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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs1138358          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:G/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_001114735.1:c.117T>G
NM_004049.2:c.117T>G
NM_004049.3:c.117T>G
NP_001108207.1:p.Asn39Lys
NP_004040.1:p.Asn39Lys
NT_010194.16:g.51053665A>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 ss48418000 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1138358 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
ss1545750LEE|897960fwd/BG/Ttccaagcaaaacgtccagagtgctacaaaagttgcgttctcagtccaaaaagaagtggaa09/13/0010/10/0386cDNAunknown
ss2982425AFFX|AFFX_SNP-1168fwd/BG/Tgcaaaacgtccagagtgctacaaaagttgcgttctcagtccaaaaagaag05/21/0110/10/03100Genomicunknown
ss4431282LEE|e897960fwd/BG/Ttccaagcaaaacgtccagagtgctacaaaagttgcgttctcagtccaaaaagaagtggaa04/26/0210/10/03106cDNAunknown
ss4929433YUSUKE|IMS-JST094677byFreqfwd/BG/Ttccaagcaaaacgtccagagtgctacaaaagttgcgttctcagtccaaaaagaagtggaa07/29/0210/10/03108Genomicunknown
ss24064940PERLEGEN|afd3566966byFreqrev/TA/Cttccacttctttttggactgagaacgcaacttttgtagcactctggacgttttgcttgga08/10/0409/13/04123Genomicunknown
ss48418000APPLERA_GI|hCV7509654byFreqfwd/BG/Ttccaagcaaaacgtccagagtgctacaaaagttgcgttctcagtccaaaaagaagtggaa09/28/0511/03/06126Genomicunknown
ss65725336ILLUMINA|Human1-rs1138358fwd/BG/Ttccaagcaaaacgtccagagtgctacaaaagttgcgttctcagtccaaaaagaagtggaa10/10/0610/10/06127Genomicunknown
ss66668183ILLUMINA|HumanHap300v1.1_rs1138358fwd/TG/Ttccaagcaaaacgtccagagtgctacaaaagttgcgttctcagtccaaaaagaagtggaa11/09/0611/09/06127Genomicunknown
ss66930305ILLUMINA|HumanHap550v1.1_rs1138358fwd/BG/Ttccaagcaaaacgtccagagtgctacaaaagttgcgttctcagtccaaaaagaagtggaa11/14/0611/14/06127Genomicunknown
ss67088086ILLUMINA|HumanHap650Yv1.0_rs1138358fwd/BG/Ttccaagcaaaacgtccagagtgctacaaaagttgcgttctcagtccaaaaagaagtggaa11/14/0611/14/06127Genomicunknown
ss69182211PERLEGEN|PGP03566966byFreqrev/TA/Cttccacttctttttggactgagaacgcaacttttgtagcactctggacgttttgcttgga01/30/0708/14/07127Genomicunknown
ss70393588ILLUMINA|HumanHap300v2.0_rs1138358fwd/BG/Ttccaagcaaaacgtccagagtgctacaaaagttgcgttctcagtccaaaaagaagtggaa04/18/0711/18/07127Genomicunknown
ss70528288ILLUMINA|HumanHap550v3.0__rs1138358fwd/BG/Ttccaagcaaaacgtccagagtgctacaaaagttgcgttctcagtccaaaaagaagtggaa04/20/0703/30/08130Genomicunknown
ss71058566ILLUMINA|HumanHap650Yv3.0_rs1138358fwd/BG/Ttccaagcaaaacgtccagagtgctacaaaagttgcgttctcagtccaaaaagaagtggaa04/23/0704/23/07127Genomicunknown
ss74807849AFFY|SNP_M-179140fwd/BG/Ttccaagcaaaacgtccagagtgctacaaaagttgcgttctcagtccaaaaagaagtggaa08/09/0708/09/07128Genomicunknown
ss75605905ILLUMINA|ILMN_Human_1M_rs1138358fwd/BG/Ttccaagcaaaacgtccagagtgctacaaaagttgcgttctcagtccaaaaagaagtggaa08/28/0708/29/07129Genomicunknown
ss83559265HGSV|Cor18956_SNV_20070510.chr15_78050400rev/TA/Cttccacttctttttggactgagaacgcaacttttgtagcactctggacgttttgcttgga11/30/0712/05/07130Genomicunknown
ss83687535KRIBB_YJKIM|KHS519569fwd/BG/Ttccaagcaaaacgtccagagtgctacaaaagttgcgttctcagtccaaaaagaagtggaa12/04/0712/05/07130Genomicunknown
ss86348150CANCER-GENOME|1554rev/TA/Cttccacttctttttggactgagaacgcaacttttgtagcactctggacgttttgcttgga01/25/0801/25/08129Genomicunknown
ss90225503BCMHGSC_JDW|JWB-0883470rev/TA/Cttccacttctttttggactgagaacgcaacttttgtagcactctggacgttttgcttgga02/26/0802/29/08129Genomicunknown
ss106443785BGI|BGI_rs1138358rev/TA/Cttccacttctttttggactgagaacgcaacttttgtagcactctggacgttttgcttgga09/15/0806/18/09130Genomicunknown
ss1144368861000GENOMES|NA19240_2008_12_16_2872379_chr15_78050400rev/TA/Cttccacttctttttggactgagaacgcaacttttgtagcactctggacgttttgcttgga12/18/0812/18/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1138358|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=130
 ACAGCCTACG CACGAAAGTG ACTAGGAGGA AGGATATTAT AAAGTGATGC AAACAGAAAT
 TCCACCAGCC TCCATGTATC ATCATGTGTC ATAACTCAGT CAAGCTCAGT GAGCATTCTC
 AGCACATTGC CTCAACAGCT TCAAGGTGAG CCAGCTCAAG ACTTTGCTCT CCACCAGGCA
 GAAGATGACA GACTGTGAAT TTGGATATAT TTACAGGCTG GCTCAGGACT ATCTGCAGTG
 CGTCCTACAG ATACCACAAC CTGGATCAGG TCCAAGCAAA ACGTCCAGAG TGCTACAAAA
 K
 GTTGCGTTCT CAGTCCAAAA AGAAGTGGAA AAGAATCTGA AGTCATGCTT GGACAATGTT
 AATGTTGTGT CCGTAGACAC TGCCAGAACA CTATTCAACC AAGTGATGGA AAAGGAGTTT
 GAAGACGGCA TCATTAACTG GGGAAGAATT GTAACCATAT TTGCATTTGA AGGTATTCTC
 ATCAAGAAAC TTCTACGACA GCAAATTGCC CCGGATGTGG ATACCTATAA GGAGATTTCA
 TATTTTGTTG CGGAGTTCAT AATGAATAAC ACAGGAGAAT GGATAAGGCA AAACGGAGGC

