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We and others in a variety of ethnic groups have previously described associations of various SNPs of the uncoupling protein genes UCP2 and UCP3 (located within 17 kb of each other on chromosome 11q13) with both central fat disposition and BMI. The aim of this study was to do a replication study in South Indian subjects using a family based approach and selecting SNP's by' a priori hypothesis' defined by a previous association with obesity/waits in other studies and/or functional data. Five SNPs were studied; 1 by Ampliflour (UCP2-866 rs659366), 1 by SNAPSHOT (UCP3Y210Y rs2075577), 2 by TaqMan (UCP3-55 rs1800849, UCP2 A55V rs660339) and one by PCR-RFLP (UCP2 exon 8 INDEL) in 882 South Indian participants from 236 families ascertained from community based study of healthy families living in Chennai, India. Statistical analysis was performed using SOLAR and anthropometric variables were corrected for age and sex. The QTLD analysis showed the BMI was associated to the UCP3 rs1800849 (AA 23.9±0.29, AB 23.5±0.32, BB 23.0±0.5, p=0.027) and UCP3 rs2075577 (AA 24.6±0.37, AB 24.0±0.30, BB 23.4±0.39, p=0.022). Waist circumference to the UCP2 rs660339 (AA 84.3±0A8, AB 85.1±0.41, BB 85.9±0.65, p=0.028). Body fat percentage to UCP2 rs660339 (AA 22.9±0.31, AB 23.2±0.27, BB 23.5±0.42, p=0.048) and UCP2 rs659366 (AA 22.7±0.31, AB 22.9±0.26, BB 23.27±0.41, p=0.076). This detailed analysis confirms associations between anthropometric traits and the UCP2/UCP3 locus but that separate SNPs are associated with either BMI or fat distribution. [ABSTRACT FROM AUTHOR]