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Reference SNP (refSNP) Cluster Report: rs4815617                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:111/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS PheGenI
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.0397/199 (1000 Genomes)
T=0.0660/8290 (TOPMED)
HGVS Names
  • CM000682.2:g.3846662C>T
  • NC_000020.10:g.3827309C>T
  • NC_000020.11:g.3846662C>T
  • NG_030028.1:g.4864C>T
  • NM_001206491.1:c.-557C>T
  • NM_020746.4:c.-309C>T
  • NR_037921.1:n.-137C>T
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 ss167702083 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4815617 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
ss6647666WI_SSAHASNP|NT_011387.8_3767309byFreqfwd/BC/Tccctggaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccgagccc02/12/0310/25/06111Genomicunknown
ss66263972AFFY|SNP_A-4294093byFreqfwd/BC/Tcgagactgcgcgccccagcaaaaaatcaggtc10/27/0603/31/08127Genomicunknown
ss66684873ILLUMINA|HumanHap300v1.1_rs4815617fwd/BC/Tccctggaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccgagccc11/09/0611/09/06127Genomicunknown
ss67381738ILLUMINA|HumanHap550v1.1_rs4815617fwd/BC/Tccctggaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccgagccc11/14/0611/14/06127Genomicunknown
ss67759534ILLUMINA|HumanHap650Yv1.0_rs4815617fwd/BC/Tccctggaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccgagccc11/14/0611/14/06127Genomicunknown
ss70827521ILLUMINA|HumanHap550v3.0__rs4815617rev/TA/Ggggctcggagaaccgacctgattttttgctggggcgcgcagtctcgagcaacttccaggg04/20/0703/31/08130Genomicunknown
ss71409777ILLUMINA|HumanHap650Yv3.0_rs4815617fwd/BC/Tccctggaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccgagccc04/23/0704/23/07127Genomicunknown
ss75594736ILLUMINA|ILMN_Human_1M_rs4815617fwd/BC/Tccctggaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccgagccc08/28/0708/29/07129Genomicunknown
ss76409040AFFY|AFFY_6_1M_SNP_A-4294093fwd/BC/Tcgagactgcgcgccccagcaaaaaatcaggtc08/28/0708/30/07129Genomicunknown
ss79196966ILLUMINA|HumanHap300v2.0_rs4815617fwd/BC/Tccctggaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccgagccc04/18/0711/18/07130Genomicunknown
ss84363626KRIBB_YJKIM|KHS693722fwd/BC/Tccctggaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccgagccc12/04/0712/07/07130Genomicunknown
ss122397914ILLUMINA|HumanCNV370v1_C_rs4815617fwd/BC/Tccctggaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccgagccc04/14/0904/15/09131Genomicunknown
ss154319999ILLUMINA|Human610_Quadv1_B_rs4815617-128_T_R_1501788752rev/TA/Ggggctcggagaaccgacctgattttttgctggggcgcgcagtctcgagcaacttccaggg06/18/0906/20/09131Genomicunknown
ss159496659ILLUMINA|Human660W-Quad_v1_A_rs4815617-128_T_R_1501788752rev/TA/Ggggctcggagaaccgacctgattttttgctggggcgcgcagtctcgagcaacttccaggg07/06/0907/07/09131Genomicunknown
ss160715661ILLUMINA|HumanOmni1-Quad_v1-0_B_rs4815617-128_T_R_1501788752rev/TA/Ggggctcggagaaccgacctgattttttgctggggcgcgcagtctcgagcaacttccaggg08/04/0910/04/09131Genomicunknown
ss167702083COMPLETE_GENOMICS|NA07022_36_chr20_3775309fwd/BC/Tccctggaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccgagccc09/30/0909/30/09132Genomicunknown
ss171931235ILLUMINA|HumanCNV370-Quadv3_C_rs4815617-128_T_R_1501788752rev/TA/Ggggctcggagaaccgacctgattttttgctggggcgcgcagtctcgagcaacttccaggg10/01/0910/04/09132Genomicunknown
ss173498122AFFY|GenomeWideSNP_5_SNP_A-4294093fwd/BC/Tcgagactgcgcgccccagcaaaaaatcaggtc10/01/0910/03/09132Genomicunknown
ss173827613ILLUMINA|Human1M-Duov3_B_rs4815617-128_T_R_1501788752rev/TA/Ggggctcggagaaccgacctgattttttgctggggcgcgcagtctcgagcaacttccaggg10/01/0910/04/09132Genomicunknown
ss208741363BCM-HGSC-SUB|BCM_CMT_1011-3209857fwd/BC/Tccctggaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccgagccc03/15/1003/20/10132Genomicunknown
ss2109520871000GENOMES|CEU.trio.3.2010_164309_chr20_3775309fwd/BC/Tccctggaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccgagccc03/29/1003/29/10132Genomicunknown
ss2377418491000GENOMES|pilot_1_CEU_7346478_chr20_3775309fwd/C/Tccctggaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccgagccc05/01/1005/01/10132Genomicunknown
ss481060600ILLUMINA|HumanOmni2.5-4v1_B_rs4815617-128_T_R_1735639701fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg01/30/1210/28/16137Genomicunknown
ss481082354ILLUMINA|HumanOmniExpress-12v1_C_rs4815617-131_T_R_1857705518fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg01/30/1210/27/16137Genomicunknown
