In the 1000 genome browser, for some snps you have synonyms. Very often, they are on the same chromosome and close to each other. I guess this is just a build problem.
But I found a snp (rs16960052) with a synonym snp on an other chromosome, with different allele frequency and different flanking sequence. Why this is happening?
When your search for rs16960052 in 1000 genome browser, it give you another snp (rs16960063). When you look for this snp, it said they are synonyms but they are not on the same chromosome.