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Reference SNP (refSNP) Cluster Report: rs2020908                 ** other **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:94/142
Map to Genome Build:106/Weight
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMed
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/G (FWD)
Allele Origin:C:germline
G:germline
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:other
MAF/MinorAlleleCount:G=0.0020/10
MAF Source:1000 Genomes
HGVS Names
  • NC_000002.11:g.48026308C>G
  • NC_000002.12:g.47799169C>G
  • NG_007111.1:g.21023C>G
  • NM_000179.2:c.1186C>G
  • NM_001281492.1:c.796C>G
  • NM_001281493.1:c.280C>G
  • NM_001281494.1:c.280C>G
  • NP_000170.1:p.Leu396Val
  • NP_001268421.1:p.Leu266Val
  • NP_001268422.1:p.Leu94Val
  • NP_001268423.1:p.Leu94Val
  • XM_005264271.1:c.889C>G
  • XP_005264328.1:p.Leu297Val
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 ss4384594 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2020908 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
ss2924019UWGC|gtbp-e4+f559fwd/BC/Gcctgatcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaattctt09/17/0110/10/03101Genomicunknown
ss3188801HGBASE|SNP000064539fwd/BC/Gtcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaa07/23/0110/10/0398cDNAunknown
ss4384594EGP_SNPS|MSH6-016940byFreqfwd/BC/Gcctgatcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaattctt03/15/0210/25/06103Genomicunknown
ss37042839ICRCG|MSH1-396fwd/C/Gcctgatcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaattctt04/04/0504/21/05125Genomicunknown
ss74809502AFFY|SNP_M-182291fwd/BC/Gcctgatcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaattctt08/09/0708/09/07128Genomicunknown
ss86344855CANCER-GENOME|4449fwd/C/Gcctgatcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaattctt01/25/0801/25/08129Genomicunknown
ss97035917HUMANGENOME_JCVI|1103658091309fwd/C/Gcctgatcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaattctt03/28/0803/28/08130Genomicunknown
ss143899721ENSEMBL|ENSSNP4354644fwd/C/Gcctgatcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaattctt12/08/0810/20/09131Genomicunknown
ss160489389ILLUMINA|HumanOmni1-Quad_v1-0_B_rs2020908-128_T_R_1562132711rev/C/Gaagaattgaggaaatcctcaggcacatagatgtagatgcatcaaaatcggggtgatcagg08/04/0910/02/09131Genomicunknown
ss2311542951000GENOMES|pilot_1_CEU_758924_chr2_47879812fwd/C/Gcctgatcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaattctt05/01/1005/01/10132Genomicunknown
ss292262977PJP|SNP_1769335_chr2_47879812fwd/C/Gcctgatcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaattctt01/21/1101/21/11134Genomicunknown
ss342059159NHLBI-ESP|ESP2500-chr2-48026308byFreqfwd/C/Gcctgatcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaattctt03/25/1109/05/14134Genomicunknown
ss472343115CORRELAGEN|MSH6_1186C_G_060311fwd/C/Gcctgatcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaattctt11/18/1111/22/11136Genomicunknown
ss480383662ILLUMINA|HumanOmni2.5-4v1_B_rs2020908-128_T_R_1735681586rev/C/Gaagaattgaggaaatcctcaggcacatagatgtagatgcatcaaaatcggggtgatcagg01/30/1201/31/12137Genomicunknown
ss480396321ILLUMINA|HumanOmniExpress-12v1_C_rs2020908-131_T_R_1853408862rev/C/Gaagaattgaggaaatcctcaggcacatagatgtagatgcatcaaaatcggggtgatcagg01/30/1201/31/12137Genomicunknown
ss481172986ILLUMINA|HumanOmni1-Quad_v1-0_C_rs2020908-131_T_R_1865560706rev/C/Gaagaattgaggaaatcctcaggcacatagatgtagatgcatcaaaatcggggtgatcagg01/30/1201/31/12137Genomicunknown
ss484989413ILLUMINA|HumanOmni2.5-4v1_D_rs2020908-131_T_R_1853408862rev/C/Gaagaattgaggaaatcctcaggcacatagatgtagatgcatcaaaatcggggtgatcagg01/30/1202/04/12137Genomicunknown
ss4898152491000GENOMES|20110521_exome_341235_chr2_48026308fwd/C/Gcctgatcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaattctt02/10/1202/21/12137Genomicunknown
ss491318701EXOME_CHIP|nonsyn_34928_chr_2_48026308fwd/C/Gcctgatcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaattctt03/05/1203/05/12137Genomicunknown
ss491783036CLINSEQ_SNP|SNV-chr2-47879812byFreqfwd/C/Gtcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaa03/06/1209/05/14137Genomicunknown
ss537023699ILLUMINA|HumanOmni5-4v1_B__rs2020908-131_T_R_1893170226rev/C/Gaagaattgaggaaatcctcaggcacatagatgtagatgcatcaaaatcggggtgatcagg06/22/1207/03/12138Genomicunknown
ss538293054MMR_WOODS|MSH6_complex_44fwd/C/Gcctgatcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaattctt07/31/1210/25/12137Genomicunknown
ss779025604ILLUMINA|HumanOmni25Exome-8v1_A_rs2020908-131_T_R_1865560706fwd/C/Gaagaattgaggaaatcctcaggcacatagatgtagatgcatcaaaatcggggtgatcagg05/30/1305/30/13142Genomicunknown
ss782941022ILLUMINA|HumanOmni2.5-4v1_H_rs2020908-131_T_R_1853408862fwd/C/Gaagaattgaggaaatcctcaggcacatagatgtagatgcatcaaaatcggggtgatcagg05/30/1305/31/13142Genomicunknown
ss783903599ILLUMINA|HumanOmniExpressExome-8v1_A_rs2020908-131_T_R_1893170226fwd/C/Gaagaattgaggaaatcctcaggcacatagatgtagatgcatcaaaatcggggtgatcagg05/31/1305/31/13142Genomicunknown
ss834488251ILLUMINA|HumanOmni2.5-8v1_A_rs2020908-131_T_R_1865560706fwd/C/Gaagaattgaggaaatcctcaggcacatagatgtagatgcatcaaaatcggggtgatcagg09/18/1309/18/13142Genomicunknown
ss976788939EVA-GONL|EVA-GONL_rs2020908fwd/C/Gtcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaa04/23/1404/23/14142Genomicunknown
ss12970647741000GENOMES|PHASE3_V1_8044844fwd/C/Gtcaccccgattttgatgcatctacatctatgtgcctgaggatttcctcaa08/16/1408/16/14142Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2020908|allelePos=256|totalLen=511|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=142
 AAAAGGAAAA GCTCTAGGAA GGAAACGCCC TCAGCCACCA AACAAGCAAC TAGCATTTCA
 TCAGAAACCA AGAATACTTT GAGAGCTTTC TCTGCCCCTC AAAATTCTGA ATCCCAAGCC
 CACGTTAGTG GAGGTGGTGA TGACAGTAGT CGCCCTACTG TTTGGTATCA TGAAACTTTA
 GAATGGCTTA AGGAGGAAAA GAGAAGAGAT GAGCACAGGA GGAGGCCTGA TCACCCCGAT
 TTTGATGCAT CTACA
 S
 TCTATGTGCC TGAGGATTTC CTCAATTCTT GTACTCCTGG GATGAGGAAG TGGTGGCAGA
 TTAAGTCTCA GAACTTTGAT CTTGTCATCT GTTACAAGGT GGGGAAATTT TATGAGCTGT
 ACCACATGGA TGCTCTTATT GGAGTCAGTG AACTGGGGCT GGTATTCATG AAAGGCAACT
 GGGCCCATTC TGGCTTTCCT GAAATTGCAT TTGGCCGTTA TTCAGATTCC CTGGTGCAGA
 AGGGCTATAA AGTAG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
U54777 ABBA01075176
dbSNP Blast Analysis
UniGene Cluster ID
445052
3D structure mapping
NP_000170  

  Population Diversity (in rs orientation) back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/G
G/G
HWPC
G
ss143899721ENSEMBL_Venter 2IG 1.000 0.500 0.500
ss231154295pilot_1_CEU_low_coverage_panel 120AF 0.983 0.017
ss2924019NIHPDRGlobal 88IG 0.977 0.023 1.000 0.989 0.011
ss342059159ESP_Cohort_Populations 4518GF 0.991 0.009 1.000 0.995 0.005
ss4384594PDR90Global 180IG 0.989 0.011 1.000 0.994 0.006
CEPH 184AF 1.000
HapMap-CEUEuropean 120IG 0.983 0.017 1.000 0.992 0.008
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 88IG 0.977 0.023 1.000 0.989 0.011
HapMap-YRISub-Saharan African 120IG 1.000 1.000
GScTr12003 192AF 0.990 0.010
ENSEMBL_Venter 2IG 1.000 1.000
ss491783036CSAgilent 1323GF 0.989 0.011 0.994 0.005
ss97035917J. Craig Venter 2IG 1.000 0.500 0.500

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.004+/-0.044617501450

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNYESYES

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