Hi Ivan, The only difference in the table between these two SNPs is the strand orientation. We obtain the rsIDs and genomic locations directly from dbSNP, who considers both of these SNPs valid (http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3871692 and http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs62635282).
Feel free to contact dbSNP at snp-admin at ncbi.nlm.nih.gov if you have any questions about these SNPs. I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary --------------------- Mary Goldman UCSC Bioinformatics Group On 6/11/10 10:31 PM, Ivan Adzhubey wrote: > Hi, > > I found about 3% of SNPs in hg19.snp131 table have exactly identical > annotations (chromosome, position, observed alleles, etc) except for different > rsIDs. An example is listed below. Is this a bug or a feature? > > Thanks, > Ivan > > mysql> select * from snp131 where chrom='chr1' and chromStart=12197 and > chromEnd=12198\G > *************************** 1. row *************************** > bin: 585 > chrom: chr1 > chromStart: 12197 > chromEnd: 12198 > name: rs3871692 > score: 0 > strand: - > refNCBI: G > refUCSC: G > observed: C/G > molType: genomic > class: single > valid: unknown > avHet: 0 > avHetSE: 0 > func: missense > locType: exact > weight: 3 > *************************** 2. row *************************** > bin: 585 > chrom: chr1 > chromStart: 12197 > chromEnd: 12198 > name: rs62635282 > score: 0 > strand: + > refNCBI: G > refUCSC: G > observed: C/G > molType: genomic > class: single > valid: unknown > avHet: 0 > avHetSE: 0 > func: missense > locType: exact > weight: 3 > 2 rows in set (3.52 sec) > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
