The difference in result yield between an Entrez search and a direct search on you local database is due to the fact that Entrez only returns SNPs with clear mapping to the current genome build.

To get the same results that you got from Entrez by using a direct SQL query, use an example sql (located in the data dictionary entry for SNPContigLoc), which allows you to find all refSNPs that have unique mapping positions.

Getting the same results that you got from a direct SQL query by using Entrez is not possible right now. Before I explain, please note the definitions for mapping weight available online.

If you use your use your SNPContigLoc example (mentioned above) to make a direct query of your local database for a SNP with hits on chromosome1 in the 1:6000 bp range, you will find all SNPs (including high mapping weight SNPs). The problem is, though, if you do an Entrez search for the same, you will only find mapping weight 1 SNPs for chromosome 1 in the 1:6000 range, since Entrez separately indexes mapping weight 2 SNPs in the chrMulti table, and does not index location. So searching Entrez using 1:6000 will not find those SNPs that have a mapping weight of 2. (08/09/07)

Seqview displayed the SNPs that are located on PRKAA1 mRNA. Most of the remaining SNPs are located in the intron and are not displayed. (1/12/05)

There are 49948 SNPs that have mapping information but have weight=0(unmapped) in the SNPMapInfo table. The SNPs you mention are among those SNPs that have weight=0, and therefore did not make it into Entrez since Entrez keeps mapping information only for weight 1 and weight 2 SNPs. (02/21/08)

These SNPs hit unplaced contigs on reference assembly. I will make sure they make it to Entrez (albeit without mapping info) in the next build. (02/21/08)