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Reference SNP (refSNP) Cluster Report: rs774359                 
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
Association:NHGRI GWAS PheGenI
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.1955/979 (1000 Genomes)
C=0.2264/28432 (TOPMED)
HGVS Names
  • CM000671.2:g.27561051T>C
  • NC_000009.11:g.27561049T>C
  • NC_000009.12:g.27561051T>C
  • NG_031977.1:g.17816A>G
  • NM_001256054.1:c.665+534A>G
  • NM_001256054.2:c.665+534A>G
  • NM_018325.4:c.665+534A>G
  • NM_145005.6:c.*530A>G
Links , Linkout
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 ss280166896 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs774359 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
ss893264KWOK|OVLP-000804-113570fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca09/01/0010/10/0386Genomic99 %
ss1569144KWOK|OVLP-000925-33883byFreqrev/TA/Gtggcaataatagtaatagtacctaatgtgtgggttgttataagcattgagtaagataaat10/04/0004/07/0487Genomic99 %
ss1569832KWOK|OVLP-000925-44659fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca10/04/0010/10/0387Genomic99 %
ss3638774SC_JCM|AC016237.4_19151fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca09/24/0110/10/03100Genomicunknown
ss10519002BCM_SSAHASNP|chr9.NT_008413.15_27551050fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca06/29/0310/10/03116Genomicunknown
ss12930735SC_SNP|NT_008413.15_27551050fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca10/21/0310/31/03119Genomicunknown
ss17284477CSHL-HAPMAP|CSHL-HuAA-200402.chr9.NT_008413.16_27551049fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca02/17/0403/04/04120Genomicunknown
ss43893295ABI|hCV3137384fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca07/18/0507/18/05126Genomicunknown
ss65744147ILLUMINA|Human1-rs774359fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca10/10/0610/10/06127Genomicunknown
ss66659929ILLUMINA|HumanHap300v1.1_rs774359fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca11/09/0611/09/06127Genomicunknown
ss67825208ILLUMINA|HumanHap550v1.1_rs774359fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca11/14/0611/14/06127Genomicunknown
ss67987774ILLUMINA|HumanHap650Yv1.0_rs774359fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca11/14/0611/15/06127Genomicunknown
ss70947080ILLUMINA|HumanHap550v3.0__rs774359rev/TA/Gtggcaataatagtaatagtacctaatgtgtgggttgttataagcattgagtaagataaat04/20/0703/31/08130Genomicunknown
ss71552296ILLUMINA|HumanHap650Yv3.0_rs774359fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca04/23/0704/23/07127Genomicunknown
ss75500076ILLUMINA|ILMN_Human_1M_rs774359fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca08/28/0708/29/07129Genomicunknown
ss79268469ILLUMINA|HumanHap300v2.0_rs774359fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca04/18/0711/18/07130Genomicunknown
ss83560170KRIBB_YJKIM|KHS489892fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca12/04/0712/05/07130Genomicunknown
ss115716389ILLUMINA-UK|NA18507_000046802_NCBI36.1_chr9_27551049fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca01/15/0901/16/09130Genomic99 %
ss122825160ILLUMINA|HumanCNV370v1_C_rs774359fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca04/14/0904/15/09131Genomicunknown
ss154444312ILLUMINA|Human610_Quadv1_B_rs774359-128_T_R_1501868892rev/TA/Gtggcaataatagtaatagtacctaatgtgtgggttgttataagcattgagtaagataaat06/18/0906/20/09131Genomicunknown
ss159619207ILLUMINA|Human660W-Quad_v1_A_rs774359-128_T_R_1501868892rev/TA/Gtggcaataatagtaatagtacctaatgtgtgggttgttataagcattgagtaagataaat07/06/0907/07/09131Genomicunknown
ss160909848ILLUMINA|HumanOmni1-Quad_v1-0_B_rs774359-128_T_R_1512237425rev/TA/Gtggcaataatagtaatagtacctaatgtgtgggttgttataagcattgagtaagataaat08/04/0910/05/09131Genomicunknown
ss163994090COMPLETE_GENOMICS|NA07022_36_chr9_27551049fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca09/29/0909/29/09132Genomicunknown
ss172340709ILLUMINA|HumanCNV370-Quadv3_C_rs774359-128_T_R_1501868892rev/TA/Gtggcaataatagtaatagtacctaatgtgtgggttgttataagcattgagtaagataaat10/01/0910/04/09132Genomicunknown
ss174525851ILLUMINA|Human1M-Duov3_B_rs774359-128_T_R_1501868892rev/TA/Gtggcaataatagtaatagtacctaatgtgtgggttgttataagcattgagtaagataaat10/01/0910/04/09132Genomicunknown
ss2107481161000GENOMES|YRI.trio.3.2010_874787_chr9_27551049fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca03/29/1003/29/10132Genomicunknown
ss2241994691000GENOMES|pilot_1_YRI_6009152_chr9_27551049fwd/C/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca04/22/1004/22/10132Genomicunknown
ss2347812271000GENOMES|pilot_1_CEU_4385856_chr9_27551049fwd/C/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca05/01/1005/01/10132Genomicunknown
ss2415631171000GENOMES|pilot_1_CHB+JPT_3448194_chr9_27551049fwd/C/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca05/01/1005/01/10132Genomicunknown
ss280166896GMI|GMI_AK_SNP_4487169fwd/C/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca12/16/1012/16/10137Genomicunknown
ss285995303GMI|GMI_NA10851_SNP_2008076fwd/C/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca12/17/1012/17/10138Genomicunknown
ss481661054ILLUMINA|HumanOmni2.5-4v1_B_rs774359-128_T_R_1767957209fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat01/30/1210/29/16137Genomicunknown
ss481691779ILLUMINA|HumanOmniExpress-12v1_C_rs774359-131_T_R_1857373264fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat01/30/1210/27/16137Genomicunknown
ss482658516ILLUMINA|HumanOmni1-Quad_v1-0_C_rs774359-131_T_R_1865265442fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat01/30/1208/28/15146Genomicunknown
ss485625204ILLUMINA|HumanOmni2.5-4v1_D_rs774359-131_T_R_1857373264fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat01/30/1210/28/16137Genomicunknown
ss491421501EXOME_CHIP|.GWAS._137727_chr_9_27561049fwd/BC/Tatttatcttactcaatgcttataacaacccacacattaggtactattactattattgcca03/05/1203/05/12137Genomicunknown
ss537508591ILLUMINA|HumanOmni5-4v1_B_rs774359-131_T_R_1885472883fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat06/22/1208/29/15146Genomicunknown
ss655767715SSMP|9_27561049fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat12/14/1202/12/15138Genomicunknown
ss778984652ILLUMINA|HumanOmni25Exome-8v1_A_rs774359-131_T_R_1865265442fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat05/30/1307/10/15146Genomicunknown
ss780686739ILLUMINA|HumanOmni25Exome-8v1_A_exm-rs774359-131_T_R_1990494142fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat05/30/1307/10/15146Genomicunknown
ss783258214ILLUMINA|HumanOmni2.5-4v1_H_rs774359-131_T_R_1857373264fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat05/30/1307/29/15146Genomicunknown
ss783360271ILLUMINA|HumanOmniExpressExome-8v1_A_exm-rs774359-131_T_R_1990494142fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat05/31/1306/19/15146Genomicunknown
ss784211701ILLUMINA|HumanOmniExpressExome-8v1_A_rs774359-131_T_R_1885472883fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat05/31/1306/19/15146Genomicunknown
ss825598987ILLUMINA|HumanCNV370v1_C_rs774359-126_T_R_IFB1135526219:0fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat06/24/1311/21/14144Genomicunknown
ss832519098ILLUMINA|HumanOmniExpress-12v1_H_rs774359-131_T_R_1857373264fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat09/17/1306/19/15146Genomicunknown
ss834446840ILLUMINA|HumanOmni2.5-8v1_A_rs774359-131_T_R_1865265442fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat09/18/1307/29/15146Genomicunknown