  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
U29680 Hs.227817
dbSNP Blast Analysis
UniGene Cluster ID
227817

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source G/G
 G/T
 T/T
 HWP G
 T
ss24064940 AFD_EUR_PANEL European 48 IG 0.292 0.708 0.439 0.146 0.854
AFD_AFR_PANEL African American 46 IG 0.261 0.522 0.217 1.000 0.522 0.478
AFD_CHN_PANEL Asian 48 IG 0.208 0.583 0.208 0.439 0.500 0.500
ss48418000 HapMap-CEU European 120 IG 0.033 0.433 0.533 0.251 0.250 0.750
HapMap-HCB Asian 90 IG 0.289 0.422 0.289 0.317 0.500 0.500
HapMap-JPT Asian 88 IG 0.318 0.432 0.250 0.403 0.534 0.466
HapMap-YRI Sub-Saharan African 120 IG 0.367 0.433 0.200 0.403 0.583 0.417
AGI_ASP population multiple 72 IG 0.028 0.556 0.417 0.100 0.306 0.694
ss4929433 CEPH 184 AF 0.300 0.700
ss69182211 HapMap-CEU European 120 GF 0.033 0.433 0.533 0.250 0.750
HapMap-HCB Asian 90 GF 0.289 0.422 0.289 0.500 0.500
HapMap-JPT Asian 90 GF 0.311 0.422 0.267 0.522 0.478
HapMap-YRI Sub-Saharan African 120 GF 0.367 0.433 0.200 0.583 0.417

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.492+/-0.061 1302 1091 276 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwithHapMapFreqWith1000GenomeData
Validated by: ILLUMINA
 UNKNOWN YES UNKNOWN

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Revised: May 25, 2006 1:38 PM .