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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs3743193          
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:C
Clinical Association:unknown
HGVS Names
NM_014918.3:c.1075C>T
NP_055733.2:p.Pro359Ser
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 ss43698698 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3743193 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
ss4929200YUSUKE|IMS-JST094414byFreqfwd/BC/Tattcataaagaggacctccagctgggaatcctccctccttcatgaggtttcagccccgcc07/29/0210/10/03107Genomicunknown
ss20005370CSHL-HAPMAP|CSHL-HuFF-200402.chr15.NT_035325.5_3160664rev/TA/Gggcggggctgaaacctcatgaaggagggaggattcccagctggaggtcctctttatgaat02/21/0403/04/04120Genomicunknown
ss24126517PERLEGEN|afd4160526byFreqrev/TA/Gggcggggctgaaacctcatgaaggagggaggattcccagctggaggtcctctttatgaat08/10/0409/13/04123Genomicunknown
ss35077041KYUGEN|QH09648fwd/BC/Tattcataaagaggacctccagctgggaatcctccctccttcatgaggtttcagccccgcc03/04/05125Genomicunknown
ss43698698ABI|hCV1156345byFreqrev/TA/Gggcggggctgaaacctcatgaaggagggaggattcccagctggaggtcctctttatgaat07/18/0511/03/06126Genomicunknown
ss65727625ILLUMINA|Human1-rs3743193fwd/BC/Tattcataaagaggacctccagctgggaatcctccctccttcatgaggtttcagccccgcc10/10/0610/10/06127Genomicunknown
ss66616496ILLUMINA|HumanHap300v1.1_rs3743193fwd/TC/Tattcataaagaggacctccagctgggaatcctccctccttcatgaggtttcagccccgcc11/09/0611/09/06127Genomicunknown
ss67298685ILLUMINA|HumanHap550v1.1_rs3743193fwd/BC/Tattcataaagaggacctccagctgggaatcctccctccttcatgaggtttcagccccgcc11/14/0611/14/06127Genomicunknown
ss67703282ILLUMINA|HumanHap650Yv1.0_rs3743193fwd/BC/Tattcataaagaggacctccagctgggaatcctccctccttcatgaggtttcagccccgcc11/14/0611/14/06127Genomicunknown
ss69188429PERLEGEN|PGP04160526byFreqrev/TA/Gggcggggctgaaacctcatgaaggagggaggattcccagctggaggtcctctttatgaat01/30/0703/31/08127Genomicunknown
ss70777313ILLUMINA|HumanHap550v3.0__rs3743193fwd/BC/Tattcataaagaggacctccagctgggaatcctccctccttcatgaggtttcagccccgcc04/20/0703/30/08130Genomicunknown
ss71353449ILLUMINA|HumanHap650Yv3.0_rs3743193fwd/BC/Tattcataaagaggacctccagctgggaatcctccctccttcatgaggtttcagccccgcc04/23/0704/23/07127Genomicunknown
ss75479760ILLUMINA|ILMN_Human_1M_rs3743193fwd/BC/Tattcataaagaggacctccagctgggaatcctccctccttcatgaggtttcagccccgcc08/28/0708/29/07129Genomicunknown
ss76768369AFFY|AFFY_6_1M_SNP_A-8629771fwd/BC/Tcctccagctgggaatcctccctccttcatgag08/28/0708/30/07130Genomicunknown
ss79164099ILLUMINA|HumanHap300v2.0_rs3743193fwd/BC/Tattcataaagaggacctccagctgggaatcctccctccttcatgaggtttcagccccgcc04/18/0711/18/07130Genomicunknown
ss84164460KRIBB_YJKIM|KHS648564fwd/BC/Tattcataaagaggacctccagctgggaatcctccctccttcatgaggtttcagccccgcc12/04/0712/06/07130Genomicunknown
ss96840874HUMANGENOME_JCVI|1103645704782rev/TA/Gggcggggctgaaacctcatgaaggagggaggattcccagctggaggtcctctttatgaat03/27/0803/27/08130Genomicunknown
ss1091051191000GENOMES|CEU.trio.12.15.2008_3234794_chr15_99536450rev/TA/Gggcggggctgaaacctcatgaaggagggaggattcccagctggaggtcctctttatgaat12/15/0812/16/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3743193|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 ATACAATACT AAATTTGTGA TCTCTTTTTT TTCCTGTAAC AGATGCAGCA GCTTTTTTAT
 GAGAATTACG AGCAGAACAA AAAGGGGTAC ATTAGAGATC TCCATAACAG TAAAATTCAC
 CAAGCTATCA CATTACACCC CAACAAAAAC CCACCCTACC AGTACAGGCT CCACAGCTAC
 ATGCTGAGCC GCAAGATATC CGAGCTCCGC CATCGCACAA TACAGCTGCA CCGCGAAATT
 GTCCTGATGA GCAAATACAG CAACACAGAA ATTCATAAAG AGGACCTCCA GCTGGGAATC
 Y
 CTCCCTCCTT CATGAGGTTT CAGCCCCGCC AGCGAGAGGA GATTCTGGAA TGGGAGTTTC
 TGACTGGAAA ATACTTGTAT TCGGCAGTTG ACGGCCAGCC CCCTCGAAGA GGAATGGACT
 CCGCCCAGAG GGAAGCCTTG GACGACATTG TCATGCAGGT CATGGAGATG ATCAATGCCA
 ACGCCAAGAC CAGAGGGCGC ATCATTGACT TCAAAGAGAT CCAGTACGGC TACCGCCGGG
 TGAACCCCAT GTATGGGGCT GAGTACATCC TGGACCTGCT GCTTCTGTAC AAAAAGCACA

