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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2062988          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:94/130
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_018706.5:c.1821C>G
NP_061176.3:p.Ile607Met
NT_077569.2:g.6506001C>G
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 ss2974308 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2062988 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
ss2974308TSC-CSHL|TSC1097619byFreqfwd/TC/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac01/29/0110/30/0494Genomicunknown
ss4926021YUSUKE|IMS-JST090877byFreqfwd/TC/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac07/29/0210/10/03108Genomicunknown
ss14738035SC_SNP|NT_077569.2_6506001fwd/TC/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac11/12/0311/22/03119Genomicunknown
ss16249542CGAP-GAI|1498143fwd/TC/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac11/18/0311/22/03120cDNAunknown
ss19159070CSHL-HAPMAP|CSHL-HuDD-200402.chr10.NT_077569.2_6506001fwd/TC/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac02/20/0403/04/04120Genomicunknown
ss20671836SSAHASNP|WGSA-200403-chr10.chr10.NT_077569.2_6506001fwd/TC/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac03/18/0403/19/04123Genomicunknown
ss23243374PERLEGEN|afd4500744byFreqfwd/TC/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac08/10/0409/13/04123Genomicunknown
ss28510365MGC_GENOME_DIFF|BC002477x29800963-C6506001Gfwd/TC/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac08/25/0408/25/04126cDNAunknown
ss38554906ABI|hCV11374245byFreqfwd/C/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac07/15/0511/02/06126Genomicunknown
ss65726106ILLUMINA|Human1-rs2062988fwd/TC/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac10/10/0610/10/06127Genomicunknown
ss69070767PERLEGEN|PGP04500744byFreqfwd/C/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac01/30/0708/14/07127Genomicunknown
ss74807285AFFY|SNP_M-178243fwd/TC/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac08/09/0708/09/07128Genomicunknown
ss76555080AFFY|AFFY_6_1M_SNP_A-8416112rev/C/Gtctcctggcaaaccacattgcatgcctctgac08/28/0708/30/07129Genomicunknown
ss82841043HGSV|Cor18555_SNV_20070510.chr10_12183111fwd/C/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac11/27/0712/03/07130Genomicunknown
ss88099024BCMHGSC_JDW|JWB-0236830fwd/C/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac02/26/0802/27/08129Genomicunknown
ss97536231HUMANGENOME_JCVI|1103649863856fwd/C/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac03/29/0803/29/08130Genomicunknown
ss104861721KRIBB_YJKIM|KHS1254039fwd/C/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac07/10/0807/10/08130Genomicunknown
ss1092391121000GENOMES|CEU.trio.12.15.2008_2296969_chr10_12183111fwd/C/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac12/15/0812/16/08130Genomicunknown
ss119036632ILLUMINA-UK|NA18507_000018781_NCBI36.1_chr10_12183111fwd/C/Gtcgtggaactttcagtcagaggcatgcaatgtggtttgccaggagacggatgacacctac01/21/0901/22/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2062988|allelePos=168|totalLen=1166|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=130
 GAAAATTCTC AGGATTAAGC CAGTATATAA GAATTTACAG TCACCACACC TTATTATTAG
 GTTATTTATG GGAATCTGAC TTTTTTTTTC TTGCTTGCTT AAGGTTTTAA TGTTCGTCTA
 AGTGGCCAAG ATGTTGGTCG TGGAACTTTC AGTCAGAGGC ATGCAAT
 S
 GTGGTTTGCC AGGAGACGGA TGACACCTAC ATCCCCCTGA ACCATATGGA CCCAAATCAG
 AAGGGGTTTC TAGAGGTGAG ATGTTTCTAT AGCTGTTGTA AAATCCAGGT GCCAACGATT
 ACACTTCCAG GATTCTTAGA ACAAGTAGGA AGGAGTGCTG GCAACTTTGG GTTCAGTACT
 TTTGGAAGTA AAGGAGTGCT AAATGGGTGG ATGAGGTGGG TCTGTCAATT TGGAATGCAA
 GTAACCCCTA GAGAGTAGGC TGGAGCTTTC TTCTTCTGGT GACATATCTG TAATCATGTA
 AATGTCAAAT CAATGTGTGT TTTGTCAACT CAAAGTTGAC ATTATCATCT GCATATTGCT
 GTAATTCATT AAAGTTAGTC AAAGATATGG ATAAGTCAGT ATTCCTTGCC TACTTAAGGA
 TAGCAAAATC GCACATCCTC AAGGTTACCT GTTCCCTAAG GTATGATTGG CTTGACGAAT
 GTACACATAA CCGTGTAttt ctttcttttt tttcggagac ttaatcttgc tctgttgccc
 acagctggag gacaatggtg ccatcttggc tcactgcaac ctccacctcc caggctcang
 ggatcctcat gtttcagcct cccgagtagc tgggaccacg ggaatgaggt gccattcctg
 gctaattttt ttatttttag tagatggaat ttcaccatgt tgcccaggct ggtcttgaac
 tcctggcctc aagcagtcca cctgccttgg cctcccaaag cactggaagt ataggtgtga
 gccactgcac ccagccAGAT ATAACCATGT ATTTCTGTGT GGCAGCCTCT GTGCCCTCTG
 TAGTGCCTTA AGGATAGTAG TGGAGTCTTT TCATTTATTT ATCTCAAACA ATTATTCAAG
 TGTCTAGCAC ATGATGTTTA TGAAAATAAC TTATTCCTTA AGGTAAGTTG AGTGGCATGT
 CATCTTCTTT CCTACTCTAG CCATTAGTTT GAGAACAT

  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_077569 ABBA01034672 BC002477 BI870429
dbSNP Blast Analysis
UniGene Cluster ID
104980

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/G
 G/G
 HWP C
 G
ss23243374 AFD_EUR_PANEL European 48 IG 0.042 0.458 0.500 0.439 0.271 0.729
AFD_AFR_PANEL African American 46 IG 0.652 0.348 0.025 0.326 0.674
AFD_CHN_PANEL Asian 48 IG 0.042 0.250 0.708 0.655 0.167 0.833
ss2974308 CEPH 184 AF 0.220 0.780
HapMap-CEU European 120 IG 0.333 0.667 0.150 0.167 0.833
HapMap-HCB Asian 90 IG 0.022 0.489 0.489 0.100 0.267 0.733
HapMap-JPT Asian 88 IG 0.045 0.386 0.568 0.752 0.239 0.761
HapMap-YRI Sub-Saharan African 120 IG 0.217 0.650 0.133 0.020 0.542 0.458
CHMJ Asian 74 IG 0.257 0.743
ss38554906 AoD_African_American 90 AF 0.340 0.660
AoD_Caucasian 92 AF 0.210 0.790
AoD_Chinese 90 AF 0.330 0.670
AoD_Japanese 90 AF 0.300 0.700
ss4926021 JBIC-allele 1256 AF 0.262 0.738
ss69070767 HapMap-CEU European 120 GF 0.333 0.667 0.167 0.833
HapMap-HCB Asian 90 GF 0.022 0.489 0.489 0.267 0.733
HapMap-JPT Asian 90 GF 0.044 0.378 0.578 0.233 0.767
HapMap-YRI Sub-Saharan African 120 GF 0.217 0.650 0.133 0.542 0.458

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.422+/-0.182 1264 1052 276 0

  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 .