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Reference SNP (refSNP) Cluster Report: rs12979860                 ** With drug-response allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:121/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:With drug-response allele [ClinVar]
MAF/MinorAlleleCount:T=0.3558/1782 (1000 Genomes)
T=0.3907/49056 (TOPMED)
HGVS Names
  • CM000681.2:g.39248147C>T
  • NC_000019.10:g.39248147C>T
  • NC_000019.9:g.39738787C>T
  • NG_042193.1:g.1825G>A
  • NG_055295.1:g.5710G>A
  • NM_001276254.2:c.151-152G>A
  • NR_074079.1:n.429-152G>A
Links , Linkout
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 ss283208441 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12979860 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
ss21535512SSAHASNP|WGSA-200403-chr19.chr19.NT_011109.15_12007005fwd/BC/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc03/20/0403/20/04121Genomicunknown
ss41007958ABI|hCV7820464byFreqfwd/BC/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc07/17/0509/05/14126Genomicunknown
ss75310850ILLUMINA|ILMN_Human_1M_rs12979860fwd/BC/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc08/28/0708/29/07129Genomicunknown
ss78402638HGSV|Cor12878_SNV_20070510.chr19_44430627fwd/BC/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc10/17/0710/19/07129Genomicunknown
ss90972021BCMHGSC_JDW|JWB-1168952fwd/BC/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc02/26/0803/01/08129Genomicunknown
ss96306171HUMANGENOME_JCVI|1103691143510fwd/BC/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc03/26/0803/26/08130Genomicunknown
ss1113725021000GENOMES|CEU.trio.12.15.2008_3617486_chr19_44430627fwd/BC/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc12/17/0812/17/08130Genomicunknown
ss1151275721000GENOMES|NA19240_2008_12_16_3258494_chr19_44430627fwd/BC/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc12/19/0812/19/08130Genomicunknown
ss117704479ILLUMINA-UK|NA18507_000044813_NCBI36.1_chr19_44430627fwd/BC/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc01/19/0901/20/09130Genomic99 %
ss119820267KRIBB_YJKIM|KHS1860650fwd/BC/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc02/04/0902/05/09131Genomicunknown
ss123417708ILLUMINA|HumanCNV370v1_C_rs12979860fwd/BC/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc04/14/0904/15/09131Genomicunknown
ss137673719ENSEMBL|ENSSNP6430537fwd/BC/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc05/15/0905/16/09131Genomicunknown
ss153304285ILLUMINA|Human610_Quadv1_B_rs12979860-128_T_R_1514278295rev/TA/Gggagcgcggagtgcaattcaaccctggttccgccttcggggagctccctggttcagtaca06/18/0906/19/09131Genomicunknown
ss160310582ILLUMINA|HumanOmni1-Quad_v1-0_B_rs12979860-128_T_R_1514278295rev/TA/Gggagcgcggagtgcaattcaaccctggttccgccttcggggagctccctggttcagtaca08/04/0910/02/09131Genomicunknown
ss169725740COMPLETE_GENOMICS|NA19240_36_chr19_44430627fwd/BC/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc10/01/0910/01/09132Genomicunknown
ss170267528ILLUMINA|HumanCNV370-Quadv3_C_rs12979860-128_T_R_1514278295rev/TA/Gggagcgcggagtgcaattcaaccctggttccgccttcggggagctccctggttcagtaca10/01/0910/03/09132Genomicunknown
ss172294859ILLUMINA|Human1M-Duov3_B_rs12979860-128_T_R_1514278295rev/TA/Gggagcgcggagtgcaattcaaccctggttccgccttcggggagctccctggttcagtaca10/01/0910/02/09132Genomicunknown
ss208491878BCM-HGSC-SUB|BCM_CMT_1011-3121431fwd/BC/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc03/15/1003/19/10132Genomicunknown
ss2281382701000GENOMES|pilot_1_YRI_9947953_chr19_44430627fwd/C/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc04/22/1004/22/10132Genomicunknown
ss2376761231000GENOMES|pilot_1_CEU_7280752_chr19_44430627fwd/C/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc05/01/1005/01/10132Genomicunknown
ss2438826051000GENOMES|pilot_1_CHB+JPT_5767682_chr19_44430627fwd/C/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc05/01/1005/01/10132Genomicunknown
ss283208441GMI|GMI_AK_SNP_7528862fwd/C/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc12/16/1012/16/10137Genomicunknown
ss292249552PJP|SNP_1755910_chr19_44430627fwd/C/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc01/21/1101/21/11134Genomicunknown
