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Reference SNP (refSNP) Cluster Report: rs1050368                 **Clinical Channel**
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/T (REV)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.0645/7373 (ExAC)
T=0.0292/3669 (TOPMED)
HGVS Names
  • CM000668.2:g.31356301G>A
  • CM000668.2:g.31356301G>T
  • NC_000006.11:g.31324078G>A
  • NC_000006.11:g.31324078G>T
  • NC_000006.12:g.31356301G>A
  • NC_000006.12:g.31356301G>T
  • NG_023187.1:g.5912C>A
  • NG_023187.1:g.5912C>T
  • NM_005514.7:c.485C>A
  • NM_005514.7:c.485C>T
  • NP_005505.2:p.Thr162Lys
  • NP_005505.2:p.Thr162Met
  • NR_106951.1:n.-985C>A
  • NR_106951.1:n.-985C>T
  • NT_113891.2:g.2836765G>T
  • NT_113891.3:g.2836659G>A
  • NT_113891.3:g.2836659G>T
  • NT_167246.1:g.2670534G>T
  • NT_167246.2:g.2664914G>A
  • NT_167246.2:g.2664914G>T
  • NT_167247.1:g.2703870G>T
  • NT_167247.2:g.2698285G>A
  • NT_167247.2:g.2698285G>T
  • NT_167248.1:g.2617593G>T
  • NT_167248.2:g.2611997G>A
  • NT_167248.2:g.2611997G>T
  • NT_167249.1:g.2657838G>T
  • NT_167249.2:g.2658540G>A
  • NT_167249.2:g.2658540G>T
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 ss491381604 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1050368 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
ss1524966LEE|402092fwd/TA/Caggacctgcgctcctggaccgccgcggacaggcggctcagatcacccagcgcaagtggga09/13/0010/10/0386cDNAunknown
ss4394496LEE|ge402092fwd/TA/Caggacctgcgctcctggaccgccgcggacaggcggctcagatcacccagcgcaagtggga04/25/0210/10/03106cDNAunknown
ss4415688LEE|e402092fwd/TA/Caggacctgcgctcctggaccgccgcggacaggcggctcagatcacccagcgcaagtggga04/26/0210/10/03106cDNAunknown
ss24797033SEQUENOM|sqnm144192fwd/TA/Caggacctgcgctcctggaccgccgcggacaggcggctcagatcacccagcgcaagtggga06/18/0406/18/04123cDNAunknown
ss3331827151000GENOMES|20100804_snps_4826252_chr6_31324078rev/G/Ttcccacttgcgctgggtgatctgagccgcctgtccgcggcggtccaggagcgcaggtcct03/22/1103/22/11137Genomicunknown
ss491381604EXOME_CHIP|nonsyn_97830_chr_6_31324078rev/BG/Ttcccacttgcgctgggtgatctgagccgcctgtccgcggcggtccaggagcgcaggtcct03/05/1203/05/12137Genomicunknown
ss491884864CLINSEQ_SNP|SNV-chr6-31432057byFreqrev/BG/Tcttgcgctgggtgatctgagccgcctgtccgcggcggtccaggagcgcag03/06/1209/05/14137Genomicunknown
ss539212310DBMHC|NG_023187.1:g.5912C>Afwd/TA/Caggacctgagctcctggaccgcggcggacacgcggctcagatcacccagcgcaagtggga10/03/1210/03/12137Genomicunknown
ss982762129EVA-GONL|EVA-GONL_rs1050368rev/BG/Tcttgcgctgggtgatctgagccgcctgtccgcggcggtccaggagcgcag04/23/1404/24/14142Genomicunknown
ss1688228661EVA_EXAC|EVA_EXAC_3249792rev/G/Tcttgcgctgggtgatctgagccgcctgtccgcggcggtccaggagcgcag03/04/1503/04/15144Genomicunknown
ss1688228662EVA_EXAC|EVA_EXAC_3249793rev/A/Gcttgcgctgggtgatctgagccgcctgtccgcggcggtccaggagcgcag03/04/1503/04/15144Genomicunknown
ss1711120648EVA_MGP|EVA_XIMO_236408rev/BG/Tcttgcgctgggtgatctgagccgcctgtccgcggcggtccaggagcgcag03/09/1503/09/15144Genomicunknown
ss1926014023WEILL_CORNELL_DGM|SNV:chr6:31324078rev/BG/Tcttgcgctgggtgatctgagccgcctgtccgcggcggtccaggagcgcag10/16/1510/17/15147Genomicunknown
ss2151805346USC_VALOUEV|NC_000006.11:g.31324078G>Trev/G/Tcttgcgctgggtgatctgagccgcctgtccgcggcggtccaggagcgcag11/17/1611/17/16150Genomicunknown
ss2282937691HUMAN_LONGEVITY|HLI-6-31356301-G-Trev/G/Tcttgcgctgggtgatctgagccgcctgtccgcggcggtccaggagcgcag11/18/1611/18/16150Genomicunknown
ss2735645612GNOMAD|exomes_rs1050368rev/A/G/Tcttgcgctgggtgatctgagccgcctgtccgcggcggtccaggagcgcag05/17/1705/17/17151Genomicunknown
ss2747580720GNOMAD|coding_rs1050368rev/G/Tcttgcgctgggtgatctgagccgcctgtccgcggcggtccaggagcgcag05/17/1705/17/17151Genomicunknown
ss2837409828GNOMAD|rs1050368rev/G/Tcttgcgctgggtgatctgagccgcctgtccgcggcggtccaggagcgcag05/18/1705/18/17151Genomicunknown
ss2998790559SWEGEN|NC_000006.11:g.31324078G>Trev/G/Tcttgcgctgggtgatctgagccgcctgtccgcggcggtccaggagcgcag05/30/1705/30/17151Genomicunknown
ss3493805977TOPMED|TOPMed_freeze_5?chr6:31,356,301-01rev/A/Gcttgcgctgggtgatctgagccgcctgtccgcggcggtccaggagcgcag10/05/1710/05/17151Genomicunknown
ss3493805978TOPMED|TOPMed_freeze_5?chr6:31,356,301-02rev/G/Tcttgcgctgggtgatctgagccgcctgtccgcggcggtccaggagcgcag10/05/1710/05/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1050368|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='A/C/T'|mol=Genomic|build=151
 GGGTTGGTCG GGGCGGGGCG GGGCTCGGGG GACTGGGCTG ACCGCGGGGC CGGGGCCAGG
 GTCTCACACC CTCCAGAGCA TGTACGGCTG CGACGTGGGG CCGGACGGGC GCCTCCTCCG
 CGGGCATGAC CAGTACGCCT ACGACGGCAA GGATTACATC GCCCTGAACG AGGACCTGCG
 CTCCTGGACC GCCGCGGACA
 H
 GGCGGCTCAG ATCACCCAGC GCAAGTGGGA GGCGGCCCGT GAGGCGGAGC AGCGGAGAGC
 CTACCTGGAG GGCGAGTGCG TGGAGTGGCT CCGCAGATAC CTGGAGAACG GGAAGGACAA
 GCTGGAGCGC GCTGGTACCA GGGGCAGTGG GGAGCCTTCC CCATCTCCTA TAGGTCGCCG
 GGGATGGCCT CCCACGAGAA

  NCBI Resource Links back to top
Submitter-Referenced
dbSTSGenBank
sqnm144192 NC_000006 Hs.248038 Hs.277477
dbSNP Blast Analysis
UniGene Cluster ID
77961
3D structure mapping
NP_005505  

dbMHC locus: HLA-B
  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs1050368 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/C
C/C
HWPA
C
T
ss1688228661ExAc_Aggregated_Populations120438AF 0.064580950.93541908
ss1688228662ExAc_Aggregated_Populations112724AF 0.999432270.00056776
ss491884864CSAgilent 889GF0.171000000.829000000.438578000.085500000.91450000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.122+/-0.2150000

  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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