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Reference SNP(refSNP) Cluster Report: rs2397118          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/130
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_153699.1:c.163G>A
NP_714543.1:p.Val55Ile
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 ss3360496 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2397118 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
ss3360496TSC-CSHL|TSC1613720byFreqfwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa09/20/0110/25/06100Genomicunknown
ss6498251WI_SSAHASNP|NT_007592.11_43498250fwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa02/12/0310/10/03111Genomicunknown
ss17113108CSHL-HAPMAP|CSHL-HuAA-200402.chr6.NT_007592.13_43498251fwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa02/17/0403/04/04120Genomicunknown
ss22455332SSAHASNP|WGSA-200403-chr6.chr6.NT_007592.13_43498251fwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa03/21/0403/21/04121Genomicunknown
ss23265904PERLEGEN|afd4635908byFreqfwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa08/10/0409/13/04124Genomicunknown
ss42859237ABI|hCV26549095fwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa07/18/0507/18/05126Genomicunknown
ss68366171CSHL-HAPMAP|sanger:assay:1729587:1byFreqfwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa01/11/0701/16/07127NAunknown
ss68977278PERLEGEN|PGP04635908byFreqfwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa01/30/0708/14/07127Genomicunknown
ss76886478SI_EXO|NT_007592.14_43559374fwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa09/20/0709/20/07129Genomicunknown
ss77425979HGSV|Cor12156_SNV_20070510.chr6_52809102fwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa10/09/0710/12/07129Genomicunknown
ss83327967HGSV|Cor19240_SNV_20070510.chr6_52809102fwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa11/30/0712/04/07130Genomicunknown
ss84168796PHARMGKB_AB_DME|PS206045_PA147546758_301fwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa12/06/0712/09/07130Genomicunknown
ss93461253BCMHGSC_JDW|JWB-2140642fwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa02/26/0803/04/08129Genomicunknown
ss98393793HUMANGENOME_JCVI|1103652868800fwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa03/31/0803/31/08130Genomicunknown
ss105439845SNP500CANCER|GSTA5-02rev/TA/Gttctaagatgggagtttgctgttccagcaataccaatggttgagattgacgggatgaagc09/05/0809/05/08130Genomicunknown
ss106000973BGI|BGI_rs2397118fwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa09/12/0806/19/09130Genomicunknown
ss1101282911000GENOMES|CEU.trio.12.15.2008_1521065_chr6_52809102fwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa12/15/0812/17/08130Genomicunknown
ss1143721841000GENOMES|NA19240_2008_12_16_1363927_chr6_52809102fwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa12/18/0812/18/08130Genomicunknown
ss116469782ILLUMINA-UK|NA18507_000078405_NCBI36.1_chr6_52809102fwd/BC/Tgcttcatcccgtcaatctcaaccattggtattgctggaacagcaaactcccatcttagaa01/17/0901/17/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2397118|allelePos=500|totalLen=973|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CTTCCCTCCC CAGGCCTTCA TCTACAGACT CTCAGACATT CTATGCCTTG CCCTACGCTG
