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Reference SNP (refSNP) Cluster Report: rs9576827                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:G=0.2454/1229 (1000 Genomes)
G=0.1150/14436 (TOPMED)
HGVS Names
  • CM000675.2:g.39506244A>G
  • NC_000013.10:g.40080381A>G
  • NC_000013.11:g.39506244A>G
  • NM_005780.2:c.385+94588T>C
  • XR_941893.2:n.501+521A>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 ss281684919 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9576827 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
ss13300639SC_SNP|NT_024524.12_8654872byFreqfwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa10/22/0310/25/06119Genomicunknown
ss24056247PERLEGEN|afd0952799byFreqfwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa08/10/0409/13/04123Genomicunknown
ss66822258ILLUMINA|HumanHap300v1.1_rs9576827fwd/BA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa11/09/0611/09/06127Genomicunknown
ss67933137ILLUMINA|HumanHap550v1.1_rs9576827fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa11/14/0611/15/06127Genomicunknown
ss68052173ILLUMINA|HumanHap650Yv1.0_rs9576827fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa11/14/0611/15/06127Genomicunknown
ss69132184PERLEGEN|PGP00952799byFreqfwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa01/30/0703/31/08127Genomicunknown
ss71616878ILLUMINA|HumanHap650Yv3.0_rs9576827fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa04/23/0704/23/07127Genomicunknown
ss74832750AFFY|SNP_M-589975fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa08/09/0708/09/07128Genomicunknown
ss75861287ILLUMINA|ILMN_Human_1M_rs9576827fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa08/28/0708/29/07129Genomicunknown
ss79300567ILLUMINA|HumanHap300v2.0_rs9576827fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa04/18/0711/18/07130Genomicunknown
ss84839462KRIBB_YJKIM|KHS825913fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa12/04/0712/08/07130Genomicunknown
ss98274757ILLUMINA|HumanHap550v3.0__rs9576827fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa04/20/0703/31/08130Genomicunknown
ss103113643BGI|BGI_rs9576827fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa06/05/0806/17/09131Genomicunknown
ss1127181711000GENOMES|CEU.trio.12.15.2008_2882366_chr13_38978381fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa12/18/0812/18/08130Genomicunknown
ss123016980ILLUMINA|HumanCNV370v1_C_rs9576827fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa04/14/0904/15/09131Genomicunknown
ss154502228ILLUMINA|Human610_Quadv1_B_rs9576827-127_T_F_1501892063fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa06/18/0906/20/09131Genomicunknown
ss154699400GMI|GMI_SNP_73870002fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa06/24/0906/24/09131Genomicunknown
ss159676081ILLUMINA|Human660W-Quad_v1_A_rs9576827-128_T_F_1501892063fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa07/06/0907/07/09131Genomicunknown
ss161000735ILLUMINA|HumanOmni1-Quad_v1-0_B_rs9576827-128_T_F_1501892063fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa08/04/0910/05/09131Genomicunknown
ss172483110ILLUMINA|HumanCNV370-Quadv3_C_rs9576827-127_T_F_1501892063fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa10/01/0910/04/09132Genomicunknown
ss174871001ILLUMINA|Human1M-Duov3_B_rs9576827-127_T_F_1501892063fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa10/01/0910/05/09132Genomicunknown
ss199114739BUSHMAN|BUSHMAN-chr13-38978380byFreqfwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa02/16/1009/05/14132Genomicunknown
ss208604246BCM-HGSC-SUB|BCM_CMT_1011-2496316fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa03/15/1003/19/10132Genomicunknown
ss209093966ILLUMINA|ALS_iSelect_272541_A_rs9576827-127_T_F_IFB1223186854fwd/TA/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa03/24/1003/24/10132Genomicunknown
ss2261458491000GENOMES|pilot_1_YRI_7955532_chr13_38978381fwd/A/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa04/22/1004/22/10132Genomicunknown
ss2362238121000GENOMES|pilot_1_CEU_5828441_chr13_38978381fwd/A/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa05/01/1005/01/10132Genomicunknown
ss2427244521000GENOMES|pilot_1_CHB+JPT_4609529_chr13_38978381fwd/A/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa05/01/1005/01/10132Genomicunknown
ss281684919GMI|GMI_AK_SNP_6005308fwd/A/Gctgtgatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctaccataaaa12/16/1012/16/10137Genomicunknown
ss481941010ILLUMINA|HumanOmni2.5-4v1_B_rs9576827-128_T_F_1782907716fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca01/30/1210/28/16137Genomicunknown
