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SUPPLEMENTARY ONLINE MATERIAL

Common variants in the GDF5-BFZB region are associated with variation in human height

Serena Sanna1, 2*, Anne U. Jackson1*, Ramaiah Nagaraja3, Cristen J. Willer1, Wei-Min Chen1,4,

Lori L. Bonnycastle5, Haiqing Shen6, Nicholas Timpson7,8, Guillaume Lettre9, Gianluca Usala2,

Peter S. Chines5, Heather M. Stringham1, Mariano Dei2, Sandra Lai2, Giuseppe Albai2, Laura

Crisponi2, Silvia Naitza2, Kimberly F. Doheny10, Elizabeth W. Pugh10, Yoav Ben-Shlomo7, Shah

Ebrahim11, Debbie A. Lawlor7,8, Richard N. Bergman12, Richard M. Watanabe12,13, Manuela

Uda2, Jaakko Tuomilehto14, Josef Coresh15, Joel N. Hirschhorn9, Alan R. Shuldiner6,16, David

Schlessinger3, Francis S. Collins5, George Davey Smith7,8, Eric Boerwinkle17, Antonio Cao2,

Michael Boehnke1, Gonçalo R. Abecasis1, ¶, Karen L. Mohlke18, ¶

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SUPPLEMENTARY METHODS

Genotype imputation:

We imputed genotypes for all polymorphic HapMap SNPs in the FUSION and SardiNIA studies

using a Hidden Markov Model programmed in MACH1,2. Imputation allowed us to evaluate

association at the same SNPs in the two studies even though genotyping was performed using

different GWA platforms. The imputation method combines genotype data from each sample

with the HapMap CEU samples (July 2006 phased haplotype release) and then infers the

unobserved genotypes probabilistically. The inference relies on the identification of stretches of

haplotype shared between study samples and individuals in the HapMap CEU reference panel.

For each individual, we summarized imputation results in an “allele dosage” defined as the

expected number of copies of the minor allele at each position (a fractional value between 0.0

and 2.0). As previously described, we estimated r2 between each imputed genotype and the true

underlying genotypes1. We chose an estimated r2>0.3 as a threshold to flag and discard low

quality imputed SNPs. In a previous analysis of 521 SNPs that were both imputed and genotyped

in the FUSION study, the mean allelic error rate of excluded SNPs (r2≤0.3) was 7.5% whereas

the mean allelic error rate of included SNPs (r2>0.3) was 1.4%1. At this threshold we expect to

exclude most of the poorly imputed markers (70% in the previous data set) without removing

many of the successfully imputed markers (0.5%).

FUSION GWAS quality control:

Genotypes for a total of 304,560 SNPs that had minor allele frequency (MAF) >1% and passed

quality checks evaluating data completeness (≥90.0%), Hardy-Weinberg equilibrium (p≥10-6),

reproducibility in duplicate samples and Mendelian inheritance (≤3 total discrepancies in a

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combined set of 79 duplicate samples and 122 parent-offspring sets) were used as input for the

imputation procedure. The average predicted r2 between imputed allele counts and true

genotypes was .89. We evaluated quality of the imputed genotypes by comparing imputed

genotypes for 521 markers with those obtained by genotyping 1,190 individuals and observed an

error rate of 1.40% per imputed allele, in line with expectations1,2.

SardiNIA GWAS quality control:

In parallel to the strategy used in the FUSION study, we first used the 356,359 SNPs in this set

that had MAF>5% and passed the same quality control filters to estimate genotypes for all the

polymorphic SNPs genotyped by the HapMap consortium. In the SardiNIA GWAS, the average

predicted r2 between imputed allele counts and true genotypes was 0.86. We compared imputed

genotypes with those obtained by genotyping the Affymetrix Mapping 10K array in 436

individuals across 5,305 markers and observed an estimated error rate of 2.17% per allele, in line

with expectations1.

SAMPLE DESCRIPTION:

FUSION Stage 2 Samples (N = 2,466)

The FUSION study includes a series of type 2 diabetes (T2D) cases and controls approximately

frequency matched to take into account age, sex, and birth province within Finland2. Stage 2

samples do not overlap with the individuals used in the initial genome-wide association scan

(GWAS). Clinical height measurements were available for 1,208 T2D and 1,258 normal glucose

tolerant individuals. SNPs were genotyped using the iPLEX Gold assay or the homogeneous

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mass extension (hME) MassARRAY system (Sequenom, San Diego, CA). Association analysis

was performed as in the GWAS samples.

Diabetes Genetics Initiative (DGI, N = 2,985)

In the Diabetes Genetics Initiative case-control study of T2D3, height measurements were

available for 1,517 cases of T2D and 1,468 non-diabetic control individuals from Finland and

Sweden matched for age, sex, and BMI. Genotypes for rs6060369 were obtained from

Affymetrix Mapping 500K array data, and genotypes for rs143383 were imputed using MACH1.

Details of the design and data collection methods of DGI samples have been described

previously3.

Old Order Amish (N = 2,711)

The Old Order Amish individuals examined here were enrolled in ongoing family studies of

diabetes, osteoporosis, and cardiovascular traits, and have been described previously4,5. Study

subjects were examined either at the Amish Research Clinic in Strasburg, Pennsylvania, or at

their homes. Height was measured using a stadiometer with shoes removed. All protocols were

approved by the Institutional Review Board at the University of Maryland and informed consent

was obtained in all subjects, including permission to use their DNA for a variety of genetic traits.

Among the 2,711 Amish individuals examined here, 861 were genotyped for rs6060369 on the

Affymetrix Mapping 500K array and the additional samples were genotyped with the TaqMan

allelic discrimination assay. The Old Order Amish samples consist of very large Amish

pedigrees, and the evidence for association was evaluated using variance components analysis

implemented in SOLAR6.

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Atherosclerosis Risk in Communities Study (ARIC, N = 15,792)

The Atherosclerosis Risk in Communities (ARIC) study is a population-based cohort study of

atherosclerosis and its clinical sequelae in 15,792 individuals, aged 45-65 years at baseline7.

Participants were selected in 1987 from four communities: Forsyth County, NC, Jackson, MS,

northwestern suburbs of Minneapolis, MN, and Washington County, MD. The cohort was

intended to be representative of the racial and ethnic make-up of the communities, except in

Jackson, MS, where all participants are African American. Height was measured by wall

stadiometer and sitting height was measured by having the participant sit on a stool 32 inches

high. Genotyping of two SNPs reported here was performed using the TaqMan allelic

discrimination assay. Association analysis was performed as in the GWAS samples.

Caerphilly (N = 1,389)

Caerphilly is a cohort study of white, European men (97.4% were born in the UK) aged 45-59

years at entry in 1979-838,9. Subjects were recruited from the town of Caerphilly, UK and five

adjacent villages. Men were selected using the electoral role and general practitioner records.

Anthropometric measurements were taken repeatedly over several phases. The height

measurements reported here were obtained during the first phase of data collection. Ethical

approval was provided for research in the Caerphilly cohort by the South East Wales Research

Ethics Committee. Genotyping was performed by KBiosciences (Hoddesdon, UK) using

fluorescence-based competitive allele-specific PCR (KASPar) technology. Association analysis

was performed as in the GWA samples.

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BWHHS (N = 3,685)

The British Women’s Heart and Health Study (BWHHS) consists of female participants, aged 60

to 79 years and recruited between April 1999 and March 2001. Initially, 4,286 women were

randomly selected from 23 British towns and were interviewed, clinically examined, and

completed medical questionnaires. Methods used at baseline assessment have been previously

described10. Ethical approval for the study was granted by local ethics committees for each of the

23 towns in which participants live. Each woman gave written consent for use of stored blood

samples for genetic studies of heart disease risk. Genotyping was performed by KBiosciences

(Hoddesdon, UK) using their fluorescence-based competitive allele-specific PCR (KASPar)

technology. Association analysis was performed as in the GWAS samples.

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References:

1. Li, Y., Willer, C.J., Ding, J., Scheet, P. & Abecasis, G.R. Markov model for rapid haplotyping and genotype imputation in genome wide studies. Nature Genetics, Submitted. http://www.sph.umich.edu/csg/abecasis/MACH/ (2007).

2. Scott, L.J. et al. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 316, 1341-5 (2007).

3. Diabetes Genetics Initiative. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 316, 1331-6 (2007).

4. Hsueh, W.C. et al. Diabetes in the Old Order Amish: characterization and heritability analysis of the Amish Family Diabetes Study. Diabetes Care 23, 595-601 (2000).

