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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2071561          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:96/130
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_002278.3:c.665C>A
NP_002269.3:p.Ser222Tyr
NT_010755.15:g.3346364G>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 ss78143570 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2071561 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
ss2985222YUSUKE|IMS-JST007093byFreqfwd/TA/Cgcaaggctgacctggaggcccaggttgagtcctgaaggaggagctgatgtgcctcaaaaa05/24/0110/10/0396Genomicunknown
ss3186606HGBASE|SNP000572190fwd/TA/Cgctgacctggaggcccaggttgagtcctgaaggaggagctgatgtgcctc07/09/0110/10/0398Genomicunknown
ss24098671PERLEGEN|afd4229180byFreqrev/BG/Ttttttgaggcacatcagctcctccttcaggactcaacctgggcctccaggtcagccttgc08/10/0409/13/04123Genomicunknown
ss65726148ILLUMINA|Human1-rs2071561fwd/TA/Cgcaaggctgacctggaggcccaggttgagtcctgaaggaggagctgatgtgcctcaaaaa10/10/0610/10/06127Genomicunknown
ss69196309PERLEGEN|PGP04229180byFreqrev/BG/Ttttttgaggcacatcagctcctccttcaggactcaacctgggcctccaggtcagccttgc01/30/0708/14/07127Genomicunknown
ss74806067AFFY|SNP_M-174503fwd/TA/Cgcaaggctgacctggaggcccaggttgagtcctgaaggaggagctgatgtgcctcaaaaa08/09/0708/09/07128Genomicunknown
ss78143570HGSV|Cor12878_SNV_20070510.chr17_36875594rev/BG/Ttttttgaggcacatcagctcctccttcaggactcaacctgggcctccaggtcagccttgc10/17/0710/18/07129Genomicunknown
ss81904843HGSV|Cor18555_SNV_20070510.chr17_36875594rev/BG/Ttttttgaggcacatcagctcctccttcaggactcaacctgggcctccaggtcagccttgc11/27/0712/01/07130Genomicunknown
ss90587795BCMHGSC_JDW|JWB-1021258rev/BG/Ttttttgaggcacatcagctcctccttcaggactcaacctgggcctccaggtcagccttgc02/26/0802/29/08129Genomicunknown
ss103345971BGI|BGI_rs2071561rev/BG/Ttttttgaggcacatcagctcctccttcaggactcaacctgggcctccaggtcagccttgc06/06/0806/18/09130Genomicunknown
ss1097632021000GENOMES|CEU.trio.12.15.2008_3398549_chr17_36875594rev/BG/Ttttttgaggcacatcagctcctccttcaggactcaacctgggcctccaggtcagccttgc12/15/0812/16/08130Genomicunknown
ss118054007ILLUMINA-UK|NA18507_000043068_NCBI36.1_chr17_36875594rev/BG/Ttttttgaggcacatcagctcctccttcaggactcaacctgggcctccaggtcagccttgc01/20/0901/20/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2071561|allelePos=201|totalLen=567|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=130
 GAGGGTTGGA AAGTGCCGGC AGTTTAAGGC CTTCCCTGAG TTCTGCATTC TGTTTCACCC
 TTGGTTGCTG ACCCTGTCCT TGTGCAGGTA CGAGGCAGAG CTGGCCATGC GGCAGCTGGT
 GGAGGCCGAC ATCAATGGCC TGCGCAGGAT CCTGGATGAT CTCACTCTGT GCAAGGCTGA
 CCTGGAGGCC CAGGTTGAGT
 M
 CCTGAAGGAG GAGCTGATGT GCCTCAAAAA GAACCATGAG GAGGTGAGGC TGGAAGTCCC
 GCTGAAGTGG CCCCGGGAAG CAGAGGGGGA GGAACGTGGG GTATGGGGTT GGATAGGCGT
 GGGTTGAAAT TCCCAAGCCT GCCACATGTT GTTTTAGTGA CTTTGCCCAA TTTATGGAAT
 CTTCCTGAGC CTCCTCTTCT GTAAAATGGG GACAACATGA TCACGCAGGG TTATTGTGAG
 GATTTAATGG ACAGGATATG GATCATGGAA ATCCCCAAGG CATGGGTATG AAACACCTGC
 CACTTGGTCA ACTCTCAGAA GTGTAGCCCC CTTCCCTTCT GCATTTCCTG GGCTAGTGTG
