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Reference SNP (refSNP) Cluster Report: rs16940342                 ** With Benign allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:123/149
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwithHapMapFreqWith1000GenomeData
Citation:PubMed
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:A:germline
C:germline
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:With Benign allele [ClinVar]
MAF/MinorAlleleCount:G=0.1999/1001 (1000 Genomes)
HGVS Names
  • NC_000016.10:g.23633265A>G
  • NC_000016.9:g.23644586A>G
  • NG_007406.1:g.13093T>C
  • NM_024675.3:c.1684+1597T>C
  • XM_005255578.1:c.1684+1597T>C
  • XM_011545946.2:c.1690+1597T>C
  • XM_011545947.2:c.1690+1597T>C
  • XM_011545948.2:c.799+1597T>C
  • XM_017023671.1:c.1690+1597T>C
  • XM_017023672.1:c.1684+1597T>C
  • XM_017023673.1:c.1684+1597T>C
  • XR_243309.1:n.1884+1597T>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 ss282475772 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs16940342 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
ss23965509PERLEGEN|afd3704097byFreqfwd/TA/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa08/10/0409/13/04123Genomicunknown
ss69341621PERLEGEN|PGP03704097byFreqfwd/TA/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa01/30/0703/31/08127Genomicunknown
ss75050298ILLUMINA|ILMN_Human_1M_rs16940342fwd/TA/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa08/28/0708/29/07129Genomicunknown
ss90348755BCMHGSC_JDW|JWB-0931503byFreqfwd/TA/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa02/26/0809/05/14129Genomicunknown
ss103286658BGI|BGI_rs16940342fwd/TA/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa06/06/0806/18/09131Genomicunknown
ss1092624481000GENOMES|CEU.trio.12.15.2008_3273486_chr16_23552087fwd/TA/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa12/16/0812/16/08130Genomicunknown
ss119855061KRIBB_YJKIM|KHS1880331fwd/TA/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa02/04/0902/05/09131Genomicunknown
ss136634199ENSEMBL|ENSSNP11091550fwd/TA/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa05/11/0905/15/09131Genomicunknown
ss157198990GMI|GMI_SNP_39766245fwd/TA/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa06/24/0906/25/09131Genomicunknown
ss160399978ILLUMINA|HumanOmni1-Quad_v1-0_B_rs16940342-128_T_F_1513994108fwd/TA/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa08/04/0910/02/09131Genomicunknown
ss172670720ILLUMINA|Human1M-Duov3_B_rs16940342-128_T_F_1513994108fwd/TA/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa10/01/0910/02/09132Genomicunknown
ss201554788BUSHMAN|BUSHMAN-chr16-23552086fwd/TA/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa02/16/1003/07/10132Genomicunknown
ss2116988071000GENOMES|YRI.trio.3.2010_1309485_chr16_23552087fwd/TA/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa03/29/1003/30/10132Genomicunknown
ss2271907941000GENOMES|pilot_1_YRI_9000477_chr16_23552087fwd/A/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa04/22/1004/22/10132Genomicunknown
ss2369882091000GENOMES|pilot_1_CEU_6592838_chr16_23552087fwd/A/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa05/01/1005/01/10132Genomicunknown
ss2433358291000GENOMES|pilot_1_CHB+JPT_5220906_chr16_23552087fwd/A/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa05/01/1005/01/10132Genomicunknown
ss255584168BL|SNP32806_16_23552087fwd/TA/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa08/20/1008/20/10134Genomicunknown
ss282475772GMI|GMI_AK_SNP_6796173fwd/A/Gcttatagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgcacataa12/16/1012/16/10137Genomicunknown
ss469105180MTISCHKOWITZ|NM_024675.3:c.1684+1597A>Grev/TA/Gttatgtgcaaaaataggtagcaggctgctcgtaccattggacatggacttggtctataag08/05/1108/19/11135Genomicunknown
ss480113276ILLUMINA|HumanOmni2.5-4v1_B_rs16940342-128_T_F_1768187613fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca01/30/1210/28/16137Genomicunknown
ss480122188ILLUMINA|HumanOmniExpress-12v1_C_rs16940342-131_T_F_1854056145fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca01/30/1210/27/16137Genomicunknown
ss480816842ILLUMINA|HumanOmni1-Quad_v1-0_C_rs16940342-131_T_F_1865453701fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca01/30/1208/28/15146Genomicunknown
ss484854506ILLUMINA|HumanOmni2.5-4v1_D_rs16940342-131_T_F_1854056145fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca01/30/1210/27/16137Genomicunknown
ss536922416ILLUMINA|HumanOmni5-4v1_B_rs16940342-131_T_F_1866537715fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca06/22/1208/29/15146Genomicunknown
ss564840967TISHKOFF|snp_chr16_23644586fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca11/22/1211/23/12138Genomicunknown
ss660592755SSMP|16_23644586fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca12/14/1202/13/15138Genomicunknown
ss778821607ILLUMINA|HumanOmni25Exome-8v1_A_rs16940342-131_T_F_1866537715fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca05/30/1307/10/15142Genomicunknown
ss782873761ILLUMINA|HumanOmni2.5-4v1_H_rs16940342-131_T_F_1854056145fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca05/30/1307/29/15142Genomicunknown
ss783837747ILLUMINA|HumanOmniExpressExome-8v1_A_rs16940342-131_T_F_1967891248fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca05/31/1306/19/15142Genomicunknown
ss832127961ILLUMINA|HumanOmniExpress-12v1_H_rs16940342-131_T_F_1854056145fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca09/17/1306/18/15144Genomicunknown
ss834281958ILLUMINA|HumanOmni2.5-8v1_A_rs16940342-131_T_F_1866537715fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca09/18/1307/29/15142Genomicunknown
ss992382775EVA-GONL|EVA-GONL_rs16940342fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca04/23/1404/30/14142Genomicunknown
ss1080555188JMKIDD_LAB|HGDP_WGS_chr16_23644586fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca07/10/1407/12/14142Genomicunknown
ss13557792211000GENOMES|PHASE3_V1_69201136fwd/A/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca08/16/1408/16/14142Genomicunknown
ss1397713025HAMMER_LAB|HAMMER_LAB_rs16940342fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca09/30/1409/30/14146Genomicunknown
ss1427808190DDI|DDI_rs16940342fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca11/04/1411/04/14144Genomicunknown
ss1577875768EVA_GENOME_DK|EVA_GENOME_DK_snv_rs16940342fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca02/19/1502/19/15144Genomicunknown
ss1634205577EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_16_23644586_38259892fwd/A/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca03/04/1503/04/15144Genomicunknown
ss1677199610EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_16_23644586_38259892fwd/A/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca03/04/1503/04/15144Genomicunknown
ss1696417119EVA_DECODE|EVA_DECODE_16_23552087_211407_rs16940342fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca03/02/1503/04/15144Genomicunknown
ss1713532606EVA_SVP|EVA_SVP_1226973fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca03/12/1503/12/15144Genomicunknown
ss1752187074ILLUMINA|OmniExpressExome-8v1-1_B_rs16940342-131_T_F_1967891248fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca05/27/1506/09/15146Genomicunknown
ss1808466070HAMMER_LAB|Hsieh_7492217fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca07/15/1507/16/15146Genomicunknown
ss1935805663WEILL_CORNELL_DGM|SNV:chr16:23644586fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca10/16/1510/19/15147Genomicunknown
ss1968241079GENOMED|rs16940342fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca02/16/1602/16/16147Genomicunknown
