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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2916414          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:101/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/T
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_177998.1:c.927T>A
NP_819056.1:p.Asp309Glu
NT_006051.17:g.287079A>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 ss44525925 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2916414 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
ss4114268SC_JCM|AC011744.6_162841fwd/BA/Tcaggcccaggactgcgcccaccatgacccctcagacttgaactgcatcttctggtgctga10/15/0110/10/03101Genomicunknown
ss14313257WI_SSAHASNP|chr4.NT_006051.16_287079fwd/BA/Tcaggcccaggactgcgcccaccatgacccctcagacttgaactgcatcttctggtgctga11/05/0311/22/03119Genomicunknown
ss22069504SSAHASNP|WGSA-200403-chr4.chr4.NT_006051.16_287079fwd/BA/Tcaggcccaggactgcgcccaccatgacccctcagacttgaactgcatcttctggtgctga03/20/0403/20/04121Genomicunknown
ss44525925ABI|hCV15849710byFreqfwd/A/Tcaggcccaggactgcgcccaccatgacccctcagacttgaactgcatcttctggtgctga07/19/0511/03/06126Genomicunknown
ss48430396APPLERA_GI|hCV15849710byFreqrev/A/Ttcagcaccagaagatgcagttcaagtctgaggggtcatggtgggcgcagtcctgggcctg10/02/0511/03/06126Genomicunknown
ss68888576PERLEGEN|PGP04759251byFreqfwd/A/Tcaggcccaggactgcgcccaccatgacccctcagacttgaactgcatcttctggtgctga01/30/0703/31/08127Genomicunknown
ss74808475AFFY|SNP_M-180055fwd/BA/Tcaggcccaggactgcgcccaccatgacccctcagacttgaactgcatcttctggtgctga08/09/0708/09/07128Genomicunknown
ss78793983HGSV|Cor12878_SNV_20070510.chr4_4317706fwd/A/Tcaggcccaggactgcgcccaccatgacccctcagacttgaactgcatcttctggtgctga10/17/0710/20/07129Genomicunknown
ss84383347HGSV|Cor18555_SNV_20070510.chr4_4317706fwd/A/Tcaggcccaggactgcgcccaccatgacccctcagacttgaactgcatcttctggtgctga11/27/0712/07/07130Genomicunknown
ss86179691HGSV|Cor18517_SNV_20070510.chr4_4317706fwd/A/Tcaggcccaggactgcgcccaccatgacccctcagacttgaactgcatcttctggtgctga12/06/0712/11/07130Genomicunknown
ss92447518BCMHGSC_JDW|JWB-1728101fwd/A/Tcaggcccaggactgcgcccaccatgacccctcagacttgaactgcatcttctggtgctga02/26/0803/03/08129Genomicunknown
ss1116888211000GENOMES|NA19240_2008_12_16_814003_chr4_4250535fwd/A/Tcaggcccaggactgcgcccaccatgacccctcagacttgaactgcatcttctggtgctga12/16/0812/17/08130Genomicunknown
ss1128621881000GENOMES|CEU.trio.12.15.2008_901900_chr4_4250535fwd/A/Tcaggcccaggactgcgcccaccatgacccctcagacttgaactgcatcttctggtgctga12/15/0812/18/08130Genomicunknown
ss116846680ILLUMINA-UK|NA18507_000006417_NCBI36.1_chr4_4250535fwd/A/Tcaggcccaggactgcgcccaccatgacccctcagacttgaactgcatcttctggtgctga01/18/0901/18/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2916414|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=130
 GATTGAGCCC CAGGAGATAA GCCAGGAGCC CGAGGCAGTG CCCACCAAGA GGTCCGAGTC
 CAGTTTGCGG GCCGGATTTT TGGACTCATC CAGTGACTTC TCGTCTATCC TGTAAATCCG
 GATTCCAGCC AGCCCCGCAG CCCCCATAAG CATCAGCAGG GTGATGGCAT ACAGGTAGAA
 CATGATGAGT GCCGACTCGC TCTTGGTCTT GGAGCGCCCA ATATGAATCA GGTATACCAC
 CACCACAGCA ATGGTGGCGG CCAGCACGGT CAGGCCCAGG ACTGCGCCCA CCATGACCCC
 W
 TCAGACTTGA ACTGCATCTT CTGGTGCTGA TGGCTGTCAA CTTTGCGCCC GATGTTCTTC
 CACAGGACGT AGAGCATTGT GGAGGCCAGG ATCTGATACT CTATGTTGAA GGGGTAGAGG
 TAGTAGATCC CGTGGGAGAT GGCAGTGCAC AGAGTTGGGG GCGTGCAGTT ACACTGCGGT
 GTGTGGTCAT CTAAAACTAG GGGAGACAGG TAGATCACAC AGGAGGGCGA TTAGCAGGTG
 CAAGGGGGAA CAGAAAAGCA CAGAAAACTG TTTCCACCGT GGATTCAGGC TTGGGTCTTC

  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
GenBank
NT_006051 AC015709 AF276255
dbSNP Blast Analysis
UniGene Cluster ID
534544

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/T
 T/T
 HWP A
 T
ss44525925 HapMap-CEU European 120 IG 0.100 0.300 0.600 0.150 0.250 0.750
HapMap-HCB Asian 90 IG 0.111 0.489 0.400 0.655 0.356 0.644
HapMap-JPT Asian 88 IG 0.068 0.545 0.386 0.200 0.341 0.659
HapMap-YRI Sub-Saharan African 120 IG 0.167 0.500 0.333 1.000 0.417 0.583
ss48430396 AGI_ASP population multiple 62 IG 0.129 0.387 0.484 0.527 0.323 0.677
ss68888576 HapMap-CEU European 120 GF 0.100 0.300 0.600 0.250 0.750
HapMap-HCB Asian 90 GF 0.111 0.489 0.400 0.356 0.644
HapMap-JPT Asian 90 GF 0.067 0.556 0.378 0.344 0.656
HapMap-YRI Sub-Saharan African 120 GF 0.167 0.500 0.333 0.417 0.583
Concordant Genotype Total Sample A/A A/T T/T
ss44525925 523 33 120 114
ss48430396 39 15 12 4
ss68888576 268 33 121 114
RefSNP Genotype Summary Total Individual A/A A/T T/T
rs2916414 564 48 133 118
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
5237 ss44525925 T/T CSHL-HAPMAP HapMap-YRI NA18501 YOR004.03 r27_ch4_YRI_bcm:genotype_0002
5237 ss68888576 A/T CSHL-HAPMAP HapMap-YRI NA18501 YOR004.03 chr4-HapMap-YRI
5302 ss44525925 A/T CSHL-HAPMAP HapMap-YRI NA19140 YOR071.02 r27_ch4_YRI_bcm:genotype_0002
5302 ss68888576 T/T CSHL-HAPMAP HapMap-YRI NA19140 YOR071.02 chr4-HapMap-YRI
Genotype data submitted for564 samples from564 individualsIndividual with multiple genotypes submission:270

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .