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Reference SNP (refSNP) Cluster Report: rs41281338                 ** With other allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:127/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/G/T (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With other allele [ClinVar]
MAF/MinorAlleleCount:C=0.0144/750 (ExAC)
C=0.0066/33 (1000 Genomes)
C=0.0082/102 (GO-ESP)
C=0.0071/886 (TOPMED)
HGVS Names
  • CM000672.2:g.71803310G>C
  • NC_000010.10:g.73563067G>C
  • NC_000010.10:g.73563067G>T
  • NC_000010.11:g.71803310G>C
  • NG_008835.1:g.411364G>C
  • NG_008835.1:g.411364G>T
  • NM_001171933.1:c.1042G>C
  • NM_001171933.1:c.1042G>T
  • NM_001171934.1:c.1042G>C
  • NM_001171934.1:c.1042G>T
  • NM_022124.5:c.7762G>C
  • NM_022124.5:c.7762G>T
  • NP_001165404.1:p.Glu348Gln
  • NP_001165404.1:p.Glu348Ter
  • NP_001165405.1:p.Glu348Gln
  • NP_001165405.1:p.Glu348Ter
  • NP_071407.4:p.Glu2588Gln
  • NP_071407.4:p.Glu2588Ter
  • XP_006718003.1:p.Glu2653Gln
  • XP_006718005.1:p.Glu2631Gln
  • XP_011538341.1:p.Glu2652Gln
  • XP_011538344.1:p.Glu2623Gln
  • XP_011538345.1:p.Glu2653Gln
  • XP_011538346.1:p.Glu2608Gln
  • XP_011538347.1:p.Glu2653Gln
  • XP_011538348.1:p.Glu2473Gln
  • XP_011538349.1:p.Glu2259Gln
  • XP_011538354.1:p.Glu1429Gln
  • XP_016871988.1:p.Glu2633Gln
  • XP_016871989.1:p.Glu2611Gln
  • XP_016871990.1:p.Glu1799Gln
  • XP_016871991.1:p.Glu1799Gln
  • XP_016871992.1:p.Glu1256Gln
  • XP_016871993.1:p.Glu1066Gln
  • XP_016871994.1:p.Glu1015Gln
  • XP_016871995.1:p.Glu956Gln
  • XP_016871996.1:p.Glu620Gln
  • XP_016871997.1:p.Glu348Gln
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 ss52058339 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs41281338 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
ss52058339SI_EXO|NT_008583.16_22114222fwd/C/Gagtctgaccgtggtggccacagatggtggaagcccccactctggggcaccaccatgctcc03/29/0603/29/06127Genomicunknown
ss3362171651000GENOMES|20100804_snps_7860706_chr10_73563067fwd/C/Gagtctgaccgtggtggccacagatggtggaagcccccactctggggcaccaccatgctcc03/22/1103/22/11134Genomicunknown
ss491436726EXOME_CHIP|nonsyn_152952_chr_10_73563067fwd/C/Gagtctgaccgtggtggccacagatggtggaagcccccactctggggcaccaccatgctcc03/05/1203/05/12137Genomicunknown
ss491627212CLINSEQ_SNP|SNV-chr10-73233073byFreqfwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat03/06/1209/05/14137Genomicunknown
ss712951721NHLBI-ESP|ESP6500SI-chr10-73563067fwd/C/Gagtctgaccgtggtggccacagatggtggaagcccccactctggggcaccaccatgctcc02/20/1302/20/13138Genomicunknown
ss783573655ILLUMINA|HumanOmniExpressExome-8v1_A_exm832831-0_T_F_1920973486fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat05/31/1306/18/15146Genomicunknown
ss987636323EVA-GONL|EVA-GONL_rs41281338fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat04/23/1404/25/14142Genomicunknown
ss1067513696JMKIDD_LAB|HGDP_exomes_chr10_73563067fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat07/09/1407/09/14142Genomicunknown
ss1077098031JMKIDD_LAB|HGDP_WGS_chr10_73563067fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat07/10/1407/11/14142Genomicunknown
ss13379881201000GENOMES|PHASE3_V1_50664532fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat08/16/1408/16/14142Genomicunknown
ss1597308381EVA_DECODE|EVA_DECODE_10_73233073_564366_rs41281338fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat03/02/1503/03/15144Genomicunknown
ss1624859225EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_10_73563067_27975561fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat03/04/1503/04/15144Genomicunknown
ss1667853258EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_10_73563067_27975561fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat03/04/1503/04/15144Genomicunknown
ss1689946142EVA_EXAC|EVA_EXAC_5099691fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat03/04/1503/04/15144Genomicunknown
ss1711260699EVA_MGP|EVA_XIMO_376459fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat03/09/1503/09/15144Genomicunknown
