SUPPLEMENTARY DATA Page Supplementary Text …………………………………………………………………………………

SUPPLEMENTARY DATA Page Supplementary Text …………………………………………………………………………………. 2 Discovery Cohort Descriptions ……………………………………………………………………. 2 Translational Cohort Descriptions …………………………………………………………………. 6 Clinical characteristics of the Translation cohorts ………………………………………………… 7 References …………………………………………………………………………………………. 8

Supplementary Table 1. Pearson’s correlation matrix for T2D-related quantitative traits in the Discovery cohorts. A) Euglycemic clamp cohorts including MACAD, HTN-IR, NIDDM-Athero and B) FSIGT cohorts including IRAS, IRAS Family, BetaGene, TRIPOD. …………………………...... 10

Supplementary Table 2. Top Discovery hits (P<1.00x10‐4) from the GUARDIAN Consortium. SNPs with evidence of association are tabulated by trait (a. MCRI, b. SI+M, c. SI, d. M, e. AIRg, f. DI, g. SG) in order of genomic position. ...…………………………………………………………...... 11

Supplementary Table 3. Top Discovery hits from the GUARDIAN Consortium ordered by trait. … 41

Supplementary Table 4. Top Discovery hits from the GUARDIAN Consortium ordered by trait with conditional analyses performed at loci with multiple signals of association or in close proximity to previously identified T2D loci. ……………………………………………………………………... 42

Supplementary Table 5. Association with reported type 2 diabetes (T2D) susceptibility loci (a. MCRI, b. SI+M, c. SI, d. M, e. AIRg, f. DI, and g. SG) in GUARDIAN Hispanic Americans (nmax=3,787). Index SNPs reaching genome‐wide significance (P<5.0E‐08) for association with T2D were selected from the NHGRI GWAS catalog. ……………………………………………………… 43

Supplementary Table 6. All SNPs from GWAS of T2D-related quantitative traits with Translation to T2D in Mexican-origin cohorts ordered by trait from the Discovery stage. ……………………….. 65

Supplementary Table 7. Top regions from GWAS of T2D-related quantitative traits with translation to T2D in Mexican-origin. ………………………………………………………………… 86

Supplementary Table 8. Top regions from GWAS of T2D-related quantitative traits with translation to T2D in Mexican-origin cohorts ordered by trait from the Discovery stage with conditional analyses performed at loci with multiple signals of association or in close proximity to previously identified T2D loci. ………………………………………………………………………... 87

Supplementary Figure 1. Power to detect association with T2D (n=6,463 T2D cases and 9,232 controls) with an α of 5.00x10-8 at minor allele frequencies (MAF) ranging from 0.05-0.45. ……….. 89

Supplementary Figure 2. Regional plots of loci with evidence of association (P<2.00x10-6) in the Discovery meta-analysis. A) GNA15 rs2302063 with MCRI/T2D, B) MFSD8 rs1602084 with SI+M/T2D, C) MYT1L/TSSC1 rs896232 with SI+M/T2D, D) HAAO/SFP36L2/THADA rs1978648 with SI/T2D, E) C15orf59 rs4887140 with SI/T2D, F) HMGN3/LCA5 rs196701 with SI/T2D, G) KLF12/LINC00347 rs10492494 with M/T2D, H) LOC646736/IRS1 rs11683087 with M/T2D, I) MTNR1B rs10830963 with AIRg/T2D, J) CDKAL1 rs2206734 with AIRg/T2D, K) PEX5L/TTC14 rs6803803 with AIRg/T2D, L) SOHLH2 rs2149423 with DI/T2D, M) SNAPC4 rs3812570 with DI/T2D, N) BCL6/LPP rs523079 with SG/T2D, O) GCKR rs780093 with SG/T2D, and P) MYH14 rs788338 with SG/T2D. ……………………………………………………...... 91

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Discovery Cohort Descriptions

BetaGene. BetaGene was a family study designed to identify genetic determinants of beta-cell function (1). BetaGene recruited non-diabetic women with a history of gestational diabetes mellitus (GDM), their adult family members, and women without history of GDM. GUARDIAN includes 1217 of these individuals in 390 pedigrees, 238 families of probands with previous GDM and 152 families of probands with normal pregnancies. Recruitment occurred in the Los Angeles area. Insulin sensitivity was obtained by FSIGT. Other phenotypes include OGTT and total body fat by DXA scan.

TRIPOD. The Troglitazone in the Prevention of Diabetes (TRIPOD) study was designed to address the impact of troglitazone treatment on -cell function and glucose levels in women with prior GDM (2). TRIPOD recruited non-diabetic women with history of GDM in the Los Angeles area; family members were not recruited. GUARDIAN includes baseline (pre-intervention) data from 217 of these individuals. Insulin sensitivity was obtained by tolbutamide-modified FSIGT. Other phenotypes include OGTT and carotid intima-media thickness by B-mode ultrasonography.

IRAS. The Insulin Resistance Atherosclerosis Study (IRAS) was an epidemiologic cohort study designed to examine the relationship between insulin resistance and carotid atherosclerosis across a range of glucose tolerance (3). Individuals of self-reported Mexican-American ethnicity were recruited in San Antonio, TX and San Luis Valley, CO. Recruitment was balanced across age and glucose tolerance status. GUARDIAN includes 194 individuals from the IRAS. Insulin sensitivity was obtained by FSIGT. Other phenotypes include OGTT and carotid intima-media thickness by B-mode ultrasonography.

IRAS Family Study. The Insulin Resistance Atherosclerosis Study (IRAS) Family Study was a family study designed to examine the genetic and epidemiologic basis of glucose homeostasis traits and abdominal adiposity; details of the IRAS Family Study are described elsewhere (4).

Briefly, self-reported Mexican pedigrees were recruited in San Antonio, TX and San Luis Valley, CO. Probands with large families were recruited from the initial non-family-based IRAS Study (3), which was modestly enriched for impaired glucose tolerance and T2D. GUARDIAN includes 1040 individuals in 88 pedigrees from the IRAS Family Study. Insulin sensitivity was obtained by FSIGT. Other phenotypes include abdominal fat areas measured by computed tomography scan and total body fat by dual X-ray absorptiometry (DXA) scan.

HTN-IR. The Hypertension-Insulin Resistance Family Study (HTN-IR) was designed as a family study to examine the genetic basis of hypertension and insulin resistance (5). Family members of probands with documented hypertension were recruited in the Los Angeles area. GUARDIAN includes 708 of these individuals from 156 families. Insulin sensitivity was obtained by euglycemic clamp. Other phenotypes include OGTT, carotid intima-media thickness by B-mode ultrasonography, and salt sensitivity.

MACAD. The Mexican-American Coronary Artery Disease (MACAD) Study was designed as a family study to examine the genetic basis of coronary artery disease and insulin resistance (6). Family members of probands with documented coronary artery disease were recruited from the Los Angeles area. GUARDIAN includes 772 of these individuals from 208 families. Insulin sensitivity was obtained by euglycemic clamp. Other phenotypes include OGTT, carotid intima- media thickness by B-mode ultrasonography, total body fat by DXA scan, and post-heparin lipase activity assessment.

NIDDM-Athero. The NIDDM-Atherosclerosis Study was designed as a family study to examine the genetic basis of subclinical atherosclerosis and diabetes (7). Family members of probands with T2D were recruited in the Los Angeles area. GUARDIAN includes 188 of these individuals from 93 families. Insulin sensitivity was obtained by euglycemic clamp. Other phenotypes include OGTT and carotid intima-media thickness by B-mode ultrasonography.

Translation Cohort Descriptions

MESA. The Multi-Ethnic Study of Atherosclerosis (MESA) was initiated in 2000 to investigate the prevalence, correlates, and progression of subclinical cardiovascular disease (CVD) in a population-based sample of 6,814 men and women aged 45-84 years (8). Participant who were free of clinically apparent CVD were recruited from portions of 6 US communities: Baltimore City and Baltimore County, Maryland; Chicago, Illinois; Forsyth County, North Carolina; Los Angeles County, California; Northern Manhattan and the Bronx, New York; and St. Paul, Minnesota. Each field site recruited from locally available sources, which included lists of residents, lists of dwellings, and telephone exchanges. Twenty-two percent (1494) of the cohort is Hispanic; this analysis was limited to Hispanic participants who were classified as ‘Mexican’ via principal component analysis (all Caribbean Hispanics were excluded in this study). The PCA classified ‘Mexicans’ were mainly self-identified as Mexican, South America, or Central- American. Diabetes was defined as fasting glucose >126 mg/dL or use of hypoglycemic medication at baseline.

MESA Family. The MESA Family Study is an ancillary study to MESA. This study recruited family members specifically for genetic analysis. Participants in the MESA Family Study include 2,128 individuals from 528 families. Similarly, this analysis considers only those families classified as ‘Mexican’ via principal component analysis. Diabetes was defined as fasting glucose ≥126 mg/dL or use of insulin or hypoglycemic medication.

LALES. The Los Angeles Latino Eye Study (LALES) is a population-based study of 6357 Latinos, living in six census tracts in the city of La Puente, Los Angeles County, California (9). All subjects were 40 years of age and older. Written, informed consent was obtained from all participants. The data obtained from LALES have been used to document the prevalence, incidence, and impact of visual impairment in Latinos. GWAS data from 1,768 samples was used for in silico translation.

Starr County. The Starr County study participants were selected from genetic and epidemiological resources developed in the Mexican-American population in Starr County, TX (10). Diabetes was defined using the 1997 ADA criteria. Of 931 successfully genotyped case samples, 837 unrelated individuals were used for in silico translation. A representative type 2

©2014 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db14-0732/-/DC1 SUPPLEMENTARY DATA diabetes control sample was selected from a systematic survey of the primary population centers of Starr County conducted from 2002 to 2006.

WHI. The Women’s Health Initiative (WHI) consisted of multiple components including an observational study and clinical trial cohorts of postmenopausal women in the US (11). All participating institutions obtained Institutional Review Board approval. WHI SHARe included a total sample of 3,642 self-identified Mexican or Hispanic origin subjects from WHI, who had consented to genetic research. Type 2 diabetes was defined by self-report as ever being treated for diabetes (insulin shots or oral hypoglycemic medication) when participants were not pregnant. Medical histories were obtained at baseline and updates on disease status were obtained through self-administered questionnaires or contact with clinical staff every 6 months for the randomized clinical trial or annually for the observational study participants. Prevalent type 2 diabetes was identified from self-report in the baseline medical history. Incident type 2 diabetes was identified as first-time use of hypoglycemic medication after baseline. Both prevalent and incident cases were used for in silico translation.

SIGMA. The Slim Initiative in Genomic Medicine for the Americas (SIGMA) Type 2 Diabetes Consortium was conducted to characterize the genetic basis of type 2 diabetes in Mexican and other Latin American populations (12). Four cohorts contributed to the SIGMA GWAS. Diabetes in Mexico Study: A prospective cohort residing in Mexico City, Mexico, including 690 cases (defined as either a previous T2D diagnosis or fasting glucose levels above 125 mg/dL; individuals with fasting glycemia between 100-125 mg/dL were excluded) and 472 controls who were unrelated healthy subjects older than 45 years and with fasting glucose levels below 100 mg/dL. Mexico City Diabetes Study: A prospective cohort residing in Mexico City, Mexico, including 287 cases (defined using the ADA criteria, fasting glucose 126 mg/dL or more or 2 hr post 75 gr of glucose load 200 or more; in addition, a participant diagnosed as diabetic by a physician and under pharmacologic therapy for diabetes was considered as diabetic regardless the blood glucose levels) and 613 participants without diabetes ever as diagnosed by ADA criteria. UNAM/INCMNSZ Diabetes Study: A prospective cohort residing in Mexico City, Mexico, including 815 cases (defined in accordance with ADA criteria, fasting plasma glucose values ≥126 mg/dL, current treatment with a hypoglycemic agent, or casual glucose values ≥200 mg/dL) and 1,138 control subjects who were recruited from a cohort of adults aged 45 years or

©2014 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db14-0732/-/DC1 SUPPLEMENTARY DATA older among government employees, blue collar workers and subjects seeking for attention in medical units for any condition besides those considered as exclusion criteria. Normoglycemic status was defined as having a fasting plasma glucose concentration < 100 mg/dl and no previous history of hyperglycemia, gestational diabetes or use of metformin. Multiethnic Cohort: A case- control study conducted in Los Angeles, California, USA, including 2056 cases defined as (a) a self-report of diabetes on the baseline questionnaire, 2nd questionnaire or 3rd questionnaire; and (b) self-report of taking medication for T2D at the time of blood draw; and (c) no diagnosis of T1D in the absence of a T2D diagnosis from the OSHPD (California Residents). Controls (n=2,143) were defined as: (a) no self-report of diabetes; (b) no use of medications for T2D at the time of blood draw; and (c) no diabetes diagnosis (type 1 or 2) from the OSHPD, Hawaii Medical Service Association (HMSA) or Kaiser Permanente Hawaii (KPH) registries.

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Clinical characteristics of the Translation cohorts.

Gender Age BMI Sample Size (% female) (range) (range) Genotyping Platform Case Control Case Control Case Control Case Control 57 37 31.7 29.6 Affy 6.0 Starr County, TX 805 340 60 70 (25-87) (26-77) (15.4-60.8) (18.4-55.3) Imputed to 1000G 62 60 34 29.4 Affy 6.0 MESA Family 81 304 62 56 (45-85) (41-90) (22.3-56.3) (17.3-50.1) Imputed to 1000G 64 61 31.6 29.2 Affy 6.0 MESA 221 886 47 52 (45-84) (44-84) (19.6-49.8) (17.6-52.5) Imputed to 1000G 60 60 31.5 28.3 Affy 6.0 WHI 614 2869 100 100 (50-78) (50-79) (18.4-55.3) (17.2-60.9) 58 60 32.4 29.2 Illumina OmniExpress LALES 894 467 57 50 (40-88) (40-92) (17.7–58.5) (14.6-52.1) 58 58 29.5 27.5 Illumina 2.5M SIGMA 3848* 4366* 57 57 (19-89) (34-94) (15.0-67.8) (11.0-57.4) Imputed to 1000G *47% of cases and 51% of controls from Mexico City, Mexico.

REFERENCES

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Patterson N, Aguilar-Delfin I, Martinez-Hernandez A, Centeno-Cruz F, Mendoza-Caamal E, Revilla-Monsalve C, Islas-Andrade S, Cordova E, Rodriguez-Arellano E, Soberon X, Gonzalez-Villalpando ME, Henderson BE, Monroe K, Wilkens L, Kolonel LN, Le Marchand L, Riba L, Ordonez-Sanchez ML, Rodriguez-Guillen R, Cruz-Bautista I, Rodriguez-Torres M, Munoz-Hernandez LL, Saenz T, Gomez D, Alvirde U, Onofrio RC, Brodeur WM, Gage D, Murphy J, Franklin J, Mahan S, Ardlie K, Crenshaw AT, Winckler W, Prufer K, Shunkov MV, Sawyer S, Stenzel U, Kelso J, Lek M, Sankararaman S, Macarthur DG, Derevianko AP, Paabo S, Gopal S, Grammatikos JA, Smith IC, Bullock KH, Deik AA, Souza AL, Pierce KA, Clish CB, Fennell T, Farjoun Y, Genomics Platform B, Gabriel S, Gross MD, Pereira MA, Seielstad M, Koh WP, Tai ES, Flannick J, Fontanillas P, Morris A, Teslovich TM, Atzmon G, Blangero J, Bowden DW, Chambers J, Shin Cho Y, Duggirala R, Glaser B, Hanis C, Kooner J, Laakso M, Lee JY, Ying Teo Y, Wilson JG, Puppala S, Farook VS, Thameem F, Abboud HE, Defronzo RA, Jenkinson CP, Lehman DM, Curran JE, Cortes ML: Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico. Nature, 2013

A) MCRI M DI MCRI 0.172 0.14 M 0.423 DI

B) SI Sg AIRg DI MCRI SI 0.29436 -0.3181 0.421 0.6555 Sg 0.2193 0.5312 0.02974 AIRg 0.4597 -0.32868 DI 0.17068 MCRI

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Supplementary Table 2. Top Discovery hits (P<1.00x10‐4) from the GUARDIAN Consortium. SNPs with evidence of association are tabulated by trait (a. MCRI, b. SI+M, c. SI, d. M, e. AIRg, f. DI, g. SG) in order of genomic position. For each SNP, position from Build hg19 is listed with the nearest annotated RefSeq gene.

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a. MCRI (nmax=3,787)

Direction of Association Ref (BetaGene, HTN, Allele IRAS, IRASFS, Marker Chr Position Gene ref/nonref Freq β±SE Best model MACAD, NIDDM) Best p‐value rs4350219 1 19858807 T/C 0.244 0.24 ± 0.07 dom ++++++ 7.45E‐05 rs11247954 1 26741285 LIN28A A/G 0.179 0.26 ± 0.08 dom +++++‐ 9.76E‐05 rs2278979 1 26877708 RPS6KA1 A/G 0.405 0.31 ± 0.07 dom ++++++ 3.16E‐05 rs3790645 1 26884864 RPS6KA1 A/G 0.421 0.34 ± 0.07 dom ++++++ 6.07E‐06 rs1064196 1 26887592 RPS6KA1 C/T 0.424 0.34 ± 0.07 dom ++++++ 9.75E‐06 rs282177 1 26899125 RPS6KA1 T/C 0.451 0.34 ± 0.08 dom ++‐++? 3.30E‐05 rs6697598 1 241105515 RGS7 C/T 0.042 ‐0.60 ± 0.15 dom ‐‐‐‐‐? 1.88E‐05 rs6718111 2 8201262 LINC00299 C/T 0.487 ‐0.19 ± 0.05 add ‐‐‐‐‐‐ 9.33E‐05 rs1044280 2 8871342 KIDINS220 A/C 0.287 0.19 ± 0.07 dom ++++++ 6.97E‐05 rs7572039 2 31061392 T/G 0.078 0.36 ± 0.10 dom ++++++ 2.74E‐05 rs6745880 2 171105318 MYO3B G/A 0.138 ‐0.30 ± 0.09 dom ‐‐+‐‐‐ 7.34E‐05 rs13024014 2 173530946 T/C 0.023 ‐0.62 ± 0.19 dom ‐+‐‐‐? 9.17E‐05 rs11688831 2 199299078 A/G 0.384 ‐0.14 ± 0.05 add ‐‐‐‐‐‐ 7.08E‐05 rs6741187 2 222065721 T/C 0.010 2.15 ± 0.72 dom +?++?? 8.62E‐05 rs9847647 3 19813225 G/A 0.024 0.58 ± 0.18 dom +++++? 8.50E‐05 rs13321674 3 51704721 C/T 0.009 ‐1.57 ± 0.38 dom ‐?‐‐‐? 7.70E‐05 rs6444236 3 187225416 G/A 0.195 0.22 ± 0.07 dom ++++++ 8.73E‐05 rs16835397 4 4268642 T/C 0.018 ‐0.71 ± 0.21 dom ‐‐‐‐‐? 1.85E‐05 rs2124794 4 62290634 LPHN3 A/G 0.437 ‐0.15 ± 0.05 add ‐‐+‐‐‐ 5.27E‐05 rs6821028 4 62293449 LPHN3 A/C 0.376 ‐0.13 ± 0.05 add ‐‐‐‐‐‐ 1.03E‐04 rs6822279 4 99745705 C/A 0.406 ‐0.21 ± 0.06 add ‐?‐‐‐‐ 2.33E‐05 rs7728957 5 64505977 ADAMTS6 G/T 0.075 0.30 ± 0.10 dom +++++‐ 9.73E‐05 rs7726659 5 74478078 ANKRD31 G/A 0.015 ‐0.90 ± 0.25 dom ‐‐‐‐‐? 4.58E‐05 rs4957640 5 111601600 EPB41L4A C/T 0.048 ‐0.41 ± 0.14 dom ‐‐‐‐‐? 5.85E‐05 rs523848 6 15830025 A/G 0.467 0.20 ± 0.05 add ++++++ 3.48E‐05 rs220933 6 15845797 C/T 0.421 ‐0.19 ± 0.05 add ‐‐‐‐‐+ 9.83E‐05

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rs3749855 6 17283321 RBM24 G/T 0.057 ‐0.52 ± 0.12 dom ‐‐‐‐‐? 5.04E‐06 rs6938736 6 22441270 C/T 0.469 0.22 ± 0.05 add +++++? 7.64E‐05 rs13219760 6 110761189 SLC22A16 G/A 0.111 0.35 ± 0.09 dom +++++‐ 3.15E‐06 rs723685 6 110763875 SLC22A16 G/A 0.114 0.33 ± 0.09 dom +++++‐ 8.04E‐06 rs17166951 7 13302054 A/C 0.06 0.42 ± 0.12 dom +‐+++? 8.25E‐05 rs4629751 7 16825580 G/T 0.284 0.26 ± 0.07 dom ++++++ 9.58E‐05 rs10251809 7 32044030 PDE1C T/C 0.180 ‐0.25 ± 0.08 dom ‐‐‐‐‐‐ 4.28E‐05 rs1597137 8 464083 C8orf42 C/T 0.365 0.18 ± 0.05 add ++++++ 7.91E‐05 rs11136431 8 1791433 ARHGEF10 T/C 0.383 0.14 ± 0.05 add ++++++ 6.90E‐05 rs6651438 8 1794023 ARHGEF10 C/T 0.377 0.20 ± 0.06 add ++++?+ 9.10E‐05 rs13258014 8 4165460 CSMD1 T/C 0.392 0.26 ± 0.07 add +?+++? 7.99E‐05 rs4434590 8 100860657 VPS13B T/C 0.161 ‐0.29 ± 0.08 dom ‐‐‐‐‐‐ 8.09E‐05 rs6468694 8 100865836 VPS13B A/G 0.125 ‐0.34 ± 0.08 dom ‐‐‐‐‐‐ 2.13E‐05 rs4409375 8 100889987 A/C 0.143 ‐0.33 ± 0.08 dom ‐‐‐‐‐‐ 3.64E‐05 rs13253073 8 100897383 COX6C A/C 0.129 ‐0.35 ± 0.08 dom ‐‐‐‐‐‐ 5.89E‐06 rs12544943 8 100903890 COX6C G/A 0.129 ‐0.34 ± 0.08 dom ‐‐‐‐‐‐ 6.90E‐06 rs7851513 9 9842176 PTPRD A/C 0.129 0.38 ± 0.09 dom ++++++ 2.72E‐05 rs7025024 9 25816219 G/A 0.342 ‐0.18 ± 0.05 add ‐‐‐‐‐‐ 8.33E‐05 rs6602203 10 17596121 T/C 0.403 ‐0.32 ± 0.07 dom ‐‐‐‐‐‐ 4.80E‐06 rs10825203 10 55798117 PCDH15 A/C 0.268 0.23 ± 0.07 dom ++++++ 5.80E‐05 rs1911409 10 55806316 PCDH15 G/A 0.243 0.23 ± 0.07 dom ++++++ 5.05E‐05 rs716594 10 112006311 MXI1 A/G 0.019 ‐0.65 ± 0.21 dom ‐‐‐‐‐? 3.84E‐05 rs11016332 10 130363802 G/A 0.008 2.07 ± 0.49 dom +?++?? 4.72E‐05 rs7944706 11 10331311 A/G 0.285 0.31 ± 0.07 dom ++++++ 4.70E‐05 rs2449501 11 20044696 NAV2 G/A 0.198 ‐0.22 ± 0.07 dom ‐‐+‐‐‐ 1.27E‐05 rs16918932 11 29309078 G/T 0.003 3.45 ± 0.84 dom +??+?? 4.38E‐05 rs10400279 11 36270057 G/A 0.058 ‐0.31 ± 0.12 dom ‐‐‐‐‐? 8.87E‐05 rs7124 11 57174559 PRG2 A/G 0.003 8.24 ± 1.81 dom ??+??? 8.33E‐06 rs1784499 11 73359236 PLEKHB1 T/C 0.018 0.97 ± 0.22 dom +++++? 5.50E‐06 rs2510094 11 102981300 DYNC2H1 C/T 0.044 0.45 ± 0.14 dom +++++? 5.69E‐05 rs1334870 13 54838415 A/C 0.309 ‐0.26 ± 0.07 dom ‐‐‐‐‐+ 8.31E‐05 rs9565115 13 75269569 G/A 0.364 ‐0.22 ± 0.07 dom ‐‐‐‐‐? 9.23E‐05 rs9530368 13 75270057 C/A 0.358 ‐0.22 ± 0.07 dom ‐‐‐‐‐? 6.37E‐05

SUPPLEMENTARY DATA

rs6576136 14 28737460 C/T 0.381 0.18 ± 0.06 add +++++? 9.18E‐05 rs2210313 14 40835874 G/A 0.085 0.32 ± 0.10 dom +++++? 1.01E‐04 rs2031271 14 42344822 LRFN5 C/A 0.158 0.23 ± 0.08 dom ++++++ 3.73E‐05 rs8003026 14 72482760 RGS6 G/T 0.003 3.07 ± 0.75 dom +?++?? 4.04E‐05 rs10147864 14 97919601 C/T 0.005 3.27 ± 0.86 dom +??+?? 6.21E‐05 rs637568 15 29692391 FAM189A1 G/A 0.027 ‐0.46 ± 0.17 dom ‐‐‐‐‐? 8.96E‐05 rs11853158 15 56364902 A/G 0.320 ‐0.18 ± 0.06 add ‐‐‐‐‐+ 6.96E‐05 rs2718934 15 56557418 G/A 0.466 ‐0.17 ± 0.05 add ‐‐+‐‐+ 2.50E‐05 rs8032549 15 56572176 G/A 0.328 ‐0.18 ± 0.05 add ‐‐‐‐‐+ 7.52E‐05 rs11857306 15 56746003 MNS1 C/A 0.341 ‐0.19 ± 0.05 add ‐‐‐‐‐+ 7.27E‐05 rs12441883 15 58456850 ALDH1A2 A/G 0.370 0.23 ± 0.07 dom +++++‐ 3.60E‐05 rs7172809 15 77819676 A/G 0.484 0.18 ± 0.05 add +++++? 9.20E‐06 rs2701405 15 87539918 AGBL1 A/C 0.486 ‐0.23 ± 0.06 add ‐‐‐‐?‐ 2.15E‐05 rs781856 17 3950224 ZZEF1 A/G 0.014 0.94 ± 0.25 dom +++++? 7.06E‐06 rs4790177 17 4067900 ANKFY1 T/C 0.012 0.95 ± 0.28 dom +++++? 4.21E‐05 rs2325989 17 4199320 UBE2G1 G/A 0.015 1.10 ± 0.26 dom ++++‐? 5.63E‐05 rs1986507 17 10082301 GAS7 A/G 0.152 ‐0.26 ± 0.08 dom ‐‐+‐‐‐ 9.92E‐05 rs4791426 17 10752513 A/G 0.098 ‐0.16 ± 0.09 dom ‐‐‐‐‐‐ 6.50E‐05 rs2274892 17 16852027 TNFRSF13B G/T 0.372 ‐0.16 ± 0.05 add ‐‐‐‐‐+ 7.67E‐05 rs16530 17 37357034 RPL19 T/C 0.099 ‐0.34 ± 0.09 dom ‐‐‐‐‐‐ 6.22E‐05 rs9912528 17 77387550 RBFOX3 C/T 0.150 0.27 ± 0.08 dom ++++++ 1.65E‐05 rs2339345 18 49957255 DCC A/C 0.343 ‐0.25 ± 0.06 add ‐‐‐‐‐? 7.80E‐06 rs11872993 18 71104519 T/C 0.006 ‐1.74 ± 0.49 dom ‐?‐+‐? 8.65E‐05 rs2276210 18 74587458 ZNF236 A/G 0.015 ‐0.89 ± 0.24 dom ‐‐‐‐‐? 9.92E‐05 rs3786947 19 3114229 GNA11 A/G 0.222 ‐0.28 ± 0.07 dom ‐‐‐‐‐+ 1.21E‐05 rs2302063 19 3150418 GNA15 A/C 0.336 ‐0.29 ± 0.07 dom ‐‐‐‐‐‐ 7.31E‐08 rs7247790 19 5311412 PTPRS G/T 0.185 ‐0.28 ± 0.08 dom ‐‐‐‐‐‐ 6.88E‐05

SUPPLEMENTARY DATA

b. SI+M (nmax=4,153)

Direction of Association (BetaGene, HTN, IRAS, IRASFS, Ref MACAD, Allele Best NIDDM, Best p‐ Marker Chr Position Gene ref/nonref Freq β±SE SI β±SE M model TRIPOD) value rs10492966 1 8598005 RERE T/C 0.258 0.10 ± 0.08 18.42 ± 5.67 dom +++++‐+ 1.01E‐04 rs3766466 1 54505437 TMEM59 A/C 0.047 ‐0.21 ± 0.16 ‐25.2 ± 9.4 dom ‐‐+‐‐0‐ 7.39E‐05 rs6685355 1 79458347 ELTD1 C/A 0.326 ‐0.13 ± 0.06 ‐18.36 ± 4.25 add +‐‐‐‐‐‐ 6.27E‐05 rs7411591 1 86683345 A/G 0.119 0.26 ± 0.10 13.79 ± 6.51 dom +++++‐+ 6.56E‐05 rs1507290 1 86684713 G/A 0.206 0.23 ± 0.09 11.58 ± 5.6 dom +++++‐+ 6.54E‐05 rs4658244 1 92069188 A/G 0.359 ‐0.06 ± 0.06 ‐13.2 ± 4.07 add ‐‐+‐‐‐‐ 9.64E‐05 rs1256941 1 201392764 TNNI1 A/C 0.128 0.33 ± 0.09 7.02 ± 6.36 dom +++++‐+ 9.52E‐05 rs9427477 1 202032235 T/G 0.345 ‐0.21 ± 0.06 ‐9.95 ± 4.09 add ‐‐‐‐‐‐‐ 1.03E‐04 rs6719442 2 2722295 A/G 0.185 ‐0.29 ± 0.08 ‐11.55 ± 5.87 dom ‐‐‐‐‐+‐ 1.53E‐06 rs896232 2 2732877 T/C 0.282 ‐0.2 ± 0.06 ‐12.27 ± 4.23 add ‐‐‐‐‐‐‐ 1.26E‐06 rs12620694 2 2763051 A/G 0.170 ‐0.38 ± 0.08 ‐12.42 ± 5.82 dom ‐‐‐‐‐+‐ 3.29E‐06 rs13411840 2 29973281 ALK C/A 0.046 ‐0.28 ± 0.16 ‐33.75 ± 8.94 dom ‐‐‐‐‐‐‐ 2.69E‐06 rs4233921 2 37354149 EIF2AK2 A/G 0.301 ‐0.12 ± 0.07 ‐13.79 ± 4.09 add ‐‐+‐‐‐‐ 2.11E‐06 rs1044158 2 85826132 TMEM150A A/G 0.303 ‐0.14 ± 0.08 ‐16.93 ± 5.39 dom ‐‐‐‐‐‐‐ 4.74E‐05 rs6733550 2 85828014 TMEM150A G/T 0.303 ‐0.13 ± 0.08 ‐17.47 ± 5.4 dom ‐‐‐‐‐‐‐ 5.44E‐05 rs207910 2 217018422 XRCC5 G/A 0.150 0.09 ± 0.09 17.1 ± 6.27 dom +++++++ 4.51E‐05 rs7426289 2 218966315 T/C 0.490 0.15 ± 0.06 11.06 ± 3.81 add ++++++‐ 5.47E‐05 rs6723449 2 218997580 CXCR2 C/T 0.474 0.15 ± 0.06 10.56 ± 3.82 add ++‐+++‐ 6.39E‐05 rs6767721 3 87630433 G/T 0.071 0.29 ± 0.12 14.74 ± 8 dom +++++++ 5.90E‐05 rs843532 3 196482211 PAK2 C/T 0.057 0.29 ± 0.12 29.38 ± 9.08 dom +++++++ 9.23E‐06 rs10007938 4 32452973 G/A 0.241 0.20 ± 0.08 15.78 ± 5.5 dom ++++++‐ 4.74E‐05 rs10023791 4 99425353 TSPAN5 A/G 0.426 0.15 ± 0.06 9.35 ± 3.86 add +‐+++++ 4.31E‐05 rs1602084 4 128843480 MFSD8 G/A 0.042 0.43 ± 0.16 20.7 ± 9.19 dom +++++++ 5.20E‐07

SUPPLEMENTARY DATA

rs34766684 4 146023924 ABCE1 C/T 0.008 0.79 ± 0.3 43.66 ± 28.57 dom ++++00+ 5.11E‐05 rs6815953 4 183109012 ODZ3 T/G 0.431 0.19 ± 0.06 9.47 ± 3.97 add +++++++ 3.14E‐05 rs16894006 5 24833120 C/T 0.020 ‐0.48 ± 0.18 ‐31.85 ± 15.38 dom ‐‐‐‐‐0‐ 4.38E‐05 rs7732393 5 114018075 AK097686 C/T 0.087 0.30 ± 0.10 16.44 ± 7.86 dom +++++0‐ 4.40E‐05 rs7724522 5 142081559 C/T 0.038 ‐0.57 ± 0.13 ‐18.32 ± 11.87 dom ‐‐‐‐+0+ 5.11E‐05 rs29848 5 151449400 AK001582 T/G 0.328 0.17 ± 0.06 15.44 ± 4.21 add ++++++‐ 5.08E‐05 rs3129963 6 32380208 G/A 0.138 0.28 ± 0.09 22.25 ± 6.51 dom +++++++ 4.47E‐05 rs9268530 6 32383223 C/T 0.128 0.27 ± 0.09 23.44 ± 6.66 dom +++++++ 3.71E‐05 rs3135382 6 32383441 G/T 0.128 0.27 ± 0.09 23.09 ± 6.67 dom +++++++ 4.41E‐05 rs2001098 6 32383837 A/G 0.128 0.27 ± 0.09 23.51 ± 6.66 dom +++++++ 3.82E‐05 rs2001097 6 32383858 T/G 0.128 0.27 ± 0.09 23.45 ± 6.65 dom +++++++ 3.69E‐05 rs2227138 6 32384500 T/C 0.110 0.22 ± 0.10 24.9 ± 7 dom +++++++ 7.04E‐05 rs3135376 6 32385470 G/A 0.128 0.27 ± 0.09 23.45 ± 6.65 dom +++++++ 3.69E‐05 rs3135375 6 32385573 A/G 0.128 0.27 ± 0.09 23.41 ± 6.66 dom +++++++ 3.78E‐05 rs3135374 6 32385605 A/C 0.128 0.27 ± 0.09 23.45 ± 6.65 dom +++++++ 3.69E‐05 rs3135372 6 32385782 A/C 0.128 0.27 ± 0.09 23.45 ± 6.65 dom +++++++ 4.21E‐05 rs2187820 6 32385873 T/C 0.128 0.27 ± 0.09 23.46 ± 6.66 dom +++++++ 3.71E‐05 rs2395161 6 32387752 C/A 0.128 0.27 ± 0.09 23.45 ± 6.65 dom +++++++ 3.79E‐05 rs2395162 6 32387780 T/G 0.128 0.27 ± 0.09 23.45 ± 6.65 dom +++++++ 3.70E‐05 rs3135366 6 32388709 C/T 0.129 0.27 ± 0.09 23.27 ± 6.65 dom +++++++ 3.61E‐05 rs3135356 6 32391516 A/G 0.127 0.28 ± 0.09 20.36 ± 6.67 dom +++++++ 1.01E‐04 rs1041885 6 32412809 HLA‐DRA A/T 0.140 0.27 ± 0.09 20.45 ± 6.51 dom +++++++ 1.01E‐04 rs7749057 6 32448904 G/A 0.131 0.21 ± 0.09 21.37 ± 6.6 dom +++++++ 4.18E‐05 rs7785730 7 28096199 JAZF1 G/A 0.131 ‐0.17 ± 0.09 ‐17.84 ± 6.61 dom ‐‐‐‐‐+‐ 8.23E‐05 rs24003 7 30748323 INMT C/T 0.471 ‐0.14 ± 0.06 ‐12.91 ± 4.15 add ‐‐‐‐‐0+ 6.24E‐05 rs2726051 7 36155071 C/A 0.223 0.25 ± 0.08 14.29 ± 5.53 dom +++++++ 5.27E‐05 rs17141982 7 70133502 AUTS2 T/C 0.340 0.20 ± 0.08 9.1 ± 5.58 dom ++++++‐ 9.89E‐05 rs10268984 7 98963340 ARPC1A T/C 0.103 ‐0.20 ± 0.10 ‐16.38 ± 7.12 dom ‐‐‐‐‐‐‐ 5.59E‐05 rs3177186 7 98984399 ARPC1A T/C 0.105 ‐0.19 ± 0.10 ‐16.45 ± 7.12 dom ‐‐‐‐‐‐‐ 6.58E‐05 rs7799219 7 123895098 EU233817 T/C 0.228 0.24 ± 0.08 14.82 ± 5.58 dom +++++++ 6.95E‐05 rs12682418 8 62891832 A/G 0.065 0.24 ± 0.12 25.42 ± 8.47 dom +++++++ 1.01E‐04 rs12675420 8 62924308 T/C 0.069 0.27 ± 0.12 23.61 ± 8.33 dom +++++++ 8.87E‐05 rs6475448 9 20497142 MLLT3 G/A 0.303 ‐0.06 ± 0.06 ‐18.68 ± 4.43 add ‐‐‐+‐0‐ 3.31E‐05

rs10966384 9 24672959 C/T 0.057 ‐0.24 ± 0.12 ‐23.3 ± 9.47 dom ‐‐‐‐‐‐‐ 9.06E‐05 rs4817 9 33917498 UBE2R2 C/T 0.314 ‐0.14 ± 0.06 ‐8.04 ± 4.3 add ‐‐‐‐‐‐+ 7.96E‐05 rs10739874 9 105991203 BC035187 C/T 0.092 0.22 ± 0.10 27.16 ± 8.11 dom +++++0+ 1.00E‐04 rs4837024 9 128739400 T/C 0.465 0.16 ± 0.09 22.18 ± 5.96 dom +++++++ 8.73E‐05 rs10904919 10 17334745 T/C 0.374 ‐0.27 ± 0.06 ‐10.32 ± 10.74 add ‐0‐‐0‐‐ 1.03E‐04 rs2688789 10 17733014 STAM G/A 0.419 ‐0.08 ± 0.06 ‐14.73 ± 3.84 add ‐‐‐+‐‐‐ 9.47E‐05 rs12413935 10 85453920 G/T 0.020 ‐0.73 ± 0.23 ‐44.19 ± 19.71 dom ‐‐‐‐00+ 4.11E‐05 rs1223629 10 95906315 PLCE1 A/G 0.039 ‐0.74 ± 0.17 ‐17.55 ± 11.1 dom ‐‐‐‐‐0‐ 3.05E‐06 rs10870303 10 134191811 LRRC27 G/A 0.429 ‐0.13 ± 0.06 ‐4.07 ± 3.89 add ‐‐+‐+‐‐ 1.02E‐04 rs10160242 11 108498885 C/T 0.058 0.41 ± 0.11 5.25 ± 9.53 dom +‐+++0+ 6.26E‐05 rs948178 11 113195595 TTC12 A/G 0.337 0.21 ± 0.08 13.09 ± 5.42 dom +++++++ 9.43E‐05 rs3781827 11 121411041 SORL1 G/A 0.434 0.10 ± 0.06 10.77 ± 5.33 add +0++++‐ 6.12E‐05 rs1479451 12 23836547 SOX5 A/C 0.199 0.21 ± 0.08 10.02 ± 5.65 dom +++++++ 3.79E‐05 rs11180162 12 75081042 C/T 0.189 0.20 ± 0.08 7.9 ± 5.74 dom +++++‐+ 8.30E‐05 rs11108203 12 96100594 NTN4 T/C 0.069 ‐0.47 ± 0.12 ‐17.93 ± 8.36 dom ‐‐‐‐‐0‐ 4.07E‐05 rs10860482 12 100038835 ANKS1B C/T 0.372 0.09 ± 0.06 13.33 ± 4.09 add +++++++ 9.80E‐05 rs7974375 12 118585698 T/G 0.104 ‐0.13 ± 0.10 ‐23.88 ± 6.93 dom ‐‐+‐‐‐+ 8.96E‐05 rs17512574 12 118788003 TAOK3 T/C 0.110 ‐0.08 ± 0.09 ‐29.28 ± 6.72 dom ‐‐+‐‐‐+ 3.19E‐05 rs673078 12 118791441 TAOK3 C/A 0.125 ‐0.08 ± 0.09 ‐30.26 ± 6.55 dom ‐‐+‐‐‐+ 4.71E‐06 rs884844 12 118814838 SUDS3 T/C 0.113 ‐0.07 ± 0.09 ‐28.67 ± 6.67 dom ‐‐+‐‐‐+ 6.71E‐05 rs7305647 12 118855566 SUDS3 A/G 0.105 ‐0.08 ± 0.09 ‐29.15 ± 6.88 dom ‐‐+‐‐‐+ 5.90E‐05 rs4772128 13 99385553 SLC15A1 A/G 0.029 ‐0.51 ± 0.18 ‐20.52 ± 12.21 dom ‐‐‐‐‐0‐ 5.57E‐05 rs12717423 14 52940827 TXNDC16 G/A 0.253 ‐0.21 ± 0.08 ‐10.05 ± 5.5 dom ‐‐‐‐‐‐‐ 3.87E‐05 rs10129385 14 52959478 TXNDC16 C/T 0.253 ‐0.21 ± 0.08 ‐9.92 ± 5.48 dom ‐‐‐‐‐‐‐ 5.48E‐05 rs2617235 15 42758738 ZFP106 C/T 0.366 0.14 ± 0.06 14.3 ± 4.02 add +++++++ 9.05E‐05 rs10454039 15 42832534 C/T 0.429 0.14 ± 0.06 13.79 ± 3.94 add +++++++ 7.78E‐06 rs10851411 15 42859235 HAUS2 T/G 0.428 0.14 ± 0.06 12.78 ± 3.93 add +++++++ 5.64E‐06 rs2241998 15 42869028 STARD9 A/G 0.417 0.12 ± 0.06 11.94 ± 3.93 add +++++++ 7.70E‐05 rs7497796 15 55136506 A/C 0.376 0.17 ± 0.08 21.92 ± 5.65 dom +++++++ 2.63E‐05 rs12438945 15 55226570 C/A 0.230 0.19 ± 0.08 23.49 ± 5.54 dom +++++++ 5.38E‐05 rs11631474 15 67934167 MAP2K5 G/A 0.262 ‐0.24 ± 0.08 ‐6.71 ± 5.56 dom ‐‐‐‐‐+‐ 3.72E‐05 rs884202 15 68054388 MAP2K5 A/G 0.381 ‐0.10 ± 0.06 ‐8.87 ± 4.16 add ‐‐‐‐‐‐‐ 9.64E‐05 rs7178383 15 99159956 C/T 0.332 ‐0.16 ± 0.08 ‐19.57 ± 5.48 dom ‐‐‐‐‐‐+ 8.42E‐05

SUPPLEMENTARY DATA

rs4624233 17 38955961 KRT28 A/G 0.137 ‐0.28 ± 0.09 ‐17.68 ± 6.28 dom ‐‐‐‐+‐+ 2.46E‐05 rs7219451 17 38957002 C/T 0.380 ‐0.17 ± 0.06 ‐15.91 ± 4.04 add ‐‐‐‐‐‐+ 3.92E‐06 rs10558 17 38991003 TMEM99 C/T 0.138 ‐0.31 ± 0.09 ‐16.19 ± 6.25 dom ‐‐‐‐+‐+ 1.48E‐05 rs9303297 17 39005990 T/C 0.138 ‐0.31 ± 0.09 ‐17.14 ± 6.28 dom ‐‐‐‐+‐+ 9.98E‐06 rs3760333 17 39023875 C/T 0.173 ‐0.31 ± 0.09 ‐13.41 ± 5.81 dom ‐‐‐‐+‐‐ 2.09E‐05 rs2291447 17 43212963 ACBD4 T/G 0.346 ‐0.24 ± 0.06 ‐10.49 ± 4.16 add ‐‐‐‐‐‐‐ 7.95E‐05 rs2192990 17 68801676 A/C 0.122 0.12 ± 0.10 15.54 ± 6.44 dom +++++++ 1.04E‐04 rs691336 17 76518426 DNAH17 T/C 0.263 ‐0.27 ± 0.08 ‐7.68 ± 5.54 dom ‐‐‐‐+‐‐ 2.77E‐05 rs759635 19 3351890 C/T 0.460 0.20 ± 0.06 12.32 ± 3.92 add +++++++ 1.20E‐05 rs3108582 19 37221835 G/A 0.293 0.21 ± 0.08 17.6 ± 5.5 dom +++++++ 1.01E‐04 rs6133145 20 4576230 A/C 0.400 0.15 ± 0.08 13.34 ± 6.02 dom +++++0‐ 4.52E‐05 rs6139486 20 4578080 A/G 0.366 0.14 ± 0.08 12.06 ± 5.52 dom ++++++‐ 7.29E‐05 rs6075733 20 20856254 C/T 0.346 ‐0.06 ± 0.06 ‐18.29 ± 4.13 add ‐‐+‐‐‐‐ 3.40E‐05 rs8130631 21 35535498 T/C 0.101 0.26 ± 0.10 16.36 ± 7.38 dom +++++0+ 5.21E‐05 rs1061325 22 19184095 CLTCL1 C/T 0.451 0.12 ± 0.10 ‐13.72 ± 9.23 rec ‐‐‐‐00‐ 9.96E‐05

SUPPLEMENTARY DATA

c. SI (nmax=2,549)

Direction of Association (BetaGene, IRAS, Ref Allele IRASFS, Best p‐ Marker Chr Position Gene ref/nonref Freq β±SE Best model TRIPOD) value rs880554 1 19954014 MINOS1 T/G 0.278 0.21 ± 0.08 dom +‐++ 3.87E‐05 rs17385225 1 164475201 A/G 0.134 0.28 ± 0.10 dom ++++ 4.87E‐05 rs1256941 1 201392764 TNNI1 A/C 0.126 0.33 ± 0.09 dom ++++ 1.03E‐04 rs6719442 2 2722295 A/G 0.18 ‐0.29 ± 0.08 dom ‐‐‐‐ 1.53E‐05 rs12620694 2 2763051 A/G 0.162 ‐0.38 ± 0.08 dom ‐‐‐‐ 3.42E‐05 rs1978648 2 43371542 T/C 0.328 0.2 ± 0.06 add ++++ 5.31E‐07 rs4952971 2 43373119 A/G 0.438 0.18 ± 0.06 add ++++ 2.31E‐05 rs10167465 2 43397176 G/A 0.419 0.19 ± 0.06 add ++++ 9.30E‐05 rs12464602 2 43397614 G/A 0.424 0.38 ± 0.10 rec ++++ 7.28E‐06 rs1044710 2 211297355 LANCL1 A/G 0.395 ‐0.2 ± 0.06 add ‐‐‐‐ 8.93E‐05 rs6782551 3 74922055 A/G 0.014 0.57 ± 0.22 dom ++++ 9.04E‐05 rs1872552 3 85049088 CADM2 A/G 0.444 ‐0.20 ± 0.06 add ‐‐‐‐ 8.59E‐05 rs716975 4 38349236 T/C 0.226 ‐0.27 ± 0.08 dom ‐‐‐‐ 9.86E‐06 rs7690543 4 68056613 T/C 0.177 0.28 ± 0.09 dom ++++ 2.34E‐06 rs1848056 4 125755019 T/C 0.484 0.09 ± 0.06 add +‐++ 3.21E‐05 rs9997902 4 125763629 A/G 0.49 0.10 ± 0.06 add +‐++ 2.29E‐05 rs1602084 4 128843480 MFSD8 G/A 0.038 0.43 ± 0.16 dom ++++ 3.10E‐06 rs11943562 4 167652786 C/T 0.130 ‐0.25 ± 0.09 dom ‐‐‐+ 6.27E‐05 rs17069175 4 181226698 A/G 0.241 ‐0.27 ± 0.08 dom ‐‐‐‐ 7.04E‐05 rs6868526 5 5399472 C/T 0.188 0.27 ± 0.09 dom +++‐ 2.22E‐05 rs16875556 5 5402163 A/G 0.167 0.26 ± 0.09 dom +++‐ 3.47E‐05 rs7717247 5 27839258 C/A 0.136 ‐0.33 ± 0.09 dom ‐‐‐+ 4.16E‐05 rs462647 5 81080808 C/T 0.334 0.32 ± 0.08 dom ++++ 8.79E‐05 rs6880017 5 81185254 G/A 0.314 ‐0.17 ± 0.06 add ‐‐‐+ 7.51E‐05 rs17155849 5 103142399 T/C 0.290 ‐0.29 ± 0.08 dom ‐‐‐‐ 7.13E‐05

SUPPLEMENTARY DATA

rs1898910 5 124555847 A/C 0.161 ‐0.38 ± 0.09 dom ‐‐‐+ 6.60E‐06 rs1042711 5 148206348 SH3TC2 C/T 0.212 0.31 ± 0.08 dom ++++ 9.07E‐05 rs12194985 6 6892411 T/G 0.032 ‐0.40 ± 0.17 dom ‐‐‐‐ 8.50E‐05 rs10080664 6 15864284 A/G 0.384 0.15 ± 0.06 add ++++ 9.95E‐05 rs4716224 6 18161563 KDM1B A/G 0.306 ‐0.19 ± 0.08 dom ‐‐‐‐ 9.37E‐05 rs724941 6 76723011 IMPG1 C/T 0.446 0.17 ± 0.06 add +++‐ 9.34E‐05 rs2148261 6 76736996 IMPG1 T/C 0.449 0.15 ± 0.06 add ++++ 3.41E‐05 rs943086 6 76755221 IMPG1 G/A 0.449 0.15 ± 0.06 add ++++ 6.49E‐05 rs196705 6 80138778 T/C 0.123 ‐0.36 ± 0.10 dom ‐‐‐+ 9.35E‐06 rs196701 6 80147187 C/T 0.128 ‐0.35 ± 0.10 dom ‐‐‐‐ 1.37E‐06 rs17062582 6 133789961 EYA4 A/G 0.144 ‐0.18 ± 0.09 dom ‐‐‐‐ 1.02E‐04 rs7803642 7 21641629 DNAH11 T/C 0.321 ‐0.18 ± 0.06 add ‐‐‐‐ 9.92E‐05 rs9406428 9 11463799 C/T 0.132 0.33 ± 0.09 dom ++++ 7.63E‐05 rs10964496 9 20248264 A/G 0.091 0.34 ± 0.10 dom +++‐ 5.14E‐05 rs10811340 9 20283406 G/A 0.098 0.27 ± 0.10 dom +++‐ 7.35E‐05 rs1581979 9 23407435 C/A 0.310 ‐0.18 ± 0.06 add ‐‐‐‐ 8.14E‐05 rs10780305 9 81978708 A/G 0.431 0.15 ± 0.06 add ++++ 8.69E‐06 rs10867395 9 82118185 C/T 0.304 0.13 ± 0.08 dom ++++ 6.04E‐05 rs1885984 9 119078249 PAPPA T/C 0.009 ‐0.79 ± 0.25 dom ‐?‐‐ 9.14E‐05 rs2819042 10 10230151 A/C 0.455 ‐0.18 ± 0.06 add ‐‐‐‐ 1.38E‐05 rs2819039 10 10232363 C/T 0.456 ‐0.19 ± 0.06 add ‐‐‐‐ 1.61E‐05 rs359297 10 17333680 A/G 0.213 ‐0.28 ± 0.08 dom ‐‐‐‐ 5.10E‐05 rs11817459 10 17594247 G/T 0.396 ‐0.14 ± 0.06 add ‐‐‐‐ 7.01E‐05 rs12256421 10 17614097 A/G 0.387 ‐0.2 ± 0.06 add ‐‐‐‐ 9.07E‐05 rs945296 10 26704514 C/T 0.305 0.2 ± 0.06 add ++++ 1.02E‐04 rs1223629 10 95906315 PLCE1 A/G 0.038 ‐0.74 ± 0.17 dom ‐‐‐‐ 4.72E‐06 rs10870301 10 134186772 LRRC27 C/T 0.435 ‐0.12 ± 0.06 add ‐+‐‐ 7.93E‐05 rs4443996 10 134191005 LRRC27 C/A 0.441 ‐0.11 ± 0.06 add ‐+‐‐ 9.70E‐05 rs10870302 10 134191738 LRRC27 T/G 0.436 ‐0.13 ± 0.06 add ‐+‐‐ 9.64E‐05 rs10870303 10 134191811 LRRC27 G/A 0.436 ‐0.13 ± 0.06 add ‐+‐‐ 6.94E‐05 rs4568920 10 134324451 T/C 0.077 ‐0.29 ± 0.12 dom ‐+‐‐ 7.13E‐05 rs7117567 11 7715079 OVCH2 G/A 0.356 ‐0.21 ± 0.06 add ‐‐‐‐ 8.87E‐05 rs121704 11 17904634 SERGEF G/A 0.474 0.15 ± 0.06 add +++‐ 5.97E‐05

SUPPLEMENTARY DATA

rs10160242 11 108498885 C/T 0.060 0.41 ± 0.11 dom ++++ 4.33E‐06 rs2368785 12 260682 IQSEC3 C/T 0.150 0.19 ± 0.09 dom +‐++ 4.51E‐05 rs1947234 12 39450491 A/C 0.197 0.13 ± 0.08 dom ++++ 7.83E‐05 rs7136587 12 39487541 A/G 0.136 0.17 ± 0.09 dom +‐++ 1.01E‐04 rs10785139 12 75089475 C/T 0.307 0.19 ± 0.06 add ++++ 5.31E‐05 rs9554019 13 27951711 A/G 0.061 ‐0.36 ± 0.13 dom ‐‐‐‐ 2.76E‐05 rs17376318 13 108013050 FAM155A C/T 0.119 ‐0.41 ± 0.10 dom ‐‐‐‐ 4.00E‐05 rs9559508 13 109805793 MYO16 T/C 0.240 ‐0.17 ± 0.08 dom ‐+‐‐ 9.54E‐05 rs2383580 14 34749512 A/C 0.161 0.29 ± 0.08 dom ++++ 7.06E‐05 rs10129961 14 34767305 A/G 0.146 0.33 ± 0.09 dom ++++ 2.25E‐05 rs17123946 14 51929722 G/A 0.251 ‐0.29 ± 0.08 dom ‐‐‐‐ 9.17E‐05 rs10498430 14 51942961 T/C 0.243 ‐0.30 ± 0.08 dom ‐‐‐‐ 4.05E‐05 rs17123969 14 51946458 G/A 0.245 ‐0.30 ± 0.08 dom ‐‐‐‐ 5.36E‐05 rs4901281 14 52980190 TXNDC16 A/C 0.148 ‐0.29 ± 0.09 dom ‐‐‐‐ 5.98E‐05 rs11631474 15 67934167 MAP2K5 G/A 0.272 ‐0.24 ± 0.08 dom ‐‐‐‐ 3.36E‐05 rs896598 15 74036629 C15orf59 A/G 0.119 0.37 ± 0.10 dom ++++ 5.83E‐07 rs4887140 15 74046663 G/T 0.143 0.31 ± 0.10 add ++++ 6.91E‐08 rs2415230 15 74059081 A/G 0.171 0.26 ± 0.09 dom ++++ 7.20E‐06 rs27230 16 3434699 ZNF434 G/A 0.107 ‐0.23 ± 0.09 dom ‐‐‐+ 5.85E‐05 rs16530 17 37357034 RPL19 T/C 0.102 ‐0.33 ± 0.10 dom ‐‐‐‐ 2.97E‐05 rs691336 17 76518426 DNAH17 T/C 0.261 ‐0.27 ± 0.08 dom ‐‐‐‐ 2.91E‐05 rs6139479 20 4566415 A/G 0.308 0.23 ± 0.08 dom ++++ 9.73E‐05 rs6100794 20 58799036 AX747739 T/C 0.012 ‐0.63 ± 0.24 dom ‐‐‐+ 4.80E‐06

SUPPLEMENTARY DATA

d. M (nmax=1,604)

Direction of Association (HTN, Ref Allele Best MACAD, Best p‐ Marker Chr Position Gene ref/nonref Freq β±SE model NIDDM) value rs2235438 1 4849384 BC037321 T/C 0.357 15.45 ± 4.12 add +++ 3.95E‐05 rs2744761 1 26040514 MAN1C1 G/T 0.229 ‐21.75 ± 5.8 dom ‐‐‐ 5.54E‐05 rs11209072 1 67908644 G/A 0.393 ‐22.54 ± 5.52 dom ‐‐‐ 7.60E‐05 rs12135476 1 69649328 A/G 0.118 ‐31.54 ± 6.61 dom ‐‐‐ 3.75E‐06 rs10493454 1 69659840 G/A 0.136 ‐29.41 ± 6.22 dom ‐‐‐ 6.08E‐06 rs4650135 1 69684997 C/T 0.157 ‐29.56 ± 6.00 dom ‐‐‐ 2.31E‐06 rs6685355 1 79458347 ELTD1 C/A 0.311 ‐18.36 ± 4.25 add ‐‐‐ 1.33E‐05 rs1886644 1 85350658 LPAR3 C/A 0.295 ‐22.90 ± 5.42 dom ‐‐‐ 6.28E‐06 rs13375429 1 112103322 ADORA3 A/G 0.015 107.86 ± 27.77 dom ?+? 1.03E‐04 rs11582424 1 154363985 C/A 0.292 20.19 ± 5.41 dom +++ 1.02E‐04 rs6665426 1 200148319 A/G 0.309 ‐19.74 ± 5.46 dom ‐‐‐ 8.31E‐05 rs17047682 1 218523025 TGFB2 G/A 0.078 ‐31.01 ± 7.63 dom ‐‐‐ 1.19E‐05 rs6681101 1 242243325 A/G 0.401 ‐23.30 ± 6.08 dom ‐‐? 9.80E‐05 rs10926618 1 242251696 PLD5 T/C 0.386 ‐23.32 ± 6.02 dom ‐‐? 8.79E‐05 rs7558483 2 11537452 T/C 0.244 ‐19.51 ± 5.58 dom ‐‐‐ 7.39E‐05 rs17031893 2 44283172 G/A 0.101 27.41 ± 6.78 dom +++ 9.83E‐05 rs7595513 2 46687867 G/A 0.198 ‐22.09 ± 5.80 dom ‐‐‐ 6.66E‐05 rs2138397 2 86974049 RMND5A A/G 0.442 ‐24.39 ± 5.86 dom ‐‐‐ 3.71E‐05 rs10179986 2 134864344 G/A 0.467 ‐17.78 ± 3.89 add ‐‐‐ 7.95E‐06 rs1996589 2 134865196 C/T 0.230 ‐21.95 ± 5.57 dom ‐‐‐ 3.97E‐05 rs4953902 2 134876049 C/A 0.140 ‐25.81 ± 6.31 dom ‐‐‐ 1.41E‐05 rs1111961 2 134880830 G/A 0.158 ‐25.37 ± 6.10 dom ‐‐‐ 1.40E‐05 rs13030335 2 142231898 LRP1B A/G 0.382 ‐33.45 ± 8.00 rec ‐‐? 4.13E‐05 rs10178963 2 142349495 LRP1B C/A 0.446 24.53 ± 6.30 dom ++? 9.64E‐05 rs1546676 2 154509239 A/G 0.325 23.62 ± 5.49 dom +++ 8.00E‐06 rs2178704 2 227579207 G/A 0.244 25.31 ± 5.41 dom +++ 8.83E‐05

SUPPLEMENTARY DATA

rs11683087 2 227586606 G/A 0.412 20.54 ± 3.87 add +++ 7.42E‐07 rs2251692 2 227589780 A/G 0.483 17.31 ± 3.84 add +++ 1.98E‐05 rs10205233 2 227614005 IRS1 T/C 0.185 23.19 ± 4.75 add ‐++ 2.35E‐05 rs16822640 2 227647907 IRS1 T/G 0.210 20.51 ± 4.61 add ‐++ 1.04E‐04 rs11130721 3 6008503 C/A 0.070 ‐33.07 ± 8.52 dom ‐‐‐ 7.00E‐05 rs2596937 3 9480906 SETD5 C/T 0.238 ‐17.41 ± 4.43 add ‐‐‐ 9.76E‐05 rs2279440 3 9518511 SETD5 T/C 0.203 ‐21.57 ± 4.63 add ‐‐‐ 3.31E‐06 rs17050395 3 9533974 G/A 0.235 ‐17.84 ± 4.48 add ‐‐‐ 8.31E‐05 rs3806667 3 9860880 ARPC4‐TTLL3 G/T 0.272 ‐20.45 ± 5.51 dom ‐‐+ 2.79E‐05 rs13106 3 12624580 MKRN2 A/G 0.028 126.46 ± 30.51 dom ??+ 3.41E‐05 rs635787 3 32466487 CMTM7 A/G 0.453 ‐22.82 ± 5.22 add ?‐‐ 1.24E‐05 rs9682976 3 60118879 FHIT T/C 0.152 ‐24.49 ± 6.11 dom ‐‐‐ 5.93E‐05 rs17062321 3 60122156 FHIT T/C 0.163 ‐24.84 ± 5.99 dom ‐‐‐ 2.39E‐05 rs12493716 3 106777359 LOC100302640 G/A 0.253 ‐16.3 ± 4.47 add ‐‐‐ 9.21E‐05 rs3773155 3 127438528 MGLL G/A 0.110 25.12 ± 6.87 dom +++ 4.27E‐05 rs12487584 3 132300293 ACAD11 T/C 0.284 19.13 ± 4.34 add +++ 2.87E‐05 rs13094259 3 142444625 TRPC1 T/G 0.091 ‐29.40 ± 7.77 dom ‐‐? 9.10E‐05 rs9824464 3 167635899 LOC646168 T/C 0.468 27.97 ± 7.05 rec ++‐ 8.41E‐05 rs11920292 3 188246257 LPP T/C 0.509 28.44 ± 6.08 add ?+? 2.90E‐06 rs11709891 3 188248624 LPP C/T 0.510 27.77 ± 6.06 add ?+? 4.54E‐06 rs1426260 3 188260703 LPP T/C 0.501 27.98 ± 6.08 add ?+? 4.25E‐06 rs10937355 3 188289697 LPP T/C 0.306 ‐23.26 ± 5.41 dom ‐‐‐ 4.12E‐05 rs12511127 4 5142212 STK32B G/A 0.325 ‐16.49 ± 4.07 add ‐‐‐ 6.59E‐05 rs6448852 4 12017993 C/T 0.468 15.04 ± 3.88 add +++ 5.55E‐05 rs1025877 4 12074137 G/A 0.455 ‐14.32 ± 3.91 add ‐‐‐ 9.65E‐05 rs4834882 4 12108239 T/C 0.314 18.23 ± 4.13 add +++ 2.08E‐05 rs1382751 4 12138827 C/T 0.316 17.13 ± 4.16 add +++ 7.86E‐05 rs9997603 4 66438114 EPHA5 T/G 0.080 ‐31.75 ± 7.58 dom ‐‐‐ 1.54E‐05 rs4320186 4 66483593 EPHA5 A/G 0.079 ‐30.58 ± 7.68 dom ‐‐‐ 2.41E‐05 rs11930824 4 161451545 A/G 0.445 29.13 ± 5.90 dom ++? 7.46E‐05 rs4627838 4 175602762 GLRA3 A/C 0.427 19.97 ± 5.71 dom ++‐ 7.25E‐05 rs4695784 4 175608905 GLRA3 T/C 0.426 19.97 ± 5.71 dom ++‐ 7.25E‐05 rs2448425 5 55917956 C/T 0.494 ‐15.23 ± 3.95 add ‐‐‐ 3.69E‐05

SUPPLEMENTARY DATA

rs6877846 5 81160103 A/G 0.328 20.99 ± 5.55 dom +++ 5.27E‐05 rs4835696 5 137972584 A/G 0.383 35.18 ± 8.27 rec ++? 1.74E‐05 rs13361457 5 152797679 T/C 0.477 23.81 ± 5.60 add ?++ 9.63E‐06 rs1019507 5 152798614 C/A 0.409 ‐18.01 ± 4.10 add ‐‐‐ 2.10E‐05 rs1465417 5 153790531 GALNT10 T/C 0.198 ‐20.39 ± 5.87 dom ‐‐+ 7.72E‐05 rs322394 5 172157768 C/T 0.360 ‐15.83 ± 4.02 add ‐‐‐ 3.38E‐05 rs241439 6 32797537 TAP2 G/T 0.426 18.67 ± 5.34 add ?++ 9.23E‐05 rs16884633 6 53902171 MLIP A/G 0.234 ‐23.78 ± 5.58 dom ‐‐‐ 3.67E‐05 rs987672 6 77410315 G/A 0.358 ‐17.03 ± 3.98 add ‐‐‐ 9.05E‐05 rs665791 6 106674850 ATG5 G/A 0.328 18.17 ± 4.21 add +++ 8.39E‐06 rs484621 6 106734408 ATG5 T/C 0.323 18.89 ± 4.22 add +++ 4.12E‐06 rs490010 6 106740458 ATG5 A/G 0.316 18.72 ± 4.23 add +++ 5.91E‐06 rs510432 6 106774030 T/C 0.341 16.93 ± 4.17 add +++ 2.61E‐05 rs9637984 6 170275554 G/A 0.245 19.29 ± 4.45 add +++ 3.63E‐05 rs4134409 6 170279658 A/G 0.245 19.26 ± 4.45 add +++ 3.79E‐05 rs2282909 7 28844815 CREB5 T/G 0.409 22.37 ± 5.70 dom +++ 1.05E‐04 rs11768415 7 52347667 A/G 0.519 ‐17.74 ± 4.17 add ‐‐? 2.80E‐05 rs11764734 7 52356515 T/C 0.520 ‐18.43 ± 4.20 add ‐‐? 1.41E‐05 rs296307 7 52432938 T/C 0.470 ‐15.67 ± 4.05 add ‐‐‐ 8.25E‐05 rs296316 7 52439967 T/C 0.369 ‐16.72 ± 4.15 add ‐‐‐ 9.52E‐05 rs2188256 7 88213062 C/T 0.179 ‐21.95 ± 5.85 dom ‐‐‐ 6.79E‐05 rs1588422 7 97329406 T/C 0.278 44.15 ± 10.17 rec ++? 3.19E‐05 rs2968865 7 124810399 AX746567 G/A 0.459 29.85 ± 7.01 rec ++? 1.40E‐05 rs441606 8 17903046 A/G 0.462 26.11 ± 6.49 dom ++? 9.48E‐05 rs17197236 8 25193338 DOCK5 G/A 0.034 54.29 ± 11.11 dom +++ 7.13E‐06 rs13267838 8 25196710 DOCK5 T/G 0.035 54.96 ± 10.96 dom +++ 4.03E‐06 rs13252932 8 25198091 DOCK5 T/C 0.049 47.71 ± 9.20 dom +++ 5.17E‐06 rs11780263 8 27823832 SCARA5 A/G 0.210 ‐16.34 ± 4.67 add ‐‐+ 6.64E‐05 rs9650426 8 27827391 SCARA5 C/T 0.334 15.63 ± 4.06 add +++ 6.38E‐05 rs4732617 8 27829251 SCARA5 G/A 0.330 20.45 ± 5.52 dom +++ 1.02E‐04 rs1715350 8 50396852 T/G 0.258 ‐19.15 ± 4.39 add ‐‐‐ 7.31E‐05 rs4737430 8 57303823 A/G 0.404 17.9 ± 5.57 dom ++‐ 6.71E‐05 rs660416 8 102465300 A/G 0.337 ‐16.42 ± 4.07 add ‐‐‐ 5.79E‐05

SUPPLEMENTARY DATA

rs633142 8 102466767 T/G 0.337 ‐16.14 ± 4.08 add ‐‐‐ 8.10E‐05 rs618854 8 102467706 T/C 0.343 ‐16.61 ± 4.06 add ‐‐‐ 5.04E‐05 rs4333664 9 6556948 GLDC T/C 0.432 16.94 ± 3.95 add +++ 1.15E‐05 rs224025 9 20309831 T/C 0.449 ‐23.94 ± 5.98 dom ‐‐? 4.00E‐05 rs6475448 9 20497142 MLLT3 G/A 0.316 ‐18.68 ± 4.43 add ‐‐? 1.89E‐05 rs17781302 9 24142314 C/A 0.178 21.35 ± 5.03 add +++ 6.10E‐05 rs17060946 9 77808519 G/A 0.068 37.86 ± 8.30 dom +++ 2.56E‐06 rs7030420 9 77809075 G/A 0.080 29.63 ± 7.63 dom +++ 5.75E‐05 rs12001098 9 110407586 A/G 0.106 27.75 ± 7.15 dom ++? 1.00E‐04 rs1888221 9 117778355 A/G 0.310 19.08 ± 4.30 add +++ 2.52E‐06 rs10828046 10 20676173 A/G 0.157 ‐23.63 ± 6.04 dom ‐‐‐ 4.18E‐05 rs17100713 10 84510336 NRG3 T/C 0.017 104.22 ± 24.6 dom ?+? 2.28E‐05 rs11202465 10 89366214 G/A 0.007 146.07 ± 36.66 dom ?+? 6.76E‐05 rs17099236 10 92484110 A/G 0.114 28.87 ± 6.89 dom +++ 5.13E‐05 rs1488933 11 17267029 T/C 0.448 30.81 ± 7.44 rec ++‐ 2.76E‐05 rs10841497 12 20524202 PDE3A G/T 0.356 17.05 ± 4.02 add +++ 3.17E‐05 rs7964191 12 20551038 PDE3A C/T 0.150 24.85 ± 6.10 dom +++ 5.20E‐05 rs10770655 12 20574060 PDE3A C/A 0.180 23.56 ± 5.90 dom +++ 9.20E‐05 rs7311799 12 84718394 A/C 0.469 ‐27.14 ± 6.83 rec ‐‐? 9.33E‐05 rs17512574 12 118788003 TAOK3 T/C 0.11 ‐29.28 ± 6.72 dom ‐‐‐ 7.24E‐06 rs673078 12 118791441 TAOK3 C/A 0.124 ‐30.26 ± 6.55 dom ‐‐‐ 2.41E‐06 rs884844 12 118814838 SUDS3 T/C 0.111 ‐28.67 ± 6.67 dom ‐‐‐ 6.48E‐06 rs7305647 12 118855566 SUDS3 A/G 0.103 ‐29.15 ± 6.88 dom ‐‐‐ 6.15E‐06 rs11059101 12 127874250 C/T 0.100 ‐25.34 ± 7.18 dom ‐‐‐ 9.30E‐05 rs4760067 12 130611682 T/C 0.432 ‐23.40 ± 5.73 dom ‐‐‐ 2.54E‐05 rs2874868 13 36356679 MAB21L1 G/T 0.233 16.78 ± 5.49 dom ++‐ 6.40E‐05 rs7329452 13 39000963 G/T 0.498 ‐23.70 ± 6.11 dom ‐‐‐ 3.64E‐05 rs4520736 13 59174647 C/T 0.415 ‐21.75 ± 5.23 add ‐?‐ 2.56E‐05 rs4885169 13 74900793 A/G 0.239 ‐23.04 ± 5.58 dom ‐‐‐ 5.31E‐06 rs1041515 13 74905950 C/T 0.243 ‐21.78 ± 4.53 add ‐‐‐ 5.14E‐07 rs7992923 13 74907043 A/G 0.427 ‐13.94 ± 3.94 add ‐‐‐ 7.86E‐05 rs1331765 13 74907933 G/A 0.372 ‐15.35 ± 4.04 add ‐‐‐ 2.15E‐05 rs10492494 13 74920186 A/C 0.240 ‐22.02 ± 4.55 add ‐‐‐ 5.04E‐07

SUPPLEMENTARY DATA

rs2325620 13 74927727 T/C 0.069 ‐34.55 ± 8.40 dom ‐‐? 3.28E‐05 rs2325622 13 74932425 A/C 0.247 ‐21.66 ± 4.51 add ‐‐‐ 5.61E‐07 rs9543599 13 74937657 C/T 0.433 ‐13.69 ± 3.94 add ‐‐‐ 8.26E‐05 rs555647 13 98632349 IPO5 G/A 0.403 20.89 ± 5.72 dom +++ 8.65E‐05 rs9559222 13 108699887 A/G 0.424 ‐43.53 ± 11.20 rec ?‐? 1.01E‐04 rs6572117 14 42360633 LRFN5 T/C 0.374 ‐29.20 ± 7.08 dom ‐?‐ 9.45E‐05 rs17120327 14 49073392 A/G 0.199 ‐22.43 ± 5.65 dom ‐‐‐ 3.06E‐05 rs7154149 14 49075564 A/G 0.204 ‐21.10 ± 5.62 dom ‐‐‐ 1.01E‐04 rs12050106 14 49084116 A/G 0.204 ‐21.07 ± 5.63 dom ‐‐‐ 1.04E‐04 rs7165441 15 27828539 G/A 0.408 22.79 ± 5.63 dom +++ 6.52E‐05 rs2222314 15 46405908 T/G 0.455 ‐25.24 ± 5.89 dom ‐‐‐ 1.64E‐05 rs7497796 15 55136506 A/C 0.384 21.92 ± 5.65 dom +++ 4.56E‐05 rs12438478 15 55159177 G/T 0.248 22.72 ± 5.49 dom +++ 2.98E‐05 rs17818867 15 55175350 C/T 0.255 19.09 ± 4.48 add +++ 1.24E‐05 rs11637842 15 55200927 A/G 0.225 20.78 ± 4.62 add +++ 1.43E‐05 rs12438945 15 55226570 C/A 0.230 21.63 ± 4.59 add +++ 4.34E‐06 rs17238052 15 55259099 G/A 0.235 22.68 ± 5.53 dom +++ 9.39E‐05 rs1076471 16 54100518 FTO A/G 0.244 ‐21.36 ± 5.52 dom ‐‐‐ 1.01E‐04 rs17175749 16 86343912 T/G 0.036 47.74 ± 11.31 dom ++? 2.46E‐05 rs3826347 17 64970002 CACNG4 G/A 0.424 25.26 ± 6.14 dom ++? 4.44E‐05 rs740559 17 64971249 CACNG4 A/G 0.446 24.31 ± 6.28 dom ++? 1.04E‐04 rs907900 17 77345200 RBFOX3 C/T 0.011 126.16 ± 30.94 dom ?+? 4.54E‐05 rs6501303 17 77430593 RBFOX3 A/G 0.046 33.3 ± 10.26 dom ++‐ 4.32E‐05 rs11872936 18 7352783 T/C 0.009 152.75 ± 35.1 dom ?+? 1.35E‐05 rs626410 18 65855591 A/C 0.398 16.55 ± 3.99 add +++ 2.88E‐05 rs12961613 18 66309996 T/C 0.229 ‐22.84 ± 5.59 dom ‐‐‐ 6.23E‐05 rs10408924 19 9253139 ZNF317 G/T 0.370 22.59 ± 5.62 dom +++ 9.94E‐05 rs892024 19 33399344 CEP89 A/G 0.168 ‐23.28 ± 5.87 dom ‐‐‐ 8.92E‐05 rs864140 20 3088010 LOC100134015 A/G 0.294 21.29 ± 5.54 dom +++ 1.04E‐04 rs913555 20 3090124 LOC100134015 A/G 0.295 21.8 ± 5.54 dom +++ 6.92E‐05 rs911112 20 3144664 ProSAPiP1 T/C 0.254 22.86 ± 5.65 dom +++ 6.70E‐05 rs6075733 20 20856254 C/T 0.346 ‐18.29 ± 4.13 add ‐‐‐ 8.61E‐06 rs11907984 20 20862068 T/C 0.370 ‐16.12 ± 4.10 add ‐‐‐ 9.28E‐05

SUPPLEMENTARY DATA

rs4813402 20 20889803 C/T 0.366 ‐16.68 ± 4.03 add ‐‐‐ 5.21E‐05 rs6137217 20 20997702 T/C 0.349 24.96 ± 5.54 dom +++ 9.01E‐06 rs1028444 20 22267058 C/T 0.404 26.33 ± 6.24 dom ++? 5.22E‐06 rs4813452 20 22276813 G/T 0.382 24.54 ± 6.20 dom ++? 2.16E‐05 rs17192831 20 22281954 T/C 0.386 24.83 ± 6.21 dom ++? 1.64E‐05 rs819136 20 32848719 ASIP A/G 0.103 29.44 ± 7.35 dom ++? 8.26E‐05 rs6018406 20 45941326 ZMYND8 C/A 0.247 18.51 ± 4.50 add +++ 5.91E‐05 rs155004 20 57870356 G/A 0.283 ‐24.33 ± 5.43 dom ‐‐‐ 2.48E‐05 rs2277827 21 47986001 DIP2A G/T 0.435 29.78 ± 7.30 rec ++? 1.02E‐04 rs763040 22 44763606 BC037321 A/G 0.205 22.54 ± 5.70 dom +++ 6.91E‐05

SUPPLEMENTARY DATA

e. AIRg (nmax=2,548)

Direction of Association (BetaGene, IRAS, Ref Allele Best IRASFS, Best p‐ Marker Chr Position Gene ref/nonref Freq β±SE model TRIPOD) value rs2784739 1 8497558 RERE G/T 0.243 ‐1.98 ± 0.45 dom ‐‐‐‐ 1.91E‐05 rs11121182 1 8522553 RERE A/C 0.270 ‐1.92 ± 0.44 dom ‐‐‐‐ 5.01E‐05 rs10492966 1 8598005 RERE T/C 0.273 ‐1.96 ± 0.44 dom ‐‐‐‐ 4.70E‐05 rs10492965 1 8598127 RERE A/G 0.271 ‐1.93 ± 0.44 dom ‐‐‐‐ 5.08E‐05 rs11121203 1 8648240 RERE C/T 0.286 ‐1.86 ± 0.44 dom ‐‐‐‐ 4.42E‐05 rs12061717 1 55024928 ACOT11 T/C 0.080 ‐2.10 ± 0.61 dom ‐+‐‐ 2.66E‐05 rs7537721 1 88514479 A/G 0.010 8.45 ± 1.80 dom +?++ 2.92E‐05 rs11185362 1 104561488 G/A 0.309 ‐1.65 ± 0.44 dom ‐‐‐‐ 3.21E‐05 rs961490 1 227219076 CDC42BPA T/C 0.003 43.04 ± 10.6 dom ?+?? 6.62E‐05 rs17018659 2 4211781 G/A 0.004 10.57 ± 2.50 dom +++? 5.39E‐05 rs2053797 2 46370892 PRKCE A/G 0.162 1.89 ± 0.49 dom +‐++ 5.02E‐05 rs4953320 2 46374529 PRKCE C/T 0.099 2.13 ± 0.57 dom +‐++ 8.13E‐05 rs10200604 2 56575020 CCDC85A A/G 0.314 ‐1.33 ± 0.34 add ‐‐‐‐ 8.09E‐05 rs1345516 2 64703286 A/C 0.420 1.04 ± 0.32 add ++++ 4.11E‐05 rs6756027 2 64720254 A/G 0.432 1.09 ± 0.31 add ++++ 6.05E‐05 rs6546079 2 64725466 G/T 0.438 1.08 ± 0.31 add +‐++ 6.66E‐05 rs13002043 2 64726449 A/G 0.437 1.07 ± 0.31 add +‐++ 7.92E‐05 rs7594935 2 235255122 T/C 0.116 1.91 ± 0.54 dom ++++ 2.88E‐05 rs9809000 3 154268934 G/A 0.080 2.17 ± 0.65 dom +++‐ 2.76E‐05 rs6803803 3 180116563 C/T 0.002 17.53 ± 3.72 dom +++? 1.64E‐06 rs17013808 4 89004957 A/G 0.056 ‐3.15 ± 0.80 dom ‐‐‐‐ 4.05E‐05 rs11943562 4 167652786 C/T 0.130 1.71 ± 0.51 dom +‐++ 2.39E‐05 rs3893856 5 111163 A/G 0.096 2.09 ± 0.58 dom +++‐ 7.21E‐05 rs10041174 5 11710193 CTNND2 G/A 0.080 ‐2.59 ± 0.65 dom ‐‐‐‐ 2.36E‐05 rs11750248 5 52153066 ITGA1 T/C 0.068 2.43 ± 0.62 dom ++++ 2.88E‐05

