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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs1899          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:36/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_016013.2:c.-266A>G
NM_016013.2:c.26G>A
NP_057097.2:p.Arg9His
NT_010194.16:g.12479789C>T
Links , Linkout

SNP Details are organized in the following sections:
Submission Fasta Resource GeneView Map Diversity Validation

  Submitter records for this RefSNP Cluster back to top
The submission ss43779357 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1899 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
ss1924WIAF|WIAF-3863byFreqfwd/TA/Ggtaccatggctttggttcacaaattgctgctggtacttattttctcagaaaattctctaa01/23/9904/07/0436Genomicunknown
ss1529957LEE|524195fwd/TA/Ggtaccatggctttggttcacaaattgctgctggtacttattttctcagaaaattctctaa09/13/0010/10/0386cDNAunknown
ss4419484LEE|e524195fwd/TA/Ggtaccatggctttggttcacaaattgctgctggtacttattttctcagaaaattctctaa04/26/0210/10/03106cDNAunknown
ss16242711CGAP-GAI|1482672fwd/TA/Ggtaccatggctttggttcacaaattgctgctggtacttattttctcagaaaattctctaa11/18/0311/22/03120cDNAunknown
ss17538177CSHL-HAPMAP|CSHL-HuCC-200402.chr15.NT_010194.16_12479789byFreqrev/BC/Tttagagaattttctgagaaaataagtaccagcagcaatttgtgaaccaaagccatggtac02/19/0405/16/04120Genomicunknown
ss43779357ABI|hCV8219526byFreqrev/BC/Tttagagaattttctgagaaaataagtaccagcagcaatttgtgaaccaaagccatggtac07/18/0511/03/06126Genomicunknown
ss48413285APPLERA_GI|hCV8219526byFreqrev/BC/Tttagagaattttctgagaaaataagtaccagcagcaatttgtgaaccaaagccatggtac09/28/0511/03/06126Genomicunknown
ss65726005ILLUMINA|Human1-rs1899fwd/TA/Ggtaccatggctttggttcacaaattgctgctggtacttattttctcagaaaattctctaa10/10/0610/10/06127Genomicunknown
ss66198203AFFY|SNP_A-2274606rev/BC/Tgagaaaataagtaccagcagcaatttgtgaac10/27/0610/27/06127Genomicunknown
ss66578453ILLUMINA|HumanHap300v1.1_rs1899fwd/BA/Ggtaccatggctttggttcacaaattgctgctggtacttattttctcagaaaattctctaa11/09/0611/09/06127Genomicunknown
ss67205010ILLUMINA|HumanHap550v1.1_rs1899fwd/TA/Ggtaccatggctttggttcacaaattgctgctggtacttattttctcagaaaattctctaa11/14/0611/14/06127Genomicunknown
ss67597360ILLUMINA|HumanHap650Yv1.0_rs1899fwd/TA/Ggtaccatggctttggttcacaaattgctgctggtacttattttctcagaaaattctctaa11/14/0611/14/06127Genomicunknown
ss69174605PERLEGEN|PGP04752071byFreqrev/BC/Tttagagaattttctgagaaaataagtaccagcagcaatttgtgaaccaaagccatggtac01/30/0708/14/07127Genomicunknown
ss70683238ILLUMINA|HumanHap550v3.0__rs1899rev/BC/Tttagagaattttctgagaaaataagtaccagcagcaatttgtgaaccaaagccatggtac04/20/0703/30/08130Genomicunknown
ss71247214ILLUMINA|HumanHap650Yv3.0_rs1899fwd/TA/Ggtaccatggctttggttcacaaattgctgctggtacttattttctcagaaaattctctaa04/23/0704/23/07127Genomicunknown
ss74918664ILLUMINA|ILMN_Human_1M_rs1899fwd/TA/Ggtaccatggctttggttcacaaattgctgctggtacttattttctcagaaaattctctaa08/28/0708/29/07129Genomicunknown
ss76282697AFFY|AFFY_6_1M_SNP_A-2274606rev/BC/Tgagaaaataagtaccagcagcaatttgtgaac08/28/0708/30/07129Genomicunknown
ss79099993ILLUMINA|HumanHap300v2.0_rs1899fwd/TA/Ggtaccatggctttggttcacaaattgctgctggtacttattttctcagaaaattctctaa04/18/0711/18/07130Genomicunknown
ss83344921KRIBB_YJKIM|KHS439532fwd/TA/Ggtaccatggctttggttcacaaattgctgctggtacttattttctcagaaaattctctaa12/04/0712/04/07130Genomicunknown
ss1087647471000GENOMES|CEU.trio.12.15.2008_3151460_chr15_39476524rev/BC/Tttagagaattttctgagaaaataagtaccagcagcaatttgtgaaccaaagccatggtac12/15/0812/16/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1899|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 GAGGCTACAG TGAGCTGTGA TTGTGCCACT GTACCCAGCC TGGGCCACAG AGCAAGACCT
 TGTCTCAAAT AATAATAATA ATAATAGTAA ACAAATAAGT TAACAAACTT CAAAATACCT
 GATTTCTGTT GAATTTGAAA TTGTGATGCA TTCATTGCTA TGCTGATAAT TCTTCAATGT
 CTCTTCTGTT ATAGGTAGAA TTGGGCTATT TGCTGAAGCT TCTTGGTGGC CCTTGCTAGC
 CCAGGAAGAA ACTTACATTT TGATTTTTTT GTACCATGGC TTTGGTTCAC AAATTGCTGC
 R
 TGGTACTTAT TTTCTCAGAA AATTCTCTAA GCCAACTTCT GCCTTGTATC CATTTTTGGG
 TATTCGCTTT GCAGAGTATT CCAGTAGTCT TCAGAAACCA GTGGCTTCTC CTGGCAAAGC
 CTCCTCACAG AGGAAGACTG AAGGGGATTT GCAAGGAGAT CACCAGAAAG AAGTTGCTTT
 GGATATAACT TCTTCTGAGG AGAAGCCTGA TGTTAGTTTC GATAAAGCAA TTAGAGATGA
 AGCAATATAC CATTTTAGGC TTTTGAAGGA TGAAATTGTG GATCATTGGA GAGGACCGGA

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
dbSTS GenBank
G44219 NT_010194 BF689899 Hs.106529
dbSNP Blast Analysis
UniGene Cluster ID
106529

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/G
 G/G
 HWP A
 G
ss17538177 CEPH 184 AF 0.360 0.640
ss1924 HydatidiformMoles Tissue 10 IG 0.200 0.800 0.050 0.200 0.800
ss43779357 HapMap-CEU European 120 IG 0.017 0.317 0.667 0.479 0.175 0.825
HapMap-HCB Asian 90 IG 0.022 0.978 1.000 0.011 0.989
HapMap-JPT Asian 88 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 120 IG 0.017 0.283 0.700 0.655 0.158 0.842
AoD_African_American 90 AF 0.240 0.760
AoD_Caucasian 92 AF 0.270 0.730
AoD_Chinese 90 AF 0.020 0.980
AoD_Japanese 90 AF 0.020 0.980
ss48413285 AGI_ASP population multiple 70 IG 0.286 0.714 0.343 0.143 0.857
ss69174605 HapMap-CEU European 120 GF 0.017 0.317 0.667 0.175 0.825
HapMap-HCB Asian 90 GF 0.022 0.978 0.011 0.989
HapMap-JPT Asian 90 GF 1.000 1.000
HapMap-YRI Sub-Saharan African 120 GF 0.017 0.283 0.700 0.158 0.842
ss76282697 ICMHP 8 IG 1.000 1.000

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.182+/-0.241 1255 1045 270 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwithHapMapFreqWith1000GenomeData
Validated by: ILLUMINA
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .