Identification of SNPs on chromosome 6 by GWAS of asthma
GWAS was performed with LR using 1,386 asthmatic patients and 5,205 controls with 4,935,875 SNPs. Figure E2 shows a quantile-quantile (QQ) plot for LR, which demonstrated that the distribution of the observedP values was consistent with the expected distribution except for a few significant SNPs with a genomic inflation factor 1.035. MDS plots showed no evidence of population stratification (Figure E3), and our analyses were statistically valid. Manhattan plots of the genome demonstrated that only 4 SNPs met genome-wide significance (Figure 1).
Table 2 shows the results for the most significant 10 SNPs. If there were several genome-wide significant SNPs in the same LD block, the result for the most significant SNP was included. According to Table 2, rs1770 was the most significant SNP (p =4.5×10-10). The genomic region of rs1770 on chromosome 6 is shown in Figure 2, demonstrating that rs1770 was located near Human leukocyte antigen (HLA)-DQB1. The second most significant SNP was rs9271469, and it was also a genome-wide significant SNP (p =3.74×10-8). It was located in the intergenic region of HLA-DRB1 (dist=31017) and HLA-DQA1 (dist=16553).