (1.09-1.20)
      +       2.45E-06   1.17 (1.10-1.24)
 -+-++-+-     1.97E-04   1.07 (1.03-1.11)
++-+++++      1.28E-05   1.06 (1.03-1.09)
 + +- +-+     2.05E-06   1.08 (1.04-1.11)
      + ---   1.24E-04   1.10 (1.05-1.15)
 + ++ +-+     4.14E-08   1.11 (1.07-1.15)
 + ++ -+-     2.46E-06   1.08 (1.04-1.11)
  + +- +-     8.31E-05   1.10 (1.05-1.15)
      - --+   1.01E-05   1.08 (1.04-1.12)
++-+++-+      2.75E-08   1.10 (1.07-1.14)
 - + +++      2.09E-05   1.07 (1.04-1.11)
 ++---+-+     2.09E-02   1.04 (1.00-1.09)
     + -++    4.58E-05   1.15 (1.08-1.21)
        --+   5.39E-05   1.18 (1.09-1.26)
 + + +++      4.68E-06   1.10 (1.06-1.14)
 + ++ +++     1.82E-09   1.10 (1.07-1.13)
++++++++      1.11E-08   1.15 (1.10-1.20)
 + +- +++     1.20E-06   1.10 (1.06-1.14)
  - +- ++-    4.94E-05   1.07 (1.03-1.10)
 + + +++      1.13E-07   1.09 (1.06-1.12)
  - + -++     2.01E-05   1.12 (1.07-1.17)
   - +- -+-   2.05E-04   1.06 (1.03-1.09)
  - +- +-+    1.52E-05   1.07 (1.04-1.10)
+++++--+      8.87E-07   1.11 (1.07-1.16)
     - +++    3.25E-06   1.08 (1.05-1.12)
 ---++++      2.52E-03   1.05 (1.02-1.09)
 + ++ +++     1.87E-06   1.08 (1.05-1.11)
  ---++-+-    3.73E-05   1.06 (1.03-1.08)
+++++--+      2.85E-06   1.07 (1.04-1.09)
 + +- +++     2.49E-06   1.08 (1.04-1.11)
  + - -++     3.22E-04   1.09 (1.04-1.13)
  - - +++     3.16E-04   1.07 (1.03-1.11)
+-++++++      2.60E-10   1.09 (1.06-1.12)
-+++++++      1.05E-06   1.23 (1.14-1.31)
    -- --     4.87E-02   1.03 (1.00-1.07)
     + +--    3.19E-05   1.08 (1.04-1.12)
     + +--    8.17E-05   1.15 (1.08-1.22)
     - +-+    3.88E-05   1.10 (1.05-1.15)
     + ++-    6.83E-05   1.15 (1.08-1.21)
   + +--      7.55E-05   1.07 (1.03-1.11)
n Table S5) which were followed-up in 8 independent
                                                      .
 sample. Stage 2 is replication sample (reported as
                                                      .
 2 (reported as two-tailed weighted (1/SE) meta p -
                                                      .
ates p <5E-08 for Stage 1 and Combined, and
                                                      .
n samples: + is same direction; - is opposite
                                                      .
  bp is the base position (HG18). Within the MHC
                                                      .
showed strong replication: 7 of 22 SNPs
                                                      .
Ps having p <0.05, far in excess of chance
                                                      .
                                                      .
his table for completeness since these SNPs were      .
                                                      .
Supplementary Table 7: Genome-Wide Significant Loci.             .
                                   GWS p <0.05          GWS
Location                           Stage Stage 2        Stages
                                   1       Replication 1&2
                        Novel GWS loci
1p21.3                               no        yes        yes
2q32.3                               no        yes        yes
8p23.2                               no        yes        yes
8q21.3                               yes       yes        yes
10q24.32-q24.33                      yes       yes        yes
                    GWS previous reports
2q32.1                               no        NA*        NA*
6p21.32-p22.1                        yes       yes        yes
11q24.2                              yes       no         no
18q21.2                              yes       yes        yes
                                                                 .
Note: Four loci above (2q32.1, 6p21.32-p22.1, 11q24.2, and
                                                                 .
18q21.2) were previously reported to be genome-wide
                                                                 .
significant (GWS) [10,13,18,93]; please note that the studied
                                                                 .
samples here contained most of the samples used in those
                                                                 .
previous GWAS. We provide replication for two of those,
                                                                 .
