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Reference SNP (refSNP) Cluster Report: rs2462692                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/T (REV)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.0323/162 (1000 Genomes)
A=0.0432/5426 (TOPMED)
HGVS Names
  • CM000672.2:g.7102293T>A
  • CM000672.2:g.7102293T>G
  • NC_000010.10:g.7144255T>G
  • NC_000010.11:g.7102293T>A
  • NC_000010.11:g.7102293T>G
  • XR_001747351.1:n.363+17338A>C
  • XR_001747351.1:n.363+17338A>T
  • XR_001747352.1:n.363+17338A>C
  • XR_001747352.1:n.363+17338A>T
  • XR_001747354.1:n.363+17338A>C
  • XR_001747354.1:n.363+17338A>T
  • XR_930623.2:n.363+17338A>C
  • XR_930623.2:n.363+17338A>T
  • XR_930624.2:n.363+17338A>C
  • XR_930624.2:n.363+17338A>T
  • XR_930625.2:n.363+17338A>C
  • XR_930625.2:n.363+17338A>T
  • XR_930626.2:n.363+17338A>C
  • XR_930626.2:n.363+17338A>T
  • XR_930627.2:n.363+17338A>C
  • XR_930627.2:n.363+17338A>T
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 ss16092113 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2462692 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
ss3452343SC_JCM|AC073378.2_100000fwd/TA/Caagaagcctttcccaatatttggcagcagagtcatattggctctaggatgatatttctca09/24/0110/10/03100Genomicunknown
ss12084518WI_SSAHASNP|chr10.NT_077569.2_1507151rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt07/04/0310/10/03116Genomicunknown
ss16092113SC_SNP|NT_077569.2_1507151byFreqrev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt11/18/0310/30/04120Genomicunknown
ss16472939CSHL-HAPMAP|CSHL-HuAA-200402.chr10.NT_077569.2_1507151rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt02/17/0403/04/04120Genomicunknown
ss19162515CSHL-HAPMAP|CSHL-HuDD-200402.chr10.NT_077569.2_1507151rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt02/20/0403/04/04120Genomicunknown
ss24538594PERLEGEN|afd2203879byFreqrev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt08/10/0409/13/04123Genomicunknown
ss38625228ABI|hCV56390rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt07/15/0507/15/05126Genomicunknown
ss66743525ILLUMINA|HumanHap300v1.1_rs2462692fwd/TA/Caagaagcctttcccaatatttggcagcagagtcatattggctctaggatgatatttctca11/09/0611/09/06127Genomicunknown
ss67255860ILLUMINA|HumanHap550v1.1_rs2462692fwd/TA/Caagaagcctttcccaatatttggcagcagagtcatattggctctaggatgatatttctca11/14/0611/14/06127Genomicunknown
ss67654212ILLUMINA|HumanHap650Yv1.0_rs2462692fwd/TA/Caagaagcctttcccaatatttggcagcagagtcatattggctctaggatgatatttctca11/14/0611/14/06127Genomicunknown
ss70734209ILLUMINA|HumanHap550v3.0__rs2462692fwd/TA/Caagaagcctttcccaatatttggcagcagagtcatattggctctaggatgatatttctca04/20/0703/30/08130Genomicunknown
ss71304131ILLUMINA|HumanHap650Yv3.0_rs2462692fwd/TA/Caagaagcctttcccaatatttggcagcagagtcatattggctctaggatgatatttctca04/23/0704/23/07127Genomicunknown
ss75711396ILLUMINA|ILMN_Human_1M_rs2462692fwd/TA/Caagaagcctttcccaatatttggcagcagagtcatattggctctaggatgatatttctca08/28/0708/29/07129Genomicunknown
ss79136068ILLUMINA|HumanHap300v2.0_rs2462692fwd/TA/Caagaagcctttcccaatatttggcagcagagtcatattggctctaggatgatatttctca04/18/0711/18/07130Genomicunknown
ss80221345HGSV|Cor18507_SNV_20070510.chr10_7184261rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt11/23/0711/25/07130Genomicunknown
ss83803151HGSV|Cor18956_SNV_20070510.chr10_7184261rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt11/30/0712/05/07130Genomicunknown
ss84051369KRIBB_YJKIM|KHS616514fwd/TA/Caagaagcctttcccaatatttggcagcagagtcatattggctctaggatgatatttctca12/04/0712/06/07130Genomicunknown
ss85768711HGSV|Cor18517_SNV_20070510.chr10_7184261rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt12/06/0712/10/07130Genomicunknown