 TTGGCTGGAG TCTAGCCTCT GAAGTTCTGA GTACCTGAAT CATGATTCCC CATCCTCCTC
 AGTTCATAGG GTTTATGAGT GTCTGGAAAC CTCAGTCAGG TTGCAGGATC CATGGACTGC
 ATCCTCTTTT AGAATCACCC TTGCCTGAAC CCTCCCCATG TTCACTGTTC CCTCATCTCC
 ATGGGACTCT GCAATACTGG ACCTCAGCGT GCATCCTCAA GACCCAGCCT GCTGCTGGTC
 ATGATGCCCT GCCATGGTCC CACCCACTCA AAGAAGGACT TAAATCACTC TGTGTTCTCT
 GTGGATGGAA GAACAGAAAA TATACCATAC AGGGCTCTCT CCTTCATGTC TTTCCCATAA
 AGGTTGTATT TGCTGGCAAT GTAGTTAAGA ATGGCTCTGG TCTGCACCAG CTTCATCCCG
 TCAATCTCAA CCATTGGTA
 Y
 TTGCTGGAAC AGCAAACTCC CATCTTAGAA AGAAGAAAAA AAAAGGAGTA TGAAGTGTCT
 ATGAAACCCA CCCTTTTGGG ATGAAAAAAA TGGTTATGGA AATGACTAAA TTTGTGAAAT
 GAAAAAGAAA TTATTGCCTG TTAAGTTTTC ACTTGAAACA ACttttttcc ttgttttgtt
 ttttgagaca gagtctcact ctgtcaccca ggctggagtg cagtgggacg atctcagctc
 actgtaacct ctgcctcctg ggttcaagca attctcctac ctcagcctcc tgagtagctg
 ggattacagg catgtgccaa catacccagc taatttttgt atttttagta gagacgtgat
 ctcatcatgt tggccaaact ggtctcgaac tcctgacctc aaatgatcca cccgcctcag
 cctctcgaag agctgggatt acaggtgtga gccaccatac ccggccCAAA CAA

  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_007592.14 ABBA01050547
dbSNP Blast Analysis
UniGene Cluster ID
553652

  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
ss105439845 P1 202 GF 0.040 0.208 0.752 0.144 0.856
CAUC1 60 GF 0.100 0.900 0.050 0.950
AFR1 48 GF 0.083 0.375 0.542 0.271 0.729
HISP1 46 GF 0.087 0.913 0.043 0.957
PAC1 48 GF 0.083 0.292 0.625 0.229 0.771
P2 418 GF 0.005 0.191 0.804 0.100 0.900
CAUC2 118 GF 0.119 0.881 0.059 0.941
AFR2 120 GF 0.250 0.750 0.125 0.875
P3 536 GF 0.015 0.168 0.817 0.099 0.901
CAUC3 128 GF 0.047 0.953 0.023 0.977
AFR3 146 GF 0.027 0.301 0.671 0.178 0.822
HISP3 94 GF 1.000 1.000
PAC3 168 GF 0.024 0.238 0.738 0.143 0.857
ASI2 180 GF 0.011 0.200 0.789 0.111 0.889
ss23265904 AFD_EUR_PANEL European 48 IG 0.042 0.958 1.000 0.021 0.979
AFD_AFR_PANEL African American 44 IG 0.273 0.727 0.479 0.136 0.864
AFD_CHN_PANEL Asian 48 IG 0.208 0.792 0.584 0.104 0.896
ss3360496 HapMap-CEU European 118 IG 0.119 0.881 0.655 0.059 0.941
HapMap-HCB Asian 90 IG 0.222 0.778 0.403 0.111 0.889
HapMap-JPT Asian 90 IG 0.022 0.178 0.800 0.527 0.111 0.889
HapMap-YRI Sub-Saharan African 120 IG 0.250 0.750 0.273 0.125 0.875
ss68977278 HapMap-CEU European 120 GF 0.117 0.883 0.058 0.942
HapMap-HCB Asian 90 GF 0.222 0.778 0.111 0.889
HapMap-JPT Asian 90 GF 0.044 0.156 0.800 0.122 0.878
HapMap-YRI Sub-Saharan African 120 GF 0.250 0.750 0.125 0.875
ss84168796 PA147546759 356 AF 0.093 0.907
Concordant Genotype Total Sample C/C C/T T/T
ss23265904 71 12 58
ss3360496 524 2 52 214
ss68977278 269 2 52 215
ss98393793 1 1
RefSNP Genotype Summary Total Individual C/C C/T T/T
rs2397118 582 2 63 266
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
5224 ss3360496 C/T CSHL-HAPMAP HapMap-JPT NA18974 JA18974 r27_ch6_JPT_perlegen:genotyping_1.0.0
5224 ss68977278 C/C CSHL-HAPMAP HapMap-JPT NA18974 JA18974 chr6-HapMap-JPT
Genotype data submitted for597 samples from582 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
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .