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Reference SNP (refSNP) Cluster Report: rs398101                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:80/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:G=0.1340/506 (1000 Genomes)
G=0.2019/25348 (TOPMED)
HGVS Names
  • CM000685.2:g.139541798A>G
  • NC_000023.10:g.138623957A>G
  • NC_000023.11:g.139541798A>G
  • NG_007994.1:g.16063A>G
  • NM_000133.3:c.391+609A>G
  • NM_001313913.1:c.277+4412A>G
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 ss287651539 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs398101 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
ss517296SC_JCM|AL033403.1_15117fwd/TA/Gatccctgaatttgactatattgattacatcaaaatgttacatagcaaccttagaatcctt07/12/0010/10/0380Genomicunknown
ss5604507PGA-UW-FHCRC|F9-012651byFreqfwd/TA/Gatccctgaatttgactatattgattacatcaaaatgttacatagcaaccttagaatcctt12/03/0204/07/04110Genomicunknown
ss48397551THOWARDEMORY|F9-A14078Gfwd/TA/Gatccctgaatttgactatattgattacatcaaaatgttacatagcaaccttagaatcctt09/01/0509/01/05126Genomicunknown
ss52086790PGA-UW-FHCRC|F9_012651byFreqfwd/TA/Gatccctgaatttgactatattgattacatcaaaatgttacatagcaaccttagaatcctt04/28/0608/14/07127Genomicunknown
ss163304633COMPLETE_GENOMICS|NA07022_36_chrX_138451623fwd/TA/Gatccctgaatttgactatattgattacatcaaaatgttacatagcaaccttagaatcctt09/29/0909/29/09132Genomicunknown
ss173678620ILLUMINA|Human1M-Duov3_B_rs398101-127_T_F_1518192346fwd/TA/Gatccctgaatttgactatattgattacatcaaaatgttacatagcaaccttagaatcctt10/01/0910/04/09132Genomicunknown
ss287651539GMI|GMI_NA10851_SNP_3664362fwd/A/Gatccctgaatttgactatattgattacatcaaaatgttacatagcaaccttagaatcctt12/17/1012/17/10138Genomicunknown
ss3418368991000GENOMES|20100804_snps_588570_chrX_138623957fwd/TA/Gatccctgaatttgactatattgattacatcaaaatgttacatagcaaccttagaatcctt03/25/1103/25/11134Genomicunknown
ss537211403ILLUMINA|HumanOmni5-4v1_B_rs398101-131_T_F_1908413150fwd/TA/Gtgaatttgactatattgattacatcaaaatgttacatagcaaccttagaa06/22/1208/28/15146Genomicunknown
ss567064495TISHKOFF|snp_chrX_138623957fwd/TA/Gtgaatttgactatattgattacatcaaaatgttacatagcaaccttagaa11/22/1211/23/12138Genomicunknown
ss663043592SSMP|X_138623957fwd/TA/Gtgaatttgactatattgattacatcaaaatgttacatagcaaccttagaa12/14/1202/14/15138Genomicunknown
ss1083159152JMKIDD_LAB|HGDP_WGS_chrX_138623957fwd/TA/Gtgaatttgactatattgattacatcaaaatgttacatagcaaccttagaa07/10/1407/12/14142Genomicunknown
ss1432129130DDI|DDI_rs398101fwd/TA/Gtgaatttgactatattgattacatcaaaatgttacatagcaaccttagaa11/04/1411/05/14144Genomicunknown
ss15563580321000GENOMES|PHASE3_chrX_3131714byFreqfwd/TA/Gtgaatttgactatattgattacatcaaaatgttacatagcaaccttagaa08/16/1408/07/15144Genomicunknown
ss1583522398EVA_GENOME_DK|EVA_GENOME_DK_snv_rs398101fwd/TA/Gtgaatttgactatattgattacatcaaaatgttacatagcaaccttagaa02/19/1502/20/15144Genomicunknown
ss1641626762EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_X_138623957_46438268fwd/A/Gtgaatttgactatattgattacatcaaaatgttacatagcaaccttagaa03/04/1503/04/15144Genomicunknown
ss1684620795EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_X_138623957_46438268fwd/A/Gtgaatttgactatattgattacatcaaaatgttacatagcaaccttagaa03/04/1503/04/15144Genomicunknown
ss1939767755WEILL_CORNELL_DGM|SNV:chrX:138623957fwd/TA/Gtgaatttgactatattgattacatcaaaatgttacatagcaaccttagaa10/16/1510/19/15147Genomicunknown
ss2159264187USC_VALOUEV|NC_000023.10:g.138623957A>Gfwd/A/Gtgaatttgactatattgattacatcaaaatgttacatagcaaccttagaa11/17/1611/17/16150Genomicunknown
