NCBI
dbSNP

PubMed Nucleotide Protein Genome Structure PopSet Taxonomy OMIM Books SNP
Search for SNP on NCBI Reference Assembly
transparent GIF
Spacer gif
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Reference SNP (refSNP) Cluster Report: rs718712                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/141
Map to Genome Build:106/Weight
Validation Status:byClusterbyFreqwithHapMapFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (REV)
Allele Origin:
Ancestral Allele:C
Variation Viewer:unknown
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.309/674
MAF Source:1000 Genomes
HGVS Names
  • NC_000020.11:g.8785361G>A
  • NG_028168.1:g.657713G>A
  • NM_015192.3:c.3112-3088G>A
  • NM_182734.2:c.3112-3088G>A
  • NT_011387.9:g.8725361G>A
  • XM_006723555.1:c.3112-3088G>A
Links
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 ss283295586 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs718712 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
ss58929TSC-CSHL|TSC0042766byFreqfwd/BC/Tgtagtccacataccagtggcaagagcatcacagggagcacattagaaatgtaagttctcg09/06/0004/07/0486Genomic95 %
ss24084311PERLEGEN|afd4377102byFreqrev/TA/Gcgagaacttacatttctaatgtgctccctgtgatgctcttgccactggtatgtggactac08/10/0409/13/04123Genomicunknown
ss41365478ABI|hCV2229875byFreqrev/TA/Gcgagaacttacatttctaatgtgctccctgtgatgctcttgccactggtatgtggactac07/17/0508/14/07126Genomicunknown
ss66350123AFFY|SNP_A-1967649byFreqfwd/BC/Tagtggcaagagcatcacagggagcacattaga10/29/0608/14/07127Genomicunknown
ss76060986AFFY|AFFY_6_1M_SNP_A-1967649fwd/BC/Tagtggcaagagcatcacagggagcacattaga08/28/0708/29/07129Genomicunknown
ss81434319KRIBB_YJKIM|KHS60504fwd/BC/Tgtagtccacataccagtggcaagagcatcacagggagcacattagaaatgtaagttctcg11/30/0711/30/07130Genomicunknown
ss106178199BGI|BGI_rs718712rev/TA/Gcgagaacttacatttctaatgtgctccctgtgatgctcttgccactggtatgtggactac09/13/0806/18/09130Genomicunknown
ss1117001931000GENOMES|CEU.trio.12.15.2008_3657381_chr20_8714008rev/TA/Gcgagaacttacatttctaatgtgctccctgtgatgctcttgccactggtatgtggactac12/17/0812/17/08130Genomicunknown
ss117479169ILLUMINA-UK|NA18507_000013026_NCBI36.1_chr20_8714008rev/TA/Gcgagaacttacatttctaatgtgctccctgtgatgctcttgccactggtatgtggactac01/19/0901/19/09130Genomic99 %
ss167785639COMPLETE_GENOMICS|NA07022_36_chr20_8714008rev/TA/Gcgagaacttacatttctaatgtgctccctgtgatgctcttgccactggtatgtggactac09/30/0909/30/09132Genomicunknown
ss171883811COMPLETE_GENOMICS|NA20431_36_chr20_8714008rev/TA/Gcgagaacttacatttctaatgtgctccctgtgatgctcttgccactggtatgtggactac10/01/0910/01/09132Genomicunknown
ss172361630AFFY|GenomeWideSNP_5_SNP_A-1967649fwd/BC/Tagtggcaagagcatcacagggagcacattaga10/01/0910/02/09132Genomicunknown
ss203826652BUSHMAN|BUSHMAN-chr20-8714007rev/TA/Gcgagaacttacatttctaatgtgctccctgtgatgctcttgccactggtatgtggactac02/16/1003/09/10132Genomicunknown
ss208715508BCM-HGSC-SUB|BCM_CMT_1011-3196896rev/TA/Gcgagaacttacatttctaatgtgctccctgtgatgctcttgccactggtatgtggactac03/15/1003/20/10132Genomicunknown
ss2119948381000GENOMES|YRI.trio.3.2010_1456302_chr20_8714008rev/TA/Gcgagaacttacatttctaatgtgctccctgtgatgctcttgccactggtatgtggactac03/29/1003/31/10132Genomicunknown
ss2282499531000GENOMES|pilot_1_YRI_10059636_chr20_8714008rev/A/Gcgagaacttacatttctaatgtgctccctgtgatgctcttgccactggtatgtggactac04/22/1004/22/10132Genomicunknown
ss2377579031000GENOMES|pilot_1_CEU_7362532_chr20_8714008rev/A/Gcgagaacttacatttctaatgtgctccctgtgatgctcttgccactggtatgtggactac05/01/1005/01/10132Genomicunknown
ss2439454571000GENOMES|pilot_1_CHB+JPT_5830534_chr20_8714008rev/A/Gcgagaacttacatttctaatgtgctccctgtgatgctcttgccactggtatgtggactac05/01/1005/01/10132Genomicunknown
ss255472297BL|SNP10597_20_8714008rev/TA/Gcgagaacttacatttctaatgtgctccctgtgatgctcttgccactggtatgtggactac08/20/1008/20/10134Genomicunknown
ss283295586GMI|GMI_AK_SNP_7616007rev/A/Gcgagaacttacatttctaatgtgctccctgtgatgctcttgccactggtatgtggactac12/16/1012/16/10137Genomicunknown
ss566128208TISHKOFF|snp_chr20_8766008rev/TA/Gacttacatttctaatgtgctccctgtgatgctcttgccactggtatgtgg11/22/1211/23/12138Genomicunknown
ss661999285SSMP|20_8766008rev/TA/Gcgagaacttacatttctaatgtgctccctggatgctcttgccactggtatgtggactaca12/14/1212/17/12138Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs718712|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=138
 ATCATTCACC TGACTTCAGA ATATTTTCTT GATTATGCCA GCATCTGCTC ACATGTGCTG
 TTTCCCTTCC GCCTACTGCC TTTATCCTCA GCAGCATCGG CCTCCAGTCA ATATTGAGAC
 TAAGCTGGAG AACTCACAGA CCTTCTGCCC ACTCAGTTCT GACTTTTATG TTGGTTTGGT
 GTCAGGCTCC ACACCACTGT CAGTGCCACA CTCCCTCCAG ACTCCCCAGA AGTTCCCTGT
 CTGCCACGTC CTTTTGCCTC CCTCTTGGCT CCCATCACAC CCCCTGCATT TGCCCTTTAC
 CCCTTGCAGA ACAAGTTTCC ACCTCCTGTG GTCCCAGAAC ACACACTTAT CTAAACTATC
 TGATTCAGCC ACGATGCAAT GGATATTTAT TAAGCACCTA CTAAATAGCA GGCACTGTTC
 TAGAAACTCT GAGCTGATGA CCTGGCTTTC TAGATCTTGC TACTCAAAGT GTAGTCCACA
 TACCAGTGGC AAGAGCATCA
 Y
 CAGGGAGCAC ATTAGAAATG TAAGTTCTCG GGCCCTACTC CAGATCAACT AAGTCAGAAT
 CTACATGTTC AACAAAATTC CCAGGAGATT TGAGTGCACA TTAGAGTTTG AAAAGCATTG
 TCTTGGTGGT TGTGGAAGAT GGAGACAATC TGGAAGAAAC CATTTCAATT TCTCTCTGCC
 CCTTCCCTTT CTAAGCCAGC CTTAGGTAAT TCTCCCCTTT GACTGCCCAG ATAACTCTGG
 GTGTTGGCCC CCTAATTGGT TTTTCCTACA GGGTATCATT TACAGACATA CCTTTTGTAT
 GTAAATATCT TATTATTGCT CCCACAAAGG GATGTCACCA TTTCAACCTT CCATTCTTAA
 TAAATGTTTA GAATCCCAGG CTCTAGACAA AATAGGCACT GAAAAAAATG ATTGTGAATG
 AAATCTTTTA AGTTTCAAAA CTACACTGGA CCCGACCTCA GCGATAGCTC TGAAAGCTCA
 CATTCAAGCC ACAGGCTGCC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000020.6
dbSNP Blast Analysis

