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Acknowledgements

The principal funder of this project was the Wellcome Trust.

Case collections were funded by: Arthritis Research Campaign, BDA Research, British Heart Foundation, British Hypertension Society, Diabetes UK, Glaxo-Smith Kline Research and Development, Juvenile Diabetes Research Foundation, National Association for Colitis and Crohn's disease, SHERT (The Scottish Hospitals Endowment Research Trust), St Bartholomew's and The Royal London Charitable Foundation, UK Medical Research Council, UK NHS R&D and the Wellcome Trust.

Statistical analyses were funded by a Commonwealth Scholarship, EU, EPSRC, Fundação para a Ciência e a Tecnologia (Portugal), National Institutes of Health, National Science Foundation and the Wellcome Trust.

We acknowledge the many physicians, research fellows and research nurses who contributed to the various case collections, and the collection teams and senior management of the UK Blood Services responsible for the UK Blood Services Collection. For the 1958 Birth Cohort, venous blood collection was funded by the UK Medical Research Council and cell-line production, DNA extraction and processing by the Juvenile Diabetes Research Foundation and the Wellcome Trust.

We recognize the contributions of: P. Shepherd (1958 Birth Cohort); those at Affymetrix responsible for genotype assay optimization, data production and data delivery (particularly S. Cawley, R. Mei, H. Fakhrai-Rad, H. Francis-Land, R. Pillai); L. Forty, G. Fraser, J. Heron, S. Hyde, A. Massey; F. Oyebode, E. Russell, M. Sinclair, A. Stern, N. Walker and S. Zammitt (recruitment and phenotypic assessment of BD cases); M. Yuille, B. Ollier and the UK DNA Banking Network and members of the BHF Family Heart Study Research Group (CAD case recruitment and DNA provision); S. Goldthorpe, D. Soars and J. Whittaker for CD collections; J. Pembroke, M. Bruce, S. Colville-Stewart, K. Edwards, L. Gatherer, C. Gemmell, K. Gilmour, S. Hampson, S. Hood, J. Hunt, J. Hussein, J. Jamieson, J. Kent, D. Lloyd, K. MacFarlane, S. Mellow, A. Nixon, J. Pheby, D. Picton, F. Porteus, P. Whitworth, K. Witte, A. Zawadzka, C. Mein and the Barts and The London Genome Centre (HT sample collection); H. Withers, the research nurses and the membership of the British Society for Paediatric Endocrinology and Diabetes (T1D case recruitment); and M. Sampson, S. O'Rahilly, S. Howell, M. Murphy and A. Wilson (T2D case recruitment).

Essential informatics support was provided by the administration, systems, bioinformatics, data services and DNA teams of the JDRF/WT DIL; the Web System teams at the Sanger Institute (particularly R. Pettett); D. Holland and R. Vincent. T. Dibling, C. Hind, D. Simpkin, P. Ewels and D. Moore provided genotyping assistance.

Personal support was provided by: Arthritis Research Campaign (A.B., H.Do., S.E., P.G., S.H., A.H., S.J., C.P., A.S., D.S., W.T., J.Wo.); British Heart Foundation (S.G.B., N.J.S., A.Do., C.W.); Cancer Research UK (D.Ea.); Diabetes UK (R.M.F.); Cure Crohn's and Colitis Fund (F.R.C.); CORE (C.M.O.); SIM (G.B.); Leverhulme Trust (A.P.M.); Throne-Holst Foundation (C.M.L.); UK Medical Research Council (D.P.K., M.D.T., J.R.P.); Vandervell Foundation (M.N.W.); and Wellcome Trust (D.G.C., L.R.C., C.M., J.Sat., M.T., A.T.H., E.Z., C.B., S.J.B., A.C., K.D., J.Gh., R.G., S.E.H., A.K., E.K., R.McG., S.P., R.R., P.Wh., D.W., P.De.).

Affymetrix GeneChip Mapping 500K Set Arrays 250K_Nsp_SNP and 250K_Sty2_SNP are deposited in NCBI GEO under accession numbers GPL3718 and GPL3720, respectively.