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Reference SNP (refSNP) Cluster Report: rs1800562                 ** With Pathogenic allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:89/147
Map to Genome Build:107/Weight 1
Validation Status:byClusterbyFreqwithHapMapFreqWith1000GenomeData
Citation:PubMed
Association:NHGRI GWAS PheGenI
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:A:germline
G:germline
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With Pathogenic allele [ClinVar]
MAF/MinorAlleleCount:A=0.0324/3937 (ExAC)
A=0.0126/63 (1000 Genomes)
A=0.0475/618 (GO-ESP)
HGVS Names
  • NC_000006.11:g.26093141G>A
  • NC_000006.12:g.26092913G>A
  • NG_008720.2:g.10633G>A
  • NM_000410.3:c.845G>A
  • NM_001300749.1:c.845G>A
  • NM_139003.2:c.527G>A
  • NM_139004.2:c.569G>A
  • NM_139006.2:c.803G>A
  • NM_139007.2:c.581G>A
  • NM_139008.2:c.539G>A
  • NM_139009.2:c.776G>A
  • NM_139010.2:c.305G>A
  • NM_139011.2:c.77-206G>A
  • NP_000401.1:p.Cys282Tyr
  • NP_001287678.1:p.Cys282Tyr
  • NP_620572.1:p.Cys176Tyr
  • NP_620573.1:p.Cys190Tyr
  • NP_620575.1:p.Cys268Tyr
  • NP_620576.1:p.Cys194Tyr
  • NP_620577.1:p.Cys180Tyr
  • NP_620578.1:p.Cys259Tyr
  • NP_620579.1:p.Cys102Tyr
  • XM_005249040.1:c.836G>A
  • XM_011514543.1:c.845G>A
  • XM_011514544.1:c.836G>A
  • XP_005249097.1:p.Cys279Tyr
  • XP_011512845.1:p.Cys282Tyr
  • XP_011512846.1:p.Cys279Tyr
  • XR_241893.1:n.967G>A
  • XR_241893.2:n.967G>A
  • XR_241894.1:n.892G>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 ss95209990 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1800562 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
ss2420669HGBASE|SNP000003443fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat11/07/0010/10/0389Genomicunknown
ss5586582SNP500CANCER|HFE-02byFreqfwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc09/26/0204/07/04113Genomicunknown
ss24365242PERLEGEN|afd4061885byFreqfwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc08/10/0409/13/04123Genomicunknown
ss65843448KRIBB_YJKIM|KHS19242fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc10/17/0611/15/06127Genomicunknown
ss66077890AFFY|SNP_A-1905121byFreqrev/BC/Ttgggtgctccacctggacgtatatctctgctc10/27/0608/14/07127Genomicunknown
ss66577872ILLUMINA|HumanHap300v1.1_rs1800562fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc11/09/0611/09/06127Genomicunknown
ss67197007ILLUMINA|HumanHap550v1.1_rs1800562fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc11/14/0611/14/06127Genomicunknown
ss67585966ILLUMINA|HumanHap650Yv1.0_rs1800562fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc11/14/0611/14/06127Genomicunknown
ss68969475PERLEGEN|PGP04061885byFreqfwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc01/30/0708/14/07127Genomicunknown
ss70675219ILLUMINA|HumanHap550v3.0__rs1800562fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc04/20/0703/30/08130Genomicunknown
ss71238231ILLUMINA|HumanHap650Yv3.0_rs1800562fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc04/23/0704/23/07127Genomicunknown
ss74935970ILLUMINA|ILMN_Human_1M_rs1800562fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc08/28/0708/29/07129Genomicunknown
ss76015380AFFY|AFFY_6_1M_SNP_A-1905121rev/BC/Ttgggtgctccacctggacgtatatctctgctc08/28/0708/29/07129Genomicunknown
ss79094227ILLUMINA|HumanHap300v2.0_rs1800562fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc04/18/0711/18/07130Genomicunknown
ss83877451KRIBB_YJKIM|KHS563046fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc12/04/0712/06/07130Genomicunknown
ss95209990EGP_SNPS|HFE-007633byFreqfwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc03/12/0803/07/10129Genomicunknown
ss121814162ILLUMINA|HumanCNV370v1_C_rs1800562fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc04/14/0904/14/09131Genomicunknown
ss153736398ILLUMINA|Human610_Quadv1_B_rs1800562-128_T_F_1501686021fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc06/18/0906/19/09131Genomicunknown
ss159329747ILLUMINA|Human660W-Quad_v1_A_rs1800562-128_T_F_1501686021fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc07/06/0907/07/09131Genomicunknown
ss159711412SEATTLESEQ|HFE-26201120fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc07/10/0907/10/09131Genomicunknown
ss170436801AFFY|GenomeWideSNP_5_SNP_A-1905121rev/BC/Ttgggtgctccacctggacgtatatctctgctc10/01/0910/02/09132Genomicunknown
ss170815449ILLUMINA|HumanCNV370-Quadv3_C_rs1800562-128_T_F_1501686021fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc10/01/0910/03/09132Genomicunknown
ss172924829ILLUMINA|Human1M-Duov3_B_rs1800562-128_T_F_1501686021fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc10/01/0910/02/09132Genomicunknown
ss209087069ILLUMINA|ALS_iSelect_272541_A_rs1800562-127_T_F_IFB1223202273fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc03/24/1003/24/10132Genomicunknown
ss2333707591000GENOMES|pilot_1_CEU_2975388_chr6_26201120fwd/A/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc05/01/1005/01/10132Genomicunknown
ss244285028ILLUMINA|CVDSNP55v1_A_rs1800562fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc06/10/1006/10/10132Genomicunknown
ss244317425OMICIA|2010_April_001_072_HFE_235200_0001fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc06/16/1006/16/10132Genomicunknown
ss288288919OMIM-CURATED-RECORDS|6333fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc12/21/1012/21/10133Genomicunknown
ss342203133NHLBI-ESP|ESP2500-chr6-26093141byFreqfwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc03/25/1109/05/14134Genomicunknown
ss410868036ILLUMINA|Cardio-Metabo_Chip_11395247_A_chr6_26201120fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc06/07/1106/07/11135Genomicunknown
ss410916049ILLUMINA|Cardio-Metabo_Chip_11395247_A_rs1800562fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc06/07/1106/07/11135Genomicunknown
ss469996319PAGE_STUDY|PAGE_CALiCo_Y2_rs1800562fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat10/04/1110/04/11137Genomicunknown
ss483420740ILLUMINA|HumanOmni2.5-4v1_D_kgp4787068-0_T_F_1805808302fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc01/30/1202/02/12137Genomicunknown
ss485221593ILLUMINA|HumanOmni2.5-4v1_B_SNP6-26201120-0_T_F_1613642169fwd/TA/Gtaccccctggggaagagcagagatatacgtcnnnnnggagcacccaggcctggatcagcc01/30/1202/04/12137Genomicunknown
ss4909210291000GENOMES|20110521_exome_428827_chr6_26093141fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc02/10/1202/21/12137Genomicunknown
ss491378673EXOME_CHIP|nonsyn_94899_chr_6_26093141fwd/TA/Gtaccccctggggaagagcagagatatacgtccaggtggagcacccaggcctggatcagcc03/05/1203/05/12137Genomicunknown
ss491881988CLINSEQ_SNP|SNV-chr6-26201120byFreqfwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat03/06/1209/05/14137Genomicunknown
