Data detail |
| info Data name | Screening Information |
| info DOI | 10.18908/lsdba.nbdc00114-003 |
| 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
|
| info Simple search URL | http://togodb.biosciencedbc.jp/togodb/view/jsnp_screen#en |
| 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 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 |
|