ss88084160BCMHGSC_JDW|JWB-0230712rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt02/26/0802/27/08129Genomicunknown
ss97618745HUMANGENOME_JCVI|1103649852945rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt03/29/0803/29/08130Genomicunknown
ss106653956BGI|BGI_rs2462692rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt09/16/0806/17/09130Genomicunknown
ss1092037071000GENOMES|CEU.trio.12.15.2008_2287928_chr10_7184261rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt12/16/0812/16/08130Genomicunknown
ss1153153611000GENOMES|NA19240_2008_12_16_2066760_chr10_7184261rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt12/19/0812/19/08130Genomicunknown
ss119008387ILLUMINA-UK|NA18507_000011650_NCBI36.1_chr10_7184261rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt01/21/0901/22/09130Genomic99 %
ss122041391ILLUMINA|HumanCNV370v1_C_rs2462692fwd/TA/Caagaagcctttcccaatatttggcagcagagtcatattggctctaggatgatatttctca04/14/0904/15/09131Genomicunknown
ss131666171ENSEMBL|ENSSNP6719169rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt05/11/0905/13/09131Genomicunknown
ss137939352ENSEMBL|ENSSNP439286rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt12/08/0810/16/09131Genomicunknown
ss153914039ILLUMINA|Human610_Quadv1_B_rs2462692-128_T_F_1501760330fwd/TA/Caagaagcctttcccaatatttggcagcagagtcatattggctctaggatgatatttctca06/18/0906/20/09131Genomicunknown
ss154535878GMI|GMI_SNP_121920244rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt06/24/0906/24/09131Genomicunknown
ss167759930COMPLETE_GENOMICS|NA07022_36_chr10_7184261rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt09/30/0909/30/09132Genomicunknown
ss168997698COMPLETE_GENOMICS|NA19240_36_chr10_7184261rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt10/01/0910/04/09132Genomicunknown
ss170387993COMPLETE_GENOMICS|NA20431_36_chr10_7184261rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt10/01/0910/04/09132Genomicunknown
ss171267984ILLUMINA|HumanCNV370-Quadv3_C_rs2462692-128_T_F_1501760330fwd/TA/Caagaagcctttcccaatatttggcagcagagtcatattggctctaggatgatatttctca10/01/0910/03/09132Genomicunknown
ss173357048ILLUMINA|Human1M-Duov3_B_rs2462692-128_T_F_1501760330fwd/TA/Caagaagcctttcccaatatttggcagcagagtcatattggctctaggatgatatttctca10/01/0910/03/09132Genomicunknown
ss201106935BUSHMAN|BUSHMAN-chr10-7184260rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt02/16/1003/07/10132Genomicunknown
ss207024396BCM-HGSC-SUB|BCM_CMT_1011-1964417rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt03/15/1003/18/10132Genomicunknown
ss2245487751000GENOMES|pilot_1_YRI_6358458_chr10_7184261rev/G/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt04/22/1004/22/10132Genomicunknown
ss2350415461000GENOMES|pilot_1_CEU_4646175_chr10_7184261rev/G/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt05/01/1005/01/10132Genomicunknown
ss2417764581000GENOMES|pilot_1_CHB+JPT_3661535_chr10_7184261rev/G/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt05/01/1005/01/10132Genomicunknown
ss254032846BL|SNP12472_10_7184261rev/BG/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt08/19/1008/19/10134Genomicunknown
ss280468170GMI|GMI_AK_SNP_4788487rev/A/Gtgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt12/16/1012/16/10137Genomicunknown
ss286124122GMI|GMI_NA10851_SNP_2136903rev/G/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt12/17/1012/17/10138Genomicunknown
ss290901858PJP|SNP_408216_chr10_7184261rev/G/Ttgagaaatatcatcctagagccaatatgactctgctgccaaatattgggaaaggcttctt01/21/1101/21/11134Genomicunknown
