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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs3127328          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:103/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_003181.2:c.1066G>A
NP_003172.1:p.Gly356Ser
NT_007422.13:g.8859386C>T
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 ss71644674 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3127328 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
ss4374094SC_JCM|AL627443.6_100798fwd/BC/Tctgctgcctgggagcccggggtgacggcgcgttgctcacagaccacaggctggggtactg02/19/0210/10/03103Genomicunknown
ss5920697SC_JCM|NT_007422.10_5500976fwd/BC/Tctgctgcctgggagcccggggtgacggcgcgttgctcacagaccacaggctggggtactg01/10/0310/10/03111Genomicunknown
ss23676534PERLEGEN|afd4356979byFreqfwd/BC/Tctgctgcctgggagcccggggtgacggcgcgttgctcacagaccacaggctggggtactg08/10/0409/13/04123Genomicunknown
ss44775384ABI|hCV25614384byFreqfwd/BC/Tctgctgcctgggagcccggggtgacggcgcgttgctcacagaccacaggctggggtactg07/19/0511/03/06126Genomicunknown
ss48426976APPLERA_GI|hCV25614384byFreqrev/TA/Gcagtaccccagcctgtggtctgtgagcaacgcgccgtcaccccgggctcccaggcagcag09/28/0511/03/06126Genomicunknown
ss71644674SI_EXO|NT_007422.13_8859386byFreqfwd/BC/Tctgctgcctgggagcccggggtgacggcgcgttgctcacagaccacaggctggggtactg05/07/0703/31/08127Genomicunknown
ss74871635ILLUMINA|ILMN_Human_1M_rs3127328fwd/BC/Tctgctgcctgggagcccggggtgacggcgcgttgctcacagaccacaggctggggtactg08/28/0708/29/07129Genomicunknown
ss93603238BCMHGSC_JDW|JWB-2252652fwd/BC/Tctgctgcctgggagcccggggtgacggcgcgttgctcacagaccacaggctggggtactg02/26/0803/04/08129Genomicunknown
ss98562188HUMANGENOME_JCVI|1103705068265fwd/BC/Tctgctgcctgggagcccggggtgacggcgcgttgctcacagaccacaggctggggtactg04/01/0804/01/08130Genomicunknown
ss1131031741000GENOMES|NA19240_2008_12_16_1504269_chr6_166492035fwd/BC/Tctgctgcctgggagcccggggtgacggcgcgttgctcacagaccacaggctggggtactg12/18/0812/18/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3127328|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TGCCGTGTGC TCCTCCACTG CTTTGAAAAG GAAGTTACTG AGGCTGCATT TCCTTCTTAA
 CCTGAGACTG CCACTGGGTA CCTAGTAGGT CAATCCAGTC ACCACTGGCT GCCACGACAA
 AAAGTCACTG CATCTTTCGG GACCTGGGCC TTGCTGCTTC ACATGGAAGG TGGCGACACA
 GGTGTCCATG AGGCTATGAG GCGGCCTTGG GCTGCGGCGT CGTACTGGCT GTCCACGATG
 TCTGTGGCCG CGGCCGCCCC TTCGTACAGT GGGGATCCCG AGGAAGAGGG CGCCGAGACC
 GGATGGGTGA GGGGTGTGTA GTGCGCGGGG GAGCCCCGGA AGAACTGGGC CCCCAGCCCG
 TTGGACACGG CTGCTGCCTG GGAGCCCGGG GTGACGGCGC
 Y
 GTTGCTCACA GACCACAGGC TGGGGTACTG ACTGCAACAG AAAGACACCA GTGAGCAGGG
 CCTGGGCAGG GGCTGCAGGC CAGCTAAGGA TGGAAAAACA CACCAGAAAT CCCATTCGGA
 GTGACTGTGT AATATGACAG TTTTCTTCTT TCAAACAGGT CATTTTCTCC AAATTATTAA
 AGGACTCACA AGCACATTCT GTGATGTATA GAAGTTATTG TCGTATCTAT TAATAAGAAA
 CAAAATCATC AGGAAGATGA CTGAAAAGAT TATTCACATA TTCAGAGCTC ATGAAAGAGC
 GCTGTTAAGT TTCACTGCGA AAGACTCATA CCAGGCCAGC CGCAGTGGGT GATGCCTGTA
 ATCCCAGTAC TTTGGGAGGC CAAGGCAGGT GGATCAGCTG

  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_007422.13 ABBA01015077 AC016432
dbSNP Blast Analysis
UniGene Cluster ID
389457

  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
ss23676534 AFD_EUR_PANEL European 48 IG 0.833 0.167 0.752 0.917 0.083
AFD_AFR_PANEL African American 46 IG 0.478 0.478 0.043 0.403 0.717 0.283
AFD_CHN_PANEL Asian 48 IG 0.917 0.083 1.000 0.958 0.042
ss44775384 HapMap-CEU European 120 IG 0.750 0.250 0.273 0.875 0.125
HapMap-HCB Asian 84 IG 0.952 0.048 1.000 0.976 0.024
HapMap-JPT Asian 86 IG 0.907 0.093 0.752 0.953 0.047
HapMap-YRI Sub-Saharan African 120 IG 0.717 0.250 0.033 0.655 0.842 0.158
ss48426976 AGI_ASP population multiple 44 IG 0.727 0.227 0.045 0.527 0.841 0.159
ss71644674 HapMap-CEU European 120 IG 0.750 0.250 0.875 0.125
HapMap-HCB Asian 84 IG 0.952 0.048 0.976 0.024
HapMap-JPT Asian 86 IG 0.907 0.093 0.953 0.047
HapMap-YRI Sub-Saharan African 120 IG 0.717 0.250 0.033 0.842 0.158

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.189+/-0.242 708 585 15 0

  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 .