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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1285933          
refSNP ID: rs1285933
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:87/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NT_007914.14:g.2218701G>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 ss2024698 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1285933 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
ss2024698KWOK|OVLP-000925-631413byFreqfwd/TA/Gccagaagcacattggaaaaccatcacaggggctgaagaagagtgacagaatctgtttaat10/06/0008/05/0487Genomic99 %
ss2478303SC_JCM|AC011654.4_163353fwd/TA/Gccagaagcacattggaaaaccatcacaggggctgaagaagagtgacagaatctgtttaat11/03/0010/10/0392Genomicunknown
ss6512750WI_SSAHASNP|NT_007914.10_2185446fwd/TA/Gccagaagcacattggaaaaccatcacaggggctgaagaagagtgacagaatctgtttaat02/12/0310/10/03111Genomicunknown
ss14548531WUGSC_SSAHASNP|chr7.NT_007914.13_2218701fwd/TA/Gccagaagcacattggaaaaccatcacaggggctgaagaagagtgacagaatctgtttaat11/05/0311/22/03120Genomicunknown
ss44832213ABI|hCV9506735fwd/TA/Gccagaagcacattggaaaaccatcacaggggctgaagaagagtgacagaatctgtttaat07/19/0507/19/05126Genomicunknown
ss65785535ILLUMINA|Human1-rs1285933fwd/TA/Gccagaagcacattggaaaaccatcacaggggctgaagaagagtgacagaatctgtttaat10/10/0610/10/06127Genomicunknown
ss66105475AFFY|SNP_A-1991517byFreqrev/BC/Tgtcactcttcttcagcccctgtgatggttttc10/27/0608/14/07127Genomicunknown
ss66798702ILLUMINA|HumanHap300v1.1_rs1285933fwd/BA/Gccagaagcacattggaaaaccatcacaggggctgaagaagagtgacagaatctgtttaat11/09/0611/09/06127Genomicunknown
ss67042629ILLUMINA|HumanHap550v1.1_rs1285933fwd/TA/Gccagaagcacattggaaaaccatcacaggggctgaagaagagtgacagaatctgtttaat11/14/0611/14/06127Genomicunknown
ss67367500ILLUMINA|HumanHap650Yv1.0_rs1285933fwd/TA/Gccagaagcacattggaaaaccatcacaggggctgaagaagagtgacagaatctgtttaat11/14/0611/14/06127Genomicunknown
ss70416757ILLUMINA|HumanHap300v2.0_rs1285933fwd/TA/Gccagaagcacattggaaaaccatcacaggggctgaagaagagtgacagaatctgtttaat04/18/0711/18/07127Genomicunknown
ss70586509ILLUMINA|HumanHap550v3.0__rs1285933fwd/TA/Gccagaagcacattggaaaaccatcacaggggctgaagaagagtgacagaatctgtttaat04/20/0703/30/08130Genomicunknown
ss71129501ILLUMINA|HumanHap650Yv3.0_rs1285933fwd/TA/Gccagaagcacattggaaaaccatcacaggggctgaagaagagtgacagaatctgtttaat04/23/0704/23/07127Genomicunknown
ss75858812ILLUMINA|ILMN_Human_1M_rs1285933fwd/TA/Gccagaagcacattggaaaaccatcacaggggctgaagaagagtgacagaatctgtttaat08/28/0708/29/07129Genomicunknown
ss76078895AFFY|AFFY_6_1M_SNP_A-1991517rev/BC/Tgtcactcttcttcagcccctgtgatggttttc08/28/0708/29/07130Genomicunknown
ss83712603KRIBB_YJKIM|KHS525515fwd/TA/Gccagaagcacattggaaaaccatcacaggggctgaagaagagtgacagaatctgtttaat12/04/0712/05/07130Genomicunknown
ss86113531HGSV|Cor18517_SNV_20070510.chr7_141080333fwd/TA/Gccagaagcacattggaaaaccatcacaggggctgaagaagagtgacagaatctgtttaat12/06/0712/11/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1285933|allelePos=5001|totalLen=5318|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 ttttatttcc ttgagcagtg gtttgtagtt ctccttgaag aggtccttca catcccttgt
 aagttggatt cctaggtatt ttattctctt tgaagcaatt gtgaatggga gttcacccat
 gatttggctc tctgtttgtc tgttgttggt gtataagaat gcttgtgatt tttgtacatt
 gattttgtat cctgagactt tgctgaagtt gcttatcagc ttaaggagat tttgggctga
 gacgatgggg ttttctagat aaacaatcat gtcatctgca aacagggaca atttgacttc
 ctcttttcct aattgaatac cctttatttc cttctcctgc ctgattgccc tggccagaac
 ttccaacact atgttgaata ggagcggtga gagagggcat ccctgtcttg tgccggtttt
 caaagggaat gcttccagtt tttgcccatt cagtatgata ttggctgtgg gtttgtcata
 gatagctctt attattttga aatacgtccc atcaatacct aatttattga gagtttttag
 catgaagagt tgttgaattt tgtcaaaggc tttttctgca tctattgaga taatcatgtg
 gtttttgtct ttggctctgt ttatatgctg gattacattt attgatttgc gtatattgaa
 ccagccttgc atcccaggga tgaagcccac ttgatcatgg tggataagct ttttgatgtg
 ctgctggatt cggtttgcca gtattttatt gaggattttt gcatcaatgt tcatcaagga
 tattggtcta aaattctctt ttttggttgt gtctctgccc ggctttggta tcagaatgat
 gctggcctca taaaatgagt tagggaggat tccctctttt tctattgatt ggaatagttt
 cagaaggaat ggtaccagtt cctccttgta cctctggtag aattcggctg tgaatccatc
 tggtcctgga ctctttttgg ttggtaaact attgattatt gccacaattt cagagcctgt
 tattggtcga ttcagagatt caacttcttc ctggtttagt cttgggagag tgtatgtgtc
 gaggaatgta tccatttctt ctagattttc tagtttattt gcgtagaggc gtttgtagta
 ttctctgatg gtagtttgta tttctgtggg atcggtggtg atatcccctt tatcattttt
 tattgtgtct atttgattct tctctctttt tttctttatt agtcttgcta gcggtctatc
 aattttgttg atcctttcaa aaaaccagct cctggattca ttgatttttt gaagggtttt
 ttgtgtctct atttccttca gttctgctct gattttagtt atttcttgcc ttctgctagc
 ttttgaatgt gtttgctctt gcttttctag ttcttttaat tgtgatgtta gggtgtcaat
 tttggatctt tcctgctttc tcttgtaggc atttagtgct ataaatttcc ctctacacac
 tgctttgaat gcgtcccaga gattctggta tgtggtgtct ttgttctcgt tggtttcaaa
 gaacatcttt atttctgcct tcatttcgtt atgtacccag tagtcattca ggagcaggtt
 gttcagtttc catgtagttg agcggctttg agtgagattc ttaatcctga gttctagttt
 gattgcactg tggtctgaga gatagtttgt tataatttct gttcttttac atttgctgag
 gagagcttta cttccaacta tgtggtcaat tttggaatag gtgtggtgtg gtgctgaaaa
 aaatgtatat tctgttgatt tggggtggag agttctgtag atgtctatta ggtctgcttg
 gtgcagagct gagttcaatt cctgggtatc cttgttgact ttctgtctcg ttgatctgtc
 taatgttgac agtggggtgt taaagtctcc cattattaat gtgtgggagt ctaagtctct
 ttgtaggtca ttgaggactt gctttatgaa tctgggtgct cctgtattgg gtgcataaat
 atttaggata gttagctcct cttgttgaat tgatcccttt accattatgt aatggccttc
 tttgtctctt ttgatctttg ttggtttaaa gtctgtttta tcagagacta ggattgcaac
 ccctgccttt ttttgttttc catttgcttg gtagatcttc ctccatcctt ttattttgag
 cctatgtgtg tctctgcacg tgagatgggt ttcctgaata cagcacactg atgggtcttg
 actctttatc caacttgcca gtctgtgtct tttaattgca gaatttagtc catttatatt
 taaagttaat attgttatgt gtgaatttga tcctgtcatt atgatgttag ctggtgattt
 tgctcattag ttgatgcagt ttcttcctag tctcgatggt ctttacattt tggcatgatt
 ttgcagcggc tggtaccggt tgttcctttc catgtttagc gcttccttca ggagctcttt
 tagggcaggc ctggtggtga caaaatctct caacatttgc ttgtctataa agtattttat
 ttctccttca cttatgaagg ttagtttggc tggatatgaa attctgggtt gaaaattctt
 ttctttaaga atgttgaata ttggccccca ctctcttctg gcttgtaggg tttctgccga
 gagatccgct gttattctga tgggctttcc tttgagggta acccgacctt tctctctggc
 tgcccttaac attttttcct tcatttcaac tttggtgaat ctgacaatta tgtgtcttgg
 agttgctctt ctcgaggagt atctttgtgg cgttctctgt atttcctgaa tctgaacgtt
 ggcctgcctt gctagattgg ggaagttctc ctggataata tcctgcagag tgttttccaa
 cttggttcca ttctccacat cactttcagg tacaccaatc agacgtagat ttggtctttt
 cacatagtcc catatttctt ggaggctttg ctcatttctt tttattcttt tttctctaaa
 cttcccttct cgcttcattt cattcatttc atcttccatt gctgataccc tttcttccag
 ttgatcgcat cggctcctga ggcttctgca ttcttcacgt agttctcgag ccttggtttt
 cagctccatc agctccttta agcacttctc tgtattggtt attctagtta tacattcttc
 taaatttttt tcaaagtttt caacttcttt gcctttggtt tgaatgtcct cccgtagctc
 agagtaattt gatcgtctga agccttcttc tctcagctcg tcaaaatcat tctccatcca
 gctttgttct gttgctggtg aggaactgcg ttcctttgga ggaggagagg cgctctgcgt
 tttagagttt ccagtttttc tgttctgttt tttccccatc tttgtggttt tatctacttt
 tggtctttga tgatggtgat gtacagatgg gttttcggtg tagatgtcct ttctggttgt
 tagttttcct tctaacagac aggaccctca gctgcaggtc tgttggaata ccctgccgtg
 tgaggtgtca gtgtgcccct gctggggggt gcctcccagt taggctgctc gggggtcagg
 agtcagggac ccacttgagg aggcagtctg cccgttctca gatctccagc tgcgtgctgg
 gagaaccact gctctcttca aagctgtcag acagggacac ttaagtctgc agaggttact
 gctgtctttt tgtttgtctg tgccctgccc ccagaggtgg agcctacaga ggcaggcagg
 cctccttgag ctgtggtggg ctccacccag ttcgagcttc ccggctgctt tgtttaccta
 agcaagcctg ggcaatggcg ggcgcccctc ccccagcctc gttgccgcct tgcagtttga
 tctcagactg ctgtgctagc aatcagtgag attccgtggg cgtaggaccc tccgagccag
 gtgtgggata tagtctcgtg gtgcgccgtt tcttaagccg gtctgaaaag cgcaatattc
 gggtgggagt gacccgattt tccaggtgcg tccgtcaccc ctttctttga ctcggaaagg
 gaactccctg accccttgcg cttcccaggt gaggcaatgc ctcgccctgc ttcggctcgc
 gcacggtgcg cacacacact ggcctgcgcc cactgtctgg cactccctag tgagatgaac
 ccggtacctc agatggaaat gcagaaatca ccgtcttctg cgtcgctcac gctgggagtt
 gtagaccgga gctgttccta ttcggccatc ttggctcctc cctcTCTTTT TTTTAAAatt
 atactttaag tcctagggta catgtgcaca atgtgcaggt ttgttacata tgtatacatg
 tgccatgttg gtgtgctgca cccactaact tatcatttat attaggtatt tctcctaatg
 ctgtccctcc cctctcctca caccccacga caggccctgg tgtgtgatgt tccctgcctg
 gtgtccaagt gctctcatta ttcaattccc acctatgagt gagaatatgt ggtgtttggt
 tttctgtctt tgcgatagct tgctcagaat gatggtttcc agcttcatcc atgtccctac
 aaaggacatg aactctcatc cttttttgtg gctgcatagt attccatggt gtatatgtgc
 cacattttct taatccagtc tatcactgat ggacatttgg gttggttcca agtctttgct
 attgtgaata gtgccacaat aaacatacgt gtgcatgtgt ctttatagta gcgtgattta
 taatcctttg ggtatatacc cagtaatggg atcactgggt caaatggtat ttctagttct
 agatccttga ggaatcgcca cactgaGCCT TTtaaggatg tttgctcttt ccagaagcac
 attggaaaac catcacaggg
 R
 gctgaagaag agtgacagaa tctgtttaat gttttaacaa gatcatcctg gttgctggat
 gaacaataca cgaaaggaca ataaagggag aaggatgaag gccagatgga gattgcaTCA
 GTTAGATTTT GCTATACGAG AGATAACCAG AAAACTCCAG TGGTATACAG TGATAAGTTT
 TTATTTTTGT GCTTAGAGTT TCAGCTGATC TAGGGTGGCT CTGCTGATCT CAGGTGGATT
 TGTTCGTGAG TCTAAGGGTT GGATGGGGGT TGGCTGACCT AGGCTGGGCC CACATTTGAG
 GTCATGAAAA GTGTGTC

  GeneView back to top
GeneView via analysis of contig annotation: CLEC5A C-type lectin domain family 5, member A
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_007914->NM_013252
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_007914->NM_013252->NP_0373842218701reverse3' near gene

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1285933 maps exactly once on NCBI human chromosome 7
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
7NW_001839073.12224008135923555plusAalt_assembly_8HuRefHuRefview5000
7NW_923640.139107396136348645plusGalt_assembly_1CeleraCeleraview5000
7NT_079596.241000928140965360plusGalt_assembly_2CRA_TCAGchr7v2CRA_TCAGchr7v2view5000
7NT_007914.142218701141273618plusGref_assemblyreferencereferenceview5000

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_007914 AC073647 AC073647.3
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss2024698HapMap-CEUEuropean 120IG 0.183 0.650 0.167 0.020 0.508 0.492
HapMap-HCBAsian 90IG 0.044 0.311 0.644 1.000 0.200 0.800
HapMap-JPTAsian 88IG 0.023 0.364 0.614 0.439 0.205 0.795
HapMap-YRISub-Saharan African 120IG 0.367 0.483 0.150 1.000 0.608 0.392
ss66105475HapMap-CEUEuropean 118GF 0.169 0.661 0.169 0.500 0.500
HapMap-HCBAsian 90GF 0.044 0.311 0.644 0.200 0.800
HapMap-JPTAsian 90GF 0.022 0.356 0.622 0.200 0.800
HapMap-YRISub-Saharan African 120GF 0.367 0.483 0.150 0.608 0.392

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.482+/-0.0942702102690

  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 .