The top SNP in the GWAS meta-analysis, rs2504235, located on chromosome 13q12.2, surpassed the genome-wide significance threshold (OR=1.16, p=2.1×10−8, Table 1; Figure S6). rs2504235 lies within an intron of FLT3, encoding FMS-like tyrosine kinase 3. No other SNPs achieved genome-wide significance, although rs1933437, a common FLT3 missense variant (Thr227Met) that lies 11.4 kb away from and is in strong LD with rs2504235 (r2=0.93), had a p-value of p=8.2×10−8 (Table S3). Across the genome, 39 LD-independent index SNPs with p<1×10−5 were identified by LD pruning (r2<0.2) followed by conditional association analyses controlling for the most significant SNP within each 2 Mb window and manual inspection of regional association plots to confirm the presence of supporting statistical evidence of association from nearby SNPs (Tables S3 and S4). The top 10 LD-independent index SNPs are presented in Table 1.
