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Reference SNP (refSNP) Cluster Report: rs3049448                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:102/141
Map to Genome Build:106/Weight
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:DIV:
deletion/insertion variation
RefSNP Alleles:-/TCTGATCC (FWD)
Allele Origin:
Ancestral Allele:Not available
Clinical Channel:unknown
Clinical Significance:NA
MAF/MinorAlleleCount:-=0.455/990
MAF Source:1000 Genomes
HGVS Names
  • NC_000013.11:g.95475162_95475169delGGATCAGA
  • NM_001160100.1:c.157+41172_157+41179delGGATCAGA
  • NM_182848.3:c.214+41115_214+41122delGGATCAGA
  • NT_009952.15:g.9222183_9222190delGGATCAGA
Links , Linkout
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 ss287911201 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3049448 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
ss4280663TSC-CSHL|TSC1590652fwd/B-/TCTGATCCccctggcagggagctgctgccgtctgatccgagttgtgggacagcactgggtgtgtgctc11/09/0110/10/03102Genomicunknown
ss49852098MARSHFIELD|MID-2546byFreqfwd/-/TCTGATCCccctggcagggagctgctgccgtctgatccgagttgtgggacagcactgggtgtgtgctc12/13/0511/03/06126Genomicunknown
ss77953077HGSV|Cor12156_DIV_20070510.chr13_94925416-94925425_1rev/-/GGATCAGAacccagtgctgtcccacaactcggatcagacggcagcagctccctgccagggattaagag10/15/0710/16/07137Genomicunknown
ss80818460HGSV|Cor12878_DIV_20070510.chr13_94925416-94925425_1rev/-/GGATCAGAacccagtgctgtcccacaactcggatcagacggcagcagctccctgccagggattaagag11/26/0711/26/07137Genomicunknown
ss287911201GMI|GMI_NA10851_INDEL_244486rev/-/GGATCAGAgagcacacacccagtgctgtcccacaactcggatcagacggcagcagctccctgccaggg04/26/1012/22/10138Genomicunknown
ss289197707GMI|GMI_AK_INDEL_871251rev/-/GGATCAGAgagcacacacccagtgctgtcccacaactcggatcagacggcagcagctccctgccaggg12/20/1012/28/11137Genomicunknown
ss3275621261000GENOMES|JPTCHB_chr13_94925408_indelrev/-/GGATCAGAgagcacacacccagtgctgtcccacaactcggatcagacggcagcagctccctgccaggg03/11/1104/03/11135Genomicunknown
ss3276700431000GENOMES|CEU_chr13_94925408_indelrev/-/GGATCAGAgagcacacacccagtgctgtcccacaactcggatcagacggcagcagctccctgccaggg03/11/1104/03/11135Genomicunknown
ss3281091441000GENOMES|YRI_chr13_94925408_indelrev/-/GGATCAGAgagcacacacccagtgctgtcccacaactcggatcagacggcagcagctccctgccaggg03/11/1104/03/11135Genomicunknown
ss5000758901000GENOMES|20110316_indels_chr13_96127407_96127414rev/-/GGATCAGAcacacccagtgctgtcccacaactcggatcagacggcagcagctccctgc03/19/1203/20/12137Genomicunknown
ss552325947LUNTER|CEU_13_94925409-94925416rev/-/GGATCAGAcacacccagtgctgtcccacaactcggatcagacggcagcagctccctgc11/21/1211/21/12138Genomic95 %
ss552640380LUNTER|YRI_13_94925409-94925416rev/-/GGATCAGAcacacccagtgctgtcccacaactcggatcagacggcagcagctccctgc11/21/1211/21/12138Genomic95 %
ss553533258LUNTER|JPTCHB_13_94925409-94925416rev/-/GGATCAGAcacacccagtgctgtcccacaactcggatcagacggcagcagctccctgc11/21/1211/21/12138Genomic95 %
ss554713890TISHKOFF|del_chr13_96127416-96127423rev/-/GGATCAGAgtgctgtcccacaactcggatcagacggcagcagctccctgccagggatt11/22/1211/22/12138Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3049448|allelePos=501|totalLen=1001|taxid=9606|snpclass=2|alleles='-/TCTGATCC'|mol=Genomic|build=138
 CCCTTGCCAC CTTCCTGGAG CTCCAAGCCA GTCACCCTCA CCAGGGGCCC AGAGGCCATT
 GGGGCAAACA GCACTGAAAC TCTTTCAAAC CCTGCTGGCC ACTTCCCTCC CTTGGGGAGC
 AGCAGAGAAG CCCACTGGTG GCCAGTGCTC AGTCAGCACA GCTGAGGTGG GCTGGCAAAA
 CTCCTGGCTC TCTCTGTCTC CGAGAATTGG CTGGGGCATC TGATGGTGGT TGCAGAGCCT
 CATCTCCCCT CTCTTGAACT TAGCGGAGAT CAGGCTCAGC AGATCTGCCC AGGTCCCCAG
 GAGGCCGGGC TGGTTACAGT CTCTGGGGAC CAGGTGCTCC CCTTTTGAAC CAAGGTTATT
 TCTCCCAACC AGGGAGCTTC CATAATCACA GGGATGTCCC CTGACCCCAT CCCTACAAAT
 ATGTAGAGTG CAAGGGAGCA GGCAGCAGGG GGCAGGGGTG GGCTCTTAAT CCCTGGCAGG
 GAGCTGCTGC CGTCTGATCC
 N
 GAGTTGTGGG ACAGCACTGG GTGTGTGCTC CTACTTCCTG GCTTATAGGT TTCCTCCTCT
 GTGTGGCACC AGCATGTGTG TCCTTGACTC CTTAGCAGAG AGGAGCCAAT TCACTCTGTC
 TGTGAAGCCA AAACACAAGA GACCTGCAAG TTTTGAACCC TCCTCTCCAC CAAGATGTGA
 GACGTATACT GGCAGATCCC TGAGATCCCA TTAGGCTCAG GCCCTCCACC CACCGCCTCT
 TCTGGGCTCA AGCCTCCCTC TGGCACCTGC AGCACAGAAC AGCCTCCTCC AGCCTGGCTC
 CACGCCTGCC CCACCCCCAT CTTCCTCCAC CCTACCCCCT GGAATGAGCT TCCCAAAAGG
 CAGATCTTAC CAGGTCTCTC TCCTCCTTGG AGCACTTATC AATCTCTACT TGCCTTTTCC
 ATTCTCTTCT CCCCATCCGT TTCTACATAT GGGTTTCCTC CCCAGTTTCA CTGAGACAGG
 GCCATTGCCC TTGCAGGCCT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
AL357061.19 NT_009952.14
dbSNP Blast Analysis

  Population Diversity (in rs orientation) back to top

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceHWP-
TCTGATCC
ss49852098European 200AF 0.355 0.645
Japanese 50AF 0.454 0.546
African 42AF 0.436 0.564
CORIELL_M44PDR 88AF 0.395 0.605
AMERICAN_INDIAN 50AF 0.325 0.675

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0000ALFRED: The Allele Frequency Database

  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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