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Reference SNP (refSNP) Cluster Report: rs1456669                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:88/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.1641/822 (1000 Genomes)
A=0.1314/16502 (TOPMED)
HGVS Names
  • CM000665.2:g.148217848C>A
  • NC_000003.11:g.147935635C>A
  • NC_000003.12:g.148217848C>A
  • XR_924565.1:n.86+2662G>T
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 ss277394243 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1456669 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
ss2274411TSC-CSHL|TSC0688859fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat10/20/0010/25/0688Genomic95 %
ss6009353SC_JCM|NT_005775.12_2455756fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat01/10/0310/10/03111Genomicunknown
ss20180421CSHL-HAPMAP|CSHL-HuFF-200402.chr3.NT_005612.14_54430789fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat02/21/0403/04/04120Genomicunknown
ss23882277PERLEGEN|afd4602473byFreqfwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat08/10/0409/13/04123Genomicunknown
ss44383027ABI|hCV7625769byFreqfwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat07/18/0511/03/06126Genomicunknown
ss65808702ILLUMINA|Human1-rs1456669fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat10/10/0610/10/06127Genomicunknown
ss66128719AFFY|SNP_A-2066494byFreqfwd/TA/Caatttttgcagctgacattttaccacttcttg10/27/0608/14/07127Genomicunknown
ss66672055ILLUMINA|HumanHap300v1.1_rs1456669fwd/BA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat11/09/0611/09/06127Genomicunknown
ss67108852ILLUMINA|HumanHap550v1.1_rs1456669fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat11/14/0611/14/06127Genomicunknown
ss67445410ILLUMINA|HumanHap650Yv1.0_rs1456669fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat11/14/0611/14/06127Genomicunknown
ss70434113ILLUMINA|HumanHap300v2.0_rs1456669fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat04/18/0711/18/07127Genomicunknown
ss70620283ILLUMINA|HumanHap550v3.0__rs1456669fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat04/20/0703/30/08130Genomicunknown
ss71168903ILLUMINA|HumanHap650Yv3.0_rs1456669fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat04/23/0704/23/07127Genomicunknown
ss75557120ILLUMINA|ILMN_Human_1M_rs1456669fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat08/28/0708/29/07129Genomicunknown
ss76132190AFFY|AFFY_6_1M_SNP_A-2066494fwd/TA/Caatttttgcagctgacattttaccacttcttg08/28/0708/30/07129Genomicunknown
ss83783014KRIBB_YJKIM|KHS542256fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat12/04/0712/05/07130Genomicunknown
ss121704867ILLUMINA|HumanCNV370v1_C_rs1456669fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat04/14/0904/14/09131Genomicunknown
ss153448793ILLUMINA|Human610_Quadv1_B_rs1456669-128_T_F_1501664810fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat06/18/0906/19/09131Genomicunknown
ss156324261GMI|GMI_SNP_191148163fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat06/24/0906/25/09131Genomicunknown
ss159272174ILLUMINA|Human660W-Quad_v1_A_rs1456669-128_T_F_1501664810fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat07/06/0907/06/09131Genomicunknown
ss161401684ENSEMBL|ENSSNP2060685byFreqfwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat09/24/0903/07/10131Genomicunknown
ss162707303COMPLETE_GENOMICS|NA07022_36_chr3_149418325fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat09/28/0909/29/09132Genomicunknown
ss167310846COMPLETE_GENOMICS|NA20431_36_chr3_149418325fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat09/30/0909/30/09132Genomicunknown
ss170530452ILLUMINA|HumanCNV370-Quadv3_C_rs1456669-128_T_F_1501664810fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat10/01/0910/03/09132Genomicunknown
ss172516033ILLUMINA|Human1M-Duov3_B_rs1456669-128_T_F_1501664810fwd/TA/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat10/01/0910/02/09132Genomicunknown
ss172597162AFFY|GenomeWideSNP_5_SNP_A-2066494fwd/TA/Caatttttgcagctgacattttaccacttcttg10/01/0910/02/09132Genomicunknown
ss2204902851000GENOMES|pilot_1_YRI_2299968_chr3_149418325fwd/A/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat04/22/1004/22/10132Genomicunknown
ss2320780641000GENOMES|pilot_1_CEU_1682693_chr3_149418325fwd/A/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat05/01/1005/01/10132Genomicunknown
ss2394392661000GENOMES|pilot_1_CHB+JPT_1324343_chr3_149418325fwd/A/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat05/01/1005/01/10132Genomicunknown
ss277394243GMI|GMI_AK_SNP_1714453fwd/A/Cggatataaatgcttaatttttgcagctgacattttaccacttcttgcttcctcattatat12/16/1012/16/10137Genomicunknown
ss536875101ILLUMINA|HumanOmni5-4v1_B_rs1456669-131_T_F_1908714048fwd/TA/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat06/22/1208/28/15146Genomicunknown
ss557017066TISHKOFF|snp_chr3_147935635fwd/TA/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat11/22/1211/23/12138Genomicunknown
ss650748536SSMP|3_147935635fwd/TA/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat12/14/1202/10/15138Genomicunknown
ss825403387ILLUMINA|HumanCNV370v1_C_rs1456669-126_T_F_IFB1152231029:0fwd/TA/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat06/24/1311/21/14147Genomicunknown
ss979283890EVA-GONL|EVA-GONL_rs1456669fwd/TA/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat04/23/1404/24/14142Genomicunknown
ss1070923959JMKIDD_LAB|HGDP_WGS_chr3_147935635fwd/TA/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat07/10/1407/10/14142Genomicunknown
ss13066327631000GENOMES|PHASE3_V1_18004398fwd/A/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat08/16/1408/16/14142Genomicunknown
ss1580229417EVA_GENOME_DK|EVA_GENOME_DK_snv_rs1456669fwd/TA/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat02/19/1502/20/15144Genomicunknown
ss1588774808EVA_DECODE|EVA_DECODE_3_149418325_1152451_rs1456669fwd/TA/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat03/02/1503/03/15144Genomicunknown
ss1608463563EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_3_147935635_9976206fwd/A/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat03/04/1503/04/15144Genomicunknown
ss1651457596EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_3_147935635_9976206fwd/A/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat03/04/1503/04/15144Genomicunknown
ss1712620861EVA_SVP|EVA_SVP_315260fwd/TA/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat03/12/1503/12/15144Genomicunknown
ss1800199063HAMMER_LAB|Hsieh_1895028fwd/TA/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat07/15/1507/15/15146Genomicunknown
ss1922507371WEILL_CORNELL_DGM|SNV:chr3:147935635fwd/TA/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat10/16/1510/17/15147Genomicunknown
ss1958615878ILLUMINA|JHU_3.147935634-1_T_F_2223582170fwd/TA/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat11/13/1511/13/15147Genomicunknown
ss1969549919GENOMED|rs1456669fwd/TA/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat02/16/1602/16/16147Genomicunknown
ss2021824695JJLAB|SNP2327250fwd/TA/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat08/29/1608/30/16149Genomicunknown
ss2149921085USC_VALOUEV|NC_000003.11:g.147935635C>Afwd/A/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat11/17/1611/17/16150Genomicunknown
ss2256816092HUMAN_LONGEVITY|HLI-3-148217848-C-Afwd/A/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat11/18/1611/18/16150Genomicunknown
ss2424195858TOPMED|3_147935635_C/Afwd/A/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat11/19/1611/19/16150Genomicunknown
ss2705334244GRF|rs1456669fwd/A/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat02/13/1702/13/17151Genomicunknown
ss2800485146GNOMAD|rs1456669fwd/A/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat05/18/1705/18/17151Genomicunknown
ss2993385574SWEGEN|NC_000003.11:g.147935635C>Afwd/A/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat05/30/1705/30/17151Genomicunknown
ss3022298103ILLUMINA|MEGA_Consortium_v2_15070954_A2_JHU_3.147935634-1_T_F_2223582170fwd/A/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat06/28/1706/28/17151Genomicunknown
ss3024680073BIOINF_KMB_FNS_UNIBA|3.148217848C>Afwd/A/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat07/05/1707/05/17151Genomicunknown
ss3345320691CSHL|rs1456669fwd/A/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat10/02/1710/02/17151Genomicunknown
ss3408640497TOPMED|TOPMed_freeze_5?chr3:148,217,848fwd/A/Ctaaatgcttaatttttgcagctgacattttaccacttcttgcttcctcat10/03/1710/03/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1456669|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=151
 ATGTTCATTG GGTTGTACCC ACTTTGAAGT TATATTTGTC TTCAACCTAT CCCTGTTCCC
 AGGAAATGAA ACAATGTGCT GATAATGAAT CAATAATATG TTGATACCGT GCATGGGATT
 AATCAAGAGC CCTTATTCTC TTTCAGGACA ATTTCAAGCT GCCAGTTATC AGCAGACGCA
 TGCAAGCTGG AGAGTAAGCC AAGCACATGC TTGATAGAAA CAATCAGGCT GCACATACTA
 ACCTTAGCAG TGAAATTCAG AAACGGCCTT TTGAGTTTCT AGGCCCCAAA GCTAGAAATG
 CACACAACCT TAGGTTAAAT ACCAATCCCC TCATTCTCTC CTTGGGTCAA CTAGTACACA
 TTCAAATTAC TTAACCTTGA GTTGCTTCTC TTGTAGTGAA GACACTAACT TACCTTTTCC
 TTTATACTTG AGAGGAGTAT CTAATTAAAA TAAAGATTTT CTCCACATTT GGATATAAAT
 GCTTAATTTT TGCAGCTGAC
 M
 ATTTTACCAC TTCTTGCTTC CTCATTATAT ATTGAGTAAA TATCAACTTC ATAGAGTAGA
 ATAAACCATT ACAGCTCTGA TTAAAGTGAC CCTAACAATC TGCTGTTGAT TGCCTCCTTC
 AGGGAGAATT CATTGATAAA TAATAATATA AGGAAACAAA AGATGCTATT TTAGTTGCTC
 TACTAAAAAC CAATTCTTAG AAGTAAGGCA ATATAAAAAC AATAAAAAGT TTGTTTGTTC
 CTCTTTTTAT TTTCCCCACT TAAAATTATA TGGCAATAAA ACATTCTTTC TATTCCAACT
 CTCTAATTTT ACACATGAAA AAATATATAA CTAGAAAAGT AAAAGGTACT GTCCCACCTT
 CACCAAGTTA GTTGTTTCCA GAATGTTGAT TCAGTTAAAA TTCTACACTT ACAGATTCTA
 TCTGCACTTT CCCTGACTTT ACTGACTTCT AAACTCCAGA CCTGATTCTT TATCTGGGTG
 GGCAGTGTTC TTACTCAATA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_005775.12
dbSNP Blast Analysis

  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.
SourceA/A
A/C
C/C
HWPA
C
ss1306632763EAS 1008AF 0.214300010.78570002
EUR 1006AF 0.127200010.87279999
AFR 1322AF 0.100600000.89940006
AMR 694AF 0.211799990.78820002
SAS 978AF 0.202500000.79750001
ss161401684ENSEMBL_celera 4IG0.50000000 0.50000000 0.500000000.50000000
ss162707303CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss167310846PGP 2IG1.00000000 1.00000000
ss220490285pilot_1_YRI_low_coverage_panel 118AF 0.084745760.91525424
ss232078064pilot_1_CEU_low_coverage_panel 120AF 0.125000000.87500000
ss23882277AFD_EUR_PANELEuropean 48IG 0.250000000.750000000.751830000.125000000.87500000
AFD_AFR_PANELAfrican American 46IG 0.217391300.782608691.000000000.108695650.89130437
AFD_CHN_PANELAsian 48IG0.208333330.375000000.416666660.294266000.395833340.60416669
ss239439266pilot_1_CHB+JPT_low_coverage_panel 120AF 0.208333330.79166669
ss44383027HapMap-CEUEuropean 226IG0.017699110.141592920.840707960.200325000.088495570.91150445
HapMap-HCBAsian 86IG0.093023260.465116290.441860470.751830000.325581400.67441863
HapMap-JPTAsian 172IG0.069767450.337209310.593023240.527089000.238372090.76162791
HapMap-YRISub-Saharan African 226IG0.008849560.123893800.867256640.583882000.070796460.92920351
HAPMAP-ASW 98IG 0.183673470.816326561.000000000.091836740.90816325
HAPMAP-CHBAsian 82IG0.073170730.463414640.463414640.583882000.304878060.69512194
HAPMAP-CHD 168IG0.047619050.476190480.476190480.150222000.285714300.71428573
HAPMAP-GIH 176IG0.068181820.329545470.602272750.479500000.232954550.76704544
HAPMAP-LWK 180IG 0.166666670.833333310.751830000.083333340.91666669
HAPMAP-MEX 100IG0.020000000.280000000.699999991.000000000.160000000.83999997
HAPMAP-MKK 286IG0.006993010.167832170.825174811.000000000.090909090.90909094
HAPMAP-TSI 176IG0.011363640.227272730.761363630.751830000.125000000.87500000
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss66128719HapMap-CEUEuropean 118IG0.033898310.169491530.796610180.150222000.118644070.88135594
HapMap-HCBAsian 90IG0.088888890.466666670.444444450.654721000.322222230.67777777
HapMap-JPTAsian 90IG0.022222220.355555560.622222240.479500000.200000000.80000001
HapMap-YRISub-Saharan African 120IG0.016666670.066666670.916666690.025056000.050000000.94999999
ss76132190ICMHP 8IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.274+/-0.2490000ALFRED: The Allele Frequency Database

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNPNCBI
UNKNOWNUNKNOWNUNKNOWN

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