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Reference SNP (refSNP) Cluster Report: rs11983225                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/147
Map to Genome Build:107/Weight 1
Validation Status:byClusterbyFreqwithHapMapFreqWith1000GenomeData
Citation:PubMed
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.1456/729 (1000 Genomes)
HGVS Names
  • NC_000007.13:g.87161520T>C
  • NC_000007.14:g.87532204T>C
  • NG_011513.1:g.186045A>G
  • NM_000927.4:c.2482-707A>G
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 ss17951424 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11983225 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
ss17951424CSHL-HAPMAP|CSHL-HuCC-200402.chr7.NT_007933.13_12395736byFreqfwd/BC/Tgtcagtttagtccatcactctataatttagccagcacatctcctctaccctggaaatatt02/19/0410/26/06120Genomicunknown
ss20398889GOLD|IVS 20+4254 A>Grev/TA/Gaatatttccagggtagaggagatgtgctggctaaattatagagtgatggactaaactgac02/23/0403/04/04121Genomicunknown
ss23402576PERLEGEN|afd0601741byFreqfwd/BC/Tgtcagtttagtccatcactctataatttagccagcacatctcctctaccctggaaatatt08/10/0409/13/04123Genomicunknown
ss35072214EGP_SNPS|ABCB1-182982byFreqrev/TA/Gaatatttccagggtagaggagatgtgctggctaaattatagagtgatggactaaactgac03/02/0511/02/06125Genomicunknown
ss69021332PERLEGEN|PGP00601741byFreqfwd/BC/Tgtcagtttagtccatcactctataatttagccagcacatctcctctaccctggaaatatt01/30/0703/31/08127Genomicunknown
ss75254921ILLUMINA|ILMN_Human_1M_rs11983225fwd/BC/Tgtcagtttagtccatcactctataatttagccagcacatctcctctaccctggaaatatt08/28/0708/29/07129Genomicunknown
ss1123116631000GENOMES|CEU.trio.12.15.2008_1804943_chr7_86999456fwd/BC/Tgtcagtttagtccatcactctataatttagccagcacatctcctctaccctggaaatatt12/17/0812/17/08130Genomicunknown
ss1140524851000GENOMES|NA19240_2008_12_16_1623669_chr7_86999456fwd/BC/Tgtcagtttagtccatcactctataatttagccagcacatctcctctaccctggaaatatt12/18/0812/18/08130Genomicunknown
ss119738042KRIBB_YJKIM|KHS1827268fwd/BC/Tgtcagtttagtccatcactctataatttagccagcacatctcctctaccctggaaatatt02/04/0902/05/09131Genomicunknown
ss160023312ILLUMINA|HumanOmni1-Quad_v1-0_B_rs11983225-128_T_R_1514200716rev/TA/Gaatatttccagggtagaggagatgtgctggctaaattatagagtgatggactaaactgac08/04/0910/01/09131Genomicunknown
ss164774568COMPLETE_GENOMICS|NA19240_36_chr7_86999456fwd/BC/Tgtcagtttagtccatcactctataatttagccagcacatctcctctaccctggaaatatt09/29/0909/30/09132Genomicunknown
ss171768616ILLUMINA|Human1M-Duov3_B_rs11983225-128_T_R_1514200716rev/TA/Gaatatttccagggtagaggagatgtgctggctaaattatagagtgatggactaaactgac10/01/0910/01/09132Genomicunknown
ss2231879981000GENOMES|pilot_1_YRI_4997681_chr7_86999456fwd/C/Tgtcagtttagtccatcactctataatttagccagcacatctcctctaccctggaaatatt04/22/1004/22/10132Genomicunknown
ss2340639691000GENOMES|pilot_1_CEU_3668598_chr7_86999456fwd/C/Tgtcagtttagtccatcactctataatttagccagcacatctcctctaccctggaaatatt05/01/1005/01/10132Genomicunknown
ss2410019641000GENOMES|pilot_1_CHB+JPT_2887041_chr7_86999456fwd/C/Tgtcagtttagtccatcactctataatttagccagcacatctcctctaccctggaaatatt05/01/1005/01/10132Genomicunknown
ss479644404ILLUMINA|HumanOmni2.5-4v1_B_rs11983225-128_T_R_1615264789rev/TA/Gaatatttccagggtagaggagatgtgctggctaaattatagagtgatggactaaactgac01/30/1201/30/12137Genomicunknown
ss479649648ILLUMINA|HumanOmniExpress-12v1_C_rs11983225-131_T_R_1857361547rev/TA/Gaatatttccagggtagaggagatgtgctggctaaattatagagtgatggactaaactgac01/30/1201/30/12137Genomicunknown
ss480159103ILLUMINA|HumanOmni1-Quad_v1-0_C_rs11983225-131_T_R_1865497162fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa01/30/1208/28/15146Genomicunknown
ss484620899ILLUMINA|HumanOmni2.5-4v1_D_rs11983225-131_T_R_1857361547rev/TA/Gaatatttccagggtagaggagatgtgctggctaaattatagagtgatggactaaactgac01/30/1202/04/12137Genomicunknown
ss536743493ILLUMINA|HumanOmni5-4v1_B__rs11983225-131_T_R_1889500894fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa06/22/1208/29/15146Genomicunknown
ss560134813TISHKOFF|snp_chr7_87161520fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa11/22/1211/23/12138Genomicunknown
ss654533855SSMP|7_87161520fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa12/14/1202/11/15138Genomicunknown
ss778771416ILLUMINA|HumanOmni25Exome-8v1_A_rs11983225-131_T_R_1865497162fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa05/30/1307/09/15146Genomicunknown
ss782757256ILLUMINA|HumanOmni2.5-4v1_H_rs11983225-131_T_R_1857361547fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa05/30/1307/29/15146Genomicunknown
ss783723775ILLUMINA|HumanOmniExpressExome-8v1_A_rs11983225-131_T_R_1889500894fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa05/31/1306/19/15146Genomicunknown
ss832009464ILLUMINA|HumanOmniExpress-12v1_H_rs11983225-131_T_R_1857361547fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa09/17/1306/19/15146Genomicunknown
ss834231263ILLUMINA|HumanOmni2.5-8v1_A_rs11983225-131_T_R_1865497162fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa09/18/1307/28/15146Genomicunknown
ss984507039EVA-GONL|EVA-GONL_rs11983225fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa04/23/1404/24/14142Genomicunknown
ss1074771621JMKIDD_LAB|HGDP_WGS_chr7_87161520fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa07/10/1407/11/14142Genomicunknown
ss13260145581000GENOMES|PHASE3_V1_38217441fwd/C/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa08/16/1408/16/14142Genomicunknown
ss1582294143EVA_GENOME_DK|EVA_GENOME_DK_snv_rs11983225fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa02/19/1502/20/15144Genomicunknown
ss1594082919EVA_DECODE|EVA_DECODE_7_86999456_691112_rs11983225fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa03/02/1503/03/15144Genomicunknown
ss1618630781EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_7_87161520_21154899fwd/C/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa03/04/1503/04/15144Genomicunknown
ss1661624814EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_7_87161520_21154899fwd/C/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa03/04/1503/04/15144Genomicunknown
ss1712968790EVA_SVP|EVA_SVP_663157fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa03/12/1503/12/15144Genomicunknown
ss1752698138ILLUMINA|OmniExpressExome-8v1-1_B_rs11983225-131_T_R_2087474927fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa05/27/1506/09/15146Genomicunknown
ss1805098552HAMMER_LAB|Hsieh_4111450fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa07/15/1507/16/15146Genomicunknown
ss1927770173WEILL_CORNELL_DGM|SNV:chr7:87161520fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa10/16/1510/17/15147Genomicunknown
ss1959029256ILLUMINA|7:87161520-T-C-0_T_R_2304288718fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa11/13/1511/13/15147Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs11983225|allelePos=201|totalLen=701|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=147
 ATCTTCCCCT TGAATTCCAG AGGGAGTCTG AAGCATGACT TTCACTAGTG TGCACTGAGT
 TCCAGCTCTA AAGCCAGAAG TCAAACTGCA AAGTGAATTT AATCCACCAC TGTATAATGT
 CCAACTGTAA ACCAGATTTC CAACTCTGAA ACCAAAAGTC AAGCTACAAA GTCAGTTTAG
 TCCATCACTC TATAATTTAG
 Y
 CCAGCACATC TCCTCTACCC TGGAAATATT CTGTGCCCTC AAGCCATTCC AAATGCCTGC
 CCTGGCCCCA GACCTGCCTT TTCtgaaaag gggctgggta aaataaggct gagatctact
 gggctacatt cccaggaggt taggcattct aagtcacagg atgcgacagg aggtcagcac
 aagatacagg tcgctaagac cttgctgata aaacaagctg tggtaaagaa gccagccaaa
 tcctaccaaa atcaagatgg tgacaaaagt gacctctggt tgttctcact gctcattata
 cgctaattat aatgtattag catgctcaaa gacacaccag cgccatgaca atttacaaat
 gccatggcaa cgttacccta tatggtctaa aaatgggagg aaccctcagt tctgagaaga
 gcccacccct tttcctagga aactcatgaa taatccaccc cttgtttagc atgtaatcaa
 gaagtaacaa taagtataAG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_007933
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
ss1326014558EAS 1008AF 0.069400000.93059999
EUR 1006AF 0.134200010.86580002
AFR 1322AF 0.203500000.79650003
AMR 694AF 0.112400000.88760000
SAS 978AF 0.181000010.81900001
ss164774568YRISub-Saharan African 2IG 1.00000000 0.500000000.50000000
ss17951424HapMap-CEUEuropean 226IG0.008849560.274336280.716814160.294266000.146017700.85398233
HapMap-HCBAsian 86IG 0.069767450.930232581.000000000.034883720.96511626
HapMap-JPTAsian 172IG0.023255810.162790700.813953460.250592000.104651160.89534885
HapMap-YRISub-Saharan African 226IG0.079646020.398230080.522123871.000000000.278761060.72123891
HAPMAP-ASW 98IG0.040816330.346938790.612244901.000000000.214285720.78571427
HAPMAP-CHBAsian 82IG 0.073170730.926829281.000000000.036585360.96341461
HAPMAP-CHD 170IG 0.070588240.929411771.000000000.035294120.96470588
HAPMAP-GIH 176IG0.022727270.318181810.659090940.527089000.181818190.81818181
HAPMAP-LWK 180IG0.088888890.344444450.566666660.317310000.261111110.73888886
HAPMAP-MEX 100IG 0.239999990.759999990.654721000.120000000.88000000
HAPMAP-MKK 286IG0.069930070.321678310.608391580.273322000.230769230.76923078
HAPMAP-TSI 176IG0.011363640.272727280.715909060.438578000.147727270.85227275
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss223187998pilot_1_YRI_low_coverage_panel 118AF 0.203389820.79661018
ss23402576AFD_EUR_PANELEuropean 48IG0.041666670.166666670.791666690.250592000.125000000.87500000
AFD_AFR_PANELAfrican American 44IG0.045454550.227272730.727272750.527089000.159090910.84090906
AFD_CHN_PANELAsian 48IG 0.083333340.916666691.000000000.041666670.95833331
ss234063969pilot_1_CEU_low_coverage_panel 120AF 0.175000000.82499999
ss241001964pilot_1_CHB+JPT_low_coverage_panel 120AF 0.083333340.91666669
ss35072214EGP_YORUB-PANELSub-Saharan African 22IG0.090909090.090909090.818181810.050043000.136363640.86363637
EGP_HISP-PANELHispanic 44IG 0.090909090.909090941.000000000.045454550.95454544
EGP_CEPH-PANELEuropean 44IG 0.318181810.681818190.654721000.159090910.84090906
EGP_AD-PANELAfrican American 30IG0.066666670.266666680.666666690.527089000.200000000.80000001
EGP_ASIAN-PANELAsian 46IG 0.086956520.913043501.000000000.043478260.95652175
ss69021332HapMap-CEUEuropean 120IG0.016666670.300000010.683333340.583882000.166666670.83333331
HapMap-HCBAsian 90IG 0.066666670.933333341.000000000.033333340.96666664
HapMap-JPTAsian 90IG0.022222220.155555560.822222230.371093000.100000000.89999998
HapMap-YRISub-Saharan African 120IG0.050000000.400000010.550000010.654721000.250000000.75000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.249+/-0.250128810772900

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqWith1000GenomeDataUNKNOWNUNKNOWNYES

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