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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs1995641          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:92/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_003241.3:c.937G>A
NP_003232.2:p.Glu313Lys
NT_022517.17:g.44883393G>A
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 ss44381942 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1995641 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
ss2908742TSC-CSHL|TSC0883067fwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg01/03/0110/10/0392Genomicunknown
ss3234748YUSUKE|IMS-JST044833byFreqfwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg09/05/0110/10/03100Genomicunknown
ss10036569BCM_SSAHASNP|chr3.NT_005825.15_2634026byFreqfwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg06/27/0304/07/04116Genomicunknown
ss44381942ABI|hCV11987512byFreqfwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg07/18/0511/03/06126Genomicunknown
ss48406451APPLERA_GI|hCV11987512byFreqfwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg09/28/0511/03/06126Genomicunknown
ss66080126AFFY|SNP_A-1911787byFreqfwd/TA/Gtgtgaatgagaatggcagaaaatcaccagtat10/27/0608/14/07127Genomicunknown
ss66642421ILLUMINA|HumanHap300v1.1_rs1995641fwd/BA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg11/09/0611/09/06127Genomicunknown
ss67213682ILLUMINA|HumanHap550v1.1_rs1995641fwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg11/14/0611/14/06127Genomicunknown
ss67607147ILLUMINA|HumanHap650Yv1.0_rs1995641fwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg11/14/0611/14/06127Genomicunknown
ss68860337PERLEGEN|PGP04767838byFreqfwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg01/30/0708/14/07127Genomicunknown
ss70691943ILLUMINA|HumanHap550v3.0__rs1995641fwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg04/20/0703/30/08130Genomicunknown
ss71257020ILLUMINA|HumanHap650Yv3.0_rs1995641fwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg04/23/0704/23/07127Genomicunknown
ss75512878ILLUMINA|ILMN_Human_1M_rs1995641fwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg08/28/0708/29/07129Genomicunknown
ss76020254AFFY|AFFY_6_1M_SNP_A-1911787fwd/TA/Gtgtgaatgagaatggcagaaaatcaccagtat08/28/0708/29/07129Genomicunknown
ss79106203ILLUMINA|HumanHap300v2.0_rs1995641fwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg04/18/0711/18/07130Genomicunknown
ss83939554KRIBB_YJKIM|KHS578504fwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg12/04/0712/06/07130Genomicunknown
ss92074790BCMHGSC_JDW|JWB-1587153fwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg02/26/0803/02/08129Genomicunknown
ss1100961281000GENOMES|NA19240_2008_12_16_619390_chr3_44918393fwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg12/16/0812/17/08130Genomicunknown
ss1116377941000GENOMES|CEU.trio.12.15.2008_690844_chr3_44918393fwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg12/15/0812/17/08130Genomicunknown
ss117069298ILLUMINA-UK|NA18507_000066815_NCBI36.1_chr3_44918393fwd/TA/Gacggtggacacctatgtgaatgagaatggcagaaaatcaccagtatgacccacgactctg01/18/0901/18/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1995641|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 ACAAGTGGAC AGGCAGTGCC CCGATCCTGC AGCAGTACTA CAACACGAAG CAGGCTGTGT
 GCTTTGGCCA GTGCTGGGTG TTTGCTGGGA TCCTGACTAC AGGTAAGTGG CAGATCCAGG
 GGCTGAGGGG AGAGGTCCCA AGGGAGGGAC TCCCAGCCCC CACAGTTGCC AACCACCCCA
 CCCTGGATCA TTTCAGTGCT GAGAGCGTTG GGCATCCCAG CACGCAGTGT GACAGGCTTC
 GATTCAGCTC ACGACACAGA AAGGAACCTC ACGGTGGACA CCTATGTGAA TGAGAATGGC
 R
 AGAAAATCAC CAGTATGACC CACGACTCTG TCTGGTAGGG TTCCTCCTTC TCAACCTGCC
 CTGTCTCCTT CTCCCAGGAA TTTTCTTTTT TCTTTTTAGA AACAGGGTCT CTCGCTAGTT
 TGCCCAGGCT GGTCTTGAAC TGGTGTCAAG CAGTCCTCCT GCCTTAGCCT CCCAGGTAGC
 TGTGATTCCA GGTGCAAGCC ACCATGCGTG GCATCCCAGG AGTTTTTTAG CCCAAGCCCA
 GTCTCCAGGC CCTCCCAACC CAGAGATTCT GCTGAGCTGT GGGGCCCCTT CAGCCTCCCT

  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_005825
dbSNP Blast Analysis
UniGene Cluster ID
438265

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/G
 G/G
 HWP A
 G
ss10036569 CEPH 184 AF 0.320 0.680
ss3234748 JBIC-allele 1496 AF 0.834 0.166
ss44381942 HapMap-CEU European 120 IG 0.233 0.467 0.300 0.655 0.467 0.533
HapMap-HCB Asian 90 IG 0.711 0.267 0.022 1.000 0.844 0.156
HapMap-JPT Asian 88 IG 0.523 0.386 0.091 0.752 0.716 0.284
HapMap-YRI Sub-Saharan African 120 IG 0.233 0.500 0.267 1.000 0.483 0.517
AoD_African_American 90 AF 0.550 0.450
AoD_Caucasian 92 AF 0.340 0.660
AoD_Chinese 90 AF 0.720 0.280
AoD_Japanese 90 AF 0.810 0.190
ss48406451 AGI_ASP population multiple 78 IG 0.179 0.487 0.333 1.000 0.423 0.577
ss66080126 HapMap-CEU European 118 GF 0.237 0.475 0.288 0.475 0.525
HapMap-HCB Asian 90 GF 0.711 0.267 0.022 0.844 0.156
HapMap-JPT Asian 90 GF 0.533 0.378 0.089 0.722 0.278
HapMap-YRI Sub-Saharan African 120 GF 0.233 0.500 0.267 0.483 0.517
ss68860337 HapMap-CEU European 120 GF 0.233 0.467 0.300 0.467 0.533
HapMap-HCB Asian 90 GF 0.689 0.289 0.022 0.833 0.167
HapMap-JPT Asian 90 GF 0.533 0.378 0.089 0.722 0.278
HapMap-YRI Sub-Saharan African 120 GF 0.233 0.483 0.283 0.475 0.525
ss76020254 ICMHP 10 IG 0.200 0.800 0.600 0.400
Concordant Genotype Total Sample A/A A/G G/G
ss44381942 1204 345 540 295
ss48406451 39 7 19 13
ss66080126 266 96 113 57
ss68860337 267 96 113 58
ss76020254 5 1 4
RefSNP Genotype Summary Total Individual A/A A/G G/G
rs1995641 1251 363 570 314
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
254 ss44381942 A/G CSHL-HAPMAP HapMap-CEU NA10856 CEPH1350.01 r27_ch3_CEU_illumina:human_1m_beadchip 407227
254 ss66080126 A/G CSHL-HAPMAP HapMap-CEU NA10856 CEPH1350.01 chr3-HapMap-CEU
254 ss68860337 G/G CSHL-HAPMAP HapMap-CEU NA10856 CEPH1350.01 chr3-HapMap-CEU
5191 ss44381942 A/A CSHL-HAPMAP HapMap-HCB NA18593 CH18593 r27_ch3_CHB_illumina:human_1m_beadchip 407227
5191 ss66080126 A/A CSHL-HAPMAP HapMap-HCB NA18593 CH18593 chr3-HapMap-HCB
5191 ss68860337 A/G CSHL-HAPMAP HapMap-HCB NA18593 CH18593 chr3-HapMap-HCB
5273 ss44381942 A/G CSHL-HAPMAP HapMap-YRI NA19101 YOR042.03 r27_ch3_YRI_illumina:human_1m_beadchip 407227
5273 ss66080126 A/G CSHL-HAPMAP HapMap-YRI NA19101 YOR042.03 chr3-HapMap-YRI
5273 ss68860337 G/G CSHL-HAPMAP HapMap-YRI NA19101 YOR042.03 chr3-HapMap-YRI
Genotype data submitted for1251 samples from1251 individualsIndividual with multiple genotypes submission:270

  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, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .