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Reference SNP (refSNP) Cluster Report: rs3828917                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:107/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G/T (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.0489/245 (1000 Genomes)
T=0.0353/4428 (TOPMED)
HGVS Names
  • CM000668.2:g.31498140G>A
  • CM000668.2:g.31498140G>T
  • NC_000006.11:g.31465917G>T
  • NC_000006.12:g.31498140G>A
  • NC_000006.12:g.31498140G>T
  • NG_021405.1:g.5063G>A
  • NG_021405.1:g.5063G>T
  • NM_001289160.1:c.-27+3145G>A
  • NM_001289160.1:c.-27+3145G>T
  • NM_001289161.1:c.-54G>A
  • NM_001289161.1:c.-54G>T
  • NM_005931.4:c.-54G>A
  • NM_005931.4:c.-54G>T
  • NT_113891.3:g.2975480G>A
  • NT_113891.3:g.2975480G>T
  • NT_167244.1:g.2780624G>T
  • NT_167244.2:g.2830708G>A
  • NT_167244.2:g.2830708G>T
  • NT_167245.2:g.2745748T=
  • NT_167245.2:g.2745748T>A
  • NT_167245.2:g.2745748T>G
  • NT_167247.2:g.2840094G>A
  • NT_167247.2:g.2840094G>T
  • NT_167248.2:g.2754040G>A
  • NT_167248.2:g.2754040G>T
  • NT_167249.2:g.2797435G>A
  • NT_167249.2:g.2797435G>T
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 ss278726600 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3828917 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
ss5015417YUSUKE|IMS-JST190472byFreqfwd/BG/Ttgactaaatttccacggggtcttctcaccgtttcattcagttggccactgctgagcagct08/12/0210/25/06107Genomicunknown
ss52085722SI_MHC_SNP|AL663061.8_5811_GTbyFreqfwd/BG/Ttgactaaatttcgacggggtcttctcacggtttcattcagttggccactgctgagcagct04/10/0603/31/08127Genomicunknown
ss65845827KRIBB_YJKIM|KHS21623byFreqfwd/BG/Ttgactaaatttccacggggtcttctcaccgtttcattcagttggccactgctgagcagct10/17/0612/16/06127Genomicunknown
ss75238054ILLUMINA|ILMN_Human_1M_rs3828917fwd/BG/Ttgactaaatttccacggggtcttctcaccgtttcattcagttggccactgctgagcagct08/28/0708/29/07129Genomicunknown
ss119466529KRIBB_YJKIM|KHS1628776fwd/BG/Ttgactaaatttcgacggggtcttctcacggtttcattcagttggccactgctgagcagct02/04/0902/04/09131Genomicunknown
ss160649035ILLUMINA|HumanOmni1-Quad_v1-0_B_rs3828917-128_T_R_1561719491rev/TA/Cagctgctcagcagtggccaactgaatgaaaccgtgagaagaccccgtcgaaatttagtca08/04/0910/04/09131Genomicunknown
ss2333988401000GENOMES|pilot_1_CEU_3003469_chr6_31573896fwd/G/Ttgactaaatttcgacggggtcttctcacggtttcattcagttggccactgctgagcagct05/01/1005/01/10132Genomicunknown
ss2404695751000GENOMES|pilot_1_CHB+JPT_2354652_chr6_31573896fwd/G/Ttgactaaatttcgacggggtcttctcacggtttcattcagttggccactgctgagcagct05/01/1005/01/10132Genomicunknown
ss244297886ILLUMINA|CVDSNP55v1_A_rs3828917rev/TA/Cagctgctcagcagtggccaactgaatgaaacggtgagaagaccccgtggaaatttagtca06/10/1006/10/10135Genomicunknown
ss278726600GMI|GMI_AK_SNP_3046839fwd/G/Ttgactaaatttcgacggggtcttctcacggtttcattcagttggccactgctgagcagct12/16/1012/16/10137Genomicunknown
ss410931041ILLUMINA|Cardio-Metabo_Chip_11395247_A_rs3828917rev/TA/Cagctgctcagcagtggccaactgaatgaaaccgtgagaagaccccgtcgaaatttagtca06/07/1106/07/11137Genomicunknown
ss481810789ILLUMINA|HumanOmni1-Quad_v1-0_C_rs3828917-131_T_R_1858947008fwd/BG/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag01/30/1208/28/15146Genomicunknown
ss537201815ILLUMINA|HumanOmni5-4v1_B_rs3828917-131_T_R_1885843244fwd/BG/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag06/22/1208/29/15146Genomicunknown
ss778704341ILLUMINA|HumanOmni25Exome-8v1_A_rs3828917-131_T_R_1885843244fwd/BG/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag05/30/1307/09/15146Genomicunknown
ss834163388ILLUMINA|HumanOmni2.5-8v1_A_rs3828917-131_T_R_1885843244fwd/BG/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag09/18/1307/28/15146Genomicunknown
ss982765521EVA-GONL|EVA-GONL_rs3828917fwd/BG/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag04/23/1404/24/14142Genomicunknown
ss13195567641000GENOMES|PHASE3_V1_31489041fwd/G/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag08/16/1408/16/14142Genomicunknown
ss1397449839HAMMER_LAB|HAMMER_LAB_rs3828917fwd/BG/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag09/30/1409/30/14146Genomicunknown
ss1592309437EVA_DECODE|EVA_DECODE_6_31573896_273475_rs3828917fwd/BG/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag03/02/1503/03/15144Genomicunknown
ss1615276665EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_6_31465917_17466062fwd/G/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag03/04/1503/04/15144Genomicunknown
ss1658270698EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_6_31465917_17466062fwd/G/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag03/04/1503/04/15144Genomicunknown
ss1711120947EVA_MGP|EVA_XIMO_236707fwd/BG/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag03/09/1503/09/15144Genomicunknown
ss1712850944EVA_SVP|EVA_SVP_545311fwd/BG/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag03/12/1503/12/15144Genomicunknown
ss1926017963WEILL_CORNELL_DGM|SNV:chr6:31465917fwd/BG/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag10/16/1510/17/15147Genomicunknown
ss2023641992JJLAB|SNP4144547fwd/BG/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag08/29/1608/30/16149Genomicunknown
ss2151808362USC_VALOUEV|NC_000006.11:g.31465917G>Tfwd/G/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag11/17/1611/17/16150Genomicunknown
ss2451317816TOPMED|6_31465917_G/Tfwd/G/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag11/20/1611/20/16150Genomicunknown
ss2634429680ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs3828917-131_T_R_20874786fwd/G/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag02/02/1702/02/17151Genomicunknown
ss2837423111GNOMAD|rs3828917fwd/G/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag05/18/1705/18/17151Genomicunknown
ss2985361868AFFY|Axiom_PsorMich_Affx-28458030fwd/G/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag05/24/1705/24/17151Genomicunknown
ss2998795233SWEGEN|NC_000006.11:g.31465917G>Tfwd/G/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag05/30/1705/30/17151Genomicunknown
ss3493834642TOPMED|TOPMed_freeze_5?chr6:31,498,140-01fwd/A/Gaaatttcgacggggtcttctcacggtttcattcagttggccactgctgag10/05/1710/05/17151Genomicunknown
ss3493834643TOPMED|TOPMed_freeze_5?chr6:31,498,140-02fwd/G/Taaatttcgacggggtcttctcacggtttcattcagttggccactgctgag10/05/1710/05/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3828917|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G/T'|mol=Genomic|build=151
 TGGAAACAGG TCTGCAAATC TGGTCACTGG TCTCATTGCA GTAACGCTGT GCGCGGTTGA
 GGGAGTGTAT TGGGAGAAAA ACCACGCGTT GTCTGTCCCG GAAGGAACAA GCCAGTGAGA
 GCCGGCCTGA TGGGAGGACC GGCGAAAGGG GCTTGGTGAA GCCCGCGCTC CTTGGGGGTG
 GGAATGCGGG GATGGGGTGG TCGCGATGCA GGGAGGGCGA CAGGGTCCAG GTCGTGCTCA
 TAAGTTTGGA GCTGTACTCT CAGCTACTCG GGGCTGGTCC TTGATTTTGG CTGCGCTCGC
 GCACGCTCCC CCTTTTCTGG CCGCCAGGTC CCGCCTTCTA AATTTCCCCA GGTCTCCAGG
 CCGCTAGAAT TTTCTCTTCT GAACGTGGCC CCGCCCTCTC CACTCATGAT TGGCCCTAAG
 TTCCGGGCCT CAGTTTTCAC TGGATAAGCG GTCGCTGAGC GGGGCGCAGG TGACTAAATT
 TCGACGGGGT CTTCTCACGG
 D
 TTTCATTCAG TTGGCCACTG CTGAGCAGCT GAGAAGGTGG CGACGTAGGG GCCATGGGGC
 TGGGCCGGGT CCTGCTGTTT CTGGCCGTCG CCTTCCCTTT TGCACCCCCG GCAGCCGCCG
 CTGGTGAGTG GGGTTCCTGG CGGTCCCCGG CGGAGCGGGA GCGGCGGGGC GTTTCCGGGG
 GTCCGGGTGG GTTGCCGCGA GCGCTGTGCG GTCAGGGCGG GGCTCAGGTG TGCTGTCTGG
 AGTGCAGGGA GCTGGACGCC GCCTGTTCCC GCCACACCTC AGCCCTGCTT TCCCATCTCC
 CGTCTCTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTCTTTCTG AGACGGAGTC
 TCTGTCGCCT AGGCTGTAGT GCAGTGGCGC GATCTTGGCT CACTGCAAGC GCCGCCTCCC
 GGGTTCACGC CATTCTCCTG CCTCAGCCTC CCTAGTAGCT GGGACTACAG GCGCCCGCCA
 CCACGCCCGG CTAATTTTTT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_023426.1
dbSNP Blast Analysis
UniGene Cluster ID
211580

  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.
SourceG/G
G/T
T/T
HWPG
T
ss1319556764EAS 1008AF 0.970200000.02980000
EUR 1006AF 0.952300010.04770000
AFR 1322AF 0.974999960.02500000
AMR 694AF 0.948099970.05190000
SAS 978AF 0.899800000.10020000
ss233398840pilot_1_CEU_low_coverage_panel 120AF 0.958333310.04166667
ss240469575pilot_1_CHB+JPT_low_coverage_panel 120AF 0.983333350.01666667
ss5015417YRISub-Saharan African 114IG1.00000000 1.00000000
CHBAsian 90IG0.911111120.08888889 1.000000000.955555560.04444445
JPTAsian 88IG0.977272750.02272727 1.000000000.988636370.01136364
CEUEuropean 120IG0.899999980.10000000 1.000000000.949999990.05000000
ss52085722HapMap-CEUEuropean 226IG0.884955760.11504425 1.000000000.942477880.05752213
HapMap-HCBAsian 86IG0.906976760.09302326 1.000000000.953488350.04651163
HapMap-JPTAsian 172IG0.953488350.04651163 1.000000000.976744170.02325581
HapMap-YRISub-Saharan African 226IG0.991150440.00884956 1.000000000.995575250.00442478
HAPMAP-ASW 98IG0.959183690.04081633 1.000000000.979591850.02040816
HAPMAP-CHBAsian 82IG0.951219500.04878049 1.000000000.975609780.02439024
HAPMAP-CHD 170IG0.952941180.04705882 1.000000000.976470590.02352941
HAPMAP-GIH 176IG0.681818190.306818190.011363640.294266000.835227250.16477273
HAPMAP-LWK 180IG0.911111120.08888889 1.000000000.955555560.04444445
HAPMAP-MEX 100IG0.899999980.10000000 1.000000000.949999990.05000000
HAPMAP-MKK 286IG0.755244730.237762240.006993010.342782000.874125900.12587413
HAPMAP-TSI 176IG0.931818190.06818182 1.000000000.965909060.03409091
ss65845827KHP1 180AF0.933333340.06666667 0.751830000.966666640.03333334

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.093+/-0.1950000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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