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Reference SNP (refSNP) Cluster Report: rs4520945                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:111/147
Map to Genome Build:107/Weight 1
Validation Status:byClusterbyFreqwithHapMapFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.1956/23617 (ExAC)
A=0.1901/952 (1000 Genomes)
A=0.1441/1769 (GO-ESP)
HGVS Names
  • NC_000019.10:g.8975642G>A
  • NC_000019.9:g.9086318G>A
  • NM_024690.2:c.5497C>T
  • NP_078966.2:p.Leu1833Phe
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 ss283119764 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4520945 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
ss6095520SC_JCM|NT_011176.12_487673fwd/TA/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg01/10/0310/10/03111Genomicunknown
ss44178315ABI|hCV26737041byFreqfwd/TA/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg07/18/0511/03/06126Genomicunknown
ss67342756ILLUMINA|HumanHap550v1.1_rs4520945fwd/TA/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg11/14/0611/14/06127Genomicunknown
ss67737529ILLUMINA|HumanHap650Yv1.0_rs4520945fwd/TA/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg11/14/0611/14/06127Genomicunknown
ss68230473ILLUMINA|HumanHap250Sv1.0_rs4520945fwd/TA/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg12/06/0612/07/06127Genomicunknown
ss69377128SI_EXO|NT_011295.10_349120byFreqfwd/TA/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg04/12/0703/31/08127Genomicunknown
ss70807899ILLUMINA|HumanHap550v3.0__rs4520945rev/BC/Tccatcaatggaggtgacaccatggatttcttcactctcagtaatgcccccaataccacag04/20/0703/30/08130Genomicunknown
ss71387700ILLUMINA|HumanHap650Yv3.0_rs4520945fwd/TA/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg04/23/0704/23/07127Genomicunknown
ss74818499AFFY|SNP_M-318260fwd/TA/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg08/09/0708/09/07128Genomicunknown
ss75642723ILLUMINA|ILMN_Human_1M_rs4520945fwd/TA/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg08/28/0708/29/07129Genomicunknown
ss84284240KRIBB_YJKIM|KHS675229fwd/TA/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg12/04/0712/06/07130Genomicunknown
ss103422077BGI|BGI_rs4520945fwd/TA/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg06/06/0806/17/09131Genomicunknown
ss1110620081000GENOMES|CEU.trio.12.15.2008_3579355_chr19_8947318fwd/TA/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg12/17/0812/17/08130Genomicunknown
ss154298582ILLUMINA|Human610_Quadv1_B_rs4520945-127_B_R_1502215904rev/BC/Tccatcaatggaggtgacaccatggatttcttcactctcagtaatgcccccaataccacag06/18/0906/20/09131Genomicunknown
ss159475467ILLUMINA|Human660W-Quad_v1_A_rs4520945-128_B_R_1502215904rev/BC/Tccatcaatggaggtgacaccatggatttcttcactctcagtaatgcccccaataccacag07/06/0907/07/09131Genomicunknown
ss160684649ILLUMINA|HumanOmni1-Quad_v1-0_B_rs4520945-128_B_R_1502215904rev/BC/Tccatcaatggaggtgacaccatggatttcttcactctcagtaatgcccccaataccacag08/04/0910/04/09131Genomicunknown
ss171480248COMPLETE_GENOMICS|NA20431_36_chr19_8947318fwd/TA/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg10/01/0910/01/09132Genomicunknown
ss173746666ILLUMINA|Human1M-Duov3_B_rs4520945-127_B_R_1502215904rev/BC/Tccatcaatggaggtgacaccatggatttcttcactctcagtaatgcccccaataccacag10/01/0910/04/09132Genomicunknown
ss2280357671000GENOMES|pilot_1_YRI_9845450_chr19_8947318fwd/A/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg04/22/1004/22/10132Genomicunknown
ss2375985951000GENOMES|pilot_1_CEU_7203224_chr19_8947318fwd/A/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg05/01/1005/01/10132Genomicunknown
ss2438215091000GENOMES|pilot_1_CHB+JPT_5706586_chr19_8947318fwd/A/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg05/01/1005/01/10132Genomicunknown
ss283119764GMI|GMI_AK_SNP_7440183fwd/A/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg12/16/1012/16/10137Genomicunknown
ss480962239ILLUMINA|HumanOmni2.5-4v1_B_rs4520945-128_B_R_1781048776rev/BC/Tccatcaatggaggtgacaccatggatttcttcactctcagtaatgcccccaataccacag01/30/1201/31/12137Genomicunknown
ss480982168ILLUMINA|HumanOmniExpress-12v1_C_rs4520945-131_B_R_1857609349rev/BC/Tccatcaatggaggtgacaccatggatttcttcactctcagtaatgcccccaataccacag01/30/1201/31/12137Genomicunknown
ss481952784ILLUMINA|HumanOmni1-Quad_v1-0_C_rs4520945-131_B_R_1865628314fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt01/30/1208/28/15146Genomicunknown
ss485276032ILLUMINA|HumanOmni2.5-4v1_D_rs4520945-131_B_R_1857609349rev/BC/Tccatcaatggaggtgacaccatggatttcttcactctcagtaatgcccccaataccacag01/30/1202/04/12137Genomicunknown
ss491539428EXOME_CHIP|nonsyn_255654_chr_19_9086318fwd/TA/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg03/05/1203/06/12137Genomicunknown
ss491757441CLINSEQ_SNP|SNV-chr19-8947318byFreqfwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt03/06/1209/05/14137Genomicunknown
ss537242642ILLUMINA|HumanOmni5-4v1_B__rs4520945-131_B_R_1894834164fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt06/22/1208/29/15146Genomicunknown
ss565846618TISHKOFF|snp_chr19_9086318fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt11/22/1211/23/12138Genomicunknown
ss661701881SSMP|19_9086318fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt12/14/1202/14/15138Genomicunknown
ss713476138NHLBI-ESP|ESP6500SI-chr19-9086318fwd/TA/Gctgtggtattgggggcattactgagagtgaagaaatccatggtgtcacctccattgatgg02/20/1302/20/13138Genomicunknown
ss778910057ILLUMINA|HumanOmni25Exome-8v1_A_rs4520945-131_B_R_1865628314fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt05/30/1307/10/15146Genomicunknown
ss780740596ILLUMINA|HumanOmni25Exome-8v1_A_exm1422057-0_B_R_1920931825fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt05/30/1307/10/15146Genomicunknown
ss783083943ILLUMINA|HumanOmni2.5-4v1_H_rs4520945-131_B_R_1857609349fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt05/30/1307/29/15146Genomicunknown
ss783417842ILLUMINA|HumanOmniExpressExome-8v1_A_exm1422057-0_B_R_1920931825fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt05/31/1306/19/15146Genomicunknown
ss784041511ILLUMINA|HumanOmniExpressExome-8v1_A_rs4520945-131_B_R_1894834164fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt05/31/1306/19/15146Genomicunknown
ss832342311ILLUMINA|HumanOmniExpress-12v1_H_rs4520945-131_B_R_1857609349fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt09/17/1306/18/15146Genomicunknown
ss834371396ILLUMINA|HumanOmni2.5-8v1_A_rs4520945-131_B_R_1865628314fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt09/18/1307/29/15146Genomicunknown
ss974504022JMKIDD_LAB|KhoeSan_Exomes_chr19_9086318fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt03/06/1403/06/14142Genomicunknown
ss994075210EVA-GONL|EVA-GONL_rs4520945fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt04/23/1405/01/14142Genomicunknown
ss1067583989JMKIDD_LAB|HGDP_exomes_chr19_9086318fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt07/09/1407/09/14142Genomicunknown
ss1081750404JMKIDD_LAB|HGDP_WGS_chr19_9086318fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt07/10/1407/12/14142Genomicunknown
ss13623049641000GENOMES|PHASE3_V1_75991594fwd/A/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt08/16/1408/16/14142Genomicunknown
ss1397754618HAMMER_LAB|HAMMER_LAB_rs4520945fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt09/30/1409/30/14146Genomicunknown
ss1428332335DDI|DDI_rs4520945fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt11/04/1411/04/14144Genomicunknown
ss1578551090EVA_GENOME_DK|EVA_GENOME_DK_snv_rs4520945fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt02/19/1502/20/15144Genomicunknown
ss1584114058EVA_FINRISK|EVA_FINRISK_rs4520945fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt02/27/1502/27/15144Genomicunknown
ss1637541717EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_19_9086318_41934795fwd/A/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt03/04/1503/04/15144Genomicunknown
ss1680535750EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_19_9086318_41934795fwd/A/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt03/04/1503/04/15144Genomicunknown
ss1693347650EVA_EXAC|EVA_EXAC_8762947fwd/A/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt03/04/1503/04/15144Genomicunknown
ss1698136024EVA_DECODE|EVA_DECODE_19_8947318_76823_rs4520945fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt03/02/1503/05/15144Genomicunknown
ss1711497646EVA_MGP|EVA_XIMO_613406fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt03/09/1503/09/15144Genomicunknown
ss1713650167EVA_SVP|EVA_SVP_1344246fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt03/12/1503/12/15144Genomicunknown
ss1752300570ILLUMINA|OmniExpressExome-8v1-1_B_exm1422057-0_B_R_1920931825fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt05/27/1506/09/15146Genomicunknown
ss1752300571ILLUMINA|OmniExpressExome-8v1-1_B_rs4520945-131_B_R_1894834164fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt05/27/1506/09/15146Genomicunknown
ss1917931944ILLUMINA|HumanExome-12v1-1_B_exm1422057-0_B_R_1920931825fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt10/16/1510/16/15147Genomicunknown
ss1937558950WEILL_CORNELL_DGM|SNV:chr19:9086318fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt10/16/1510/19/15147Genomicunknown
ss1946526820ILLUMINA|HumanCoreExome-12v1-0_C_exm1422057-0_B_R_1920931825fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt10/29/1510/29/15147Genomicunknown
ss1959838418ILLUMINA|exm1422057-0_B_R_1920931825fwd/TA/Ggtattgggggcattactgagagtgaagaaatccatggtgtcacctccatt11/13/1511/13/15147Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4520945|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=147
 TGTCTGCACA GAAACTTTTT CTGAAGAAAC TGCATGTAGT GGTTGAGTGG ACTGTTCAAT
 TGTGCCTGTA CTGGTCCATA CAATTGTTGG TGGGGTGATG GGAGAATGTG TCATGGGTGC
 TGAGTTGATG TCTGGTCCTG AGGTTATGCC TGTAGAAATG ACTTCTTCCA CTGGAATGGA
 TGAAAAAGGC AATGTTAAGC TTATGGCCCT GTTTCCAGGA GTGGAAGTCA AAGTGGTCTC
 TGCTCCAGGA GCTGAGGTCT CAGGTCGGGG ATGGATTGAA GAAGACACTT CACTCTTCTC
 TGTGTAAGTC ATGGAAGTGT GAGTGCTGTT TCCCATAGAC AGGGACTTAG AAGAGGTATC
 AGAGCCGTTT TCCAATCTGG AGGCTCTAGT GACACCAGTA TTCAATGACC TGTCAGTGGC
 CAAAGTCCCT GCAGAGCTGG TGTGCACCCC ATGGCTGAGG TCAAGTGAAT CTGTGGTATT
 GGGGGCATTA CTGAGAGTGA
 R
 AGAAATCCAT GGTGTCACCT CCATTGATGG AGTTGGAGAT GGAAGATCCA TAGAGGCAGT
 TCTGAGTTTT TCTTTTCCTG TATTTTCAGT GCTTCCCAAA GCTGTGGACA TAAGGGTAGC
 TGAGCTGGAC TCTGTCCTTG CTGAAGACTT GGAGATGTCT GAGGTCATAA CTGTGGTGAC
 CTCCTTGGTC CAAAATGTGC TGCCCCCTAT GAATTCCACA TCAGGAGTTG TAGGAGATGA
 GGTTAGAGGG ATGCTTGTGC TCATCTGGCT TCCTTCAGCA TAGCTGGGTT CAAGAGAGGA
 GGAGAGAGCT GTATTTCCCT GTGTGTTCAG CCTTGGGCTG CTTCCCTTAC TAGAATCTGT
 GACTCCTTCA GTAGTTGACT CAGAAAGGAC AGAGGAAACT CTTCCTAATG ACTGGCTGAT
 GCTTCTTCCT GGAGCACTAG TAACAAGGAG TCCCATTGTC CCAGCCATAG AGACAGTGGC
 TGTAGAACTT CTTCTTTCCA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011295.10
dbSNP Blast Analysis
UniGene Cluster ID
432676

  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/G
G/G
HWPA
G
ss1362304964EAS 1008AF 0.303600010.69639999
EUR 1006AF 0.171999990.82800001
AFR 1322AF 0.071100000.92890006
AMR 694AF 0.270899980.72909999
SAS 978AF 0.195300000.80469996
ss1693347650ExAc_Aggregated_Populations120910AF 0.195401530.80459845
ss171480248PGP 2IG 1.00000000 0.500000000.50000000
ss228035767pilot_1_YRI_low_coverage_panel 118AF 0.101694910.89830506
ss237598595pilot_1_CEU_low_coverage_panel 120AF 0.141666670.85833335
ss243821509pilot_1_CHB+JPT_low_coverage_panel 120AF 0.358333320.64166665
ss491757441CSAgilent 589GF0.034000000.305000010.661000011.000000000.186500000.81349999
ss69377128HapMap-CEUEuropean 226IG0.026548670.265486720.707964601.000000000.159292040.84070796
HapMap-HCBAsian 86IG0.093023260.348837200.558139560.479500000.267441870.73255813
HapMap-JPTAsian 172IG0.127906980.546511650.325581400.250592000.401162800.59883720
HapMap-YRISub-Saharan African 226IG0.008849560.159292040.831858401.000000000.088495570.91150445
HAPMAP-ASW 98IG0.020408160.102040820.877551020.150222000.071428570.92857140
HAPMAP-CHBAsian 82IG0.121951220.390243890.487804890.527089000.317073170.68292683
HAPMAP-CHD 170IG0.094117650.388235300.517647090.654721000.288235310.71176469
HAPMAP-GIH 176IG0.034090910.204545450.761363630.250592000.136363640.86363637
HAPMAP-LWK 180IG 0.100000000.899999981.000000000.050000000.94999999
HAPMAP-MEX 100IG0.060000000.319999990.620000000.654721000.220000000.77999997
HAPMAP-MKK 286IG 0.146853150.853146850.751830000.073426570.92657346
HAPMAP-TSI 176IG0.022727270.250000000.727272751.000000000.147727270.85227275
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ENSEMBL_Venter 2IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.315+/-0.2411210100500ALFRED: 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
byClusterbyFreqwithHapMapFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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