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Reference SNP (refSNP) Cluster Report: rs713598                 ** With drug-response allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS PheGenI
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/G (REV)
Allele Origin:C:germline
G:germline
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:With drug-response allele [ClinVar]
MAF/MinorAlleleCount:G=0.4459/54099 (ExAC)
C=0.4952/2480 (1000 Genomes)
G=0.4306/5600 (GO-ESP)
G=0.4628/58111 (TOPMED)
HGVS Names
  • CM000669.2:g.141973545C>G
  • NC_000007.13:g.141673345C>G
  • NC_000007.14:g.141973545C>G
  • NG_016141.1:g.5229G>C
  • NM_176817.4:c.145G>C
  • NP_789787.4:p.Ala49Pro
  • NW_003571040.1:g.115496C>G
Links
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' to see variant in the new NCBI variation viewer) back to top

  GeneView back to top

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Submitter records for this RefSNP Cluster back to top
The submission ss279562746 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs713598 during BLAST analysis for the current build.


NCBI
Assay ID
Handle|Submitter IDValidation
Status
ss to rs
Orientation
/Strand
Alleles5' Near Seq 30 bp3' Near Seq 30 bpEntry
Date
Update
Date
Build
Added
Molecule
Type
Freq
Warning
Ancestral
Allele
Success
Rate
ss22130TSC-CSHL|TSC0001741byFreqfwd/BC/Ggtgaatttttgggatgtagtgaagaggcagcactgagcaacagtgattgtgtgctgctgt09/06/0004/07/0486Genomic95 %
ss17154212CSHL-HAPMAP|CSHL-HuAA-200402.chr7.NT_007914.13_2264897rev/TC/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac02/17/0403/04/04120Genomicunknown
ss24483498PERLEGEN|afd1590235byFreqrev/TC/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac08/10/0409/13/04123Genomicunknown
ss44783818ABI|hCV8876467byFreqrev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac07/19/0511/03/06126Genomicunknown
ss65729202ILLUMINA|Human1-rs713598fwd/BC/Ggtgaatttttgggatgtagtgaagaggcagcactgagcaacagtgattgtgtgctgctgt10/10/0610/10/06127Genomicunknown
ss69030484PERLEGEN|PGP01590235byFreqrev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac01/30/0708/14/07127Genomicunknown
ss74808534AFFY|SNP_M-180610fwd/BC/Ggtgaatttttgggatgtagtgaagaggcagcactgagcaacagtgattgtgtgctgctgt08/09/0708/09/07128Genomicunknown
ss77737990HGSV|Cor12156_SNV_20070510.chr7_141126529rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac10/09/0710/14/07129Genomicunknown
ss93779282BCMHGSC_JDW|JWB-2384067rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac02/26/0803/05/08129Genomicunknown
ss105578894BGI|BGI_rs713598rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac09/10/0806/18/09130Genomicunknown
ss1125932961000GENOMES|CEU.trio.12.15.2008_1870300_chr7_141319814rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac12/17/0812/17/08130Genomicunknown
ss116349055ILLUMINA-UK|NA18507_000174284_NCBI36.1_chr7_141319814rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac01/16/0901/17/09130Genomic99 %
ss143028377ENSEMBL|ENSSNP7035176rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac06/05/0906/05/09131Genomicunknown
ss155604577GMI|GMI_SNP_125280058rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac06/24/0906/24/09131Genomicunknown
ss159715888SEATTLESEQ|TAS2R38-141319814rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac07/10/0907/10/09131Genomicunknown
ss160851236ILLUMINA|HumanOmni1-Quad_v1-0_B_rs713598-128_B_F_1562546526fwd/C/Ggtgaatttttgggatgtagtgaagaggcagcactgagcaacagtgattgtgtgctgctgt08/04/0910/04/09131Genomicunknown
ss162791450COMPLETE_GENOMICS|NA07022_36_chr7_141319814rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac09/28/0909/29/09132Genomicunknown
ss165558649COMPLETE_GENOMICS|NA19240_36_chr7_141319814rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac09/29/0909/30/09132Genomicunknown