6p21.32-p22.1 (MHC) and 18q21.2 (TCF4 ), in Stage 2 here,
                                                                 .
but not for the other two loci, 2q32.1 (ZNF804A ) and
                                                                 .
11q24.2 (NRGN ). We found two novel GWS loci in Stage 1
                                                                 .
(8q21.3 and 10q24.32-q24.33), which we both replicated in
                                                                 .
Stage 2. In addition, when combining Stages 1 and 2, we
                                                                 .
detected three more novel GWS loci (1p21.3, 2q32.3, and
                                                                 .
8p23.2). NA* indicates that for this locus (ZNF804A ), no
                                                                 .
SNPs were selected for Stage 2 replication genotyping since
                                                                 .
none met the Stage 1 discovery criteria of an association
Supplementary Table 8. 17 genes (our of 301 predicted MIR137 targets) with >=1
"hotspot" of p <1E-04.
Gene                      Chr                Best Z           p -value    SNP
C10orf26                   10                  5.59           2.23E-08    rs11191580
TCF4                       18                  5.58           2.35E-08    rs17512836
CSMD1                       8                  5.20           1.96E-07    rs10503256
CACNA1C                    12                  4.94           7.77E-07    rs7972947
SLC12A2                     5                  4.64           3.53E-06    rs17675435
CALN1                       7                  4.56           5.16E-06    rs12699131
GRIA1                       5                  4.49           7.23E-06    rs12522297
ST13                       22                  4.46           8.39E-06    rs5758209
CSDC2                      22                  4.46           8.39E-06    rs5758209
LUZP2                      11                  4.32           1.58E-05    rs7131395
GLIS2                      16                  4.17           3.00E-05    rs3747600
EPHA7                       6                  4.17           3.01E-05    rs1492967
CADPS2                      7                  4.07           4.78E-05    rs6968240
RGS6                       14                  4.00           6.37E-05    rs714975
TBC1D12                    10                  3.96           7.36E-05    rs2253635
FAM78A                      9                  3.96           7.59E-05    rs12553392
C20orf108                  20                  3.96           7.61E-05    rs1926065
Note: Recombination hotspots are defined according to hapmap.org for HG18 [94], and
LD blocks are defined as the region between hotspots. Each LD block is then assigned
an association score corresponding to the best score across the block. A gene's footprint
is defined as the largest of its transcripts plus 110kb upstream and 50kb downstream to
include regulatory sequence [95]. Genes are assigned every LD block that their footprint
overlaps, and in this table we show the Z-score (p -value) for the top-scoring LD-block for
each of 17 genes, found in the list of 301 predicted MIR137 targets, that show at least
one hotspot with p <1E-04.
.
.




.
.
.
.
.
.
.
.
.
Supplementary Table 9: Results of score analysis of aggregate effects of common SNPs.
            Dataset                                                   R^2 for each pT value
Training          Test             0.0001 0.001         0.01     0.05      0.1     0.2      0.3
ISC               Cardiff           0.002    0.006      0.013    0.031    0.031   0.033    0.033
ISC               MGS               0.002    0.005      0.020    0.027    0.025   0.025    0.026
                  7
ISC+MGS+Cardiff new datasets 0.009           0.015      0.035    0.051    0.054   0.057    0.058
            Dataset                                                    P for each pT value
ISC               Cardiff          ###### ###### ###### ###### ###### ###### ######
ISC               MGS              ###### ###### ###### ###### ###### ###### ######
                  7
ISC+MGS+Cardiff new datasets ###### ###### ###### ###### ###### ###### ######
Note: pT = this proportion of SNPs, ordered from lowest to highest p -values, were selected based on results from
training dataset, to form quantitative scores for test dataset subjects.
on SNPs.
alue
            0.4     0.5     1.0
           0.030   0.029   0.029
           0.026   0.026   0.025
           0.058   0.058   0.058
lue
           ###### ###### ######
           ###### ###### ######
           ###### ###### ######
ected based on results from the .
                                .
Supplementary Table 10. Notable genes in highly significant regions (GWS or selected for replication) in PGC-SZ analyses, contrasted with BP and ASD findings.
                                                                                Most
                                                                                significant
                                                                     Cytogeneti regional       Stage 1 Stage 2 Combined
Gene          Gene name                                     Disorder c band     SNP            p -value p -value p -value    Comment                                                                    Reference
DPYD          dihydropyrimidine dehydrogenase               ASD      1p21.3     rs1625579       5.72E-07 2.65E-06   1.59E-11 MR, microcephaly, ASD, and seizures.                                       [96-97]
                                                                                                                             microRNA 137 is involved in neurogenesis.
miR-137       microRNA 137                                            1p21.3        rs1625579   5.72E-07 2.65E-06   1.59E-11 TCF4 , CACNA1C , CALN1 , and CSMD1 are microRNA                            [98]
                                                                                                                             137predicted targets.
              v-akt murine thymoma viral oncogene                                                                            Deletion and translocation of AKT3 has been reported in
AKT3                                                                  1q44          rs6703335  3.26E-06 2.19E-03    5.47E-08                                                                            [99-101]
              homolog 3                                                                                                      microcephaly and agenesis of the corpus callosum.
                                                                                                                             Non-coding RNA.
PCGEM1        prostate-specific transcript 1                          2q32.3        rs17662626 3.09E-06 1.70E-03    4.65E-08                                                                            [102]
                                                                                                                             Overexpressed in prostate cancer.
              arf-GAP with GTPase, ankyrin repeat and
AGAP1         PH 9 (centaurin, gamma 2 isoform---           ASD       2q37.2        rs13025591    1.07E-06        0.13    5.92E-06 Candidate gene for autism.                                           [103]
              CENTG2)
GNL3          guanine nucleotide binding protein-like 3
                                                                                                                                   SNPs in 3p21.1 reported to be associated in BP.
              IMA (never in mitosis gene a)-related
NEK4                                                                                                                               R^2=0.40 between rs2239547 and rs1042779 (p =1.8E-07 in BP).
              kinase 4                                      BP        3p21.1        rs2239547     2.25E-06 3.15E-03       6.02E-08                                                              [104]
                                                                                                                                    rs1042779 has a SZ-PGC Stage 1 p =5.14E-05; same associated
ITIH3         inter-alpha (globulin) inhibitor H3
                                                                                                                                   allele (A).
ITIH4         inter-alpha globulin inhibitor H4
TRIM26        tripartite motif-containing 26                SCZ       6p21.33       rs2021722     4.30E-11 1.55E-03       2.18E-12 Involved in innate immunity .                                        [105]
                                                                                                                                   Protective role of histones against intrauterine infections and
HIST1H2BL histone cluster 1, H2B type 1-L                   SCZ       6p22.1        rs17693963    1.56E-10 4.00E-03       4.03E-11                                                                      [106]
                                                                                                                                   epigenetic mechanisms.
MAD1L1        mitotic arrest deficient-like 1                         7p22.3        rs10226475    5.06E-08     0.19       1.28E-05
CALN1         calneuron 1                                             7q11.22       rs12699131    5.16E-06 3.21E-02       2.05E-06 Target of miR-137; brain-specific.                                   [107]
                                                                                                                                   Linkage peak in SZ in 8p23.3-p21.2
                                                                                                                                                                                                        [17,108,10
CSMD1         CUB and Sushi multiple domains 1              SCZ       8p23.2        rs10503253    3.84E-07 7.60E-03       4.14E-08 Duplication with breakpoint in CSMD1 was reported associated
                                                                                                                                                                                                        9]
                                                                                                                                   with speech delay, autism and learning difficulties.
                                                                                                                                   Translocation with a breakpoint within MMP16 was reporeted
MMP16         matrix metallopeptidase 16                    ASD       8q21.3        rs7004633     1.45E-08        0.01    2.75E-08                                                                      [110]
                                                                                                                                   associated with developmental delay and autism.

                                                                                                                                     The same association direction in all replications; the same
                                                                                                                                     associated region as in a reported BP locus in GWAS, r^2=0.37
ANK3          ankyrin 3                                     BP        10q21.2       rs16915157    4.44E-06        0.10    4.68E-06                                                                      [111]
                                                                                                                                     with the BP-associated (p =1.3E-08) SNP rs1938526 that has a
                                                                                                                                     Stage 1 p =0.006 with the same associated allele G as in BP.

              phosphoinositide-3-kinase, class 2, alpha                                                                            PIK3C2A expression reported to be downregulated in the frontal
PIK3C2A                                                               11p15.1       rs4356203     1.91E-06 6.78E-03       1.13E-07                                                                      [112]
              polypeptide                                                                                                          cortex of suicide completers.
              potassium inwardly-rectifying channel,                                                                               Mouse model carrying mutation in KCNJ11 shows impairment of
KCNJ11                                                                11p15.1       rs4356203     1.91E-06 6.78E-03       1.13E-07                                                                      [113]
              subfamily J, member 11                                                                                               locomotor activity.
                                                                                                                                   Reported GWS SCZ locus, but the associated SNP and NRGN
NRGN          neurogranin                                   SCZ       11q24.2       rs548181      2.91E-08        0.07    8.87E-07                                                                      [18]
                                                                                                                                   are ~845 kb apart.

                                                                                                                                     The same association direction in all replications; the same
                                                                                                                                     associated region as in a reported BP locus in GWAS, r^2=1.0
CACNA1C       voltage-dependent L-type calcium channel      BP        12p13.33      rs4765905     8.92E-07        0.07    1.87E-06                                                                      [111]
                                                                                                                                     with the BP-associated SNP (p =7.0E-08) rs1006737 that has a
                                                                                                                                     Stage 1 p =1.17E-06 with the same associated allele A as in BP.

                                                                                                                                     Reported GWS SCZ locus; but not in LD (r^2=0.002) with the
TCF4          transcription factor 4                        SCZ       18q21.2       rs12966547    1.00E-06 2.29E-05       2.60E-10                                                                      [18]
                                                                                                                                     reported associated SNP rs9960767.
TXNRD2         thioredoxin reductase 2
                                                                                                                                        rs7289747 is within 22q deletion syndrome (VCSF).
COMT           catechol-O-methyltransferase
                                                              SCZ      22q11.21      rs7289747       9.67E-06        0.37    6.83E-05 COMT is a SCZ candidate gene.                                          SZGene
               armadillo repeat gene deleted in
ARVCF                                                                                                                                   rs7289747 is not in LD with rs4680 (Val/Met).
               velocardiofacial syndrome
Notes: Disorders column refers to genes previously reported associated with bipolar disorder (BP), previously implicated in autism spectrum disorders (ASD), or previously implicated in schizophrenia association    .
or linkage studies (SCZ). The most significant regional SNPs are within the same LD interval where the gene are located. SZGene from www.schizophreniaforum.org. Stage 1 is discovery GWAS sample.                    .
Stage 2 is replication sample (reported as single-tailed weighted (1/SE) meta p -value). Combined includes Stages 1 and 2 (reported as two-tailed weighted (1/SE) meta p -value). Bolding indicates p <5E-08 for      .
Stage 1 and Combined, and indicates p <0.05 for Stage 2. Although no SNPs at the 2q32.1 locus of ZNF804A (zinc finger protein 804A ) were selected for Stage 2 replication genotyping since none met the Stage        .
1 discovery criteria of an association p <2E-05, genome wide significant association to schizophrenia has been reported elsewhere between rs1344706 at ZNF804A [93] with an estimated OR of 1.10 (CI: 1.07-           .
1.14). The PGC sample, the majority of which was included in the earlier study, is consistent with that association, although reflecting a smaller sample size than the earlier study [93] (which had 21,274          .
schizophrenia/bipolar disorder cases and 38,675 controls), a slightly weaker effect (OR=1.08; CI: 1.04-1.12), and more modest evidence for association (p =1.8E-04).                                                  .
Supplementary Table 11. Joint analysis of PGC-SZ and PGC-BP datasets.

                                                                       Frequency Frequency
SNP           Chr bp                p -value OR (95% CI) Alleles Cases               Controls Info
rs4765905 12 2,219,845 7.01E-09 1.11 (1.07-1.15) CG                       0.350        0.329     ####
rs2239547        3 ######## 7.83E-09 1.12 (1.08-1.16) TC                  0.743        0.723     ####
rs10994359 10 ######## 2.45E-08 1.22 (1.15-1.29) CT                       0.069        0.059     ####
Notes: bp is the base position (HG18). Alleles are listed with risk allele first; frequency (in 16,374 joint SZ
and BP cases, and 14,044 joint controls, respectively) and OR (odds ratio, and their 95% CI, confidence
interval) refer to the risk allele. Bolding of p -values indicates p <5E-08.
             Gene
             CACNA1C
             ITIH3/4
             ANK3
y (in 16,374 joint SZ   .
5% CI, confidence       .
                        .
                        .
                                                                          .
Supplementary Table 12. Power Analyses for Stage 1 (GWAS Discovery).      .
            p <5E-08 at            p <2E-05 at             p <1E-03 at              .
         allele frequency       allele frequency        allele frequency            .
