I'm currently studying SNPs in a particular gene associated with neuropsychiatric disorders. The SNPs of interest are found in introns. Since the gene I'm studying is very large, I'm having a really difficult time finding a database that is not focused on the exons.
For exon/intron structure, use UC Santa Cruz's genome browser. The link below is to human, but you can change that in the pull-down menu to other genomes.
http://genome.ucsc.edu/cgi-bin/hgBlat
I actually tried UCSC, Ensembl, intronDB and another database with no luck! But thank you for your response!
In the NCBI SNP database you can specify exact position of SNPs. Here is an example, change the parameters for your gene.
https://www.ncbi.nlm.nih.gov/snp/?term=6%5BChromosome%5D+AND+1500000%3A3000000%5BBase+Position%5D
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