Usage of "By SNP 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 SNP feature", you can set filters about SNP features.

To get JSNP data, you need to pass through 3 steps.
1st step is to specify a region that JSNPs are mapped.
2nd step is to specify features of JSNPs.
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.	(click to zoom in)
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.	(click to zoom in)
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.	(click to zoom in)
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.	(click to zoom in)

Data schema

This is a data schema in this tool.

field name	description
snp_id	an ID of JSNP
snp_type	the snp type: SNP or IND(insertion/deletion)
na_var	a nucleic acids variation
5_flank_seq	a 5'-flanking sequence of the snp
3_flank_seq	a 3'-flanking sequence of the snp
for_primer	a forward primer sequence
back_primer	a backward primer sequence
product_size	a primer product size
contig_acc	an ACC of genomic contig (RefSeq NT) that the snp is mapped
contig_start	a start position of the snp in the genomic contig
contig_end	an end position of the snp in the genomic contig
contig_direc	a direction of the flanking sequences against the genomic contig
chr	a chromosome number that the snp is mapped
chr_start	a start position of the snp in the chromosome
chr_end	an end position of the snp in the chromosome
chr_direct	a direction of the flanking sequences against the chromosome
hit_count	the number of hit (mapped positions of the snp against genome)
freq	allele frequencies of the snp
gene_na_acc	an ACC of gene (RefSeq NM/XM) that the snp is mapped
gene_aa_acc	an ACC of gene (RefSeq NP/XP) that the snp is mapped
locus_id	an ID of gene (Locus Link) that the snp is mapped
symbol	a symbol of gene that the snp is mapped
gene_direct	a direction of the flanking sequences against a direction of gene in chromosome: if a direction of the flanking sequences in chromosome "+" and a direction of gene in chromosome "+", this is "+"; if "-" and "-", this is "+"; if "+" and "-", this is "-"; if "-" and "+", this is "-"
str_type	a gene structure that the snp is mapped: CDS, exon, intron, 5'-UTR, 3'-UTR
aa_var	an amino acids variation
codon_var	a codon variation
codon_posi	the snp postion in the codon
dbsnp_rs_id	dbSNP identifier(NCBI reference ID)
dbsnp_ss_id	dbSNP identifier(NCBI assay ID)