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Reference SNP (refSNP) Cluster Report: rs1800592                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:89/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (REV)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.4683/2345 (1000 Genomes)
C=0.4134/51914 (TOPMED)
HGVS Names
  • CM000666.2:g.140572807T>C
  • NC_000004.11:g.141493961T>C
  • NC_000004.12:g.140572807T>C
  • NG_012139.1:g.999A>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 ss277963866 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1800592 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
ss2420701HGBASE|SNP000003489fwd/TA/Gatttctgattgaccacagtttgatcagtgcatttgttaatgtgttctaca11/07/0010/10/0389Genomicunknown
ss11642597WI_SSAHASNP|chr4.NT_016606.15_3013626rev/BC/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg07/03/0310/10/03116Genomicunknown
ss24222120PERLEGEN|afd4261365byFreqrev/BC/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg08/10/0409/13/04123Genomicunknown
ss78168503HGSV|Cor12878_SNV_20070510.chr4_141851566rev/BC/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg10/17/0710/18/07129Genomicunknown
ss78774410HGSV|Cor18507_SNV_20070510.chr4_141851566rev/BC/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg10/19/0710/20/07129Genomicunknown
ss84878234HGSV|Cor18517_SNV_20070510.chr4_141851566rev/BC/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg12/06/0712/08/07130Genomicunknown
ss105869396BGI|BGI_rs1800592rev/BC/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg09/12/0806/18/09130Genomicunknown
ss1084029201000GENOMES|CEU.trio.12.15.2008_1102117_chr4_141713411rev/BC/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg12/15/0812/15/08130Genomicunknown
ss1107028701000GENOMES|NA19240_2008_12_16_993592_chr4_141713411rev/BC/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg12/17/0812/17/08130Genomicunknown
ss117214935ILLUMINA-UK|NA18507_000189637_NCBI36.1_chr4_141713411byFreqrev/BC/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg01/18/0909/05/14130Genomic99 %
ss157988442GMI|GMI_SNP_74834252rev/BC/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg06/24/0906/25/09131Genomicunknown
ss164548262COMPLETE_GENOMICS|NA19240_36_chr4_141713411rev/BC/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg09/29/0909/29/09132Genomicunknown
ss199267247BUSHMAN|BUSHMAN-chr4-141713410rev/BC/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg02/16/1003/06/10132Genomicunknown
ss2212541571000GENOMES|pilot_1_YRI_3063840_chr4_141713411rev/C/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg04/22/1004/22/10132Genomicunknown
ss2326301761000GENOMES|pilot_1_CEU_2234805_chr4_141713411rev/C/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg05/01/1005/01/10132Genomicunknown
ss2398706141000GENOMES|pilot_1_CHB+JPT_1755691_chr4_141713411rev/C/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg05/01/1005/01/10132Genomicunknown
ss277963866GMI|GMI_AK_SNP_2284099rev/C/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg12/16/1012/16/10137Genomicunknown
ss285020096GMI|GMI_NA10851_SNP_1032869rev/C/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg12/17/1012/17/10138Genomicunknown
ss293203208PJP|SNP_2709566_chr4_141713411rev/C/Tgaaaatgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaatcgctg01/21/1101/21/11134Genomicunknown
ss479574564ILLUMINA|HumanOmni2.5-4v1_D_kgp11133384-0_T_R_1811698403rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat01/30/1210/28/16137Genomicunknown
ss484710676ILLUMINA|HumanOmni2.5-4v1_B_SNP4-141713411-0_T_R_1632829687rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat01/30/1210/28/16137Genomicunknown
ss533101895ILLUMINA|HumanOmni5-4v1_B_kgp11133384-0_T_R_1811698403rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat06/22/1208/28/15146Genomicunknown
ss557902916TISHKOFF|snp_chr4_141493961rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat11/22/1211/23/12138Genomicunknown
ss651721107SSMP|4_141493961rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat12/14/1202/10/15138Genomicunknown
ss779612122ILLUMINA|HumanOmni25Exome-8v1_A_kgp11133384-0_T_R_1811698403rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat05/30/1307/09/15146Genomicunknown
ss781015451ILLUMINA|HumanOmni2.5-4v1_H_kgp11133384-0_T_R_1811698403rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat05/30/1307/28/15146Genomicunknown
ss835084348ILLUMINA|HumanOmni2.5-8v1_A_kgp11133384-0_T_R_1811698403rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat09/18/1307/28/15146Genomicunknown
ss980760451EVA-GONL|EVA-GONL_rs1800592rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat04/23/1404/24/14142Genomicunknown
ss1072019667JMKIDD_LAB|HGDP_WGS_chr4_141493961rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat07/10/1407/11/14142Genomicunknown
ss13121188761000GENOMES|PHASE3_V1_23728128rev/C/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat08/16/1408/16/14142Genomicunknown
ss1430074479DDI|DDI_rs1800592rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat11/04/1411/05/14144Genomicunknown
ss1580810136EVA_GENOME_DK|EVA_GENOME_DK_snv_rs1800592rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat02/19/1502/20/15144Genomicunknown
ss1590272571EVA_DECODE|EVA_DECODE_4_141713411_1116811_rs1800592rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat03/02/1503/03/15144Genomicunknown
