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Reference SNP (refSNP) Cluster Report: rs1800012                 ** With other allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:89/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:G/T (REV)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With other allele [ClinVar]
MAF/MinorAlleleCount:A=0.0911/456 (1000 Genomes)
A=0.1311/16468 (TOPMED)
HGVS Names
  • CM000679.2:g.50200388C>A
  • NC_000017.10:g.48277749C=
  • NC_000017.10:g.48277749C>A
  • NC_000017.11:g.50200388C=
  • NC_000017.11:g.50200388C>A
  • NG_007400.1:g.6252G=
  • NG_007400.1:g.6252G>T
  • NM_000088.3:c.104-441G=
  • NM_000088.3:c.104-441G>T
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 ss90608198 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1800012 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
ss2420069HGBASE|SNP000002635fwd/BG/Tcgccaccccacctgcccagggaatggggcgggatgagggctggacctccc11/07/0010/10/0389Genomicunknown
ss12568597CUORCGL|SNP7byFreqfwd/BG/Tgcccccgccaccccacatgcccagggaatggggcgggatgagggatggacctcccttctc07/08/0310/25/06119Genomicunknown
ss82504792HGSV|Cor19240_SNV_20070510.chr17_45632748rev/TA/Cgagaagggaggtccagccctcatcccgccccattccctgggcaggtggggtggcgggggc11/30/0712/03/07130Genomicunknown
ss90608198BCMHGSC_JDW|JWB-1028179rev/TA/Cgagaagggaggtccagccctcatcccgccccattccctgggcaggtggggtggcgggggc02/26/0802/29/08129Genomicunknown
ss1135938891000GENOMES|NA19240_2008_12_16_3065520_chr17_45632748rev/TA/Cgagaagggaggtccagccctcatcccgccccattccctgggcaggtggggtggcgggggc12/18/0812/18/08130Genomicunknown
ss137100918ENSEMBL|ENSSNP11248250rev/TA/Cgagaagggaggtccagccctcatcccgccccattccctgggcaggtggggtggcgggggc05/15/0905/16/09131Genomicunknown
ss168259526COMPLETE_GENOMICS|NA07022_36_chr17_45632748rev/TA/Cgagaagggaggtccagccctcatcccgccccattccctgggcaggtggggtggcgggggc09/30/0909/30/09132Genomicunknown
ss169747438COMPLETE_GENOMICS|NA19240_36_chr17_45632748rev/TA/Cgagaagggaggtccagccctcatcccgccccattccctgggcaggtggggtggcgggggc10/01/0910/01/09132Genomicunknown
ss2275677491000GENOMES|pilot_1_YRI_9377432_chr17_45632748rev/A/Cgagaagggaggtccagccctcatcccgccccattccctgggcaggtggggtggcgggggc04/22/1004/22/10132Genomicunknown
ss2372608731000GENOMES|pilot_1_CEU_6865502_chr17_45632748rev/A/Cgagaagggaggtccagccctcatcccgccccattccctgggcaggtggggtggcgggggc05/01/1005/01/10132Genomicunknown
ss483634850ILLUMINA|HumanOmni2.5-4v1_B_SNP17-45632748-0_T_F_1620066921rev/TA/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg01/30/1210/28/16137Genomicunknown
ss483915769ILLUMINA|HumanOmni2.5-4v1_D_kgp747462-0_T_F_1810634178rev/TA/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg01/30/1210/27/16137Genomicunknown
ss536109747ILLUMINA|HumanOmni5-4v1_B_kgp747462-0_T_F_1810634178rev/TA/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg06/22/1208/29/15146Genomicunknown
ss565299670TISHKOFF|snp_chr17_48277749rev/TA/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg11/22/1211/23/12138Genomicunknown
ss661107881SSMP|17_48277749rev/TA/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg12/14/1202/14/15138Genomicunknown
ss780456394ILLUMINA|HumanOmni25Exome-8v1_A_kgp747462-0_T_F_1810634178rev/TA/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg05/30/1307/10/15146Genomicunknown
ss782401504ILLUMINA|HumanOmni2.5-4v1_H_kgp747462-0_T_F_1810634178rev/TA/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg05/30/1307/29/15146Genomicunknown
ss835946405ILLUMINA|HumanOmni2.5-8v1_A_kgp747462-0_T_F_1810634178rev/TA/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg09/18/1307/29/15146Genomicunknown
ss993157475EVA-GONL|EVA-GONL_rs1800012rev/TA/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg04/23/1404/30/14142Genomicunknown
ss1081090037JMKIDD_LAB|HGDP_WGS_chr17_48277749rev/TA/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg07/10/1407/12/14142Genomicunknown
ss13588490761000GENOMES|PHASE3_V1_72390038rev/A/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg08/16/1408/16/14142Genomicunknown
ss1578177113EVA_GENOME_DK|EVA_GENOME_DK_snv_rs1800012rev/TA/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg02/19/1502/19/15144Genomicunknown
ss1635745530EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_17_48277749_39953007rev/A/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg03/04/1503/04/15144Genomicunknown
ss1678739563EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_17_48277749_39953007rev/A/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg03/04/1503/04/15144Genomicunknown
ss1697200930EVA_DECODE|EVA_DECODE_17_45632748_326939_rs1800012rev/TA/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg03/02/1503/04/15144Genomicunknown
ss1808803658HAMMER_LAB|Hsieh_7831290rev/TA/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg07/15/1507/16/15146Genomicunknown
ss1936619871WEILL_CORNELL_DGM|SNV:chr17:48277749rev/TA/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg10/16/1510/19/15147Genomicunknown
ss1959752878ILLUMINA|17:48277749-C-A-0_T_F_2304247553rev/TA/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg11/13/1511/13/15147Genomicunknown
ss2029085703JJLAB|SNP9588258rev/TA/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg08/29/1608/31/16149Genomicunknown
ss2157562012USC_VALOUEV|NC_000017.10:g.48277749C>Arev/A/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg11/17/1611/17/16150Genomicunknown
ss2217220263HUMAN_LONGEVITY|HLI-17-50200388-C-Arev/A/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg11/18/1611/18/16150Genomicunknown
ss2382375712TOPMED|17_48277749_C/Arev/A/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg11/19/1611/19/16150Genomicunknown
ss2633402395ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp747462-0_T_F_1810634178rev/A/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg02/02/1702/02/17151Genomicunknown
ss2633402396ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs1800012-131_T_R_19001369rev/A/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg02/02/1702/02/17151Genomicunknown
ss2950468044GNOMAD|rs1800012rev/A/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg05/23/1705/23/17151Genomicunknown
ss3015622666SWEGEN|NC_000017.10:g.48277749C>Arev/A/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg05/30/1705/30/17151Genomicunknown
ss3021786860ILLUMINA|MEGA_Consortium_v2_15070954_A2_17:48277749-C-A-0_T_F_2304247553rev/A/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg06/28/1706/28/17151Genomicunknown
ss3028364634BIOINF_KMB_FNS_UNIBA|17.50200388C>Arev/A/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg07/05/1707/05/17151Genomicunknown
ss3264204262TOPMED|TOPMed_freeze_5?chr17:50,200,388rev/A/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg10/01/1710/01/17151Genomicunknown
ss3351765888CSHL|rs1800012rev/A/Cgggaggtccagccctcatcccgccccattccctgggcaggtggggtggcg10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1800012|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=151
 GAGTGGTTAG CTAACTTCTG GACTATTTGC GGACTTTTTG GTTCTTTGGC TAAAAGTGAC
 CTGGAGGCAT TGGCTGGCTT TGGGGGACTG GGGATGGCCC CGAGAGCGGG CTTTTAAGAT
 GTCTAGGTGC TGGAGGTTAG GGTGTCTCCT AATTTTGAGG TACATTTCAA GTCTTGGGGG
 GGCCTCCCTT CCAATCAGCC GCTCCCATTC TCCTAGCCCC GCCCCCGCCA CCCCACCTGC
 CCAGGGAATG
 K
 GGGCGGGATG AGGGCTGGAC CTCCCTTCTC TCCTCCCTCG CCCTCCTCCT GTCTCTACCA
 CGCAAGCCAC TCCCCACGAG CCTGCCCTCC CGATGGGGCC CCTCCTATTC TCCCCCCGCC
 CTCCCCCTCT CACCCTGTGG TTTTTATTTC ACTTGGCTTC AGCGCCAATG GGCTGAGGTT
 GGAGTTGGAA GCCACCGCGG ACTAAAGCTT TGTTTAAATT CCTGAGAACT GGAAAGAGTT
 ACAGCCTCCC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000017
dbSNP Blast Analysis
OMIM
120150.0051
166710

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs1800012 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceG/G
G/T
HWPG
T
ss12568597American Caucasians 1855AF 0.811999980.18799999
ss1358849076EAS 1008AF 0.999000010.00100000
EUR 1006AF 0.811100010.18890001
AFR 1322AF 0.936500010.06350000
AMR 694AF 0.876100060.12390000
SAS 978AF 0.902899980.09710000
ss137100918ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss168259526CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss169747438YRISub-Saharan African 2IG 1.00000000 0.500000000.50000000
ss227567749pilot_1_YRI_low_coverage_panel 118AF 0.983050820.01694915
ss237260873pilot_1_CEU_low_coverage_panel 120AF 0.866666670.13333334
ss90608198ENSEMBL_Venter 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.166+/-0.2350000

  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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