ss198400233BUSHMAN|BUSHMAN-chr7-141319813rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac02/16/1003/06/10132Genomicunknown
ss207985013BCM-HGSC-SUB|BCM_CMT_1011-1460796rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac03/15/1003/19/10132Genomicunknown
ss2233761531000GENOMES|pilot_1_YRI_5185836_chr7_141319814rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac04/22/1004/22/10132Genomicunknown
ss2341996941000GENOMES|pilot_1_CEU_3804323_chr7_141319814rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac05/01/1005/01/10132Genomicunknown
ss2411059391000GENOMES|pilot_1_CHB+JPT_2991016_chr7_141319814rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac05/01/1005/01/10132Genomicunknown
ss244308110ILLUMINA|CVDSNP55v1_A_rs713598fwd/C/Ggtgaatttttgggatgtagtgaagaggcagcactgagcaacagtgattgtgtgctgctgt06/10/1006/10/10132Genomicunknown
ss275516291OMICIA|2010_April_001_099_TAS2R38_607751_0001rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac11/30/1008/29/12137Genomicunknown
ss279562746GMI|GMI_AK_SNP_3882993rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac12/16/1012/16/10137Genomicunknown
ss285733856GMI|GMI_NA10851_SNP_1746629rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac12/17/1012/17/10138Genomicunknown
ss290489992OMIM-CURATED-RECORDS|15176fwd/C/Ggtgaatttttgggatgtagtgaagaggcagcactgagcaacagtgattgtgtgctgctgt01/19/1101/19/11133Genomicunknown
ss293981219PJP|SNP_3487577_chr7_141319814rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac01/21/1101/21/11134Genomicunknown
ss342248500NHLBI-ESP|ESP2500-chr7-141673345byFreqrev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac03/25/1109/05/14134Genomicunknown
ss410946891ILLUMINA|Cardio-Metabo_Chip_11395247_A_rs713598fwd/C/Ggtgaatttttgggatgtagtgaagaggcagcactgagcaacagtgattgtgtgctgctgt06/07/1106/07/11135Genomicunknown
ss482483245ILLUMINA|HumanOmni1-Quad_v1-0_C_rs713598-131_B_F_1863410361rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa01/30/1208/28/15146Genomicunknown
ss483625861ILLUMINA|HumanOmni2.5-4v1_D_kgp5899594-0_B_R_1807900798fwd/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa01/30/1210/28/16137Genomicunknown
ss485364689ILLUMINA|HumanOmni2.5-4v1_B_SNP7-141319814-0_T_R_1632511169fwd/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa01/30/1210/29/16137Genomicunknown
ss4909558831000GENOMES|20110521_exome_463681_chr7_141673345rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac02/10/1202/21/12137Genomicunknown
ss491406769EXOME_CHIP|nonsyn_122995_chr_7_141673345rev/C/Gacagcagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaattcac03/05/1203/05/12137Genomicunknown
ss491916397CLINSEQ_SNP|SNV-chr7-141319814byFreqrev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa03/06/1209/05/14137Genomicunknown
ss535829774ILLUMINA|HumanOmni5-4v1_B_kgp5899594-0_B_R_1807900798rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa06/22/1208/29/15146Genomicunknown
ss560356338TISHKOFF|snp_chr7_141673345rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa11/22/1211/23/12138Genomicunknown
ss654769282SSMP|7_141673345rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa12/14/1202/11/15138Genomicunknown
ss780632440ILLUMINA|HumanOmni25Exome-8v1_A_kgp5899594-0_B_R_1807900798rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa05/30/1307/10/15142Genomicunknown
ss782256280ILLUMINA|HumanOmni2.5-4v1_H_kgp5899594-0_B_R_1807900798rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa05/30/1307/29/15142Genomicunknown
ss783549719ILLUMINA|HumanOmniExpressExome-8v1_A_exm663431-0_B_R_1918492260rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa05/31/1306/19/15142Genomicunknown
ss836126355ILLUMINA|HumanOmni2.5-8v1_A_kgp5899594-0_B_R_1807900798rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa09/18/1307/29/15142Genomicunknown
ss974466192JMKIDD_LAB|KhoeSan_Exomes_chr7_141673345rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa03/06/1403/06/14142Genomicunknown
ss984891381EVA-GONL|EVA-GONL_rs713598rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa04/23/1404/24/14142Genomicunknown
ss1067492963JMKIDD_LAB|HGDP_exomes_chr7_141673345rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa07/09/1407/09/14142Genomicunknown
ss1075049392JMKIDD_LAB|HGDP_WGS_chr7_141673345rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa07/10/1407/11/14142Genomicunknown
ss13274874961000GENOMES|PHASE3_V1_39752739rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa08/16/1408/16/14142Genomicunknown
ss1397508451HAMMER_LAB|HAMMER_LAB_rs713598rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa09/30/1409/30/14146Genomicunknown
ss1431305168DDI|DDI_rs713598rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa11/04/1411/05/14144Genomicunknown
ss1582436480EVA_GENOME_DK|EVA_GENOME_DK_snv_rs713598rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa02/19/1502/20/15144Genomicunknown
ss1584055542EVA_FINRISK|EVA_FINRISK_rs713598rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa02/27/1502/27/15144Genomicunknown
ss1594481316EVA_DECODE|EVA_DECODE_7_141319814_1089512_rs713598rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa03/02/1503/03/15144Genomicunknown
ss1619405472EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_7_141673345_22010231rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa03/04/1503/04/15144Genomicunknown
ss1662399505EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_7_141673345_22010231rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa03/04/1503/04/15144Genomicunknown
ss1688982373EVA_EXAC|EVA_EXAC_4063567rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa03/04/1503/04/15144Genomicunknown
ss1711182653EVA_MGP|EVA_XIMO_298413rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa03/09/1503/09/15144Genomicunknown
ss1752668345ILLUMINA|OmniExpressExome-8v1-1_B_exm663431-0_B_R_2060142311rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa05/27/1506/09/15146Genomicunknown
ss1805260467HAMMER_LAB|Hsieh_4273920rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa07/15/1507/16/15146Genomicunknown
ss1917823089ILLUMINA|HumanExome-12v1-1_B_exm663431-0_B_R_2060142311rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa10/16/1510/16/15147Genomicunknown
ss1928146604WEILL_CORNELL_DGM|SNV:chr7:141673345rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa10/16/1510/17/15147Genomicunknown
ss1946222884ILLUMINA|HumanCoreExome-12v1-0_C_exm663431-0_B_R_2060142311rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa10/29/1510/29/15147Genomicunknown
ss1959058334ILLUMINA|exm663431-0_B_R_1918492260rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa11/13/1511/13/15147Genomicunknown
ss1970835830GENOMED|rs713598rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa02/16/1602/16/16149Genomicunknown
ss2024762743JJLAB|SNP5265298rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa08/29/1608/30/16149Genomicunknown
ss2298591809HUMAN_LONGEVITY|HLI-7-141973545-C-Grev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa11/18/1611/18/16150Genomicunknown
ss3026170436BIOINF_KMB_FNS_UNIBA|7.141973545C>Grev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa07/05/1707/05/17151Genomicunknown
ss3546734211TOPMED|TOPMed_freeze_5?chr7:141,973,545rev/C/Gagcacacaatcactgttgctcagtgctgcctcttcactacatcccaaaaa10/06/1710/06/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs713598|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=151
 TTTTGTTTGC ATCCGTGATG CTGTGCTATG GCCTTCTGGG AAGGCGGTTG TACAGGAACA