ss479852468ILLUMINA|HumanOmni2.5-4v1_B_rs12979860-128_T_R_1773296419fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc01/30/1210/28/16137Genomicunknown
ss479860037ILLUMINA|HumanOmniExpress-12v1_C_rs12979860-131_T_R_1854045649fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc01/30/1210/27/16137Genomicunknown
ss480459004ILLUMINA|HumanOmni1-Quad_v1-0_C_rs12979860-131_T_R_1854045649fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc01/30/1208/28/15146Genomicunknown
ss484724746ILLUMINA|HumanOmni2.5-4v1_D_rs12979860-131_T_R_1854045649fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc01/30/1210/28/16137Genomicunknown
ss491546752EXOME_CHIP|.GWAS._262978_chr_19_39738787fwd/BC/Ttgtactgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgcgctcc03/05/1203/06/12137Genomicunknown
ss565980822TISHKOFF|snp_chr19_39738787fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc11/22/1211/23/12138Genomicunknown
ss661845347SSMP|19_39738787fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc12/14/1202/14/15138Genomicunknown
ss782809075ILLUMINA|HumanOmni2.5-4v1_H_rs12979860-131_T_R_1854045649fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc05/30/1307/29/15146Genomicunknown
ss825673338ILLUMINA|HumanCNV370v1_C_rs12979860-126_T_R_IFB1185506880:0fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc06/24/1311/21/14144Genomicunknown
ss832062221ILLUMINA|HumanOmniExpress-12v1_H_rs12979860-131_T_R_1854045649fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc09/17/1306/18/15146Genomicunknown
ss994296026EVA-GONL|EVA-GONL_rs12979860fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc04/23/1405/01/14142Genomicunknown
ss1081901677JMKIDD_LAB|HGDP_WGS_chr19_39738787fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc07/10/1407/12/14142Genomicunknown
ss13631504151000GENOMES|PHASE3_V1_76873332fwd/C/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc08/16/1408/16/14142Genomicunknown
ss1428402826DDI|DDI_rs12979860fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc11/04/1411/04/14144Genomicunknown
ss1637961936EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_19_39738787_42403139fwd/C/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc03/04/1503/04/15144Genomicunknown
ss1680955969EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_19_39738787_42403139fwd/C/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc03/04/1503/04/15144Genomicunknown
ss1698349552EVA_DECODE|EVA_DECODE_19_44430627_290357_rs12979860fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc03/02/1503/05/15144Genomicunknown
ss1711512534EVA_MGP|EVA_XIMO_628294fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc03/09/1503/09/15144Genomicunknown
ss1713662429EVA_SVP|EVA_SVP_1356508fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc03/12/1503/12/15144Genomicunknown
ss1752284784ILLUMINA|OmniExpressExome-8v1-1_B_rs12979860-131_T_R_1885473526fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc05/27/1506/09/15146Genomicunknown
ss1809306058HAMMER_LAB|Hsieh_8335925fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc07/15/1507/16/15146Genomicunknown
ss1937789874WEILL_CORNELL_DGM|SNV:chr19:39738787fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc10/16/1510/19/15147Genomicunknown
ss1959863218ILLUMINA|rs12979860-131_T_R_1885473526fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc11/13/1511/13/15147Genomicunknown
ss2029674034JJLAB|SNP10176589fwd/BC/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc08/29/1608/31/16149Genomicunknown
ss2158214106USC_VALOUEV|NC_000019.9:g.39738787C>Tfwd/C/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc11/17/1611/17/16150Genomicunknown
ss2391450936TOPMED|19_39738787_C/Tfwd/C/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc11/19/1611/19/16150Genomicunknown
ss2633539536ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs12979860-131_T_R_1885473fwd/C/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc02/02/1702/02/17151Genomicunknown
ss2702824666GRF|rs12979860fwd/C/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc02/13/1702/13/17151Genomicunknown
