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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2274327          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/130
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_001215.2:c.164C>T
NP_001206.2:p.Thr55Met
NT_021937.18:g.3546773C>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 ss76894700 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2274327 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
ss3210072YUSUKE|IMS-JST070156byFreqfwd/BC/Tagagacagtcgcctatcaacctacagaggagaaggtgcggtacaacccctccttgaaggg09/05/0110/10/03100Genomicunknown
ss24241367PERLEGEN|afd0985576byFreqfwd/BC/Tagagacagtcgcctatcaacctacagaggagaaggtgcggtacaacccctccttgaaggg08/10/0409/13/04123Genomicunknown
ss44036472ABI|hCV1739308byFreqfwd/BC/Tagagacagtcgcctatcaacctacagaggagaaggtgcggtacaacccctccttgaaggg07/18/0511/03/06126Genomicunknown
ss48420280APPLERA_GI|hCV1739308byFreqfwd/BC/Tagagacagtcgcctatcaacctacagaggagaaggtgcggtacaacccctccttgaaggg09/28/0511/03/06126Genomicunknown
ss65726461ILLUMINA|Human1-rs2274327fwd/BC/Tagagacagtcgcctatcaacctacagaggagaaggtgcggtacaacccctccttgaaggg10/10/0610/10/06127Genomicunknown
ss66151801AFFY|SNP_A-2135926byFreqfwd/BC/Tatcaacctacagaggagaaggtgcggtacaac10/27/0608/14/07127Genomicunknown
ss66644487ILLUMINA|HumanHap300v1.1_rs2274327fwd/TC/Tagagacagtcgcctatcaacctacagaggagaaggtgcggtacaacccctccttgaaggg11/09/0611/09/06127Genomicunknown
ss67240346ILLUMINA|HumanHap550v1.1_rs2274327fwd/BC/Tagagacagtcgcctatcaacctacagaggagaaggtgcggtacaacccctccttgaaggg11/14/0611/14/06127Genomicunknown
ss67636978ILLUMINA|HumanHap650Yv1.0_rs2274327fwd/BC/Tagagacagtcgcctatcaacctacagaggagaaggtgcggtacaacccctccttgaaggg11/14/0611/14/06127Genomicunknown
ss68758121PERLEGEN|PGP00985576byFreqfwd/BC/Tagagacagtcgcctatcaacctacagaggagaaggtgcggtacaacccctccttgaaggg01/30/0708/14/07127Genomicunknown
ss70718686ILLUMINA|HumanHap550v3.0__rs2274327rev/TA/Gcccttcaaggaggggttgtaccgcaccttctcctctgtaggttgataggcgactgtctct04/20/0703/30/08130Genomicunknown
ss71286899ILLUMINA|HumanHap650Yv3.0_rs2274327fwd/BC/Tagagacagtcgcctatcaacctacagaggagaaggtgcggtacaacccctccttgaaggg04/23/0704/23/07127Genomicunknown
ss75523904ILLUMINA|ILMN_Human_1M_rs2274327fwd/BC/Tagagacagtcgcctatcaacctacagaggagaaggtgcggtacaacccctccttgaaggg08/28/0708/29/07129Genomicunknown
ss76182378AFFY|AFFY_6_1M_SNP_A-2135926fwd/BC/Tatcaacctacagaggagaaggtgcggtacaac08/28/0708/30/07129Genomicunknown
ss76894700SI_EXO|NT_021937.18_3546773fwd/BC/Tagagacagtcgcctatcaacctacagaggagaaggtgcggtacaacccctccttgaaggg09/20/0709/20/07129Genomicunknown
ss79125165ILLUMINA|HumanHap300v2.0_rs2274327fwd/BC/Tagagacagtcgcctatcaacctacagaggagaaggtgcggtacaacccctccttgaaggg04/18/0711/18/07130Genomicunknown
ss84015993KRIBB_YJKIM|KHS602640fwd/BC/Tagagacagtcgcctatcaacctacagaggagaaggtgcggtacaacccctccttgaaggg12/04/0712/06/07130Genomicunknown
ss99185006HUMANGENOME_JCVI|1103675017482fwd/BC/Tagagacagtcgcctatcaacctacagaggagaaggtgcggtacaacccctccttgaaggg04/03/0804/03/08130Genomicunknown
ss1079804611000GENOMES|CEU.trio.12.15.2008_11331_chr1_8931993fwd/BC/Tagagacagtcgcctatcaacctacagaggagaaggtgcggtacaacccctccttgaaggg12/15/0812/15/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2274327|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GTGACACAGC GAGACCCTGT CTCAAAAAAA AAAAAAAAAG ACTTCCATTG ATTTCAAAAC
 ACTGTCTTGC TCCCAGGGCC AGCAGTTGCC ACAGGAAAGT TAGAGGTTAG CACCAAAGCC
 CCCCAAACAC CAGAGTCCTT GGAGTTGACC TCGTTGTCTT TTTGGCCTCC TTCTGGGGGA
 CCTGCTTCTG CTTTCTGGAA GGTGCCTCCG TGGGTCCCCG CCCAGCAGGC CCTGGCCTCT
 GGCCTCTGGC CTGGTGAGGT TCCTCCAGAG TGGGCGCAGC CAGGCAGCCC CTTGAACTGT
 GTCTTTCCTG TCTTAGAAGG GGCACTGGAC GAAGCGCACT GGCCACAGCA CTACCCCGCC
 TGTGGGGGCC AGAGACAGTC GCCTATCAAC CTACAGAGGA
 Y
 GAAGGTGCGG TACAACCCCT CCTTGAAGGG GCTCAATATG ACAGGCTATG AGACCCAGGC
 AGGGGAGTTC CCCATGGTCA ACAATGGCCA CACAGGTAAG AGGAAGGGGT GGTGAGGGGC
 TCCAGTCCAT GGGCAGCCTG CAGGGGAAGG CAGGTTACAC GTGTCCCTGC CAGGAATGGC
 TTGCACAGAG ACACAGAGCA CGGCCTCAGA GCTGGAGGCC TCGAACATGA GGGTCGAACA
 TGAGGGCTGA CTGGCCCCGA AACCTAGTGG CTCTTCCAGA GAGGGCAGCA TCCATCTTTC
 GACTCAACTC CCTGCTGGTC CCTTCCTGCA GCGTTATCCT CTTACCCGAG CTCACCCAAC
 CCACCCAGCA GGTGACAGGC AGGACAGGCC GTGCTGCTGA

  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_021937.18 ABBA01035528
dbSNP Blast Analysis
UniGene Cluster ID
100322

  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
 N
 T
ss24241367 AFD_EUR_PANEL European 48 IG 0.417 0.500 0.083 0.584 0.667 0.333
AFD_AFR_PANEL African American 46 IG 0.696 0.217 0.087 0.150 0.804 0.196
AFD_CHN_PANEL Asian 48 IG 0.625 0.375 0.273 0.812 0.188
CHMJ Asian 74 IG 0.689 0.027 0.284
ss3210072 JBIC-allele 1500 AF 0.743 0.257
ss44036472 HapMap-CEU European 120 IG 0.433 0.467 0.100 0.752 0.667 0.333
HapMap-HCB Asian 90 IG 0.489 0.444 0.067 0.584 0.711 0.289
HapMap-JPT Asian 88 IG 0.636 0.273 0.091 0.150 0.773 0.227
HapMap-YRI Sub-Saharan African 118 IG 0.898 0.102 0.752 0.949 0.051
AoD_African_American 90 AF 0.890 0.110
AoD_Caucasian 92 AF 0.530 0.470
AoD_Chinese 90 AF 0.770 0.230
AoD_Japanese 90 AF 0.850 0.150
ss48420280 AGI_ASP population multiple 72 IG 0.444 0.417 0.139 0.655 0.653 0.347
ss66151801 HapMap-CEU European 118 GF 0.424 0.475 0.102 0.661 0.339
