About This Database

Allele Frequency Data

Data description

Data name

DOI

10.18908/lsdba.nbdc00042-001

Description of data contents

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

Data file

File name :

dbqsnp_frequency.zip

File URL :

https://dbarchive.biosciencedbc.jp/data/dbqsnp/LATEST/dbqsnp_frequency.zip

File size :

159 KB

Simple search URL

http://togodb.biosciencedbc.jp/togodb/view/dbqsnp_frequency#en

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 unpublished) and lupus erythematosus patients were also included (Miyagawa et al. 2008; Sakaguchi et al. unpublished).

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.

Number of data entries

16,503 entries

Data detail

Data item	Description
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