disease associated snp

jialovelyjia · 05-17-2012, 01:22 AM

I want to find SNPs which are associated with autoimmune disease.I have searched the HuGE Navigator,but there are only some kinds of autoimmune diseases which have associated snps.Could someone tell me some databases or teach me some approaches to solute my problem?(It is the best,if the disease names are MeSH term.)
Thank you!

Veleno · 05-17-2012, 01:47 AM

try this http://robosnp.org/

Richard Finney · 05-17-2012, 04:54 AM

The GWAS catalog from NIH might have what you're looking for:

http://www.genome.gov/gwastudies/

Tab delimited text file is here : http://www.genome.gov/admin/gwascatalog.txt

Example :
-bash-3.00$ head -1 gwascatalog.txt | cut -f12,13,14,15
Chr_id Chr_pos Reported Gene(s) Mapped_gene
-bash-3.00$ grep -i lupus gwascatalog.txt | cut -f12,13,14,15 | head
4 109046960 LEF1 LEF1
4 87958395 AFF1 AFF1
8 11343973 BLK FAM167A - BLK
6 32605884 HLA-DR3 HLA-DQA1
22 21939675 UBE2L3 UBE2L3
1 53629585 SLC1A7 SLC1A7 - CPT2
1 189723623 Intergenic RPS3AP9 - FAM5C
7 128617466 IRF5 TNPO3
2 181513729 Intergenic CWC22 - FTHL20

jialovelyjia · 05-17-2012, 05:21 PM

Quote:

Originally Posted by Veleno

try this http://robosnp.org/

Thank you for your answer!
I have tried the website,but I can't find the snps which are associated with autoimmune diseases.Do I use it wrongly?

jialovelyjia · 05-17-2012, 06:50 PM

Quote:

Originally Posted by Richard Finney

The GWAS catalog from NIH might have what you're looking for:

http://www.genome.gov/gwastudies/

Tab delimited text file is here : http://www.genome.gov/admin/gwascatalog.txt

Example :
-bash-3.00$ head -1 gwascatalog.txt | cut -f12,13,14,15
Chr_id Chr_pos Reported Gene(s) Mapped_gene
-bash-3.00$ grep -i lupus gwascatalog.txt | cut -f12,13,14,15 | head
4 109046960 LEF1 LEF1
4 87958395 AFF1 AFF1
8 11343973 BLK FAM167A - BLK
6 32605884 HLA-DR3 HLA-DQA1
22 21939675 UBE2L3 UBE2L3
1 53629585 SLC1A7 SLC1A7 - CPT2
1 189723623 Intergenic RPS3AP9 - FAM5C
7 128617466 IRF5 TNPO3
2 181513729 Intergenic CWC22 - FTHL20

Thank you for your answer!
I have tried the website,but the snps on it are same as those which are on the HuGE Navigator.In addition,I want to find snps instead of genes.

jialovelyjia · 05-20-2012, 06:08 PM

I can't find more disease associated snps.Could somebody help me?Thank you!

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05-17-2012, 01:22 AM	#1
jialovelyjia Junior Member Location: China Join Date: Sep 2010 Posts: 6	disease associated snp I want to find SNPs which are associated with autoimmune disease.I have searched the HuGE Navigator,but there are only some kinds of autoimmune diseases which have associated snps.Could someone tell me some databases or teach me some approaches to solute my problem?(It is the best,if the disease names are MeSH term.) Thank you!

05-17-2012, 01:47 AM	#2
Veleno Member Location: UK Join Date: Aug 2011 Posts: 15	try this http://robosnp.org/

05-17-2012, 04:54 AM	#3
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 410	The GWAS catalog from NIH might have what you're looking for: http://www.genome.gov/gwastudies/ Tab delimited text file is here : http://www.genome.gov/admin/gwascatalog.txt Example : -bash-3.00$ head -1 gwascatalog.txt \| cut -f12,13,14,15 Chr_id Chr_pos Reported Gene(s) Mapped_gene -bash-3.00$ grep -i lupus gwascatalog.txt \| cut -f12,13,14,15 \| head 4 109046960 LEF1 LEF1 4 87958395 AFF1 AFF1 8 11343973 BLK FAM167A - BLK 6 32605884 HLA-DR3 HLA-DQA1 22 21939675 UBE2L3 UBE2L3 1 53629585 SLC1A7 SLC1A7 - CPT2 1 189723623 Intergenic RPS3AP9 - FAM5C 7 128617466 IRF5 TNPO3 2 181513729 Intergenic CWC22 - FTHL20

05-20-2012, 06:08 PM	#6
jialovelyjia Junior Member Location: China Join Date: Sep 2010 Posts: 6	I can't find more disease associated snps.Could somebody help me?Thank you!