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Reference SNP (refSNP) Cluster Report: rs650108                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:83/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqbySubmitterwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.4427/2217 (1000 Genomes)
A=0.3222/40453 (TOPMED)
HGVS Names
  • CM000673.2:g.102838056G>A
  • NC_000011.10:g.102838056G>A
  • NC_000011.9:g.102708787G>A
  • NG_012100.1:g.10556C>T
  • NM_002422.4:c.1229+495C>T
  • NW_003871077.1:g.6291G>A
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 ss281148966 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs650108 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
ss823058SC_JCM|AP001018.2_82940rev/BC/Ttaacactactatatgattttcaagggctactctaacctcacccacttgtcacctctacct07/27/0010/10/0383Genomicunknown
ss1996466KWOK|OVLP-000925-224781fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta10/06/0010/10/0387Genomic99 %
ss1996814KWOK|OVLP-000925-230142rev/BC/Ttaacactactatatgattttcaagggctactctaacctcacccacttgtcacctctacct10/06/0010/10/0387Genomic99 %
ss2037849KWOK|OVLP-000925-198774fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta10/06/0010/10/0387Genomic98 %
ss2044367KWOK|OVLP-000925-213777fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta10/06/0010/10/0387Genomic97 %
ss2064519KWOK|OVLP-000925-194851fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta10/07/0010/10/0387Genomic95 %
ss4251064PGA-UW-FHCRC|MMP3-008354byFreqrev/BC/Ttaacactactatatgattttcaagggctactctaacctcacccacttgtcacctctacct11/06/0104/07/04102Genomicunknown
ss10691537BCM_SSAHASNP|chr11.NT_033899.5_6252628fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta06/29/0310/10/03116Genomicunknown
ss12161346WI_SSAHASNP|chr11.NT_033899.5_6252628fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta07/04/0310/10/03116Genomicunknown
ss24073617PERLEGEN|afd0611837byFreqfwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta08/10/0409/13/04123Genomicunknown
ss38754222ABI|hCV785965byFreqfwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta07/16/0511/02/06126Genomicunknown
ss66147859AFFY|SNP_A-2123046byFreqfwd/TA/Gagtgggtgaggttagagtagcccttgaaaatc10/27/0608/14/07127Genomicunknown
ss76173227AFFY|AFFY_6_1M_SNP_A-2123046fwd/TA/Gagtgggtgaggttagagtagcccttgaaaatc08/28/0708/30/07129Genomicunknown
ss78088884HGSV|Cor12878_SNV_20070510.chr11_102213997fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta10/17/0710/17/07129Genomicunknown
ss81430995KRIBB_YJKIM|KHS57180fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta11/30/0711/30/07130Genomicunknown
ss84427005HGSV|Cor19129_SNV_20070510.chr11_102213997fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta12/06/0712/07/07130Genomicunknown
ss88752069BCMHGSC_JDW|JWB-0471954fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta02/26/0802/28/08129Genomicunknown
ss102994708BGI|BGI_rs650108fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta06/05/0810/20/09131Genomicunknown
ss1109764391000GENOMES|CEU.trio.12.15.2008_2611633_chr11_102213997fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta12/17/0812/17/08130Genomicunknown
ss119948484ILLUMINA-UK|NA18507_000133050_NCBI36.1_chr11_102213997fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta01/21/0902/06/09131Genomic99 %
ss132785899ENSEMBL|ENSSNP10494098fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta05/11/0905/14/09131Genomicunknown
ss156723542GMI|GMI_SNP_70151411fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta06/24/0906/25/09131Genomicunknown
ss174019671ILLUMINA|Human1M-Duov3_B_rs650108-128_T_F_1510647844fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta10/01/0910/04/09132Genomicunknown
