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Reference SNP (refSNP) Cluster Report: rs3024505                 **Clinical Channel**
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:102/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS PheGenI
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (REV)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.0863/432 (1000 Genomes)
A=0.1054/13235 (TOPMED)
HGVS Names
  • CM000663.2:g.206766559G>A
  • NC_000001.10:g.206939904G>A
  • NC_000001.11:g.206766559G>A
  • NG_012088.1:g.10936C>T
  • NW_003871057.1:g.757413G>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' 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 ss276190027 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3024505 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
ss4250398PGA-UW-FHCRC|IL10-006976byFreqfwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc11/06/0104/07/04102Genomicunknown
ss7987594IIPGA-WEISS-MARTINEZ|IIPGA-IL10_8290byFreqfwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc04/10/0304/07/04114Genomicunknown
ss52087170PGA-UW-FHCRC|IL10_008290byFreqfwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc04/28/0603/31/08127Genomicunknown
ss66072349AFFY|SNP_A-1888978byFreqfwd/BC/Ttgagtaaacactagtcccctcacgctctgcct10/27/0603/31/08127Genomicunknown
ss66584331ILLUMINA|HumanHap300v1.1_rs3024505fwd/TC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc11/09/0611/09/06127Genomicunknown
ss67288635ILLUMINA|HumanHap550v1.1_rs3024505fwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc11/14/0611/14/06127Genomicunknown
ss67691865ILLUMINA|HumanHap650Yv1.0_rs3024505fwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc11/14/0611/14/06127Genomicunknown
ss70767207ILLUMINA|HumanHap550v3.0__rs3024505fwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc04/20/0703/30/08130Genomicunknown
ss71341981ILLUMINA|HumanHap650Yv3.0_rs3024505fwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc04/23/0704/23/07127Genomicunknown
ss74914623ILLUMINA|ILMN_Human_1M_rs3024505fwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc08/28/0708/29/07129Genomicunknown
ss76003700AFFY|AFFY_6_1M_SNP_A-1888978byFreqfwd/BC/Ttgagtaaacactagtcccctcacgctctgcct08/28/0703/07/10129Genomicunknown
ss79157294ILLUMINA|HumanHap300v2.0_rs3024505fwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc04/18/0711/18/07130Genomicunknown
ss84143961KRIBB_YJKIM|KHS644731fwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc12/04/0712/06/07130Genomicunknown
ss1088942021000GENOMES|CEU.trio.12.15.2008_234133_chr1_205006527rev/TA/Ggaccagggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttttttcc12/16/0812/16/08130Genomicunknown
ss122163994ILLUMINA|HumanCNV370v1_C_rs3024505fwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc04/14/0904/15/09131Genomicunknown
ss154252137ILLUMINA|Human610_Quadv1_B_rs3024505-128_B_F_1501750121fwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc06/18/0906/20/09131Genomicunknown
ss159429080ILLUMINA|Human660W-Quad_v1_A_rs3024505-128_B_F_1501750121fwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc07/06/0907/07/09131Genomicunknown
ss160607512ILLUMINA|HumanOmni1-Quad_v1-0_B_rs3024505-128_B_F_1501750121fwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc08/04/0910/04/09131Genomicunknown
ss170277447AFFY|GenomeWideSNP_5_SNP_A-1888978fwd/BC/Ttgagtaaacactagtcccctcacgctctgcct10/01/0910/02/09132Genomicunknown
ss171525306ILLUMINA|HumanCNV370-Quadv3_C_rs3024505-128_B_F_1501750121fwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc10/01/0910/04/09132Genomicunknown
ss173554345ILLUMINA|Human1M-Duov3_B_rs3024505-128_B_F_1501750121fwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc10/01/0910/04/09132Genomicunknown
ss2188451121000GENOMES|pilot_1_YRI_654795_chr1_205006527rev/A/Ggaccagggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttttttcc04/22/1004/22/10132Genomicunknown
ss2308733981000GENOMES|pilot_1_CEU_478027_chr1_205006527rev/A/Ggaccagggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttttttcc05/01/1005/01/10132Genomicunknown
ss2384914171000GENOMES|pilot_1_CHB+JPT_376494_chr1_205006527rev/A/Ggaccagggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttttttcc05/01/1005/01/10132Genomicunknown
ss253777542BL|SNP195919_1_205006527rev/TA/Ggaccagggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttttttcc08/18/1008/19/10134Genomicunknown
ss276190027GMI|GMI_AK_SNP_510194rev/A/Ggaccagggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttttttcc12/16/1012/16/10137Genomicunknown
ss284215973GMI|GMI_NA10851_SNP_228739rev/A/Ggaccagggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttttttcc12/17/1012/17/10138Genomicunknown
ss410927934ILLUMINA|Cardio-Metabo_Chip_11395247_A_rs3024505fwd/BC/Tggaaaaaaatgagctgagtaaacactagtcccctcacgctctgcctgggcagccctggtc06/07/1106/07/11135Genomicunknown
ss480743584ILLUMINA|HumanOmni2.5-4v1_B_rs3024505-128_B_F_1735648519rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt01/30/1210/28/16137Genomicunknown
ss480759416ILLUMINA|HumanOmniExpress-12v1_C_rs3024505-131_B_F_1853466096rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt01/30/1210/27/16137Genomicunknown
ss481644500ILLUMINA|HumanOmni1-Quad_v1-0_C_rs3024505-131_B_F_1853466096rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt01/30/1208/28/15146Genomicunknown
ss485166541ILLUMINA|HumanOmni2.5-4v1_D_rs3024505-131_B_F_1853466096rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt01/30/1210/27/16137Genomicunknown
ss491309617EXOME_CHIP|.GWAS._25844_chr_1_206939904rev/TA/Ggaccagggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttttttcc03/05/1203/05/12137Genomicunknown
ss537158291ILLUMINA|HumanOmni5-4v1_B_rs3024505-131_B_F_1908385947rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt06/22/1208/28/15146Genomicunknown
ss648651773SSMP|1_206939904rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt12/14/1202/10/15138Genomicunknown
ss778514899ILLUMINA|HumanOmni25Exome-8v1_A_rs3024505-131_B_F_1853466096rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt05/30/1307/09/15146Genomicunknown
ss780684149ILLUMINA|HumanOmni25Exome-8v1_A_exm-rs3024505-131_B_F_1990482203rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt05/30/1307/09/15146Genomicunknown
ss783029497ILLUMINA|HumanOmni2.5-4v1_H_rs3024505-131_B_F_1853466096rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt05/30/1307/28/15146Genomicunknown
ss783357580ILLUMINA|HumanOmniExpressExome-8v1_A_exm-rs3024505-131_B_F_1990482203rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt05/31/1306/18/15146Genomicunknown
ss783989239ILLUMINA|HumanOmniExpressExome-8v1_A_rs3024505-131_B_F_1908385947rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt05/31/1306/18/15146Genomicunknown
ss825487812ILLUMINA|HumanCNV370v1_C_rs3024505-114_B_F_IFB1151452839:0rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt06/24/1311/21/14144Genomicunknown
ss832287106ILLUMINA|HumanOmniExpress-12v1_H_rs3024505-131_B_F_1853466096rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt09/17/1306/18/15146Genomicunknown
ss833971206ILLUMINA|HumanOmni2.5-8v1_A_rs3024505-131_B_F_1853466096rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt09/18/1307/28/15146Genomicunknown
ss976069308EVA-GONL|EVA-GONL_rs3024505rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt04/23/1404/23/14142Genomicunknown
ss1068546048JMKIDD_LAB|HGDP_WGS_chr1_206939904rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt07/10/1407/10/14142Genomicunknown
ss12943702921000GENOMES|PHASE3_V1_5240759rev/A/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt08/16/1408/16/14142Genomicunknown
ss1397270039HAMMER_LAB|HAMMER_LAB_rs3024505rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt09/30/1409/30/14146Genomicunknown
ss1426090596DDI|DDI_rs3024505rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt11/04/1411/04/14144Genomicunknown
ss1574629470EVA_GENOME_DK|EVA_GENOME_DK_snv_rs3024505rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt02/19/1502/19/15144Genomicunknown
ss1585464325EVA_DECODE|EVA_DECODE_1_205006527_1335082_rs3024505rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt03/02/1503/02/15144Genomicunknown
ss1601987430EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_206939904_2871770rev/A/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt03/04/1503/04/15144Genomicunknown
ss1644981463EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_206939904_2871770rev/A/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt03/04/1503/04/15144Genomicunknown
ss1712399219EVA_SVP|EVA_SVP_93771rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt03/12/1503/12/15144Genomicunknown
ss1751894396ILLUMINA|OmniExpressExome-8v1-1_B_exm-rs3024505-131_B_F_1990482203rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt05/27/1506/09/15146Genomicunknown
ss1751894397ILLUMINA|OmniExpressExome-8v1-1_B_rs3024505-131_B_F_1908385947rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt05/27/1506/09/15146Genomicunknown
ss1917741436ILLUMINA|HumanExome-12v1-1_B_exm-rs3024505-131_B_F_1990482203rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt10/16/1510/16/15147Genomicunknown
ss1919296207WEILL_CORNELL_DGM|SNV:chr1:206939904rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt10/16/1510/16/15147Genomicunknown
ss1946021279ILLUMINA|HumanCoreExome-12v1-0_C_exm-rs3024505-131_B_F_1990482203rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt10/29/1510/29/15147Genomicunknown
ss1958351106ILLUMINA|exm-rs3024505-131_B_F_1990482203rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt11/13/1511/13/15147Genomicunknown
ss1966653844AMU|chr1_206939904rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt01/29/1601/29/16147Genomicunknown
ss1966955195GENOMED|rs3024505rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt02/16/1602/16/16149Genomicunknown
ss2020168963JJLAB|SNP671518rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt08/29/1608/30/16149Genomicunknown
ss2094856674ILLUMINA|Immuno_BeadChip_11419691_B_imm_1_205006527-1_B_R_1670133751rev/TA/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt09/27/1609/27/16150Genomicunknown
ss2169516168HUMAN_LONGEVITY|HLI-1-206766559-G-Arev/A/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt11/18/1611/18/16150Genomicunknown
ss2635006395ILLUMINA|Cancer_BeadChip_11459870_A_rs3024505-128_B_F_1735648519rev/A/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt02/02/1702/02/17151Genomicunknown
ss3023844418BIOINF_KMB_FNS_UNIBA|1.206766559G>Arev/A/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt07/05/1707/05/17151Genomicunknown
ss3101610265TOPMED|TOPMed_freeze_5?chr1:206,766,559rev/A/Ggggctgcccaggcagagcgtgaggggactagtgtttactcagctcatttt09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3024505|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 TTGGCCAGGC TGGTTAGGAA CTCCTGGCCT CAAGTGATCC GCCTGCCTCA GTCTCCCAAA
 TTGCTGGGAT TACAGGCGTG AGCCACCACA CCCGGCCAGG GGAAGTTTTT AGGGTGAATA
 CAAATTGCCT GGGTTATCCT GAGGATTAAG ATAATGAGCT AACAGGGCTT CTGGCACTAG
 GAGATGTTCG CAGTGCGTAT AGTTGGTTGT TATTGGTTAT CACAACCAAA AACTCCCGCC
 AAATCCTCTT TGAGCTGAGA TCAGAGGCAA CAGGGCTGGA CCCAACAGAG TTGAAAATAA
 GCAAATTAGC CCACTTGAGA GGATAGCCAA GGACATAAGC TGCTGCTCTT TCTGTCCCCT
 CTCTGAGCCA CCAGACAAAT GTGAGATTGG CTTCTGACTG CGGTCTGCTG GGAGGGGCAC
