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Reference SNP (refSNP) Cluster Report: rs56379106                 ** With Benign allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:129/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:With Benign allele [ClinVar]
MAF/MinorAlleleCount:T=0.0031/379 (ExAC)
T=0.0012/6 (1000 Genomes)
T=0.0055/72 (GO-ESP)
T=0.0038/474 (TOPMED)
HGVS Names
  • CM000670.2:g.18222237C>T
  • NC_000008.10:g.18079746C>T
  • NC_000008.11:g.18222237C>T
  • NG_012245.2:g.56776C>T
  • NM_000662.7:c.190C>T
  • NM_001160170.3:c.190C>T
  • NM_001160171.3:c.190C>T
  • NM_001160172.3:c.190C>T
  • NM_001160173.3:c.190C>T
  • NM_001160174.2:c.190C>T
  • NM_001160175.3:c.376C>T
  • NM_001160176.3:c.376C>T
  • NM_001160179.2:c.190C>T
  • NM_001291962.1:c.376C>T
  • NP_000653.3:p.Arg64Trp
  • NP_001153642.1:p.Arg64Trp
  • NP_001153643.1:p.Arg64Trp
  • NP_001153644.1:p.Arg64Trp
  • NP_001153645.1:p.Arg64Trp
  • NP_001153646.1:p.Arg64Trp
  • NP_001153647.1:p.Arg126Trp
  • NP_001153648.1:p.Arg126Trp
  • NP_001153651.1:p.Arg64Trp
  • NP_001278891.1:p.Arg126Trp
  • XP_005273734.1:p.Arg126Trp
  • XP_005273735.1:p.Arg64Trp
  • XP_005273736.1:p.Arg64Trp
  • XP_006716473.1:p.Arg64Trp
  • XP_011542989.1:p.Arg126Trp
  • XP_011542990.1:p.Arg126Trp
  • XP_011542991.1:p.Arg64Trp
  • XP_016869436.1:p.Arg126Trp
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 ss105439097 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs56379106 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
ss75246482ILLUMINA|ILMN_Human_1M_SNP6fwd/BC/Tgccatttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaatcatc08/28/0708/29/07129Genomicunknown
ss105434751AFFY_DM3_1|DMET3B14970fwd/BC/Tgccatttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaatcatc09/03/0809/03/08130Genomicunknown
ss105439097SNP500CANCER|NAT1-19byFreqfwd/BC/Tgccatttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaatcatc09/05/0809/05/14130Genomicunknown
ss161088682ILLUMINA|HumanOmni1-Quad_v1-0_B_SNP6-0_B_F_1514230379fwd/BC/Tgccatttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaatcatc08/04/0910/05/09131Genomicunknown
ss169136510ILLUMINA|Human1M-Duov3_B_SNP6-unknown_B_F_1514230379fwd/BC/Tgccatttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaatcatc10/01/0910/01/09132Genomicunknown
ss3347240061000GENOMES|20100804_snps_6367547_chr8_18079746fwd/C/Tgccatttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaatcatc03/22/1103/22/11134Genomicunknown
ss342253577NHLBI-ESP|ESP2500-chr8-18079746byFreqfwd/BC/Tgccatttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaatcatc03/25/1109/05/14134Genomicunknown
ss483025726ILLUMINA|HumanOmni1-Quad_v1-0_C_SNP6-0_B_F_1853019320fwd/BC/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa01/30/1208/28/15146Genomicunknown
ss4909607051000GENOMES|20110521_exome_468503_chr8_18079746fwd/BC/Tgccatttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaatcatc02/10/1202/21/12137Genomicunknown
ss491410739EXOME_CHIP|nonsyn_126965_chr_8_18079746fwd/BC/Tgccatttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaatcatc03/05/1203/05/12137Genomicunknown
ss491921824CLINSEQ_SNP|SNV-chr8-18124026byFreqfwd/BC/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa03/06/1209/05/14137Genomicunknown
ss537652788ILLUMINA|HumanOmni5-4v1_B_SNP6-0_B_F_1853019320fwd/BC/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa06/22/1208/29/15146Genomicunknown
ss780867809ILLUMINA|HumanOmni25Exome-8v1_A_exm685613-0_B_F_1923019585fwd/BC/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa05/30/1307/10/15146Genomicunknown
ss783552740ILLUMINA|HumanOmniExpressExome-8v1_A_exm685613-0_B_F_1923019585fwd/BC/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa05/31/1306/19/15146Genomicunknown
ss985254175EVA-GONL|EVA-GONL_rs56379106fwd/BC/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa04/23/1404/25/14142Genomicunknown
ss13288471041000GENOMES|PHASE3_V1_41157943fwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa08/16/1408/16/14142Genomicunknown
ss1594843093EVA_DECODE|EVA_DECODE_8_18124026_221803_rs56379106fwd/BC/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa03/02/1503/03/15144Genomicunknown
ss1620096451EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_8_18079746_22757057fwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa03/04/1503/04/15144Genomicunknown
ss1663090484EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_8_18079746_22757057fwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa03/04/1503/04/15144Genomicunknown
ss1689107595EVA_EXAC|EVA_EXAC_4197000fwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa03/04/1503/04/15144Genomicunknown
ss1711194373EVA_MGP|EVA_XIMO_310133fwd/BC/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa03/09/1503/09/15144Genomicunknown
ss1752722033ILLUMINA|OmniExpressExome-8v1-1_B_exm685613-0_B_F_1923019585fwd/BC/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa05/27/1506/09/15146Genomicunknown
ss1917826192ILLUMINA|HumanExome-12v1-1_B_exm685613-0_B_F_1923019585fwd/BC/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa10/16/1510/16/15147Genomicunknown
ss1946231045ILLUMINA|HumanCoreExome-12v1-0_C_exm685613-0_B_F_1923019585fwd/BC/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa10/29/1510/29/15147Genomicunknown
ss1959092237ILLUMINA|exm685613-0_B_F_1923019585fwd/BC/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa11/13/1511/13/15147Genomicunknown
ss2024970095JJLAB|SNP5472650fwd/BC/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa08/29/1608/30/16149Genomicunknown
ss2301150648HUMAN_LONGEVITY|HLI-8-18222237-C-Tfwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa11/18/1611/18/16150Genomicunknown
ss2470808490TOPMED|8_18079746_C/Tfwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa11/20/1611/20/16150Genomicunknown
ss2634717594ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_SNP6-0_B_F_1853019320fwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa02/02/1702/02/17151Genomicunknown
ss2711131551ILLUMINA|Consortium-OncoArray_15047405_A_rs56379106-131_B_F_1889936295fwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa03/22/1703/22/17151Genomicunknown
ss2737016325GNOMAD|exomes_rs56379106fwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa05/17/1705/17/17151Genomicunknown
ss2748005836GNOMAD|coding_rs56379106fwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa05/17/1705/17/17151Genomicunknown
ss2863915011GNOMAD|rs56379106fwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa05/19/1705/19/17151Genomicunknown
ss2985432566AFFY|Axiom_PsorMich_Affx-31855735fwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa05/24/1705/24/17151Genomicunknown
ss2986074620AFFY|Axiom_Smokesc1_Affx-31855735fwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa05/24/1705/24/17151Genomicunknown
ss3002777601SWEGEN|NC_000008.10:g.18079746C>Tfwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa05/30/1705/30/17151Genomicunknown
ss3022824282ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm685613-0_B_F_1923019585fwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa06/28/1706/28/17151Genomicunknown
ss3348073217CSHL|rs56379106fwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa10/02/1710/02/17151Genomicunknown
ss3555475054TOPMED|TOPMed_freeze_5?chr8:18,222,237fwd/C/Tttttgatcaagttgtgagaagaaatggggtggatggtgtctccaggtcaa10/06/1710/06/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs56379106|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 ATAACCATTG TATTTTTACA TGTTTAAAAT ATAGCCATAA TTAGCCTACT CAAATCCAAG
 TGTAAAAGTA AWATGWTTTG CTTTCGTTTT GTTTTCCTTG CTTAGGGGAT CATGGACATT
 GAAGCATATC TKGAAAGAAT TGGCTATAAG AAGTCTAGGA ACAAATTGGA CTTGGAAACA
 TTAACTGACA TTCTTCAACA CCAGATCYGA GCTGTTCCCT TTGAGAACCT TAACATCCAT
 TGTGGGGATG CCATGGACTT AGGCTTAGAG GCCATTTTTG ATCAAGTTGT GAGAAGAAAT
 Y
 GGGGTGGATG GTGTCTCCAG GTCAATCATC TTCTGTACTG GGCTCTGACC ACTATTGGTT
 TTGAGACCAC GATGTTGGGA GGGTATGTTT ACAGCACTCC AGCCAAAAAA TACAGCACTG
 GCATGATTCA CCTTCTCCTG CAGGTGACCA TTGATGGCAN NAACTACATT GTYGATGCTG
 GGTTTGGACG CTCATACCAG ATGTGGCAGC CYCTGGAGTT AATTTCTGGG AAGGATCAGC
 CTCMGGTGCC TTGTRTCTTC CGTTTGACRG AAGAGAATGG ATTCTGGTAT CTAGACCAAA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000008
dbSNP Blast Analysis
3D structure mapping
NP_000653  NP_001153642  NP_001153643  NP_001153644  NP_001153645  NP_001153646  NP_001153647  NP_001153648  NP_001153651  

  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
ss105439097P2 420GF0.990476190.00952381 1.000000000.995238070.00476190
CAUC2 120GF0.966666640.03333334 1.000000000.983333350.01666667
AFR2 120GF1.00000000 1.00000000
P3 554GF0.996389870.00361011 1.000000000.998194930.00180505
CAUC3 130GF0.984615390.01538462 1.000000000.992307660.00769231
AFR3 150GF1.00000000 1.00000000
HISP3 98GF1.00000000 1.00000000
PAC3 176GF1.00000000 1.00000000
ASI2 180GF1.00000000 1.00000000
ss1328847104EAS 1008AF 1.00000000
EUR 1006AF 0.994999950.00500000
AFR 1322AF 0.999199990.00080000
AMR 694AF 1.00000000
SAS 978AF 1.00000000
ss1689107595ExAc_Aggregated_Populations121412AF 0.996878390.00312160
ss342253577ESP_Cohort_Populations 4550GF0.988571410.01142857 1.000000000.994285700.00571429
ss491921824CSAgilent 1323GF0.994000020.00600000 1.000000000.996999980.00300000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.006+/-0.0550000

  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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