ss656257197SSMP|10_7144255rev/BG/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc12/14/1202/12/15138Genomicunknown
ss825466586ILLUMINA|HumanCNV370v1_C_rs2462692-126_T_F_IFB1136227073:0rev/BG/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc06/24/1311/21/14144Genomicunknown
ss987164844EVA-GONL|EVA-GONL_rs2462692rev/BG/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc04/23/1404/25/14142Genomicunknown
ss1076737366JMKIDD_LAB|HGDP_WGS_chr10_7144255rev/BG/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc07/10/1407/11/14142Genomicunknown
ss13361567981000GENOMES|PHASE3_V1_48756796rev/A/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc08/16/1408/16/14142Genomicunknown
ss13361567991000GENOMES|PHASE3_V1_48756797rev/G/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc08/16/1408/16/14142Genomicunknown
ss1426211573DDI|DDI_rs2462692rev/BG/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc11/04/1411/04/14144Genomicunknown
ss1574895678EVA_GENOME_DK|EVA_GENOME_DK_snv_rs2462692rev/BG/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc02/19/1502/19/15144Genomicunknown
ss1596813269EVA_DECODE|EVA_DECODE_10_7184261_69247_rs2462692rev/BG/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc03/02/1503/03/15144Genomicunknown
ss1623926166EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_10_7144255_26948328rev/G/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc03/04/1503/04/15144Genomicunknown
ss1666920199EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_10_7144255_26948328rev/G/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc03/04/1503/04/15144Genomicunknown
ss1713154911EVA_SVP|EVA_SVP_849278rev/BG/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc03/12/1503/12/15144Genomicunknown
ss1806241939HAMMER_LAB|Hsieh_5259388rev/BG/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc07/15/1507/16/15146Genomicunknown
ss1930486746WEILL_CORNELL_DGM|SNV:chr10:7144255rev/BG/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc10/16/1510/17/15147Genomicunknown
ss1967051509GENOMED|rs2462692rev/BG/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc02/16/1602/16/16147Genomicunknown
ss2025966461JJLAB|SNP6469016rev/BG/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc08/29/1608/30/16149Genomicunknown
ss2154208830USC_VALOUEV|NC_000010.10:g.7144255T>Grev/G/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc11/17/1611/17/16150Genomicunknown
ss2172411102HUMAN_LONGEVITY|HLI-10-7102293-T-A,Grev/A/G/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc11/18/1611/18/16150Genomicunknown
ss2335120755TOPMED|10_7144255_T/Grev/G/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc11/19/1611/19/16150Genomicunknown
ss2627452400SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV4103450rev/G/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc01/06/1701/06/17151Genomicunknown
ss2698433242GRF|rs2462692rev/G/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc02/13/1702/13/17151Genomicunknown
ss2710702004ILLUMINA|Consortium-OncoArray_15047405_A_rs2462692-131_T_F_1893189719rev/G/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc03/22/1703/22/17151Genomicunknown
ss2885178543GNOMAD|rs2462692rev/A/G/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc05/19/1705/19/17151Genomicunknown
ss3005887933SWEGEN|NC_000010.10:g.7144255T>Grev/G/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc05/30/1705/30/17151Genomicunknown
ss3026766987BIOINF_KMB_FNS_UNIBA|10.7102293T>Grev/G/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc07/05/1707/05/17151Genomicunknown
ss3110829360TOPMED|TOPMed_freeze_5?chr10:7,102,293-01rev/A/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc09/29/1709/29/17151Genomicunknown
