Usage of "By Gene feature"

This is a data retrieval tool that provides JSNP data.
You can narrow the data down by some filters, and select an output format.
In "By Gene feature", you can set filters about gene features.

To get JSNP data, you need to pass through 3 steps.
1st step is to specify a region that genes are mapped.
2nd step is to specify features of genes.
3rd step is to select an output format.

1. Region setting In this page, you can retrieve data from the entire genome, an entire chromosome or a region on a particular chromosome.
2. Feature setting In this page, you can retrieve a subset of SNPs with JSNP ID, dbSNP ID, minor allele frequencies, gene structure, and so on. If you select some filters, they will automatically be retrieved with a Boolean "AND" processing. If multiple ID or words are entered in a search box, they will automatically be retrieved with a Boolean "OR" processing.
3. Output format setting In this page, options allow you to define which data should be included in the output, and you can select an output format from pull down menus.
4. Output You can export the data to a uncompressed or gzipped file in the format selected among HTML, fixed width text, CSV (Comma Separated Value),tab-separated text, Microsoft Excel or XML.

Data schema

This is a data schema in this tool.

field name	description
gene_acc	an ACC of gene (RefSeq NP/XP)
contig_acc	an ACC of genomic contig (RefSeq NT) that the gene is mapped
contig_start	a start position of the gene in the genomic contig
contig_end	an end position of the gene in the genomic contig
contig_direc	a direction of the gene sequences against the genomic contig
chr	a chromosome number that the gene is mapped
chr_start	a start position of the gene in the chromosome
chr_end	an end position of the gene in the chromosome
chr_direct	a direction of the gene against the chromosome
locus_id	an ID of the gene (Locus Link)
symbol	a symbol of the gene
alias	symbol aliases of the gene
omim	an OMIM ID related with the gene
express	tissues in which the gene expresses (this data is extracted from UniGene)
snp3000	JSNPs around the gene: from 3Kb-upstream of "chr_start" to 3kb-downstream of "chr_end"