  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_035325.6 ABBA01020527
dbSNP Blast Analysis
UniGene Cluster ID
110488

  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
ss24126517 AFD_EUR_PANEL European 48 IG 0.958 0.042 1.000 0.979 0.021
AFD_AFR_PANEL African American 46 IG 0.913 0.087 1.000 0.957 0.043
AFD_CHN_PANEL Asian 48 IG 0.667 0.208 0.125 0.050 0.771 0.229
ss43698698 HapMap-CEU European 120 IG 0.833 0.167 0.527 0.917 0.083
HapMap-HCB Asian 90 IG 0.644 0.311 0.044 1.000 0.800 0.200
HapMap-JPT Asian 88 IG 0.432 0.455 0.114 1.000 0.659 0.341
HapMap-YRI Sub-Saharan African 120 IG 0.883 0.117 0.655 0.942 0.058
AoD_African_American 90 AF 0.950 0.050
AoD_Caucasian 92 AF 0.820 0.180
ss4929200 JBIC-allele 1464 AF 0.753 0.247
ss69188429 HapMap-CEU European 120 GF 0.833 0.167 0.917 0.083
HapMap-HCB Asian 90 GF 0.644 0.333 0.022 0.811 0.189
HapMap-JPT Asian 90 GF 0.444 0.467 0.089 0.678 0.322
HapMap-YRI Sub-Saharan African 120 GF 0.883 0.117 0.942 0.058
Concordant Genotype Total Sample C/C C/T T/T
ss24126517 71
ss43698698 1205
ss69188429 268
ss96840874 1
RefSNP Genotype Summary Total Individual C/C C/T T/T
rs3743193 1264
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
5180 ss43698698 A/A CSHL-HAPMAP HapMap-HCB NA18623 CH18623 r27_ch15_CHB_affymetrix:genomewidesnp_6.0 842781
5180 ss69188429 A/G CSHL-HAPMAP HapMap-HCB NA18623 CH18623 chr15-HapMap-HCB
5210 ss43698698 A/A CSHL-HAPMAP HapMap-JPT NA18961 JA18961 r27_ch15_JPT_affymetrix:genomewidesnp_6.0 842781
5210 ss69188429 A/G CSHL-HAPMAP HapMap-JPT NA18961 JA18961 chr15-HapMap-JPT
Genotype data submitted for1279 samples from1264 individualsIndividual with multiple genotypes submission:276

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqWith1000GenomeData UNKNOWN YES YES

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Revised: May 25, 2006 1:38 PM .