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Reference SNP (refSNP) Cluster Report: rs3131969                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:103/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (REV)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.3215/1610 (1000 Genomes)
A=0.3006/37751 (TOPMED)
HGVS Names
  • CM000663.2:g.818802A>G
  • NC_000001.10:g.754182A>G
  • NC_000001.11:g.818802A>G
  • NR_103536.1:n.912A>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 ss275680750 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3131969 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
ss4379445SC_JCM|AL669831.2_57031fwd/BC/Tacgaggtgcaaacctgagagtggaggcgaaggagtccggagggcggggactgcaggccga02/19/0210/10/03103Genomicunknown
ss5764269SC_JCM|NT_004350.12_154820rev/TA/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt01/10/0310/10/03111Genomicunknown
ss6851730WI_SSAHASNP|NT_034471.1_308569rev/TA/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt02/12/0310/10/03111Genomicunknown
ss16450729CSHL-HAPMAP|CSHL-HuAA-200402.chr1.NT_034471.3_232814byFreqrev/TA/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt02/17/0404/07/04120Genomicunknown
ss19145708CSHL-HAPMAP|CSHL-HuDD-200402.chr1.NT_034471.3_232814rev/TA/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt02/20/0403/04/04120Genomicunknown
ss75167618ILLUMINA|ILMN_Human_1M_rs3131969fwd/BC/Tacgaggtgcaaacctgagagtggaggcgaaggagtccggagggcggggactgcaggccga08/28/0708/29/07129Genomicunknown
ss83853235HGSV|Cor18555_SNV_20070510.chr1_794045byFreqrev/TA/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt11/27/0709/05/14130Genomicunknown
ss84702724HGSV|Cor19240_SNV_20070510.chr1_794045rev/TA/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt11/30/0712/07/07130Genomicunknown
ss87155670BCMHGSC_JDW|JWB-0000095rev/TA/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt02/26/0802/26/08129Genomicunknown
ss97913186HUMANGENOME_JCVI|1103675000050rev/TA/Gtcggcctgcagtccccgccctccggactccttcgcctccgctctcaggtttgcacctcgt03/30/0803/30/08130Genomicunknown
ss105111648BGI|BGI_rs3131969rev/TA/Gtcggcctgcagtccccgccctccggactccttcgcctccgctctcaggtttgcacctcgt08/06/0806/16/09131Genomicunknown
ss118438211ILLUMINA-UK|NA18507_000000025_NCBI36.1_chr1_744045rev/TA/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt01/21/0901/21/09130Genomic99 %
ss137752187ENSEMBL|ENSSNP11472200rev/TA/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt05/15/0905/16/09131Genomicunknown
ss138898877ENSEMBL|ENSSNP261408rev/TA/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt12/08/0810/16/09131Genomicunknown
ss173568266ILLUMINA|Human1M-Duov3_B_rs3131969-128_B_F_1514139062fwd/BC/Tacgaggtgcaaacctgagagtggaggcgaaggagtccggagggcggggactgcaggccga10/01/0910/04/09132Genomicunknown
ss197885393BUSHMAN|BUSHMAN-chr1-744044rev/TA/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt02/16/1003/05/10132Genomicunknown
ss205529665BCM-HGSC-SUB|BCM_CMT_1011-243748rev/TA/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt03/15/1003/16/10132Genomicunknown
ss2181903651000GENOMES|pilot_1_YRI_48_chr1_744045rev/A/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt04/22/1004/22/10132Genomicunknown
ss2381149541000GENOMES|pilot_1_CHB+JPT_31_chr1_744045rev/A/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt05/01/1005/01/10132Genomicunknown
ss252864068BL|SNP130_1_744045rev/TA/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt08/18/1008/18/10134Genomicunknown
ss275680750GMI|GMI_AK_SNP_911rev/A/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt12/16/1012/16/10137Genomicunknown
ss283987357GMI|GMI_NA10851_SNP_123rev/A/Gtcggcctgcagtccccgccctccggactccttcgcctccactctcaggtttgcacctcgt12/17/1012/17/10138Genomicunknown
ss537165055ILLUMINA|HumanOmni5-4v1_B_rs3131969-131_B_F_1908388817rev/TA/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac06/22/1208/28/15146Genomicunknown
ss553710355TISHKOFF|snp_chr1_754182rev/TA/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac11/22/1211/22/12138Genomicunknown
ss647516080SSMP|1_754182rev/TA/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac12/14/1202/09/15138Genomicunknown
ss974769230EVA-GONL|EVA-GONL_rs3131969rev/TA/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac04/23/1404/23/14142Genomicunknown
ss1067612325JMKIDD_LAB|HGDP_WGS_chr1_754182rev/TA/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac07/10/1407/10/14142Genomicunknown
ss12893388451000GENOMES|PHASE3_V1_3568rev/A/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac08/16/1408/16/14142Genomicunknown
ss1397238516HAMMER_LAB|HAMMER_LAB_rs3131969rev/TA/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac09/30/1407/15/15146Genomicunknown
ss1425684794DDI|DDI_rs3131969rev/TA/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac11/04/1411/04/14144Genomicunknown
ss1573851131EVA_GENOME_DK|EVA_GENOME_DK_snv_rs3131969rev/TA/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac02/19/1502/19/15144Genomicunknown
ss1599378269EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_754182_156rev/A/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac03/04/1503/04/15144Genomicunknown
ss1642372302EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_754182_156rev/A/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac03/04/1503/04/15144Genomicunknown
ss1712305457EVA_SVP|EVA_SVP_9rev/TA/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac03/12/1503/12/15144Genomicunknown
ss1793705689HAMMER_LAB|Hsieh_179rev/TA/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac07/15/1507/15/15146Genomicunknown
ss1917960141WEILL_CORNELL_DGM|SNV:chr1:754182rev/TA/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac10/16/1510/16/15147Genomicunknown
ss1966667316GENOMED|rs3131969rev/TA/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac02/16/1602/16/16147Genomicunknown
ss2019498340JJLAB|SNP895rev/TA/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac08/29/1608/30/16149Genomicunknown
ss2147484253USC_VALOUEV|NC_000001.10:g.754182A>Grev/A/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac11/17/1611/17/16150Genomicunknown
ss2321502714TOPMED|1_754182_A/Grev/A/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac11/19/1611/19/16150Genomicunknown
ss2624264749SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV328rev/A/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac01/06/1701/06/17151Genomicunknown
ss2697374444GRF|rs3131969rev/A/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac02/13/1702/13/17151Genomicunknown
ss2750636588GNOMAD|rs3131969rev/A/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac05/17/1705/17/17151Genomicunknown
ss2986148552SWEGEN|NC_000001.10:g.754182A>Grev/A/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac05/30/1705/30/17151Genomicunknown
