Supplementary information for: A functional variation in BRAP confers risk of myocardial infarction in Asian populations

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1 Supplementary information for: A functional variation in BRAP confers risk of myocardial infarction in Asian populations Kouichi Ozaki 1, Hiroshi Sato 2, Katsumi Inoue 3, Tatsuhiko Tsunoda 4, Yasuhiko Sakata 2, Hiroya Mizuno 2, Tsung-Hsien Lin 5,6, Yoshinari Miyamoto 7, Asako Aoki 1, Yoshihiro Onouchi 1, Sheng-Hsiung Sheu 5,6, Shiro Ikegawa 7, Keita Odashiro 3, Masakiyo Nobuyoshi 3, Suh-Hang H. Juo 8,9,10, Masatsugu Hori 2, Yusuke Nakamura 11, and Toshihiro Tanaka 1 1, Laboratory for Cardiovascular Diseases, Center for Genomic Medicine, RIKEN, Yokohama, Japan 2, Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan 3, Department of Cardiology, Kokura Memorial Hospital, Kitakyushu , Japan 4, Laboratory for Medical Informatics, Center for Genomic Medicine, RIKEN, Yokohama, Japan 5, Division of Cardiology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan 6, Department of Internal Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan 7, Laboratory for Bone and Joint Disease, Center for Genomic Medicine, RIKEN, Tokyo, Japan 8, Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan 9, Graduate Institute of Medical Genetics, Kaohsiung Medical University, Kaohsiung, Taiwan 10, Center of Excellence for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan 11, Center for Genomic Medicine, RIKEN, Yokohama, Japan

2 Supplementary Table 1 Identified SNPs in BRAP dbsnp ID SNP Position in BRAP* Position in NT_ Chromosome position MAF - G>A 5'-flanking rs C>T 5'-flanking G>C 5'-flanking rs G>A 5'-flanking rs C>T intron C>T intron A>C intron C>T intron A>G intron T>C intron rs T>C intron rs A>G intron rs A>G intron rs A>G intron A>G intron C>T intron G>A intron rs T>A intron rs A>G intron rs C>T intron T>G intron rs A>G exon5 90, R241R T>C intron C>T intron C>T intron rs A>G intron A>G intron rs T>A intron rs T>G intron C>T intron rs C>T intron C>A intron A>G intron T>A intron T>A intron C>G intron rs C>T exon8 51, V341V rs A>G intron rs A>C intron T>A intron rs C>T intron rs A>C intron rs C>T intron rs A>G intron T>A intron C>T intron C>G intron rs T>G intron A>G intron rs C>T intron ; The variant was not registerd in dbsnp database (Build 129) MAF; minor allele frequency * Nucleotide numbering is according to the mutation nomenclature 23

3 Supplementary Table 2 Clustering of SNPs by tagger program tag SNPs Clustered SNPs by tagger program rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs rs intron7 212 rs rs rs rs

4 Supplementary Table 3 First stage association analyses of six tag SNPs in BRAP dbsnp ID MAF* Comparison of allele frequency Cases Controls OR** (95% CI) P value rs ( ) 0.12 rs ( ) 0.39 rs ( ) rs ( ) 0.87 intron ( ) 0.27 rs ( ) 0.30 *; minor allele frequency **; odds ratio

5 Supplementary Table 4 Haplotype association analysis Haplotype Haplotype frequency Comparison of haplotype Haplotype effect (vs. CCAATA) MI Control χ 2 P Odds ratio (95% CI) P CCAATA CCGATA ( ) CTAATG ( ) 0.64 CCAGAG ( ) 0.26 TCAGTG ( ) 0.29 Global P = by conditional log-likelihood for the haplotype set.

6 Supplementary Table 5 Regression analysis of six tag SNPs Single-locus test P when SNP added to rs Single-locus test P when rs added to SNP dbsnp ID Single-locus test (multiplicative OR) Addition of dominance effect P P rs rs rs rs intron rs

7 Supplementary Table 6 Clinical parameters of MI patients and the BRAP SNP (rs ) genotype variable Population Genotype AA (±SD) AG (±SD) GG (±SD) F value P value age (year) Japanese (11.4) 64.4 (10.9) 63.1 (11.0) Japanese (11.4) 63.5 (10.9) 66.2 (10.1) Taiwanese 61.9(14.2) 62.6(12.2) 61.3(12.1) HbA1c (%) Japanese (1.4) 6.0 (1.5) 6.4 (1.4) Japanese (1.0) 5.6 (1.0) 6.2 (1.9) Taiwanese 7.9 (1.9) 7.6 (2.1) 7.8 (1.5) TC (mg/dl) Japanese (35.4) (44.7) (31.7) Japanese (34.2) (35.2) (39.8) Taiwanese 197.2(46.8) 203.5(45.2) 199.0(34.9) HDL (mg/dl) Japanese (11.6) 38.5 (10.6) 39.3 (11.0) Japanese (10.4) 36.8 (9.4) 35.3 (8.5) Taiwanese 36.3(10.8) 38.7(10.7) 34.4(11.1) TG (mg/dl) Japanese (69.6) (80.8) (66.3) Japanese (68.2) (88.7) (53.9) Taiwanese 148.8(142.9) 156.0(119.6) 168.1(105.8) BMI (kg/m 2 ) Japanese (3.4) 23.7 (3.3) 23.5 (3.6) Japanese (3.7) 23.5 (3.1) 23.4 (3.4) Taiwanese 25.1(3.6) 25.4(3.4) 25.8(3.0) UA (mg/dl) Japanese (1.6) 6.0 (1.5) 6.0 (1.6) Japanese (1.6) 5.8 (1.4) 6.1 (1.4) Taiwanese 6.7 (2.0) 6.2 (2.0) 6.9 (1.7)