ss535631718ILLUMINA|HumanOmni5-4v1_B__kgp4787068-0_T_F_1805808302fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat06/22/1208/29/15146Genomicunknown
ss778678728ILLUMINA|HumanOmni25Exome-8v1_A_kgp4787068-0_T_F_1805808302fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat05/30/1307/09/15146Genomicunknown
ss780846250ILLUMINA|HumanOmni25Exome-8v1_A_exm521729-0_T_F_1921904613fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat05/30/1307/09/15146Genomicunknown
ss782153615ILLUMINA|HumanOmni2.5-4v1_H_kgp4787068-0_T_F_1805808302fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat05/30/1307/28/15146Genomicunknown
ss783529810ILLUMINA|HumanOmniExpressExome-8v1_A_exm521729-0_T_F_1921904613fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat05/31/1306/19/15146Genomicunknown
ss825424745ILLUMINA|HumanCNV370v1_C_rs1800562-123_T_F_IFB1151450742:0fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat06/24/1311/21/14144Genomicunknown
ss834137257ILLUMINA|HumanOmni2.5-8v1_A_kgp4787068-0_T_F_1805808302fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat09/18/1307/28/15146Genomicunknown
ss974459122JMKIDD_LAB|KhoeSan_Exomes_chr6_26093141fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat03/06/1403/06/14142Genomicunknown
ss982706046EVA-GONL|EVA-GONL_rs1800562fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat04/23/1404/24/14142Genomicunknown
ss13194045381000GENOMES|PHASE3_V1_31329085fwd/A/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat08/16/1408/16/14142Genomicunknown
ss1397445372HAMMER_LAB|HAMMER_LAB_rs1800562fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat09/30/1409/30/14146Genomicunknown
ss1581580354EVA_GENOME_DK|EVA_GENOME_DK_snv_rs1800562fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat02/19/1502/20/15144Genomicunknown
ss1584044193EVA_FINRISK|EVA_FINRISK_rs1800562fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat02/27/1502/27/15144Genomicunknown
ss1592256986EVA_DECODE|EVA_DECODE_6_26201120_221021_rs1800562fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat03/02/1503/03/15144Genomicunknown
ss1615189586EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_6_26093141_17368924fwd/A/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat03/04/1503/04/15144Genomicunknown
ss1658183619EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_6_26093141_17368924fwd/A/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat03/04/1503/04/15144Genomicunknown
ss1688187541EVA_EXAC|EVA_EXAC_3205069fwd/A/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat03/04/1503/04/15144Genomicunknown
ss1711114875EVA_MGP|EVA_XIMO_230635fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat03/09/1503/09/15144Genomicunknown
ss1752621306ILLUMINA|OmniExpressExome-8v1-1_B_exm521729-0_T_F_1921904613fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat05/27/1506/09/15146Genomicunknown
ss1917800125ILLUMINA|HumanExome-12v1-1_B_exm521729-0_T_F_1921904613fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat10/16/1510/16/15147Genomicunknown
ss1925958677WEILL_CORNELL_DGM|SNV:chr6:26093141fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat10/16/1510/17/15147Genomicunknown
ss1946170221ILLUMINA|HumanCoreExome-12v1-0_C_exm521729-0_T_F_1921904613fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat10/29/1510/29/15147Genomicunknown
ss1958872924ILLUMINA|exm521729-0_T_F_1921904613fwd/TA/Gcctggggaagagcagagatatacgtccaggtggagcacccaggcctggat11/13/1511/13/15147Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1800562|allelePos=256|totalLen=511|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=147
 TCCTCATCCT TCCTCTTTCC TGTCAAGTGC CTCCTTTGGT GAAGGTGACA CATCATGTGA
 CCTCTTCAGT GACCACTCTA CGGTGTCGGG CCTTGAACTA CTACCCCCAG AACATCACCA
 TGAAGTGGCT GAAGGATAAG CAGCCAATGG ATGCCAAGGA GTTCGAACCT AAAGACGTAT
 TGCCCAATGG GGATGGGACC TACCAGGGCT GGATAACCTT GGCTGTACCC CCTGGGGAAG
 AGCAGAGATA TACGT
 R
 CCAGGTGGAG CACCCAGGCC TGGATCAGCC CCTCATTGTG ATCTGGGGTA TGTGACTGAT
 GAGAGCCAGG AGCTGAGAAA ATCTATTGGG GGTTGAGAGG AGTGCCTGAG GAGGTAATTA
 TGGCAGTGAG ATGAGGATCT GCTCTTTGTT AGGGGGTGGG CTGAGGGTGG CAATCAAAGG
 CTTTAACTTG CTTTTTCTGT TTTAGAGCCC TCACCGTCTG GCACCCTAGT CATTGGAGTC
 ATCAGTGGAA TTGCT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
Y09803
dbSNP Blast Analysis
UniGene Cluster ID
233325
3D structure mapping
NP_000401  NP_620572  NP_620573  NP_620575  NP_620577  NP_620578  NP_620579  
OMIM
613609.0001
235200.0001

  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
ss1319404538EAS 1008AF 1.00000000
EUR 1006AF 0.042700000.95730001
AFR 1322AF 0.002300000.99769998
AMR 694AF 0.021600000.97839999
SAS 978AF 0.002000000.99800003
ss1688187541ExAc_Aggregated_Populations121412AF 0.032426780.96757323
ss233370759pilot_1_CEU_low_coverage_panel 120AF 0.033333340.96666664
ss24365242AFD_EUR_PANELEuropean 48IG 0.166666670.833333311.000000000.083333340.91666669
AFD_AFR_PANELAfrican American 44IG 1.00000000 1.00000000
AFD_CHN_PANELAsian 48IG 1.00000000 1.00000000
ss342203133ESP_Cohort_Populations 4552GF0.001757470.091388400.906854150.654721000.047451670.95254833
ss491881988CSAgilent 1321GF0.006000000.080000000.913999970.025056000.046000000.95400000
ss5586582P1 204AF 0.059000000.941000041.000000000.029000000.97100002
CAUC1 62AF 0.129000010.870999991.000000000.065000010.93500000
AFR1 48AF 1.00000000 1.00000000
HISP1 46AF 0.087000000.913000051.000000000.043000000.95699996
PAC1 48AF 1.00000000 1.00000000
CEPH 184AF 0.289999990.70999998
ss65843448KHP1 180AF 1.00000000 1.00000000
ss66077890HapMap-CEUEuropean 118IG 0.084745760.915254241.000000000.042372880.95762712
HapMap-HCBAsian 90IG 1.00000000 1.00000000
HapMap-JPTAsian 90IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
ss76015380ICMHP 10IG 1.00000000 1.00000000
ss95209990HapMap-CEUEuropean 226IG 0.106194690.893805331.000000000.053097340.94690263
HapMap-HCBAsian 90IG 1.00000000 1.00000000
HapMap-JPTAsian 88IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
EGP_YORUB-PANELSub-Saharan African 24IG 1.00000000 1.00000000
EGP_HISP-PANELHispanic 38IG 1.00000000 1.00000000
EGP_CEPH-PANELEuropean 42IG 0.095238100.904761911.000000000.047619050.95238096
EGP_AD-PANELAfrican American 28IG 1.00000000 1.00000000
EGP_ASIAN-PANELAsian 46IG 1.00000000 1.00000000
HAPMAP-ASW 98IG 0.020408160.979591851.000000000.010204080.98979592
HAPMAP-CHD 170IG 0.011764710.988235291.000000000.005882350.99411762
HAPMAP-GIH 176IG 0.011363640.988636371.000000000.005681820.99431819
HAPMAP-MEX 98IG 0.020408160.979591851.000000000.010204080.98979592
HAPMAP-TSI 176IG 0.056818180.943181811.000000000.028409090.97159094
ENSEMBL_Watson 2IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.063+/-0.16610318482890ALFRED: 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
byClusterbyFreqwithHapMapFreqWith1000GenomeDataUNKNOWNUNKNOWNYES

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