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One of the challenges facing us in India, translating recent discoveries of chronic disease associated SNPs into clinical domain for prevention, is the lack of knowledge about the frequency of the polymorphism in our population. Hence, using available HapMap data has become a norm. However, it is anticipated that population genomics in India could be different from the HapMap Caucasian population. Relative disease risk prediction based on relevant SNPs, both for personalized medicine and for population genetics, has little value without accurate information of population allele frequencies. We report allele frequency of 384 SNPs directly related to chronic disease risk and metabolic traits in the Indian population. Materials and methods We report the allele in a random sample of 146 individuals and compare them with the data reported in HapMap Caucasian population (n = 112). Genotyping was performed using Illumina golden gate genotyping assay following DNA extraction from saliva. Allele frequencies were determined by direct gene count method. Results GWAS studies confirmed 384 SNPs to be associated with disease risk (364) of Diabetes Type 1 and 2 (54 & 118 respectively), Coronary artery disease(71), myocardial infarction(9), cardiac failure(24), sudden cardiac arrest (38), atrial fibrillation(9), hypertension(18), obesity(10), metabolic syndrome(2) and stroke(11); or were associated with metabolic traits (20). The master table of their ‘rs’ id, chromosomes, location and association is presented. Of the 384 SNPs, 44 were not in H-W equilibrium and were omitted. HapMap data were not available for 13 SNPs. We are reporting their allele frequencyon the Indian population for the first time. Of the remaining 307 disease association SNPs, statistically significant difference (p 10% (considered major in population genetics) was found in 42% (130 of 307). Of the 20 metabolic association SNPs, 50% (10 of 20) had statistically significant difference and in all of them it was >10%.

Population allele frequencies of disease associated SNPs in India: a paradigm shift from HapMap