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Reference SNP (refSNP) Cluster Report: rs10880908                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.4553/2280 (1000 Genomes)
C=0.4653/58432 (TOPMED)
HGVS Names
  • CM000674.2:g.46085273T>C
  • NC_000012.11:g.46479056T>C
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 ss16278656 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10880908 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
ss16278656SC_SNP|NT_029419.10_8622362byFreqfwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc11/18/0305/17/04120Genomicunknown
ss17448066CSHL-HAPMAP|CSHL-HuCC-200402.chr12.NT_029419.10_8622362fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc02/19/0403/04/04120Genomicunknown
ss18500099SC_SNP|SC-CHR9-12_NA11321-200402.chr12.NT_029419.10_8622362fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc02/20/0403/04/04120Genomicunknown
ss20866431SSAHASNP|WGSA-200403-chr12.chr12.NT_029419.10_8622362fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc03/19/0403/19/04121Genomicunknown
ss40198098ABI|hCV11694229fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc07/16/0507/16/05126Genomicunknown
ss66825914ILLUMINA|HumanHap300v1.1_rs10880908fwd/TC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc11/09/0611/09/06127Genomicunknown
ss66907375ILLUMINA|HumanHap550v1.1_rs10880908fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc11/14/0611/14/06127Genomicunknown
ss67034391ILLUMINA|HumanHap650Yv1.0_rs10880908fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc11/14/0611/14/06127Genomicunknown
ss70383406ILLUMINA|HumanHap300v2.0_rs10880908fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc04/18/0711/18/07127Genomicunknown
ss70504902ILLUMINA|HumanHap550v3.0__rs10880908rev/TA/Gggaaagtccaagcattcattgatggtctgctaagttatgagaaaatctgtgaaaggaaat04/20/0703/30/08130Genomicunknown
ss71031347ILLUMINA|HumanHap650Yv3.0_rs10880908fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc04/23/0704/23/07127Genomicunknown
ss75885380ILLUMINA|ILMN_Human_1M_rs10880908fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc08/28/0708/29/07129Genomicunknown
ss76705227AFFY|AFFY_6_1M_SNP_A-8566492fwd/BC/Tattttctcataacttagcagaccatcaatgaa08/28/0708/30/07130Genomicunknown
ss85022546KRIBB_YJKIM|KHS877303fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc12/04/0712/08/07130Genomicunknown
ss85528035HGSV|Cor19129_SNV_20070510.chr12_44765323fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc12/06/0712/09/07130Genomicunknown
ss97306929HUMANGENOME_JCVI|1103649431547fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc03/28/0803/28/08130Genomicunknown
ss1118896031000GENOMES|CEU.trio.12.15.2008_2729572_chr12_44765323fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc12/17/0812/17/08130Genomicunknown
ss121409854ILLUMINA|HumanCNV370v1_C_rs10880908fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc04/14/0904/14/09131Genomicunknown
ss133148071ENSEMBL|ENSSNP5677340fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc05/11/0905/14/09131Genomicunknown
ss137450201ENSEMBL|ENSSNP747882fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc12/08/0810/15/09131Genomicunknown
ss152860370ILLUMINA|Human610_Quadv1_B_rs10880908-127_T_R_1501613535rev/TA/Gggaaagtccaagcattcattgatggtctgctaagttatgagaaaatctgtgaaaggaaat06/18/0906/19/09131Genomicunknown
ss159150012ILLUMINA|Human660W-Quad_v1_A_rs10880908-128_T_R_1501613535rev/TA/Gggaaagtccaagcattcattgatggtctgctaagttatgagaaaatctgtgaaaggaaat07/06/0907/06/09131Genomicunknown
ss169691854ILLUMINA|HumanCNV370-Quadv3_C_rs10880908-127_T_R_1501613535rev/TA/Gggaaagtccaagcattcattgatggtctgctaagttatgagaaaatctgtgaaaggaaat10/01/0910/02/09132Genomicunknown
ss170695303ILLUMINA|Human1M-Duov3_B_rs10880908-127_T_R_1501613535rev/TA/Gggaaagtccaagcattcattgatggtctgctaagttatgagaaaatctgtgaaaggaaat10/01/0910/01/09132Genomicunknown
ss175112971COMPLETE_GENOMICS|NA20431_36_chr12_44765323fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc10/01/0910/05/09132Genomicunknown
ss208002870BCM-HGSC-SUB|BCM_CMT_1011-2291672fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc03/15/1003/19/10132Genomicunknown
ss2112777531000GENOMES|YRI.trio.3.2010_1099148_chr12_44765323fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc03/29/1003/30/10132Genomicunknown
ss2257354181000GENOMES|pilot_1_YRI_7545101_chr12_44765323fwd/C/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc04/22/1004/22/10132Genomicunknown
ss2359220591000GENOMES|pilot_1_CEU_5526688_chr12_44765323fwd/C/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc05/01/1005/01/10132Genomicunknown
ss2424836761000GENOMES|pilot_1_CHB+JPT_4368753_chr12_44765323fwd/C/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc05/01/1005/01/10132Genomicunknown
ss255087323BL|SNP56746_12_44765323fwd/BC/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc08/19/1008/20/10134Genomicunknown
ss281382210GMI|GMI_AK_SNP_5702599fwd/C/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc12/16/1012/16/10137Genomicunknown
ss291434233PJP|SNP_940591_chr12_44765323fwd/C/Tatttcctttcacagattttctcataacttagcagaccatcaatgaatgcttggactttcc01/21/1101/21/11134Genomicunknown
ss536647863ILLUMINA|HumanOmni5-4v1_B_rs10880908-131_T_R_1908663467fwd/BC/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac06/22/1208/29/15146Genomicunknown
ss563144586TISHKOFF|snp_chr12_46479056fwd/BC/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac11/22/1211/23/12138Genomicunknown
ss658695291SSMP|12_46479056fwd/BC/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac12/14/1202/13/15138Genomicunknown
ss825352896ILLUMINA|HumanCNV370v1_C_rs10880908-126_T_R_IFB1154978838:0fwd/BC/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac06/24/1311/21/14144Genomicunknown
ss989494892EVA-GONL|EVA-GONL_rs10880908fwd/BC/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac04/23/1404/25/14142Genomicunknown
ss1078434864JMKIDD_LAB|HGDP_WGS_chr12_46479056fwd/BC/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac07/10/1407/12/14142Genomicunknown
ss13448630831000GENOMES|PHASE3_V1_57819736fwd/C/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac08/16/1408/16/14142Genomicunknown
ss1426923092DDI|DDI_rs10880908fwd/BC/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac11/04/1411/04/14144Genomicunknown
ss1576260397EVA_GENOME_DK|EVA_GENOME_DK_snv_rs10880908fwd/BC/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac02/19/1502/19/15144Genomicunknown
ss1599165108EVA_DECODE|EVA_DECODE_12_44765323_344531_rs10880908fwd/BC/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac03/02/1503/04/15144Genomicunknown
ss1628513229EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_12_46479056_31988769fwd/C/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac03/04/1503/04/15144Genomicunknown
ss1671507262EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_12_46479056_31988769fwd/C/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac03/04/1503/04/15144Genomicunknown
ss1713324844EVA_SVP|EVA_SVP_1019211fwd/BC/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac03/12/1503/12/15144Genomicunknown
ss1807228395HAMMER_LAB|Hsieh_6249638fwd/BC/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac07/15/1507/16/15146Genomicunknown
ss1932859375WEILL_CORNELL_DGM|SNV:chr12:46479056fwd/BC/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac10/16/1510/17/15147Genomicunknown
ss1967582569GENOMED|rs10880908fwd/BC/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac02/16/1602/16/16147Genomicunknown
ss2027180984JJLAB|SNP7683539fwd/BC/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac08/29/1608/30/16149Genomicunknown
ss2155516075USC_VALOUEV|NC_000012.11:g.46479056T>Cfwd/C/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac11/17/1611/17/16150Genomicunknown
ss2189470106HUMAN_LONGEVITY|HLI-12-46085273-T-Cfwd/C/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac11/18/1611/18/16150Genomicunknown
ss2353400276TOPMED|12_46479056_T/Cfwd/C/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac11/19/1611/19/16150Genomicunknown
ss2699857810GRF|rs10880908fwd/C/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac02/13/1702/13/17151Genomicunknown
ss2910058082GNOMAD|rs10880908fwd/C/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac05/22/1705/22/17151Genomicunknown
ss3009623539SWEGEN|NC_000012.11:g.46479056T>Cfwd/C/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac05/30/1705/30/17151Genomicunknown
ss3027398784BIOINF_KMB_FNS_UNIBA|12.46085273T>Cfwd/C/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac07/05/1707/05/17151Genomicunknown
ss3169874788TOPMED|TOPMed_freeze_5?chr12:46,085,273fwd/C/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac09/30/1709/30/17151Genomicunknown
ss3350047282CSHL|rs10880908fwd/C/Tctttcacagattttctcataacttagcagaccatcaatgaatgcttggac10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs10880908|allelePos=990|totalLen=2990|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 TTGTTAAATG GTTTGTCTCA AGTCTTGTCA TATGTTGTTG GTGCAGCCTG ATCTCTGTTT
 ATTGAGGAGA CAGAAAAGGT GACTGTCATG GGTGTCACTG GCTGGAGCCA GCATTGCAGG
 CAGTAAAATA ATTTACCAAG ACAGTTGTAG GTAAAACAAA AAAGCAGATT TATTGGAGGG
 AAAGTACATT GCAAGGAAGC AATGGGCAGC ACAGCAGAGA AGGGGCTTTC TGCAAAGAGG
 CAGGGGCTGG ATTGAAGTTT TATAGGCTAT TCACAGAACA AGGACGTGCT GCTGGGGCTA
 TGTGGAGAGC AAGGTAATTG TGCCAGTGGT TTGTTTGTGA TTAGCTGTCT CTTGGAATAA
 TTGTTCTCCC CCACCTGGGA CCCCTTCCTT GTTGCTGATT ACTTATTAAG ACTCCACATC
 CCCCCCACCC CCAAGTCCCA ATAGAAAAAC AATGACAAAT CTTTGGCATT GGGGTGGAAG
 TTTCATCTTC CAACTACTTC CTGCTGACTG TGGGTGTAAC GCTGACTCTA CCTATGGTTT
 TTGGTCTGTC AAGAGACCCT GTGAGTCATT GTCCTGGATT GTGGGACTTA GGATATTAGA
 TCTTGCTGGA GGGACTCATC AAACAGCGGG AGCATGTCAA GGCAAAGCTC GTGTCCAGCT
 GAATCCAGGG GAGATCATAA AGGTAGCAGG CATCACTGGG GAGAGACTGA TCTCATTCAC
 AGCATCACTT GAAAGAAACT GCTGAATTCT AGAAGATAAA ATTTTCTTTC TTAAGTCAGT
 TACCAAAAAG GCAAAGGAAA ACCTCTTGCA ATGTGACGTT TTTCCTTATT GGAAGCCAAT
 TTAGATAACC TGGAAGTTAA ACTCAGCGAA AAAGTGTTTG AATTTAATTA GACACAGCAT
 AAGGAACCAA TTTTAGAGAG ACTATTGTGT CTTAATTACA TACAACATCC CTTTTATAAA
 TTTCCTTTCA CAGATTTTCT CATAACTTA
 Y
 GCAGACCATC AATGAATGCT TGGACTTTCC GACTTGTCCT AAACATACCT CTTTTTAAAC
 AACCAGTCAT TTTACTTTAG GAAAAGAATT TCCCACACAA GATCCTTTCT CATAGAAAAT
 CTCTTTTTTA TAACCTTCCT TACAAAAAAC TACCTCTTTA CCTTTATAAC CCTTGAATTA
 GACAAAAGTC ATTTTTCTTC TGTTAGGAAG TTATGGTTTG TATCACATGT TGCTGTGCAA
 GTCCTGTGAA AGGGGAGCAG ATGAGGAGGT GATCTACATA CTGTAGAAGC TATCCCTCCC
 CCAAGAGATT GCTCGGTTAG ATTTCTTGCT AGTGTTTGTC TGAATAAGTG TGGGCTATTT
 TTAAACCTTT GAGGTAGGAC TATCTAGGTT GAAGATATTG GCTAAAAATT TAGGTAGCTT
 TTCCAGGAGA AACAGGGCTA GTAGAGAGAA AGATGAATTC AGAGCTTGGG TAAATTTTAA
 GCATGCATCC ATCTTGATAA TTATATTTTT GCCCCAAAGG GATGTGGGTT ATTTAGACAT
 ACCAGGGACT GGTGCAAGAA TAGTAATTGA TTTCTTAAGT AATATAAAGG GGTATTAATT
 CTTTTTCTTC TGGAGGATGG GGGTGCCATT TGCCCCCGTT ACCCAACAGG ATTTGGAGAA
 CAGTTGCTCA GAGAAGATTA GTACAGTGTA GGCAGCTCTT GAACCTAAAA GGGAAATGTA
 AAATTTTACT TGCTGCCTCC AGAGTTGCCC TTGGATTTGT CTTGTTGATG ACCATGTCCA
 ATTTGGAAGC CAGTTGGAGC AGAGGGCCCC TTCAGCTCAA GGCCATTGGG TGTTGGGACT
 CTGTCCCATG GTGTCTTTGA CAGTCCTGTT TCTAGTGACC AAGATTGTGA CAGAGTGGGC
 AAGCCACATG CGGCTTTTTT CCATTTATTC CATTGGGGCA GTTTGCCTTC CAGTGGACTG
 ATCTTCTTCA CTGATGGCAG TTACCTGGAG GCGTGTCCCT AGGGCAGCCT AGAGGGGGCT
 GGGGATTTGT AAAACAACCA AGAATTGAGC CTGACTCTTG TCCCTGAGTT TTTCTTTCTC
 CTTAGCCCTG TCCTTCTTAT TCTGCTTCTG GTTATAAGAG ACTGAGGGGA CTAATTTCAG
 GATTTCTTGC ATAGGAACCA TGCTGTATTA CATGAGAAAA TTAGACATTT CTTTTTGAGA
 GTTTGAGGGT CAAATTTATC CCAATGCTTT AAAATGCAGC CTGAGGGTGA CTCTGAGGGA
 ATGGAAGGAC TTTGTCCCAT GATGGGACTG ATGGGAAAGA ACATCCACTA GGGATATGAA
 CCACAGTTTC TCTTGGGGGA TCCTGCCAAG TGAAAAGGGT TCCACTCACA TCTGCTGAGT
 GACTCTGAGA TGCACTTTCC AAAGGGGCAT CCCACCTATT GGAAAGGATC TTCTGGTGCT
 AGGGCCTTAT GGTGGATGAA CACTGGGTGA GTGACCCAAG GTCAGTCCCG GTACAAATTA
 TCCTGGGTGG CCAGCCCAGG CACGAGTTCC TCTGGGCGTT CAATCCAAGT ACGAGGGGAA
 GAGGTTGAGG AAAGACTCAC TGTCCCAATG CTGTTTTGGA TCAGCTGGCT TAAGATGTTT
 GGAGCAGGTG GCTGGCTGTC TTTATGGGAG AATTTAGAAT AAGAAAGAGG GGGTATTAGT
 TCCCCCAAAA CATGTGTGGG TTTGCCCTAG TCAAGCTTCT TCTGCCTATT GTGCTACACA
 TAGGGATTGG GGACTTTTGA CCAGAAAGGA TAGGAAAGAG CCTTCTTTCC TTCTAAGCAA
 GGCTGCCAAA TCTGTTCACT GCTTGGCCTT CAGCCTATCC CAGGAAGTGC CGTGACCAGT
 GGCCATCAGT TGCCAGAGGG ATGCTAGAGT TTGTTCATGG GAAGACTGAA AAGGAAAGCA
 AACGCTGAAC TCTCACTTGA TTGGGCATCA GCAGTCAGAA GTTTTACCAT GTGAACCTTC
 AATTTTCTCT GGGCTTGGAC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_029419 ABBA01031454
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.
SourceC/C
C/T
T/T
HWPC
T
ss133148071ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss1344863083EAS 1008AF 0.313499990.68650001
EUR 1006AF 0.481099990.51890004
AFR 1322AF 0.505299990.49470001
AMR 694AF 0.488500030.51150000
SAS 978AF 0.483599990.51640004
ss137450201ENSEMBL_Venter 2IG 1.00000000 0.500000000.50000000
ENSEMBL_celera 2IG1.00000000 1.00000000
ss16278656HapMap-CEUEuropean 224IG0.205357150.464285700.330357130.583882000.437500000.56250000
HapMap-HCBAsian 86IG0.116279070.465116290.418604641.000000000.348837200.65116280
HapMap-JPTAsian 172IG0.162790700.569767420.267441870.200325000.447674420.55232561
HapMap-YRISub-Saharan African 226IG0.265486720.442477880.292035400.250592000.486725660.51327431
HAPMAP-ASW 98IG0.346938790.448979590.204081640.583882000.571428600.42857143
HAPMAP-CHBAsian 80IG0.025000000.425000010.550000010.273322000.237500000.76249999
HAPMAP-CHD 168IG0.047619050.476190480.476190480.150222000.285714300.71428573
HAPMAP-GIH 174IG0.241379310.540229860.218390810.479500000.511494280.48850575
HAPMAP-LWK 180IG0.255555570.500000000.244444441.000000000.505555570.49444443
HAPMAP-MEX 100IG0.280000000.579999980.140000000.200325000.569999990.43000001
HAPMAP-MKK 286IG0.272727280.447552440.279720280.250592000.496503500.50349653
HAPMAP-TSI 176IG0.227272730.454545470.318181810.438578000.454545470.54545456
ss175112971PGP 2IG1.00000000 1.00000000
ss225735418pilot_1_YRI_low_coverage_panel 118AF 0.491525410.50847459
ss235922059pilot_1_CEU_low_coverage_panel 120AF 0.400000010.60000002
ss242483676pilot_1_CHB+JPT_low_coverage_panel 120AF 0.425000010.57499999
ss97306929J. Craig Venter 2IG 1.00000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.496+/-0.0450000ALFRED: 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_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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