ss3110829361TOPMED|TOPMed_freeze_5?chr10:7,102,293-02rev/G/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc09/29/1709/29/17151Genomicunknown
ss3348946050CSHL|rs2462692rev/G/Taatatcatcctagagccaatatgactctgctgccaaatattgggaaaggc10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2462692|allelePos=812|totalLen=1012|taxid=9606|snpclass=1|alleles='A/C/T'|mol=Genomic|build=151
 AGTGATTACT GTGAATGGGC CTGAAAATCT CCACTTAGTT CTTTTCCACC AGCTAGAAGC
 AGAGGACTCC AGAGAGGGTG GCCAGTGCTG CAAGATGCAA AAGCCTGGGA TCCTGAGTCA
 CCACCTGGAA GAAGGAATGA GCTGACCAGG AATGCCAGCA TCAGGCCATT ATGTGAGCAA
 GAGAGAAACT TCCGTTGTGT GAAGCCGTTG AAATTTATGG GTGATATGGT TGGGCTCTGT
 GTCCCCACCC TAAATCTCAT CTTGAATTGT AACAATCCCC ACGTGTCAAG GGTGGAACCA
 GGTGGAAGTA ATTGAATCAT GAGAGCAGTT ACCTCCAGCT GTTCTGGTGA TAGTGAGTCA
 GTTCTCACGA GATCTGATGG TTTTATAAGA GGCTTTCCAC CCTGTGCTTA GCACTTCTCC
 TGGCTGCTGC GATGTGAAGG ATGTGTTTGC TTCCTCTCGC ACCTTGATTA TAAGTTTCCT
 GAGGCCTTCC CCAGCCATGC TGAATTGTAA GTCAGTTAAA CCTCTTTCCT TGATAAATTA
 TCCAGTCTCG GGTATGTCTT TACTAGCAGT GTGAGAACGG AATAATATAA GGGGTTATTT
 ATTAAAGCAG TAGCCTTAAC TTTATTGAAT CTTTTCTTTG ATGGAGTGTT TATTGTCCCA
 GCTCTAATTG CTATGAAAAC CTTACTCACA CTGAGCTAAA AGCTGCCTTC CCAGGAGTGA
 CTCCAACCCA TGGGCTACTG TTTTGCCTTT TCAGCGTGCA CAGATGTATT TCCTCTTCAT
 CAAGAAGCCT TTCCCAATAT TTGGCAGCAG A
 H
 GTCATATTGG CTCTAGGATG ATATTTCTCA TTTCTTCATT TATGGCTGCA GTGCACAGTA
 GCAAATGATT AGAGTTTTAA CCTCAGAGCT AAACAGACTC TCTCCTAGAG AGTTCCTTTT
 CTCCCTGACT CTTCCCAAAA CTCAGCAGTC ATCCCAAGGC TCTTACACCA AGAATTGTCC
 TAACTTTGGA TTGAAGCCAT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_077569 ABBA01034753 AL590095
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs2462692 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/C
C/C
HWPA
C
ss119008387YRI 2IG 1.00000000 1.00000000
ss131666171ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss137939352ENSEMBL_Venter 2IG 1.00000000 0.500000000.50000000
ENSEMBL_celera 4IG 1.00000000 1.00000000
ss16092113HapMap-CEUEuropean 226IG 0.150442480.849557520.751830000.075221240.92477876
HapMap-HCBAsian 86IG 1.00000000 1.00000000
HapMap-JPTAsian 172IG 0.058139540.941860441.000000000.029069770.97093022
HapMap-YRISub-Saharan African 226IG0.008849560.026548670.964601760.001000000.022123890.97787613
HAPMAP-ASW 98IG 0.020408160.979591851.000000000.010204080.98979592
HAPMAP-CHBAsian 82IG 0.024390240.975609781.000000000.012195120.98780489
HAPMAP-CHD 170IG 0.011764710.988235291.000000000.005882350.99411762
HAPMAP-GIH 176IG 0.056818180.943181811.000000000.028409090.97159094
HAPMAP-LWK 180IG 0.077777780.922222201.000000000.038888890.96111113
HAPMAP-MKK 286IG0.006993010.188811180.804195820.751830000.101398600.89860141
HAPMAP-TSI 176IG0.011363640.170454550.818181811.000000000.096590910.90340906
ss167759930CEUEuropean 2IG 1.00000000 1.00000000
ss168997698YRISub-Saharan African 2IG 1.00000000 1.00000000
ss170387993PGP 2IG 1.00000000 1.00000000
ss224548775pilot_1_YRI_low_coverage_panel 118AF 0.008474580.99152541
ss235041546pilot_1_CEU_low_coverage_panel 120AF 0.083333340.91666669
ss241776458pilot_1_CHB+JPT_low_coverage_panel 120AF 1.00000000
ss24538594AFD_EUR_PANELEuropean 48IG 0.125000000.875000001.000000000.062500000.93750000
AFD_AFR_PANELAfrican American 46IG 0.043478260.956521751.000000000.021739130.97826087
AFD_CHN_PANELAsian 48IG 1.00000000 1.00000000
ss97618745J. Craig Venter 2IG 1.00000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.067+/-0.1710000ALFRED: 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
byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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