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Reference SNP (refSNP) Cluster Report: rs138235491                 ** With untested allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:134/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:With untested allele [ClinVar]
MAF/MinorAlleleCount:C=0.0006/66 (ExAC)
C=0.0012/6 (1000 Genomes)
C=0.0020/24 (GO-ESP)
C=0.0023/290 (TOPMED)
HGVS Names
  • CM000663.2:g.25306681T>C
  • NC_000001.10:g.25633172T>C
  • NC_000001.11:g.25306681T>C
  • NG_007494.1:g.39192T>C
  • NM_001127691.2:c.939+3222T>C
  • NM_001282867.1:c.527T>C
  • NM_001282868.1:c.939+3222T>C
  • NM_001282869.1:c.1025T>C
  • NM_001282870.1:c.1025T>C
  • NM_001282871.1:c.1025T>C
  • NM_001282872.1:c.1025T>C
  • NM_001321772.1:c.-67+30359A>G
  • NM_016124.4:c.1025T>C
  • NP_001269796.1:p.Ile176Thr
  • NP_001269798.1:p.Ile342Thr
  • NP_001269799.1:p.Ile342Thr
  • NP_001269800.1:p.Ile342Thr
  • NP_001269801.1:p.Ile342Thr
  • NP_057208.2:p.Ile342Thr
  • NR_135787.1:n.1215+30359A>G
  • NR_135788.1:n.277+31297A>G
  • NR_135789.1:n.1215+30359A>G
  • NR_135790.1:n.1425-1860A>G
  • NR_135791.1:n.1484A>G
  • NR_135792.1:n.1216-1860A>G
  • NR_135793.1:n.1269+215A>G
  • XP_005246016.1:p.Ile342Thr
  • XP_005246017.1:p.Ile342Thr
  • XP_005246018.1:p.Ile342Thr
  • XP_005246019.1:p.Ile342Thr
  • XP_005246021.1:p.Ile191Thr
  • XP_016857504.1:p.Ile342Thr
  • XR_241226.1:n.426+215A>G
  • XR_946736.1:n.1180T>C
  • XR_946737.1:n.1094+3222T>C
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 ss341945949 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs138235491 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
ss3284846961000GENOMES|20100804_snps_128232_chr1_25633172fwd/C/Ttcagcttgctgggtctgcttggagagatcactacattgtgctgctggtgcttgataccgt03/22/1103/22/11134Genomicunknown
ss341945949NHLBI-ESP|ESP2500-chr1-25633172byFreqfwd/BC/Ttcagcttgctgggtctgcttggagagatcactacattgtgctgctggtgcttgataccgt03/25/1109/05/14134Genomicunknown
ss491289453EXOME_CHIP|nonsyn_5680_chr_1_25633172fwd/BC/Ttcagcttgctgggtctgcttggagagatcactacattgtgctgctggtgcttgataccgt03/05/1203/05/12137Genomicunknown
ss749602138ROSENBERGLAB|CHR1_25505759fwd/BC/Ttcagcttgctgggtctgcttggagagatcactacattgtgctgctggtgcttgataccgt04/26/1304/26/13142Genomicunknown
ss1067418349JMKIDD_LAB|HGDP_exomes_chr1_25633172fwd/BC/Tttgctgggtctgcttggagagatcactacattgtgctgctggtgcttgat07/09/1407/09/14142Genomicunknown
ss1067744310JMKIDD_LAB|HGDP_WGS_chr1_25633172fwd/BC/Tttgctgggtctgcttggagagatcactacattgtgctgctggtgcttgat07/10/1407/10/14142Genomicunknown
ss12900895761000GENOMES|PHASE3_V1_783920fwd/C/Tttgctgggtctgcttggagagatcactacattgtgctgctggtgcttgat08/16/1408/16/14142Genomicunknown
ss1685398932EVA_EXAC|EVA_EXAC_194756fwd/C/Tttgctgggtctgcttggagagatcactacattgtgctgctggtgcttgat03/04/1503/04/15144Genomicunknown
ss1918172211WEILL_CORNELL_DGM|SNV:chr1:25633172fwd/BC/Tttgctgggtctgcttggagagatcactacattgtgctgctggtgcttgat10/16/1510/16/15147Genomicunknown
ss2731264984GNOMAD|exomes_rs138235491fwd/C/Tttgctgggtctgcttggagagatcactacattgtgctgctggtgcttgat05/17/1705/17/17151Genomicunknown
ss2746262178GNOMAD|coding_rs138235491fwd/C/Tttgctgggtctgcttggagagatcactacattgtgctgctggtgcttgat05/17/1705/17/17151Genomicunknown
ss2752823449GNOMAD|rs138235491fwd/C/Tttgctgggtctgcttggagagatcactacattgtgctgctggtgcttgat05/17/1705/17/17151Genomicunknown
ss3071295053TOPMED|TOPMed_freeze_5?chr1:25,306,681fwd/C/Tttgctgggtctgcttggagagatcactacattgtgctgctggtgcttgat09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs138235491|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 CCCCGATGAT GTGAGTGCAC ATTCAAGTCT GAGAAGGGCT TCTTTGAGGT GAGCCTTAGT
 GCCCATCCCC CTTTGGTGGC CCCGGATACC AAGGGTGTGT GAAAGGGGTG GGTAGGGAAT
 ATGGGTCTCA CCTGCCAATC TGCTTATAAT AACACTTGTC CACAGGGGTG TTGTAACCGA
 GTGCTGGGGA TTCCCCACAG CTCCATCATG GGCTACAACT TCAGCTTGCT GGGTCTGCTT
 GGAGAGATCA
 Y
 CTACATTGTG CTGCTGGTGC TTGATACCGT CGGAGCCGGC AATGGCATGT GGGTCACTGG
 GCTTACCCCC CATCCCCTTA ACACTCCCCT CCAACTCAGG AAGAAATGTG TGCAGAGTCC
 TTAGCTGGGG CGTGTGCACT CGGGGCCAGG TGCTCAGTAG GCTTCGGTGA ATATTTGTTG
 GCTGATTTAT TCAGAAATTC TGTCCAGCCC CTACCTTGGA TGGATTTATC ACCTCTCCAG
 GCCACCTCTT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000001
dbSNP Blast Analysis
3D structure mapping
NP_057208  

  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/C
C/T
T/T
HWPC
T
ss1290089576EAS 1008AF 1.00000000
EUR 1006AF 1.00000000
AFR 1322AF 0.003800000.99620003
AMR 694AF 0.001400000.99859995
SAS 978AF 1.00000000
ss1685398932ExAc_Aggregated_Populations113214AF 0.000591800.99940819
ss341945949ESP_Cohort_Populations 4032GF 0.004464290.995535731.000000000.002232140.99776787

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.001+/-0.0250000

  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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