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Reference SNP(refSNP) Cluster Report: rs9939609                 **Clinical Channel**
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/137
Map to Genome Build:37.4
Validation Status:byFreq
Citation:PubMed
Association:NHGRI GWAS PheGenI
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/T
Allele Origin:
Ancestral Allele:A
Clinical Channel:link to VariationViewerlink to OMIM
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.355/776
MAF Source:1000 Genomes
HGVS Names
NC_000016.9:g.53820527T>A
NG_012969.1:g.87653T>A
NM_001080432.2:c.46-23525T>A
NT_010498.15:g.7434726T>A
Links , Linkout
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

  Submitter records for this RefSNP Cluster back to top
The submission ss491508391 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9939609 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
ss13778861BCM_SSAHASNP|chr16.NT_010498.14_2544445byFreqfwd/TA/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct11/05/0303/31/08119Genomicunknown
ss24411520PERLEGEN|afd3713426byFreqfwd/TA/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct08/10/0409/13/04123Genomicunknown
ss66219980AFFY|SNP_A-4249009byFreqrev/BA/Ttatccaagtgcatcacaaattcacagcagtcg10/27/0603/31/08127Genomicunknown
ss76366276AFFY|AFFY_6_1M_SNP_A-4249009rev/A/Ttatccaagtgcatcacaaattcacagcagtcg08/28/0708/30/07129Genomicunknown
ss78017758HGSV|Cor12878_SNV_20070510.chr16_52378028fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct10/17/0710/17/07129Genomicunknown
ss81498838HGSV|Cor19240_SNV_20070510.chr16_52378028fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct11/30/0711/30/07130Genomicunknown
ss82632678KRIBB_YJKIM|KHS297529fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct11/30/0712/03/07130Genomicunknown
ss90396704BCMHGSC_JDW|JWB-0947071fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct02/26/0802/29/08129Genomicunknown
ss103295301BGI|BGI_rs9939609fwd/A/Tttctagrttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct06/06/0806/18/09131Genomicunknown
ss1093313231000GENOMES|CEU.trio.12.15.2008_3291811_chr16_52378028fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct12/16/0812/16/08130Genomicunknown
ss1151042901000GENOMES|NA19240_2008_12_16_2956425_chr16_52378028fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct12/19/0812/19/08130Genomicunknown
ss118256364ILLUMINA-UK|NA18507_000053621_NCBI36.1_chr16_52378028fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct01/20/0901/21/09130Genomic99 %
ss120252622WTCCC|NT_010498.15_7434726_CEPHfwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct04/10/0904/10/09131Genomicunknown
ss136729437ENSEMBL|ENSSNP11133643fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct05/11/0905/15/09131Genomicunknown
ss168226664COMPLETE_GENOMICS|NA07022_36_chr16_52378028fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct09/30/0909/30/09132Genomicunknown
ss169759008COMPLETE_GENOMICS|NA19240_36_chr16_52378028fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct10/01/0910/01/09132Genomicunknown
ss171258868COMPLETE_GENOMICS|NA20431_36_chr16_52378028fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct10/01/0910/01/09132Genomicunknown
ss173394511AFFY|GenomeWideSNP_5_SNP_A-4249009rev/A/Ttatccaagtgcatcacaaattcacagcagtcg10/01/0910/03/09132Genomicunknown
ss181834432PAGE_STUDY|PAGE_CALiCo_rs9939609fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct12/14/0912/23/10132Genomicunknown
ss201707335BUSHMAN|BUSHMAN-chr16-52378027fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct02/16/1003/08/10132Genomicunknown
ss207479464BCM-HGSC-SUB|BCM_CMT_1011-2792605fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct03/15/1003/19/10132Genomicunknown
ss2272477131000GENOMES|pilot_1_YRI_9057396_chr16_52378028fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct04/22/1004/22/10132Genomicunknown
ss230384217WTCCC|NT_010498.15_7434726_3Tfwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct04/30/1004/30/10132Genomicunknown
ss2370290521000GENOMES|pilot_1_CEU_6633681_chr16_52378028fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct05/01/1005/01/10132Genomicunknown
ss2433672971000GENOMES|pilot_1_CHB+JPT_5252374_chr16_52378028fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct05/01/1005/01/10132Genomicunknown
ss244316144ILLUMINA|CVDSNP55v1_A_rs9939609fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct06/10/1006/10/10132Genomicunknown
ss255710131BL|SNP57986_16_52378028fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct08/20/1008/20/10134Genomicunknown
ss291845391PJP|SNP_1351749_chr16_52378028fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct01/21/1101/21/11134Genomicunknown
ss410816955ILLUMINA|Cardio-Metabo_Chip_11395247_A_chr16_52378028rev/A/Tagagtaacagagactatccaagtgcatcacaaattcacagcagtcgcaaggaacctagaa06/07/1106/07/11135Genomicunknown
ss469414612PAGE_STUDY|PAGE_MEC_Y1_rs9939609fwd/A/Tggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgtt09/26/1109/26/11137Genomicunknown
ss491508391EXOME_CHIP|.GWAS._224617_chr_16_53820527fwd/A/Tttctaggttccttgcgactgctgtgaatttgtgatgcacttggatagtctctgttactct03/05/1203/05/12137Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs9939609|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=137
 TATCTTTTGG CAGATCAGAA CATAATGAAA ATAAAATAAA AAAATTCAAA ACTGGCTCTT
 GAATGAAATA GGATTCAGAA GAGATGATCT CAAATCTACT TTATGAGATA ATGTCCTTTT
 TAAAAATAAA CACTAACATC AGTTATGCAT TTAGAATGTC TGAATTATTA TTCTAGGTTC
 CTTGCGACTG CTGTGAATTT
 W
 GTGATGCACT TGGATAGTCT CTGTTACTCT AAAGTTTTAA TAGGTAACAG TCAGAAATGG
 AGTGGGAGAG CATAAAAGCA AACTGAAATG CAAATAGCTG GTACCCTGAA GCCATTAACT
 TTAAGCTGGT TATTCCTGAC CTACTGTTTG GACATAAGAT GGTAGAGAGG CTGAGTGTGA
 CTTGAACATT TGTTCCTTAG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010498.15
dbSNP Blast Analysis
OMIM
125853
612460