ss2962824156GNOMAD|rs12979860fwd/C/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc05/23/1705/23/17151Genomicunknown
ss2985141451AFFY|Axiom_PsorMich_Affx-15940455fwd/C/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc05/24/1705/24/17151Genomicunknown
ss2985771909AFFY|Axiom_Smokesc1_Affx-15940455fwd/C/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc05/24/1705/24/17151Genomicunknown
ss3017465689SWEGEN|NC_000019.9:g.39738787C>Tfwd/C/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc05/30/1705/30/17151Genomicunknown
ss3021904980ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs12979860-138_T_R_2258077703fwd/C/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc06/28/1706/28/17151Genomicunknown
ss3028669069BIOINF_KMB_FNS_UNIBA|19.39248147C>Tfwd/C/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc07/05/1707/05/17151Genomicunknown
ss3293195516TOPMED|TOPMed_freeze_5?chr19:39,248,147fwd/C/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc10/02/1710/02/17151Genomicunknown
ss3352301434CSHL|rs12979860fwd/C/Ttgaaccagggagctccccgaaggcggaaccagggttgaattgcactccgc10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12979860|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 GGCCTGAGGA TGCAGAGAAG CTGGCGGGGG AGAGGGGCGG CGGGGCGCGG CCGTCACTCA
 CGCAGGCCGC CACATCCCTC CCCGCGGCCG CCAGCAGCTC CAGGATCGGG CCGGCGCCGG
 GGAGCAGCTC CGAGCGGTGC AGGCCGCTGA GCACTGCCTG GGCGTCCGCG ATGCCCCGGG
 CCACGTGGCG GAGCCGAGCG CAGGACTGCG GGGACGAGAG GGCGTTAGAG CGGGCCGCGC
 CCGGGCCATG CCTCTCCCGC CCACTCCCGG GCCTCACCGA TGGCCGCGGA GGATCCCTCC
 TGGGGCGGAA GGAGCAGTTG CGCTGCCCCC AGCTCAGCGC CTCTTCCTCC TGCGGGACAA
 GCGGCGCTTA TCGCATACGG CTAGGCCCCC TCGCCAGGGC CCCTAACCTC TGCACAGTCT
 GGGATTCCTG GACGTGGATG GGTACTGGCA GCGCACGGTC GTGCCTGTCG TGTACTGAAC
 CAGGGAGCTC CCCGAAGGCG
 Y
 GAACCAGGGT TGAATTGCAC TCCGCGCTCC CCCAGCAAAG CCCCTCGCCC CGACCTGGAG
 CCGAGTCCTC CCGGCAGGGC TCCCTTCTGT GATTGACCCT GAGCCTGCGT TCGCGCTGAC
 GACGGGGACT GCGGGGGTCT CGTGGTGGGA ATTGTGGGCG CTGACATAGG AGAGGCGCCT
 GCTGGGCGCT AGGACGCAGG ACCCCTTGGG ACAGGAACGG GTGTATGGGA ACCCGGTGGG
 GCCAGGGTCC CAGGGGGCAC AGGGGCTGGG CGGTGACTTA CGTAGCGGTC CCTCAGCGCC
 TTGGCAGCCG CCAGCGTCCG GGGCTCCAGC GAGCGGTAGT GCGAGAGCAG GCAGCGCCGG
 GGGGCCTTCT GCGATCACCG TGCACAGGAC CCACAGCCCC GCGGCCACTG CGGCCCAGAC
 ACTCGGCCGC ATCTCTGCTT CTGCAGCAGG CGAGAGACGT CAGGGAAGCC AAAGAGAGGG
 TCCAGCGCGT CCAGCCCCCC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011109 ABBA01040723
dbSNP Blast Analysis
OMIM
609532
607402

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss117704479YRI 2IG 1.00000000 0.500000000.50000000
ss1363150415EAS 1008AF 0.919600010.08040000
EUR 1006AF 0.690900030.30910000
AFR 1322AF 0.330599990.66939998
AMR 694AF 0.600899990.39910001
SAS 978AF 0.766900000.23310000
ss137673719ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss169725740YRISub-Saharan African 2IG 1.00000000 1.00000000
ss228138270pilot_1_YRI_low_coverage_panel 118AF 0.305084740.69491524
ss237676123pilot_1_CEU_low_coverage_panel 120AF 0.741666670.25833333
ss243882605pilot_1_CHB+JPT_low_coverage_panel 120AF 0.941666660.05833333
ss283208441LTG_NCI_NIH-HapMap-CEU 180IG0.477777780.411111120.111111110.654721000.683333340.31666666
LTG_NCI_NIH-HapMap-YRI 180IG0.077777780.400000010.522222221.000000000.277777790.72222221
LTG_NCI_NIH-HapMap-CHB_JPT 180IG0.866666670.13333334 1.000000000.933333340.06666667
ss41007958HapMap-HCBAsian 86IG0.930232580.06976745 1.000000000.965116260.03488372
HapMap-JPTAsian 166IG0.795180740.20481928 0.654721000.897590340.10240964
HapMap-YRISub-Saharan African 224IG0.098214280.419642870.482142871.000000000.308035700.69196427
HAPMAP-CHBAsian 80IG0.800000010.20000000 1.000000000.899999980.10000000
HAPMAP-GIH 176IG0.556818190.363636370.079545450.654721000.738636370.26136363
HAPMAP-LWK 178IG0.202247190.595505600.202247190.099721000.500000000.50000000
HAPMAP-MEX 98IG0.285714300.551020380.163265300.438578000.561224460.43877551
ss96306171J. Craig Venter 2IG 1.00000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.458+/-0.1380000ALFRED: The Allele Frequency Database

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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