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Reference SNP (refSNP) Cluster Report: rs868014                 ** With Benign allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (REV)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:With Benign allele [ClinVar]
MAF/MinorAlleleCount:A=0.0129/193 (ExAC)
A=0.0671/336 (1000 Genomes)
A=0.0659/8272 (TOPMED)
HGVS Names
  • CM000663.2:g.11789390A>G
  • NC_000001.10:g.11849447A>G
  • NC_000001.11:g.11789390A>G
  • NG_013351.1:g.21714T>C
  • NM_001010881.1:c.4294A>G
  • NM_001330358.1:c.*1290T>C
  • NM_005957.4:c.*1290T>C
  • NP_001010881.1:p.Arg1432Gly
  • XP_003118893.3:p.Arg1432Gly
  • XP_011539571.2:p.Arg1477Gly
  • XP_011539573.2:p.Arg1459Gly
  • XP_011539574.1:p.Arg1477Gly
  • XP_011539576.2:p.Arg1432Gly
  • XP_011539577.2:p.Arg1432Gly
  • XP_011539578.1:p.Pro1445=
  • XP_011539579.1:p.Arg1414Gly
  • XP_011539582.2:p.Arg904Gly
  • XP_011539583.2:p.Arg904Gly
  • XP_016856551.1:p.Arg1477Gly
  • XP_016856552.1:p.Arg1477Gly
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 ss275715257 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs868014 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
ss1289986TSC-CSHL|TSC0122605byFreqfwd/BC/Tctctgccccagcccccaccccgcggtgctcggcggcttcctgtccactctcggggccctt09/06/0010/25/0686Genomic95 %
ss9808964BCM_SSAHASNP|chr1.NT_021937.15_2361381rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag06/27/0310/10/03116Genomicunknown
ss16447737CSHL-HAPMAP|CSHL-HuAA-200402.chr1.NT_021937.16_5976506rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag02/17/0403/04/04120Genomicunknown
ss20474315SSAHASNP|WGSA-200403-chr1.chr1.NT_021937.16_5976506rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag03/18/0403/18/04121Genomicunknown
ss43969199ABI|hCV8861306rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag07/18/0507/18/05126Genomicunknown
ss70457151EGP_SNPS|MTHFR-015678byFreqfwd/BC/Tctgccccaagcccccaaccccgcggtgctcggcggcttcctgtccactctcggggccctt04/19/0708/14/07127Genomicunknown
ss77727388HGSV|Cor12156_SNV_20070510.chr1_11783713rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag10/09/0710/14/07129Genomicunknown
ss87223157BCMHGSC_JDW|JWB-0011018rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag02/26/0802/26/08129Genomicunknown
ss97919654HUMANGENOME_JCVI|1103675022557rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag03/30/0803/30/08130Genomicunknown
ss105121468BGI|BGI_rs868014rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag08/06/0806/16/09131Genomicunknown
ss118499936ILLUMINA-UK|NA18507_000014209_NCBI36.1_chr1_11772034rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag01/21/0901/21/09130Genomic99 %
ss137797980ENSEMBL|ENSSNP11488336rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag05/15/0905/16/09131Genomicunknown
ss139264791ENSEMBL|ENSSNP23767rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag12/08/0810/16/09131Genomicunknown
ss154641436GMI|GMI_SNP_37507543rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag06/24/0906/24/09131Genomicunknown
ss161040058ILLUMINA|HumanOmni1-Quad_v1-0_B_SNP1-11772034-0_T_F_1588082484rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag08/04/0910/05/09131Genomicunknown
ss163078962COMPLETE_GENOMICS|NA19240_36_chr1_11772034rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag09/29/0909/29/09132Genomicunknown
ss163832319COMPLETE_GENOMICS|NA07022_36_chr1_11772034rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag09/28/0909/29/09132Genomicunknown
ss198024724BUSHMAN|BUSHMAN-chr1-11772033rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag02/16/1003/05/10132Genomicunknown
ss205479648BCM-HGSC-SUB|BCM_CMT_1011-218918rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag03/15/1003/16/10132Genomicunknown
ss2104674951000GENOMES|YRI.trio.3.2010_6388_chr1_11772034rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag03/29/1003/29/10132Genomicunknown
ss2182384041000GENOMES|pilot_1_YRI_48087_chr1_11772034rev/A/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag04/22/1004/22/10132Genomicunknown
ss2304276091000GENOMES|pilot_1_CEU_32238_chr1_11772034rev/A/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag05/01/1005/01/10132Genomicunknown
ss2381428051000GENOMES|pilot_1_CHB+JPT_27882_chr1_11772034rev/A/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag05/01/1005/01/10132Genomicunknown
ss244313347ILLUMINA|CVDSNP55v1_A_rs868014rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggtgggggctggggcagag06/10/1006/10/10132Genomicunknown
ss252918132BL|SNP13910_1_11772034rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag08/18/1008/18/10134Genomicunknown
ss275715257GMI|GMI_AK_SNP_35418rev/A/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag12/16/1012/16/10137Genomicunknown
ss290623940PJP|SNP_130298_chr1_11772034rev/A/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag01/21/1101/21/11134Genomicunknown
ss410765827ILLUMINA|Cardio-Metabo_Chip_11395247_A_chr1_11772034rev/TA/Gaagggccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttggggcag06/07/1106/07/11135Genomicunknown
ss479430024ILLUMINA|HumanOmni1-Quad_v1-0_C_kgp6894723-0_T_F_1821309598rev/TA/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg01/30/1208/28/15146Genomicunknown
ss536006156ILLUMINA|HumanOmni5-4v1_B_kgp6894723-0_T_F_1821309598rev/TA/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg06/22/1208/28/15146Genomicunknown
ss553801659TISHKOFF|snp_chr1_11849447rev/TA/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg11/22/1211/22/12138Genomicunknown
ss647577725SSMP|1_11849447rev/TA/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg12/14/1202/09/15138Genomicunknown
ss1067672489JMKIDD_LAB|HGDP_WGS_chr1_11849447rev/TA/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg07/10/1407/10/14142Genomicunknown
ss12897008971000GENOMES|PHASE3_V1_379833rev/A/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg08/16/1408/16/14142Genomicunknown
ss1425713649DDI|DDI_rs868014rev/TA/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg11/04/1411/04/14144Genomicunknown
ss1573889265EVA_GENOME_DK|EVA_GENOME_DK_snv_rs868014rev/TA/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg02/19/1502/19/15144Genomicunknown
ss1599557424EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_11849447_196848rev/A/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg03/04/1503/04/15144Genomicunknown
ss1642551457EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_11849447_196848rev/A/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg03/04/1503/04/15144Genomicunknown
ss1685303868EVA_EXAC|EVA_EXAC_93382rev/A/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg03/04/1503/04/15144Genomicunknown
ss1710888330EVA_MGP|EVA_XIMO_5082rev/TA/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg03/09/1503/09/15144Genomicunknown
ss1793911284HAMMER_LAB|Hsieh_42400rev/TA/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg07/15/1507/15/15146Genomicunknown
ss1918059991WEILL_CORNELL_DGM|SNV:chr1:11849447rev/TA/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg10/16/1510/16/15147Genomicunknown
ss1966685435GENOMED|rs868014rev/TA/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg02/16/1602/16/16147Genomicunknown
ss2019543862JJLAB|SNP46417rev/TA/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg08/29/1608/30/16149Genomicunknown
ss2094782410ILLUMINA|Immuno_BeadChip_11419691_B_rs868014-131_T_R_1852957445rev/TA/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg09/27/1609/27/16150Genomicunknown
ss2094952941ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs868014-131_T_R_1852957445rev/TA/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg09/27/1609/27/16150Genomicunknown
ss2147541906USC_VALOUEV|NC_000001.10:g.11849447A>Grev/A/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg11/17/1611/17/16150Genomicunknown
ss2160086010HUMAN_LONGEVITY|HLI-1-11789390-A-Grev/A/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg11/18/1611/18/16150Genomicunknown
ss2322243884TOPMED|1_11849447_A/Grev/A/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg11/19/1611/19/16150Genomicunknown
ss2624288319SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV29529rev/A/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg01/06/1701/06/17151Genomicunknown
ss2697438479GRF|rs868014rev/A/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg02/13/1702/13/17151Genomicunknown
ss2731121226GNOMAD|exomes_rs868014rev/A/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg05/17/1705/17/17151Genomicunknown
ss2746215680GNOMAD|coding_rs868014rev/A/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg05/17/1705/17/17151Genomicunknown
ss2751673408GNOMAD|rs868014rev/A/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg05/17/1705/17/17151Genomicunknown
ss2986303377SWEGEN|NC_000001.10:g.11849447A>Grev/A/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg05/30/1705/30/17151Genomicunknown
ss3068710128TOPMED|TOPMed_freeze_5?chr1:11,789,390rev/A/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg09/28/1709/28/17151Genomicunknown
ss3343319548CSHL|rs868014rev/A/Gccccgagagtggacaggaagccgccgagcaccgcggggttgggggcttgg10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs868014|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 GCCTGTGCAG CAGCCCAGCT TCCTGGTGTA TTTTTCAGGT AGGCCCTTGT CCTGCCAGCT
 GCCTTCCTCA TCCCCTCGTC CTGTCCCAGA GGTTATCTGC CTGGCCTGGC TCCCCACGAG
 TCACCTGCAA GCCCCAGGGC CTGGGGGCAG TGACTGGCAG GTGCAGATGG GCTGTTTCGT
 GTAGTGGAAG AGCAGCCTGA TGGCCAAGGG GGTGGACGCA ATTGTGGGAT GTCCTCTTTA
 CTCCCTTCCT GGCCTCACTG GCTGGGGCAG AGGGGCAGCC GCTAGGAGAG ACTGAAAGCA
 GCAGCTAGGA CTGAGGAGTG GGTTTTATTG TCCTTCAGAG CTCTTCAAGC TGTCCCCTCT
 GTCATCACTC CCTGGATGTG TGGGGCATGG TTCCTTCCCT GGGAAGGCTA AGTTCAGTTC
 TGTTTTTTAT TCTATGAGAA CAAGTCACAG CTGCAGCTGG GCCCCATGCT CTGCCCCAAG
 CCCCCAACCC CGCGGTGCTC
 Y
 GGCGGCTTCC TGTCCACTCT CGGGGCCCTT GGGGCCTGGC TTGCTCCAGG GTCTTGGGCT
 ACTGGCAGCT CCTCTCCTTG GGCTCCTGGC TGCCAGGCGT TGGTGCCACT TCTTAAAGGC
 CTGGAACCAG GGAGGAGAGG AAATGCTATT GTTGTGGGCT TTCTCCGGGG TCTGTGCTGT
 GCCTGCTAGA GCAACCCCTG TACCCAGCTC CTTTTGTCCC CAGGGCCCCT CCCTCTGCCC
 CAAGCAGCCA GCCAGTCTTG CCTAGGCCAA ATGCACAAGC TCAGAATAGA TCTGATGGTG
 AGCTGGGAAG CTGTACTCAG AGCAGAGCAA ATGAGGGAGG GGGCGCTCAG GACCCAGGCC
 CTCCATGGGC TAGTGTGAGT GGCAGCCATG CCTCATGCCA CACCTTCTTC GCAAACTGAT
 GGACCGGGTG GGCCTGGCCT GAGCTGGGGC CACAAATCAA AGCAAGGGCT CCAGCATCCA
 GCCTGTGTGT TCTGTAATGG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_021937 ABBA01003060
dbSNP Blast Analysis
UniGene Cluster ID
214142

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs868014 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss118499936YRI 2IG 1.00000000 0.500000000.50000000
ss1289700897EAS 1008AF 1.00000000
EUR 1006AF 1.00000000
AFR 1322AF 0.759500030.24050000
AMR 694AF 0.974099990.02590000
SAS 978AF 1.00000000
ss1289986WICGR1_caucasianEuropean 92IG1.00000000 1.00000000
HapMap-CEUEuropean 120IG1.00000000 1.00000000
HapMap-HCBAsian 90IG1.00000000 1.00000000
HapMap-JPTAsian 88IG1.00000000 1.00000000
HapMap-YRISub-Saharan African 118IG0.610169470.338983060.050847461.000000000.779661000.22033899
ss137797980ENSEMBL_Watson 2IG1.00000000 1.00000000
ss139264791ENSEMBL_Venter 2IG1.00000000 1.00000000
ENSEMBL_celera 2IG1.00000000 1.00000000
ss163078962YRISub-Saharan African 2IG 1.00000000 0.500000000.50000000
ss163832319CEUEuropean 2IG1.00000000 1.00000000
ss1685303868ExAc_Aggregated_Populations 21798AF 0.975731730.02426828
ss218238404pilot_1_YRI_low_coverage_panel 118AF 0.771186410.22881356
ss230427609pilot_1_CEU_low_coverage_panel 120AF 1.00000000
ss238142805pilot_1_CHB+JPT_low_coverage_panel 120AF 1.00000000
ss70457151PDR90-PANEL 174AF 0.959770140.04022989
ss97919654J. Craig Venter 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.025+/-0.1100000

  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_SSAHASNPNCBI
UNKNOWNUNKNOWNYES

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