ss986462875EVA-GONL|EVA-GONL_rs774359fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat04/23/1404/25/14142Genomicunknown
ss1076231508JMKIDD_LAB|HGDP_WGS_chr9_27561049fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat07/10/1407/11/14142Genomicunknown
ss13334862031000GENOMES|PHASE3_V1_45974197fwd/C/Ttcttactcaatgcttataacaacccacacattaggtactattactattat08/16/1408/16/14142Genomicunknown
ss1431795330DDI|DDI_rs774359fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat11/04/1411/05/14144Genomicunknown
ss1583047349EVA_GENOME_DK|EVA_GENOME_DK_snv_rs774359fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat02/19/1502/20/15144Genomicunknown
ss1596097994EVA_DECODE|EVA_DECODE_9_27551049_274614_rs774359fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat03/02/1503/03/15144Genomicunknown
ss1622554734EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_9_27561049_25436589fwd/C/Ttcttactcaatgcttataacaacccacacattaggtactattactattat03/04/1503/04/15144Genomicunknown
ss1665548767EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_9_27561049_25436589fwd/C/Ttcttactcaatgcttataacaacccacacattaggtactattactattat03/04/1503/04/15144Genomicunknown
ss1713102299EVA_SVP|EVA_SVP_796666fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat03/12/1503/12/15144Genomicunknown
ss1752773742ILLUMINA|OmniExpressExome-8v1-1_B_exm-rs774359-131_T_R_1990494142fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat05/27/1506/09/15146Genomicunknown
ss1752773743ILLUMINA|OmniExpressExome-8v1-1_B_rs774359-131_T_R_1885472883fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat05/27/1506/09/15146Genomicunknown
ss1805944194HAMMER_LAB|Hsieh_4960359fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat07/15/1507/16/15146Genomicunknown
ss1917835426ILLUMINA|HumanExome-12v1-1_B_exm-rs774359-131_T_R_1990494142fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat10/16/1510/16/15147Genomicunknown
ss1929746706WEILL_CORNELL_DGM|SNV:chr9:27561049fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat10/16/1510/17/15147Genomicunknown
ss1946256146ILLUMINA|HumanCoreExome-12v1-0_C_exm-rs774359-131_T_R_1990494142fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat10/29/1510/29/15147Genomicunknown
ss1959176068ILLUMINA|exm-rs774359-131_T_R_1990494142fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat11/13/1511/13/15147Genomicunknown
ss1971188964GENOMED|rs774359fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat02/16/1602/16/16147Genomicunknown
ss2025584837JJLAB|SNP6087392fwd/BC/Ttcttactcaatgcttataacaacccacacattaggtactattactattat08/29/1608/30/16149Genomicunknown
ss2153810454USC_VALOUEV|NC_000009.11:g.27561049T>Cfwd/C/Ttcttactcaatgcttataacaacccacacattaggtactattactattat11/17/1611/17/16150Genomicunknown
ss2310601383HUMAN_LONGEVITY|HLI-9-27561051-T-Cfwd/C/Ttcttactcaatgcttataacaacccacacattaggtactattactattat11/18/1611/18/16150Genomicunknown
ss2480697287TOPMED|9_27561049_T/Cfwd/C/Ttcttactcaatgcttataacaacccacacattaggtactattactattat11/20/1611/20/16150Genomicunknown
ss2634855674ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs774359-131_T_R_188547288fwd/C/Ttcttactcaatgcttataacaacccacacattaggtactattactattat02/02/1702/02/17151Genomicunknown
ss2709616784GRF|rs774359fwd/C/Ttcttactcaatgcttataacaacccacacattaggtactattactattat02/13/1702/13/17151Genomicunknown
ss2877059332GNOMAD|rs774359fwd/C/Ttcttactcaatgcttataacaacccacacattaggtactattactattat05/19/1705/19/17151Genomicunknown
ss2985459261AFFY|Axiom_PsorMich_Affx-33607261fwd/C/Ttcttactcaatgcttataacaacccacacattaggtactattactattat05/24/1705/24/17151Genomicunknown
ss2986105329AFFY|Axiom_Smokesc1_Affx-33607261fwd/C/Ttcttactcaatgcttataacaacccacacattaggtactattactattat05/24/1705/24/17151Genomicunknown
ss3004609262SWEGEN|NC_000009.11:g.27561049T>Cfwd/C/Ttcttactcaatgcttataacaacccacacattaggtactattactattat05/30/1705/30/17151Genomicunknown
