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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs16891982          **clinically associated**
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:123/130
Map to Genome Build:36.3
Citation:NHGRI GWAS PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/G
Ancestral Allele:C
Clinical Association:link to VariationViewerlink to OMIM
HGVS Names
NM_001012509.1:c.1122C>G
NM_016180.3:c.1122C>G
NP_001012527.1:p.Phe374Leu
NP_057264.3:p.Phe374Leu
NT_006576.15:g.33924450C>G
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 ss44669869 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs16891982 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
ss23456916PERLEGEN|afd3693051byFreqfwd/BC/Gataaagtgaggaaaacacggagttgatgcaaagccccaacatccaacctcgactcctctt08/10/0409/13/04123Genomicunknown
ss28510204MGC_GENOME_DIFF|BC064405x37550355-C16403799Gfwd/BC/Gataaagtgaggaaaacacggagttgatgcaaagccccaacatccaacctcgactcctctt08/25/0408/25/04126cDNAunknown
ss44669869ABI|hCV2842665byFreqfwd/C/Gataaagtgaggaaaacacggagttgatgcaaagccccaacatccaacctcgactcctctt07/19/0511/03/06126Genomicunknown
ss68931899PERLEGEN|PGP03693051byFreqfwd/C/Gataaagtgaggaaaacacggagttgatgcaaagccccaacatccaacctcgactcctctt01/30/0703/31/08127Genomicunknown
ss74816457AFFY|SNP_M-312845fwd/BC/Gataaagtgaggaaaacacggagttgatgcaaagccccaacatccaacctcgactcctctt08/09/0708/09/07128Genomicunknown
ss74858559ILLUMINA|ILMN_Human_1M_rs16891982fwd/C/Gataaagtgaggaaaacacggagttgatgcaaagccccaacatccaacctcgactcctctt08/28/0708/29/07129Genomicunknown
ss78414960HGSV|Cor12878_SNV_20070510.chr5_33987450fwd/C/Gataaagtgaggaaaacacggagttgatgcaaagccccaacatccaacctcgactcctctt10/17/0710/19/07129Genomicunknown
ss86270034CORNELL|hCV2842665fwd/C/Gataaagtgaggaaaacacggagttgatgcaaagccccaacatccaacctcgactcctctt01/21/0801/21/08129Genomicunknown
ss93054654BCMHGSC_JDW|JWB-1961143fwd/C/Gataaagtgaggaaaacacggagttgatgcaaagccccaacatccaacctcgactcctctt02/26/0803/03/08129Genomicunknown
ss98610228HUMANGENOME_JCVI|1103654071247fwd/C/Gataaagtgaggaaaacacggagttgatgcaaagccccaacatccaacctcgactcctctt04/01/0804/01/08130Genomicunknown
ss1089477551000GENOMES|CEU.trio.12.15.2008_1241468_chr5_33987450fwd/C/Gataaagtgaggaaaacacggagttgatgcaaagccccaacatccaacctcgactcctctt12/15/0812/16/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs16891982|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=130
 TTCCCTTTCA TTTTCCAGAG AAACTTGATC AGGAACCCAC TGATTCCAAG AGCAAAGTAA
 TCAGTGAGGA AATGACACCT AGAATTCATG ATGAAAAAAG GATGCTTTAT ATGGTCCTTT
 TTAAGGTGAT AGTTTTTCCT GACGTCCATA GATTTATTAA GAATCTGGTA TTTTAAACAG
 TAGGAAATAC ACATAGAAAT ATCAAATCCA AGTTGTGCTA GACCAGAAAC TTTTAGAAGA
 CATCCTTAGG AGAGAGAAAG ACTTACAAGA ATAAAGTGAG GAAAACACGG AGTTGATGCA
 S
 AAGCCCCAAC ATCCAACCTC GACTCCTCTT TCGTAGATGA GAAACTCTGT GGAGTTGTGT
 GCACTATAGG GATCCCCGCG GTACACAATC TGAAAGAGAG ATTGGAGGCT GTTGAGGTAC
 AAATGCAATG TAGTAAGAAC CCTTCTCATG CACTCTGCTT CTCCACCTCT GGGGAGCAAA
 TGTCCCTGCC TGAGGGACCC TTTCTAGAGT ACAGAGCTGA TGCTGTCATG ACCAAGTCGC
 ATCCTATCAC ATCTTCATTC AAGGACCTAT CAGAAATCTA ATGCTTGCTG CATCAGATCT

  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
NC_000005.8 ABBA01066761 BC064405
dbSNP Blast Analysis
UniGene Cluster ID
278962
OMIM
606202

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/G
 G/G
 HWP C
 G
ss23456916 AFD_EUR_PANEL European 48 IG 1.000 1.000
AFD_AFR_PANEL African American 46 IG 0.826 0.174 0.655 0.913 0.087
AFD_CHN_PANEL Asian 48 IG 1.000 1.000
ss44669869 HapMap-CEU European 116 IG 0.034 0.966 0.017 0.983
HapMap-HCB Asian 88 IG 0.977 0.023 0.989 0.011
HapMap-JPT Asian 82 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 114 IG 1.000 1.000
ss68931899 HapMap-CEU European 120 GF 0.033 0.967 0.017 0.983
HapMap-HCB Asian 90 GF 0.978 0.022 0.989 0.011
HapMap-JPT Asian 90 GF 1.000 1.000
HapMap-YRI Sub-Saharan African 120 GF 1.000 1.000

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict		 Additional Freq. Data
0.418+/-0.185 582 459 15 0 ALFRED: The Allele Frequency Database

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqWith1000GenomeData UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .