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Reference SNP (refSNP) Cluster Report: rs56053398                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:129/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.0003/38 (ExAC)
T=0.0016/8 (1000 Genomes)
T=0.0010/13 (GO-ESP)
T=0.0012/150 (TOPMED)
HGVS Names
  • CM000663.2:g.59905038C>T
  • NC_000001.10:g.60370710C>G
  • NC_000001.10:g.60370710C>T
  • NC_000001.11:g.59905038C>T
  • NG_007931.1:g.26714G>A
  • NG_007931.1:g.26714G>C
  • NM_000775.3:c.1024G>A
  • NM_000775.3:c.1024G>C
  • NP_000766.2:p.Asp342Asn
  • NP_000766.2:p.Asp342His
  • NR_134981.1:n.1055+2748G>A
  • NR_134981.1:n.1055+2748G>C
  • NR_134982.1:n.1076G>A
  • NR_134982.1:n.1076G>C
  • XR_246240.1:n.1030+2748G>A
  • XR_246240.1:n.1030+2748G>C
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 ss105439414 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs56053398 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
ss75254473ILLUMINA|ILMN_Human_1M_SNP43fwd/BC/Ttcggctgctgcccctggccaatcactctgtaatctcagcttgtactttttctggtaaaga08/28/0708/29/07129Genomicunknown
ss105434280AFFY_DM3_1|DMET3B11625fwd/BC/Ttcggctgctgcccctggccaatcactctgtaatctcagcttgtactttttctggtaaaga09/03/0809/03/08130Genomicunknown
ss105439414SNP500CANCER|CYP2J2-02byFreqrev/TA/Gtctttaccagaaaaagtacaagctgagattacagagtgattggccaggggcagcagccga09/05/0809/05/14130Genomicunknown
ss161082651ILLUMINA|HumanOmni1-Quad_v1-0_B_SNP43-0_T_R_1514230373rev/TA/Gtctttaccagaaaaagtacaagctgagattacagagtgattggccaggggcagcagccga08/04/0910/05/09131Genomicunknown
ss169136389ILLUMINA|Human1M-Duov3_B_SNP43-unknown_T_R_1514230373rev/TA/Gtctttaccagaaaaagtacaagctgagattacagagtgattggccaggggcagcagccga10/01/0910/01/09132Genomicunknown
ss198505218BUSHMAN|BUSHMAN-chr1-60143297fwd/C/Gtcggctgctgcccctggccaatcactctgtaatctcagcttgtactttttctggtaaaga02/16/1003/06/10132Genomicunknown
ss341967404NHLBI-ESP|ESP2500-chr1-60370710byFreqfwd/BC/Ttcggctgctgcccctggccaatcactctgtaatctcagcttgtactttttctggtaaaga03/25/1109/05/14134Genomicunknown
ss483025702ILLUMINA|HumanOmni1-Quad_v1-0_C_SNP43-0_T_R_1853084289fwd/BC/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt01/30/1208/28/15146Genomicunknown
ss4886699491000GENOMES|20110521_exome_11738_chr1_60370710fwd/BC/Ttcggctgctgcccctggccaatcactctgtaatctcagcttgtactttttctggtaaaga02/10/1202/13/12137Genomicunknown
ss491294679EXOME_CHIP|nonsyn_10906_chr_1_60370710fwd/BC/Ttcggctgctgcccctggccaatcactctgtaatctcagcttgtactttttctggtaaaga03/05/1203/05/12137Genomicunknown
ss537652781ILLUMINA|HumanOmni5-4v1_B_SNP43-0_T_R_1853084289fwd/BC/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt06/22/1208/28/15146Genomicunknown
ss780862027ILLUMINA|HumanOmni25Exome-8v1_A_exm64046-0_T_R_1919172578fwd/BC/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt05/30/1307/09/15146Genomicunknown
ss783546507ILLUMINA|HumanOmniExpressExome-8v1_A_exm64046-0_T_R_1919172578fwd/BC/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt05/31/1306/18/15146Genomicunknown
ss12910343381000GENOMES|PHASE3_V1_1766424fwd/C/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt08/16/1408/16/14142Genomicunknown
ss1685573517EVA_EXAC|EVA_EXAC_382304fwd/C/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt03/04/1503/04/15144Genomicunknown
ss1751927320ILLUMINA|OmniExpressExome-8v1-1_B_exm64046-0_T_R_1919172578fwd/BC/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt05/27/1506/09/15146Genomicunknown
ss1917729429ILLUMINA|HumanExome-12v1-1_B_exm64046-0_T_R_1919172578fwd/BC/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt10/16/1510/16/15147Genomicunknown
ss1945996437ILLUMINA|HumanCoreExome-12v1-0_C_exm64046-0_T_R_1919172578fwd/BC/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt10/29/1510/29/15147Genomicunknown
ss1958276229ILLUMINA|exm64046-0_T_R_1919172578fwd/BC/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt11/13/1511/13/15147Genomicunknown
ss2162796853HUMAN_LONGEVITY|HLI-1-59905038-C-Tfwd/C/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt11/18/1611/18/16150Genomicunknown
ss2325042689TOPMED|1_60370710_C/Tfwd/C/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt11/19/1611/19/16150Genomicunknown
ss2632520421ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_SNP43-0_T_R_1853084289fwd/C/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt02/02/1702/02/17151Genomicunknown
ss2710673007ILLUMINA|Consortium-OncoArray_15047405_A_rs56053398-131_T_R_2077149028fwd/C/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt03/22/1703/22/17151Genomicunknown
ss2731538144GNOMAD|exomes_rs56053398fwd/C/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt05/17/1705/17/17151Genomicunknown
ss2746343571GNOMAD|coding_rs56053398fwd/C/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt05/17/1705/17/17151Genomicunknown
ss2755540095GNOMAD|rs56053398fwd/C/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt05/17/1705/17/17151Genomicunknown
ss3021091221ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm64046-0_T_R_1919172578fwd/C/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt06/28/1706/28/17151Genomicunknown
ss3077546123TOPMED|TOPMed_freeze_5?chr1:59,905,038fwd/C/Ttgctgcccctggccaatcactctgtaatctcagcttgtactttttctggt09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs56053398|allelePos=302|totalLen=602|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 ATCTAGTATT ATATCAGGTA TAAGATATCT TTTTCTTCCA TTTAAATGAT TCCTTAGGAC
 AAGAATAAAT GTCACTTCTC AAGTTCAAGT TTCTACCCCC CTAAAAGATG GGCTTGAAGA
 TCTGCTTAAT TACCTTGGGC AGGTGGTACC CAGCCAAAGT GGTATCAACT GTCACTTCCC
 TGGGNAACGT TCWGGGGGAT GATGTTGCCC ATTCTCTGCA CCTCATGGAT GACAGCATTG
 GTGTAGGGCA TGGACTCCCG GGCGGCTGTG CTCGGCTGCT GCCCCTGGCC AATCACTCTG
 T
 Y
 AATCTCAGCT TGTACTTTTT CTGGTAAAGA GGGAAGGGTT CTATTATTTT TTAAACTTTT
 ATGCTTTATT ATAAAGAGGT ATGAGTGGTC TCCAAGATGT CATCTGTTGT ATTTCAATTA
 GTGACCAGGT TGCAAGAAAT AAAATGGTTC TTAACCTTTT GAAAGGCTTA TTCAGAAAAC
 TACCACCTCT GTAAATCTCC TTGAGCCTGG TTAGGCTATG GGATGGAATG ACCAGGATTA
 ATATGGCTAA ACTTCATTAC ATCAGACCCC AGCGGACTTG GTGTCTGGTG AAGACCCACT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000001
dbSNP Blast Analysis
3D structure mapping
NP_000766  

  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
ss105439414P1 204GF0.990196050.00980392 1.000000000.995098050.00490196
CAUC1 62GF1.00000000 1.00000000
AFR1 48GF0.958333310.04166667 1.000000000.979166690.02083333
HISP1 46GF1.00000000 1.00000000
PAC1 48GF1.00000000 1.00000000
P3 558GF0.992831530.00716846 1.000000000.996415790.00358423
CAUC3 132GF1.00000000 1.00000000
AFR3 150GF0.973333360.02666667 1.000000000.986666680.01333333
HISP3 98GF1.00000000 1.00000000
PAC3 178GF1.00000000 1.00000000
ss1291034338EAS 1008AF 1.00000000
EUR 1006AF 1.00000000
AFR 1322AF 0.993900000.00610000
AMR 694AF 1.00000000
SAS 978AF 1.00000000
ss1685573517ExAc_Aggregated_Populations121412AF 0.999687020.00031298
ss341967404ESP_Cohort_Populations 4552GF0.997803150.00219684 1.000000000.998901610.00109842

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.001+/-0.0180000

  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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