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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs4329          
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_000789.2:c.2059-460C>A
NM_152830.1:c.337-460C>A
NT_010783.14:g.20215469A>G
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 ss10853271 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4329 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
ss4718DEBNICK|dcp1-11663fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc05/03/9912/23/0336Genomicunknown
ss3199026YUSUKE|IMS-JST014948byFreqfwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc08/07/0110/10/0398Genomicunknown
ss6877013WI_SSAHASNP|NT_035428.2_988011fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc02/12/0310/10/03111Genomicunknown
ss10853271BCM_SSAHASNP|chr17.NT_010783.13_16855390byFreqfwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc06/30/0310/25/06116Genomicunknown
ss14741106SC_SNP|NT_010783.14_20215469fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc11/12/0311/22/03119Genomicunknown
ss16730754CSHL-HAPMAP|CSHL-HuAA-200402.chr17.NT_010783.14_20215469fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc02/17/0403/04/04120Genomicunknown
ss23142639PARC|ACE-011379byFreqfwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc05/07/0405/16/04126Genomicunknown
ss44043702ABI|hCV1247713byFreqfwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc07/18/0511/03/06126Genomicunknown
ss66650517ILLUMINA|HumanHap300v1.1_rs4329fwd/BA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc11/09/0611/09/06127Genomicunknown
ss67327339ILLUMINA|HumanHap550v1.1_rs4329fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc11/14/0611/14/06127Genomicunknown
ss67728725ILLUMINA|HumanHap650Yv1.0_rs4329fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc11/14/0611/14/06127Genomicunknown
ss69365648PHARMGKB_PARC|PS205301_PA141144424_11379byFreqfwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc03/22/0708/14/07127Genomicunknown
ss70800152ILLUMINA|HumanHap550v3.0__rs4329fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc04/20/0703/30/08130Genomicunknown
ss71378877ILLUMINA|HumanHap650Yv3.0_rs4329fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc04/23/0704/23/07127Genomicunknown
ss75522195ILLUMINA|ILMN_Human_1M_rs4329fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc08/28/0708/29/07129Genomicunknown
ss76665718AFFY|AFFY_6_1M_SNP_A-8527087rev/BC/Ttttgtgctcagccaaaaggcagggaatgaggg08/28/0708/30/07129Genomicunknown
ss79179520ILLUMINA|HumanHap300v2.0_rs4329fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc04/18/0711/18/07130Genomicunknown
ss83346404KRIBB_YJKIM|KHS439889fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc12/04/0712/04/07130Genomicunknown
ss84149329PHARMGKB_PARC|PS206642_PA151794545_11379fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc12/06/0712/10/07130Genomicunknown
ss84149347PHARMGKB_PARC|PS206642_PA151795005_11379fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc12/06/0712/10/07130Genomicunknown
ss90634014BCMHGSC_JDW|JWB-1038649fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc02/26/0802/29/08129Genomicunknown
ss1098558951000GENOMES|CEU.trio.12.15.2008_3421259_chr17_58917190fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc12/15/0812/16/08130Genomicunknown
ss1137106031000GENOMES|NA19240_2008_12_16_3080148_chr17_58917190fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc12/18/0812/18/08130Genomicunknown
ss118097364ILLUMINA-UK|NA18507_000064300_NCBI36.1_chr17_58917190fwd/TA/Gacacttcctctttaccctcattccctgccttttggctgagcacaaattatgccactgagc01/20/0901/20/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4329|allelePos=601|totalLen=919|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 CGggccgggc gcggtggctc acgcctgtaa tcccagcact ttgggagggg gaggcgggcg
 gatcacgagg tcagatcaag accatcctgg ctaacacggt gaaaccccat ctctagtaaa
 aatacaaaaa ttagccgggt gtggtggcga gcacctgtag tcccagtact caggaggctg
 aggcaggaga atggcatgaa cccgggaggc agagcttgca gtgagccgag atggcaccac
 tgcactccag cctgggcgac agagcgagac tccatcaaaa aaaaaaaaaa aaaaaaCTCA
 ATTTCAGATT TTGATGAACA TTTACTCAAT GCCTGAGCAA TTCTTCTTTC CTTAAAAATC
 AGTctctggg aggcctaggt gggaggatca cttgaagcca ggagttggag actagcctgg
 gcaacatagc aagatcccat ctctattcaa acaaacaaat aaacaaaaaT CAATCTCTAG
 TAACAGAATA ATTTGTACAT AAATAAGTGG TGCTCAAGTC GTTTTTTAAA AGATTGAAAG
 CCTCTGTTTG TCTCCTCTAC AAAAGGGGCT ACACTTCCTC TTTACCCTCA TTCCCTGCCT
 R
 TTTGGCTGAG CACAAATTAT GCCACTGAGC CACACACTGT TACTGTTCCT TGGCACTTTG
 ATCTGTTGCC TCATCTTTTT CTCAACAGCC TTGCAAAATT GGTGAGCTTA TTCCCATTTT
 ACAGATGGGA TTTGATATTA ACTCTGAGGT TCAGAAAGGC CACAGAGCTA ATACCAAGCT
 GGCTCCTTCC TAAGGGCCTT TACGACACTT GGGGGTCTTC TCTTCTCTGC CCCTGCCTGG
 ATATGTGTTG CTTGACCGCA GGCATCCAGG GAGGGTGAGT ACTGCATCCA GGACGTTATC
 AGCGTCCAGC TTGCAGAG

  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_010783
dbSNP Blast Analysis

  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
ss10853271 HapMap-CEU European 120 IG 0.267 0.417 0.317 0.251 0.475 0.525
HapMap-HCB Asian 90 IG 0.022 0.444 0.533 0.244 0.756
HapMap-JPT Asian 90 IG 0.156 0.556 0.289 0.433 0.567
HapMap-YRI Sub-Saharan African 120 IG 0.317 0.450 0.233 0.542 0.458
ss23142639 PARC-EUROPEAN-PANEL European 32 AF 0.500 0.500
ss3199026 JBIC-allele 900 AF 0.363 0.637
ss44043702 AoD_African_American 90 AF 0.570 0.430
AoD_Caucasian 92 AF 0.560 0.440
AoD_Chinese 90 AF 0.310 0.690
AoD_Japanese 90 AF 0.380 0.620
ss69365648 PA141144429 946 AF 0.569 0.431
ss84149329 PA151794546 76 AF 0.592 0.408
ss84149347 PA151795006 76 AF 0.592 0.408

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.492+/-0.064 1207 1002 0 0

  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 YES

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Revised: May 25, 2006 1:38 PM .