ss481974401ILLUMINA|HumanOmniExpress-12v1_C_rs9576827-131_T_F_1857675241fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca01/30/1210/27/16137Genomicunknown
ss482930425ILLUMINA|HumanOmni1-Quad_v1-0_C_rs9576827-131_T_F_1865253963fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca01/30/1208/28/15146Genomicunknown
ss485764206ILLUMINA|HumanOmni2.5-4v1_D_rs9576827-131_T_F_1857675241fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca01/30/1210/27/16137Genomicunknown
ss537613879ILLUMINA|HumanOmni5-4v1_B_rs9576827-131_T_F_1866908739fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca06/22/1208/29/15146Genomicunknown
ss563622849TISHKOFF|snp_chr13_40080381fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca11/22/1211/23/12138Genomicunknown
ss659221816SSMP|13_40080381fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca12/14/1202/13/15138Genomicunknown
ss779014702ILLUMINA|HumanOmni25Exome-8v1_A_rs9576827-131_T_F_1866908739fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca05/30/1307/10/15142Genomicunknown
ss783327916ILLUMINA|HumanOmni2.5-4v1_H_rs9576827-131_T_F_1857675241fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca05/30/1307/29/15142Genomicunknown
ss784279686ILLUMINA|HumanOmniExpressExome-8v1_A_rs9576827-131_T_F_1866908739fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca05/31/1306/18/15142Genomicunknown
ss825631085ILLUMINA|HumanCNV370v1_C_rs9576827-123_T_F_IFB1137361867:0fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca06/24/1311/21/14144Genomicunknown
ss832589644ILLUMINA|HumanOmniExpress-12v1_H_rs9576827-131_T_F_1857675241fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca09/17/1306/18/15144Genomicunknown
ss833186794ILLUMINA|Human660W-Quad_v1_C_rs9576827-131_T_F_1857675241fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca09/18/1307/02/15142Genomicunknown
ss833777622ILLUMINA|Human660W-Quad_v1_H_rs9576827-131_T_F_1857675241fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca09/18/1307/02/15142Genomicunknown
ss834477204ILLUMINA|HumanOmni2.5-8v1_A_rs9576827-131_T_F_1866908739fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca09/18/1307/29/15142Genomicunknown
ss990313242EVA-GONL|EVA-GONL_rs9576827fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca04/23/1404/25/14142Genomicunknown
ss1079027615JMKIDD_LAB|HGDP_WGS_chr13_40080381fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca07/10/1407/12/14142Genomicunknown
ss13479289831000GENOMES|PHASE3_V1_61019070fwd/A/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca08/16/1408/16/14142Genomicunknown
ss1427166267DDI|DDI_rs9576827fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca11/04/1411/04/14144Genomicunknown
ss1576743646EVA_GENOME_DK|EVA_GENOME_DK_snv_rs9576827fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca02/19/1502/19/15144Genomicunknown
ss1630124870EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_13_40080381_33768128fwd/A/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca03/04/1503/04/15144Genomicunknown
ss1673118903EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_13_40080381_33768128fwd/A/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca03/04/1503/04/15144Genomicunknown
ss1684833560EVA_DECODE|EVA_DECODE_13_38978381_171688_rs9576827fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca03/02/1503/04/15144Genomicunknown
ss1713385409EVA_SVP|EVA_SVP_1079776fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca03/12/1503/12/15144Genomicunknown
ss1752103565ILLUMINA|OmniExpressExome-8v1-1_B_rs9576827-131_T_F_2031153236fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca05/27/1506/09/15146Genomicunknown
ss1933681594WEILL_CORNELL_DGM|SNV:chr13:40080381fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca10/16/1510/17/15147Genomicunknown
ss2027599465JJLAB|SNP8102020fwd/TA/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca08/29/1608/31/16149Genomicunknown
ss2155964141USC_VALOUEV|NC_000013.10:g.40080381A>Gfwd/A/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca11/17/1611/17/16150Genomicunknown
ss2195737382HUMAN_LONGEVITY|HLI-13-39506244-A-Gfwd/A/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca11/18/1611/18/16150Genomicunknown
ss2359848168TOPMED|13_40080381_A/Gfwd/A/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca11/19/1611/19/16150Genomicunknown
ss2628289132SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV5162415fwd/A/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca01/06/1701/06/17151Genomicunknown
ss2633054813ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs9576827-131_T_F_20311532fwd/A/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca02/02/1702/02/17151Genomicunknown
ss2635044725ILLUMINA|Cancer_BeadChip_11459870_A_rs9576827-128_T_F_1782907716fwd/A/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca02/02/1702/02/17151Genomicunknown
ss2700338735GRF|rs9576827fwd/A/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca02/13/1702/13/17151Genomicunknown
ss2918810254GNOMAD|rs9576827fwd/A/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca05/23/1705/23/17151Genomicunknown
ss2985637484AFFY|Axiom_Smokesc1_Affx-9317817fwd/A/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca05/24/1705/24/17151Genomicunknown
ss3010899547SWEGEN|NC_000013.10:g.40080381A>Gfwd/A/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca05/30/1705/30/17151Genomicunknown
ss3027616500BIOINF_KMB_FNS_UNIBA|13.39506244A>Gfwd/A/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca07/05/1707/05/17151Genomicunknown
ss3190763440TOPMED|TOPMed_freeze_5?chr13:39,506,244fwd/A/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca09/30/1709/30/17151Genomicunknown
ss3350420392CSHL|rs9576827fwd/A/Gatcaacagtgcggttaatagatgtgttaggaaaacaagaagaggctacca10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs9576827|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 CTCTCTTGGT TCCTTCTAAA GCTGAGAAAC TTCATTAGGT CTGTACCCAC TACAGATTTC
 CAGTGATAGA GTGAAGGGTA TTATCCACTT TTATACATTT TCTAAATGAC ATTTTGTCTA
 TATTACAAAT GAAAATATTA TCCTCTAAAC AAGGATGCAT TATCTTACTG CCACAGAGGA
 GCTATCAATA ATTTCTCAGT CCTCATCATT TATTATAAAG GATCTGCGGA ACATCTCTCC
 TTTTAACCTC TAACCACTCA ACTCAGATAA AGCCTGCATT CAAAACTGAT CACCTTGTCA
 TGCAGGTGAT CAAGCAAGAA CTATCTCTTT TTACAGACAA AACAGCCCCA AGTATAATAA
 TATGGTTTTA TACTACACTA TGATCTTTTA CATTACTTCC TTACAATAAC AGTTTCTAGG
 GAACAATATG ATTTCCAATA TTCAGCTCTG GCTTCTGTGG ACGTAATATT CTGTGATCAA
 CAGTGCGGTT AATAGATGTG
 R
 TTAGGAAAAC AAGAAGAGGC TACCATAAAA ATGTATGTGA AAGAGCACCT GAGGGTCCCG
 CTGCTAATTC CTTGGCCAAG TTCTTAACAA GGGGTGAGGA TCCTAATGGT GTTCAGTGAT
 GAATACGAAG ACCAACTGTG AGAAAGGACC TCAGAGAAGA TAGTAAACAT TTGTCAAAGT
 TGAGTCCCAT GGGATTTCAC GCTCTTCTGA GCAGTGGAAA CCAAAATCAC CTAATTTTCT
 ATCCAGCCAG GCTAGGATGA TGATCCACAG TGAGAAACAT TTCACACTAA AGTCATTTAT
 TTTATTTTAT TTCATTTCAT TTTTTGCTTG TGACCCCTAA ATTAATAAGG GCCACCGCCA
 CTCAGCAGCT TAATCAACAG AGCTCCATCA TTCTGTCAGC TCCTTAAGAA GCATAAGAAA
 GCAAGTCAGG GTGGGAAAGG GTTGAATGGC AGAGAAGGAA GGAGGTGGGA TAGGGAGGTG
 GGGGGGAAGG TGTGGAAAAA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_024524
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.
SourceA/A
A/G
G/G
HWPA
G
ss13300639HapMap-CEUEuropean 120IG0.816666660.18333334 0.751830000.908333360.09166667
HapMap-HCBAsian 82IG0.170731710.390243890.439024390.317310000.365853670.63414633
HapMap-JPTAsian 168IG0.107142860.488095220.404761910.527089000.351190480.64880955
HapMap-YRISub-Saharan African 118IG0.830508470.16949153 1.000000000.915254240.08474576
HAPMAP-ASW 96IG0.437500000.479166660.083333340.527089000.677083310.32291666
HAPMAP-CHBAsian 80IG0.075000000.400000010.524999981.000000000.275000010.72500002
HAPMAP-CHD 166IG0.132530120.445783140.421686741.000000000.355421690.64457834
HAPMAP-GIH 176IG0.511363630.397727280.090909090.751830000.710227250.28977272
HAPMAP-LWK 180IG0.622222240.300000010.077777780.200325000.772222220.22777778
HAPMAP-MKK 282IG0.687943280.283687950.028368791.000000000.829787250.17021276
HAPMAP-TSI 176IG0.761363630.23863636 0.583882000.880681810.11931818
ENSEMBL_Watson 2IG1.00000000 1.00000000
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss1347928983EAS 1008AF 0.373000000.62699997
EUR 1006AF 0.914500000.08550000
AFR 1322AF 0.921299990.07870000
AMR 694AF 0.929400030.07060000
SAS 978AF 0.633900050.36610001
ss199114739BUSHMAN_POP2 2IG 1.00000000 0.500000000.50000000
BANTU 2IG 1.00000000 0.500000000.50000000
ss226145849pilot_1_YRI_low_coverage_panel 118AF 0.906779650.09322034
ss236223812pilot_1_CEU_low_coverage_panel 120AF 0.916666690.08333334
ss24056247AFD_EUR_PANELEuropean 48IG0.875000000.12500000 1.000000000.937500000.06250000
AFD_AFR_PANELAfrican American 46IG0.782608690.21739130 1.000000000.891304370.10869565
AFD_CHN_PANELAsian 48IG0.291666660.416666660.291666660.438578000.500000000.50000000
ss242724452pilot_1_CHB+JPT_low_coverage_panel 120AF 0.383333330.61666667
ss69132184HapMap-CEUEuropean 120IG0.816666660.18333334 0.751830000.908333360.09166667
HapMap-HCBAsian 90IG0.155555560.377777790.466666670.273322000.344444450.65555555
HapMap-JPTAsian 90IG0.177777780.511111140.311111121.000000000.433333340.56666666
HapMap-YRISub-Saharan African 120IG0.833333310.16666667 1.000000000.916666690.08333334

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.370+/-0.2190000ALFRED: 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
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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