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Reference SNP (refSNP) Cluster Report: rs2880301                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:101/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreq
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (REV)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
NA
HGVS Names
  • CM000675.2:g.19526394C>T
  • NC_000013.10:g.20100534C>T
  • NC_000013.11:g.19526394C>T
  • NM_001141968.1:c.-236+10202G>A
  • NM_130785.3:c.-44+10202G>A
  • NM_199254.2:c.-44+10202G>A
  • NR_073485.1:n.281-23117G>A
  • NR_073487.1:n.168+10202G>A
Links
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' to see variant in the new NCBI variation viewer) back to top

  GeneView back to top

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Submitter records for this RefSNP Cluster back to top
The submission ss4071484 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2880301 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
ss4071484TSC-CSHL|TSC1742199byFreqfwd/TA/Gtggatggcctccaggcttttaggcttttagctggattgctgcaaaggacatgatcttgtt10/02/0108/14/07101Genomicunknown
ss66466589AFFY|SNP_A-2257575byFreqrev/BC/Tctttgcagcaatccagctaaaagcctaaaagc10/29/0603/31/08142Genomicunknown
ss76270147AFFY|AFFY_6_1M_SNP_A-2257575byFreqrev/BC/Tctttgcagcaatccagctaaaagcctaaaagc08/28/0703/07/10142Genomicunknown
ss81899094KRIBB_YJKIM|KHS157600fwd/TA/Gtggatggcctccaggcttttaggcttttagctggattgctgcaaaggacatgatcttgtt11/30/0712/01/07130Genomicunknown
ss173053522AFFY|GenomeWideSNP_5_SNP_A-2257575rev/BC/Tctttgcagcaatccagctaaaagcctaaaagc10/01/0910/02/09142Genomicunknown
ss173520832ILLUMINA|Human1M-Duov3_B_rs2880301-128_T_F_1511722193fwd/TA/Gtggatggcctccaggcttttaggcttttagctggattgctgcaaaggacatgatcttgtt10/01/0910/03/09132Genomicunknown
ss1397650506HAMMER_LAB|HAMMER_LAB_rs2880301rev/BC/Tgatcatgtcctttgcagcaatccagctaaaagcctaaaagcctggaggcc09/30/1409/30/14146Genomicunknown
ss1713372203EVA_SVP|EVA_SVP_1066570rev/BC/Tgatcatgtcctttgcagcaatccagctaaaagcctaaaagcctggaggcc03/12/1503/12/15144Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2880301|allelePos=501|totalLen=1000|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=146
 CTCTTCTCTT ATTGAGAAGA GATTACCTTT ACATCAATAT TAACCATTTT GATATACTGA
 GATATAATTC AGTTGGTTCA TGACTGTGCC AATAGCTCCA TTTTTATATA CAAATAGACA
 TGCCTAAATC CAGTTTTTTT TGTATGCACA TTTTATTTAA TTAATtttta acttttattt
 taggttcaag ggtacatgtg caggtttgtt atatatgtaa attttgtgtc atgggggttt
 gatgcacgga ttgttttgtc actcaggtga taagcatagt acctgatagg tagctttttg
 atactcacca tcctccagcc tccaaccctc aagtaggccc caatgtctgt tgttcccata
 tttgtgccca tgtgtactca atgtttaact cccacttata agtgagaaca tgaggtattt
 ggtttcctgt tcctgtgtta gtttgcttag aataattttt aagctggagc tggatggcct
 ccaggctttt aggcttttag
 R
 ctggattgct gcaaaggaca tgatcttgtt tttattttat ggctgcatag tattccatgg
 tatatgtgtg ccacattttt taaattcagt tcaccattga tgggcaccta gctaaattct
 gtgtctttgc cattgtgaat agtgctgcga tgaacatatg tgtgcatgtg tcttcatggt
 agaatgatat ttatattcct gtgggtatat actcagtaat gggattgctg ggtcacaggg
 taattctcaa gttctttgag aaatcaccaa actgctttcc ataatggctg aactaattta
 catacccagc agtagtgtat aagcattccc tttcctctgt aactttgcca gcatctattt
 tttggctttt tattaatagc tattctgact ggtatgatat ggtatctcat tgtagttttg
 atttgcattt ctctagtatt agtgatgttg agcatttttt catgtttgtt agctgtgtgt
 atgtcttttg agaagtgtc

  NCBI Resource Links back to top
Submitter-Referenced
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) Note: rs2880301 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss4071484HapMap-CEUEuropean 222IG 0.477477490.522522510.050043000.238738750.76126128
HapMap-HCBAsian 86IG 0.511627910.488372090.150222000.255813960.74418604
HapMap-JPTAsian 168IG 0.500000000.500000000.050043000.250000000.75000000
HapMap-YRISub-Saharan African 120IG 0.500000000.500000000.099721000.250000000.75000000
HAPMAP-ASW 94IG 0.361702110.638297860.402784000.180851060.81914896
HAPMAP-CHBAsian 82IG 0.487804890.512195110.200325000.243902440.75609756
HAPMAP-CHD 170IG 0.482352940.517647090.099721000.241176470.75882351
HAPMAP-GIH 174IG0.011494250.494252860.494252860.010028000.258620680.74137932
HAPMAP-LWK 174IG 0.482758610.517241360.099721000.241379310.75862068
HAPMAP-MKK 276IG0.007246380.463768120.528985500.002501000.239130440.76086956
HAPMAP-TSI 170IG 0.482352940.517647090.099721000.241176470.75882351
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss76270147ICMHP 4IG0.50000000 0.50000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.366+/-0.2210000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqUNKNOWNUNKNOWNUNKNOWN

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