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Reference SNP (refSNP) Cluster Report: rs10799824                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.1695/849 (1000 Genomes)
A=0.1815/22788 (TOPMED)
HGVS Names
  • CM000663.2:g.19514680G>A
  • NC_000001.10:g.19841174G>A
  • NC_000001.11:g.19514680G>A
  • XR_001737920.1:n.144-3441G>A
  • XR_947017.2:n.1179-2102C>T
  • XR_947019.1:n.188+1684G>A
  • XR_947020.2:n.144-3441G>A
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 ss275742309 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10799824 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
ss18189274SC_SNP|SC-CHR1_NA17109-200402.chr1.NT_004610.16_644424byFreqfwd/TA/Gcactgattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaacaagc02/20/0410/26/06120Genomicunknown
ss18281062SC_SNP|SC-CHR1_NA07340-200402.chr1.NT_004610.16_644424fwd/TA/Gcactgattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaacaagc02/20/0403/04/04120Genomicunknown
ss19135889CSHL-HAPMAP|CSHL-HuDD-200402.chr1.NT_004610.16_644424fwd/TA/Gcactgattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaacaagc02/20/0403/04/04120Genomicunknown
ss75077711ILLUMINA|ILMN_Human_1M_rs10799824fwd/TA/Gcactgattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaacaagc08/28/0708/29/07129Genomicunknown
ss77415593HGSV|Cor12156_SNV_20070510.chr1_19586480fwd/TA/Gcactgattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaacaagc10/09/0710/12/07129Genomicunknown
ss119639244KRIBB_YJKIM|KHS1790550fwd/TA/Gcactgattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaacaagc02/04/0902/05/09131Genomicunknown
ss154727610GMI|GMI_SNP_36623104fwd/TA/Gcactgattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaacaagc06/24/0906/24/09131Genomicunknown
ss159922549ILLUMINA|HumanOmni1-Quad_v1-0_B_rs10799824-128_T_F_1514021920fwd/TA/Gcactgattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaacaagc08/04/0910/01/09131Genomicunknown
ss170549372ILLUMINA|Human1M-Duov3_B_rs10799824-128_T_F_1514021920fwd/TA/Gcactgattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaacaagc10/01/0910/01/09132Genomicunknown
ss198122809BUSHMAN|BUSHMAN-chr1-19713760fwd/TA/Gcactgattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaacaagc02/16/1003/05/10132Genomicunknown
ss2182691921000GENOMES|pilot_1_YRI_78875_chr1_19713761fwd/A/Gcactgattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaacaagc04/22/1004/22/10132Genomicunknown
ss2304512901000GENOMES|pilot_1_CEU_55919_chr1_19713761fwd/A/Gcactgattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaacaagc05/01/1005/01/10132Genomicunknown
ss2381618281000GENOMES|pilot_1_CHB+JPT_46905_chr1_19713761fwd/A/Gcactgattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaacaagc05/01/1005/01/10132Genomicunknown
ss252962356BL|SNP25056_1_19713761fwd/TA/Gcactgattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaacaagc08/18/1008/18/10134Genomicunknown
ss275742309GMI|GMI_AK_SNP_62472fwd/A/Gcactgattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaacaagc12/16/1012/16/10137Genomicunknown
ss290706298PJP|SNP_212656_chr1_19713761fwd/A/Gcactgattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaacaagc01/21/1101/21/11134Genomicunknown
ss479354420ILLUMINA|HumanOmni2.5-4v1_B_rs10799824-128_T_F_1765265344fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa01/30/1210/28/16137Genomicunknown
ss479357363ILLUMINA|HumanOmniExpress-12v1_C_rs10799824-131_T_F_1857149281fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa01/30/1210/27/16137Genomicunknown
ss479756143ILLUMINA|HumanOmni1-Quad_v1-0_C_rs10799824-131_T_F_1865235859fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa01/30/1208/28/15146Genomicunknown
ss484477358ILLUMINA|HumanOmni2.5-4v1_D_rs10799824-131_T_F_1857149281fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa01/30/1210/27/16137Genomicunknown
ss536636157ILLUMINA|HumanOmni5-4v1_B_rs10799824-131_T_F_1891352230fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa06/22/1208/28/15146Genomicunknown
ss553861135TISHKOFF|snp_chr1_19841174fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa11/22/1211/22/12138Genomicunknown
ss647621716SSMP|1_19841174fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa12/14/1202/09/15138Genomicunknown
ss778365300ILLUMINA|HumanOmni25Exome-8v1_A_rs10799824-131_T_F_1865235859fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa05/30/1307/09/15146Genomicunknown
ss782685212ILLUMINA|HumanOmni2.5-4v1_H_rs10799824-131_T_F_1857149281fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa05/30/1307/28/15146Genomicunknown
ss783653592ILLUMINA|HumanOmniExpressExome-8v1_A_rs10799824-131_T_F_1891352230fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa05/31/1306/18/15146Genomicunknown
ss831936063ILLUMINA|HumanOmniExpress-12v1_H_rs10799824-131_T_F_1857149281fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa09/17/1306/18/15146Genomicunknown
ss833820126ILLUMINA|HumanOmni2.5-8v1_A_rs10799824-131_T_F_1865235859fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa09/18/1307/28/15146Genomicunknown
ss974917970EVA-GONL|EVA-GONL_rs10799824fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa04/23/1404/23/14142Genomicunknown
ss1067714829JMKIDD_LAB|HGDP_WGS_chr1_19841174fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa07/10/1407/10/14142Genomicunknown
ss12899265821000GENOMES|PHASE3_V1_614259fwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa08/16/1408/16/14142Genomicunknown
ss1425736023DDI|DDI_rs10799824fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa11/04/1411/04/14144Genomicunknown
ss1573923830EVA_GENOME_DK|EVA_GENOME_DK_snv_rs10799824fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa02/19/1502/19/15144Genomicunknown
ss1584275605EVA_DECODE|EVA_DECODE_1_19713761_146341_rs10799824fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa03/02/1503/02/15144Genomicunknown
ss1599669424EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_19841174_320132fwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa03/04/1503/04/15144Genomicunknown
ss1642663457EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_19841174_320132fwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa03/04/1503/04/15144Genomicunknown
ss1712315815EVA_SVP|EVA_SVP_10367fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa03/12/1503/12/15144Genomicunknown
ss1751890193ILLUMINA|OmniExpressExome-8v1-1_B_rs10799824-131_T_F_1891352230fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa05/27/1506/09/15146Genomicunknown
ss1918129281WEILL_CORNELL_DGM|SNV:chr1:19841174fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa10/16/1510/16/15147Genomicunknown
ss1945986979ILLUMINA|HumanCoreExome-12v1-0_C_rs10799824-131_T_F_1891352230fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa10/29/1510/29/15147Genomicunknown
ss1958249541ILLUMINA|rs10799824-131_T_F_1891352230fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa11/13/1511/13/15147Genomicunknown
ss1966699001GENOMED|rs10799824fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa02/16/1602/16/16147Genomicunknown
ss2019576258JJLAB|SNP78813fwd/TA/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa08/29/1608/30/16149Genomicunknown
ss2147579534USC_VALOUEV|NC_000001.10:g.19841174G>Afwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa11/17/1611/17/16150Genomicunknown
ss2160500756HUMAN_LONGEVITY|HLI-1-19514680-G-Afwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa11/18/1611/18/16150Genomicunknown
ss2322683360TOPMED|1_19841174_G/Afwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa11/19/1611/19/16150Genomicunknown
ss2624304388SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV48832fwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa01/06/1701/06/17151Genomicunknown
ss2632486055ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs10799824-131_T_F_1891352fwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa02/02/1702/02/17151Genomicunknown
ss2697483891GRF|rs10799824fwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa02/13/1702/13/17151Genomicunknown
ss2710667238ILLUMINA|Consortium-OncoArray_15047405_A_rs10799824-131_T_F_1891352230fwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa03/22/1703/22/17151Genomicunknown
ss2752353062GNOMAD|rs10799824fwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa05/17/1705/17/17151Genomicunknown
ss2985500380AFFY|Axiom_Smokesc1_Affx-6494721fwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa05/24/1705/24/17151Genomicunknown
ss2986420015SWEGEN|NC_000001.10:g.19841174G>Afwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa05/30/1705/30/17151Genomicunknown
ss3021062877ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs10799824-138_T_F_2264352721fwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa06/28/1706/28/17151Genomicunknown
ss3023553093BIOINF_KMB_FNS_UNIBA|1.19514680G>Afwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa07/05/1707/05/17151Genomicunknown
ss3070210335TOPMED|TOPMed_freeze_5?chr1:19,514,680fwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa09/28/1709/28/17151Genomicunknown
ss3343353800CSHL|rs10799824fwd/A/Gattccttgacaagtttccaaaagtggaacagagcaactgtttggtttgaa10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs10799824|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 CTGGAGTGCA GTGACACGAT TTTGGCTCAC TGCAACCTCT GTCTCCTGGG TTCAAGCAAT
 TCTCTGCCTC AGTCTCCTGA GGAGCTGGTA TTACAGGCGC CCACCCCCAC GCCCGGCTAA
 TTTTTGTATT TTTGGTAGAG ACTGGGTTTC ATCATCTTGG CCAGGCTGGT CTTGAACTCC
 GGACCTCATG ATTCATCCGC CTTGGCCTTC CAAAGTGCTG GGATTACAGG TGTGAGCCAC
 TGTGCCCAGC CTGGGAATTC TAAAAAAGGA CTTAGTCTCC GTTGTCTAGG CTGGGCACTG
 GACAGTTGAC CAGAGGCTCA ACCGGATGCC TTCGAGAGGG CCCTGGAGAA CTGAGAGGTC
 TGCGGTTCAA TGGTCAGGGG AGAAGGAGGA ATGTTCCCGG GCCTTGGTTT CTCCTTGGAT
 TGAATTCAGT CTACACAAGG GCCTCTTGGG GCCCGAGTTG TCTAAGTAAA CACTGATTCC
 TTGACAAGTT TCCAAAAGTG
 R
 GAACAGAGCA ACTGTTTGGT TTGAACAAGC TGTGCTCTGT AAACCACCAC TTGCATATGA
 CCAGGGCCCC GTGTAAATAT TTTAGCTACA GATGGAAAGA ACATAACTTT TTTTGAAATC
 CCATCACTTC ACTGCTAGAC TTATAATGAA TTATGTGTTG TCTCTATTTG CTGTTAGACT
 TAAAATGAAT TATGTGTTAT TTCTATTTGT TGGGAGGTCC AGTTCTCTAA TTTAATTGTA
 GGCTGCTTAG ATGTGCCTCT ACTGAGACTG CTAGGGTTTG GGGAAAGCAC AGTAAAGAAC
 ATGCCACTTT TGGCCGGGCG CAGTGGCTCA CGCCTGTAAT CCCAGCACTT TGGGAGGCCA
 AGGCGGGCAG ATCACCTGAG GTCAGGAGTT CGAGACCAGC CTGGCCAACA TGGTGAAACC
 CTGTCTCTAT TAAAAAATAC AAAAATTAGC TGGGCGTGGT GGCAGGCGCC TTAATCCCAG
 CTACTTGGGA GGCAGAGGCA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_004610
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
ss1289926582EAS 1008AF 0.127000000.87300003
EUR 1006AF 0.142100010.85790002
AFR 1322AF 0.255699990.74430001
AMR 694AF 0.194500000.80550003
SAS 978AF 0.107400000.89260006
ss18189274HapMap-CEUEuropean 226IG0.026548670.318584080.654867230.583882000.185840710.81415927
HapMap-HCBAsian 86IG0.023255810.209302320.767441870.751830000.127906980.87209302
HapMap-JPTAsian 172IG0.011627910.209302320.779069781.000000000.116279070.88372093
HapMap-YRISub-Saharan African 226IG0.061946900.371681420.566371681.000000000.247787610.75221241
HAPMAP-ASW 98IG0.061224490.387755100.551020381.000000000.255102040.74489796
HAPMAP-CHBAsian 82IG0.024390240.243902440.731707331.000000000.146341460.85365856
HAPMAP-CHD 170IG0.011764710.141176480.847058830.583882000.082352940.91764706
HAPMAP-GIH 176IG0.011363640.159090910.829545440.751830000.090909090.90909094
HAPMAP-LWK 180IG0.088888890.455555560.455555560.654721000.316666660.68333334
HAPMAP-MEX 100IG0.040000000.180000010.779999970.150222000.130000000.87000000
HAPMAP-MKK 286IG0.160839160.412587400.426573430.200325000.367132870.63286716
HAPMAP-TSI 176IG0.056818180.215909090.727272750.050043000.164772730.83522725
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss198122809BANTU 2IG 1.00000000 0.500000000.50000000
ss218269192pilot_1_YRI_low_coverage_panel 118AF 0.288135590.71186441
ss230451290pilot_1_CEU_low_coverage_panel 120AF 0.183333340.81666666
ss238161828pilot_1_CHB+JPT_low_coverage_panel 120AF 0.150000010.85000002

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.282+/-0.2480000

  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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