ss1611332165EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_4_141493961_13127945rev/C/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat03/04/1503/04/15144Genomicunknown
ss1654326198EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_4_141493961_13127945rev/C/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat03/04/1503/04/15144Genomicunknown
ss1802306438HAMMER_LAB|Hsieh_2513319rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat07/15/1507/15/15146Genomicunknown
ss1924001504WEILL_CORNELL_DGM|SNV:chr4:141493961rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat10/16/1510/17/15147Genomicunknown
ss1958725456ILLUMINA|4:141493961-T-C-0_T_R_2304235668rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat11/13/1511/13/15147Genomicunknown
ss1969889942GENOMED|rs1800592rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat02/16/1602/16/16147Genomicunknown
ss2022588169JJLAB|SNP3090724rev/BC/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat08/29/1608/30/16149Genomicunknown
ss2150719785USC_VALOUEV|NC_000004.11:g.141493961T>Crev/C/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat11/17/1611/17/16150Genomicunknown
ss2267774235HUMAN_LONGEVITY|HLI-4-140572807-T-Crev/C/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat11/18/1611/18/16150Genomicunknown
ss2435672433TOPMED|4_141493961_T/Crev/C/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat11/20/1611/20/16150Genomicunknown
ss2625790657SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV1970126rev/C/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat01/06/1701/06/17151Genomicunknown
ss2634186480ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp11133384-0_T_R_18116984rev/C/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat02/02/1702/02/17151Genomicunknown
ss2706211264GRF|rs1800592rev/C/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat02/13/1702/13/17151Genomicunknown
ss2816129217GNOMAD|rs1800592rev/C/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat05/18/1705/18/17151Genomicunknown
ss2995681078SWEGEN|NC_000004.11:g.141493961T>Crev/C/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat05/30/1705/30/17151Genomicunknown
ss3022421146ILLUMINA|MEGA_Consortium_v2_15070954_A2_4:141493961-T-C-0_T_R_2304235668rev/C/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat06/28/1706/28/17151Genomicunknown
ss3025071376BIOINF_KMB_FNS_UNIBA|4.140572807T>Crev/C/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat07/05/1707/05/17151Genomicunknown
ss3345998958CSHL|rs1800592rev/C/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat10/02/1710/02/17151Genomicunknown
ss3444767147TOPMED|TOPMed_freeze_5?chr4:140,572,807rev/C/Ttgtagaacacattaacaaatgcactgatcaaactgtggtcaatcagaaat10/04/1710/04/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1800592|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 AAAATAGACT TTCTCTTGGC TCAGTGTATA CTGCCAAATT GTTTTCCAAA AAAATTGTGT
 CAATGTATAA CACCATCACT AATATAGTAT TGATATTATG GTTATTACAT TTTAAAATTC
 ATAATTTGTA ATTATAACAT TCATAATTTA TTACTATTTA TAATATTAAT GTAAATGTAT
 ATTATATATA AATGTTATAG TAATTATAAC TTTGGTAGTG ACAAAGTATT AATTTATTAG
 GTGAAGTATA TGCTTTTTTA TTAGTGATAA TAAATATATC CTCTCTCCCA TTATAAAAGT
 TTGTATTTCT TCTTTTAGAA ATTGATTCTT CTGTCATTTG CACATTTATC TGTATAATTA
 TAACAGGGTA TTTCCCAGTG GTGGCTAATG AGAGAATTAT GGGAAAGTAT AGAACACTAT
 TCAAATGCAA AGCACTGTAT GATTTTTATT TAATAGGAAG ACATTTTGTG CAGCGATTTC
 TGATTGACCA CAGTTTGATC
 R
 AGTGCATTTG TTAATGTGTT CTACATTTTC AAAAAGGAAA GGAGAATTTG TTACATTCAG
 AACTTGCTGC CACTCCTTTG CTACGTCATA AAGGGTCAGT TGCCCTTGCT CATACTGACC
 TATTCTTTAC CTCTCTGCTT CTTCTTTGTG CCAGAAGAGT AGAAATCTGA CCCTTTGGGG
 ATACCACCCT CTCCCCTACT GCTCTCTCCA ACCTGAGGCA AACTTTCTCC TACTTCCCAG
 AGCCTGTCAG AAGTGGTGAA GCCAGCCTGC TCCTTGGAAT CCAGAACTAC TTTCAGAATC
 TTGAACTTCT GTGACCTCTC AGGGTCCCCT TGTGTGAAGT TTTTGACGTC AGCTTCTCCT
 GTGACCCTTA GAAGTCACTC TTGTGTCTAG CACATCCCAG GTGCTCAGTC ACCATTGAAC
 TACAGTCATA CTATCTCCTG GCAAAGGCTC TTAACTGTCC ATGTTAGCCT GATATTAATA
 TCCTGGAAGC TTATACTGTC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
U28479
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs1800592 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss117214935ENSEMBL_Watson 2IG1.00000000 1.00000000
YRI 2IG 1.00000000 1.00000000
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss1312118876EAS 1008AF 0.534699980.46529999
EUR 1006AF 0.763400020.23660001
AFR 1322AF 0.265500010.73449999
AMR 694AF 0.593699990.40630001
SAS 978AF 0.606300060.39370000
ss164548262YRISub-Saharan African 2IG 1.00000000 0.500000000.50000000
ss221254157pilot_1_YRI_low_coverage_panel 118AF 0.211864410.78813559
ss232630176pilot_1_CEU_low_coverage_panel 120AF 0.725000020.27500001
ss239870614pilot_1_CHB+JPT_low_coverage_panel 120AF 0.550000010.44999999
ss24222120AFD_EUR_PANELEuropean 48IG0.583333310.333333340.083333340.654721000.750000000.25000000
AFD_AFR_PANELAfrican American 46IG0.086956520.521739130.391304340.479500000.347826090.65217394
AFD_CHN_PANELAsian 48IG0.208333330.541666690.250000000.751830000.479166660.52083331

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.498+/-0.0320000

  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:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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