ss2320717719HUMAN_LONGEVITY|HLI-X-139541798-A-Gfwd/A/Gtgaatttgactatattgattacatcaaaatgttacatagcaaccttagaa11/18/1611/18/16150Genomicunknown
ss2983897743GNOMAD|rs398101fwd/A/Gtgaatttgactatattgattacatcaaaatgttacatagcaaccttagaa05/23/1705/23/17151Genomicunknown
ss3020696083SWEGEN|NC_000023.10:g.138623957A>Gfwd/A/Gtgaatttgactatattgattacatcaaaatgttacatagcaaccttagaa05/30/1705/30/17151Genomicunknown
ss3029127156BIOINF_KMB_FNS_UNIBA|X.139541798A>Gfwd/A/Gtgaatttgactatattgattacatcaaaatgttacatagcaaccttagaa07/05/1707/05/17151Genomicunknown
ss3623243470TOPMED|TOPMed_freeze_5?chrX:139,541,798fwd/A/Gtgaatttgactatattgattacatcaaaatgttacatagcaaccttagaa10/07/1710/07/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs398101|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 TTGATGCTTA TAAACATTTC ATTTGTAGTG ATAGTTTTCA GGATATGAGT TCAAGAAGCT
 ACATTAAAAT CAATAACAAT ATTTGGTAAC TAATATTAAG TAATAATGAT GTTCCACTCA
 CTTATTAATC TTTAATACAA CCGTATGTGG TTAGTACTAT CATTATGCGC ATTCTATGCA
 GATGAGAAAA CCGCAACTCC AACGGCCAAA AATTACAGAG GCATAAATGG TTTAGACAGG
 ACTTAAACTT CAGTGTGACC AAAACCCATG CTTCTAACTA CTATATTCAA AACTCAGAGA
 AAACTGAACC CAGAAAATTG AAATCATGAC TAAATTGCTA TCAACATAGG TAGTGAAAGT
 CAATTAAGTA CAGAACTGGA GTATGACTGG CCAATTATCC CATATAATGG GAATTCTCCA
 CATGTACAAA CCACTTCATA TGCTAAACTT GTTGACAACA TTCAAAGCTC ATCCCTGAAT
 TTGACTATAT TGATTACATC
 R
 AAAATGTTAC ATAGCAACCT TAGAATCCTT GTGTACCTTT TCTTCTCAAA GCCTAGATTA
 TTTCTTTTTC CGACGTTTCA GTAATTGGAG CAGTAAACCC CAGTGTCCCT TACCTACTTG
 TTTATTACCT CCAGATGCAA TATTACTGGT ACTGTGATTG AGAAACGCAC ACAGTGCTAA
 TGAGGAATTC ACTTTCTACT CTGACACTCT GGAAGAATAG AGATGCAATC CTAAGGAAGA
 ATTTAACACC ACAGGCTACA TGACTAAGGA TAAAGAGTAG AAAATTAGCA GGACTCTATT
 AAGGCATTAC AGCAATCCAC CTGACAGATG AAAAAGGCAT GAAATGAAAT GAAATGTAGC
 AGCTACACTC GTCCTATTGA GAAAGGAAAA AAGTCACCTG TAATGTTGTT CAGAAATCCT
 TTCAGTACTA AAAAATTCAT TGACCATCTT CCTTTAGTCT CGAAAATTTC TTAGAAGGTA
 AAAAAAGGAA AAGGTGACAG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000023 K02402
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/G
A/A
A/G
G
G/G
HWP0
A
G
ss1556358032EAS 1008AF 0.999000010.00100000
EUR 1006AF 0.761399980.23860000
AFR 1322AF 0.940999980.05900000
AMR 694AF 0.904900010.09509999
SAS 978AF 0.876300040.12370000
ss163304633CEUEuropean 1IG 1.00000000 1.00000000
ss52086790HSP_GENO_PANEL 120IG0.28333333 0.583333310.11666667 0.016666670.301194000.141666670.783333360.07500000
YRI_GENO_PANELSub-Saharan African 120IG0.466666670.033333340.466666670.03333334 0.199888000.250000000.716666640.03333334
AAM_GENO_PANELAfrican American 124IG0.06451613 0.774193530.14516129 0.016129030.740818000.032258060.879032250.08870967
CEU_GENO_PANELEuropean 120IG0.349999990.150000010.233333330.18333334 0.083333340.150318000.250000000.500000000.25000000
CHB_GENO_PANELAsian 90IG0.48888889 0.51111114 0.200325000.244444440.75555557
JPT_GENO_PANELAsian 90IG0.48888889 0.51111114 0.200325000.244444440.75555557
ss5604507PGA-AFRICAN-PANELAfrican American 48IG0.458333340.041666670.416666660.08333334 0.606531000.250000000.687500000.06250000
PGA-EUROPEAN-PANELEuropean 46IG0.347826090.173913050.173913050.17391305 0.130434780.272532000.260869560.434782590.30434781
ENSEMBL_Venter 2IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.232+/-0.2490000ALFRED: 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
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNYES

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