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Reference SNP (refSNP) Cluster Report: rs3813867                 ** With other allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:107/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/G (FWD)
Allele Origin:C:germline
G:germline
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With other allele [ClinVar]
MAF/MinorAlleleCount:C=0.0853/427 (1000 Genomes)
C=0.0559/7017 (TOPMED)
HGVS Names
  • CM000672.2:g.133526101G>A
  • CM000672.2:g.133526101G>C
  • NC_000010.10:g.135339605G>C
  • NC_000010.11:g.133526101G>A
  • NC_000010.11:g.133526101G>C
  • NG_008383.1:g.3739G>A
  • NG_008383.1:g.3739G>C
  • NG_055447.1:g.2551G>A
  • NG_055447.1:g.2551G>C
  • NM_000773.3:c.-1295G>A
  • NM_000773.3:c.-1295G>C
  • XR_001747676.1:n.1257C>G
  • XR_001747676.1:n.1257C>T
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 ss280844095 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3813867 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
ss5000278YUSUKE|IMS-JST174068byFreqfwd/BC/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac08/12/0211/22/03107Genomicunknown
ss5586446SNP500CANCER|CYP2E1-09byFreqfwd/BC/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac09/26/0204/07/04116Genomicunknown
ss6312564KIDDLAB|SI000693SbyFreqfwd/BC/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac01/17/0310/10/03111Genomicunknown
ss16489663CSHL-HAPMAP|CSHL-HuAA-200402.chr10.NT_017795.16_495184fwd/BC/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac02/17/0403/04/04120Genomicunknown
ss24093286PERLEGEN|afd4394396byFreqfwd/BC/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac08/10/0409/13/04123Genomicunknown
ss39809760ABI|hCV2431875byFreqrev/C/Ggtcattggttgtgctgcacctaacactgcactctcctgaaccaagaaggggcgttggcct07/16/0511/02/06126Genomicunknown
ss84155504PHARMGKB_AB_DME|PS206239_PA150068017_301byFreqfwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac12/06/0709/05/14130Genomicunknown
ss84556327HGSV|Cor19129_SNV_20070510.chr10_135228486fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac12/06/0712/07/07130Genomicunknown
ss97699209HUMANGENOME_JCVI|1103694101431fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac03/29/0803/30/08130Genomicunknown
ss102929654BGI|BGI_rs3813867fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac06/05/0810/20/09131Genomicunknown
ss1098963241000GENOMES|CEU.trio.12.15.2008_2466965_chr10_135189595fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac12/16/0812/16/08130Genomicunknown
ss138752737ENSEMBL|ENSSNP350337fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac12/08/0810/16/09131Genomicunknown
ss154272293ILLUMINA|Human610_Quadv1_B_rs3813867-128_B_F_1526886039fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac06/18/0906/20/09131Genomicunknown
ss155789328GMI|GMI_SNP_75303692fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac06/24/0906/24/09131Genomicunknown
ss159449023ILLUMINA|Human660W-Quad_v1_A_rs3813867-128_B_F_1526886039fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac07/06/0907/07/09131Genomicunknown
ss160646514ILLUMINA|HumanOmni1-Quad_v1-0_B_rs3813867-128_B_F_1526886039fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac08/04/0910/04/09131Genomicunknown
ss173651389ILLUMINA|Human1M-Duov3_B_rs3813867-128_B_F_1526886039fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac10/01/0910/04/09132Genomicunknown
ss202249083BUSHMAN|BUSHMAN-chr10-135189594byFreqfwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac02/16/1009/05/14132Genomicunknown
ss2250417721000GENOMES|pilot_1_YRI_6851455_chr10_135189595fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac04/22/1004/22/10132Genomicunknown
ss2354078521000GENOMES|pilot_1_CEU_5012481_chr10_135189595fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac05/01/1005/01/10132Genomicunknown
ss2420703101000GENOMES|pilot_1_CHB+JPT_3955387_chr10_135189595fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac05/01/1005/01/10132Genomicunknown
ss244297639ILLUMINA|CVDSNP55v1_A_rs3813867fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac06/10/1006/10/10132Genomicunknown
ss280844095GMI|GMI_AK_SNP_5164432fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac12/16/1012/16/10137Genomicunknown
ss290971413PJP|SNP_477771_chr10_135189595fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac01/21/1101/21/11134Genomicunknown
ss480848222ILLUMINA|HumanOmni2.5-4v1_B_rs3813867-128_B_F_1616871375fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca01/30/1210/28/16137Genomicunknown
ss480865688ILLUMINA|HumanOmniExpress-12v1_C_rs3813867-131_B_F_1853480667fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca01/30/1210/27/16137Genomicunknown
ss481800821ILLUMINA|HumanOmni1-Quad_v1-0_C_rs3813867-131_B_F_1865768329fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca01/30/1208/28/15146Genomicunknown
ss485219008ILLUMINA|HumanOmni2.5-4v1_D_rs3813867-131_B_F_1853480667fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca01/30/1210/27/16137Genomicunknown
ss537199361ILLUMINA|HumanOmni5-4v1_B_rs3813867-131_B_F_1893174615fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca06/22/1208/29/15146Genomicunknown
ss562324940TISHKOFF|snp_chr10_135339605fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca11/22/1211/23/12138Genomicunknown
ss657634149SSMP|10_135339605fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca12/14/1202/12/15138Genomicunknown
ss780632776ILLUMINA|HumanOmni25Exome-8v1_A_rs3813867-131_B_F_1893174615fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca05/30/1307/10/15146Genomicunknown
ss783055456ILLUMINA|HumanOmni2.5-4v1_H_rs3813867-131_B_F_1853480667fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca05/30/1307/29/15146Genomicunknown
ss784013750ILLUMINA|HumanOmniExpressExome-8v1_A_rs3813867-131_B_F_1893174615fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca05/31/1306/18/15146Genomicunknown
ss832313353ILLUMINA|HumanOmniExpress-12v1_H_rs3813867-131_B_F_1853480667fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca09/17/1306/18/15146Genomicunknown
ss836126701ILLUMINA|HumanOmni2.5-8v1_A_rs3813867-131_B_F_1893174615fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca09/18/1307/29/15146Genomicunknown
ss988110209EVA-GONL|EVA-GONL_rs3813867fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca04/23/1404/25/14142Genomicunknown
ss1077434940JMKIDD_LAB|HGDP_WGS_chr10_135339605fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca07/10/1407/12/14142Genomicunknown
ss13397592581000GENOMES|PHASE3_V1_52507259fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca08/16/1408/16/14142Genomicunknown
ss1505810970OMIM-CURATED-RECORDS|SCV000038665.136523fwd/C/Gaggccaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaaccaatgac12/08/1412/08/14142Genomicunknown
ss1575464140EVA_GENOME_DK|EVA_GENOME_DK_snv_rs3813867fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca02/19/1502/19/15144Genomicunknown
ss1597789164EVA_DECODE|EVA_DECODE_10_135189595_1045165_rs3813867fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca03/02/1503/04/15144Genomicunknown
ss1625812972EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_10_135339605_29021964fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca03/04/1503/04/15144Genomicunknown
ss1668807005EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_10_135339605_29021964fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca03/04/1503/04/15144Genomicunknown
ss1751957702ILLUMINA|OmniExpressExome-8v1-1_B_rs3813867-131_B_F_1893174615fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca05/27/1506/09/15146Genomicunknown
ss1931468849WEILL_CORNELL_DGM|SNV:chr10:135339605fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca10/16/1510/17/15147Genomicunknown
ss1967268981GENOMED|rs3813867fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca02/16/1602/16/16147Genomicunknown
ss2026475043JJLAB|SNP6977598fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca08/29/1608/30/16149Genomicunknown
ss2154758231USC_VALOUEV|NC_000010.10:g.135339605G>Cfwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca11/17/1611/17/16150Genomicunknown
ss2179510489HUMAN_LONGEVITY|HLI-10-133526101-G-Cfwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca11/18/1611/18/16150Genomicunknown
ss2342623541TOPMED|10_135339605_G/Cfwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca11/19/1611/19/16150Genomicunknown
ss2627706832SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV4420710fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca01/06/1701/06/17151Genomicunknown
ss2632788388ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs3813867-131_B_F_18931746fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca02/02/1702/02/17151Genomicunknown
ss2699023323GRF|rs3813867fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca02/13/1702/13/17151Genomicunknown
ss2895305891GNOMAD|rs3813867fwd/A/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca05/19/1705/19/17151Genomicunknown
ss3007433529SWEGEN|NC_000010.10:g.135339605G>Cfwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca05/30/1705/30/17151Genomicunknown
ss3134812612TOPMED|TOPMed_freeze_5?chr10:133,526,101-01fwd/A/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca09/29/1709/29/17151Genomicunknown
ss3134812613TOPMED|TOPMed_freeze_5?chr10:133,526,101-02fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca09/29/1709/29/17151Genomicunknown
ss3349401339CSHL|rs3813867fwd/C/Gaacgccccttcttggttcaggagagtgcagtgttaggtgcagcacaacca10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3813867|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/C/G'|mol=Genomic|build=151
 CTCCAGGGCA CGCGGGTCCC GCCTGGGATG TGCACACTCA GGTGAGCTGC ACAGACAAGG
 TGTCCTCAGC CCAGGGGAGC CAGAGGCCTG CTCTGCCTCT CCACCCTGAT GCTTCCTGTT
 CTCACCCCAC CAAAGCCAAG GCTTCAATTT CAGTCTGTGG GGAGCTGACT CTGCTGCTCT
 CAAGCACTAG AAGAAGGAAC CAGTAATCGA GGAAACTTGT GGACCCCAAT GGGTGTCTGT
 CCCGGCCAGG CCTGGCTGGG CCCACACAGG ACAACAGGGT TCAGGGGTCT GGACAGCTGT
 TTCTGCCCAG GGAATTGTCC CTGCCACCTC ACACTGGCCA CTGGAAAGGA AAGAGAGGAG
 GAGGCGGCAG GCTAACCCAC CCGTGAGCCA GTCGAGTCTA CATTGTCAGT TCTCACCTCG
 AGGGGTGCCA AAAACCAGAG GGAAGCAAAG GCCCCTGAAG CCTCTGCCAG AGGCCAACGC
 CCCTTCTTGG TTCAGGAGAG
 V
 TGCAGTGTTA GGTGCAGCAC AACCAATGAC TTGCTTATGT GGCTAATAAA TTGTCAAGAG
 AAAAACTGGG TTAGAATGCA ATATATAGTA TGTAGTCTCA TTTTTGTATA AATACAAGTA
 TAGAATGGCA TAACTCAAAA TCCACAAGTG ATTTGGCTGG ATTGTAAATG ACTTTTATTT
 TCTTCATTTC TCATCATATT TTCTATTATA CATAAAGATT CATTGTTAAT ATAAAAGTAC
 AAAATTGCAA CCTATGAATT AAGAACTTCT ATATATTGCC AGTTAGAAGA CAGAATGAAA
 AACATTCTCT TCATTCTAAC CACACACACA AAAAAGCTCC ACAAAATACC TATGGACTAC
 CTTCATAGAA GGTGGAAGAG GGTCTGTATG AAGAAAATAA TTAATACATG AAAGAAGAAG
 CTAGTCAATG TGGAGCTCTA TTGTGTCCCG GGATCAACAA AGACAAGATA TCTTTAAAAT
 CGTCTTCTAA ATTTACCCTA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_028298.2 ABBA01006221
dbSNP Blast Analysis
OMIM
124040.0001

  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/G
G/G
HWPC
G
ss1339759258EAS 1008AF 0.202400000.79759997
EUR 1006AF 0.040800000.95920002
AFR 1322AF 0.066599990.93340003
AMR 694AF 0.122500000.87750000
SAS 978AF 0.009200000.99079996
ss138752737ENSEMBL_Venter 2IG 1.00000000 0.500000000.50000000
ss202249083BUSHMAN_POP2 2IG 1.00000000 0.500000000.50000000
BANTU 2IG 1.00000000 0.500000000.50000000
ss225041772pilot_1_YRI_low_coverage_panel 118AF 0.067796610.93220341
ss235407852pilot_1_CEU_low_coverage_panel 120AF 0.058333330.94166666
ss24093286AFD_EUR_PANELEuropean 44IG 0.045454550.954545441.000000000.022727270.97727275
AFD_AFR_PANELAfrican American 42IG 0.190476190.809523821.000000000.095238100.90476191
AFD_CHN_PANELAsian 48IG0.041666670.291666660.666666691.000000000.187500000.81250000
ss242070310pilot_1_CHB+JPT_low_coverage_panel 120AF 0.216666670.78333336
ss39809760HapMap-CEUEuropean 120IG 0.133333340.866666671.000000000.066666670.93333334
HapMap-HCBAsian 90IG0.111111110.355555560.533333360.371093000.288888900.71111113
HapMap-JPTAsian 88IG0.045454550.318181810.636363631.000000000.204545450.79545456
HapMap-YRISub-Saharan African 120IG 0.133333340.866666671.000000000.066666670.93333334
AoD_African_American 90AF 0.080000000.92000002
AoD_Caucasian 92AF 0.010000000.99000001
AoD_Chinese 90AF 0.190000000.81000000
AoD_Japanese 90AF 0.220000000.77999997
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss5000278JBIC-allele 1310AF 0.208400000.79159999
ss5586446P1 204AF 0.029000000.971000021.000000000.015000000.98500001
CAUC1 62AF 1.00000000 1.00000000
AFR1 48AF 1.00000000 1.00000000
HISP1 46AF 1.00000000 1.00000000
PAC1 48AF 0.125000000.875000001.000000000.063000000.93700004
ss6312564PO000020C 182AF 0.040000000.95999998
ss84155504PA150068018 356AF 0.123595510.87640452
ss97699209J. Craig Venter 2IG 1.00000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.156+/-0.2320000ALFRED: 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
byClusterbyFreqwithHapMapFreqWith1000GenomeDataUNKNOWNUNKNOWNYES

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