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Reference SNP (refSNP) Cluster Report: rs5400                 ** With other allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:52/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (REV)
Allele Origin:C:germline
T:germline
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:With other allele [ClinVar]
MAF/MinorAlleleCount:A=0.1540/18691 (ExAC)
A=0.2153/1078 (1000 Genomes)
A=0.2397/3117 (GO-ESP)
A=0.2235/28070 (TOPMED)
HGVS Names
  • CM000665.2:g.171014511G>A
  • NC_000003.11:g.170732300G>A
  • NC_000003.12:g.171014511G>A
  • NG_008108.1:g.17469C>T
  • NM_000340.1:c.329C>T
  • NM_001278658.1:c.14+4020C>T
  • NM_001278659.1:c.-66C>T
  • NP_000331.1:p.Thr110Ile
  • XP_011511389.1:p.Thr95Ile
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 ss44383054 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs5400 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
ss6865ARAVINDA|CHAK00479byFreqfwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga06/29/9904/07/0452Genomicunknown
ss12587280IBARROSO|SLC2A2_T110IbyFreqfwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga08/06/0304/07/04117Genomicunknown
ss19544170CSHL-HAPMAP|CSHL-HuDD-200402.chr3.NT_005612.14_77227458byFreqrev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag02/20/0405/16/04120Genomicunknown
ss22887952IMCJ-GDT|IMCJ-SLC2A2_4-ctfwd/BC/Tctntatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga03/22/0403/22/04121Genomicunknown
ss44383054ABI|hCV3142148byFreqrev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag07/18/0511/03/06126Genomicunknown
ss48405807APPLERA_GI|hCV3142148byFreqfwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga09/28/0511/03/06126Genomicunknown
ss66685972ILLUMINA|HumanHap300v1.1_rs5400fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga11/09/0611/09/06127Genomicunknown
ss67415224ILLUMINA|HumanHap550v1.1_rs5400fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga11/14/0611/14/06127Genomicunknown
ss67778414ILLUMINA|HumanHap650Yv1.0_rs5400fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga11/14/0611/14/06127Genomicunknown
ss68882391PERLEGEN|PGP04231739rev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag01/30/0701/30/07127Genomicunknown
ss70844411ILLUMINA|HumanHap550v3.0__rs5400fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga04/20/0703/31/08130Genomicunknown
ss71428793ILLUMINA|HumanHap650Yv3.0_rs5400fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga04/23/0704/23/07127Genomicunknown
ss74809390AFFY|SNP_M-182036fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga08/09/0708/09/07128Genomicunknown
ss75878286ILLUMINA|ILMN_Human_1M_rs5400fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga08/28/0708/29/07129Genomicunknown
ss76870165CGM_KYOTO|12640rev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag09/12/0709/12/07129cDNAunknown
ss79207922ILLUMINA|HumanHap300v2.0_rs5400fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga04/18/0711/18/07130Genomicunknown
ss83346835KRIBB_YJKIM|KHS439994fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga12/04/0712/04/07130Genomicunknown
ss92370096BCMHGSC_JDW|JWB-1699330rev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag02/26/0803/02/08129Genomicunknown
ss95212663CNG|19335446rev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag03/13/0803/13/08129Genomicunknown
ss1113419311000GENOMES|NA19240_2008_12_16_771557_chr3_172214994rev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag12/17/0812/17/08130Genomicunknown
ss1126887711000GENOMES|CEU.trio.12.15.2008_859767_chr3_172214994rev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag12/17/0812/17/08130Genomicunknown
ss117376100ILLUMINA-UK|NA18507_000220920_NCBI36.1_chr3_172214994rev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag01/18/0901/19/09130Genomic99 %
ss120037065ILLUMINA|GS0007123-OPA_Ober-rs5400rev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag02/24/0902/24/09131Genomicunknown
ss122463338ILLUMINA|HumanCNV370v1_C_rs5400fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga04/14/0904/15/09131Genomicunknown
ss139291785ENSEMBL|ENSSNP5782030rev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag05/18/0905/18/09131Genomicunknown
ss154338015ILLUMINA|Human610_Quadv1_B_rs5400-127_B_F_1501830682fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga06/18/0906/20/09131Genomicunknown
ss159514587ILLUMINA|Human660W-Quad_v1_A_rs5400-128_B_F_1501830682fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga07/06/0907/07/09131Genomicunknown
ss159706523SEATTLESEQ|SLC2A2-172214994rev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag07/10/0907/10/09131Genomicunknown
ss160741162ILLUMINA|HumanOmni1-Quad_v1-0_B_rs5400-128_B_F_1501830682fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga08/04/0910/04/09131Genomicunknown
ss161415881ENSEMBL|ENSSNP2089081byFreqrev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag09/24/0903/07/10131Genomicunknown
ss164960281COMPLETE_GENOMICS|NA19240_36_chr3_172214994rev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag09/29/0909/30/09132Genomicunknown
ss172025181ILLUMINA|HumanCNV370-Quadv3_C_rs5400-127_B_F_1501830682fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga10/01/0910/04/09132Genomicunknown
ss173916965ILLUMINA|Human1M-Duov3_B_rs5400-127_B_F_1501830682fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga10/01/0910/04/09132Genomicunknown
ss203519004BUSHMAN|BUSHMAN-chr3-172214993byFreqrev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag02/16/1009/05/14132Genomicunknown
ss2205763531000GENOMES|pilot_1_YRI_2386036_chr3_172214994rev/A/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag04/22/1004/22/10132Genomicunknown
ss2321409761000GENOMES|pilot_1_CEU_1745605_chr3_172214994rev/A/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag05/01/1005/01/10132Genomicunknown
ss2394890961000GENOMES|pilot_1_CHB+JPT_1374173_chr3_172214994rev/A/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag05/01/1005/01/10132Genomicunknown
ss244303010ILLUMINA|CVDSNP55v1_A_rs5400fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga06/10/1006/10/10132Genomicunknown
ss292973219PJP|SNP_2479577_chr3_172214994rev/A/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag01/21/1101/21/11134Genomicunknown
ss342152109NHLBI-ESP|ESP2500-chr3-170732300byFreqrev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag03/25/1109/05/14134Genomicunknown
ss410849260ILLUMINA|Cardio-Metabo_Chip_11395247_A_chr3_172214994rev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag06/07/1106/07/11135Genomicunknown
ss481142116ILLUMINA|HumanOmni2.5-4v1_B_rs5400-128_B_F_1768762456rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga01/30/1210/28/16137Genomicunknown
ss481164303ILLUMINA|HumanOmniExpress-12v1_C_rs5400-131_B_F_1857745699rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga01/30/1210/27/16137Genomicunknown
ss482153344ILLUMINA|HumanOmni1-Quad_v1-0_C_rs5400-131_B_F_1865616714rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga01/30/1208/28/15146Genomicunknown
ss485366167ILLUMINA|HumanOmni2.5-4v1_D_rs5400-131_B_F_1857745699rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga01/30/1210/28/16137Genomicunknown
ss4908779071000GENOMES|20110521_exome_385705_chr3_170732300rev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag02/10/1202/21/12137Genomicunknown
ss491348894EXOME_CHIP|nonsyn_65121_chr_3_170732300rev/TA/Gtccccaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctggatacag03/05/1203/05/12137Genomicunknown
ss491845413CLINSEQ_SNP|SNV-chr3-172214994byFreqrev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga03/06/1209/05/14137Genomicunknown