5. Streeten, E.A. et al. Reduced incidence of hip fracture in the Old Order Amish. J Bone Miner Res 19, 308-13 (2004).

6. Almasy, L. & Blangero, J. Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet 62, 1198-211 (1998).

7. ARIC Investigators. The Atherosclerosis Risk in Communities (ARIC) Study: design and objectives Am J Epidemiol 129, 687-702 (1989).

8. The Caerphilly and Speedwell Collaborative Group. Caerphilly and Speedwell collaborative heart disease studies. J Epidemiol Community Health 38, 259-62 (1984).

9. Fehily, A.M., Butland, B.K. & Yarnell, J.W. Body fatness and frame size: the Caerphilly study. Eur J Clin Nutr 44, 107-11 (1990).

10. Lawlor, D.A., Bedford, C., Taylor, M. & Ebrahim, S. Geographical variation in cardiovascular disease, risk factors, and their control in older women: British Women's Heart and Health Study. J Epidemiol Community Health 57, 134-40 (2003).

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SUPPLEMENTARY FIGURE LEGENDS: Supplementary Figure 1: Summary of genome-wide association scan for height. Combined

genome-wide association scan results for SardiNIA and FUSION plotted as –log10 p-value. The

position of GDF5 – BFZB is noted.

Supplementary Figure 2: Quantile-quantile plot of SNPs associated with height in the

SardiNIA and FUSION studies. Red symbols represent all genotyped and imputed SNPs. Blue

symbols represent all genotyped and imputed SNPs not located within 250 kb of rs6060369. The

gray area corresponds to the 90% confidence region from a null distribution of p-values

(generated from 100 simulations).

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Supplementary Table 1. Association between HMGA2 SNPs rs1042725 and rs7968682 and height.

rs1042725 N Allele freq (C) Effect (se) cm Effect (se) standardized

% Variance explained P-value

FUSION T2D stage 1 1,073 .525 .023 (.249) .024 (.043) .03 .575 FUSION NGT stage 1 1,279 .526 .391 (.231) .041 (.044) .18 .354

SardiNIA 4,305 .447 .366 (.194) .046 (.022) .24 .058 Stage 1 meta-analysis .031

rs7968682 N Allele freq (G) Effect (se) cm Effect (se) standardized

% Variance explained P-value

FUSION T2D stage 1 1,073 .508 .119 (.255) .044 (.039) .08 .123 FUSION NGT stage 1 1,279 .513 .320 (.239) .052 (.040) .13 .202

SardiNIA 4,305 .420 .356 (.197) .044 (.022) .21 .077 Stage 1 meta-analysis .0093

Association results are shown for an additive genetic model. Height means (SD) in cm are shown.

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Supplementary Table 2. The most strongly associated independent signals for height in the FUSION and SardiNIA GWAS meta-analysis. Locus Association Signal Nearby Genes

SNP Chr Position

(Mb) Allele

(tall/short) Freq * (tall)

Effect (cm) P-value

rs725908 20 33.4 T/C 0.402 0.586 1.8 x 10-7 GDF5 - BFZB

rs17690232 4 55.1 C/G 0.801 0.855 3.9 x 10-7 PDGFRA

rs4932217 15 87.7 A/C 0.580 0.660 8.4 x 10-7 POLG

rs724016 3 142.6 G/A 0.363 0.611 1.2 x 10-6 ZBTB38

rs10078095 5 78.8 C/T 0.215 0.897 3.1 x 10-6 HOMER1 Chromosome assignments, position, and gene annotations all refer to NCBI Build 35. Alleles are ordered such that the first allele (“tall”) is associated with increased height. Effect sizes are measured as additive effects, which correspond to the average change in phenotype when one “short” allele is replaced with one “tall” allele. For each locus, the most strongly associated SNP is indicated together with nearby genes. SNPs in bold were imputed in both FUSION and SardiNIA. *Weighted average of the allele frequency in FUSION T2D, FUSION NGT, and SardiNIA.

