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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs772436          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NT_005334.15:g.2667956C>T
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 ss1458404 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs772436 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
ss884175KWOK|OVLP-000804-68763rev/TA/Gtgcaggtcacttattttggaaagtggaatcgaaaagagtaatataagaaaggaagtagag09/01/0010/10/0386Genomic99 %
ss1458404TSC-CSHL|TSC0013222byFreqfwd/BC/Tctctacttcctttcttatattactcttttcgattccactttccaaaataagtgacctgca09/07/0004/07/0492Genomic95 %
ss2558949SC_JCM|AC072053.1_105447rev/TA/Gtgcaggtcacttattttggaaagtggaatcgaaaagagtaatataagaaaggaagtagag11/03/0010/10/0392Genomicunknown
ss5157193TSC-CSHL|TSC0220503rev/TA/Gtgcaggtcacttattttggaaagtggaatcgaaaagagtaatataagaaaggaagtagag09/19/0210/10/03108Genomicunknown
ss5509183TSC-CSHL|TSC0588827rev/TA/Gtgcaggtcacttattttggaaagtggaatcgaaaagagtaatataagaaaggaagtagag09/21/0210/10/03108Genomicunknown
ss9944046BCM_SSAHASNP|chr2.NT_005334.13_2660515fwd/BC/Tctctacttcctttcttatattactcttttcgattccactttccaaaataagtgacctgca06/27/0310/10/03116Genomicunknown
ss24251704PERLEGEN|afd1223397byFreqfwd/BC/Tctctacttcctttcttatattactcttttcgattccactttccaaaataagtgacctgca08/10/0409/13/04123Genomicunknown
ss44342820ABI|hCV8349946byFreqfwd/BC/Tctctacttcctttcttatattactcttttcgattccactttccaaaataagtgacctgca07/18/0511/03/06126Genomicunknown
ss65943881AFFY|SNP_A-1683146rev/TA/Ggtcacttattttggaaagtggaatcgaaaagagtaatataagaaaggaag10/26/0610/26/06127Genomicunknown
ss66096153AFFY|SNP_A-1962014byFreqrev/TA/Gtttggaaagtggaatcgaaaagagtaatataa10/27/0608/14/07127Genomicunknown
ss66851919ILLUMINA|HumanHap300v1.1_rs772436fwd/TC/Tctctacttcctttcttatattactcttttcgattccactttccaaaataagtgacctgca11/09/0611/09/06127Genomicunknown
ss67822846ILLUMINA|HumanHap550v1.1_rs772436fwd/BC/Tctctacttcctttcttatattactcttttcgattccactttccaaaataagtgacctgca11/14/0611/14/06127Genomicunknown
ss67986278ILLUMINA|HumanHap650Yv1.0_rs772436fwd/BC/Tctctacttcctttcttatattactcttttcgattccactttccaaaataagtgacctgca11/14/0611/15/06127Genomicunknown
ss68403386CSHL-HAPMAP|perlegen:assay:24707.1223397:1byFreqfwd/BC/Tctctacttcctttcttatattactcttttcgattccactttccaaaataagtgacctgca01/11/0701/16/07127NAunknown
ss70945890ILLUMINA|HumanHap550v3.0__rs772436rev/TA/Gtgcaggtcacttattttggaaagtggaatcgaaaagagtaatataagaaaggaagtagag04/20/0703/31/08130Genomicunknown
ss71550793ILLUMINA|HumanHap650Yv3.0_rs772436fwd/BC/Tctctacttcctttcttatattactcttttcgattccactttccaaaataagtgacctgca04/23/0704/23/07127Genomicunknown
ss75920140ILLUMINA|ILMN_Human_1M_rs772436fwd/BC/Tctctacttcctttcttatattactcttttcgattccactttccaaaataagtgacctgca08/28/0708/29/07129Genomicunknown
ss76056835AFFY|AFFY_6_1M_SNP_A-1962014rev/TA/Gtttggaaagtggaatcgaaaagagtaatataa08/28/0708/29/07129Genomicunknown
ss79267812ILLUMINA|HumanHap300v2.0_rs772436fwd/BC/Tctctacttcctttcttatattactcttttcgattccactttccaaaataagtgacctgca04/18/0711/18/07130Genomicunknown
ss83559737KRIBB_YJKIM|KHS489799fwd/BC/Tctctacttcctttcttatattactcttttcgattccactttccaaaataagtgacctgca12/04/0712/05/07130Genomicunknown
ss91047007BCMHGSC_JDW|JWB-1197007fwd/BC/Tctctacttcctttcttatattactcttttcgattccactttccaaaataagtgacctgca02/26/0803/01/08129Genomicunknown
ss1092043401000GENOMES|CEU.trio.12.15.2008_309809_chr2_7751272fwd/BC/Tctctacttcctttcttatattactcttttcgattccactttccaaaataagtgacctgca12/15/0812/16/08130Genomicunknown
ss1122418641000GENOMES|NA19240_2008_12_16_281686_chr2_7751272fwd/BC/Tctctacttcctttcttatattactcttttcgattccactttccaaaataagtgacctgca12/16/0812/17/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs772436|allelePos=89|totalLen=848|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CCCAGGTATC CCCAGTCACC ACCGGCAGTA ATCAGCTTGG TAAACACCCC TAGTTTACCT
 CTACTTCCTT TCTTATATTA CTCTTTTC
 Y
 GATTCCACTT TCCAAAATAA GTGACCTGCA TCCACACCCT GCCTGAAGCT CTGCTTTTTG
 GGCTCTACTG GCTAAGACAG AGGCCACTTG ATACTGACCT TCATATTTAT GTGCAGCCTT
 GGCCCCTGGC TTATCTGCAG ATACATTCCA CGATTTGCGT CACATACATC AAATCTAACG
 AACAATTCCC ACTATGTAGC CTAAGTTACA CCTGTATTAG ATATTGAGGA TCTACCAGTG
 CCAATGAATC ATCCTTATCT CCAAGAAACT CTCACTTTAG TGTGGAAGAC AGATAGGCAA
 ATGGGCAGTT ACAGTGGGGA GGAATCCTTC ATGCTGCAAT TCAGTAAAGA TCATGTTCTT
 TCATCCTGAG CAACAGTAAT TTCCACTCAC CTCTGTATGC GGAGAAAGCC TCAGATGAGG
 CTATTTGCCA ATTAGTCAGT TAAAATGGAG AAACAGAACA TCTGACCAGT CTGCCCTTAG
 ACAGTACCCA TCCACGAGGA TATACAGTGT CCCCCGCCCC GGGCTCACAC AGGCATGATA
 CTCTTGTCCA CCAAGGCTCC AGGGCCCTCA GCCACACCCT TTCGATTAGA GTAAACAGGA
 AACTACTATC AACTGTCACA TTGCACATTC ACAATGAAAC CTATTTTCCT GGGTAAAAAC
 TCGGCATTAT ATAGATAAGA AACCAGCCCA GGGAAGGGGA GGGACTTCCC CAAGGAAAAC
 TGCCAATTAA TAACGGGTTT AGACAAGAAC CTTGGCTAC

  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_005334 AC011936 AC072053.1
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP C
 T
ss1458404 TSC_42_AA 82 AF 0.634 0.366
TSC_42_C 84 AF 0.310 0.690
TSC_42_A 82 AF 0.720 0.280
AfAm African American 8 IG 0.500 0.500 0.250 0.750
Caucasian European 24 IG 0.417 0.583 0.371 0.208 0.792
Asian Asian 10 IG 1.000 0.050 0.500 0.500
CEPH European 12 IG 0.167 0.500 0.333 1.000 0.417 0.583
PDpanel Global 38 IG 0.211 0.579 0.211 0.527 0.500 0.500
HapMap-CEU European 120 IG 0.083 0.433 0.483 1.000 0.300 0.700
HapMap-HCB Asian 90 IG 0.422 0.489 0.089 0.479 0.667 0.333
HapMap-JPT Asian 88 IG 0.591 0.341 0.068 0.655 0.761 0.239
HapMap-YRI Sub-Saharan African 120 IG 0.583 0.400 0.017 0.200 0.783 0.217
ss24251704 AFD_EUR_PANEL European 48 IG 0.167 0.542 0.292 0.655 0.438 0.562
AFD_AFR_PANEL African American 46 IG 0.565 0.217 0.217 0.020 0.674 0.326
AFD_CHN_PANEL Asian 48 IG 0.625 0.333 0.042 1.000 0.792 0.208
ss44342820 AoD_African_American 90 AF 0.680 0.320
AoD_Caucasian 92 AF 0.270 0.730
ss66096153 HapMap-CEU European 118 GF 0.085 0.441 0.475 0.305 0.695
HapMap-HCB Asian 90 GF 0.422 0.489 0.089 0.667 0.333
HapMap-JPT Asian 90 GF 0.578 0.356 0.067 0.756 0.244
HapMap-YRI Sub-Saharan African 120 GF 0.583 0.400 0.017 0.783 0.217
ss76056835 ICMHP 10 IG 0.200 0.200 0.600 0.300 0.700
Concordant Genotype Total Sample C/C C/T T/T
ss1458404 1252 555 479 195
ss24251704 71 32 26 13
ss66096153 268
ss76056835 5
RefSNP Genotype Summary Total Individual C/C C/T T/T
rs772436 1310 584 497 204
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
5229 ss1458404 N/N CSHL-HAPMAP HapMap-JPT NA18992 JA18992 r27_ch2_JPT_illumina:human_1m_beadchip
5229 ss66096153 A/G CSHL-HAPMAP HapMap-JPT NA18992 JA18992 chr2-HapMap-JPT
Genotype data submitted for1329 samples from1310 individualsIndividual with multiple genotypes submission:279

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .