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Reference SNP (refSNP) Cluster Report: rs2353398                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/T (FWD)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.2398/1201 (1000 Genomes)
T=0.3421/42958 (TOPMED)
HGVS Names
  • CM000666.2:g.144601606T>A
  • NC_000004.11:g.145522758T>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 ss11233059 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2353398 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
ss3308737TSC-CSHL|TSC1479106fwd/BA/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt09/20/0110/10/03100Genomicunknown
ss6025836SC_JCM|NT_016606.12_137072fwd/BA/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt01/10/0310/10/03111Genomicunknown
ss11233059SC_JCM|chr4.NT_016606.15_7042423byFreqfwd/BA/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt07/03/0310/25/06117Genomicunknown
ss11634426WI_SSAHASNP|chr4.NT_016606.15_7042423fwd/BA/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt07/03/0310/10/03117Genomicunknown
ss14601197WI_SSAHASNP|chr4.NT_016606.16_7070814fwd/BA/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt11/05/0311/22/03123Genomicunknown
ss22138100SSAHASNP|WGSA-200403-chr4.chr4.NT_016606.16_7070814fwd/BA/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt03/20/0403/21/04121Genomicunknown
ss42392767ABI|hCV15988402fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt07/17/0507/18/05126Genomicunknown
ss78256457HGSV|Cor12878_SNV_20070510.chr4_145880363fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt10/17/0710/18/07129Genomicunknown
ss92816411BCMHGSC_JDW|JWB-1867772fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt02/26/0803/03/08129Genomicunknown
ss98871769HUMANGENOME_JCVI|1103654576016fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt04/01/0804/02/08130Genomicunknown
ss105872059BGI|BGI_rs2353398fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt09/12/0806/18/09130Genomicunknown
ss1084267211000GENOMES|CEU.trio.12.15.2008_1108189_chr4_145742208fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt12/15/0812/15/08130Genomicunknown
ss1107469321000GENOMES|NA19240_2008_12_16_998985_chr4_145742208fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt12/17/0812/17/08130Genomicunknown
ss117224759ILLUMINA-UK|NA18507_000194374_NCBI36.1_chr4_145742208fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt01/18/0901/18/09131Genomic99 %
ss135104635ENSEMBL|ENSSNP2300425fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt12/08/0810/15/09131Genomicunknown
ss139940195ENSEMBL|ENSSNP12689619fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt05/18/0905/19/09131Genomicunknown
ss158022935GMI|GMI_SNP_41884710fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt06/24/0906/25/09131Genomicunknown
ss162631616COMPLETE_GENOMICS|NA07022_36_chr4_145742208fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt09/28/0909/29/09132Genomicunknown
ss164616394COMPLETE_GENOMICS|NA19240_36_chr4_145742208fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt09/29/0909/29/09132Genomicunknown
ss199301091BUSHMAN|BUSHMAN-chr4-145742207fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt02/16/1003/06/10132Genomicunknown
ss206414401BCM-HGSC-SUB|BCM_CMT_1011-877599fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt03/15/1003/17/10132Genomicunknown
ss2212692411000GENOMES|pilot_1_YRI_3078924_chr4_145742208fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt04/22/1004/22/10132Genomicunknown
ss2326406211000GENOMES|pilot_1_CEU_2245250_chr4_145742208fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt05/01/1005/01/10132Genomicunknown
ss2398787911000GENOMES|pilot_1_CHB+JPT_1763868_chr4_145742208fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt05/01/1005/01/10132Genomicunknown
ss253596896BL|SNP159102_4_145742208fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt08/18/1008/18/10134Genomicunknown
ss277975534GMI|GMI_AK_SNP_2295767fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt12/16/1012/16/10137Genomicunknown
ss285025648GMI|GMI_NA10851_SNP_1038421fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt12/17/1012/17/10138Genomicunknown
ss293218269PJP|SNP_2724627_chr4_145742208fwd/A/Taaaaagaatattccacagacatttttatactaaaagtggaatgaacaatattattcactt01/21/1101/21/11134Genomicunknown
ss651740664SSMP|4_145522758fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt12/14/1202/10/15138Genomicunknown
ss980790443EVA-GONL|EVA-GONL_rs2353398fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt04/23/1404/24/14142Genomicunknown
ss1072041224JMKIDD_LAB|HGDP_WGS_chr4_145522758fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt07/10/1407/11/14142Genomicunknown
ss13122336061000GENOMES|PHASE3_V1_23847455fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt08/16/1408/16/14142Genomicunknown
ss1430085693DDI|DDI_rs2353398fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt11/04/1411/05/14144Genomicunknown
ss1580821634EVA_GENOME_DK|EVA_GENOME_DK_snv_rs2353398fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt02/19/1502/20/15144Genomicunknown
ss1590303080EVA_DECODE|EVA_DECODE_4_145742208_1147320_rs2353398fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt03/02/1503/03/15144Genomicunknown
ss1611389559EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_4_145522758_13190833fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt03/04/1503/04/15144Genomicunknown
ss1654383592EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_4_145522758_13190833fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt03/04/1503/04/15144Genomicunknown
ss1802343421HAMMER_LAB|Hsieh_2525254fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt07/15/1507/15/15146Genomicunknown
ss1924032713WEILL_CORNELL_DGM|SNV:chr4:145522758fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt10/16/1510/17/15147Genomicunknown
ss1958727168ILLUMINA|rs2353398-138_T_R_2264358894fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt11/13/1511/13/15147Genomicunknown
ss1969897607GENOMED|rs2353398fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt02/16/1602/16/16147Genomicunknown
ss2022602961JJLAB|SNP3105516fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt08/29/1608/30/16149Genomicunknown
ss2150734259USC_VALOUEV|NC_000004.11:g.145522758T>Afwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt11/17/1611/17/16150Genomicunknown
ss2267986490HUMAN_LONGEVITY|HLI-4-144601606-T-Afwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt11/18/1611/18/16150Genomicunknown
ss2435916975TOPMED|4_145522758_T/Afwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt11/20/1611/20/16150Genomicunknown
ss2625797917SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV1980494fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt01/06/1701/06/17151Genomicunknown
ss2706228575GRF|rs2353398fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt02/13/1702/13/17151Genomicunknown
ss2816460826GNOMAD|rs2353398fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt05/18/1705/18/17151Genomicunknown
ss2985932384AFFY|Axiom_Smokesc1_Affx-23573724fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt05/24/1705/24/17151Genomicunknown
ss2995727546SWEGEN|NC_000004.11:g.145522758T>Afwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt05/30/1705/30/17151Genomicunknown
ss3022423201ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs2353398-138_T_R_2264358894fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt06/28/1706/28/17151Genomicunknown
ss3025078717BIOINF_KMB_FNS_UNIBA|4.144601606T>Afwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt07/05/1707/05/17151Genomicunknown
ss3346011958CSHL|rs2353398fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt10/02/1710/02/17151Genomicunknown
ss3445518743TOPMED|TOPMed_freeze_5?chr4:144,601,606fwd/A/Tgaatattccacagacatttttatactaaaagtggaatgaacaatattatt10/04/1710/04/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2353398|allelePos=794|totalLen=4541|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=151
 ATATTAAGGA TTTCCATTAC ATGAAGAACA CCATGGAAAA CGTTGACAAA CTGATGAAGG
 CTGGAGaaat tatttaaaat ttctaaaatt aataaGTGAT TAATATCTGA AATATATCAG
 AAAGTCTTAC AAATCAAACA ATAACAACAA AAACAGACCA TAATTTTTTT AAATGGCCAA
 AATAAGATCC TCAGAAGAGA TAAACAAAAG ACAATCACAT TAGAAATAGa gtcattaaga
 aattacagaa actcaaaaat gatgagatat tacattacac ctattgtatt tgaaaaatca
 gaaaacatca tcatagctca tgatgtcaga gacatgggaa cacttgtgtg ctgctgaaag
 gagggtagaa gagtgtgtac aaactatcag tgtttactca aattgggtat acacttctct
 atgacccagc aatctcattg ttgggtttca atattccaaa gacaaggccg ggcgtggcgg
 ctcacgcctg tgattccaac attttgggag gtcaaagtgg gtggatcacc tgaggtcagg
 agttcgagac cagcctggcc aacatggtga aaccctatct ctactaaaag tacaaaaaaa
 tcagccaggt gtggtggtgc gtgcctggag tcccagctgc ttgggaggct gaggcaggag
 aatctcttga acccaggagg cacagattgc agtgagccga gatggggaca ctgcactcca
 gtctgggtga cagagtgaga ctccatctca aaaaaaaaaa aaaaaaaaga atattccaca
 gacattttta tac
 W
 taaaagtgga atgaacaata ttattcactt caatgttatt tgatagtaaa ggattggaaa
 cagtctaagt atccatttct gagggaatgc ataaataaaa aatgagagat actaccataa
 aatgttacat ggaggctaaa aatgaaagga ttgaaagtac acacagcaac gtggatggat
 cttaaaatat aatgttgaag gaaaaacagt aaataacata attgtatata tagccaaata
 tatataaata tttatgtaaa ttaaaaatac acaggttggg tgcagttgct catgcttgta
 atgccagcac ttcgggaggc ctaggcagga ggattgcttg agcccaggag tttgagacca
 gcctgaccaa gatggccaga cttcatccgt acaaaaaata aaaaataaat tagccaggta
 tggtggccta cgcctgtagt ctcagctact ggagaggctg aggcaggaga ctcttttaag
 cccaagattc aaggcactat gattacacca ctgcactcca acctgggcaa cagagcgaca
 ccccatctct aaaaatatat gtatgtatac atagacttgt gatacatcca tacaatgaaa
 tacgactcaC TAGACTAggc cctccatatc cacaggttct gcatcctcag attctaccaa
 cttccagtag aaaatattca gaaaaaaaaa tttaaaaaac cacaataaca ataaaataac
 agcaaagaaa aataacaata aaataatacc aataaaaata tagtataaca actatttaca
 tagcatttac attgtgttag gtattataag taatctatag atgatttaaa gtatatgaga
 ggatatgcat aggttatatg caaatactgt gccattttat ataagatact cgagcattta
 caaattgtgt acggggagtc tggaggggaa ctcttggaac cactcgatat attctgaggg
 atgactTTaa taataaagaa tgaactactg atgcatgcaa caacttggat agatttcgtg
 ggaattgtgc tcagcagaaa aaaagccaat ctcaaaaggt tggcatacaa atccaagaaa
 tacagagaac ctcagataga tactatataa aacaatcatc cccaagtcac atagtcaaca
 gattcaccaa cgccaacaaa aagaaaaaaa tcttaaaggc agctagagag gaatcaagtc
 acatacagag cgagcttcat caggcagacc tctcagcaga aatcttacaa gccagaagat
 attgagggcc tattttcagc atctttaaag aaaagaaatt ccaaccaaga atttcatatc
 ctgccaaaat aagcttcata agtgaaggag aaataaaatc ctcagacaag ctaatattga
 aggaatttgt ttcaactaga tcagccttcc atgaggttct tgaaggagtg ctaaacatgg
 aatcaaaaga ataacacctg ctactggcta ggcgcagtgg ctcacacctg taatcccagc
 actttgagag gccaaggcag gcggatcacc tgaggtcggg agttcaagtc cagcctgacc
 aacatggaga aaccctgtct ctactaaaaa tacaaaatta gctgggtgtg gtggcatatg
 cctgtaatcc cagctacttg tgaggctgag gcaggagaat tgcttaaacc tgggaggcag
 aggttgcaat gagcccagat tgcaccattg cactcctgcc tgggcaacaa gagtgaaact
 ccgtcaaaaa aaaaaaaaaa aaagaataac acctgctacc acacaaacac atgtaagcat
 atagcccaca ggcactataa agtaactaca caatcacaca atcaagtcta tataacaacc
 agctaaaaat atgatgacaa gatcaaaatc acacatatca atattaacct taaatgtaaa
 tggactaagc acccccactt ggaagacatg gagtggaaag ctaaataaaa aggcaagatc
 caacctgttt aatggcattc acagaatcaa agtaaaggaa tgaagaacaa tctaccatgc
 aaacagaaac aaaaggagaa aaggagtcac tattcttgtA TATatttgtg tctctgccca
 aatttcatgt tgaattgGAG GAGGTGCCTG CTtgtgtgtc acctctttcc cctttatttt
 ctctctctct ctctcctgtc accatgtgaa gaaggtcttt gctccccctt tgccttctgc
 tatgattgta aggttcctga ggccacccag tcatgcttcc tgctaagctt ggtgaattga
 attgtgagtc cattaagcct ctttgcttca taaattatcc agtcttaggt agttctttat
 agcagtgtta aaatggacta atgcaAcatt acataatgat acagggtaca atccaacaaa
 aaaacttaac tatcttaaat atatacacac ccaacatcag agcacacaga ttcataaaat
 atgttatttg tggcctacaa aaagacttag acaaccacac agtaatagtg agagacttca
 acaccctact gacagcatta gactgattat taaggtagaa aactaaGATt ttctgcatat
 ggctagccag ttttcccagc accatttact gaataggaca tccttttccc attgcttgtt
 tttggcaggt ttgttgaaga tcagatggtt gtagatatgt ggtgtcattt ctgaggtctc
 tgttctgctc cattggtcta tttgtctgtt ttggtaccag taccatgctg ttttggttac
 tgtagccttg tagtatagct tgaagtcagg tagcatgatg cccccagctt tgttctcttt
 gcttaggatt gtcttggcta tatggggtct tctctgattc catatgaaat ttaaaatagt
 tttttctaat tctgtgaaga atgtcaatag tagtttgatg ggaatAAAAC CATCAAATAA
 GAACAAATCA ACCCCACTGC Taccatggaa tactacacag ccataaaaag aatgcagtca
 tgtcctttga agcaacatgg atggagctgg aggaaattat cctatgcaaa ttaatgcagg
 aacagtctcc taagcaaatt aacataggaa cagaaaacca aataacacat gttctttctc
 ataagtggga gctaaagatt ggctactcat gaacataaaa tggcaacagt agacactgga
 gactactaga tggaggaggg agttgacatg aaaaactacc cattgagtcc tatgctcact
 acctgggtgc aatataccca tataacaaat ctgcacatgt acttcctgta tctgaaataa
 aagttgaaaT TTAAATTTTT AAATTtttat ttatttattt atttatttTA ATTTTTACTA
 TCATTATTAt tttttttttt tttcttgaga cagagtttcg ctctgtcgcc caggctggag
 tgcagtggcg ccatctcggc tcactgcaag ctccgcctcc cgggttcacg ccattctcct
 gcctcagcct cccgagtagc tgggactaca ggcacccgcc accatgccca gctaattttt
 tgtatttttt tagtagagac ggggtttcac cgtgttagcc aggatggtct caatctcctg
 accttgtgat ctgcccgcct cagcctccca aagtgctggg attacaggca tgaAAAGAAT
 TTTAAATATT AAAAAGGTAT CGACTACTTG ATAGGTACTG TTCTTAACAA GAACTTTTGG
 GAAGAATTTT ACAATCCATA AAACGTA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_016606.12 ABBA01070017
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/T
T/T
HWPA
T
ss11233059HapMap-CEUEuropean 120IG0.183333340.566666660.250000000.294266000.466666670.53333336
HapMap-HCBAsian 82IG0.439024390.56097561 0.099721000.719512220.28048781
HapMap-JPTAsian 88IG0.681818190.250000000.068181820.200325000.806818190.19318181
HapMap-YRISub-Saharan African 120IG0.850000020.15000001 1.000000000.925000010.07500000
ss117224759YRI 2IG1.00000000 1.00000000
ss1312233606EAS 1008AF 0.777800020.22220001
EUR 1006AF 0.521900000.47810000
AFR 1322AF 0.934200050.06580000
AMR 694AF 0.654200020.34580001
SAS 978AF 0.827200000.17280000
ss135104635ENSEMBL_Venter 2IG1.00000000 1.00000000
ss139940195ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss162631616CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss164616394YRISub-Saharan African 2IG1.00000000 1.00000000
ss221269241pilot_1_YRI_low_coverage_panel 118AF 0.915254240.08474576
ss232640621pilot_1_CEU_low_coverage_panel 120AF 0.491666670.50833333
ss239878791pilot_1_CHB+JPT_low_coverage_panel 120AF 0.783333360.21666667
ss98871769J. Craig Venter 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.365+/-0.2220000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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