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Supplementary Table 3. Association between rs6060369 (allele C) and height by gender. Males Females

Standing height N Effect (se) standardized p-value N Effect (se)

standardized p-value

FUSION T2D stage 1+ 617 .086 (.060) .152 467 .073 (.067) .274 FUSION NGT stage 1+ 640 .111 (.057) .053 647 .137 (.058) .018

SardiNIA 1,883 .092 (.038) .015 2,415 .100 (.034) .0036 Stage 1 meta-analysis 3,140 0.095 6.94 x 10-4 3,529 0.103 1.34 x 10-4 FUSION T2D stage 2 690 .092 (.054) .093 464 .030 (.063) .641 FUSION NGT stage 2 728 .118 (.050) .019 475 .061 (.064) .340

DGI T2D+ 887 .112 (.052) .029 630 .002 (.056) .966 DGI controls+ 553 .068 (.059) .252 537 .070 (.060) .242

Old Order Amish 1,253 .100 (.040) .012 1,458 .060 (.036) .087 ARIC European Americans 5,124 .016 (.020) .429 5,762 .064 (.019) .0006 ARIC African Americans 1,468 .075 (.040) .062 2,394 .017 (.032) .580

Caerphilly 1,097 .083 (.042) .055 - - - BWHHS - - - 3,652 .093 (.240) 9.71 x 10-5

Stage 2 meta-analysis 11,800 0.059 1.00 x 10-5 15,372 0.060 1.77 x 10-7 Standing height meta-analysis 14,940 0.066 4.25 x 10-8 18,901 0.068 2.03 x 10-10

Sitting height ARIC European Americans 5,119 .024 (.020) .228 5,757 .053 (.018) .0040 ARIC African Americans 1,468 .052 (.040) .194 2,393 -.041 (.031) .185

Caerphilly 1,092 .087 (.041) .038 - - - BWHHS - - - 3,655 .100 (.023) 1.73 x 10-5

Sitting height meta-analysis 7,679 0.038 .0195 11,805 0.049 .00014 Standardized effects indicate the amount of increased height in standard deviation units, on average, for each additional copy of the C allele. P-values correspond to standardized effects. +Genotypes for individuals not successfully genotyped for this marker were imputed to increase the call rate to 100%.

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Supplementary Table 4. SNPs in the GDF5 – BFZB region showing p-value < 0.001 in the combined SardiNIA and FUSION GWAS.

SNP Position (bp)

Allele tall/short

Frequency* (tall allele) SardiNIA FUSION

NGT FUSION

T2D Combined

GWAS Gene

rs725908 33,431,481 T/C 0.397 2.64 x 10-5 1.76 x 10-2 4.74 x 10-2 1.84 x 10-7 BFZB(Intron) rs1406949 33,369,318 A/C 0.395 4.63 x 10-4 1.88 x 10-3 6.64 x 10-2 8.26 x 10-7 BFZB(Intron) rs1406948 33,369,033 A/G 0.394 4.81 x 10-4 1.86 x 10-3 6.44 x 10-2 8.30 x 10-7 BFZB(Intron) rs6060369 33,370,575 C/T 0.401 4.35 x 10-4 2.36 x 10-3 7.19 x 10-2 9.73 x 10-7 BFZB(Intron) rs6088791 33,371,323 C/T 0.402 4.34 x 10-4 2.39 x 10-3 7.42 x 10-2 1.01 x 10-6 BFZB(Intron) rs2425062 33,386,980 G/A 0.405 4.55 x 10-4 2.92 x 10-3 7.13 x 10-2 1.17 x 10-6 BFZB(Intron) rs6060373 33,377,622 G/A 0.404 4.55 x 10-4 2.63 x 10-3 7.75 x 10-2 1.18 x 10-6 BFZB(Intron) rs6060371 33,376,736 T/G 0.404 4.55 x 10-4 2.61 x 10-3 7.79 x 10-2 1.18 x 10-6 BFZB(Intron) rs224329 33,482,993 T/C 0.396 3.38 x 10-4 9.23 x 10-3 4.64 x 10-2 1.35 x 10-6 rs6142374 33,448,982 C/T 0.398 2.82 x 10-4 1.44 x 10-2 4.81 x 10-2 1.64 x 10-6 BFZB(Intron) rs6087704 33,464,472 C/T 0.397 3.48 x 10-4 1.09 x 10-2 4.90 x 10-2 1.66 x 10-6 BFZB(Intron) rs6088820 33,450,712 T/C 0.397 3.01 x 10-4 1.33 x 10-2 4.90 x 10-2 1.67 x 10-6 BFZB(Intron) rs6579234 33,446,899 A/G 0.398 2.83 x 10-4 1.49 x 10-2 4.78 x 10-2 1.69 x 10-6 BFZB(Intron) rs3795159 33,359,676 G/C 0.387 7.05 x 10-4 1.75 x 10-3 9.17 x 10-2 1.69 x 10-6 BFZB(Intron) rs6060402 33,468,654 T/C 0.397 3.67 x 10-4 1.06 x 10-2 4.87 x 10-2 1.71 x 10-6 rs1886691 33,449,685 T/C 0.398 2.98 x 10-4 1.39 x 10-2 4.85 x 10-2 1.71 x 10-6 BFZB(Intron) rs6142379 33,462,681 A/G 0.397 3.52 x 10-4 1.14 x 10-2 4.94 x 10-2 1.76 x 10-6 BFZB(Intron) rs6142373 33,446,728 T/A 0.398 3.00 x 10-4 1.55 x 10-2 4.76 x 10-2 1.84 x 10-6 BFZB(Intron) rs878639 33,357,877 G/A 0.386 7.82 x 10-4 1.83 x 10-3 9.03 x 10-2 1.92 x 10-6 BFZB(Intron) rs6579235 33,459,359 T/A 0.397 3.87 x 10-4 1.17 x 10-2 4.96 x 10-2 1.98 x 10-6 BFZB(Intron) rs6088823 33,457,679 G/T 0.397 3.84 x 10-4 1.18 x 10-2 4.96 x 10-2 1.99 x 10-6 BFZB(Intron) rs6142376 33,456,175 T/A 0.397 3.72 x 10-4 1.24 x 10-2 4.96 x 10-2 1.99 x 10-6 BFZB(Intron) rs6088815 33,439,888 G/C 0.399 3.25 x 10-4 1.75 x 10-2 4.66 x 10-2 2.17 x 10-6 BFZB(Intron) rs4911179 33,436,313 A/C 0.399 3.30 x 10-4 1.81 x 10-2 4.64 x 10-2 2.25 x 10-6 BFZB(Intron)

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SNP Position (bp)

Allele tall/short

Frequency* (tall allele) SardiNIA FUSION

NGT FUSION

T2D Combined

GWAS Gene

rs6088813 33,438,595 C/A 0.399 3.33 x 10-4 1.81 x 10-2 4.64 x 10-2 2.27 x 10-6 BFZB(Intron) rs4911496 33,435,467 C/T 0.399 3.38 x 10-4 1.81 x 10-2 4.64 x 10-2 2.31 x 10-6 BFZB(Intron)

rs4911494+ 33,435,328 C/T 0.399 3.40 x 10-4 1.81 x 10-2 4.64 x 10-2 2.32 x 10-6 BFZB(Exon); BFZB(Intron)

rs4911180 33,436,362 G/A 0.399 3.48 x 10-4 1.81 x 10-2 4.64 x 10-2 2.38 x 10-6 BFZB(Intron) rs6141548 33,434,499 A/G 0.399 3.54 x 10-4 1.79 x 10-2 4.67 x 10-2 2.42 x 10-6 BFZB(Intron) rs6060355 33,353,475 A/G 0.383 6.70 x 10-4 3.23 x 10-3 9.35 x 10-2 2.46 x 10-6 rs1540927 33,394,758 A/G 0.398 4.27 x 10-4 1.53 x 10-2 5.40 x 10-2 2.93 x 10-6 BFZB(Intron) rs224333 33,487,376 A/G 0.388 1.15 x 10-3 5.89 x 10-3 3.75 x 10-2 2.98 x 10-6 GDF5(Intron) rs6142358 33,423,722 C/T 0.398 4.40 x 10-4 1.72 x 10-2 4.85 x 10-2 3.01 x 10-6 BFZB(Intron) rs1570004 33,421,667 A/T 0.398 4.45 x 10-4 1.71 x 10-2 4.89 x 10-2 3.05 x 10-6 BFZB(Intron) rs745931 33,419,418 A/T 0.398 4.48 x 10-4 1.68 x 10-2 4.96 x 10-2 3.07 x 10-6 BFZB(Intron) rs4911491 33,410,699 C/G 0.398 4.51 x 10-4 1.61 x 10-2 5.14 x 10-2 3.08 x 10-6 BFZB(Intron) rs2248393 33,389,517 G/C 0.398 4.54 x 10-4 1.51 x 10-2 5.49 x 10-2 3.12 x 10-6 BFZB(Intron) rs4911178 33,416,034 G/A 0.398 4.76 x 10-4 1.65 x 10-2 5.03 x 10-2 3.26 x 10-6 BFZB(Intron) rs4911492 33,415,213 G/A 0.398 4.77 x 10-4 1.64 x 10-2 5.06 x 10-2 3.27 x 10-6 BFZB(Intron) rs6060378 33,386,415 G/T 0.382 5.04 x 10-4 4.36 x 10-3 1.78 x 10-1 4.36 x 10-6 BFZB(Intron) rs2425060 33,378,115 C/T 0.382 5.02 x 10-4 4.14 x 10-3 1.92 x 10-1 4.56 x 10-6 BFZB(Intron) rs2425056 33,372,659 A/G 0.381 5.06 x 10-4 3.77 x 10-3 2.08 x 10-1 4.73 x 10-6 BFZB(Intron) rs6060370 33,373,166 C/T 0.381 5.06 x 10-4 3.83 x 10-3 2.09 x 10-1 4.79 x 10-6 BFZB(Intron) rs6087709 33,481,358 G/C 0.352 1.87 x 10-4 3.34 x 10-2 1.83 x 10-1 7.96 x 10-6 rs1204656 33,446,260 G/A 0.356 2.10 x 10-4 4.53 x 10-2 1.38 x 10-1 8.65 x 10-6 BFZB(Intron) rs2145082 33,368,740 T/C 0.359 7.42 x 10-4 1.51 x 10-2 1.29 x 10-1 1.12 x 10-5 BFZB(Intron) rs1210224 33,444,274 T/C 0.352 2.18 x 10-4 8.78 x 10-2 1.13 x 10-1 1.35 x 10-5 BFZB(Intron)

rs17323916 33,373,995 A/G 0.361 4.70 x 10-4 1.03 x 10-2 3.08 x 10-1 1.39 x 10-5 BFZB(Intron) rs6088792 33,373,198 T/C 0.361 5.00 x 10-4 1.02 x 10-2 3.12 x 10-1 1.50 x 10-5 BFZB(Intron)

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SNP Position (bp)

Allele tall/short

Frequency* (tall allele) SardiNIA FUSION

NGT FUSION

T2D Combined

GWAS Gene

rs941665 33,406,695 C/T 0.356 3.11 x 10-4 4.67 x 10-2 1.74 x 10-1 1.61 x 10-5 BFZB(Intron) rs941664 33,403,387 G/C 0.356 3.26 x 10-4 4.63 x 10-2 1.79 x 10-1 1.73 x 10-5 BFZB(Intron) rs143383 33,489,397 G/A 0.403 6.73 x 10-3 3.70 x 10-3 7.10 x 10-2 2.70 x 10-5 GDF5(Exon) rs143384 33,489,170 G/A 0.422 3.29 x 10-3 5.63 x 10-3 1.79 x 10-1 3.65 x 10-5 GDF5(Exon) rs6088832 33,469,590 T/C 0.322 1.81 x 10-4 1.35 x 10-1 2.80 x 10-1 4.42 x 10-5 rs6120880 33,292,822 G/C 0.460 1.07 x 10-3 5.02 x 10-2 2.00 x 10-1 6.31 x 10-5 MMP24(Intron) rs2425019 33,282,831 G/A 0.491 7.53 x 10-4 8.60 x 10-2 1.92 x 10-1 6.89 x 10-5 MMP24(Intron) rs6088765 33,262,941 G/T 0.473 2.01 x 10-3 8.58 x 10-2 1.66 x 10-1 1.50 x 10-4 rs6088747 33,218,265 T/G 0.509 3.29 x 10-4 1.83 x 10-1 5.57 x 10-1 2.27 x 10-4 rs2069952 33,227,612 T/C 0.498 6.59 x 10-4 1.89 x 10-1 5.50 x 10-1 4.08 x 10-4 PROCR(Intron) rs1415774 33,229,277 G/A 0.498 6.60 x 10-4 1.94 x 10-1 5.45 x 10-1 4.13 x 10-4 rs6060285 33,234,148 T/G 0.498 6.64 x 10-4 1.98 x 10-1 5.40 x 10-1 4.19 x 10-4 rs2065979 33,231,351 C/T 0.498 6.75 x 10-4 1.96 x 10-1 5.43 x 10-1 4.22 x 10-4 rs4911478 33,246,286 A/C 0.498 6.72 x 10-4 2.08 x 10-1 5.30 x 10-1 4.32 x 10-4 rs633198 33,242,095 T/C 0.498 6.78 x 10-4 2.08 x 10-1 5.30 x 10-1 4.35 x 10-4 rs1577924 33,247,949 C/G 0.498 6.82 x 10-4 2.08 x 10-1 5.30 x 10-1 4.37 x 10-4 rs6058202 33,241,644 G/A 0.498 6.83 x 10-4 2.08 x 10-1 5.30 x 10-1 4.38 x 10-4 rs8114671 33,252,803 C/A 0.498 6.86 x 10-4 2.07 x 10-1 5.30 x 10-1 4.39 x 10-4 rs2093058 33,254,942 G/A 0.498 6.94 x 10-4 2.07 x 10-1 5.32 x 10-1 4.44 x 10-4 rs6142324 33,252,704 C/T 0.498 6.99 x 10-4 2.08 x 10-1 5.30 x 10-1 4.46 x 10-4

SNPs in bold were imputed in both FUSION and SardiNIA (not genotyped in either study). Positions are from NCBI Build 35. The annotation indicates if the SNPs are located in exons or introns of any of the isoforms of a gene. *Weighted average of the allele frequency in SardiNIA, FUSION cases and FUSION controls. + rs4911494 is in an exon or intron depending on the BFZB isoform.

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Supplementary Table 5. Association between rs143383 (allele G) and height by gender. Males Females

Standing height N Effect (se) standardized p-value N Effect (se)

standardized p-value

FUSION T2D stage 1+ 617 .114 (.066) .083 467 .055 (.072) .441 FUSION NGT stage 1+ 640 .130 (.062) .035 647 .109 (.064) .086

SardiNIA 1,883 .068 (.039) .081 2,415 .070 (.035) .046 Stage 1 meta-analysis 3,140 0.090 .0021 3,529 0.075 .0076 FUSION T2D stage 2 692 .069 (.054) .202 475 .042 (.064) .516 FUSION NGT stage 2 743 .119 (.050) .018 473 .037 (.065) .570

DGI T2D+ 887 .128 (.053) .016 630 .026 (.056) .640 DGI controls+ 553 .040 (.061) .509 537 .101 (.061) .099

Old Order Amish - - - - - - ARIC European Americans 5,115 .012 (.020) .534 5,746 .069 (.019) .0002 ARIC African Americans 1,477 .128 (.057) .025 2,406 .071 (.044) .108

Caerphilly - - - - - - BWHHS - - - - - -

Stage 2 meta-analysis 9,467 0.055 .0012 10,267 0.066 1.60 x 10-5 Standing height meta-analysis 12,607 0.064 1.38 x 10-5 13,796 0.068 3.97 x 10-7

Sitting height ARIC European Americans 5,110 .018 (.020) .363 5,741 .050 (.019) .0071 ARIC African Americans 1,477 .065 (.056) .246 2,405 -.088 (.043) .042

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Sitting height meta-analysis 6,587 0.028 .210 8,146 0.012 .248 Standardized effects indicate the amount of increased height in standard deviation units, on average, for each additional copy of the C allele. P-values correspond to standardized effects. +Genotypes for individuals not successfully genotyped for this marker were imputed to increase the call rate to 100%.

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Supplementary Figure 2: Quantile-quantile plot of SNPs associated with height in the SardiNIA and FUSION studies. Red symbols represent all genotyped and imputed SNPs. Blue symbols represent all genotyped and imputed SNPs not located within 250 kb of rs6060369. The gray area corresponds to the 90% confidence region from a null distribution of p-values (generated from 100 simulations).