This help document answers the following questions:

• What type of information can I get from cgd snp database?
• When should I use this query form?
• How do I use this query form?
• what values are acceptable in each of the query form fields?
• How do I narrow my query?
• How do I interpret the summary results of my query?
• How do I interpret the detail results of my query?

Type of information you can get from cgd snp database

• SNP-gene association (nearest genes,gene type,genes with single/multiple isoforms,...)
• SNP-transcript association
• SNP-EXON association (exon rank,terminal exons,internal exons,...)
• SNP-functional implication (stop gained,stop lost, coding synonymous,...)
• SNP-protein association
• SNP location (Intergenic,Intron,Exon,UTRs,...)
• SNP-phenotype association
• SNP-GO association
• SNP-LD association
• SNP quality (conflict between sources,bad cluster windows,..)
• SNP minor allele frequency

When should I use this query form?
You can use this Query Form for the following cases:

• You have a single snp ID (chromosome:bp_position)
• You have multiple or a range of snp IDs (chromosome1:bp_position chromosome2:bp_position chromosome1:bp_position1-bp_position2)
• You have a single Gene ID, Name or Symbol
• You have multiple Gene IDs, Names or Symbols
• You have a single Ensembl protein ID
• You have multiple Ensembl protein IDs
• You have a single phenotype term ID, or phenotype term
• You have multiple phenotype term IDs, or phenotype terms
• You have a single GO term ID, or GO term
• You have multiple GO term IDs, or GO terms

How do I use this query form?
We either do a simple query by

Simple query

Input data	Data Description	Data format
A single snp ID	A single base pair position on the genome	chromosome:bp_position
Multiple or a range of snp IDs	Multiple base pair position on same chromsome or on different chromosomes. Consecutive entries are separated by commas character	chromosome1:bp_position1 chromosome1:bp_position2 chromosome2:bp_position1 chromosome1:bp_position1-bp_position2
A single/multiple Gene ID, or Symbol	Ensembl geneid;Entrez geneid;MGI geneid,gene name,gene symbol	Consecutive entries are separated by a commas character
Single/Multiple Ensembl transcript ID(s)	Using Ensembl transcript(s) to query for snps	Consecutive entries are separated by commas character
A single/Multiple Ensembl protein ID(s)	Using Ensembl protein ID(s) to query for snps	Consecutive entries are separated by a commas character
A single/Multiple MGI phenotype term ID(s)	Using MGI phenotype term ID(s) to query for snps	Consecutive entries are separated by a commas character
A single/Multiple MGI phenotype term(s)	Using MGI phenotype term(s) to query for snps	Consecutive entries are separated by a "|" character
A single/Multiple GO term ID(s)	Using GO term ID(s) to query for snps	Consecutive entries are separated by a commas character
A single/Multiple GO term(s)	Using GO term(s) to query for snps	Consecutive entries are separated by a "|" character

File upload

Input data	Data Description	Data format
A list of single snp IDs	A file containing a list of single base pair position on the genome. One entry per line	chromosome:bp_position
A list of Ensembl Gene IDs	A file containing a list of Ensembl geneids	One entry per line
A list of Entrez Gene IDs	A file containing a list of Entrez geneids	One entry per line
A list of MGI Gene IDs	A file containing a list of MGI geneids	One entry per line
A list of MGI Gene symbols	A file containing a list of MGI Gene symbols	One entry per line
A list of MGI phenotype term IDs	A file containing a list of MGI phenotype term IDs	One entry per line
A list of MGI phenotype terms	A file containing a list of MGI phenotype terms	One entry per line
A list of GO term IDs	A file containing a list of GO term IDs	One entry per line
A list of GO terms	A file containing a list of GO terms	One entry per line