8 Supplementary Table 7 Relationship between non-genetic factors and rs among MI cases Non-genetic factors (p-value) Panel Gender Diabetes Hypertension Hyperlipidemia Smoking Japanese Japanese Taiwanese

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11 Supplementary Note Clinical ascertainment and description of study populations Japanese population We have been conducting a district-based survey named the Osaka Acute Coronary Insufficiency study (OACIS) 21 to assess the clinical variables, therapeutic procedures and consequent clinical events in patients with MI in the Osaka area. Both cohorts used in this study comprised of patients who were admitted to 25 collaborating hospitals within one week of onset. The diagnosis of definite MI required two of the following three criteria: (1) a clinical history of central chest pressure, pain, or tightness lasting for 30 min or more, (2) ST-segment elevation greater than 0.1 mv in at least one standard or 2 precordial leads, and (3) a rise in serum creatine kinase concentration to greater than twice the normal laboratory value. For first cohort, patients (n = 2,475) were recruited between April 1998 and December The clinical characteristics are the following; mean age: 63.9 ± 10.1, gender (male %): 77.6, hypertension (%): 52.8, smoking (%): 65.7, past history of MI (%): 11.8, body mass index (kg/m2): 23.7 ± 3.4, HbA1c (%): 6.2 ± 1.4, total cholesterol (mg/dl): ± 34.7, HDL cholesterol (mg/dl): 38.9 ± 11.1, and triglyceride (mg/dl): ± For second cohort, patients (n = 862) were recruited between January 2004 and December The clinical characteristics are the following; mean age: 64.1 ± 11.0, gender (male %): 79.8, hypertension (%): 58.8, smoking (%): 65.7, past history of MI (%): 12.3, body mass index (kg/m2): 23.9 ± 3.4, HbA1c (%): 5.9 ± 1.2, total cholesterol (mg/dl): ± 35.2, HDL cholesterol (mg/dl): 37.1 ± 9.7, and triglyceride (mg/dl): ± Control population for first cohort (n = 2,778) were recruited from several medical institutes in Japan; mean age (year) and gender (male %) were 53.4 ± 18.4 and 28.0, respectively. For second cohort, they (n = 1,113) were from other distinct medical institutes in Japan; mean age (year) and gender (male %) were 49.5 ± 15.4 and 74.3, respectively. All subjects were Japanese and provided written informed consent to participate in the study, or their parents gave them when they were under 20 years old, according to the process approved by the Ethical Committee at Center for Genomic Medicine, RIKEN.

12 Taiwanese population The diagnosis of MI in the Taiwanese samples was based on two of the following three conditions (1) A documented history of myocardial infarction, (2) Pathological Q wave over EKG [any Q wave in leads V1 through V3, Q wave to 30 ms (0.03 s) in leads I, II, avl, avf, V4, V5, or V6. (The Q wave changes must be present in any two contiguous leads, and be to 1 mm in depth.)], or (3) Markers of myocardial cell death recovered from blood samples [maximal concentration of troponin T (> 0.1) or I (> 0.4) exceeding the decision limit] on at least one occasion during the first 24 h after the index clinical event. The 349 MI subjects were recruited at the Kaohsiung Medical University at the two intervals (from 2001 to 2004 and from 2006 to 2008). The clinical characteristics are as follows: mean age: 62.1 ± 13.1, gender (male %): 75.3, hypertension (%): 61.8, body mass index (kg/m 2 ): 25.3 ± 3.5, HbA1c: 7.8 ± 1.9, total cholesterol (mg/dl): ± 45.1, HDL cholesterol (mg/dl): 37.2 ± 10.9, LDL cholesterol (mg/dl): ± 39.5, triglyceride (mg/dl): ± 129.0, and uric acid (mg/dl): 6.6 ± 2.0. The control subjects (n=994) were stroke- and MI-free volunteers who participated in the health screening program conducted by the medical staff from Kaohsiung Medical University Hospital between January 2006 and December The clinical characteristics for the controls are as follows: mean age: 55.7 ± 12.8, sex (male%): 42.4, hypertension (%): 27.2, body mass index (kg/m 2 ): 24.5 ± 3.6, total cholesterol (mg/dl): ± 36.1, HDL cholesterol (mg/dl): 56.8 ± 14.1, LDL cholesterol (mg/dl): ± 34.0, triglyceride (mg/dl): ± 78.0 and uric acid (mg/dl): 6.2 ± 4.1. The study protocols and methods were approved by the Institutional Review Board (IRB) of the Kaohsiung Medical University Hospital and by the Ethical Committee at Center for genomic medicine, RIKEN.