OR     0.05 0.10 0.20 0.40    0.05 0.10 0.20 0.40     0.05 0.10 0.20 0.40
 1.10   0% 1% 8% 29%           2% 11% 42% 74%         14% 41% 78% 95%
 1.15   2% 18% 70% 95%        17% 60% 95% 99%         50% 89% 99% 99%
 1.20  14% 69% 99% 99%        53% 95% 99% 99%         86% 99% 99% 99%
Power figures at representative and relevant ORs (ORs of 1.10, 1.15, and 1.20)      .
and allele frequencies (0.05, 0.10, 0.20, and 0.40) are displayed for the Stage 1   .
GWAS (discovery) analysis.                                                          .
Supplementary Table 13. Data Collection Procedures for Schizophrenia GWAS Studies.
                                                      Cardiff        ISC -        ISC -    ISC -   ISC -
Phenotypic Score Item || Stage 1 site                 UK      CATIE Aberdeen Cardiff Dublin Edinburgh
Used a structured psychiatric interview               yes     yes    yes          yes      yes     yes
Systematic interviewer training                       yes     yes    yes          yes      yes     yes
Systematic quality control of diagnostic accuracy yes         no     yes          yes      yes     yes
Reliability trials                                    yes     yes    yes          no       yes     no
Review of medical record information                  yes     yes    yes          yes      yes     yes
Best-estimate diagnostic procedure                    yes     no     yes          yes      yes     yes
Specific inclusion and exclusion criteria utilized    yes     yes    yes          yes      yes     yes
MDs or PhDs make final diagnostic determination yes           yes    yes          yes      yes     yes
                                                      yes
Special additional training for the final diagnostician       yes    yes          yes      yes     yes
Note: Samples meeting at least 7 of the 9 criteria were judged of high quality. One study (ISC - SW1-2) used a fundamentally d
was requested, provided [3], and approved by the group. Abbreviations: Collection names as in Table 1.
              ISC -   ISC -        ISC - ISC -         SGENE SGENE -             SGENE - SGENE - SGENE - Zucker
              London Portugal SW1 SW2 MGS - Bonn Copenhagen Munich                             TOP3        UCLA       Hillside
              yes     yes          no     no    yes    yes       yes             yes          yes         yes         yes
              yes     yes          no     no    yes    yes       yes             yes          yes         yes         yes
              yes     yes          no     no    yes    yes       yes             yes          yes         yes         yes
              no      yes          no     no    yes    yes       no              yes          yes         no          yes
              yes     yes          yes    yes   yes    yes       yes             yes          yes         yes         yes
              yes     yes          no     no    yes    yes       yes             yes          yes         no          yes
              yes     yes          yes    yes   yes    yes       yes             yes          yes         yes         yes
              yes     yes          yes    yes   yes    yes       yes             no           yes         yes         yes
              yes     yes          no     no    yes    yes       yes             yes          yes         yes         no
W1-2) used a fundamentally different ascertainment methodology; further empirical support for the validity of this approach
 ble 1.
.
.
.
Supplementary Table 14. Interaction Analysis of Table 1 SNPs.
Table 1 SNP      rs11191580 rs1625579 rs548181 rs12966547 rs17512836 rs17662626
rs7914558            0.948          0.944        0.318          0.076             0.213           0.006
 rs11191580           NA            0.696        0.075          0.392             0.621           0.083
rs1625579             NA             NA          0.667          0.124             0.651           0.187
 rs548181             NA             NA            NA           0.067             0.797           0.884
rs12966547            NA             NA            NA             NA              0.865           0.293
rs17512836            NA             NA            NA             NA                NA            0.434
rs17662626            NA             NA            NA             NA                NA              NA
rs2021722             NA             NA            NA             NA                NA              NA
rs10503253            NA             NA            NA             NA                NA              NA
Note: We tested for interaction between each of these loci (all pairs of loci in Table 1 tested) in a logistic regression model that
main effect of each SNP. The p -value for only the interaction term is reported in this table -- none were significant when correc
number of pairs tested.
                rs2021722 rs10503253 rs7004633
                    0.264       0.384           0.260
                    0.766       0.098           0.642
                    0.557       0.494           0.944
                    0.607       0.620           0.318
                    0.390       0.212           0.161
                    0.670       0.943           0.786
                    0.725       0.770           0.864
                     NA         0.587           0.449
                     NA            NA           0.058
d) in a logistic regression model that included the     .
-- none were significant when correcting for the        .
                                                        .
                                                        .

				
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