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Life Science Database Archive
JSNP

Screening Information

Data detail

info Data name Screening Information
info DOI 
info 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 .

info Data file 
File name:
jsnp_screen.zip
File URL:
https://dbarchive.biosciencedbc.jp/data/jsnp/LATEST/jsnp_screen.zip
File size:
15.6 MB
info Simple search URL 
info 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.

info Data analysis method 

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

info Number of data entries 

197,195 entries

Data itemDescription
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