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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1428974          
refSNP ID: rs1428974
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:88/129
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_004172.3:c.181+801T>C
NT_006576.15:g.36582264T>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 ss44643679 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1428974 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
ss2237177TSC-CSHL|TSC0638514byFreqfwd/BC/Ttttgaccaaaccaatacagaaatccttagatgacaaacatatacgccaatgccaggttgt10/20/0004/07/0488Genomic95 %
ss10256697BCM_SSAHASNP|chr5.NT_006576.13_19036252fwd/BC/Ttttgaccaaaccaatacagaaatccttagatgacaaacatatacgccaatgccaggttgt06/27/0310/10/03116Genomicunknown
ss23749159PERLEGEN|afd4589196byFreqfwd/BC/Ttttgaccaaaccaatacagaaatccttagatgacaaacatatacgccaatgccaggttgt08/10/0409/13/04123Genomicunknown
ss44643679ABI|hCV7583496byFreqfwd/BC/Ttttgaccaaaccaatacagaaatccttagatgacaaacatatacgccaatgccaggttgt07/19/0511/03/06126Genomicunknown
ss76855048AFFY|AFFY_6_1M_SNP_A-8716510rev/TA/Ggcgtatatgtttgtcatctaaggatttctgta08/28/0708/30/07129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1428974|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=129
 TCTCACCCAG CAACTGGGAA AGGTAGATTG GGGAAAATGT TAACACAGAT CTCTTTCATT
 CATTGCTTTG CAGAGCCTGC CATAACCAGC TATACCTTTT TTTGAATCAT TTCCATCTCT
 TACTAATTTA GCAGGGTTGA CAGCAATCTG TACTAATAAA ATATTATTGT TTTGTTTTGT
 TTATTGATCT TAAAAGTTAT AGTTTATTAC TTATGGGTGG CATTGATCCT ACTTTAAAAT
 ATAGCTGAAA AAACCTACTT ATTTGGAATT TTTGACCAAA CCAATACAGA AATCCTTAGA
 Y
 TGACAAACAT ATACGCCAAT GCCAGGTTGT AAAAATATTC CAACTTAACC TACCAATTTG
 CCACCAAAAA AGAGGCATTC AGTACCGTTT TAATCTCTAC TTTGGAGTTT GCCAAGATTT
 CCATCAACTT TAAAGAGGTA ATGATTTAAT AAAGATTAAG AAAATTCTGT AGTGTGTAAA
 TATAACTTTT TTCAAGAAAA TTGAATTCTT AAATTGTAGA CAAATGAAGT ATAGCAGGAG
 AGTTTGTCAC AAGATTTTAG ATACATCCCA TTTTAACATC ATTGTCTTCC ATTAGTAATC

  GeneView back to top
GeneView via analysis of contig annotation: SLC1A3 solute carrier family 1 (glial high affinity glutamate transporter), member 3
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_006576->NM_004172
svfunction
HuRefNW_001838933->NM_004172
svfunction
CeleraNW_922596->NM_004172
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_006576->NM_004172->NP_00416336582264forwardintron
HuRefNW_001838933->NM_004172->NP_004163905179forwardintron
CeleraNW_922596->NM_004172->NP_0041632206949forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1428974 maps exactly once on NCBI human chromosome 5
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
5NW_922596.1220694936496435plusTalt_assembly_1CeleraCeleraview300
5NW_001838933.190517936562568plusTalt_assembly_8HuRefHuRefview300
5NT_006576.153658226436645264plusTref_assemblyreferencereferenceview300

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_006576
dbSNP Blast Analysis
GenBank HTGS Finished:
AC010631.6 NC_000005.8

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
C/C
C/T
T/T
HWPC
T
ss2237177SC_12_AAsian 24AF 1.000 1.000
SC_12_AAAfrican American 22AF 0.818 0.182 0.001 0.090 0.910
SC_12_CEuropean 24AF 1.000 1.000
SC_95_CEuropean 90IG 1.000 1.000
ss23749159AFD_EUR_PANELEuropean 48IG 1.000 1.000
AFD_AFR_PANELAfrican American 46IG 0.043 0.261 0.696 0.752 0.174 0.826
AFD_CHN_PANELAsian 48IG 1.000 1.000
ss44643679HapMap-CEUEuropean 120IG 1.000 1.000
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 90IG 1.000 1.000
HapMap-YRISub-Saharan African 120IG 0.050 0.300 0.650 0.655 0.200 0.800
Concordant GenotypeTotal SampleA/AA/GC/CC/TT/T
ss22371771142476
ss23749159661461
ss44643679268423241
RefSNP Genotype SummaryTotal IndividualA/AA/GC/CC/TT/T
rs142897440124527326
Discordant Genotypes:
Indiviudal
SampleID		SubSNP(ss)GenotypePopulation
Handle		Submitter
Population		Submitter
SampleID		SampleID
Alias		Submission
Batch		NCBI
ProbeID
114ss2237177A/ATSC-CSHLSC_12_CCEPH1331.12TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
114ss2237177T/TTSC-CSHLSC_95_CCEPH1331.12TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
229ss2237177A/ATSC-CSHLSC_12_CCEPH1347.02TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
229ss2237177N/NTSC-CSHLSC_95_CCEPH1347.02TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
229ss44643679T/TCSHL-HAPMAPHapMap-CEUNA10859CEPH1347.02r23_ch5_CEU_perlegen:genotyping_1.0.03041127
230ss2237177A/ATSC-CSHLSC_12_CCEPH1347.03TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
230ss2237177T/TTSC-CSHLSC_95_CCEPH1347.03TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
231ss2237177A/ATSC-CSHLSC_12_CCEPH1347.04TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
231ss2237177T/TTSC-CSHLSC_95_CCEPH1347.04TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
429ss2237177A/ATSC-CSHLSC_12_CCEPH1416.01TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
429ss2237177T/TTSC-CSHLSC_95_CCEPH1416.01TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
429ss44643679T/TCSHL-HAPMAPHapMap-CEUNA10835CEPH1416.01r23_ch5_CEU_perlegen:genotyping_1.0.03041127
430ss2237177A/ATSC-CSHLSC_12_CCEPH1416.02TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
430ss2237177T/TTSC-CSHLSC_95_CCEPH1416.02TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
840ss2237177A/ATSC-CSHLSC_12_AANA17109TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
840ss23749159T/TPERLEGENAFD_AFR_PANELNA1710971_IND_CHR_5
845ss2237177A/GTSC-CSHLSC_12_AANA17114TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
845ss23749159C/TPERLEGENAFD_AFR_PANELNA1711471_IND_CHR_5
846ss2237177A/ATSC-CSHLSC_12_AANA17115TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
846ss23749159T/TPERLEGENAFD_AFR_PANELNA1711571_IND_CHR_5
865ss2237177A/ATSC-CSHLSC_12_AANA17134TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
865ss23749159T/TPERLEGENAFD_AFR_PANELNA1713471_IND_CHR_5
867ss2237177A/GTSC-CSHLSC_12_AANA17136TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
867ss23749159C/TPERLEGENAFD_AFR_PANELNA1713671_IND_CHR_5
Genotype data submitted for472 samples from401 individualsIndividual with multiple genotypes submission:63

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP, NCBI
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .