Mapping of PARK2 and PACRG Overlapping Regulatory Region Reveals LD Structure and Functional Variants in Association with Leprosy in Unrelated Indian Population Groups
Figure 3
A schematic lay-out of the BIN structure (r2≥0.80) in the regulatory region of the PARK2 and PACRG genes in North Indian and East Indian-Orissa and Vietnamese population for 41 SNPs spanning 148 Kb region of Chromosome 6q26, where 36 SNPs are common to both Vietnamese and Indian population and 5 significant SNPs (No. 20, 22, 23, 26, 32) are exclusively studied in the Indian population.
[It may be noted that a similar BIN structure was observed in the North-Indian and East-Indian-Orissa populations]. Physical location of the studied chromosomal region is given in Mb on top. Vietnamese population information of Mira et al, 2004 and common SNPs between Indian and Vietnamese population (Alter et al, 2012) was shared by Prof. Schurr. Rest of the SNPs & BIN structure information was retrieved from Alter et al (2012). SNPs in star shape indicate the significant association (in two respective populations-Indian and Vietnamese). 11 significantly associated SNPs in studied Indian populations are distributed in two BINs (BIN 1 with 8 and BIN 2 with 3 SNPs). Distribution of significant SNPs in Vietnamese population is shown in BIN 1, BIN 2 and BIN3. SNPs, rs10945859 (No. 1) and rs9347684 (No. 9), although shared significance in both the Indian and Vietnamese population, but these showed no significant difference in expression in in vitro reporter assay for the alternative alleles. Each SNP is designated by a No. ranging from 1 to 41 according to increasing order of the chromosomal position. Filled Black Star - Significant SNPs in Indian (North and East Indian-Orissa) population, Unfilled Star - Significant SNPs in Vietnamese population, Filled Black Dot - Non-Significant SNPs in North and East Indian-Orissa population, Unfilled Dot - Non-Significant SNPs in Vietnamese population, Black Circled Dot and Black Circled Star SNPs (No. 5, 7, 8, 24, 35) studied by us earlier [26].