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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs227778          
refSNP ID: rs227778
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:79/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_003494.2:c.4509+1040A>G
NT_022184.14:g.50688170A>G
Links

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 ss1642511 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs227778 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
ss294976KWOK|OVLP-000621-291965fwd/BC/Tacaagccgcctacagatggctaagctgaaaagtcctctgtaacacacatccactggggct06/30/0010/10/0379Genomic97 %
ss1210124KWOK|OVLP-000804-122539fwd/BC/Tacaagccgcctacagatggctaagctgaaaagtcctctgtaacacacatccactggggct09/02/0010/10/0386Genomic97 %
ss1642511KWOK|OVLP-000925-453376byFreqfwd/BC/Tacaagccgcctacagatggctaagctgaaaagtcctctgtaacacacatccactggggct10/04/0010/25/0687Genomic97 %
ss2577284SC_JCM|AJ007973.1_20216rev/TA/Gagccccagtggatgtgtgttacagaggacttttcagcttagccatctgtaggcggcttgt11/03/0010/10/03117Genomicunknown
ss3069759TSC-CSHL|TSC1161001rev/TA/Gagccccagtggatgtgtgttacagaggacttttcagcttagccatctgtaggcggcttgt06/07/0110/10/0396Genomicunknown
ss9999875BCM_SSAHASNP|chr2.NT_022184.12_50688165rev/TA/Gagccccagtggatgtgtgttacagaggacttttcagcttagccatctgtaggcggcttgt06/27/0310/10/03116Genomicunknown
ss41696673ABI|hCV26432281rev/TA/Gagccccagtggatgtgtgttacagaggacttttcagcttagccatctgtaggcggcttgt07/17/0507/17/05126Genomicunknown
ss67240863ILLUMINA|HumanHap550v1.1_rs227778fwd/BC/Tacaagccgcctacagatggctaagctgaaaagtcctctgtaacacacatccactggggct11/14/0611/14/06127Genomicunknown
ss67637543ILLUMINA|HumanHap650Yv1.0_rs227778fwd/BC/Tacaagccgcctacagatggctaagctgaaaagtcctctgtaacacacatccactggggct11/14/0611/14/06127Genomicunknown
ss68201105ILLUMINA|HumanHap250Sv1.0_rs227778fwd/BC/Tacaagccgcctacagatggctaagctgaaaagtcctctgtaacacacatccactggggct12/06/0612/07/06127Genomicunknown
ss68818913PERLEGEN|PGP04877224byFreqrev/TA/Gagccccagtggatgtgtgttacagaggacttttcagcttagccatctgtaggcggcttgt01/30/0708/14/07127Genomicunknown
ss70719207ILLUMINA|HumanHap550v3.0__rs227778rev/TA/Gagccccagtggatgtgtgttacagaggacttttcagcttagccatctgtaggcggcttgt04/20/0703/30/08130Genomicunknown
ss71287468ILLUMINA|HumanHap650Yv3.0_rs227778fwd/BC/Tacaagccgcctacagatggctaagctgaaaagtcctctgtaacacacatccactggggct04/23/0704/23/07127Genomicunknown
ss75544641ILLUMINA|ILMN_Human_1M_rs227778fwd/BC/Tacaagccgcctacagatggctaagctgaaaagtcctctgtaacacacatccactggggct08/28/0708/29/07129Genomicunknown
ss76714618AFFY|AFFY_6_1M_SNP_A-8576058fwd/BC/Tgatggctaagctgaaaagtcctctgtaacaca08/28/0708/30/07129Genomicunknown
ss83393922KRIBB_YJKIM|KHS451096fwd/BC/Tacaagccgcctacagatggctaagctgaaaagtcctctgtaacacacatccactggggct12/04/0712/04/07130Genomicunknown
ss84711610HGSV|Cor19240_SNV_20070510.chr2_71783888rev/TA/Gagccccagtggatgtgtgttacagaggacttttcagcttagccatctgtaggcggcttgt11/30/0712/07/07130Genomicunknown
ss91205278BCMHGSC_JDW|JWB-1257982rev/TA/Gagccccagtggatgtgtgttacagaggacttttcagcttagccatctgtaggcggcttgt02/26/0803/01/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs227778|allelePos=891|totalLen=1409|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GCCAAAAGAA TCACCTGAAA GCCCAGGCCA CCTGCTACCC TGACAAGCTT CAACTCTCTC
 TCATCCAGTC CCCTCCAAAG GGCTCTTGGG GCCTTTCCTA TGTGTCTAAC AGCCTGTGCC
 CACCTCTCAT TTTCTCCTCT CCAAGCCTGG GAGGTAATTG CGGGGTACAG AGTCTCCCCC
 ATTTATAATC CAGAAGTAGT gttgccagat ttagtaagtg aaaatacaca atttccagtt
 aaatctgaat ttcaaataaa taactgatac agaacggggt caggtaagtg ctgggtagag
 gaggacggtg tccctggcga gggcttcatc ccccgggcct gtgcccacag gcctagggag
 gacaggcatt tctgttttct tgcccaaatg ctgcatttcc caagaccatc ctggcctgcc
 acacccccat tctgtgccta taaaaacccc caagacccta gcgggcagaa acacaagttg
 ctggacatcg agaggaacac acaagcagag gaacacacaa gcggcgggat gtcgagaagg
 acccactggc gtaggagcac accaacaggc ctcagcaggc cagcaggcca ttgaccagcg
 gaacaacgtg gagtttggtc ctggtggtgg gaggagagtc caggccactg agcagcgcga
 ctccagggga aaaccacctt cccattccat ctcccttctg gctccccaat ctgctgagag
 ctacttccac ccagtaaaac cttgcactca atctccaagc ccacgtgcga tccaattctt
 tcagtacacc aaggcaagaa accccgggat acagaaagcc ctctgtgctt gtgataaggc
 aggggtctaa ttgagctaac acaagccgcc tacagatggc taagctgaaa
 Y
 agtcctctgt aacacacatc cactggggct tcagctgtaa acattcacct ctggacactg
 ctgtggggtt ggagccccgc aacctgccca tctgcatgtt cccctagagg tgtgagcagc
 agggcactga agaagccagc cacaccccca ctgcacaccc tgcaaggggg ataagggaac
 ttttcctgtt tcataaccaa taatttttaa agaaatatgc cccgtgcaat atttgatgca
 tgctgatatt aaaaaactat tcattgttca tctgaaattc aaatgtgact gggcatcctg
 aattttaact ggcaacccTA GCCAGGAGAC CATGCAACTC CTTTAAGGAG TAATTTCTGA
 GTCACCTCTG ATTATCTTCT TTAAAAGTAG TCTACTTTTT CAAAGCATAA TTATATTTGT
 ATAATTTCCT CAAAATACCA CAATTTGGCT GACTCATTTC TGTTTTTTTC CACAGAAACA
 GGGTTTCCCA TATTTTCAGA TTTGTAGGTA ATTTTCTG

