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Reference SNP (refSNP) Cluster Report: rs140018158                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:134/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.00006/7 (ExAC)
T=0.0002/1 (1000 Genomes)
T=0.0002/3 (GO-ESP)
T=0.0004/45 (TOPMED)
HGVS Names
  • CM000678.2:g.88841002C>T
  • NC_000016.10:g.88841002C>T
  • NC_000016.9:g.88907410C>T
  • NG_008667.1:g.20965G>A
  • NM_000512.4:c.412G>A
  • NM_001323543.1:c.-144G>A
  • NM_001323544.1:c.430G>A
  • NP_000503.1:p.Val138Ile
  • NP_001310473.1:p.Val144Ile
  • XP_005256358.1:p.Val138Ile
  • XP_005256359.1:p.Val144Ile
  • XP_011521284.1:p.Val144Ile
  • XP_016878600.1:p.Val144Ile
  • XP_016878601.1:p.Val144Ile
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 ss342437133 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs140018158 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
ss342437133NHLBI-ESP|ESP2500-chr16-88907410fwd/BC/Tggcgtggccaggagacttaccacttgccgaaatcttgctgacgtagccggccttcttcag03/25/1103/27/11134Genomicunknown
ss4647591151000GENOMES|20101123_snps_10926345_chr16_88907410fwd/C/Tggcgtggccaggagacttaccacttgccgaaatcttgctgacgtagccggccttcttcag07/20/1107/20/11135Genomicunknown
ss13575148791000GENOMES|PHASE3_V1_70999054fwd/C/Tggccaggagacttaccacttgccgaaatcttgctgacgtagccggccttc08/16/1408/16/14142Genomicunknown
ss1692468325EVA_EXAC|EVA_EXAC_7816796fwd/C/Tggccaggagacttaccacttgccgaaatcttgctgacgtagccggccttc03/04/1503/04/15144Genomicunknown
ss1808658353HAMMER_LAB|Hsieh_7685373fwd/BC/Tggccaggagacttaccacttgccgaaatcttgctgacgtagccggccttc07/15/1507/16/15146Genomicunknown
ss1959710069ILLUMINA|16:88907410-CT-0_T_R_2299447387fwd/BC/Tggccaggagacttaccacttgccgaaatcttgctgacgtagccggccttc11/13/1511/13/15147Genomicunknown
ss2214730076HUMAN_LONGEVITY|HLI-16-88841002-C-Tfwd/C/Tggccaggagacttaccacttgccgaaatcttgctgacgtagccggccttc11/18/1611/18/16150Genomicunknown
ss2379552964TOPMED|16_88907410_C/Tfwd/C/Tggccaggagacttaccacttgccgaaatcttgctgacgtagccggccttc11/19/1611/19/16150Genomicunknown
ss2742240956GNOMAD|exomes_rs140018158fwd/C/Tggccaggagacttaccacttgccgaaatcttgctgacgtagccggccttc05/17/1705/17/17151Genomicunknown
ss2749624898GNOMAD|coding_rs140018158fwd/C/Tggccaggagacttaccacttgccgaaatcttgctgacgtagccggccttc05/17/1705/17/17151Genomicunknown
ss2946568214GNOMAD|rs140018158fwd/C/Tggccaggagacttaccacttgccgaaatcttgctgacgtagccggccttc05/23/1705/23/17151Genomicunknown
ss3021740336ILLUMINA|MEGA_Consortium_v2_15070954_A2_16:88907410-CT-0_T_R_2299447387fwd/C/Tggccaggagacttaccacttgccgaaatcttgctgacgtagccggccttc06/28/1706/28/17151Genomicunknown
ss3254721241TOPMED|TOPMed_freeze_5?chr16:88,841,002fwd/C/Tggccaggagacttaccacttgccgaaatcttgctgacgtagccggccttc10/01/1710/01/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs140018158|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 GAGTCTGATG CCGCAGGATA CTCGCGGCCG TGGGACCAGC CTGGTGACCT GAGATCCTGC
 TGGCAAGGTC ACGCTGGCCT GCACAGGGAC GCTGGAGACA CCTGAACACA CCCAGAATCA
 GCTGCCGTTT CCCACCCAAG ACACCCTCCT CATTTGGAAA CTTGTGGCCA TGTCCCTTGG
 AACCAAGGCC AGGAAGTGGA TGGAGCAGGA CGCCTGGGCA GGCGTGGCCA GGAGACTTAC
 CACTTGCCGA
 Y
 AATCTTGCTG ACGTAGCCGG CCTTCTTCAG AAGCTCCGGC AGGAGCTGCT CCGAGTCTGG
 GATGCCGCCC ACAATCTCCT GCGGTGTGTA GGCTGGAAGA GCAGCGCTGG GTGAGCCCCG
 AGGAGACCCC GAGAAGCTGC CACCAACCCC ATCCTAACAG GACACTGGGG GCTGCGTCCA
 CACATCCTAA CAGGACACTG GCCCCTCGGG GTCAAAGGCT GTGCCTGGGG GCTGCGCGTC
 CACAGGGCAT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000016
dbSNP Blast Analysis
3D structure mapping
NP_000503  

  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
ss1357514879EAS 1008AF 1.00000000
EUR 1006AF 1.00000000
AFR 1322AF 0.999199990.00080000
AMR 694AF 1.00000000
SAS 978AF 1.00000000
ss1692468325ExAc_Aggregated_Populations121408AF 0.999942360.00005766
ss342437133ESP_Cohort_Populations 4550GF0.999560420.00043956 1.000000000.999780240.00021978

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.000+/-0.0080000

  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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