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Reference SNP(refSNP) Cluster Report: rs7566605          **clinically associated**
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/130
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/G
Ancestral Allele:G
Clinical Association:link to VariationViewerlink to OMIM
HGVS Names
NT_022135.15:g.7543947C>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 ss44147645 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs7566605 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
ss11450462WI_SSAHASNP|chr2.NT_022135.13_7543767byFreqfwd/TC/Gctgccaagtacttaacaatggatatttgatgtggtcctttaggtctgtaccagggtggtt07/03/0310/25/06116Genomicunknown
ss14877947PERLEGEN|PS00776426byFreqrev/BC/Gaaccaccctggtacagacctaaaggaccacatcaaatatccattgttaagtacttggcag11/13/0304/07/04119Genomicunknown
ss21633044SSAHASNP|WGSA-200403-chr2.chr2.NT_022135.13_7543767fwd/TC/Gctgccaagtacttaacaatggatatttgatgtggtcctttaggtctgtaccagggtggtt03/20/0403/20/04121Genomicunknown
ss23938610PERLEGEN|afd0776426byFreqfwd/TC/Gctgccaagtacttaacaatggatatttgatgtggtcctttaggtctgtaccagggtggtt08/10/0409/13/04123Genomicunknown
ss44147645ABI|hCV29404113byFreqfwd/C/Gctgccaagtacttaacaatggatatttgatgtggtcctttaggtctgtaccagggtggtt07/18/0511/03/06126Genomicunknown
ss66003987AFFY|SNP_A-1669246rev/BC/Gccctggtacagacctaaaggaccacatcaaatatccattgttaagtactt10/26/0610/26/06127Genomicunknown
ss66096985AFFY|SNP_A-1964628byFreqrev/BC/Gagacctaaaggaccacatcaaatatccattgt10/27/0603/31/08127Genomicunknown
ss68382656CSHL-HAPMAP|perlegen:assay:24708.776426:1byFreqfwd/C/Gctgccaagtacttaacaatggatatttgatgtggtcctttaggtctgtaccagggtggtt01/11/0701/16/07127NAunknown
ss68825460PERLEGEN|PGP00776426byFreqfwd/C/Gctgccaagtacttaacaatggatatttgatgtggtcctttaggtctgtaccagggtggtt01/30/0703/31/08127Genomicunknown
ss76058863AFFY|AFFY_6_1M_SNP_A-1964628rev/C/Gagacctaaaggaccacatcaaatatccattgt08/28/0708/29/07129Genomicunknown
ss77256321HGSV|Cor12156_SNV_20070510.chr2_118552255fwd/C/Gctgccaagtacttaacaatggatatttgatgtggtcctttaggtctgtaccagggtggtt10/09/0710/12/07129Genomicunknown
ss82448141KRIBB_YJKIM|KHS254819fwd/C/Gctgccaagtacttaacaatggatatttgatgtggtcctttaggtctgtaccagggtggtt11/30/0712/02/07130Genomicunknown
ss91312313BCMHGSC_JDW|JWB-1294435fwd/C/Gctgccaagtacttaacaatggatatttgatgtggtcctttaggtctgtaccagggtggtt02/26/0803/01/08129Genomicunknown
ss96420541HUMANGENOME_JCVI|1103658196312fwd/C/Gctgccaagtacttaacaatggatatttgatgtggtcctttaggtctgtaccagggtggtt03/26/0803/26/08130Genomicunknown
ss1098153261000GENOMES|CEU.trio.12.15.2008_452417_chr2_118552495fwd/C/Gctgccaagtacttaacaatggatatttgatgtggtcctttaggtctgtaccagggtggtt12/15/0812/16/08130Genomicunknown
ss1108022011000GENOMES|NA19240_2008_12_16_411696_chr2_118552495fwd/C/Gctgccaagtacttaacaatggatatttgatgtggtcctttaggtctgtaccagggtggtt12/16/0812/17/08130Genomicunknown
ss117842972ILLUMINA-UK|NA18507_000147519_NCBI36.1_chr2_118552495fwd/C/Gctgccaagtacttaacaatggatatttgatgtggtcctttaggtctgtaccagggtggtt01/19/0901/20/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs7566605|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=130
 CTTTCTATAT TTTTAATTGG CAAATTGTAT ATGCGTTTTT ATTAGCTCAC TATGATCGCT
 GAGCTGATAT GGGGAAAAAA ATGGAAACAC AAACTCTGAT TACATTTATT TCAACCGAGA
 GATGAAGGAA ACAAAGGTCC AGATTGGGTA CTAACTGGCT CAAGGTCACC TAGCTAGTTA
 GCTGAAGTAC AAGGACTTGA AGTTGATCTA ATGTTCTCTC TCCTACCTCC CTCCAATACC
 CCATCGGAAT TGAAATCATT GCAATAGCCA CTGCCAAGTA CTTAACAATG GATATTTGAT
 S
 GTGGTCCTTT AGGTCTGTAC CAGGGTGGTT TTCAGTTTTT TACTTCATCA GCACAGGAAG
 GCAAGGACAT CGCACTGACT CTCATATTTC ATCCTTAGCT CTCGATTCCC TTGGTTTTAC
 ATTTCTGACT CTTCCTTCAG TTTCTTGTAG GGCTTTATGA TTTAATTTAA TTTCAGCTTA
 TGGCTGGCTT TGGTACCCAG AAGAGTGGTA ATTTGTCCTT TAAATTATTC ACCCAGGGGA
 GTCGGTGTTC TTAGAAAACG AGGCGGGGAG AACCTATAAG CTTCATCCCA GCAGAGGGAC

  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
NT_022135 ABBA01045944
dbSNP Blast Analysis
OMIM
608660

  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
 N
ss11450462 CHMJ Asian 74 IG 0.405 0.581 0.014
ss14877947 AfAm African American 12 IG 0.167 0.833 0.020 0.167 0.833
Caucasian European 22 IG 0.091 0.455 0.455 1.000 0.318 0.682
Asian Asian 12 IG 0.833 0.167 0.100 0.417 0.583
CEPH European 12 IG 0.167 0.833 1.000 0.083 0.917
PDpanel Global 44 IG 0.091 0.273 0.636 0.317 0.227 0.773
ss23938610 AFD_EUR_PANEL European 48 IG 0.542 0.458 0.100 0.271 0.729
AFD_AFR_PANEL African American 46 IG 0.087 0.304 0.609 0.439 0.239 0.761
AFD_CHN_PANEL Asian 48 IG 0.167 0.375 0.458 0.403 0.354 0.646
ss44147645 HapMap-CEU European 120 IG 0.067 0.417 0.517 0.752 0.275 0.725
HapMap-HCB Asian 90 IG 0.156 0.400 0.444 0.317 0.356 0.644
HapMap-JPT Asian 88 IG 0.159 0.500 0.341 1.000 0.409 0.591
HapMap-YRI Sub-Saharan African 120 IG 0.083 0.300 0.617 0.251 0.233 0.767
ss66096985 HapMap-CEU European 118 GF 0.068 0.407 0.525 0.271 0.729
HapMap-HCB Asian 90 GF 0.156 0.400 0.444 0.356 0.644
HapMap-JPT Asian 90 GF 0.156 0.489 0.356 0.400 0.600
HapMap-YRI Sub-Saharan African 120 GF 0.083 0.300 0.617 0.233 0.767
ss68825460 HapMap-CEU European 120 GF 0.067 0.417 0.517 0.275 0.725
HapMap-HCB Asian 90 GF 0.156 0.400 0.444 0.356 0.644
HapMap-JPT Asian 90 GF 0.156 0.489 0.356 0.400 0.600
HapMap-YRI Sub-Saharan African 120 GF 0.083 0.300 0.617 0.233 0.767
ss76058863 ICMHP 10 IG 0.400 0.600 0.200 0.800

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.421+/-0.183 1314 1096 282 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .