Single nucleotide polymorphisms (SNPs) can change polyadenylation signals. Poly(A) signal (PAS) plays an important role during polyadenylation process. Therefore, the selection of poly(A) sites may be affected by the appearance of SNPs. With the rapid development of the next-generation high-throughput DNA sequencing techniques, more and more SNPs are discovered, but not all the SNPs can lead to the change of the poly(A) sites. Here a pipeline named ESAP (extract SNPs associating with polyadenylation) was designed that can extract the SNPs affecting poly(A) sites. ESAP uses poly(A) prediction program PASS to compute the base prediction scores which are used to identify the difference of poly(A) sites because of the existence of SNPs. Finally, the SNPs are classified into ÂlikelyÂ, ÂprobableÂ, ÂunlikelyÂ according to their effect on poly(A) sites. 569,859 SNPs fromArabidopsisÂ Bur-0 and 40,026 poly(A) site clusters (PACs) from Arabidopsis Thaliana are analyzed. Total 160 SNPs that can affect PAS (PAS-SNPs)were found, including 84 ÂlikelyÂ, 38 ÂprobableÂ.