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Reference SNP (refSNP) Cluster Report: rs1055933                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/147
Map to Genome Build:107/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.1002/502 (1000 Genomes)
HGVS Names
  • NC_000011.10:g.63956703G>A
  • NC_000011.9:g.63724175G>A
  • NM_001300800.1:c.*2224G>A
  • NM_024771.3:c.*2224G>A
  • XM_005274295.1:c.*2224G>A
  • XM_005274296.1:c.*2224G>A
  • XM_005274297.1:c.*2224G>A
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 ss16543653 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1055933 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
ss1535091LEE|644109fwd/TA/Gttttgagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagcactttg09/13/0010/10/0386cDNAunknown
ss4397338LEE|ge644109fwd/TA/Gttttgagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagcactttg04/25/0210/10/03106cDNAunknown
ss4423657LEE|e644109fwd/TA/Gttttgagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagcactttg04/26/0210/10/03106cDNAunknown
ss15912998SC_SNP|NT_033903.6_8897217fwd/TA/Gttttgagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagcactttg11/17/0311/22/03120Genomicunknown
ss16543653CSHL-HAPMAP|CSHL-HuAA-200402.chr11.NT_033903.6_8897217byFreqfwd/TA/Gttttgagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagcactttg02/17/0405/16/04120Genomicunknown
ss39942171ABI|hCV11662759fwd/TA/Gttttgagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagcactttg07/16/0507/16/05126Genomicunknown
ss97392256HUMANGENOME_JCVI|1103649706330fwd/TA/Gttttgagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagcactttg03/29/0803/29/08130Genomicunknown
ss144115043ENSEMBL|ENSSNP4461093fwd/TA/Gttttgagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagcactttg12/08/0810/20/09131Genomicunknown
ss159910744ILLUMINA|HumanOmni1-Quad_v1-0_B_rs1055933-128_T_F_1562528761fwd/TA/Gttttgagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagcactttg08/04/0910/01/09131Genomicunknown
ss2252809841000GENOMES|pilot_1_YRI_7090667_chr11_63480751fwd/A/Gttttgagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagcactttg04/22/1004/22/10132Genomicunknown
ss2355893101000GENOMES|pilot_1_CEU_5193939_chr11_63480751fwd/A/Gttttgagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagcactttg05/01/1005/01/10132Genomicunknown
ss255225976BL|SNP84476_11_63480751fwd/TA/Gttttgagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagcactttg08/19/1008/20/10134Genomicunknown
ss291060789PJP|SNP_567147_chr11_63480751fwd/A/Gttttgagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagcactttg01/21/1101/21/11134Genomicunknown
ss479708860ILLUMINA|HumanOmni1-Quad_v1-0_C_rs1055933-131_T_F_1863270536fwd/TA/Gagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagca01/30/1208/28/15146Genomicunknown
ss482867220ILLUMINA|HumanOmni2.5-4v1_B_SNP11-63480751-0_T_F_1618504361fwd/TA/Gttttgagaaacagcaggcatggctgagtgcgnnnnntacacctgtaatcccagcactttg01/30/1202/02/12137Genomicunknown
ss483613807ILLUMINA|HumanOmni2.5-4v1_D_kgp5836153-0_T_F_1797816793fwd/TA/Gttttgagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagcactttg01/30/1202/02/12137Genomicunknown
ss535818348ILLUMINA|HumanOmni5-4v1_B__kgp5836153-0_T_F_1797816793fwd/TA/Gagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagca06/22/1208/29/15146Genomicunknown
ss562607214TISHKOFF|snp_chr11_63724175fwd/TA/Gagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagca11/22/1211/23/12138Genomicunknown
ss658119036SSMP|11_63724175fwd/TA/Gagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagca12/14/1202/12/15138Genomicunknown
ss779511861ILLUMINA|HumanOmni25Exome-8v1_A_kgp5836153-0_T_F_1797816793fwd/TA/Gagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagca05/30/1307/10/15146Genomicunknown
ss782250289ILLUMINA|HumanOmni2.5-4v1_H_kgp5836153-0_T_F_1797816793fwd/TA/Gagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagca05/30/1307/29/15146Genomicunknown
ss834982231ILLUMINA|HumanOmni2.5-8v1_A_kgp5836153-0_T_F_1797816793fwd/TA/Gagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagca09/18/1307/29/15146Genomicunknown
ss988603027EVA-GONL|EVA-GONL_rs1055933fwd/TA/Gagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagca04/23/1404/25/14142Genomicunknown
ss1077787497JMKIDD_LAB|HGDP_WGS_chr11_63724175fwd/TA/Gagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagca07/10/1407/12/14142Genomicunknown
ss13415869391000GENOMES|PHASE3_V1_54407822fwd/A/Gagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagca08/16/1408/16/14142Genomicunknown
ss1575756937EVA_GENOME_DK|EVA_GENOME_DK_snv_rs1055933fwd/TA/Gagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagca02/19/1502/19/15144Genomicunknown
ss1598265159EVA_DECODE|EVA_DECODE_11_63480751_474948_rs1055933fwd/TA/Gagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagca03/02/1503/04/15144Genomicunknown
ss1626751722EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_11_63724175_30051761fwd/A/Gagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagca03/04/1503/04/15144Genomicunknown
ss1669745755EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_11_63724175_30051761fwd/A/Gagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagca03/04/1503/04/15144Genomicunknown
ss1711296500EVA_MGP|EVA_XIMO_412260fwd/TA/Gagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagca03/09/1503/09/15144Genomicunknown
ss1931961874WEILL_CORNELL_DGM|SNV:chr11:63724175fwd/TA/Gagaaacagcaggcatggctgagtgcgtggcttacacctgtaatcccagca10/16/1510/17/15147Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1055933|allelePos=211|totalLen=711|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=147
 TGGGTGCTTG GTGCCATACC CTGCTCACCC TAGTCTCTGC AGGCCATGTC CTGAAGGGTT
 CCTCAGGAGG TCGGGACTAG GGTGGGAGAG GCACTATCTG AGACCTGCAA TCACTCTTGT
 TGGTCTTGAG CCCATTCATT TCCAAAACAT CCATCTTTCT CCACTTCCCC CAGGTCTTGG
 TTTTGAGAAA CAGCAGGCAT ggctgagtgc
 R
 gtggcttaca cctgtaatcc cagcactttg ggaggctgag gcaggcgggt cacctgaggt
 caggagttca agaccagcct ggtcaacatg gcaaaagccc atctctacta aaaaatacaa
 aaatcagcca ggcgtggttg tggcctgtaa tcccagctac tcgggaggct gaggcaggag
 actcgcttga acccaggagg tggaggttgt ggtgagctga gatcacgcca ttgcactcca
 gcctaggcga cagagtgaga ctccatctca aaaaaaaaaa aaagagaaaC ATAGCAGGCC
 TTTTTTACCA GGCTTTTTGT GTTTTGTTTG TTTGTTTGGA GCATGTTAAG ATTTTTTTAA
 GATTTTTAAA ATTTTAGTTA TATCCACCCT ATTTCAGGTT ATTTTTGTTG GTGTCAAGTA
 TGTATAGGAC ATGTGAATGG TTCTTTTTAA TTTTTTTTTA AGAGGAAATT TGGAAGATAA
 ACTCCTTGAT ATATATATAT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_033903 ABBA01003282 Hs.139189
dbSNP Blast Analysis
UniGene Cluster ID
523753

  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.
SourceA/A
G/G
HWPA
G
ss1341586939EAS 1008AF 0.007900000.99210000
EUR 1006AF 0.280300020.71969998
AFR 1322AF 0.012900000.98709995
AMR 694AF 0.100899990.89910001
SAS 978AF 0.127800000.87220001
ss144115043ENSEMBL_Venter 2IG1.00000000 1.00000000
ss16543653CEPH 184AF 0.250000000.75000000
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss225280984pilot_1_YRI_low_coverage_panel 118AF 0.008474580.99152541
ss235589310pilot_1_CEU_low_coverage_panel 120AF 0.208333330.79166669
ss97392256J. Craig Venter 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.180+/-0.2403300

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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