ss482076797ILLUMINA|HumanOmni1-Quad_v1-0_C_rs4815617-131_T_R_1865282748fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg01/30/1208/28/15146Genomicunknown
ss485325338ILLUMINA|HumanOmni2.5-4v1_D_rs4815617-131_T_R_1857705518fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg01/30/1210/28/16137Genomicunknown
ss491557663EXOME_CHIP|.GWAS._273889_chr_20_3827309fwd/BC/Tccctggaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccgagccc03/05/1203/06/12137Genomicunknown
ss537278687ILLUMINA|HumanOmni5-4v1_B_rs4815617-131_T_R_1866551395fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg06/22/1208/29/15146Genomicunknown
ss661972685SSMP|20_3827309fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg12/14/1202/14/15138Genomicunknown
ss778920635ILLUMINA|HumanOmni25Exome-8v1_A_rs4815617-131_T_R_1866551395fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg05/30/1307/10/15146Genomicunknown
ss780685382ILLUMINA|HumanOmni25Exome-8v1_A_exm-rs4815617-131_T_R_1990492630fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg05/30/1307/10/15146Genomicunknown
ss783108480ILLUMINA|HumanOmni2.5-4v1_H_rs4815617-131_T_R_1857705518fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg05/30/1307/29/15146Genomicunknown
ss783358868ILLUMINA|HumanOmniExpressExome-8v1_A_exm-rs4815617-131_T_R_1990492630fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg05/31/1306/19/15146Genomicunknown
ss784065540ILLUMINA|HumanOmniExpressExome-8v1_A_rs4815617-131_T_R_1967907704fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg05/31/1306/19/15146Genomicunknown
ss825527484ILLUMINA|HumanCNV370v1_C_rs4815617-111_T_R_IFB1135757159:0fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg06/24/1311/21/14144Genomicunknown
ss832367128ILLUMINA|HumanOmniExpress-12v1_H_rs4815617-131_T_R_1857705518fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg09/17/1306/18/15146Genomicunknown
ss834382063ILLUMINA|HumanOmni2.5-8v1_A_rs4815617-131_T_R_1866551395fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg09/18/1307/29/15146Genomicunknown
ss994487100EVA-GONL|EVA-GONL_rs4815617fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg04/23/1405/01/14142Genomicunknown
ss1082031732JMKIDD_LAB|HGDP_WGS_chr20_3827309fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg07/10/1407/12/14142Genomicunknown
ss13638761051000GENOMES|PHASE3_V1_77629350fwd/C/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg08/16/1408/16/14142Genomicunknown
ss1397761738HAMMER_LAB|HAMMER_LAB_rs4815617fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg09/30/1409/30/14146Genomicunknown
ss1579415231EVA_GENOME_DK|EVA_GENOME_DK_snv_rs4815617fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg02/19/1502/20/15144Genomicunknown
ss1638308764EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_20_3827309_42791359fwd/C/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg03/04/1503/04/15144Genomicunknown
ss1681302797EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_20_3827309_42791359fwd/C/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg03/04/1503/04/15144Genomicunknown
ss1698541763EVA_DECODE|EVA_DECODE_20_3775309_31536_rs4815617fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg03/02/1503/05/15144Genomicunknown
ss1713675033EVA_SVP|EVA_SVP_1369112fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg03/12/1503/12/15144Genomicunknown
ss1752385857ILLUMINA|OmniExpressExome-8v1-1_B_exm-rs4815617-131_T_R_1990492630fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg05/27/1506/09/15146Genomicunknown
ss1752385858ILLUMINA|OmniExpressExome-8v1-1_B_rs4815617-131_T_R_1967907704fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg05/27/1506/09/15146Genomicunknown
ss1917944461ILLUMINA|HumanExome-12v1-1_B_exm-rs4815617-131_T_R_1990492630fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg10/16/1510/16/15147Genomicunknown
ss1937996205WEILL_CORNELL_DGM|SNV:chr20:3827309fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg10/16/1510/19/15147Genomicunknown
ss1946545891ILLUMINA|HumanCoreExome-12v1-0_C_exm-rs4815617-131_T_R_1990492630fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg10/29/1510/29/15147Genomicunknown
ss1959894139ILLUMINA|exm-rs4815617-131_T_R_1990492630fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg11/13/1511/13/15147Genomicunknown
ss2029775088JJLAB|SNP10277643fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg08/29/1608/31/16149Genomicunknown
ss2094809419ILLUMINA|Immuno_BeadChip_11419691_B_rs4815617-131_T_R_1866551395fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg09/27/1609/27/16150Genomicunknown
ss2095112965ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs4815617-131_T_R_1866551395fwd/BC/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg09/27/1609/27/16150Genomicunknown
ss2158329314USC_VALOUEV|NC_000020.10:g.3827309C>Tfwd/C/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg11/17/1611/17/16150Genomicunknown
ss2240937361HUMAN_LONGEVITY|HLI-20-3846662-C-Tfwd/C/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg11/18/1611/18/16150Genomicunknown
ss2407403548TOPMED|20_3827309_C/Tfwd/C/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg11/19/1611/19/16150Genomicunknown
ss2633769737ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_SoL-rs4815617-131_T_R_2131fwd/C/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg02/02/1702/02/17151Genomicunknown
ss2633769738ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs4815617-131_T_R_19679077fwd/C/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg02/02/1702/02/17151Genomicunknown
ss2964909857GNOMAD|rs4815617fwd/C/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg05/23/1705/23/17151Genomicunknown
ss2985208332AFFY|Axiom_PsorMich_Affx-16693821fwd/C/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg05/24/1705/24/17151Genomicunknown
ss2985828739AFFY|Axiom_Smokesc1_Affx-16693821fwd/C/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg05/24/1705/24/17151Genomicunknown
ss3017790731SWEGEN|NC_000020.10:g.3827309C>Tfwd/C/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg05/30/1705/30/17151Genomicunknown
ss3022096197ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm-rs4815617-131_T_R_1990492630fwd/C/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg06/28/1706/28/17151Genomicunknown
ss3028719545BIOINF_KMB_FNS_UNIBA|20.3846662C>Tfwd/C/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg07/05/1707/05/17151Genomicunknown
ss3352394743CSHL|rs4815617fwd/C/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg10/02/1710/02/17151Genomicunknown
ss3353737577TOPMED|TOPMed_freeze_5?chr20:3,846,662fwd/C/Tgaagttgctcgagactgcgcgccccagcaaaaaatcaggtcggttctccg10/03/1710/03/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4815617|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 CTTGCCCCTG TGACTTCAGC GGCACCCAAC GTTTATTGGG CACTAACTGT ATGCCAGGCC
 ATGGGGGTGC CGGAGAGAAC GACACGAAGA CCCTCACCCC TCAAAGTTCC CAGGGGGAGG
 AGGGGCTGCT TCACTTGGGA AGCGTGGGGA TGGAATTCTC AGCCCCCCGA TGACTCCGAG
 GCCGGCCACC TGCCTGGTTT CTGGCCGGAC ACCGGACTTC CCCTGGAAGT TGCTCGAGAC
 TGCGCGCCCC
 Y
 AGCAAAAAAT CAGGTCGGTT CTCCGAGCCC AGTCTAGCGC TTCCCGACCC GCAAACCAAG
 GCCCAGTGAC CGTCCCCGCT GCGCAGCCGC CTGCGTCGCC AGCCAACCAC GCGCGGCCGA
 GTAGCCCCGC CCCTCCACAT GGCCAATGGC CGCGCGCTCT GCCCGCCCCG CCTCCTCGCT
 GCGGGAAGGG TCCTGGGCCC CGGGCGGCGG TCGCCAGGTC TCAGGGCCGG GGGTACCCGA
 GGTAAGATCG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000020
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
ss1363876105EAS 1008AF 0.995000000.00500000
EUR 1006AF 0.895599960.10439999
AFR 1322AF 0.991699930.00830000
AMR 694AF 0.949599980.05040000
SAS 978AF 0.956000030.04400000
ss167702083CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss237741849pilot_1_CEU_low_coverage_panel 120AF 0.958333310.04166667
ss66263972HapMap-CEUEuropean 118IG0.779661000.22033899 0.751830000.889830530.11016949
HapMap-HCBAsian 90IG1.00000000 1.00000000
HapMap-JPTAsian 90IG1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG1.00000000 1.00000000
ss6647666HapMap-CEUEuropean 226IG0.823008840.159292040.017699110.342782000.902654890.09734514
HapMap-HCBAsian 86IG1.00000000 1.00000000
HapMap-JPTAsian 88IG1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG1.00000000 1.00000000
HAPMAP-ASW 98IG0.959183690.04081633 1.000000000.979591850.02040816
HAPMAP-CHBAsian 82IG0.975609780.02439024 1.000000000.987804890.01219512
HAPMAP-GIH 176IG0.920454560.07954545 1.000000000.960227250.03977273
HAPMAP-MEX 100IG0.899999980.10000000 1.000000000.949999990.05000000
HAPMAP-MKK 286IG0.972027960.02797203 1.000000000.986014010.01398601
HAPMAP-TSI 176IG0.784090940.204545450.011363641.000000000.886363630.11363637
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss76409040ICMHP 6IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.076+/-0.1800000ALFRED: 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
byClusterbyFreqwith2hitWith1000GenomeData
DoubleHit found by:  NCBI
UNKNOWNUNKNOWNUNKNOWN

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