The PCR and SNP primer(s) information provided in the database are based on human reference SNPs defined by NCBI based on the release, Build 103. There are nearly 1.7 million defined rsSNPs in this database. The database is searchable currently only by using the assigned “rs” number for a given SNP. Please refer to the NCBI dbSNP website for more information and obtaining the rs number: http://www.ncbi.nlm.nih.gov/SNP/index.html

*CLICK HERE TO SEARCH THE SNP DATABASE BY RS NUMBER

 

1 159,892 2 126,105 3 109,680 4 96,953 5 1263,161 6 120,786 7 62,011 8 85,252 9 71,845 10 88,344 11 100,449 12 75,554 13 64,740 14 55,135 15 32,959 16 49,017 17 42,886 18 53,485 19 31,303 20 38,215 21 39,286 22 26,128 X 38,571 Y 1,083 TOTAL 1695,870

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This database is provided solely as a research tool and no commercial exploitation of the information is permitted. This information is provided at no charge and will remain freely available. The information here was kindly provided by Dr. Pui-Yan Kwok and associates. Primer design was accomplished using a method similar to that published recently by Vieux, E.F., Kwok, P-Y and Miller, R. D. in BioTechniques (June 2002) Vol. 32. Supplement: “SNPs: Discovery of Marker Disease, ppgs. 28-32, with the following specifications:

Parameter	Criteria
TARGET	SNP_POSITION, 20
PRIMER_OPT_SIZE	23
PRIMER_MAX_SIZE	26
PRIMER_MIN_SIZE	20
PRIMER_OPT_TM	55
PRIMER_MAX_TM	56
PRIMER_MIN_TM	54
PRIMER_PRODUCT_SIZE_RANGE	80 - 300
PRIMER_PRODUCT_OPT_SIZE	250
PRIMER_PAIR_WT-PRODUCT_SIZE_LT	0.2
PRIMER_PAIR_WT-PRODUCT_SIZE_GT	0.2
PRIMER_MIN_GC	20
PRIMER_MAX_GC	50
PRIMER_SALT_CONC	50
PRIMER_SELF_ANY	8
PRIMER_SELF_END	3
PRIMER_DNA_CONC	40
PRIMER_GC_CLAMP	0
PRIMER_MAX_END_STABILITY	8
PRIMER_EXPLAIN_FLAG	1
PRIMER_NUM_RETURN	1

In most cases both a forward and reverse SNP has been identified. In those cases, one of the two SNP primers is defined as the “preferred SNP primer” which should be tried first. As very few of these primers for rsSNPs, (currently numbering in the low 1,000’s) have actually been validated, it is recommended that both SNP primers be tried and validated for a given SNP. In many cases, one of the primers will clearly outperform the other primer and going forward only that primer need be used for future genotyping analyses.

As this is truly a research reference site, we would like to encourage users of this database to send an e-mail to snps@perkinelmer.com about both successes and failures of those sequences contained within. Any suggestions about how to improve this site and database utility would also be appreciated.

THIS DATABASE IS PROVIDED BY THE PERKINELMER LIFE SCIENCES “AS IS'” VIA SNPSCORING.COM AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PERKINELMER LIFE SCIENCES BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.