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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs2021937          
refSNP ID: rs2021937
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:94/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_152447.2:c.-197+36140A>G
NT_026437.11:g.23113655A>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 ss43623107 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2021937 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
ss2925549TSC-CSHL|TSC0900829fwd/TA/Gtaagaaaatgtataaagatctttctttaggtatattttatgtccttcccctgtgtcctcc01/26/0110/25/0694Genomicunknown
ss3647240SC_JCM|AC016914.5_8605fwd/TA/Gtaagaaaatgtataaagatctttctttaggtatattttatgtccttcccctgtgtcctcc09/24/0110/10/03100Genomicunknown
ss43623107ABI|hCV11608218byFreqfwd/TA/Gtaagaaaatgtataaagatctttctttaggtatattttatgtccttcccctgtgtcctcc07/18/0511/03/06126Genomicunknown
ss66740646ILLUMINA|HumanHap300v1.1_rs2021937fwd/BA/Gtaagaaaatgtataaagatctttctttaggtatattttatgtccttcccctgtgtcctcc11/09/0611/09/06127Genomicunknown
ss70694223ILLUMINA|HumanHap550v3.0__rs2021937rev/BC/Tggaggacacaggggaaggacataaaatatacctaaagaaagatctttatacattttctta04/20/0703/30/08130Genomicunknown
ss71259571ILLUMINA|HumanHap650Yv3.0_rs2021937fwd/TA/Gtaagaaaatgtataaagatctttctttaggtatattttatgtccttcccctgtgtcctcc04/23/0704/23/07127Genomicunknown
ss75701037ILLUMINA|ILMN_Human_1M_rs2021937fwd/TA/Gtaagaaaatgtataaagatctttctttaggtatattttatgtccttcccctgtgtcctcc08/28/0708/29/07129Genomicunknown
ss79107849ILLUMINA|HumanHap300v2.0_rs2021937fwd/TA/Gtaagaaaatgtataaagatctttctttaggtatattttatgtccttcccctgtgtcctcc04/18/0711/18/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2021937|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 TTAAATCTAT CATGCATTTA GGAATATAAT TGCAAGCTGC TGTTTAAAGT TTTGATAGTG
 TAATATCTGA AAATTATATA CCTATCCTAC TTTACTTAAT ATGCGTCCAG TTTTGTTAGT
 TATCATGAAC CATGTACCAC ACAGTTTGGC AGGGTTGGGT AAGGAGATAG TCGGAGTGTG
 TGTTTTGTGT GTGTGTGTGT TATGTATATG TGTGTGTACT GGCAGAGGTT GAATTAAACC
 CTGTGATAAA AAAGGAATCA AGGCTTATCC TAAGAAAATG TATAAAGATC TTTCTTTAGG
 R
 TATATTTTAT GTCCTTCCCC TGTGTCCTCC AACTTTCAGT CGCTCCATTA TTTGATAGTT
 TAATTCTCAG ATGCTGAGGA TCAGAACAGA TGGATGCAGA AATTCTGGGA GAATCTTGGC
 TGAAGATGTG GGTTTCTCTT CTGCAAAGAA CACAAGATCA GAGAATCTTT AAAATGAGAT
 GGGAATAAAT TTCAGGGATC ATATTTGACA TTCTAAATTA AAACATGGTT TCTTTTTTAT
 GGTCTAAAAG CAGCTGTCTA GTTCCTTTAG AACAACCACA GTAAGGTAAC TAAAGCATAA

  GeneView back to top
GeneView via analysis of contig annotation: LRFN5 leucine rich repeat and fibronectin type III domain containing 5
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_026437->NM_152447
function
HuRefNW_001838111->NM_152447
function
CeleraNW_925539->NM_152447
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_026437->NM_152447->NP_68966023113655forwardintron
HuRefNW_001838111->NM_152447->NP_689660925201forwardintron
CeleraNW_925539->NM_152447->NP_68966021916706forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs2021937 maps exactly once on NCBI human chromosome 14
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
14NW_925539.12191670621974584plusAalt_assembly_1CeleraCeleraview300
14NW_001838111.192520122224211plusAalt_assembly_8HuRefHuRefview300
14NT_026437.112311365541183655plusAref_assemblyreferencereferenceview300

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
AC016914 AL121821
dbSNP Blast Analysis
GenBank HTGS Finished:
AL121821.7

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss43623107HapMap-CEUEuropean 120IG 0.350 0.550 0.100 0.200 0.625 0.375
HapMap-HCBAsian 90IG 0.978 0.022 1.000 0.989 0.011
HapMap-JPTAsian 90IG 1.000 1.000
HapMap-YRISub-Saharan African 118IG 0.678 0.288 0.034 1.000 0.822 0.178

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.269+/-0.24927021000

  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 .