  GeneView back to top
GeneView via analysis of contig annotation: DYSF dysferlin, limb girdle muscular dystrophy 2B (autosomal recessive)
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_022184->NM_003494
function
HuRefNW_001838769->NM_003494
function
CeleraNW_927719->NM_003494
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_022184->NM_003494->NP_00348550688170forwardintron
HuRefNW_001838769->NM_003494->NP_00348541705999forwardintron
CeleraNW_927719->NM_003494->NP_00348571654662forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs227778 maps exactly once on NCBI human chromosome 2
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
2NW_001838769.14170599971609755minusGalt_assembly_8HuRefHuRefview890
2NW_927719.17165466271722727minusAalt_assembly_1CeleraCeleraview890
2NT_022184.145068817071725741minusAref_assemblyreferencereferenceview890

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_022184 AC010147 AJ007973.1
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1642511HapMap-CEUEuropean 116IG 0.569 0.362 0.069 1.000 0.750 0.250
HapMap-HCBAsian 90IG 0.556 0.400 0.044 0.584 0.756 0.244
HapMap-JPTAsian 90IG 0.244 0.444 0.311 0.479 0.467 0.533
HapMap-YRISub-Saharan African 120IG 0.167 0.517 0.317 0.752 0.425 0.575
ss68818913HapMap-CEUEuropean 120GF 0.567 0.350 0.083 0.742 0.258
HapMap-HCBAsian 90GF 0.556 0.400 0.044 0.756 0.244
HapMap-JPTAsian 90GF 0.244 0.444 0.311 0.467 0.533
HapMap-YRISub-Saharan African 120GF 0.167 0.517 0.317 0.425 0.575

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.482+/-0.0942702102700

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqUNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .