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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2070418          
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:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_003253.2:c.739G>A
NP_003244.2:p.Gly247Arg
NT_011512.10:g.18300421C>T
Links

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 ss48430186 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2070418 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
ss2983650YUSUKE|IMS-JST005230fwd/BC/Tagtagcctgcaaatttgctccccggccccagtttgctgtcactccagagtttttctgagc05/24/0110/10/0396Genomicunknown
ss3185562HGBASE|SNP000571146rev/TA/Ggaaaaactctggagtgacagcaaactggggccggggagcaaatttgcagg07/09/0110/10/0398Genomicunknown
ss48430186APPLERA_GI|hCV25471643byFreqfwd/BC/Tagtagcctgcaaatttgctccccggcccccgtttgctgtcactccagagtttttctgagc10/02/0511/03/06126Genomicunknown
ss65726123ILLUMINA|Human1-rs2070418fwd/BC/Tagtagcctgcaaatttgctccccggccccagtttgctgtcactccagagtttttctgagc10/10/0610/10/06127Genomicunknown
ss66579646ILLUMINA|HumanHap300v1.1_rs2070418fwd/TC/Tagtagcctgcaaatttgctccccggccccagtttgctgtcactccagagtttttctgagc11/09/0611/09/06127Genomicunknown
ss67221905ILLUMINA|HumanHap550v1.1_rs2070418fwd/BC/Tagtagcctgcaaatttgctccccggccccagtttgctgtcactccagagtttttctgagc11/14/0611/14/06127Genomicunknown
ss67616324ILLUMINA|HumanHap650Yv1.0_rs2070418fwd/BC/Tagtagcctgcaaatttgctccccggccccagtttgctgtcactccagagtttttctgagc11/14/0611/14/06127Genomicunknown
ss69252169PERLEGEN|PGP04781492byFreqfwd/BC/Tagtagcctgcaaatttgctccccggcccccgtttgctgtcactccagagtttttctgagc01/30/0708/14/07127Genomicunknown
ss70700195ILLUMINA|HumanHap550v3.0__rs2070418rev/TA/Ggctcagaaaaactctggagtgacagcaaacgggggccggggagcaaatttgcaggctact04/20/0703/30/08130Genomicunknown
ss71266218ILLUMINA|HumanHap650Yv3.0_rs2070418fwd/BC/Tagtagcctgcaaatttgctccccggcccccgtttgctgtcactccagagtttttctgagc04/23/0704/23/07127Genomicunknown
ss74956097ILLUMINA|ILMN_Human_1M_rs2070418fwd/BC/Tagtagcctgcaaatttgctccccggcccccgtttgctgtcactccagagtttttctgagc08/28/0708/29/07129Genomicunknown
ss79112186ILLUMINA|HumanHap300v2.0_rs2070418fwd/BC/Tagtagcctgcaaatttgctccccggcccccgtttgctgtcactccagagtttttctgagc04/18/0711/18/07130Genomicunknown
ss83964069KRIBB_YJKIM|KHS586029fwd/BC/Tagtagcctgcaaatttgctccccggcccccgtttgctgtcactccagagtttttctgagc12/04/0712/06/07130Genomicunknown
ss1124303851000GENOMES|CEU.trio.12.15.2008_3756018_chr21_31560421fwd/BC/Tagtagcctgcaaatttgctccccggcccccgtttgctgtcactccagagtttttctgagc12/15/0812/17/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2070418|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TTCTAAGAGC AAAGTCATGC ACTTAAAGAG TCATGCACCA TTCCCAAAAT ATTGAAACAA
 ATTTCAATCA CTTTACCTGA GTTGTTTTAG CTCTTCTGCC TTGCATGCTG TTGCTATGGC
 TAATTTGTGG GTTGGTGGCA CCTTCAGAGA GACAGTGAGA TTTCCTACAG GGAAGTGTGT
 TATAATTACT GTACGGAGGA GTCTCTTCAG CAGCAGCTGG TGGCATCTTA TGGTTTGCAA
 GATTGGGAAT ATCAGACACC AAATTCCGAC AGTAGCCTGC AAATTTGCTC CCCGGCCCCC
 Y
 GTTTGCTGTC ACTCCAGAGT TTTTCTGAGC ATACAAGTCA CCCAAGGAAT TGGCTCTCTG
 ACAGGTGCTG AGCTGCCGCG GACTCGCCCG CGTTTCCATC CCCCGAGCCT CCTCGCAGTC
 CTTCTCTTCG GCGGAACCCA AGATTTCTTC GTTGCTTGTT AAATGTTCTT GGCTCAGATC
 AGAGAGTGAG AATTCCAGGC TGTCCTCCCG CCAGATGTCT GCAGATTTGG AGCGTTTCTT
 CTTAAAGCTC GCCGTCTCCA TGAAAGTGGG CCCATTGGAT GTATAGGAAT GCTGCCTCCT

  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
NC_000021.7
dbSNP Blast Analysis
UniGene Cluster ID
517228

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/G
 C/C
 C/T
 G/G
 T/T
 HWP A
 C
 G
 T
ss48430186 HapMap-CEU European 120 IG 0.783 0.200 0.017 1.000 0.883 0.117
HapMap-HCB Asian 84 IG 0.286 0.548 0.167 0.479 0.560 0.440
HapMap-JPT Asian 86 IG 0.535 0.302 0.163 0.100 0.686 0.314
HapMap-YRI Sub-Saharan African 120 IG 1.000 1.000
AGI_ASP population multiple 78 IG 0.026 0.154 0.821 0.317 0.103 0.897
ss69252169 HapMap-CEU European 120 GF 0.817 0.167 0.017 0.900 0.100
HapMap-HCB Asian 90 GF 0.378 0.489 0.133 0.622 0.378
HapMap-JPT Asian 90 GF 0.511 0.311 0.178 0.667 0.333
HapMap-YRI Sub-Saharan African 120 GF 0.983 0.017 0.992 0.008
Concordant Genotype Total Sample A/A A/G C/C C/T G/G T/T
ss48430186 1234 1 6 795 242 32 60
RefSNP Genotype Summary Total Individual A/A A/G C/C C/T G/G T/T
rs2070418 1246 1 6 795 242 32 60
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
229 ss48430186 C/T CSHL-HAPMAP HapMap-CEU NA10859 CEPH1347.02 r27_ch21_CEU_illumina:human_1m_beadchip 927892
255 ss48430186 C/C CSHL-HAPMAP HapMap-CEU NA10855 CEPH1350.02 r27_ch21_CEU_illumina:human_1m_beadchip 927892
265 ss48430186 C/T CSHL-HAPMAP HapMap-CEU NA11832 CEPH1350.13 r27_ch21_CEU_illumina:human_1m_beadchip 927892
348 ss48430186 N/N CSHL-HAPMAP HapMap-CEU NA10860 CEPH1362.01 r27_ch21_CEU_illumina:human_1m_beadchip 927892
620 ss48430186 C/T CSHL-HAPMAP HapMap-CEU NA12874 CEPH1459.11 r27_ch21_CEU_illumina:human_1m_beadchip 927892
5151 ss48430186 T/T CSHL-HAPMAP HapMap-HCB NA18558 CH18558 r27_ch21_CHB_illumina:human_1m_beadchip 927892
5157 ss48430186 N/N CSHL-HAPMAP HapMap-HCB NA18540 CH18540 r27_ch21_CHB_illumina:human_1m_beadchip 927892
5177 ss48430186 C/T CSHL-HAPMAP HapMap-HCB NA18594 CH18594 r27_ch21_CHB_illumina:human_1m_beadchip 927892
5184 ss48430186 C/T CSHL-HAPMAP HapMap-HCB NA18579 CH18579 r27_ch21_CHB_illumina:human_1m_beadchip 927892
5211 ss48430186 C/C CSHL-HAPMAP HapMap-JPT NA18972 JA18972 r27_ch21_JPT_illumina:human_1m_beadchip 927892
5218 ss48430186 C/T CSHL-HAPMAP HapMap-JPT NA18978 JA18978 r27_ch21_JPT_illumina:human_1m_beadchip 927892
5249 ss48430186 C/C CSHL-HAPMAP HapMap-YRI NA18516 YOR013.03 r27_ch21_YRI_illumina:golden_gate_1.0.0 927892
Genotype data submitted for1246 samples from1246 individualsIndividual with multiple genotypes submission:0

  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 .