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Reference SNP (refSNP) Cluster Report: rs2000974                 ** With Benign allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:92/141
Map to Genome Build:106/Weight
Validation Status:byClusterbyFreq
Citation:PubMed
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:C:germline
T:germline
Ancestral Allele:C
Clinical Channel:Link to VarView pending
Clinical Significance:With Benign allele [ClinVar]
MAF/MinorAlleleCount:T=0.029/31
MAF Source:1000 Genomes
HGVS Names
  • NC_012920.1:m.1048C>T
Links
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' or 'Contig Pos' column value to see variation in NCBI sequence 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 ss2915465 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2000974 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
ss2915465TSC-CSHL|TSC0922470fwd/BC/Taactacgaaagtggctttaacatatctgaaacacaatagctaagacccaaactgggatta01/03/0110/10/0392Genomicunknown
ss4044489SC_JCM|V00662.1_1048fwd/BC/Tgactacgaaagtggctttaacatatctgaaacacaatagctaagacccaaactgggatta09/26/0110/10/03104Genomicunknown
ss35124309SSAHASNP|TA-079.chrM_1050fwd/BC/Tgactacgaaagtggctttaacatatctgaaacacaatagctaagacccaaactgggatta03/11/05125Genomicunknown
ss46525661BROAD|mt1048fwd/BC/Tnactacgaaagtggctttaacatatctgaaacacaatagctaagacccaaactgggatta04/25/0507/21/05126Genomicunknown
ss66863464ILLUMINA|HumanHap550v1.1_MitoC1050Tfwd/BC/Tgactacgaaagtggctttaacatatctgaaacacaatagctaagacccaaactgggatta11/14/0611/14/06127Genomicunknown
ss66932018ILLUMINA|HumanHap650Yv1.0_MitoC1050Tfwd/BC/Tgactacgaaagtggctttaacatatctgaaacacaatagctaagacccaaactgggatta11/14/0611/14/06127Genomicunknown
ss68074772ILLUMINA|HumanHap250Sv1.0_MitoC1050Tfwd/BC/Tgactacgaaagtggctttaacatatctgaaacacaatagctaagacccaaactgggatta12/06/0612/07/06127Genomicunknown
ss70458823ILLUMINA|HumanHap550v3.0__MitoC1050Tfwd/BC/Tgactacgaaagtggctttaacatatctgaaacacaatagctaagacccaaactgggatta04/20/0703/29/08130Genomicunknown
ss70979363ILLUMINA|HumanHap650Yv3.0_MitoC1050Tfwd/BC/Tgactacgaaagtggctttaacatatctgaaacacaatagctaagacccaaactgggatta04/23/0704/23/07127Genomicunknown
ss75878487ILLUMINA|ILMN_Human_1M_MitoC1050Tfwd/BC/Tgactacgaaagtggctttaacatatctgaaacacaatagctaagacccaaactgggatta08/28/0708/29/07129Genomicunknown
ss76713257AFFY|AFFY_6_1M_SNP_A-8574535fwd/BC/Tctttaacatatctgaaacacaatagctaagac08/28/0708/30/07130Genomicunknown
ss244317134LMM-PCPGM|11613163fwd/BC/Tgactacgaaagtggctttaacatatctgaaacacaatagctaagacccaaactgggatta06/15/1006/15/10136Genomicunknown
ss491581292EXOME_CHIP|mitoch_297518_chr_MT_1048fwd/BC/Tgactacgaaagtggctttaacatatctgaaacacaatagctaagacccaaactgggatta03/05/1203/06/12137Genomicunknown
ss567117901TISHKOFF|snp_chrM_1048fwd/BC/Tcgaaagtggctttaacatatctgaaacacaatagctaagacccaaactgg11/22/1211/23/12138Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2000974|allelePos=57|totalLen=608|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=138
 TAAAAAACTC CAGTTGACAC AAAATAAACT ACGAAAGTGG CTTTAACATA TCTGAA
 Y
 ACACAATAGC TAAGACCCAA ACTGGGATTA GATACCCCAC TATGCTTAGC CCTAAACCTC
 AACAGTTAAA TCAACAAAAC TGCTCGCCAG AACACTACGA GCCACAGCTT AAAACTCAAA
 GGACCTGGCG GTGCTTCATA TCCCTCTAGA GGAGCCTGTT CTGTAATCGA TAAACCCCGA
 TCAACCTCAC CACCTCTTGC TCAGCCTATA TACCGCCATC TTCAGCAAAC CCTGATGAAG
 GCTACAAAGT AAGCGCAAGT ACCCACGTAA AGACGTTAGG TCAAGGTGTA GCCCATGAGG
 TGGCAAGAAA TGGGCTACAT TTTCTACCCC AGAAAACTAC GATAGCCCTT ATGAAACTTA
 AGGGTCGAAG GTGGATTTAG CAGTAAACTG AGAGTAGAGT GCTTAGTTGA ACAGGGCCCT
 GAAGCGCGTA CACACCGCCC GTCACCCTCC TCAAGTATAC TTCAAAGGAC ATTTAACTAA
 AACCCCTACG CATTTATATA GAGGAGACAA GTCGTAACAT GGTAAGTGTA CTGGAAAGTG
 CACTTGGACG A

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
V00662 AX039612 D38112 X62996 X93334
dbSNP Blast Analysis

  Population Diversity (in rs orientation) back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
T/T
HWPC
T
ss2915465HapMap-CEUEuropean 120IG 1.000 1.000
HapMap-HCBAsian 86IG 0.953 0.047 0.001 0.953 0.047
HapMap-JPTAsian 172IG 0.988 0.012 0.001 0.988 0.012
HapMap-YRISub-Saharan African 226IG 0.973 0.027 0.001 0.973 0.027
HAPMAP-ASW 98IG 0.878 0.122 0.001 0.878 0.122
HAPMAP-CHBAsian 82IG 0.976 0.024 0.001 0.976 0.024
HAPMAP-CHD 170IG 0.988 0.012 0.001 0.988 0.012
HAPMAP-LWK 180IG 0.822 0.178 0.001 0.822 0.178
HAPMAP-MKK 286IG 0.713 0.287 0.001 0.713 0.287

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.056+/-0.1580000

  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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