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Supplementary information for: A functional variation in BRAP confers risk of myocardial infarction in Asian populations Kouichi Ozaki1, Hiroshi Sato2, Katsumi Inoue3, Tatsuhiko Tsunoda4, Yasuhiko Sakata2, Hiroya Mizuno2, Tsung-Hsien Lin5,6, Yoshinari Miyamoto7, Asako Aoki1, Yoshihiro Onouchi1, Sheng-Hsiung Sheu5,6, Shiro Ikegawa7, Keita Odashiro3, Masakiyo Nobuyoshi3, Suh-Hang H. Juo8,9,10, Masatsugu Hori2, Yusuke Nakamura11, and Toshihiro Tanaka1 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 802-8555, 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

Nature Genetics: doi:10.1038/ng.326

dbSNP ID SNP Position in BRAP* Position in NT_009775.16 Chromosome position MAF- G>A 5'-flanking -3146 2696394 110611268 0.003

rs608814 C>T 5'-flanking -2876 2696124 110610998 0.061- G>C 5'-flanking -2815 2696063 110610937 0.013

rs649406 G>A 5'-flanking -2326 2695574 110610448 0.152rs601663 C>T intron1 231 2692793 110607667 0.065

- C>T intron1 256 2692768 110607642 0.003- A>C intron1 315 2692709 110607583 0.013- C>T intron1 1950 2691039 110605913 0.008- A>G intron1 2173 2690851 110605725 0.016- T>C intron2 421 2690038 110604912 0.005

rs12580069 T>C intron2 696 2689763 110604637 0.312rs646275 A>G intron2 780 2689679 110604553 0.151

rs11066001 A>G intron3 270 2688680 110603554 0.292rs847895 A>G intron3 865 2688085 110602959 0.168

- A>G intron4 595 2685869 110600743 0.003- C>T intron4 1269 2685195 110600069 0.005- G>A intron4 2138 2684326 110599200 0.003

rs11065999 T>A intron4 3105 2683359 110598233 0.311rs7136874 A>G intron4 3297 2683167 110598041 0.149rs12427276 C>T intron4 3447 2683017 110597891 0.168

- T>G intron4 3857 2682607 110597481 0.031rs3782886 A>G exon5 90, R241R 2679998 110594872 0.301

- T>C intron5 3630 2676457 110591242 0.003- C>T intron5 3911 2676176 110587331 0.013- C>T intron5 3973 2676114 110583358 0.003

rs3742001 A>G intron6 295 2672657 110587531 0.154- A>G intron6 558 2672394 110586973 0.003

rs10849966 T>A intron6 2670 2670282 110584303 0.058rs11065995 T>G intron6 2688 2670264 110585138 0.011

- C>T intron6 3864 2669088 110583962 0.005rs10774634 C>T intron6 4198 2668754 110583628 0.151

- C>A intron6 4301 2668651 110583525 0.005- A>G intron7 36 2667877 110582751 0.003- T>A intron7 45 2667868 110582742 0.003- T>A intron7 212 2667701 110582575 0.087- C>G intron7 1154 2666759 110581633 0.003

rs3742002 C>T exon8 51, V341V 2666608 110581482 0.011rs10774633 A>G intron9 251 2665798 110580672 0.309rs12307990 A>C intron9 922 2665127 110580001 0.312

- T>A intron9 1752 2664297 110579171 0.003rs7977828 C>T intron9 1774 2664275 110579149 0.152rs2285727 A>C intron10 292 2662587 110577461 0.145rs12579287 C>T intron10 2556 2660323 110575197 0.136rs12582964 A>G intron10 2591 2660288 110575162 0.139

- T>A intron11 103 2657149 110572023 0.003- C>T intron11 202 2657050 110571924 0.016- C>G intron11 353 2656899 110571773 0.005

rs10744773 T>G intron11 933 2656319 110571193 0.151- A>G intron11 944 2656308 110571182 0.003

rs10774632 C>T intron11 1240 2656012 110570886 0.151-; The variant was not registerd in dbSNP database (Build 129)MAF; minor allele frequency* Nucleotide numbering is according to the mutation nomenclature23

Supplementary Table 1 Identified SNPs in BRAP


Supplementary Table 2 Clustering of SNPs by tagger programtag SNPs Clustered SNPs by tagger programrs601663 rs608814 rs10849966rs12427276 rs847895rs3782886 rs11066001rs3742001 rs649406 rs646275 rs7136874 rs10774634 rs7977828 rs2285727 rs12579287 rs12582964 rs10744773 rs10774632intron7 212rs10774633 rs12580069 rs11065999 rs12307990


dbSNP IDCases Controls OR** (95% CI) P value

rs601663 0.08 0.05 1.33 (0.92-1.91) 0.12rs12427276 0.18 0.20 1.11 (0.88-1.41) 0.39rs3782886 0.35 0.28 1.38 (1.13-1.68) 0.0014rs3742001 0.15 0.15 1.02 (0.86-1.72) 0.87intron7 212 0.07 0.08 1.22 (0.86-1.72) 0.27rs10774633 0.33 0.35 1.11 (0.91-1.35) 0.30

**; odds ratio

MAF* Comparison of allele frequencySupplementary Table 3 First stage association analyses of six tag SNPs in BRAP

*; minor allele frequency


Supplementary Table 4 Haplotype association analysisHaplotype

MI Control χ2 P Odds ratio (95% CI) PCCAATA 0.321 0.368 4.70 0.03 - -CCGATA 0.343 0.281 8.37 0.0038 1.47 (1.15 - 1.86) 0.0018CTAATG 0.178 0.199 1.39 0.24 1.07 (0.80 - 1.41) 0.64CCAGAG 0.069 0.08 0.91 0.4 0.80 (0.54 - 1.18) 0.26TCAGTG 0.074 0.055 2.79 0.095 1.25 (0.83 - 1.89) 0.29Global P = 0.0057 by conditional log-likelihood for the haplotype set.

Haplotype frequency Comparison of haplotype Haplotype effect (vs. CCAATA)


dbSNP IDSingle-locus test

(multiplicative OR)Addition of

dominance effect

Single-locus test Pwhen SNP added to

rs3783886

Single-locus test Pwhen rs3783886

added to SNPP P

rs601663 0.10 0.05 0.10 0.00067rs12427276 0.39 0.97 0.89 0.00099rs3782886 0.0011 0.99 - -rs3742001 0.86 0.25 0.37 0.00059intron7 212 0.26 0.72 0.71 0.0011rs10774633 0.28 0.40 0.66 0.00070

Supplementary Table 5 Regression analysis of six tag SNPs


GenotypeAA (±SD) AG (±SD) GG (±SD)

age (year) Japanese 1 63.7 (11.4) 64.4 (10.9) 63.1 (11.0) 1.85 0.16Japanese 2 64.4 (11.4) 63.5 (10.9) 66.2 (10.1) 1.61 0.20Taiwanese 61.9(14.2) 62.6(12.2) 61.3(12.1) 0.22 0.80

HbA1c (%) Japanese 1 6.2 (1.4) 6.0 (1.5) 6.4 (1.4) 1.33 0.27Japanese 2 6.0 (1.0) 5.6 (1.0) 6.2 (1.9) 2.13 0.12Taiwanese 7.9 (1.9) 7.6 (2.1) 7.8 (1.5) 0.29 0.75

TC (mg/dl) Japanese 1 188.3 (35.4) 189.6 (44.7) 190.8 (31.7) 0.41 0.66Japanese 2 182.2 (34.2) 183.9 (35.2) 187.2 (39.8) 0.35 0.71Taiwanese 197.2(46.8) 203.5(45.2) 199.0(34.9) 2.22 0.11

HDL (mg/dl) Japanese 1 39.4 (11.6) 38.5 (10.6) 39.3 (11.0) 0.88 0.42Japanese 2 37.9 (10.4) 36.8 (9.4) 35.3 (8.5) 1.17 0.31Taiwanese 36.3(10.8) 38.7(10.7) 34.4(11.1) 2.66 0.07

TG (mg/dl) Japanese 1 145.0 (69.6) 144.7 (80.8) 147.7 (66.3) 0.18 0.84Japanese 2 141.7 (68.2) 146.4 (88.7) 156.7 (53.9) 0.62 0.54Taiwanese 148.8(142.9) 156.0(119.6) 168.1(105.8) 0.35 0.70

BMI (kg/m2) Japanese 1 23.7 (3.4) 23.7 (3.3) 23.5 (3.6) 0.40 0.11Japanese 2 24.4 (3.7) 23.5 (3.1) 23.4 (3.4) 4.38 0.01Taiwanese 25.1(3.6) 25.4(3.4) 25.8(3.0) 0.61 0.55

UA (mg/dl) Japanese 1 6.1 (1.6) 6.0 (1.5) 6.0 (1.6) 1.24 0.29Japanese 2 6.1 (1.6) 5.8 (1.4) 6.1 (1.4) 1.34 0.25Taiwanese 6.7 (2.0) 6.2 (2.0) 6.9 (1.7) 2.85 0.06

Supplementary Table 6 Clinical parameters of MI patients and the BRAP SNP (rs11066001) genotype

variable F value P valuePopulation


Panel Gender Diabetes Hypertension Hyperlipidemia SmokingJapanese 1 0.08 0.85 0.99 0.09 0.18Japanese 2 0.04 0.92 0.99 0.72 0.26Taiwanese 0.05 0.56 0.18 0.19 0.16

Non-genetic factors (p-value)

Supplementary Table 7 Relationship between non-genetic factors and rs11066001 amongMI cases


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 2003. 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): 189.2 ± 34.7, HDL cholesterol (mg/dl): 38.9 ± 11.1, and triglyceride (mg/dl): 145.2 ± 74.5. For second cohort, patients (n = 862) were recruited between January 2004 and December 2005. 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): 183.5 ± 35.2, HDL cholesterol (mg/dl): 37.1 ± 9.7, and triglyceride (mg/dl): 142.9 ± 65.2. 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.


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/m2): 25.3 ± 3.5, HbA1c: 7.8 ± 1.9, total cholesterol (mg/dl): 198.2 ± 45.1, HDL cholesterol (mg/dl): 37.2 ± 10.9, LDL cholesterol (mg/dl): 133.4 ± 39.5, triglyceride (mg/dl): 153.9 ± 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 2007. 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/m2): 24.5 ± 3.6, total cholesterol (mg/dl): 188.4 ± 36.1, HDL cholesterol (mg/dl): 56.8 ± 14.1, LDL cholesterol (mg/dl): 122.9 ± 34.0, triglyceride (mg/dl): 119.8 ± 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.


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