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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs1426654          **clinically associated**
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:88/130
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:G
Clinical Association:link to VariationViewerlink to OMIM
HGVS Names
NM_205850.2:c.331A>G
NP_995322.1:p.Thr111Ala
NT_010194.16:g.19217041A>G
Links

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 ss43742806 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1426654 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
ss2233714TSC-CSHL|TSC0633716byFreqfwd/TA/Ggcccttggattgtctcaggatgttgcaggccaactttcatggcagcgggcagttcagctc10/20/0010/25/0688Genomic95 %
ss3462402SC_JCM|AC090526.3_146711fwd/TA/Ggcccttggattgtctcaggatgttgcaggccaactttcatggcagcgggcagttcagctc09/24/0110/10/03100Genomicunknown
ss12321463WI_SSAHASNP|chr15.NT_010194.15_19216095fwd/TA/Ggcccttggattgtctcaggatgttgcaggccaactttcatggcagcgggcagttcagctc07/04/0310/10/03116Genomicunknown
ss19327142CSHL-HAPMAP|CSHL-HuDD-200402.chr15.NT_010194.16_19217041fwd/TA/Ggcccttggattgtctcaggatgttgcaggccaactttcatggcagcgggcagttcagctc02/20/0403/04/04120Genomicunknown
ss43742806ABI|hCV2908190byFreqfwd/TA/Ggcccttggattgtctcaggatgttgcaggccaactttcatggcagcgggcagttcagctc07/18/0511/03/06126Genomicunknown
ss65725648ILLUMINA|Human1-rs1426654fwd/TA/Ggcccttggattgtctcaggatgttgcaggccaactttcatggcagcgggcagttcagctc10/10/0610/10/06127Genomicunknown
ss69175592PERLEGEN|PGP04749428byFreqfwd/TA/Ggcccttggattgtctcaggatgttgcaggccaactttcatggcagcgggcagttcagctc01/30/0708/14/07127Genomicunknown
ss69356387PERLEGEN|PS04749428fwd/TA/Ggcccttggattgtctcaggatgttgcaggccaactttcatggcagcgggcagttcagctc02/16/0702/16/07127Genomicunknown
ss74806079AFFY|SNP_M-174264fwd/TA/Ggcccttggattgtctcaggatgttgcaggccaactttcatggcagcgggcagttcagctc08/09/0708/09/07128Genomicunknown
ss74865056ILLUMINA|ILMN_Human_1M_rs1426654fwd/TA/Ggcccttggattgtctcaggatgttgcaggccaactttcatggcagcgggcagttcagctc08/28/0708/29/07129Genomicunknown
ss80703511HGSV|Cor18507_SNV_20070510.chr15_46213776fwd/TA/Ggcccttggattgtctcaggatgttgcaggccaactttcatggcagcgggcagttcagctc11/26/0711/26/07130Genomicunknown
ss83526066HGSV|Cor18555_SNV_20070510.chr15_46213776fwd/TA/Ggcccttggattgtctcaggatgttgcaggccaactttcatggcagcgggcagttcagctc11/27/0712/05/07130Genomicunknown
ss85617502HGSV|Cor19129_SNV_20070510.chr15_46213776fwd/TA/Ggcccttggattgtctcaggatgttgcaggccaactttcatggcagcgggcagttcagctc12/06/0712/09/07130Genomicunknown
ss106427081BGI|BGI_rs1426654fwd/TA/Ggcccttggattgtctcaggatgttgcaggccaactttcatggcagcgggcagttcagctc09/15/0806/18/09130Genomicunknown
ss1141351701000GENOMES|NA19240_2008_12_16_2834391_chr15_46213776fwd/TA/Ggcccttggattgtctcaggatgttgcaggccaactttcatggcagcgggcagttcagctc12/18/0812/18/08130Genomicunknown
ss118216307ILLUMINA-UK|NA18507_000032135_NCBI36.1_chr15_46213776fwd/TA/Ggcccttggattgtctcaggatgttgcaggccaactttcatggcagcgggcagttcagctc01/20/0901/21/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1426654|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 TGAACGCTTT TCTGGGTTCC AAATAACCCT ATGTTTGGCA CTCAGGATAT TCCCTTTAGT
 CTCCTGGCCT TCCCTCACCC TTTCTATAGA AGCATTAAGT AATGAAGTCA TAAAGAAGCA
 AAACATTGGA CTCTTTTAAT CTGTGTATTT TATTTTTCTA GTTTAATAGT GGTTTTATGT
 GAAGCTGTAG CTTTGAGTAT CTATTGTGTT TAGTTGTAAA GACATACTCT TTCACTTTAT
 TAGGCATAAC AATCATTTCA TTTATGTTCA GCCCTTGGAT TGTCTCAGGA TGTTGCAGGC
 R
 CAACTTTCAT GGCAGCGGGC AGTTCAGCTC CTGAATTAGT TACTGCTTTC CTAGGTAAAT
 ATTGCTCCTT ATACTTCTTG CTTACTCAGT GTGATTTTTA TTTTCTTCAA GTTAACACTA
 ACTTAGCTGG TACTATCTTG CACATAGGTG TATTTATCAC AAAGGGAGAT ATTGGCATTA
 GCACCATCCT TGGATCTGCA ATTTATAATC TCCTTGGCAT CTGTGCTGCC TGTGGTTTGC
 TATCTAATAC GGTATGTAAC AAAACCATTC AACAAAATGT ATTGTCTTAA AAAATTCTAA

  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_010194 AC009823 AC066612 AC090267 AC090269
dbSNP Blast Analysis
UniGene Cluster ID
553672
OMIM
609802.0001

  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
ss2233714 Nigeria(AFR) 95 AF 0.020 0.980
European_American(EUA) 114 AF 1.000
African_American(AFA) 95 AF 0.190 0.810
Mexican_American(MAM) 90 AF 0.500 0.500
East_Asian(EAS) 80 AF 0.030 0.970
South_Asian(SAS) 87 AF 0.820 0.180
Mexican(MXN) 94 AF 0.380 0.620
Puerto_Rican(PRN) 95 AF 0.590 0.410
Amerindian(MAYAN) 72 AF 0.050 0.950
ss43742806 HapMap-CEU European 116 IG 1.000 1.000
HapMap-HCB Asian 90 IG 0.022 0.978 1.000 0.011 0.989
HapMap-JPT Asian 88 IG 0.023 0.977 1.000 0.011 0.989
HapMap-YRI Sub-Saharan African 120 IG 0.050 0.950 1.000 0.025 0.975
AoD_African_American 90 AF 0.270 0.730
AoD_Caucasian 92 AF 0.980 0.020
AoD_Chinese 90 AF 0.010 0.990
ss69175592 HapMap-CEU European 120 GF 0.950 0.050 0.975 0.025
HapMap-HCB Asian 90 GF 0.022 0.978 0.011 0.989
HapMap-JPT Asian 90 GF 0.022 0.978 0.022 0.978
HapMap-YRI Sub-Saharan African 120 GF 0.050 0.950 0.025 0.975
Concordant Genotype Total Sample A/A A/G G/G
ss43742806 1202 298 170 631
RefSNP Genotype Summary Total Individual A/A A/G G/G
rs1426654 1207 298 170 631
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
188 ss43742806 A/A CSHL-HAPMAP HapMap-CEU NA10851 CEPH1344.01 r27_ch15_CEU_illumina:golden_gate_1.1.0
410 ss43742806 A/A CSHL-HAPMAP HapMap-CEU NA12155 CEPH1408.12 r27_ch15_CEU_illumina:golden_gate_1.1.0
546 ss43742806 A/A CSHL-HAPMAP HapMap-CEU NA12761 CEPH1447.10 r27_ch15_CEU_illumina:golden_gate_1.1.0
636 ss43742806 A/A CSHL-HAPMAP HapMap-CEU NA12891 CEPH1463.15 r27_ch15_CEU_illumina:golden_gate_1.1.0
5208 ss43742806 A/G CSHL-HAPMAP HapMap-JPT NA18969 JA18969 r27_ch15_JPT_illumina:human_1m_beadchip
Genotype data submitted for1207 samples from1207 individualsIndividual with multiple genotypes submission: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, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .