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Reference SNP (refSNP) Cluster Report: rs58285195                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:129/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.0598/7262 (ExAC)
C=0.0601/301 (1000 Genomes)
C=0.0537/698 (GO-ESP)
C=0.0582/7302 (TOPMED)
HGVS Names
  • CM000681.2:g.41116300T>C
  • NC_000019.10:g.41116300T>C
  • NC_000019.9:g.41622205T>C
  • NG_007930.1:g.6853T>C
  • NM_000774.4:c.112T>C
  • NP_000765.2:p.Ser38Pro
  • NR_135528.1:n.184T>C
  • XP_005258629.1:p.Ser38Pro
  • XP_011524853.1:p.Ser38Pro
  • XP_011524854.1:p.Ser38Pro
  • XP_011524855.1:p.Ser113Pro
  • XP_011524857.1:p.Ser113Pro
  • XP_016881873.1:p.Ser113Pro
  • XP_016881874.1:p.Ser113Pro
  • XP_016881875.1:p.Ser113Pro
  • XP_016881876.1:p.Ser113Pro
  • XR_243905.1:n.209T>C
  • XR_243906.1:n.212T>C
  • XR_430190.3:n.515T>C
  • XR_935755.1:n.327T>C
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 ss105440185 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs58285195 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
ss84157974PHARMGKB_AB_DME|PS206198_PA149588897_301byFreqfwd/BC/Tggaaagctgcctccgggacccagacccctccaatcctgggaaacctgctgctgctttgct12/06/0709/05/14129Genomicunknown
ss86251332CORNELL|hCV25650083byFreqfwd/BC/Tggaaagctgcctccgggacccagacccctccaatcctgggaaacctgctgctgctttgct01/21/0809/05/14130Genomicunknown
ss95212510APPLERA_GI|hCV25650083fwd/BC/Tggaaagctgcctccgggacccagacccctccaatcctgggaaacctgctgctgctttgct11/30/0503/13/08130Genomicunknown
ss105434261AFFY_DM3_1|DMET3B11457fwd/BC/Tggaaagctgcctccgggacccagacccctccaatcctgggaaacctgctgctgctttgct09/03/0809/03/08130Genomicunknown
ss105440185SNP500CANCER|CYP2F1-02byFreqfwd/BC/Tggaaagctgcctncrggacccagacccctccaatcctgggaaacctgctgctgctttgct09/05/0809/05/14130Genomicunknown
ss161063814ILLUMINA|HumanOmni1-Quad_v1-0_B_SNP19-46314045-0_T_R_1588136180rev/TA/Gagcaaagcagcagcaggtttcccaggattggaggggtctgggtcccggaggcagctttcc08/04/0910/05/09131Genomicunknown
ss203757132BUSHMAN|BUSHMAN-chr19-46314044byFreqfwd/BC/Tggaaagctgcctccgggacccagacccctccaatcctgggaaacctgctgctgctttgct02/16/1009/05/14132Genomicunknown
ss2281443551000GENOMES|pilot_1_YRI_9954038_chr19_46314045fwd/C/Tggaaagctgcctccgggacccagacccctccaatcctgggaaacctgctgctgctttgct04/22/1004/22/10132Genomicunknown
ss2376808551000GENOMES|pilot_1_CEU_7285484_chr19_46314045fwd/C/Tggaaagctgcctccgggacccagacccctccaatcctgggaaacctgctgctgctttgct05/01/1005/01/10132Genomicunknown
ss342499044NHLBI-ESP|ESP2500-chr19-41622205byFreqfwd/BC/Tggaaagctgcctccgggacccagacccctccaatcctgggaaacctgctgctgctttgct03/25/1109/05/14134Genomicunknown
ss479418405ILLUMINA|HumanOmni1-Quad_v1-0_C_kgp5872389-0_T_R_1816078710fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct01/30/1208/28/15146Genomicunknown
ss483620881ILLUMINA|HumanOmni2.5-4v1_D_kgp5872389-0_T_R_1816078710fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct01/30/1210/28/16137Genomicunknown
ss483829471ILLUMINA|HumanOmni2.5-4v1_B_SNP19-46314045-0_T_R_1628559552fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct01/30/1210/28/16137Genomicunknown
ss4911596941000GENOMES|20110521_exome_667492_chr19_41622205fwd/BC/Tggaaagctgcctccgggacccagacccctccaatcctgggaaacctgctgctgctttgct02/10/1202/22/12137Genomicunknown
ss491547701EXOME_CHIP|nonsyn_263927_chr_19_41622205fwd/BC/Tggaaagctgcctccgggacccagacccctccaatcctgggaaacctgctgctgctttgct03/05/1203/06/12137Genomicunknown
ss491767804CLINSEQ_SNP|SNV-chr19-46314045byFreqfwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct03/06/1209/05/14137Genomicunknown
ss535824984ILLUMINA|HumanOmni5-4v1_B_kgp5872389-0_T_R_1816078710fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct06/22/1208/29/15146Genomicunknown
ss565989346TISHKOFF|snp_chr19_41622205fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct11/22/1211/23/12138Genomicunknown
ss661854277SSMP|19_41622205fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct12/14/1202/14/15138Genomicunknown
ss778680193ILLUMINA|HumanOmni25Exome-8v1_A_kgp5872389-0_T_R_1816078710fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct05/30/1307/10/15146Genomicunknown
ss782253796ILLUMINA|HumanOmni2.5-4v1_H_kgp5872389-0_T_R_1816078710fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct05/30/1307/29/15146Genomicunknown
ss834138747ILLUMINA|HumanOmni2.5-8v1_A_kgp5872389-0_T_R_1816078710fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct09/18/1307/29/15146Genomicunknown
ss994310202EVA-GONL|EVA-GONL_rs58285195fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct04/23/1405/01/14142Genomicunknown
ss1067589718JMKIDD_LAB|HGDP_exomes_chr19_41622205fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct07/09/1407/09/14142Genomicunknown
ss1081910942JMKIDD_LAB|HGDP_WGS_chr19_41622205fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct07/10/1407/12/14142Genomicunknown
ss13632059991000GENOMES|PHASE3_V1_76931145fwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct08/16/1408/16/14142Genomicunknown
ss1397757892HAMMER_LAB|HAMMER_LAB_rs58285195fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct09/30/1409/30/14146Genomicunknown
ss1428405870DDI|DDI_rs58285195fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct11/04/1411/04/14144Genomicunknown
ss1578643856EVA_GENOME_DK|EVA_GENOME_DK_snv_rs58285195fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct02/19/1502/20/15144Genomicunknown
ss1584117716EVA_FINRISK|EVA_FINRISK_rs58285195fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct02/27/1502/27/15144Genomicunknown
ss1637988852EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_19_41622205_42433098fwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct03/04/1503/04/15144Genomicunknown
ss1680982885EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_19_41622205_42433098fwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct03/04/1503/04/15144Genomicunknown
ss1693618744EVA_EXAC|EVA_EXAC_9053678fwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct03/04/1503/04/15144Genomicunknown
ss1711514170EVA_MGP|EVA_XIMO_629930fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct03/09/1503/09/15144Genomicunknown
ss1809312338HAMMER_LAB|Hsieh_8342233fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct07/15/1507/16/15146Genomicunknown
ss1937803893WEILL_CORNELL_DGM|SNV:chr19:41622205fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct10/16/1510/19/15147Genomicunknown
ss1959865383ILLUMINA|kgp5872389-0_T_R_1816078710fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct11/13/1511/13/15147Genomicunknown
ss1971464720AMU|chr19:41622205fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct03/02/1603/02/16147Genomicunknown
ss2029681315JJLAB|SNP10183870fwd/BC/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct08/29/1608/31/16149Genomicunknown
ss2158222381USC_VALOUEV|NC_000019.9:g.41622205T>Cfwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct11/17/1611/17/16150Genomicunknown
ss2225835383HUMAN_LONGEVITY|HLI-19-41116300-T-Cfwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct11/18/1611/18/16150Genomicunknown
ss2391567343TOPMED|19_41622205_T/Cfwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct11/19/1611/19/16150Genomicunknown
ss2633541211ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_SoL-kgp5872389-0_T_R_21311fwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct02/02/1702/02/17151Genomicunknown
ss2633541212ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp5872389-0_T_R_181607871fwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct02/02/1702/02/17151Genomicunknown
ss2702833309GRF|rs58285195fwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct02/13/1702/13/17151Genomicunknown
ss2710883078ILLUMINA|Consortium-OncoArray_15047405_A_rs58285195-131_T_R_2060816565fwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct03/22/1703/22/17151Genomicunknown
