How To Get Chromosome Position Given Rs Number?

Calendar 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.