About This Database

Allele Frequency

Data description

Data name

Allele Frequency

DOI

10.18908/lsdba.nbdc00114-002

Description of data contents

Polymorphism allele frequencies in Japanese. Out of 84651 polymorphisms, 13 and 39 SNPs are assayed in three (POP_*) and two (RIKEN_japanese_*) panels, respectively. Derived from "Flat files" ftp://ftp.hgc.jp/pub/hgc/db/snp/alleleFreq140508.txt

Data file

File name :

jsnp_allele_freq.zip

File URL :

https://dbarchive.biosciencedbc.jp/data/jsnp/LATEST/jsnp_allele_freq.zip

File size :

1.4 MB

Simple search URL

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

Data acquisition method

Multiplex PCR were done using the same primers as those for polymorphism screening, and templates from Japanese shown in Panel_ID description. Genotypes were determined with the invader assay (JBIC-allele and RIKEN_japanese_*), TaqMan assay (RIKEN-allele) or direct sequencing / allelic discrimination chemistries / restriction enzyme genotyping (POP_*).

Data analysis method

Number of data entries

84,716 entries

Data detail

Data item	Description
JSNP ID	JSNP ID
Panel_ID	ID of the pool of Japanese individuals where the frequency was examined JBIC-allele - 752 anonymous unrelated Japanese volunteers RIKEN-allele - 893 anonymous unrelated Japanese volunteers POP_102 - 144 unrelated Japanese volunteers with rheumatoid arthritis under informed consent POP_103 - 16 unrelated Japanese volunteers with adult-onset Still's disease under informed consent POP_104 - 92 healthy unrelated Japanese volunteers under informed consent RIKEN_japanese_normal_weight - 711 unrelated japanese normal weight volunteers ( body mass index <= 25kg/m2 ) RIKEN_japanese_obese - 796 unrelated japanese obese patients ( body mass index >= 30kg/m2 )
dbSNP ss#	dbSNP ss (submitted SNP) number assigned
dbSNP rs#	dbSNP rs (reference SNP) number assigned
allele-1	allele-1
allele-2	allele-2
allele-1 frequency	allele-1 frequency
allele-2 frequency	allele-2 frequency
the number of chromosomes examined	the number of chromosomes where the frequency was examined (sample size)