 ACTGCC

  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
X90761.1
dbSNP Blast Analysis
UniGene Cluster ID
41752

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/C
 C/C
 HWP A
 C
 N
ss24098671 AFD_EUR_PANEL European 46 IG 0.130 0.609 0.261 0.254 0.435 0.565
AFD_AFR_PANEL African American 46 IG 0.391 0.609 0.251 0.196 0.804
AFD_CHN_PANEL Asian 48 IG 0.250 0.625 0.125 0.200 0.562 0.438
HapMap-CEU European 120 IG 0.267 0.533 0.200 0.584 0.533 0.467
HapMap-HCB Asian 90 IG 0.244 0.667 0.089 0.020 0.578 0.422
HapMap-JPT Asian 88 IG 0.409 0.477 0.114 1.000 0.648 0.352
HapMap-YRI Sub-Saharan African 120 IG 0.050 0.333 0.617 1.000 0.217 0.783
CHMJ Asian 74 IG 0.514 0.338 0.149
ss2985222 JBIC-allele 1498 AF 0.585 0.415
ss69196309 HapMap-CEU European 120 GF 0.183 0.600 0.217 0.483 0.517
HapMap-HCB Asian 90 GF 0.067 0.556 0.378 0.344 0.656
HapMap-JPT Asian 90 GF 0.200 0.556 0.244 0.478 0.522
HapMap-YRI Sub-Saharan African 120 GF 0.017 0.333 0.650 0.183 0.817
Concordant Genotype Total Sample A/A A/C C/C
ss24098671 69
ss78143570 452
RefSNP Genotype Summary Total Individual A/A A/C C/C
rs2071561 581
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
157 ss78143570 G/G CSHL-HAPMAP HapMap-CEU NA12144 CEPH1334.10 r27_ch17_CEU_illumina:golden_gate_1.0.0
159 ss78143570 G/T CSHL-HAPMAP HapMap-CEU NA12146 CEPH1334.12 r27_ch17_CEU_illumina:golden_gate_1.0.0
161 ss78143570 T/T CSHL-HAPMAP HapMap-CEU NA07029 CEPH1340.01 r27_ch17_CEU_illumina:golden_gate_1.0.0
171 ss78143570 G/T CSHL-HAPMAP HapMap-CEU NA07022 CEPH1340.11 r27_ch17_CEU_illumina:golden_gate_1.0.0
185 ss78143570 T/T CSHL-HAPMAP HapMap-CEU NA07055 CEPH1341.12 r27_ch17_CEU_illumina:golden_gate_1.0.0
186 ss78143570 T/T CSHL-HAPMAP HapMap-CEU NA06993 CEPH1341.13 r27_ch17_CEU_illumina:golden_gate_1.0.0
199 ss78143570 G/T CSHL-HAPMAP HapMap-CEU NA12056 CEPH1344.12 r27_ch17_CEU_illumina:golden_gate_1.0.0
200 ss78143570 T/T CSHL-HAPMAP HapMap-CEU NA12057 CEPH1344.13 r27_ch17_CEU_illumina:golden_gate_1.0.0
214 ss78143570 G/G CSHL-HAPMAP HapMap-CEU NA07345 CEPH1345.13 r27_ch17_CEU_illumina:golden_gate_1.0.0
225 ss78143570 T/T CSHL-HAPMAP HapMap-CEU NA12043 CEPH1346.11 r27_ch17_CEU_illumina:golden_gate_1.0.0
239 ss78143570 G/T CSHL-HAPMAP HapMap-CEU NA11882 CEPH1347.15 r27_ch17_CEU_illumina:golden_gate_1.0.0
242 ss24098671 T/T PERLEGEN AFD_EUR_PANEL NA10854 71_IND_CHR_17 846088
242 ss78143570 T/T CSHL-HAPMAP HapMap-CEU NA10854 CEPH1349.02 r27_ch17_CEU_illumina:golden_gate_1.0.0
253 ss78143570 T/T CSHL-HAPMAP HapMap-CEU NA11840 CEPH1349.14 r27_ch17_CEU_illumina:golden_gate_1.0.0
254 ss78143570 T/T CSHL-HAPMAP HapMap-CEU NA10856 CEPH1350.01 r27_ch17_CEU_illumina:golden_gate_1.0.0
363 ss78143570 T/T CSHL-HAPMAP HapMap-CEU NA11995 CEPH1362.16 r27_ch17_CEU_illumina:golden_gate_1.0.0
373 ss78143570 T/T CSHL-HAPMAP HapMap-CEU NA12264 CEPH1375.11 r27_ch17_CEU_illumina:golden_gate_1.0.0
400 ss24098671 G/G PERLEGEN AFD_EUR_PANEL NA10831 71_IND_CHR_17 846088
400 ss78143570 G/G CSHL-HAPMAP HapMap-CEU NA10831 CEPH1408.02 r27_ch17_CEU_illumina:golden_gate_1.0.0
411 ss78143570 G/G CSHL-HAPMAP HapMap-CEU NA12156 CEPH1408.13 r27_ch17_CEU_illumina:golden_gate_1.0.0
457 ss78143570 G/G CSHL-HAPMAP HapMap-CEU NA10839 CEPH1420.02 r27_ch17_CEU_illumina:golden_gate_1.0.0
538 ss78143570 G/G CSHL-HAPMAP HapMap-CEU NA12753 CEPH1447.02 r27_ch17_CEU_illumina:golden_gate_1.0.0
545 ss78143570 G/T CSHL-HAPMAP HapMap-CEU NA12760 CEPH1447.09 r27_ch17_CEU_illumina:golden_gate_1.0.0
548 ss78143570 G/T CSHL-HAPMAP HapMap-CEU NA12763 CEPH1447.12 r27_ch17_CEU_illumina:golden_gate_1.0.0
566 ss78143570 G/T CSHL-HAPMAP HapMap-CEU NA12802 CEPH1454.02 r27_ch17_CEU_illumina:golden_gate_1.0.0
623 ss78143570 G/T CSHL-HAPMAP HapMap-CEU NA12878 CEPH1463.02 r27_ch17_CEU_illumina:golden_gate_1.0.0
5135 ss78143570 G/T CSHL-HAPMAP HapMap-YRI NA19128 YOR077.03 r27_ch17_YRI_illumina:golden_gate_1.0.0
5137 ss78143570 G/T CSHL-HAPMAP HapMap-YRI NA19131 YOR101.02 r27_ch17_YRI_illumina:golden_gate_1.0.0
5140 ss78143570 G/T CSHL-HAPMAP HapMap-YRI NA19099 YOR105.02 r27_ch17_YRI_illumina:golden_gate_1.0.0
5146 ss78143570 G/G CSHL-HAPMAP HapMap-YRI NA19238 YOR117.02 r27_ch17_YRI_illumina:golden_gate_1.0.0
5148 ss78143570 T/T CSHL-HAPMAP HapMap-HCB NA18526 CH18526 r27_ch17_CHB_illumina:golden_gate_1.0.0
5149 ss78143570 G/T CSHL-HAPMAP HapMap-HCB NA18524 CH18524 r27_ch17_CHB_illumina:golden_gate_1.0.0
5150 ss78143570 G/T CSHL-HAPMAP HapMap-HCB NA18529 CH18529 r27_ch17_CHB_illumina:golden_gate_1.0.0
5151 ss78143570 T/T CSHL-HAPMAP HapMap-HCB NA18558 CH18558 r27_ch17_CHB_illumina:golden_gate_1.0.0
5152 ss78143570 G/T CSHL-HAPMAP HapMap-HCB NA18532 CH18532 r27_ch17_CHB_illumina:golden_gate_1.0.0
5156 ss78143570 G/T CSHL-HAPMAP HapMap-HCB NA18603 CH18603 r27_ch17_CHB_illumina:golden_gate_1.0.0
5157 ss78143570 T/T CSHL-HAPMAP HapMap-HCB NA18540 CH18540 r27_ch17_CHB_illumina:golden_gate_1.0.0
5158 ss78143570 G/T CSHL-HAPMAP HapMap-HCB NA18605 CH18605 r27_ch17_CHB_illumina:golden_gate_1.0.0
5160 ss78143570 G/T CSHL-HAPMAP HapMap-HCB NA18545 CH18545 r27_ch17_CHB_illumina:golden_gate_1.0.0
5163 ss78143570 G/T CSHL-HAPMAP HapMap-HCB NA18609 CH18609 r27_ch17_CHB_illumina:golden_gate_1.0.0
5164 ss78143570 T/T CSHL-HAPMAP HapMap-HCB NA18550 CH18550 r27_ch17_CHB_illumina:golden_gate_1.0.0
5165 ss78143570 T/T CSHL-HAPMAP HapMap-HCB NA18608 CH18608 r27_ch17_CHB_illumina:golden_gate_1.0.0
5168 ss78143570 T/T CSHL-HAPMAP HapMap-HCB NA18555 CH18555 r27_ch17_CHB_illumina:golden_gate_1.0.0
5171 ss78143570 T/T CSHL-HAPMAP HapMap-HCB NA18563 CH18563 r27_ch17_CHB_illumina:golden_gate_1.0.0
5173 ss78143570 G/T CSHL-HAPMAP HapMap-HCB NA18612 CH18612 r27_ch17_CHB_illumina:golden_gate_1.0.0
5174 ss78143570 G/G CSHL-HAPMAP HapMap-HCB NA18571 CH18571 r27_ch17_CHB_illumina:golden_gate_1.0.0
5175 ss78143570 T/T CSHL-HAPMAP HapMap-HCB NA18620 CH18620 r27_ch17_CHB_illumina:golden_gate_1.0.0
