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About This Database

Screening Information

Data description
Data name
Screening Information
DOI
10.18908/lsdba.nbdc00114-003
Description of data contents
Information from polymorphism screening experiments. Derived from "Each Type of variation Found in Location in Gene" in "Data Contributions" http://snp.ims.u-tokyo.ac.jp/data_roots.html .
Data file
File name :
jsnp_screen.zip
File URL :
File size :
15.6 MB
Simple search URL
http://togodb.biosciencedbc.jp/togodb/view/jsnp_screen#en
Data acquisition method

Exons, promotor regions and introns selected from human genomic sequences in GenBank and RefSeq were PCR amplified using DNA from 24 (IMS-JST), 48 (RIKEN) or 40 (TJWU) individuals as templates, and sequenced with capillary sequencers.

Data analysis method

PolyPhred was used to assist verification of SNPs by eye inspection.

Number of data entries

197,195 entries

Data detail
Data item Description
JSNP ID

JSNP ID

In Gene

type of gene region where the polymorphism

promoter*1: annotated in GenBank entries
promoter*2: predicted by GENSCAN
promoter*3: putative promoter (1.5kb upstream of the initiation position of mRNA records in the RefSeq)
CDS*1: annotated in GenBank entries either positively or passively
CDS*2: predicted by GENSCAN
CDS*3: extracted by homology search with cDNA
exon*1: annotated in GenBank entries either positively or passively
exon*3: extracted by homology search with mRNA/cDNA/Unigene records
intron*1: annotated in GenBank entries or intervened by Exon*1 and CDS*1
intron*2: intervened by CDS*2
intron*3: intervened by exon*3 and CDS*3
others: surrounding regions of genes

Type

type of polymorphisms

SNP: single nucleotide polymorphism
IND: insertion/deletion
MIC: microsatelite

Frequencies

minor allele frequencies in dbSNP; number in brackets means JSNP original allele frequency

allele

allele observed

dbSNP ss#

dbSNP ss (submitted SNP) number assigned

dbSNP rs#

dbSNP rs (reference SNP) number assigned

HGVbase-ID

ID in HGCbase

5' assay

5' flanking sequence

3' assay

3' flanking sequence

Screened Accession

accession No. of the sequence for polymorphism screening

Screened Position

position of the polymorphism in the sequence for polymorphism screening

Screened Symbol

gene name related to the sequence for polymorphism screening

Screened OMIM-ID

OMIM ID related to the sequence for polymorphism screening