SUPPLEMENTARY DATA

rs1545696 5 122102442 A/G 0.282 ‐1.60 ± 0.44 dom ‐‐‐‐ 4.93E‐05 rs6887101 5 122109207 A/G 0.270 ‐1.70 ± 0.44 dom ‐‐‐‐ 1.24E‐05 rs10071705 5 122132725 SNX2 T/C 0.273 ‐1.65 ± 0.44 dom ‐‐‐‐ 1.52E‐05 rs193541 5 122253304 SNX24 C/T 0.253 ‐1.71 ± 0.44 dom ‐‐‐‐ 7.64E‐06 rs17149748 5 122267367 SNX24 G/A 0.093 ‐2.14 ± 0.57 dom ‐‐‐‐ 5.70E‐05 rs6891052 5 122358015 T/G 0.092 ‐2.31 ± 0.56 dom ‐‐‐‐ 2.32E‐05 rs10476419 5 162296335 G/A 0.010 4.71 ± 2.26 dom +‐++ 8.86E‐05 rs10078423 5 162312823 G/A 0.005 7.29 ± 2.36 dom +?+? 4.94E‐05 rs10051450 5 162378040 T/C 0.005 7.39 ± 2.36 dom +?+? 3.14E‐05 rs12198482 6 15218671 C/A 0.213 1.65 ± 0.46 dom ++++ 8.95E‐05 rs4712523 6 20657564 CDKAL1 G/A 0.315 ‐1.17 ± 0.33 add ‐‐‐‐ 1.60E‐05 rs6456369 6 20660365 CDKAL1 C/T 0.350 ‐0.98 ± 0.32 add ‐+‐‐ 5.17E‐05 rs7754840 6 20661250 CDKAL1 C/G 0.310 ‐1.26 ± 0.33 add ‐‐‐‐ 3.83E‐06 rs7756992 6 20679709 CDKAL1 G/A 0.309 ‐1.13 ± 0.34 add ‐‐‐‐ 1.01E‐04 rs9368222 6 20686996 CDKAL1 A/C 0.262 ‐1.46 ± 0.35 add ‐‐‐‐ 1.28E‐06 rs2206734 6 20694884 CDKAL1 T/C 0.194 ‐2.05 ± 0.45 dom ‐‐‐‐ 1.02E‐06 rs1040558 6 20713706 CDKAL1 G/A 0.218 ‐1.92 ± 0.44 dom ‐‐‐‐ 5.52E‐06 rs6935599 6 20717095 CDKAL1 G/A 0.245 ‐1.73 ± 0.44 dom ‐‐‐‐ 5.83E‐05 rs10946403 6 20717404 CDKAL1 G/A 0.242 ‐1.74 ± 0.44 dom ‐‐‐‐ 5.56E‐05 rs9358357 6 20719145 CDKAL1 G/A 0.247 ‐1.77 ± 0.44 dom ‐‐‐+ 3.60E‐05 rs9356746 6 20720279 CDKAL1 C/T 0.193 ‐1.73 ± 0.45 dom ‐‐‐+ 3.29E‐05 rs3873380 6 31262438 HLA‐B T/C 0.408 1.55 ± 0.46 dom +‐++ 4.50E‐05 rs236358 6 36800611 CPNE5 A/C 0.427 1.05 ± 0.32 add +++‐ 3.39E‐05 rs35473403 6 43480822 YIPF3 T/C 0.002 16.32 ± 4.38 dom ++?? 7.58E‐05 rs7750450 6 55714563 BMP5 C/T 0.322 1.40 ± 0.34 add ++++ 6.21E‐05 rs17082388 6 120892140 G/A 0.236 1.67 ± 0.45 dom ++‐+ 1.49E‐05 rs11963462 6 121021878 C/T 0.232 1.60 ± 0.45 dom ++‐+ 6.06E‐05 rs2358010 6 121028021 A/C 0.232 1.59 ± 0.45 dom ++‐+ 6.50E‐05 rs9321207 6 130397238 L3MBTL3 A/G 0.365 ‐0.97 ± 0.32 add ‐‐‐+ 7.43E‐05 rs4897370 6 130466676 SAMD3 G/A 0.346 1.43 ± 0.44 dom ++++ 3.80E‐05 rs11970367 6 138544807 KIAA1244 A/G 0.006 11.97 ± 3.94 dom ++++ 9.07E‐05 rs2038586 6 158091108 ZDHHC14 T/C 0.184 1.97 ± 0.48 dom ++++ 1.49E‐05 rs9295206 6 163326692 PACRG G/A 0.400 ‐1.18 ± 0.32 add ‐‐‐‐ 4.78E‐05

SUPPLEMENTARY DATA

rs7779074 7 22986107 FAM126A A/G 0.101 2.13 ± 0.60 dom ++++ 9.56E‐05 rs10230193 7 50364626 IKZF1 A/G 0.479 ‐1.79 ± 0.53 rec ‐+‐‐ 7.09E‐06 rs10232215 7 92097166 G/A 0.248 1.96 ± 0.44 dom ++++ 4.41E‐05 rs2111200 7 92140397 PEX1 T/C 0.251 1.96 ± 0.44 dom ++++ 3.21E‐05 rs10237822 7 93760001 G/T 0.025 3.94 ± 1.18 dom +++‐ 3.53E‐05 rs10242768 7 93784157 C/T 0.022 3.94 ± 1.13 dom +++‐ 6.87E‐05 rs17881463 7 100495687 T/C 0.003 43.04 ± 10.60 dom ?+?? 6.62E‐05 rs11779094 8 10666813 SOX7 A/G 0.075 ‐2.18 ± 0.64 dom ‐‐‐+ 8.16E‐05 rs11203714 8 15477945 TUSC3 G/T 0.217 1.11 ± 0.46 dom +‐+‐ 1.00E‐04 rs4645564 8 15494159 TUSC3 T/C 0.210 1.04 ± 0.46 dom +‐+‐ 1.04E‐04 rs7000560 8 16993943 C/A 0.476 2.00 ± 0.49 dom ++++ 3.35E‐05 rs4922265 8 16996435 A/C 0.469 2.11 ± 0.49 dom ++++ 6.61E‐06 rs6988635 8 95744466 DPY19L4 G/A 0.444 1.18 ± 0.31 add ++++ 7.73E‐05 rs7018475 9 22137685 G/T 0.323 ‐1.64 ± 0.34 add ‐‐‐‐ 4.90E‐06 rs13301551 9 25683697 T/C 0.075 2.39 ± 0.62 dom ++++ 8.39E‐05 rs2295926 9 101593825 GALNT12 C/T 0.348 ‐1.61 ± 0.44 dom ‐‐‐‐ 2.21E‐05 rs7341705 9 107651348 ABCA1 C/T 0.003 13.32 ± 4.28 dom +‐++ 1.77E‐05 rs9696881 9 109274146 BC017988 G/A 0.233 ‐1.47 ± 0.45 dom ‐‐‐‐ 6.80E‐05 rs1602111 9 109277184 BC017988 C/A 0.233 ‐1.53 ± 0.45 dom ‐‐‐‐ 2.16E‐05 rs2287005 9 113791313 LPAR1 C/T 0.068 2.61 ± 0.66 dom +++‐ 6.49E‐05 rs7036846 9 119798885 ASTN2 C/T 0.005 10.86 ± 2.43 dom ++++ 9.25E‐06 rs12348950 9 123327435 CDK5RAP2 C/T 0.469 1.95 ± 0.53 rec ++++ 5.73E‐05 rs1128905 9 139253839 GPSM1 T/C 0.435 ‐1.05 ± 0.32 add ‐‐‐‐ 8.83E‐05 rs10870202 9 139257411 DNLZ T/C 0.430 ‐1.04 ± 0.32 add ‐‐‐+ 5.37E‐05 rs10781496 9 139261086 CARD9 A/G 0.493 ‐1.07 ± 0.32 add ‐‐‐‐ 6.97E‐05 rs2855022 10 70849959 SRGN G/A 0.465 ‐1.72 ± 0.53 rec ‐‐‐+ 2.73E‐05 rs7919192 10 93660727 C/T 0.216 ‐1.45 ± 0.46 dom ‐‐‐+ 5.00E‐05 rs10509794 10 107460228 C/T 0.004 7.64 ± 2.29 dom +‐+‐ 1.02E‐04 rs6584696 10 107578214 C/T 0.026 4.14 ± 0.99 dom ++++ 2.66E‐05 rs2129969 11 45586169 G/A 0.477 1.14 ± 0.32 add ++++ 2.10E‐05 rs10838488 11 45596965 C/T 0.479 1.14 ± 0.32 add ++++ 2.70E‐05 rs510398 11 66054823 YIF1A C/T 0.003 12.63 ± 2.96 dom +?++ 4.37E‐06 rs11227856 11 67377758 NDUFV1 T/C 0.005 6.51 ± 2.48 dom +‐++ 5.34E‐05

SUPPLEMENTARY DATA rs12295232 11 67379575 NDUFV1 A/G 0.005 6.51 ± 2.48 dom +‐++ 5.38E‐05 rs10082595 11 67383433 T/C 0.005 6.51 ± 2.48 dom +‐++ 5.40E‐05 rs11227870 11 67400566 TBX10 A/G 0.005 6.63 ± 2.50 dom +‐++ 6.28E‐05 rs10898909 11 72952496 A/G 0.404 1.41 ± 0.33 add +++‐ 4.03E‐06 rs3847554 11 92668826 T/C 0.343 ‐1.64 ± 0.32 add ‐‐‐‐ 1.08E‐06 rs1387153 11 92673828 T/C 0.220 ‐2.55 ± 0.45 dom ‐‐‐‐ 2.21E‐09 rs2166706 11 92691532 C/T 0.308 ‐1.70 ± 0.33 add ‐‐‐‐ 1.24E‐06 rs10830961 11 92694757 G/A 0.331 ‐1.59 ± 0.33 add ‐‐‐‐ 1.91E‐06 rs10830963 11 92708710 MTNR1B G/C 0.220 ‐2.76 ± 0.45 dom ‐‐‐‐ 5.23E‐12 rs686413 11 117537710 DSCAML1 A/G 0.327 ‐1.19 ± 0.33 add ‐‐‐‐ 5.67E‐05 rs12292105 11 117983479 TMPRSS4 G/T 0.024 3.77 ± 1.18 dom ++++ 3.77E‐05 rs11216770 11 117983801 TMPRSS4 T/C 0.024 3.78 ± 1.18 dom ++++ 3.67E‐05 rs7927108 11 134038949 NCAPD3 T/G 0.004 10.54 ± 2.49 dom +++‐ 4.35E‐05 rs7962050 12 1031454 RAD52 G/A 0.323 1.20 ± 0.33 add +++‐ 7.67E‐05 rs247352 12 14900457 C/T 0.013 4.42 ± 1.49 dom +‐++ 9.24E‐05 rs12816878 12 23155705 AK094733 T/C 0.283 1.31 ± 0.35 add ++++ 9.69E‐05 rs3847896 12 23159966 AK094733 C/T 0.453 1.12 ± 0.31 add +++‐ 6.47E‐05 rs1489076 12 29129874 T/C 0.377 ‐1.37 ± 0.33 add ‐‐‐‐ 1.97E‐05 rs11049971 12 29130200 T/C 0.376 ‐1.37 ± 0.33 add ‐‐‐‐ 1.78E‐05 rs1489078 12 29141413 G/A 0.376 ‐1.34 ± 0.33 add ‐‐‐‐ 2.48E‐05 rs11113214 12 107588082 G/A 0.219 ‐1.93 ± 0.47 dom ‐‐‐‐ 6.21E‐05 rs3026485 12 110782027 ATP2A2 C/T 0.002 15.24 ± 5.06 dom +?+? 6.78E‐06 rs16940879 12 110928719 G/A 0.003 11.03 ± 4.51 dom +?+‐ 6.21E‐05 rs10774579 12 121405210 C/T 0.252 1.59 ± 0.44 dom ++++ 7.01E‐05 rs10744163 12 124383950 DNAH10 T/C 0.200 1.75 ± 0.46 dom ++++ 2.66E‐05 rs9553849 13 27082326 A/G 0.199 1.57 ± 0.47 dom +‐++ 6.70E‐05 rs9670049 13 31692454 C/T 0.176 1.81 ± 0.47 dom ++++ 9.20E‐05 rs9585660 13 101962642 NALCN A/G 0.006 8.29 ± 2.16 dom +?++ 2.60E‐05 rs7158254 14 37264674 SLC25A21 C/T 0.007 7.18 ± 1.90 dom +++‐ 3.91E‐05 rs1690356 15 55301874 A/C 0.003 13.41 ± 3.63 dom +??+ 1.47E‐05 rs2701405 15 87539918 AGBL1 A/C 0.485 0.91 ± 0.30 add +++‐ 8.78E‐05 rs2570133 15 87604296 C/T 0.416 ‐1.00 ± 0.31 add ‐‐‐+ 6.64E‐05 rs428233 16 1085393 C/A 0.295 1.54 ± 0.44 dom ++++ 9.59E‐05

SUPPLEMENTARY DATA

rs12921387 16 25978823 HS3ST4 C/T 0.223 ‐1.76 ± 0.45 dom ‐‐‐‐ 9.72E‐05 rs7192071 16 78953857 WWOX G/A 0.024 4.34 ± 1.03 dom ++++ 7.30E‐05 rs16953087 17 420033 VPS53 C/T 0.13 ‐1.81 ± 0.52 dom ‐‐‐‐ 3.26E‐05 rs1006703 17 3865399 ATP2A3 T/C 0.087 2.13 ± 0.57 dom +++‐ 2.65E‐06 rs2619996 17 71703758 T/C 0.042 3.15 ± 0.81 dom ++++ 7.69E‐05 rs899596 17 71735485 G/A 0.230 2.20 ± 0.45 dom ++++ 2.64E‐06 rs9947929 18 6662650 T/C 0.193 1.87 ± 0.45 dom +++‐ 2.15E‐05 rs9955097 18 7965469 PTPRM C/A 0.004 11.62 ± 2.75 dom +?++ 3.10E‐05 rs9950590 18 8043661 PTPRM T/C 0.005 11.99 ± 2.72 dom +?++ 5.19E‐06 rs2068732 18 26236729 C/A 0.120 2.42 ± 0.53 dom ++++ 6.85E‐05 rs12608167 18 71893294 G/A 0.264 1.36 ± 0.35 add ++++ 2.48E‐05 rs4567819 18 74894653 T/C 0.469 1.09 ± 0.31 add ++++ 1.01E‐04 rs153508 19 34009392 PEPD T/C 0.362 1.01 ± 0.33 add ++++ 7.18E‐05 rs33845 19 34014316 A/G 0.361 1.00 ± 0.33 add ++++ 7.03E‐05 rs6030572 20 41598995 PTPRT C/A 0.175 ‐1.96 ± 0.47 dom ‐‐‐‐ 8.83E‐05 rs17646111 21 34954782 DONSON A/G 0.237 ‐1.57 ± 0.45 dom ‐‐‐‐ 3.16E‐05 rs1892700 21 35016137 DONSON A/G 0.236 ‐1.52 ± 0.45 dom ‐‐‐‐ 5.02E‐05 rs5752933 22 29902192 C/A 0.230 2.11 ± 0.45 dom ++++ 1.36E‐05

f. DI (nmax=3,083)

Direction of Association (BetaGene, IRAS, IRASFS, MACAD, Ref Allele NIDDM, Best p‐ Marker Chr Position Gene ref/nonref Freq β±SE Best model TRIPOD) value rs2985125 1 17004186 G/A 0.052 3.11 ± 0.85 dom ++++?+ 3.02E‐05 rs16866049 1 35836440 ZMYM4 G/A 0.002 21.17 ± 5.11 dom +?+??? 3.08E‐05 rs513553 1 182494063 RGSL1 G/A 0.262 ‐1.83 ± 0.49 dom ‐‐‐+‐‐ 8.14E‐05 rs185580 1 182519861 RGSL1 A/G 0.227 ‐1.47 ± 0.50 dom ‐+‐‐‐‐ 9.30E‐05 rs266549 1 182528269 RGSL1 T/C 0.229 ‐1.59 ± 0.50 dom ‐‐‐‐‐‐ 6.29E‐05 rs474939 1 182538615 A/G 0.239 ‐1.69 ± 0.49 dom ‐‐‐‐‐‐ 3.59E‐05 rs10919851 1 200187504 C/T 0.442 ‐1.16 ± 0.36 add ‐‐‐‐?+ 5.29E‐05 rs6427807 1 200189305 A/C 0.462 1.15 ± 0.36 add ++++?‐ 6.79E‐05 rs7603311 2 49041322 C/T 0.441 1.44 ± 0.36 add ++++?+ 2.30E‐05 rs4482537 2 49052255 T/C 0.404 1.38 ± 0.36 add ++++?+ 5.52E‐05 rs17492567 2 50212116 NRXN1 C/T 0.089 2.54 ± 0.65 dom ++++?+ 4.51E‐05 rs12986646 2 52372389 A/G 0.044 2.64 ± 0.89 dom +‐++?‐ 8.76E‐05 rs881952 2 60888202 C/T 0.477 ‐2.30 ± 0.52 dom ‐‐‐‐++ 4.59E‐06 rs1366828 2 83753456 T/C 0.452 ‐1.99 ± 0.53 dom ‐‐‐‐?‐ 9.92E‐05 rs6753918 2 137214258 C/T 0.012 6.77 ± 1.65 dom ++++?+ 2.54E‐05 rs7560169 2 142148511 LRP1B T/C 0.388 1.57 ± 0.49 dom +++++‐ 8.79E‐05 rs684428 2 220505265 SLC4A3 T/C 0.170 1.61 ± 0.52 dom ++++‐‐ 8.27E‐05 rs7559293 2 236422975 AGAP1 A/G 0.408 1.95 ± 0.51 dom +++++‐ 6.75E‐05 rs28415051 3 66008918 MAGI1 G/A 0.003 15.79 ± 6.09 dom +++??‐ 5.80E‐05 rs7629006 3 96801930 EPHA6 A/G 0.371 2.25 ± 0.49 dom ++++‐+ 1.33E‐05 rs9832209 3 96825782 EPHA6 A/G 0.356 2.00 ± 0.49 dom ++++++ 5.13E‐05 rs602149 3 185244569 LIPH T/G 0.059 ‐2.95 ± 0.81 dom ‐‐‐‐?+ 4.20E‐05 rs612304 3 185251001 LIPH C/T 0.059 ‐3.25 ± 0.81 dom ‐‐‐‐?‐ 3.31E‐05

SUPPLEMENTARY DATA

rs233991 4 104665738 A/C 0.457 ‐2.07 ± 0.65 rec ‐‐‐‐?‐ 8.69E‐05 rs1520323 4 125146503 T/C 0.021 ‐3.68 ± 1.19 dom ‐‐‐‐?‐ 6.82E‐05 rs467650 5 97969453 C/T 0.271 1.94 ± 0.49 dom +++‐++ 3.33E‐05 rs4712428 6 10203618 MRDS1 T/C 0.326 2.08 ± 0.48 dom +++‐‐+ 3.43E‐05 rs9470003 6 35337931 PPARD C/G 0.011 8.07 ± 2.39 dom ++++?+ 3.92E‐05 rs13193467 6 85211681 T/C 0.132 ‐2.10 ± 0.57 dom ‐‐‐‐?‐ 4.66E‐05 rs1510292 6 124371914 NKAIN2 A/G 0.060 ‐3.05 ± 0.81 dom ‐+‐‐?‐ 5.10E‐05 rs17086954 6 156337304 G/A 0.220 2.02 ± 0.49 dom +++‐++ 2.71E‐05 rs10225719 7 12691988 SCIN T/C 0.418 ‐2.17 ± 0.62 dom ‐‐‐?‐+ 3.17E‐05 rs10267836 7 30755583 INMT T/C 0.041 3.20 ± 0.90 dom +‐++?‐ 6.27E‐06 rs1346111 7 49742459 C/T 0.226 ‐2.04 ± 0.49 dom ‐‐‐‐‐‐ 2.28E‐05 rs10278107 7 125278195 C/T 0.477 ‐1.90 ± 0.53 dom ‐‐‐‐‐‐ 5.14E‐05 rs12539028 7 154812950 A/G 0.435 ‐1.74 ± 0.52 dom ‐‐‐‐‐‐ 8.46E‐05 rs1077489 8 6635669 T/C 0.072 ‐2.37 ± 0.75 dom ‐+‐‐?‐ 9.47E‐05 rs12546336 8 39620015 ADAM2 A/G 0.333 1.65 ± 0.48 dom ++++++ 9.24E‐05 rs13253406 8 143200557 G/T 0.390 ‐1.77 ± 0.46 add ‐‐‐??‐ 6.65E‐05 rs2382470 9 14387817 NFIB A/G 0.255 ‐1.59 ± 0.49 dom ‐‐‐‐‐+ 2.02E‐05 rs2020927 9 107553185 ABCA1 G/A 0.161 ‐1.74 ± 0.53 dom ‐+‐‐‐‐ 5.74E‐05 rs10121901 9 107553524 ABCA1 G/A 0.161 ‐1.74 ± 0.53 dom ‐+‐‐‐‐ 5.63E‐05 rs2066720 9 107554069 ABCA1 T/C 0.161 ‐1.74 ± 0.53 dom ‐+‐‐‐‐ 5.74E‐05 rs11145750 9 139259249 CARD9 A/G 0.474 ‐1.69 ± 0.53 dom ‐+‐‐‐+ 2.71E‐05 rs3812560 9 139269905 T/C 0.465 ‐1.83 ± 0.52 dom ‐+‐‐?+ 6.16E‐06 rs3812570 9 139275204 SNAPC4 A/C 0.461 ‐1.87 ± 0.52 dom ‐+‐‐?+ 1.72E‐06 rs4266763 9 139289825 SNAPC4 A/G 0.489 ‐2.00 ± 0.54 dom ‐+‐‐?+ 3.46E‐06 rs8413 9 139323311 INPP5E T/C 0.470 ‐1.77 ± 0.52 dom ‐‐‐‐?+ 2.83E‐05 rs10870194 9 139327034 INPP5E A/G 0.446 ‐1.58 ± 0.51 dom ‐+‐‐?+ 5.86E‐05 rs10781542 9 139327439 INPP5E A/G 0.446 ‐1.59 ± 0.51 dom ‐+‐‐?+ 5.77E‐05 rs1148233 10 31461599 T/C 0.008 8.86 ± 2.17 dom ++++?+ 9.09E‐06 rs1414894 10 89785190 C/T 0.286 1.67 ± 0.48 dom ++++‐+ 4.62E‐05 rs2488069 10 94505421 G/T 0.002 ‐18.48 ± 5.14 dom ‐‐‐??‐ 5.73E‐05 rs7081634 10 94685886 EXOC6 G/A 0.002 ‐22.06 ± 5.64 dom ‐?‐??‐ 2.62E‐05 rs17108007 10 94711701 EXOC6 C/T 0.002 ‐21.94 ± 5.65 dom ‐?‐??‐ 2.84E‐05 rs7909248 10 94721776 EXOC6 T/G 0.002 ‐22.02 ± 5.65 dom ‐?‐??‐ 2.70E‐05

SUPPLEMENTARY DATA

rs17093817 10 94740586 EXOC6 G/A 0.002 ‐22.00 ± 5.63 dom ‐?‐??‐ 2.66E‐05 rs835252 10 94749417 EXOC6 G/A 0.002 ‐22.01 ± 5.65 dom ‐?‐??‐ 2.72E‐05 rs835237 10 94754464 EXOC6 A/G 0.002 ‐21.96 ± 5.65 dom ‐?‐??‐ 2.84E‐05 rs835242 10 94756734 EXOC6 C/T 0.002 ‐22.02 ± 5.64 dom ‐?‐??‐ 2.69E‐05 rs835243 10 94757548 EXOC6 G/A 0.002 ‐21.99 ± 5.66 dom ‐?‐??‐ 2.80E‐05 rs835246 10 94761707 EXOC6 A/G 0.002 ‐22.01 ± 5.65 dom ‐?‐??‐ 2.71E‐05 rs835254 10 94763426 EXOC6 G/A 0.002 ‐22.01 ± 5.65 dom ‐?‐??‐ 2.71E‐05 rs835255 10 94765333 EXOC6 A/G 0.002 ‐22.01 ± 5.65 dom ‐?‐??‐ 2.71E‐05 rs9420601 10 94771867 EXOC6 A/G 0.002 ‐22.76 ± 6.29 dom ‐?‐??? 7.36E‐05 rs7068036 10 95315193 T/C 0.156 1.94 ± 0.55 dom +‐++?+ 6.79E‐05 rs2237896 11 2858440 KCNQ1 A/G 0.247 1.64 ± 0.51 dom ++++?‐ 1.57E‐05 rs2237897 11 2858546 KCNQ1 T/C 0.251 1.75 ± 0.51 dom ++++?‐ 7.04E‐06 rs5241 11 14990543 CALCA T/G 0.016 5.81 ± 1.55 dom +++‐?+ 9.58E‐05 rs4756016 11 45699134 G/A 0.416 1.50 ± 0.51 dom +‐++++ 4.61E‐05 rs744434 11 65847982 PACS1 G/T 0.003 15.07 ± 3.98 dom +++??+ 5.45E‐05 rs3847554 11 92668826 T/C 0.339 ‐2.19 ± 0.48 dom ‐‐‐++‐ 1.03E‐04 rs1387153 11 92673828 T/C 0.220 ‐3.20 ± 0.51 dom ‐‐‐+?‐ 1.32E‐09 rs2166706 11 92691532 C/T 0.308 ‐2.29 ± 0.48 dom ‐‐‐++‐ 4.46E‐05 rs10830961 11 92694757 G/A 0.328 ‐2.37 ± 0.48 dom ‐‐‐++‐ 7.43E‐06 rs10830963 11 92708710 MTNR1B G/C 0.218 ‐3.40 ± 0.51 dom ‐‐‐+?‐ 1.03E‐11 rs1351571 11 98408860 T/C 0.472 ‐1.31 ± 0.44 add ‐+‐??+ 4.20E‐05 rs17108749 11 108796817 DDX10 G/T 0.009 ‐9.79 ± 2.41 dom ‐‐‐??‐ 7.57E‐05 rs7971324 12 3098924 TEAD4 C/A 0.056 3.44 ± 0.81 dom ++++?+ 5.00E‐05 rs17107718 12 70488764 T/C 0.054 2.52 ± 0.85 dom ++++?‐ 6.92E‐05 rs7304911 12 129705400 TMEM132D T/C 0.223 ‐1.40 ± 0.49 dom ‐+‐‐‐‐ 2.69E‐05 rs1537435 13 27909319 T/C 0.316 1.61 ± 0.48 dom ++++++ 5.12E‐05 rs17085484 13 27930039 C/T 0.318 1.52 ± 0.49 dom ++++++ 8.64E‐05 rs17085485 13 27936526 G/T 0.228 1.51 ± 0.49 dom ++++++ 7.43E‐05 rs870767 13 27938560 G/A 0.233 1.53 ± 0.49 dom +‐++++ 5.87E‐05 rs2764026 13 36291051 MAB21L1 G/A 0.282 ‐1.77 ± 0.48 dom ‐‐‐‐‐+ 6.43E‐05 rs9575380 13 36708286 G/A 0.281 1.66 ± 0.48 dom ++++++ 7.91E‐05 rs9575437 13 36731208 G/A 0.296 2.02 ± 0.48 dom ++++++ 2.08E‐05 rs9575445 13 36731586 A/G 0.285 1.88 ± 0.48 dom ++++++ 1.48E‐05

SUPPLEMENTARY DATA

rs1328641 13 36745029 SOHLH2 T/C 0.227 1.96 ± 0.49 dom ++++++ 1.96E‐05 rs2149423 13 36772381 SOHLH2 G/A 0.315 2.18 ± 0.48 dom ++++++ 3.67E‐07 rs2054715 15 59607007 MYO1E C/T 0.172 ‐1.35 ± 0.55 dom ‐+‐‐?+ 6.02E‐05 rs11073891 15 90363995 C/A 0.274 1.37 ± 0.48 dom +‐++‐+ 9.68E‐05 rs4238710 16 84546021 A/G 0.310 ‐2.08 ± 0.48 dom ‐‐‐‐‐‐ 3.68E‐05 rs2326274 16 84546108 T/G 0.308 ‐2.1 ± 0.48 dom ‐‐‐‐‐‐ 3.97E‐05 rs9891963 17 2875114 RAP1GAP2 T/C 0.038 ‐3.23 ± 1.01 dom ‐‐‐+?+ 8.32E‐05 rs654136 18 48464204 ME2 T/C 0.359 ‐1.43 ± 0.49 dom ‐+‐‐‐‐ 9.26E‐05 rs4073064 18 59532727 RNF152 C/T 0.010 ‐10.09 ± 2.54 dom ‐‐‐??‐ 7.42E‐05 rs2541872 18 63632952 A/G 0.385 ‐1.93 ± 0.5 dom ‐‐‐‐?‐ 9.90E‐05 rs2587374 18 63638807 A/G 0.250 ‐2.07 ± 0.48 dom ‐‐‐‐‐‐ 5.93E‐05 rs4802566 19 49632309 PPFIA3 T/C 0.392 1.77 ± 0.50 dom ++++++ 2.84E‐05 rs1217356 20 4170187 G/A 0.450 ‐2.35 ± 0.63 dom ‐‐‐??‐ 5.21E‐05 rs6076157 20 23862844 G/A 0.479 2.09 ± 0.55 dom ++++?+ 9.63E‐05 rs8128305 21 27861993 CYYR1 A/G 0.250 1.61 ± 0.49 dom +++++‐ 1.63E‐05 rs219628 21 27865420 CYYR1 C/T 0.255 1.4 ± 0.49 dom +++++‐ 5.01E‐05 rs2833555 21 33285149 HUNK T/C 0.079 ‐2.93 ± 0.73 dom ‐‐‐‐?‐ 6.09E‐05 rs133937 22 33395851 SYN3 C/A 0.335 1.65 ± 0.50 dom ++++++ 6.74E‐05

SUPPLEMENTARY DATA

g. SG (nmax=2,542)

Direction of Association (BetaGene, IRAS, IRASFS, MACAD, Ref Allele NIDDM, Best p‐ Marker Chr Position Gene ref/nonref Freq β±SE Best model TRIPOD) value rs1674879 1 4497217 T/C 0.079 0.19 ± 0.05 dom ++++ 5.99E‐05 rs780593 1 4507743 C/T 0.081 0.19 ± 0.05 dom ++++ 1.03E‐04 rs1572823 1 19889959 T/C 0.125 ‐0.14 ± 0.04 dom ‐‐‐‐ 6.36E‐05 rs11805807 1 155064844 T/C 0.004 1.14 ± 0.27 dom +??? 2.89E‐05 rs563988 1 182474160 RGSL1 C/T 0.268 ‐0.11 ± 0.04 dom ‐+‐‐ 9.29E‐05 rs471910 1 182474704 RGSL1 C/T 0.269 ‐0.11 ± 0.04 dom ‐+‐‐ 5.55E‐05 rs7570259 2 23202248 A/C 0.002 1.59 ± 0.35 dom +??? 5.51E‐06 rs1049817 2 27550967 GTF3C2 A/G 0.464 0.11 ± 0.03 add ++++ 1.89E‐05 rs11684134 2 27558252 GTF3C2 A/G 0.436 0.1 ± 0.03 add ++++ 5.99E‐05 rs10205219 2 27568565 GTF3C2 T/C 0.463 0.11 ± 0.03 add ++++ 3.42E‐05 rs4665969 2 27574953 GTF3C2 T/C 0.468 0.11 ± 0.03 add ++++ 1.44E‐05 rs6716894 2 27583273 A/G 0.468 0.11 ± 0.03 add ++++ 3.40E‐05 rs7586601 2 27584666 A/G 0.425 0.11 ± 0.03 add ++++ 3.20E‐05 rs11695549 2 27586155 C/A 0.479 ‐0.11 ± 0.03 add ‐‐‐‐ 3.21E‐05 rs2280737 2 27589810 EIF2B4 T/C 0.469 0.11 ± 0.03 add ++++ 3.38E‐05 rs7602534 2 27592423 EIF2B4 C/T 0.465 0.11 ± 0.03 add ++++ 5.06E‐05 rs12475426 2 27599132 SNX17 G/A 0.459 0.11 ± 0.03 add ++++ 8.93E‐05 rs13472 2 27600239 ZNF513 G/A 0.469 0.11 ± 0.03 add ++++ 4.28E‐05 rs1260342 2 27663416 NRBP1 G/T 0.46 0.11 ± 0.03 add ++++ 1.02E‐04 rs4803 2 27667297 KRTCAP3 A/G 0.459 0.11 ± 0.03 add ++++ 8.09E‐05 rs11126999 2 27670307 IFT172 G/A 0.474 0.11 ± 0.03 add ++++ 3.09E‐05 rs704795 2 27716494 FNDC4 G/A 0.460 0.11 ± 0.03 add ++++ 7.12E‐05 rs1260320 2 27722416 GCKR G/A 0.467 0.11 ± 0.03 add ++++ 9.73E‐05

SUPPLEMENTARY DATA

rs2293571 2 27729480 GCKR G/A 0.476 0.12 ± 0.03 add ++++ 1.98E‐05 rs1260326 2 27730940 GCKR T/C 0.335 0.13 ± 0.03 add ++++ 4.04E‐06 rs780094 2 27741237 GCKR T/C 0.341 0.14 ± 0.03 add ++++ 1.97E‐06 rs780093 2 27742603 GCKR T/C 0.341 0.14 ± 0.03 add ++++ 1.12E‐06 rs11681351 2 27743423 GCKR G/A 0.479 0.11 ± 0.03 add ++++ 3.35E‐05 rs4852424 2 70283210 PCBP1‐AS1 G/A 0.382 ‐0.15 ± 0.04 dom ‐‐‐‐ 5.50E‐05 rs3755388 2 70310878 PCBP1‐AS1 G/A 0.388 ‐0.15 ± 0.04 dom ‐‐‐‐ 6.51E‐05 rs6743318 2 70373677 G/T 0.392 ‐0.15 ± 0.04 dom ‐‐‐‐ 4.91E‐05 rs14234 2 70524142 FAM136A A/G 0.412 0.10 ± 0.03 add ++++ 2.34E‐05 rs9816690 3 82046207 BC031255 A/G 0.055 0.23 ± 0.06 dom ++++ 7.44E‐05 rs11927192 3 183730657 ABCC5 A/G 0.004 0.77 ± 0.2 dom +?++ 5.32E‐05 rs523079 3 187615862 T/C 0.069 0.25 ± 0.06 dom +‐++ 1.53E‐07 rs13059988 3 187624906 T/G 0.063 0.22 ± 0.06 dom +‐++ 3.40E‐07 rs10000105 4 53623677 A/G 0.002 1.32 ± 0.34 dom +?++ 7.67E‐05 rs3775781 4 70595637 SULT1B1 T/C 0.027 ‐0.38 ± 0.10 dom ‐‐‐‐ 3.26E‐05 rs1011631 4 82440730 T/C 0.328 0.09 ± 0.03 add +‐++ 9.08E‐05 rs6871313 5 2397617 G/A 0.372 0.1 ± 0.03 add ++++ 4.12E‐05 rs6885718 5 31657655 PDZD2 G/A 0.081 0.22 ± 0.05 dom ++++ 4.62E‐05 rs17165293 5 126183502 A/G 0.041 0.28 ± 0.07 dom ++++ 8.94E‐05 rs7708035 5 161834699 A/G 0.003 1.71 ± 0.45 dom +++? 1.99E‐05 rs28011 5 179407229 RNF130 C/T 0.325 ‐0.08 ± 0.03 add ‐+‐‐ 8.59E‐05 rs4700708 5 179529895 RASGEF1C A/G 0.419 ‐0.08 ± 0.03 add ‐+‐‐ 6.82E‐05 rs2064197 6 8998811 G/A 0.164 ‐0.19 ± 0.04 dom ‐‐‐‐ 7.23E‐06 rs699986 6 49731027 G/A 0.472 ‐0.18 ± 0.05 rec ‐‐‐‐ 6.24E‐05 rs696718 6 49752742 T/G 0.473 ‐0.18 ± 0.05 rec ‐‐‐‐ 9.37E‐05 rs367274 6 90622187 T/C 0.418 0.12 ± 0.03 add ++++ 2.51E‐05 rs7744034 6 135143748 A/G 0.253 0.13 ± 0.04 dom +++‐ 5.45E‐05 rs11752655 6 135160309 G/A 0.081 0.19 ± 0.05 dom +++‐ 1.12E‐05 rs12536973 7 10062341 G/A 0.312 ‐0.11 ± 0.03 add ‐‐‐‐ 5.09E‐05 rs4720914 7 10915448 C/T 0.132 ‐0.17 ± 0.04 dom ‐‐‐‐ 8.42E‐05 rs16876733 7 10945193 C/A 0.129 ‐0.17 ± 0.04 dom ‐‐‐‐ 5.24E‐05 rs539518 7 73753250 CLIP2 T/C 0.366 0.09 ± 0.03 add +‐+‐ 9.40E‐05 rs1421221 8 97004203 C/T 0.385 ‐0.11 ± 0.03 add ‐‐‐‐ 9.91E‐05

SUPPLEMENTARY DATA

rs883952 9 71514651 PIP5K1B G/A 0.478 0.10 ± 0.03 add ++++ 5.56E‐05 rs12313180 12 30308868 T/C 0.336 0.14 ± 0.03 add ++++ 5.88E‐06 rs4931283 12 30334071 G/A 0.322 0.16 ± 0.04 dom ++++ 1.34E‐05 rs909013 12 30334754 G/A 0.317 0.16 ± 0.04 dom ++++ 1.75E‐05 rs17518256 12 30339648 C/A 0.295 0.17 ± 0.04 dom ++++ 1.32E‐05 rs10843647 12 30341934 T/G 0.331 0.17 ± 0.04 dom ++++ 4.13E‐06 rs11837387 12 73467487 C/T 0.001 2.02 ± 0.42 dom ++?? 2.22E‐05 rs17042107 12 76600231 C/T 0.038 0.3 ± 0.08 dom ++++ 1.03E‐04 rs11104268 12 76627445 G/A 0.042 0.33 ± 0.08 dom ++++ 6.74E‐06 rs7296900 12 104177668 NT5DC3 T/C 0.453 0.12 ± 0.03 add ++++ 4.05E‐05 rs11113179 12 107452785 CRY1 T/C 0.286 ‐0.12 ± 0.03 add ‐‐‐‐ 1.28E‐05 rs7319628 13 34502705 RFC3 A/G 0.006 0.95 ± 0.23 dom +++‐ 2.21E‐05 rs17081477 13 35134265 C/T 0.013 0.44 ± 0.13 dom +++‐ 3.83E‐05 rs1748124 13 52455098 C/T 0.480 ‐0.11 ± 0.03 add ‐‐‐+ 8.53E‐05 rs9550193 13 113324324 C13orf35 T/G 0.351 ‐0.12 ± 0.03 add ‐‐‐‐ 3.19E‐05 rs2145516 14 26129412 A/G 0.457 0.09 ± 0.03 add +‐++ 8.88E‐05 rs12432901 14 26494469 A/G 0.105 ‐0.18 ± 0.05 dom ‐‐‐‐ 4.44E‐05 rs7140895 14 49724328 C/T 0.123 0.17 ± 0.05 dom ++++ 9.31E‐05 rs2353498 15 24150918 T/C 0.329 0.1 ± 0.03 add +‐++ 4.06E‐05 rs1429751 15 34116858 RYR3 C/T 0.253 0.14 ± 0.04 dom ++++ 9.22E‐05 rs17650440 15 52504036 MYO5C A/G 0.004 2.09 ± 0.44 dom ???+ 6.17E‐06 rs9964 15 102194288 TARSL2 C/T 0.450 0.16 ± 0.05 rec ++++ 8.62E‐05 rs516667 15 102204031 TARSL2 G/A 0.448 0.16 ± 0.05 rec ++++ 5.02E‐05 rs12901450 15 102224341 TARSL2 A/G 0.449 0.17 ± 0.05 rec ++++ 4.27E‐05 rs2456491 15 102305129 T/C 0.461 0.18 ± 0.05 rec ++++ 2.47E‐05 rs1115936 16 7171923 RBFOX1 G/A 0.363 ‐0.13 ± 0.04 dom ‐+‐‐ 5.22E‐05 rs7203944 16 54438254 G/A 0.314 0.12 ± 0.03 add ++++ 1.03E‐04 rs4783122 16 82535037 G/A 0.243 ‐0.16 ± 0.04 dom ‐‐‐‐ 3.56E‐05 rs7202949 16 82593560 G/A 0.474 ‐0.09 ± 0.03 add ‐‐‐‐ 9.47E‐05 rs4299147 16 82883338 CDH13 T/C 0.410 0.10 ± 0.03 add ++++ 8.86E‐05 rs1559310 16 82918371 CDH13 G/T 0.437 ‐0.11 ± 0.03 add ‐‐‐‐ 4.08E‐05 rs11150514 16 82923464 CDH13 G/T 0.414 0.10 ± 0.03 add ++++ 4.41E‐05 rs12933472 16 82924685 CDH13 A/G 0.435 ‐0.12 ± 0.03 add ‐‐‐‐ 8.16E‐06

©2014 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db13-1829/-/DC1 SUPPLEMENTARY DATA rs11150519 16 82934307 CDH13 G/A 0.441 ‐0.11 ± 0.03 add ‐‐‐‐ 4.32E‐05 rs6565127 16 83152261 CDH13 G/A 0.373 0.09 ± 0.03 add ++++ 6.14E‐05 rs1559438 16 83308559 CDH13 C/T 0.476 0.09 ± 0.03 add +‐++ 6.67E‐05 rs7499978 16 85065085 KIAA0513 A/G 0.434 0.11 ± 0.03 add ++++ 5.49E‐05 rs16947417 17 13143819 G/T 0.053 0.26 ± 0.06 dom ++++ 2.24E‐05 rs9896748 17 64939574 T/G 0.070 0.27 ± 0.06 dom +++‐ 2.37E‐05 rs94312 18 7806492 PTPRM G/A 0.049 ‐0.27 ± 0.07 dom ‐‐‐‐ 8.39E‐05 rs2048132 18 73694904 T/G 0.225 0.16 ± 0.04 dom ++++ 2.16E‐05 rs6566045 18 75650801 C/T 0.289 0.14 ± 0.04 dom ++++ 4.52E‐05 rs1106581 19 293934 A/G 0.451 0.10 ± 0.03 add ++++ 9.35E‐05 rs2291004 19 37997952 ZNF793 A/C 0.153 0.16 ± 0.04 dom +++‐ 3.82E‐05 rs788338 19 50778543 MYH14 C/T 0.287 ‐0.17 ± 0.04 dom ‐‐‐+ 1.66E‐06 rs788332 19 50782462 MYH14 A/C 0.264 ‐0.16 ± 0.04 dom ‐‐‐‐ 1.77E‐05 rs2278998 19 50939737 MYBPC2 C/A 0.343 0.11 ± 0.03 add ++++ 1.00E‐04 rs2004423 19 50939867 MYBPC2 A/G 0.325 0.12 ± 0.03 add ++++ 4.51E‐05 rs4802723 19 51172786 SHANK1 G/A 0.150 ‐0.16 ± 0.04 dom ‐‐‐‐ 1.90E‐05 rs4802724 19 51173218 SHANK1 C/A 0.151 ‐0.16 ± 0.04 dom ‐‐‐‐ 1.81E‐05 rs2825882 21 21283010 C/T 0.474 ‐0.10 ± 0.03 add ‐‐‐+ 9.16E‐05 rs9974077 21 43835771 UBASH3A T/G 0.259 0.13 ± 0.04 dom ++++ 3.44E‐05

SUPPLEMENTARY DATA

Supplementary Table 3. Top Discovery hits from the GUARDIAN Consortium ordered by trait.

Model 1§ Model 2|| SNP Chr Position* Gene Name Alleles† RAF‡ Trait Beta P-value Beta P-value rs2302063 19 3150418 GNA15 A/C 0.34 MCRI -0.29 7.31E-08 -0.19 1.47E-05 rs1602084 4 128843480 MFSD8 G/A 0.041 SI+M 8.97 5.20E-07 11.15 7.29E-05 rs896232 2 2732877 MYT1L / TSSC1 T/C 0.29 SI+M -5.28 1.26E-06 -6.44 4.43E-04 rs6719442 2 2722295 MYT1L / TSSC1 A/G 0.18 SI+M -5.03 1.53E-06 -4.79 5.06E-04 ¶ rs1978648 2 43371542 HAAO / ZFP36L2 / THADA T/C 0.32 SI 0.20 5.31E-07 0.10 2.11E-05 rs896598 15 74036629 C15orf59 A/G 0.12 SI 0.37 5.83E-07 0.28 7.14E-07 rs4887140 15 74046663 C15orf59 / TBC1D21 G/T 0.14 SI 0.31 6.91E-08 0.18 1.35E-06 rs196701 6 80147187 HMGN3 / LCA5 C/T 0.13 SI -0.35 1.37E-06 -0.10 9.02E-03 rs10492494 13 74920186 KLF12 / LINC00347 A/C 0.24 M -22.00 5.04E-07 -15.71 8.82E-05 rs11683087 2 227586606 LOC646736 / IRS1# G/A 0.41 M 20.54 7.42E-07 17.45 8.25E-06 ** rs10830963 11 92708710 MTNR1B G/C 0.22 AIRg -2.76 5.23E-12 -2.81 3.22E-13 †† rs1387153 11 92673828 FAT3 / MTNR1B T/C 0.22 AIRg -2.55 2.21E-09 -2.62 2.16E-10 ‡‡ rs2206734 6 20694884 CDKAL1 T/C 0.20 AIRg -2.05 1.02E-06 -1.90 5.03E-06 §§ rs3847554 11 92668826 FAT3 / MTNR1B A/G 0.34 AIRg -1.64 1.08E-06 -1.70 1.27E-07 |||| rs9368222 6 20686996 CDKAL1 A/C 0.26 AIRg -1.46 1.28E-06 -1.36 4.74E-06 rs6803803 3 180116563 PEX5L / TTC14 C/T 0.0030 AIRg 17.53 1.64E-06 17.25 9.29E-07 rs10830963 11 92708710 MTNR1B** G/C 0.23 DI -3.40 1.03E-11 -3.36 3.25E-12 rs1387153 11 92673828 FAT3 / MTNR1B†† T/C 0.22 DI -3.20 1.32E-09 -3.11 7.51E-10 rs2149423 13 36772381 CCDC169-SOHLH2; SOHLH2 G/A 0.32 DI 2.18 3.67E-07 2.07 7.35E-07 rs3812570 9 139275204 SNAPC4 A/C 0.46 DI -1.87 1.72E-06 -1.63 5.89E-06 rs523079 3 187615862 BCL6 / LPP T/C 0.069 SG 0.25 1.53E-07 0.25 3.82E-08 ¶¶ rs780093 2 27742603 GCKR T/C 0.34 SG 0.14 1.12E-06 0.13 3.11E-06 rs788338 19 50778543 MYH14 C/T 0.29 SG -0.17 1.66E-06 -0.17 1.98E-06 Independent signals (r2<0.80) with evidence of association (P<2.00E-06) with the nearest annotated RefSeq gene(s) listed. *Build hg19, †Reference Allele/Other Allele, ‡Reference Allele Frequency, §Model 1 covariates included age, gender, study site (in multi- center recruitment studies), and admixture proportions, ||Model 2 covariates included age, gender, study site (in multi-center recruitment studies), admixture proportions, and BMI, ¶Previously identified T2D locus (THADA rs7578597; r2=0.0079, #Previously identified T2D locus (IRS1 rs2943641; r2=0.04), **Previously identified T2D locus (MTNR1B rs1387153; r2=0.69), ††Previously identified T2D locus (MTNR1B rs1387153), ‡‡Previously identified T2D locus (CDKAL1 rs7754840; r2=0.42), §§Previously identified T2D locus (MTNR1B rs1387153; r2=0.54), ||||Previously identified T2D locus (CDKAL1 rs7754840; r2=0.72), ¶¶Previously identified T2D locus (GCKR rs780094; r2=0.98)

SUPPLEMENTARY DATA Supplementary Table 4. Top Discovery hits from the GUARDIAN Consortium ordered by trait with conditional analyses performed at loci with multiple signals of association or in close proximity to previously identified T2D loci.

Conditional Analysis SNP Chr:Position* Gene Name Alleles† RAF‡ Trait Beta P-value SNP r2§ P-value rs2302063 19:3150418 GNA15 A/C 0.336 MCRI -0.29 7.31E-08 rs1602084 4:128843480 MFSD8 G/A 0.041 SI+M 8.97 5.20E-07 rs896232 2:2732877 MYT1L / TSSC1 T/C 0.291SI+M -5.28 1.26E-06 rs6719442 2:2722295 MYT1L / TSSC1 A/G 0.184 SI+M -5.03 1.53E-06 rs896232 0.37 8.21E-03 || || rs1978648 2:43371542 HAAO / ZFP36L2 / THADA T/C 0.324 SI 0.20 5.31E-07 rs7578597 0.0079 6.88E-07 rs896598 15:74036629 C15orf59 A/G 0.116 SI 0.37 5.83E-07 rs4887140 15:74046663 C15orf59 / TBC1D21 G/T 0.139 SI 0.31 6.91E-08 rs896598 0.79 3.41E-02 rs196701 6:80147187 HMGN3 / LCA5 C/T 0.132 SI -0.35 1.37E-06 rs10492494 13:74920186 KLF12 / LINC00347 A/C 0.240 M -22.02 5.04E-07 rs11683087 2:227586606 LOC646736 / IRS1|| G/A 0.412M 20.547.42E-07 rs2943641|| 0.04 1.29E-06 || || rs10830963 11:92708710 MTNR1B G/C 0.220AIRg -2.76 5.23E-12 rs1387153 0.69 8.67E-05 || || rs1387153 11:92673828 FAT3 / MTNR1B T/C 0.220AIRg -2.55 2.21E-09 rs10830963 0.69 8.27E-01 || || rs2206734 6:20694884 CDKAL1 T/C 0.198AIRg -2.05 1.02E-06 rs7754840 0.42 9.37E-03 || || rs3847554 11:92668826 FAT3 / MTNR1B A/G 0.341AIRg -1.64 1.08E-06 rs1387153 0.54 3.66E-01 rs10830963 0.36 5.95E-01 || || rs9368222 6:20686996 CDKAL1 A/C 0.264AIRg -1.46 1.28E-06 rs7754840 0.72 8.19E-02 rs2206734 0.57 3.06E-01 rs6803803 3:180116563 PEX5L / TTC14 C/T 0.003 AIRg 17.53 1.64E-06 rs10830963 11:92708710 MTNR1B|| G/C 0.230DI -3.401.03E-11 rs1387153|| 0.69 4.31E-04 rs1387153 11:92673828 FAT3 / MTNR1B|| T/C 0.220DI -3.201.32E-09 rs10830963|| 0.69 7.27E-01 rs2149423 13:36772381 CCDC169-SOHLH2; SOHLH2 G/A 0.315 DI 2.18 3.67E-07 rs3812570 9:139275204 SNAPC4 A/C 0.461 DI -1.87 1.72E-06 rs523079 3:187615862 BCL6 / LPP T/C 0.069 SG 0.25 1.53E-07 || || rs780093 2:27742603 GCKR T/C 0.341SG 0.14 1.12E-06 rs780094 0.98 1.05E-01 rs788338 19:50778543 MYH14 C/T 0.287 SG -0.17 1.66E-06 Independent signals (r2<0.80) with evidence of association (P<2.00E-06) with the nearest annotated RefSeq gene(s) listed. *Build hg19, †Reference Allele/Other Allele, ‡Reference Allele Frequency, §Correlation from the largest set of unrelated individuals from BetaGene ||Previously identified T2D locus

SUPPLEMENTARY DATA

Supplementary Table 5A. Association with reported type 2 diabetes (T2D) susceptibility loci with MCRI in GUARDIAN Hispanic Americans (nmax=3,787). Index SNPs reaching genome‐wide significance (P<5.0E‐08) for association with T2D were selected from the NHGRI GWAS catalog (http://www.genome.gov/gwastudies). When the index variable was unavailable in GUARDIAN, a suitable proxy was selected using the HapMap 3 MEX (Mexican ancestry in Los Angeles, California) population.

2 Index r Position Alleles Heterogeneity Additive Ref Proxy Gene(s) Beta SE SNP (MEX) (hg19) Risk Ref/Alt P-value P-value rs10923931 1 rs2793831 1.00 1:120523902 NOTCH2 T T/C 0.05 0.09 0.10 0.80 rs2075423 29 1:212221342 PROX1 G - - - - - rs17106184 28 rs1278516 1.00 1:50900021 FAF1 G G/A 0.22 0.12 0.072 0.71 rs6723108 30 2:135479980 TMEM163 T T/G 0.08 0.07 0.012 0.68 rs7560163 2 2:151637936 RND3 / FABP5P10 C - - - - - rs7593730 3 2:161171454 RBMS1 C - - - - - rs3923113 4 2:165501849 EIF3EP3 / SNORA70F A - - - - - rs7578326 5 rs13405357 0.90 2:227022036 LOC646736 A A/G -0.12 0.06 0.53 0.048 rs2943641 31 2:227093745 IRS1 C C/T -0.16 0.06 0.15 0.24 rs780094 29 2:27741237 GCKR C C/T -0.09 0.05 0.82 0.050 rs7578597 1 2:43732823 THADA T T/C 0.12 0.11 0.42 0.52 rs243021 5 2:60584819 BCL11A A A/G -0.07 0.05 0.017 0.18 rs11708067 29 3:123065778 ADCY5 A A/G 0.03 0.06 0.20 0.37 rs1801282 3:12393125 PPARG C C/G -0.11 0.08 0.67 0.38 rs4402960 6 3:185511687 IGF2BP2 T T/G 0.05 0.06 0.25 0.92 rs16861329 4 rs16861317 1.00 3:186664728 ST6GAL1 G G/A 0.12 0.05 0.0050 0.71 rs6808574 28 3:187740523 LPP C C/T -0.01 0.06 0.086 0.43 rs7612463 32 3:23336450 UBE2E2 C C/A -0.19 0.11 0.52 0.081 rs831571 8 rs35837 0.92 3:64013249 PSMD6 / PRICKLE2-AS1 C C/T 0.05 0.09 0.67 0.72 rs4607103 1 3:64711904 ADAMTS9-AS2 C C/T 0.07 0.05 0.24 0.090 rs7656416 9 4:1254535 CTBP1-AS1 / MAEA C - - - - - rs6815464 8 4:1309901 MAEA C - - - - - rs6813195 28 4:153739925 TMEM154 C - - - - - rs1801214 5 4:6303022 WFS1 T - - - - - rs702634 28 5:53271420 ARL15 A A/G -0.02 0.07 0.31 0.77 rs459193 33 5:55842508 ANKRD55 G - - - - - rs4457053 5 5:76424949 ZBED3-AS1 G G/A -0.02 0.05 0.36 0.48 rs10946398 12 rs7754840 0.96 6:20661250 CDKAL1 C C/G 0.16 0.05 0.0025 0.0087 rs3130501 28 6:31136453 POU5F1-TCF19 G G/A -0.11 0.06 0.81 0.061

SUPPLEMENTARY DATA

rs9470794 8 rs3800364 0.83 6:38121211 ZFAND3 C G/A 0.04 0.12 0.82 0.94 rs1535500 8 6:39284050 KCNK16 T - - - - - rs1048886 15 6:71289189 C6orf57 G G/A -0.01 0.07 0.92 0.62 rs9505118 28 6:7290437 SSR1-RREB1 A A/G 0.05 0.05 0.14 0.82 rs6467136 8 7:127164958 ZNF800 / GCC1 G - - - - - rs10229583 16 7:127246903 FSCN3 / PAX4 G G/A 0.09 0.07 0.88 0.27 rs972283 5 7:130466854 KLF14 / MIR29A G G/A -0.02 0.05 0.14 0.50 rs17168486 29 7:14898282 DGKB T T/C 0.08 0.05 0.34 0.084 rs864745 1 rs1635852 1.00 7:28189411 JAZF1 T T/C -0.06 0.07 0.68 0.16 rs10278336 29 7:44211888 GCK A - - - - - rs13266634 11 8:118184783 SLC30A8 C C/T 0.09 0.06 0.41 0.11 rs515071 9 rs508419 1.00 8:41522991 ANK1 C G/A 0.05 0.06 0.65 0.60 rs896854 5 rs4735337 0.81 8:95973465 TP53INP1 T T/C 0.04 0.05 0.83 0.33 rs10811661 6 9:22134094 CDKN2B-AS1 / DMRTA1 T - - - - - rs7018475 18 9:22137685 CDKN2B-AS1 / DMRTA1 T T/G -0.11 0.06 0.26 0.030 rs7041847 8 9:4287466 GLIS3 A - - - - - rs13292136 5 9:81952128 KRT18P24 / CHCHD2P9 C - - - - - rs2796441 33 9:84308948 TLE1 G G/A 0.07 0.06 0.87 0.39 rs17584499 20 9:8879118 PTPRD T T/C 0.12 0.06 0.82 0.11 rs7903146 22 10:114758349 TCF7L2 T T/C 0.04 0.06 0.64 0.92 rs10886471 19 10:121149403 GRK5 C C/T -0.06 0.07 0.25 0.17 rs12779790 1 10:12328010 CDC123 / MIR4480 G - - - - - rs1802295 4 10:70931474 VPS26A A A/G -0.10 0.06 0.43 0.064 rs12571751 33 10:80612637 ZMIZ1 A - - - - - rs1111875 11 rs10882101 1.00 10:94462427 HHEX / EXOC6 C C/T -0.06 0.05 0.33 0.23 rs2334499 35 11:1696849 DUSP8 T T/C 0.05 0.05 0.22 0.46 rs5219 6 11:17409572 KCNJ11 T T/C -0.06 0.05 0.93 0.27 rs231362 5 11:2691471 KCNQ1;KCNQ1OT1 G G/A 0.09 0.05 0.92 0.13 rs2237892 24 11:2839751 KCNQ1 C C/T -0.10 0.06 0.47 0.096 rs1552224 5 11:72433098 ARAP1 A A/C 0.12 0.11 0.14 0.12 rs1387153 5 11:92673828 FAT3 / MTNR1B T T/C -0.02 0.06 0.88 0.35 rs7305618 17 12:121402932 RPL12P33 / HNF1A-AS1 C C/T 0.10 0.07 0.54 0.24 rs7957197 5 12:121460686 OASL T - - - - - rs4275659 28 12:123447928 MPHOSPH9 C C/T -0.02 0.05 0.32 0.25 rs10842994 33 12:27965150 KLHDC5 C C/T 0.02 0.07 0.51 0.67 rs11063069 34 12:4374373 CCND2 G G/A -0.09 0.08 0.66 0.48

SUPPLEMENTARY DATA

rs1531343 5 rs2612067 1.00 12:66170163 RPSAP52 C G/T 0.08 0.10 0.73 0.15 rs2261181 5 12:66212318 HMGA2 T T/C 0.06 0.11 0.94 0.40 rs7961581 1 12:71663102 TSPAN8 / LGR5 C C/T -0.11 0.07 0.20 0.11 rs9552911 26 13:23864657 SGCG G - - - - - rs1359790 23 13:80717156 NDFIP2 / SPRY2 G - - - - - rs7403531 19 15:38822905 RASGRP1 T T/C 0.02 0.05 0.20 0.24 rs7172432 27 15:62396389 C2CD4A / C2CD4B A - - - - - rs7178572 4 rs11857294 0.86 15:77596725 HMG20A G C/T -0.10 0.05 0.035 0.0053 rs11634397 5 15:80432222 ZFAND6 / FAH G G/A 0.13 0.05 0.054 0.093 rs2028299 4 15:90374257 AP3S2;C15orf38-AP3S2 C C/A 0.09 0.06 0.26 0.51 rs8042680 5 15:91521337 PRC1 A A/C 0.03 0.05 0.082 0.33 rs8050136 12 16:53816275 FTO A A/C -0.14 0.06 0.019 0.34 rs7202877 33 16:75247245 BCAR1 T T/G 0.17 0.10 0.46 0.057 rs391300 20 17:2216258 SRR G G/A -0.02 0.05 0.10 0.99 rs13342232 36 17:6945940 SLC16A11 G - - - - - rs4430796 19 17:36098040 HNF1B G G/A 0.05 0.05 0.89 0.28 rs12970134 33 18:57884750 MC4R A A/G -0.08 0.07 0.26 0.16 rs8090011 14 18:7068462 LAMA1 G - - - - - rs10401969 33 19:19407718 CILP2 C C/T 0.04 0.13 0.016 0.95 rs3786897 8 19:33893008 PEPD A A/G 0.03 0.06 0.68 0.18 rs6017317 8 20:42946966 FITM2 / R3HDML G - - - - - rs4812829 4 rs2144908 1.00 20:42985717 HNF4A A A/G 0.04 0.05 0.66 0.20 rs12010175 19 X:152862638 FAM58A G - - - - - rs5945326 5 X:152899922 KRT18P48 / DUSP9 A - - - - -

SUPPLEMENTARY DATA

Supplementary Table 5B. Association with reported type 2 diabetes (T2D) susceptibility loci with SI+M in GUARDIAN Hispanic Americans (nmax=4,153). Index SNPs reaching genome‐wide significance (P<5.0E‐08) for association with T2D were selected from the NHGRI GWAS catalog (http://www.genome.gov/gwastudies). When the index SNP was unavailable in GUARDIAN, a suitable proxy was selected using the HapMap 3 MEX (Mexican ancestry in Los Angeles, California) population.

2 Index r Position Alleles Heterogeneity Additive Ref Proxy Gene(s) Beta SE SNP (MEX) (hg19) Risk Ref/Alt P-value P-value rs10923931 1 rs2793831 1.00 1:120523902 NOTCH2 T T/C 0.22 2.46 0.82 0.55 rs2075423 29 1:212221342 PROX1 G - - - - - rs17106184 28 rs1278516 1.00 1:50900021 FAF1 G G/A -0.70 3.64 0.85 0.26 rs6723108 30 2:135479980 TMEM163 T T/G -1.67 2.45 0.24 0.73 rs7560163 2 2:151637936 RND3 / FABP5P10 C - - - - - rs7593730 3 2:161171454 RBMS1 C - - - - - rs3923113 4 2:165501849 EIF3EP3 / SNORA70F A - - - - - rs7578326 5 rs13405357 0.90 2:227022036 LOC646736 A A/G 2.44 1.94 0.10 0.60 rs2943641 31 2:227093745 IRS1 C C/T 0.85 2.11 0.099 0.16 rs780094 29 2:27741237 GCKR C C/T -1.09 1.72 0.99 0.098 rs7578597 1 2:43732823 THADA T T/C 3.69 3.65 0.94 0.15 rs243021 5 2:60584819 BCL11A A A/G 1.24 1.69 0.12 0.53 rs11708067 29 3:123065778 ADCY5 A A/G 0.51 1.89 0.47 0.76 rs1801282 3:12393125 PPARG C C/G 2.70 2.75 0.51 0.64 rs4402960 6 3:185511687 IGF2BP2 T T/G -0.01 1.98 0.12 0.95 rs16861329 4 rs16861317 1.00 3:186664728 ST6GAL1 G G/A 0.07 1.80 0.14 0.072 rs6808574 28 3:187740523 LPP C C/T -1.95 2.14 0.12 0.66 rs7612463 32 3:23336450 UBE2E2 C C/A -2.64 3.13 0.52 0.26 rs831571 8 rs35837 0.92 3:64013249 PSMD6 / PRICKLE2-AS1 C C/T -0.74 2.90 0.97 0.71 rs4607103 1 3:64711904 ADAMTS9-AS2 C C/T -2.29 1.76 0.03 0.41 rs7656416 9 4:1254535 CTBP1-AS1 / MAEA C - - - - - rs6815464 8 4:1309901 MAEA C - - - - - rs6813195 28 4:153739925 TMEM154 C - - - - - rs1801214 5 4:6303022 WFS1 T - - - - - rs702634 28 5:53271420 ARL15 A A/G -4.60 2.22 0.73 0.041 rs459193 33 5:55842508 ANKRD55 G - - - - - rs4457053 5 5:76424949 ZBED3-AS1 G G/A 0.88 1.71 0.94 0.79 rs10946398 12 rs7754840 0.96 6:20661250 CDKAL1 C C/G 0.52 1.77 0.019 0.0081 rs3130501 28 6:31136453 POU5F1-TCF19 G G/A 1.43 1.95 0.57 0.75

SUPPLEMENTARY DATA

rs9470794 8 rs3800364 0.83 6:38121211 ZFAND3 C G/A 4.43 3.25 0.99 0.022 rs1535500 8 6:39284050 KCNK16 T - - - - - rs1048886 15 6:71289189 C6orf57 G G/A -0.15 2.09 0.40 0.36 rs9505118 28 6:7290437 SSR1-RREB1 A A/G 1.09 1.67 0.095 0.90 rs6467136 8 7:127164958 ZNF800 / GCC1 G - - - - - rs10229583 16 7:127246903 FSCN3 / PAX4 G G/A -1.64 2.24 0.73 0.80 rs972283 5 7:130466854 KLF14 / MIR29A G G/A -2.74 1.67 0.49 0.014 rs17168486 29 7:14898282 DGKB T T/C 1.28 1.68 0.71 0.21 rs864745 1 rs1635852 1.00 7:28189411 JAZF1 T T/C -4.20 1.62 0.41 0.068 rs10278336 29 7:44211888 GCK A - - - - - rs13266634 11 8:118184783 SLC30A8 C C/T 1.25 1.92 0.10 0.21 rs515071 9 rs508419 1.00 8:41522991 ANK1 C G/A 1.83 2.09 0.94 0.73 rs896854 5 rs4735337 0.81 8:95973465 TP53INP1 T T/C 2.08 1.54 0.67 0.35 rs10811661 6 9:22134094 CDKN2B-AS1 / DMRTA1 T - - - - - rs7018475 18 9:22137685 CDKN2B-AS1 / DMRTA1 T T/G -1.75 1.79 0.97 0.22 rs7041847 8 9:4287466 GLIS3 A - - - - - rs13292136 5 9:81952128 KRT18P24 / CHCHD2P9 C - - - - - rs2796441 33 9:84308948 TLE1 G G/A -2.14 1.65 0.41 0.86 rs17584499 20 9:8879118 PTPRD T T/C -1.01 1.98 0.15 0.41 rs7903146 22 10:114758349 TCF7L2 T T/C 0.33 1.87 0.76 0.34 rs10886471 19 10:121149403 GRK5 C C/T -0.16 1.48 0.60 0.30 rs12779790 1 10:12328010 CDC123 / MIR4480 G - - - - - rs1802295 4 10:70931474 VPS26A A A/G -4.82 1.94 0.32 0.0094 rs12571751 33 10:80612637 ZMIZ1 A - - - - - rs1111875 11 rs10882101 1.00 10:94462427 HHEX / EXOC6 C C/T -0.79 1.72 0.13 0.66 rs2334499 35 11:1696849 DUSP8 T T/C -2.48 1.59 0.16 0.31 rs5219 6 11:17409572 KCNJ11 T T/C 2.75 1.71 0.19 0.85 rs231362 5 11:2691471 KCNQ1;KCNQ1OT1 G G/A -0.81 1.79 0.23 0.18 rs2237892 24 11:2839751 KCNQ1 C C/T 1.75 1.84 0.36 0.48 rs1552224 5 11:72433098 ARAP1 A A/C 3.34 3.15 0.47 0.31 rs1387153 5 11:92673828 FAT3 / MTNR1B T T/C -2.52 1.87 0.61 0.013 rs7305618 17 12:121402932 RPL12P33 / HNF1A-AS1 C C/T 1.20 2.15 0.90 0.084 rs7957197 5 12:121460686 OASL T - - - - - rs4275659 28 12:123447928 MPHOSPH9 C C/T 0.55 1.64 0.61 0.37 rs10842994 33 12:27965150 KLHDC5 C C/T -1.58 2.47 0.079 0.95 rs11063069 34 12:4374373 CCND2 G G/A -1.71 2.31 0.99 0.15

SUPPLEMENTARY DATA

rs1531343 5 rs2612067 1.00 12:66170163 RPSAP52 C G/T -0.11 3.01 0.30 0.26 rs2261181 5 12:66212318 HMGA2 T T/C 0.01 3.29 0.52 0.45 rs7961581 1 12:71663102 TSPAN8 / LGR5 C C/T -4.73 2.20 0.051 0.094 rs9552911 26 13:23864657 SGCG G - - - - - rs1359790 23 13:80717156 NDFIP2 / SPRY2 G - - - - - rs7403531 19 15:38822905 RASGRP1 T T/C 0.47 1.70 0.58 0.63 rs7172432 27 15:62396389 C2CD4A / C2CD4B A - - - - - rs7178572 4 rs11857294 0.86 15:77596725 HMG20A G C/T -2.51 1.70 0.40 0.067 rs11634397 5 15:80432222 ZFAND6 / FAH G G/A 1.41 1.55 0.79 0.14 rs2028299 4 15:90374257 AP3S2;C15orf38-AP3S2 C C/A 1.75 2.24 0.94 0.017 rs8042680 5 15:91521337 PRC1 A A/C 2.33 1.83 0.17 0.25 rs8050136 12 16:53816275 FTO A A/C -4.64 1.93 0.78 0.0019 rs7202877 33 16:75247245 BCAR1 T T/G -0.79 2.89 0.16 0.62 rs391300 20 17:2216258 SRR G G/A 1.39 1.71 0.31 0.24 rs13342232 36 17:6945940 SLC16A11 G - - - - - rs4430796 19 17:36098040 HNF1B G G/A 1.87 1.69 0.36 0.16 rs12970134 33 18:57884750 MC4R A A/G 1.96 2.36 0.36 0.65 rs8090011 14 18:7068462 LAMA1 G - - - - - rs10401969 33 19:19407718 CILP2 C C/T 4.84 3.67 0.015 0.48 rs3786897 8 19:33893008 PEPD A A/G -4.10 1.89 0.10 0.85 rs6017317 8 20:42946966 FITM2 / R3HDML G - - - - - rs4812829 4 rs2144908 1.00 20:42985717 HNF4A A A/G 3.58 1.72 0.56 0.0046 rs12010175 19 X:152862638 FAM58A G - - - - - rs5945326 5 X:152899922 KRT18P48 / DUSP9 A - - - - -

SUPPLEMENTARY DATA

Supplementary Table 5C. Association with reported type 2 diabetes (T2D) susceptibility loci with SI in GUARDIAN Hispanic Americans (nmax=2,549). Index SNPs reaching genome‐wide significance (P<5.0E‐08) for association with T2D were selected from the NHGRI GWAS catalog (http://www.genome.gov/gwastudies). When the index variable was unavailable in GUARDIAN, a suitable proxy was selected using the HapMap 3 MEX (Mexican ancestry in Los Angeles, California) population.

2 Index r Position Alleles Heterogeneity Additive Ref Proxy Gene(s) Beta SE SNP (MEX) (hg19) Risk Ref/Alt P-value P-value rs10923931 1 rs2793831 1.00 1:120523902 NOTCH2 T T/C -0.01 0.09 0.77 0.45 rs2075423 29 1:212221342 PROX1 G - - - - - rs17106184 28 rs1278516 1.00 1:50900021 FAF1 G G/A 0.07 0.14 0.85 0.13 rs6723108 30 2:135479980 TMEM163 T T/G 0.02 0.07 0.23 0.23 rs7560163 2 2:151637936 RND3 / FABP5P10 C - - - - - rs7593730 3 2:161171454 RBMS1 C - - - - - rs3923113 4 2:165501849 EIF3EP3 / SNORA70F A - - - - - rs7578326 5 rs13405357 0.90 2:227022036 LOC646736 A A/G -0.06 0.06 0.89 0.092 rs2943641 31 2:227093745 IRS1 C C/T -0.12 0.07 0.34 0.031 rs780094 29 2:27741237 GCKR C C/T -0.05 0.06 0.92 0.12 rs7578597 1 2:43732823 THADA T T/C 0.15 0.11 0.90 0.23 rs243021 5 2:60584819 BCL11A A A/G 0.02 0.06 0.083 0.16 rs11708067 29 3:123065778 ADCY5 A A/G -0.07 0.07 0.26 0.73 rs1801282 3:12393125 PPARG C C/G -0.12 0.09 0.54 0.18 rs4402960 6 3:185511687 IGF2BP2 T T/G -0.02 0.06 0.036 0.94 rs16861329 4 rs16861317 1.00 3:186664728 ST6GAL1 G G/A 0.04 0.06 0.18 0.054 rs6808574 28 3:187740523 LPP C C/T 0.09 0.07 0.21 0.56 rs7612463 32 3:23336450 UBE2E2 C C/A 0.01 0.11 0.25 0.43 rs831571 8 rs35837 0.92 3:64013249 PSMD6 / PRICKLE2-AS1 C C/T 0.02 0.09 0.93 0.59 rs4607103 1 3:64711904 ADAMTS9-AS2 C C/T 0.04 0.06 0.021 0.70 rs7656416 9 4:1254535 CTBP1-AS1 / MAEA C - - - - - rs6815464 8 4:1309901 MAEA C - - - - - rs6813195 28 4:153739925 TMEM154 C - - - - - rs1801214 5 4:6303022 WFS1 T - - - - - rs702634 28 5:53271420 ARL15 A A/G -0.07 0.07 0.54 0.31 rs459193 33 5:55842508 ANKRD55 G - - - - - rs4457053 5 5:76424949 ZBED3-AS1 G G/A -0.02 0.06 0.99 0.77 rs10946398 12 rs7754840 0.96 6:20661250 CDKAL1 C C/G 0.08 0.06 0.015 0.00094 rs3130501 28 6:31136453 POU5F1-TCF19 G G/A -0.07 0.07 0.74 0.46

SUPPLEMENTARY DATA

rs9470794 8 rs3800364 0.83 6:38121211 ZFAND3 C G/A 0.21 0.12 0.91 0.061 rs1535500 8 6:39284050 KCNK16 T - - - - - rs1048886 15 6:71289189 C6orf57 G G/A 0.08 0.08 0.42 0.37 rs9505118 28 6:7290437 SSR1-RREB1 A A/G -0.11 0.06 0.063 0.65 rs6467136 8 7:127164958 ZNF800 / GCC1 G - - - - - rs10229583 16 7:127246903 FSCN3 / PAX4 G G/A 0.09 0.08 0.75 0.37 rs972283 5 7:130466854 KLF14 / MIR29A G G/A -0.06 0.06 0.24 0.047 rs17168486 29 7:14898282 DGKB T T/C 0.09 0.06 0.65 0.22 rs864745 1 rs1635852 1.00 7:28189411 JAZF1 T T/C -0.03 0.06 0.82 0.44 rs10278336 29 7:44211888 GCK A - - - - - rs13266634 11 8:118184783 SLC30A8 C C/T 0.10 0.07 0.021 0.24 rs515071 9 rs508419 1.00 8:41522991 ANK1 C G/A 0.02 0.07 0.86 0.74 rs896854 5 rs4735337 0.81 8:95973465 TP53INP1 T T/C -0.03 0.06 0.54 0.87 rs10811661 6 9:22134094 CDKN2B-AS1 / DMRTA1 T - - - - - rs7018475 18 9:22137685 CDKN2B-AS1 / DMRTA1 T T/G -0.04 0.06 0.79 0.40 rs7041847 8 9:4287466 GLIS3 A - - - - - rs13292136 5 9:81952128 KRT18P24 / CHCHD2P9 C - - - - - rs2796441 33 9:84308948 TLE1 G G/A 0.03 0.06 0.56 0.30 rs17584499 20 9:8879118 PTPRD T T/C 0.12 0.07 0.83 0.10 rs7903146 22 10:114758349 TCF7L2 T T/C 0.03 0.06 0.39 0.27 rs10886471 19 10:121149403 GRK5 C C/T -0.09 0.06 0.47 0.26 rs12779790 1 10:12328010 CDC123 / MIR4480 G - - - - - rs1802295 4 10:70931474 VPS26A A A/G -0.07 0.07 0.86 0.085 rs12571751 33 10:80612637 ZMIZ1 A - - - - - rs1111875 11 rs10882101 1.00 10:94462427 HHEX / EXOC6 C C/T -0.05 0.06 0.17 0.54 rs2334499 35 11:1696849 DUSP8 T T/C -0.09 0.06 0.088 0.96 rs5219 6 11:17409572 KCNJ11 T T/C -0.03 0.06 0.57 0.11 rs231362 5 11:2691471 KCNQ1;KCNQ1OT1 G G/A 0.15 0.06 0.21 0.036 rs2237892 24 11:2839751 KCNQ1 C C/T 0.03 0.07 0.19 0.85 rs1552224 5 11:72433098 ARAP1 A A/C -0.02 0.10 0.38 0.65 rs1387153 5 11:92673828 FAT3 / MTNR1B T T/C -0.16 0.07 0.33 0.032 rs7305618 17 12:121402932 RPL12P33 / HNF1A-AS1 C C/T 0.06 0.08 0.82 0.12 rs7957197 5 12:121460686 OASL T - - - - - rs4275659 28 12:123447928 MPHOSPH9 C C/T -0.09 0.06 0.66 0.23 rs10842994 33 12:27965150 KLHDC5 C C/T 0.02 0.08 0.38 0.96 rs11063069 34 12:4374373 CCND2 G G/A -0.05 0.08 0.90 0.21

SUPPLEMENTARY DATA

rs1531343 5 rs2612067 1.00 12:66170163 RPSAP52 C G/T 0.23 0.11 0.14 0.19 rs2261181 5 12:66212318 HMGA2 T T/C 0.18 0.11 0.32 0.37 rs7961581 1 12:71663102 TSPAN8 / LGR5 C C/T 0.07 0.07 0.05 0.44 rs9552911 26 13:23864657 SGCG G - - - - - rs1359790 23 13:80717156 NDFIP2 / SPRY2 G - - - - - rs7403531 19 15:38822905 RASGRP1 T T/C 0.00 0.06 0.80 0.51 rs7172432 27 15:62396389 C2CD4A / C2CD4B A - - - - - rs7178572 4 rs11857294 0.86 15:77596725 HMG20A G C/T -0.04 0.06 0.95 0.19 rs11634397 5 15:80432222 ZFAND6 / FAH G G/A 0.06 0.06 0.89 0.22 rs2028299 4 15:90374257 AP3S2;C15orf38-AP3S2 C C/A 0.11 0.07 0.87 0.024 rs8042680 5 15:91521337 PRC1 A A/C -0.07 0.06 0.065 0.53 rs8050136 12 16:53816275 FTO A A/C -0.12 0.07 0.58 0.026 rs7202877 33 16:75247245 BCAR1 T T/G -0.03 0.11 0.066 0.42 rs391300 20 17:2216258 SRR G G/A 0.08 0.06 0.17 0.53 rs13342232 36 17:6945940 SLC16A11 G - - - - - rs4430796 19 17:36098040 HNF1B G G/A -0.04 0.06 0.18 0.48 rs12970134 33 18:57884750 MC4R A A/G 0.03 0.08 0.22 0.87 rs8090011 14 18:7068462 LAMA1 G - - - - - rs10401969 33 19:19407718 CILP2 C C/T 0.14 0.15 0.12 0.82 rs3786897 8 19:33893008 PEPD A A/G 0.04 0.06 0.36 0.20 rs6017317 8 20:42946966 FITM2 / R3HDML G - - - - - rs4812829 4 rs2144908 1.00 20:42985717 HNF4A A A/G 0.12 0.06 0.35 0.076 rs12010175 19 X:152862638 FAM58A G - - - - - rs5945326 5 X:152899922 KRT18P48 / DUSP9 A - - - - -

SUPPLEMENTARY DATA

Supplementary Table 5D. Association with reported type 2 diabetes (T2D) susceptibility loci with M in GUARDIAN Hispanic Americans (nmax=1604). Index SNPs reaching genome‐wide significance (P<5.0E‐08) for association with T2D were selected from the NHGRI GWAS catalog (http://www.genome.gov/gwastudies). When the index variable was unavailable in GUARDIAN, a suitable proxy was selected using the HapMap 3 MEX (Mexican ancestry in Los Angeles, California) population.

