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Reference SNP (refSNP) Cluster Report: rs11740298                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwithHapMapFreqWith1000GenomeData
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=0.1715/859 (1000 Genomes)
T=0.2259/28369 (TOPMED)
HGVS Names
  • CM000667.2:g.150112892C>T
  • NC_000005.10:g.150112892C>T
  • NC_000005.9:g.149492455C>T
  • NG_012303.1:g.5481G>A
  • NG_023367.1:g.47968G>A
  • NM_005211.3:c.-181+369G>A
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 ss285282219 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11740298 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
ss17056543CSHL-HAPMAP|CSHL-HuAA-200402.chr5.NT_029289.10_10655391byFreqfwd/BC/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc02/17/0410/26/06120Genomicunknown
ss66951106ILLUMINA|HumanHap550v1.1_rs11740298fwd/BC/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc11/14/0611/14/06127Genomicunknown
ss67113849ILLUMINA|HumanHap650Yv1.0_rs11740298fwd/BC/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc11/14/0611/14/06127Genomicunknown
ss68111968ILLUMINA|HumanHap250Sv1.0_rs11740298fwd/BC/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc12/06/0612/07/06127Genomicunknown
ss68953554PERLEGEN|PGP03328095byFreqfwd/BC/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc01/30/0703/31/08127Genomicunknown
ss70539794ILLUMINA|HumanHap550v3.0__rs11740298rev/TA/Ggaaacggcatcttcatttgagtgggtgcggaaggacctcattttggaaccacaggcctcc04/20/0703/30/08130Genomicunknown
ss71071704ILLUMINA|HumanHap650Yv3.0_rs11740298fwd/BC/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc04/23/0704/23/07127Genomicunknown
ss75446540ILLUMINA|ILMN_Human_1M_rs11740298fwd/BC/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc08/28/0708/29/07129Genomicunknown
ss77137201HGSV|Cor12156_SNV_20070510.chr5_149472648fwd/BC/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc10/09/0710/11/07129Genomicunknown
ss85132298KRIBB_YJKIM|KHS907425fwd/BC/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc12/04/0712/08/07130Genomicunknown
ss98775855HUMANGENOME_JCVI|1103654256087byFreqfwd/BC/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc04/01/0803/07/10130Genomicunknown
ss1095089451000GENOMES|CEU.trio.12.15.2008_1386886_chr5_149472648fwd/BC/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc12/16/0812/16/08130Genomicunknown
ss142532303ENSEMBL|ENSSNP9062869fwd/BC/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc12/08/0810/16/09131Genomicunknown
ss153047273ILLUMINA|Human610_Quadv1_B_rs11740298-128_T_R_1502099753rev/TA/Ggaaacggcatcttcatttgagtgggtgcggaaggacctcattttggaaccacaggcctcc06/18/0906/19/09131Genomicunknown
ss159186856ILLUMINA|Human660W-Quad_v1_A_rs11740298-128_T_R_1502099753rev/TA/Ggaaacggcatcttcatttgagtgggtgcggaaggacctcattttggaaccacaggcctcc07/06/0907/06/09131Genomicunknown
ss159999453ILLUMINA|HumanOmni1-Quad_v1-0_B_rs11740298-128_T_R_1502099753rev/TA/Ggaaacggcatcttcatttgagtgggtgcggaaggacctcattttggaaccacaggcctcc08/04/0910/01/09131Genomicunknown
ss162763392COMPLETE_GENOMICS|NA07022_36_chr5_149472648fwd/BC/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc09/28/0909/29/09132Genomicunknown
ss171512148ILLUMINA|Human1M-Duov3_B_rs11740298-128_T_R_1502099753rev/TA/Ggaaacggcatcttcatttgagtgggtgcggaaggacctcattttggaaccacaggcctcc10/01/0910/01/09132Genomicunknown
ss206738482BCM-HGSC-SUB|BCM_CMT_1011-1039344fwd/BC/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc03/15/1003/18/10132Genomicunknown
ss2220337261000GENOMES|pilot_1_YRI_3843409_chr5_149472648fwd/C/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc04/22/1004/22/10132Genomicunknown
ss2331959821000GENOMES|pilot_1_CEU_2800611_chr5_149472648fwd/C/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc05/01/1005/01/10132Genomicunknown
ss2403091661000GENOMES|pilot_1_CHB+JPT_2194243_chr5_149472648fwd/C/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc05/01/1005/01/10132Genomicunknown
ss285282219GMI|GMI_NA10851_SNP_1294992fwd/C/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc12/17/1012/17/10138Genomicunknown
ss293492151PJP|SNP_2998509_chr5_149472648fwd/C/Tggaggcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgccgtttc01/21/1101/21/11134Genomicunknown
ss479580662ILLUMINA|HumanOmni2.5-4v1_B_rs11740298-128_T_R_1768930693fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc01/30/1210/28/16137Genomicunknown
ss479584987ILLUMINA|HumanOmniExpress-12v1_C_rs11740298-131_T_R_1857319189fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc01/30/1210/27/16137Genomicunknown
ss480063597ILLUMINA|HumanOmni1-Quad_v1-0_C_rs11740298-131_T_R_1865594050fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc01/30/1208/28/15146Genomicunknown
ss484589085ILLUMINA|HumanOmni2.5-4v1_D_rs11740298-131_T_R_1857319189fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc01/30/1210/28/16137Genomicunknown
ss558791398TISHKOFF|snp_chr5_149492455fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc11/22/1211/23/12138Genomicunknown
ss652695298SSMP|5_149492455fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc12/14/1202/11/15138Genomicunknown
ss782741326ILLUMINA|HumanOmni2.5-4v1_H_rs11740298-131_T_R_1857319189fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc05/30/1307/28/15146Genomicunknown
ss831993258ILLUMINA|HumanOmniExpress-12v1_H_rs11740298-131_T_R_1857319189fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc09/17/1306/18/15146Genomicunknown
ss982253790EVA-GONL|EVA-GONL_rs11740298fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc04/23/1404/24/14142Genomicunknown
ss1073137412JMKIDD_LAB|HGDP_WGS_chr5_149492455fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc07/10/1407/11/14142Genomicunknown
ss13177295011000GENOMES|PHASE3_V1_29579786fwd/C/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc08/16/1408/16/14142Genomicunknown
ss1581399952EVA_GENOME_DK|EVA_GENOME_DK_snv_rs11740298fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc02/19/1502/20/15144Genomicunknown
ss1591786567EVA_DECODE|EVA_DECODE_5_149472648_1117272_rs11740298fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc03/02/1503/03/15144Genomicunknown
ss1614287886EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_5_149492455_16373372fwd/C/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc03/04/1503/04/15144Genomicunknown
ss1657281919EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_5_149492455_16373372fwd/C/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc03/04/1503/04/15144Genomicunknown
ss1712809985EVA_SVP|EVA_SVP_504352fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc03/12/1503/12/15144Genomicunknown
ss1752556015ILLUMINA|OmniExpressExome-8v1-1_B_rs11740298-131_T_R_1889524915fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc05/27/1506/09/15146Genomicunknown
ss1925507726WEILL_CORNELL_DGM|SNV:chr5:149492455fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc10/16/1510/17/15147Genomicunknown
ss1958834028ILLUMINA|rs11740298-138_T_R_2276339750fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc11/13/1511/13/15147Genomicunknown
ss2023361686JJLAB|SNP3864241fwd/BC/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc08/29/1608/30/16149Genomicunknown
ss2151520221USC_VALOUEV|NC_000005.9:g.149492455C>Tfwd/C/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc11/17/1611/17/16150Genomicunknown
ss2279232005HUMAN_LONGEVITY|HLI-5-150112892-C-Tfwd/C/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc11/18/1611/18/16150Genomicunknown
ss2447550836TOPMED|5_149492455_C/Tfwd/C/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc11/20/1611/20/16150Genomicunknown
ss2634356053ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs11740298-131_T_R_1889524fwd/C/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc02/02/1702/02/17151Genomicunknown
ss2635150310ILLUMINA|Cancer_BeadChip_11459870_A_rs11740298-128_T_R_1768930693fwd/C/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc02/02/1702/02/17151Genomicunknown
ss2707089948GRF|rs11740298fwd/C/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc02/13/1702/13/17151Genomicunknown
ss2832248535GNOMAD|rs11740298fwd/C/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc05/18/1705/18/17151Genomicunknown
ss2997996977SWEGEN|NC_000005.9:g.149492455C>Tfwd/C/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc05/30/1705/30/17151Genomicunknown
ss3022542253ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs11740298-138_T_R_2276339750fwd/C/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc06/28/1706/28/17151Genomicunknown
ss3025462669BIOINF_KMB_FNS_UNIBA|5.150112892C>Tfwd/C/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc07/05/1707/05/17151Genomicunknown
ss3346682727CSHL|rs11740298fwd/C/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc10/02/1710/02/17151Genomicunknown
ss3482057643TOPMED|TOPMed_freeze_5?chr5:150,112,892fwd/C/Tcctgtggttccaaaatgaggtccttccgcacccactcaaatgaagatgcc10/04/1710/04/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs11740298|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 GTAGTCAGAT TTTTATCAAC CTTTGTCTTA GTGTGGCATC TAGCTCCATT TATCCCTGGG
 GAAACTGAGG CCTGATGTGG TGTAATCCAC TCAAGTTCCC ATAAGGAGCA GGCCTGAGAC
 ACAGGGAGCT GAGATCTTCT GACCTCCAGA CAGAGGCTTT TGCACCAGCA AAGATAATCC
 CTGTCTGGAA TGTGGGCTAG TTATTTTCTT TACAAGGCAG ATCCGGGTAT CACCTCATTC
 AACTCCTGCC ACAGCTAGAA GAGAAGTCAC AGGCTCTGGG TGTTTTCTGA AGCCAGGATC
 CCTGGGATGG TGGGCTTTGT ATGGCCAGGC CTTATAGCCG TCGGGTATTT TCCCTGGTGT
 GGCTCAGCTG CCCCTGAGTT GGCGGCTGGG CCTGTGAGTC AGAGCTGTCC CATGGCTCCA
 TTCTTTTCCC CACTTGAAGC CACAGCCCCA GACTCCTGGA GGCAGTCCAG GGAGGCCTGT
 GGTTCCAAAA TGAGGTCCTT
 Y
 CCGCACCCAC TCAAATGAAG ATGCCGTTTC CCCAGCTCAG AGAGAGCAAG GGAGGGGCTA
 AGGACACACA GTGATGGATC TGAGGCTGAC ATCTGGTCCA CCTCAAGTGA GCCAAGTACA
 GGACTCTGGG CCCAGGTGGG AGGGCCCTAG CACTCTGTCC CCTGCCCCCA GCAACCCTAT
 TGCCCCTGGC CCTGTGTTGC TGCCGGGGTC CCACAGGCCT GGGCTCGGCA GGAGAGCCTA
 TGACTCATGC CGGCCCCACA ACCCCTGAGA TGCTGCAGCC GTGAGGGGTC TGGGTCCTGC
 CAGGTCTACA CCTCTCTGCC CTCAAAGCCA CAGCCTGGTC GCCACCCTAT TCCCTCCCCT
 GTCCTTACCC TGGCCGCAGT TCCCTCCGCT TCCTCTCTTC CTCTTCCTCT TCCTCTTCTC
 TCTTCTCCAC CTTCTCCTCA CTTCGTGCTC TCACGCTTTT GGACACTCTG TCTGCCCTTC
 TCCTACCTGG GGCCTGATCA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_029289 ABBA01026285
dbSNP Blast Analysis

  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
ss1317729501EAS 1008AF 0.894799950.10520000
EUR 1006AF 0.704800010.29519999
AFR 1322AF 0.972000000.02800000
AMR 694AF 0.770899950.22910000
SAS 978AF 0.734200000.26580000
ss142532303ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss162763392CEUEuropean 2IG 1.00000000 1.00000000
ss222033726pilot_1_YRI_low_coverage_panel 118AF 0.957627120.04237288
ss233195982pilot_1_CEU_low_coverage_panel 120AF 0.574999990.42500001
ss240309166pilot_1_CHB+JPT_low_coverage_panel 120AF 0.941666660.05833333
ss68953554HapMap-CEUEuropean 120IG0.349999990.516666650.133333340.527089000.608333350.39166668
HapMap-HCBAsian 90IG0.866666670.13333334 1.000000000.933333340.06666667
HapMap-JPTAsian 90IG0.866666670.13333334 1.000000000.933333340.06666667
HapMap-YRISub-Saharan African 120IG0.916666690.08333334 1.000000000.958333310.04166667
ss98775855HapMap-CEUEuropean 222IG0.378378390.477477490.144144151.000000000.617117110.38288289
HapMap-HCBAsian 84IG0.857142870.14285715 1.000000000.928571400.07142857
HapMap-JPTAsian 168IG0.833333310.16666667 0.751830000.916666690.08333334
HapMap-YRISub-Saharan African 224IG0.910714270.08928572 1.000000000.955357130.04464286
J. Craig Venter 2IG 1.00000000 0.500000000.50000000
HAPMAP-ASW 98IG0.877551020.12244898 1.000000000.938775540.06122449
HAPMAP-CHBAsian 82IG0.853658560.121951220.024390240.200325000.914634170.08536585
HAPMAP-CHD 170IG0.741176490.235294120.023529411.000000000.858823540.14117648
HAPMAP-GIH 176IG0.522727250.409090910.068181821.000000000.727272750.27272728
HAPMAP-LWK 178IG0.988764050.01123596 1.000000000.994382020.00561798
HAPMAP-MEX 100IG0.579999980.360000010.060000001.000000000.759999990.23999999
HAPMAP-MKK 284IG0.922535240.07746479 1.000000000.961267590.03873239
HAPMAP-TSI 174IG0.482758610.459770110.057471260.254213000.712643680.28735632

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.284+/-0.2480000ALFRED: 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
byClusterbyFreqwithHapMapFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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