========================================================================== JSNP data Flat File ========================================================================== URL : ftp://ftp.hgc.jp/pub/hgc/db/snp/ -- JSNP Rel.42 was released May 8, 2014 - IMS-JST SNP Database (JSNP) Release 42 was released. Release 42 consists of 197,195 SNPs. rsID numbers are based on NCBI's dbSNP build 139. - Release 42 consists of 84,651 SNPs with allele frequency data. -- JSNP Rel.41 was released March 27, 2013 - IMS-JST SNP Database (JSNP) Release 41 was released. Release 41 consists of 197,195 SNPs. rsID numbers are based on NCBI's dbSNP build 137. - Release 41 consists of 84,651 SNPs with allele frequency data. -- JSNP Rel.40 was released April 4, 2012 - IMS-JST SNP Database (JSNP) Release 40 was released. Release 40 consists of 197,195 SNPs. rsID numbers are based on NCBI's dbSNP build 135. - Release 40 consists of 84,651 SNPs with allele frequency data. -- JSNP Rel.39 was released October 14, 2011 - IMS-JST SNP Database (JSNP) Release 39 was released. Release 39 consists of 197,195 SNPs. rsID numbers are based on NCBI's dbSNP build 134. - Release 39 consists of 84,651 SNPs with allele frequency data. -- JSNP Rel.38 was released October 18, 2010 - IMS-JST SNP Database (JSNP) Release 38 was released. Release 38 consists of 197,195 SNPs. rsID numbers are based on NCBI's dbSNP build 131. - Release 38 consists of 84,651 SNPs with allele frequency data. -- JSNP Rel.37 was released November 26, 2009 - IMS-JST SNP Database (JSNP) Release 37 was released. Release 37 consists of 197,195 SNPs. rsID numbers are based on NCBI's dbSNP build 130. - Release 37 consists of 84,651 SNPs with allele frequency data. - Release 37 was released without new ftp files. -- JSNP Rel.36 was released August 11, 2009 - IMS-JST SNP Database (JSNP) Release 36 was released. Release 36 consists of 197,195 SNPs. rsID numbers are based on NCBI's dbSNP build 130. - Release 36 consists of 84,651 SNPs with allele frequency data. -- JSNP Rel.35 was released October 28, 2008 - IMS-JST SNP Database (JSNP) Release 35 was released. Release 35 consists of 197,195 SNPs. rsID numbers are based on NCBI's dbSNP build 129. - Release 35 consists of 84,651 SNPs with allele frequency data. -- JSNP Rel.33 was released April 21, 2008 - IMS-JST SNP Database (JSNP) Release 33 was released. Release 33 consists of 197,195 SNPs. rsID numbers are based on NCBI's dbSNP build 128. - Release 33 consists of 84,651 SNPs with allele frequency data. - FTP data format for allele frequency data was changed. dbSNP ss number and dbSNP rs number were added. -- JSNP Rel.32 was released October 31, 2007 - The JSNP550typed is released. This new dataset consists of 515,286 SNPs with genotyping information participated by 934 Japanese volunteers. - The data download has been available on http://snp.ims.u-tokyo.ac.jp/map/cgi-bin/downloadTypingData.cgi -- JSNP Rel.31 was released June 25, 2007 - IMS-JST SNP Database (JSNP) Release 31 was released. Release 31 consists of 197,157 SNPs. rsID numbers are based on NCBI's dbSNP build 127. - Release 31 consists of 84,618 SNPs with allele frequency data. Release Date : January 11, 2007 -- JSNP Rel.30 was released January 11, 2007 - IMS-JST SNP Database (JSNP) Release 30 was released. Release 30 consists of 197,157 SNPs. rsID numbers are based on NCBI's dbSNP build 126. - Allele frequency flat file was the same as in release 25. Release Date : September 5, 2006 -- JSNP Rel.29 was released September 5, 2006 - IMS-JST SNP Database (JSNP) Release 29 was released. Release 29 consists of 197,157 SNPs. rsID numbers are based on NCBI's dbSNP build 126. - Allele frequency flat file was the same as in release 25. Release Date : May 30, 2006 -- JSNP Rel.28 was released May 30, 2006 - IMS-JST SNP Database (JSNP) Release 28 was released. Release 28 consists of 197,157 SNPs. - Allele frequency flat file was the same as in release 25. -- JSNP Rel.27 was released January 11, 2006 - IMS-JST SNP Database (JSNP) Release 27 was released. Release 27 consists of 197,151 SNPs. - Allele frequency flat file was the same as in release 25. -- JSNP Rel.26 was released November 17, 2005 - IMS-JST SNP Database (JSNP) Release 26 was released. Release 26 consists of 197,151 SNPs. rsID numbers are based on NCBI's dbSNP build 125. - Allele frequency flat file was the same as in release 25. Release Date : September 7, 2005 -- JSNP Rel.25 was released September 7, 2005 - IMS-JST SNP Database (JSNP) Release 25 was released. Release 25 consists of 195,151 SNPs. rsID numbers are based on NCBI's dbSNP build 124. - Release 25 consists of 84,612 SNPs with allele frequency data. - The allele frequency flat file's name and its data format have been changed. Panel_ID was added following JSNP_ID. Release Date : May 16, 2005 -- JSNP Rel.24 was released May 16, 2005 - IMS-JST SNP Database (JSNP) Release 24 was released. Release 24 consists of 195,134 SNPs. rsID numbers are based on NCBI's dbSNP build 124. - Allele frequency flat file was the same as in release 23. Release Date : November 25, 2004 -- JSNP Rel.23 was released November 25, 2004 - IMS-JST SNP Database (JSNP) Release 23 was released. Release 23 consists of 195,134 SNPs. rsID numbers are based on NCBI's dbSNP build 123. - Release 23 consists of 84,599 SNPs with allele frequency data. Release Date : September 15, 2004 -- JSNP Rel.22 was released September 15, 2004 - IMS-JST SNP Database (JSNP) Release 22 was released. Release 22 consists of 195,059 SNPs. rsID numbers are based on NCBI's dbSNP build 122. - Allele frequency flat file was the same as in release 19. Release Date : May 20, 2004 -- JSNP Rel.21 was released May 20, 2004 - IMS-JST SNP Database (JSNP) Release 21 was released. Release 21 consists of 195,059 SNPs. rsID numbers are based on NCBI's dbSNP build 120. - Allele frequency flat file was the same as in release 19. Release Date : Mar 31, 2004 -- JSNP Rel.20 was released Mar 31, 2004 - IMS-JST SNP Database (JSNP) Release 20 was released. Release 20 consists of 195,059 SNPs. - Allele frequency flat file was the same as in release 19. Release Date : Dec 3, 2003 -- JSNP Rel.19 was released Dec 3, 2003 - IMS-JST SNP Database (JSNP) Release 19 was released. Release 19 consists of 195,059 SNPs. - Release 19 consists of 84,566 SNPs with allele frequency data. Release Date : July 31, 2003 -- JSNP Rel.18 was released July 31, 2003 - IMS-JST SNP Database (JSNP) Release 18 was released. Release 18 consists of 195,059 SNPs. - Release 18 consists of 84,560 SNPs with allele frequency data. Release Date : May 30, 2003 -- JSNP Rel.17 was released May 30, 2003 - IMS-JST SNP Database (JSNP) Release 17 was released. Release 17 consists of 195,059 SNPs. - Release 17 consists of 84,557 SNPs with allele frequency data. Release Date : Mar 12, 2003 -- JSNP Rel.16 was released Mar 12, 2003 - IMS-JST SNP Database (JSNP) Release 16 was released. Release 16 consists of 194,393 SNPs. - Allele frequency flat file was the same as in release 14. -- JSNP Rel.15 was released Jan 23, 2003 - IMS-JST SNP Database (JSNP) Release 15 was released. Release 15 consists of 194,393 SNPs. - Allele frequency flat file was the same as in release 14. -- JSNP Rel.14 was released Dec 25, 2002 - IMS-JST SNP Database (JSNP) Release 14 was released. Release 14 consists of 194,393 SNPs. - Release 14 consists of 78,570 SNPs with allele frequency data. -- JSNP Rel.13 was released Oct 21, 2002 - IMS-JST SNP Database (JSNP) Release 13 was released. Release 13 consists of 193,037 SNPs. - Allele frequency flat file was the same as in release 11. -- JSNP Rel.12 was released Oct 1, 2002 - IMS-JST SNP Database (JSNP) Release 12 was released. Release 12 consists of 