How To Get Chromosome Position Given Rs Number?

How To Get Chromosome Position Given Rs Number?

February 27, 2021
Application
primer design, multiplex PCR, Bioinformatics, SNP

Introduction #

We have a list of SNP rs numbers, like:

rs1002315756
rs1003815568
rs1004109382
rs1004635980
rs1008829651

And we want the genome positions for each SNPS, the results should like:

#chrom	chromStart	chromEnd	name	ref	altCount	alts	shiftBases	freqSourceCount	minorAlleleFreq	majorAllele	minorAllele	maxFuncImpact	class	ucscNotes	_dataOffset	_dataLen
chr1	51453	51454	rs1004109382	C	1	T,	0	0				0	snv	rareSome,rareAll,	409400514	36
chr1	51594	51599	rs1004635980	GGGGG	1	GGGG,	4	12	-inf,-inf,0.000127421,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,	,,GGGGG,,,,,,,,,,	,,GGGG,,,,,,,,,,	0	delins	rareSome,rareAll,overlapDiffClass,	461755619	105
chr1	10042	10043	rs1008829651	T	1	A,	0	0				1986	snv	rareSome,rareAll,	878656298	46
chr1	10320	10321	rs1002315756	C	1	T,	0	12	-inf,-inf,-inf,-inf,-inf,0.00102617,-inf,-inf,-inf,-inf,-inf,-inf,	,,,,,C,,,,,,,	,,,,,T,,,,,,,	1986	snv	rareSome,rareAll,overlapDiffClass,	230771761	107
chr1	52763	52764	rs1003815568	T	1	A,	0	0				0	snv	rareSome,rareAll,	380161821	36

Method #

UCSC Table Browser do this job perfectly, thanks.

  1. Visit: https://genome.ucsc.edu/cgi-bin/hgTables.
  2. On the “Table Browser” page, select proper parameters, as “Step 1” in the following picture shows. UCSC Table Browser first step
  3. Click “paste list” in red box labeled as “Step 2”, paste your rs number list as following picture shows, , then click “submit”. UCSC Table Browser second step
  4. Click “get output” labeled as “Step 3”.
  5. We get the genome positions as well as other information, done. UCSC Table Browser result