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Reference SNP (refSNP) Cluster Report: rs10513025                 **Clinical Channel**
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/151
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:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.0517/259 (1000 Genomes)
C=0.0551/6923 (TOPMED)
HGVS Names
  • CM000667.2:g.9623510T>C
  • NC_000005.9:g.9623622T>C
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 ss116470207 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10513025 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
ss14911994PERLEGEN|PS03122623byFreqfwd/BC/Tttggcctctcctcttttcacttgtgcatgatctctatggggtttctgtttcctttctttg11/13/0304/07/04119Genomicunknown
ss66017600AFFY|SNP_A-1726701rev/TA/Gaaaggaaacagaaaccccatagagatcatgcacaagtgaaaagaggagag10/26/0610/26/06127Genomicunknown
ss66506870AFFY|SNP_A-4210816byFreqrev/TA/Gagaaaccccatagagatcatgcacaagtgaaa10/29/0603/31/08127Genomicunknown
ss76329837AFFY|AFFY_6_1M_SNP_A-4210816byFreqrev/TA/Gagaaaccccatagagatcatgcacaagtgaaa08/28/0703/07/10129Genomicunknown
ss82742325KRIBB_YJKIM|KHS315561fwd/BC/Tttggcctctcctcttttcacttgtgcatgatctctatggggtttctgtttcctttctttg11/30/0712/03/07130Genomicunknown
ss116470207ILLUMINA-UK|NA18507_000017571_NCBI36.1_chr5_9676622byFreqfwd/BC/Tttggcctctcctcttttcacttgtgcatgatctctatggggtttctgtttcctttctttg01/17/0909/05/14130Genomic99 %
ss159907289ILLUMINA|HumanOmni1-Quad_v1-0_B_rs10513025-128_T_R_1572948866rev/TA/Gcaaagaaaggaaacagaaaccccatagagatcatgcacaagtgaaaagaggagaggccaa08/04/0910/01/09131Genomicunknown
ss173281468AFFY|GenomeWideSNP_5_SNP_A-4210816rev/TA/Gagaaaccccatagagatcatgcacaagtgaaa10/01/0910/03/09132Genomicunknown
ss199869541BUSHMAN|BUSHMAN-chr5-9676621fwd/BC/Tttggcctctcctcttttcacttgtgcatgatctctatggggtttctgtttcctttctttg02/16/1003/06/10132Genomicunknown
ss2215120801000GENOMES|pilot_1_YRI_3321763_chr5_9676622fwd/C/Tttggcctctcctcttttcacttgtgcatgatctctatggggtttctgtttcctttctttg04/22/1004/22/10132Genomicunknown
ss2328254031000GENOMES|pilot_1_CEU_2430032_chr5_9676622fwd/C/Tttggcctctcctcttttcacttgtgcatgatctctatggggtttctgtttcctttctttg05/01/1005/01/10132Genomicunknown
ss479694971ILLUMINA|HumanOmni1-Quad_v1-0_C_rs10513025-131_T_R_1863293136fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt01/30/1208/28/15146Genomicunknown
ss491364427EXOME_CHIP|.GWAS._80654_chr_5_9623622fwd/BC/Tttggcctctcctcttttcacttgtgcatgatctctatggggtttctgtttcctttctttg03/05/1203/05/12137Genomicunknown
ss558198144TISHKOFF|snp_chr5_9623622fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt11/22/1211/23/12138Genomicunknown
ss780680579ILLUMINA|HumanOmni25Exome-8v1_A_exm-rs10513025-131_T_R_1990487117fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt05/30/1307/09/15146Genomicunknown
ss783353859ILLUMINA|HumanOmniExpressExome-8v1_A_exm-rs10513025-131_T_R_1990487117fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt05/31/1306/19/15146Genomicunknown
ss981239704EVA-GONL|EVA-GONL_rs10513025fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt04/23/1404/24/14142Genomicunknown
ss1072383382JMKIDD_LAB|HGDP_WGS_chr5_9623622fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt07/10/1407/11/14142Genomicunknown
ss13138702471000GENOMES|PHASE3_V1_25556213fwd/C/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt08/16/1408/16/14142Genomicunknown
ss1430243353DDI|DDI_rs10513025fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt11/04/1411/05/14144Genomicunknown
ss1581008670EVA_GENOME_DK|EVA_GENOME_DK_snv_rs10513025fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt02/19/1502/20/15144Genomicunknown
ss1590755507EVA_DECODE|EVA_DECODE_5_9676622_86188_rs10513025fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt03/02/1503/03/15144Genomicunknown
ss1612257246EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_5_9623622_14146134fwd/C/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt03/04/1503/04/15144Genomicunknown
ss1655251279EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_5_9623622_14146134fwd/C/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt03/04/1503/04/15144Genomicunknown
ss1712743443EVA_SVP|EVA_SVP_437810fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt03/12/1503/12/15144Genomicunknown
ss1752591006ILLUMINA|OmniExpressExome-8v1-1_B_exm-rs10513025-131_T_R_1990487117fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt05/27/1506/09/15146Genomicunknown
ss1803047237HAMMER_LAB|Hsieh_2727704fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt07/15/1507/15/15146Genomicunknown
ss1917787981ILLUMINA|HumanExome-12v1-1_B_exm-rs10513025-131_T_R_1990487117fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt10/16/1510/16/15147Genomicunknown
ss1924499856WEILL_CORNELL_DGM|SNV:chr5:9623622fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt10/16/1510/17/15147Genomicunknown
ss1946138199ILLUMINA|HumanCoreExome-12v1-0_C_exm-rs10513025-131_T_R_1990487117fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt10/29/1510/29/15147Genomicunknown
ss1958766122ILLUMINA|exm-rs10513025-131_T_R_1990487117fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt11/13/1511/13/15147Genomicunknown
ss2022847381JJLAB|SNP3349936fwd/BC/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt08/29/1608/30/16149Genomicunknown
ss2271304279HUMAN_LONGEVITY|HLI-5-9623510-T-Cfwd/C/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt11/18/1611/18/16150Genomicunknown
ss2439291139TOPMED|5_9623622_T/Cfwd/C/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt11/20/1611/20/16150Genomicunknown
ss2634244936ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs10513025-131_T_R_1885472fwd/C/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt02/02/1702/02/17151Genomicunknown
ss2634244937ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_seq-rs10513025-131_T_R_213fwd/C/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt02/02/1702/02/17151Genomicunknown
ss2821052666GNOMAD|rs10513025fwd/C/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt05/18/1705/18/17151Genomicunknown
ss2985315478AFFY|Axiom_PsorMich_Affx-27219941fwd/C/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt05/24/1705/24/17151Genomicunknown
ss2996425172SWEGEN|NC_000005.9:g.9623622T>Cfwd/C/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt05/30/1705/30/17151Genomicunknown
ss3022465423ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm-rs10513025-131_T_R_1990487117fwd/C/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt06/28/1706/28/17151Genomicunknown
ss3455989773TOPMED|TOPMed_freeze_5?chr5:9,623,510fwd/C/Tctctcctcttttcacttgtgcatgatctctatggggtttctgtttccttt10/04/1710/04/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs10513025|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 AAGCTTTAGA CTTCCCCGGT CCCCATTGTT TTCACTCCTT CCTCTAGCCT GTTCCAAACA
 GGAGCTGCTC CTGCAGGAGT GTGAACAGTA ACAGGGCTGC TGAACAGCCA CAGCCAGTGC
 ACGACACAAG TGAGAATGAA CCTGTGTCTT GGAGGTGCTG CAGTCCTGGT GCCATTTTGT
 CCCGCAGCAA AAGCAGCTCC ACATACCTTT GATTGTTCCC TTGGCCTCTC CTCTTTTCAC
 TTGTGCATGA
 Y
 TCTCTATGGG GTTTCTGTTT CCTTTCTTTG CCAGGTACTT TTACATGTGC TGTTTCCTTT
 TTCTAGAATT AGCTGTCCTC CAAAACCTGT GACTGATTAT TAGGGGGAAG CATACAAAAC
 TGTCATTGTT GCAGATAGAA AGTCATCAAA GTCTAGCAGT TTCCTAAGGT TAACATAACT
 AAAAACAACA ATGGCAGCAG CCAGGCATTG TGCTGGGAAC TGGGTTCCAC TAACCCCTCA
 GCTCCTCTCA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000005
dbSNP Blast Analysis
OMIM
209850

  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
ss116470207HapMap-CEUEuropean 226IG0.008849560.070796460.920354010.099721000.044247790.95575219
HapMap-HCBAsian 86IG 0.023255810.976744171.000000000.011627910.98837209
HapMap-JPTAsian 90IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 226IG 0.185840710.814159270.654721000.092920360.90707964
HAPMAP-ASW 98IG 0.102040820.897959171.000000000.051020410.94897962
HAPMAP-CHBAsian 82IG 1.00000000 1.00000000
HAPMAP-CHD 170IG 0.011764710.988235291.000000000.005882350.99411762
HAPMAP-GIH 176IG 0.034090910.965909061.000000000.017045460.98295456
HAPMAP-LWK 180IG0.022222220.200000000.777777790.527089000.122222220.87777776
HAPMAP-MEX 100IG 0.120000000.880000001.000000000.060000000.94000000
HAPMAP-MKK 286IG0.020979020.251748260.727272751.000000000.146853150.85314685
HAPMAP-TSI 176IG 0.159090910.840909060.751830000.079545450.92045456
ENSEMBL_Watson 2IG 1.00000000 1.00000000
YRI 2IG 1.00000000 0.500000000.50000000
ss1313870247EAS 1008AF 0.001000000.99900001
EUR 1006AF 0.045700000.95430005
AFR 1322AF 0.119500000.88050002
AMR 694AF 0.036000000.96399999
SAS 978AF 0.029700000.97030002
ss14911994AfAmAfrican American 12IG 0.166666670.83333331 0.083333340.91666669
CaucasianEuropean 24IG 0.083333340.916666691.000000000.041666670.95833331
AsianAsian 12IG 1.00000000 1.00000000
CEPHEuropean 10IG 1.00000000 1.00000000
PDpanelGlobal 46IG 0.217391300.782608691.000000000.108695650.89130437
ss199869541BANTU 2IG 1.00000000 0.500000000.50000000
ss221512080pilot_1_YRI_low_coverage_panel 118AF 0.118644070.88135594
ss232825403pilot_1_CEU_low_coverage_panel 120AF 0.033333340.96666664
ss66506870HapMap-CEUEuropean 118IG0.016949150.050847460.932203410.004998000.042372880.95762712
HapMap-HCBAsian 90IG 0.022222220.977777781.000000000.011111110.98888886
HapMap-JPTAsian 90IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG 0.166666670.833333311.000000000.083333340.91666669
ss76329837ICMHP 10IG0.20000000 0.80000001 0.200000000.80000001

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.098+/-0.1990000

  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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