2 Index r Position Alleles Heterogeneity Additive Ref Proxy Gene(s) Beta SE SNP (MEX) (hg19) Risk Ref/Alt P-value P-value rs10923931 1 rs2793831 1.00 1:120523902 NOTCH2 T T/C 0.62 6.68 0.35 1.00 rs2075423 29 1:212221342 PROX1 G - - - - - rs17106184 28 rs1278516 1.00 1:50900021 FAF1 G G/A -2.03 9.91 0.75 0.88 rs6723108 30 2:135479980 TMEM163 T T/G -4.00 5.82 0.48 0.35 rs7560163 2 2:151637936 RND3 / FABP5P10 C - - - - - rs7593730 3 2:161171454 RBMS1 C - - - - - rs3923113 4 2:165501849 EIF3EP3 / SNORA70F A - - - - - rs7578326 5 rs13405357 0.90 2:227022036 LOC646736 A A/G 5.87 4.59 0.058 0.20 rs2943641 31 2:227093745 IRS1 C C/T 2.18 5.00 0.11 0.63 rs780094 29 2:27741237 GCKR C C/T -2.51 4.09 0.91 0.48 rs7578597 1 2:43732823 THADA T T/C 8.55 8.66 0.54 0.40 rs243021 5 2:60584819 BCL11A A A/G 2.90 4.02 0.48 0.45 rs11708067 29 3:123065778 ADCY5 A A/G 1.30 4.48 0.47 0.96 rs1801282 3:12393125 PPARG C C/G 6.58 6.52 0.70 0.36 rs4402960 6 3:185511687 IGF2BP2 T T/G 0.00 4.70 0.45 0.85 rs16861329 4 rs16861317 1.00 3:186664728 ST6GAL1 G G/A 0.10 4.28 0.12 0.64 rs6808574 28 3:187740523 LPP C C/T -4.75 5.08 0.20 0.15 rs7612463 32 3:23336450 UBE2E2 C C/A -7.18 8.49 0.88 0.40 rs831571 8 rs35837 0.92 3:64013249 PSMD6 / PRICKLE2-AS1 C C/T -1.79 6.88 0.72 0.94 rs4607103 1 3:64711904 ADAMTS9-AS2 C C/T -5.49 4.18 0.11 0.40 rs7656416 9 4:1254535 CTBP1-AS1 / MAEA C - - - - - rs6815464 8 4:1309901 MAEA C - - - - - rs6813195 28 4:153739925 TMEM154 C - - - - - rs1801214 5 4:6303022 WFS1 T - - - - - rs702634 28 5:53271420 ARL15 A A/G -10.81 5.28 0.76 0.044 rs459193 33 5:55842508 ANKRD55 G - - - - - rs4457053 5 5:76424949 ZBED3-AS1 G G/A 2.12 4.06 0.60 0.43 rs10946398 12 rs7754840 0.96 6:20661250 CDKAL1 C C/G 1.13 4.21 0.72 0.93 rs3130501 28 6:31136453 POU5F1-TCF19 G G/A 3.49 4.62 0.23 0.67

SUPPLEMENTARY DATA rs9470794 8 rs3800364 0.83 6:38121211 ZFAND3 C G/A 11.70 8.83 0.93 0.19 rs1535500 8 6:39284050 KCNK16 T - - - - - rs1048886 15 6:71289189 C6orf57 G G/A -0.45 4.96 0.19 0.73 rs9505118 28 6:7290437 SSR1-RREB1 A A/G 2.75 3.97 0.26 0.44 rs6467136 8 7:127164958 ZNF800 / GCC1 G - - - - - rs10229583 16 7:127246903 FSCN3 / PAX4 G G/A -4.01 5.32 0.56 0.47 rs972283 5 7:130466854 KLF14 / MIR29A G G/A -6.42 3.96 0.53 0.15 rs17168486 29 7:14898282 DGKB T T/C 2.91 3.99 0.37 0.63 rs864745 1 rs1635852 1.00 7:28189411 JAZF1 T T/C -13.90 5.39 0.20 0.021 rs10278336 29 7:44211888 GCK A - - - - - rs13266634 11 8:118184783 SLC30A8 C C/T 2.83 4.57 0.71 0.60 rs515071 9 rs508419 1.00 8:41522991 ANK1 C G/A 4.32 4.95 0.94 0.34 rs896854 5 rs4735337 0.81 8:95973465 TP53INP1 T T/C 5.71 4.18 0.74 0.18 rs10811661 6 9:22134094 CDKN2B-AS1 / DMRTA1 T - - - - - rs7018475 18 9:22137685 CDKN2B-AS1 / DMRTA1 T T/G -4.11 4.24 0.93 0.36 rs7041847 8 9:4287466 GLIS3 A - - - - - rs13292136 5 9:81952128 KRT18P24 / CHCHD2P9 C - - - - - rs2796441 33 9:84308948 TLE1 G G/A -7.03 5.36 0.86 0.17 rs17584499 20 9:8879118 PTPRD T T/C -2.55 4.69 0.053 0.45 rs7903146 22 10:114758349 TCF7L2 T T/C 0.75 4.45 0.97 0.87 rs10886471 19 10:121149403 GRK5 C C/T -0.41 6.44 1.00 0.95 rs12779790 1 10:12328010 CDC123 / MIR4480 G - - - - - rs1802295 4 10:70931474 VPS26A A A/G -11.34 4.60 0.050 0.045 rs12571751 33 10:80612637 ZMIZ1 A - - - - - rs1111875 11 rs10882101 1.00 10:94462427 HHEX / EXOC6 C C/T -1.81 4.08 0.10 0.96 rs2334499 35 11:1696849 DUSP8 T T/C -5.77 3.77 0.55 0.12 rs5219 6 11:17409572 KCNJ11 T T/C 6.57 4.05 0.55 0.083 rs231362 5 11:2691471 KCNQ1;KCNQ1OT1 G G/A -2.12 4.24 0.66 0.64 rs2237892 24 11:2839751 KCNQ1 C C/T 4.11 4.36 0.47 0.37 rs1552224 5 11:72433098 ARAP1 A A/C 7.96 7.47 0.32 0.28 rs1387153 5 11:92673828 FAT3 / MTNR1B T T/C -6.57 5.08 0.83 0.20 rs7305618 17 12:121402932 RPL12P33 / HNF1A-AS1 C C/T 2.77 5.10 0.56 0.41 rs7957197 5 12:121460686 OASL T - - - - - rs4275659 28 12:123447928 MPHOSPH9 C C/T 1.42 3.89 0.32 0.96 rs10842994 33 12:27965150 KLHDC5 C C/T -3.78 5.86 0.016 0.87 rs11063069 34 12:4374373 CCND2 G G/A -4.55 6.28 0.95 0.46

SUPPLEMENTARY DATA rs1531343 5 rs2612067 1.00 12:66170163 RPSAP52 C G/T -0.58 7.15 0.51 0.88 rs2261181 5 12:66212318 HMGA2 T T/C -0.23 7.80 0.49 0.94 rs7961581 1 12:71663102 TSPAN8 / LGR5 C C/T -11.34 5.21 0.14 0.09 rs9552911 26 13:23864657 SGCG G - - - - - rs1359790 23 13:80717156 NDFIP2 / SPRY2 G - - - - - rs7403531 19 15:38822905 RASGRP1 T T/C 1.10 4.03 0.17 0.96 rs7172432 27 15:62396389 C2CD4A / C2CD4B A - - - - - rs7178572 4 rs11857294 0.86 15:77596725 HMG20A G C/T -5.90 4.04 0.054 0.20 rs11634397 5 15:80432222 ZFAND6 / FAH G G/A 3.75 4.20 0.18 0.42 rs2028299 4 15:90374257 AP3S2;C15orf38-AP3S2 C C/A 4.00 5.32 0.73 0.32 rs8042680 5 15:91521337 PRC1 A A/C 5.63 4.35 0.44 0.28 rs8050136 12 16:53816275 FTO A A/C -10.84 4.58 0.57 0.028 rs7202877 33 16:75247245 BCAR1 T T/G -2.10 7.86 0.60 0.81 rs391300 20 17:2216258 SRR G G/A 3.19 4.05 0.40 0.28 rs13342232 36 17:6945940 SLC16A11 G - - - - - rs4430796 19 17:36098040 HNF1B G G/A 4.48 4.00 0.52 0.17 rs12970134 33 18:57884750 MC4R A A/G 4.60 5.60 0.46 0.35 rs8090011 14 18:7068462 LAMA1 G - - - - - rs10401969 33 19:19407718 CILP2 C C/T 12.91 9.96 0.0049 0.38 rs3786897 8 19:33893008 PEPD A A/G -9.78 4.48 0.35 0.054 rs6017317 8 20:42946966 FITM2 / R3HDML G - - - - - rs4812829 4 rs2144908 1.00 20:42985717 HNF4A A A/G 8.33 4.09 0.58 0.020 rs12010175 19 X:152862638 FAM58A G - - - - - rs5945326 5 X:152899922 KRT18P48 / DUSP9 A - - - - -

SUPPLEMENTARY DATA

Supplementary Table 5E. Association with reported type 2 diabetes (T2D) susceptibility loci with AIRg in GUARDIAN Hispanic Americans (nmax=2,548). Index SNPs reaching genome‐wide significance (P<5.0E‐08) for association with T2D were selected from the NHGRI GWAS catalog (http://www.genome.gov/gwastudies). When the index variable was unavailable in GUARDIAN, a suitable proxy was selected using the HapMap 3 MEX (Mexican ancestry in Los Angeles, California) population.

2 Index r Position Alleles Heterogeneity Additive Ref Proxy Gene(s) Beta SE SNP (MEX) (hg19) Risk Ref/Alt P-value P-value rs10923931 1 rs2793831 1.00 1:120523902 NOTCH2 T T/C -0.81 0.49 0.25 0.14 rs2075423 29 1:212221342 PROX1 G - - - - - rs17106184 28 rs1278516 1.00 1:50900021 FAF1 G G/A -1.32 0.77 0.64 0.021 rs6723108 30 2:135479980 TMEM163 T T/G -0.21 0.45 0.65 0.30 rs7560163 2 2:151637936 RND3 / FABP5P10 C - - - - - rs7593730 3 2:161171454 RBMS1 C - - - - - rs3923113 4 2:165501849 EIF3EP3 / SNORA70F A - - - - - rs7578326 5 rs13405357 0.90 2:227022036 LOC646736 A A/G 0.03 0.35 0.30 0.63 rs2943641 31 2:227093745 IRS1 C C/T 0.23 0.39 0.94 0.42 rs780094 29 2:27741237 GCKR C C/T -0.61 0.32 0.45 0.16 rs7578597 1 2:43732823 THADA T T/C -0.77 0.63 0.52 0.29 rs243021 5 2:60584819 BCL11A A A/G 0.31 0.32 0.66 0.52 8.85E- rs11708067 29 3:123065778 ADCY5 A A/G -1.01 0.37 0.097 05 rs1801282 3:12393125 PPARG C C/G 1.05 0.49 0.66 0.013 rs4402960 6 3:185511687 IGF2BP2 T T/G -0.76 0.35 0.81 0.016 rs16861329 4 rs16861317 1.00 3:186664728 ST6GAL1 G G/A -0.25 0.34 0.32 0.12 rs6808574 28 3:187740523 LPP C C/T -0.26 0.39 0.20 0.26 rs7612463 32 3:23336450 UBE2E2 C C/A 1.26 0.61 0.11 0.20 rs831571 8 rs35837 0.92 3:64013249 PSMD6 / PRICKLE2-AS1 C C/T 0.46 0.52 0.011 0.99 rs4607103 1 3:64711904 ADAMTS9-AS2 C C/T 0.36 0.34 0.64 0.093 rs7656416 9 4:1254535 CTBP1-AS1 / MAEA C - - - - - rs6815464 8 4:1309901 MAEA C - - - - - rs6813195 28 4:153739925 TMEM154 C - - - - - rs1801214 5 4:6303022 WFS1 T - - - - - rs702634 28 5:53271420 ARL15 A A/G -0.26 0.41 0.28 0.45 rs459193 33 5:55842508 ANKRD55 G - - - - - rs4457053 5 5:76424949 ZBED3-AS1 G G/A -0.69 0.33 0.71 0.027 rs10946398 12 rs7754840 0.96 6:20661250 CDKAL1 C C/G -1.26 0.33 0.72 3.8E-06 rs3130501 28 6:31136453 POU5F1-TCF19 G G/A 0.10 0.38 0.81 0.64

SUPPLEMENTARY DATA

rs9470794 8 rs3800364 0.83 6:38121211 ZFAND3 C G/A 0.66 0.69 0.80 0.50 rs1535500 8 6:39284050 KCNK16 T - - - - - rs1048886 15 6:71289189 C6orf57 G G/A 0.07 0.41 0.044 0.61 rs9505118 28 6:7290437 SSR1-RREB1 A A/G 0.14 0.33 0.14 0.64 rs6467136 8 7:127164958 ZNF800 / GCC1 G - - - - - rs10229583 16 7:127246903 FSCN3 / PAX4 G G/A -1.12 0.43 0.58 0.0028 rs972283 5 7:130466854 KLF14 / MIR29A G G/A -0.11 0.33 0.31 0.94 rs17168486 29 7:14898282 DGKB T T/C -0.78 0.33 0.70 0.033 rs864745 1 rs1635852 1.00 7:28189411 JAZF1 T T/C 0.06 0.33 0.79 0.83 rs10278336 29 7:44211888 GCK A - - - - - rs13266634 11 8:118184783 SLC30A8 C C/T -0.50 0.37 0.30 0.021 rs515071 9 rs508419 1.00 8:41522991 ANK1 C G/A -0.30 0.40 0.93 0.61 rs896854 5 rs4735337 0.81 8:95973465 TP53INP1 T T/C -0.25 0.31 0.54 0.35 rs10811661 6 9:22134094 CDKN2B-AS1 / DMRTA1 T - - - - - rs7018475 18 9:22137685 CDKN2B-AS1 / DMRTA1 T T/G 1.64 0.34 0.18 4.9E-06 rs7041847 8 9:4287466 GLIS3 A - - - - - rs13292136 5 9:81952128 KRT18P24 / CHCHD2P9 C - - - - - rs2796441 33 9:84308948 TLE1 G G/A -0.31 0.31 0.68 0.46 rs17584499 20 9:8879118 PTPRD T T/C -1.27 0.38 0.20 0.0037 rs7903146 22 10:114758349 TCF7L2 T T/C -1.03 0.36 0.090 2.5E-04 rs10886471 19 10:121149403 GRK5 C C/T 0.43 0.32 0.45 0.15 rs12779790 1 10:12328010 CDC123 / MIR4480 G - - - - - rs1802295 4 10:70931474 VPS26A A A/G 0.51 0.37 0.91 0.17 rs12571751 33 10:80612637 ZMIZ1 A - - - - - rs1111875 11 rs10882101 1.00 10:94462427 HHEX / EXOC6 C C/T 0.29 0.33 0.58 0.51 rs2334499 35 11:1696849 DUSP8 T T/C 0.19 0.32 0.025 0.55 rs5219 6 11:17409572 KCNJ11 T T/C -0.10 0.32 0.91 0.86 rs231362 5 11:2691471 KCNQ1;KCNQ1OT1 G G/A -0.29 0.34 0.30 0.49 rs2237892 24 11:2839751 KCNQ1 C C/T -0.73 0.36 0.053 0.0077 rs1552224 5 11:72433098 ARAP1 A A/C -1.71 0.62 0.89 0.0015 rs1387153 5 11:92673828 FAT3 / MTNR1B T T/C -1.99 0.36 0.43 2.3E-08 rs7305618 17 12:121402932 RPL12P33 / HNF1A-AS1 C C/T -1.60 0.45 0.30 5.8E-04 rs7957197 5 12:121460686 OASL T - - - - - rs4275659 28 12:123447928 MPHOSPH9 C C/T 0.53 0.32 0.67 0.18 rs10842994 33 12:27965150 KLHDC5 C C/T -0.94 0.44 0.41 0.11 rs11063069 34 12:4374373 CCND2 G G/A -0.17 0.49 0.24 0.60

SUPPLEMENTARY DATA

rs1531343 5 rs2612067 1.00 12:66170163 RPSAP52 C G/T -0.82 0.60 0.84 0.21 rs2261181 5 12:66212318 HMGA2 T T/C -0.54 0.64 0.75 0.47 rs7961581 1 12:71663102 TSPAN8 / LGR5 C C/T -0.15 0.39 0.027 0.54 rs9552911 26 13:23864657 SGCG G - - - - - rs1359790 23 13:80717156 NDFIP2 / SPRY2 G - - - - - rs7403531 19 15:38822905 RASGRP1 T T/C -0.14 0.32 0.47 0.39 rs7172432 27 15:62396389 C2CD4A / C2CD4B A - - - - - rs7178572 4 rs11857294 0.86 15:77596725 HMG20A G C/T -0.05 0.33 0.59 0.88 rs11634397 5 15:80432222 ZFAND6 / FAH G G/A 0.14 0.31 0.26 0.35 rs2028299 4 15:90374257 AP3S2;C15orf38-AP3S2 C C/A -0.72 0.38 0.19 0.011 rs8042680 5 15:91521337 PRC1 A A/C -0.28 0.33 0.096 0.42 rs8050136 12 16:53816275 FTO A A/C 0.33 0.36 0.82 0.30 rs7202877 33 16:75247245 BCAR1 T T/G -0.94 0.63 0.0035 0.049 rs391300 20 17:2216258 SRR G G/A 0.08 0.34 0.80 0.82 rs13342232 36 17:6945940 SLC16A11 G - - - - - rs4430796 19 17:36098040 HNF1B G G/A -0.83 0.32 0.75 0.008 rs12970134 33 18:57884750 MC4R A A/G -0.18 0.43 0.24 0.95 rs8090011 14 18:7068462 LAMA1 G - - - - - rs10401969 33 19:19407718 CILP2 C C/T 0.37 0.81 0.62 0.25 rs3786897 8 19:33893008 PEPD A A/G -0.28 0.35 0.33 0.27 rs6017317 8 20:42946966 FITM2 / R3HDML G - - - - - rs4812829 4 rs2144908 1.00 20:42985717 HNF4A A A/G -0.12 0.31 0.92 0.70 rs12010175 19 X:152862638 FAM58A G - - - - - rs5945326 5 X:152899922 KRT18P48 / DUSP9 A - - - - -

SUPPLEMENTARY DATA

Supplementary Table 5F. Association with reported type 2 diabetes (T2D) susceptibility loci with DI in GUARDIAN Hispanic Americans (nmax=3,083). Index SNPs reaching genome‐wide significance (P<5.0E‐08) for association with T2D were selected from the NHGRI GWAS catalog (http://www.genome.gov/gwastudies). When the index variable was unavailable in GUARDIAN, a suitable proxy was selected using the HapMap 3 MEX (Mexican ancestry in Los Angeles, California) population.

2 Index r Position Alleles Heterogeneity Additive Ref Proxy Gene(s) Beta SE SNP (MEX) (hg19) Risk Ref/Alt P-value P-value rs10923931 1 rs2793831 1.00 1:120523902 NOTCH2 T T/C -0.14 0.56 0.064 0.59 rs2075423 29 1:212221342 PROX1 G - - - - - rs17106184 28 rs1278516 1.00 1:50900021 FAF1 G G/A -1.08 0.88 0.94 0.11 rs6723108 30 2:135479980 TMEM163 T T/G 0.35 0.52 0.87 0.36 rs7560163 2 2:151637936 RND3 / FABP5P10 C - - - - - rs7593730 3 2:161171454 RBMS1 C - - - - - rs3923113 4 2:165501849 EIF3EP3 / SNORA70F A - - - - - rs7578326 5 rs13405357 0.90 2:227022036 LOC646736 A A/G -0.44 0.39 0.033 0.60 rs2943641 31 2:227093745 IRS1 C C/T -0.26 0.43 1.82E-04 1.00 rs780094 29 2:27741237 GCKR C C/T -0.75 0.36 0.98 0.044 rs7578597 1 2:43732823 THADA T T/C 0.13 0.72 0.94 0.75 rs243021 5 2:60584819 BCL11A A A/G -0.02 0.35 0.53 0.46 rs11708067 29 3:123065778 ADCY5 A A/G -1.17 0.40 0.095 0.0016 rs1801282 3:12393125 PPARG C C/G 0.34 0.55 0.84 0.29 rs4402960 6 3:185511687 IGF2BP2 T T/G -0.95 0.38 0.023 0.043 rs16861329 4 rs16861317 1.00 3:186664728 ST6GAL1 G G/A -0.48 0.37 0.49 0.31 rs6808574 28 3:187740523 LPP C C/T 0.42 0.43 0.50 0.71 rs7612463 32 3:23336450 UBE2E2 C C/A 0.36 0.69 0.022 0.41 rs831571 8 rs35837 0.92 3:64013249 PSMD6 / PRICKLE2-AS1 C C/T 0.03 0.61 0.24 0.67 rs4607103 1 3:64711904 ADAMTS9-AS2 C C/T 0.21 0.37 0.17 0.30 rs7656416 9 4:1254535 CTBP1-AS1 / MAEA C - - - - - rs6815464 8 4:1309901 MAEA C - - - - - rs6813195 28 4:153739925 TMEM154 C - - - - - rs1801214 5 4:6303022 WFS1 T - - - - - rs702634 28 5:53271420 ARL15 A A/G -0.86 0.45 0.71 0.043 rs459193 33 5:55842508 ANKRD55 G - - - - - rs4457053 5 5:76424949 ZBED3-AS1 G G/A -0.94 0.36 0.50 0.012 rs10946398 12 rs7754840 0.96 6:20661250 CDKAL1 C C/G -0.28 0.37 0.016 0.094 rs3130501 28 6:31136453 POU5F1-TCF19 G G/A -0.15 0.42 0.31 0.69

©2014 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db13-1829/-/DC1 SUPPLEMENTARY DATA rs9470794 8 rs3800364 0.83 6:38121211 ZFAND3 C G/A 1.40 0.79 0.92 0.10 rs1535500 8 6:39284050 KCNK16 T - - - - - rs1048886 15 6:71289189 C6orf57 G G/A -0.11 0.45 0.27 0.85 rs9505118 28 6:7290437 SSR1-RREB1 A A/G 0.03 0.36 0.071 0.79 rs6467136 8 7:127164958 ZNF800 / GCC1 G - - - - - rs10229583 16 7:127246903 FSCN3 / PAX4 G G/A -0.85 0.50 0.60 0.064 rs972283 5 7:130466854 KLF14 / MIR29A G G/A -0.67 0.36 0.27 0.033 rs17168486 29 7:14898282 DGKB T T/C -0.37 0.36 0.17 0.74 rs864745 1 rs1635852 1.00 7:28189411 JAZF1 T T/C -0.49 0.44 0.89 0.28 rs10278336 29 7:44211888 GCK A - - - - - rs13266634 11 8:118184783 SLC30A8 C C/T -0.77 0.40 0.79 0.018 rs515071 9 rs508419 1.00 8:41522991 ANK1 C G/A -0.07 0.44 0.92 0.79 rs896854 5 rs4735337 0.81 8:95973465 TP53INP1 T T/C -0.21 0.35 0.95 0.43 rs10811661 6 9:22134094 CDKN2B-AS1 / DMRTA1 T - - - - - rs7018475 18 9:22137685 CDKN2B-AS1 / DMRTA1 T T/G 1.32 0.37 0.17 3.9E-04 rs7041847 8 9:4287466 GLIS3 A - - - - - rs13292136 5 9:81952128 KRT18P24 / CHCHD2P9 C - - - - - rs2796441 33 9:84308948 TLE1 G G/A -0.01 0.34 0.36 0.63 rs17584499 20 9:8879118 PTPRD T T/C -0.58 0.42 0.70 0.33 rs7903146 22 10:114758349 TCF7L2 T T/C -1.06 0.40 0.08 5.8E-05 rs10886471 19 10:121149403 GRK5 C C/T 0.12 0.37 0.66 0.90 rs12779790 1 10:12328010 CDC123 / MIR4480 G - - - - - rs1802295 4 10:70931474 VPS26A A A/G 0.13 0.41 0.55 0.99 rs12571751 33 10:80612637 ZMIZ1 A - - - - - rs1111875 11 rs10882101 1.00 10:94462427 HHEX / EXOC6 C C/T 0.32 0.36 0.51 0.49 rs2334499 35 11:1696849 DUSP8 T T/C -0.49 0.35 0.07 0.39 rs5219 6 11:17409572 KCNJ11 T T/C -0.29 0.35 0.23 0.18 rs231362 5 11:2691471 KCNQ1;KCNQ1OT1 G G/A 0.71 0.37 0.12 0.19 rs2237892 24 11:2839751 KCNQ1 C C/T -0.88 0.41 0.0007 0.0035 rs1552224 5 11:72433098 ARAP1 A A/C -1.65 0.71 0.50 0.016 rs1387153 5 11:92673828 FAT3 / MTNR1B T T/C -2.69 0.42 0.0046 5.7E-09 rs7305618 17 12:121402932 RPL12P33 / HNF1A-AS1 C C/T -0.46 0.50 0.98 0.26 rs7957197 5 12:121460686 OASL T - - - - - rs4275659 28 12:123447928 MPHOSPH9 C C/T 0.06 0.35 0.82 0.96 rs10842994 33 12:27965150 KLHDC5 C C/T -0.91 0.50 0.70 0.21 rs11063069 34 12:4374373 CCND2 G G/A -0.79 0.56 0.69 0.40

SUPPLEMENTARY DATA

rs1531343 5 rs2612067 1.00 12:66170163 RPSAP52 C G/T 0.19 0.68 0.15 0.68 rs2261181 5 12:66212318 HMGA2 T T/C 0.08 0.72 0.14 0.85 rs7961581 1 12:71663102 TSPAN8 / LGR5 C C/T -0.36 0.45 0.94 0.31 rs9552911 26 13:23864657 SGCG G - - - - - rs1359790 23 13:80717156 NDFIP2 / SPRY2 G - - - - - rs7403531 19 15:38822905 RASGRP1 T T/C -0.08 0.35 0.61 0.81 rs7172432 27 15:62396389 C2CD4A / C2CD4B A - - - - - rs7178572 4 rs11857294 0.86 15:77596725 HMG20A G C/T -0.33 0.36 0.16 0.28 rs11634397 5 15:80432222 ZFAND6 / FAH G G/A 0.51 0.36 0.80 0.052 rs2028299 4 15:90374257 AP3S2;C15orf38-AP3S2 C C/A 0.14 0.44 0.014 0.72 rs8042680 5 15:91521337 PRC1 A A/C -0.24 0.36 0.68 0.64 rs8050136 12 16:53816275 FTO A A/C -0.21 0.39 0.86 0.51 rs7202877 33 16:75247245 BCAR1 T T/G -0.51 0.72 0.48 0.48 rs391300 20 17:2216258 SRR G G/A 0.01 0.37 0.96 0.90 rs13342232 36 17:6945940 SLC16A11 G - - - - - rs4430796 19 17:36098040 HNF1B G G/A -0.72 0.35 0.038 0.20 rs12970134 33 18:57884750 MC4R A A/G -0.08 0.50 0.68 0.91 rs8090011 14 18:7068462 LAMA1 G - - - - - rs10401969 33 19:19407718 CILP2 C C/T 2.02 0.92 0.12 0.008 rs3786897 8 19:33893008 PEPD A A/G 0.29 0.38 0.68 0.86 rs6017317 8 20:42946966 FITM2 / R3HDML G - - - - - rs4812829 4 rs2144908 1.00 20:42985717 HNF4A A A/G 0.02 0.34 0.59 0.96 rs12010175 19 X:152862638 FAM58A G - - - - - rs5945326 5 X:152899922 KRT18P48 / DUSP9 A - - - - -

SUPPLEMENTARY DATA

Supplementary Table 5G. Association with reported type 2 diabetes (T2D) susceptibility loci with SG in GUARDIAN Hispanic Americans (nmax=2,542). Index SNPs reaching genome‐wide significance (P<5.0E‐08) for association with T2D were selected from the NHGRI GWAS catalog (http://www.genome.gov/gwastudies). When the index variable was unavailable in GUARDIAN, a suitable proxy was selected using the HapMap 3 MEX (Mexican ancestry in Los Angeles, California) population.

2 Index r Position Alleles Heterogeneity Additive Ref Proxy Gene(s) Beta SE SNP (MEX) (hg19) Risk Ref/Alt P-value P-value rs10923931 1 rs2793831 1.00 1:120523902 NOTCH2 T T/C -0.01 0.04 0.23 0.67 rs2075423 29 1:212221342 PROX1 G - - - - - rs17106184 28 rs1278516 1.00 1:50900021 FAF1 G G/A -0.07 0.07 0.34 0.063 rs6723108 30 2:135479980 TMEM163 T T/G 0.03 0.04 0.18 0.20 rs7560163 2 2:151637936 RND3 / FABP5P10 C - - - - - rs7593730 3 2:161171454 RBMS1 C - - - - - rs3923113 4 2:165501849 EIF3EP3 / SNORA70F A - - - - - rs7578326 5 rs13405357 0.90 2:227022036 LOC646736 A A/G -0.04 0.03 0.86 0.28 rs2943641 31 2:227093745 IRS1 C C/T -0.05 0.03 0.18 0.12 rs780094 29 2:27741237 GCKR C C/T -0.14 0.03 0.29 1.97E-06 rs7578597 1 2:43732823 THADA T T/C 0.06 0.05 0.79 0.13 rs243021 5 2:60584819 BCL11A A A/G -0.03 0.03 0.17 0.076 rs11708067 29 3:123065778 ADCY5 A A/G -0.05 0.03 0.97 0.12 rs1801282 3:12393125 PPARG C C/G 0.03 0.04 0.96 0.51 rs4402960 6 3:185511687 IGF2BP2 T T/G -0.07 0.03 0.048 0.0075 rs16861329 4 rs16861317 1.00 3:186664728 ST6GAL1 G G/A -0.01 0.03 0.47 0.65 rs6808574 28 3:187740523 LPP C C/T -0.02 0.03 0.28 0.58 rs7612463 32 3:23336450 UBE2E2 C C/A 0.02 0.05 0.11 0.99 rs831571 8 rs35837 0.92 3:64013249 PSMD6 / PRICKLE2-AS1 C C/T 0.07 0.04 0.019 0.26 rs4607103 1 3:64711904 ADAMTS9-AS2 C C/T -0.05 0.03 0.92 0.054 rs7656416 9 4:1254535 CTBP1-AS1 / MAEA C - - - - - rs6815464 8 4:1309901 MAEA C - - - - - rs6813195 28 4:153739925 TMEM154 C - - - - - rs1801214 5 4:6303022 WFS1 T - - - - - rs702634 28 5:53271420 ARL15 A A/G -0.04 0.03 0.51 0.28 rs459193 33 5:55842508 ANKRD55 G - - - - - rs4457053 5 5:76424949 ZBED3-AS1 G G/A -0.05 0.03 0.72 0.046 rs10946398 12 rs7754840 0.96 6:20661250 CDKAL1 C C/G -0.02 0.03 0.33 0.29 rs3130501 28 6:31136453 POU5F1-TCF19 G G/A 0.03 0.03 0.98 0.36

SUPPLEMENTARY DATA

rs9470794 8 rs3800364 0.83 6:38121211 ZFAND3 C G/A 0.04 0.06 0.67 0.58 rs1535500 8 6:39284050 KCNK16 T - - - - - rs1048886 15 6:71289189 C6orf57 G G/A 0.04 0.04 0.21 0.48 rs9505118 28 6:7290437 SSR1-RREB1 A A/G -0.05 0.03 0.15 0.20 rs6467136 8 7:127164958 ZNF800 / GCC1 G - - - - - rs10229583 16 7:127246903 FSCN3 / PAX4 G G/A 0.00 0.04 0.88 0.98 rs972283 5 7:130466854 KLF14 / MIR29A G G/A -0.02 0.03 0.062 0.44 rs17168486 29 7:14898282 DGKB T T/C -0.03 0.03 0.80 0.22 rs864745 1 rs1635852 1.00 7:28189411 JAZF1 T T/C 0.03 0.03 0.33 0.29 rs10278336 29 7:44211888 GCK A - - - - - rs13266634 11 8:118184783 SLC30A8 C C/T -0.04 0.03 0.16 0.070 rs515071 9 rs508419 1.00 8:41522991 ANK1 C G/A 0.00 0.03 0.41 0.67 rs896854 5 rs4735337 0.81 8:95973465 TP53INP1 T T/C 0.00 0.03 0.28 0.93 rs10811661 6 9:22134094 CDKN2B-AS1 / DMRTA1 T - - - - - rs7018475 18 9:22137685 CDKN2B-AS1 / DMRTA1 T T/G 0.04 0.03 0.24 0.41 rs7041847 8 9:4287466 GLIS3 A - - - - - rs13292136 5 9:81952128 KRT18P24 / CHCHD2P9 C - - - - - rs2796441 33 9:84308948 TLE1 G G/A -0.01 0.03 0.20 0.93 rs17584499 20 9:8879118 PTPRD T T/C 0.00 0.03 0.91 0.85 rs7903146 22 10:114758349 TCF7L2 T T/C 0.01 0.03 0.20 0.96 rs10886471 19 10:121149403 GRK5 C C/T -0.04 0.03 0.91 0.19 rs12779790 1 10:12328010 CDC123 / MIR4480 G - - - - - rs1802295 4 10:70931474 VPS26A A A/G -0.02 0.03 0.44 0.44 rs12571751 33 10:80612637 ZMIZ1 A - - - - - rs1111875 11 rs10882101 1.00 10:94462427 HHEX / EXOC6 C C/T -0.01 0.03 0.51 0.62 rs2334499 35 11:1696849 DUSP8 T T/C -0.04 0.03 0.59 0.10 rs5219 6 11:17409572 KCNJ11 T T/C -0.06 0.03 0.29 0.0076 rs231362 5 11:2691471 KCNQ1;KCNQ1OT1 G G/A 0.04 0.03 0.66 0.15 rs2237892 24 11:2839751 KCNQ1 C C/T 0.00 0.03 0.44 0.95 rs1552224 5 11:72433098 ARAP1 A A/C 0.02 0.05 0.98 0.75 rs1387153 5 11:92673828 FAT3 / MTNR1B T T/C -0.12 0.03 0.39 3.0E-04 rs7305618 17 12:121402932 RPL12P33 / HNF1A-AS1 C C/T -0.08 0.04 0.71 0.049 rs7957197 5 12:121460686 OASL T - - - - - rs4275659 28 12:123447928 MPHOSPH9 C C/T 0.00 0.03 0.45 1.00 rs10842994 33 12:27965150 KLHDC5 C C/T -0.02 0.04 0.29 0.86 rs11063069 34 12:4374373 CCND2 G G/A -0.04 0.04 0.31 0.47

©2014 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db13-1829/-/DC1 SUPPLEMENTARY DATA rs1531343 5 rs2612067 1.00 12:66170163 RPSAP52 C G/T -0.04 0.05 0.25 0.56 rs2261181 5 12:66212318 HMGA2 T T/C -0.05 0.05 0.33 0.33 rs7961581 1 12:71663102 TSPAN8 / LGR5 C C/T -0.01 0.03 0.78 0.93 rs9552911 26 13:23864657 SGCG G - - - - - rs1359790 23 13:80717156 NDFIP2 / SPRY2 G - - - - - rs7403531 19 15:38822905 RASGRP1 T T/C 0.02 0.03 0.12 0.94 rs7172432 27 15:62396389 C2CD4A / C2CD4B A - - - - - rs7178572 4 rs11857294 0.86 15:77596725 HMG20A G C/T -0.04 0.03 0.29 0.42 rs11634397 5 15:80432222 ZFAND6 / FAH G G/A 0.01 0.03 0.35 0.32 rs2028299 4 15:90374257 AP3S2;C15orf38-AP3S2 C C/A -0.01 0.03 0.0055 0.93 rs8042680 5 15:91521337 PRC1 A A/C -0.01 0.03 0.73 0.78 rs8050136 12 16:53816275 FTO A A/C -0.02 0.03 0.21 0.48 rs7202877 33 16:75247245 BCAR1 T T/G 0.07 0.05 0.24 0.23 rs391300 20 17:2216258 SRR G G/A 0.01 0.03 0.67 0.52 rs13342232 36 17:6945940 SLC16A11 G - - - - - rs4430796 19 17:36098040 HNF1B G G/A -0.04 0.03 0.26 0.14 rs12970134 33 18:57884750 MC4R A A/G -0.03 0.04 0.76 0.51 rs8090011 14 18:7068462 LAMA1 G - - - - - rs10401969 33 19:19407718 CILP2 C C/T 0.06 0.07 0.13 0.27 rs3786897 8 19:33893008 PEPD A A/G 0.02 0.03 0.40 0.83 rs6017317 8 20:42946966 FITM2 / R3HDML G - - - - - rs4812829 4 rs2144908 1.00 20:42985717 HNF4A A A/G -0.02 0.03 0.49 0.57 rs12010175 19 X:152862638 FAM58A G - - - - - rs5945326 5 X:152899922 KRT18P48 / DUSP9 A - - - - -

SUPPLEMENTARY DATA REFERENCES

1. Zeggini et al. Meta‐analysis of genome‐wide association data and large‐scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet 40:638‐645, 2008 2. Palmer et al. A genome‐wide association search for type 2 diabetes genes in African Americans. PLoS One 7:e29202, 2012 3. Qi et al. Genetic variants at 2q24 are associated with susceptibility to type 2 diabetes. Hum Mol Genet 19:2706‐2715, 2010 4. Kooner et al. Genome‐wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci. Nat Genet 43:984‐989, 2011 5. Voight et al. Twelve type 2 diabetes susceptibility loci identified through large‐scale association analysis. Nat Genet 42:579‐589, 2010 6. Scott et al. A genome‐wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 316:1341‐1345, 2007 7. Unoki et al. SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations. Nat Genet 40:1098‐1102, 2008 8. Cho et al. Meta‐analysis of genome‐wide association studies identifies eight new loci for type 2 diabetes in east Asians. Nat Genet 44:67‐72, 2012 9. Imamura et al. A single‐nucleotide polymorphism in ANK1 is associated with susceptibility to type 2 diabetes in Japanese populations. Hum Mol Genet 21:3042‐3049, 2012 10. Takeuchi et al. Confirmation of multiple risk Loci and genetic impacts by a genome‐wide association study of type 2 diabetes in the Japanese population. Diabetes 58:1690‐1699, 2009 11. Saxena et al. Genome‐wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 316:1331‐1336, 2007 12. Zeggini et al. Replication of genome‐wide association signals in UK samples reveals risk loci for type 2 diabetes. Science 316:1336‐1341, 2007 13. Steinthorsdottir et al. A variant in CDKAL1 influences insulin response and risk of type 2 diabetes. Nat Genet 39:770‐775, 2007 14. Perry et al. Stratifying type 2 diabetes cases by BMI identifies genetic risk variants in LAMA1 and enrichment for risk variants in lean compared to obese cases. PLoS Genet 8:e1002741, 2012 15. Sim et al. Transferability of type 2 diabetes implicated loci in multi‐ethnic cohorts from Southeast Asia. PLoS Genet 7:e1001363, 2011 16. Ma et al. Genome‐wide association study in a Chinese population identifies a susceptibility locus for type 2 diabetes at 7q32 near PAX4. Diabetologia 56:1291‐1305, 2013 17. Parra et al. Genome‐wide association study of type 2 diabetes in a sample from Mexico City and a meta‐analysis of a Mexican‐American sample from Starr County, Texas. Diabetologia 54:2038‐2046, 2011 18. Huang et al. 1000 Genomes‐based imputation identifies novel and refined associations for the Wellcome Trust Case Control Consortium phase 1 Data. Eur J Hum Genet 20:801‐805, 2012 19. Li et al. A genome‐wide association study identifies GRK5 and RASGRP1 as type 2 diabetes loci in Chinese Hans. Diabetes 62:291‐298, 2013 20. Tsai et al. A genome‐wide association study identifies susceptibility variants for type 2 diabetes in Han Chinese. PLoS Genet 6:e1000847, 2010 21. WTCCC Genome‐wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447:661‐678, 2007 22. Sladek at al. A genome‐wide association study identifies novel risk loci for type 2 diabetes. Nature 445:881‐885, 2007 23. Shu et al. Identification of new genetic risk variants for type 2 diabetes. PLoS Genet 6:e1001127, 2010 24. Yasuda et al. Variants in KCNQ1 are associated with susceptibility to type 2 diabetes mellitus. Nat Genet 40:1092‐1097, 2008 25. Cui et al. A genome‐wide association study confirms previously reported loci for type 2 diabetes in Han Chinese. PLoS One 6:e22353, 2011 26. Saxena et al. Genome‐wide association study identifies a novel locus contributing to type 2 diabetes susceptibility in Sikhs of Punjabi origin from India. Diabetes 62:1746‐1755, 2013 27. Yamauchi et al. A genome‐wide association study in the Japanese population identifies susceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A‐C2CD4B. Nat Genet 42:864‐868, 2010

SUPPLEMENTARY DATA Supplementary Table 6. All SNPs from GWAS of T2D-related quantitative traits with Translation to T2D in Mexican-origin cohorts ordered by trait from the Discovery stage.

Discovery Cohort Translational Cohort Discovery and Translational Marker Chr Position Gene RA/ RA Trait Beta P‐value OR (95%CI) P‐value Meta‐Analysis Nonref Frequency P‐value rs4350219 1 19858807 MCRI 0.24 7.45E‐05 T/C 0.244 0.93 (0.86‐1.00) 1.40E‐01 1.21E‐04 rs11247954 1 26741285 LIN28A MCRI 0.26 9.76E‐05 A/G 0.179 1.03 (0.93‐1.14) 4.97E‐01 2.29E‐02 rs2278979 1 26877708 RPS6KA1 MCRI 0.31 3.16E‐05 A/G 0.405 1.06 (0.99‐1.13) 4.33E‐01 1.69E‐02 rs3790645 1 26884864 RPS6KA1 MCRI 0.34 6.07E‐06 A/G 0.421 1.05 (0.98‐1.12) 8.57E‐01 2.13E‐03 rs1064196 1 26887592 RPS6KA1 MCRI 0.34 9.75E‐06 C/T 0.424 1.04 (0.97‐1.11) 7.54E‐01 3.66E‐03 rs282177 1 26899125 RPS6KA1 MCRI 0.34 3.30E‐05 T/C 0.451 1.07 (1.00‐1.15) 3.62E‐01 2.20E‐02 rs7549785 1 159277868 FCER1A MCRI 0.34 7.92E‐04 A/G 0.163 1.22 (1.11‐1.35) 1.66E‐03 8.82E‐01 rs12742834 1 240107121 MCRI 0.22 1.94E‐04 C/T 0.245 1.06 (0.98‐1.16) 8.27E‐01 1.31E‐02 rs6697598 1 241105515 RGS7 MCRI ‐0.60 1.88E‐05 C/T 0.042 0.99 (0.82‐1.19) 3.16E‐01 2.05E‐02 rs6718111 2 8201262 LINC00299 MCRI ‐0.19 9.33E‐05 C/T 0.487 0.99 (0.92‐1.06) 2.49E‐01 5.14E‐02 rs1044280 2 8871342 KIDINS220 MCRI 0.19 6.97E‐05 A/C 0.287 0.99 (0.92‐1.07) 8.72E‐01 3.43E‐03 rs7572039 2 31061392 MCRI 0.36 2.74E‐05 T/G 0.078 1.10 (0.97‐1.24) 1.59E‐01 4.88E‐02 rs10197417 2 70881592 ADD2 MCRI ‐0.15 7.00E‐04 T/C 0.411 0.98 (0.91‐1.05) 4.51E‐01 6.23E‐02 rs6745880 2 171105318 MYO3B MCRI ‐0.30 7.34E‐05 G/A 0.138 0.97 (0.88‐1.07) 6.61E‐01 1.84E‐03 rs13024014 2 173530946 MCRI ‐0.62 9.17E‐05 T/C 0.023 0.96 (0.77‐1.20) 4.36E‐01 2.67E‐02 rs11688831 2 199299078 MCRI ‐0.14 7.08E‐05 A/G 0.384 1.01 (0.94‐1.09) 7.27E‐01 2.24E‐03 rs12373582 2 209069303 MCRI 0.37 1.80E‐04 G/A 0.084 0.94 (0.81‐1.08) 7.64E‐01 4.22E‐03 rs6741187 2 222065721 MCRI 2.15 8.62E‐05 T/C 0.010 1.06 (0.54‐2.08) 9.35E‐01 6.54E‐03 rs6798029 3 10763460 MCRI ‐0.29 5.17E‐04 A/G 0.254 0.90 (0.84‐0.98) 2.33E‐02 3.95E‐01 rs13321674 3 51704721 MCRI ‐1.57 7.70E‐05 C/T 0.009 0.60 (0.35‐1.01) 1.96E‐01 5.99E‐02 rs381062 3 55267391 MCRI 0.43 3.11E‐04 A/G 0.061 1.11 (0.98‐1.26) 2.56E‐01 8.07E‐02 rs726737 3 142860107 MCRI ‐0.15 7.83E‐04 A/G 0.320 0.90 (0.83‐0.97) 7.54E‐03 6.27E‐01 rs13064954 3 156854742 MCRI 0.23 6.36E‐04 A/G 0.107 1.08 (0.96‐1.22) 7.68E‐02 2.44E‐01 rs13325944 3 157057390 VEPH1 MCRI 0.19 9.82E‐04 A/G 0.145 1.06 (0.96‐1.17) 6.37E‐02 3.08E‐01 rs9830704 3 187222367 MCRI 0.21 3.06E‐04 T/C 0.164 1.04 (0.95‐1.14) 8.69E‐01 7.61E‐03

SUPPLEMENTARY DATA rs16835397 4 4268642 MCRI ‐0.71 1.85E‐05 T/C 0.018 0.83 (0.64‐1.06) 5.52E‐01 9.12E‐03 rs2124794 4 62290634 LPHN3 MCRI ‐0.15 5.27E‐05 A/G 0.437 0.98 (0.92‐1.06) 9.53E‐01 3.73E‐03 rs6822279 4 99745705 MCRI ‐0.21 2.33E‐05 C/A 0.406 0.93 (0.87‐0.99) 1.50E‐02 2.04E‐01 rs7726659 5 74478078 ANKRD31 MCRI ‐0.90 4.58E‐05 G/A 0.015 0.97 (0.75‐1.26) 6.08E‐01 1.17E‐02 rs6874765 5 147298847 MCRI ‐4.50 2.02E‐04 A/G 0.005 1.16 (0.34‐4.01) 6.09E‐01 2.79E‐03 rs523848 6 15830025 MCRI 0.20 3.48E‐05 A/G 0.467 0.96 (0.90‐1.03) 3.56E‐01 3.44E‐04 rs220933 6 15845797 MCRI ‐0.19 9.83E‐05 C/T 0.421 1.07 (0.99‐1.14) 3.83E‐01 7.51E‐04 rs9370836 6 15856619 MCRI 0.23 1.19E‐04 C/T 0.442 0.94 (0.88‐1.00) 2.19E‐01 3.30E‐04 rs3749855 6 17283321 RBM24 MCRI ‐0.52 5.04E‐06 G/T 0.057 0.96 (0.82‐1.11) 6.94E‐01 4.56E‐04 rs6938736 6 22441270 MCRI 0.22 7.64E‐05 C/T 0.469 0.96 (0.90‐1.03) 1.42E‐01 1.26E‐04 rs9295552 6 22540765 MCRI ‐0.28 7.11E‐04 T/C 0.300 1.04 (0.97‐1.12) 2.64E‐01 1.45E‐03 rs9449095 6 81313076 MCRI 0.44 3.88E‐04 G/A 0.046 0.97 (0.84‐1.12) 2.04E‐01 6.58E‐04 rs13219760 6 110761189 SLC22A16 MCRI 0.35 3.15E‐06 G/A 0.111 0.94 (0.84‐1.05) 8.13E‐01 5.34E‐04 rs723685 6 110763875 SLC22A16 MCRI 0.33 8.04E‐06 G/A 0.114 1.04 (0.94‐1.15) 2.54E‐01 1.88E‐02 rs17166951 7 13302054 MCRI 0.42 8.25E‐05 A/C 0.060 0.93 (0.79‐1.10) 7.71E‐01 2.79E‐03 rs4629751 7 16825580 MCRI 0.26 9.58E‐05 G/T 0.284 0.97 (0.90‐1.05) 4.80E‐01 1.12E‐03 rs10251809 7 32044030 PDE1C MCRI ‐0.25 4.28E‐05 T/C 0.180 0.95 (0.86‐1.04) 4.06E‐01 2.12E‐02 rs10246021 7 100692680 MUC17 MCRI 0.29 2.01E‐04 T/G 0.470 0.96 (0.90‐1.03) 3.36E‐02 3.60E‐05 rs11136431 8 1791433 ARHGEF10 MCRI 0.14 6.90E‐05 T/C 0.383 0.99 (0.93‐1.07) 2.65E‐01 3.16E‐04 rs6651438 8 1794023 ARHGEF10 MCRI 0.20 9.10E‐05 C/T 0.377 0.90 (0.84‐0.96) 3.40E‐02 1.98E‐05 rs13258014 8 4165460 CSMD1 MCRI 0.26 7.99E‐05 T/C 0.392 0.98 (0.91‐1.05) 5.32E‐01 1.23E‐03 rs17128106 8 19146926 MCRI 2.97 1.37E‐04 A/G 0.003 0.53 (0.25‐1.13) 1.00E‐01 1.14E‐04 rs4434590 8 100860657 VPS13B MCRI ‐0.29 8.09E‐05 T/C 0.161 1.00 (0.92‐1.09) 5.65E‐01 1.73E‐02 rs13253073 8 100897383 COX6C MCRI ‐0.35 5.89E‐06 A/C 0.129 0.93 (0.85‐1.02) 2.08E‐01 2.07E‐02 rs12544943 8 100903890 COX6C MCRI ‐0.34 6.90E‐06 G/A 0.129 0.91 (0.83‐1.00) 1.44E‐01 3.19E‐02 rs13257834 8 122322450 MCRI ‐0.22 9.10E‐04 G/A 0.248 1.01 (0.94‐1.08) 4.27E‐01 3.65E‐03 rs7851513 9 9842176 PTPRD MCRI 0.38 2.72E‐05 A/C 0.129 0.98 (0.89‐1.07) 3.41E‐01 2.72E‐04 rs10960561 9 12275924 MCRI ‐0.19 4.19E‐04 A/G 0.256 1.03 (0.90‐1.17) 8.23E‐02 1.97E‐04 rs7025024 9 25816219 MCRI ‐0.18 8.33E‐05 G/A 0.342 0.94 (0.87‐1.01) 4.12E‐01 2.76E‐02 rs16923334 9 106556113 MCRI ‐0.54 6.75E‐04 C/T 0.028 0.94 (0.77‐1.14) 3.16E‐01 9.01E‐02 rs6602203 10 17596121 MCRI ‐0.32 4.80E‐06 T/C 0.403 1.02 (0.95‐1.09) 5.86E‐01 2.96E‐04 rs10825203 10 55798117 PCDH15 MCRI 0.23 5.80E‐05 A/C 0.268 0.94 (0.87‐1.01) 5.86E‐02 2.91E‐05

SUPPLEMENTARY DATA rs1911409 10 55806316 PCDH15 MCRI 0.23 5.05E‐05 G/A 0.243 1.00 (0.93‐1.08) 2.89E‐01 3.00E‐04 rs716594 10 112006311 MXI1 MCRI ‐0.65 3.84E‐05 A/G 0.019 0.74 (0.57‐0.96) 7.50E‐02 9.85E‐02 rs11016332 10 130363802 MCRI 2.07 4.72E‐05 G/A 0.008 0.74 (0.37‐1.50) 7.84E‐01 7.30E‐03 rs7944706 11 10331311 MCRI 0.31 4.70E‐05 A/G 0.285 1.04 (0.97‐1.11) 9.33E‐02 9.07E‐02 rs2449501 11 20044696 NAV2 MCRI ‐0.22 1.27E‐05 G/A 0.198 0.97 (0.89‐1.07) 7.91E‐01 1.06E‐03 rs16918932 11 29309078 MCRI 3.45 4.38E‐05 G/T 0.003 0.43 (0.11‐1.70) 6.30E‐01 1.23E‐03 rs10400279 11 36270057 MCRI ‐0.31 8.87E‐05 G/A 0.058 1.06 (0.93‐1.20) 6.57E‐01 2.03E‐03 rs2510094 11 102981300 DYNC2H1 MCRI 0.45 5.69E‐05 C/T 0.044 0.88 (0.74‐1.05) 4.90E‐01 8.54E‐04 rs7131741 12 78251906 NAV3 MCRI 0.25 4.30E‐04 G/T 0.211 0.97 (0.89‐1.07) 6.72E‐01 2.85E‐02 rs2059765 12 115030724 MCRI ‐0.29 4.19E‐04 A/G 0.228 1.07 (0.98‐1.17) 1.25E‐01 3.44E‐04 rs17075764 13 52100949 MCRI 0.37 5.41E‐04 G/A 0.042 1.10 (0.83‐1.45) 4.00E‐01 2.35E‐03 rs1334870 13 54838415 MCRI ‐0.26 8.31E‐05 A/C 0.309 0.98 (0.90‐1.06) 4.44E‐01 8.86E‐04 rs9530368 13 75270057 MCRI ‐0.22 6.37E‐05 C/A 0.358 0.92 (0.86‐0.99) 2.43E‐01 4.54E‐02 rs1930224 13 96897559 HS6ST3 MCRI 0.25 3.69E‐04 T/C 0.131 0.99 (0.88‐1.10) 4.38E‐01 2.16E‐03 rs6576136 14 28737460 MCRI 0.18 9.18E‐05 C/T 0.381 1.01 (0.94‐1.08) 5.90E‐01 1.71E‐02 rs1680727 14 34507353 MCRI 0.19 5.13E‐04 C/T 0.336 1.06 (0.98‐1.14) 6.13E‐01 3.58E‐02 rs2031271 14 42344822 LRFN5 MCRI 0.23 3.73E‐05 C/A 0.158 1.10 (1.00‐1.21) 6.74E‐02 1.05E‐01 rs8003026 14 72482760 RGS6 MCRI 3.07 4.04E‐05 G/T 0.003 1.84 (0.85‐3.97) 1.17E‐01 7.25E‐02 rs8014528 14 91305899 MCRI ‐0.20 3.03E‐04 C/T 0.348 1.04 (0.96‐1.12) 5.45E‐02 9.07E‐05 rs10147864 14 97919601 MCRI 3.27 6.21E‐05 C/T 0.005 0.76 (0.12‐4.83) 5.88E‐01 1.31E‐03 rs637568 15 29692391 FAM189A1 MCRI ‐0.46 8.96E‐05 G/A 0.027 1.17 (0.92‐1.48) 6.61E‐01 2.07E‐03 rs10518808 15 55562142 RAB27A MCRI 0.22 4.70E‐04 A/G 0.215 0.94 (0.86‐1.02) 2.73E‐01 1.16E‐03 rs11853158 15 56364902 MCRI ‐0.18 6.96E‐05 A/G 0.320 0.91 (0.84‐0.98) 1.79E‐02 2.55E‐01 rs2718934 15 56557418 MCRI ‐0.17 2.50E‐05 G/A 0.466 0.94 (0.88‐1.01) 2.44E‐01 3.11E‐02 rs8032549 15 56572176 MCRI ‐0.18 7.52E‐05 G/A 0.328 0.92 (0.86‐0.99) 1.65E‐02 2.70E‐01 rs2244373 15 57622887 MCRI ‐0.15 4.42E‐04 C/T 0.212 1.06 (0.97‐1.15) 3.65E‐01 1.78E‐03 rs12441883 15 58456850 ALDH1A2 MCRI 0.23 3.60E‐05 A/G 0.370 1.00 (0.93‐1.08) 9.40E‐01 2.93E‐03 rs3784334 15 68610384 ITGA11 MCRI 0.25 4.38E‐04 G/T 0.183 1.03 (0.94‐1.13) 7.62E‐01 2.31E‐02 rs7172809 15 77819676 MCRI 0.18 9.20E‐06 A/G 0.484 1.12 (1.04‐1.20) 1.49E‐02 1.57E‐01 rs2701405 15 87539918 AGBL1 MCRI ‐0.23 2.15E‐05 A/C 0.486 1.02 (0.95‐1.09) 8.93E‐01 1.94E‐03 rs4843249 16 87652026 JPH3 MCRI 0.18 5.22E‐04 G/A 0.465 0.98 (0.91‐1.06) 2.90E‐01 8.83E‐02 rs781856 17 3950224 ZZEF1 MCRI 0.94 7.06E‐06 A/G 0.014 1.09 (0.83‐1.43) 7.79E‐01 2.91E‐03

SUPPLEMENTARY DATA rs4790177 17 4067900 ANKFY1 MCRI 0.95 4.21E‐05 T/C 0.012 1.26 (0.77‐2.06) 3.52E‐01 2.53E‐02 rs8065822 17 4171848 MCRI 1.21 2.19E‐04 C/A 0.009 1.42 (0.83‐2.43) 4.18E‐01 4.13E‐02 rs2325989 17 4199320 UBE2G1 MCRI 1.10 5.63E‐05 G/A 0.015 1.09 (0.85‐1.41) 3.55E‐01 2.82E‐02 rs1986507 17 10082301 GAS7 MCRI ‐0.26 9.92E‐05 A/G 0.152 1.02 (0.93‐1.12) 8.68E‐01 8.41E‐03 rs2274892 17 16852027 TNFRSF13B MCRI ‐0.16 7.67E‐05 G/T 0.372 0.92 (0.86‐0.98) 1.30E‐02 2.99E‐01 rs9911767 17 70376204 MCRI 0.12 6.78E‐04 A/G 0.386 0.99 (0.92‐1.07) 3.38E‐01 8.44E‐02 rs9912528 17 77387550 RBFOX3 MCRI 0.27 1.65E‐05 C/T 0.150 1.05 (0.95‐1.15) 4.48E‐01 1.21E‐02 rs2339345 18 49957255 DCC MCRI ‐0.25 7.80E‐06 A/C 0.343 1.05 (0.99‐1.13) 3.75E‐01 1.52E‐04 rs1008632 18 58869249 MCRI 0.22 4.19E‐04 T/C 0.312 0.99 (0.92‐1.07) 6.36E‐01 3.08E‐02 rs11872993 18 71104519 MCRI ‐1.74 8.65E‐05 T/C 0.006 0.44 (0.21‐0.90) 1.88E‐01 6.51E‐02 rs2276210 18 74587458 ZNF236 MCRI ‐0.89 9.92E‐05 A/G 0.015 0.90 (0.70‐1.17) 7.25E‐01 1.23E‐02 rs3786947 19 3114229 GNA11 MCRI ‐0.28 1.21E‐05 A/G 0.222 1.05 (0.95‐1.16) 2.42E‐01 8.79E‐05 rs7247790 19 5311412 PTPRS MCRI ‐0.28 6.88E‐05 G/T 0.185 0.95 (0.86‐1.06) 5.34E‐01 1.76E‐02 rs6013784 20 52365120 MCRI 0.18 9.56E‐04 T/C 0.167 1.04 (0.95‐1.14) 7.29E‐01 3.66E‐02 rs9983598 21 17903973 LINC00478 MCRI 3.86 1.06E‐04 T/C 0.002 0.51 (0.04‐6.14) 7.20E‐01 2.76E‐03 rs6685355 1 79458347 ELTD1 SI+M ‐7.81 6.27E‐05 C/A 0.326 0.97 (0.91‐1.05) 4.28E‐01 2.32E‐02 rs1507290 1 86684713 SI+M 5.01 6.54E‐05 G/A 0.206 0.98 (0.90‐1.07) 8.85E‐01 6.51E‐03 rs896232 2 2732877 SI+M ‐5.28 1.26E‐06 T/C 0.282 1.00 (0.92‐1.08) 4.05E‐01 4.54E‐03 rs13411840 2 29973281 ALK SI+M ‐14.39 2.69E‐06 C/A 0.046 0.87 (0.75‐1.00) 6.03E‐02 4.66E‐02 rs7581057 2 115958079 DPP10 SI+M ‐5.47 1.74E‐04 G/A 0.056 1.29 (1.10‐1.50) 6.67E‐03 4.82E‐06 rs207910 2 217018422 XRCC5 SI+M 7.26 4.51E‐05 G/A 0.150 0.95 (0.85‐1.07) 7.04E‐01 8.90E‐03 rs6767721 3 87630433 SI+M 6.37 5.90E‐05 G/T 0.071 1.08 (0.95‐1.23) 5.94E‐01 1.38E‐02 rs9853442 3 177191797 SI+M ‐5.68 4.21E‐04 A/G 0.485 1.00 (0.94‐1.08) 8.47E‐01 1.84E‐02 rs10007938 4 32452973 SI+M 6.76 4.74E‐05 G/A 0.241 1.00 (0.92‐1.08) 9.48E‐01 3.47E‐03 rs10023791 4 99425353 TSPAN5 SI+M 4.03 4.31E‐05 A/G 0.426 1.02 (0.96‐1.10) 3.04E‐01 3.03E‐02 rs6815953 4 183109012 ODZ3 SI+M 4.10 3.14E‐05 T/G 0.431 0.92 (0.86‐0.99) 1.25E‐02 2.47E‐06 rs16894006 5 24833120 SI+M ‐12.02 4.38E‐05 C/T 0.020 0.91 (0.68‐1.22) 4.62E‐01 1.78E‐02 rs7724522 5 142081559 SI+M ‐7.09 5.11E‐05 C/T 0.038 1.14 (0.94‐1.37) 1.10E‐01 6.51E‐05 rs29848 5 151449400 AK001582 SI+M 6.61 5.08E‐05 T/G 0.328 1.06 (0.98‐1.13) 3.27E‐01 2.99E‐02 rs2001097 6 32383858 SI+M 10.04 3.69E‐05 T/G 0.128 1.04 (0.75‐1.42) 8.29E‐01 5.70E‐03 rs2227138 6 32384500 SI+M 10.62 7.04E‐05 T/C 0.110 0.92 (0.62‐1.38) 3.55E‐01 5.31E‐04 rs3135376 6 32385470 SI+M 10.04 3.69E‐05 G/A 0.128 1.04 (0.75‐1.42) 8.32E‐01 5.65E‐03

SUPPLEMENTARY DATA rs2395161 6 32387752 SI+M 10.04 3.79E‐05 C/A 0.128 1.04 (0.75‐1.42) 8.29E‐01 5.77E‐03 rs3135366 6 32388709 SI+M 9.96 3.61E‐05 C/T 0.129 0.95 (0.76‐1.18) 7.76E‐01 1.80E‐03 rs558015 6 137899792 SI+M ‐4.84 1.45E‐04 A/G 0.470 0.98 (0.92‐1.05) 8.86E‐01 9.73E‐03 rs24003 7 30748323 INMT SI+M ‐4.83 6.24E‐05 C/T 0.471 1.02 (0.95‐1.09) 2.81E‐01 3.27E‐04 rs2726051 7 36155071 SI+M 6.17 5.27E‐05 C/A 0.223 1.07 (0.98‐1.16) 1.77E‐01 5.68E‐02 rs17141982 7 70133502 AUTS2 SI+M 3.95 9.89E‐05 T/C 0.340 0.99 (0.92‐1.06) 2.23E‐01 3.01E‐04 rs10268984 7 98963340 ARPC1A SI+M ‐7.02 5.59E‐05 T/C 0.103 1.09 (0.99‐1.20) 1.96E‐01 1.67E‐04 rs3177186 7 98984399 ARPC1A SI+M ‐7.04 6.58E‐05 T/C 0.105 1.03 (0.73‐1.47) 8.64E‐01 3.24E‐03 rs7799219 7 123895098 EU233817 SI+M 6.38 6.95E‐05 T/C 0.228 0.94 (0.86‐1.04) 1.41E‐01 1.17E‐04 rs12675420 8 62924308 SI+M 10.10 8.87E‐05 T/C 0.069 1.10 (0.96‐1.27) 7.17E‐01 1.19E‐02 rs6475448 9 20497142 MLLT3 SI+M ‐6.91 3.31E‐05 G/A 0.303 0.98 (0.91‐1.06) 5.97E‐01 9.37E‐04 rs10966384 9 24672959 SI+M ‐9.96 9.06E‐05 C/T 0.057 0.86 (0.74‐1.01) 7.07E‐02 1.36E‐01 rs4817 9 33917498 UBE2R2 SI+M ‐3.47 7.96E‐05 C/T 0.314 0.93 (0.86‐1.00) 8.88E‐02 1.13E‐01 rs10739874 9 105991203 BC035187 SI+M 10.13 1.00E‐04 C/T 0.092 1.05 (0.95‐1.17) 5.58E‐01 1.95E‐02 rs1176191 9 105993267 BC035187 SI+M 10.03 1.77E‐04 T/C 0.090 1.05 (0.95‐1.15) 5.46E‐01 2.62E‐02 rs2688789 10 17733014 STAM SI+M ‐6.25 9.47E‐05 G/A 0.419 1.00 (0.93‐1.07) 4.65E‐01 1.05E‐03 rs12413935 10 85453920 SI+M ‐10.34 4.11E‐05 G/T 0.020 0.95 (0.75‐1.21) 6.14E‐01 1.13E‐03 rs948178 11 113195595 TTC12 SI+M 5.63 9.43E‐05 A/G 0.337 1.04 (0.96‐1.12) 6.89E‐01 2.33E‐03 rs3781827 11 121411041 SORL1 SI+M 3.38 6.12E‐05 G/A 0.434 0.97 (0.91‐1.04) 5.36E‐01 1.07E‐03 rs11180162 12 75081042 SI+M 3.44 8.30E‐05 C/T 0.189 1.05 (0.97‐1.15) 4.38E‐01 2.55E‐02 rs10860482 12 100038835 ANKS1B SI+M 5.67 9.80E‐05 C/T 0.372 1.07 (1.00‐1.15) 2.30E‐01 5.68E‐02 rs7974375 12 118585698 SI+M ‐10.14 8.96E‐05 T/G 0.104 0.91 (0.82‐1.03) 1.93E‐01 6.45E‐02 rs17512574 12 118788003 TAOK3 SI+M ‐12.38 3.19E‐05 T/C 0.110 0.96 (0.87‐1.07) 2.92E‐01 2.81E‐02 rs673078 12 118791441 TAOK3 SI+M ‐12.79 4.71E‐06 C/A 0.125 0.88 (0.80‐0.98) 6.71E‐02 5.21E‐02 rs884844 12 118814838 SUDS3 SI+M ‐12.12 6.71E‐05 T/C 0.113 0.90 (0.81‐1.01) 1.84E‐02 2.50E‐01 rs7305647 12 118855566 SUDS3 SI+M ‐12.32 5.90E‐05 A/G 0.105 0.96 (0.86‐1.06) 2.40E‐01 4.45E‐02 rs4772128 13 99385553 SLC15A1 SI+M ‐7.87 5.57E‐05 A/G 0.029 0.81 (0.58‐1.14) 5.32E‐01 1.60E‐02 rs12717423 14 52940827 TXNDC16 SI+M ‐4.35 3.87E‐05 G/A 0.253 1.02 (0.94‐1.10) 7.64E‐01 1.79E‐03 rs10129385 14 52959478 TXNDC16 SI+M ‐4.30 5.48E‐05 C/T 0.253 1.03 (0.96‐1.11) 3.47E‐01 4.35E‐04 rs2617235 15 42758738 ZFP106 SI+M 6.10 9.05E‐05 C/T 0.366 0.95 (0.88‐1.02) 5.46E‐01 1.40E‐03 rs10851411 15 42859235 HAUS2 SI+M 5.46 5.64E‐06 T/G 0.428 0.96 (0.89‐1.03) 7.23E‐01 5.40E‐04 rs2241998 15 42869028 STARD9 SI+M 5.10 7.70E‐05 A/G 0.417 1.00 (0.94‐1.07) 4.71E‐01 2.23E‐02

SUPPLEMENTARY DATA rs7497796 15 55136506 SI+M 9.33 2.63E‐05 A/C 0.376 0.99 (0.92‐1.06) 7.74E‐01 5.61E‐03 rs12438945 15 55226570 SI+M 10.00 5.38E‐05 C/A 0.230 1.01 (0.93‐1.10) 3.51E‐01 2.81E‐02 rs884202 15 68054388 MAP2K5 SI+M ‐3.79 9.64E‐05 A/G 0.381 0.97 (0.90‐1.04) 5.72E‐01 1.84E‐02 rs7178383 15 99159956 SI+M ‐8.34 8.42E‐05 C/T 0.332 1.00 (0.93‐1.09) 5.91E‐01 1.64E‐02 rs4624233 17 38955961 KRT28 SI+M ‐7.61 2.46E‐05 A/G 0.137 1.02 (0.92‐1.14) 4.08E‐01 3.60E‐04 rs7219451 17 38957002 SI+M ‐6.80 3.92E‐06 C/T 0.380 1.08 (1.00‐1.16) 1.06E‐02 3.97E‐07 rs10558 17 38991003 TMEM99 SI+M ‐7.00 1.48E‐05 C/T 0.138 1.06 (0.96‐1.17) 1.18E‐01 3.08E‐05 rs9303297 17 39005990 SI+M ‐7.40 9.98E‐06 T/C 0.138 1.06 (0.96‐1.16) 1.73E‐01 4.34E‐05 rs3760333 17 39023875 SI+M ‐5.83 2.09E‐05 C/T 0.173 1.05 (0.96‐1.15) 9.73E‐02 2.90E‐05 rs2291447 17 43212963 ACBD4 SI+M ‐4.56 7.95E‐05 T/G 0.346 1.00 (0.93‐1.07) 8.85E‐01 3.82E‐03 rs6133145 20 4576230 SI+M 6.23 4.52E‐05 A/C 0.400 0.99 (0.92‐1.07) 4.24E‐01 5.60E‐04 rs6139486 20 4578080 SI+M 5.16 7.29E‐05 A/G 0.366 0.96 (0.89‐1.03) 4.80E‐01 9.53E‐04 rs6075733 20 20856254 SI+M ‐7.74 3.40E‐05 C/T 0.346 0.99 (0.92‐1.06) 9.15E‐01 2.65E‐03 rs1061325 22 19184095 CLTCL1 SI+M ‐3.28 9.96E‐05 C/T 0.451 1.02 (0.95‐1.09) 5.01E‐01 1.25E‐03 rs17385225 1 164475201 SI 0.28 4.87E‐05 A/G 0.134 0.99 (0.84‐1.17) 5.60E‐01 1.39E‐02 rs6719442 2 2722295 SI ‐0.29 1.53E‐05 A/G 0.180 1.05 (0.96‐1.15) 4.33E‐01 3.03E‐04 rs12620694 2 2763051 SI ‐0.38 3.42E‐05 A/G 0.162 1.03 (0.95‐1.13) 7.09E‐01 1.40E‐03 rs1978648 2 43371542 SI 0.20 5.31E‐07 T/C 0.328 1.03 (0.96‐1.11) 3.08E‐01 4.72E‐03 rs4952971 2 43373119 SI 0.18 2.31E‐05 A/G 0.438 1.00 (0.93‐1.07) 8.08E‐01 1.55E‐03 rs10167465 2 43397176 SI 0.19 9.30E‐05 G/A 0.419 0.98 (0.91‐1.06) 8.93E‐01 4.25E‐03 rs1044710 2 211297355 LANCL1 SI ‐0.20 8.93E‐05 A/G 0.395 1.03 (0.96‐1.11) 5.43E‐01 1.37E‐03 rs6782551 3 74922055 SI 0.57 9.04E‐05 A/G 0.014 0.80 (0.42‐1.54) 7.97E‐02 6.14E‐05 rs1872552 3 85049088 CADM2 SI ‐0.20 8.59E‐05 A/G 0.444 1.01 (0.95‐1.07) 6.62E‐01 2.03E‐03 rs716975 4 38349236 SI ‐0.27 9.86E‐06 T/C 0.226 1.03 (0.95‐1.12) 8.57E‐01 2.71E‐03 rs7690543 4 68056613 SI 0.28 2.34E‐06 T/C 0.177 1.05 (0.96‐1.15) 3.76E‐01 6.67E‐03 rs1848056 4 125755019 SI 0.09 3.21E‐05 T/C 0.484 0.98 (0.91‐1.05) 3.41E‐01 3.02E‐04 rs9997902 4 125763629 SI 0.10 2.29E‐05 A/G 0.490 0.95 (0.89‐1.00) 1.15E‐01 3.98E‐05 rs1602084 4 128843480 MFSD8 SI 0.43 3.10E‐06 G/A 0.038 1.05 (0.85‐1.29) 5.78E‐01 3.68E‐03 rs11943562 4 167652786 SI ‐0.25 6.27E‐05 C/T 0.130 0.96 (0.86‐1.07) 2.49E‐01 4.39E‐02 rs17069175 4 181226698 SI ‐0.27 7.04E‐05 A/G 0.241 0.99 (0.91‐1.07) 4.28E‐01 7.49E‐04 rs6868526 5 5399472 SI 0.27 2.22E‐05 C/T 0.188 1.05 (0.96‐1.14) 6.91E‐01 6.56E‐03 rs16875556 5 5402163 SI 0.26 3.47E‐05 A/G 0.167 1.01 (0.92‐1.12) 7.85E‐01 1.81E‐03

©2014 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db13-1829/-/DC1 SUPPLEMENTARY DATA rs7717247 5 27839258 SI ‐0.33 4.16E‐05 C/A 0.136 0.99 (0.89‐1.10) 7.57E‐01 1.83E‐03 rs462647 5 81080808 SI 0.32 8.79E‐05 C/T 0.334 1.07 (0.99‐1.15) 4.37E‐02 1.78E‐01 rs6880017 5 81185254 SI ‐0.17 7.51E‐05 G/A 0.314 0.97 (0.90‐1.04) 5.61E‐01 1.69E‐02 rs17155849 5 103142399 SI ‐0.29 7.13E‐05 T/C 0.290 1.02 (0.94‐1.10) 5.96E‐01 1.46E‐03 rs1898910 5 124555847 SI ‐0.38 6.60E‐06 A/C 0.161 1.02 (0.93‐1.12) 7.04E‐01 3.52E‐03 rs1042711 5 148206348 SH3TC2 SI 0.31 9.07E‐05 C/T 0.212 1.04 (0.97‐1.11) 6.40E‐01 1.48E‐02 rs12194985 6 6892411 SI ‐0.40 8.50E‐05 T/G 0.032 1.17 (0.97‐1.43) 3.04E‐01 4.55E‐04 rs10080664 6 15864284 SI 0.15 9.95E‐05 A/G 0.384 0.95 (0.89‐1.02) 3.04E‐01 5.04E‐04 rs4716224 6 18161563 KDM1B SI ‐0.19 9.37E‐05 A/G 0.306 1.00 (0.93‐1.07) 8.23E‐01 9.20E‐03 rs724941 6 76723011 IMPG1 SI 0.17 9.34E‐05 C/T 0.446 0.93 (0.87‐1.00) 7.11E‐01 2.49E‐03 rs943086 6 76755221 IMPG1 SI 0.15 6.49E‐05 G/A 0.449 1.00 (0.93‐1.07) 3.15E‐01 3.46E‐02 rs196701 6 80147187 SI ‐0.35 1.37E‐06 C/T 0.128 0.93 (0.84‐1.03) 5.03E‐02 4.23E‐02 rs7803642 7 21641629 DNAH11 SI ‐0.18 9.92E‐05 T/C 0.321 1.05 (0.98‐1.13) 9.62E‐01 6.55E‐03 rs9406428 9 11463799 SI 0.33 7.63E‐05 C/T 0.132 0.96 (0.86‐1.06) 7.62E‐02 5.10E‐05 rs10964496 9 20248264 SI 0.34 5.14E‐05 A/G 0.091 0.95 (0.85‐1.06) 9.58E‐01 3.73E‐03 rs10811340 9 20283406 SI 0.27 7.35E‐05 G/A 0.098 0.93 (0.83‐1.03) 8.57E‐01 3.38E‐03 rs1581979 9 23407435 SI ‐0.18 8.14E‐05 C/A 0.310 0.95 (0.89‐1.03) 4.25E‐01 2.63E‐02 rs10780305 9 81978708 SI 0.15 8.69E‐06 A/G 0.431 0.97 (0.91‐1.04) 5.95E‐01 4.31E‐04 rs1885984 9 119078249 PAPPA SI ‐0.79 9.14E‐05 T/C 0.009 0.64 (0.35‐1.19) 1.90E‐01 6.57E‐02 rs2819042 10 10230151 SI ‐0.18 1.38E‐05 A/C 0.455 0.99 (0.92‐1.06) 8.34E‐01 1.27E‐03 rs359297 10 17333680 SI ‐0.28 5.10E‐05 A/G 0.213 1.03 (0.95‐1.12) 8.39E‐01 6.51E‐03 rs12256421 10 17614097 SI ‐0.20 9.07E‐05 A/G 0.387 1.00 (0.94‐1.08) 5.42E‐01 1.95E‐02 rs1223629 10 95906315 PLCE1 SI ‐0.74 4.72E‐06 A/G 0.038 0.98 (0.83‐1.16) 4.29E‐01 7.44E‐03 rs10870301 10 134186772 LRRC27 SI ‐0.12 7.93E‐05 C/T 0.435 0.98 (0.92‐1.05) 4.49E‐01 2.41E‐02 rs4443996 10 134191005 LRRC27 SI ‐0.11 9.70E‐05 C/A 0.441 0.97 (0.91‐1.04) 3.22E‐01 3.98E‐02 rs10870302 10 134191738 LRRC27 SI ‐0.13 9.64E‐05 T/G 0.436 0.98 (0.92‐1.05) 4.06E‐01 3.01E‐02 rs10870303 10 134191811 LRRC27 SI ‐0.13 6.94E‐05 G/A 0.436 0.99 (0.92‐1.06) 8.09E‐01 8.24E‐03 rs4568920 10 134324451 SI ‐0.29 7.13E‐05 T/C 0.077 0.98 (0.86‐1.11) 2.63E‐01 4.36E‐02 rs7117567 11 7715079 OVCH2 SI ‐0.21 8.87E‐05 G/A 0.356 1.02 (0.93‐1.11) 7.59E‐01 2.80E‐03 rs121704 11 17904634 SERGEF SI 0.15 5.97E‐05 G/A 0.474 1.06 (0.98‐1.13) 5.16E‐02 1.44E‐01 rs10160242 11 108498885 SI 0.41 4.33E‐06 C/T 0.060 1.11 (0.93‐1.33) 7.79E‐01 2.29E‐03 rs2368785 12 260682 IQSEC3 SI 0.19 4.51E‐05 C/T 0.150 1.03 (0.93‐1.13) 9.50E‐02 8.83E‐02

©2014 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db13-1829/-/DC1 SUPPLEMENTARY DATA rs1947234 12 39450491 SI 0.13 7.83E‐05 A/C 0.197 1.02 (0.93‐1.11) 8.21E‐01 8.47E‐03 rs10785139 12 75089475 SI 0.19 5.31E‐05 C/T 0.307 1.04 (0.96‐1.12) 6.92E‐01 9.95E‐03 rs9554019 13 27951711 SI ‐0.36 2.76E‐05 A/G 0.061 1.02 (0.80‐1.30) 7.86E‐01 5.56E‐03 rs17376318 13 108013050 FAM155A SI ‐0.41 4.00E‐05 C/T 0.119 0.98 (0.87‐1.11) 7.08E‐01 8.30E‐03 rs9559508 13 109805793 MYO16 SI ‐0.17 9.54E‐05 T/C 0.240 0.95 (0.88‐1.03) 5.34E‐01 2.04E‐02 rs10129961 14 34767305 SI 0.33 2.25E‐05 A/G 0.146 1.07 (0.97‐1.18) 2.02E‐01 3.62E‐02 rs17123946 14 51929722 SI ‐0.29 9.17E‐05 G/A 0.251 1.09 (1.00‐1.18) 1.50E‐01 1.54E‐04 rs10498430 14 51942961 SI ‐0.30 4.05E‐05 T/C 0.243 1.11 (1.02‐1.20) 7.37E‐02 3.08E‐05 rs17123969 14 51946458 SI ‐0.30 5.36E‐05 G/A 0.245 1.11 (1.02‐1.21) 2.37E‐01 2.22E‐04 rs4901281 14 52980190 TXNDC16 SI ‐0.29 5.98E‐05 A/C 0.148 1.03 (0.94‐1.14) 4.55E‐01 7.63E‐04 rs11631474 15 67934167 MAP2K5 SI ‐0.24 3.36E‐05 G/A 0.272 0.98 (0.91‐1.06) 8.76E‐01 4.77E‐03 rs896598 15 74036629 C15orf59 SI 0.37 5.83E‐07 A/G 0.119 1.07 (0.96‐1.19) 9.72E‐02 1.83E‐02 rs4887140 15 74046663 SI 0.31 6.91E‐08 G/T 0.143 0.97 (0.88‐1.07) 2.93E‐01 2.14E‐03 rs2415230 15 74059081 SI 0.26 7.20E‐06 A/G 0.171 1.07 (0.98‐1.17) 2.01E‐01 2.33E‐02 rs27230 16 3434699 ZNF434 SI ‐0.23 5.85E‐05 G/A 0.107 0.94 (0.84‐1.04) 6.25E‐01 1.26E‐02 rs16530 17 37357034 RPL19 SI ‐0.33 2.97E‐05 T/C 0.102 0.97 (0.86‐1.10) 7.24E‐01 1.36E‐03 rs691336 17 76518426 DNAH17 SI ‐0.27 2.91E‐05 T/C 0.261 0.98 (0.91‐1.06) 6.97E‐01 7.36E‐03 rs6139479 20 4566415 SI 0.23 9.73E‐05 A/G 0.308 0.94 (0.87‐1.02) 3.82E‐01 7.41E‐04 rs6100794 20 58799036 AX747739 SI ‐0.63 4.80E‐06 T/C 0.012 1.10 (0.60‐2.02) 8.27E‐01 7.02E‐04 rs2235438 1 4849384 BC037321 M 15.45 3.95E‐05 T/C 0.357 1.09 (1.01‐1.18) 7.53E‐02 9.92E‐02 rs2744761 1 26040514 MAN1C1 M ‐21.75 5.54E‐05 G/T 0.229 1.06 (0.97‐1.16) 8.04E‐01 7.47E‐03 rs11209072 1 67908644 M ‐22.54 7.60E‐05 G/A 0.393 1.05 (0.98‐1.12) 2.03E‐01 2.18E‐04 rs12135476 1 69649328 M ‐31.54 3.75E‐06 A/G 0.118 0.99 (0.89‐1.10) 9.13E‐01 1.41E‐03 rs10493454 1 69659840 M ‐29.41 6.08E‐06 G/A 0.136 1.00 (0.91‐1.09) 7.50E‐01 6.16E‐04 rs4650135 1 69684997 M ‐29.56 2.31E‐06 C/T 0.157 1.01 (0.92‐1.11) 8.17E‐01 4.57E‐04 rs1886644 1 85350658 LPAR3 M ‐22.90 6.28E‐06 C/A 0.295 0.93 (0.86‐1.00) 5.01E‐02 7.05E‐02 rs6665426 1 200148319 M ‐19.74 8.31E‐05 A/G 0.309 0.94 (0.87‐1.03) 3.54E‐01 3.34E‐02 rs17047682 1 218523025 TGFB2 M ‐31.01 1.19E‐05 G/A 0.078 1.09 (0.90‐1.31) 1.11E‐01 2.39E‐05 rs10926618 1 242251696 PLD5 M ‐23.32 8.79E‐05 T/C 0.386 1.02 (0.95‐1.10) 8.50E‐01 3.65E‐03 rs7558483 2 11537452 M ‐19.51 7.39E‐05 T/C 0.244 0.98 (0.91‐1.07) 9.67E‐01 4.63E‐03 rs17031893 2 44283172 M 27.41 9.83E‐05 G/A 0.101 0.93 (0.84‐1.03) 3.59E‐01 6.67E‐04 rs7595513 2 46687867 M ‐22.09 6.66E‐05 G/A 0.198 0.94 (0.86‐1.02) 4.35E‐01 2.33E‐02

SUPPLEMENTARY DATA rs2138397 2 86974049 RMND5A M ‐24.39 3.71E‐05 A/G 0.442 1.00 (0.93‐1.07) 9.03E‐01 4.64E‐03 rs2889323 2 105039687 M ‐14.31 3.60E‐04 C/A 0.436 1.01 (0.94‐1.09) 7.85E‐01 6.61E‐03 rs10179986 2 134864344 M ‐17.78 7.95E‐06 G/A 0.467 1.00 (0.93‐1.07) 8.77E‐01 2.30E‐03 rs1996589 2 134865196 M ‐21.95 3.97E‐05 C/T 0.230 0.95 (0.88‐1.03) 7.90E‐01 6.58E‐03 rs4953902 2 134876049 M ‐25.81 1.41E‐05 C/A 0.140 0.95 (0.86‐1.05) 7.10E‐01 4.99E‐03 rs1111961 2 134880830 M ‐25.37 1.40E‐05 G/A 0.158 0.96 (0.87‐1.05) 6.47E‐01 5.99E‐03 rs13030335 2 142231898 LRP1B M ‐33.45 4.13E‐05 A/G 0.382 0.89 (0.83‐0.96) 9.78E‐04 5.70E‐01 rs10178963 2 142349495 LRP1B M 24.53 9.64E‐05 C/A 0.446 1.12 (1.04‐1.20) 6.83E‐03 3.98E‐01 rs1546676 2 154509239 M 23.62 8.00E‐06 A/G 0.325 1.02 (0.95‐1.10) 5.20E‐01 6.88E‐03 rs1429411 2 198144002 ANKRD44 M 21.71 4.09E‐04 G/A 0.436 1.07 (1.00‐1.14) 1.19E‐01 1.62E‐01 rs2178704 2 227579207 M 25.31 8.83E‐05 G/A 0.244 0.94 (0.87‐1.03) 1.39E‐01 1.34E‐04 rs11683087 2 227586606 M 20.54 7.42E‐07 G/A 0.412 1.02 (0.94‐1.11) 8.38E‐01 7.92E‐04 rs2251692 2 227589780 M 17.31 1.98E‐05 A/G 0.483 1.04 (0.97‐1.11) 6.73E‐01 6.56E‐03 rs10205233 2 227614005 IRS1 M 23.19 2.35E‐05 T/C 0.185 0.97 (0.89‐1.06) 2.18E‐01 1.13E‐04 rs2596937 3 9480906 SETD5 M ‐17.41 9.76E‐05 C/T 0.238 1.00 (0.93‐1.08) 2.32E‐01 5.60E‐02 rs2279440 3 9518511 SETD5 M ‐21.57 3.31E‐06 T/C 0.203 1.04 (0.96‐1.13) 9.13E‐01 1.32E‐03 rs17050395 3 9533974 M ‐17.84 8.31E‐05 G/A 0.235 0.96 (0.89‐1.03) 5.60E‐02 1.52E‐01 rs3806667 3 9860880 ARPC4‐TTLL3 M ‐20.45 2.79E‐05 G/T 0.272 1.03 (0.95‐1.11) 3.99E‐01 3.71E‐04 rs13106 3 12624580 MKRN2 M 126.46 3.41E‐05 A/G 0.028 0.90 (0.50‐1.62) 3.16E‐01 2.74E‐04 rs635787 3 32466487 CMTM7 M ‐22.82 1.24E‐05 A/G 0.453 0.98 (0.91‐1.06) 2.10E‐01 2.75E‐02 rs9682976 3 60118879 FHIT M ‐24.49 5.93E‐05 T/C 0.152 1.02 (0.93‐1.13) 7.28E‐01 2.03E‐03 rs17062321 3 60122156 FHIT M ‐24.84 2.39E‐05 T/C 0.163 1.03 (0.94‐1.14) 6.51E‐01 9.42E‐04 rs9854367 3 102259425 M 27.76 3.04E‐04 C/T 0.092 0.94 (0.84‐1.05) 6.85E‐01 4.50E‐03 rs12493716 3 106777359 LOC100302640 M ‐16.30 9.21E‐05 G/A 0.253 0.96 (0.88‐1.04) 3.71E‐01 3.30E‐02 rs12487584 3 132300293 ACAD11 M 19.13 2.87E‐05 T/C 0.284 1.06 (0.98‐1.15) 2.27E‐01 3.53E‐02 rs13094259 3 142444625 TRPC1 M ‐29.40 9.10E‐05 T/G 0.091 1.05 (0.94‐1.17) 5.03E‐02 3.31E‐05 rs9824464 3 167635899 LOC646168 M 27.97 8.41E‐05 T/C 0.468 0.98 (0.91‐1.04) 9.28E‐01 4.45E‐03 rs1426260 3 188260703 LPP M 27.98 4.25E‐06 T/C 0.501 1.01 (0.94‐1.08) 7.67E‐01 2.35E‐03 rs10937355 3 188289697 LPP M ‐23.26 4.12E‐05 T/C 0.306 0.97 (0.90‐1.05) 9.71E‐01 4.05E‐03 rs12511127 4 5142212 STK32B M ‐16.49 6.59E‐05 G/A 0.325 1.04 (0.97‐1.12) 6.18E‐01 1.50E‐03 rs6448852 4 12017993 M 15.04 5.55E‐05 C/T 0.468 0.95 (0.89‐1.02) 2.39E‐01 2.31E‐04 rs1025877 4 12074137 M ‐14.32 9.65E‐05 G/A 0.455 1.02 (0.96‐1.08) 9.44E‐01 5.00E‐03

SUPPLEMENTARY DATA rs4834882 4 12108239 M 18.23 2.08E‐05 T/C 0.314 1.00 (0.93‐1.08) 9.93E‐01 2.57E‐03 rs9997603 4 66438114 EPHA5 M ‐31.75 1.54E‐05 T/G 0.080 1.01 (0.90‐1.13) 9.81E‐01 2.36E‐03 rs4320186 4 66483593 EPHA5 M ‐30.58 2.41E‐05 A/G 0.079 1.08 (0.95‐1.23) 3.57E‐01 2.76E‐04 rs1023514 4 108239396 M 7.76 5.36E‐02 A/G 0.413 1.07 (1.00‐1.15) 1.22E‐01 7.86E‐01 rs11930824 4 161451545 M 29.13 7.46E‐05 A/G 0.445 0.99 (0.93‐1.06) 3.48E‐01 5.30E‐04 rs4627838 4 175602762 GLRA3 M 19.97 7.25E‐05 A/C 0.427 1.02 (0.95‐1.09) 5.38E‐01 1.78E‐02 rs4695784 4 175608905 GLRA3 M 19.97 7.25E‐05 T/C 0.426 1.01 (0.94‐1.07) 7.84E‐01 8.99E‐03 rs6877846 5 81160103 M 20.99 5.27E‐05 A/G 0.328 1.02 (0.95‐1.10) 3.16E‐01 3.16E‐02 rs4835696 5 137972584 M 35.18 1.74E‐05 A/G 0.383 0.95 (0.88‐1.02) 2.35E‐01 1.06E‐04 rs13361457 5 152797679 M 23.81 9.63E‐06 T/C 0.477 1.04 (0.97‐1.12) 1.18E‐01 4.31E‐02 rs1019507 5 152798614 M ‐18.01 2.10E‐05 C/A 0.409 0.99 (0.93‐1.07) 4.74E‐01 1.24E‐02 rs1465417 5 153790531 GALNT10 M ‐20.39 7.72E‐05 T/C 0.198 0.98 (0.90‐1.06) 4.60E‐01 2.30E‐02 rs322394 5 172157768 M ‐15.83 3.38E‐05 C/T 0.360 1.17 (1.09‐1.26) 7.87E‐04 1.12E‐07 rs241439 6 32797537 TAP2 M 18.67 9.23E‐05 G/T 0.426 0.94 (0.87‐1.00) 6.69E‐01 2.16E‐03 rs16884633 6 53902171 MLIP M ‐23.78 3.67E‐05 A/G 0.234 0.97 (0.89‐1.06) 6.21E‐01 1.08E‐03 rs987672 6 77410315 M ‐17.03 9.05E‐05 G/A 0.358 1.03 (0.96‐1.11) 7.05E‐01 1.24E‐02 rs665791 6 106674850 ATG5 M 18.17 8.39E‐06 G/A 0.328 0.88 (0.82‐0.94) 5.92E‐02 7.32E‐06 rs484621 6 106734408 ATG5 M 18.89 4.12E‐06 T/C 0.323 0.95 (0.88‐1.02) 3.23E‐01 7.64E‐05 rs490010 6 106740458 ATG5 M 18.72 5.91E‐06 A/G 0.316 0.88 (0.82‐0.94) 9.35E‐02 1.14E‐05 rs510432 6 106774030 M 16.93 2.61E‐05 T/C 0.341 0.94 (0.88‐1.01) 1.47E‐01 6.38E‐05 rs4134409 6 170279658 M 19.26 3.79E‐05 A/G 0.245 0.89 (0.80‐0.99) 3.50E‐01 3.51E‐04 rs10267935 7 34885503 AAA1 M ‐26.04 3.55E‐04 A/C 0.105 0.99 (0.90‐1.10) 7.77E‐01 2.01E‐02 rs11768415 7 52347667 M ‐17.74 2.80E‐05 A/G 0.519 1.00 (0.93‐1.06) 6.10E‐01 9.28E‐03 rs11764734 7 52356515 M ‐18.43 1.41E‐05 T/C 0.520 0.97 (0.91‐1.05) 3.22E‐01 1.78E‐02 rs296307 7 52432938 M ‐15.67 8.25E‐05 T/C 0.470 0.97 (0.91‐1.04) 4.34E‐01 2.57E‐02 rs296316 7 52439967 M ‐16.72 9.52E‐05 T/C 0.369 0.93 (0.86‐1.00) 2.59E‐02 2.37E‐01 rs2188256 7 88213062 M ‐21.95 6.79E‐05 C/T 0.179 0.97 (0.89‐1.06) 8.44E‐01 3.11E‐03 rs1588422 7 97329406 M 44.15 3.19E‐05 T/C 0.278 1.00 (0.93‐1.07) 9.93E‐01 3.20E‐03 rs2968865 7 124810399 AX746567 M 29.85 1.40E‐05 G/A 0.459 0.99 (0.93‐1.06) 8.79E‐01 3.04E‐03 rs441606 8 17903046 M 26.11 9.48E‐05 A/G 0.462 0.92 (0.86‐0.99) 8.73E‐02 7.21E‐05 rs17197236 8 25193338 DOCK5 M 54.29 7.13E‐06 G/A 0.034 0.89 (0.73‐1.08) 1.64E‐01 3.21E‐05 rs13267838 8 25196710 DOCK5 M 54.96 4.03E‐06 T/G 0.035 0.90 (0.75‐1.08) 1.45E‐01 1.78E‐05

©2014 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db13-1829/-/DC1 SUPPLEMENTARY DATA rs13252932 8 25198091 DOCK5 M 47.71 5.17E‐06 T/C 0.049 0.89 (0.75‐1.04) 6.61E‐02 6.11E‐06 rs11780263 8 27823832 SCARA5 M ‐16.34 6.64E‐05 A/G 0.210 0.92 (0.84‐1.00) 1.21E‐02 2.95E‐01 rs9650426 8 27827391 SCARA5 M 15.63 6.38E‐05 C/T 0.334 0.97 (0.90‐1.05) 2.58E‐01 2.87E‐04 rs1715350 8 50396852 M ‐19.15 7.31E‐05 T/G 0.258 1.08 (1.00‐1.17) 2.91E‐01 3.84E‐04 rs4737430 8 57303823 M 17.90 6.71E‐05 A/G 0.404 0.98 (0.91‐1.05) 7.97E‐01 2.69E‐03 rs633142 8 102466767 M ‐16.14 8.10E‐05 T/G 0.337 0.93 (0.87‐0.99) 3.99E‐02 1.82E‐01 rs618854 8 102467706 M ‐16.61 5.04E‐05 T/C 0.343 0.93 (0.87‐1.00) 4.21E‐02 1.53E‐01 rs4333664 9 6556948 GLDC M 16.94 1.15E‐05 T/C 0.432 0.99 (0.92‐1.06) 7.79E‐01 3.70E‐03 rs17781302 9 24142314 M 21.35 6.10E‐05 C/A 0.178 1.09 (0.93‐1.27) 3.36E‐01 3.12E‐02 rs17060946 9 77808519 M 37.86 2.56E‐06 G/A 0.068 0.87 (0.75‐1.01) 6.89E‐02 3.99E‐06 rs7030420 9 77809075 M 29.63 5.75E‐05 G/A 0.080 0.95 (0.83‐1.09) 5.25E‐01 9.87E‐04 rs1888221 9 117778355 M 19.08 2.52E‐06 A/G 0.310 0.97 (0.90‐1.05) 8.52E‐01 5.40E‐04 rs17099236 10 92484110 M 28.87 5.13E‐05 A/G 0.114 0.96 (0.86‐1.07) 6.47E‐01 1.44E‐03 rs4564313 11 6083952 M ‐13.19 1.49E‐03 A/G 0.489 0.94 (0.88‐1.00) 2.72E‐02 4.94E‐01 rs1488933 11 17267029 M 30.81 2.76E‐05 T/C 0.448 1.08 (1.01‐1.16) 8.21E‐02 8.27E‐02 rs10841497 12 20524202 PDE3A M 17.05 3.17E‐05 G/T 0.356 1.05 (0.91‐1.22) 9.35E‐02 7.90E‐02 rs7964191 12 20551038 PDE3A M 24.85 5.20E‐05 C/T 0.150 1.12 (1.02‐1.24) 3.05E‐02 1.83E‐01 rs10770655 12 20574060 PDE3A M 23.56 9.20E‐05 C/A 0.180 1.12 (1.02‐1.23) 2.71E‐02 2.29E‐01 rs7311799 12 84718394 M ‐27.14 9.33E‐05 A/C 0.469 1.00 (0.93‐1.07) 7.60E‐01 2.89E‐03 rs11059101 12 127874250 M ‐25.34 9.30E‐05 C/T 0.100 0.99 (0.75‐1.31) 8.71E‐01 8.07E‐03 rs4760067 12 130611682 M ‐23.40 2.54E‐05 T/C 0.432 0.94 (0.88‐1.01) 2.16E‐01 3.55E‐02 rs2874868 13 36356679 MAB21L1 M 16.78 6.40E‐05 G/T 0.233 0.94 (0.87‐1.02) 7.78E‐01 2.48E‐03 rs7329452 13 39000963 M ‐23.70 3.64E‐05 G/T 0.498 0.97 (0.92‐1.03) 8.55E‐01 2.30E‐03 rs4520736 13 59174647 M ‐21.75 2.56E‐05 C/T 0.415 0.99 (0.92‐1.07) 8.42E‐01 4.57E‐03 rs4885169 13 74900793 M ‐23.04 5.31E‐06 A/G 0.239 1.10 (1.01‐1.19) 6.90E‐01 4.64E‐04 rs1041515 13 74905950 M ‐21.78 5.14E‐07 C/T 0.243 1.08 (1.00‐1.18) 7.18E‐01 1.41E‐04 rs7992923 13 74907043 M ‐13.94 7.86E‐05 A/G 0.427 1.05 (0.99‐1.13) 6.37E‐01 1.78E‐03 rs1331765 13 74907933 M ‐15.35 2.15E‐05 G/A 0.372 1.06 (0.99‐1.14) 6.38E‐01 8.46E‐04 rs10492494 13 74920186 M ‐22.02 5.04E‐07 A/C 0.240 1.11 (1.02‐1.20) 4.22E‐01 3.77E‐05 rs2325622 13 74932425 M ‐21.66 5.61E‐07 A/C 0.247 1.07 (0.99‐1.16) 9.52E‐01 3.42E‐04 rs9554374 13 97580064 M 20.73 4.37E‐04 T/G 0.387 1.07 (0.99‐1.15) 8.82E‐01 1.72E‐02 rs2389751 13 97584304 M 15.52 2.13E‐04 A/G 0.411 1.02 (0.95‐1.09) 4.73E‐01 1.77E‐03

SUPPLEMENTARY DATA rs555647 13 98632349 IPO5 M 20.89 8.65E‐05 G/A 0.403 1.00 (0.93‐1.07) 4.15E‐01 8.00E‐04 rs6572117 14 42360633 LRFN5 M ‐29.20 9.45E‐05 T/C 0.374 0.98 (0.91‐1.05) 2.70E‐01 4.76E‐02 rs17120327 14 49073392 M ‐22.43 3.06E‐05 A/G 0.199 1.03 (0.95‐1.12) 8.15E‐01 1.85E‐03 rs7165441 15 27828539 M 22.79 6.52E‐05 G/A 0.408 1.01 (0.94‐1.08) 4.83E‐01 2.00E‐02 rs17818867 15 55175350 M 19.09 1.24E‐05 C/T 0.255 1.01 (0.93‐1.09) 5.38E‐01 7.94E‐03 rs11637842 15 55200927 M 20.78 1.43E‐05 A/G 0.225 1.01 (0.93‐1.09) 6.06E‐01 6.86E‐03 rs17238052 15 55259099 M 22.68 9.39E‐05 G/A 0.235 1.03 (0.95‐1.11) 1.65E‐01 7.52E‐02 rs3826347 17 64970002 CACNG4 M 25.26 4.44E‐05 G/A 0.424 1.00 (0.93‐1.07) 9.15E‐01 4.92E‐03 rs6501303 17 77430593 RBFOX3 M 33.30 4.32E‐05 A/G 0.046 0.95 (0.80‐1.12) 1.30E‐01 7.43E‐05 rs626410 18 65855591 M 16.55 2.88E‐05 A/C 0.398 0.96 (0.90‐1.03) 6.99E‐01 1.23E‐03 rs12961613 18 66309996 M ‐22.84 6.23E‐05 T/C 0.229 1.07 (0.94‐1.21) 1.26E‐01 9.10E‐05 rs10408924 19 9253139 ZNF317 M 22.59 9.94E‐05 G/T 0.370 0.97 (0.90‐1.04) 4.57E‐01 1.05E‐03 rs892024 19 33399344 CEP89 M ‐23.28 8.92E‐05 A/G 0.168 1.00 (0.92‐1.10) 8.53E‐01 3.71E‐03 rs913555 20 3090124 LOC100134015 M 21.80 6.92E‐05 A/G 0.295 1.01 (0.94‐1.09) 8.91E‐01 6.59E‐03 rs911112 20 3144664 ProSAPiP1 M 22.86 6.70E‐05 T/C 0.254 1.00 (0.93‐1.09) 7.46E‐01 2.31E‐03 rs11907984 20 20862068 M ‐16.12 9.28E‐05 T/C 0.370 0.99 (0.92‐1.07) 7.18E‐01 2.53E‐03 rs4813402 20 20889803 M ‐16.68 5.21E‐05 C/T 0.366 0.99 (0.92‐1.06) 8.26E‐01 2.56E‐03 rs6137217 20 20997702 M 24.96 9.01E‐06 T/C 0.349 0.96 (0.89‐1.03) 6.94E‐01 6.31E‐04 rs6047982 20 22246450 M 12.85 6.23E‐04 G/T 0.419 0.98 (0.92‐1.06) 4.66E‐01 3.34E‐03 rs6113604 20 22252275 M 22.01 1.22E‐04 T/C 0.369 1.03 (0.96‐1.10) 6.89E‐01 2.69E‐03 rs4815102 20 22255173 CR627206 M 21.95 1.39E‐04 T/G 0.371 0.99 (0.92‐1.06) 3.79E‐01 9.13E‐04 rs1028444 20 22267058 M 26.33 5.22E‐06 C/T 0.404 1.02 (0.96‐1.10) 8.62E‐01 8.26E‐04 rs4813452 20 22276813 M 24.54 2.16E‐05 G/T 0.382 1.03 (0.96‐1.11) 7.51E‐01 1.25E‐03 rs17192831 20 22281954 M 24.83 1.64E‐05 T/C 0.386 0.98 (0.91‐1.05) 2.33E‐01 9.99E‐05 rs6018406 20 45941326 ZMYND8 M 18.51 5.91E‐05 C/A 0.247 0.88 (0.79‐0.97) 1.06E‐01 6.84E‐05 rs155004 20 57870356 M ‐24.33 2.48E‐05 G/A 0.283 0.95 (0.87‐1.04) 2.50E‐01 3.01E‐02 rs1573708 22 36427484 M 14.69 2.25E‐03 T/C 0.488 0.95 (0.89‐1.03) 6.46E‐01 1.30E‐02 rs763040 22 44763606 M 22.54 6.91E‐05 A/G 0.205 1.04 (0.96‐1.13) 8.50E‐01 7.36E‐03 rs2784739 1 8497558 RERE AIRg ‐1.98 1.91E‐05 G/T 0.243 1.01 (0.93‐1.10) 2.97E‐01 2.23E‐02 rs11121182 1 8522553 RERE AIRg ‐1.92 5.01E‐05 A/C 0.270 0.87 (0.81‐0.94) 4.40E‐03 3.93E‐01 rs10492966 1 8598005 RERE AIRg ‐1.96 4.70E‐05 T/C 0.273 0.87 (0.81‐0.94) 3.27E‐03 4.25E‐01 rs11121203 1 8648240 RERE AIRg ‐1.86 4.42E‐05 C/T 0.286 0.96 (0.88‐1.03) 5.20E‐02 1.30E‐01

©2014 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db13-1829/-/DC1 SUPPLEMENTARY DATA rs12061717 1 55024928 ACOT11 AIRg ‐2.10 2.66E‐05 T/C 0.080 0.95 (0.84‐1.08) 1.96E‐01 3.97E‐02 rs13375344 1 73500168 AIRg 16.86 3.10E‐05 A/C 0.002 2.77 (0.48‐16.12) 2.69E‐01 3.04E‐02 rs7537721 1 88514479 AIRg 8.45 2.92E‐05 A/G 0.010 0.79 (0.33‐1.90) 1.72E‐01 8.85E‐05 rs11185362 1 104561488 AIRg ‐1.65 3.21E‐05 G/A 0.309 1.06 (0.98‐1.14) 4.67E‐01 5.50E‐04 rs17018659 2 4211781 AIRg 10.57 5.39E‐05 G/A 0.004 1.35 (0.45‐4.06) 4.11E‐01 2.30E‐02 rs2053797 2 46370892 PRKCE AIRg 1.89 5.02E‐05 A/G 0.162 0.91 (0.83‐1.00) 1.42E‐02 4.21E‐06 rs4953320 2 46374529 PRKCE AIRg 2.13 8.13E‐05 C/T 0.099 0.95 (0.84‐1.07) 1.71E‐01 1.74E‐04 rs1345516 2 64703286 AIRg 1.04 4.11E‐05 A/C 0.420 0.95 (0.88‐1.02) 2.04E‐01 1.46E‐04 rs6756027 2 64720254 AIRg 1.09 6.05E‐05 A/G 0.432 0.95 (0.88‐1.02) 3.87E‐01 5.65E‐04 rs13002043 2 64726449 AIRg 1.07 7.92E‐05 A/G 0.437 0.99 (0.93‐1.05) 9.29E‐01 4.32E‐03 rs9809000 3 154268934 AIRg 2.17 2.76E‐05 G/A 0.080 0.99 (0.89‐1.11) 6.97E‐01 1.20E‐03 rs6803803 3 180116563 AIRg 17.53 1.64E‐06 C/T 0.002 0.63 (0.25‐1.59) 4.23E‐01 7.64E‐05 rs17013808 4 89004957 AIRg ‐3.15 4.05E‐05 A/G 0.056 1.03 (0.88‐1.20) 6.78E‐01 1.39E‐03 rs3893856 5 111163 AIRg 2.09 7.21E‐05 A/G 0.096 0.95 (0.85‐1.05) 5.26E‐01 1.14E‐03 rs10041174 5 11710193 CTNND2 AIRg ‐2.59 2.36E‐05 G/A 0.080 1.07 (0.95‐1.21) 5.16E‐01 5.62E‐04 rs11750248 5 52153066 ITGA1 AIRg 2.43 2.88E‐05 T/C 0.068 1.22 (1.07‐1.39) 1.75E‐02 2.02E‐01 rs6887101 5 122109207 AIRg ‐1.70 1.24E‐05 A/G 0.270 0.98 (0.91‐1.05) 4.56E‐01 1.04E‐02 rs193541 5 122253304 SNX24 AIRg ‐1.71 7.64E‐06 C/T 0.253 0.98 (0.91‐1.06) 4.08E‐01 9.90E‐03 rs17149748 5 122267367 SNX24 AIRg ‐2.14 5.70E‐05 G/A 0.093 0.94 (0.84‐1.06) 3.63E‐01 2.76E‐02 rs6891052 5 122358015 AIRg ‐2.31 2.32E‐05 T/G 0.092 0.92 (0.82‐1.04) 2.39E‐01 3.08E‐02 rs10476419 5 162296335 AIRg 4.71 8.86E‐05 G/A 0.010 1.23 (0.61‐2.47) 3.66E‐01 3.29E‐02 rs10078423 5 162312823 AIRg 7.29 4.94E‐05 G/A 0.005 0.87 (0.38‐1.97) 7.94E‐01 7.26E‐03 rs10051450 5 162378040 AIRg 7.39 3.14E‐05 T/C 0.005 1.20 (0.50‐2.91) 5.10E‐01 1.32E‐02 rs4712523 6 20657564 CDKAL1 AIRg ‐1.17 1.60E‐05 G/A 0.315 1.03 (0.96‐1.11) 2.64E‐01 1.23E‐04 rs6456369 6 20660365 CDKAL1 AIRg ‐0.98 5.17E‐05 C/T 0.350 1.09 (1.01‐1.17) 2.97E‐02 1.09E‐05 rs7754840 6 20661250 CDKAL1 AIRg ‐1.26 3.83E‐06 C/G 0.310 1.10 (1.02‐1.18) 9.77E‐03 3.50E‐07 rs9368222 6 20686996 CDKAL1 AIRg ‐1.46 1.28E‐06 A/C 0.262 1.12 (1.00‐1.25) 3.31E‐03 3.78E‐08 rs2206734 6 20694884 CDKAL1 AIRg ‐2.05 1.02E‐06 T/C 0.194 1.19 (1.09‐1.30) 1.41E‐03 1.11E‐08 rs1040558 6 20713706 CDKAL1 AIRg ‐1.92 5.52E‐06 G/A 0.218 1.15 (1.05‐1.24) 5.05E‐03 2.04E‐07 rs6935599 6 20717095 CDKAL1 AIRg ‐1.73 5.83E‐05 G/A 0.245 1.03 (0.96‐1.11) 2.01E‐01 1.80E‐04 rs10946403 6 20717404 CDKAL1 AIRg ‐1.74 5.56E‐05 G/A 0.242 1.09 (1.01‐1.18) 5.25E‐03 1.41E‐06 rs9358357 6 20719145 CDKAL1 AIRg ‐1.77 3.60E‐05 G/A 0.247 1.16 (1.07‐1.26) 2.64E‐03 4.46E‐07

SUPPLEMENTARY DATA rs9356746 6 20720279 CDKAL1 AIRg ‐1.73 3.29E‐05 C/T 0.193 1.16 (1.06‐1.27) 8.95E‐03 1.71E‐06 rs3873380 6 31262438 HLA‐B AIRg 1.55 4.50E‐05 T/C 0.408 0.89 (0.70‐1.12) 3.21E‐01 3.35E‐04 rs35473403 6 43480822 YIPF3 AIRg 16.32 7.58E‐05 T/C 0.002 1.02 (0.32‐3.29) 9.73E‐01 5.53E‐03 rs7750450 6 55714563 BMP5 AIRg 1.40 6.21E‐05 C/T 0.322 0.92 (0.86‐0.99) 4.67E‐02 2.26E‐05 rs11963462 6 121021878 AIRg 1.60 6.06E‐05 C/T 0.232 1.09 (1.00‐1.19) 1.72E‐01 6.13E‐02 rs9321207 6 130397238 L3MBTL3 AIRg ‐0.97 7.43E‐05 A/G 0.365 0.97 (0.90‐1.04) 5.05E‐01 1.98E‐02 rs4897370 6 130466676 SAMD3 AIRg 1.43 3.80E‐05 G/A 0.346 0.97 (0.90‐1.04) 8.71E‐01 2.46E‐03 rs2038586 6 158091108 ZDHHC14 AIRg 1.97 1.49E‐05 T/C 0.184 0.92 (0.81‐1.05) 6.47E‐02 1.26E‐05 rs9295206 6 163326692 PACRG AIRg ‐1.18 4.78E‐05 G/A 0.400 1.00 (0.93‐1.07) 9.75E‐01 3.76E‐03 rs7779074 7 22986107 FAM126A AIRg 2.13 9.56E‐05 A/G 0.101 1.17 (1.05‐1.32) 2.90E‐02 2.24E‐01 rs10232215 7 92097166 AIRg 1.96 4.41E‐05 G/A 0.248 0.95 (0.88‐1.03) 7.07E‐01 1.61E‐03 rs2111200 7 92140397 PEX1 AIRg 1.96 3.21E‐05 T/C 0.251 0.96 (0.88‐1.05) 4.02E‐01 1.89E‐02 rs10237822 7 93760001 AIRg 3.94 3.53E‐05 G/T 0.025 1.03 (0.81‐1.31) 3.89E‐01 2.06E‐02 rs10242768 7 93784157 AIRg 3.94 6.87E‐05 C/T 0.022 1.10 (0.84‐1.46) 1.60E‐01 6.87E‐02 rs11779094 8 10666813 SOX7 AIRg ‐2.18 8.16E‐05 A/G 0.075 1.10 (0.94‐1.27) 7.19E‐01 2.36E‐03 rs7000560 8 16993943 AIRg 2.00 3.35E‐05 C/A 0.476 1.04 (0.97‐1.12) 8.77E‐01 4.74E‐03 rs4922265 8 16996435 AIRg 2.11 6.61E‐06 A/C 0.469 1.00 (0.93‐1.07) 8.54E‐01 9.11E‐04 rs6988635 8 95744466 DPY19L4 AIRg 1.18 7.73E‐05 G/A 0.444 0.96 (0.89‐1.03) 5.33E‐01 1.21E‐03 rs7018475 9 22137685 AIRg ‐1.64 4.90E‐06 G/T 0.323 1.09 (1.02‐1.17) 2.34E‐03 7.31E‐08 rs13301551 9 25683697 AIRg 2.39 8.39E‐05 T/C 0.075 0.97 (0.85‐1.11) 1.80E‐01 1.92E‐04 rs2295926 9 101593825 GALNT12 AIRg ‐1.61 2.21E‐05 C/T 0.348 0.92 (0.82‐1.04) 1.08E‐01 6.23E‐02 rs7341705 9 107651348 ABCA1 AIRg 13.32 1.77E‐05 C/T 0.003 1.02 (0.49‐2.10) 3.82E‐01 1.56E‐02 rs1602111 9 109277184 BC017988 AIRg ‐1.53 2.16E‐05 C/A 0.233 1.00 (0.93‐1.08) 9.49E‐01 3.09E‐03 rs2287005 9 113791313 LPAR1 AIRg 2.61 6.49E‐05 C/T 0.068 1.08 (0.92‐1.26) 7.63E‐01 9.03E‐03 rs7036846 9 119798885 ASTN2 AIRg 10.86 9.25E‐06 C/T 0.005 1.11 (0.57‐2.17) 6.67E‐01 5.82E‐04 rs10870202 9 139257411 DNLZ AIRg ‐1.04 5.37E‐05 T/C 0.430 1.12 (1.05‐1.20) 2.08E‐02 7.10E‐06 rs7919192 10 93660727 AIRg ‐1.45 5.00E‐05 C/T 0.216 0.92 (0.84‐1.01) 6.01E‐01 1.25E‐02 rs6584696 10 107578214 AIRg 4.14 2.66E‐05 C/T 0.026 0.82 (0.66‐1.02) 2.70E‐01 1.77E‐04 rs2129969 11 45586169 AIRg 1.14 2.10E‐05 G/A 0.477 0.91 (0.85‐0.98) 2.38E‐02 4.10E‐06 rs510398 11 66054823 YIF1A AIRg 12.63 4.37E‐06 C/T 0.003 1.89 (0.65‐5.53) 6.85E‐01 3.07E‐03 rs11227856 11 67377758 NDUFV1 AIRg 6.51 5.34E‐05 T/C 0.005 1.77 (0.88‐3.55) 4.86E‐01 1.81E‐02 rs10898909 11 72952496 AIRg 1.41 4.03E‐06 A/G 0.404 0.94 (0.86‐1.02) 9.27E‐02 8.64E‐06

SUPPLEMENTARY DATA rs3847554 11 92668826 AIRg ‐1.64 1.08E‐06 T/C 0.343 1.07 (1.00‐1.15) 1.96E‐01 1.29E‐05 rs1387153 11 92673828 AIRg ‐2.55 2.21E‐09 T/C 0.220 1.07 (0.98‐1.16) 1.97E‐01 2.72E‐07 rs2166706 11 92691532 AIRg ‐1.70 1.24E‐06 C/T 0.308 1.07 (0.99‐1.15) 2.47E‐01 2.17E‐05 rs10830961 11 92694757 AIRg ‐1.59 1.91E‐06 G/A 0.331 1.07 (0.99‐1.15) 2.41E‐01 2.70E‐05 rs10830963 11 92708710 MTNR1B AIRg ‐2.76 5.23E‐12 G/C 0.220 1.08 (1.00‐1.18) 1.83E‐01 5.86E‐09 rs686413 11 117537710 DSCAML1 AIRg ‐1.19 5.67E‐05 A/G 0.327 0.94 (0.88‐1.00) 1.03E‐01 9.00E‐02 rs12292105 11 117983479 TMPRSS4 AIRg 3.77 3.77E‐05 G/T 0.024 0.92 (0.73‐1.16) 9.00E‐01 2.68E‐03 rs7927108 11 134038949 NCAPD3 AIRg 10.54 4.35E‐05 T/G 0.004 0.82 (0.35‐1.93) 5.25E‐01 8.36E‐04 rs7962050 12 1031454 RAD52 AIRg 1.20 7.67E‐05 G/A 0.323 0.96 (0.89‐1.03) 2.74E‐01 3.56E‐04 rs247352 12 14900457 AIRg 4.42 9.24E‐05 C/T 0.013 1.20 (0.94‐1.52) 5.40E‐01 1.98E‐02 rs12816878 12 23155705 AK094733 AIRg 1.31 9.69E‐05 T/C 0.283 0.98 (0.91‐1.05) 8.61E‐01 3.97E‐03 rs3847896 12 23159966 AK094733 AIRg 1.12 6.47E‐05 C/T 0.453 0.94 (0.88‐1.01) 1.16E‐01 8.32E‐05 rs1489076 12 29129874 AIRg ‐1.37 1.97E‐05 T/C 0.377 0.97 (0.91‐1.04) 4.26E‐01 1.41E‐02 rs11049971 12 29130200 AIRg ‐1.37 1.78E‐05 T/C 0.376 0.98 (0.91‐1.05) 3.78E‐01 1.59E‐02 rs1489078 12 29141413 AIRg ‐1.34 2.48E‐05 G/A 0.376 0.98 (0.92‐1.06) 6.42E‐01 7.97E‐03 rs11113214 12 107588082 AIRg ‐1.93 6.21E‐05 G/A 0.219 1.08 (0.99‐1.17) 6.07E‐01 1.40E‐03 rs3026485 12 110782027 ATP2A2 AIRg 15.24 6.78E‐06 C/T 0.002 2.54 (0.96‐6.73) 4.64E‐02 7.61E‐02 rs16940879 12 110928719 AIRg 11.03 6.21E‐05 G/A 0.003 1.51 (0.68‐3.37) 3.93E‐01 2.59E‐02 rs10774579 12 121405210 AIRg 1.59 7.01E‐05 C/T 0.252 0.97 (0.89‐1.06) 1.46E‐01 1.24E‐04 rs10744163 12 124383950 DNAH10 AIRg 1.75 2.66E‐05 T/C 0.200 0.97 (0.89‐1.06) 2.32E‐01 1.36E‐04 rs9553849 13 27082326 AIRg 1.57 6.70E‐05 A/G 0.199 0.86 (0.79‐0.94) 1.29E‐02 4.70E‐06 rs9670049 13 31692454 AIRg 1.81 9.20E‐05 C/T 0.176 1.02 (0.94‐1.10) 3.81E‐01 3.19E‐02 rs9585660 13 101962642 NALCN AIRg 8.29 2.60E‐05 A/G 0.006 1.55 (0.82‐2.94) 6.36E‐02 9.64E‐02 rs7158254 14 37264674 SLC25A21 AIRg 7.18 3.91E‐05 C/T 0.007 1.22 (0.74‐2.01) 5.50E‐01 1.29E‐02 rs1690356 15 55301874 AIRg 13.41 1.47E‐05 A/C 0.003 0.95 (0.29‐3.07) 9.94E‐01 2.14E‐03 rs2570133 15 87604296 AIRg ‐1.00 6.64E‐05 C/T 0.416 1.03 (0.95‐1.10) 6.31E‐01 1.58E‐03 rs9935964 16 66216144 AIRg 28.14 9.57E‐08 A/G 0.001 2.15 (0.21‐22.37) 5.63E‐01 7.71E‐04 rs7192071 16 78953857 WWOX AIRg 4.34 7.30E‐05 G/A 0.024 0.94 (0.77‐1.15) 6.35E‐01 1.69E‐03 rs16953087 17 420033 VPS53 AIRg ‐1.81 3.26E‐05 C/T 0.130 1.02 (0.93‐1.13) 9.47E‐01 3.84E‐03 rs1006703 17 3865399 ATP2A3 AIRg 2.13 2.65E‐06 T/C 0.087 0.92 (0.81‐1.05) 8.38E‐01 5.30E‐04 rs2619996 17 71703758 AIRg 3.15 7.69E‐05 T/C 0.042 0.97 (0.81‐1.17) 8.86E‐01 7.06E‐03 rs899596 17 71735485 AIRg 2.20 2.64E‐06 G/A 0.230 0.98 (0.90‐1.06) 5.32E‐01 1.67E‐04

