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Reference SNP (refSNP) Cluster Report: rs6679677                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.0258/129 (1000 Genomes)
A=0.0587/7374 (TOPMED)
HGVS Names
  • CM000663.2:g.113761186C>A
  • NC_000001.10:g.114303808C>A
  • NC_000001.11:g.113761186C>A
  • NM_001323041.1:c.-2309G>T
  • NM_001323042.1:c.-1445G>T
  • NM_001323043.1:c.-2194G>T
  • NM_001323044.1:c.-2693G>T
  • NM_001323045.1:c.-2404G>T
  • NM_001323046.1:c.-2663G>T
  • NM_001323047.1:c.-2309G>T
  • NM_001323048.1:c.-2194G>T
  • NM_001323049.1:c.-2483G>T
  • NM_001323050.1:c.-2404G>T
  • NM_001323051.1:c.-2693G>T
  • NM_001323052.1:c.-2194G>T
  • NM_001323053.1:c.-2309G>T
  • NR_136564.1:n.-1646G>T
  • NR_136565.1:n.-1646G>T
  • NR_136566.1:n.-1646G>T
  • NR_136567.1:n.-1646G>T
  • NR_136568.1:n.-1646G>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 ss284124179 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6679677 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
ss9855676BCM_SSAHASNP|chr1.NT_019273.15_4739612byFreqfwd/TA/Cagcgaacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatttattc06/27/0310/25/06116Genomicunknown
ss66195856AFFY|SNP_A-2267906byFreqfwd/TA/Cgaatccttgctcccaacaataatctgtgatct10/27/0603/31/08127Genomicunknown
ss75187089ILLUMINA|ILMN_Human_1M_rs6679677fwd/TA/Cagcgaacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatttattc08/28/0708/29/07129Genomicunknown
ss76277608AFFY|AFFY_6_1M_SNP_A-2267906fwd/TA/Cgaatccttgctcccaacaataatctgtgatct08/28/0708/30/07129Genomicunknown
ss82287139KRIBB_YJKIM|KHS221799fwd/TA/Cagcgaacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatttattc11/30/0712/02/07130Genomicunknown
ss87727249BCMHGSC_JDW|JWB-0108047fwd/TA/Cagcgaacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatttattc02/26/0802/26/08129Genomicunknown
ss1085374781000GENOMES|CEU.trio.12.15.2008_147268_chr1_114105331fwd/TA/Cagcgaacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatttattc12/16/0812/16/08130Genomicunknown
ss138063450ENSEMBL|ENSSNP11610775fwd/TA/Cagcgaacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatttattc05/15/0905/16/09131Genomicunknown
ss160797216ILLUMINA|HumanOmni1-Quad_v1-0_B_rs6679677-128_T_F_1514147467fwd/TA/Cagcgaacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatttattc08/04/0910/04/09131Genomicunknown
ss173097150AFFY|GenomeWideSNP_5_SNP_A-2267906fwd/TA/Cgaatccttgctcccaacaataatctgtgatct10/01/0910/03/09132Genomicunknown
ss174066187ILLUMINA|Human1M-Duov3_B_rs6679677-128_T_F_1514147467fwd/TA/Cagcgaacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatttattc10/01/0910/04/09132Genomicunknown
ss2306986761000GENOMES|pilot_1_CEU_303305_chr1_114105331fwd/A/Cagcgaacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatttattc05/01/1005/01/10132Genomicunknown
ss244305931ILLUMINA|CVDSNP55v1_A_rs6679677fwd/TA/Cagcgaacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatttattc06/10/1006/10/10132Genomicunknown
ss284124179GMI|GMI_NA10851_SNP_136945fwd/A/Cagcgaacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatttattc12/17/1012/17/10138Genomicunknown
ss290602301PJP|SNP_108659_chr1_114105331fwd/A/Cagcgaacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatttattc01/21/1101/21/11134Genomicunknown
ss410942626ILLUMINA|Cardio-Metabo_Chip_11395247_A_rs6679677fwd/TA/Cagcgaacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatttattc06/07/1106/07/11135Genomicunknown
ss482321868ILLUMINA|HumanOmni1-Quad_v1-0_C_rs6679677-131_T_F_1852938599fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt01/30/1208/28/15146Genomicunknown
ss491298565EXOME_CHIP|.GWAS._14792_chr_1_114303808fwd/TA/Cagcgaacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatttattc03/05/1203/05/12137Genomicunknown
ss536071794ILLUMINA|HumanOmni5-4v1_B_kgp7261981-0_T_F_1902337139fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt06/22/1208/28/15146Genomicunknown
ss648324073SSMP|1_114303808fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt12/14/1202/09/15138Genomicunknown
ss780685963ILLUMINA|HumanOmni25Exome-8v1_A_exm-rs6679677-131_T_F_1990493246fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt05/30/1307/09/15146Genomicunknown
ss783359469ILLUMINA|HumanOmniExpressExome-8v1_A_exm-rs6679677-131_T_F_1990493246fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt05/31/1306/18/15146Genomicunknown
ss975588088EVA-GONL|EVA-GONL_rs6679677fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt04/23/1404/23/14142Genomicunknown
ss1068205979JMKIDD_LAB|HGDP_WGS_chr1_114303808fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt07/10/1407/10/14142Genomicunknown
ss12925005711000GENOMES|PHASE3_V1_3295341fwd/A/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt08/16/1408/16/14142Genomicunknown
ss1397257914HAMMER_LAB|HAMMER_LAB_rs6679677fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt09/30/1409/30/14146Genomicunknown
ss1574334304EVA_GENOME_DK|EVA_GENOME_DK_snv_rs6679677fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt02/19/1502/19/15144Genomicunknown
ss1584968956EVA_DECODE|EVA_DECODE_1_114105331_839708_rs6679677fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt03/02/1503/02/15144Genomicunknown
ss1601026481EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_114303808_1814024fwd/A/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt03/04/1503/04/15144Genomicunknown
ss1644020514EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_114303808_1814024fwd/A/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt03/04/1503/04/15144Genomicunknown
ss1712364443EVA_SVP|EVA_SVP_58995fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt03/12/1503/12/15144Genomicunknown
ss1751864539ILLUMINA|OmniExpressExome-8v1-1_B_exm-rs6679677-131_T_F_1990493246fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt05/27/1506/09/15146Genomicunknown
ss1917732850ILLUMINA|HumanExome-12v1-1_B_exm-rs6679677-131_T_F_1990493246fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt10/16/1510/16/15147Genomicunknown
ss1946005555ILLUMINA|HumanCoreExome-12v1-0_C_exm-rs6679677-131_T_F_1990493246fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt10/29/1510/29/15147Genomicunknown
ss1958304653ILLUMINA|exm-rs6679677-131_T_F_1990493246fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt11/13/1511/13/15147Genomicunknown
ss2019918574JJLAB|SNP421129fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt08/29/1608/30/16149Genomicunknown
ss2094847235ILLUMINA|Immuno_BeadChip_11419691_B_imm_1_114105331-1_T_F_1670121127fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt09/27/1609/27/16150Genomicunknown
ss2094972618ILLUMINA|InfiniumImmunoArray-24v2-0_A_imm_1_114105331-1_T_F_2310582006fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt09/27/1609/27/16150Genomicunknown
ss2094972620ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs6679677-138_T_F_2264362982fwd/TA/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt09/27/1609/27/16150Genomicunknown
ss2147937374USC_VALOUEV|NC_000001.10:g.114303808C>Afwd/A/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt11/17/1611/17/16150Genomicunknown
ss2165854231HUMAN_LONGEVITY|HLI-1-113761186-C-Afwd/A/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt11/18/1611/18/16150Genomicunknown
ss2328219153TOPMED|1_114303808_C/Afwd/A/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt11/19/1611/19/16150Genomicunknown
ss2632565409ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_seq-rs6679677-131_T_F_2130fwd/A/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt02/02/1702/02/17151Genomicunknown
