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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs550712          
refSNP ID: rs550712
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:83/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/C
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_004437.2:c.1668+663C>A
NM_203342.1:c.1827+663C>A
NM_203343.1:c.2229+663C>A
NT_004610.18:g.12263965C>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 ss16386905 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs550712 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
ss721643SC_JCM|AC025145.2_74020fwd/TA/Cgagagtgggttgatctagataatttctgggctgagtgctaaaattctatatttttatgtt07/27/0010/10/0383Genomicunknown
ss1660551KWOK|OVLP-000925-511322fwd/TA/Cgagagtgggttgatctagataatttctgggctgagtgctaaaattctatatttttatgtt10/05/0010/10/0387Genomic84 %
ss1660558KWOK|OVLP-000925-515114fwd/TA/Cgagagtgggttgatctagataatttctgggctgagtgctaaaattctatatttttatgtt10/05/0010/10/0387Genomic84 %
ss11406563WI_SSAHASNP|chr1.NT_004538.14_632579fwd/TA/Cgagagtgggttgatctagataatttctgggctgagtgctaaaattctatatttttatgtt07/03/0310/10/03116Genomicunknown
ss16386905CSHL-HAPMAP|CSHL-HuAA-200402.chr1.NT_004538.15_628929byFreqfwd/TA/Cgagagtgggttgatctagataatttctgggctgagtgctaaaattctatatttttatgtt02/17/0410/26/06120Genomicunknown
ss19097321CSHL-HAPMAP|CSHL-HuDD-200402.chr1.NT_004538.15_628929fwd/TA/Cgagagtgggttgatctagataatttctgggctgagtgctaaaattctatatttttatgtt02/20/0403/04/04120Genomicunknown
ss20454991SSAHASNP|WGSA-200403-chr1.chr1.NT_004538.15_628929fwd/TA/Cgagagtgggttgatctagataatttctgggctgagtgctaaaattctatatttttatgtt03/18/0403/18/04121Genomicunknown
ss23859278PERLEGEN|afd4540192byFreqfwd/TA/Cgagagtgggttgatctagataatttctgggctgagtgctaaaattctatatttttatgtt08/10/0409/13/04123Genomicunknown
ss75149582ILLUMINA|ILMN_Human_1M_rs550712fwd/TA/Cgagagtgggttgatctagataatttctgggctgagtgctaaaattctatatttttatgtt08/28/0708/29/07129Genomicunknown
ss77178064HGSV|Cor12156_SNV_20070510.chr1_29260239fwd/TA/Cgagagtgggttgatctagataatttctgggctgagtgctaaaattctatatttttatgtt10/09/0710/11/07129Genomicunknown
ss87324213BCMHGSC_JDW|JWB-0028023fwd/TA/Cgagagtgggttgatctagataatttctgggctgagtgctaaaattctatatttttatgtt02/26/0802/26/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs550712|allelePos=480|totalLen=708|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=129
 AGCCAGGAAA TGTAATGGAA AGAACATGAG CTTTGGATTC CAAGACTTGA TTCAATTGCT
 GGTTCTTAAT ATATTCTAGC TGttaactct ctgggcctcc attttgcatc tgtaagatga
 agatgatagt atctccctct cagggttgtt gtgagaatca ggtgaaatac tggatgaaca
 gctggtggca catggtgagc tcagttaaat ggagctattg ttATTCCGAA GGTAAAGGTA
 CCTGAACCCA TGCTAGACAA CATCAAAACA AAGGGAAGCA TGCCCCTACC CTTAGAGAGC
 TGTAACAGCC GAGAAGACAC GAGCGGGAGC ATAGTATGGT GGACAAGACA CCAGCAGACT
 Cgaaacttgt tttctgccct acatctctaa cttgctgtgt gaccttgggc aaatcacttt
 tccgctgatt tttttctcct ttcctaaaag agagtgggtt gatctagata atttctggg
 M
 ctgagtgcta aaattctata tttttatgTT AATTGGGTGC TAATTGTGTG CTGCAAGCAA
 TTAGCAAATA ATAAGGTCAG GATTAATGTT CCCAGTTCTC TGCTGGGTGA GGTTAGAACA
 GTAAAGCTGC AGAGAAGAGG GGGTGGAAGA GATTGCATGC AAATGCTTCT GGAATCGTTG
 ACTGGGTTGC TGGAGCAATA ATTCTGTGGC CTTTTTATGC TGATATGC

  GeneView back to top
GeneView via analysis of contig annotation: EPB41 erythrocyte membrane protein band 4.1 (elliptocytosis 1, RH-linked)
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_004610->NM_004437
svfunction
referenceNT_004610->NM_203342
svfunction
referenceNT_004610->NM_203343
svfunction
HuRefNW_001838576->NM_004437
svfunction
HuRefNW_001838576->NM_203342
svfunction
HuRefNW_001838576->NM_203343
svfunction
CeleraNW_921351->NM_004437
svfunction
CeleraNW_921351->NM_203342
svfunction
CeleraNW_921351->NM_203343
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_004610->NM_004437->NP_00442812263965forwardintron
referenceNT_004610->NM_203342->NP_97621712263965forwardintron
referenceNT_004610->NM_203343->NP_97621812263965forwardintron
HuRefNW_001838576->NM_004437->NP_0044283336561forwardintron
HuRefNW_001838576->NM_203342->NP_9762173336561forwardintron
HuRefNW_001838576->NM_203343->NP_9762183336561forwardintron
CeleraNW_921351->NM_004437->NP_0044283696630forwardintron
CeleraNW_921351->NM_203342->NP_9762173696630forwardintron
CeleraNW_921351->NM_203343->NP_9762183696630forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs550712 maps exactly once on NCBI human chromosome 1
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
1NW_001838576.1333656127691739plusAalt_assembly_8HuRefHuRefview479
1NW_921351.1369663027835772plusAalt_assembly_1CeleraCeleraview479
1NT_004610.181226396529312210plusCref_assemblyreferencereferenceview479

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_004538 AL354986 AL354986.3 AL357500.5
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AL357500.17 NC_000001.9 AC135897.1 AL354986.4 AL513012.4

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/C
C/C
HWPA
C
ss16386905HapMap-CEUEuropean 120IG 0.617 0.300 0.083 0.251 0.767 0.233
HapMap-HCBAsian 90IG 0.200 0.489 0.311 1.000 0.444 0.556
HapMap-JPTAsian 90IG 0.200 0.489 0.311 1.000 0.444 0.556
HapMap-YRISub-Saharan African 120IG 0.133 0.400 0.467 0.439 0.333 0.667
ss23859278AFD_EUR_PANELEuropean 48IG 0.625 0.333 0.042 1.000 0.792 0.208
AFD_AFR_PANELAfrican American 46IG 0.174 0.478 0.348 1.000 0.413 0.587
AFD_CHN_PANELAsian 48IG 0.292 0.458 0.250 0.752 0.521 0.479

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.499+/-0.02333226090

  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 .