ss3022920578ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm-rs774359-131_T_R_1990494142fwd/C/Ttcttactcaatgcttataacaacccacacattaggtactattactattat06/28/1706/28/17151Genomicunknown
ss3026581096BIOINF_KMB_FNS_UNIBA|9.27561051T>Cfwd/C/Ttcttactcaatgcttataacaacccacacattaggtactattactattat07/05/1707/05/17151Genomicunknown
ss3348589859CSHL|rs774359fwd/C/Ttcttactcaatgcttataacaacccacacattaggtactattactattat10/02/1710/02/17151Genomicunknown
ss3585807367TOPMED|TOPMed_freeze_5?chr9:27,561,051fwd/C/Ttcttactcaatgcttataacaacccacacattaggtactattactattat10/07/1710/07/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs774359|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 TATTTATTGA AATACCATCA TTTTATAGCT GAAGAAATTG ACATGTAGAG AGATTAAGTG
 ACTTACTTAA AGTCAAATGG GATTTAAAAT GATGTATGAA AGGCTGACAC TGAACAGATA
 CAGGACTAAA GTGCTTCTGA TTCAAGCCAT TAAGGCTCTT AGGTTAAACA CACTCATGCC
 TCTGATACTC CATCATGAGC CTAAAGGAAA AGACTGTGAA CATAAAAGTG AATACTTTAT
 ACTTTTACTT CTCTTTTATT AAAAGTAAAA TTTCATGAAA ATCTGTAACT GTGAAGAAAC
 TTTAAAACAG AATATAAGAT AATACATGTA AAGCAACTAG TAAAGGAACT AACATGTAGG
 CACTCAACAA ATACTGGCTA TTTCTAGAAG AAATGTAAAT AGGAAATGTT AGCTATGAGC
 TATTATTAAG TGTTTTTATG TTCCAGGCAC TGTTCTAAGT GCTTTATATT ATTTATCTTA
 CTCAATGCTT ATAACAACCC
 Y
 ACACATTAGG TACTATTACT ATTATTGCCA TTTTACAGAT GAGGAAATAG GTGTATAGAG
 AATTCAGGCA CCTTGCCCAC GGGTACACAG CATTAATCCA GGGAGTCTGG TTTAAGGGCA
 CAAACTCTTA AGTACTAAAC TCCACTGCTG GATGGAAAAA GATCAGTATA AATATGAATA
 ATTTTGTTCT ACGCCTAAAT AACTTAAGTT CATCTACAGT ACAACTTAAT ATGAAAGGAT
 TCTGTTAGCT TTAATGAGAA GTAAAACAAG AAACCAGAAT CAAGCAAGGG GCCATGATTT
 CTTGTCTGGG ATGGAAACTC GGTTTCTTTA AATAGCAAAT GGAATAACAC CAAATATATA
 TAGAAATATA ATGAGTGAAA AATAACACAA ATTTAAGCAA CAGTTCAAAT ACGTAATGTC
 CCTAGAACAA TCTAAGTAGA CAGTCTGTTA TTTTCTTTCT TCCAAATCTT GTCATAGGTG
 AGCATAAGAT GGTATCTGCT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_008413 AC025611 AL139116 AL355585 AL355585.4 AL355585.5 AL451123
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.
SourceC/C
C/T
T/T
HWPC
T
ss115716389YRI 2IG 1.00000000 0.500000000.50000000
ss1333486203EAS 1008AF 0.095200000.90480000
EUR 1006AF 0.252500000.74750000
AFR 1322AF 0.245099990.75489998
AMR 694AF 0.159899990.84010005
SAS 978AF 0.198400010.80159998
ss1569144HapMap-CEUEuropean 226IG0.097345140.336283180.566371680.150222000.265486720.73451328
HapMap-HCBAsian 86IG 0.162790700.837209281.000000000.081395350.91860467
HapMap-JPTAsian 172IG 0.139534890.860465111.000000000.069767450.93023258
HapMap-YRISub-Saharan African 224IG0.008928570.303571430.687500000.200325000.160714280.83928573
HAPMAP-ASW 98IG0.040816330.265306120.693877580.654721000.173469390.82653064
HAPMAP-CHBAsian 80IG 0.175000000.824999991.000000000.087500000.91250002
HAPMAP-CHD 170IG0.011764710.164705890.823529421.000000000.094117650.90588236
HAPMAP-GIH 176IG0.022727270.284090910.693181811.000000000.164772730.83522725
HAPMAP-LWK 180IG0.088888890.422222230.488888891.000000000.300000010.69999999
HAPMAP-MEX 100IG0.020000000.080000000.899999980.050043000.060000000.94000000
HAPMAP-MKK 284IG0.056338030.408450690.535211270.479500000.260563370.73943663
HAPMAP-TSI 176IG0.079545450.420454530.500000001.000000000.289772720.71022725
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss163994090CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss224199469pilot_1_YRI_low_coverage_panel 118AF 0.144067790.85593218
ss234781227pilot_1_CEU_low_coverage_panel 120AF 0.250000000.75000000
ss241563117pilot_1_CHB+JPT_low_coverage_panel 120AF 0.066666670.93333334

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.315+/-0.2420000ALFRED: The Allele Frequency Database

  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
UNKNOWNUNKNOWNUNKNOWN

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