190,562 SNPs which were the same as in release 11. - Allele frequency flat file was the same as in release 11. -- JSNP Rel.11 was released Jul 17, 2002 - IMS-JST SNP Database (JSNP) Release 11 was released. Release 11 consists of 190,562 SNPs. - Allele frequency flat file was added. This file provides a list of JSNP ID with allele frequency. Release 11 consists of 78,570 SNPs with allele frequency data. -- JSNP Rel.10 was released Mar 26, 2002 - IMS-JST SNP Database (JSNP) Release 10 was released. Release 10 consists of 164,117 SNPs. -- JSNP Rel.9 was released Jan 23, 2002 - IMS-JST SNP Database (JSNP) Release 9 was released. Release 9 consists of 151,727 SNPs. -- JSNP Rel.8 was released Oct 11, 2001 - IMS-JST SNP Database (JSNP) Release 8 was released. Release 8 consists of 117,427 SNPs. -- JSNP Rel.7 was released Aug 9, 2001 - IMS-JST SNP Database (JSNP) Release 7 was released. Release 7 consists of 104,192 SNPs. - FTP data format was changed. Additional data was added into defline as dbSNP ss number and dbSNP rs number. -- JSNP Rel.6 was released Jun 11, 2001 - IMS-JST SNP Database (JSNP) Release 6 was released. Release 6 consists of 77,141 SNPs. -- JSNP Rel.5 was released Mar 30, 2001 - IMS-JST SNP Database (JSNP) Release 5 was released. Release 5 consists of 56,332 SNPs. -- JSNP Rel.4 was released Dec 26, 2000 - IMS-JST SNP Database (JSNP) Release 4 was released. Release 4 consists of 34,064 SNPs. -- JSNP Rel.3 was released Oct 20, 2000 - IMS-JST SNP Database (JSNP) Release 3 was released. Release 3 consists of 22,882 SNPs. -- JSNP Rel.2 was released Aug 10, 2000 - IMS-JST SNP Database (JSNP) Release 2 was released. Release 2 consists of 10,131 SNPs. - FTP data format was changed. Additional data was added into defline as comment_type which mainly contains repeat sequence information in SNP and flanking sequence. -- JSNP Rel.1 was released Jul 7, 2000 - IMS-JST SNP Database (JSNP) Release 1 was released. Release 1 consists of 6,830 SNPs. ========================================================================== -------------- FASTA sequence -------------- This format provides the flanking sequence for each report of variations in IMS-JST SNP DB. This data format is typically used for BLAST applications. File Notes --------------- ---------------------------------------- imsSNP140508.fas Contains SNP sequences in FASTA format imsSNP140508.fas.gz Compressed by GNU zip archive of the SNP file imsSNP140508.fas.Z Compressed archive of the SNP file imsIND140508.fas Contains INS/DEL variation sequences in FASTA format imsIND140508.fas.gz Compressed by GNU zip archive of the INS/DEL file imsIND140508.fas.Z Compressed archive of the INS/DEL file *** FASTA format and data structure *** SNP Example ; >gnl|JSNP_SNP|IMS-JST000001 allelePos=61 total len=121|AB001517.1 Pos=2580||TMEM1|2924062|2020943|| CAAGTCCTGG TCATCCCCAG CCAAGATGAC CACGTCCTGG AAGTCAGTGT AACATGACAA Y GCCAGGGTGA ACACACGCCA CTTCCCAGCT AGGAGTGCAC TTTATGGGAC TGTGACTGGA SNP Structure ; 1st line (define for FASTA records) ; >(object_type=general)|(database name)|(IMS-JST_SNP DB ID) (offset of SNP in sequence) (total length of sequence)|(Accession No._version No.) (offset of SNP in record)|(comment_type)|(gene symbol) |(dbSNP ss number) |(dbSNP rs number)|(JSNP previous ID)|(JSNP reference ID) (JSNP reference ID) "comment_type" represents following contents : comment_type Notes -------------- ----------------------------------------------- 1 SNP is present in repeat sequence 2 repeat sequence exists in flanking sequence "gene symbol" is derived from LocusLink, Genbank and Unigene for additional information of the position where the SNP was found. 2nd line ; 5' flanking sequence 3rd line ; variation (The appropriate IUPAC nucleotide ambiguity letter is applied.) 4th line ; 3' flanking sequence INS/DEL Example; >gnl|JSNP_InsDel_MIC|IMS-JST078455_Major allelePos=60^61 total len=120|AC000041.1 Pos=15852^15853|2||4477854|3216870|| GGACTAGGCT GGTTGAGAAT CTGGATTTCT GACACACACT CACACACACA CACACACACA TACACACAAA TTTTTTTGAG ATGTGGTTTC ATGTTGCCCA GATTGGTCTC AAATTCCTCA >gnl|JSNP_InsDel_MIC|IMS-JST078455_Minor allelePos=61..62 total len=122|AC000041.1 Pos=15852^15853|2||4477854|3216870|| GGACTAGGCT GGTTGAGAAT CTGGATTTCT GACACACACT CACACACACA CACACACACA CA TACACACAAA TTTTTTTGAG ATGTGGTTTC ATGTTGCCCA GATTGGTCTC AAATTCCTCA INS/DEL Structure; >(object_type=general)|(database datatype)|(JSNP ID)_(Major/Minor) (offset of INS/DEL in sequence) (total length of sequence)|(Accession No._version No.) (offset of INS/DEL in record)|(comment_type)|(gene symbol)|(dbSNP ss number) |(dbSNP rs number)|(JSNP previous ID)|(JSNP reference ID) (JSNP reference ID) In "database datatype", if the INS/DEL type is microsatellite, "JSNP_InsDel_MIC" is shown here. The other is JSP_InsDel_IND. In "offset of INS/DEL in sequence", "^" shows the position where the base(s) is (are) present in another allele sequence and ".." shows the position where the base(s) is (are) absent there. In "offset of INS/DEL in record", "^" shows the position where the base(s) is (are) present in the following sequence and ".." shows the position where the base(s) is (are) absent there. "comment_type" represents following contents : comment_type Notes -------------- ----------------------------------------------- 1 INS/DEL is present in repeat sequence 2 repeat sequence exists in flanking sequence "gene symbol" is derived from LocusLink, Genbank and Unigene for additional information of the position where the SNP was found. 2nd line ; 5' flanking sequence 3rd line ; The extra base(s) is shown in the longer sequence, as this line is omitted for the shorter sequence. 4th line ; 3' flanking sequence =============================================================================== ---------------- Allele frequency ---------------- This file provides a list of JSNP ID with Panel_ID and allele frequency data. Output is a tab-delimited report with the format: JSNP-ID Panel_ID allele-1 allele-2 allele-1_frequency allele-2_frequency the number of chromosomes examined dbSNP ss number dbSNP rs number ------- -------- -------- -------- ------------------ ------------------ ---------------------------------- --------------- --------------- File Notes ---------------------- ------------------------------ alleleFreq140508.txt Contains allele frequencies in txt format alleleFreq140508.txt.gz Compressed by GNU zip archive of the allele frequncy file alleleFreq140508.txt.Z Compressed archive of the allele frequency file *** Panel_ID list *** POP_J 24 anonymous unrelated Japanese individuals POP_J_RIKENSNPRC 48 anonymous unrelated Japanese individuals JBIC-allele 752 anonymous unrelated Japanese volunteers RIKEN-allele 893 anonymous unrelated Japanese volunteers POP_101 40 Japanese genomic DNA obtained from PBMCs (Peripheral blood mononuclear cells) POP_102 144 unrelated Japanese volunteers with rheumatoid arthritis under informed consent POP_103 16 unrelated Japanese volunteers with adult-onset Still's disease under informed consent POP_104 92 healthy unrelated Japanese volunteers under informed consent RIKEN_japanese_normal_weight 711 unrelated japanese normal weight volunteers ( body mass index <= 25kg/m2 ) RIKEN_japanese_obese 796 unrelated japanese obese patients ( body mass index >= 30kg/m2 ) =============================================================================== ---------------- Amended entries ---------------- These files provide lists of JSNP IDs which have amended in release 27. File Notes ---------------------- ------------------------------ FTPamended060111.txt Contains JSNP IDs amended in the ftp files XMLamended060111.txt Contains JSNP IDs amendes in the XML files based on Screened information