NCBI

NLM

PubMed Nucleotide Protein Genome Structure PopSet Taxonomy OMIM Books SNP
Search for SNP on NCBI Reference Assembly
Spacer gif
BUILD 129
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Reference SNP(refSNP) Cluster Report: rs338196          
refSNP ID: rs338196
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:79/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_001098424.1:c.318+20936A>G
NM_004087.2:c.318+20936A>G
NT_029928.12:g.1608348T>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 ss1691978 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs338196 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
ss431058KWOK|OVLP-000621-328374fwd/BC/Tcatttggtagaacctatcaaatagtaagcatatcaatgttgttattactattattaatat06/30/0010/10/0379Genomic99 %
ss501082SC_JCM|AL121981.11_117950rev/TA/Gatattaataatagtaataacaacattgatatgcttactatttgataggttctaccaaatg07/12/0010/10/0380Genomicunknown
ss1102754KWOK|OVLP-000804-204775fwd/BC/Tcatttggtagaacctatcaaatagtaagcatatcaatgttgttattactattattaatat09/02/0010/10/0387Genomic99 %
ss1691978KWOK|OVLP-000925-360287byFreqfwd/BC/Tcatttggtagaacctatcaaatagtaagcatatcaatgttgttattactattattaatat10/05/0010/25/0687Genomic99 %
ss10074871BCM_SSAHASNP|chr3.NT_029928.10_1608348fwd/BC/Tcatttggtagaacctatcaaatagtaagcatatcaatgttgttattactattattagtat06/27/0310/10/03116Genomicunknown
ss16991979CSHL-HAPMAP|CSHL-HuAA-200402.chr3.NT_029928.11_1608348fwd/BC/Tcatttggtagaacctatcaaatagtaagcatatcaatgttgttattactattattagtat02/17/0403/04/04120Genomicunknown
ss23713562PERLEGEN|afd0714115byFreqfwd/BC/Tcatttggtagaacctatcaaatagtaagcatatcaatgttgttattactattattagtat08/10/0409/13/04123Genomicunknown
ss42074089ABI|hCV1333400fwd/BC/Tcatttggtagaacctatcaaatagtaagcatatcaatgttgttattactattattagtat07/17/0507/17/05126Genomicunknown
ss74854981AFFY|SNP_M-614958fwd/BC/Tcatttggtagaacctatcaaatagtaagcatatcaatgttgttattactattattagtat08/09/0708/09/07128Genomicunknown
ss76758818AFFY|AFFY_6_1M_SNP_A-8620143fwd/BC/Ttatcaaatagtaagcatatcaatgttgttatt08/28/0708/30/07129Genomicunknown
ss80549052HGSV|Cor18507_SNV_20070510.chr3_198476924fwd/BC/Tcatttggtagaacctatcaaatagtaagcatatcaatgttgttattactattattagtat11/23/0711/26/07130Genomicunknown
ss92432701BCMHGSC_JDW|JWB-1723015fwd/BC/Tcatttggtagaacctatcaaatagtaagcatatcaatgttgttattactattattagtat02/26/0803/03/08129Genomicunknown
ss1116340451000GENOMES|NA19240_2008_12_16_807297_chr3_198473011fwd/BC/Tcatttggtagaacctatcaaatagtaagcatatcaatgttgttattactattattagtat12/16/0812/17/08130Genomicunknown
ss1128366281000GENOMES|CEU.trio.12.15.2008_895700_chr3_198473011fwd/BC/Tcatttggtagaacctatcaaatagtaagcatatcaatgttgttattactattattagtat12/15/0812/18/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs338196|allelePos=253|totalLen=1455|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 ATAAGGAAGA GTATTATCTG CAATTTTTGT CCACAAAGTT TCCTCACAGT TTACAGATAT
 TATGAATGAC CTCAAGTTCA AACAACTGAA CTGTTCCTAC TTGCCTCTTA TACCCCATTC
 CTCCTCCTAA CATTTCAAAT ACACATGGAC TGCACTAACA ACTTTCAGAC TAAACCACAT
 TTCACTGTTA AGCgttatga aaaggagtta atacatatat accatttggt agaacctatc
 aaatagtaag ca
 Y
 tatcaatgtt gttattactA TTATTAATAT GTATCAAATT ACAGCCTTTT ATTTAAAGCC
 TAACAGGGTA TACTTGAGAC AGGCCCAATG GGACTTTACC TTACTTtatc taatggggct
 gttgtgtgag gattaaataa tatacacagg gcacttagaa taatgcTGAC TTGTTAGGTC
 AATAGTGGCA ATAAATAGTG CAACAGTGCT CAGTAAATGC CAGCTACAGC TATAGATCTA
 Ttgtggtata atatgaaata tattcggtct ttgtttctgt cagagtgcct aaaactcttg
 gaaattccta agtaatggga aggtcttctt ttgttcatga caagcccttt ggatcacagc
 taatgctaat gaggtaactt aaagtgagac ccctagaaag cctcaggatg aggctcatca
 ccagaaagac cacgggatta gaggattaga gggttagagg gctggaactt tcagctccac
 ccaccaacct ccaggaaagg ggcaggggtt gggggctgGA GATCAAGCTC TATAAAAACT
 CTTAACAACA TGTGATGTGC TTTTGGGTTG GCAAAGGCAA GCTGGGAAGG CTGAGGACTC
 CAACTCTACC AGGatagaag ctcctgcact tgggaccctt ccagaccttg ccctatgtat
 ctctttttct ggctgttcat ctgtatcctt tataacatct tttataataa actagtaaac
 gcatttccct gagttctgta agccatccta gcaaattaac caaacccaag gaaggggttg
 tgtgaacccc aatttaaaac tagtcagtca gaagcatagg tcacaatcta ctatttccat
 ctaaatgggg gcagtcttgt ggggctgagc ccccaacctg tgggatctga cactatactt
 cagagactac tactatctcc aagtagacac tgccagaact gtatttacgt agagactact
 actacctcca agcagatagt gtcagaattg aattatagga cacccagtag gtgtccactg
 gaaaagcttc accaaaaacc tcctcacaca tctagtcagc acagaagtgt gctgtgttga
 gagcagaggg aaaaaatggt ttTTCTCCTC TCAGACCTAA ATACATATGT ATGTAGCTAT
 GTAAATGTCA TCATGGGCCA ACACATCCCT TATCCCATGC AGGATATAGC CTGGAAATTA
 CA

  GeneView back to top
GeneView via analysis of contig annotation: DLG1 discs, large homolog 1 (Drosophila)
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_029928->NM_001098424
svfunction
referenceNT_029928->NM_004087
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_029928->NM_001098424->NP_0010918941608348reverseintron
referenceNT_029928->NM_004087->NP_0040781608348reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs338196 maps exactly once on NCBI human chromosome 3
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
3NW_001838889.11319561194287810plusTalt_assembly_8HuRefHuRefview252
3NW_921873.11255383195573903plusTalt_assembly_1CeleraCeleraview252
3NT_029928.121608348198473011plusTref_assemblyreferencereferenceview252

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_029928 AC018707 AL121981.14 AL121981.17
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AL121981.17 AL592305.4

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1691978HapMap-CEUEuropean 116IG 0.086 0.500 0.414 0.371 0.336 0.664
HapMap-HCBAsian 88IG 0.159 0.841 0.584 0.080 0.920
HapMap-JPTAsian 90IG 0.022 0.222 0.756 1.000 0.133 0.867
HapMap-YRISub-Saharan African 118IG 0.051 0.407 0.542 0.584 0.254 0.746
ss23713562AFD_EUR_PANELEuropean 46IG 0.087 0.391 0.522 1.000 0.283 0.717
AFD_AFR_PANELAfrican American 46IG 0.087 0.435 0.478 1.000 0.304 0.696
AFD_CHN_PANELAsian 48IG 0.292 0.708 0.439 0.146 0.854

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.344+/-0.23233226090

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreq
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

GENERAL: Contact Us | Homepage | Announcements |dbSNP Summary | Genome | FTP SERVER | Build History | Handle Request
DOCUMENTATION: FAQ | Searchable FAQ Archive | Overview | How to Submit | RefSNP Summary Info | Database Schema
SEARCH: Entrez SNP | Blast SNP | Batch Query | By Submitter |New Batches | Method | Population | Publication | Batch | Locus Info | Between Marker
HAPLOTYPE:Submission | Specifications | Sample HapSet | Sample Individual
NCBI: PubMed | Entrez | BLAST | OMIM | Taxonomy | Structure

Disclaimer     Privacy statement

Revised: May 25, 2006 1:38 PM .