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Reference SNP (refSNP) Cluster Report: rs2290349                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (REV)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:G=0.0408/4957 (ExAC)
G=0.0413/207 (1000 Genomes)
G=0.0335/436 (GO-ESP)
G=0.0397/4980 (TOPMED)
HGVS Names
  • CM000672.2:g.4839743A>G
  • NC_000010.10:g.4881935A>G
  • NC_000010.11:g.4839743A>G
  • NM_001040177.2:c.597A>G
  • NM_001271021.1:c.582+2162A>G
  • NM_001271025.1:c.460-2678A>G
  • NP_001035267.1:p.Pro199=
  • NR_073125.1:n.745A>G
  • NR_073126.1:n.659A>G
  • NR_073127.1:n.730+2162A>G
  • XP_011518017.1:p.Pro220=
  • XP_011518020.1:p.Pro220=
  • XP_011518021.1:p.Pro220=
  • XP_011518022.1:p.Pro220=
  • XP_011518024.1:p.Pro220=
  • XP_011518027.1:p.Pro220=
  • XP_016872232.1:p.Pro220=
  • XP_016872233.1:p.Pro220=
  • XP_016872234.1:p.Pro95=
  • XR_001747220.1:n.1042A>G
  • XR_001747221.1:n.712A>G
  • XR_001747222.1:n.1042A>G
  • XR_001747223.1:n.1743+2162A>G
  • XR_930518.2:n.1041A>G
  • XR_930519.2:n.1042A>G
  • XR_930520.2:n.1041A>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 ss280458380 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2290349 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
ss3232204YUSUKE|IMS-JST042289byFreqfwd/BC/Taaaactgatcagattcttctgagtaagatagggtggcactcaatctataacagaatcata09/05/0110/10/03100Genomicunknown
ss24075174PERLEGEN|afd2201590byFreqrev/TA/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt08/10/0409/13/04123Genomicunknown
ss48420508APPLERA_GI|hCV15884414byFreqfwd/BC/Taaaactgatcagattcttctgagtaagatagggtggcactcaatctataacagaatcata09/28/0511/03/06126Genomicunknown
ss66237480AFFY|SNP_A-4266918byFreqfwd/BC/Ttcttctgagtaagatagggtggcactcaatct10/27/0608/14/07127Genomicunknown
ss66542930ILLUMINA|HumanHap300v1.1_rs2290349fwd/TC/Taaaactgatcagattcttctgagtaagatagggtggcactcaatctataacagaatcata11/09/0611/09/06127Genomicunknown
ss67242959ILLUMINA|HumanHap550v1.1_rs2290349fwd/BC/Taaaactgatcagattcttctgagtaagatagggtggcactcaatctataacagaatcata11/14/0611/14/06127Genomicunknown
ss67639794ILLUMINA|HumanHap650Yv1.0_rs2290349fwd/BC/Taaaactgatcagattcttctgagtaagatagggtggcactcaatctataacagaatcata11/14/0611/14/06127Genomicunknown
ss69068226PERLEGEN|PGP02201590byFreqrev/TA/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt01/30/0708/14/07127Genomicunknown
ss70721303ILLUMINA|HumanHap550v3.0__rs2290349rev/TA/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt04/20/0703/30/08130Genomicunknown
ss71289718ILLUMINA|HumanHap650Yv3.0_rs2290349fwd/BC/Taaaactgatcagattcttctgagtaagatagggtggcactcaatctataacagaatcata04/23/0704/23/07127Genomicunknown
ss75228811ILLUMINA|ILMN_Human_1M_rs2290349fwd/BC/Taaaactgatcagattcttctgagtaagatagggtggcactcaatctataacagaatcata08/28/0708/29/07129Genomicunknown
ss76383310AFFY|AFFY_6_1M_SNP_A-4266918fwd/BC/Ttcttctgagtaagatagggtggcactcaatct08/28/0708/30/07129Genomicunknown
ss76899268SI_EXO|NT_077567.3_4821935byFreqrev/TA/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt09/20/0709/05/14129Genomicunknown
ss79127137ILLUMINA|HumanHap300v2.0_rs2290349fwd/BC/Taaaactgatcagattcttctgagtaagatagggtggcactcaatctataacagaatcata04/18/0711/18/07130Genomicunknown
ss84023875KRIBB_YJKIM|KHS605088fwd/BC/Taaaactgatcagattcttctgagtaagatagggtggcactcaatctataacagaatcata12/04/0712/06/07130Genomicunknown
ss102848940BGI|BGI_rs2290349rev/TA/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt06/05/0806/17/09131Genomicunknown
ss121988887ILLUMINA|HumanCNV370v1_C_rs2290349fwd/BC/Taaaactgatcagattcttctgagtaagatagggtggcactcaatctataacagaatcata04/14/0904/15/09131Genomicunknown
ss153900185ILLUMINA|Human610_Quadv1_B_rs2290349-128_T_R_1501711907rev/TA/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt06/18/0906/20/09131Genomicunknown
ss158126451GMI|GMI_SNP_122555021rev/TA/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt06/24/0906/25/09131Genomicunknown
ss159378015ILLUMINA|Human660W-Quad_v1_A_rs2290349-128_T_R_1501711907rev/TA/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt07/06/0907/07/09131Genomicunknown
ss161341656ENSEMBL|ENSSNP403326byFreqrev/TA/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt09/24/0903/07/10131Genomicunknown
ss170330950COMPLETE_GENOMICS|NA20431_36_chr10_4871935rev/TA/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt10/01/0910/04/09132Genomicunknown
ss171166908ILLUMINA|HumanCNV370-Quadv3_C_rs2290349-128_T_R_1501711907rev/TA/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt10/01/0910/03/09132Genomicunknown
ss173258504ILLUMINA|Human1M-Duov3_B_rs2290349-128_T_R_1501711907rev/TA/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt10/01/0910/03/09132Genomicunknown
ss173436411AFFY|GenomeWideSNP_5_SNP_A-4266918fwd/BC/Ttcttctgagtaagatagggtggcactcaatct10/01/0910/03/09132Genomicunknown
ss2350317481000GENOMES|pilot_1_CEU_4636377_chr10_4871935rev/A/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt05/01/1005/01/10132Genomicunknown
ss2417688121000GENOMES|pilot_1_CHB+JPT_3653889_chr10_4871935rev/A/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt05/01/1005/01/10132Genomicunknown
ss280458380GMI|GMI_AK_SNP_4778697rev/A/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt12/16/1012/16/10137Genomicunknown
ss342291531NHLBI-ESP|ESP2500-chr10-4881935byFreqrev/TA/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt03/25/1109/05/14134Genomicunknown
ss479822047ILLUMINA|HumanOmni2.5-4v1_D_kgp11804084-0_T_F_1814683105rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca01/30/1210/27/16137Genomicunknown
ss482598275ILLUMINA|HumanOmni2.5-4v1_B_SNP10-4871935-0_T_F_1621072826rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca01/30/1210/28/16137Genomicunknown
ss4909914501000GENOMES|20110521_exome_499248_chr10_4881935rev/TA/Gtatgattctgttatagattgagtgccaccctatcttactcagaagaatctgatcagtttt02/10/1202/21/12137Genomicunknown
ss491620533CLINSEQ_SNP|SNV-chr10-4871935byFreqrev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca03/06/1209/05/14137Genomicunknown
ss533308468ILLUMINA|HumanOmni5-4v1_B_kgp11804084-0_T_F_1814683105rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca06/22/1208/29/15146Genomicunknown
ss656241542SSMP|10_4881935rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca12/14/1202/12/15138Genomicunknown
ss779482804ILLUMINA|HumanOmni25Exome-8v1_A_kgp11804084-0_T_F_1814683105rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca05/30/1307/10/15142Genomicunknown
ss781077161ILLUMINA|HumanOmni2.5-4v1_H_kgp11804084-0_T_F_1814683105rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca05/30/1307/29/15142Genomicunknown
ss825457655ILLUMINA|HumanCNV370v1_C_rs2290349-126_T_R_IFB1136441836:0rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca06/24/1311/21/14144Genomicunknown
ss834952845ILLUMINA|HumanOmni2.5-8v1_A_kgp11804084-0_T_F_1814683105rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca09/18/1307/29/15142Genomicunknown
ss974473713JMKIDD_LAB|KhoeSan_Exomes_chr10_4881935rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca03/06/1403/06/14142Genomicunknown
ss987143556EVA-GONL|EVA-GONL_rs2290349rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca04/23/1404/25/14142Genomicunknown
ss1067510437JMKIDD_LAB|HGDP_exomes_chr10_4881935rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca07/09/1407/09/14142Genomicunknown
ss1076721420JMKIDD_LAB|HGDP_WGS_chr10_4881935rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca07/10/1407/11/14142Genomicunknown
ss13360818381000GENOMES|PHASE3_V1_48678487rev/A/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca08/16/1408/16/14142Genomicunknown
ss1574877175EVA_GENOME_DK|EVA_GENOME_DK_snv_rs2290349rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca02/19/1502/19/15144Genomicunknown
ss1584066531EVA_FINRISK|EVA_FINRISK_rs2290349rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca02/27/1502/27/15144Genomicunknown
ss1596790744EVA_DECODE|EVA_DECODE_10_4871935_46722_rs2290349rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca03/02/1503/03/15144Genomicunknown
ss1623887064EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_10_4881935_26904745rev/A/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca03/04/1503/04/15144Genomicunknown
ss1666881097EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_10_4881935_26904745rev/A/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca03/04/1503/04/15144Genomicunknown
ss1689798221EVA_EXAC|EVA_EXAC_4940284rev/A/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca03/04/1503/04/15144Genomicunknown
ss1711246069EVA_MGP|EVA_XIMO_361829rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca03/09/1503/09/15144Genomicunknown
ss1713152896EVA_SVP|EVA_SVP_847263rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca03/12/1503/12/15144Genomicunknown
ss1930463215WEILL_CORNELL_DGM|SNV:chr10:4881935rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca10/16/1510/17/15147Genomicunknown
ss2025954188JJLAB|SNP6456743rev/TA/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca08/29/1608/30/16149Genomicunknown
ss2172272321HUMAN_LONGEVITY|HLI-10-4839743-A-Grev/A/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca11/18/1611/18/16150Genomicunknown
ss2334971610TOPMED|10_4881935_A/Grev/A/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca11/19/1611/19/16150Genomicunknown
ss2627445639SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV4095618rev/A/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca01/06/1701/06/17151Genomicunknown
ss2632667743ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp11804084-0_T_F_18146831rev/A/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca02/02/1702/02/17151Genomicunknown
ss2698418585GRF|rs2290349rev/A/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca02/13/1702/13/17151Genomicunknown
ss2738085491GNOMAD|exomes_rs2290349rev/A/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca05/17/1705/17/17151Genomicunknown
ss2748338200GNOMAD|coding_rs2290349rev/A/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca05/17/1705/17/17151Genomicunknown
ss2884974620GNOMAD|rs2290349rev/A/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca05/19/1705/19/17151Genomicunknown
ss3005853747SWEGEN|NC_000010.10:g.4881935A>Grev/A/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca05/30/1705/30/17151Genomicunknown
ss3026760128BIOINF_KMB_FNS_UNIBA|10.4839743A>Grev/A/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca07/05/1707/05/17151Genomicunknown
ss3110370092TOPMED|TOPMed_freeze_5?chr10:4,839,743rev/A/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca09/29/1709/29/17151Genomicunknown
ss3348934365CSHL|rs2290349rev/A/Gttctgttatagattgagtgccaccctatcttactcagaagaatctgatca10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2290349|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 TCTCTTAGCT GATCTTGGGA GCACAGTACA GCTGCAGGAG GGCCTGGGTA AAGATGACAG
 CAGGCTTTGC CTCATCCAAC CATGGAGAGG CCTGGGGAGC ATCCTTGTCA GGAGGTCAGA
 AGGGGGCTGA CACCCTGGTG GGGAACTCAG CAAAGGGGTC ACTCCAGGCT GATTTACGTC
 CCTGAAGAGG TCCTGACCCT CCCAGGGCAG CCCACTCACA GCCACTCCCT GGCTTCCAAT
 AATAAACCAT GCCTTCAATC CCAGGCTTGA GAGGTGTGGA CAGCCCCCTA TAGTACCATC
 CCTCCACACC CTGTCAAAAC CTCCATTAAG CCCTCCCTCA GTCATCCCAA GGAAATGAGA
