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Reference SNP (refSNP) Cluster Report: rs2033962                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:94/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqbySubmitterwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G/T (REV)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.1725/864 (1000 Genomes)
A=0.1987/24946 (TOPMED)
HGVS Names
  • CM000664.2:g.157781929A>C
  • CM000664.2:g.157781929A>T
  • NC_000002.11:g.158638441A>C
  • NC_000002.12:g.157781929A>C
  • NC_000002.12:g.157781929A>T
  • NG_008004.1:g.98183T>A
  • NG_008004.1:g.98183T>G
  • NM_001105.4:c.68-1329T>A
  • NM_001105.4:c.68-1329T>G
  • NM_001111067.2:c.68-1329T>A
  • NM_001111067.2:c.68-1329T>G
  • NM_001347663.1:c.68-1329T>A
  • NM_001347663.1:c.68-1329T>G
  • NM_001347664.1:c.68-1329T>A
  • NM_001347664.1:c.68-1329T>G
  • NM_001347665.1:c.68-1329T>A
  • NM_001347665.1:c.68-1329T>G
  • NM_001347666.1:c.68-1329T>A
  • NM_001347666.1:c.68-1329T>G
  • NM_001347667.1:c.68-1329T>A
  • NM_001347667.1:c.68-1329T>G
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 ss276749976 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2033962 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
ss2943023TSC-CSHL|TSC1047479byFreqfwd/BG/Tctatgtgccatagacctttggagggagctcgaaagctgaatttcctaatatgaacagtgc01/29/0104/07/0494Genomicunknown
ss11445439WI_SSAHASNP|chr2.NT_005403.13_8797780rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag07/03/0310/10/03116Genomicunknown
ss16302435SC_SNP|NT_005403.14_8847859rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag11/18/0311/22/03120Genomicunknown
ss21650216SSAHASNP|WGSA-200403-chr2.chr2.NT_005403.14_8847859rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag03/20/0403/20/04121Genomicunknown
ss23251837PERLEGEN|afd1360361byFreqrev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag08/10/0409/13/04123Genomicunknown
ss44172854ABI|hCV11649878rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag07/18/0507/18/05126Genomicunknown
ss83958518HGSV|Cor18956_SNV_20070510.chr2_158463949rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag11/30/0712/06/07130Genomicunknown
ss91408774BCMHGSC_JDW|JWB-1330653rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag02/26/0803/01/08129Genomicunknown
ss96441007HUMANGENOME_JCVI|1103658265071rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag03/26/0803/26/08130Genomicunknown
ss103615554BGI|BGI_rs2033962rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag06/06/0806/18/09131Genomicunknown
ss1101228491000GENOMES|CEU.trio.12.15.2008_504996_chr2_158346687rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag12/17/0812/17/08130Genomicunknown
ss1111540141000GENOMES|NA19240_2008_12_16_457074_chr2_158346687rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag12/17/0812/17/08130Genomicunknown
ss117937584ILLUMINA-UK|NA18507_000195291_NCBI36.1_chr2_158346687rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag01/19/0901/20/09130Genomic99 %
ss136094111ENSEMBL|ENSSNP1643341rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag12/08/0810/15/09131Genomicunknown
ss138562012ENSEMBL|ENSSNP6298824rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag05/15/0905/18/09131Genomicunknown
ss157883941GMI|GMI_SNP_46989752rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag06/24/0906/25/09131Genomicunknown
ss164630205COMPLETE_GENOMICS|NA19240_36_chr2_158346687rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag09/29/0909/29/09132Genomicunknown
ss165494445COMPLETE_GENOMICS|NA07022_36_chr2_158346687rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag09/29/0909/30/09132Genomicunknown
ss167343408COMPLETE_GENOMICS|NA20431_36_chr2_158346687rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag09/30/0909/30/09132Genomicunknown
ss201262180BUSHMAN|BUSHMAN-chr2-158346686rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag02/16/1003/07/10132Genomicunknown
ss205642231BCM-HGSC-SUB|BCM_CMT_1011-300022rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag03/15/1003/16/10132Genomicunknown
ss2196062061000GENOMES|pilot_1_YRI_1415889_chr2_158346687rev/A/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag04/22/1004/22/10132Genomicunknown
ss2314330711000GENOMES|pilot_1_CEU_1037700_chr2_158346687rev/A/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag05/01/1005/01/10132Genomicunknown
ss2389272311000GENOMES|pilot_1_CHB+JPT_812308_chr2_158346687rev/A/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag05/01/1005/01/10132Genomicunknown
ss253610428BL|SNP164705_2_158346687rev/TA/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag08/18/1008/18/10134Genomicunknown
ss276749976GMI|GMI_AK_SNP_1070185rev/A/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag12/16/1012/16/10137Genomicunknown
ss284468706GMI|GMI_NA10851_SNP_481477rev/A/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag12/17/1012/17/10138Genomicunknown
ss292408243PJP|SNP_1914601_chr2_158346687rev/A/Cgcactgttcatattaggaaattcagctttcgagctccctccaaaggtctatggcacatag01/21/1101/21/11134Genomicunknown
ss555981720TISHKOFF|snp_chr2_158638441rev/TA/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca11/22/1211/23/12138Genomicunknown
ss649624071SSMP|2_158638441rev/TA/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca12/14/1202/10/15138Genomicunknown
ss977546233EVA-GONL|EVA-GONL_rs2033962rev/TA/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca04/23/1404/23/14142Genomicunknown
ss1069633351JMKIDD_LAB|HGDP_WGS_chr2_158638441rev/TA/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca07/10/1407/10/14142Genomicunknown
ss13000568691000GENOMES|PHASE3_V1_11156677rev/A/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca08/16/1408/16/14142Genomicunknown
ss1428793052DDI|DDI_rs2033962rev/TA/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca11/04/1411/04/14144Genomicunknown
ss1579160321EVA_GENOME_DK|EVA_GENOME_DK_snv_rs2033962rev/TA/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca02/19/1502/20/15144Genomicunknown
ss1586980929EVA_DECODE|EVA_DECODE_2_158346687_1182842_rs2033962rev/TA/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca03/02/1503/03/15144Genomicunknown
ss1604948791EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_2_158638441_6119732rev/A/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca03/04/1503/04/15144Genomicunknown
ss1647942824EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_2_158638441_6119732rev/A/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca03/04/1503/04/15144Genomicunknown
ss1797780908HAMMER_LAB|Hsieh_1176344rev/TA/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca07/15/1507/15/15146Genomicunknown
ss1920799841WEILL_CORNELL_DGM|SNV:chr2:158638441rev/TA/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca10/16/1510/16/15147Genomicunknown
ss1968931843GENOMED|rs2033962rev/TA/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca02/16/1602/16/16147Genomicunknown
ss2020929627JJLAB|SNP1432182rev/TA/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca08/29/1608/30/16149Genomicunknown
ss2148995368USC_VALOUEV|NC_000002.11:g.158638441A>Crev/A/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca11/17/1611/17/16150Genomicunknown
ss2235803463HUMAN_LONGEVITY|HLI-2-157781929-A-Crev/A/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca11/18/1611/18/16150Genomicunknown
ss2402198523TOPMED|2_158638441_A/Crev/A/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca11/19/1611/19/16150Genomicunknown
ss2624969595SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV903559rev/A/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca01/06/1701/06/17151Genomicunknown
ss2703628028GRF|rs2033962rev/A/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca02/13/1702/13/17151Genomicunknown
ss2781752419GNOMAD|rs2033962rev/A/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca05/17/1705/17/17151Genomicunknown
ss2985188389AFFY|Axiom_PsorMich_Affx-18313061rev/A/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca05/24/1705/24/17151Genomicunknown
ss2985810138AFFY|Axiom_Smokesc1_Affx-18313061rev/A/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca05/24/1705/24/17151Genomicunknown
ss2990715244SWEGEN|NC_000002.11:g.158638441A>Crev/A/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca05/30/1705/30/17151Genomicunknown
ss3024227096BIOINF_KMB_FNS_UNIBA|2.157781929A>Crev/A/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca07/05/1707/05/17151Genomicunknown
ss3327817506TOPMED|TOPMed_freeze_5?chr2:157,781,929-01rev/A/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca10/02/1710/02/17151Genomicunknown
ss3327817507TOPMED|TOPMed_freeze_5?chr2:157,781,929-02rev/A/Tgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca10/02/1710/02/17151Genomicunknown
ss3344562113CSHL|rs2033962rev/A/Cgttcatattaggaaattcagctttcgagctccctccaaaggtctatggca10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2033962|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G/T'|mol=Genomic|build=151
 GCTCATTAAG AATGTTTGAG GGCTCTTGAT TCTCAGGGGT GAGACTGGTG ACATACATAG
 ACTGTCAGCG GCTATTTTGG ATTTTCTGCT TTCAGGCATG TCTTTGCTCT TGGATGAGCC
 CCTTGTGGTT TTCAAAGGAA CTAGCAAGTC AATTATAAAT AGAAGGCTGT GTCTGTGTGT
 CTGCATGCAC TTACTCTGTG GGACGAGGCA CCCACATTAC AGTGGGCAGT GAACTATTTT
 TCCACTTCTT TGAAGAGGGA AGAAGAAAGA TTAAGAATGC TTTTCTCTTT TTGAGATAAC
 CCACATCTCT ACACACACCC ACACAAATCT GTGTAAATGA ACTTGACATT TTCAAAGACC
 TTACCTTAAG GTCTCCTCTG GAAAGCACAG CCACCCAACC TGTTATTTTA AGAAAGAAGC
 ATTTATCTCC TAGACCCACT ACTGAGGGTT CAGGGATTAG AAGGCAGCCT CTATGTGCCA
 TAGACCTTTG GAGGGAGCTC
 D
 GAAAGCTGAA TTTCCTAATA TGAACAGTGC TTCGGCAAAA GTGGCCTCAG CTAACTAATC
 AGTGGCCTCT AGGACTTGGC TGTTTACATT TTATCCTCTG TTTCCTTCCC CACTAGTAGA
 AACTGTGGGA CCAGCAAGTC TAAACTAATC ATACTGACAA GGGAAGAGAA AAGAGTAATG
 TGAAAATGCA GATGCAAATA AGTATTCTCA GAAAGAGACA ATTAAGCAGA GTGATTAGAT
 GTGCTTCCCT GATCATCCGT TTCTGCCTCT TTCCATTGCA CCTTGAACTC CCTAGGTGTG
 TATTCTTCCA GTGGTCCCAC CTGTCACCTT ACTGTTCAAA CATTATTCGG TTCTCTTGGT
 CTCCTTGTGC CCTCATTCTC CATATTTGGC ACCATTTTTT TCCTGCCAGC CAAAAATTCT
 TAAGCAGGTG TTAATTCCCA CTATAATCTA TGTAAACTTT AGTGTTACCA CTAGTGAAAA
 AGTTAGTCTA GGCATCTAGC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_005403 ABBA01004847
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs2033962 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceG/G
G/T
T/T
HWPG
T
ss117937584YRI 2IG 1.00000000 0.500000000.50000000
ss1300056869EAS 1008AF 0.928600010.07140000
EUR 1006AF 0.824999990.17500000
AFR 1322AF 0.730000020.27000001
AMR 694AF 0.850100040.14990000
SAS 978AF 0.841499980.15850000
ss136094111ENSEMBL_Venter 2IG1.00000000 1.00000000
ss138562012ENSEMBL_Watson 2IG1.00000000 1.00000000
ss164630205YRISub-Saharan African 2IG1.00000000 1.00000000
ss165494445CEUEuropean 2IG1.00000000 1.00000000
ss167343408PGP 2IG 1.00000000 0.500000000.50000000
ss201262180BANTU 2IG 1.00000000 0.500000000.50000000
ss219606206pilot_1_YRI_low_coverage_panel 118AF 0.720339000.27966103
ss231433071pilot_1_CEU_low_coverage_panel 120AF 0.774999980.22499999
ss23251837AFD_EUR_PANELEuropean 48IG0.750000000.166666670.083333340.099721000.833333310.16666667
AFD_AFR_PANELAfrican American 42IG0.571428600.380952390.047619051.000000000.761904780.23809524
AFD_CHN_PANELAsian 48IG0.833333310.16666667 1.000000000.916666690.08333334
ss238927231pilot_1_CHB+JPT_low_coverage_panel 120AF 0.866666670.13333334
ss2943023HapMap-CEUEuropean 120IG0.633333330.36666667 0.317310000.816666660.18333334
HapMap-HCBAsian 90IG0.800000010.177777780.022222220.527089000.888888900.11111111
HapMap-JPTAsian 88IG0.772727250.22727273 0.751830000.886363630.11363637
HapMap-YRISub-Saharan African 120IG0.550000010.400000010.050000000.654721000.750000000.25000000
ss96441007J. Craig Venter 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.286+/-0.2470000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitWith1000GenomeData
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNPNCBI
UNKNOWNUNKNOWNUNKNOWN

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