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. 2009 Feb 27;58(6):1403–1410. doi: 10.2337/db08-1514

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© 2009 by the American Diabetes Association.

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FIG. 2. — Summary of genome-wide association results for the chromosome 7p, 9q, 11p, and 13q loci. A: Genome-wide association scan and imputed data for the chromosome 7p locus. rs39059 (solid red triangle) is located at position IVS1 + 21350 relative to exon 1 of CHN2 isoform 2 and is in tight linkage disequilibrium with rs39075 (r² = 0.96), located at position IVS1 + 42572. rs39059 and rs39075 reside −69,318 and −90,540 kb, respectively, upstream of CPVL isoforms 1 and 2. A third alternate transcript (isoform 3) is predicted for CPVL and contains an exon that extends to intron 1 of CHN2. rs39059 and rs39075 are located at positions −20579 and −41801, respectively, relative to this transcript. ▲, SNPs genotyped on the Affymetrix array (n = 163); △, imputed SNPs (n = 694). *Imputed SNP rs39075 was genotyped in the GoKinD samples to confirm the imputation. B: Genome-wide association scan and imputed data for the chromosome 9q locus. A total of 100 genotyped SNPs from the Affymetrix array data and 450 imputed SNPs are shown. rs10868025 (solid red triangle) is located at position −10829 relative to FRMD3's transcription start site. rs10868025 is in complete linkage disequilibrium (r² = 1.0) and only 253 bp from imputed SNP rs13289150 (△ superimposed on rs10868025). rs1888747, located at position −2204, is in partial linkage disequilibrium (r² = 0.81) with rs10868025. *Imputed SNP rs1888747 was genotyped in the GoKinD samples to confirm the imputation. C: Genome-wide association scan and imputed data for the chromosome 11p locus. A total of 33 genotyped SNPs from the Affymetrix array data and 190 imputed SNPs are shown. rs739401 and rs451041 (solid red triangles) are in strong linkage disequilibrium (r² = 0.97). rs739401 is located in intron 16 (isoforms a and c)/17 (isoforms b and d) of the CARS gene (position IVS16 + 687/IVS17 + 687). rs451041 is located in intron 4 (isoforms a and c)/5 (isoforms b and d), position IVS4 − 203/IVS5 − 203). D: Genome-wide association scan and imputed data for the chromosome 13q locus. A total of 68 genotyped SNPs from the Affymetrix array data and 268 imputed SNPs are shown. Seven lead SNPs (rs1041466, rs1411766, rs17412858, rs6492208, rs2391777, rs7989848, and rs9521445) from this region are indicated in red. rs1411766 and rs17412858 are in complete linkage disequilibrium (r² = 1.0). Similarly, rs6492208 and rs2391777 are in complete linkage disequilibrium (r² = 1.0). rs7989848 and rs9521445 are in strong linkage disequilibrium (r² = 0.87), whereas only modest linkage disequilibrium exists between all other SNP pairs (r² = 0.30–0.65). The two nearest genes are MYO16 and IRS2, located ∼384 kb centromeric and 120 kb telomeric of this region, respectively.