SUPPLEMENTARY DATA rs9955097 18 7965469 PTPRM AIRg 11.62 3.10E‐05 C/A 0.004 0.64 (0.19‐2.10) 4.54E‐01 5.11E‐04 rs9950590 18 8043661 PTPRM AIRg 11.99 5.19E‐06 T/C 0.005 0.48 (0.19‐1.19) 1.47E‐01 2.15E‐05 rs2068732 18 26236729 AIRg 2.42 6.85E‐05 C/A 0.120 1.08 (0.97‐1.19) 9.87E‐02 9.94E‐02 rs12608167 18 71893294 AIRg 1.36 2.48E‐05 G/A 0.264 1.01 (0.93‐1.09) 8.70E‐01 1.95E‐03 rs33845 19 34014316 AIRg 1.00 7.03E‐05 A/G 0.361 1.03 (0.96‐1.11) 7.03E‐01 1.11E‐02 rs6030572 20 41598995 PTPRT AIRg ‐1.96 8.83E‐05 C/A 0.175 0.96 (0.88‐1.05) 4.28E‐01 2.70E‐02 rs17646111 21 34954782 DONSON AIRg ‐1.57 3.16E‐05 A/G 0.237 1.07 (0.99‐1.16) 7.21E‐01 1.40E‐03 rs1892700 21 35016137 DONSON AIRg ‐1.52 5.02E‐05 A/G 0.236 1.01 (0.93‐1.09) 2.99E‐01 3.29E‐02 rs5752933 22 29902192 AIRg 2.11 1.36E‐05 C/A 0.230 1.00 (0.91‐1.10) 9.23E‐01 1.66E‐03 rs2985125 1 17004186 DI 3.11 3.02E‐05 G/A 0.052 1.01 (0.70‐1.45) 9.82E‐01 3.02E‐03 rs16866049 1 35836440 ZMYM4 DI 21.17 3.08E‐05 G/A 0.002 1.18 (0.38‐3.65) 7.18E‐01 7.10E‐03 rs513553 1 182494063 RGSL1 DI ‐1.83 8.14E‐05 G/A 0.262 1.08 (1.00‐1.17) 7.92E‐02 5.64E‐05 rs185580 1 182519861 RGSL1 DI ‐1.47 9.30E‐05 A/G 0.227 1.04 (0.95‐1.13) 3.41E‐01 5.89E‐04 rs266549 1 182528269 RGSL1 DI ‐1.59 6.29E‐05 T/C 0.229 0.99 (0.91‐1.08) 4.60E‐01 8.02E‐04 rs474939 1 182538615 DI ‐1.69 3.59E‐05 A/G 0.239 1.06 (0.97‐1.15) 2.15E‐01 1.45E‐04 rs10919851 1 200187504 DI ‐1.16 5.29E‐05 C/T 0.442 0.98 (0.91‐1.05) 7.31E‐01 1.92E‐03 rs6427807 1 200189305 DI 1.15 6.79E‐05 A/C 0.462 1.05 (0.98‐1.12) 6.41E‐01 1.29E‐02 rs7603311 2 49041322 DI 1.44 2.30E‐05 C/T 0.441 1.04 (0.97‐1.12) 2.94E‐01 2.44E‐02 rs4482537 2 49052255 DI 1.38 5.52E‐05 T/C 0.404 1.05 (0.98‐1.12) 2.62E‐01 3.95E‐02 rs17492567 2 50212116 NRXN1 DI 2.54 4.51E‐05 C/T 0.089 0.99 (0.89‐1.10) 3.21E‐01 2.90E‐02 rs12986646 2 52372389 DI 2.64 8.76E‐05 A/G 0.044 0.90 (0.75‐1.08) 8.01E‐01 9.44E‐03 rs881952 2 60888202 DI ‐2.30 4.59E‐06 C/T 0.477 0.94 (0.88‐1.01) 1.17E‐01 3.30E‐02 rs6753918 2 137214258 DI 6.77 2.54E‐05 C/T 0.012 0.96 (0.77‐1.19) 8.94E‐01 3.93E‐03 rs7560169 2 142148511 LRP1B DI 1.57 8.79E‐05 T/C 0.388 1.02 (0.95‐1.10) 6.30E‐01 1.50E‐02 rs684428 2 220505265 SLC4A3 DI 1.61 8.27E‐05 T/C 0.170 0.97 (0.88‐1.06) 9.15E‐01 6.76E‐03 rs7559293 2 236422975 AGAP1 DI 1.95 6.75E‐05 A/G 0.408 1.03 (0.96‐1.11) 2.65E‐01 4.25E‐02 rs28415051 3 66008918 MAGI1 DI 15.79 5.80E‐05 G/A 0.003 0.79 (0.44‐1.40) 7.93E‐01 2.46E‐03 rs9832209 3 96825782 EPHA6 DI 2.00 5.13E‐05 A/G 0.356 1.07 (1.00‐1.15) 5.20E‐02 1.36E‐01 rs602149 3 185244569 LIPH DI ‐2.95 4.20E‐05 T/G 0.059 1.10 (0.95‐1.28) 6.29E‐01 1.20E‐03 rs612304 3 185251001 LIPH DI ‐3.25 3.31E‐05 C/T 0.059 1.07 (0.92‐1.25) 9.49E‐01 3.85E‐03 rs1520323 4 125146503 DI ‐3.68 6.82E‐05 T/C 0.021 0.99 (0.78‐1.25) 9.94E‐01 4.95E‐03 rs467650 5 97969453 DI 1.94 3.33E‐05 C/T 0.271 1.01 (0.93‐1.09) 8.86E‐01 4.61E‐03

©2014 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db13-1829/-/DC1 SUPPLEMENTARY DATA rs6902991 6 78060981 DI ‐0.52 1.58E‐01 T/C 0.534 1.03 (0.96‐1.10) 1.47E‐01 4.30E‐02 rs13193467 6 85211681 DI ‐2.10 4.66E‐05 T/C 0.132 1.02 (0.92‐1.13) 5.99E‐01 1.15E‐03 rs1510292 6 124371914 NKAIN2 DI ‐3.05 5.10E‐05 A/G 0.060 0.90 (0.78‐1.03) 1.69E‐01 5.85E‐02 rs17086954 6 156337304 DI 2.02 2.71E‐05 G/A 0.220 0.92 (0.85‐1.00) 1.77E‐01 8.74E‐05 rs10225719 7 12691988 SCIN DI ‐2.17 3.17E‐05 T/C 0.418 1.01 (0.94‐1.08) 5.45E‐01 7.52E‐04 rs10267836 7 30755583 INMT DI 3.20 6.27E‐06 T/C 0.041 0.95 (0.81‐1.12) 9.93E‐01 1.37E‐03 rs1346111 7 49742459 DI ‐2.04 2.28E‐05 C/T 0.226 1.00 (0.92‐1.08) 1.49E‐01 4.83E‐02 rs10278107 7 125278195 DI ‐1.90 5.14E‐05 C/T 0.477 1.05 (0.99‐1.11) 2.10E‐01 1.76E‐04 rs12539028 7 154812950 DI ‐1.74 8.46E‐05 A/G 0.435 1.03 (0.96‐1.11) 5.08E‐01 1.16E‐03 rs1077489 8 6635669 DI ‐2.37 9.47E‐05 T/C 0.072 1.06 (0.91‐1.23) 5.84E‐01 1.76E‐02 rs12546336 8 39620015 ADAM2 DI 1.65 9.24E‐05 A/G 0.333 1.06 (0.99‐1.14) 2.26E‐01 5.63E‐02 rs2891781 8 124608162 DI ‐1.38 4.34E‐03 T/C 0.537 0.97 (0.90‐1.04) 1.06E‐01 3.82E‐01 rs13253406 8 143200557 DI ‐1.77 6.65E‐05 G/T 0.390 1.01 (0.95‐1.07) 9.75E‐01 5.14E‐03 rs2382470 9 14387817 NFIB DI ‐1.59 2.02E‐05 A/G 0.255 0.95 (0.88‐1.02) 7.38E‐01 5.48E‐03 rs2020927 9 107553185 ABCA1 DI ‐1.74 5.74E‐05 G/A 0.161 0.95 (0.87‐1.03) 4.55E‐01 2.05E‐02 rs10121901 9 107553524 ABCA1 DI ‐1.74 5.63E‐05 G/A 0.161 0.96 (0.87‐1.05) 6.85E‐01 1.04E‐02 rs2066720 9 107554069 ABCA1 DI ‐1.74 5.74E‐05 T/C 0.161 0.95 (0.87‐1.04) 5.79E‐01 1.42E‐02 rs11145750 9 139259249 CARD9 DI ‐1.69 2.71E‐05 A/G 0.474 1.11 (1.04‐1.18) 2.77E‐02 6.06E‐06 rs10781499 9 139266405 CARD9 DI ‐0.97 4.13E‐02 G/A 0.491 1.07 (1.01‐1.15) 1.53E‐01 1.42E‐02 rs4077515 9 139266496 CARD9 DI ‐0.89 5.71E‐02 C/T 0.491 1.08 (1.01‐1.15) 1.48E‐01 1.79E‐02 rs3812560 9 139269905 DI ‐1.83 6.16E‐06 T/C 0.465 1.09 (1.02‐1.16) 1.89E‐01 3.71E‐05 rs3812570 9 139275204 SNAPC4 DI ‐1.87 1.72E‐06 A/C 0.461 1.07 (0.99‐1.14) 4.93E‐02 1.81E‐06 rs4266763 9 139289825 SNAPC4 DI ‐2.00 3.46E‐06 A/G 0.489 1.10 (1.03‐1.18) 1.23E‐02 4.34E‐07 rs8413 9 139323311 INPP5E DI ‐1.77 2.83E‐05 T/C 0.470 1.07 (1.00‐1.15) 3.83E‐02 9.62E‐06 rs10870194 9 139327034 INPP5E DI ‐1.58 5.86E‐05 A/G 0.446 1.07 (1.01‐1.14) 3.40E‐01 4.38E‐04 rs10781542 9 139327439 INPP5E DI ‐1.59 5.77E‐05 A/G 0.446 1.06 (0.99‐1.14) 7.76E‐02 4.28E‐05 rs1148233 10 31461599 DI 8.86 9.09E‐06 T/C 0.008 1.29 (0.70‐2.38) 8.19E‐01 2.92E‐03 rs1414894 10 89785190 DI 1.67 4.62E‐05 C/T 0.286 1.02 (0.95‐1.10) 9.05E‐01 5.17E‐03 rs2488069 10 94505421 DI ‐18.48 5.73E‐05 G/T 0.002 2.34 (0.90‐6.07) 2.63E‐01 2.76E‐04 rs7081634 10 94685886 EXOC6 DI ‐22.06 2.62E‐05 G/A 0.002 2.24 (0.87‐5.80) 1.40E‐01 5.87E‐05 rs7068036 10 95315193 DI 1.94 6.79E‐05 T/C 0.156 0.99 (0.88‐1.11) 9.89E‐01 5.01E‐03 rs2237896 11 2858440 KCNQ1 DI 1.64 1.57E‐05 A/G 0.247 0.75 (0.69‐0.82) 2.90E‐13 2.13E‐16

SUPPLEMENTARY DATA rs2237897 11 2858546 KCNQ1 DI 1.75 7.04E‐06 T/C 0.251 0.73 (0.68‐0.79) 1.89E‐19 1.24E‐21 rs5241 11 14990543 CALCA DI 5.81 9.58E‐05 T/G 0.016 1.22 (0.74‐2.01) 3.22E‐01 3.97E‐02 rs4756016 11 45699134 DI 1.50 4.61E‐05 G/A 0.416 1.00 (0.94‐1.07) 8.85E‐01 2.85E‐03 rs744434 11 65847982 PACS1 DI 15.07 5.45E‐05 G/T 0.003 0.82 (0.38‐1.77) 8.63E‐01 2.93E‐03 rs1351571 11 98408860 DI ‐1.31 4.20E‐05 T/C 0.472 1.02 (0.95‐1.09) 7.58E‐01 1.84E‐03 rs17108749 11 108796817 DDX10 DI ‐9.79 7.57E‐05 G/T 0.009 2.10 (0.91‐4.88) 1.31E‐01 1.11E‐04 rs7971324 12 3098924 TEAD4 DI 3.44 5.00E‐05 C/A 0.056 0.81 (0.70‐0.94) 6.09E‐02 2.75E‐05 rs17107718 12 70488764 DI 2.52 6.92E‐05 T/C 0.054 1.05 (0.92‐1.21) 9.50E‐01 5.61E‐03 rs7304911 12 129705400 TMEM132D DI ‐1.40 2.69E‐05 T/C 0.223 1.04 (0.96‐1.14) 4.63E‐01 4.88E‐04 rs1537435 13 27909319 DI 1.61 5.12E‐05 T/C 0.316 0.97 (0.91‐1.04) 4.77E‐01 7.61E‐04 rs17085484 13 27930039 DI 1.52 8.64E‐05 C/T 0.318 0.97 (0.90‐1.04) 5.01E‐01 1.15E‐03 rs870767 13 27938560 DI 1.53 5.87E‐05 G/A 0.233 1.02 (0.90‐1.15) 6.17E‐01 1.40E‐03 rs2764026 13 36291051 MAB21L1 DI ‐1.77 6.43E‐05 G/A 0.282 0.93 (0.86‐1.00) 3.26E‐01 3.31E‐02 rs9575437 13 36731208 DI 2.02 2.08E‐05 G/A 0.296 1.08 (1.00‐1.16) 1.46E‐01 4.76E‐02 rs9575445 13 36731586 DI 1.88 1.48E‐05 A/G 0.285 1.01 (0.93‐1.10) 2.58E‐01 2.36E‐02 rs1328641 13 36745029 SOHLH2 DI 1.96 1.96E‐05 T/C 0.227 1.10 (1.02‐1.20) 5.84E‐02 9.28E‐02 rs2149423 13 36772381 SOHLH2 DI 2.18 3.67E‐07 G/A 0.315 1.01 (0.94‐1.09) 2.95E‐01 4.30E‐03 rs2054715 15 59607007 MYO1E DI ‐1.35 6.02E‐05 C/T 0.172 1.06 (0.96‐1.16) 6.85E‐01 1.79E‐03 rs11073891 15 90363995 DI 1.37 9.68E‐05 C/A 0.274 1.03 (0.94‐1.13) 4.94E‐01 1.19E‐03 rs4238710 16 84546021 DI ‐2.08 3.68E‐05 A/G 0.310 0.98 (0.91‐1.06) 8.69E‐01 2.41E‐03 rs2326274 16 84546108 DI ‐2.10 3.97E‐05 T/G 0.308 1.03 (0.96‐1.11) 5.31E‐01 8.11E‐04 rs9891963 17 2875114 RAP1GAP2 DI ‐3.23 8.32E‐05 T/C 0.038 0.99 (0.84‐1.15) 5.55E‐01 1.80E‐02 rs654136 18 48464204 ME2 DI ‐1.43 9.26E‐05 T/C 0.359 0.95 (0.88‐1.02) 9.87E‐02 1.10E‐01 rs4073064 18 59532727 RNF152 DI ‐10.09 7.42E‐05 C/T 0.010 1.18 (0.37‐3.73) 9.68E‐01 5.55E‐03 rs2541872 18 63632952 DI ‐1.93 9.90E‐05 A/G 0.385 0.97 (0.91‐1.05) 9.18E‐01 7.37E‐03 rs2587374 18 63638807 DI ‐2.07 5.93E‐05 A/G 0.250 0.95 (0.88‐1.04) 6.46E‐01 1.19E‐02 rs4802566 19 49632309 PPFIA3 DI 1.77 2.84E‐05 T/C 0.392 0.95 (0.88‐1.03) 2.25E‐01 1.34E‐04 rs219628 21 27865420 CYYR1 DI 1.40 5.01E‐05 C/T 0.255 0.98 (0.91‐1.06) 5.33E‐01 9.37E‐04 rs2833555 21 33285149 HUNK DI ‐2.93 6.09E‐05 T/C 0.079 1.02 (0.90‐1.14) 1.18E‐01 8.16E‐05 rs133937 22 33395851 SYN3 DI 1.65 6.74E‐05 C/A 0.335 0.94 (0.87‐1.01) 7.94E‐01 2.67E‐03 rs1674879 1 4497217 SG 0.19 5.99E‐05 T/C 0.079 1.00 (0.88‐1.14) 9.07E‐01 5.86E‐03 rs1572823 1 19889959 SG ‐0.14 6.36E‐05 T/C 0.125 1.07 (0.97‐1.18) 5.69E‐01 1.23E‐03

SUPPLEMENTARY DATA rs11805807 1 155064844 SG 1.14 2.89E‐05 T/C 0.004 0.55 (0.16‐1.91) 3.20E‐01 2.52E‐04 rs563988 1 182474160 RGSL1 SG ‐0.11 9.29E‐05 C/T 0.268 1.07 (0.99‐1.16) 6.42E‐02 4.65E‐05 rs471910 1 182474704 RGSL1 SG ‐0.11 5.55E‐05 C/T 0.269 1.05 (0.98‐1.14) 2.59E‐01 2.63E‐04 rs7570259 2 23202248 SG 1.59 5.51E‐06 A/C 0.002 0.79 (0.29‐2.17) 8.19E‐01 2.28E‐03 rs11684134 2 27558252 GTF3C2 SG 0.10 5.99E‐05 A/G 0.436 0.93 (0.87‐1.00) 1.05E‐01 6.77E‐05 rs4665969 2 27574953 GTF3C2 SG 0.11 1.44E‐05 T/C 0.468 0.96 (0.89‐1.02) 2.08E‐01 7.58E‐05 rs6716894 2 27583273 SG 0.11 3.40E‐05 A/G 0.468 0.96 (0.91‐1.02) 1.99E‐01 1.23E‐04 rs7586601 2 27584666 SG 0.11 3.20E‐05 A/G 0.425 0.94 (0.88‐1.01) 5.98E‐02 1.94E‐05 rs11695549 2 27586155 SG ‐0.11 3.21E‐05 C/A 0.479 1.04 (0.97‐1.11) 2.41E‐01 1.63E‐04 rs7602534 2 27592423 EIF2B4 SG 0.11 5.06E‐05 C/T 0.465 0.97 (0.91‐1.04) 3.37E‐01 3.93E‐04 rs13472 2 27600239 ZNF513 SG 0.11 4.28E‐05 G/A 0.469 0.97 (0.91‐1.04) 2.44E‐01 2.01E‐04 rs4803 2 27667297 KRTCAP3 SG 0.11 8.09E‐05 A/G 0.459 0.98 (0.91‐1.05) 3.46E‐01 5.54E‐04 rs11126999 2 27670307 IFT172 SG 0.11 3.09E‐05 G/A 0.474 0.98 (0.92‐1.05) 3.41E‐01 2.95E‐04 rs704795 2 27716494 FNDC4 SG 0.11 7.12E‐05 G/A 0.460 0.98 (0.91‐1.05) 3.23E‐01 4.51E‐04 rs1260320 2 27722416 GCKR SG 0.11 9.73E‐05 G/A 0.467 0.98 (0.92‐1.05) 3.80E‐01 7.32E‐04 rs2293571 2 27729480 GCKR SG 0.12 1.98E‐05 G/A 0.476 0.94 (0.86‐1.02) 1.61E‐01 6.09E‐05 rs1260326 2 27730940 GCKR SG 0.13 4.04E‐06 T/C 0.335 0.96 (0.89‐1.03) 5.58E‐02 3.99E‐06 rs780093 2 27742603 GCKR SG 0.14 1.12E‐06 T/C 0.341 0.96 (0.90‐1.03) 2.07E‐01 1.46E‐05 rs11681351 2 27743423 GCKR SG 0.11 3.35E‐05 G/A 0.479 0.96 (0.90‐1.03) 2.83E‐01 2.22E‐04 rs4852424 2 70283210 PCBP1‐AS1 SG ‐0.15 5.50E‐05 G/A 0.382 1.00 (0.93‐1.07) 7.39E‐01 2.02E‐03 rs3755388 2 70310878 PCBP1‐AS1 SG ‐0.15 6.51E‐05 G/A 0.388 1.07 (1.00‐1.15) 2.45E‐01 2.67E‐04 rs6743318 2 70373677 SG ‐0.15 4.91E‐05 G/T 0.392 1.01 (0.93‐1.10) 5.35E‐01 9.33E‐04 rs14234 2 70524142 FAM136A SG 0.10 2.34E‐05 A/G 0.412 0.98 (0.91‐1.05) 5.66E‐01 6.84E‐04 rs9816690 3 82046207 BC031255 SG 0.23 7.44E‐05 A/G 0.055 1.09 (0.94‐1.26) 8.23E‐01 8.22E‐03 rs11927192 3 183730657 ABCC5 SG 0.77 5.32E‐05 A/G 0.004 1.03 (0.39‐2.78) 4.88E‐01 1.79E‐02 rs523079 3 187615862 SG 0.25 1.53E‐07 T/C 0.069 0.92 (0.81‐1.05) 3.39E‐01 1.14E‐05 rs13059988 3 187624906 SG 0.22 3.40E‐07 T/G 0.063 1.01 (0.86‐1.17) 6.78E‐01 9.62E‐05 rs10000105 4 53623677 SG 1.32 7.67E‐05 A/G 0.002 0.95 (0.12‐7.74) 3.83E‐01 6.41E‐04 rs3775781 4 70595637 SULT1B1 SG ‐0.38 3.26E‐05 T/C 0.027 0.88 (0.71‐1.08) 1.58E‐01 5.25E‐02 rs1011631 4 82440730 SG 0.09 9.08E‐05 T/C 0.328 1.06 (0.99‐1.14) 3.84E‐01 3.14E‐02 rs6871313 5 2397617 SG 0.10 4.12E‐05 G/A 0.372 1.12 (1.05‐1.21) 3.04E‐02 1.71E‐01 rs6885718 5 31657655 PDZD2 SG 0.22 4.62E‐05 G/A 0.081 1.06 (0.90‐1.26) 2.68E‐01 3.60E‐02

SUPPLEMENTARY DATA rs17165293 5 126183502 SG 0.28 8.94E‐05 A/G 0.041 1.01 (0.82‐1.24) 6.68E‐01 1.36E‐02 rs7708035 5 161834699 SG 1.71 1.99E‐05 A/G 0.003 1.71 (0.64‐4.56) 1.98E‐01 3.52E‐02 rs28011 5 179407229 RNF130 SG ‐0.08 8.59E‐05 C/T 0.325 1.05 (0.97‐1.13) 5.41E‐01 1.33E‐03 rs4700708 5 179529895 RASGEF1C SG ‐0.08 6.82E‐05 A/G 0.419 1.03 (0.96‐1.10) 5.13E‐01 1.04E‐03 rs2064197 6 8998811 SG ‐0.19 7.23E‐06 G/A 0.164 1.18 (1.08‐1.30) 7.01E‐04 2.56E‐08 rs367274 6 90622187 SG 0.12 2.51E‐05 T/C 0.418 1.07 (1.00‐1.15) 4.86E‐02 1.13E‐01 rs7744034 6 135143748 SG 0.13 5.45E‐05 A/G 0.253 0.95 (0.88‐1.03) 2.32E‐01 2.17E‐04 rs11752655 6 135160309 SG 0.19 1.12E‐05 G/A 0.081 0.91 (0.81‐1.02) 6.90E‐02 1.13E‐05 rs16876733 7 10945193 SG ‐0.17 5.24E‐05 C/A 0.129 1.02 (0.92‐1.13) 9.52E‐01 3.71E‐03 rs539518 7 73753250 CLIP2 SG 0.09 9.40E‐05 T/C 0.366 0.99 (0.93‐1.07) 7.40E‐01 2.73E‐03 rs1421221 8 97004203 SG ‐0.11 9.91E‐05 C/T 0.385 1.00 (0.94‐1.07) 6.75E‐01 1.41E‐02 rs883952 9 71514651 PIP5K1B SG 0.10 5.56E‐05 G/A 0.478 1.02 (0.95‐1.09) 7.38E‐01 8.95E‐03 rs12313180 12 30308868 SG 0.14 5.88E‐06 T/C 0.336 0.98 (0.91‐1.07) 7.41E‐01 2.98E‐03 rs4931283 12 30334071 SG 0.16 1.34E‐05 G/A 0.322 1.02 (0.95‐1.09) 9.22E‐01 2.61E‐03 rs909013 12 30334754 SG 0.16 1.75E‐05 G/A 0.317 1.02 (0.95‐1.09) 9.82E‐01 2.26E‐03 rs17518256 12 30339648 SG 0.17 1.32E‐05 C/A 0.295 0.99 (0.92‐1.07) 6.30E‐01 6.14E‐03 rs10843647 12 30341934 SG 0.17 4.13E‐06 T/G 0.331 1.00 (0.93‐1.07) 6.81E‐01 3.03E‐03 rs11837387 12 73467487 SG 2.02 2.22E‐05 C/T 0.001 2.96 (1.26‐6.92) 5.74E‐02 9.78E‐02 rs11104268 12 76627445 SG 0.33 6.74E‐06 G/A 0.042 1.04 (0.87‐1.25) 8.66E‐01 9.58E‐04 rs7296900 12 104177668 NT5DC3 SG 0.12 4.05E‐05 T/C 0.453 0.97 (0.91‐1.04) 9.58E‐02 4.50E‐05 rs11113179 12 107452785 CRY1 SG ‐0.12 1.28E‐05 T/C 0.286 0.99 (0.91‐1.07) 5.74E‐01 7.19E‐03 rs7319628 13 34502705 RFC3 SG 0.95 2.21E‐05 A/G 0.006 1.35 (0.56‐3.25) 3.94E‐01 1.66E‐02 rs17081477 13 35134265 SG 0.44 3.83E‐05 C/T 0.013 1.23 (0.81‐1.85) 2.62E‐01 3.42E‐02 rs1748124 13 52455098 SG ‐0.11 8.53E‐05 C/T 0.480 0.96 (0.90‐1.03) 3.35E‐01 3.60E‐02 rs9550193 13 113324324 C13orf35 SG ‐0.12 3.19E‐05 T/G 0.351 1.07 (0.99‐1.17) 1.16E‐01 5.03E‐05 rs2145516 14 26129412 SG 0.09 8.88E‐05 A/G 0.457 0.94 (0.87‐1.01) 2.91E‐02 1.60E‐05 rs12432901 14 26494469 SG ‐0.18 4.44E‐05 A/G 0.105 0.97 (0.87‐1.09) 5.37E‐01 1.43E‐02 rs7140895 14 49724328 SG 0.17 9.31E‐05 C/T 0.123 0.98 (0.89‐1.08) 5.29E‐01 1.33E‐03 rs1429751 15 34116858 RYR3 SG 0.14 9.22E‐05 C/T 0.253 1.03 (0.95‐1.11) 7.11E‐01 1.23E‐02 rs1115936 16 7171923 RBFOX1 SG ‐0.13 5.22E‐05 G/A 0.363 1.02 (0.95‐1.10) 7.93E‐01 7.47E‐03 rs4783122 16 82535037 SG ‐0.16 3.56E‐05 G/A 0.243 1.01 (0.93‐1.09) 9.90E‐01 3.37E‐03 rs7202949 16 82593560 SG ‐0.09 9.47E‐05 G/A 0.474 1.01 (0.95‐1.09) 5.97E‐01 1.72E‐03

SUPPLEMENTARY DATA

rs4299147 16 82883338 CDH13 SG 0.10 8.86E‐05 T/C 0.410 0.96 (0.89‐1.03) 2.05E‐01 2.44E‐04

rs1559310 16 82918371 CDH13 SG ‐0.11 4.08E‐05 G/T 0.437 1.04 (0.97‐1.11) 3.11E‐01 2.98E‐04

rs11150514 16 82923464 CDH13 SG 0.10 4.41E‐05 G/T 0.414 0.94 (0.88‐1.01) 4.40E‐01 5.93E‐04

rs12933472 16 82924685 CDH13 SG ‐0.12 8.16E‐06 A/G 0.435 1.06 (0.99‐1.14) 9.55E‐02 1.47E‐05

rs11150519 16 82934307 CDH13 SG ‐0.11 4.32E‐05 G/A 0.441 1.05 (0.98‐1.12) 1.37E‐01 7.99E‐05

rs1559438 16 83308559 CDH13 SG 0.09 6.67E‐05 C/T 0.476 1.04 (0.95‐1.13) 8.39E‐01 3.04E‐03

rs16947417 17 13143819 SG 0.26 2.24E‐05 G/T 0.053 1.07 (0.90‐1.27) 9.35E‐02 7.00E‐02

rs9896748 17 64939574 SG 0.27 2.37E‐05 T/G 0.070 0.91 (0.80‐1.03) 1.60E‐01 6.82E‐05

rs94312 18 7806492 PTPRM SG ‐0.27 8.39E‐05 G/A 0.049 0.97 (0.82‐1.16) 3.68E‐01 3.20E‐02

rs2048132 18 73694904 SG 0.16 2.16E‐05 T/G 0.225 1.01 (0.93‐1.11) 9.16E‐01 3.40E‐03

rs6566045 18 75650801 SG 0.14 4.52E‐05 C/T 0.289 0.96 (0.89‐1.04) 2.42E‐01 2.05E‐04

rs2291004 19 37997952 ZNF793 SG 0.16 3.82E‐05 A/C 0.153 0.89 (0.82‐0.97) 9.88E‐03 2.18E‐06

rs788338 19 50778543 MYH14 SG ‐0.17 1.66E‐06 C/T 0.287 0.97 (0.89‐1.05) 7.42E‐01 1.61E‐03

rs788332 19 50782462 MYH14 SG ‐0.16 1.77E‐05 A/C 0.264 0.98 (0.86‐1.13) 8.03E‐01 4.26E‐03

rs2004423 19 50939867 MYBPC2 SG 0.12 4.51E‐05 A/G 0.325 0.97 (0.89‐1.05) 2.63E‐01 2.36E‐04

rs4802723 19 51172786 SHANK1 SG ‐0.16 1.90E‐05 G/A 0.150 1.03 (0.94‐1.14) 9.26E‐01 2.00E‐03

rs4802724 19 51173218 SHANK1 SG ‐0.16 1.81E‐05 C/A 0.151 1.01 (0.89‐1.13) 8.80E‐01 3.44E‐03

rs2825882 21 21283010 SG ‐0.10 9.16E‐05 C/T 0.474 1.06 (0.99‐1.14) 9.78E‐01 5.34E‐03

rs9984764 21 27497497 APP SG 0.81 2.06E‐05 A/G 0.997 0.82 (0.29‐2.28) 5.58E‐01 6.13E‐04

rs9974077 21 43835771 UBASH3A SG 0.13 3.44E‐05 T/G 0.259 1.02 (0.94‐1.10) 9.59E‐01 3.02E‐03

SUPPLEMENTARY DATA Supplementary Table 7. Top regions from GWAS of T2D-related quantitative traits with translation to T2D in Mexican-origin cohorts ordered by trait from the Discovery stage.

§ || ‡ Model 1 Model 2 Marker Chr Position* Gene RA† RAF Trait Beta P-value Beta P-value rs7219451 17 38957002 KRT28 / KRT10 SI +M C 0.38 -6.8 3.92E-06 -5.86 1.43E-04 rs6815953 4 183109012 TENM3 SI +M T 0.431 4.10 3.14E-05 3.59 3.53E-04 rs7581057 2 115958079 DPP10 SI +M G 0.056 -5.47 1.74E-04 -4.52 9.35E-03 rs322394 5 172157768 NEURL1B / DUSP1 M C 0.36 -15.8 3.38E-05 -13.94 8.64E-05 rs17060946 9 77808519 OSTF1 / PCSK5 M G 0.068 37.86 2.56E-06 31.94 2.94E-05 rs13252932 8 25198091 DOCK5 M T 0.049 47.71 5.17E-06 39.14 5.93E-05 ¶ rs10830963 11 92708710 MTNR1B AIRg G 0.22 -2.76 5.23E-12 -2.81 3.22E-13 # rs2206734 6 20694884 CDKAL1 AIRg T 0.194 -2.05 1.02E-06 -1.90 5.03E-06 ** rs7018475 9 22137685 CDKN2B-AS1 / DMRTA1 AIRg G 0.323 -1.64 4.90E-06 -1.60 8.24E-06 †† rs1387153 11 92673828 MTNR1B AIRg T 0.22 -2.55 2.21E-09 -2.62 2.16E-10 rs2129969 11 45586169 PRDN11 / CHST1 AIRg G 0.477 1.14 2.10E-05 1.21 4.56E-06 rs2053797 2 46370892 PRKCE AIRg A 0.162 1.89 5.02E-05 1.81 6.75E-05 rs9553849 13 27082326 CDK8 / WASF3 AIRg A 0.199 1.57 6.70E-05 1.54 6.07E-05 rs10870202 9 139257411 DNLZ AIRg T 0.43 -1.04 5.37E-05 -1.06 2.09E-05 rs10898909 11 72952496 P2RY2 AIRg A 0.404 1.41 4.03E-06 1.31 7.78E-06 rs2237897 11 2858546 KCNQ1‡‡ DI A 0.251 1.75 7.04E-06 1.82 1.59E-06 rs4266763 9 139289825 SNAPC4 DI A 0.489 -2.00 3.46E-06 -1.93 3.35E-06 rs2064197 6 8998811 SLC35B3 / TFAP2A SG G 0.164 -0.19 7.23E-06 -0.19 7.31E-06 rs2291004 19 37997952 ZNF793 SG A 0.153 0.16 3.82E-05 0.15 1.97E-05 §§ rs1260326 2 27730940 GCKR SG T 0.335 0.13 4.04E-06 0.13 1.43E-05 SNPs with evidence of association with the nearest annotated RefSeq gene(s) listed. *Build hg19, †Reference Allele, ‡Reference Allele Frequency, §Model 1 covariates included age, gender, study site (in multi-center recruitment studies), and admixture proportions, ||Model 2 covariates included age, gender, study site (in multi-center recruitment studies), admixture proportions, and BMI, ¶Previously identified T2D locus (MTNR1B rs1387153, r2=0.69), #Previously identified T2D locus (CDKAL1 rs7754840, r2=0.42), **Previously identified T2D locus (CDKN2B rs7018475), ††Previously identified T2D locus (MTNR1B rs1387153), ‡‡Previously identified T2D locus (KCNQ1 rs2237892, r2=0.90; and KCNQ1 rs231362, r2=0.038), §§Previously identified T2D locus (GCKR rs780094, r2=0.91).

SUPPLEMENTARY DATA Supplementary Table 8. Top regions from GWAS of T2D-related quantitative traits with translation to T2D in Mexican-origin cohorts ordered by trait from the Discovery stage with conditional analyses performed at loci with multiple signals of association or in close proximity to previously identified T2D loci. Discovery Cohorts Translation Cohorts Discovery and Conditional Analysis Translation Marker Chr:Position* Gene OR Trait RAF‡ Beta P-value P-value Meta-Analysis SNP r2|| P-value (95% CI)§ P-value 1.08 rs7219451 17:38957002 KRT28 / KRT10 S +M 0.380 (C) -6.80 3.92E-06 1.06E-02 3.97E-07 I (1.00‐1.16) 0.92 rs6815953 4:183109012 TENM3 S +M 0.431 (T) 4.10 3.14E-05 1.25E-02 2.47E-06 I (0.86‐0.99) 1.29 rs7581057 2:115958079 DPP10 S +M 0.056 (G) -5.47 1.74E-04 6.67E-03 4.82E-06 I (1.10‐1.50) 1.17 rs322394 5:172157768 NEURL1B / DUSP1 M 0.360 (C) -15.83 3.38E-05 7.87E-04 1.12E-07 (1.09‐1.26) 0.87 rs17060946 9:77808519 OSTF1 / PCSK5 M 0.068 (G) 37.86 2.56E-06 6.89E-02 3.99E-06 (0.75‐1.01) 0.89 rs13252932 8:25198091 DOCK5 M 0.049 (T) 47.71 5.17E-06 6.61E-02 6.11E-06 (0.75‐1.04) 1.08 rs10830963 11:92708710 MTNR1B AIR 0.220 (G) -2.76 5.23E-12 rs1387153¶ 0.69 8.67E-05 1.83E-01 5.86E-09 g (1.00‐1.18) 1.19 rs2206734 6:20694884 CDKAL1 AIR 0.194 (T) -2.05 1.02E-06 rs7754840¶ 0.42 9.37E-03 1.41E-03 1.11E-08 g (1.09‐1.30) CDKN2B-AS1 / 1.09 rs7018475 9:22137685 AIR 0.323 (G) -1.64 4.90E-06 2.34E-03 7.31E-08 DMRTA1 g (1.02‐1.17) 1.07 rs1387153 11:92673828 MTNR1B AIR 0.220 (T) -2.55 2.21E-09 1.97E-01 2.72E-07 g (0.98‐1.16) 0.91 rs2129969 11:45586169 PRDN11 / CHST1 AIR 0.477 (G) 1.14 2.10E-05 2.38E-02 4.10E-06 g (0.85‐0.98) 0.91 rs2053797 2:46370892 PRKCE AIR 0.162 (A) 1.89 5.02E-05 1.42E-02 4.21E-06 g (0.83‐1.00) 0.86 rs9553849 13:27082326 CDK8 / WASF3 AIR 0.199 (A) 1.57 6.70E-05 1.29E-02 4.70E-06 g (0.79‐0.94) 1.12 rs10870202 9:139257411 DNLZ AIR 0.430 (T) -1.04 5.37E-05 2.08E-02 7.10E-06 g (1.05‐1.20) 0.94 rs10898909 11:72952496 P2RY2 AIR 0.404 (A) 1.41 4.03E-06 9.27E-02 8.64E-06 g (0.86‐1.02) rs2237892¶ 0.90 1.57E-04 0.73 rs2237897 11:2858546 KCNQ1†† DI 0.251 (A) 1.75 7.04E-06 1.89E-19 1.24E-21 rs231362¶ 0.038 1.06E-05 (0.68‐0.79) 1.10 rs4266763 9:139289825 SNAPC4 DI 0.489 (A) -2.00 3.46E-06 1.23E-02 4.34E-07 (1.03‐1.18) 0.94 rs2064197 6:8998811 SLC35B3 / TFAP2A S 0.164 (G) -0.19 7.23E-06 7.01E-04 2.56E-08 G (0.87‐1.01) 0.89 rs2291004 19:37997952 ZNF793 S 0.153 (A) 0.16 3.82E-05 9.88E-03 2.18E-06 G (0.82‐0.97) 0.96 rs1260326 2:27730940 GCKR S 0.335 (T) 0.13 4.04E-06 rs780094¶ 0.91 9.62E-01 5.58E-02 3.99E-06 G (0.89‐1.03)

SUPPLEMENTARY DATA SNPs with evidence of association with the nearest annotated RefSeq gene(s) listed. *Build hg19, †Reference Allele, ‡Reference Allele Frequency, §Odds Ratio (OR) and 95% Confidence Interval (95% CI), ||Correlation from the largest set of unrelated individuals from BetaGene ¶Previously identified T2D locus

Supplementary Figure 1. Power to detect association with T2D (n=6,463 T2D cases and 9,232 controls) with an α of 5.00x10-8 at minor allele frequencies (MAF) ranging from 0.05-0.45.

Supplementary Figure 2. Regional plots of loci with evidence of association (P<2.00x10-6) in the Discovery meta-analysis. A) GNA15 rs2302063 with MCRI/T2D, B) MFSD8 rs1602084 with

SI+M/T2D, C) MYT1L/TSSC1 rs896232 with SI+M/T2D, D) HAAO/SFP36L2/THADA rs1978648 with SI/T2D, E) C15orf59 rs4887140 with SI/T2D, F) HMGN3/LCA5 rs196701 with SI/T2D, G) KLF12/LINC00347 rs10492494 with M/T2D, H) LOC646736/IRS1 rs11683087 with M/T2D, I) MTNR1B rs10830963 with AIRg/T2D, J) CDKAL1 rs2206734 with AIRg/T2D, K) PEX5L/TTC14 rs6803803 with AIRg/T2D, L) SOHLH2 rs2149423 with DI/T2D, M) SNAPC4 rs3812570 with DI/T2D, N) BCL6/LPP rs523079 with SG/T2D, O) GCKR rs780093 with SG/T2D, and P) MYH14 rs788338 with SG. Genotyped SNPs passing quality control measures across all Discovery cohorts are plotted with their Discovery meta-analysis p-values (as -log10 values) as a function of genomic position (hg19). In each panel, the index variant is represented by a diamond, with the discovery results denoted in red and the discovery and translational meta- analysis denoted in purple. Estimated recombination rates (taken from HapMap) are plotted to reflect the local LD structure. Color of additional variants indicates correlation with the index SNP (red, r2≥0.80; orange, 0.60≤r2<0.80; green, 0.40≤r2<0.60; blue, 0.20≤r2<0.40; white, r2<0.20; gray no r2 value available) based on pairwise r2 values from HapMap. Gene annotations were taken from the University of California Santa Cruz genome browser.

A) B) C)

D) E) F)

G) H) I)

J) K) L)

M) N) O)