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Reference SNP (refSNP) Cluster Report: rs11983225                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/141
Map to Genome Build:106/Weight
Validation Status:byClusterbyFreqwithHapMapFreqWith1000GenomeData
Citation:PubMed
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:T
Clinical Channel:unknown
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.132/287
MAF Source:1000 Genomes
HGVS Names
  • NC_000007.14:g.87532204T>C
  • NG_011513.1:g.186045A>G
  • NM_000927.4:c.2482-707A>G
  • NT_007933.16:g.25025425T>C
Links
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' or 'Contig Pos' column value to see variation in NCBI sequence 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_1865497162rev/TA/Gaatatttccagggtagaggagatgtgctggctaaattatagagtgatggactaaactgac01/30/1201/31/12137Genomicunknown
ss484620899ILLUMINA|HumanOmni2.5-4v1_D_rs11983225-131_T_R_1857361547rev/TA/Gaatatttccagggtagaggagatgtgctggctaaattatagagtgatggactaaactgac01/30/1202/04/12137Genomicunknown
ss536743493ILLUMINA|HumanOmni5-4v1_B__rs11983225-131_T_R_1889500894rev/TA/Gaatatttccagggtagaggagatgtgctggctaaattatagagtgatggactaaactgac06/22/1207/01/12138Genomicunknown
ss560134813TISHKOFF|snp_chr7_87161520fwd/BC/Ttttagtccatcactctataatttagccagcacatctcctctaccctggaa11/22/1211/23/12138Genomicunknown
ss654533855SSMP|7_87161520fwd/BC/Tgtcagtttagtccatcactctataatttagcagcacatctcctctaccctggaaatattc12/14/1212/14/12138Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs11983225|allelePos=201|totalLen=701|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=138
 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 (in rs orientation) back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss164774568YRISub-Saharan African 2IG 1.000 0.500 0.500
ss17951424HapMap-CEUEuropean 226IG 0.009 0.274 0.717 0.294 0.146 0.854
HapMap-HCBAsian 86IG 0.070 0.930 1.000 0.035 0.965
HapMap-JPTAsian 172IG 0.023 0.163 0.814 0.251 0.105 0.895
HapMap-YRISub-Saharan African 226IG 0.080 0.398 0.522 1.000 0.279 0.721
HAPMAP-ASW 98IG 0.041 0.347 0.612 1.000 0.214 0.786
HAPMAP-CHBAsian 82IG 0.073 0.927 1.000 0.037 0.963
HAPMAP-CHD 170IG 0.071 0.929 1.000 0.035 0.965
HAPMAP-GIH 176IG 0.023 0.318 0.659 0.527 0.182 0.818
HAPMAP-LWK 180IG 0.089 0.344 0.567 0.317 0.261 0.739
HAPMAP-MEX 100IG 0.240 0.760 0.655 0.120 0.880
HAPMAP-MKK 286IG 0.070 0.322 0.608 0.273 0.231 0.769
HAPMAP-TSI 176IG 0.011 0.273 0.716 0.439 0.148 0.852
ENSEMBL_Watson 2IG 1.000 1.000
ENSEMBL_Venter 2IG 1.000 1.000
ss223187998pilot_1_YRI_low_coverage_panel 118AF 0.203 0.797
ss23402576AFD_EUR_PANELEuropean 48IG 0.042 0.167 0.792 0.251 0.125 0.875
AFD_AFR_PANELAfrican American 44IG 0.045 0.227 0.727 0.527 0.159 0.841
AFD_CHN_PANELAsian 48IG 0.083 0.917 1.000 0.042 0.958
ss234063969pilot_1_CEU_low_coverage_panel 120AF 0.175 0.825
ss241001964pilot_1_CHB+JPT_low_coverage_panel 120AF 0.083 0.917
ss35072214EGP_YORUB-PANELSub-Saharan African 22IG 0.091 0.091 0.818 0.050 0.136 0.864
EGP_HISP-PANELHispanic 44IG 0.091 0.909 1.000 0.045 0.955
EGP_CEPH-PANELEuropean 44IG 0.318 0.682 0.655 0.159 0.841
EGP_AD-PANELAfrican American 30IG 0.067 0.267 0.667 0.527 0.200 0.800
EGP_ASIAN-PANELAsian 46IG 0.087 0.913 1.000 0.043 0.957
ss69021332HapMap-CEUEuropean 120IG 0.017 0.300 0.683 0.584 0.167 0.833
HapMap-HCBAsian 90IG 0.067 0.933 1.000 0.033 0.967
HapMap-JPTAsian 90IG 0.022 0.156 0.822 0.371 0.100 0.900
HapMap-YRISub-Saharan African 120IG 0.050 0.400 0.550 0.655 0.250 0.750

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.229+/-0.249128810772900

  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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