ss3066395957TOPMED|TOPMed_freeze_5?chr1:818,802rev/A/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac09/28/1709/28/17151Genomicunknown
ss3343272394CSHL|rs3131969rev/A/Gctgcagtccccgccctccggactccttcgcctccactctcaggtttgcac10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3131969|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 TAGCAAACAA CTTCAAAAAA CCTCTGTGGC TTGAAAACAC AAAGTTTAAT CACTTGTCCA
 TGCTTCTCTT CCACTGCAGG CTGGGGGTAG CTCCTGTATC CTCAGGCCCA GGTGAGATAA
 TTTTCCCATC CTGAGCACTG CCAGGCTCAT GGCAGAGGGG AGGGTGCAGG AACGTTGTGC
 GGCTTTTAAA GTTTCTGCCA ATAAGGGGCA GAGTCACTTC CATTCCGTTC CATTGGCTGG
 GCCTGACCAC GGGACAAGTA GCAGAACCTT TCCATCCAGG AGAAACAGAG AGTGTCTGGA
 GGAAGAATAC ACACTGTCCC CAACTCCCAG AGTTAATGCT GTGAATTCAT CAACAGGATG
 ATACACTTGC CTCACTGGCT TTTTGTTCCA ATAGACAGAA TCATAGAGTC TTGTTGTGCT
 GAGAGCCTTG TAGGTCACGC AGTCCAGGGA TGCAAAATTA GAAGACAATG ACGAGGTGCA
 AACCTGAGAG TGGAGGCGAA
 Y
 GGAGTCCGGA GGGCGGGGAC TGCAGGCCGA GCACACACCC CACCGGGGAG CAGCCATCTC
 AGCTGCAGCC GACGTTGCCC TAGAGAGATG AATGCAGGCC CAATGTTGGC AGCTATTCCA
 ATGTGAAAGA AACTAAAAAT CCAGACTTTT ATGTAACAAT ATTCTAATAT TTACAACATT
 AATCAGCTGG GGGAAAAAGT GTCCACAGAA CTTTTGCAGC CTGTGAGCCA CCCATTTCTA
 CCCAAATTCA GCCCAAACCT CTAACTGCAC AAGCTCACAC AAATAGAGAA AGCCAGGAAA
 AGTATCCAGA ACTCCACATG CACTTCACTA CTCACAGGGG CCTCCAGCCC TGGTAAGCAT
 GGGAACCACA CATGTAAACA CTGAGGTGCC CTGCCACGCC AGTGAAGTGC ATGCTGCTCG
 TGTGTGACCC ATTTTTAACC CCTAAAGGCA TAAAACACGA ATACTGTGAA TTCAGTTAAT
 AAGTTGAATT TACACCAGTC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_034471 ABBA01016000 AC000386 AF198096
dbSNP Blast Analysis
UniGene Cluster ID
521342

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs3131969 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss118438211YRI 2IG1.00000000 1.00000000
ss1289338845EAS 1008AF 0.733100000.26689997
EUR 1006AF 0.871800010.12819999
AFR 1322AF 0.352499990.64749998
AMR 694AF 0.756500010.24349999
SAS 978AF 0.808799980.19120000
ss137752187ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss138898877ENSEMBL_Venter 2IG1.00000000 1.00000000
ENSEMBL_celera 2IG1.00000000 1.00000000
ss197885393BUSHMAN_POP2 2IG 1.00000000 0.500000000.50000000
ss218190365pilot_1_YRI_low_coverage_panel 118AF 0.372881350.62711865
ss238114954pilot_1_CHB+JPT_low_coverage_panel 120AF 0.625000000.37500000
ss83853235HapMap-CEUEuropean 226IG0.743362840.238938050.017699111.000000000.862831830.13716814
HapMap-HCBAsian 82IG0.463414640.487804890.048780490.254213000.707317050.29268292
HapMap-JPTAsian 168IG0.452380960.369047610.178571430.099721000.636904780.36309522
HapMap-YRISub-Saharan African 222IG0.081081080.405405400.513513511.000000000.283783790.71621621
HAPMAP-ASW 96IG0.208333330.500000000.291666661.000000000.458333340.54166669
HAPMAP-CHBAsian 82IG0.609756110.39024389 0.371093000.804878060.19512194
HAPMAP-CHD 168IG0.642857130.250000000.107142860.010028000.767857130.23214285
HAPMAP-GIH 176IG0.636363630.340909090.022727270.402784000.806818190.19318181
HAPMAP-LWK 178IG0.123595510.483146070.393258420.751830000.365168540.63483149
HAPMAP-MEX 100IG0.620000000.319999990.060000000.654721000.779999970.22000000
HAPMAP-MKK 274IG0.124087590.562043790.313868610.099721000.405109490.59489053
HAPMAP-TSI 176IG0.840909060.136363640.022727270.150222000.909090940.09090909
ss97913186J. Craig Venter 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.436+/-0.1670000

  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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