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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2241883          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:98/130
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_001443.1:c.280A>G
NP_001434.1:p.Thr94Ala
NT_022184.14:g.67167610T>C
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 ss76895520 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2241883 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
ss3197965YUSUKE|IMS-JST013887byFreqfwd/BC/Tgttcggtcacagacttgatgtttttgaaagtgtcaccagtttattgtcaccttccaactg08/07/0110/10/0398Genomicunknown
ss24160905PERLEGEN|afd1280288byFreqfwd/BC/Tgttcggtcacagacttgatgtttttgaaagtgtcaccagtttattgtcaccttccaactg08/10/0409/13/04123Genomicunknown
ss48430047APPLERA_GI|hCV25473098byFreqfwd/BC/Tgttcggtcacagacttgatgtttttgaaagtgtcaccagtttattgtcaccttccaactg10/02/0511/03/06126Genomicunknown
ss65726333ILLUMINA|Human1-rs2241883fwd/BC/Tgttcggtcacagacttgatgtttttgaaagtgtcaccagtttattgtcaccttccaactg10/10/0610/10/06127Genomicunknown
ss66162987AFFY|SNP_A-2170840byFreqrev/TA/Gcaataaactggtgacactttcaaaaacatcaa10/27/0608/14/07127Genomicunknown
ss66580731ILLUMINA|HumanHap300v1.1_rs2241883fwd/BC/Tgttcggtcacagacttgatgtttttgaaagtgtcaccagtttattgtcaccttccaactg11/09/0611/09/06127Genomicunknown
ss67237002ILLUMINA|HumanHap550v1.1_rs2241883fwd/BC/Tgttcggtcacagacttgatgtttttgaaagtgtcaccagtttattgtcaccttccaactg11/14/0611/14/06127Genomicunknown
ss67633247ILLUMINA|HumanHap650Yv1.0_rs2241883fwd/BC/Tgttcggtcacagacttgatgtttttgaaagtgtcaccagtttattgtcaccttccaactg11/14/0611/14/06127Genomicunknown
ss68821923PERLEGEN|PGP01280288byFreqfwd/BC/Tgttcggtcacagacttgatgtttttgaaagtgtcaccagtttattgtcaccttccaactg01/30/0708/14/07127Genomicunknown
ss70715329ILLUMINA|HumanHap550v3.0__rs2241883rev/TA/Gcagttggaaggtgacaataaactggtgacactttcaaaaacatcaagtctgtgaccgaac04/20/0703/30/08130Genomicunknown
ss71283157ILLUMINA|HumanHap650Yv3.0_rs2241883fwd/BC/Tgttcggtcacagacttgatgtttttgaaagtgtcaccagtttattgtcaccttccaactg04/23/0704/23/07127Genomicunknown
ss74917991ILLUMINA|ILMN_Human_1M_rs2241883fwd/BC/Tgttcggtcacagacttgatgtttttgaaagtgtcaccagtttattgtcaccttccaactg08/28/0708/29/07129Genomicunknown
ss76207793AFFY|AFFY_6_1M_SNP_A-2170840rev/TA/Gcaataaactggtgacactttcaaaaacatcaa08/28/0708/30/07129Genomicunknown
ss76895520SI_EXO|NT_022184.14_67167610fwd/BC/Tgttcggtcacagacttgatgtttttgaaagtgtcaccagtttattgtcaccttccaactg09/20/0709/20/07129Genomicunknown
ss79122777ILLUMINA|HumanHap300v2.0_rs2241883fwd/BC/Tgttcggtcacagacttgatgtttttgaaagtgtcaccagtttattgtcaccttccaactg04/18/0711/18/07130Genomicunknown
ss84006240KRIBB_YJKIM|KHS599567fwd/BC/Tgttcggtcacagacttgatgtttttgaaagtgtcaccagtttattgtcaccttccaactg12/04/0712/06/07130Genomicunknown
ss91247879BCMHGSC_JDW|JWB-1272390fwd/BC/Tgttcggtcacagacttgatgtttttgaaagtgtcaccagtttattgtcaccttccaactg02/26/0803/01/08129Genomicunknown
ss97057729HUMANGENOME_JCVI|1103658156629fwd/BC/Tgttcggtcacagacttgatgtttttgaaagtgtcaccagtttattgtcaccttccaactg03/28/0803/28/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2241883|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GACTGTGCCA GGCTTGTAAG CTGCCATAAT ATGACCATGA ATGGGATTCT CTTTATAAAC
 GCTAAATGGG CAAAGGCATT TATGAAGCAC CCTGGGCATG CAGGGCAGGT GGAGGCCTCT
 GTGGCTGGTT GGTTGCGCTG AGCAGAAAGG ATTAGTGATA ATGTGTGTAA ACTGCCTGGG
 ACATGATGGA TCCTCAGTAA GTGCTGGCAG ATACTGACCA CAGGAAAGAA GTTTGGGGGT
 TGGAGGGTGG AGGGGTGGCA TTAGGGTATG TGAGCCGCTC CCCATGCTTC ACCTCCCCTC
 TCCCCTCAAG CACTGGGAGC CACACGCTCA GAGCACCACC AACTTACATT GGTGATTATG
 TCGCCGTTGA GTTCGGTCAC AGACTTGATG TTTTTGAAAG
 Y
 TGTCACCAGT TTATTGTCAC CTTCCAACTG AACCACTGTC TGCAGGGAAC AGAGAGGTGA
 CCTGTGAGGA AGGGGTGGTG GGGGGCAAGA GCCTTGCTAA TGAAGTTGCT TCCTTTGCAC
 AGGTCTCAGC TCATAACAAC CAAAATGCTC TGGTTCCTAT GATCCCAAGC CTCTAGTTCT
 CTGGCTCCAA ATAGAAGTGA GGTGCATTTA AGAACTAAAT AAAATGTCAC GACTTCTTTT
 GTCAGAACTT TAATTCATGG CATGTGATCT AGAAATGAGC ATGGAACACC TAAGTGGCCC
 CAAATACAAA TGCTAAAATC AAATCAAGTA AAATCTCAAT TCTCCCAAGC TAATGGAGGG
 AGGTAGTGGC AAAATTCAAA TATTGACCAG TAGAGAATAC

  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_022184.14 ABBA01018805
dbSNP Blast Analysis
UniGene Cluster ID
380135

  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
 N
 T
ss24160905 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 0.304 0.696 0.403 0.152 0.848
AFD_CHN_PANEL Asian 48 IG 0.583 0.417 0.050 0.292 0.708
CHMJ Asian 74 IG 0.135 0.014 0.851
ss3197965 JBIC-allele 1486 AF 0.244 0.756
ss48430047 HapMap-CEU European 120 IG 0.083 0.417 0.500 1.000 0.292 0.708
HapMap-HCB Asian 90 IG 0.022 0.244 0.733 1.000 0.144 0.856
HapMap-JPT Asian 88 IG 0.068 0.364 0.568 1.000 0.250 0.750
HapMap-YRI Sub-Saharan African 120 IG 0.033 0.233 0.733 0.527 0.150 0.850
AGI_ASP population multiple 62 IG 0.613 0.323 0.065 0.752 0.774 0.226
ss66162987 HapMap-CEU European 118 GF 0.085 0.424 0.492 0.297 0.703
HapMap-HCB Asian 90 GF 0.022 0.244 0.733 0.144 0.856
HapMap-JPT Asian 90 GF 0.067 0.356 0.578 0.244 0.756
HapMap-YRI Sub-Saharan African 120 GF 0.033 0.233 0.733 0.150 0.850
ss68821923 HapMap-CEU European 120 GF 0.083 0.417 0.500 0.292 0.708
HapMap-HCB Asian 90 GF 0.022 0.244 0.733 0.144 0.856
HapMap-JPT Asian 90 GF 0.067 0.356 0.578 0.244 0.756
HapMap-YRI Sub-Saharan African 120 GF 0.033 0.233 0.733 0.150 0.850
ss76207793 ICMHP 6 IG 0.333 0.667 0.333 0.667

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.390+/-0.252 1300 1085 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
byClusterbyFreqwithHapMapFreq UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .