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Reference SNP (refSNP) Cluster Report: rs78779412                 ** With Benign allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:131/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/G/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:With Benign allele [ClinVar]
MAF/MinorAlleleCount:G=0.0022/264 (ExAC)
G=0.0082/41 (1000 Genomes)
G=0.0077/100 (GO-ESP)
G=0.0064/806 (TOPMED)
HGVS Names
  • CM000664.2:g.202515016C>G
  • CM000664.2:g.202515016C>T
  • NC_000002.11:g.203379739C>G
  • NC_000002.11:g.203379739C>T
  • NC_000002.12:g.202515016C>G
  • NC_000002.12:g.202515016C>T
  • NG_009363.1:g.143690C>G
  • NG_009363.1:g.143690C>T
  • NM_001204.6:c.621+37C>G
  • NM_001204.6:c.621+37C>T
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 ss219759265 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs78779412 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
ss2197592651000GENOMES|pilot_1_YRI_1568948_chr2_203087984fwd/C/Gttgccgttagattatggactgttgtttctatgtgatactagacctggaacagtgacttca04/22/1004/22/10132Genomicunknown
ss4898476101000GENOMES|20110521_exome_357215_chr2_203379739fwd/C/Gttgccgttagattatggactgttgtttctatgtgatactagacctggaacagtgacttca02/10/1202/21/12137Genomicunknown
ss533849149ILLUMINA|HumanOmni5-4v1_B_kgp14554867-0_T_F_1900072515fwd/C/Ggttagattatggactgttgtttctatgtgatactagacctggaacagtga06/22/1208/28/15146Genomicunknown
ss712477774NHLBI-ESP|ESP6500SI-chr2-203379739fwd/C/Gttgccgttagattatggactgttgtttctatgtgatactagacctggaacagtgacttca02/20/1302/20/13138Genomicunknown
ss13012527161000GENOMES|PHASE3_V1_12405501fwd/C/Ggttagattatggactgttgtttctatgtgatactagacctggaacagtga08/16/1408/16/14142Genomicunknown
ss13012527171000GENOMES|PHASE3_V1_12405502fwd/C/Tgttagattatggactgttgtttctatgtgatactagacctggaacagtga08/16/1408/16/14142Genomicunknown
ss1558284760BGI|AMD_SNP13762fwd/BC/Tgttagattatggactgttgtttctatgtgatactagacctggaacagtga02/05/1502/05/15144Genomicunknown
ss1686688620EVA_EXAC|EVA_EXAC_1585852fwd/C/Ggttagattatggactgttgtttctatgtgatactagacctggaacagtga03/04/1503/04/15144Genomicunknown
ss1686688621EVA_EXAC|EVA_EXAC_1585853fwd/C/Tgttagattatggactgttgtttctatgtgatactagacctggaacagtga03/04/1503/04/15144Genomicunknown
ss1798205670HAMMER_LAB|Hsieh_1303459fwd/C/Ggttagattatggactgttgtttctatgtgatactagacctggaacagtga07/15/1507/15/15146Genomicunknown
ss1921104849WEILL_CORNELL_DGM|SNV:chr2:203379739fwd/C/Ggttagattatggactgttgtttctatgtgatactagacctggaacagtga10/16/1510/16/15147Genomicunknown
ss2238327345HUMAN_LONGEVITY|HLI-2-202515016-C-G,Tfwd/C/G/Tgttagattatggactgttgtttctatgtgatactagacctggaacagtga11/18/1611/18/16150Genomicunknown
ss2404772838TOPMED|2_203379739_C/Gfwd/C/Ggttagattatggactgttgtttctatgtgatactagacctggaacagtga11/19/1611/19/16150Genomicunknown
ss2703806877GRF|rs78779412fwd/C/Tgttagattatggactgttgtttctatgtgatactagacctggaacagtga02/13/1702/13/17151Genomicunknown
ss2733259612GNOMAD|exomes_rs78779412fwd/C/G/Tgttagattatggactgttgtttctatgtgatactagacctggaacagtga05/17/1705/17/17151Genomicunknown
ss2746858646GNOMAD|coding_rs78779412fwd/C/G/Tgttagattatggactgttgtttctatgtgatactagacctggaacagtga05/17/1705/17/17151Genomicunknown
ss2785207774GNOMAD|rs78779412fwd/C/G/Tgttagattatggactgttgtttctatgtgatactagacctggaacagtga05/17/1705/17/17151Genomicunknown
ss3335804317TOPMED|TOPMed_freeze_5?chr2:202,515,016-01fwd/C/Ggttagattatggactgttgtttctatgtgatactagacctggaacagtga10/02/1710/02/17151Genomicunknown
ss3335804318TOPMED|TOPMed_freeze_5?chr2:202,515,016-02fwd/C/Tgttagattatggactgttgtttctatgtgatactagacctggaacagtga10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs78779412|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='C/G/T'|mol=Genomic|build=151
 ATTATAAAAA GTGTAAAAAG ATATTCATTT TAAGAAAACC ATATATTAGT AACCTGTTTC
 CTGTTCTTAT AGGAGACCGT AAACAAGGTC TTCACAGTAT GAACATGATG GAGGCAGCAG
 CATCCGAACC CTCTCTTGAT CTAGATAATC TGAAACTGTT GGAGGTAAGT TTGCCGTTAG
 ATTATGGACT GTTGTTTCTA
 B
 TGTGATACTA GACCTGGAAC AGTGACTTCA TTCAATCATT AAGACATTCA TTCATTTATT
 TAACCCTATT TACTAAATTA CAATTTTTTG TCAAGGCCTA TTCTAGGCAC TAGGAACATA
 GGTGAACAAT GTCTCCTGGG GCTTCTATTT GAATTGGGGA GTCTACAGAC AGGTACAGGA
 ATGTATAATA TAATTGCAAG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000002
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceHWPC
G
T
ss1686688620ExAc_Aggregated_Populations121371AF 0.997824850.00217515
ss1686688621ExAc_Aggregated_Populations121148AF 0.99966156 0.00033843
ss219759265pilot_1_YRI_low_coverage_panel 118AF 0.974576290.02542373

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.005+/-0.0500000

  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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