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Reference SNP (refSNP) Cluster Report: rs1702294                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:89/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G/T (REV)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.1599/801 (1000 Genomes)
T=0.1490/18704 (TOPMED)
HGVS Names
  • CM000663.2:g.98036428T>A
  • CM000663.2:g.98036428T>C
  • NC_000001.10:g.98501984T>C
  • NC_000001.11:g.98036428T>A
  • NC_000001.11:g.98036428T>C
  • NR_046105.1:n.814+9580A>G
  • NR_046105.1:n.814+9580A>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 ss275941279 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1702294 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
ss2535972SC_JCM|AC027691.9_168487fwd/TA/Gtaggttttcctattttattaattataaacataactgtaaataactatgttcattctcttt11/03/0010/10/0389Genomicunknown
ss3970808SC_JCM|AL391725.3_42521rev/BC/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta09/25/0110/10/03100Genomicunknown
ss20610236SSAHASNP|WGSA-200403-chr1.chr1.NT_028050.13_6690928rev/BC/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta03/18/0403/18/04121Genomicunknown
ss82195545HGSV|Cor19240_SNV_20070510.chr1_98214005rev/BC/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta11/30/0712/02/07130Genomicunknown
ss87650195BCMHGSC_JDW|JWB-0091009rev/BC/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta02/26/0802/26/08129Genomicunknown
ss97960699HUMANGENOME_JCVI|1103675171310rev/BC/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta03/30/0803/30/08130Genomicunknown
ss106588941BGI|BGI_rs1702294rev/BC/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta09/16/0806/16/09130Genomicunknown
ss1084437981000GENOMES|CEU.trio.12.15.2008_124350_chr1_98274572rev/BC/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta12/15/0812/15/08130Genomicunknown
ss1108744531000GENOMES|NA19240_2008_12_16_114559_chr1_98274572rev/BC/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta12/17/0812/17/08130Genomicunknown
ss118912792ILLUMINA-UK|NA18507_000113689_NCBI36.1_chr1_98274572rev/BC/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta01/21/0901/21/09130Genomic99 %
ss138043414ENSEMBL|ENSSNP6211318rev/BC/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta05/15/0905/16/09131Genomicunknown
ss138845290ENSEMBL|ENSSNP293075rev/BC/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta12/08/0810/16/09131Genomicunknown
ss155401482GMI|GMI_SNP_237948938rev/BC/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta06/24/0906/24/09131Genomicunknown
ss163718402COMPLETE_GENOMICS|NA19240_36_chr1_98274572rev/BC/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta09/29/0909/29/09132Genomicunknown
ss164853112COMPLETE_GENOMICS|NA07022_36_chr1_98274572rev/BC/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta09/28/0909/30/09132Genomicunknown
ss198819699BUSHMAN|BUSHMAN-chr1-98274571rev/BC/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta02/16/1003/06/10132Genomicunknown
ss205144368BCM-HGSC-SUB|BCM_CMT_1011-52050rev/BC/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta03/15/1003/15/10132Genomicunknown
ss2185428951000GENOMES|pilot_1_YRI_352578_chr1_98274572rev/C/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta04/22/1004/22/10132Genomicunknown
ss2306523131000GENOMES|pilot_1_CEU_256942_chr1_98274572rev/C/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta05/01/1005/01/10132Genomicunknown
ss2383203931000GENOMES|pilot_1_CHB+JPT_205470_chr1_98274572rev/C/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta05/01/1005/01/10132Genomicunknown
ss275941279GMI|GMI_AK_SNP_261442rev/C/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta12/16/1012/16/10137Genomicunknown
ss284103788GMI|GMI_NA10851_SNP_116554rev/C/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta12/17/1012/17/10138Genomicunknown
ss290578442PJP|SNP_84800_chr1_98274572rev/C/Taaagagaatgaacatagttatttacagttatgtttataattaataaaataggaaaaccta01/21/1101/21/11134Genomicunknown
ss648245968SSMP|1_98501984rev/BC/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa12/14/1202/09/15138Genomicunknown
ss975471014EVA-GONL|EVA-GONL_rs1702294rev/BC/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa04/23/1404/23/14142Genomicunknown
ss1068119253JMKIDD_LAB|HGDP_WGS_chr1_98501984rev/BC/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa07/10/1407/10/14142Genomicunknown
ss12920642111000GENOMES|PHASE3_V1_2840370rev/C/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa08/16/1408/16/14142Genomicunknown
ss1425907995DDI|DDI_rs1702294rev/BC/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa11/04/1411/04/14144Genomicunknown
ss1574262353EVA_GENOME_DK|EVA_GENOME_DK_snv_rs1702294rev/BC/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa02/19/1502/19/15144Genomicunknown
ss1584848852EVA_DECODE|EVA_DECODE_1_98274572_719602_rs1702294rev/BC/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa03/02/1503/02/15144Genomicunknown
ss1600793368EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_98501984_1558137rev/C/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa03/04/1503/04/15144Genomicunknown
ss1643787401EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_98501984_1558137rev/C/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa03/04/1503/04/15144Genomicunknown
ss1794791824HAMMER_LAB|Hsieh_300734rev/BC/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa07/15/1507/15/15146Genomicunknown
ss1918671101WEILL_CORNELL_DGM|SNV:chr1:98501984rev/BC/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa10/16/1510/16/15147Genomicunknown
ss1966818031GENOMED|rs1702294rev/BC/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa02/16/1602/16/16147Genomicunknown
ss2019856717JJLAB|SNP359272rev/BC/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa08/29/1608/30/16149Genomicunknown
ss2147875616USC_VALOUEV|NC_000001.10:g.98501984T>Crev/C/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa11/17/1611/17/16150Genomicunknown
ss2164938537HUMAN_LONGEVITY|HLI-1-98036428-T-Crev/C/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa11/18/1611/18/16150Genomicunknown
ss2327287062TOPMED|1_98501984_T/Crev/C/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa11/19/1611/19/16150Genomicunknown
ss2697802816GRF|rs1702294rev/C/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa02/13/1702/13/17151Genomicunknown
ss2758513756GNOMAD|rs1702294rev/C/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa05/17/1705/17/17151Genomicunknown
ss2985519735AFFY|Axiom_Smokesc1_Affx-16285296rev/C/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa05/24/1705/24/17151Genomicunknown
ss2987288308SWEGEN|NC_000001.10:g.98501984T>Crev/C/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa05/30/1705/30/17151Genomicunknown
ss3023692031BIOINF_KMB_FNS_UNIBA|1.98036428T>Crev/C/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa07/05/1707/05/17151Genomicunknown
ss3084364451TOPMED|TOPMed_freeze_5?chr1:98,036,428-01rev/A/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa09/28/1709/28/17151Genomicunknown
ss3084364452TOPMED|TOPMed_freeze_5?chr1:98,036,428-02rev/C/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa09/28/1709/28/17151Genomicunknown
ss3343590710CSHL|rs1702294rev/C/Tgaatgaacatagttatttacagttatgtttataattaataaaataggaaa10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1702294|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G/T'|mol=Genomic|build=151
 TCCTCGTACA TATGTTGCTT AACAACAAGG ATACATTCTG AGAAACACAT CCTTAGGCAA
 TTTTGGCATT GTAGTAACAA CCTAGAATGT ACTTACAGAA ACCTATATGG TATAGCCTAC
 TATACACCTA GACTGTATGG CAGCCTACTG CTCTTAGGCT GGAAACCTGT ACAGCCACAT
 GTTACTATAC TGAATAATGT AGCCCATTGT AACACAATGG TAAGTATTTG TGAATCTAAA
 CACTCTAAAT ATAGAAAAGG TATAGTAGGA ATACAGTATT ACAAGTTTAT GGGATCACCA
 TTGTATATCT AGCCTGTCAT TGATACATAC ACCATTATGT GCCATATGAC TACCAAATCA
 TTCCTCTATC ATAGCATTGA GGGTTCACTA GAAAAATGGT GTAACTATCT TTGTTTTAAA
 TTCATCAAGA TAGAAAGTTG ATATCCTTTT GACCATTTAA TCCCATTTAA TAGGTTTTCC
 TATTTTATTA ATTATAAACA
 D
 TAACTGTAAA TAACTATGTT CATTCTCTTT CTAAAGTTTT TTAAAAAGGT TGTAGATATA
 ATCCCAAGAT AGGTAGGTAG ATAGACAGAC AGACTAACTT TTTAAAATCT ATTGTCTTGC
 TCAACTGAAA ATAATCCAGT GGAAAAATTG GCACTGAGAA GCCACACCTA AAATAATCAA
 TATTTTGTCC AAAGAAAAAT ATTTTATGGA TTCACATAAT TTGGCCAAGA ACAAAATGTT
 TTAAATTGTG TAAAGGATAG ATATTAATCC TCATACCAGC TAATTAAGCT TCTTCTGTAC
 AACATACAGT TTTAAGTTAA CAGTAATTAA TATAGCCAGC TTGGAACCTC AGGAAGCTAA
 AGCCAGCAAG TGCTTTTTGG TTCACTCGAG AGGATGCGGT TTGATTGCTG GCGCCAGTAA
 ACAGGTTGGG AATTGTCAAC ATTGTAATTA GCAGCAAGTT TCTGGATTCT CTGCCTGCCA
 GACTAGTGGG CTGATGCTTG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_028050 ABBA01045470 AC027691 AL391725
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs1702294 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/G
G/G
HWPA
G
ss118912792YRI 2IG 1.00000000 1.00000000
ss1292064211EAS 1008AF 0.070400010.92960000
EUR 1006AF 0.209700000.79030001
AFR 1322AF 0.171700000.82830000
AMR 694AF 0.106600000.89340001
SAS 978AF 0.222900000.77709997
ss138043414ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss138845290ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss163718402YRISub-Saharan African 2IG1.00000000 0.500000000.50000000
ss164853112CEUEuropean 2IG 1.00000000 1.00000000
ss218542895pilot_1_YRI_low_coverage_panel 118AF 0.194915250.80508476
ss230652313pilot_1_CEU_low_coverage_panel 120AF 0.208333330.79166669
ss238320393pilot_1_CHB+JPT_low_coverage_panel 120AF 0.041666670.95833331
ss97960699J. Craig Venter 2IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.269+/-0.2490000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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