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Reference SNP (refSNP) Cluster Report: rs903901                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
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=0.1162/582 (1000 Genomes)
A=0.0637/7995 (TOPMED)
HGVS Names
  • CM000663.2:g.2378754G>A
  • NC_000001.10:g.2310193G>A
  • NC_000001.11:g.2378754G>A
  • NM_001301060.1:c.538-4197C>T
  • NM_024848.2:c.538-4197C>T
  • NR_125361.1:n.1029C>T
  • XR_241042.1:n.756-4197C>T
  • XR_946762.1:n.756-4197C>T
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 ss43934077 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs903901 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
ss1336330TSC-CSHL|TSC0181560byFreqfwd/TA/Gccgtctcccaccgaggatgttctggaggactgtggggcctgcccaagccctcgggtcctg09/06/0004/07/0486Genomic95 %
ss43934077ABI|hCV8861414byFreqrev/BC/Tcaggacccgagggcttgggcaggccccacagtcctccagaacatcctcggtgggagacgg07/18/0511/03/06126Genomicunknown
ss66821021ILLUMINA|HumanHap300v1.1_rs903901fwd/BA/Gccgtctcccaccgaggatgttctggaggactgtggggcctgcccaagccctcgggtcctg11/09/0611/09/06127Genomicunknown
ss67891558ILLUMINA|HumanHap550v1.1_rs903901fwd/TA/Gccgtctcccaccgaggatgttctggaggactgtggggcctgcccaagccctcgggtcctg11/14/0611/14/06127Genomicunknown
ss68027894ILLUMINA|HumanHap650Yv1.0_rs903901fwd/TA/Gccgtctcccaccgaggatgttctggaggactgtggggcctgcccaagccctcgggtcctg11/14/0611/15/06127Genomicunknown
ss71592538ILLUMINA|HumanHap650Yv3.0_rs903901fwd/TA/Gccgtctcccaccgaggatgttctggaggactgtggggcctgcccaagccctcgggtcctg04/23/0704/23/07127Genomicunknown
ss75845305ILLUMINA|ILMN_Human_1M_rs903901fwd/TA/Gccgtctcccaccgaggatgttctggaggactgtggggcctgcccaagccctcgggtcctg08/28/0708/29/07129Genomicunknown
ss79288188ILLUMINA|HumanHap300v2.0_rs903901fwd/TA/Gccgtctcccaccgaggatgttctggaggactgtggggcctgcccaagccctcgggtcctg04/18/0711/18/07130Genomicunknown
ss83603570KRIBB_YJKIM|KHS499774fwd/TA/Gccgtctcccaccgaggatgttctggaggactgtggggcctgcccaagccctcgggtcctg12/04/0712/05/07130Genomicunknown
ss98233003ILLUMINA|HumanHap550v3.0__rs903901rev/BC/Tcaggacccgagggcttgggcaggccccacagtcctccagaacatcctcggtgggagacgg04/20/0703/31/08130Genomicunknown
ss122942956ILLUMINA|HumanCNV370v1_C_rs903901fwd/TA/Gccgtctcccaccgaggatgttctggaggactgtggggcctgcccaagccctcgggtcctg04/14/0904/15/09131Genomicunknown
ss154479716ILLUMINA|Human610_Quadv1_B_rs903901-128_B_R_1501882123rev/BC/Tcaggacccgagggcttgggcaggccccacagtcctccagaacatcctcggtgggagacgg06/18/0906/20/09131Genomicunknown
ss159654129ILLUMINA|Human660W-Quad_v1_A_rs903901-128_B_R_1501882123rev/BC/Tcaggacccgagggcttgggcaggccccacagtcctccagaacatcctcggtgggagacgg07/06/0907/07/09131Genomicunknown
ss160965562ILLUMINA|HumanOmni1-Quad_v1-0_B_rs903901-128_B_R_1501882123rev/BC/Tcaggacccgagggcttgggcaggccccacagtcctccagaacatcctcggtgggagacgg08/04/0910/05/09131Genomicunknown
ss172427030ILLUMINA|HumanCNV370-Quadv3_C_rs903901-128_B_R_1501882123rev/BC/Tcaggacccgagggcttgggcaggccccacagtcctccagaacatcctcggtgggagacgg10/01/0910/04/09132Genomicunknown
ss174776220ILLUMINA|Human1M-Duov3_B_rs903901-128_B_R_1501882123rev/BC/Tcaggacccgagggcttgggcaggccccacagtcctccagaacatcctcggtgggagacgg10/01/0910/05/09132Genomicunknown
ss2181961051000GENOMES|pilot_1_YRI_5788_chr1_2300053fwd/A/Gccgtctcccaccgaggatgttctggaggactgtggggcctgcccaagccctcgggtcctg04/22/1004/22/10132Genomicunknown
ss2303995031000GENOMES|pilot_1_CEU_4132_chr1_2300053fwd/A/Gccgtctcccaccgaggatgttctggaggactgtggggcctgcccaagccctcgggtcctg05/01/1005/01/10132Genomicunknown
ss2381187531000GENOMES|pilot_1_CHB+JPT_3830_chr1_2300053fwd/A/Gccgtctcccaccgaggatgttctggaggactgtggggcctgcccaagccctcgggtcctg05/01/1005/01/10132Genomicunknown
ss252871896BL|SNP2386_1_2300053fwd/TA/Gccgtctcccaccgaggatgttctggaggactgtggggcctgcccaagccctcgggtcctg08/18/1008/18/10134Genomicunknown
ss481834747ILLUMINA|HumanOmni2.5-4v1_B_rs903901-128_B_R_1782954368fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg01/30/1210/28/16137Genomicunknown
ss481867314ILLUMINA|HumanOmniExpress-12v1_C_rs903901-131_B_R_1857555397fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg01/30/1210/27/16137Genomicunknown
ss482825445ILLUMINA|HumanOmni1-Quad_v1-0_C_rs903901-131_B_R_1865287903fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg01/30/1208/28/15146Genomicunknown
ss485711881ILLUMINA|HumanOmni2.5-4v1_D_rs903901-131_B_R_1857555397fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg01/30/1210/27/16137Genomicunknown
ss537573993ILLUMINA|HumanOmni5-4v1_B_rs903901-131_B_R_1866875164fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg06/22/1208/28/15146Genomicunknown
ss553723765TISHKOFF|snp_chr1_2310193fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg11/22/1211/22/12138Genomicunknown
ss647526791SSMP|1_2310193fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg12/14/1202/09/15138Genomicunknown
ss778632155ILLUMINA|HumanOmni25Exome-8v1_A_rs903901-131_B_R_1866875164fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg05/30/1307/09/15146Genomicunknown
ss783301560ILLUMINA|HumanOmni2.5-4v1_H_rs903901-131_B_R_1857555397fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg05/30/1307/28/15146Genomicunknown
ss784253834ILLUMINA|HumanOmniExpressExome-8v1_A_rs903901-131_B_R_1866875164fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg05/31/1306/18/15146Genomicunknown
ss825618706ILLUMINA|HumanCNV370v1_C_rs903901-126_B_R_IFB1153052060:0fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg06/24/1311/21/14144Genomicunknown
ss832562912ILLUMINA|HumanOmniExpress-12v1_H_rs903901-131_B_R_1857555397fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg09/17/1306/18/15146Genomicunknown
ss834089787ILLUMINA|HumanOmni2.5-8v1_A_rs903901-131_B_R_1866875164fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg09/18/1307/28/15146Genomicunknown
ss974783240EVA-GONL|EVA-GONL_rs903901fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg04/23/1404/23/14142Genomicunknown
ss1067619637JMKIDD_LAB|HGDP_WGS_chr1_2310193fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg07/10/1407/10/14142Genomicunknown
ss12893988591000GENOMES|PHASE3_V1_65934fwd/A/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg08/16/1408/16/14142Genomicunknown
ss1573855570EVA_GENOME_DK|EVA_GENOME_DK_snv_rs903901fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg02/19/1502/19/15144Genomicunknown
ss1584142835EVA_DECODE|EVA_DECODE_1_2300053_13574_rs903901fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg03/02/1503/02/15144Genomicunknown
ss1599402595EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_2310193_27001fwd/A/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg03/04/1503/04/15144Genomicunknown
ss1642396628EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_2310193_27001fwd/A/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg03/04/1503/04/15144Genomicunknown
ss1712306052EVA_SVP|EVA_SVP_604fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg03/12/1503/12/15144Genomicunknown
ss1751904515ILLUMINA|OmniExpressExome-8v1-1_B_rs903901-131_B_R_1866875164fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg05/27/1506/09/15146Genomicunknown
ss1793747693HAMMER_LAB|Hsieh_6452fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg07/15/1507/15/15146Genomicunknown
ss1917977185WEILL_CORNELL_DGM|SNV:chr1:2310193fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg10/16/1510/16/15147Genomicunknown
ss2019505176JJLAB|SNP7731fwd/TA/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg08/29/1608/30/16149Genomicunknown
ss2147493837USC_VALOUEV|NC_000001.10:g.2310193G>Afwd/A/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg11/17/1611/17/16150Genomicunknown
ss2159471917HUMAN_LONGEVITY|HLI-1-2378754-G-Afwd/A/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg11/18/1611/18/16150Genomicunknown
ss2321625744TOPMED|1_2310193_G/Afwd/A/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg11/19/1611/19/16150Genomicunknown
ss2632466906ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs903901-131_B_R_186687516fwd/A/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg02/02/1702/02/17151Genomicunknown
ss2634995426ILLUMINA|Cancer_BeadChip_11459870_A_rs903901-128_B_R_1782954368fwd/A/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg02/02/1702/02/17151Genomicunknown
ss2697385716GRF|rs903901fwd/A/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg02/13/1702/13/17151Genomicunknown
ss2750816465GNOMAD|rs903901fwd/A/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg05/17/1705/17/17151Genomicunknown
ss2986175550SWEGEN|NC_000001.10:g.2310193G>Afwd/A/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg05/30/1705/30/17151Genomicunknown
ss3066796911TOPMED|TOPMed_freeze_5?chr1:2,378,754fwd/A/Gtcccaccgaggatgttctggaggactgtggggcctgcccaagccctcggg09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs903901|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 CCCCGGTTGG GCATTCCCAC ACACGCCCAG CTGAGGAGAG GAGGCTCGGG GACTGCGGCA
 GGCAAAGCCG CCCAGAAGGA GCCACCTGCT CCGTGCAGTG AGCAGGTGCT CGGCACCCAG
 CGGCAACTCC GGGAAAGCTG GCGTGTGAGA CAGCCAACAC TCACGGCGCA GCTGATACAG
 CCAGGGATGC CCGGAGGGCC GCGCTGCTGC CAACATGGGT AGGAGACACT CTGATGTGCA
 CACACACGTG TGGCCTCTAC TCTGTCTGCT CCGTCTCCCA CCGAGGATGT TCTGGAGGAC
 R
 TGTGGGGCCT GCCCAAGCCC TCGGGTCCTG GGAGGTCGAG CAGTAAGCTG TAAACTAGGA
 GTGTGGGGGA CGGAGATGGC TGAGGCGTCA CAGGCTGGTG GGGGTGCTCG TGGCCCAGGA
 CCTCTGTGGC TTCCGGGACC GGCCTGAGCC GCGTGGCTCC TGTCCCTGTG GAAGAGGAGC
 CTTCTCTGCT TTGGGATCCG CTGTTCTTAT TTTCCGTCAG AAGAAGCTGT AACACGTTTA
 TTTTCAGGAA TGCATTTTTT TCTAGAATGC ATTTTTAAAA AAAGGTTCTT CATAGAGCTT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000001 AC025802.3
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.
SourceA/A
A/G
G/G
HWPA
G
ss1289398859EAS 1008AF 0.068500000.93150002
EUR 1006AF 0.053700000.94629997
AFR 1322AF 0.065100000.93489999
AMR 694AF 0.113800000.88620001
SAS 978AF 0.300599990.69940001
ss1336330TSC_42_AA 84AF 0.060000000.94000000
TSC_42_C 82AF 0.049000010.95100003
TSC_42_A 82AF 0.110000010.88999993
ss218196105pilot_1_YRI_low_coverage_panel 118AF 0.101694910.89830506
ss230399503pilot_1_CEU_low_coverage_panel 120AF 0.100000000.89999998
ss238118753pilot_1_CHB+JPT_low_coverage_panel 120AF 0.083333340.91666669
ss43934077HapMap-CEUEuropean 226IG 0.185840710.814159270.654721000.092920360.90707964
HapMap-HCBAsian 86IG 0.139534890.860465111.000000000.069767450.93023258
HapMap-JPTAsian 172IG 0.151162790.848837201.000000000.075581390.92441863
HapMap-YRISub-Saharan African 226IG 0.176991150.823008840.751830000.088495570.91150445
HAPMAP-ASW 98IG 0.122448980.877551021.000000000.061224490.93877554
HAPMAP-CHBAsian 82IG 0.073170730.926829281.000000000.036585360.96341461
HAPMAP-CHD 168IG0.011904760.071428570.916666690.099721000.047619050.95238096
HAPMAP-GIH 174IG0.080459770.482758610.436781620.342782000.321839090.67816091
HAPMAP-LWK 180IG 0.088888890.911111121.000000000.044444450.95555556
HAPMAP-MEX 100IG 0.239999990.759999990.654721000.120000000.88000000
HAPMAP-MKK 286IG0.013986010.083916080.902097880.020022000.055944060.94405591
HAPMAP-TSI 174IG0.011494250.091954020.896551730.200325000.057471260.94252872
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
0.205+/-0.2460000ALFRED: 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
byClusterbyFreqwith2hitWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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