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Reference SNP (refSNP) Cluster Report: rs3213119                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:106/147
Map to Genome Build:107/Weight 1
Validation Status:byClusterbyFreqwithHapMapFreqWith1000GenomeData
Citation:PubMed
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:G/T (REV)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.0206/2480 (ExAC)
A=0.0120/60 (1000 Genomes)
A=0.0220/286 (GO-ESP)
HGVS Names
  • NC_000005.10:g.159316780C>A
  • NC_000005.9:g.158743788C>A
  • NG_009618.1:g.18694G>T
  • NM_002187.2:c.892G>T
  • NP_002178.2:p.Val298Phe
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 ss42475737 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3213119 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
ss4473662PGA-UW-FHCRC|IL12B-011702fwd/BG/Tagagtcttcacggacaagacctcagccacgtcatctgccgcaaaaatgccagcattagcg05/30/0210/10/03106Genomicunknown
ss22257719SSAHASNP|WGSA-200403-chr5.chr5.NT_023133.11_3553346rev/TA/Ccgctaatgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaagactct03/21/0403/21/04121Genomicunknown
ss28525220JDRF_WT_DIL|DIL5272fwd/BG/Tagagtcttcacggacaagacctcagccacgtcatctgccgcaaaaatgccagcattagcg11/03/0411/03/04124Genomicunknown
ss42475737ABI|hCV31985602rev/TA/Ccgctaatgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaagactct07/18/0507/18/05126Genomicunknown
ss48295088SNP500CANCER|IL12B-10byFreqfwd/BG/Tagagtcttcacggacaagacctcagccacgtcatctgccgcaaaaatgccagcattagcg08/19/0511/03/06126Genomicunknown
ss66538568SHGC|751fwd/BG/Tagagtcttcacggacaagacctcagccacgtcatctgccgcaaaaatgccagcattagcg11/07/0611/07/06127Genomicunknown
ss68955661PERLEGEN|PGP04775567byFreqrev/TA/Ccgctaatgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaagactct01/30/0703/31/08127Genomicunknown
ss74814704AFFY|SNP_M-307665fwd/BG/Tagagtcttcacggacaagacctcagccacgtcatctgccgcaaaaatgccagcattagcg08/09/0708/09/07128Genomicunknown
ss76868591CGM_KYOTO|9980rev/TA/Ccgctaatgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaagactct09/12/0709/12/07129cDNAunknown
ss98781162HUMANGENOME_JCVI|1103654271819rev/TA/Ccgctaatgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaagactct04/01/0804/01/08130Genomicunknown
ss144221316ENSEMBL|ENSSNP10140902rev/TA/Ccgctaatgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaagactct12/08/0810/17/09131Genomicunknown
ss160616301ILLUMINA|HumanOmni1-Quad_v1-0_B_rs3213119-128_B_F_1510647001fwd/BG/Tagagtcttcacggacaagacctcagccacgtcatctgccgcaaaaatgccagcattagcg08/04/0910/04/09131Genomicunknown
ss173575529ILLUMINA|Human1M-Duov3_B_rs3213119-128_B_F_1510647001fwd/BG/Tagagtcttcacggacaagacctcagccacgtcatctgccgcaaaaatgccagcattagcg10/01/0910/04/09132Genomicunknown
ss2332224761000GENOMES|pilot_1_CEU_2827105_chr5_158676366rev/A/Ccgctaatgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaagactct05/01/1005/01/10132Genomicunknown
ss244294310ILLUMINA|CVDSNP55v1_A_rs3213119fwd/BG/Tagagtcttcacggacaagacctcagccacgtcatctgccgcaaaaatgccagcattagcg06/10/1006/10/10132Genomicunknown
ss293504854PJP|SNP_3011212_chr5_158676366rev/A/Ccgctaatgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaagactct01/21/1101/21/11134Genomicunknown
ss342195917NHLBI-ESP|ESP2500-chr5-158743788byFreqrev/TA/Ccgctaatgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaagactct03/25/1109/05/14134Genomicunknown
ss480768377ILLUMINA|HumanOmni2.5-4v1_B_rs3213119-128_B_F_1747440452fwd/BG/Tagagtcttcacggacaagacctcagccacgtcatctgccgcaaaaatgccagcattagcg01/30/1201/31/12137Genomicunknown
