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Reference SNP (refSNP) Cluster Report: rs3825932                 **Clinical Channel**
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:107/151
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=0.3680/1843 (1000 Genomes)
C=0.4767/59860 (TOPMED)
HGVS Names
  • CM000677.2:g.78943104T>C
  • NC_000015.10:g.78943104T>C
  • NC_000015.9:g.79235446T>C
  • NG_009614.1:g.6975A>G
  • NM_001319137.1:c.-985+1787A>G
  • NM_004390.4:c.91+1787A>G
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 ss282329257 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3825932 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
ss5012413YUSUKE|IMS-JST187182fwd/BC/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct08/12/0210/10/03107Genomicunknown
ss16663703CSHL-HAPMAP|CSHL-HuAA-200402.chr15.NT_010194.16_50025766byFreqfwd/BC/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct02/17/0410/26/06120Genomicunknown
ss17531556CSHL-HAPMAP|CSHL-HuCC-200402.chr15.NT_010194.16_50025766fwd/BC/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct02/19/0403/04/04120Genomicunknown
ss21233438SSAHASNP|WGSA-200403-chr15.chr15.NT_010194.16_50025766fwd/BC/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct03/19/0403/19/04121Genomicunknown
ss43689710ABI|hCV26390332fwd/BC/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct07/18/0507/18/05126Genomicunknown
ss66261722AFFY|SNP_A-4291786byFreqrev/TA/Gccagaataatctctccgaggcaaactggtagt10/27/0603/31/08127Genomicunknown
ss75245662ILLUMINA|ILMN_Human_1M_rs3825932fwd/BC/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct08/28/0708/29/07129Genomicunknown
ss76406823AFFY|AFFY_6_1M_SNP_A-4291786rev/TA/Gccagaataatctctccgaggcaaactggtagt08/28/0708/30/07130Genomicunknown
ss78183649HGSV|Cor12878_SNV_20070510.chr15_77022501fwd/BC/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct10/17/0710/18/07129Genomicunknown
ss81968261KRIBB_YJKIM|KHS168423fwd/BC/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct11/30/0712/01/07130Genomicunknown
ss103254546BGI|BGI_rs3825932fwd/BC/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct06/06/0806/18/09131Genomicunknown
ss132424993ENSEMBL|ENSSNP1142023byFreqfwd/BC/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct12/08/0803/07/10131Genomicunknown
ss160648532ILLUMINA|HumanOmni1-Quad_v1-0_B_rs3825932-128_T_R_1514216144rev/TA/Gagattattctggccccagaataatctctccgaggcaaactggtagtcaattgtcctaaac08/04/0910/04/09131Genomicunknown
ss171368497COMPLETE_GENOMICS|NA20431_36_chr15_77022501fwd/BC/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct10/01/0910/01/09132Genomicunknown
ss173493218AFFY|GenomeWideSNP_5_SNP_A-4291786rev/TA/Gccagaataatctctccgaggcaaactggtagt10/01/0910/03/09132Genomicunknown
ss173656758ILLUMINA|Human1M-Duov3_B_rs3825932-128_T_R_1514216144rev/TA/Gagattattctggccccagaataatctctccgaggcaaactggtagtcaattgtcctaaac10/01/0910/04/09132Genomicunknown
ss207388756BCM-HGSC-SUB|BCM_CMT_1011-2762457fwd/BC/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct03/15/1003/18/10132Genomicunknown
ss2269891261000GENOMES|pilot_1_YRI_8798809_chr15_77022501fwd/C/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct04/22/1004/22/10132Genomicunknown
ss2368466761000GENOMES|pilot_1_CEU_6451305_chr15_77022501fwd/C/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct05/01/1005/01/10132Genomicunknown
ss2432215901000GENOMES|pilot_1_CHB+JPT_5106667_chr15_77022501fwd/C/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct05/01/1005/01/10132Genomicunknown
ss255136007BL|SNP66483_15_77022501fwd/BC/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct08/19/1008/20/10134Genomicunknown
ss282329257GMI|GMI_AK_SNP_6649656fwd/C/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct12/16/1012/16/10137Genomicunknown
ss286987860GMI|GMI_NA10851_SNP_3000651fwd/C/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct12/17/1012/17/10138Genomicunknown
ss291758026PJP|SNP_1264384_chr15_77022501fwd/C/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct01/21/1101/21/11134Genomicunknown
ss410931007ILLUMINA|Cardio-Metabo_Chip_11395247_A_rs3825932rev/TA/Gagattattctggccccagaataatctctccgaggcaaactggtagtcaattgtcctaaac06/07/1106/07/11135Genomicunknown
ss480854453ILLUMINA|HumanOmni2.5-4v1_B_rs3825932-128_T_R_1660355004fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat01/30/1210/28/16137Genomicunknown
ss480872439ILLUMINA|HumanOmniExpress-12v1_C_rs3825932-131_T_R_1852961835fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat01/30/1210/27/16137Genomicunknown
ss481808787ILLUMINA|HumanOmni1-Quad_v1-0_C_rs3825932-131_T_R_1865384196fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat01/30/1208/28/15146Genomicunknown
ss485222210ILLUMINA|HumanOmni2.5-4v1_D_rs3825932-131_T_R_1852961835fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat01/30/1210/27/16137Genomicunknown
ss491498078EXOME_CHIP|.GWAS._214304_chr_15_79235446fwd/BC/Tgtttaggacaattgactaccagtttgcctcggagagattattctggggccagaataatct03/05/1203/05/12137Genomicunknown
ss564595206TISHKOFF|snp_chr15_79235446fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat11/22/1211/23/12138Genomicunknown
ss660333164SSMP|15_79235446fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat12/14/1202/13/15138Genomicunknown
ss780684750ILLUMINA|HumanOmni25Exome-8v1_A_exm-rs3825932-131_T_R_1990491951fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat05/30/1307/10/15146Genomicunknown
ss783057055ILLUMINA|HumanOmni2.5-4v1_H_rs3825932-131_T_R_1852961835fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat05/30/1307/29/15146Genomicunknown
ss783358214ILLUMINA|HumanOmniExpressExome-8v1_A_exm-rs3825932-131_T_R_1990491951fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat05/31/1306/18/15146Genomicunknown
ss832314967ILLUMINA|HumanOmniExpress-12v1_H_rs3825932-131_T_R_1852961835fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat09/17/1306/18/15146Genomicunknown
ss991985019EVA-GONL|EVA-GONL_rs3825932fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat04/23/1404/30/14142Genomicunknown
ss1080269088JMKIDD_LAB|HGDP_WGS_chr15_79235446fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat07/10/1407/12/14142Genomicunknown
ss13542422971000GENOMES|PHASE3_V1_67606521fwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat08/16/1408/16/14142Genomicunknown
ss1427686776DDI|DDI_rs3825932fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat11/04/1411/04/14144Genomicunknown
ss1577714295EVA_GENOME_DK|EVA_GENOME_DK_snv_rs3825932fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat02/19/1502/19/15144Genomicunknown
ss1633414653EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_15_79235446_37395581fwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat03/04/1503/04/15144Genomicunknown
ss1676408686EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_15_79235446_37395581fwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat03/04/1503/04/15144Genomicunknown
ss1696011092EVA_DECODE|EVA_DECODE_15_77022501_425676_rs3825932fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat03/02/1503/04/15144Genomicunknown
ss1713504410EVA_SVP|EVA_SVP_1198777fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat03/12/1503/12/15144Genomicunknown
ss1752172617ILLUMINA|OmniExpressExome-8v1-1_B_exm-rs3825932-131_T_R_1990491951fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat05/27/1506/09/15146Genomicunknown
ss1752172618ILLUMINA|OmniExpressExome-8v1-1_B_rs3825932-131_T_R_1885473348fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat05/27/1506/09/15146Genomicunknown
ss1808289455HAMMER_LAB|Hsieh_7314815fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat07/15/1507/16/15146Genomicunknown
ss1917899456ILLUMINA|HumanExome-12v1-1_B_exm-rs3825932-131_T_R_1990491951fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat10/16/1510/16/15147Genomicunknown
ss1935388375WEILL_CORNELL_DGM|SNV:chr15:79235446fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat10/16/1510/18/15147Genomicunknown
ss1946399529ILLUMINA|HumanCoreExome-12v1-0_C_exm-rs3825932-131_T_R_1990491951fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat10/29/1510/29/15147Genomicunknown
ss1959629092ILLUMINA|exm-rs3825932-131_T_R_1990491951fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat11/13/1511/13/15147Genomicunknown
ss1968153390GENOMED|rs3825932fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat02/16/1602/16/16147Genomicunknown
ss2028475706JJLAB|SNP8978261fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat08/29/1608/31/16149Genomicunknown
ss2094886975ILLUMINA|Immuno_BeadChip_11419691_B_imm_15_77022501-1_T_R_1670085947fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat09/27/1609/27/16150Genomicunknown
ss2095060645ILLUMINA|InfiniumImmunoArray-24v2-0_A_imm_15_77022501-1_T_R_2310671538fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat09/27/1609/27/16150Genomicunknown
ss2095060646ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs3825932-138_T_R_2264335340fwd/BC/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat09/27/1609/27/16150Genomicunknown
ss2156884557USC_VALOUEV|NC_000015.9:g.79235446T>Cfwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat11/17/1611/17/16150Genomicunknown
ss2208377507HUMAN_LONGEVITY|HLI-15-78943104-T-Cfwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat11/18/1611/18/16150Genomicunknown
ss2372868244TOPMED|15_79235446_T/Cfwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat11/19/1611/19/16150Genomicunknown
ss2633254336ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_SoL-rs3825932-131_T_R_2131fwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat02/02/1702/02/17151Genomicunknown
ss2633254337ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs3825932-131_T_R_18854733fwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat02/02/1702/02/17151Genomicunknown
ss2633254338ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_seq-rs3825932-131_T_R_2130fwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat02/02/1702/02/17151Genomicunknown
ss2701365618GRF|rs3825932fwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat02/13/1702/13/17151Genomicunknown
ss2937141983GNOMAD|rs3825932fwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat05/23/1705/23/17151Genomicunknown
ss2985047886AFFY|Axiom_PsorMich_Affx-12017636fwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat05/24/1705/24/17151Genomicunknown
ss2985689622AFFY|Axiom_Smokesc1_Affx-12017636fwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat05/24/1705/24/17151Genomicunknown
ss3013599187SWEGEN|NC_000015.9:g.79235446T>Cfwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat05/30/1705/30/17151Genomicunknown
ss3021652312ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm-rs3825932-131_T_R_1990491951fwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat06/28/1706/28/17151Genomicunknown
ss3028062161BIOINF_KMB_FNS_UNIBA|15.78943104T>Cfwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat07/05/1707/05/17151Genomicunknown
ss3232780069TOPMED|TOPMed_freeze_5?chr15:78,943,104fwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat10/01/1710/01/17151Genomicunknown
ss3351201153CSHL|rs3825932fwd/C/Tggacaattgactaccagtttgcctcggagagattattctggggccagaat10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3825932|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 CAGATATGAA CGATTTATTA CCGTTTTGTC TTTTTGTTTG CTGTCCCTAT TGTTTTTATA
 CCCATGGGTT CAGGTTCAGA TTGAATGAGA GGAAAGAGGT TCCCCCTTGC CTTCAGGGGC
 TCTCTCCCAG TTTTAGCAAA GAGGACACTT GGAAATAAAA GGTCTGTAAA TGGATTTCCA
 GAACACTCTC TGCCGGCATC ACTTGAAATA TCTTCCTGTT TCCCCAAGGA TCCATACCTC
 CAGTGTGAAG ATCACTACCA CACAGCATTT AGATCTCCGT TTTTGGGTCT CGAACCTGTT
 CCAGAGACCA ATCTATGGCC GTTTTCCCTG GGGAAAATGC ACATTTCCTC AACATGGCTC
 CCTTTAGGGT TTCAGGGGAT TCCAGATCTT GATTAAGGGC CCTGCTGCAG CTGAGGGCTT
 TAGAGGAAGA CAGACCTCAA CTCAGGACAA GAGTTGGAGG CAGGGTTTGA GTTTAGGACA
 ATTGACTACC AGTTTGCCTC
 Y
 GGAGAGATTA TTCTGGGGCC AGAATAATCT GCTGGTGAAC CGTGCCTTAC CCTAAAATAG
 ATCCATTCCA ATCTAGTCAG GACTTTAAAA GTGCCATAAT ACCTTGCCTG GATTTACAGC
 AGGTTTCAGG AAAGTACAGT ATTCCCCTGT TTGTTTGTTT GTTTGTTTTA GATGGAGTCT
 TACTCTGTCA CCCAGGCTGG AGTGATCGCC ACCTCTCAGT TTCAAGCGAT TCTCCTGCCC
 CAGCCTCCTG AGTACCTGGG ATTACAGGCA CCTGGCTACC ACACCCAGCT AATTTTTGTA
 TTTTTAGTAG AGACAGGGTT TCACCATGTT GGCCAGGCTG CTCTCGAACT CCTGACCTAA
 AGTGATCCGA CTGCCTCGGT CTCCCAAATT GCTGAGATTA CAGGTGTGAG CCACCGCAGC
 CGGTCCCTGA CTCCTGTTTT AGTACAGCTC CTGGGCTACA AACGGTTTCT TACAATTTTA
 AATGGTTAGA AGAAACATAT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010284.1
dbSNP Blast Analysis
OMIM
222100

  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
ss132424993ENSEMBL_Venter 2IG1.00000000 1.00000000
ENSEMBL_celera 4IG0.50000000 0.50000000 0.500000000.50000000
ss1354242297EAS 1008AF 0.095200000.90480000
EUR 1006AF 0.660000030.34000000
AFR 1322AF 0.162600000.83740002
AMR 694AF 0.407800020.59219998
SAS 978AF 0.598200020.40179998
ss16663703HapMap-CEUEuropean 226IG0.469026540.451327440.079646020.527089000.694690290.30530974
HapMap-HCBAsian 86IG 0.302325580.697674390.583882000.151162790.84883720
HapMap-JPTAsian 172IG0.023255810.162790700.813953460.250592000.104651160.89534885
HapMap-YRISub-Saharan African 226IG0.026548670.230088500.743362840.583882000.141592920.85840708
HAPMAP-ASW 98IG 0.448979590.551020380.250592000.224489790.77551019
HAPMAP-CHBAsian 82IG 0.121951220.878048781.000000000.060975610.93902439
HAPMAP-CHD 166IG0.012048190.156626510.831325290.751830000.090361450.90963858
HAPMAP-GIH 174IG0.390804590.436781620.172413800.479500000.609195410.39080459
HAPMAP-LWK 180IG0.066666670.366666670.566666661.000000000.250000000.75000000
HAPMAP-MEX 100IG0.239999990.560000000.200000000.402784000.519999980.47999999
HAPMAP-MKK 286IG0.083916080.391608390.524475510.751830000.279720280.72027969
HAPMAP-TSI 176IG0.352272720.431818190.215909090.273322000.568181810.43181819
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss171368497PGP 2IG 1.00000000 0.500000000.50000000
ss226989126pilot_1_YRI_low_coverage_panel 118AF 0.110169490.88983053
ss236846676pilot_1_CEU_low_coverage_panel 120AF 0.699999990.30000001
ss243221590pilot_1_CHB+JPT_low_coverage_panel 120AF 0.125000000.87500000
ss66261722HapMap-CEUEuropean 118IG0.457627120.423728820.118644070.751830000.669491530.33050847
HapMap-HCBAsian 90IG 0.288888900.711111130.583882000.144444450.85555553
HapMap-JPTAsian 90IG0.022222220.200000000.777777790.654721000.122222220.87777776
HapMap-YRISub-Saharan African 120IG0.033333340.150000010.816666660.099721000.108333330.89166665
ss76406823ICMHP 4IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.465+/-0.1270000

  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_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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