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Life Science Database Archive
dbQSNP

Allele Frequency Data

Data detail

info Data name Allele Frequency Data
info DOI 
info Description of data contents 

SNP allele frequencies in Japanese and European populations, determined by quantitative fluorescent PCR-SSCP analysis of pooled DNA.

info Data file 
File name:
dbqsnp_frequency.zip
File URL:
https://dbarchive.biosciencedbc.jp/data/dbqsnp/LATEST/dbqsnp_frequency.zip
File size:
159 KB
info Simple search URL 
info Data acquisition method 

Most of SNPs described here were initially collected by Sanger sequencing of transcription start sites (TSSs) of 8 randomly picked Japanese. Short fragments harboring the SNPs were further analyzed for their allele frequencies in several populations using quantitative fluorescent PCR-SSCP analysis of pooled DNA samples (Kukita et al. 2002; Baba et al. 2003: Tahira et al. 2005). A part of the results of association study of breast cancer patients (Miyagi et al. unpublished) and lupus erythematosus patients were also included (Miyagawa et al. 2008; Sakaguchi et al. unpublished).

info Data analysis method 

Data analysis of fluorescent SSCP analysis was performed using QUISCA software that was integrated in dbQSNP system (Higasa et al. 2002; Sasaki et al. 2001; Tahira et al. 2005). SNPs in dbQSNP were submitted to dbSNP of NCBI under the handle name of KYUGEN, and refSNP ID #s were identified or given.

info Number of data entries 

16,503 entries

Data itemDescription
dbQSNP_id dbQSNP ID.
strand Orientation of the STS compared with contig sequence of GenBank (NT sequence, NCBI Build 36) . Note that SNPs are always described as sequences in forward strand of the STS.
contig_id ID of genomic contigs that showed highest homology to the STS (NT sequence, NCBI Build 36)
rs# dbSNP accession for the refSNP (dbSNP Build 128)
allele_1 sequence of allele 1
allele_2 sequence of allele 2
AF_allele_1 allele frequency of allele 1
AF_allele_2 allele frequency of allele 2
pool_id ID of pooled DNA (see below, DNA samples were extracted from peripheral blood lymphocytes)
"CAU200", prepared from Caucasian Panel of 200, obtained from CORIELL (HD200, https://www.coriell.org) was used as the Caucasian pool in a large part of this study. "CP" (combined CEPH parents, prepared by us from 45 CEPH core family collection) and "COP" (HD100 from CORIELL) were also used.

"JSA426", prepared from DNA derived from apparently healthy individuals enrolled at Kyushu area was used as the Japanese pool in a large part of study. Other pools derived from healthy individuals enrolled at various area of Japan were also used. Those were; JPK, JPK2, JPK3, JCM253, NCEP, NCL_P, NCP269, NCE_SP and JNCL_SP.

The allele frequency data of pools derived from breast cancer patients (BREP, BRLP, JBRE_SP, JBRL_SP) and pools derived from systemic lupus erythematosus patients (SLEP264, SLEP183), obtained in association studies of each diseases, are also included
#individual The number of individuals in the pool