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Reference SNP (refSNP) Cluster Report: rs16147                 **Clinical Channel**
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:54/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqbySubmitterwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (REV)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.4830/2419 (1000 Genomes)
C=0.4894/61452 (TOPMED)
HGVS Names
  • CM000669.2:g.24283791T>C
  • NC_000007.13:g.24323410T>C
  • NC_000007.14:g.24283791T>C
  • NG_016148.1:g.4604T>C
  • NM_000905.3:c.-485T>C
  • XR_001745121.1:n.473+35566A>G
  • XR_001745122.1:n.345-86762A>G
  • XR_001745123.1:n.473+35566A>G
  • XR_001745124.1:n.473+35566A>G
  • XR_001745125.1:n.473+35566A>G
  • XR_001745126.1:n.473+35566A>G
  • XR_001745127.1:n.345-28092A>G
  • XR_001745129.1:n.473+35566A>G
  • XR_001745130.1:n.473+35566A>G
  • XR_001745131.1:n.473+35566A>G
  • XR_001745132.1:n.473+35566A>G
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 ss279227313 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs16147 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
ss18571ACEVAN|CHAK01126fwd/TA/Ggattcttgtctcctgccaacaggactaccacccactgggtgccggagtaggaagcacctg09/09/9912/23/0354Genomicunknown
ss129179TSC-CSHL|TSC0102148byFreqfwd/TA/Ggattcttgtctcctgccaacaggactaccacccactgggtgccggagtaggaagcacctg09/06/0004/07/0486Genomic95 %
ss4253015ACEVAN|ABACUS89fwd/TA/Ggattcttgtctcctgccaacaggactaccacccactgggtgccggagtaggaagcacctg11/07/0110/10/03102Genomicunknown
ss5585343TSC-CSHL|TSC0319257byFreqfwd/TA/Ggattcttgtctcctgccaacaggactaccacccactgggtgccggagtaggaagcacctg09/21/0208/05/04108Genomicunknown
ss13447573SC_SNP|NT_007819.13_23617018rev/BC/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc10/23/0310/31/03120Genomicunknown
ss24434036PERLEGEN|afd0535752byFreqrev/BC/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc08/10/0409/13/04123Genomicunknown
ss44783552ABI|hCV2267279rev/BC/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc07/19/0507/19/05126Genomicunknown
ss51854374STEJUSTINE-REGGEN|631_-471fwd/TA/Ggattcttgtctcctgccaacaggactaccacccactgggtgccggagtaggaagcacctg02/16/0602/16/06126Genomicunknown
ss75057317ILLUMINA|ILMN_Human_1M_rs16147fwd/TA/Ggattcttgtctcctgccaacaggactaccacccactgggtgccggagtaggaagcacctg08/28/0708/29/07129Genomicunknown
ss83126754HGSV|Cor18555_SNV_20070510.chr7_24096650rev/BC/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc11/27/0712/04/07130Genomicunknown
ss93645676BCMHGSC_JDW|JWB-2284706rev/BC/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc02/26/0803/04/08129Genomicunknown
ss104409830BGI|BGI_rs16147rev/BC/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc06/08/0806/17/09131Genomicunknown
ss1116834861000GENOMES|CEU.trio.12.15.2008_1722673_chr7_24289935rev/BC/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc12/17/0812/17/08130Genomicunknown
ss1134716371000GENOMES|NA19240_2008_12_16_1550594_chr7_24289935rev/BC/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc12/18/0812/18/08130Genomicunknown
ss119339716KRIBB_YJKIM|KHS1501963fwd/TA/Ggattcttgtctcctgccaacaggactaccacccactgggtgccggagtaggaagcacctg02/04/0902/04/09131Genomicunknown
ss142756870ENSEMBL|ENSSNP6112858rev/BC/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc06/05/0906/05/09131Genomicunknown
ss158145538GMI|GMI_SNP_48298763rev/BC/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc06/24/0906/25/09131Genomicunknown
ss160378891ILLUMINA|HumanOmni1-Quad_v1-0_B_rs16147-128_T_F_1514031819fwd/TA/Ggattcttgtctcctgccaacaggactaccacccactgggtgccggagtaggaagcacctg08/04/0910/02/09131Genomicunknown
