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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs701865          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/130
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/T
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_006204.3:c.808T>A
NP_006195.3:p.Ser270Thr
NT_030059.12:g.14130299T>A
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 ss1477173 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs701865 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
ss1477173TSC-CSHL|TSC0095248byFreqfwd/TA/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg09/07/0004/07/0486Genomic95 %
ss1527861LEE|477191fwd/TA/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg09/13/0010/10/0386cDNAunknown
ss3908287SC_JCM|AL157396.7_8242fwd/TA/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg09/25/0110/10/03100Genomicunknown
ss16509960CSHL-HAPMAP|CSHL-HuAA-200402.chr10.NT_030059.11_14130299fwd/TA/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg02/17/0403/04/04120Genomicunknown
ss20728816SSAHASNP|WGSA-200403-chr10.chr10.NT_030059.11_14130299fwd/TA/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg03/18/0403/19/04121Genomicunknown
ss23580834PERLEGEN|afd2289224byFreqfwd/TA/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg08/10/0409/13/04123Genomicunknown
ss38563661ABI|hCV7626668byFreqfwd/A/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg07/15/0511/02/06126Genomicunknown
ss48404787APPLERA_GI|hCV7626668byFreqrev/A/Tcaatggagtatcgttcacagttcagatatgtctaaccgtgtagagcgctttgtgaaactg09/28/0511/03/06126Genomicunknown
ss65729146ILLUMINA|Human1-rs701865fwd/TA/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg10/10/0610/10/06127Genomicunknown
ss68400148CSHL-HAPMAP|sanger:assay:1729417:1byFreqfwd/A/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg01/11/0701/16/07127NAunknown
ss69087957PERLEGEN|PGP02289224byFreqfwd/A/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg01/30/0708/14/07127Genomicunknown
ss74809088AFFY|SNP_M-181666fwd/TA/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg08/09/0708/09/07128Genomicunknown
ss74891353ILLUMINA|ILMN_Human_1M_rs701865fwd/A/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg08/28/0708/29/07129Genomicunknown
ss76426511AFFY|AFFY_6_1M_SNP_A-8287426fwd/A/Tgctctacacggttagacatatctgaactgtga08/28/0708/30/07129Genomicunknown
ss76890732SI_EXO|NT_030059.12_14130299fwd/A/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg09/20/0709/20/07129Genomicunknown
ss78779284HGSV|Cor12878_SNV_20070510.chr10_95371763fwd/A/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg10/17/0710/20/07129Genomicunknown
ss81012585HGSV|Cor18507_SNV_20070510.chr10_95371763fwd/A/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg11/26/0711/27/07130Genomicunknown
ss104824383KRIBB_YJKIM|KHS1216719fwd/A/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg07/10/0807/10/08130Genomicunknown
ss1096628471000GENOMES|CEU.trio.12.15.2008_2407434_chr10_95371763fwd/A/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg12/15/0812/16/08130Genomicunknown
ss119272489ILLUMINA-UK|NA18507_000120233_NCBI36.1_chr10_95371763fwd/A/Tcagtttcacaaagcgctctacacggttagacatatctgaactgtgaacgatactccattg01/21/0901/22/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs701865|allelePos=186|totalLen=945|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=130
 TTATTTTATC TTGATGCACC TCATGTTTTC TTGTGGTGAA TGCTCTATCT CTCCATAGCA
 TACTTTATTC TAACTGTTTT CTTTTTGATA CCTACTTTCA GATCCTTATG TGGTCAGCCA
 ATAAAGTATT TGAAGAACTC ACAGATGTTG AGCGACAGTT TCACAAAGCG CTCTACACGG
 TTAGA
 W
 CATATCTGAA CTGTGAACGA TACTCCATTG GACTGCTGGA CATGACCAAG GAGAAGGTTC
 TTATTATTCT ACACATTTTG TCTCATCTCA CATCGCCTAT ATAACACACA CCACAGGAAA
 TGTGATCCTT AAAAAACAGA TACACTATGT AAATAATTAG TCATGATTGA TGACAAGAAC
 AGAGGTAAAA GTGTGTGTCT TGGAGCAAAA AAGATGTAGG CTTGAATCTT GGTTTTTCCA
 CTTCCTAGTA ATATGGGTTT TCAGCAAGTC TGTTTTTTTT TTACATTAat taatagacta
 tttttagagt agtattgaca gaaaaattga ttataaagta cggagtttcc tcttccctcc
 caatctcctc tcccagtttc cctgttatta atatcttgca ttagtgtggt gtgatgaatc
 aatattgata tattattatt aactaaagtc catagtttac atgagggttc atcctttgtg
 cagttctctg ggttttgaca aatgtgtaat gtcatatatc tgctactaca gtatcagaca
 gactactttc agtgcctcaa agccctctgt gcttcacata ttcaaccttt cctcacccct
 tccaaactcc tggtagccac aggttttttt ttgttttttt tttgttgttt tttttttttt
 gctgtttcta tagtttttgc cttttccaga atgccatata gttggaatca tacagtatgt
 agctttcaga cGAAAGTGCA GTTTGATTGC TACAAGGCT

  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
U31973 AL356214 AL356214.6 Hs.93173 X94354 X94354.1
dbSNP Blast Analysis
UniGene Cluster ID
93173

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/T
 T/T
 HWP A
 N
 T
ss1477173 CEPH 184 AF 0.450 0.550
HapMap-CEU European 120 IG 0.200 0.450 0.350 0.584 0.425 0.575
HapMap-HCB Asian 90 IG 0.244 0.444 0.311 0.479 0.467 0.533
HapMap-JPT Asian 88 IG 0.295 0.568 0.136 0.273 0.580 0.420
HapMap-YRI Sub-Saharan African 120 IG 0.200 0.533 0.267 0.584 0.467 0.533
CHMJ Asian 74 IG 0.500 0.014 0.486
ss23580834 AFD_EUR_PANEL European 44 IG 0.227 0.409 0.364 0.439 0.432 0.568
AFD_AFR_PANEL African American 40 IG 0.150 0.650 0.200 0.200 0.475 0.525
AFD_CHN_PANEL Asian 44 IG 0.318 0.636 0.045 0.100 0.636 0.364
ss38563661 AoD_African_American 90 AF 0.540 0.460
AoD_Caucasian 92 AF 0.440 0.560
AoD_Chinese 90 AF 0.490 0.510
AoD_Japanese 90 AF 0.480 0.520
ss48404787 AGI_ASP population multiple 74 IG 0.162 0.541 0.297 0.584 0.432 0.568
ss69087957 HapMap-CEU European 120 GF 0.200 0.450 0.350 0.425 0.575
HapMap-HCB Asian 90 GF 0.244 0.444 0.311 0.467 0.533
HapMap-JPT Asian 90 GF 0.289 0.578 0.133 0.578 0.422
HapMap-YRI Sub-Saharan African 120 GF 0.200 0.533 0.267 0.467 0.533

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.499+/-0.020 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
byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Validated by: ILLUMINA
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .