The independent contributions of all traits, covariates, SNPs, and haplotypes were determined by multiple regression analysis. Association between haplotypes and T2D or metabolic traits were tested by Haploview (version 4.0, Broad Institute of MIT and Harvard, USA) and PHASE software (version 2.1, UW Tech-Transfer Digital Ventures, University of Washington, Seattle, WA, USA) [24] . When using PHASE software, the probability thresholds were set at 90% for haplotype inference to deal with ambiguous haplotypes. It was only used to infer the haplotype of each individual and thus the case-control permutation test was not conducted. The PHASE-imputed haplotypes were counted 20 times using different seed numbers. No difference between runs was detected.