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Reference SNP (refSNP) Cluster Report: rs4825261                 ** With untested allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:111/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/G/T (FWD)
Allele Origin:A:unknown
C:germline
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:With untested allele [ClinVar]
MAF/MinorAlleleCount:A=0.2894/36335 (TOPMED)
HGVS Names
  • CM000685.2:g.18579749C>A
  • CM000685.2:g.18579749C>G
  • CM000685.2:g.18579749C>T
  • NC_000023.10:g.18597869C>A
  • NC_000023.10:g.18597869C>T
  • NC_000023.11:g.18579749C>A
  • NC_000023.11:g.18579749C>G
  • NC_000023.11:g.18579749C>T
  • NG_008475.1:g.159145C>A
  • NG_008475.1:g.159145C>G
  • NG_008475.1:g.159145C>T
  • NM_001037343.1:c.283-99C>A
  • NM_001037343.1:c.283-99C>G
  • NM_001037343.1:c.283-99C>T
  • NM_001323289.1:c.283-99C>A
  • NM_001323289.1:c.283-99C>G
  • NM_001323289.1:c.283-99C>T
  • NM_003159.2:c.283-99C>A
  • NM_003159.2:c.283-99C>G
  • NM_003159.2:c.283-99C>T
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 ss283705432 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4825261 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
ss6664169WI_SSAHASNP|NT_011586.9_1070457fwd/TA/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg02/12/0310/10/03111Genomicunknown
ss8181487SC_SNP|NT_011586.9_1070457byFreqfwd/TA/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg04/16/0310/25/06114Genomicunknown
ss8528157SC_SNP|NT_011757.12_5512336fwd/TA/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg05/23/0310/10/03116Genomicunknown
ss24230211PERLEGEN|afd3867116byFreqfwd/TA/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg08/10/0409/13/04123Genomicunknown
ss75140478ILLUMINA|ILMN_Human_1M_rs4825261fwd/TA/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg08/28/0708/29/07129Genomicunknown
ss84928787HGSV|Cor19129_SNV_20070510.chrX_18357526fwd/TA/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg12/06/0712/08/07130Genomicunknown
ss105717298BGI|BGI_rs4825261fwd/TA/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg09/10/0806/18/09130Genomicunknown
ss119490268KRIBB_YJKIM|KHS1652515fwd/TA/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg02/04/0902/04/09131Genomicunknown
ss161780648ENSEMBL|ENSSNP3116094fwd/TA/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg09/24/0909/25/09131Genomicunknown
ss163048851COMPLETE_GENOMICS|NA07022_36_chrX_18507790fwd/TA/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg09/29/0909/29/09132Genomicunknown
ss173831802ILLUMINA|Human1M-Duov3_B_rs4825261-127_T_F_1514108728fwd/TA/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg10/01/0910/04/09132Genomicunknown
ss208890042BCM-HGSC-SUB|BCM_CMT_1011-3345477fwd/TA/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg03/15/1003/20/10132Genomicunknown
ss2121570141000GENOMES|YRI.trio.3.2010_1536944_chrX_18507790fwd/TA/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg03/29/1003/31/10132Genomicunknown
ss283705432GMI|GMI_AK_SNP_8025875fwd/A/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg12/16/1012/16/10137Genomicunknown
ss294530825PJP|SNP_4037183_chrX_18507790fwd/A/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg01/21/1101/21/11134Genomicunknown
