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Some months ago, I used the CHIP SNPper tool to obtain annotation on lists of SNPs for a QTL study. I was under the impression that SNPper cross-referenced dbSNP and UCSC for its annotation. The former defines a SNP as part of a gene if it is within <2kb upstream or <0.5 kb downstream. However, SNPper returned gene names for several SNPs that were 5kb or more upstream. Does anybody know what SNPper's cutoff is? Evidently, it is using a less stringent criterion than dbSNP.
