|
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 |
|