ss162138891COMPLETE_GENOMICS|NA07022_36_chr7_24289935rev/BC/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc09/28/0909/28/09132Genomicunknown
ss163839736COMPLETE_GENOMICS|NA19240_36_chr7_24289935rev/BC/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc09/29/0909/29/09132Genomicunknown
ss166287421COMPLETE_GENOMICS|NA20431_36_chr7_24289935rev/BC/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc09/30/0909/30/09132Genomicunknown
ss203083472BUSHMAN|BUSHMAN-chr7-24289934rev/BC/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc02/16/1003/09/10132Genomicunknown
ss208086442BCM-HGSC-SUB|BCM_CMT_1011-1494481rev/BC/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc03/15/1003/19/10132Genomicunknown
ss2229658231000GENOMES|pilot_1_YRI_4775506_chr7_24289935rev/C/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc04/22/1004/22/10132Genomicunknown
ss2338921711000GENOMES|pilot_1_CEU_3496800_chr7_24289935rev/C/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc05/01/1005/01/10132Genomicunknown
ss2408644321000GENOMES|pilot_1_CHB+JPT_2749509_chr7_24289935rev/C/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc05/01/1005/01/10132Genomicunknown
ss279227313GMI|GMI_AK_SNP_3547558rev/C/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc12/16/1012/16/10137Genomicunknown
ss294031488PJP|SNP_3537846_chr7_24289935rev/C/Tcaggtgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaagaatc01/21/1101/21/11134Genomicunknown
ss480053119ILLUMINA|HumanOmni2.5-4v1_B_rs16147-128_T_F_1735654615rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa01/30/1210/28/16137Genomicunknown
ss480061721ILLUMINA|HumanOmniExpress-12v1_C_rs16147-131_T_F_1853347052rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa01/30/1210/27/16137Genomicunknown
ss480732874ILLUMINA|HumanOmni1-Quad_v1-0_C_rs16147-131_T_F_1865335834rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa01/30/1208/28/15146Genomicunknown
ss484824480ILLUMINA|HumanOmni2.5-4v1_D_rs16147-131_T_F_1853347052rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa01/30/1210/28/16137Genomicunknown
ss536901568ILLUMINA|HumanOmni5-4v1_B_rs16147-131_T_F_1908823154rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa06/22/1208/29/15146Genomicunknown
ss559872479TISHKOFF|snp_chr7_24323410rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa11/22/1211/23/12138Genomicunknown
ss654225646SSMP|7_24323410rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa12/14/1202/11/15138Genomicunknown
ss778815227ILLUMINA|HumanOmni25Exome-8v1_A_rs16147-131_T_F_1865335834rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa05/30/1307/09/15146Genomicunknown
ss782858802ILLUMINA|HumanOmni2.5-4v1_H_rs16147-131_T_F_1853347052rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa05/30/1307/29/15146Genomicunknown
ss783823190ILLUMINA|HumanOmniExpressExome-8v1_A_rs16147-131_T_F_1908823154rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa05/31/1306/19/15146Genomicunknown
ss832112795ILLUMINA|HumanOmniExpress-12v1_H_rs16147-131_T_F_1853347052rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa09/17/1306/19/15146Genomicunknown
ss834275526ILLUMINA|HumanOmni2.5-8v1_A_rs16147-131_T_F_1865335834rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa09/18/1307/28/15146Genomicunknown
ss984058692EVA-GONL|EVA-GONL_rs16147rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa04/23/1404/24/14142Genomicunknown
ss1074447259JMKIDD_LAB|HGDP_WGS_chr7_24323410rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa07/10/1407/11/14142Genomicunknown
ss13243273891000GENOMES|PHASE3_V1_36460571rev/C/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa08/16/1408/16/14142Genomicunknown
ss1431059882DDI|DDI_rs16147rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa11/04/1411/05/14144Genomicunknown
ss1582114398EVA_GENOME_DK|EVA_GENOME_DK_snv_rs16147rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa02/19/1502/20/15144Genomicunknown
ss1593627472EVA_DECODE|EVA_DECODE_7_24289935_235653_rs16147rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa03/02/1503/03/15144Genomicunknown
ss1617783840EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_7_24323410_20218748rev/C/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa03/04/1503/04/15144Genomicunknown
ss1660777873EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_7_24323410_20218748rev/C/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa03/04/1503/04/15144Genomicunknown
ss1712939469EVA_SVP|EVA_SVP_633836rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa03/12/1503/12/15144Genomicunknown
ss1752679167ILLUMINA|OmniExpressExome-8v1-1_B_rs16147-131_T_F_1908823154rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa05/27/1506/09/15146Genomicunknown
ss1804914757HAMMER_LAB|Hsieh_3926890rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa07/15/1507/16/15146Genomicunknown
ss1927304002WEILL_CORNELL_DGM|SNV:chr7:24323410rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa10/16/1510/17/15147Genomicunknown
ss1958996001ILLUMINA|7:24323410-T-C-0_T_R_2304237870rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa11/13/1511/13/15147Genomicunknown
ss1970650345GENOMED|rs16147rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa02/16/1602/16/16147Genomicunknown
ss2024328647JJLAB|SNP4831202rev/BC/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa08/29/1608/30/16149Genomicunknown
ss2152524830USC_VALOUEV|NC_000007.13:g.24323410T>Crev/C/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa11/17/1611/17/16150Genomicunknown
ss2292487041HUMAN_LONGEVITY|HLI-7-24283791-T-Crev/C/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa11/18/1611/18/16150Genomicunknown
ss2461346667TOPMED|7_24323410_T/Crev/C/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa11/20/1611/20/16150Genomicunknown
ss2626653331SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV3083850rev/C/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa01/06/1701/06/17151Genomicunknown
ss2634580549ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs16147-131_T_F_1908823154rev/C/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa02/02/1702/02/17151Genomicunknown
ss2708181717GRF|rs16147rev/C/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa02/13/1702/13/17151Genomicunknown
ss2850876902GNOMAD|rs16147rev/C/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa05/19/1705/19/17151Genomicunknown
ss2986033747AFFY|Axiom_Smokesc1_Affx-30221200rev/C/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa05/24/1705/24/17151Genomicunknown
ss3000786601SWEGEN|NC_000007.13:g.24323410T>Crev/C/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa05/30/1705/30/17151Genomicunknown
ss3022717549ILLUMINA|MEGA_Consortium_v2_15070954_A2_7:24323410-T-C-0_T_R_2304237870rev/C/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa06/28/1706/28/17151Genomicunknown
ss3025958560BIOINF_KMB_FNS_UNIBA|7.24283791T>Crev/C/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa07/05/1707/05/17151Genomicunknown
ss3347485762CSHL|rs16147rev/C/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa10/02/1710/02/17151Genomicunknown
ss3525053010TOPMED|TOPMed_freeze_5?chr7:24,283,791rev/C/Tgcttcctactccggcacccagtgggtggtagtcctgttggcaggagacaa10/06/1710/06/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs16147|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 GGGTCGTAGC ACTCACGGTG GCTGGCGCGC GGGCGTGGCT GGGCGGCAAG TACTATGCTG