ss1751979561ILLUMINA|OmniExpressExome-8v1-1_B_exm832831-0_T_F_2060150545fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat05/27/1506/09/15146Genomicunknown
ss1917848174ILLUMINA|HumanExome-12v1-1_B_exm832831-0_T_F_2060150545fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat10/16/1510/16/15147Genomicunknown
ss1931002086WEILL_CORNELL_DGM|SNV:chr10:73563067fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat10/16/1510/17/15147Genomicunknown
ss1946285745ILLUMINA|HumanCoreExome-12v1-0_C_exm832831-0_T_F_2060150545fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat10/29/1510/29/15147Genomicunknown
ss1959273087ILLUMINA|exm832831-0_T_F_1920973486fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat11/13/1511/13/15147Genomicunknown
ss2026228775JJLAB|SNP6731330fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat08/29/1608/30/16149Genomicunknown
ss2154503049USC_VALOUEV|NC_000010.10:g.73563067G>Cfwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat11/17/1611/17/16150Genomicunknown
ss2175875469HUMAN_LONGEVITY|HLI-10-71803310-G-C,Tfwd/C/G/Tgaccgtggtggccacagatggtggaagcccccactctggggcaccaccat11/18/1611/18/16150Genomicunknown
ss2338915021TOPMED|10_73563067_G/Cfwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat11/19/1611/19/16150Genomicunknown
ss2738316207GNOMAD|exomes_rs41281338fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat05/17/1705/17/17151Genomicunknown
ss2748410252GNOMAD|coding_rs41281338fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat05/17/1705/17/17151Genomicunknown
ss2890317328GNOMAD|rs41281338fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat05/19/1705/19/17151Genomicunknown
ss2985561583AFFY|Axiom_Smokesc1_Affx-3604661fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat05/24/1705/24/17151Genomicunknown
ss3006704764SWEGEN|NC_000010.10:g.73563067G>Cfwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat05/30/1705/30/17151Genomicunknown
ss3021251829ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm832831-0_T_F_1920973486fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat06/28/1706/28/17151Genomicunknown
ss3123363686TOPMED|TOPMed_freeze_5?chr10:71,803,310fwd/C/Ggaccgtggtggccacagatggtggaagcccccactctggggcaccaccat09/29/1709/29/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs41281338|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='C/G/T'|mol=Genomic|build=151
 GTGCTGGATG TCAATGACTG CCGGCCACAG TTCTCCAAGC CCCAGTTCAG CACAAGCGTG
 TATGAGAATG AGCCGGCGGG CACCTCGGTC ATCACCATGA TGGCCACTGA CCAGGATGAA
 GGTCCCAATG GAGAGTTGAC CTACTCACTT GAGGGCCCTG GCGTGGGTAT GTGGCCTTCC
 TTGGACACCC ATGATGTCTT GGGGGGTGGG AGGGGGAGGC CTGCCAGCCC AGGCCAGGAG
 TAGAGGGAAG CGTGGGAAGG ATGTCTCAAC CAGAGCTACT CTCCTGCTCC CACTGCCAGA
 GGCCTTCCAT GTGGACATGG ACTCGGGCTT GGTGACCACA CAGCGGCCAC TGCAGTCCTA
 CGAGAAGTTC AGTCTGACCG TGGTGGCCAC AGATGGTGGA
 B
 AGCCCCCACT CTGGGGCACC ACCATGCTCC TGGTGGAGGT CATCGACGTC AATGACAACC
 GCCCTGTCTT TGTGCGCCCA CCCAACGGCA CCATCCTCCA CATCAGAGAG GTACTCCTGC
 CCCGAGGGCC TCCTGCCCAC CAGTATTTCC TTCTTCCAGC TGTGGCCTAG AAGAGTGGAA
 GCACCCCACT CTAAAGGTGG GGAAACTTGG CTTCAGGAAA GTAGCTCCAG GAAAAAAAAA
 ACTTTTTTAA TTAAATAAAA GTTTGTAAAG GTGGGAAAAC TGAGGCCGGA GAAGGAAGCA
 GACCTGCCCA GTGCCACACA GGGCAGTATT GAACAGTGGT TACTATATGG GCTGTGCTAG
 TAAAAGATCT TTGGTTTGGC CAGGTGCAGT GGCTCACACC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_008583.16
dbSNP Blast Analysis
3D structure mapping
NP_001165404  NP_001165405  NP_071407  

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/G
G/G
HWPC
G
ss1337988120EAS 1008AF 1.00000000
EUR 1006AF 0.009900000.99009997
AFR 1322AF 0.000800000.99919999
AMR 694AF 0.005800000.99419999
SAS 978AF 0.018400000.98160005
ss1689946142ExAc_Aggregated_Populations120642AF 0.008396740.99160326
ss491627212CSAgilent 457GF0.017000000.982999981.000000000.008500000.99150002
ss52058339ENSEMBL_Watson 2IG 1.00000000 1.00000000
ENSEMBL_Venter 2IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.028+/-0.1160000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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