ss3413408461000GENOMES|20100804_snps_92550_chrX_18597869fwd/TA/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg03/23/1103/23/11134Genomicunknown
ss537279970ILLUMINA|HumanOmni5-4v1_B_rs4825261-131_T_F_1908444028fwd/TA/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg06/22/1208/28/15146Genomicunknown
ss538296403CHWRETT|CDKL5: c.283-99C>Afwd/TA/Ctagaaagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatgctttg08/08/1208/08/12137Genomicunknown
ss566785212TISHKOFF|snp_chrX_18597869fwd/TA/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg11/22/1211/23/12138Genomicunknown
ss1082815155JMKIDD_LAB|HGDP_WGS_chrX_18597869fwd/TA/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg07/10/1407/12/14142Genomicunknown
ss1432011040DDI|DDI_rs4825261fwd/TA/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg11/04/1411/05/14144Genomicunknown
ss1583339739EVA_GENOME_DK|EVA_GENOME_DK_snv_rs4825261fwd/TA/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg02/19/1502/20/15144Genomicunknown
ss1640415708EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_X_18597869_45113565fwd/A/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg03/04/1503/04/15144Genomicunknown
ss1683409741EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_X_18597869_45113565fwd/A/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg03/04/1503/04/15144Genomicunknown
ss1711578182EVA_MGP|EVA_XIMO_693942fwd/TA/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg03/09/1503/09/15144Genomicunknown
ss1939182575WEILL_CORNELL_DGM|SNV:chrX:18597869fwd/TA/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg10/16/1510/19/15147Genomicunknown
ss1971350023GENOMED|rs4825261fwd/TA/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg02/16/1602/16/16147Genomicunknown
ss2158968624USC_VALOUEV|NC_000023.10:g.18597869C>Afwd/A/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg11/17/1611/17/16150Genomicunknown
ss2316003520HUMAN_LONGEVITY|HLI-X-18579749-C-A,Tfwd/A/C/Tagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg11/18/1611/18/16150Genomicunknown
ss2629672790SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV6916356fwd/A/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg01/06/1701/06/17151Genomicunknown
ss2710097077GRF|rs4825261fwd/A/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg02/13/1702/13/17151Genomicunknown
ss2976933635GNOMAD|rs4825261fwd/A/C/Tagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg05/23/1705/23/17151Genomicunknown
ss2985481514AFFY|Axiom_PsorMich_Affx-34746162fwd/A/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg05/24/1705/24/17151Genomicunknown
ss2986127910AFFY|Axiom_Smokesc1_Affx-34746162fwd/A/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg05/24/1705/24/17151Genomicunknown
ss3019694792SWEGEN|NC_000023.10:g.18597869C>Afwd/A/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg05/30/1705/30/17151Genomicunknown
ss3029014367BIOINF_KMB_FNS_UNIBA|X.18579749C>Afwd/A/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg07/05/1707/05/17151Genomicunknown
ss3606383365TOPMED|TOPMed_freeze_5?chrX:18,579,749-01fwd/A/Cagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg10/07/1710/07/17151Genomicunknown
ss3606383366TOPMED|TOPMed_freeze_5?chrX:18,579,749-02fwd/C/Gagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg10/07/1710/07/17151Genomicunknown
ss3606383367TOPMED|TOPMed_freeze_5?chrX:18,579,749-03fwd/C/Tagcaaaacaattaaaaaaaaaagcttgtattggatgaattattctagatg10/07/1710/07/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4825261|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/C/G/T'|mol=Genomic|build=151
 ATGAATTTTA GTTATAATGG TCTCTGACTC CAAATTAAGG TTTTTGAATA TTGAATTGTA
 GGGGGTCTGT GACTCTTTAT TTCAATAGTA TTTTCTGGCC TGTTTGAATT TTTGTACTAA
 ATGTATTGAT CATTTTTAAT TTTGGACATT TTTTTTTCTA CTAAGAATAT TTCGTGGATC
 TTCCAGGTGT ATTTTCAAGG CTTGATTTTT ATCACAAGAT TCTGTTGCAG AGATACAGCA
 CACTGTGTTT AAAAAGGCTC TTTCCCCCCT TTATACATTA CAGTGTCATA TTTCTACTTT
 GTATTGCTTT TCTCTTCTAA TTATTCTAAA ATAATGCCTG AAAACCTTTA GGGAGAGTGA
 AAAGTATACA GGGTTATTAT TTGGGGTAGC ATTAGGGAAT AGTAAAAATG GAATTCCTCA
 TAAAAGAAAG CCCCAATTTT AATGCTGATT CAGCATGAGA AAGTTGTAGA TAGAAAGCAA
 AACAATTAAA AAAAAAAGCT
 N
 TGTATTGGAT GAATTATTCT AGATGCTTTG TAAAATTGTT AATACATAAT TTACGGGCCT
 ACCTAATTTG GGAAATAATG ACTCTATTTA ATTTTTAGAA TATGCTCGAA TTGCTGGAAG
 AAATGCCAAA TGGAGTTCCA CCTGAGAAAG TAAAAAGCTA CATCTATCAG CTAATCAAGG
 CTATTCACTG GTGCCATAAG AATGATATTG TCCATCGAGG TGAGTATGAG ATTTTTAAAA
 TGGAAAATAT TAAAACATCA AATAAAGTTA AGAGTATTTC ACATGTTACT GTCTTTAAGA
 ATATTTTCAT AAGCATTGGC ATTGCCATTT AAATTAAATA TATTTTGAAA GTGCAAGACA
 TGAGAAATAT TTGCTCTCCA TATCTCCTTT TCTATCACCA AAAGGATGGA TTACAAATTT
 ATTTGGATAT TGTGGTGAGA TCTTTACATT TGTATAACTA TTATAGATCC ACTCCCAATT
 GTAGAAATGC CTAGTGATAT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011757
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.
Source0/A
0/C
A
A/A
A/C
C
C/C
N
HWP0
A
C
N
ss161780648ENSEMBL_celera 4IG 0.50000000 0.50000000 0.250000000.75000000
ss163048851CEUEuropean 1IG 1.00000000 1.00000000
ss24230211AFD_EUR_PANELEuropean 48IG0.208333330.33333334 0.041666670.20833333 0.20833333 0.449329000.270833340.250000000.47916666
AFD_AFR_PANELAfrican American 46IG0.043478260.43478259 0.043478260.04347826 0.43478259 0.099759000.239130440.086956520.67391306
AFD_CHN_PANELAsian 46IG 0.304347810.17391305 0.52173913 0.00250100 0.391304340.60869563
ss8181487HapMap-CEUEuropean 226IG 0.194690270.25663716 0.54867256 0.00100000 0.323008840.67699116
HapMap-HCBAsian 86IG 0.325581400.25581396 0.41860464 0.00250100 0.453488380.54651165
HapMap-JPTAsian 170IG 0.329411770.25882354 0.41176471 0.00100000 0.458823530.54117650
HapMap-YRISub-Saharan African 226IG 0.035398230.15044248 0.81415927 0.02002200 0.110619470.88938051
CHMJAsian 74IG 0.47297296 0.51351351 0.01351351 0.472972960.513513510.01351351
HAPMAP-ASW 98IG 0.061224490.18367347 0.75510204 0.05004300 0.153061230.84693879
HAPMAP-CHBAsian 82IG 0.341463420.36585367 0.29268292 0.09972100 0.524390220.47560975
HAPMAP-CHD 170IG 0.411764710.23529412 0.35294119 0.00100000 0.529411790.47058824
HAPMAP-GIH 176IG 0.250000000.26136363 0.48863637 0.00100000 0.380681810.61931819
HAPMAP-LWK 180IG 0.05555556 0.94444442 1.00000000 0.027777780.97222221
HAPMAP-MEX 100IG 0.460000010.31999999 0.22000000 0.02505600 0.620000000.38000000
HAPMAP-MKK 282IG 0.163120570.14184397 0.69503546 0.00100000 0.234042560.76595747
HAPMAP-TSI 176IG 0.238636360.26136363 0.50000000 0.00100000 0.369318190.63068181
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
0.437+/-0.1670000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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