Supplementary Table 1. Association and linkage studies with suggestive markers near gsx1 (chr13:28,366,780-28,368,089) Phenotype / Disorder Cross-disorder: scz/mdd/bip Schizophrenia Antisocial behavior Schizophrenia ADHD+Conduct disorder Schizophrenia Tobacco use ADHD Antisocial personality Schizophrenia Bipolar Schizophrenia Bipolar Schizophrenia Schizophrenia Marker rs7326068 rs2985662 D13S1304 rs9512730 rs9512900 rs2491222 D13S217 rs1792040 D13S289 D13S171 D13S1493 D13S1293 D13S1 D13S1491 D13S894* Position 21,209,762 22,449,838 27,370,019 28,076,894 28,429,988 28,607,666 29,271,791 29,377,193 31,165,654 33,153,912 33,908,691 34,638,154 36,991,143 38,463,261 38,738,457 p value / LOD <0.00005 6.00E-04 3.20E-04 4.50E-06 8.50E-06 Z = 2.1 LOD 1.3 1.75E-05 LOD 2.1 LOD 1.6 LOD 1.6 LOD 1.8 Z = 1.4 LOD 3.0 LOD 3.6 Distance to Gsx1 (bp) -7,157,572 -5,917,496 -997,315 -290,440 62,654 240,332 904,457 1,009,859 2,798,320 4,786,578 5,541,357 6,270,820 8,623,809 10,095,927 10,371,123 Note Ref 1 2 3 Additional linked SNPs 4 5 Peak: rs720083 at 30,348,987 6 7 Additional linked SNPs * Genome wide significance was indicated for D13S894. References for Table 1 1. Huang J, Perlis RH, Lee PH, Rush AJ, Fava M, Sachs GS et al. Cross-disorder genomewide analysis of schizophrenia, bipolar disorder, and depression. Am J Psychiatry 2010; 167(10): 1254-1263. 2. Kirov G, Zaharieva I, Georgieva L, Moskvina V, Nikolov I, Cichon S et al. A genome-wide association study in 574 schizophrenia trios using DNA pooling. Mol Psychiatry 2009; 14(8): 796-803. 3. Gizer IR, Ehlers CL, Vieten C, Feiler HS, Gilder DA, Wilhelmsen KC. Genomewide linkage scan of antisocial behavior, depression, and impulsive substance use in the UCSF family alcoholism study. Psychiatr Genet 2012; 22(5): 235-244. 4. Sullivan PF, Lin D, Tzeng JY, van den Oord E, Perkins D, Stroup TS et al. Genomewide association for schizophrenia in the CATIE study: results of stage 1. Mol Psychiatry 2008; 13(6): 570-584. 5. Anney RJ, Lasky-Su J, O'Dushlaine C, Kenny E, Neale BM, Mulligan A et al. Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. Am J Med Genet B Neuropsychiatr Genet 2008; 147B(8): 1369-1378. 8 9 10 11 12 13 14 15 6. Hong KS, Won H-H, Cho E-Y, Jeun HO, Cho S-S, Lee Y-S et al. Genome-widely significant evidence of linkage of schizophrenia to chromosomes 2p24.3 and 6q27 in an SNP-Based analysis of Korean families. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics 2009; 150B(5): 647-652. 7. Ehlers C, Wilhelmsen K. Genomic screen for loci associated with tobacco usage in Mission Indians. BMC Medical Genetics 2006; 7(1): 9. 8. Sonuga-Barke EJ, Lasky-Su J, Neale BM, Oades R, Chen W, Franke B et al. Does parental expressed emotion moderate genetic effects in ADHD? An exploration using a genome wide association scan. Am J Med Genet B Neuropsychiatr Genet 2008; 147B(8): 1359-1368. 9. Ehlers CL, Gilder DA, Slutske WS, Lind PA, Wilhelmsen KC. Externalizing disorders in American Indians: comorbidity and a genome wide linkage analysis. Am J Med Genet B Neuropsychiatr Genet 2008; 147B(6): 690-698. 10. Wijsman EM, Rosenthal EA, Hall D, Blundell ML, Sobin C, Heath SC et al. Genome-wide scan in a large complex pedigree with predominantly male schizophrenics from the island of Kosrae: evidence for linkage to chromosome 2q. Mol Psychiatry 2003; 8(7): 695-705, 643. 11. McInnis MG, Lan TH, Willour VL, McMahon FJ, Simpson SG, Addington AM et al. Genome-wide scan of bipolar disorder in 65 pedigrees: supportive evidence for linkage at 8q24, 18q22, 4q32, 2p12, and 13q12. Mol Psychiatry 2003; 8(3): 288-298. 12. Shaw SH, Kelly M, Smith AB, Shields G, Hopkins PJ, Loftus J et al. A genomewide search for schizophrenia susceptibility genes. Am J Med Genet 1998; 81(5): 364-376. 13. Ginns EI, Ott J, Egeland JA, Allen CR, Fann CS, Pauls DL et al. A genome-wide search for chromosomal loci linked to bipolar affective disorder in the Old Order Amish. Nat Genet 1996; 12(4): 431-435. 14. Maziade M, Roy MA, Chagnon YC, Cliche D, Fournier JP, Montgrain N et al. Shared and specific susceptibility loci for schizophrenia and bipolar disorder: a dense genome scan in Eastern Quebec families. Mol Psychiatry 2005; 10(5): 486499. 15. Camp NJ, Neuhausen SL, Tiobech J, Polloi A, Coon H, Myles-Worsley M. Genomewide multipoint linkage analysis of seven extended Palauan pedigrees with schizophrenia, by a Markov-chain Monte Carlo method. Am J Hum Genet 2001; 69(6): 1278-1289.