ss2028689873JJLAB|SNP9192428fwd/TA/Gagaccaagtccatgtccaatggtacgagcagcctgctacctatttttgca08/29/1608/31/16149Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs16940342|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=149
 ATGTAGCTGC AGTTTACTAC AATTATAGCA GACTATTTCA AACTACTGGC TGGGCCTGGT
 GGCTCACGCC TGTAATCCCA GCACTTTGGG AGGCCGAGGT GGGTAGATCA CCTGAGGTCA
 GGAGATAGAG ACCAGCCTGG CCAACATGGC AAAAACCCAT CTCTACTGAA AATATAAAAA
 TTAGCTGGGT GTGGTGGTGG GCACCTGTAA TCTCAGCTAC TCAGGGGGCT GAGGTGGGAG
 AATCGCTTGA ACCTGGGAGG CAGAGGTTGC AGTGAGCTGA GATAGCGCCA CTGCACCCTA
 TCCGGGGCGA CAAGGGTGAA ACTGTCTCAA CAACAATAAA AAAAAACTAC TGTGTAAAAA
 ACAGTATTTC TAGATTACTG GATTGCCTAC TTTTTGATGA CTTTGTATCC TTGTTCGCTT
 AAAAGATGAT GAAAAGTCAC AATTATTATT TTTGGATTAA TTAGTCACAG CTTATAGACC
 AAGTCCATGT CCAATGGTAC
 R
 GAGCAGCCTG CTACCTATTT TTGCACATAA AGTTGTTTTT TTGTTTTAGG AACTTGGCTG
 TAAAGTGCAT ATAAAGGTGC GTTGGAACAC AGTCACAGTT ACAAGTTGAC TGGCTGCTCT
 GGCACATAGC TGAGTAGTTG AGACAGACAG AACACAAAGA CTAAAATCTG TGCTATCTGG
 CCCATTCTAG AAAGTATGCT GATCCCTAGT TTAGAGCCAC AATGAATTAC CCAGATTTTG
 TGCTTAGTTC ATCAGATATG ATTAAATTCT CAGTAAATGA ATTGAAAGTT TAAATTACAA
 TGTATCGTTG CTGCCCATCC TCCAAAATTC TGTGTCCCTT GGAGGCCTTA GAGACACTGC
 ATTAGATATT TTATCCAAAA AAGTTGCTTA GGCCTTTTCA TTACATGATG ACTTCTAAAA
 GAGATAGTCA GTGGAGTCTT AGTCTTGTTT TTTTTTGAGA GAGGGTTTTG CTCTATCACC
 CAGACTGGAG TGCAGTGGTG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000016.8
dbSNP Blast Analysis
OMIM
114480

  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.
SourceA
A/A
A/G
G
G/G
HWPA
G
ss1355779221EAS 1008AF 0.827400030.17260000
EUR 1006AF 0.859799980.14020000
AFR 1322AF 0.760999980.23900001
AMR 694AF 0.763700010.23630001
SAS 978AF 0.789399980.21060000
ss136634199ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss201554788BUSHMAN_POP2 2IG 1.00000000 0.500000000.50000000
ss227190794pilot_1_YRI_low_coverage_panel 118AF 0.762711880.23728813
ss236988209pilot_1_CEU_low_coverage_panel 120AF 0.908333360.09166667
ss23965509AFD_EUR_PANELEuropean 48IG 0.875000000.12500000 1.000000000.937500000.06250000
AFD_AFR_PANELAfrican American 46IG 0.739130440.26086956 0.751830000.869565190.13043478
AFD_CHN_PANELAsian 48IG 0.458333340.50000000 0.041666670.317310000.708333310.29166666
CHMJAsian 74IG0.78378379 0.21621622 0.783783790.21621622
ss243335829pilot_1_CHB+JPT_low_coverage_panel 120AF 0.824999990.17500000
ss69341621HapMap-CEUEuropean 120IG 0.816666660.16666667 0.016666670.583882000.899999980.10000000
HapMap-HCBAsian 90IG 0.622222240.28888890 0.088888890.200325000.766666650.23333333
HapMap-JPTAsian 90IG 0.644444470.31111112 0.044444451.000000000.800000010.20000000
HapMap-YRISub-Saharan African 120IG 0.683333340.28333333 0.033333341.000000000.824999990.17500000
ss90348755HapMap-CEUEuropean 226IG 0.796460150.19469027 0.008849561.000000000.893805330.10619469
HapMap-HCBAsian 86IG 0.627906980.27906978 0.093023260.200325000.767441870.23255815
HapMap-JPTAsian 172IG 0.662790720.31395349 0.023255810.583882000.819767420.18023255
HapMap-YRISub-Saharan African 226IG 0.628318610.29203540 0.079646020.099721000.774336280.22566372
HAPMAP-ASW 98IG 0.673469360.26530612 0.061224490.294266000.806122420.19387755
HAPMAP-CHBAsian 82IG 0.414634140.53658539 0.048780490.150222000.682926830.31707317
HAPMAP-CHD 170IG 0.611764730.36470589 0.023529410.294266000.794117630.20588236
HAPMAP-GIH 176IG 0.670454560.27272728 0.056818180.250592000.806818190.19318181
HAPMAP-LWK 180IG 0.577777800.36666667 0.055555561.000000000.761111140.23888889
HAPMAP-MEX 100IG 0.639999990.31999999 0.040000001.000000000.800000010.20000000
HAPMAP-MKK 286IG 0.405594410.48251748 0.111888110.527089000.646853150.35314685
HAPMAP-TSI 176IG 0.818181810.17045455 0.011363641.000000000.903409060.09659091
ENSEMBL_Venter 2IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.320+/-0.240126710562760

  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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