ss2744020602GNOMAD|exomes_rs58285195fwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct05/17/1705/17/17151Genomicunknown
ss2750196038GNOMAD|coding_rs58285195fwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct05/17/1705/17/17151Genomicunknown
ss2962986399GNOMAD|rs58285195fwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct05/23/1705/23/17151Genomicunknown
ss2985142541AFFY|Axiom_PsorMich_Affx-15966699fwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct05/24/1705/24/17151Genomicunknown
ss2985775101AFFY|Axiom_Smokesc1_Affx-15966699fwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct05/24/1705/24/17151Genomicunknown
ss3017490540SWEGEN|NC_000019.9:g.41622205T>Cfwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct05/30/1705/30/17151Genomicunknown
ss3293559263TOPMED|TOPMed_freeze_5?chr19:41,116,300fwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct10/02/1710/02/17151Genomicunknown
ss3352307816CSHL|rs58285195fwd/C/Tgctgcctccgggacccagacccctccaatcctgggaaacctgctgctgct10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs58285195|allelePos=303|totalLen=603|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 GTTGACTATC TCTGCCTCTT TCCTCCTTTC TCCCTCCCTT CCCCATCCCC TGGCCTCTCC
 CTGTCTCCTT CTCTCCATCT GCCTTCATTT CCAGGGCCTA GGGAAGGTAA GTCCCAGGGG
 AGATGGAAAG GAGGGATCAG CGATGTCCTC TCCCACTTTG CCCTCCACAC GCCAGCAGCT
 GCCTTCACCA TGGACAGCAT AAGNCNACAG CCATCTTACT CCTGCTCCTG GCTCTCGTCT
 GTCTGCTCCT GACCCTAAGC TCAAGAGATA AGGGAAAGCT GCCTNCRGGA CCCAGACCCC
 TC
 Y
 CAATCCTGGG AAACCTGCTG CTGCTTTGCT CCCAAGACAT GCTGACTTCT CTCACTAAGG
 TGCAAGGCCC TTAGCTTGGG TGATGGTGGA AGGATAAGGA GGAGGGGTCC CATGGCCACA
 GGCCCCCCTG TAACTTCTGT CTTCCTACCC TCAGCTGAGC AAGGAGTATG GCTCCATGTA
 CACAGTGCAC CTGGGACCCA GGCGGGTGGT GGTCCTCAGC GGGTACCAAG CTGTGAAGGA
 GGCCCTGGTG GACCAGGGAG AGGAGTTTAG TGGCCSCGGT GACTACCCTG CCTTTTTCAA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000019
dbSNP Blast Analysis
3D structure mapping
NP_000765  

  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.
SourceC/C
C/T
T/T
HWPC
T
ss105440185P1 200GF 0.120000000.880000001.000000000.060000000.94000000
CAUC1 58GF 0.034482760.965517221.000000000.017241380.98275864
AFR1 48GF 0.291666660.708333310.751830000.145833330.85416669
HISP1 46GF 0.086956520.913043501.000000000.043478260.95652175
PAC1 48GF 0.083333340.916666691.000000000.041666670.95833331
P2 418GF 0.081339710.918660281.000000000.040669850.95933014
CAUC2 120GF 0.133333340.866666671.000000000.066666670.93333334
AFR2 120GF 0.066666670.933333341.000000000.033333340.96666664
P3 544GF0.003676470.172794120.823529420.402784000.090073530.90992647
CAUC3 132GF 0.090909090.909090941.000000000.045454550.95454544
AFR3 146GF0.013698630.246575340.739726010.751830000.136986300.86301368
HISP3 94GF 0.297872330.702127640.583882000.148936170.85106385
PAC3 172GF 0.104651160.895348851.000000000.052325580.94767439
ASI2 178GF 0.056179780.943820241.000000000.028089890.97191012
ss1363205999EAS 1008AF 0.028800000.97119999
EUR 1006AF 0.042700000.95730001
AFR 1322AF 0.067300000.93270004
AMR 694AF 0.079300000.92070001
SAS 978AF 0.086900000.91310000
ss1693618744ExAc_Aggregated_Populations121412AF 0.059821110.94017887
ss203757132BUSHMAN_POP 4IG 1.00000000 0.500000000.50000000
BUSHMAN_POP2 2IG 1.00000000 0.500000000.50000000
ss228144355pilot_1_YRI_low_coverage_panel 118AF 0.025423730.97457629
ss237680855pilot_1_CEU_low_coverage_panel 120AF 0.041666670.95833331
ss342499044ESP_Cohort_Populations 4552GF0.002636200.104130050.893233720.751830000.054701230.94529879
ss491767804CSAgilent 1319GF0.003000000.079000000.917999980.479500000.042500000.95749998
ss84157974PA149588898 356AF 0.058988760.94101125
ss86251332AGI_ASP_populationmultiple 68IG 0.147058830.852941161.000000000.073529410.92647058

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.112+/-0.2090000

  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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