  Population Diversity (in rs orientation) Note: rs718712 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
ss117479169YRI 2IG 1.000 0.500 0.500
ss167785639CEUEuropean 2IG 1.000 0.500 0.500
ss171883811PGP 2IG 1.000 0.500 0.500
ss203826652BANTU 2IG 1.000 0.500 0.500
ss228249953pilot_1_YRI_low_coverage_panel 118AF 0.636 0.364
ss237757903pilot_1_CEU_low_coverage_panel 120AF 0.733 0.267
ss24084311AFD_EUR_PANELEuropean 48IG 0.625 0.375 0.527 0.812 0.188
AFD_AFR_PANELAfrican American 46IG 0.478 0.348 0.174 0.273 0.652 0.348
AFD_CHN_PANELAsian 48IG 0.292 0.500 0.208 1.000 0.542 0.458
ss243945457pilot_1_CHB+JPT_low_coverage_panel 120AF 0.650 0.350
ss41365478HapMap-CEUEuropean 224IG 0.509 0.420 0.071 0.752 0.719 0.281
HapMap-HCBAsian 86IG 0.488 0.372 0.140 0.317 0.674 0.326
HapMap-JPTAsian 172IG 0.465 0.419 0.116 0.752 0.674 0.326
HapMap-YRISub-Saharan African 226IG 0.425 0.469 0.106 0.655 0.659 0.341
HAPMAP-ASW 98IG 0.510 0.388 0.102 0.655 0.704 0.296
HAPMAP-CHBAsian 82IG 0.439 0.463 0.098 1.000 0.671 0.329
HAPMAP-CHD 170IG 0.353 0.541 0.106 0.200 0.624 0.376
HAPMAP-GIH 176IG 0.398 0.455 0.148 1.000 0.625 0.375
HAPMAP-LWK 180IG 0.522 0.411 0.067 0.752 0.728 0.272
HAPMAP-MEX 100IG 0.500 0.400 0.100 0.752 0.700 0.300
HAPMAP-MKK 284IG 0.458 0.415 0.127 0.439 0.665 0.335
HAPMAP-TSI 176IG 0.398 0.455 0.148 1.000 0.625 0.375
ENSEMBL_Watson 2IG 1.000 1.000
ENSEMBL_Venter 2IG 1.000 1.000
ss58929AfAmAfrican American 12IG 0.833 0.167 0.917 0.083
CaucasianEuropean 22IG 0.455 0.455 0.091 1.000 0.682 0.318
AsianAsian 12IG 0.667 0.167 0.167 0.750 0.250
CEPHEuropean 10IG 1.000 1.000
PDpanelGlobal 40IG 0.750 0.250 1.000 0.875 0.125
ss76060986ICMHP 10IG 1.000 1.000
Concordant GenotypeTotal SampleC/CC/TT/T
ss1174791691
ss1677856391
ss1718838111
ss2038266521
ss2408431170
ss413654781200
ss589294935122
ss7606098655
RefSNP Genotype SummaryTotal IndividualC/CC/TT/T
rs718712131640122
Discordant Genotypes:
Indiviudal
SampleID
SubSNP(ss)GenotypePopulation
Handle
Submitter
Population
Submitter
SampleID
SampleID
Alias
Submission
Batch
NCBI
ProbeID
215ss24084311A/GPERLEGENAFD_EUR_PANELNA1085771_IND_CHR_20
215ss41365478N/NCSHL-HAPMAPHapMap-CEUNA10857CEPH1346.01r27_ch20_CEU_affymetrix:genomewidesnp_6.0
374ss41365478A/ACSHL-HAPMAPHapMap-CEUNA12234CEPH1375.12r27_ch20_CEU_affymetrix:genomewidesnp_6.0
620ss41365478A/GCSHL-HAPMAPHapMap-CEUNA12874CEPH1459.11r27_ch20_CEU_affymetrix:genomewidesnp_6.0
5137ss41365478A/GCSHL-HAPMAPHapMap-YRINA19131YOR101.02r27_ch20_YRI_affymetrix:genomewidesnp_6.0
5168ss41365478G/GCSHL-HAPMAPHapMap-HCBNA18555CH18555r27_ch20_CHB_affymetrix:genomewidesnp_6.0
5231ss41365478G/GCSHL-HAPMAPHapMap-JPTNA18998JA18998r27_ch20_JPT_affymetrix:genomewidesnp_6.0
5263ss41365478G/GCSHL-HAPMAPHapMap-YRINA18861YOR024.02r27_ch20_YRI_affymetrix:genomewidesnp_6.0
5283ss41365478N/NCSHL-HAPMAPHapMap-YRINA19205YOR048.01r27_ch20_YRI_affymetrix:genomewidesnp_6.0
5301ss41365478G/GCSHL-HAPMAPHapMap-YRINA19142YOR071.01r27_ch20_YRI_affymetrix:genomewidesnp_6.0
Genotype data submitted for1338 samples from1316 individualsIndividual with multiple genotypes submission:22

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

GENERAL: Contact Us | Homepage | Announcements |dbSNP Summary | Genome | FTP SERVER | Build History | Handle Request
DOCUMENTATION: FAQ | Searchable FAQ Archive | Overview | How to Submit | RefSNP Summary Info | Database Schema
SEARCH: Entrez SNP | Blast SNP | Batch Query | By Submitter |New Batches | Method | Population | Publication | Batch | Locus Info | Between Marker
NCBI: PubMed | Entrez | BLAST | OMIM | Taxonomy | Structure

Disclaimer     Privacy statement