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Data description
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Data name
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Integrated List
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DOI
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10.18908/lsdba.nbdc00114-005
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Description of data contents
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List of data from "Mapping Information" and "Screening Information" put together every polymorphism (unless the polymorphism is mapped on two or more chromosomes).
Derived from "Show List by Chromosome" of "Show List of SNPs" http://snp.ims.u-tokyo.ac.jp/search_list.html .
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Data file
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File name :
jsnp_list.zip
File URL :
File size :
17.9 MB
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Simple search URL
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http://togodb.biosciencedbc.jp/togodb/view/jsnp_list#en
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Data acquisition method
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From "Screening Information" and"Mapping Information"
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Data analysis method
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-
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Number of data entries
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198,236 entries
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Data detail
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Data item
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Description
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| JSNP ID |
JSNP ID |
| Chromosome |
Chromosome number |
| Location |
cytogenetic band |
| Evidence of Location |
information source of cytogenic band
- GenBank "/chromosome" and "/map"
- EntrezGene "CHR" and "MAP"
- UniGene "CHROMOSOME" and "CYTOBAND" |
| In Gene |
Type of gene region
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 |
| Mapping Accession |
accession No. of the mapped sequence |
| Mapping Position |
position of the polymorphism in the mapped sequence |
| Mapping Symbol |
gene name relevant to the mapped sequence |
| Mapping OMIM-ID |
OMIM ID relevant to the mapped 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 relevant to the sequence for polymorphism screening |
| Screened OMIM-ID |
OMIM ID relevant to the sequence for polymorphism screening |
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