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Reference SNP (refSNP) Cluster Report: rs5030839                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:113/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
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:T=0.0027/326 (ExAC)
T=0.0028/14 (1000 Genomes)
T=0.0028/36 (GO-ESP)
T=0.0025/319 (TOPMED)
HGVS Names
  • CM000670.2:g.18222606C>T
  • NC_000008.10:g.18080115C>T
  • NC_000008.11:g.18222606C>T
  • NG_012245.2:g.57145C>T
  • NM_000662.7:c.559C>T
  • NM_001160170.3:c.559C>T
  • NM_001160171.3:c.559C>T
  • NM_001160172.3:c.559C>T
  • NM_001160173.3:c.559C>T
  • NM_001160174.2:c.559C>T
  • NM_001160175.3:c.745C>T
  • NM_001160176.3:c.745C>T
  • NM_001160179.2:c.559C>T
  • NM_001291962.1:c.745C>T
  • NP_000653.3:p.Arg187Ter
  • NP_001153642.1:p.Arg187Ter
  • NP_001153643.1:p.Arg187Ter
  • NP_001153644.1:p.Arg187Ter
  • NP_001153645.1:p.Arg187Ter
  • NP_001153646.1:p.Arg187Ter
  • NP_001153647.1:p.Arg249Ter
  • NP_001153648.1:p.Arg249Ter
  • NP_001153651.1:p.Arg187Ter
  • NP_001278891.1:p.Arg249Ter
  • XP_005273734.1:p.Arg249Ter
  • XP_005273735.1:p.Arg187Ter
  • XP_005273736.1:p.Arg187Ter
  • XP_006716473.1:p.Arg187Ter
  • XP_011542989.1:p.Arg249Ter
  • XP_011542990.1:p.Arg249Ter
  • XP_011542991.1:p.Arg187Ter
  • XP_016869436.1:p.Arg249Ter
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 ss342253585 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs5030839 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
ss7986004HGBASE|SNP001494153fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa03/19/0310/10/03113Genomicunknown
ss48295916SNP500CANCER|NAT1-10fwd/BC/Tcattctgatctcctagaagacagcaaatacraaaaatctactcctttactcttaagcctc08/19/0509/12/05126Genomicunknown
ss75246247ILLUMINA|ILMN_Human_1M_rs5030839fwd/BC/Tcattctgatctcctagaagacagcaaatacraaaaatctactcctttactcttaagcctc08/28/0708/29/07129Genomicunknown
ss119497783KRIBB_YJKIM|KHS1660030fwd/BC/Tcattctgatctcctagaagacagcaaatacraaaaatctactcctttactcttaagcctc02/04/0902/04/09131Genomicunknown
ss173907686ILLUMINA|Human1M-Duov3_B_rs5030839-128_B_F_1514219358fwd/BC/Tcattctgatctcctagaagacagcaaatacraaaaatctactcctttactcttaagcctc10/01/0910/04/09132Genomicunknown
ss3347240081000GENOMES|20100804_snps_6367549_chr8_18080115fwd/C/Tcattctgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaagcctc03/22/1103/22/11134Genomicunknown
ss342253585NHLBI-ESP|ESP2500-chr8-18080115byFreqfwd/BC/Tcattctgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaagcctc03/25/1109/05/14134Genomicunknown
ss481130403ILLUMINA|HumanOmni2.5-4v1_B_rs5030839-128_B_F_1649462974fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa01/30/1210/29/16137Genomicunknown
ss481152436ILLUMINA|HumanOmniExpress-12v1_C_rs5030839-131_B_F_1857741328fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa01/30/1210/27/16137Genomicunknown
ss482141973ILLUMINA|HumanOmni1-Quad_v1-0_C_rs5030839-131_B_F_1865379438fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa01/30/1208/28/15146Genomicunknown
ss485360228ILLUMINA|HumanOmni2.5-4v1_D_rs5030839-131_B_F_1857741328fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa01/30/1210/28/16137Genomicunknown
ss4909607091000GENOMES|20110521_exome_468507_chr8_18080115fwd/BC/Tcattctgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaagcctc02/10/1202/21/12137Genomicunknown
ss491410742EXOME_CHIP|stopgl_126968_chr_8_18080115fwd/BC/Tcattctgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaagcctc03/05/1203/05/12137Genomicunknown
ss491921829CLINSEQ_SNP|SNV-chr8-18124395fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa03/06/1203/13/12137Genomicunknown
ss537304737ILLUMINA|HumanOmni5-4v1_B_rs5030839-131_B_F_1889936637fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa06/22/1208/29/15146Genomicunknown
ss778556160ILLUMINA|HumanOmni25Exome-8v1_A_rs5030839-131_B_F_1865379438fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa05/30/1307/10/15146Genomicunknown
ss780867812ILLUMINA|HumanOmni25Exome-8v1_A_exm685632-0_B_F_1923008391fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa05/30/1307/10/15146Genomicunknown
ss783125803ILLUMINA|HumanOmni2.5-4v1_H_rs5030839-131_B_F_1857741328fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa05/30/1307/29/15146Genomicunknown
ss783552743ILLUMINA|HumanOmniExpressExome-8v1_A_exm685632-0_B_F_1923008391fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa05/31/1306/19/15146Genomicunknown
ss784082424ILLUMINA|HumanOmniExpressExome-8v1_A_rs5030839-131_B_F_1889936637fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa05/31/1306/19/15146Genomicunknown
ss832384641ILLUMINA|HumanOmniExpress-12v1_H_rs5030839-131_B_F_1857741328fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa09/17/1306/19/15146Genomicunknown
ss834012960ILLUMINA|HumanOmni2.5-8v1_A_rs5030839-131_B_F_1865379438fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa09/18/1307/29/15146Genomicunknown
ss985254178EVA-GONL|EVA-GONL_rs5030839fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa04/23/1404/25/14142Genomicunknown
ss1067495857JMKIDD_LAB|HGDP_exomes_chr8_18080115fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa07/09/1407/09/14142Genomicunknown
ss1075324500JMKIDD_LAB|HGDP_WGS_chr8_18080115fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa07/10/1407/11/14142Genomicunknown
ss13288471181000GENOMES|PHASE3_V1_41157957fwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa08/16/1408/16/14142Genomicunknown
ss1594843096EVA_DECODE|EVA_DECODE_8_18124395_221806_rs5030839fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa03/02/1503/03/15144Genomicunknown
ss1620096459EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_8_18080115_22757065fwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa03/04/1503/04/15144Genomicunknown
ss1663090492EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_8_18080115_22757065fwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa03/04/1503/04/15144Genomicunknown
ss1689107685EVA_EXAC|EVA_EXAC_4197093fwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa03/04/1503/04/15144Genomicunknown
ss1711194377EVA_MGP|EVA_XIMO_310137fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa03/09/1503/09/15144Genomicunknown
ss1752722037ILLUMINA|OmniExpressExome-8v1-1_B_rs5030839-131_B_F_1889936637fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa05/27/1506/09/15146Genomicunknown
ss1946231053ILLUMINA|HumanCoreExome-12v1-0_C_exm685632-0_B_F_1923008391fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa10/29/1510/29/15147Genomicunknown
ss1959092251ILLUMINA|exm685632-0_B_F_1923008391fwd/BC/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa11/13/1511/13/15147Genomicunknown
ss2301150671HUMAN_LONGEVITY|HLI-8-18222606-C-Tfwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa11/18/1611/18/16150Genomicunknown
ss2470808523TOPMED|8_18080115_C/Tfwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa11/20/1611/20/16150Genomicunknown
ss2634717605ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_SoL-rs5030839-131_B_F_2131fwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa02/02/1702/02/17151Genomicunknown
ss2634717606ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_exm685632-0_B_F_1923008391fwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa02/02/1702/02/17151Genomicunknown
ss2634717607ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs5030839-131_B_F_18899366fwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa02/02/1702/02/17151Genomicunknown
ss2711131558ILLUMINA|Consortium-OncoArray_15047405_A_exm685632-0_B_F_1923008391fwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa03/22/1703/22/17151Genomicunknown
ss2737016437GNOMAD|exomes_rs5030839fwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa05/17/1705/17/17151Genomicunknown
ss2748005862GNOMAD|coding_rs5030839fwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa05/17/1705/17/17151Genomicunknown
ss2863915037GNOMAD|rs5030839fwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa05/19/1705/19/17151Genomicunknown
ss2985432570AFFY|Axiom_PsorMich_Affx-31855744fwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa05/24/1705/24/17151Genomicunknown
ss2986074623AFFY|Axiom_Smokesc1_Affx-31855744fwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa05/24/1705/24/17151Genomicunknown
ss3002777605SWEGEN|NC_000008.10:g.18080115C>Tfwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa05/30/1705/30/17151Genomicunknown
ss3022824292ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm685632-0_B_F_1923008391fwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa06/28/1706/28/17151Genomicunknown
ss3555475138TOPMED|TOPMed_freeze_5?chr8:18,222,606fwd/C/Ttgatctcctagaagacagcaaatacgaaaaatctactcctttactcttaa10/06/1710/06/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs5030839|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 TGGCATGATT CACCTTCTCC TGCAGGTGAC CATTGATGGC AGGAACTACA TTGTCGATGC
 TGGGTTTGGA CGCTCATACC AGATGTGGCA GCCTCTGGAG TTAATTTCTG GGAAGGATCA
 GCCTCAGGTG CCTTGTGTCT TCCGTTTGAC GGAAGAGAAT GGATTCTGGT ATCTAGACCA
 AATCAGAAGG GAACAGTACA TTCCAAATGA AGAATTTCTT CATTCTGATC TCCTAGAAGA
 CAGCAAATAC
 Y
 GAAAAATCTA CTCCTTTACT CTTAAGCCTC GAACAATTGA AGATTTTGAG TCTATGAATA
 CATACCTGCA GACATCTCCA TCATCTGTGT TTACTAGTAA ATCATTTTGT TCCTTGCAGA
 CCCCAGATGG GGTTCACTGT TTGGTGGGCT TCACCCTCAC CCATAGGAGA TTCAATTATA
 AGGACAATAC AGATCTAATA GAGTTCAAGA CTCTGAGTGA GGAAGAAATA GAAAAAGTGC
 TGAAAAATAT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_030737
dbSNP Blast Analysis
UniGene Cluster ID
155956
3D structure mapping
NP_000653  NP_001153642  NP_001153643  NP_001153644  NP_001153645  NP_001153646  NP_001153647  NP_001153648  NP_001153651  

  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
ss1328847118EAS 1008AF 1.00000000
EUR 1006AF 0.991099950.00890000
AFR 1322AF 0.998499990.00150000
AMR 694AF 0.995700000.00430000
SAS 978AF 1.00000000
ss1689107685ExAc_Aggregated_Populations121410AF 0.997314870.00268512
ss342253585ESP_Cohort_Populations 4528GF0.996466460.00353357 1.000000000.998233200.00176678
ss48295916P1 202AF1.00000000 1.00000000
CAUC1 62AF1.00000000 1.00000000
AFR1 48AF1.00000000 1.00000000
HISP1 46AF1.00000000 1.00000000
PAC1 46AF1.00000000 1.00000000
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss491921829CSAgilent 1321GF0.997000040.00300000 1.000000000.998499990.00150000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.005+/-0.0520000

  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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