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Reference SNP (refSNP) Cluster Report: rs425105                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:80/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqbySubmitterWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS PheGenI
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=0.1426/714 (1000 Genomes)
C=0.1546/19409 (TOPMED)
HGVS Names
  • CM000681.2:g.46705224T>C
  • NC_000019.10:g.46705224T>C
  • NC_000019.9:g.47208481T>C
  • NM_001079880.1:c.512-575A>G
  • NM_001079881.1:c.512-575A>G
  • NM_001079882.1:c.41-575A>G
  • NM_016457.4:c.512-575A>G
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 ss283228972 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs425105 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
ss562252SC_JCM|AC025983.3_217byFreqfwd/TA/Ggggaggactagaaggaggtgcttaccatagggactggggctgggtcagagctttggcggg07/12/0004/07/0480Genomicunknown
ss65792928ILLUMINA|Human1-rs425105fwd/TA/Ggggaggactagaaggaggtgcttaccatagggactggggctgggtcagagctttggcggg10/10/0610/10/06127Genomicunknown
ss66618031ILLUMINA|HumanHap300v1.1_rs425105fwd/TA/Ggggaggactagaaggaggtgcttaccatagggactggggctgggtcagagctttggcggg11/09/0611/09/06127Genomicunknown
ss67321191ILLUMINA|HumanHap550v1.1_rs425105fwd/TA/Ggggaggactagaaggaggtgcttaccatagggactggggctgggtcagagctttggcggg11/14/0611/14/06127Genomicunknown
ss67725202ILLUMINA|HumanHap650Yv1.0_rs425105fwd/TA/Ggggaggactagaaggaggtgcttaccatagggactggggctgggtcagagctttggcggg11/14/0611/14/06127Genomicunknown
ss70797079ILLUMINA|HumanHap550v3.0__rs425105fwd/TA/Ggggaggactagaaggaggtgcttaccatagggactggggctgggtcagagctttggcggg04/20/0703/30/08130Genomicunknown
ss71375355ILLUMINA|HumanHap650Yv3.0_rs425105fwd/TA/Ggggaggactagaaggaggtgcttaccatagggactggggctgggtcagagctttggcggg04/23/0704/23/07127Genomicunknown
ss75455458ILLUMINA|ILMN_Human_1M_rs425105fwd/TA/Ggggaggactagaaggaggtgcttaccatagggactggggctgggtcagagctttggcggg08/28/0708/29/07129Genomicunknown
ss79177564ILLUMINA|HumanHap300v2.0_rs425105fwd/TA/Ggggaggactagaaggaggtgcttaccatagggactggggctgggtcagagctttggcggg04/18/0711/18/07130Genomicunknown
ss80065560HGSV|Cor18507_SNV_20070510.chr19_51900321rev/BC/Tcccgccaaagctctgacccagccccagtccctatggtaagcacctccttctagtcctccc11/23/0711/24/07130Genomicunknown
ss83451193KRIBB_YJKIM|KHS464730fwd/TA/Ggggaggactagaaggaggtgcttaccatagggactggggctgggtcagagctttggcggg12/04/0712/05/07130Genomicunknown
ss117720927ILLUMINA-UK|NA18507_000052885_NCBI36.1_chr19_51900321byFreqrev/BC/Tcccgccaaagctctgacccagccccagtccctatggtaagcacctccttctagtcctccc01/19/0909/05/14130Genomic99 %
ss122284061ILLUMINA|HumanCNV370v1_C_rs425105fwd/TA/Ggggaggactagaaggaggtgcttaccatagggactggggctgggtcagagctttggcggg04/14/0904/15/09131Genomicunknown
ss154286808ILLUMINA|Human610_Quadv1_B_rs425105-128_T_F_1501772098fwd/TA/Ggggaggactagaaggaggtgcttaccatagggactggggctgggtcagagctttggcggg06/18/0906/20/09131Genomicunknown
ss159463739ILLUMINA|Human660W-Quad_v1_A_rs425105-128_T_F_1501772098fwd/TA/Ggggaggactagaaggaggtgcttaccatagggactggggctgggtcagagctttggcggg07/06/0907/07/09131Genomicunknown
ss160667962ILLUMINA|HumanOmni1-Quad_v1-0_B_rs425105-128_T_F_1512138951fwd/TA/Ggggaggactagaaggaggtgcttaccatagggactggggctgggtcagagctttggcggg08/04/0910/04/09131Genomicunknown
ss168267128COMPLETE_GENOMICS|NA07022_36_chr19_51900321rev/BC/Tcccgccaaagctctgacccagccccagtccctatggtaagcacctccttctagtcctccc09/30/0909/30/09132Genomicunknown
ss171759346ILLUMINA|HumanCNV370-Quadv3_C_rs425105-128_T_F_1501772098fwd/TA/Ggggaggactagaaggaggtgcttaccatagggactggggctgggtcagagctttggcggg10/01/0910/04/09132Genomicunknown
ss173702740ILLUMINA|Human1M-Duov3_B_rs425105-128_T_F_1501772098fwd/TA/Ggggaggactagaaggaggtgcttaccatagggactggggctgggtcagagctttggcggg10/01/0910/04/09132Genomicunknown
ss203769721BUSHMAN|BUSHMAN-chr19-51900320rev/BC/Tcccgccaaagctctgacccagccccagtccctatggtaagcacctccttctagtcctccc02/16/1003/09/10132Genomicunknown
ss2281625251000GENOMES|pilot_1_YRI_9972208_chr19_51900321rev/C/Tcccgccaaagctctgacccagccccagtccctatggtaagcacctccttctagtcctccc04/22/1004/22/10132Genomicunknown
ss2376939661000GENOMES|pilot_1_CEU_7298595_chr19_51900321rev/C/Tcccgccaaagctctgacccagccccagtccctatggtaagcacctccttctagtcctccc05/01/1005/01/10132Genomicunknown
ss2438959721000GENOMES|pilot_1_CHB+JPT_5781049_chr19_51900321rev/C/Tcccgccaaagctctgacccagccccagtccctatggtaagcacctccttctagtcctccc05/01/1005/01/10132Genomicunknown
ss255711177BL|SNP58142_19_51900321rev/BC/Tcccgccaaagctctgacccagccccagtccctatggtaagcacctccttctagtcctccc08/20/1008/20/10134Genomicunknown
ss283228972GMI|GMI_AK_SNP_7549393rev/C/Tcccgccaaagctctgacccagccccagtccctatggtaagcacctccttctagtcctccc12/16/1012/16/10137Genomicunknown
ss481886561ILLUMINA|HumanOmni1-Quad_v1-0_C_rs425105-131_T_F_1858938200rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc01/30/1208/28/15146Genomicunknown
ss483488559ILLUMINA|HumanOmni2.5-4v1_D_kgp5156231-0_T_R_1816412538rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc01/30/1210/28/16137Genomicunknown
ss483837109ILLUMINA|HumanOmni2.5-4v1_B_SNP19-51900321-0_T_R_1628545556rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc01/30/1210/28/16137Genomicunknown
ss491550184EXOME_CHIP|.GWAS._266410_chr_19_47208481rev/BC/Tcccgccaaagctctgacccagccccagtccctatggtaagcacctccttctagtcctccc03/05/1203/06/12137Genomicunknown
ss535697228ILLUMINA|HumanOmni5-4v1_B_kgp5156231-0_T_R_1816412538rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc06/22/1208/29/15146Genomicunknown
ss566016253TISHKOFF|snp_chr19_47208481rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc11/22/1211/23/12138Genomicunknown
ss661882803SSMP|19_47208481rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc12/14/1202/14/15138Genomicunknown
ss780296379ILLUMINA|HumanOmni25Exome-8v1_A_kgp5156231-0_T_R_1816412538rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc05/30/1307/10/15146Genomicunknown
ss780684958ILLUMINA|HumanOmni25Exome-8v1_A_exm-rs425105-131_T_F_1990492166rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc05/30/1307/10/15146Genomicunknown
ss782187671ILLUMINA|HumanOmni2.5-4v1_H_kgp5156231-0_T_R_1816412538rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc05/30/1307/29/15146Genomicunknown
ss783358432ILLUMINA|HumanOmniExpressExome-8v1_A_exm-rs425105-131_T_F_1990492166rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc05/31/1306/19/15146Genomicunknown
ss825508082ILLUMINA|HumanCNV370v1_C_rs425105-80_T_F_IFB1135375864:0rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc06/24/1311/21/14144Genomicunknown
ss835783007ILLUMINA|HumanOmni2.5-8v1_A_kgp5156231-0_T_R_1816412538rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc09/18/1307/29/15146Genomicunknown
ss994352848EVA-GONL|EVA-GONL_rs425105rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc04/23/1405/01/14142Genomicunknown
ss1081939892JMKIDD_LAB|HGDP_WGS_chr19_47208481rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc07/10/1407/12/14142Genomicunknown
ss13633813231000GENOMES|PHASE3_V1_77113487rev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc08/16/1408/16/14142Genomicunknown
ss1428417631DDI|DDI_rs425105rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc11/04/1411/04/14144Genomicunknown
ss1578658986EVA_GENOME_DK|EVA_GENOME_DK_snv_rs425105rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc02/19/1502/20/15144Genomicunknown
ss1638069787EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_19_47208481_42523406rev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc03/04/1503/04/15144Genomicunknown
ss1681063820EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_19_47208481_42523406rev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc03/04/1503/04/15144Genomicunknown
ss1698408195EVA_DECODE|EVA_DECODE_19_51900321_349000_rs425105rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc03/02/1503/05/15144Genomicunknown
ss1713665709EVA_SVP|EVA_SVP_1359788rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc03/12/1503/12/15144Genomicunknown
ss1752289320ILLUMINA|OmniExpressExome-8v1-1_B_exm-rs425105-131_T_F_2058874244rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc05/27/1506/09/15146Genomicunknown
ss1809332235HAMMER_LAB|Hsieh_8362211rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc07/15/1507/16/15146Genomicunknown
ss1917939443ILLUMINA|HumanExome-12v1-1_B_exm-rs425105-131_T_F_2058874244rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc10/16/1510/16/15147Genomicunknown
ss1937850831WEILL_CORNELL_DGM|SNV:chr19:47208481rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc10/16/1510/19/15147Genomicunknown
ss1946538377ILLUMINA|HumanCoreExome-12v1-0_C_exm-rs425105-131_T_F_2058874244rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc10/29/1510/29/15147Genomicunknown
ss1959871807ILLUMINA|exm-rs425105-131_T_F_1990492166rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc11/13/1511/13/15147Genomicunknown
ss2029702187JJLAB|SNP10204742rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc08/29/1608/31/16149Genomicunknown
ss2094899411ILLUMINA|Immuno_BeadChip_11419691_B_imm_19_51900321-1_T_R_1670102160rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc09/27/1609/27/16150Genomicunknown
ss2095085367ILLUMINA|InfiniumImmunoArray-24v2-0_A_imm_19_51900321-1_T_R_2310677393rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc09/27/1609/27/16150Genomicunknown
ss2095085368ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs425105-138_T_F_2264360873rev/BC/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc09/27/1609/27/16150Genomicunknown
ss2158246769USC_VALOUEV|NC_000019.9:g.47208481T>Crev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc11/17/1611/17/16150Genomicunknown
ss2226123726HUMAN_LONGEVITY|HLI-19-46705224-T-Crev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc11/18/1611/18/16150Genomicunknown
ss2391939503TOPMED|19_47208481_T/Crev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc11/19/1611/19/16150Genomicunknown
ss2629348160SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV6512765rev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc01/06/1701/06/17151Genomicunknown
ss2633545991ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp5156231-0_T_R_181641253rev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc02/02/1702/02/17151Genomicunknown
ss2702859822GRF|rs425105rev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc02/13/1702/13/17151Genomicunknown
ss2963490736GNOMAD|rs425105rev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc05/23/1705/23/17151Genomicunknown
ss2985145522AFFY|Axiom_PsorMich_Affx-16045760rev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc05/24/1705/24/17151Genomicunknown
ss2985776161AFFY|Axiom_Smokesc1_Affx-16045760rev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc05/24/1705/24/17151Genomicunknown
ss3017564785SWEGEN|NC_000019.9:g.47208481T>Crev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc05/30/1705/30/17151Genomicunknown
ss3021913749ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm-rs425105-131_T_F_1990492166rev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc06/28/1706/28/17151Genomicunknown
ss3028681502BIOINF_KMB_FNS_UNIBA|19.46705224T>Crev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc07/05/1707/05/17151Genomicunknown
ss3294695114TOPMED|TOPMed_freeze_5?chr19:46,705,224rev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc10/02/1710/02/17151Genomicunknown
ss3352327449CSHL|rs425105rev/C/Tcaaagctctgacccagccccagtccctatggtaagcacctccttctagtc10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs425105|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 ACCTCTGCCT CCTGGGTTCA AGTGATTCTC CTGCCTCAGC CTCCGGAGTA GCTGGGATTA
 CAGGCGTGTG CCACTACACC CGGCTAAGTT TTGTATTTTT AGTAGAGATG GGGTTTTGCC
 ATGTTGGCCA GTGTGGTCTC AAACTCCTGA CCTCAAGTGA TCCGCCGGCC TTGGCCTCCC
 AAAGTGCTGG GATTACAGGC GTGAGCCACC ATGCGTGGCC CACACTACTA AGATTTAATC
 ACACTACTTA GGGATTGCCT GGATTCCAGG TCTACAGAAA AGAGAAAGTG GGGTACAGGG
 GGTGAGCAGA CCTGGAGGGA TAGTGACCTT AGGGGTGGGG GTGAGGAGAG GCATTTTCTT
 TTGGAAAGTT GGGGTTGGGG AAAGAGGGGG AACCAAAGGG GCCTCAGAAA AAGGAAGGTC
 AGGGTTAGAA GGGGGAACAG GTGTCTCTAG GGAGATGGAC AGGAGTTTTG GGGAGGACTA
 GAAGGAGGTG CTTACCATAG
 R
 GGACTGGGGC TGGGTCAGAG CTTTGGCGGG GACTTTTGAG GCATCCATTG TTGCAGTGGG
 AAAAGGTGGG GTGTGAGGCG CGTTCAGGGC CTGGGGGGCA GATGGGGTGA TGTCGGGGCT
 ACAAGCTGGA ACTAGGGGTG GAGCTTTGGA GGGAACCTTT GAGGTATCCC TTGTTGGAGT
 GGGAAAATTT TGGGTGTGAG GCGTGTTCAG GGTCTGGGGG ACAGATGGGG TGATGGCAGG
 GCTACAAGCT GAAACTGGGG ACAGAGCTTT GGGGGGAGCC TTTGAGGTGT CCCTTGTTGG
 AGTGAGAAAA GGGGTGTGGG TGTGTTCAGG GTCTGGGGGA CAGATGGGGT GATGGTGGGG
 CTACAAGCTG GAACTTGGGG CAGAACTCTA AGGAGGGGTG GGCCTGAAGG GGCTGATACA
 CTTACGGATA GTAGTGCCTT TTGGAGGAGA TCGTGCTGGC GGGGGGTGAT GGGACAGGAC
 CAGGTGAGAG ATTGGGTGGA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000019 AC008635
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs425105 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
ss117720927HapMap-CEUEuropean 226IG0.699115040.283185840.017699110.583882000.840707960.15929204
HapMap-HCBAsian 86IG0.720930220.27906978 0.654721000.860465110.13953489
HapMap-JPTAsian 172IG0.744186040.244186040.011627910.654721000.866279070.13372093
HapMap-YRISub-Saharan African 226IG0.752212410.212389380.035398230.200325000.858407080.14159292
HAPMAP-ASW 98IG0.795918350.20408164 0.751830000.897959170.10204082
HAPMAP-CHBAsian 80IG0.699999990.275000010.025000001.000000000.837499980.16249999
HAPMAP-CHD 170IG0.588235320.364705890.047058821.000000000.770588220.22941177
HAPMAP-GIH 176IG0.784090940.204545450.011363641.000000000.886363630.11363637
HAPMAP-LWK 180IG0.800000010.188888890.011111111.000000000.894444470.10555556
HAPMAP-MEX 100IG0.680000010.280000000.040000000.751830000.819999990.18000001
HAPMAP-MKK 286IG0.790209770.188811180.020979020.371093000.884615360.11538462
HAPMAP-TSI 176IG0.681818190.295454530.022727270.751830000.829545440.17045455
ENSEMBL_Watson 2IG1.00000000 1.00000000
YRI 2IG 1.00000000 0.500000000.50000000
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss1363381323EAS 1008AF 0.831299960.16870001
EUR 1006AF 0.826999960.17299999
AFR 1322AF 0.872899950.12710001
AMR 694AF 0.884700000.11530001
SAS 978AF 0.875299990.12469999
ss168267128CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss203769721BUSHMAN_POP2 2IG 1.00000000 0.500000000.50000000
ss228162525pilot_1_YRI_low_coverage_panel 118AF 0.889830530.11016949
ss237693966pilot_1_CEU_low_coverage_panel 120AF 0.833333310.16666667
ss243895972pilot_1_CHB+JPT_low_coverage_panel 120AF 0.858333350.14166667
ss562252CEPH 184AF 0.730000020.27000001

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.244+/-0.2500000ALFRED: 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
byClusterbyFreqbySubmitterWith1000GenomeData
Validated by: ILLUMINA
UNKNOWNUNKNOWNUNKNOWN

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