Schematic representation of the JAK2 locus. (A) Loci of SNPs are shown as black dots. Two SNPs included in the 46/1 haplotype are shown at the right end (rs12343867) and left end (rs10974944). A new candidate SNP is shown in the middle of those, near exon 13. Primers used for sequencing, a forward primer (int-12F) and four reverse primers (int-12-R, exon13-R, int-13R, and int-14R), are shown. (B) Location of primers used for allele-specific PCR. The larger fragment (3158 bp) was amplified using a forward primer (int-12F) and two sets of reverse primers (exon14-R or V617F-R) that can discriminate two alleles with or without JAK2 V617F. The smaller fragment was amplified using two forward primers (exon 14-F or V617F-F) and one reverse primer (int-14R). Detailed information on primers is given in Additional File 1.