ss203137441BUSHMAN|BUSHMAN-chr11-102213996fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta02/16/1003/09/10132Genomicunknown
ss2111877961000GENOMES|YRI.trio.3.2010_1054641_chr11_102213997fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta03/29/1003/30/10132Genomicunknown
ss2254300181000GENOMES|pilot_1_YRI_7239701_chr11_102213997fwd/A/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta04/22/1004/22/10132Genomicunknown
ss2356960671000GENOMES|pilot_1_CEU_5300696_chr11_102213997fwd/A/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta05/01/1005/01/10132Genomicunknown
ss2422988831000GENOMES|pilot_1_CHB+JPT_4183960_chr11_102213997fwd/A/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta05/01/1005/01/10132Genomicunknown
ss244305171ILLUMINA|CVDSNP55v1_A_rs650108fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta06/10/1006/10/10132Genomicunknown
ss281148966GMI|GMI_AK_SNP_5469355fwd/A/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta12/16/1012/16/10137Genomicunknown
ss286445882GMI|GMI_NA10851_SNP_2458671fwd/A/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta12/17/1012/17/10138Genomicunknown
ss291127229PJP|SNP_633587_chr11_102213997fwd/A/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta01/21/1101/21/11134Genomicunknown
ss410941414ILLUMINA|Cardio-Metabo_Chip_11395247_A_rs650108fwd/TA/Gaggtagaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtagtgtta06/07/1106/07/11135Genomicunknown
ss537357510ILLUMINA|HumanOmni5-4v1_B_rs650108-131_T_F_1908481062fwd/TA/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag06/22/1208/29/15146Genomicunknown
ss562788118TISHKOFF|snp_chr11_102708787fwd/TA/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag11/22/1211/23/12138Genomicunknown
ss658310777SSMP|11_102708787fwd/TA/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag12/14/1202/13/15138Genomicunknown
ss988900740EVA-GONL|EVA-GONL_rs650108fwd/TA/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag04/23/1404/25/14142Genomicunknown
ss1077999597JMKIDD_LAB|HGDP_WGS_chr11_102708787fwd/TA/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag07/10/1407/12/14142Genomicunknown
ss13427304911000GENOMES|PHASE3_V1_55597563fwd/A/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag08/16/1408/16/14142Genomicunknown
ss1426743241DDI|DDI_rs650108fwd/TA/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag11/04/1411/04/14144Genomicunknown
ss1575917255EVA_GENOME_DK|EVA_GENOME_DK_snv_rs650108fwd/TA/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag02/19/1502/19/15144Genomicunknown
ss1598564912EVA_DECODE|EVA_DECODE_11_102213997_774710_rs650108fwd/TA/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag03/02/1503/04/15144Genomicunknown
ss1627334779EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_11_102708787_30691250fwd/A/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag03/04/1503/04/15144Genomicunknown
ss1670328812EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_11_102708787_30691250fwd/A/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag03/04/1503/04/15144Genomicunknown
ss1806970799HAMMER_LAB|Hsieh_5991014fwd/TA/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag07/15/1507/16/15146Genomicunknown
ss1932263433WEILL_CORNELL_DGM|SNV:chr11:102708787fwd/TA/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag10/16/1510/17/15147Genomicunknown
ss1959380791ILLUMINA|rs650108-138_T_F_2258075205fwd/TA/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag11/13/1511/13/15147Genomicunknown
ss1967443784GENOMED|rs650108fwd/TA/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag02/16/1602/16/16149Genomicunknown
ss2026876150JJLAB|SNP7378705fwd/TA/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag08/29/1608/30/16149Genomicunknown
ss2185212272HUMAN_LONGEVITY|HLI-11-102838056-G-Afwd/A/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag11/18/1611/18/16150Genomicunknown
ss2635029834ILLUMINA|Cancer_BeadChip_11459870_A_rs650108-128_T_F_1630044035fwd/A/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag02/02/1702/02/17151Genomicunknown
ss3027236887BIOINF_KMB_FNS_UNIBA|11.102838056G>Afwd/A/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag07/05/1707/05/17151Genomicunknown
ss3154853327TOPMED|TOPMed_freeze_5?chr11:102,838,056fwd/A/Ggaggtgacaagtgggtgaggttagagtagcccttgaaaatcatatagtag09/30/1709/30/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs650108|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 AATGGTACTG TAAAGAGTTC TGAAAGCCAT ATCTCCATCC GGAACAGGGG CCGCATCCTG
 CTGTATGTAG CACATGCTGT TTGTCATCAT ATTTCTTAAG CCTGGACAGA AAGAACCTTA
 ATCATCTTTC TGTCACAAAG ACATGAAAGT GTGAACATAT ATATAAAGTG AATTGAATCA
 ACATCTAAAA TGCAATTTTA ATTCCCTACC ACAATTGGCC CATATATGCC TGCTGTCCCC
 TCCCCTGCAC ATCTAAATCT TCTCTGGTGG CCTCCTGGGA AAAGGGATTA GGATAAGAAG
 CAAAGCACAG TAAGTGTGTT TTTAGCCCAT TGGCTGGATA TCAGATGGTC GGCCTCGATG
 TCTCAAAGTC TGGCCAAATG ACCCAGGAAT CAACCTGTCT GTGAGTGTTG GGTTGTATCC
 ATAAACTGGA CTGCTATTGA TCATCATCTC TTAAATGAGC CATCATTATC AGGTAGAGGT
 GACAAGTGGG TGAGGTTAGA
 R
 GTAGCCCTTG AAAATCATAT AGTAGTGTTA GGAAGACAAA ACAAACACAC AATGAGACAG
 TGACAAACAC ACAGTGAGAC AGTGAGCCAA ACTAAAAGAC AATGGGAAGG GAACGCTAAA
 TTGCGGTCTG GGTTCTCAGA ACATTTTCCC AATGGGTCTA AAGTCCACGA GGGAAAGCTG
 CATGGAGGTG ATGAGACTTG AGCCAGGACT TGAAGGATGG GCAAGATTTG AATAGGTTGA
 GGAGAGAAGA GGGGGCTCCA GGCAGGTGGG GTGACAGCAC CAAGGGAAGC ACCAGCCAAC
 TGCACTTGGG ACTGAAAGCA GGAGAGCCTA AGGTGCTGCT GTTTTAAAGT AAGAACTTTC
 CCACAGTTGT CTGAAGTCCC ATCCTTCCTA CTAAGAGAGA AGCAGGCCTA AGGTTGGGGT
 GGGGGATTTC CTTAGTAAAA GAAACTAATT TCCCTAATTA GGCTCCATAC AAAGTCATTT
 CTCTTGCATC TCACCTCCAG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_033899 AP000619 AP000789 AP001144 AP001144.2 U78045 U78045.1
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.
SourceA/A
A/G
G/G
HWPA
G
ss119948484YRI 2IG 1.00000000 0.500000000.50000000
ss132785899ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss1342730491EAS 1008AF 0.586300020.41370001
EUR 1006AF 0.286300000.71370000
AFR 1322AF 0.307100000.69290000
AMR 694AF 0.521600010.47840002
SAS 978AF 0.582799970.41720000
ss203137441BUSHMAN_POP2 2IG 1.00000000 0.500000000.50000000
ss225430018pilot_1_YRI_low_coverage_panel 118AF 0.322033910.67796612
ss235696067pilot_1_CEU_low_coverage_panel 120AF 0.258333330.74166667
ss24073617AFD_EUR_PANELEuropean 48IG0.041666670.291666660.666666691.000000000.187500000.81250000
AFD_AFR_PANELAfrican American 46IG0.086956520.478260870.434782590.751830000.326086970.67391306
AFD_CHN_PANELAsian 48IG0.208333330.583333310.208333330.438578000.500000000.50000000
ss242298883pilot_1_CHB+JPT_low_coverage_panel 120AF 0.658333360.34166667
ss38754222HapMap-CEUEuropean 120IG0.050000000.349999990.600000021.000000000.224999990.77499998
HapMap-HCBAsian 90IG0.377777790.466666670.155555561.000000000.611111100.38888890
HapMap-JPTAsian 90IG0.377777790.466666670.155555561.000000000.611111100.38888890
HapMap-YRISub-Saharan African 120IG0.100000000.416666660.483333321.000000000.308333340.69166666
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss4251064PGA-AFRICAN-PANELAfrican American 48IG0.125000000.458333340.416666661.000000000.354166660.64583331
PGA-EUROPEAN-PANELEuropean 46IG0.043478260.304347810.652173941.000000000.195652170.80434781
ss76173227ICMHP 8IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.493+/-0.0570000

  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_SSAHASNPNCBI
UNKNOWNUNKNOWNYES

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