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Reference SNP (refSNP) Cluster Report: rs2236609                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:98/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
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=0.3409/1707 (1000 Genomes)
G=0.3476/43646 (TOPMED)
HGVS Names
  • CM000683.2:g.34449813A>G
  • NC_000021.8:g.35822111A>G
  • NC_000021.9:g.34449813A>G
  • NG_009091.1:g.66503T>C
  • NM_000219.3:c.-50-129T>C
  • NM_000219.5:c.-50-129T>C
  • NM_001127668.3:c.-50-129T>C
  • NM_001127669.3:c.-50-129T>C
  • NM_001127670.1:c.-50-129T>C
  • NM_001127670.3:c.-50-129T>C
  • NM_001270402.2:c.-50-129T>C
  • NM_001270403.2:c.-50-129T>C
  • NM_001270404.2:c.-50-129T>C
  • NM_001270405.2:c.-50-129T>C
  • NM_001330065.1:c.-41-129T>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 ss283531392 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2236609 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
ss3191064YUSUKE|IMS-JST016975byFreqfwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc08/07/0110/10/0398Genomicunknown
ss10984150BCM_SSAHASNP|chr21.NT_011512.8_21482506fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc06/30/0310/10/03116Genomicunknown
ss12509502WI_SSAHASNP|chr21.NT_011512.8_21482506fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc07/04/0310/10/03116Genomicunknown
ss20135270CSHL-HAPMAP|CSHL-HuFF-200402.chr21.NT_011512.9_21482507fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc02/21/0403/04/04120Genomicunknown
ss21810032SSAHASNP|WGSA-200403-chr21.chr21.NT_011512.9_21482507fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc03/20/0403/20/04121Genomicunknown
ss41478924ABI|hCV11388336byFreqfwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc07/17/0511/03/06126Genomicunknown
ss65625592RSG_JCVI|KCNE1-003756_003757-A_GbyFreqfwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc08/16/0612/16/06127Genomicunknown
ss76871375CGM_KYOTO|13850fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc09/12/0709/12/07129cDNAunknown
ss76887738SI_EXO|NT_011512.10_21483981byFreqfwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc09/20/0709/05/14129Genomicunknown
ss77201876HGSV|Cor12156_SNV_20070510.chr21_34743981fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc10/09/0710/11/07129Genomicunknown
ss81588290HGSV|Cor18555_SNV_20070510.chr21_34743981fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc11/27/0711/30/07130Genomicunknown
ss82027724HGSV|Cor18956_SNV_20070510.chr21_34743981fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc11/30/0712/02/07130Genomicunknown
ss91828311BCMHGSC_JDW|JWB-1492163fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc02/26/0803/02/08129Genomicunknown
ss105108590PHARMGKB_PAT|PS207029_PA157925986_210byFreqfwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc07/23/0809/05/14130Genomicunknown
ss106211807BGI|BGI_rs2236609fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc09/13/0806/18/09130Genomicunknown
ss1124472151000GENOMES|CEU.trio.12.15.2008_3760123_chr21_34743981fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc12/17/0812/17/08130Genomicunknown
ss1138501441000GENOMES|NA19240_2008_12_16_3398468_chr21_34743981fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc12/18/0812/18/08130Genomicunknown
ss117514529ILLUMINA-UK|NA18507_000033434_NCBI36.1_chr21_34743981fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc01/19/0901/19/09130Genomic99 %
ss121083673PHARMGKB_PAT|PS207033_PA158084502_210byFreqfwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc04/14/0909/05/14131Genomicunknown
ss135610819ENSEMBL|ENSSNP1971290fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc12/08/0810/14/09131Genomicunknown
ss138311760ENSEMBL|ENSSNP6457454fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc05/15/0905/17/09131Genomicunknown
ss167957562COMPLETE_GENOMICS|NA07022_36_chr21_34743981fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc09/30/0909/30/09132Genomicunknown
ss169397011COMPLETE_GENOMICS|NA19240_36_chr21_34743981fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc10/01/0910/01/09132Genomicunknown
ss171991907COMPLETE_GENOMICS|NA20431_36_chr21_34743981fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc10/01/0910/01/09132Genomicunknown
ss204008519BUSHMAN|BUSHMAN-chr21-34743980fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc02/16/1003/10/10132Genomicunknown
ss208794557BCM-HGSC-SUB|BCM_CMT_1011-3249990fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc03/15/1003/20/10132Genomicunknown
ss2285489901000GENOMES|pilot_1_YRI_10358673_chr21_34743981fwd/A/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc04/22/1004/22/10132Genomicunknown
ss2379710241000GENOMES|pilot_1_CEU_7575653_chr21_34743981fwd/A/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc05/01/1005/01/10132Genomicunknown
ss2441119971000GENOMES|pilot_1_CHB+JPT_5997074_chr21_34743981fwd/A/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc05/01/1005/01/10132Genomicunknown
ss255928009BL|SNP29864_21_34743981fwd/TA/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc08/20/1008/20/10134Genomicunknown
ss283531392GMI|GMI_AK_SNP_7851813fwd/A/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc12/16/1012/16/10137Genomicunknown
ss287525993GMI|GMI_NA10851_SNP_3538784fwd/A/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc12/17/1012/17/10138Genomicunknown
ss292705172PJP|SNP_2211530_chr21_34743981fwd/A/Gggggtgagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatgccttc01/21/1101/21/11134Genomicunknown
ss410840628ILLUMINA|Cardio-Metabo_Chip_11395247_A_chr21_34743981rev/BC/Tgaaggcattgcacagacccaagatggcacagccatggcctgtggagtgtcagctcacccc06/07/1106/07/11135Genomicunknown
ss479585733ILLUMINA|HumanOmni2.5-4v1_D_kgp11162887-0_B_R_1819939594fwd/TA/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg01/30/1210/28/16137Genomicunknown
ss484264173ILLUMINA|HumanOmni2.5-4v1_B_SNP21-34743981-0_B_R_1631679977fwd/TA/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg01/30/1210/28/16137Genomicunknown
ss533110856ILLUMINA|HumanOmni5-4v1_B_kgp11162887-0_B_R_1819939594fwd/TA/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg06/22/1208/29/15146Genomicunknown
ss566478096TISHKOFF|snp_chr21_35822111fwd/TA/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg11/22/1211/23/12138Genomicunknown
ss662388084SSMP|21_35822111fwd/TA/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg12/14/1202/14/15138Genomicunknown
ss779614165ILLUMINA|HumanOmni25Exome-8v1_A_kgp11162887-0_B_R_1819939594fwd/TA/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg05/30/1307/10/15146Genomicunknown
ss781018196ILLUMINA|HumanOmni2.5-4v1_H_kgp11162887-0_B_R_1819939594fwd/TA/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg05/30/1307/29/15146Genomicunknown
ss835086432ILLUMINA|HumanOmni2.5-8v1_A_kgp11162887-0_B_R_1819939594fwd/TA/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg09/18/1307/29/15146Genomicunknown
ss995090810EVA-GONL|EVA-GONL_rs2236609fwd/TA/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg04/23/1405/01/14142Genomicunknown
ss1082478723JMKIDD_LAB|HGDP_WGS_chr21_35822111fwd/TA/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg07/10/1407/12/14142Genomicunknown
ss13661914541000GENOMES|PHASE3_V1_80040982fwd/A/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg08/16/1408/16/14142Genomicunknown
ss1429176047DDI|DDI_rs2236609fwd/TA/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg11/04/1411/04/14144Genomicunknown
ss1639507255EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_21_35822111_44109229fwd/A/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg03/04/1503/04/15144Genomicunknown
ss1682501288EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_21_35822111_44109229fwd/A/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg03/04/1503/04/15144Genomicunknown
ss1699160849EVA_DECODE|EVA_DECODE_21_34743981_180899_rs2236609fwd/TA/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg03/02/1503/05/15144Genomicunknown
ss1809673541HAMMER_LAB|Hsieh_8705012fwd/TA/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg07/15/1507/16/15146Genomicunknown
ss1938641539WEILL_CORNELL_DGM|SNV:chr21:35822111fwd/TA/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg10/16/1510/19/15147Genomicunknown
ss1969218640GENOMED|rs2236609fwd/TA/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg02/16/1602/16/16147Genomicunknown
ss2030092203JJLAB|SNP10594758fwd/TA/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg08/29/1608/31/16149Genomicunknown
ss2158696619USC_VALOUEV|NC_000021.8:g.35822111A>Gfwd/A/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg11/17/1611/17/16150Genomicunknown
ss2412250633TOPMED|21_35822111_A/Gfwd/A/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg11/19/1611/19/16150Genomicunknown
ss2629544943SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV6760085fwd/A/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg01/06/1701/06/17151Genomicunknown
ss2633844959ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp11162887-0_B_R_18199395fwd/A/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg02/02/1702/02/17151Genomicunknown
ss2704426662GRF|rs2236609fwd/A/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg02/13/1702/13/17151Genomicunknown
ss3018851439SWEGEN|NC_000021.8:g.35822111A>Gfwd/A/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg05/30/1705/30/17151Genomicunknown
ss3352706371CSHL|rs2236609fwd/A/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg10/02/1710/02/17151Genomicunknown
ss3370186804TOPMED|TOPMed_freeze_5?chr21:34,449,813fwd/A/Ggagctgacactccacaggccatggctgtgccatcttgggtctgtgcaatg10/03/1710/03/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2236609|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 CATAGCACGA CCTGTAGCTC TCCAGGACCC GGGCCTGGAC ATAGGCCTTG TCCTTCTCTT
 GCCAGGCATC GGACTCGATG TAGACGTTGA ATGGGTCGTT CGAGTGCTCC AGCTTCTTGG
 AGCGGATGTA GCTCAGCATG ATGCCCAGGG TGAAGAAGCC GAAGAATCCC AGTACCATGA
 GGACGTAGAG GGCCTCCAGC TTGCCGTCAC TGCTGCGGGG GGACCTGCGG GCCAGGCCCG
 ACATGTTGCC ACCCTGCTGA ACTGTCTCCT GCCACAGCTT GGTCAGAAAG GGCGTCACCG
 CTGTGGTGTT AGACAGGATC ATCCTGGGCA TTAAGGTTCC ACTGCTGCAG CTCAAACTTC
 CCAGGCACAC CTCTTAAAGG AAAAATGCAA CCCCAAATCA AAAAGTACGT ATTGGCCAAA
 ACCCACACGT ACGCACACAC ACGTATACAA TTTTAAAATC TCAGGTGAGA GGGGTGAGCT
 GACACTCCAC AGGCCATGGC
 R
 TGTGCCATCT TGGGTCTGTG CAATGCCTTC TCTTGATAGA TGAATGGATA CATTGATTCC
 CTTCTATTTC CATCCACCAC TCCAATCTCC ACCCCTATAG GTGACCATCA GAATGAGCTT
 CTTTAATATG CATTGCTGCA TATTGTGGCG TATGGGGTTG CATGTGTGCA TTTTGGTTTA
 CCTAAATGGT ATCAGGTCAT CCAACTCATT CAGTCTCCTT CTTTTTCCTC ATGACTGTGC
 TTTTGTGGCT CACTTGCGGT GCTGGGTGTG TGCATTCCCT TGCTTCCAAT GTTTGTATAC
 AACCCATGGT GAACACCCAC TTCTTTTCTC TGCCTTCTCC CCCAGAGATG GACACTGCTG
 TGGCTGCTGA CTCCATAAAC AAGGGGGAGA CAAATATCCC CATCCTTGAC CTCCTATGGA
 CCTAAAAAAA ATCACGCATC TCATACAACT AGTTCCTGGC AGCTTATGCA AGACTAGTCA
 GACTGGTTGC CCTTGGAAGC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011512.10
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
ss105108590PA157925987 374AF 0.360962570.63903743
ss117514529YRI 2IG 1.00000000 0.500000000.50000000
ss121083673PA158084503 750AF 0.397333320.60266668
ss135610819ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss1366191454EAS 1008AF 0.298599990.70140004
EUR 1006AF 0.390699980.60930002
AFR 1322AF 0.276899990.72310001
AMR 694AF 0.403499990.59650004
SAS 978AF 0.375299990.62470001
ss138311760ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss167957562CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss169397011YRISub-Saharan African 2IG 1.00000000 1.00000000
ss171991907PGP 2IG 1.00000000 0.500000000.50000000
ss228548990pilot_1_YRI_low_coverage_panel 118AF 0.237288130.76271188
ss237971024pilot_1_CEU_low_coverage_panel 120AF 0.400000010.60000002
ss244111997pilot_1_CHB+JPT_low_coverage_panel 120AF 0.391666680.60833335
ss3191064JBIC-allele 1076AF 0.243499980.75650001
ss65625592R31_MEXLA 92IG0.108695650.586956500.304347810.150222000.402173910.59782606
R31_HANLA 94IG0.148936170.382978740.468085110.317310000.340425520.65957445
R31_AAAfrican American 94IG0.063829790.404255330.531914891.000000000.265957440.73404253
R31_CAUEuropean 94IG0.212765960.446808520.340425520.583882000.436170220.56382978
ss76887738HapMap-YRISub-Saharan African 120IG0.066666670.333333340.600000020.654721000.233333330.76666665

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.449+/-0.1510000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNYES

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