 GGTGGCTGGG GAAGCCCTAC TCAAAGCCCC GTGACTTAGA GGAGAGAGGA GGAAAAAAAT
 GAGCTGAGTA AACACTAGTC
 Y
 CCCTCACGCT CTGCCTGGGC AGCCCTGGTC TGGGGAAGGC TGGGAGCGGA CAGGCTGTGG
 TCAGTTTTTC AGTAAGACCT GACTCACTTC GGTTAAAGTA ACCATAGGAA GGAAGTGGGA
 AACATCAAAG CGAAAATTCT GAGATGAAAG GGTAGGAGTA AGAATGGAGG TTAGCAGAAG
 ATAAGGAGAG GGGGCCTGAA GCTCTCTACT CTGAGGCTGT CCATCCTGAA CTGAAGAAGA
 CATCCTGAGT CTGTGAAAGG AAAATCTTGG GGCCTCAAAA TCACCAAGCT AAAGGGAAAA
 GTCAAGCTGG GAACTACTCA GGGCAAACCT GCCTCCCATT CTATTCAAAG TCATCCCTCT
 GTTCACTGAG ATAGATGCAT ATCTGATAGC CTCCTTTGGA AAAGAATCAG AAACTCAAAA
 GAATGCAACC ATTTGTCTCT TACCTACCTG TGACCTGGAA GCCCCTTCCC TGCTTTGAGT
 TGTCCCCATC TTTCTGGATG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_021877.12
dbSNP Blast Analysis
OMIM
612381
222100

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs3024505 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1294370292EAS 1008AF 0.972199980.02780000
EUR 1006AF 0.832000020.16800000
AFR 1322AF 0.968200030.03180000
AMR 694AF 0.917899970.08210000
SAS 978AF 0.860899980.13910000
ss218845112pilot_1_YRI_low_coverage_panel 118AF 0.974576290.02542373
ss230873398pilot_1_CEU_low_coverage_panel 120AF 0.808333340.19166666
ss238491417pilot_1_CHB+JPT_low_coverage_panel 120AF 0.983333350.01666667
ss4250398PGA-AFRICAN-PANELAfrican American 46AF 0.913042960.08695700
PGA-EUROPEAN-PANELEuropean 44AF 0.772727010.22727300
HapMap-CEUEuropean 226IG0.654867230.327433620.017699110.294266000.818584080.18141593
HapMap-HCBAsian 84IG0.976190450.02380952 1.000000000.988095220.01190476
HapMap-JPTAsian 170IG0.988235290.01176471 1.000000000.994117620.00588235
HapMap-YRISub-Saharan African 222IG0.964028780.03597122 1.000000000.981981990.01801802
HAPMAP-ASW 96IG0.962264180.03773585 1.000000000.979166690.02083333
HAPMAP-CHBAsian 82IG0.975609780.02439024 1.000000000.987804890.01219512
HAPMAP-CHD 168IG0.940476180.05952381 1.000000000.970238090.02976190
HAPMAP-GIH 174IG0.643678190.333333340.022988510.438578000.810344820.18965517
HAPMAP-LWK 172IG0.895348850.093023260.011627910.200325000.941860440.05813954
HAPMAP-MEX 98IG0.893333320.10666667 1.000000000.948979620.05102041
HAPMAP-MKK 274IG0.963503660.021897810.014598540.001000000.974452560.02554744
HAPMAP-TSI 172IG0.662790720.290697660.046511630.583882000.808139560.19186047
ENSEMBL_Venter 2IG1.00000000 1.00000000
Control 432IG0.777777790.212962970.009259260.583882000.884259280.11574074
ss52087170HSP_GENO_PANEL 120IG0.866666670.13333334 1.000000000.933333340.06666667
YRI_GENO_PANELSub-Saharan African 120IG0.966666640.03333334 1.000000000.983333350.01666667
AAM_GENO_PANELAfrican American 122IG0.901639340.09836066 1.000000000.950819670.04918033
CEU_GENO_PANELEuropean 120IG0.666666690.316666660.016666670.479500000.824999990.17500000
CHB_GENO_PANELAsian 88IG0.977272750.02272727 1.000000000.988636370.01136364
JPT_GENO_PANELAsian 90IG0.977777780.02222222 1.000000000.988888860.01111111
ss66072349HapMap-CEUEuropean 118IG0.661016940.322033910.016949150.479500000.822033880.17796610
HapMap-HCBAsian 90IG0.977777780.02222222 1.000000000.988888860.01111111
HapMap-JPTAsian 90IG0.977777780.02222222 1.000000000.988888860.01111111
HapMap-YRISub-Saharan African 120IG0.966666640.03333334 1.000000000.983333350.01666667
ss76003700ICMHP 10IG0.600000020.200000000.20000000 0.699999990.30000001
ss7987594D-0African American 46IG0.826086940.17391305 1.000000000.913043500.08695652
E-0European 40IG0.600000020.40000001 0.527089000.800000010.20000000
E-1European 6IG0.333333340.66666669 0.666666690.33333334

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.158+/-0.2320000ALFRED: 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
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNYES

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