ss537309149ILLUMINA|HumanOmni5-4v1_B_rs5400-131_B_F_1894016976rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga06/22/1208/28/15146Genomicunknown
ss557112506TISHKOFF|snp_chr3_170732300rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga11/22/1211/23/12138Genomicunknown
ss650858580SSMP|3_170732300rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga12/14/1202/10/15138Genomicunknown
ss778929207ILLUMINA|HumanOmni25Exome-8v1_A_rs5400-131_B_F_1865616714rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga05/30/1307/09/15146Genomicunknown
ss780824039ILLUMINA|HumanOmni25Exome-8v1_A_exm364452-0_B_R_1922184752rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga05/30/1307/09/15146Genomicunknown
ss783128731ILLUMINA|HumanOmni2.5-4v1_H_rs5400-131_B_F_1857745699rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga05/30/1307/28/15146Genomicunknown
ss783506601ILLUMINA|HumanOmniExpressExome-8v1_A_exm364452-0_B_R_1922184752rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga05/31/1306/19/15146Genomicunknown
ss784085288ILLUMINA|HumanOmniExpressExome-8v1_A_rs5400-131_B_F_1894016976rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga05/31/1306/19/15146Genomicunknown
ss825538440ILLUMINA|HumanCNV370v1_C_rs5400-126_B_F_IFB1153915219:0rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga06/24/1311/21/14147Genomicunknown
ss832387609ILLUMINA|HumanOmniExpress-12v1_H_rs5400-131_B_F_1857745699rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga09/17/1306/18/15146Genomicunknown
ss834390725ILLUMINA|HumanOmni2.5-8v1_A_rs5400-131_B_F_1865616714rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga09/18/1307/28/15146Genomicunknown
ss974450665JMKIDD_LAB|KhoeSan_Exomes_chr3_170732300rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga03/06/1403/06/14142Genomicunknown
ss979450726EVA-GONL|EVA-GONL_rs5400rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga04/23/1404/24/14142Genomicunknown
ss1067456971JMKIDD_LAB|HGDP_exomes_chr3_170732300rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga07/09/1407/09/14142Genomicunknown
ss1071050288JMKIDD_LAB|HGDP_WGS_chr3_170732300rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga07/10/1407/10/14142Genomicunknown
ss13072548441000GENOMES|PHASE3_V1_18655073rev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga08/16/1408/16/14142Genomicunknown
ss1397358961HAMMER_LAB|HAMMER_LAB_rs5400rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga09/30/1409/30/14146Genomicunknown
ss1429670297DDI|DDI_rs5400rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga11/04/1411/05/14144Genomicunknown
ss1457615359CLINVAR|SCV000152787fwd/BC/Tctgtatccagctttgcagttggtggaatgatgcatcattctttggtgggtggcttgggga11/23/1411/23/14142Genomicunknown
ss1580294605EVA_GENOME_DK|EVA_GENOME_DK_snv_rs5400rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga02/19/1502/20/15144Genomicunknown
ss1584031569EVA_FINRISK|EVA_FINRISK_rs5400rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga02/27/1502/27/15144Genomicunknown
ss1588945194EVA_DECODE|EVA_DECODE_3_172214994_1322840_rs5400rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga03/02/1503/03/15144Genomicunknown
ss1608794935EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_3_170732300_10341122rev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga03/04/1503/04/15144Genomicunknown
ss1651788968EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_3_170732300_10341122rev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga03/04/1503/04/15144Genomicunknown
ss1687292263EVA_EXAC|EVA_EXAC_2234992rev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga03/04/1503/04/15144Genomicunknown
ss1711041144EVA_MGP|EVA_XIMO_156904rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga03/09/1503/09/15144Genomicunknown
ss1712631203EVA_SVP|EVA_SVP_325570rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga03/12/1503/12/15144Genomicunknown
ss1752452277ILLUMINA|OmniExpressExome-8v1-1_B_exm364452-0_B_R_1922184752rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga05/27/1506/09/15146Genomicunknown
ss1752452278ILLUMINA|OmniExpressExome-8v1-1_B_rs5400-131_B_F_1894016976rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga05/27/1506/09/15146Genomicunknown
ss1800428446HAMMER_LAB|Hsieh_1964857rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga07/15/1507/15/15146Genomicunknown
ss1917775075ILLUMINA|HumanExome-12v1-1_B_exm364452-0_B_R_1922184752rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga10/16/1510/16/15147Genomicunknown
ss1922671395WEILL_CORNELL_DGM|SNV:chr3:170732300rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga10/16/1510/17/15147Genomicunknown
ss1946102248ILLUMINA|HumanCoreExome-12v1-0_C_exm364452-0_B_R_1922184752rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga10/29/1510/29/15147Genomicunknown
ss1946102249ILLUMINA|HumanCoreExome-12v1-0_C_rs5400-131_B_F_1894016976rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga10/29/1510/29/15147Genomicunknown
ss1958628150ILLUMINA|exm364452-0_B_R_1922184752rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga11/13/1511/13/15147Genomicunknown
ss1958628151ILLUMINA|rs5400-131_B_F_1894016976rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga11/13/1511/13/15147Genomicunknown
ss2021910983JJLAB|SNP2413538rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga08/29/1608/30/16149Genomicunknown
ss2094814156ILLUMINA|Immuno_BeadChip_11419691_B_rs5400-131_B_F_1865616714rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga09/27/1609/27/16150Genomicunknown
ss2095140185ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs5400-131_B_F_1865616714rev/TA/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga09/27/1609/27/16150Genomicunknown
ss2150008491USC_VALOUEV|NC_000003.11:g.170732300G>Arev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga11/17/1611/17/16150Genomicunknown
ss2258125308HUMAN_LONGEVITY|HLI-3-171014511-G-Arev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga11/18/1611/18/16150Genomicunknown
ss2425521044TOPMED|3_170732300_G/Arev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga11/19/1611/19/16150Genomicunknown
ss2634043006ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs5400-131_B_F_1894016976rev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga02/02/1702/02/17151Genomicunknown
ss2710992344ILLUMINA|Consortium-OncoArray_15047405_A_rs5400-131_B_F_1894016976rev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga03/22/1703/22/17151Genomicunknown
ss2734198441GNOMAD|exomes_rs5400rev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga05/17/1705/17/17151Genomicunknown
ss2747138921GNOMAD|coding_rs5400rev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga05/17/1705/17/17151Genomicunknown
ss2802284089GNOMAD|rs5400rev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga05/18/1705/18/17151Genomicunknown
ss2985276355AFFY|Axiom_PsorMich_Affx-21655969rev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga05/24/1705/24/17151Genomicunknown
ss2993635817SWEGEN|NC_000003.11:g.170732300G>Arev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga05/30/1705/30/17151Genomicunknown
ss3022312919ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm364452-0_B_R_1922184752rev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga06/28/1706/28/17151Genomicunknown
ss3022312920ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs5400-138_B_F_2264232882rev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga06/28/1706/28/17151Genomicunknown
ss3024723705BIOINF_KMB_FNS_UNIBA|3.171014511G>Arev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga07/05/1707/05/17151Genomicunknown
ss3345393490CSHL|rs5400rev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga10/02/1710/02/17151Genomicunknown
ss3412766757TOPMED|TOPMed_freeze_5?chr3:171,014,511rev/A/Gaagccacccaccaaagaatgatgcatcattccaccaactgcaaagctgga10/03/1710/03/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs5400|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 ACGTAACAAA CACTTTAAAG ACAAAAACAA AAATACATAG AATGTTTGAA ATAGTAAAGC
 TATTTTTCTT TATCTCCTAG GTAATAATAT CTCACTATAG ACATGTTTTG GGTGTTCCAC
 TGGATGACCG AAAAGCTATC AACAACTATG TTATCAACAG TACAGATGAA CTGCCCACAA
 TCTCATACTC AATGAACCCA AAACCAACCC CTTGGGCTGA GGAAGAGACT GTGGCAGCTG
 CTCAACTAAT CACCATGCTC TGGTCCCTGT CTGTATCCAG CTTTGCAGTT GGTGGAATGA
 Y
 TGCATCATTC TTTGGTGGGT GGCTTGGGGA CACACTTGGA AGGTAGGCAA ATTTCATAAA
 TAAGCATAAA CAGAAACTTT CATATTTTCA TTTTCCTAAC ACTTGTTTAG AAAAATATTA
 TCTTTCTTCT TGTGGAATAG CTTTAGAGTT GTTTTTTCAA CTCATGACCC TATGAGGCAT
 ATCAGTGTTA GATCAAATCA ATGAAAAAAG CTGTTGCGAC AGTTTGGTTA ATTGTTCAGA
 CATTTATACC AAACATGAGT TTTGTGTGTA TTTCTAGATA ATTGCTTTGA TCCTCTAGCT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_005612.14
dbSNP Blast Analysis
UniGene Cluster ID
167584

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs5400 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
ss117376100YRI 2IG 1.00000000 0.500000000.50000000
ss12587280ELY 921AF 0.860000010.14000000
ss1307254844EAS 1008AF 0.984099980.01590000
EUR 1006AF 0.864799980.13519999
AFR 1322AF 0.510599970.48940000
AMR 694AF 0.828500030.17150001
SAS 978AF 0.836400030.16360000
ss139291785ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss161415881ENSEMBL_celera 4IG0.50000000 0.50000000 0.500000000.50000000
ss164960281YRISub-Saharan African 2IG 1.00000000 0.500000000.50000000
ss1687292263ExAc_Aggregated_Populations121412AF 0.846053120.15394689
ss19544170CEPH 184AF 0.699999990.30000001
ss203519004BUSHMAN_POP 4IG 1.00000000 0.500000000.50000000
BANTU 2IG 1.00000000 0.500000000.50000000
ss220576353pilot_1_YRI_low_coverage_panel 118AF 0.483050850.51694918
ss232140976pilot_1_CEU_low_coverage_panel 120AF 0.850000020.15000001
ss239489096pilot_1_CHB+JPT_low_coverage_panel 120AF 0.975000020.02500000
ss342152109ESP_Cohort_Populations 4550GF0.577142830.334945050.087912090.001000000.744615380.25538462
ss44383054HapMap-HCBAsian 86IG0.953488350.04651163 1.000000000.976744170.02325581
HapMap-JPTAsian 172IG0.953488350.04651163 1.000000000.976744170.02325581
HapMap-YRISub-Saharan African 226IG0.185840710.557522120.256637160.200325000.464601760.53539824
AoD_African_American 90AF 0.529999970.47000000
AoD_Caucasian 92AF 0.880000000.12000000
AoD_Japanese 90AF 0.990000010.01000000
HAPMAP-ASW 98IG0.387755100.428571430.183673470.479500000.602040830.39795917
HAPMAP-CHBAsian 82IG0.975609780.02439024 1.000000000.987804890.01219512
HAPMAP-CHD 168IG0.976190450.02380952 1.000000000.988095220.01190476
HAPMAP-GIH 176IG0.693181810.250000000.056818180.150222000.818181810.18181819
HAPMAP-LWK 180IG0.255555570.588888880.155555560.099721000.550000010.44999999
HAPMAP-MEX 100IG0.600000020.340000000.060000001.000000000.769999980.23000000
HAPMAP-MKK 286IG0.433566420.447552440.118881121.000000000.657342670.34265736
HAPMAP-TSI 176IG0.727272750.238636360.034090910.479500000.846590940.15340909
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss48405807AGI_ASP populationmultiple 78IG0.615384640.282051300.102564100.150222000.756410240.24358974
ss491845413CSAgilent 1324GF0.741258740.235764240.022977020.527089000.859140870.14085914
ss6865HYP1 80AF 0.899999980.10000000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict		Additional Freq. Data
0.261+/-0.2500000ALFRED: 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
byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Validated by: ILLUMINA
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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