 CCTGGATTTA TTAATCTTGC ATCACCCAAG AGGTAGAACC ATCAGTCTTC CACCCTATGA
 TAAGCTCTTA CGTGTATCCA AGAGATGTTC TAGAGAAACA ACATCCCTCT AAGTTTCCTG
 CCAGAACTTT TTATGCGCTC GCTTTGGGAT AGATCTAGGC AAAGAGCTGG ATGCTTTGTG
 AAGGAAAGGT CCTGGCTTGG AACGTACATT TACCTTTCTG CACTGGGTGG CAACCAGGTC
 TTTAGATTAG CCAACTAGAG AAGAGAAGTA GAATAGCCAA TTAGAGAAGT GACATCATGT
 TGACTCTAAC TCGCATCCGC ACTGTGTCCT ATGAAGTCAG GAGTACATTT CTGTTCATTT
 CAGTCCTGGA GTTTGCAGTG GGGTTTCTGA CCAATGCCTT CGTTTTCTTG GTGAATTTTT
 GGGATGTAGT GAAGAGGCAG
 S
 CACTGAGCAA CAGTGATTGT GTGCTGCTGT GTCTCAGCAT CAGCCGGCTT TTCCTGCATG
 GACTGCTGTT CCTGAGTGCT ATCCAGCTTA CCCACTTCCA GAAGTTGAGT GAACCACTGA
 ACCACAGCTA CCAAGCCATC ATCATGCTAT GGATGATTGC AAACCAAGCC AACCTCTGGC
 TTGCTGCCTG CCTCAGCCTG CTTTACTGCT CCAAGCTCAT CCGTTTCTCT CACACCTTCC
 TGATCTGCTT GGCAAGCTGG GTCTCCAGGA AGATCTCCCA GATGCTCCTG GGTATTATTC
 TTTGCTCCTG CATCTGCACT GTCCTCTGTG TTTGGTGCTT TTTTAGCAGA CCTCACTTCA
 CAGTCACAAC TGTGCTATTC ATGAATAACA ATACAAGGCT CAACTGGCAG ATTAAAGATC
 TCAATTTATT TTATTCCTTT CTCTTCTGCT ATCTGTGGTC TGTGCCTCCT TTCCTATTGT
 TTCTGGTTTC TTCTGGGATG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_007914 AC073647.1
dbSNP Blast Analysis
UniGene Cluster ID
553500
OMIM
607751.0001

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs713598 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/G
G/G
HWPC
G
ss116349055YRI 2IG 1.00000000 0.500000000.50000000
ss1327487496EAS 1008AF 0.675599990.32440001
EUR 1006AF 0.422500010.57750005
AFR 1322AF 0.475000020.52499998
AMR 694AF 0.658500020.34150001
SAS 978AF 0.344599990.65539998
ss143028377ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss162791450CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss165558649YRISub-Saharan African 2IG1.00000000 1.00000000
ss1688982373ExAc_Aggregated_Populations121412AF 0.445763200.55423683
ss198400233BUSHMAN_POP 2IG 1.00000000 0.500000000.50000000
ss22130TSC_42_AA 72AF 0.459999980.54000002
TSC_42_C 83AF 0.397590370.60240966
TSC_42_A 83AF 0.807228920.19277108
ss223376153pilot_1_YRI_low_coverage_panel 118AF 0.423728820.57627118
ss234199694pilot_1_CEU_low_coverage_panel 120AF 0.358333320.64166665
ss241105939pilot_1_CHB+JPT_low_coverage_panel 120AF 0.574999990.42500001
ss24483498AFD_EUR_PANELEuropean 48IG0.208333330.541666690.250000000.751830000.479166660.52083331
AFD_AFR_PANELAfrican American 46IG0.173913050.565217380.260869560.527089000.456521750.54347825
AFD_CHN_PANELAsian 48IG0.500000000.333333340.166666670.250592000.666666690.33333334
ss342248500ESP_Cohort_Populations 4550GF0.191208790.505494530.303296720.273322000.443956050.55604398
ss44783818HapMap-CEUEuropean 118IG0.186440680.491525410.322033911.000000000.432203380.56779659
HapMap-HCBAsian 90IG0.466666670.422222230.111111111.000000000.677777770.32222223
HapMap-JPTAsian 88IG0.295454530.477272720.227272731.000000000.534090940.46590909
HapMap-YRISub-Saharan African 120IG0.200000000.383333330.416666660.150222000.391666680.60833335
AoD_African_American 90AF 0.449999990.55000001
AoD_Caucasian 92AF 0.380000000.62000000
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss491916397CSAgilent 1322GF0.190809190.512487530.296703280.371093000.447052960.55294704
ss69030484HapMap-CEUEuropean 120IG0.183333340.483333320.333333341.000000000.425000010.57499999
HapMap-HCBAsian 90IG0.466666670.422222230.111111111.000000000.677777770.32222223
HapMap-JPTAsian 90IG0.288888900.488888890.222222221.000000000.533333360.46666667
HapMap-YRISub-Saharan African 120IG0.200000000.383333330.416666660.150222000.391666680.60833335

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.494+/-0.0540000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNPNCBI
UNKNOWNUNKNOWNUNKNOWN

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