  Population Diversity back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA
A/A
A/T
T/T
HWPA
T
ss118256364YRI 2IG 1.000 0.500 0.500
ss120252622ENSEMBL_Venter 2IG 1.000 1.000
ss136729437ENSEMBL_Watson 2IG 1.000 0.500 0.500
ss168226664CEUEuropean 2IG 1.000 0.500 0.500
ss169759008YRISub-Saharan African 2IG 1.000 0.500 0.500
ss171258868PGP 2IG 1.000 0.500 0.500
ss201707335BUSHMAN_POP2 2IG 1.000 0.500 0.500
BANTU 1IG 1.000 1.000
ss227247713pilot_1_YRI_low_coverage_panel 118AF 0.559 0.441
ss237029052pilot_1_CEU_low_coverage_panel 120AF 0.450 0.550
ss243367297pilot_1_CHB+JPT_low_coverage_panel 120AF 0.150 0.850
ss24411520AFD_EUR_PANELEuropean 46IG 0.087 0.609 0.304 0.200 0.391 0.609
AFD_AFR_PANELAfrican American 46IG 0.087 0.478 0.435 0.752 0.326 0.674
AFD_CHN_PANELAsian 48IG 0.042 0.250 0.708 0.655 0.167 0.833
ss66219980HapMap-CEUEuropean 118IG 0.119 0.661 0.220 0.010 0.449 0.551
HapMap-HCBAsian 90IG 0.244 0.756 0.655 0.122 0.878
HapMap-JPTAsian 90IG 0.089 0.178 0.733 0.010 0.178 0.822
HapMap-YRISub-Saharan African 120IG 0.250 0.533 0.217 0.655 0.517 0.483
ss76366276ICMHP 6IG 1.000 1.000
ss90396704HapMap-CEUEuropean 226IG 0.177 0.566 0.257 0.150 0.460 0.540
HapMap-HCBAsian 86IG 0.233 0.767 0.752 0.116 0.884
HapMap-JPTAsian 172IG 0.035 0.302 0.663 1.000 0.186 0.814
HapMap-YRISub-Saharan African 222IG 0.243 0.532 0.225 0.527 0.509 0.491
HAPMAP-ASW 98IG 0.224 0.510 0.265 1.000 0.480 0.520
HAPMAP-CHBAsian 82IG 0.049 0.268 0.683 0.527 0.183 0.817
HAPMAP-CHD 170IG 0.024 0.271 0.706 1.000 0.159 0.841
HAPMAP-GIH 176IG 0.091 0.352 0.557 0.371 0.267 0.733
HAPMAP-LWK 180IG 0.400 0.433 0.167 0.439 0.617 0.383
HAPMAP-MKK 284IG 0.268 0.521 0.211 0.655 0.528 0.472
HAPMAP-TSI 176IG 0.250 0.432 0.318 0.251 0.466 0.534
Concordant GenotypeTotal SampleAA/AA/TT/T
ss11825636411
ss12025262211
ss13672943711
ss16822666411
ss16975900811
ss17125886811
ss201707335211
ss244115207153134
ss6621998026810512340
ss76366276541
ss903967041129212489403
RefSNP Genotype SummaryTotal IndividualAA/AA/TT/T
rs993960911961325529474
Discordant Genotypes:
Indiviudal
SampleID		SubSNP(ss)GenotypePopulation
Handle		Submitter
Population		Submitter
SampleID		SampleID
Alias		Submission
Batch		NCBI
ProbeID
5229ss66219980T/TCSHL-HAPMAPHapMap-JPTNA18992JA18992chr16-HapMap-JPT
5229ss90396704N/NCSHL-HAPMAPHapMap-JPTNA18992JA18992r27_ch16_JPT_affymetrix:genomewidesnp_6.0
Genotype data submitted for1213 samples from1196 individualsIndividual with multiple genotypes submission:275

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

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