Get the snp id (rs) from the name of genes

Question

[Ahmed]

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.

Answer 1

[Pierre Lindenbaum]

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 |
+-------+-------+--------------+------------+----------+

[Ahmed]

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

[Pierre Lindenbaum]

any mysql driver for python or R...

Answer 2

[GenoMax]

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