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Reference SNP (refSNP) Cluster Report: rs57865060                 ** With other 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:C:germline
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:With other allele [ClinVar]
MAF/MinorAlleleCount:T=0.0142/1426 (ExAC)
T=0.0104/52 (1000 Genomes)
T=0.0037/48 (GO-ESP)
T=0.0045/571 (TOPMED)
HGVS Names
  • CM000664.2:g.38074704C>T
  • NC_000002.11:g.38301847C>T
  • NC_000002.12:g.38074704C>T
  • NG_008386.2:g.6398G>A
  • NM_000104.3:c.685G>A
  • NP_000095.2:p.Glu229Lys
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 ss105439411 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs57865060 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
ss84155912PHARMGKB_AB_DME|PS206235_PA150030528_301byFreqfwd/BC/Ttgcccgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaactcggg12/06/0709/05/14129Genomicunknown
ss105434424AFFY_DM3_1|DMET3B12482fwd/BC/Ttgcccgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaactcggg09/03/0809/03/08130Genomicunknown
ss105439411SNP500CANCER|CYP1B1-185byFreqrev/TA/Gcccgagttccgtgagctgctcagccacaacaagagttcgggcgcacggtgggcgcgggca09/05/0809/05/14130Genomicunknown
ss3295514981000GENOMES|20100804_snps_1195034_chr2_38301847fwd/C/Ttgcccgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaactcggg03/22/1103/22/11134Genomicunknown
ss342056016NHLBI-ESP|ESP2500-chr2-38301847byFreqfwd/BC/Ttgcccgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaactcggg03/25/1109/05/14134Genomicunknown
ss4898124641000GENOMES|20110521_exome_339870_chr2_38301847fwd/BC/Ttgcccgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaactcggg02/10/1202/21/12137Genomicunknown
ss491317867EXOME_CHIP|nonsyn_34094_chr_2_38301847fwd/BC/Ttgcccgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaactcggg03/05/1203/05/12137Genomicunknown
ss491782022CLINSEQ_SNP|SNV-chr2-38155351byFreqfwd/BC/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac03/06/1209/05/14137Genomicunknown
ss536414975ILLUMINA|HumanOmni5-4v1_B_kgp919372-0_T_R_1904607631fwd/BC/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac06/22/1208/28/15146Genomicunknown
ss649072409SSMP|2_38301847fwd/BC/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac12/14/1202/10/15138Genomicunknown
ss976704543EVA-GONL|EVA-GONL_rs57865060fwd/BC/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac04/23/1404/23/14142Genomicunknown
ss12967343141000GENOMES|PHASE3_V1_7702863fwd/C/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac08/16/1408/16/14142Genomicunknown
ss1457611151CLINVAR|SCV000087422rev/TA/Gcccgagttccgtgagctgctcagccacaacaagagttcgggcgcacggtgggcgcgggca11/23/1411/23/14142Genomicunknown
ss1584018103EVA_FINRISK|EVA_FINRISK_rs57865060fwd/BC/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac02/27/1502/27/15144Genomicunknown
ss1586111888EVA_DECODE|EVA_DECODE_2_38155351_313778_rs57865060fwd/BC/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac03/02/1503/02/15144Genomicunknown
ss1603247834EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_2_38301847_4256504fwd/C/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac03/04/1503/04/15144Genomicunknown
ss1646241867EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_2_38301847_4256504fwd/C/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac03/04/1503/04/15144Genomicunknown
ss1686272001EVA_EXAC|EVA_EXAC_1135443fwd/C/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac03/04/1503/04/15144Genomicunknown
ss1919938682WEILL_CORNELL_DGM|SNV:chr2:38301847fwd/BC/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac10/16/1510/16/15147Genomicunknown
ss1946037836ILLUMINA|HumanCoreExome-12v1-0_C_kgp919372-0_T_R_1904607631fwd/BC/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac10/29/1510/29/15147Genomicunknown
ss1958408515ILLUMINA|kgp919372-0_T_R_1904607631fwd/BC/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac11/13/1511/13/15147Genomicunknown
ss2229222222HUMAN_LONGEVITY|HLI-2-38074704-C-Tfwd/C/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac11/18/1611/18/16150Genomicunknown
ss2395146136TOPMED|2_38301847_C/Tfwd/C/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac11/19/1611/19/16150Genomicunknown
ss2633598868ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp919372-0_T_R_1904607631fwd/C/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac02/02/1702/02/17151Genomicunknown
ss2710897229ILLUMINA|Consortium-OncoArray_15047405_A_kgp919372-0_T_R_1904607631fwd/C/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac03/22/1703/22/17151Genomicunknown
ss2732609465GNOMAD|exomes_rs57865060fwd/C/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac05/17/1705/17/17151Genomicunknown
ss2746663487GNOMAD|coding_rs57865060fwd/C/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac05/17/1705/17/17151Genomicunknown
ss2772048345GNOMAD|rs57865060fwd/C/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac05/17/1705/17/17151Genomicunknown
ss2985165053AFFY|Axiom_PsorMich_Affx-20007576fwd/C/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac05/24/1705/24/17151Genomicunknown
ss2989311017SWEGEN|NC_000002.11:g.38301847C>Tfwd/C/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac05/30/1705/30/17151Genomicunknown
ss3021960998ILLUMINA|MEGA_Consortium_v2_15070954_A2_kgp919372-0_T_R_1904607631fwd/C/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac06/28/1706/28/17151Genomicunknown
ss3304618873TOPMED|TOPMed_freeze_5?chr2:38,074,704fwd/C/Tgcgcccaccgtgcgcccgaactcttgttgtggctgagcagctcacggaac10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs57865060|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 CGAAGATGTC AGTGATAGTG GCCGGTAMGT TCTCCAAATC CAGCCGCGCG CCACCACCGT
 GCGAGTCCCC GGCCGCCTTC TTTTCCGCAG AGAGGATAAA GGCGTCCATC ATGTCGCGGG
 GGGCGGCCCC GGGCCGAAGG CTTTCGCAGT GCCTCAAGAA CTTGTCCAGG ATGAAGTTGC
 TGAAGTTGMG GTTGAGCTGC TCGAATTCGC GGAAAACGGT GCGCACCGGG TTGGGGAAGT
 ACTRCAGCCA GGGCATSACG TCCACCAGGC TGCCCGCGCC CACCGTGCGC CCGAACTCTT
 Y
 GTTGTGGCTG AGCAGCTCAC GGAACTCGGG GWCGTCGTGG MTGTAGCGGC AGCCGAAACA
 CACGGCAYTC ATGACGTTGG CCACGGCCAC RAYGGTCAGC GGCCTCGGGT CGAGGAAGGC
 KCCGTCCGCG CTGCCGCGCA CCAGCAGCGC CACCAGCTCG CGCGCCTCGC TCAGCACGTG
 GCCCTCGAGG ACTTGGCGGC TGCGCGGCTG GCGCGTGAAG AAGTTGCGCA TCATGCTGTG
 GGCTGCGCGC CGCTGCACCT TCCAGTGCTC CGAGTAGTGG CCGAAAGCCA TGCTGCGGCC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000002
dbSNP Blast Analysis
3D structure mapping
NP_000095  
OMIM
120200

  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
ss105439411P2 420GF0.995238070.00476190 1.000000000.997619030.00238095
CAUC2 120GF0.983333350.01666667 1.000000000.991666670.00833333
AFR2 120GF1.00000000 1.00000000
P3 544GF0.974264680.02573529 1.000000000.987132370.01286765
CAUC3 128GF0.984375000.01562500 1.000000000.992187500.00781250
AFR3 148GF1.00000000 1.00000000
HISP3 94GF1.00000000 1.00000000
PAC3 174GF0.931034510.06896552 1.000000000.965517220.03448276
ASI2 180GF1.00000000 1.00000000
ss1296734314EAS 1008AF 1.00000000
EUR 1006AF 0.995999990.00400000
AFR 1322AF 1.00000000
AMR 694AF 0.997100060.00290000
SAS 978AF 0.953000010.04700000
ss1686272001ExAc_Aggregated_Populations120912AF 0.987974700.01202527
ss342056016ESP_Cohort_Populations 3576GF0.995525720.00447427 1.000000000.997762860.00223714
ss491782022CSAgilent 611GF0.977000000.02300000 1.000000000.988500000.01150000
ss84155912PA150030529 354AF 0.994350250.00564972

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.028+/-0.1150000

  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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