5182 ss78143570 G/T CSHL-HAPMAP HapMap-HCB NA18577 CH18577 r27_ch17_CHB_illumina:golden_gate_1.0.0
5185 ss78143570 G/T CSHL-HAPMAP HapMap-HCB NA18632 CH18632 r27_ch17_CHB_illumina:golden_gate_1.0.0
5187 ss78143570 G/T CSHL-HAPMAP HapMap-HCB NA18633 CH18633 r27_ch17_CHB_illumina:golden_gate_1.0.0
5188 ss78143570 G/T CSHL-HAPMAP HapMap-HCB NA18635 CH18635 r27_ch17_CHB_illumina:golden_gate_1.0.0
5190 ss78143570 G/T CSHL-HAPMAP HapMap-HCB NA18636 CH18636 r27_ch17_CHB_illumina:golden_gate_1.0.0
5191 ss78143570 G/T CSHL-HAPMAP HapMap-HCB NA18593 CH18593 r27_ch17_CHB_illumina:golden_gate_1.0.0
5196 ss78143570 T/T CSHL-HAPMAP HapMap-JPT NA18943 JA18943 r27_ch17_JPT_illumina:golden_gate_1.0.0
5205 ss78143570 T/T CSHL-HAPMAP HapMap-JPT NA18953 JA18953 r27_ch17_JPT_illumina:golden_gate_1.0.0
5207 ss78143570 T/T CSHL-HAPMAP HapMap-JPT NA18959 JA18959 r27_ch17_JPT_illumina:golden_gate_1.0.0
5208 ss78143570 T/T CSHL-HAPMAP HapMap-JPT NA18969 JA18969 r27_ch17_JPT_illumina:golden_gate_1.0.0
5210 ss78143570 T/T CSHL-HAPMAP HapMap-JPT NA18961 JA18961 r27_ch17_JPT_illumina:golden_gate_1.0.0
5211 ss78143570 T/T CSHL-HAPMAP HapMap-JPT NA18972 JA18972 r27_ch17_JPT_illumina:golden_gate_1.0.0
5212 ss78143570 G/T CSHL-HAPMAP HapMap-JPT NA18965 JA18965 r27_ch17_JPT_illumina:golden_gate_1.0.0
5213 ss78143570 G/T CSHL-HAPMAP HapMap-JPT NA18973 JA18973 r27_ch17_JPT_illumina:golden_gate_1.0.0
5215 ss78143570 T/T CSHL-HAPMAP HapMap-JPT NA18975 JA18975 r27_ch17_JPT_illumina:golden_gate_1.0.0
5223 ss78143570 G/T CSHL-HAPMAP HapMap-JPT NA18971 JA18971 r27_ch17_JPT_illumina:golden_gate_1.0.0
5225 ss78143570 T/T CSHL-HAPMAP HapMap-JPT NA18987 JA18987 r27_ch17_JPT_illumina:golden_gate_1.0.0
5226 ss78143570 G/T CSHL-HAPMAP HapMap-JPT NA18990 JA18990 r27_ch17_JPT_illumina:golden_gate_1.0.0
5235 ss78143570 T/T CSHL-HAPMAP HapMap-JPT NA19007 JA19007 r27_ch17_JPT_illumina:golden_gate_1.0.0
5258 ss78143570 G/G CSHL-HAPMAP HapMap-YRI NA18853 YOR018.03 r27_ch17_YRI_illumina:golden_gate_1.0.0
5259 ss78143570 G/T CSHL-HAPMAP HapMap-YRI NA18857 YOR023.01 r27_ch17_YRI_illumina:golden_gate_1.0.0
5265 ss78143570 G/T CSHL-HAPMAP HapMap-YRI NA18914 YOR028.01 r27_ch17_YRI_illumina:golden_gate_1.0.0
5267 ss78143570 G/T CSHL-HAPMAP HapMap-YRI NA18913 YOR028.03 r27_ch17_YRI_illumina:golden_gate_1.0.0
5293 ss78143570 G/G CSHL-HAPMAP HapMap-YRI NA19159 YOR056.02 r27_ch17_YRI_illumina:golden_gate_1.0.0
5294 ss78143570 T/T CSHL-HAPMAP HapMap-YRI NA19160 YOR056.03 r27_ch17_YRI_illumina:golden_gate_1.0.0
5300 ss78143570 T/T CSHL-HAPMAP HapMap-YRI NA19119 YOR060.03 r27_ch17_YRI_illumina:golden_gate_1.0.0
5302 ss78143570 G/T CSHL-HAPMAP HapMap-YRI NA19140 YOR071.02 r27_ch17_YRI_illumina:golden_gate_1.0.0
5310 ss78143570 G/T CSHL-HAPMAP HapMap-YRI NA19129 YOR077.01 r27_ch17_YRI_illumina:golden_gate_1.0.0
Genotype data submitted for596 samples from581 individualsIndividual with multiple genotypes submission:15

  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 .