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Reference SNP (refSNP) Cluster Report: rs591058                 ** With Benign allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:83/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:With Benign allele [ClinVar]
MAF/MinorAlleleCount:T=0.4263/51479 (ExAC)
T=0.3552/1779 (1000 Genomes)
T=0.4584/5961 (GO-ESP)
T=0.4350/54625 (TOPMED)
HGVS Names
  • CM000673.2:g.102840607T>C
  • NC_000011.10:g.102840607T>C
  • NC_000011.9:g.102711338T>C
  • NG_012100.1:g.8005A>G
  • NM_002422.4:c.626-14A>G
  • NW_003871077.1:g.8842T>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 ss281148972 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs591058 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
ss762820SC_JCM|AP000789.2_136193fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac07/27/0010/10/0383Genomicunknown
ss1994893KWOK|OVLP-000925-200777fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac10/06/0010/10/0387Genomic99 %
ss1995128KWOK|OVLP-000925-205116fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac10/06/0010/10/0387Genomic99 %
ss2044369KWOK|OVLP-000925-213779fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac10/06/0010/10/0387Genomic97 %
ss2830083TSC-CSHL|TSC1008489byFreqfwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac01/03/0110/25/0692Genomicunknown
ss2984777YUSUKE|IMS-JST006590byFreqfwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac05/24/0110/25/0696Genomicunknown
ss4251051PGA-UW-FHCRC|MMP3-005803byFreqrev/TA/Ggtatttaaaaaataagtaactattgttctcatttcttaaatagggaccaatttatttctc11/06/0104/07/04102Genomicunknown
ss38672890ABI|hCV785960byFreqfwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac07/16/0511/02/06126Genomicunknown
ss52080035SI_EXO|NT_033899.7_6273754byFreqfwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac03/29/0608/14/07127Genomicunknown
ss66538920SHGC|1143byFreqrev/TA/Ggtatttaaaaaataagtaactattgttctcatttcttaaatagggaccaatttatttctc11/08/0612/16/06127Genomicunknown
ss71640584SHGC|1921byFreqrev/TA/Ggtatttaaaaaataagtaactattgttctcatttcttaaatagggaccaatttatttctc04/27/0708/14/07127Genomicunknown
ss75137632ILLUMINA|ILMN_Human_1M_rs591058fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac08/28/0708/29/07129Genomicunknown
ss76873808CGM_KYOTO|720775fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac09/12/0709/12/07129cDNAunknown
ss88752077BCMHGSC_JDW|JWB-0471956fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac02/26/0802/28/08129Genomicunknown
ss102994710BGI|BGI_rs591058fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac06/05/0810/20/09130Genomicunknown
ss104796501KRIBB_YJKIM|KHS1101122fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac06/09/0806/09/08130Genomicunknown
ss1109764891000GENOMES|CEU.trio.12.15.2008_2611639_chr11_102216548fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac12/17/0812/17/08130Genomicunknown
ss119359327KRIBB_YJKIM|KHS1521574fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac02/04/0902/04/09131Genomicunknown
ss119948486ILLUMINA-UK|NA18507_000133052_NCBI36.1_chr11_102216548fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac01/21/0902/06/09131Genomic99 %
ss132785903ENSEMBL|ENSSNP10494099fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac05/11/0905/14/09131Genomicunknown
ss156723557GMI|GMI_SNP_33985241fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac06/24/0906/25/09131Genomicunknown
ss173936617ILLUMINA|Human1M-Duov3_B_rs591058-128_B_F_1514110805fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac10/01/0910/04/09132Genomicunknown
ss203137461BUSHMAN|BUSHMAN-chr11-102216547fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac02/16/1003/09/10132Genomicunknown
ss2111878031000GENOMES|YRI.trio.3.2010_1054644_chr11_102216548fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac03/29/1003/30/10132Genomicunknown
ss2254300251000GENOMES|pilot_1_YRI_7239708_chr11_102216548fwd/C/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac04/22/1004/22/10132Genomicunknown
ss2356960771000GENOMES|pilot_1_CEU_5300706_chr11_102216548fwd/C/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac05/01/1005/01/10132Genomicunknown
ss2422988891000GENOMES|pilot_1_CHB+JPT_4183966_chr11_102216548fwd/C/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac05/01/1005/01/10132Genomicunknown
ss281148972GMI|GMI_AK_SNP_5469361fwd/C/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac12/16/1012/16/10137Genomicunknown
ss286445884GMI|GMI_NA10851_SNP_2458673fwd/C/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac12/17/1012/17/10138Genomicunknown
ss4910279291000GENOMES|20110521_exome_535727_chr11_102711338fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac02/10/1202/22/12137Genomicunknown
ss491653108CLINSEQ_SNP|SNV-chr11-102216548byFreqfwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta03/06/1209/05/14137Genomicunknown
ss532990668ILLUMINA|HumanOmni5-4v1_B_kgp10774834-0_T_R_1907861133fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta06/22/1208/29/15146Genomicunknown
ss562788131TISHKOFF|snp_chr11_102711338fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta11/22/1211/23/12138Genomicunknown
ss658310794SSMP|11_102711338fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta12/14/1202/13/15138Genomicunknown
ss713054290NHLBI-ESP|ESP6500SI-chr11-102711338fwd/BC/Tgagaaataaattggtccctatttaagaaatgagaacaatagttacttattttttaaatac02/20/1302/20/13138Genomicunknown
ss974480936JMKIDD_LAB|KhoeSan_Exomes_chr11_102711338fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta03/06/1403/06/14142Genomicunknown
ss988900758EVA-GONL|EVA-GONL_rs591058fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta04/23/1404/25/14142Genomicunknown
ss1067527660JMKIDD_LAB|HGDP_exomes_chr11_102711338fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta07/09/1407/09/14142Genomicunknown
ss1077999609JMKIDD_LAB|HGDP_WGS_chr11_102711338fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta07/10/1407/12/14142Genomicunknown
ss13427305641000GENOMES|PHASE3_V1_55597638fwd/C/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta08/16/1408/16/14142Genomicunknown
ss1426743245DDI|DDI_rs591058fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta11/04/1411/04/14144Genomicunknown
ss1575917275EVA_GENOME_DK|EVA_GENOME_DK_snv_rs591058fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta02/19/1502/19/15144Genomicunknown
ss1584077719EVA_FINRISK|EVA_FINRISK_rs591058fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta02/27/1502/27/15144Genomicunknown
ss1598564933EVA_DECODE|EVA_DECODE_11_102216548_774731_rs591058fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta03/02/1503/04/15144Genomicunknown
ss1627334830EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_11_102711338_30691303fwd/C/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta03/04/1503/04/15144Genomicunknown
ss1670328863EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_11_102711338_30691303fwd/C/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta03/04/1503/04/15144Genomicunknown
ss1690608186EVA_EXAC|EVA_EXAC_5811320fwd/C/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta03/04/1503/04/15144Genomicunknown
ss1711306875EVA_MGP|EVA_XIMO_422635fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta03/09/1503/09/15144Genomicunknown
ss1713280435EVA_SVP|EVA_SVP_974802fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta03/12/1503/12/15144Genomicunknown
ss1806970804HAMMER_LAB|Hsieh_5991019fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta07/15/1507/16/15146Genomicunknown
ss1932263453WEILL_CORNELL_DGM|SNV:chr11:102711338fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta10/16/1510/17/15147Genomicunknown
ss1967443790GENOMED|rs591058fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta02/16/1602/16/16149Genomicunknown
ss2026876160JJLAB|SNP7378715fwd/BC/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta08/29/1608/30/16149Genomicunknown
ss2185212433HUMAN_LONGEVITY|HLI-11-102840607-T-Cfwd/C/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta11/18/1611/18/16150Genomicunknown
ss2635029839ILLUMINA|Cancer_BeadChip_11459870_A_rs591058-128_B_F_1630044029fwd/C/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta02/02/1702/02/17151Genomicunknown
ss3027236895BIOINF_KMB_FNS_UNIBA|11.102840607T>Cfwd/C/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta07/05/1707/05/17151Genomicunknown
ss3154853807TOPMED|TOPMed_freeze_5?chr11:102,840,607fwd/C/Tataaattggtccctatttaagaaatgagaacaatagttacttatttttta09/30/1709/30/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs591058|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 CCTGTCTTTA AAGATCAGGA TTTCTCCCCT CAGAGTGCTG ACAGCATCAA AGGACAAAGC
 AGGATCACAG TTGGCTGGCG TCCCAGGTTC TGGAGGGACA GGTTCCGTGG GTACCAGGGG
 GGTCTCAGGG GAGTCAGGGG GAGGTCCTAA AGGGAACATT AGGGGAAATG TGATACGTTT
 CAATATATGC CCATTTGTAT GCTTTCCAAA CATTCTCACG GTGCTTTGAA CTAAATCATA
 AATACTTTAT GTAGCATTTG AAAGCTCTTC TGAAGACCAT CATTGCAAAA CTACAATGGC
 TGATTTTCCC AGTGTCACTC ACCATAGAGG GACTGAATGC CATTTATATC ATCTTGAGAC
 AGGCGGAACC GAGTCAGGTC TGTGAGTGAG TGATAGAGTG GGTACATCAA AGCTTCAGTG
 TTGGCTGAGT GAAAGAGACC CAGGGAGTGG CCAATTTCAT GAGCAGCAAC GAGAAATAAA
 TTGGTCCCTA TTTAAGAAAT
 Y
 GAGAACAATA GTTACTTATT TTTTAAATAC ATGTGCATTA CACAGGTCTG CTGTGCATTG
 TATTGGTTTT TACTTCTTGG AACCACACAG GGCTTTTTAC ACCTTGTTTG TTGGTTAATT
 GAACAATTGA CTAATTACAC ACTTAATGGA AAGCTAAGTG TATTTTAAAA CTCATACCTG
 TAATCAATCT TTGAGATTGA TTTCCCAGTT ACATCCACTT GCCCCCCATG GCCCCAAACC
 CACCCCCAGC CTCACAAGCA TATTAACTCC AGAAGAACCA GATCCCTTTT CTTGTACTCA
 GGAATGGAAT GAACCCACTT GCTTAGCATA TCAGATATTT ACCTTCATTT GTCAATGCAA
 AGCTAAACAC TGTTTTAATA TATTTACATT TGCCATTTGC AGTCTCAGTT AAAGGAAACT
 ATATTCATGT TAATTGATAA TGTCTCAGCC TCATCATCAT GAAGTACATA TTGAGACTAA
 AAACATGAAT AATGATAGAT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
U78045.1 AP000619 AP000789.2 AP001018 AP001018.2 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.
SourceC/C
C/T
T/T
HWPC
T
ss119948486YRI 2IG 1.00000000 0.500000000.50000000
ss132785903ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss1342730564EAS 1008AF 0.667700050.33230001
EUR 1006AF 0.528799950.47119999
AFR 1322AF 0.644500020.35550001
AMR 694AF 0.672900020.32710001
SAS 978AF 0.720900000.27910000
ss1690608186ExAc_Aggregated_Populations121408AF 0.572153390.42784661
ss225430025pilot_1_YRI_low_coverage_panel 118AF 0.601694940.39830509
ss235696077pilot_1_CEU_low_coverage_panel 120AF 0.441666660.55833334
ss242298889pilot_1_CHB+JPT_low_coverage_panel 120AF 0.741666670.25833333
ss2984777JBIC-allele 1488AF 0.672699990.32730001
ss38672890AoD_African_American 90AF 0.540000020.46000001
AoD_Caucasian 92AF 0.490000010.50999999
AoD_Chinese 90AF 0.680000010.31999999
AoD_Japanese 90AF 0.690000000.31000000
ss4251051PGA-AFRICAN-PANELAfrican American 44IG0.454545470.363636370.181818190.317310000.636363630.36363637
PGA-EUROPEAN-PANELEuropean 46IG0.086956520.478260870.434782590.751830000.326086970.67391306
ss491653108CSAgilent 1297GF0.254000010.515999970.230000000.438578000.512000020.48800001
ss52080035HapMap-CEUEuropean 226IG0.185840710.513274310.300884960.751830000.442477880.55752212
HapMap-HCBAsian 86IG0.511627910.372093020.116279070.479500000.697674390.30232558
HapMap-JPTAsian 172IG0.488372090.453488380.058139540.317310000.715116260.28488371
HapMap-YRISub-Saharan African 226IG0.362831860.522123870.115044250.250592000.623893800.37610620
HAPMAP-ASW 98IG0.367346940.510204080.122448980.583882000.622448980.37755102
HAPMAP-CHBAsian 82IG0.487804890.439024390.073170730.751830000.707317050.29268292
HAPMAP-CHD 170IG0.447058830.423529420.129411770.654721000.658823550.34117648
HAPMAP-GIH 176IG0.579545440.363636370.056818181.000000000.761363630.23863636
HAPMAP-LWK 180IG0.600000020.344444450.055555561.000000000.772222220.22777778
HAPMAP-MEX 100IG0.440000000.419999990.140000000.654721000.649999980.34999999
HAPMAP-MKK 286IG0.412587400.475524490.111888110.654721000.650349680.34965035
HAPMAP-TSI 176IG0.329545470.420454530.250000000.150222000.539772750.46022728
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss66538920R24 48AF 0.630000000.37000000
ss71640584F24 48AF 0.460000010.54000002

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.489+/-0.0730000

  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
UNKNOWNUNKNOWNYES

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