ss480784182ILLUMINA|HumanOmniExpress-12v1_C_rs3213119-131_B_F_1857428829fwd/BG/Tagagtcttcacggacaagacctcagccacgtcatctgccgcaaaaatgccagcattagcg01/30/1201/31/12137Genomicunknown
ss481679742ILLUMINA|HumanOmni1-Quad_v1-0_C_rs3213119-131_B_F_1857428829rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag01/30/1208/28/15146Genomicunknown
ss485178915ILLUMINA|HumanOmni2.5-4v1_D_rs3213119-131_B_F_1857428829fwd/BG/Tagagtcttcacggacaagacctcagccacgtcatctgccgcaaaaatgccagcattagcg01/30/1202/04/12137Genomicunknown
ss4909153391000GENOMES|20110521_exome_423137_chr5_158743788rev/TA/Ccgctaatgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaagactct02/10/1202/21/12137Genomicunknown
ss491374973EXOME_CHIP|nonsyn_91199_chr_5_158743788rev/TA/Ccgctaatgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaagactct03/05/1203/05/12137Genomicunknown
ss491877193CLINSEQ_SNP|SNV-chr5-158676366byFreqrev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag03/06/1209/05/14137Genomicunknown
ss537168362ILLUMINA|HumanOmni5-4v1_B__rs3213119-131_B_F_1889527364rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag06/22/1208/29/15146Genomicunknown
ss778889877ILLUMINA|HumanOmni25Exome-8v1_A_rs3213119-131_B_F_1857428829rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag05/30/1307/09/15146Genomicunknown
ss780843456ILLUMINA|HumanOmni25Exome-8v1_A_exm500154-0_B_R_1921172043rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag05/30/1307/09/15146Genomicunknown
ss783035629ILLUMINA|HumanOmni2.5-4v1_H_rs3213119-131_B_F_1857428829rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag05/30/1307/28/15146Genomicunknown
ss783526878ILLUMINA|HumanOmniExpressExome-8v1_A_exm500154-0_B_R_1921172043rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag05/31/1306/19/15146Genomicunknown
ss783995165ILLUMINA|HumanOmniExpressExome-8v1_A_rs3213119-131_B_F_1889527364rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag05/31/1306/19/15146Genomicunknown
ss832293290ILLUMINA|HumanOmniExpress-12v1_H_rs3213119-131_B_F_1857428829rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag09/17/1306/18/15146Genomicunknown
ss834350975ILLUMINA|HumanOmni2.5-8v1_A_rs3213119-131_B_F_1857428829rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag09/18/1307/28/15146Genomicunknown
ss982321563EVA-GONL|EVA-GONL_rs3213119rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag04/23/1404/24/14142Genomicunknown
ss1067473354JMKIDD_LAB|HGDP_exomes_chr5_158743788rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag07/09/1407/09/14142Genomicunknown
ss1073188602JMKIDD_LAB|HGDP_WGS_chr5_158743788rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag07/10/1407/11/14142Genomicunknown
ss13179882401000GENOMES|PHASE3_V1_29848944rev/A/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag08/16/1408/16/14142Genomicunknown
ss1397432886HAMMER_LAB|HAMMER_LAB_rs3213119rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag09/30/1409/30/14146Genomicunknown
ss1584042412EVA_FINRISK|EVA_FINRISK_rs3213119rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag02/27/1502/27/15144Genomicunknown
ss1591859644EVA_DECODE|EVA_DECODE_5_158676366_1190351_rs3213119rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag03/02/1503/03/15144Genomicunknown
ss1614429603EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_5_158743788_16528332rev/A/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag03/04/1503/04/15144Genomicunknown
ss1657423636EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_5_158743788_16528332rev/A/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag03/04/1503/04/15144Genomicunknown
ss1688067154EVA_EXAC|EVA_EXAC_3074784rev/A/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag03/04/1503/04/15144Genomicunknown
ss1711104707EVA_MGP|EVA_XIMO_220467rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag03/09/1503/09/15144Genomicunknown
ss1752559440ILLUMINA|OmniExpressExome-8v1-1_B_exm500154-0_B_R_1921172043rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag05/27/1506/09/15146Genomicunknown
ss1752559441ILLUMINA|OmniExpressExome-8v1-1_B_rs3213119-131_B_F_2087477901rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag05/27/1506/09/15146Genomicunknown
ss1917796968ILLUMINA|HumanExome-12v1-1_B_exm500154-0_B_R_1921172043rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag10/16/1510/16/15147Genomicunknown
ss1946161221ILLUMINA|HumanCoreExome-12v1-0_C_exm500154-0_B_R_1921172043rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag10/29/1510/29/15147Genomicunknown
ss1958839680ILLUMINA|exm500154-0_B_R_1921172043rev/TA/Catgctggcatttttgcggcagatgacgtggctgaggtcttgtccgtgaag11/13/1511/13/15147Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3213119|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=147
 GGCAAGGCAA TTGTGCTAGA AAGATGAAAG CTGGGCCAAA CGATTTCTCC CTCAAGGGCT
 TACAAAGTAC AAAAGCTGCA CCTACATGTG GAGTGTCTGC CAGTAGGTGG TGCAAGTTCT
 ATGCACACCC CTGTGAATTG CAAGCACAGT GCCCTAAGAC CAAGATGGGC TTGTTTTGGG
 AGAGTATGCA TTGCAGAAAC AGGCTCAGCT TACCCTGTGA CTATGTTGCC AAGGGGTCTT
 CACAGCTTTC CTTCTCTTTT GCAGAAAGAT AGAGTCTTCA CGGACAAGAC CTCAGCCACG
 K
 TCATCTGCCG CAAAAATGCC AGCATTAGCG TGCGGGCCCA GGACCGCTAC TATAGCTCAT
 CTTGGAGCGA ATGGGCATCT GTGCCCTGCA GTTAGGTGAG CAGGCCCTCA AAGGCCAGCC
 CAGGCCTGCA CTCTCAGTGC ACCTGGATGC AGGGATATGA TTGGGGGCTG TGTTGGAGAG
 GAAAGGGGGA TGGAGTGGCC AGCACCCAGT TGCCAGAATC AGAAACATAC ATTTATTCAC
 TAACAGATAT TTATTTGGTG CCTTTGTTAT GTAGGACACT GTGCTGGCCA CAGGGATATT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_023133.12 ABBA01044239
dbSNP Blast Analysis
UniGene Cluster ID
674
3D structure mapping
NP_002178  

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs3213119 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceG/G
G/T
T/T
HWPG
T
ss1317988240EAS 1008AF 1.00000000
EUR 1006AF 0.963199970.03680000
AFR 1322AF 0.997699980.00230000
AMR 694AF 0.972599980.02740000
SAS 978AF 0.998999950.00100000
ss144221316ENSEMBL_Venter 2IG 1.00000000 0.500000000.50000000
ss1688067154ExAc_Aggregated_Populations121402AF 0.979530810.02046918
ss233222476pilot_1_CEU_low_coverage_panel 120AF 0.941666660.05833333
ss342195917ESP_Cohort_Populations 4550GF0.958681340.040879120.000439561.000000000.979120850.02087912
ss42475737HapMap-CEUEuropean 116IG0.982758640.01724138 1.000000000.991379320.00862069
HapMap-HCBAsian 90IG1.00000000 1.00000000
HapMap-JPTAsian 88IG1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG1.00000000 1.00000000
ENSEMBL_Watson 2IG1.00000000 1.00000000
ss4473662PGA-AFRICAN-PANELAfrican American 44IG1.00000000 1.00000000
PGA-EUROPEAN-PANELEuropean 42IG0.952380960.04761905 1.000000000.976190450.02380952
ss48295088P1 196AF0.968999980.03100000 1.000000000.985000010.01500000
CAUC1 62AF0.967999990.03200000 1.000000000.983999970.01600000
AFR1 46AF1.00000000 1.00000000
HISP1 42AF0.904999970.09500000 1.000000000.952000020.04800000
PAC1 46AF1.00000000 1.00000000
ss491877193CSAgilent 1317GF0.939000010.058000000.003000000.150222000.967999990.03200000
ss66538568R24 46AF 0.980000020.02000000
ss98781162J. Craig Venter 2IG 1.00000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.040+/-0.136560438150

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqWith1000GenomeDataUNKNOWNUNKNOWNYES

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