 AGGTGGCATC TACTTCCCAG TCGGACTCTG ACTAACACAC CACTGAGGTA TCCTTACCAC
 GAGCCACCAA GAGGACGGTA AGCAGTCACG GACACATCTC TGGATTGGCA AAAACTGATC
 AGATTCTTCT GAGTAAGATA
 Y
 GGGTGGCACT CAATCTATAA CAGAATCATA GCTTACATAA AATTCAGACC ACTAGTGTTC
 AAGAAAAGCT CTACAAGAGA AGACCTGCGT CAAAGTCTTG GCTGTCACCG AGTAGCCATG
 GGGCCCAGCT CCAGGCCTAA GTGTTTCTGT TGTGAGGAGT CTGGACAGAG CAATCTCCAA
 GAGGCCAGCA GGTGTCATGG TCTCTGAGTC CACGGCCTTG GGGACACCTA CATCATCTGA
 ATGTTCCAAT ACCACCTGCT CTGCAGGGCC TTCCCTGAGC ACTCAGATAA AGATTGTTAA
 CACACCATAG CTCTCATCTC CCCCGGCCTT TATTTTCCTC TACAGCATCT ATCACTATCT
 GACATCTCAT AGATTTTACA TATTTGCTCA CTGTCTTTCT GTGTCACCAA GATCTAAGCC
 TCATGAAGAT AGAGATTTTT GTTTGAATTT GTTTTGTTCA TAGATGTCTC ACCAACACTA
 AGAACAATCT AGACATGTAG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_077567.3
dbSNP Blast Analysis
UniGene Cluster ID
537121
3D structure mapping
NP_001035267  

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs2290349 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1336081838EAS 1008AF 0.103200000.89680004
EUR 1006AF 0.048700000.95130002
AFR 1322AF 0.003000000.99700004
AMR 694AF 0.044700000.95530003
SAS 978AF 0.019400000.98060000
ss161341656ENSEMBL_celera 4IG0.50000000 0.50000000 0.500000000.50000000
ss1689798221ExAc_Aggregated_Populations121412AF 0.040827930.95917207
ss170330950PGP 2IG 1.00000000 0.500000000.50000000
ss235031748pilot_1_CEU_low_coverage_panel 120AF 0.050000000.94999999
ss24075174AFD_EUR_PANELEuropean 48IG 0.125000000.875000001.000000000.062500000.93750000
AFD_AFR_PANELAfrican American 46IG 1.00000000 1.00000000
AFD_CHN_PANELAsian 48IG0.041666670.166666670.791666690.250592000.125000000.87500000
ss241768812pilot_1_CHB+JPT_low_coverage_panel 120AF 0.108333330.89166665
ss3232204JBIC-allele 1494AF 0.129100010.87090003
ss342291531ESP_Cohort_Populations 4550GF0.000879120.058021980.941098931.000000000.029890110.97010988
ss48420508AGI_ASP populationmultiple 78IG 0.051282050.948717951.000000000.025641030.97435898
ss491620533CSAgilent 1323GF0.002000000.080000000.917999981.000000000.042000000.95800000
ss66237480HapMap-CEUEuropean 118IG 0.118644070.881355941.000000000.059322030.94067794
HapMap-HCBAsian 90IG 0.244444440.755555570.654721000.122222220.87777776
HapMap-JPTAsian 90IG 0.155555560.844444451.000000000.077777780.92222220
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
ss69068226HapMap-CEUEuropean 120IG 0.116666670.883333331.000000000.058333330.94166666
HapMap-HCBAsian 90IG 0.244444440.755555570.654721000.122222220.87777776
HapMap-JPTAsian 90IG 0.155555560.844444451.000000000.077777780.92222220
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
ss76383310ICMHP 10IG 1.00000000 1.00000000
ss76899268HapMap-CEUEuropean 226IG 0.097345140.902654891.000000000.048672570.95132744
HapMap-HCBAsian 86IG 0.255813960.744186040.654721000.127906980.87209302
HapMap-JPTAsian 172IG 0.186046510.813953460.751830000.093023260.90697676
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
HAPMAP-ASW 98IG 0.040816330.959183691.000000000.020408160.97959185
HAPMAP-CHBAsian 82IG 0.170731710.829268281.000000000.085365850.91463417
HAPMAP-CHD 170IG0.023529410.211764710.764705900.583882000.129411770.87058824
HAPMAP-GIH 176IG 0.056818180.943181811.000000000.028409090.97159094
HAPMAP-MEX 100IG0.020000000.080000000.899999980.050043000.060000000.94000000
HAPMAP-TSI 176IG 0.159090910.840909060.751830000.079545450.92045456
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ENSEMBL_Venter 2IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.078+/-0.1820000ALFRED: 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
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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