 TCGGGCGAGC GTCTCCGAGG GGTGAGAGCC AGCGGATGGG GTGCAGAGAG CGGGTCGCGA
 CAGGGCTTTT ATGGAGCTTC CTCGCCGCGG CAGGAGGGGC CTCGGGCAGT CACGCTTGGG
 TGACTCCCAC CCGCCACTTC CCGCCCCTGA GTGGCGGGGG GAGGGGGCTG GAACCGCAGC
 CGCACGAGTG TCGACTTAGG GAGCCACCCA CACCCCAACC CTCCCGCCCC AGGCACTGCC
 TGAAGAAGCG GGGCCTGGGA CCGCGTGAGC GAGGCAGCGC ACTCCGAGCG CGCTGGACAA
 CACCAAAGCC CAAGTATCTG CCCTCGGGCA GTGCCCGATC CCTGCTTTCC TTCTTTCCTT
 CTTTCCTTCA CGCCCCGTCT AGTCCTGCCA GAGATAGGAG CAGCCCAGAC GATTCTTGTC
 TCCTGCCAAC AGGACTACCA
 R
 CCCACTGGGT GCCGGAGTAG GAAGCACCTG AATCCTCTTT GTGGTGGGGC ATCTCCACGA
 CTAGCGCGGC ATCCTCGCCG GGCACAACTG CGCGCTGTTG GAGTGAGGCA ACTGGGCGCA
 CAGATTTTTC CTGTACTTAG AACAAGTCGG AGGCAGCTGC CGGAAGTCTC CGGCTAGAGG
 GTCCCAAAGC TGCGCTCCCC ACCCCACCCC CGCCCGTGGT TTCAGGGGCT TCTGCCCCTT
 CTCTCAGCTG GTTTTTCTAG ATCAGCCTTC CTCAAGTACT CGCTCAGACG CAGCGAGCCA
 GGCTCGGTCG AGACATGAGT GTGGCGACTC AAAATTCCCC AGAGGGGGAA CACGGTAAAC
 CTATTCCCCC AGTTTGCTGA AAAAGAGCCA CGCTTCCAGC TTCTAGAGAC TCTTTTAAGC
 TCAATTTTAA AAATATATAT TTTTTCTTTT TTGGTCCAAA GTGACGGTGG TTAAATGAAC
 AACAGTTTCT GTCTTATTTA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_007819
dbSNP Blast Analysis
OMIM
162640

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs16147 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss129179TSC_42_AA 84AF 0.699999990.30000001
TSC_42_C 84AF 0.509999990.49000001
TSC_42_A 78AF 0.259999990.74000001
ss1324327389EAS 1008AF 0.359100010.64090002
EUR 1006AF 0.493000000.50699997
AFR 1322AF 0.636900010.36309999
AMR 694AF 0.332899990.66710001
SAS 978AF 0.499000010.50099999
ss142756870ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss162138891CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss163839736YRISub-Saharan African 2IG 1.00000000 0.500000000.50000000
ss166287421PGP 2IG 1.00000000 1.00000000
ss203083472BUSHMAN_POP2 2IG 1.00000000 0.500000000.50000000
ss222965823pilot_1_YRI_low_coverage_panel 118AF 0.576271180.42372882
ss233892171pilot_1_CEU_low_coverage_panel 120AF 0.474999990.52499998
ss240864432pilot_1_CHB+JPT_low_coverage_panel 120AF 0.358333320.64166665
ss24434036AFD_EUR_PANELEuropean 48IG0.041666670.708333310.250000000.020022000.395833340.60416669
AFD_AFR_PANELAfrican American 46IG0.478260870.478260870.043478260.402784000.717391310.28260869
AFD_CHN_PANELAsian 48IG0.083333340.375000000.541666691.000000000.270833340.72916669
ss5585343HapMap-CEUEuropean 226IG0.283185840.415929200.300884960.099721000.491150440.50884956
HapMap-HCBAsian 86IG0.139534890.441860470.418604641.000000000.360465110.63953489
HapMap-JPTAsian 172IG0.104651160.418604640.476744171.000000000.313953490.68604654
HapMap-YRISub-Saharan African 226IG0.398230080.433628320.168141590.371093000.615044240.38495576
7 65AF 0.669399980.33059999
HAPMAP-ASW 98IG0.448979590.428571430.122448981.000000000.663265290.33673468
HAPMAP-CHBAsian 82IG0.073170730.487804890.439024390.438578000.317073170.68292683
HAPMAP-CHD 170IG0.152941180.435294120.411764710.583882000.370588240.62941176
HAPMAP-GIH 176IG0.272727280.534090940.193181810.527089000.539772750.46022728
HAPMAP-LWK 180IG0.322222230.488888890.188888891.000000000.566666660.43333334
HAPMAP-MEX 100IG0.120000000.340000000.540000020.250592000.289999990.70999998
HAPMAP-MKK 286IG0.244755240.587412600.167832170.050043000.538461570.46153846
HAPMAP-TSI 176IG0.193181810.545454560.261363630.371093000.465909090.53409094
ENSEMBL_Venter 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.499+/-0.0170000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitWith1000GenomeData
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP, NCBI
UNKNOWNUNKNOWNYES

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