HapMap-HCB Asian 90 GF 0.489 0.444 0.067 0.711 0.289
HapMap-JPT Asian 90 GF 0.644 0.267 0.089 0.778 0.222
HapMap-YRI Sub-Saharan African 120 GF 0.900 0.100 0.950 0.050
ss68758121 HapMap-CEU European 120 GF 0.467 0.433 0.100 0.683 0.317
HapMap-HCB Asian 90 GF 0.489 0.444 0.067 0.711 0.289
HapMap-JPT Asian 90 GF 0.644 0.267 0.089 0.778 0.222
HapMap-YRI Sub-Saharan African 120 GF 0.850 0.133 0.017 0.917 0.083
ss76182378 ICMHP 8 IG 0.750 0.250 0.750 0.250
Concordant Genotype Total Sample C/C C/T T/T
ss24241367 71 41 26 4
ss48420280 38 16 15 5
ss66151801 263 167 81 15
ss68758121 264 168 81 15
ss76182378 6 4 1 1
ss76894700 1201 717 366 80
ss99185006 1 1
RefSNP Genotype Summary Total Individual C/C C/T T/T
rs2274327 1307 784 411 91
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
535 ss66151801 C/T CSHL-HAPMAP HapMap-CEU NA12750 CEPH1444.13 chr1-HapMap-CEU
535 ss68758121 C/C CSHL-HAPMAP HapMap-CEU NA12750 CEPH1444.13 chr1-HapMap-CEU
535 ss76894700 C/T CSHL-HAPMAP HapMap-CEU NA12750 CEPH1444.13 r27_ch1_CEU_illumina:human_1m_beadchip
618 ss66151801 C/T CSHL-HAPMAP HapMap-CEU NA12872 CEPH1459.09 chr1-HapMap-CEU
618 ss68758121 C/C CSHL-HAPMAP HapMap-CEU NA12872 CEPH1459.09 chr1-HapMap-CEU
618 ss76894700 C/T CSHL-HAPMAP HapMap-CEU NA12872 CEPH1459.09 r27_ch1_CEU_illumina:human_1m_beadchip
5249 ss66151801 C/C CSHL-HAPMAP HapMap-YRI NA18516 YOR013.03 chr1-HapMap-YRI
5249 ss68758121 C/T CSHL-HAPMAP HapMap-YRI NA18516 YOR013.03 chr1-HapMap-YRI
5249 ss76894700 C/C CSHL-HAPMAP HapMap-YRI NA18516 YOR013.03 r27_ch1_YRI_illumina:human_1m_beadchip
5276 ss66151801 C/C CSHL-HAPMAP HapMap-YRI NA19138 YOR043.03 chr1-HapMap-YRI
5276 ss68758121 T/T CSHL-HAPMAP HapMap-YRI NA19138 YOR043.03 chr1-HapMap-YRI
5276 ss76894700 N/N CSHL-HAPMAP HapMap-YRI NA19138 YOR043.03 r27_ch1_YRI_illumina:human_1m_beadchip
5277 ss66151801 C/C CSHL-HAPMAP HapMap-YRI NA19202 YOR045.01 chr1-HapMap-YRI
5277 ss68758121 C/T CSHL-HAPMAP HapMap-YRI NA19202 YOR045.01 chr1-HapMap-YRI
5277 ss76894700 C/C CSHL-HAPMAP HapMap-YRI NA19202 YOR045.01 r27_ch1_YRI_illumina:human_1m_beadchip
5278 ss66151801 C/C CSHL-HAPMAP HapMap-YRI NA19201 YOR045.02 chr1-HapMap-YRI
5278 ss68758121 C/T CSHL-HAPMAP HapMap-YRI NA19201 YOR045.02 chr1-HapMap-YRI
5278 ss76894700 C/C CSHL-HAPMAP HapMap-YRI NA19201 YOR045.02 r27_ch1_YRI_illumina:human_1m_beadchip
Genotype data submitted for1322 samples from1307 individualsIndividual with multiple genotypes submission:276

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqWith1000GenomeData UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .