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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs3828357          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:107/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_001015050.1:c.403G>A
NP_001015050.1:p.Asp135Asn
NR_024250.1:c.1432T>C
NR_024251.1:c.1530T>C
NT_005612.15:g.32143502T>C
XR_037841.1:c.787A>G
XR_040853.1:c.1815T>C
XR_041463.1:c.1907T>C
XR_041464.1:c.1910T>C
XR_041465.1:c.1906T>C
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 ss5473867 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3828357 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
ss5014850YUSUKE|IMS-JST189856fwd/BC/Tcccatcggagctgctgcgactcccgcaggtcttccaaaactggtttagcttgcctgcagg08/12/0210/10/03107Genomicunknown
ss5473867TSC-CSHL|TSC0881908byFreqrev/TA/Gcctgcaggcaagctaaaccagttttggaagacctgcgggagtcgcagcagctccgatggg09/21/0210/25/06113Genomicunknown
ss16947998CSHL-HAPMAP|CSHL-HuAA-200402.chr3.NT_005612.14_32143510fwd/BC/Tcccatcggagctgctgcgactcccgcaggtcttccaaaactggtttagcttgcctgcagg02/17/0403/04/04120Genomicunknown
ss23956263PERLEGEN|afd4398951byFreqfwd/BC/Tcccatcggagctgctgcgactcccgcaggtcttccaaaactggtttagcttgcctgcagg08/10/0409/13/04126Genomicunknown
ss41939649ABI|hCV27495086fwd/BC/Tcccatcggagctgctgcgactcccgcaggtcttccaaaactggtttagcttgcctgcagg07/17/0507/17/05126Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3828357|allelePos=475|totalLen=625|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=126
 CACATCCCTG GGCTTACGAT GCAGCAGGTG CTTTTTTCAA GACAGGAATC AAAATGTTAG
 GAACACGGCA GAAAGGTGAC ACCTGGAGAC CAAACGCAGG ATAAGGAGTA CTGCAGAGGT
 CACAGGGAAG TCACAGAACA GTAATACGCT AGCAGGGGCA TGGGGCATGA AGAACAGAAG
 AAGAGAGGAA GTGTTTCCGA GCCTCCGGAA AAGAAATCAG AGCCAAGCAC AGCTTCCCGG
 GTCACAGAAC CAATTCATTC ACCAGGCGGC ACCACTGCCG TCATTTCAGC TTCTGGCCAC
 TGGGAGGCGC TGCTCAAAAG GGTTTGCCCT GAGACTCCGA GAAGAAGCTG CGGGAAGGAC
 AGCAGGGGTC CCGGGGTTTT AGCCTCTGGC CCAGGAGTTG TATGTCCATA ACCAAAGGGA
 GCACAGTCTG CACCCAGCTC TCATCCCATC GGAGCTGCTG CGACTCCCGC AGGT
 Y
 CTTCCAAAAC TGGTTTAGCT TGCCTGCAGG ATCAGGAAAG TTTGAGAAAA GCATCTGCAA
 AAAAATAAAG AGCAGAGCTT ACCTCATTGC CTGTCCCCAC CCCATCCCAG GTCACCACCT
 GGCTGACCCC AGGTCCCCGA CCCAACAACA

  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_022411.6
dbSNP Blast Analysis
UniGene Cluster ID
553949

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP C
 T
ss23956263 AFD_EUR_PANEL European 48 IG 0.042 0.625 0.333 0.100 0.354 0.646
AFD_AFR_PANEL African American 46 IG 0.130 0.348 0.522 0.403 0.304 0.696
AFD_CHN_PANEL Asian 48 IG 0.167 0.500 0.333 1.000 0.417 0.583
ss5473867 HapMap-CEU European 120 IG 0.200 0.467 0.333 0.752 0.433 0.567
HapMap-HCB Asian 90 IG 0.444 0.556 0.100 0.222 0.778
HapMap-JPT Asian 90 IG 0.067 0.422 0.511 0.278 0.722
HapMap-YRI Sub-Saharan African 120 IG 0.400 0.600 0.100 0.200 0.800

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.425+/-0.179 581 459 15 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .