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Reference SNP (refSNP) Cluster Report: rs13048019                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:121/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS PheGenI
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:T=0.0913/457 (1000 Genomes)
T=0.1295/16259 (TOPMED)
HGVS Names
  • CM000683.2:g.31545981C>T
  • NC_000021.8:g.32918294C>T
  • NC_000021.9:g.31545981C>T
  • NM_001353688.1:c.-707+12946G>A
  • NM_001353689.1:c.-489+12946G>A
  • NM_001353690.1:c.-369+12946G>A
  • NM_001353691.1:c.-518+12946G>A
  • NM_001353692.1:c.-312+12946G>A
  • NM_001353693.1:c.-422+12607G>A
  • NM_003253.2:c.-422+12946G>A
  • NM_003253.3:c.-422+12946G>A
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 ss283523899 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs13048019 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
ss21813868SSAHASNP|WGSA-200403-chr21.chr21.NT_011512.9_18578741fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat03/20/0403/20/04121Genomicunknown
ss44278846ABI|hCV3272642byFreqfwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat07/18/0511/03/06126Genomicunknown
ss66540994ILLUMINA|HumanHap300v1.1_rs13048019fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat11/09/0611/09/06127Genomicunknown
ss67054254ILLUMINA|HumanHap550v1.1_rs13048019fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat11/14/0611/14/06127Genomicunknown
ss67380941ILLUMINA|HumanHap650Yv1.0_rs13048019fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat11/14/0611/14/06127Genomicunknown
ss70418645ILLUMINA|HumanHap300v2.0_rs13048019fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat04/18/0711/18/07127Genomicunknown
ss70592504ILLUMINA|HumanHap550v3.0__rs13048019fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat04/20/0703/30/08130Genomicunknown
ss71136392ILLUMINA|HumanHap650Yv3.0_rs13048019fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat04/23/0704/23/07127Genomicunknown
ss75549251ILLUMINA|ILMN_Human_1M_rs13048019fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat08/28/0708/29/07129Genomicunknown
ss85295828KRIBB_YJKIM|KHS953135fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat12/04/0712/08/07130Genomicunknown
ss91822452BCMHGSC_JDW|JWB-1489998fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat02/26/0803/02/08129Genomicunknown
ss96145586HUMANGENOME_JCVI|1103643107151fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat03/25/0803/25/08130Genomicunknown
ss121616703ILLUMINA|HumanCNV370v1_C_rs13048019fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat04/14/0904/14/09131Genomicunknown
ss135613692ENSEMBL|ENSSNP1968334fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat12/08/0810/14/09131Genomicunknown
ss138308639ENSEMBL|ENSSNP6561947fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat05/15/0905/17/09131Genomicunknown
ss153312164ILLUMINA|Human610_Quadv1_B_rs13048019-128_B_F_1501650979fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat06/18/0906/19/09131Genomicunknown
ss159243192ILLUMINA|Human660W-Quad_v1_A_rs13048019-128_B_F_1501650979fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat07/06/0907/06/09131Genomicunknown
ss167914000COMPLETE_GENOMICS|NA07022_36_chr21_31840165fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat09/30/0909/30/09132Genomicunknown
ss170279795ILLUMINA|HumanCNV370-Quadv3_C_rs13048019-128_B_F_1501650979fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat10/01/0910/03/09132Genomicunknown
ss172312221ILLUMINA|Human1M-Duov3_B_rs13048019-128_B_F_1501650979fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat10/01/0910/02/09132Genomicunknown
ss2379632171000GENOMES|pilot_1_CEU_7567846_chr21_31840165fwd/C/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat05/01/1005/01/10132Genomicunknown
ss2441061481000GENOMES|pilot_1_CHB+JPT_5991225_chr21_31840165fwd/C/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat05/01/1005/01/10132Genomicunknown
ss255911410BL|SNP26955_21_31840165fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat08/20/1008/20/10134Genomicunknown
ss283523899GMI|GMI_AK_SNP_7844320fwd/C/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat12/16/1012/16/10137Genomicunknown
ss292701900PJP|SNP_2208258_chr21_31840165fwd/C/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat01/21/1101/21/11134Genomicunknown
ss491565041EXOME_CHIP|.GWAS._281267_chr_21_32918294fwd/BC/Tatttttctgattatacaagtaactactactatcacaaaatctttcaaagttagagaaaat03/05/1203/06/12137Genomicunknown
ss536829238ILLUMINA|HumanOmni5-4v1_B_rs13048019-131_B_F_1888146453fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag06/22/1208/29/15146Genomicunknown
ss566464112TISHKOFF|snp_chr21_32918294fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag11/22/1211/23/12138Genomicunknown
ss662374799SSMP|21_32918294fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag12/14/1202/14/15138Genomicunknown
ss780681679ILLUMINA|HumanOmni25Exome-8v1_A_exm-rs13048019-131_B_F_1990479306fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag05/30/1307/10/15146Genomicunknown
ss783355008ILLUMINA|HumanOmniExpressExome-8v1_A_exm-rs13048019-131_B_F_1990479306fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag05/31/1306/19/15146Genomicunknown
ss825387919ILLUMINA|HumanCNV370v1_C_rs13048019-126_B_F_IFB1136463117:0fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag06/24/1311/21/14147Genomicunknown
ss995069819EVA-GONL|EVA-GONL_rs13048019fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag04/23/1405/01/14142Genomicunknown
ss1082463290JMKIDD_LAB|HGDP_WGS_chr21_32918294fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag07/10/1407/12/14142Genomicunknown
ss13661097451000GENOMES|PHASE3_V1_79955494fwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag08/16/1408/16/14142Genomicunknown
ss1429170344DDI|DDI_rs13048019fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag11/04/1411/04/14144Genomicunknown
ss1579644178EVA_GENOME_DK|EVA_GENOME_DK_snv_rs13048019fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag02/19/1502/20/15144Genomicunknown
ss1639463152EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_21_32918294_44060003fwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag03/04/1503/04/15144Genomicunknown
ss1682457185EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_21_32918294_44060003fwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag03/04/1503/04/15144Genomicunknown
ss1699139137EVA_DECODE|EVA_DECODE_21_31840165_159187_rs13048019fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag03/02/1503/05/15144Genomicunknown
ss1713719529EVA_SVP|EVA_SVP_1413608fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag03/12/1503/12/15144Genomicunknown
ss1752405403ILLUMINA|OmniExpressExome-8v1-1_B_exm-rs13048019-131_B_F_1990479306fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag05/27/1506/09/15146Genomicunknown
ss1809663917HAMMER_LAB|Hsieh_8695347fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag07/15/1507/16/15146Genomicunknown
ss1917950778ILLUMINA|HumanExome-12v1-1_B_exm-rs13048019-131_B_F_1990479306fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag10/16/1510/16/15147Genomicunknown
ss1938621792WEILL_CORNELL_DGM|SNV:chr21:32918294fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag10/16/1510/19/15147Genomicunknown
ss1946561752ILLUMINA|HumanCoreExome-12v1-0_C_exm-rs13048019-131_B_F_1990479306fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag10/29/1510/29/15147Genomicunknown
ss1959948469ILLUMINA|rs13048019-138_B_F_2264355349fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag11/13/1511/13/15147Genomicunknown
ss1966654454AMU|chr21_32918294fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag01/29/1601/29/16147Genomicunknown
ss1969214134GENOMED|rs13048019fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag02/16/1602/16/16147Genomicunknown
ss2030081828JJLAB|SNP10584383fwd/BC/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag08/29/1608/31/16149Genomicunknown
ss2158684665USC_VALOUEV|NC_000021.8:g.32918294C>Tfwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag11/17/1611/17/16150Genomicunknown
ss2245417441HUMAN_LONGEVITY|HLI-21-31545981-C-Tfwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag11/18/1611/18/16150Genomicunknown
ss2412074248TOPMED|21_32918294_C/Tfwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag11/19/1611/19/16150Genomicunknown
ss2633841929ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs13048019-131_B_F_1888146fwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag02/02/1702/02/17151Genomicunknown
ss2633841930ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_seq-rs13048019-131_T_R_213fwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag02/02/1702/02/17151Genomicunknown
ss2635109174ILLUMINA|Cancer_BeadChip_11459870_A_rs13048019-128_B_F_1782894671fwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag02/02/1702/02/17151Genomicunknown
ss2971299745GNOMAD|rs13048019fwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag05/23/1705/23/17151Genomicunknown
ss2985226269AFFY|Axiom_PsorMich_Affx-17798425fwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag05/24/1705/24/17151Genomicunknown
ss2985844121AFFY|Axiom_Smokesc1_Affx-17798425fwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag05/24/1705/24/17151Genomicunknown
ss3018817647SWEGEN|NC_000021.8:g.32918294C>Tfwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag05/30/1705/30/17151Genomicunknown
ss3022154346ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm-rs13048019-131_B_F_1990479306fwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag06/28/1706/28/17151Genomicunknown
ss3022154347ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs13048019-138_B_F_2264355349fwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag06/28/1706/28/17151Genomicunknown
ss3028879125BIOINF_KMB_FNS_UNIBA|21.31545981C>Tfwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag07/05/1707/05/17151Genomicunknown
ss3352696708CSHL|rs13048019fwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag10/02/1710/02/17151Genomicunknown
ss3369670460TOPMED|TOPMed_freeze_5?chr21:31,545,981fwd/C/Ttctgattatacaagtaactactactatcacaaaatctttcaaagttagag10/03/1710/03/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs13048019|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 TTTGGGACAT TCAGAGAAGA TGGGATCATT CATGAACCAG GAGGCAATCC TAGAGAAAAG
 CTGAAGTCAT GAGACACAAC CATGATTGGG ACTGTGGATA TAAGACTAGT GTCTAAGGAG
 AAAGGGGAAA AAAGGGGAGG CACTCAACCC TCCAAGGTCA ACAATGTTCT GATGACTGAG
 GGTCTTGGTT CAATCCCAGC CTGAAAGGAT CCATTAATAG CGCTAATCCT TCCATTGAGA
 TTTAATCACT GGGCTCCTCT GTGGCCCCCA CTGGCTTTCT CATCTTTGTT CACTCTGACA
 GAGCCCACAT ATTCTTTATT CTTCCCAAGG TCCTTGTTGT TAAGAGGAAC ACTTTGTGAT
 TAATCTCCAT GTGTAAAGTG GATTACAAAA CGAGAAAATA TGACTTTGGG GGGCTTAAGT
 GTCCACTAGT CACACCCATT CAAAGATGAA GGTGTATATT CATTAATGTG ATTTTTCTGA
 TTATACAAGT AACTACTACT
 Y
 ATCACAAAAT CTTTCAAAGT TAGAGAAAAT CATACAGAAG AAAATAAGTT GCTTTTATAC
 AGGAAGAGAA AAAAATTGTT TTAATTTATT TTAAAAAAAA TTTTTAATAA AAGAAAATAA
 CAACCACCCT TAATCTCAAC ACTAAAGAAT ATTTATAATG GGTATTCTGG CACACTTTAT
 GTAATGAAAA GAGGTATTTG TAATTTAAAA AAAAAAAAAA ACTGTGATGG AATCTTCCAG
 AAGAATTACC CAGGTAGAAG GAAAAAAAAA TGTTAAAAAG AAACCAGAGG CCAGGCTCAG
 TGGCTCACAC CTGTAATCTC AGCACTTTGG GAGGTCCAGG CAGGCAGATC ACGAGGTCAG
 GAGTTCGAGA CCAGCCTGGC CAACATGGCG AAACCCCATG TCTACTAAAA ATACAAAAAT
 GAGCCAGGCA TGGTGGCGCA TGCCTGTAAT CCCAGCTACT CAGGAGGCTG AGGAAGGAGA
 ATCGCTTGAA ACCAGGAGGT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011512 ABBA01057288
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
ss135613692ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss1366109745EAS 1008AF 0.985099970.01490000
EUR 1006AF 0.831000030.16900001
AFR 1322AF 0.958399950.04160000
AMR 694AF 0.816999970.18300000
SAS 978AF 0.907999990.09200000
ss138308639ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss167914000CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss237963217pilot_1_CEU_low_coverage_panel 120AF 0.850000020.15000001
ss244106148pilot_1_CHB+JPT_low_coverage_panel 120AF 0.991666670.00833333
ss44278846HapMap-CEUEuropean 120IG0.699999990.30000001 0.479500000.850000020.15000001
HapMap-HCBAsian 90IG1.00000000 1.00000000
HapMap-JPTAsian 86IG1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG0.933333340.06666667 1.000000000.966666640.03333334
HAPMAP-ASW 96IG0.708333310.29166666 0.583882000.854166690.14583333
HAPMAP-CHD 166IG0.867469910.13253012 1.000000000.933734950.06626506
HAPMAP-GIH 172IG0.767441870.186046510.046511630.050043000.860465110.13953489
HAPMAP-LWK 176IG0.886363630.090909090.022727270.010028000.931818190.06818182
HAPMAP-MKK 284IG0.880281690.11971831 1.000000000.940140840.05985916
ss96145586J. Craig Venter 2IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.166+/-0.2350000ALFRED: 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
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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