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Reference SNP (refSNP) Cluster Report: rs11642015                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwithHapMapFreqWith1000GenomeData
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=0.2284/1144 (1000 Genomes)
T=0.2897/36381 (TOPMED)
HGVS Names
  • CM000678.2:g.53768582C>T
  • NC_000016.10:g.53768582C>T
  • NC_000016.9:g.53802494C>T
  • NG_012969.1:g.69620C>T
  • NM_001080432.2:c.46-41558C>T
  • XR_001751980.1:n.232-41558C>T
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 ss287077117 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11642015 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
ss16703696CSHL-HAPMAP|CSHL-HuAA-200402.chr16.NT_010498.14_2526412fwd/BC/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg02/17/0403/04/04120Genomicunknown
ss24411330PERLEGEN|afd3713463byFreqfwd/BC/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg08/10/0409/13/04123Genomicunknown
ss43905324ABI|hCV2031268fwd/BC/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg07/18/0507/18/05126Genomicunknown
ss77712468HGSV|Cor12156_SNV_20070510.chr16_52359995fwd/BC/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg10/09/0710/14/07129Genomicunknown
ss90396614BCMHGSC_JDW|JWB-0947035fwd/BC/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg02/26/0802/29/08129Genomicunknown
ss103295254BGI|BGI_rs11642015fwd/BC/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg06/06/0806/18/09131Genomicunknown
ss1093311231000GENOMES|CEU.trio.12.15.2008_3291754_chr16_52359995fwd/BC/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg12/16/0812/16/08130Genomicunknown
ss120252547WTCCC|NT_010498.15_7416693_CEPHfwd/BC/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg04/10/0904/10/09131Genomicunknown
ss136729313ENSEMBL|ENSSNP6455158fwd/BC/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg05/11/0905/15/09131Genomicunknown
ss161781796ENSEMBL|ENSSNP1224308fwd/BC/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg09/24/0909/25/09131Genomicunknown
ss168226139COMPLETE_GENOMICS|NA07022_36_chr16_52359995fwd/BC/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg09/30/0909/30/09132Genomicunknown
ss171258478COMPLETE_GENOMICS|NA20431_36_chr16_52359995fwd/BC/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg10/01/0910/01/09132Genomicunknown
ss207634277BCM-HGSC-SUB|BCM_CMT_1011-2843996fwd/BC/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg03/15/1003/19/10132Genomicunknown
ss2272476321000GENOMES|pilot_1_YRI_9057315_chr16_52359995fwd/C/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg04/22/1004/22/10132Genomicunknown
ss230384193WTCCC|NT_010498.15_7416693_3Tfwd/BC/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg04/30/1004/30/10132Genomicunknown
ss2370289871000GENOMES|pilot_1_CEU_6633616_chr16_52359995fwd/C/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg05/01/1005/01/10132Genomicunknown
ss2433672311000GENOMES|pilot_1_CHB+JPT_5252308_chr16_52359995fwd/C/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg05/01/1005/01/10132Genomicunknown
ss255709893BL|SNP57938_16_52359995fwd/BC/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg08/20/1008/20/10134Genomicunknown
ss287077117GMI|GMI_NA10851_SNP_3089908fwd/C/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg12/17/1012/17/10138Genomicunknown
ss410816889ILLUMINA|Cardio-Metabo_Chip_11395247_A_chr16_52359995rev/TA/Gcctatccatcccaccaaggtcctgctacacgagttgcccctttgtgcatcaaaagggaaa06/07/1106/07/11135Genomicunknown
ss411630473BROAD_NHGRI_T2D|T2D_targeted_CEU_rs11642015fwd/BC/Ttttcccttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatggatagg06/17/1106/17/11147Genomicunknown
ss564906389TISHKOFF|snp_chr16_53802494fwd/BC/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg11/22/1211/23/12138Genomicunknown
ss660678239SSMP|16_53802494fwd/BC/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg12/14/1202/14/15138Genomicunknown
ss992500100EVA-GONL|EVA-GONL_rs11642015fwd/BC/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg04/23/1404/30/14142Genomicunknown
ss1080630523JMKIDD_LAB|HGDP_WGS_chr16_53802494fwd/BC/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg07/10/1407/12/14142Genomicunknown
ss13562930941000GENOMES|PHASE3_V1_69733380fwd/C/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg08/16/1408/16/14142Genomicunknown
ss1427850431DDI|DDI_rs11642015fwd/BC/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg11/04/1411/04/14144Genomicunknown
ss1577917880EVA_GENOME_DK|EVA_GENOME_DK_snv_rs11642015fwd/BC/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg02/19/1502/19/15144Genomicunknown
ss1634446359EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_16_53802494_38524997fwd/C/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg03/04/1503/04/15144Genomicunknown
