Get the snp id (rs) from the name of genes
2
0
Entering edit mode
7 weeks ago
Ahmed • 0

I have a list of genes and I want to see all available SNP related to those genes. so I need to get the SNP ID (rs) from the gene name by using python or R.

snp rs gene • 385 views
ADD COMMENT
1
Entering edit mode
7 weeks ago

using mysql/ucsc

$ mysql  -h  genome-mysql.cse.ucsc.edu -A -u genome -D hg19 -e 'select distinct G.chrom,N.value,S.name,S.chromStart,S.chromEnd from ensemblToGeneName as N,ensGene as G,snp151 as S where G.name= N.name and N.value="SCN5A" and S.chrom=G.chrom and NOT(S.chromEnd <= G.txStart OR S.chromStart>=G.txEnd) limit 10'
+-------+-------+--------------+------------+----------+
| chrom | value | name         | chromStart | chromEnd |
+-------+-------+--------------+------------+----------+
| chr3  | SCN5A | rs1048869186 |   38589554 | 38589555 |
| chr3  | SCN5A | rs1364237131 |   38589555 | 38589556 |
| chr3  | SCN5A | rs34095914   |   38589561 | 38589561 |
| chr3  | SCN5A | rs756210830  |   38589562 | 38589563 |
| chr3  | SCN5A | rs1318679164 |   38589570 | 38589571 |
| chr3  | SCN5A | rs887720794  |   38589571 | 38589572 |
| chr3  | SCN5A | rs41258455   |   38589581 | 38589582 |
| chr3  | SCN5A | rs1383871535 |   38589584 | 38589585 |
| chr3  | SCN5A | rs1399904090 |   38589588 | 38589589 |
| chr3  | SCN5A | rs913120201  |   38589591 | 38589592 |
+-------+-------+--------------+------------+----------+
ADD COMMENT
0
Entering edit mode

Thanks , is there any python or R package does this?

ADD REPLY
0
Entering edit mode

any mysql driver for python or R...

ADD REPLY
1
Entering edit mode
7 weeks ago
GenoMax 110k

Using EntrezDirect:

$ esearch -db snp -query "SCN5A [GENE] AND human [orgn]" | esummary | xtract -pattern DocumentSummary -element CHR,NAME,SNP_ID,CHRPOS 
3   SCN5A   2089406557  3:38641066
3   SCN5A   2077235231  3:38610317
3   SCN5A   2074172389  3:38618406
3   SCN5A   2065689680  3:38581366
3   SCN5A   2062935810  3:38651659
ADD COMMENT

Login before adding your answer.

Traffic: 2471 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6