ss2635002482ILLUMINA|Cancer_BeadChip_11459870_A_rs6679677-128_T_F_1616887918fwd/A/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt02/02/1702/02/17151Genomicunknown
ss2759755700GNOMAD|rs6679677fwd/A/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt05/17/1705/17/17151Genomicunknown
ss2984871516AFFY|Axiom_PsorMich_Affx-4560687fwd/A/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt05/24/1705/24/17151Genomicunknown
ss2985522540AFFY|Axiom_Smokesc1_Affx-4560687fwd/A/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt05/24/1705/24/17151Genomicunknown
ss2987466727SWEGEN|NC_000001.10:g.114303808C>Afwd/A/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt05/30/1705/30/17151Genomicunknown
ss3021122706ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm-rs6679677-131_T_F_1990493246fwd/A/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt06/28/1706/28/17151Genomicunknown
ss3023723837BIOINF_KMB_FNS_UNIBA|1.113761186C>Afwd/A/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt07/05/1707/05/17151Genomicunknown
ss3087256079TOPMED|TOPMed_freeze_5?chr1:113,761,186fwd/A/Cacaaggtctgaatccttgctcccaacaataatctgtgatcttaagcaatt09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6679677|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=151
 ACTGAGGCAG GAGGATCGTC TGAGTCCACG AGTTCGAGGC TGTAGTGAGC TATGATTGCA
 CCACTGCACT TCGGCCTAGG CAACAGAGAC CTGTCTCAAA TAAAGTAAAA ATTATTTTAC
 CCTTATTTTT ATATTGCACA CATTGGCAGT GGTTTCCTTC TGCTTTTGCT CCTTGACAGC
 TTTTCCTTTC CTTAGTGCTA AACATTACAA TTCTGTTGAG CTTCAAGACA AATGGCCAAC
 TTGAAAAAAG AGATAAATGA CAAGTGAAAA ACGTCGAATT TTGCACACGT AAATATTTAA
 CCTCAATTAC ATTAATAGCA AAAGTACTTT ACTTCACTGT TTGGCACACA GATTTTCAGG
 GAGTGTCTGG AGGAACTGAA TCAGGTAAGA AGTATTAGAG AATAGTGGTA AGTAGTAAAC
 CATTTTTCAG GTGCCCTGTT GGAAACTATT CAGTGCTTCC TGCGGCTACC AGCGAACAAG
 GTCTGAATCC TTGCTCCCAA
 M
 CAATAATCTG TGATCTTAAG CAATTTATTC AACTAACAAG CCTGTTTTCT CACCTGTATT
 ATGGAGATAG TCACCTTCTT AAGGATGTGA GGATTAAATG AGAAACCCTC ATATAAACTG
 CCTGGCCCAT GGCAGTTACT CAAAAAATGT GAAGTCCCTT TCTTTTCCTT TCCTAGACAG
 AACCAAAGGC TATCAGTGCT TAGGACAGGT ACCTCAATTA AAGATAACTT CACACAAAAA
 CTGATGAGGA AAGAAATCCA TTTTGTTGTG TCACATTAAT ACATCAATGA CATAAAAGTC
 TATACGCCAT CTTCATTAAT ACTCAATGCA CTTTCAAGAA AATCCACATC ACCAGAATAA
 AAATTTAAGA CTGTCCTCTT TTAAGTAGAT ACACACCAAT TTAAGCAATT AAGAGGCATT
 AACTACAACA AATGTCAAGT GTATTTTTTC TTCTTCCCCC AAACTAATTG CATCTCAATA
 TGGATGGAAT TTTCCCCAGA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_019273
dbSNP Blast Analysis

  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
A/C
C/C
HWPA
C
ss1292500571EAS 1008AF 1.00000000
EUR 1006AF 0.091500010.90850002
AFR 1322AF 0.002300000.99769998
AMR 694AF 0.030300000.96969998
SAS 978AF 0.013300000.98670000
ss138063450ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss230698676pilot_1_CEU_low_coverage_panel 120AF 0.125000000.87500000
ss66195856HapMap-CEUEuropean 118IG 0.271186440.728813590.583882000.135593220.86440676
HapMap-HCBAsian 90IG 1.00000000 1.00000000
HapMap-JPTAsian 90IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
ss76277608ICMHP 10IG 0.200000000.80000001 0.100000000.89999998
ss9855676HapMap-CEUEuropean 226IG0.008849560.212389380.778761090.654721000.115044250.88495576
HapMap-HCBAsian 90IG 1.00000000 1.00000000
HapMap-JPTAsian 88IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
HAPMAP-ASW 98IG 0.040816330.959183691.000000000.020408160.97959185
HAPMAP-GIH 176IG 0.011363640.988636371.000000000.005681820.99431819
HAPMAP-MEX 100IG0.020000000.060000000.920000020.010028000.050000000.94999999
HAPMAP-MKK 286IG 0.006993010.993007001.000000000.003496500.99650347
HAPMAP-TSI 174IG 0.137931030.862068951.000000000.068965520.93103451
ENSEMBL_Venter 2IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.050+/-0.1500000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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