ss1677440392EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_16_53802494_38524997fwd/C/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg03/04/1503/04/15144Genomicunknown
ss1696534469EVA_DECODE|EVA_DECODE_16_52359995_328759_rs11642015fwd/BC/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg03/02/1503/04/15144Genomicunknown
ss1935936090WEILL_CORNELL_DGM|SNV:chr16:53802494fwd/BC/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg10/16/1510/19/15147Genomicunknown
ss1959679139ILLUMINA|16:53802494-C-T-0_T_R_2304225842fwd/BC/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg11/13/1511/13/15147Genomicunknown
ss2028750112JJLAB|SNP9252667fwd/BC/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg08/29/1608/31/16149Genomicunknown
ss2157186395USC_VALOUEV|NC_000016.9:g.53802494C>Tfwd/C/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg11/17/1611/17/16150Genomicunknown
ss2212256777HUMAN_LONGEVITY|HLI-16-53768582-C-Tfwd/C/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg11/18/1611/18/16150Genomicunknown
ss2377185886TOPMED|16_53802494_C/Tfwd/C/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg11/19/1611/19/16150Genomicunknown
ss2701709712GRF|rs11642015fwd/C/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg02/13/1702/13/17151Genomicunknown
ss2710833103ILLUMINA|Consortium-OncoArray_15047405_A_chr16_53802494_C_T-100_B_F_21989fwd/C/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg03/22/1703/22/17151Genomicunknown
ss2943151863GNOMAD|rs11642015fwd/C/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg05/23/1705/23/17151Genomicunknown
ss3014532453SWEGEN|NC_000016.9:g.53802494C>Tfwd/C/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg05/30/1705/30/17151Genomicunknown
ss3021706697ILLUMINA|MEGA_Consortium_v2_15070954_A2_16:53802494-C-T-0_T_R_2304225842fwd/C/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg06/28/1706/28/17151Genomicunknown
ss3028193543BIOINF_KMB_FNS_UNIBA|16.53768582C>Tfwd/C/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg07/05/1707/05/17151Genomicunknown
ss3246853303TOPMED|TOPMed_freeze_5?chr16:53,768,582fwd/C/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg10/01/1710/01/17151Genomicunknown
ss3351456665CSHL|rs11642015fwd/C/Tcttttgatgcacaaaggggcaactcgtgtagcaggaccttggtgggatgg10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs11642015|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 GGCCTGGGCA CAAGTATGAT ATTTAAGTAG ATGCTTAGTG ACTGATTGAT GTCTCCAAAC
 ATTTGGGATT TCCTTCCACA TTTGCCATAG CACAGCTTGT TTTATGTCTT TTCTAAAATG
 GTCTAGGTAC CTGACATCCT TTGATCCTTC ATATGGTTAC ACTCAAAAGG AGCCATATGA
 ATTTTGACCA TTTGCACATC TGCCTGTCTT TTTGGTTAGC TGCCAGATAG AGCTCAGGTT
 TTAAATCCTT TGCAGTTAAA AGAGATAATA AATGTTAACA TTCCTAGTAC AGTGCCTGGC
 ACAGAATGTG TAAATATCAT TTGATTCGGA AACATGACTG CTGGTCAATT CGGCCTCCAG
 GGAGACAAAA CTAAGGGGTG GGGTTGTGGC TTTTTTTGAG GTAGGGGATG GAATAGATAT
 TTCTTACCCG AGTAGAAGAT GATGCCGGGG GATCTAATGC TTCTTTTAAA TTTCCCTTTT
 GATGCACAAA GGGGCAACTC
 Y
 GTGTAGCAGG ACCTTGGTGG GATGGATAGG CAGCTTTGTA AGTGGAGAAA TGGCCTCTGT
 TTAGCTTATG AGCACAGAGT CATTTTGGGG GTGGTTTATG AGTCATCTGA AATATGCATT
 TAATCTAGAT TTGTGGCCTG CTTGGTGAGG CTGCTGCTTT TTTATGATCT CAAGTGTCTT
 GTCCATGTCA AAACTTGCCT TGTTTTTTTG TTTACTTTGA ATCAGAAAAA TGTTCACAAC
 CACCCTTGGA ATTCCTCCTC AAGTGTGCGT TTGGTCACAT CACCCCTGGC TACCACCAGT
 ACATGACTGT TTATTTTGGA TGTCCTTTTC TGATGTTCAG CTAATTTAAC CCACAATGAA
 GTTAATCCTT GCTTCTTTGG AAAAGTACAG ATTTACTTAT TAGCTGCCTT CCAGAGACAT
 TTGCATTTTC ATGAAAGCGA GTATATAATT ACATTGACTT TTGGACTCAT CTACCCACAT
 ATGTGGTGGG CGCCTTTTGA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010498.15
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
ss120252547ENSEMBL_Venter 2IG1.00000000 1.00000000
ss1356293094EAS 1008AF 0.832299950.16769999
EUR 1006AF 0.567600010.43239999
AFR 1322AF 0.944000010.05600000
AMR 694AF 0.760799940.23920001
SAS 978AF 0.693300010.30670002
ss136729313ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss161781796ENSEMBL_celera 2IG 1.00000000 1.00000000
ss168226139CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss171258478PGP 2IG 1.00000000 0.500000000.50000000
ss227247632pilot_1_YRI_low_coverage_panel 118AF 0.957627120.04237288
ss237028987pilot_1_CEU_low_coverage_panel 120AF 0.541666690.45833334
ss243367231pilot_1_CHB+JPT_low_coverage_panel 120AF 0.850000020.15000001
ss24411330AFD_EUR_PANELEuropean 48IG0.333333340.583333310.083333340.250592000.625000000.37500000
AFD_AFR_PANELAfrican American 46IG0.826086940.17391305 1.000000000.913043500.08695652
AFD_CHN_PANELAsian 48IG0.708333310.250000000.041666670.654721000.833333310.16666667

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.353+/-0.2280000

  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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